Query         gi|254780725|ref|YP_003065138.1| response regulator receiver protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 427
No_of_seqs    291 out of 3794
Neff          7.5 
Searched_HMMs 39220
Date          Sun May 29 20:05:25 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780725.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG4963 CpaE Flp pilus assembl 100.0       0       0  383.4  24.2  359   22-422     5-365 (366)
  2 CHL00175 minD septum-site dete 100.0       0       0  323.3  27.2  261  157-425     9-279 (279)
  3 TIGR01968 minD_bact septum sit 100.0       0       0  317.6  15.6  254  161-421     1-272 (272)
  4 PRK10818 cell division inhibit 100.0       0       0  304.0  25.0  256  160-422     1-269 (270)
  5 TIGR01969 minD_arch cell divis 100.0       0       0  301.4  21.1  231  162-402     1-233 (258)
  6 TIGR03371 cellulose_yhjQ cellu 100.0 3.1E-40 8.4E-45  266.6  25.5  234  162-403     2-244 (246)
  7 COG0455 flhG Antiactivator of  100.0 3.6E-39 9.1E-44  260.0  27.5  258  161-424     2-262 (262)
  8 pfam00142 Fer4_NifH 4Fe-4S iro 100.0 1.2E-37   3E-42  250.7  25.1  256  162-422     1-266 (269)
  9 COG2894 MinD Septum formation  100.0 1.1E-38 2.8E-43  257.0  18.2  257  160-423     1-272 (272)
 10 cd02040 NifH NifH gene encodes 100.0 1.3E-37 3.3E-42  250.4  23.5  257  162-423     2-268 (270)
 11 cd02036 MinD Bacterial cell di 100.0 8.5E-36 2.2E-40  239.3  19.7  176  163-393     1-179 (179)
 12 PRK13233 nifH nitrogenase redu 100.0 4.3E-35 1.1E-39  234.9  22.6  259  161-423     2-270 (275)
 13 pfam06564 YhjQ YhjQ protein. T 100.0 1.8E-35 4.7E-40  237.2  20.3  225  162-402     2-237 (244)
 14 PRK13232 nifH nitrogenase redu 100.0 5.8E-35 1.5E-39  234.2  22.1  257  162-423     2-267 (273)
 15 PRK13235 nifH nitrogenase redu 100.0 1.6E-34 4.2E-39  231.4  23.1  256  162-423     2-269 (274)
 16 PRK13230 nitrogenase reductase 100.0 2.5E-33 6.5E-38  224.0  22.6  255  162-422     2-279 (292)
 17 PRK11670 putative ATPase; Prov 100.0 1.2E-32 2.9E-37  220.0  22.2  232  159-405   105-354 (369)
 18 cd02032 Bchl_like This family  100.0 1.7E-32 4.4E-37  218.9  22.8  251  163-422     2-265 (267)
 19 PHA02518 ParA-like protein; Pr 100.0 9.5E-33 2.4E-37  220.5  20.0  206  162-404     1-209 (211)
 20 PRK13185 chlL protochlorophyll 100.0 2.5E-31 6.5E-36  211.7  24.4  253  161-422     2-266 (269)
 21 PRK13231 nitrogenase reductase 100.0 1.4E-31 3.6E-36  213.3  22.9  250  162-423     3-261 (264)
 22 TIGR03453 partition_RepA plasm 100.0 4.1E-31 1.1E-35  210.4  22.0  236  158-398   101-368 (387)
 23 PRK13869 plasmid-partitioning  100.0 4.9E-31 1.3E-35  210.0  19.7  234  160-398   120-385 (405)
 24 CHL00072 chlL photochlorophyll 100.0 2.9E-30 7.4E-35  205.2  22.0  251  163-422     2-265 (271)
 25 PRK10037 cell division protein 100.0 2.3E-30 5.8E-35  205.9  21.4  224  162-401     2-236 (250)
 26 PRK13234 nifH nitrogenase redu 100.0 4.5E-30 1.2E-34  204.1  22.8  257  161-422     4-271 (293)
 27 pfam01656 CbiA CobQ/CobB/MinD/ 100.0 5.5E-31 1.4E-35  209.7  16.8  202  164-369     1-210 (212)
 28 PRK13236 nitrogenase reductase 100.0 5.5E-30 1.4E-34  203.5  20.9  259  160-423     5-273 (295)
 29 COG1192 Soj ATPases involved i 100.0 1.6E-29   4E-34  200.7  21.0  239  161-404     2-254 (259)
 30 PRK13705 plasmid-partitioning  100.0 3.6E-29 9.1E-34  198.5  20.6  222  157-385   102-353 (388)
 31 PHA02519 plasmid partition pro 100.0 1.4E-28 3.5E-33  195.0  22.5  223  157-385   102-353 (387)
 32 cd02117 NifH_like This family  100.0 1.8E-29 4.5E-34  200.4  15.4  202  162-366     1-212 (212)
 33 TIGR01287 nifH nitrogenase iro 100.0 1.4E-28 3.6E-33  194.9  18.1  258  162-423     1-270 (278)
 34 cd03111 CpaE_like This protein 100.0 5.1E-29 1.3E-33  197.6  12.7  105  163-337     1-106 (106)
 35 cd03110 Fer4_NifH_child This p 100.0 9.6E-28 2.4E-32  189.8  16.2  177  163-364     1-179 (179)
 36 KOG3022 consensus              100.0 2.9E-26 7.4E-31  180.7  21.5  232  157-403    43-294 (300)
 37 COG1348 NifH Nitrogenase subun  99.9 4.1E-26   1E-30  179.7  18.5  259  162-425     2-271 (278)
 38 pfam09140 MipZ ATPase MipZ. Mi  99.9   1E-25 2.6E-30  177.3  16.4  209  162-386     1-234 (261)
 39 PRK09841 cryptic autophosphory  99.9 4.6E-25 1.2E-29  173.3  17.7  192  142-341   511-706 (726)
 40 COG1149 MinD superfamily P-loo  99.9 1.3E-24 3.4E-29  170.4  19.1  230  162-402     2-282 (284)
 41 COG3640 CooC CO dehydrogenase   99.9 1.3E-24 3.3E-29  170.5  19.0  228  163-402     2-252 (255)
 42 PRK11519 tyrosine kinase; Prov  99.9 2.1E-24 5.4E-29  169.2  19.2  175  158-340   523-700 (720)
 43 TIGR03029 EpsG chain length de  99.9 1.5E-24 3.9E-29  170.0  18.0  171  160-337   102-274 (274)
 44 cd02038 FleN-like FleN is a me  99.9 1.2E-25   3E-30  176.9  12.2  133  163-364     1-139 (139)
 45 COG0489 Mrp ATPases involved i  99.9 1.3E-23 3.3E-28  164.4  18.6  202  158-369    54-261 (265)
 46 cd02033 BchX Chlorophyllide re  99.9 6.6E-23 1.7E-27  160.0  20.2  251  159-423    29-294 (329)
 47 TIGR03018 pepcterm_TyrKin exop  99.9 5.6E-23 1.4E-27  160.4  18.0  194  134-336     5-207 (207)
 48 TIGR01281 DPOR_bchL light-inde  99.9 3.5E-23   9E-28  161.7  15.5  256  162-422     1-272 (275)
 49 TIGR01007 eps_fam capsular exo  99.9 5.5E-23 1.4E-27  160.5  13.7  178  160-343    18-198 (207)
 50 cd02037 MRP-like MRP (Multiple  99.9 1.2E-22 3.1E-27  158.4  15.2  157  163-367     1-169 (169)
 51 pfam07015 VirC1 VirC1 protein.  99.9 3.4E-21 8.7E-26  149.5  21.1  207  162-401     2-219 (231)
 52 PRK13849 putative crown gall t  99.9 6.3E-21 1.6E-25  147.8  17.1  185  162-379     2-191 (231)
 53 cd00550 ArsA_ATPase Oxyanion-t  99.9 4.5E-21 1.1E-25  148.8  13.7  198  162-365     1-238 (254)
 54 cd02035 ArsA ArsA ATPase funct  99.9 1.1E-20 2.8E-25  146.4  12.6  171  164-342     1-184 (217)
 55 cd02042 ParA ParA and ParB of   99.9 1.5E-20 3.8E-25  145.5  12.3  101  163-336     1-104 (104)
 56 TIGR02016 BchX chlorophyllide   99.8 9.2E-19 2.3E-23  134.5  15.5  229  162-405     1-253 (355)
 57 PRK10923 glnG nitrogen regulat  99.7 2.2E-15 5.7E-20  113.7  17.2  177   28-213     3-213 (469)
 58 pfam02374 ArsA_ATPase Anion-tr  99.7 4.4E-16 1.1E-20  118.1  13.4  172  164-341     3-248 (304)
 59 PRK11361 acetoacetate metaboli  99.7 5.9E-15 1.5E-19  111.1  17.2  180   23-213     1-218 (457)
 60 PRK10365 transcriptional regul  99.7 6.4E-15 1.6E-19  110.9  16.7  166   28-202     5-201 (441)
 61 TIGR01818 ntrC nitrogen regula  99.7 2.4E-15 6.1E-20  113.5  14.5  156   35-197     5-192 (471)
 62 COG2204 AtoC Response regulato  99.6 1.2E-13   3E-18  103.1  16.4  163   30-200     6-201 (464)
 63 TIGR01005 eps_transp_fam exopo  99.6 7.9E-14   2E-18  104.2  12.4  177  160-343   559-742 (778)
 64 PRK10046 dpiA two-component re  99.5 4.3E-13 1.1E-17   99.7  14.9  119   29-151     5-123 (225)
 65 cd02034 CooC The accessory pro  99.5 1.5E-13 3.8E-18  102.5   9.9  111  164-304     2-116 (116)
 66 PRK10430 DNA-binding transcrip  99.5 2.3E-12 5.8E-17   95.2  14.5  113   35-149     7-120 (239)
 67 PRK10693 response regulator of  99.5 6.4E-12 1.6E-16   92.5  15.2  119   25-150     4-124 (337)
 68 cd01983 Fer4_NifH The Fer4_Nif  99.4 1.4E-12 3.5E-17   96.6  10.7   95  163-336     1-99  (99)
 69 PRK11083 DNA-binding response   99.4 2.2E-11 5.5E-16   89.2  15.4  117   30-153     5-122 (229)
 70 cd00156 REC Signal receiver do  99.4 8.6E-12 2.2E-16   91.7  13.1  108   35-149     3-112 (113)
 71 COG4753 Response regulator con  99.4 9.1E-12 2.3E-16   91.5  12.8  103   50-154    22-124 (475)
 72 pfam00072 Response_reg Respons  99.4   2E-11 5.2E-16   89.4  13.9  106   35-147     5-111 (111)
 73 TIGR00345 arsA arsenite-activa  99.4 1.8E-12 4.7E-17   95.8   8.2  171  166-340     1-268 (330)
 74 PRK09836 DNA-binding transcrip  99.4 3.8E-11 9.6E-16   87.7  14.2  115   31-152     3-118 (226)
 75 PRK09390 fixJ response regulat  99.4 1.6E-11   4E-16   90.1  12.1  117   28-151     3-120 (202)
 76 PRK10610 chemotaxis regulatory  99.4 5.7E-11 1.5E-15   86.6  14.8  120   28-151     5-125 (129)
 77 PRK09581 pleD response regulat  99.4 4.8E-11 1.2E-15   87.1  14.0  114   27-149     3-119 (457)
 78 PRK10336 DNA-binding transcrip  99.4 3.2E-11 8.2E-16   88.1  13.0  113   33-152     5-118 (219)
 79 PRK09468 ompR osmolarity respo  99.3 5.3E-11 1.4E-15   86.8  13.9  116   30-152     7-123 (239)
 80 PRK10161 transcriptional regul  99.3 1.1E-10 2.9E-15   84.8  13.5  117   31-153     5-123 (229)
 81 PRK11517 transcriptional regul  99.3 1.4E-10 3.5E-15   84.3  13.7  114   31-152     3-117 (223)
 82 COG0745 OmpR Response regulato  99.3 2.9E-10 7.5E-15   82.2  14.8  116   32-154     4-120 (229)
 83 CHL00148 orf27 Ycf27; Reviewed  99.3   9E-11 2.3E-15   85.4  11.7  115   30-152     8-123 (240)
 84 PRK10710 DNA-binding transcrip  99.3 1.1E-10 2.9E-15   84.8  11.8  118   25-152     9-127 (240)
 85 PRK10643 DNA-binding transcrip  99.3 2.4E-10 6.2E-15   82.7  13.4  115   31-152     3-118 (222)
 86 PRK10816 DNA-binding transcrip  99.3 2.2E-10 5.7E-15   83.0  12.9  112   34-152     6-118 (223)
 87 PRK09483 response regulator; P  99.3 3.9E-10   1E-14   81.5  14.0  118   30-151     3-120 (216)
 88 TIGR02154 PhoB phosphate regul  99.2 1.1E-10 2.8E-15   84.9  10.9  149   34-206     8-158 (226)
 89 PRK09935 transcriptional regul  99.2 4.5E-10 1.1E-14   81.1  13.8  119   29-151     4-122 (210)
 90 PRK13435 response regulator; P  99.2 6.8E-10 1.7E-14   80.0  13.1  113   31-154     4-119 (141)
 91 PRK10651 transcriptional regul  99.2 4.5E-10 1.1E-14   81.1  12.0  119   29-151     7-125 (216)
 92 PRK10701 DNA-binding transcrip  99.2 2.7E-10 6.9E-15   82.4  10.8  114   31-152     4-118 (240)
 93 PRK10955 DNA-binding transcrip  99.2 3.6E-10 9.3E-15   81.7  11.3  110   34-152     7-117 (232)
 94 PRK10529 DNA-binding transcrip  99.2   4E-10   1E-14   81.4  11.3  114   31-152     4-118 (225)
 95 COG4565 CitB Response regulato  99.2 1.1E-09 2.9E-14   78.6  13.1  113   35-150     6-118 (224)
 96 COG0003 ArsA Predicted ATPase   99.2 9.4E-11 2.4E-15   85.3   7.5   51  163-215     3-53  (322)
 97 PRK11173 two-component respons  99.2 1.1E-09 2.9E-14   78.6  12.8  116   27-152     4-120 (237)
 98 PRK10766 DNA-binding transcrip  99.2 5.2E-10 1.3E-14   80.7  10.8  115   30-152     4-119 (224)
 99 PRK10403 transcriptional regul  99.2 1.5E-09 3.9E-14   77.9  13.2  120   29-152     7-126 (215)
100 PRK13557 histidine kinase; Pro  99.2 2.7E-09 6.8E-14   76.3  14.1   11  331-341   459-469 (538)
101 PRK00742 chemotaxis-specific m  99.1 1.1E-08 2.9E-13   72.5  17.0  163   28-200     2-192 (345)
102 PRK09958 DNA-binding transcrip  99.1 2.8E-09 7.2E-14   76.2  13.6  111   36-151     8-118 (204)
103 PRK13856 two-component respons  99.1 3.6E-09 9.1E-14   75.6  14.0  112   32-151     5-118 (241)
104 PRK10840 transcriptional regul  99.1 6.9E-09 1.7E-13   73.8  14.8  120   28-151     3-125 (216)
105 COG4566 TtrR Response regulato  99.1 1.6E-09 4.1E-14   77.7  11.5  116   31-152     7-122 (202)
106 PRK01077 cobyrinic acid a,c-di  99.1   8E-09   2E-13   73.4  14.9  178  162-377     4-192 (451)
107 TIGR01387 cztR_silR_copR heavy  99.1 9.6E-11 2.5E-15   85.2   5.0  142   35-191     5-165 (219)
108 TIGR02915 PEP_resp_reg putativ  99.1 6.2E-10 1.6E-14   80.2   8.9  139   59-200    24-202 (451)
109 PRK05703 flhF flagellar biosyn  99.1 2.1E-08 5.3E-13   70.9  16.0  202  118-361   155-377 (412)
110 PRK12555 chemotaxis-specific m  99.1 1.9E-08 4.9E-13   71.1  15.4  139   30-175     3-168 (340)
111 COG2197 CitB Response regulato  99.1 2.1E-08 5.4E-13   70.8  15.1  115   34-152     6-120 (211)
112 COG4567 Response regulator con  99.0   9E-09 2.3E-13   73.1  12.7  114   30-150    11-125 (182)
113 PRK11107 hybrid sensory histid  99.0 3.5E-08   9E-13   69.5  14.8  111   29-148   537-648 (920)
114 PRK11466 hybrid sensory histid  99.0 1.7E-08 4.3E-13   71.4  13.1  118   27-150   680-798 (912)
115 PRK10360 DNA-binding transcrip  99.0 2.5E-08 6.3E-13   70.4  13.8  108   37-151    10-117 (196)
116 PRK11091 aerobic respiration c  99.0 2.8E-08 7.2E-13   70.1  14.1  129   18-153   515-646 (779)
117 PRK10841 hybrid sensory kinase  99.0 3.8E-08 9.7E-13   69.3  14.4   21  300-320   826-846 (947)
118 KOG2825 consensus               98.9 8.2E-09 2.1E-13   73.4   9.6  173  161-342    18-267 (323)
119 PRK09959 hybrid sensory histid  98.9 9.2E-08 2.4E-12   66.9  14.2  115   28-149   958-1073(1197)
120 TIGR02875 spore_0_A sporulatio  98.9 9.8E-08 2.5E-12   66.7  13.2  121   29-152     3-124 (270)
121 COG1797 CobB Cobyrinic acid a,  98.9 1.5E-07 3.7E-12   65.7  13.8  200  163-401     2-212 (451)
122 PRK10100 DNA-binding transcrip  98.8 9.3E-08 2.4E-12   66.9  11.9  112   35-152    16-127 (216)
123 PRK12374 putative dithiobiotin  98.8 6.7E-07 1.7E-11   61.6  15.4  192  161-369     2-206 (231)
124 PRK00090 bioD dithiobiotin syn  98.8 1.2E-07 3.1E-12   66.2  10.7  187  163-369     1-204 (223)
125 COG3437 Response regulator con  98.8 2.3E-07 5.8E-12   64.5  11.5  115   28-148    14-131 (360)
126 PRK13886 conjugal transfer pro  98.7 2.9E-07 7.3E-12   63.9  11.6  143  161-339     2-156 (241)
127 PRK13896 cobyrinic acid a,c-di  98.7 1.3E-06 3.2E-11   59.9  13.4  179  162-381     2-190 (432)
128 TIGR00313 cobQ cobyric acid sy  98.7 3.3E-08 8.5E-13   69.6   5.0  193  164-369     1-227 (502)
129 PRK10416 cell division protein  98.7 4.7E-06 1.2E-10   56.4  15.9  179  161-376   295-496 (499)
130 COG3706 PleD Response regulato  98.6 1.9E-06 4.8E-11   58.8  13.3  119   28-152   132-252 (435)
131 PRK11475 DNA-binding transcrip  98.6 7.1E-07 1.8E-11   61.5  10.1   93   57-151    21-114 (205)
132 PRK13837 two-component VirA-li  98.5 4.8E-06 1.2E-10   56.3  13.3   59  329-387   744-803 (831)
133 COG0784 CheY FOG: CheY-like re  98.5 1.1E-05 2.9E-10   54.0  14.9  117   29-150     6-124 (130)
134 COG3947 Response regulator con  98.5 4.6E-06 1.2E-10   56.4  12.5  149   37-194     9-167 (361)
135 COG1703 ArgK Putative periplas  98.5 1.1E-05 2.8E-10   54.1  13.3  186  160-378    50-240 (323)
136 PRK11697 putative two-componen  98.4 7.9E-06   2E-10   55.0  12.3  112   33-151     5-117 (239)
137 TIGR00959 ffh signal recogniti  98.4 5.3E-05 1.3E-09   49.9  16.4  186  139-361    78-279 (439)
138 PRK06995 flhF flagellar biosyn  98.4 1.7E-05 4.4E-10   52.9  13.7  242  118-404   119-394 (404)
139 PRK00784 cobyric acid synthase  98.4 7.4E-06 1.9E-10   55.2  11.4  198  160-367     2-229 (492)
140 TIGR03499 FlhF flagellar biosy  98.4 1.5E-06 3.9E-11   59.4   7.8  131  118-284   137-282 (282)
141 COG0541 Ffh Signal recognition  98.4   6E-05 1.5E-09   49.6  16.0  173  161-371   100-290 (451)
142 PRK10867 signal recognition pa  98.4 6.8E-05 1.7E-09   49.2  16.1  173  162-371   101-291 (453)
143 PRK06731 flhF flagellar biosyn  98.4 2.7E-05 6.9E-10   51.7  13.5  169  159-369    73-256 (270)
144 pfam00448 SRP54 SRP54-type pro  98.4 6.6E-05 1.7E-09   49.3  15.2  144  162-342     2-154 (196)
145 PRK09435 arginine/ornithine tr  98.3 4.3E-05 1.1E-09   50.5  13.6  167  159-357    47-218 (325)
146 pfam03308 ArgK ArgK protein. T  98.3 1.1E-05 2.7E-10   54.2  10.4  165  160-357    28-195 (267)
147 PRK13768 GTPase; Provisional    98.3 1.9E-05 4.9E-10   52.6  11.4  181  163-376     4-199 (253)
148 PRK12727 flagellar biosynthesi  98.3 3.5E-05 8.8E-10   51.1  12.6  184  117-341   292-495 (557)
149 PRK12726 flagellar biosynthesi  98.2 3.4E-05 8.6E-10   51.1  11.8  163  158-362   203-375 (407)
150 PRK00771 signal recognition pa  98.2 0.00013 3.3E-09   47.6  14.6  171  162-371    98-285 (433)
151 COG1341 Predicted GTPase or GT  98.2 2.2E-05 5.5E-10   52.3  10.5  153  134-308    47-212 (398)
152 cd03115 SRP The signal recogni  98.2 0.00017 4.3E-09   46.8  14.8  160  163-360     2-170 (173)
153 COG0132 BioD Dethiobiotin synt  98.2 8.8E-05 2.3E-09   48.6  13.3  188  162-369     3-207 (223)
154 TIGR00064 ftsY signal recognit  98.2 0.00023 5.7E-09   46.1  14.7  220  112-374    37-283 (284)
155 KOG0519 consensus               98.1 4.6E-05 1.2E-09   50.3  10.7   57  329-385   710-770 (786)
156 PRK05632 phosphate acetyltrans  98.1 0.00039   1E-08   44.6  14.9   36   77-114    98-136 (702)
157 COG3707 AmiR Response regulato  98.1 4.7E-05 1.2E-09   50.3   9.7   80   66-148    40-119 (194)
158 KOG0781 consensus               98.1 4.2E-05 1.1E-09   50.5   9.3  189  119-340   343-542 (587)
159 PRK12724 flagellar biosynthesi  98.1 0.00055 1.4E-08   43.7  14.9  208  118-368   158-403 (432)
160 PRK12723 flagellar biosynthesi  98.1 0.00019 4.9E-09   46.5  12.4  162  159-362   172-345 (388)
161 COG2403 Predicted GTPase [Gene  98.0  0.0011 2.7E-08   41.9  16.2  198   93-327    71-299 (449)
162 PRK13558 bacterio-opsin activa  98.0 3.8E-05 9.7E-10   50.8   8.6   97   50-150    35-131 (674)
163 PRK11889 flhF flagellar biosyn  98.0 8.8E-05 2.3E-09   48.6   9.3  169  159-369   239-422 (436)
164 COG0552 FtsY Signal recognitio  98.0 0.00011 2.7E-09   48.1   9.5  175  161-374   139-338 (340)
165 TIGR00379 cobB cobyrinic acid   97.9  0.0008   2E-08   42.7  12.9  198  164-401     2-218 (464)
166 PRK05537 bifunctional sulfate   97.8 0.00045 1.1E-08   44.2  11.0  145  120-283   357-501 (568)
167 pfam10609 ParA ParA/MinD ATPas  97.8 9.3E-05 2.4E-09   48.4   7.1   63  275-339     1-65  (81)
168 cd01886 EF-G Elongation factor  97.7  0.0018 4.6E-08   40.5  12.7  149  164-364     2-154 (270)
169 cd04169 RF3 RF3 subfamily.  Pe  97.7  0.0014 3.5E-08   41.2  12.1  156  162-365     3-162 (267)
170 pfam03029 ATP_bind_1 Conserved  97.7 0.00016 4.1E-09   47.0   7.0  151  170-341     4-167 (234)
171 TIGR00750 lao LAO/AO transport  97.7  0.0041   1E-07   38.3  14.8  158  160-345    37-199 (333)
172 cd03109 DTBS Dethiobiotin synt  97.7 0.00056 1.4E-08   43.6   9.4  126  164-364     1-134 (134)
173 TIGR02956 TMAO_torS TMAO reduc  97.6 0.00078   2E-08   42.7   9.9  113   30-150   763-886 (1052)
174 cd04170 EF-G_bact Elongation f  97.6  0.0019 4.9E-08   40.3  11.8   89  273-364    62-154 (268)
175 PRK09361 radB DNA repair and r  97.6  0.0019 4.9E-08   40.3  11.7   40  159-200    21-60  (224)
176 cd04168 TetM_like Tet(M)-like   97.6   0.001 2.6E-08   42.0  10.2   85  273-360    62-149 (237)
177 COG2201 CheB Chemotaxis respon  97.6  0.0062 1.6E-07   37.2  16.3  161   30-198     3-191 (350)
178 KOG0780 consensus               97.6  0.0023 5.8E-08   39.9  11.3  174  161-373   101-293 (483)
179 PRK00741 prfC peptide chain re  97.5  0.0035 8.9E-08   38.7  11.7   73   34-106    83-162 (526)
180 cd01394 radB RadB. The archaea  97.5  0.0034 8.8E-08   38.8  11.2   40  159-200    17-56  (218)
181 COG0468 RecA RecA/RadA recombi  97.4  0.0046 1.2E-07   38.0  11.6  142  156-340    55-197 (279)
182 KOG1532 consensus               97.4  0.0025 6.3E-08   39.7  10.0  181  157-356    15-214 (366)
183 COG1419 FlhF Flagellar GTP-bin  97.4 0.00047 1.2E-08   44.1   5.7  186  115-341   151-351 (407)
184 pfam03796 DnaB_C DnaB-like hel  97.4  0.0072 1.8E-07   36.8  11.8   47  159-206    17-63  (186)
185 cd03114 ArgK-like The function  97.3  0.0063 1.6E-07   37.2  10.8  146  163-339     1-148 (148)
186 pfam00009 GTP_EFTU Elongation   97.3  0.0024   6E-08   39.8   8.5   67  273-342    65-133 (185)
187 TIGR02237 recomb_radB DNA repa  97.3  0.0015 3.9E-08   41.0   7.5  146  159-340    10-160 (223)
188 TIGR03600 phage_DnaB phage rep  97.3  0.0009 2.3E-08   42.4   6.3  111  163-282   195-313 (421)
189 cd00984 DnaB_C DnaB helicase C  97.1   0.005 1.3E-07   37.8   8.9   47  159-206    11-57  (242)
190 cd01122 GP4d_helicase GP4d_hel  97.1  0.0032 8.1E-08   39.0   7.9   46  159-205    28-73  (271)
191 PRK08082 consensus              97.1  0.0043 1.1E-07   38.2   8.4   46  160-206   202-247 (453)
192 cd01125 repA Hexameric Replica  97.1  0.0031 7.9E-08   39.0   7.7  111  163-282     2-119 (239)
193 cd01891 TypA_BipA TypA (tyrosi  97.1  0.0038 9.6E-08   38.5   8.1   77  274-353    64-143 (194)
194 PRK05595 replicative DNA helic  97.1  0.0015 3.9E-08   41.0   6.0   46  160-206   200-245 (444)
195 PRK06749 replicative DNA helic  97.1  0.0033 8.3E-08   38.9   7.5   40  163-203   187-226 (428)
196 cd01393 recA_like RecA is a  b  97.1   0.011 2.8E-07   35.6  10.2   47  157-204    15-66  (226)
197 PRK05636 replicative DNA helic  97.0  0.0034 8.7E-08   38.8   7.3  115  160-282   266-385 (507)
198 PRK07263 consensus              97.0  0.0025 6.3E-08   39.6   6.5   46  160-206   202-247 (453)
199 PRK05748 replicative DNA helic  97.0  0.0024 6.2E-08   39.7   6.3   46  160-206   202-247 (448)
200 PRK09191 two-component respons  97.0   0.013 3.3E-07   35.2   9.8   85   60-149   166-251 (261)
201 PRK13351 elongation factor G;   96.9   0.033 8.3E-07   32.8  12.3   17  260-276   451-467 (687)
202 PRK07004 replicative DNA helic  96.9   0.004   1E-07   38.4   6.7   44  163-206   214-257 (460)
203 cd00881 GTP_translation_factor  96.9  0.0052 1.3E-07   37.7   7.2   81  274-357    61-145 (189)
204 PRK06696 uridine kinase; Valid  96.8  0.0048 1.2E-07   37.9   6.8   61  138-203     6-66  (227)
205 pfam00154 RecA recA bacterial   96.8   0.036 9.2E-07   32.5  13.1   45  157-203    48-92  (322)
206 PRK08760 replicative DNA helic  96.8  0.0061 1.6E-07   37.2   7.2   46  160-206   228-273 (476)
207 KOG1533 consensus               96.8  0.0019   5E-08   40.3   4.5  103  165-287     6-109 (290)
208 TIGR00455 apsK adenylylsulfate  96.8   0.019 4.8E-07   34.2   9.5  114  157-283    15-128 (187)
209 PRK08840 replicative DNA helic  96.8  0.0044 1.1E-07   38.1   6.1   46  160-206   216-261 (464)
210 PRK07471 DNA polymerase III su  96.8   0.041   1E-06   32.2  11.4  147  139-311    22-182 (363)
211 cd00983 recA RecA is a  bacter  96.8   0.042 1.1E-06   32.1  12.7   45  157-203    51-95  (325)
212 KOG0078 consensus               96.8   0.042 1.1E-06   32.1  11.4  111  278-406    64-179 (207)
213 PRK06904 replicative DNA helic  96.7   0.006 1.5E-07   37.3   6.5  114  160-282   220-342 (472)
214 cd01885 EF2 EF2 (for archaea a  96.7   0.017 4.4E-07   34.5   8.7   66  273-341    71-138 (222)
215 TIGR01425 SRP54_euk signal rec  96.6   0.014 3.5E-07   35.1   7.8  172  161-371   121-311 (453)
216 TIGR00347 bioD dethiobiotin sy  96.6  0.0073 1.9E-07   36.8   6.3  161  166-336     2-187 (187)
217 PRK00889 adenylylsulfate kinas  96.6   0.036 9.1E-07   32.5   9.8   82  160-251     3-84  (175)
218 PRK08506 replicative DNA helic  96.6  0.0083 2.1E-07   36.4   6.4   42  160-203   192-233 (473)
219 PRK08694 consensus              96.6  0.0059 1.5E-07   37.3   5.6   44  160-204   217-260 (468)
220 PRK08006 replicative DNA helic  96.6  0.0075 1.9E-07   36.7   6.1   46  160-206   223-268 (471)
221 PRK06321 replicative DNA helic  96.6    0.01 2.6E-07   35.9   6.8   41  163-203   227-267 (472)
222 PRK09165 replicative DNA helic  96.5  0.0099 2.5E-07   35.9   6.6   40  163-202   206-259 (484)
223 pfam01583 APS_kinase Adenylyls  96.5   0.038 9.6E-07   32.4   9.4   58  161-224     2-59  (157)
224 PRK09354 recA recombinase A; P  96.5   0.063 1.6E-06   31.0  12.5   45  157-203    56-100 (350)
225 cd03288 ABCC_SUR2 The SUR doma  96.5   0.022 5.5E-07   33.9   8.0   41  159-201    45-85  (257)
226 PRK05541 adenylylsulfate kinas  96.4   0.041 1.1E-06   32.1   9.2  108  158-283     4-111 (176)
227 cd01890 LepA LepA subfamily.    96.4   0.014 3.5E-07   35.1   6.6   84  274-360    66-152 (179)
228 cd04167 Snu114p Snu114p subfam  96.4   0.056 1.4E-06   31.4   9.7   64  274-340    70-135 (213)
229 TIGR00176 mobB molybdopterin-g  96.4   0.024 6.1E-07   33.6   7.7  102  163-281     1-103 (165)
230 PRK10789 putative multidrug tr  96.3   0.069 1.8E-06   30.8   9.9  150  159-314   339-516 (569)
231 cd01123 Rad51_DMC1_radA Rad51_  96.3   0.081 2.1E-06   30.4  11.7   46  158-204    16-66  (235)
232 COG1763 MobB Molybdopterin-gua  96.3   0.037 9.3E-07   32.5   8.4   98  161-281     2-99  (161)
233 COG3706 PleD Response regulato  96.3   0.016 4.2E-07   34.6   6.4   86   62-151    18-103 (435)
234 PRK11176 lipid transporter ATP  96.2   0.038 9.7E-07   32.3   8.0   41  159-201   366-406 (581)
235 TIGR02640 gas_vesic_GvpN gas v  96.2  0.0081 2.1E-07   36.5   4.5   45  159-208    19-63  (265)
236 PRK09270 frcK putative fructos  96.2   0.017 4.2E-07   34.6   6.1   71  128-201     3-74  (230)
237 PRK09581 pleD response regulat  96.2   0.059 1.5E-06   31.2   8.9   85   63-148   185-270 (457)
238 cd04112 Rab26 Rab26 subfamily.  96.2   0.097 2.5E-06   29.9  10.4  116  274-407    49-169 (191)
239 COG0529 CysC Adenylylsulfate k  96.2   0.081 2.1E-06   30.3   9.5  113  157-284    19-131 (197)
240 COG1492 CobQ Cobyric acid synt  96.1    0.03 7.5E-07   33.0   7.1  194  162-370     2-231 (486)
241 cd03289 ABCC_CFTR2 The CFTR su  96.1   0.028 7.1E-07   33.2   6.9   41  158-201    27-67  (275)
242 COG3279 LytT Response regulato  96.0    0.05 1.3E-06   31.6   8.0  107   39-151    12-118 (244)
243 pfam00071 Ras Ras family. Incl  96.0    0.12   3E-06   29.4  10.7  110  274-401    47-161 (162)
244 COG0305 DnaB Replicative DNA h  96.0   0.047 1.2E-06   31.8   7.6   40  163-202   197-236 (435)
245 cd04121 Rab40 Rab40 subfamily.  96.0    0.12 3.1E-06   29.3  11.2  112  274-404    54-170 (189)
246 PRK05506 bifunctional sulfate   96.0     0.1 2.6E-06   29.8   9.2  112  157-283   439-550 (613)
247 TIGR01618 phage_P_loop phage n  96.0   0.015 3.9E-07   34.8   5.1  182  162-391    14-211 (229)
248 KOG2749 consensus               95.9    0.12 3.2E-06   29.2  10.9   96  104-207    47-147 (415)
249 cd04114 Rab30 Rab30 subfamily.  95.9    0.13 3.3E-06   29.1  10.0  110  274-401    55-169 (169)
250 cd04166 CysN_ATPS CysN_ATPS su  95.9   0.043 1.1E-06   32.0   6.9  103  273-384    75-186 (208)
251 PRK07773 replicative DNA helic  95.8   0.055 1.4E-06   31.4   7.4   46  160-206   202-247 (868)
252 PRK06067 flagellar accessory p  95.8    0.14 3.5E-06   28.9   9.9   43  159-203    30-72  (241)
253 cd01866 Rab2 Rab2 subfamily.    95.8    0.15 3.8E-06   28.8  10.6  113  273-403    51-168 (168)
254 PRK00007 elongation factor G;   95.8    0.15 3.8E-06   28.7  12.4   40   65-104   117-157 (693)
255 PRK08533 flagellar accessory p  95.7    0.15 3.8E-06   28.7  12.2  104  159-283    22-126 (230)
256 PRK09302 circadian clock prote  95.7    0.15 3.9E-06   28.7   9.7   97  159-282   264-364 (501)
257 cd04144 Ras2 Ras2 subfamily.    95.7   0.081 2.1E-06   30.4   7.8  135  274-426    46-188 (190)
258 PRK03846 adenylylsulfate kinas  95.7   0.023 5.8E-07   33.7   5.0   63  157-225    20-82  (198)
259 cd01861 Rab6 Rab6 subfamily.    95.7    0.16   4E-06   28.6   9.8  110  273-400    47-161 (161)
260 TIGR02868 CydC ABC transporter  95.7    0.05 1.3E-06   31.6   6.7   60  134-203   368-427 (566)
261 PRK05124 cysN sulfate adenylyl  95.7   0.035   9E-07   32.6   5.9   67  273-341   105-173 (475)
262 COG0467 RAD55 RecA-superfamily  95.6    0.13 3.3E-06   29.1   8.7   48  157-206    19-66  (260)
263 pfam03205 MobB Molybdopterin g  95.6   0.038 9.8E-07   32.3   6.0   42  163-206     2-44  (122)
264 PRK05506 bifunctional sulfate   95.6   0.038 9.8E-07   32.3   5.9   13  271-283   391-403 (613)
265 cd03228 ABCC_MRP_Like The MRP   95.5   0.052 1.3E-06   31.5   6.4   41  159-201    26-66  (171)
266 cd04125 RabA_like RabA-like su  95.5    0.13 3.4E-06   29.1   8.4  116  273-406    47-167 (188)
267 PRK03003 engA GTP-binding prot  95.5    0.19 4.7E-06   28.1  19.1  192   78-341   118-335 (474)
268 cd04117 Rab15 Rab15 subfamily.  95.5    0.18 4.5E-06   28.3   8.9  110  273-400    47-161 (161)
269 PRK11174 cysteine/glutathione   95.5    0.12 3.1E-06   29.3   8.0   41  159-202   374-414 (588)
270 smart00382 AAA ATPases associa  95.4   0.039   1E-06   32.3   5.5   41  161-203     2-42  (148)
271 cd03116 MobB Molybdenum is an   95.4   0.052 1.3E-06   31.5   6.1   40  162-203     2-41  (159)
272 cd01865 Rab3 Rab3 subfamily.    95.4    0.19   5E-06   28.0   9.9  111  274-402    49-164 (165)
273 cd00477 FTHFS Formyltetrahydro  95.4     0.2 5.1E-06   27.9  14.8  100  305-407   332-446 (524)
274 PRK05973 replicative DNA helic  95.4    0.18 4.6E-06   28.2   8.7   45  160-206    63-107 (237)
275 cd03252 ABCC_Hemolysin The ABC  95.4   0.045 1.2E-06   31.9   5.6   42  159-202    26-67  (237)
276 pfam01268 FTHFS Formate--tetra  95.4    0.21 5.3E-06   27.8  16.3   89  314-407   360-461 (555)
277 PRK13657 cyclic beta-1,2-gluca  95.3   0.037 9.4E-07   32.5   4.8   36  159-196   359-394 (585)
278 PRK07667 uridine kinase; Provi  95.2   0.066 1.7E-06   30.9   6.1   44  158-203    10-54  (190)
279 pfam00931 NB-ARC NB-ARC domain  95.2   0.016   4E-07   34.7   2.9   25  160-185    18-42  (285)
280 cd02028 UMPK_like Uridine mono  95.2   0.038 9.8E-07   32.3   4.8   40  163-204     1-40  (179)
281 TIGR03172 probable selenium-de  95.2    0.23 5.8E-06   27.6  12.1  127  163-307     1-137 (232)
282 PRK09518 bifunctional cytidyla  95.2    0.23 5.8E-06   27.6  19.2   79  274-357   499-590 (714)
283 smart00175 RAB Rab subfamily o  95.2    0.23   6E-06   27.5  10.0  111  274-402    48-163 (164)
284 TIGR02012 tigrfam_recA protein  95.2    0.12 3.1E-06   29.2   7.3   46  156-203    50-95  (322)
285 cd03254 ABCC_Glucan_exporter_l  95.2   0.038 9.8E-07   32.3   4.7   43  158-202    26-68  (229)
286 cd03248 ABCC_TAP TAP, the Tran  95.1   0.069 1.8E-06   30.8   5.8   28  159-187    38-65  (226)
287 cd01867 Rab8_Rab10_Rab13_like   95.1    0.25 6.4E-06   27.3  10.9  111  274-402    51-166 (167)
288 PRK11107 hybrid sensory histid  95.1    0.25 6.4E-06   27.3  16.5  117   29-151   669-787 (920)
289 cd03278 ABC_SMC_barmotin Barmo  95.0    0.16 4.2E-06   28.5   7.6   28  159-188    21-48  (197)
290 cd02027 APSK Adenosine 5'-phos  95.0   0.042 1.1E-06   32.1   4.5   54  163-222     1-54  (149)
291 PTZ00099 rab6; Provisional      95.0    0.27 6.8E-06   27.2  10.1  113  274-404    28-145 (176)
292 cd01868 Rab11_like Rab11-like.  95.0    0.27 6.9E-06   27.1   9.7  109  274-400    51-164 (165)
293 PRK07560 elongation factor EF-  95.0    0.27 6.9E-06   27.1   9.9   18  259-276   437-454 (730)
294 COG1484 DnaC DNA replication p  94.9   0.079   2E-06   30.4   5.8   38  160-199   104-141 (254)
295 cd03246 ABCC_Protease_Secretio  94.9    0.13 3.2E-06   29.2   6.8   36  159-196    26-61  (173)
296 pfam07755 DUF1611 Protein of u  94.9    0.28 7.2E-06   27.0  14.2  247   63-363    24-294 (302)
297 KOG0744 consensus               94.9    0.13 3.2E-06   29.1   6.7  152  160-315   176-336 (423)
298 TIGR00416 sms DNA repair prote  94.8     0.1 2.6E-06   29.7   6.2  158  161-341   103-290 (481)
299 cd03244 ABCC_MRP_domain2 Domai  94.8    0.11 2.8E-06   29.5   6.3   41  159-201    28-68  (221)
300 COG1124 DppF ABC-type dipeptid  94.8    0.18 4.7E-06   28.2   7.3   68  158-228    30-111 (252)
301 cd03249 ABC_MTABC3_MDL1_MDL2 M  94.7    0.13 3.2E-06   29.1   6.3   41  159-201    27-67  (238)
302 cd03291 ABCC_CFTR1 The CFTR su  94.7   0.042 1.1E-06   32.1   3.8   29  158-187    60-88  (282)
303 cd03245 ABCC_bacteriocin_expor  94.7   0.069 1.7E-06   30.8   4.9   38  159-198    28-65  (220)
304 PRK11819 putative ABC transpor  94.7    0.28 7.2E-06   27.0   8.1   28  159-187   348-375 (556)
305 PRK12740 elongation factor G;   94.7    0.21 5.2E-06   27.9   7.3   17  260-276   436-452 (670)
306 COG4988 CydD ABC-type transpor  94.7   0.071 1.8E-06   30.7   5.0  125  159-290   345-491 (559)
307 PRK04328 hypothetical protein;  94.6     0.1 2.6E-06   29.7   5.8   44  158-203    21-64  (250)
308 cd02023 UMPK Uridine monophosp  94.6   0.066 1.7E-06   30.9   4.7  177  163-366     1-181 (198)
309 COG1066 Sms Predicted ATP-depe  94.6    0.34 8.5E-06   26.6  10.2   64  126-200    66-129 (456)
310 PRK12739 elongation factor G;   94.6    0.34 8.7E-06   26.5  13.6   37   66-103   117-155 (693)
311 pfam06745 KaiC KaiC. This fami  94.5    0.11 2.9E-06   29.5   5.7   45  158-203    16-60  (231)
312 PRK09112 DNA polymerase III su  94.5    0.35 8.9E-06   26.4  11.3   51  131-187    14-70  (352)
313 cd01860 Rab5_related Rab5-rela  94.5    0.36 9.1E-06   26.4   9.9  109  274-400    49-162 (163)
314 PRK09554 feoB ferrous iron tra  94.5    0.36 9.1E-06   26.4   8.9   10  277-286   484-493 (772)
315 PRK06217 hypothetical protein;  94.4    0.31 7.8E-06   26.8   7.8  175  162-401     2-178 (185)
316 PRK08261 fabG 3-ketoacyl-(acyl  94.4    0.37 9.4E-06   26.3  12.9  119   75-202    77-242 (447)
317 COG1123 ATPase components of v  94.4    0.12 3.1E-06   29.3   5.7   66  159-226   315-394 (539)
318 PRK10751 molybdopterin-guanine  94.4    0.15 3.7E-06   28.8   6.1   40  162-203     3-42  (170)
319 cd03251 ABCC_MsbA MsbA is an e  94.4    0.13 3.4E-06   29.0   5.9   43  158-202    25-67  (234)
320 cd04113 Rab4 Rab4 subfamily.    94.4    0.38 9.6E-06   26.2  10.1  109  274-400    48-161 (161)
321 cd01883 EF1_alpha Eukaryotic e  94.3    0.15 3.9E-06   28.7   6.0   67  273-341    75-150 (219)
322 cd03253 ABCC_ATM1_transporter   94.3    0.11 2.8E-06   29.6   5.3   43  158-202    24-66  (236)
323 COG3598 RepA RecA-family ATPas  94.3    0.38 9.8E-06   26.2  11.2   47  159-206    87-142 (402)
324 pfam08419 consensus             94.3    0.05 1.3E-06   31.6   3.6   65  115-183    28-96  (116)
325 PRK11160 cysteine/glutathione   94.3    0.21 5.3E-06   27.8   6.7   41  159-201   365-405 (575)
326 cd04148 RGK RGK subfamily.  Th  94.2     0.4   1E-05   26.1  11.6  110  275-402    50-164 (221)
327 PRK09519 recA recombinase A; R  94.2     0.4   1E-05   26.1  11.8   12  330-341   684-695 (790)
328 PRK04220 2-phosphoglycerate ki  94.2   0.056 1.4E-06   31.3   3.6   25  162-186    92-116 (306)
329 TIGR00763 lon ATP-dependent pr  94.2   0.033 8.5E-07   32.7   2.4   33  157-190   445-478 (941)
330 PRK08181 transposase; Validate  94.2    0.28 7.3E-06   27.0   7.2  117   60-200    19-143 (269)
331 cd01894 EngA1 EngA1 subfamily.  94.2    0.14 3.7E-06   28.8   5.6   67  274-343    44-120 (157)
332 PRK01889 ribosome-associated G  94.2    0.42 1.1E-05   26.0   9.8   96   79-184   113-216 (353)
333 pfam00485 PRK Phosphoribulokin  94.2   0.048 1.2E-06   31.7   3.2  185  163-367     1-191 (196)
334 COG1160 Predicted GTPases [Gen  94.1    0.42 1.1E-05   26.0  15.1  210   78-357    84-318 (444)
335 PRK06547 hypothetical protein;  94.1   0.093 2.4E-06   30.0   4.6   37  158-198    12-48  (184)
336 cd01887 IF2_eIF5B IF2/eIF5B (i  94.1    0.22 5.5E-06   27.7   6.4   66  274-342    49-116 (168)
337 cd00154 Rab Rab family.  Rab G  94.1    0.37 9.5E-06   26.3   7.6   78  273-350    47-127 (159)
338 cd03229 ABC_Class3 This class   94.0    0.19 4.8E-06   28.1   6.0   28  158-186    23-50  (178)
339 cd04122 Rab14 Rab14 subfamily.  94.0    0.44 1.1E-05   25.8   8.6  111  273-401    49-164 (166)
340 COG1663 LpxK Tetraacyldisaccha  94.0    0.23   6E-06   27.5   6.4   70  132-203    18-89  (336)
341 pfam08423 Rad51 Rad51. Rad51 i  93.9    0.46 1.2E-05   25.7  11.6   46  158-204    40-90  (261)
342 cd01869 Rab1_Ypt1 Rab1/Ypt1 su  93.9    0.47 1.2E-05   25.7  10.9  112  273-402    49-165 (166)
343 cd03297 ABC_ModC_molybdenum_tr  93.9    0.14 3.7E-06   28.8   5.2   26  160-186    22-47  (214)
344 cd04163 Era Era subfamily.  Er  93.8    0.11 2.8E-06   29.5   4.5   65  275-342    51-125 (168)
345 PRK13409 putative ATPase RIL;   93.8    0.49 1.2E-05   25.5   7.8  140  159-309   363-515 (590)
346 PRK00139 murE UDP-N-acetylmura  93.7    0.34 8.8E-06   26.5   6.9   35  159-197    98-132 (481)
347 TIGR02632 RhaD_aldol-ADH rhamn  93.7   0.061 1.6E-06   31.1   3.0  248   28-319   257-563 (709)
348 cd04155 Arl3 Arl3 subfamily.    93.7    0.29 7.5E-06   26.9   6.5   83  274-358    57-143 (173)
349 cd04115 Rab33B_Rab33A Rab33B/R  93.7    0.51 1.3E-05   25.4   9.7  109  274-400    50-168 (170)
350 cd04123 Rab21 Rab21 subfamily.  93.7    0.51 1.3E-05   25.4   8.6  111  273-401    47-162 (162)
351 COG2074 2-phosphoglycerate kin  93.7     0.2   5E-06   28.0   5.6  237  118-402    39-287 (299)
352 PRK05480 uridine kinase; Provi  93.7    0.14 3.6E-06   28.8   4.8  182  161-366     6-188 (209)
353 cd03257 ABC_NikE_OppD_transpor  93.6    0.19 4.8E-06   28.1   5.4   44  158-203    28-71  (228)
354 cd01121 Sms Sms (bacterial rad  93.6    0.16   4E-06   28.6   5.0   53  137-199    66-118 (372)
355 PRK02006 murD UDP-N-acetylmura  93.6    0.52 1.3E-05   25.4  11.5  119   64-197    18-154 (501)
356 COG2274 SunT ABC-type bacterio  93.6    0.09 2.3E-06   30.1   3.7   42  159-202   497-538 (709)
357 pfam02421 FeoB_N Ferrous iron   93.6    0.31 7.8E-06   26.8   6.4   79  274-357    45-135 (188)
358 KOG0635 consensus               93.6    0.28 7.1E-06   27.1   6.2  108  159-284    29-139 (207)
359 COG0378 HypB Ni2+-binding GTPa  93.6    0.54 1.4E-05   25.3   8.6   45  161-208    13-58  (202)
360 cd04147 Ras_dva Ras-dva subfam  93.5    0.54 1.4E-05   25.3   8.5  111  274-402    46-164 (198)
361 cd01120 RecA-like_NTPases RecA  93.5    0.16 4.1E-06   28.5   4.9   38  164-203     2-39  (165)
362 PRK10875 recD exonuclease V su  93.5    0.44 1.1E-05   25.8   7.1   74  134-210   127-210 (607)
363 cd04127 Rab27A Rab27a subfamil  93.5    0.55 1.4E-05   25.2  10.0  111  275-403    63-179 (180)
364 cd01895 EngA2 EngA2 subfamily.  93.5    0.23 5.8E-06   27.6   5.6   79  274-355    49-140 (174)
365 PRK11147 ABC transporter ATPas  93.4    0.36 9.2E-06   26.4   6.6  146  159-312   343-501 (632)
366 PRK00093 engA GTP-binding prot  93.4    0.58 1.5E-05   25.1  17.6  207   79-358    85-313 (438)
367 pfam02702 KdpD Osmosensitive K  93.4    0.36 9.1E-06   26.4   6.5   44  158-202     1-44  (211)
368 PRK08233 hypothetical protein;  93.3    0.59 1.5E-05   25.0   9.1  156  161-365     3-160 (182)
369 PRK08691 DNA polymerase III su  93.3    0.48 1.2E-05   25.6   7.0   33  116-148   322-354 (704)
370 cd02025 PanK Pantothenate kina  93.2    0.32 8.2E-06   26.7   6.1   39  163-202     1-40  (220)
371 PRK08939 primosomal protein Dn  93.2    0.38 9.6E-06   26.3   6.4   75  121-199   119-193 (306)
372 pfam02492 cobW CobW/HypB/UreG,  93.2    0.61 1.5E-05   25.0  13.0  156  164-355     2-163 (174)
373 cd01889 SelB_euk SelB subfamil  93.2    0.26 6.6E-06   27.2   5.6   66  273-341    66-133 (192)
374 PRK10419 nikE nickel transport  93.2     0.1 2.6E-06   29.7   3.5   43  158-202    35-77  (266)
375 cd04152 Arl4_Arl7 Arl4/Arl7 su  93.2    0.62 1.6E-05   24.9   8.8  118  274-405    51-174 (183)
376 PRK03003 engA GTP-binding prot  93.1    0.52 1.3E-05   25.4   7.0   33  162-197   120-152 (474)
377 cd04171 SelB SelB subfamily.    93.1    0.23 5.9E-06   27.5   5.2   66  275-342    51-118 (164)
378 TIGR02928 TIGR02928 orc1/cdc6   93.1    0.64 1.6E-05   24.8   9.5  186  139-372    26-219 (383)
379 cd03290 ABCC_SUR1_N The SUR do  93.1    0.22 5.5E-06   27.7   5.0   37  158-196    24-60  (218)
380 cd04120 Rab12 Rab12 subfamily.  93.1    0.64 1.6E-05   24.8   9.9  115  274-406    48-168 (202)
381 PRK08327 acetolactate synthase  93.0    0.66 1.7E-05   24.7  13.7   23  172-195   230-252 (568)
382 PRK06526 transposase; Provisio  93.0    0.18 4.7E-06   28.2   4.5  116   60-200    12-135 (254)
383 KOG2004 consensus               93.0    0.11 2.9E-06   29.4   3.5   32  158-190   435-466 (906)
384 PRK00652 lpxK tetraacyldisacch  92.9    0.41   1E-05   26.0   6.2   70  132-202    17-90  (334)
385 PTZ00301 uridine kinase; Provi  92.9    0.26 6.7E-06   27.2   5.3  184  162-367     4-190 (210)
386 PRK12339 2-phosphoglycerate ki  92.9    0.12   3E-06   29.4   3.4   24  163-186     4-27  (197)
387 pfam01695 IstB IstB-like ATP b  92.8    0.23 5.9E-06   27.6   4.9   40  159-200    45-84  (178)
388 PRK10636 putative ABC transpor  92.8    0.69 1.8E-05   24.6   7.4  142  159-312   336-491 (638)
389 PRK09140 2-dehydro-3-deoxy-6-p  92.8     0.7 1.8E-05   24.6   8.6   69   79-149    35-103 (206)
390 TIGR02203 MsbA_lipidA lipid A   92.8   0.076 1.9E-06   30.5   2.4  120   61-199   298-423 (603)
391 PRK10790 putative multidrug tr  92.8     0.7 1.8E-05   24.6   9.2   41  159-201   365-405 (593)
392 pfam09818 ABC_ATPase Predicted  92.8    0.17 4.4E-06   28.4   4.1  118   77-203   220-351 (447)
393 PRK10522 multidrug transporter  92.7    0.71 1.8E-05   24.5   7.4   42  159-202   347-388 (547)
394 cd04154 Arl2 Arl2 subfamily.    92.7    0.66 1.7E-05   24.8   7.1   83  274-358    57-143 (173)
395 KOG1805 consensus               92.7    0.41 1.1E-05   26.0   6.0  129  161-306   684-829 (1100)
396 cd01124 KaiC KaiC is a circadi  92.7    0.23   6E-06   27.5   4.8   36  166-202     3-38  (187)
397 PRK08904 consensus              92.6    0.74 1.9E-05   24.5   8.1   86   60-148    16-101 (207)
398 PRK09183 transposase/IS protei  92.6    0.25 6.3E-06   27.4   4.8  112   60-200    15-138 (258)
399 cd04124 RabL2 RabL2 subfamily.  92.6    0.74 1.9E-05   24.4   8.1  107  273-401    47-158 (161)
400 COG1116 TauB ABC-type nitrate/  92.6     0.6 1.5E-05   25.0   6.7   53  158-213    26-81  (248)
401 PRK08118 topology modulation p  92.6     0.2 5.2E-06   27.9   4.3   94  162-313     2-95  (167)
402 KOG1534 consensus               92.6    0.75 1.9E-05   24.4   8.7  104  164-287     6-110 (273)
403 KOG4658 consensus               92.6     0.2 5.1E-06   27.9   4.3   44  137-187   161-204 (889)
404 PRK07455 keto-hydroxyglutarate  92.5    0.76 1.9E-05   24.4   8.5   87   60-149    19-105 (210)
405 cd01884 EF_Tu EF-Tu subfamily.  92.4    0.39   1E-05   26.1   5.6   67  274-342    64-132 (195)
406 cd01888 eIF2_gamma eIF2-gamma   92.4    0.39 9.9E-06   26.2   5.6   65  275-341    83-150 (203)
407 TIGR03201 dearomat_had 6-hydro  92.4    0.79   2E-05   24.3  10.2   49  157-212   163-211 (349)
408 cd01879 FeoB Ferrous iron tran  92.4    0.63 1.6E-05   24.9   6.6   59  295-358    73-133 (158)
409 cd03250 ABCC_MRP_domain1 Domai  92.3    0.16   4E-06   28.6   3.5   28  158-186    28-55  (204)
410 PRK07261 topology modulation p  92.3    0.23   6E-06   27.5   4.3   32  163-199     2-33  (171)
411 TIGR03594 GTPase_EngA ribosome  92.3    0.54 1.4E-05   25.3   6.2  216   68-357    72-311 (429)
412 cd00878 Arf_Arl Arf (ADP-ribos  92.3    0.75 1.9E-05   24.4   6.9   83  274-358    42-128 (158)
413 TIGR02397 dnaX_nterm DNA polym  92.3    0.21 5.2E-06   27.9   4.0  159  140-327    20-227 (363)
414 PRK12338 hypothetical protein;  92.2    0.15 3.9E-06   28.7   3.3   30  163-196     5-34  (320)
415 cd04134 Rho3 Rho3 subfamily.    92.2    0.83 2.1E-05   24.1  10.0  129  273-408    46-181 (189)
416 cd01878 HflX HflX subfamily.    92.2    0.84 2.1E-05   24.1   8.4   52  291-342   115-167 (204)
417 KOG2968 consensus               92.2    0.84 2.1E-05   24.1  11.3   57  263-319   696-753 (1158)
418 COG1160 Predicted GTPases [Gen  92.2    0.49 1.2E-05   25.6   5.8   18  107-124   179-198 (444)
419 cd00009 AAA The AAA+ (ATPases   92.2    0.23 5.9E-06   27.6   4.2   39  160-200    18-56  (151)
420 cd03294 ABC_Pro_Gly_Bertaine T  92.2    0.39 9.9E-06   26.2   5.3   42  158-201    47-88  (269)
421 cd04137 RheB Rheb (Ras Homolog  92.2    0.84 2.2E-05   24.1  11.0  119  274-410    48-172 (180)
422 cd03369 ABCC_NFT1 Domain 2 of   92.1    0.87 2.2E-05   24.0   8.5   41  159-201    32-72  (207)
423 COG1493 HprK Serine kinase of   92.0    0.88 2.2E-05   24.0   9.0   89   94-183    69-166 (308)
424 PTZ00141 elongation factor 1 a  92.0    0.27 6.8E-06   27.2   4.3   14  102-115   106-119 (443)
425 PRK05855 short chain dehydroge  92.0    0.22 5.7E-06   27.6   3.9  155  105-269   232-421 (582)
426 PRK05564 DNA polymerase III su  92.0    0.89 2.3E-05   23.9  10.0   42  140-187    10-51  (313)
427 pfam05729 NACHT NACHT domain.   91.9     0.2   5E-06   28.0   3.6   27  162-189     1-27  (165)
428 cd03258 ABC_MetN_methionine_tr  91.9    0.46 1.2E-05   25.7   5.5   43  158-202    28-70  (233)
429 PRK12377 putative replication   91.9    0.33 8.5E-06   26.6   4.7   68  126-198    61-136 (248)
430 PRK06872 DNA polymerase III su  91.9    0.92 2.3E-05   23.9   8.4   32  117-148   319-350 (696)
431 cd03256 ABC_PhnC_transporter A  91.9    0.61 1.6E-05   25.0   6.0   43  158-202    24-66  (241)
432 PRK13506 formate--tetrahydrofo  91.8    0.44 1.1E-05   25.8   5.3   52  157-212    50-104 (577)
433 PRK12337 2-phosphoglycerate ki  91.8    0.19 4.9E-06   28.0   3.4   26  161-186   261-286 (492)
434 PRK08116 hypothetical protein;  91.8    0.33 8.4E-06   26.6   4.6   38  160-199   107-144 (262)
435 PRK05718 keto-hydroxyglutarate  91.8    0.93 2.4E-05   23.8   7.9   86   60-148    21-106 (212)
436 cd00876 Ras Ras family.  The R  91.8    0.93 2.4E-05   23.8  10.6  110  273-400    45-160 (160)
437 cd03247 ABCC_cytochrome_bd The  91.8    0.93 2.4E-05   23.8   7.1   36  159-196    26-61  (178)
438 PRK12317 elongation factor 1-a  91.6    0.65 1.6E-05   24.8   6.0   64  275-340    85-152 (426)
439 PRK10490 sensor protein KdpD;   91.6    0.97 2.5E-05   23.7   8.5   21   60-85     90-110 (895)
440 PRK10070 glycine betaine trans  91.6    0.98 2.5E-05   23.7   7.2   96  117-222    17-127 (400)
441 PRK08782 consensus              91.6    0.98 2.5E-05   23.7   9.5   87   60-149    23-109 (219)
442 COG1072 CoaA Panthothenate kin  91.6    0.99 2.5E-05   23.7   7.9   72  163-240    84-157 (283)
443 pfam02572 CobA_CobO_BtuR ATP:c  91.5    0.84 2.1E-05   24.1   6.5   37  160-199     3-39  (172)
444 TIGR01846 type_I_sec_HlyB type  91.5    0.24   6E-06   27.5   3.6  107  159-291   489-607 (703)
445 TIGR03375 type_I_sec_LssB type  91.4    0.29 7.4E-06   26.9   4.0   37  159-198   489-525 (694)
446 cd03261 ABC_Org_Solvent_Resist  91.4    0.62 1.6E-05   24.9   5.7   39  158-198    23-61  (235)
447 TIGR02173 cyt_kin_arch cytidyl  91.4    0.15 3.7E-06   28.8   2.4  108  164-315     2-112 (173)
448 TIGR01394 TypA_BipA GTP-bindin  91.4   0.056 1.4E-06   31.3   0.3  126  275-406    70-203 (609)
449 PRK00089 era GTP-binding prote  91.4     0.2 5.1E-06   27.9   3.1  115  158-342     6-130 (296)
450 cd04136 Rap_like Rap-like subf  91.4       1 2.6E-05   23.5  10.1  109  274-400    48-162 (163)
451 pfam02399 Herpes_ori_bp Origin  91.3    0.62 1.6E-05   24.9   5.6  162   22-207   128-322 (829)
452 COG4167 SapF ABC-type antimicr  91.2    0.23 5.9E-06   27.5   3.3   49  158-208    36-84  (267)
453 TIGR00972 3a0107s01c2 phosphat  91.2     1.1 2.8E-05   23.4   8.4   50  159-209    25-78  (248)
454 PRK12771 putative glutamate sy  91.2     1.1 2.8E-05   23.4  16.2   70  135-212   107-180 (560)
455 cd01863 Rab18 Rab18 subfamily.  91.1     1.1 2.8E-05   23.4   8.7  108  274-400    48-161 (161)
456 cd04176 Rap2 Rap2 subgroup.  T  91.1     1.1 2.8E-05   23.4  10.7  108  275-400    49-162 (163)
457 PRK11823 DNA repair protein Ra  91.1    0.47 1.2E-05   25.6   4.8   34  164-199    92-125 (454)
458 cd04153 Arl5_Arl8 Arl5/Arl8 su  91.0    0.94 2.4E-05   23.8   6.3   82  274-357    58-143 (174)
459 cd04150 Arf1_5_like Arf1-Arf5-  91.0    0.85 2.2E-05   24.1   6.1   83  274-358    43-129 (159)
460 cd01864 Rab19 Rab19 subfamily.  91.0    0.73 1.9E-05   24.5   5.7  109  274-400    51-165 (165)
461 PRK13505 formate--tetrahydrofo  90.9    0.59 1.5E-05   25.0   5.1   90  313-407   359-462 (556)
462 PTZ00336 elongation factor 1-a  90.9    0.42 1.1E-05   26.0   4.3   12  296-307   108-119 (449)
463 cd04160 Arfrp1 Arfrp1 subfamil  90.6    0.92 2.3E-05   23.9   6.0   81  274-356    49-133 (167)
464 PRK08104 consensus              90.6     1.2 3.1E-05   23.1   8.0   67   79-148    40-106 (212)
465 cd04158 ARD1 ARD1 subfamily.    90.6     1.1 2.9E-05   23.3   6.4  118  273-404    41-164 (169)
466 cd00879 Sar1 Sar1 subfamily.    90.5     1.2 3.2E-05   23.1   7.0   85  274-360    62-150 (190)
467 PTZ00265 multidrug resistance   90.4     0.7 1.8E-05   24.6   5.2   43  159-203   409-452 (1467)
468 PRK07003 DNA polymerase III su  90.4     1.3 3.2E-05   23.0   9.0   33  116-148   322-354 (816)
469 PRK07952 DNA replication prote  90.4    0.56 1.4E-05   25.2   4.7   33  163-197    98-130 (242)
470 cd02029 PRK_like Phosphoribulo  90.4    0.54 1.4E-05   25.3   4.6   38  163-202     1-38  (277)
471 smart00177 ARF ARF-like small   90.4     1.1 2.8E-05   23.3   6.2  112  274-400    56-173 (175)
472 PRK13507 formate--tetrahydrofo  90.3    0.69 1.7E-05   24.6   5.1   92  313-407   389-491 (587)
473 PRK04308 murD UDP-N-acetylmura  90.3     1.3 3.3E-05   22.9  12.0  118   63-197    15-142 (445)
474 KOG0448 consensus               90.2     1.3 3.4E-05   22.9   6.7   76  276-354   207-287 (749)
475 COG0572 Udk Uridine kinase [Nu  90.2    0.46 1.2E-05   25.7   4.1  185  159-367     6-191 (218)
476 PRK06015 keto-hydroxyglutarate  90.2     1.3 3.4E-05   22.9  10.0   86   60-148    21-106 (212)
477 pfam07279 DUF1442 Protein of u  90.2     1.3 3.4E-05   22.9  10.9   73  110-197     3-76  (218)
478 cd04141 Rit_Rin_Ric Rit/Rin/Ri  90.2     1.3 3.4E-05   22.9  10.0  114  274-405    49-168 (172)
479 cd03215 ABC_Carb_Monos_II This  90.1     1.4 3.5E-05   22.8   7.5   45  157-203    22-66  (182)
480 cd04149 Arf6 Arf6 subfamily.    90.0     1.3 3.4E-05   22.8   6.4   83  274-358    52-138 (168)
481 PRK04213 GTP-binding protein;   90.0     1.4 3.5E-05   22.8   6.4   42  315-359   112-153 (195)
482 PRK00049 elongation factor Tu;  90.0    0.82 2.1E-05   24.2   5.3   66  274-341    75-142 (397)
483 pfam01935 DUF87 Domain of unkn  90.0    0.61 1.5E-05   25.0   4.6   43  161-204    23-65  (218)
484 PRK07133 DNA polymerase III su  90.0     1.4 3.5E-05   22.8   9.3   43  140-188    24-66  (718)
485 COG0028 IlvB Thiamine pyrophos  90.0     1.4 3.5E-05   22.8  14.0   77   34-114    21-98  (550)
486 cd00880 Era_like Era (E. coli   89.9     0.7 1.8E-05   24.6   4.9   64  276-342    46-118 (163)
487 cd04161 Arl2l1_Arl13_like Arl2  89.9    0.99 2.5E-05   23.7   5.6   85  273-359    41-129 (167)
488 pfam01081 Aldolase KDPG and KH  89.9     1.4 3.5E-05   22.8   8.3   85   61-148    15-99  (196)
489 COG4987 CydC ABC-type transpor  89.9    0.54 1.4E-05   25.3   4.2   39  159-199   362-400 (573)
490 TIGR02770 nickel_nikD nickel i  89.8    0.31 7.8E-06   26.8   3.0  203  158-395     9-236 (239)
491 COG4108 PrfC Peptide chain rel  89.8     1.3 3.3E-05   23.0   6.1   19  287-305    95-113 (528)
492 cd04111 Rab39 Rab39 subfamily.  89.8     1.4 3.6E-05   22.7  10.3  112  276-405    53-170 (211)
493 PRK07994 DNA polymerase III su  89.8     1.4 3.6E-05   22.7   8.4   46  105-150   146-191 (643)
494 cd03230 ABC_DR_subfamily_A Thi  89.8     1.4 3.6E-05   22.7   7.1   42  158-201    23-64  (173)
495 cd00877 Ran Ran (Ras-related n  89.8     1.4 3.6E-05   22.7  11.4  111  274-405    48-163 (166)
496 pfam00025 Arf ADP-ribosylation  89.8     1.4 3.6E-05   22.7   9.9  111  274-399    57-173 (174)
497 PRK11831 putative ABC transpor  89.8    0.78   2E-05   24.3   5.0   41  158-200    31-71  (269)
498 PRK12810 gltD glutamate syntha  89.8     1.4 3.7E-05   22.7   9.6   72  134-213   111-187 (472)
499 TIGR01054 rgy reverse gyrase;   89.8    0.41 1.1E-05   26.0   3.6  150  118-281    44-216 (1843)
500 PRK10787 DNA-binding ATP-depen  89.7    0.42 1.1E-05   25.9   3.6   53  137-190   325-377 (784)

No 1  
>COG4963 CpaE Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]
Probab=100.00  E-value=0  Score=383.42  Aligned_cols=359  Identities=31%  Similarity=0.472  Sum_probs=293.5

Q ss_pred             HHCCCCCEEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHH
Q ss_conf             64018730599983898999999988641100202237306998999999861899849999805987677889998885
Q gi|254780725|r   22 SMCSLPRISVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAE  101 (427)
Q Consensus        22 ~~~~~~~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~  101 (427)
                      ..+..++.+...+|..-.+...+...  +.++..+-.-...|.-.....++.-.+.+-..+.+.....++.+--++    
T Consensus         5 ~~a~~~~~~~~~i~~~s~~~v~~~~~--~~~~~~~~~~~~~~~d~~~~~~~~f~~~~~~~~~~~~~~~~d~~~~~~----   78 (366)
T COG4963           5 MMEMGVLFLAILITPASNHGVNIANG--MQLILNLDLINKKDADFLSLVHSIFVDEGAEPLGSETARLADIKNIKE----   78 (366)
T ss_pred             HHCCCCEEECEEEEECCCCCCCHHHH--HHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCEEEECCCHHHHHHHHH----
T ss_conf             10245332021688725666204220--477765432113672022123314578775431332011135555566----


Q ss_pred             HCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHH
Q ss_conf             32899808998168718999999976562643189998999997631023322234567537999746988775689999
Q gi|254780725|r  102 VCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHN  181 (427)
Q Consensus       102 ~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~n  181 (427)
                                         ....+++|+.|++..+.               ...+.++.||+++|+|+|||+|.||+|+|
T Consensus        79 -------------------~~~~~~a~~~~~v~~~~---------------~s~s~~~~~r~iafl~akgg~g~stlA~n  124 (366)
T COG4963          79 -------------------NLAAIRAGVNDCVDIES---------------DSISIAQQGRELAFLGAKGGVGTSTLAHN  124 (366)
T ss_pred             -------------------HHHHHHHHHHHEEECCC---------------CCCHHHHHCEEEEEEEECCCCCHHHHHHH
T ss_conf             -------------------77887642101000245---------------65012110328999960588666899999


Q ss_pred             HHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCH
Q ss_conf             99999962699499997879898603343899878988863184561243376532024898068724876120320799
Q gi|254780725|r  182 CAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDE  261 (427)
Q Consensus       182 LA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~  261 (427)
                      +||.++...+..|+|+|+|+++|+.+++|++++.+++++++++|+|+|+.++++.++++.+||++++++.++...+++..
T Consensus       125 ~a~~l~~~~~~~v~L~DL~~~~G~~~~~l~~~~a~~i~~~~~~peRLDq~lld~~~~~~~~~l~ll~a~~~~~~~~d~~~  204 (366)
T COG4963         125 LAKGLAILSGAAVLLVDLDLQGGTAALYLDQDPAFGIAEAVKQPERLDQVLLDSLLTRLASGLKLLAAPTELAKNYDLKT  204 (366)
T ss_pred             HHHHHHHHCCCCEEEEECCCCCCCHHHHCCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCEEECCCCCHHHHCCCCC
T ss_conf             99998641487389997688876123430787214589886097876078777898616887633037744565215331


Q ss_pred             HHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCC
Q ss_conf             99999899985128889973888889899999862012543578776889999999999998198767538999565898
Q gi|254780725|r  262 KMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTP  341 (427)
Q Consensus       262 ~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~  341 (427)
                      +.+..+++.++..||+||+|+|+.|.+|+..+|..||.+++|++++++|+|+++++++.+++.++++.++++|+|+++.+
T Consensus       205 ~~~~~Ll~~~~~~~~~vV~Dlp~~~~~~t~~vL~~Sd~iviv~e~sl~slR~ak~lld~l~~~r~~~~~p~lv~n~~~~~  284 (366)
T COG4963         205 GAVERLLDLLRGSFDFVVVDLPNIWTDWTRQVLSGSDEIVIVAEPSLASLRNAKELLDELKRLRPNDPKPILVLNRVGVP  284 (366)
T ss_pred             CHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCC
T ss_conf             26999999764028838971897662589999862884999963638989999999999997377988956886522788


Q ss_pred             CCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCC--CCHHHHHHH
Q ss_conf             752005999999848953799068799999988479618988899989999999999985221223211--105899998
Q gi|254780725|r  342 KKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIANLLVDFSRVLMGRVTVSKPQ--SAMYTKIKK  419 (427)
Q Consensus       342 ~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~~~~~La~~i~gr~~~~~~k--~~~~~~l~~  419 (427)
                      +.++  .++|++.+|.+....+|+|+..+..|.|+|+|+.|.+|++|+++++.++++.+.++....+.+  +++.+.+.+
T Consensus       285 ~~~~--~~dl~~~~~i~~~~~~p~d~~~~~~A~n~g~~l~E~~~~~~~~k~l~~la~~l~~~~~~~r~~~~~~l~~~l~k  362 (366)
T COG4963         285 KRPE--PSDLEEILGIESLLVLPFDPALFGDAANNGRMLSEVDPGSPAAKALAQLAQSLGGRISGERRKKLRGLGKLLGK  362 (366)
T ss_pred             CCCC--HHHHHHHHCCCHHCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH
T ss_conf             8999--99998884884001366770544444206960222377875889999999985376672101357889999877


Q ss_pred             HHH
Q ss_conf             742
Q gi|254780725|r  420 IFN  422 (427)
Q Consensus       420 lf~  422 (427)
                      +|+
T Consensus       363 ~~~  365 (366)
T COG4963         363 LFR  365 (366)
T ss_pred             HHC
T ss_conf             504


No 2  
>CHL00175 minD septum-site determining protein; Validated
Probab=100.00  E-value=0  Score=323.35  Aligned_cols=261  Identities=19%  Similarity=0.275  Sum_probs=226.8

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCC--CCHHHHHCCCCCHHHHHHH
Q ss_conf             45675379997469887756899999999996269949999787989860334389987--8988863184561243376
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPI--NSISDAIYPVGRIDKAFVS  234 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~--~~l~d~l~~~~rlD~~~l~  234 (427)
                      .+..+|||+|.|+||||||||+|+|||++||+ .|++|+++|+|+++++++.+||+++.  +++.+++.+..++++..+.
T Consensus         9 ~~~m~kiIaV~s~KGGVGKTT~a~NLa~aLA~-~G~kVlliD~D~~~~n~~~~lg~~~~~~~~~~~vl~g~~~l~~~~i~   87 (279)
T CHL00175          9 VATMTRIIVITSGKGGVGKTTTTANLGMSIAR-LGYRVALIDADIGLRNLDLLLGLENRVVYTAMEVLEGECRLDQALIR   87 (279)
T ss_pred             HCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCEEE
T ss_conf             25988699997489984489999999999997-89988999578999987532686666667476640787664301342


Q ss_pred             HHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHH-CCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHH
Q ss_conf             532024898068724876120320799999998999851-2888997388888989999986201254357877688999
Q gi|254780725|r  235 RLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQ-IFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRN  313 (427)
Q Consensus       235 ~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~-~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~  313 (427)
                      .   ...++++++++..... .+.+..+.+..+++.++. .|||||||||++++.++.+++..||.+++|++|++.++++
T Consensus        88 ~---~~~~~l~ll~~~~~~~-~~~~~~~~~~~ll~~l~~~~yDyiiID~ppgl~~~~~~al~aad~viIvttpe~~al~d  163 (279)
T CHL00175         88 D---KRWPNLSLLPISKNRQ-RYNVTRKNMNMLVDSLKERNYDYILIDCPAGIDVGFINAIAPAKEAIVVTTPEITAIRD  163 (279)
T ss_pred             C---CCCCCEEEEECCCHHH-HHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHCCEEEEECCCCHHHHHH
T ss_conf             5---7778779997897054-45741999999999997279999998189988899999999789069978997899999


Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEECCCCCC---CCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHH
Q ss_conf             99999999981987675389995658987---520059999998489537990687999999884796189888999899
Q gi|254780725|r  314 SKNLIDVLKKLRPADKPPYLVLNQVKTPK---KPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIA  390 (427)
Q Consensus       314 a~~ll~~l~~~~~~~~~~~iVlNr~~~~~---~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a  390 (427)
                      ++++++.++..+.  ..+.+|+|++.+..   ......+++++.++.+..+.||+|+.+ .+|.++|+|+....|+|+.+
T Consensus       164 a~~~i~~~~~~~~--~~~~lvvN~~~~~~~~~~~~~~~~~~~~~l~v~~lg~IP~D~~v-~~a~~~G~Pvv~~~P~S~~a  240 (279)
T CHL00175        164 ADRVAGLLEANGI--YNIKLLVNRVRPDMIKANDMMSVRDVQEMLGIPLLGAIPEDENV-IISTNRGEPLVLKKKLTLSG  240 (279)
T ss_pred             HHHHHHHHHHCCC--CCCEEEECCCCCCCCCCCCCCCHHHHHHHHCCCEEEECCCCHHH-HHCCCCCEEEEEECCCCHHH
T ss_conf             9999999997599--86213533564554354553449999997199346576787789-86130690589849999999


Q ss_pred             HHHHHHHHHHHCCCCC----CCCCCCHHHHHHHHHHHHH
Q ss_conf             9999999998522122----3211105899998742340
Q gi|254780725|r  391 NLLVDFSRVLMGRVTV----SKPQSAMYTKIKKIFNMKC  425 (427)
Q Consensus       391 ~~~~~La~~i~gr~~~----~~~k~~~~~~l~~lf~rk~  425 (427)
                      ++|.+||++|.|+..+    ....++++++|+++|+||.
T Consensus       241 ~a~~~iA~~l~~~~~~~~~~~~~~~~~~~kl~~~f~~~~  279 (279)
T CHL00175        241 IAFENAARRLVGKQVYFIDLDSPSKGPLKRLRRFFLGRS  279 (279)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCC
T ss_conf             999999999957876766555445659999999856689


No 3  
>TIGR01968 minD_bact septum site-determining protein MinD; InterPro: IPR010223   This entry describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE . MinD is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. In plants, chloroplast division requires the dimerisation of stromal MinD . The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model.; GO: 0016887 ATPase activity, 0000918 selection of site for barrier septum formation.
Probab=100.00  E-value=0  Score=317.58  Aligned_cols=254  Identities=20%  Similarity=0.346  Sum_probs=227.1

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCC--CCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             5379997469887756899999999996269949999787989860334389987--89888631845612433765320
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPI--NSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~--~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      +++|.|+|+||||||||+++||+.+||+ .|+||+|||+|..--++++.||++.+  |++.|++.+..++++++++.   
T Consensus         1 ~~viViTSGKGGVGKTTtTANlG~aLA~-lG~kVvliD~DiGLRNLD~~lGLEnRivYt~vDVveG~C~l~qALikD---   76 (272)
T TIGR01968         1 ARVIVITSGKGGVGKTTTTANLGTALAR-LGKKVVLIDADIGLRNLDLLLGLENRIVYTLVDVVEGECRLQQALIKD---   76 (272)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCC---
T ss_conf             9589998178897735898999999996-198289995475703457774231035453554324842110010012---


Q ss_pred             CCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHC--CCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf             248980687248761203207999999989998512--888997388888989999986201254357877688999999
Q gi|254780725|r  239 FYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQI--FPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKN  316 (427)
Q Consensus       239 ~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~--yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~  316 (427)
                      +..++|+|||+..+-+ -+.++++.+..+++.|++.  |||||||||.+......+|...||..++|++|+++|+|++.|
T Consensus        77 Kr~~NL~LLpAsQ~rd-K~~~~~E~~~~lv~~Lk~~~~FDYviIDcPAGIE~GF~nAv~~Ad~AiVVttPEvsavRDADR  155 (272)
T TIGR01968        77 KRLENLYLLPASQTRD-KDAVTPEQMKKLVNELKEEEHFDYVIIDCPAGIESGFRNAVAPADEAIVVTTPEVSAVRDADR  155 (272)
T ss_pred             CCCHHHHHHHHHHCCC-CCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHCCEEEEEECCCCCCHHHHHH
T ss_conf             6752356636530236-134697789999999854379307997378774356899875268358987787451002556


Q ss_pred             HHHHHHHCCCCCC-----CCEEEEECCCCC---CCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCC-C
Q ss_conf             9999998198767-----538999565898---752005999999848953799068799999988479618988899-9
Q gi|254780725|r  317 LIDVLKKLRPADK-----PPYLVLNQVKTP---KKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPK-S  387 (427)
Q Consensus       317 ll~~l~~~~~~~~-----~~~iVlNr~~~~---~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~-s  387 (427)
                      ++-.|...+.-.+     +.++|+||..+.   +..-++.+|+.+.|+.++.++||.|.+. -.|.|.|.|++. .++ |
T Consensus       156 vIGlLea~~~i~~~GEE~~~~LivNR~rP~mV~~G~Mlsi~Dv~~~L~i~LiGviPeD~~i-I~stN~GEP~vl-~~~L~  233 (272)
T TIGR01968       156 VIGLLEAKGNIEEKGEEVKIKLIVNRLRPEMVKKGDMLSIDDVLEILSIPLIGVIPEDEEI-IVSTNKGEPVVL-NKKLS  233 (272)
T ss_pred             HHHHHCCCCCCCCCCCEEEEEEEEECCCHHHHHCCCCCCHHHHHHHCCCCCEEEECCCCCE-EEEECCCEEEEE-CCCCC
T ss_conf             7524212455445776464347785156477416898278999986088616863299865-766456143544-60026


Q ss_pred             HHHHHHHHHHHHHHCCCC-----CCCCCCCHHHHHHHHH
Q ss_conf             899999999999852212-----2321110589999874
Q gi|254780725|r  388 AIANLLVDFSRVLMGRVT-----VSKPQSAMYTKIKKIF  421 (427)
Q Consensus       388 ~~a~~~~~La~~i~gr~~-----~~~~k~~~~~~l~~lf  421 (427)
                      ..+++|+.+|++|.|+.-     -..++|++|..|+++|
T Consensus       234 ~~g~Af~~~ArRi~G~~vpf~~d~~~~~kG~~~~i~~~F  272 (272)
T TIGR01968       234 RAGKAFENIARRILGEEVPFEDDLEEQKKGFFARIKRFF  272 (272)
T ss_pred             HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCHHHHHHHCC
T ss_conf             167889999875348864303334043022789987409


No 4  
>PRK10818 cell division inhibitor MinD; Provisional
Probab=100.00  E-value=0  Score=304.05  Aligned_cols=256  Identities=20%  Similarity=0.268  Sum_probs=211.9

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCC--CCHHHHHCCCCCHHHHHHHHHH
Q ss_conf             75379997469887756899999999996269949999787989860334389987--8988863184561243376532
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPI--NSISDAIYPVGRIDKAFVSRLP  237 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~--~~l~d~l~~~~rlD~~~l~~~l  237 (427)
                      .+|||+|.|+||||||||+|+|||++||+ .|++|++||+|++.++++.++|.++.  +++.+++.+...+++..+..  
T Consensus         1 M~rvIaV~s~KGGVGKTT~avNLA~aLA~-~G~kVlliD~D~~~~n~~~~lg~~~~~~~~~~~vl~g~~~l~~~~i~~--   77 (270)
T PRK10818          1 MARIIVVTSGKGGVGKTTSSAAIATGLAQ-KGKKTVVIDFDIGLRNLDLIMGCERRVVYDFVNVIQGDATLNQALIKD--   77 (270)
T ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCHHHHEEEC--
T ss_conf             97499997899984189999999999997-799689996899998887345767766666898836998588905446--


Q ss_pred             HCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHH-CCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf             024898068724876120320799999998999851-2888997388888989999986201254357877688999999
Q gi|254780725|r  238 VFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQ-IFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKN  316 (427)
Q Consensus       238 ~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~-~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~  316 (427)
                       +..++++++|++...+ ...+..+.+..+++.+.. .|||||||||++++..+..++.+||.+++|++|++.+++++++
T Consensus        78 -~~~~~l~ilpa~~~~~-~~~~~~~~~~~~l~~l~~~~yDyIiID~ppgl~~~~~~al~aad~vlvv~tpe~~al~da~~  155 (270)
T PRK10818         78 -KRTENLYILPASQTRD-KDALTREGVAKVLDDLKAMDFEFIVCDSPAGIETGALMALYFADEAIITTNPEVSSVRDSDR  155 (270)
T ss_pred             -CCCCCEEEECCCCHHH-HHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHCCEEEEECCCCHHHHHHHHH
T ss_conf             -8769979979996476-75545999999999777659989998899986689999998589689973897889987999


Q ss_pred             HHHHHHHCC------CCCCCCEEEEECCCCCC---CCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             999999819------87675389995658987---520059999998489537990687999999884796189888999
Q gi|254780725|r  317 LIDVLKKLR------PADKPPYLVLNQVKTPK---KPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS  387 (427)
Q Consensus       317 ll~~l~~~~------~~~~~~~iVlNr~~~~~---~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s  387 (427)
                      +++.+....      ...-..++++|++++.+   ...+..+++++.++.+..+.||+|+++ .+|.+.|+|++ ++|+|
T Consensus       156 ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lg~IP~d~~v-~eA~~~G~Pvv-~~p~s  233 (270)
T PRK10818        156 ILGILASKSRRAENGEEPIKEHLLLTRYNPGRVSRGDMLSMEDVLEILRIKLVGVIPEDQSV-LRASNQGEPVI-LDINA  233 (270)
T ss_pred             HHHHHHHHHHHHHCCCCCHHCCEEEEEECHHHCCHHHHCCHHHHHHHCCCEEEEECCCCHHH-HHHCCCCCCEE-ECCCC
T ss_conf             99999987776533520100125884245312321100129999973288069980797469-88522799879-89999


Q ss_pred             HHHHHHHHHHHHHHCCCCCC-CCCCCHHHHHHHHHH
Q ss_conf             89999999999985221223-211105899998742
Q gi|254780725|r  388 AIANLLVDFSRVLMGRVTVS-KPQSAMYTKIKKIFN  422 (427)
Q Consensus       388 ~~a~~~~~La~~i~gr~~~~-~~k~~~~~~l~~lf~  422 (427)
                      +.+++|.+||+++.|+..+. ...+++.++|+|+||
T Consensus       234 ~~a~Ay~~lA~~ll~~~~p~~~~~~~~~~~~~~~fg  269 (270)
T PRK10818        234 DAGKAYADTVERLLGEERPFRFIEEEKKGFLKRLFG  269 (270)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHCC
T ss_conf             899999999999956877765544332348887008


No 5  
>TIGR01969 minD_arch cell division ATPase MinD; InterPro: IPR010224   Proper placement of the bacterial cell division site requires the site-specific inactivation of other potential division sites. In Escherichia coli, selection of the correct mid-cell site is mediated by the MinC, MinD and MinE proteins. Several members of this family are found in archaeal genomes but their function is uncharacterised. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins.    This entry represents the archaeal MinD family. The exact roles of the various archaeal MinD homologs are unknown. .
Probab=100.00  E-value=0  Score=301.37  Aligned_cols=231  Identities=19%  Similarity=0.259  Sum_probs=216.1

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCC-CCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             3799974698877568999999999962699499997879898603343899-878988863184561243376532024
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKD-PINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~-~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      |+|+|.|+|||+||||+++|||.+||+ .|++|+++|.|..+.|+.+.||++ -+.||+|+|.+--+     ++.++..+
T Consensus         1 r~I~iASGKGGtGKTT~tANLgVALA~-~Gk~V~~~DADI~MANL~LiLgmE~~~VTLhDVLAGeA~-----i~DAIY~g   74 (258)
T TIGR01969         1 RIITIASGKGGTGKTTITANLGVALAK-LGKKVLVLDADITMANLELILGMEDKPVTLHDVLAGEAD-----IKDAIYEG   74 (258)
T ss_pred             CEEEEEECCCCCCHHHEEEHHHHHHHH-CCCEEEEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCC-----HHHHCCCC
T ss_conf             988999778898614000007788986-097689994676677689884468889675221344561-----00110028


Q ss_pred             CCC-EEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             898-0687248761203207999999989998512888997388888989999986201254357877688999999999
Q gi|254780725|r  241 AEN-LSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLID  319 (427)
Q Consensus       241 ~~g-L~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~  319 (427)
                      +.| ++++|++-+++..---.++.+..++..+.+.|||++||+|.+....+..+|..||+.++|++|+.+|+.++-++.-
T Consensus        75 p~GnV~V~PagvSLEg~rKA~~~~L~dV~~~i~~~~D~lLIDAPAGL~~~a~~Al~~a~elLLVvNPEi~SItDaLK~k~  154 (258)
T TIGR01969        75 PEGNVKVIPAGVSLEGLRKADPDKLEDVLKEIIDDTDFLLIDAPAGLERDAVTALAAADELLLVVNPEISSITDALKVKI  154 (258)
T ss_pred             CCCCEEEECCCCCHHHCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHH
T ss_conf             89844785061221000126833328999987204377887478983378999998618664866765446777889999


Q ss_pred             HHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf             99981987675389995658987520059999998489537990687999999884796189888999899999999999
Q gi|254780725|r  320 VLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIANLLVDFSRV  399 (427)
Q Consensus       320 ~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~~~~~La~~  399 (427)
                      ..++++  -..+++|+||+... ..+++.++++..|+.++.++||.||+. ++|...|.|++...|+||+|++|.+||+.
T Consensus       155 va~~lG--t~ilG~vlNRv~~~-~tel~~~eiE~iLevPVl~~vPEDP~V-R~AAa~G~P~V~~~P~SpAA~A~~eLA~~  230 (258)
T TIGR01969       155 VAEKLG--TAILGVVLNRVTRD-KTELGREEIEAILEVPVLGVVPEDPEV-RRAAAFGEPVVVYSPNSPAAQAFMELAAE  230 (258)
T ss_pred             HHHHCC--CCEEEEEEEECCCC-CCCCCHHHHHHHHCCCEEEEECCCHHH-HHHHHCCCCEEEECCCCHHHHHHHHHHHH
T ss_conf             987608--83246899602366-663788899988479738985698434-45642485368847998789999999999


Q ss_pred             HHC
Q ss_conf             852
Q gi|254780725|r  400 LMG  402 (427)
Q Consensus       400 i~g  402 (427)
                      |.|
T Consensus       231 l~G  233 (258)
T TIGR01969       231 LAG  233 (258)
T ss_pred             HHC
T ss_conf             718


No 6  
>TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ. Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (PMID:16930487), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.
Probab=100.00  E-value=3.1e-40  Score=266.55  Aligned_cols=234  Identities=18%  Similarity=0.193  Sum_probs=190.8

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCC--CCCHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf             37999746988775689999999999626994999978798986033438998--7898886318456124337653202
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDP--INSISDAIYPVGRIDKAFVSRLPVF  239 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~--~~~l~d~l~~~~rlD~~~l~~~l~~  239 (427)
                      |+|+|.+.||||||||+|+|||++||+ .|++|++||+|+| |++..+||.++  ..++.+.+.....     ++....+
T Consensus         2 kiIav~n~KGGVGKTT~avNLA~~La~-~G~rVLlIDlDpQ-~~l~~~~g~~~~~~~~l~~~~~~~~~-----~~~~~~~   74 (246)
T TIGR03371         2 KVIAIVGIKGGVGRTTLTAALASALKL-LGEPVLAIDLDPQ-NLLRLHFGMDWSVRDGWARALLAGED-----WRAAAYR   74 (246)
T ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCC-CCHHHHCCCCCCCCCCHHHHHHCCCC-----HHHHHEE
T ss_conf             399997599985499999999999996-8997899975999-85032248887534569999827998-----8895255


Q ss_pred             CCCCEEEEECCCC-CC---CHHCCCHHHHHHHHHHHH-HCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHH
Q ss_conf             4898068724876-12---032079999999899985-128889973888889899999862012543578776889999
Q gi|254780725|r  240 YAENLSILTAPAM-LS---RTYDFDEKMIVPVLDILE-QIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNS  314 (427)
Q Consensus       240 ~~~gL~lL~a~~~-~~---~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a  314 (427)
                      +.+|+++++++.. ..   .........+..++..++ ..||||||||||+++..+.++|.+||.+++|++|+..++...
T Consensus        75 ~~~~~~~ip~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~~~D~viiD~pp~l~~~~~~al~aad~vlipv~~~~~s~~~~  154 (246)
T TIGR03371        75 SSDGVLFLPYGTLSADEREAYQAHDAGWLARLLQQLDLAARDWVLIDLPRGPSPITDQALAAADLVLVVVNADAACYATL  154 (246)
T ss_pred             CCCCEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHCCEEEEEECCCHHHHHHH
T ss_conf             78982897089847778987604478999999986303679889994899874999999998894799818998999999


Q ss_pred             HHHHHHHHHCCCCCCCCEEEEECCCCCCCCHH-HHHHHHHHHCCCEE-EEECCCHHHHHHHHHCCCCEEEECCCCHHHHH
Q ss_conf             99999999819876753899956589875200-59999998489537-99068799999988479618988899989999
Q gi|254780725|r  315 KNLIDVLKKLRPADKPPYLVLNQVKTPKKPEI-SISDFCAPLGITPS-AIIPFDGAVFGMSANSGKMIHEVDPKSAIANL  392 (427)
Q Consensus       315 ~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i-~~~~~~~~lg~~~~-~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~~  392 (427)
                      .+++..+.+...+...+++|+||++..+.... ..+.+++.++.++. ..||+|.+ +.+|...|+|+.+++|+|+.+++
T Consensus       155 ~~~~~~~~~~~~~~~~~~iv~n~~~~~~~~~~~~~~~l~~~~~~~~~~~~I~~~~~-v~eA~~~g~pv~~~~p~S~aa~~  233 (246)
T TIGR03371       155 HQLALALLARSVPPDGIHYLINQFQPARQLSRDVRAVLRATLGSRLLPMFVHRDEA-VAEALARGTPVFNYAPHSQAAHD  233 (246)
T ss_pred             HHHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCHH-HHHHHHCCCCCEEECCCCHHHHH
T ss_conf             99999999842776751788630264015899999999997498816226899779-99999769982669958989999


Q ss_pred             HHHHHHHHHCC
Q ss_conf             99999998522
Q gi|254780725|r  393 LVDFSRVLMGR  403 (427)
Q Consensus       393 ~~~La~~i~gr  403 (427)
                      |++||++|..|
T Consensus       234 y~~LA~~ll~~  244 (246)
T TIGR03371       234 IRTLAFWLLTK  244 (246)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999996


No 7  
>COG0455 flhG Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]
Probab=100.00  E-value=3.6e-39  Score=260.00  Aligned_cols=258  Identities=21%  Similarity=0.301  Sum_probs=222.4

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCC-HHHHHCCCCCHHHHHHHHHHHC
Q ss_conf             537999746988775689999999999626994999978798986033438998789-8886318456124337653202
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINS-ISDAIYPVGRIDKAFVSRLPVF  239 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~-l~d~l~~~~rlD~~~l~~~l~~  239 (427)
                      .++|+|.|+||||||||+++|++..+++..+++|+++|+|+.+++++..||+++..+ +.+++.+..++.+     ....
T Consensus         2 ~~~Iav~SgKGGvGKTtitanlga~~~~~~~k~V~~iDaD~g~~nL~~~~g~~~~~~~l~dvL~~~~~~~D-----i~~~   76 (262)
T COG0455           2 TKVIAVVSGKGGVGKTTITANLGAALAALGGKVVLLIDADLGLGNLSLLLGVESKPTTLHDVLAGEASIED-----IIYE   76 (262)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCHHHHHCCCCCCCCHHHHHHCCCCHHH-----EEEE
T ss_conf             78999984588756898998699999964897699996588887288885888885509999707787768-----0231


Q ss_pred             CC-CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             48-98068724876120320799999998999851288899738888898999998620125435787768899999999
Q gi|254780725|r  240 YA-ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLI  318 (427)
Q Consensus       240 ~~-~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll  318 (427)
                      .+ .|++++|+...+.....+.++.+..++..+...||||++|+|++.+..+...+..+|.+++|++|+..++.++..++
T Consensus        77 ~~~~gl~vipg~~~~~~~~~~~~~~~~~~~~~l~~~~D~iliD~~aGl~~~~~~~~~~sd~~viVt~pe~~si~~A~~~i  156 (262)
T COG0455          77 TPQDGLYVLPGGSGLEDLAKLDPEDLEDVIKELEELYDYILIDTGAGLSRDTLSFILSSDELVIVTTPEPTSITDAYKTI  156 (262)
T ss_pred             CCCCCEEEEECCCCHHHHHHCCHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHCCCEEEEECCCCCHHHHHHHHH
T ss_conf             57689899607887688861698889999999875299999968999668889998736817999279852089999999


Q ss_pred             HHHHHCCCCCCCCEEEEECCCCCCCC-HHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHH
Q ss_conf             99998198767538999565898752-00599999984895379906879999998847961898889998999999999
Q gi|254780725|r  319 DVLKKLRPADKPPYLVLNQVKTPKKP-EISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIANLLVDFS  397 (427)
Q Consensus       319 ~~l~~~~~~~~~~~iVlNr~~~~~~~-~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~~~~~La  397 (427)
                      +++...........+|+|+++..+.. +...+..+..........+|+|+ .+.++...|.|+....|+|+++++|.+||
T Consensus       157 ~~~~~~~~~~~~~~vV~N~v~~~~e~~~~~~~~~~~~~~~~~~~~i~~~~-~v~~a~~~g~p~~~~~p~s~as~ai~~lA  235 (262)
T COG0455         157 KILSKLGLDLLGRRVVLNRVRSTKEGVDVAALLIQVVKQVPVLQVIPFDP-EVRRALAEGKPIVLYSPNSKASQAIKELA  235 (262)
T ss_pred             HHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEECCCH-HHHHHHHCCCCEEEECCCCHHHHHHHHHH
T ss_conf             99997387643315899703666654678999999997077434715675-78998624986797288978999999999


Q ss_pred             HHHHCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             998522122321110589999874234
Q gi|254780725|r  398 RVLMGRVTVSKPQSAMYTKIKKIFNMK  424 (427)
Q Consensus       398 ~~i~gr~~~~~~k~~~~~~l~~lf~rk  424 (427)
                      ..+.+......++.+..++++++|+++
T Consensus       236 ~~l~~~~~~~~~~~~~~~~~~~~~~~~  262 (262)
T COG0455         236 AKLAGLPEPKAPRRGFISKIKRLLKRR  262 (262)
T ss_pred             HHHHCCCCCCCCCCCHHHHHHHHHCCC
T ss_conf             998605566774311279999885069


No 8  
>pfam00142 Fer4_NifH 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family.
Probab=100.00  E-value=1.2e-37  Score=250.71  Aligned_cols=256  Identities=16%  Similarity=0.190  Sum_probs=197.8

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      |+||| ++||||||||+++|||.+||+ .|+||+++|+|+|.++++.++|..+.+++.|.+.....+++..++..+....
T Consensus         1 r~iai-~GKGGVGKTTtsvNLA~aLA~-~GkrVlliDaD~~~~~~~~llg~~~~~~l~d~l~~~~~~~~~~~~~vi~~~~   78 (269)
T pfam00142         1 RKIAI-YGKGGIGKSTTSQNTSAALAE-MGKKVLIVGCDPKADSTRLILGGKAQPTIIDTLREKGLVEDVELEDVVKKGY   78 (269)
T ss_pred             CEEEE-ECCCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCCCCCHHHHCCCCCCCCHHHHHCCCCCCCCCCHHHHEECCC
T ss_conf             95899-899976889999999999998-7990999845899874144438988884787760467702240745013377


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHHH-----HCCCEEEECCCCCCCH--HH-HHHHHHCCCCCCCCCCCHHHHHH
Q ss_conf             9806872487612032079999999899985-----1288899738888898--99-99986201254357877688999
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDILE-----QIFPLVILDVPHVWNS--WT-QEVLTLSDKVVITTSLDLAGLRN  313 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~-----~~yd~VIiD~p~~~~~--~~-~~~L~~AD~vviV~~p~~~slr~  313 (427)
                      .++.++++....... ......+...++.++     ..|||+++|+++....  .. ......||.+++|++|+..++.+
T Consensus        79 ~gv~~i~~~~~e~~~-~~~~~~~~~~~~~l~~~~~~~~~DyiliD~~g~~~~~~~~~~i~~~~A~~viiv~t~E~~al~~  157 (269)
T pfam00142        79 GGIRCVESGGPEPGV-GCAGRGVITAIDLLEELGAYDDLDFVLYDVLGDVVCGGFAMPIREGKAQEVYIVTSGEMMALYA  157 (269)
T ss_pred             CCCEEEECCCCCCCC-CCCHHHHHHHHHHHHHHCCHHCCCEEEEECCCCEEECCCCCCHHHCCCCEEEEEECCCHHHHHH
T ss_conf             872688689986563-2110789999999998210212888985336740243400533443588799982894789999


Q ss_pred             HHHHHHHHHHCC--CCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHH
Q ss_conf             999999999819--876753899956589875200599999984895379906879999998847961898889998999
Q gi|254780725|r  314 SKNLIDVLKKLR--PADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIAN  391 (427)
Q Consensus       314 a~~ll~~l~~~~--~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~  391 (427)
                      +.++++.+.+..  .+-....+|+|+.... ...-..+++.+.++.++...||.|.. +.+|...|+|+.+++|+|+.++
T Consensus       158 a~~l~~~i~~~~~~~~~~i~giv~n~~~~~-~~~~~~~~~~~~~~~~~lg~IP~d~~-v~eA~~~g~pv~~~~P~S~~A~  235 (269)
T pfam00142       158 ANNICKGILKYAKSGGVRLGGLICNSRKVD-DERELIDAFAEALGTQMIHFVPRDNI-VQKAELNKQTVIEYAPTCNQAK  235 (269)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEEEECCCCCC-HHHHHHHHHHHHHCCCEEEECCCCHH-HHHHHHCCCCEEEECCCCHHHH
T ss_conf             999999999985057962789982686541-15799999999819947997799826-8754234981799899998999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             9999999985221223211105899998742
Q gi|254780725|r  392 LLVDFSRVLMGRVTVSKPQSAMYTKIKKIFN  422 (427)
Q Consensus       392 ~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~  422 (427)
                      +|.+||++|..+.+...|++-...-|.+++.
T Consensus       236 ay~~LA~~il~~~~~~~p~p~~~~~~~~~~~  266 (269)
T pfam00142       236 EYRELARKIIENPEGIIPTPLTMDELEELLV  266 (269)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
T ss_conf             9999999998589998888699889999999


No 9  
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=100.00  E-value=1.1e-38  Score=257.03  Aligned_cols=257  Identities=20%  Similarity=0.301  Sum_probs=222.2

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCC--CCHHHHHCCCCCHHHHHHHHHH
Q ss_conf             75379997469887756899999999996269949999787989860334389987--8988863184561243376532
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPI--NSISDAIYPVGRIDKAFVSRLP  237 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~--~~l~d~l~~~~rlD~~~l~~~l  237 (427)
                      .+++|.|.|.||||||||.++|++.+||. .|++|++||+|...-++.+.+|++..  +.+.+++....++.+++++.  
T Consensus         1 M~~iIVvTSGKGGVGKTTttAnig~aLA~-~GkKv~liD~DiGLRNLDlimGlE~RiVYd~vdVi~g~~~l~QALIkD--   77 (272)
T COG2894           1 MARIIVVTSGKGGVGKTTTTANIGTALAQ-LGKKVVLIDFDIGLRNLDLIMGLENRIVYDLVDVIEGEATLNQALIKD--   77 (272)
T ss_pred             CCEEEEEECCCCCCCCCCHHHHHHHHHHH-CCCEEEEEECCCCCHHHHHHHCCCCEEEEEEHHHHCCCCCHHHHHHCC--
T ss_conf             96499994488876743106778999997-398599996676720446664342015654013444766365676403--


Q ss_pred             HCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHH-HCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf             02489806872487612032079999999899985-12888997388888989999986201254357877688999999
Q gi|254780725|r  238 VFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILE-QIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKN  316 (427)
Q Consensus       238 ~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~  316 (427)
                       +..++|++||+..+-+. ..++++.+..+++.|+ ..||||++|+|.+.......++..||..++|++|+++|+|++.|
T Consensus        78 -Kr~~nL~lLPAsQtrdK-dalt~E~v~~vv~eL~~~~fDyIi~DsPAGIE~G~~~A~~~Ad~AiVVtnPEvSsVRDsDR  155 (272)
T COG2894          78 -KRLENLFLLPASQTRDK-DALTPEGVKKVVNELKAMDFDYIIIDSPAGIEQGFKNAVYFADEAIVVTNPEVSSVRDSDR  155 (272)
T ss_pred             -CCCCCEEECCCCCCCCC-CCCCHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHCCCEEEEECCCCCCCCCCCHH
T ss_conf             -56785266144323672-2279999999999997669988996484067788886541026379974887554234112


Q ss_pred             HHHHHHHCC----C-CCCCCEEEEECCCCC---CCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCH
Q ss_conf             999999819----8-767538999565898---75200599999984895379906879999998847961898889998
Q gi|254780725|r  317 LIDVLKKLR----P-ADKPPYLVLNQVKTP---KKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSA  388 (427)
Q Consensus       317 ll~~l~~~~----~-~~~~~~iVlNr~~~~---~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~  388 (427)
                      ++-.|....    . ...+.++++||+++.   +..-++.+|+.+.|..++.++||.|... -.|.|.|.|+.. .+++.
T Consensus       156 iiGlLesk~~rae~~~~~~~~llvnR~~p~~v~~GeMlsv~Dv~~iL~i~liGiiPed~~V-i~asN~GePv~l-~~~~~  233 (272)
T COG2894         156 IIGLLESKSRRAEIGEEPKEHLLLNRYRPEMVKRGEMLSVEDVLEILSIPLIGVIPEDQDV-LRASNKGEPVIL-DDNSD  233 (272)
T ss_pred             HEEEHHCCCCHHHCCCCCCCEEEEECCCHHHHCCCCCCCHHHHHHHHCCCEEEEECCCHHH-EEECCCCCCEEE-CCCCH
T ss_conf             2020121454233077666348997168888115772539999997477447760485333-000478887675-78751


Q ss_pred             HHHHHHHHHHHHHCCCCCC----CCCCCHHHHHHHHHHH
Q ss_conf             9999999999985221223----2111058999987423
Q gi|254780725|r  389 IANLLVDFSRVLMGRVTVS----KPQSAMYTKIKKIFNM  423 (427)
Q Consensus       389 ~a~~~~~La~~i~gr~~~~----~~k~~~~~~l~~lf~r  423 (427)
                      ++++|..++++|.|...+-    .++++++++++++|++
T Consensus       234 a~~Ay~d~arRllGe~vp~~~~~~~kkg~~~~l~~~~~~  272 (272)
T COG2894         234 AGKAYRDIARRLLGEEVPFRFLEEEKKGFLARLKGGFSG  272 (272)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             779999999997088866322134441299998655259


No 10 
>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.
Probab=100.00  E-value=1.3e-37  Score=250.44  Aligned_cols=257  Identities=17%  Similarity=0.211  Sum_probs=192.0

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      |+|||.| ||||||||+++|||.+||+ .|++|+++|+|+|.+++..+++..+.+++.+.+....... ..++..+....
T Consensus         2 r~Iai~G-KGGVGKTTtavNLA~aLa~-~GkkVlliDaDpq~~~t~~l~g~~~~~~~~~~l~~~~~~~-~~~~~~i~~~~   78 (270)
T cd02040           2 RQIAIYG-KGGIGKSTTTQNLSAALAE-MGKKVMIVGCDPKADSTRLLLGGKAIPTVLDTLREKGEVE-LELEDVIFEGF   78 (270)
T ss_pred             CEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCCCCHHHHHCCCCCCCCHHHHHHHCCCCC-CCHHHHEECCC
T ss_conf             5899979-9857789999999999998-7994999865799851346529988882899887527776-53889613376


Q ss_pred             CCEEEEECCCCCCCHH-----CCCHHHHHHHHHHHHHCCCEEEECCCCCCC--HHHHH-HHHHCCCCCCCCCCCHHHHHH
Q ss_conf             9806872487612032-----079999999899985128889973888889--89999-986201254357877688999
Q gi|254780725|r  242 ENLSILTAPAMLSRTY-----DFDEKMIVPVLDILEQIFPLVILDVPHVWN--SWTQE-VLTLSDKVVITTSLDLAGLRN  313 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~-----~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~--~~~~~-~L~~AD~vviV~~p~~~slr~  313 (427)
                      +|+.++++........     .+....+...+..+...||||++|+.....  ..+.. ....||.+++|++|++.++.+
T Consensus        79 ~gv~~ip~~~~~~~~~~~gr~~~~~~~ll~~l~~~~~~~D~iliD~lg~~~~~~~~~~i~~~~ad~viiv~t~e~~al~~  158 (270)
T cd02040          79 GGIKCVESGGPEPGVGCAGRGVITAINLLEELGAYEDDLDFVIYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMALYA  158 (270)
T ss_pred             CCCEEEECCCCCCCCHHCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCHHHHCCCCEEEEECCCCHHHHHH
T ss_conf             77064105996435121240078899999985434406988998235633321232303553388799962881899999


Q ss_pred             HHHHHHHHHHCCCC-CCCCE-EEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHH
Q ss_conf             99999999981987-67538-99956589875200599999984895379906879999998847961898889998999
Q gi|254780725|r  314 SKNLIDVLKKLRPA-DKPPY-LVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIAN  391 (427)
Q Consensus       314 a~~ll~~l~~~~~~-~~~~~-iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~  391 (427)
                      +.++++.+...... ..++. +|.|+... ....-..++|++.++.++...||+|.. +.+|..+|+|+.+++|+|+.++
T Consensus       159 ~~~l~k~i~~~~~~~~~~l~gvv~~~~~~-~~~~~~~~~~~~~~~~~~l~~IP~d~~-v~EA~~~g~pi~~~~P~S~~A~  236 (270)
T cd02040         159 ANNICKGILKYAKSGGVRLGGLICNSRNT-DREDELIDAFAKRLGTQMIHFVPRDNV-VQRAELRGKTVIEYDPESKQAD  236 (270)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEEECCCCC-CHHHHHHHHHHHHHCCCEEEECCCCHH-HHHHHHCCCEEEEECCCCHHHH
T ss_conf             99999999999834697479998378665-137899999999859952877799717-8751342970799798998999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             99999999852212232111058999987423
Q gi|254780725|r  392 LLVDFSRVLMGRVTVSKPQSAMYTKIKKIFNM  423 (427)
Q Consensus       392 ~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~r  423 (427)
                      +|.+||++|..+..+..|++---..|.++|+.
T Consensus       237 ay~~LA~eii~~~~~~~p~p~~~~~~~~~~~~  268 (270)
T cd02040         237 EYRELARKIVENKLLVIPTPLEMDELEELLME  268 (270)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
T ss_conf             99999999984899989888997899999996


No 11 
>cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.
Probab=100.00  E-value=8.5e-36  Score=239.27  Aligned_cols=176  Identities=22%  Similarity=0.325  Sum_probs=151.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCC--CCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             79997469887756899999999996269949999787989860334389987--8988863184561243376532024
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPI--NSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~--~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      ||+|+|+||||||||+|+|||++||+ .|++|++||+|+++++++..++.+..  +++.|                    
T Consensus         1 iIav~s~KGGVGKTT~a~NLA~aLa~-~g~~vllvD~D~~~~~l~~~~~~~~~~~~~~~~--------------------   59 (179)
T cd02036           1 VIVVTSGKGGVGKTTTTANLGTALAQ-LGYKVVLIDADLGLRNLDLILGLENRVVYTLHD--------------------   59 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCCHHHCCCCCCCCCHHHC--------------------
T ss_conf             98997399987099999999999997-799189995899999836661765566531311--------------------


Q ss_pred             CCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             89806872487612032079999999899985128889973888889899999862012543578776889999999999
Q gi|254780725|r  241 AENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDV  320 (427)
Q Consensus       241 ~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~  320 (427)
                           ++++                          ||||+|+|++++..+..++..||.+++|++|+..+++++.++++.
T Consensus        60 -----vl~g--------------------------D~viiD~ppg~~~~~~~~l~~ad~vlvv~~p~~~sl~~~~~~~~~  108 (179)
T cd02036          60 -----VLAG--------------------------DYILIDSPAGIERGFITAIAPADEALLVTTPEISSLRDADRVKGL  108 (179)
T ss_pred             -----CCCC--------------------------CEEEEECCCCCCHHHHHHHHHCCCCEECCCCCHHHHHHHHHHHHH
T ss_conf             -----2669--------------------------999997999988899999984681256378858899999999999


Q ss_pred             HHHCCCCCCCCEEEEECCCCCC-CCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHHHH
Q ss_conf             9981987675389995658987-520059999998489537990687999999884796189888999899999
Q gi|254780725|r  321 LKKLRPADKPPYLVLNQVKTPK-KPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIANLL  393 (427)
Q Consensus       321 l~~~~~~~~~~~iVlNr~~~~~-~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~~~  393 (427)
                      +++.+.  ..+++|+||++... ......+++++.+|.++.+.||+|.. +.+|.++|+|+.+++|+|+.+++|
T Consensus       109 ~~~~~~--~~~~vv~Nr~~~~~~~~~~~~~~~~~~l~~~vlg~IP~d~~-v~eA~~~g~Pv~~~~P~s~aA~ay  179 (179)
T cd02036         109 LEALGI--KVVGVIVNRVRPDMVEGGDMVEDIEEILGVPLLGVIPEDPA-VIRATNRGEPVVLNKPKSPAAQAY  179 (179)
T ss_pred             HHHCCC--CEEEEEECCCCCCCCCHHHHHHHHHHHCCCCEEEECCCCHH-HHHHHHCCCEEEEECCCCHHHHCC
T ss_conf             982599--64699984546766636779999998559967988779889-999876795389879999566309


No 12 
>PRK13233 nifH nitrogenase reductase; Reviewed
Probab=100.00  E-value=4.3e-35  Score=234.91  Aligned_cols=259  Identities=15%  Similarity=0.194  Sum_probs=200.5

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             53799974698877568999999999962699499997879898603343899878988863184561243376532024
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      .|.|||+| |||+||||+++|||.+||+..|++|++||+|++..++.+.++..+..++.|.+..... +...++..+...
T Consensus         2 ~~~iaiyG-KGGIGKSTTt~NLaaALA~l~GkrVl~IgcDPk~dST~~l~g~~~~~tv~d~l~~~~~-~~~~~e~ii~~g   79 (275)
T PRK13233          2 TRKIAIYG-KGGIGKSTTTQNTAAAMAHFHDKKVFIHGCDPKADSTRLILGGKPQTTMMDTLRELGE-EKVTPDKVIKTG   79 (275)
T ss_pred             CCEEEEEC-CCCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHCCCCCCCCHHHHHHHCCC-CCCCHHHHHHCC
T ss_conf             73899989-9854465459999999996479889997978876136776089878839999986288-755388887537


Q ss_pred             CCCEEEEECCCCCC-----CHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCC--HHHHHH-HHHCCCCCCCCCCCHHHHH
Q ss_conf             89806872487612-----032079999999899985128889973888889--899999-8620125435787768899
Q gi|254780725|r  241 AENLSILTAPAMLS-----RTYDFDEKMIVPVLDILEQIFPLVILDVPHVWN--SWTQEV-LTLSDKVVITTSLDLAGLR  312 (427)
Q Consensus       241 ~~gL~lL~a~~~~~-----~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~--~~~~~~-L~~AD~vviV~~p~~~slr  312 (427)
                      ..|+.++.++....     ....+....+..-++.....||||++|++....  ..+..+ ...||+|++|+++++.|+.
T Consensus        80 ~~gv~cVEaGgp~pG~gcagrgii~~~~lle~~~~~~~~~D~Vl~DvLGdVvcGgFa~Pir~~~AdeV~IVts~E~msL~  159 (275)
T PRK13233         80 FKGIRCVESGGPEPGVGCAGRGVITAITLMEEHGAYEDDLDFVFFDVLGDVVCGGFAMPIRDGKAQEVYIVASGEMMALY  159 (275)
T ss_pred             CCCCEEEECCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCHHHHH
T ss_conf             89857986899986665576312358888998097434688899841561105551034313668889999468379999


Q ss_pred             HHHHHHHHHHHC--CCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHH
Q ss_conf             999999999981--987675389995658987520059999998489537990687999999884796189888999899
Q gi|254780725|r  313 NSKNLIDVLKKL--RPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIA  390 (427)
Q Consensus       313 ~a~~ll~~l~~~--~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a  390 (427)
                      .+.++.+.+.+.  +.+.+-..+|+|+.+.+. .+...++|++.++.++...||+|.. +.+|..+|++++|++|.|+.+
T Consensus       160 aannI~~~l~~~~~~~~~~l~Gii~N~r~~~~-e~~~v~~fa~~ig~~vi~~IPr~~~-V~~Ae~~~~tVie~~P~S~~A  237 (275)
T PRK13233        160 AANNICKGLVKYAEQSGVRLGGIICNSRNVDG-ELELLEEFTDAIGTQLIHFVPRDNI-VQKAEFNKKTVVEFDPTCNQA  237 (275)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEEEECCCCCC-HHHHHHHHHHHHCCCEEEECCCCHH-HHHHHHCCCEEEEECCCCHHH
T ss_conf             99999999999850589638999971788860-7999999999859957997789778-887787397679989999799


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             999999999852212232111058999987423
Q gi|254780725|r  391 NLLVDFSRVLMGRVTVSKPQSAMYTKIKKIFNM  423 (427)
Q Consensus       391 ~~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~r  423 (427)
                      ++|++||+.|........|++-....|+.+..+
T Consensus       238 ~~Y~~LAk~I~~n~~~~~P~pl~~~el~~~~~~  270 (275)
T PRK13233        238 HEYKELARKIIENKNFVIPKPMTMDELEEMVVK  270 (275)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
T ss_conf             999999999985899978888998999999998


No 13 
>pfam06564 YhjQ YhjQ protein. This family consists of several bacterial YhjQ proteins. The function of this family is unknown. However, the family does contain a P-loop sequence motif suggesting a nucleotide binding function.
Probab=100.00  E-value=1.8e-35  Score=237.19  Aligned_cols=225  Identities=15%  Similarity=0.226  Sum_probs=167.8

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCC--CCCHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf             37999746988775689999999999626994999978798986033438998--7898886318456124337653202
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDP--INSISDAIYPVGRIDKAFVSRLPVF  239 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~--~~~l~d~l~~~~rlD~~~l~~~l~~  239 (427)
                      |||+|.|.||||||||+++|||++|++ .|++|++||+|+| +.+.+.||.+.  ..++...+.....     ++....+
T Consensus         2 kiIai~s~KGGVGKTT~t~nLa~aLa~-~G~rVLlID~Dpq-~~l~~~~g~~~~~~~g~~~~~l~~~~-----~~~~~~~   74 (244)
T pfam06564         2 AVLALQGVRGGVGTTSLTAALGWALQQ-LGESVLVIDASPD-NLLRLHFNVDFDHSDGWARAELDGRP-----WRDAALR   74 (244)
T ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCC-CCCCCCCCCCCCCCCCHHHHHHCCCC-----HHHHHEE
T ss_conf             299996699986199999999999997-7995899968987-42102358886434414899875997-----7774445


Q ss_pred             CCCCEEEEECCCCC-CCHHCC-----CHHHHHHHHHHHH--HCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHH
Q ss_conf             48980687248761-203207-----9999999899985--128889973888889899999862012543578776889
Q gi|254780725|r  240 YAENLSILTAPAML-SRTYDF-----DEKMIVPVLDILE--QIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGL  311 (427)
Q Consensus       240 ~~~gL~lL~a~~~~-~~~~~~-----~~~~l~~ll~~l~--~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~sl  311 (427)
                      ..+|++++|.+... ...+.+     ....+...+..+.  ..||||+||||++.+..+.+++..||.+++|++||..+.
T Consensus        75 ~~~gl~llP~g~l~~~~~~~~~~~~~~~~~l~~~l~~l~~~~~yD~iliD~Pp~l~~l~~~al~aad~vLv~v~~d~~s~  154 (244)
T pfam06564        75 YTPGLDLLPFGQLTGAERENLQQLQPDLGAWAQRLQLLKASGQYRWILLDLPQGFSPLTRQLLELADVTLAVVHADANCH  154 (244)
T ss_pred             ECCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHCCCEEEEECCCHHHH
T ss_conf             26975897289974789998986544379999987642135789999997999968999999997696089968885899


Q ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHH-HHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHH
Q ss_conf             9999999999981987675389995658987520059-999998489537990687999999884796189888999899
Q gi|254780725|r  312 RNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISI-SDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIA  390 (427)
Q Consensus       312 r~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~-~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a  390 (427)
                      ..       +.+ +.......+++||+++.++..... ..+.+.++......||.|.. +.+|...|+|+.+++|+|+.+
T Consensus       155 ~~-------l~~-~~~~~~~~ilvn~~d~~~~l~~d~~~~~~~~~~~~l~~~I~rd~~-l~EA~a~g~pv~~yaP~S~aA  225 (244)
T pfam06564       155 IR-------LHQ-QALPAGCHLLINDFRIGSQLQDDLYQLWLQSQRRLLPIVVHRDEA-MAEALAAKQPLGEYRPDSLAA  225 (244)
T ss_pred             HH-------HHH-CCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEECCCCH-HHHHHHCCCCHHHCCCCCHHH
T ss_conf             99-------732-334467748864245576899999999998608725755079882-989986799554538699899


Q ss_pred             HHHHHHHHHHHC
Q ss_conf             999999999852
Q gi|254780725|r  391 NLLVDFSRVLMG  402 (427)
Q Consensus       391 ~~~~~La~~i~g  402 (427)
                      ++|..||.++.-
T Consensus       226 ~dy~~LA~w~l~  237 (244)
T pfam06564       226 EEVLTLANWCLL  237 (244)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999998


No 14 
>PRK13232 nifH nitrogenase reductase; Reviewed
Probab=100.00  E-value=5.8e-35  Score=234.15  Aligned_cols=257  Identities=14%  Similarity=0.140  Sum_probs=194.6

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      |-|+|+| ||||||||+++|||.+||+ .|+||++||+|++..++..+++..+.+++.|.+..... +..-++..+.+..
T Consensus         2 ~~iaiyG-KGGVGKSTTt~NLaAALA~-~GkkVL~IgcDPk~dsT~~l~gg~~~~tvld~l~~~~~-~~~~l~~v~~~g~   78 (273)
T PRK13232          2 RQIAIYG-KGGIGKSTTTQNLTAALST-MGNKILLVGCDPKADSTRMLLGGLNQKTVLDTLRSEGD-EGVDLDVVMQPGF   78 (273)
T ss_pred             CEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCCCHHHHHHHCCCCCCCHHHHHHHCCC-CCCCHHHEEECCC
T ss_conf             5799979-9866588789999999997-79969998978844277788589988879999986185-6563666154288


Q ss_pred             CCEEEEECCCCCCCH-----HCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHH---HHHHCCCCCCCCCCCHHHHHH
Q ss_conf             980687248761203-----207999999989998512888997388888989999---986201254357877688999
Q gi|254780725|r  242 ENLSILTAPAMLSRT-----YDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQE---VLTLSDKVVITTSLDLAGLRN  313 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~-----~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~---~L~~AD~vviV~~p~~~slr~  313 (427)
                      .++.++.+.......     ..+..-.+..-+......||||++|++.........   ....|+++++|+++++.++..
T Consensus        79 ~gv~cve~ggp~~g~gcagrgii~~~~lle~l~~~~~~~Dyvl~Dvlgdvvcggfa~P~~~~~A~evlIVts~E~~slya  158 (273)
T PRK13232         79 GDIKCVESGGPEPGVGCAGRGIITSIGLLENLGAYTDDLDYVFYDVLGDVVCGGFAMPIREGKAKEIYIVASGELMAIYA  158 (273)
T ss_pred             CCEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCHHHHHH
T ss_conf             97389868998767654530478888899970832147988999414733236531442016576899980760888999


Q ss_pred             HHHHHHHHHHCCC-CCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHHH
Q ss_conf             9999999998198-767538999565898752005999999848953799068799999988479618988899989999
Q gi|254780725|r  314 SKNLIDVLKKLRP-ADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIANL  392 (427)
Q Consensus       314 a~~ll~~l~~~~~-~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~~  392 (427)
                      +.++++.+++... ..+--.+|+|+.+.... +.-.++|++.++.++...||+|..+ .+|..+|+|+++++|+|+.+++
T Consensus       159 annI~k~i~~~~~~~~rl~GiI~n~r~~~~~-~e~v~~fa~~~g~~vi~~IPr~~~v-~~A~~~g~tvie~~P~S~~A~a  236 (273)
T PRK13232        159 ANNICKGLAKFAKGGARLGGIICNSRNVDGE-RELLEAFAKKLGSQLIHFVPRDNIV-QRAEINRKTVIDFDPESNQAKE  236 (273)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEEECCCCCCH-HHHHHHHHHHCCCCEEEECCCCHHH-HHHHHCCCEEEEECCCCHHHHH
T ss_conf             9999999999962188501488505577638-9999999997199669978997788-7648729835897999979999


Q ss_pred             HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             9999999852212232111058999987423
Q gi|254780725|r  393 LVDFSRVLMGRVTVSKPQSAMYTKIKKIFNM  423 (427)
Q Consensus       393 ~~~La~~i~gr~~~~~~k~~~~~~l~~lf~r  423 (427)
                      |.+||+.|..+.....|++-....|..|+.+
T Consensus       237 Y~~LA~~I~~~~~~~~P~pl~~~el~~~~~~  267 (273)
T PRK13232        237 YLTLAHNVQNNDKLVVPTPLPMEELEAMMVE  267 (273)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
T ss_conf             9999999985899877887998999999998


No 15 
>PRK13235 nifH nitrogenase reductase; Reviewed
Probab=100.00  E-value=1.6e-34  Score=231.37  Aligned_cols=256  Identities=14%  Similarity=0.130  Sum_probs=193.3

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      |.|||+| ||||||||+++|||.+||+ .|++|++||+|++..++...+|..+..++.|.+....  +...++..+.+..
T Consensus         2 ~~iaiyG-KGGVGKSTtt~NLaAALA~-~GkkVl~IgcDPk~dsT~~L~gg~~~~tvld~l~~~~--~~~~ledvi~~g~   77 (274)
T PRK13235          2 RKVAIYG-KGGIGKSTTTQNTVAGLAE-MGKKVMVVGCDPKADSTRLLLGGLQQKTVLDTLREEG--EDVELEDIIKEGY   77 (274)
T ss_pred             CEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCCCCHHHHHHCCCCCCCHHHHHHHCC--CCCCHHHHEEECC
T ss_conf             6799979-9855476789999999997-8997999898984536678738998997899998628--7767789443178


Q ss_pred             CCEEEEECCCCC-C-CHHCCCHHHHHHHHHHHH-----HCCCEEEECCCCCCCHHHHHH---HHHCCCCCCCCCCCHHHH
Q ss_conf             980687248761-2-032079999999899985-----128889973888889899999---862012543578776889
Q gi|254780725|r  242 ENLSILTAPAML-S-RTYDFDEKMIVPVLDILE-----QIFPLVILDVPHVWNSWTQEV---LTLSDKVVITTSLDLAGL  311 (427)
Q Consensus       242 ~gL~lL~a~~~~-~-~~~~~~~~~l~~ll~~l~-----~~yd~VIiD~p~~~~~~~~~~---L~~AD~vviV~~p~~~sl  311 (427)
                      .++.+..++... . ....-..-....+++.+.     ..||||++|++.........+   ...||+|++|+++++.||
T Consensus        78 ~gi~cveaggp~pg~gcagrgii~~~~~L~~l~~~~~~~~~DyVl~DvLGdvvcggFa~pir~~~A~eV~IVts~E~~AL  157 (274)
T PRK13235         78 GNTRCTESGGPEPGVGCAGRGIITSVNLLEQLGAYDDEWNLDYVFYDVLGDVVCGGFAMPIRDGKAEEIYIVCSGEMMAM  157 (274)
T ss_pred             CCEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCHHHH
T ss_conf             98189868998756675763152589999881775433577689981378531245115510065878999916836899


Q ss_pred             HHHHHHHHHHHHCC--CCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHH
Q ss_conf             99999999999819--8767538999565898752005999999848953799068799999988479618988899989
Q gi|254780725|r  312 RNSKNLIDVLKKLR--PADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAI  389 (427)
Q Consensus       312 r~a~~ll~~l~~~~--~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~  389 (427)
                      ..+.++++.+++.+  ...+-..+|+|+.+.... .-..++|++.++.++.+.||+|.. +.+|..+|+++++++|+|+.
T Consensus       158 ~aannI~k~i~~~~~~~~~~l~Gii~N~r~~~~~-~~~v~~fa~~~g~~vi~~IPr~~~-V~~Ae~~~~tVie~~P~S~~  235 (274)
T PRK13235        158 YAANNICKGILKYADAGGVRLGGLICNSRKVDNE-REMIEELARKLGTQMIHFVPRDNM-VQRAEINRKTVIDYDPTHGQ  235 (274)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCH-HHHHHHHHHHCCCCEEEECCCCHH-HHHHHHCCCEEEEECCCCHH
T ss_conf             9999999999999743795488999736778757-899999999749936997589458-89998739778997899879


