Query         gi|254780806|ref|YP_003065219.1| chromosome partitioning protein A [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 265
No_of_seqs    125 out of 8007
Neff          8.9 
Searched_HMMs 39220
Date          Sun May 29 20:09:21 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780806.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR03453 partition_RepA plasm 100.0       0       0  358.2  14.8  254    2-256   100-379 (387)
  2 TIGR03371 cellulose_yhjQ cellu 100.0       0       0  353.7  16.5  243    7-258     2-245 (246)
  3 PRK13869 plasmid-partitioning  100.0       0       0  352.8  14.0  253    3-256   118-396 (405)
  4 TIGR01969 minD_arch cell divis 100.0       0       0  349.7  14.2  231    7-256     1-233 (258)
  5 PRK10818 cell division inhibit 100.0       0       0  332.3  15.3  245    6-260     2-252 (270)
  6 CHL00175 minD septum-site dete 100.0       0       0  328.7  15.6  242    4-260    11-256 (279)
  7 TIGR01968 minD_bact septum sit 100.0       0       0  336.6   8.1  243    6-260     1-252 (272)
  8 PRK13705 plasmid-partitioning  100.0       0       0  328.5  15.1  254    2-257   102-379 (388)
  9 PHA02519 plasmid partition pro 100.0       0       0  328.5  14.8  254    3-257   103-379 (387)
 10 pfam06564 YhjQ YhjQ protein. T 100.0       0       0  329.8  12.7  238    7-260     2-241 (244)
 11 COG1192 Soj ATPases involved i 100.0       0       0  312.9  16.6  254    5-261     1-257 (259)
 12 PHA02518 ParA-like protein; Pr 100.0       0       0  302.3  16.4  210    7-259     1-210 (211)
 13 pfam00142 Fer4_NifH 4Fe-4S iro 100.0       0       0  297.8  14.6  241    7-260     1-250 (269)
 14 cd02040 NifH NifH gene encodes 100.0       0       0  294.6  16.0  239    7-259     2-250 (270)
 15 PRK13230 nitrogenase reductase 100.0 1.4E-45       0  286.8  16.0  242    7-258     2-261 (292)
 16 PRK11670 putative ATPase; Prov 100.0 2.9E-44       0  277.9  19.0  242    5-263   106-358 (369)
 17 COG2894 MinD Septum formation  100.0   7E-45       0  281.7   9.1  242    6-259     2-250 (272)
 18 cd02036 MinD Bacterial cell di 100.0 1.3E-43       0  274.2  13.2  178    8-247     1-179 (179)
 19 PRK13232 nifH nitrogenase redu 100.0 1.2E-42       0  268.4  14.8  237    7-259     2-249 (273)
 20 PRK13235 nifH nitrogenase redu 100.0 4.1E-42       0  265.3  15.7  238    7-258     2-250 (274)
 21 PRK10037 cell division protein 100.0 1.3E-42       0  268.2  11.7  236    7-258     2-239 (250)
 22 PRK13233 nifH nitrogenase redu 100.0 2.5E-41       0  260.7  15.5  239    6-259     2-252 (275)
 23 COG0455 flhG Antiactivator of  100.0 4.8E-41 1.4E-45  259.1  14.6  236    5-257     1-241 (262)
 24 pfam01656 CbiA CobQ/CobB/MinD/ 100.0 7.6E-40   2E-44  252.1  10.3  204    9-226     1-212 (212)
 25 cd02032 Bchl_like This family  100.0 1.3E-37 3.2E-42  239.2  14.6  234    8-258     2-247 (267)
 26 PRK13231 nitrogenase reductase 100.0 7.9E-37   2E-41  234.5  15.6  233    6-258     2-242 (264)
 27 cd02117 NifH_like This family  100.0 9.5E-38 2.4E-42  239.9  10.7  201    7-221     1-212 (212)
 28 PRK13185 chlL protochlorophyll 100.0 2.8E-36 7.1E-41  231.3  15.4  237    6-258     2-248 (269)
 29 pfam09140 MipZ ATPase MipZ. Mi 100.0 1.6E-36 4.1E-41  232.7  13.2  210    7-240     1-234 (261)
 30 KOG3022 consensus              100.0 1.5E-35 3.9E-40  227.0  15.5  240    4-260    45-297 (300)
 31 CHL00072 chlL photochlorophyll 100.0 1.8E-34 4.5E-39  220.8  13.3  235    8-258     2-247 (271)
 32 PRK13236 nitrogenase reductase 100.0 5.9E-33 1.5E-37  211.9  16.3  243    1-258     1-254 (295)
 33 pfam07015 VirC1 VirC1 protein. 100.0 3.7E-33 9.4E-38  213.1  15.3  212    7-256     2-220 (231)
 34 PRK13234 nifH nitrogenase redu 100.0 3.7E-32 9.3E-37  207.3  15.4  239    5-258     3-252 (293)
 35 TIGR01287 nifH nitrogenase iro 100.0 1.4E-32 3.4E-37  209.8  12.8  238    7-258     1-251 (278)
 36 TIGR01281 DPOR_bchL light-inde 100.0 7.1E-32 1.8E-36  205.6  16.2  236    7-257     1-252 (275)
 37 PRK13849 putative crown gall t 100.0 7.3E-32 1.8E-36  205.5  15.3  195    7-240     2-201 (231)
 38 cd03110 Fer4_NifH_child This p 100.0   3E-32 7.8E-37  207.7   8.9  177    9-219     2-179 (179)
 39 COG4963 CpaE Flp pilus assembl 100.0 1.5E-30 3.9E-35  197.8  11.8  236    4-257   102-344 (366)
 40 COG3640 CooC CO dehydrogenase  100.0 1.1E-28 2.7E-33  187.0  14.5  229    8-257     2-253 (255)
 41 TIGR01007 eps_fam capsular exo 100.0   7E-30 1.8E-34  194.0   8.4  180    1-195    14-197 (207)
 42 COG0489 Mrp ATPases involved i 100.0 1.1E-28 2.7E-33  187.0  13.1  205    4-225    55-262 (265)
 43 PRK11519 tyrosine kinase; Prov 100.0 6.2E-29 1.6E-33  188.4  11.0  179    1-195   521-702 (720)
 44 COG1348 NifH Nitrogenase subun 100.0 1.1E-28 2.7E-33  187.0  11.7  239    7-259     2-251 (278)
 45 cd02037 MRP-like MRP (Multiple 100.0   8E-29   2E-33  187.8   9.9  158    8-222     1-169 (169)
 46 PRK09841 cryptic autophosphory 100.0 1.7E-28 4.4E-33  185.8  10.8  179    1-195   526-707 (726)
 47 cd02042 ParA ParA and ParB of  100.0 2.8E-28 7.3E-33  184.5   8.2  104    8-189     1-104 (104)
 48 cd02038 FleN-like FleN is a me  99.9 1.9E-27 4.9E-32  179.7  10.2  120    8-205     1-120 (139)
 49 COG1149 MinD superfamily P-loo  99.9 1.5E-26 3.7E-31  174.6  14.1  234    7-255     2-281 (284)
 50 cd00550 ArsA_ATPase Oxyanion-t  99.9   1E-27 2.6E-32  181.3   7.3  195    7-210     1-229 (254)
 51 cd02033 BchX Chlorophyllide re  99.9 5.6E-26 1.4E-30  171.2  14.3  237    2-257    27-275 (329)
 52 TIGR03029 EpsG chain length de  99.9 1.2E-26 3.2E-31  175.0  10.8  173    3-190   100-274 (274)
 53 cd02035 ArsA ArsA ATPase funct  99.9 7.4E-27 1.9E-31  176.3   7.5  172    9-194     1-183 (217)
 54 TIGR03018 pepcterm_TyrKin exop  99.9 7.2E-25 1.8E-29  164.7  10.9  171    2-189    31-207 (207)
 55 cd03111 CpaE_like This protein  99.9 5.6E-24 1.4E-28  159.5   7.8  105    8-190     1-106 (106)
 56 pfam02374 ArsA_ATPase Anion-tr  99.8 6.9E-21 1.7E-25  141.4   7.4  180    7-194     2-248 (304)
 57 TIGR02016 BchX chlorophyllide   99.8 2.9E-18 7.4E-23  126.1   8.7  203    7-226     1-223 (355)
 58 cd02034 CooC The accessory pro  99.7 1.2E-17 3.1E-22  122.5   7.5  115    9-153     2-116 (116)
 59 TIGR00345 arsA arsenite-activa  99.7   5E-18 1.3E-22  124.7   5.1   46   11-56      1-48  (330)
 60 cd01983 Fer4_NifH The Fer4_Nif  99.7 9.7E-17 2.5E-21  117.2   7.2   78    8-168     1-81  (99)
 61 COG0003 ArsA Predicted ATPase   99.7 7.5E-17 1.9E-21  117.9   4.6  126    6-136     2-138 (322)
 62 TIGR01005 eps_transp_fam exopo  99.5 1.2E-14   3E-19  105.0   5.9  183    5-201   559-747 (778)
 63 KOG2825 consensus               99.3 3.7E-12 9.5E-17   90.5   6.4   53    6-58     18-70  (323)
 64 PRK00090 bioD dithiobiotin syn  98.9 4.5E-09 1.1E-13   72.5   8.4  193    8-225     1-205 (223)
 65 pfam00448 SRP54 SRP54-type pro  98.8 1.9E-08 4.9E-13   68.8   8.5  161    6-213     1-170 (196)
 66 TIGR00959 ffh signal recogniti  98.8 4.7E-09 1.2E-13   72.3   5.3  176    4-225   100-287 (439)
 67 PRK12374 putative dithiobiotin  98.8 7.6E-08 1.9E-12   65.3   9.7  196    7-225     3-207 (231)
 68 cd03115 SRP The signal recogni  98.8 6.3E-08 1.6E-12   65.8   9.0  159    8-213     2-169 (173)
 69 COG1703 ArgK Putative periplas  98.8 1.8E-07 4.5E-12   63.1  11.1  150    5-194    50-202 (323)
 70 PRK12726 flagellar biosynthesi  98.7 4.7E-08 1.2E-12   66.5   7.9   42    4-46    204-245 (407)
 71 PRK13896 cobyrinic acid a,c-di  98.7 2.7E-08 6.8E-13   68.0   6.6  173    7-225     2-179 (432)
 72 PRK10416 cell division protein  98.7 9.2E-08 2.3E-12   64.8   9.1  165    3-213   292-470 (499)
 73 PRK00784 cobyric acid synthase  98.7 6.1E-08 1.6E-12   65.8   7.7  208    5-222     2-229 (492)
 74 pfam03308 ArgK ArgK protein. T  98.7 3.3E-07 8.4E-12   61.6  11.4  164    4-209    27-193 (267)
 75 PRK01077 cobyrinic acid a,c-di  98.7 6.7E-08 1.7E-12   65.6   7.7  171    6-224     3-184 (451)
 76 PRK05703 flhF flagellar biosyn  98.7 6.3E-08 1.6E-12   65.7   7.4  168    3-224   207-390 (412)
 77 COG0541 Ffh Signal recognition  98.7 3.9E-08 9.9E-13   67.0   6.2  164    4-213    98-269 (451)
 78 TIGR00313 cobQ cobyric acid sy  98.7 2.4E-08 6.1E-13   68.2   4.9  198   11-224     3-227 (502)
 79 PRK06731 flhF flagellar biosyn  98.7 1.4E-07 3.6E-12   63.7   8.3   43    3-46     72-114 (270)
 80 PRK11889 flhF flagellar biosyn  98.7 8.6E-08 2.2E-12   65.0   6.9  173    3-227   238-425 (436)
 81 PRK09435 arginine/ornithine tr  98.6 8.9E-07 2.3E-11   59.0  11.2  166    3-208    46-215 (325)
 82 PRK12724 flagellar biosynthesi  98.6 1.6E-07 4.1E-12   63.4   7.3  169    3-225   220-405 (432)
 83 pfam03029 ATP_bind_1 Conserved  98.6 1.4E-07 3.6E-12   63.8   6.9  103   14-140     3-106 (234)
 84 PRK00771 signal recognition pa  98.6 2.1E-07 5.5E-12   62.7   6.9  161    5-213    96-264 (433)
 85 PRK10867 signal recognition pa  98.6 2.3E-07   6E-12   62.4   6.9  163    4-213    98-270 (453)
 86 TIGR00750 lao LAO/AO transport  98.5 5.6E-07 1.4E-11   60.2   8.5  212    4-256    36-265 (333)
 87 PRK06995 flhF flagellar biosyn  98.5 2.8E-07   7E-12   62.0   6.8  170    4-226   174-358 (404)
 88 PRK13768 GTPase; Provisional    98.5 1.2E-06 3.1E-11   58.2   8.9  161    9-194     5-175 (253)
 89 COG1797 CobB Cobyrinic acid a,  98.5 4.2E-07 1.1E-11   60.9   6.4  171    8-225     2-183 (451)
 90 PRK13886 conjugal transfer pro  98.5 2.6E-07 6.7E-12   62.1   5.1   41    6-46      2-42  (241)
 91 PRK12723 flagellar biosynthesi  98.5 1.1E-06 2.9E-11   58.4   8.3   43    3-46    171-217 (388)
 92 cd04169 RF3 RF3 subfamily.  Pe  98.4   8E-07   2E-11   59.3   7.0   92  121-220    68-162 (267)
 93 COG1419 FlhF Flagellar GTP-bin  98.4 1.5E-06 3.9E-11   57.7   8.1  172    4-226   201-385 (407)
 94 pfam10609 ParA ParA/MinD ATPas  98.4 1.9E-07 4.9E-12   62.9   2.4   62  124-191     1-64  (81)
 95 cd01886 EF-G Elongation factor  98.3   1E-06 2.6E-11   58.7   5.8   91  121-219    61-154 (270)
 96 PRK12727 flagellar biosynthesi  98.3   9E-07 2.3E-11   59.0   5.1  168    4-226   346-529 (557)
 97 KOG0781 consensus               98.3 9.6E-07 2.5E-11   58.8   5.2  156    3-193   375-542 (587)
 98 KOG0780 consensus               98.3 3.2E-06 8.2E-11   55.8   7.5   43    3-46     98-140 (483)
 99 COG0552 FtsY Signal recognitio  98.3 1.9E-06 4.9E-11   57.1   6.1  165    3-213   136-314 (340)
100 cd04170 EF-G_bact Elongation f  98.3 1.5E-06 3.9E-11   57.7   5.3   92  122-220    62-155 (268)
101 cd03109 DTBS Dethiobiotin synt  98.2   8E-06   2E-10   53.5   8.6   63  150-219    72-134 (134)
102 COG0132 BioD Dethiobiotin synt  98.2 1.7E-05 4.3E-10   51.6  10.1  194    6-224     2-207 (223)
103 PRK00741 prfC peptide chain re  98.2 3.9E-06   1E-10   55.3   6.7   90  122-219    77-169 (526)
104 cd04168 TetM_like Tet(M)-like   98.2 2.6E-06 6.7E-11   56.3   5.3   87  122-215    62-150 (237)
105 TIGR03499 FlhF flagellar biosy  98.2 1.9E-06 4.9E-11   57.1   3.8   41    5-46    193-235 (282)
106 TIGR00064 ftsY signal recognit  98.2 4.6E-06 1.2E-10   54.9   5.7  166    2-213    78-259 (284)
107 cd03114 ArgK-like The function  98.1 1.4E-05 3.6E-10   52.1   8.0  123    8-158     1-125 (148)
108 KOG1532 consensus               98.1 5.6E-06 1.4E-10   54.4   5.9  115    5-142    18-134 (366)
109 PRK05632 phosphate acetyltrans  98.1 4.6E-05 1.2E-09   49.1  10.1  164    6-194     1-175 (702)
110 TIGR01425 SRP54_euk signal rec  98.0 1.8E-05 4.6E-10   51.4   6.0  146    3-195   118-274 (453)
111 TIGR00379 cobB cobyrinic acid   97.9 3.3E-05 8.5E-10   49.9   6.7  174    9-225     2-187 (464)
112 COG1341 Predicted GTPase or GT  97.9 9.7E-05 2.5E-09   47.2   8.3   40    8-48     75-115 (398)
113 KOG1533 consensus               97.8 1.3E-05 3.2E-10   52.3   2.8  105   14-140     9-113 (290)
114 TIGR00455 apsK adenylylsulfate  97.7 3.3E-05 8.4E-10   49.9   4.0   57    8-65     21-78  (187)
115 PRK00007 elongation factor G;   97.6 0.00029 7.5E-09   44.3   7.5   89  123-219    75-166 (693)
116 PRK07667 uridine kinase; Provi  97.4 0.00036 9.1E-09   43.9   5.2   44    1-45      7-52  (190)
117 pfam07755 DUF1611 Protein of u  97.4  0.0019 4.8E-08   39.7   8.8  170    5-220   112-296 (302)
118 COG0529 CysC Adenylylsulfate k  97.2 0.00039 9.9E-09   43.7   4.2   60    3-63     20-80  (197)
119 cd03116 MobB Molybdenum is an   97.1 0.00095 2.4E-08   41.4   5.3   41    6-47      1-41  (159)
120 pfam00009 GTP_EFTU Elongation   97.1  0.0012 3.1E-08   40.8   5.8   79  122-207    65-146 (185)
121 KOG1534 consensus               97.1 0.00068 1.7E-08   42.2   4.5  107   10-139     6-113 (273)
122 COG1492 CobQ Cobyric acid synt  97.1  0.0014 3.6E-08   40.4   5.7  203    8-225     3-231 (486)
123 TIGR02237 recomb_radB DNA repa  97.1  0.0013 3.4E-08   40.5   5.6   43    6-50     11-53  (223)
124 PRK05541 adenylylsulfate kinas  97.1  0.0015 3.7E-08   40.3   5.8   43    3-46      4-46  (176)
125 pfam03205 MobB Molybdopterin g  97.0  0.0021 5.3E-08   39.4   6.3   41    8-49      2-44  (122)
126 TIGR00347 bioD dethiobiotin sy  97.0  0.0025 6.3E-08   39.0   6.5   28   16-43      7-34  (187)
127 PRK12740 elongation factor G;   96.9 0.00084 2.2E-08   41.7   3.0   91  122-219    58-150 (670)
128 PRK03846 adenylylsulfate kinas  96.8  0.0022 5.6E-08   39.3   5.0   54    3-57     21-75  (198)
129 PRK00652 lpxK tetraacyldisacch  96.8  0.0022 5.5E-08   39.3   4.9   40    5-44     48-88  (334)
130 pfam01583 APS_kinase Adenylyls  96.8  0.0025 6.4E-08   38.9   5.1   52    5-57      1-53  (157)
131 PRK06696 uridine kinase; Valid  96.8  0.0031 7.8E-08   38.4   5.5   37    8-45     28-64  (227)
132 PRK13351 elongation factor G;   96.8   0.001 2.7E-08   41.1   3.1   90  123-219    72-163 (687)
133 PRK08533 flagellar accessory p  96.8  0.0035 8.9E-08   38.1   5.7  100    9-131    26-125 (230)
134 COG0480 FusA Translation elong  96.8   0.002   5E-08   39.5   4.3   84  123-213    75-160 (697)
135 TIGR00176 mobB molybdopterin-g  96.8  0.0018 4.5E-08   39.8   4.1   39    8-47      1-39  (165)
136 PRK00313 lpxK tetraacyldisacch  96.7  0.0024 6.2E-08   39.0   4.6   39    6-44     51-90  (332)
137 PRK10751 molybdopterin-guanine  96.7  0.0034 8.6E-08   38.2   5.2   40    7-47      3-42  (170)
138 PRK00889 adenylylsulfate kinas  96.7  0.0046 1.2E-07   37.4   5.7   54    4-58      2-56  (175)
139 pfam02606 LpxK Tetraacyldisacc  96.6  0.0031 7.8E-08   38.4   4.6   39    5-43     34-73  (318)
140 cd01125 repA Hexameric Replica  96.6   0.036 9.2E-07   32.1   9.9   26    8-33      2-27  (239)
141 PRK05506 bifunctional sulfate   96.6  0.0024 6.1E-08   39.0   3.9   79  122-208    85-166 (613)
142 TIGR02640 gas_vesic_GvpN gas v  96.5  0.0052 1.3E-07   37.0   5.2   31   14-47     28-58  (265)
143 PRK07560 elongation factor EF-  96.5  0.0033 8.4E-08   38.2   4.1   63  124-194    87-152 (730)
144 PRK09361 radB DNA repair and r  96.5  0.0068 1.7E-07   36.4   5.5   38    7-44     23-60  (224)
145 PRK01906 tetraacyldisaccharide  96.5  0.0045 1.2E-07   37.4   4.5   39    5-43     55-94  (339)
146 PRK05480 uridine kinase; Provi  96.5  0.0074 1.9E-07   36.2   5.6   41    1-44      1-41  (209)
147 PRK05537 bifunctional sulfate   96.4  0.0043 1.1E-07   37.5   3.8   58    3-61    389-448 (568)
148 cd02027 APSK Adenosine 5'-phos  96.4  0.0057 1.5E-07   36.8   4.4   36   11-46      3-38  (149)
149 cd00984 DnaB_C DnaB helicase C  96.3    0.01 2.6E-07   35.3   5.6   37    8-44     14-51  (242)
150 cd02028 UMPK_like Uridine mono  96.3  0.0083 2.1E-07   35.9   5.1   37    8-45      1-37  (179)
151 PRK12739 elongation factor G;   96.3  0.0034 8.7E-08   38.1   3.1   90  123-219    74-165 (693)
152 cd01394 radB RadB. The archaea  96.3  0.0096 2.4E-07   35.5   5.3   37    8-44     20-56  (218)
153 COG3367 Uncharacterized conser  96.2   0.043 1.1E-06   31.7   8.4  178    3-225   145-331 (339)
154 PRK00089 era GTP-binding prote  96.2   0.035 8.9E-07   32.2   7.8   38    2-46      4-41  (296)
155 TIGR01618 phage_P_loop phage n  96.2  0.0033 8.5E-08   38.2   2.6  106    8-164    15-124 (229)
156 pfam03796 DnaB_C DnaB-like hel  96.2    0.01 2.6E-07   35.4   5.0   36    9-44     21-57  (186)
157 cd01890 LepA LepA subfamily.    96.1  0.0057 1.5E-07   36.8   3.5   84  123-213    66-151 (179)
158 KOG2749 consensus               96.1   0.017 4.4E-07   34.0   5.8   45    5-50    102-147 (415)
159 PRK12377 putative replication   96.1   0.012   3E-07   35.0   4.9   33   11-43    105-137 (248)
160 COG1763 MobB Molybdopterin-gua  96.1   0.011 2.9E-07   35.1   4.7   40    6-46      2-41  (161)
161 pfam02572 CobA_CobO_BtuR ATP:c  96.0   0.013 3.3E-07   34.8   4.8   38    4-43      2-39  (172)
162 COG2874 FlaH Predicted ATPases  95.9   0.035 8.9E-07   32.2   6.8  107    9-139    30-136 (235)
163 TIGR01166 cbiO cobalt ABC tran  95.9   0.046 1.2E-06   31.5   7.4  158    1-177    13-177 (190)
164 cd01891 TypA_BipA TypA (tyrosi  95.9  0.0067 1.7E-07   36.4   3.0   80  123-209    64-145 (194)
165 cd01122 GP4d_helicase GP4d_hel  95.9   0.022 5.5E-07   33.5   5.6   39    5-44     29-68  (271)
166 PRK06526 transposase; Provisio  95.9   0.017 4.5E-07   34.0   5.1   32   13-44    104-135 (254)
167 COG1663 LpxK Tetraacyldisaccha  95.9  0.0093 2.4E-07   35.6   3.7   42    6-47     47-89  (336)
168 PRK06749 replicative DNA helic  95.9   0.027 6.8E-07   32.9   5.9   40    5-45    185-224 (428)
169 cd02023 UMPK Uridine monophosp  95.8   0.018 4.6E-07   33.9   4.9   35    8-45      1-35  (198)
170 COG1484 DnaC DNA replication p  95.8   0.018 4.7E-07   33.9   4.9   37    6-43    105-141 (254)
171 PRK09302 circadian clock prote  95.8    0.02 5.1E-07   33.6   5.1   38    6-44     24-62  (501)
172 cd01124 KaiC KaiC is a circadi  95.8   0.019 4.9E-07   33.7   4.9   35   10-44      2-36  (187)
173 TIGR01394 TypA_BipA GTP-bindin  95.7  0.0061 1.6E-07   36.6   2.2  126  124-258    70-201 (609)
174 cd00561 CobA_CobO_BtuR ATP:cor  95.7   0.021 5.2E-07   33.6   4.7   37    5-43      2-38  (159)
175 TIGR03600 phage_DnaB phage rep  95.7   0.028   7E-07   32.8   5.3   40    5-45    193-233 (421)
176 TIGR01054 rgy reverse gyrase;   95.6   0.013 3.4E-07   34.7   3.5   35    7-42    100-135 (1843)
177 PRK08181 transposase; Validate  95.6   0.025 6.4E-07   33.1   4.9   32   13-44    112-143 (269)
178 PRK06547 hypothetical protein;  95.6   0.022 5.6E-07   33.4   4.5   37    3-44     12-48  (184)
179 pfam00485 PRK Phosphoribulokin  95.6   0.012 2.9E-07   35.0   3.1   36    8-44      1-36  (196)
180 PRK09183 transposase/IS protei  95.5   0.026 6.6E-07   33.0   4.8   31   13-43    107-137 (258)
181 PRK05595 replicative DNA helic  95.5   0.038 9.6E-07   32.0   5.6   40    5-45    200-240 (444)
182 PRK07952 DNA replication prote  95.5   0.025 6.4E-07   33.1   4.7   33   11-43    100-132 (242)
183 COG1159 Era GTPase [General fu  95.5   0.092 2.3E-06   29.8   7.5   40    1-47      1-40  (298)
184 PRK05748 replicative DNA helic  95.5    0.04   1E-06   31.9   5.6   40    5-45    202-242 (448)
185 PRK08506 replicative DNA helic  95.5   0.042 1.1E-06   31.8   5.7   40    5-45    192-231 (473)
186 cd01120 RecA-like_NTPases RecA  95.5    0.03 7.7E-07   32.6   4.9   35   11-45      3-37  (165)
187 PRK07004 replicative DNA helic  95.4   0.036 9.1E-07   32.2   5.2   40    5-45    212-252 (460)
188 TIGR01393 lepA GTP-binding pro  95.4   0.014 3.6E-07   34.5   3.0   85  122-213    69-155 (598)
189 pfam00154 RecA recA bacterial   95.4   0.025 6.4E-07   33.1   4.3   53    5-58     51-105 (322)
190 pfam00931 NB-ARC NB-ARC domain  95.3    0.02 5.2E-07   33.6   3.7   26    3-29     16-41  (285)
191 PRK05433 GTP-binding protein L  95.2   0.019 4.9E-07   33.7   3.4   82  123-211    73-156 (601)
192 PRK13506 formate--tetrahydrofo  95.2   0.033 8.4E-07   32.4   4.5   40    3-42     51-93  (577)
193 pfam01695 IstB IstB-like ATP b  95.2   0.044 1.1E-06   31.7   5.2   36    7-43     48-83  (178)
194 PRK04328 hypothetical protein;  95.2   0.046 1.2E-06   31.6   5.2   36    9-44     26-61  (250)
195 COG3598 RepA RecA-family ATPas  95.2   0.038 9.7E-07   32.0   4.8   36    8-43     90-135 (402)
196 PRK07263 consensus              95.2   0.059 1.5E-06   30.9   5.7   40    5-45    202-242 (453)
197 TIGR03172 probable selenium-de  95.0   0.038 9.8E-07   32.0   4.4   31    8-41      1-31  (232)
198 PRK07414 cob(I)yrinic acid a,c  95.0   0.058 1.5E-06   30.9   5.3   37    5-43     21-57  (178)
199 PRK08082 consensus              95.0   0.065 1.7E-06   30.7   5.5   40    5-45    202-242 (453)
200 PRK05636 replicative DNA helic  95.0   0.069 1.8E-06   30.5   5.6   40    5-45    266-306 (507)
201 COG0467 RAD55 RecA-superfamily  95.0   0.064 1.6E-06   30.7   5.4   40    5-45     22-61  (260)
202 COG0523 Putative GTPases (G3E   95.0    0.26 6.7E-06   27.1   8.5   34    9-44      3-36  (323)
203 COG2403 Predicted GTPase [Gene  94.9    0.05 1.3E-06   31.3   4.7   37    7-43    127-163 (449)
204 cd00983 recA RecA is a  bacter  94.9   0.078   2E-06   30.2   5.7   53    5-58     54-108 (325)
205 TIGR01085 murE UDP-N-acetylmur  94.9   0.056 1.4E-06   31.0   5.0   39    2-43     84-122 (494)
206 PRK13505 formate--tetrahydrofo  94.9   0.044 1.1E-06   31.6   4.4   51    3-55     51-104 (556)
207 PRK04308 murD UDP-N-acetylmura  94.9   0.054 1.4E-06   31.1   4.8   38    2-42    106-143 (445)
208 cd00477 FTHFS Formyltetrahydro  94.8   0.045 1.2E-06   31.6   4.3   40    3-42     35-77  (524)
209 PRK08939 primosomal protein Dn  94.8   0.096 2.4E-06   29.7   5.9   37    6-43    157-193 (306)
210 pfam01268 FTHFS Formate--tetra  94.7    0.04   1E-06   31.9   3.9   40    3-42     51-93  (555)
211 PRK08694 consensus              94.7   0.077   2E-06   30.2   5.2   40    5-45    217-257 (468)
212 PRK08840 replicative DNA helic  94.7   0.087 2.2E-06   29.9   5.5   40    5-45    216-256 (464)
213 PRK09270 frcK putative fructos  94.7    0.11 2.9E-06   29.2   6.1   38    7-45     35-74  (230)
214 KOG0635 consensus               94.6   0.083 2.1E-06   30.0   5.2   55    5-60     30-85  (207)
215 PRK13507 formate--tetrahydrofo  94.6   0.054 1.4E-06   31.1   4.3   40    3-42     60-102 (587)
216 PRK09401 reverse gyrase; Revie  94.6   0.045 1.1E-06   31.6   3.8   36    6-42     93-128 (1176)
217 PRK10218 GTP-binding protein;   94.5   0.029 7.5E-07   32.7   2.7   81  122-209    66-148 (607)
218 PRK06067 flagellar accessory p  94.5   0.095 2.4E-06   29.7   5.3   36    9-44     34-69  (241)
219 COG0468 RecA RecA/RadA recombi  94.5   0.096 2.4E-06   29.7   5.3   38    6-44     60-97  (279)
220 PRK09165 replicative DNA helic  94.4    0.12 3.1E-06   29.0   5.8   40    5-45    204-258 (484)
221 smart00382 AAA ATPases associa  94.4   0.066 1.7E-06   30.6   4.3   39    7-46      3-41  (148)
222 TIGR02928 TIGR02928 orc1/cdc6   94.4    0.11 2.7E-06   29.4   5.4   36   11-46     47-87  (383)
223 PRK08116 hypothetical protein;  94.3   0.081 2.1E-06   30.1   4.7   33   11-43    112-144 (262)
224 PRK08760 replicative DNA helic  94.1    0.14 3.6E-06   28.7   5.6   40    5-45    228-268 (476)
225 COG4988 CydD ABC-type transpor  94.1   0.018 4.5E-07   34.0   0.9   31    4-35    345-376 (559)
226 PRK11174 cysteine/glutathione   94.1   0.036 9.1E-07   32.2   2.4   37    4-43    374-410 (588)
227 cd01393 recA_like RecA is a  b  94.1    0.12 3.1E-06   29.1   5.1   37    8-44     20-62  (226)
228 PRK04690 murD UDP-N-acetylmura  94.0    0.14 3.5E-06   28.8   5.3   35    5-42    114-148 (468)
229 KOG0462 consensus               94.0   0.064 1.6E-06   30.7   3.6   84  123-213   124-209 (650)
230 PRK08006 replicative DNA helic  94.0    0.17 4.4E-06   28.2   5.7   40    5-45    223-263 (471)
231 cd00881 GTP_translation_factor  93.9   0.033 8.4E-07   32.4   1.9   82  123-211    61-145 (189)
232 PRK04220 2-phosphoglycerate ki  93.9   0.081 2.1E-06   30.1   3.9   26    7-32     92-117 (306)
233 PRK08233 hypothetical protein;  93.9    0.14 3.6E-06   28.7   5.1   37    4-43      1-37  (182)
234 TIGR03574 selen_PSTK L-seryl-t  93.8    0.11 2.9E-06   29.2   4.6   36   10-45      2-37  (249)
235 PTZ00301 uridine kinase; Provi  93.8    0.21 5.5E-06   27.6   5.9   40    5-45      2-43  (210)
236 PRK09354 recA recombinase A; P  93.8    0.21 5.3E-06   27.7   5.8   51    5-58     59-113 (350)
237 pfam08433 KTI12 Chromatin asso  93.8    0.11 2.9E-06   29.3   4.4   36   10-45      2-37  (266)
238 pfam01935 DUF87 Domain of unkn  93.6    0.13 3.3E-06   28.9   4.5   40    6-48     23-63  (218)
239 PRK01390 murD UDP-N-acetylmura  93.6    0.18 4.7E-06   28.0   5.3   34    5-41    113-146 (457)
240 cd01889 SelB_euk SelB subfamil  93.6   0.069 1.8E-06   30.5   3.1   81  122-209    66-149 (192)
241 PRK05973 replicative DNA helic  93.5     0.2   5E-06   27.9   5.3   36   10-45     67-102 (237)
242 PRK11545 gntK gluconate kinase  93.4   0.088 2.2E-06   29.9   3.4   36    3-44      5-40  (177)
243 PRK06321 replicative DNA helic  93.4    0.22 5.7E-06   27.5   5.5   40    5-45    225-265 (472)
244 pfam06745 KaiC KaiC. This fami  93.3     0.2 5.2E-06   27.8   5.2   36    9-44     21-57  (231)
245 PRK00139 murE UDP-N-acetylmura  93.2    0.15 3.8E-06   28.6   4.3   38    3-43     97-134 (481)
246 cd01123 Rad51_DMC1_radA Rad51_  93.2    0.27 6.8E-06   27.1   5.6   39    7-45     19-63  (235)
247 COG1110 Reverse gyrase [DNA re  93.2    0.18 4.6E-06   28.1   4.8   37    5-42     96-132 (1187)
248 pfam00071 Ras Ras family. Incl  93.2    0.23 5.8E-06   27.5   5.3  109  124-255    48-161 (162)
249 PRK07261 topology modulation p  93.2    0.17 4.2E-06   28.3   4.5   32    7-43      2-33  (171)
250 PRK06904 replicative DNA helic  93.1    0.23 5.9E-06   27.4   5.2   40    5-45    220-260 (472)
251 cd01866 Rab2 Rab2 subfamily.    93.1     0.4   1E-05   26.1   6.4  111  124-257    53-168 (168)
252 pfam04851 ResIII Type III rest  93.1    0.23 5.9E-06   27.4   5.1   34    6-41     19-52  (103)
253 PRK02006 murD UDP-N-acetylmura  93.0    0.24 6.1E-06   27.4   5.1   34    5-41    121-154 (501)
254 cd01121 Sms Sms (bacterial rad  93.0    0.24   6E-06   27.4   5.1   35   10-44     85-119 (372)
255 PRK03333 coaE dephospho-CoA ki  92.9    0.28 7.2E-06   26.9   5.4   31    8-45      3-33  (394)
256 PRK06835 DNA replication prote  92.9     0.2 5.2E-06   27.8   4.7   30   14-43    190-219 (330)
257 PRK03803 murD UDP-N-acetylmura  92.9    0.21 5.3E-06   27.7   4.7   35    4-41    107-141 (448)
258 PRK08118 topology modulation p  92.9    0.18 4.5E-06   28.1   4.3   32    7-42      2-33  (167)
259 PRK03369 murD UDP-N-acetylmura  92.8    0.27 6.9E-06   27.0   5.2   35    5-42    116-150 (487)
260 KOG1805 consensus               92.8    0.12   3E-06   29.2   3.3   34   10-43    688-721 (1100)
261 pfam02223 Thymidylate_kin Thym  92.8    0.16   4E-06   28.4   3.9   30   16-46      5-34  (186)
262 cd00009 AAA The AAA+ (ATPases   92.7     0.2   5E-06   27.8   4.4   38    6-44     19-56  (151)
263 PRK01710 murD UDP-N-acetylmura  92.7    0.24 6.1E-06   27.4   4.8   35    4-41    115-149 (458)
264 COG0857 Pta BioD-like N-termin  92.7    0.28   7E-06   27.0   5.1   37    6-42      2-38  (354)
265 cd02025 PanK Pantothenate kina  92.7    0.27 6.8E-06   27.1   5.0   37    8-45      1-39  (220)
266 COG4240 Predicted kinase [Gene  92.7    0.23 5.8E-06   27.5   4.7   37    8-44     51-88  (300)
267 COG0572 Udk Uridine kinase [Nu  92.7    0.24 6.2E-06   27.3   4.8   38    5-45      7-44  (218)
268 PRK03806 murD UDP-N-acetylmura  92.6    0.26 6.5E-06   27.2   4.9   36    3-41    102-137 (438)
269 KOG4658 consensus               92.6    0.13 3.4E-06   28.9   3.3   25    7-32    180-204 (889)
270 PRK06278 cobyrinic acid a,c-di  92.5    0.77   2E-05   24.4   8.9  168    5-215   243-421 (482)
271 TIGR01313 therm_gnt_kin carboh  92.5   0.081 2.1E-06   30.1   2.2   39   14-52      5-46  (175)
272 COG1072 CoaA Panthothenate kin  92.5    0.41   1E-05   26.0   5.8   43    3-45     78-122 (283)
273 TIGR00437 feoB ferrous iron tr  92.5   0.063 1.6E-06   30.7   1.6   85  124-217    41-137 (733)
274 PRK00698 tmk thymidylate kinas  92.4    0.47 1.2E-05   25.7   6.0   37    5-42      2-38  (204)
275 PRK00683 murD UDP-N-acetylmura  92.3    0.19 4.9E-06   27.9   3.9   35    4-41    100-134 (418)
276 PRK13764 ATPase; Provisional    92.3    0.19 4.9E-06   27.9   3.8   39    4-43    257-295 (605)
277 PRK04663 murD UDP-N-acetylmura  92.2    0.29 7.4E-06   26.8   4.7   35    4-41    106-140 (438)
278 cd04144 Ras2 Ras2 subfamily.    92.2    0.54 1.4E-05   25.3   6.1  111  128-258    51-166 (190)
279 COG1618 Predicted nucleotide k  92.1    0.36 9.1E-06   26.4   5.1   39    4-43      3-41  (179)
280 cd01887 IF2_eIF5B IF2/eIF5B (i  92.0    0.11 2.9E-06   29.2   2.5   78  123-207    49-128 (168)
281 pfam05729 NACHT NACHT domain.   92.0     0.2   5E-06   27.8   3.7   26    7-33      1-26  (165)
282 cd04111 Rab39 Rab39 subfamily.  91.9    0.91 2.3E-05   24.0   7.9  112  128-261    56-172 (211)
283 cd01885 EF2 EF2 (for archaea a  91.9   0.068 1.7E-06   30.6   1.1   64  123-193    72-137 (222)
284 cd02029 PRK_like Phosphoribulo  91.8    0.35 8.9E-06   26.4   4.7   37    8-45      1-37  (277)
285 PRK12339 2-phosphoglycerate ki  91.7     0.2 5.2E-06   27.8   3.4   25    6-31      3-27  (197)
286 cd01672 TMPK Thymidine monopho  91.6    0.48 1.2E-05   25.6   5.2   34    9-43      3-36  (200)
287 PRK01438 murD UDP-N-acetylmura  91.6    0.43 1.1E-05   25.9   5.0   35    4-41    120-154 (481)
288 PRK01368 murD UDP-N-acetylmura  91.5    0.42 1.1E-05   25.9   4.9   35    4-41    102-136 (450)
289 COG4088 Predicted nucleotide k  91.5    0.23 5.7E-06   27.5   3.5   37    9-45      3-39  (261)
290 PRK06217 hypothetical protein;  91.5    0.27   7E-06   27.0   3.9   31    8-44      3-33  (185)
291 PRK13721 conjugal transfer ATP  91.5    0.44 1.1E-05   25.8   4.9   34   11-44    478-511 (864)
292 cd01883 EF1_alpha Eukaryotic e  91.5    0.12   3E-06   29.2   2.0   70  122-194    75-150 (219)
293 PRK02472 murD UDP-N-acetylmura  91.4    0.36 9.2E-06   26.3   4.5   35    4-41    110-144 (450)
294 TIGR00041 DTMP_kinase thymidyl  91.4    0.22 5.6E-06   27.6   3.4   28   14-41      9-37  (211)
295 cd04166 CysN_ATPS CysN_ATPS su  91.4    0.18 4.6E-06   28.1   2.9   66  122-193    75-142 (208)
296 PRK09554 feoB ferrous iron tra  91.3    0.11 2.9E-06   29.2   1.9   20    8-28      5-24  (772)
297 TIGR01082 murC UDP-N-acetylmur  91.3    0.29 7.5E-06   26.8   3.9   40    1-44    104-144 (491)
298 cd04167 Snu114p Snu114p subfam  91.3   0.095 2.4E-06   29.7   1.4   63  124-193    71-135 (213)
299 COG2759 MIS1 Formyltetrahydrof  91.2    0.18 4.5E-06   28.1   2.7   51    3-55     49-102 (554)
300 PRK07933 thymidylate kinase; V  91.0    0.32 8.2E-06   26.6   3.9   34    9-43      3-36  (213)
301 PRK05986 cob(I)yrinic acid a,c  91.0    0.24 6.2E-06   27.3   3.3   39    3-43     20-58  (190)
302 TIGR00763 lon ATP-dependent pr  91.0    0.27 6.8E-06   27.1   3.5   88    3-92    446-586 (941)
303 COG1120 FepC ABC-type cobalami  91.0    0.25 6.5E-06   27.2   3.4   38    4-43     26-63  (258)
304 PRK13973 thymidylate kinase; P  91.0    0.74 1.9E-05   24.5   5.7   39    5-45      2-40  (216)
305 cd04122 Rab14 Rab14 subfamily.  91.0     1.1 2.9E-05   23.4   6.7  109  125-256    52-165 (166)
306 PRK05876 short chain dehydroge  90.9    0.34 8.6E-06   26.5   3.9   41    1-46      1-41  (275)
307 COG0771 MurD UDP-N-acetylmuram  90.9    0.47 1.2E-05   25.7   4.7   33    5-40    109-141 (448)
308 PRK06194 hypothetical protein;  90.9    0.35 8.9E-06   26.4   4.0   41    1-46      1-41  (301)
309 TIGR02475 CobW cobalamin biosy  90.9     0.2   5E-06   27.9   2.7   31    9-42      6-37  (349)
310 PRK09825 idnK D-gluconate kina  90.8    0.26 6.6E-06   27.2   3.3   34    5-44      2-35  (176)
311 PRK02705 murD UDP-N-acetylmura  90.8    0.44 1.1E-05   25.8   4.4   35    4-41    107-141 (459)
312 cd01897 NOG NOG1 is a nucleola  90.8    0.16 4.2E-06   28.3   2.2   28    8-42      2-29  (168)
313 PRK00141 murD UDP-N-acetylmura  90.7    0.59 1.5E-05   25.1   5.0   34    5-41    122-155 (476)
314 TIGR02173 cyt_kin_arch cytidyl  90.7    0.21 5.3E-06   27.7   2.7   25    9-33      2-26  (173)
315 COG3973 Superfamily I DNA and   90.7    0.42 1.1E-05   25.9   4.3   36    7-42    226-267 (747)
316 cd04141 Rit_Rin_Ric Rit/Rin/Ri  90.7    0.94 2.4E-05   23.9   6.0  112  125-258    51-167 (172)
317 pfam02562 PhoH PhoH-like prote  90.4    0.58 1.5E-05   25.1   4.8   35    8-42     20-56  (205)
318 TIGR02770 nickel_nikD nickel i  90.4    0.29 7.4E-06   26.9   3.2   27    4-31     10-36  (239)
319 cd01867 Rab8_Rab10_Rab13_like   90.4     1.1 2.7E-05   23.6   6.1  110  125-257    53-167 (167)
320 PRK12297 obgE GTPase ObgE; Rev  90.3    0.31   8E-06   26.7   3.3   85  122-210   204-301 (429)
321 PRK12299 obgE GTPase ObgE; Rev  90.3    0.44 1.1E-05   25.8   4.1   86  123-210   205-301 (334)
322 pfam05970 DUF889 PIF1 helicase  90.3    0.46 1.2E-05   25.7   4.1   28   14-41      1-28  (418)
323 PRK12298 obgE GTPase ObgE; Rev  90.3    0.29 7.3E-06   26.9   3.1   87  123-211   206-306 (380)
324 pfam00437 GSPII_E Type II/IV s  90.2    0.35 8.9E-06   26.4   3.4   43  210-252   210-255 (283)
325 cd01888 eIF2_gamma eIF2-gamma   90.1    0.27 6.8E-06   27.1   2.8   81  124-209    83-166 (203)
326 COG0125 Tmk Thymidylate kinase  90.0    0.97 2.5E-05   23.8   5.7   38    5-43      2-39  (208)
327 cd04109 Rab28 Rab28 subfamily.  89.9    0.82 2.1E-05   24.2   5.2  113  126-258    52-169 (215)
328 PRK06398 aldose dehydrogenase;  89.9    0.52 1.3E-05   25.4   4.2   41    1-46      1-41  (256)
329 PRK13695 putative NTPase; Prov  89.8    0.68 1.7E-05   24.7   4.7   30    9-38      5-34  (174)
330 cd04121 Rab40 Rab40 subfamily.  89.8    0.93 2.4E-05   23.9   5.4  110  125-258    56-170 (189)
331 cd04112 Rab26 Rab26 subfamily.  89.8     1.4 3.5E-05   22.9   6.3  109  125-258    51-166 (191)
332 TIGR02012 tigrfam_recA protein  89.8       1 2.6E-05   23.6   5.6   39    5-44     54-92  (322)
333 COG0305 DnaB Replicative DNA h  89.7    0.92 2.3E-05   24.0   5.3   39    5-44    195-234 (435)
334 PRK12338 hypothetical protein;  89.7    0.38 9.7E-06   26.2   3.4   36    4-44      2-37  (320)
335 KOG2004 consensus               89.7    0.25 6.5E-06   27.2   2.5   30    3-33    435-464 (906)
336 cd04140 ARHI_like ARHI subfami  89.7    0.67 1.7E-05   24.7   4.6   68  125-193    50-120 (165)
337 cd01869 Rab1_Ypt1 Rab1/Ypt1 su  89.7     1.5 3.8E-05   22.7   6.9  110  124-256    51-165 (166)
338 COG3903 Predicted ATPase [Gene  89.6    0.41 1.1E-05   26.0   3.5   44    8-52     15-59  (414)
339 COG4108 PrfC Peptide chain rel  89.6    0.41   1E-05   26.0   3.4   91  127-225    84-179 (528)
340 cd01898 Obg Obg subfamily.  Th  89.5    0.39   1E-05   26.1   3.3   27    9-42      3-29  (170)
341 pfam03266 DUF265 Protein of un  89.4    0.55 1.4E-05   25.2   4.0   28   11-38      3-30  (168)
342 COG3451 VirB4 Type IV secretor  89.3    0.84 2.1E-05   24.2   4.9   46   10-55    439-486 (796)
343 TIGR00503 prfC peptide chain r  89.3    0.35 8.8E-06   26.4   2.9  103  128-238    84-192 (530)
344 PRK09519 recA recombinase A; R  89.2     1.2 3.1E-05   23.2   5.7   39    5-44     59-97  (790)
345 PRK06761 hypothetical protein;  89.2    0.94 2.4E-05   23.9   5.1   39    6-45      2-41  (281)
346 PRK13898 type IV secretion sys  89.2    0.96 2.4E-05   23.8   5.1   32   14-45    453-484 (800)
347 PRK05124 cysN sulfate adenylyl  89.1    0.34 8.8E-06   26.4   2.8   79  122-208   105-186 (475)
348 TIGR01087 murD UDP-N-acetylmur  89.1    0.92 2.3E-05   23.9   4.9   33    5-40    109-141 (476)
349 cd02022 DPCK Dephospho-coenzym  89.0    0.56 1.4E-05   25.2   3.8   31    8-45      1-31  (179)
350 TIGR00682 lpxK tetraacyldisacc  89.0    0.65 1.6E-05   24.8   4.1   40    5-44     31-71  (342)
351 TIGR01137 cysta_beta cystathio  89.0    0.77   2E-05   24.4   4.5  112   24-162   193-316 (527)
352 COG0481 LepA Membrane GTPase L  88.9    0.45 1.1E-05   25.8   3.2   22  114-135   354-375 (603)
353 COG1102 Cmk Cytidylate kinase   88.9    0.42 1.1E-05   25.9   3.1   28    8-39      2-29  (179)
354 pfam02492 cobW CobW/HypB/UreG,  88.9     0.8 2.1E-05   24.3   4.5   36    9-45      2-37  (174)
355 PRK07429 phosphoribulokinase;   88.9     1.1 2.9E-05   23.4   5.3   38    5-45      7-44  (331)
356 PRK04195 replication factor C   88.8     0.9 2.3E-05   24.0   4.7   32    9-43     42-73  (403)
357 smart00175 RAB Rab subfamily o  88.7     1.5   4E-05   22.6   5.9  110  125-257    50-164 (164)
358 PRK03839 putative kinase; Prov  88.7     0.8   2E-05   24.3   4.4   28    8-39      2-29  (180)
359 pfam07726 AAA_3 ATPase family   88.7       1 2.6E-05   23.7   5.0   32   12-46      4-35  (131)
360 KOG1969 consensus               88.6    0.84 2.1E-05   24.2   4.5   37    4-43    323-359 (877)
361 TIGR00631 uvrb excinuclease AB  88.5    0.45 1.1E-05   25.8   3.0   26   14-42     36-61  (667)
362 cd01862 Rab7 Rab7 subfamily.    88.5     1.7 4.4E-05   22.3   6.0  116  125-260    50-172 (172)
363 pfam06418 CTP_synth_N CTP synt  88.5     1.4 3.5E-05   23.0   5.5   45    6-50      1-46  (275)
364 PRK09112 DNA polymerase III su  88.5    0.54 1.4E-05   25.3   3.4   22   12-33     50-71  (352)
365 cd04139 RalA_RalB RalA/RalB su  88.5     1.6   4E-05   22.6   5.8  112  124-257    48-164 (164)
366 COG5623 CLP1 Predicted GTPase   88.4    0.97 2.5E-05   23.8   4.7   40    6-46     99-138 (424)
367 PRK11929 putative bifunctional  88.3     1.5 3.9E-05   22.7   5.6   39    2-43    107-145 (953)
368 TIGR00337 PyrG CTP synthase; I  88.2     1.4 3.5E-05   22.9   5.3   47    4-50      2-49  (571)
369 cd00755 YgdL_like Family of ac  88.2    0.57 1.5E-05   25.2   3.4   36    4-46     10-46  (231)
370 cd04163 Era Era subfamily.  Er  88.2    0.29 7.4E-06   26.9   1.9   28    7-41      4-31  (168)
371 TIGR02203 MsbA_lipidA lipid A   88.1    0.41 1.1E-05   26.0   2.6   44    4-50    386-430 (603)
372 COG1855 ATPase (PilT family) [  87.9     0.7 1.8E-05   24.6   3.7   36    5-41    262-297 (604)
373 PRK11331 5-methylcytosine-spec  87.9    0.85 2.2E-05   24.1   4.1   57    3-59    190-249 (459)
374 cd01884 EF_Tu EF-Tu subfamily.  87.9    0.47 1.2E-05   25.7   2.8   67  123-195    64-132 (195)
375 cd04114 Rab30 Rab30 subfamily.  87.9       2 5.1E-05   22.0   6.1  108  125-255    57-169 (169)
376 cd01895 EngA2 EngA2 subfamily.  87.9    0.34 8.8E-06   26.4   2.1   27    8-41      4-30  (174)
377 pfam08423 Rad51 Rad51. Rad51 i  87.8     1.4 3.6E-05   22.9   5.2   40    6-45     42-87  (261)
378 PRK05506 bifunctional sulfate   87.7    0.25 6.4E-06   27.2   1.3   56    4-60    441-497 (613)
379 PRK11823 DNA repair protein Ra  87.6     1.3 3.4E-05   23.0   5.0   35    9-44     92-126 (454)
380 TIGR02632 RhaD_aldol-ADH rhamn  87.6     1.1 2.8E-05   23.5   4.6   38    4-46    422-459 (709)
381 cd04154 Arl2 Arl2 subfamily.    87.6    0.68 1.7E-05   24.7   3.5   25    1-27     10-34  (173)
382 PRK07471 DNA polymerase III su  87.5     1.2   3E-05   23.3   4.6   27    7-34     40-66  (363)
383 cd04123 Rab21 Rab21 subfamily.  87.5     1.1 2.9E-05   23.4   4.5  109  124-255    49-162 (162)
384 cd02026 PRK Phosphoribulokinas  87.4    0.62 1.6E-05   24.9   3.2   35    8-45      1-35  (273)
385 cd01863 Rab18 Rab18 subfamily.  87.4     2.1 5.4E-05   21.8   6.1  107  124-253    49-160 (161)
386 PRK05380 pyrG CTP synthetase;   87.4     1.9 4.8E-05   22.1   5.7   45    6-50      2-47  (534)
387 PRK13873 conjugal transfer ATP  87.3     1.6   4E-05   22.6   5.2   32   14-45    448-480 (815)
388 cd03113 CTGs CTP synthetase (C  87.3     1.4 3.5E-05   22.9   4.9   39   12-50      7-45  (255)
389 PRK12337 2-phosphoglycerate ki  87.3    0.73 1.9E-05   24.5   3.5   25    7-31    262-286 (492)
390 cd01127 TrwB Bacterial conjuga  87.2     1.8 4.5E-05   22.3   5.4   47    5-54     41-87  (410)
391 TIGR00618 sbcc exonuclease Sbc  87.2    0.66 1.7E-05   24.8   3.2   29    8-38     31-59  (1063)
392 TIGR02528 EutP ethanolamine ut  87.1    0.37 9.4E-06   26.3   1.9   37    7-45      1-37  (144)
393 PRK10773 murF UDP-N-acetylmura  87.1    0.85 2.2E-05   24.1   3.7   35    3-40     97-131 (452)
394 TIGR03575 selen_PSTK_euk L-ser  86.9     1.1 2.8E-05   23.5   4.2   37    9-45      1-38  (340)
395 PRK12826 3-ketoacyl-(acyl-carr  86.9     1.1 2.8E-05   23.5   4.2   41    1-46      1-41  (253)
396 TIGR01846 type_I_sec_HlyB type  86.9    0.61 1.6E-05   25.0   2.9  122    4-146   489-615 (703)
397 PTZ00265 multidrug resistance   86.9     1.5 3.8E-05   22.7   4.9   41    4-46    409-451 (1467)
398 cd00154 Rab Rab family.  Rab G  86.8       1 2.5E-05   23.7   4.0   65  125-193    50-117 (159)
399 TIGR03420 DnaA_homol_Hda DnaA   86.8     1.3 3.3E-05   23.0   4.5   38    6-44     38-75  (226)
400 COG1428 Deoxynucleoside kinase  86.7    0.92 2.3E-05   23.9   3.7   32    4-39      2-33  (216)
401 cd01868 Rab11_like Rab11-like.  86.6     2.3   6E-05   21.6   5.8  107  125-254    53-164 (165)
402 PRK05872 short chain dehydroge  86.6     1.1 2.7E-05   23.6   4.0   41    1-46      4-44  (296)
403 pfam06414 Zeta_toxin Zeta toxi  86.5     1.5 3.8E-05   22.7   4.7   39    3-44      9-47  (191)
404 PRK07773 replicative DNA helic  86.4     2.2 5.7E-05   21.7   5.6   39    5-44    202-241 (868)
405 PRK13640 cbiO cobalt transport  86.4    0.98 2.5E-05   23.8   3.8   29    4-33     32-60  (283)
406 COG1217 TypA Predicted membran  86.4    0.57 1.5E-05   25.1   2.5   81  122-209    66-148 (603)
407 PRK13644 cbiO cobalt transport  86.2    0.85 2.2E-05   24.1   3.4   35    4-40     26-61  (274)
408 PRK13830 conjugal transfer pro  86.2     1.7 4.3E-05   22.4   4.9   33   13-45    462-495 (818)
409 COG0370 FeoB Fe2+ transport sy  86.2    0.64 1.6E-05   24.8   2.7   32  186-217   113-145 (653)
410 PRK08589 short chain dehydroge  86.1     1.1 2.8E-05   23.5   3.9   41    1-46      1-41  (272)
411 PRK00421 murC UDP-N-acetylmura  85.9     1.3 3.3E-05   23.1   4.1   36    4-42    106-142 (459)
412 COG2074 2-phosphoglycerate kin  85.9    0.85 2.2E-05   24.1   3.2   26    5-31     88-113 (299)
413 cd04127 Rab27A Rab27a subfamil  85.8     2.6 6.6E-05   21.3   6.5  110  125-257    64-179 (180)
414 pfam02421 FeoB_N Ferrous iron   85.8     0.7 1.8E-05   24.6   2.8   19    8-27      1-19  (188)
415 PRK10875 recD exonuclease V su  85.7     2.1 5.3E-05   21.9   5.1   27    7-33    162-188 (607)
416 cd04171 SelB SelB subfamily.    85.7    0.75 1.9E-05   24.5   2.8   80  124-209    51-133 (164)
417 pfam01121 CoaE Dephospho-CoA k  85.6     1.5   4E-05   22.6   4.4   31    8-45      2-32  (179)
418 TIGR02729 Obg_CgtA GTP-binding  85.6     0.5 1.3E-05   25.5   1.9   67  125-193   210-294 (296)
419 COG1066 Sms Predicted ATP-depe  85.5     1.9 4.9E-05   22.1   4.9   34   10-44     96-129 (456)
420 TIGR00073 hypB hydrogenase acc  85.5    0.97 2.5E-05   23.8   3.4   41    8-50     36-76  (225)
421 smart00487 DEXDc DEAD-like hel  85.4     1.8 4.5E-05   22.3   4.6   32   11-42     28-61  (201)
422 COG4962 CpaF Flp pilus assembl  85.3    0.71 1.8E-05   24.6   2.6   16   13-28    179-194 (355)
423 cd02020 CMPK Cytidine monophos  85.3     0.9 2.3E-05   24.0   3.1   23    8-31      1-23  (147)
424 PRK10536 hypothetical protein;  85.3     1.1 2.8E-05   23.5   3.6   30    6-35     73-102 (262)
425 PRK13632 cbiO cobalt transport  85.2    0.87 2.2E-05   24.1   3.0   38    4-43     34-71  (273)
426 PRK06912 acoL dihydrolipoamide  85.1    0.77   2E-05   24.4   2.7   38    6-50      1-38  (458)
427 PRK12829 short chain dehydroge  85.1     1.3 3.4E-05   23.0   3.9   41    1-46      6-46  (264)
428 cd03257 ABC_NikE_OppD_transpor  85.0       1 2.7E-05   23.6   3.3   28    4-32     29-56  (228)
429 PRK08862 short chain dehydroge  85.0    0.94 2.4E-05   23.9   3.1   39    4-47      3-41  (227)
430 cd02021 GntK Gluconate kinase   85.0    0.85 2.2E-05   24.1   2.9   30   11-45      3-32  (150)
431 COG0378 HypB Ni2+-binding GTPa  85.0     2.5 6.5E-05   21.4   5.3   39    7-47     14-52  (202)
432 TIGR02868 CydC ABC transporter  85.0       1 2.7E-05   23.6   3.3   41    4-46    385-426 (566)
433 PRK00300 gmk guanylate kinase;  84.9     1.2 3.1E-05   23.2   3.6   27    1-28      2-28  (208)
434 PRK08324 short chain dehydroge  84.8       2 5.1E-05   21.9   4.7   40    3-47    418-457 (676)
435 COG0194 Gmk Guanylate kinase [  84.8     1.3 3.3E-05   23.1   3.7   23    5-28      3-25  (191)
436 pfam10412 TrwB_AAD_bind Type I  84.7     2.9 7.4E-05   21.0   6.0   47    3-52     12-58  (386)
437 TIGR02880 cbbX_cfxQ CbbX prote  84.6     1.3 3.2E-05   23.1   3.6   37    7-44     59-99  (284)
438 PRK13648 cbiO cobalt transport  84.6     1.2 3.1E-05   23.2   3.6   27    4-31     33-59  (269)
439 PRK10463 hydrogenase nickel in  84.5     1.3 3.3E-05   23.1   3.6   39    8-48    106-144 (290)
440 pfam08245 Mur_ligase_M Mur lig  84.4     1.5 3.8E-05   22.7   3.9   27   16-42      3-29  (188)
441 PRK05057 aroK shikimate kinase  84.2     1.9 4.9E-05   22.1   4.4   37    1-45      1-37  (172)
442 TIGR02211 LolD_lipo_ex lipopro  84.2    0.76 1.9E-05   24.4   2.4   24    4-28     29-52  (221)
443 cd03290 ABCC_SUR1_N The SUR do  84.2     1.2 3.1E-05   23.2   3.4   36    4-40     25-60  (218)
444 TIGR02746 TraC-F-type type-IV   84.0     2.4 6.2E-05   21.5   4.9   46    9-55    492-538 (900)
445 pfam07693 KAP_NTPase KAP famil  84.0     3.1   8E-05   20.8   6.0   42    4-46     18-59  (301)
446 PRK10789 putative multidrug tr  84.0     2.7 6.8E-05   21.3   5.0   37    4-43    339-376 (569)
447 PRK13394 3-hydroxybutyrate deh  84.0     1.8 4.6E-05   22.3   4.2   40    1-45      2-41  (262)
448 PRK13631 cbiO cobalt transport  84.0     1.3 3.4E-05   23.0   3.5   36    4-40     50-85  (320)
449 cd03291 ABCC_CFTR1 The CFTR su  83.9     1.3 3.3E-05   23.1   3.4   28    4-32     61-88  (282)
450 PRK10846 bifunctional folylpol  83.9     2.5 6.3E-05   21.4   4.8   37    2-41     45-81  (416)
451 cd04174 Rnd1_Rho6 Rnd1/Rho6 su  83.8     1.6 4.2E-05   22.5   3.9  104  143-257    82-190 (232)
452 cd01853 Toc34_like Toc34-like   83.7    0.93 2.4E-05   23.9   2.6   29    8-43     33-61  (249)
453 PRK12296 obgE GTPase ObgE; Rev  83.7    0.87 2.2E-05   24.1   2.5   81  123-207   205-308 (495)
454 PRK13642 cbiO cobalt transport  83.6     1.2 3.2E-05   23.2   3.2   38    4-43     31-68  (277)
455 PRK13645 cbiO cobalt transport  83.6    0.81 2.1E-05   24.3   2.3   35    4-40     35-70  (289)
456 COG3265 GntK Gluconate kinase   83.5    0.49 1.3E-05   25.5   1.1   32   15-51      3-37  (161)
457 PRK12898 secA preprotein trans  83.4    0.52 1.3E-05   25.4   1.2   33   11-43    135-167 (673)
458 COG4167 SapF ABC-type antimicr  83.4    0.93 2.4E-05   23.9   2.5   36    4-40     37-72  (267)
459 cd04155 Arl3 Arl3 subfamily.    83.3     1.6   4E-05   22.6   3.6   25    1-27     10-34  (173)
460 PRK06484 short chain dehydroge  83.3     1.8 4.6E-05   22.2   3.9   40    2-46      1-40  (530)
461 cd03249 ABC_MTABC3_MDL1_MDL2 M  83.3     1.5 3.7E-05   22.8   3.5   37    4-43     27-64  (238)
462 PRK13633 cobalt transporter AT  83.2     1.4 3.7E-05   22.8   3.4   36    4-40     35-70  (281)
463 PRK13650 cbiO cobalt transport  83.2     1.4 3.5E-05   22.9   3.3   37    4-43     28-65  (276)
464 PRK12814 putative NADPH-depend  83.1     2.7 6.9E-05   21.2   4.8   50    2-57    189-238 (652)
465 TIGR03015 pepcterm_ATPase puta  83.1     1.9 4.8E-05   22.1   4.0   42    5-47     41-82  (269)
466 PRK07454 short chain dehydroge  83.0       2 5.1E-05   22.0   4.1   41    1-46      1-41  (241)
467 cd03261 ABC_Org_Solvent_Resist  83.0     1.5 3.9E-05   22.7   3.4   26    4-30     24-49  (235)
468 COG0237 CoaE Dephospho-CoA kin  82.9     2.4 6.2E-05   21.5   4.5   32    6-44      2-33  (201)
469 PRK10787 DNA-binding ATP-depen  82.9     1.3 3.3E-05   23.1   3.1   29    3-32    346-374 (784)
470 COG2274 SunT ABC-type bacterio  82.9     1.5 3.9E-05   22.6   3.5   37    4-43    497-534 (709)
471 cd03248 ABCC_TAP TAP, the Tran  82.8     1.5 3.7E-05   22.8   3.3   37    4-43     38-75  (226)
472 cd03289 ABCC_CFTR2 The CFTR su  82.8     1.3 3.3E-05   23.0   3.1   37    4-43     28-64  (275)
473 TIGR03345 VI_ClpV1 type VI sec  82.8     1.6   4E-05   22.6   3.5   32   13-44    214-252 (852)
474 KOG2859 consensus               82.7     2.2 5.7E-05   21.7   4.3   46    2-48     34-85  (293)
475 COG1100 GTPase SAR1 and relate  82.7     1.3 3.3E-05   23.1   3.0   38    6-45      6-43  (219)
476 PRK13646 cbiO cobalt transport  82.6     1.6 4.1E-05   22.5   3.5   40    4-44     31-70  (286)
477 cd03808 GT1_cap1E_like This fa  82.6     2.4   6E-05   21.5   4.3   35    7-43      1-35  (359)
478 pfam07728 AAA_5 AAA domain (dy  82.5    0.85 2.2E-05   24.1   2.0   33   12-46      4-36  (139)
479 pfam00910 RNA_helicase RNA hel  82.4     1.7 4.2E-05   22.5   3.5   23   12-34      3-25  (105)
480 PRK06500 short chain dehydroge  82.4     1.8 4.7E-05   22.2   3.7   41    1-46      1-41  (249)
481 PRK06172 short chain dehydroge  82.4     1.7 4.4E-05   22.4   3.5   38    4-46      5-42  (253)
482 cd01879 FeoB Ferrous iron tran  82.3     1.1 2.7E-05   23.6   2.4   15   14-28      3-17  (158)
483 PRK13700 conjugal transfer pro  82.3     3.7 9.4E-05   20.4   5.3   40    4-44    183-222 (732)
484 cd04113 Rab4 Rab4 subfamily.    82.2     2.3   6E-05   21.6   4.2  107  125-254    50-161 (161)
485 PRK13651 cobalt transporter AT  82.2     1.4 3.7E-05   22.8   3.1   41    4-45     31-71  (304)
486 COG0770 MurF UDP-N-acetylmuram  82.2     1.9 4.9E-05   22.1   3.7   30    3-35    100-129 (451)
487 cd02024 NRK1 Nicotinamide ribo  82.1     1.8 4.7E-05   22.2   3.6   32    8-44      1-32  (187)
488 PRK06921 hypothetical protein;  82.1     3.3 8.3E-05   20.7   4.9   28   14-41    123-151 (265)
489 cd03288 ABCC_SUR2 The SUR doma  82.1     1.8 4.7E-05   22.2   3.6   36    4-42     45-81  (257)
490 CHL00181 cbbX CbbX; Provisiona  82.0     2.1 5.3E-05   21.9   3.9   29    7-36     60-88  (287)
491 TIGR01966 RNasePH ribonuclease  82.0    0.94 2.4E-05   23.9   2.1   21   28-48    100-121 (237)
492 PRK13853 type IV secretion sys  81.9     3.7 9.4E-05   20.4   5.1   32   14-45    433-468 (789)
493 TIGR02982 heterocyst_DevA ABC   81.9    0.94 2.4E-05   23.9   2.1   21    9-29     33-53  (220)
494 PRK12825 fabG 3-ketoacyl-(acyl  81.9     2.1 5.3E-05   21.9   3.8   40    1-45      2-41  (250)
495 pfam00996 GDI GDP dissociation  81.9    0.75 1.9E-05   24.5   1.5   37   17-55     11-48  (439)
496 cd03112 CobW_like The function  81.8       2 5.2E-05   21.9   3.7   35    9-45      2-36  (158)
497 cd03251 ABCC_MsbA MsbA is an e  81.8     1.8 4.5E-05   22.3   3.4   37    4-43     26-63  (234)
498 PRK13635 cbiO cobalt transport  81.8     1.7 4.4E-05   22.3   3.4   28    4-32     31-58  (279)
499 cd04137 RheB Rheb (Ras Homolog  81.7     2.8 7.2E-05   21.1   4.5  112  124-258    49-166 (180)
500 PRK13643 cbiO cobalt transport  81.7     1.7 4.2E-05   22.4   3.3   24    4-28     30-53  (288)