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             9999999999852212232111058999987423
Q gi|254780725|r  390 ANLLVDFSRVLMGRVTVSKPQSAMYTKIKKIFNM  423 (427)
Q Consensus       390 a~~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~r  423 (427)
                      +++|++||++|........|++-....|.+|+..
T Consensus       236 A~~Yr~LA~~I~~n~~~~~p~pl~~~el~~l~~~  269 (274)
T PRK13235        236 ADEYRALARKIDENEMFVIPKPLEIEELESLLIE  269 (274)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
T ss_conf             9999999999983899867885998999999998


No 16 
>PRK13230 nitrogenase reductase-like protein; Reviewed
Probab=100.00  E-value=2.5e-33  Score=224.04  Aligned_cols=255  Identities=18%  Similarity=0.199  Sum_probs=177.3

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHH---------
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433---------
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAF---------  232 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~---------  232 (427)
                      |.|||+| ||||||||+|+|||.+||. .|++|++||+|+|..++.-+.+-....++.|.+.... +|...         
T Consensus         2 ~~ia~yG-KGGVGKTTTavNLAaALA~-~GkkVLlID~DPqgnaTs~L~~g~~~~tv~d~~~~~~-~~~~~l~~~~~~~~   78 (292)
T PRK13230          2 KQIAFYG-KGGIGKSTTVCNLAAALSK-SGKKVIVVGCDPKHDCTSNLRGGEDIPTVLDVLREKG-IDKLGIETIIRENL   78 (292)
T ss_pred             CEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHCC-CCCCCHHHHCCCCC
T ss_conf             6799917-9985789899999999998-7995999776797754253015987752999998617-54222333203244


Q ss_pred             --HHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHH-------CCCEEEECCCCCCCH---HHHHHHHHCCCC
Q ss_conf             --76532024898068724876120320799999998999851-------288899738888898---999998620125
Q gi|254780725|r  233 --VSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQ-------IFPLVILDVPHVWNS---WTQEVLTLSDKV  300 (427)
Q Consensus       233 --l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~-------~yd~VIiD~p~~~~~---~~~~~L~~AD~v  300 (427)
                        .+..+....+++.++.++...... ......+....+.+++       .|||+++|++.....   .+...+..||.|
T Consensus        79 ~~~~dii~~~~~gv~~ve~g~~~~g~-g~~gr~~~~~~~ll~~~~~~~~~~~D~vl~D~lg~~~~~g~~~p~~~~~Ad~V  157 (292)
T PRK13230         79 LKKEDIIYEGFNGIYCVEAGGPKPGY-GCAGRGVIVVIDLLKKMNVFEELGVDVVLYDVLGDVVCGGFAMPLRMGLADQI  157 (292)
T ss_pred             CCHHHEEECCCCCEEEEECCCCCCCC-CCCHHHHHHHHHHHHHHCCHHHHCCCEEEECCCCCCCCCCCCCCCHHCCCCEE
T ss_conf             65232222267862786168987664-11314789999999981312330876575034355664642156202018989


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCC--CCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCC
Q ss_conf             4357877688999999999999819--87675389995658987520059999998489537990687999999884796
Q gi|254780725|r  301 VITTSLDLAGLRNSKNLIDVLKKLR--PADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGK  378 (427)
Q Consensus       301 viV~~p~~~slr~a~~ll~~l~~~~--~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~  378 (427)
                      ++|++++..+|.++.++++.+++..  .+..--.+|.|+..... ..-..++|++.++.++...||++.++ .+|...|+
T Consensus       158 lIp~q~E~~ALeg~~~l~~tI~~~~~~~~~~l~Giv~n~r~~l~-~~~vv~e~~~~fg~~v~~~IPrnv~l-~EAps~G~  235 (292)
T PRK13230        158 YVVTSSDYMALYAANNICKGIKQFAKRGGSTLGGIIYNVRGSMD-AFDIVSEFASKLNTNIIGKVPNSNII-NEAEIDGK  235 (292)
T ss_pred             EEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCC-HHHHHHHHHHHHCCEEEEECCCCCHH-HHCCCCCC
T ss_conf             99727389999999999999999984579757999970898864-78999999998299159967996063-41430498


Q ss_pred             CEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             18988899989999999999985221223211105899998742
Q gi|254780725|r  379 MIHEVDPKSAIANLLVDFSRVLMGRVTVSKPQSAMYTKIKKIFN  422 (427)
Q Consensus       379 pi~e~~p~s~~a~~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~  422 (427)
                      |+.+++|+|+.+++|.+||++|........|+.-.-..|..||+
T Consensus       236 pvi~ydP~S~gA~aY~~LA~ei~en~~~~~p~pl~~~~l~~l~~  279 (292)
T PRK13230        236 TAIEYAPDSEISKIYRELAEKIYENNTGTIPNPLENEQIMQIGK  279 (292)
T ss_pred             CEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
T ss_conf             24897989978999999999999679997888899899999999


No 17 
>PRK11670 putative ATPase; Provisional
Probab=100.00  E-value=1.2e-32  Score=220.01  Aligned_cols=232  Identities=15%  Similarity=0.144  Sum_probs=170.9

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             67537999746988775689999999999626994999978798986033438998789888631845612433765320
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      ...+||+|.|+||||||||+|+|||.+||+ .|++|+++|+|+++.++..+||.+......        .|...+..   
T Consensus       105 ~v~~vIAVaSGKGGVGKSTvavNLA~ALA~-~G~kVgllDADi~Gpsip~mlG~~~~~~~~--------~d~~~i~P---  172 (369)
T PRK11670        105 GVKNIIAVSSGKGGVGKSSTAVNLALALAA-EGAKVGILDADIYGPSIPTMLGAENQRPTS--------PDGTHMAP---  172 (369)
T ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCCCHHHCCCCCCCCC--------CCCCEECC---
T ss_conf             868899998589988899999999999996-699378982478887650230665456646--------88966376---


Q ss_pred             CCCCCEEEEECCCCC--CCHH----CCCHHHHHHHH-HHHHHCCCEEEECCCCCCCHHHHHH--HHHCCCCCCCCCCCHH
Q ss_conf             248980687248761--2032----07999999989-9985128889973888889899999--8620125435787768
Q gi|254780725|r  239 FYAENLSILTAPAML--SRTY----DFDEKMIVPVL-DILEQIFPLVILDVPHVWNSWTQEV--LTLSDKVVITTSLDLA  309 (427)
Q Consensus       239 ~~~~gL~lL~a~~~~--~~~~----~~~~~~l~~ll-~~l~~~yd~VIiD~p~~~~~~~~~~--L~~AD~vviV~~p~~~  309 (427)
                      ....|+.+.+..--.  +...    ......+.+++ +.....|||+|||+|++.++....+  ....+.+++|++|...
T Consensus       173 ~~~~gi~~~S~g~l~~~~~~~iwRgp~~~~al~q~l~~~~wg~lDyLIID~PPGtgDi~Ltl~q~v~~~gavvVTTPq~~  252 (369)
T PRK11670        173 IMAHGLATNSIGYLVTDDNAMVWRGPMASKALMQMLQETLWPDLDYLVLDMPPGTGDIQLTLAQNIPVTGAVVVTTPQDI  252 (369)
T ss_pred             CCCCCEEEEECCCCCCCCCCHHHCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEEECCCCHH
T ss_conf             00058125302202376640222130167999998777433788889983799875277788764576607996277376


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCEEEEECCCC--CC---C----CHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCE
Q ss_conf             8999999999999819876753899956589--87---5----2005999999848953799068799999988479618
Q gi|254780725|r  310 GLRNSKNLIDVLKKLRPADKPPYLVLNQVKT--PK---K----PEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMI  380 (427)
Q Consensus       310 slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~--~~---~----~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi  380 (427)
                      ++.++.+.+.++++.+.  ..+.+|.||...  +.   .    +.-..+++++.++.+..+.||.|+.. .++.+.|+|+
T Consensus       253 Al~Da~k~i~m~~k~~v--pilGiVeNMs~~~c~~c~~~~~iFg~gg~e~~a~~~~v~lLG~IP~d~~I-~ea~d~G~Pv  329 (369)
T PRK11670        253 ALIDAKKGIVMFEKVEV--PVLGIVENMSMHICSNCGHHEPIFGTGGAEKLAEKYHTQLLGQMPLHISL-REDLDRGTPT  329 (369)
T ss_pred             HHHHHHHHHHHHHHCCC--CCEEEEECCCCCCCCCCCCCCEECCCCCHHHHHHHHCCCEEEECCCCHHH-HHHCCCCCCE
T ss_conf             99999999999985488--85068863633336899971001366609999998399879979898899-9618599856


Q ss_pred             EEECCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             9888999899999999999852212
Q gi|254780725|r  381 HEVDPKSAIANLLVDFSRVLMGRVT  405 (427)
Q Consensus       381 ~e~~p~s~~a~~~~~La~~i~gr~~  405 (427)
                      +...|+|+.+++|.+||++|..+-.
T Consensus       330 V~~~P~S~aA~Af~~iA~~la~~~~  354 (369)
T PRK11670        330 VVSRPESEFTAIYRQLADRVAAQLY  354 (369)
T ss_pred             EEECCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9828999899999999999999996


No 18 
>cd02032 Bchl_like This family of proteins contains bchL and chlL. Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen.
Probab=100.00  E-value=1.7e-32  Score=218.93  Aligned_cols=251  Identities=15%  Similarity=0.175  Sum_probs=189.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCC-CHHHHHHHHHHHCCC
Q ss_conf             7999746988775689999999999626994999978798986033438998789888631845-612433765320248
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVG-RIDKAFVSRLPVFYA  241 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~-rlD~~~l~~~l~~~~  241 (427)
                      +|||+| |||+||||+++||+.+||+ .|++|++||+|+...++ ..|.-...+++.|.+...+ +.+...++..+.+..
T Consensus         2 kiaiyG-KGGIGKSTttaNl~aaLA~-~G~kVl~IgcDpk~Dst-~~L~g~~~~tvld~l~~~~~~~~~~~~~d~v~~g~   78 (267)
T cd02032           2 VLAVYG-KGGIGKSTTSSNLSVALAK-RGKKVLQIGCDPKHDST-FTLTGFLIPTVIDILEEVDFHYEELWPEDVIYEGY   78 (267)
T ss_pred             EEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCCHHHH-HHHCCCCCCCHHHHHHHHCCCHHHCCHHHHHHCCC
T ss_conf             799977-9965787789999999998-79959997789951556-75269886839999986088666414778753076


Q ss_pred             CCEEEEECCCCCCC--HHC-CCHHHHHHHHH--HHHHCCCEEEECCCCCCC-HHHHHHHHHCCCCCCCCCCCHHHHHHHH
Q ss_conf             98068724876120--320-79999999899--985128889973888889-8999998620125435787768899999
Q gi|254780725|r  242 ENLSILTAPAMLSR--TYD-FDEKMIVPVLD--ILEQIFPLVILDVPHVWN-SWTQEVLTLSDKVVITTSLDLAGLRNSK  315 (427)
Q Consensus       242 ~gL~lL~a~~~~~~--~~~-~~~~~l~~ll~--~l~~~yd~VIiD~p~~~~-~~~~~~L~~AD~vviV~~p~~~slr~a~  315 (427)
                      .|+.++.++.....  ... .-...+ .+++  .+.+.||||++|++...- ......+..||++++|++++..|++++.
T Consensus        79 ~gv~cvEaGgP~pg~Gcagrgi~~~~-~lL~~l~~~~~~D~Vl~DvlgdVvcgGFa~pi~~Ad~~~iVTs~e~~sl~aAn  157 (267)
T cd02032          79 GGVDCVEAGGPPAGAGCGGYVVGETV-KLLKELNLFEEYDVILFDVLGDVVCGGFAAPLNYADYALIVTDNDFDSIFAAN  157 (267)
T ss_pred             CCCEEEECCCCCCCCCCCCCCHHHHH-HHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCEEEEEECCCHHHHHHHH
T ss_conf             78457665899999887764048999-99987166434778999536654456656761006889999567187899999


Q ss_pred             HHHHHHHHCC--CCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCH----H
Q ss_conf             9999999819--876753899956589875200599999984895379906879999998847961898889998----9
Q gi|254780725|r  316 NLIDVLKKLR--PADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSA----I  389 (427)
Q Consensus       316 ~ll~~l~~~~--~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~----~  389 (427)
                      |+...+++..  .+.+--.+|+|+.+    ..-..++|++.++.++.+.||+|.. +.+|.++|+|++|+.|.++    .
T Consensus       158 ~I~~~i~~~~~~~~~rl~GlI~Nr~~----~~~~i~~fa~~lg~~lig~VP~d~~-V~~se~~g~tvie~~p~~~~~s~~  232 (267)
T cd02032         158 RIAAAVREKAKTYKVRLAGLIANRTD----KTDLIDKFVEAVGMPVLAVLPLIED-IRRSRVKGKTLFEMDESDEELAYR  232 (267)
T ss_pred             HHHHHHHHHHHCCCCCCCEEEEECCC----CHHHHHHHHHHHCCCEEEECCCCHH-HHHHHHCCCEEEEECCCCCHHHHH
T ss_conf             99999999753379764227874698----5789999999729946996699338-899987398689848998437899


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             999999999985221223211105899998742
Q gi|254780725|r  390 ANLLVDFSRVLMGRVTVSKPQSAMYTKIKKIFN  422 (427)
Q Consensus       390 a~~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~  422 (427)
                      ++.|++||+.|....+...|++-....|..||+
T Consensus       233 a~~Yr~LA~~i~~n~~~~~P~pl~~~el~~l~~  265 (267)
T cd02032         233 CDYYLLIADQLLAGPEGVVPEPLGDREIFDLLG  265 (267)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
T ss_conf             999999999998399986776699899999862


No 19 
>PHA02518 ParA-like protein; Provisional
Probab=100.00  E-value=9.5e-33  Score=220.52  Aligned_cols=206  Identities=15%  Similarity=0.176  Sum_probs=155.2

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      |||+|.+.||||||||+|+|||.+|++ .|++|++||+|+|. ++..++...            +.              
T Consensus         1 KIIav~n~KGGvGKTT~a~nLA~~la~-~G~~VlliD~DpQ~-s~~~w~~~r------------~~--------------   52 (211)
T PHA02518          1 KIIAVLNQKGGAGKTTVATNLASWLHA-DGHKVLLVDLDPQG-SSTDWAEAR------------EE--------------   52 (211)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHH-CCCCEEEEECCCCC-CHHHHHHHC------------CC--------------
T ss_conf             989998089997499999999999997-89948999779996-788999852------------26--------------


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             98068724876120320799999998999851288899738888898999998620125435787768899999999999
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVL  321 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l  321 (427)
                       +..+++.       ... ...+..-+..+...|||||||+|+..+..+..+|..||.+++|+.|+..++..+.++++.+
T Consensus        53 -~~~~~~~-------~~~-~~~~~~~l~~~~~~yD~viID~pp~~~~~~~~al~aaD~vliP~~ps~~d~~~~~~~~~~i  123 (211)
T PHA02518         53 -GEPLIPV-------VRM-GKSIRADLPKVASGYDYVVVDGAPQDSELARAALRIADMVLIPVQPSPFDIWAAPDLVELI  123 (211)
T ss_pred             -CCCCCCH-------HHC-CHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHCCEEEEECCCCHHHHHHHHHHHHHH
T ss_conf             -8997401-------213-6779999997406788899889997429999999958969996378687899999999999


Q ss_pred             HH---CCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Q ss_conf             98---198767538999565898752005999999848953799068799999988479618988899989999999999
Q gi|254780725|r  322 KK---LRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIANLLVDFSR  398 (427)
Q Consensus       322 ~~---~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~~~~~La~  398 (427)
                      +.   .+.+.....++.|+...+.+.....++..+.++.+++-....+...+.+|...|+++.|+.|+|+.+++|..|++
T Consensus       124 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~v~~t~I~~r~~~~~a~~~G~~V~e~~~~~~aa~e~~~L~~  203 (211)
T PHA02518        124 KARQEVTDGLPKFAFIISRAIKNTQLYREARKALAGYGLPILRNGTTQRVAYADAAEAGGSVLELPEDDKAAEEIIQLVK  203 (211)
T ss_pred             HHHHHHCCCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCCHHEECCCCHHHHHHHHHHH
T ss_conf             99998665675168886235866569999999999869981068198878999999759976109979999999999999


Q ss_pred             HHHCCC
Q ss_conf             985221
Q gi|254780725|r  399 VLMGRV  404 (427)
Q Consensus       399 ~i~gr~  404 (427)
                      +|..|.
T Consensus       204 Eil~r~  209 (211)
T PHA02518        204 ELFRGI  209 (211)
T ss_pred             HHHHHH
T ss_conf             999863


No 20 
>PRK13185 chlL protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional
Probab=100.00  E-value=2.5e-31  Score=211.74  Aligned_cols=253  Identities=13%  Similarity=0.134  Sum_probs=192.3

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCC-CHHHHHHHHHHHC
Q ss_conf             537999746988775689999999999626994999978798986033438998789888631845-6124337653202
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVG-RIDKAFVSRLPVF  239 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~-rlD~~~l~~~l~~  239 (427)
                      +++|+|+| |||+||||+++|++.+||+ .|++|++||+|+...++-.+.| ...+++.|.+...+ +.++..++..+.+
T Consensus         2 ~~~iaiyG-KGGIGKSTttaNlsaALA~-~GkkV~~IgcDPk~DsT~~L~g-~~~~tild~l~~~~~~~~~~~~ed~~~~   78 (269)
T PRK13185          2 ALVLAVYG-KGGIGKSTTSSNLSAALAK-LGKKVLQIGCDPKHDSTFTLTG-KLVPTVIDILEEVDFHSEELRPEDFVFE   78 (269)
T ss_pred             CEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCCCCCHHHCCC-CCCCCHHHHHHHCCCCHHHCCHHHHHHC
T ss_conf             53999978-9954788899999999997-6993899818997323011259-9878789999743876021256677633


Q ss_pred             CCCCEEEEECCCC-CC--CHHCCCHHHHHHHHHHH--HHCCCEEEECCCCCCC-HHHHHHHHHCCCCCCCCCCCHHHHHH
Q ss_conf             4898068724876-12--03207999999989998--5128889973888889-89999986201254357877688999
Q gi|254780725|r  240 YAENLSILTAPAM-LS--RTYDFDEKMIVPVLDIL--EQIFPLVILDVPHVWN-SWTQEVLTLSDKVVITTSLDLAGLRN  313 (427)
Q Consensus       240 ~~~gL~lL~a~~~-~~--~~~~~~~~~l~~ll~~l--~~~yd~VIiD~p~~~~-~~~~~~L~~AD~vviV~~p~~~slr~  313 (427)
                      ...|+.++-++.. +.  .....-...+ .+++.+  .+.||||++|++...- ......+..||++++|++++..+++.
T Consensus        79 G~~gv~cvEaGGP~pG~GCaGrgi~~~~-~~L~~~~~~~~~D~Vl~DvlgdVvCGGFa~Pi~~Ad~~~IVts~e~~al~a  157 (269)
T PRK13185         79 GYNGVDCVEAGGPPAGTGCGGYVVGETV-KLLKEHHLLDDYDVILFDVLGDVVCGGFAAPLQYADYALIVTANDFDSIFA  157 (269)
T ss_pred             CCCCCEEEECCCCCCCCCCCCCCHHHHH-HHHHHCCCCCCCCEEEEECCCCCCCCCCCCCHHCCCEEEEEECCHHHHHHH
T ss_conf             7677056643899998776764318999-999872874337879995367433365557510088899992530878999


Q ss_pred             HHHHHHHHHHC--CCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHH
Q ss_conf             99999999981--9876753899956589875200599999984895379906879999998847961898889998999
Q gi|254780725|r  314 SKNLIDVLKKL--RPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIAN  391 (427)
Q Consensus       314 a~~ll~~l~~~--~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~  391 (427)
                      +.|++..+.+.  +.+.+--.+|+|+.+.    .-..++|.+.+|.++.+.||+|. .+.+|.++|++++|..|.|+.++
T Consensus       158 AnnI~~~i~~~a~~~~~rl~GiI~Nr~~~----~d~v~~fa~~~g~~vl~~IP~~~-~V~~se~~g~TviE~~p~~~~a~  232 (269)
T PRK13185        158 ANRIAAAIQAKAKNYKVRLAGVIANRSGG----TDQIDKFNERVGLRTLAHVPDLD-AIRRSRLKGKTLFEMEETDELEE  232 (269)
T ss_pred             HHHHHHHHHHHHHCCCCCCCEEEEECCCC----HHHHHHHHHHHCCCEEEECCCCH-HHHHHHHCCCEEEEECCCCHHHH
T ss_conf             99999999865301585323257616883----77999999986997699789978-89999874986788589981789


Q ss_pred             ---HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             ---9999999985221223211105899998742
Q gi|254780725|r  392 ---LLVDFSRVLMGRVTVSKPQSAMYTKIKKIFN  422 (427)
Q Consensus       392 ---~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~  422 (427)
                         +|++||+.|.+..++..|++-.-..|..||+
T Consensus       233 v~~~Yr~LA~~i~~~~~~~~P~pl~~~el~~l~~  266 (269)
T PRK13185        233 VQNEYLRLADQLLAGPEPLVPKPLKDREIFDLLS  266 (269)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
T ss_conf             9999999999998289987888899899999974


No 21 
>PRK13231 nitrogenase reductase-like protein; Reviewed
Probab=100.00  E-value=1.4e-31  Score=213.30  Aligned_cols=250  Identities=20%  Similarity=0.195  Sum_probs=193.4

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      |.|+|+| |||+||||+++|||.+||.  +++|++||+|+...++...+|. ..+++.|.+......   .++..+.+..
T Consensus         3 ~~iAiyG-KGGIGKSTt~~NlaaalA~--g~rVl~igcDpk~dst~~L~G~-~~ptvl~~l~~~~~~---~~~dvv~~g~   75 (264)
T PRK13231          3 KKIAIYG-KGGIGKSTTVSNMAAAYSS--DNSTLVIGCDPKADTTRTLVGK-RIPTVLDTLKDNRQP---ELEDIIYEGY   75 (264)
T ss_pred             EEEEEEC-CCCCCHHHHHHHHHHHHHC--CCCEEEECCCCCCCHHHHHHCC-CCCCHHHHHHHCCCC---CHHHHEEECC
T ss_conf             2899978-9854788899999999987--9977998568885024676199-988388986312777---7656312178


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHH---HH---HHHHHHCCCEEEECCCCCCCHHHHH---HHHHCCCCCCCCCCCHHHHH
Q ss_conf             980687248761203207999999---98---9998512888997388888989999---98620125435787768899
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIV---PV---LDILEQIFPLVILDVPHVWNSWTQE---VLTLSDKVVITTSLDLAGLR  312 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~---~l---l~~l~~~yd~VIiD~p~~~~~~~~~---~L~~AD~vviV~~p~~~slr  312 (427)
                      .|+.++.++.. ..........+.   .+   +..+...+|||++|++........+   ....||++++|++++..||.
T Consensus        76 ~gi~cvesGgp-epg~gcagrgi~~~~~lLe~~~~~~~~~D~vl~Dvlgdvvcggfa~Pir~~~Adev~IVts~e~msLy  154 (264)
T PRK13231         76 NNTLCVESGGP-EPGVGCAGRGVIVAMNLLEKLGVFDNDPDVVIYDVLGDVVCGGFSVPLREDYADEVYIVTSGEYMSLY  154 (264)
T ss_pred             CCEEEEECCCC-CCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEECCCCCCCCCEEEEEECCCHHHHH
T ss_conf             98499737998-87766565217689899987264224798799943587205667045542669889999478589999


Q ss_pred             HHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHHH
Q ss_conf             99999999998198767538999565898752005999999848953799068799999988479618988899989999
Q gi|254780725|r  313 NSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIANL  392 (427)
Q Consensus       313 ~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~~  392 (427)
                      ++.++.+.+++.+.  +--.+|+|+.+.+.. .-..++|++.+|.++.+.||+|.. +.+|...|++++|..|.|+.+++
T Consensus       155 aAnnI~~~i~~~~~--rl~GiI~N~r~~~~e-~~iv~~fa~~~g~~vl~~IPr~~~-V~~ae~~~~tVie~~P~S~~A~~  230 (264)
T PRK13231        155 AANNIAKGIKKLKG--KLGGIICNCRNVKNE-VEIVSEFASLIGSRIIGIIPRSNL-VQESELKASTVVETFPESSQASI  230 (264)
T ss_pred             HHHHHHHHHHHHCC--CCCEEEEECCCCCCH-HHHHHHHHHHCCCCEEEECCCCHH-HHHHHHCCCEEEEECCCCHHHHH
T ss_conf             99999999999546--442089606898877-999999999719968996689478-88888629758997989889999


Q ss_pred             HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             9999999852212232111058999987423
Q gi|254780725|r  393 LVDFSRVLMGRVTVSKPQSAMYTKIKKIFNM  423 (427)
Q Consensus       393 ~~~La~~i~gr~~~~~~k~~~~~~l~~lf~r  423 (427)
                      |++||+.|........|+.-....|.+||..
T Consensus       231 Yr~LA~~I~~~~~~~~P~pl~~~~l~~~~~~  261 (264)
T PRK13231        231 YSELANNIMNNQEFTTPEPMDIEEFEEFFYS  261 (264)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
T ss_conf             9999999985899978887998999999998


No 22 
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=100.00  E-value=4.1e-31  Score=210.45  Aligned_cols=236  Identities=15%  Similarity=0.135  Sum_probs=170.5

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCC------CCHHHHHCCCCCHHHH
Q ss_conf             5675379997469887756899999999996269949999787989860334389987------8988863184561243
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPI------NSISDAIYPVGRIDKA  231 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~------~~l~d~l~~~~rlD~~  231 (427)
                      +...+||+|.+.||||||||+|+|||++||. .|+|||+||+|+| |++..+||..|.      .++.+++...+.  ..
T Consensus       101 g~~~~VIav~N~KGGVGKTTtav~LA~~LA~-~G~RVLvIDLDPQ-anlT~~~G~~pe~d~~~~~tl~~~l~~d~~--~~  176 (387)
T TIGR03453       101 GEHLQVIAVTNFKGGSGKTTTSAHLAQYLAL-RGYRVLAIDLDPQ-ASLSALFGFQPEFDVGENETLYGAIRYDDE--RR  176 (387)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEECCCH-HHHHHHCCCCCCCCCCCCCCHHHHHHCCCC--CC
T ss_conf             9988089997888765699999999999997-7998899953701-678875289843466756429999844556--68


Q ss_pred             HHHHHHHC-CCCCEEEEECCCCCCCHHC---------CC-----HHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHH
Q ss_conf             37653202-4898068724876120320---------79-----999999899985128889973888889899999862
Q gi|254780725|r  232 FVSRLPVF-YAENLSILTAPAMLSRTYD---------FD-----EKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTL  296 (427)
Q Consensus       232 ~l~~~l~~-~~~gL~lL~a~~~~~~~~~---------~~-----~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~  296 (427)
                      .+...+.+ +.+||+++|+...+...+.         ..     ...+...++.++..||||||||||.++..+.++|.+
T Consensus       177 ~l~~~i~~T~~~~LdliPa~~~L~~~E~~~~~~l~~~~~~~~~f~~rL~~aL~~v~d~YD~IlIDcPPsLg~lT~nAL~A  256 (387)
T TIGR03453       177 PLSEIIRKTYFPGLDLIPGNLELMEFEHETPRALSRGAGGDTIFFARVGEALAEVEDDYDVVVIDCPPQLGFLTLSALCA  256 (387)
T ss_pred             CHHHHHHCCCCCCEEEECCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHH
T ss_conf             79996114799996896598899998898899997431100269999999999766029999995898513999999998


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHH-------HHHHHCC--CCCCCCEEEEECCCCCCCCHH-HHHHHHHHHCCCE-EEEECC
Q ss_conf             0125435787768899999999-------9999819--876753899956589875200-5999999848953-799068
Q gi|254780725|r  297 SDKVVITTSLDLAGLRNSKNLI-------DVLKKLR--PADKPPYLVLNQVKTPKKPEI-SISDFCAPLGITP-SAIIPF  365 (427)
Q Consensus       297 AD~vviV~~p~~~slr~a~~ll-------~~l~~~~--~~~~~~~iVlNr~~~~~~~~i-~~~~~~~~lg~~~-~~~IP~  365 (427)
                      ||.+++++.|+...+..+.+++       +.+++.+  .+..-++++++|+++....+. -.+.+.+.+|..+ ...||.
T Consensus       257 Ad~vlIPv~p~~ld~~s~~qfl~~~~~l~~~i~~~g~~~~~d~~~~LlT~~d~~~~~~~~v~~~~r~~fg~~vl~~~i~~  336 (387)
T TIGR03453       257 ATAVLITVHPQMLDVMSMSQFLLMTGDLLGVVRDAGGNLSYDWMRYLVTRYEPNDGPQAQMVAFMRSLFGEHVLTNPMLK  336 (387)
T ss_pred             CCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCEEEH
T ss_conf             19408788871777999999999999999999971677676405776451789984699999999998506542362016


Q ss_pred             CHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Q ss_conf             799999988479618988899989999999999
Q gi|254780725|r  366 DGAVFGMSANSGKMIHEVDPKSAIANLLVDFSR  398 (427)
Q Consensus       366 D~~~~~~A~~~G~pi~e~~p~s~~a~~~~~La~  398 (427)
                      . ..+++|...+++|.|..+..-..+.|.+.-+
T Consensus       337 S-~ai~~A~~~~~TiyE~~~~~~~r~ty~Ra~e  368 (387)
T TIGR03453       337 S-TAISDAGLTKQTLYEVERSQFTRSTYDRAME  368 (387)
T ss_pred             H-HHHHHHHHHCCCEEEECCCCCCHHHHHHHHH
T ss_conf             7-9998637637935987746589899999999


No 23 
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=100.00  E-value=4.9e-31  Score=209.97  Aligned_cols=234  Identities=13%  Similarity=0.085  Sum_probs=169.5

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCC------CHHHHHCCCCCHHHHHH
Q ss_conf             753799974698877568999999999962699499997879898603343899878------98886318456124337
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPIN------SISDAIYPVGRIDKAFV  233 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~------~l~d~l~~~~rlD~~~l  233 (427)
                      ..+||+|.+.||||||||+|+|||++||. .|++||+||+|+| |++..+||..|..      ++.+++...+.  ...+
T Consensus       120 ~~kVIaVaN~KGGVGKTTtav~LA~~LA~-~G~RVLlIDLDPQ-gnlS~~lG~~pe~d~~~~~tl~~~l~~d~~--~~~l  195 (405)
T PRK13869        120 HLQVIAVTNFKGGSGKTTTSAHLAQYLAL-QGYRVLAVDLDPQ-ASLSALLGVLPETDVGANETLYAAIRYDDT--RRPL  195 (405)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEECCHH-HHHHHHHCCCCCCCCCCHHHHHHHHHCCCC--CCCH
T ss_conf             98289997888776599999999999997-7998899964561-788898089854566531359999844545--5879


Q ss_pred             HHHHH-CCCCCEEEEECCCCCCCHHCCC--------------HHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCC
Q ss_conf             65320-2489806872487612032079--------------99999989998512888997388888989999986201
Q gi|254780725|r  234 SRLPV-FYAENLSILTAPAMLSRTYDFD--------------EKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSD  298 (427)
Q Consensus       234 ~~~l~-~~~~gL~lL~a~~~~~~~~~~~--------------~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD  298 (427)
                      ...+. .+.+||+++|+...+...+...              ...+...++.+...||||||||||.++..+.++|.+||
T Consensus       196 ~~~I~~T~~~~LdlIPa~l~L~~~E~~~~~~l~~~~~~~~~~~~rl~~~L~~v~d~YDvIiIDcPPsLg~lT~nAL~AAd  275 (405)
T PRK13869        196 RDVIRPTYFDGLHLVPGNLELMEFEHTTPKALSDRGTRDGLFFTRVAQAFDEVADDYDVVVIDCPPQLGFLTLSGLCAAT  275 (405)
T ss_pred             HHHCCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHC
T ss_conf             99521679999689589889999888759998743315568999999999864412998999599826599999999828


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHH-------HCCCCC--CCCEEEEECCCCCCCCH-HHHHHHHHHHCCCEE-EEECCCH
Q ss_conf             254357877688999999999999-------819876--75389995658987520-059999998489537-9906879
Q gi|254780725|r  299 KVVITTSLDLAGLRNSKNLIDVLK-------KLRPAD--KPPYLVLNQVKTPKKPE-ISISDFCAPLGITPS-AIIPFDG  367 (427)
Q Consensus       299 ~vviV~~p~~~slr~a~~ll~~l~-------~~~~~~--~~~~iVlNr~~~~~~~~-i~~~~~~~~lg~~~~-~~IP~D~  367 (427)
                      .++|++.|+...+..+.+++..+.       +.+.+.  .-++++++|++...... ...+.+.+.+|-.+. ..||.. 
T Consensus       276 ~vlIPv~pe~ld~~s~~qfl~~~~~l~~~~~~~~~~~~~dfir~LlTr~d~~~~~~~~v~~~lr~~fg~~Vl~~~i~~S-  354 (405)
T PRK13869        276 SMVITVHPQMLDIASMSQFLLMTRDLLGVVKEAGGNLQYDFIRYLLTRYEPQDAPQTKVTALLRNMFEDHVLTNPMVKS-  354 (405)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCHHH-
T ss_conf             6386489608789999999999999999999707887854045631406899825999999999998788860807377-


Q ss_pred             HHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Q ss_conf             9999988479618988899989999999999
Q gi|254780725|r  368 AVFGMSANSGKMIHEVDPKSAIANLLVDFSR  398 (427)
Q Consensus       368 ~~~~~A~~~G~pi~e~~p~s~~a~~~~~La~  398 (427)
                      ..+++|....++|.|..+..-..+.|.+.-+
T Consensus       355 ~ais~A~~~~~TvyE~~~~~~~r~Ty~Ra~e  385 (405)
T PRK13869        355 AAVSDAGLTKQTLYEIGRENLTRSTYDRAME  385 (405)
T ss_pred             HHHHHHHHHCCCEEEECCCCCCHHHHHHHHH
T ss_conf             9999868744962876505278899999999


No 24 
>CHL00072 chlL photochlorophyllide reductase subunit L
Probab=99.98  E-value=2.9e-30  Score=205.23  Aligned_cols=251  Identities=14%  Similarity=0.161  Sum_probs=188.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCC-CHHHHHHHHHHHCCC
Q ss_conf             7999746988775689999999999626994999978798986033438998789888631845-612433765320248
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVG-RIDKAFVSRLPVFYA  241 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~-rlD~~~l~~~l~~~~  241 (427)
                      .|+|+| |||+||||+++|++.+||. .|++|++|++|+...++.. |.-...+++.|.+...+ +.+...++..+.+.-
T Consensus         2 ~iaiyG-KGGIGKSTtsaNlsaaLA~-~GkkVl~IGcDpk~DsT~~-L~g~~~~tvld~l~~~~~~~~~~~~edvi~~G~   78 (271)
T CHL00072          2 KIAVYG-KGGIGKSTTSCNISIALAR-RGKKVLQIGCDPKHDSTFT-LTGFLIPTIIDTLQSKDYHYEDVWPEDVIYKGY   78 (271)
T ss_pred             EEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCHHHHHHH-HCCCCCCCHHHHHHHHCCCCCCCCHHHHHHCCC
T ss_conf             699978-9854485889999999998-7997999789973777740-069988859999975378732164999985277


Q ss_pred             CCEEEEECCCC-CC--CHHCCCHHHHHHHHHHHH--HCCCEEEECCCCCCC-HHHHHHHHHCCCCCCCCCCCHHHHHHHH
Q ss_conf             98068724876-12--032079999999899985--128889973888889-8999998620125435787768899999
Q gi|254780725|r  242 ENLSILTAPAM-LS--RTYDFDEKMIVPVLDILE--QIFPLVILDVPHVWN-SWTQEVLTLSDKVVITTSLDLAGLRNSK  315 (427)
Q Consensus       242 ~gL~lL~a~~~-~~--~~~~~~~~~l~~ll~~l~--~~yd~VIiD~p~~~~-~~~~~~L~~AD~vviV~~p~~~slr~a~  315 (427)
                      .|+.++-++.. +.  .....-...+ .+++.+.  +.||||+.|++...- ......+..||++++|++++..|++.+.
T Consensus        79 ~gi~cvEaGGPepGvGCaGrgi~~~i-~lL~~l~~~~d~D~V~yDvlgDVVCGGFa~Pi~~Ad~~~iVts~e~malyaAN  157 (271)
T CHL00072         79 GGVDCVEAGGPPAGAGCGGYVVGETV-KLLKELNAFYEYDVILFDVLGDVVCGGFAAPLNYADYCIIITDNGFDALFAAN  157 (271)
T ss_pred             CCCEEEECCCCCCCCCCCCCCCHHHH-HHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCEEEEEECCCHHHHHHHH
T ss_conf             88466543899988777886519999-99997376213888999447765565456750008889999567088999999


Q ss_pred             HHHHHHHHCC--CCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHH----
Q ss_conf             9999999819--8767538999565898752005999999848953799068799999988479618988899989----
Q gi|254780725|r  316 NLIDVLKKLR--PADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAI----  389 (427)
Q Consensus       316 ~ll~~l~~~~--~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~----  389 (427)
                      |+...+++..  ...+--.+|+|+.+   ..+ -.++|.+.+|.++.+.||.|. .+.+|.++|++++|..|.|+-    
T Consensus       158 nI~~~i~~~a~~~~~rl~GiI~N~~~---~~~-~v~~fa~~~g~~~i~~iPrd~-~V~~ae~~~~TviE~~p~s~~~~~~  232 (271)
T CHL00072        158 RIAASVREKARTHPLRLAGLVGNRTS---KRD-LIDKYVEACPMPVLEVLPLIE-DIRVSRVKGKTLFEMAESEPSLNYV  232 (271)
T ss_pred             HHHHHHHHHHHCCCCCCCEEEECCCC---CHH-HHHHHHHHCCCCEEEECCCCC-HHHHHHHCCCCEEECCCCCHHHHHH
T ss_conf             99999999730468644436522688---378-999999973996698568711-6689997488204228998247899


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             999999999985221223211105899998742
Q gi|254780725|r  390 ANLLVDFSRVLMGRVTVSKPQSAMYTKIKKIFN  422 (427)
Q Consensus       390 a~~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~  422 (427)
                      ++.|++||+.|.+......|+.-....|..||+
T Consensus       233 ~~~Yr~LA~~I~~n~~~~iP~pl~~~el~~ll~  265 (271)
T CHL00072        233 CDFYLNIADQLLSQPEGVVPKELPDRELFSLLS  265 (271)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH
T ss_conf             999999999997399986688788799999999


No 25 
>PRK10037 cell division protein; Provisional
Probab=99.98  E-value=2.3e-30  Score=205.88  Aligned_cols=224  Identities=15%  Similarity=0.204  Sum_probs=168.8

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCC--CCCCHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf             3799974698877568999999999962699499997879898603343899--87898886318456124337653202
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKD--PINSISDAIYPVGRIDKAFVSRLPVF  239 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~--~~~~l~d~l~~~~rlD~~~l~~~l~~  239 (427)
                      ++|++.|.||||||||+++||||+|++ .|++|++||+|++ +.+.+.||++  ...|++.++.+.+.     ++....+
T Consensus         2 ~iial~s~kGGVGkTTltAnLA~aL~~-~g~~VlaID~dpq-N~Lrlhfg~~~~~~~Gwa~a~l~g~~-----W~~a~~~   74 (250)
T PRK10037          2 AILGLQGVRGGVGTTSITAALAWSLQM-LGENVLVIDACPD-NLLRLSFNVDFTHRQGWARALLDGQD-----WRDAGLR   74 (250)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCHH-HHHHHHCCCCCCCCCCHHHHHHCCCC-----HHHHHHH
T ss_conf             379996078887689999999999997-7991899957825-66787549985447729999856997-----8999850


Q ss_pred             CCCCEEEEECCCCC-CCHHCCCH--HHHHHHHHHH-----HHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHH
Q ss_conf             48980687248761-20320799--9999989998-----5128889973888889899999862012543578776889
Q gi|254780725|r  240 YAENLSILTAPAML-SRTYDFDE--KMIVPVLDIL-----EQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGL  311 (427)
Q Consensus       240 ~~~gL~lL~a~~~~-~~~~~~~~--~~l~~ll~~l-----~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~sl  311 (427)
                      ..+|+.++|.+... ++...+..  +....++..+     ...|++||+|+|++.++.+..++..||.+++|+.||..|.
T Consensus        75 ~~~gl~~LPfG~l~~~~~~~~~~~~~~~~~l~~~l~~l~~~~~~~~vliD~P~g~s~~~~~~l~~AD~vLvVv~aDa~s~  154 (250)
T PRK10037         75 YTSQLDLLPFGQLSIEEQENPQHWQTTLGDICSALQQLKASGRYQWILLDLPRGASPLTRQLLSLCDHSLAIVNVDANCH  154 (250)
T ss_pred             CCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHCCEEEEEECCCHHHH
T ss_conf             56993697278799899863887765179999998620025789989996599982999999985787899836787789


Q ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHH-HHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHH
Q ss_conf             9999999999981987675389995658987520059999-998489537990687999999884796189888999899
Q gi|254780725|r  312 RNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDF-CAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIA  390 (427)
Q Consensus       312 r~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~-~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a  390 (427)
                      -.   +..   +..  ....++++|++++.+.-.....++ .+.++.....+|..|. .+.+|...++|+.+++|.|.++
T Consensus       155 ~~---L~q---~~~--~~g~~~liNq~~~~s~l~~Dl~~l~~q~~~~llp~~IHrDe-av~EAlA~~~~v~~y~P~SqAa  225 (250)
T PRK10037        155 IR---LHQ---QAL--PAGAHILINDLRIGSQLQDDLYQLWLQSQRRLLPMLIHRDE-AMAECLAAKQPLGEYRSDSLAA  225 (250)
T ss_pred             HH---HHH---HCC--CCCCCEEECCCCCHHHHHHHHHHHHHHHCCCCCCEEECCCC-HHHHHHHCCCCCCCCCCCCHHH
T ss_conf             98---734---214--78982775166711046699999999744241556751754-6899986599874759757788


Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999985
Q gi|254780725|r  391 NLLVDFSRVLM  401 (427)
Q Consensus       391 ~~~~~La~~i~  401 (427)
                      ++|..||.+..
T Consensus       226 ~D~~~LA~W~l  236 (250)
T PRK10037        226 EEILTLANWCL  236 (250)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 26 
>PRK13234 nifH nitrogenase reductase; Reviewed
Probab=99.98  E-value=4.5e-30  Score=204.05  Aligned_cols=257  Identities=13%  Similarity=0.162  Sum_probs=199.3

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             53799974698877568999999999962699499997879898603343899878988863184561243376532024
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      =|.|+|+| |||+||||+++||+.+||+ .|+||++|.+|+...++.++++.....++.+.+......++.-++..+...
T Consensus         4 mr~IAiYG-KGGIGKSTtssNlsAAlA~-~G~rVl~IGCDPK~DSTr~Llgg~~~~Tvld~~~~~~~~ed~~ledvv~~G   81 (293)
T PRK13234          4 LRQIAFYG-KGGIGKSTTSQNTLAALVE-MGQKILIVGCDPKADSTRLILNAKAQDTVLSLAAEAGSVEDLELEDVMKIG   81 (293)
T ss_pred             CCEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCCCHHHHHHHCCCCCCCHHHHHHHCCCCCCCCHHHHHHCC
T ss_conf             75799977-9844587789999999997-799699974898316568762899997088998764981215387897437


Q ss_pred             CCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHH-----CCCEEEECCCCC-CCHHHHHHH--HHCCCCCCCCCCCHHHHH
Q ss_conf             898068724876120320799999998999851-----288899738888-898999998--620125435787768899
Q gi|254780725|r  241 AENLSILTAPAMLSRTYDFDEKMIVPVLDILEQ-----IFPLVILDVPHV-WNSWTQEVL--TLSDKVVITTSLDLAGLR  312 (427)
Q Consensus       241 ~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~-----~yd~VIiD~p~~-~~~~~~~~L--~~AD~vviV~~p~~~slr  312 (427)
                      ..|+....++.. +.........+...++.|.+     .||||+.|+... .......-+  ..||++++|+..+..|+.
T Consensus        82 ~~gI~CVEsGGP-ePGvGCAGRGIitai~~Le~lga~ed~D~V~yDVLGDVVCGGFAmPir~g~A~evyIVtSge~msly  160 (293)
T PRK13234         82 YKGIKCVESGGP-EPGVGCAGRGVITSINFLEENGAYDDVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALY  160 (293)
T ss_pred             CCCEEEEECCCC-CCCCCCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCHHHHH
T ss_conf             798489768998-9988877713146788887718765799999956776651475566545887689999467187999


Q ss_pred             HHHHHHHHHHHC--CCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHH
Q ss_conf             999999999981--987675389995658987520059999998489537990687999999884796189888999899
Q gi|254780725|r  313 NSKNLIDVLKKL--RPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIA  390 (427)
Q Consensus       313 ~a~~ll~~l~~~--~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a  390 (427)
                      .+.|+.+.+.+.  +.+.+--.+|+|+-+.+.. +--+++|++.+|.++.+.||+|. .+.+|..+|++++|.+|.|+.+
T Consensus       161 AANnI~~~i~~~~~~g~~rlgGlI~N~r~~~~e-~~~v~~fa~~~gt~ii~~IPrs~-~v~~aE~~~~TviE~~P~s~~A  238 (293)
T PRK13234        161 AANNIAKGILKYANSGGVRLGGLICNERQTDRE-LELAEALAKRLGSKLIHFVPRDN-IVQHAELRRMTVIEYAPDSKQA  238 (293)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCH-HHHHHHHHHHHCCCEEEECCCCH-HHHHHHHCCCEEEEECCCCHHH
T ss_conf             999999999998632696246899717898537-99999999984993799779968-8999997397778968898799


Q ss_pred             HHHHHHHHHHHCCC-CCCCCCCCHHHHHHHHHH
Q ss_conf             99999999985221-223211105899998742
Q gi|254780725|r  391 NLLVDFSRVLMGRV-TVSKPQSAMYTKIKKIFN  422 (427)
Q Consensus       391 ~~~~~La~~i~gr~-~~~~~k~~~~~~l~~lf~  422 (427)
                      +.|++||+.|.... +..-|++-....|+.|+.
T Consensus       239 ~~Yr~LA~~I~~n~~~~~iP~Pl~~~eL~~l~~  271 (293)
T PRK13234        239 GEYRALAEKIHANSGKGTIPTPITMEELEDMLM  271 (293)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH
T ss_conf             999999999984788700188899899999999


No 27 
>pfam01656 CbiA CobQ/CobB/MinD/ParA nucleotide binding domain. This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from S.typhimurium, and CobQ from R. capsulatus. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family.
Probab=99.98  E-value=5.5e-31  Score=209.66  Aligned_cols=202  Identities=19%  Similarity=0.209  Sum_probs=148.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCH-HHHHHHHHH--HCC
Q ss_conf             99974698877568999999999962699499997879898603343899878988863184561-243376532--024
Q gi|254780725|r  164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRI-DKAFVSRLP--VFY  240 (427)
Q Consensus       164 Iav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rl-D~~~l~~~l--~~~  240 (427)
                      |+|+|+||||||||+|+|||++||+ .|++|+++|+|+|+++...+++..+.....+........ .........  ..+
T Consensus         1 Iav~s~KGGVGKTT~a~nLA~~la~-~G~rVlliD~D~q~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (212)
T pfam01656         1 IAIAGTKGGVGKTTLAANLARALAK-RGYRVLLIDLDPQANLTSSLGKGPDLIDVLKEGLEIVDAQPLQHIAAAIVPSRN   79 (212)
T ss_pred             CEEECCCCCHHHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCHHHHCCCCCCCCCCCCCCHHCCCCCHHHHHHEEECCCC
T ss_conf             9897689980699999999999997-899789983899996258865876434444441010112100245642224555


Q ss_pred             CCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             89806872487612032079999999899985128889973888889899999862012543578776889999999999
Q gi|254780725|r  241 AENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDV  320 (427)
Q Consensus       241 ~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~  320 (427)
                      .+++.++++...+.... .........+..++..|||||+|+|++++..+..++..+|.+++|++|+..|+++++++++.
T Consensus        80 ~~~l~l~p~~~~~~~~~-~~~~~~~~~~~~~~~~~D~viiD~pp~~~~~~~~al~~ad~vivv~~p~~~sl~~~~~l~~~  158 (212)
T pfam01656        80 LDPLLLIPSNLSLANFE-SELILEGGEEGLIKLAYDYVIIDGAPGLGELTANALVAADILVVPIEPEGVAVLGAQRLLEL  158 (212)
T ss_pred             CCCEEEECCCHHHHHHH-HHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf             58746533501566777-77799999987666049989994799755999999983998999948976999999999999


Q ss_pred             HHHCCCCCCCCEEEEECCCCCCCCHH--HHHHHHHHHCCCE---EEEECCCHHH
Q ss_conf             99819876753899956589875200--5999999848953---7990687999
Q gi|254780725|r  321 LKKLRPADKPPYLVLNQVKTPKKPEI--SISDFCAPLGITP---SAIIPFDGAV  369 (427)
Q Consensus       321 l~~~~~~~~~~~iVlNr~~~~~~~~i--~~~~~~~~lg~~~---~~~IP~D~~~  369 (427)
                      +++.+.  +..++|+||++.......  ..+.+++..+.+.   ...||+|...
T Consensus       159 ~~~l~~--~~~gvV~N~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ip~d~~v  210 (212)
T pfam01656       159 VERLGL--KILGVVLNKVDRGDERHLDKEIEALERKTGIPVLLLLGVIPRDLAL  210 (212)
T ss_pred             HHHCCC--CCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCC
T ss_conf             998599--6229999148899836630789999999789975140411687766


No 28 
>PRK13236 nitrogenase reductase; Reviewed
Probab=99.97  E-value=5.5e-30  Score=203.54  Aligned_cols=259  Identities=14%  Similarity=0.169  Sum_probs=200.4

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf             75379997469887756899999999996269949999787989860334389987898886318456124337653202
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVF  239 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~  239 (427)
                      .=|.|||+| |||+||||+++|++.+||+ .|++|++|.+|+...++.++++-....++.+.+......++..++..+..
T Consensus         5 ~mk~IAiYG-KGGIGKSTts~NlsAAlA~-~G~rVl~IGCDPK~DSTr~Llgg~~~~tvld~~~e~~~~ed~~ledvv~~   82 (295)
T PRK13236          5 NIRQIAFYG-KGGIGKSTTSQNTLAAMAE-MGQRILIVGCDPKADSTRLMLHSKAQTTVLHLAAERGAVEDLELEEVMLT   82 (295)
T ss_pred             CCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCCCHHHHHHHCCCCCCCHHHHHHHHCCCCCCCHHHHHHC
T ss_conf             761899967-9843475789999999997-79969997889802667876389999718888876098444548887422


Q ss_pred             CCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHH-----HCCCEEEECCCCC-CCHHHHHHHH--HCCCCCCCCCCCHHHH
Q ss_conf             489806872487612032079999999899985-----1288899738888-8989999986--2012543578776889
Q gi|254780725|r  240 YAENLSILTAPAMLSRTYDFDEKMIVPVLDILE-----QIFPLVILDVPHV-WNSWTQEVLT--LSDKVVITTSLDLAGL  311 (427)
Q Consensus       240 ~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~-----~~yd~VIiD~p~~-~~~~~~~~L~--~AD~vviV~~p~~~sl  311 (427)
                      .-.|+....++.. +.........+...++.|.     +.||||+.|+... .......-+.  .||++++|+..+..++
T Consensus        83 G~~Gi~CvEsGGP-ePGvGCAGRGIitai~lLee~ga~e~~D~V~yDVLGDVVCGGFAmPir~g~A~evyiVtSge~mal  161 (295)
T PRK13236         83 GFRGVRCVESGGP-EPGVGCAGRGIITAINFLEENGAYQDLDFVSYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMAM  161 (295)
T ss_pred             CCCCCEEEECCCC-CCCCCCCCCEEEEHHHHHHHCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEECCCHHHH
T ss_conf             6588379878999-998988886254056679871985569989885057753267546566787648999956818899


Q ss_pred             HHHHHHHHHHHHC--CCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHH
Q ss_conf             9999999999981--98767538999565898752005999999848953799068799999988479618988899989
Q gi|254780725|r  312 RNSKNLIDVLKKL--RPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAI  389 (427)
Q Consensus       312 r~a~~ll~~l~~~--~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~  389 (427)
                      ..+.|+.+.+++.  +.+.+--.+|+|+-+.+... --+++|++.+|.++.+.||+|. .+.+|..+|++++|..|.|+.
T Consensus       162 yAANNI~~~i~~~a~~g~~rlgGiI~N~r~~~~e~-~~v~~fa~~~gt~ii~~iPr~~-~V~~ae~~~~TviE~~P~s~~  239 (295)
T PRK13236        162 YAANNIARGILKYAHTGGVRLGGLICNSRNVDREI-ELIETLAKRLNTQMIHFVPRDN-IVQHAELRRMTVNEYAPDSNQ  239 (295)
T ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCHH-HHHHHHHHHHCCCEEEECCCCH-HHHHHHHCCCEEEEECCCCHH
T ss_conf             99999999999997426970358996078887479-9999999981992699657838-888999739876887889779


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             9999999999852212232111058999987423
Q gi|254780725|r  390 ANLLVDFSRVLMGRVTVSKPQSAMYTKIKKIFNM  423 (427)
Q Consensus       390 a~~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~r  423 (427)
                      ++.|++||+.|....+...|++-....|..|+..
T Consensus       240 A~~Yr~LA~~i~~n~~~~vP~Pl~~~eL~~l~~~  273 (295)
T PRK13236        240 GNEYRILAKKIINNDKLTIPTPIEMEELEELLIE  273 (295)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
T ss_conf             9999999999985899867898998899999998


No 29 
>COG1192 Soj ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=99.97  E-value=1.6e-29  Score=200.75  Aligned_cols=239  Identities=22%  Similarity=0.304  Sum_probs=175.1

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCC--CCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             5379997469887756899999999996269949999787989860334389987--89888631845612433765320
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPI--NSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~--~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      .++|+|.+.||||||||+|+|||.+||...|++|++||+|+| +++..+|+.++.  ....+++......  ........
T Consensus         2 ~~iI~v~n~KGGvGKTT~a~nLa~~La~~~~~kVLliDlDpQ-~s~t~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~   78 (259)
T COG1192           2 MKIIAVANQKGGVGKTTTAVNLAAALAKRGGKKVLLIDLDPQ-GSLTSWLGLRPDLEGDLYNLLSGLKER--PDILDYTV   78 (259)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC-CCHHHHHCCCCCCCCCHHHHHHCCCCC--CCHHHCCC
T ss_conf             769999857888519999999999999838997899978999-417778466643231036676323332--21022034


Q ss_pred             CCCCCEEEEECCCCCCC--HHCC----CHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHH
Q ss_conf             24898068724876120--3207----99999998999851288899738888898999998620125435787768899
Q gi|254780725|r  239 FYAENLSILTAPAMLSR--TYDF----DEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLR  312 (427)
Q Consensus       239 ~~~~gL~lL~a~~~~~~--~~~~----~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr  312 (427)
                       ..++++++|+..++..  ....    ....+..+++.....|||||+|+|+..+..+.+++.+||.++++++++..++.
T Consensus        79 -~~~~l~~ip~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~yD~iiID~pp~l~~l~~nal~asd~vliP~~~~~~~~~  157 (259)
T COG1192          79 -VIEGLDLIPSNIDLAEGAEIELNAVAKELLLKRLLDPVKDDYDYIIIDTPPSLGVLTLNALAAADHVLIPVQPEFLDLE  157 (259)
T ss_pred             -CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHHCCEEECCCCCHHHHH
T ss_conf             -4567312357600010045665421178999999752026999899899986167779999982755670475086898


Q ss_pred             HHHHHHHHHHHC---CCCC-CCCEEEEECCCCCCC-CHHHHHHHHHHHCCC-EEEEECCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             999999999981---9876-753899956589875-200599999984895-3799068799999988479618988899
Q gi|254780725|r  313 NSKNLIDVLKKL---RPAD-KPPYLVLNQVKTPKK-PEISISDFCAPLGIT-PSAIIPFDGAVFGMSANSGKMIHEVDPK  386 (427)
Q Consensus       313 ~a~~ll~~l~~~---~~~~-~~~~iVlNr~~~~~~-~~i~~~~~~~~lg~~-~~~~IP~D~~~~~~A~~~G~pi~e~~p~  386 (427)
                      ....+++.+...   ..+. ....++.|++..... .....+...+.++.+ ....||... .+.++...|+|+.+..++
T Consensus       158 ~l~~~~~~i~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~-~~~~a~~~g~~~~~~~~~  236 (259)
T COG1192         158 GLEQLLNTLEDLLKLRRNKLIVVGILITRFDSRTKLADEVLQELKQLLGDPVLKTKIPRRV-AYREAAAEGKPLYEYDPK  236 (259)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCH-HHHHHHHCCCCEEEECCC
T ss_conf             8999999999999852453232567435347420157899999997514311114476532-688788749801550787


Q ss_pred             CHHHHHHHHHHHHHHCCC
Q ss_conf             989999999999985221
Q gi|254780725|r  387 SAIANLLVDFSRVLMGRV  404 (427)
Q Consensus       387 s~~a~~~~~La~~i~gr~  404 (427)
                      ++.++.+.++++.+..+.
T Consensus       237 ~~~~~~~~~~~~e~~~~~  254 (259)
T COG1192         237 SKAAEEYYELAKELLEEL  254 (259)
T ss_pred             CHHHHHHHHHHHHHHHHH
T ss_conf             557999999999999975


No 30 
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=99.97  E-value=3.6e-29  Score=198.54  Aligned_cols=222  Identities=14%  Similarity=0.133  Sum_probs=160.8

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCCCCCCHHHCCCCCCCC------HHHHHCCCCCHH
Q ss_conf             456753799974698877568999999999962699499997-8798986033438998789------888631845612
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLAD-LDLPYGTANINFDKDPINS------ISDAIYPVGRID  229 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvD-lDl~~g~~~~~l~~~~~~~------l~d~l~~~~rlD  229 (427)
                      .+....||+|.+.||||||||+|+|||.+||. .|+|||+|| +|+| +++..++|..|...      +...... ++.+
T Consensus       102 ~g~~~~VIAVaNqKGGvGKTTTavnLA~~LAl-~G~RVLlID~LDPQ-anlT~~~G~~pd~~~~~~~tl~~~~~~-~~~~  178 (388)
T PRK13705        102 EDEFPPVIGVAAHKGGVYKTSVSVHLAQDLAL-KGLRVLLVEGNDPQ-GTASMYHGWVPDLHIHAEDTLLPFYLG-EKDD  178 (388)
T ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCC-CCCCCCCCCCCCCCCCCCCHHHHHHHC-CCCC
T ss_conf             99987289995278885599999999999997-79908999587888-656435688887665644302477614-6665


Q ss_pred             HHHHHHHHH-CCCCCEEEEECCCCCCCHHC-C------------CHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHH
Q ss_conf             433765320-24898068724876120320-7------------999999989998512888997388888989999986
Q gi|254780725|r  230 KAFVSRLPV-FYAENLSILTAPAMLSRTYD-F------------DEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLT  295 (427)
Q Consensus       230 ~~~l~~~l~-~~~~gL~lL~a~~~~~~~~~-~------------~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~  295 (427)
                         +...+. .+.+||+++|+...+...+. +            ....++..++.+...||||||||||..+..+.++|.
T Consensus       179 ---~~~~I~~T~~~gLDlIPs~l~L~~~E~el~~~~~~~~~~~~~~~~Lr~aL~~v~d~YD~IlIDcPPsLG~LTiNAL~  255 (388)
T PRK13705        179 ---AAYAIKPTCWPGLDIIPSCLALHRIETELMGKFDEGKLPTDPHLMLRLAIETVAHDYDVIVIDSAPNLGIGTINVVC  255 (388)
T ss_pred             ---HHHEEECCCCCCEEEECCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHH
T ss_conf             ---54504347889979970898999999999775531232225899999999862503999999589717799999999


Q ss_pred             HCCCCCCCCCCCHHHHHHHHHHHHHHHH-------CCCCCCCCEEEEECCCCCCCCHHH--HHHHHHHHCCCEEEEECCC
Q ss_conf             2012543578776889999999999998-------198767538999565898752005--9999998489537990687
Q gi|254780725|r  296 LSDKVVITTSLDLAGLRNSKNLIDVLKK-------LRPADKPPYLVLNQVKTPKKPEIS--ISDFCAPLGITPSAIIPFD  366 (427)
Q Consensus       296 ~AD~vviV~~p~~~slr~a~~ll~~l~~-------~~~~~~~~~iVlNr~~~~~~~~i~--~~~~~~~lg~~~~~~IP~D  366 (427)
                      +||.++|++.|+.-.+-.+.+++..+..       .+.. ..++++++|+++...++-.  ..-+.+.+|-.+...--..
T Consensus       256 AAd~vlIPv~p~~lD~~S~~qFl~m~~~l~~~~~~~g~~-~~~r~L~Tr~e~~d~~q~~~m~~~lr~~fg~~vl~~~i~~  334 (388)
T PRK13705        256 AADVLIVPTPAELFDYTSALQFFDMLRDLLKNVDLKGFE-PDVRILLTKYSNANGSQSPWMEEQIRDAWGSMVLKNVVRE  334 (388)
T ss_pred             HHCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHH
T ss_conf             808548678940776999999999999999998751777-6348998725899987899999999999767776362257


Q ss_pred             HHHHHHHHHCCCCEEEECC
Q ss_conf             9999998847961898889
Q gi|254780725|r  367 GAVFGMSANSGKMIHEVDP  385 (427)
Q Consensus       367 ~~~~~~A~~~G~pi~e~~p  385 (427)
                      ...+++|....++|.|...
T Consensus       335 S~aI~~A~~~~~TlyE~~~  353 (388)
T PRK13705        335 TDEVGKGQIRMRTVFEQAI  353 (388)
T ss_pred             HHHHHHHHHHCCCCEECCC
T ss_conf             8999872652073010244


No 31 
>PHA02519 plasmid partition protein SopA; Reviewed
Probab=99.97  E-value=1.4e-28  Score=194.96  Aligned_cols=223  Identities=15%  Similarity=0.100  Sum_probs=160.8

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCCCCCCHHHCCCCCCC------CHHHHHCCCCCHH
Q ss_conf             456753799974698877568999999999962699499997-879898603343899878------9888631845612
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLAD-LDLPYGTANINFDKDPIN------SISDAIYPVGRID  229 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvD-lDl~~g~~~~~l~~~~~~------~l~d~l~~~~rlD  229 (427)
                      .+....||+|.+.||||||||+|+|||.+||. .|+|||+|| +|+| +++..++|..|..      ++...... ++. 
T Consensus       102 ~~~~~~VIAVaN~KGGVGKTTTavnLA~~LAl-~G~RVL~ID~lDPQ-aslS~~~G~~pd~~~~~~~t~~~~~~~-~~~-  177 (387)
T PHA02519        102 DDKNPVVLAVMSHKGGVYKTSSAVHTAQWLAL-QGHRVLLIEGNDPQ-GTASMYHGYVPDLHIHADDTLLPFYLG-ERD-  177 (387)
T ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCC-CCCCCCCCCCCCCCCCCCCHHHHHHHC-CCC-
T ss_conf             98875289986168877699999999999997-69968999598852-004314588887664655413577615-755-


Q ss_pred             HHHHHHHH-HCCCCCEEEEECCCCCCCHHCC-------------CHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHH
Q ss_conf             43376532-0248980687248761203207-------------999999989998512888997388888989999986
Q gi|254780725|r  230 KAFVSRLP-VFYAENLSILTAPAMLSRTYDF-------------DEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLT  295 (427)
Q Consensus       230 ~~~l~~~l-~~~~~gL~lL~a~~~~~~~~~~-------------~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~  295 (427)
                        .++..+ ..+.+||+++|+...+...+.-             ....+...++.+...||||||||||..+..+.++|.
T Consensus       178 --~~~~~I~~T~~~gLDlIPa~l~L~~~E~el~~~~~~~~~~~~~~~~L~~aL~~v~d~YDvVlIDcPPsLG~LTlNAL~  255 (387)
T PHA02519        178 --NAEYAIKPTCWPGLDIIPSCLALHRIETDLMQYHDAGKLPHPPHLMLRAAIESVWDNYDIIVIDSAPNLGTGTINVVC  255 (387)
T ss_pred             --CHHHHEECCCCCCEEEECCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHH
T ss_conf             --577603368989967974888999999999878743142234899999998752346998999799736899999999


Q ss_pred             HCCCCCCCCCCCHHHHHHHHHHHHHHHH------CCCCCCCCEEEEECCCCCCCCHH--HHHHHHHHHCCCEEEEECCCH
Q ss_conf             2012543578776889999999999998------19876753899956589875200--599999984895379906879
Q gi|254780725|r  296 LSDKVVITTSLDLAGLRNSKNLIDVLKK------LRPADKPPYLVLNQVKTPKKPEI--SISDFCAPLGITPSAIIPFDG  367 (427)
Q Consensus       296 ~AD~vviV~~p~~~slr~a~~ll~~l~~------~~~~~~~~~iVlNr~~~~~~~~i--~~~~~~~~lg~~~~~~IP~D~  367 (427)
                      +||.++|++.|++..+-.+.+++..+..      ......-++++++|+++...+.-  -...+.+.+|-.+....-...
T Consensus       256 AAd~vlIPv~p~~ld~~S~~qFl~m~~~l~~~v~~~g~~~~~r~LiTr~ep~d~~q~~~m~~~lR~~fg~~vl~~~i~~S  335 (387)
T PHA02519        256 AADVIVVATPAELFDYVSVLQFFTMLLDLLATVDLGGFEPVVRLLLTKYSLTVGNQSRWMEEQIRNTWGSMVLRQVVRVT  335 (387)
T ss_pred             HCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHH
T ss_conf             82965868896387799999999999999999862378750468775358999888999999999998788864623587


Q ss_pred             HHHHHHHHCCCCEEEECC
Q ss_conf             999998847961898889
Q gi|254780725|r  368 AVFGMSANSGKMIHEVDP  385 (427)
Q Consensus       368 ~~~~~A~~~G~pi~e~~p  385 (427)
                      ..+++|....++|.|...
T Consensus       336 ~aI~~A~~~~qTlYE~~~  353 (387)
T PHA02519        336 DEVGKGQIKMRTVFEQAA  353 (387)
T ss_pred             HHHHHHHHHCCCCEECCC
T ss_conf             999973651274121354


No 32 
>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the  protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase. Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.
Probab=99.97  E-value=1.8e-29  Score=200.43  Aligned_cols=202  Identities=16%  Similarity=0.166  Sum_probs=148.4

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      |.|||+| ||||||||+++|||.+||+ .|+||+++|+|++..++...++.....++.+.+......+...++..+....
T Consensus         1 ~~iaiyG-KGGVGKTTts~NLaaaLA~-~G~rVl~iD~Dp~~~st~~L~g~~~~~~i~~~~~~~~~~~~~~~~~ii~~g~   78 (212)
T cd02117           1 RQIAIYG-KGGIGKSTTSQNLSAALAE-MGKKVLQVGCDPKADSTRLLLGGKAPTTILELAAEDGHVEDLELEDVIFEGF   78 (212)
T ss_pred             CEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCCCCHHHCCCCCCCCHHHHHHHHCCCCCEEEEEEEEECC
T ss_conf             9599988-9835687789999999998-6996999903899873303119977871999987527866445667899668


Q ss_pred             CCEEEEECCCCCCCHH-----CCCHHHHHHHHHHHHHCCCEEEECCCCCCCH--HHH-HHHHHCCCCCCCCCCCHHHHHH
Q ss_conf             9806872487612032-----0799999998999851288899738888898--999-9986201254357877688999
Q gi|254780725|r  242 ENLSILTAPAMLSRTY-----DFDEKMIVPVLDILEQIFPLVILDVPHVWNS--WTQ-EVLTLSDKVVITTSLDLAGLRN  313 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~-----~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~--~~~-~~L~~AD~vviV~~p~~~slr~  313 (427)
                      .|+.++++........     ......+..-+..+...||||++|+......  .+. -....||++++|++|+..|+.+
T Consensus        79 ~gv~~veaggp~~g~~~ag~~i~~~~~ll~~~~~~~~~~D~IliD~lGdvv~~gf~~pi~~~~Ad~vlIvtt~E~~Al~~  158 (212)
T cd02117          79 GGVKCVESGGPEPGVGCAGRGVITAVNLLEKEGFAEDDLDVVLYDVLGDVVCGGFAMPIREGKADEIYIVTSGEFMALYA  158 (212)
T ss_pred             CCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEECCCCCCCCCCCCCEEEEECCCCHHHHHH
T ss_conf             87089988997767654541178899999974100257999999658854035633432116688899980693578898


Q ss_pred             HHHHHHHHHHC--CCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCC
Q ss_conf             99999999981--987675389995658987520059999998489537990687
Q gi|254780725|r  314 SKNLIDVLKKL--RPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFD  366 (427)
Q Consensus       314 a~~ll~~l~~~--~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D  366 (427)
                      +.++++.++..  +.+.+-..+|.||.+.... +...++|++.+|.++.+.||+|
T Consensus       159 a~~l~k~I~~~~~~~n~~l~GiI~N~~~~~~~-~~~i~~f~~~~g~~vl~~IP~d  212 (212)
T cd02117         159 ANNICKGIRKYAKSGGVRLGGLICNSRNTDRE-TELIDAFAERLGTQVIHFVPRD  212 (212)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEEEECCCCCCH-HHHHHHHHHHHCCEEEEECCCC
T ss_conf             89999999999736798148999846788864-9999999998399189974899


No 33 
>TIGR01287 nifH nitrogenase iron protein; InterPro: IPR005977    The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene , . Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes . It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .; GO: 0016163 nitrogenase activity, 0009399 nitrogen fixation, 0016612 molybdenum-iron nitrogenase complex.
Probab=99.97  E-value=1.4e-28  Score=194.87  Aligned_cols=258  Identities=16%  Similarity=0.209  Sum_probs=208.3

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             379997469887756899999999996269-9499997879898603343899878988863184561243376532024
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFA-METLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~-~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      |-|||+| |||.||||+..|++.+||.. + ++|+++-+||-.-++.++++-.+..|+.|.++..+.++..-++..+...
T Consensus         1 rqiAiYG-KGGIGKSTT~~N~~AAla~~-gdkkVl~~GCDPKaDsTr~l~Gg~~~~TVLd~lre~G~ve~~~~e~v~~~G   78 (278)
T TIGR01287         1 RQIAIYG-KGGIGKSTTTQNIAAALAEM-GDKKVLVVGCDPKADSTRLLLGGKAQPTVLDVLREKGAVEDVELEDVIKEG   78 (278)
T ss_pred             CEEEEEC-CCCCCCCHHHHHHHHHHHHH-CCCEEEEEECCCCCCHHHHHHCCCCCCHHHHHHHHCCCCCCCCCCHHHEEC
T ss_conf             9488862-78867006888999999862-495589972388520234651774455489999856871144510220016


Q ss_pred             CCCEEEEECC-CCC----CCHHCCCHHHHHHHHHHHHH-CCCEEEEC-CCCCCCHHHHHHHH--HCCCCCCCCCCCHHHH
Q ss_conf             8980687248-761----20320799999998999851-28889973-88888989999986--2012543578776889
Q gi|254780725|r  241 AENLSILTAP-AML----SRTYDFDEKMIVPVLDILEQ-IFPLVILD-VPHVWNSWTQEVLT--LSDKVVITTSLDLAGL  311 (427)
Q Consensus       241 ~~gL~lL~a~-~~~----~~~~~~~~~~l~~ll~~l~~-~yd~VIiD-~p~~~~~~~~~~L~--~AD~vviV~~p~~~sl  311 (427)
                      -.+++..-++ +.|    .-.--+..=.+..-....++ .-|||+.| ++.........-+.  .|++|++|++.|+.++
T Consensus        79 f~girCVESGGPePGVGCAGRGvItai~lL~~~g~y~dLdlD~V~YDVLGDVVCGGFAmP~R~g~A~eiYiVtSge~MAl  158 (278)
T TIGR01287        79 FGGIRCVESGGPEPGVGCAGRGVITAIDLLEELGAYEDLDLDVVIYDVLGDVVCGGFAMPLREGLAQEIYIVTSGEMMAL  158 (278)
T ss_pred             CCCEEEEEECCCCCCCCCCCCHHEEEEHHHHHCCCCCCCCCCEEEEEECCCEEECCCCCHHHCCCCCEEEEECCCHHHHH
T ss_conf             88318885076878952068711201337753378731167768984236556566036100588654888603406789


Q ss_pred             HHHHHHHHHHHHCC--CCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHH
Q ss_conf             99999999999819--8767538999565898752005999999848953799068799999988479618988899989
Q gi|254780725|r  312 RNSKNLIDVLKKLR--PADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAI  389 (427)
Q Consensus       312 r~a~~ll~~l~~~~--~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~  389 (427)
                      ..|+|+.+=+.+..  ...+.=.+|.|.-......|+ .++|++.+|..+.+.+|.|. .+.+|+-+++++.|++|.|..
T Consensus       159 YAANNI~kGI~kYa~~GGv~LGG~IcN~R~~~~e~El-~~~fA~~lgtq~i~~VPrs~-~V~~AEl~~~TVIE~dP~s~q  236 (278)
T TIGR01287       159 YAANNIAKGILKYAKSGGVRLGGIICNSRNVDDEKEL-VDEFAKKLGTQLIHFVPRSN-IVQKAELEKKTVIEYDPESEQ  236 (278)
T ss_pred             HHHHHHHHHHHHHHHCCCCEECCEEECCCCCCCHHHH-HHHHHHHHCCEEEEECCCCC-CCHHHHHCCCCEEEECCCCHH
T ss_conf             9997887778999753882222478714576217899-99999873770675217885-212787368845633887157


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             9999999999852212232111058999987423
Q gi|254780725|r  390 ANLLVDFSRVLMGRVTVSKPQSAMYTKIKKIFNM  423 (427)
Q Consensus       390 a~~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~r  423 (427)
                      |+.|++||+.|.......-|++-....|..++.+
T Consensus       237 A~~YR~LA~~I~~N~~~~iP~Pl~~~eL~~~~~~  270 (278)
T TIGR01287       237 ANEYRELAKKIYENEEFVIPTPLEMEELEELLMK  270 (278)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
T ss_conf             8999999999982578527998987899999987


No 34 
>cd03111 CpaE_like This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains 7 genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF. These genes are clustered together on chromosome.
Probab=99.96  E-value=5.1e-29  Score=197.58  Aligned_cols=105  Identities=36%  Similarity=0.584  Sum_probs=101.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886318456124337653202489
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAE  242 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~  242 (427)
                      ||+|+|+|||+|+||+|+|+||+||++.+++|+|+|+|+|||+                                     
T Consensus         1 vi~~~~~kGGvG~Tt~A~nlA~~la~~~~~~v~lvDldlqfGd-------------------------------------   43 (106)
T cd03111           1 VIAFIGAKGGVGATTLAANLAVALAKEAGRRVLLVDLDLQFGD-------------------------------------   43 (106)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC-------------------------------------
T ss_conf             9899728998668999999999999841993899965467799-------------------------------------


Q ss_pred             CEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             80687248761203207999999989998512888997388888989999986201254357877688999999999999
Q gi|254780725|r  243 NLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLK  322 (427)
Q Consensus       243 gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~  322 (427)
                                                       ||||+|+|+.|++|+..+++.||.+++|++|+++++|+++|+++.++
T Consensus        44 ---------------------------------d~VVvD~~~~~~~~~~~al~~ad~i~lv~~~~lp~lrn~kr~l~~l~   90 (106)
T cd03111          44 ---------------------------------DYVVVDLGRSLDEVSLAALDQADRVFLVTQQDLPSIRNAKRLLELLR   90 (106)
T ss_pred             ---------------------------------CEEEECCCCCCCHHHHHHHHHCCEEEEEECCCHHHHHHHHHHHHHHH
T ss_conf             ---------------------------------78999186553889999998679799980677489997999999999


Q ss_pred             HCCCC-CCCCEEEEEC
Q ss_conf             81987-6753899956
Q gi|254780725|r  323 KLRPA-DKPPYLVLNQ  337 (427)
Q Consensus       323 ~~~~~-~~~~~iVlNr  337 (427)
                      .++++ +.++++|+||
T Consensus        91 ~l~~~~~~ki~lVvNR  106 (106)
T cd03111          91 VLDYSLPAKIELVLNR  106 (106)
T ss_pred             HCCCCCCCCEEEEECC
T ss_conf             8499973656998579


No 35 
>cd03110 Fer4_NifH_child This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.
Probab=99.96  E-value=9.6e-28  Score=189.76  Aligned_cols=177  Identities=19%  Similarity=0.227  Sum_probs=129.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCC-CCCHHHHHHHHHHHCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886318-45612433765320248
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYP-VGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~-~~rlD~~~l~~~l~~~~  241 (427)
                      .|+|+|+||||||||+|+|||..+     ++|+++|+|++.++.+.+|+.++.......... ...++....      +.
T Consensus         1 kIaV~SgKGGVGKTT~a~nLA~~l-----~~V~liD~D~~~~n~~~~l~~~~~~~~~~~~~~~~~~~~~~~~------~~   69 (179)
T cd03110           1 QIAVISGKGGTGKTTVTAALAALL-----KNVVLADCDVDAPNLHLFLKPEIEEEEDFIVGGKKAVIDPELC------IS   69 (179)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHC-----CCCEEEEECCCCCCHHHHCCCCCCCCEEEEECCCCCEECHHHH------HH
T ss_conf             989995899860999999999974-----2871999418998577771876563212230465335150665------32


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHH-HHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             98068724876120320799999998-99985128889973888889899999862012543578776889999999999
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPV-LDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDV  320 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~l-l~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~  320 (427)
                      .++.           ..+.......+ .......|||||+|+|++.+..+..++..+|.+++|++|+..++++++++++.
T Consensus        70 ~g~~-----------~~~~~~~~~~~~~~~~~~~~D~viiD~Ppg~~~~~~~al~~ad~~iiVttP~~~si~d~~r~i~l  138 (179)
T cd03110          70 CGLC-----------GKLVTEVRKHAKEIAKAEGAELIIIDGPPGIGCPVIASLTGADAALLVTEPTPSGLHDLERAVEL  138 (179)
T ss_pred             CCCH-----------HHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHH
T ss_conf             3517-----------68899999999998644379989981899975789999973994999819947899999999999


Q ss_pred             HHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEEC
Q ss_conf             99819876753899956589875200599999984895379906
Q gi|254780725|r  321 LKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIP  364 (427)
Q Consensus       321 l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP  364 (427)
                      +++.+.   ++.+|+||++......-..+++.+.++.++.+.||
T Consensus       139 ~~~~~~---~~gvV~Nr~~~~~~~~~~i~~~~~~~~vp~LG~iP  179 (179)
T cd03110         139 VRHFGI---PVGVVINKYDLNDEIAEEIEDYCEEEGIPILGKIP  179 (179)
T ss_pred             HHHCCC---CEEEEEECCCCCCCCHHHHHHHHHHHCCCEEEECC
T ss_conf             998299---78999968878876348999999980999898387


No 36 
>KOG3022 consensus
Probab=99.95  E-value=2.9e-26  Score=180.67  Aligned_cols=232  Identities=20%  Similarity=0.189  Sum_probs=176.2

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHH
Q ss_conf             45675379997469887756899999999996269949999787989860334389987898886318456124337653
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRL  236 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~  236 (427)
                      ....-++|+|.+.||||||||+++|||++||+ .+.+|.++|.|+...++..++|.+.+. +.   .....+-++     
T Consensus        43 l~~vk~iI~VlSGKGGVGKSTvt~nla~~La~-~g~~vglLD~Dl~GPSiP~m~g~e~~~-~~---~~~~g~~Pv-----  112 (300)
T KOG3022          43 LSGVKHIILVLSGKGGVGKSTVTVNLALALAS-EGKKVGLLDADLCGPSIPRMMGLEGEV-VH---QSDNGWIPV-----  112 (300)
T ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHC-CCCCEEEEEECCCCCCCHHHCCCCCCE-EE---ECCCCCEEE-----
T ss_conf             13454589998678877616899999999861-797179975035587705340877744-55---048874144-----


Q ss_pred             HHCCCCCEEEEECCCCCC---CHHCC----CHHHHHHHHHHH-HHCCCEEEECCCCCCCHHHHHHHHHCCC---CCCCCC
Q ss_conf             202489806872487612---03207----999999989998-5128889973888889899999862012---543578
Q gi|254780725|r  237 PVFYAENLSILTAPAMLS---RTYDF----DEKMIVPVLDIL-EQIFPLVILDVPHVWNSWTQEVLTLSDK---VVITTS  305 (427)
Q Consensus       237 l~~~~~gL~lL~a~~~~~---~~~~~----~~~~l~~ll~~l-~~~yd~VIiD~p~~~~~~~~~~L~~AD~---vviV~~  305 (427)
                        ....++.+++..--+.   ....+    ...++.+++... ....||+|||+||+.++....+...+-.   .++|++
T Consensus       113 --~~~~~l~~mS~gfLl~~~~~~vIwRGpkk~~~I~qflk~vdwg~lDyLviDtPPGtsDehls~~~~~~~~~gAviVTT  190 (300)
T KOG3022         113 --VVNKNLKLMSMGFLLKPRDDSVIWRGPKKNSMIKQFLKDVDWGELDYLVIDTPPGTSDEHLSLVQFLRESDGAVIVTT  190 (300)
T ss_pred             --EECCCEEEEEEEEECCCCCCCCEEECHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHEEECCCCCCCEEEEEC
T ss_conf             --443876788756432888766265454788999999716887776779995899987014310000445573499817


Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCC--CCCCH-------HHHHHHHHHHCCCEEEEECCCHHHHHHHHHC
Q ss_conf             77688999999999999819876753899956589--87520-------0599999984895379906879999998847
Q gi|254780725|r  306 LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKT--PKKPE-------ISISDFCAPLGITPSAIIPFDGAVFGMSANS  376 (427)
Q Consensus       306 p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~--~~~~~-------i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~  376 (427)
                      |.-.++.++++-++++++.+.  +-+.+|-||..-  ++-.+       -..+++++.+|.+....||-|+.. .++.+.
T Consensus       191 PQ~vAl~Dv~K~i~fc~K~~I--~ilGvVENMs~f~Cp~C~~~~~iF~~gGg~~l~~~~glp~Lg~iPld~~i-~~~~d~  267 (300)
T KOG3022         191 PQEVALQDVRKEIDFCRKAGI--PILGVVENMSGFVCPKCGHSTNIFGSGGGERLAEELGLPLLGSLPLDPLI-AESSDS  267 (300)
T ss_pred             CHHHHHHHHHHHHHHHHHCCC--CEEEEEECCCCCCCCCCCCCCEECCCCCHHHHHHHCCCCEEEECCCCHHH-HHHCCC
T ss_conf             205566888865026664598--56888962555307887875533367628999987299757506788799-975348


Q ss_pred             CCCEEEECCCCHHHHHHHHHHHHHHCC
Q ss_conf             961898889998999999999998522
Q gi|254780725|r  377 GKMIHEVDPKSAIANLLVDFSRVLMGR  403 (427)
Q Consensus       377 G~pi~e~~p~s~~a~~~~~La~~i~gr  403 (427)
                      |+|+++..|.|+++++|.++++.|...
T Consensus       268 G~~~v~~~p~s~~~~af~~i~~~i~~~  294 (300)
T KOG3022         268 GVPFVEEYPDSPASEAFEDIAEKLVEQ  294 (300)
T ss_pred             CCEEEECCCCCHHHHHHHHHHHHHHHH
T ss_conf             983476079956999999999999986


No 37 
>COG1348 NifH Nitrogenase subunit NifH (ATPase) [Inorganic ion transport and metabolism]
Probab=99.95  E-value=4.1e-26  Score=179.72  Aligned_cols=259  Identities=15%  Similarity=0.216  Sum_probs=197.5

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      |.|||+| |||.||||++.|++.+||. .|++|++|-+|+...++-+++|-...+++.|.++........-++..+.+.-
T Consensus         2 r~iAiYG-KGGIGKSTts~N~aAAla~-~GkkVl~vGCDPKaDSTr~Llgg~~ipTVld~lre~~~~e~~~ledvi~~Gf   79 (278)
T COG1348           2 RQIAIYG-KGGIGKSTTSQNLAAALAE-LGKKVLIVGCDPKADSTRLLLGGKAIPTVLDTLREKGEVEDLELEDVIFTGF   79 (278)
T ss_pred             CEEEEEC-CCCCCCCHHHHHHHHHHHH-CCCEEEEECCCCCCCHHHHHHCCCCCCHHHHHHHHCCCCCCCCHHHHEECCC
T ss_conf             3799962-7876731267789999997-2981799747987632777747866656999998618644588778212067


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHH------HHHCCCEEEECCCCC-CCHHHHHHHH--HCCCCCCCCCCCHHHHH
Q ss_conf             98068724876120320799999998999------851288899738888-8989999986--20125435787768899
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDI------LEQIFPLVILDVPHV-WNSWTQEVLT--LSDKVVITTSLDLAGLR  312 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~------l~~~yd~VIiD~p~~-~~~~~~~~L~--~AD~vviV~~p~~~slr  312 (427)
                      .|+.+.-++..... -......+..-++.      .....|+|+.|+... .......-+.  .||.+++|++.++.++.
T Consensus        80 ~gv~CVEsGGPepG-vGCAGRGVitai~~Le~lgaf~~~~DvviyDVLGDVVCGGFAmPiReg~AdeiyIVtSge~MalY  158 (278)
T COG1348          80 GGVKCVESGGPEPG-VGCAGRGVITAINLLEELGAFEEDLDVVIYDVLGDVVCGGFAMPIREGYADEIYIVTSGEMMALY  158 (278)
T ss_pred             CCEEEEECCCCCCC-CCCCCCHHHHHHHHHHHHCCCCCCCCEEEEECCCCEEECCEEEEHHCCCCCEEEEEECCCHHHHH
T ss_conf             85377425998999-88465119999999998187301287899953577347460002002666379999568358999


Q ss_pred             HHHHHHHHHHHCC--CCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHH
Q ss_conf             9999999999819--87675389995658987520059999998489537990687999999884796189888999899
Q gi|254780725|r  313 NSKNLIDVLKKLR--PADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIA  390 (427)
Q Consensus       313 ~a~~ll~~l~~~~--~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a  390 (427)
                      .+.|+.+-+++..  .+.+.-.++.|+-+..... --.+.|++.+|.++.+.||+|. .+.+|..+|+++.|.+|.|..+
T Consensus       159 AANNI~kgi~k~a~~~~~rLgGiIcNsR~~~~e~-e~v~~fa~~igt~li~~vPr~~-ivq~aE~~~kTvie~~P~s~~a  236 (278)
T COG1348         159 AANNIAKGIRKYAKTGGVRLGGIICNSRSVDRER-ELVEAFAERLGTQLIHFVPRDN-IVQKAELNGKTVIEYAPDSNQA  236 (278)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCHH-HHHHHHHHHHCCCEEEECCCHH-HHHHHHHCCCCHHHHCCCHHHH
T ss_conf             9889999999987337963145774577764379-9999999984885276335127-8899987486611318462489


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             99999999985221223211105899998742340
Q gi|254780725|r  391 NLLVDFSRVLMGRVTVSKPQSAMYTKIKKIFNMKC  425 (427)
Q Consensus       391 ~~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~rk~  425 (427)
                      +.|++||+.|.......-|+.-....|..++.+.+
T Consensus       237 ~~yr~LA~~I~~n~~~vip~pl~~eele~~~~~~~  271 (278)
T COG1348         237 EEYRELAKKILENEKGVVPTPLSDEELEELLLEFG  271 (278)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHC
T ss_conf             99999999998377875678878789999999835


No 38 
>pfam09140 MipZ ATPase MipZ. MipZ is an ATPase that forms a complex with the chromosome partitioning protein ParB near the chromosomal origin of replication. It is responsible for the temporal and spatial regulation of FtsZ ring formation.
Probab=99.94  E-value=1e-25  Score=177.32  Aligned_cols=209  Identities=14%  Similarity=0.173  Sum_probs=129.1

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      +||+|.+.||||||||+|+|||.+||+ .|++|++||+|+|++++..+++-....  .+    ...++        ...+
T Consensus         1 hIIaVaNqKGGvGKTTtavnLA~aLA~-~G~rVllIDlDpqq~slt~~l~nr~~~--~~----~~~~~--------l~~P   65 (261)
T pfam09140         1 HVIVVGNEKGGSGKSTTAVHVAVALLY-LGARVATIDLDLRQRTLTRYIENRAAT--AE----RTGLD--------LPVP   65 (261)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCHHHHHHHHHHH--HH----HCCCC--------CCCC
T ss_conf             979997178987299999999999998-899789997999998512344303556--55----13865--------3466


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH----
Q ss_conf             9806872487612032079999999899985128889973888889899999862012543578776889999999----
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNL----  317 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~l----  317 (427)
                      ....+..........+......+...+..+...|||||||||++.+..+.+++.+||.+++|.+++...+....++    
T Consensus        66 ~~~~l~~~~~~~~~~~~~~~~~L~~al~~l~~~yDfIlIDcPPsl~~Lt~nAl~aAD~vIiPlq~sf~dld~L~~vd~~~  145 (261)
T pfam09140        66 KHLCLPDDVSEVFDGESADDARLEEAVADLEQDADFIVIDTPGSDSPLSRLAHSRADTLVTPLNDSFVDFDLLGQVDPET  145 (261)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHCEEEECCCHHHHHHHHHHHCCHHH
T ss_conf             53445506777613455789999999999875799999969985739999999983987632440155143352137034


Q ss_pred             ---------HHHH---HHCCC--CCC--CCEEEEECCCCCC-CCHHH----HHHHHHHHCCCEEEEECCCHHHHHHHHHC
Q ss_conf             ---------9999---98198--767--5389995658987-52005----99999984895379906879999998847
Q gi|254780725|r  318 ---------IDVL---KKLRP--ADK--PPYLVLNQVKTPK-KPEIS----ISDFCAPLGITPSAIIPFDGAVFGMSANS  376 (427)
Q Consensus       318 ---------l~~l---~~~~~--~~~--~~~iVlNr~~~~~-~~~i~----~~~~~~~lg~~~~~~IP~D~~~~~~A~~~  376 (427)
                               .+.+   ++.+.  +..  ...++-||...-. +....    .++..+.+|..+..-+ .+...|.+-.-.
T Consensus       146 ~~i~~~s~y~e~vw~~r~~ra~~~~~~idwivlrnRl~~~~~rnk~~~~~~l~~Ls~rigfr~~~g~-~eRviyRelfp~  224 (261)
T pfam09140       146 FKVTRPSFYAEMVWEARKKRAQADRAPIDWIVLRNRLSTLEARNKRRVEDALNELSKRVGFRVAPGF-SERVIYRELFPR  224 (261)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC-CHHHHHHHHCCC
T ss_conf             3213621789999999998743689886479980562188878889999999999764075225774-313578776246


Q ss_pred             CCCEEEECCC
Q ss_conf             9618988899
Q gi|254780725|r  377 GKMIHEVDPK  386 (427)
Q Consensus       377 G~pi~e~~p~  386 (427)
                      |..+.+..+.
T Consensus       225 gltl~dl~~~  234 (261)
T pfam09140       225 GLTLLDLKDL  234 (261)
T ss_pred             CCCHHCCCCC
T ss_conf             7714118512


No 39 
>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional
Probab=99.94  E-value=4.6e-25  Score=173.26  Aligned_cols=192  Identities=15%  Similarity=0.162  Sum_probs=156.5

Q ss_pred             HHHHHHHCCCCCC-CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHH
Q ss_conf             9997631023322-234567537999746988775689999999999626994999978798986033438998789888
Q gi|254780725|r  142 IINSISAIFTPQE-EGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISD  220 (427)
Q Consensus       142 l~~ai~~~~~~~~-~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d  220 (427)
                      +.++++.+.+.-. ......+|+|.|+|+-.|.||||+|.|||..+|. .|++|+|||+|+..+.++.+|+.....|+.+
T Consensus       511 ~~Ea~R~lrt~l~~~~~~~~~kvi~vTS~~pgEGKSt~a~nLA~~~A~-~G~rvLLID~DlRrp~l~~~~~~~~~~GLs~  589 (726)
T PRK09841        511 AVEAVRALRTSLHFAMMETENNILMITGATPDSGKTFVSSTLAAVIAQ-SDQKVLFIDADLRRGYSHNLFTVSNEHGLSE  589 (726)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCCCCCHHHHCCCCCCCCHHH
T ss_conf             999999999988875268888689997799999779999999999984-7995999828877710776159999987799


Q ss_pred             HHCCCCCHHHHHHHHHHHCC-CCCEEEEECCC-CCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCC-HHHHHHHHHC
Q ss_conf             63184561243376532024-89806872487-612032079999999899985128889973888889-8999998620
Q gi|254780725|r  221 AIYPVGRIDKAFVSRLPVFY-AENLSILTAPA-MLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWN-SWTQEVLTLS  297 (427)
Q Consensus       221 ~l~~~~rlD~~~l~~~l~~~-~~gL~lL~a~~-~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~-~~~~~~L~~A  297 (427)
                      ++.+...+++..     .+. .++|++|+++. .++..+.+....+..+++.++..|||||||+||... ..+..+...+
T Consensus       590 ~L~g~~~~~~~i-----~~~~~~~ldvl~aG~~p~nP~elL~s~~~~~ll~~l~~~yD~IIiDtPPvl~v~Da~~l~~~~  664 (726)
T PRK09841        590 YLAGKDELNKVI-----QHFGKGGFDVITRGQVPPNPSELLMRDRMRQLLEWANDHYDLVIVDTPPMLAVSDAAVVGRSV  664 (726)
T ss_pred             HHCCCCCHHHHC-----CCCCCCCEEEEECCCCCCCHHHHHCCHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHC
T ss_conf             838999889933-----027989989982899997989995876999999999813999999199965341599999978


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCC
Q ss_conf             12543578776889999999999998198767538999565898
Q gi|254780725|r  298 DKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTP  341 (427)
Q Consensus       298 D~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~  341 (427)
                      |.+++|+......-....+.++.+.+.+.  +..++|+|.+...
T Consensus       665 D~~l~Vvr~g~T~~~~~~~a~~~l~~~~~--~v~G~vlN~v~~~  706 (726)
T PRK09841        665 GTSLLVARFGLNTAKEVSLSMQRLEQAGV--NIKGAILNGVIKR  706 (726)
T ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHHCCC--CEEEEEECCCCCC
T ss_conf             95999997996889999999999997899--7589998288656


No 40 
>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]
Probab=99.94  E-value=1.3e-24  Score=170.42  Aligned_cols=230  Identities=17%  Similarity=0.243  Sum_probs=166.4

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCC---------------
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845---------------
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVG---------------  226 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~---------------  226 (427)
                      +.|+|.|+|||+||||+++|||..|+.  ..+++|+|+|....+.+++|+.+....-.......-               
T Consensus         2 m~vAV~sGKGGtGKTTva~~la~~l~~--~~~~~l~DcDVe~PNl~l~l~~e~~~~~e~~~~~~p~i~~e~C~~CG~C~~   79 (284)
T COG1149           2 MQVAVASGKGGTGKTTVAANLAVLLGD--KYKLVLADCDVEAPNLHLLLGVEVLEEEEVIRGEIPEIDPEKCIRCGKCAE   79 (284)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHCC--CCCEEEEECCCCCCCCCEEECCCHHHHHHHHHHHCCCCCHHHCCCCCCHHH
T ss_conf             279996368877702289999998366--522477765778998616744501135677875046037577430172687


Q ss_pred             --CHHHHHH-H--HH----HHCCCCCEEEEECCCC---------------------------CCCHHCCCHHHHHHHHHH
Q ss_conf             --6124337-6--53----2024898068724876---------------------------120320799999998999
Q gi|254780725|r  227 --RIDKAFV-S--RL----PVFYAENLSILTAPAM---------------------------LSRTYDFDEKMIVPVLDI  270 (427)
Q Consensus       227 --rlD~~~l-~--~~----l~~~~~gL~lL~a~~~---------------------------~~~~~~~~~~~l~~ll~~  270 (427)
                        +.+...+ +  ..    ...++-|...+..|..                           ++-.+.-+..-+..+...
T Consensus        80 vC~f~Ai~~~~~~~~~~~~~lC~GCgaC~~~CP~~AI~~~~~~~G~i~~~~~~~g~~li~g~l~vGe~~s~~lV~~~kk~  159 (284)
T COG1149          80 VCRFGAIVVLPGGKPVLNPDLCEGCGACSIVCPEPAIEEEPVVIGKIYESKTDYGFPLISGRLNVGEEESGKLVTALKKH  159 (284)
T ss_pred             HCCCCEEEECCCCCEECCCCCCCCCCCCEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHHHHHHH
T ss_conf             67888089737886002802026766333247876555432000389998768996368874467844451378999875


Q ss_pred             HHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             85128889973888889899999862012543578776889999999999998198767538999565898752005999
Q gi|254780725|r  271 LEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       271 l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      ..+..+++|||+|++.+....+++..+|.+++|++|+++++.+.+|+++.++.++..   ..+|+||++... .  ..++
T Consensus       160 a~E~~~~~IIDsaaG~gCpVi~sl~~aD~ai~VTEPTp~glhD~kr~~el~~~f~ip---~~iViNr~~~g~-s--~ie~  233 (284)
T COG1149         160 AKELADLLIIDSAAGTGCPVIASLKGADLAILVTEPTPFGLHDLKRALELVEHFGIP---TGIVINRYNLGD-S--EIEE  233 (284)
T ss_pred             HHHHCCEEEEECCCCCCCHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCC---EEEEEECCCCCC-H--HHHH
T ss_conf             565321258857997897177764168779998168852366899999999983995---499996677772-0--8999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHC
Q ss_conf             9998489537990687999999884796189888999899999999999852
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIANLLVDFSRVLMG  402 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~~~~~La~~i~g  402 (427)
                      +.+..|.++.+.||||... .++..+|.|+.+  +.++-+..+...+.++..
T Consensus       234 ~~~e~gi~il~~IPyd~~i-~~~~~~g~~~~~--~~~k~~~~~~~~~~~~~~  282 (284)
T COG1149         234 YCEEEGIPILGEIPYDKDI-PEAYVNGEPFVE--PDSKEAEAILEEAEKLKE  282 (284)
T ss_pred             HHHHCCCCEEEECCCCHHH-HHHHHCCCCCCC--CCCHHHHHHHHHHHHHHC
T ss_conf             8887399726878864258-999857885313--552688999999999870


No 41 
>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]
Probab=99.94  E-value=1.3e-24  Score=170.53  Aligned_cols=228  Identities=18%  Similarity=0.234  Sum_probs=174.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCC-CC---HHHHHCC----CCCHH-----
Q ss_conf             79997469887756899999999996269949999787989860334389987-89---8886318----45612-----
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPI-NS---ISDAIYP----VGRID-----  229 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~-~~---l~d~l~~----~~rlD-----  229 (427)
                      +|+|.| |||+||||+|+-|+..+..+.+.+|+.||.|+ ..+++..||++.+ ..   ..+.++.    ....+     
T Consensus         2 kIaI~G-KGG~GKTtiaalll~~l~~~~~~~VLvVDaDp-d~nL~~~LGve~~~~~lg~~~e~~~k~~~a~~~~~~~~~f   79 (255)
T COG3640           2 KIAITG-KGGVGKTTIAALLLKRLLSKGGYNVLVVDADP-DSNLPEALGVEEPMKYLGGKRELLKKRTGAEPGGPPGEMF   79 (255)
T ss_pred             EEEEEC-CCCCCHHHHHHHHHHHHHHCCCCEEEEEECCC-CCCHHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCC
T ss_conf             699965-99765899999999999864895499994899-9990776299998755300899999986147899955300


Q ss_pred             ------HHHHHHHHHCCCCCEEEEECCCCC---CCHHCCCHHHHHHHHHHHHHC-CCEEEECCCCCCCHHHHHHHHHCCC
Q ss_conf             ------433765320248980687248761---203207999999989998512-8889973888889899999862012
Q gi|254780725|r  230 ------KAFVSRLPVFYAENLSILTAPAML---SRTYDFDEKMIVPVLDILEQI-FPLVILDVPHVWNSWTQEVLTLSDK  299 (427)
Q Consensus       230 ------~~~l~~~l~~~~~gL~lL~a~~~~---~~~~~~~~~~l~~ll~~l~~~-yd~VIiD~p~~~~~~~~~~L~~AD~  299 (427)
                            ..+.+.++...+ .+.+|.-+..-   ...+-.-...++.+++.+..+ |++||+|+-.+..+..+.....+|.
T Consensus        80 k~~~~~~di~~e~~~e~~-~~~LLvmGkie~~GeGC~Cp~~allR~~l~~l~~~~~e~VivDtEAGiEHfgRg~~~~vD~  158 (255)
T COG3640          80 KENPLVSDLPDEYLVENG-DIDLLVMGKIEEGGEGCACPMNALLRRLLRHLILNRYEVVIVDTEAGIEHFGRGTIEGVDL  158 (255)
T ss_pred             CCCCCHHHHHHHHHHHCC-CCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHCCCCCCCCCE
T ss_conf             137543351698850068-8007995255679974316278999999999751667489996334566656563257877


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCC
Q ss_conf             54357877688999999999999819876753899956589875200599999984895379906879999998847961
Q gi|254780725|r  300 VVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKM  379 (427)
Q Consensus       300 vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~p  379 (427)
                      +++|++|+.-|++.++++-++..+++  -.++.+|+|++...   +......+..++.++.++||||++.+ ++...|.|
T Consensus       159 vivVvDpS~~sl~taeri~~L~~elg--~k~i~~V~NKv~e~---e~~~~~~~~~~~~~vlg~iP~d~~v~-~~dl~G~p  232 (255)
T COG3640         159 VIVVVDPSYKSLRTAERIKELAEELG--IKRIFVVLNKVDEE---EELLRELAEELGLEVLGVIPYDPEVV-EADLKGEP  232 (255)
T ss_pred             EEEEECCCHHHHHHHHHHHHHHHHHC--CCEEEEEEEECCCH---HHHHHHHHHCCCCEEEEECCCCHHHH-HCCCCCCC
T ss_conf             99995787788888999999998718--75499999503411---57777653227974899716987887-42256884


Q ss_pred             EEEECCCCHHHHHHHHHHHHHHC
Q ss_conf             89888999899999999999852
Q gi|254780725|r  380 IHEVDPKSAIANLLVDFSRVLMG  402 (427)
Q Consensus       380 i~e~~p~s~~a~~~~~La~~i~g  402 (427)
                      +.+. |  ...+++.++++.|..
T Consensus       233 l~~~-~--~v~~~i~~I~~~l~~  252 (255)
T COG3640         233 LNEE-P--EVLKEIEEIAERLIK  252 (255)
T ss_pred             CCCC-H--HHHHHHHHHHHHHHH
T ss_conf             2123-5--557899999999985


No 42 
>PRK11519 tyrosine kinase; Provisional
Probab=99.93  E-value=2.1e-24  Score=169.22  Aligned_cols=175  Identities=14%  Similarity=0.177  Sum_probs=150.0

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHH
Q ss_conf             56753799974698877568999999999962699499997879898603343899878988863184561243376532
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLP  237 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l  237 (427)
                      ...+|+|.|+|+-.|.||||+|+|||..+|. .|+||+|||+|+..+.++.+|+.....|+.+++.+...++..     +
T Consensus       523 ~~~~~vi~vTS~~pgEGKSt~a~nLA~~~A~-~G~rvLLID~DlRrp~l~~~~~~~~~~GLs~~L~g~~~~~~~-----i  596 (720)
T PRK11519        523 QAQNNVLMMTGVSPSIGKTFVCANLAAVISQ-TNKRVLLIDCDMRKGYTHELLGTNNVNGLSEILIGQGDITTA-----A  596 (720)
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCCHHHHHCCCCCCCCHHHHCCCCCCHHHH-----C
T ss_conf             8887679997089999789999999999983-799199993877770167753999999859980799978997-----0


Q ss_pred             HCC-CCCEEEEECCC-CCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCC-HHHHHHHHHCCCCCCCCCCCHHHHHHH
Q ss_conf             024-89806872487-612032079999999899985128889973888889-899999862012543578776889999
Q gi|254780725|r  238 VFY-AENLSILTAPA-MLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWN-SWTQEVLTLSDKVVITTSLDLAGLRNS  314 (427)
Q Consensus       238 ~~~-~~gL~lL~a~~-~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~-~~~~~~L~~AD~vviV~~p~~~slr~a  314 (427)
                      .+. -++|++|+++. .++..+.+....+..+++.++..|||||||+||... ..+..+...+|.+++|+..........
T Consensus       597 ~~~~~~~l~vl~~G~~~pnp~elL~s~~~~~ll~~l~~~yD~IIiDtpPv~~v~Da~~la~~aD~~l~Vvr~g~t~~~~v  676 (720)
T PRK11519        597 KPTSIANFDLIPRGQVPPNPSELLMSERFAELVAWASKNYDLVLIDTPPILAVTDAAIVGRHVGTTLMVARYAVNTLKEV  676 (720)
T ss_pred             CCCCCCCEEEECCCCCCCCHHHHHCCHHHHHHHHHHHHHCCEEEEECCCCCCCHHHHHHHHHCCEEEEEEECCCCCHHHH
T ss_conf             35798998997699999498998387599999999985299999939996523589999997897999998995789999


Q ss_pred             HHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf             99999999819876753899956589
Q gi|254780725|r  315 KNLIDVLKKLRPADKPPYLVLNQVKT  340 (427)
Q Consensus       315 ~~ll~~l~~~~~~~~~~~iVlNr~~~  340 (427)
                      ...++.+.+.+.  ...++|+|++..
T Consensus       677 ~~a~~~l~~~~~--~v~G~VlN~v~~  700 (720)
T PRK11519        677 ETSLSRFEQNGI--PVKGVILNSIFR  700 (720)
T ss_pred             HHHHHHHHHCCC--CEEEEEECCCCC
T ss_conf             999999996899--748999889766


No 43 
>TIGR03029 EpsG chain length determinant protein tyrosine kinase EpsG. The proteins in this family are homologs of the EpsG protein found in Methylobacillus strain 12S and are generally found in operons with other Eps homologs. The protein is believed to function as the protein tyrosine kinase component of the chain length regulator (along with the transmembrane component EpsF).
Probab=99.93  E-value=1.5e-24  Score=170.03  Aligned_cols=171  Identities=23%  Similarity=0.245  Sum_probs=147.1

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf             75379997469887756899999999996269949999787989860334389987898886318456124337653202
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVF  239 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~  239 (427)
                      ..|.++|+|+..|.||||+|+|||+.+|+ .|+||+|||+|+..+.++.+||++...|+.+++.+...++....    ..
T Consensus       102 ~~~~LaItS~~pGEGKS~vAaNLA~~~Aq-~G~RvLLVDaDLRrP~lh~~f~l~~~~GLs~vL~g~~~l~~i~~----~~  176 (274)
T TIGR03029       102 GRKALAVVSAKSGEGCSYIAANLAIVFSQ-LGEKTLLIDANLRDPVQHRNFKLSEQRGLSDILAGRSDLEVITH----IP  176 (274)
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCCHHHHHHCCCCCCCHHHHHCCCCCHHHEEE----CC
T ss_conf             88389996899999899999999999996-79919999588888447797599997687888459998899051----58


Q ss_pred             CCCCEEEEECCCC-CCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC-CHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             4898068724876-1203207999999989998512888997388888-9899999862012543578776889999999
Q gi|254780725|r  240 YAENLSILTAPAM-LSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVW-NSWTQEVLTLSDKVVITTSLDLAGLRNSKNL  317 (427)
Q Consensus       240 ~~~gL~lL~a~~~-~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~-~~~~~~~L~~AD~vviV~~p~~~slr~a~~l  317 (427)
                      ..++|++|+++.. ++..+.+....+..+++.++..||+||+|+||.. ...+..+...+|-+++|+..+....++.++.
T Consensus       177 ~~~nL~VLpaG~~ppnP~eLL~s~~~~~ll~~l~~~yD~IIiDTPPvl~~sDA~ila~~aDg~LlVvR~~~T~~~~l~~a  256 (274)
T TIGR03029       177 ALENLSVLPAGAIPPNPQELLARPAFTDLLNKVMGDYDVVIVDTPSAEHSSDAQIVATRARGTLIVSRVNETRLHELTSL  256 (274)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCCHHHHHHHHCCEEEEEEECCCCCHHHHHHH
T ss_conf             98997899699999897998735899999999984099999938986554349999986897999996898889999999


Q ss_pred             HHHHHHCCCCCCCCEEEEEC
Q ss_conf             99999819876753899956
Q gi|254780725|r  318 IDVLKKLRPADKPPYLVLNQ  337 (427)
Q Consensus       318 l~~l~~~~~~~~~~~iVlNr  337 (427)
                      ++.+++.+.  +..++|+|+
T Consensus       257 ~~~L~~~g~--~VlGvVLNq  274 (274)
T TIGR03029       257 KEHLSGVGV--RVVGAVLNQ  274 (274)
T ss_pred             HHHHHHCCC--CEEEEEECC
T ss_conf             999997799--668998487


No 44 
>cd02038 FleN-like FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by influencing FleQ activity.
Probab=99.93  E-value=1.2e-25  Score=176.92  Aligned_cols=133  Identities=23%  Similarity=0.353  Sum_probs=111.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886318456124337653202489
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAE  242 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~  242 (427)
                      ||+|.|+||||||||+++|||.+||+ .|++|+++|+|+..+++                                    
T Consensus         1 vi~v~sgKgGvGkt~~~~nLa~~la~-~G~~vll~D~D~g~an~------------------------------------   43 (139)
T cd02038           1 IIAVTSGKGGVGKTNISANLALALAK-LGKRVLLLDADLGLANL------------------------------------   43 (139)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCC------------------------------------
T ss_conf             98996499998399999999999997-89969999898999657------------------------------------


Q ss_pred             CEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             80687248761203207999999989998512888997388888989999986201254357877688999999999999
Q gi|254780725|r  243 NLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLK  322 (427)
Q Consensus       243 gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~  322 (427)
                                                     +||||++|+|++.+..+..++..||.+++|++|++.|+.+++++++.+.
T Consensus        44 -------------------------------~~D~viiD~~aG~~~~~~~~~~~ad~~lvV~tpeptSi~DAYalIK~l~   92 (139)
T cd02038          44 -------------------------------DYDYIIIDTGAGISDNVLDFFLAADEVIVVTTPEPTSITDAYALIKKLA   92 (139)
T ss_pred             -------------------------------CCCEEEEECCCCCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHH
T ss_conf             -------------------------------9999999489998778999999589579995897067999999999999


Q ss_pred             HCCCCCCCCEEEEECCCCCCCCHHHHHHHHHH----HCC--CEEEEEC
Q ss_conf             81987675389995658987520059999998----489--5379906
Q gi|254780725|r  323 KLRPADKPPYLVLNQVKTPKKPEISISDFCAP----LGI--TPSAIIP  364 (427)
Q Consensus       323 ~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~----lg~--~~~~~IP  364 (427)
                      +.. +...+++|+||+..++..+...+.|.+.    |+.  +..+.||
T Consensus        93 ~~~-~~~~~~lvvN~v~s~~ea~~~~~~l~~v~~kfL~v~l~~lG~IP  139 (139)
T cd02038          93 KQL-RVLNFRVVVNRAESPKEGKKVFKRLSNVSNRFLGLSLDYLGFIP  139 (139)
T ss_pred             HHC-CCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEECC
T ss_conf             963-99975999956899999999999999999998099831071485


No 45 
>COG0489 Mrp ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=99.92  E-value=1.3e-23  Score=164.37  Aligned_cols=202  Identities=23%  Similarity=0.197  Sum_probs=159.0

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHH
Q ss_conf             56753799974698877568999999999962699499997879898603343899878988863184561243376532
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLP  237 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l  237 (427)
                      ....++|+|.++|||+||||+|+|||+++|+ .|++|+++|+|+...+.+.+|+.+...++.+.+.+..      +....
T Consensus        54 ~~~~~~I~V~S~kgGvGKStva~nLA~alA~-~G~rVlliDaD~~gps~~~~l~~~~~~g~~~~~~g~~------~~~~~  126 (265)
T COG0489          54 KGVKNVIAVTSGKGGVGKSTVAVNLAAALAQ-LGKRVLLLDADLRGPSIPRMLGLENLPGLTELLAGEA------LEPVI  126 (265)
T ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCCCCHHHCCCCCCCCCCCCCCCCC------CCCCE
T ss_conf             5666189997589987568999999999996-3993899967466986355408986556541137871------14322


Q ss_pred             HCC-CCCEEEEECCCCC-CCHHCCCHHHHHHHHHHHHHC-CCEEEECCCCCCCHHHHHHHHH-CCCCCCCCCCCHHHHHH
Q ss_conf             024-8980687248761-203207999999989998512-8889973888889899999862-01254357877688999
Q gi|254780725|r  238 VFY-AENLSILTAPAML-SRTYDFDEKMIVPVLDILEQI-FPLVILDVPHVWNSWTQEVLTL-SDKVVITTSLDLAGLRN  313 (427)
Q Consensus       238 ~~~-~~gL~lL~a~~~~-~~~~~~~~~~l~~ll~~l~~~-yd~VIiD~p~~~~~~~~~~L~~-AD~vviV~~p~~~slr~  313 (427)
                      ... -+.++++.....+ .....+...++.+++..++.. |||||||+||+.......++.. .|-+++|++|.......
T Consensus       127 ~~~~~~~lsi~~~~~~p~~~r~~l~s~~~~qll~~~~~~~~D~vIID~PP~~g~~d~~i~~~~~~g~viVt~p~~~~~~~  206 (265)
T COG0489         127 QHDGIKVLSILPLGPVPVIPRGLLGSKAMLQLLEDVLWGEYDYVIIDTPPGTGDADATVLQRIPDGVVIVTTPGKTALED  206 (265)
T ss_pred             ECCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHCCCEEEEEECCCCCHHHH
T ss_conf             02665504788328899894677633899999999745688889996999864277788751388599996677355999


Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEECCCCCC--CCHHHHHHHHHHHCCCEEEEECCCHHH
Q ss_conf             99999999981987675389995658987--520059999998489537990687999
Q gi|254780725|r  314 SKNLIDVLKKLRPADKPPYLVLNQVKTPK--KPEISISDFCAPLGITPSAIIPFDGAV  369 (427)
Q Consensus       314 a~~ll~~l~~~~~~~~~~~iVlNr~~~~~--~~~i~~~~~~~~lg~~~~~~IP~D~~~  369 (427)
                      +++.++.+++.+.  .-+.+|.|+.....  .++-..+.+.+.++ +....+|.+...
T Consensus       207 v~ka~~~~~~~~~--~vlGvv~Nm~~~~~~~~~~g~~~~~~~~~~-~~~g~~p~~~~~  261 (265)
T COG0489         207 VKKAIDMLEKAGI--PVLGVVENMSYFICPRCGEGGGEKYAERYG-PYLGSIPLDPSA  261 (265)
T ss_pred             HHHHHHHHHHCCC--CEEEEEECCCCCCCCCCCCCCHHHHHHHHC-CCCCCCCCCHHH
T ss_conf             9999999987499--347999668666665557885233566511-102668867454


No 46 
>cd02033 BchX Chlorophyllide reductase converts chlorophylls into bacteriochlorophylls by reducing the chlorin B-ring. This family contains the X subunit of this three-subunit enzyme. Sequence and structure similarity between bchX, protochlorophyllide reductase L subunit (bchL and chlL) and nitrogenase Fe protein (nifH gene) suggest their functional similarity. Members of the BchX family serve as the unique electron donors to their respective catalytic subunits (bchN-bchB, bchY-bchZ and nitrogenase component 1). Mechanistically, they hydrolyze ATP and transfer electrons through a Fe4-S4 cluster.
Probab=99.92  E-value=6.6e-23  Score=159.99  Aligned_cols=251  Identities=18%  Similarity=0.194  Sum_probs=182.8

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCC-CHHHHHHHHHH
Q ss_conf             67537999746988775689999999999626994999978798986033438998789888631845-61243376532
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVG-RIDKAFVSRLP  237 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~-rlD~~~l~~~l  237 (427)
                      ...|+|||+| |||+||||++.|++.+||+ .|++|+.|-+|+...++.++|+-....++.|.+.... ..+...++..+
T Consensus        29 k~~~~IAiYG-KGGIGKSTts~NlsAAlA~-~GkkVm~IGCDPKaDSTrlLlgG~~~~TVLd~~~~~~~~~e~v~~~dv~  106 (329)
T cd02033          29 KKTQIIAIYG-KGGIGKSFTLANLSYMMAQ-QGKRVLLIGCDPKSDTTSLLFGGKACPTIIETSAKKKLAGEEVQIGDVC  106 (329)
T ss_pred             CCCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCCCCHHHHCCCCCCCCHHHHHHHHCCCCCCCCCHHHEE
T ss_conf             4454999976-8843561688999999997-7996999788884603341058988840999998728864434250178


Q ss_pred             HCCCCCEEEEEC-CCCCCC----HHCCCHHHHHHHHHHH---HHCCCEEEECCCCC-CCHHHHHHH--HHCCCCCCCCCC
Q ss_conf             024898068724-876120----3207999999989998---51288899738888-898999998--620125435787
Q gi|254780725|r  238 VFYAENLSILTA-PAMLSR----TYDFDEKMIVPVLDIL---EQIFPLVILDVPHV-WNSWTQEVL--TLSDKVVITTSL  306 (427)
Q Consensus       238 ~~~~~gL~lL~a-~~~~~~----~~~~~~~~l~~ll~~l---~~~yd~VIiD~p~~-~~~~~~~~L--~~AD~vviV~~p  306 (427)
                      .+. .|+...-+ +..+..    ..-+..  + .+++.+   ...+|||+.|+-.. .......-+  ..|++|++|+..
T Consensus       107 ~~g-~Gv~CvEsGGPEPGvGCAGRGIIta--i-~lLe~lg~~~~d~D~V~yDVLGDVVCGGFAmPiR~g~A~evyIVtSg  182 (329)
T cd02033         107 FKR-DGVFAMELGGPEVGRGCGGRGIIHG--F-ELLEKLGFHDWDFDYVLLDFLGDVVCGGFGLPIARDMAQKVIVVGSN  182 (329)
T ss_pred             ECC-CCEEEEECCCCCCCCCCCCCCHHHH--H-HHHHHCCCCCCCCCEEEEECCCCEEECCCCCCCCCCCCCEEEEEECC
T ss_conf             625-9988986679999876788730136--6-78776377525899999922453566463353356876289999678


Q ss_pred             CHHHHHHHHHHHHHHHHC---CCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEE
Q ss_conf             768899999999999981---98767538999565898752005999999848953799068799999988479618988
Q gi|254780725|r  307 DLAGLRNSKNLIDVLKKL---RPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEV  383 (427)
Q Consensus       307 ~~~slr~a~~ll~~l~~~---~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~  383 (427)
                      +..|+..+.|+.+-+...   +.+.+.-.+|+|+-+..  .+  .+.|++.+|.++.+.||.|..+...+.+ .+++  .
T Consensus       183 E~MalyAANNI~~~i~~~a~~gg~vrl~GlI~N~~~~~--~e--~e~fa~~~g~~~l~~vP~d~~iRr~~~~-y~iv--~  255 (329)
T cd02033         183 DLQSLYVANNVCNAVEYFRKLGGNVGVAGMVINKDDGT--GE--AQAFAAHAGIPILAAIPADEELRRKSAA-YQIV--G  255 (329)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCC--HH--HHHHHHHCCCCEEEECCCCHHHHHHHHH-CCCC--C
T ss_conf             08899988789999999986389710115986068872--49--9999997199579963787788765430-2603--4


Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             8999899999999999852212232111058999987423
Q gi|254780725|r  384 DPKSAIANLLVDFSRVLMGRVTVSKPQSAMYTKIKKIFNM  423 (427)
Q Consensus       384 ~p~s~~a~~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~r  423 (427)
                      .|.++.+..|++||..|...+. ..|+.--...|..||+-
T Consensus       256 ~p~~~~~~~f~~LA~~i~~~~p-~~P~pl~~deL~~Lf~~  294 (329)
T cd02033         256 RPGTTWGPLFEQLATNVAEAPP-MRPKPLSQDELLGLFSS  294 (329)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCC-CCCCCCCHHHHHHHHCC
T ss_conf             8761589999999997612798-77899898999876354


No 47 
>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase. Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.
Probab=99.91  E-value=5.6e-23  Score=160.45  Aligned_cols=194  Identities=22%  Similarity=0.229  Sum_probs=151.0

Q ss_pred             CCCCCH-HHHHHHHHH-CCC-CCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHC
Q ss_conf             189998-999997631-023-32223456753799974698877568999999999962699499997879898603343
Q gi|254780725|r  134 IEPLSV-ADIINSISA-IFT-PQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINF  210 (427)
Q Consensus       134 ~~P~~~-~~l~~ai~~-~~~-~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l  210 (427)
                      ..|.++ .|-.+.++. +.. .......+.+|+|.|+|+..|.||||+|.|||.++|+..+++|+|||+|+..++++.+|
T Consensus         5 ~~P~s~~aEa~R~lRt~l~~~~~~~~~~~~~kvi~VTS~~pgeGKTtva~nLA~~lA~~~~~~VLLVDaDlr~p~l~~~l   84 (207)
T TIGR03018         5 NSPRSRIAEEFRKIKRPLLANAFSANRKKNNNLIMVTSSLPGEGKSFTAINLAISLAQEYDKTVLLIDADLRRPSLHRTL   84 (207)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHC
T ss_conf             89999899999999998766410103467880999978999998899999999999972498599995357899710013


Q ss_pred             CCCCCCCHHHHHCCCC-CHHHHHHHHHHHCC-CCCEEEEECCCCCCC-HHCCCHHHHHHHHHHHHHCCC--EEEECCCCC
Q ss_conf             8998789888631845-61243376532024-898068724876120-320799999998999851288--899738888
Q gi|254780725|r  211 DKDPINSISDAIYPVG-RIDKAFVSRLPVFY-AENLSILTAPAMLSR-TYDFDEKMIVPVLDILEQIFP--LVILDVPHV  285 (427)
Q Consensus       211 ~~~~~~~l~d~l~~~~-rlD~~~l~~~l~~~-~~gL~lL~a~~~~~~-~~~~~~~~l~~ll~~l~~~yd--~VIiD~p~~  285 (427)
                      +.++..|+.|.+.+.. .++..     +.+. .++|++++++..... .+.+....+..+++.+++.||  |||||+||.
T Consensus        85 ~~~~~~Gl~d~L~~~~~~l~~~-----i~~~~~~~l~vlpag~~~~~~~~ll~s~~~~~li~~lr~~yd~~~VIiDtPPv  159 (207)
T TIGR03018        85 GLEAEPGLSDCLLDPVLDLADV-----LVPTNIGRLSLLPAGRRHPNPTELLASQRMRSLLHELARRYPDRIIIIDTPPL  159 (207)
T ss_pred             CCCCCCCHHHHHCCCCCCHHHH-----EECCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf             8899998567743899875672-----34268875557516898996676542699999999999737965799838962


Q ss_pred             CC-HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf             89-8999998620125435787768899999999999981987675389995
Q gi|254780725|r  286 WN-SWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLN  336 (427)
Q Consensus       286 ~~-~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlN  336 (427)
                      .. ..+..+...+|-+++|+.......+...+.++.|+.    ..-+++|+|
T Consensus       160 l~~~Da~~la~~~D~vllVvr~~~t~~~~v~~a~~~L~~----~~vlG~VlN  207 (207)
T TIGR03018       160 LVFSEARALARLVGQIVLVVEEGRTTQEAVKEALSALES----CKVLGVVLN  207 (207)
T ss_pred             CCCHHHHHHHHHCCEEEEEEECCCCCHHHHHHHHHHHCC----CCEEEEEEC
T ss_conf             232369999996896999997998789999999998668----980699969


No 48 
>TIGR01281 DPOR_bchL light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein; InterPro: IPR005971    Synonym: dark protochlorophyllide reductase    Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite.    The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulphur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase . ; GO: 0005524 ATP binding, 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction.
Probab=99.91  E-value=3.5e-23  Score=161.69  Aligned_cols=256  Identities=14%  Similarity=0.174  Sum_probs=196.5

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCC-CHHHHHHHHHHHCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845-61243376532024
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVG-RIDKAFVSRLPVFY  240 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~-rlD~~~l~~~l~~~  240 (427)
                      +++||+| |||+||||+++||+.+||+ .|+|||=|-|||-+ |....|--.-.+|+.|+|..-+ +.++..-+..+-+.
T Consensus         1 ~~lAvYG-KGGiGKSTTssNLSvA~A~-~GkkVlQIGCDPKh-DSTFTLtg~L~PTvidvL~~~~yH~E~v~~eD~iy~G   77 (275)
T TIGR01281         1 MILAVYG-KGGIGKSTTSSNLSVALAK-KGKKVLQIGCDPKH-DSTFTLTGKLIPTVIDVLDAVNYHYEDVEPEDVIYTG   77 (275)
T ss_pred             CEEEEEC-CCCCCCHHHHHHHHHHHHH-CCCEEEEECCCCCC-CCCCCCCCCCCCCEEEECCCCCCCEEECCCCCEEEEC
T ss_conf             9688863-8887700467899999984-69918985257888-8774544741674644225676303103337877834


Q ss_pred             CCCEEEEECCCCCCCHH---CCCHHHHHHHHHHH--HHCCCEEEEC-CCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHH
Q ss_conf             89806872487612032---07999999989998--5128889973-888889899999862012543578776889999
Q gi|254780725|r  241 AENLSILTAPAMLSRTY---DFDEKMIVPVLDIL--EQIFPLVILD-VPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNS  314 (427)
Q Consensus       241 ~~gL~lL~a~~~~~~~~---~~~~~~l~~ll~~l--~~~yd~VIiD-~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a  314 (427)
                      =.|++++-++..|.-.-   .+=.+. -.||+.+  -+.||+||.| ++........+-|..||.-+||+.-|..||-.|
T Consensus        78 Y~GVd~vEaGGPPAGsGCGGYVVGeT-VKLLke~~~~~~yDVilFDVLGDVVCGGFAaPL~YAd~aLvva~NDFDalFAA  156 (275)
T TIGR01281        78 YGGVDCVEAGGPPAGSGCGGYVVGET-VKLLKELDVLDEYDVILFDVLGDVVCGGFAAPLQYADYALVVAANDFDALFAA  156 (275)
T ss_pred             CCCEEEEECCCCCCCCCCCCEEECCH-HHHHHHCCHHHHCCEEEEEECCCEEECCCCCHHHHHCCEEEEECCCCHHHHHH
T ss_conf             68568871473689888987471522-45566526334289799962575551754641123212566610772178999


Q ss_pred             HHHHHHHHHC--C-CCCCCCEEEEECCCCC-CCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC---
Q ss_conf             9999999981--9-8767538999565898-7520059999998489537990687999999884796189888999---
Q gi|254780725|r  315 KNLIDVLKKL--R-PADKPPYLVLNQVKTP-KKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS---  387 (427)
Q Consensus       315 ~~ll~~l~~~--~-~~~~~~~iVlNr~~~~-~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s---  387 (427)
                      +|+...+++.  + +.-+--.+|-||+... ..+.--.+.|.+..+.++...+|+- +.+++|--.|.++.|+.+..   
T Consensus       157 NRia~av~~K~~~Gy~vkLAGiIaNR~~~~yGGGtdlle~F~~~~~~~~l~~~P~~-d~IR~SRl~g~TlFEmee~~p~~  235 (275)
T TIGR01281       157 NRIAAAVREKAKSGYDVKLAGIIANRVDKEYGGGTDLLEKFAERVGTPVLGVVPRL-DEIRRSRLKGKTLFEMEESGPEL  235 (275)
T ss_pred             HHHHHHHHHHHCCCCEEEEEEEEECCCCCCCCCCCCHHHHHHHHCCCCEEEECCCH-HHCCHHHHCCCCEEECCCCCCCH
T ss_conf             99999999984179707873266312113117871568999986288322007771-11020101586123015899658


Q ss_pred             -HHHHHHHHHHHHHHCC-CCCCCCCCCHHHHHHHHHH
Q ss_conf             -8999999999998522-1223211105899998742
Q gi|254780725|r  388 -AIANLLVDFSRVLMGR-VTVSKPQSAMYTKIKKIFN  422 (427)
Q Consensus       388 -~~a~~~~~La~~i~gr-~~~~~~k~~~~~~l~~lf~  422 (427)
                       ...+.|.+||+.|..+ ++..-|+...--.+..||+
T Consensus       236 ~~~~~~y~~~A~~LL~~Gp~~~vp~~~~dR~~F~ll~  272 (275)
T TIGR01281       236 EEVTAEYLKMAEYLLAKGPEGVVPKPLADREIFELLG  272 (275)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC
T ss_conf             8999999999999986388973677410158998734


No 49 
>TIGR01007 eps_fam capsular exopolysaccharide family; InterPro: IPR005702    This family describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis (EPS). At least 13 genes EpsA to EpsM in streptococcus species seem to direct the EPS proteins and share high homology. ; GO: 0030234 enzyme regulator activity, 0045227 capsule polysaccharide biosynthetic process.
Probab=99.90  E-value=5.5e-23  Score=160.48  Aligned_cols=178  Identities=21%  Similarity=0.251  Sum_probs=151.6

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCC-CCCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             7537999746988775689999999999626994999978798986033438998-789888631845612433765320
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDP-INSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~-~~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      .=|+++|.|.|-|-||||+.+|+||++|+ .|.||||||.|+..++....|+..- ..||.+.|.+...+.+..-+.   
T Consensus        18 e~K~l~itS~~~~eGKsT~S~NiA~~fAq-aGyKTLlIDgD~R~sv~~~~Fk~~n~~~GLtn~L~g~~dl~~~i~~T---   93 (207)
T TIGR01007        18 EIKVLLITSVKAGEGKSTTSANIAVSFAQ-AGYKTLLIDGDMRNSVMSGTFKSQNKIKGLTNFLSGNTDLSDAICET---   93 (207)
T ss_pred             CEEEEEEEECCCCCCCEEEEHHHHHHHHH-CCCEEEEEECCCCCCCEEEEECCCCCCCCCHHHHCCCCCHHHHHHCC---
T ss_conf             70589984110588862410788999985-68558887546586603678658887656333221454533342026---


Q ss_pred             CCCCCEEEEEC-CCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHH-HHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf             24898068724-8761203207999999989998512888997388888989999-986201254357877688999999
Q gi|254780725|r  239 FYAENLSILTA-PAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQE-VLTLSDKVVITTSLDLAGLRNSKN  316 (427)
Q Consensus       239 ~~~~gL~lL~a-~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~-~L~~AD~vviV~~p~~~slr~a~~  316 (427)
                      +.+++|.++++ |-.|...+.+....|..+++.++..|||||||+||.-.-.-.+ ....+|..++|+...--.=+..+.
T Consensus        94 ~isenL~vi~sG~vPPNPt~LL~s~~F~~l~e~~~~~fD~iiiDTPPig~V~DAai~a~~~d~~~LV~~A~~~~k~~v~K  173 (207)
T TIGR01007        94 NISENLDVITSGPVPPNPTELLQSSNFKTLIETLRKYFDYIIIDTPPIGTVIDAAIIARAVDASILVTDAGKIKKREVKK  173 (207)
T ss_pred             CCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHCCEEEEEECCCCCHHHHHH
T ss_conf             54678727517887877547888899999999987168889995188666788999998729779887225326467899


Q ss_pred             HHHHHHHCCCCCCCCEEEEECCCCCCC
Q ss_conf             999999819876753899956589875
Q gi|254780725|r  317 LIDVLKKLRPADKPPYLVLNQVKTPKK  343 (427)
Q Consensus       317 ll~~l~~~~~~~~~~~iVlNr~~~~~~  343 (427)
                      ..+.|++.+  ..-+++|||+++..+.
T Consensus       174 AK~~LEq~G--~~~LGvvLNK~d~s~~  198 (207)
T TIGR01007       174 AKEQLEQAG--SKFLGVVLNKVDISVD  198 (207)
T ss_pred             HHHHHHHHC--CCEEEEEECCCCCCCC
T ss_conf             999998617--8411588888257655


No 50 
>cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.
Probab=99.90  E-value=1.2e-22  Score=158.38  Aligned_cols=157  Identities=25%  Similarity=0.276  Sum_probs=121.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886318456124337653202489
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAE  242 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~  242 (427)
                      ||+|.++||||||||+++|||.+|++ .|++|+++|+|....+...++            +                   
T Consensus         1 vi~v~s~kggvgkst~~~~la~~l~~-~g~~v~~~d~di~gpsip~~~------------r-------------------   48 (169)
T cd02037           1 VIAVMSGKGGVGKSTVAVNLALALAK-LGYKVGLLDADIYGPSIPKMW------------R-------------------   48 (169)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEEEECCCCCCCEEE------------E-------------------
T ss_conf             98997499988199999999999998-799789997137999755012------------0-------------------


Q ss_pred             CEEEEECCCCCCCHHCCCHHHHHHHH-HHHHHCCCEEEECCCCCCCHHHHHHH--HHCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             80687248761203207999999989-99851288899738888898999998--6201254357877688999999999
Q gi|254780725|r  243 NLSILTAPAMLSRTYDFDEKMIVPVL-DILEQIFPLVILDVPHVWNSWTQEVL--TLSDKVVITTSLDLAGLRNSKNLID  319 (427)
Q Consensus       243 gL~lL~a~~~~~~~~~~~~~~l~~ll-~~l~~~yd~VIiD~p~~~~~~~~~~L--~~AD~vviV~~p~~~slr~a~~ll~  319 (427)
                            +|        .....+.+++ +.....+||+|||+|++.++....+.  ..+|.+++|++|+..|+.++++.++
T Consensus        49 ------Gp--------~~~~~i~q~l~~~~w~~lDyLIID~PPGtgD~~lt~~~~~~~d~~IvVTTP~~~s~~Da~r~i~  114 (169)
T cd02037          49 ------GP--------MKMGAIKQFLTDVDWGELDYLVIDMPPGTGDEHLTLAQSLPIDGAVIVTTPQEVALDDVRKAID  114 (169)
T ss_pred             ------CH--------HHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHH
T ss_conf             ------47--------3899999999852546678899968999870778798750567479994695889999999999


Q ss_pred             HHHHCCCCCCCCEEEEECCCC--C---CC----CHHHHHHHHHHHCCCEEEEECCCH
Q ss_conf             999819876753899956589--8---75----200599999984895379906879
Q gi|254780725|r  320 VLKKLRPADKPPYLVLNQVKT--P---KK----PEISISDFCAPLGITPSAIIPFDG  367 (427)
Q Consensus       320 ~l~~~~~~~~~~~iVlNr~~~--~---~~----~~i~~~~~~~~lg~~~~~~IP~D~  367 (427)
                      ++++.+.  ..+.+|.||...  +   ++    ++-..+++++.++.+..+.||.||
T Consensus       115 ~~~~~~i--~i~GvVeNMs~~~c~~c~~~~~ifg~~~~~~la~~~~i~~Lg~IP~dp  169 (169)
T cd02037         115 MFKKVNI--PILGVVENMSYFVCPHCGKKIYIFGKGGGEKLAEELGVPLLGKIPLDP  169 (169)
T ss_pred             HHHHCCC--CEEEEEECCCCCCCCCCCCEEECCCCCHHHHHHHHHCCCEEEECCCCC
T ss_conf             9997599--707999879666079999735278884499999995999898728999


No 51 
>pfam07015 VirC1 VirC1 protein. This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon which enhances T-DNA processing probably does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA.
Probab=99.90  E-value=3.4e-21  Score=149.49  Aligned_cols=207  Identities=15%  Similarity=0.092  Sum_probs=136.9

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      ++|+|.+.|||+||||++.|||.+++. .|++|+++|+|+|.. +..+.         +.-...+..+            
T Consensus         2 ~vi~~~~~KGG~GKtT~a~~la~~~~~-~g~~V~liD~Dpq~s-~~~W~---------~~a~~~~~~~------------   58 (231)
T pfam07015         2 QLITFCSFKGGAGKTTALMGLCSALAS-DGKRVALFEADENRP-LTKWR---------ENALRKGTWD------------   58 (231)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCC-HHHHH---------HHHHHCCCCC------------
T ss_conf             379996179986599999999999996-899599996899868-89999---------9876468888------------


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHHH-HCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             9806872487612032079999999899985-128889973888889899999862012543578776889999999999
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDILE-QIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDV  320 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~  320 (427)
                      +...+...         .....+...++.+. ..|||||||+|+..+.++..++..||.|+++++|+...+..+.+.+++
T Consensus        59 ~~~~v~~~---------~~~~~l~~~~~~~~~~~yD~VIIDtpg~~s~~~~~AI~~ADlVLIP~qpSplD~~~a~~t~~~  129 (231)
T pfam07015        59 PACEIFNA---------DELPLLEQAYEHAEGSGFDYALADTHGGSSELNNTIIASSDLLLIPTMLTPLDIDEALATYRY  129 (231)
T ss_pred             CCCCEECC---------CCHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHCCEEEECCCCCHHHHHHHHHHHHH
T ss_conf             76522205---------660158999998865799989983998575899999997898997789982339999999999


Q ss_pred             HHHC---CCCCCCCEEEEECCCCCCCCHHHHHHHHHHHC-CCEEEEECCCHHHHHHHHHCCCCEEEECCCC------HHH
Q ss_conf             9981---98767538999565898752005999999848-9537990687999999884796189888999------899
Q gi|254780725|r  321 LKKL---RPADKPPYLVLNQVKTPKKPEISISDFCAPLG-ITPSAIIPFDGAVFGMSANSGKMIHEVDPKS------AIA  390 (427)
Q Consensus       321 l~~~---~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg-~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s------~~a  390 (427)
                      +.+.   ...+-+..++++|+... +.......+.+.++ .+++-+--.+...|......|....+....+      +.+
T Consensus       130 i~~~~~~~~~~ip~avl~tRv~~~-~~~~~~~~i~e~le~lpvl~t~i~eR~AF~~if~~G~l~~~l~~~~~~~~~~~a~  208 (231)
T pfam07015       130 VIELLLTENLAIPTAILRQRVPVG-RLTSSQRFCSDMLEQLPVFDCPMHERDAFAAMKERGMLHITLENLSQIPSMRLAL  208 (231)
T ss_pred             HHHHHHHHCCCCCEEEEEEECCCC-CCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCHHCCCCCCCCCHHHHH
T ss_conf             999999737899803345511400-0217899999999649854354202899999998046200026877785112899


Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999985
Q gi|254780725|r  391 NLLVDFSRVLM  401 (427)
Q Consensus       391 ~~~~~La~~i~  401 (427)
                      +.++.+++.+.
T Consensus       209 ~n~~~~~~e~~  219 (231)
T pfam07015       209 RNLRTAMEDLD  219 (231)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 52 
>PRK13849 putative crown gall tumor protein VirC1; Provisional
Probab=99.88  E-value=6.3e-21  Score=147.84  Aligned_cols=185  Identities=13%  Similarity=0.101  Sum_probs=122.9

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      ++|+|.+.|||+||||+|.|||.++++ .|.+|+++|+|+|. ++..+..         .....+..            .
T Consensus         2 ~vi~~~~~KGG~GKtT~a~~la~~~~~-~g~~v~~iD~Dpq~-s~~~W~e---------~a~~~~~~------------~   58 (231)
T PRK13849          2 KLLTFCSFKGGAGKTTALMGLCAALAS-DGKRVALFEADENR-PLTRWKE---------NALRSNTW------------D   58 (231)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCC-CHHHHHH---------HHHHCCCC------------C
T ss_conf             379996189987699999999999997-89959999689986-8899998---------76525898------------8


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHH-HHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             980687248761203207999999989998-5128889973888889899999862012543578776889999999999
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDIL-EQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDV  320 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l-~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~  320 (427)
                      +...+...         .....+....+.. .+.|||||||+|+..+.+...++..||.|+|+++|+...++.+.+.+++
T Consensus        59 ~~~~v~~~---------~~~~~l~~~~e~~~~~~~D~VIIDtpg~~s~~~~~Ai~~ADLVLIP~qPSp~D~~~a~~tv~~  129 (231)
T PRK13849         59 PACEVYAA---------DELPLLEAAYEDAELQGFDYALADTHGGSSELNNTIIASSNLLLIPTMLTPLDIDEALSTYRY  129 (231)
T ss_pred             CCCCEEEC---------CCHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHCCEEEECCCCCHHHHHHHHHHHHH
T ss_conf             77523405---------652578999988753699889981899775899999997898997799986679999999999


Q ss_pred             HHHC---CCCCCCCEEEEECCCCCCCCHHHHHHHHHHHC-CCEEEEECCCHHHHHHHHHCCCC
Q ss_conf             9981---98767538999565898752005999999848-95379906879999998847961
Q gi|254780725|r  321 LKKL---RPADKPPYLVLNQVKTPKKPEISISDFCAPLG-ITPSAIIPFDGAVFGMSANSGKM  379 (427)
Q Consensus       321 l~~~---~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg-~~~~~~IP~D~~~~~~A~~~G~p  379 (427)
                      +.+.   .-.+-+..+++||+.... ..-..+.+.+.+. .+++-+--.+...|.+=...|..
T Consensus       130 i~~~~~~~~~~ip~~vlltRv~a~~-~t~~~~~i~~~le~lPvl~T~i~eR~Af~~i~~~G~L  191 (231)
T PRK13849        130 VIELLLSENLAIPTAILRQRVPVGR-LTTSQRAMSDMLESLPVVDSPMHERDAFAAMKERGML  191 (231)
T ss_pred             HHHHHHHHCCCCCEEEEEEECCHHH-HCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCH
T ss_conf             9999997287886566654050454-0688999999996299555530227999999983514


No 53 
>cd00550 ArsA_ATPase Oxyanion-translocating ATPase (ArsA).  This ATPase is involved in transport of arsenite, antimonite or other oxyanions across biological membranes in all three kingdoms of life.  ArsA contains a highly conserved AAA motif present in the AAA+ ATPase superfamily associated with a variety of cellular activities.   To form a functional ATP-driven pump, ArsA interacts with the permease ArsB, which is a channel-forming integral membrane protein. One of the most interesting features of ArsA is the allosteric activation by its transport substrates.  A divalent cation, typically Mg2+, is required for its enzymatic activity.
Probab=99.87  E-value=4.5e-21  Score=148.76  Aligned_cols=198  Identities=18%  Similarity=0.227  Sum_probs=113.2

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHH--HH---HCCCCCHHHH-HHHH
Q ss_conf             3799974698877568999999999962699499997879898603343899878988--86---3184561243-3765
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSIS--DA---IYPVGRIDKA-FVSR  235 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~--d~---l~~~~rlD~~-~l~~  235 (427)
                      |+| |+++||||||||+|+|+|..||+ .|+||+|||.|++ .+++-.||.+...+..  +.   +... .+|.. .++.
T Consensus         1 r~i-~~~GKGGVGKTT~AaalA~~lA~-~G~kVLlvstDPa-hsLsd~f~~~~~~~~~~v~~~~nL~a~-eid~~~~~~~   76 (254)
T cd00550           1 RYI-FFGGKGGVGKTTISAATAVRLAE-QGKKVLLVSTDPA-HSLSDSFNQEFGKGPTPVKGVENLSAM-EIDPQEALEE   76 (254)
T ss_pred             CEE-EEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCC-CCHHHHHCCCCCCCCCEECCCCCCEEE-EECHHHHHHH
T ss_conf             989-99689855489999999999996-8994999958986-448898488667887110366884578-7288999999


Q ss_pred             HHHCCCCCEEEEECCCCCCCH-------HCC-CHHHHHHHHHHHH-HCCCEEEECCCCCC-----------CHHHHHHHH
Q ss_conf             320248980687248761203-------207-9999999899985-12888997388888-----------989999986
Q gi|254780725|r  236 LPVFYAENLSILTAPAMLSRT-------YDF-DEKMIVPVLDILE-QIFPLVILDVPHVW-----------NSWTQEVLT  295 (427)
Q Consensus       236 ~l~~~~~gL~lL~a~~~~~~~-------~~~-~~~~l~~ll~~l~-~~yd~VIiD~p~~~-----------~~~~~~~L~  295 (427)
                      ......+.+.-...+...+..       ..+ ..-.+..+++.+. ..||+||+||||.-           -.|....|.
T Consensus        77 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~PG~~E~~~l~~i~~~~~~~~yD~IViDtaPTGhtLrlL~lP~~l~~~~~~L~  156 (254)
T cd00550          77 YRQEVLEPIEANLLLEMLKGILEEELESPGIEEIAAFDEFSRYIDEAEYDVVVFDTAPTGHTLRLLSLPTVLSWAREILS  156 (254)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHCHHHHHHHHHHCC
T ss_conf             99999998863225566888899986398589999999999997606998899889985679987515699999998537


Q ss_pred             H--CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCH------------HHHHHHHHHHCCCEEE
Q ss_conf             2--0125435787768899999999999981987675389995658987520------------0599999984895379
Q gi|254780725|r  296 L--SDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPE------------ISISDFCAPLGITPSA  361 (427)
Q Consensus       296 ~--AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~------------i~~~~~~~~lg~~~~~  361 (427)
                      .  ...+++|++|+..++..++|++..++..+.+.  ..+|+||+-++....            --.+++++.++-.+..
T Consensus       157 d~~~t~~~lV~~PE~~~v~Et~R~~~~L~~~~i~v--~~vvvN~v~p~~~~~~~~~~~r~~~q~~~l~~i~~~f~~~~v~  234 (254)
T cd00550         157 DPERTSFRLVCIPEKMSLYETERAIQELAKYGIDV--DAVIVNQLLPEDVTNCPFLEARREIQQKYLEEIEELFSDLPVA  234 (254)
T ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCC--CEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEE
T ss_conf             95655899997787216999999999999779998--9799958808776889999999999999999999870589679


Q ss_pred             EECC
Q ss_conf             9068
Q gi|254780725|r  362 IIPF  365 (427)
Q Consensus       362 ~IP~  365 (427)
                      .+|.
T Consensus       235 ~vp~  238 (254)
T cd00550         235 KLPL  238 (254)
T ss_pred             EECC
T ss_conf             8157


No 54 
>cd02035 ArsA ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes respectively. Arsenic efflux in bacteria is catalyzed by either ArsB alone or by ArsAB complex. The ATP-coupled pump, however, is more efficient. ArsA is composed of two homologous halves, A1 and A2, connected by a short linker sequence.
Probab=99.85  E-value=1.1e-20  Score=146.35  Aligned_cols=171  Identities=19%  Similarity=0.229  Sum_probs=96.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCC-CCCHHH-HHHHHHHHCCC
Q ss_conf             9997469887756899999999996269949999787989860334389987898886318-456124-33765320248
Q gi|254780725|r  164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYP-VGRIDK-AFVSRLPVFYA  241 (427)
Q Consensus       164 Iav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~-~~rlD~-~~l~~~l~~~~  241 (427)
                      |.|+++||||||||+|+|+|.++|+ .|+||++||+|++.+.....     ..++.+.... ....+. ....+......
T Consensus         1 i~~~sGKGGVGKTTvAaalA~~lA~-~G~rvLlvs~DPah~l~d~~-----~~~L~~~~~~~~~e~~~~~~~~~v~~~~~   74 (217)
T cd02035           1 VIFFTGKGGVGKTTIAAATAVRLAE-EGKKVLLVSTDPAHNLSDKG-----LPNLSDAFIVEDPEIAPNLYREEVDATRR   74 (217)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCCCCCCC-----CCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             9899789966199999999999996-89949999589876653234-----79865135888766679999875016665


Q ss_pred             CCEEEEECCC---CCC-CHHCCCH-HHHHHHHHHH-HHCCCEEEECCCCCCCH---HHHHHHHHCC--CCCCCCCCCHHH
Q ss_conf             9806872487---612-0320799-9999989998-51288899738888898---9999986201--254357877688
Q gi|254780725|r  242 ENLSILTAPA---MLS-RTYDFDE-KMIVPVLDIL-EQIFPLVILDVPHVWNS---WTQEVLTLSD--KVVITTSLDLAG  310 (427)
Q Consensus       242 ~gL~lL~a~~---~~~-~~~~~~~-~~l~~ll~~l-~~~yd~VIiD~p~~~~~---~~~~~L~~AD--~vviV~~p~~~s  310 (427)
                      ..........   ... ....+.+ -.+..+.+.+ ...|||||+|+||.-..   .....|...+  .+++|++|+..+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~pg~~E~~~l~~~~~~~~~~~yD~IVvDtpPTGhtlrlL~~~~L~d~~~t~~~lVt~Pe~~~  154 (217)
T cd02035          75 VERAWGGEGGLMLELAAALPGIEELASLLAVFREFSEGLYDVIVFDTAPTGHTLRLLVRELLTDPERTSFRLVTLPEKLP  154 (217)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHHCCCCCCEEEEEECCCCCH
T ss_conf             33311001145677761599789999999999998548998899828985569998678872488876799995776217


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf             99999999999981987675389995658987
Q gi|254780725|r  311 LRNSKNLIDVLKKLRPADKPPYLVLNQVKTPK  342 (427)
Q Consensus       311 lr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~  342 (427)
                      +.+++|++..++..+.+  ...+|+||+-++.
T Consensus       155 ~~et~r~~~~L~~~gi~--v~~vVvN~v~p~~  184 (217)
T cd02035         155 LYETERAITELALYGIP--VDAVVVNRVLPAE  184 (217)
T ss_pred             HHHHHHHHHHHHHCCCC--CCEEEEECCCCCC
T ss_conf             99999999999977998--8989895882787


No 55 
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=99.85  E-value=1.5e-20  Score=145.52  Aligned_cols=101  Identities=28%  Similarity=0.388  Sum_probs=89.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886318456124337653202489
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAE  242 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~  242 (427)
                      +|+|.+.||||||||++.|||..+++ .|.+|+++|+|+|                                        
T Consensus         1 vi~~~n~KGGvGKtt~~~~la~~~a~-~g~~vl~iD~DpQ----------------------------------------   39 (104)
T cd02042           1 VIAVANQKGGVGKTTTAVNLAAALAR-RGKRVLLIDLDPQ----------------------------------------   39 (104)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCC----------------------------------------
T ss_conf             99997389987689999999999997-7992999977988----------------------------------------


Q ss_pred             CEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH-
Q ss_conf             8068724876120320799999998999851288899738888898999998620125435787768899999999999-
Q gi|254780725|r  243 NLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVL-  321 (427)
Q Consensus       243 gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l-  321 (427)
                                                      |||||+|+|+..+..+..++..||.+++|+.|+..+++...++++.+ 
T Consensus        40 --------------------------------yD~iiIDtpp~~~~~~~~al~~aD~viiP~~p~~~~~~~~~~~~~~~~   87 (104)
T cd02042          40 --------------------------------YDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSPLDLDGLEKLLETLI   87 (104)
T ss_pred             --------------------------------CCEEEEECCCCCCHHHHHHHHHCCEEEEECCCCHHHHHHHHHHHHHHH
T ss_conf             --------------------------------888999794999899999999789999983698899999999999999


Q ss_pred             --HHCCCCCCCCEEEEE
Q ss_conf             --981987675389995
Q gi|254780725|r  322 --KKLRPADKPPYLVLN  336 (427)
Q Consensus       322 --~~~~~~~~~~~iVlN  336 (427)
                        +..++......+|+|
T Consensus        88 ~~~~~~~~~~~~~~v~~  104 (104)
T cd02042          88 LEDRLNPDLDILGILPT  104 (104)
T ss_pred             HHHHHCCCCEEEEEEEC
T ss_conf             99976999889999809


No 56 
>TIGR02016 BchX chlorophyllide reductase iron protein subunit X; InterPro: IPR010246   This entry represents the X subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase , . This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase. This subunit is homologous to the nitrogenase component II, or 'iron' protein.; GO: 0005524 ATP binding, 0016628 oxidoreductase activity acting on the CH-CH group of donors NAD or NADP as acceptor, 0051539 4 iron 4 sulfur cluster binding, 0015979 photosynthesis, 0030494 bacteriochlorophyll biosynthetic process.
Probab=99.82  E-value=9.2e-19  Score=134.54  Aligned_cols=229  Identities=19%  Similarity=0.220  Sum_probs=161.8

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCC---CCHHHH-----HH
Q ss_conf             3799974698877568999999999962699499997879898603343899878988863184---561243-----37
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPV---GRIDKA-----FV  233 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~---~rlD~~-----~l  233 (427)
                      |+|||+| |||.|||.+.+||...||. .++|||++-|||..-+++.+||-..-+|+.|+...-   .|-+++     .+
T Consensus         1 r~iAiYG-KGG~GKSFtttNLs~~~A~-mgkRVL~lGCDPKhDst~~LFGGislPT~~ev~~ekk~agreEev~~~dv~F   78 (355)
T TIGR02016         1 RIIAIYG-KGGIGKSFTTTNLSAKLAL-MGKRVLQLGCDPKHDSTSALFGGISLPTVIEVFAEKKEAGREEEVKVSDVVF   78 (355)
T ss_pred             CEEEEEC-CCCCCHHHHHHHHHHHHHH-HCCCEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEEE
T ss_conf             9588974-8898667898999999997-4682354057897332221367866750889999986518732056611787


Q ss_pred             HHHHHCCCCCEEEEEC-CCCC----CCHHCCCHHHHHHHHHHHHHCCCEEEEC-CCCC-----CCHHHHHHHHHCCCCCC
Q ss_conf             6532024898068724-8761----2032079999999899985128889973-8888-----89899999862012543
Q gi|254780725|r  234 SRLPVFYAENLSILTA-PAML----SRTYDFDEKMIVPVLDILEQIFPLVILD-VPHV-----WNSWTQEVLTLSDKVVI  302 (427)
Q Consensus       234 ~~~l~~~~~gL~lL~a-~~~~----~~~~~~~~~~l~~ll~~l~~~yd~VIiD-~p~~-----~~~~~~~~L~~AD~vvi  302 (427)
                      ++.+...+..++=+-- +...    .-.--+..-.+.+=+....=.+|||++| ++..     -.+.++.   .|.+|+|
T Consensus        79 k~~I~~~~~~vyg~ElGGPeVGRGCGGRGIi~GFd~LEKlG~~~W~~D~vlmDFLGDVVCGGFatPlaRs---laeeVi~  155 (355)
T TIGR02016        79 KRDIMNFAATVYGIELGGPEVGRGCGGRGIIFGFDLLEKLGLFEWELDFVLMDFLGDVVCGGFATPLARS---LAEEVIV  155 (355)
T ss_pred             ECCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHCCCCCCCHHHEEEECCCCEEECCCCCHHHHH---HHCCEEE
T ss_conf             2336889874578881787115546875310102566552744000200020005867756644312353---2024377


Q ss_pred             CCCCCHHHHHHHHHHHH---HHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHH--HHHHHCC
Q ss_conf             57877688999999999---999819876753899956589875200599999984895379906879999--9988479
Q gi|254780725|r  303 TTSLDLAGLRNSKNLID---VLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVF--GMSANSG  377 (427)
Q Consensus       303 V~~p~~~slr~a~~ll~---~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~--~~A~~~G  377 (427)
                      ++.-|..||..++|+.+   ++++++.+.+-..+|+||=+-    .=..+.|++.++.++.+.||+|.++.  ..+-.-.
T Consensus       156 ~~sNDrQSly~aNNic~A~~YFr~~GGr~~llGlvvNrDDG----sG~A~~fA~~~gipvLa~iP~d~~~Rdmddsfdfa  231 (355)
T TIGR02016       156 VTSNDRQSLYVANNICSAAEYFRKLGGRSKLLGLVVNRDDG----SGVAEAFAKEVGIPVLAKIPLDRKVRDMDDSFDFA  231 (355)
T ss_pred             EECCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCC----CCHHHHHHHHCCCCEEEECCCCCHHCCHHCCCHHE
T ss_conf             61374368888866988999998618860467889864688----71898989870993475267650010000000120


Q ss_pred             CCEEEECCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             6189888999899999999999852212
Q gi|254780725|r  378 KMIHEVDPKSAIANLLVDFSRVLMGRVT  405 (427)
Q Consensus       378 ~pi~e~~p~s~~a~~~~~La~~i~gr~~  405 (427)
                      .-+    |  .+.+.+.+||..+.+...
T Consensus       232 ikl----P--evGeP~K~lA~~i~~~~~  253 (355)
T TIGR02016       232 IKL----P--EVGEPFKELADDILLALA  253 (355)
T ss_pred             EEC----C--CCCCHHHHHHHHHHHHHC
T ss_conf             206----7--667647899999997424


No 57 
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=99.71  E-value=2.2e-15  Score=113.71  Aligned_cols=177  Identities=16%  Similarity=0.216  Sum_probs=131.4

Q ss_pred             CEEEEEEECCHHHHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             30599983898999999988641100202237-30699899999986189984999980598767788999888532899
Q gi|254780725|r   28 RISVHVFCVTDTLYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSG  106 (427)
Q Consensus        28 ~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~  106 (427)
                      +..|...-+++.....+.....+     .+.. +...+..+|.+.+... .|++||+|+.||.+++++.+.++.+. .|.
T Consensus         3 k~kILiVDDd~~~r~~l~~~L~~-----~g~~v~~a~~~~~al~~l~~~-~~dlvl~Di~mP~~~Gl~ll~~lr~~-~~~   75 (469)
T PRK10923          3 RGIVWVVDDDSSIRWVLERALAG-----AGLTCTTFENGNEVLEALASK-TPDVLLSDIRMPGMDGLALLKQIKQR-HPM   75 (469)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHH-----CCCEEEEECCHHHHHHHHHCC-CCCEEEECCCCCCCCHHHHHHHHHHC-CCC
T ss_conf             99799994989999999999987-----799899989999999998669-99999878999998999999999842-989


Q ss_pred             CEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCC--------CCCCC--------------------
Q ss_conf             80899816871899999997656264318999899999763102332--------22345--------------------
Q gi|254780725|r  107 TKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQ--------EEGKG--------------------  158 (427)
Q Consensus       107 ~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~--------~~~~~--------------------  158 (427)
                      ++|||++.++|+....++|++|+.|||.||+++++++.++.+.....        .+...                    
T Consensus        76 ~pvIviT~~~~~~~av~A~~~GA~dyL~KP~~~~~L~~~v~ral~~~~~~~~~~~~~~~~~~~~liG~S~~m~~v~~~i~  155 (469)
T PRK10923         76 LPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHYQEQQQPRNIQVNGPTTDIIGEAPAMQDVFRIIG  155 (469)
T ss_pred             CCEEEEECCCCHHHHHHHHHCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEECCHHHHHHHHHHH
T ss_conf             97899989999899999985570443008899999999999999999998654431210675565468999999999999


Q ss_pred             ---CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC--HHHCCCC
Q ss_conf             ---675379997469887756899999999996269949999787989860--3343899
Q gi|254780725|r  159 ---SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA--NINFDKD  213 (427)
Q Consensus       159 ---~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~--~~~l~~~  213 (427)
                         ..-.-|-+.| --|+||.++|..+ +..+.+.+.+-+.|||..-..+.  ..+||.+
T Consensus       156 ~~a~~~~pVLI~G-E~GTGK~~~Ar~I-H~~S~r~~~pfi~vnC~~~~~~~~e~eLFG~~  213 (469)
T PRK10923        156 RLSRSSISVLING-ESGTGKELVAHAL-HRHSPRAKAPFIALNMAAIPKDLIESELFGHE  213 (469)
T ss_pred             HHHCCCCCEEEEC-CCCCCHHHHHHHH-HHCCCCCCCCCEEEECCCCCHHHHHHHHHCCC
T ss_conf             9858899789989-8982699999999-97488779995787678899778999970876


No 58 
>pfam02374 ArsA_ATPase Anion-transporting ATPase. This Pfam family represents a conserved domain, which is sometimes repeated, in an anion-transporting ATPase. The ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell.
Probab=99.70  E-value=4.4e-16  Score=118.05  Aligned_cols=172  Identities=17%  Similarity=0.226  Sum_probs=99.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHH-----HCCCCCHHH-HHHHHHH
Q ss_conf             9997469887756899999999996269949999787989860334389987898886-----318456124-3376532
Q gi|254780725|r  164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDA-----IYPVGRIDK-AFVSRLP  237 (427)
Q Consensus       164 Iav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~-----l~~~~rlD~-~~l~~~l  237 (427)
                      |-|+++||||||||+|+.+|..+|+ .|+||+++-.|+.. +++-.|+++-......+     +... .+|. ..+++..
T Consensus         3 ~i~~~GKGGVGKTT~AaA~A~~~A~-~G~rvLlvStDPAh-sL~D~~~~~~g~~pt~V~~~~nL~a~-eiD~~~~~~~~~   79 (304)
T pfam02374         3 WIFFGGKGGVGKTTVSCATAVRLSE-QGKKVLLVSTDPAH-SLSDSFNQKFGHEPTKIKGVENLSAM-EIDPQMELEEYR   79 (304)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCC-HHHHHHCCCCCCCCEEECCCCCCEEE-EECHHHHHHHHH
T ss_conf             9999579857489999999999995-89929999469721-48898488679996151588982798-727899999999


Q ss_pred             HCCCCCEE-EEECCCCCCC--------HHCC-CHHHHHHHHHHHH-HCCCEEEECCCCCCCH------------HH----
Q ss_conf             02489806-8724876120--------3207-9999999899985-1288899738888898------------99----
Q gi|254780725|r  238 VFYAENLS-ILTAPAMLSR--------TYDF-DEKMIVPVLDILE-QIFPLVILDVPHVWNS------------WT----  290 (427)
Q Consensus       238 ~~~~~gL~-lL~a~~~~~~--------~~~~-~~~~l~~ll~~l~-~~yd~VIiD~p~~~~~------------~~----  290 (427)
                      ......+. ++. ......        ...+ ..-.+..+.+.+. ..||+||+|+||.-..            |.    
T Consensus        80 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~PG~~E~~al~~i~~~~~~~~yD~VV~DtaPTGhtLrlL~lP~~l~~~l~~~~  158 (304)
T pfam02374        80 GEVQDPINAVLG-ADMLEGILAEELSSLPGIDEIASFDEFKKYMDEGEYDVVIFDTAPTGHTLRLLSLPTVLSWYLEKII  158 (304)
T ss_pred             HHHHHHHHHHHC-HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHCCHHHHHHHHHHHH
T ss_conf             999999986512-2126678999983699899999999999999717887699668981779988616899999999999


Q ss_pred             ---------------------------------------HHHHHHC--CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             ---------------------------------------9998620--12543578776889999999999998198767
Q gi|254780725|r  291 ---------------------------------------QEVLTLS--DKVVITTSLDLAGLRNSKNLIDVLKKLRPADK  329 (427)
Q Consensus       291 ---------------------------------------~~~L~~A--D~vviV~~p~~~slr~a~~ll~~l~~~~~~~~  329 (427)
                                                             ...|...  ..+++|+.|+..++..+.|++..|+..+.+..
T Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~L~dp~~T~f~lV~~pe~~~i~Et~R~~~~L~~~~i~v~  238 (304)
T pfam02374       159 KLKNKIGPLAKPFKGPMGGSCLPEALESLEETKEQIEKAREILSDPERTSFRLVCIPEKMSLYETERAIQELAKYGIDVD  238 (304)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCC
T ss_conf             89998899988774013567627899999999999999999854989749999837984379999999999997799889


Q ss_pred             CCEEEEECCCCC
Q ss_conf             538999565898
Q gi|254780725|r  330 PPYLVLNQVKTP  341 (427)
Q Consensus       330 ~~~iVlNr~~~~  341 (427)
                        .+|+||+-+.
T Consensus       239 --~vvvNrvlp~  248 (304)
T pfam02374       239 --AVIVNQVLPE  248 (304)
T ss_pred             --EEEECCCCCC
T ss_conf             --7988077888


No 59 
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=99.69  E-value=5.9e-15  Score=111.11  Aligned_cols=180  Identities=15%  Similarity=0.196  Sum_probs=130.4

Q ss_pred             HCCCCCEEEEEEECCHHHHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHH
Q ss_conf             4018730599983898999999988641100202237-306998999999861899849999805987677889998885
Q gi|254780725|r   23 MCSLPRISVHVFCVTDTLYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAE  101 (427)
Q Consensus        23 ~~~~~~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~  101 (427)
                      |.+++||-|  --+++.....+....+     +.+.. ...++..+|.+.+.... |++||+|+.+|++++++.|..+.+
T Consensus         1 M~~~~rILI--VDDd~~ir~~l~~~L~-----~~G~~V~~a~~~~~Al~~l~~~~-~DlvllDi~mP~~~Glell~~ir~   72 (457)
T PRK11361          1 MTAINRILI--VDDEDNVRRMLSTAFA-----LQGFETHCANNGRTALHLFADIH-PDVVLMDIRMPEMDGIKALKEMRS   72 (457)
T ss_pred             CCCCCCEEE--ECCCHHHHHHHHHHHH-----HCCCEEEEECCHHHHHHHHHCCC-CCEEEEECCCCCCCHHHHHHHHHH
T ss_conf             999992899--8399999999999999-----77998999899999999986689-899998287999999999999982


Q ss_pred             HCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCC----------C--CCCC-----------
Q ss_conf             3289980899816871899999997656264318999899999763102332----------2--2345-----------
Q gi|254780725|r  102 VCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQ----------E--EGKG-----------  158 (427)
Q Consensus       102 ~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~----------~--~~~~-----------  158 (427)
                      . .|.++||+++.+.++....++|+.|+.|||.||++.+++...+.+.+...          .  ....           
T Consensus        73 ~-~p~~pvIvlTa~~~~~~av~A~k~GA~Dyl~KPf~~~~L~~~v~rAl~~~~l~~~~~~l~~~~~~~~~~~~lig~S~~  151 (457)
T PRK11361         73 H-ETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSMKKEIRHLHQALSTSWQWGHILTNSPA  151 (457)
T ss_pred             C-CCCCCEEEEECCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEECCHH
T ss_conf             0-989938999689998999999975966325699999999999999999988777776665432012456774546999


Q ss_pred             ------------CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC--HHHCCCC
Q ss_conf             ------------675379997469887756899999999996269949999787989860--3343899
Q gi|254780725|r  159 ------------SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA--NINFDKD  213 (427)
Q Consensus       159 ------------~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~--~~~l~~~  213 (427)
                                  ..-.-|-+.| --|+||..+|-.+ +..+.+...+-+-|||---..+.  ..+||-+
T Consensus       152 m~~v~~~i~~~A~s~~~VLI~G-EsGTGKe~~Ar~I-H~~S~r~~~pFv~vnc~ai~~~l~eseLFG~~  218 (457)
T PRK11361        152 MMDICKDTAKIALSQASVLISG-ESGTGKELIARAI-HYNSRRAKGPFIKVNCAALPESLLESELFGHE  218 (457)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEC-CCCCCHHHHHHHH-HHHCCCCCCCEEEEECCCCCHHHHHHHHHCCC
T ss_conf             9999999999848899589988-9985789999999-98379889983876478798577899971876


No 60 
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=99.68  E-value=6.4e-15  Score=110.90  Aligned_cols=166  Identities=12%  Similarity=0.181  Sum_probs=128.0

Q ss_pred             CEEEEEEECCHHHHHHHHHHHHHHHHHHCEE-EEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             3059998389899999998864110020223-730699899999986189984999980598767788999888532899
Q gi|254780725|r   28 RISVHVFCVTDTLYSVVERSKIDPRMSQVNM-RITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSG  106 (427)
Q Consensus        28 ~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~-~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~  106 (427)
                      .+.|..-.+++.....++....     +.+. .....+..+|++.+.... |++|++|+.+++.++++.|.++... +|.
T Consensus         5 ~~~ILIVDDd~~~~~~l~~~L~-----~~G~~v~~a~~~~~al~~l~~~~-~DlvllD~~mp~~~Gl~lL~~l~~~-~p~   77 (441)
T PRK10365          5 NIDILVVDDDISHCTILQALLR-----GWGYNVALANSGRQALEQVREQV-FDLVLCDVRMAEMDGIATLKEIKAL-NPA   77 (441)
T ss_pred             CCEEEEECCCHHHHHHHHHHHH-----HCCCEEEEECCHHHHHHHHHCCC-CCEEEECCCCCCCCHHHHHHHHHHH-CCC
T ss_conf             9859998398999999999999-----77998999899999999986489-9999988999999899999999842-989


Q ss_pred             CEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCC-----------CCCC-----------------
Q ss_conf             808998168718999999976562643189998999997631023322-----------2345-----------------
Q gi|254780725|r  107 TKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQE-----------EGKG-----------------  158 (427)
Q Consensus       107 ~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~-----------~~~~-----------------  158 (427)
                      ++||||+.++|+....++|+.|+.|||.||++.+++..++.+.+....           ...+                 
T Consensus        78 ~pvIviT~~~~~~~av~A~k~GA~Dyl~KP~~~~~L~~~i~~al~~~~~~~~~~~~~~~~~~~liG~S~am~~v~~~i~~  157 (441)
T PRK10365         78 IPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHSIDAETPAVSASQFGMVGKSPAMQHLLSEIAL  157 (441)
T ss_pred             CCEEEEECCCCHHHHHHHHHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHCCHHCCCCCCCCEECCHHHHHHHHHHHH
T ss_conf             82899969999899999998285123407888999999999999999876520000122257866689999999999999


Q ss_pred             --CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             --67537999746988775689999999999626994999978798
Q gi|254780725|r  159 --SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       159 --~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                        ..-.-|-+.| --|+||..+|-.+ +..+.+.+.+-+.|||-.-
T Consensus       158 ~A~s~~pVLI~G-E~GTGK~~~Ar~I-H~~S~r~~~pfv~vnC~~l  201 (441)
T PRK10365        158 VAPSEATVLIHG-DSGTGKELVARAI-HASSARSEKPLVTLNCAAL  201 (441)
T ss_pred             HHCCCCCEEEEC-CCCHHHHHHHHHH-HHCCCCCCCCCEEEECCCC
T ss_conf             848899489989-9981099999999-9657877898079878989


No 61 
>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=99.68  E-value=2.4e-15  Score=113.55  Aligned_cols=156  Identities=16%  Similarity=0.233  Sum_probs=123.9

Q ss_pred             ECCHHHHHHHHHHHHHHHHHHCEEEEEC-CCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             3898999999988641100202237306-998999999861899849999805987677889998885328998089981
Q gi|254780725|r   35 CVTDTLYSVVERSKIDPRMSQVNMRITR-GSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIG  113 (427)
Q Consensus        35 ~~~~~~~~~~~~~~~drr~~~~~~~v~~-g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig  113 (427)
                      -+|....-++++|     |.+++..|.. ++-+.++.++...|+|++||.|+.||+.|+++.|.++.+. .|..||||++
T Consensus         5 DDD~siR~VL~~A-----L~~~g~~v~~f~~A~~~l~~l~~~p~pD~~~tD~rMPg~~Gl~LL~~ik~~-~P~LPVIvM~   78 (471)
T TIGR01818         5 DDDRSIRWVLEKA-----LSRAGIEVRTFDNAASVLRALAREPQPDLLITDVRMPGEDGLDLLKQIKKR-HPKLPVIVMT   78 (471)
T ss_pred             ECCCHHHHHHHHH-----HHHCCCEEEEHHHHHHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHC-CCCCCEEEEC
T ss_conf             6471899999999-----966695453113189999998447999879861226882489999999850-8999779871


Q ss_pred             CCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCCCC-------------------C------------CCCE
Q ss_conf             68718999999976562643189998999997631023322234-------------------5------------6753
Q gi|254780725|r  114 DTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQEEGK-------------------G------------SSGC  162 (427)
Q Consensus       114 ~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~~-------------------~------------~~gr  162 (427)
                      .++|......+.+.|+.|||+||++.+|.+.-+.|......+..                   |            ....
T Consensus        79 A~~dl~~Av~a~~~GAfEYLpKPFD~de~v~lv~RA~~~~~~~~~~~~~~~~~~~~~~liG~aPAMQevfR~igRL~~~~  158 (471)
T TIGR01818        79 AHSDLDSAVAAYQRGAFEYLPKPFDLDEAVTLVERALAHAQEQVALELDAGEAEDSAELIGEAPAMQEVFRAIGRLSRSD  158 (471)
T ss_pred             CCHHHHHHHHHHHCCCHHCCCCCCCHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCC
T ss_conf             30678999999735830217698766889999998610300122200012101256212368851689999999751696


Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             79997469887756899999999996269949999
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLA  197 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLv  197 (427)
                      +-..+++-.|+||=-+|..|=. .+.+...+=+-+
T Consensus       159 l~VlI~GESGTGKELVA~ALH~-~s~R~~~PFiAl  192 (471)
T TIGR01818       159 LSVLINGESGTGKELVARALHR-HSPRARGPFIAL  192 (471)
T ss_pred             CEEEEECCCCCCHHHHHHHHHC-CCCCCCCCCEEE
T ss_conf             0588855757758999998401-375557773273


No 62 
>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]
Probab=99.60  E-value=1.2e-13  Score=103.15  Aligned_cols=163  Identities=16%  Similarity=0.221  Sum_probs=126.0

Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             59998389899999998864110020223730699899999986189984999980598767788999888532899808
Q gi|254780725|r   30 SVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKV  109 (427)
Q Consensus        30 ~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~V  109 (427)
                      +|...-++......+....++-.    +..+...+..+|.+++... .|++|++|+.|+..++++.|.++.+. +|+++|
T Consensus         6 ~iLvVDDd~~ir~~l~~~L~~~G----~~v~~a~~~~~al~~i~~~-~~~lvl~Di~mp~~~Gl~ll~~i~~~-~~~~pV   79 (464)
T COG2204           6 RILVVDDDPDIRELLEQALELAG----YEVVTAESAEEALEALSES-PFDLVLLDIRMPGMDGLELLKEIKSR-DPDLPV   79 (464)
T ss_pred             CEEEEECCHHHHHHHHHHHHHCC----CEEEEECCHHHHHHHHHCC-CCCEEEEECCCCCCCHHHHHHHHHHH-CCCCCE
T ss_conf             78999297899999999999769----7489858999999998628-99989981678999669999999963-899988


Q ss_pred             EEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCC---CC-----C------C-----------------
Q ss_conf             998168718999999976562643189998999997631023322---23-----4------5-----------------
Q gi|254780725|r  110 IVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQE---EG-----K------G-----------------  158 (427)
Q Consensus       110 ivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~---~~-----~------~-----------------  158 (427)
                      |+|+.+.|+....++|+.|+.|||.||++++.+..++.+.+....   +.     .      .                 
T Consensus        80 I~~Tg~g~i~~AV~A~k~GA~Dfl~KP~~~~~L~~~v~ral~~~~~~~e~~~~~~~~~~~~~~liG~S~am~~l~~~i~k  159 (464)
T COG2204          80 IVMTGHGDIDTAVEALRLGAFDFLEKPFDLDRLLAIVERALELRELQRENRRSLKRAKSLGGELVGESPAMQQLRRLIAK  159 (464)
T ss_pred             EEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             99828899999999985570333218999999999999999876532221000001345567752069999999999999


Q ss_pred             --CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             --675379997469887756899999999996269949999787
Q gi|254780725|r  159 --SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLD  200 (427)
Q Consensus       159 --~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlD  200 (427)
                        ..---|-+. +-.|+||-.+|-.+ +..+.+.+.+-+-|.|-
T Consensus       160 vA~s~a~VLI~-GESGtGKElvAr~I-H~~S~R~~~PFVavNca  201 (464)
T COG2204         160 VAPSDASVLIT-GESGTGKELVARAI-HQASPRAKGPFIAVNCA  201 (464)
T ss_pred             HHCCCCCEEEE-CCCCCCHHHHHHHH-HHHCCCCCCCCEEEECC
T ss_conf             84779978997-78987589999999-86074458992563346


No 63 
>TIGR01005 eps_transp_fam exopolysaccharide transport protein family; InterPro: IPR005700    The bacterial exopolysaccharide transport protein is part of a large genetic locus which is associated with exopolysaccharide (EPS) biosynthesis. Detailed molecular characterization and gene fusion analysis revealed at least seven gene products are involved in the overall regulation, which among other things, include exopolysaccharide biosynthesis, property of conferring virulence and exopolysaccharide export.; GO: 0015542 sugar efflux transmembrane transporter activity, 0006859 extracellular carbohydrate transport.
Probab=99.56  E-value=7.9e-14  Score=104.20  Aligned_cols=177  Identities=20%  Similarity=0.206  Sum_probs=143.9

Q ss_pred             CCE-EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             753-7999746988775689999999999626994999978798986033438998789888631845612433765320
Q gi|254780725|r  160 SGC-SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       160 ~gr-vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      ..+ +|.+.++..++||+.|+.|++..||. .|+|++|||.|..-+.++.+|+..+..||.|.+.+..-+..    ..-.
T Consensus       559 e~~Pvv~~~~p~p~~Gks~i~an~aaliA~-ggkR~llidad~rk~~l~q~~~~~~~~GL~d~LaG~rs~~~----~~~~  633 (778)
T TIGR01005       559 ESEPVVALASPLPDVGKSIIEANLAALIAA-GGKRVLLIDADIRKAALSQILVKAEKSGLLDLLAGERSLEL----DVKA  633 (778)
T ss_pred             CCCCEEEECCCCCCCCHHHHHHHHHHHHHC-CCCCEEEECCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHH----HCCC
T ss_conf             898758856888866568899999999832-68717873267760555644214788853755642465663----0340


Q ss_pred             CCCCCEEEEECC----CCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHH-HHHCCCCC-CCCCCCHHHHH
Q ss_conf             248980687248----7612032079999999899985128889973888889899999-86201254-35787768899
Q gi|254780725|r  239 FYAENLSILTAP----AMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEV-LTLSDKVV-ITTSLDLAGLR  312 (427)
Q Consensus       239 ~~~~gL~lL~a~----~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~-L~~AD~vv-iV~~p~~~slr  312 (427)
                      ....++.+|+++    -.....+.+-..+...+++..+..|||||||+|+...-....+ -..++.++ +|+.-+...++
T Consensus       634 ~~~~~l~~l~~GGas~~~h~~~eLLaspa~~~l~~~ar~~~D~vvvd~~~~~pV~d~~a~a~la~~~lslvt~~~r~~~~  713 (778)
T TIGR01005       634 EVAAKLDILDAGGASLLRHNSSELLASPAMVELVENARSAYDLVVVDVAAVAPVADAKALAALADLVLSLVTEYDRSVVE  713 (778)
T ss_pred             CCCCCCHHHHCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHCCEEEECCCHHHHHHHHHHHHHCCCEEEHHEEEECCEEHH
T ss_conf             23677112334761247888415321668899999886518857745531248999999742242002001111441044


Q ss_pred             HHHHHHHHHHHCCCCCCCCEEEEECCCCCCC
Q ss_conf             9999999999819876753899956589875
Q gi|254780725|r  313 NSKNLIDVLKKLRPADKPPYLVLNQVKTPKK  343 (427)
Q Consensus       313 ~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~  343 (427)
                      .....++.+...+.  .-..+|+|+.++...
T Consensus       714 ~~r~~~~~~~~~n~--~v~gV~ln~ldpn~~  742 (778)
T TIGR01005       714 LVRELLKSLSRLNS--EVLGVVLNKLDPNEL  742 (778)
T ss_pred             HHHHHHHHHHHCCC--EEEEEEECCCCCCCH
T ss_conf             42887754453186--045665045575201


No 64 
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=99.55  E-value=4.3e-13  Score=99.67  Aligned_cols=119  Identities=13%  Similarity=0.214  Sum_probs=95.9

Q ss_pred             EEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             05999838989999999886411002022373069989999998618998499998059876778899988853289980
Q gi|254780725|r   29 ISVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTK  108 (427)
Q Consensus        29 ~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~  108 (427)
                      ++|.---+++..+..+....+  ++..-......++..+|.+.+... .|++|++|+.+|.+++++.+.+|.+. .+.++
T Consensus         5 i~VLIVEDd~~v~~~l~~~L~--~~~gf~~V~~A~~~~eA~~~l~~~-~pDLvLLDi~LPd~~Glell~~lr~~-~~~~~   80 (225)
T PRK10046          5 LTLLIVEDETPLAEMHAEYIR--HIPGFSQILLAGNLAQARMMIERF-KPGLILLDNYLPDGRGINLLHELVQA-HYPGD   80 (225)
T ss_pred             CEEEEEECCHHHHHHHHHHHH--HCCCCEEEEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCHHHHHHHHHHH-CCCCC
T ss_conf             869999598999999999997--289954999989999999999735-99999982898999799999999964-87998


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             8998168718999999976562643189998999997631023
Q gi|254780725|r  109 VIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       109 Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      ||+|+..+|....+++++.||.|||+||++.+++.+++.+...
T Consensus        81 VI~iTA~~d~~~~~~Al~~Ga~DYLvKPf~~erl~~~L~~y~~  123 (225)
T PRK10046         81 VVFTTAASDMETVSEAVRCGVFDYLIKPIAYERLGQTLTRFRQ  123 (225)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCCCEECCCCHHHHHHHHHHHHH
T ss_conf             8999689999999999974998310289999999999999999


No 65 
>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.
Probab=99.51  E-value=1.5e-13  Score=102.53  Aligned_cols=111  Identities=23%  Similarity=0.194  Sum_probs=77.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCC-
Q ss_conf             9997469887756899999999996269949999787989860334389987898886318456124337653202489-
Q gi|254780725|r  164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAE-  242 (427)
Q Consensus       164 Iav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~-  242 (427)
                      |+|.| ||||||||+++++|.+|++ .+++|++||.|+.  ++..                          ++.....+ 
T Consensus         2 ia~~G-KGGvGKtt~~~~la~~l~~-~g~~vl~iD~Dp~--dlpe--------------------------~~~~~~~~~   51 (116)
T cd02034           2 IAITG-KGGVGKTTIAALLARYLAE-KGKPVLAIDADPD--DLPE--------------------------RLSVEVGEI   51 (116)
T ss_pred             EEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCC--CCHH--------------------------HHCEECCCC
T ss_conf             78988-9977499999999999997-8996999989897--1235--------------------------542331787


Q ss_pred             -CEEEEECCCCCCCH-HCCCHHHHHHHHHHH-HHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCC
Q ss_conf             -80687248761203-207999999989998-512888997388888989999986201254357
Q gi|254780725|r  243 -NLSILTAPAMLSRT-YDFDEKMIVPVLDIL-EQIFPLVILDVPHVWNSWTQEVLTLSDKVVITT  304 (427)
Q Consensus       243 -gL~lL~a~~~~~~~-~~~~~~~l~~ll~~l-~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~  304 (427)
                       .+.++......... +-.....++.+++.+ ...|+|||+|++.+..+..+......|.+++|.
T Consensus        52 ~~l~~lg~~~~~g~GC~C~~n~ll~~~l~~l~~~~~~~VvvD~eAGiEHl~Rg~~~~vD~livVs  116 (116)
T cd02034          52 KLLLVMGMGRPGGEGCYCPENALLNALLRHLVLTRDEQVVVDTEAGLEHLGRGTAEGVDLLVVVN  116 (116)
T ss_pred             CEEEEEECCCCCCCCEECCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHCCHHHCCCEEEEEC
T ss_conf             07999973435899408825789999999970679989999678548777300664399999969


No 66 
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=99.48  E-value=2.3e-12  Score=95.20  Aligned_cols=113  Identities=19%  Similarity=0.298  Sum_probs=90.2

Q ss_pred             ECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHC-CCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             3898999999988641100202237306998999999861-899849999805987677889998885328998089981
Q gi|254780725|r   35 CVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSD-SSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIG  113 (427)
Q Consensus        35 ~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~-~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig  113 (427)
                      ++|+...+-+.+..-+ +...-++.-...+..+|.+.+.. ...||+||+|+.+|.+++++.|..|.+. .|.++||+|+
T Consensus         7 VEDD~~v~~~~~~~l~-~~~gf~vv~~a~t~~eA~~~l~~~~~~~DLILLDi~mPd~~Glell~~lR~~-~~~~~VI~IT   84 (239)
T PRK10430          7 VDDDAMVAELNRRYVA-QIPGFQCCGTASTLEKAKEIIFNSDTPIDLILLDIYMQQENGLDLLPVLHEA-GCKSDVIVIS   84 (239)
T ss_pred             EECCHHHHHHHHHHHH-HCCCCEEEEEECCHHHHHHHHHCCCCCCCEEEECCCCCCCCHHHHHHHHHHH-CCCCEEEEEE
T ss_conf             9298999999999985-1899089999899999999996579998589978999999789999999985-8998199997


Q ss_pred             CCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHC
Q ss_conf             687189999999765626431899989999976310
Q gi|254780725|r  114 DTNDVSLYRALISNHVSEYLIEPLSVADIINSISAI  149 (427)
Q Consensus       114 ~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~  149 (427)
                      ..+|....+++++.||.|||+||++.+.+.+++.+-
T Consensus        85 a~~d~~~v~~Al~~Ga~DYLiKPf~~~rl~~~L~~y  120 (239)
T PRK10430         85 SAADAATIKDSLHYGVVDYLIKPFQASRFEEALTGW  120 (239)
T ss_pred             ECCCHHHHHHHHHCCCHHHEECCCCHHHHHHHHHHH
T ss_conf             268899999999839503048999999999999999


No 67 
>PRK10693 response regulator of RpoS; Provisional
Probab=99.46  E-value=6.4e-12  Score=92.46  Aligned_cols=119  Identities=18%  Similarity=0.230  Sum_probs=93.9

Q ss_pred             CCCCEEEEEEECCHHHHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHC
Q ss_conf             18730599983898999999988641100202237-30699899999986189984999980598767788999888532
Q gi|254780725|r   25 SLPRISVHVFCVTDTLYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVC  103 (427)
Q Consensus        25 ~~~~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~  103 (427)
                      |+-.-.|..--+++.....+....     .+.+.. +...+..+|++.+... .|++||+|+.||..++++.+++|++. 
T Consensus         4 pl~gkkILIVDDd~~~r~~l~~~L-----~~~G~~V~~A~nG~eAl~~l~~~-~pDLIi~Dl~MP~mdGlell~~lr~~-   76 (337)
T PRK10693          4 PLVGKQILIVEDEPVFRSLLDSWF-----SSLGATTVLAADGVDALELLGGF-TPDLMICDIAMPRMNGLKFVEHLRNR-   76 (337)
T ss_pred             CCCCCEEEEECCCHHHHHHHHHHH-----HHCCCEEEEECCHHHHHHHHHCC-CCCEEEEECCCCCCCHHHHHHHHHHH-
T ss_conf             888998999949999999999999-----97899999989999999998658-99999996899999989999999985-


Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCC-CHHHHHHHHHHCC
Q ss_conf             8998089981687189999999765626431899-9899999763102
Q gi|254780725|r  104 DSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPL-SVADIINSISAIF  150 (427)
Q Consensus       104 ~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~-~~~~l~~ai~~~~  150 (427)
                      .+.++||+++..+|..-..+++++||.|||.||+ +..++.+++.+..
T Consensus        77 ~~~~PVIvlTa~~~~~d~v~al~~GA~DyL~KPI~d~~~Lr~~v~a~l  124 (337)
T PRK10693         77 GDQTPVLVISATENMADIAKALRLGVEDVLLKPVKDLNRLREAVFACL  124 (337)
T ss_pred             CCCCEEEEEECCCCHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHH
T ss_conf             899649999868999999999974995899789699999999999875


No 68 
>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
Probab=99.44  E-value=1.4e-12  Score=96.57  Aligned_cols=95  Identities=27%  Similarity=0.347  Sum_probs=78.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886318456124337653202489
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAE  242 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~  242 (427)
                      +|+|.|.| |+||||+|+|||..|++ .|++|+++|                                            
T Consensus         1 ~i~~~~~k-GvGKTT~a~~La~~la~-~g~~Vl~vD--------------------------------------------   34 (99)
T cd01983           1 VIVVTGKG-GVGKTTLAANLAAALAK-RGKRVLLID--------------------------------------------   34 (99)
T ss_pred             CEEEECCC-CCCHHHHHHHHHHHHHH-CCCEEEEEC--------------------------------------------
T ss_conf             98985899-77689999999999998-899699986--------------------------------------------


Q ss_pred             CEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHH---HHHHHHCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             806872487612032079999999899985128889973888889899---99986201254357877688999999999
Q gi|254780725|r  243 NLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWT---QEVLTLSDKVVITTSLDLAGLRNSKNLID  319 (427)
Q Consensus       243 gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~---~~~L~~AD~vviV~~p~~~slr~a~~ll~  319 (427)
                                                       |||++|+|+..+...   ..++..+|.++++++|+..++....+..+
T Consensus        35 ---------------------------------d~iiiD~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~   81 (99)
T cd01983          35 ---------------------------------DYVLIDTPPGLGLLVLLCLLALLAADLVIIVTTPEALAVLGARRLTE   81 (99)
T ss_pred             ---------------------------------CCEEECCCCCCCHHHHHHHHHHHHCCEEEEECCCCHHHHHHHHHHHH
T ss_conf             ---------------------------------71788589988846899998787589589965984889999999999


Q ss_pred             HHHH-CCCCCCCCEEEEE
Q ss_conf             9998-1987675389995
Q gi|254780725|r  320 VLKK-LRPADKPPYLVLN  336 (427)
Q Consensus       320 ~l~~-~~~~~~~~~iVlN  336 (427)
                      .... .........+++|
T Consensus        82 ~~~~~~~~~~~~~~vv~n   99 (99)
T cd01983          82 VVLELAIEGLRPVGVVVN   99 (99)
T ss_pred             HHHHHCCCCCCEEEEECC
T ss_conf             999841069815788539


No 69 
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=99.42  E-value=2.2e-11  Score=89.20  Aligned_cols=117  Identities=11%  Similarity=0.163  Sum_probs=96.2

Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHHCEEEEE-CCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             59998389899999998864110020223730-69989999998618998499998059876778899988853289980
Q gi|254780725|r   30 SVHVFCVTDTLYSVVERSKIDPRMSQVNMRIT-RGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTK  108 (427)
Q Consensus        30 ~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~-~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~  108 (427)
                      .|..--+++.....+...     |.+.+..|. ..+..+|.+.+... .|++||+|++++..++++.+.+|++. .++++
T Consensus         5 kILiVEDd~~l~~~l~~~-----L~~~g~~v~~~~~~~~al~~~~~~-~~DlvilDi~LP~~~G~~l~~~iR~~-~~~~p   77 (229)
T PRK11083          5 TILLVEDEQAIADTLVYA-----LQSEGFTVEWFERGLPALDKLRQQ-PPDLVILDVGLPDISGFELCRQLRAF-HPALP   77 (229)
T ss_pred             EEEEEECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHHC-CCCEEEECCCCCCCCHHHHHHHHHHH-CCCCE
T ss_conf             999996999999999999-----998899999989999999999718-99899973889998768899999970-89972


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCC
Q ss_conf             899816871899999997656264318999899999763102332
Q gi|254780725|r  109 VIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQ  153 (427)
Q Consensus       109 Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~  153 (427)
                      ||+++..++..-....++.|+.||+.||+++.+|.+.+..++.+.
T Consensus        78 II~lta~~~~~d~i~~l~~GADDYl~KPf~~~EL~aRi~a~lrR~  122 (229)
T PRK11083         78 VIFLTARSDEVDRLVGLEIGADDYVAKPFSPREVAARVRTILRRV  122 (229)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHH
T ss_conf             999836789899999997599877308742899999999999764


No 70 
>cd00156 REC Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers
Probab=99.41  E-value=8.6e-12  Score=91.67  Aligned_cols=108  Identities=17%  Similarity=0.280  Sum_probs=90.7

Q ss_pred             ECCHH-HHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             38989-99999988641100202237-30699899999986189984999980598767788999888532899808998
Q gi|254780725|r   35 CVTDT-LYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVI  112 (427)
Q Consensus        35 ~~~~~-~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivi  112 (427)
                      ++|+. ....+....+.     .+.. ....+..+|++.+... .|++||+|+.+|..++++.+.++++. .|.++||++
T Consensus         3 VDD~~~~~~~l~~~L~~-----~g~~v~~a~~g~~al~~~~~~-~~dlvi~D~~mP~~~G~el~~~ir~~-~~~~pvI~l   75 (113)
T cd00156           3 VDDDPLIRELLRRLLEK-----EGYEVVEAEDGEEALALLAEE-KPDLILLDIMMPGMDGLELLRRIRKR-GPDIPIIFL   75 (113)
T ss_pred             ECCCHHHHHHHHHHHHH-----CCCEEEEECCHHHHHHHHHHC-CCCEEEECCCCCCCCCHHHHHHHHHH-CCCCCEEEE
T ss_conf             92729999999999998-----899999989999999998757-99999977999898726999999985-899959999


Q ss_pred             ECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHC
Q ss_conf             1687189999999765626431899989999976310
Q gi|254780725|r  113 GDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAI  149 (427)
Q Consensus       113 g~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~  149 (427)
                      +..++.....++++.|+.+|+.||++..++..++.++
T Consensus        76 T~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~v~~~  112 (113)
T cd00156          76 TAHGDDEDAVEALKAGADDYLTKPFSPEELLARIRAL  112 (113)
T ss_pred             ECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
T ss_conf             7878999999999768978996989999999999986


No 71 
>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
Probab=99.40  E-value=9.1e-12  Score=91.52  Aligned_cols=103  Identities=17%  Similarity=0.329  Sum_probs=90.1

Q ss_pred             HHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCC
Q ss_conf             11002022373069989999998618998499998059876778899988853289980899816871899999997656
Q gi|254780725|r   50 DPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHV  129 (427)
Q Consensus        50 drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv  129 (427)
                      |..=-+.++.-.+-+...|.+.++..+ |++||.|+.||..+|++.++.+.+. .|.+.+|+++..+|-.-.+.+|+.||
T Consensus        22 ~w~~~g~eiVgtA~NG~eAleli~e~~-pDiviTDI~MP~mdGLdLI~~ike~-~p~~~~IILSGy~eFeYak~Am~lGV   99 (475)
T COG4753          22 DWEALGIEVVGTAANGKEALELIQETQ-PDIVITDINMPGMDGLDLIKAIKEQ-SPDTEFIILSGYDEFEYAKKAMKLGV   99 (475)
T ss_pred             CHHHCCCEEEEECCCHHHHHHHHHHCC-CCEEEEECCCCCCCHHHHHHHHHHH-CCCCEEEEEECCCHHHHHHHHHHCCC
T ss_conf             856369757875145799999987349-9789981578887579999999974-99853999846420589999986185


Q ss_pred             CEEECCCCCHHHHHHHHHHCCCCCC
Q ss_conf             2643189998999997631023322
Q gi|254780725|r  130 SEYLIEPLSVADIINSISAIFTPQE  154 (427)
Q Consensus       130 ~dyl~~P~~~~~l~~ai~~~~~~~~  154 (427)
                      .|||.||++..++..++.++.+.-.
T Consensus       100 ~dYLLKP~~k~eL~~~L~ki~~kl~  124 (475)
T COG4753         100 KDYLLKPVDKAELEEALKKIIGKLE  124 (475)
T ss_pred             HHHEECCCCHHHHHHHHHHHHHHHH
T ss_conf             2122076989999999999999999


No 72 
>pfam00072 Response_reg Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.
Probab=99.39  E-value=2e-11  Score=89.38  Aligned_cols=106  Identities=14%  Similarity=0.217  Sum_probs=89.3

Q ss_pred             ECCHHHHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             3898999999988641100202237-306998999999861899849999805987677889998885328998089981
Q gi|254780725|r   35 CVTDTLYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIG  113 (427)
Q Consensus        35 ~~~~~~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig  113 (427)
                      -+++.....+....+.     .+.. ....+..+|++.++.. .|++||+|+.+|..++++.+.++++. .|.++||+++
T Consensus         5 DD~~~~~~~l~~~L~~-----~g~~v~~a~~g~~al~~~~~~-~~dlvi~Di~mP~~dG~el~~~ir~~-~~~~piI~~T   77 (111)
T pfam00072         5 DDDPLIRELLRQLLEK-----EGYVVAEADDGEEALELLKEK-RPDLILLDIRMPGMDGLELLRRIRRR-PPTTPVIVLT   77 (111)
T ss_pred             ECCHHHHHHHHHHHHH-----CCCEEEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCHHHHHHHHHHC-CCCCEEEEEE
T ss_conf             8989999999999998-----899999989999999999847-99899995368995015799999735-9998099997


Q ss_pred             CCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHH
Q ss_conf             6871899999997656264318999899999763
Q gi|254780725|r  114 DTNDVSLYRALISNHVSEYLIEPLSVADIINSIS  147 (427)
Q Consensus       114 ~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~  147 (427)
                      ..++.....+++++|+.||+.||++..++.++++
T Consensus        78 ~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~ir  111 (111)
T pfam00072        78 AHGDEEDAVEALKAGANDFLSKPFDPEELVAALR  111 (111)
T ss_pred             CCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHCC
T ss_conf             5089999999997798779949999899998529


No 73 
>TIGR00345 arsA arsenite-activated ATPase (arsA); InterPro: IPR003348   This ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell.    In Escherichia coli an anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773. This ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance .   The ArsA and ArsB proteins form a membrane-bound pump that functions as an oxyanion-translocating ATPase. The ArsC protein is an arsenate reductase that reduces arsenate to arsenite, which is subsequently pumped out of the cell .; GO: 0005524 ATP binding, 0006820 anion transport, 0016020 membrane.
Probab=99.38  E-value=1.8e-12  Score=95.81  Aligned_cols=171  Identities=21%  Similarity=0.258  Sum_probs=95.0

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCCHHHCCCCCCCCHH-----HHHCCCCCHHH---------
Q ss_conf             974698877568999999999962-699499997879898603343899878988-----86318456124---------
Q gi|254780725|r  166 FIGSRGGVGSSTIAHNCAFSIASV-FAMETLLADLDLPYGTANINFDKDPINSIS-----DAIYPVGRIDK---------  230 (427)
Q Consensus       166 v~g~KGGvGkTTiA~nLA~~LA~~-~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~-----d~l~~~~rlD~---------  230 (427)
                      |+|+||||||||+++..|..||++ .|++||||=-||.+ +++-.|+.+-+++..     +-|... .+|+         
T Consensus         1 f~gGKGGVGKTt~SaAtA~~lAe~qPGkkvLl~STDPAH-sL~D~F~~e~G~~~~kv~g~eNL~~~-EIDp~~al~~y~~   78 (330)
T TIGR00345         1 FFGGKGGVGKTTISAATAIRLAEQQPGKKVLLVSTDPAH-SLSDVFEQELGHEPTKVKGVENLSAV-EIDPQAALEEYRA   78 (330)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCH-HHHHHHHHHHCCCCCEEECCCCCEEE-EECHHHHHHHHHH
T ss_conf             977878823888999999999851899779998408600-27886113217773032058985555-1037899998799


Q ss_pred             ---HHHHHHHHCCCCCE-EEEEC-------C----CCCCCHHCCCHHHHHHHHHHHH-HC---CCEEEECCCC-------
Q ss_conf             ---33765320248980-68724-------8----7612032079999999899985-12---8889973888-------
Q gi|254780725|r  231 ---AFVSRLPVFYAENL-SILTA-------P----AMLSRTYDFDEKMIVPVLDILE-QI---FPLVILDVPH-------  284 (427)
Q Consensus       231 ---~~l~~~l~~~~~gL-~lL~a-------~----~~~~~~~~~~~~~l~~ll~~l~-~~---yd~VIiD~p~-------  284 (427)
                         .+.+++......|+ +.|-.       .    .-|.-.+-..-..+...++... ..   ||+||+|+.|       
T Consensus        79 rvf~~~~~i~~~~~~~~~~~l~~ql~~~~~~dltGsiPGiDE~~~F~~~~k~~~~~~~~e~etyD~vIfDTAPTGHTLRL  158 (330)
T TIGR00345        79 RVFKLKEQIKQNLSLGVVDMLEDQLEGAALSDLTGSIPGIDEIAAFDEFLKHMDEAELNERETYDVVIFDTAPTGHTLRL  158 (330)
T ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHH
T ss_conf             99999999860678873202799999877775227998588999999999876543215676234688716974677753


Q ss_pred             -----CCCHHHH-------------------------------------------------HHHHH--CCCCCCCCCCCH
Q ss_conf             -----8898999-------------------------------------------------99862--012543578776
Q gi|254780725|r  285 -----VWNSWTQ-------------------------------------------------EVLTL--SDKVVITTSLDL  308 (427)
Q Consensus       285 -----~~~~~~~-------------------------------------------------~~L~~--AD~vviV~~p~~  308 (427)
                           .|+.|..                                                 .+|.-  =..+++|+.|+-
T Consensus       159 L~lP~~~~~~~~~~~k~~~~~g~~~~~~~~~Lpf~G~~~~l~~~~~l~~~~e~Ke~~~~~~~~l~DP~~T~f~~V~~pE~  238 (330)
T TIGR00345       159 LQLPEVLSKFLEKFIKLREKLGPMLKLFKELLPFMGAGESLEDDEALEKLEELKEQIEAAREVLSDPERTSFVLVVIPEK  238 (330)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCC
T ss_conf             10023679999874356777889887664105789898878778999989999999999999724998516888860262


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf             88999999999999819876753899956589
Q gi|254780725|r  309 AGLRNSKNLIDVLKKLRPADKPPYLVLNQVKT  340 (427)
Q Consensus       309 ~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~  340 (427)
                      .++..+.|++..|...+....  .||+|++-+
T Consensus       239 ~~l~E~~R~~~~L~~Y~~~~~--~vIvN~vLP  268 (330)
T TIGR00345       239 MSLYESERAHKELKKYGIKVD--AVIVNQVLP  268 (330)
T ss_pred             CCHHHHHHHHHHHHHCCCCCC--EEEECCCCC
T ss_conf             427899999999986498504--478702257


No 74 
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=99.37  E-value=3.8e-11  Score=87.73  Aligned_cols=115  Identities=9%  Similarity=0.189  Sum_probs=96.2

Q ss_pred             EEEEECCHHHHHHHHHHHHHHHHHHCEEEEE-CCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             9998389899999998864110020223730-699899999986189984999980598767788999888532899808
Q gi|254780725|r   31 VHVFCVTDTLYSVVERSKIDPRMSQVNMRIT-RGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKV  109 (427)
Q Consensus        31 ~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~-~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~V  109 (427)
                      |..--++......+...     |.+.+..|. ..+..+|.+.+... .|++||+|+.+|..++++.+.++++. .+++||
T Consensus         3 ILiVEDd~~l~~~l~~~-----L~~~G~~v~~a~~g~~a~~~~~~~-~~DlvilDi~lP~~~G~~l~~~iR~~-~~~~PI   75 (226)
T PRK09836          3 LLIVEDEKKTGEYLTKG-----LTEAGFVVDLADNGLNGYHLAMTG-DYDLIILDIMLPDVNGWDIVRMLRSA-NKGMPI   75 (226)
T ss_pred             EEEEECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHHC-CCCEEEECCCCCCCCCCCHHHHHHHH-CCCCEE
T ss_conf             99993999999999999-----987899999989999999998518-99999988999999872043567761-679609


Q ss_pred             EEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             9981687189999999765626431899989999976310233
Q gi|254780725|r  110 IVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       110 ivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      |+++..+|..-...++..|+.||+.||++..++.+.+..++.+
T Consensus        76 I~Lta~~~~~d~i~~l~~GADDYl~KPf~~~EL~aRi~allrr  118 (226)
T PRK09836         76 LLLTALGTIEHRVKGLELGADDYLVKPFAFAELLARVRTLLRR  118 (226)
T ss_pred             EEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCC
T ss_conf             9994458988999999769968863687679999999999662


No 75 
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=99.37  E-value=1.6e-11  Score=90.06  Aligned_cols=117  Identities=14%  Similarity=0.158  Sum_probs=92.0

Q ss_pred             CEEEEEEECCHHHHHHHHHHHHHHHHHHCEEEE-ECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             305999838989999999886411002022373-0699899999986189984999980598767788999888532899
Q gi|254780725|r   28 RISVHVFCVTDTLYSVVERSKIDPRMSQVNMRI-TRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSG  106 (427)
Q Consensus        28 ~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v-~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~  106 (427)
                      |-+|.---+.+-....++...+     ...+.| ...+..++.+.+... .|+++|+|+++|+.++++.+.+|.+. .|.
T Consensus         3 k~tIliVDDh~~vr~gl~~lL~-----~~~~~v~~~~~~~~~l~~~~~~-~pdlvllDi~mP~~~G~e~l~~l~~~-~p~   75 (202)
T PRK09390          3 KGVVHVVDDDEAMRDSLAFLLD-----SAGFEVRLFESAQAFLDALPGL-RFGCVVTDVRMPGIDGIELLRRLKAR-GSP   75 (202)
T ss_pred             CCEEEEECCCHHHHHHHHHHHH-----HCCCEEEEECCHHHHHHHHHCC-CCCEEEECCCCCCCCCHHHHHHHHHC-CCC
T ss_conf             9979998499999999999999-----8899899989999999997657-97999877999998960799998722-899


Q ss_pred             CEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             808998168718999999976562643189998999997631023
Q gi|254780725|r  107 TKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       107 ~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      ++||+++.+.|.....+++++|+++|+.||.+.+++++++.+.+.
T Consensus        76 ~~vivlT~~~~~~~~~~al~~GA~gyl~K~~~~~~L~~aI~~~l~  120 (202)
T PRK09390         76 LPVIVMTGHGDVPLAVEAMKLGAIDFIEKPFEDERLIGAIERALA  120 (202)
T ss_pred             CCEEEEEECCCHHHHHHHHHCCCHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             867999745748888999982946445599999999999999997


No 76 
>PRK10610 chemotaxis regulatory protein CheY; Provisional
Probab=99.36  E-value=5.7e-11  Score=86.62  Aligned_cols=120  Identities=13%  Similarity=0.135  Sum_probs=97.9

Q ss_pred             CEEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHC-CCC
Q ss_conf             3059998389899999998864110020223730699899999986189984999980598767788999888532-899
Q gi|254780725|r   28 RISVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVC-DSG  106 (427)
Q Consensus        28 ~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~-~p~  106 (427)
                      ++.|..--+++.....++...+...+.   .-....+..+|++.+... .|++|++|..+|..++++.+..+++.. .+.
T Consensus         5 ~lrILivDD~~~~r~~l~~~L~~~g~~---~v~~a~~g~~al~~~~~~-~~Dlil~D~~MP~~dG~el~~~ir~~~~~~~   80 (129)
T PRK10610          5 ELKFLVVDDFSTMRRIVRNLLKELGFN---NVEEAEDGVDALNKLQAG-GFGFVISDWNMPNMDGLELLKTIRADGAMSA   80 (129)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCC---EEEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCHHHHHHHHHHCCCCCC
T ss_conf             989999979899999999999986997---899989999999999858-9999998189999989999999985777789


Q ss_pred             CEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             808998168718999999976562643189998999997631023
Q gi|254780725|r  107 TKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       107 ~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      +|||+++...+.....+++++|+.+||.||++..++.+.+.+++.
T Consensus        81 ~Pii~~T~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~vl~  125 (129)
T PRK10610         81 LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFE  125 (129)
T ss_pred             CCEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHH
T ss_conf             968999886899999999986998899898999999999999997


No 77 
>PRK09581 pleD response regulator PleD; Reviewed
Probab=99.35  E-value=4.8e-11  Score=87.06  Aligned_cols=114  Identities=16%  Similarity=0.229  Sum_probs=88.9

Q ss_pred             CCEEEEEEECC-HHHHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHH-C
Q ss_conf             73059998389-8999999988641100202237-3069989999998618998499998059876778899988853-2
Q gi|254780725|r   27 PRISVHVFCVT-DTLYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEV-C  103 (427)
Q Consensus        27 ~~~~~~~f~~~-~~~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~-~  103 (427)
                      +||-|   ++| +....++...     |.+.+.. +...+..+|++.+... .|++|++|+.||++++++.+.+|.+. .
T Consensus         3 ~rILi---VdD~~~~~~~l~~~-----L~~~~y~v~~a~~G~eAL~~~~~~-~PDLILlDi~MP~mdG~ev~r~Lk~~~~   73 (457)
T PRK09581          3 ARILV---VDDIPANVKLLEAK-----LLAEYYTVLTASSGAEAIEICERE-QPDIILLDVMMPGMDGFEVCRRLKSDPA   73 (457)
T ss_pred             CCEEE---ECCCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCHHHHHHHHHCCCC
T ss_conf             71999---94989999999999-----987899999989999999999718-9998999287799999999999965988


Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHC
Q ss_conf             8998089981687189999999765626431899989999976310
Q gi|254780725|r  104 DSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAI  149 (427)
Q Consensus       104 ~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~  149 (427)
                      ...+|||+++..+|.....+++++|+.|||.||++..++...++.+
T Consensus        74 ~~~iPVIvlTa~~d~e~~~~al~~GA~DYL~KP~~~~~L~~ri~~l  119 (457)
T PRK09581         74 TAHIPVVMVTALDDPSDRVRGLEAGADDFLTKPINDVALFARVKSL  119 (457)
T ss_pred             CCCCEEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
T ss_conf             8998499997899999999998648878998999989999999999


No 78 
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=99.35  E-value=3.2e-11  Score=88.13  Aligned_cols=113  Identities=9%  Similarity=0.153  Sum_probs=94.7

Q ss_pred             EEECCHHHHHHHHHHHHHHHHHHCEEEEE-CCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             98389899999998864110020223730-69989999998618998499998059876778899988853289980899
Q gi|254780725|r   33 VFCVTDTLYSVVERSKIDPRMSQVNMRIT-RGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIV  111 (427)
Q Consensus        33 ~f~~~~~~~~~~~~~~~drr~~~~~~~v~-~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Viv  111 (427)
                      .--+++.....+...     |.+.+..|. ..+..+|.+.+... .|+++|+|+.+|..++++.+.++++. .+.+|||+
T Consensus         5 lVEDd~~l~~~l~~~-----L~~~g~~V~~a~~g~~a~~~~~~~-~~DlvilDi~lP~~dG~~l~~~iR~~-~~~~PII~   77 (219)
T PRK10336          5 LIEDDMLIGDGIKTG-----LSKMGFSVDWFTQGRQGKEALYSA-PYDAVILDLTLPGMDGRDILREWREK-GQREPVLI   77 (219)
T ss_pred             EEECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHCC-CCCEEEEECCCCCCCCCCCCCCHHHH-CCCCCEEE
T ss_conf             993899999999999-----998799999989999999998628-96999997999999856310104652-78887899


Q ss_pred             EECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             81687189999999765626431899989999976310233
Q gi|254780725|r  112 IGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       112 ig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      ++..++..-..+.+.+|+.||+.||+++.++.+.+..++.+
T Consensus        78 lta~~~~~d~i~~l~~GAdDYl~KPf~~~eL~ari~allrr  118 (219)
T PRK10336         78 LTARDALAERVEGLRLGADDYLCKPFALIEVAARLEALMRR  118 (219)
T ss_pred             EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH
T ss_conf             80689999999999769988868897679999999999611


No 79 
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=99.35  E-value=5.3e-11  Score=86.81  Aligned_cols=116  Identities=13%  Similarity=0.202  Sum_probs=95.4

Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHHCEEEEE-CCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             59998389899999998864110020223730-69989999998618998499998059876778899988853289980
Q gi|254780725|r   30 SVHVFCVTDTLYSVVERSKIDPRMSQVNMRIT-RGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTK  108 (427)
Q Consensus        30 ~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~-~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~  108 (427)
                      .|..--+++.....+....     .+.+..|. ..+..+|.+.+... .|++||+|+.+|+.++++.+..|++. .+.+|
T Consensus         7 kILiVEDd~~~~~~l~~~L-----~~~g~~v~~a~~~~~a~~~~~~~-~~DlvilDi~lp~~dG~~l~~~iR~~-~~~~p   79 (239)
T PRK09468          7 KILVVDDDMRLRALLERYL-----TEQGFQVRSAANAEQMDRLLTRE-SFHLMVLDLMLPGEDGLSICRRLRSQ-NNPTP   79 (239)
T ss_pred             EEEEEECCHHHHHHHHHHH-----HHCCCEEEEECCHHHHHHHHHHC-CCCEEEECCCCCCCCCCHHHHHHHHH-CCCCC
T ss_conf             8999909999999999999-----98899999989999999999758-99899987899888873467778750-57877


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             89981687189999999765626431899989999976310233
Q gi|254780725|r  109 VIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       109 Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      ||+++..+|..-...++..|+.||+.||++..+|.+.+..++.+
T Consensus        80 II~LTa~~~~~d~i~~l~~GADDYi~KPf~~~EL~aRI~allrR  123 (239)
T PRK09468         80 IIMLTAKGEEVDRIVGLEMGADDYLPKPFNPRELLARIRAVLRR  123 (239)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH
T ss_conf             89994667878999999769868855899989999999999863


No 80 
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=99.30  E-value=1.1e-10  Score=84.79  Aligned_cols=117  Identities=14%  Similarity=0.199  Sum_probs=96.2

Q ss_pred             EEEEECCHHHHHHHHHHHHHHHHHHCEEEE-ECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHH-CCCCCE
Q ss_conf             999838989999999886411002022373-069989999998618998499998059876778899988853-289980
Q gi|254780725|r   31 VHVFCVTDTLYSVVERSKIDPRMSQVNMRI-TRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEV-CDSGTK  108 (427)
Q Consensus        31 ~~~f~~~~~~~~~~~~~~~drr~~~~~~~v-~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~-~~p~~~  108 (427)
                      |..--+++.....+...     |.+.+..| ...+..+|.+.+... .|+++|+|+.+|..++++.+..|++. +.+++|
T Consensus         5 ILiVEDd~~l~~~l~~~-----L~~~g~~v~~a~~g~~a~~~l~~~-~~DliilDi~lP~~dG~~~~~~ir~~~~~~~~P   78 (229)
T PRK10161          5 ILVVEDEAPIREMVCFV-----LEQNGFQPVEAEDYDSAVNQLNEP-WPDLILLDWMLPGGSGIQFIKHLKRESMTRDIP   78 (229)
T ss_pred             EEEEECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHCC-CCCEEEEECCCCCCCCHHHHHHHHHCCCCCCCC
T ss_conf             99995999999999999-----997799999989999999998528-998999978998876335878877502468975


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCC
Q ss_conf             899816871899999997656264318999899999763102332
Q gi|254780725|r  109 VIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQ  153 (427)
Q Consensus       109 Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~  153 (427)
                      ||+++..++..-....+..|+.||+.||+++.+|++.+..++.+.
T Consensus        79 II~lta~~~~~d~v~gl~~GADDYl~KPf~~~EL~aRi~a~lrR~  123 (229)
T PRK10161         79 VVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRI  123 (229)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHC
T ss_conf             899955666577999987698765208999899999999997123


No 81 
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=99.30  E-value=1.4e-10  Score=84.26  Aligned_cols=114  Identities=15%  Similarity=0.202  Sum_probs=95.7

Q ss_pred             EEEEECCHHHHHHHHHHHHHHHHHHCEEEEE-CCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             9998389899999998864110020223730-699899999986189984999980598767788999888532899808
Q gi|254780725|r   31 VHVFCVTDTLYSVVERSKIDPRMSQVNMRIT-RGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKV  109 (427)
Q Consensus        31 ~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~-~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~V  109 (427)
                      |..--++++....+...     |.+.+..|. ..+..+|.+.+... .|++||+|+.+|..++++.+..+++.  ..+||
T Consensus         3 ILiVEDd~~l~~~l~~~-----L~~~g~~V~~a~~g~~al~~~~~~-~~DlvilDi~lP~~dG~~l~~~iR~~--~~~pI   74 (223)
T PRK11517          3 ILLIEDNQRTQEWVTQG-----LSEAGYVIDAVSDGRDGLYLALKD-DYALIILDIMLPGMDGWQILQTLRTA--KQTPV   74 (223)
T ss_pred             EEEEECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHCC-CCCEEEECCCCCCCCHHHHHHHHHHC--CCCCE
T ss_conf             99996989999999999-----998899999989999999998528-99999984999873689999999856--88648


Q ss_pred             EEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             9981687189999999765626431899989999976310233
Q gi|254780725|r  110 IVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       110 ivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      |+++..++..-....+..|+.||+.||++..++.+.+..++.+
T Consensus        75 I~lta~~~~~d~i~~l~~GADDYl~KPf~~~EL~aRi~a~lrr  117 (223)
T PRK11517         75 ICLTARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQ  117 (223)
T ss_pred             EEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCC
T ss_conf             9995655657899999839877620897789999999999641


No 82 
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=99.29  E-value=2.9e-10  Score=82.24  Aligned_cols=116  Identities=16%  Similarity=0.246  Sum_probs=95.7

Q ss_pred             EEEECCHHHHHHHHHHHHHHHHHHCEEEEEC-CCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             9983898999999988641100202237306-998999999861899849999805987677889998885328998089
Q gi|254780725|r   32 HVFCVTDTLYSVVERSKIDPRMSQVNMRITR-GSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVI  110 (427)
Q Consensus        32 ~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~-g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vi  110 (427)
                      ..--++++....+...     +.+.++.|.. .+..+|.+.....  |++||+|+.+|..++++.+.++++.-...+|||
T Consensus         4 LiveDd~~i~~~l~~~-----L~~~G~~v~~~~~~~~a~~~~~~~--~dlviLD~~lP~~dG~~~~~~iR~~~~~~~PIi   76 (229)
T COG0745           4 LLVEDDPELAELLKEY-----LEEEGYEVDVAADGEEALEAAREQ--PDLVLLDLMLPDLDGLELCRRLRAKKGSGPPII   76 (229)
T ss_pred             EEEECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHCC--CCEEEEECCCCCCCHHHHHHHHHHCCCCCCCEE
T ss_conf             9991888999999999-----987597899978989999997269--999999889998568999999985168999889


Q ss_pred             EEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCC
Q ss_conf             98168718999999976562643189998999997631023322
Q gi|254780725|r  111 VIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQE  154 (427)
Q Consensus       111 vig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~  154 (427)
                      +++...+..-....+.+|+.||+.||+++.++.+.+..++.+..
T Consensus        77 ~Lta~~~~~d~v~gl~~GADDYl~KPf~~~EL~ARi~a~lRR~~  120 (229)
T COG0745          77 VLTARDDEEDRVLGLEAGADDYLTKPFSPRELLARLRALLRRNA  120 (229)
T ss_pred             EEECCCCHHHHHHHHHCCCHHHCCCCCCHHHHHHHHHHHHCCCC
T ss_conf             99668728889999975634233488998999999999967365


No 83 
>CHL00148 orf27 Ycf27; Reviewed
Probab=99.28  E-value=9e-11  Score=85.41  Aligned_cols=115  Identities=18%  Similarity=0.284  Sum_probs=95.6

Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             599983898999999988641100202237-3069989999998618998499998059876778899988853289980
Q gi|254780725|r   30 SVHVFCVTDTLYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTK  108 (427)
Q Consensus        30 ~~~~f~~~~~~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~  108 (427)
                      .|..--++++....+....     .+.+.. ....+..+|.+.+... .|++||+|+++|..++++.+.+|++.  .++|
T Consensus         8 kILiVEDd~~l~~~l~~~L-----~~~G~~v~~a~~g~~a~~~~~~~-~~DlviLDi~LP~~dG~~l~~~iR~~--~~~P   79 (240)
T CHL00148          8 KILVVDDEASIRRILETRL-----SIIGYEVITASDGEEALKLFHQE-QPDLVILDVMMPKLDGYGVCQEIRKE--SDVP   79 (240)
T ss_pred             EEEEEECCHHHHHHHHHHH-----HHCCCEEEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCCCEEEECCCCC--CCCC
T ss_conf             2999939899999999999-----97899999989999999999747-99999997999988866305414037--9954


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             89981687189999999765626431899989999976310233
Q gi|254780725|r  109 VIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       109 Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      ||+++..++..-....+.+|+.||+.||+++.+|.+.+..++.+
T Consensus        80 II~LTa~~~~~d~v~gl~~GADDYi~KPf~~~EL~aRi~allrr  123 (240)
T CHL00148         80 IIMLTALGDVSDRITGLELGADDYVVKPFSPKELEARIRSVLRR  123 (240)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH
T ss_conf             89981678989999999769978952784479999999999866


No 84 
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=99.27  E-value=1.1e-10  Score=84.77  Aligned_cols=118  Identities=14%  Similarity=0.206  Sum_probs=96.9

Q ss_pred             CCCCEEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEE-CCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHC
Q ss_conf             1873059998389899999998864110020223730-699899999986189984999980598767788999888532
Q gi|254780725|r   25 SLPRISVHVFCVTDTLYSVVERSKIDPRMSQVNMRIT-RGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVC  103 (427)
Q Consensus        25 ~~~~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~-~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~  103 (427)
                      .-|||-|  --+++.....+...     |.+.++.|. ..+..+|.+.+... .|++||+|++++..++++.+.+|++. 
T Consensus         9 ~~~kILl--VEDd~~l~~~l~~~-----L~~~g~~V~~a~~~~eal~~~~~~-~~DliilDi~lp~~~Gl~l~~~lr~~-   79 (240)
T PRK10710          9 NTPRILI--VEDEPKLGQLLIDY-----LRAASYAPTLISHGDEVLPYVRQT-PPDLILLDLMLPGTDGLTLCREIRRF-   79 (240)
T ss_pred             CCCEEEE--EECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHHC-CCCEEEECCCCCCCCCCCCHHHHHCC-
T ss_conf             9887999--92989999999999-----998899999989999999999737-99899987999888776321122115-


Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             8998089981687189999999765626431899989999976310233
Q gi|254780725|r  104 DSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       104 ~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                       ++++||+++...+..-...++.+|+.||+.||++..++.+.+..+..+
T Consensus        80 -~~~piI~lta~~~~~~~~~al~~GAddYl~KPf~~~eLlari~~~lrr  127 (240)
T PRK10710         80 -SDIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTILRR  127 (240)
T ss_pred             -CCCCEEEECCCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHHHHH
T ss_conf             -764689981678889999999869987600776538999999999845


No 85 
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=99.26  E-value=2.4e-10  Score=82.74  Aligned_cols=115  Identities=11%  Similarity=0.171  Sum_probs=94.6

Q ss_pred             EEEEECCHHHHHHHHHHHHHHHHHHCEEEEE-CCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             9998389899999998864110020223730-699899999986189984999980598767788999888532899808
Q gi|254780725|r   31 VHVFCVTDTLYSVVERSKIDPRMSQVNMRIT-RGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKV  109 (427)
Q Consensus        31 ~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~-~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~V  109 (427)
                      |.---+++.....+...     |.+.++.|. .++..+|.+.+.... |+++|+|+.++..++++.+.++.+. .+.+||
T Consensus         3 ILlVEDd~~~~~~l~~~-----L~~~g~~V~~a~~~~ea~~~~~~~~-~DlvilDi~lp~~~G~~l~~~ir~~-~~~~pI   75 (222)
T PRK10643          3 ILIVEDDTLLLQGLILA-----AQTEGYACDGVSTAREAEQSLESGH-YSLVVLDLGLPDEDGLHFLARIRQK-KYTLPV   75 (222)
T ss_pred             EEEEECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHHCC-CCEEEEECCCCCCCCHHHHHHHHHC-CCCCCE
T ss_conf             99992889999999999-----9978999999899999999997489-9899996888998622689999834-899889


Q ss_pred             EEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             9981687189999999765626431899989999976310233
Q gi|254780725|r  110 IVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       110 ivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      |+++..++..-...++.+|+.||+.||++..++.+.+..+...
T Consensus        76 I~lt~~~~~~~~~~~l~~GAddyi~KP~~~~eL~ari~~~lrr  118 (222)
T PRK10643         76 LILTARDTLEDRIAGLDVGADDYLVKPFALEELHARIRALLRR  118 (222)
T ss_pred             EEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH
T ss_conf             9982103678899999759977643887689999999999703


No 86 
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=99.26  E-value=2.2e-10  Score=82.95  Aligned_cols=112  Identities=13%  Similarity=0.245  Sum_probs=92.7

Q ss_pred             EECCHHHHHHHHHHHHHHHHHHCEEEE-ECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             838989999999886411002022373-0699899999986189984999980598767788999888532899808998
Q gi|254780725|r   34 FCVTDTLYSVVERSKIDPRMSQVNMRI-TRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVI  112 (427)
Q Consensus        34 f~~~~~~~~~~~~~~~drr~~~~~~~v-~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivi  112 (427)
                      --++......+...     +...+..| ...+..+|.+.+... .|+++|+|+.+++.++++.+.++++. .+.+|||++
T Consensus         6 vEdd~~~~~~l~~~-----L~~~g~~V~~a~~~~~al~~~~~~-~~dlvilD~~lp~~~G~~l~~~ir~~-~~~~piI~l   78 (223)
T PRK10816          6 VEDNALLRHHLKVQ-----LQDAGHQVDAAEDAKEADYYLNEH-LPDIAIVDLGLPDEDGLSLIRRWRSN-DVSLPILVL   78 (223)
T ss_pred             EECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCCCCCCCCHHCC-CCCCCEEEE
T ss_conf             95989999999999-----997899999989999999999757-99899997999898864001201104-898768999


Q ss_pred             ECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             1687189999999765626431899989999976310233
Q gi|254780725|r  113 GDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       113 g~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      +..++..-..+++.+|+.||+.||++..++...+..+..+
T Consensus        79 ta~~~~~~~~~al~~Gaddyl~KP~~~~eL~arv~~~lrr  118 (223)
T PRK10816         79 TARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRR  118 (223)
T ss_pred             ECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHHHCC
T ss_conf             4445677899999869988641897778999999999665


No 87 
>PRK09483 response regulator; Provisional
Probab=99.25  E-value=3.9e-10  Score=81.46  Aligned_cols=118  Identities=12%  Similarity=0.185  Sum_probs=96.0

Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             59998389899999998864110020223730699899999986189984999980598767788999888532899808
Q gi|254780725|r   30 SVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKV  109 (427)
Q Consensus        30 ~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~V  109 (427)
                      .|.-.-+.+-+...++...+.  .....+.....+..++++.+... .|+++|+|+.+++.++++.+.++... .|.++|
T Consensus         3 ~VlIvDDh~l~r~gl~~~L~~--~~~~~vv~~a~~~~~~l~~~~~~-~pDvvllDl~lp~~~Gl~~~~~i~~~-~p~~~v   78 (216)
T PRK09483          3 NVLLVDDHELVRAGIRRILED--IKGIKVVGEASCGEDAVKWCRTN-AVDVVLMDMNMPGIGGLEATRKILRS-TPDVKI   78 (216)
T ss_pred             EEEEECCCHHHHHHHHHHHHH--CCCCEEEEEECCHHHHHHHHHHC-CCCEEEECCCCCCCCCHHHHHHHHHH-CCCCCE
T ss_conf             899984999999999999974--89958999989999999999855-99999986889898752377888740-899857


Q ss_pred             EEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             998168718999999976562643189998999997631023
Q gi|254780725|r  110 IVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       110 ivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      |+++...|.....+++++|++.|+.|+.+++++.+++..+..
T Consensus        79 ivls~~~~~~~~~~al~~Ga~gyl~K~~~~~~l~~ai~~v~~  120 (216)
T PRK09483         79 IMLTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHS  120 (216)
T ss_pred             EEECCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHC
T ss_conf             863056632889999974887899479999999999999985


No 88 
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB; InterPro: IPR011879    PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself . It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006817 phosphate transport.
Probab=99.25  E-value=1.1e-10  Score=84.89  Aligned_cols=149  Identities=13%  Similarity=0.184  Sum_probs=113.7

Q ss_pred             EECCHHHHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCC-CCCEEEE
Q ss_conf             83898999999988641100202237-306998999999861899849999805987677889998885328-9980899
Q gi|254780725|r   34 FCVTDTLYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCD-SGTKVIV  111 (427)
Q Consensus        34 f~~~~~~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~-p~~~Viv  111 (427)
                      --+.++..++|.-.     |.+.+++ +++++...|....... .||||++|=..|+.+|++.+.+|+..-. ..+|||.
T Consensus         8 VEDE~AirEl~~~~-----L~~~gy~v~~A~d~~~A~~~~~E~-~PDLILLDWMLPG~SGIel~R~Lr~~~~Tr~iPIIM   81 (226)
T TIGR02154         8 VEDEPAIRELIAYN-----LEKAGYDVVEAGDGDEALTLINER-LPDLILLDWMLPGTSGIELARRLRREPETRAIPIIM   81 (226)
T ss_pred             EECCHHHHHHHHHH-----HCCCCCEEEEECCHHHHHHHHHCC-CCCEEEECCCCCCCCHHHHHHHHCCCCCCCCCCEEE
T ss_conf             70826899999998-----416894699807979999998607-998899614789975699998734763314888177


Q ss_pred             EECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             81687189999999765626431899989999976310233222345675379997469887756899999999996269
Q gi|254780725|r  112 IGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFA  191 (427)
Q Consensus       112 ig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~  191 (427)
                      ++...+-.--..-+..||.||++||+++.||++-|+.++.+..|..  ...+|.|-+-               .|=. ..
T Consensus        82 LTARGeE~Drv~GLetGADDYvtKPFSp~EL~ARikAVLRR~~P~~--~~~~i~~~~l---------------~lD~-~~  143 (226)
T TIGR02154        82 LTARGEEEDRVRGLETGADDYVTKPFSPRELLARIKAVLRRIRPEL--SDEVIEVGDL---------------ELDP-VA  143 (226)
T ss_pred             EECCCCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHHHCCCHHH--HCCEEEECCE---------------EECC-CC
T ss_conf             4055560001131136887503678865889999999983167124--2020110347---------------7751-02


Q ss_pred             CCEEEEECCCCCCCC
Q ss_conf             949999787989860
Q gi|254780725|r  192 METLLADLDLPYGTA  206 (427)
Q Consensus       192 ~~VlLvDlDl~~g~~  206 (427)
                      +||..-+-.+.-|-+
T Consensus       144 HRV~~~~~~~~lGPT  158 (226)
T TIGR02154       144 HRVKRGGQPLELGPT  158 (226)
T ss_pred             CEEEECCEECCCCCH
T ss_conf             404313602146870


No 89 
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=99.24  E-value=4.5e-10  Score=81.12  Aligned_cols=119  Identities=13%  Similarity=0.212  Sum_probs=97.4

Q ss_pred             EEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             05999838989999999886411002022373069989999998618998499998059876778899988853289980
Q gi|254780725|r   29 ISVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTK  108 (427)
Q Consensus        29 ~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~  108 (427)
                      ++|.---+.+-+...++...+.  ...-.+....++..++++.+...+ ||++|+|+++++.++++.+..+.+. .|+++
T Consensus         4 ~~VlIvDDh~l~r~gl~~~l~~--~~~~~vv~~a~~~~~~~~~l~~~~-~DvvllD~~lp~~~g~~~i~~i~~~-~p~~~   79 (210)
T PRK09935          4 ASVIIMDEHPIVRMSIEVLLQK--NSNIQVVLKTDDSRITIDYLRTYP-VDLVILDIELPGTDGFTLLKRIKQI-QETVK   79 (210)
T ss_pred             CEEEEECCCHHHHHHHHHHHHC--CCCEEEEEEECCHHHHHHHHHHCC-CCEEEECCCCCCCCCCCHHHHHHHH-CCCCC
T ss_conf             8899985969999999999962--989289999899999999997479-9999988999998864056789873-89970


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             8998168718999999976562643189998999997631023
Q gi|254780725|r  109 VIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       109 Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      |++++...|.....+++++|++.|+.|+.+.+++..++..+..
T Consensus        80 ilvls~~~~~~~~~~a~~~Ga~g~l~K~~~~~~l~~ai~~v~~  122 (210)
T PRK09935         80 VLFLSSKSECFYAGRAIRAGANGFVSKRKDLNDIYNAVQMILS  122 (210)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHC
T ss_conf             8997176729999999966877688678999999999999985


No 90 
>PRK13435 response regulator; Provisional
Probab=99.20  E-value=6.8e-10  Score=79.99  Aligned_cols=113  Identities=12%  Similarity=0.161  Sum_probs=84.9

Q ss_pred             EEEEECCHHHHHHHHHHHHHHHHHHCEEE-E-ECCCHHHHHHHHHCCCCCCEEEEECCCC-CCCHHHHHHHHHHHCCCCC
Q ss_conf             99983898999999988641100202237-3-0699899999986189984999980598-7677889998885328998
Q gi|254780725|r   31 VHVFCVTDTLYSVVERSKIDPRMSQVNMR-I-TRGSIAEAVSCFSDSSTPDLIIVQTKVD-SREVLSALEPLAEVCDSGT  107 (427)
Q Consensus        31 ~~~f~~~~~~~~~~~~~~~drr~~~~~~~-v-~~g~~~~A~~~~~~~~~P~~iivd~~~~-~~~~~~~l~~la~~~~p~~  107 (427)
                      |..--++......++...     .+.+.. + ..++..+|++..+.. .|+++++|++++ +.++++.+.+|.+  .+++
T Consensus         4 ILIVEDe~~i~~~l~~~L-----~~~G~~vv~~A~~~~eAl~~~~~~-~PDlvllDi~LpdG~~G~e~~r~l~~--~~~i   75 (141)
T PRK13435          4 VLIVEDEALIALELEKLL-----EEAGHQVVGIASTSEQALALGRRA-QPDVALVDIRLADGPTGVEVARRLSI--DGGV   75 (141)
T ss_pred             EEEECCCHHHHHHHHHHH-----HHCCCEEEEEECCHHHHHHHHHCC-CCCEEEECCCCCCCCCHHHHHHHHHH--CCCC
T ss_conf             999899899999999999-----987997999759999999997659-99899978878999989999999987--5998


Q ss_pred             EEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCC
Q ss_conf             08998168718999999976562643189998999997631023322
Q gi|254780725|r  108 KVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQE  154 (427)
Q Consensus       108 ~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~  154 (427)
                      +||.++.+.|.   ...+.+|+.||+.||+++.++.+++.++..+..
T Consensus        76 pvI~lTa~~d~---~~~~~aGA~dyl~KPf~~~eL~~ai~~~~~rr~  119 (141)
T PRK13435         76 EVIFMTANPER---VGHDFAGALGVIAKPYSLRQVARALSYVAARRV  119 (141)
T ss_pred             CEEEEECCHHH---HHHHHCCCCCEEECCCCHHHHHHHHHHHHHHCC
T ss_conf             38999777998---601345998589899998999999999997156


No 91 
>PRK10651 transcriptional regulator NarL; Provisional
Probab=99.20  E-value=4.5e-10  Score=81.10  Aligned_cols=119  Identities=13%  Similarity=0.182  Sum_probs=97.2

Q ss_pred             EEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             05999838989999999886411002022373069989999998618998499998059876778899988853289980
Q gi|254780725|r   29 ISVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTK  108 (427)
Q Consensus        29 ~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~  108 (427)
                      |+|.-.-+.+-....++...+.  ...-.+.....+..+|++.+...+ |+++|+|+++++.++++.+.+|.+. .|.++
T Consensus         7 irVlIvDDh~l~r~gl~~~L~~--~~~~~vv~~a~~~~ea~~~~~~~~-pDlvllDl~lp~~~G~~~~~~l~~~-~~~~~   82 (216)
T PRK10651          7 ATILLIDDHPMLRTGVKQLISM--APDITVVGEASNGEQGIELAESLD-PDLILLDLNMPGMNGLETLDKLREK-SLSGR   82 (216)
T ss_pred             CEEEEECCCHHHHHHHHHHHHH--CCCEEEEEEECCHHHHHHHHHHCC-CCEEEEECCCCCCCCCCCCCCCCCC-CCCCC
T ss_conf             7899983999999999999975--899389999899999999987079-9999995999998887642323345-78874


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             8998168718999999976562643189998999997631023
Q gi|254780725|r  109 VIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       109 Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      ||+++..++.....+++++|+.+|+.||.+.+++++++..+..
T Consensus        83 iivlt~~~~~~~~~~al~~Ga~gyl~K~~~~~~L~~ai~~v~~  125 (216)
T PRK10651         83 IVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAA  125 (216)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHC
T ss_conf             6763055418899999966987898378999999999999985


No 92 
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=99.20  E-value=2.7e-10  Score=82.45  Aligned_cols=114  Identities=8%  Similarity=0.136  Sum_probs=90.0

Q ss_pred             EEEEECCHHHHHHHHHHHHHHHHHHCEEEEE-CCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             9998389899999998864110020223730-699899999986189984999980598767788999888532899808
Q gi|254780725|r   31 VHVFCVTDTLYSVVERSKIDPRMSQVNMRIT-RGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKV  109 (427)
Q Consensus        31 ~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~-~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~V  109 (427)
                      |..--+++.....+...     |.+.++.|. ..+..+|.+.+... .|++||+|+++|+.++++.+.+|++.  ..+||
T Consensus         4 ILlVEDd~~l~~~l~~~-----L~~~g~~v~~a~~g~~a~~~~~~~-~~DlvilDi~LP~~dG~~l~~~iR~~--~~~Pi   75 (240)
T PRK10701          4 IVFVEDDAEVGSLIAAY-----LAKHDIDVTVEPRGDRAEETILRE-QPDLVLLDIMLPGKDGMTICRDLRPK--WSGPI   75 (240)
T ss_pred             EEEEECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCCCEEEEECCCC--CCCCE
T ss_conf             99997999999999999-----988799999989999999998617-99999992899767887876311025--89878


Q ss_pred             EEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             9981687189999999765626431899989999976310233
Q gi|254780725|r  110 IVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       110 ivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      |+++..++..-....+..|+.|||.||+++.++++.++..+..
T Consensus        76 I~lta~~~~~d~v~gl~~GADDYl~KPf~~~eL~aRi~a~lrr  118 (240)
T PRK10701         76 VLLTSLDSDMNHILALEMGACDYILKTTPPAVLLARLRLHLRQ  118 (240)
T ss_pred             EEEEECCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH
T ss_conf             9994057578899999768877641799879999999999965


No 93 
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=99.19  E-value=3.6e-10  Score=81.66  Aligned_cols=110  Identities=15%  Similarity=0.231  Sum_probs=90.0

Q ss_pred             EECCHHHHHHHHHHHHHHHHHHCEEEE-ECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             838989999999886411002022373-0699899999986189984999980598767788999888532899808998
Q gi|254780725|r   34 FCVTDTLYSVVERSKIDPRMSQVNMRI-TRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVI  112 (427)
Q Consensus        34 f~~~~~~~~~~~~~~~drr~~~~~~~v-~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivi  112 (427)
                      --+++.....+...     |.+.++.| ...+..+|.+.+..  .|++||+|+.+|+.++++.+.++++.  ..+|||++
T Consensus         7 VEDd~~l~~~l~~~-----L~~~G~~V~~a~~g~~al~~l~~--~~DlvilDi~LP~~dG~~l~~~iR~~--~~~PII~l   77 (232)
T PRK10955          7 VDDDRELTSLLKEL-----LEMEGFNVIVAHDGEQALDLLDD--SIDLLLLDVMMPKKNGIDTLKALRQT--HQTPVIML   77 (232)
T ss_pred             EECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHC--CCCEEEEECCCCCCCCCCCCCEEECC--CCCCEEEE
T ss_conf             96989999999999-----98889999998999999999648--98999991899988867230124407--88878998


Q ss_pred             ECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             1687189999999765626431899989999976310233
Q gi|254780725|r  113 GDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       113 g~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      +..++..-....++.|+.||+.||+++.++.+.+..++.+
T Consensus        78 ta~~~~~d~i~~l~~GADDYl~KPf~~~eL~ari~allrR  117 (232)
T PRK10955         78 TARGSELDRVLGLELGADDYLPKPFNDRELVARIRAILRR  117 (232)
T ss_pred             ECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHHHCC
T ss_conf             0556768899999769757633899989999999999761


No 94 
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=99.19  E-value=4e-10  Score=81.42  Aligned_cols=114  Identities=16%  Similarity=0.271  Sum_probs=93.5

Q ss_pred             EEEEECCHHHHHHHHHHHHHHHHHHCEEEE-ECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             999838989999999886411002022373-0699899999986189984999980598767788999888532899808
Q gi|254780725|r   31 VHVFCVTDTLYSVVERSKIDPRMSQVNMRI-TRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKV  109 (427)
Q Consensus        31 ~~~f~~~~~~~~~~~~~~~drr~~~~~~~v-~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~V  109 (427)
                      |..--++++....+...     +.+.+..| ...+..+|...+... .|+++|+|+.+|..++++.+..+++.  ..++|
T Consensus         4 ILivEDd~~l~~~l~~~-----L~~~g~~V~~a~~~~~al~~~~~~-~~DlviLDi~lP~~dG~~l~~~iR~~--~~~pI   75 (225)
T PRK10529          4 VLIVEDEQAIRRFLRTA-----LEGDGMRVFEAETLQRGLLEAATR-KPDLIILDLGLPDGDGIEFIRDLRQW--SAIPV   75 (225)
T ss_pred             EEEEECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCCCCCEEEEECC--CCCCE
T ss_conf             99997989999999999-----998899999979999999986117-99899980788888876331000127--99878


Q ss_pred             EEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             9981687189999999765626431899989999976310233
Q gi|254780725|r  110 IVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       110 ivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      |+++..++..-....+..|+.||+.||+++.++.+.+..++.+
T Consensus        76 I~lta~~~~~d~i~~l~~GADDYl~KPf~~~eL~aRi~a~lrr  118 (225)
T PRK10529         76 IVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRR  118 (225)
T ss_pred             EEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH
T ss_conf             9995468989999999769876540785459999999999714


No 95 
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=99.17  E-value=1.1e-09  Score=78.63  Aligned_cols=113  Identities=19%  Similarity=0.320  Sum_probs=90.7

Q ss_pred             ECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEEC
Q ss_conf             38989999999886411002022373069989999998618998499998059876778899988853289980899816
Q gi|254780725|r   35 CVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGD  114 (427)
Q Consensus        35 ~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~  114 (427)
                      .+|+..-+-|++-.- ..+..-+.....+++++|...+..- .|+||++|+-+|.+++++.|..+.+. ...+-||+|+.
T Consensus         6 iEDD~mVaeih~~yv-~~~~gF~~vg~A~~~~ea~~~i~~~-~pDLILLDiYmPd~~Gi~lL~~ir~~-~~~~DVI~iTA   82 (224)
T COG4565           6 IEDDPMVAEIHRRYV-KQIPGFSVVGTAGTLEEAKMIIEEF-KPDLILLDIYMPDGNGIELLPELRSQ-HYPVDVIVITA   82 (224)
T ss_pred             ECCCHHHHHHHHHHH-HHCCCCEEEEEECCHHHHHHHHHHH-CCCEEEEEECCCCCCCHHHHHHHHHC-CCCCCEEEEEC
T ss_conf             708658999999999-7389953898606499999999840-89979996026798507799999846-89978899953


Q ss_pred             CCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCC
Q ss_conf             871899999997656264318999899999763102
Q gi|254780725|r  115 TNDVSLYRALISNHVSEYLIEPLSVADIINSISAIF  150 (427)
Q Consensus       115 ~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~  150 (427)
                      .+|....++++|.||-|||.||+..+-+..++.+-.
T Consensus        83 A~d~~tI~~alr~Gv~DYLiKPf~~eRl~~aL~~y~  118 (224)
T COG4565          83 ASDMETIKEALRYGVVDYLIKPFTFERLQQALTRYR  118 (224)
T ss_pred             CCHHHHHHHHHHCCCHHHEECCEEHHHHHHHHHHHH
T ss_conf             443789999996582322056340999999999999


No 96 
>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=99.17  E-value=9.4e-11  Score=85.27  Aligned_cols=51  Identities=31%  Similarity=0.400  Sum_probs=40.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPI  215 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~  215 (427)
                      .|.|+++||||||||+|+.+|+.+|+. |++|++|-.|+. .+++-.|+.+-.
T Consensus         3 riv~f~GKGGVGKTT~aaA~A~~lA~~-g~kvLlvStDPA-hsL~d~f~~elg   53 (322)
T COG0003           3 RIVFFTGKGGVGKTTIAAATAVKLAES-GKKVLLVSTDPA-HSLGDVFDLELG   53 (322)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHC-CCCEEEEEECCC-CCHHHHHCCCCC
T ss_conf             799993688545899999999999975-990799984898-744765423047


No 97 
>PRK11173 two-component response regulator; Provisional
Probab=99.17  E-value=1.1e-09  Score=78.64  Aligned_cols=116  Identities=10%  Similarity=0.149  Sum_probs=92.5

Q ss_pred             CCEEEEEEECCHHHHHHHHHHHHHHHHHHCEEEE-ECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCC
Q ss_conf             7305999838989999999886411002022373-069989999998618998499998059876778899988853289
Q gi|254780725|r   27 PRISVHVFCVTDTLYSVVERSKIDPRMSQVNMRI-TRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDS  105 (427)
Q Consensus        27 ~~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v-~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p  105 (427)
                      |+|-|  --+++.....+...     +...++.| ..++..+|.+.+... .|++||+|+.++..++++.+.++++.  .
T Consensus         4 ~~ILi--VEDD~~~~~~l~~~-----L~~~G~~V~~a~~~~ea~~~l~~~-~~DlvilDi~lp~~~G~~l~~~iR~~--~   73 (237)
T PRK11173          4 PHILI--VEDELVTRNTLKSI-----FEAEGYDVFEATDGAEMHQILSEN-DINLVIMDINLPGKNGLLLARELREQ--A   73 (237)
T ss_pred             CEEEE--EECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHCC-CCCEEEEECCCCCCCCHHHHHHHHHC--C
T ss_conf             98999--95989999999999-----998899999989999999998638-99899993899988730355566516--8


Q ss_pred             CCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             98089981687189999999765626431899989999976310233
Q gi|254780725|r  106 GTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       106 ~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      .+++|+++..++..-...++.+|++||+.||++..++...+..++.+
T Consensus        74 ~~piI~lta~~~~~~~i~~l~~GaddYi~KPf~~~EL~arv~~~l~r  120 (237)
T PRK11173         74 NVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSR  120 (237)
T ss_pred             CCCEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH
T ss_conf             84789994325778899999769767887898879999999999866


No 98 
>PRK10766 DNA-binding transcriptional regulator TorR; Provisional
Probab=99.16  E-value=5.2e-10  Score=80.74  Aligned_cols=115  Identities=13%  Similarity=0.174  Sum_probs=93.0

Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHHCEEEEE-CCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             59998389899999998864110020223730-69989999998618998499998059876778899988853289980
Q gi|254780725|r   30 SVHVFCVTDTLYSVVERSKIDPRMSQVNMRIT-RGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTK  108 (427)
Q Consensus        30 ~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~-~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~  108 (427)
                      .|..--+++.....+...     |.+.++.|. ..+..+|.+.+... .|+++|+|+.++..++++.+..+++.  .+++
T Consensus         4 kILlVEDD~~l~~~l~~~-----L~~~g~~V~~~~~~~~a~~~l~~~-~~DlvilDi~lp~~~G~el~~~iR~~--~~~p   75 (224)
T PRK10766          4 HILVVEDEPVTRARLQGY-----FEQEGYRVSEAASGAGMREIMQNQ-HVDLILLDINLPGEDGLMLTRELRSR--STVG   75 (224)
T ss_pred             EEEEECCCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHHC-CCCEEEECCCCCCCCCCCHHHHHHHC--CCCC
T ss_conf             199991999999999999-----998799999989999999999608-99999988999988766137676304--7855


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             89981687189999999765626431899989999976310233
Q gi|254780725|r  109 VIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       109 Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      ||+++..++..-...++++|+.||+.||++..++...+..++.+
T Consensus        76 iI~lta~~~~~~~i~al~~GaddYl~KPf~~~eL~ari~allrR  119 (224)
T PRK10766         76 IILVTGRTDSIDRIVGLEMGADDYVTKPFELRELLVRVKNLLWR  119 (224)
T ss_pred             EEEECCCCCHHHHHHHHHCCCHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             68633558989999999849414513999889999999999725


No 99 
>PRK10403 transcriptional regulator NarP; Provisional
Probab=99.16  E-value=1.5e-09  Score=77.86  Aligned_cols=120  Identities=16%  Similarity=0.118  Sum_probs=96.5

Q ss_pred             EEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             05999838989999999886411002022373069989999998618998499998059876778899988853289980
Q gi|254780725|r   29 ISVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTK  108 (427)
Q Consensus        29 ~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~  108 (427)
                      |.|.-.-+.+-....++...+.  .....+.-...+..++++.+... .||++|+|+.+++.++++.+..|.+. .|.++
T Consensus         7 irIlIvDD~~l~r~gl~~~L~~--~~~~~vv~~a~~~~~~~~~~~~~-~pDlvllD~~lp~~~G~~~~~~l~~~-~p~~~   82 (215)
T PRK10403          7 FQVLIVDDHPLMRRGVRQLLEL--DPGFEVVAEAGDGASAIDLANRL-DIDVILLDLNMKGMSGLDTLNALRRD-GVTAQ   82 (215)
T ss_pred             CEEEEECCCHHHHHHHHHHHHH--CCCEEEEEEECCHHHHHHHHHHC-CCCEEEECCCCCCCCCCCHHHHHHHC-CCCCC
T ss_conf             5799983989999999999975--89928999989999999998644-99899980899899874123356541-88773


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             89981687189999999765626431899989999976310233
Q gi|254780725|r  109 VIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       109 Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      ||+++...+.....+++++|++.|+.|+.++.++..++..+...
T Consensus        83 iivlt~~~~~~~~~~al~~Ga~gyl~K~~~~~~l~~ai~~v~~G  126 (215)
T PRK10403         83 IIILTVSDASSDIFALIDAGADGYLLKDSDPEVLLEAIRAGAKG  126 (215)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCC
T ss_conf             68863243236789987468766884899999999999999849


No 100
>PRK13557 histidine kinase; Provisional
Probab=99.15  E-value=2.7e-09  Score=76.34  Aligned_cols=11  Identities=18%  Similarity=0.344  Sum_probs=4.8

Q ss_pred             CEEEEECCCCC
Q ss_conf             38999565898
Q gi|254780725|r  331 PYLVLNQVKTP  341 (427)
Q Consensus       331 ~~iVlNr~~~~  341 (427)
                      +-+|+.-..+|
T Consensus       459 ~Dlvl~D~~MP  469 (538)
T PRK13557        459 VDLLFTDLIMP  469 (538)
T ss_pred             CCEEEECCCCC
T ss_conf             88998877799


No 101
>PRK00742 chemotaxis-specific methylesterase; Provisional
Probab=99.14  E-value=1.1e-08  Score=72.49  Aligned_cols=163  Identities=14%  Similarity=0.208  Sum_probs=107.1

Q ss_pred             CEEEEEEECCHHHHHHHHHHHHHHHHHHCEEEE--ECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCC
Q ss_conf             305999838989999999886411002022373--069989999998618998499998059876778899988853289
Q gi|254780725|r   28 RISVHVFCVTDTLYSVVERSKIDPRMSQVNMRI--TRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDS  105 (427)
Q Consensus        28 ~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v--~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p  105 (427)
                      +|.|...-++......++...+.    ...+.|  ...+..+|++.+... .||+|++|+.|+.+|+++.++++.+.+ |
T Consensus         2 kirVLIVDDs~~~R~~l~~~L~~----~~~~eVv~~A~nG~eAl~~~~~~-~pDvVllDi~MP~mdGie~l~~I~~~~-p   75 (345)
T PRK00742          2 KIRVLVVDDSAFMRRLLSEILNS----DPDIEVVGTARDGLEAVEKIKKL-NPDVITLDVEMPVMDGIEALRKIMALR-P   75 (345)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHH----CCCEEEEEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCHHHHHHHHHHHC-C
T ss_conf             82699992988999999999972----89908999989999999998860-999999837889998799999999758-9


Q ss_pred             CCEEEEEECC--CCHHHHHHHHHCCCCEEECCCCC-----HHH----HHHHHHHCCCCC-----C----------CCCCC
Q ss_conf             9808998168--71899999997656264318999-----899----999763102332-----2----------23456
Q gi|254780725|r  106 GTKVIVIGDT--NDVSLYRALISNHVSEYLIEPLS-----VAD----IINSISAIFTPQ-----E----------EGKGS  159 (427)
Q Consensus       106 ~~~Vivig~~--~d~~l~r~l~r~Gv~dyl~~P~~-----~~~----l~~ai~~~~~~~-----~----------~~~~~  159 (427)
                       ++||+++..  .+.....++++.|+.||+.||..     ..+    |++.++.+....     .          .....
T Consensus        76 -~pVimvSs~~~~~~~~~~~Al~~GA~D~i~KP~~~~~~~~~~~~~~L~~ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (345)
T PRK00742         76 -TPVVMVSSLTERGAEITLEALELGAVDFVPKPFLGISEGMDAAAELLAEKVRAAARAARLAAAAPAAAPAALKAAPSGS  154 (345)
T ss_pred             -CCEEEEEECCCCCHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             -8779997225556599999997592248957888765329999999999999985186556788888888887777788


Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             75379997469887756899999999996269949999787
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLD  200 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlD  200 (427)
                      ..++|++..+-||..+  +..=|. .|-......++++-.=
T Consensus       155 ~~~vV~IGaStGGp~a--L~~il~-~Lp~~~p~pivivQHm  192 (345)
T PRK00742        155 SEKLVAIGASTGGPEA--LQKVLT-QLPANFPAPIVIVQHM  192 (345)
T ss_pred             CCCEEEEEECCCCHHH--HHHHHH-HCCCCCCCCEEEEECC
T ss_conf             8718999837568999--999998-5898899748999658


No 102
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=99.13  E-value=2.8e-09  Score=76.18  Aligned_cols=111  Identities=14%  Similarity=0.178  Sum_probs=90.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECC
Q ss_conf             89899999998864110020223730699899999986189984999980598767788999888532899808998168
Q gi|254780725|r   36 VTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDT  115 (427)
Q Consensus        36 ~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~  115 (427)
                      +.+-....++...+..   ...+.-...+..++++.+... .||++|+|+++++.++++.+..+.+.+ |.++|++++..
T Consensus         8 Dh~lvr~gl~~ll~~~---~~~vv~~~~~~~~~l~~~~~~-~pDvvllDl~lp~~~G~~~~~~ir~~~-~~~~viv~s~~   82 (204)
T PRK09958          8 DHPLAIAAIRNLLIKN---DIEILAELTEGGSAVQRVETL-KPDIVIIDVDIPGVNGIQVLETLRKRQ-YSGIIIIVSAK   82 (204)
T ss_pred             CCHHHHHHHHHHHHHC---CCEEEEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCCHHHHHHHHHHC-CCEEEEEEECC
T ss_conf             9899999999999868---998999979999999998743-979999958999998416788898727-98059999724


Q ss_pred             CCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             718999999976562643189998999997631023
Q gi|254780725|r  116 NDVSLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       116 ~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      +|.....+++++|++.|+.|..+.+++.+++..+..
T Consensus        83 ~~~~~~~~a~~~Ga~g~l~K~~~~~~l~~aI~~v~~  118 (204)
T PRK09958         83 NDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKN  118 (204)
T ss_pred             CCCHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHC
T ss_conf             652114433526863799789999999999999977


No 103
>PRK13856 two-component response regulator VirG; Provisional
Probab=99.13  E-value=3.6e-09  Score=75.59  Aligned_cols=112  Identities=12%  Similarity=0.210  Sum_probs=86.9

Q ss_pred             EEEECCHHHHHHHHHHHHHHHHHHCEEEE-ECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             99838989999999886411002022373-06998999999861899849999805987677889998885328998089
Q gi|254780725|r   32 HVFCVTDTLYSVVERSKIDPRMSQVNMRI-TRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVI  110 (427)
Q Consensus        32 ~~f~~~~~~~~~~~~~~~drr~~~~~~~v-~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vi  110 (427)
                      .---++++....+...     |...++.| ...+..+|.+.+... .|+++|+|+++|..++++.+..+++.  ..+++|
T Consensus         5 LlVEDD~~l~~~l~~~-----L~~~g~~v~~a~~~~~~~~~l~~~-~~DlvIlDi~lp~~~Gl~~~~~ir~~--~~~pii   76 (241)
T PRK13856          5 LVIDDDVAMRHLIVEY-----LTIHAFKVTAVADSQQFNRVLSSE-TVDVVVVDLNLGREDGLEIVRSLATK--SDVPII   76 (241)
T ss_pred             EEEECCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHCC-CCCEEEEECCCCCCCCHHHHHHHCCC--CCCCEE
T ss_conf             9996989999999999-----987799999989999999998659-99999996999876613455564036--997369


Q ss_pred             EEEC-CCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             9816-8718999999976562643189998999997631023
Q gi|254780725|r  111 VIGD-TNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       111 vig~-~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      +++. ..|..--..++..|+.|||.||++..++++.+..++.
T Consensus        77 ilt~~~~~~~d~i~~l~~GADDYl~KPf~~~EL~aRi~~~lr  118 (241)
T PRK13856         77 IISGDRLEEADKVVALELGATDFIAKPFGTREFLARIRVALR  118 (241)
T ss_pred             EEECCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHH
T ss_conf             997267878999999876998899777677799999999987


No 104
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=99.11  E-value=6.9e-09  Score=73.83  Aligned_cols=120  Identities=9%  Similarity=0.127  Sum_probs=93.1

Q ss_pred             CEEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCC---CCHHHHHHHHHHHCC
Q ss_conf             30599983898999999988641100202237306998999999861899849999805987---677889998885328
Q gi|254780725|r   28 RISVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDS---REVLSALEPLAEVCD  104 (427)
Q Consensus        28 ~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~---~~~~~~l~~la~~~~  104 (427)
                      +|.|.---+.+-....++...+.  .....+.-...+..++++.+... .|+++|+|+++|+   .++++.+..+.+. .
T Consensus         3 ~irIlIvDDh~lvr~Gl~~~L~~--~~~~~vvg~a~~~~~~~~~~~~~-~pDvvllDl~mpg~~~~dGl~~~~~i~~~-~   78 (216)
T PRK10840          3 NMNVIIADDHPIVLFGIRKSLEQ--IEWVNVVGEFEDSTALINNLPKL-DAHVLITDLSMPGDKYGDGITLIKYIKRH-F   78 (216)
T ss_pred             CCEEEEECCHHHHHHHHHHHHCC--CCCCEEEEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCCCCHHHHHHHHHHH-C
T ss_conf             88899988979999999999815--99968999879999999998623-98989982677999887899999999985-8


Q ss_pred             CCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             99808998168718999999976562643189998999997631023
Q gi|254780725|r  105 SGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       105 p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      |+++||+++.+++.....+++++|++.|+.|-..++++..++..+..
T Consensus        79 p~~~vivls~~~~~~~v~~al~~Ga~Gyl~K~~~~~~L~~AI~~v~~  125 (216)
T PRK10840         79 PSLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQK  125 (216)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHC
T ss_conf             99808998477878999999858974899878999999999999987


No 105
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=99.11  E-value=1.6e-09  Score=77.69  Aligned_cols=116  Identities=15%  Similarity=0.241  Sum_probs=92.6