No 1  
>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=0  Score=358.23  Aligned_cols=254  Identities=25%  Similarity=0.402  Sum_probs=209.4

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCC---CCCCCEEEEEE---CCCCHH
Q ss_conf             876874999980889888899999999999987995999987877680112124633---34541167630---257712
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELY---DRKYSSYDLLI---EEKNIN   75 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~---~~~~ti~~~l~---~~~~l~   75 (265)
                      +..++|||+|.|+||||||||+|+|||++||.+|+|||+||+|||||+|.+||..+.   ....++++.+.   ...++.
T Consensus       100 ~g~~~~VIav~N~KGGVGKTTtav~LA~~LA~~G~RVLvIDLDPQanlT~~~G~~pe~d~~~~~tl~~~l~~d~~~~~l~  179 (387)
T TIGR03453       100 GGEHLQVIAVTNFKGGSGKTTTSAHLAQYLALRGYRVLAIDLDPQASLSALFGFQPEFDVGENETLYGAIRYDDERRPLS  179 (387)
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCCCCCCCCCCCCCHHHHHHCCCCCCCHH
T ss_conf             99988089997888765699999999999997799889995370167887528984346675642999984455668799


Q ss_pred             HCCCCCCCCCEEECCCCCCCCCCCCCCC----CCCCC----CHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHH
Q ss_conf             1024444442000148874577500012----32222----102333224765102782033101333222210112331
Q gi|254780806|r   76 QILIQTAIPNLSIIPSTMDLLGIEMILG----GEKDR----LFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAAD  147 (265)
Q Consensus        76 ~~i~~~~~~~l~iipa~~~~~~~~~~l~----~~~~~----~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad  147 (265)
                      +++.+|.++|||+|||+..+.+++..+.    .....    ..+|++.|. .+.++||||||||||++|.+|.|+|.|||
T Consensus       180 ~~i~~T~~~~LdliPa~~~L~~~E~~~~~~l~~~~~~~~~f~~rL~~aL~-~v~d~YD~IlIDcPPsLg~lT~nAL~AAd  258 (387)
T TIGR03453       180 EIIRKTYFPGLDLIPGNLELMEFEHETPRALSRGAGGDTIFFARVGEALA-EVEDDYDVVVIDCPPQLGFLTLSALCAAT  258 (387)
T ss_pred             HHHHCCCCCCEEEECCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH-HHHCCCCEEEEECCCCCCHHHHHHHHHCC
T ss_conf             96114799996896598899998898899997431100269999999999-76602999999589851399999999819


Q ss_pred             HCCCCCCCCCHHHHHHHHHHHHHHHHHHH-----HHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCH
Q ss_conf             00111112311378887533577765543-----2026774310020231253100112689998808520156267868
Q gi|254780806|r  148 SILVPLQCEFFALEGLSQLLETVEEVRRT-----VNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNV  222 (265)
Q Consensus       148 ~viip~~p~~~s~~~~~~~~~~i~~~~~~-----~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~  222 (265)
                      .+|||+.|+++++.++.+++.++..+...     .+.++++.++++|||++++..+.++.+.+++.||..++.+.||.+.
T Consensus       259 ~vlIPv~p~~ld~~s~~qfl~~~~~l~~~i~~~g~~~~~d~~~~LlT~~d~~~~~~~~v~~~~r~~fg~~vl~~~i~~S~  338 (387)
T TIGR03453       259 AVLITVHPQMLDVMSMSQFLLMTGDLLGVVRDAGGNLSYDWMRYLVTRYEPNDGPQAQMVAFMRSLFGEHVLTNPMLKST  338 (387)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCEEEHHH
T ss_conf             40878887177799999999999999999997167767640577645178998469999999999850654236201679


Q ss_pred             HHHHHHHCCCCEEEECCCCH-------HHHHHHHHHHHHHH
Q ss_conf             89877737985799979998-------99999999999999
Q gi|254780806|r  223 RISEAPSYGKPAIIYDLKCA-------GSQAYLKLASELIQ  256 (265)
Q Consensus       223 ~i~~a~~~g~pv~~~~p~s~-------~a~~~~~la~el~~  256 (265)
                      ++.+|...+++|+++++...       +.+.+.....||.+
T Consensus       339 ai~~A~~~~~TiyE~~~~~~~r~ty~Ra~e~~d~v~~ei~~  379 (387)
T TIGR03453       339 AISDAGLTKQTLYEVERSQFTRSTYDRAMESLDAVNAEIEG  379 (387)
T ss_pred             HHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             99863763793598774658989999999999999999999


No 2  
>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=0  Score=353.74  Aligned_cols=243  Identities=24%  Similarity=0.294  Sum_probs=202.1

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCE
Q ss_conf             49999808898888999999999999879959999878776801121246333454116763025771210244444420
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNL   86 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l   86 (265)
                      |||+|+|+||||||||+|+|||++||+.|+||++||+|||++++.+||.++. ...++.+.+....++.+++.+ ..+|+
T Consensus         2 kiIav~n~KGGVGKTT~avNLA~~La~~G~rVLlIDlDpQ~~l~~~~g~~~~-~~~~l~~~~~~~~~~~~~~~~-~~~~~   79 (246)
T TIGR03371         2 KVIAIVGIKGGVGRTTLTAALASALKLLGEPVLAIDLDPQNLLRLHFGMDWS-VRDGWARALLAGEDWRAAAYR-SSDGV   79 (246)
T ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHCCCCCC-CCCCHHHHHHCCCCHHHHHEE-CCCCE
T ss_conf             3999975999854999999999999968997899975999850322488875-345699998279988895255-78982


Q ss_pred             EECCCCC-CCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             0014887-457750001232222102333224765102782033101333222210112331001111123113788875
Q gi|254780806|r   87 SIIPSTM-DLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQ  165 (265)
Q Consensus        87 ~iipa~~-~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~~  165 (265)
                      +++|++. .....+.....   ...++.+.+...-.+.||||||||||+++.++.++|.+||.+++|++|+++|+.++.+
T Consensus        80 ~~ip~~~~~~~~~~~~~~~---~~~~l~~~l~~l~~~~~D~viiD~pp~l~~~~~~al~aad~vlipv~~~~~s~~~~~~  156 (246)
T TIGR03371        80 LFLPYGTLSADEREAYQAH---DAGWLARLLQQLDLAARDWVLIDLPRGPSPITDQALAAADLVLVVVNADAACYATLHQ  156 (246)
T ss_pred             EEEECCCCCHHHHHHHCCC---CHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHCCEEEEEECCCHHHHHHHHH
T ss_conf             8970898477789876044---7899999998630367988999489987499999999889479981899899999999


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCCHHHH
Q ss_conf             33577765543202677431002023125310011268999880852015626786889877737985799979998999
Q gi|254780806|r  166 LLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGSQ  245 (265)
Q Consensus       166 ~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s~~a~  245 (265)
                      ++..+.....    +....++|+||+++++..++++.+.+++.|+..++.+.||++..+.+|...|+||++|.|+|++++
T Consensus       157 ~~~~~~~~~~----~~~~~~iv~n~~~~~~~~~~~~~~~l~~~~~~~~~~~~I~~~~~v~eA~~~g~pv~~~~p~S~aa~  232 (246)
T TIGR03371       157 LALALLARSV----PPDGIHYLINQFQPARQLSRDVRAVLRATLGSRLLPMFVHRDEAVAEALARGTPVFNYAPHSQAAH  232 (246)
T ss_pred             HHHHHHHHCC----CCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCEEECCCCHHHH
T ss_conf             9999998427----767517886302640158999999999974988162268997799999976998266995898999


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999999
Q gi|254780806|r  246 AYLKLASELIQQE  258 (265)
Q Consensus       246 ~~~~la~el~~~~  258 (265)
                      +|++||+||++|.
T Consensus       233 ~y~~LA~~ll~~l  245 (246)
T TIGR03371       233 DIRTLAFWLLTKL  245 (246)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9999999999963


No 3  
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=100.00  E-value=0  Score=352.82  Aligned_cols=253  Identities=22%  Similarity=0.391  Sum_probs=205.8

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCC---CCCCEEEEEE---CCCCHHH
Q ss_conf             768749999808898888999999999999879959999878776801121246333---4541167630---2577121
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYD---RKYSSYDLLI---EEKNINQ   76 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~---~~~ti~~~l~---~~~~l~~   76 (265)
                      ..+.|||+|.|+||||||||+|+|||.+||.+|+|||+||+|||||+|.+||+.+..   ...++++.+.   ...++.+
T Consensus       118 ~~~~kVIaVaN~KGGVGKTTtav~LA~~LA~~G~RVLlIDLDPQgnlS~~lG~~pe~d~~~~~tl~~~l~~d~~~~~l~~  197 (405)
T PRK13869        118 SEHLQVIAVTNFKGGSGKTTTSAHLAQYLALQGYRVLAVDLDPQASLSALLGVLPETDVGANETLYAAIRYDDTRRPLRD  197 (405)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCHHH
T ss_conf             99982899978887765999999999999977998899964561788898089854566531359999844545587999


Q ss_pred             CCCCCCCCCEEECCCCCCCCCCCCCCC----CCCCC----CHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHH
Q ss_conf             024444442000148874577500012----32222----1023332247651027820331013332222101123310
Q gi|254780806|r   77 ILIQTAIPNLSIIPSTMDLLGIEMILG----GEKDR----LFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADS  148 (265)
Q Consensus        77 ~i~~~~~~~l~iipa~~~~~~~~~~l~----~~~~~----~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~  148 (265)
                      ++.+|.++|||+|||+.++..++....    ....+    ..++.+.|. .+.++||||||||||++|.+|.|+|+|||.
T Consensus       198 ~I~~T~~~~LdlIPa~l~L~~~E~~~~~~l~~~~~~~~~~~~rl~~~L~-~v~d~YDvIiIDcPPsLg~lT~nAL~AAd~  276 (405)
T PRK13869        198 VIRPTYFDGLHLVPGNLELMEFEHTTPKALSDRGTRDGLFFTRVAQAFD-EVADDYDVVVIDCPPQLGFLTLSGLCAATS  276 (405)
T ss_pred             HCCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCCEEEEECCCCHHHHHHHHHHHHCE
T ss_conf             5216799996895898899998887599987433155689999999998-644129989995998265999999998286


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHH---HHH--CCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHH
Q ss_conf             011111231137888753357776554---320--267743100202312531001126899988085201562678688
Q gi|254780806|r  149 ILVPLQCEFFALEGLSQLLETVEEVRR---TVN--SALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVR  223 (265)
Q Consensus       149 viip~~p~~~s~~~~~~~~~~i~~~~~---~~~--~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~  223 (265)
                      +|||+.|+++++.++.+++.++..+..   ..+  ....+.++++|||++++..+.++.+.+++.||..|+.+.||++..
T Consensus       277 vlIPv~pe~ld~~s~~qfl~~~~~l~~~~~~~~~~~~~dfir~LlTr~d~~~~~~~~v~~~lr~~fg~~Vl~~~i~~S~a  356 (405)
T PRK13869        277 MVITVHPQMLDIASMSQFLLMTRDLLGVVKEAGGNLQYDFIRYLLTRYEPQDAPQTKVTALLRNMFEDHVLTNPMVKSAA  356 (405)
T ss_pred             EEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf             38648960878999999999999999999970788785404563140689982599999999999878886080737799


Q ss_pred             HHHHHHCCCCEEEECCCC-------HHHHHHHHHHHHHHH
Q ss_conf             987773798579997999-------899999999999999
Q gi|254780806|r  224 ISEAPSYGKPAIIYDLKC-------AGSQAYLKLASELIQ  256 (265)
Q Consensus       224 i~~a~~~g~pv~~~~p~s-------~~a~~~~~la~el~~  256 (265)
                      +.+|....++|++.++..       ++.+.+.....||.+
T Consensus       357 is~A~~~~~TvyE~~~~~~~r~Ty~Ra~e~~d~v~~ei~~  396 (405)
T PRK13869        357 VSDAGLTKQTLYEIGRENLTRSTYDRAMESLDAVNSEIEA  396 (405)
T ss_pred             HHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             9986874496287650527889999999999999999999


No 4  
>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=349.67  Aligned_cols=231  Identities=29%  Similarity=0.497  Sum_probs=202.0

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC-CCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCC
Q ss_conf             499998088988889999999999998799599998787-7680112124633345411676302577121024444442
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP-QGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPN   85 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~-q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~   85 (265)
                      |+|+|.|+||||||||+|+|||++||++|++|++||+|. .+||+..||++  +.+-|++|+|.++.+++|+|+.++.+|
T Consensus         1 r~I~iASGKGGtGKTT~tANLgVALA~~Gk~V~~~DADI~MANL~LiLgmE--~~~VTLhDVLAGeA~i~DAIY~gp~Gn   78 (258)
T TIGR01969         1 RIITIASGKGGTGKTTITANLGVALAKLGKKVLVLDADITMANLELILGME--DKPVTLHDVLAGEADIKDAIYEGPEGN   78 (258)
T ss_pred             CEEEEEECCCCCCHHHEEEHHHHHHHHCCCEEEEEECCHHHHHHHHHHCCC--CCCCCCCCCCCCCCCHHHHCCCCCCCC
T ss_conf             988999778898614000007788986097689994676677689884468--889675221344561001100288984


Q ss_pred             EEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             00014887457750001232222102333224765102782033101333222210112331001111123113788875
Q gi|254780806|r   86 LSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQ  165 (265)
Q Consensus        86 l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~~  165 (265)
                      +.|+|++.+|.++-.      .+..+|.+.+. .+.+.|||+|||||+|++.-+..+|.+||.+++|++||++|+.++-+
T Consensus        79 V~V~PagvSLEg~rK------A~~~~L~dV~~-~i~~~~D~lLIDAPAGL~~~a~~Al~~a~elLLVvNPEi~SItDaLK  151 (258)
T TIGR01969        79 VKVIPAGVSLEGLRK------ADPDKLEDVLK-EIIDDTDFLLIDAPAGLERDAVTALAAADELLLVVNPEISSITDALK  151 (258)
T ss_pred             EEEECCCCCHHHCCC------CCHHHHHHHHH-HHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCHHHHHHHHH
T ss_conf             478506122100012------68333289999-87204377887478983378999998618664866765446777889


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCEEECC-CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCCHHH
Q ss_conf             33577765543202677431002023125-31001126899988085201562678688987773798579997999899
Q gi|254780806|r  166 LLETVEEVRRTVNSALDIQGIILTMFDSR-NSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGS  244 (265)
Q Consensus       166 ~~~~i~~~~~~~~~~~~~~~iv~N~~~~~-~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s~~a  244 (265)
                      +.    .+.++.+  +.++|+|+||+... +.+.   .++++..+..+|+. +||+|+.+++|..+|.|++.|+|+|++|
T Consensus       152 ~k----~va~~lG--t~ilG~vlNRv~~~~tel~---~~eiE~iLevPVl~-~vPEDP~VR~AAa~G~P~V~~~P~SpAA  221 (258)
T TIGR01969       152 VK----IVAEKLG--TAILGVVLNRVTRDKTELG---REEIEAILEVPVLG-VVPEDPEVRRAAAFGEPVVVYSPNSPAA  221 (258)
T ss_pred             HH----HHHHHCC--CCEEEEEEEECCCCCCCCC---HHHHHHHHCCCEEE-EECCCHHHHHHHHCCCCEEEECCCCHHH
T ss_conf             99----9987608--8324689960236666378---88999884797389-8569843445642485368847998789


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780806|r  245 QAYLKLASELIQ  256 (265)
Q Consensus       245 ~~~~~la~el~~  256 (265)
                      |+|.+||.+|.+
T Consensus       222 ~A~~eLA~~l~G  233 (258)
T TIGR01969       222 QAFMELAAELAG  233 (258)
T ss_pred             HHHHHHHHHHHC
T ss_conf             999999999718


No 5  
>PRK10818 cell division inhibitor MinD; Provisional
Probab=100.00  E-value=0  Score=332.32  Aligned_cols=245  Identities=25%  Similarity=0.373  Sum_probs=195.4

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC-CCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCC-CC
Q ss_conf             749999808898888999999999999879959999878-7768011212463334541167630257712102444-44
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD-PQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQT-AI   83 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D-~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~-~~   83 (265)
                      +|||+|+|+||||||||+|+|||++||++|+||++||+| +++|++.++|++. ...+++.+++.+++.+++++++. ..
T Consensus         2 ~rvIaV~s~KGGVGKTT~avNLA~aLA~~G~kVlliD~D~~~~n~~~~lg~~~-~~~~~~~~vl~g~~~l~~~~i~~~~~   80 (270)
T PRK10818          2 ARIIVVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFDIGLRNLDLIMGCER-RVVYDFVNVIQGDATLNQALIKDKRT   80 (270)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCC-CCCCCHHHHHCCCCCHHHHEEECCCC
T ss_conf             74999978999841899999999999977996899968999988873457677-66666898836998588905446876


Q ss_pred             CCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHH
Q ss_conf             42000148874577500012322221023332247651027820331013332222101123310011111231137888
Q gi|254780806|r   84 PNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGL  163 (265)
Q Consensus        84 ~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~  163 (265)
                      +|++++|++.... .  .   ... ...+.+.+....+.+|||||||||||++..+.+++.+||.+++|++|+++|++++
T Consensus        81 ~~l~ilpa~~~~~-~--~---~~~-~~~~~~~l~~l~~~~yDyIiID~ppgl~~~~~~al~aad~vlvv~tpe~~al~da  153 (270)
T PRK10818         81 ENLYILPASQTRD-K--D---ALT-REGVAKVLDDLKAMDFEFIVCDSPAGIETGALMALYFADEAIITTNPEVSSVRDS  153 (270)
T ss_pred             CCEEEECCCCHHH-H--H---HHH-HHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHCCEEEEECCCCHHHHHHH
T ss_conf             9979979996476-7--5---545-9999999997776599899988999866899999985896899738978899879


Q ss_pred             HHHHHHHHHHHHHHHCCCC--CCCCCCCEEECCCHHHHHH--HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECC
Q ss_conf             7533577765543202677--4310020231253100112--68999880852015626786889877737985799979
Q gi|254780806|r  164 SQLLETVEEVRRTVNSALD--IQGIILTMFDSRNSLSQQV--VSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDL  239 (265)
Q Consensus       164 ~~~~~~i~~~~~~~~~~~~--~~~iv~N~~~~~~~~~~~~--~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p  239 (265)
                      +++++.+.....+.+....  ..++++||+++......+.  .+++.+.++.+++. +||+|..+.+|.+.|+|++ ++|
T Consensus       154 ~~ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lg-~IP~d~~v~eA~~~G~Pvv-~~p  231 (270)
T PRK10818        154 DRILGILASKSRRAENGEEPIKEHLLLTRYNPGRVSRGDMLSMEDVLEILRIKLVG-VIPEDQSVLRASNQGEPVI-LDI  231 (270)
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHCCEEEEEECHHHCCHHHHCCHHHHHHHCCCEEEE-ECCCCHHHHHHCCCCCCEE-ECC
T ss_conf             99999999877765335201001258842453123211001299999732880699-8079746988522799879-899


Q ss_pred             CCHHHHHHHHHHHHHHHHHHH
Q ss_conf             998999999999999999986
Q gi|254780806|r  240 KCAGSQAYLKLASELIQQERH  260 (265)
Q Consensus       240 ~s~~a~~~~~la~el~~~~~~  260 (265)
                      +|+++++|++||++|++++++
T Consensus       232 ~s~~a~Ay~~lA~~ll~~~~p  252 (270)
T PRK10818        232 NADAGKAYADTVERLLGEERP  252 (270)
T ss_pred             CCHHHHHHHHHHHHHHCCCCC
T ss_conf             998999999999999568777


No 6  
>CHL00175 minD septum-site determining protein; Validated
Probab=100.00  E-value=0  Score=328.72  Aligned_cols=242  Identities=26%  Similarity=0.374  Sum_probs=196.7