Q ss_pred             EEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             99983898999999988641100202237306998999999861899849999805987677889998885328998089
Q gi|254780725|r   31 VHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVI  110 (427)
Q Consensus        31 ~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vi  110 (427)
                      ||..-+|+.....+...     +..+++++..-....+.-.-....-|-.+|+|+.||+.++++..++|++. .+..|||
T Consensus         7 V~vVDDD~~vr~al~~L-----l~s~G~~v~~~~s~~~fL~~~~~~~pGclllDvrMPg~sGlelq~~L~~~-~~~~PVI   80 (202)
T COG4566           7 VHVVDDDESVRDALAFL-----LESAGFQVKCFASAEEFLAAAPLDRPGCLLLDVRMPGMSGLELQDRLAER-GIRLPVI   80 (202)
T ss_pred             EEEECCCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHHC-CCCCCEE
T ss_conf             89976848899999999-----98389536650479999830667889769985578888508999999953-9998879


Q ss_pred             EEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             981687189999999765626431899989999976310233
Q gi|254780725|r  111 VIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       111 vig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      +|+.+.||....++|++|+-|||.||++..++++++.+.+..
T Consensus        81 fiTGhgDIpmaV~AmK~GAvDFLeKP~~~q~Lldav~~Al~~  122 (202)
T COG4566          81 FLTGHGDIPMAVQAMKAGAVDFLEKPFSEQDLLDAVERALAR  122 (202)
T ss_pred             EEECCCCHHHHHHHHHCCHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             982788728999999742156774788548999999999998


No 106
>PRK01077 cobyrinic acid a,c-diamide synthase; Validated
Probab=99.11  E-value=8e-09  Score=73.41  Aligned_cols=178  Identities=13%  Similarity=0.131  Sum_probs=108.9

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      +-|-|.|...|+||||+++-|..+|++ +|.+|.-.-.                        +|+-+|+.+.....-+..
T Consensus         4 p~lmI~gt~S~~GKT~vt~gL~r~l~~-rG~~VapFK~------------------------GPDyIdp~~~~~a~g~~~   58 (451)
T PRK01077          4 PALVIAAPASGSGKTTVTLGLMRALRR-RGLRVQPFKV------------------------GPDYIDPAFHAAATGRPS   58 (451)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHH-CCCCCCCCCC------------------------CCCCCCHHHHHHHHCCCC
T ss_conf             879998689999789999999999996-8794575357------------------------857629899999978975


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC-----------CHHHHHHHHHCCCCCCCCCCCHHH
Q ss_conf             980687248761203207999999989998512888997388888-----------989999986201254357877688
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVW-----------NSWTQEVLTLSDKVVITTSLDLAG  310 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~-----------~~~~~~~L~~AD~vviV~~p~~~s  310 (427)
                      .+|          ..+.+.++.+..++....+.+|++||.--.+.           +....+-+..+. |++|++.+-. 
T Consensus        59 ~nL----------D~~l~~~~~v~~~~~~~~~~~D~~viEG~mGlyDG~~~~~~~gS~aeiA~~l~~P-ViLViD~~~~-  126 (451)
T PRK01077         59 RNL----------DSWMMGEDLVRALFARAAGGADIAVIEGVMGLFDGAGGDPDKGSTADIARLLGAP-VVLVVDASGM-  126 (451)
T ss_pred             CCC----------CHHHCCHHHHHHHHHHHCCCCCEEEEEECHHCCCCCCCCCCCCCHHHHHHHHCCC-EEEEECCCCH-
T ss_conf             358----------8344899999999997546688899850101134545677777789999870998-8999846620-


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCC
Q ss_conf             9999999999998198767538999565898752005999999848953799068799999988479
Q gi|254780725|r  311 LRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSG  377 (427)
Q Consensus       311 lr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G  377 (427)
                      .+....++.-+....+...-..+|+|++..++..++-.+.++ .+|.++.++||++....-..-..|
T Consensus       127 ~~s~aa~v~G~~~~~~~~~I~GvIlNk~~g~~h~~ll~~~ie-~~gvpvlG~lP~~~~l~lpeRHLG  192 (451)
T PRK01077        127 AQSAAALVLGFARFDPDLNIAGVILNRVGSERHYQLLREALE-ELGLPVLGALPRDAALALPERHLG  192 (451)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHHHHHHHHH-HCCCCEEEEECCCCCCCCCCCCCC
T ss_conf             899999999999759778774899624787668999999998-639957986157633456421257


No 107
>TIGR01387 cztR_silR_copR heavy metal response regulator; InterPro: IPR006291   Members of this family contain a response regulator receiver domain and an associated transcriptional regulatory region. This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members are encoded by genes adjacent to genes which code for a member of the heavy metal sensor histidine kinase family (IPR006290 from INTERPRO), its partner in the two-component response regulator system. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0007600 sensory perception.
Probab=99.10  E-value=9.6e-11  Score=85.22  Aligned_cols=142  Identities=12%  Similarity=0.147  Sum_probs=110.4

Q ss_pred             ECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEEC
Q ss_conf             38989999999886411002022373069989999998618998499998059876778899988853289980899816
Q gi|254780725|r   35 CVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGD  114 (427)
Q Consensus        35 ~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~  114 (427)
                      -+.|-|++-++++     |+.++..|...+==--.-|++.+.-=++||+|++.|++|+++-|++|++- ...+||+.++.
T Consensus         5 EDeqkT~~YlqqG-----LsE~GYvvD~~~nG~DGL~lA~~~~Y~liILDvmLPG~DGW~vl~~LR~~-~~~~PVl~LTA   78 (219)
T TIGR01387         5 EDEQKTAEYLQQG-----LSESGYVVDIASNGRDGLHLAEKDDYDLIILDVMLPGMDGWQVLKALRRS-GKETPVLFLTA   78 (219)
T ss_pred             ECCCCHHHHHHCC-----CCCCCEEEEEEECCCCHHHHCCCCCCEEEEEECCCCCCCHHHHHHHHHCC-CCCCCEEEEEC
T ss_conf             3086026765305-----20123479887768624754368883089963258895068999998407-89873488833


Q ss_pred             CCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCCCCC-------------------CCCEEEEEEECCCCCCH
Q ss_conf             87189999999765626431899989999976310233222345-------------------67537999746988775
Q gi|254780725|r  115 TNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQEEGKG-------------------SSGCSISFIGSRGGVGS  175 (427)
Q Consensus       115 ~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~~~-------------------~~grvIav~g~KGGvGk  175 (427)
                      .+++.--.+-+..||.|||+||++-.||++.++.++..+.....                   |.++.|..++       
T Consensus        79 ~D~v~DkvkGLd~GAdDYLvKPF~F~ELlARvR~~LR~~~~~~~~evl~i~DL~~D~~~~~v~R~~~~I~LT~-------  151 (219)
T TIGR01387        79 RDSVADKVKGLDLGADDYLVKPFEFAELLARVRTLLRRSESLESTEVLEIADLELDVVRRRVFRGSKRIELTR-------  151 (219)
T ss_pred             CCCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEECCCEECCCEEEEEECCEEEEECH-------
T ss_conf             7884543530114786541378776037999998767752037676268605575121038875682687303-------


Q ss_pred             HHHHHHHHHHHHHHCC
Q ss_conf             6899999999996269
Q gi|254780725|r  176 STIAHNCAFSIASVFA  191 (427)
Q Consensus       176 TTiA~nLA~~LA~~~~  191 (427)
                        ==..|=+.|.++.|
T Consensus       152 --kEF~LL~lL~~r~G  165 (219)
T TIGR01387       152 --KEFALLELLMRRTG  165 (219)
T ss_pred             --HHHHHHHHHHHHCC
T ss_conf             --67899999997488


No 108
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator; InterPro: IPR014264   Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC (see Q06065 from SWISSPROT). These proteins have a Fis family DNA binding sequence, a response regulator receiver domain, and sigma-54 interaction domain. They are found strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system  common in Gram-positive bacteria, where members of IPR014265 from INTERPRO and IPR014266 from INTERPRO also occur..
Probab=99.10  E-value=6.2e-10  Score=80.23  Aligned_cols=139  Identities=14%  Similarity=0.179  Sum_probs=110.0

Q ss_pred             EEECCCHHHHHHHHHCCCCCCEEEEECCCCC-----CCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEE
Q ss_conf             7306998999999861899849999805987-----67788999888532899808998168718999999976562643
Q gi|254780725|r   59 RITRGSIAEAVSCFSDSSTPDLIIVQTKVDS-----REVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSEYL  133 (427)
Q Consensus        59 ~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~-----~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl  133 (427)
                      .+-++.=..|+..++.+. |.||.+|++.||     ..+|..|+++-++ .|.||||||+..+|-.=..+++++||+||.
T Consensus        24 ~~~A~DR~sAiA~vRRhe-P~VVTLDLGLPPd~d~a~EGl~~L~qIL~~-~P~TKVIViTGN~~r~NAlkAi~lGAYDFy  101 (451)
T TIGR02915        24 VAVAADRESAIALVRRHE-PAVVTLDLGLPPDADGASEGLAALQQILAI-APDTKVIVITGNDDRENALKAIGLGAYDFY  101 (451)
T ss_pred             EEEECCHHHHHHHHHCCC-CCEEECCCCCCCCCCCHHHHHHHHHHHHHH-CCCCEEEEEECCCCCHHHHHHHHCCCCCCC
T ss_conf             355347578999860569-964773675578988745899999999963-898048998668983889999643751013


Q ss_pred             CCCCCHHHHHHHHHHCCCCC-------------CCCCC----------------------CCCEEEEEEECCCCCCHHHH
Q ss_conf             18999899999763102332-------------22345----------------------67537999746988775689
Q gi|254780725|r  134 IEPLSVADIINSISAIFTPQ-------------EEGKG----------------------SSGCSISFIGSRGGVGSSTI  178 (427)
Q Consensus       134 ~~P~~~~~l~~ai~~~~~~~-------------~~~~~----------------------~~grvIav~g~KGGvGkTTi  178 (427)
                      .||++++.|.=.|.|.|.-.             .++..                      ..+-+-+++=+=.|+||=-+
T Consensus       102 qKP~d~d~L~liv~RAf~L~~Le~ENRrL~~~~~~Gst~~~Gli~~~~~m~kic~tIekvA~sd~TvllLGESGTGKEV~  181 (451)
T TIGR02915       102 QKPIDPDVLKLIVDRAFRLYTLETENRRLQSALGGGSTALEGLITSSPGMQKICRTIEKVAPSDITVLLLGESGTGKEVL  181 (451)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCCHHHHHHHHHHHCCCCCEEEEECCCCCHHHHH
T ss_conf             57875789999999988888888876998740688741036522068506789888652120000130104667117899


Q ss_pred             HHHHHHHHHHHCCCCEEEEECC
Q ss_conf             9999999996269949999787
Q gi|254780725|r  179 AHNCAFSIASVFAMETLLADLD  200 (427)
Q Consensus       179 A~nLA~~LA~~~~~~VlLvDlD  200 (427)
                      |-.+ +.++.+..++-+-|.|-
T Consensus       182 ArA~-H~~S~R~~~~FVAINCA  202 (451)
T TIGR02915       182 ARAL-HELSDRKDKRFVAINCA  202 (451)
T ss_pred             HHHH-HHHCCCCCCCEEEEECC
T ss_conf             9898-42057897773444167


No 109
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=99.08  E-value=2.1e-08  Score=70.88  Aligned_cols=202  Identities=17%  Similarity=0.204  Sum_probs=109.7

Q ss_pred             HHHHHHHHHCCCCEEECC--------CCCHHHHHHHHHHC----CCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             899999997656264318--------99989999976310----233222345675379997469887756899999999
Q gi|254780725|r  118 VSLYRALISNHVSEYLIE--------PLSVADIINSISAI----FTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFS  185 (427)
Q Consensus       118 ~~l~r~l~r~Gv~dyl~~--------P~~~~~l~~ai~~~----~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~  185 (427)
                      -.+|..|++.|+++.+..        -....+..+.+.+.    +..........+|+|+|+| --||||||+.+=||..
T Consensus       155 ~~l~~~L~~~Gvs~~la~~l~~~~~~~~~~~~~~~~l~~~L~~~l~~~~~~~~~~~~vvalVG-PTGVGKTTTiAKLAA~  233 (412)
T PRK05703        155 AKLYKRLKESGLSPEIADKLLKLLLEDMNPREAWRYLLELLANMLPTRVEDILEQGGVVALVG-PTGVGKTTTLAKLAAR  233 (412)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEC-CCCCCHHHHHHHHHHH
T ss_conf             999999998699999999999986642897999999999999757888766545673699988-8887567699999999


Q ss_pred             HHHHCCC-CEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHH
Q ss_conf             9962699-499997879898603343899878988863184561243376532024898068724876120320799999
Q gi|254780725|r  186 IASVFAM-ETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMI  264 (427)
Q Consensus       186 LA~~~~~-~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l  264 (427)
                      ++...++ +|.||-+|..--.+.-.                       |+.+..-  -|+.+-.         -.+++.+
T Consensus       234 ~~l~~~~~kV~lIT~DtyRigA~eQ-----------------------Lk~Ya~i--lgvp~~v---------~~~~~~l  279 (412)
T PRK05703        234 YALEEGKDKVALITLDTYRIGAVEQ-----------------------LKTYAKI--MGIPVKV---------AYDPKEL  279 (412)
T ss_pred             HHHHCCCCEEEEEEECCCCHHHHHH-----------------------HHHHHHH--CCCEEEE---------ECCHHHH
T ss_conf             9997299817999837677779999-----------------------9999997--1973798---------4799999


Q ss_pred             HHHHHHHHHCCCEEEECCCCCC--CHHH----HHHHHH--CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf             9989998512888997388888--9899----999862--0125435787768899999999999981987675389995
Q gi|254780725|r  265 VPVLDILEQIFPLVILDVPHVW--NSWT----QEVLTL--SDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLN  336 (427)
Q Consensus       265 ~~ll~~l~~~yd~VIiD~p~~~--~~~~----~~~L~~--AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlN  336 (427)
                      ...++.++ .+|+|+||++...  +...    ...+..  .+.+++|...+ ..-++..++++.+...++.    .+|+.
T Consensus       280 ~~al~~~~-~~dlILIDTaG~s~~d~~~~~eL~~~~~~~~~~~~~LVlsat-~~~~dl~~i~~~f~~~~~~----~lI~T  353 (412)
T PRK05703        280 AKALEQLA-NCDLILIDTAGRSQRDPRLISELKALIENSKPIDVYLVLSAT-TKYRDLKDIVKHFSRLPLD----GLILT  353 (412)
T ss_pred             HHHHHHHC-CCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCEEEEECCC-CCHHHHHHHHHHHCCCCCC----EEEEE
T ss_conf             99998715-899799968988978999999999998624887189997598-9989999999984679998----79997


Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCEEE
Q ss_conf             6589875200599999984895379
Q gi|254780725|r  337 QVKTPKKPEISISDFCAPLGITPSA  361 (427)
Q Consensus       337 r~~~~~~~~i~~~~~~~~lg~~~~~  361 (427)
                      +.+.....- ..=.+.-..+.++.+
T Consensus       354 KlDEt~~~G-~il~~~~~~~lplsy  377 (412)
T PRK05703        354 KLDETSSLG-SILSLLIESGLPISY  377 (412)
T ss_pred             EECCCCCCC-HHHHHHHHHCCCEEE
T ss_conf             112899862-999999998879699


No 110
>PRK12555 chemotaxis-specific methylesterase; Provisional
Probab=99.07  E-value=1.9e-08  Score=71.06  Aligned_cols=139  Identities=11%  Similarity=0.149  Sum_probs=95.7

Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHHCEEEE--ECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             5999838989999999886411002022373--06998999999861899849999805987677889998885328998
Q gi|254780725|r   30 SVHVFCVTDTLYSVVERSKIDPRMSQVNMRI--TRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGT  107 (427)
Q Consensus        30 ~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v--~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~  107 (427)
                      .|...-++.-....+++..+.    ...+.|  ...+..+|++.+... .||+|++|+.|+.+|+++.+++|.+.+ | +
T Consensus         3 rVLIVDDs~~~R~~l~~~L~~----~~~~eVv~~A~~g~eAl~~~~~~-~pDvVllDi~MP~mdGie~l~~I~~~~-p-~   75 (340)
T PRK12555          3 NVGIVDDSALAREALRRIIAR----RPDHRVLGVATDGLQARDLCKAQ-PPDVVLLDLEMPRMDGLTFLRRIMRRR-P-C   75 (340)
T ss_pred             EEEEEECCHHHHHHHHHHHHH----CCCCEEEEEECCHHHHHHHHHHH-CCCEEEEECCCCCCCHHHHHHHHHHHC-C-C
T ss_conf             899990988999999999960----99948999989999999998861-999999727889998799999999878-9-9


Q ss_pred             EEEEEECC--CCHHHHHHHHHCCCCEEECCCCC-----H----HHHHHHHHHCCCC---C-------C----CCCCCCCE
Q ss_conf             08998168--71899999997656264318999-----8----9999976310233---2-------2----23456753
Q gi|254780725|r  108 KVIVIGDT--NDVSLYRALISNHVSEYLIEPLS-----V----ADIINSISAIFTP---Q-------E----EGKGSSGC  162 (427)
Q Consensus       108 ~Vivig~~--~d~~l~r~l~r~Gv~dyl~~P~~-----~----~~l~~ai~~~~~~---~-------~----~~~~~~gr  162 (427)
                      +||+++..  .+.....+++++|+.||+.||..     .    .++++.++.+...   .       .    .......+
T Consensus        76 PVimvSs~~~~~~~~~~~AL~~GA~D~i~KP~~~~~~~~~~~~~~L~~ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (340)
T PRK12555         76 PVLIVSSLTEAGASITYEALGAGALDAVDKPKLGIGRGLDAYAQELLAKIDQAARALVRRLARAAAPAPAAPAPFRTTEK  155 (340)
T ss_pred             CEEEEEECCCCCHHHHHHHHHCCHHHEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             86998503565769999999779776684788775531999999999999998644245678888888998765578887


Q ss_pred             EEEEEECCCCCCH
Q ss_conf             7999746988775
Q gi|254780725|r  163 SISFIGSRGGVGS  175 (427)
Q Consensus       163 vIav~g~KGGvGk  175 (427)
                      +|++.++-||..+
T Consensus       156 vv~IGaSTGGp~a  168 (340)
T PRK12555        156 LVAIGASAGGTEA  168 (340)
T ss_pred             EEEEEECCCCHHH
T ss_conf             8999968899999


No 111
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=99.05  E-value=2.1e-08  Score=70.81  Aligned_cols=115  Identities=15%  Similarity=0.169  Sum_probs=90.7

Q ss_pred             EECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             83898999999988641100202237306998999999861899849999805987677889998885328998089981
Q gi|254780725|r   34 FCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIG  113 (427)
Q Consensus        34 f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig  113 (427)
                      ..+.+-...-++...+...  .-.+....++..++++.+. ...|+++++|+++|+.++++.+..|.+. .|.++|++++
T Consensus         6 vDDh~l~r~gl~~~L~~~~--~~~vv~~a~~~~~~l~~~~-~~~pdvvl~Dl~mP~~~G~e~~~~l~~~-~p~~~vvvlt   81 (211)
T COG2197           6 VDDHPLVREGLRQLLELEP--DLEVVGEASNGEEALDLAR-ELKPDVVLLDLSMPGMDGLEALKQLRAR-GPDIKVVVLT   81 (211)
T ss_pred             ECCCHHHHHHHHHHHHHCC--CCEEEEEECCHHHHHHHHH-CCCCCEEEEECCCCCCCHHHHHHHHHHH-CCCCEEEEEE
T ss_conf             8097779999999998689--9669998278899999851-3799889983788998759999999986-8997299996


Q ss_pred             CCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             687189999999765626431899989999976310233
Q gi|254780725|r  114 DTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       114 ~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      ..++.....+++++|++.|+.|+.+++++.+++..+...
T Consensus        82 ~~~~~~~v~~~l~~Ga~gyl~K~~~~~~l~~ai~~v~~G  120 (211)
T COG2197          82 AHDDPAYVIRALRAGADGYLLKDASPEELVEAIRAVAAG  120 (211)
T ss_pred             CCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCC
T ss_conf             778989999999779969986799999999999999758


No 112
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=99.04  E-value=9e-09  Score=73.09  Aligned_cols=114  Identities=17%  Similarity=0.272  Sum_probs=93.4

Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             599983898999999988641100202237-3069989999998618998499998059876778899988853289980
Q gi|254780725|r   30 SVHVFCVTDTLYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTK  108 (427)
Q Consensus        30 ~~~~f~~~~~~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~  108 (427)
                      |..-.-+|......+.+++     .+-++. +...+..+++...++. +|...+||+....++++..++.|++. +++++
T Consensus        11 ~lllvdDD~~f~~~LaRa~-----e~RGf~v~~a~~~~eal~~art~-~PayAvvDlkL~~gsGL~~i~~lr~~-~~d~r   83 (182)
T COG4567          11 SLLLVDDDTPFLRTLARAM-----ERRGFAVVTAESVEEALAAARTA-PPAYAVVDLKLGDGSGLAVIEALRER-RADMR   83 (182)
T ss_pred             EEEEECCCHHHHHHHHHHH-----HCCCCEEEEECCHHHHHHHHHCC-CCCEEEEEEEECCCCCHHHHHHHHHC-CCCCE
T ss_conf             0589618769999999998-----60686257614499999998517-98528898640688746899999824-97643


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCC
Q ss_conf             899816871899999997656264318999899999763102
Q gi|254780725|r  109 VIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIF  150 (427)
Q Consensus       109 Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~  150 (427)
                      +||++....|....++++.|+.|||.||.+.+++.+++.+-.
T Consensus        84 ivvLTGy~sIATAV~AvKlGA~~YLaKPAdaDdi~aAl~~~~  125 (182)
T COG4567          84 IVVLTGYASIATAVEAVKLGACDYLAKPADADDILAALLRRE  125 (182)
T ss_pred             EEEEECCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCC
T ss_conf             898845117999999998624554079777689999986027


No 113
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=99.01  E-value=3.5e-08  Score=69.46  Aligned_cols=111  Identities=14%  Similarity=0.117  Sum_probs=56.1

Q ss_pred             EEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHH-HHHHCCCCC
Q ss_conf             0599983898999999988641100202237306998999999861899849999805987677889998-885328998
Q gi|254780725|r   29 ISVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEP-LAEVCDSGT  107 (427)
Q Consensus        29 ~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~-la~~~~p~~  107 (427)
                      -+|..+...+..+..+.......     +..|.....   .+.+.. ...++++++..++..+....+.. +...+....
T Consensus       537 ~~vlvve~~~~~~~~l~~~L~~~-----g~~v~~~~~---~~~l~~-~~~D~~li~~~~~~~~~~~~~~~~l~~~~~~~~  607 (920)
T PRK11107        537 KRLLYVEPNSLAAQATLDLLSET-----PLEVTYSPT---LSQLPE-AHYDYLLLGCPVTFREPLTMLHERLAKAKSMTD  607 (920)
T ss_pred             CEEEEECCCHHHHHHHHHHHHHC-----CCEEEECCC---HHHHHC-CCCCEEEECCCCCCCCHHHHHHHHHHHHCCCCC
T ss_conf             76999769778999999999974-----964575178---877513-688879961666665406678999863003578


Q ss_pred             EEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHH
Q ss_conf             08998168718999999976562643189998999997631
Q gi|254780725|r  108 KVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISA  148 (427)
Q Consensus       108 ~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~  148 (427)
                      .++++....+...+..+.+.|+..+|.+|+....+..++..
T Consensus       608 ~~il~~~s~~~~~~~~~~~~~~~~~L~kPv~~~~L~~~L~~  648 (920)
T PRK11107        608 FLILALPCHEQVNAEQLKQPGADACLSKPLSETRLLPALLT  648 (920)
T ss_pred             CEEEEECCCCHHHHHHHHHCCCCHHCCCCCCHHHHHHHHHC
T ss_conf             46997156434557887642530211277768899998722


No 114
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=99.01  E-value=1.7e-08  Score=71.40  Aligned_cols=118  Identities=10%  Similarity=0.103  Sum_probs=93.2

Q ss_pred             CCEEEEEEECCHHHHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCC
Q ss_conf             730599983898999999988641100202237-3069989999998618998499998059876778899988853289
Q gi|254780725|r   27 PRISVHVFCVTDTLYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDS  105 (427)
Q Consensus        27 ~~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p  105 (427)
                      +...|..- +|.++...+-...    +.+.+.. ....+..+|++.+......|+|+.|+.||.+|+++...+|++. .|
T Consensus       680 ~~lrVLvV-EDn~~N~~v~~~~----L~~lG~~v~~A~nG~eAle~l~~~~~fDlVLmDi~MP~mDG~eatr~iR~~-~~  753 (912)
T PRK11466        680 DGLRLLLI-EDNPLTQRITVEM----LNTSGAQVVAVGNAAQALETLQNSEPFAAALVDFDLPDYDGITLARQLAQQ-YP  753 (912)
T ss_pred             CCCEEEEE-ECCHHHHHHHHHH----HHHCCCEEEEECCHHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHC-CC
T ss_conf             88869999-4878899999999----998699899989999999999718998589876999999899999999861-99


Q ss_pred             CCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCC
Q ss_conf             980899816871899999997656264318999899999763102
Q gi|254780725|r  106 GTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIF  150 (427)
Q Consensus       106 ~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~  150 (427)
                      .+|+|.++.+.-..-.++.+.+|..+||.||++..++.+.+.+..
T Consensus       754 ~~pIIAlTA~a~~ed~~~~l~aGmd~~L~KPv~~~~L~~~l~~~l  798 (912)
T PRK11466        754 SLVLIGFSAHVIDETLRQRTSSLFRGIIPKPVPREVLGQLLAHYL  798 (912)
T ss_pred             CCCEEEECCCCCHHHHHHHHHCCCCCEECCCCCHHHHHHHHHHHH
T ss_conf             997899779878899999997699877549899999999999984


No 115
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=99.00  E-value=2.5e-08  Score=70.40  Aligned_cols=108  Identities=15%  Similarity=0.135  Sum_probs=85.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCC
Q ss_conf             98999999988641100202237306998999999861899849999805987677889998885328998089981687
Q gi|254780725|r   37 TDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTN  116 (427)
Q Consensus        37 ~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~  116 (427)
                      .+-....+....+.  -....+.-..++..++++.+... .|+++|+|+.+++.++++.+.++.    ++++||+++...
T Consensus        10 h~l~r~gl~~~l~~--~~~~~vv~~~~~~~~~l~~~~~~-~~dvvllD~~mp~~~g~~~~~~l~----~~~~vivls~~~   82 (196)
T PRK10360         10 HLIVRSGFAQLLGL--EPDLQVVAEFGSGREALAGLPGR-GVQVCICDISMPDISGLELLSQLP----KGMATIMLSVHD   82 (196)
T ss_pred             CHHHHHHHHHHHHC--CCCEEEEEEECCHHHHHHHHHHC-CCCEEEECCCCCCCCCHHHHHHHH----CCCCEEEEEECC
T ss_conf             79999999999812--99959999989999999988744-999999878878862077999984----387489997307


Q ss_pred             CHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             18999999976562643189998999997631023
Q gi|254780725|r  117 DVSLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       117 d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      |....++++++|+..|+.|...++++.+++..+..
T Consensus        83 ~~~~~~~a~~~Ga~g~l~K~~~~~el~~aI~~v~~  117 (196)
T PRK10360         83 SPALVEQALNAGARGFLSKRCSPDELIAAVHTVAT  117 (196)
T ss_pred             CHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHC
T ss_conf             59999999975998899778999999999999986


No 116
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.00  E-value=2.8e-08  Score=70.06  Aligned_cols=129  Identities=14%  Similarity=0.197  Sum_probs=95.8

Q ss_pred             HHHHHHCCCCCEEEEEEECCHHHHHHHHHHHHHHHHHHCEEEE-ECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHH
Q ss_conf             0677640187305999838989999999886411002022373-069989999998618998499998059876778899
Q gi|254780725|r   18 NLSESMCSLPRISVHVFCVTDTLYSVVERSKIDPRMSQVNMRI-TRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSAL   96 (427)
Q Consensus        18 ~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v-~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l   96 (427)
                      ...+.-.+.|...|..--+.+....+++.-     |.+-+.+| ...+..+|++.+... .+++|+.|+.||.+|+++..
T Consensus       515 ~~~~~~~~~~~lrILvVEDn~iN~~V~~~~-----L~~lG~~v~~A~nG~eALe~~~~~-~fDLILMDiqMP~MDG~Eat  588 (779)
T PRK11091        515 AFDEDDMPLPALNILLVEDIELNVIVARSL-----LEKLGNSVDVAMTGKDALEMFKPG-EYDLVLLDIQLPDMTGLDVA  588 (779)
T ss_pred             CCCCCCCCCCCCEEEEECCCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHCCC-CCCEEEEECCCCCCCHHHHH
T ss_conf             556666688888189986889999999999-----997599999989999999985069-99989982899999789999


Q ss_pred             HHHHHHCCCC--CEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCC
Q ss_conf             9888532899--80899816871899999997656264318999899999763102332
Q gi|254780725|r   97 EPLAEVCDSG--TKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQ  153 (427)
Q Consensus        97 ~~la~~~~p~--~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~  153 (427)
                      .++++.....  +|+|+++...- .--.+.+.+|.+|||.||++..+|.+.+.+.+...
T Consensus       589 r~IR~~~~~~~~~PIIALTAna~-~d~~~~l~aGMdd~L~KPi~~~~L~~~l~~~~~~~  646 (779)
T PRK11091        589 RELRERYGREDLPPLVALTANVL-KDKQEYLDAGMDDVLSKPLSVPALTAMIKKFWDTQ  646 (779)
T ss_pred             HHHHHCCCCCCCCCEEEEECCCC-HHHHHHHHCCCCCEEECCCCHHHHHHHHHHHHCCC
T ss_conf             99984257689992798818741-76999997699847518898999999999984645


No 117
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=98.99  E-value=3.8e-08  Score=69.27  Aligned_cols=21  Identities=5%  Similarity=0.022  Sum_probs=9.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHH
Q ss_conf             543578776889999999999
Q gi|254780725|r  300 VVITTSLDLAGLRNSKNLIDV  320 (427)
Q Consensus       300 vviV~~p~~~slr~a~~ll~~  320 (427)
                      .++|++=+.....-.+.+++.
T Consensus       826 rILVVEDNpINq~VL~~~L~~  846 (947)
T PRK10841        826 MILVVDDHPINRRLLADQLGS  846 (947)
T ss_pred             EEEEECCCHHHHHHHHHHHHH
T ss_conf             899990789999999999997


No 118
>KOG2825 consensus
Probab=98.94  E-value=8.2e-09  Score=73.36  Aligned_cols=173  Identities=20%  Similarity=0.297  Sum_probs=95.8

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCC----CCC--CCHHHHHCCCCCHHHH---
Q ss_conf             5379997469887756899999999996269949999787989860334389----987--8988863184561243---
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDK----DPI--NSISDAIYPVGRIDKA---  231 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~----~~~--~~l~d~l~~~~rlD~~---  231 (427)
                      ...+-|+|+||||||||.++.||..+|.. +.+|++|--|+..+ +.-.|++    .|.  .|... +...+ +|+.   
T Consensus        18 slKwifVGGKGGVGKTTcs~sLAvqla~~-r~~vLiISTDPAHN-lSDAF~qkftk~pt~V~Gf~n-LfAME-IDp~~e~   93 (323)
T KOG2825          18 SLKWIFVGGKGGVGKTTCSCSLAVQLAKV-RESVLIISTDPAHN-LSDAFSQKFTKTPTKVEGFEN-LFAME-IDPNVEM   93 (323)
T ss_pred             EEEEEEECCCCCCCCCCHHHHHHHHHHCC-CCCEEEEECCCCCC-HHHHHHHHHCCCCCCCCCHHH-HEEEE-CCCCHHH
T ss_conf             03699976767767653126899998616-88647861685311-678888775179830357223-10232-2872444


Q ss_pred             ------HHHHHHHCCCCCEEEEEC--CCCCCCHHCCCHHHHHHHHHHHH-HCCCEEEECCCCCCC---------------
Q ss_conf             ------376532024898068724--87612032079999999899985-128889973888889---------------
Q gi|254780725|r  232 ------FVSRLPVFYAENLSILTA--PAMLSRTYDFDEKMIVPVLDILE-QIFPLVILDVPHVWN---------------  287 (427)
Q Consensus       232 ------~l~~~l~~~~~gL~lL~a--~~~~~~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p~~~~---------------  287 (427)
                            +....-....+|..++.-  ..-+.-.+..+   +..++...+ -+|+.||.|+.|.-.               
T Consensus        94 ~~~~~m~~~~~~n~~~~g~g~l~e~~~~~Pgideams---fae~~klvk~~~F~~vVFDTAPTGHTLRlL~fP~~lek~l  170 (323)
T KOG2825          94 GDMPEMFGNAANNEGSDGKGMLQELANAFPGIDEAMS---FAEVMKLVKGMNFDVVVFDTAPTGHTLRLLQFPTTLEKGL  170 (323)
T ss_pred             HHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCHHHHHH---HHHHHHHHHCCCCCEEEECCCCCCCEEHHHCCCHHHHHHH
T ss_conf             1567875300212466523279998731888057775---8999988630664069951588764102521526899999


Q ss_pred             -----------HHH------------------------HHHHH---------HCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             -----------899------------------------99986---------2012543578776889999999999998
Q gi|254780725|r  288 -----------SWT------------------------QEVLT---------LSDKVVITTSLDLAGLRNSKNLIDVLKK  323 (427)
Q Consensus       288 -----------~~~------------------------~~~L~---------~AD~vviV~~p~~~slr~a~~ll~~l~~  323 (427)
                                 +..                        +..+.         .....+.|+-++..|+..+.|++..|.+
T Consensus       171 gKl~~l~~k~~pm~sq~~sm~g~~~~~~~~l~~kle~~~~~i~~vn~qFkdpd~TtFVcVcI~eflslyEteRliqeL~k  250 (323)
T KOG2825         171 GKLLSLKNKIGPMLSQMGSMFGMEDAGADDLAGKLEELLEVIEKVNEQFKDPDCTTFVCVCIAEFLSLYETERLIQELAK  250 (323)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_conf             99988998878899987635254557777899999999999999999707998725999877888868889999999986


Q ss_pred             CCCCCCCCEEEEECCCCCC
Q ss_conf             1987675389995658987
Q gi|254780725|r  324 LRPADKPPYLVLNQVKTPK  342 (427)
Q Consensus       324 ~~~~~~~~~iVlNr~~~~~  342 (427)
                      .+....  .+|+||.-.+.
T Consensus       251 ~~idth--nIIVNQLL~~~  267 (323)
T KOG2825         251 QGIDTH--NIIVNQLLFPD  267 (323)
T ss_pred             CCCCCC--CEEEEECCCCC
T ss_conf             488611--20133023799


No 119
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=98.92  E-value=9.2e-08  Score=66.89  Aligned_cols=115  Identities=13%  Similarity=0.131  Sum_probs=76.0

Q ss_pred             CEEEEEEECCHHHHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             30599983898999999988641100202237-30699899999986189984999980598767788999888532899
Q gi|254780725|r   28 RISVHVFCVTDTLYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSG  106 (427)
Q Consensus        28 ~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~  106 (427)
                      +.+|..--+.+....+++.-     |.+-+.+ ....+..+|++.+... .+|+|+.|+.||.+|+++...++++. .+.
T Consensus       958 ~l~ILvVeDn~~Nr~ll~~~-----L~~lG~~v~~a~nG~eAl~~~~~~-~fDlILmDi~MP~MDG~e~tr~IR~~-~~~ 1030 (1197)
T PRK09959        958 KLSILIADDHPTNRLLLKRQ-----LNLLGYDVDEATDGVQALHKVSMQ-HYDLLITDVNMPNMDGFELTRKLREQ-NSS 1030 (1197)
T ss_pred             CCEEEEECCCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHCC-CCCEEEECCCCCCCCHHHHHHHHHCC-CCC
T ss_conf             98799979989999999999-----998399999989999999997669-99999987978999899999999646-986


Q ss_pred             CEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHC
Q ss_conf             8089981687189999999765626431899989999976310
Q gi|254780725|r  107 TKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAI  149 (427)
Q Consensus       107 ~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~  149 (427)
                      +|+|.++......-..+++.+|..|||.||++.++|...+.+.
T Consensus      1031 ~PIialTA~a~~~~~~~cl~aGMdd~L~KPi~l~~L~~~L~~~ 1073 (1197)
T PRK09959       1031 LPIWGLTANAQANEREKGLNCGMNLCLFKPLTLDVLKTHLSQL 1073 (1197)
T ss_pred             CCEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
T ss_conf             9489997999999999999769983451889899999999853


No 120
>TIGR02875 spore_0_A sporulation transcription factor Spo0A; InterPro: IPR012052   Members of this group are response regulators/transcription factors that contain CheY-like receiver (phosphoacceptor) domain and a unique DNA-binding domain. Spo0A controls the entry of Bacillus subtilis into the developmental process of sporulation . Activation of the Spo0A transcription factor by phosphorylation serves as a developmental checkpoint and to integrate several physiological signals that control entry into the sporulation pathway. The signals are generated by conditions of nutrient deprivation, high cell density, the Krebs cycle, DNA replication, DNA damage, and some aspect of the chromosome partitioning machinery .  Activated Spo0A has multiple functions . It represses promoters (such as the abrB promoter) by binding to sites (0A boxes) downstream from the transcription start site. Spo0A also activates transcription from promoters used by two forms of RNA polymerase that differ by containing either the major sigma factor, sigma A (e.g. the spoIIE and spoIIG promoters) or the alternate sigma factor, sigma H (e.g. the spoIIA promoter). At promoters activated by Spo0A, the 0A boxes lie upstream of the transcription-initiation site.; GO: 0003677 DNA binding, 0005509 calcium ion binding, 0000160 two-component signal transduction system (phosphorelay), 0042173 regulation of sporulation, 0045449 regulation of transcription, 0050906 detection of stimulus during sensory perception.
Probab=98.88  E-value=9.8e-08  Score=66.72  Aligned_cols=121  Identities=11%  Similarity=0.200  Sum_probs=95.1

Q ss_pred             EEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCC-CC
Q ss_conf             05999838989999999886411002022373069989999998618998499998059876778899988853289-98
Q gi|254780725|r   29 ISVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDS-GT  107 (427)
Q Consensus        29 ~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p-~~  107 (427)
                      |.|.---++-|-.+.++.=..-  -..-.+--.+-+..+|++..+++. ||+||+|+=||=.||+..||+|++.... ..
T Consensus         3 Iri~i~DDNkEFc~lL~eY~~~--Q~D~EVvG~A~nG~~a~~~I~~q~-PD~vvLDIIMPhLDGiGVLEKl~~~~~~~~P   79 (270)
T TIGR02875         3 IRIVIADDNKEFCNLLKEYLAA--QEDMEVVGVAHNGVDALELIKEQK-PDVVVLDIIMPHLDGIGVLEKLNEIELKARP   79 (270)
T ss_pred             EEEEEEECCHHHHHHHHHHHHC--CCCEEEEEECCCHHHHHHHHHHCC-CCEEEECCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             2899982888999999999852--898389974147689999996089-9899951504300057999998898874489


Q ss_pred             EEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             089981687189999999765626431899989999976310233
Q gi|254780725|r  108 KVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       108 ~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      +||.++...=-..-+++|..||+-|++||++.+-|...++.++..
T Consensus        80 ~vi~LsAfGQE~ITqrA~~LGADYYvlKPfDle~L~~RIRQl~~~  124 (270)
T TIGR02875        80 RVIMLSAFGQEKITQRAVALGADYYVLKPFDLEILAARIRQLAEG  124 (270)
T ss_pred             CEEEEECCCHHHHHHHHHHCCCCCEEECHHHHHHHHHHHHHHHCC
T ss_conf             588852237558999999728981566504178899999986246


No 121
>COG1797 CobB Cobyrinic acid a,c-diamide synthase [Coenzyme metabolism]
Probab=98.87  E-value=1.5e-07  Score=65.66  Aligned_cols=200  Identities=14%  Similarity=0.140  Sum_probs=125.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886318456124337653202489
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAE  242 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~  242 (427)
                      -|.+.|...|+||||++..|..+|.+ +|.+|--.       -                 ..|+-+|+.+...+.-+.+-
T Consensus         2 ~vvIAg~~SG~GKTTvT~glm~aL~~-rg~~Vqpf-------K-----------------vGPDYIDP~~H~~atG~~sr   56 (451)
T COG1797           2 AVVIAGTSSGSGKTTVTLGLMRALRR-RGLKVQPF-------K-----------------VGPDYIDPGYHTAATGRPSR   56 (451)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHH-CCCCCCCC-------C-----------------CCCCCCCCHHHHHHHCCCCC
T ss_conf             35995488888589999999999986-68721665-------5-----------------68786381356676388567


Q ss_pred             CEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCC--------CC-CHHHHHHHHHCC-CCCCCCCCCHHHHH
Q ss_conf             806872487612032079999999899985128889973888--------88-989999986201-25435787768899
Q gi|254780725|r  243 NLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPH--------VW-NSWTQEVLTLSD-KVVITTSLDLAGLR  312 (427)
Q Consensus       243 gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~--------~~-~~~~~~~L~~AD-~vviV~~p~~~slr  312 (427)
                      +|          +.+.+.++.+..++....+.+|+.||.-=-        .. ...+..+...-+ -|++|++..-.|- 
T Consensus        57 NL----------D~~mm~~~~v~~~f~~~~~~adi~vIEGVMGLfDG~~~~~~~gSTA~lAk~l~~PVvLVid~~~~s~-  125 (451)
T COG1797          57 NL----------DSWMMGEEGVRALFARAAADADIAVIEGVMGLFDGRGSATDTGSTADLAKLLGAPVVLVVDASGLSR-  125 (451)
T ss_pred             CC----------CHHHCCHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCHHHHHHHHCCCEEEEEECCCHHH-
T ss_conf             77----------6544699899999998627898799961230236887776777799999985999899995752257-


Q ss_pred             HHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCC-CEEEECCCCHHHH
Q ss_conf             999999999981987675389995658987520059999998489537990687999999884796-1898889998999
Q gi|254780725|r  313 NSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGK-MIHEVDPKSAIAN  391 (427)
Q Consensus       313 ~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~-pi~e~~p~s~~a~  391 (427)
                      .+..++.-++...+...--.+|+||+++.+..++-.+.+++..+.++.+.||.+..+--..--.|- |..|   ...+..
T Consensus       126 S~AAiv~G~~~fdp~v~iaGVIlNrVgserH~~llr~Ale~~~gv~vlG~lpr~~~l~lp~RHLGLV~a~E---~~~~~~  202 (451)
T COG1797         126 SVAAIVKGFKHFDPDVNIAGVILNRVGSERHYELLRDALEEYTGVPVLGYLPRDDDLELPSRHLGLVPASE---RLELEA  202 (451)
T ss_pred             HHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCHH---HHHHHH
T ss_conf             89999988986199882578997247778899999987553279857987427855678541326534303---444899


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999985
Q gi|254780725|r  392 LLVDFSRVLM  401 (427)
Q Consensus       392 ~~~~La~~i~  401 (427)
                      -+..++..+.
T Consensus       203 ~~~~~a~~v~  212 (451)
T COG1797         203 KLEALAEVVE  212 (451)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999998


No 122
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=98.84  E-value=9.3e-08  Score=66.88  Aligned_cols=112  Identities=7%  Similarity=0.138  Sum_probs=84.9

Q ss_pred             ECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEEC
Q ss_conf             38989999999886411002022373069989999998618998499998059876778899988853289980899816
Q gi|254780725|r   35 CVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGD  114 (427)
Q Consensus        35 ~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~  114 (427)
                      ..++.....-...-.+-.+   .+.+...+...+.+.+.   .|++|++|+.++..++++...++-..-.|.++||+++.
T Consensus        16 ~~dp~l~~~~~a~~l~e~l---~v~~~l~~~~~al~~~~---~pdViLmDi~mp~~~gi~~~~e~i~~~~p~~kVliLTt   89 (216)
T PRK10100         16 ITKPSLQATALLQHLKQSL---AITGKLHNIQRSLDDIS---SGSIILLDMMEADKKLIHYWQDTLSRKNNNIKILLLNT   89 (216)
T ss_pred             ECCCHHHHHHHHHHHHHHH---HHHHEECCHHHHHHHCC---CCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEC
T ss_conf             5584299999999889876---47630247766776447---99989984887883089999999972599977999968


Q ss_pred             CCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             87189999999765626431899989999976310233
Q gi|254780725|r  115 TNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       115 ~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      .+|......++++|++.|+.|-.++++++++|+.+...
T Consensus        90 ~dd~e~v~~al~aGa~GyllK~~~~~~Li~aIr~v~~G  127 (216)
T PRK10100         90 PEDYPYREIENWPHINGVFYAMEDQERVVNGLQGVLRG  127 (216)
T ss_pred             CCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCC
T ss_conf             87489999997658766766899999999999999879


No 123
>PRK12374 putative dithiobiotin synthetase; Provisional
Probab=98.81  E-value=6.7e-07  Score=61.58  Aligned_cols=192  Identities=10%  Similarity=0.070  Sum_probs=119.5

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             53799974698877568999999999962699499997879898603343899878988863184561243376532024
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      .|-+-|.|..-+||||.+++.|..++.+ .|.+|...-- .+.|....      ..++.       .-|...+.......
T Consensus         2 mk~~FITGTDTdVGKT~vsaaL~~~l~~-~G~~v~~~KP-VasG~~~~------~~g~~-------~~Da~~l~~~~~~~   66 (231)
T PRK12374          2 LKRFFITGTDTSVGKTVVSRALLQALAS-QGKSVAGYKP-VAKGSKET------PEGLR-------NKDALVLQSVSTIE   66 (231)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEEEE-EECCCCCC------CCCCC-------HHHHHHHHHHHCCC
T ss_conf             9647998789995399999999999997-8994888856-88399668------99872-------47899999873789


Q ss_pred             CC-----CEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCH------HHHHHHHHCC-CCCCCCCCCH
Q ss_conf             89-----8068724876120320799999998999851288899738888898------9999986201-2543578776
Q gi|254780725|r  241 AE-----NLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNS------WTQEVLTLSD-KVVITTSLDL  308 (427)
Q Consensus       241 ~~-----gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~------~~~~~L~~AD-~vviV~~p~~  308 (427)
                      .+     -+.+-+..........+....+..-+..+.+.||++||.-..+|-.      ........-+ -+++|+...+
T Consensus        67 ~~~~~vnP~~~~~~~aa~~~~~~id~~~i~~~~~~l~~~~d~vlVEGAGG~~vPl~~~~~~~Dl~~~l~lPVILV~~~~L  146 (231)
T PRK12374         67 LPYEAVNPIALSEEESSVAHSCPINYTLISNGLANLTDKVDHVVVEGTGGWRSLMNDLRPLSEWVVQEQLPVLMVVGIQE  146 (231)
T ss_pred             CCHHHCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHCCEEEEECCCCEEECCCCCCHHHHHHHHCCCCEEEEECCCC
T ss_conf             99887197668866577445485789999999999885579799977986213047651499999983999999988986


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCC-CHHHHHHHHHHHCCCEEEEECCCHHH
Q ss_conf             88999999999999819876753899956589875-20059999998489537990687999
Q gi|254780725|r  309 AGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKK-PEISISDFCAPLGITPSAIIPFDGAV  369 (427)
Q Consensus       309 ~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~-~~i~~~~~~~~lg~~~~~~IP~D~~~  369 (427)
                      .++-.+--.++.+++.+.  .-..+|+|++++... .+-..+.+++.++.++.+.|||-++.
T Consensus       147 G~INHtLLT~eal~~~gl--~l~G~I~N~~~p~~~~~~e~i~~L~~~~~~P~LG~iP~l~~~  206 (231)
T PRK12374        147 GCINHALLTAQAIANDGL--PLIGWVANRINPGLAHYAEIIDVLGKKLPAPLIGELPYLPRA  206 (231)
T ss_pred             CHHHHHHHHHHHHHHCCC--CEEEEEEEEECCCHHHHHHHHHHHHHHCCCCEEEECCCCCCC
T ss_conf             848899999999997899--579999983679704678899999985599978868999998


No 124
>PRK00090 bioD dithiobiotin synthetase; Reviewed
Probab=98.77  E-value=1.2e-07  Score=66.17  Aligned_cols=187  Identities=13%  Similarity=0.108  Sum_probs=113.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886318456124337653202489
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAE  242 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~  242 (427)
                      +|-|.|..-|||||++++.|+..|.+ .|.+|...-- .+.|.-.   +.             ..-|..++.+......+
T Consensus         1 ~ifI~GT~T~vGKT~vt~~L~~~l~~-~G~~v~~~KP-v~tG~~~---~~-------------~~~Da~~~~~~~~~~~~   62 (223)
T PRK00090          1 VLFVTGTDTGVGKTVVTAALAQALRE-QGYRVAGYKP-VQSGCDG---GL-------------RNGDALALQRLSGLPLD   62 (223)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEECE-EEECCCC---CC-------------CCHHHHHHHHHHCCCCC
T ss_conf             98998689997699999999999997-8994899751-2048988---99-------------72799999998089998


Q ss_pred             ----CEEEEECCCCCC-----CHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC-CH-----HHHHHHHHCC-CCCCCCCC
Q ss_conf             ----806872487612-----03207999999989998512888997388888-98-----9999986201-25435787
Q gi|254780725|r  243 ----NLSILTAPAMLS-----RTYDFDEKMIVPVLDILEQIFPLVILDVPHVW-NS-----WTQEVLTLSD-KVVITTSL  306 (427)
Q Consensus       243 ----gL~lL~a~~~~~-----~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~-~~-----~~~~~L~~AD-~vviV~~p  306 (427)
                          +...+..|..+.     ....+..+.+...++.+++.||++||.-..++ .+     .........+ -+++|+..
T Consensus        63 ~~~~~p~~~~~p~sP~~aa~~~g~~i~~~~i~~~~~~l~~~~d~vlvEGaGGl~~Pl~~~~~~~Dla~~l~~pvILV~~~  142 (223)
T PRK00090         63 YELVNPYRFEEPLSPHLAARLEGVTIDLEKISAALRELAQQADLVLVEGAGGLLVPLTDDLTLADLAAQLQLPVILVVGV  142 (223)
T ss_pred             HHHHCCCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHCCCEEEEECC
T ss_conf             67605402588989899999909846899999999999831898999468865567567878899999968898999769


Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCC-CHHHHHHHHHHHCCCEEEEECCCHHH
Q ss_conf             7688999999999999819876753899956589875-20059999998489537990687999
Q gi|254780725|r  307 DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKK-PEISISDFCAPLGITPSAIIPFDGAV  369 (427)
Q Consensus       307 ~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~-~~i~~~~~~~~lg~~~~~~IP~D~~~  369 (427)
                      .+.++-.+.-.++.+++.+.  +-..+|+|++..... .....+.+++..|.++.+.|||-++.
T Consensus       143 ~lG~inhtllt~eal~~~gl--~v~GvI~N~~~~~~~~~~~~~~~l~~~~gvPvLG~iP~~~~~  204 (223)
T PRK00090        143 KLGCINHTLLTLEAIRARGL--PLAGWVANGVPPEGLRHAENLATLAELLPAPLLGRLPYLAEL  204 (223)
T ss_pred             CCCHHHHHHHHHHHHHHCCC--CEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEECCCCCCC
T ss_conf             88809999998999996899--489999968588366777689999985499889975899998


No 125
>COG3437 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]
Probab=98.75  E-value=2.3e-07  Score=64.50  Aligned_cols=115  Identities=17%  Similarity=0.292  Sum_probs=91.6

Q ss_pred             CEEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             30599983898999999988641100202237306998999999861899849999805987677889998885328998
Q gi|254780725|r   28 RISVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGT  107 (427)
Q Consensus        28 ~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~  107 (427)
                      +++|.---+.+.....+.+..   ||...++. ...+.+.|.+....++ |+++++|++++.+++.+.+.+|... .|.|
T Consensus        14 ~~~vl~vDD~~~~~~~~~~lL---~~~~y~v~-~ae~g~~a~kl~~~~~-~dlvllD~~mp~mdg~ev~~~lk~~-~p~t   87 (360)
T COG3437          14 KLTVLLVDDEPDNLEALRQLL---RMIGYRVI-EAENGEEALKLLQEEP-PDLVLLDVRMPEMDGAEVLNKLKAM-SPST   87 (360)
T ss_pred             CCEEEEECCCHHHHHHHHHHH---HHCCCCEE-EECCCHHHHHHHCCCC-CCEEEEECCCCCCCHHHHHHHHHHC-CCCC
T ss_conf             014889658666899999999---74264146-4147507788751168-8567764257776599999998724-9765


Q ss_pred             E---EEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHH
Q ss_conf             0---8998168718999999976562643189998999997631
Q gi|254780725|r  108 K---VIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISA  148 (427)
Q Consensus       108 ~---Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~  148 (427)
                      .   |++++...|.....+++..|+.||+.||+++.++...+..
T Consensus        88 ~~ip~i~lT~~~d~~~~~~~~~~g~~dyl~KP~~~~~l~~rv~~  131 (360)
T COG3437          88 RRIPVILLTAYADSEDRQRALEAGADDYLSKPISPKELVARVSS  131 (360)
T ss_pred             CCCCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             65325998605876999999972477775288988999999999


No 126
>PRK13886 conjugal transfer protein TraL; Provisional
Probab=98.73  E-value=2.9e-07  Score=63.86  Aligned_cols=143  Identities=17%  Similarity=0.086  Sum_probs=88.9

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             53799974698877568999999999962699499997879898603343899878988863184561243376532024
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      ++|=-|.+.|||||||.+|.-||.++.. .+.++..+|.|+-.++.+-+-.++                           
T Consensus         2 a~IH~vlqgKGGVGKS~va~~LaQY~~~-~~~~~~~iDTDpvN~tf~~ykal~---------------------------   53 (241)
T PRK13886          2 AKIHMVLQGKGGVGKSMIAATIAQYKAG-KGQKPLCIDTDPVNATFEGYKALN---------------------------   53 (241)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCCCEEECCCCCCCHHHCCCCC---------------------------
T ss_conf             7599985588863099999999999983-599985560899970534214367---------------------------


Q ss_pred             CCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCC-HHH--------HHHHHHCCCC---CCCCCCCH
Q ss_conf             89806872487612032079999999899985128889973888889-899--------9998620125---43578776
Q gi|254780725|r  241 AENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWN-SWT--------QEVLTLSDKV---VITTSLDL  308 (427)
Q Consensus       241 ~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~-~~~--------~~~L~~AD~v---viV~~p~~  308 (427)
                      ...+.++       ...++....++.+++.+...=+-+|||.+.+.- +..        ..++....+-   ..|++.. 
T Consensus        54 v~~i~I~-------e~~~i~~r~FD~l~E~i~~~~~~~VID~GAstfvPL~~Yl~eN~v~~ll~e~G~~v~iH~vi~GG-  125 (241)
T PRK13886         54 VRRLNIM-------DGDEINTRNFDALVEMIASTEGDVIIDNGASSFVPLSHYLISNQVPALLQDMGHELVVHTVVTGG-  125 (241)
T ss_pred             CEEEEEE-------CCCCCCHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHHHCCHHHHHHHCCCEEEEEEEECCC-
T ss_conf             5577752-------38865666668999998568998899885176778999998788699999779739999984598-


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEEEEECCC
Q ss_conf             8899999999999981987675389995658
Q gi|254780725|r  309 AGLRNSKNLIDVLKKLRPADKPPYLVLNQVK  339 (427)
Q Consensus       309 ~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~  339 (427)
                      .++.++.+.+..+-..=+...++.+++|.+.
T Consensus       126 qa~~DT~~gl~~l~~~~~~~~~~VVWlN~~~  156 (241)
T PRK13886        126 QALLDTVSGFAQLASQFPAECLFVVWLNPYW  156 (241)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCEEEEECCCC
T ss_conf             4277899999999986587787899974887


No 127
>PRK13896 cobyrinic acid a,c-diamide synthase; Provisional
Probab=98.67  E-value=1.3e-06  Score=59.92  Aligned_cols=179  Identities=8%  Similarity=-0.044  Sum_probs=106.3

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      |-|.+.|...|+||||++.-|..+|++ +|.+|--.-.                        +|+-+|+.+...+.-+-.
T Consensus         2 kgilIAa~~SgsGKTtvt~gL~~aL~~-rG~~Vq~FK~------------------------GPDYIDP~~h~~a~G~~~   56 (432)
T PRK13896          2 DGVVLAGTSSGVGKTVATLAVLQALAD-AGYDVQPAKA------------------------GPDFIDPSHHEAVVDTPS   56 (432)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHH-CCCCCCCCCC------------------------CCCCCCHHHHHHHHCCCC
T ss_conf             628997789999899999999999997-8496376666------------------------847519899999968984


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC------CHHHHHHHHHCCCCCCCCCCCHHHHHHHH
Q ss_conf             980687248761203207999999989998512888997388888------98999998620125435787768899999
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVW------NSWTQEVLTLSDKVVITTSLDLAGLRNSK  315 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~------~~~~~~~L~~AD~vviV~~p~~~slr~a~  315 (427)
                      -+|+.          +..+++.+..++  .+...|+.||.---+.      +....+-+... -|++|++..-.+-.- .
T Consensus        57 ~NLD~----------~m~~~~~v~~~~--~~~~aDiaviEGvMGLyDG~~~Sta~lA~~l~~-PVvLVvd~~~~~~s~-a  122 (432)
T PRK13896         57 RSLDP----------WLSGEDGMRRTY--WRGTGDVCVVEGMMGLYDGTVASTAAVAEELDL-PVVLVVDAKAGMESV-A  122 (432)
T ss_pred             CCCCH----------HHCCHHHHHHHH--HHCCCCEEEEEECCCCCCCCCCCHHHHHHHHCC-CEEEEEECCHHHHHH-H
T ss_conf             46891----------018989999999--727998699961232457887758999998499-989999332018889-9


Q ss_pred             HHHHHHHHCCCC----CCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEE
Q ss_conf             999999981987----675389995658987520059999998489537990687999999884796189
Q gi|254780725|r  316 NLIDVLKKLRPA----DKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIH  381 (427)
Q Consensus       316 ~ll~~l~~~~~~----~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~  381 (427)
                      .++.-++...+.    -.-..+|+|++.+++..+.-.+.+++  +.++.+.||.+....-.+-..|-...
T Consensus       123 A~v~G~~~f~~~~~~d~~iaGVIlN~v~s~rh~~~l~~al~~--~i~vlG~lPr~~~l~lp~RHLGL~~~  190 (432)
T PRK13896        123 ATALGFQAYADRAGVDIDVAGVLAQRAHGGRHADGIRDALPD--ELTYFGRVPPRSDLEIPDRHLGLHMG  190 (432)
T ss_pred             HHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHC--CCCEEEEECCCCCCCCCCCCCCCCCC
T ss_conf             999999972412476524766884267758899999999870--89489884247778984102598733


No 128
>TIGR00313 cobQ cobyric acid synthase CobQ; InterPro: IPR004459 Cobyric acid synthase (CobQ) catalyses amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide in the biosynthesis of cobalamin. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolysed for each amidation .; GO: 0003824 catalytic activity, 0009236 cobalamin biosynthetic process.
Probab=98.66  E-value=3.3e-08  Score=69.60  Aligned_cols=193  Identities=18%  Similarity=0.250  Sum_probs=121.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCC-----CCCCCHHHH-------HCCCCCHHHH
Q ss_conf             9997469887756899999999996269949999787989860334389-----987898886-------3184561243
Q gi|254780725|r  164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDK-----DPINSISDA-------IYPVGRIDKA  231 (427)
Q Consensus       164 Iav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~-----~~~~~l~d~-------l~~~~rlD~~  231 (427)
                      |-|.|+..-.|||++++.|...||+ +|.+|.      +|-..+.-||-     +.+-+++.+       +....++++.
T Consensus         1 iMV~GTsS~AGKs~l~AaLCRiL~r-rGy~VA------PFKsQNMSLNSfvt~~~~EiA~AQ~~QA~AAGieP~~~mNPv   73 (502)
T TIGR00313         1 IMVVGTSSSAGKSLLTAALCRILAR-RGYRVA------PFKSQNMSLNSFVTAEGGEIAIAQALQALAAGIEPSVHMNPV   73 (502)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHC-CCCCCC------CCHHHHHHHHHHHCCCCCEEEHHHHHHHHHCCCCCCCCCCCC
T ss_conf             9542011540289999999999852-788127------850110101333113787551376899986387886234871


Q ss_pred             HHHHHHHCCCCCEEEEECCCCCCCHH-------CCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHH----------HHHH
Q ss_conf             37653202489806872487612032-------079999999899985128889973888889899----------9998
Q gi|254780725|r  232 FVSRLPVFYAENLSILTAPAMLSRTY-------DFDEKMIVPVLDILEQIFPLVILDVPHVWNSWT----------QEVL  294 (427)
Q Consensus       232 ~l~~~l~~~~~gL~lL~a~~~~~~~~-------~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~----------~~~L  294 (427)
                      +|+.---- .+.+=++--|..-....       +...+.+..-++.|.+.|||||+--..+..+..          .+-+
T Consensus        74 LLKPkgdf-~SQviv~G~a~g~~~~~~Y~~~~~d~~~~~i~eSle~L~~~Yd~vv~EGAGS~AEINL~~rDLaN~~iA~~  152 (502)
T TIGR00313        74 LLKPKGDF-TSQVIVHGRAVGDMNAQEYYKNKVDFLLKAIKESLEILAEEYDLVVIEGAGSPAEINLKERDLANMRIAEL  152 (502)
T ss_pred             CCCCCCCC-EEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCHHHHHHHH
T ss_conf             01678884-66789841124667615677799999999999999875202888998268871000533157224789864


Q ss_pred             HHCCCCCCCCCCCH----HHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCC-CHHHHHHHHHHHCCCEEEEECCCHHH
Q ss_conf             62012543578776----88999999999999819876753899956589875-20059999998489537990687999
Q gi|254780725|r  295 TLSDKVVITTSLDL----AGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKK-PEISISDFCAPLGITPSAIIPFDGAV  369 (427)
Q Consensus       295 ~~AD~vviV~~p~~----~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~-~~i~~~~~~~~lg~~~~~~IP~D~~~  369 (427)
                      ..|| +++|++=|.    +|+..|..||+.=.+.    .-=.+|+||++-... -+-..+.+|+.-|.++.++||||-.+
T Consensus       153 ~~A~-~iLvADIDRGGVFAsi~GTl~LL~~~~r~----liKG~vINkfRG~~~vL~~GI~~lEelTGiPVLGv~PY~~~l  227 (502)
T TIGR00313       153 ADAD-VILVADIDRGGVFASIYGTLKLLPEEERK----LIKGIVINKFRGNVDVLESGIEKLEELTGIPVLGVLPYDENL  227 (502)
T ss_pred             CCCC-EEEEEECCCCCCHHHHHHHHHHCCCCCCC----EECEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCC
T ss_conf             3976-79997507774324337466618834575----003068835468724434456899885484234465012577


No 129
>PRK10416 cell division protein FtsY; Provisional
Probab=98.66  E-value=4.7e-06  Score=56.40  Aligned_cols=179  Identities=15%  Similarity=0.146  Sum_probs=107.6

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             53799974698877568999999999962699499997879898603343899878988863184561243376532024
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      -.||.|+| --|+||||...-||..+.+ .|++|+|+=+|..-..+--.|                       ....  -
T Consensus       295 P~VIl~vG-vNG~GKTTTigKLA~~~~~-~gkkVllaA~DTfRaAAieQL-----------------------~~w~--~  347 (499)
T PRK10416        295 PFVILMVG-VNGVGKTTTIGKLARQFEQ-QGKSVMLAAGDTFRAAAVEQL-----------------------QVWG--Q  347 (499)
T ss_pred             CEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEEEECCCCHHHHHHH-----------------------HHHH--C
T ss_conf             87999974-7878789899999999997-799537884066756899999-----------------------9984--2


Q ss_pred             CCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHH---H------HHHHH-----HCCCCCCCCCC
Q ss_conf             8980687248761203207999999989998512888997388888989---9------99986-----20125435787
Q gi|254780725|r  241 AENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSW---T------QEVLT-----LSDKVVITTSL  306 (427)
Q Consensus       241 ~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~---~------~~~L~-----~AD~vviV~~p  306 (427)
                      ..++.++.....-+..    .-.+..+-..-.+.||+||+|+..+...-   .      ..++.     .-+.+++|.+.
T Consensus       348 r~~v~vi~~~~g~Dpa----~V~~dai~~a~~~~~DvviiDTAGRl~~~~~LM~EL~ki~rvi~k~~~~aP~e~lLVlDa  423 (499)
T PRK10416        348 RNNIPVIAQHTGADSA----SVIFDAIQAAKARNVDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPHEVMLTIDA  423 (499)
T ss_pred             CCCCEEEECCCCCCHH----HHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEC
T ss_conf             4573698368999979----999999999997299989985776432609999999999999972378999748999778


Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEE---------EECCCHHHHHHHHHC
Q ss_conf             7688999999999999819876753899956589875200599999984895379---------906879999998847
Q gi|254780725|r  307 DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSA---------IIPFDGAVFGMSANS  376 (427)
Q Consensus       307 ~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~---------~IP~D~~~~~~A~~~  376 (427)
                      ...  .|+.+-.+.+.+.   ..--++|+.+.+...++-+ .=.+...++.++.+         .-||++.-|..|...
T Consensus       424 ~tG--Qna~~qak~F~e~---~~ltGiIlTKlDGtAKGG~-~lsi~~~~~~PI~fiG~GE~idDL~~F~~~~Fv~aLf~  496 (499)
T PRK10416        424 STG--QNAVSQAKLFHEA---VGLTGITLTKLDGTAKGGV-IFSVADQFGIPIRYIGVGERIEDLRPFKADDFIEALFA  496 (499)
T ss_pred             CCC--HHHHHHHHHHHHC---CCCCEEEEECCCCCCCCHH-HHHHHHHHCCCEEEEECCCCHHHCCCCCHHHHHHHHHC
T ss_conf             767--7899999998442---7997599965677885259-99999998839599867988220667798999999844


No 130
>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]
Probab=98.63  E-value=1.9e-06  Score=58.83  Aligned_cols=119  Identities=14%  Similarity=0.227  Sum_probs=92.1

Q ss_pred             CEEEEEEECCHHHHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCC-C
Q ss_conf             30599983898999999988641100202237-306998999999861899849999805987677889998885328-9
Q gi|254780725|r   28 RISVHVFCVTDTLYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCD-S  105 (427)
Q Consensus        28 ~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~-p  105 (427)
                      ...|.+--+.......+++.     |.+.+.. ..+.+-..|...+.+. .|++||+|..++..|+++...++...-. .
T Consensus       132 ~~kILvvdD~~~~~~~l~~~-----L~~~g~~v~~a~~~~~Al~~~~e~-~~dlil~d~~mp~~dg~el~~~lr~~~~t~  205 (435)
T COG3706         132 PKKILVVDDDATQRERLRRI-----LQVEGFRVVEATDGEEALLQLAEL-PPDLVLLDANMPDMDGLELCTRLRQLERTR  205 (435)
T ss_pred             CCEEEEECCCHHHHHHHHHH-----HHHCCCEEEEECCHHHHHHHHHCC-CCCEEEEECCCCCCCHHHHHHHHHCCCCCC
T ss_conf             75089974807799999999-----875363366515989999997468-985899955787667899999972444445


Q ss_pred             CCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             98089981687189999999765626431899989999976310233
Q gi|254780725|r  106 GTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTP  152 (427)
Q Consensus       106 ~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~  152 (427)
                      .++||.++...|....-++++.|+.||+.+|++..++...+.+.+..
T Consensus       206 ~ipii~~~~~~d~~~~~~Af~~G~~Dyi~kPi~~~~l~~Rl~~~l~~  252 (435)
T COG3706         206 DIPIILLSSKDDDELVVRAFELGVNDYITKPIEEGELRARLRRQLRR  252 (435)
T ss_pred             CCCEEEEECCCCHHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHHHH
T ss_conf             66389995266347899999768851673477879999999999985


No 131
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=98.59  E-value=7.1e-07  Score=61.46  Aligned_cols=93  Identities=19%  Similarity=0.185  Sum_probs=76.3

Q ss_pred             EEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCC-HHHHHHHHHCCCCEEECC
Q ss_conf             2373069989999998618998499998059876778899988853289980899816871-899999997656264318
Q gi|254780725|r   57 NMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTND-VSLYRALISNHVSEYLIE  135 (427)
Q Consensus        57 ~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d-~~l~r~l~r~Gv~dyl~~  135 (427)
                      ++.-..++.++|+.+.... .|++++.|+++|..++++.+.+|+..+ |+++|||++.+++ ..+...++..|++.|+.|
T Consensus        21 ~vv~e~~~g~EAl~~~~~~-~v~~~LmDi~mP~~dGL~~~~~L~r~~-P~vriLVLTm~d~e~~v~~aL~~aga~Gyl~K   98 (205)
T PRK11475         21 HIFSSQSSFQDAMSRISFS-AVIFSLSAMRSERREGLSCLTELAIKF-PRMRRLVIADDDIEARLIGSLSPSPLDGVLSK   98 (205)
T ss_pred             EEEECCCCHHHHHHCCCCC-CCEEEEECCCCCCCCHHHHHHHHHHHC-CCCEEEEEECCCCHHHHHHHHHHHHCCEEEEC
T ss_conf             9950545699998628866-643898538999976699999999978-99718999747687999999998416688856


Q ss_pred             CCCHHHHHHHHHHCCC
Q ss_conf             9998999997631023
Q gi|254780725|r  136 PLSVADIINSISAIFT  151 (427)
Q Consensus       136 P~~~~~l~~ai~~~~~  151 (427)
                      ....+++.+++.....
T Consensus        99 ~~~~~eL~~Ai~~~~~  114 (205)
T PRK11475         99 ASTLEILQQELFLSLN  114 (205)
T ss_pred             CCCHHHHHHHHHHHHC
T ss_conf             7889999999999870


No 132
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=98.54  E-value=4.8e-06  Score=56.33  Aligned_cols=59  Identities=15%  Similarity=0.014  Sum_probs=20.7

Q ss_pred             CCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCH-HHHHHHHHCCCCEEEECCCC
Q ss_conf             753899956589875200599999984895379906879-99999884796189888999
Q gi|254780725|r  329 KPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDG-AVFGMSANSGKMIHEVDPKS  387 (427)
Q Consensus       329 ~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~-~~~~~A~~~G~pi~e~~p~s  387 (427)
                      ..+-+|+.-+.++..+.............-+....-|.. ....++...|...+...|-+
T Consensus       744 ~~~DLvltD~~p~~~g~~~~~~l~~~~p~lpVilsg~~~~~~~~~~~~~~~~~fL~KPfs  803 (831)
T PRK13837        744 KRFDLVLVDQPSLGDSQLAIAALHAAAPTLPIILAGSSLKMAAREALATAIAEILPKPIS  803 (831)
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHCCCCEEEEECCCCHHHHHCHHHCCCCEEEECCCC
T ss_conf             985399988999998799999998618997499976881443311022266706509999


No 133
>COG0784 CheY FOG: CheY-like receiver [Signal transduction mechanisms]
Probab=98.53  E-value=1.1e-05  Score=54.03  Aligned_cols=117  Identities=15%  Similarity=0.255  Sum_probs=87.2

Q ss_pred             EEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCH-HHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             0599983898999999988641100202237306998-999999861899849999805987677889998885328998
Q gi|254780725|r   29 ISVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSI-AEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGT  107 (427)
Q Consensus        29 ~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~-~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~  107 (427)
                      ..|..-.+++.....++....+..   ..+ ....+. .+|++.+....-|+++++|..++..++++.+.++... .+.+
T Consensus         6 ~~vLivdD~~~~~~~~~~~l~~~g---~~v-~~a~~~~~~al~~~~~~~~~dlii~D~~mp~~~G~~~~~~l~~~-~~~~   80 (130)
T COG0784           6 LRVLVVDDEPVNRRLLKRLLEDLG---YEV-VEAADGEEEALELLRELPQPDLILLDINMPGMDGIELLRRLRAR-GPNI   80 (130)
T ss_pred             CEEEEECCCHHHHHHHHHHHHHCC---CEE-EEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHH-CCCC
T ss_conf             889997899999999999998779---789-99578399999998627899999980688788889999999971-8999


Q ss_pred             EEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHH-HHHHHHHCC
Q ss_conf             0899816871899999997656264318999899-999763102
Q gi|254780725|r  108 KVIVIGDTNDVSLYRALISNHVSEYLIEPLSVAD-IINSISAIF  150 (427)
Q Consensus       108 ~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~-l~~ai~~~~  150 (427)
                      +||+++...+.....++++.|+.+|+.||+...+ +...+....
T Consensus        81 pvv~~t~~~~~~~~~~~~~~g~~~~l~kP~~~~~~l~~~i~~~~  124 (130)
T COG0784          81 PVILLTAYADEADRERALAAGADDYLTKPIFLEEELLAALRRLL  124 (130)
T ss_pred             CEEEEECCCCHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHH
T ss_conf             68999867867659999976876897589987999999999998


No 134
>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]
Probab=98.51  E-value=4.6e-06  Score=56.45  Aligned_cols=149  Identities=17%  Similarity=0.199  Sum_probs=98.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHCEEEEECCC-HHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECC
Q ss_conf             9899999998864110020223730699-899999986189984999980598767788999888532899808998168
Q gi|254780725|r   37 TDTLYSVVERSKIDPRMSQVNMRITRGS-IAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDT  115 (427)
Q Consensus        37 ~~~~~~~~~~~~~drr~~~~~~~v~~g~-~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~  115 (427)
                      +......+-.-     ++++|..+..-+ ..+|.+.+. +-.|+++++|+.++..++++..++..+.. +.+++|.|+.+
T Consensus         9 d~a~~~~l~~i-----Ls~~~~~~~~~~~~~eal~~Le-~~kpDLifldI~mp~~ngiefaeQvr~i~-~~v~iifIssh   81 (361)
T COG3947           9 DAAIVKLLSVI-----LSRAGHEVRSCSHPVEALDLLE-VFKPDLIFLDIVMPYMNGIEFAEQVRDIE-SAVPIIFISSH   81 (361)
T ss_pred             HHHHHHHHHHH-----HHHCCCHHHCCCCHHHHHHHHH-HCCCCEEEEEEECCCCCHHHHHHHHHHHH-CCCCEEEEECC
T ss_conf             38999999999-----9861102100688788999998-43887799985237860878999998753-14868999630


Q ss_pred             CCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCCC-CCCCCEEEEEEECC-----CCCC---HHHHHHHHHHHH
Q ss_conf             71899999997656264318999899999763102332223-45675379997469-----8877---568999999999
Q gi|254780725|r  116 NDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQEEG-KGSSGCSISFIGSR-----GGVG---SSTIAHNCAFSI  186 (427)
Q Consensus       116 ~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~-~~~~grvIav~g~K-----GGvG---kTTiA~nLA~~L  186 (427)
                      ..-..-+.-|.  ..|||+||++++.|-+++.+......+. ....+..|..+|.-     -|.-   .|+=|..|=..|
T Consensus        82 ~eya~dsf~~n--~~dYl~KPvt~ekLnraIdr~~k~ve~~~eee~~~~iscfgg~ev~~rqg~~vkWis~KA~ELFayL  159 (361)
T COG3947          82 AEYADDSFGMN--LDDYLPKPVTPEKLNRAIDRRLKRVELTAEEESGTQISCFGGTEVVLRQGQQVKWISRKALELFAYL  159 (361)
T ss_pred             HHHHHHHCCCC--HHHHCCCCCCHHHHHHHHHHHHCCCCCCCHHCCCEEEEECCCEEEECCCCCEEEEHHHHHHHHHHHH
T ss_conf             56523203556--6754168888889999999874024444100137046750640012347842230136799999999


Q ss_pred             HHHCCCCE
Q ss_conf             96269949
Q gi|254780725|r  187 ASVFAMET  194 (427)
Q Consensus       187 A~~~~~~V  194 (427)
                      -.+.|+.|
T Consensus       160 v~hkgk~v  167 (361)
T COG3947         160 VEHKGKEV  167 (361)
T ss_pred             HHHCCCCC
T ss_conf             98248855


No 135
>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]
Probab=98.46  E-value=1.1e-05  Score=54.12  Aligned_cols=186  Identities=15%  Similarity=0.167  Sum_probs=112.0

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCC-CCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             753799974698877568999999999962699499997879898-6033438998789888631845612433765320
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYG-TANINFDKDPINSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g-~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      ...+|.+.| -+|+||||+.--|...|.+ .|.+|.++=-|+... +-+..||            +.-|+..     .. 
T Consensus        50 ~a~viGITG-~PGaGKSTli~~L~~~l~~-~G~rVaVlAVDPSSp~TGGsiLG------------DRiRM~~-----~~-  109 (323)
T COG1703          50 NAHVIGITG-VPGAGKSTLIEALGRELRE-RGHRVAVLAVDPSSPFTGGSILG------------DRIRMQR-----LA-  109 (323)
T ss_pred             CCCEEEECC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEECCCCCCCCCCCCC------------CHHHHHH-----HC-
T ss_conf             983787317-9988668899999999997-79678999988999987853012------------0766776-----44-


Q ss_pred             CCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHH-HCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHH-HHHHH
Q ss_conf             2489806872487612032079999999899985-128889973888889899999862012543578776889-99999
Q gi|254780725|r  239 FYAENLSILTAPAMLSRTYDFDEKMIVPVLDILE-QIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGL-RNSKN  316 (427)
Q Consensus       239 ~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~sl-r~a~~  316 (427)
                       ..+|+++=+.|..- ....++... ...+..+. ..||+|||.+- +.+..-..+...+|.+++|+.|....= ...|.
T Consensus       110 -~~~~vFiRs~~srG-~lGGlS~at-~~~i~~ldAaG~DvIIVETV-GvGQsev~I~~~aDt~~~v~~pg~GD~~Q~iK~  185 (323)
T COG1703         110 -VDPGVFIRSSPSRG-TLGGLSRAT-REAIKLLDAAGYDVIIVETV-GVGQSEVDIANMADTFLVVMIPGAGDDLQGIKA  185 (323)
T ss_pred             -CCCCEEEEECCCCC-CCHHHHHHH-HHHHHHHHHCCCCEEEEEEC-CCCCCHHHHHHHCCEEEEEECCCCCCHHHHHHH
T ss_conf             -69981784268776-510166889-99999998618988999814-788415577652166899965788827888874


Q ss_pred             HHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCE--EEEECCCHHHHHHHHHCCC
Q ss_conf             9999998198767538999565898752005999999848953--7990687999999884796
Q gi|254780725|r  317 LIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITP--SAIIPFDGAVFGMSANSGK  378 (427)
Q Consensus       317 ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~--~~~IP~D~~~~~~A~~~G~  378 (427)
                      =+     +...+   .+|+|+++. +..+....++..++....  ...-++.|.++..+...|+
T Consensus       186 Gi-----mEiaD---i~vINKaD~-~~A~~a~r~l~~al~~~~~~~~~~~W~ppv~~t~A~~g~  240 (323)
T COG1703         186 GI-----MEIAD---IIVINKADR-KGAEKAARELRSALDLLREVWRENGWRPPVVTTSALEGE  240 (323)
T ss_pred             HH-----HHHHH---EEEEECCCH-HHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCC
T ss_conf             14-----65403---356725672-658999999999997511454236888864676413577


No 136
>PRK11697 putative two-component response-regulatory protein YehT; Provisional
Probab=98.44  E-value=7.9e-06  Score=55.01  Aligned_cols=112  Identities=11%  Similarity=0.213  Sum_probs=80.3

Q ss_pred             EEECCHHH-HHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             98389899-99999886411002022373069989999998618998499998059876778899988853289980899
Q gi|254780725|r   33 VFCVTDTL-YSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIV  111 (427)
Q Consensus        33 ~f~~~~~~-~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Viv  111 (427)
                      +-|+|+.. ...++.-.++  .....+....++..+|++.+... .||++++|+.+++.+|++.+..|..  +..+.+|.
T Consensus         5 ~I~DDe~~~~~~l~~~l~~--~~~i~~~~~~~~~~eal~~~~~~-~~DllfLDI~m~~~~G~ela~~l~~--~~~~~iIF   79 (239)
T PRK11697          5 LIVDDEPLAREELRELLQE--EGDIEIVGECSNAIEALGAIHRL-KPDVVFLDIQMPRISGLELVGMLDP--EHMPYIVF   79 (239)
T ss_pred             EEECCCHHHHHHHHHHHHH--CCCEEEEEEECCHHHHHHHHHHC-CCCEEEECCCCCCCCHHHHHHHHCC--CCCCEEEE
T ss_conf             9996999999999999975--87989999989999999999853-9999998399869599999998373--34986999


Q ss_pred             EECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             8168718999999976562643189998999997631023
Q gi|254780725|r  112 IGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       112 ig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      ++.+.+-  ..++.+.++.|||.||++.+++..++.++..
T Consensus        80 vT~~~e~--a~~af~~~a~dYllKP~~~e~l~~~l~r~~~  117 (239)
T PRK11697         80 VTAFDEY--AIKAFEEHAFDYLLKPIDPARLAKTLARLRQ  117 (239)
T ss_pred             EECCHHH--HHHHHHCCCCEEEECCCCHHHHHHHHHHHHH
T ss_conf             9586899--9999730972665389999999999999999


No 137
>TIGR00959 ffh signal recognition particle protein; InterPro: IPR004780    The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane.    This entry represents various SRP subunits.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=98.44  E-value=5.3e-05  Score=49.94  Aligned_cols=186  Identities=13%  Similarity=0.113  Sum_probs=111.2

Q ss_pred             HHHHHHHHHHC---CCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHH-HHHHCCCCEEEEECCCCCCCCHHHCCCCC
Q ss_conf             89999976310---233222345675379997469887756899999999-99626994999978798986033438998
Q gi|254780725|r  139 VADIINSISAI---FTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFS-IASVFAMETLLADLDLPYGTANINFDKDP  214 (427)
Q Consensus       139 ~~~l~~ai~~~---~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~-LA~~~~~~VlLvDlDl~~g~~~~~l~~~~  214 (427)
                      .++|++-+..-   -..-.....+ =-+|-++| ==|.||||++.=||.+ |-+..+++||||=||++-..+-       
T Consensus        78 ~eEL~~~LG~~~~E~~~L~~~~~~-P~vilmvG-LQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~yRPAA~-------  148 (439)
T TIGR00959        78 HEELVAILGGKGRESAELKLAEKR-PTVILMVG-LQGSGKTTTAGKLALYLLKKKEGKKVLLVACDLYRPAAI-------  148 (439)
T ss_pred             HHHHHHHCCCCCCCCCCCCCCCCC-CEEEEEEC-CCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCCCHHHH-------
T ss_conf             689998516667325675556786-83899731-378857889999999999986389703403210347899-------


Q ss_pred             CCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEE-CCCCCC--CHHCCCHHHHHHHHHHHH-HCCCEEEECCCCCCCHH-
Q ss_conf             7898886318456124337653202489806872-487612--032079999999899985-12888997388888989-
Q gi|254780725|r  215 INSISDAIYPVGRIDKAFVSRLPVFYAENLSILT-APAMLS--RTYDFDEKMIVPVLDILE-QIFPLVILDVPHVWNSW-  289 (427)
Q Consensus       215 ~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~-a~~~~~--~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p~~~~~~-  289 (427)
                                    |+  |.....+  =|+.+++ -+..-.  .+-    +-.++.++.++ ..||+|||||..+..-. 
T Consensus       149 --------------~Q--L~~Lg~Q--~gVpvf~h~~~~~~p~~Pv----~ia~~Al~~Ak~~~~D~vI~DTAGRL~ID~  206 (439)
T TIGR00959       149 --------------EQ--LKVLGEQ--VGVPVFAHLGKGQSPDDPV----EIARQALEEAKENGFDVVIVDTAGRLQIDE  206 (439)
T ss_pred             --------------HH--HHHHHHH--CCCCCCCCCCCCCCCCCHH----HHHHHHHHHHHHCCCCEEEEECCCCHHHHH
T ss_conf             --------------99--9997675--2887110047888988778----999999999997489789972675125559


Q ss_pred             --H-----HHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEE
Q ss_conf             --9-----99986201254357877688999999999999819876753899956589875200599999984895379
Q gi|254780725|r  290 --T-----QEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSA  361 (427)
Q Consensus       290 --~-----~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~  361 (427)
                        .     ......-|++++|++  -.+=.++-++-+.+.+ +  -.--++|+.+.+...|+-... .+...+|.|+-+
T Consensus       207 ~LM~EL~~iK~~~nP~EiLlVvD--aM~GQdAvn~A~~F~e-~--lgltG~vltK~DGDaRGGAAL-S~~~~tg~PIKF  279 (439)
T TIGR00959       207 ELMEELAEIKEILNPDEILLVVD--AMTGQDAVNTAKTFNE-R--LGLTGVVLTKLDGDARGGAAL-SVRSVTGKPIKF  279 (439)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCH--HCCHHHHHHHHHHHCC-C--CCCCEEEEECCCCCCHHHHHH-HHHHHHCCCEEE
T ss_conf             99999999988868870541220--1021699999986366-0--013547885475660578999-999996896188


No 138
>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=98.42  E-value=1.7e-05  Score=52.89  Aligned_cols=242  Identities=12%  Similarity=0.068  Sum_probs=127.4

Q ss_pred             HHHHHHHHHCCCCEEEC--------CCCCHHH----HHHHHHHCCCC--CCCCCCCCCEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             89999999765626431--------8999899----99976310233--2223456753799974698877568999999
Q gi|254780725|r  118 VSLYRALISNHVSEYLI--------EPLSVAD----IINSISAIFTP--QEEGKGSSGCSISFIGSRGGVGSSTIAHNCA  183 (427)
Q Consensus       118 ~~l~r~l~r~Gv~dyl~--------~P~~~~~----l~~ai~~~~~~--~~~~~~~~grvIav~g~KGGvGkTTiA~nLA  183 (427)
                      ..+|++++++|+++-+.        .-.+...    +...+.+...-  ........|+|++++| -=||||||+.+-||
T Consensus       119 ~~l~~~L~~~g~~~~la~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~ggV~alVG-PTGVGKTTTiAKLA  197 (404)
T PRK06995        119 GALFRHLLAAGFSAQLVRMLLENLPAGDDAQAAMDWARSVLASNLPVLGSEDALMERGGVFALVG-PTGVGKTTTTAKLA  197 (404)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHCCCCEEEEEC-CCCCCHHHHHHHHH
T ss_conf             99999999879999999999984703389789999999999974666666531011475589866-88876375899999


Q ss_pred             HHHHHHCC-CCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHH
Q ss_conf             99996269-94999978798986033438998789888631845612433765320248980687248761203207999
Q gi|254780725|r  184 FSIASVFA-METLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEK  262 (427)
Q Consensus       184 ~~LA~~~~-~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~  262 (427)
                      ....-+.| .+|.||-+|..--.+.-.|                       +.+..-  -|+.+-.         -.+++
T Consensus       198 Ar~~l~~g~~kVaLIT~DTYRIgAvEQL-----------------------ktYa~I--lgvPv~v---------v~~~~  243 (404)
T PRK06995        198 ARCVMRHGASKVALLTTDSYRIGGHEQL-----------------------RIYGKI--LGVPVHA---------VKDAA  243 (404)
T ss_pred             HHHHHHHCCCCEEEEECCCCCHHHHHHH-----------------------HHHHHH--CCCEEEE---------ECCHH
T ss_conf             9999983898379997687547899999-----------------------999987--5955999---------59999


Q ss_pred             HHHHHHHHHHHCCCEEEECCCCCC--CHHH---HHHHHHC---CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEE
Q ss_conf             999989998512888997388888--9899---9998620---1254357877688999999999999819876753899
Q gi|254780725|r  263 MIVPVLDILEQIFPLVILDVPHVW--NSWT---QEVLTLS---DKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLV  334 (427)
Q Consensus       263 ~l~~ll~~l~~~yd~VIiD~p~~~--~~~~---~~~L~~A---D~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iV  334 (427)
                      .+...++.++ .+|+|+||++...  +...   ...|..+   ..+++|...+. .-++.+.+++.++..++    -.+|
T Consensus       244 eL~~aL~~l~-~~dlILIDTaGrs~rD~~~~e~l~~l~~~~~~~~~~LVLsat~-~~~dl~~i~~~f~~~~~----~~~I  317 (404)
T PRK06995        244 DLRLALAELR-NKHIVLIDTVGMSQRDRMVSEQIAMLHGAGAPVQRLLLLNATS-HGDTLNEVVQAYRGPGL----AGCI  317 (404)
T ss_pred             HHHHHHHHHC-CCCEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCC-CHHHHHHHHHHHCCCCC----CEEE
T ss_conf             9999999708-9999998099989768889999999973578852899977989-99999999998446999----8399


Q ss_pred             EECCCCCCCCHHHHHHHHHHHCCCEEEE-----ECCCH------HHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCC
Q ss_conf             9565898752005999999848953799-----06879------999998847961898889998999999999998522
Q gi|254780725|r  335 LNQVKTPKKPEISISDFCAPLGITPSAI-----IPFDG------AVFGMSANSGKMIHEVDPKSAIANLLVDFSRVLMGR  403 (427)
Q Consensus       335 lNr~~~~~~~~i~~~~~~~~lg~~~~~~-----IP~D~------~~~~~A~~~G~pi~e~~p~s~~a~~~~~La~~i~gr  403 (427)
                      +.+.+.....- ..=.+.-..+.++..+     +|.|.      .++..|.....   +.+|-+.-..++.-+.....++
T Consensus       318 ~TKLDEt~~~G-~iln~~~~~~lPlsy~T~GQ~VPeDi~~A~~~~Lv~ra~~~~~---~~~~~~~~~~~~~~~~~~~~~~  393 (404)
T PRK06995        318 LTKLDEAASLG-GALDTVIRHKLPLHYVSNGQRVPEDLHVANAKFLLHRAFCAPR---EGSPFVPQDDEMPLLLAALAAR  393 (404)
T ss_pred             EECCCCCCCHH-HHHHHHHHHCCCEEEECCCCCCCCCHHCCCHHHHHHHHHHCCC---CCCCCCCCCCHHHHHHHHHHCC
T ss_conf             83040679723-9999999978985998189958421210898999999862645---5899998800799999876414


Q ss_pred             C
Q ss_conf             1
Q gi|254780725|r  404 V  404 (427)
Q Consensus       404 ~  404 (427)
                      .
T Consensus       394 ~  394 (404)
T PRK06995        394 S  394 (404)
T ss_pred             C
T ss_conf             6


No 139
>PRK00784 cobyric acid synthase; Provisional
Probab=98.40  E-value=7.4e-06  Score=55.20  Aligned_cols=198  Identities=13%  Similarity=0.155  Sum_probs=111.9

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCC-CCCCHHHHHCC-------CCCHHHH
Q ss_conf             753799974698877568999999999962699499997879898603343899-87898886318-------4561243
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKD-PINSISDAIYP-------VGRIDKA  231 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~-~~~~l~d~l~~-------~~rlD~~  231 (427)
                      .+|.|-|.|+..++|||++++.|...+++ .|.+|.=  +-.|.=..+.+...+ -+-+.+.+++.       .-+.++.
T Consensus         2 ~~k~lMv~GT~S~vGKS~l~aaLCRi~~~-~G~~VaP--FKaQNMslNs~vt~dG~EigrAQ~~QA~Aag~~p~v~MNPI   78 (492)
T PRK00784          2 MAKALMVQGTTSDAGKSTLVAGLCRILAR-RGLRVAP--FKAQNMSLNSAVTADGGEIGRAQALQAEAAGVEPSVDMNPV   78 (492)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHH-CCCCCCC--CCHHHCCCCCEECCCCCEEHHHHHHHHHHCCCCCCCCCCCE
T ss_conf             86305888678887799999999999995-8985578--57022466517889998336999999998699997676887


Q ss_pred             HHHHHHHCCCCCEEEEECCCCCC-----CHHCC---CHHHHHHHHHHHHHCCCEEEECCCCCCCHHH--------HHHHH
Q ss_conf             37653202489806872487612-----03207---9999999899985128889973888889899--------99986
Q gi|254780725|r  232 FVSRLPVFYAENLSILTAPAMLS-----RTYDF---DEKMIVPVLDILEQIFPLVILDVPHVWNSWT--------QEVLT  295 (427)
Q Consensus       232 ~l~~~l~~~~~gL~lL~a~~~~~-----~~~~~---~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~--------~~~L~  295 (427)
                      +|+..-.   .+-.++--+....     ..++.   -...+...++.|+..||+||+.-..+..+..        ..+..
T Consensus        79 LLKP~gd---~~SQVIv~Gk~~g~~~a~~Y~~~~~~~~~~v~~a~~~L~~~~d~iV~EGAGSpaEiNL~~~Di~Nm~~A~  155 (492)
T PRK00784         79 LLKPQSD---TGSQVIVQGKVVGNMDARDYHDYKPRLLEAVLESLDRLAAEYDLVVVEGAGSPAEINLRDRDIANMGFAE  155 (492)
T ss_pred             EECCCCC---CCCEEEECCEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCCCHHHHHHHHHHH
T ss_conf             7631899---8867999997875313999998699999999999999886588999935898200265220024289998


Q ss_pred             HCC-CCCCCCCCC----HHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCC-CHHHHHHHHHHHCCCEEEEECCCH
Q ss_conf             201-254357877----688999999999999819876753899956589875-200599999984895379906879
Q gi|254780725|r  296 LSD-KVVITTSLD----LAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKK-PEISISDFCAPLGITPSAIIPFDG  367 (427)
Q Consensus       296 ~AD-~vviV~~p~----~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~-~~i~~~~~~~~lg~~~~~~IP~D~  367 (427)
                      .++ -|++|.+-|    .+++..+..+++.-.+.    .-..+|+|++.-... -+-..+.+++..|.++.++|||..
T Consensus       156 ~~~apviLV~DIdRGGvfAsl~GT~~lL~~~eR~----li~G~IiNKFRGD~~ll~pG~~~le~~tg~PvlGviP~~~  229 (492)
T PRK00784        156 AADAPVILVADIDRGGVFASLVGTLALLSPEERA----RVKGFVINKFRGDISLLEPGLDWLEELTGIPVLGVLPYLD  229 (492)
T ss_pred             HCCCCEEEEEECCCCCHHHHHHHHHHHCCHHHHH----HEEEEEEEEECCCHHHHCCHHHHHHHHHCCCCEEEECCCC
T ss_conf             6599889999756764268776388759998871----1589999764587466355999999986898068614656


No 140
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=98.40  E-value=1.5e-06  Score=59.42  Aligned_cols=131  Identities=19%  Similarity=0.221  Sum_probs=79.5

Q ss_pred             HHHHHHHHHCCCCEEECCC--------CCHHH----HHHHHHHCCCCC--CCCCCCCCEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             8999999976562643189--------99899----999763102332--223456753799974698877568999999
Q gi|254780725|r  118 VSLYRALISNHVSEYLIEP--------LSVAD----IINSISAIFTPQ--EEGKGSSGCSISFIGSRGGVGSSTIAHNCA  183 (427)
Q Consensus       118 ~~l~r~l~r~Gv~dyl~~P--------~~~~~----l~~ai~~~~~~~--~~~~~~~grvIav~g~KGGvGkTTiA~nLA  183 (427)
                      -.+|..|++.|+++.+..-        .+.++    +...|.+.+.-.  .......+++|+|+| --||||||+.+=||
T Consensus       137 ~~l~~~L~~~gv~~~~~~~l~~~~~~~~~~~~~~~~l~~~L~~~i~~~~~~~~~~~~~~vi~lvG-PTGVGKTTTiAKLA  215 (282)
T TIGR03499       137 AKLYERLEEAGVSEELARELLEKLPERADAESAWRWLREALENMLPVKPEEDEILEQGGVIALVG-PTGVGKTTTLAKLA  215 (282)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEC-CCCCCHHHHHHHHH
T ss_conf             99999999869999999999997460299789999999999964777887655445672799977-88875788999999


Q ss_pred             HHHHHHC-CCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHH
Q ss_conf             9999626-994999978798986033438998789888631845612433765320248980687248761203207999
Q gi|254780725|r  184 FSIASVF-AMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEK  262 (427)
Q Consensus       184 ~~LA~~~-~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~  262 (427)
                      +.++... +++|.||-+|..--.+.-.|     .+.++++                    |+.+-.         -.++.
T Consensus       216 a~~~l~~~~~~V~lIT~DtyRigA~eQL-----k~ya~il--------------------~vp~~v---------v~~~~  261 (282)
T TIGR03499       216 ARFVLEHGKKKVALITTDTYRIGAVEQL-----KTYAKIL--------------------GVPVKV---------ARDPK  261 (282)
T ss_pred             HHHHHHCCCCCEEEEEECCCCHHHHHHH-----HHHHHHH--------------------CCEEEE---------ECCHH
T ss_conf             9999973899679998077767899999-----9999995--------------------974899---------39999


Q ss_pred             HHHHHHHHHHHCCCEEEECCCC
Q ss_conf             9999899985128889973888
Q gi|254780725|r  263 MIVPVLDILEQIFPLVILDVPH  284 (427)
Q Consensus       263 ~l~~ll~~l~~~yd~VIiD~p~  284 (427)
                      .+...++.++ .+|+|+||++.
T Consensus       262 ~l~~~l~~~~-~~d~IlIDTaG  282 (282)
T TIGR03499       262 ELAKALERLR-DKDLILIDTAG  282 (282)
T ss_pred             HHHHHHHHCC-CCCEEEEECCC
T ss_conf             9999998657-98999981979


No 141
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=98.40  E-value=6e-05  Score=49.58  Aligned_cols=173  Identities=14%  Similarity=0.145  Sum_probs=102.0

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             53799974698877568999999999962699499997879898603343899878988863184561243376532024
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      --+|-++| =-|.||||.+.-||++|.+ .+++|+||-+|.+-..+-                     |+  |+....+ 
T Consensus       100 P~vImmvG-LQGsGKTTt~~KLA~~lkk-~~~kvllVaaD~~RpAA~---------------------eQ--L~~La~q-  153 (451)
T COG0541         100 PTVILMVG-LQGSGKTTTAGKLAKYLKK-KGKKVLLVAADTYRPAAI---------------------EQ--LKQLAEQ-  153 (451)
T ss_pred             CEEEEEEE-CCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCHHHH---------------------HH--HHHHHHH-
T ss_conf             85899981-5679748689999999997-499458985056786899---------------------99--9999986-


Q ss_pred             CCCEEEEECCCCCCCHHCCCHHHHHHHHHHHH-HCCCEEEECCCCCCCHH--H------HHHHHHCCCCCCCCCCCHHHH
Q ss_conf             89806872487612032079999999899985-12888997388888989--9------999862012543578776889
Q gi|254780725|r  241 AENLSILTAPAMLSRTYDFDEKMIVPVLDILE-QIFPLVILDVPHVWNSW--T------QEVLTLSDKVVITTSLDLAGL  311 (427)
Q Consensus       241 ~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p~~~~~~--~------~~~L~~AD~vviV~~p~~~sl  311 (427)
                       -++.+++.... ..+.+    -...-++.++ ..||+||||+.......  .      .......|++++|++....  
T Consensus       154 -~~v~~f~~~~~-~~Pv~----Iak~al~~ak~~~~DvvIvDTAGRl~ide~Lm~El~~Ik~~~~P~E~llVvDam~G--  225 (451)
T COG0541         154 -VGVPFFGSGTE-KDPVE----IAKAALEKAKEEGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAMIG--  225 (451)
T ss_pred             -CCCCEECCCCC-CCHHH----HHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCC--
T ss_conf             -09853167788-99799----99999999997499889996887330309999999999855398748998764445--


Q ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEE---------EECCCHHHHH
Q ss_conf             99999999999819876753899956589875200599999984895379---------9068799999
Q gi|254780725|r  312 RNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSA---------IIPFDGAVFG  371 (427)
Q Consensus       312 r~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~---------~IP~D~~~~~  371 (427)
                      .++.+..+.+.+.   -.--.+|+.+.+...++-... .+....|.|+-+         .=||+|+-+.
T Consensus       226 QdA~~~A~aF~e~---l~itGvIlTKlDGdaRGGaAL-S~~~~tg~PIkFiGtGEki~dLE~F~P~R~a  290 (451)
T COG0541         226 QDAVNTAKAFNEA---LGITGVILTKLDGDARGGAAL-SARAITGKPIKFIGTGEKIDDLEPFHPDRFA  290 (451)
T ss_pred             HHHHHHHHHHHHH---CCCCEEEEECCCCCCCCHHHH-HHHHHHCCCEEEEECCCCCCCCCCCCHHHHH
T ss_conf             6789999998662---698649997146787622888-5699878985997458873547774958899


No 142
>PRK10867 signal recognition particle protein; Provisional
Probab=98.39  E-value=6.8e-05  Score=49.25  Aligned_cols=173  Identities=10%  Similarity=0.094  Sum_probs=99.8

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      .+|-++| =-|+||||.+.-||.++-...+++|+++-+|..-..+--.|                       +....+  
T Consensus       101 ~VIm~vG-LqGsGKTTT~aKLA~~lk~k~~k~vllvaaDt~RpaA~eQL-----------------------~~la~~--  154 (453)
T PRK10867        101 AVVLMAG-LQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPAAIKQL-----------------------ETLAEQ--  154 (453)
T ss_pred             EEEEEEC-CCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHH-----------------------HHHHHH--
T ss_conf             6999974-68885185899999999973898379855887705899999-----------------------999985--


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHH-HHHHCCCEEEECCCCCCCHHH--------HHHHHHCCCCCCCCCCCHHHHH
Q ss_conf             9806872487612032079999999899-985128889973888889899--------9998620125435787768899
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLD-ILEQIFPLVILDVPHVWNSWT--------QEVLTLSDKVVITTSLDLAGLR  312 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~-~l~~~yd~VIiD~p~~~~~~~--------~~~L~~AD~vviV~~p~~~slr  312 (427)
                      -++.++..+..-+ +..+    ...-++ .-...||+||+|+........        ..-....|++++|.+....  .
T Consensus       155 ~~v~~~~~~~~~d-p~~i----a~~a~~~ak~~~~DvvivDTAGRl~~d~~Lm~El~~i~~~~~P~e~llV~Da~~G--Q  227 (453)
T PRK10867        155 VGVDFFPSDVGQK-PVDI----VNAALKEAKLKFYDVLLVDTAGRLHVDEAMMDEIKQVHASINPVETLFVVDAMTG--Q  227 (453)
T ss_pred             CCCCEECCCCCCC-HHHH----HHHHHHHHHHCCCCEEEEECCCCHHCCHHHHHHHHHHHHHHCCCCEEEEEECCCC--H
T ss_conf             1980436788998-8999----9999999997799999997876012108889999999876378713797432235--6


Q ss_pred             HHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEE---------EECCCHHHHH
Q ss_conf             9999999999819876753899956589875200599999984895379---------9068799999
Q gi|254780725|r  313 NSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSA---------IIPFDGAVFG  371 (427)
Q Consensus       313 ~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~---------~IP~D~~~~~  371 (427)
                      ++.+..+.+.+.-   .--.+|+.+.+...++-... .+....|.|+.+         .-||+|.-|.
T Consensus       228 ~a~~~a~~F~~~~---~~~gvIlTKlDgdarGG~al-S~~~~t~~PI~FiG~GEk~ddle~F~p~r~a  291 (453)
T PRK10867        228 DAANTAKAFNEAL---PLTGVVLTKVDGDARGGAAL-SIRHITGKPIKFLGVGEKTDALEPFHPDRIA  291 (453)
T ss_pred             HHHHHHHHHHHHC---CCCEEEEECCCCCCCCHHHH-HHHHHHCCCCEEEECCCCCCCCCCCCHHHHH
T ss_conf             6899999999855---98707875046787613898-9999978696788669982458876848999


No 143
>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=98.36  E-value=2.7e-05  Score=51.72  Aligned_cols=169  Identities=14%  Similarity=0.138  Sum_probs=93.5

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             67537999746988775689999999999626994999978798986033438998789888631845612433765320
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      ..-++|.++| =-|+||||.++-||+.+.. .+++|+++=+|..-..+--.|                       +.+..
T Consensus        73 ~~~~vI~lvG-~~G~GKTTT~AKLA~~~~~-~~~kV~lia~DtyR~aA~eQL-----------------------k~~a~  127 (270)
T PRK06731         73 KEVQTIALIG-PTGVGKTTTLAKMAWQFHG-KKKTVGFITTDHSRIGTVQQL-----------------------QDYVK  127 (270)
T ss_pred             CCCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEECCCCHHHHHHH-----------------------HHHHH
T ss_conf             9981899988-8989889999999999986-799089998388888899999-----------------------99999


Q ss_pred             CCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHH--CCCEEEECCCCCCC--HHH-HHH---HH--HCCCCCCCCCCCH
Q ss_conf             24898068724876120320799999998999851--28889973888889--899-999---86--2012543578776
Q gi|254780725|r  239 FYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQ--IFPLVILDVPHVWN--SWT-QEV---LT--LSDKVVITTSLDL  308 (427)
Q Consensus       239 ~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~--~yd~VIiD~p~~~~--~~~-~~~---L~--~AD~vviV~~p~~  308 (427)
                      .  -++.+....         .+..+...+..++.  .||+|+||+.....  ... ..+   +.  ..|++++|...+.
T Consensus       128 ~--l~v~~~~~~---------~~~~~~~~~~~~~~~~~~DvilIDTAGR~~~d~~lm~el~~~~~~~~p~~~~Lvldas~  196 (270)
T PRK06731        128 T--IGFEVIAVR---------DEAAMTRALTYFKEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASM  196 (270)
T ss_pred             H--HCCCEECCC---------CHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEECCC
T ss_conf             8--199535458---------87899999999999769999999799987146999999999860638987999986877


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEE-----ECCCHHH
Q ss_conf             889999999999998198767538999565898752005999999848953799-----0687999
Q gi|254780725|r  309 AGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAI-----IPFDGAV  369 (427)
Q Consensus       309 ~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~-----IP~D~~~  369 (427)
                       .-.++.+..+.++..+    .-++|+++.+...++-. .=.+....+.|+.+.     ||.|-+.
T Consensus       197 -~~~~~~~~~~~f~~~~----i~gvIlTKlD~ta~gG~-als~~~~~~~PI~fig~Ge~VpeDi~~  256 (270)
T PRK06731        197 -KSKDMIEIITNFKDIH----IDGIVFTKFDETASSGE-LLKIPAVSSAPIVLMTDGQDVKKNIHI  256 (270)
T ss_pred             -CHHHHHHHHHHHCCCC----CCEEEEECCCCCCCCCH-HHHHHHHHCCCEEEEECCCCCHHHHHC
T ss_conf             -7699999999807799----98899965358997729-999999988597999459997021413


No 144
>pfam00448 SRP54 SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
Probab=98.35  E-value=6.6e-05  Score=49.33  Aligned_cols=144  Identities=12%  Similarity=0.123  Sum_probs=74.6

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      +||+++| --||||||..+-||+.+.. .+++|.+|-+|.....+.-.|                       +.+...  
T Consensus         2 ~vi~lvG-ptGvGKTTTiaKLAa~~~~-~~~~V~lit~Dt~R~gA~eQL-----------------------~~ya~~--   54 (196)
T pfam00448         2 NVILLVG-LQGSGKTTTIAKLAAYLKK-QGKKVLLVAADTFRAAAIEQL-----------------------KQLAER--   54 (196)
T ss_pred             EEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCHHHHHHH-----------------------HHHHHH--
T ss_conf             6999989-9999889999999999997-799289997587768899999-----------------------999986--


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHH-HHCCCEEEECCCCCC--CHHH----HHHHH--HCCCCCCCCCCCHHHHH
Q ss_conf             980687248761203207999999989998-512888997388888--9899----99986--20125435787768899
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDIL-EQIFPLVILDVPHVW--NSWT----QEVLT--LSDKVVITTSLDLAGLR  312 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l-~~~yd~VIiD~p~~~--~~~~----~~~L~--~AD~vviV~~p~~~slr  312 (427)
                      -++.+...... ...    ...+...++.+ .+.||+|+||++...  +...    .....  ..+.+++|..+.... .
T Consensus        55 l~v~~~~~~~~-~d~----~~~~~~~l~~~~~~~~D~IlIDTaGr~~~d~~~~~el~~~~~~~~~~~~~LVl~a~~~~-~  128 (196)
T pfam00448        55 LGVPVFGSGTG-SDP----AAVAFDAVEKAKAENYDVVLVDTAGRLQNDKNLMDELKKIKRVIAPDEVLLVLDATTGQ-N  128 (196)
T ss_pred             CCCEEEECCCC-CCH----HHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCC-C
T ss_conf             39817814877-787----89999999998846899999989998747677899999998522873028998567782-1


Q ss_pred             HHHHHHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf             999999999981987675389995658987
Q gi|254780725|r  313 NSKNLIDVLKKLRPADKPPYLVLNQVKTPK  342 (427)
Q Consensus       313 ~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~  342 (427)
                      .......+.+..++    -.+|+++.+...
T Consensus       129 ~~~~~~~f~~~~~~----~~~I~TKlDet~  154 (196)
T pfam00448       129 ALNQAKAFNEAVGI----TGVILTKLDGDA  154 (196)
T ss_pred             HHHHHHHHHHHCCC----CCEEEEEECCCC
T ss_conf             37899987600477----626888405788


No 145
>PRK09435 arginine/ornithine transport system ATPase; Provisional
Probab=98.32  E-value=4.3e-05  Score=50.45  Aligned_cols=167  Identities=15%  Similarity=0.179  Sum_probs=98.3

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC-CHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHH
Q ss_conf             67537999746988775689999999999626994999978798986-03343899878988863184561243376532
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGT-ANINFDKDPINSISDAIYPVGRIDKAFVSRLP  237 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~-~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l  237 (427)
                      ..+.+|.|.| -.|+||||+.-.|+..+.. .|++|.++=.||...- -+..||            +.-|+...      
T Consensus        47 g~a~~iGiTG-~pG~GKStli~~l~~~~~~-~g~~v~vlavDPsS~~sgGaiLG------------Dr~Rm~~~------  106 (325)
T PRK09435         47 GNALRIGITG-VPGVGKSTFIEALGMHLIE-QGHKVAVLAVDPSSTRTGGSILG------------DKTRMERL------  106 (325)
T ss_pred             CCCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEECCCCCCCCCCHHH------------HHHHHHHH------
T ss_conf             9825997427-9998688999999999996-79858999978999988861010------------38888761------


Q ss_pred             HCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHH-HCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHH-HHHHH
Q ss_conf             02489806872487612032079999999899985-12888997388888989999986201254357877688-99999
Q gi|254780725|r  238 VFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILE-QIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAG-LRNSK  315 (427)
Q Consensus       238 ~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~s-lr~a~  315 (427)
                       ...++.++=+.+.. .....++.. ....+..+. ..||+|+|.+= +.+..-..+...+|.++++..|.... +...|
T Consensus       107 -~~~~~~fiRs~~sr-g~lgg~~~~-~~~~~~~~~a~g~d~i~iETv-GvGQ~e~~v~~~~d~~~~~~~p~~GD~~Q~~K  182 (325)
T PRK09435        107 -SRHPNAFIRPSPSS-GTLGGVARK-TRETMLLCEAAGFDVILVETV-GVGQSETAVAGMVDFFLLLQLPGAGDELQGIK  182 (325)
T ss_pred             -CCCCCEEEEECCCC-CCCCCCCHH-HHHHHHHHHHCCCCEEEEEEC-CCCHHHHHHHHHCCEEEEEECCCCCCHHHHHH
T ss_conf             -47998488406778-886773354-999999999779998999706-77714889987426688883588760889988


Q ss_pred             HHHHHHHHCCCCCCCCEEEEECCCCCCC--CHHHHHHHHHHHCC
Q ss_conf             9999999819876753899956589875--20059999998489
Q gi|254780725|r  316 NLIDVLKKLRPADKPPYLVLNQVKTPKK--PEISISDFCAPLGI  357 (427)
Q Consensus       316 ~ll~~l~~~~~~~~~~~iVlNr~~~~~~--~~i~~~~~~~~lg~  357 (427)
                      +=+     ....+   .+|+|+++.+..  ......++..++..
T Consensus       183 ~GI-----mEiaD---i~vVNKaDgd~~~~A~~t~~e~~~aL~l  218 (325)
T PRK09435        183 KGI-----MELAD---LIVINKADGDNHTAARRAAAEYRSALRL  218 (325)
T ss_pred             HHH-----HHHCC---EEEEECCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             657-----75042---6899776755658999999999999860


No 146
>pfam03308 ArgK ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems.
Probab=98.31  E-value=1.1e-05  Score=54.21  Aligned_cols=165  Identities=15%  Similarity=0.197  Sum_probs=99.4

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCC-CCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             753799974698877568999999999962699499997879898-6033438998789888631845612433765320
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYG-TANINFDKDPINSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g-~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      .+.+|.+.| -+|+||||+.-.|...+.+ .+++|.++=-||... +-+..||            +.-|+...       
T Consensus        28 ~a~~iGiTG-~PGaGKStli~~l~~~~~~-~g~~vaVlAvDPSS~~sgGaiLG------------Dr~RM~~~-------   86 (267)
T pfam03308        28 RAHRVGITG-VPGAGKSTLIEALGMELRR-RGHRVAVLAVDPSSPFTGGSILG------------DRTRMQRL-------   86 (267)
T ss_pred             CCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEECCCCCCCCCCCCC------------CHHHHHHH-------
T ss_conf             955998768-9988799999999999996-89868999978999888863001------------07777650-------


Q ss_pred             CCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHH-CCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHH-HHHHHH
Q ss_conf             24898068724876120320799999998999851-2888997388888989999986201254357877688-999999
Q gi|254780725|r  239 FYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQ-IFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAG-LRNSKN  316 (427)
Q Consensus       239 ~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~-~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~s-lr~a~~  316 (427)
                      ...++.++=+.+.. .....++.. ....+..+.. .||+|+|.+- +.+..-..+...+|.+++|..|.... +...|+
T Consensus        87 ~~~~~vfiRs~~sr-g~lGGls~~-t~~~i~lleaaGfD~IivETV-GVGQsE~~v~~~aD~~llv~~Pg~GDeiQ~iKa  163 (267)
T pfam03308        87 AVDPGAFIRSSPSR-GALGGLSRA-TREAILLLDAAGFDVIIIETV-GVGQSEVDIANMADTFVLVTIPGGGDDLQGIKA  163 (267)
T ss_pred             CCCCCEEEEECCCC-CCCCCCCHH-HHHHHHHHHHCCCCEEEEECC-CCCCCCHHHHHHCCEEEEEECCCCCHHHHHHHH
T ss_conf             58998588645778-888871476-999999999779999999247-777530355541576899955887608889875


Q ss_pred             HHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCC
Q ss_conf             99999981987675389995658987520059999998489
Q gi|254780725|r  317 LIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGI  357 (427)
Q Consensus       317 ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~  357 (427)
                      =+     ....+   .+|+|+++.+. .+....+++.++..
T Consensus       164 GI-----mEiaD---i~vVNKaD~~~-A~~~~~~l~~~l~l  195 (267)
T pfam03308       164 GL-----MEIAD---IYVVNKADLPG-AERTARELRSALHL  195 (267)
T ss_pred             HH-----HHHCC---EEEEECCCHHH-HHHHHHHHHHHHHC
T ss_conf             37-----65354---89996676476-99999999999851


No 147
>PRK13768 GTPase; Provisional
Probab=98.29  E-value=1.9e-05  Score=52.61  Aligned_cols=181  Identities=17%  Similarity=0.204  Sum_probs=100.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886318456124337653202489
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAE  242 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~  242 (427)
                      .+-|+| --|.||||....+...+.. .++++.+|.|||..-..    .-+|.-.+.|.+.         ++..+.++. 
T Consensus         4 ~~~ViG-paGSGKsT~~~~l~~~l~~-~~r~~~vvNLDPA~e~~----pY~~~iDIRd~i~---------~~dVM~~~~-   67 (253)
T PRK13768          4 IVFFLG-TAGSGKTTLVGALSDWLEE-QGYDVAIVNLDPAVEYL----PYKPDIDVREYVS---------AREIMRKYG-   67 (253)
T ss_pred             EEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCC----CCCCCCCHHHHCC---------HHHHHHHHC-
T ss_conf             899989-9999889999999999997-69975999789866589----9998863786178---------999998819-


Q ss_pred             CEEEEECCC-CCCCHHCCCHHHHHHHHHHHHH-CCCEEEECCCCCCCHHH--------HHHHHHCCCCCCCCCCCHHHHH
Q ss_conf             806872487-6120320799999998999851-28889973888889899--------9998620125435787768899
Q gi|254780725|r  243 NLSILTAPA-MLSRTYDFDEKMIVPVLDILEQ-IFPLVILDVPHVWNSWT--------QEVLTLSDKVVITTSLDLAGLR  312 (427)
Q Consensus       243 gL~lL~a~~-~~~~~~~~~~~~l~~ll~~l~~-~yd~VIiD~p~~~~~~~--------~~~L~~AD~vviV~~p~~~slr  312 (427)
                       |    +|. .+-...++-...+.++.+.+.. .-||+|+|||.+..-.+        ...|......++|---|..-..
T Consensus        68 -L----GPNGali~~~e~l~~~~d~l~~~i~~~~~dY~i~D~PGQiElft~~~~~~~i~~~L~~~~~~~~v~l~D~~~~~  142 (253)
T PRK13768         68 -L----GPNGALIASVDLLLTKAEEIKEEIERLDADYVLVDTPGQMELFAFRESGRYLVEKLSSGSKSLSVYLIDAVLAK  142 (253)
T ss_pred             -C----CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCEEEEECCHHHHHHHHHHHCCCCEEEEEEECHHHHC
T ss_conf             -8----96468999999999989999999851588759982687443222340799999998636862899984505637


Q ss_pred             HHHHHHHHH-----HHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHC
Q ss_conf             999999999-----9819876753899956589875200599999984895379906879999998847
Q gi|254780725|r  313 NSKNLIDVL-----KKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANS  376 (427)
Q Consensus       313 ~a~~ll~~l-----~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~  376 (427)
                      +...++..+     ...+.. -+...|+|+++.-+.  ...+++.+.+.         |+..+..+.+.
T Consensus       143 ~~~~fiS~~L~a~s~m~~l~-lP~inVlsK~Dll~~--~~~~~i~~~~~---------D~~~l~~~l~~  199 (253)
T PRK13768        143 DPSDFVSLLLLALSVQLRLG-LPQIPVLNKIDLLSE--EELERIRKWLE---------DPETLLEELKL  199 (253)
T ss_pred             CHHHHHHHHHHHHHHHHHCC-CCEEEEEEHHHCCCH--HHHHHHHHHHC---------CHHHHHHHHHC
T ss_conf             88799999999999999739-997998676862783--77999999862---------99999999850


No 148
>PRK12727 flagellar biosynthesis regulator FlhF; Provisional
Probab=98.29  E-value=3.5e-05  Score=51.06  Aligned_cols=184  Identities=15%  Similarity=0.200  Sum_probs=97.8

Q ss_pred             CHHHHHHHHHCCCCEEECC--------CCCHHH----HHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             1899999997656264318--------999899----9997631023322234567537999746988775689999999
Q gi|254780725|r  117 DVSLYRALISNHVSEYLIE--------PLSVAD----IINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAF  184 (427)
Q Consensus       117 d~~l~r~l~r~Gv~dyl~~--------P~~~~~----l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~  184 (427)
                      -..+++.|+++|++.-|..        -.+..+    +...|.+-+.-.....-..|-|++++| --||||||..+-||+
T Consensus       292 ra~L~krL~~~GfS~~Lar~L~~~lP~~~~~~~a~~~ll~~La~~Lpv~~~d~~~~gGv~AlvG-pTGvGKTTT~aKlAa  370 (557)
T PRK12727        292 RAQALELMDDYGFDAGLTRDVAMQIPADTELHRGRGLMLGLLSKRLPVAPVDPLERGGVIALVG-PTGAGKTTTIAKLAQ  370 (557)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHCCCEEEEEC-CCCCCCHHHHHHHHH
T ss_conf             8999999997669999999999748332788899999999999628777775154076478743-777673117999999


Q ss_pred             HHHHHCC-CCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHH
Q ss_conf             9996269-949999787989860334389987898886318456124337653202489806872487612032079999
Q gi|254780725|r  185 SIASVFA-METLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKM  263 (427)
Q Consensus       185 ~LA~~~~-~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~  263 (427)
                      .++.++| .+|.||-.|..-=.+            .|-+..-.        +++     |+.+-..         .+...
T Consensus       371 ~~~~~~g~~~valit~DtyRiga------------~eQL~~y~--------~il-----gvpv~~~---------~~~~~  416 (557)
T PRK12727        371 RFAAQHAPRDVALVTTDTQRVGG------------REQLHSYG--------RQL-----GIAVHEA---------DSAES  416 (557)
T ss_pred             HHHHHCCCCEEEEEECCCCCHHH------------HHHHHHHH--------HHH-----CCEEEEE---------CCHHH
T ss_conf             99997399818999726640879------------99999999--------983-----9757982---------89999


Q ss_pred             HHHHHHHHHHCCCEEEECCCCCC--CHH-H--HHHHHHCCCC--CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf             99989998512888997388888--989-9--9998620125--435787768899999999999981987675389995
Q gi|254780725|r  264 IVPVLDILEQIFPLVILDVPHVW--NSW-T--QEVLTLSDKV--VITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLN  336 (427)
Q Consensus       264 l~~ll~~l~~~yd~VIiD~p~~~--~~~-~--~~~L~~AD~v--viV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlN  336 (427)
                      +..++..++ .+++|+||+....  +.. .  ...|.....+  ++|...+ ...+....+++.++...+    -++|+.
T Consensus       417 l~~~l~~l~-~~~lvliDTaG~~~rd~~~~~~~~~l~~~~~~~~~Lvl~a~-~~~~~l~~~~~~~~~~~~----~~~i~T  490 (557)
T PRK12727        417 LLDLLERLR-DYKLVLIDTAGMGQRDRALAAQLNWLRAARQVTSLLVLPAN-AHFSDLDEVVRRFAHAKP----QGVVLT  490 (557)
T ss_pred             HHHHHHHHC-CCCEEEEECCCCCCCCHHHHHHHHHHHCCCCCCEEEEEECC-CCHHHHHHHHHHHCCCCC----CEEEEE
T ss_conf             999999836-99989994999884699999999987514776359999688-998999999998537998----748996


Q ss_pred             CCCCC
Q ss_conf             65898
Q gi|254780725|r  337 QVKTP  341 (427)
Q Consensus       337 r~~~~  341 (427)
                      +.+..
T Consensus       491 KlDE~  495 (557)
T PRK12727        491 KLDET  495 (557)
T ss_pred             ECCCC
T ss_conf             14367


No 149
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=98.25  E-value=3.4e-05  Score=51.13  Aligned_cols=163  Identities=13%  Similarity=0.132  Sum_probs=85.2

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHH
Q ss_conf             56753799974698877568999999999962699499997879898603343899878988863184561243376532
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLP  237 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l  237 (427)
                      -..|+||+++| --|+||||.+.-||+.+.. .|++|+|+=+|..-..+.-.|            .       .+-++. 
T Consensus       203 l~~g~VIaLVG-vnGvGKTTTiAKLA~~l~~-~gkkV~LVAaDTFRaAAiEQL------------k-------~~g~rl-  260 (407)
T PRK12726        203 LSNHRIISLIG-QTGVGKTTTLVKLGWQLLK-QNRTVGFITTDTFRSGAVEQF------------Q-------GYADKL-  260 (407)
T ss_pred             ECCCCEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCHHHHHHH------------H-------HHHHHH-
T ss_conf             03690899989-9989789999999999997-799179997066778899999------------9-------999997-


Q ss_pred             HCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHH--HHHCCCEEEECCCCCCCH--HHHHHHH------HCCCCCCCCCCC
Q ss_conf             024898068724876120320799999998999--851288899738888898--9999986------201254357877
Q gi|254780725|r  238 VFYAENLSILTAPAMLSRTYDFDEKMIVPVLDI--LEQIFPLVILDVPHVWNS--WTQEVLT------LSDKVVITTSLD  307 (427)
Q Consensus       238 ~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~--l~~~yd~VIiD~p~~~~~--~~~~~L~------~AD~vviV~~p~  307 (427)
                           ++.+..+. +        +..+...+..  ....+|+|+||+......  ....-|.      .-+..++|.+..
T Consensus       261 -----gVpV~~~~-d--------pa~l~~av~~~a~~~~~DvVIIDTAGRl~~d~~Lm~EL~ki~~vi~P~~~lLV~dag  326 (407)
T PRK12726        261 -----DVELIVAT-S--------PAELEEAVQYMTYVNCVDHILIDTVGRNYLAEESVSEISAYTDVVHPDLTCFTFSSG  326 (407)
T ss_pred             -----CCEEEEEC-C--------HHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf             -----96499818-8--------899999999998628999899969998813499999999987332896699993675


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEE
Q ss_conf             6889999999999998198767538999565898752005999999848953799
Q gi|254780725|r  308 LAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAI  362 (427)
Q Consensus       308 ~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~  362 (427)
                      ..    ...+.+.+..... ..--.+|+.+.+...++-. .=.+...++.++.++
T Consensus       327 ~~----~~~v~qa~~~~~~-v~ItGiILTKLDgtAKGG~-aLSi~~~~~lPI~fI  375 (407)
T PRK12726        327 MK----SADVMTILPKLAE-IPIDGFIITKMDETTRIGD-LYTVMQETNLPVLYM  375 (407)
T ss_pred             CC----HHHHHHHHHHHCC-CCCCEEEEEECCCCCCCCH-HHHHHHHHCCCEEEE
T ss_conf             66----9999999987047-9998799970147898539-999999988897999


No 150
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=98.24  E-value=0.00013  Score=47.56  Aligned_cols=171  Identities=16%  Similarity=0.143  Sum_probs=98.5

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      -||-++| =-|+||||.++-||.++.+ .|++|+|+-+|.....+--.                       |+....+  
T Consensus        98 ~Vim~vG-lqGsGKTTT~aKLA~~~kk-~g~kv~lvaaDt~RpaA~eQ-----------------------L~~la~~--  150 (433)
T PRK00771         98 QTILLVG-LQGSGKTTTAAKLARYFQK-KGLKVGVICADTWRPGAYEQ-----------------------LKQLCEK--  150 (433)
T ss_pred             EEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCHHHHHH-----------------------HHHHHHH--
T ss_conf             5899973-7889789999999999997-79946785067883689999-----------------------9999986--


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHH--------HHHHHHCCCCCCCCCCCHHHHHH
Q ss_conf             9806872487612032079999999899985128889973888889899--------99986201254357877688999
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWT--------QEVLTLSDKVVITTSLDLAGLRN  313 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~--------~~~L~~AD~vviV~~p~~~slr~  313 (427)
                      -++.++..+..-+ +..+    ...-+..++ .||+||+|+........        ..-....|++++|.+....  .+
T Consensus       151 ~~v~~~~~~~~~d-p~~i----~~~a~~~~k-~~DvviiDTAGRl~~d~~Lm~El~~i~~~~~P~e~llV~Da~~G--Q~  222 (433)
T PRK00771        151 INVPFYGDPKEKD-AVKI----VKEGLEKLK-KVDVIIVDTAGRHKLEKDLIEEMKQIKEITKPDEVILVIDATIG--QQ  222 (433)
T ss_pred             CCCCCCCCCCCCC-HHHH----HHHHHHHHC-CCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCC--HH
T ss_conf             3887317889999-9999----999999845-69889997765210409999999999877579768998654422--67


Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEE---------EECCCHHHHH
Q ss_conf             999999999819876753899956589875200599999984895379---------9068799999
Q gi|254780725|r  314 SKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSA---------IIPFDGAVFG  371 (427)
Q Consensus       314 a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~---------~IP~D~~~~~  371 (427)
                      +.+..+.+.+.-   .--.+|+++.+...++-... .+....|.|+.+         .-||+|+-+.
T Consensus       223 a~~~a~~F~~~~---~i~gvIlTKlDgdarGGaaL-Si~~~t~~PI~FiG~GEk~~dle~F~p~r~a  285 (433)
T PRK00771        223 ASEQAKAFKEAV---GIGGIIITKLDGTAKGGGAL-SAVAETGAPIKFIGTGETIDDLEPFDPKRFI  285 (433)
T ss_pred             HHHHHHHHHHHC---CCCEEEEECCCCCCCCCHHH-HHHHHHCCCCEEEECCCCCCCCCCCCHHHHH
T ss_conf             899999998753---88737997256788730542-1898878995688617872148866808899


No 151
>COG1341 Predicted GTPase or GTP-binding protein [General function prediction only]
Probab=98.23  E-value=2.2e-05  Score=52.32  Aligned_cols=153  Identities=13%  Similarity=0.202  Sum_probs=87.2

Q ss_pred             CCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHH-----
Q ss_conf             189998999997631023322234567537999746988775689999999999626994999978798986033-----
Q gi|254780725|r  134 IEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANI-----  208 (427)
Q Consensus       134 ~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~-----  208 (427)
                      .-|.+..+..+-+..............+ ++.++|.+ .+||||+++-||--+-. +|.+|.++|+|..+.+...     
T Consensus        47 e~P~d~~~~~e~i~~~~~~~~~~~~~~~-~vmvvG~v-DSGKSTLt~~LaN~~l~-rG~~v~iiDaDvGQ~ei~pPg~IS  123 (398)
T COG1341          47 EVPEDRSEPLEEIADTWESKSESAGKVG-VVMVVGPV-DSGKSTLTTYLANKLLA-RGRKVAIIDADVGQSEIGPPGFIS  123 (398)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCHHCCCCC-EEEEECCC-CCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCCCCCCCCEEE
T ss_conf             2816763178997632244201206873-89998986-76788999999988764-474189996899976667974677