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC-CCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCC-
Q ss_conf             68749999808898888999999999999879959999878-7768011212463334541167630257712102444-
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD-PQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQT-   81 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D-~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~-   81 (265)
                      .-+|||+|+|+||||||||+|+|||++||+.|+||++||+| +++|++.+||++.. ..+++.+++.+.+.++++++.. 
T Consensus        11 ~m~kiIaV~s~KGGVGKTT~a~NLa~aLA~~G~kVlliD~D~~~~n~~~~lg~~~~-~~~~~~~vl~g~~~l~~~~i~~~   89 (279)
T CHL00175         11 TMTRIIVITSGKGGVGKTTTTANLGMSIARLGYRVALIDADIGLRNLDLLLGLENR-VVYTAMEVLEGECRLDQALIRDK   89 (279)
T ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCC-CCCCHHHHCCCCCCCCCCEEECC
T ss_conf             98869999748998448999999999999789988999578999987532686666-66747664078766430134257


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHH
Q ss_conf             44420001488745775000123222210233322476510278203310133322221011233100111112311378
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALE  161 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~  161 (265)
                      ..+|++++|++........    .   ...+.+.+....+.+|||||||||||++.++.+++.+||++|+|++|+++|++
T Consensus        90 ~~~~l~ll~~~~~~~~~~~----~---~~~~~~ll~~l~~~~yDyiiID~ppgl~~~~~~al~aad~viIvttpe~~al~  162 (279)
T CHL00175         90 RWPNLSLLPISKNRQRYNV----T---RKNMNMLVDSLKERNYDYILIDCPAGIDVGFINAIAPAKEAIVVTTPEITAIR  162 (279)
T ss_pred             CCCCEEEEECCCHHHHHHH----H---HHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHCCEEEEECCCCHHHHH
T ss_conf             7787799978970544574----1---99999999999727999999818998889999999978906997899789999


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHH--HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECC
Q ss_conf             88753357776554320267743100202312531001--1268999880852015626786889877737985799979
Q gi|254780806|r  162 GLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQ--QVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDL  239 (265)
Q Consensus       162 ~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~--~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p  239 (265)
                      ++++++++++..      .....++|+||+.+......  .....+++.++.++++ .||+|..+.+|.+.|+|+..+.|
T Consensus       163 da~~~i~~~~~~------~~~~~~lvvN~~~~~~~~~~~~~~~~~~~~~l~v~~lg-~IP~D~~v~~a~~~G~Pvv~~~P  235 (279)
T CHL00175        163 DADRVAGLLEAN------GIYNIKLLVNRVRPDMIKANDMMSVRDVQEMLGIPLLG-AIPEDENVIISTNRGEPLVLKKK  235 (279)
T ss_pred             HHHHHHHHHHHC------CCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHCCCEEE-ECCCCHHHHHCCCCCEEEEEECC
T ss_conf             999999999975------99862135335645543545534499999971993465-76787789861306905898499


Q ss_pred             CCHHHHHHHHHHHHHHHHHHH
Q ss_conf             998999999999999999986
Q gi|254780806|r  240 KCAGSQAYLKLASELIQQERH  260 (265)
Q Consensus       240 ~s~~a~~~~~la~el~~~~~~  260 (265)
                      +|+++++|.+||++|++++..
T Consensus       236 ~S~~a~a~~~iA~~l~~~~~~  256 (279)
T CHL00175        236 LTLSGIAFENAARRLVGKQVY  256 (279)
T ss_pred             CCHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999999999578767


No 7  
>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=336.62  Aligned_cols=243  Identities=28%  Similarity=0.415  Sum_probs=203.7

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC-CCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC-C
Q ss_conf             7499998088988889999999999998799599998787-7680112124633345411676302577121024444-4
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP-QGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA-I   83 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~-q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~-~   83 (265)
                      ++||+|+|+||||||||+|+||+.+||++|+||++||+|. ..||+..||++.+ .-||+.|++.++|.+++|.++.+ +
T Consensus         1 ~~viViTSGKGGVGKTTtTANlG~aLA~lG~kVvliD~DiGLRNLD~~lGLEnR-ivYt~vDVveG~C~l~qALikDKr~   79 (272)
T TIGR01968         1 ARVIVITSGKGGVGKTTTTANLGTALARLGKKVVLIDADIGLRNLDLLLGLENR-IVYTLVDVVEGECRLQQALIKDKRL   79 (272)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHCCCHH-HHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             958999817889773589899999999619828999547570345777423103-5453554324842110010012675


Q ss_pred             CCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCC--CCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHH
Q ss_conf             4200014887457750001232222102333224765102--78203310133322221011233100111112311378
Q gi|254780806|r   84 PNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSD--FSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALE  161 (265)
Q Consensus        84 ~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~--yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~  161 (265)
                      +||.++|+++........    ++.   + +.|...|.++  |||||||||+|++.-..+|+..||.+||||+||..|++
T Consensus        80 ~NL~LLpAsQ~rdK~~~~----~E~---~-~~lv~~Lk~~~~FDYviIDcPAGIE~GF~nAv~~Ad~AiVVttPEvsavR  151 (272)
T TIGR01968        80 ENLYLLPASQTRDKDAVT----PEQ---M-KKLVNELKEEEHFDYVIIDCPAGIESGFRNAVAPADEAIVVTTPEVSAVR  151 (272)
T ss_pred             HHHHHHHHHHCCCCCCCC----HHH---H-HHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHCCEEEEEECCCCCCHH
T ss_conf             235663653023613469----778---9-99999985437930799737877435689987526835898778745100


Q ss_pred             HHHHHHHHHHHHHHHHH--CCCCCCCCCCCEEECCCHHHHHH--HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEE
Q ss_conf             88753357776554320--26774310020231253100112--689998808520156267868898777379857999
Q gi|254780806|r  162 GLSQLLETVEEVRRTVN--SALDIQGIILTMFDSRNSLSQQV--VSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIY  237 (265)
Q Consensus       162 ~~~~~~~~i~~~~~~~~--~~~~~~~iv~N~~~~~~~~~~~~--~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~  237 (265)
                      +++|+++.++......+  .... .++|+||++|.-...-++  .+++.+.++.++++ +||+|+.+-.|.+.|.|+.+-
T Consensus       152 DADRvIGlLea~~~i~~~GEE~~-~~LivNR~rP~mV~~G~Mlsi~Dv~~~L~i~LiG-viPeD~~iI~stN~GEP~vl~  229 (272)
T TIGR01968       152 DADRVIGLLEAKGNIEEKGEEVK-IKLIVNRLRPEMVKKGDMLSIDDVLEILSIPLIG-VIPEDEEIIVSTNKGEPVVLN  229 (272)
T ss_pred             HHHHHHHHHCCCCCCCCCCCEEE-EEEEEECCCHHHHHCCCCCCHHHHHHHCCCCCEE-EECCCCCEEEEECCCEEEEEC
T ss_conf             25567524212455445776464-3477851564774168982789999860886168-632998657664561435446


Q ss_pred             CCC-CHHHHHHHHHHHHHHHHHHH
Q ss_conf             799-98999999999999999986
Q gi|254780806|r  238 DLK-CAGSQAYLKLASELIQQERH  260 (265)
Q Consensus       238 ~p~-s~~a~~~~~la~el~~~~~~  260 (265)
                       ++ |.++++|+++|++|.+++.+
T Consensus       230 -~~L~~~g~Af~~~ArRi~G~~vp  252 (272)
T TIGR01968       230 -KKLSRAGKAFENIARRILGEEVP  252 (272)
T ss_pred             -CCCCHHHHHHHHHHHHHCCCCCC
T ss_conf             -00261678899998753488643


No 8  
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=100.00  E-value=0  Score=328.46  Aligned_cols=254  Identities=25%  Similarity=0.377  Sum_probs=204.7

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE-CCCCCCCCHHHCCCCCC---CCCCEEEEE-ECCCCHHH
Q ss_conf             87687499998088988889999999999998799599998-78776801121246333---454116763-02577121
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLID-LDPQGNASTGLGIELYD---RKYSSYDLL-IEEKNINQ   76 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID-~D~q~~~~~~l~~~~~~---~~~ti~~~l-~~~~~l~~   76 (265)
                      +.+++.||+|.|+||||||||+|+|||.+||.+|+|||+|| +|||||+|.+||+.+..   ...+++... .+..++.+
T Consensus       102 ~g~~~~VIAVaNqKGGvGKTTTavnLA~~LAl~G~RVLlID~LDPQanlT~~~G~~pd~~~~~~~tl~~~~~~~~~~~~~  181 (388)
T PRK13705        102 EDEFPPVIGVAAHKGGVYKTSVSVHLAQDLALKGLRVLLVEGNDPQGTASMYHGWVPDLHIHAEDTLLPFYLGEKDDAAY  181 (388)
T ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCHHH
T ss_conf             99987289995278885599999999999997799089995878886564356888876656443024776146665545


Q ss_pred             CCCCCCCCCEEECCCCCCCCCCCCCCCCCC-------CCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHC
Q ss_conf             024444442000148874577500012322-------2210233322476510278203310133322221011233100
Q gi|254780806|r   77 ILIQTAIPNLSIIPSTMDLLGIEMILGGEK-------DRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSI  149 (265)
Q Consensus        77 ~i~~~~~~~l~iipa~~~~~~~~~~l~~~~-------~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~v  149 (265)
                      +|.+|.++|||+|||+..+..+|..+....       ....+|++.|. .+.++||||||||||++|.+|.|+|.|||.+
T Consensus       182 ~I~~T~~~gLDlIPs~l~L~~~E~el~~~~~~~~~~~~~~~~Lr~aL~-~v~d~YD~IlIDcPPsLG~LTiNAL~AAd~v  260 (388)
T PRK13705        182 AIKPTCWPGLDIIPSCLALHRIETELMGKFDEGKLPTDPHLMLRLAIE-TVAHDYDVIVIDSAPNLGIGTINVVCAADVL  260 (388)
T ss_pred             EEECCCCCCEEEECCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-HHHHCCCEEEEECCCCHHHHHHHHHHHHCEE
T ss_conf             043478899799708989999999997755312322258999999998-6250399999958971779999999980854


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHH---CCCCCCCCCCCEEECCCHHHHH-HHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf             11111231137888753357776554320---2677431002023125310011-2689998808520156267868898
Q gi|254780806|r  150 LVPLQCEFFALEGLSQLLETVEEVRRTVN---SALDIQGIILTMFDSRNSLSQQ-VVSDVRKNLGGKVYNTVIPRNVRIS  225 (265)
Q Consensus       150 iip~~p~~~s~~~~~~~~~~i~~~~~~~~---~~~~~~~iv~N~~~~~~~~~~~-~~~~l~~~~~~~v~~~~Ip~~~~i~  225 (265)
                      |||+.|+++++.+..+++.++..+.+..+   .... .++++|||+++...+.+ +...+++.||..|+.+.++.+.++.
T Consensus       261 lIPv~p~~lD~~S~~qFl~m~~~l~~~~~~~g~~~~-~r~L~Tr~e~~d~~q~~~m~~~lr~~fg~~vl~~~i~~S~aI~  339 (388)
T PRK13705        261 IVPTPAELFDYTSALQFFDMLRDLLKNVDLKGFEPD-VRILLTKYSNANGSQSPWMEEQIRDAWGSMVLKNVVRETDEVG  339 (388)
T ss_pred             EECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-EEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             867894077699999999999999999875177763-4899872589998789999999999976777636225789998


Q ss_pred             HHHHCCCCEEEECCC---C-----HHHHHHHHHHHHHHHH
Q ss_conf             777379857999799---9-----8999999999999999
Q gi|254780806|r  226 EAPSYGKPAIIYDLK---C-----AGSQAYLKLASELIQQ  257 (265)
Q Consensus       226 ~a~~~g~pv~~~~p~---s-----~~a~~~~~la~el~~~  257 (265)
                      +|....++|++...+   +     ++-+.+.....||.+.
T Consensus       340 ~A~~~~~TlyE~~~~~~~~~~ty~RA~es~d~v~~Ei~~~  379 (388)
T PRK13705        340 KGQIRMRTVFEQAIDQRSSTGAWRNALSIWEPVCNEIFDR  379 (388)
T ss_pred             HHHHHCCCCEECCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7265207301024444657799999999999999999999


No 9  
>PHA02519 plasmid partition protein SopA; Reviewed
Probab=100.00  E-value=0  Score=328.46  Aligned_cols=254  Identities=24%  Similarity=0.317  Sum_probs=203.7

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE-CCCCCCCCHHHCCCCCC---CCCCEEEEE-ECCCCHHHC
Q ss_conf             7687499998088988889999999999998799599998-78776801121246333---454116763-025771210
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLID-LDPQGNASTGLGIELYD---RKYSSYDLL-IEEKNINQI   77 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID-~D~q~~~~~~l~~~~~~---~~~ti~~~l-~~~~~l~~~   77 (265)
                      .+++.||+|+|.||||||||+|+|||.+||.+|+|||+|| +|||||+|.+||+.+..   ...+++... .+..++.++
T Consensus       103 ~~~~~VIAVaN~KGGVGKTTTavnLA~~LAl~G~RVL~ID~lDPQaslS~~~G~~pd~~~~~~~t~~~~~~~~~~~~~~~  182 (387)
T PHA02519        103 DKNPVVLAVMSHKGGVYKTSSAVHTAQWLALQGHRVLLIEGNDPQGTASMYHGYVPDLHIHADDTLLPFYLGERDNAEYA  182 (387)
T ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCHHHH
T ss_conf             88752899861688776999999999999976996899959885200431458888766465541357761575557760


Q ss_pred             CCCCCCCCEEECCCCCCCCCCCCCCCCCCC-------CCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCC
Q ss_conf             244444420001488745775000123222-------2102333224765102782033101333222210112331001
Q gi|254780806|r   78 LIQTAIPNLSIIPSTMDLLGIEMILGGEKD-------RLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSIL  150 (265)
Q Consensus        78 i~~~~~~~l~iipa~~~~~~~~~~l~~~~~-------~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~vi  150 (265)
                      |.+|.++|||+|||+..+..+|..+.....       ...+|++.|. .+.++||||||||||++|.+|.|+|.|||.+|
T Consensus       183 I~~T~~~gLDlIPa~l~L~~~E~el~~~~~~~~~~~~~~~~L~~aL~-~v~d~YDvVlIDcPPsLG~LTlNAL~AAd~vl  261 (387)
T PHA02519        183 IKPTCWPGLDIIPSCLALHRIETDLMQYHDAGKLPHPPHLMLRAAIE-SVWDNYDIIVIDSAPNLGTGTINVVCAADVIV  261 (387)
T ss_pred             EECCCCCCEEEECCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-HHHCCCCEEEEECCCCHHHHHHHHHHHCCEEE
T ss_conf             33689899679748889999999998787431422348999999987-52346998999799736899999999829658


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHH--CCCCCCCCCCCEEECCCH-HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHH
Q ss_conf             1111231137888753357776554320--267743100202312531-0011268999880852015626786889877
Q gi|254780806|r  151 VPLQCEFFALEGLSQLLETVEEVRRTVN--SALDIQGIILTMFDSRNS-LSQQVVSDVRKNLGGKVYNTVIPRNVRISEA  227 (265)
Q Consensus       151 ip~~p~~~s~~~~~~~~~~i~~~~~~~~--~~~~~~~iv~N~~~~~~~-~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a  227 (265)
                      ||+.|+++++.++.+++.++..+.+..+  ......++++|||+++.. .++.+...+++.||..|+...++.+.+|.+|
T Consensus       262 IPv~p~~ld~~S~~qFl~m~~~l~~~v~~~g~~~~~r~LiTr~ep~d~~q~~~m~~~lR~~fg~~vl~~~i~~S~aI~~A  341 (387)
T PHA02519        262 VATPAELFDYVSVLQFFTMLLDLLATVDLGGFEPVVRLLLTKYSLTVGNQSRWMEEQIRNTWGSMVLRQVVRVTDEVGKG  341 (387)
T ss_pred             ECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             68896387799999999999999999862378750468775358999888999999999998788864623587999973


Q ss_pred             HHCCCCEEEECC---CC-----HHHHHHHHHHHHHHHH
Q ss_conf             737985799979---99-----8999999999999999
Q gi|254780806|r  228 PSYGKPAIIYDL---KC-----AGSQAYLKLASELIQQ  257 (265)
Q Consensus       228 ~~~g~pv~~~~p---~s-----~~a~~~~~la~el~~~  257 (265)
                      ....++|++...   .+     ++-+.+.....||.+.
T Consensus       342 ~~~~qTlYE~~~~~~~tr~ty~RA~es~d~v~~EI~e~  379 (387)
T PHA02519        342 QIKMRTVFEQAANQRSTLNAWRNAVAIWEPVCAEIFND  379 (387)
T ss_pred             HHHCCCCEECCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             65127412135434558899999999999999999999


No 10 
>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=0  Score=329.75  Aligned_cols=238  Identities=19%  Similarity=0.248  Sum_probs=189.4

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCE
Q ss_conf             49999808898888999999999999879959999878776801121246333454116763025771210244444420
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNL   86 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l   86 (265)
                      |||+|.|+||||||||+|+|||++|+++|+|||+||+|||++++.+||++.... .++...+.+..++.+.+++. .+|+
T Consensus         2 kiIai~s~KGGVGKTT~t~nLa~aLa~~G~rVLlID~Dpq~~l~~~~g~~~~~~-~g~~~~~l~~~~~~~~~~~~-~~gl   79 (244)
T pfam06564         2 AVLALQGVRGGVGTTSLTAALGWALQQLGESVLVIDASPDNLLRLHFNVDFDHS-DGWARAELDGRPWRDAALRY-TPGL   79 (244)
T ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCC-CCHHHHHHCCCCHHHHHEEE-CCCE
T ss_conf             299996699986199999999999997799589996898742102358886434-41489987599777744452-6975


Q ss_pred             EECCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHH-HHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             00148874577500012-3222210233322476-510278203310133322221011233100111112311378887
Q gi|254780806|r   87 SIIPSTMDLLGIEMILG-GEKDRLFRLDKALSVQ-LTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLS  164 (265)
Q Consensus        87 ~iipa~~~~~~~~~~l~-~~~~~~~~l~~~l~~~-l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~  164 (265)
                      +++|++ .+...+.... ........+.+.+... ...+||||||||||+++.++.+++.+||.+++|++||..|...+.
T Consensus        80 ~llP~g-~l~~~~~~~~~~~~~~~~~l~~~l~~l~~~~~yD~iliD~Pp~l~~l~~~al~aad~vLv~v~~d~~s~~~l~  158 (244)
T pfam06564        80 DLLPFG-QLTGAERENLQQLQPDLGAWAQRLQLLKASGQYRWILLDLPQGFSPLTRQLLELADVTLAVVHADANCHIRLH  158 (244)
T ss_pred             EEEECC-CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHCCCEEEEECCCHHHHHHHH
T ss_conf             897289-9747899989865443799999876421357899999979999689999999976960899688858999973


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCCHHH
Q ss_conf             53357776554320267743100202312531001126899988085201562678688987773798579997999899
Q gi|254780806|r  165 QLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGS  244 (265)
Q Consensus       165 ~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s~~a  244 (265)
                                ++...  ...++++||++++...++++...+++.++. ++.++||+|+++.+|...|+|+++|+|+|+++
T Consensus       159 ----------~~~~~--~~~~ilvn~~d~~~~l~~d~~~~~~~~~~~-~l~~~I~rd~~l~EA~a~g~pv~~yaP~S~aA  225 (244)
T pfam06564       159 ----------QQALP--AGCHLLINDFRIGSQLQDDLYQLWLQSQRR-LLPIVVHRDEAMAEALAAKQPLGEYRPDSLAA  225 (244)
T ss_pred             ----------HCCCC--CCCEEEEECCCHHHHHHHHHHHHHHHHHCC-CCCEEECCCCHHHHHHHCCCCHHHCCCCCHHH
T ss_conf             ----------23344--677488642455768999999999986087-25755079882989986799554538699899


Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999999999986
Q gi|254780806|r  245 QAYLKLASELIQQERH  260 (265)
Q Consensus       245 ~~~~~la~el~~~~~~  260 (265)
                      ++|+.||.|++.+.+.
T Consensus       226 ~dy~~LA~w~l~~~~~  241 (244)
T pfam06564       226 EEVLTLANWCLLHYSR  241 (244)
T ss_pred             HHHHHHHHHHHHHHCC
T ss_conf             9999999999986433


No 11 
>COG1192 Soj ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=100.00  E-value=0  Score=312.87  Aligned_cols=254  Identities=44%  Similarity=0.661  Sum_probs=208.9

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCC-C
Q ss_conf             8749999808898888999999999999-8799599998787768011212463334541167630257712102444-4
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQT-A   82 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~-~   82 (265)
                      ..+||+|+|.||||||||+|+|||++|| ..|+|||+||+|||+++|.+||.+.. ...+..+++.......+....+ .
T Consensus         1 ~~~iI~v~n~KGGvGKTT~a~nLa~~La~~~~~kVLliDlDpQ~s~t~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~   79 (259)
T COG1192           1 MMKIIAVANQKGGVGKTTTAVNLAAALAKRGGKKVLLIDLDPQGSLTSWLGLRPD-LEGDLYNLLSGLKERPDILDYTVV   79 (259)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHCCCCC-CCCCHHHHHHCCCCCCCHHHCCCC
T ss_conf             9769999857888519999999999999838997899978999417778466643-231036676323332210220344


Q ss_pred             CCCEEECCCCCCCCC-CCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHH
Q ss_conf             442000148874577-5000123222210233322476510278203310133322221011233100111112311378
Q gi|254780806|r   83 IPNLSIIPSTMDLLG-IEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALE  161 (265)
Q Consensus        83 ~~~l~iipa~~~~~~-~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~  161 (265)
                      .++++++|++.++.. .+..+. .......+.+.+. .+.++||||||||||+++.++.+++.+||.+++|++|+.+++.
T Consensus        80 ~~~l~~ip~~~~l~~~~~~~~~-~~~~~~~l~~~~~-~~~~~yD~iiID~pp~l~~l~~nal~asd~vliP~~~~~~~~~  157 (259)
T COG1192          80 IEGLDLIPSNIDLAEGAEIELN-AVAKELLLKRLLD-PVKDDYDYIIIDTPPSLGVLTLNALAAADHVLIPVQPEFLDLE  157 (259)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHH-HHHHHHHHHHHHH-HHCCCCCEEEECCCCCHHHHHHHHHHHHCCEEECCCCCHHHHH
T ss_conf             5673123576000100456654-2117899999975-2026999899899986167779999982755670475086898


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC
Q ss_conf             88753357776554320267743100202312531001126899988085201562678688987773798579997999
Q gi|254780806|r  162 GLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC  241 (265)
Q Consensus       162 ~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s  241 (265)
                      ++.++++.+..+.+.....+...++++|+++.++..+.+.+..+++.++..++.+.||.+..+.++...|.|+..+++++
T Consensus       158 ~l~~~~~~i~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~a~~~g~~~~~~~~~~  237 (259)
T COG1192         158 GLEQLLNTLEDLLKLRRNKLIVVGILITRFDSRTKLADEVLQELKQLLGDPVLKTKIPRRVAYREAAAEGKPLYEYDPKS  237 (259)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC
T ss_conf             89999999999998524532325674353474201578999999975143111144765326887887498015507875


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999999999867
Q gi|254780806|r  242 AGSQAYLKLASELIQQERHR  261 (265)
Q Consensus       242 ~~a~~~~~la~el~~~~~~~  261 (265)
                      +++++|.++++|++++....
T Consensus       238 ~~~~~~~~~~~e~~~~~~~~  257 (259)
T COG1192         238 KAAEEYYELAKELLEELLKL  257 (259)
T ss_pred             HHHHHHHHHHHHHHHHHHHC
T ss_conf             57999999999999975431


No 12 
>PHA02518 ParA-like protein; Provisional
Probab=100.00  E-value=0  Score=302.29  Aligned_cols=210  Identities=26%  Similarity=0.371  Sum_probs=172.9

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCE
Q ss_conf             49999808898888999999999999879959999878776801121246333454116763025771210244444420
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNL   86 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l   86 (265)
                      |||+|+|+||||||||+|+|||++|+++|+||++||+|||++++.|+.......            +             
T Consensus         1 KIIav~n~KGGvGKTT~a~nLA~~la~~G~~VlliD~DpQ~s~~~w~~~r~~~~------------~-------------   55 (211)
T PHA02518          1 KIIAVLNQKGGAGKTTVATNLASWLHADGHKVLLVDLDPQGSSTDWAEAREEGE------------P-------------   55 (211)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHCCCCC------------C-------------
T ss_conf             989998089997499999999999997899489997799967889998522689------------9-------------


Q ss_pred             EECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             00148874577500012322221023332247651027820331013332222101123310011111231137888753
Q gi|254780806|r   87 SIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQL  166 (265)
Q Consensus        87 ~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~~~  166 (265)
                       ++|..    ...          ..+...+ ..+.++||||||||||+.+.++.+++.+||.+|+|+.|+.+++.++..+
T Consensus        56 -~~~~~----~~~----------~~~~~~l-~~~~~~yD~viID~pp~~~~~~~~al~aaD~vliP~~ps~~d~~~~~~~  119 (211)
T PHA02518         56 -LIPVV----RMG----------KSIRADL-PKVASGYDYVVVDGAPQDSELARAALRIADMVLIPVQPSPFDIWAAPDL  119 (211)
T ss_pred             -CCCHH----HCC----------HHHHHHH-HHHCCCCCEEEECCCCCCHHHHHHHHHHCCEEEEECCCCHHHHHHHHHH
T ss_conf             -74012----136----------7799999-9740678889988999742999999995896999637868789999999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCCHHHHH
Q ss_conf             35777655432026774310020231253100112689998808520156267868898777379857999799989999
Q gi|254780806|r  167 LETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGSQA  246 (265)
Q Consensus       167 ~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s~~a~~  246 (265)
                      ++.++..+. .+..+...+++.|+++.++...+++.+.+ +.++.+++.+.|+++..+.+|...|.||++|+|+++++++
T Consensus       120 ~~~i~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~~~~~l-~~~~~~v~~t~I~~r~~~~~a~~~G~~V~e~~~~~~aa~e  197 (211)
T PHA02518        120 VELIKARQE-VTDGLPKFAFIISRAIKNTQLYREARKAL-AGYGLPILRNGTTQRVAYADAAEAGGSVLELPEDDKAAEE  197 (211)
T ss_pred             HHHHHHHHH-HCCCCCEEEEEEECCCCCCHHHHHHHHHH-HHCCCCCCCCCCCCCHHHHHHHHCCCCHHEECCCCHHHHH
T ss_conf             999999998-66567516888623586656999999999-9869981068198878999999759976109979999999


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999998
Q gi|254780806|r  247 YLKLASELIQQER  259 (265)
Q Consensus       247 ~~~la~el~~~~~  259 (265)
                      |+.|++|+++|.+
T Consensus       198 ~~~L~~Eil~r~~  210 (211)
T PHA02518        198 IIQLVKELFRGIS  210 (211)
T ss_pred             HHHHHHHHHHHHC
T ss_conf             9999999998634


No 13 
>pfam00142 Fer4_NifH 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family.
Probab=100.00  E-value=0  Score=297.81  Aligned_cols=241  Identities=20%  Similarity=0.327  Sum_probs=178.9

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCC-CCHHHCCCCCCCCCCEEEEEECCCCHHHC----CCCC
Q ss_conf             499998088988889999999999998799599998787768-01121246333454116763025771210----2444
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGN-ASTGLGIELYDRKYSSYDLLIEEKNINQI----LIQT   81 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~-~~~~l~~~~~~~~~ti~~~l~~~~~l~~~----i~~~   81 (265)
                      |+|+| |+||||||||+|+|||.+||++|+||++||+|||++ .+..||..+   .+++++++.++..+.+.    ++..
T Consensus         1 r~iai-~GKGGVGKTTtsvNLA~aLA~~GkrVlliDaD~~~~~~~~llg~~~---~~~l~d~l~~~~~~~~~~~~~vi~~   76 (269)
T pfam00142         1 RKIAI-YGKGGIGKSTTSQNTSAALAEMGKKVLIVGCDPKADSTRLILGGKA---QPTIIDTLREKGLVEDVELEDVVKK   76 (269)
T ss_pred             CEEEE-ECCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHCCCCC---CCCHHHHHCCCCCCCCCCHHHHEEC
T ss_conf             95899-8999768899999999999987990999845899874144438988---8847877604677022407450133


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHH-HHHHCCCCCCEEEECCCCCC---CCCCHHHHHHHCCCCCCCCC
Q ss_conf             444200014887457750001232222102333224-76510278203310133322---22101123310011111231
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALS-VQLTSDFSYIFLDCPPSFNL---LTMNAMAAADSILVPLQCEF  157 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~-~~l~~~yD~IiiD~pp~~~~---~~~~al~aad~viip~~p~~  157 (265)
                      ...+++++|++....+...  ..  .......+.+. ...+++||||||||++.+..   ....+..+||.+++|++|++
T Consensus        77 ~~~gv~~i~~~~~e~~~~~--~~--~~~~~~~~~l~~~~~~~~~DyiliD~~g~~~~~~~~~~i~~~~A~~viiv~t~E~  152 (269)
T pfam00142        77 GYGGIRCVESGGPEPGVGC--AG--RGVITAIDLLEELGAYDDLDFVLYDVLGDVVCGGFAMPIREGKAQEVYIVTSGEM  152 (269)
T ss_pred             CCCCCEEEECCCCCCCCCC--CH--HHHHHHHHHHHHHCCHHCCCEEEEECCCCEEECCCCCCHHHCCCCEEEEEECCCH
T ss_conf             7787268868998656321--10--7899999999982102128889853367402434005334435887999828947


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEE
Q ss_conf             13788875335777655432026774310020231253100112689998808520156267868898777379857999
Q gi|254780806|r  158 FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIY  237 (265)
Q Consensus       158 ~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~  237 (265)
                      +|++++.++++.+.+.++..  ++++.|++.|+.  +....++..+++.+.++.++++ .||+|..+.+|...|+|+++|
T Consensus       153 ~al~~a~~l~~~i~~~~~~~--~~~i~giv~n~~--~~~~~~~~~~~~~~~~~~~~lg-~IP~d~~v~eA~~~g~pv~~~  227 (269)
T pfam00142       153 MALYAANNICKGILKYAKSG--GVRLGGLICNSR--KVDDERELIDAFAEALGTQMIH-FVPRDNIVQKAELNKQTVIEY  227 (269)
T ss_pred             HHHHHHHHHHHHHHHHHCCC--CCEEEEEEECCC--CCCHHHHHHHHHHHHHCCCEEE-ECCCCHHHHHHHHCCCCEEEE
T ss_conf             89999999999999985057--962789982686--5411579999999981994799-779982687542349817998


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             79998999999999999999986
Q gi|254780806|r  238 DLKCAGSQAYLKLASELIQQERH  260 (265)
Q Consensus       238 ~p~s~~a~~~~~la~el~~~~~~  260 (265)
                      +|+|++|++|++||+||+++.+.
T Consensus       228 ~P~S~~A~ay~~LA~~il~~~~~  250 (269)
T pfam00142       228 APTCNQAKEYRELARKIIENPEG  250 (269)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             99998999999999999858999


No 14 
>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=0  Score=294.63  Aligned_cols=239  Identities=22%  Similarity=0.346  Sum_probs=180.4

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEE----ECCCCHHHCCCCCC
Q ss_conf             49999808898888999999999999879959999878776801121246333454116763----02577121024444
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLL----IEEKNINQILIQTA   82 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l----~~~~~l~~~i~~~~   82 (265)
                      |+|+|. +||||||||+|+|||.+||+.|+||++||+|||++.+..+...  ...+++++.+    ....++.+++.+ .
T Consensus         2 r~Iai~-GKGGVGKTTtavNLA~aLa~~GkkVlliDaDpq~~~t~~l~g~--~~~~~~~~~l~~~~~~~~~~~~~i~~-~   77 (270)
T cd02040           2 RQIAIY-GKGGIGKSTTTQNLSAALAEMGKKVMIVGCDPKADSTRLLLGG--KAIPTVLDTLREKGEVELELEDVIFE-G   77 (270)
T ss_pred             CEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHCCC--CCCCCHHHHHHHCCCCCCCHHHHEEC-C
T ss_conf             589997-9985778999999999999879949998657998513465299--88882899887527776538896133-7


Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHH------HHHHCCCCCCCC
Q ss_conf             44200014887457750001232222102333224765102782033101333222210112------331001111123
Q gi|254780806|r   83 IPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMA------AADSILVPLQCE  156 (265)
Q Consensus        83 ~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~------aad~viip~~p~  156 (265)
                      .+|++++|++......+...... .....+.+.+. .++++||||||||   ++..+++.+.      .||.+++|++|+
T Consensus        78 ~~gv~~ip~~~~~~~~~~~gr~~-~~~~~ll~~l~-~~~~~~D~iliD~---lg~~~~~~~~~~i~~~~ad~viiv~t~e  152 (270)
T cd02040          78 FGGIKCVESGGPEPGVGCAGRGV-ITAINLLEELG-AYEDDLDFVIYDV---LGDVVCGGFAMPIREGKAQEIYIVTSGE  152 (270)
T ss_pred             CCCCEEEECCCCCCCCHHCCCCH-HHHHHHHHHHH-HHHCCCCEEEEEC---CCCCCCCHHHCHHHHCCCCEEEEECCCC
T ss_conf             67706410599643512124007-88999999854-3440698899823---5633321232303553388799962881


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEE
Q ss_conf             11378887533577765543202677431002023125310011268999880852015626786889877737985799
Q gi|254780806|r  157 FFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAII  236 (265)
Q Consensus       157 ~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~  236 (265)
                      ++|++++.++++.+..+++..+.  ++.+++.|+.  ++...++..+++.+.++.+++. .||++..+.+|..+|+|+++
T Consensus       153 ~~al~~~~~l~k~i~~~~~~~~~--~l~gvv~~~~--~~~~~~~~~~~~~~~~~~~~l~-~IP~d~~v~EA~~~g~pi~~  227 (270)
T cd02040         153 MMALYAANNICKGILKYAKSGGV--RLGGLICNSR--NTDREDELIDAFAKRLGTQMIH-FVPRDNVVQRAELRGKTVIE  227 (270)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCC--EEEEEEECCC--CCCHHHHHHHHHHHHHCCCEEE-ECCCCHHHHHHHHCCCEEEE
T ss_conf             89999999999999999834697--4799983786--6513789999999985995287-77997178751342970799


Q ss_pred             ECCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             97999899999999999999998
Q gi|254780806|r  237 YDLKCAGSQAYLKLASELIQQER  259 (265)
Q Consensus       237 ~~p~s~~a~~~~~la~el~~~~~  259 (265)
                      |+|+|++|++|++||+|++++.+
T Consensus       228 ~~P~S~~A~ay~~LA~eii~~~~  250 (270)
T cd02040         228 YDPESKQADEYRELARKIVENKL  250 (270)
T ss_pred             ECCCCHHHHHHHHHHHHHHHCCC
T ss_conf             79899899999999999984899


No 15 
>PRK13230 nitrogenase reductase-like protein; Reviewed
Probab=100.00  E-value=1.4e-45  Score=286.80  Aligned_cols=242  Identities=24%  Similarity=0.312  Sum_probs=177.6

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEEC----CCCHHHC-----
Q ss_conf             4999980889888899999999999987995999987877680112124633345411676302----5771210-----
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIE----EKNINQI-----   77 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~----~~~l~~~-----   77 (265)
                      |.|+|. +||||||||+|+|||.+||..|+|||+||||||+|+|..|+....  ..++++.+.+    ...+.+.     
T Consensus         2 ~~ia~y-GKGGVGKTTTavNLAaALA~~GkkVLlID~DPqgnaTs~L~~g~~--~~tv~d~~~~~~~~~~~l~~~~~~~~   78 (292)
T PRK13230          2 KQIAFY-GKGGIGKSTTVCNLAAALSKSGKKVIVVGCDPKHDCTSNLRGGED--IPTVLDVLREKGIDKLGIETIIRENL   78 (292)
T ss_pred             CEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCCCC--CCHHHHHHHHCCCCCCCHHHHCCCCC
T ss_conf             679991-799857898999999999987995999776797754253015987--75299999861754222333203244


Q ss_pred             -----CCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCC---CCCCCCHHHHHHHC
Q ss_conf             -----2444444200014887457750001232222102333224765102782033101333---22221011233100
Q gi|254780806|r   78 -----LIQTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSF---NLLTMNAMAAADSI  149 (265)
Q Consensus        78 -----i~~~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~---~~~~~~al~aad~v  149 (265)
                           ++....+++.+++++....+..............+.+ +.....-.|||+++|+++..   +..+-..+.+||.+
T Consensus        79 ~~~~dii~~~~~gv~~ve~g~~~~g~g~~gr~~~~~~~ll~~-~~~~~~~~~D~vl~D~lg~~~~~g~~~p~~~~~Ad~V  157 (292)
T PRK13230         79 LKKEDIIYEGFNGIYCVEAGGPKPGYGCAGRGVIVVIDLLKK-MNVFEELGVDVVLYDVLGDVVCGGFAMPLRMGLADQI  157 (292)
T ss_pred             CCHHHEEECCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHH-HCCHHHHCCCEEEECCCCCCCCCCCCCCCHHCCCCEE
T ss_conf             652322222678627861689876641131478999999998-1312330876575034355664642156202018989


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHH-HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf             111112311378887533577765543202677431002023125310-0112689998808520156267868898777
Q gi|254780806|r  150 LVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSL-SQQVVSDVRKNLGGKVYNTVIPRNVRISEAP  228 (265)
Q Consensus       150 iip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~-~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~  228 (265)
                      +||+++|.++++++.+++++++.++.+.+  ..+.|+|.|   .++.. ..++.++++++|+.+++.+ ||++..+++|.
T Consensus       158 lIp~q~E~~ALeg~~~l~~tI~~~~~~~~--~~l~Giv~n---~r~~l~~~~vv~e~~~~fg~~v~~~-IPrnv~l~EAp  231 (292)
T PRK13230        158 YVVTSSDYMALYAANNICKGIKQFAKRGG--STLGGIIYN---VRGSMDAFDIVSEFASKLNTNIIGK-VPNSNIINEAE  231 (292)
T ss_pred             EEEECCHHHHHHHHHHHHHHHHHHHHCCC--CEEEEEEEE---CCCCCCHHHHHHHHHHHHCCEEEEE-CCCCCHHHHCC
T ss_conf             99727389999999999999999984579--757999970---8988647899999999829915996-79960634143


Q ss_pred             HCCCCEEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             379857999799989999999999999999
Q gi|254780806|r  229 SYGKPAIIYDLKCAGSQAYLKLASELIQQE  258 (265)
Q Consensus       229 ~~g~pv~~~~p~s~~a~~~~~la~el~~~~  258 (265)
                      .+|+|+++|+|+|+.|++|++||+||++..
T Consensus       232 s~G~pvi~ydP~S~gA~aY~~LA~ei~en~  261 (292)
T PRK13230        232 IDGKTAIEYAPDSEISKIYRELAEKIYENN  261 (292)
T ss_pred             CCCCCEEEECCCCHHHHHHHHHHHHHHHCC
T ss_conf             049824897989978999999999999679


No 16 
>PRK11670 putative ATPase; Provisional
Probab=100.00  E-value=2.9e-44  Score=277.91  Aligned_cols=242  Identities=23%  Similarity=0.253  Sum_probs=183.7

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCC
Q ss_conf             8749999808898888999999999999879959999878776-801121246333454116763025771210244444
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAI   83 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~-~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~   83 (265)
                      -.+||+|+|+||||||||+|+|||.+||++|+||+++|+|.+| |++.+||.+...  .+..+    .    ..+.+...
T Consensus       106 v~~vIAVaSGKGGVGKSTvavNLA~ALA~~G~kVgllDADi~Gpsip~mlG~~~~~--~~~~d----~----~~i~P~~~  175 (369)
T PRK11670        106 VKNIIAVSSGKGGVGKSSTAVNLALALAAEGAKVGILDADIYGPSIPTMLGAENQR--PTSPD----G----THMAPIMA  175 (369)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHCCCCCC--CCCCC----C----CEECCCCC
T ss_conf             68899998589988899999999999996699378982478887650230665456--64688----9----66376000


Q ss_pred             CCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCC--CCCHHHHHHHCCCCCCCCCHHHH
Q ss_conf             4200014887457750001232222102333224765102782033101333222--21011233100111112311378
Q gi|254780806|r   84 PNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLL--TMNAMAAADSILVPLQCEFFALE  161 (265)
Q Consensus        84 ~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~--~~~al~aad~viip~~p~~~s~~  161 (265)
                      .++.+++-+.-........+..+.....+.+++....|++|||+|||||||+|+.  +.......+.+++|++|+..|+.
T Consensus       176 ~gi~~~S~g~l~~~~~~~iwRgp~~~~al~q~l~~~~wg~lDyLIID~PPGtgDi~Ltl~q~v~~~gavvVTTPq~~Al~  255 (369)
T PRK11670        176 HGLATNSIGYLVTDDNAMVWRGPMASKALMQMLQETLWPDLDYLVLDMPPGTGDIQLTLAQNIPVTGAVVVTTPQDIALI  255 (369)
T ss_pred             CCEEEEECCCCCCCCCCHHHCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEEECCCCHHHHH
T ss_conf             58125302202376640222130167999998777433788889983799875277788764576607996277376999


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCEE---ECCCHHH-----HHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCC
Q ss_conf             887533577765543202677431002023---1253100-----11268999880852015626786889877737985
Q gi|254780806|r  162 GLSQLLETVEEVRRTVNSALDIQGIILTMF---DSRNSLS-----QQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKP  233 (265)
Q Consensus       162 ~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~---~~~~~~~-----~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~p  233 (265)
                      ++.+.+.++++.      +++++|+|.||.   .++....     +.-.+++.+.|+.++++ .||.|..+.++.+.|+|
T Consensus       256 Da~k~i~m~~k~------~vpilGiVeNMs~~~c~~c~~~~~iFg~gg~e~~a~~~~v~lLG-~IP~d~~I~ea~d~G~P  328 (369)
T PRK11670        256 DAKKGIVMFEKV------EVPVLGIVENMSMHICSNCGHHEPIFGTGGAEKLAEKYHTQLLG-QMPLHISLREDLDRGTP  328 (369)
T ss_pred             HHHHHHHHHHHC------CCCCEEEEECCCCCCCCCCCCCCEECCCCCHHHHHHHHCCCEEE-ECCCCHHHHHHCCCCCC
T ss_conf             999999999854------88850688636333368999710013666099999983998799-79898899961859985


Q ss_pred             EEEECCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             799979998999999999999999986774
Q gi|254780806|r  234 AIIYDLKCAGSQAYLKLASELIQQERHRKE  263 (265)
Q Consensus       234 v~~~~p~s~~a~~~~~la~el~~~~~~~~~  263 (265)
                      ++.+.|+|+++++|++||+++.++.-.+.+
T Consensus       329 vV~~~P~S~aA~Af~~iA~~la~~~~~~~~  358 (369)
T PRK11670        329 TVVSRPESEFTAIYRQLADRVAAQLYWQGE  358 (369)
T ss_pred             EEEECCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             698289998999999999999999965146


No 17 
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=100.00  E-value=7e-45  Score=281.70  Aligned_cols=242  Identities=29%  Similarity=0.419  Sum_probs=200.3

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC-CCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC-C
Q ss_conf             7499998088988889999999999998799599998787-7680112124633345411676302577121024444-4
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP-QGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA-I   83 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~-q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~-~   83 (265)
                      +|+|+|.|+||||||||+++||+.+||++|+||++||+|. ..|++..+|++.. .-|++.|++.+++.+++++++.+ .
T Consensus         2 ~~iIVvTSGKGGVGKTTttAnig~aLA~~GkKv~liD~DiGLRNLDlimGlE~R-iVYd~vdVi~g~~~l~QALIkDKr~   80 (272)
T COG2894           2 ARIIVVTSGKGGVGKTTTTANIGTALAQLGKKVVLIDFDIGLRNLDLIMGLENR-IVYDLVDVIEGEATLNQALIKDKRL   80 (272)
T ss_pred             CEEEEEECCCCCCCCCCHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHCCCCE-EEEEEHHHHCCCCCHHHHHHCCCCC
T ss_conf             649999448887674310677899999739859999667672044666434201-5654013444766365676403567


Q ss_pred             CCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH-CCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHH
Q ss_conf             42000148874577500012322221023332247651-02782033101333222210112331001111123113788
Q gi|254780806|r   84 PNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLT-SDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEG  162 (265)
Q Consensus        84 ~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~-~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~  162 (265)
                      +||.++|+++.......    .++....+.+    .+. .+||||++|||+|+.....+|++.||..++|++|+..|+++
T Consensus        81 ~nL~lLPAsQtrdKdal----t~E~v~~vv~----eL~~~~fDyIi~DsPAGIE~G~~~A~~~Ad~AiVVtnPEvSsVRD  152 (272)
T COG2894          81 ENLFLLPASQTRDKDAL----TPEGVKKVVN----ELKAMDFDYIIIDSPAGIEQGFKNAVYFADEAIVVTNPEVSSVRD  152 (272)
T ss_pred             CCEEECCCCCCCCCCCC----CHHHHHHHHH----HHHHCCCCEEEECCCCHHHHHHHHHHHCCCEEEEECCCCCCCCCC
T ss_conf             85266144323672227----9999999999----997669988996484067788886541026379974887554234


Q ss_pred             HHHHHHHHHHHHHHH--HCCCCCCCCCCCEEECCCHHHHHH--HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEEC
Q ss_conf             875335777655432--026774310020231253100112--6899988085201562678688987773798579997
Q gi|254780806|r  163 LSQLLETVEEVRRTV--NSALDIQGIILTMFDSRNSLSQQV--VSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYD  238 (265)
Q Consensus       163 ~~~~~~~i~~~~~~~--~~~~~~~~iv~N~~~~~~~~~~~~--~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~  238 (265)
                      +.|++..++....+.  +..+ ..++++||+++.....-++  .+++.+.+..++++ +||+|+.+.+|++.|.|+.. .
T Consensus       153 sDRiiGlLesk~~rae~~~~~-~~~llvnR~~p~~v~~GeMlsv~Dv~~iL~i~liG-iiPed~~Vi~asN~GePv~l-~  229 (272)
T COG2894         153 SDRIIGLLESKSRRAEIGEEP-KEHLLLNRYRPEMVKRGEMLSVEDVLEILSIPLIG-VIPEDQDVLRASNKGEPVIL-D  229 (272)
T ss_pred             CHHHEEEHHCCCCHHHCCCCC-CCEEEEECCCHHHHCCCCCCCHHHHHHHHCCCEEE-EECCCHHHEEECCCCCCEEE-C
T ss_conf             112202012145423307766-63489971688881157725399999974774477-60485333000478887675-7


Q ss_pred             CCCHHHHHHHHHHHHHHHHHH
Q ss_conf             999899999999999999998
Q gi|254780806|r  239 LKCAGSQAYLKLASELIQQER  259 (265)
Q Consensus       239 p~s~~a~~~~~la~el~~~~~  259 (265)
                      +++.++++|.++|++|++++.
T Consensus       230 ~~~~a~~Ay~d~arRllGe~v  250 (272)
T COG2894         230 DNSDAGKAYRDIARRLLGEEV  250 (272)
T ss_pred             CCCHHHHHHHHHHHHHHCCCC
T ss_conf             875177999999999708886


No 18 
>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=1.3e-43  Score=274.17  Aligned_cols=178  Identities=31%  Similarity=0.463  Sum_probs=151.3

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCE
Q ss_conf             999980889888899999999999987995999987877-6801121246333454116763025771210244444420
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNL   86 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l   86 (265)
                      ||+|+|+||||||||+|+|||++||++|+||++||+||| ++++..++.+.. ..+++                     .
T Consensus         1 iIav~s~KGGVGKTT~a~NLA~aLa~~g~~vllvD~D~~~~~l~~~~~~~~~-~~~~~---------------------~   58 (179)
T cd02036           1 VIVVTSGKGGVGKTTTTANLGTALAQLGYKVVLIDADLGLRNLDLILGLENR-VVYTL---------------------H   58 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCC-CCCHH---------------------H
T ss_conf             9899739998709999999999999779918999589999983666176556-65313---------------------1


Q ss_pred             EECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             00148874577500012322221023332247651027820331013332222101123310011111231137888753
Q gi|254780806|r   87 SIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQL  166 (265)
Q Consensus        87 ~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~~~  166 (265)
                      ++++                                 .|||||||||+++..+.+++.+||.+++|++|+.+|++++.++
T Consensus        59 ~vl~---------------------------------gD~viiD~ppg~~~~~~~~l~~ad~vlvv~~p~~~sl~~~~~~  105 (179)
T cd02036          59 DVLA---------------------------------GDYILIDSPAGIERGFITAIAPADEALLVTTPEISSLRDADRV  105 (179)
T ss_pred             CCCC---------------------------------CCEEEEECCCCCCHHHHHHHHHCCCCEECCCCCHHHHHHHHHH
T ss_conf             1266---------------------------------9999997999988899999984681256378858899999999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCCHHHHH
Q ss_conf             35777655432026774310020231253100112689998808520156267868898777379857999799989999
Q gi|254780806|r  167 LETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGSQA  246 (265)
Q Consensus       167 ~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s~~a~~  246 (265)
                      .+++++.      +.+..++|+||++++....++..+++++.++.+++. .||+|..+.+|...|+|+.++.|+|+++++
T Consensus       106 ~~~~~~~------~~~~~~vv~Nr~~~~~~~~~~~~~~~~~~l~~~vlg-~IP~d~~v~eA~~~g~Pv~~~~P~s~aA~a  178 (179)
T cd02036         106 KGLLEAL------GIKVVGVIVNRVRPDMVEGGDMVEDIEEILGVPLLG-VIPEDPAVIRATNRGEPVVLNKPKSPAAQA  178 (179)
T ss_pred             HHHHHHC------CCCEEEEEECCCCCCCCCHHHHHHHHHHHCCCCEEE-ECCCCHHHHHHHHCCCEEEEECCCCHHHHC
T ss_conf             9999825------996469998454676663677999999855996798-877988999987679538987999956630


Q ss_pred             H
Q ss_conf             9
Q gi|254780806|r  247 Y  247 (265)
Q Consensus       247 ~  247 (265)
                      |
T Consensus       179 y  179 (179)
T cd02036         179 Y  179 (179)
T ss_pred             C
T ss_conf             9


No 19 
>PRK13232 nifH nitrogenase reductase; Reviewed
Probab=100.00  E-value=1.2e-42  Score=268.41  Aligned_cols=237  Identities=23%  Similarity=0.376  Sum_probs=181.2

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHH-CCCCCCCCCCEEEEEECC----CCHHHCCCCC
Q ss_conf             49999808898888999999999999879959999878776801121-246333454116763025----7712102444
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGL-GIELYDRKYSSYDLLIEE----KNINQILIQT   81 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l-~~~~~~~~~ti~~~l~~~----~~l~~~i~~~   81 (265)
                      |-|+|. +|||+||||+|+|||.+||+.|+||++||||||++.|..+ |...   .+|+.|.+.+.    .++++.+. .
T Consensus         2 ~~iaiy-GKGGVGKSTTt~NLaAALA~~GkkVL~IgcDPk~dsT~~l~gg~~---~~tvld~l~~~~~~~~~l~~v~~-~   76 (273)
T PRK13232          2 RQIAIY-GKGGIGKSTTTQNLTAALSTMGNKILLVGCDPKADSTRMLLGGLN---QKTVLDTLRSEGDEGVDLDVVMQ-P   76 (273)
T ss_pred             CEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHCCCC---CCCHHHHHHHCCCCCCCHHHEEE-C
T ss_conf             579997-998665887899999999977996999897884427778858998---88799999861856563666154-2


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHH------HHHHCCCCCCC
Q ss_conf             444200014887457750001232222102333224765102782033101333222210112------33100111112
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMA------AADSILVPLQC  155 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~------aad~viip~~p  155 (265)
                      ...++.+++++....+........... ..+.+.+. .+.++|||||+|+   ++..+++++.      .|+.+++|+++
T Consensus        77 g~~gv~cve~ggp~~g~gcagrgii~~-~~lle~l~-~~~~~~Dyvl~Dv---lgdvvcggfa~P~~~~~A~evlIVts~  151 (273)
T PRK13232         77 GFGDIKCVESGGPEPGVGCAGRGIITS-IGLLENLG-AYTDDLDYVFYDV---LGDVVCGGFAMPIREGKAKEIYIVASG  151 (273)
T ss_pred             CCCCEEEEECCCCCCCCCCCCHHHHHH-HHHHHHCC-CCCCCCCEEEEEC---CCCCCCCCCCCCCCCCCCCEEEEEECC
T ss_conf             889738986899876765453047888-88999708-3214798899941---473323653144201657689998076


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEE
Q ss_conf             31137888753357776554320267743100202312531001126899988085201562678688987773798579
Q gi|254780806|r  156 EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAI  235 (265)
Q Consensus       156 ~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~  235 (265)
                      |++|++++.++.+.++++.+.   ..++.|+|.|+-+  ....+++.+++.++++.+++. +||+|..+++|..+|+|++
T Consensus       152 E~~slyaannI~k~i~~~~~~---~~rl~GiI~n~r~--~~~~~e~v~~fa~~~g~~vi~-~IPr~~~v~~A~~~g~tvi  225 (273)
T PRK13232        152 ELMAIYAANNICKGLAKFAKG---GARLGGIICNSRN--VDGERELLEAFAKKLGSQLIH-FVPRDNIVQRAEINRKTVI  225 (273)
T ss_pred             CHHHHHHHHHHHHHHHHHHHC---CCCEEEEEEECCC--CCCHHHHHHHHHHHCCCCEEE-ECCCCHHHHHHHHCCCEEE
T ss_conf             088899999999999999621---8850148850557--763899999999971996699-7899778876487298358


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             997999899999999999999998
Q gi|254780806|r  236 IYDLKCAGSQAYLKLASELIQQER  259 (265)
Q Consensus       236 ~~~p~s~~a~~~~~la~el~~~~~  259 (265)
                      +|+|+|+.|++|++||++|.++.+
T Consensus       226 e~~P~S~~A~aY~~LA~~I~~~~~  249 (273)
T PRK13232        226 DFDPESNQAKEYLTLAHNVQNNDK  249 (273)
T ss_pred             EECCCCHHHHHHHHHHHHHHHCCC
T ss_conf             979999799999999999985899


No 20 
>PRK13235 nifH nitrogenase reductase; Reviewed
Probab=100.00  E-value=4.1e-42  Score=265.33  Aligned_cols=238  Identities=21%  Similarity=0.327  Sum_probs=180.2

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHH-CCCCCCCCCCEEEEEEC---CCCHHHCCCCCC
Q ss_conf             49999808898888999999999999879959999878776801121-24633345411676302---577121024444
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGL-GIELYDRKYSSYDLLIE---EKNINQILIQTA   82 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l-~~~~~~~~~ti~~~l~~---~~~l~~~i~~~~   82 (265)
                      |-|+|. +|||+||||+|+|||.+||++|+||++||||||++.|..+ |..   ...|+.|.+..   ...+++++. ..
T Consensus         2 ~~iaiy-GKGGVGKSTtt~NLaAALA~~GkkVl~IgcDPk~dsT~~L~gg~---~~~tvld~l~~~~~~~~ledvi~-~g   76 (274)
T PRK13235          2 RKVAIY-GKGGIGKSTTTQNTVAGLAEMGKKVMVVGCDPKADSTRLLLGGL---QQKTVLDTLREEGEDVELEDIIK-EG   76 (274)
T ss_pred             CEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHCCC---CCCCHHHHHHHCCCCCCHHHHEE-EC
T ss_conf             679997-99855476789999999997899799989898453667873899---89978999986287767789443-17


Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH-HCCCCCCEEEECCCCCCCCCCHHH------HHHHCCCCCCC
Q ss_conf             44200014887457750001232222102333224765-102782033101333222210112------33100111112
Q gi|254780806|r   83 IPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQL-TSDFSYIFLDCPPSFNLLTMNAMA------AADSILVPLQC  155 (265)
Q Consensus        83 ~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l-~~~yD~IiiD~pp~~~~~~~~al~------aad~viip~~p  155 (265)
                      ..++.+++++....+....-.........|. .+.... ..+||||++||   ++..+++++.      +||.++||+++
T Consensus        77 ~~gi~cveaggp~pg~gcagrgii~~~~~L~-~l~~~~~~~~~DyVl~Dv---LGdvvcggFa~pir~~~A~eV~IVts~  152 (274)
T PRK13235         77 YGNTRCTESGGPEPGVGCAGRGIITSVNLLE-QLGAYDDEWNLDYVFYDV---LGDVVCGGFAMPIRDGKAEEIYIVCSG  152 (274)
T ss_pred             CCCEEEEECCCCCCCCCCCCCHHHHHHHHHH-HCCCCCCCCCCCEEEEEC---CCCCCCCCCCCCCCCCCCCEEEEEECC
T ss_conf             8981898689987566757631525899998-817754335776899813---785312451155100658789999168


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEE
Q ss_conf             31137888753357776554320267743100202312531001126899988085201562678688987773798579
Q gi|254780806|r  156 EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAI  235 (265)
Q Consensus       156 ~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~  235 (265)
                      |++|++++.++.+.+++++++.+  .++.|++.|+.+..  ..++..+++.+.++.+++. +||+|..+++|..+|+||+
T Consensus       153 E~~AL~aannI~k~i~~~~~~~~--~~l~Gii~N~r~~~--~~~~~v~~fa~~~g~~vi~-~IPr~~~V~~Ae~~~~tVi  227 (274)
T PRK13235        153 EMMAMYAANNICKGILKYADAGG--VRLGGLICNSRKVD--NEREMIEELARKLGTQMIH-FVPRDNMVQRAEINRKTVI  227 (274)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCC--CEEEEEEEECCCCC--CHHHHHHHHHHHCCCCEEE-ECCCCHHHHHHHHCCCEEE
T ss_conf             36899999999999999974379--54889997367787--5789999999974993699-7589458899987397789


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             99799989999999999999999
Q gi|254780806|r  236 IYDLKCAGSQAYLKLASELIQQE  258 (265)
Q Consensus       236 ~~~p~s~~a~~~~~la~el~~~~  258 (265)
                      +|+|+|+.|++|++||++|++.+
T Consensus       228 e~~P~S~~A~~Yr~LA~~I~~n~  250 (274)
T PRK13235        228 DYDPTHGQADEYRALARKIDENE  250 (274)
T ss_pred             EECCCCHHHHHHHHHHHHHHHCC
T ss_conf             97899879999999999998389


No 21 
>PRK10037 cell division protein; Provisional
Probab=100.00  E-value=1.3e-42  Score=268.24  Aligned_cols=236  Identities=19%  Similarity=0.243  Sum_probs=184.6

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCE
Q ss_conf             49999808898888999999999999879959999878776801121246333454116763025771210244444420
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNL   86 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l   86 (265)
                      |+|++.|.||||||||+|+|||++|++.|++|++||+|||..+..+||++..+. .++...+.+..++.+++.+ +.+|+
T Consensus         2 ~iial~s~kGGVGkTTltAnLA~aL~~~g~~VlaID~dpqN~Lrlhfg~~~~~~-~Gwa~a~l~g~~W~~a~~~-~~~gl   79 (250)
T PRK10037          2 AILGLQGVRGGVGTTSITAALAWSLQMLGENVLVIDACPDNLLRLSFNVDFTHR-QGWARALLDGQDWRDAGLR-YTSQL   79 (250)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHCCCCCCCC-CCHHHHHHCCCCHHHHHHH-CCCCC
T ss_conf             379996078887689999999999997799189995782566787549985447-7299998569978999850-56993


Q ss_pred             EECCCCCCCCCCCCCCCCC-CCCCHHHHHHH-HHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             0014887457750001232-22210233322-476510278203310133322221011233100111112311378887
Q gi|254780806|r   87 SIIPSTMDLLGIEMILGGE-KDRLFRLDKAL-SVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLS  164 (265)
Q Consensus        87 ~iipa~~~~~~~~~~l~~~-~~~~~~l~~~l-~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~  164 (265)
                      +++|.+. +...+....+. ......+...+ ......+||+|||||||+.++.+..++..||.+++|+.||..|.--+.
T Consensus        80 ~~LPfG~-l~~~~~~~~~~~~~~~~~l~~~l~~l~~~~~~~~vliD~P~g~s~~~~~~l~~AD~vLvVv~aDa~s~~~L~  158 (250)
T PRK10037         80 DLLPFGQ-LSIEEQENPQHWQTTLGDICSALQQLKASGRYQWILLDLPRGASPLTRQLLSLCDHSLAIVNVDANCHIRLH  158 (250)
T ss_pred             EEEECCC-CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHCCEEEEEECCCHHHHHHHH
T ss_conf             6972787-998998638877651799999986200257899899965999829999999857878998367877899873


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCCHHH
Q ss_conf             53357776554320267743100202312531001126899988085201562678688987773798579997999899
Q gi|254780806|r  165 QLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGS  244 (265)
Q Consensus       165 ~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s~~a  244 (265)
                      +         +...   .-.++++|++++.+.+++++...+++..+ ..++.+|++|+++.||..+++|+.+|+|.|.++
T Consensus       159 q---------~~~~---~g~~~liNq~~~~s~l~~Dl~~l~~q~~~-~llp~~IHrDeav~EAlA~~~~v~~y~P~SqAa  225 (250)
T PRK10037        159 Q---------QALP---AGAHILINDLRIGSQLQDDLYQLWLQSQR-RLLPMLIHRDEAMAECLAAKQPLGEYRSDSLAA  225 (250)
T ss_pred             H---------HCCC---CCCCEEECCCCCHHHHHHHHHHHHHHHCC-CCCCEEECCCCHHHHHHHCCCCCCCCCCCCHHH
T ss_conf             4---------2147---89827751667110466999999997442-415567517546899986599874759757788


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999999999999
Q gi|254780806|r  245 QAYLKLASELIQQE  258 (265)
Q Consensus       245 ~~~~~la~el~~~~  258 (265)
                      ++|..||.|.+-..
T Consensus       226 ~D~~~LA~W~l~~~  239 (250)
T PRK10037        226 EEILTLANWCLLHY  239 (250)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999999860


No 22 
>PRK13233 nifH nitrogenase reductase; Reviewed
Probab=100.00  E-value=2.5e-41  Score=260.72  Aligned_cols=239  Identities=21%  Similarity=0.331  Sum_probs=182.8

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCCHH-HCCCCCCCCCCEEEEEEC----CCCHHHCCC
Q ss_conf             7499998088988889999999999998-7995999987877680112-124633345411676302----577121024
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLDPQGNASTG-LGIELYDRKYSSYDLLIE----EKNINQILI   79 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~D~q~~~~~~-l~~~~~~~~~ti~~~l~~----~~~l~~~i~   79 (265)
                      +|.|+|. +|||+||||+++|||.+||+ .|+||++||||||++.|.. ++..+   .+|+.|++.+    ...++++ +
T Consensus         2 ~~~iaiy-GKGGIGKSTTt~NLaaALA~l~GkrVl~IgcDPk~dST~~l~g~~~---~~tv~d~l~~~~~~~~~~e~i-i   76 (275)
T PRK13233          2 TRKIAIY-GKGGIGKSTTTQNTAAAMAHFHDKKVFIHGCDPKADSTRLILGGKP---QTTMMDTLRELGEEKVTPDKV-I   76 (275)
T ss_pred             CCEEEEE-CCCCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHCCCCC---CCCHHHHHHHCCCCCCCHHHH-H
T ss_conf             7389998-9985446545999999999647988999797887613677608987---883999998628875538888-7


Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHH------HHHHCCCCC
Q ss_conf             44444200014887457750001232222102333224765102782033101333222210112------331001111
Q gi|254780806|r   80 QTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMA------AADSILVPL  153 (265)
Q Consensus        80 ~~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~------aad~viip~  153 (265)
                      .+...|+.+++++....+........... ..+.+.+. .+.++||||++|+++   ..++..+.      .||.+++|+
T Consensus        77 ~~g~~gv~cVEaGgp~pG~gcagrgii~~-~~lle~~~-~~~~~~D~Vl~DvLG---dVvcGgFa~Pir~~~AdeV~IVt  151 (275)
T PRK13233         77 KTGFKGIRCVESGGPEPGVGCAGRGVITA-ITLMEEHG-AYEDDLDFVFFDVLG---DVVCGGFAMPIRDGKAQEVYIVA  151 (275)
T ss_pred             HCCCCCCEEEECCCCCCCCCCCCCCHHHH-HHHHHHHC-CCCCCCCEEEEECCC---CCCCCCCCCCCCCCCCCEEEEEE
T ss_conf             53789857986899986665576312358-88899809-743468889984156---11055510343136688899994


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCC
Q ss_conf             12311378887533577765543202677431002023125310011268999880852015626786889877737985
Q gi|254780806|r  154 QCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKP  233 (265)
Q Consensus       154 ~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~p  233 (265)
                      ++|++|+.++.++.+.+.++..+.+  .++.|+|.|+-+  .....+..+++.+.++.+++. +||+|..+++|..+|++
T Consensus       152 s~E~msL~aannI~~~l~~~~~~~~--~~l~Gii~N~r~--~~~e~~~v~~fa~~ig~~vi~-~IPr~~~V~~Ae~~~~t  226 (275)
T PRK13233        152 SGEMMALYAANNICKGLVKYAEQSG--VRLGGIICNSRN--VDGELELLEEFTDAIGTQLIH-FVPRDNIVQKAEFNKKT  226 (275)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCC--CEEEEEEEECCC--CCCHHHHHHHHHHHHCCCEEE-ECCCCHHHHHHHHCCCE
T ss_conf             6837999999999999999850589--638999971788--860799999999985995799-77897788877873976


Q ss_pred             EEEECCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             79997999899999999999999998
Q gi|254780806|r  234 AIIYDLKCAGSQAYLKLASELIQQER  259 (265)
Q Consensus       234 v~~~~p~s~~a~~~~~la~el~~~~~  259 (265)
                      |++|+|+|+.+++|++||++|++...
T Consensus       227 Vie~~P~S~~A~~Y~~LAk~I~~n~~  252 (275)
T PRK13233        227 VVEFDPTCNQAHEYKELARKIIENKN  252 (275)
T ss_pred             EEEECCCCHHHHHHHHHHHHHHHCCC
T ss_conf             79989999799999999999985899


No 23 
>COG0455 flhG Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]
Probab=100.00  E-value=4.8e-41  Score=259.12  Aligned_cols=236  Identities=26%  Similarity=0.378  Sum_probs=183.4

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHH-HHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC
Q ss_conf             874999980889888899999999-999987995999987877-680112124633345411676302577121024444
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLS-TALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA   82 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA-~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~   82 (265)
                      .+++|+|.|+||||||||+|+||+ ..++..|++|++||+|+. +|++..||++..  +.++.+++.++++++|+++++.
T Consensus         1 ~~~~Iav~SgKGGvGKTtitanlga~~~~~~~k~V~~iDaD~g~~nL~~~~g~~~~--~~~l~dvL~~~~~~~Di~~~~~   78 (262)
T COG0455           1 MTKVIAVVSGKGGVGKTTITANLGAALAALGGKVVLLIDADLGLGNLSLLLGVESK--PTTLHDVLAGEASIEDIIYETP   78 (262)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCHHHHHCCCCC--CCCHHHHHHCCCCHHHEEEECC
T ss_conf             97899998458875689899869999996489769999658888728888588888--5509999707787768023157


Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHH
Q ss_conf             44200014887457750001232222102333224765102782033101333222210112331001111123113788
Q gi|254780806|r   83 IPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEG  162 (265)
Q Consensus        83 ~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~  162 (265)
                      .+||++||++.++.++-..   .++   .+..++ ..+...||||+||||||++.-+..++..||.+|+|++|++.++.+
T Consensus        79 ~~gl~vipg~~~~~~~~~~---~~~---~~~~~~-~~l~~~~D~iliD~~aGl~~~~~~~~~~sd~~viVt~pe~~si~~  151 (262)
T COG0455          79 QDGLYVLPGGSGLEDLAKL---DPE---DLEDVI-KELEELYDYILIDTGAGLSRDTLSFILSSDELVIVTTPEPTSITD  151 (262)
T ss_pred             CCCEEEEECCCCHHHHHHC---CHH---HHHHHH-HHHHHCCCEEEEECCCCCCHHHHHHHHHCCCEEEEECCCCCHHHH
T ss_conf             6898996078876888616---988---899999-998752999999689996688899987368179992798520899


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCC--CCCCEEECCCHHHHHHHHHHHHH-HCCCCCCCCCCCCHHHHHHHHCCCCEEEECC
Q ss_conf             87533577765543202677431--00202312531001126899988-0852015626786889877737985799979
Q gi|254780806|r  163 LSQLLETVEEVRRTVNSALDIQG--IILTMFDSRNSLSQQVVSDVRKN-LGGKVYNTVIPRNVRISEAPSYGKPAIIYDL  239 (265)
Q Consensus       163 ~~~~~~~i~~~~~~~~~~~~~~~--iv~N~~~~~~~~~~~~~~~l~~~-~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p  239 (265)
                      +..+++.+.....      ...+  +|+||+++.. ..++....+.+. ...+.+ .++|++..+.++...|.|+..+.|
T Consensus       152 A~~~i~~~~~~~~------~~~~~~vV~N~v~~~~-e~~~~~~~~~~~~~~~~~~-~~i~~~~~v~~a~~~g~p~~~~~p  223 (262)
T COG0455         152 AYKTIKILSKLGL------DLLGRRVVLNRVRSTK-EGVDVAALLIQVVKQVPVL-QVIPFDPEVRRALAEGKPIVLYSP  223 (262)
T ss_pred             HHHHHHHHHHCCC------CCCCCEEEEEECCCCC-CHHHHHHHHHHHHHHCCCE-EEECCCHHHHHHHHCCCCEEEECC
T ss_conf             9999999997387------6433158997036666-5467899999999707743-471567578998624986797288


Q ss_pred             CCHHHHHHHHHHHHHHHH
Q ss_conf             998999999999999999
Q gi|254780806|r  240 KCAGSQAYLKLASELIQQ  257 (265)
Q Consensus       240 ~s~~a~~~~~la~el~~~  257 (265)
                      +|++++++++||..+.+.
T Consensus       224 ~s~as~ai~~lA~~l~~~  241 (262)
T COG0455         224 NSKASQAIKELAAKLAGL  241 (262)
T ss_pred             CCHHHHHHHHHHHHHHCC
T ss_conf             978999999999998605


No 24 
>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=100.00  E-value=7.6e-40  Score=252.12  Aligned_cols=204  Identities=34%  Similarity=0.464  Sum_probs=144.1

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCC---CEEEEEECCCCHHH-CCCC-CCC
Q ss_conf             999808898888999999999999879959999878776801121246333454---11676302577121-0244-444
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKY---SSYDLLIEEKNINQ-ILIQ-TAI   83 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~---ti~~~l~~~~~l~~-~i~~-~~~   83 (265)
                      |+|.|+||||||||+|+|||++||++|+||++||+|||++.+..|+........   +............+ .+.. ...
T Consensus         1 Iav~s~KGGVGKTT~a~nLA~~la~~G~rVlliD~D~q~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (212)
T pfam01656         1 IAIAGTKGGVGKTTLAANLARALAKRGYRVLLIDLDPQANLTSSLGKGPDLIDVLKEGLEIVDAQPLQHIAAAIVPSRNL   80 (212)
T ss_pred             CEEECCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHCCCCCCCCCCCCCCHHCCCCCHHHHHHEEECCCCC
T ss_conf             98976899806999999999999978997899838999962588658764344444410101121002456422245555


Q ss_pred             CCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHH
Q ss_conf             42000148874577500012322221023332247651027820331013332222101123310011111231137888
Q gi|254780806|r   84 PNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGL  163 (265)
Q Consensus        84 ~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~  163 (265)
                      ++++++|++..+...+...        .........++++||||||||||+++..+.+++.+||.+++|++|+..|++++
T Consensus        81 ~~l~l~p~~~~~~~~~~~~--------~~~~~~~~~~~~~~D~viiD~pp~~~~~~~~al~~ad~vivv~~p~~~sl~~~  152 (212)
T pfam01656        81 DPLLLIPSNLSLANFESEL--------ILEGGEEGLIKLAYDYVIIDGAPGLGELTANALVAADILVVPIEPEGVAVLGA  152 (212)
T ss_pred             CCEEEECCCHHHHHHHHHH--------HHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHCCCEEEEEECCCHHHHHHH
T ss_conf             8746533501566777777--------99999987666049989994799755999999983998999948976999999


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHH-HHHHHHHHHHHCCC--CCCCCCCCCHHHHH
Q ss_conf             75335777655432026774310020231253100-11268999880852--01562678688987
Q gi|254780806|r  164 SQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLS-QQVVSDVRKNLGGK--VYNTVIPRNVRISE  226 (265)
Q Consensus       164 ~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~-~~~~~~l~~~~~~~--v~~~~Ip~~~~i~~  226 (265)
                      .++++.+++++      +++.|+|+|||+.+...+ .+....+++..+.+  ++.++||+|..+.+
T Consensus       153 ~~l~~~~~~l~------~~~~gvV~N~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ip~d~~v~~  212 (212)
T pfam01656       153 QRLLELVERLG------LKILGVVLNKVDRGDERHLDKEIEALERKTGIPVLLLLGVIPRDLALSE  212 (212)
T ss_pred             HHHHHHHHHCC------CCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCC
T ss_conf             99999999859------9622999914889983663078999999978997514041168776687


No 25 
>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=1.3e-37  Score=239.15  Aligned_cols=234  Identities=22%  Similarity=0.234  Sum_probs=176.7

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCC------CHHHCCCCC
Q ss_conf             99998088988889999999999998799599998787768011212463334541167630257------712102444
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEK------NINQILIQT   81 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~------~l~~~i~~~   81 (265)
                      +|+|. +|||+||||+|+||+.+||++|+||++|||||..+.+..|.-   ...+|+.|++.+.+      .+++.+. .
T Consensus         2 kiaiy-GKGGIGKSTttaNl~aaLA~~G~kVl~IgcDpk~Dst~~L~g---~~~~tvld~l~~~~~~~~~~~~~d~v~-~   76 (267)
T cd02032           2 VLAVY-GKGGIGKSTTSSNLSVALAKRGKKVLQIGCDPKHDSTFTLTG---FLIPTVIDILEEVDFHYEELWPEDVIY-E   76 (267)
T ss_pred             EEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHCC---CCCCCHHHHHHHHCCCHHHCCHHHHHH-C
T ss_conf             79997-799657877899999999987995999778995155675269---886839999986088666414778753-0


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHH-HHHCCCCCCEEEECCCCC-CCCCCHHHHHHHCCCCCCCCCHH
Q ss_conf             4442000148874577500012322221023332247-651027820331013332-22210112331001111123113
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSV-QLTSDFSYIFLDCPPSFN-LLTMNAMAAADSILVPLQCEFFA  159 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~-~l~~~yD~IiiD~pp~~~-~~~~~al~aad~viip~~p~~~s  159 (265)
                      ...|+.++.++..-.+....-....    ...+.|.. .+.++||||++|+++..- -.+.+.+..||.+++|++||++|
T Consensus        77 g~~gv~cvEaGgP~pg~Gcagrgi~----~~~~lL~~l~~~~~~D~Vl~DvlgdVvcgGFa~pi~~Ad~~~iVTs~e~~s  152 (267)
T cd02032          77 GYGGVDCVEAGGPPAGAGCGGYVVG----ETVKLLKELNLFEEYDVILFDVLGDVVCGGFAAPLNYADYALIVTDNDFDS  152 (267)
T ss_pred             CCCCCEEEECCCCCCCCCCCCCCHH----HHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCEEEEEECCCHHH
T ss_conf             7678457665899999887764048----999999871664347789995366544566567610068899995671878


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECC
Q ss_conf             78887533577765543202677431002023125310011268999880852015626786889877737985799979
Q gi|254780806|r  160 LEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDL  239 (265)
Q Consensus       160 ~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p  239 (265)
                      ++.+.++.+.++....+.+  .+..|+|.|+.+     .+++++++.+.++.+++. +||+|..+.+|...|+||+++.|
T Consensus       153 l~aAn~I~~~i~~~~~~~~--~rl~GlI~Nr~~-----~~~~i~~fa~~lg~~lig-~VP~d~~V~~se~~g~tvie~~p  224 (267)
T cd02032         153 IFAANRIAAAVREKAKTYK--VRLAGLIANRTD-----KTDLIDKFVEAVGMPVLA-VLPLIEDIRRSRVKGKTLFEMDE  224 (267)
T ss_pred             HHHHHHHHHHHHHHHHCCC--CCCCEEEEECCC-----CHHHHHHHHHHHCCCEEE-ECCCCHHHHHHHHCCCEEEEECC
T ss_conf             9999999999999753379--764227874698-----578999999972994699-66993388999873986898489


Q ss_pred             CCH----HHHHHHHHHHHHHHHH
Q ss_conf             998----9999999999999999
Q gi|254780806|r  240 KCA----GSQAYLKLASELIQQE  258 (265)
Q Consensus       240 ~s~----~a~~~~~la~el~~~~  258 (265)
                      +++    .++.|++||+.|++..
T Consensus       225 ~~~~~s~~a~~Yr~LA~~i~~n~  247 (267)
T cd02032         225 SDEELAYRCDYYLLIADQLLAGP  247 (267)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             98437899999999999998399


No 26 
>PRK13231 nitrogenase reductase-like protein; Reviewed
Probab=100.00  E-value=7.9e-37  Score=234.51  Aligned_cols=233  Identities=20%  Similarity=0.305  Sum_probs=177.7

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCC--CHHHCCCCCCC
Q ss_conf             7499998088988889999999999998799599998787768011212463334541167630257--71210244444
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEK--NINQILIQTAI   83 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~--~l~~~i~~~~~   83 (265)
                      -|.|+|. +|||+||||+++|||.+|| .|+||++|||||+++.|..|.-.   ..+|+.+.+.+..  ++.+.+.+ .+
T Consensus         2 m~~iAiy-GKGGIGKSTt~~NlaaalA-~g~rVl~igcDpk~dst~~L~G~---~~ptvl~~l~~~~~~~~~dvv~~-g~   75 (264)
T PRK13231          2 LKKIAIY-GKGGIGKSTTVSNMAAAYS-SDNSTLVIGCDPKADTTRTLVGK---RIPTVLDTLKDNRQPELEDIIYE-GY   75 (264)
T ss_pred             CEEEEEE-CCCCCCHHHHHHHHHHHHH-CCCCEEEECCCCCCCHHHHHHCC---CCCCHHHHHHHCCCCCHHHHEEE-CC
T ss_conf             4289997-8985478889999999998-79977998568885024676199---98838898631277776563121-78


Q ss_pred             CCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHH------HHHHHCCCCCCCCC
Q ss_conf             420001488745775000123222210233322476510278203310133322221011------23310011111231
Q gi|254780806|r   84 PNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAM------AAADSILVPLQCEF  157 (265)
Q Consensus        84 ~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al------~aad~viip~~p~~  157 (265)
                      .|+.+++++..-.+....-.........|.+ + ..++.++|||++|+.+..   ++..+      ..||.+++|+++|+
T Consensus        76 ~gi~cvesGgpepg~gcagrgi~~~~~lLe~-~-~~~~~~~D~vl~Dvlgdv---vcggfa~Pir~~~Adev~IVts~e~  150 (264)
T PRK13231         76 NNTLCVESGGPEPGVGCAGRGVIVAMNLLEK-L-GVFDNDPDVVIYDVLGDV---VCGGFSVPLREDYADEVYIVTSGEY  150 (264)
T ss_pred             CCEEEEECCCCCCCCCCCCCHHHHHHHHHHH-H-CCCCCCCCEEEEECCCCC---CCCCEECCCCCCCCCEEEEEECCCH
T ss_conf             9849973799887766565217689899987-2-642247987999435872---0566704554266988999947858


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEE
Q ss_conf             13788875335777655432026774310020231253100112689998808520156267868898777379857999
Q gi|254780806|r  158 FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIY  237 (265)
Q Consensus       158 ~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~  237 (265)
                      +|+.++.++.+.+++++.      ++.|+|.|+.+..  ...++.+++.+.+|.+++. .||++..+++|...|+||+++
T Consensus       151 msLyaAnnI~~~i~~~~~------rl~GiI~N~r~~~--~e~~iv~~fa~~~g~~vl~-~IPr~~~V~~ae~~~~tVie~  221 (264)
T PRK13231        151 MSLYAANNIAKGIKKLKG------KLGGIICNCRNVK--NEVEIVSEFASLIGSRIIG-IIPRSNLVQESELKASTVVET  221 (264)
T ss_pred             HHHHHHHHHHHHHHHHCC------CCCEEEEECCCCC--CHHHHHHHHHHHCCCCEEE-ECCCCHHHHHHHHCCCEEEEE
T ss_conf             999999999999999546------4420896068988--7799999999971996899-668947888888629758997


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q ss_conf             799989999999999999999
Q gi|254780806|r  238 DLKCAGSQAYLKLASELIQQE  258 (265)
Q Consensus       238 ~p~s~~a~~~~~la~el~~~~  258 (265)
                      .|.|+.++.|++||++|.+..
T Consensus       222 ~P~S~~A~~Yr~LA~~I~~~~  242 (264)
T PRK13231        222 FPESSQASIYSELANNIMNNQ  242 (264)
T ss_pred             CCCCHHHHHHHHHHHHHHHCC
T ss_conf             989889999999999998589


No 27 
>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=100.00  E-value=9.5e-38  Score=239.87  Aligned_cols=201  Identities=23%  Similarity=0.354  Sum_probs=150.8

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEEC-----CCCHHHCCCCC
Q ss_conf             4999980889888899999999999987995999987877680112124633345411676302-----57712102444
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIE-----EKNINQILIQT   81 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~-----~~~l~~~i~~~   81 (265)
                      |.|+|. +||||||||+++|||.+||++||||++||||||++.+..+.-.  ...+++.+++..     +..+++.+. +
T Consensus         1 ~~iaiy-GKGGVGKTTts~NLaaaLA~~G~rVl~iD~Dp~~~st~~L~g~--~~~~~i~~~~~~~~~~~~~~~~~ii~-~   76 (212)
T cd02117           1 RQIAIY-GKGGIGKSTTSQNLSAALAEMGKKVLQVGCDPKADSTRLLLGG--KAPTTILELAAEDGHVEDLELEDVIF-E   76 (212)
T ss_pred             CEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCHHHCCC--CCCCCHHHHHHHHCCCCCEEEEEEEE-E
T ss_conf             959998-8983568778999999999869969999038998733031199--77871999987527866445667899-6


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHH------HHHCCCCCCC
Q ss_conf             4442000148874577500012322221023332247651027820331013332222101123------3100111112
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAA------ADSILVPLQC  155 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~a------ad~viip~~p  155 (265)
                      ...|++++|++....+.+............+.+ +. ..+++||||||||   ++..+++++.+      ||.+++|++|
T Consensus        77 g~~gv~~veaggp~~g~~~ag~~i~~~~~ll~~-~~-~~~~~~D~IliD~---lGdvv~~gf~~pi~~~~Ad~vlIvtt~  151 (212)
T cd02117          77 GFGGVKCVESGGPEPGVGCAGRGVITAVNLLEK-EG-FAEDDLDVVLYDV---LGDVVCGGFAMPIREGKADEIYIVTSG  151 (212)
T ss_pred             CCCCEEEEECCCCCCCCCCCCCHHHHHHHHHHH-HH-HHCCCCCEEEEEC---CCCCEECCCCCCCCCCCCCEEEEECCC
T ss_conf             688708998899776765454117889999997-41-0025799999965---885403563343211668889998069


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             311378887533577765543202677431002023125310011268999880852015626786
Q gi|254780806|r  156 EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRN  221 (265)
Q Consensus       156 ~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~  221 (265)
                      |++|++++.++++.++.++++.+  +++.|+|.||.+..  ...+..+++.+.+|.+++. +||+|
T Consensus       152 E~~Al~~a~~l~k~I~~~~~~~n--~~l~GiI~N~~~~~--~~~~~i~~f~~~~g~~vl~-~IP~d  212 (212)
T cd02117         152 EFMALYAANNICKGIRKYAKSGG--VRLGGLICNSRNTD--RETELIDAFAERLGTQVIH-FVPRD  212 (212)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCC--CCEEEEEEECCCCC--CHHHHHHHHHHHHCCEEEE-ECCCC
T ss_conf             35788988999999999973679--81489998467888--6499999999983991899-74899


No 28 
>PRK13185 chlL protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional
Probab=100.00  E-value=2.8e-36  Score=231.32  Aligned_cols=237  Identities=19%  Similarity=0.237  Sum_probs=177.7

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCC------CHHHCCC
Q ss_conf             7499998088988889999999999998799599998787768011212463334541167630257------7121024
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEK------NINQILI   79 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~------~l~~~i~   79 (265)
                      +++|+|. +|||+||||+++||+.+||++|+||++|||||..+.+..|.-   ...+|+.|++.+..      .+++.+.
T Consensus         2 ~~~iaiy-GKGGIGKSTttaNlsaALA~~GkkV~~IgcDPk~DsT~~L~g---~~~~tild~l~~~~~~~~~~~~ed~~~   77 (269)
T PRK13185          2 ALVLAVY-GKGGIGKSTTSSNLSAALAKLGKKVLQIGCDPKHDSTFTLTG---KLVPTVIDILEEVDFHSEELRPEDFVF   77 (269)
T ss_pred             CEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHCCC---CCCCCHHHHHHHCCCCHHHCCHHHHHH
T ss_conf             5399997-899547888999999999976993899818997323011259---987878999974387602125667763


Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CCCCCHHHHHHHCCCCCCCCCH
Q ss_conf             444442000148874577500012322221023332247651027820331013332-2221011233100111112311
Q gi|254780806|r   80 QTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFN-LLTMNAMAAADSILVPLQCEFF  158 (265)
Q Consensus        80 ~~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~-~~~~~al~aad~viip~~p~~~  158 (265)
                       ..+.++.++.++..-.+....-.........|.+ +  .+.++||||++|+++..- --..+.+..||.+++|+.+|++
T Consensus        78 -~G~~gv~cvEaGGP~pG~GCaGrgi~~~~~~L~~-~--~~~~~~D~Vl~DvlgdVvCGGFa~Pi~~Ad~~~IVts~e~~  153 (269)
T PRK13185         78 -EGYNGVDCVEAGGPPAGTGCGGYVVGETVKLLKE-H--HLLDDYDVILFDVLGDVVCGGFAAPLQYADYALIVTANDFD  153 (269)
T ss_pred             -CCCCCCEEEECCCCCCCCCCCCCCHHHHHHHHHH-C--CCCCCCCEEEEECCCCCCCCCCCCCHHCCCEEEEEECCHHH
T ss_conf             -3767705664389999877676431899999987-2--87433787999536743336555751008889999253087


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEEC
Q ss_conf             37888753357776554320267743100202312531001126899988085201562678688987773798579997
Q gi|254780806|r  159 ALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYD  238 (265)
Q Consensus       159 s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~  238 (265)
                      |++.+.++...++....+.  ..++.|+|.|+.+     ..++++++.+..|.+++. +||+|..+.+|..+|+|++++.
T Consensus       154 al~aAnnI~~~i~~~a~~~--~~rl~GiI~Nr~~-----~~d~v~~fa~~~g~~vl~-~IP~~~~V~~se~~g~TviE~~  225 (269)
T PRK13185        154 SIFAANRIAAAIQAKAKNY--KVRLAGVIANRSG-----GTDQIDKFNERVGLRTLA-HVPDLDAIRRSRLKGKTLFEME  225 (269)
T ss_pred             HHHHHHHHHHHHHHHHHCC--CCCCCEEEEECCC-----CHHHHHHHHHHHCCCEEE-ECCCCHHHHHHHHCCCEEEEEC
T ss_conf             8999999999998653015--8532325761688-----377999999986997699-7899788999987498678858


Q ss_pred             CCCHHHH---HHHHHHHHHHHHH
Q ss_conf             9998999---9999999999999
Q gi|254780806|r  239 LKCAGSQ---AYLKLASELIQQE  258 (265)
Q Consensus       239 p~s~~a~---~~~~la~el~~~~  258 (265)
                      |.+..++   +|++||+.|++..
T Consensus       226 p~~~~a~v~~~Yr~LA~~i~~~~  248 (269)
T PRK13185        226 ETDELEEVQNEYLRLADQLLAGP  248 (269)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             99817899999999999998289


No 29 
>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=100.00  E-value=1.6e-36  Score=232.71  Aligned_cols=210  Identities=25%  Similarity=0.323  Sum_probs=132.9