Q ss_pred             -HCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCC
Q ss_conf             -4389987898886318456124337653202489806872487612032079999999899985128889973888889
Q gi|254780725|r  209 -NFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWN  287 (427)
Q Consensus       209 -~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~  287 (427)
                       .+-..+..++.+                   ....=..+.+..++...+.---..+.++.+.+....|+|+||||....
T Consensus       124 L~~~~s~~~~L~~-------------------l~~~~~~FvG~isP~~~~~~~i~~v~rL~~~a~~~~~~ilIdT~GWi~  184 (398)
T COG1341         124 LAFPESPVISLSE-------------------LEPFTLYFVGSISPQGFPGRYIAGVARLVDLAKKEADFILIDTDGWIK  184 (398)
T ss_pred             EECCCCCCCCHHH-------------------CCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCCEE
T ss_conf             4125677777777-------------------586522798514777776899999999999865168779996998430


Q ss_pred             HHH-----HHHHH--HCCCCCCCCCCCH
Q ss_conf             899-----99986--2012543578776
Q gi|254780725|r  288 SWT-----QEVLT--LSDKVVITTSLDL  308 (427)
Q Consensus       288 ~~~-----~~~L~--~AD~vviV~~p~~  308 (427)
                      .|.     .+.+.  ..|.|+.+-+...
T Consensus       185 G~~g~elk~~li~~ikP~~Ii~l~~~~~  212 (398)
T COG1341         185 GWGGLELKRALIDAIKPDLIIALERANE  212 (398)
T ss_pred             CCHHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf             7427899999886509778999314453


No 152
>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.
Probab=98.22  E-value=0.00017  Score=46.84  Aligned_cols=160  Identities=15%  Similarity=0.152  Sum_probs=85.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886318456124337653202489
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAE  242 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~  242 (427)
                      ||.++| --||||||..+-||+.+.+ .+++|.+|-+|..-..+.-.|                       +.+...  -
T Consensus         2 Vi~lvG-ptGvGKTTTiaKLA~~~~~-~~~kV~lit~Dt~R~gA~eQL-----------------------~~~a~~--l   54 (173)
T cd03115           2 VILLVG-LQGVGKTTTAAKLALYLKK-KGKKVLLVAADTYRPAAIEQL-----------------------RVLGEQ--V   54 (173)
T ss_pred             EEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCHHHHHHH-----------------------HHHHHH--C
T ss_conf             999989-9999889999999999997-699289997488757799999-----------------------999997--4


Q ss_pred             CEEEEECCCCCCCHHCCCHHHHHHHHHHH-HHCCCEEEECCCCCC--CHHH----HHHHH--HCCCCCCCCCCCHHHHHH
Q ss_conf             80687248761203207999999989998-512888997388888--9899----99986--201254357877688999
Q gi|254780725|r  243 NLSILTAPAMLSRTYDFDEKMIVPVLDIL-EQIFPLVILDVPHVW--NSWT----QEVLT--LSDKVVITTSLDLAGLRN  313 (427)
Q Consensus       243 gL~lL~a~~~~~~~~~~~~~~l~~ll~~l-~~~yd~VIiD~p~~~--~~~~----~~~L~--~AD~vviV~~p~~~slr~  313 (427)
                      ++.+....... ..    ...+...++.. .+.||+|+||++...  +...    ...+.  ..+.+++|......  .+
T Consensus        55 ~v~~~~~~~~~-~~----~~~~~~~~~~~~~~~~D~IlIDTaGr~~~d~~~~~el~~l~~~~~p~~~~LVl~a~~~--~~  127 (173)
T cd03115          55 GVPVFEEGEGK-DP----VSIAKRAIEHAREENFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDAMTG--QD  127 (173)
T ss_pred             CCEEEECCCCC-CH----HHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCEEECCCCCH--HH
T ss_conf             98599227755-87----9999999999875689989997888787999999999999864489721574246550--65


Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEE
Q ss_conf             99999999981987675389995658987520059999998489537
Q gi|254780725|r  314 SKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPS  360 (427)
Q Consensus       314 a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~  360 (427)
                      +.+....+.+. .  ..-++|+.+.+...+.-... .+....+.|+.
T Consensus       128 ~~~~~~~f~~~-~--~~~~~I~TKlDet~~~G~~l-s~~~~~~~Pi~  170 (173)
T cd03115         128 AVNQAKAFNEA-L--GITGVILTKLDGDARGGAAL-SIRAVTGKPIK  170 (173)
T ss_pred             HHHHHHHHHHC-C--CCCEEEEEEECCCCCCCHHH-HHHHHHCCCEE
T ss_conf             89999998742-7--99789997143899757999-99999890908


No 153
>COG0132 BioD Dethiobiotin synthetase [Coenzyme metabolism]
Probab=98.21  E-value=8.8e-05  Score=48.56  Aligned_cols=188  Identities=15%  Similarity=0.131  Sum_probs=121.4

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC-
Q ss_conf             3799974698877568999999999962699499997879898603343899878988863184561243376532024-
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY-  240 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~-  240 (427)
                      +.+-|.|.-=|||||.++..|+.++.. .|.+|...--= |.|.-.       ...         .-|...+.+..... 
T Consensus         3 ~~~fVtGTDT~VGKTv~S~aL~~~l~~-~g~~~~~~KPV-qsG~~~-------~~~---------~~D~~~l~~~~~~~~   64 (223)
T COG0132           3 KRFFVTGTDTGVGKTVVSAALAQALKQ-QGYSVAGYKPV-QTGSEE-------TAE---------NSDALVLQRLSGLDL   64 (223)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEECCE-EECCCC-------CCC---------CCHHHHHHHHCCCCC
T ss_conf             369998279996499999999999996-89705987752-217877-------899---------745999998519986


Q ss_pred             ---CCCEEEEECCCCCCCH-----HCCCHHHHHHHHHHHHHCCCEEEECCCCCCC-HHH-----H-HHHHHCCCCCCCCC
Q ss_conf             ---8980687248761203-----2079999999899985128889973888889-899-----9-99862012543578
Q gi|254780725|r  241 ---AENLSILTAPAMLSRT-----YDFDEKMIVPVLDILEQIFPLVILDVPHVWN-SWT-----Q-EVLTLSDKVVITTS  305 (427)
Q Consensus       241 ---~~gL~lL~a~~~~~~~-----~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~-~~~-----~-~~L~~AD~vviV~~  305 (427)
                         .-..+-+..|..+.-.     ..+..+.+..-+..+...||+|+|--..+|. +.+     . -+-...--+++|+.
T Consensus        65 ~~~~~~py~f~~P~sPhlAa~~eg~~I~~~~l~~~l~~l~~~~d~vlVEGAGGl~vPl~~~~~~~D~~~~~~lpvILV~~  144 (223)
T COG0132          65 SYELINPYRFKEPLSPHLAAELEGRTIDLEKLSQGLRQLLKKYDLVLVEGAGGLLVPLTEEYTFADLAVQLQLPVILVVG  144 (223)
T ss_pred             CCCCCCCEECCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHCCCCEEEEECCCCEEEECCCCCCHHHHHHHCCCCEEEEEC
T ss_conf             63354335307888847778764893569999878885405467899967873333257865299999980999999966


Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHH-HHHHHHCCCEEEEECCCHHH
Q ss_conf             77688999999999999819876753899956589875200599-99998489537990687999
Q gi|254780725|r  306 LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISIS-DFCAPLGITPSAIIPFDGAV  369 (427)
Q Consensus       306 p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~-~~~~~lg~~~~~~IP~D~~~  369 (427)
                      ..+.++-.+---++.+++.+.+  -..+|.|+..+......... .+.+.++.+..+.+|+-++.
T Consensus       145 ~~LGtINHtlLt~eal~~~gl~--l~G~I~n~~~~~~~~~~~~~~~l~~~~~~p~~g~~p~~~~~  207 (223)
T COG0132         145 IKLGTINHTLLTVEALRARGLP--LAGWVANGINPELDHYAEINATLLKRIGAPLLGIIPYLPES  207 (223)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCC--EEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf             7757787999999999977998--78999726788555788889999974289743405577663


No 154
>TIGR00064 ftsY signal recognition particle-docking protein FtsY; InterPro: IPR004390   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).  This family includes the cell division ABC transporter and the periplasmic substrate-binding protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In Escherichia coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.; GO: 0005525 GTP binding.
Probab=98.17  E-value=0.00023  Score=46.06  Aligned_cols=220  Identities=16%  Similarity=0.177  Sum_probs=131.1

Q ss_pred             EECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             81687189999999765626431899989999976310233222345675379997469887756899999999996269
Q gi|254780725|r  112 IGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFA  191 (427)
Q Consensus       112 ig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~  191 (427)
                      --...+....++++..=..+++..-.+..........-    .......--||.|+| ==|+||||.-.=||..+.. .|
T Consensus        37 ~~~~~~~~~~~e~~~~~l~~~~~~~~~~~~~~~~~~~~----~~~~~~kp~Vil~VG-VNG~GKTTTIaKLA~~l~~-~G  110 (284)
T TIGR00064        37 GKKVKDEEKLKEILKEALKEILKEILDKDTLLDLEQIE----ELPEEKKPNVILFVG-VNGVGKTTTIAKLANKLKK-QG  110 (284)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH----HCCCCCCCEEEEEEE-EECCCHHHHHHHHHHHHHH-CC
T ss_conf             35577078999999999999874112321133443344----301478977999984-4088601028899999987-49


Q ss_pred             CCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCC-CCCHHCCCHHHHHHHHHH
Q ss_conf             9499997879898603343899878988863184561243376532024898068724876-120320799999998999
Q gi|254780725|r  192 METLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAM-LSRTYDFDEKMIVPVLDI  270 (427)
Q Consensus       192 ~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~-~~~~~~~~~~~l~~ll~~  270 (427)
                      ++|+|.=.|.- --++              +.+        |+.+..  .-|..|...... -|.    ..-.|+.+-..
T Consensus       111 k~V~laAgDTF-RAAA--------------~EQ--------L~~Wa~--R~gv~vi~~~~gn~DP----AaV~fDAi~~A  161 (284)
T TIGR00064       111 KSVLLAAGDTF-RAAA--------------IEQ--------LEVWAK--RLGVDVIKQKEGNADP----AAVIFDAIQAA  161 (284)
T ss_pred             CEEEEECCCHH-HHHH--------------HHH--------HHHHHH--HHCCEEEECCCCCCCC----HHHHHHHHHHH
T ss_conf             90899827524-7999--------------999--------999898--8387554078898871----78999989999


Q ss_pred             HHHCCCEEEECCCCCCCH---HH------HHHH------HHCCCCCCCCCCCHH--HHHHHHHHHHHHHHCCCCCCCCEE
Q ss_conf             851288899738888898---99------9998------620125435787768--899999999999981987675389
Q gi|254780725|r  271 LEQIFPLVILDVPHVWNS---WT------QEVL------TLSDKVVITTSLDLA--GLRNSKNLIDVLKKLRPADKPPYL  333 (427)
Q Consensus       271 l~~~yd~VIiD~p~~~~~---~~------~~~L------~~AD~vviV~~p~~~--slr~a~~ll~~l~~~~~~~~~~~i  333 (427)
                      -.++||+|++||..++..   ..      ..++      .+-+++++|.+.+..  ++.+++.+-+.+       .-=++
T Consensus       162 k~~niDvvliDTAGRLqnk~NLm~EL~KI~RV~~k~~~~~aP~e~lLVlDAt~Gqna~~QA~~F~eav-------~ltGi  234 (284)
T TIGR00064       162 KARNIDVVLIDTAGRLQNKVNLMDELKKIKRVIKKVDPVDAPDEVLLVLDATTGQNALEQAKVFNEAV-------GLTGI  234 (284)
T ss_pred             HHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHC-------CCCEE
T ss_conf             87499789973475454662039999999998732102578755754220222030899999986540-------68858


Q ss_pred             EEECCCCCCCCHHHHHHHHHHHCCCEEEE---------ECCCHHHHHHHH
Q ss_conf             99565898752005999999848953799---------068799999988
Q gi|254780725|r  334 VLNQVKTPKKPEISISDFCAPLGITPSAI---------IPFDGAVFGMSA  374 (427)
Q Consensus       334 VlNr~~~~~~~~i~~~~~~~~lg~~~~~~---------IP~D~~~~~~A~  374 (427)
                      ||.+.+...++-+. =.+...++.|+...         .|||+..|.++.
T Consensus       235 iLTKLDg~AKGG~~-l~i~~~l~~Pv~~~G~GE~~dDL~~Fd~~~fv~~L  283 (284)
T TIGR00064       235 ILTKLDGTAKGGII-LAIAYELKLPVKFIGVGEKIDDLAPFDADWFVEAL  283 (284)
T ss_pred             EEECCCCCCHHHHH-HHHHHHHCCCEEEEECCCCHHHHCCCCHHHHHHHC
T ss_conf             99634688037899-98899857976998548873320147978998750


No 155
>KOG0519 consensus
Probab=98.15  E-value=4.6e-05  Score=50.32  Aligned_cols=57  Identities=9%  Similarity=-0.011  Sum_probs=25.5

Q ss_pred             CCCEEEEECCCCCCC-CHHHHHHHHHHHC--CCEEEE-ECCCHHHHHHHHHCCCCEEEECC
Q ss_conf             753899956589875-2005999999848--953799-06879999998847961898889
Q gi|254780725|r  329 KPPYLVLNQVKTPKK-PEISISDFCAPLG--ITPSAI-IPFDGAVFGMSANSGKMIHEVDP  385 (427)
Q Consensus       329 ~~~~iVlNr~~~~~~-~~i~~~~~~~~lg--~~~~~~-IP~D~~~~~~A~~~G~pi~e~~p  385 (427)
                      ....+|+--+.+|.. +....+++.+..+  .++.+. ---++....+....|.--....|
T Consensus       710 ~~y~~ifmD~qMP~mDG~e~~~~irk~~~~~~pIvAlTa~~~~~~~~~c~~~Gmd~yl~KP  770 (786)
T KOG0519         710 HSYDVIFMDLQMPEMDGYEATREIRKKERWHLPIVALTADADPSTEEECLEVGMDGYLSKP  770 (786)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHCCCEEECCC
T ss_conf             8632799975775555499999998751678877997468757889999982876467463


No 156
>PRK05632 phosphate acetyltransferase; Reviewed
Probab=98.11  E-value=0.00039  Score=44.56  Aligned_cols=36  Identities=25%  Similarity=0.435  Sum_probs=14.4

Q ss_pred             CCCEEEEECCCCCC-CHH-HHH-HHHHHHCCCCCEEEEEEC
Q ss_conf             98499998059876-778-899-988853289980899816
Q gi|254780725|r   77 TPDLIIVQTKVDSR-EVL-SAL-EPLAEVCDSGTKVIVIGD  114 (427)
Q Consensus        77 ~P~~iivd~~~~~~-~~~-~~l-~~la~~~~p~~~Vivig~  114 (427)
                      .-|+||||-..... ... ..+ .++|..  =|.+||.+..
T Consensus        98 ~~DvVLVEGs~~~~~~~~~~~lNa~IAkn--LgA~VILV~~  136 (702)
T PRK05632         98 DCDVVLVEGLVPTRKHPFALSLNAEIAKN--LGAEVILVSS  136 (702)
T ss_pred             CCCEEEEECCCCCCCCCCHHHHHHHHHHH--CCCCEEEEEC
T ss_conf             89989994888788986044335999997--6998899963


No 157
>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]
Probab=98.08  E-value=4.7e-05  Score=50.26  Aligned_cols=80  Identities=23%  Similarity=0.427  Sum_probs=62.0

Q ss_pred             HHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHH
Q ss_conf             99999986189984999980598767788999888532899808998168718999999976562643189998999997
Q gi|254780725|r   66 AEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINS  145 (427)
Q Consensus        66 ~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~a  145 (427)
                      -.+.+..... -||+||+|+.+|..+..+.+-...+  .+..++|++..++|.....+++.+|+.-|+++|+++..+...
T Consensus        40 ~~~~~~~~~~-~pDvVildie~p~rd~~e~~~~~~~--~~~~piv~lt~~s~p~~i~~a~~~Gv~ayivkpi~~~rl~p~  116 (194)
T COG3707          40 LEAVEVCERL-QPDVVILDIEMPRRDIIEALLLASE--NVARPIVALTAYSDPALIEAAIEAGVMAYIVKPLDESRLLPI  116 (194)
T ss_pred             CCCCHHHHHC-CCCEEEEECCCCCCCHHHHHHHHHC--CCCCCEEEEECCCCHHHHHHHHHCCCEEEEECCCCHHHHHHH
T ss_conf             4750677852-9987999667877328999898605--899878999716785899999973874988347654210479


Q ss_pred             HHH
Q ss_conf             631
Q gi|254780725|r  146 ISA  148 (427)
Q Consensus       146 i~~  148 (427)
                      +.-
T Consensus       117 L~v  119 (194)
T COG3707         117 LDV  119 (194)
T ss_pred             HHH
T ss_conf             999


No 158
>KOG0781 consensus
Probab=98.07  E-value=4.2e-05  Score=50.54  Aligned_cols=189  Identities=16%  Similarity=0.184  Sum_probs=107.2

Q ss_pred             HHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             99999997656264318999899999763102332223456753799974698877568999999999962699499997
Q gi|254780725|r  119 SLYRALISNHVSEYLIEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLAD  198 (427)
Q Consensus       119 ~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvD  198 (427)
                      ...+++|+---. -+..|-..-|+.+-|.+.-.   ..   .-=+|+|+| --||||||--+-+|++|-+ .+.+|+++-
T Consensus       343 ~Tvk~Al~daLv-QILTP~~sVDlLrdI~~ar~---~k---rPYvi~fvG-VNGVGKSTNLAKIayWLlq-NkfrVlIAA  413 (587)
T KOG0781         343 STVKEALRDALV-QILTPQRSVDLLRDIMSARR---RK---RPYVISFVG-VNGVGKSTNLAKIAYWLLQ-NKFRVLIAA  413 (587)
T ss_pred             HHHHHHHHHHHH-HHCCCCCHHHHHHHHHHHHH---CC---CCEEEEEEE-ECCCCCCCHHHHHHHHHHH-CCCEEEEEE
T ss_conf             999999999999-87388730669999999874---68---975999982-1476651329999999985-783699986


Q ss_pred             CCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHH-HCCCE
Q ss_conf             87989860334389987898886318456124337653202489806872487612032079999999899985-12888
Q gi|254780725|r  199 LDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILE-QIFPL  277 (427)
Q Consensus       199 lDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~-~~yd~  277 (427)
                      ||.--+.+--.|                   .+..++.-.-+++.+.++..+-.-+     ...-....+...+ +.||+
T Consensus       414 CDTFRsGAvEQL-------------------rtHv~rl~~l~~~~v~lfekGYgkd-----~a~vak~AI~~a~~~gfDv  469 (587)
T KOG0781         414 CDTFRSGAVEQL-------------------RTHVERLSALHGTMVELFEKGYGKD-----AAGVAKEAIQEARNQGFDV  469 (587)
T ss_pred             CCCHHHHHHHHH-------------------HHHHHHHHHHCCCHHHHHHHHCCCC-----HHHHHHHHHHHHHHCCCCE
T ss_conf             243124478999-------------------9999999874552048886104778-----2899999999998669878


Q ss_pred             EEECCCCCCCH--HHHHHH------HHCCCCCCCCCCCH--HHHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf             99738888898--999998------62012543578776--88999999999999819876753899956589
Q gi|254780725|r  278 VILDVPHVWNS--WTQEVL------TLSDKVVITTSLDL--AGLRNSKNLIDVLKKLRPADKPPYLVLNQVKT  340 (427)
Q Consensus       278 VIiD~p~~~~~--~~~~~L------~~AD~vviV~~p~~--~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~  340 (427)
                      |++|+......  ..+..|      ..-|.|+.|.+.=+  .|+..++.+-+.+.....+..--.+++.+++.
T Consensus       470 vLiDTAGRmhn~~~LM~~L~kl~~~n~pD~i~~VgEALVG~dsvdq~~~Fn~al~d~~~~r~iDgilltK~DT  542 (587)
T KOG0781         470 VLIDTAGRMHNNAPLMTSLAKLIKVNKPDLILFVGEALVGNDSVDQLKKFNRALADHSTPRLIDGILLTKFDT  542 (587)
T ss_pred             EEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEHHHHHCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCH
T ss_conf             9983544334780678999999744798659985055527558999999999874489744234378871250


No 159
>PRK12724 flagellar biosynthesis regulator FlhF; Provisional
Probab=98.07  E-value=0.00055  Score=43.68  Aligned_cols=208  Identities=15%  Similarity=0.171  Sum_probs=105.7

Q ss_pred             HHHHHHHHHCCCCEEECC-----------CCCH---H----HHHHHHHHCCCC-CC--CCCC-CCCEEEEEEECCCCCCH
Q ss_conf             899999997656264318-----------9998---9----999976310233-22--2345-67537999746988775
Q gi|254780725|r  118 VSLYRALISNHVSEYLIE-----------PLSV---A----DIINSISAIFTP-QE--EGKG-SSGCSISFIGSRGGVGS  175 (427)
Q Consensus       118 ~~l~r~l~r~Gv~dyl~~-----------P~~~---~----~l~~ai~~~~~~-~~--~~~~-~~grvIav~g~KGGvGk  175 (427)
                      ..+|..+++.|+++-+..           |.+.   .    .+...+...... .+  ...+ ...|+|+|+|. =||||
T Consensus       158 ~~l~~~L~~~~~~~~~~~~i~~~l~~~~~~~d~~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~kvi~lVGP-TGVGK  236 (432)
T PRK12724        158 QRLGERLVREGMSQSYVEEMASKLEERLSPVDQGRNHNVTERAVTYLEERVSVDSDLFSGTGKNQRKVVFFVGP-TGSGK  236 (432)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHCCCCCCCEEEEEECC-CCCCH
T ss_conf             99999998756688999999999987538100110678999999999987147740110357777629999899-99888


Q ss_pred             HHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCC
Q ss_conf             68999999999962699499997879898603343899878988863184561243376532024898068724876120
Q gi|254780725|r  176 STIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSR  255 (427)
Q Consensus       176 TTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~  255 (427)
                      ||..+=||..++-..+++|.||=.|..-=.+.-.|     .+.++++                    |+.+-.       
T Consensus       237 TTTiAKLAA~~~l~~~kkVaLIT~DTYRIgAvEQL-----ktYa~Il--------------------~iPv~v-------  284 (432)
T PRK12724        237 TTSIAKLAAKYFLHMGKSVSLYTTDNYRIAAIEQL-----KRYADTM--------------------GMPFYP-------  284 (432)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHH-----HHHHHHH--------------------CCCEEE-------
T ss_conf             99999999999997499279995266537799999-----9999985--------------------994599-------


Q ss_pred             HHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCH--H----HHHHHHH---CC--CCCCCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf             320799999998999851288899738888898--9----9999862---01--25435787768899999999999981
Q gi|254780725|r  256 TYDFDEKMIVPVLDILEQIFPLVILDVPHVWNS--W----TQEVLTL---SD--KVVITTSLDLAGLRNSKNLIDVLKKL  324 (427)
Q Consensus       256 ~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~--~----~~~~L~~---AD--~vviV~~p~~~slr~a~~ll~~l~~~  324 (427)
                        -.++..+...+..  ..+|+|+||+......  .    ....+..   .+  ++++|...+. .-++.+.+++.+...
T Consensus       285 --v~~~~el~~al~~--~~~DlILIDTAGrS~rd~~~~~eL~~ll~~~~~~~~ie~~LVLSaTt-k~~dl~~ii~~f~~l  359 (432)
T PRK12724        285 --VKDIKKFKETLAR--DGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTS-SYHHTLTVLKAYESL  359 (432)
T ss_pred             --EECHHHHHHHHHH--CCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEECCC-CHHHHHHHHHHHCCC
T ss_conf             --5189999999985--69999999299989789999999999998636678851799997889-989999999984269


Q ss_pred             CCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEE-----ECCCHH
Q ss_conf             98767538999565898752005999999848953799-----068799
Q gi|254780725|r  325 RPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAI-----IPFDGA  368 (427)
Q Consensus       325 ~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~-----IP~D~~  368 (427)
                      .+.    .+|+.+.+-....- +.=.+....+.++...     +|.|-.
T Consensus       360 ~~~----~lIfTKLDET~s~G-~ilni~~~~~~PisYiT~GQ~VPdDI~  403 (432)
T PRK12724        360 NYR----RILLTKLDEADFLG-SFLELADTYSKSFTYLSVGQEVPFDIL  403 (432)
T ss_pred             CCC----EEEEEECCCCCCCC-HHHHHHHHHCCCEEEEECCCCCCCCHH
T ss_conf             998----49997122779866-999999998898699808997971733


No 160
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=98.06  E-value=0.00019  Score=46.51  Aligned_cols=162  Identities=12%  Similarity=0.089  Sum_probs=88.1

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC---CEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHH
Q ss_conf             6753799974698877568999999999962699---4999978798986033438998789888631845612433765
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAM---ETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSR  235 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~---~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~  235 (427)
                      ..+|||+++| --||||||+.+-||..++-..++   +|.||-+|..--.+.-.|     .+.++.+             
T Consensus       172 ~k~~vi~lVG-PTGvGKTTTiAKLAa~~~l~~~~k~~~V~lit~DtyRigAveQL-----ktya~il-------------  232 (388)
T PRK12723        172 LKKRIFILVG-PTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQI-----QTYGDIM-------------  232 (388)
T ss_pred             CCCEEEEEEC-CCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCHHHHHHH-----HHHHHHH-------------
T ss_conf             5762899989-98875787999999999986267677379998078758899999-----9999997-------------


Q ss_pred             HHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCH------HHHHHHHHC--C-CCCCCCCC
Q ss_conf             32024898068724876120320799999998999851288899738888898------999998620--1-25435787
Q gi|254780725|r  236 LPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNS------WTQEVLTLS--D-KVVITTSL  306 (427)
Q Consensus       236 ~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~------~~~~~L~~A--D-~vviV~~p  306 (427)
                             |+.+-..         .+...+...+..+ ..||+|+||++.....      .....+...  | .+++|...
T Consensus       233 -------~vp~~v~---------~~~~dl~~~l~~~-~~~D~IlIDTAGrs~~d~~~~~el~~~~~~~~~~~~~~Lvlsa  295 (388)
T PRK12723        233 -------GIPVKAI---------ESFKDLKEEITQS-KDFDLVLIDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSS  295 (388)
T ss_pred             -------CCCEEEE---------CCHHHHHHHHHHH-CCCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEECC
T ss_conf             -------8806985---------7889999999972-4999999958998856899999999999741898459999879


Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEE
Q ss_conf             76889999999999998198767538999565898752005999999848953799
Q gi|254780725|r  307 DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAI  362 (427)
Q Consensus       307 ~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~  362 (427)
                      +. .-++...+++.+...++    -.+|+.+.+.....- ..=.+....+.++...
T Consensus       296 t~-~~~d~~~i~~~f~~~~~----~~~I~TKlDEt~~~G-~~l~~~~~~~~Pi~yi  345 (388)
T PRK12723        296 TT-KTSDIKEIFHQFSPFSY----KTVIFTKLDETTCVG-NLISLIHEMRKEVSYV  345 (388)
T ss_pred             CC-CHHHHHHHHHHHCCCCC----CEEEEEECCCCCCCC-HHHHHHHHHCCCEEEE
T ss_conf             89-99999999998427999----849998322789866-9999999988886999


No 161
>COG2403 Predicted GTPase [General function prediction only]
Probab=98.04  E-value=0.0011  Score=41.95  Aligned_cols=198  Identities=14%  Similarity=0.152  Sum_probs=107.9

Q ss_pred             HHHHHHHHHHCCCCCEEEEEECCCC---HHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEC
Q ss_conf             8899988853289980899816871---8999999976562643189998999997631023322234567537999746
Q gi|254780725|r   93 LSALEPLAEVCDSGTKVIVIGDTND---VSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGS  169 (427)
Q Consensus        93 ~~~l~~la~~~~p~~~Vivig~~~d---~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~  169 (427)
                      ..+|+.+-+-.+-+.-|+..++..-   ..+...++.+|+.=.+..|.+.....                .-.+|+|++.
T Consensus        71 ~~~lek~ire~~VD~~VlaySDvs~e~v~~IaS~vLs~GA~f~~~gP~et~~~~----------------ekPviaV~at  134 (449)
T COG2403          71 YDDLEKIIREKDVDIVVLAYSDVSYEHVFRIASRVLSAGADFKELGPKETMLKL----------------EKPVIAVTAT  134 (449)
T ss_pred             HHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHCCCEEEEECCCHHHHHH----------------CCCEEEEEEE
T ss_conf             899999998707661687701289899878999997478536872752776651----------------4855999972


Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHH-----HHHHHHHHCCCCCE
Q ss_conf             9887756899999999996269949999787989860334389987898886318456124-----33765320248980
Q gi|254780725|r  170 RGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDK-----AFVSRLPVFYAENL  244 (427)
Q Consensus       170 KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~-----~~l~~~l~~~~~gL  244 (427)
                      +-|+|||+++.-+|..|.+ +|.++|.|-.-...+      |..+..+. +.+...+.+|.     ..-+.+.....-+.
T Consensus       135 rtg~GKsaVS~~v~r~l~e-rgyrv~vVrhPmiy~------~~~ieitv-e~~~k~edld~ha~t~eereeye~~I~tg~  206 (449)
T COG2403         135 RTGVGKSAVSRYVARLLRE-RGYRVCVVRHPMIYR------GDRIEITV-ERLAKLEDLDRHAATDEEREEYESYIPTGG  206 (449)
T ss_pred             CCCCCHHHHHHHHHHHHHH-CCCCEEEEECCEEEC------CCCCHHHH-HHHHCHHHCCCCCCCHHHHHHHHHCCCCCC
T ss_conf             3665567888999999986-698237995570233------77310018-977377652642255666887874364355


Q ss_pred             EEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHH-----------------------HHHHHHCCCCC
Q ss_conf             6872487612032079999999899985128889973888889899-----------------------99986201254
Q gi|254780725|r  245 SILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWT-----------------------QEVLTLSDKVV  301 (427)
Q Consensus       245 ~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~-----------------------~~~L~~AD~vv  301 (427)
                      -++++            ..+..++.......|+|++|-+...-+..                       .--+..||.+ 
T Consensus       207 ~vlAG------------vdy~~vlke~~~~aD~IlwdGgnndfPfvkpd~~Ivvvda~rpg~ei~~~pGe~~irlAD~V-  273 (449)
T COG2403         207 GVLAG------------VDYGTVLKEGEKEADFILWDGGNNDFPFVKPDLHIVVVDALRPGEEIGSFPGELRIRLADLV-  273 (449)
T ss_pred             CEEEE------------EEHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCEEEEECCCCCCHHHCCCCCCEEEEECCEE-
T ss_conf             34652------------04899998776415589994888778852577059993388872565268773153221289-


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf             35787768899999999999981987
Q gi|254780725|r  302 ITTSLDLAGLRNSKNLIDVLKKLRPA  327 (427)
Q Consensus       302 iV~~p~~~slr~a~~ll~~l~~~~~~  327 (427)
                      +++-.+.++.....++.+.+++.++.
T Consensus       274 IItkveea~~~kvrkI~~~I~~iNP~  299 (449)
T COG2403         274 IITKVEEAMAEKVRKIVRNIEEINPK  299 (449)
T ss_pred             EEECCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             99613513367899999999860998


No 162
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.04  E-value=3.8e-05  Score=50.81  Aligned_cols=97  Identities=13%  Similarity=0.112  Sum_probs=77.3

Q ss_pred             HHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCC
Q ss_conf             11002022373069989999998618998499998059876778899988853289980899816871899999997656
Q gi|254780725|r   50 DPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHV  129 (427)
Q Consensus        50 drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv  129 (427)
                      |++|..--..-..-+..+|.+.+.... -+-|+.|-.|+..++++.|+++++. +|..|+|+++...+-...++++.+||
T Consensus        35 ~~~~~~~~~~~~~~~~~~a~~r~~~~~-~DCvv~dy~~~~~dGieLLe~vRe~-~p~lP~Il~t~~gsE~vas~AI~AGv  112 (674)
T PRK13558         35 DLDEDGRFDVTQIRDFVAARDRVDDPD-IDCVVAVHEPDGFDGVAFLEAVRQT-HAEFPVVVVPTAVDEDVARRAVDADA  112 (674)
T ss_pred             CCCCCCCCCEEEECCHHHHHHHHCCCC-CCEEEECCCCCCCCHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHCH
T ss_conf             566677421276323888986531589-8769965657888679999998613-89998899956785899999875163


Q ss_pred             CEEECCCCCHHHHHHHHHHCC
Q ss_conf             264318999899999763102
Q gi|254780725|r  130 SEYLIEPLSVADIINSISAIF  150 (427)
Q Consensus       130 ~dyl~~P~~~~~l~~ai~~~~  150 (427)
                      .+||.+  +..+....+....
T Consensus       113 t~Ylp~--~~~~~~~~~~~~i  131 (674)
T PRK13558        113 TGLVPA--VSEDATAAIADRI  131 (674)
T ss_pred             HHHCCC--CCHHHHHHHHHHH
T ss_conf             643344--7176899999999


No 163
>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=97.97  E-value=8.8e-05  Score=48.56  Aligned_cols=169  Identities=14%  Similarity=0.133  Sum_probs=90.1

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             67537999746988775689999999999626994999978798986033438998789888631845612433765320
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      ..-..||++|. -||||||..+-||+.+.. .+++|.||-.|..-=.+.            |=|..-.        +++ 
T Consensus       239 ~~~q~IALVGP-TGVGKTTTIAKLAArf~~-~~KkVALITtDTYRIGAV------------EQLKTYA--------eIM-  295 (436)
T PRK11889        239 KEVQTIALIGP-TGVGKTTTLAKMAWQFHG-KKKTVGFITTDHSRIGTV------------QQLQDYV--------KTI-  295 (436)
T ss_pred             HHCEEEEEECC-CCCCHHHHHHHHHHHHHC-CCCEEEEEECCCCHHHHH------------HHHHHHH--------HHH-
T ss_conf             41717999899-998889999999999861-698089998066347699------------9999999--------984-


Q ss_pred             CCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHH--CCCEEEECCCCCCC--HHH----HHHHHH--CCCCCCCCCCCH
Q ss_conf             24898068724876120320799999998999851--28889973888889--899----999862--012543578776
Q gi|254780725|r  239 FYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQ--IFPLVILDVPHVWN--SWT----QEVLTL--SDKVVITTSLDL  308 (427)
Q Consensus       239 ~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~--~yd~VIiD~p~~~~--~~~----~~~L~~--AD~vviV~~p~~  308 (427)
                          ++.+...         .++..+...+..++.  .||+|+||+.....  ...    ...+..  .+.+++|...+.
T Consensus       296 ----gVPV~VV---------~dp~eL~~AL~~lkdka~~DLILIDTAGRS~RD~~~I~EL~~~l~~~~p~ev~LVLSATT  362 (436)
T PRK11889        296 ----GFEVIAV---------RDEAAMTRALTYFKEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASM  362 (436)
T ss_pred             ----CCCEEEE---------CCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEECCC
T ss_conf             ----9943996---------888999999998763368888999298988468999999999985127771699997889


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEE-----ECCCHHH
Q ss_conf             889999999999998198767538999565898752005999999848953799-----0687999
Q gi|254780725|r  309 AGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAI-----IPFDGAV  369 (427)
Q Consensus       309 ~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~-----IP~D~~~  369 (427)
                       .-++.+.+++.++..++    -.+|+.+.+..... -..=.+....+.++...     +|.|...
T Consensus       363 -K~~DL~eIi~rF~~l~i----dglIfTKLDET~Sl-G~ILNv~~~s~LPIsYvTdGQ~VPEDIev  422 (436)
T PRK11889        363 -KSKDMIEIITNFKDIHI----DGIVFTKFDETASS-GELLKIPAVSSAPIVLMTDGQDVKKNIHI  422 (436)
T ss_pred             -CHHHHHHHHHHHCCCCC----CEEEEEECCCCCCC-HHHHHHHHHHCCCEEEECCCCCCCCCHHH
T ss_conf             -98999999997257998----82899713256870-37888998839987997899858753000


No 164
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=97.95  E-value=0.00011  Score=48.09  Aligned_cols=175  Identities=18%  Similarity=0.199  Sum_probs=105.0

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             53799974698877568999999999962699499997879898603343899878988863184561243376532024
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      --+|.|+| --|+||||...-||..+-+ .|++|++.=+|.-- ..+              +.+..    ..-++     
T Consensus       139 p~Vil~vG-VNG~GKTTTIaKLA~~l~~-~g~~VllaA~DTFR-AaA--------------iEQL~----~w~er-----  192 (340)
T COG0552         139 PFVILFVG-VNGVGKTTTIAKLAKYLKQ-QGKSVLLAAGDTFR-AAA--------------IEQLE----VWGER-----  192 (340)
T ss_pred             CEEEEEEE-CCCCCHHHHHHHHHHHHHH-CCCEEEEEECCHHH-HHH--------------HHHHH----HHHHH-----
T ss_conf             67999993-4888637179999999997-89869998233478-999--------------99999----99999-----


Q ss_pred             CCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHH---------HHHHHHC-----CCCCCCCCC
Q ss_conf             89806872487612032079999999899985128889973888889899---------9998620-----125435787
Q gi|254780725|r  241 AENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWT---------QEVLTLS-----DKVVITTSL  306 (427)
Q Consensus       241 ~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~---------~~~L~~A-----D~vviV~~p  306 (427)
                       -|..++.....    .+...-.++.+-..-.+.||+|++|+..+...-.         ..++...     ++++++.+.
T Consensus       193 -~gv~vI~~~~G----~DpAaVafDAi~~Akar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~llvlDA  267 (340)
T COG0552         193 -LGVPVISGKEG----ADPAAVAFDAIQAAKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDA  267 (340)
T ss_pred             -HCCEEECCCCC----CCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEC
T ss_conf             -59927825999----9808999999999997699999996755445736689999999998464568998428999775


Q ss_pred             --CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEE---------EECCCHHHHHHHH
Q ss_conf             --7688999999999999819876753899956589875200599999984895379---------9068799999988
Q gi|254780725|r  307 --DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSA---------IIPFDGAVFGMSA  374 (427)
Q Consensus       307 --~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~---------~IP~D~~~~~~A~  374 (427)
                        -..++..++.+-+.+.       --.+|+.+.+...++-+ .=.+...++.|+..         ..|||++.|..+.
T Consensus       268 ttGqnal~QAk~F~eav~-------l~GiIlTKlDgtAKGG~-il~I~~~l~~PI~fiGvGE~~~DL~~Fd~~~fv~~L  338 (340)
T COG0552         268 TTGQNALSQAKIFNEAVG-------LDGIILTKLDGTAKGGI-ILSIAYELGIPIKFIGVGEGYDDLRPFDAEWFVDAL  338 (340)
T ss_pred             CCCHHHHHHHHHHHHHCC-------CCEEEEEECCCCCCCCE-EEEHHHHHCCCEEEEECCCCHHHCCCCCHHHHHHHH
T ss_conf             647568999999987528-------86699970246777624-350888869997998578884432006999999986


No 165
>TIGR00379 cobB cobyrinic acid a,c-diamide synthase; InterPro: IPR004484 This family describes cobyrinic acid a,c-diamide synthase, the cobB (cbiA in Salmonella) protein of cobalamin biosynthesis. It is responsible for the amidation of cobyrinic acid to cobyrinic acid a,c-diamide via the intermediate formation of cobyrinic acid c-monoamide or hydrogenobrynic acid. NH(2) groups are provided by glutamine and one molecule of ATP hydrogenolyzed for each amidation .; GO: 0042242 cobyrinic acid ac-diamide synthase activity, 0009236 cobalamin biosynthetic process.
Probab=97.88  E-value=0.0008  Score=42.67  Aligned_cols=198  Identities=18%  Similarity=0.152  Sum_probs=114.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             99974698877568999999999962699499997879898603343899878988863184561243376532024898
Q gi|254780725|r  164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAEN  243 (427)
Q Consensus       164 Iav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~g  243 (427)
                      |.+.|...+||||||++.+=.+|+++ +.+|       |.=-+                 +||-+|+.+           
T Consensus         2 VviAGt~S~vGKT~I~~g~m~~L~~~-~~~V-------Q~fKV-----------------GPDYIDP~f-----------   45 (464)
T TIGR00379         2 VVIAGTSSKVGKTTISTGIMKALSRR-KLEV-------QPFKV-----------------GPDYIDPSF-----------   45 (464)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHCC-CCCC-------CCEEE-----------------CCCCCCCCC-----------
T ss_conf             78830568754789999999998618-6324-------65442-----------------587437884-----------


Q ss_pred             EEEEE-C--CCCCCCHHCCCHHHHHHHHHHHHHCC--CEEEECCCC---------CCCH--HHHHHHHHCCC-CCCCCCC
Q ss_conf             06872-4--87612032079999999899985128--889973888---------8898--99999862012-5435787
Q gi|254780725|r  244 LSILT-A--PAMLSRTYDFDEKMIVPVLDILEQIF--PLVILDVPH---------VWNS--WTQEVLTLSDK-VVITTSL  306 (427)
Q Consensus       244 L~lL~-a--~~~~~~~~~~~~~~l~~ll~~l~~~y--d~VIiD~p~---------~~~~--~~~~~L~~AD~-vviV~~p  306 (427)
                       |-++ +  .+.+| ...++...+..++....+.-  |+-||--=.         ..++  -|.++...-|. ||+|++.
T Consensus        46 -H~~aTGr~sRNLD-sF~~~~~~i~~~F~~~~~~~Gs~~s~IEGv~GLYdg~Py~a~~d~gStA~vAk~L~~PvvLv~n~  123 (464)
T TIGR00379        46 -HTLATGRKSRNLD-SFFMSEAQIKELFIRHSKGAGSDVSIIEGVRGLYDGIPYSAISDKGSTASVAKALDAPVVLVVNA  123 (464)
T ss_pred             -CCCCCCCCCCCCC-HHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCEEEEEEC
T ss_conf             -5411478666768-53302899999999861347896579727413436768877687751889999865988999956


Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHH-CCCEEEEECCCHHHHHHHHHCC-CCEEEEC
Q ss_conf             7688999999999999819876753899956589875200599999984-8953799068799999988479-6189888
Q gi|254780725|r  307 DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPL-GITPSAIIPFDGAVFGMSANSG-KMIHEVD  384 (427)
Q Consensus       307 ~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~l-g~~~~~~IP~D~~~~~~A~~~G-~pi~e~~  384 (427)
                      . .=-|.+..++.=.+...++..--++|+||++..+..+.....+++.. |.++.++||+..++-..---.| .|-.|. 
T Consensus       124 ~-~L~~saaAiv~Gy~~fdp~V~l~GVILN~V~~~rH~~k~k~A~e~L~Pgi~vlG~~pR~~~l~~p~RHLGLVpa~E~-  201 (464)
T TIGR00379       124 K-RLSRSAAAIVLGYRSFDPDVKLKGVILNRVGSERHLEKLKTAVEKLAPGIEVLGVIPRKEDLKVPDRHLGLVPAVER-  201 (464)
T ss_pred             C-HHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCC-
T ss_conf             4-03357867764134308983178788731077446899999988636894588777367532147754653166135-


Q ss_pred             CCCHHHHHHHHHHHHHH
Q ss_conf             99989999999999985
Q gi|254780725|r  385 PKSAIANLLVDFSRVLM  401 (427)
Q Consensus       385 p~s~~a~~~~~La~~i~  401 (427)
                      -+....+-+..|+..+.
T Consensus       202 l~~~~~~~~~~la~~~e  218 (464)
T TIGR00379       202 LDEIIQQILDWLAEVVE  218 (464)
T ss_pred             CCHHHHHHHHHHHHHHH
T ss_conf             31789999999999999


No 166
>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated
Probab=97.83  E-value=0.00045  Score=44.21  Aligned_cols=145  Identities=18%  Similarity=0.186  Sum_probs=78.3

Q ss_pred             HHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             99999976562643189998999997631023322234567537999746988775689999999999626994999978
Q gi|254780725|r  120 LYRALISNHVSEYLIEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADL  199 (427)
Q Consensus       120 l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDl  199 (427)
                      -.|+.++.|..  ++.-++..++++.+++.    -|...+.|-+|=++| =.|.||||||..|...|-+..++.|.++|-
T Consensus       357 elr~~L~~G~~--IPeWft~PeV~~eLrr~----~PPr~~~G~tiwlTG-LsgsGKsTiA~al~~~L~~~~~~~v~lLDG  429 (568)
T PRK05537        357 ELRRRLREGLE--IPEWFSFPEVVAELRRT----YPPRHKQGFTVFFTG-LSGAGKSTIAKALMAKLMEMRGRPVTLLDG  429 (568)
T ss_pred             HHHHHHHCCCC--CCCCCCCHHHHHHHHHH----CCCCCCCCEEEEEEC-CCCCCHHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             99999867998--99553877899999985----687445864999845-788877699999999999718927999546


Q ss_pred             CCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEE
Q ss_conf             79898603343899878988863184561243376532024898068724876120320799999998999851288899
Q gi|254780725|r  200 DLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVI  279 (427)
Q Consensus       200 Dl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VI  279 (427)
                      |.--..++..||    ++-.|-..+..|+..  +-+.+..  .|+-++.+.-.+...   ..+..+.+++.. ..|=-|.
T Consensus       430 D~~R~~l~~dLg----fs~~dR~enirR~~~--va~~~~~--~g~i~i~a~isP~~~---~R~~~r~~~~~~-~~f~ev~  497 (568)
T PRK05537        430 DVVRKHLSSELG----FSKEDRDLNILRIGF--VASEITK--NGGIAICAPIAPYRA---TRREVREMIEAF-GAFIEVY  497 (568)
T ss_pred             HHHHHHHCCCCC----CCHHHHHHHHHHHHH--HHHHHHH--CCCEEEEEECCCCHH---HHHHHHHHHCCC-CCEEEEE
T ss_conf             888742155789----898899999999999--9999985--897899950699979---999999985237-9779999


Q ss_pred             ECCC
Q ss_conf             7388
Q gi|254780725|r  280 LDVP  283 (427)
Q Consensus       280 iD~p  283 (427)
                      ||+|
T Consensus       498 v~~p  501 (568)
T PRK05537        498 VATP  501 (568)
T ss_pred             ECCC
T ss_conf             7898


No 167
>pfam10609 ParA ParA/MinD ATPase like. This family contains ATPases involved in plasmid partitioning. It also contains the cytosolic Fe-S cluster assembling factor NBP35 which is required for biogenesis and export of both ribosomal subunits.
Probab=97.80  E-value=9.3e-05  Score=48.41  Aligned_cols=63  Identities=24%  Similarity=0.205  Sum_probs=54.5

Q ss_pred             CCEEEECCCCCCCHHHHHHHHH--CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCC
Q ss_conf             8889973888889899999862--0125435787768899999999999981987675389995658
Q gi|254780725|r  275 FPLVILDVPHVWNSWTQEVLTL--SDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVK  339 (427)
Q Consensus       275 yd~VIiD~p~~~~~~~~~~L~~--AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~  339 (427)
                      .||+|||+||+.++....+++.  .+..++|++|...|+..++|.++++++.+.  .-+.+|-||..
T Consensus         1 LDyLiiD~PPGTgD~~ltl~~~~~~~~~ivVTTP~~ls~~dv~r~i~~~~~~~i--~ilGiVENMs~   65 (81)
T pfam10609         1 LDYLIIDMPPGTGDEHLTLAQSLPVDGAVIVTTPQDVALLDVRKAIDMFKKLNV--PILGIVENMSY   65 (81)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHHCCC--CEEEEEECCCC
T ss_conf             989999489996789999997488577699809859999999999999998499--61899977975


No 168
>cd01886 EF-G Elongation factor G (EF-G) subfamily.  Translocation is mediated by EF-G (also called translocase).  The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA.  This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule.  EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit.  The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit.  To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it.  The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well.  The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site.  This group conta
Probab=97.73  E-value=0.0018  Score=40.52  Aligned_cols=149  Identities=15%  Similarity=0.138  Sum_probs=92.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             99974698877568999999999962699499997879898603343899878988863184561243376532024898
Q gi|254780725|r  164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAEN  243 (427)
Q Consensus       164 Iav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~g  243 (427)
                      |+++| .+|.||||++=.+.+. +.... +.-=||    .|++-.++                  ++.-.+|       +
T Consensus         2 iai~g-H~gaGKTtL~EalL~~-ag~i~-r~G~v~----~g~tv~D~------------------~~eE~~R-------~   49 (270)
T cd01886           2 IGIIA-HIDAGKTTTTERILYY-TGRIH-KIGEVH----GGGATMDF------------------MEQERER-------G   49 (270)
T ss_pred             EEEEE-CCCCCHHHHHHHHHHH-CCCCC-CCCEEC----CCCCCCCC------------------CHHHHHC-------C
T ss_conf             89996-8999988999999986-68735-581553----89755668------------------4889876-------8


Q ss_pred             EEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCH--HHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             068724876120320799999998999851288899738888898--999998620125435787768899999999999
Q gi|254780725|r  244 LSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNS--WTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVL  321 (427)
Q Consensus       244 L~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~--~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l  321 (427)
                      .++-++.....                 ...+-+-++|+|...+.  .+..+|..+|..++|+...-.---.+.++.+.+
T Consensus        50 isi~~~~~~~~-----------------w~~~~inliDTPG~~DF~~e~~~aL~~~D~AviVv~a~~GVe~~T~~~w~~~  112 (270)
T cd01886          50 ITIQSAATTCF-----------------WKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQA  112 (270)
T ss_pred             CEEECCEEEEE-----------------ECCEEEEEEECCCCHHHHHHHHHHHHHHCEEEEEEECCCCHHHHHHHHHHHH
T ss_conf             70733668999-----------------8998999986969678899999998775559999846764426369999889


Q ss_pred             HHCCCCCCCCEEEEECCCCCCC-CHHHHHHHHHHHCCCEE-EEEC
Q ss_conf             9819876753899956589875-20059999998489537-9906
Q gi|254780725|r  322 KKLRPADKPPYLVLNQVKTPKK-PEISISDFCAPLGITPS-AIIP  364 (427)
Q Consensus       322 ~~~~~~~~~~~iVlNr~~~~~~-~~i~~~~~~~~lg~~~~-~~IP  364 (427)
                      ++.+.   +..+++|+.+.+.. ..-..+++++.+|.++. ..+|
T Consensus       113 ~~~~l---P~i~fINKmDre~ad~~~~l~~i~~~lg~~~vp~~~P  154 (270)
T cd01886         113 DRYNV---PRIAFVNKMDRTGADFFRVVEQIREKLGANPVPLQLP  154 (270)
T ss_pred             HHCCC---CEEEEEECCCCCCCCCHHHHHHHHHHHCCCEEEEEEE
T ss_conf             98499---9899998878778871668999999858973889856


No 169
>cd04169 RF3 RF3 subfamily.  Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria.  Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide.  The class II release factor RF3 then initiates the release of the class I RF from the ribosome.  RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state.  GDP/GTP exchange occurs, followed by the release of the class I RF.  Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome.  RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts.
Probab=97.73  E-value=0.0014  Score=41.20  Aligned_cols=156  Identities=15%  Similarity=0.143  Sum_probs=93.8

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      |-|+++| .+|+||||++=.|.+.- .. -.+.--|+.....|++..++                  ++.-.+|      
T Consensus         3 Rniai~g-H~gaGKTtL~EalL~~~-G~-i~r~G~V~~~~~~g~t~~D~------------------~~eE~~R------   55 (267)
T cd04169           3 RTFAIIS-HPDAGKTTLTEKLLLFG-GA-IREAGAVKARKSRKHATSDW------------------MEIEKQR------   55 (267)
T ss_pred             CEEEEEC-CCCCCHHHHHHHHHHHC-CC-CCCCCEEEECCCCCCCCCCC------------------HHHHHHC------
T ss_conf             1799984-79999899999999866-86-33385463036888604688------------------7999865------


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCH--HHHHHHHHCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             98068724876120320799999998999851288899738888898--9999986201254357877688999999999
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNS--WTQEVLTLSDKVVITTSLDLAGLRNSKNLID  319 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~--~~~~~L~~AD~vviV~~p~~~slr~a~~ll~  319 (427)
                       |.++-++.....                 ...+.+=+||+|...+.  .+..+|..+|..++|+...-.---.+.++.+
T Consensus        56 -~iSi~~~~~~~~-----------------w~~~kinliDTPG~~DF~~e~~~al~v~D~AviVv~a~~GVe~~T~~~w~  117 (267)
T cd04169          56 -GISVTSSVMQFE-----------------YRDCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFE  117 (267)
T ss_pred             -CCEEECCEEEEE-----------------ECCEEEEEEECCCCHHHHHHHHHHHHHHHCEEEEEECCCCCCHHHHHHHH
T ss_conf             -944863637887-----------------89989999979697789999999998864547995256665355899999


Q ss_pred             HHHHCCCCCCCCEEEEECCCCCCC-CHHHHHHHHHHHCCCE-EEEECC
Q ss_conf             999819876753899956589875-2005999999848953-799068
Q gi|254780725|r  320 VLKKLRPADKPPYLVLNQVKTPKK-PEISISDFCAPLGITP-SAIIPF  365 (427)
Q Consensus       320 ~l~~~~~~~~~~~iVlNr~~~~~~-~~i~~~~~~~~lg~~~-~~~IP~  365 (427)
                      +.++.+.   +..+++|+.+.... ..-..+++++.+|.++ ...+|.
T Consensus       118 ~a~~~~i---P~iifINKmDr~~adf~~~l~~i~~~lg~~~vpi~lPi  162 (267)
T cd04169         118 VCRLRGI---PIITFINKLDREGRDPLELLDEIEEELGIDCTPLTWPI  162 (267)
T ss_pred             HHHHCCC---CEEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEE
T ss_conf             9997299---97999853456789878999999998687751168775


No 170
>pfam03029 ATP_bind_1 Conserved hypothetical ATP binding protein. Members of this family are found in a range of archaea and eukaryotes and have hypothesized ATP binding activity.
Probab=97.70  E-value=0.00016  Score=46.98  Aligned_cols=151  Identities=19%  Similarity=0.158  Sum_probs=84.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEEC
Q ss_conf             98877568999999999962699499997879898603343899878988863184561243376532024898068724
Q gi|254780725|r  170 RGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTA  249 (427)
Q Consensus       170 KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a  249 (427)
                      --|+||||....+...+.. .++++.+|.|||..-...    -++.-.+.|.+.         ++..+....  |  =| 
T Consensus         4 paGSGKTT~~~~l~~~l~~-~~r~~~vvNLDPA~e~~p----Y~~~iDIrd~i~---------~~dvM~~~~--L--GP-   64 (234)
T pfam03029         4 GAGSGKTTFVGALSEILPL-RGRSVYVVNLDPAAENLP----YEADIDIRELIT---------VADVMEDYG--L--GP-   64 (234)
T ss_pred             CCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCCC----CCCCCCHHHHCC---------HHHHHHHCC--C--CC-
T ss_conf             8989889999999999997-799759997898665899----987771787467---------999999829--8--97-


Q ss_pred             CCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHH--------HHHHHHCCCCCCCCCCCHHHHHHHHHHHHH-
Q ss_conf             87612032079999999899985128889973888889899--------999862012543578776889999999999-
Q gi|254780725|r  250 PAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWT--------QEVLTLSDKVVITTSLDLAGLRNSKNLIDV-  320 (427)
Q Consensus       250 ~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~--------~~~L~~AD~vviV~~p~~~slr~a~~ll~~-  320 (427)
                      ...+-...++-...+.++.+.+....+|+++|+|.+..-++        ...|... .++.|.--|..-+.+...++.. 
T Consensus        65 NGali~~me~l~~~~d~l~~~l~~~~~y~l~DtPGQiElf~~~~~~~~i~~~L~~~-~~~~v~l~D~~~~~d~~~fis~~  143 (234)
T pfam03029        65 NGALTVAMDFGRITLDWLLEELEYEDDYYLFDTPGQIELFTHWDSLARGVEALEAS-RLGAVYLVDTRRLTDPIDFFSGL  143 (234)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEEECCHHHHHHHHHHHCC-CEEEEEEECHHHHCCHHHHHHHH
T ss_conf             38999999999999999999852557769983698357654002699999997128-73899984257746888899999


Q ss_pred             ----HHHCCCCCCCCEEEEECCCCC
Q ss_conf             ----998198767538999565898
Q gi|254780725|r  321 ----LKKLRPADKPPYLVLNQVKTP  341 (427)
Q Consensus       321 ----l~~~~~~~~~~~iVlNr~~~~  341 (427)
                          ....+.. -+...|+|+++.-
T Consensus       144 L~a~s~m~~l~-lP~vnvlsK~Dl~  167 (234)
T pfam03029       144 LYALSIMLRLG-LPFVVALNKFDLL  167 (234)
T ss_pred             HHHHHHHHHCC-CCEEEEECCHHCC
T ss_conf             99999999748-9944310004135


No 171
>TIGR00750 lao LAO/AO transport system ATPase; InterPro: IPR005129   Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli K-12, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK  resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase..
Probab=97.70  E-value=0.0041  Score=38.33  Aligned_cols=158  Identities=15%  Similarity=0.201  Sum_probs=95.6

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCC-CCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             753799974698877568999999999962699499997879898-6033438998789888631845612433765320
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYG-TANINFDKDPINSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g-~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      ++.+|.|+| --|+||||+---|.-.|-+ .|++|.+|=-||... |-+..||            +.-|++...-...+ 
T Consensus        37 nA~~vG~TG-~PGaGKSTl~~~l~~~lrR-rG~~VaViAvDP~SPfTGGsiLG------------Dr~Rm~~~asrkql-  101 (333)
T TIGR00750        37 NAHVVGITG-VPGAGKSTLVEKLIMELRR-RGLKVAVIAVDPSSPFTGGSILG------------DRLRMQRLASRKQL-  101 (333)
T ss_pred             CCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEECCCCCCCCHHHHH------------HHHHHHHHHHHHHH-
T ss_conf             907876646-8888577799999899976-59768999887975975514545------------68877544222233-


Q ss_pred             CCCCCEEEEECCCCCCCHHCCCH--HHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf             24898068724876120320799--9999989998512888997388888989999986201254357877688999999
Q gi|254780725|r  239 FYAENLSILTAPAMLSRTYDFDE--KMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKN  316 (427)
Q Consensus       239 ~~~~gL~lL~a~~~~~~~~~~~~--~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~  316 (427)
                      -..+|.++=|.|..-. .-.++.  ..+-.+++.  -.||+|+|-|= +.+..--.+...+|.+++|+-|..-.=     
T Consensus       102 W~dPg~FIRs~ptrG~-lGGls~at~~~~~lldA--~G~DVI~vETV-GVGQSEVdi~~~aDT~v~v~~pg~GDd-----  172 (333)
T TIGR00750       102 WTDPGVFIRSMPTRGS-LGGLSKATRELVKLLDA--AGYDVILVETV-GVGQSEVDIINMADTFVVVTIPGTGDD-----  172 (333)
T ss_pred             HCCCCCEECCCCCCCC-HHHHHHHHHHHHHHHHH--CCCCEEEEEEE-CCCHHHHHHHHHHCEEEEEECCCCCCH-----
T ss_conf             2289856767766675-25787999999999986--38987999841-575248788734150589854887834-----


Q ss_pred             HHHHHHH--CCCCCCCCEEEEECCCCCCCCH
Q ss_conf             9999998--1987675389995658987520
Q gi|254780725|r  317 LIDVLKK--LRPADKPPYLVLNQVKTPKKPE  345 (427)
Q Consensus       317 ll~~l~~--~~~~~~~~~iVlNr~~~~~~~~  345 (427)
                       +..+|+  +...|   .+|+|+.+.+...+
T Consensus       173 -~Q~iKaG~mEiaD---I~VVNKaD~~~a~~  199 (333)
T TIGR00750       173 -VQGIKAGVMEIAD---IYVVNKADGEGAEE  199 (333)
T ss_pred             -HHHHHHHHHEEEE---EEEEECCCCCCHHH
T ss_conf             -6666544302324---87881688766589


No 172
>cd03109 DTBS Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms. The enzyme catalyzes formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon dioxide. The enzyme utilizes carbon dioxide instead of hydrogen carbonate as substrate and is dependent on ATP and divalent metal ions as cofactors.
Probab=97.67  E-value=0.00056  Score=43.64  Aligned_cols=126  Identities=13%  Similarity=0.092  Sum_probs=90.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             99974698877568999999999962699499997879898603343899878988863184561243376532024898
Q gi|254780725|r  164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAEN  243 (427)
Q Consensus       164 Iav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~g  243 (427)
                      |..+|.--|||||.+++.|+.+|.+ .|.+|...-  +.                                         
T Consensus         1 ~~~~GTdT~VGKT~vt~~l~~~l~~-~G~~v~~~K--Pv-----------------------------------------   36 (134)
T cd03109           1 IMGFGTGTDIGKTVATAILARALKE-KGYRVAPLK--PV-----------------------------------------   36 (134)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEEC--HH-----------------------------------------
T ss_conf             9575278887689999999999997-799177875--66-----------------------------------------


Q ss_pred             EEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC------CHHHHHHHHHC-CCCCCCCCCCHHHHHHHHH
Q ss_conf             0687248761203207999999989998512888997388888------98999998620-1254357877688999999
Q gi|254780725|r  244 LSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVW------NSWTQEVLTLS-DKVVITTSLDLAGLRNSKN  316 (427)
Q Consensus       244 L~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~------~~~~~~~L~~A-D~vviV~~p~~~slr~a~~  316 (427)
                                                   +.||+|++.-..+|      .......+... --+++|+...+.++-.+--
T Consensus        37 -----------------------------~t~D~vlVEGaGG~~vPl~~~~~~~Dl~~~l~~pvIlV~~~~LG~INhtlL   87 (134)
T cd03109          37 -----------------------------QTYDFVLVEGAGGLCVPLKEDFTNADVAKELNLPAILVTSAGLGSINHAFL   87 (134)
T ss_pred             -----------------------------HCCCEEEEECCCCEEECCCCCCCHHHHHHHHCCCEEEEECCCCCHHHHHHH
T ss_conf             -----------------------------727989998897746003898629999997099989997788785899999


Q ss_pred             HHHHHHHCCCCCCCCEEEEECCCCCC-CCHHHHHHHHHHHCCCEEEEEC
Q ss_conf             99999981987675389995658987-5200599999984895379906
Q gi|254780725|r  317 LIDVLKKLRPADKPPYLVLNQVKTPK-KPEISISDFCAPLGITPSAIIP  364 (427)
Q Consensus       317 ll~~l~~~~~~~~~~~iVlNr~~~~~-~~~i~~~~~~~~lg~~~~~~IP  364 (427)
                      .++.+++.+.+  ...+|+|++.... ..+...+.+++..+.++.+++|
T Consensus        88 t~eal~~~gi~--v~G~i~N~~~~~~~~~~~N~~~I~~~t~vPvLG~vP  134 (134)
T cd03109          88 TIEAARIKGII--LNGVLGNVIVEKEGLATLNVETIERLTGIPVLGIVP  134 (134)
T ss_pred             HHHHHHHCCCC--EEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEECC
T ss_conf             99999987992--889999467997106787599999974999778288


No 173
>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=97.65  E-value=0.00078  Score=42.74  Aligned_cols=113  Identities=17%  Similarity=0.352  Sum_probs=89.5

Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHHCEEEE-ECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCC-C-
Q ss_conf             5999838989999999886411002022373-069989999998618998499998059876778899988853289-9-
Q gi|254780725|r   30 SVHVFCVTDTLYSVVERSKIDPRMSQVNMRI-TRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDS-G-  106 (427)
Q Consensus        30 ~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v-~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p-~-  106 (427)
                      .|. -+||=+.-..|-.++    +.+=+.+| -+-+...|.+.+.....-|++++|++.|..||++-+.+|....+. . 
T Consensus       763 ~vL-lVEDN~vN~~VA~gf----L~~LGH~VtlA~s~~~A~~c~~~~~~FD~aLLDI~LPD~dGVtL~~~L~~~~~~k~~  837 (1052)
T TIGR02956       763 RVL-LVEDNEVNQMVAQGF----LERLGHKVTLAESGQSALRCFHQDHRFDLALLDINLPDGDGVTLLQQLRAIYKAKND  837 (1052)
T ss_pred             EEE-EEECCHHHHHHHHHH----HHCCCCEEEHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             132-464474779999999----842794472085499999998548876754551578898656789999999973204


Q ss_pred             -----CEEEEEECC---CCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCC
Q ss_conf             -----808998168---71899999997656264318999899999763102
Q gi|254780725|r  107 -----TKVIVIGDT---NDVSLYRALISNHVSEYLIEPLSVADIINSISAIF  150 (427)
Q Consensus       107 -----~~Vivig~~---~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~  150 (427)
                           .|.|.++.+   .|+..|+   .+|+..||.||+...+|.+.|.+.+
T Consensus       838 ~~~~p~k~iAvSAHVf~Edv~~y~---~aGF~G~laKPl~~~~L~~~l~~~l  886 (1052)
T TIGR02956       838 SQDEPVKFIAVSAHVFNEDVAQYL---AAGFDGFLAKPLVEEQLVAMLAKIL  886 (1052)
T ss_pred             CCCCCCCEEEEEHHHHHHHHHHHH---HHHCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             445677722211334477699997---5302663479987788999999987


No 174
>cd04170 EF-G_bact Elongation factor G (EF-G) subfamily.  Translocation is mediated by EF-G (also called translocase).  The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA.  This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule.  EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit.  The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G.  On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit.  To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it.  The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well.  The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site.  This group
Probab=97.64  E-value=0.0019  Score=40.35  Aligned_cols=89  Identities=12%  Similarity=0.205  Sum_probs=69.5

Q ss_pred             HCCCEEEECCCCCCC--HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCC-CHHHHH
Q ss_conf             128889973888889--89999986201254357877688999999999999819876753899956589875-200599
Q gi|254780725|r  273 QIFPLVILDVPHVWN--SWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKK-PEISIS  349 (427)
Q Consensus       273 ~~yd~VIiD~p~~~~--~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~-~~i~~~  349 (427)
                      +.+-+-+||+|...+  ..+..+|..+|..++|+.+.-.-=-++.++.+.+++.+.   +..+++|+++.+.. ..-..+
T Consensus        62 ~~~~inliDTPG~~DF~~e~~~aL~v~D~Av~Vida~~GVe~~T~~~w~~~~~~~i---P~i~fINKmDr~~ad~~~~l~  138 (268)
T cd04170          62 KGHKINLIDTPGYADFVGETRAALRAADAALVVVSAQSGVEVGTEKLWEFADEAGI---PRIIFINKMDRERADFDKTLA  138 (268)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCC---CEEEEEECCCCCCCCHHHHHH
T ss_conf             99799998698975799999998404783999941875476879999999998599---989999787878996477999


Q ss_pred             HHHHHHCCCEE-EEEC
Q ss_conf             99998489537-9906
Q gi|254780725|r  350 DFCAPLGITPS-AIIP  364 (427)
Q Consensus       350 ~~~~~lg~~~~-~~IP  364 (427)
                      ++++.++.++. ..+|
T Consensus       139 ~i~~~lg~~~vp~~~P  154 (268)
T cd04170         139 ALQEAFGRPVVPLQLP  154 (268)
T ss_pred             HHHHHHCCCEEEEEEE
T ss_conf             9999868984999966


No 175
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=97.63  E-value=0.0019  Score=40.31  Aligned_cols=40  Identities=20%  Similarity=0.285  Sum_probs=33.7

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             675379997469887756899999999996269949999787
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLD  200 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlD  200 (427)
                      ..|.++-++| --|+||||++..+|...+. .|.+|+++|..
T Consensus        21 ~~G~itei~G-~pG~GKTtl~lq~a~~~~~-~g~~vlYidtE   60 (224)
T PRK09361         21 ERGTITQIYG-PPGSGKTNICIQLAVEAAR-QGKKVIYIDTE   60 (224)
T ss_pred             CCCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEECCC
T ss_conf             8887999989-9998599999999999997-49909996787


No 176
>cd04168 TetM_like Tet(M)-like subfamily.  Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria.  Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site.  This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative.  Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G.  EF-G and Tet(M) compete for binding on the ribosomes.  Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind.  Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity.  These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.
Probab=97.62  E-value=0.001  Score=42.00  Aligned_cols=85  Identities=14%  Similarity=0.136  Sum_probs=65.3

Q ss_pred             HCCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCC-CHHHHH
Q ss_conf             12888997388888--989999986201254357877688999999999999819876753899956589875-200599
Q gi|254780725|r  273 QIFPLVILDVPHVW--NSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKK-PEISIS  349 (427)
Q Consensus       273 ~~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~-~~i~~~  349 (427)
                      ..+.+-+||+|...  ...+..+|..+|..++|+.+.-.---.+.++++.+++.+.+   ..+++|+.+.+.. .....+
T Consensus        62 ~~~~~n~iDtPG~~dF~~e~~~al~~~D~av~Vv~a~~Gv~~~t~~~~~~~~~~~~P---~iifiNKmDre~adf~~~l~  138 (237)
T cd04168          62 EDTKVNLIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILWRLLRKLNIP---TIIFVNKIDRAGADLEKVYQ  138 (237)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCHHHHHHHHHHCCCC---EEEEEECCCCCCCCHHHHHH
T ss_conf             998799988988465666898897634816999965888223449999999985998---59986244578999999999


Q ss_pred             HHHHHHCCCEE
Q ss_conf             99998489537
Q gi|254780725|r  350 DFCAPLGITPS  360 (427)
Q Consensus       350 ~~~~~lg~~~~  360 (427)
                      ++++.++.++.
T Consensus       139 ~i~~~l~~~~~  149 (237)
T cd04168         139 EIKEKLSSDIV  149 (237)
T ss_pred             HHHHHHCCCEE
T ss_conf             99999789747


No 177
>COG2201 CheB Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]
Probab=97.57  E-value=0.0062  Score=37.23  Aligned_cols=161  Identities=13%  Similarity=0.151  Sum_probs=97.8

Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             59998389899999998864110020223730699899999986189984999980598767788999888532899808
Q gi|254780725|r   30 SVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKV  109 (427)
Q Consensus        30 ~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~V  109 (427)
                      .|..--++.-...+|.+..+.  -.+..+-....+...|++....- .||+|.+|+.|+-+|+++.|+.+-..  ..++|
T Consensus         3 rVlvVddsal~R~~i~~~l~~--~~~i~vv~~a~ng~~a~~~~~~~-~PDVi~ld~emp~mdgl~~l~~im~~--~p~pV   77 (350)
T COG2201           3 RVLVVDDSALMRKVISDILNS--DPDIEVVGTARNGREAIDKVKKL-KPDVITLDVEMPVMDGLEALRKIMRL--RPLPV   77 (350)
T ss_pred             EEEEECCCHHHHHHHHHHHHC--CCCEEEEEECCCHHHHHHHHHHC-CCCEEEEECCCCCCCHHHHHHHHHCC--CCCCE
T ss_conf             799985819999999999830--89737997337879999999722-99789972566445479999998447--99868


Q ss_pred             EEEECCCC--HHHHHHHHHCCCCEEECCCCCH---------HHHHHHHHHCCC-------CC----CC------CCCCCC
Q ss_conf             99816871--8999999976562643189998---------999997631023-------32----22------345675
Q gi|254780725|r  110 IVIGDTND--VSLYRALISNHVSEYLIEPLSV---------ADIINSISAIFT-------PQ----EE------GKGSSG  161 (427)
Q Consensus       110 ivig~~~d--~~l~r~l~r~Gv~dyl~~P~~~---------~~l~~ai~~~~~-------~~----~~------~~~~~g  161 (427)
                      |+++....  -..-.+++..|+.||+.+|...         .++++-+.....       .+    .+      .....-
T Consensus        78 imvsslt~~g~~~t~~al~~gAvD~i~kp~~~i~~~~~~~~~~l~~kv~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  157 (350)
T COG2201          78 IMVSSLTEEGAEATLEALELGAVDFIAKPSGGISLGLDEVAELLIEKVRAAARQNRKSLRTPEPPRAPAFRPVKPGPAAR  157 (350)
T ss_pred             EEEECCCCCCHHHHHHHHHCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             99951452137999999845742132178765444667889999999998752442013566778754357777778876


Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             3799974698877568999999999962699499997
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLAD  198 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvD  198 (427)
                      ++|++..+-||..+  +..=|.. |-...+..++++-
T Consensus       158 ~iV~IGaStGGp~A--L~~il~~-lP~~~p~pvvIvQ  191 (350)
T COG2201         158 KIVAIGASTGGPAA--LRAVLPA-LPADFPAPVVIVQ  191 (350)
T ss_pred             CEEEEEECCCCHHH--HHHHHHH-CCCCCCCCEEEEE
T ss_conf             38999947899999--9999975-8988899879994


No 178
>KOG0780 consensus
Probab=97.57  E-value=0.0023  Score=39.88  Aligned_cols=174  Identities=15%  Similarity=0.142  Sum_probs=94.5

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             53799974698877568999999999962699499997879898603343899878988863184561243376532024
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      --||-|+|- -|+||||..+-+|+++-+ .|.+++||=.|..-..+-                     |+.-  ....+ 
T Consensus       101 psVimfVGL-qG~GKTTtc~KlA~y~kk-kG~K~~LvcaDTFRagAf---------------------DQLk--qnA~k-  154 (483)
T KOG0780         101 PSVIMFVGL-QGSGKTTTCTKLAYYYKK-KGYKVALVCADTFRAGAF---------------------DQLK--QNATK-  154 (483)
T ss_pred             CCEEEEEEC-CCCCCCEEHHHHHHHHHH-CCCCEEEEEECCCCCCHH---------------------HHHH--HHHHH-
T ss_conf             708999830-578863008999999984-687245776022453068---------------------9999--87674-


Q ss_pred             CCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCH---HHHHHHH-----HCCCCCCCCCCCHHHHH
Q ss_conf             898068724876120320799999998999851288899738888898---9999986-----20125435787768899
Q gi|254780725|r  241 AENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNS---WTQEVLT-----LSDKVVITTSLDLAGLR  312 (427)
Q Consensus       241 ~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~---~~~~~L~-----~AD~vviV~~p~~~slr  312 (427)
                       .++.+..+....+ +..+.   ...+-..=+++||+||+|+......   ...++.+     .-|.++.|.+.+..-  
T Consensus       155 -~~iP~ygsyte~d-pv~ia---~egv~~fKke~fdvIIvDTSGRh~qe~sLfeEM~~v~~ai~Pd~vi~VmDasiGQ--  227 (483)
T KOG0780         155 -ARVPFYGSYTEAD-PVKIA---SEGVDRFKKENFDVIIVDTSGRHKQEASLFEEMKQVSKAIKPDEIIFVMDASIGQ--  227 (483)
T ss_pred             -HCCEEEECCCCCC-HHHHH---HHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCH--
T ss_conf             -0770684036655-58999---9999988863972899827873012489999999998515987389998562007--


Q ss_pred             HHHHHHHHHHHCCCCCCCCEEEEECCCCCCCC--HHHHHHHHHHHCCCEEE---------EECCCHHHHHHH
Q ss_conf             99999999998198767538999565898752--00599999984895379---------906879999998
Q gi|254780725|r  313 NSKNLIDVLKKLRPADKPPYLVLNQVKTPKKP--EISISDFCAPLGITPSA---------IIPFDGAVFGMS  373 (427)
Q Consensus       313 ~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~--~i~~~~~~~~lg~~~~~---------~IP~D~~~~~~A  373 (427)
                      ++......+++   ...--.+++.+.+...++  -++.   ..+.+.++..         .=|||++.|...
T Consensus       228 aae~Qa~aFk~---~vdvg~vIlTKlDGhakGGgAlSa---VaaTksPIiFIGtGEhmdDlE~F~pk~Fvsr  293 (483)
T KOG0780         228 AAEAQARAFKE---TVDVGAVILTKLDGHAKGGGALSA---VAATKSPIIFIGTGEHMDDLEPFDPKPFVSR  293 (483)
T ss_pred             HHHHHHHHHHH---HHCCCEEEEEECCCCCCCCCEEEE---HHHHCCCEEEEECCCCCCCCCCCCHHHHHHH
T ss_conf             67999998877---615403799722567777734530---3540798799816755111577780779998


No 179
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=97.52  E-value=0.0035  Score=38.73  Aligned_cols=73  Identities=15%  Similarity=0.135  Sum_probs=38.1

Q ss_pred             EECCHHHHHHHHHHHHHHHHHHCEEEE-EC-CCH----HHHHHHHHCCCCCCEEEEE-CCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             838989999999886411002022373-06-998----9999998618998499998-0598767788999888532899
Q gi|254780725|r   34 FCVTDTLYSVVERSKIDPRMSQVNMRI-TR-GSI----AEAVSCFSDSSTPDLIIVQ-TKVDSREVLSALEPLAEVCDSG  106 (427)
Q Consensus        34 f~~~~~~~~~~~~~~~drr~~~~~~~v-~~-g~~----~~A~~~~~~~~~P~~iivd-~~~~~~~~~~~l~~la~~~~p~  106 (427)
                      +.++|-........-.--|..-..+-| .. .|+    ...-+.++....|-+++|- ++-+..+....|++|.+.....
T Consensus        83 liDTPGh~DF~~e~~raL~a~D~Av~Vida~~GVe~qTe~~w~~~~~~~iP~i~FINKmDR~~ad~~~~l~ei~~~lg~~  162 (526)
T PRK00741         83 LLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKGVEPQTRKLMEVCRLRDTPIFTFINKLDRDGREPLELLDEIEEVLGIA  162 (526)
T ss_pred             EEECCCCHHHHHHHHHHHHHHCEEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             99098946778999999987375999997775523336899999886399889999656767898789887788874787


No 180
>cd01394 radB RadB. The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.
Probab=97.47  E-value=0.0034  Score=38.79  Aligned_cols=40  Identities=23%  Similarity=0.282  Sum_probs=33.5

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             675379997469887756899999999996269949999787
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLD  200 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlD  200 (427)
                      ..|.++-++| -.|+||||++..+|...++ .+.+|+++|.-
T Consensus        17 ~~G~it~i~G-~pG~GKStl~lq~a~~~~~-~g~~v~YidtE   56 (218)
T cd01394          17 ERGTVTQVYG-PPGTGKTNIAIQLAVETAG-QGKKVAYIDTE   56 (218)
T ss_pred             CCCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEECC
T ss_conf             7887999989-9998499999999999863-69869999665


No 181
>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]
Probab=97.45  E-value=0.0046  Score=38.01  Aligned_cols=142  Identities=15%  Similarity=0.104  Sum_probs=75.8

Q ss_pred             CCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHH
Q ss_conf             34567537999746988775689999999999626994999978798986033438998789888631845612433765
Q gi|254780725|r  156 GKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSR  235 (427)
Q Consensus       156 ~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~  235 (427)
                      +.-+.|+|+=|+| -.|.||||+|++++... +..+.+++.||.--.+.                    |+|+     ..
T Consensus        55 GGl~~g~ItEiyG-~~gsGKT~lal~~~~~a-q~~g~~a~fIDtE~~l~--------------------p~r~-----~~  107 (279)
T COG0468          55 GGLPRGRITEIYG-PESSGKTTLALQLVANA-QKPGGKAAFIDTEHALD--------------------PERA-----KQ  107 (279)
T ss_pred             CCCCCCEEEEEEC-CCCCCHHHHHHHHHHHH-HCCCCEEEEEECCCCCC--------------------HHHH-----HH
T ss_conf             8865535899846-88765466899998886-53798089995899989--------------------9999-----99


Q ss_pred             HHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHH-HHHHH
Q ss_conf             32024898068724876120320799999998999851288899738888898999998620125435787768-89999
Q gi|254780725|r  236 LPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLA-GLRNS  314 (427)
Q Consensus       236 ~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~-slr~a  314 (427)
                      ......+++.+.-.. +.+.    ..+.+..+.....+.++.||||.-...-+   ..... |       ..+. --|..
T Consensus       108 l~~~~~d~l~v~~~~-~~e~----q~~i~~~~~~~~~~~i~LvVVDSvaa~~r---~~~~~-d-------~~~~~~~r~l  171 (279)
T COG0468         108 LGVDLLDNLLVSQPD-TGEQ----QLEIAEKLARSGAEKIDLLVVDSVAALVR---AEEIE-D-------GHLGLRARLL  171 (279)
T ss_pred             HHHHHHCCEEEECCC-CHHH----HHHHHHHHHHHCCCCCCEEEEECCCCCCH---HHHCC-C-------CHHHHHHHHH
T ss_conf             887542153686689-7799----99999999875468878899825743463---65548-5-------3489999999


Q ss_pred             HHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf             99999999819876753899956589
Q gi|254780725|r  315 KNLIDVLKKLRPADKPPYLVLNQVKT  340 (427)
Q Consensus       315 ~~ll~~l~~~~~~~~~~~iVlNr~~~  340 (427)
                      .+.+..+........-..++.||+..
T Consensus       172 s~~l~~L~~~a~~~~~~vi~~NQv~~  197 (279)
T COG0468         172 SKALRKLTRLANKYNTAVIFTNQVRA  197 (279)
T ss_pred             HHHHHHHHHHHHHCCCEEEEECCEEE
T ss_conf             99999999999974958999784034


No 182
>KOG1532 consensus
Probab=97.43  E-value=0.0025  Score=39.68  Aligned_cols=181  Identities=16%  Similarity=0.191  Sum_probs=96.2

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHH
Q ss_conf             45675379997469887756899999999996269949999787989860334389987898886318456124337653
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRL  236 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~  236 (427)
                      ..+.-.+|.|+| --|.||||+..-|-.++.. .+.+.-+|.||+.--.+..-.|++-    .|.+         -.+..
T Consensus        15 ~~~~p~~ilVvG-MAGSGKTTF~QrL~~hl~~-~~~ppYviNLDPAv~~vpy~aniDI----RDtV---------kYkEv   79 (366)
T KOG1532          15 AIQRPVIILVVG-MAGSGKTTFMQRLNSHLHA-KKTPPYVINLDPAVRNVPYPANIDI----RDTV---------KYKEV   79 (366)
T ss_pred             CCCCCCEEEEEE-CCCCCCHHHHHHHHHHHHH-CCCCCEEEECCHHHHCCCCCCCCCH----HHHH---------HHHHH
T ss_conf             556870799994-4778841399999999862-3699808867888854888667756----6543---------09999


Q ss_pred             HHCCC--CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCH--H------HHHHHHHCC-CC--CCC
Q ss_conf             20248--98068724876120320799999998999851288899738888898--9------999986201-25--435
Q gi|254780725|r  237 PVFYA--ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNS--W------TQEVLTLSD-KV--VIT  303 (427)
Q Consensus       237 l~~~~--~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~--~------~~~~L~~AD-~v--viV  303 (427)
                      |.++.  ++=.++.+    -......-+.+..+++.....++||+||+|.+...  |      ....|..+- .|  ++|
T Consensus        80 MkqY~LGPNGgI~Ts----LNLF~tk~dqv~~~iek~~~~~~~~liDTPGQIE~FtWSAsGsIIte~lass~ptvv~Yvv  155 (366)
T KOG1532          80 MKQYQLGPNGGIVTS----LNLFATKFDQVIELIEKRAEEFDYVLIDTPGQIEAFTWSASGSIITETLASSFPTVVVYVV  155 (366)
T ss_pred             HHHHCCCCCCCHHHH----HHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCEEEEEECCCCCCHHHHHHHCCCEEEEEEE
T ss_conf             998388998640335----8999987899999999742204779974888068998427850158667613985999994


Q ss_pred             CCCCHHH-HHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCC--CHHHH---HHHHHHHC
Q ss_conf             7877688-999999999999819876753899956589875--20059---99999848
Q gi|254780725|r  304 TSLDLAG-LRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKK--PEISI---SDFCAPLG  356 (427)
Q Consensus       304 ~~p~~~s-lr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~--~~i~~---~~~~~~lg  356 (427)
                      -+|...+ ..=..+++-.+.-+-...-+..+|+|+.+..+.  ..-..   +.|.+++.
T Consensus       156 Dt~rs~~p~tFMSNMlYAcSilyktklp~ivvfNK~Dv~d~~fa~eWm~DfE~FqeAl~  214 (366)
T KOG1532         156 DTPRSTSPTTFMSNMLYACSILYKTKLPFIVVFNKTDVSDSEFALEWMTDFEAFQEALN  214 (366)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             47767884169988999999998626876999714344561889999999999999997


No 183
>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]
Probab=97.37  E-value=0.00047  Score=44.11  Aligned_cols=186  Identities=13%  Similarity=0.158  Sum_probs=98.0

Q ss_pred             CCCHHHHHHHHHCCCCEEEC----CCCC-HHHHHHHHHHCCCCCCCC-CCCCCEEEEEEECCCCCCHHHHHHHHHHHHH-
Q ss_conf             87189999999765626431----8999-899999763102332223-4567537999746988775689999999999-
Q gi|254780725|r  115 TNDVSLYRALISNHVSEYLI----EPLS-VADIINSISAIFTPQEEG-KGSSGCSISFIGSRGGVGSSTIAHNCAFSIA-  187 (427)
Q Consensus       115 ~~d~~l~r~l~r~Gv~dyl~----~P~~-~~~l~~ai~~~~~~~~~~-~~~~grvIav~g~KGGvGkTTiA~nLA~~LA-  187 (427)
                      ..-..++++++++|++--+.    .... ...+...+..+.....+. -...+++|+++| --||||||.-+-|||... 
T Consensus       151 ~~~~~~i~~~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~vi~LVG-PTGVGKTTTlAKLAar~~~  229 (407)
T COG1419         151 PTRLNLINELLRAGLELEILDMKDESYEDLRYFSEKLRKLLLSLIENLIVEQKRVIALVG-PTGVGKTTTLAKLAARYVM  229 (407)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEC-CCCCCHHHHHHHHHHHHHH
T ss_conf             046999999999756413331322222123217999999887644111124685799989-9887588799999999975


Q ss_pred             HHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHH
Q ss_conf             62699499997879898603343899878988863184561243376532024898068724876120320799999998
Q gi|254780725|r  188 SVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPV  267 (427)
Q Consensus       188 ~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~l  267 (427)
                      ....++|.+|-+|..-=.+.-.|     .+.++.+                    ++.+-         .-.++..+...
T Consensus       230 ~~~~~kVaiITtDtYRIGA~EQL-----k~Ya~im--------------------~vp~~---------vv~~~~el~~a  275 (407)
T COG1419         230 LKKKKKVAIITTDTYRIGAVEQL-----KTYADIM--------------------GVPLE---------VVYSPKELAEA  275 (407)
T ss_pred             HCCCCCEEEEEECCCHHHHHHHH-----HHHHHHH--------------------CCCEE---------EECCHHHHHHH
T ss_conf             32576068997144115289999-----9999986--------------------99559---------96399999999


Q ss_pred             HHHHHHCCCEEEECCCCCC--CHHH----HHHHHH--CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCC
Q ss_conf             9998512888997388888--9899----999862--0125435787768899999999999981987675389995658
Q gi|254780725|r  268 LDILEQIFPLVILDVPHVW--NSWT----QEVLTL--SDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVK  339 (427)
Q Consensus       268 l~~l~~~yd~VIiD~p~~~--~~~~----~~~L~~--AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~  339 (427)
                      +..++ +||+|+||+-...  +...    .+.+..  ...+++|...+. ..++.+.+++.++...+.    .+++.+.+
T Consensus       276 i~~l~-~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~-K~~dlkei~~~f~~~~i~----~~I~TKlD  349 (407)
T COG1419         276 IEALR-DCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATT-KYEDLKEIIKQFSLFPID----GLIFTKLD  349 (407)
T ss_pred             HHHHH-CCCEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCC-CHHHHHHHHHHHCCCCCC----EEEEECCC
T ss_conf             99853-1888999689988337899999999970356621799984576-468899999972458866----16897133


Q ss_pred             CC
Q ss_conf             98
Q gi|254780725|r  340 TP  341 (427)
Q Consensus       340 ~~  341 (427)
                      -.
T Consensus       350 ET  351 (407)
T COG1419         350 ET  351 (407)
T ss_pred             CC
T ss_conf             56


No 184
>pfam03796 DnaB_C DnaB-like helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=97.36  E-value=0.0072  Score=36.81  Aligned_cols=47  Identities=21%  Similarity=0.232  Sum_probs=37.0

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             675379997469887756899999999996269949999787989860
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      +.|. +.++++.-|+|||+++.|+|..+|.+.|.+|+++.+......+
T Consensus        17 ~~G~-l~vi~g~pg~GKS~~~~~~a~~~a~~~g~~Vl~~slEm~~~~~   63 (186)
T pfam03796        17 QKGD-LIIIAARPSMGKTAFALNIARNAALKQDKPVLFFSLEMSAEQL   63 (186)
T ss_pred             CCCC-EEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHH
T ss_conf             8881-7999967999879999999999999709966875475529999


No 185
>cd03114 ArgK-like The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.
Probab=97.29  E-value=0.0063  Score=37.18  Aligned_cols=146  Identities=14%  Similarity=0.170  Sum_probs=82.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCC-CCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             799974698877568999999999962699499997879898-6033438998789888631845612433765320248
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYG-TANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g-~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      ||.+.| -+|+||||+.-.|...+.+ .+++|.++=-|+... +-...||        |.+    |....       ...
T Consensus         1 viGitG-~pGaGKStLi~~l~~~~~~-~g~~VaVlavDPsS~~sgGalLG--------DRi----Rm~~~-------~~~   59 (148)
T cd03114           1 VIGITG-VPGAGKSTLIDALITALRA-RGKRVAVLAIDPSSPFSGGAILG--------DRI----RMERH-------ASD   59 (148)
T ss_pred             CEEECC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEECCCCCCCCCCCHH--------HHH----HHHHH-------CCC
T ss_conf             976258-9978789999999999997-89837999968887866862032--------354----53441-------579


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHHH-HCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             9806872487612032079999999899985-128889973888889899999862012543578776889999999999
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDILE-QIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDV  320 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~  320 (427)
                      ++.++-+.+..-. ...+ .......+..+. ..||+|+|.+-. .+.........+|.+++|..|..-.--..+     
T Consensus        60 ~~vfiRs~atrg~-~ggl-a~~~~~~i~~l~~~g~D~IiIETvG-vGQse~~i~~~aD~~i~v~~p~~GD~iQ~~-----  131 (148)
T cd03114          60 PGVFIRSLATRGF-LGGL-SRATPEVIRVLDAAGFDVIIVETVG-VGQSEVDIASMADTTVVVMAPGAGDDIQAI-----  131 (148)
T ss_pred             CCEEEEECCCCCC-CCCH-HHHHHHHHHHHHHCCCCEEEEECCC-CCCCHHHHHHHCCEEEEEECCCCCCHHHHC-----
T ss_conf             9836863466665-4204-6889999999997599989997487-775602655435669999636887377611-----


Q ss_pred             HHHCCCCCCCCEEEEECCC
Q ss_conf             9981987675389995658
Q gi|254780725|r  321 LKKLRPADKPPYLVLNQVK  339 (427)
Q Consensus       321 l~~~~~~~~~~~iVlNr~~  339 (427)
                       |. +.-...=.+|+|+.+
T Consensus       132 -K~-gi~e~aDl~vvNK~D  148 (148)
T cd03114         132 -KA-GIMEIADIVVVNKAD  148 (148)
T ss_pred             -CC-CHHHCCCEEEEECCC
T ss_conf             -22-852124699993789


No 186
>pfam00009 GTP_EFTU Elongation factor Tu GTP binding domain. This domain contains a P-loop motif, also found in several other families such as pfam00071, pfam00025 and pfam00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.
Probab=97.28  E-value=0.0024  Score=39.79  Aligned_cols=67  Identities=12%  Similarity=0.158  Sum_probs=49.2

Q ss_pred             HCCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf             1288899738888--898999998620125435787768899999999999981987675389995658987
Q gi|254780725|r  273 QIFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPK  342 (427)
Q Consensus       273 ~~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~  342 (427)
                      ..+.+.++|+|..  +...+..++..+|.+++|++.+-.-...+++++..++..+   .++.+++|+++...
T Consensus        65 ~~~~i~~iDtPGh~~f~~~~~~~l~~aD~~vlVvda~~G~~~qt~~~~~~~~~~~---~p~iv~vNKiD~v~  133 (185)
T pfam00009        65 KKRHINIIDTPGHVDFTKEMIRGAAQADGAILVVDAVEGVMPQTREHLLLAKQLG---VPIIVFINKMDRVD  133 (185)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHHHHHHHHC---CCEEEEEECCCCCC
T ss_conf             8936899989987143999999986465642999867685323099999999828---98799997732777


No 187
>TIGR02237 recomb_radB DNA repair and recombination protein RadB; InterPro: IPR011939    This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO) and DMC1 (IPR011940 from INTERPRO), and archaeal RadA (IPR011938 from INTERPRO) ,, .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=97.28  E-value=0.0015  Score=40.97  Aligned_cols=146  Identities=16%  Similarity=0.121  Sum_probs=78.2

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHH-
Q ss_conf             6753799974698877568999999999962699499997879898603343899878988863184561243376532-
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLP-  237 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l-  237 (427)
                      ..|-|.=++| -||+|||++|.-+|..-++ .|++|+.||--=.+                    +++|+-+..-.+.+ 
T Consensus        10 E~G~iTQiYG-p~G~GKTn~c~~~a~~a~~-~Gk~v~YiDTEGGL--------------------S~ER~~q~~~~~~~D   67 (223)
T TIGR02237        10 ERGIITQIYG-PPGSGKTNICLILAVNAAR-QGKKVVYIDTEGGL--------------------SPERFKQIAEDRALD   67 (223)
T ss_pred             CCCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCC--------------------HHHHHHHHHHCCCCC
T ss_conf             2035889875-8998678999999999986-18958999628983--------------------289999986305889


Q ss_pred             -HCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHC---CCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHH
Q ss_conf             -0248980687248761203207999999989998512---888997388888989999986201254357877688999
Q gi|254780725|r  238 -VFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQI---FPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRN  313 (427)
Q Consensus       238 -~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~---yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~  313 (427)
                       -+..+++-+.-+ .++    .-...++......+...   ++.||+|+-.   ...+.-....+.-      ...-.+.
T Consensus        68 ~e~~~~~~iv~~~-~~f----~eQ~~ai~~~~~~~~~~G~~~~LvVvDs~t---~~YRle~~~d~nk------~~~~~~~  133 (223)
T TIGR02237        68 PERVLSNVIVFEV-FDF----DEQEVAIQKTSKLIDRDGDKADLVVVDSFT---ALYRLERSDDRNK------QISLNRE  133 (223)
T ss_pred             HHHHHCCEEEECC-CCH----HHHHHHHHHHHHHHHCCCCEEEEEEEECCH---HHHHHCCCCCCHH------HHHHHHH
T ss_conf             8888415355235-356----789999999999986068833148881533---4542025786025------6799999


Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf             999999999819876753899956589
Q gi|254780725|r  314 SKNLIDVLKKLRPADKPPYLVLNQVKT  340 (427)
Q Consensus       314 a~~ll~~l~~~~~~~~~~~iVlNr~~~  340 (427)
                      ..+=+..|-.+.-...-.-+|-||+-.
T Consensus       134 l~~Ql~~Ll~lArk~~~AVviTNQvy~  160 (223)
T TIGR02237       134 LARQLTLLLSLARKKDLAVVITNQVYT  160 (223)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEEEEE
T ss_conf             999999999998764997899711588


No 188
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=97.27  E-value=0.0009  Score=42.37  Aligned_cols=111  Identities=18%  Similarity=0.204  Sum_probs=59.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHC-CCCCCCCHHHHHCCCCCHHHHHHHHHH---H
Q ss_conf             799974698877568999999999962699499997879898603343-899878988863184561243376532---0
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINF-DKDPINSISDAIYPVGRIDKAFVSRLP---V  238 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l-~~~~~~~l~d~l~~~~rlD~~~l~~~l---~  238 (427)
                      -..|++++-|+|||++|.|+|...|...|.+|++.-+....-.+..-+ -....-....+ ..+ ++...-+++..   .
T Consensus       195 ~LiIiaARPsmGKTafalnia~n~A~~~g~~Vl~fSLEMs~eql~~R~la~~s~i~~~~i-~~g-~l~~~~~~~~~~a~~  272 (421)
T TIGR03600       195 DLIVIGARPSMGKTTLALNIAENVALREGKPVLFFSLEMSAEQLGERLLASKSGINTGNI-RTG-RFNDSDFNRLLNAVD  272 (421)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHCCCCHHHH-HCC-CCCHHHHHHHHHHHH
T ss_conf             689998546787459999999999986698389992579999999999998548977666-528-999899999999999


Q ss_pred             CCC-CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHC---CCEEEECC
Q ss_conf             248-980687248761203207999999989998512---88899738
Q gi|254780725|r  239 FYA-ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQI---FPLVILDV  282 (427)
Q Consensus       239 ~~~-~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~---yd~VIiD~  282 (427)
                      ... ..|++       +....++...++..+..++..   -++||||.
T Consensus       273 ~l~~~~l~i-------~d~~~~ti~~ir~~~r~~~~~~~~l~livIDY  313 (421)
T TIGR03600       273 RLSEKDLYI-------DDTGGLTVAQIRSIARRIKRKKGGLDLIVVDY  313 (421)
T ss_pred             HHHCCCEEE-------ECCCCCCHHHHHHHHHHHHHHCCCCCEEEECH
T ss_conf             861687899-------66998876789999999998628986999757


No 189
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the  chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=97.14  E-value=0.005  Score=37.80  Aligned_cols=47  Identities=23%  Similarity=0.311  Sum_probs=37.1

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             675379997469887756899999999996269949999787989860
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      +.| -+.++++.-|+||||++.|+|+.+|.+.|.+|+++=+......+
T Consensus        11 ~~G-~L~vi~a~~g~GKS~~~~~la~~~a~~~g~~V~~~SlEm~~~~~   57 (242)
T cd00984          11 QPG-DLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEMSKEQL   57 (242)
T ss_pred             CCC-CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHH
T ss_conf             998-18999968999999999999999999779959999333538899


No 190
>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.
Probab=97.12  E-value=0.0032  Score=38.98  Aligned_cols=46  Identities=17%  Similarity=0.276  Sum_probs=36.8

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC
Q ss_conf             67537999746988775689999999999626994999978798986
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGT  205 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~  205 (427)
                      +.|. +.|+++.-|+|||+++.++|..++.+.|.+|+++-+......
T Consensus        28 ~~Ge-L~viaarpg~GKT~f~~~~a~~~~~~~g~~vl~~SlEm~~~~   73 (271)
T cd01122          28 RKGE-LIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEEPVVR   73 (271)
T ss_pred             CCCC-EEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCHHH
T ss_conf             9980-899996899869999999999999976990899970499999


No 191
>PRK08082 consensus
Probab=97.11  E-value=0.0043  Score=38.21  Aligned_cols=46  Identities=17%  Similarity=0.222  Sum_probs=36.5

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             75379997469887756899999999996269949999787989860
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      .|. ..|++++-|+|||++|.|+|+.+|.+.+.+|++.-+......+
T Consensus       202 ~g~-LiviaaRPsmGKTa~alnia~~~a~~~~~~V~~fSlEM~~~~l  247 (453)
T PRK08082        202 RND-LIIVAARPSVGKTAFALNIAQNVATKTDENVAIFSLEMGADQL  247 (453)
T ss_pred             CCC-EEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHH
T ss_conf             585-7999867887578999999999998559948997313898999


No 192
>cd01125 repA Hexameric Replicative Helicase RepA.  RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.
Probab=97.11  E-value=0.0031  Score=39.04  Aligned_cols=111  Identities=17%  Similarity=0.187  Sum_probs=51.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC-CCCCCHHHCCCC-CCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             799974698877568999999999962699499997879-898603343899-878988863184561243376532024
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDL-PYGTANINFDKD-PINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl-~~g~~~~~l~~~-~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      .++++-+.||+|||+++..+|.++|.  |.+.+-..... ..|. -+|+..+ +...+..      |+....-.......
T Consensus         2 ~v~~l~g~gG~GKS~lal~lAl~vA~--G~~~~g~~~~~~~~G~-Vly~~~Ed~~~~l~r------Rl~a~~~~~~~~~~   72 (239)
T cd01125           2 YVSALVAPGGTGKSSLLLVLALAMAL--GKNLFGGGLKVTEPGR-VVYLSAEDPREEIHR------RLEAILQHLEPDDA   72 (239)
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCE-EEEEECCCCHHHHHH------HHHHHHHHCCCCCC
T ss_conf             38999808998889999999999975--9965689854687761-999978899899999------99999986386655


Q ss_pred             CCCEEEEECCCCC----CCHHCCCHHHHHHHHHHHH-HCCCEEEECC
Q ss_conf             8980687248761----2032079999999899985-1288899738
Q gi|254780725|r  241 AENLSILTAPAML----SRTYDFDEKMIVPVLDILE-QIFPLVILDV  282 (427)
Q Consensus       241 ~~gL~lL~a~~~~----~~~~~~~~~~l~~ll~~l~-~~yd~VIiD~  282 (427)
                      ..++.+.+....+    ..........+..+++.+. ..++.||||+
T Consensus        73 ~~rl~~~~~~~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~LVViDp  119 (239)
T cd01125          73 GDRLFIDSGRIQPISIAREGRIIVVPEFERIIEQLLIRRIDLVVIDP  119 (239)
T ss_pred             CCCEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEECC
T ss_conf             54166415566644133577210148999999997458998999838


No 193
>cd01891 TypA_BipA TypA (tyrosine phosphorylated protein A)/BipA subfamily.  BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants.  BipA was originally described as a protein that is induced in Salmonella typhimurium after exposure to bactericidal/permeability-inducing protein (a cationic antimicrobial protein produced by neutrophils), and has since been identified in E. coli as well.  The properties thus far described for BipA are related to its role in the process of pathogenesis by enteropathogenic E. coli.  It appears to be involved in the regulation of several processes important for infection, including rearrangements of the cytoskeleton of the host, bacterial resistance to host defense peptides, flagellum-mediated cell motility, and expression of K5 capsular genes.  It has been proposed that BipA may utilize a novel mechanism to regulate the expression of target genes.  In addition, BipA from enteropathogenic E. co
Probab=97.11  E-value=0.0038  Score=38.54  Aligned_cols=77  Identities=18%  Similarity=0.335  Sum_probs=54.0

Q ss_pred             CCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCC-CHHHHHH
Q ss_conf             288899738888--8989999986201254357877688999999999999819876753899956589875-2005999
Q gi|254780725|r  274 IFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKK-PEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~-~~i~~~~  350 (427)
                      .+-+-++|+|..  +.......+..+|..++|+...-.-.-++++.+....+.+.   ++.+++|+++.+.. .+...++
T Consensus        64 ~~~~n~IDtPGH~dF~~~~~~~~~~~D~ailVVdA~~Gv~~QT~~~l~~a~~~~~---~~iv~iNK~D~~~a~~~~v~~e  140 (194)
T cd01891          64 DTKINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALELGL---KPIVVINKIDRPDARPEEVVDE  140 (194)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCC---CEEEEEECCCCCCCCHHHHHHH
T ss_conf             9889999899847777789877643446789865378975899999999987299---7499885645898889999999


Q ss_pred             HHH
Q ss_conf             999
Q gi|254780725|r  351 FCA  353 (427)
Q Consensus       351 ~~~  353 (427)
                      +.+
T Consensus       141 i~~  143 (194)
T cd01891         141 VFD  143 (194)
T ss_pred             HHH
T ss_conf             999


No 194
>PRK05595 replicative DNA helicase; Provisional
Probab=97.10  E-value=0.0015  Score=40.96  Aligned_cols=46  Identities=22%  Similarity=0.190  Sum_probs=36.4

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             75379997469887756899999999996269949999787989860
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      .|.. .|++++-|+|||++|.|+|...|...|.+|++.-+......+
T Consensus       200 ~GdL-iiiaaRP~mGKTa~alnia~~~a~~~g~~V~~fSlEMs~~ql  245 (444)
T PRK05595        200 KGDM-ILIAARPSMGKTTFALNIAEYAALREGKSVVIFSLEMSKEQL  245 (444)
T ss_pred             CCCE-EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHH
T ss_conf             5777-999857989807999999999998669937999588999999


No 195
>PRK06749 replicative DNA helicase; Provisional
Probab=97.07  E-value=0.0033  Score=38.92  Aligned_cols=40  Identities=20%  Similarity=0.311  Sum_probs=33.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             79997469887756899999999996269949999787989
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      -..|++++-|+|||++|.|+|...|+ .|.+|++.-+....
T Consensus       187 ~LiviaaRPsmGKTa~alnia~~~a~-~g~~v~~fSlEMs~  226 (428)
T PRK06749        187 DFVVLGARPSMGKTAFALNVGLHAAK-SGAAVGLFSLEMSS  226 (428)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCH
T ss_conf             68999627989768999999999996-49927998378999


No 196
>cd01393 recA_like RecA is a  bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response.  RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57.  Archaea have the RecA-like homologs radA and radB.
Probab=97.06  E-value=0.011  Score=35.64  Aligned_cols=47  Identities=13%  Similarity=0.153  Sum_probs=34.7

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH-----CCCCEEEEECCCCCC
Q ss_conf             456753799974698877568999999999962-----699499997879898
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASV-----FAMETLLADLDLPYG  204 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~-----~~~~VlLvDlDl~~g  204 (427)
                      .-+.|+++-++| ..|+|||+++.++|......     .+.+|+.||..-.|.
T Consensus        15 Gip~G~ItEi~G-~~gsGKT~l~lqla~~~q~~~~~~~~~g~vvyIDtE~~f~   66 (226)
T cd01393          15 GIPTGRITEIFG-EFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFR   66 (226)
T ss_pred             CCCCCEEEEEEC-CCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCC
T ss_conf             988883999999-9999899999999999854221169996199995577531


No 197
>PRK05636 replicative DNA helicase; Provisional
Probab=97.03  E-value=0.0034  Score=38.80  Aligned_cols=115  Identities=17%  Similarity=0.237  Sum_probs=59.3

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHH-HCCCCCCCCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             7537999746988775689999999999626994999978798986033-438998789888631845612433765320
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANI-NFDKDPINSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~-~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      .|. ..|++++-|+|||++|.|+|...|...+.+|++.-+....-.+.. ++-....-.+..+-  ..++++.-++++..
T Consensus       266 ~G~-LiIiAARPsmGKTalAlnia~n~A~~~g~~v~~fSLEMs~~ql~~Rlla~~s~V~~~~ir--~g~l~~~~~~~l~~  342 (507)
T PRK05636        266 GGQ-MIIVAARPGVGKSTIALDFMRSASIKNNKASVIFSLEMSKSEIVMRLLSAEAEVRLADMR--GGKMDEDAWEKLVQ  342 (507)
T ss_pred             CCC-EEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCHHHHH--CCCCCHHHHHHHHH
T ss_conf             356-799973787866899999999999876993799715699899999999984798878885--58878899999999


Q ss_pred             CCC--CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHC--CCEEEECC
Q ss_conf             248--980687248761203207999999989998512--88899738
Q gi|254780725|r  239 FYA--ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQI--FPLVILDV  282 (427)
Q Consensus       239 ~~~--~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~--yd~VIiD~  282 (427)
                      ...  ..+.+     -.+....++...+..-...+++.  .++||||.
T Consensus       343 a~~~l~~~pl-----~IdD~~~lti~~Ira~aRrlk~~~~l~livVDY  385 (507)
T PRK05636        343 RLGKIAQAPI-----FIDDSANLTMMEIRSKARRLKQKHDLKMIVVDY  385 (507)
T ss_pred             HHHHHHHCCE-----EEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEH
T ss_conf             9999861988-----998499976999999999998617999899845


No 198
>PRK07263 consensus
Probab=97.02  E-value=0.0025  Score=39.65  Aligned_cols=46  Identities=13%  Similarity=0.161  Sum_probs=36.8

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             75379997469887756899999999996269949999787989860
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      .|.. .|++++-|+|||++|.|+|...|...+.+|++.-+......+
T Consensus       202 ~GdL-iviaaRPsmGKTa~alnia~~iA~~~~~~V~~fSlEMs~~ql  247 (453)
T PRK07263        202 PDQL-IILAARPAVGKTAFVLNIAQNVGTKQKKTVAIFSLEMGAESL  247 (453)
T ss_pred             CCCE-EEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHH
T ss_conf             7868-999727888478999999999998559828999246998999


No 199
>PRK05748 replicative DNA helicase; Provisional
Probab=97.01  E-value=0.0024  Score=39.72  Aligned_cols=46  Identities=17%  Similarity=0.235  Sum_probs=36.0

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             75379997469887756899999999996269949999787989860
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      .|. ..|++++-|+|||++|.|+|...|...+.+|++.-+......+
T Consensus       202 ~g~-LiviaaRP~mGKTa~alnia~~~a~~~~~~v~~fSlEM~~~~l  247 (448)
T PRK05748        202 PND-LIIVAARPSVGKTAFALNIAQNVATKTDKNVAIFSLEMGAESL  247 (448)
T ss_pred             CCC-EEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHH
T ss_conf             673-7999847998768999999999998569808998177888899


No 200
>PRK09191 two-component response regulator; Provisional
Probab=96.97  E-value=0.013  Score=35.23  Aligned_cols=85  Identities=18%  Similarity=0.183  Sum_probs=62.9

Q ss_pred             EECCCHHHHHHHHHCCCCCCEEEEECCCCC-CCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCC
Q ss_conf             306998999999861899849999805987-6778899988853289980899816871899999997656264318999
Q gi|254780725|r   60 ITRGSIAEAVSCFSDSSTPDLIIVQTKVDS-REVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLS  138 (427)
Q Consensus        60 v~~g~~~~A~~~~~~~~~P~~iivd~~~~~-~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~  138 (427)
                      -...+..+|++..... .|+++++|++..+ .++++...++.+.  -++|||-|+...|--+-.+-.+ .+. ++.||++
T Consensus       166 GiA~t~~eAl~la~~~-~PDlvL~DI~L~d~~sGIdaa~~I~~~--~~iPvIFiTAyperlltg~~~e-p~~-li~KPf~  240 (261)
T PRK09191        166 GIARTRAEAVALAKKT-RPGLILADIQLADGSSGIDAVNDILKT--FDVPVIFITAFPERLLTGERPE-PAF-LITKPFQ  240 (261)
T ss_pred             EEECCHHHHHHHHHCC-CCCEEEEEEECCCCCCHHHHHHHHHHH--CCCCEEEECCCHHHHCCCCCCC-CCE-EECCCCC
T ss_conf             7627899999997425-989899953479998799999999982--8999899777846530278888-740-3569898


Q ss_pred             HHHHHHHHHHC
Q ss_conf             89999976310
Q gi|254780725|r  139 VADIINSISAI  149 (427)
Q Consensus       139 ~~~l~~ai~~~  149 (427)
                      ++.+..+++..
T Consensus       241 ~~~v~aai~qA  251 (261)
T PRK09191        241 PDTVKAAISQA  251 (261)
T ss_pred             HHHHHHHHHHH
T ss_conf             89999999999


No 201
>PRK13351 elongation factor G; Reviewed
Probab=96.90  E-value=0.033  Score=32.77  Aligned_cols=17  Identities=24%  Similarity=0.249  Sum_probs=7.4

Q ss_pred             CHHHHHHHHHHHHHCCC
Q ss_conf             99999998999851288
Q gi|254780725|r  260 DEKMIVPVLDILEQIFP  276 (427)
Q Consensus       260 ~~~~l~~ll~~l~~~yd  276 (427)
                      .+-+++.+++.|++.|.
T Consensus       451 GElHLe~~l~~L~~~f~  467 (687)
T PRK13351        451 GELHLEIALERLRREFK  467 (687)
T ss_pred             CHHHHHHHHHHHHHHHC
T ss_conf             89999999998888719


No 202
>PRK07004 replicative DNA helicase; Provisional
Probab=96.89  E-value=0.004  Score=38.36  Aligned_cols=44  Identities=11%  Similarity=0.283  Sum_probs=35.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             79997469887756899999999996269949999787989860
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      -..|++++-|+|||++|.|+|...|.+.|.+|++.-+....-.+
T Consensus       214 dLiIIAARPsmGKTafAlniA~n~A~~~g~~V~~FSLEMs~eql  257 (460)
T PRK07004        214 ELIIVAGRPSMGKTAFSMNIGEYVAVEYGLPVAVFSMEMPGTQL  257 (460)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHH
T ss_conf             57999736876426999999999987258866998477999999


No 203
>cd00881 GTP_translation_factor GTP translation factor family.  This family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation.  In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function.
Probab=96.88  E-value=0.0052  Score=37.68  Aligned_cols=81  Identities=14%  Similarity=0.170  Sum_probs=58.1

Q ss_pred             CCCEEEECCCCCCC--HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCC--CHHHHH
Q ss_conf             28889973888889--89999986201254357877688999999999999819876753899956589875--200599
Q gi|254780725|r  274 IFPLVILDVPHVWN--SWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKK--PEISIS  349 (427)
Q Consensus       274 ~yd~VIiD~p~~~~--~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~--~~i~~~  349 (427)
                      .+.+.++|+|....  ..+..++..+|.+++|+...-.--..+++.+..++..+   .++.+++|+++....  .+...+
T Consensus        61 ~~~i~~iDTPGh~~f~~~~~~~l~~aD~ailvVda~~G~~~qt~~~~~~~~~~~---~p~iv~iNKiD~~~~~~~~~~~~  137 (189)
T cd00881          61 DRRVNFIDTPGHEDFSSEVIRGLSVSDGAILVVDANEGVQPQTREHLRIAREGG---LPIIVAINKIDRVGEEDLEEVLR  137 (189)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCC---CCEEEEEECCCCCCHHHHHHHHH
T ss_conf             989999969981889999999986468569999879899878999999999769---98799998971877562999999


Q ss_pred             HHHHHHCC
Q ss_conf             99998489
Q gi|254780725|r  350 DFCAPLGI  357 (427)
Q Consensus       350 ~~~~~lg~  357 (427)
                      ++.+.++.
T Consensus       138 ei~~~l~~  145 (189)
T cd00881         138 EIKELLGL  145 (189)
T ss_pred             HHHHHHHH
T ss_conf             99999875


No 204
>PRK06696 uridine kinase; Validated
Probab=96.85  E-value=0.0048  Score=37.89  Aligned_cols=61  Identities=15%  Similarity=0.117  Sum_probs=42.8

Q ss_pred             CHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             989999976310233222345675379997469887756899999999996269949999787989
Q gi|254780725|r  138 SVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       138 ~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      +..+++..|........++.+   -+|+|-| -.|+||||+|..|+..|.. .|.+|+.+-.|-..
T Consensus         6 ~r~~~~~~~~~~i~~~~p~rp---l~VgIdG-~~gSGKTTlA~~La~~L~~-~G~~V~~v~~Ddf~   66 (227)
T PRK06696          6 NRKQVVKEIANHILTLNLTRP---LRVAIDG-ITASGKTTFANELAEEIKK-RGRPVIRASIDDFH   66 (227)
T ss_pred             CHHHHHHHHHHHHHHCCCCCC---EEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEECCCCCC
T ss_conf             287899999999983599986---8999778-9987879999999999974-69948997154434


No 205
>pfam00154 RecA recA bacterial DNA recombination protein. RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyses an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination.
Probab=96.85  E-value=0.036  Score=32.50  Aligned_cols=45  Identities=18%  Similarity=0.149  Sum_probs=36.1

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             45675379997469887756899999999996269949999787989
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      .-+.||++.++| .-++||||+|.++... ++..|..++.+|....+
T Consensus        48 GlP~GRi~ei~G-~essGKTtlal~~ia~-aQk~gg~~~~iD~E~a~   92 (322)
T pfam00154        48 GLPKGRIIEIYG-PESSGKTTLALHAIAE-AQKAGGTAAFIDAEHAL   92 (322)
T ss_pred             CCCCCEEEEEEC-CCCCCHHHHHHHHHHH-HHHCCCEEEEEEHHHHC
T ss_conf             977870899988-9877789999999999-97349938998536605


No 206
>PRK08760 replicative DNA helicase; Provisional
Probab=96.84  E-value=0.0061  Score=37.24  Aligned_cols=46  Identities=15%  Similarity=0.121  Sum_probs=36.1

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             75379997469887756899999999996269949999787989860
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      .|. ..|++++-|+|||++|.|+|...|.+.++.|++.-+....-.+
T Consensus       228 ~G~-LiViaaRPsmGKTalalnia~~~A~~~~~~V~~fSLEMs~~ql  273 (476)
T PRK08760        228 PTD-LIILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSMEMSASQL  273 (476)
T ss_pred             CCC-EEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHH
T ss_conf             777-7999877887478999999999998379978997036999999


No 207
>KOG1533 consensus
Probab=96.81  E-value=0.0019  Score=40.30  Aligned_cols=103  Identities=17%  Similarity=0.154  Sum_probs=64.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             99746988775689999999999626994999978798986033438998789888631845612433765320248980
Q gi|254780725|r  165 SFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENL  244 (427)
Q Consensus       165 av~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL  244 (427)
                      .|+| -.|.||||-.......++. .|+++.+|.+|+...+...    ++...|.+++..         +..+.++.   
T Consensus         6 vVIG-PPgSGKsTYc~g~~~fls~-~gr~~~vVNLDPaNd~~~Y----~~~v~I~elit~---------edvm~~~~---   67 (290)
T KOG1533           6 VVIG-PPGSGKSTYCNGMSQFLSA-IGRPVAVVNLDPANDNLPY----ECAVDIRELITV---------EDVMEELG---   67 (290)
T ss_pred             EEEC-CCCCCCCCHHHHHHHHHHH-HCCCEEEEECCCCCCCCCC----CCCCCHHHHCCH---------HHHHHHHC---
T ss_conf             8876-9999853113209999997-4896279956876567888----776519997139---------99999858---


Q ss_pred             EEEECCCCCCCHHCCCHHHHHHHHHHHHH-CCCEEEECCCCCCC
Q ss_conf             68724876120320799999998999851-28889973888889
Q gi|254780725|r  245 SILTAPAMLSRTYDFDEKMIVPVLDILEQ-IFPLVILDVPHVWN  287 (427)
Q Consensus       245 ~lL~a~~~~~~~~~~~~~~l~~ll~~l~~-~yd~VIiD~p~~~~  287 (427)
                       +=|-+ .+--..+.-+..+.+++..++. ...|+++|+|.+..
T Consensus        68 -LGPNg-~l~yc~E~l~~~idwl~~~l~~~~~~Y~lFDcPGQVE  109 (290)
T KOG1533          68 -LGPNG-ALKYCMEYLEANIDWLLEKLKPLTDHYVLFDCPGQVE  109 (290)
T ss_pred             -CCCCH-HHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCEE
T ss_conf             -79961-2799999998544999997452347489995798279


No 208
>TIGR00455 apsK adenylylsulfate kinase; InterPro: IPR002891 Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulphate. This domain contains an ATP binding P-loop motif .; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity transferring phosphorus-containing groups, 0000103 sulfate assimilation.
Probab=96.79  E-value=0.019  Score=34.22  Aligned_cols=114  Identities=22%  Similarity=0.208  Sum_probs=74.2

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHH
Q ss_conf             45675379997469887756899999999996269949999787989860334389987898886318456124337653
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRL  236 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~  236 (427)
                      ....|-||=++| =.|.||||||..|.-.|-+ .|.++-++|-|-=--.+...||    ++=.|=..+..|+-++.  +.
T Consensus        15 ~~h~g~vlWlTG-LSGsGKsTiA~Al~~~L~~-~G~~~~~LDGDnvR~gL~~dLG----FS~~DR~eNIRRigEVa--~L   86 (187)
T TIGR00455        15 NKHRGVVLWLTG-LSGSGKSTIANALEKKLEK-KGYRVYVLDGDNVRHGLNKDLG----FSEEDRKENIRRIGEVA--KL   86 (187)
T ss_pred             CCCCEEEEEEEC-CCCCHHHHHHHHHHHHHHH-CCCEEEEECCCEEECCCCCCCC----CCHHHHCCCCCEEHHHH--HH
T ss_conf             279738985116-8856357999999999996-6974999758634247788888----88567056883532646--77


Q ss_pred             HHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCC
Q ss_conf             20248980687248761203207999999989998512888997388
Q gi|254780725|r  237 PVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVP  283 (427)
Q Consensus       237 l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p  283 (427)
                      ++  ..|+=+|.+--.|.+   ...+.++.+++..--.|-=|.||||
T Consensus        87 ~~--~~G~i~ltsfISPyR---~~R~~vR~~~~~~Gl~F~Evfv~~P  128 (187)
T TIGR00455        87 LV--RNGVIVLTSFISPYR---ADRQMVRELIEEGGLEFIEVFVKCP  128 (187)
T ss_pred             HH--HCCEEEEEEEECCCH---HHHHHHHHHHHCCCEEEEEEECCCC
T ss_conf             76--479389984217766---6789998875405736899721788


No 209
>PRK08840 replicative DNA helicase; Provisional
Probab=96.78  E-value=0.0044  Score=38.13  Aligned_cols=46  Identities=20%  Similarity=0.236  Sum_probs=35.9

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             75379997469887756899999999996269949999787989860
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      .|. ..|++++-|+|||++|.|+|...|...+.+|++.-+....-.+
T Consensus       216 ~G~-LiviaaRPsmGKTalalnia~n~a~~~~~~v~~fSlEMs~~ql  261 (464)
T PRK08840        216 GSD-LIIVAARPSMGKTTFAMNLCENAAMDQDKPVLIFSLEMPAEQL  261 (464)
T ss_pred             CCC-EEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHH
T ss_conf             576-7999837987368999999999999659967997677998999


No 210
>PRK07471 DNA polymerase III subunit delta'; Validated
Probab=96.78  E-value=0.041  Score=32.16  Aligned_cols=147  Identities=14%  Similarity=0.082  Sum_probs=76.9

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCH
Q ss_conf             89999976310233222345675379997469887756899999999996269949999787989860334389987898
Q gi|254780725|r  139 VADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSI  218 (427)
Q Consensus       139 ~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l  218 (427)
                      -++..+.+.+.+.     .+|...-+-|.|. -|+||+|+|..+|.+|-.. + ...    +...+.....+..++.+..
T Consensus        22 qe~~~~~L~~a~~-----~grl~HA~Lf~Gp-~GiGK~tlA~~~A~~ll~~-~-~~~----~~~~~~~~~~l~~~~~~p~   89 (363)
T PRK07471         22 HAAAEAALLDAYR-----SGRLHHAWLIGGP-QGIGKATLAYRMARFLLAT-P-PPG----GDAVFPPPASLAVDPDHPV   89 (363)
T ss_pred             HHHHHHHHHHHHH-----CCCCCCEEEEECC-CCCCHHHHHHHHHHHHHCC-C-CCC----CCCCCCCHHHHCCCCCCCH
T ss_conf             1999999999998-----5997645876799-9818899999999998579-9-977----7776787053125877728


Q ss_pred             HHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCC---CCCHHCCCHHHHHHHHHHHH-----HCCCEEEECCCCCCCHHH
Q ss_conf             8863184561243376532024898068724876---12032079999999899985-----128889973888889899
Q gi|254780725|r  219 SDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAM---LSRTYDFDEKMIVPVLDILE-----QIFPLVILDVPHVWNSWT  290 (427)
Q Consensus       219 ~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~---~~~~~~~~~~~l~~ll~~l~-----~~yd~VIiD~p~~~~~~~  290 (427)
                      ...+              .....+++.++..+.+   ......+..+.++.+.+.+.     ..|-++|||-+..++...
T Consensus        90 ~r~i--------------~~~~hpdl~~i~r~~d~k~~~~~~~I~Vd~iR~l~~~~~~~p~~g~~kV~IId~ad~mn~~a  155 (363)
T PRK07471         90 ARRI--------------AAGAHGGLLTLERSWNEKGKRLRTVITVDEVRETIGFFGLTAAEGGWRVVIVDTADEMNANA  155 (363)
T ss_pred             HHHH--------------HCCCCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCEEEEEECHHHHCHHH
T ss_conf             9999--------------52699984667620011333212445399999999997248524896699986878738899


Q ss_pred             HHHHHH------CCCCCCCCCCCHHHH
Q ss_conf             999862------012543578776889
Q gi|254780725|r  291 QEVLTL------SDKVVITTSLDLAGL  311 (427)
Q Consensus       291 ~~~L~~------AD~vviV~~p~~~sl  311 (427)
                      .++|..      ...+++.++.++..+
T Consensus       156 aNALLK~LEEPP~~t~fiLit~~~~~l  182 (363)
T PRK07471        156 ANALLKVLEEPPARSLLLLVSHAPARL  182 (363)
T ss_pred             HHHHHHHHCCCCCCEEEEEEECCHHHC
T ss_conf             999999721589883899863997777


No 211
>cd00983 recA RecA is a  bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response.  RecA couples ATP hydrolysis to DNA strand exchange.
Probab=96.77  E-value=0.042  Score=32.12  Aligned_cols=45  Identities=18%  Similarity=0.180  Sum_probs=36.1

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             45675379997469887756899999999996269949999787989
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      .-+.||++.++| .-++||||+|.++... ++..|..++++|....+
T Consensus        51 GiP~GRivei~G-~essGKTtlal~~ia~-aQk~gg~~~~iDaE~a~   95 (325)
T cd00983          51 GYPKGRIIEIYG-PESSGKTTLALHAIAE-AQKLGGTVAFIDAEHAL   95 (325)
T ss_pred             CCCCCEEEEEEC-CCCCCHHHHHHHHHHH-HHHCCCEEEEEEHHHCC
T ss_conf             966880899988-9877799999999999-87359839999625425


No 212
>KOG0078 consensus
Probab=96.76  E-value=0.042  Score=32.08  Aligned_cols=111  Identities=14%  Similarity=0.195  Sum_probs=71.2

Q ss_pred             EEECCCCC--CCHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHH
Q ss_conf             99738888--89899999862012543578-7768899999999999981987675389995658987520059999998
Q gi|254780725|r  278 VILDVPHV--WNSWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAP  354 (427)
Q Consensus       278 VIiD~p~~--~~~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~  354 (427)
                      -++|+..+  ....+......|+-+++|-. -+--|..|..++++.+++......+..+|=|+++...+           
T Consensus        64 QiWDtaGQerf~ti~~sYyrgA~gi~LvyDitne~Sfeni~~W~~~I~e~a~~~v~~~LvGNK~D~~~~-----------  132 (207)
T KOG0078          64 QIWDTAGQERFRTITTAYYRGAMGILLVYDITNEKSFENIRNWIKNIDEHASDDVVKILVGNKCDLEEK-----------  132 (207)
T ss_pred             EEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCC-----------
T ss_conf             999724305678899999865482499998452577777999999998637888748985114121013-----------


Q ss_pred             HCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHCCCCC
Q ss_conf             489537990687999999884796189888999--8999999999998522122
Q gi|254780725|r  355 LGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMGRVTV  406 (427)
Q Consensus       355 lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~gr~~~  406 (427)
                            -.+|.+... .-|...|.+..|.+++.  -+-++|.+||+.|..+.+.
T Consensus       133 ------R~V~~e~ge-~lA~e~G~~F~EtSAk~~~NI~eaF~~La~~i~~k~~~  179 (207)
T KOG0078         133 ------RQVSKERGE-ALAREYGIKFFETSAKTNFNIEEAFLSLARDILQKLED  179 (207)
T ss_pred             ------CCCCHHHHH-HHHHHHCCEEEECCCCCCCCHHHHHHHHHHHHHHHCCH
T ss_conf             ------335679999-99998498279713367998899999999999863662


No 213
>PRK06904 replicative DNA helicase; Validated
Probab=96.72  E-value=0.006  Score=37.32  Aligned_cols=114  Identities=13%  Similarity=0.139  Sum_probs=60.0

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHH-HCCCCCCCCHHHHHCCCCCHHHHHHHHH--
Q ss_conf             7537999746988775689999999999626994999978798986033-4389987898886318456124337653--
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANI-NFDKDPINSISDAIYPVGRIDKAFVSRL--  236 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~-~l~~~~~~~l~d~l~~~~rlD~~~l~~~--  236 (427)
                      .|. ..|++++-|+|||++|.|+|...|...+.+|++.-+....-.+.. ++-....-....+ .....++..-+++.  
T Consensus       220 ~g~-LiViAaRPsmGKTa~alnia~n~A~~~~~~V~~fSLEM~~~~l~~R~ls~~s~v~~~~i-~~g~~l~~~e~~~~~~  297 (472)
T PRK06904        220 PSD-LIIVAARPSMGKTTFAMNLCENAAMASEKPVLVFSLEMPAEQIMMRMLASLSRVDQTKI-RTGQNLDQQDWAKISS  297 (472)
T ss_pred             CCC-EEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHCCCCHHHH-HCCCCCHHHHHHHHHH
T ss_conf             575-79997379875689999999999995599579977879999999999998649998886-4688560999999999


Q ss_pred             -HHCCC--CCEEEEECCCCCCCHHCCCHHHHHHHHHHH-HH--CCCEEEECC
Q ss_conf             -20248--980687248761203207999999989998-51--288899738
Q gi|254780725|r  237 -PVFYA--ENLSILTAPAMLSRTYDFDEKMIVPVLDIL-EQ--IFPLVILDV  282 (427)
Q Consensus       237 -l~~~~--~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l-~~--~yd~VIiD~  282 (427)
                       .....  +++++-       ....++...+..-...+ +.  .-++||||.
T Consensus       298 ~~~~l~~~~~l~id-------d~~~~t~~~i~~~~r~~~~~~~~l~~vvIDY  342 (472)
T PRK06904        298 TVGMFKQKPNLYID-------DSSGLTPTELRSRARRVYRENGGLSLIMVDY  342 (472)
T ss_pred             HHHHHHCCCCEEEE-------CCCCCCHHHHHHHHHHHHHHCCCCCEEEEEH
T ss_conf             99998468981684-------6999999999999999998738997899638