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC-CCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCC
Q ss_conf             499998088988889999999999998799599998787-7680112124633345411676302577121024444442
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP-QGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPN   85 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~-q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~   85 (265)
                      .||+|.|+||||||||+|+|||.+||++|+||++||+|| |++++.+++-...     ..    ...            +
T Consensus         1 hIIaVaNqKGGvGKTTtavnLA~aLA~~G~rVllIDlDpqq~slt~~l~nr~~-----~~----~~~------------~   59 (261)
T pfam09140         1 HVIVVGNEKGGSGKSTTAVHVAVALLYLGARVATIDLDLRQRTLTRYIENRAA-----TA----ERT------------G   59 (261)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHH-----HH----HHC------------C
T ss_conf             97999717898729999999999999889978999799999851234430355-----65----513------------8


Q ss_pred             EEE-CCCCCCCCCCCCCCCC-CCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHH
Q ss_conf             000-1488745775000123-22221023332247651027820331013332222101123310011111231137888
Q gi|254780806|r   86 LSI-IPSTMDLLGIEMILGG-EKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGL  163 (265)
Q Consensus        86 l~i-ipa~~~~~~~~~~l~~-~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~  163 (265)
                      +++ +|....+...+..+.. ......+|.+.+. .+.++||||||||||+++.++.+++.+||.+|+|+++|.++++++
T Consensus        60 ~~l~~P~~~~l~~~~~~~~~~~~~~~~~L~~al~-~l~~~yDfIlIDcPPsl~~Lt~nAl~aAD~vIiPlq~sf~dld~L  138 (261)
T pfam09140        60 LDLPVPKHLCLPDDVSEVFDGESADDARLEEAVA-DLEQDADFIVIDTPGSDSPLSRLAHSRADTLVTPLNDSFVDFDLL  138 (261)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHCCCCEEEEECCCCCCHHHHHHHHHHCEEEECCCHHHHHHHHH
T ss_conf             6534665344550677761345578999999999-987579999996998573999999998398763244015514335


Q ss_pred             HHHH-------------HHH---HHHHHHH-HCCCCCCCCCCCEEECCCHHHH----HHHHHHHHHHCCCCCCCCCCCCH
Q ss_conf             7533-------------577---7655432-0267743100202312531001----12689998808520156267868
Q gi|254780806|r  164 SQLL-------------ETV---EEVRRTV-NSALDIQGIILTMFDSRNSLSQ----QVVSDVRKNLGGKVYNTVIPRNV  222 (265)
Q Consensus       164 ~~~~-------------~~i---~~~~~~~-~~~~~~~~iv~N~~~~~~~~~~----~~~~~l~~~~~~~v~~~~Ip~~~  222 (265)
                      .++-             +++   .+.+... ..+++.. ++-||........+    +.++++.+..|-.+.+ -+.+..
T Consensus       139 ~~vd~~~~~i~~~s~y~e~vw~~r~~ra~~~~~~idwi-vlrnRl~~~~~rnk~~~~~~l~~Ls~rigfr~~~-g~~eRv  216 (261)
T pfam09140       139 GQVDPETFKVTRPSFYAEMVWEARKKRAQADRAPIDWI-VLRNRLSTLEARNKRRVEDALNELSKRVGFRVAP-GFSERV  216 (261)
T ss_pred             HHCCHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCEE-EEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC-CCCHHH
T ss_conf             21370343213621789999999998743689886479-9805621888788899999999997640752257-743135


Q ss_pred             HHHHHHHCCCCEEEECCC
Q ss_conf             898777379857999799
Q gi|254780806|r  223 RISEAPSYGKPAIIYDLK  240 (265)
Q Consensus       223 ~i~~a~~~g~pv~~~~p~  240 (265)
                      .+.+-.-.|.++.+..+.
T Consensus       217 iyRelfp~gltl~dl~~~  234 (261)
T pfam09140       217 IYRELFPRGLTLLDLKDL  234 (261)
T ss_pred             HHHHHCCCCCCHHCCCCC
T ss_conf             787762467714118512


No 30 
>KOG3022 consensus
Probab=100.00  E-value=1.5e-35  Score=226.96  Aligned_cols=240  Identities=20%  Similarity=0.249  Sum_probs=185.1

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC
Q ss_conf             68749999808898888999999999999879959999878776-80112124633345411676302577121024444
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA   82 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~-~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~   82 (265)
                      +-..+|+|.|+||||||||+|+|||++||..|++|.++|.|.-| |+..+||.+.+.    .++.-.+   +...   ..
T Consensus        45 ~vk~iI~VlSGKGGVGKSTvt~nla~~La~~g~~vglLD~Dl~GPSiP~m~g~e~~~----~~~~~~g---~~Pv---~~  114 (300)
T KOG3022          45 GVKHIILVLSGKGGVGKSTVTVNLALALASEGKKVGLLDADLCGPSIPRMMGLEGEV----VHQSDNG---WIPV---VV  114 (300)
T ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHCCCCCCE----EEECCCC---CEEE---EE
T ss_conf             454589998678877616899999999861797179975035587705340877744----5504887---4144---44


Q ss_pred             CCCEEECCCCCCCCC-CCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHH---HHHCCCCCCCCCH
Q ss_conf             442000148874577-500012322221023332247651027820331013332222101123---3100111112311
Q gi|254780806|r   83 IPNLSIIPSTMDLLG-IEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAA---ADSILVPLQCEFF  158 (265)
Q Consensus        83 ~~~l~iipa~~~~~~-~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~a---ad~viip~~p~~~  158 (265)
                      ..|+.++.-+.-+.. .+...+..+....+++++|.+.-|++.||++||||||.++..+.....   +|..++|++|...
T Consensus       115 ~~~l~~mS~gfLl~~~~~~vIwRGpkk~~~I~qflk~vdwg~lDyLviDtPPGtsDehls~~~~~~~~~gAviVTTPQ~v  194 (300)
T KOG3022         115 NKNLKLMSMGFLLKPRDDSVIWRGPKKNSMIKQFLKDVDWGELDYLVIDTPPGTSDEHLSLVQFLRESDGAVIVTTPQEV  194 (300)
T ss_pred             CCCEEEEEEEEECCCCCCCCEEECHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHEEECCCCCCCEEEEECCHHH
T ss_conf             38767887564328887662654547889999997168877767799958999870143100004455734998172055


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEE---CCCHHH-----HHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC
Q ss_conf             3788875335777655432026774310020231---253100-----11268999880852015626786889877737
Q gi|254780806|r  159 ALEGLSQLLETVEEVRRTVNSALDIQGIILTMFD---SRNSLS-----QQVVSDVRKNLGGKVYNTVIPRNVRISEAPSY  230 (265)
Q Consensus       159 s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~---~~~~~~-----~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~  230 (265)
                      ++.++.+-++++++.      +++++|+|.||..   +.....     ..--+.+.+.+|.+.+. .||.|..+.++.+.
T Consensus       195 Al~Dv~K~i~fc~K~------~I~ilGvVENMs~f~Cp~C~~~~~iF~~gGg~~l~~~~glp~Lg-~iPld~~i~~~~d~  267 (300)
T KOG3022         195 ALQDVRKEIDFCRKA------GIPILGVVENMSGFVCPKCGHSTNIFGSGGGERLAEELGLPLLG-SLPLDPLIAESSDS  267 (300)
T ss_pred             HHHHHHHHHHHHHHC------CCCEEEEEECCCCCCCCCCCCCCEECCCCCHHHHHHHCCCCEEE-ECCCCHHHHHHCCC
T ss_conf             668888650266645------98568889625553078878755333676289999872997575-06788799975348


Q ss_pred             CCCEEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             985799979998999999999999999986
Q gi|254780806|r  231 GKPAIIYDLKCAGSQAYLKLASELIQQERH  260 (265)
Q Consensus       231 g~pv~~~~p~s~~a~~~~~la~el~~~~~~  260 (265)
                      |.|+++..|.|.++++|.+++.+|.+.-..
T Consensus       268 G~~~v~~~p~s~~~~af~~i~~~i~~~~~~  297 (300)
T KOG3022         268 GVPFVEEYPDSPASEAFEDIAEKLVEQLSS  297 (300)
T ss_pred             CCEEEECCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             983476079956999999999999986120


No 31 
>CHL00072 chlL photochlorophyllide reductase subunit L
Probab=100.00  E-value=1.8e-34  Score=220.81  Aligned_cols=235  Identities=21%  Similarity=0.200  Sum_probs=176.1

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCC------CHHHCCCCC
Q ss_conf             99998088988889999999999998799599998787768011212463334541167630257------712102444
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEK------NINQILIQT   81 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~------~l~~~i~~~   81 (265)
                      .|+|. +|||+||||+++|++.+||++|+||++|+|||..+.+..|.-   ...+|+.|++.++.      .+++++. .
T Consensus         2 ~iaiy-GKGGIGKSTtsaNlsaaLA~~GkkVl~IGcDpk~DsT~~L~g---~~~~tvld~l~~~~~~~~~~~~edvi~-~   76 (271)
T CHL00072          2 KIAVY-GKGGIGKSTTSCNISIALARRGKKVLQIGCDPKHDSTFTLTG---FLIPTIIDTLQSKDYHYEDVWPEDVIY-K   76 (271)
T ss_pred             EEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHCC---CCCCCHHHHHHHHCCCCCCCCHHHHHH-C
T ss_conf             69997-898544858899999999987997999789973777740069---988859999975378732164999985-2


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCC-CCCCHHHHHHHCCCCCCCCCHHH
Q ss_conf             44420001488745775000123222210233322476510278203310133322-22101123310011111231137
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNL-LTMNAMAAADSILVPLQCEFFAL  160 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~-~~~~al~aad~viip~~p~~~s~  160 (265)
                      ...|+.++.++..-.+....-.........|.+ +.  ..++||||++|+++..-. -..+.+..||.+++|+++|++|+
T Consensus        77 G~~gi~cvEaGGPepGvGCaGrgi~~~i~lL~~-l~--~~~d~D~V~yDvlgDVVCGGFa~Pi~~Ad~~~iVts~e~mal  153 (271)
T CHL00072         77 GYGGVDCVEAGGPPAGAGCGGYVVGETVKLLKE-LN--AFYEYDVILFDVLGDVVCGGFAAPLNYADYCIIITDNGFDAL  153 (271)
T ss_pred             CCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHH-CC--CCCCCCEEEEECCCCCCCCCCCCCCCCCCEEEEEECCCHHHH
T ss_conf             778846654389998877788651999999997-37--621388899944776556545675000888999956708899


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCC
Q ss_conf             88875335777655432026774310020231253100112689998808520156267868898777379857999799
Q gi|254780806|r  161 EGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLK  240 (265)
Q Consensus       161 ~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~  240 (265)
                      +.+.++.+.++++....+  .++.|+|.|+.+     .+++++++.+..|.+++. .||+|..+.+|..+|+|++++.|.
T Consensus       154 yaANnI~~~i~~~a~~~~--~rl~GiI~N~~~-----~~~~v~~fa~~~g~~~i~-~iPrd~~V~~ae~~~~TviE~~p~  225 (271)
T CHL00072        154 FAANRIAASVREKARTHP--LRLAGLVGNRTS-----KRDLIDKYVEACPMPVLE-VLPLIEDIRVSRVKGKTLFEMAES  225 (271)
T ss_pred             HHHHHHHHHHHHHHHCCC--CCCCEEEECCCC-----CHHHHHHHHHHCCCCEEE-ECCCCCHHHHHHHCCCCEEECCCC
T ss_conf             999999999999730468--644436522688-----378999999973996698-568711668999748820422899


Q ss_pred             CHH----HHHHHHHHHHHHHHH
Q ss_conf             989----999999999999999
Q gi|254780806|r  241 CAG----SQAYLKLASELIQQE  258 (265)
Q Consensus       241 s~~----a~~~~~la~el~~~~  258 (265)
                      ++.    ++.|++||+.|++..
T Consensus       226 s~~~~~~~~~Yr~LA~~I~~n~  247 (271)
T CHL00072        226 EPSLNYVCDFYLNIADQLLSQP  247 (271)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCC
T ss_conf             8247899999999999997399


No 32 
>PRK13236 nitrogenase reductase; Reviewed
Probab=100.00  E-value=5.9e-33  Score=211.89  Aligned_cols=243  Identities=18%  Similarity=0.283  Sum_probs=184.6

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCC-----CHH
Q ss_conf             987687499998088988889999999999998799599998787768011212463334541167630257-----712
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEK-----NIN   75 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~-----~l~   75 (265)
                      |.+++-|.|+|. +|||+||||++.||+.+||++|+||++|.|||..+.|..|.-  .....++.+++....     .++
T Consensus         1 ~~~~~mk~IAiY-GKGGIGKSTts~NlsAAlA~~G~rVl~IGCDPK~DSTr~Llg--g~~~~tvld~~~e~~~~ed~~le   77 (295)
T PRK13236          1 MTDENIRQIAFY-GKGGIGKSTTSQNTLAAMAEMGQRILIVGCDPKADSTRLMLH--SKAQTTVLHLAAERGAVEDLELE   77 (295)
T ss_pred             CCCCCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHC--CCCCCCHHHHHHHHCCCCCCCHH
T ss_conf             986776189996-798434757899999999977996999788980266787638--99997188888760984445488


Q ss_pred             HCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHH------HHHHC
Q ss_conf             102444444200014887457750001232222102333224765102782033101333222210112------33100
Q gi|254780806|r   76 QILIQTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMA------AADSI  149 (265)
Q Consensus        76 ~~i~~~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~------aad~v  149 (265)
                      +++. ..+.|+.++.++..-.+....-.........|.+. .  ..++||||+.|.   +++..+..+.      .||.+
T Consensus        78 dvv~-~G~~Gi~CvEsGGPePGvGCAGRGIitai~lLee~-g--a~e~~D~V~yDV---LGDVVCGGFAmPir~g~A~ev  150 (295)
T PRK13236         78 EVML-TGFRGVRCVESGGPEPGVGCAGRGIITAINFLEEN-G--AYQDLDFVSYDV---LGDVVCGGFAMPIREGKAQEI  150 (295)
T ss_pred             HHHH-CCCCCCEEEECCCCCCCCCCCCCEEEEHHHHHHHC-C--CCCCCCEEEEEE---CCCCCCCCCCCCCCCCCCCEE
T ss_conf             8742-26588379878999998988886254056679871-9--855699898850---577532675465667876489


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHH
Q ss_conf             11111231137888753357776554320267743100202312531001126899988085201562678688987773
Q gi|254780806|r  150 LVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPS  229 (265)
Q Consensus       150 iip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~  229 (265)
                      ++|+..|++|+..+.++.+.+.++..+.+.  ++.|+|.|+-  +.....++.+++.+..|.+++. .||+|..+++|-.
T Consensus       151 yiVtSge~malyAANNI~~~i~~~a~~g~~--rlgGiI~N~r--~~~~e~~~v~~fa~~~gt~ii~-~iPr~~~V~~ae~  225 (295)
T PRK13236        151 YIVTSGEMMAMYAANNIARGILKYAHTGGV--RLGGLICNSR--NVDREIELIETLAKRLNTQMIH-FVPRDNIVQHAEL  225 (295)
T ss_pred             EEEECCCHHHHHHHHHHHHHHHHHHHCCCC--CEEEEEEECC--CCCCHHHHHHHHHHHHCCCEEE-ECCCCHHHHHHHH
T ss_conf             999568188999999999999999742697--0358996078--8874799999999981992699-6578388889997


Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             79857999799989999999999999999
Q gi|254780806|r  230 YGKPAIIYDLKCAGSQAYLKLASELIQQE  258 (265)
Q Consensus       230 ~g~pv~~~~p~s~~a~~~~~la~el~~~~  258 (265)
                      ++++|+++.|.|..++.|++||+.|++..
T Consensus       226 ~~~TviE~~P~s~~A~~Yr~LA~~i~~n~  254 (295)
T PRK13236        226 RRMTVNEYAPDSNQGNEYRILAKKIINND  254 (295)
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHCC
T ss_conf             39876887889779999999999998589


No 33 
>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=100.00  E-value=3.7e-33  Score=213.07  Aligned_cols=212  Identities=22%  Similarity=0.231  Sum_probs=153.0

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCE
Q ss_conf             49999808898888999999999999879959999878776801121246333454116763025771210244444420
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNL   86 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l   86 (265)
                      +||+|.|+|||+||||++.|||.+++.+|++|++||+|||++++.|.-.....   ..         ..        +..
T Consensus         2 ~vi~~~~~KGG~GKtT~a~~la~~~~~~g~~V~liD~Dpq~s~~~W~~~a~~~---~~---------~~--------~~~   61 (231)
T pfam07015         2 QLITFCSFKGGAGKTTALMGLCSALASDGKRVALFEADENRPLTKWRENALRK---GT---------WD--------PAC   61 (231)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHC---CC---------CC--------CCC
T ss_conf             37999617998659999999999999689959999689986889999987646---88---------88--------765


Q ss_pred             EECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             00148874577500012322221023332247651027820331013332222101123310011111231137888753
Q gi|254780806|r   87 SIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQL  166 (265)
Q Consensus        87 ~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~~~  166 (265)
                      .+....               ....+.+.+...-...||||||||||+.+.++..++..||.++||++|+++++..+.+.
T Consensus        62 ~v~~~~---------------~~~~l~~~~~~~~~~~yD~VIIDtpg~~s~~~~~AI~~ADlVLIP~qpSplD~~~a~~t  126 (231)
T pfam07015        62 EIFNAD---------------ELPLLEQAYEHAEGSGFDYALADTHGGSSELNNTIIASSDLLLIPTMLTPLDIDEALAT  126 (231)
T ss_pred             CEECCC---------------CHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHCCEEEECCCCCHHHHHHHHHH
T ss_conf             222056---------------60158999998865799989983998575899999997898997789982339999999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCEEECCCHHH-HHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC----
Q ss_conf             35777655432026774310020231253100-1126899988085201562678688987773798579997999----
Q gi|254780806|r  167 LETVEEVRRTVNSALDIQGIILTMFDSRNSLS-QQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC----  241 (265)
Q Consensus       167 ~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~-~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s----  241 (265)
                      ++.+++..+..+..+.. .+++||+....... .....++.+.  .++|.+.|.++.+|.+....|....+....+    
T Consensus       127 ~~~i~~~~~~~~~~ip~-avl~tRv~~~~~~~~~~~i~e~le~--lpvl~t~i~eR~AF~~if~~G~l~~~l~~~~~~~~  203 (231)
T pfam07015       127 YRYVIELLLTENLAIPT-AILRQRVPVGRLTSSQRFCSDMLEQ--LPVFDCPMHERDAFAAMKERGMLHITLENLSQIPS  203 (231)
T ss_pred             HHHHHHHHHHHCCCCCE-EEEEEECCCCCCCHHHHHHHHHHHC--CCCCCCCCCCHHHHHHHHHHCCCCHHCCCCCCCCC
T ss_conf             99999999973789980-3345511400021789999999964--98543542028999999980462000268777851


Q ss_pred             --HHHHHHHHHHHHHHH
Q ss_conf             --899999999999999
Q gi|254780806|r  242 --AGSQAYLKLASELIQ  256 (265)
Q Consensus       242 --~~a~~~~~la~el~~  256 (265)
                        ++++.++.+++|+..
T Consensus       204 ~~~a~~n~~~~~~e~~~  220 (231)
T pfam07015       204 MRLALRNLRTAMEDLDR  220 (231)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             12899999999999999


No 34 
>PRK13234 nifH nitrogenase reductase; Reviewed
Probab=100.00  E-value=3.7e-32  Score=207.27  Aligned_cols=239  Identities=19%  Similarity=0.274  Sum_probs=178.6

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCC-----CHHHCCC
Q ss_conf             87499998088988889999999999998799599998787768011212463334541167630257-----7121024
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEK-----NINQILI   79 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~-----~l~~~i~   79 (265)
                      .=|-|+|. +|||+||||++.||+.+||++|+||++|.|||..+.|..|.-  .....|+.+++....     .+++++.
T Consensus         3 ~mr~IAiY-GKGGIGKSTtssNlsAAlA~~G~rVl~IGCDPK~DSTr~Llg--g~~~~Tvld~~~~~~~~ed~~ledvv~   79 (293)
T PRK13234          3 ALRQIAFY-GKGGIGKSTTSQNTLAALVEMGQKILIVGCDPKADSTRLILN--AKAQDTVLSLAAEAGSVEDLELEDVMK   79 (293)
T ss_pred             CCCEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHC--CCCCCCHHHHHHHCCCCCCCCHHHHHH
T ss_conf             77579997-798445877899999999977996999748983165687628--999970889987649812153878974


Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHH------HHHHCCCCC
Q ss_conf             44444200014887457750001232222102333224765102782033101333222210112------331001111
Q gi|254780806|r   80 QTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMA------AADSILVPL  153 (265)
Q Consensus        80 ~~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~------aad~viip~  153 (265)
                       ....|+.++.++..-.+....-.........|.+ +.  +.++||||+.|.   +++..+..+.      .||.+++|+
T Consensus        80 -~G~~gI~CVEsGGPePGvGCAGRGIitai~~Le~-lg--a~ed~D~V~yDV---LGDVVCGGFAmPir~g~A~evyIVt  152 (293)
T PRK13234         80 -IGYKGIKCVESGGPEPGVGCAGRGVITSINFLEE-NG--AYDDVDYVSYDV---LGDVVCGGFAMPIRENKAQEIYIVM  152 (293)
T ss_pred             -CCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHH-CC--CCCCCCEEEEEC---CCCCCCCCCCCCCCCCCCCEEEEEE
T ss_conf             -3779848976899899888777131467888877-18--765799999956---7766514755665458876899994


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCC
Q ss_conf             12311378887533577765543202677431002023125310011268999880852015626786889877737985
Q gi|254780806|r  154 QCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKP  233 (265)
Q Consensus       154 ~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~p  233 (265)
                      ..|+.|+..+.++.+.+..+..+.+.  ++.|+|.|+-+  .....++.+++.+..+.+++. +||+|..+++|-.++++
T Consensus       153 Sge~mslyAANnI~~~i~~~~~~g~~--rlgGlI~N~r~--~~~e~~~v~~fa~~~gt~ii~-~IPrs~~v~~aE~~~~T  227 (293)
T PRK13234        153 SGEMMALYAANNIAKGILKYANSGGV--RLGGLICNERQ--TDRELELAEALAKRLGSKLIH-FVPRDNIVQHAELRRMT  227 (293)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCC--EEEEEEEECCC--CCCHHHHHHHHHHHHCCCEEE-ECCCCHHHHHHHHCCCE
T ss_conf             67187999999999999998632696--24689971789--853799999999984993799-77996889999973977


Q ss_pred             EEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             7999799989999999999999999
Q gi|254780806|r  234 AIIYDLKCAGSQAYLKLASELIQQE  258 (265)
Q Consensus       234 v~~~~p~s~~a~~~~~la~el~~~~  258 (265)
                      |+++.|.|..++.|++||+.|.+..
T Consensus       228 viE~~P~s~~A~~Yr~LA~~I~~n~  252 (293)
T PRK13234        228 VIEYAPDSKQAGEYRALAEKIHANS  252 (293)
T ss_pred             EEEECCCCHHHHHHHHHHHHHHHCC
T ss_conf             7896889879999999999998478


No 35 
>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=100.00  E-value=1.4e-32  Score=209.79  Aligned_cols=238  Identities=23%  Similarity=0.337  Sum_probs=190.0

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCC-CCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECC---CC--HHHCCCC
Q ss_conf             49999808898888999999999999879-959999878776801121246333454116763025---77--1210244
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIG-ENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEE---KN--INQILIQ   80 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g-~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~---~~--l~~~i~~   80 (265)
                      |-|||. +|||.||||++.|+|.+||..| |||+++-|||.++.|..|.-  .....|+.|+|.+.   +.  +++ ++.
T Consensus         1 rqiAiY-GKGGIGKSTT~~N~~AAla~~gdkkVl~~GCDPKaDsTr~l~G--g~~~~TVLd~lre~G~ve~~~~e~-v~~   76 (278)
T TIGR01287         1 RQIAIY-GKGGIGKSTTTQNIAAALAEMGDKKVLVVGCDPKADSTRLLLG--GKAQPTVLDVLREKGAVEDVELED-VIK   76 (278)
T ss_pred             CEEEEE-CCCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHC--CCCCCHHHHHHHHCCCCCCCCCCH-HHE
T ss_conf             948886-2788670068889999998624955899723885202346517--744554899998568711445102-200


Q ss_pred             CCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHC-CCCCCEEEECCCCCCCCCCHHHH------HHHCCCCC
Q ss_conf             444420001488745775000123222210233322476510-27820331013332222101123------31001111
Q gi|254780806|r   81 TAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTS-DFSYIFLDCPPSFNLLTMNAMAA------ADSILVPL  153 (265)
Q Consensus        81 ~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~-~yD~IiiD~pp~~~~~~~~al~a------ad~viip~  153 (265)
                      ..+.++.++-|+-+--+....-..-.-....|.+.  ....+ +.|||++|.   +|+..+-.++.      ||.+.||+
T Consensus        77 ~Gf~girCVESGGPePGVGCAGRGvItai~lL~~~--g~y~dLdlD~V~YDV---LGDVVCGGFAmP~R~g~A~eiYiVt  151 (278)
T TIGR01287        77 EGFGGIRCVESGGPEPGVGCAGRGVITAIDLLEEL--GAYEDLDLDVVIYDV---LGDVVCGGFAMPLREGLAQEIYIVT  151 (278)
T ss_pred             ECCCCEEEEEECCCCCCCCCCCCHHEEEEHHHHHC--CCCCCCCCCEEEEEE---CCCEEECCCCCHHHCCCCCEEEEEC
T ss_conf             16883188850768789520687112013377533--787311677689842---3655656603610058865488860


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCC
Q ss_conf             12311378887533577765543202677431002023125310011268999880852015626786889877737985
Q gi|254780806|r  154 QCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKP  233 (265)
Q Consensus       154 ~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~p  233 (265)
                      .-|+++++.+.++-+-|.++..+.+..  .-|||-|.  .+.....|+++++.+.+|..++. +||+|..+++|-.++++
T Consensus       152 Sge~MAlYAANNI~kGI~kYa~~GGv~--LGG~IcN~--R~~~~e~El~~~fA~~lgtq~i~-~VPrs~~V~~AEl~~~T  226 (278)
T TIGR01287       152 SGEMMALYAANNIAKGILKYAKSGGVR--LGGIICNS--RNVDDEKELVDEFAKKLGTQLIH-FVPRSNIVQKAELEKKT  226 (278)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCE--ECCEEECC--CCCCCHHHHHHHHHHHHCCEEEE-ECCCCCCCHHHHHCCCC
T ss_conf             340678999978877789997538822--22478714--57621789999999873770675-21788521278736884


Q ss_pred             EEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             7999799989999999999999999
Q gi|254780806|r  234 AIIYDLKCAGSQAYLKLASELIQQE  258 (265)
Q Consensus       234 v~~~~p~s~~a~~~~~la~el~~~~  258 (265)
                      |.||+|.|..|+.|+.||+.|.+.+
T Consensus       227 VIE~dP~s~qA~~YR~LA~~I~~N~  251 (278)
T TIGR01287       227 VIEYDPESEQANEYRELAKKIYENE  251 (278)
T ss_pred             EEEECCCCHHHHHHHHHHHHHHHCC
T ss_conf             5633887157899999999998257


No 36 
>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=100.00  E-value=7.1e-32  Score=205.58  Aligned_cols=236  Identities=25%  Similarity=0.320  Sum_probs=188.8

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEEC----CCC--HHHCCCC
Q ss_conf             4999980889888899999999999987995999987877680112124633345411676302----577--1210244
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIE----EKN--INQILIQ   80 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~----~~~--l~~~i~~   80 (265)
                      +||||. +|||+||||+++||+.++|++|||||-|-|||.-++|..|--..   .+|+.|+|..    .++  ..|.|+ 
T Consensus         1 ~~lAvY-GKGGiGKSTTssNLSvA~A~~GkkVlQIGCDPKhDSTFTLtg~L---~PTvidvL~~~~yH~E~v~~eD~iy-   75 (275)
T TIGR01281         1 MILAVY-GKGGIGKSTTSSNLSVALAKKGKKVLQIGCDPKHDSTFTLTGKL---IPTVIDVLDAVNYHYEDVEPEDVIY-   75 (275)
T ss_pred             CEEEEE-CCCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCCC---CCCEEEECCCCCCCEEECCCCCEEE-
T ss_conf             968886-38887700467899999984699189852578888774544741---6746442256763031033378778-


Q ss_pred             CCCCCEEECCCCCCCCCCCCCC--CCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHH----HHHHHCCCCCC
Q ss_conf             4444200014887457750001--23222210233322476510278203310133322221011----23310011111
Q gi|254780806|r   81 TAIPNLSIIPSTMDLLGIEMIL--GGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAM----AAADSILVPLQ  154 (265)
Q Consensus        81 ~~~~~l~iipa~~~~~~~~~~l--~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al----~aad~viip~~  154 (265)
                      +.+.|+|++-++-.+++...=-  ..+.  ...|++ +  .+-++||+|++|.   +|+..+-.+    ..||+.+|++.
T Consensus        76 ~GY~GVd~vEaGGPPAGsGCGGYVVGeT--VKLLke-~--~~~~~yDVilFDV---LGDVVCGGFAaPL~YAd~aLvva~  147 (275)
T TIGR01281        76 TGYGGVDCVEAGGPPAGSGCGGYVVGET--VKLLKE-L--DVLDEYDVILFDV---LGDVVCGGFAAPLQYADYALVVAA  147 (275)
T ss_pred             ECCCCEEEEECCCCCCCCCCCCEEECCH--HHHHHH-C--CHHHHCCEEEEEE---CCCEEECCCCCHHHHHCCEEEEEC
T ss_conf             3468568871473689888987471522--455665-2--6334289799962---575551754641123212566610


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCE
Q ss_conf             23113788875335777655432026774310020231253100112689998808520156267868898777379857
Q gi|254780806|r  155 CEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPA  234 (265)
Q Consensus       155 p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv  234 (265)
                      =+.-|+=.+.|+-..+.+..++ +.+++..|||-||++.+..-..+.++...+..+.+++. ++|+-+.|++|-..|+++
T Consensus       148 NDFDalFAANRia~av~~K~~~-Gy~vkLAGiIaNR~~~~yGGGtdlle~F~~~~~~~~l~-~~P~~d~IR~SRl~g~Tl  225 (275)
T TIGR01281       148 NDFDALFAANRIAAAVREKAKS-GYDVKLAGIIANRVDKEYGGGTDLLEKFAERVGTPVLG-VVPRLDEIRRSRLKGKTL  225 (275)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCC-CCEEEEEEEEECCCCCCCCCCCCHHHHHHHHCCCCEEE-ECCCHHHCCHHHHCCCCE
T ss_conf             7721789999999999998417-97078732663121131178715689999862883220-077711102010158612


Q ss_pred             EEECCCC----HHHHHHHHHHHHHHHH
Q ss_conf             9997999----8999999999999999
Q gi|254780806|r  235 IIYDLKC----AGSQAYLKLASELIQQ  257 (265)
Q Consensus       235 ~~~~p~s----~~a~~~~~la~el~~~  257 (265)
                      +|++|..    ...+.|.++|+.|++|
T Consensus       226 FEmee~~p~~~~~~~~y~~~A~~LL~~  252 (275)
T TIGR01281       226 FEMEESGPELEEVTAEYLKMAEYLLAK  252 (275)
T ss_pred             EECCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             301589965889999999999999863


No 37 
>PRK13849 putative crown gall tumor protein VirC1; Provisional
Probab=100.00  E-value=7.3e-32  Score=205.53  Aligned_cols=195  Identities=18%  Similarity=0.212  Sum_probs=141.6

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCE
Q ss_conf             49999808898888999999999999879959999878776801121246333454116763025771210244444420
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNL   86 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l   86 (265)
                      +||+|.|+|||+||||++.|||..++.+|++|++||+|||++++.|.........            +.        +..
T Consensus         2 ~vi~~~~~KGG~GKtT~a~~la~~~~~~g~~v~~iD~Dpq~s~~~W~e~a~~~~~------------~~--------~~~   61 (231)
T PRK13849          2 KLLTFCSFKGGAGKTTALMGLCAALASDGKRVALFEADENRPLTRWKENALRSNT------------WD--------PAC   61 (231)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHCCC------------CC--------CCC
T ss_conf             3799961899876999999999999978995999968998688999987652589------------88--------775


Q ss_pred             EECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             00148874577500012322221023332247651027820331013332222101123310011111231137888753
Q gi|254780806|r   87 SIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQL  166 (265)
Q Consensus        87 ~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~~~  166 (265)
                      .+...            ..   ...+...+...-...||||||||||+.+.++..++..||.+|||+.|+++++..+.++
T Consensus        62 ~v~~~------------~~---~~~l~~~~e~~~~~~~D~VIIDtpg~~s~~~~~Ai~~ADLVLIP~qPSp~D~~~a~~t  126 (231)
T PRK13849         62 EVYAA------------DE---LPLLEAAYEDAELQGFDYALADTHGGSSELNNTIIASSNLLLIPTMLTPLDIDEALST  126 (231)
T ss_pred             CEEEC------------CC---HHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHCCEEEECCCCCHHHHHHHHHH
T ss_conf             23405------------65---2578999988753699889981899775899999997898997799986679999999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCEEECC--CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCC---EEEECCC
Q ss_conf             3577765543202677431002023125--310011268999880852015626786889877737985---7999799
Q gi|254780806|r  167 LETVEEVRRTVNSALDIQGIILTMFDSR--NSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKP---AIIYDLK  240 (265)
Q Consensus       167 ~~~i~~~~~~~~~~~~~~~iv~N~~~~~--~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~p---v~~~~p~  240 (265)
                      ++.+++..+..+.+++. .+++||+...  +...+.+.+.+ +  +.++|++.|+++.+|.+-...|.-   +.+..|.
T Consensus       127 v~~i~~~~~~~~~~ip~-~vlltRv~a~~~t~~~~~i~~~l-e--~lPvl~T~i~eR~Af~~i~~~G~Lh~~l~~~~~~  201 (231)
T PRK13849        127 YRYVIELLLSENLAIPT-AILRQRVPVGRLTTSQRAMSDML-E--SLPVVDSPMHERDAFAAMKERGMLHLTLLNLSTD  201 (231)
T ss_pred             HHHHHHHHHHHCCCCCE-EEEEEECCHHHHCHHHHHHHHHH-H--CCCCCCCCCHHHHHHHHHHHHCCHHHHHHHCCCC
T ss_conf             99999999972878865-66654050454068899999999-6--2995555302279999999835146889865999


No 38 
>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=99.97  E-value=3e-32  Score=207.73  Aligned_cols=177  Identities=23%  Similarity=0.281  Sum_probs=120.4

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCEE
Q ss_conf             999808898888999999999999879959999878776-8011212463334541167630257712102444444200
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLS   87 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~-~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l~   87 (265)
                      |+|+|+||||||||+|+|||.    .++||++||+|+|+ |+..+|+.+.... ......   ...            ..
T Consensus         2 IaV~SgKGGVGKTT~a~nLA~----~l~~V~liD~D~~~~n~~~~l~~~~~~~-~~~~~~---~~~------------~~   61 (179)
T cd03110           2 IAVISGKGGTGKTTVTAALAA----LLKNVVLADCDVDAPNLHLFLKPEIEEE-EDFIVG---GKK------------AV   61 (179)
T ss_pred             EEEEECCCCCHHHHHHHHHHH----HCCCCEEEEECCCCCCHHHHCCCCCCCC-EEEEEC---CCC------------CE
T ss_conf             899958998609999999999----7428719994189985777718765632-122304---653------------35


Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf             01488745775000123222210233322476510278203310133322221011233100111112311378887533
Q gi|254780806|r   88 IIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLL  167 (265)
Q Consensus        88 iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~~~~  167 (265)
                      +.|......+....+.     .....+.+....+++|||||||||||++..+.+++.+||.+++|++|+++|++++.+++
T Consensus        62 ~~~~~~~~~g~~~~~~-----~~~~~~~~~~~~~~~~D~viiD~Ppg~~~~~~~al~~ad~~iiVttP~~~si~d~~r~i  136 (179)
T cd03110          62 IDPELCISCGLCGKLV-----TEVRKHAKEIAKAEGAELIIIDGPPGIGCPVIASLTGADAALLVTEPTPSGLHDLERAV  136 (179)
T ss_pred             ECHHHHHHCCCHHHHH-----HHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCHHHHHHHHHHH
T ss_conf             1506653235176889-----99999999986443799899818999757899999739949998199478999999999


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             5777655432026774310020231253100112689998808520156267
Q gi|254780806|r  168 ETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIP  219 (265)
Q Consensus       168 ~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip  219 (265)
                      ++++++    +.  ++ ++|+||++.+.....+ .+++.+.++.++++ .||
T Consensus       137 ~l~~~~----~~--~~-gvV~Nr~~~~~~~~~~-i~~~~~~~~vp~LG-~iP  179 (179)
T cd03110         137 ELVRHF----GI--PV-GVVINKYDLNDEIAEE-IEDYCEEEGIPILG-KIP  179 (179)
T ss_pred             HHHHHC----CC--CE-EEEEECCCCCCCCHHH-HHHHHHHHCCCEEE-ECC
T ss_conf             999982----99--78-9999688788763489-99999980999898-387


No 39 
>COG4963 CpaE Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]
Probab=99.97  E-value=1.5e-30  Score=197.76  Aligned_cols=236  Identities=23%  Similarity=0.333  Sum_probs=191.3

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCC-
Q ss_conf             687499998088988889999999999998-7995999987877-6801121246333454116763025771210244-
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLDPQ-GNASTGLGIELYDRKYSSYDLLIEEKNINQILIQ-   80 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~-   80 (265)
                      +++|+++|.+.|||+|-||+|.|+|+.++. .++.|+++|+|-| |+...+|+.++.   .++.++..+++.+++.... 
T Consensus       102 ~~~r~iafl~akgg~g~stlA~n~a~~l~~~~~~~v~L~DL~~~~G~~~~~l~~~~a---~~i~~~~~~peRLDq~lld~  178 (366)
T COG4963         102 QQGRELAFLGAKGGVGTSTLAHNLAKGLAILSGAAVLLVDLDLQGGTAALYLDQDPA---FGIAEAVKQPERLDQVLLDS  178 (366)
T ss_pred             HHCEEEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHCCCCCH---HHHHHHHCCHHHHHHHHHHH
T ss_conf             103289999605886668999999999864148738999768887612343078721---45898860978760787778


Q ss_pred             ---CCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCC
Q ss_conf             ---44442000148874577500012322221023332247651027820331013332222101123310011111231
Q gi|254780806|r   81 ---TAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEF  157 (265)
Q Consensus        81 ---~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~  157 (265)
                         ...++++++|+..++..+......   ...+|    ...++..||+|++|.|-.+.+|+...|..||.++++++|+.
T Consensus       179 ~~~~~~~~l~ll~a~~~~~~~~d~~~~---~~~~L----l~~~~~~~~~vV~Dlp~~~~~~t~~vL~~Sd~iviv~e~sl  251 (366)
T COG4963         179 LLTRLASGLKLLAAPTELAKNYDLKTG---AVERL----LDLLRGSFDFVVVDLPNIWTDWTRQVLSGSDEIVIVAEPSL  251 (366)
T ss_pred             HHHCCCCCCEEECCCCCHHHHCCCCCC---HHHHH----HHHHHCCCCEEEECCCCCCCHHHHHHHHCCCEEEEEECCCH
T ss_conf             986168876330377445652153312---69999----99764028838971897662589999862884999963638


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHH-HHHHHCCCCEEE
Q ss_conf             1378887533577765543202677431002023125310011268999880852015626786889-877737985799
Q gi|254780806|r  158 FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRI-SEAPSYGKPAII  236 (265)
Q Consensus       158 ~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i-~~a~~~g~pv~~  236 (265)
                      .|++.+.++++.+++++..    .+...+|+|||..+....   .+++.+.++.+.+. .+|.|... ..|.++|+++.+
T Consensus       252 ~slR~ak~lld~l~~~r~~----~~~p~lv~n~~~~~~~~~---~~dl~~~~~i~~~~-~~p~d~~~~~~A~n~g~~l~E  323 (366)
T COG4963         252 ASLRNAKELLDELKRLRPN----DPKPILVLNRVGVPKRPE---PSDLEEILGIESLL-VLPFDPALFGDAANNGRMLSE  323 (366)
T ss_pred             HHHHHHHHHHHHHHHHCCC----CCCCEEEEEECCCCCCCC---HHHHHHHHCCCHHC-CCCCCCHHHHHHHCCCCCCCC
T ss_conf             9899999999999973779----889568865227888999---99998884884001-366770544444206960222


Q ss_pred             ECCCCHHHHHHHHHHHHHHHH
Q ss_conf             979998999999999999999
Q gi|254780806|r  237 YDLKCAGSQAYLKLASELIQQ  257 (265)
Q Consensus       237 ~~p~s~~a~~~~~la~el~~~  257 (265)
                      .+|++++++++..++..+..+
T Consensus       324 ~~~~~~~~k~l~~la~~l~~~  344 (366)
T COG4963         324 VDPGSPAAKALAQLAQSLGGR  344 (366)
T ss_pred             CCCCCHHHHHHHHHHHHHCCC
T ss_conf             377875889999999985376


No 40 
>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]
Probab=99.96  E-value=1.1e-28  Score=187.05  Aligned_cols=229  Identities=23%  Similarity=0.314  Sum_probs=160.2

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHC-CCCEEEEECCCCCCCCHHHCCCCC-CCCCCEEEEEEC---------------
Q ss_conf             999980889888899999999999987-995999987877680112124633-345411676302---------------
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAI-GENVLLIDLDPQGNASTGLGIELY-DRKYSSYDLLIE---------------   70 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~-g~rVllID~D~q~~~~~~l~~~~~-~~~~ti~~~l~~---------------   70 (265)
                      +|+|+ +|||+||||+|+-||..+..+ |++||+||+||..|++..||++.. +.-....+++..               
T Consensus         2 kIaI~-GKGG~GKTtiaalll~~l~~~~~~~VLvVDaDpd~nL~~~LGve~~~~~lg~~~e~~~k~~~a~~~~~~~~~fk   80 (255)
T COG3640           2 KIAIT-GKGGVGKTTIAALLLKRLLSKGGYNVLVVDADPDSNLPEALGVEEPMKYLGGKRELLKKRTGAEPGGPPGEMFK   80 (255)
T ss_pred             EEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             69996-59976589999999999986489549999489999907762999987553008999999861478999553001


Q ss_pred             -C---CCHH-HCCCCCCCCCEEECCCC-CCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHH
Q ss_conf             -5---7712-10244444420001488-7457750001232222102333224765102782033101333222210112
Q gi|254780806|r   71 -E---KNIN-QILIQTAIPNLSIIPST-MDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMA  144 (265)
Q Consensus        71 -~---~~l~-~~i~~~~~~~l~iipa~-~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~  144 (265)
                       .   .++. +.++  ..++++++.-+ +.-.+-.+ ..   ....+++++|.....++|||||+||.+|+.++.+....
T Consensus        81 ~~~~~~di~~e~~~--e~~~~~LLvmGkie~~GeGC-~C---p~~allR~~l~~l~~~~~e~VivDtEAGiEHfgRg~~~  154 (255)
T COG3640          81 ENPLVSDLPDEYLV--ENGDIDLLVMGKIEEGGEGC-AC---PMNALLRRLLRHLILNRYEVVIVDTEAGIEHFGRGTIE  154 (255)
T ss_pred             CCCCHHHHHHHHHH--HCCCCCEEEECCCCCCCCCC-CC---HHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHCCCCCC
T ss_conf             37543351698850--06880079952556799743-16---27899999999975166748999633456665656325


Q ss_pred             HHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHH
Q ss_conf             33100111112311378887533577765543202677431002023125310011268999880852015626786889
Q gi|254780806|r  145 AADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRI  224 (265)
Q Consensus       145 aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i  224 (265)
                      .+|.+|+|+.|+.-|++.+.++.+..+.    .+  ++..++|+|+++..    .+.+.......+.+++. +||+|..+
T Consensus       155 ~vD~vivVvDpS~~sl~taeri~~L~~e----lg--~k~i~~V~NKv~e~----e~~~~~~~~~~~~~vlg-~iP~d~~v  223 (255)
T COG3640         155 GVDLVIVVVDPSYKSLRTAERIKELAEE----LG--IKRIFVVLNKVDEE----EELLRELAEELGLEVLG-VIPYDPEV  223 (255)
T ss_pred             CCCEEEEEECCCHHHHHHHHHHHHHHHH----HC--CCEEEEEEEECCCH----HHHHHHHHHCCCCEEEE-ECCCCHHH
T ss_conf             7877999957877888889999999987----18--75499999503411----57777653227974899-71698788


Q ss_pred             HHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf             877737985799979998999999999999999
Q gi|254780806|r  225 SEAPSYGKPAIIYDLKCAGSQAYLKLASELIQQ  257 (265)
Q Consensus       225 ~~a~~~g~pv~~~~p~s~~a~~~~~la~el~~~  257 (265)
                      .++...|.|++.+.   .+.+++.++++.+++.
T Consensus       224 ~~~dl~G~pl~~~~---~v~~~i~~I~~~l~~~  253 (255)
T COG3640         224 VEADLKGEPLNEEP---EVLKEIEEIAERLIKL  253 (255)
T ss_pred             HHCCCCCCCCCCCH---HHHHHHHHHHHHHHHC
T ss_conf             74225688421235---5578999999999850


No 41 
>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=99.96  E-value=7e-30  Score=193.95  Aligned_cols=180  Identities=23%  Similarity=0.315  Sum_probs=139.7

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCC
Q ss_conf             9876874999980889888899999999999987995999987877-680112124633345411676302577121024
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYSSYDLLIEEKNINQILI   79 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~   79 (265)
                      |++..-|+++|.|-|-|.||||+++|+|+++|+.||||||||.|.- ..++-.|..  .+...++.++|.+..+++|+|.
T Consensus        14 ~a~~e~K~l~itS~~~~eGKsT~S~NiA~~fAqaGyKTLlIDgD~R~sv~~~~Fk~--~n~~~GLtn~L~g~~dl~~~i~   91 (207)
T TIGR01007        14 GAEQEIKVLLITSVKAGEGKSTTSANIAVSFAQAGYKTLLIDGDMRNSVMSGTFKS--QNKIKGLTNFLSGNTDLSDAIC   91 (207)
T ss_pred             CCCCCEEEEEEEECCCCCCCEEEEHHHHHHHHHCCCEEEEEECCCCCCCEEEEECC--CCCCCCCHHHHCCCCCHHHHHH
T ss_conf             35787058998411058886241078899998568558887546586603678658--8876563332214545333420


Q ss_pred             CCCC-CCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHH--HHHCCCCCCCC
Q ss_conf             4444-42000148874577500012322221023332247651027820331013332222101123--31001111123
Q gi|254780806|r   80 QTAI-PNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAA--ADSILVPLQCE  156 (265)
Q Consensus        80 ~~~~-~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~a--ad~viip~~p~  156 (265)
                      .|.. +||+||+|++-+-.-...+.     ...+.+ |.+.+++.|||||||||| ++..+.+++.+  +|..|+|+..+
T Consensus        92 ~T~isenL~vi~sG~vPPNPt~LL~-----s~~F~~-l~e~~~~~fD~iiiDTPP-ig~V~DAai~a~~~d~~~LV~~A~  164 (207)
T TIGR01007        92 ETNISENLDVITSGPVPPNPTELLQ-----SSNFKT-LIETLRKYFDYIIIDTPP-IGTVIDAAIIARAVDASILVTDAG  164 (207)
T ss_pred             CCCCCCCCEEECCCCCCCCHHHHHH-----HHHHHH-HHHHHHCCCCEEEEEECC-CCHHHHHHHHHHHHCCEEEEEECC
T ss_conf             2654678727517887877547888-----899999-999987168889995188-666788999998729779887225


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCC
Q ss_conf             113788875335777655432026774310020231253
Q gi|254780806|r  157 FFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRN  195 (265)
Q Consensus       157 ~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~  195 (265)
                      ...-+.+.+..+.+++.    +.  .++|||+|+++...
T Consensus       165 ~~~k~~v~KAK~~LEq~----G~--~~LGvvLNK~d~s~  197 (207)
T TIGR01007       165 KIKKREVKKAKEQLEQA----GS--KFLGVVLNKVDISV  197 (207)
T ss_pred             CCCHHHHHHHHHHHHHH----CC--CEEEEEECCCCCCC
T ss_conf             32646789999999861----78--41158888825765


No 42 
>COG0489 Mrp ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=99.96  E-value=1.1e-28  Score=187.01  Aligned_cols=205  Identities=23%  Similarity=0.337  Sum_probs=148.3

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC
Q ss_conf             68749999808898888999999999999879959999878776-80112124633345411676302577121024444
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA   82 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~-~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~   82 (265)
                      +..++|+|.|+|||+||||+++|||.++|++|+||++||+|..+ +...+|+.+..   ..+.+.+.+.. +.+++....
T Consensus        55 ~~~~~I~V~S~kgGvGKStva~nLA~alA~~G~rVlliDaD~~gps~~~~l~~~~~---~g~~~~~~g~~-~~~~~~~~~  130 (265)
T COG0489          55 GVKNVIAVTSGKGGVGKSTVAVNLAAALAQLGKRVLLLDADLRGPSIPRMLGLENL---PGLTELLAGEA-LEPVIQHDG  130 (265)
T ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCHHHCCCCCC---CCCCCCCCCCC-CCCCEECCC
T ss_conf             66618999758998756899999999999639938999674669863554089865---56541137871-143220266


Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHH-HHHHCCCCCCCCCHHHH
Q ss_conf             44200014887457750001232222102333224765102782033101333222210112-33100111112311378
Q gi|254780806|r   83 IPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMA-AADSILVPLQCEFFALE  161 (265)
Q Consensus        83 ~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~-aad~viip~~p~~~s~~  161 (265)
                      ..++++++...     ....+...-....+.++|.+..|.+||||||||||+.+..-...+. ..|.+++|++|......
T Consensus       131 ~~~lsi~~~~~-----~p~~~r~~l~s~~~~qll~~~~~~~~D~vIID~PP~~g~~d~~i~~~~~~g~viVt~p~~~~~~  205 (265)
T COG0489         131 IKVLSILPLGP-----VPVIPRGLLGSKAMLQLLEDVLWGEYDYVIIDTPPGTGDADATVLQRIPDGVVIVTTPGKTALE  205 (265)
T ss_pred             CCEEEEEECCC-----CCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHCCCEEEEEECCCCCHHH
T ss_conf             55047883288-----9989467763389999999974568888999699986427778875138859999667735599


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHH-HHHHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf             8875335777655432026774310020231253100-112689998808520156267868898
Q gi|254780806|r  162 GLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLS-QQVVSDVRKNLGGKVYNTVIPRNVRIS  225 (265)
Q Consensus       162 ~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~-~~~~~~l~~~~~~~v~~~~Ip~~~~i~  225 (265)
                      .+.+.+++++..      +.+++|+|.||........ .---+...+.|+ +.+. .+|.+....
T Consensus       206 ~v~ka~~~~~~~------~~~vlGvv~Nm~~~~~~~~~~g~~~~~~~~~~-~~~g-~~p~~~~~~  262 (265)
T COG0489         206 DVKKAIDMLEKA------GIPVLGVVENMSYFICPRCGEGGGEKYAERYG-PYLG-SIPLDPSAR  262 (265)
T ss_pred             HHHHHHHHHHHC------CCCEEEEEECCCCCCCCCCCCCCHHHHHHHHC-CCCC-CCCCCHHHH
T ss_conf             999999999874------99347999668666665557885233566511-1026-688674544


No 43 
>PRK11519 tyrosine kinase; Provisional
Probab=99.96  E-value=6.2e-29  Score=188.41  Aligned_cols=179  Identities=21%  Similarity=0.329  Sum_probs=138.4

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCC
Q ss_conf             9876874999980889888899999999999987995999987877-680112124633345411676302577121024
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYSSYDLLIEEKNINQILI   79 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~   79 (265)
                      +.++.+|||.|.|.-.|.||||+++|||..+|+.|+||||||+|.. +.++.+|+...   ..++.+++.+..++.++|.
T Consensus       521 ~~~~~~~vi~vTS~~pgEGKSt~a~nLA~~~A~~G~rvLLID~DlRrp~l~~~~~~~~---~~GLs~~L~g~~~~~~~i~  597 (720)
T PRK11519        521 MMQAQNNVLMMTGVSPSIGKTFVCANLAAVISQTNKRVLLIDCDMRKGYTHELLGTNN---VNGLSEILIGQGDITTAAK  597 (720)
T ss_pred             CCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHCCCCC---CCCHHHHCCCCCCHHHHCC
T ss_conf             4688876799970899997899999999999837991999938777701677539999---9985998079997899703


Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCH--HHHHHHCCCCCCCCC
Q ss_conf             444442000148874577500012322221023332247651027820331013332222101--123310011111231
Q gi|254780806|r   80 QTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNA--MAAADSILVPLQCEF  157 (265)
Q Consensus        80 ~~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~a--l~aad~viip~~p~~  157 (265)
                      ++..+|||+||++.....-...+.+     .++.+.+ ..++.+||||||||||-.. .+...  -..+|.++.|+....
T Consensus       598 ~~~~~~l~vl~~G~~~pnp~elL~s-----~~~~~ll-~~l~~~yD~IIiDtpPv~~-v~Da~~la~~aD~~l~Vvr~g~  670 (720)
T PRK11519        598 PTSIANFDLIPRGQVPPNPSELLMS-----ERFAELV-AWASKNYDLVLIDTPPILA-VTDAAIVGRHVGTTLMVARYAV  670 (720)
T ss_pred             CCCCCCEEEECCCCCCCCHHHHHCC-----HHHHHHH-HHHHHHCCEEEEECCCCCC-CHHHHHHHHHCCEEEEEEECCC
T ss_conf             5798998997699999498998387-----5999999-9998529999993999652-3589999997897999998995


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCC
Q ss_conf             13788875335777655432026774310020231253
Q gi|254780806|r  158 FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRN  195 (265)
Q Consensus       158 ~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~  195 (265)
                      .....+...++.+..      .+.++.|+|+|.++++.
T Consensus       671 t~~~~v~~a~~~l~~------~~~~v~G~VlN~v~~~~  702 (720)
T PRK11519        671 NTLKEVETSLSRFEQ------NGIPVKGVILNSIFRRA  702 (720)
T ss_pred             CCHHHHHHHHHHHHH------CCCCEEEEEECCCCCCC
T ss_conf             789999999999996------89974899988976665


No 44 
>COG1348 NifH Nitrogenase subunit NifH (ATPase) [Inorganic ion transport and metabolism]
Probab=99.96  E-value=1.1e-28  Score=187.03  Aligned_cols=239  Identities=24%  Similarity=0.358  Sum_probs=178.9

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECC-----CCHHHCCCCC
Q ss_conf             49999808898888999999999999879959999878776801121246333454116763025-----7712102444
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEE-----KNINQILIQT   81 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~-----~~l~~~i~~~   81 (265)
                      |.|+|. +|||.||||++.|+|.+||..|+||++|-|||.++.|..|.-  -...+|+.|.+.+.     ..+++.+. +
T Consensus         2 r~iAiY-GKGGIGKSTts~N~aAAla~~GkkVl~vGCDPKaDSTr~Llg--g~~ipTVld~lre~~~~e~~~ledvi~-~   77 (278)
T COG1348           2 RQIAIY-GKGGIGKSTTSQNLAAALAELGKKVLIVGCDPKADSTRLLLG--GKAIPTVLDTLREKGEVEDLELEDVIF-T   77 (278)
T ss_pred             CEEEEE-CCCCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHC--CCCCCHHHHHHHHCCCCCCCCHHHHEE-C
T ss_conf             379996-278767312677899999972981799747987632777747--866656999998618644588778212-0


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHH------HHHHCCCCCCC
Q ss_conf             444200014887457750001232222102333224765102782033101333222210112------33100111112
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMA------AADSILVPLQC  155 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~------aad~viip~~p  155 (265)
                      ...++.++-|+..-.+....-.........|.+ |. ...+..|||++|.   +++..+..++      -||++.+|+.-
T Consensus        78 Gf~gv~CVEsGGPepGvGCAGRGVitai~~Le~-lg-af~~~~DvviyDV---LGDVVCGGFAmPiReg~AdeiyIVtSg  152 (278)
T COG1348          78 GFGGVKCVESGGPEPGVGCAGRGVITAINLLEE-LG-AFEEDLDVVIYDV---LGDVVCGGFAMPIREGYADEIYIVTSG  152 (278)
T ss_pred             CCCCEEEEECCCCCCCCCCCCCHHHHHHHHHHH-HC-CCCCCCCEEEEEC---CCCEEECCEEEEHHCCCCCEEEEEECC
T ss_conf             678537742599899988465119999999998-18-7301287899953---577347460002002666379999568


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEE
Q ss_conf             31137888753357776554320267743100202312531001126899988085201562678688987773798579
Q gi|254780806|r  156 EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAI  235 (265)
Q Consensus       156 ~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~  235 (265)
                      +++++..+.++.+-+.++..+.+.  +.-|++-|.=  +....++++..+.+.+|.+++. .||++..+++|-.+|++|.
T Consensus       153 e~MalYAANNI~kgi~k~a~~~~~--rLgGiIcNsR--~~~~e~e~v~~fa~~igt~li~-~vPr~~ivq~aE~~~kTvi  227 (278)
T COG1348         153 EMMALYAANNIAKGIRKYAKTGGV--RLGGIICNSR--SVDRERELVEAFAERLGTQLIH-FVPRDNIVQKAELNGKTVI  227 (278)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCC--CEEEEEECCC--CCCCHHHHHHHHHHHHCCCEEE-ECCCHHHHHHHHHCCCCHH
T ss_conf             358999988999999998733796--3145774577--7643799999999984885276-3351278899987486611


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             997999899999999999999998
Q gi|254780806|r  236 IYDLKCAGSQAYLKLASELIQQER  259 (265)
Q Consensus       236 ~~~p~s~~a~~~~~la~el~~~~~  259 (265)
                      ++.|+|..++.|++||+.+++.++
T Consensus       228 e~~P~s~~a~~yr~LA~~I~~n~~  251 (278)
T COG1348         228 EYAPDSNQAEEYRELAKKILENEK  251 (278)
T ss_pred             HHCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             318462489999999999983778


No 45 
>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=99.96  E-value=8e-29  Score=187.77  Aligned_cols=158  Identities=23%  Similarity=0.346  Sum_probs=116.6

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCE
Q ss_conf             9999808898888999999999999879959999878776-801121246333454116763025771210244444420
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNL   86 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~-~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l   86 (265)
                      ||+|.|+||||||||+++|||.+|+++|+||+++|+|..+ |++.               ++.+                
T Consensus         1 vi~v~s~kggvgkst~~~~la~~l~~~g~~v~~~d~di~gpsip~---------------~~rG----------------   49 (169)
T cd02037           1 VIAVMSGKGGVGKSTVAVNLALALAKLGYKVGLLDADIYGPSIPK---------------MWRG----------------   49 (169)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCE---------------EEEC----------------
T ss_conf             989974999881999999999999987997899971379997550---------------1204----------------


Q ss_pred             EECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCC--CCCHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             0014887457750001232222102333224765102782033101333222--21011233100111112311378887
Q gi|254780806|r   87 SIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLL--TMNAMAAADSILVPLQCEFFALEGLS  164 (265)
Q Consensus        87 ~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~--~~~al~aad~viip~~p~~~s~~~~~  164 (265)
                                         +.....+.+++....|+++||+|||+|||.|+.  +......+|.+++|++|+..|+.++.
T Consensus        50 -------------------p~~~~~i~q~l~~~~w~~lDyLIID~PPGtgD~~lt~~~~~~~d~~IvVTTP~~~s~~Da~  110 (169)
T cd02037          50 -------------------PMKMGAIKQFLTDVDWGELDYLVIDMPPGTGDEHLTLAQSLPIDGAVIVTTPQEVALDDVR  110 (169)
T ss_pred             -------------------HHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHCCCCCEEEEECCCHHHHHHHH
T ss_conf             -------------------7389999999985254667889996899987077879875056747999469588999999


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCEEE---CC-----CHHHHHHHHHHHHHHCCCCCCCCCCCCH
Q ss_conf             5335777655432026774310020231---25-----3100112689998808520156267868
Q gi|254780806|r  165 QLLETVEEVRRTVNSALDIQGIILTMFD---SR-----NSLSQQVVSDVRKNLGGKVYNTVIPRNV  222 (265)
Q Consensus       165 ~~~~~i~~~~~~~~~~~~~~~iv~N~~~---~~-----~~~~~~~~~~l~~~~~~~v~~~~Ip~~~  222 (265)
                      +.++++++.      +.++.|+|.||..   +.     .-....-.+++.+.++.+++. .||.|.
T Consensus       111 r~i~~~~~~------~i~i~GvVeNMs~~~c~~c~~~~~ifg~~~~~~la~~~~i~~Lg-~IP~dp  169 (169)
T cd02037         111 KAIDMFKKV------NIPILGVVENMSYFVCPHCGKKIYIFGKGGGEKLAEELGVPLLG-KIPLDP  169 (169)
T ss_pred             HHHHHHHHC------CCCEEEEEECCCCCCCCCCCCEEECCCCCHHHHHHHHHCCCEEE-ECCCCC
T ss_conf             999999975------99707999879666079999735278884499999995999898-728999


No 46 
>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional
Probab=99.96  E-value=1.7e-28  Score=185.81  Aligned_cols=179  Identities=18%  Similarity=0.274  Sum_probs=138.3

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCC
Q ss_conf             9876874999980889888899999999999987995999987877-680112124633345411676302577121024
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYSSYDLLIEEKNINQILI   79 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~   79 (265)
                      +.++..|||.|.|.--|.||||+|+|||..+|+.|+||+|||||.. +.++..|+...   ..++.+++.+..++.++|.
T Consensus       526 ~~~~~~kvi~vTS~~pgEGKSt~a~nLA~~~A~~G~rvLLID~DlRrp~l~~~~~~~~---~~GLs~~L~g~~~~~~~i~  602 (726)
T PRK09841        526 MMETENNILMITGATPDSGKTFVSSTLAAVIAQSDQKVLFIDADLRRGYSHNLFTVSN---EHGLSEYLAGKDELNKVIQ  602 (726)
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHCCCCC---CCCHHHHHCCCCCHHHHCC
T ss_conf             2688886899977999997799999999999847995999828877710776159999---9877998389998899330


Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHH--HHHHHCCCCCCCCC
Q ss_conf             4444420001488745775000123222210233322476510278203310133322221011--23310011111231
Q gi|254780806|r   80 QTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAM--AAADSILVPLQCEF  157 (265)
Q Consensus        80 ~~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al--~aad~viip~~p~~  157 (265)
                      ++..+|||+||++.....-...+.+     .++.+.| ..++.+||||||||||-+. .+...+  ..+|.++.|+....
T Consensus       603 ~~~~~~ldvl~aG~~p~nP~elL~s-----~~~~~ll-~~l~~~yD~IIiDtPPvl~-v~Da~~l~~~~D~~l~Vvr~g~  675 (726)
T PRK09841        603 HFGKGGFDVITRGQVPPNPSELLMR-----DRMRQLL-EWANDHYDLVIVDTPPMLA-VSDAAVVGRSVGTSLLVARFGL  675 (726)
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHCC-----HHHHHHH-HHHHHCCCEEEEECCCCCC-CCHHHHHHHHCCEEEEEEECCC
T ss_conf             2798998998289999798999587-----6999999-9998139999991999653-4159999997895999997996


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCC
Q ss_conf             13788875335777655432026774310020231253
Q gi|254780806|r  158 FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRN  195 (265)
Q Consensus       158 ~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~  195 (265)
                      .....+.+.++.+..      .+.++.|+|+|.++.+.
T Consensus       676 T~~~~~~~a~~~l~~------~~~~v~G~vlN~v~~~~  707 (726)
T PRK09841        676 NTAKEVSLSMQRLEQ------AGVNIKGAILNGVIKRA  707 (726)
T ss_pred             CCHHHHHHHHHHHHH------CCCCEEEEEECCCCCCC
T ss_conf             889999999999997------89975899982886566


No 47 
>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=99.95  E-value=2.8e-28  Score=184.54  Aligned_cols=104  Identities=59%  Similarity=0.872  Sum_probs=93.7

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCEE
Q ss_conf             99998088988889999999999998799599998787768011212463334541167630257712102444444200
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLS   87 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l~   87 (265)
                      +|+|.|.||||||||+++|||+.+++.|+||++||+|||                                         
T Consensus         1 vi~~~n~KGGvGKtt~~~~la~~~a~~g~~vl~iD~DpQ-----------------------------------------   39 (104)
T cd02042           1 VIAVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQ-----------------------------------------   39 (104)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCC-----------------------------------------
T ss_conf             999973899876899999999999977992999977988-----------------------------------------


Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf             01488745775000123222210233322476510278203310133322221011233100111112311378887533
Q gi|254780806|r   88 IIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLL  167 (265)
Q Consensus        88 iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~~~~  167 (265)
                                                          ||||||||||+.+..+.+++.+||++++|+.|+.++++++.+++
T Consensus        40 ------------------------------------yD~iiIDtpp~~~~~~~~al~~aD~viiP~~p~~~~~~~~~~~~   83 (104)
T cd02042          40 ------------------------------------YDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSPLDLDGLEKLL   83 (104)
T ss_pred             ------------------------------------CCEEEEECCCCCCHHHHHHHHHCCEEEEECCCCHHHHHHHHHHH
T ss_conf             ------------------------------------88899979499989999999978999998369889999999999


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             5777655432026774310020
Q gi|254780806|r  168 ETVEEVRRTVNSALDIQGIILT  189 (265)
Q Consensus       168 ~~i~~~~~~~~~~~~~~~iv~N  189 (265)
                      +.+... +..++.....++++|
T Consensus        84 ~~~~~~-~~~~~~~~~~~~v~~  104 (104)
T cd02042          84 ETLILE-DRLNPDLDILGILPT  104 (104)
T ss_pred             HHHHHH-HHHCCCCEEEEEEEC
T ss_conf             999999-976999889999809


No 48 
>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=99.95  E-value=1.9e-27  Score=179.72  Aligned_cols=120  Identities=28%  Similarity=0.421  Sum_probs=96.2

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCEE
Q ss_conf             99998088988889999999999998799599998787768011212463334541167630257712102444444200
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLS   87 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l~   87 (265)
                      ||+|.|+||||||||+++|||.+|+++|+||+++|+|...                                    .|+ 
T Consensus         1 vi~v~sgKgGvGkt~~~~nLa~~la~~G~~vll~D~D~g~------------------------------------an~-   43 (139)
T cd02038           1 IIAVTSGKGGVGKTNISANLALALAKLGKRVLLLDADLGL------------------------------------ANL-   43 (139)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC------------------------------------CCC-
T ss_conf             9899649999839999999999999789969999898999------------------------------------657-


Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf             01488745775000123222210233322476510278203310133322221011233100111112311378887533
Q gi|254780806|r   88 IIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLL  167 (265)
Q Consensus        88 iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~~~~  167 (265)
                                                         +|||||||+|||.+..+...+.+||.+++|++||+.|+.+++.++
T Consensus        44 -----------------------------------~~D~viiD~~aG~~~~~~~~~~~ad~~lvV~tpeptSi~DAYalI   88 (139)
T cd02038          44 -----------------------------------DYDYIIIDTGAGISDNVLDFFLAADEVIVVTTPEPTSITDAYALI   88 (139)
T ss_pred             -----------------------------------CCCEEEEECCCCCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHH
T ss_conf             -----------------------------------999999948999877899999958957999589706799999999


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHH
Q ss_conf             57776554320267743100202312531001126899
Q gi|254780806|r  168 ETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDV  205 (265)
Q Consensus       168 ~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l  205 (265)
                      +.+..   ..+  ....++|+||++.. ...++..+.+
T Consensus        89 K~l~~---~~~--~~~~~lvvN~v~s~-~ea~~~~~~l  120 (139)
T cd02038          89 KKLAK---QLR--VLNFRVVVNRAESP-KEGKKVFKRL  120 (139)
T ss_pred             HHHHH---HCC--CCCEEEEEECCCCH-HHHHHHHHHH
T ss_conf             99999---639--99759999568999-9999999999


No 49 
>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]
Probab=99.95  E-value=1.5e-26  Score=174.57  Aligned_cols=234  Identities=21%  Similarity=0.231  Sum_probs=153.3

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEE-E--EEECC-CC--------
Q ss_conf             4999980889888899999999999987995999987877-6801121246333454116-7--63025-77--------
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYSSY-D--LLIEE-KN--------   73 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~-~--~l~~~-~~--------   73 (265)
                      +-|+|.|+|||+||||+++|||..|+.. +|++++|+|.- .|+..+|+.+..+...-+. .  .+..+ +.        
T Consensus         2 m~vAV~sGKGGtGKTTva~~la~~l~~~-~~~~l~DcDVe~PNl~l~l~~e~~~~~e~~~~~~p~i~~e~C~~CG~C~~v   80 (284)
T COG1149           2 MQVAVASGKGGTGKTTVAANLAVLLGDK-YKLVLADCDVEAPNLHLLLGVEVLEEEEVIRGEIPEIDPEKCIRCGKCAEV   80 (284)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHCCC-CCEEEEECCCCCCCCCEEECCCHHHHHHHHHHHCCCCCHHHCCCCCCHHHH
T ss_conf             2799963688777022899999983665-224777657789986167445011356778750460375774301726876


Q ss_pred             -HHHCCCCCCCCCEEECC------------CCCC---------------CCCCC-C----CCCCCCCCCHHHHHHHHHHH
Q ss_conf             -12102444444200014------------8874---------------57750-0----01232222102333224765
Q gi|254780806|r   74 -INQILIQTAIPNLSIIP------------STMD---------------LLGIE-M----ILGGEKDRLFRLDKALSVQL  120 (265)
Q Consensus        74 -l~~~i~~~~~~~l~iip------------a~~~---------------~~~~~-~----~l~~~~~~~~~l~~~l~~~l  120 (265)
                       -.++++--..++..+.|            ...+               ..... .    .+.-.......|.+.+....
T Consensus        81 C~f~Ai~~~~~~~~~~~~~lC~GCgaC~~~CP~~AI~~~~~~~G~i~~~~~~~g~~li~g~l~vGe~~s~~lV~~~kk~a  160 (284)
T COG1149          81 CRFGAIVVLPGGKPVLNPDLCEGCGACSIVCPEPAIEEEPVVIGKIYESKTDYGFPLISGRLNVGEEESGKLVTALKKHA  160 (284)
T ss_pred             CCCCEEEECCCCCEECCCCCCCCCCCCEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHHHHHHHH
T ss_conf             78880897378860028020267663332478765554320003899987689963688744678444513789998755


Q ss_pred             HCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             10278203310133322221011233100111112311378887533577765543202677431002023125310011
Q gi|254780806|r  121 TSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       121 ~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      .+..|++|||+|||.+.-...++..+|++|+|++|.++++.++.++++..+.++.    +   .++|+||++....   +
T Consensus       161 ~E~~~~~IIDsaaG~gCpVi~sl~~aD~ai~VTEPTp~glhD~kr~~el~~~f~i----p---~~iViNr~~~g~s---~  230 (284)
T COG1149         161 KELADLLIIDSAAGTGCPVIASLKGADLAILVTEPTPFGLHDLKRALELVEHFGI----P---TGIVINRYNLGDS---E  230 (284)
T ss_pred             HHHCCEEEEECCCCCCCHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCC----C---EEEEEECCCCCCH---H
T ss_conf             6532125885799789717776416877999816885236689999999998399----5---4999966777720---8


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH
Q ss_conf             2689998808520156267868898777379857999799989999999999999
Q gi|254780806|r  201 VVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGSQAYLKLASELI  255 (265)
Q Consensus       201 ~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s~~a~~~~~la~el~  255 (265)
                       +++..+..|.+++. .||+|..+.++..+|.|+..  ++++.+..+...+.++.
T Consensus       231 -ie~~~~e~gi~il~-~IPyd~~i~~~~~~g~~~~~--~~~k~~~~~~~~~~~~~  281 (284)
T COG1149         231 -IEEYCEEEGIPILG-EIPYDKDIPEAYVNGEPFVE--PDSKEAEAILEEAEKLK  281 (284)
T ss_pred             -HHHHHHHCCCCEEE-ECCCCHHHHHHHHCCCCCCC--CCCHHHHHHHHHHHHHH
T ss_conf             -99988873997268-78864258999857885313--55268899999999987


No 50 
>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=99.94  E-value=1e-27  Score=181.29  Aligned_cols=195  Identities=19%  Similarity=0.269  Sum_probs=112.8

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEE----EEECCCCHHHCCCCCC
Q ss_conf             499998088988889999999999998799599998787768011212463334541167----6302577121024444
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYD----LLIEEKNINQILIQTA   82 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~----~l~~~~~l~~~i~~~~   82 (265)
                      |+| |.++||||||||+|+++|..||+.|+|||+||.||+.|++..|+....... +...    +...+-+....+.+ .
T Consensus         1 r~i-~~~GKGGVGKTT~AaalA~~lA~~G~kVLlvstDPahsLsd~f~~~~~~~~-~~v~~~~nL~a~eid~~~~~~~-~   77 (254)
T cd00550           1 RYI-FFGGKGGVGKTTISAATAVRLAEQGKKVLLVSTDPAHSLSDSFNQEFGKGP-TPVKGVENLSAMEIDPQEALEE-Y   77 (254)
T ss_pred             CEE-EEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHCCCCCCCC-CEECCCCCCEEEEECHHHHHHH-H
T ss_conf             989-996898554899999999999968994999958986448898488667887-1103668845787288999999-9


Q ss_pred             CCC-EEECCCCCCCCCCCC----CC-CCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCC---CCC--------CHHH-
Q ss_conf             442-000148874577500----01-23222210233322476510278203310133322---221--------0112-
Q gi|254780806|r   83 IPN-LSIIPSTMDLLGIEM----IL-GGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNL---LTM--------NAMA-  144 (265)
Q Consensus        83 ~~~-l~iipa~~~~~~~~~----~l-~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~---~~~--------~al~-  144 (265)
                      +.. .+.+.+.......+.    .+ ....+....+.+.+...-+++||||||||||.-..   +..        ..|. 
T Consensus        78 ~~~v~~~~~~~~~~~~~~~~~~~~~~~PG~~E~~~l~~i~~~~~~~~yD~IViDtaPTGhtLrlL~lP~~l~~~~~~L~d  157 (254)
T cd00550          78 RQEVLEPIEANLLLEMLKGILEEELESPGIEEIAAFDEFSRYIDEAEYDVVVFDTAPTGHTLRLLSLPTVLSWAREILSD  157 (254)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHCHHHHHHHHHHCCC
T ss_conf             99999988632255668888999863985899999999999976069988998899856799875156999999985379


Q ss_pred             -HHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCC-----------HHHHHHHHHHHHHHC
Q ss_conf             -331001111123113788875335777655432026774310020231253-----------100112689998808
Q gi|254780806|r  145 -AADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRN-----------SLSQQVVSDVRKNLG  210 (265)
Q Consensus       145 -aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~-----------~~~~~~~~~l~~~~~  210 (265)
                       ....+++|++|+.+++..+.|++..++..      ++++.++|+||+-+..           ..+++.++++++.|+
T Consensus       158 ~~~t~~~lV~~PE~~~v~Et~R~~~~L~~~------~i~v~~vvvN~v~p~~~~~~~~~~~r~~~q~~~l~~i~~~f~  229 (254)
T cd00550         158 PERTSFRLVCIPEKMSLYETERAIQELAKY------GIDVDAVIVNQLLPEDVTNCPFLEARREIQQKYLEEIEELFS  229 (254)
T ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHHHC------CCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             565589999778721699999999999977------999897999588087768899999999999999999998705


No 51 
>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=99.94  E-value=5.6e-26  Score=171.15  Aligned_cols=237  Identities=20%  Similarity=0.227  Sum_probs=169.8

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECC------CCHH
Q ss_conf             8768749999808898888999999999999879959999878776801121246333454116763025------7712
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEE------KNIN   75 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~------~~l~   75 (265)
                      +.|++|+|+|. +|||.||||++.|++.+||++|+||++|-|||.++.|..|.-  .....|+.|.+...      ..+.
T Consensus        27 ~~k~~~~IAiY-GKGGIGKSTts~NlsAAlA~~GkkVm~IGCDPKaDSTrlLlg--G~~~~TVLd~~~~~~~~~e~v~~~  103 (329)
T cd02033          27 PTKKTQIIAIY-GKGGIGKSFTLANLSYMMAQQGKRVLLIGCDPKSDTTSLLFG--GKACPTIIETSAKKKLAGEEVQIG  103 (329)
T ss_pred             CCCCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHCCC--CCCCCHHHHHHHHCCCCCCCCCHH
T ss_conf             75445499997-688435616889999999977996999788884603341058--988840999998728864434250


Q ss_pred             HCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHH------HHHC
Q ss_conf             1024444442000148874577500012322221023332247651027820331013332222101123------3100
Q gi|254780806|r   76 QILIQTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAA------ADSI  149 (265)
Q Consensus        76 ~~i~~~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~a------ad~v  149 (265)
                      +.+.+.  .|+.++-++..-.+....-.........|.+ +. ....++|||++|.   +++..+..+++      ||.+
T Consensus       104 dv~~~g--~Gv~CvEsGGPEPGvGCAGRGIItai~lLe~-lg-~~~~d~D~V~yDV---LGDVVCGGFAmPiR~g~A~ev  176 (329)
T cd02033         104 DVCFKR--DGVFAMELGGPEVGRGCGGRGIIHGFELLEK-LG-FHDWDFDYVLLDF---LGDVVCGGFGLPIARDMAQKV  176 (329)
T ss_pred             HEEECC--CCEEEEECCCCCCCCCCCCCCHHHHHHHHHH-CC-CCCCCCCEEEEEC---CCCEEECCCCCCCCCCCCCEE
T ss_conf             178625--9988986679999876788730136678776-37-7525899999922---453566463353356876289


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHH
Q ss_conf             11111231137888753357776554320267743100202312531001126899988085201562678688987773
Q gi|254780806|r  150 LVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPS  229 (265)
Q Consensus       150 iip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~  229 (265)
                      +||+.-+++|+..+.++.+.+..++...+ +.++.|+|.|+-+..    .+ .+.+.+..|.+++. .||++..+++...
T Consensus       177 yIVtSgE~MalyAANNI~~~i~~~a~~gg-~vrl~GlI~N~~~~~----~e-~e~fa~~~g~~~l~-~vP~d~~iRr~~~  249 (329)
T cd02033         177 IVVGSNDLQSLYVANNVCNAVEYFRKLGG-NVGVAGMVINKDDGT----GE-AQAFAAHAGIPILA-AIPADEELRRKSA  249 (329)
T ss_pred             EEEECCCHHHHHHHHHHHHHHHHHHHCCC-CCCEEEEEEECCCCC----HH-HHHHHHHCCCCEEE-ECCCCHHHHHHHH
T ss_conf             99967808899988789999999986389-710115986068872----49-99999971995799-6378778876543


Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf             7985799979998999999999999999
Q gi|254780806|r  230 YGKPAIIYDLKCAGSQAYLKLASELIQQ  257 (265)
Q Consensus       230 ~g~pv~~~~p~s~~a~~~~~la~el~~~  257 (265)
                      +...+  +.|.++.+.-|+.||+.+.+.
T Consensus       250 ~y~iv--~~p~~~~~~~f~~LA~~i~~~  275 (329)
T cd02033         250 AYQIV--GRPGTTWGPLFEQLATNVAEA  275 (329)
T ss_pred             HCCCC--CCCCCHHHHHHHHHHHHHHHC
T ss_conf             02603--487615899999999976127


No 52 
>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=99.94  E-value=1.2e-26  Score=174.97  Aligned_cols=173  Identities=20%  Similarity=0.277  Sum_probs=133.4

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCC
Q ss_conf             76874999980889888899999999999987995999987877-68011212463334541167630257712102444
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYSSYDLLIEEKNINQILIQT   81 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~   81 (265)
                      +..-|.++|+|...|.||||+++|||..+|+.|+||++||+|.- ..+..+|+++..   .++.+++.+..++.+++..+
T Consensus       100 ~~~~~~LaItS~~pGEGKS~vAaNLA~~~Aq~G~RvLLVDaDLRrP~lh~~f~l~~~---~GLs~vL~g~~~l~~i~~~~  176 (274)
T TIGR03029       100 SEGRKALAVVSAKSGEGCSYIAANLAIVFSQLGEKTLLIDANLRDPVQHRNFKLSEQ---RGLSDILAGRSDLEVITHIP  176 (274)
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHCCCCC---CCHHHHHCCCCCHHHEEECC
T ss_conf             788838999689999989999999999999679919999588888447797599997---68788845999889905158


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCC-CCCCHHHHHHHCCCCCCCCCHHH
Q ss_conf             44420001488745775000123222210233322476510278203310133322-22101123310011111231137
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNL-LTMNAMAAADSILVPLQCEFFAL  160 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~-~~~~al~aad~viip~~p~~~s~  160 (265)
                      ..+||+++|++.....-...+.     ..++.+.+ ..++.+||||||||||-... -....-..+|.+++|+..+....
T Consensus       177 ~~~nL~VLpaG~~ppnP~eLL~-----s~~~~~ll-~~l~~~yD~IIiDTPPvl~~sDA~ila~~aDg~LlVvR~~~T~~  250 (274)
T TIGR03029       177 ALENLSVLPAGAIPPNPQELLA-----RPAFTDLL-NKVMGDYDVVIVDTPSAEHSSDAQIVATRARGTLIVSRVNETRL  250 (274)
T ss_pred             CCCCEEEEECCCCCCCHHHHHH-----HHHHHHHH-HHHHHHCCEEEEECCCCCCCCHHHHHHHHCCEEEEEEECCCCCH
T ss_conf             9899789969999989799873-----58999999-99984099999938986554349999986897999996898889


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCE
Q ss_conf             888753357776554320267743100202
Q gi|254780806|r  161 EGLSQLLETVEEVRRTVNSALDIQGIILTM  190 (265)
Q Consensus       161 ~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~  190 (265)
                      ..+.+.++.++..      +.++.|+|+|+
T Consensus       251 ~~l~~a~~~L~~~------g~~VlGvVLNq  274 (274)
T TIGR03029       251 HELTSLKEHLSGV------GVRVVGAVLNQ  274 (274)
T ss_pred             HHHHHHHHHHHHC------CCCEEEEEECC
T ss_conf             9999999999977------99668998487


No 53 
>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=99.94  E-value=7.4e-27  Score=176.29  Aligned_cols=172  Identities=21%  Similarity=0.170  Sum_probs=97.4

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEEC---CCCHHHCCCC---CC
Q ss_conf             99980889888899999999999987995999987877680112124633345411676302---5771210244---44
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIE---EKNINQILIQ---TA   82 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~---~~~l~~~i~~---~~   82 (265)
                      |.|.++||||||||+|+|+|.++|+.|+|||+||+||+.+++..+..       ++.+....   +.........   ..
T Consensus         1 i~~~sGKGGVGKTTvAaalA~~lA~~G~rvLlvs~DPah~l~d~~~~-------~L~~~~~~~~~e~~~~~~~~~v~~~~   73 (217)
T cd02035           1 VIFFTGKGGVGKTTIAAATAVRLAEEGKKVLLVSTDPAHNLSDKGLP-------NLSDAFIVEDPEIAPNLYREEVDATR   73 (217)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCC-------CCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             98997899661999999999999968994999958987665323479-------86513588876667999987501666


Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCC---CCCCCHHHHH--HHCCCCCCCCC
Q ss_conf             442000148874577500012322221023332247651027820331013332---2221011233--10011111231
Q gi|254780806|r   83 IPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFN---LLTMNAMAAA--DSILVPLQCEF  157 (265)
Q Consensus        83 ~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~---~~~~~al~aa--d~viip~~p~~  157 (265)
                      .......+...........+. ..+....+.+........+||||||||||+-.   .+....|...  ..+++|++|+.
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~p-g~~E~~~l~~~~~~~~~~~yD~IVvDtpPTGhtlrlL~~~~L~d~~~t~~~lVt~Pe~  152 (217)
T cd02035          74 RVERAWGGEGGLMLELAAALP-GIEELASLLAVFREFSEGLYDVIVFDTAPTGHTLRLLVRELLTDPERTSFRLVTLPEK  152 (217)
T ss_pred             HHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHHCCCCCCEEEEEECCCC
T ss_conf             533311001145677761599-7899999999999985489988998289855699986788724888767999957762


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECC
Q ss_conf             1378887533577765543202677431002023125
Q gi|254780806|r  158 FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSR  194 (265)
Q Consensus       158 ~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~  194 (265)
                      .++..+.+++..++..      ++.+.++|+||+-|.
T Consensus       153 ~~~~et~r~~~~L~~~------gi~v~~vVvN~v~p~  183 (217)
T cd02035         153 LPLYETERAITELALY------GIPVDAVVVNRVLPA  183 (217)
T ss_pred             CHHHHHHHHHHHHHHC------CCCCCEEEEECCCCC
T ss_conf             1799999999999977------998898989588278


No 54 
>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=99.92  E-value=7.2e-25  Score=164.68  Aligned_cols=171  Identities=25%  Similarity=0.381  Sum_probs=128.9

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEEEEEECC-CCHHHCC
Q ss_conf             87687499998088988889999999999998-7995999987877-6801121246333454116763025-7712102
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLDPQ-GNASTGLGIELYDRKYSSYDLLIEE-KNINQIL   78 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~~~l~~~-~~l~~~i   78 (265)
                      .+++.|||.|.|...|.||||+++|||.++|+ .|+||++||+|.. ++++.+|+....   .++.+++.+. .++.+++
T Consensus        31 ~~~~~kvi~VTS~~pgeGKTtva~nLA~~lA~~~~~~VLLVDaDlr~p~l~~~l~~~~~---~Gl~d~L~~~~~~l~~~i  107 (207)
T TIGR03018        31 RKKNNNLIMVTSSLPGEGKSFTAINLAISLAQEYDKTVLLIDADLRRPSLHRTLGLEAE---PGLSDCLLDPVLDLADVL  107 (207)
T ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHCCCCCC---CCHHHHHCCCCCCHHHHE
T ss_conf             46788099997899999889999999999997249859999535789971001388999---985677438998756723


Q ss_pred             CCCCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCC--CCEEEECCCCCCC-CCCHHHHHHHCCCCCCC
Q ss_conf             44444420001488745775000123222210233322476510278--2033101333222-21011233100111112
Q gi|254780806|r   79 IQTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFS--YIFLDCPPSFNLL-TMNAMAAADSILVPLQC  155 (265)
Q Consensus        79 ~~~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD--~IiiD~pp~~~~~-~~~al~aad~viip~~p  155 (265)
                      .++..++++++|++.........+.     ..++.+.+ ..++++||  |||||+||-+..- .......+|.+++|+..
T Consensus       108 ~~~~~~~l~vlpag~~~~~~~~ll~-----s~~~~~li-~~lr~~yd~~~VIiDtPPvl~~~Da~~la~~~D~vllVvr~  181 (207)
T TIGR03018       108 VPTNIGRLSLLPAGRRHPNPTELLA-----SQRMRSLL-HELARRYPDRIIIIDTPPLLVFSEARALARLVGQIVLVVEE  181 (207)
T ss_pred             ECCCCCCEEEEECCCCCCCHHHHHH-----HHHHHHHH-HHHHHHCCCCEEEEECCCCCCCHHHHHHHHHCCEEEEEEEC
T ss_conf             4268875557516898996676542-----69999999-99997379657998389622323699999968969999979


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             3113788875335777655432026774310020
Q gi|254780806|r  156 EFFALEGLSQLLETVEEVRRTVNSALDIQGIILT  189 (265)
Q Consensus       156 ~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N  189 (265)
                      +......+.+.++.++        +.+++|+|+|
T Consensus       182 ~~t~~~~v~~a~~~L~--------~~~vlG~VlN  207 (207)
T TIGR03018       182 GRTTQEAVKEALSALE--------SCKVLGVVLN  207 (207)
T ss_pred             CCCCHHHHHHHHHHHC--------CCCEEEEEEC
T ss_conf             9878999999999866--------8980699969


No 55 
>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=99.90  E-value=5.6e-24  Score=159.46  Aligned_cols=105  Identities=32%  Similarity=0.459  Sum_probs=91.3