No 214
>cd01885 EF2 EF2 (for archaea and eukarya).  Translocation requires hydrolysis of a molecule of GTP and is mediated by EF-G in bacteria and by eEF2 in eukaryotes.  The eukaryotic elongation factor eEF2 is a GTPase involved in the translocation of the peptidyl-tRNA from the A site to the P site on the ribosome.  The 95-kDa protein is highly conserved, with 60% amino acid sequence identity between the human and yeast proteins.  Two major mechanisms are known to regulate protein elongation and both involve eEF2.  First, eEF2 can be modulated by reversible phosphorylation.  Increased levels of phosphorylated eEF2 reduce elongation rates presumably because phosphorylated eEF2 fails to bind the ribosomes.  Treatment of mammalian cells with agents that raise the cytoplasmic Ca2+ and cAMP levels reduce elongation rates by activating the kinase responsible for phosphorylating eEF2.  In contrast, treatment of cells with insulin increases elongation rates by promoting eEF2 dephosphorylation.  Seco
Probab=96.69  E-value=0.017  Score=34.46  Aligned_cols=66  Identities=18%  Similarity=0.256  Sum_probs=50.8

Q ss_pred             HCCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCC
Q ss_conf             1288899738888--89899999862012543578776889999999999998198767538999565898
Q gi|254780725|r  273 QIFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTP  341 (427)
Q Consensus       273 ~~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~  341 (427)
                      ..|-+-+||+|..  +......++..+|-+++|+...-.-.-++++.++...+.+.   ++.+++|+.+..
T Consensus        71 ~~~~inlIDTPGH~dF~~ev~~al~~~DgailVVDa~eGv~~qT~~vl~~a~~~~l---~~il~iNKiDRl  138 (222)
T cd01885          71 NEYLINLIDSPGHVDFSSEVTAALRLCDGALVVVDAVEGVCVQTETVLRQALKERV---KPVLVINKIDRL  138 (222)
T ss_pred             CCEEEEEEECCCHHHHHHHHHHHHHHCCEEEEEECCCCCCCHHHHHHHHHHHHCCC---CEEEEEECCCCC
T ss_conf             86389997288569899999999985681799610457857789999999998599---979999890365


No 215
>TIGR01425 SRP54_euk signal recognition particle protein SRP54; InterPro: IPR006325    The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane.    This entry represents the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species.; GO: 0005525 GTP binding, 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=96.62  E-value=0.014  Score=35.08  Aligned_cols=172  Identities=15%  Similarity=0.164  Sum_probs=92.8

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             53799974698877568999999999962699499997879898603343899878988863184561243376532024
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      ..||-|+|- =|.||||..+=||++.- ++|.+++||=+|.--..+---|.++                  ..+.-+.-+
T Consensus       121 ~~ViMfVGL-QGaGKTTtctKLA~YYk-~rGfK~~lvCADTFRAGAFdQLkqN------------------A~kA~iPFY  180 (453)
T TIGR01425       121 SSVIMFVGL-QGAGKTTTCTKLAYYYK-RRGFKPALVCADTFRAGAFDQLKQN------------------ATKAKIPFY  180 (453)
T ss_pred             CEEEEEEEC-CCCCHHHHHHHHHHHHH-CCCCCEEEECCCCCCCCHHHHHHHH------------------HHHCCCCCC
T ss_conf             215888621-48871566878777763-2664325651775423248999874------------------764489712


Q ss_pred             CCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCH---HHHHHHH-----HCCCCCCCCCCCHH--H
Q ss_conf             898068724876120320799999998999851288899738888898---9999986-----20125435787768--8
Q gi|254780725|r  241 AENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNS---WTQEVLT-----LSDKVVITTSLDLA--G  310 (427)
Q Consensus       241 ~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~---~~~~~L~-----~AD~vviV~~p~~~--s  310 (427)
                      ++  +.   +.+|-.   +-   ++-+-..=++.||.|||||..+.-.   ...+...     .-|.++.|.+.+.-  +
T Consensus       181 Gs--y~---E~DPVk---iA---~EGv~~Fk~E~~diIivDTSGRHkQe~~LF~Em~qv~~Ai~Pd~iifVMDGsIGQAA  249 (453)
T TIGR01425       181 GS--YL---ESDPVK---IA---SEGVEKFKKEKFDIIIVDTSGRHKQEEELFEEMVQVAEAIKPDSIIFVMDGSIGQAA  249 (453)
T ss_pred             CC--CC---CCCCEE---EE---CCCHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHH
T ss_conf             01--04---898707---80---020113221278479983798732258888998768633499836998066166788


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEE---------EECCCHHHHH
Q ss_conf             999999999999819876753899956589875200599999984895379---------9068799999
Q gi|254780725|r  311 LRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSA---------IIPFDGAVFG  371 (427)
Q Consensus       311 lr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~---------~IP~D~~~~~  371 (427)
                      -..|+.    ++..   ..--.+|+.+.+-...+-=....++ +-..|+..         .=+||++.|-
T Consensus       250 ~~QAkA----FK~~---~~vGSvIiTKLDGHAkGGGALSAVA-ATKsPiiFIGTGEhv~d~E~F~~~~Fv  311 (453)
T TIGR01425       250 FSQAKA----FKDS---VEVGSVIITKLDGHAKGGGALSAVA-ATKSPIIFIGTGEHVDDFEIFDAEPFV  311 (453)
T ss_pred             HHHHHH----HHHC---CCCEEEEEECCCCCCCCCHHHHHHH-HHCCCEEEECCCCCCCCCCCCCCCCHH
T ss_conf             999998----6300---3500388751567767623788987-535977981377502760578997147


No 216
>TIGR00347 bioD dethiobiotin synthase; InterPro: IPR004472 The enzyme is involved in biotin biosynthesis and catalyses the reaction (CO2 + 7,8-diaminononanoate + ATP = dethiobiotin + phosphate + ADP). The enzyme binds ATP and requires magnesium as a co-factor. The Thr residue at position seven of the seed alignment is necessary for the binding of ATP.; GO: 0004141 dethiobiotin synthase activity, 0005524 ATP binding, 0009102 biotin biosynthetic process.
Probab=96.61  E-value=0.0073  Score=36.78  Aligned_cols=161  Identities=13%  Similarity=0.142  Sum_probs=86.5

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC--HHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             97469887756899999999996269949999787989860--3343899878988863184561243376532024898
Q gi|254780725|r  166 FIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA--NINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAEN  243 (427)
Q Consensus       166 v~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~--~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~g  243 (427)
                      |.|.-=|||||.++.+||..|-+ .|.+|.+.=.= +.|.-  .-.|-.+....+-+......++|+     -+.-.+  
T Consensus         2 vTGtDT~VGKT~~ss~La~~lk~-~G~~~g~~Kpv-~tG~~~~~~dL~~~D~~~L~~~~~~~~~~~~-----Pi~~~P--   72 (187)
T TIGR00347         2 VTGTDTGVGKTVVSSALAKKLKK-AGYSVGYYKPV-QTGIEETAEDLRNEDTELLQNISGTALDLDG-----PIEVNP--   72 (187)
T ss_pred             CEEEECCCCHHHHHHHHHHHHHH-CCCCEEEECCH-HCCCCCCCCCCHHHHHHHHHHHHHHHHHCCC-----CEEECC--
T ss_conf             10224586178998999999997-59852511200-0157667763105679999876544321389-----844266--


Q ss_pred             EEEEECCCCCC-----CHHCCCHHHHHHHHH----HHHHCCCEEEECCCCCC-CHHHHHHHHHCC-------------CC
Q ss_conf             06872487612-----032079999999899----98512888997388888-989999986201-------------25
Q gi|254780725|r  244 LSILTAPAMLS-----RTYDFDEKMIVPVLD----ILEQIFPLVILDVPHVW-NSWTQEVLTLSD-------------KV  300 (427)
Q Consensus       244 L~lL~a~~~~~-----~~~~~~~~~l~~ll~----~l~~~yd~VIiD~p~~~-~~~~~~~L~~AD-------------~v  300 (427)
                       ..|..|..|.     +.-.+..+.+..-+.    .+++.|||+||--..+| .+..++-...||             .+
T Consensus        73 -~~F~~PlsP~~A~~~Eg~~i~~~~~~~~~~naye~l~~~~d~~lVEGAGG~~vP~~r~~~t~~D~i~~~ietsGh~L~~  151 (187)
T TIGR00347        73 -YAFALPLSPHIAAKQEGRPIDLEELSKHLRNAYEELEEKYDFVLVEGAGGLCVPITREEYTVADLIKLLIETSGHQLPV  151 (187)
T ss_pred             -CCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEE
T ss_conf             -3205688625888617783268889878878999999717917998336242666612457999999998505882027


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf             435787768899999999999981987675389995
Q gi|254780725|r  301 VITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLN  336 (427)
Q Consensus       301 viV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlN  336 (427)
                      ++|+.+.+-++-.+---.+.+++.+....-..+|+|
T Consensus       152 ilV~r~~LGtiNHt~Lt~~~~~~~Gl~shl~G~i~N  187 (187)
T TIGR00347       152 ILVVRVKLGTINHTLLTVEAARQTGLKSHLAGVILN  187 (187)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEEEEC
T ss_conf             987468646067999999999977994443545619


No 217
>PRK00889 adenylylsulfate kinase; Provisional
Probab=96.60  E-value=0.036  Score=32.53  Aligned_cols=82  Identities=24%  Similarity=0.257  Sum_probs=50.4

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf             75379997469887756899999999996269949999787989860334389987898886318456124337653202
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVF  239 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~  239 (427)
                      .|-+|=++| -.|.||||+|-.|...|.. .+.++.++|.|---    ..|+.+..++..|-..+..|+..  +-..+..
T Consensus         3 kg~viWltG-lsgSGKTTia~~l~~~L~~-~~~~~~~LDGD~lR----~~l~~~lgfs~~dR~~n~~r~~~--la~~l~~   74 (175)
T PRK00889          3 RGVTVWFTG-LSGAGKTTISHALAEKLRA-RGYPVEVLDGDIVR----TNLSKGLGFSKEDRDTNIRRIGF--VAHLLTR   74 (175)
T ss_pred             CCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEECCHHHH----HHHCCCCCCCHHHHHHHHHHHHH--HHHHHHH
T ss_conf             888999889-8999999999999999998-69967997768888----75367889898999999999999--9999981


Q ss_pred             CCCCEEEEECCC
Q ss_conf             489806872487
Q gi|254780725|r  240 YAENLSILTAPA  251 (427)
Q Consensus       240 ~~~gL~lL~a~~  251 (427)
                        .|+.++.+.-
T Consensus        75 --~g~~vIvs~i   84 (175)
T PRK00889         75 --HGVIVLVSAI   84 (175)
T ss_pred             --CCCEEEEEEC
T ss_conf             --8986888504


No 218
>PRK08506 replicative DNA helicase; Provisional
Probab=96.58  E-value=0.0083  Score=36.42  Aligned_cols=42  Identities=19%  Similarity=0.331  Sum_probs=33.7

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             75379997469887756899999999996269949999787989
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      .|. ..|++++-|+|||++|.|+|...+. .+.+|++.-|....
T Consensus       192 ~gd-LiIIAARPsmGKTAfAlniA~~~a~-~~~~V~~FSLEMs~  233 (473)
T PRK08506        192 KGD-LIIIAARPSMGKTTLVLNMVLKALN-QGKGVAFFSLEMPA  233 (473)
T ss_pred             CCC-EEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCH
T ss_conf             562-7999507998678999999999996-59965898224799


No 219
>PRK08694 consensus
Probab=96.58  E-value=0.0059  Score=37.33  Aligned_cols=44  Identities=14%  Similarity=0.198  Sum_probs=34.9

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCC
Q ss_conf             753799974698877568999999999962699499997879898
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYG  204 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g  204 (427)
                      .|. ..|++++-|+|||++|.|+|+..|.+.+.+|++.-+....-
T Consensus       217 ~G~-LiVIaaRPsmGKTalalnia~~~a~~~~~~V~~fSLEMs~~  260 (468)
T PRK08694        217 PGD-LIIVAGRPSMGKTAFSINIAEHVAVEGKLPVAVFSMEMGGA  260 (468)
T ss_pred             CCC-EEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCHH
T ss_conf             784-79996178653789999999999984798479977889999


No 220
>PRK08006 replicative DNA helicase; Provisional
Probab=96.56  E-value=0.0075  Score=36.69  Aligned_cols=46  Identities=20%  Similarity=0.260  Sum_probs=35.8

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             75379997469887756899999999996269949999787989860
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      .|. ..|++++-|+|||++|.|+|...|...+.+|++.-+....-.+
T Consensus       223 ~G~-LiviaaRPsmGKTalalnia~~~a~~~~~~V~~fSlEMs~~ql  268 (471)
T PRK08006        223 PSD-LIIVAARPSMGKTTFAMNLCENAAMLQDKPVLIFSLEMPGEQI  268 (471)
T ss_pred             CCC-EEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHH
T ss_conf             173-8999946998769999999999998669957998167999999


No 221
>PRK06321 replicative DNA helicase; Provisional
Probab=96.56  E-value=0.01  Score=35.85  Aligned_cols=41  Identities=15%  Similarity=0.229  Sum_probs=32.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             79997469887756899999999996269949999787989
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      -..|++++-|+|||++|.|+|+..|...+.+|++.-+....
T Consensus       227 dliviaaRPsmGKTalalnia~~~a~~~~~~v~~fSLEMs~  267 (472)
T PRK06321        227 NLMILAARPAMGKTALALNIAENFCFQNRLPVGIFSLEMTV  267 (472)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCH
T ss_conf             57998538999779999999999998569946997577999


No 222
>PRK09165 replicative DNA helicase; Provisional
Probab=96.54  E-value=0.0099  Score=35.94  Aligned_cols=40  Identities=20%  Similarity=0.314  Sum_probs=30.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHH--------------CCCCEEEEECCCC
Q ss_conf             799974698877568999999999962--------------6994999978798
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASV--------------FAMETLLADLDLP  202 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~--------------~~~~VlLvDlDl~  202 (427)
                      -..|++++-|+|||++|.|+|...|+.              .|.+|++.-+...
T Consensus       206 dLiIIAARPsmGKTafaLniA~n~A~~~~~~~~~~~~~~~~~g~~V~~FSLEMs  259 (484)
T PRK09165        206 DLIILAGRPSMGKTALATNIAFNAAKAYLREAQPDGSKKAVNGGVVGFFSLEMS  259 (484)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCC
T ss_conf             379996079997789999999999987410222233211368984899947799


No 223
>pfam01583 APS_kinase Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif.
Probab=96.51  E-value=0.038  Score=32.39  Aligned_cols=58  Identities=28%  Similarity=0.302  Sum_probs=41.6

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCC
Q ss_conf             5379997469887756899999999996269949999787989860334389987898886318
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYP  224 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~  224 (427)
                      |.||=|+| -.|+||||+|..|...|.. .+.+|.++|.|---.    .|+.+..++..+-..+
T Consensus         2 G~viW~TG-LsGsGKTTlA~~l~~~L~~-~~~~~~~LDGD~~R~----~l~~dlgys~~~R~~n   59 (157)
T pfam01583         2 GCTVWFTG-LSGSGKSTIANALERKLFA-QGISVYVLDGDNVRH----GLNKDLGFSEEDRTEN   59 (157)
T ss_pred             CEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEECCHHHHC----CCCCCCCCCHHHHHHH
T ss_conf             88999889-8999999999999999997-599779976887750----1257779898999999


No 224
>PRK09354 recA recombinase A; Provisional
Probab=96.51  E-value=0.063  Score=31.03  Aligned_cols=45  Identities=16%  Similarity=0.143  Sum_probs=36.0

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             45675379997469887756899999999996269949999787989
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      .-+.||+|-++| .-+.||||+|.+.... ++..|.-++.+|....+
T Consensus        56 G~P~GRivEi~G-~esSGKTtlal~~iae-aQk~Gg~~a~iDaE~al  100 (350)
T PRK09354         56 GLPKGRIVEIYG-PESSGKTTLALHAIAE-AQKAGGTAAFIDAEHAL  100 (350)
T ss_pred             CCCCCCEEEEEC-CCCCCHHHHHHHHHHH-HHHCCCCEEEEEECCCC
T ss_conf             967870899988-9877799999999999-99759947999600027


No 225
>cd03288 ABCC_SUR2 The SUR domain 2.  The sulfonylurea receptor SUR is an ATP binding cassette (ABC) protein of the ABCC/MRP family.  Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel.  Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism.  It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.
Probab=96.48  E-value=0.022  Score=33.87  Aligned_cols=41  Identities=17%  Similarity=0.335  Sum_probs=27.9

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             6753799974698877568999999999962699499997879
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDL  201 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl  201 (427)
                      ..|..|+++| +-|+||||+.--+.-.+.-. ..++.+=+.|+
T Consensus        45 ~~Ge~vaIvG-~sGsGKSTL~~ll~gl~~p~-~G~I~idg~di   85 (257)
T cd03288          45 KPGQKVGICG-RTGSGKSSLSLAFFRMVDIF-DGKIVIDGIDI   85 (257)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHHCCCCC-CCEEEECCEEH
T ss_conf             7999999999-99981999999996056678-88899998996


No 226
>PRK05541 adenylylsulfate kinase; Provisional
Probab=96.42  E-value=0.041  Score=32.15  Aligned_cols=108  Identities=14%  Similarity=0.035  Sum_probs=60.5

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHH
Q ss_conf             56753799974698877568999999999962699499997879898603343899878988863184561243376532
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLP  237 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l  237 (427)
                      ...|.+|=++| =.|+||||+|..|...|-. .|.+|.++|.|---    ..|+.. .++..+-..+..|..  .+-..+
T Consensus         4 ~~kg~viW~TG-LsGSGKTTiA~~l~~~L~~-~g~~~~~LDGD~lR----~~~~~~-gfs~~~R~~n~~r~~--~lak~l   74 (176)
T PRK05541          4 KPNGYVIWITG-LAGSGKTTIAKALYERLKL-KYSNVIYLDGDELR----EIFGHS-GYDKESRIEMALKRA--KLAAFL   74 (176)
T ss_pred             CCCCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEECCHHHH----HHHCCC-CCCHHHHHHHHHHHH--HHHHHH
T ss_conf             88867999789-9999899999999999997-59977998868999----873658-989999999999999--999998


Q ss_pred             HCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCC
Q ss_conf             0248980687248761203207999999989998512888997388
Q gi|254780725|r  238 VFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVP  283 (427)
Q Consensus       238 ~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p  283 (427)
                      .  ..|+.++.+.-.+...       .+......-..|=-|.+|+|
T Consensus        75 ~--~~g~~vIvs~isp~~~-------~R~~~R~~~~~~~EVyv~~p  111 (176)
T PRK05541         75 A--DQGMIVIVTTISMFNE-------IYAYNRKHLPNYFEVYLKCD  111 (176)
T ss_pred             H--HCCCCEEEEECCCCHH-------HHHHHHHHCCCCEEEEEECC
T ss_conf             6--4698036752279899-------99999974887689999489


No 227
>cd01890 LepA LepA subfamily.  LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome.  LepA is ubiquitous in bacteria and eukaryota (e.g. yeast GUF1p), but is missing from archaea.  This pattern of phyletic distribution suggests that LepA evolved through a duplication of the EF-G gene in bacteria, followed by early transfer into the eukaryotic lineage, most likely from the promitochondrial endosymbiont.  Yeast GUF1p is not essential and mutant cells did not reveal any marked phenotype.
Probab=96.41  E-value=0.014  Score=35.12  Aligned_cols=84  Identities=15%  Similarity=0.161  Sum_probs=59.9

Q ss_pred             CCCEEEECCCCCCCH--HHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC-CCHHHHHH
Q ss_conf             288899738888898--999998620125435787768899999999999981987675389995658987-52005999
Q gi|254780725|r  274 IFPLVILDVPHVWNS--WTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPK-KPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~~~~--~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~-~~~i~~~~  350 (427)
                      .|-+-++|+|.....  ....++..+|.+++|+...-.--.++.+.++.....+.   ++.+++|+++... ..+...++
T Consensus        66 ~~~in~iDtPGh~dF~~~~~~al~~~D~allVVda~~Gv~~qT~~~~~~a~~~~~---p~ivviNKiD~~~ad~~~v~~~  142 (179)
T cd01890          66 EYLLNLIDTPGHVDFSYEVSRSLAACEGALLLVDATQGVEAQTLANFYLALENNL---EIIPVINKIDLPSADPERVKQQ  142 (179)
T ss_pred             CEEEEEEECCCCCCCHHHHHHHHHHHCEEEEEEECCCCCCHHHHHHHHHHHHCCC---CEEEEEECCCCCCCCHHHHHHH
T ss_conf             1489999899864517789889975442789986477873748999999987699---8899986555677899999999


Q ss_pred             HHHHHCCCEE
Q ss_conf             9998489537
Q gi|254780725|r  351 FCAPLGITPS  360 (427)
Q Consensus       351 ~~~~lg~~~~  360 (427)
                      +++.+|....
T Consensus       143 i~~~~g~~~~  152 (179)
T cd01890         143 IEDVLGLDPS  152 (179)
T ss_pred             HHHHHCCCCC
T ss_conf             9998688976


No 228
>cd04167 Snu114p Snu114p subfamily.  Snu114p is one of several proteins that make up the U5 small nuclear ribonucleoprotein (snRNP) particle.  U5 is a component of the spliceosome, which catalyzes the splicing of pre-mRNA to remove introns.  Snu114p is homologous to EF-2, but typically contains an additional N-terminal domain not found in Ef-2.  This protein is part of the GTP translation factor family and the Ras superfamily, characterized by five G-box motifs.
Probab=96.39  E-value=0.056  Score=31.35  Aligned_cols=64  Identities=25%  Similarity=0.247  Sum_probs=50.9

Q ss_pred             CCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf             2888997388888--989999986201254357877688999999999999819876753899956589
Q gi|254780725|r  274 IFPLVILDVPHVW--NSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKT  340 (427)
Q Consensus       274 ~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~  340 (427)
                      .|-+-++|+|...  ...+..++..+|-+++|++..-.-.-++++.++...+.+.   ++.+++|+.+.
T Consensus        70 ~~~inlIDTPGH~dF~~ev~~al~~~DgailVVDa~eGv~~qT~~~l~~a~~~~l---~~ilviNKiDR  135 (213)
T cd04167          70 SYLFNIIDTPGHVNFMDEVAAALRLSDGVVLVVDVVEGVTSNTERLIRHAILEGL---PIVLVINKIDR  135 (213)
T ss_pred             EEEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCC---CEEEEEECCCC
T ss_conf             0578778898724179999988863776799998788875779999999998699---98999988234


No 229
>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein B; InterPro: IPR004435   The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cisdithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism , .    In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which coverts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner . MoCF is the active co-factor in eukaryotic and some prokaryotic molybdoenzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdoenzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF . Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 () of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) .   The MobB domain is similar to that of the urease accessory protein UreG and the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocentres of their respective target enzymes. It is involved in the final step of molybdenum-cofactor biosynthesis. While its precise function has not been identified it is thought to be involved in the transfer of a guanine dinucleotide moiety to molybdopterin, as it shows GTP-binding and weak GTPase activity . The MobB protein (P32125 from SWISSPROT) from Escherichia coli, which is comprised of this domain, is a homodimer . Each molecule is composed of two distinct regions - an outer region comprised of 6 beta-strands and three alpha helices, and an inner region comprised of a two-strand beta hairpin followed by an alpha helix. These regions require interaction with the second monomer to allow proper folding to occur. The two monomers are intertwined and form an extensive 16-stranded beta-sheet. While the active site could not be positively identified, the presence of highly conserved residues suggests the substrate binding site occurs in the central solvent channel.; GO: 0005525 GTP binding, 0006777 Mo-molybdopterin cofactor biosynthetic process.
Probab=96.37  E-value=0.024  Score=33.62  Aligned_cols=102  Identities=16%  Similarity=0.224  Sum_probs=60.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886318456124337653202489
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAE  242 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~  242 (427)
                      |++|+| .-+.||||+...+.-.|.. +|.+|..|=.+.+ |.-...++-+-.-+..-.        +.--+..+.....
T Consensus         1 v~~i~G-~k~SGKTtL~~~l~~~L~~-~Gy~V~~IKH~gh-G~H~~~~d~~GkDs~rhr--------~AGA~~v~~~~~~   69 (165)
T TIGR00176         1 VLQIVG-YKNSGKTTLIERLVKALKA-RGYRVATIKHDGH-GHHDFDIDKEGKDSYRHR--------EAGADAVIVASSE   69 (165)
T ss_pred             CEEEEE-ECCCCHHHHHHHHHHHHHC-CCCCEEEEEECCC-CCCCCEECCCCCCCHHHH--------HCCCCEEEEECCC
T ss_conf             937896-2588678999999999970-7995089860898-887565279987313321--------0436278866790


Q ss_pred             CEEEEECCCCCCCHHCCCHHHHHHHHHHHHH-CCCEEEEC
Q ss_conf             8068724876120320799999998999851-28889973
Q gi|254780725|r  243 NLSILTAPAMLSRTYDFDEKMIVPVLDILEQ-IFPLVILD  281 (427)
Q Consensus       243 gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~-~yd~VIiD  281 (427)
                      +..++..      .....+..+..+|..+.. .||+|+|-
T Consensus        70 ~~~~~~~------~~g~~e~~L~~~l~~~~~~~~D~~LvE  103 (165)
T TIGR00176        70 RYAVMTE------TQGEEELDLEALLKRLADRELDIILVE  103 (165)
T ss_pred             EEEEEEE------CCCCCCCCHHHHHHHCCCCCCCEEEEE
T ss_conf             6899875------289998787999864285526878985


No 230
>PRK10789 putative multidrug transporter membrane\ATP-binding components; Provisional
Probab=96.34  E-value=0.069  Score=30.76  Aligned_cols=150  Identities=14%  Similarity=0.114  Sum_probs=68.9

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHH------HCCCCC---CCCHHHHHCC--CCC
Q ss_conf             67537999746988775689999999999626994999978798986033------438998---7898886318--456
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANI------NFDKDP---INSISDAIYP--VGR  227 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~------~l~~~~---~~~l~d~l~~--~~r  227 (427)
                      +.|+.++++| +-|+||||++--+...+.-. ..++.+=+-|+..=+...      +..++|   ..++.|-+.-  ++-
T Consensus       339 ~~Ge~vaIVG-~SGsGKSTLl~LL~g~y~p~-~G~I~idg~di~~i~~~~lR~~I~~V~Q~~~LF~~TI~eNI~lg~~~~  416 (569)
T PRK10789        339 KPGQMLGICG-PTGSGKSTLLSLIQRHFDVS-EGDIRFHDIPLTKLQLDSWRSRLAVVSQTPFLFSDTVANNIALGRPDA  416 (569)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHHHHHCC-CCCEEEECEECCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHCCCCCC
T ss_conf             8997899879-99998799999999776426-787465010134257688863147658875025662999986579776


Q ss_pred             HHHH--------HHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHH--HHHHHHHHCCCEEEECCCCC-CCHHHHH----
Q ss_conf             1243--------3765320248980687248761203207999999--98999851288899738888-8989999----
Q gi|254780725|r  228 IDKA--------FVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIV--PVLDILEQIFPLVILDVPHV-WNSWTQE----  292 (427)
Q Consensus       228 lD~~--------~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~--~ll~~l~~~yd~VIiD~p~~-~~~~~~~----  292 (427)
                      -++.        -++..+.+.++|++-.-+..    ...++.+.-+  .+-..+-...+.+|+|=|.. .+..+..    
T Consensus       417 ~~eei~~a~~~a~l~~~i~~lp~G~dT~ige~----G~~LSGGQrQRialARAll~~p~iliLDEaTSaLD~~tE~~i~~  492 (569)
T PRK10789        417 TQQEIEHVARLASVHEDILRLPQGYDTEVGER----GVMLSGGQKQRISIARALLLNAEILILDDALSAVDGRTEHQILH  492 (569)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC----CCCCCHHHHHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHH
T ss_conf             54589999998555687643755323712688----89969999999999999954999899808766689999999999


Q ss_pred             HHHH--CCCCCCCCCCCHHHHHHH
Q ss_conf             9862--012543578776889999
Q gi|254780725|r  293 VLTL--SDKVVITTSLDLAGLRNS  314 (427)
Q Consensus       293 ~L~~--AD~vviV~~p~~~slr~a  314 (427)
                      .+..  .+..++++...+..++++
T Consensus       493 ~l~~~~~~~T~i~IaHRlsti~~a  516 (569)
T PRK10789        493 NLRQWGEGRTVIISAHRLSALTEA  516 (569)
T ss_pred             HHHHHCCCCEEEEECCCHHHHHHC
T ss_conf             999974999899971588889859


No 231
>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .
Probab=96.32  E-value=0.081  Score=30.36  Aligned_cols=46  Identities=15%  Similarity=0.266  Sum_probs=33.7

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHH-----HCCCCEEEEECCCCCC
Q ss_conf             5675379997469887756899999999996-----2699499997879898
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIAS-----VFAMETLLADLDLPYG  204 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~-----~~~~~VlLvDlDl~~g  204 (427)
                      -+.|.++-++| -.|+|||+++..+|.....     ..+.+|++||..-.|.
T Consensus        16 i~~G~itEi~G-~~GsGKTql~lqla~~~~~~~~~~g~~~~vvyIdtE~~f~   66 (235)
T cd01123          16 IETGSITEIFG-EFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFR   66 (235)
T ss_pred             CCCCEEEEEEC-CCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCC
T ss_conf             64787999999-9998499999999999842475367896299995367758


No 232
>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]
Probab=96.31  E-value=0.037  Score=32.47  Aligned_cols=98  Identities=12%  Similarity=0.122  Sum_probs=57.2

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             53799974698877568999999999962699499997879898603343899878988863184561243376532024
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      -+|++|+|-| ++||||+.-.+...|.. +|.+|..|-...+..++    +.+-.-+        -|.-.         .
T Consensus         2 ~~Il~ivG~k-~SGKTTLie~lv~~L~~-~G~rVa~iKH~hh~~~~----D~~GkDs--------~r~~~---------a   58 (161)
T COG1763           2 MKILGIVGYK-NSGKTTLIEKLVRKLKA-RGYRVATVKHAHHDFDL----DKPGKDT--------YRHRK---------A   58 (161)
T ss_pred             CCEEEEEECC-CCCHHHHHHHHHHHHHH-CCCEEEEEEECCCCCCC----CCCCCCC--------CHHHC---------C
T ss_conf             7289999627-99734289999999975-79379999865877777----8898766--------10003---------5


Q ss_pred             CCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEEC
Q ss_conf             89806872487612032079999999899985128889973
Q gi|254780725|r  241 AENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILD  281 (427)
Q Consensus       241 ~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD  281 (427)
                      +....+++++.............+..++..+...+|+|++-
T Consensus        59 Ga~~~v~~s~~~~~~~~~~~~~~L~~vl~~l~~~~D~vLVE   99 (161)
T COG1763          59 GADQVVVASDHRTALMTRTPDRDLDAVLSRLDPLLDLVLVE   99 (161)
T ss_pred             CCCEEEEECCCEEEEEEECCCCCHHHHHHHCCCCCCEEEEE
T ss_conf             66349995597899998268768999997427556799995


No 233
>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]
Probab=96.26  E-value=0.016  Score=34.60  Aligned_cols=86  Identities=12%  Similarity=0.205  Sum_probs=67.6

Q ss_pred             CCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHH
Q ss_conf             69989999998618998499998059876778899988853289980899816871899999997656264318999899
Q gi|254780725|r   62 RGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVAD  141 (427)
Q Consensus        62 ~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~  141 (427)
                      ..+...|...+.... |+.+++|+.++++++++....+.+  .|.+ |+.++...+..---+...+|+.+++++|+....
T Consensus        18 a~~g~~~l~~~~~~~-~~~~lld~~m~~~~~~~~~~~lk~--~~~~-~v~~t~~~~~~~~~~~~~~~~~~~l~~~~~~~~   93 (435)
T COG3706          18 AKKGLIALAILLDHK-PDYKLLDVMMPGMDGFELCRRLKA--EPAT-VVMVTALDDSAPRVRGLKAGADDFLTKPVNDSQ   93 (435)
T ss_pred             CCCHHHHHHHHHCCC-CCEEEEECCCCCCCCHHHHHHHHC--CCCC-EEEEEECCCCCCCHHHHHHHHHHHCCCCCCHHH
T ss_conf             254277999974489-874874100688673019987635--8751-699860378777556776313441367777177


Q ss_pred             HHHHHHHCCC
Q ss_conf             9997631023
Q gi|254780725|r  142 IINSISAIFT  151 (427)
Q Consensus       142 l~~ai~~~~~  151 (427)
                      +......++.
T Consensus        94 ~~~r~~~l~~  103 (435)
T COG3706          94 LFLRAKSLVR  103 (435)
T ss_pred             HHHHHHHHCC
T ss_conf             8875266314


No 234
>PRK11176 lipid transporter ATP-binding/permease protein; Provisional
Probab=96.21  E-value=0.038  Score=32.35  Aligned_cols=41  Identities=34%  Similarity=0.415  Sum_probs=28.4

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             6753799974698877568999999999962699499997879
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDL  201 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl  201 (427)
                      +.|+.++++| +-|+||||++-=+...+--. ..++.+=+-|+
T Consensus       366 ~~G~~vaiVG-~SGsGKSTL~~LL~gly~p~-~G~I~idg~di  406 (581)
T PRK11176        366 PAGKTVALVG-RSGSGKSTIANLLTRFYDID-EGEILLDGHDL  406 (581)
T ss_pred             CCCCEEECCC-CCCCCHHHHHHHHHHHCCCC-CCEEEECCEEH
T ss_conf             9994431228-99986789999998536678-87487898851


No 235
>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN; InterPro: IPR013462    The GvpN protein is associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy , . It belongs to a larger family of ATPases .; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0031412 gas vesicle organization and biogenesis, 0031411 gas vesicle.
Probab=96.20  E-value=0.0081  Score=36.50  Aligned_cols=45  Identities=24%  Similarity=0.344  Sum_probs=37.1

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHH
Q ss_conf             67537999746988775689999999999626994999978798986033
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANI  208 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~  208 (427)
                      ..|.-|-|.|. -|+||||+|.++|.    .++++|+++-.|-++++..+
T Consensus        19 ~~G~PvHl~GP-aG~GKT~LA~hvA~----~r~RPV~l~~Gd~eL~~~DL   63 (265)
T TIGR02640        19 KSGYPVHLRGP-AGTGKTTLAMHVAR----KRDRPVVLINGDAELTTSDL   63 (265)
T ss_pred             CCCCCEEEECC-CCCCHHHHHHHHHH----HCCCCEEEEECCCCCCCCCC
T ss_conf             27886674478-88556899999997----36896899865823265442


No 236
>PRK09270 frcK putative fructose transport system kinase; Reviewed
Probab=96.19  E-value=0.017  Score=34.57  Aligned_cols=71  Identities=13%  Similarity=0.177  Sum_probs=43.5

Q ss_pred             CCCEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCC
Q ss_conf             5626431899989999976310233222345675379997469887756899999999996269-9499997879
Q gi|254780725|r  128 HVSEYLIEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFA-METLLADLDL  201 (427)
Q Consensus       128 Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~-~~VlLvDlDl  201 (427)
                      ++.++...+...++..+-+........  .+..=.+|++.| -.|+||||+|..|+..|.+... ..++++-+|-
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~rR~lIgIaG-~pGSGKSTlA~~l~~~L~~~~~~~~~~~vpmDG   74 (230)
T PRK09270          3 TVNGLDVQAQYLDELIEEVHKPLMLAA--EPQRRTVVGIAG-PPGAGKSTLAETLWEALSQQGPELPAIQVPMDG   74 (230)
T ss_pred             EECCEEEEEEECHHHHHHHHHHHHHHC--CCCCEEEEEEEC-CCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCC
T ss_conf             146616674514566899999998715--999718999989-998899999999999986237998579973653


No 237
>PRK09581 pleD response regulator PleD; Reviewed
Probab=96.18  E-value=0.059  Score=31.20  Aligned_cols=85  Identities=16%  Similarity=0.257  Sum_probs=59.7

Q ss_pred             CCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCC-CCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHH
Q ss_conf             998999999861899849999805987677889998885328-9980899816871899999997656264318999899
Q gi|254780725|r   63 GSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCD-SGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVAD  141 (427)
Q Consensus        63 g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~-p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~  141 (427)
                      +...++.... ....|++++++..++..+++.....+..... .+++++.+...++.......+..|++||+.+|.+..+
T Consensus       185 ~~~~~~l~~~-~~~~~d~~i~~~~~~~~~~~~~~~~~r~~~~~~~~~i~~~~~~~~~~~~~~~~~~g~~d~~~~~~~~~e  263 (457)
T PRK09581        185 SDPEEALIRA-AEGNYDLIIVSASFENYDPLRLCSQLRSKERTRYVPILLLVDEDEDPRLVKALELGVNDYLMRPIDKNE  263 (457)
T ss_pred             CCHHHHHHHH-CCCCCCEEEECCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHCCCCEEEECCCCHHH
T ss_conf             4869999874-357976899756567664689999997143435732999956886166766641465228843786275


Q ss_pred             HHHHHHH
Q ss_conf             9997631
Q gi|254780725|r  142 IINSISA  148 (427)
Q Consensus       142 l~~ai~~  148 (427)
                      +...+..
T Consensus       264 ~~~r~~~  270 (457)
T PRK09581        264 LLARVRT  270 (457)
T ss_pred             HHHHHHH
T ss_conf             5587999


No 238
>cd04112 Rab26 Rab26 subfamily.  First identified in rat pancreatic acinar cells, Rab26 is believed to play a role in recruiting mature granules to the plasma membrane upon beta-adrenergic stimulation.  Rab26 belongs to the Rab functional group III, which are considered key regulators of intracellular vesicle transport during exocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
Probab=96.17  E-value=0.097  Score=29.87  Aligned_cols=116  Identities=15%  Similarity=0.102  Sum_probs=76.6

Q ss_pred             CCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             2888997388888--9899999862012543578-776889999999999998198767538999565898752005999
Q gi|254780725|r  274 IFPLVILDVPHVW--NSWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      .+.+-|+|++..-  .......+..+|.+++|.+ -+..|+.+...+++.+++......++.+|-|+.+......++.++
T Consensus        49 ~v~l~iwDtaG~e~~~~l~~~~~~~a~~~ilvydit~~~Sf~~l~~w~~~i~~~~~~~~~iilVGNK~DL~~~r~V~~~e  128 (191)
T cd04112          49 KVKLQIWDTAGQERFRSVTHAYYRDAHALLLLYDITNKASFDNIRAWLTEIKEYAQEDVVIMLLGNKADMSGERVVKRED  128 (191)
T ss_pred             EEEEEEEECCCCCCCCCCHHHHHHCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCHHH
T ss_conf             99999997998633464647771177778999727988999999999999998666785389861246553026799999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHCCCCCC
Q ss_conf             9998489537990687999999884796189888999--89999999999985221223
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMGRVTVS  407 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~gr~~~~  407 (427)
                      .++                  -|...|.+..|.+.+.  -+-+.|..|++.|..+....
T Consensus       129 ~~~------------------~a~~~~~~f~EtSAkt~~nI~e~F~~i~~~i~~~~~~~  169 (191)
T cd04112         129 GER------------------LAKEYGVPFMETSAKTGLNVELAFTAVAKELKHRKYEQ  169 (191)
T ss_pred             HHH------------------HHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             999------------------99982997999854898097999999999998742279


No 239
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=96.17  E-value=0.081  Score=30.33  Aligned_cols=113  Identities=28%  Similarity=0.273  Sum_probs=64.2

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHH
Q ss_conf             45675379997469887756899999999996269949999787989860334389987898886318456124337653
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRL  236 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~  236 (427)
                      .+..|.+|=|.| =.|.||||||..|.-.|-. .|..|-++|-|----.+    +.+-.++-.|-..+..|+-.  +.+.
T Consensus        19 ~~~~~~viW~TG-LSGsGKSTiA~ale~~L~~-~G~~~y~LDGDnvR~gL----~~dLgFs~edR~eniRRvae--vAkl   90 (197)
T COG0529          19 KGQKGAVIWFTG-LSGSGKSTIANALEEKLFA-KGYHVYLLDGDNVRHGL----NRDLGFSREDRIENIRRVAE--VAKL   90 (197)
T ss_pred             HCCCCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEECCHHHHHCC----CCCCCCCHHHHHHHHHHHHH--HHHH
T ss_conf             279985999646-8888787999999999997-59758985574676500----57889786789999999999--9999


Q ss_pred             HHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCC
Q ss_conf             202489806872487612032079999999899985128889973888
Q gi|254780725|r  237 PVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPH  284 (427)
Q Consensus       237 l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~  284 (427)
                      +..  .|+-++.+--.+.+.   ..+..+.++..  ..|=-|.||+|-
T Consensus        91 l~d--aG~iviva~ISP~r~---~R~~aR~~~~~--~~FiEVyV~~pl  131 (197)
T COG0529          91 LAD--AGLIVIVAFISPYRE---DRQMARELLGE--GEFIEVYVDTPL  131 (197)
T ss_pred             HHH--CCEEEEEEEECCCHH---HHHHHHHHHCC--CCEEEEEECCCH
T ss_conf             987--890899975173099---99999997276--862899957989


No 240
>COG1492 CobQ Cobyric acid synthase [Coenzyme metabolism]
Probab=96.13  E-value=0.03  Score=33.04  Aligned_cols=194  Identities=12%  Similarity=0.192  Sum_probs=101.1

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCC--CCCC---C---HHHHHCC-C---CCHH
Q ss_conf             379997469887756899999999996269949999787989860334389--9878---9---8886318-4---5612
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDK--DPIN---S---ISDAIYP-V---GRID  229 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~--~~~~---~---l~d~l~~-~---~rlD  229 (427)
                      +.|-|.|.-..+|||++++.|...+++ .|.+|.      +|-..+..||-  .+.-   +   +.+++.. .   -+..
T Consensus         2 ~~iMv~GT~S~~GKS~~~aglcRi~~~-~G~~V~------PFK~QNMsLNs~it~~G~EIgraQ~~QA~Aa~i~p~v~mN   74 (486)
T COG1492           2 KAIMVQGTTSDAGKSFLVAGLCRILAR-RGYRVA------PFKSQNMSLNSAITPGGGEIGRAQALQALAAGIEPSVHMN   74 (486)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHHH-CCCCCC------CCHHHHCCCCCEECCCCCEEEHHHHHHHHHCCCCCCCCCC
T ss_conf             853787214776546752453488873-577547------8706543466078779968755066789873998743428


Q ss_pred             HHHHHHHHHCCCC-CEEEEECCCCCCCHHCC---------CHHHHHHHHHHHHHCCCEEEECCCCCCCHH--------HH
Q ss_conf             4337653202489-80687248761203207---------999999989998512888997388888989--------99
Q gi|254780725|r  230 KAFVSRLPVFYAE-NLSILTAPAMLSRTYDF---------DEKMIVPVLDILEQIFPLVILDVPHVWNSW--------TQ  291 (427)
Q Consensus       230 ~~~l~~~l~~~~~-gL~lL~a~~~~~~~~~~---------~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~--------~~  291 (427)
                      +.+|+    ++++ +..++.-..........         -...+...++.+.+.||+|++--..+..+.        ..
T Consensus        75 PvLLK----P~sd~~sQVIv~G~~~G~~s~~~yy~~~~~~l~~~v~~s~~~l~~~~d~Vv~EGAGSpaEiNlr~~Di~Nm  150 (486)
T COG1492          75 PVLLK----PCSDTGSQVIVMGKDIGRKSAVEYYQEGKGLLWVAVKESLERLDREYDVVVIEGAGSPAEINLRDRDIANM  150 (486)
T ss_pred             CEEEE----ECCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHCCCCCCCCCCE
T ss_conf             77870----35888447999463446657178899988999999999998754105589996379823227663661100


Q ss_pred             HHHHHCC-CCCCCCCCCH----HHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCC-CHHHHHHHHHHHCCCEEEEECC
Q ss_conf             9986201-2543578776----88999999999999819876753899956589875-2005999999848953799068
Q gi|254780725|r  292 EVLTLSD-KVVITTSLDL----AGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKK-PEISISDFCAPLGITPSAIIPF  365 (427)
Q Consensus       292 ~~L~~AD-~vviV~~p~~----~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~-~~i~~~~~~~~lg~~~~~~IP~  365 (427)
                      .+...+| -+++|.+=|.    +|+..+..++..-.+.    .--.+++|++.-... -+-..+.+++..|.+++.++||
T Consensus       151 ~~a~~~dapvILV~DIdRGGvfAsl~GT~~lL~~~~r~----~VkG~iINkFRGd~~ll~~gik~Le~~tg~~vlGv~P~  226 (486)
T COG1492         151 GVAEIADAPVILVGDIDRGGVFASLYGTLALLPESDRA----LVKGFIINKFRGDESLLDPGLKWLEELTGVPVLGVLPY  226 (486)
T ss_pred             EEEHHCCCCEEEEEEECCCCEEEEEEEHHEECCHHHHC----CEEEEEEEEECCCHHHHHHHHHHHHHHHCCEEEEECCC
T ss_conf             22023389889999511564541730212236876760----01479996317987887459999998619746756525


Q ss_pred             CHHHH
Q ss_conf             79999
Q gi|254780725|r  366 DGAVF  370 (427)
Q Consensus       366 D~~~~  370 (427)
                      .....
T Consensus       227 ~~~~~  231 (486)
T COG1492         227 LKDAL  231 (486)
T ss_pred             CCCCC
T ss_conf             55455


No 241
>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2.  The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia.  Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole.  In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells.  CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.
Probab=96.11  E-value=0.028  Score=33.18  Aligned_cols=41  Identities=20%  Similarity=0.299  Sum_probs=27.9

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             56753799974698877568999999999962699499997879
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDL  201 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl  201 (427)
                      -..|.+++++| +-|+||||+.--|.-.+..  ...+.+=+.|.
T Consensus        27 I~~Ge~vaIvG-~sGsGKSTLl~lL~gl~~~--~G~I~idg~~i   67 (275)
T cd03289          27 ISPGQRVGLLG-RTGSGKSTLLSAFLRLLNT--EGDIQIDGVSW   67 (275)
T ss_pred             ECCCCEEEEEC-CCCCCHHHHHHHHHHHCCC--CCEEEECCEEC
T ss_conf             87999999999-9999799999999603578--95399998806


No 242
>COG3279 LytT Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]
Probab=96.04  E-value=0.05  Score=31.61  Aligned_cols=107  Identities=11%  Similarity=0.220  Sum_probs=76.3

Q ss_pred             HHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCH
Q ss_conf             99999998864110020223730699899999986189984999980598767788999888532899808998168718
Q gi|254780725|r   39 TLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDV  118 (427)
Q Consensus        39 ~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~  118 (427)
                      .+..-++.-..  .+.........++...+.+.+... .|+++++|+.++..++++....++.. +|...|+.+..+++-
T Consensus        12 ~~~~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~fldI~~~~~~G~ela~~i~~~-~~~~~Ivfvt~~~~~   87 (244)
T COG3279          12 LAREELRRILN--EIPDIEIVGEAENGEEALQLLQGL-RPDLVFLDIAMPDINGIELAARIRKG-DPRPAIVFVTAHDEY   87 (244)
T ss_pred             HHHHHHHHHHH--HHHHCCHHHHHCCHHHHHHHHHCC-CCCEEEEEECCCCCCHHHHHHHHCCC-CCCCEEEEEEEHHHH
T ss_conf             67999999988--744211113312303178887602-57769997237652449999986156-988539999861543


Q ss_pred             HHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             999999976562643189998999997631023
Q gi|254780725|r  119 SLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       119 ~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      ..  .+-...+-||+.||.+...+...+.++..
T Consensus        88 a~--~afev~a~d~i~kp~~~~~l~~~l~~~~~  118 (244)
T COG3279          88 AV--AAFEVEALDYLLKPISEERLAKTLERLRR  118 (244)
T ss_pred             HH--HHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             23--33133466774285426899999999888


No 243
>pfam00071 Ras Ras family. Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.
Probab=96.00  E-value=0.12  Score=29.37  Aligned_cols=110  Identities=13%  Similarity=0.151  Sum_probs=71.4

Q ss_pred             CCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             2888997388888--9899999862012543578-776889999999999998198767538999565898752005999
Q gi|254780725|r  274 IFPLVILDVPHVW--NSWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      .+.+.++|++...  .......+..+|.+++|.. -+..|+.....+++.+.+......++.+|-|+.+.+....++.++
T Consensus        47 ~~~~~i~Dt~G~e~~~~~~~~~~~~ad~~iivfd~~~~~S~~~i~~~~~~i~~~~~~~~piilvgnK~Dl~~~~~i~~~e  126 (162)
T pfam00071        47 TVKLQIWDTAGQERFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADDNVPIVLVGNKCDLEDQRVVSTEE  126 (162)
T ss_pred             EEEEEEEECCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCHHHCCCCCHHH
T ss_conf             99999997898720467889986257655042348988999999999999998579886288997524746518899999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHH
Q ss_conf             9998489537990687999999884796189888999--89999999999985
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLM  401 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~  401 (427)
                                        .-..|...|.+..|.+.++  -+-+.|..|+++|.
T Consensus       127 ------------------~~~~a~~~~~~y~e~Sak~g~gI~~~F~~i~~~il  161 (162)
T pfam00071       127 ------------------GEALAKELGLPFMETSAKTNENVEEAFEELAREIL  161 (162)
T ss_pred             ------------------HHHHHHHHCCEEEEECCCCCCCHHHHHHHHHHHHC
T ss_conf             ------------------99999980997999737888299999999999967


No 244
>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]
Probab=95.98  E-value=0.047  Score=31.79  Aligned_cols=40  Identities=20%  Similarity=0.338  Sum_probs=32.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             7999746988775689999999999626994999978798
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      -.-+++++.|.|||++|.|+|..+|....++|++.=+-..
T Consensus       197 dLiilAaRP~mGKTafalnia~n~a~~~~~~v~iFSLEM~  236 (435)
T COG0305         197 DLIIVAARPGMGKTALALNIALNAAADGRKPVAIFSLEMS  236 (435)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf             7799716899975899999999999855897599982679


No 245
>cd04121 Rab40 Rab40 subfamily.  This subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous.  In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle.  Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components.  Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide d
Probab=95.98  E-value=0.12  Score=29.30  Aligned_cols=112  Identities=14%  Similarity=0.222  Sum_probs=76.0

Q ss_pred             CCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             288899738888--89899999862012543578-776889999999999998198767538999565898752005999
Q gi|254780725|r  274 IFPLVILDVPHV--WNSWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      .+.+-|+|++..  +......-+..|+-+++|.+ -+..|+.+..++++.+++..++ -++.+|-|+++......++.+ 
T Consensus        54 ~v~l~iwDtaGqe~f~~l~~~y~r~a~~~ilvyDvt~~~Sf~~l~~w~~~i~~~~~~-~p~iLVGNK~DL~~~r~V~~e-  131 (189)
T cd04121          54 RVKLQLWDTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHAPG-VPKILVGNRLHLAFKRQVATE-  131 (189)
T ss_pred             EEEEEEECCCCCCCHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCC-CCEEEEEECCCHHHCCCCCHH-
T ss_conf             999999817886221167898866337048982279889999999999999997689-878996132550330889999-


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHCCC
Q ss_conf             9998489537990687999999884796189888999--89999999999985221
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMGRV  404 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~gr~  404 (427)
                                       +...-|...|.+..|.+.+.  -+.+.|..|++.+.-+.
T Consensus       132 -----------------e~~~~A~~~~~~f~EtSAk~g~nV~e~F~~l~~~il~~~  170 (189)
T cd04121         132 -----------------QAQAYAERNGMTFFEVSPLCNFNITESFTELARIVLMRH  170 (189)
T ss_pred             -----------------HHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             -----------------999999988999999600679398999999999999865


No 246
>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
Probab=95.97  E-value=0.1  Score=29.77  Aligned_cols=112  Identities=22%  Similarity=0.279  Sum_probs=59.9

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHH
Q ss_conf             45675379997469887756899999999996269949999787989860334389987898886318456124337653
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRL  236 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~  236 (427)
                      .+..|.+|=|+| -.|.||||||..|...|-. .|.++.++|.|---..    |+.+..++-.|-..+..|+-..  .++
T Consensus       439 ~g~~~~~iw~tG-lsgsGKstiA~~le~~L~~-~g~~~~~LDGd~lR~g----l~~dlgf~~~dR~enirR~~ev--a~l  510 (613)
T PRK05506        439 KGQKPATVWFTG-LSGSGKSTIANLVERRLHA-LGRHTYVLDGDNVRHG----LNRDLGFTDADRVENIRRVAEV--ARL  510 (613)
T ss_pred             HCCCCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEECCHHHHHH----HCCCCCCCHHHHHHHHHHHHHH--HHH
T ss_conf             489976999977-8989747999999999997-7998799880898741----0457797989999999999999--999


Q ss_pred             HHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCC
Q ss_conf             20248980687248761203207999999989998512888997388
Q gi|254780725|r  237 PVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVP  283 (427)
Q Consensus       237 l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p  283 (427)
                      +.  ..|+-++.+.-.+...   ..+..+.++..  ..|--|.+|+|
T Consensus       511 ~~--~aG~i~i~a~iSp~~~---~R~~~r~~~~~--~~f~Ev~v~~~  550 (613)
T PRK05506        511 MA--DAGLIVLVSFISPFRE---ERELARALIGE--GEFVEVFVDTP  550 (613)
T ss_pred             HH--HCCCEEEEECCCCCHH---HHHHHHHHCCC--CCEEEEEEECC
T ss_conf             98--6898899975889989---99999975788--87899999089


No 247
>TIGR01618 phage_P_loop phage nucleotide-binding protein; InterPro: IPR006505   These sequences represent an uncharacterised family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of these proteins is unknown..
Probab=95.97  E-value=0.015  Score=34.81  Aligned_cols=182  Identities=16%  Similarity=0.178  Sum_probs=93.0

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      -.|-++| |||.||||++=+        ...+++++|+|-..-                +|.+                .
T Consensus        14 ~~~lIYG-~~G~GKTS~~K~--------l~GktL~l~~D~SSk----------------VL~G----------------~   52 (229)
T TIGR01618        14 FRYLIYG-KPGLGKTSTIKY--------LPGKTLVLSLDKSSK----------------VLAG----------------D   52 (229)
T ss_pred             CEEEEEC-CCCCCCCCEEEE--------CCCCEEEEECCCCCC----------------CCCC----------------C
T ss_conf             3688875-898872305664--------588789883678644----------------3468----------------9


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEEC-CCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             9806872487612032079999999899985128889973-888889899999862012543578776889999999999
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILD-VPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDV  320 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD-~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~  320 (427)
                      ++++++-+..+.......-.+.+.++.......||-|||| +.+....|....=..+-.-..+-.+++.-+...  +++.
T Consensus        53 ~nvdiim~~~d~~~~~~~~~e~~~~~~~~~~~~Y~niViDNis~lq~~~L~~~gr~~K~~~~p~~q~Y~~~~~~--~~d~  130 (229)
T TIGR01618        53 ENVDIIMADLDDEKPIQEMVEFYKELQNIQAEEYDNIVIDNISELQKLWLINLGREAKNGRSPELQHYQKLDLY--FLDL  130 (229)
T ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCHHHCCCEEEEECHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHH--HHHH
T ss_conf             98338998606998478999999997322534576589814278999999846844245788650003688899--9999


Q ss_pred             HHHCCC-CCCCCEEEEECCCCCC-------------CCHHHHHHHHHHHCCC-EEEEECCCHHHHHHHHHCCCCEEEECC
Q ss_conf             998198-7675389995658987-------------5200599999984895-379906879999998847961898889
Q gi|254780725|r  321 LKKLRP-ADKPPYLVLNQVKTPK-------------KPEISISDFCAPLGIT-PSAIIPFDGAVFGMSANSGKMIHEVDP  385 (427)
Q Consensus       321 l~~~~~-~~~~~~iVlNr~~~~~-------------~~~i~~~~~~~~lg~~-~~~~IP~D~~~~~~A~~~G~pi~e~~p  385 (427)
                      ++-+.. ...  .+|..=++...             .+.+..+-+-..+|.. +.+.|-..++. ++-..  +.+.....
T Consensus       131 ~~vl~~l~~~--~i~~tAwe~~~~~~~e~G~iy~ry~pdir~kvlN~~lgl~DvVaRl~~~~~t-G~eev--Rg~~L~~~  205 (229)
T TIGR01618       131 LTVLKELKNK--NIYVTAWEDTNQLSLESGQIYNRYLPDIREKVLNAFLGLTDVVARLVKNAKT-GEEEV--RGFILDPS  205 (229)
T ss_pred             HHHHHHCCCC--EEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCC-CHHHC--CCEEECCC
T ss_conf             9999855898--7999876566753401146687666775478876550333234567656888-81131--32355599


Q ss_pred             CCHHHH
Q ss_conf             998999
Q gi|254780725|r  386 KSAIAN  391 (427)
Q Consensus       386 ~s~~a~  391 (427)
                      ++-+||
T Consensus       206 ~G~yAK  211 (229)
T TIGR01618       206 KGNYAK  211 (229)
T ss_pred             CCCCCC
T ss_conf             872121


No 248
>KOG2749 consensus
Probab=95.94  E-value=0.12  Score=29.20  Aligned_cols=96  Identities=20%  Similarity=0.240  Sum_probs=54.6

Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHCCC--CEEECCCCC---HHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHH
Q ss_conf             89980899816871899999997656--264318999---8999997631023322234567537999746988775689
Q gi|254780725|r  104 DSGTKVIVIGDTNDVSLYRALISNHV--SEYLIEPLS---VADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTI  178 (427)
Q Consensus       104 ~p~~~Vivig~~~d~~l~r~l~r~Gv--~dyl~~P~~---~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTi  178 (427)
                      ++++++.+.+-+.-. +  +  -.|.  .+|+..--.   -..+..++...-. ......+.|..+.++|. --+||||+
T Consensus        47 ~~~~k~aifTw~Gct-l--e--v~G~t~~~YVs~eTpM~~ylNlH~ale~~R~-~~e~~~~~GPrv~vVGp-~d~GKsTl  119 (415)
T KOG2749          47 PNGMKVAIFTWQGCT-L--E--VEGTTEVEYVSDETPMVLYLNLHAALEKRRM-QAEEESSYGPRVMVVGP-TDVGKSTL  119 (415)
T ss_pred             CCCCEEEEEEEECCE-E--E--EECCCCCEEECCCCCHHHHHHHHHHHHHHHH-HHHHHHCCCCEEEEECC-CCCCHHHH
T ss_conf             888558999982638-9--9--9435241585189873000139999999866-55420025977999898-76566789


Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCCCCH
Q ss_conf             99999999962699499997879898603
Q gi|254780725|r  179 AHNCAFSIASVFAMETLLADLDLPYGTAN  207 (427)
Q Consensus       179 A~nLA~~LA~~~~~~VlLvDlDl~~g~~~  207 (427)
                      +--|-.+..+ .|++.+.+|+|+++|...
T Consensus       120 ~r~L~nyavk-~gr~Plfv~LDvgQ~sit  147 (415)
T KOG2749         120 CRILLNYAVK-QGRRPLFVELDVGQGSIT  147 (415)
T ss_pred             HHHHHHHHHH-CCCCCEEEECCCCCCCEE
T ss_conf             9999999987-178653897479997244


No 249
>cd04114 Rab30 Rab30 subfamily.  Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.  Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=95.91  E-value=0.13  Score=29.13  Aligned_cols=110  Identities=17%  Similarity=0.178  Sum_probs=73.8

Q ss_pred             CCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             2888997388888--98999998620125435787-76889999999999998198767538999565898752005999
Q gi|254780725|r  274 IFPLVILDVPHVW--NSWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      .+.+-|.|++..-  .......+..||.+++|... +..|+.+.+.+++.+++...+..++.+|-|+.+.....+++.++
T Consensus        55 ~v~l~iwDtaG~e~~~~l~~~~~~~a~~~ilvydvt~~~Sf~~l~~w~~~i~~~~~~~~~~ilVGNK~DL~~~r~v~~~~  134 (169)
T cd04114          55 KIKLQIWDTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNKIDLAERREVSQQR  134 (169)
T ss_pred             EEEEEEEECCCCCCCCCCHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHCCCCCHHH
T ss_conf             99999998999844451557774236645998148988899999999999998689886389731134345417889999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHH
Q ss_conf             9998489537990687999999884796189888999--89999999999985
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLM  401 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~  401 (427)
                      .                  -.-|..+|.+..|.+.+.  -+-+.|..||++|.
T Consensus       135 ~------------------~~~a~~~~~~~~E~SAktg~nV~e~F~~la~~li  169 (169)
T cd04114         135 A------------------EEFSDAQDMYYLETSAKESDNVEKLFLDLACRLI  169 (169)
T ss_pred             H------------------HHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHC
T ss_conf             9------------------9999988999999868988088999999999879


No 250
>cd04166 CysN_ATPS CysN_ATPS subfamily.  CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes.  ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate.  CysD, which catalyzes ATP hydrolysis, is a member of the ATP pyrophosphatase (ATP PPase) family.  CysN hydrolysis of GTP is required for CysD hydrolysis of ATP; however, CysN hydrolysis of GTP is not dependent on CysD hydrolysis of ATP.  CysN is an example of lateral gene transfer followed by acquisition of new function.  In many organisms, an ATPS exists which is not GTP-dependent and shares no sequence or structural similarity to CysN.
Probab=95.85  E-value=0.043  Score=32.04  Aligned_cols=103  Identities=17%  Similarity=0.172  Sum_probs=67.6

Q ss_pred             HCCCEEEECCCCCCC--HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHH--
Q ss_conf             128889973888889--8999998620125435787768899999999999981987675389995658987520059--
Q gi|254780725|r  273 QIFPLVILDVPHVWN--SWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISI--  348 (427)
Q Consensus       273 ~~yd~VIiD~p~~~~--~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~--  348 (427)
                      ..+.|+++|+|....  .........+|..++|+...-.-..++++.+..++.++.  +.+.+++|+++.-.-.+-..  
T Consensus        75 ~~~~~~iiDtPGH~dfi~nmi~gas~aD~ailVVda~~G~~~QT~eh~~~~~~lgi--~~iIv~vNKmD~v~~~e~~f~~  152 (208)
T cd04166          75 PKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGVLEQTRRHSYILSLLGI--RHVVVAVNKMDLVDYSEEVFEE  152 (208)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCC--CEEEEEEECCCCCCCCHHHHHH
T ss_conf             99269998789628899999999863774799997588872789999999997499--8399999885768999899999


Q ss_pred             -----HHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEEC
Q ss_conf             -----999998489537990687999999884796189888
Q gi|254780725|r  349 -----SDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVD  384 (427)
Q Consensus       349 -----~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~  384 (427)
                           ..|.+.++.+....||-.       ...|.-+.+-.
T Consensus       153 i~~~~~~~l~~~~~~~~~~IPiS-------a~~GdNi~~~s  186 (208)
T cd04166         153 IVADYLAFAAKLGIEDITFIPIS-------ALDGDNVVSRS  186 (208)
T ss_pred             HHHHHHHHHHHCCCCCCEEEEEE-------CCCCCCCCCCC
T ss_conf             99999999997499887199812-------67788878699


No 251
>PRK07773 replicative DNA helicase; Validated
Probab=95.84  E-value=0.055  Score=31.39  Aligned_cols=46  Identities=22%  Similarity=0.324  Sum_probs=36.2

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             75379997469887756899999999996269949999787989860
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      .|.. .+++++-|+|||++|.|+|...|...+.+|++.-+....-.+
T Consensus       202 ~~~l-~i~a~rp~~GKt~~~~~~a~~~a~~~~~~v~~FSLEMs~~ql  247 (868)
T PRK07773        202 PGQM-IIVAARPGVGKSTLGLDFARSCSIRHRLASVIFSLEMSKEEI  247 (868)
T ss_pred             CCCE-EEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHH
T ss_conf             7767-999828977777899999999998659965897305678899


No 252
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=95.84  E-value=0.14  Score=28.93  Aligned_cols=43  Identities=14%  Similarity=0.166  Sum_probs=35.5

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             675379997469887756899999999996269949999787989
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      +.|.++.+.| --|+|||+++..+++..++ .|.+++++-++..-
T Consensus        30 p~g~~~li~G-~~G~GKt~~~~~f~~~~~~-~g~~~~~~~~ee~~   72 (241)
T PRK06067         30 PFGSLILIEG-ENDTGKSVLSQQFVWGALN-QGKRGLAITTENTS   72 (241)
T ss_pred             CCCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEECCCH
T ss_conf             7990899980-7998879999999999986-79829999942899


No 253
>cd01866 Rab2 Rab2 subfamily.  Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key featur
Probab=95.76  E-value=0.15  Score=28.75  Aligned_cols=113  Identities=11%  Similarity=0.162  Sum_probs=76.5

Q ss_pred             HCCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             12888997388888--98999998620125435787-7688999999999999819876753899956589875200599
Q gi|254780725|r  273 QIFPLVILDVPHVW--NSWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       273 ~~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      ..+.+-|.|++..-  .......+..+|.+++|.+. +..|+.+...+++.++....+..++.+|-|+.+......++.+
T Consensus        51 ~~~~l~iwDt~G~e~~~~l~~~~~~~a~~~ilvydit~~~Sf~~l~~w~~~i~~~~~~~~~iiLVGNK~DL~~~r~V~~~  130 (168)
T cd01866          51 KQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCDLESRREVSYE  130 (168)
T ss_pred             EEEEEEEEECCCCCCCCCCHHHHHHHHCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCHHHCCCCCHH
T ss_conf             99999999799973346255888664368999344587799999999999999867999659984342354540778999


Q ss_pred             HHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHCC
Q ss_conf             99998489537990687999999884796189888999--8999999999998522
Q gi|254780725|r  350 DFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMGR  403 (427)
Q Consensus       350 ~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~gr  403 (427)
                      +                  .-.-|...|-+..|.+.+.  -+.+.|..|++.|..|
T Consensus       131 e------------------~~~~a~~~~~~~~E~SAk~~~nV~~~F~~l~~~i~~k  168 (168)
T cd01866         131 E------------------GEAFAKEHGLIFMETSAKTASNVEEAFINTAKEIYEK  168 (168)
T ss_pred             H------------------HHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHC
T ss_conf             9------------------9999998699999976788808899999999999739


No 254
>PRK00007 elongation factor G; Reviewed
Probab=95.75  E-value=0.15  Score=28.73  Aligned_cols=40  Identities=10%  Similarity=0.165  Sum_probs=20.3

Q ss_pred             HHHHHHHHHCCCCCCEEEEE-CCCCCCCHHHHHHHHHHHCC
Q ss_conf             89999998618998499998-05987677889998885328
Q gi|254780725|r   65 IAEAVSCFSDSSTPDLIIVQ-TKVDSREVLSALEPLAEVCD  104 (427)
Q Consensus        65 ~~~A~~~~~~~~~P~~iivd-~~~~~~~~~~~l~~la~~~~  104 (427)
                      ......+....-.|-++++- ++-...+....++++.+...
T Consensus       117 T~~v~r~a~~~~lp~i~fINK~Dr~~ad~~~~l~~i~~~l~  157 (693)
T PRK00007        117 SETVWRQADKYKVPRIVFVNKMDRTGADFLRVVEQIKDRLG  157 (693)
T ss_pred             HHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHC
T ss_conf             99999999875989699997977899998999999999859


No 255
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=95.74  E-value=0.15  Score=28.68  Aligned_cols=104  Identities=13%  Similarity=0.142  Sum_probs=59.6

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             67537999746988775689999999999626994999978798986033438998789888631845612433765320
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      +.|.++.+.| .-|+|||+++..++|...+ .|.+|+++-....               ..+.+.+.+.+.-..-+ ...
T Consensus        22 p~gs~~li~G-~~GtGKsi~~~~~~~~~l~-~g~~~~yis~e~t---------------~~~~i~qm~s~g~di~~-~~~   83 (230)
T PRK08533         22 PFGSIILIEG-DESTGKSILSQRLAYGFLQ-NGYSVSYVSSQLT---------------TTEFIKQMMSLGYDINK-KLI   83 (230)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEECCC---------------HHHHHHHHHHCCCCCHH-HHH
T ss_conf             8984899986-8998789999999999987-8986999994389---------------99999999986998179-975


Q ss_pred             CCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHH-HCCCEEEECCC
Q ss_conf             2489806872487612032079999999899985-12888997388
Q gi|254780725|r  239 FYAENLSILTAPAMLSRTYDFDEKMIVPVLDILE-QIFPLVILDVP  283 (427)
Q Consensus       239 ~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p  283 (427)
                        ...|.+++.-.... ........+..+++..+ ...|+||||.=
T Consensus        84 --~G~l~~i~~~~~~~-~~~~~~~~L~~ll~~~~~~~~dvIIIDSl  126 (230)
T PRK08533         84 --SGKLLYIPVYPLLS-GNSEKRDFLDKLMNTRRFYEKDVVIIDSL  126 (230)
T ss_pred             --CCCEEEEECCCCCC-CHHHHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             --79679996134335-40457899999973266437989999053


No 256
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=95.73  E-value=0.15  Score=28.65  Aligned_cols=97  Identities=16%  Similarity=0.131  Sum_probs=56.3

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCH---HHCCCCCCCCHHHHHCCCCCHHHHHHHH
Q ss_conf             6753799974698877568999999999962699499997879898603---3438998789888631845612433765
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTAN---INFDKDPINSISDAIYPVGRIDKAFVSR  235 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~---~~l~~~~~~~l~d~l~~~~rlD~~~l~~  235 (427)
                      ..|.++.+.| --|+||||+|.+++++-++ .|.+++++-++-.-..+-   ..+|.+                   ++.
T Consensus       264 ~~GsstLi~G-p~GtGKTtla~qFl~~~a~-~GE~~l~~~FeE~~~~l~~~a~~~G~d-------------------l~~  322 (501)
T PRK09302        264 FRGSIILVSG-ATGTGKTLLVSKFAEAACR-RGERCLLFAFEESRAQLVRNATSWGID-------------------LEE  322 (501)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEEEEECCHHHHHHHHHHCCCC-------------------HHH
T ss_conf             5894699988-9998889999999999986-599089999967999999999973998-------------------488


Q ss_pred             HHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHH-CCCEEEECC
Q ss_conf             32024898068724876120320799999998999851-288899738
Q gi|254780725|r  236 LPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQ-IFPLVILDV  282 (427)
Q Consensus       236 ~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~-~yd~VIiD~  282 (427)
                      +..  ...|.+.........    ..+.+..+.+...+ ....||||-
T Consensus       323 ~~~--~G~l~i~~~~p~~~~----~~e~~~~i~~~v~~~~~~rVvIDs  364 (501)
T PRK09302        323 MER--KGLLKIICARPESTG----LEDHLQIIKREIEEFKPSRVAVDP  364 (501)
T ss_pred             HHH--CCCEEEEEECCCCCC----HHHHHHHHHHHHHHCCCCEEEECC
T ss_conf             874--894799983700059----899999999999972998999958


No 257
>cd04144 Ras2 Ras2 subfamily.  The Ras2 subfamily, found exclusively in fungi, was first identified in Ustilago maydis.  In U. maydis, Ras2 is regulated by Sql2, a protein that is homologous to GEFs (guanine nucleotide exchange factors) of the CDC25 family.  Ras2 has been shown to induce filamentous growth, but the signaling cascade through which Ras2 and Sql2 regulate cell morphology is not known.  Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid.  Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.
Probab=95.70  E-value=0.081  Score=30.35  Aligned_cols=135  Identities=17%  Similarity=0.208  Sum_probs=76.7

Q ss_pred             CCCEEEECCCCCCC--HHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHC---CCCCCCCEEEEECCCCCCCCHHH
Q ss_conf             28889973888889--899999862012543578-7768899999999999981---98767538999565898752005
Q gi|254780725|r  274 IFPLVILDVPHVWN--SWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKL---RPADKPPYLVLNQVKTPKKPEIS  347 (427)
Q Consensus       274 ~yd~VIiD~p~~~~--~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~---~~~~~~~~iVlNr~~~~~~~~i~  347 (427)
                      .+.+-|+|++..-.  ......+..||.+++|.. -+..|+.+...+.+.+...   .....++.+|-|+++......++
T Consensus        46 ~~~l~iwDtaG~e~~~~l~~~~~r~a~~~ilVydvtd~~SF~~l~~w~~~i~~~~~~~~~~~piiLVGNK~Dl~~~r~V~  125 (190)
T cd04144          46 PCMLEVLDTAGQEEYTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVYEREVS  125 (190)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHCCCCC
T ss_conf             99999998999731167889982367658999727977899999999999999853379995289514553503305789


Q ss_pred             HHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             9999998489537990687999999884796189888999--89999999999985221223211105899998742340
Q gi|254780725|r  348 ISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMGRVTVSKPQSAMYTKIKKIFNMKC  425 (427)
Q Consensus       348 ~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~rk~  425 (427)
                      .++                .+  .-|...|....|.+.+.  -+-+.|..|++.|..+.............-+..-++||
T Consensus       126 ~~e----------------~~--~~a~~~~~~~~E~SAk~~~nV~e~F~~l~~~i~~~~~~~~~~~~~~~~~~~~~k~~c  187 (190)
T cd04144         126 TEE----------------GA--ALARRLGCEFIEASAKTNVNVERAFYTLVRALRQQRQGGQGPKGGPTKKKEKKKRKC  187 (190)
T ss_pred             HHH----------------HH--HHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf             999----------------99--999980998999735888097999999999999877435788888776778789888


Q ss_pred             C
Q ss_conf             3
Q gi|254780725|r  426 F  426 (427)
Q Consensus       426 ~  426 (427)
                      +
T Consensus       188 ~  188 (190)
T cd04144         188 V  188 (190)
T ss_pred             E
T ss_conf             7


No 258
>PRK03846 adenylylsulfate kinase; Provisional
Probab=95.70  E-value=0.023  Score=33.74  Aligned_cols=63  Identities=25%  Similarity=0.235  Sum_probs=44.7

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCC
Q ss_conf             456753799974698877568999999999962699499997879898603343899878988863184
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPV  225 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~  225 (427)
                      .+..|.+|=++| -.|.||||+|-.|...|.. .+.+++++|.|---.    .|+.+..++..+-..+.
T Consensus        20 ~~~kg~viWlTG-LSGSGKTTlA~~L~~~L~~-~~~~~~~LDGD~lR~----~l~~dlgfs~~dR~~n~   82 (198)
T PRK03846         20 HGHKGVVLWFTG-LSGSGKSTVAGALEEALHE-LGVHTYLLDGDNVRH----GLCSDLGFSDADRKENI   82 (198)
T ss_pred             HCCCCEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEECHHHHHH----HHCCCCCCCHHHHHHHH
T ss_conf             689986999879-9999889999999999997-599759977799987----43667898999999999


No 259
>cd01861 Rab6 Rab6 subfamily.  Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate
Probab=95.69  E-value=0.16  Score=28.58  Aligned_cols=110  Identities=18%  Similarity=0.174  Sum_probs=72.1

Q ss_pred             HCCCEEEECCCCCCC--HHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             128889973888889--899999862012543578-77688999999999999819876753899956589875200599
Q gi|254780725|r  273 QIFPLVILDVPHVWN--SWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       273 ~~yd~VIiD~p~~~~--~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      ..+.+-|+|++....  ......+..+|.+++|.. -+..|+.++.++++.++.......++.+|-|+.+......++.+
T Consensus        47 ~~~~l~i~D~~g~e~~~~~~~~~~~~~~~~ilvfd~t~~~Sf~~~~~w~~~i~~~~~~~~~ivlvGnK~Dl~~~r~v~~~  126 (161)
T cd01861          47 KTVRLQLWDTAGQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDKRQVSTE  126 (161)
T ss_pred             EEEEEEEEECCCCHHHHHHHHHHHHHHCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHCCCCCHH
T ss_conf             99999999799853157888988665258999984799899999999999999865789849996102110221778999


Q ss_pred             HHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHH
Q ss_conf             99998489537990687999999884796189888999--8999999999998
Q gi|254780725|r  350 DFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVL  400 (427)
Q Consensus       350 ~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i  400 (427)
                      +                  ...-|...|-+..|.+.++  -+.+.|..||+.|
T Consensus       127 e------------------~~~~a~~~~~~y~E~Sak~~~nV~e~F~~la~~l  161 (161)
T cd01861         127 E------------------GEKKAKELNAMFIETSAKAGHNVKELFRKIASAL  161 (161)
T ss_pred             H------------------HHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHC
T ss_conf             9------------------9999998499899983477808899999999709


No 260
>TIGR02868 CydC ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC; InterPro: IPR014223   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    This entry represents CydC, a member of a heterodimeric ATP-binding cassette-type transporter (ABC transporter). It is involved in the export of glutathione from the cytoplasm to the periplasm and is required for the assembly of both cytochrome c and cytochrome bd , , .; GO: 0042626 ATPase activity coupled to transmembrane movement of substances, 0006810 transport, 0016021 integral to membrane.
Probab=95.67  E-value=0.05  Score=31.62  Aligned_cols=60  Identities=18%  Similarity=0.253  Sum_probs=42.1

Q ss_pred             CCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             1899989999976310233222345675379997469887756899999999996269949999787989
Q gi|254780725|r  134 IEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       134 ~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      -||-+.....+.|.=        .-+.|+.|+|+| ..|+||||++.-|+-.|.=. +-+|.|=|.+++.
T Consensus       368 ~~pg~~~~vl~~V~L--------~l~~G~r~Ai~G-~SG~GKsTLL~~L~G~l~P~-~G~vtl~G~~~~~  427 (566)
T TIGR02868       368 GYPGAPPNVLDGVSL--------DLPPGERVAILG-PSGSGKSTLLATLAGLLDPL-QGEVTLDGVPVSS  427 (566)
T ss_pred             ECCCCCHHHHCCCCC--------CCCCCCCEEEEC-CCCCCHHHHHHHHHHHCCCC-CCCEEECCCCHHH
T ss_conf             269873465427864--------113886089866-88765789999998402899-9917877732432


No 261
>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional
Probab=95.67  E-value=0.035  Score=32.57  Aligned_cols=67  Identities=12%  Similarity=0.086  Sum_probs=45.3

Q ss_pred             HCCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCC
Q ss_conf             1288899738888--89899999862012543578776889999999999998198767538999565898
Q gi|254780725|r  273 QIFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTP  341 (427)
Q Consensus       273 ~~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~  341 (427)
                      ..+.|+|+|+|..  +..........||..++|+..+-.-+.++++-+..++.++.  +.+.+++|+++.-
T Consensus       105 ~~r~~~i~DaPGH~~f~~NMitGas~aD~aiLvVdA~~G~~~QTreH~~i~~llGI--~~iIVaVNKMDlV  173 (475)
T PRK05124        105 EKRKFIIADTPGHEQYTRNMATGASTCDLAILLIDARKGVLDQTRRHSFIATLLGI--KHLVVAVNKMDLV  173 (475)
T ss_pred             CCEEEEEEECCCHHHHHHHHHHHHHHCCEEEEEEECCCCCHHHHHHHHHHHHHCCC--CEEEEEEECHHCC
T ss_conf             87689997379638778889888876788999998988947888999999986599--8599998504313


No 262
>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]
Probab=95.64  E-value=0.13  Score=29.09  Aligned_cols=48  Identities=15%  Similarity=0.126  Sum_probs=40.3

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             45675379997469887756899999999996269949999787989860
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      .-+.|+++.|.| .-|+|||+++.++++..++. |.+|++|-++-...++
T Consensus        19 G~p~g~~~lI~G-~pGsGKT~f~~qfl~~~~~~-ge~vlyvs~~e~~~~l   66 (260)
T COG0467          19 GLPRGSVVLITG-PPGTGKTIFALQFLYEGARE-GEPVLYVSTEESPEEL   66 (260)
T ss_pred             CCCCCCEEEEEE-CCCCCHHHHHHHHHHHHHHC-CCEEEEEEEECCHHHH
T ss_conf             988997899993-89986899999999977626-9858999920698999


No 263
>pfam03205 MobB Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
Probab=95.64  E-value=0.038  Score=32.35  Aligned_cols=42  Identities=14%  Similarity=0.211  Sum_probs=33.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCE-EEEECCCCCCCC
Q ss_conf             79997469887756899999999996269949-999787989860
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMET-LLADLDLPYGTA  206 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~V-lLvDlDl~~g~~  206 (427)
                      +|.|+|. -++||||++-.|...+.+ .|.++ +++|+|+..+..
T Consensus         2 ~v~i~G~-~~sGKttl~~~L~~~~~~-~g~~~~~~~~~d~gq~~~   44 (122)
T pfam03205         2 IVLVVGP-KDSGKTTLIRKLLNYLKR-RGYRVAVVKHLDHGQGEI   44 (122)
T ss_pred             EEEEECC-CCCCHHHHHHHHHHHHHH-CCCCEEEEEECCCCCCCC
T ss_conf             7999948-999899999999999998-799448999899998776


No 264
>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
Probab=95.62  E-value=0.038  Score=32.34  Aligned_cols=13  Identities=8%  Similarity=0.082  Sum_probs=7.9

Q ss_pred             HHHCCCEEEECCC
Q ss_conf             8512888997388
Q gi|254780725|r  271 LEQIFPLVILDVP  283 (427)
Q Consensus       271 l~~~yd~VIiD~p  283 (427)
                      .+..-.||+||--
T Consensus       391 n~~tGsFILID~~  403 (613)
T PRK05506        391 NRTTGSFILIDRL  403 (613)
T ss_pred             CCCCCCEEEEECC
T ss_conf             8666658999889


No 265
>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export.  They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins.  The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities.  The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD).  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=95.54  E-value=0.052  Score=31.51  Aligned_cols=41  Identities=24%  Similarity=0.358  Sum_probs=29.0

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             6753799974698877568999999999962699499997879
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDL  201 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl  201 (427)
                      +.|.+++++| +-|+||||+.--+.-.+.-. ..++.+-+-|+
T Consensus        26 ~~Ge~i~ivG-~sGsGKSTLl~ll~gl~~p~-~G~I~i~g~~i   66 (171)
T cd03228          26 KPGEKVAIVG-PSGSGKSTLLKLLLRLYDPT-SGEILIDGVDL   66 (171)
T ss_pred             CCCCEEEEEC-CCCCHHHHHHHHHHCCCCCC-CCEEEECCEEC
T ss_conf             5998999999-99983999999997677589-74899999998


No 266
>cd04125 RabA_like RabA-like subfamily.  RabA was first identified in D. discoideum, where its expression levels were compared to other Rabs in growing and developing cells.  The RabA mRNA levels were below the level of detection by Northern blot analysis, suggesting a very low level of expression.  The function of RabA remains unknown.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
Probab=95.54  E-value=0.13  Score=29.05  Aligned_cols=116  Identities=12%  Similarity=0.121  Sum_probs=76.8

Q ss_pred             HCCCEEEECCCCCCC--HHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             128889973888889--899999862012543578-77688999999999999819876753899956589875200599
Q gi|254780725|r  273 QIFPLVILDVPHVWN--SWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       273 ~~yd~VIiD~p~~~~--~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      ..+.+-|+|++..-.  ......+..||.+++|.+ -+..|+.+...+++.++...+...++.+|-|+.+......++.+
T Consensus        47 ~~~~l~iwDtaG~e~~~~l~~~~~~~a~~~ilvydit~~~Sf~~l~~w~~~i~~~~~~~~~iilvgNK~DL~~~r~V~~~  126 (188)
T cd04125          47 KIIKLQIWDTNGQERFRSLNNSYYRGAHGYLLVYDVTDQESFENLKFWINEINRYARENVIKVIVANKSDLVNNKVVDSN  126 (188)
T ss_pred             EEEEEEEEECCCCHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCHHHHHHCCCCCHH
T ss_conf             99999999899971045789998637867999803898789999999999999878986624510013447660679999


Q ss_pred             HHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHCCCCC
Q ss_conf             99998489537990687999999884796189888999--8999999999998522122
Q gi|254780725|r  350 DFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMGRVTV  406 (427)
Q Consensus       350 ~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~gr~~~  406 (427)
                      +.                  -.-|...|-+..|.+.+.  -+-+.|..|++.+..+...
T Consensus       127 e~------------------~~~a~~~~~~~~E~SAktg~nV~e~F~~l~~~i~~~~~~  167 (188)
T cd04125         127 IA------------------KSFCDSLNIPFFETSAKQSINVEEAFILLVKLIIKRLEE  167 (188)
T ss_pred             HH------------------HHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             99------------------999998699899974788909899999999999998761


No 267
>PRK03003 engA GTP-binding protein EngA; Reviewed
Probab=95.49  E-value=0.19  Score=28.13  Aligned_cols=192  Identities=16%  Similarity=0.166  Sum_probs=107.3

Q ss_pred             CCEEE--EECCCCCC-CHHHHHHHHHHHCCCCCEEEEEECCCC----HHHHHHHHHCCCCEEECC----CCCHHHHHHHH
Q ss_conf             84999--98059876-778899988853289980899816871----899999997656264318----99989999976
Q gi|254780725|r   78 PDLII--VQTKVDSR-EVLSALEPLAEVCDSGTKVIVIGDTND----VSLYRALISNHVSEYLIE----PLSVADIINSI  146 (427)
Q Consensus        78 P~~ii--vd~~~~~~-~~~~~l~~la~~~~p~~~Vivig~~~d----~~l~r~l~r~Gv~dyl~~----P~~~~~l~~ai  146 (427)
                      -++|+  ||....-. .-.+-.+.|..   .+.+|+++-.--|    -..+-+..+.|..+.+.-    -....+|.+.+
T Consensus       118 aD~IlfVvD~~~glt~~D~eia~~LRk---~~kpviLVvNK~D~~~~~~~~~efy~LGf~~~i~ISA~Hg~Gi~dLld~i  194 (474)
T PRK03003        118 ADAVLFVVDATVGATATDEAVARLLRR---SGKPVFLAANKVDSERGEADAAALWSLGLGEPHPVSALHGRGVADLLDAV  194 (474)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHH---CCCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEHHCCCCHHHHHHHH
T ss_conf             999999996898988789999999875---39977998675566210234899997579986996020378979999999


Q ss_pred             HHCCCCCC--CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCC
Q ss_conf             31023322--2345675379997469887756899999999996269949999787989860334389987898886318
Q gi|254780725|r  147 SAIFTPQE--EGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYP  224 (427)
Q Consensus       147 ~~~~~~~~--~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~  224 (427)
                      ...+....  ........-||++| |..+||||+.-.    |..  ..+++ +  +...|++-            |.   
T Consensus       195 ~~~l~~~~~~~~~~~~~~rIAIvG-rPNvGKStL~N~----llg--~~r~i-v--s~~~GTTR------------Ds---  249 (474)
T PRK03003        195 LAALPEVPEVGSAVGGPRRVALVG-KPNVGKSSLLNK----LAG--EERSV-V--HDVAGTTV------------DP---  249 (474)
T ss_pred             HHHCCCCCCCCCCCCCCCEEEEEC-CCCCCHHHHHHH----HHC--CCCEE-E--CCCCCCCC------------CC---
T ss_conf             974877664433457762799980-899878899999----858--97567-4--58998515------------44---


Q ss_pred             CCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC-------------CHHHH
Q ss_conf             45612433765320248980687248761203207999999989998512888997388888-------------98999
Q gi|254780725|r  225 VGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVW-------------NSWTQ  291 (427)
Q Consensus       225 ~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~-------------~~~~~  291 (427)
                         ++..+                                      -.....|+++|++..-             ..-+.
T Consensus       250 ---I~~~~--------------------------------------~~~~~~~~liDTAGiRrk~kv~~~iE~~s~~rtl  288 (474)
T PRK03003        250 ---VDSLI--------------------------------------ELGGKVWRFVDTAGLRRKVGQASGHEFYASLRTH  288 (474)
T ss_pred             ---EEEEE--------------------------------------EECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             ---05899--------------------------------------9999899999898766355334314589999999


Q ss_pred             HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCC
Q ss_conf             99862012543578776889999999999998198767538999565898
Q gi|254780725|r  292 EVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTP  341 (427)
Q Consensus       292 ~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~  341 (427)
                      .++..||.+++|++.+..--..=.+++..+.+.+   +.+.+++|+++.-
T Consensus       289 ~aI~~advvilviDa~egit~QD~~Ia~~v~~~g---k~~IivvNKwDLv  335 (474)
T PRK03003        289 AAIDAAEVAVVLIDASEPLTEQDQRVLSMVIEAG---RALVLAFNKWDLV  335 (474)
T ss_pred             HHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHHC---CCEEEEEECHHCC
T ss_conf             9987335579998546587499999999999809---9579999714416


No 268
>cd04117 Rab15 Rab15 subfamily.  Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic trafficking.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.  Due to
Probab=95.47  E-value=0.18  Score=28.28  Aligned_cols=110  Identities=9%  Similarity=0.112  Sum_probs=74.0

Q ss_pred             HCCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             12888997388888--9899999862012543578-77688999999999999819876753899956589875200599
Q gi|254780725|r  273 QIFPLVILDVPHVW--NSWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       273 ~~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      ..+.+-|.|++...  .......+..|+.+++|.+ -+..|+.+...+++.+.+..+...++.+|-|+++.....+++  
T Consensus        47 ~~i~l~iwDtaGqe~~~~~~~~y~r~a~~~ilvyDvt~~~Sf~~l~~w~~~i~~~~~~~~~~ilVgNK~Dl~~~r~v~--  124 (161)
T cd04117          47 IKVRIQIWDTAGQERYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQKRQVG--  124 (161)
T ss_pred             EEEEEEEEECCCCCCCCCCHHHHHHHHCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCHHHCCCCC--
T ss_conf             999999997999602363558887641688996148988999999999999998789986499987327878627799--


Q ss_pred             HHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHH
Q ss_conf             99998489537990687999999884796189888999--8999999999998
Q gi|254780725|r  350 DFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVL  400 (427)
Q Consensus       350 ~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i  400 (427)
                                     .+ +...-|...|.+..|.+.+.  -+-+.|..|++.|
T Consensus       125 ---------------~~-~~~~~a~~~~~~~~etSAk~~~nV~e~F~~l~~~i  161 (161)
T cd04117         125 ---------------DE-QGNKLAKEYGMDFFETSACTNSNIKESFTRLTELV  161 (161)
T ss_pred             ---------------HH-HHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHC
T ss_conf             ---------------99-99999998699799967789829899999999649


No 269
>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=95.45  E-value=0.12  Score=29.27  Aligned_cols=41  Identities=12%  Similarity=0.290  Sum_probs=27.5

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             67537999746988775689999999999626994999978798
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      +.|.+++++| +.|+||||++--+.... -. ..++.+=+-|+.
T Consensus       374 ~~Ge~vaIVG-~SGsGKSTl~~LL~g~~-p~-~G~I~i~g~di~  414 (588)
T PRK11174        374 PAGQRVALVG-PSGAGKTSLLNALLGFL-PY-QGSLKINGIELR  414 (588)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHHHC-CC-CCEEEECCEECC
T ss_conf             4997899989-99864999999998728-98-838999998603


No 270
>smart00382 AAA ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Probab=95.45  E-value=0.039  Score=32.29  Aligned_cols=41  Identities=22%  Similarity=0.237  Sum_probs=32.0

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             5379997469887756899999999996269949999787989
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      ++.+.++| .-|+||||++..+|..+... ...++.++.+...
T Consensus         2 ~~~ill~G-~~GsGKTtl~~~la~~~~~~-~~~v~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVG-PPGSGKTTLARALARELGPP-GGGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEEC-CCCHHHHHHHHHHHHHHCCC-CCCEEEEEHHHHH
T ss_conf             97899999-99702999999999872668-9968998759989


No 271
>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.
Probab=95.44  E-value=0.052  Score=31.54  Aligned_cols=40  Identities=18%  Similarity=0.275  Sum_probs=35.7

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             379997469887756899999999996269949999787989
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      |+|+|+| .-|+||||+...|...|.. +|.+|..|=.|.+.
T Consensus         2 kii~ivG-~snSGKTTLi~kli~~l~~-~G~~V~~iKH~~H~   41 (159)
T cd03116           2 KVIGFVG-YSGSGKTTLLEKLIPALSA-RGLRVAVIKHDHHD   41 (159)
T ss_pred             EEEEEEE-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEECCCC
T ss_conf             2999996-7999999999999999997-79859899734767


No 272
>cd01865 Rab3 Rab3 subfamily.  The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D.  All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression.  Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules.  Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promot
Probab=95.43  E-value=0.19  Score=28.01  Aligned_cols=111  Identities=11%  Similarity=0.102  Sum_probs=75.3

Q ss_pred             CCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             288899738888--898999998620125435787-76889999999999998198767538999565898752005999
Q gi|254780725|r  274 IFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      .+.+-++|++..  ........+..+|-+++|.+. +..|+.+...+++.++...+...++.+|-|+.+......++.++
T Consensus        49 ~i~l~iwDtaGqe~~~~l~~~y~~~a~~~ilvydit~~~Sf~~~~~w~~~i~~~~~~~~~iilvgNK~DL~~~r~v~~~~  128 (165)
T cd01865          49 RVKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDMEDERVVSSER  128 (165)
T ss_pred             EEEEEEEECCCCCCCCCCHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHCCCCCHHH
T ss_conf             99999996999834554415441135448998517887999999999999998689872599960242355518899999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHC
Q ss_conf             9998489537990687999999884796189888999--899999999999852
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMG  402 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~g  402 (427)
                      .                  -.-|...|.+..|.+.+.  -+.+.|..|++.|..
T Consensus       129 ~------------------~~~a~~~~~~~~E~SAk~~~nV~e~F~~l~~~i~~  164 (165)
T cd01865         129 G------------------RQLADQLGFEFFEASAKENINVKQVFERLVDIICD  164 (165)
T ss_pred             H------------------HHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHC
T ss_conf             9------------------99999869979997689890889999999999962


No 273
>cd00477 FTHFS Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2 fixation (acetogenesis) and the glycine synthase/reductase pathways of purinolysis. The key physiological role of this enzyme in acetogens is to catalyze the formylation of tetrahydrofolate, an initial step in the reduction of carbon dioxide and other one-carbon precursors to acetate. In purinolytic organisms, the enzymatic reaction is reversed, liberating formate from 10-formyltetrahydrofolate with concurrent production of ATP.
Probab=95.40  E-value=0.2  Score=27.93  Aligned_cols=100  Identities=14%  Similarity=0.220  Sum_probs=57.8

Q ss_pred             CCCHHHHH----HHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHH-HHHHHHHHCCCEEEEECCC---------HHHH
Q ss_conf             87768899----99999999998198767538999565898752005-9999998489537990687---------9999
Q gi|254780725|r  305 SLDLAGLR----NSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEIS-ISDFCAPLGITPSAIIPFD---------GAVF  370 (427)
Q Consensus       305 ~p~~~slr----~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~-~~~~~~~lg~~~~~~IP~D---------~~~~  370 (427)
                      ++++..++    |..+-++-+++.+   -++.+.+|++......|+. .+++++..|.+....=.|.         -+.+
T Consensus       332 ~en~~al~~G~~NL~~Hi~N~~~fg---vpvVVAIN~F~~DT~~Ei~~i~~~~~~~G~~~av~~~~a~GG~Ga~~LA~~V  408 (524)
T cd00477         332 EENLEALEKGFANLRKHIENIKKFG---VPVVVAINKFSTDTDAELALVRKLAEEAGAFVAVSEHWAEGGKGAVELAEAV  408 (524)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCC---CCEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEECHHHHCCCCHHHHHHHH
T ss_conf             6699999978766999998898628---9759995378998689999999999977996998062551551089999999


Q ss_pred             HHHHHCCCCEE-EECCCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf             99884796189-88899989999999999985221223
Q gi|254780725|r  371 GMSANSGKMIH-EVDPKSAIANLLVDFSRVLMGRVTVS  407 (427)
Q Consensus       371 ~~A~~~G~pi~-e~~p~s~~a~~~~~La~~i~gr~~~~  407 (427)
                      .++..+..++- .+...-++.+-+..+|++|.|.....
T Consensus       409 v~~~~~~~~f~~lY~~~~~l~eKI~~IA~~IYgA~~V~  446 (524)
T cd00477         409 IEACEQPSEFKFLYDLEDPLEDKIETIAKKIYGADGVE  446 (524)
T ss_pred             HHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEE
T ss_conf             99860788866657999999999999999735988587


No 274
>PRK05973 replicative DNA helicase; Provisional
Probab=95.39  E-value=0.18  Score=28.22  Aligned_cols=45  Identities=16%  Similarity=0.253  Sum_probs=34.6

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             75379997469887756899999999996269949999787989860
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA  206 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~  206 (427)
                      .|-.| +++++-|.|||+++.|+|+..++ .|+.|++.-+......+
T Consensus        63 PGDLI-IlAARPsMGKTafaLnla~~A~k-~g~~v~fFSLEM~~~ql  107 (237)
T PRK05973         63 PGDLV-LLGARPGQGKTLLGLELAVEAMK-SGRTGVFFTLEYTEKDV  107 (237)
T ss_pred             CCCEE-EEECCCCCCHHHHHHHHHHHHHH-HCCCEEEEEECCCHHHH
T ss_conf             86779-99428988789999999999999-59966999615999999


No 275
>cd03252 ABCC_Hemolysin The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E. coli.  The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane.  HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB.  This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport.  Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.
Probab=95.37  E-value=0.045  Score=31.91  Aligned_cols=42  Identities=24%  Similarity=0.321  Sum_probs=28.9

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             67537999746988775689999999999626994999978798
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      +.|..++++| +-|.||||+.--|.-.+.-. ..++.+=+.|+.
T Consensus        26 ~~G~~vaivG-~sGsGKSTll~ll~gl~~p~-~G~I~i~g~di~   67 (237)
T cd03252          26 KPGEVVGIVG-RSGSGKSTLTKLIQRFYVPE-NGRVLVDGHDLA   67 (237)
T ss_pred             CCCCEEEEEC-CCCCHHHHHHHHHHCCCCCC-CCEEEECCEECC
T ss_conf             7999999999-99985999999996776579-878999999955


No 276
>pfam01268 FTHFS Formate--tetrahydrofolate ligase.
Probab=95.35  E-value=0.21  Score=27.84  Aligned_cols=89  Identities=15%  Similarity=0.260  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHH-HHHHHHHHCCCEEEEECCC---------HHHHHHHHHCC---CCE
Q ss_conf             9999999998198767538999565898752005-9999998489537990687---------99999988479---618
Q gi|254780725|r  314 SKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEIS-ISDFCAPLGITPSAIIPFD---------GAVFGMSANSG---KMI  380 (427)
Q Consensus       314 a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~-~~~~~~~lg~~~~~~IP~D---------~~~~~~A~~~G---~pi  380 (427)
                      ..+-++-+++.+   -++.+.+|++......|+. .+++++..|.+....=.|.         -+.+.++....   +++
T Consensus       360 L~~Hi~N~~~fG---~pvVVAIN~F~~DT~~Ei~~i~~~~~~~g~~~~~s~~wa~GG~Ga~~LA~~Vv~~~~~~~~f~~l  436 (555)
T pfam01268       360 LEKHIENVKKFG---VPVVVAINRFPTDTDAELALVRELCEEAGAEAAVSEHWAKGGEGAIELAEAVVEACEKPSNFKPL  436 (555)
T ss_pred             HHHHHHHHHHCC---CCEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEEHHHCCCCCHHHHHHHHHHHHCCCCCCCCC
T ss_conf             999999999719---97699944789987999999999999869989994045405767699999999996088887665


Q ss_pred             EEECCCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf             988899989999999999985221223
Q gi|254780725|r  381 HEVDPKSAIANLLVDFSRVLMGRVTVS  407 (427)
Q Consensus       381 ~e~~p~s~~a~~~~~La~~i~gr~~~~  407 (427)
                        +...-++.+-+..+|++|.|.....
T Consensus       437 --Y~~~~~l~eKIe~IA~~IYGA~~V~  461 (555)
T pfam01268       437 --YDLELSLEEKIETIATEIYGADGVE  461 (555)
T ss_pred             --CCCCCCHHHHHHHHHHHCCCCCCEE
T ss_conf             --7998899999999999715888577


No 277
>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional
Probab=95.25  E-value=0.037  Score=32.46  Aligned_cols=36  Identities=17%  Similarity=0.230  Sum_probs=26.6

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             67537999746988775689999999999626994999
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLL  196 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlL  196 (427)
                      +.|+.|+++| +-|+||||++-=|...+.-.. .++.+
T Consensus       359 ~~Ge~vaiVG-~SGsGKSTL~~LL~gly~p~~-G~I~i  394 (585)
T PRK13657        359 KPGQTVAIVG-PTGAGKSTLINLLHRVFDPQS-GRIRI  394 (585)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHHHCCCCC-CCEEE
T ss_conf             5998899988-989869999999860157887-96758


No 278
>PRK07667 uridine kinase; Provisional
Probab=95.23  E-value=0.066  Score=30.88  Aligned_cols=44  Identities=11%  Similarity=0.061  Sum_probs=33.5

Q ss_pred             CCCCE-EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             56753-79997469887756899999999996269949999787989
Q gi|254780725|r  158 GSSGC-SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       158 ~~~gr-vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      .+.+| +|++-| .+|+||||+|..|+..|.. .+.++.++-.|-..
T Consensus        10 ~~~~r~iIgIaG-~sgSGKTTla~~L~~~l~~-~~~~v~v~~~Dd~~   54 (190)
T PRK07667         10 HKENRFILGIDG-LSRSGKTTFVANLKENMKQ-EGIPFHIFHIDDHI   54 (190)
T ss_pred             CCCCEEEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCC
T ss_conf             759869999779-8978899999999999866-59837999666242


No 279
>pfam00931 NB-ARC NB-ARC domain.
Probab=95.22  E-value=0.016  Score=34.72  Aligned_cols=25  Identities=28%  Similarity=0.453  Sum_probs=20.8

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             75379997469887756899999999
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFS  185 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~  185 (427)
                      .-+||+++| -||+||||+|..+-..
T Consensus        18 ~~~vI~I~G-~gGiGKTtLA~~v~~~   42 (285)
T pfam00931        18 NLGVVGIVG-MGGVGKTTLAKQIYND   42 (285)
T ss_pred             CCEEEEEEC-CCCCCHHHHHHHHHCC
T ss_conf             953999889-9956399999999716


No 280
>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).
Probab=95.22  E-value=0.038  Score=32.33  Aligned_cols=40  Identities=20%  Similarity=0.305  Sum_probs=33.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCC
Q ss_conf             799974698877568999999999962699499997879898
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYG  204 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g  204 (427)
                      +|++.| -.|+||||+|..|+..|.. .+.++.++-+|-..-
T Consensus         1 iIgIaG-~SgSGKTT~a~~L~~~l~~-~~~~~~vis~D~yy~   40 (179)
T cd02028           1 VVGIAG-PSGSGKTTFAKKLSNQLRV-NGIGPVVISLDDYYV   40 (179)
T ss_pred             CEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCC
T ss_conf             989989-8977899999999999846-488539995466645


No 281
>TIGR03172 probable selenium-dependent hydroxylase accessory protein YqeC. This uncharacterized protein family includes YqeC from Escherichia coli. A phylogenetic profiling analysis shows correlation with SelD, the selenium donor protein, even in species where SelD contributes to neither selenocysteine nor selenouridine biosynthesis. Instead, this family, and families TIGR03309 and TIGR03310 appear to mark selenium-dependent molybdenum hydroxylase maturation systems.
Probab=95.21  E-value=0.23  Score=27.58  Aligned_cols=127  Identities=13%  Similarity=0.147  Sum_probs=61.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886318456124337653202489
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAE  242 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~  242 (427)
                      ||+|+|+   =||||+-..||..+.. .|++|++-      -|+.+++-....+.  ..+...+   ...... ..+...
T Consensus         1 VIs~VGa---GGKTS~m~~LA~e~~~-~G~~VlvT------TTT~m~~P~~~~~~--~~~~~~d---~~~~~~-~~~~~~   64 (232)
T TIGR03172         1 VIAFVGA---GGKTSTMFWLAAEYRK-EGYRVLVT------TTTRMFLPEPPLYD--YFLTSHD---GWVRDQ-VTKDTP   64 (232)
T ss_pred             CEEEECC---CCHHHHHHHHHHHHHH-CCCCEEEE------CCCCCCCCCCCCCC--EEEECCH---HHHHHH-HHCCCC
T ss_conf             9899889---8799999999999987-69909998------89665678700166--2650625---777777-650466


Q ss_pred             CE--EEEEC-CCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCC-------CCCHHHHHHHHHCCCCCCCCCCC
Q ss_conf             80--68724-87612032079999999899985128889973888-------88989999986201254357877
Q gi|254780725|r  243 NL--SILTA-PAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPH-------VWNSWTQEVLTLSDKVVITTSLD  307 (427)
Q Consensus       243 gL--~lL~a-~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~-------~~~~~~~~~L~~AD~vviV~~p~  307 (427)
                      ..  ...++ +..-.....++++.+..+.+  ...||+|+|-.-.       .|..+-...-..+|.|+.|+..+
T Consensus        65 ~~~~~~~~~~~~~~~K~~g~~~e~~~~l~~--~~~~D~vLiEADGAk~~plKaP~~~EPvIP~~t~~VI~V~g~~  137 (232)
T TIGR03172        65 RIAGIEFSALPRVSGKVRGFTPSTVDDLSD--FQHFDVILVEADGAKCRPLKAPSDHEPVIPKSSTTVIGVAGIS  137 (232)
T ss_pred             CEEEEEEECCCCCCCCEECCCHHHHHHHHH--CCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEECHH
T ss_conf             414579840577689551689999999984--5667789997576578816488989994788788899970577


No 282
>PRK09518 bifunctional cytidylate kinase/GTP-binding protein; Reviewed
Probab=95.21  E-value=0.23  Score=27.57  Aligned_cols=79  Identities=8%  Similarity=0.024  Sum_probs=52.1

Q ss_pred             CCCEEEECCCCCC------C-------HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf             2888997388888------9-------89999986201254357877688999999999999819876753899956589
Q gi|254780725|r  274 IFPLVILDVPHVW------N-------SWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKT  340 (427)
Q Consensus       274 ~yd~VIiD~p~~~------~-------~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~  340 (427)
                      .-.|.+||+..--      .       .-+..++..||.+++|++.+..--.+=.+++..+.+.+   +.+.+|+|+++.
T Consensus       499 g~~~~lIDTAGiRkk~k~~~~iE~~S~~rt~~aI~~adVvllviDA~~git~QD~~Ia~~i~~~g---k~~IivvNKWDL  575 (714)
T PRK09518        499 GKDWLFVDTAGIRRKQKKLTGAEYYASLRTQAAIERCELALILFDASQPISEQDLRVMSMAVDAG---RALVLAFNKWDL  575 (714)
T ss_pred             CEEEEEEECHHCCCCCCCCCCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHHC---CCEEEEEECHHC
T ss_conf             97899998600152443254322799999999886588999998677675289999999999859---937999961430


Q ss_pred             CCCCHHHHHHHHHHHCC
Q ss_conf             87520059999998489
Q gi|254780725|r  341 PKKPEISISDFCAPLGI  357 (427)
Q Consensus       341 ~~~~~i~~~~~~~~lg~  357 (427)
                      -..  ...+.+++.+..
T Consensus       576 v~~--~~~~~~~~~i~~  590 (714)
T PRK09518        576 MDE--FRRQRLEREIDT  590 (714)
T ss_pred             CCH--HHHHHHHHHHHH
T ss_conf             686--689999999997


No 283
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=95.18  E-value=0.23  Score=27.52  Aligned_cols=111  Identities=15%  Similarity=0.176  Sum_probs=71.4

Q ss_pred             CCCEEEECCCCCCC--HHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             28889973888889--8999998620125435787-76889999999999998198767538999565898752005999
Q gi|254780725|r  274 IFPLVILDVPHVWN--SWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~~~--~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      .+.+-++|++....  ......+..+|.+++|.+. +..|+.+...+++.++.......++.+|-|+.+.....+++.++
T Consensus        48 ~~~l~iwDt~G~e~~~~l~~~~~~~~~~~ilvfdi~~~~Sf~~i~~w~~~i~~~~~~~~piilvgnK~Dl~~~r~V~~~e  127 (164)
T smart00175       48 RVKLQIWDTAGQERFRSITSSYYRGAVGALLVYDITNRESFENLKNWLKELREYADPNVVIMLVGNKSDLEDQRQVSREE  127 (164)
T ss_pred             EEEEEEEECCCCHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCEEECCCCCCHHHHCCCCHHH
T ss_conf             99999996799446647799883366536884368998999999999999998679998255116456856518799999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHC
Q ss_conf             9998489537990687999999884796189888999--899999999999852
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMG  402 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~g  402 (427)
                      ..                  .-|...|.+..|.+.+.  -+.+.|..|++.+..
T Consensus       128 ~~------------------~~a~~~~~~~~e~SAk~~~~v~e~F~~l~~~i~k  163 (164)
T smart00175      128 AE------------------AFAEEHGLPFFETSAKTNTNVEEAFEELAREILK  163 (164)
T ss_pred             HH------------------HHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHC
T ss_conf             99------------------9999849979998316690889999999999971


No 284
>TIGR02012 tigrfam_recA protein RecA; InterPro: IPR001553   The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response . In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs . RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage .    RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved , ,  among eubacterial species. It is also found in the chloroplast of plants . RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, -strand 3, the loop C-terminal to -strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and -strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation [Lusetti and Cox, Annu. Rev. Biochem. 2002. 71:71-100.]. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between -strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at -strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at -strand 2 and the loop C-terminal to that strand, all of which are greater than 90
Probab=95.16  E-value=0.12  Score=29.25  Aligned_cols=46  Identities=20%  Similarity=0.190  Sum_probs=36.8

Q ss_pred             CCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             345675379997469887756899999999996269949999787989
Q gi|254780725|r  156 GKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       156 ~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      +.-+.||||=++|. --.||||+|.+.- +=++..|.-+..||....+
T Consensus        50 GG~P~GRi~EiYGp-ESsGKTTLal~~i-A~~Qk~Gg~~afiDAEHAl   95 (322)
T TIGR02012        50 GGLPKGRIIEIYGP-ESSGKTTLALHVI-AEAQKAGGVAAFIDAEHAL   95 (322)
T ss_pred             CCCCCCEEEEEECC-CCCCHHHHHHHHH-HHHHHCCCEEEEEECHHHC
T ss_conf             98987507998548-9884789999999-9997439838998451303


No 285
>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein.  In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor.  This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export.  The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD).  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=95.15  E-value=0.038  Score=32.34  Aligned_cols=43  Identities=16%  Similarity=0.278  Sum_probs=29.4

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             567537999746988775689999999999626994999978798
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      -+.|..++++| +-|+||||+.--+.-.+.-..| .+.+=+.|+.
T Consensus        26 i~~Ge~vaivG-~sGsGKSTLl~ll~gl~~p~~G-~I~idg~~i~   68 (229)
T cd03254          26 IKPGETVAIVG-PTGAGKTTLINLLMRFYDPQKG-QILIDGIDIR   68 (229)
T ss_pred             ECCCCEEEEEC-CCCCHHHHHHHHHHCCCCCCCC-EEEECCEECC
T ss_conf             87999999999-9998099999999668667873-8999999954


No 286
>cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules.  Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells.  Subsequently, virus-infected or malignantly transformed cells can be eliminated.  TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.
Probab=95.09  E-value=0.069  Score=30.77  Aligned_cols=28  Identities=21%  Similarity=0.271  Sum_probs=23.7

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             67537999746988775689999999999
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIA  187 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA  187 (427)
                      +.|++++++| .-|+||||++--+.-.+.
T Consensus        38 ~~Ge~vaIvG-~sGsGKSTL~~ll~gl~~   65 (226)
T cd03248          38 HPGEVTALVG-PSGSGKSTVVALLENFYQ   65 (226)
T ss_pred             CCCCEEEEEC-CCCCHHHHHHHHHHCCCC
T ss_conf             2999999999-999849999999964546


No 287
>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2.  Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhi
Probab=95.09  E-value=0.25  Score=27.34  Aligned_cols=111  Identities=14%  Similarity=0.145  Sum_probs=73.2

Q ss_pred             CCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             2888997388888--9899999862012543578-776889999999999998198767538999565898752005999
Q gi|254780725|r  274 IFPLVILDVPHVW--NSWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      .+.+-|.|++...  .......+..+|.+++|.+ -+..|+.+...+++.+.+......++.+|-|+++......++.++
T Consensus        51 ~i~l~iwDt~G~e~~~~~~~~y~~~a~~~ilvfdit~~~Sf~~~~~w~~~i~~~~~~~~~~ilVgNK~Dl~~~r~v~~~e  130 (167)
T cd01867          51 KIKLQIWDTAGQERFRTITTAYYRGAMGIILVYDITDEKSFENIRNWMRNIEEHASEDVERMLVGNKCDMEEKRVVSKEE  130 (167)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHCCCCCHHH
T ss_conf             99999998999700116679985650588995568987999999999999998669997057642124502307799999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHC
Q ss_conf             9998489537990687999999884796189888999--899999999999852
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMG  402 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~g  402 (427)
                      .+                  .-|...|.+..|.+.+.  -+.+.|..|++.|..
T Consensus       131 ~~------------------~~a~~~~~~~~e~SAktg~nI~e~F~~l~~~i~~  166 (167)
T cd01867         131 GE------------------ALADEYGIKFLETSAKANINVEEAFFTLAKDIKK  166 (167)
T ss_pred             HH------------------HHHHHHCCEEEEECCCCCCCHHHHHHHHHHHHHH
T ss_conf             99------------------9999809969998225790789999999999970


No 288
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=95.08  E-value=0.25  Score=27.33  Aligned_cols=117  Identities=14%  Similarity=0.145  Sum_probs=91.3

Q ss_pred             EEEEEEECCHHHHHHHHHHHHHHHHHHCEEE-EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHH-CCCC
Q ss_conf             0599983898999999988641100202237-3069989999998618998499998059876778899988853-2899
Q gi|254780725|r   29 ISVHVFCVTDTLYSVVERSKIDPRMSQVNMR-ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEV-CDSG  106 (427)
Q Consensus        29 ~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~-v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~-~~p~  106 (427)
                      ++|..--+++.-..++..-.++     -+.. ....+..+|++.+...+ +++|+.|+.||.+||++...++++. ....
T Consensus       669 lrVLvVEDN~iN~~vi~~lL~~-----lG~~v~~A~nG~eAle~~~~~~-fDLILMDiqMP~MDG~eATr~IR~~~~~~~  742 (920)
T PRK11107        669 LTVMAVDDNPANLKLIGALLEE-----QVEHVVLCDSGHQAVELAKQRP-FDLIFMDIQMPGMDGIRACELIRQLPHNQN  742 (920)
T ss_pred             CEEEEECCCHHHHHHHHHHHHH-----CCCEEEEECCHHHHHHHHHCCC-CCEEEECCCCCCCCHHHHHHHHHHCCCCCC
T ss_conf             7499984889999999999998-----4988999899999999974799-978998899999989999999981867898


Q ss_pred             CEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCC
Q ss_conf             808998168718999999976562643189998999997631023
Q gi|254780725|r  107 TKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFT  151 (427)
Q Consensus       107 ~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~  151 (427)
                      +|||+++.+.-..--.+++.+|.+|||.||++..+|...+.+...
T Consensus       743 ~PIIAlTA~a~~~dre~cl~aGMddyLtKPI~~~~L~~~L~~~~~  787 (920)
T PRK11107        743 TPIIAVTAHAMAGERERLLGAGMDDYLAKPIDEAALKQVLLRWKP  787 (920)
T ss_pred             CEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHHCC
T ss_conf             959999799898999999977999387287999999999998678


No 289
>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function.  Barmotin belongs to the SMC protein family.  SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains.  Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins.  The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases.  The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w
Probab=95.04  E-value=0.16  Score=28.48  Aligned_cols=28  Identities=21%  Similarity=0.462  Sum_probs=22.4

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHH
Q ss_conf             675379997469887756899999999996
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIAS  188 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~  188 (427)
                      +.| +++++| .-|+||||+.--+.+.+..
T Consensus        21 p~G-itaIvG-psGsGKSTLl~~i~~~lg~   48 (197)
T cd03278          21 PPG-LTAIVG-PNGSGKSNIIDAIRWVLGE   48 (197)
T ss_pred             CCC-EEEEEC-CCCCCHHHHHHHHHHHHCC
T ss_conf             898-289999-9999889999999987477


No 290
>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.
Probab=94.99  E-value=0.042  Score=32.12  Aligned_cols=54  Identities=26%  Similarity=0.136  Sum_probs=36.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHH
Q ss_conf             799974698877568999999999962699499997879898603343899878988863
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAI  222 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l  222 (427)
                      ||=|+| -.|+||||+|-.|.-.|.. .+.++.++|.|---.    .|+.+..++..+-.
T Consensus         1 ViW~tG-LsgsGKTTlA~~l~~~L~~-~~~~~~~lDGD~iR~----~l~~~lgys~~~R~   54 (149)
T cd02027           1 VIWLTG-LSGSGKSTIARALEEKLFQ-RGRPVYVLDGDNVRH----GLNKDLGFSREDRE   54 (149)
T ss_pred             CEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEECCHHHHH----HHCCCCCCCHHHHH
T ss_conf             989879-9999999999999999998-699759977488997----73655598878899


No 291
>PTZ00099 rab6; Provisional
Probab=94.98  E-value=0.27  Score=27.16  Aligned_cols=113  Identities=16%  Similarity=0.150  Sum_probs=78.8

Q ss_pred             CCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCC-HHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             288899738888--8989999986201254357877-6889999999999998198767538999565898752005999
Q gi|254780725|r  274 IFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLD-LAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~-~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      .+.+-|+|++..  +......-...|+-+++|..-+ ..|+.+...+++.+.+....+.++.+|-|+.+......++.++
T Consensus        28 ~v~l~IWDTAGqE~f~sl~~~y~r~a~~~ilVyDit~~~SF~~l~~W~~~i~~~~~~~~~iiLVGNK~DL~~~r~V~~ee  107 (176)
T PTZ00099         28 PVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEE  107 (176)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCHHHHCCCCHHH
T ss_conf             99999997998634135768870798679998504207789999999999998538877439998556558616859999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHCCC
Q ss_conf             9998489537990687999999884796189888999--89999999999985221
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMGRV  404 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~gr~  404 (427)
                                        ...-|...|.+..|.+.++  -+.+.|..||++|....
T Consensus       108 ------------------~~~~A~~~~~~f~EtSAktg~nV~e~F~~la~~i~~~~  145 (176)
T PTZ00099        108 ------------------GMQKAQEYNTMFHETSAKAGHNIKVLFKKIAAKLPNLD  145 (176)
T ss_pred             ------------------HHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHCCHH
T ss_conf             ------------------99999985999999848999498999999999860802


No 292
>cd01868 Rab11_like Rab11-like.  Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP
Probab=94.97  E-value=0.27  Score=27.14  Aligned_cols=109  Identities=9%  Similarity=0.065  Sum_probs=70.4

Q ss_pred             CCCEEEECCCCCCC--HHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             28889973888889--8999998620125435787-76889999999999998198767538999565898752005999
Q gi|254780725|r  274 IFPLVILDVPHVWN--SWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~~~--~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      .+.+-|+|++..-.  .....-+..++.+++|.+. +..|+.+...+++.++...+...++.+|-|+.+......++.++
T Consensus        51 ~~~l~iwDtaG~e~~~~~~~~~~~~a~~~ilvydit~~~Sf~~i~~w~~~i~~~~~~~~~iilVgnK~DL~~~r~Vs~~e  130 (165)
T cd01868          51 TIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKKQTFENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTEE  130 (165)
T ss_pred             EEEEEEEECCCCHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHCCCCHHH
T ss_conf             99999998999721267899873320514898626988999999999999998555773598702347868857888999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHH
Q ss_conf             9998489537990687999999884796189888999--8999999999998
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVL  400 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i  400 (427)
                      .                  -.-|..+|-+..|.+.++  -+.+.|..|+++|
T Consensus       131 ~------------------~~~a~~~~~~~~E~SAk~g~nV~e~F~~l~~~i  164 (165)
T cd01868         131 A------------------KAFAEKNGLSFIETSALDGTNVEEAFKQLLTEI  164 (165)
T ss_pred             H------------------HHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             9------------------999998599799967888929899999999986


No 293
>PRK07560 elongation factor EF-2; Reviewed
Probab=94.96  E-value=0.27  Score=27.12  Aligned_cols=18  Identities=6%  Similarity=0.054  Sum_probs=10.0

Q ss_pred             CCHHHHHHHHHHHHHCCC
Q ss_conf             799999998999851288
Q gi|254780725|r  259 FDEKMIVPVLDILEQIFP  276 (427)
Q Consensus       259 ~~~~~l~~ll~~l~~~yd  276 (427)
                      +.+-+++.+++.|++.|.
T Consensus       437 mGElHLei~~~rL~~~f~  454 (730)
T PRK07560        437 MGELHLEVITYRIKRDYG  454 (730)
T ss_pred             CCHHHHHHHHHHHHHHHC
T ss_conf             289999999999999848


No 294
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=94.95  E-value=0.079  Score=30.41  Aligned_cols=38  Identities=18%  Similarity=0.325  Sum_probs=32.8

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             7537999746988775689999999999626994999978
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADL  199 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDl  199 (427)
                      .++-+.++| +.|+|||.+|+.+|..+. ..|.+|+.+..
T Consensus       104 ~~~nl~l~G-~~G~GKthLa~Ai~~~l~-~~g~sv~f~~~  141 (254)
T COG1484         104 RGENLVLLG-PPGVGKTHLAIAIGNELL-KAGISVLFITA  141 (254)
T ss_pred             CCCCEEEEC-CCCCCHHHHHHHHHHHHH-HCCCEEEEEEH
T ss_conf             588289989-999879999999999999-83984999885


No 295
>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain.  They export degradative enzymes by using a type I protein secretion system and  lack an N-terminal signal peptide, but contain a C-terminal secretion signal.  The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP).  For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli.  The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior.  HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels.  The spectrum of transport substra
Probab=94.92  E-value=0.13  Score=29.18  Aligned_cols=36  Identities=28%  Similarity=0.316  Sum_probs=26.9

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             67537999746988775689999999999626994999
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLL  196 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlL  196 (427)
                      +.|..++++| .-|+||||+.--++-.+.-. ..++.+
T Consensus        26 ~~G~~vaIvG-~sGsGKSTLl~ll~gl~~p~-~G~i~i   61 (173)
T cd03246          26 EPGESLAIIG-PSGSGKSTLARLILGLLRPT-SGRVRL   61 (173)
T ss_pred             CCCCEEEEEC-CCCCHHHHHHHHHHCCCCCC-CCEEEE
T ss_conf             5999999999-99980999999996666679-998999


No 296
>pfam07755 DUF1611 Protein of unknown function (DUF1611). This region is found in a number of hypothetical bacterial and archaeal proteins. The region is approximately 350 residues long. A member of this family is thought to associate with another subunit to form an H+-transporting ATPase, but no evidence has been found to support this.
Probab=94.89  E-value=0.28  Score=27.01  Aligned_cols=247  Identities=17%  Similarity=0.181  Sum_probs=140.9

Q ss_pred             CCHHHHHHHHHCCCCCCEEEEECCCCCCCH-HHHHHHHHHHCCCCCEEEEEEC---CCCHHHHHHHHHCCCCEE-ECCCC
Q ss_conf             998999999861899849999805987677-8899988853289980899816---871899999997656264-31899
Q gi|254780725|r   63 GSIAEAVSCFSDSSTPDLIIVQTKVDSREV-LSALEPLAEVCDSGTKVIVIGD---TNDVSLYRALISNHVSEY-LIEPL  137 (427)
Q Consensus        63 g~~~~A~~~~~~~~~P~~iivd~~~~~~~~-~~~l~~la~~~~p~~~Vivig~---~~d~~l~r~l~r~Gv~dy-l~~P~  137 (427)
                      +++.+|.+     ..|+.+|+-+...+..+ -+-...+.+....|..|+---+   .+|..+...+-+.|+.=+ +.+|-
T Consensus        24 ~sl~eA~~-----~g~~~liiGiA~~GG~lp~~w~~~i~~Ai~~GldIvsGLH~~L~ddp~l~~~A~~~g~~i~DvR~p~   98 (302)
T pfam07755        24 SSLEEALA-----AGADTLIIGIAPSGGVLPEAWREVLLEALEAGLDVVSGLHEFLSDDPELAAAAKKHGVQIIDVRKPP   98 (302)
T ss_pred             CCHHHHHH-----CCCCEEEEEECCCCCCCCHHHHHHHHHHHHCCCCEEHHHHHHHHCCHHHHHHHHHCCCEEEEECCCC
T ss_conf             76999986-----6999899974168884898999999999982892623357775148989999998699799915899


Q ss_pred             CHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCC
Q ss_conf             98999997631023322234567537999746988775689999999999626994999978798986033438998789
Q gi|254780725|r  138 SVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINS  217 (427)
Q Consensus       138 ~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~  217 (427)
                      .  +    + .++..  ......+++|.++|.---+||=|.|..|..++-+ +|.++..+=-    |-++++..   .+|
T Consensus        99 ~--~----~-~~~~g--~~~~~~~~rvl~vGTDcavGK~tTal~l~~~l~~-~Gi~a~fiaT----GQTGili~---g~G  161 (302)
T pfam07755        99 V--D----L-PVATG--KAREVKAKRVLTVGTDCAVGKMTTALELERALRE-RGLNAAFVAT----GQTGILIA---GYG  161 (302)
T ss_pred             C--C----C-CCCCC--CCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHH-CCCCEEEEEC----CCCEEEEE---CCE
T ss_conf             9--8----8-65768--4014798789996057334078999999999997-7998479972----76136881---524


Q ss_pred             HHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC-----CHHHHH
Q ss_conf             888631845612433765320248980687248761203207999999989998512888997388888-----989999
Q gi|254780725|r  218 ISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVW-----NSWTQE  292 (427)
Q Consensus       218 l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~-----~~~~~~  292 (427)
                      +.        +|.+                        ..++-..+++.++-...+..|++||---.+.     +..+..
T Consensus       162 v~--------iDav------------------------~~DFvaGavE~~v~~~~~~~d~iiIEGQgSL~hP~y~gvsl~  209 (302)
T pfam07755       162 VP--------LDAV------------------------PADFVAGAVEALVLDAAEEDDWIVIEGQGSLSHPAYSGVTLG  209 (302)
T ss_pred             EE--------ECCC------------------------HHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCHH
T ss_conf             78--------4322------------------------476676789999986454678799916543236656654598


Q ss_pred             HHHH--CCCCCCCCCCCH-----------HHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC-CCHHHHHHHHHHHCCC
Q ss_conf             9862--012543578776-----------8899999999999981987675389995658987-5200599999984895
Q gi|254780725|r  293 VLTL--SDKVVITTSLDL-----------AGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPK-KPEISISDFCAPLGIT  358 (427)
Q Consensus       293 ~L~~--AD~vviV~~p~~-----------~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~-~~~i~~~~~~~~lg~~  358 (427)
                      .|..  .|.+++...|..           +++...-++.+.+....++.+-+.+-+|..+... ......+++++.++.+
T Consensus       210 lL~Gs~Pd~lIL~H~p~R~~~~~~~~~~iP~l~~~i~l~e~~a~~~~~~kvvgIslNt~~l~~~ea~~~~~~~~~~~glP  289 (302)
T pfam07755       210 LLHGSQPDALVLCHRPGRKHRRGFPHYPLPPLEEEIELIEALAGTTPPAKVVGISLNTRGLSEAEAREAIERIEEELGLP  289 (302)
T ss_pred             HHCCCCCCEEEEECCCCCCEECCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             86078998699963789862278766889998999999999736479973999995578799999999999999998997


Q ss_pred             EEEEE
Q ss_conf             37990
Q gi|254780725|r  359 PSAII  363 (427)
Q Consensus       359 ~~~~I  363 (427)
                      +.-.+
T Consensus       290 v~Dp~  294 (302)
T pfam07755       290 VTDPV  294 (302)
T ss_pred             EEECC
T ss_conf             47121


No 297
>KOG0744 consensus
Probab=94.89  E-value=0.13  Score=29.14  Aligned_cols=152  Identities=13%  Similarity=0.096  Sum_probs=84.8

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHC---CCCEEEEECCCCCCCCHHHCCCCCC------CCHHHHHCCCCCHHH
Q ss_conf             7537999746988775689999999999626---9949999787989860334389987------898886318456124
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVF---AMETLLADLDLPYGTANINFDKDPI------NSISDAIYPVGRIDK  230 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~---~~~VlLvDlDl~~g~~~~~l~~~~~------~~l~d~l~~~~rlD~  230 (427)
                      --|+|-+.| -.|+|||+++-.||..|+-+.   -.+..+|..+.+ +--.-+|+-...      +-|.|++...+.+=-
T Consensus       176 ~NRliLlhG-PPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinsh-sLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVf  253 (423)
T KOG0744         176 WNRLILLHG-PPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSH-SLFSKWFSESGKLVAKMFQKIQELVEDRGNLVF  253 (423)
T ss_pred             EEEEEEEEC-CCCCCHHHHHHHHHHHHEEEECCCCCCCEEEEEEHH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEE
T ss_conf             414899857-999882279999987514652376444069997046-788988712113899999999999717896899


Q ss_pred             HHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHH
Q ss_conf             33765320248980687248761203207999999989998512888997388888989999986201254357877688
Q gi|254780725|r  231 AFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAG  310 (427)
Q Consensus       231 ~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~s  310 (427)
                      ++++..-.-...+=...++...-+...  -..++..-++.+++.-+++|+-+..-....-.+..+.||.+..|..|+..+
T Consensus       254 vLIDEVESLa~aR~s~~S~~EpsDaIR--vVNalLTQlDrlK~~~NvliL~TSNl~~siD~AfVDRADi~~yVG~Pt~~a  331 (423)
T KOG0744         254 VLIDEVESLAAARTSASSRNEPSDAIR--VVNALLTQLDRLKRYPNVLILATSNLTDSIDVAFVDRADIVFYVGPPTAEA  331 (423)
T ss_pred             EEEHHHHHHHHHHHHHHCCCCCCHHHH--HHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHHHHEEECCCCCHHH
T ss_conf             980787888999875413799821899--999999989986047977999626267777888611754211038963999


Q ss_pred             HHHHH
Q ss_conf             99999
Q gi|254780725|r  311 LRNSK  315 (427)
Q Consensus       311 lr~a~  315 (427)
                      ++...
T Consensus       332 i~~Il  336 (423)
T KOG0744         332 IYEIL  336 (423)
T ss_pred             HHHHH
T ss_conf             99999


No 298
>TIGR00416 sms DNA repair protein RadA; InterPro: IPR004504   RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ).   RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=94.85  E-value=0.1  Score=29.69  Aligned_cols=158  Identities=20%  Similarity=0.257  Sum_probs=83.0

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCH---HHCCCCCCCCHHHHHCCCCCHHHHHHHHHH
Q ss_conf             53799974698877568999999999962699499997879898603---343899878988863184561243376532
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTAN---INFDKDPINSISDAIYPVGRIDKAFVSRLP  237 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~---~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l  237 (427)
                      |-. -.+|+.-|+||||+-..++..||++ ..+||+|=..=...-+.   .-||      +.+.....            
T Consensus       103 Gsl-iLiGG~PG~GKSTLLLqV~~~LA~~-~~~~LYVsGEES~~Q~klRA~RLG------it~~~~~s------------  162 (481)
T TIGR00416       103 GSL-ILIGGDPGIGKSTLLLQVACQLAKN-SMKVLYVSGEESLQQIKLRATRLG------ITDLVEPS------------  162 (481)
T ss_pred             CCE-EEECCCCCCCHHHHHHHHHHHHHHC-CCCEEEEEECCHHHHHHHHHHHCC------CCCCCCHH------------
T ss_conf             416-9846889963567899999998404-881689972301677888875455------32478702------------


Q ss_pred             HCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECC------------CCCCCH---HHHHHHHHC--CCC
Q ss_conf             024898068724876120320799999998999851288899738------------888898---999998620--125
Q gi|254780725|r  238 VFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDV------------PHVWNS---WTQEVLTLS--DKV  300 (427)
Q Consensus       238 ~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~------------p~~~~~---~~~~~L~~A--D~v  300 (427)
                       +..+|+.-|+....+.-..+.+-+.+...++.+  +|.++|||.            |.+.+.   .|..++..|  +.|
T Consensus       163 -qaqdGinnlahdG~L~~L~Et~~e~I~~~~e~~--~P~~~ViDSIQ~ly~~di~SaPGSVsQVRE~t~~Lmr~AKt~~i  239 (481)
T TIGR00416       163 -QAQDGINNLAHDGNLYVLSETNLEQICAEIEEL--NPQVVVIDSIQTLYLPDISSAPGSVSQVRECTAELMRLAKTRGI  239 (481)
T ss_pred             -HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHH--CCCEEEEECCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             -344324543026753215757989999999852--99489991421000000025888423888999999876521686


Q ss_pred             --CCCC----CCCHHHHHHHHHHHHHHHHC-CCCC---CCCEEEEECCCCC
Q ss_conf             --4357----87768899999999999981-9876---7538999565898
Q gi|254780725|r  301 --VITT----SLDLAGLRNSKNLIDVLKKL-RPAD---KPPYLVLNQVKTP  341 (427)
Q Consensus       301 --viV~----~p~~~slr~a~~ll~~l~~~-~~~~---~~~~iVlNr~~~~  341 (427)
                        ++|-    +.+++.=|-..+++|..=-. +-.+   +-++=+=||+++.
T Consensus       240 aifiVGHVTKeGsiAGPkvLEH~vD~vLyfeGd~~~~~R~LRS~KNRFGat  290 (481)
T TIGR00416       240 AIFIVGHVTKEGSIAGPKVLEHMVDTVLYFEGDRDSRFRILRSVKNRFGAT  290 (481)
T ss_pred             CEEEEEEECCCCCCCCCHHHHHHHHHHEECCCCCCCCCCHHHCCCCCCCCC
T ss_conf             579970043567543404666343311011588753444010001567873


No 299
>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.  This family is also known as MRP (mulrtidrug resisitance-associated protein).  Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear.  The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed.  MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
Probab=94.82  E-value=0.11  Score=29.52  Aligned_cols=41  Identities=20%  Similarity=0.338  Sum_probs=28.2

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             6753799974698877568999999999962699499997879
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDL  201 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl  201 (427)
                      ..|.+++++| +-|+||||+.--++-.+.-. ...+.+=+.|+
T Consensus        28 ~~Ge~v~ivG-~sGsGKSTLl~ll~gl~~p~-~G~I~i~g~~i   68 (221)
T cd03244          28 KPGEKVGIVG-RTGSGKSSLLLALFRLVELS-SGSILIDGVDI   68 (221)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHCCCCCC-CCEEEECCEEC
T ss_conf             6998999999-99998999999996797189-84899999996


No 300
>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]
Probab=94.76  E-value=0.18  Score=28.17  Aligned_cols=68  Identities=18%  Similarity=0.149  Sum_probs=41.8

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCC---------CCHH-----HCCCCCCCCHHHHHC
Q ss_conf             56753799974698877568999999999962699499997879898---------6033-----438998789888631
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYG---------TANI-----NFDKDPINSISDAIY  223 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g---------~~~~-----~l~~~~~~~l~d~l~  223 (427)
                      -..|.+++++| ..|+||||++--++-...-  ..-.+.+|...-..         .+.+     +--++|..++.+.+.
T Consensus        30 i~~Ge~lgivG-eSGsGKSTL~r~l~Gl~~p--~~G~I~~~G~~~~~~~~~~~~~~~VQmVFQDp~~SLnP~~tv~~~l~  106 (252)
T COG1124          30 IERGETLGIVG-ESGSGKSTLARLLAGLEKP--SSGSILLDGKPLAPKKRAKAFYRPVQMVFQDPYSSLNPRRTVGRILS  106 (252)
T ss_pred             ECCCCEEEEEC-CCCCCHHHHHHHHHCCCCC--CCCEEEECCCCCCCCCCCHHHCCCEEEEECCCCCCCCCCHHHHHHHH
T ss_conf             64897899984-8989888999999565678--88628988840576653033304506995187224684101989974


Q ss_pred             CCCCH
Q ss_conf             84561
Q gi|254780725|r  224 PVGRI  228 (427)
Q Consensus       224 ~~~rl  228 (427)
                      .+-+.
T Consensus       107 Epl~~  111 (252)
T COG1124         107 EPLRP  111 (252)
T ss_pred             HHHCC
T ss_conf             24303


No 301
>cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1.  In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD.  MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.
Probab=94.70  E-value=0.13  Score=29.15  Aligned_cols=41  Identities=24%  Similarity=0.406  Sum_probs=27.8

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             6753799974698877568999999999962699499997879
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDL  201 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl  201 (427)
                      +.|..|+++| +-|+||||+.--|.-.+.-. ..++.+=+.|+
T Consensus        27 ~~G~~iaIvG-~sGsGKSTLl~ll~gl~~p~-~G~I~idg~~i   67 (238)
T cd03249          27 PPGKTVALVG-SSGCGKSTVVSLLERFYDPT-SGEILLDGVDI   67 (238)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHHCCCCC-CCEEEECCEEC
T ss_conf             6999999999-99998999999982386188-51899999992


No 302
>cd03291 ABCC_CFTR1 The CFTR subfamily domain 1.  The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia.  Use of the term assembly of a functional ion channel implies the coming together of subunits, or at least smaller not-yet functional components of the active whole.  In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells.  CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.
Probab=94.69  E-value=0.042  Score=32.12  Aligned_cols=29  Identities=14%  Similarity=0.182  Sum_probs=23.7

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             567537999746988775689999999999
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIA  187 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA  187 (427)
                      -+.|..|+++| +-|+||||+.--+.-.+-
T Consensus        60 I~~Ge~vaIVG-~sGSGKSTLl~lL~gl~~   88 (282)
T cd03291          60 IEKGEMLAITG-STGSGKTSLLMLILGELE   88 (282)
T ss_pred             ECCCCEEEEEC-CCCCHHHHHHHHHHCCCC
T ss_conf             84999999999-999819999999957872


No 303
>cd03245 ABCC_bacteriocin_exporters ABC-type bacteriocin exporters. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2.  A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.
Probab=94.69  E-value=0.069  Score=30.79  Aligned_cols=38  Identities=29%  Similarity=0.322  Sum_probs=26.6

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             6753799974698877568999999999962699499997
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLAD  198 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvD  198 (427)
                      ..|..|+++| +-|+||||+.--+.-.+.-. ...+.+=+
T Consensus        28 ~~G~~v~ivG-~sGsGKSTLl~ll~gl~~p~-~G~I~i~g   65 (220)
T cd03245          28 RAGEKVAIIG-RVGSGKSTLLKLLAGLYKPT-SGSVLLDG   65 (220)
T ss_pred             CCCCEEEEEC-CCCCHHHHHHHHHHCCCCCC-CCEEEECC
T ss_conf             7999999999-99985999999996725478-65899999


No 304
>PRK11819 putative ABC transporter ATP-binding protein; Reviewed
Probab=94.68  E-value=0.28  Score=27.01  Aligned_cols=28  Identities=25%  Similarity=0.321  Sum_probs=22.3

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             67537999746988775689999999999
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIA  187 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA  187 (427)
                      +.|.+|+++| .-|+||||+.-.++-.+.
T Consensus       348 ~~Ge~iaivG-~NGsGKSTLlk~l~G~~~  375 (556)
T PRK11819        348 PPGGIVGIIG-PNGAGKSTLFKMITGQEQ  375 (556)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHCCCC
T ss_conf             7882478988-987758899999838656


No 305
>PRK12740 elongation factor G; Reviewed
Probab=94.68  E-value=0.21  Score=27.87  Aligned_cols=17  Identities=18%  Similarity=0.235  Sum_probs=7.4

Q ss_pred             CHHHHHHHHHHHHHCCC
Q ss_conf             99999998999851288
Q gi|254780725|r  260 DEKMIVPVLDILEQIFP  276 (427)
Q Consensus       260 ~~~~l~~ll~~l~~~yd  276 (427)
                      .+-+++.+++.|++.|.
T Consensus       436 GElHLei~l~~Lr~~f~  452 (670)
T PRK12740        436 GELHLEVALERLKRKYG  452 (670)
T ss_pred             CHHHHHHHHHHHHHHHC
T ss_conf             98999999999989869


No 306
>COG4988 CydD ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]
Probab=94.66  E-value=0.071  Score=30.68  Aligned_cols=125  Identities=18%  Similarity=0.169  Sum_probs=61.1

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC------HHHCCCCC---CCCHHHHH--CCCCC
Q ss_conf             675379997469887756899999999996269949999787989860------33438998---78988863--18456
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA------NINFDKDP---INSISDAI--YPVGR  227 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~------~~~l~~~~---~~~l~d~l--~~~~r  227 (427)
                      +.|+.++++| +.|+||||+..-++-.++-.. ....+=|.|+..=+.      -.+.+++|   ..++.|-+  ..++.
T Consensus       345 ~~g~~talvG-~SGaGKSTLl~lL~G~~~~~~-G~I~vng~~l~~l~~~~~~k~i~~v~Q~p~lf~gTireNi~l~~~~~  422 (559)
T COG4988         345 KAGQLTALVG-ASGAGKSTLLNLLLGFLAPTQ-GEIRVNGIDLRDLSPEAWRKQISWVSQNPYLFAGTIRENILLARPDA  422 (559)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHCCCCCCC-CEEEECCCCCCCCCHHHHHHHEEEECCCCCCCCCCHHHHHHCCCCCC
T ss_conf             4896799988-999978999999847577778-44888993100068778886724627998405641887773168767


Q ss_pred             --------HHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHH--HHHHHHCCCEEEECCCCC-CCHHH
Q ss_conf             --------1243376532024898068724876120320799999998--999851288899738888-89899
Q gi|254780725|r  228 --------IDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPV--LDILEQIFPLVILDVPHV-WNSWT  290 (427)
Q Consensus       228 --------lD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~l--l~~l~~~yd~VIiD~p~~-~~~~~  290 (427)
                              ++.+-+...+.. ++||+-.-+..    ...++.+..+++  -..+-..-+++++|=|.. .+..+
T Consensus       423 s~e~i~~al~~a~l~~~v~~-p~GLdt~ige~----G~~LSgGQ~QRlaLARAll~~~~l~llDEpTA~LD~et  491 (559)
T COG4988         423 SDEEIIAALDQAGLLEFVPK-PDGLDTVIGEG----GAGLSGGQAQRLALARALLSPASLLLLDEPTAHLDAET  491 (559)
T ss_pred             CHHHHHHHHHHHCHHHHHCC-CCCCCCCCCCC----CCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCCCCHHH
T ss_conf             89999999998257876167-77643302158----88778999999999998558888898548756798767


No 307
>PRK04328 hypothetical protein; Provisional
Probab=94.63  E-value=0.1  Score=29.68  Aligned_cols=44  Identities=11%  Similarity=0.110  Sum_probs=36.0

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             5675379997469887756899999999996269949999787989
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      -+.|.++.+.| .-|+|||++|.++++.-++ .|.+++++-++-..
T Consensus        21 lp~gs~~Lv~G-~pGtGKT~la~qFl~~g~~-~GE~~lyis~eE~~   64 (250)
T PRK04328         21 IPERNVVLLSG-GPGTGKSIFSQQFLWNGLQ-MGEPGIYVALEEHP   64 (250)
T ss_pred             CCCCEEEEEEE-CCCCCHHHHHHHHHHHHHH-CCCCEEEEEEECCH
T ss_conf             87996999982-8999989999999999987-69977999972799


No 308
>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.
Probab=94.60  E-value=0.066  Score=30.90  Aligned_cols=177  Identities=16%  Similarity=0.080  Sum_probs=76.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHH---HCCCCCHHHHHHHHHHHC
Q ss_conf             79997469887756899999999996269949999787989860334389987898886---318456124337653202
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDA---IYPVGRIDKAFVSRLPVF  239 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~---l~~~~rlD~~~l~~~l~~  239 (427)
                      +|++.| ..|+||||+|-.|+..|   .+.+|+++.+|-..-+.      .+..-....   ...|+-+|-.++...+..
T Consensus         1 iIgI~G-~sgsGKTT~a~~L~~~l---~~~~v~~i~~D~yy~~~------~~~~~~~~~~~~fd~p~a~d~~~l~~~L~~   70 (198)
T cd02023           1 IIGIAG-GSGSGKTTVAEEIIEQL---GNPKVVIISQDSYYKDL------SHEELEERKNNNYDHPDAFDFDLLISHLQD   70 (198)
T ss_pred             CEEEEC-CCCCCHHHHHHHHHHHH---CCCCEEEEECCCCCCCC------CCCCHHHHCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             989889-99885999999999980---99985899788888798------604387843678789226449999999999


Q ss_pred             CCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCC-HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             489806872487612032079999999899985128889973888889-8999998620125435787768899999999
Q gi|254780725|r  240 YAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWN-SWTQEVLTLSDKVVITTSLDLAGLRNSKNLI  318 (427)
Q Consensus       240 ~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~-~~~~~~L~~AD~vviV~~p~~~slr~a~~ll  318 (427)
                      ...|-.+-.      ..+++.......-...+ ...++||++--..+. +..+   ...|..+.+-.+  ..+|-.+|+.
T Consensus        71 L~~g~~i~~------p~Yd~~t~~r~~~~~~i-~~~~iiIvEGi~~l~~~~lr---~~~D~kIfid~~--~d~rl~Rri~  138 (198)
T cd02023          71 LKNGKSVEI------PVYDFKTHSRLKETVTV-YPADVIILEGILALYDKELR---DLMDLKIFVDTD--ADVRLIRRIE  138 (198)
T ss_pred             HHCCCCCCC------CCEECCCCCCCCCCEEE-CCCCEEEEECHHHCCCHHHH---HHHHCEEEEECC--HHHHHHHHHH
T ss_conf             864897612------31003457546772796-58865998253430688888---674023786178--9999999998


Q ss_pred             HHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCC
Q ss_conf             999981987675389995658987520059999998489537990687
Q gi|254780725|r  319 DVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFD  366 (427)
Q Consensus       319 ~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D  366 (427)
                      .-..+.+....   -|++++....+  ...+.|-+......+.+||+.
T Consensus       139 RD~~eRg~~~~---~v~~~~~~~v~--p~~~~~i~P~k~~ADlIi~~~  181 (198)
T cd02023         139 RDIVERGRDLE---SVINQYLKFVK--PMHEQFIEPTKRYADVIIPRG  181 (198)
T ss_pred             HHHHHHCCCHH---HHHHHHHHHHH--HHHHHHCCCCHHCCCEEECCC
T ss_conf             76988589999---99999998607--879986524151473897899


No 309
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=94.59  E-value=0.34  Score=26.55  Aligned_cols=64  Identities=19%  Similarity=0.256  Sum_probs=43.1

Q ss_pred             HCCCCEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             765626431899989999976310233222345675379997469887756899999999996269949999787
Q gi|254780725|r  126 SNHVSEYLIEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLD  200 (427)
Q Consensus       126 r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlD  200 (427)
                      .....|+--.|....++-+.+..-+.        .|-+| .+|..-|+||||+-..++..+|.+ + +|++|--.
T Consensus        66 ~i~~~~~~Ri~tg~~EldRVLGGG~V--------~Gs~i-LIgGdPGIGKSTLLLQva~~lA~~-~-~vLYVsGE  129 (456)
T COG1066          66 DIELEEEPRISTGIEELDRVLGGGLV--------PGSVI-LIGGDPGIGKSTLLLQVAARLAKR-G-KVLYVSGE  129 (456)
T ss_pred             CCEEEECCCCCCCHHHHHHHHCCCCC--------CCCEE-EECCCCCCCHHHHHHHHHHHHHHC-C-CEEEEECC
T ss_conf             01122224235781888765367723--------66179-973689877989999999998705-9-57999677


No 310
>PRK12739 elongation factor G; Reviewed
Probab=94.56  E-value=0.34  Score=26.51  Aligned_cols=37  Identities=14%  Similarity=0.282  Sum_probs=14.3

Q ss_pred             HHHHHHHHCCCCCCEEEEECCCC--CCCHHHHHHHHHHHC
Q ss_conf             99999986189984999980598--767788999888532
Q gi|254780725|r   66 AEAVSCFSDSSTPDLIIVQTKVD--SREVLSALEPLAEVC  103 (427)
Q Consensus        66 ~~A~~~~~~~~~P~~iivd~~~~--~~~~~~~l~~la~~~  103 (427)
                      ...+.+....-.|-++++- .++  ..+.-..++++.+..
T Consensus       117 ~~v~rqa~~~~lp~il~iN-KiDR~~ad~~~~~~~i~~~l  155 (693)
T PRK12739        117 ETVWRQADKYGVPRIVFVN-KMDRIGADFFRVVEQIKDRL  155 (693)
T ss_pred             HHHHHHHHHCCCCEEEEEE-CCCCCCCCHHHHHHHHHHHH
T ss_conf             9999999986989699997-97889999899999999985


No 311
>pfam06745 KaiC KaiC. This family represents a conserved region within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria.
Probab=94.52  E-value=0.11  Score=29.45  Aligned_cols=45  Identities=16%  Similarity=0.221  Sum_probs=35.2

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             5675379997469887756899999999996269949999787989
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      -+.|.++.+.| .-|+|||++|..+++.-+.+.|.+|+++-++-..
T Consensus        16 i~~gs~~LI~G-~pGsGKT~la~qfl~~ga~~~ge~~lYis~ee~~   60 (231)
T pfam06745        16 IPEGRVVLITG-GPGTGKTIFGLQFLYNGALEYGEPGVYVTLEEPP   60 (231)
T ss_pred             CCCCEEEEEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCH
T ss_conf             82996999985-8972599999999999998658968999813799


No 312
>PRK09112 DNA polymerase III subunit delta'; Validated
Probab=94.52  E-value=0.35  Score=26.44  Aligned_cols=51  Identities=20%  Similarity=0.315  Sum_probs=33.9

Q ss_pred             EEECCCCCHHHH------HHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             643189998999------997631023322234567537999746988775689999999999
Q gi|254780725|r  131 EYLIEPLSVADI------INSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIA  187 (427)
Q Consensus       131 dyl~~P~~~~~l------~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA  187 (427)
                      |..+.|-+..++      .+.+.+.+.     .+|...-+-|.|. -|+||||+|-.+|..|-
T Consensus        14 ~g~p~Pr~~~~liGq~~~~~~L~~a~~-----~gRl~HA~Lf~GP-~GiGKaTlA~~~A~~Ll   70 (352)
T PRK09112         14 DGVPSPSENNRLFGHEEARAFLAQAYR-----EGRLHHALLFEGP-EGIGKATLAFHLANHIL   70 (352)
T ss_pred             CCCCCCCCHHHHCCHHHHHHHHHHHHH-----CCCCCCEEEEECC-CCCCHHHHHHHHHHHHH
T ss_conf             999896446462786999999999998-----4996524653589-98089999999999986


No 313
>cd01860 Rab5_related Rab5-related subfamily.  This subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways.  In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence mo
Probab=94.48  E-value=0.36  Score=26.39  Aligned_cols=109  Identities=14%  Similarity=0.187  Sum_probs=67.9

Q ss_pred             CCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             2888997388888--98999998620125435787-76889999999999998198767538999565898752005999
Q gi|254780725|r  274 IFPLVILDVPHVW--NSWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      .+.+-|+|++...  .......+..||.+++|.+. +..|+.+++.+++.+++...+..++.+|-|+.+......++.++
T Consensus        49 ~v~l~iwDtaG~e~~~~~~~~~~~~a~~~ilvydit~~~Sf~~~~~w~~~i~~~~~~~~~iilVgnK~DL~~~r~V~~~e  128 (163)
T cd01860          49 TVKFEIWDTAGQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQRNASPNIIIALVGNKADLESKRQVSTEE  128 (163)
T ss_pred             EEEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCHHHCCCCCHHH
T ss_conf             99999997999710027889885167714999818997999999999999998559872367755335756508999999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHH
Q ss_conf             9998489537990687999999884796189888999--8999999999998
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVL  400 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i  400 (427)
                      ..                  .-|...|-+..|.+.+.  -+.+.|..|+++|
T Consensus       129 ~~------------------~~a~~~~~~~~E~SAk~~~nV~e~F~~l~~~i  162 (163)
T cd01860         129 AQ------------------EYADENGLLFFETSAKTGENVNELFTEIAKKL  162 (163)
T ss_pred             HH------------------HHHHHCCCEEEEECCCCCCCHHHHHHHHHHHC
T ss_conf             99------------------99998299799986265907899999999858


No 314
>PRK09554 feoB ferrous iron transport protein B; Reviewed
Probab=94.47  E-value=0.36  Score=26.38  Aligned_cols=10  Identities=10%  Similarity=0.398  Sum_probs=4.4

Q ss_pred             EEEECCCCCC
Q ss_conf             8997388888
Q gi|254780725|r  277 LVILDVPHVW  286 (427)
Q Consensus       277 ~VIiD~p~~~  286 (427)
                      .-|..+|+..
T Consensus       484 pfvmELPpYr  493 (772)
T PRK09554        484 PFVMELPVYH  493 (772)
T ss_pred             CCEEECCCCC
T ss_conf             7477379878


No 315
>PRK06217 hypothetical protein; Validated
Probab=94.44  E-value=0.31  Score=26.80  Aligned_cols=175  Identities=15%  Similarity=0.078  Sum_probs=80.0

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      +.|.|+| -+|.||||++..||..+    +.+  .+|+|-.+     .+.-+|+++.                       
T Consensus         2 ~rI~i~G-~sGsGkSTla~~La~~l----~~~--~~~lD~~~-----W~p~~~pf~~-----------------------   46 (185)
T PRK06217          2 MRIHITG-ASGSGTTTLGAALAEAL----DLP--HLDTDDFF-----WLPTDPPFTT-----------------------   46 (185)
T ss_pred             CEEEEEC-CCCCCHHHHHHHHHHHH----CCC--EEECCCCE-----ECCCCCCCCC-----------------------
T ss_conf             6799978-99887899999999975----989--68645553-----5689997564-----------------------


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             98068724876120320799999998999851288899738888898999998620125435787768899999999999
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVL  321 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l  321 (427)
                                     ..-.++....+...+...=.+|+ |  .....|....+..+|.||.+..|..-.+...++  ...
T Consensus        47 ---------------kR~~~eR~~ll~~~~~~~~~WV~-s--Gs~~~wgd~l~p~~DlvVfL~lP~~irl~Rlr~--RE~  106 (185)
T PRK06217         47 ---------------KREPEERLRLLLEDLRDSEGWIL-S--GSLLGWGDPLEPLFDLVVFLYIPPELRLERLRL--REE  106 (185)
T ss_pred             ---------------CCCHHHHHHHHHHHHHCCCCEEE-E--CCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHH--HHH
T ss_conf             ---------------37999999999998637999899-5--775232321134356899982898999999999--999


Q ss_pred             HHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCC-HHHH-HHHHHCCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf             981987675389995658987520059999998489537990687-9999-99884796189888999899999999999
Q gi|254780725|r  322 KKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFD-GAVF-GMSANSGKMIHEVDPKSAIANLLVDFSRV  399 (427)
Q Consensus       322 ~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D-~~~~-~~A~~~G~pi~e~~p~s~~a~~~~~La~~  399 (427)
                      .  +++++        ..+...-+..-.+|-+-....-....+-. -+.. ........|++..+...++.+-+..+.+.
T Consensus       107 ~--RyG~r--------i~pgGdm~~~~~~Fl~Wa~~YD~~~~~gRsl~~He~Wl~~~~cPVlrldg~~~~~~~~~~vl~~  176 (185)
T PRK06217        107 Q--RYGNR--------ILPGGDMHKASLEFLEWAAQYDNAGPEGRSLAAHEQWLADQSCPVLRLDGDLTVEERLAQVLAA  176 (185)
T ss_pred             H--HCCCC--------CCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHH
T ss_conf             8--60786--------6899418888899999998678898776449999999952898679976989899999999999


Q ss_pred             HH
Q ss_conf             85
Q gi|254780725|r  400 LM  401 (427)
Q Consensus       400 i~  401 (427)
                      +.
T Consensus       177 ~~  178 (185)
T PRK06217        177 LN  178 (185)
T ss_pred             HH
T ss_conf             74


No 316
>PRK08261 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=94.42  E-value=0.37  Score=26.31  Aligned_cols=119  Identities=13%  Similarity=0.205  Sum_probs=74.5

Q ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHH-------HHCCCCCEEEEEECCCC----HH--------------HHHHHHHCCC
Q ss_conf             89984999980598767788999888-------53289980899816871----89--------------9999997656
Q gi|254780725|r   75 SSTPDLIIVQTKVDSREVLSALEPLA-------EVCDSGTKVIVIGDTND----VS--------------LYRALISNHV  129 (427)
Q Consensus        75 ~~~P~~iivd~~~~~~~~~~~l~~la-------~~~~p~~~Vivig~~~d----~~--------------l~r~l~r~Gv  129 (427)
                      .....-++.|..+- .++ ++|.+|.       ....|.-+|||||..-+    +.              +-.| +|.|+
T Consensus        77 ~~~~~~~v~da~~~-~~~-~~l~~~~~~~~~~~r~l~~~~rvvv~g~~p~~~~~~~~~~a~~~legf~rs~~ke-~~~g~  153 (447)
T PRK08261         77 GDKFGALVFDATGI-TDP-EELKQLYEFFHPLLRNLAPCGRVVVLGRPPETAADPAQAIAQRALEGFTRSLGKE-LRRGA  153 (447)
T ss_pred             CCCCCEEEEECCCC-CCH-HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHCCCHHHHHHHHHHHHHHHHHHHH-HHCCC
T ss_conf             77633699977789-998-9999999999999873377760899437802237999999998777889989999-72684


Q ss_pred             CEEE--CCCCCHHHHHHHHHHCCCCCC--------------------CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             2643--189998999997631023322--------------------234567537999746988775689999999999
Q gi|254780725|r  130 SEYL--IEPLSVADIINSISAIFTPQE--------------------EGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIA  187 (427)
Q Consensus       130 ~dyl--~~P~~~~~l~~ai~~~~~~~~--------------------~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA  187 (427)
                      .--|  +.|-....+..+++-++.+..                    -.++=.||+..|+|+..|+|+.     +|..||
T Consensus       154 t~~l~~v~~~~~~~~~~~lrf~ls~~sa~v~gq~~~v~~~~~~~~~~~~~pL~GKVALVTGAArGIG~A-----IA~~LA  228 (447)
T PRK08261        154 TAQLVYVAPGAETGLESTLRFFLSPRSAYVSGQVVRVGAADAAPPADWDRPLAGKVALVTGAARGIGAA-----IAEVLA  228 (447)
T ss_pred             EEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCEEEEECCCCHHHHH-----HHHHHH
T ss_conf             367999788840011552424406663311253899638988898887888999989991725789999-----999999


Q ss_pred             HHCCCCEEEEECCCC
Q ss_conf             626994999978798
Q gi|254780725|r  188 SVFAMETLLADLDLP  202 (427)
Q Consensus       188 ~~~~~~VlLvDlDl~  202 (427)
                      + .|.+|+++|.+-.
T Consensus       229 r-eGA~VVi~Di~~a  242 (447)
T PRK08261        229 R-DGAHVVCLDVPQA  242 (447)
T ss_pred             H-CCCEEEEEECCHH
T ss_conf             8-6999999827114


No 317
>COG1123 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]
Probab=94.41  E-value=0.12  Score=29.25  Aligned_cols=66  Identities=20%  Similarity=0.245  Sum_probs=42.1

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC--CCCCC------------CHHHCCCCCCCCHHHHHCC
Q ss_conf             675379997469887756899999999996269949999787--98986------------0334389987898886318
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLD--LPYGT------------ANINFDKDPINSISDAIYP  224 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlD--l~~g~------------~~~~l~~~~~~~l~d~l~~  224 (427)
                      +.|.+++++| ..|+||||+|--++-.+-- .+..+.+.+-|  +..+.            .+.+..++|..++.+.+..
T Consensus       315 ~~GE~lglVG-eSGsGKSTlar~i~gL~~P-~~G~i~~~g~~~~~~~~~~~~~r~~~QmvFQdp~~SLnPr~tV~~~i~e  392 (539)
T COG1123         315 REGETLGLVG-ESGSGKSTLARILAGLLPP-SSGSIIFDGQDLDLTGGELRRLRRRIQMVFQDPYSSLNPRMTVGDILAE  392 (539)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHCCCCC-CCCEEEEECCCCCCCCCHHHHHHHHEEEEEECCCCCCCCCCCHHHHHHH
T ss_conf             3887899988-9999989999999487788-8844999276556552314552420379996762336700069999874


Q ss_pred             CC
Q ss_conf             45
Q gi|254780725|r  225 VG  226 (427)
Q Consensus       225 ~~  226 (427)
                      +-
T Consensus       393 pL  394 (539)
T COG1123         393 PL  394 (539)
T ss_pred             HH
T ss_conf             78


No 318
>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional
Probab=94.40  E-value=0.15  Score=28.76  Aligned_cols=40  Identities=10%  Similarity=0.084  Sum_probs=35.2

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             379997469887756899999999996269949999787989
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      .||+|+| ..|+||||+...|--.|.. +|.+|..|-.+.+.
T Consensus         3 Pii~ivG-~s~SGKTTLi~kli~~l~~-~G~rV~~IKH~~H~   42 (170)
T PRK10751          3 PLLAIAA-WSGTGKTTLLKKLIPALCA-RGIRPGLIKHTHHD   42 (170)
T ss_pred             CEEEEEE-CCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCC
T ss_conf             7799994-6999999999999999998-79849999457778


No 319
>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=94.40  E-value=0.13  Score=29.03  Aligned_cols=43  Identities=19%  Similarity=0.247  Sum_probs=28.5

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             567537999746988775689999999999626994999978798
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      -+.|..|+++| +-|+||||+.--+.-.+.-. ...+.+=+.|..
T Consensus        25 i~~Ge~i~IvG-~sGsGKSTLl~ll~gl~~p~-~G~I~i~g~~i~   67 (234)
T cd03251          25 IPAGETVALVG-PSGSGKSTLVNLIPRFYDVD-SGRILIDGHDVR   67 (234)
T ss_pred             ECCCCEEEEEC-CCCCHHHHHHHHHHCCCCCC-CCEEEECCEECC
T ss_conf             87999999998-99982999999996676678-868999999966


No 320
>cd04113 Rab4 Rab4 subfamily.  Rab4 has been implicated in numerous functions within the cell.  It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A.  Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane.  It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to p
Probab=94.36  E-value=0.38  Score=26.23  Aligned_cols=109  Identities=12%  Similarity=0.143  Sum_probs=70.3

Q ss_pred             CCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             2888997388888--9899999862012543578-776889999999999998198767538999565898752005999
Q gi|254780725|r  274 IFPLVILDVPHVW--NSWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      .+.+-|+|++...  .......+..||.+++|.+ -+..|+.+...+++.++....+..++.+|-|+.+.....+++.++
T Consensus        48 ~~~l~iwDtaG~e~~~~~~~~~~~~a~~~ilvydit~~~Sf~~~~~w~~~i~~~~~~~~~iilVgNK~Dl~~~r~V~~~e  127 (161)
T cd04113          48 RVKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITNRTSFEALPTWLSDARALASPNIVVILVGNKSDLADQREVTFLE  127 (161)
T ss_pred             EEEEEEEECCCCHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHCCCCCHHH
T ss_conf             99999998999701226789984057778995368988999999999999998679996498603434400037889999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHH
Q ss_conf             9998489537990687999999884796189888999--8999999999998
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVL  400 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i  400 (427)
                      .                +  .-|..+|-+..|.+.+.  -+-+.|.+||++|
T Consensus       128 ~----------------~--~~a~~~~~~~~E~SAk~~~nV~e~F~~la~~i  161 (161)
T cd04113         128 A----------------S--RFAQENGLLFLETSALTGENVEEAFLKCARSI  161 (161)
T ss_pred             H----------------H--HHHHHCCCEEEEECCCCCCCHHHHHHHHHHHC
T ss_conf             9----------------9--99998599799974156905899999999709


No 321
>cd01883 EF1_alpha Eukaryotic elongation factor 1 (EF1) alpha subfamily.  EF1 is responsible for the GTP-dependent binding of aminoacyl-tRNAs to the ribosomes.  EF1 is composed of four subunits: the alpha chain which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains.  This subfamily is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF1-alpha) and eukaryotes (eEF1-alpha).  eEF1-alpha interacts with the actin of the eukaryotic cytoskeleton and may thereby play a role in cellular transformation and apoptosis.  EF-Tu can have no such role in bacteria.  In humans, the isoform eEF1A2 is overexpressed in 2/3 of breast cancers and has been identified as a putative oncogene.  This subfamily also includes Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation in
Probab=94.33  E-value=0.15  Score=28.67  Aligned_cols=67  Identities=13%  Similarity=0.175  Sum_probs=49.0

Q ss_pred             HCCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCCHHHH-------HHHHHHHHHHHHCCCCCCCCEEEEECCCCC
Q ss_conf             1288899738888--89899999862012543578776889-------999999999998198767538999565898
Q gi|254780725|r  273 QIFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLDLAGL-------RNSKNLIDVLKKLRPADKPPYLVLNQVKTP  341 (427)
Q Consensus       273 ~~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~~~sl-------r~a~~ll~~l~~~~~~~~~~~iVlNr~~~~  341 (427)
                      ..+.+.++|+|..  +...+...+..+|..++|+...-...       ..+++.+..++.++.  +.+-+++|+++..
T Consensus        75 ~~~~~~iiDtPGH~df~~~mi~g~~~ad~ailvvda~~g~~e~g~~~~~QTreH~~l~~~lGi--k~iIVavNKMD~v  150 (219)
T cd01883          75 EKYRFTILDAPGHRDFVPNMITGASQADVAVLVVDARKGEFEAGFEKGGQTREHALLARTLGV--KQLIVAVNKMDDV  150 (219)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHCCC--CEEEEEEECCCCC
T ss_conf             993699987897266788999877531668999985767510366777659999999998499--7489999875368


No 322
>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria.  Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=94.33  E-value=0.11  Score=29.56  Aligned_cols=43  Identities=21%  Similarity=0.224  Sum_probs=29.4

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             567537999746988775689999999999626994999978798
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      -+.|..++++| +-|+||||+.--|.-.+.-. ..++.+=+.|+.
T Consensus        24 i~~Ge~v~ivG-~sGsGKSTLl~ll~gl~~p~-~G~I~idg~di~   66 (236)
T cd03253          24 IPAGKKVAIVG-PSGSGKSTILRLLFRFYDVS-SGSILIDGQDIR   66 (236)
T ss_pred             ECCCCEEEEEC-CCCCCHHHHHHHHCCCCCCC-CCEEEECCEECC
T ss_conf             86999999999-99998999999974385488-748999999923


No 323
>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]
Probab=94.33  E-value=0.38  Score=26.18  Aligned_cols=47  Identities=23%  Similarity=0.337  Sum_probs=31.6

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHH---CC------CCEEEEECCCCCCCC
Q ss_conf             6753799974698877568999999999962---69------949999787989860
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASV---FA------METLLADLDLPYGTA  206 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~---~~------~~VlLvDlDl~~g~~  206 (427)
                      +.| +..++-+-||+||||++.-|..+|+.-   .|      .+|++|-+.+.-.++
T Consensus        87 r~g-~~~~~~gdsg~GKttllL~l~IalaaG~~lfG~~v~epGkvlyvslEl~re~~  142 (402)
T COG3598          87 RKG-YVSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELYREDI  142 (402)
T ss_pred             HCC-EEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCHHHH
T ss_conf             517-05898448862376899999999986477745335588807999822686889


No 324
>pfam08419 consensus
Probab=94.32  E-value=0.05  Score=31.61  Aligned_cols=65  Identities=25%  Similarity=0.361  Sum_probs=41.9

Q ss_pred             CCCHHHHHHHHHCCCCEEE----CCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             8718999999976562643----18999899999763102332223456753799974698877568999999
Q gi|254780725|r  115 TNDVSLYRALISNHVSEYL----IEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCA  183 (427)
Q Consensus       115 ~~d~~l~r~l~r~Gv~dyl----~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA  183 (427)
                      ..|+.+||+.+...+.+=+    .+|++.......+..++.. .| .  .-.||=|+|..||.||||.|-.|-
T Consensus        28 ~e~P~~yrR~~a~~~~~e~~~~~~~~~~lk~WQ~~l~~~l~~-~P-d--dRtI~Wvygp~GgeGKStfak~L~   96 (116)
T pfam08419        28 LEDPSTYRRCLARKAMEEFRKEAAWPLDLRPWQDEVESLLEE-EP-D--DRTIIWVYGPNGGEGKSTFAKHLG   96 (116)
T ss_pred             HHCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC-CC-C--CCEEEEEECCCCCCCHHHHHHHHH
T ss_conf             307158889999871899987512667651699999999836-99-8--746999985899866428888642


No 325
>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=94.31  E-value=0.21  Score=27.82  Aligned_cols=41  Identities=24%  Similarity=0.353  Sum_probs=28.1

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             6753799974698877568999999999962699499997879
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDL  201 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl  201 (427)
                      +.|+.++++| .-|+||||++.-|...+--. ..++.+=+-|+
T Consensus       365 ~~Ge~vaiVG-~SGsGKSTL~~LL~r~ydp~-~G~I~idG~di  405 (575)
T PRK11160        365 KAGEKVALLG-RTGCGKSTLLQLLTRAWDPQ-QGEILLNGQPI  405 (575)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHCCCCCC-CCEEEECCEEC
T ss_conf             6998899988-99975999999986236789-98899998975


No 326
>cd04148 RGK RGK subfamily.  The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues.   RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function.  Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells.  RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton.  Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ra
Probab=94.24  E-value=0.4  Score=26.08  Aligned_cols=110  Identities=20%  Similarity=0.204  Sum_probs=65.3

Q ss_pred             CCEEEECCCCCCCHHHHHHHH-HCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCC-CCCCCEEEEECCCCCCCCHHHHHHH
Q ss_conf             888997388888989999986-2012543578-776889999999999998198-7675389995658987520059999
Q gi|254780725|r  275 FPLVILDVPHVWNSWTQEVLT-LSDKVVITTS-LDLAGLRNSKNLIDVLKKLRP-ADKPPYLVLNQVKTPKKPEISISDF  351 (427)
Q Consensus       275 yd~VIiD~p~~~~~~~~~~L~-~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~-~~~~~~iVlNr~~~~~~~~i~~~~~  351 (427)
                      +...++|++..-.......+. .+|.+++|-. -+..|+.++..+...+++... ...++.+|-|+.+....-+++.++ 
T Consensus        50 ~~l~i~Dt~g~e~~~~~~~~~~~ada~ilVYdvtdr~SF~~~~~~~~~l~~~~~~~~~piILVGNK~DL~~~R~Vs~eE-  128 (221)
T cd04148          50 STLVVIDHWEQEMWTEDSCMQYQGDAFVVVYSVTDRSSFERASELRIQLRRNRQLEDRPIILVGNKSDLARSREVSVQE-  128 (221)
T ss_pred             EEEEEEECCCCHHHHHHHHHHHCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCHHHHCCCCHHH-
T ss_conf             8999998987312666656530686899999646677888899999999986489995199985356668638999999-


Q ss_pred             HHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCC--CHHHHHHHHHHHHHHC
Q ss_conf             99848953799068799999988479618988899--9899999999999852
Q gi|254780725|r  352 CAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPK--SAIANLLVDFSRVLMG  402 (427)
Q Consensus       352 ~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~--s~~a~~~~~La~~i~g  402 (427)
                                     .+  .-|...|-+..|.+.+  +-+.+.|..|++.|-.
T Consensus       129 ---------------g~--~~A~~~~~~F~EtSAk~~~NV~elF~~lvrqIrl  164 (221)
T cd04148         129 ---------------GR--ACAVVFDCKFIETSAGLQHNVDELLEGIVRQIRL  164 (221)
T ss_pred             ---------------HH--HHHHHCCCEEEECCCCCCCCHHHHHHHHHHHHHH
T ss_conf             ---------------99--9999859989994579994989999999999985


No 327
>PRK09519 recA recombinase A; Reviewed
Probab=94.24  E-value=0.4  Score=26.07  Aligned_cols=12  Identities=17%  Similarity=0.348  Sum_probs=5.4

Q ss_pred             CCEEEEECCCCC
Q ss_conf             538999565898
Q gi|254780725|r  330 PPYLVLNQVKTP  341 (427)
Q Consensus       330 ~~~iVlNr~~~~  341 (427)
                      +..+|.|++.+|
T Consensus       684 ~~~vv~~k~spP  695 (790)
T PRK09519        684 AEGVVVHNCSPP  695 (790)
T ss_pred             EEEEEECCCCCC
T ss_conf             333343266897


No 328
>PRK04220 2-phosphoglycerate kinase; Provisional
Probab=94.20  E-value=0.056  Score=31.33  Aligned_cols=25  Identities=44%  Similarity=0.545  Sum_probs=21.6

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             3799974698877568999999999
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSI  186 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~L  186 (427)
                      .+|-.+|+-.||||||+|..||..|
T Consensus        92 pliILigGtsGvGKSTlA~~LA~rL  116 (306)
T PRK04220         92 PIIILIGGASGVGTSTIAFELASRL  116 (306)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             8799985899887899999999970


No 329
>TIGR00763 lon ATP-dependent protease La; InterPro: IPR004815   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This signature defines the bacterial and eukaryotic lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). This family of sequences does not include the archaeal lon homologs, IPR004663 from INTERPRO. In the eukaryotes the majority of the proteins are located in the mitochondrial matrix , . In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response .; GO: 0004176 ATP-dependent peptidase activity, 0005524 ATP binding, 0006510 ATP-dependent proteolysis.
Probab=94.20  E-value=0.033  Score=32.72  Aligned_cols=33  Identities=21%  Similarity=0.420  Sum_probs=27.9

Q ss_pred             CCCCCE-EEEEEECCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             456753-7999746988775689999999999626
Q gi|254780725|r  157 KGSSGC-SISFIGSRGGVGSSTIAHNCAFSIASVF  190 (427)
Q Consensus       157 ~~~~gr-vIav~g~KGGvGkTTiA~nLA~~LA~~~  190 (427)
                      ..-.|+ |++|+| =-|||||+||-++|-+|.+..
T Consensus       445 ~~~~GpqIlClvG-PPGVGKTSlg~SIA~ALnRkF  478 (941)
T TIGR00763       445 GKMKGPQILCLVG-PPGVGKTSLGKSIAKALNRKF  478 (941)
T ss_pred             CCCCCCEEEEEEC-CCCCCHHHHHHHHHHHHCCEE
T ss_conf             7888876787207-269542227899999968804


No 330
>PRK08181 transposase; Validated
Probab=94.19  E-value=0.28  Score=26.99  Aligned_cols=117  Identities=15%  Similarity=0.222  Sum_probs=66.6

Q ss_pred             EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCE--------
Q ss_conf             306998999999861899849999805987677889998885328998089981687189999999765626--------
Q gi|254780725|r   60 ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSE--------  131 (427)
Q Consensus        60 v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~d--------  131 (427)
                      .+..|++++.+.+..++.-         +.....+.|..|.+..        +.....-.+-|.+.++|...        
T Consensus        19 LkL~~~~~~~~~~~~~a~~---------~~~s~~e~L~~Lle~E--------~~~R~~rr~~rrlk~A~fp~~ktLe~fD   81 (269)
T PRK08181         19 LRLPTIKTLWPQFAEQADK---------EGWPAARFLAAIAEHE--------IAERARRRIERHLAEAHLPPGKTLDSFD   81 (269)
T ss_pred             CCCHHHHHHHHHHHHHHHH---------CCCCHHHHHHHHHHHH--------HHHHHHHHHHHHHHHCCCCCCCCHHHCC
T ss_conf             6852899999999999987---------5999999999999999--------9999999999999868979988865478


Q ss_pred             EECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             431899989999976310233222345675379997469887756899999999996269949999787
Q gi|254780725|r  132 YLIEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLD  200 (427)
Q Consensus       132 yl~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlD  200 (427)
                      |=..|--....+..+...     ..--+.+.-|.++| .-|+|||.+|+.|+....+ .|.+|..+.++
T Consensus        82 f~~~p~i~~~~i~~L~~~-----~~fi~~~~Nvil~G-p~GtGKThLA~Alg~~A~~-~G~~V~f~~~~  143 (269)
T PRK08181         82 FEAVPMISKAQVMALAAG-----DSWLAKGANLLLFG-PPGGGKSHLAAAIGLALIE-NGWRVLFTRTT  143 (269)
T ss_pred             CCCCCCCCHHHHHHHHCC-----CHHHHCCCEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEHH
T ss_conf             556899899999999656-----75886487089989-9998788999999999998-79939997899


No 331
>cd01894 EngA1 EngA1 subfamily.  This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains.  Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability.  A recent report suggests that E. coli Der functions in ribosome assembly and stability.
Probab=94.17  E-value=0.14  Score=28.82  Aligned_cols=67  Identities=16%  Similarity=0.192  Sum_probs=42.7

Q ss_pred             CCCEEEECCCCCC----------CHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCC
Q ss_conf             2888997388888----------989999986201254357877688999999999999819876753899956589875
Q gi|254780725|r  274 IFPLVILDVPHVW----------NSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKK  343 (427)
Q Consensus       274 ~yd~VIiD~p~~~----------~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~  343 (427)
                      .+.++++|+|...          ...+...+..||.+++|++.+..-...-.++++.+++.   ..++.+|+|+.+....
T Consensus        44 ~~~~~lvDTpG~~~~~~~~~~~~~~~~~~~i~~ad~il~viDa~~~~~~~d~~i~~~l~~~---~kp~i~v~NK~D~~~~  120 (157)
T cd01894          44 GREFILIDTGGIEPDDEGISKEIREQAELAIEEADVILFVVDGREGLTPADEEIAKYLRKS---KKPVILVVNKVDNIKE  120 (157)
T ss_pred             CEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHH---CCCEEEEEECCCCCCC
T ss_conf             9889998578755566067899999999999865907999989999998999999999984---7980999978716586


No 332
>PRK01889 ribosome-associated GTPase; Reviewed
Probab=94.16  E-value=0.42  Score=25.97  Aligned_cols=96  Identities=21%  Similarity=0.353  Sum_probs=46.8

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHHH-CCCC-CEEEEEECCC---CHHHHHHHHHC---CCCEEECCCCCHHHHHHHHHHCC
Q ss_conf             499998059876778899988853-2899-8089981687---18999999976---56264318999899999763102
Q gi|254780725|r   79 DLIIVQTKVDSREVLSALEPLAEV-CDSG-TKVIVIGDTN---DVSLYRALISN---HVSEYLIEPLSVADIINSISAIF  150 (427)
Q Consensus        79 ~~iivd~~~~~~~~~~~l~~la~~-~~p~-~~Vivig~~~---d~~l~r~l~r~---Gv~dyl~~P~~~~~l~~ai~~~~  150 (427)
                      |.+++=...++.--...|++.-.. .+.| .+|||+...+   |...+.+.++.   |+.=+.+.-.+ .+-++.+...+
T Consensus       113 D~v~IV~s~~~~fn~~rieRyLv~a~~~g~~pvivLnK~DL~~d~~~~~~~~~~~~~g~~v~~vSa~~-~~gl~~L~~~l  191 (353)
T PRK01889        113 DTVFIVCSLNHDFNLRRIERYLALAWESGAEPVVVLTKADLCEDVEEKIAEVEALAPGVPVLAVNALD-GEGVDALQAWL  191 (353)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHCCCCEEEEEECCC-CCCHHHHHHHH
T ss_conf             68999952899979789999999999869967999966556679999999999855997599997899-84789999986


Q ss_pred             CCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             3322234567537999746988775689999999
Q gi|254780725|r  151 TPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAF  184 (427)
Q Consensus       151 ~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~  184 (427)
                              ..|++++|+| ..||||||+.-.|.-
T Consensus       192 --------~~GkT~vl~G-~SGVGKSTLiN~L~g  216 (353)
T PRK01889        192 --------KPGKTVALLG-SSGVGKSTLVNALLG  216 (353)
T ss_pred             --------HCCCEEEEEC-CCCCCHHHHHHHHCC
T ss_conf             --------3497899977-888669999987565


No 333
>pfam00485 PRK Phosphoribulokinase / Uridine kinase family. In Arabidopsis the region carries two binding domains, a phosphoribosylpyrophosphate-binding domain and, at the very C-terminus, a uracil-binding domain.
Probab=94.16  E-value=0.048  Score=31.72  Aligned_cols=185  Identities=12%  Similarity=0.056  Sum_probs=78.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCC----CHHHH-HCCCCCHHHHHHHHHH
Q ss_conf             799974698877568999999999962699499997879898603343899878----98886-3184561243376532
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPIN----SISDA-IYPVGRIDKAFVSRLP  237 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~----~l~d~-l~~~~rlD~~~l~~~l  237 (427)
                      +|++.| -.|+||||+|-.|+..|.. .+.++..++.|--...-..+-+..+..    +..+. -..|+.+|-.++...+
T Consensus         1 iIgIaG-~SgSGKTT~a~~L~~~l~~-~~~~~~~~~~d~~~~~d~~~~~~~~~~~~~~~~~~~~~d~P~a~d~~ll~~~l   78 (196)
T pfam00485         1 IIGVAG-SSGAGKTTVARTFVSIFGR-EGVPAAGIEGDSFHRYDRFYMDLHMEDRKRAGNNHYSFFSPEANDFDLLYEQF   78 (196)
T ss_pred             CEEEEC-CCCCCHHHHHHHHHHHHCC-CCCCCCCCCCEEEEEECHHCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf             989989-9857199999999999660-58776412431798604102443757676514578897896623599999999


Q ss_pred             HCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCC-HHHHHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf             02489806872487612032079999999899985128889973888889-89999986201254357877688999999
Q gi|254780725|r  238 VFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWN-SWTQEVLTLSDKVVITTSLDLAGLRNSKN  316 (427)
Q Consensus       238 ~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~-~~~~~~L~~AD~vviV~~p~~~slr~a~~  316 (427)
                      .....|-.+..      ..+++.......-...+ ..-++||++--+.+. ......+.  -.|++-+..+   +|-.+|
T Consensus        79 ~~Lk~g~~i~~------P~Ydf~~~~r~~~~~~i-~p~~viIvEGi~~l~~~~ir~l~D--~kIfid~~~d---~rl~RR  146 (196)
T pfam00485        79 KELKEGGSGDK------PIYNHVTGEADPWPELI-EGADILFIEGLHGLYDERVAQLLD--LKIYVDPDID---LELIQK  146 (196)
T ss_pred             HHHHCCCCEEE------EEEECCCCCCCCCCEEC-CCCCEEEEECHHHCCCHHHHHHHC--EEEEEECCCC---HHHHHH
T ss_conf             99708994576------56751345336773661-788569994333303277887638--4799726801---999999


Q ss_pred             HHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCH
Q ss_conf             999999819876753899956589875200599999984895379906879
Q gi|254780725|r  317 LIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDG  367 (427)
Q Consensus       317 ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~  367 (427)
                      +..-..+.+..   ..-|++++.. .+  -..+.|-+......+.+||+-|
T Consensus       147 i~RD~~eRgrs---~~~v~~q~~~-v~--p~~~~fI~P~k~~ADliI~~~p  191 (196)
T pfam00485       147 IQRDMAERGHS---LEGVTDSIER-RK--PDYVNYICPQFSYADLIIQRVP  191 (196)
T ss_pred             HHHCHHHHCCC---HHHHHHHHHH-HH--HHHHHHCCCCHHHCCEEECCCC
T ss_conf             87345751999---9999999999-72--5389647478522988970699


No 334
>COG1160 Predicted GTPases [General function prediction only]
Probab=94.15  E-value=0.42  Score=25.96  Aligned_cols=210  Identities=18%  Similarity=0.229  Sum_probs=118.7

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHCCCC-CEEEEEECCCCH----HHHHHHHHCCCCEEECC----CCCHHHHHHHHHH
Q ss_conf             84999980598767788999888532899-808998168718----99999997656264318----9998999997631
Q gi|254780725|r   78 PDLIIVQTKVDSREVLSALEPLAEVCDSG-TKVIVIGDTNDV----SLYRALISNHVSEYLIE----PLSVADIINSISA  148 (427)
Q Consensus        78 P~~iivd~~~~~~~~~~~l~~la~~~~p~-~~Vivig~~~d~----~l~r~l~r~Gv~dyl~~----P~~~~~l~~ai~~  148 (427)
                      -+++|.=+++.. -+.++=+.+++...+. .|||++-.--|.    ...-+.-..|..|++.-    -....+|.+++..
T Consensus        84 ADvilfvVD~~~-Git~~D~~ia~~Lr~~~kpviLvvNK~D~~~~e~~~~efyslG~g~~~~ISA~Hg~Gi~dLld~v~~  162 (444)
T COG1160          84 ADVILFVVDGRE-GITPADEEIAKILRRSKKPVILVVNKIDNLKAEELAYEFYSLGFGEPVPISAEHGRGIGDLLDAVLE  162 (444)
T ss_pred             CCEEEEEEECCC-CCCHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCEEEEHHHCCCHHHHHHHHHH
T ss_conf             799999984887-8997899999999853998899997666730456489998647898268425535698999999997


Q ss_pred             CCC-CCCCCC-C-CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCC
Q ss_conf             023-322234-5-6753799974698877568999999999962699499997879898603343899878988863184
Q gi|254780725|r  149 IFT-PQEEGK-G-SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPV  225 (427)
Q Consensus       149 ~~~-~~~~~~-~-~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~  225 (427)
                      .+- ..+... . ...--|+++| |--|||||+-=    +|..  ..++++-|.   .|++-            |.+...
T Consensus       163 ~l~~~e~~~~~~~~~~ikiaiiG-rPNvGKSsLiN----~ilg--eeR~Iv~~~---aGTTR------------D~I~~~  220 (444)
T COG1160         163 LLPPDEEEEEEEETDPIKIAIIG-RPNVGKSSLIN----AILG--EERVIVSDI---AGTTR------------DSIDIE  220 (444)
T ss_pred             HCCCCCCCCCCCCCCCEEEEEEE-CCCCCCHHHHH----HHCC--CCEEEECCC---CCCCC------------CCEEEE
T ss_conf             56774334443567750899992-78787058887----7506--825984599---98622------------033125


Q ss_pred             CCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCC-------------CCCHHHHH
Q ss_conf             56124337653202489806872487612032079999999899985128889973888-------------88989999
Q gi|254780725|r  226 GRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPH-------------VWNSWTQE  292 (427)
Q Consensus       226 ~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~-------------~~~~~~~~  292 (427)
                      -.                                            +....|+++|+..             ....-+..
T Consensus       221 ~e--------------------------------------------~~~~~~~liDTAGiRrk~ki~e~~E~~Sv~rt~~  256 (444)
T COG1160         221 FE--------------------------------------------RDGRKYVLIDTAGIRRKGKITESVEKYSVARTLK  256 (444)
T ss_pred             EE--------------------------------------------ECCEEEEEEECCCCCCCCCCCCCEEEEEEHHHHH
T ss_conf             89--------------------------------------------9881899998778774664124268875054676


Q ss_pred             HHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCC
Q ss_conf             98620125435787768899999999999981987675389995658987520059999998489
Q gi|254780725|r  293 VLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGI  357 (427)
Q Consensus       293 ~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~  357 (427)
                      ++..||.+++|.+.+-.-...-.++..++.+.+   +.+.+|+|+++.-...+...+++++.+..
T Consensus       257 aI~~a~vvllviDa~~~~~~qD~~ia~~i~~~g---~~~vIvvNKWDl~~~~~~~~~~~k~~i~~  318 (444)
T COG1160         257 AIERADVVLLVIDATEGISEQDLRIAGLIEEAG---RGIVIVVNKWDLVEEDEATMEEFKKKLRR  318 (444)
T ss_pred             HHHHCCEEEEEEECCCCCHHHHHHHHHHHHHCC---CCEEEEEECCCCCCCHHHHHHHHHHHHHH
T ss_conf             786568899999888783688999999999758---97499997532578516679999999998


No 335
>PRK06547 hypothetical protein; Provisional
Probab=94.12  E-value=0.093  Score=29.99  Aligned_cols=37  Identities=24%  Similarity=0.283  Sum_probs=25.9

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             56753799974698877568999999999962699499997
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLAD  198 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvD  198 (427)
                      +...++|+|=| .+|.||||+|..|+..+   .+..|+=+|
T Consensus        12 ~g~~~iVaIDG-~sGaGKTTLA~~La~~~---~~~~vvHmD   48 (184)
T PRK06547         12 GGDMITVLIDG-RSGSGKTTLAGELAACW---EGSQLVHLD   48 (184)
T ss_pred             CCCEEEEEEEC-CCCCCHHHHHHHHHHHC---CCCCEEEEC
T ss_conf             99769999868-99888899999999745---798289705


No 336
>cd01887 IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily.  IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits.  As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states.  Eukaryotic IF2/eIF5Bs possess three characteristic segments, including a divergent N-terminal region followed by conserved central and C-terminal segments.  This core region is conserved among all known eukaryotic and archaeal IF2/eIF5Bs and eubacterial IF2s.
Probab=94.07  E-value=0.22  Score=27.72  Aligned_cols=66  Identities=18%  Similarity=0.244  Sum_probs=46.1

Q ss_pred             CCCEEEECCCCCCCH--HHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf             288899738888898--999998620125435787768899999999999981987675389995658987
Q gi|254780725|r  274 IFPLVILDVPHVWNS--WTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPK  342 (427)
Q Consensus       274 ~yd~VIiD~p~~~~~--~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~  342 (427)
                      .+.+.++|+|.....  .....+..+|.+++|...+-.-..+...+++.++..+   .++.+++|+++...
T Consensus        49 ~~~i~~iDTPGh~~f~~~~~~~~~~aD~~ilvvda~~g~~~~~~~~~~~l~~~~---~p~ivviNKiD~~~  116 (168)
T cd01887          49 IPGITFIDTPGHEAFTNMRARGASLTDIAILVVAADDGVMPQTIEAIKLAKAAN---VPFIVALNKIDKPN  116 (168)
T ss_pred             CCEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCC---CCEEEEEECCCCCC
T ss_conf             871899989981677999999986268899998646675458999999998769---97899998930898


No 337
>cd00154 Rab Rab family.  Rab GTPases form the largest family within the Ras superfamily.  There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways.  The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide di
Probab=94.07  E-value=0.37  Score=26.26  Aligned_cols=78  Identities=18%  Similarity=0.224  Sum_probs=52.4

Q ss_pred             HCCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             12888997388888--9899999862012543578-77688999999999999819876753899956589875200599
Q gi|254780725|r  273 QIFPLVILDVPHVW--NSWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       273 ~~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      ..+.+.++|++...  .......+..+|.+++|.. -+..|+.+.+.+++.+++......++.+|-|+.+.....+++.+
T Consensus        47 ~~~~l~iwDt~G~e~~~~l~~~~~~~~d~~ilv~d~~~~~Sf~~~~~~~~~i~~~~~~~~~iilvgnK~DL~~~~~v~~~  126 (159)
T cd00154          47 KTVKLQIWDTAGQERFRSITPSYYRGAHGAILVYDITNRESFENLDKWLKELKEYAPENIPIILVGNKIDLEDQRQVSTE  126 (159)
T ss_pred             EEEEEEEEECCCCHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHCCCCCHH
T ss_conf             99999999789826577889999754127567244898899999999999999868988826999974563011689999


Q ss_pred             H
Q ss_conf             9
Q gi|254780725|r  350 D  350 (427)
Q Consensus       350 ~  350 (427)
                      +
T Consensus       127 ~  127 (159)
T cd00154         127 E  127 (159)
T ss_pred             H
T ss_conf             9


No 338
>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=94.04  E-value=0.19  Score=28.11  Aligned_cols=28  Identities=25%  Similarity=0.268  Sum_probs=22.5

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             56753799974698877568999999999
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSI  186 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~L  186 (427)
                      -..|.+++++| ..|+||||+.--++-.+
T Consensus        23 i~~Ge~~~ivG-pSG~GKSTllr~i~Gl~   50 (178)
T cd03229          23 IEAGEIVALLG-PSGSGKSTLLRCIAGLE   50 (178)
T ss_pred             ECCCCEEEEEC-CCCCHHHHHHHHHHCCC
T ss_conf             88998999999-99983999999998599


No 339
>cd04122 Rab14 Rab14 subfamily.  Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles.  Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments.  Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation.  In addition, Rab14 is believed to play a role in the regulation of phagocytosis.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GT
Probab=94.02  E-value=0.44  Score=25.80  Aligned_cols=111  Identities=10%  Similarity=0.176  Sum_probs=72.0

Q ss_pred             HCCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             12888997388888--98999998620125435787-7688999999999999819876753899956589875200599
Q gi|254780725|r  273 QIFPLVILDVPHVW--NSWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       273 ~~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      ..+.+-|.|++..-  .......+..++-+++|.+. +..|+.+...+++.++....+..++.+|-|+++.....+++.+
T Consensus        49 ~~~~l~iwDtaG~e~~~~~~~~~~~~a~~~ilvydvt~~~Sf~~l~~w~~~~~~~~~~~~~iilVGNK~DL~~~r~V~~~  128 (166)
T cd04122          49 QKIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLEAQRDVTYE  128 (166)
T ss_pred             EEEEEEEEECCCCCCCCCCCHHHEECCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHCCCCCHH
T ss_conf             99999999899985444252111431546599725874767999999999999856999758703401574443899999


Q ss_pred             HHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHH
Q ss_conf             99998489537990687999999884796189888999--89999999999985
Q gi|254780725|r  350 DFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLM  401 (427)
Q Consensus       350 ~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~  401 (427)
                      +                  ...-|..+|.+..|.+.+.  -+.+.|..|++.|.
T Consensus       129 e------------------~~~~a~~~~~~~~E~SAk~g~nV~e~F~~l~~~i~  164 (166)
T cd04122         129 E------------------AKQFADENGLLFLECSAKTGENVEDAFLETAKKIY  164 (166)
T ss_pred             H------------------HHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHH
T ss_conf             9------------------99999986998999865878088999999999997


No 340
>COG1663 LpxK Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]
Probab=94.00  E-value=0.23  Score=27.51  Aligned_cols=70  Identities=14%  Similarity=0.130  Sum_probs=44.4

Q ss_pred             EECCCCCH-HHHHHHHHHCCCCCCCCCCCCCEEEEEEE-CCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             43189998-99999763102332223456753799974-69887756899999999996269949999787989
Q gi|254780725|r  132 YLIEPLSV-ADIINSISAIFTPQEEGKGSSGCSISFIG-SRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       132 yl~~P~~~-~~l~~ai~~~~~~~~~~~~~~grvIav~g-~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      |+.+|++- -..+..+++...... ...-...||+|.+ .-||.|||-++.-||-.|-. +|.++.++-=....
T Consensus        18 ~lL~PlS~ly~~i~~~r~~~~~~g-~~~~pvPVI~VGNltvGGtGKTP~vi~la~~l~~-rG~~~gvvSRGYgg   89 (336)
T COG1663          18 FLLLPLSWLYAFIAGLRRKLAKKG-SYRAPVPVICVGNLTVGGTGKTPVVIWLAEALQA-RGVRVGVVSRGYGG   89 (336)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCCEEEECCEEECCCCCCHHHHHHHHHHHH-CCCEEEEEECCCCC
T ss_conf             999999999999999999873246-6567887899855777789968899999999986-69736798057688


No 341
>pfam08423 Rad51 Rad51. Rad51 is a DNA repair and recombination protein and is a homologue of the bacterial ATPase RecA protein.
Probab=93.95  E-value=0.46  Score=25.71  Aligned_cols=46  Identities=13%  Similarity=0.130  Sum_probs=33.9

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHH--H---HCCCCEEEEECCCCCC
Q ss_conf             567537999746988775689999999999--6---2699499997879898
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIA--S---VFAMETLLADLDLPYG  204 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA--~---~~~~~VlLvDlDl~~g  204 (427)
                      -+.|.|.=++| -.|+|||.+++.||....  .   ..+.+|+.||..-.|.
T Consensus        40 i~~g~ITEi~G-~~gsGKTQlc~qlav~~qlp~~~gg~~g~vvyIDTEg~f~   90 (261)
T pfam08423        40 IETGSITEVFG-EFRTGKTQLCHTLCVTCQLPLEMGGGEGKALYIDTEGTFR   90 (261)
T ss_pred             CCCCEEEEEEC-CCCCCHHHHHHHHHHHHHCHHHHCCCCCEEEEEECCCCCC
T ss_conf             66772999989-9888789999999999407096569997289993688869


No 342
>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily.  Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.  Due to t
Probab=93.91  E-value=0.47  Score=25.68  Aligned_cols=112  Identities=15%  Similarity=0.192  Sum_probs=74.0

Q ss_pred             HCCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             12888997388888--9899999862012543578-77688999999999999819876753899956589875200599
Q gi|254780725|r  273 QIFPLVILDVPHVW--NSWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       273 ~~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      ..+.+-++|++...  .......+..+|.+++|.+ -+..|+.+...+++.+.+......++.+|-|+.+......++.+
T Consensus        49 ~~~~l~iwDtaG~e~~~~~~~~~~~~a~~~ilvfdit~~~Sf~~i~~w~~~i~~~~~~~~~~ilvgNK~DL~~~r~v~~~  128 (166)
T cd01869          49 KTIKLQIWDTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTDKRVVDYS  128 (166)
T ss_pred             EEEEEEEEECCCCCCCCCCHHHHHHHCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCCCHH
T ss_conf             99999999899982346267888563267799711799899999999999999867877744886132011314667999


Q ss_pred             HHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHC
Q ss_conf             99998489537990687999999884796189888999--899999999999852
Q gi|254780725|r  350 DFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMG  402 (427)
Q Consensus       350 ~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~g  402 (427)
                      +                  ...-|...|.+..|.+.+.  -+.+.|..|++.|..
T Consensus       129 ~------------------~~~~a~~~~~~~~E~SAk~g~nI~e~F~~l~~~i~k  165 (166)
T cd01869         129 E------------------AQEFADELGIPFLETSAKNATNVEQAFMTMAREIKK  165 (166)
T ss_pred             H------------------HHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHH
T ss_conf             9------------------999999839969998768780689999999999971


No 343
>cd03297 ABC_ModC_molybdenum_transporter ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=93.88  E-value=0.14  Score=28.82  Aligned_cols=26  Identities=23%  Similarity=0.183  Sum_probs=21.6

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             753799974698877568999999999
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSI  186 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~L  186 (427)
                      .|.+++++| ..|+||||+.--+|-..
T Consensus        22 ~ge~~~iiG-pSGsGKSTll~~i~GL~   47 (214)
T cd03297          22 NEEVTGIFG-ASGAGKSTLLRCIAGLE   47 (214)
T ss_pred             CCCEEEEEC-CCCCHHHHHHHHHHCCC
T ss_conf             997999999-99735999999998499


No 344
>cd04163 Era Era subfamily.  Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria.  It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA.  It also contacts several assembly elements of the 30S subunit.  Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism.  Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding.  Both domains are important for Era function.  Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.
Probab=93.85  E-value=0.11  Score=29.53  Aligned_cols=65  Identities=22%  Similarity=0.297  Sum_probs=43.2

Q ss_pred             CCEEEECCCCCCCH----------HHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf             88899738888898----------999998620125435787768899999999999981987675389995658987
Q gi|254780725|r  275 FPLVILDVPHVWNS----------WTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPK  342 (427)
Q Consensus       275 yd~VIiD~p~~~~~----------~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~  342 (427)
                      +.++++|+|.....          .+...+..+|.+++|.+.+-..-..-..+++.++..+   .++.+|+|+++.-.
T Consensus        51 ~~~~l~DtpG~~~~~~~~~~~~~~~~~~~l~~~D~il~vvD~~~~~~~~d~~i~~~l~~~~---~~~iivlNK~Dl~~  125 (168)
T cd04163          51 AQIIFVDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEPIGEGDEFILELLKKSK---TPVILVLNKIDLVK  125 (168)
T ss_pred             EEEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCHHHHHHHHHHHHCC---CCEEEEEECEEECC
T ss_conf             7899995898665145677899999998651365589999789898667799999999809---98599997887047


No 345
>PRK13409 putative ATPase RIL; Provisional
Probab=93.79  E-value=0.49  Score=25.55  Aligned_cols=140  Identities=16%  Similarity=0.208  Sum_probs=69.5

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCC-CCHHHHHHHHHH
Q ss_conf             6753799974698877568999999999962699499997879898603343899878988863184-561243376532
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPV-GRIDKAFVSRLP  237 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~-~rlD~~~l~~~l  237 (427)
                      ..|.+|+++| .-|+||||++--||-.+.-..| .+ .  .+..-+-...++..++..++.+.+... ..++...+...+
T Consensus       363 ~~GEiigIvG-~NGaGKTTLlKiLaG~lkPd~G-~V-~--~~~~isY~pQ~i~~d~~~tV~~~L~~~~~~~~~~~~~~el  437 (590)
T PRK13409        363 RKGEVIGIVG-PNGIGKTTFVKLLAGVLKPDEG-EV-D--TDLKISYKPQYIKPDYDGTVEDLLRSITDDLGSSYYKSEI  437 (590)
T ss_pred             ECCCEEEEEC-CCCCCHHHHHHHHHCCCCCCCC-EE-E--ECCEEEECCHHCCCCCCCCHHHHHHHHCCCCCHHHHHHHH
T ss_conf             0474899988-8888789999998288778874-47-5--4774873360014686881999998624422538999999


Q ss_pred             HCCCCCEEEEECCCCCC-CHHCCCHHHHHH--HHHHHHHCCCEEEECCCCCCCH-HH--------HHHHHHCCCCCCCCC
Q ss_conf             02489806872487612-032079999999--8999851288899738888898-99--------999862012543578
Q gi|254780725|r  238 VFYAENLSILTAPAMLS-RTYDFDEKMIVP--VLDILEQIFPLVILDVPHVWNS-WT--------QEVLTLSDKVVITTS  305 (427)
Q Consensus       238 ~~~~~gL~lL~a~~~~~-~~~~~~~~~l~~--ll~~l~~~yd~VIiD~p~~~~~-~~--------~~~L~~AD~vviV~~  305 (427)
                      .+   .|.+   ..-++ ....++.+...+  +...+....|+.|+|=|...-+ ..        ...+.......+|++
T Consensus       438 l~---~L~l---~~lldk~v~~LSGGEkQRvaLA~~L~~~anvLLLDEPTn~LDvE~R~~~~k~i~~~~~~~~~t~~vV~  511 (590)
T PRK13409        438 IK---PLNL---EKLLDRNVKDLSGGELQRVAIAACLSRDADLYLLDEPSAYLDVEQRLAVARAIRRIAEEKEKAALVVD  511 (590)
T ss_pred             HH---HHCC---HHHHCCCHHHCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             98---8788---86764962440989999999999866799999994898877889999999999999986697599994


Q ss_pred             CCHH
Q ss_conf             7768
Q gi|254780725|r  306 LDLA  309 (427)
Q Consensus       306 p~~~  309 (427)
                      -|..
T Consensus       512 HD~~  515 (590)
T PRK13409        512 HDIY  515 (590)
T ss_pred             CCHH
T ss_conf             7099


No 346
>PRK00139 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional
Probab=93.75  E-value=0.34  Score=26.48  Aligned_cols=35  Identities=20%  Similarity=0.100  Sum_probs=26.8

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             675379997469887756899999999996269949999
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLA  197 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLv  197 (427)
                      ...++|+|+|+   .||||++.-++..|.. .|.++.++
T Consensus        98 ~~l~vIgITGT---nGKTTt~~~l~~iL~~-~g~~~~~i  132 (481)
T PRK00139         98 DKLKLIGVTGT---NGKTTTAYLIAQILRL-LGKKAALI  132 (481)
T ss_pred             HCCCEEEEECC---CCCHHHHHHHHHHHHH-CCCCCEEE
T ss_conf             31808999589---9843499999999987-49863143


No 347
>TIGR02632 RhaD_aldol-ADH rhamnulose-1-phosphate aldolase/alcohol dehydrogenase; InterPro: IPR013454    Rhamnose is a methyl-pentose sugar which is found as a constituent of pectin within the cell walls of dicotyledonous plants and has also been found in the mucilage of a number of legume plants . RhaD from Rhizobium leguminosarum bv. trifolii is encoded by a gene occurring in a rhamnose utilisation cluster, and is necessary for growth on this compound . This protein is predicted to be a bifunctional NAD-dependent aldolase/dehydrogenase..
Probab=93.72  E-value=0.061  Score=31.09  Aligned_cols=248  Identities=18%  Similarity=0.210  Sum_probs=123.8

Q ss_pred             CEEEEEEECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHH-HHHHH-----
Q ss_conf             305999838989999999886411002022373069989999998618998499998059876778899-98885-----
Q gi|254780725|r   28 RISVHVFCVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSAL-EPLAE-----  101 (427)
Q Consensus        28 ~~~~~~f~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l-~~la~-----  101 (427)
                      |-.|-.|-+++.+.+.+... +-+||+.-+.-     +++   ||..+= -.=++||.... ..-+++| ..|.+     
T Consensus       257 r~~i~~f~D~d~vL~Fvns~-e~~~La~LGts-----CPD---HflrTK-~~PL~iD~~P~-a~d~e~~~~~l~~~~~~Y  325 (709)
T TIGR02632       257 RRKIGTFDDSDAVLEFVNSK-EAPRLAALGTS-----CPD---HFLRTK-IRPLVIDWAPD-APDLEELVAKLKEGLEAY  325 (709)
T ss_pred             CCEEEEECCCHHHHHHHHHH-CCCCHHHCCCC-----CCC---CHHHCC-CCCEEEECCCC-CCCHHHHHHHHHHHHHHH
T ss_conf             20035323747888876202-13105650676-----653---012315-35525732688-765899999999999987


Q ss_pred             ---------H---------CCCCCEEEEE--------EC-----CCCHHHHHHHHH-----CCCCEEECCCCCHH-----
Q ss_conf             ---------3---------2899808998--------16-----871899999997-----65626431899989-----
Q gi|254780725|r  102 ---------V---------CDSGTKVIVI--------GD-----TNDVSLYRALIS-----NHVSEYLIEPLSVA-----  140 (427)
Q Consensus       102 ---------~---------~~p~~~Vivi--------g~-----~~d~~l~r~l~r-----~Gv~dyl~~P~~~~-----  140 (427)
                               .         -+|...||.|        |.     .-.-.+|.+++.     .-+++|...|....     
T Consensus       326 r~dY~~YYe~~~~p~Sp~Mr~a~P~v~LvPGvGm~SfGkdk~~arva~efY~~AI~VMRGA~Av~~Y~~L~e~E~F~IEY  405 (709)
T TIGR02632       326 REDYARYYERHRRPDSPTMRDANPAVLLVPGVGMISFGKDKETARVAAEFYVNAINVMRGAEAVSEYAALPEQEAFDIEY  405 (709)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCCCCCCCCH
T ss_conf             89999997503788648888868738970771345346666667888999999997415611121025875110334101


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHH
Q ss_conf             99997631023322234567537999746988775689999999999626994999978798986033438998789888
Q gi|254780725|r  141 DIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISD  220 (427)
Q Consensus       141 ~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d  220 (427)
                      +.++ ...+...+. ++.-.+||+.|+|+-||+|+-     +|..|+.+ |-.|+++|+|...-..              
T Consensus       406 W~LE-eaKL~rmP~-ek~LA~~Va~VtGGasGIG~~-----~A~rL~~e-GAhvV~aD~d~~~a~~--------------  463 (709)
T TIGR02632       406 WALE-EAKLRRMPK-EKELARRVAFVTGGASGIGRE-----TARRLVDE-GAHVVLADLDAEAAEA--------------  463 (709)
T ss_pred             HHHH-HHHHHCCCC-CCCCCCEEEEEECCCCCHHHH-----HHHHHHHC-CCEEEEECCCHHHHHH--------------
T ss_conf             1679-998724765-967157068897388652689-----99999736-9779996236578999--------------


Q ss_pred             HHCCCCCHHHHHHHHHHHCCCCCEE-----EEEC-CCCCCCHHCCCHHHHHHHHHHHHHCC---CEEEECCCCCCCHHHH
Q ss_conf             6318456124337653202489806-----8724-87612032079999999899985128---8899738888898999
Q gi|254780725|r  221 AIYPVGRIDKAFVSRLPVFYAENLS-----ILTA-PAMLSRTYDFDEKMIVPVLDILEQIF---PLVILDVPHVWNSWTQ  291 (427)
Q Consensus       221 ~l~~~~rlD~~~l~~~l~~~~~gL~-----lL~a-~~~~~~~~~~~~~~l~~ll~~l~~~y---d~VIiD~p~~~~~~~~  291 (427)
                                 .-+.+..+++.+--     +-++ |.---..+-.+++.+...++.....|   |.||..-+-..+....
T Consensus       464 -----------va~~~~~~fG~d~a~AGsdisaCGPaiGl~~DvT~e~~v~~~f~~v~~~yGGvD~vv~nAGi~~S~p~~  532 (709)
T TIGR02632       464 -----------VAAEIVDKFGADKAVAGSDISACGPAIGLKLDVTDEEAVKAAFAEVALAYGGVDIVVNNAGIAVSSPLE  532 (709)
T ss_pred             -----------HHHHHHHHCCCCCEECCCCHHCCCCCEEEEEEECCHHHHHHHHHHHHHHHCCEEEEEECCCHHCCCCCH
T ss_conf             -----------999986313888121143200046710027631758999999999999749847876525301057702


Q ss_pred             H---HHHHCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             9---986201254357877688999999999
Q gi|254780725|r  292 E---VLTLSDKVVITTSLDLAGLRNSKNLID  319 (427)
Q Consensus       292 ~---~L~~AD~vviV~~p~~~slr~a~~ll~  319 (427)
                      .   .=...=.+=|.++...---|.+-|+++
T Consensus       533 ~t~r~~~W~l~~di~atG~FLVareA~r~~~  563 (709)
T TIGR02632       533 ETERLEEWDLNLDILATGYFLVAREAARLMR  563 (709)
T ss_pred             HHHHHHHHHHCCEEEEECCHHHHHHHHHHHH
T ss_conf             3221554320120101200358889999997


No 348
>cd04155 Arl3 Arl3 subfamily.  Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension.  In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form.  The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.  Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2).  It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery.  In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.
Probab=93.71  E-value=0.29  Score=26.91  Aligned_cols=83  Identities=12%  Similarity=0.161  Sum_probs=57.1

Q ss_pred             CCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCC-HHHHHHHHHHHH-HHHHCCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             288899738888--8989999986201254357877-688999999999-999819876753899956589875200599
Q gi|254780725|r  274 IFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLD-LAGLRNSKNLID-VLKKLRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       274 ~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~-~~slr~a~~ll~-~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      .+.+.+.|++..  ........+..+|-+++|.+.+ ..++.++...+. .++.......++.++.|+.+.+.  .++.+
T Consensus        57 ~~~~~lwD~~G~~~~~~~~~~y~~~a~~iI~VvD~td~~~~~~~~~~l~~~l~~~~~~~~PiLiv~NK~Dl~~--a~~~~  134 (173)
T cd04155          57 GFKLNVWDIGGQRAIRPYWRNYFENTDCLIYVIDSADKKRLEEAGAELVELLEEEKLAGVPVLVFANKQDLAT--AAPAE  134 (173)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCC--CCCHH
T ss_conf             9999998558751012689976555637999996675688999999999997413006983899997666777--89999


Q ss_pred             HHHHHHCCC
Q ss_conf             999984895
Q gi|254780725|r  350 DFCAPLGIT  358 (427)
Q Consensus       350 ~~~~~lg~~  358 (427)
                      ++.+.++..
T Consensus       135 eI~~~l~l~  143 (173)
T cd04155         135 EIAEALNLH  143 (173)
T ss_pred             HHHHHHCHH
T ss_conf             999985876


No 349
>cd04115 Rab33B_Rab33A Rab33B/Rab33A subfamily.  Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II.  Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells.  In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine 
Probab=93.70  E-value=0.51  Score=25.45  Aligned_cols=109  Identities=13%  Similarity=0.156  Sum_probs=71.4

Q ss_pred             CCCEEEECCCCCCC---HHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCC-CCCCCEEEEECCCCCCCCHHHH
Q ss_conf             28889973888889---899999862012543578-776889999999999998198-7675389995658987520059
Q gi|254780725|r  274 IFPLVILDVPHVWN---SWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRP-ADKPPYLVLNQVKTPKKPEISI  348 (427)
Q Consensus       274 ~yd~VIiD~p~~~~---~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~-~~~~~~iVlNr~~~~~~~~i~~  348 (427)
                      .+.+-|+|++..-.   .........+|-+++|.+ -+..|+.+.+.+++.+++... +.-++.+|-|+.+......++.
T Consensus        50 ~v~l~iwDtaG~e~~~~s~~~~~~~~a~~~ilvydvt~~~Sf~~~~~w~~~i~~~~~~~~~p~vlVGNK~DL~~~r~Vs~  129 (170)
T cd04115          50 RIKVQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQIQVPT  129 (170)
T ss_pred             EEEEEEEECCCCHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCHHHCCCCH
T ss_conf             99999997788530567778998457735799950474767999999999999865888997999999821341178799


Q ss_pred             HHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC-----HHHHHHHHHHHHH
Q ss_conf             999998489537990687999999884796189888999-----8999999999998
Q gi|254780725|r  349 SDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS-----AIANLLVDFSRVL  400 (427)
Q Consensus       349 ~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s-----~~a~~~~~La~~i  400 (427)
                      +                  +.-.-|...|.+..|.+.+.     -+-+.|..||++|
T Consensus       130 ~------------------e~~~~a~~~~~~~~E~SAK~~~~~~nV~~~F~~la~~i  168 (170)
T cd04115         130 D------------------LAQRFADAHSMPLFETSAKDPSENDHVEAIFMTLAHKL  168 (170)
T ss_pred             H------------------HHHHHHHHCCCEEEEECCCCCCCCCCHHHHHHHHHHHH
T ss_conf             9------------------99999997799999988899851708899999999996


No 350
>cd04123 Rab21 Rab21 subfamily.  The localization and function of Rab21 are not clearly defined, with conflicting data reported.  Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker.  More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site
Probab=93.69  E-value=0.51  Score=25.43  Aligned_cols=111  Identities=17%  Similarity=0.237  Sum_probs=71.0

Q ss_pred             HCCCEEEECCCCCCC--HHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             128889973888889--8999998620125435787-7688999999999999819876753899956589875200599
Q gi|254780725|r  273 QIFPLVILDVPHVWN--SWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       273 ~~yd~VIiD~p~~~~--~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      ..+.+.++|++....  ......+..+|.+++|.+. +..|+.+...+.+.+++......++.+|-|+.+.+....++.+
T Consensus        47 ~~~~l~iwDt~G~~~~~~~~~~~~~~a~~~ilv~d~t~~~Sf~~i~~~~~~i~~~~~~~~~iilvgnK~Dl~~~r~v~~~  126 (162)
T cd04123          47 KRIDLAIWDTAGQERYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLERQRVVSKS  126 (162)
T ss_pred             EEEEEEEEECCCCCCCCCCCHHHEECCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHCCCCHH
T ss_conf             99999999589973035563133011445799963899899999999999999876999746866332132540888999


Q ss_pred             HHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHH
Q ss_conf             99998489537990687999999884796189888999--89999999999985
Q gi|254780725|r  350 DFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLM  401 (427)
Q Consensus       350 ~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~  401 (427)
                      +.                  -.-|...|-+..|.+.++  -+.+.|..|+++|.
T Consensus       127 e~------------------~~~a~~~~~~y~e~Sak~g~nV~e~F~~l~~~il  162 (162)
T cd04123         127 EA------------------EEYAKSVGAKHFETSAKTGKGIEELFLSLAKRMI  162 (162)
T ss_pred             HH------------------HHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             99------------------9999982998999812788198999999999869


No 351
>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]
Probab=93.69  E-value=0.2  Score=27.97  Aligned_cols=237  Identities=14%  Similarity=0.088  Sum_probs=95.4

Q ss_pred             HHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCCC-----------CCCCCEEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             899999997656264318999899999763102332223-----------456753799974698877568999999999
Q gi|254780725|r  118 VSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQEEG-----------KGSSGCSISFIGSRGGVGSSTIAHNCAFSI  186 (427)
Q Consensus       118 ~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~-----------~~~~grvIav~g~KGGvGkTTiA~nLA~~L  186 (427)
                      ...+++|.+.|.+.     ++.+++.+....+.....+.           ....-..|-++|+-.||||||||..+|.-|
T Consensus        39 ~~i~e~L~~~~~~~-----v~~~eir~~~~~l~~k~~~e~a~rY~lwR~ir~~~~p~IILIGGasGVGkStIA~ElA~rL  113 (299)
T COG2074          39 IEIQEELKKEGIRL-----VTKDEIREVYQKLLEKGDPEVAKRYLLWRRIRKMKRPLIILIGGASGVGKSTIAGELARRL  113 (299)
T ss_pred             HHHHHHHHHCCCEE-----EEHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHC
T ss_conf             99999997579727-----6199999999999873287999999999998615787599961788777257999999972


Q ss_pred             HHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHH
Q ss_conf             96269949999787989860334389987898886318456124337653202489806872487612032079999999
Q gi|254780725|r  187 ASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVP  266 (427)
Q Consensus       187 A~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~  266 (427)
                          |-+-+ +--|.----+--.++-+-.++|..-.       ...++.+-.+..++. ++++-.  ++...+ ...+..
T Consensus       114 ----gI~~v-isTD~IREvlR~ii~~~l~PtLh~Ss-------y~Awkalr~~~~~~p-iiaGF~--dqa~~V-~~GI~~  177 (299)
T COG2074         114 ----GIRSV-ISTDSIREVLRKIISPELLPTLHTSS-------YDAWKALRDPTDENP-IIAGFE--DQASAV-MVGIEA  177 (299)
T ss_pred             ----CCCEE-ECCHHHHHHHHHHCCHHHCCHHHHHH-------HHHHHHHCCCCCCCC-HHHHHH--HHHHHH-HHHHHH
T ss_conf             ----98610-04247999999737977455356757-------799998368999961-313178--776799-988999


Q ss_pred             HHHHHHHCCCEEEECCCCCCCHH-HHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCH
Q ss_conf             89998512888997388888989-99998620125435787768899999999999981987675389995658987520
Q gi|254780725|r  267 VLDILEQIFPLVILDVPHVWNSW-TQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPE  345 (427)
Q Consensus       267 ll~~l~~~yd~VIiD~p~~~~~~-~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~  345 (427)
                      +++.+-+.-.-+|+..=+..... -...+......+++.-+|.--.+  .|+.+-.   +...      .|+-     +.
T Consensus       178 VI~RAi~eG~~lIIEGvHlVPg~i~~~~~~~n~~~~~l~i~dee~Hr--~RF~~R~---~~t~------~~rp-----~~  241 (299)
T COG2074         178 VIERAIEEGEDLIIEGVHLVPGLIKEEALGNNVFMFMLYIADEELHR--ERFYDRI---RYTH------ASRP-----GG  241 (299)
T ss_pred             HHHHHHHCCCCEEEEEEEECCCCCCHHHHCCCEEEEEEEECCHHHHH--HHHHHHH---HHHH------CCCC-----HH
T ss_conf             99999853753588742115002167661355178999838878999--9999988---8876------0596-----56


Q ss_pred             HHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHC
Q ss_conf             059999998489537990687999999884796189888999899999999999852
Q gi|254780725|r  346 ISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIANLLVDFSRVLMG  402 (427)
Q Consensus       346 i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~~~~~La~~i~g  402 (427)
                      --.+-|.+.-..       .|. ++..|-..|.|+.+   +..+....+++.+.+..
T Consensus       242 Ryl~yf~EiR~I-------~Dy-l~~~Are~gVPvI~---n~di~etv~~il~~i~~  287 (299)
T COG2074         242 RYLEYFKEIRTI-------HDY-LVERAREHGVPVIE---NDDIDETVDRILEDIRK  287 (299)
T ss_pred             HHHHHHHHHHHH-------HHH-HHHHHHHCCCCEEC---CCCHHHHHHHHHHHHHH
T ss_conf             799999999999-------999-99988865998112---53199999999999999


No 352
>PRK05480 uridine kinase; Provisional
Probab=93.66  E-value=0.14  Score=28.83  Aligned_cols=182  Identities=15%  Similarity=0.118  Sum_probs=78.0

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCH-HHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf             53799974698877568999999999962699499997879898603-34389987898886318456124337653202
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTAN-INFDKDPINSISDAIYPVGRIDKAFVSRLPVF  239 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~-~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~  239 (427)
                      --+|++.| -.|+||||+|-.|+..|.   +..+.++.+|-.+-+.. .........+    ...|+.+|-.++...+..
T Consensus         6 P~iIgIaG-~SgSGKTT~a~~L~~~l~---~~~v~vi~~D~Yy~~~~~~~~~e~~~~n----fD~P~a~d~~ll~~~L~~   77 (209)
T PRK05480          6 PIIIGIAG-GSGSGKTTVASTIYEELG---DESIAVISQDSYYKDQSHLSMEERVKTN----YDHPDAFDHDLLIEHLKA   77 (209)
T ss_pred             CEEEEEEC-CCCCCHHHHHHHHHHHCC---CCCEEEEECCCCCCCCCCCCHHHHCCCC----CCCCHHHHHHHHHHHHHH
T ss_conf             88999989-997789999999999808---6875999554412473407886812368----788267669999999999


Q ss_pred             CCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             48980687248761203207999999989998512888997388888989999986201254357877688999999999
Q gi|254780725|r  240 YAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLID  319 (427)
Q Consensus       240 ~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~  319 (427)
                      ...|-.+-      -..+++.......-...+ ..-++||++--..+....  .-...|.-+.+-.+  ..+|-.+|+..
T Consensus        78 L~~G~~v~------~P~Ydf~t~~r~~~~~~i-~~~~iiIvEGi~~l~~~~--lr~~~DlkIfid~~--~d~rl~RRi~R  146 (209)
T PRK05480         78 LKAGKAIE------IPVYDYTEHTRSKETIHV-EPKDVIILEGILLLEDER--LRDLMDIKIFVDTP--LDIRLIRRLKR  146 (209)
T ss_pred             HHCCCCCC------CCCCCCCCCCCCCCEEEE-CCCCEEEEECHHHCCCHH--HHHHHCEEEEEECC--HHHHHHHHHHH
T ss_conf             97499875------675445566557863896-698769993456406787--88652657999667--77899999997


Q ss_pred             HHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCC
Q ss_conf             99981987675389995658987520059999998489537990687
Q gi|254780725|r  320 VLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFD  366 (427)
Q Consensus       320 ~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D  366 (427)
                      -..+.+...+   -|++++....+  -..+.|-.......+.+||..
T Consensus       147 D~~eRGr~~e---~vi~q~~~~v~--p~~~~yI~P~k~~ADlII~~~  188 (209)
T PRK05480        147 DVNERGRSLE---SVINQYLSTVR--PMHLQFIEPSKRYADIIIPEG  188 (209)
T ss_pred             HHHHHCCCHH---HHHHHHHHHHH--HHHHHHCHHHHHCCEEEECCC
T ss_conf             8999788999---99999999765--769976845274240898899


No 353
>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE).  The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE).  The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis.  The molecular mechanism of nickel uptake in many bacteria and most archaea is not known.  Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides.  The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.
Probab=93.64  E-value=0.19  Score=28.07  Aligned_cols=44  Identities=20%  Similarity=0.259  Sum_probs=30.8

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             5675379997469887756899999999996269949999787989
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      -+.|.+++++| ..|+||||+.--++-.+.- ....+.+-+-|...
T Consensus        28 i~~Ge~~~iiG-~sGsGKSTLl~~i~Gl~~p-~~G~I~~~g~~i~~   71 (228)
T cd03257          28 IKKGETLGLVG-ESGSGKSTLARAILGLLKP-TSGSIIFDGKDLLK   71 (228)
T ss_pred             ECCCCEEEEEC-CCCCHHHHHHHHHHCCCCC-CCCEEEECCEECCC
T ss_conf             86998999999-9998699999999728987-88669989964677


No 354
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=93.64  E-value=0.16  Score=28.59  Aligned_cols=53  Identities=19%  Similarity=0.290  Sum_probs=36.1

Q ss_pred             CCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             998999997631023322234567537999746988775689999999999626994999978
Q gi|254780725|r  137 LSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADL  199 (427)
Q Consensus       137 ~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDl  199 (427)
                      ....|+-+.+..-+.        .|- +..+|..-|+||||+...+|..|++ .+.+|++|-.
T Consensus        66 Tgi~ElDRVLGGGiV--------pGS-vvLlgGePGIGKSTLLLQia~~la~-~~~~vLYvSG  118 (372)
T cd01121          66 TGIEELDRVLGGGLV--------PGS-VILIGGDPGIGKSTLLLQVAARLAK-RGGKVLYVSG  118 (372)
T ss_pred             CCCHHHHHHHCCCCC--------CCE-EEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEEEC
T ss_conf             783666540057730--------671-7998259988688999999999986-3993899824


No 355
>PRK02006 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=93.63  E-value=0.52  Score=25.36  Aligned_cols=119  Identities=13%  Similarity=0.136  Sum_probs=58.3

Q ss_pred             CHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHH---H-C-------CCCCEEEEEECCC------CHHHHHHHHH
Q ss_conf             98999999861899849999805987677889998885---3-2-------8998089981687------1899999997
Q gi|254780725|r   64 SIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAE---V-C-------DSGTKVIVIGDTN------DVSLYRALIS  126 (427)
Q Consensus        64 ~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~---~-~-------~p~~~Vivig~~~------d~~l~r~l~r  126 (427)
                      +..+++.++.... -.+.+.|.+..+ +-+..++..-.   . +       -.+..+||++.--      ...++..+.+
T Consensus        18 sG~a~a~~L~~~G-~~V~~~D~~~~~-~~~~~l~~~~~~~~~~~g~~~~~~~~~~d~vV~SPGI~p~~p~~~~~l~~A~~   95 (501)
T PRK02006         18 SGLAMARWCARHG-CRLRVADTREAP-PNLAALQAEGIDAEFVGGAFDPALLDGVELVALSPGLSPLEPALAALLAAARE   95 (501)
T ss_pred             HHHHHHHHHHHCC-CEEEEEECCCCC-CCHHHHHHCCCCCEEECCCCCHHHHCCCCEEEECCEECCCCCCHHHHHHHHHH
T ss_conf             8999999999789-849999899998-61999986089818977889867846899999899008888543199999998


Q ss_pred             CCCCEEECCCCCHHHH-HHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             6562643189998999-9976310233222345675379997469887756899999999996269949999
Q gi|254780725|r  127 NHVSEYLIEPLSVADI-INSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLA  197 (427)
Q Consensus       127 ~Gv~dyl~~P~~~~~l-~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLv  197 (427)
                      .|+. .+    +..|+ .+.+..+    ........|+|+|.|+.   ||||++.=+++.|.. .|.++.+.
T Consensus        96 ~gi~-i~----~eiel~~~~~~~~----~~~~~~~~~iIaVTGTn---GKTTTt~li~~iL~~-~g~~~~~~  154 (501)
T PRK02006         96 RGIP-VW----GELELFAQALAAL----GASRGYAPKVLAITGTN---GKTTTTSLTGLLCER-AGKKVAVA  154 (501)
T ss_pred             CCCC-EE----EHHHHHHHHHHHC----CCCCCCCCCEEEEECCC---CHHHHHHHHHHHHHH-CCCCEEEE
T ss_conf             7995-87----6899999887630----22235687489993899---668799999999997-69974652


No 356
>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]
Probab=93.60  E-value=0.09  Score=30.05  Aligned_cols=42  Identities=26%  Similarity=0.335  Sum_probs=29.2

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             67537999746988775689999999999626994999978798
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      +.|+.|+++| +.|+||||++-.+.-.+.-. ..++.+=+.|+.
T Consensus       497 ~~Ge~vaIvG-~SGsGKSTL~KLL~gly~p~-~G~I~~dg~dl~  538 (709)
T COG2274         497 PPGEKVAIVG-RSGSGKSTLLKLLLGLYKPQ-QGRILLDGVDLN  538 (709)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHCCCCCC-CCEEEECCEEHH
T ss_conf             7998899987-99998899999983678888-855999987278


No 357
>pfam02421 FeoB_N Ferrous iron transport protein B. Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.
Probab=93.59  E-value=0.31  Score=26.79  Aligned_cols=79  Identities=23%  Similarity=0.331  Sum_probs=37.4

Q ss_pred             CCCEEEECCCCCC--CH------HHHHHH--HHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCC
Q ss_conf             2888997388888--98------999998--6201254357877688999999999999819876753899956589875
Q gi|254780725|r  274 IFPLVILDVPHVW--NS------WTQEVL--TLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKK  343 (427)
Q Consensus       274 ~yd~VIiD~p~~~--~~------~~~~~L--~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~  343 (427)
                      .+.++++|+|...  ..      .....+  ..||.++.|.+.+-.. |+. .+...+...   ..++.+|+|+++..++
T Consensus        45 ~~~~~lvDTpGi~~~~~~~~~e~v~~~~~~~~~aDlvl~vvDa~~~e-r~l-~l~~~l~~~---~~p~IvVlNK~Dl~~~  119 (188)
T pfam02421        45 GYEIEIVDLPGTYSLSPYSEEEKVARDYLLEEKPDVIINVVDATNLE-RNL-YLTLQLLEL---GIPVVVALNMMDEAEK  119 (188)
T ss_pred             CEEEEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCHH-HHH-HHHHHHHHC---CCCEEEEECCCHHCCC
T ss_conf             16799996888501465327899999998623687369997676245-448-999999976---9988999617020100


Q ss_pred             CHH--HHHHHHHHHCC
Q ss_conf             200--59999998489
Q gi|254780725|r  344 PEI--SISDFCAPLGI  357 (427)
Q Consensus       344 ~~i--~~~~~~~~lg~  357 (427)
                      ..+  ..+.+.+.+|.
T Consensus       120 ~~~~~~~~~l~~~lg~  135 (188)
T pfam02421       120 KGIKIDIKKLSELLGV  135 (188)
T ss_pred             CCCHHHHHHHHHHCCC
T ss_conf             3652039999987399


No 358
>KOG0635 consensus
Probab=93.56  E-value=0.28  Score=27.05  Aligned_cols=108  Identities=24%  Similarity=0.252  Sum_probs=59.9

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHH---HHHH
Q ss_conf             6753799974698877568999999999962699499997879898603343899878988863184561243---3765
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKA---FVSR  235 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~---~l~~  235 (427)
                      ..|-+|=+.| -.|.||||+|+.|..+|-+ +|+-+-.+|-|----.++..|+-    .-.|-..+..|+.++   +.+ 
T Consensus        29 qkGcviWiTG-LSgSGKStlACaL~q~L~q-rgkl~Y~LDGDNvRhGLN~DL~F----~a~dR~ENIRRigeVaKLFAD-  101 (207)
T KOG0635          29 QKGCVIWITG-LSGSGKSTLACALSQALLQ-RGKLTYILDGDNVRHGLNKDLGF----KAEDRNENIRRIGEVAKLFAD-  101 (207)
T ss_pred             CCCCEEEEEC-CCCCCCHHHHHHHHHHHHH-CCCEEEEECCCCCCCCCCCCCCC----CHHHHHHHHHHHHHHHHHHHC-
T ss_conf             8996899742-5778802599999999986-58658985485401043445676----503344657888999998732-


Q ss_pred             HHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCC
Q ss_conf             3202489806872487612032079999999899985128889973888
Q gi|254780725|r  236 LPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPH  284 (427)
Q Consensus       236 ~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~  284 (427)
                            .++-.++   .+-.++....++.+.++..-  .|=-|.+|+|-
T Consensus       102 ------ag~icia---SlISPYR~dRdacRel~~~~--~FiEvfmdvpl  139 (207)
T KOG0635         102 ------AGVICIA---SLISPYRKDRDACRELLPEG--DFIEVFMDVPL  139 (207)
T ss_pred             ------CCEEEEE---HHCCCHHCCHHHHHHHCCCC--CEEEEEECCCH
T ss_conf             ------5403100---21580020579999736689--85888752868


No 359
>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]
Probab=93.56  E-value=0.54  Score=25.29  Aligned_cols=45  Identities=13%  Similarity=0.101  Sum_probs=33.4

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHH
Q ss_conf             5379997469887756899999999996269949999787989-86033
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY-GTANI  208 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~-g~~~~  208 (427)
                      -+.|.|.| --|.|||++--.+-..|..+  .+..+|-.|... -++..
T Consensus        13 ~~~i~v~G-p~GSGKTaLie~~~~~L~~~--~~~aVI~~Di~t~~Da~~   58 (202)
T COG0378          13 MLRIGVGG-PPGSGKTALIEKTLRALKDE--YKIAVITGDIYTKEDADR   58 (202)
T ss_pred             EEEEEECC-CCCCCHHHHHHHHHHHHHHH--CCEEEEECEEECHHHHHH
T ss_conf             48999617-99867899999999999752--776899640400655999


No 360
>cd04147 Ras_dva Ras-dva subfamily.  Ras-dva (Ras - dorsal-ventral anterior localization) subfamily consists of a set of proteins characterized only in Xenopus leavis, to date.  In Xenopus Ras-dva expression is activated by the transcription factor Otx2 and begins during gastrulation throughout the anterior ectoderm.  Ras-dva expression is inhibited in the anterior neural plate by factor Xanf1.  Downregulation of Ras-dva results in head development abnormalities through the inhibition of several regulators of the anterior neural plate and folds patterning, including Otx2, BF-1, Xag2, Pax6, Slug, and Sox9.  Downregulation of Ras-dva also interferes with the FGF-8a signaling within the anterior ectoderm.  Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid.  Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.
Probab=93.54  E-value=0.54  Score=25.27  Aligned_cols=111  Identities=14%  Similarity=0.164  Sum_probs=71.5

Q ss_pred             CCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCC-CCCEEEEECCC-CCCCCHHHH
Q ss_conf             2888997388888--98999998620125435787-7688999999999999819876-75389995658-987520059
Q gi|254780725|r  274 IFPLVILDVPHVW--NSWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKLRPAD-KPPYLVLNQVK-TPKKPEISI  348 (427)
Q Consensus       274 ~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~~~~~-~~~~iVlNr~~-~~~~~~i~~  348 (427)
                      .+.+-|+|++...  ......-+..||.+++|.+- +..|+.++..+++.+.+..... -++.+|-|+++ ......++.
T Consensus        46 ~v~l~i~DtaG~e~~~~l~~~~~r~a~~~ilVyDit~~~Sf~~l~~w~~~i~~~~~~~~ipiilVGNK~Dll~~~R~V~~  125 (198)
T cd04147          46 SLTLDILDTSGSYSFPAMRKLSIQNSDAFALVYAVDDPESFEEVERLREEILEVKEDKFVPIVVVGNKADSLEEERQVPA  125 (198)
T ss_pred             EEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCCCCH
T ss_conf             99999997877513014555541588668999616977999999999999999628889828999878765010478489


Q ss_pred             HHHHHHHCCCEEEEECCCHHHHHHHH-HCCCCEEEECCCC--HHHHHHHHHHHHHHC
Q ss_conf             99999848953799068799999988-4796189888999--899999999999852
Q gi|254780725|r  349 SDFCAPLGITPSAIIPFDGAVFGMSA-NSGKMIHEVDPKS--AIANLLVDFSRVLMG  402 (427)
Q Consensus       349 ~~~~~~lg~~~~~~IP~D~~~~~~A~-~~G~pi~e~~p~s--~~a~~~~~La~~i~g  402 (427)
                      ++.+                  ..|. ..+.+..|.+.+.  -+-+.|..|++.+.-
T Consensus       126 ~e~~------------------~~a~~~~~~~f~EtSAktg~nV~e~F~~l~r~i~~  164 (198)
T cd04147         126 KDAL------------------STVELDWNCGFVETSAKDNENVLEVFKELLRQANL  164 (198)
T ss_pred             HHHH------------------HHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHCC
T ss_conf             9999------------------99985599789987799994989999999999773


No 361
>cd01120 RecA-like_NTPases RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Probab=93.53  E-value=0.16  Score=28.49  Aligned_cols=38  Identities=24%  Similarity=0.321  Sum_probs=30.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             9997469887756899999999996269949999787989
Q gi|254780725|r  164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       164 Iav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                      |.++ +-.|+||||++.++|...+. .+.+|+++|..-..
T Consensus         2 ~li~-g~~g~GKttl~~~~~~~~~~-~~~~~~~~~~ee~~   39 (165)
T cd01120           2 ILVF-GPTGSGKTTLALQLALNIAT-KGGKVVYVDIEEEI   39 (165)
T ss_pred             EEEE-CCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCH
T ss_conf             8999-89999899999999999876-39979999866644


No 362
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=93.50  E-value=0.44  Score=25.80  Aligned_cols=74  Identities=22%  Similarity=0.262  Sum_probs=45.7

Q ss_pred             CCCCCHHHHHHHHHHCCCCCCCCC-------CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC---CCEEEEECCCCC
Q ss_conf             189998999997631023322234-------5675379997469887756899999999996269---949999787989
Q gi|254780725|r  134 IEPLSVADIINSISAIFTPQEEGK-------GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFA---METLLADLDLPY  203 (427)
Q Consensus       134 ~~P~~~~~l~~ai~~~~~~~~~~~-------~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~---~~VlLvDlDl~~  203 (427)
                      ..|++...+...+.++|.......       ....+-++|+++-.|+||||+.+.+-..|.+...   .++.|+   -+.
T Consensus       127 ~~~~~~~~~~~~L~~lf~~~~~~dwQk~A~a~Al~~~~~vIsGGPGTGKTttV~~lLa~l~~~~~~~~l~I~La---APT  203 (607)
T PRK10875        127 AIEVDEALLAQTLDALFPPGDEVNWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLA---APT  203 (607)
T ss_pred             CCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEE---CCH
T ss_conf             88899899999999857998885189999999875577899679998778899999999999645899708998---822


Q ss_pred             CCCHHHC
Q ss_conf             8603343
Q gi|254780725|r  204 GTANINF  210 (427)
Q Consensus       204 g~~~~~l  210 (427)
                      |-++.-|
T Consensus       204 GKAAaRL  210 (607)
T PRK10875        204 GKAAARL  210 (607)
T ss_pred             HHHHHHH
T ss_conf             8999999


No 363
>cd04127 Rab27A Rab27a subfamily.  The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b.  Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions.  Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder.  When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated 
Probab=93.50  E-value=0.55  Score=25.23  Aligned_cols=111  Identities=14%  Similarity=0.139  Sum_probs=72.6

Q ss_pred             CCEEEECCCCCC--CHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCC-CCCEEEEECCCCCCCCHHHHHH
Q ss_conf             888997388888--98999998620125435787-7688999999999999819876-7538999565898752005999
Q gi|254780725|r  275 FPLVILDVPHVW--NSWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKLRPAD-KPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       275 yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~~~~~-~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      +.+-++|++..-  .......+..|+-+++|.+. +..|+.+.+.+++.++...... .++.+|-|+++......++.++
T Consensus        63 v~l~iwDtaGqe~~~~l~~~~~~~a~~~ilvydit~~~Sf~~l~~w~~~i~~~~~~~~~~iilVGNK~DL~~~r~V~~~e  142 (180)
T cd04127          63 IHLQLWDTAGQERFRSLTTAFFRDAMGFLLIFDLTNEQSFLNVRNWMSQLQTHAYCENPDIVLCGNKADLEDQRQVSEEQ  142 (180)
T ss_pred             EEEEEEECCCCHHHHHHHHHHHHHHCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCHHHCCCCCHHH
T ss_conf             99999989886304788899987543658999689889999899999999985466898578750323667508889999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHCC
Q ss_conf             9998489537990687999999884796189888999--8999999999998522
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMGR  403 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~gr  403 (427)
                                        ...-|...|.+..|.+.+.  -+.+.|..|++.+..|
T Consensus       143 ------------------~~~~a~~~~~~~~E~SAk~g~nV~e~F~~l~~~i~~~  179 (180)
T cd04127         143 ------------------AKALADKYGIPYFETSAATGTNVEKAVERLLDLVMKR  179 (180)
T ss_pred             ------------------HHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHH
T ss_conf             ------------------9999998499799980377919899999999999972


No 364
>cd01895 EngA2 EngA2 subfamily.  This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains.  Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family.  Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.
Probab=93.47  E-value=0.23  Score=27.61  Aligned_cols=79  Identities=11%  Similarity=0.127  Sum_probs=43.7

Q ss_pred             CCCEEEECCCCCC---------C----HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf             2888997388888---------9----89999986201254357877688999999999999819876753899956589
Q gi|254780725|r  274 IFPLVILDVPHVW---------N----SWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKT  340 (427)
Q Consensus       274 ~yd~VIiD~p~~~---------~----~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~  340 (427)
                      ...++++|+|...         .    ..+..++..+|.+++|++.+-.-...-..+++.+...+   .++.+|+|+++.
T Consensus        49 ~~~~~~vDtpGi~~~~~~~~~~e~~~~~~~~~~i~~~dvil~viDa~~~~~~~d~~i~~~l~~~~---~p~iiv~NK~Dl  125 (174)
T cd01895          49 GKKYTLIDTAGIRRKGKVEEGIEKYSVLRTLKAIERADVVLLVIDATEGITEQDLRIAGLILEEG---KALVIVVNKWDL  125 (174)
T ss_pred             CEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHCC---CCEEEEEECEEC
T ss_conf             98899985788421344210688999999999998428658997589899889999999999859---986999856752


Q ss_pred             CCCCHHHHHHHHHHH
Q ss_conf             875200599999984
Q gi|254780725|r  341 PKKPEISISDFCAPL  355 (427)
Q Consensus       341 ~~~~~i~~~~~~~~l  355 (427)
                      -.......+.+.+.+
T Consensus       126 i~~~~~~~~~~~~~~  140 (174)
T cd01895         126 VEKDSKTMKEFKKEI  140 (174)
T ss_pred             CCCCHHHHHHHHHHH
T ss_conf             676477899999999


No 365
>PRK11147 ABC transporter ATPase component; Reviewed
Probab=93.44  E-value=0.36  Score=26.37  Aligned_cols=146  Identities=15%  Similarity=0.122  Sum_probs=73.1

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHH-HCCCCCCCCHHHHHCCCCC-HHH----HH
Q ss_conf             67537999746988775689999999999626994999978798986033-4389987898886318456-124----33
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANI-NFDKDPINSISDAIYPVGR-IDK----AF  232 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~-~l~~~~~~~l~d~l~~~~r-lD~----~~  232 (427)
                      +.|-.|+++| .-|+||||+.--++-.+.-..| + +-+.-++..+-... .-.+++..++.+.+..... +..    ..
T Consensus       343 ~~Ge~ialvG-~NGsGKSTLlk~l~G~l~p~~G-~-i~~g~~~~i~y~~Q~~~~l~~~~tv~~~l~~~~~~~~~~~~~r~  419 (632)
T PRK11147        343 QRGDKIALIG-PNGCGKTTLLKLMLGQLQADSG-R-IHCGTKLEVAYFDQYRAELDPEKTVMDNLAEGKQEVMVNGKPRH  419 (632)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHCCCCCCCC-E-EEECCCCEEEEEHHHHHHCCCCCCHHHHHHHCCHHCCCCHHHHH
T ss_conf             7887799988-9884277999986066689987-7-99899870775515476459768699999732321011558999


Q ss_pred             HHHHHHCCCCCEEEEECCCCCCCHHCCCHHH--HHHHHHHHHHCCCEEEECCCCC-CCHHHHHH----HHHCCCCCCCCC
Q ss_conf             7653202489806872487612032079999--9998999851288899738888-89899999----862012543578
Q gi|254780725|r  233 VSRLPVFYAENLSILTAPAMLSRTYDFDEKM--IVPVLDILEQIFPLVILDVPHV-WNSWTQEV----LTLSDKVVITTS  305 (427)
Q Consensus       233 l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~--l~~ll~~l~~~yd~VIiD~p~~-~~~~~~~~----L~~AD~vviV~~  305 (427)
                      +...+..     .++.+.........++.+.  --.+...+....+++|+|=|.. .+-.+..+    |..-+-.+++++
T Consensus       420 ~~~~L~~-----f~f~~~~~~~~v~~LSGGEk~Rl~LA~~l~~~pnlLiLDEPTNhLDi~s~e~Le~aL~~y~Gtvl~VS  494 (632)
T PRK11147        420 VLGYLQD-----FLFHPKRAMTPVKALSGGERNRLLLARLFLKPSNLLILDEPTNDLDVETLELLEELLDSYQGTLLLVS  494 (632)
T ss_pred             HHHHHHH-----HCCCHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             9999998-----57798896391553999999999999985779978999898765799999999999985898399997


Q ss_pred             CCHHHHH
Q ss_conf             7768899
Q gi|254780725|r  306 LDLAGLR  312 (427)
Q Consensus       306 p~~~slr  312 (427)
                      -|..=+.
T Consensus       495 HDr~fl~  501 (632)
T PRK11147        495 HDRQFVD  501 (632)
T ss_pred             CCHHHHH
T ss_conf             9899998


No 366
>PRK00093 engA GTP-binding protein EngA; Reviewed
Probab=93.38  E-value=0.58  Score=25.11  Aligned_cols=207  Identities=16%  Similarity=0.169  Sum_probs=111.5

Q ss_pred             CEEEEECCCCC-CCHHHHHHHHHHHCCCCCEEEEEECCCC----HHHHHHHHHCCCCEEEC----CCCCHHHHHHHHHHC
Q ss_conf             49999805987-6778899988853289980899816871----89999999765626431----899989999976310
Q gi|254780725|r   79 DLIIVQTKVDS-REVLSALEPLAEVCDSGTKVIVIGDTND----VSLYRALISNHVSEYLI----EPLSVADIINSISAI  149 (427)
Q Consensus        79 ~~iivd~~~~~-~~~~~~l~~la~~~~p~~~Vivig~~~d----~~l~r~l~r~Gv~dyl~----~P~~~~~l~~ai~~~  149 (427)
                      =+.+||..... .+-..-.+-|..   -+-+||++-.--|    -..+-+.-+.|..+.+.    .-....+|.+.+...
T Consensus        85 IlfVvD~~~git~~D~~i~~~Lrk---~~k~vilviNK~D~~~~~~~~~ef~~LGf~~~i~iSA~h~~Gi~~L~~~i~~~  161 (438)
T PRK00093         85 ILFVVDGRAGLTPADEEIAKILRK---SNKPVILVVNKVDGKKMEADAYEFYSLGLGEPYPISAEHGRGIGDLLDAILEL  161 (438)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH---CCCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHH
T ss_conf             999983776898789999999997---39978999975566320345999998368981888530566989999999854


Q ss_pred             CCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHH
Q ss_conf             23322234567537999746988775689999999999626994999978798986033438998789888631845612
Q gi|254780725|r  150 FTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRID  229 (427)
Q Consensus       150 ~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD  229 (427)
                      +....... ...-.||++| |--|||||+-=.|   +.+   .++ +++-  ..|++-            |.+...    
T Consensus       162 l~~~~~~~-~~~iriaiiG-rpNvGKStl~N~l---l~~---~r~-ivs~--~~GtTr------------D~i~~~----  214 (438)
T PRK00093        162 LPEEEEEE-EDPIKIAIIG-RPNVGKSTLINAL---LGE---ERV-IVSD--IAGTTR------------DSIDTP----  214 (438)
T ss_pred             CCCCCCCC-CCCEEEEEEC-CCCCCHHHHHHHH---HHH---HHH-HCCC--CCCCCC------------CCEEEE----
T ss_conf             88554344-5560599955-8886556788876---543---332-0479--998511------------232679----


Q ss_pred             HHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC-------------CHHHHHHHHH
Q ss_conf             433765320248980687248761203207999999989998512888997388888-------------9899999862
Q gi|254780725|r  230 KAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVW-------------NSWTQEVLTL  296 (427)
Q Consensus       230 ~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~-------------~~~~~~~L~~  296 (427)
                        +      ..                                ....|.++|++.--             ...+..++..
T Consensus       215 --~------~~--------------------------------~~~~~~~iDTaGirkk~k~~~~iE~~s~~~t~~~i~~  254 (438)
T PRK00093        215 --F------ER--------------------------------DGQKYTLIDTAGIRRRGKVTEGIEKYSVIRTLKAIER  254 (438)
T ss_pred             --E------EE--------------------------------CCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             --9------98--------------------------------9967999989898765642137889999999999864


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             01254357877688999999999999819876753899956589875200599999984895
Q gi|254780725|r  297 SDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGIT  358 (427)
Q Consensus       297 AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~  358 (427)
                      ||.+++|++.+..--..=.+++..+.+.+   +++.+++|+++.-.......+++.+.+...
T Consensus       255 ~dvvilviDa~~~~~~qD~~i~~~i~~~g---k~~ii~vNKwDLv~~~~~~~~~~~~~i~~~  313 (438)
T PRK00093        255 ADVVLLVIDATEGITEQDLRIAGLALEAG---RALVIVVNKWDLVEKDSKTMEEVKEELRRR  313 (438)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHCC---CCEEEEEECHHCCCCCHHHHHHHHHHHHHH
T ss_conf             46699999766588488899999999819---966999970222566389999999999975


No 367
>pfam02702 KdpD Osmosensitive K+ channel His kinase sensor domain. This is a family of KdpD sensor kinase proteins that regulate the kdpFABC operon responsible for potassium transport. The aligned region corresponds to the N-terminal cytoplasmic part of the protein which may be the sensor domain responsible for sensing turgor pressure.
Probab=93.37  E-value=0.36  Score=26.37  Aligned_cols=44  Identities=18%  Similarity=0.308  Sum_probs=35.4

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             567537999746988775689999999999626994999978798
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      ++.||.--|+|..-|||||--..+=|..+.+ .|.+|++-=...+
T Consensus         1 ~~rG~LkIylG~apGVGKTy~ML~eA~~l~~-~G~DVViG~vEth   44 (211)
T pfam02702         1 GRRGKLKIFLGAAPGVGKTYAMLSEAHELLE-RGVDVVIGYVETH   44 (211)
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEEEECCC
T ss_conf             9976168985359987789999999999997-8995699995379


No 368
>PRK08233 hypothetical protein; Provisional
Probab=93.31  E-value=0.59  Score=25.05  Aligned_cols=156  Identities=13%  Similarity=0.117  Sum_probs=76.5

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             53799974698877568999999999962699499997879898603343899878988863184561243376532024
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      ..||++.| --|.||||+|-.|...+   .+..++..|.+.        +...+ ..+.++...+...|           
T Consensus         3 p~IIgIaG-gSgSGKTtla~~l~~~l---~~~~~~~~D~y~--------~~~~~-~~~~~~~~~~~~~d-----------   58 (182)
T PRK08233          3 TKIITIAA-VSGGGKTTLTERLTHKL---KNSKALYFDRYD--------FDNCP-EDICKWIDDGANYS-----------   58 (182)
T ss_pred             CEEEEEEC-CCCCCHHHHHHHHHHHC---CCCEEEEECCCC--------CCCCH-HHHHHHHCCCCCCC-----------
T ss_conf             88999968-88678999999999974---677589966655--------54687-88998740677866-----------


Q ss_pred             CCCEEEEECCCCCCCHHCCCHHHHHHHHHHHH--HCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             89806872487612032079999999899985--1288899738888898999998620125435787768899999999
Q gi|254780725|r  241 AENLSILTAPAMLSRTYDFDEKMIVPVLDILE--QIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLI  318 (427)
Q Consensus       241 ~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~--~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll  318 (427)
                                       .+....+..-+..++  ..+|+||+|.+-.+...  ..-..-|.-+.|-+|  ..+|=++|+.
T Consensus        59 -----------------~~d~~~l~~~l~~l~~~~~~d~iIvEgil~l~~~--~lr~l~D~kIfVdtp--~Dirl~RRi~  117 (182)
T PRK08233         59 -----------------EWVLTPLIKDIQELIAKSNVDYIIVDYPFAYLNS--EMRQYIDVTIFIDTP--LDIAMARRIL  117 (182)
T ss_pred             -----------------HHHHHHHHHHHHHHHCCCCCCEEEEEEEHHHCCH--HHHHHHCEEEEECCC--HHHHHHHHHH
T ss_conf             -----------------6669999999999855998728999644362689--899771878997286--8999999888


Q ss_pred             HHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECC
Q ss_conf             99998198767538999565898752005999999848953799068
Q gi|254780725|r  319 DVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPF  365 (427)
Q Consensus       319 ~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~  365 (427)
                      .-+++.+.  +.+.-|++++....++  ....|.+......+..||.
T Consensus       118 RDi~Er~g--r~i~svl~qY~~~VrP--m~~~fvePsk~~ADiIId~  160 (182)
T PRK08233        118 RDFKEDTG--NEIHNDLKHYLNYARP--LYLEALDTVKPNADIVLDG  160 (182)
T ss_pred             HHHHHHCC--CCHHHHHHHHHHHHHH--HHHHHHCHHHHCCCEEEEC
T ss_conf             88777618--8789999999998788--9999857003219689858


No 369
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=93.30  E-value=0.48  Score=25.62  Aligned_cols=33  Identities=12%  Similarity=0.257  Sum_probs=19.2

Q ss_pred             CCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHH
Q ss_conf             718999999976562643189998999997631
Q gi|254780725|r  116 NDVSLYRALISNHVSEYLIEPLSVADIINSISA  148 (427)
Q Consensus       116 ~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~  148 (427)
                      .|+.||-+..-.|-+|.=..|....-+.=.+-|
T Consensus       322 e~~Ql~Yqi~l~gr~dl~~ap~~~~g~eM~lLR  354 (704)
T PRK08691        322 EQIQLYYQIAVHGKRDLSLAPDEYAGFMMTLLR  354 (704)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
T ss_conf             999999999982202255699702539999999


No 370
>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.
Probab=93.24  E-value=0.32  Score=26.68  Aligned_cols=39  Identities=23%  Similarity=0.053  Sum_probs=30.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEECCCC
Q ss_conf             7999746988775689999999999626-994999978798
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVF-AMETLLADLDLP  202 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~-~~~VlLvDlDl~  202 (427)
                      +|++.| .-|+||||+|-.|...|.+.. +.+|.++-.|-.
T Consensus         1 IIGIaG-~sgSGKST~a~~l~~~l~~~~~~~~v~ii~~D~f   40 (220)
T cd02025           1 IIGIAG-SVAVGKSTTARVLQALLSRWPDHPNVELITTDGF   40 (220)
T ss_pred             CEEEEC-CCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCC
T ss_conf             989788-9987799999999998600269994899978787


No 371
>PRK08939 primosomal protein DnaI; Reviewed
Probab=93.24  E-value=0.38  Score=26.25  Aligned_cols=75  Identities=15%  Similarity=0.215  Sum_probs=46.6

Q ss_pred             HHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             9999976562643189998999997631023322234567537999746988775689999999999626994999978
Q gi|254780725|r  121 YRALISNHVSEYLIEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADL  199 (427)
Q Consensus       121 ~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDl  199 (427)
                      =++...+...||-..+.+..+.+.++......-.  .+..+|=+-++| .-|+|||.++..+|..|++ .|.+|+++-.
T Consensus       119 pk~i~~as~~d~~~~d~~R~~a~~~a~~F~~~y~--~~~~~kGlyl~G-~~G~GKTyL~~aian~La~-~g~~v~~v~~  193 (306)
T PRK08939        119 PKDLLQATLADIDLDDLDRLDALMAALDFLEAYK--PGEKVKGLYLYG-DFGVGKTYLLAAIANELAK-KGVSSTLVHF  193 (306)
T ss_pred             CHHHHCCCHHHCCCCCHHHHHHHHHHHHHHHHHC--CCCCCCEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEH
T ss_conf             7999809898648897789999999999999737--698887788989-9999899999999999998-6992999875


No 372
>pfam02492 cobW CobW/HypB/UreG, nucleotide-binding domain. This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans.
Probab=93.24  E-value=0.61  Score=24.97  Aligned_cols=156  Identities=14%  Similarity=0.155  Sum_probs=70.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             99974698877568999999999962699499997879898603343899878988863184561243376532024898
Q gi|254780725|r  164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAEN  243 (427)
Q Consensus       164 Iav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~g  243 (427)
                      |.++++==|.||||+--++....  ..+.++.++=-|.  |...                    +|..++.+.    ...
T Consensus         2 v~iitGFLGsGKTTll~~ll~~~--~~~~~~avI~Ne~--g~~~--------------------iD~~ll~~~----~~~   53 (174)
T pfam02492         2 VTVLTGFLGSGKTTLLEHLLRDN--REGLKIAVIVNDF--GETG--------------------IDAELLRET----GAE   53 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHC--CCCCCEEEEEECC--CCHH--------------------HHHHHHHHC----CCE
T ss_conf             69993488788999999999844--4898479999336--5302--------------------079998706----961


Q ss_pred             EEEEECCCCCCC-HHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHH---HHCCCCCCCCCCCH-HHHHH-HHHH
Q ss_conf             068724876120-320799999998999851288899738888898999998---62012543578776-88999-9999
Q gi|254780725|r  244 LSILTAPAMLSR-TYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVL---TLSDKVVITTSLDL-AGLRN-SKNL  317 (427)
Q Consensus       244 L~lL~a~~~~~~-~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L---~~AD~vviV~~p~~-~slr~-a~~l  317 (427)
                      +.-+..+--.-. ..++ ...+..+.+.-...+|+|+|.+...+.+....-+   ...+.++.++++.. ..-.+ ...+
T Consensus        54 v~el~~GciCc~~~~d~-~~~l~~l~~~~~~~~d~iiIE~sGla~p~~i~~~~~~~~~~~~i~vvDa~~~~~~~~~~~~~  132 (174)
T pfam02492        54 IVELNNGCICCTIREDL-SMVLEALLELKLPRLDLLFIETTGLACPAPVLDLRSDLGLDGVVTVVDVKNFTEGEDIPEKA  132 (174)
T ss_pred             EEEECCCCCCCCCCHHH-HHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHCCCCCEEEEEEECHHHHHCCCCHHHH
T ss_conf             89974886645433369-99999998557899999999587667707777653202654599999723433002007899


Q ss_pred             HHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHH
Q ss_conf             99999819876753899956589875200599999984
Q gi|254780725|r  318 IDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPL  355 (427)
Q Consensus       318 l~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~l  355 (427)
                      .+   +....+   .+|+|+.+.-...+. .+.+++.+
T Consensus       133 ~~---Qi~~AD---~vvlNK~Dl~~~~~~-l~~~~~~i  163 (174)
T pfam02492       133 PD---QIAFAD---LIVINKTDLAPAVGA-LEKLEADL  163 (174)
T ss_pred             HH---HHHHCC---EEEEEHHHCCCCHHH-HHHHHHHH
T ss_conf             99---998769---999846653782769-99999999


No 373
>cd01889 SelB_euk SelB subfamily.  SelB is an elongation factor needed for the co-translational incorporation of selenocysteine.  Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin.  In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu).  It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner.  This allows insertion of selenocysteine at in-frame UGA stop codons.  In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence).  The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation.  Archaeal and animal mechanisms of selenocysteine incorporation are more complex.  Although the SECIS elements have different secondary structures and conserved elements between archaea and euk
Probab=93.21  E-value=0.26  Score=27.25  Aligned_cols=66  Identities=11%  Similarity=0.072  Sum_probs=50.6