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHC-CCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCE
Q ss_conf             999980889888899999999999987-9959999878776801121246333454116763025771210244444420
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAI-GENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNL   86 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~-g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l   86 (265)
                      ||+|.|.|||+||||+|+|+|++||+. |+||+++|+|+|.      |-                               
T Consensus         1 vi~~~~~kGGvG~Tt~A~nlA~~la~~~~~~v~lvDldlqf------Gd-------------------------------   43 (106)
T cd03111           1 VIAFIGAKGGVGATTLAANLAVALAKEAGRRVLLVDLDLQF------GD-------------------------------   43 (106)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC------CC-------------------------------
T ss_conf             98997289986689999999999998419938999654677------99-------------------------------


Q ss_pred             EECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             00148874577500012322221023332247651027820331013332222101123310011111231137888753
Q gi|254780806|r   87 SIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQL  166 (265)
Q Consensus        87 ~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s~~~~~~~  166 (265)
                                                            |||++|+|++++.++..++..||.++++++|+..+++++.++
T Consensus        44 --------------------------------------d~VVvD~~~~~~~~~~~al~~ad~i~lv~~~~lp~lrn~kr~   85 (106)
T cd03111          44 --------------------------------------DYVVVDLGRSLDEVSLAALDQADRVFLVTQQDLPSIRNAKRL   85 (106)
T ss_pred             --------------------------------------CEEEECCCCCCCHHHHHHHHHCCEEEEEECCCHHHHHHHHHH
T ss_conf             --------------------------------------789991865538899999986797999806774899979999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCE
Q ss_conf             357776554320267743100202
Q gi|254780806|r  167 LETVEEVRRTVNSALDIQGIILTM  190 (265)
Q Consensus       167 ~~~i~~~~~~~~~~~~~~~iv~N~  190 (265)
                      ++.++.+...   ......+|+||
T Consensus        86 l~~l~~l~~~---~~~ki~lVvNR  106 (106)
T cd03111          86 LELLRVLDYS---LPAKIELVLNR  106 (106)
T ss_pred             HHHHHHCCCC---CCCCEEEEECC
T ss_conf             9999984999---73656998579


No 56 
>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=99.83  E-value=6.9e-21  Score=141.45  Aligned_cols=180  Identities=19%  Similarity=0.259  Sum_probs=100.5

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEE---EEEECCCCHHHCCCC---
Q ss_conf             49999808898888999999999999879959999878776801121246333454116---763025771210244---
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSY---DLLIEEKNINQILIQ---   80 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~---~~l~~~~~l~~~i~~---   80 (265)
                      |+| |.++||||||||+++.+|..+|+.|+|||+|-.||--|++-.|+....+.+..+.   ++..-+-+....+..   
T Consensus         2 r~i-~~~GKGGVGKTT~AaA~A~~~A~~G~rvLlvStDPAhsL~D~~~~~~g~~pt~V~~~~nL~a~eiD~~~~~~~~~~   80 (304)
T pfam02374         2 RWI-FFGGKGGVGKTTVSCATAVRLSEQGKKVLLVSTDPAHSLSDSFNQKFGHEPTKIKGVENLSAMEIDPQMELEEYRG   80 (304)
T ss_pred             CEE-EEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHCCCCCCCCEEECCCCCCEEEEECHHHHHHHHHH
T ss_conf             199-9957985748999999999999589929999469721488984886799961515889827987278999999999


Q ss_pred             CCCCCE-EECCCCCCCCCC-CCCCC--CCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCC----------------
Q ss_conf             444420-001488745775-00012--3222210233322476510278203310133322221----------------
Q gi|254780806|r   81 TAIPNL-SIIPSTMDLLGI-EMILG--GEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTM----------------  140 (265)
Q Consensus        81 ~~~~~l-~iipa~~~~~~~-~~~l~--~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~----------------  140 (265)
                      .....+ .+.+.. ...+. ...+.  ...+....+.++....-.++||+|++||||+-..+-.                
T Consensus        81 ~~~~~~~~~~~~~-~~~~~~~~~~~~~PG~~E~~al~~i~~~~~~~~yD~VV~DtaPTGhtLrlL~lP~~l~~~l~~~~~  159 (304)
T pfam02374        81 EVQDPINAVLGAD-MLEGILAEELSSLPGIDEIASFDEFKKYMDEGEYDVVIFDTAPTGHTLRLLSLPTVLSWYLEKIIK  159 (304)
T ss_pred             HHHHHHHHHHCHH-HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHCCHHHHHHHHHHHHH
T ss_conf             9999998651221-266789999836998999999999999997178876996689817799886168999999999998


Q ss_pred             ---------------------------------------CHHHH--HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             ---------------------------------------01123--3100111112311378887533577765543202
Q gi|254780806|r  141 ---------------------------------------NAMAA--ADSILVPLQCEFFALEGLSQLLETVEEVRRTVNS  179 (265)
Q Consensus       141 ---------------------------------------~al~a--ad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~  179 (265)
                                                             ..|.-  -..+++|+.|+..++.-+.|+...++..      
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~L~dp~~T~f~lV~~pe~~~i~Et~R~~~~L~~~------  233 (304)
T pfam02374       160 LKNKIGPLAKPFKGPMGGSCLPEALESLEETKEQIEKAREILSDPERTSFRLVCIPEKMSLYETERAIQELAKY------  233 (304)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHC------
T ss_conf             99988999887740135676278999999999999999998549897499998379843799999999999977------


Q ss_pred             CCCCCCCCCCEEECC
Q ss_conf             677431002023125
Q gi|254780806|r  180 ALDIQGIILTMFDSR  194 (265)
Q Consensus       180 ~~~~~~iv~N~~~~~  194 (265)
                      ++++-++|+|++-|.
T Consensus       234 ~i~v~~vvvNrvlp~  248 (304)
T pfam02374       234 GIDVDAVIVNQVLPE  248 (304)
T ss_pred             CCCCCEEEECCCCCC
T ss_conf             998897988077888


No 57 
>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=99.76  E-value=2.9e-18  Score=126.11  Aligned_cols=203  Identities=21%  Similarity=0.292  Sum_probs=132.1

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHH-HCCCCCCCCCCEEEEEEC--------CCCHHHC
Q ss_conf             4999980889888899999999999987995999987877680112-124633345411676302--------5771210
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTG-LGIELYDRKYSSYDLLIE--------EKNINQI   77 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~-l~~~~~~~~~ti~~~l~~--------~~~l~~~   77 (265)
                      |+|||. +|||.|||.++.||.+.+|.+|+|||+|-|||..+.++. ||--   .-+|+.|++..        +..++++
T Consensus         1 r~iAiY-GKGG~GKSFtttNLs~~~A~mgkRVL~lGCDPKhDst~~LFGGi---slPT~~ev~~ekk~agreEev~~~dv   76 (355)
T TIGR02016         1 RIIAIY-GKGGIGKSFTTTNLSAKLALMGKRVLQLGCDPKHDSTSALFGGI---SLPTVIEVFAEKKEAGREEEVKVSDV   76 (355)
T ss_pred             CEEEEE-CCCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCC---CCCHHHHHHHHHHHCCCCCCEEEEEE
T ss_conf             958897-48898667898999999997468235405789733222136786---67508899999865187320566117


Q ss_pred             CCCCCCCCE----EEC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHH------HH
Q ss_conf             244444420----001-4887457750001232222102333224765102782033101333222210112------33
Q gi|254780806|r   78 LIQTAIPNL----SII-PSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMA------AA  146 (265)
Q Consensus        78 i~~~~~~~l----~ii-pa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~------aa  146 (265)
                      +.++...|.    +=+ -+++... -..=-.........|.++=. .-| ++|||+.|.   +|+..+-.+.      .|
T Consensus        77 ~Fk~~I~~~~~~vyg~ElGGPeVG-RGCGGRGIi~GFd~LEKlG~-~~W-~~D~vlmDF---LGDVVCGGFatPlaRsla  150 (355)
T TIGR02016        77 VFKRDIMNFAATVYGIELGGPEVG-RGCGGRGIIFGFDLLEKLGL-FEW-ELDFVLMDF---LGDVVCGGFATPLARSLA  150 (355)
T ss_pred             EEECCCCCCCCCEEEEEECCCCCC-CCCCCCCCCCCHHHHHHCCC-CCC-CHHHEEEEC---CCCEEECCCCCHHHHHHH
T ss_conf             872336889874578881787115-54687531010256655274-400-020002000---586775664431235320


Q ss_pred             HHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf             10011111231137888753357776554320267743100202312531001126899988085201562678688987
Q gi|254780806|r  147 DSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISE  226 (265)
Q Consensus       147 d~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~~  226 (265)
                      ..||+++.=|..|+..+.++-+..+=++. ++-..+++|+|+||=|- +.+..    ...+..+.+|+. .||.|..++.
T Consensus       151 eeVi~~~sNDrQSly~aNNic~A~~YFr~-~GGr~~llGlvvNrDDG-sG~A~----~fA~~~gipvLa-~iP~d~~~Rd  223 (355)
T TIGR02016       151 EEVIVVTSNDRQSLYVANNICSAAEYFRK-LGGRSKLLGLVVNRDDG-SGVAE----AFAKEVGIPVLA-KIPLDRKVRD  223 (355)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHHHHHHHH-CCCCEEEEEEEEECCCC-CCHHH----HHHHHCCCCEEE-ECCCCCHHCC
T ss_conf             24377613743688888669889999986-18860467889864688-71898----989870993475-2676500100


No 58 
>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=99.72  E-value=1.2e-17  Score=122.45  Aligned_cols=115  Identities=27%  Similarity=0.274  Sum_probs=78.0

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCEEE
Q ss_conf             99980889888899999999999987995999987877680112124633345411676302577121024444442000
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLSI   88 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l~i   88 (265)
                      |+| ++||||||||++++||.+|+++|++|++||+||. ++...++.+..+.                       ..+++
T Consensus         2 ia~-~GKGGvGKtt~~~~la~~l~~~g~~vl~iD~Dp~-dlpe~~~~~~~~~-----------------------~~l~~   56 (116)
T cd02034           2 IAI-TGKGGVGKTTIAALLARYLAEKGKPVLAIDADPD-DLPERLSVEVGEI-----------------------KLLLV   56 (116)
T ss_pred             EEE-ECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCC-CCHHHHCEECCCC-----------------------CEEEE
T ss_conf             789-8899774999999999999978996999989897-1235542331787-----------------------07999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCC
Q ss_conf             14887457750001232222102333224765102782033101333222210112331001111
Q gi|254780806|r   89 IPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPL  153 (265)
Q Consensus        89 ipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~  153 (265)
                      +...... +....-+    ....+++++...+..+||||++||++|+.++.+......|.+++|+
T Consensus        57 lg~~~~~-g~GC~C~----~n~ll~~~l~~l~~~~~~~VvvD~eAGiEHl~Rg~~~~vD~livVs  116 (116)
T cd02034          57 MGMGRPG-GEGCYCP----ENALLNALLRHLVLTRDEQVVVDTEAGLEHLGRGTAEGVDLLVVVN  116 (116)
T ss_pred             EECCCCC-CCCEECC----HHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHCCHHHCCCEEEEEC
T ss_conf             9734358-9940882----5789999999970679989999678548777300664399999969


No 59 
>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=99.72  E-value=5e-18  Score=124.75  Aligned_cols=46  Identities=39%  Similarity=0.506  Sum_probs=41.4

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHC--CCCEEEEECCCCCCCCHHHCCC
Q ss_conf             980889888899999999999987--9959999878776801121246
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAAI--GENVLLIDLDPQGNASTGLGIE   56 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~~--g~rVllID~D~q~~~~~~l~~~   56 (265)
                      |+.+||||||||+++.+|..+|++  |+|||||=.||--|++-.|+.+
T Consensus         1 f~gGKGGVGKTt~SaAtA~~lAe~qPGkkvLl~STDPAHsL~D~F~~e   48 (330)
T TIGR00345         1 FFGGKGGVGKTTISAATAIRLAEQQPGKKVLLVSTDPAHSLSDVFEQE   48 (330)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHH
T ss_conf             977878823888999999999851899779998408600278861132


No 60 
>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=99.68  E-value=9.7e-17  Score=117.22  Aligned_cols=78  Identities=44%  Similarity=0.678  Sum_probs=70.6

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCEE
Q ss_conf             99998088988889999999999998799599998787768011212463334541167630257712102444444200
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLS   87 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l~   87 (265)
                      +|++.+.| ||||||+++|||..|+++|+||++||                                             
T Consensus         1 ~i~~~~~k-GvGKTT~a~~La~~la~~g~~Vl~vD---------------------------------------------   34 (99)
T cd01983           1 VIVVTGKG-GVGKTTLAANLAAALAKRGKRVLLID---------------------------------------------   34 (99)
T ss_pred             CEEEECCC-CCCHHHHHHHHHHHHHHCCCEEEEEC---------------------------------------------
T ss_conf             98985899-77689999999999998899699986---------------------------------------------


Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCC---CCHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             0148874577500012322221023332247651027820331013332222---1011233100111112311378887
Q gi|254780806|r   88 IIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLT---MNAMAAADSILVPLQCEFFALEGLS  164 (265)
Q Consensus        88 iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~---~~al~aad~viip~~p~~~s~~~~~  164 (265)
                                                           |||++|+||+.+...   ..++.++|.+++|+.|+..++.+..
T Consensus        35 -------------------------------------d~iiiD~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~   77 (99)
T cd01983          35 -------------------------------------DYVLIDTPPGLGLLVLLCLLALLAADLVIIVTTPEALAVLGAR   77 (99)
T ss_pred             -------------------------------------CCEEECCCCCCCHHHHHHHHHHHHCCEEEEECCCCHHHHHHHH
T ss_conf             -------------------------------------7178858998884689999878758958996598488999999


Q ss_pred             HHHH
Q ss_conf             5335
Q gi|254780806|r  165 QLLE  168 (265)
Q Consensus       165 ~~~~  168 (265)
                      ++..
T Consensus        78 ~~~~   81 (99)
T cd01983          78 RLTE   81 (99)
T ss_pred             HHHH
T ss_conf             9999


No 61 
>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=99.66  E-value=7.5e-17  Score=117.86  Aligned_cols=126  Identities=25%  Similarity=0.315  Sum_probs=72.1

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCC----CCCCCEEEEEECCCCHHHCCCCC
Q ss_conf             74999980889888899999999999987995999987877680112124633----34541167630257712102444
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELY----DRKYSSYDLLIEEKNINQILIQT   81 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~----~~~~ti~~~l~~~~~l~~~i~~~   81 (265)
                      +|++ ++++||||||||+++.+|..+|..|+||++|-.||-.|+...|+.+..    ....++.-...   +...++.. 
T Consensus         2 ~riv-~f~GKGGVGKTT~aaA~A~~lA~~g~kvLlvStDPAhsL~d~f~~elg~~~~~I~~nL~a~ei---D~~~~l~e-   76 (322)
T COG0003           2 TRIV-FFTGKGGVGKTTIAAATAVKLAESGKKVLLVSTDPAHSLGDVFDLELGHDPRKVGPNLDALEL---DPEKALEE-   76 (322)
T ss_pred             CEEE-EEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHCCCCCCCHHHCCCCCCEEEE---CHHHHHHH-
T ss_conf             3799-993688545899999999999975990799984898744765423047851125888754660---68999999-


Q ss_pred             CCCCEE-----ECCCCC--CCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCC
Q ss_conf             444200-----014887--4577500012322221023332247651027820331013332
Q gi|254780806|r   82 AIPNLS-----IIPSTM--DLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFN  136 (265)
Q Consensus        82 ~~~~l~-----iipa~~--~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~  136 (265)
                      +++.+.     .++.+.  .....+.......+....+.++..-...++||+|++||||.-.
T Consensus        77 y~~~v~~~~~~~~~~~~l~~~~~~e~~~~PGidE~~~l~~i~e~~~~~~yD~IV~DtaPTG~  138 (322)
T COG0003          77 YWDEVKDYLARLLRTRGLGGIYADELATLPGIDEALALLKILEYYVSGEYDVIVVDTAPTGH  138 (322)
T ss_pred             HHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCHHH
T ss_conf             99999999974126554212578898609888999999999998752689889984897087


No 62 
>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=99.53  E-value=1.2e-14  Score=105.03  Aligned_cols=183  Identities=22%  Similarity=0.285  Sum_probs=127.9

Q ss_pred             CCE-EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC
Q ss_conf             874-999980889888899999999999987995999987877-680112124633345411676302577121024444
Q gi|254780806|r    5 KSR-IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA   82 (265)
Q Consensus         5 ~~k-vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~   82 (265)
                      ..+ ||.+.+..-|+||+.+..|+|..+|.-|+|+++||.|.. +.++.+|+.++   ..++.|.|.|...+...+....
T Consensus       559 e~~Pvv~~~~p~p~~Gks~i~an~aaliA~ggkR~llidad~rk~~l~q~~~~~~---~~GL~d~LaG~rs~~~~~~~~~  635 (778)
T TIGR01005       559 ESEPVVALASPLPDVGKSIIEANLAALIAAGGKRVLLIDADIRKAALSQILVKAE---KSGLLDLLAGERSLELDVKAEV  635 (778)
T ss_pred             CCCCEEEECCCCCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHCCCC---CCCHHHHHHHHHHHHHHCCCCC
T ss_conf             8987588568888665688999999998326871787326776055564421478---8853755642465663034023


Q ss_pred             CCCEEECCCCCC-C-CCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHH-HHHHCC-CCCCCCCH
Q ss_conf             442000148874-5-7750001232222102333224765102782033101333222210112-331001-11112311
Q gi|254780806|r   83 IPNLSIIPSTMD-L-LGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMA-AADSIL-VPLQCEFF  158 (265)
Q Consensus        83 ~~~l~iipa~~~-~-~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~-aad~vi-ip~~p~~~  158 (265)
                      ..++++|+++.. + ..-..+|-..+    +..+.+ ......|||++||+||-.-..-..++. .++.++ +++.=+..
T Consensus       636 ~~~l~~l~~GGas~~~h~~~eLLasp----a~~~l~-~~ar~~~D~vvvd~~~~~pV~d~~a~a~la~~~lslvt~~~r~  710 (778)
T TIGR01005       636 AAKLDILDAGGASLLRHNSSELLASP----AMVELV-ENARSAYDLVVVDVAAVAPVADAKALAALADLVLSLVTEYDRS  710 (778)
T ss_pred             CCCCHHHHCCCCCCCCCCCCHHHCCH----HHHHHH-HHHHHHCCEEEECCCHHHHHHHHHHHHHCCCEEEHHEEEECCE
T ss_conf             67711233476124788841532166----889999-9886518857745531248999999742242002001111441


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHH
Q ss_conf             3788875335777655432026774310020231253100112
Q gi|254780806|r  159 ALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQV  201 (265)
Q Consensus       159 s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~  201 (265)
                      .++-+...++.+.    +.|  -++.|||+|+.++++...+..
T Consensus       711 ~~~~~r~~~~~~~----~~n--~~v~gV~ln~ldpn~~~tkaa  747 (778)
T TIGR01005       711 VVELVRELLKSLS----RLN--SEVLGVVLNKLDPNELVTKAA  747 (778)
T ss_pred             EHHHHHHHHHHHH----HCC--CEEEEEEECCCCCCCHHHHEE
T ss_conf             0444288775445----318--604566504557520111001


No 63 
>KOG2825 consensus
Probab=99.32  E-value=3.7e-12  Score=90.45  Aligned_cols=53  Identities=38%  Similarity=0.502  Sum_probs=45.2

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCC
Q ss_conf             74999980889888899999999999987995999987877680112124633
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELY   58 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~   58 (265)
                      +.---|..+||||||||.++.||..+|.-+.+||+|-.||--|++-.|+....
T Consensus        18 slKwifVGGKGGVGKTTcs~sLAvqla~~r~~vLiISTDPAHNlSDAF~qkft   70 (323)
T KOG2825          18 SLKWIFVGGKGGVGKTTCSCSLAVQLAKVRESVLIISTDPAHNLSDAFSQKFT   70 (323)
T ss_pred             EEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHC
T ss_conf             03699976767767653126899998616886478616853116788887751


No 64 
>PRK00090 bioD dithiobiotin synthetase; Reviewed
Probab=98.95  E-value=4.5e-09  Score=72.47  Aligned_cols=193  Identities=19%  Similarity=0.227  Sum_probs=101.6

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHCCCCCCCCCCEEEEEECCC---CHHHCCCCCCC
Q ss_conf             9999808898888999999999999879959999878776-8011212463334541167630257---71210244444
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIELYDRKYSSYDLLIEEK---NINQILIQTAI   83 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~-~~~~~l~~~~~~~~~ti~~~l~~~~---~l~~~i~~~~~   83 (265)
                      +|-|...--|||||++++.|+..|+++|++|.-.=  |.. ....  +....+.. -+........   .+....++.  
T Consensus         1 ~ifI~GT~T~vGKT~vt~~L~~~l~~~G~~v~~~K--Pv~tG~~~--~~~~~Da~-~~~~~~~~~~~~~~~~p~~~~~--   73 (223)
T PRK00090          1 VLFVTGTDTGVGKTVVTAALAQALREQGYRVAGYK--PVQSGCDG--GLRNGDAL-ALQRLSGLPLDYELVNPYRFEE--   73 (223)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEC--EEEECCCC--CCCCHHHH-HHHHHHCCCCCHHHHCCCCCCC--
T ss_conf             98998689997699999999999997899489975--12048988--99727999-9999808999867605402588--


Q ss_pred             CCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCC-CCCCCCHHHHHH-------HCCCCCCC
Q ss_conf             4200014887457750001232222102333224765102782033101333-222210112331-------00111112
Q gi|254780806|r   84 PNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSF-NLLTMNAMAAAD-------SILVPLQC  155 (265)
Q Consensus        84 ~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~-~~~~~~al~aad-------~viip~~p  155 (265)
                            |.++.++   ....+..-....+.+.+. .++.+||+++|.-.+|+ .+++... ..+|       -+|+|+..
T Consensus        74 ------p~sP~~a---a~~~g~~i~~~~i~~~~~-~l~~~~d~vlvEGaGGl~~Pl~~~~-~~~Dla~~l~~pvILV~~~  142 (223)
T PRK00090         74 ------PLSPHLA---ARLEGVTIDLEKISAALR-ELAQQADLVLVEGAGGLLVPLTDDL-TLADLAAQLQLPVILVVGV  142 (223)
T ss_pred             ------CCCHHHH---HHHHCCCCCHHHHHHHHH-HHHHHCCEEEEECCCCCCCCCCCCC-CHHHHHHHHCCCEEEEECC
T ss_conf             ------9898999---999098468999999999-9983189899946886556756787-8899999968898999769


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf             3113788875335777655432026774310020231253100112689998808520156267868898
Q gi|254780806|r  156 EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRIS  225 (265)
Q Consensus       156 ~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~  225 (265)
                      ..-++-   ..+-+++.+++   ..+++.|+|+|++++......+..+.+++..|.++++ +||+...+.
T Consensus       143 ~lG~in---htllt~eal~~---~gl~v~GvI~N~~~~~~~~~~~~~~~l~~~~gvPvLG-~iP~~~~~~  205 (223)
T PRK00090        143 KLGCIN---HTLLTLEAIRA---RGLPLAGWVANGVPPEGLRHAENLATLAELLPAPLLG-RLPYLAELS  205 (223)
T ss_pred             CCCHHH---HHHHHHHHHHH---CCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEE-ECCCCCCCC
T ss_conf             888099---99998999996---8994899999685883667776899999854998899-758999989


No 65 
>pfam00448 SRP54 SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
Probab=98.84  E-value=1.9e-08  Score=68.77  Aligned_cols=161  Identities=22%  Similarity=0.266  Sum_probs=81.0

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCC
Q ss_conf             74999980889888899999999999987995999987877680112124633345411676302577121024444442
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPN   85 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~   85 (265)
                      .+||+++ +=-||||||+.+-||..+.++|++|.+|-+|....... -.+.      +..+                .-|
T Consensus         1 P~vi~lv-GptGvGKTTTiaKLAa~~~~~~~~V~lit~Dt~R~gA~-eQL~------~ya~----------------~l~   56 (196)
T pfam00448         1 PNVILLV-GLQGSGKTTTIAKLAAYLKKQGKKVLLVAADTFRAAAI-EQLK------QLAE----------------RLG   56 (196)
T ss_pred             CEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHH-HHHH------HHHH----------------HCC
T ss_conf             9699998-99999889999999999997799289997587768899-9999------9998----------------639


Q ss_pred             EEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCC---CCHH------HHHHHCCCCCCCC
Q ss_conf             000148874577500012322221023332247651027820331013332222---1011------2331001111123
Q gi|254780806|r   86 LSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLT---MNAM------AAADSILVPLQCE  156 (265)
Q Consensus        86 l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~---~~al------~aad~viip~~p~  156 (265)
                      +.+.+...           ..+....+.+.+.....++||+|||||++ .++..   +.-+      ...+.+++|..+.
T Consensus        57 v~~~~~~~-----------~~d~~~~~~~~l~~~~~~~~D~IlIDTaG-r~~~d~~~~~el~~~~~~~~~~~~~LVl~a~  124 (196)
T pfam00448        57 VPVFGSGT-----------GSDPAAVAFDAVEKAKAENYDVVLVDTAG-RLQNDKNLMDELKKIKRVIAPDEVLLVLDAT  124 (196)
T ss_pred             CEEEECCC-----------CCCHHHHHHHHHHHHHHCCCCEEEEECCC-CCCCCHHHHHHHHHHHHHCCCCCEEEEEECC
T ss_conf             81781487-----------77878999999999884689999998999-8747677899999998522873028998567


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             113788875335777655432026774310020231253100112689998808520
Q gi|254780806|r  157 FFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV  213 (265)
Q Consensus       157 ~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v  213 (265)
                      .- ...+..    +..+    ...+.+-++|+|+.|...+... +++.+.+ .+.++
T Consensus       125 ~~-~~~~~~----~~~f----~~~~~~~~~I~TKlDet~~~G~-~l~~~~~-~~~Pi  170 (196)
T pfam00448       125 TG-QNALNQ----AKAF----NEAVGITGVILTKLDGDAKGGA-ALSIAAE-TGKPI  170 (196)
T ss_pred             CC-CCHHHH----HHHH----HHHCCCCCEEEEEECCCCCCCH-HHHHHHH-HCCCE
T ss_conf             78-213789----9987----6004776268884057887529-9989999-89697


No 66 
>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=98.84  E-value=4.7e-09  Score=72.33  Aligned_cols=176  Identities=23%  Similarity=0.308  Sum_probs=91.8

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHH--HHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCC
Q ss_conf             687499998088988889999999999--998799599998787768011212463334541167630257712102444
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTA--LAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQT   81 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~--la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~   81 (265)
                      +++-||=+ .+==|+||||+|+=||++  +.+.|+||||+=||.+.-+..-                 +-..|.+   ++
T Consensus       100 ~~P~vilm-vGLQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~yRPAA~~-----------------QL~~Lg~---Q~  158 (439)
T TIGR00959       100 KRPTVILM-VGLQGSGKTTTAGKLALYLLKKKEGKKVLLVACDLYRPAAIE-----------------QLKVLGE---QV  158 (439)
T ss_pred             CCCEEEEE-ECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCCCHHHHH-----------------HHHHHHH---HC
T ss_conf             86838997-313788578899999999999863897034032103478999-----------------9999767---52


Q ss_pred             CCCCEEECC-CCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHHCCCCCCEEEECCCCCC--CCCCHHH------HHHHCCC
Q ss_conf             444200014-8874577500012322-2210233322476510278203310133322--2210112------3310011
Q gi|254780806|r   82 AIPNLSIIP-STMDLLGIEMILGGEK-DRLFRLDKALSVQLTSDFSYIFLDCPPSFNL--LTMNAMA------AADSILV  151 (265)
Q Consensus        82 ~~~~l~iip-a~~~~~~~~~~l~~~~-~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~--~~~~al~------aad~vii  151 (265)
                         |+.+.+ -..+         ..+ +.....++++...-..+||+|||||.+=+..  ..+.=|.      -=|+++.
T Consensus       159 ---gVpvf~h~~~~---------~~p~~Pv~ia~~Al~~Ak~~~~D~vI~DTAGRL~ID~~LM~EL~~iK~~~nP~EiLl  226 (439)
T TIGR00959       159 ---GVPVFAHLGKG---------QSPDDPVEIARQALEEAKENGFDVVIVDTAGRLQIDEELMEELAEIKEILNPDEILL  226 (439)
T ss_pred             ---CCCCCCCCCCC---------CCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             ---88711004788---------898877899999999999748978997267512555999999999988868870541


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf             11123113788875335777655432026774310020231253100112689998808520156267868898
Q gi|254780806|r  152 PLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRIS  225 (265)
Q Consensus       152 p~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~  225 (265)
                      |+..  ++=+      +.+ ++.+.|+..+.+-|+|++++|.-++=.-  .=.+++..|.|+ . +|--.+++.
T Consensus       227 VvDa--M~GQ------dAv-n~A~~F~e~lgltG~vltK~DGDaRGGA--ALS~~~~tg~PI-K-FiG~GEK~~  287 (439)
T TIGR00959       227 VVDA--MTGQ------DAV-NTAKTFNERLGLTGVVLTKLDGDARGGA--ALSVRSVTGKPI-K-FIGVGEKIE  287 (439)
T ss_pred             CCHH--CCHH------HHH-HHHHHHCCCCCCCEEEEECCCCCCHHHH--HHHHHHHHCCCE-E-EEECCCCCC
T ss_conf             2201--0216------999-9998636600135478854756605789--999999968961-8-884177723


No 67 
>PRK12374 putative dithiobiotin synthetase; Provisional
Probab=98.78  E-value=7.6e-08  Score=65.29  Aligned_cols=196  Identities=14%  Similarity=0.148  Sum_probs=105.3

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEE--EECCCCHHHCCCCCCCC
Q ss_conf             4999980889888899999999999987995999987877680112124633345411676--30257712102444444
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDL--LIEEKNINQILIQTAIP   84 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~--l~~~~~l~~~i~~~~~~   84 (265)
                      |-+-|...--+||||.+|+.|+.+++++|++|...=- .|.+..      ..+.+..-.|.  +.....+.     ..++
T Consensus         3 k~~FITGTDTdVGKT~vsaaL~~~l~~~G~~v~~~KP-VasG~~------~~~~g~~~~Da~~l~~~~~~~-----~~~~   70 (231)
T PRK12374          3 KRFFITGTDTSVGKTVVSRALLQALASQGKSVAGYKP-VAKGSK------ETPEGLRNKDALVLQSVSTIE-----LPYE   70 (231)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEE-EECCCC------CCCCCCCHHHHHHHHHHHCCC-----CCHH
T ss_conf             6479987899953999999999999978994888856-883996------689987247899999873789-----9988


Q ss_pred             CEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CCCCCH-----HHHHHH-CCCCCCCCC
Q ss_conf             2000148874577500012322221023332247651027820331013332-222101-----123310-011111231
Q gi|254780806|r   85 NLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFN-LLTMNA-----MAAADS-ILVPLQCEF  157 (265)
Q Consensus        85 ~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~-~~~~~a-----l~aad~-viip~~p~~  157 (265)
                        .+-|-......... .....-....+.+.+. .+.++||+++|--.+|+- +++...     ...-+. +|+|+....
T Consensus        71 --~vnP~~~~~~~aa~-~~~~~id~~~i~~~~~-~l~~~~d~vlVEGAGG~~vPl~~~~~~~Dl~~~l~lPVILV~~~~L  146 (231)
T PRK12374         71 --AVNPIALSEEESSV-AHSCPINYTLISNGLA-NLTDKVDHVVVEGTGGWRSLMNDLRPLSEWVVQEQLPVLMVVGIQE  146 (231)
T ss_pred             --HCCCCCCCCCCCCH-HHCCCCCHHHHHHHHH-HHHHHCCEEEEECCCCEEECCCCCCHHHHHHHHCCCCEEEEECCCC
T ss_conf             --71976688665774-4548578999999999-9885579799977986213047651499999983999999988986


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf             13788875335777655432026774310020231253100112689998808520156267868898
Q gi|254780806|r  158 FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRIS  225 (265)
Q Consensus       158 ~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~  225 (265)
                      -++-   ..+-+++.++.   ..+++.|+|+|++++......+.++.+++..+.++++ +||+-....
T Consensus       147 G~IN---HtLLT~eal~~---~gl~l~G~I~N~~~p~~~~~~e~i~~L~~~~~~P~LG-~iP~l~~~~  207 (231)
T PRK12374        147 GCIN---HALLTAQAIAN---DGLPLIGWVANRINPGLAHYAEIIDVLGKKLPAPLIG-ELPYLPRAE  207 (231)
T ss_pred             CHHH---HHHHHHHHHHH---CCCCEEEEEEEEECCCHHHHHHHHHHHHHHCCCCEEE-ECCCCCCCC
T ss_conf             8488---99999999997---8995799999836797046788999999855999788-689999989


No 68 
>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=98.76  E-value=6.3e-08  Score=65.77  Aligned_cols=159  Identities=23%  Similarity=0.288  Sum_probs=78.8

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCE
Q ss_conf             9999808898888999999999999879959999878776-801121246333454116763025771210244444420
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNL   86 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~-~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l   86 (265)
                      ||.++ +==||||||+.+-||..+.++|+||.+|=+|... ..---|  .      +..+                .-++
T Consensus         2 Vi~lv-GptGvGKTTTiaKLA~~~~~~~~kV~lit~Dt~R~gA~eQL--~------~~a~----------------~l~v   56 (173)
T cd03115           2 VILLV-GLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQL--R------VLGE----------------QVGV   56 (173)
T ss_pred             EEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHH--H------HHHH----------------HCCC
T ss_conf             99998-99999889999999999997699289997488757799999--9------9999----------------7498


Q ss_pred             EECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCC--CCCCCC----HHH--HHHHCCCCCCCCCH
Q ss_conf             0014887457750001232222102333224765102782033101333--222210----112--33100111112311
Q gi|254780806|r   87 SIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSF--NLLTMN----AMA--AADSILVPLQCEFF  158 (265)
Q Consensus        87 ~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~--~~~~~~----al~--aad~viip~~p~~~  158 (265)
                      .+....           ...+....+++.+...-.+.||+|+|||++-.  +.....    .+.  ..+.+++|.... .
T Consensus        57 ~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~D~IlIDTaGr~~~d~~~~~el~~l~~~~~p~~~~LVl~a~-~  124 (173)
T cd03115          57 PVFEEG-----------EGKDPVSIAKRAIEHAREENFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDAM-T  124 (173)
T ss_pred             EEEECC-----------CCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCEEECCCC-C
T ss_conf             599227-----------7558799999999998756899899978887879999999999998644897215742465-5


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             3788875335777655432026774310020231253100112689998808520
Q gi|254780806|r  159 ALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV  213 (265)
Q Consensus       159 s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v  213 (265)
                      .    ....+....+    ...+.+-++++|++|...+... +++...+ .+.|+
T Consensus       125 ~----~~~~~~~~~f----~~~~~~~~~I~TKlDet~~~G~-~ls~~~~-~~~Pi  169 (173)
T cd03115         125 G----QDAVNQAKAF----NEALGITGVILTKLDGDARGGA-ALSIRAV-TGKPI  169 (173)
T ss_pred             H----HHHHHHHHHH----HHCCCCCEEEEEEECCCCCCCH-HHHHHHH-HCCCE
T ss_conf             0----6589999998----7427997899971438997579-9999999-89090


No 69 
>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]
Probab=98.76  E-value=1.8e-07  Score=63.14  Aligned_cols=150  Identities=21%  Similarity=0.295  Sum_probs=88.5

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCC
Q ss_conf             87499998088988889999999999998799599998787768011212463334541167630257712102444444
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIP   84 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~   84 (265)
                      ++-||.+. +-+|+||||+.--|...|..+|+||.+|=-||-.         +... .++   +.+.-..++.   +..+
T Consensus        50 ~a~viGIT-G~PGaGKSTli~~L~~~l~~~G~rVaVlAVDPSS---------p~TG-Gsi---LGDRiRM~~~---~~~~  112 (323)
T COG1703          50 NAHVIGIT-GVPGAGKSTLIEALGRELRERGHRVAVLAVDPSS---------PFTG-GSI---LGDRIRMQRL---AVDP  112 (323)
T ss_pred             CCCEEEEC-CCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCC---------CCCC-CCC---CCCHHHHHHH---CCCC
T ss_conf             98378731-7998866889999999999779678999988999---------9878-530---1207667764---4699


Q ss_pred             CEEEC--CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHH-HH
Q ss_conf             20001--4887457750001232222102333224765102782033101333222210112331001111123113-78
Q gi|254780806|r   85 NLSII--PSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFA-LE  161 (265)
Q Consensus        85 ~l~ii--pa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s-~~  161 (265)
                      |+.+=  |+...+.+...          ...+.+...-+-.||+|||-|- |.|..-......+|.+++++.|..-+ ++
T Consensus       113 ~vFiRs~~srG~lGGlS~----------at~~~i~~ldAaG~DvIIVETV-GvGQsev~I~~~aDt~~~v~~pg~GD~~Q  181 (323)
T COG1703         113 GVFIRSSPSRGTLGGLSR----------ATREAIKLLDAAGYDVIIVETV-GVGQSEVDIANMADTFLVVMIPGAGDDLQ  181 (323)
T ss_pred             CEEEEECCCCCCCHHHHH----------HHHHHHHHHHHCCCCEEEEEEC-CCCCCHHHHHHHCCEEEEEECCCCCCHHH
T ss_conf             817842687765101668----------8999999998618988999814-78841557765216689996578882788


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECC
Q ss_conf             887533577765543202677431002023125
Q gi|254780806|r  162 GLSQLLETVEEVRRTVNSALDIQGIILTMFDSR  194 (265)
Q Consensus       162 ~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~  194 (265)
                      +.+.-  ++ ++.       +  =+++|++|..
T Consensus       182 ~iK~G--im-Eia-------D--i~vINKaD~~  202 (323)
T COG1703         182 GIKAG--IM-EIA-------D--IIVINKADRK  202 (323)
T ss_pred             HHHHH--HH-HHH-------H--EEEEECCCHH
T ss_conf             88741--46-540-------3--3567256726


No 70 
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=98.75  E-value=4.7e-08  Score=66.53  Aligned_cols=42  Identities=36%  Similarity=0.435  Sum_probs=38.6

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             6874999980889888899999999999987995999987877
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      ++++||.+. +=-||||||+++-||+.+.++|++|+++=+|..
T Consensus       204 ~~g~VIaLV-GvnGvGKTTTiAKLA~~l~~~gkkV~LVAaDTF  245 (407)
T PRK12726        204 SNHRIISLI-GQTGVGKTTTLVKLGWQLLKQNRTVGFITTDTF  245 (407)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf             369089998-999897899999999999977991799970667


No 71 
>PRK13896 cobyrinic acid a,c-diamide synthase; Provisional
Probab=98.75  E-value=2.7e-08  Score=67.96  Aligned_cols=173  Identities=15%  Similarity=0.196  Sum_probs=87.8

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCE
Q ss_conf             49999808898888999999999999879959999878776801121246333454116763025771210244444420
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNL   86 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l   86 (265)
                      |-|.|.....|+||||+|..|..+|+++|++|.-.-+-|-          .-|+  .++          ..+.-....||
T Consensus         2 kgilIAa~~SgsGKTtvt~gL~~aL~~rG~~Vq~FK~GPD----------YIDP--~~h----------~~a~G~~~~NL   59 (432)
T PRK13896          2 DGVVLAGTSSGVGKTVATLAVLQALADAGYDVQPAKAGPD----------FIDP--SHH----------EAVVDTPSRSL   59 (432)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCC----------CCCH--HHH----------HHHHCCCCCCC
T ss_conf             6289977899998999999999999978496376666847----------5198--999----------99968984468


Q ss_pred             EECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCC-CCHHHHHH----HCCCCCCCCCHHHH
Q ss_conf             00148874577500012322221023332247651027820331013332222-10112331----00111112311378
Q gi|254780806|r   87 SIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLT-MNAMAAAD----SILVPLQCEFFALE  161 (265)
Q Consensus        87 ~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~-~~al~aad----~viip~~p~~~s~~  161 (265)
                      |..            +....    .+++..   .....|+.||.---|+=+-. .+.-..|.    =||+|+.+.-.+. 
T Consensus        60 D~~------------m~~~~----~v~~~~---~~~~aDiaviEGvMGLyDG~~~Sta~lA~~l~~PVvLVvd~~~~~~-  119 (432)
T PRK13896         60 DPW------------LSGED----GMRRTY---WRGTGDVCVVEGMMGLYDGTVASTAAVAEELDLPVVLVVDAKAGME-  119 (432)
T ss_pred             CHH------------HCCHH----HHHHHH---HHCCCCEEEEEECCCCCCCCCCCHHHHHHHHCCCEEEEEECCHHHH-
T ss_conf             910------------18989----999999---7279986999612324578877589999984999899993320188-


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf             8875335777655432026774310020231253100112689998808520156267868898
Q gi|254780806|r  162 GLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRIS  225 (265)
Q Consensus       162 ~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~  225 (265)
                      ++.-++.-+..+....+.++++.|||+|++.+  ..|.+.+.+..+. +.++++ +||++..+.
T Consensus       120 s~aA~v~G~~~f~~~~~~d~~iaGVIlN~v~s--~rh~~~l~~al~~-~i~vlG-~lPr~~~l~  179 (432)
T PRK13896        120 SVAATALGFQAYADRAGVDIDVAGVLAQRAHG--GRHADGIRDALPD-ELTYFG-RVPPRSDLE  179 (432)
T ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEEEECCCCC--HHHHHHHHHHHHC-CCCEEE-EECCCCCCC
T ss_conf             89999999997241247652476688426775--8899999999870-894898-842477789


No 72 
>PRK10416 cell division protein FtsY; Provisional
Probab=98.73  E-value=9.2e-08  Score=64.81  Aligned_cols=165  Identities=20%  Similarity=0.284  Sum_probs=92.0

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC
Q ss_conf             76874999980889888899999999999987995999987877680112124633345411676302577121024444
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA   82 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~   82 (265)
                      .+...||-|+ +=-|+||||++.-||+.|.+.|++|+++=+|.......- .+..      |                ..
T Consensus       292 ~~~P~VIl~v-GvNG~GKTTTigKLA~~~~~~gkkVllaA~DTfRaAAie-QL~~------w----------------~~  347 (499)
T PRK10416        292 GKTPFVILMV-GVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVE-QLQV------W----------------GQ  347 (499)
T ss_pred             CCCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHH-HHHH------H----------------HC
T ss_conf             9998799997-478787898999999999977995378840667568999-9999------8----------------42


Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCC--CC-------HHH-----HHHH
Q ss_conf             442000148874577500012322221023332247651027820331013332222--10-------112-----3310
Q gi|254780806|r   83 IPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLT--MN-------AMA-----AADS  148 (265)
Q Consensus        83 ~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~--~~-------al~-----aad~  148 (265)
                      .-|+.++....           ..+......+.+.......||++||||.+-+..-.  +.       ++.     +-+.
T Consensus       348 r~~v~vi~~~~-----------g~Dpa~V~~dai~~a~~~~~DvviiDTAGRl~~~~~LM~EL~ki~rvi~k~~~~aP~e  416 (499)
T PRK10416        348 RNNIPVIAQHT-----------GADSASVIFDAIQAAKARNVDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPHE  416 (499)
T ss_pred             CCCCEEEECCC-----------CCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCE
T ss_conf             45736983689-----------9997999999999999729998998577643260999999999999997237899974


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             01111123113788875335777655432026774310020231253100112689998808520
Q gi|254780806|r  149 ILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV  213 (265)
Q Consensus       149 viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v  213 (265)
                      +++|+.... +    .   +.+... +.++..+.+-|+|+|+.|...+=.  +.-.+...++.++
T Consensus       417 ~lLVlDa~t-G----Q---na~~qa-k~F~e~~~ltGiIlTKlDGtAKGG--~~lsi~~~~~~PI  470 (499)
T PRK10416        417 VMLTIDAST-G----Q---NAVSQA-KLFHEAVGLTGITLTKLDGTAKGG--VIFSVADQFGIPI  470 (499)
T ss_pred             EEEEEECCC-C----H---HHHHHH-HHHHHCCCCCEEEEECCCCCCCCH--HHHHHHHHHCCCE
T ss_conf             899977876-7----7---899999-998442799759996567788525--9999999988395


No 73 
>PRK00784 cobyric acid synthase; Provisional
Probab=98.72  E-value=6.1e-08  Score=65.84  Aligned_cols=208  Identities=16%  Similarity=0.197  Sum_probs=107.2