Q ss_pred             HCCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCC
Q ss_conf             1288899738888--89899999862012543578776889999999999998198767538999565898
Q gi|254780725|r  273 QIFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTP  341 (427)
Q Consensus       273 ~~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~  341 (427)
                      ..|-+.++|+|..  +.......+..+|..++|+..+-.-..++++.+..++..+.   ++.+++|+++.-
T Consensus        66 ~~~~i~~IDtPGH~df~~~~~~g~~~~D~ailvVda~~G~~~QT~eh~~~~~~~~~---~~iv~iNK~D~v  133 (192)
T cd01889          66 ENLQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDATKGIQTQTAECLVIGEILCK---KLIVVLNKIDLI  133 (192)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCCC---CEEEEEECCCCC
T ss_conf             74589998779838899888888743265279998788887899999999998589---979999741278


No 374
>PRK10419 nikE nickel transporter ATP-binding protein; Provisional
Probab=93.20  E-value=0.1  Score=29.68  Aligned_cols=43  Identities=23%  Similarity=0.203  Sum_probs=27.8

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             567537999746988775689999999999626994999978798
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      -..|.+++++| ..|+||||++--++-.+.- ....+.+-+-|+.
T Consensus        35 i~~GE~l~ivG-eSGsGKSTL~r~i~gl~~p-~sG~I~~~g~~l~   77 (266)
T PRK10419         35 LKSGETVALLG-RSGCGKSTLARLLVGLESP-SQGNISWRGEPLA   77 (266)
T ss_pred             ECCCCEEEEEC-CCCCHHHHHHHHHHCCCCC-CCEEEEECCEECC
T ss_conf             88998999999-9997799999999669999-9629988999567


No 375
>cd04152 Arl4_Arl7 Arl4/Arl7 subfamily.  Arl4 (Arf-like 4) is highly expressed in testicular germ cells, and is found in the nucleus and nucleolus.  In mice, Arl4 is developmentally expressed during embryogenesis, and a role in somite formation and central nervous system differentiation has been proposed.  Arl7 has been identified as the only Arf/Arl protein to be induced by agonists of liver X-receptor and retinoid X-receptor and by cholesterol loading in human macrophages.  Arl7 is proposed to play a role in transport between a perinuclear compartment and the plasma membrane, apparently linked to the ABCA1-mediated cholesterol secretion pathway.  Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.
Probab=93.17  E-value=0.62  Score=24.91  Aligned_cols=118  Identities=14%  Similarity=0.214  Sum_probs=75.3

Q ss_pred             CCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCC-CCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             288899738888--89899999862012543578-77688999999999999819-876753899956589875200599
Q gi|254780725|r  274 IFPLVILDVPHV--WNSWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLR-PADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       274 ~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~-~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      .+.+.+.|++..  +......-...||-+++|.+ .+..++.+++..+..+.+.. ....++.+|.|+.+.+.  ..+..
T Consensus        51 ~v~l~iwDtaGqe~~r~l~~~Y~r~a~g~i~V~D~td~~~~~~~~~~l~~~~~~~~~~~~piliv~NK~Dl~~--~~~~~  128 (183)
T cd04152          51 GITFHFWDVGGQEKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITRFSENQGVPVLVLANKQDLPN--ALSVS  128 (183)
T ss_pred             EEEEEEEECCCCCCCCEEHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCC--CCCHH
T ss_conf             6799999789873451008767467867899996776889999999999997321237962999986677766--87889


Q ss_pred             HHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECC--CCHHHHHHHHHHHHHHCCCC
Q ss_conf             999984895379906879999998847961898889--99899999999999852212
Q gi|254780725|r  350 DFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDP--KSAIANLLVDFSRVLMGRVT  405 (427)
Q Consensus       350 ~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p--~s~~a~~~~~La~~i~gr~~  405 (427)
                      ++++.++..-            -+...+-.+.+.+.  +.-+.++|..|++.|..+..
T Consensus       129 ei~~~l~l~~------------~~~~~~~~i~~tSA~tG~gI~e~f~~L~~~i~~r~~  174 (183)
T cd04152         129 EVEKLLALHE------------LSASTPWHVQPACAIIGEGLQEGLEKLYEMILKRRK  174 (183)
T ss_pred             HHHHHHHHHH------------HHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             9999971999------------866699899972799796989999999999999998


No 376
>PRK03003 engA GTP-binding protein EngA; Reviewed
Probab=93.14  E-value=0.52  Score=25.39  Aligned_cols=33  Identities=15%  Similarity=0.198  Sum_probs=19.5

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             379997469887756899999999996269949999
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLA  197 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLv  197 (427)
                      -|+-|+-++  .|-|..=..+|..|-+ .+++|+||
T Consensus       120 ~IlfVvD~~--~glt~~D~eia~~LRk-~~kpviLV  152 (474)
T PRK03003        120 AVLFVVDAT--VGATATDEAVARLLRR-SGKPVFLA  152 (474)
T ss_pred             EEEEEEECC--CCCCHHHHHHHHHHHH-CCCCEEEE
T ss_conf             999999689--8988789999999875-39977998


No 377
>cd04171 SelB SelB subfamily.  SelB is an elongation factor needed for the co-translational incorporation of selenocysteine.  Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin.  In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu).  It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons.  In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence).  The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation.  Archaeal and animal mechanisms of selenocysteine incorporation are more complex.  Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryo
Probab=93.08  E-value=0.23  Score=27.52  Aligned_cols=66  Identities=18%  Similarity=0.164  Sum_probs=44.2

Q ss_pred             CCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf             88899738888--898999998620125435787768899999999999981987675389995658987
Q gi|254780725|r  275 FPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPK  342 (427)
Q Consensus       275 yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~  342 (427)
                      ..+.++|+|..  +...+...+..+|.+++|+..+-.-.......+..++..+.  +++.+|+|+++.-.
T Consensus        51 ~~i~~iDtPGh~~~~~~~~~~~~~aD~~llVvda~~g~~~q~~e~~~~~~~~~i--~~~ivvlNK~D~v~  118 (164)
T cd04171          51 KRLGFIDVPGHEKFIKNMLAGAGGIDLVLLVVAADEGIMPQTREHLEILELLGI--KRGLVVLTKADLVD  118 (164)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCC--CCEEEEEECCCCCC
T ss_conf             899999487879999999998742672589986177888889999999987388--72787346342579


No 378
>TIGR02928 TIGR02928 orc1/cdc6 family replication initiation protein; InterPro: IPR014277   This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. The proteins in this entry are found exclusively in the archaea. Several members may be found in a genome and interact with each other..
Probab=93.07  E-value=0.64  Score=24.82  Aligned_cols=186  Identities=12%  Similarity=0.121  Sum_probs=82.5

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH---CCCC-EEEEECCCCCCCCHHHCCCCC
Q ss_conf             899999763102332223456753799974698877568999999999962---6994-999978798986033438998
Q gi|254780725|r  139 VADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASV---FAME-TLLADLDLPYGTANINFDKDP  214 (427)
Q Consensus       139 ~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~---~~~~-VlLvDlDl~~g~~~~~l~~~~  214 (427)
                      ..++..+|+.+..   |+..+  .=|-++| |-|+|||.++-++.-.|.+.   ++.+ +..+-.|++.-++...     
T Consensus        26 I~~l~~~L~~~l~---PG~~P--~Ni~iYG-kTGtGKT~vt~~v~~~l~~~~~~~d~~D~~~~~~NC~~~~T~y~-----   94 (383)
T TIGR02928        26 IEELAKALRPILR---PGSRP--SNIFIYG-KTGTGKTAVTKYVMKELEEAAEDRDVRDVSTVYINCQILDTSYQ-----   94 (383)
T ss_pred             HHHHHHHHHHHHC---CCCCC--CCEEEEC-CCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCHHH-----
T ss_conf             9999999887506---74898--7258878-88987889999999999998622699715899977854684699-----


Q ss_pred             CCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHH-HCCCEEEECCCCCCCHHHHHH
Q ss_conf             7898886318456124337653202489806872487612032079999999899985-128889973888889899999
Q gi|254780725|r  215 INSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILE-QIFPLVILDVPHVWNSWTQEV  293 (427)
Q Consensus       215 ~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p~~~~~~~~~~  293 (427)
                        .+..++           ..+- +...+..+-..       ..-..+.+..+.+.+. ..++.+||            +
T Consensus        95 --~~~~L~-----------~~ln-~~~~~~~vP~t-------G~s~~~~~~~l~~~l~~~~~~~~~i------------v  141 (383)
T TIGR02928        95 --VLVELA-----------NQLN-RRGSGEEVPTT-------GLSTSEVFRELYKELNRERGDSLII------------V  141 (383)
T ss_pred             --HHHHHH-----------HHHC-CCCCCCCCCCC-------CCCHHHHHHHHHHHHHHHCCCEEEE------------E
T ss_conf             --999999-----------9851-57788889887-------7878999999999983201887999------------8


Q ss_pred             HHHCCCCCCCCCCCHHHHH-HHHHHHHHHHHCCCCCCCCEEE--EECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHH
Q ss_conf             8620125435787768899-9999999999819876753899--956589875200599999984895379906879999
Q gi|254780725|r  294 LTLSDKVVITTSLDLAGLR-NSKNLIDVLKKLRPADKPPYLV--LNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVF  370 (427)
Q Consensus       294 L~~AD~vviV~~p~~~slr-~a~~ll~~l~~~~~~~~~~~iV--lNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~  370 (427)
                      |+.-|.++ --..+-++.. -.+.|.+.=........++.+|  -|-...  +..++ .+++..|.-+-...=|||-.-.
T Consensus       142 LDEiD~Lv-~~~~d~PAyS~~LY~L~Ra~~~~~~~~~~vgvIgISND~~f--~~~Ld-~RVkSsL~~eei~FpPYdA~eL  217 (383)
T TIGR02928       142 LDEIDKLV-RKDDDDPAYSKLLYQLSRARENGDLENAKVGVIGISNDLKF--RENLD-PRVKSSLCEEEIVFPPYDAEEL  217 (383)
T ss_pred             ECCCCHHH-CCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCHH--HHHCC-CCEECCCCCCCCEECCCCHHHH
T ss_conf             62310221-58888807878853433100035778853489998657143--64457-5301324874004079886999


Q ss_pred             HH
Q ss_conf             99
Q gi|254780725|r  371 GM  372 (427)
Q Consensus       371 ~~  372 (427)
                      .+
T Consensus       218 ~~  219 (383)
T TIGR02928       218 RD  219 (383)
T ss_pred             HH
T ss_conf             99


No 379
>cd03290 ABCC_SUR1_N The SUR domain 1.  The sulfonylurea receptor SUR is an ATP transporter of the ABCC/MRP family with tandem ATPase binding domains.  Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel.  Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism.  It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.
Probab=93.07  E-value=0.22  Score=27.72  Aligned_cols=37  Identities=14%  Similarity=0.148  Sum_probs=26.4

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             567537999746988775689999999999626994999
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLL  196 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlL  196 (427)
                      -+.|.+++++| +-|+||||+.--++-.+.-. ..++.+
T Consensus        24 i~~Ge~~~IvG-~sGsGKSTLl~~l~g~~~~~-~G~I~~   60 (218)
T cd03290          24 IPTGQLTMIVG-QVGCGKSSLLLAILGEMQTL-EGKVHW   60 (218)
T ss_pred             ECCCCEEEEEC-CCCCCHHHHHHHHHCCCCCC-CCEEEE
T ss_conf             86999999999-99980999999985556567-764998


No 380
>cd04120 Rab12 Rab12 subfamily.  Rab12 was first identified in canine cells, where it was localized to the Golgi complex.  The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported.  More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic
Probab=93.06  E-value=0.64  Score=24.81  Aligned_cols=115  Identities=15%  Similarity=0.231  Sum_probs=75.2

Q ss_pred             CCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHH
Q ss_conf             288899738888--898999998620125435787-76889999999999998198767538999565898752005999
Q gi|254780725|r  274 IFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISD  350 (427)
Q Consensus       274 ~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~  350 (427)
                      .+.+-|+|++..  +...+..-+..|+-+++|.+. +..|+.+...+++.+++......++.+|-|+++......++.++
T Consensus        48 ~v~l~IWDTaGqe~f~sl~~~yyr~a~~~ilVyDit~~~SF~~l~~W~~~i~~~~~~~~~iiLVGNK~DL~~~R~Vs~~e  127 (202)
T cd04120          48 KIRLQIWDTAGQERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETDREISRQQ  127 (202)
T ss_pred             EEEEEEEECCCCCCCCCCHHHHHHHHCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHCCCCHHH
T ss_conf             99999997988612452357887641445899856888999999999999997466887189876536505317879999


Q ss_pred             HHHHHCCCEEEEECCCHHHHHHHHH-CCCCEEEECCCC--HHHHHHHHHHHHHHCCCCC
Q ss_conf             9998489537990687999999884-796189888999--8999999999998522122
Q gi|254780725|r  351 FCAPLGITPSAIIPFDGAVFGMSAN-SGKMIHEVDPKS--AIANLLVDFSRVLMGRVTV  406 (427)
Q Consensus       351 ~~~~lg~~~~~~IP~D~~~~~~A~~-~G~pi~e~~p~s--~~a~~~~~La~~i~gr~~~  406 (427)
                      .++                  -|.. +|....|.+.+.  -+.+.|..|++.|..+...
T Consensus       128 ~~~------------------~A~~~~~~~f~EtSAkt~~nV~e~F~~l~~~i~~~~~~  168 (202)
T cd04120         128 GEK------------------FAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKKMPL  168 (202)
T ss_pred             HHH------------------HHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             999------------------99827998899925899969899999999999985876


No 381
>PRK08327 acetolactate synthase catalytic subunit; Validated
Probab=92.99  E-value=0.66  Score=24.75  Aligned_cols=23  Identities=9%  Similarity=0.060  Sum_probs=10.9

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             877568999999999962699499
Q gi|254780725|r  172 GVGSSTIAHNCAFSIASVFAMETL  195 (427)
Q Consensus       172 GvGkTTiA~nLA~~LA~~~~~~Vl  195 (427)
                      |+..+--... -..|++..+.+|+
T Consensus       230 G~~~~~a~~~-l~~lae~lg~PV~  252 (568)
T PRK08327        230 GGRRAEAFAS-LDRLAEELGIPVV  252 (568)
T ss_pred             CCCHHHHHHH-HHHHHHHCCCCEE
T ss_conf             7335789999-9999875499679


No 382
>PRK06526 transposase; Provisional
Probab=92.99  E-value=0.18  Score=28.16  Aligned_cols=116  Identities=13%  Similarity=0.137  Sum_probs=68.3

Q ss_pred             EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCE--------
Q ss_conf             306998999999861899849999805987677889998885328998089981687189999999765626--------
Q gi|254780725|r   60 ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSE--------  131 (427)
Q Consensus        60 v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~d--------  131 (427)
                      .+..|++.+.+.+..++.-         ......+.|..|.+..        +....+-..-|.+.++|...        
T Consensus        12 LrL~~ma~~~~~~~~~a~~---------~~~s~~e~L~~Lle~E--------~~~R~~rr~~rrlk~A~fp~~ktLe~fd   74 (254)
T PRK06526         12 LKAPSLAGAVERLAERARA---------ESWSHEEFLAACLQRE--------VAARESHGGEGRIRAARFPSRKSLEEFD   74 (254)
T ss_pred             CCHHHHHHHHHHHHHHHHH---------CCCCHHHHHHHHHHHH--------HHHHHHHHHHHHHHHCCCCCCCCHHHCC
T ss_conf             3837899999999988876---------5999999999999999--------9999998999999977979988987678


Q ss_pred             EECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             431899989999976310233222345675379997469887756899999999996269949999787
Q gi|254780725|r  132 YLIEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLD  200 (427)
Q Consensus       132 yl~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlD  200 (427)
                      |-..|--....+..+..+      .--..+.=|.++| ..|+|||.+|+.++....+ .|.+|..+-++
T Consensus        75 ~~~~~~l~~~~i~~La~~------~fi~~~~Nvil~G-~~GtGKThLA~Alg~~A~~-~G~~v~f~~~~  135 (254)
T PRK06526         75 FDHQRSLKRDTIAHLGTL------DFVTGKENVVFLG-PPGTGKTHLAIGLGIRACQ-AGHRVLFATAA  135 (254)
T ss_pred             CCCCCCCCHHHHHHHHCC------CHHHCCCCEEEEC-CCCCCHHHHHHHHHHHHHH-CCCCEEEEEHH
T ss_conf             656789899999998637------1776588789989-9998689999999999998-69967998779


No 383
>KOG2004 consensus
Probab=92.98  E-value=0.11  Score=29.45  Aligned_cols=32  Identities=31%  Similarity=0.554  Sum_probs=27.2

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             567537999746988775689999999999626
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVF  190 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~  190 (427)
                      .-.|+|++|+| --|||||+|+-++|.+|.+..
T Consensus       435 s~qGkIlCf~G-PPGVGKTSI~kSIA~ALnRkF  466 (906)
T KOG2004         435 SVQGKILCFVG-PPGVGKTSIAKSIARALNRKF  466 (906)
T ss_pred             CCCCCEEEEEC-CCCCCCCCHHHHHHHHHCCCE
T ss_conf             67883799868-998773218999999848746


No 384
>PRK00652 lpxK tetraacyldisaccharide 4'-kinase; Reviewed
Probab=92.94  E-value=0.41  Score=26.04  Aligned_cols=70  Identities=14%  Similarity=0.116  Sum_probs=43.1

Q ss_pred             EECCCCCHH-HHHHHHHHC-CCCC-CCCCCCCCEEEEEEE-CCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             431899989-999976310-2332-223456753799974-6988775689999999999626994999978798
Q gi|254780725|r  132 YLIEPLSVA-DIINSISAI-FTPQ-EEGKGSSGCSISFIG-SRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       132 yl~~P~~~~-~l~~ai~~~-~~~~-~~~~~~~grvIav~g-~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      |+.+|++.- .++-.+++. +... .......-.||+|.+ .-||+|||-++.-||-.|.+ .|.++.++==...
T Consensus        17 ~lL~PlS~ly~~~~~lr~~~y~~~~~~~~~~~vpVI~VGNitvGGtGKTP~v~~la~~l~~-~g~~~~IlSRGYg   90 (334)
T PRK00652         17 RLLLPLSWLYGLVSGLIRLSYRLGLARPYRFPVPVISVGNLTVGGNGKTPVVIWLAEQLQA-RGVKVGVVSRGYG   90 (334)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECEEECCCCHHHHHHHHHHHHHH-CCCCEEEEECCCC
T ss_conf             9999999999999999999986056765558998999908887887779999999999997-6993678734667


No 385
>PTZ00301 uridine kinase; Provisional
Probab=92.93  E-value=0.26  Score=27.19  Aligned_cols=184  Identities=11%  Similarity=0.123  Sum_probs=84.7

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCCCCCCHH-HCCCCCCCCHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf             379997469887756899999999996269-94999978798986033-4389987898886318456124337653202
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFA-METLLADLDLPYGTANI-NFDKDPINSISDAIYPVGRIDKAFVSRLPVF  239 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~-~~VlLvDlDl~~g~~~~-~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~  239 (427)
                      -||++.| -.|+||||+|.++...|-...+ .+|.++-.|...-+... -+......+    ...|+.+|-.++...+..
T Consensus         4 ~iIgIaG-gSgSGKTT~a~~i~~~l~~~~~~~~v~ii~~D~Yy~d~~~~~~~~~~~~N----fDhP~a~D~dLl~~~L~~   78 (210)
T PTZ00301          4 TVIGISG-ASGSGKSSLSTNIVSELMAHCGPVSIGVICEDFYYRDQSNIPESERAYTN----YDHPKSLEHDLLTTHLRE   78 (210)
T ss_pred             EEEEEEC-CCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCHHHCCCCC----CCCCCCCCHHHHHHHHHH
T ss_conf             8999968-87678999999999998761499807998367667787658865627889----998230369999999999


Q ss_pred             CCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC-CHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             48980687248761203207999999989998512888997388888-98999998620125435787768899999999
Q gi|254780725|r  240 YAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVW-NSWTQEVLTLSDKVVITTSLDLAGLRNSKNLI  318 (427)
Q Consensus       240 ~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~-~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll  318 (427)
                      ...|-.+--      ..+++.......-...+ .-.++||++--..+ .+..+..+..  .|++=+..   .+|-.+|+.
T Consensus        79 Lk~Gk~I~~------P~Ydf~~h~R~~~~~~i-~p~~vIIvEGi~~l~~~~lr~l~Dl--kIFvd~~~---dirl~RRi~  146 (210)
T PTZ00301         79 LKSGKTVQI------PQYDYVHHTRSDTAVTM-TPKSVLIVEGILLFTNAELRNEMDC--LIFVDTPL---DICLIRRAK  146 (210)
T ss_pred             HHCCCCEEC------CCCCCCCCCCCCCEEEE-CCCCEEEEEEEHHCCCHHHHHHHCE--EEEECCCH---HHHHHHHHH
T ss_conf             976996344------66555677667970896-6885699971043078989977424--57734872---378899888


Q ss_pred             HHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCH
Q ss_conf             9999819876753899956589875200599999984895379906879
Q gi|254780725|r  319 DVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDG  367 (427)
Q Consensus       319 ~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~  367 (427)
                      .-+.+.+....   -|+.|+....++  ..+.|-+......+.+||+.+
T Consensus       147 RDv~eRGr~~e---~Vi~qy~~~V~P--~~~~fI~P~k~~ADiIIp~~~  190 (210)
T PTZ00301        147 RDMRERGRTFE---SVIEQYEATVRP--MYYAYVEPSKVYADIIVPSWK  190 (210)
T ss_pred             HHHHHHCCCHH---HHHHHHHHHHCC--CHHHHCCHHHHCCCEEECCCC
T ss_conf             77887588999---999999966230--588768051633618978999


No 386
>PRK12339 2-phosphoglycerate kinase; Provisional
Probab=92.86  E-value=0.12  Score=29.35  Aligned_cols=24  Identities=38%  Similarity=0.512  Sum_probs=19.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             799974698877568999999999
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSI  186 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~L  186 (427)
                      .|-++|+-.||||||+|..||..|
T Consensus         4 ~iiligG~sGvGKStla~~lA~rl   27 (197)
T PRK12339          4 TIHFIGGIPGVGKTSISGYIARHR   27 (197)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHC
T ss_conf             799985799887899999999974


No 387
>pfam01695 IstB IstB-like ATP binding protein. This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function.
Probab=92.85  E-value=0.23  Score=27.56  Aligned_cols=40  Identities=15%  Similarity=0.260  Sum_probs=33.0

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             675379997469887756899999999996269949999787
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLD  200 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlD  200 (427)
                      ..++-|.++| .-|+|||-+|+.++..+.+ .|.+|+.+-..
T Consensus        45 ~~~~Nlll~G-~~GtGKThLA~Ai~~~~~~-~g~~v~f~~~~   84 (178)
T pfam01695        45 EQAENLLLLG-PPGVGKTHLACALGHQACR-AGYSVLFTRTP   84 (178)
T ss_pred             HCCCCEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEECH
T ss_conf             1587689989-9998789999999999998-69859999616


No 388
>PRK10636 putative ABC transporter ATP-binding protein; Provisional
Probab=92.85  E-value=0.69  Score=24.62  Aligned_cols=142  Identities=20%  Similarity=0.157  Sum_probs=66.7

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCC------CCCCCHHHHHCCC-CCHHHH
Q ss_conf             675379997469887756899999999996269949999787989860334389------9878988863184-561243
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDK------DPINSISDAIYPV-GRIDKA  231 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~------~~~~~l~d~l~~~-~rlD~~  231 (427)
                      +.|..|+++| .-|+||||+.--|+-.+.-..| .+-+ .-....|    ||.+      ++..++.+.+... ......
T Consensus       336 ~~GeriaIvG-~NGsGKSTLlk~L~G~l~p~~G-~i~~-~~~v~ig----y~~Q~~~~~l~~~~t~l~~~~~~~~~~~~~  408 (638)
T PRK10636        336 VPGSRIGLLG-RNGAGKSTLIKLLAGELAPVSG-EIGL-AKGIKLG----YFAQHQLEFLRADESPLQHLARLAPQELEQ  408 (638)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHCCCCCCCCC-EEEE-CCCCCCC----CCHHHHHHHCCCHHHHHHHHHHHCHHHHHH
T ss_conf             3784799974-7871388999997288788885-6998-4444334----110767765061124999998857254699


Q ss_pred             HHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHH--HHHHHHHHHCCCEEEECCCCC-CCHHHHHHH----HHCCCCCCCC
Q ss_conf             376532024898068724876120320799999--998999851288899738888-898999998----6201254357
Q gi|254780725|r  232 FVSRLPVFYAENLSILTAPAMLSRTYDFDEKMI--VPVLDILEQIFPLVILDVPHV-WNSWTQEVL----TLSDKVVITT  304 (427)
Q Consensus       232 ~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l--~~ll~~l~~~yd~VIiD~p~~-~~~~~~~~L----~~AD~vviV~  304 (427)
                      .+..++...     .+.+..-......++.+.-  -.+...+....++.|+|=|.. .+..+..+|    ..-.-.++++
T Consensus       409 ~~r~~L~~f-----~f~~~~~~~~v~~LSGGEk~Rl~LA~~l~~~pnlLiLDEPTNhLDi~s~e~Le~aL~~y~Gtvl~V  483 (638)
T PRK10636        409 KLRDYLGGF-----GFQGDKVTEETRRFSGGEKARLVLALIVWQRPNLLLLDEPTNHLDLDMRQALTEALIDFEGALVVV  483 (638)
T ss_pred             HHHHHHHHC-----CCCHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCEEEEE
T ss_conf             999999866-----889778639113399999999999999825998899858876688899999999998489839999


Q ss_pred             CCCHHHHH
Q ss_conf             87768899
Q gi|254780725|r  305 SLDLAGLR  312 (427)
Q Consensus       305 ~p~~~slr  312 (427)
                      +-|..=+.
T Consensus       484 SHDr~fl~  491 (638)
T PRK10636        484 SHDRHLLR  491 (638)
T ss_pred             ECCHHHHH
T ss_conf             78999999


No 389
>PRK09140 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; Reviewed
Probab=92.83  E-value=0.7  Score=24.60  Aligned_cols=69  Identities=12%  Similarity=0.168  Sum_probs=54.8

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHC
Q ss_conf             49999805987677889998885328998089981687189999999765626431899989999976310
Q gi|254780725|r   79 DLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAI  149 (427)
Q Consensus        79 ~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~  149 (427)
                      .+-.+|+.+..-+.+..++.|++.. |+--.|=.|...+..-.++++.+|++ |++.|....++++...+.
T Consensus        35 Gi~~iEVTl~tp~a~~~I~~l~~~~-~~~~~iGAGTVlt~e~~~~ai~aGA~-FiVSP~~~~~vi~~a~~~  103 (206)
T PRK09140         35 GFRAIEIPLNSPDPFDSIAALVKAL-GDDALIGAGTVLSPEQVDRLADAGGR-LIVTPNIDPEVIRRAVAY  103 (206)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHC-CCCEEEEEEECCCHHHHHHHHHCCCC-EEECCCCCHHHHHHHHHC
T ss_conf             9988999179976999999999967-98659986204679999999985999-999999989999999982


No 390
>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA; InterPro: IPR011917   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 a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes .; GO: 0005524 ATP binding, 0006869 lipid transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=92.82  E-value=0.076  Score=30.51  Aligned_cols=120  Identities=20%  Similarity=0.203  Sum_probs=60.4

Q ss_pred             ECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCC----CEEEEEEC-C-CCHHHHHHHHHCCCCEEEC
Q ss_conf             0699899999986189984999980598767788999888532899----80899816-8-7189999999765626431
Q gi|254780725|r   61 TRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSG----TKVIVIGD-T-NDVSLYRALISNHVSEYLI  134 (427)
Q Consensus        61 ~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~----~~Vivig~-~-~d~~l~r~l~r~Gv~dyl~  134 (427)
                      ..|++.+=+.....-..|===+.+++.+=|.++...+.+-+..|..    +.=..+.. . .++.      -++|+ + .
T Consensus       298 T~G~f~~~~~am~~l~~PlK~Ltnv~~~~Q~gl~aAe~~F~~lD~~~E~D~G~~~~~RPv~G~~e------FR~v~-~-~  369 (603)
T TIGR02203       298 TVGDFVAFITAMILLIKPLKQLTNVSAPMQKGLAAAESVFTLLDSPPEKDTGTRALERPVRGRVE------FRNVT-F-R  369 (603)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEE------EEEEE-E-E
T ss_conf             63389999999999998887678765888777888877853127885434788268885112488------87666-6-5


Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             89998999997631023322234567537999746988775689999999999626994999978
Q gi|254780725|r  135 EPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADL  199 (427)
Q Consensus       135 ~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDl  199 (427)
                      .|-+..+.++.+.-        .-+.|++||.+| +.|.||||++.=+-...--..| + .|+|-
T Consensus       370 Yp~~~~~aL~~i~l--------~~~~G~~vALVG-RSGSGKsTlv~LlPRFy~p~~G-~-IllDG  423 (603)
T TIGR02203       370 YPGRDRPALDSISL--------VVEPGETVALVG-RSGSGKSTLVNLLPRFYEPDSG-Q-ILLDG  423 (603)
T ss_pred             ECCCCHHHHCCCCC--------EECCCCEEEEEC-CCCCHHHHHHHHCCCCCCCCCC-C-EEECC
T ss_conf             37887241236665--------115873599870-6885389998552366045888-5-65278


No 391
>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional
Probab=92.79  E-value=0.7  Score=24.58  Aligned_cols=41  Identities=24%  Similarity=0.180  Sum_probs=28.4

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             6753799974698877568999999999962699499997879
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDL  201 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl  201 (427)
                      +.|..++++| +-|+||||++--|...+--..| ++.+=+-|+
T Consensus       365 ~~Ge~vaIVG-~SGsGKSTL~~LL~rly~p~~G-~I~idG~di  405 (593)
T PRK10790        365 PSRNFVALVG-HTGSGKSTLASLLMGYYPLTEG-EIRLDGRPL  405 (593)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHHHCCCCCC-CCCCCCEEC
T ss_conf             8997899879-9988689999999985567899-416599324


No 392
>pfam09818 ABC_ATPase Predicted ATPase of the ABC class. Members of this family include various bacterial predicted ABC class ATPases.
Probab=92.78  E-value=0.17  Score=28.35  Aligned_cols=118  Identities=17%  Similarity=0.164  Sum_probs=73.8

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCC-
Q ss_conf             9849999805987677889998885328998089981687189999999765626431899989999976310233222-
Q gi|254780725|r   77 TPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQEE-  155 (427)
Q Consensus        77 ~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~-  155 (427)
                      +|.=+=+++..+....+..+.-     ..|+-+||-|..--=++..+++..||.+  .-|-+-.|++-+-.....-..+ 
T Consensus       220 SP~sL~v~~~lP~~g~v~GMGI-----p~GITlIvGGGyHGKSTLL~Ale~GVYn--HipGDGRE~VvT~~~avKiRAED  292 (447)
T pfam09818       220 SPESLEVEIELPNGGTVSGMGI-----PKGITLIVGGGYHGKSTLLEALERGVYD--HIPGDGREFVVTDPDAVKIRAED  292 (447)
T ss_pred             CCCCEEEEEECCCCCEEEECCC-----CCCEEEEECCCCCCHHHHHHHHHHCCCC--CCCCCCEEEEEECCCEEEEEECC
T ss_conf             9850389998899985564564-----7766999789877678899999827777--78899807999659658888458


Q ss_pred             -------------CCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             -------------345675379997469887756899999999996269949999787989
Q gi|254780725|r  156 -------------GKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       156 -------------~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
                                   ..-+.|+--.-++..-..|.|+-|+|+.-+|  ..|.+++|||-|...
T Consensus       293 GR~V~~vDIS~FI~~LP~G~dT~~FsT~~ASGSTSqAAnI~Eal--EaGa~~lLIDEDTsA  351 (447)
T pfam09818       293 GRSVHGVDISPFINNLPPGKDTTDFSTEDASGSTSQAANIQEAL--EAGASLLLIDEDTSA  351 (447)
T ss_pred             CCEEECEECHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHH--HCCCCEEEECCCCCC
T ss_conf             84462412338784099999877312589871699999999999--748978998356431


No 393
>PRK10522 multidrug transporter membrane component/ATP-binding component; Provisional
Probab=92.74  E-value=0.71  Score=24.53  Aligned_cols=42  Identities=26%  Similarity=0.229  Sum_probs=28.7

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             67537999746988775689999999999626994999978798
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      +.|+.++++| .-|+||||++.=|...+--. ..++.+=+-|+.
T Consensus       347 ~~Ge~vaiVG-~SGsGKSTL~~LL~r~y~p~-~G~I~idG~di~  388 (547)
T PRK10522        347 KRGELLFLIG-GNGSGKSTLAMLLTGLYQPQ-SGEILLDGKPVT  388 (547)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHCCCCCC-CCEEEECCEECC
T ss_conf             5998899989-99997799999982896699-986989999999


No 394
>cd04154 Arl2 Arl2 subfamily.  Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity.  Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix.  The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI.  Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different.  In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport.  In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.
Probab=92.73  E-value=0.66  Score=24.76  Aligned_cols=83  Identities=17%  Similarity=0.197  Sum_probs=57.6

Q ss_pred             CCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCCCC-HHHHHHHHHHHHHH-HHCCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             2888997388888--989999986201254357877-68899999999999-9819876753899956589875200599
Q gi|254780725|r  274 IFPLVILDVPHVW--NSWTQEVLTLSDKVVITTSLD-LAGLRNSKNLIDVL-KKLRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       274 ~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~p~-~~slr~a~~ll~~l-~~~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      .+.+.+.|++...  .......+..+|.+++|.+.+ ..++..++..+..+ ........++.++.|+.+.+.  ..+.+
T Consensus        57 ~~~l~iwD~~G~e~~~~~~~~y~~~a~~ii~VvD~td~~~~~~~~~~l~~ll~~~~~~~~pili~~NK~Dl~~--~~~~~  134 (173)
T cd04154          57 GYKLNIWDVGGQKTLRPYWRNYFESTDALIWVVDSSDRLRLDDCKRELKELLQEERLAGATLLILANKQDLPG--ALSEE  134 (173)
T ss_pred             CEEEEEEECCCCCCCCHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCC--CCCHH
T ss_conf             9999999668860200589997226653899985565788999999999998635415984799987656777--88999


Q ss_pred             HHHHHHCCC
Q ss_conf             999984895
Q gi|254780725|r  350 DFCAPLGIT  358 (427)
Q Consensus       350 ~~~~~lg~~  358 (427)
                      ++.+.++..
T Consensus       135 ei~~~l~l~  143 (173)
T cd04154         135 EIREALELD  143 (173)
T ss_pred             HHHHHHHHH
T ss_conf             999998687


No 395
>KOG1805 consensus
Probab=92.73  E-value=0.41  Score=26.00  Aligned_cols=129  Identities=16%  Similarity=0.179  Sum_probs=66.5

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCC----------CCCCHHHHHCCCC----
Q ss_conf             53799974698877568999999999962699499997879898603343899----------8789888631845----
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKD----------PINSISDAIYPVG----  226 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~----------~~~~l~d~l~~~~----  226 (427)
                      ++-++.+=+=.|+||||+-+.|=..|.. .|++|||.-.-.. .--++...+.          ....+.+.++...    
T Consensus       684 aedy~LI~GMPGTGKTTtI~~LIkiL~~-~gkkVLLtsyThs-AVDNILiKL~~~~i~~lRLG~~~kih~~v~e~~~~~~  761 (1100)
T KOG1805         684 AEDYALILGMPGTGKTTTISLLIKILVA-LGKKVLLTSYTHS-AVDNILIKLKGFGIYILRLGSEEKIHPDVEEFTLTNE  761 (1100)
T ss_pred             CCCHHEEECCCCCCCHHHHHHHHHHHHH-CCCEEEEEEHHHH-HHHHHHHHHHCCCCCEEECCCCCCCCHHHHHHHCCCC
T ss_conf             0332203269989812259999999997-3881899850567-8899999875067110344872224468998712344


Q ss_pred             -CH-HHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC-CHHHHHHHHHCCCCCCC
Q ss_conf             -61-2433765320248980687248761203207999999989998512888997388888-98999998620125435
Q gi|254780725|r  227 -RI-DKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVW-NSWTQEVLTLSDKVVIT  303 (427)
Q Consensus       227 -rl-D~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~-~~~~~~~L~~AD~vviV  303 (427)
                       .. +-..++..+    +...+.+.--     ..+.    ..+  .-++.|||+|||=..+. -+.....|..+...|+|
T Consensus       762 ~s~ks~~~l~~~~----~~~~IVa~TC-----lgi~----~pl--f~~R~FD~cIiDEASQI~lP~~LgPL~~s~kFVLV  826 (1100)
T KOG1805         762 TSEKSYADLKKFL----DQTSIVACTC-----LGIN----HPL--FVNRQFDYCIIDEASQILLPLCLGPLSFSNKFVLV  826 (1100)
T ss_pred             CCHHHHHHHHHHH----CCCCEEEEEC-----CCCC----CHH--HHCCCCCEEEECCCCCCCCCHHHHHHHHCCEEEEE
T ss_conf             5453399999972----8976799971-----5788----655--52142678998651111434212102112358996


Q ss_pred             CCC
Q ss_conf             787
Q gi|254780725|r  304 TSL  306 (427)
Q Consensus       304 ~~p  306 (427)
                      -++
T Consensus       827 GDh  829 (1100)
T KOG1805         827 GDH  829 (1100)
T ss_pred             CCC
T ss_conf             463


No 396
>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
Probab=92.72  E-value=0.23  Score=27.51  Aligned_cols=36  Identities=17%  Similarity=0.226  Sum_probs=29.7

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             9746988775689999999999626994999978798
Q gi|254780725|r  166 FIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       166 v~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      .+.+.-|+||||+|.++++..++ .|.+|+.+-++-.
T Consensus         3 Li~G~pGsGKT~~a~qfl~~~a~-~ge~~lyis~eE~   38 (187)
T cd01124           3 LLSGGPGTGKTTFALQFLYAGLA-RGEPGLYVTLEES   38 (187)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHH-CCCCEEEEEECCC
T ss_conf             58768999999999999999987-6997899995079


No 397
>PRK08904 consensus
Probab=92.64  E-value=0.74  Score=24.45  Aligned_cols=86  Identities=10%  Similarity=0.126  Sum_probs=60.6

Q ss_pred             EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCH
Q ss_conf             30699899999986189984999980598767788999888532899808998168718999999976562643189998
Q gi|254780725|r   60 ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSV  139 (427)
Q Consensus        60 v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~  139 (427)
                      ++..+.+.|.+....--.-.+=++|+.+...+.++.++.+++.. |+. +|=.|...+..-.++++.+|++ |++.|..-
T Consensus        16 ir~~~~~~a~~~a~al~~~Gi~~iEiTlrtp~a~~~i~~l~~~~-p~~-~vGaGTVl~~e~~~~a~~aGA~-FiVSP~~~   92 (207)
T PRK08904         16 MAIDDLSTAVDLSRALVEGGIPTLEITLRTPVGLDAIRLIAKEV-PNA-IVGAGTVTNPEQLKAVEDAGAV-FAISPGLH   92 (207)
T ss_pred             EECCCHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHC-CCC-EEEEEECCCHHHHHHHHHCCCC-EEECCCCC
T ss_conf             97699999999999999879988999579913999999999868-987-6855313689999999984999-99848998


Q ss_pred             HHHHHHHHH
Q ss_conf             999997631
Q gi|254780725|r  140 ADIINSISA  148 (427)
Q Consensus       140 ~~l~~ai~~  148 (427)
                      .++++...+
T Consensus        93 ~~v~~~a~~  101 (207)
T PRK08904         93 ESLAKAGHN  101 (207)
T ss_pred             HHHHHHHHH
T ss_conf             999999998


No 398
>PRK09183 transposase/IS protein; Provisional
Probab=92.62  E-value=0.25  Score=27.36  Aligned_cols=112  Identities=11%  Similarity=0.115  Sum_probs=65.0

Q ss_pred             EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCH
Q ss_conf             30699899999986189984999980598767788999888532899808998168718999999976562643189998
Q gi|254780725|r   60 ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSV  139 (427)
Q Consensus        60 v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~  139 (427)
                      .+..|++++.+.+..++.-         +.....+.|..|.+..        +.....-.+-|.+.+++..    .+-+.
T Consensus        15 LkL~~m~~~~~~~~~~a~~---------~~~s~~e~L~~Ll~~E--------~~~R~~rr~~r~lk~A~fp----~~ktl   73 (258)
T PRK09183         15 LQLESLISAAPALAQQAVD---------QEWSYMDFLEHLLHEE--------KLARHQRKQAMYTRMAAFP----AVKTF   73 (258)
T ss_pred             CCCHHHHHHHHHHHHHHHH---------CCCCHHHHHHHHHHHH--------HHHHHHHHHHHHHHHCCCC----CCCCH
T ss_conf             7831899999999998876---------3999999999999999--------9999999999999977999----98777


Q ss_pred             HHH------------HHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             999------------9976310233222345675379997469887756899999999996269949999787
Q gi|254780725|r  140 ADI------------INSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLD  200 (427)
Q Consensus       140 ~~l------------~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlD  200 (427)
                      +++            +..+..+      .--..+.-|.++| .-|+|||-+|+.||....+ .|.+|..+.+.
T Consensus        74 e~fDf~~~~~l~~~~i~~La~~------~fi~~~~Nvil~G-~~GtGKThLA~Alg~~A~~-~G~~v~f~~~~  138 (258)
T PRK09183         74 EEYDFTFATGAPQKQLQSLRSL------SFIERNENIVLLG-PSGVGKTHLAIALGYEAVR-AGIKVRFTTAA  138 (258)
T ss_pred             HHCCCCCCCCCCHHHHHHHHCC------CHHHCCCCEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEHH
T ss_conf             5556546886238999988258------1665588679989-9998689999999999998-79939997899


No 399
>cd04124 RabL2 RabL2 subfamily.  RabL2 (Rab-like2) subfamily.  RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share  98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-b
Probab=92.61  E-value=0.74  Score=24.42  Aligned_cols=107  Identities=11%  Similarity=0.210  Sum_probs=75.6

Q ss_pred             HCCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             1288899738888--898999998620125435787-7688999999999999819876753899956589875200599
Q gi|254780725|r  273 QIFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       273 ~~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      ..+.+-|.|++..  +.......+..|+-+++|.+- +..|+.+.+.+++.+++..+ +.++.+|-|+++...+  ..  
T Consensus        47 ~~~~l~iwDtaG~e~f~~~~~~y~~~a~~~ilvfDit~~~Sf~~~~~w~~~i~~~~~-~~p~ilVgNK~DL~~~--~~--  121 (161)
T cd04124          47 KTILVDFWDTAGQERFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYRP-EIPCIVVANKIDLDPS--VT--  121 (161)
T ss_pred             EEEEEEEEECCCCCCCCHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCC-CCCEEEEEECCCCCCH--HH--
T ss_conf             999999997999843432469973568767999968977889999999999998686-9989999997117742--58--


Q ss_pred             HHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHH
Q ss_conf             99998489537990687999999884796189888999--89999999999985
Q gi|254780725|r  350 DFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLM  401 (427)
Q Consensus       350 ~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~  401 (427)
                                     .  +....|..+|.+..|.+.+.  -+.+.|.+|++.+.
T Consensus       122 ---------------~--~~~~~a~~~~~~f~etSAk~g~nV~e~F~~l~~~~i  158 (161)
T cd04124         122 ---------------Q--KKFNFAEKHNLPLYYVSAADGTNVVKLFQDAIKLAV  158 (161)
T ss_pred             ---------------H--HHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             ---------------9--999999986991999907838097999999999998


No 400
>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=92.60  E-value=0.6  Score=25.01  Aligned_cols=53  Identities=23%  Similarity=0.186  Sum_probs=34.2

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC---CCCCCHHHCCCC
Q ss_conf             56753799974698877568999999999962699499997879---898603343899
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDL---PYGTANINFDKD  213 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl---~~g~~~~~l~~~  213 (427)
                      -..|..++++| ..||||||+---+|-...  ...-.+.+|-..   +..+.++.|...
T Consensus        26 v~~GEfvsilG-pSGcGKSTLLriiAGL~~--p~~G~V~~~g~~v~~p~~~~~~vFQ~~   81 (248)
T COG1116          26 VEKGEFVAILG-PSGCGKSTLLRLIAGLEK--PTSGEVLLDGRPVTGPGPDIGYVFQED   81 (248)
T ss_pred             ECCCCEEEEEC-CCCCCHHHHHHHHHCCCC--CCCCEEEECCCCCCCCCCCEEEEECCC
T ss_conf             77997999989-997889999999968787--777559988821578998779992667


No 401
>PRK08118 topology modulation protein; Reviewed
Probab=92.60  E-value=0.2  Score=27.88  Aligned_cols=94  Identities=19%  Similarity=0.146  Sum_probs=52.1

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
                      +-|.|+| ..|+||||+|..|+..    .+.+++-+|- +...                                     
T Consensus         2 ~rI~IiG-~~GsGKSTlAr~L~~~----~~ip~~~LD~-l~w~-------------------------------------   38 (167)
T PRK08118          2 KKIILIG-SGGSGKSTLARQLGEK----LNIPVHHLDA-LFWK-------------------------------------   38 (167)
T ss_pred             CEEEEEC-CCCCCHHHHHHHHHHH----HCCCEEECCC-EEEC-------------------------------------
T ss_conf             6799988-9998799999999998----8969796443-4766-------------------------------------


Q ss_pred             CCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHH
Q ss_conf             980687248761203207999999989998512888997388888989999986201254357877688999
Q gi|254780725|r  242 ENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRN  313 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr~  313 (427)
                            ++      ....+.+.+...++.+-.. |-=|+|-  ..+.....-+..||.|+..--|-..++..
T Consensus        39 ------~~------w~~~~~~e~~~~~~~~~~~-~~WIidG--ny~~~~~~r~~~aD~iI~Ld~p~~~~~~r   95 (167)
T PRK08118         39 ------PN------WEGVPKEEQRTVQNELVKE-DEWIIDG--NYGGTMDIRLNAADTIIFLDIPRTICLYR   95 (167)
T ss_pred             ------CC------CCCCCHHHHHHHHHHHHHC-CCEEEEC--CCHHHHHHHHHHCCEEEEECCCHHHHHHH
T ss_conf             ------89------9468889999999999838-9879947--71779987797699999985989999999


No 402
>KOG1534 consensus
Probab=92.57  E-value=0.75  Score=24.39  Aligned_cols=104  Identities=15%  Similarity=0.105  Sum_probs=61.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             99974698877568999999999962699499997879898603343899878988863184561243376532024898
Q gi|254780725|r  164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAEN  243 (427)
Q Consensus       164 Iav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~g  243 (427)
                      +-|+| --|.||||...++-...- ..|+.+-+|.||+..    ..|+-+..-.+.|++.    +|.+.-+  +.-.+.|
T Consensus         6 ~lV~G-pAgSGKSTyC~~~~~h~e-~~gRs~~vVNLDPAa----e~f~y~~~iDiRdlIs----vdDVmEd--l~~GPNG   73 (273)
T KOG1534           6 QLVMG-PAGSGKSTYCSSMYEHCE-TVGRSVHVVNLDPAA----EHFNYPVTIDIRDLIS----VDDVMED--LDLGPNG   73 (273)
T ss_pred             EEEEC-CCCCCCCHHHHHHHHHHH-HHCCEEEEEECCHHH----HHHCCCCCCCHHHHCC----HHHHHHH--HCCCCCC
T ss_conf             89874-678884307899999998-628545886268788----8608962002887521----8888888--6349986


Q ss_pred             EEEEECCCCCCCHHCCCHHHHHHHHHHHH-HCCCEEEECCCCCCC
Q ss_conf             06872487612032079999999899985-128889973888889
Q gi|254780725|r  244 LSILTAPAMLSRTYDFDEKMIVPVLDILE-QIFPLVILDVPHVWN  287 (427)
Q Consensus       244 L~lL~a~~~~~~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p~~~~  287 (427)
                              .+--..+.-.+.+.++.+..- -.-||.|+|||.+..
T Consensus        74 --------gLv~cmEyl~~NldwL~~~~Gd~eddylifDcPGQIE  110 (273)
T KOG1534          74 --------GLVYCMEYLLENLDWLEEEIGDVEDDYLIFDCPGQIE  110 (273)
T ss_pred             --------CCHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCEEE
T ss_conf             --------5203899999778887754067567779984798167


No 403
>KOG4658 consensus
Probab=92.56  E-value=0.2  Score=27.92  Aligned_cols=44  Identities=16%  Similarity=0.325  Sum_probs=29.2

Q ss_pred             CCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             998999997631023322234567537999746988775689999999999
Q gi|254780725|r  137 LSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIA  187 (427)
Q Consensus       137 ~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA  187 (427)
                      +..++.++.+-+.+.....      .+++++| -||+||||+|..+=....
T Consensus       161 VG~e~~~ekl~~~L~~d~~------~ivgi~G-MGGvGKTTL~~qi~N~~~  204 (889)
T KOG4658         161 VGLETMLEKLWNRLMEDDV------GIVGIYG-MGGVGKTTLARQIFNKFD  204 (889)
T ss_pred             CCHHHHHHHHHHHHCCCCC------CEEEEEC-CCCCCHHHHHHHHHHCCH
T ss_conf             4688999999998404799------6899988-970349999999841331


No 404
>PRK07455 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=92.54  E-value=0.76  Score=24.37  Aligned_cols=87  Identities=11%  Similarity=0.138  Sum_probs=59.7

Q ss_pred             EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCH
Q ss_conf             30699899999986189984999980598767788999888532899808998168718999999976562643189998
Q gi|254780725|r   60 ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSV  139 (427)
Q Consensus        60 v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~  139 (427)
                      ++.-....|......--.-.+=++|+.....+.++.++.|++.. |+. .|=.|..-|..-.++++.+|+. |++.|...
T Consensus        19 lr~~~~~~a~~~~~al~~gGi~~iEiTl~t~~a~~~I~~l~~~~-p~~-~iGaGTV~~~e~~~~a~~aGA~-FiVSP~~~   95 (210)
T PRK07455         19 IRAPDLELGLQMAEAVAAGGMRLIEITWNSDQPAELISQLREKL-PEC-IIGTGTLLTLEDLEEAIAAGAQ-FCFTPHVD   95 (210)
T ss_pred             EECCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHC-CCC-EEEEEECCCHHHHHHHHHCCCC-EEECCCCC
T ss_conf             97599999999999999879988999689988999999999878-996-8988818789999999986999-99868888


Q ss_pred             HHHHHHHHHC
Q ss_conf             9999976310
Q gi|254780725|r  140 ADIINSISAI  149 (427)
Q Consensus       140 ~~l~~ai~~~  149 (427)
                      .++++...+.
T Consensus        96 ~~vi~~a~~~  105 (210)
T PRK07455         96 LELIQAAVAA  105 (210)
T ss_pred             HHHHHHHHHC
T ss_conf             9999999982


No 405
>cd01884 EF_Tu EF-Tu subfamily.  This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts.  It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors.  The eukaryotic counterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this family.  EF-Tu is one of the most abundant proteins in bacteria, as well as, one of the most highly conserved, and in a number of species the gene is duplicated with identical function.  When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors.  Transfer RNA is carried to the ribosome in these complexes for protein translation.
Probab=92.42  E-value=0.39  Score=26.12  Aligned_cols=67  Identities=9%  Similarity=0.020  Sum_probs=49.6

Q ss_pred             CCCEEEECCCCCCC--HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf             28889973888889--8999998620125435787768899999999999981987675389995658987
Q gi|254780725|r  274 IFPLVILDVPHVWN--SWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPK  342 (427)
Q Consensus       274 ~yd~VIiD~p~~~~--~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~  342 (427)
                      .+.+.++|+|....  ..+...+..+|.+++|+...-.-..+++..+..++.++.  .++.+++|+++...
T Consensus        64 ~~~~~~IDtPGH~dF~~~~i~g~~~~D~aiLVVdA~eGv~~QT~eh~~la~~lgi--~~iiV~iNK~D~~~  132 (195)
T cd01884          64 NRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGV--PYIVVFLNKADMVD  132 (195)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHHCC--CCEEEEEECCCCCC
T ss_conf             8169962689607788899863511362689985277874789999999998099--96279996877898


No 406
>cd01888 eIF2_gamma eIF2-gamma (gamma subunit of initiation factor 2).  eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits.  The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit.  Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome.  The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B.  eIF2B is a heteropentamer, and the epsilon chain binds eIF2.  Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma.  It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role.  eIF2-gamma is found only in eukaryotes and archaea.  It is closely related to SelB, the sel
Probab=92.42  E-value=0.39  Score=26.16  Aligned_cols=65  Identities=11%  Similarity=0.077  Sum_probs=45.9

Q ss_pred             CCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCCHHH-HHHHHHHHHHHHHCCCCCCCCEEEEECCCCC
Q ss_conf             88899738888--8989999986201254357877688-9999999999998198767538999565898
Q gi|254780725|r  275 FPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLDLAG-LRNSKNLIDVLKKLRPADKPPYLVLNQVKTP  341 (427)
Q Consensus       275 yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~~~s-lr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~  341 (427)
                      +.|.++|+|..  +..........||..++|+..+-.. --++++-+..++.++.  +.+-+++|+++..
T Consensus        83 r~~tiiD~PGH~df~~nmi~Gas~aD~aiLvVdA~eG~~~~QT~eH~~l~~~lgv--~~iIV~vNKmDlv  150 (203)
T cd01888          83 RHVSFVDCPGHEILMATMLSGAAVMDGALLLIAANEPCPQPQTSEHLAALEIMGL--KHIIIVQNKIDLV  150 (203)
T ss_pred             EEEEEEECCCHHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHHCCC--CCEEEEEECCCCC
T ss_conf             4799986898799999999766434766898643667750779999999998499--8636775077778


No 407
>TIGR03201 dearomat_had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase. Members of this protein family are 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase, an enzyme in the anaerobic metabolism of aromatic enzymes by way of benzoyl-CoA, as seen in Thauera aromatica, Geobacter metallireducens, and Azoarcus sp. The experimentally characterized form from T. aromatica uses only NAD+, not NADP+. Note that Rhodopseudomonas palustris uses a different pathway to perform a similar degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA.
Probab=92.42  E-value=0.79  Score=24.27  Aligned_cols=49  Identities=22%  Similarity=0.273  Sum_probs=31.4

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCC
Q ss_conf             45675379997469887756899999999996269949999787989860334389
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDK  212 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~  212 (427)
                      ..+.|..+.|+|+ ||+|-      ++.++|+..|.+|..+|.+..--..+.-||.
T Consensus       163 ~v~~g~~V~V~G~-G~iGl------~a~~~ak~~Ga~Vi~vd~~~~rle~a~~~Ga  211 (349)
T TIGR03201       163 GLKKGDLVIVIGA-GGVGG------YMVQTAKAMGAAVVAIDIDPEKLEMMKGFGA  211 (349)
T ss_pred             CCCCCCEEEEECC-CHHHH------HHHHHHHHCCCEEEEEECCHHHHHHHHHCCC
T ss_conf             7899988999897-48999------9999999859979999499999999996499


No 408
>cd01879 FeoB Ferrous iron transport protein B (FeoB) subfamily.  E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions.  FeoB has been identified as part of this transport system.  FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.
Probab=92.37  E-value=0.63  Score=24.88  Aligned_cols=59  Identities=22%  Similarity=0.282  Sum_probs=29.0

Q ss_pred             HHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCC--HHHHHHHHHHHCCC
Q ss_conf             62012543578776889999999999998198767538999565898752--00599999984895
Q gi|254780725|r  295 TLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKP--EISISDFCAPLGIT  358 (427)
Q Consensus       295 ~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~--~i~~~~~~~~lg~~  358 (427)
                      ..+|.+++|.+.+-  +..-..+...+...   ..++.+|+|+++..+..  .+..+.+++.++.+
T Consensus        73 ~~~d~vl~vvD~~~--~~~~l~~~~~l~~~---~~p~ivV~NK~D~~~~~~~~~~~~~l~~~~~~~  133 (158)
T cd01879          73 EKPDLIVNVVDATN--LERNLYLTLQLLEL---GLPVVVALNMIDEAEKRGIKIDLDKLSELLGVP  133 (158)
T ss_pred             CCCCCEEEEEECCH--HHHHHHHHHHHHHC---CCCEEEEEEHHHHHHHCCCHHHHHHHHHHCCCC
T ss_conf             17871799977740--67768999999865---998899940277655225466799999871994


No 409
>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.  This family is also known as MRP (mulrtidrug resisitance-associated protein).  Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear.  The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
Probab=92.34  E-value=0.16  Score=28.58  Aligned_cols=28  Identities=18%  Similarity=0.259  Sum_probs=22.5

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             56753799974698877568999999999
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSI  186 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~L  186 (427)
                      -+.|.+++++| +-|+||||+.--++-.+
T Consensus        28 i~~Ge~~~IvG-~sGsGKSTLl~~i~G~~   55 (204)
T cd03250          28 VPKGELVAIVG-PVGSGKSSLLSALLGEL   55 (204)
T ss_pred             ECCCCEEEEEC-CCCCCHHHHHHHHCCCC
T ss_conf             76998999999-99985899999981895


No 410
>PRK07261 topology modulation protein; Provisional
Probab=92.33  E-value=0.23  Score=27.52  Aligned_cols=32  Identities=31%  Similarity=0.386  Sum_probs=23.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             7999746988775689999999999626994999978
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADL  199 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDl  199 (427)
                      -|.|+| -+|.||||+|-.|+.    ..+.+++-+|.
T Consensus         2 rI~IiG-~sGsGKSTlAr~L~~----~~~ip~~~LD~   33 (171)
T PRK07261          2 KIAIIG-YSGSGKSTLARFLGQ----HYNCPVLHLDQ   33 (171)
T ss_pred             EEEEEC-CCCCCHHHHHHHHHH----HHCCCEEEECC
T ss_conf             899988-999868999999999----87979797022


No 411
>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA. EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability.
Probab=92.31  E-value=0.54  Score=25.28  Aligned_cols=216  Identities=18%  Similarity=0.191  Sum_probs=112.2

Q ss_pred             HHHHHHCCCCCCEEEEECCCCC-CCHHHHHHHHHHHCCCCCEEEEEECCCC----HHHHHHHHHCCCCEEEC----CCCC
Q ss_conf             9999861899849999805987-6778899988853289980899816871----89999999765626431----8999
Q gi|254780725|r   68 AVSCFSDSSTPDLIIVQTKVDS-REVLSALEPLAEVCDSGTKVIVIGDTND----VSLYRALISNHVSEYLI----EPLS  138 (427)
Q Consensus        68 A~~~~~~~~~P~~iivd~~~~~-~~~~~~l~~la~~~~p~~~Vivig~~~d----~~l~r~l~r~Gv~dyl~----~P~~  138 (427)
                      +..+...+ --=+.++|..... ..-..-++-|..   -+.+|+++-.--|    -...-+.-+.|..+.+.    .-..
T Consensus        72 ~~~ai~~a-DlIlfVvD~~~git~~D~~i~~~Lrk---~~k~vilviNK~D~~~~~~~~~ef~~LG~~~~i~iSA~h~~G  147 (429)
T TIGR03594        72 AEIAIEEA-DVILFVVDGREGLTPEDEEIAKWLRK---SGKPVILVANKIDGKKEDAVAAEFYSLGFGEPIPISAEHGRG  147 (429)
T ss_pred             HHHHHHHC-CEEEEEEECCCCCCHHHHHHHHHHHH---CCCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEECCCCC
T ss_conf             99999867-99999985776898679999999987---199789999834675314569999983689868874204679


Q ss_pred             HHHHHHHHHHCCCCCCCC--CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCC
Q ss_conf             899999763102332223--456753799974698877568999999999962699499997879898603343899878
Q gi|254780725|r  139 VADIINSISAIFTPQEEG--KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPIN  216 (427)
Q Consensus       139 ~~~l~~ai~~~~~~~~~~--~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~  216 (427)
                      .++|.+.+...+......  .....-.||++| |--|||||+-=.|   +    |.+-++++-  ..|++-         
T Consensus       148 i~~L~~~i~~~l~~~~~~~~~~~~~iriaivG-rPNvGKSTl~N~l---l----~~~r~ivs~--~~GtTr---------  208 (429)
T TIGR03594       148 IGDLLDAILELLPEEEEEEEEEDGPIKIAIIG-RPNVGKSTLVNAL---L----GEERVIVSD--IAGTTR---------  208 (429)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEC-CCCCCHHHHHHHH---H----HHHHHHCCC--CCCCCC---------
T ss_conf             99999999965886655543455652699974-8876546777776---5----433321479--998631---------


Q ss_pred             CHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC----------
Q ss_conf             9888631845612433765320248980687248761203207999999989998512888997388888----------
Q gi|254780725|r  217 SISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVW----------  286 (427)
Q Consensus       217 ~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~----------  286 (427)
                         |.+...-                               .             .....|.++|++.--          
T Consensus       209 ---D~i~~~~-------------------------------~-------------~~~~~~~~iDTaGirkk~k~~~~~e  241 (429)
T TIGR03594       209 ---DSIDIPF-------------------------------E-------------RNGKKYLLIDTAGIRRKGKVTEGIE  241 (429)
T ss_pred             ---CCEEEEE-------------------------------E-------------ECCEEEEEEECCCCCCCCCCCHHHH
T ss_conf             ---0268799-------------------------------9-------------9990899998988763664230477


Q ss_pred             ---CHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCC
Q ss_conf             ---98999998620125435787768899999999999981987675389995658987520059999998489
Q gi|254780725|r  287 ---NSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGI  357 (427)
Q Consensus       287 ---~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~  357 (427)
                         ...+..++..||.++++.+.+-.--+.=.+++..+.+.+   +++.+++|+++.-+.. ...+++.+.+..
T Consensus       242 ~~s~~~t~~~i~~~dvvil~iD~~~~~~~qD~~i~~~i~~~~---k~~ii~~NK~Dli~~~-~~~~~~~~~i~~  311 (429)
T TIGR03594       242 KYSVLRTLKAIERADVVLLVLDATEGITEQDLRIAGLALEAG---KALIIVVNKWDLVKDE-KTREEFKKELRR  311 (429)
T ss_pred             HHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCC---CCEEEEEEHHHCCCCH-HHHHHHHHHHHH
T ss_conf             999999999987447799999766588488899999898739---9769999722303799-999999999998


No 412
>cd00878 Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases.  Arf proteins are activators of phospholipase D isoforms.  Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated.  Arfs are N-terminally myristoylated.  Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner.  They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site.  Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins.  Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus.  Most other Arf family proteins are so far relatively poorly characterized.  Thu
Probab=92.28  E-value=0.75  Score=24.42  Aligned_cols=83  Identities=14%  Similarity=0.234  Sum_probs=56.9

Q ss_pred             CCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHH-HHCCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             288899738888--898999998620125435787-768899999999999-9819876753899956589875200599
Q gi|254780725|r  274 IFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVL-KKLRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       274 ~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l-~~~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      .+.+.+.|++..  ........+..+|-+++|.+. +..++..++..+..+ ........++.+|.|+.+.+..  ....
T Consensus        42 ~~~l~iwDt~G~~~~~~~~~~y~~~a~~~i~V~D~t~~~s~~~~~~~~~~~~~~~~~~~~piliv~NK~Dl~~~--~~~~  119 (158)
T cd00878          42 NVSFTVWDVGGQDKIRPLWKHYYENTNGIIFVVDSSDRERIEEAKEELHKLLNEEELKGVPLLIFANKQDLPGA--LSVS  119 (158)
T ss_pred             CEEEEEEECCCCCCCCHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCC--CCHH
T ss_conf             89999998899722144899872768776899837988899999999999986605576538987605476657--8999


Q ss_pred             HHHHHHCCC
Q ss_conf             999984895
Q gi|254780725|r  350 DFCAPLGIT  358 (427)
Q Consensus       350 ~~~~~lg~~  358 (427)
                      ++.+.++..
T Consensus       120 ei~~~l~~~  128 (158)
T cd00878         120 ELIEKLGLE  128 (158)
T ss_pred             HHHHHHHHH
T ss_conf             999998587


No 413
>TIGR02397 dnaX_nterm DNA polymerase III, subunits gamma and tau; InterPro: IPR012763    This entry represents the well-conserved first N-terminal domain of DnaX, approx. 365 aa. The full-length product of the dnaX gene in Escherichia coli encodes the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the extreme thermophile Thermus thermophilis.; GO: 0003887 DNA-directed DNA polymerase activity, 0005524 ATP binding, 0006260 DNA replication, 0009360 DNA polymerase III complex.
Probab=92.26  E-value=0.21  Score=27.86  Aligned_cols=159  Identities=16%  Similarity=0.206  Sum_probs=89.3

Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHC--CCC----
Q ss_conf             99999763102332223456753799974698877568999999999962699499997879898603343--899----
Q gi|254780725|r  140 ADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINF--DKD----  213 (427)
Q Consensus       140 ~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l--~~~----  213 (427)
                      +.++++|.+...     .+|.+.-+-|.|.| ||||||+|==||-+|--. +     .|.+|- |......  +..    
T Consensus        20 ~~iv~tL~NAi~-----~~ri~HAYLF~GpR-GtGKTS~ARIfAKaLNC~-~-----~~~~PC-n~C~~C~~i~~g~~~D   86 (363)
T TIGR02397        20 EHIVKTLKNAIK-----NGRIAHAYLFSGPR-GTGKTSIARIFAKALNCQ-G-----PDGEPC-NECESCKEINSGSSLD   86 (363)
T ss_pred             HHHHHHHHHHHH-----HCCCCCEEEECCCC-CCCHHHHHHHHHHHHCCC-C-----CCCCCC-CCCCHHHHHHCCCCCC
T ss_conf             799999999997-----18966234502859-976355899999986588-7-----877877-7750227765289866


Q ss_pred             -------CCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCC-----CCCHHCCCHHHHHHHHHHHHHCCCEEEE-
Q ss_conf             -------878988863184561243376532024898068724876-----1203207999999989998512888997-
Q gi|254780725|r  214 -------PINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAM-----LSRTYDFDEKMIVPVLDILEQIFPLVIL-  280 (427)
Q Consensus       214 -------~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~-----~~~~~~~~~~~l~~ll~~l~~~yd~VIi-  280 (427)
                             +..|+.|+=        .++        +.+.+.|....     .|+.-.++.++|-.||.+|.+-=.+||+ 
T Consensus        87 viEiDAASN~gVD~IR--------~l~--------e~v~y~P~~~kYKvYIIDEVHMLS~~AFNALLKTLEEPP~hV~FI  150 (363)
T TIGR02397        87 VIEIDAASNNGVDDIR--------ELR--------ENVKYAPSKGKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFI  150 (363)
T ss_pred             EEEECCCCCCCHHHHH--------HHH--------HHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCEEEE
T ss_conf             6886486568788999--------998--------730368755443358873230286568999876522798762888


Q ss_pred             --------------------CCCCCCCHHHHHHHH---------H-CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf             --------------------388888989999986---------2-0125435787768899999999999981987
Q gi|254780725|r  281 --------------------DVPHVWNSWTQEVLT---------L-SDKVVITTSLDLAGLRNSKNLIDVLKKLRPA  327 (427)
Q Consensus       281 --------------------D~p~~~~~~~~~~L~---------~-AD~vviV~~p~~~slr~a~~ll~~l~~~~~~  327 (427)
                                          |...-.......-|.         . -..+-+++...-.|+|+|-.+++.+-....+
T Consensus       151 lATTE~~KiP~TIlSRCQrF~Fk~i~~~~i~~~L~~I~~~E~I~~e~~AL~~IA~~a~GS~RDAlsllDQ~~~~~~~  227 (363)
T TIGR02397       151 LATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSMRDALSLLDQAISFGNG  227 (363)
T ss_pred             EECCCHHHCCCCCEEECEEECCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCC
T ss_conf             73487112055402100031267899899999999999870883177899999996289610688999999982688


No 414
>PRK12338 hypothetical protein; Provisional
Probab=92.22  E-value=0.15  Score=28.65  Aligned_cols=30  Identities=37%  Similarity=0.599  Sum_probs=23.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             7999746988775689999999999626994999
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLL  196 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlL  196 (427)
                      .|.++|+-.||||||+|.-||..|    |-++++
T Consensus         5 liILiGGtSGvGKSTlAseLAsRL----gI~tvI   34 (320)
T PRK12338          5 YVILIGSASGIGKSTIASEVARRL----NIKHLI   34 (320)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHC----CCCEEE
T ss_conf             799970688876888999999851----987110


No 415
>cd04134 Rho3 Rho3 subfamily.  Rho3 is a member of the Rho family found only in fungi.  Rho3 is believed to regulate cell polarity by interacting with the diaphanous/formin family protein For3 to control both the actin cytoskeleton and microtubules.  Rho3 is also believed to have a direct role in exocytosis that is independent of its role in regulating actin polarity.  The function in exocytosis may be two-pronged: first, in the transport of post-Golgi vesicles from the mother cell to the bud, mediated by myosin (Myo2); second, in the docking and fusion of vesicles to the plasma membrane, mediated by an exocyst (Exo70) protein.  Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid.  Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.
Probab=92.22  E-value=0.83  Score=24.12  Aligned_cols=129  Identities=12%  Similarity=0.117  Sum_probs=78.2

Q ss_pred             HCCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCC-CHHHHHHHH-HHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHH
Q ss_conf             1288899738888--898999998620125435787-768899999-999999981987675389995658987520059
Q gi|254780725|r  273 QIFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSL-DLAGLRNSK-NLIDVLKKLRPADKPPYLVLNQVKTPKKPEISI  348 (427)
Q Consensus       273 ~~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p-~~~slr~a~-~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~  348 (427)
                      ..+.+-|+|++..  +..........+|.+++|-.- +..|+.+.. ++++.+++..+ ..++.+|-|+++.....+   
T Consensus        46 ~~v~l~iwDTaGqe~~~~i~~~~y~~a~~~ilvydi~~~~Sf~~v~~~w~~~i~~~~~-~~piiLVgnK~DL~~~~~---  121 (189)
T cd04134          46 LHIELSLWDTAGQEEFDRLRSLSYADTDVIMLCFSVDSPDSLENVESKWLGEIREHCP-GVKLVLVALKCDLREARN---  121 (189)
T ss_pred             EEEEEEEEECCCCCCCCHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCC-CCCEEEEEECHHCCCCHH---
T ss_conf             9999999847785000035567643786459999789878999999999999997497-997899998800465323---


Q ss_pred             HHHHHHHCCCEEEEECCCHHHHHHHHH-CCCCEEEECCCC--HHHHHHHHHHHHHHCCCCCCC
Q ss_conf             999998489537990687999999884-796189888999--899999999999852212232
Q gi|254780725|r  349 SDFCAPLGITPSAIIPFDGAVFGMSAN-SGKMIHEVDPKS--AIANLLVDFSRVLMGRVTVSK  408 (427)
Q Consensus       349 ~~~~~~lg~~~~~~IP~D~~~~~~A~~-~G~pi~e~~p~s--~~a~~~~~La~~i~gr~~~~~  408 (427)
                        ....+.......+.++ +....|.. ++.+..|.+.+.  -+-+.|.++|+.++....+.+
T Consensus       122 --~~~~~~~~~~~~is~~-eg~~~Ak~~~~~~y~EtSAkt~~nV~e~F~~lar~~l~~~~~~~  181 (189)
T cd04134         122 --ERDDLQRYGKHTISYE-EGLAVAKRINALRYLECSAKLNRGVNEAFTEAARVALNVRPPHP  181 (189)
T ss_pred             --HHHHHHHHCCCCCCHH-HHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCC
T ss_conf             --5677766304665899-99999998299789996806794989999999999973589899


No 416
>cd01878 HflX HflX subfamily.  A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily.  The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear.  HflX is widespread, but not universally represented in all three superkingdoms.
Probab=92.19  E-value=0.84  Score=24.10  Aligned_cols=52  Identities=23%  Similarity=0.247  Sum_probs=31.8

Q ss_pred             HHHHHHCCCCCCCCCCCHHH-HHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf             99986201254357877688-99999999999981987675389995658987
Q gi|254780725|r  291 QEVLTLSDKVVITTSLDLAG-LRNSKNLIDVLKKLRPADKPPYLVLNQVKTPK  342 (427)
Q Consensus       291 ~~~L~~AD~vviV~~p~~~s-lr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~  342 (427)
                      ...+..||.+++|++.+-.. ........+.++..+....++.+|+|+++...
T Consensus       115 le~i~~AD~il~vvD~s~~~~~~~~~~~~~~l~~l~~~~k~~i~V~NKiDl~~  167 (204)
T cd01878         115 LEEVAEADLLLHVVDASDPDYEEQIETVEKVLKELGAEDIPMILVLNKIDLLD  167 (204)
T ss_pred             HHHHHHCCEEEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCC
T ss_conf             99997398999999799853667799999999980655576078886704799


No 417
>KOG2968 consensus
Probab=92.19  E-value=0.84  Score=24.10  Aligned_cols=57  Identities=18%  Similarity=0.242  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHH-HHHHHHH
Q ss_conf             99998999851288899738888898999998620125435787768899-9999999
Q gi|254780725|r  263 MIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLR-NSKNLID  319 (427)
Q Consensus       263 ~l~~ll~~l~~~yd~VIiD~p~~~~~~~~~~L~~AD~vviV~~p~~~slr-~a~~ll~  319 (427)
                      .+..-+......|+.|+.-+-...+.|++..+..||.+++|...+...-. ...+++.
T Consensus       696 rl~~wL~~qEd~y~ivlY~~D~~~s~WtrrClrqaD~ILiva~g~~~pe~g~~er~l~  753 (1158)
T KOG2968         696 RLMSWLAQQEDRYRIVLYQCDFVLSNWTRRCLRQADCILIVALGDQSPEIGELERELL  753 (1158)
T ss_pred             HHHHHHHHHHHHHEEEEEEECCCCCHHHHHHHHHHCEEEEEECCCCCCHHHHHHHHHH
T ss_conf             3777887753433289999447557899999865078999963888830769999998


No 418
>COG1160 Predicted GTPases [General function prediction only]
Probab=92.18  E-value=0.49  Score=25.55  Aligned_cols=18  Identities=39%  Similarity=0.543  Sum_probs=9.3

Q ss_pred             CEEEEEECCCC--HHHHHHH
Q ss_conf             80899816871--8999999
Q gi|254780725|r  107 TKVIVIGDTND--VSLYRAL  124 (427)
Q Consensus       107 ~~Vivig~~~d--~~l~r~l  124 (427)
                      .+|-+||.-|.  ..|...+
T Consensus       179 ikiaiiGrPNvGKSsLiN~i  198 (444)
T COG1160         179 IKIAIIGRPNVGKSSLINAI  198 (444)
T ss_pred             EEEEEEECCCCCCHHHHHHH
T ss_conf             08999927878705888775


No 419
>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Probab=92.18  E-value=0.23  Score=27.56  Aligned_cols=39  Identities=18%  Similarity=0.191  Sum_probs=31.3

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             75379997469887756899999999996269949999787
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLD  200 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlD  200 (427)
                      ..+-+-++| --|+|||++|..+|+.+.. .+..++.+++.
T Consensus        18 ~~~~ill~G-ppGtGKT~la~~ia~~~~~-~~~~~~~~~~~   56 (151)
T cd00009          18 PPKNLLLYG-PPGTGKTTLARAIANELFR-PGAPFLYLNAS   56 (151)
T ss_pred             CCCEEEEEC-CCCCCHHHHHHHHHHHHCC-CCCCEEEEEHH
T ss_conf             998089989-9998865999999997121-37982785477


No 420
>cd03294 ABC_Pro_Gly_Bertaine This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea.  This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily.  The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=92.18  E-value=0.39  Score=26.16  Aligned_cols=42  Identities=21%  Similarity=0.248  Sum_probs=27.5

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             56753799974698877568999999999962699499997879
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDL  201 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl  201 (427)
                      -..|.+++++| ..|+||||+.-.++..+.- ...++.+=+-|.
T Consensus        47 i~~GE~~~ivG-~SGsGKSTLLr~i~GL~~p-~~G~I~~~G~~i   88 (269)
T cd03294          47 VREGEIFVIMG-LSGSGKSTLLRCINRLIEP-TSGKVLIDGQDI   88 (269)
T ss_pred             ECCCCEEEEEC-CCCCHHHHHHHHHHCCCCC-CCEEEEECCEEC
T ss_conf             88999999998-9984899999999759999-975999999999


No 421
>cd04137 RheB Rheb (Ras Homolog Enriched in Brain) subfamily.  Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation.  It is expressed ubiquitously, with elevated levels in muscle and brain.  Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth.  TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell.  TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb.  The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb.  Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that le
Probab=92.17  E-value=0.84  Score=24.09  Aligned_cols=119  Identities=13%  Similarity=0.117  Sum_probs=72.3

Q ss_pred             CCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHH-CCCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             288899738888--898999998620125435787-76889999999999998-19876753899956589875200599
Q gi|254780725|r  274 IFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKK-LRPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       274 ~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~-~~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      .|.+-|+|++..  +......-...++-+++|.+. +..|+.+...+.+.+.. .....-++.+|-|+.+......++.+
T Consensus        48 ~~~l~iwDtaG~e~~~~~~~~~~~~a~~~ilvydvt~~~Sf~~~~~~~~~~~~~~~~~~~piilVgNK~DL~~~r~V~~~  127 (180)
T cd04137          48 DYHLEIVDTAGQDEYSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHTQRQVSTE  127 (180)
T ss_pred             EEEEEEEECCCCCCCCHHHHHHHHHCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHCCCCHH
T ss_conf             99999998998701006679998635578999743887889999999999999758888867977653462440788999


Q ss_pred             HHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             99998489537990687999999884796189888999--89999999999985221223211
Q gi|254780725|r  350 DFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVLMGRVTVSKPQ  410 (427)
Q Consensus       350 ~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i~gr~~~~~~k  410 (427)
                      +.                +  .-|...|-+..|.+.+.  -+.+.|..|++.|.....+.+|+
T Consensus       128 e~----------------~--~~a~~~~~~f~EtSAk~g~nV~e~F~~l~~~i~k~~~~~~~~  172 (180)
T cd04137         128 EG----------------K--ELAESWGAAFLESSARENENVEEAFELLIEEIEKVENPLDPG  172 (180)
T ss_pred             HH----------------H--HHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             99----------------9--999983998999776889198999999999998863899999


No 422
>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1).  NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters.  Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear.  The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed.  MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.
Probab=92.06  E-value=0.87  Score=24.01  Aligned_cols=41  Identities=22%  Similarity=0.334  Sum_probs=28.7

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             6753799974698877568999999999962699499997879
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDL  201 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl  201 (427)
                      +.|..|+++| +-|+||||+.--+.-.+--. ...+.+=+-|+
T Consensus        32 ~~Ge~v~ivG-~sGsGKSTLl~ll~g~~~p~-~G~I~idg~di   72 (207)
T cd03369          32 KAGEKIGIVG-RTGAGKSTLILALFRFLEAE-EGKIEIDGIDI   72 (207)
T ss_pred             CCCCEEEEEC-CCCCCHHHHHHHHHHHCCCC-CCEEEECCEEC
T ss_conf             6999999999-99987999999999872888-87899999995


No 423
>COG1493 HprK Serine kinase of the HPr protein, regulates carbohydrate metabolism [Signal transduction mechanisms]
Probab=92.02  E-value=0.88  Score=23.98  Aligned_cols=89  Identities=15%  Similarity=0.244  Sum_probs=61.3

Q ss_pred             HHHHHHHHHCCCCCEEEEEECCCC--HHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCC-CCCCCCCCEEEEEEE--
Q ss_conf             899988853289980899816871--899999997656264318999899999763102332-223456753799974--
Q gi|254780725|r   94 SALEPLAEVCDSGTKVIVIGDTND--VSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQ-EEGKGSSGCSISFIG--  168 (427)
Q Consensus        94 ~~l~~la~~~~p~~~Vivig~~~d--~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~-~~~~~~~grvIav~g--  168 (427)
                      ..-.++.+.|...+|.+|++..-+  ..++-.+.+.++- .|..+....++...+...+... .+...-.|-.+.++|  
T Consensus        69 ~r~~~i~~~~~~~~P~iI~sk~~~~p~~l~~~a~~~~~p-il~s~~~ts~l~~~l~~yL~~~lA~~~~vHGvl~~I~GvG  147 (308)
T COG1493          69 ERKKRIGKLFSLDTPALIVSKGLPIPEELLDAAKKYNIP-ILTSKLSTSELSFTLTNYLSRPLAERVNVHGVLLDIFGVG  147 (308)
T ss_pred             HHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHCCCC-EEEECCHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEEEE
T ss_conf             589999997476997799978999978999998870996-6985331899999999986131052025546899994258


Q ss_pred             ----CCCCCCHHHHHHHHH
Q ss_conf             ----698877568999999
Q gi|254780725|r  169 ----SRGGVGSSTIAHNCA  183 (427)
Q Consensus       169 ----~KGGvGkTTiA~nLA  183 (427)
                          +..|+|||.+|..|=
T Consensus       148 VLItG~SG~GKSElALeLi  166 (308)
T COG1493         148 VLITGPSGAGKSELALELI  166 (308)
T ss_pred             EEEECCCCCCHHHHHHHHH
T ss_conf             9998789887768999999


No 424
>PTZ00141 elongation factor 1 alpha; Provisional
Probab=92.01  E-value=0.27  Score=27.17  Aligned_cols=14  Identities=7%  Similarity=0.261  Sum_probs=6.7

Q ss_pred             HCCCCCEEEEEECC
Q ss_conf             32899808998168
Q gi|254780725|r  102 VCDSGTKVIVIGDT  115 (427)
Q Consensus       102 ~~~p~~~Vivig~~  115 (427)
                      .+.++.-++||...
T Consensus       106 as~aD~ailvVdA~  119 (443)
T PTZ00141        106 TSQADVALLVVPAE  119 (443)
T ss_pred             HCCCCEEEEEEECC
T ss_conf             41077589999867


No 425
>PRK05855 short chain dehydrogenase; Validated
Probab=91.98  E-value=0.22  Score=27.62  Aligned_cols=155  Identities=17%  Similarity=0.167  Sum_probs=75.2

Q ss_pred             CCCEEEEEECCCC----HHHHHHHHHCCCCEEEC--------CCCC-HHHHHHHHHHCCCC----C-----------CCC
Q ss_conf             9980899816871----89999999765626431--------8999-89999976310233----2-----------223
Q gi|254780725|r  105 SGTKVIVIGDTND----VSLYRALISNHVSEYLI--------EPLS-VADIINSISAIFTP----Q-----------EEG  156 (427)
Q Consensus       105 p~~~Vivig~~~d----~~l~r~l~r~Gv~dyl~--------~P~~-~~~l~~ai~~~~~~----~-----------~~~  156 (427)
                      ..+||-+|-...|    ..+|..+-+ =+.+|-.        .|.+ ++.+.+.+......    +           .+.
T Consensus       232 ~~vPVq~iv~~~D~~v~p~l~~~~~~-w~~~l~rr~i~a~HW~p~s~P~~iA~~~~efv~~~~~~~~~~~~~~~~~~~~~  310 (582)
T PRK05855        232 THVPVQLIVPTGDPYVRPALYDDLAR-WVPRLWRREIKAGHWLPMSHPQVLAAAVAELIDAVEGGPPPRALLRARVGRPR  310 (582)
T ss_pred             CCCCEEEEEECCCCCCCHHHHCCHHH-CCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCC
T ss_conf             88877997517887769777441444-17860898603785376679899999999999863578898667335458998


Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC-HHHC---CCCCCCCHHHHHCCCCCHHHHH
Q ss_conf             45675379997469887756899999999996269949999787989860-3343---8998789888631845612433
Q gi|254780725|r  157 KGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA-NINF---DKDPINSISDAIYPVGRIDKAF  232 (427)
Q Consensus       157 ~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~-~~~l---~~~~~~~l~d~l~~~~rlD~~~  232 (427)
                      ....||++.|+|+.+|+|+.     +|..||+ .|.+|++.|.|...... ...+   |.+...-..|+ .+.+.+ ..+
T Consensus       311 ~rFsGKvAvVTGA~sGIGrA-----~A~~fA~-~GA~Vvl~Dr~~~~l~eta~ei~~~G~~a~~~~~DV-td~~av-~al  382 (582)
T PRK05855        311 GRFGGKLVVVTGAGSGIGRA-----TALAFAR-EGAEVVASDIDEAAAERTAALIRAAGAVAHAYRVDV-SDADAM-EAL  382 (582)
T ss_pred             CCCCCCEEEEECCCCHHHHH-----HHHHHHH-CCCEEEEECCCHHHHHHHHHHHHHCCCEEEEEECCC-CCHHHH-HHH
T ss_conf             87499589995875789999-----9999997-799999960799999999999995198489997558-999999-999


Q ss_pred             HHHHHHCCCCCEEEEECCCCC---CCHHCCCHHHHHHHHH
Q ss_conf             765320248980687248761---2032079999999899
Q gi|254780725|r  233 VSRLPVFYAENLSILTAPAML---SRTYDFDEKMIVPVLD  269 (427)
Q Consensus       233 l~~~l~~~~~gL~lL~a~~~~---~~~~~~~~~~l~~ll~  269 (427)
                      .+..... -.++++|--....   ....+.+.+.++.+++
T Consensus       383 ~~~v~~~-~G~iDILVNNAGI~~~g~~~d~s~e~w~~v~d  421 (582)
T PRK05855        383 AEWVGAE-HGVPDIVVNNAGIGMAGGFLDTSAEEWDRVLD  421 (582)
T ss_pred             HHHHHHH-CCCCCEEEECCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             9999997-69999999898758997803299999999998


No 426
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=91.95  E-value=0.89  Score=23.93  Aligned_cols=42  Identities=29%  Similarity=0.405  Sum_probs=30.1

Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             999997631023322234567537999746988775689999999999
Q gi|254780725|r  140 ADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIA  187 (427)
Q Consensus       140 ~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA  187 (427)
                      +.+.+.+.+...     .++.+.-+-|.| ..|+|||++|-.+|..+-
T Consensus        10 ~~i~~~L~~~i~-----~~rl~HAyLF~G-p~G~GK~~~A~~~A~~ll   51 (313)
T PRK05564         10 ENIKNRIDNSII-----KGKFSHASLIVG-EDGIGKSILAKEIANKIL   51 (313)
T ss_pred             HHHHHHHHHHHH-----CCCCCCEEEEEC-CCCCCHHHHHHHHHHHHH
T ss_conf             999999999998-----799875043279-998509999999999982


No 427
>pfam05729 NACHT NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
Probab=91.93  E-value=0.2  Score=27.97  Aligned_cols=27  Identities=22%  Similarity=0.327  Sum_probs=22.8

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             3799974698877568999999999962
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASV  189 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~  189 (427)
                      |.|.+.| ..|+||||++..+|+.+++.
T Consensus         1 r~i~i~G-~aG~GKTtll~kl~~~wa~g   27 (165)
T pfam05729         1 RTVILQG-EAGSGKTTLLQKLALLWAQG   27 (165)
T ss_pred             CEEEEEC-CCCCCHHHHHHHHHHHHHCC
T ss_conf             9899982-79898999999999999869


No 428
>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport.  Other members of this system include the MetP permease and  the MetQ substrate binding protein.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=91.91  E-value=0.46  Score=25.69  Aligned_cols=43  Identities=26%  Similarity=0.258  Sum_probs=28.3

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             567537999746988775689999999999626994999978798
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      -+.|.+++++| ..|+||||+.--++....- ....+.+-+-|..
T Consensus        28 i~~Ge~~~ivG-~SGsGKSTllr~i~gL~~p-~sG~I~~~g~~i~   70 (233)
T cd03258          28 VPKGEIFGIIG-RSGAGKSTLIRCINGLERP-TSGSVLVDGTDLT   70 (233)
T ss_pred             ECCCCEEEEEC-CCCCHHHHHHHHHHCCCCC-CCCEEEECCEECC
T ss_conf             99999999988-9805899999999679999-9808999999989


No 429
>PRK12377 putative replication protein; Provisional
Probab=91.86  E-value=0.33  Score=26.58  Aligned_cols=68  Identities=9%  Similarity=0.087  Sum_probs=41.8

Q ss_pred             HCCCCEEE------CCCCCHHHHHHHHH--HCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             76562643------18999899999763--10233222345675379997469887756899999999996269949999
Q gi|254780725|r  126 SNHVSEYL------IEPLSVADIINSIS--AIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLA  197 (427)
Q Consensus       126 r~Gv~dyl------~~P~~~~~l~~ai~--~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLv  197 (427)
                      |+|++++-      -+++.-+....++.  +-++.   .-...+.-+.|+| .-|+|||-+|+.++..+.+ .|++|+.+
T Consensus        61 rs~i~~~h~~~~f~ny~~~~~~~~~a~~~a~~~~~---~F~~~~~NlIf~G-~pGtGKTHLA~AIg~~a~~-~G~sVlF~  135 (248)
T PRK12377         61 RSGIQPLHRKCSFANYQVQNDGQRYALSQAKSIAD---ELMTGCTNFVFSG-KPGTGKNHLAAAIGNRLLA-KGRSVIVV  135 (248)
T ss_pred             CCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHHH---HHHCCCCEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEE
T ss_conf             04685376438634564578789999999999999---8731886089989-9998788999999999998-79969998


Q ss_pred             E
Q ss_conf             7
Q gi|254780725|r  198 D  198 (427)
Q Consensus       198 D  198 (427)
                      -
T Consensus       136 t  136 (248)
T PRK12377        136 T  136 (248)
T ss_pred             E
T ss_conf             8


No 430
>PRK06872 DNA polymerase III subunits gamma and tau; Provisional
Probab=91.86  E-value=0.92  Score=23.87  Aligned_cols=32  Identities=13%  Similarity=0.202  Sum_probs=18.3

Q ss_pred             CHHHHHHHHHCCCCEEECCCCCHHHHHHHHHH
Q ss_conf             18999999976562643189998999997631
Q gi|254780725|r  117 DVSLYRALISNHVSEYLIEPLSVADIINSISA  148 (427)
Q Consensus       117 d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~  148 (427)
                      |+.||-+..-.|-+|.=..|....-+-=++-|
T Consensus       319 ~~ql~Yqi~l~g~~dl~~apd~~~g~eM~lLR  350 (696)
T PRK06872        319 DVQFFYQVMVSGRKELAFAPNRRIGVEMTLLR  350 (696)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             99999999984120045699646749999999


No 431
>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system.  Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond.  Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond.  Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=91.86  E-value=0.61  Score=24.95  Aligned_cols=43  Identities=21%  Similarity=0.285  Sum_probs=29.3

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             567537999746988775689999999999626994999978798
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLP  202 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~  202 (427)
                      -..|.+++++| ..|+||||+.-.++-.+.-. ..++.+-+-|..
T Consensus        24 i~~Ge~~~iiG-psGsGKSTLl~~i~gl~~p~-~G~I~~~g~~i~   66 (241)
T cd03256          24 INPGEFVALIG-PSGAGKSTLLRCLNGLVEPT-SGSVLIDGTDIN   66 (241)
T ss_pred             ECCCCEEEEEC-CCCCHHHHHHHHHHCCCCCC-CEEEEECCEECC
T ss_conf             99998999999-99833999999997499998-559999999989


No 432
>PRK13506 formate--tetrahydrofolate ligase; Provisional
Probab=91.84  E-value=0.44  Score=25.80  Aligned_cols=52  Identities=8%  Similarity=0.077  Sum_probs=37.8

Q ss_pred             CCCCCEEEEEEE---CCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCC
Q ss_conf             456753799974---69887756899999999996269949999787989860334389
Q gi|254780725|r  157 KGSSGCSISFIG---SRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDK  212 (427)
Q Consensus       157 ~~~~grvIav~g---~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~  212 (427)
                      ..+.||.|.|.+   ..-|-||||++..|+.+|.+ .|+++++.   +...+++..||+
T Consensus        50 ~~~~gklilVTaitPTP~GEGKTTttIGL~~aL~~-lgk~~~~~---lRePSlGP~FGi  104 (577)
T PRK13506         50 DQPKGKLVIVTAVTPTPLGEGKTVTTIGLTQGLNA-LGQKVCAC---IRQPSMGPVFGV  104 (577)
T ss_pred             CCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHH-HCCCEEEE---EECCCCCCCCCC
T ss_conf             38996499998568988989841109879999987-19845899---726887874066


No 433
>PRK12337 2-phosphoglycerate kinase; Provisional
Probab=91.83  E-value=0.19  Score=28.04  Aligned_cols=26  Identities=23%  Similarity=0.388  Sum_probs=22.5

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             53799974698877568999999999
Q gi|254780725|r  161 GCSISFIGSRGGVGSSTIAHNCAFSI  186 (427)
Q Consensus       161 grvIav~g~KGGvGkTTiA~nLA~~L  186 (427)
                      -.+|..+|+-.||||||+|..||.-|
T Consensus       261 ~PiiILIGGaSGvGKSTlAseLA~RL  286 (492)
T PRK12337        261 RPLHVLLGGVSGTGKSVLAAELAYRL  286 (492)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             87699960788866888999999960


No 434
>PRK08116 hypothetical protein; Validated
Probab=91.83  E-value=0.33  Score=26.59  Aligned_cols=38  Identities=13%  Similarity=0.250  Sum_probs=30.6

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             7537999746988775689999999999626994999978
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADL  199 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDl  199 (427)
                      .++=+-++| .-|+|||.+|+.+|..|.+ .|.+|+.+..
T Consensus       107 ~~~GLll~G-~~GtGKThLa~aIa~~l~~-~g~~V~~~~~  144 (262)
T PRK08116        107 ESVGLLLWG-SPGNGKTYLAAAIANELIE-KGVPVVFVNV  144 (262)
T ss_pred             CCCEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEEEH
T ss_conf             686189989-8999899999999999998-7993999889


No 435
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=91.81  E-value=0.93  Score=23.84  Aligned_cols=86  Identities=12%  Similarity=0.200  Sum_probs=57.9

Q ss_pred             EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCH
Q ss_conf             30699899999986189984999980598767788999888532899808998168718999999976562643189998
Q gi|254780725|r   60 ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSV  139 (427)
Q Consensus        60 v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~  139 (427)
                      ++.-+...|.+....--.-.+=++|+.....+.++.++.+++.+ |+. .|=.|..-+....++++.+|++ |++.|...
T Consensus        21 lr~~~~~~a~~i~~al~~gGi~~iEiTl~tp~a~~~I~~l~~~~-p~~-~vGaGTV~~~e~~~~a~~aGA~-FiVSP~~~   97 (212)
T PRK05718         21 IVINKLEDAVPLAKALVAGGLPVLEVTLRTPAALEAIRAIRKEV-PEA-LIGAGTVLNPEQLAQAIEAGAQ-FIVSPGLT   97 (212)
T ss_pred             EECCCHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHC-CCC-EEEEEEECCHHHHHHHHHCCCC-EEECCCCC
T ss_conf             97489999999999999879978999578961999999999758-981-7965331348899999984998-99848998


Q ss_pred             HHHHHHHHH
Q ss_conf             999997631
Q gi|254780725|r  140 ADIINSISA  148 (427)
Q Consensus       140 ~~l~~ai~~  148 (427)
                      .++++...+
T Consensus        98 ~~v~~~a~~  106 (212)
T PRK05718         98 PPLLKACQD  106 (212)
T ss_pred             HHHHHHHHH
T ss_conf             999999998


No 436
>cd00876 Ras Ras family.  The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.  Ras proteins regulate cell growth, proliferation and differentiation.  Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding.  Many RasGEFs have been identified.  These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras.  Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1.  Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid.  Lipid binding is essential for membrane attachment, a key feature of m
Probab=91.80  E-value=0.93  Score=23.83  Aligned_cols=110  Identities=18%  Similarity=0.215  Sum_probs=67.6

Q ss_pred             HCCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCC-CCCCCEEEEECCCCCCCCHHHH
Q ss_conf             12888997388888--9899999862012543578-776889999999999998198-7675389995658987520059
Q gi|254780725|r  273 QIFPLVILDVPHVW--NSWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRP-ADKPPYLVLNQVKTPKKPEISI  348 (427)
Q Consensus       273 ~~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~-~~~~~~iVlNr~~~~~~~~i~~  348 (427)
                      ..+.+-++|++...  .......+..||.+++|.+ -+..|+.+...+++.+.+... ...++.+|-|+.+......++.
T Consensus        45 ~~~~l~i~Dt~g~~~~~~~~~~~~~~a~~~ilvfd~~~~~Sf~~i~~~~~~i~~~~~~~~~piilvgnK~Dl~~~~~V~~  124 (160)
T cd00876          45 ETYTLDILDTAGQEEFSAMRDLYIRQGDGFILVYSITDRESFEEIKGYREQILRVKDDEDIPIVLVGNKCDLENERQVSK  124 (160)
T ss_pred             EEEEEEEEECCCCHHHHHHHHHHHHHCCEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHCCCCCH
T ss_conf             99999999799962355788999764368999732898789999999999999972878862999997456223078999


Q ss_pred             HHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHH
Q ss_conf             999998489537990687999999884796189888999--8999999999998
Q gi|254780725|r  349 SDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVL  400 (427)
Q Consensus       349 ~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i  400 (427)
                      ++..+                  -|...|.+..|.+.++  -+.+.|..|++.|
T Consensus       125 ~e~~~------------------~a~~~~~~y~e~Sak~g~nV~e~F~~i~~~i  160 (160)
T cd00876         125 EEGKA------------------LAKEWGCPFIETSAKDNINIDEVFKLLVREI  160 (160)
T ss_pred             HHHHH------------------HHHHCCCEEEEECCCCCCCHHHHHHHHHHHC
T ss_conf             99999------------------9998499799984798949899999999729


No 437
>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis.  The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes.  CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space.  In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.
Probab=91.79  E-value=0.93  Score=23.82  Aligned_cols=36  Identities=28%  Similarity=0.350  Sum_probs=27.2

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             67537999746988775689999999999626994999
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLL  196 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlL  196 (427)
                      ..|..++++| +-|+||||+.--+.-.+.-.. .++.+
T Consensus        26 ~~Ge~~aivG-~sGsGKSTLl~~l~G~~~p~~-G~i~i   61 (178)
T cd03247          26 KQGEKIALLG-RSGSGKSTLLQLLTGDLKPQQ-GEITL   61 (178)
T ss_pred             CCCCEEEEEC-CCCCHHHHHHHHHHHCCCCCC-CEEEE
T ss_conf             6999999999-998759999999986176678-86999


No 438
>PRK12317 elongation factor 1-alpha; Reviewed
Probab=91.63  E-value=0.65  Score=24.80  Aligned_cols=64  Identities=13%  Similarity=0.182  Sum_probs=28.7

Q ss_pred             CCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCCH--HHHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf             88899738888--89899999862012543578776--88999999999999819876753899956589
Q gi|254780725|r  275 FPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLDL--AGLRNSKNLIDVLKKLRPADKPPYLVLNQVKT  340 (427)
Q Consensus       275 yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~~--~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~  340 (427)
                      +.|.++|+|..  +-..+......+|..++|+..+-  .-...+++-+..++.++.  +.+.+++|+++.
T Consensus        85 ~~~~iiD~PGH~~fi~nmi~Gas~~D~ailvV~A~~~~G~~~QT~eHl~l~~~lgi--~~iiV~vnKmD~  152 (426)
T PRK12317         85 YYFTIIDCPGHRDFVKNMITGASQADAAVLVVSARDAGGVMPQTREHVFLARTLGI--NQLIVAINKMDA  152 (426)
T ss_pred             CEEEEEECCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHCC--CEEEEEEECCCC
T ss_conf             16999878963667877874534677279999636566764778999999998099--839999953335


No 439
>PRK10490 sensor protein KdpD; Provisional
Probab=91.62  E-value=0.97  Score=23.71  Aligned_cols=21  Identities=24%  Similarity=0.431  Sum_probs=11.4

Q ss_pred             EECCCHHHHHHHHHCCCCCCEEEEEC
Q ss_conf             30699899999986189984999980
Q gi|254780725|r   60 ITRGSIAEAVSCFSDSSTPDLIIVQT   85 (427)
Q Consensus        60 v~~g~~~~A~~~~~~~~~P~~iivd~   85 (427)
                      ...-++++++..     -|++++||=
T Consensus        90 ~~e~dlda~l~r-----~P~~~lvDe  110 (895)
T PRK10490         90 ISEFDLDAALAR-----RPALILMDE  110 (895)
T ss_pred             CCCCCHHHHHHC-----CCCEEEEEC
T ss_conf             341689899853-----998899733


No 440
>PRK10070 glycine betaine transporter ATP-binding subunit; Provisional
Probab=91.60  E-value=0.98  Score=23.69  Aligned_cols=96  Identities=16%  Similarity=0.140  Sum_probs=57.3

Q ss_pred             CHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCC-CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             18999999976562643189998999997631023322-23456753799974698877568999999999962699499
Q gi|254780725|r  117 DVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQE-EGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETL  195 (427)
Q Consensus       117 d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~-~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~Vl  195 (427)
                      +..-..++++.|.+        .+++.+.-....+-.+ .-.-..|.+++++| ..|+||||+.--++..+-- ...++.
T Consensus        17 ~~~~a~~~~~~g~~--------k~ei~~~tg~~vAv~dVsl~I~~GEi~~ivG-~SGsGKSTLlr~i~gL~~P-t~G~I~   86 (400)
T PRK10070         17 HPQRAFKYIEQGLS--------KEQILEKTGLSLGVKDASLAIEEGEIFVIMG-LSGSGKSTMVRLLNRLIEP-TRGQVL   86 (400)
T ss_pred             CHHHHHHHHHCCCC--------HHHHHHHHCCEEEEECCEEEECCCCEEEEEC-CCCCHHHHHHHHHHCCCCC-CCCEEE
T ss_conf             98999999876999--------8999986499998974076887999999999-9984699999999759998-981899


Q ss_pred             EEECCCCCC-----------CCHH---HCCCCCCCCHHHHH
Q ss_conf             997879898-----------6033---43899878988863
Q gi|254780725|r  196 LADLDLPYG-----------TANI---NFDKDPINSISDAI  222 (427)
Q Consensus       196 LvDlDl~~g-----------~~~~---~l~~~~~~~l~d~l  222 (427)
                      +-+-|...-           ..++   .+++-|..++.+-+
T Consensus        87 i~G~di~~~~~~~l~~~rrr~igmVFQ~~aL~P~~TV~eNi  127 (400)
T PRK10070         87 IDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNT  127 (400)
T ss_pred             ECCEECCCCCHHHHHHHHCCCEEEEECCCCCCCCCCHHHHH
T ss_conf             99999998997898765146559995797414388888878


No 441
>PRK08782 consensus
Probab=91.58  E-value=0.98  Score=23.68  Aligned_cols=87  Identities=15%  Similarity=0.158  Sum_probs=63.0

Q ss_pred             EECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCH
Q ss_conf             30699899999986189984999980598767788999888532899808998168718999999976562643189998
Q gi|254780725|r   60 ITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSV  139 (427)
Q Consensus        60 v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~  139 (427)
                      ++.-+.+.|.+....--.-.+=++|+.+.....++.++.|++.. |+ -.|=.|...|....++++.+|++ |++.|...
T Consensus        23 ir~~~~~~a~~~~eal~~gGi~~iEiTlrt~~a~~~i~~l~~~~-p~-~~vGaGTV~~~e~~~~a~~aGA~-FiVSP~~~   99 (219)
T PRK08782         23 VTVDTLDQARRVADALLEGGLPAIELTLRTPVAIEALAMLKREL-PN-IVIGAGTVLSERQLRQSVDAGAD-FLVTPGTP   99 (219)
T ss_pred             EECCCHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHC-CC-CEEEEEEECCHHHHHHHHHCCCC-EEECCCCC
T ss_conf             97599999999999999879987999679933999999999868-99-47999970589999999984998-99878997


Q ss_pred             HHHHHHHHHC
Q ss_conf             9999976310
Q gi|254780725|r  140 ADIINSISAI  149 (427)
Q Consensus       140 ~~l~~ai~~~  149 (427)
                      .++++...+.
T Consensus       100 ~~v~~~a~~~  109 (219)
T PRK08782        100 APLARLLADA  109 (219)
T ss_pred             HHHHHHHHHC
T ss_conf             9999999981


No 442
>COG1072 CoaA Panthothenate kinase [Coenzyme metabolism]
Probab=91.56  E-value=0.99  Score=23.67  Aligned_cols=72  Identities=21%  Similarity=0.043  Sum_probs=40.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCC-EEEEECCCC-CCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf             7999746988775689999999999626994-999978798-98603343899878988863184561243376532024
Q gi|254780725|r  163 SISFIGSRGGVGSSTIAHNCAFSIASVFAME-TLLADLDLP-YGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFY  240 (427)
Q Consensus       163 vIav~g~KGGvGkTTiA~nLA~~LA~~~~~~-VlLvDlDl~-~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~  240 (427)
                      ||++.| .-|+||||+|-.|...+++....+ |-+|-.|-- .++.  .|+   ++|+.+-=..|+..|-..+-+.+...
T Consensus        84 IIgiaG-svavGKST~ar~L~~ll~~~~~~~~v~lvpmDGFhy~n~--~L~---~~glm~rKGfPeSyD~~~ll~fl~~v  157 (283)
T COG1072          84 IIGIAG-SVAVGKSTTARILQALLSRWPESPKVDLVTMDGFHYPNA--VLD---ERGLMARKGFPESYDVAALLRFLSDV  157 (283)
T ss_pred             EEEECC-CCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHH--HHH---HCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             999605-766557789999999996388987337871454546767--752---21220018998535689999999999


No 443
>pfam02572 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin adenosyltransferase, EC:2.5.1.17, involved in cobalamin (vitamin B12) biosynthesis. These enzymes catalyse the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.
Probab=91.55  E-value=0.84  Score=24.09  Aligned_cols=37  Identities=27%  Similarity=0.389  Sum_probs=29.1

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             7537999746988775689999999999626994999978
Q gi|254780725|r  160 SGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADL  199 (427)
Q Consensus       160 ~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDl  199 (427)
                      .|.+...+|  -|=||||-|..+|.-.+. .|.+|+++-+
T Consensus         3 ~G~i~iytG--~GKGKTTAAlGlalRA~G-~G~rV~ivQF   39 (172)
T pfam02572         3 KGLLIVYTG--NGKGKSTAAFGMALRALG-HGMRVGVVQF   39 (172)
T ss_pred             CCEEEEEEC--CCCCHHHHHHHHHHHHHC-CCCEEEEEEE
T ss_conf             637999957--999718899999999825-9988999999


No 444
>TIGR01846 type_I_sec_HlyB type I secretion system ATPase; InterPro: IPR010132   Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This entry contains one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane.
Probab=91.51  E-value=0.24  Score=27.48  Aligned_cols=107  Identities=16%  Similarity=0.159  Sum_probs=56.1

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             67537999746988775689999999999626994999978798986033438998789888631845612433765320
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPV  238 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~  238 (427)
                      +.|.+|.++| ..|+||||++==+=...-=++| +||+=..|+..                        .|++.|+|-+.
T Consensus       489 ~~Ge~IGIvG-pSGSGKSTLTKL~QRLYtP~~G-qVLVDG~DLA~------------------------~DP~wLRRQ~g  542 (703)
T TIGR01846       489 KPGEVIGIVG-PSGSGKSTLTKLLQRLYTPEHG-QVLVDGVDLAI------------------------ADPAWLRRQVG  542 (703)
T ss_pred             CCCEEEEEEC-CCCCCHHHHHHHHHHHCCCCCC-EEEECCCCCCC------------------------CCCCHHHHCCE
T ss_conf             7865799872-7898678999998861488887-47770300010------------------------18520102230


Q ss_pred             CC-----------CCCEEEEECCCCCCCHHCC-CHHHHHHHHHHHHHCCCEEEECCCCCCCHHHH
Q ss_conf             24-----------8980687248761203207-99999998999851288899738888898999
Q gi|254780725|r  239 FY-----------AENLSILTAPAMLSRTYDF-DEKMIVPVLDILEQIFPLVILDVPHVWNSWTQ  291 (427)
Q Consensus       239 ~~-----------~~gL~lL~a~~~~~~~~~~-~~~~l~~ll~~l~~~yd~VIiD~p~~~~~~~~  291 (427)
                      .+           .||+++--...+.+..-.. +=..-...+..+++.|+..|.-=+...+..-+
T Consensus       543 VVLQEn~LFsrSirdNI~l~~P~~~~E~Vi~AA~LAGA~dFI~~Lp~GY~T~vgE~G~~LSGGQR  607 (703)
T TIGR01846       543 VVLQENVLFSRSIRDNIALCNPGASVEHVIAAAKLAGAHDFISELPQGYNTEVGEKGANLSGGQR  607 (703)
T ss_pred             EEEECCHHHCCCHHHHHHHCCCCCCHHHHHHHHHHCCHHHHHHHCCCCCCCCCEEECCCCCCHHH
T ss_conf             23400021012278898517777698999999862185899973637677400124156673378


No 445
>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.
Probab=91.41  E-value=0.29  Score=26.94  Aligned_cols=37  Identities=27%  Similarity=0.251  Sum_probs=26.9

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             6753799974698877568999999999962699499997
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLAD  198 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvD  198 (427)
                      +.|..|+++| +.|+||||++--++-.+.-.. .. +.+|
T Consensus       489 ~~Ge~vaIvG-~sGsGKSTL~kll~Gl~~p~~-G~-i~id  525 (694)
T TIGR03375       489 RPGEKVAIIG-RIGSGKSTLLKLLLGLYQPTE-GS-VLLD  525 (694)
T ss_pred             CCCCEEEEEE-CCCCCHHHHHHHHCCCCCCCC-CE-EEEC
T ss_conf             7997899980-589878899998556758998-87-9989


No 446
>cd03261 ABC_Org_Solvent_Resistant ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=91.40  E-value=0.62  Score=24.91  Aligned_cols=39  Identities=23%  Similarity=0.232  Sum_probs=26.4

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             56753799974698877568999999999962699499997
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLAD  198 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvD  198 (427)
                      -..|.+++++| ..|+||||+.-.++-.+.- ...++.+-.
T Consensus        23 i~~Ge~~~iiG-~SGsGKSTll~~i~gL~~p-~~G~I~~~g   61 (235)
T cd03261          23 VRRGEILAIIG-PSGSGKSTLLRLIVGLLRP-DSGEVLIDG   61 (235)
T ss_pred             ECCCCEEEEEC-CCCCHHHHHHHHHHCCCCC-CCCEEEECC
T ss_conf             87998999999-9997299999999759998-985899999


No 447
>TIGR02173 cyt_kin_arch cytidylate kinase, putative; InterPro: IPR011892    Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by IPR003136 from INTERPRO.; GO: 0004127 cytidylate kinase activity, 0005524 ATP binding, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=91.38  E-value=0.15  Score=28.77  Aligned_cols=108  Identities=19%  Similarity=0.230  Sum_probs=56.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             99974698877568999999999962699499997879898603343899878988863184561243376532024898
Q gi|254780725|r  164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAEN  243 (427)
Q Consensus       164 Iav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~g  243 (427)
                      |-++|+-.|.||||+|-.||-.|+    .+-      ...|..            .++...                 .|
T Consensus         2 ~I~ISGpPGSGktTvA~~lA~~Ls----l~~------iSaG~i------------RelA~~-----------------~G   42 (173)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKLS----LKL------ISAGDI------------RELAEK-----------------MG   42 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCC----CCE------ECCCHH------------HHHHHH-----------------CC
T ss_conf             788735896864789999998639----831------202007------------889864-----------------29


Q ss_pred             EEEEECCCCCCCHHCCCHHHHHH-HHHHHHHCCCEEEECCCCCCCHHHHH-HHHHCCCCCC-CCCCCHHHHHHHH
Q ss_conf             06872487612032079999999-89998512888997388888989999-9862012543-5787768899999
Q gi|254780725|r  244 LSILTAPAMLSRTYDFDEKMIVP-VLDILEQIFPLVILDVPHVWNSWTQE-VLTLSDKVVI-TTSLDLAGLRNSK  315 (427)
Q Consensus       244 L~lL~a~~~~~~~~~~~~~~l~~-ll~~l~~~yd~VIiD~p~~~~~~~~~-~L~~AD~vvi-V~~p~~~slr~a~  315 (427)
                      |+|.-... .++..++... +++ +.+.++..-|+||=   .....|... --..||.-+. -+.+++.+-|=++
T Consensus        43 ldl~E~~~-aee~~eIDk~-iD~~~~E~A~~~~nvvlE---srlagW~~~~nG~yaD~~iyL~A~levRA~RIA~  112 (173)
T TIGR02173        43 LDLAESKY-AEENPEIDKK-IDRRIREIAEKEKNVVLE---SRLAGWILKKNGEYADVKIYLKAPLEVRARRIAK  112 (173)
T ss_pred             CCHHHHHH-HCCCCCCCHH-HHHHHHHHHCCCCCEEEE---EHHHHHHCCCCCCCCCEEEEECCCHHHHHHHHHH
T ss_conf             88777344-3058631167-537885543048966885---2054331157889675678860883332433211


No 448
>TIGR01394 TypA_BipA GTP-binding protein TypA; InterPro: IPR006298   This bacterial (and Arabidopsis) protein, termed TypA or BipA, is a GTP-binding protein. It is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.; GO: 0005525 GTP binding, 0005622 intracellular.
Probab=91.37  E-value=0.056  Score=31.35  Aligned_cols=126  Identities=17%  Similarity=0.268  Sum_probs=78.8

Q ss_pred             CCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC-CCHHHHHHH
Q ss_conf             88899738888--898999998620125435787768899999999999981987675389995658987-520059999
Q gi|254780725|r  275 FPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPK-KPEISISDF  351 (427)
Q Consensus       275 yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~-~~~i~~~~~  351 (427)
                      +-.=|||||..  ++.....+|.+.|-|+++++..---+-+|+=.++.-  +..+ -+|-+|+|+.+.|. |++...+++
T Consensus        70 ~~INIvDTPGHADFGGEVERvL~MVDGvlLlVDA~EGPMPQTrFVL~KA--L~~g-LkPIVViNKiDrp~ARP~eV~d~v  146 (609)
T TIGR01394        70 TKINIVDTPGHADFGGEVERVLGMVDGVLLLVDASEGPMPQTRFVLKKA--LELG-LKPIVVINKIDRPSARPDEVVDEV  146 (609)
T ss_pred             EEEEEEECCCCCCCCCEEEEECEEEEEEEEEEECCCCCCCCCHHHHHHH--HHCC-CCEEEEECCCCCCCCCHHHHHHHH
T ss_conf             8997781689887886588733024058999857888988534789999--9568-936999713478878837887578


Q ss_pred             HH---HHCCCEEEEECCCHHHHHHHHHCCCCEEEECC--CCHHHHHHHHHHHHHHCCCCC
Q ss_conf             99---84895379906879999998847961898889--998999999999998522122
Q gi|254780725|r  352 CA---PLGITPSAIIPFDGAVFGMSANSGKMIHEVDP--KSAIANLLVDFSRVLMGRVTV  406 (427)
Q Consensus       352 ~~---~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p--~s~~a~~~~~La~~i~gr~~~  406 (427)
                      -+   .||..=. .+  |...+-.|..+|..=.+...  ...-++.+.-|=+.|....++
T Consensus       147 FDLF~~LgA~de-QL--DFP~vYASa~~G~A~l~~~~dg~~~~~~~m~PLFd~I~~hvPa  203 (609)
T TIGR01394       147 FDLFIELGADDE-QL--DFPIVYASARAGWASLDKDKDGLDDDSEDMAPLFDAILRHVPA  203 (609)
T ss_pred             HHHHHHCCCCCC-CC--CHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCC
T ss_conf             788885388800-10--1256766523672014466577887220178999898640688


No 449
>PRK00089 era GTP-binding protein Era; Reviewed
Probab=91.36  E-value=0.2  Score=27.92  Aligned_cols=115  Identities=25%  Similarity=0.311  Sum_probs=61.6

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHH
Q ss_conf             56753799974698877568999999999962699499997879898603343899878988863184561243376532
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLP  237 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l  237 (427)
                      -|.| .|+++| +--|||||+-=.|.       |.++..+---+  ||+-                  +++..       
T Consensus         6 ~ksG-~VaivG-~PNvGKSTL~N~l~-------~~k~siVS~k~--~TTR------------------~~i~g-------   49 (296)
T PRK00089          6 FKSG-FVAIVG-RPNVGKSTLLNALV-------GQKISIVSPKP--QTTR------------------HRIRG-------   49 (296)
T ss_pred             CCEE-EEEEEC-CCCCCHHHHHHHHH-------CCCEEEECCCC--CCCC------------------CCEEE-------
T ss_conf             8379-999998-99988899999996-------89617614959--9872------------------83899-------


Q ss_pred             HCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC----------CHHHHHHHHHCCCCCCCCCCC
Q ss_conf             0248980687248761203207999999989998512888997388888----------989999986201254357877
Q gi|254780725|r  238 VFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDVPHVW----------NSWTQEVLTLSDKVVITTSLD  307 (427)
Q Consensus       238 ~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~p~~~----------~~~~~~~L~~AD~vviV~~p~  307 (427)
                              ++.                       ...+.++++|+|...          ...+..++..||.++++++.+
T Consensus        50 --------i~~-----------------------~~~~q~i~iDTpGi~~~~~~l~~~~~~~~~~ai~~aDlil~viD~~   98 (296)
T PRK00089         50 --------IVT-----------------------EDDAQIIFVDTPGIHKPKRALNRAMNKAAWSSLKDVDLVLFVVDAD   98 (296)
T ss_pred             --------EEE-----------------------ECCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCEEEEEEECC
T ss_conf             --------999-----------------------7997999998998667467787899999999997599999998578


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf             68899999999999981987675389995658987
Q gi|254780725|r  308 LAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPK  342 (427)
Q Consensus       308 ~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~  342 (427)
                      -.--..-..+++.++..   ..+..+|+|+.+.-+
T Consensus        99 ~~~~~~d~~i~~~l~~~---~kp~ilviNKiDlv~  130 (296)
T PRK00089         99 EKIGPGDEFILEKLKKV---KTPVILVLNKIDLVD  130 (296)
T ss_pred             CCCCHHHHHHHHHHHHC---CCCEEEEEEHHHHCC
T ss_conf             89898899999988874---998899954788428


No 450
>cd04136 Rap_like Rap-like subfamily.  The Rap subfamily consists of the Rap1, Rap2, and RSR1.  Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules.  Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts.   Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines.  Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands.  In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. 
Probab=91.36  E-value=1  Score=23.54  Aligned_cols=109  Identities=17%  Similarity=0.241  Sum_probs=66.9

Q ss_pred             CCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHHHHHHHC-CCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             2888997388888--98999998620125435787-768899999999999981-9876753899956589875200599
Q gi|254780725|r  274 IFPLVILDVPHVW--NSWTQEVLTLSDKVVITTSL-DLAGLRNSKNLIDVLKKL-RPADKPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       274 ~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~p-~~~slr~a~~ll~~l~~~-~~~~~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      .+.+-|+|++...  .......+..||-+++|... +..|+.+.+.+.+.+.+. .....++.+|-|+++......++.+
T Consensus        48 ~~~l~iwDtaG~e~~~~~~~~y~~~a~~~ilvydvt~~~Sf~~l~~~~~~i~~~~~~~~~piilVGnK~Dl~~~r~v~~~  127 (163)
T cd04136          48 QCMLEILDTAGTEQFTAMRDLYIKNGQGFVLVYSITSQSSFNDLQDLREQILRVKDTENVPMVLVGNKCDLEDERVVSRE  127 (163)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHCCCCHH
T ss_conf             99998645765445556789883468769997048988999999999999998618888867876235472640789999


Q ss_pred             HHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHH
Q ss_conf             99998489537990687999999884796189888999--8999999999998
Q gi|254780725|r  350 DFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANLLVDFSRVL  400 (427)
Q Consensus       350 ~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s--~~a~~~~~La~~i  400 (427)
                                      +.+  .-|...|.+..|.+.+.  .+.+.|..|++.|
T Consensus       128 ----------------~~~--~~a~~~~~~~~E~SAk~~~nV~e~F~~l~~~i  162 (163)
T cd04136         128 ----------------EGQ--ALARQWGCPFYETSAKSKINVDEVFADLVRQI  162 (163)
T ss_pred             ----------------HHH--HHHHHCCCEEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             ----------------999--99998499899974487805899999999963


No 451
>pfam02399 Herpes_ori_bp Origin of replication binding protein. This Pfam family represents the herpesvirus origin of replication binding protein, probably involved in DNA replication.
Probab=91.30  E-value=0.62  Score=24.90  Aligned_cols=162  Identities=14%  Similarity=0.196  Sum_probs=74.5

Q ss_pred             HHCCCCCEEEEEE-----ECCHHHHHHHHHHHHHHHHHHCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHH
Q ss_conf             6401873059998-----38989999999886411002022373069989999998618998499998059876778899
Q gi|254780725|r   22 SMCSLPRISVHVF-----CVTDTLYSVVERSKIDPRMSQVNMRITRGSIAEAVSCFSDSSTPDLIIVQTKVDSREVLSAL   96 (427)
Q Consensus        22 ~~~~~~~~~~~~f-----~~~~~~~~~~~~~~~drr~~~~~~~v~~g~~~~A~~~~~~~~~P~~iivd~~~~~~~~~~~l   96 (427)
                      ++.++.|++...-     --=+|....|.+--.. -|.+-      .-+++-.-.+.. .+|.+|-.|...+ .++++.|
T Consensus       128 QiESLHRV~~~ll~~YDvLILDEVMSti~QlySp-TM~~L------~~VDall~~LLr-~CprIIAMDAT~N-aqlVd~L  198 (829)
T pfam02399       128 QIESLHRVDENLLNNYDVLILDEVMSTIGQLYSP-TMRRL------KEVDALLLRLLR-NCPRIIAMDATVN-AQLVDFL  198 (829)
T ss_pred             EEECCCCCCHHHCCCCCEEEEHHHHHHHHHHHCH-HHHHH------HHHHHHHHHHHH-CCCCEEEECCHHH-HHHHHHH
T ss_conf             8511113883342566779857788888876068-88999------999999999985-4982798402042-8999999


Q ss_pred             HHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCC---------------------
Q ss_conf             98885328998089981687189999999765626431899989999976310233222---------------------
Q gi|254780725|r   97 EPLAEVCDSGTKVIVIGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQEE---------------------  155 (427)
Q Consensus        97 ~~la~~~~p~~~Vivig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~---------------------  155 (427)
                      ..|+.  +..+.|||- .......      +.=+=|+..-+..+.+..++...-.....                     
T Consensus       199 a~lRG--~~nvhvIv~-~yas~GF------S~R~c~~l~~LG~d~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (829)
T pfam02399       199 AGLRG--EENVHVIVN-TYASPGF------SNRRCTFLRTLGTDVLASVLRDEDEGAESSATPPHSPSGEPSAAISLRGA  269 (829)
T ss_pred             HHHCC--CCCEEEEEE-CCCCCCC------CCCEEEEHHHHCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             97268--880689981-4526665------66638756433648899872872212234678888876654333566556


Q ss_pred             -------CCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCH
Q ss_conf             -------3456753799974698877568999999999962699499997879898603
Q gi|254780725|r  156 -------GKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTAN  207 (427)
Q Consensus       156 -------~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~  207 (427)
                             ..-..|+-|+++++      |..-.++...+......+|+++.-.-+-+++.
T Consensus       270 tFF~eL~~rL~~G~NiCiFsS------TvsFSe~vArFc~~ft~sVLvLnS~rp~~DV~  322 (829)
T pfam02399       270 TFFGELEARLEAGKNVCLFSS------TVSFSEIVARFCARFTDSVLLLNSTRPKCDVN  322 (829)
T ss_pred             CHHHHHHHHHHCCCEEEEEEC------HHHHHHHHHHHHHHCCCEEEEECCCCCCCCCC
T ss_conf             579999999847980799944------47699999999984589089970899985502


No 452
>COG4167 SapF ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
Probab=91.22  E-value=0.23  Score=27.54  Aligned_cols=49  Identities=31%  Similarity=0.397  Sum_probs=39.9

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHH
Q ss_conf             567537999746988775689999999999626994999978798986033
Q gi|254780725|r  158 GSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANI  208 (427)
Q Consensus       158 ~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~  208 (427)
                      -+.|..++|+| +-|.||||+|--+|-.+.- .+.+.+.=|--+++|+...
T Consensus        36 L~~~QTlaiIG-~NGSGKSTLakMlaGmi~P-TsG~il~n~~~L~~~Dy~~   84 (267)
T COG4167          36 LREGQTLAIIG-ENGSGKSTLAKMLAGMIEP-TSGEILINDHPLHFGDYSF   84 (267)
T ss_pred             ECCCCEEEEEC-CCCCCHHHHHHHHHCCCCC-CCCEEEECCCCCCCCCHHH
T ss_conf             60796799982-6997475899998355589-8854878884131234676


No 453
>TIGR00972 3a0107s01c2 phosphate ABC transporter, ATP-binding protein; InterPro: IPR005670   This is a family of phosphate transport system permease proteins.; GO: 0005315 inorganic phosphate transmembrane transporter activity, 0015114 phosphate transmembrane transporter activity, 0006817 phosphate transport, 0016020 membrane.
Probab=91.18  E-value=1.1  Score=23.43  Aligned_cols=50  Identities=18%  Similarity=0.194  Sum_probs=33.3

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHH----CCCCEEEEECCCCCCCCHHH
Q ss_conf             6753799974698877568999999999962----69949999787989860334
Q gi|254780725|r  159 SSGCSISFIGSRGGVGSSTIAHNCAFSIASV----FAMETLLADLDLPYGTANIN  209 (427)
Q Consensus       159 ~~grvIav~g~KGGvGkTTiA~nLA~~LA~~----~~~~VlLvDlDl~~g~~~~~  209 (427)
                      +..+|.|++| ..||||||+-=.|=..--..    ...+|++-+-|......+..
T Consensus        25 ~~n~vTAlIG-PSGCGKSTlLR~lNRMnDl~~~~r~~G~v~f~G~dIy~~~~D~~   78 (248)
T TIGR00972        25 PKNQVTALIG-PSGCGKSTLLRSLNRMNDLVPGVRIEGKVLFDGQDIYDKKIDVV   78 (248)
T ss_pred             CCCEEEEEEC-CCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCCHH
T ss_conf             3770589877-88986789999988776407881688889864511456566878


No 454
>PRK12771 putative glutamate synthase (NADPH) small subunit; Provisional
Probab=91.17  E-value=1.1  Score=23.42  Aligned_cols=70  Identities=10%  Similarity=0.211  Sum_probs=45.3

Q ss_pred             CCCCHHHHHHHHHHCCCC----CCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHC
Q ss_conf             899989999976310233----2223456753799974698877568999999999962699499997879898603343
Q gi|254780725|r  135 EPLSVADIINSISAIFTP----QEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINF  210 (427)
Q Consensus       135 ~P~~~~~l~~ai~~~~~~----~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l  210 (427)
                      .|+....+.+.+......    ..+..++.||.|||+|+    |-.-+++  |+.|++ .|.+|-+.+-....|..- .+
T Consensus       107 ~pV~I~~lkR~~~d~~~~~~~~~~~~~~~tgkkVAVIGa----GPAGLsa--A~~La~-~G~~VtVfE~~~~~GGml-~~  178 (560)
T PRK12771        107 EAVGINAVERFLGDYAIENGWQFPPPAPDTGKRVAVIGG----GPAGLSA--AYQLRR-LGHAVTIFEAGPKLGGMM-RY  178 (560)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECC----CHHHHHH--HHHHHH-CCCEEEEECCCCCCCCEE-EC
T ss_conf             982027899999999997599789887778998999897----7899999--999997-698589967678889888-35


Q ss_pred             CC
Q ss_conf             89
Q gi|254780725|r  211 DK  212 (427)
Q Consensus       211 ~~  212 (427)
                      |+
T Consensus       179 GI  180 (560)
T PRK12771        179 GI  180 (560)
T ss_pred             CC
T ss_conf             68


No 455
>cd01863 Rab18 Rab18 subfamily.  Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex.  In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of mos
Probab=91.11  E-value=1.1  Score=23.39  Aligned_cols=108  Identities=12%  Similarity=0.169  Sum_probs=68.5

Q ss_pred             CCCEEEECCCCCC--CHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHCCCCC-CCCEEEEECCCCCCCCHHHHH
Q ss_conf             2888997388888--9899999862012543578-77688999999999999819876-753899956589875200599
Q gi|254780725|r  274 IFPLVILDVPHVW--NSWTQEVLTLSDKVVITTS-LDLAGLRNSKNLIDVLKKLRPAD-KPPYLVLNQVKTPKKPEISIS  349 (427)
Q Consensus       274 ~yd~VIiD~p~~~--~~~~~~~L~~AD~vviV~~-p~~~slr~a~~ll~~l~~~~~~~-~~~~iVlNr~~~~~~~~i~~~  349 (427)
                      .+.+-++|++...  .......+..+|.+++|.+ -+..|+.+.+.+++.++...... .++.+|-|+.+...+ .    
T Consensus        48 ~~~l~iwDt~g~~~~~~~~~~~~~~a~~~ilvfd~~~~~Sf~~i~~~~~~i~~~~~~~~~~~ilVgnK~D~~~~-~----  122 (161)
T cd01863          48 KVKLAIWDTAGQERFRTLTSSYYRGAQGVILVYDVTRRDTFTNLETWLNELETYSTNNDIVKMLVGNKIDKENR-E----  122 (161)
T ss_pred             EEEEEEEECCCCCCCCCCHHHHHHHCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCC-C----
T ss_conf             99999999999842353422441321534899767826569999999999998568888737887310440006-8----


Q ss_pred             HHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHH
Q ss_conf             99998489537990687999999884796189888999--8999999999998
Q gi|254780725|r  350 DFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKS--AIANL