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEEEEEE-------CCCCHHH
Q ss_conf             874999980889888899999999999987995999987877-68011212463334541167630-------2577121
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYSSYDLLI-------EEKNINQ   76 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~~~l~-------~~~~l~~   76 (265)
                      .+|.|-|...--+||||++++.|...|+++|+||.=.-  .| .++..+  +......-+..++++       -....++
T Consensus         2 ~~k~lMv~GT~S~vGKS~l~aaLCRi~~~~G~~VaPFK--aQNMslNs~--vt~dG~EigrAQ~~QA~Aag~~p~v~MNP   77 (492)
T PRK00784          2 MAKALMVQGTTSDAGKSTLVAGLCRILARRGLRVAPFK--AQNMSLNSA--VTADGGEIGRAQALQAEAAGVEPSVDMNP   77 (492)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCC--HHHCCCCCE--ECCCCCEEHHHHHHHHHHCCCCCCCCCCC
T ss_conf             86305888678887799999999999995898557857--022466517--88999833699999999869999767688


Q ss_pred             CCCCCCCC-CEEECCCCCCCCCCCCC-CCCCCCCC-HHHHHHHHHHHHCCCCCCEEEECCCCCCCCCC---------HHH
Q ss_conf             02444444-20001488745775000-12322221-02333224765102782033101333222210---------112
Q gi|254780806|r   77 ILIQTAIP-NLSIIPSTMDLLGIEMI-LGGEKDRL-FRLDKALSVQLTSDFSYIFLDCPPSFNLLTMN---------AMA  144 (265)
Q Consensus        77 ~i~~~~~~-~l~iipa~~~~~~~~~~-l~~~~~~~-~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~---------al~  144 (265)
                      +..+...+ +--||--+......... ........ ....+.+ ..+..+||+|++.-.++.-.+++.         |-.
T Consensus        78 ILLKP~gd~~SQVIv~Gk~~g~~~a~~Y~~~~~~~~~~v~~a~-~~L~~~~d~iV~EGAGSpaEiNL~~~Di~Nm~~A~~  156 (492)
T PRK00784         78 VLLKPQSDTGSQVIVQGKVVGNMDARDYHDYKPRLLEAVLESL-DRLAAEYDLVVVEGAGSPAEINLRDRDIANMGFAEA  156 (492)
T ss_pred             EEECCCCCCCCEEEECCEECCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHCCEEEEECCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             7763189988679999978753139999986999999999999-998865889999358982002652200242899986


Q ss_pred             HHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCH
Q ss_conf             331001111123113788875335777655432026774310020231253100112689998808520156267868
Q gi|254780806|r  145 AADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNV  222 (265)
Q Consensus       145 aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~  222 (265)
                      +---+|+|..-|.-.+  ...+..+++.+... +.. .+.|+|+|||.-...+-..-++.+++..+.++++ +||+..
T Consensus       157 ~~apviLV~DIdRGGv--fAsl~GT~~lL~~~-eR~-li~G~IiNKFRGD~~ll~pG~~~le~~tg~PvlG-viP~~~  229 (492)
T PRK00784        157 ADAPVILVADIDRGGV--FASLVGTLALLSPE-ERA-RVKGFVINKFRGDISLLEPGLDWLEELTGIPVLG-VLPYLD  229 (492)
T ss_pred             CCCCEEEEEECCCCCH--HHHHHHHHHHCCHH-HHH-HEEEEEEEEECCCHHHHCCHHHHHHHHHCCCCEE-EECCCC
T ss_conf             5998899997567642--68776388759998-871-1589999764587466355999999986898068-614656


No 74 
>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=98.71  E-value=3.3e-07  Score=61.58  Aligned_cols=164  Identities=19%  Similarity=0.245  Sum_probs=95.1

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCC
Q ss_conf             68749999808898888999999999999879959999878776801121246333454116763025771210244444
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAI   83 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~   83 (265)
                      .++.+|.|. +-.|+||||+.-.|+..+-..|+||.++=-||-...|-         + ++   |.+.....+.   ...
T Consensus        27 g~a~~iGiT-G~PGaGKStli~~l~~~~~~~g~~vaVlAvDPSS~~sg---------G-ai---LGDr~RM~~~---~~~   89 (267)
T pfam03308        27 GRAHRVGIT-GVPGAGKSTLIEALGMELRRRGHRVAVLAVDPSSPFTG---------G-SI---LGDRTRMQRL---AVD   89 (267)
T ss_pred             CCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCC---------C-CC---CCCHHHHHHH---CCC
T ss_conf             995599876-89988799999999999996898689999789998888---------6-30---0107777650---589


Q ss_pred             CCEEEC--CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHH-H
Q ss_conf             420001--4887457750001232222102333224765102782033101333222210112331001111123113-7
Q gi|254780806|r   84 PNLSII--PSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFA-L  160 (265)
Q Consensus        84 ~~l~ii--pa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s-~  160 (265)
                      +++.+=  |+...+.+...          ...+.+...-...||+|||-|- |.|.--..+...+|.++++..|..-+ +
T Consensus        90 ~~vfiRs~~srg~lGGls~----------~t~~~i~lleaaGfD~IivETV-GVGQsE~~v~~~aD~~llv~~Pg~GDei  158 (267)
T pfam03308        90 PGAFIRSSPSRGALGGLSR----------ATREAILLLDAAGFDVIIIETV-GVGQSEVDIANMADTFVLVTIPGGGDDL  158 (267)
T ss_pred             CCEEEEECCCCCCCCCCCH----------HHHHHHHHHHHCCCCEEEEECC-CCCCCCHHHHHHCCEEEEEECCCCCHHH
T ss_conf             9858864577888887147----------6999999999779999999247-7775303555415768999558876088


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHH
Q ss_conf             8887533577765543202677431002023125310011268999880
Q gi|254780806|r  161 EGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNL  209 (265)
Q Consensus       161 ~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~  209 (265)
                      +++++-   |-++     .  +  -+|+|+.|...  .+....+++..+
T Consensus       159 Q~iKaG---ImEi-----a--D--i~vVNKaD~~~--A~~~~~~l~~~l  193 (267)
T pfam03308       159 QGIKAG---LMEI-----A--D--IYVVNKADLPG--AERTARELRSAL  193 (267)
T ss_pred             HHHHHH---HHHH-----C--C--EEEEECCCHHH--HHHHHHHHHHHH
T ss_conf             898753---7653-----5--4--89996676476--999999999998


No 75 
>PRK01077 cobyrinic acid a,c-diamide synthase; Validated
Probab=98.71  E-value=6.7e-08  Score=65.63  Aligned_cols=171  Identities=19%  Similarity=0.248  Sum_probs=91.1

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCC
Q ss_conf             74999980889888899999999999987995999987877680112124633345411676302577121024444442
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPN   85 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~   85 (265)
                      -+.|.|.....|+||||+++.|..+|+++|+||.-.-+-|-     +  +++     .+.          ..+.-....|
T Consensus         3 ~p~lmI~gt~S~~GKT~vt~gL~r~l~~rG~~VapFK~GPD-----y--Idp-----~~~----------~~a~g~~~~n   60 (451)
T PRK01077          3 MPALVIAAPASGSGKTTVTLGLMRALRRRGLRVQPFKVGPD-----Y--IDP-----AFH----------AAATGRPSRN   60 (451)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCC-----C--CCH-----HHH----------HHHHCCCCCC
T ss_conf             88799986899997899999999999968794575357857-----6--298-----999----------9997897535


Q ss_pred             EEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCC-----------CCCCCHHHHHHHCCCCCC
Q ss_conf             000148874577500012322221023332247651027820331013332-----------222101123310011111
Q gi|254780806|r   86 LSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFN-----------LLTMNAMAAADSILVPLQ  154 (265)
Q Consensus        86 l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~-----------~~~~~al~aad~viip~~  154 (265)
                      ||..            +...    ..+++.+ ....++||++||----|+=           ..-.+-+..+. ||+|+.
T Consensus        61 LD~~------------l~~~----~~v~~~~-~~~~~~~D~~viEG~mGlyDG~~~~~~~gS~aeiA~~l~~P-ViLViD  122 (451)
T PRK01077         61 LDSW------------MMGE----DLVRALF-ARAAGGADIAVIEGVMGLFDGAGGDPDKGSTADIARLLGAP-VVLVVD  122 (451)
T ss_pred             CCHH------------HCCH----HHHHHHH-HHHCCCCCEEEEEECHHCCCCCCCCCCCCCHHHHHHHHCCC-EEEEEC
T ss_conf             8834------------4899----9999999-97546688899850101134545677777789999870998-899984


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHH
Q ss_conf             2311378887533577765543202677431002023125310011268999880852015626786889
Q gi|254780806|r  155 CEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRI  224 (265)
Q Consensus       155 p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i  224 (265)
                      .+-.+ .++..++..+..    +.++.++.|+|+|++..  ..|.+.++...+..|.++++ +||.+..+
T Consensus       123 ~~~~~-~s~aa~v~G~~~----~~~~~~I~GvIlNk~~g--~~h~~ll~~~ie~~gvpvlG-~lP~~~~l  184 (451)
T PRK01077        123 ASGMA-QSAAALVLGFAR----FDPDLNIAGVILNRVGS--ERHYQLLREALEELGLPVLG-ALPRDAAL  184 (451)
T ss_pred             CCCHH-HHHHHHHHHHHH----HCCCCCEEEEEEECCCC--HHHHHHHHHHHHHCCCCEEE-EECCCCCC
T ss_conf             66208-999999999997----59778774899624787--66899999999863995798-61576334


No 76 
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=98.70  E-value=6.3e-08  Score=65.75  Aligned_cols=168  Identities=24%  Similarity=0.360  Sum_probs=84.7

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCC-CEEEEECCCCC-CCCHHHCCCCCCCCCCEEEEEECCCCHHHCCC
Q ss_conf             7687499998088988889999999999998-799-59999878776-80112124633345411676302577121024
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAA-IGE-NVLLIDLDPQG-NASTGLGIELYDRKYSSYDLLIEEKNINQILI   79 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~-rVllID~D~q~-~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~   79 (265)
                      .++.|||+|+ +==||||||+.+=||..++. .|+ +|.+|=+|... ...-  .+                        
T Consensus       207 ~~~~~vvalV-GPTGVGKTTTiAKLAA~~~l~~~~~kV~lIT~DtyRigA~e--QL------------------------  259 (412)
T PRK05703        207 LEQGGVVALV-GPTGVGKTTTLAKLAARYALEEGKDKVALITLDTYRIGAVE--QL------------------------  259 (412)
T ss_pred             CCCCCEEEEE-CCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHH--HH------------------------
T ss_conf             4567369998-88887567699999999999729981799983767777999--99------------------------


Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCC---C----CHHHH--HHHCC
Q ss_conf             444442000148874577500012322221023332247651027820331013332222---1----01123--31001
Q gi|254780806|r   80 QTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLT---M----NAMAA--ADSIL  150 (265)
Q Consensus        80 ~~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~---~----~al~a--ad~vi  150 (265)
                      +++.+-          .+........+   .-|..+|.. + .++|+|||||++ .|+.-   .    ..+..  .+.++
T Consensus       260 k~Ya~i----------lgvp~~v~~~~---~~l~~al~~-~-~~~dlILIDTaG-~s~~d~~~~~eL~~~~~~~~~~~~~  323 (412)
T PRK05703        260 KTYAKI----------MGIPVKVAYDP---KELAKALEQ-L-ANCDLILIDTAG-RSQRDPRLISELKALIENSKPIDVY  323 (412)
T ss_pred             HHHHHH----------CCCEEEEECCH---HHHHHHHHH-H-CCCCEEEEECCC-CCCCCHHHHHHHHHHHHHCCCCCEE
T ss_conf             999997----------19737984799---999999987-1-589979996898-8978999999999998624887189


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC----CCCCCCCCHHH
Q ss_conf             111123113788875335777655432026774310020231253100112689998808520----15626786889
Q gi|254780806|r  151 VPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV----YNTVIPRNVRI  224 (265)
Q Consensus       151 ip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v----~~~~Ip~~~~i  224 (265)
                      +|+.+.. ..+.+..+   ++.++     .+.+.++|+|+.|....... +++.+.+. +.++    .++.||+|...
T Consensus       324 LVlsat~-~~~dl~~i---~~~f~-----~~~~~~lI~TKlDEt~~~G~-il~~~~~~-~lplsy~t~GQ~VPeDi~~  390 (412)
T PRK05703        324 LVLSATT-KYRDLKDI---VKHFS-----RLPLDGLILTKLDETSSLGS-ILSLLIES-GLPISYLTDGQRVPDDIKV  390 (412)
T ss_pred             EEECCCC-CHHHHHHH---HHHHC-----CCCCCEEEEEEECCCCCCCH-HHHHHHHH-CCCEEEEECCCCCHHHHHC
T ss_conf             9975989-98999999---99846-----79998799971128998629-99999998-8796999469997243422


No 77 
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=98.70  E-value=3.9e-08  Score=67.00  Aligned_cols=164  Identities=25%  Similarity=0.322  Sum_probs=87.4

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCC
Q ss_conf             68749999808898888999999999999879959999878776801121246333454116763025771210244444
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAI   83 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~   83 (265)
                      +..-||-++ +==|+||||++.-||.+|.++|++|++|-||.+.-...              +-|   ..+.+   +   
T Consensus        98 ~~P~vImmv-GLQGsGKTTt~~KLA~~lkk~~~kvllVaaD~~RpAA~--------------eQL---~~La~---q---  153 (451)
T COG0541          98 KPPTVILMV-GLQGSGKTTTAGKLAKYLKKKGKKVLLVAADTYRPAAI--------------EQL---KQLAE---Q---  153 (451)
T ss_pred             CCCEEEEEE-ECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHH--------------HHH---HHHHH---H---
T ss_conf             998589998-15679748689999999997499458985056786899--------------999---99998---6---


Q ss_pred             CCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCC--CC------HHHHHHHCCCCCCC
Q ss_conf             42000148874577500012322221023332247651027820331013332222--10------11233100111112
Q gi|254780806|r   84 PNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLT--MN------AMAAADSILVPLQC  155 (265)
Q Consensus        84 ~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~--~~------al~aad~viip~~p  155 (265)
                      -++++.+.+.           ..+.....++.+...-...||+|||||.+-+..-.  ..      ...--|+++.|+..
T Consensus       154 ~~v~~f~~~~-----------~~~Pv~Iak~al~~ak~~~~DvvIvDTAGRl~ide~Lm~El~~Ik~~~~P~E~llVvDa  222 (451)
T COG0541         154 VGVPFFGSGT-----------EKDPVEIAKAALEKAKEEGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDA  222 (451)
T ss_pred             CCCCEECCCC-----------CCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEC
T ss_conf             0985316778-----------89979999999999997499889996887330309999999999855398748998764


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             3113788875335777655432026774310020231253100112689998808520
Q gi|254780806|r  156 EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV  213 (265)
Q Consensus       156 ~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v  213 (265)
                      -.  =+.+.       ...+.++..+.+-|+|+|+.|...+=.-  .-.++...|.|+
T Consensus       223 m~--GQdA~-------~~A~aF~e~l~itGvIlTKlDGdaRGGa--ALS~~~~tg~PI  269 (451)
T COG0541         223 MI--GQDAV-------NTAKAFNEALGITGVILTKLDGDARGGA--ALSARAITGKPI  269 (451)
T ss_pred             CC--CHHHH-------HHHHHHHHHCCCCEEEEECCCCCCCCHH--HHHHHHHHCCCE
T ss_conf             44--56789-------9999986626986499971467876228--885699878985


No 78 
>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=98.69  E-value=2.4e-08  Score=68.23  Aligned_cols=198  Identities=16%  Similarity=0.194  Sum_probs=105.6

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEEEEEEC-------CCCHHHCCCCCC
Q ss_conf             980889888899999999999987995999987877-680112124633345411676302-------577121024444
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYSSYDLLIE-------EKNINQILIQTA   82 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~~~l~~-------~~~l~~~i~~~~   82 (265)
                      |...---+|||++|+.|=..|+++||||.=.=.  | ++|-.+.-  ..+..-.++++.+-       ....+++..+ +
T Consensus         3 V~GTsS~AGKs~l~AaLCRiL~rrGy~VAPFKs--QNMSLNSfvt--~~~~EiA~AQ~~QA~AAGieP~~~mNPvLLK-P   77 (502)
T TIGR00313         3 VVGTSSSAGKSLLTAALCRILARRGYRVAPFKS--QNMSLNSFVT--AEGGEIAIAQALQALAAGIEPSVHMNPVLLK-P   77 (502)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCHH--HHHHHHHHHC--CCCCEEEHHHHHHHHHCCCCCCCCCCCCCCC-C
T ss_conf             420115402899999999998527881278501--1010133311--3787551376899986387886234871016-7


Q ss_pred             CCCEE--ECCCCCCCCCCCCCCCCCCCCCHHHHHHHH---HHHHCCCCCCEEEECCCCCCCC----------CCHHHHHH
Q ss_conf             44200--014887457750001232222102333224---7651027820331013332222----------10112331
Q gi|254780806|r   83 IPNLS--IIPSTMDLLGIEMILGGEKDRLFRLDKALS---VQLTSDFSYIFLDCPPSFNLLT----------MNAMAAAD  147 (265)
Q Consensus        83 ~~~l~--iipa~~~~~~~~~~l~~~~~~~~~l~~~l~---~~l~~~yD~IiiD~pp~~~~~~----------~~al~aad  147 (265)
                      .+++-  ||--+....+....-. ..+...++.+.+.   ..|+.+||||++--.+|.-.++          .+-+..||
T Consensus        78 kgdf~SQviv~G~a~g~~~~~~Y-~~~~~d~~~~~i~eSle~L~~~Yd~vv~EGAGS~AEINL~~rDLaN~~iA~~~~A~  156 (502)
T TIGR00313        78 KGDFTSQVIVHGRAVGDMNAQEY-YKNKVDFLLKAIKESLEILAEEYDLVVIEGAGSPAEINLKERDLANMRIAELADAD  156 (502)
T ss_pred             CCCCEEEEEEEEECCCCCCHHHH-HHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHCCCC
T ss_conf             88846678984112466761567-77999999999999998752028889982688710005331572247898643976


Q ss_pred             HCCCCCCCCC----HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHH
Q ss_conf             0011111231----137888753357776554320267743100202312531001126899988085201562678688
Q gi|254780806|r  148 SILVPLQCEF----FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVR  223 (265)
Q Consensus       148 ~viip~~p~~----~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~  223 (265)
                      . |+|..=|.    .|+.|+-+++.      +..  ...+.|||+||+.-+...=..=++++++.-|.+|++ +||+++.
T Consensus       157 ~-iLvADIDRGGVFAsi~GTl~LL~------~~~--r~liKG~vINkfRG~~~vL~~GI~~lEelTGiPVLG-v~PY~~~  226 (502)
T TIGR00313       157 V-ILVADIDRGGVFASIYGTLKLLP------EEE--RKLIKGIVINKFRGNVDVLESGIEKLEELTGIPVLG-VLPYDEN  226 (502)
T ss_pred             E-EEEEECCCCCCHHHHHHHHHHCC------CCC--CCEECEEEECCCCCCHHHHHHHHHHHHHHCCCCEEE-EEECCCC
T ss_conf             7-99975077743243374666188------345--750030688354687244344568998854842344-6501257


Q ss_pred             H
Q ss_conf             9
Q gi|254780806|r  224 I  224 (265)
Q Consensus       224 i  224 (265)
                      .
T Consensus       227 l  227 (502)
T TIGR00313       227 L  227 (502)
T ss_pred             C
T ss_conf             7


No 79 
>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=98.66  E-value=1.4e-07  Score=63.73  Aligned_cols=43  Identities=30%  Similarity=0.356  Sum_probs=38.1

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             76874999980889888899999999999987995999987877
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      +++.++|.++ +==|+||||+++-||+.+...|++|++|=+|..
T Consensus        72 ~~~~~vI~lv-G~~G~GKTTT~AKLA~~~~~~~~kV~lia~Dty  114 (270)
T PRK06731         72 EKEVQTIALI-GPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHS  114 (270)
T ss_pred             CCCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCC
T ss_conf             7998189998-889898899999999999867990899983888


No 80 
>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=98.65  E-value=8.6e-08  Score=64.97  Aligned_cols=173  Identities=20%  Similarity=0.304  Sum_probs=87.9

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC
Q ss_conf             76874999980889888899999999999987995999987877680112124633345411676302577121024444
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA   82 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~   82 (265)
                      ||.-..|++. +=-||||||+.+-||+.++..+++|.+|-+|...-.. .=.+      .+..+           |    
T Consensus       238 ~~~~q~IALV-GPTGVGKTTTIAKLAArf~~~~KkVALITtDTYRIGA-VEQL------KTYAe-----------I----  294 (436)
T PRK11889        238 EKEVQTIALI-GPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGT-VQQL------QDYVK-----------T----  294 (436)
T ss_pred             HHHCEEEEEE-CCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCHHHH-HHHH------HHHHH-----------H----
T ss_conf             6417179998-9999888999999999986169808999806634769-9999------99999-----------8----


Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH--CCCCCCEEEECCCCCCC---CC----CHHHH--HHHCCC
Q ss_conf             442000148874577500012322221023332247651--02782033101333222---21----01123--310011
Q gi|254780806|r   83 IPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLT--SDFSYIFLDCPPSFNLL---TM----NAMAA--ADSILV  151 (265)
Q Consensus        83 ~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~--~~yD~IiiD~pp~~~~~---~~----~al~a--ad~vii  151 (265)
                       =|+.+.+.            ..+   .-+.+++. .+.  .+||+|||||.+ .|+.   ..    ..+..  .+.+++
T Consensus       295 -MgVPV~VV------------~dp---~eL~~AL~-~lkdka~~DLILIDTAG-RS~RD~~~I~EL~~~l~~~~p~ev~L  356 (436)
T PRK11889        295 -IGFEVIAV------------RDE---AAMTRALT-YFKEEARVDYILIDTAG-KNYRASETVEEMIETMGQVEPDYICL  356 (436)
T ss_pred             -HCCCEEEE------------CCH---HHHHHHHH-HHHHCCCCCEEEEECCC-CCCCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             -49943996------------888---99999999-87633688889992989-88468999999999985127771699


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC----CCCCCCCCHHHHHH
Q ss_conf             11123113788875335777655432026774310020231253100112689998808520----15626786889877
Q gi|254780806|r  152 PLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV----YNTVIPRNVRISEA  227 (265)
Q Consensus       152 p~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v----~~~~Ip~~~~i~~a  227 (265)
                      |+.... ..+.+..   .++.++     .+.+.++|+|+.|....... +++-+.+ .+.|+    -++.||+|..++.+
T Consensus       357 VLSATT-K~~DL~e---Ii~rF~-----~l~idglIfTKLDET~SlG~-ILNv~~~-s~LPIsYvTdGQ~VPEDIevA~a  425 (436)
T PRK11889        357 TLSASM-KSKDMIE---IITNFK-----DIHIDGIVFTKFDETASSGE-LLKIPAV-SSAPIVLMTDGQDVKKNIHIATA  425 (436)
T ss_pred             EEECCC-CHHHHHH---HHHHHC-----CCCCCEEEEEECCCCCCCHH-HHHHHHH-HCCCEEEECCCCCCCCCHHHCCH
T ss_conf             997889-9899999---999725-----79988289971325687037-8889988-39987997899858753000699


No 81 
>PRK09435 arginine/ornithine transport system ATPase; Provisional
Probab=98.61  E-value=8.9e-07  Score=59.04  Aligned_cols=166  Identities=20%  Similarity=0.267  Sum_probs=93.2

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC
Q ss_conf             76874999980889888899999999999987995999987877680112124633345411676302577121024444
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA   82 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~   82 (265)
                      ..++.+|.|. +-.|+||||+.-.|+..+...|++|.++=.||-...|-         + ++   |.+...+.+.   ..
T Consensus        46 ~g~a~~iGiT-G~pG~GKStli~~l~~~~~~~g~~v~vlavDPsS~~sg---------G-ai---LGDr~Rm~~~---~~  108 (325)
T PRK09435         46 TGNALRIGIT-GVPGVGKSTFIEALGMHLIEQGHKVAVLAVDPSSTRTG---------G-SI---LGDKTRMERL---SR  108 (325)
T ss_pred             CCCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCC---------C-CH---HHHHHHHHHH---CC
T ss_conf             7982599742-79998688999999999996798589999789999888---------6-10---1038888761---47


Q ss_pred             CCCEEEC--CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCHH-
Q ss_conf             4420001--4887457750001232222102333224765102782033101333222210112331001111123113-
Q gi|254780806|r   83 IPNLSII--PSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFA-  159 (265)
Q Consensus        83 ~~~l~ii--pa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~s-  159 (265)
                      .+++.+=  |+...+.+...          ...+.+...-.-.||+|||-|- |.|.--......+|.++++..|..-+ 
T Consensus       109 ~~~~fiRs~~srg~lgg~~~----------~~~~~~~~~~a~g~d~i~iETv-GvGQ~e~~v~~~~d~~~~~~~p~~GD~  177 (325)
T PRK09435        109 HPNAFIRPSPSSGTLGGVAR----------KTRETMLLCEAAGFDVILVETV-GVGQSETAVAGMVDFFLLLQLPGAGDE  177 (325)
T ss_pred             CCCEEEEECCCCCCCCCCCH----------HHHHHHHHHHHCCCCEEEEEEC-CCCHHHHHHHHHCCEEEEEECCCCCCH
T ss_conf             99848840677888677335----------4999999999779998999706-777148899874266888835887608


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHH-HHHHHHHHHHH
Q ss_conf             78887533577765543202677431002023125310-01126899988
Q gi|254780806|r  160 LEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSL-SQQVVSDVRKN  208 (265)
Q Consensus       160 ~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~-~~~~~~~l~~~  208 (265)
                      +++++.-   |-++.       +  -+|+|+.|..... .+....+++..
T Consensus       178 ~Q~~K~G---ImEia-------D--i~vVNKaDgd~~~~A~~t~~e~~~a  215 (325)
T PRK09435        178 LQGIKKG---IMELA-------D--LIVINKADGDNHTAARRAAAEYRSA  215 (325)
T ss_pred             HHHHHHH---HHHHC-------C--EEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             8998865---77504-------2--6899776755658999999999999


No 82 
>PRK12724 flagellar biosynthesis regulator FlhF; Provisional
Probab=98.61  E-value=1.6e-07  Score=63.41  Aligned_cols=169  Identities=15%  Similarity=0.211  Sum_probs=84.5

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCC
Q ss_conf             7687499998088988889999999999998-799599998787768011212463334541167630257712102444
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQT   81 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~   81 (265)
                      +.+.|||+|+ +==||||||+.+=||..++. .|++|.+|=+|... +...-.+                        ++
T Consensus       220 ~~~~kvi~lV-GPTGVGKTTTiAKLAA~~~l~~~kkVaLIT~DTYR-IgAvEQL------------------------kt  273 (432)
T PRK12724        220 KNQRKVVFFV-GPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDNYR-IAAIEQL------------------------KR  273 (432)
T ss_pred             CCCCEEEEEE-CCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCC-HHHHHHH------------------------HH
T ss_conf             7776299998-99998889999999999999749927999526653-7799999------------------------99


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCC------C-CHHHH---HH--HC
Q ss_conf             4442000148874577500012322221023332247651027820331013332222------1-01123---31--00
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLT------M-NAMAA---AD--SI  149 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~------~-~al~a---ad--~v  149 (265)
                      +.+-+. +|-       ..  ...   ...+.+.|.   ..++|+|||||.+- |+-.      + ..+.+   .+  ..
T Consensus       274 Ya~Il~-iPv-------~v--v~~---~~el~~al~---~~~~DlILIDTAGr-S~rd~~~~~eL~~ll~~~~~~~~ie~  336 (432)
T PRK12724        274 YADTMG-MPF-------YP--VKD---IKKFKETLA---RDGSELILIDTAGY-SHRNLEQLERMQSFYSCFGEKDSVEN  336 (432)
T ss_pred             HHHHHC-CCE-------EE--EEC---HHHHHHHHH---HCCCCEEEEECCCC-CCCCHHHHHHHHHHHHHHCCCCCCEE
T ss_conf             999859-945-------99--518---999999998---56999999929998-97899999999999986366788517


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC----CCCCCCCCHHHH
Q ss_conf             1111123113788875335777655432026774310020231253100112689998808520----156267868898
Q gi|254780806|r  150 LVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV----YNTVIPRNVRIS  225 (265)
Q Consensus       150 iip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v----~~~~Ip~~~~i~  225 (265)
                      ++|+... ...+.+..+   ++.+.     .+.+.++|+|+.|....... +++-+.. .+.++    .++.||+|...+
T Consensus       337 ~LVLSaT-tk~~dl~~i---i~~f~-----~l~~~~lIfTKLDET~s~G~-ilni~~~-~~~PisYiT~GQ~VPdDI~~A  405 (432)
T PRK12724        337 LLVLSST-SSYHHTLTV---LKAYE-----SLNYRRILLTKLDEADFLGS-FLELADT-YSKSFTYLSVGQEVPFDILNA  405 (432)
T ss_pred             EEEEECC-CCHHHHHHH---HHHHC-----CCCCCEEEEEECCCCCCCCH-HHHHHHH-HCCCEEEEECCCCCCCCHHHC
T ss_conf             9999788-998999999---99842-----69998499971227798669-9999999-889869980899797173335


No 83 
>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=98.61  E-value=1.4e-07  Score=63.75  Aligned_cols=103  Identities=25%  Similarity=0.370  Sum_probs=58.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC-CCCEEECCCC
Q ss_conf             889888899999999999987995999987877680112124633345411676302577121024444-4420001488
Q gi|254780806|r   14 QKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA-IPNLSIIPST   92 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~-~~~l~iipa~   92 (265)
                      +--|+||||.+..+...+...|++|.+|-+||.+. .  +   +++..-++.|.+    ++.+++.+.. .||--++   
T Consensus         3 GpaGSGKTT~~~~l~~~l~~~~r~~~vvNLDPA~e-~--~---pY~~~iDIrd~i----~~~dvM~~~~LGPNGali---   69 (234)
T pfam03029         3 GGAGSGKTTFVGALSEILPLRGRSVYVVNLDPAAE-N--L---PYEADIDIRELI----TVADVMEDYGLGPNGALT---   69 (234)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCC-C--C---CCCCCCCHHHHC----CHHHHHHHCCCCCCHHHH---
T ss_conf             98989889999999999997799759997898665-8--9---998777178746----799999982989738999---


Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCC
Q ss_conf             745775000123222210233322476510278203310133322221
Q gi|254780806|r   93 MDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTM  140 (265)
Q Consensus        93 ~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~  140 (265)
                         ..++. +.   ....|+.    ..+..+.||+|||||+....++.
T Consensus        70 ---~~me~-l~---~~~d~l~----~~l~~~~~y~l~DtPGQiElf~~  106 (234)
T pfam03029        70 ---VAMDF-GR---ITLDWLL----EELEYEDDYYLFDTPGQIELFTH  106 (234)
T ss_pred             ---HHHHH-HH---HHHHHHH----HHHCCCCCEEEEECCCCEEEEEC
T ss_conf             ---99999-99---9999999----98525577699836983576540


No 84 
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=98.57  E-value=2.1e-07  Score=62.66  Aligned_cols=161  Identities=20%  Similarity=0.273  Sum_probs=80.9

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCC
Q ss_conf             87499998088988889999999999998799599998787768011212463334541167630257712102444444
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIP   84 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~   84 (265)
                      ++-||-++ +==|+||||+++-||.++.++|++|+++-+|.......- .+                ..+.+      .-
T Consensus        96 kP~Vim~v-GlqGsGKTTT~aKLA~~~kk~g~kv~lvaaDt~RpaA~e-QL----------------~~la~------~~  151 (433)
T PRK00771         96 KPQTILLV-GLQGSGKTTTAAKLARYFQKKGLKVGVICADTWRPGAYE-QL----------------KQLCE------KI  151 (433)
T ss_pred             CCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHH-HH----------------HHHHH------HC
T ss_conf             98589997-378897899999999999977994678506788368999-99----------------99998------63


Q ss_pred             CEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCC--C------HHHHHHHCCCCCCCC
Q ss_conf             20001488745775000123222210233322476510278203310133322221--0------112331001111123
Q gi|254780806|r   85 NLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTM--N------AMAAADSILVPLQCE  156 (265)
Q Consensus        85 ~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~--~------al~aad~viip~~p~  156 (265)
                      ++.+.+...           ..+......+.+. . ...||+|||||.+-+..-..  .      -...-|+++.|+...
T Consensus       152 ~v~~~~~~~-----------~~dp~~i~~~a~~-~-~k~~DvviiDTAGRl~~d~~Lm~El~~i~~~~~P~e~llV~Da~  218 (433)
T PRK00771        152 NVPFYGDPK-----------EKDAVKIVKEGLE-K-LKKVDVIIVDTAGRHKLEKDLIEEMKQIKEITKPDEVILVIDAT  218 (433)
T ss_pred             CCCCCCCCC-----------CCCHHHHHHHHHH-H-HCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEECC
T ss_conf             887317889-----------9999999999999-8-45698899977652104099999999998775797689986544


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             113788875335777655432026774310020231253100112689998808520
Q gi|254780806|r  157 FFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV  213 (265)
Q Consensus       157 ~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v  213 (265)
                      . . +      +.+ ...+.++..+.+-|+|+|+.|...+=.-  .-.++...+.|+
T Consensus       219 ~-G-Q------~a~-~~a~~F~~~~~i~gvIlTKlDgdarGGa--aLSi~~~t~~PI  264 (433)
T PRK00771        219 I-G-Q------QAS-EQAKAFKEAVGIGGIIITKLDGTAKGGG--ALSAVAETGAPI  264 (433)
T ss_pred             C-C-H------HHH-HHHHHHHHHCCCCEEEEECCCCCCCCCH--HHHHHHHHCCCC
T ss_conf             2-2-6------789-9999998753887379972567887305--421898878995


No 85 
>PRK10867 signal recognition particle protein; Provisional
Probab=98.56  E-value=2.3e-07  Score=62.44  Aligned_cols=163  Identities=19%  Similarity=0.256  Sum_probs=83.2

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCCH-HHCCCCCCCCCCEEEEEECCCCHHHCCCCC
Q ss_conf             687499998088988889999999999998-799599998787768011-212463334541167630257712102444
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLDPQGNAST-GLGIELYDRKYSSYDLLIEEKNINQILIQT   81 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~D~q~~~~~-~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~   81 (265)
                      +...||-++ +==|+||||+++-||.++.. .|++|+++-||.+..... -|.                  .+.      
T Consensus        98 ~~p~VIm~v-GLqGsGKTTT~aKLA~~lk~k~~k~vllvaaDt~RpaA~eQL~------------------~la------  152 (453)
T PRK10867         98 QPPAVVLMA-GLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPAAIKQLE------------------TLA------  152 (453)
T ss_pred             CCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHH------------------HHH------
T ss_conf             999699997-4688851858999999999738983798558877058999999------------------999------


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCC--CC------HHHHHHHCCCCC
Q ss_conf             4442000148874577500012322221023332247651027820331013332222--10------112331001111
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLT--MN------AMAAADSILVPL  153 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~--~~------al~aad~viip~  153 (265)
                      ..-++.+.+...           ..+......+.+...-...||+|||||.+-+..-.  ..      -..--|.++.|+
T Consensus       153 ~~~~v~~~~~~~-----------~~dp~~ia~~a~~~ak~~~~DvvivDTAGRl~~d~~Lm~El~~i~~~~~P~e~llV~  221 (453)
T PRK10867        153 EQVGVDFFPSDV-----------GQKPVDIVNAALKEAKLKFYDVLLVDTAGRLHVDEAMMDEIKQVHASINPVETLFVV  221 (453)
T ss_pred             HHCCCCEECCCC-----------CCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHCCHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             851980436788-----------998899999999999977999999978760121088899999998763787137974


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             123113788875335777655432026774310020231253100112689998808520
Q gi|254780806|r  154 QCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV  213 (265)
Q Consensus       154 ~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v  213 (265)
                      .... . +.   .++..    +.++..+.+-|+|+|+.|...+=.-  .=.+....+.|+
T Consensus       222 Da~~-G-Q~---a~~~a----~~F~~~~~~~gvIlTKlDgdarGG~--alS~~~~t~~PI  270 (453)
T PRK10867        222 DAMT-G-QD---AANTA----KAFNEALPLTGVVLTKVDGDARGGA--ALSIRHITGKPI  270 (453)
T ss_pred             ECCC-C-HH---HHHHH----HHHHHHCCCCEEEEECCCCCCCCHH--HHHHHHHHCCCC
T ss_conf             3223-5-66---89999----9999855987078750467876138--989999978696


No 86 
>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=98.54  E-value=5.6e-07  Score=60.23  Aligned_cols=212  Identities=16%  Similarity=0.194  Sum_probs=113.6

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC--HHHCCCCCCCCCCEEEEEECCCCHHHCCCC-
Q ss_conf             68749999808898888999999999999879959999878776801--121246333454116763025771210244-
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS--TGLGIELYDRKYSSYDLLIEEKNINQILIQ-   80 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~--~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~-   80 (265)
                      -+|.+|-|. +-=|+||||+.--|...|-++|+||.+|=-||-..-|  ..||               +...+++.-.. 
T Consensus        36 GnA~~vG~T-G~PGaGKSTl~~~l~~~lrRrG~~VaViAvDP~SPfTGGsiLG---------------Dr~Rm~~~asrk   99 (333)
T TIGR00750        36 GNAHVVGIT-GVPGAGKSTLVEKLIMELRRRGLKVAVIAVDPSSPFTGGSILG---------------DRLRMQRLASRK   99 (333)
T ss_pred             CCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCHHHHH---------------HHHHHHHHHHHH
T ss_conf             790787664-6888857779999989997659768999887975975514545---------------688775442222


Q ss_pred             --CCCCCEEE--CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCC
Q ss_conf             --44442000--14887457750001232222102333224765102782033101333222210112331001111123
Q gi|254780806|r   81 --TAIPNLSI--IPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCE  156 (265)
Q Consensus        81 --~~~~~l~i--ipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~  156 (265)
                        -..||++|  +|+.-.+.+....       ...+.+.|   -+-.||+|||-| =|.|..=...+.++|.+|+++-|.
T Consensus       100 qlW~dPg~FIRs~ptrG~lGGls~a-------t~~~~~ll---dA~G~DVI~vET-VGVGQSEVdi~~~aDT~v~v~~pg  168 (333)
T TIGR00750       100 QLWTDPGVFIRSMPTRGSLGGLSKA-------TRELVKLL---DAAGYDVILVET-VGVGQSEVDIINMADTFVVVTIPG  168 (333)
T ss_pred             HHHCCCCCEECCCCCCCCHHHHHHH-------HHHHHHHH---HHCCCCEEEEEE-ECCCHHHHHHHHHHCEEEEEECCC
T ss_conf             3322898567677666752578799-------99999999---863898799984-157524878873415058985488


Q ss_pred             CH-HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHC-----CCCCCCCCCCCHHHHHHHHC
Q ss_conf             11-3788875335777655432026774310020231253100112689998808-----52015626786889877737
Q gi|254780806|r  157 FF-ALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLG-----GKVYNTVIPRNVRISEAPSY  230 (265)
Q Consensus       157 ~~-s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~-----~~v~~~~Ip~~~~i~~a~~~  230 (265)
                      .= .+++++.-+=   ++     .  + + +|+|+.|...-  .++...++-.|.     ..++...-+-|++-.+....
T Consensus       169 ~GDd~Q~iKaG~m---Ei-----a--D-I-~VVNKaD~~~a--~~v~~~a~~~l~l~~esvqmlsqmthadearvq~G~~  234 (333)
T TIGR00750       169 TGDDVQGIKAGVM---EI-----A--D-I-YVVNKADGEGA--EEVKTLARLMLALDLESVQMLSQMTHADEARVQKGEI  234 (333)
T ss_pred             CCCHHHHHHHHHH---EE-----E--E-E-EEEECCCCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             7834666654430---23-----2--4-8-78816887665--8999999998888888999998653333444302655


Q ss_pred             CCCEEEECCCC-----HHHHHHHHHHHHHHH
Q ss_conf             98579997999-----899999999999999
Q gi|254780806|r  231 GKPAIIYDLKC-----AGSQAYLKLASELIQ  256 (265)
Q Consensus       231 g~pv~~~~p~s-----~~a~~~~~la~el~~  256 (265)
                      +.=--.|+|.=     ---+-+.+||+.|.+
T Consensus       235 ~~r~~gW~Ppv~~tsA~~G~Gi~EL~daI~e  265 (333)
T TIGR00750       235 YRREKGWRPPVLKTSAVEGRGIDELWDAIEE  265 (333)
T ss_pred             CCHHCCCCCCEEEEECCCCCCCHHHHHHHHH
T ss_conf             1101058996388733568871678999999


No 87 
>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=98.53  E-value=2.8e-07  Score=62.02  Aligned_cols=170  Identities=20%  Similarity=0.251  Sum_probs=88.0

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CC-CCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCC
Q ss_conf             687499998088988889999999999998-79-9599998787768011212463334541167630257712102444
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAA-IG-ENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQT   81 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g-~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~   81 (265)
                      .+++|++++ +==||||||+.+-||..+.. .| +||.+|=+|...- ...-.                   +     ++
T Consensus       174 ~~ggV~alV-GPTGVGKTTTiAKLAAr~~l~~g~~kVaLIT~DTYRI-gAvEQ-------------------L-----kt  227 (404)
T PRK06995        174 ERGGVFALV-GPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRI-GGHEQ-------------------L-----RI  227 (404)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCH-HHHHH-------------------H-----HH
T ss_conf             147558986-6888763758999999999983898379997687547-89999-------------------9-----99


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCC------CHHHHH---HHCCCC
Q ss_conf             44420001488745775000123222210233322476510278203310133322221------011233---100111
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTM------NAMAAA---DSILVP  152 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~------~al~aa---d~viip  152 (265)
                      +.+=          .+........+   .-|..+|.. + .++|+|||||++ .|+.-.      ..|..+   ...++|
T Consensus       228 Ya~I----------lgvPv~vv~~~---~eL~~aL~~-l-~~~dlILIDTaG-rs~rD~~~~e~l~~l~~~~~~~~~~LV  291 (404)
T PRK06995        228 YGKI----------LGVPVHAVKDA---ADLRLALAE-L-RNKHIVLIDTVG-MSQRDRMVSEQIAMLHGAGAPVQRLLL  291 (404)
T ss_pred             HHHH----------CCCEEEEECCH---HHHHHHHHH-H-CCCCEEEEECCC-CCCCCHHHHHHHHHHHHCCCCCEEEEE
T ss_conf             9987----------59559995999---999999997-0-899999980999-897688899999999735788528999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC----CCCCCCCCHHHHH
Q ss_conf             1123113788875335777655432026774310020231253100112689998808520----1562678688987
Q gi|254780806|r  153 LQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV----YNTVIPRNVRISE  226 (265)
Q Consensus       153 ~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v----~~~~Ip~~~~i~~  226 (265)
                      ..+.. ..+.+..+   ++.++     .+.+.++|+|+.|....... +++.+.+. +.++    .++.||+|..+++
T Consensus       292 Lsat~-~~~dl~~i---~~~f~-----~~~~~~~I~TKLDEt~~~G~-iln~~~~~-~lPlsy~T~GQ~VPeDi~~A~  358 (404)
T PRK06995        292 LNATS-HGDTLNEV---VQAYR-----GPGLAGCILTKLDEAASLGG-ALDTVIRH-KLPLHYVSNGQRVPEDLHVAN  358 (404)
T ss_pred             ECCCC-CHHHHHHH---HHHHC-----CCCCCEEEEECCCCCCCHHH-HHHHHHHH-CCCEEEECCCCCCCCCHHCCC
T ss_conf             77989-99999999---99844-----69998399830406797239-99999997-898599818995842121089


No 88 
>PRK13768 GTPase; Provisional
Probab=98.48  E-value=1.2e-06  Score=58.22  Aligned_cols=161  Identities=19%  Similarity=0.278  Sum_probs=79.4

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC-CCCEE
Q ss_conf             99980889888899999999999987995999987877680112124633345411676302577121024444-44200
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA-IPNLS   87 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~-~~~l~   87 (265)
                      +.|+ +--|+||||.+..+...+...|++|.+|-+||.+.   .+.   ++..-.+.|.+    ++.+++.+.. .||=-
T Consensus         5 ~~Vi-GpaGSGKsT~~~~l~~~l~~~~r~~~vvNLDPA~e---~~p---Y~~~iDIRd~i----~~~dVM~~~~LGPNGa   73 (253)
T PRK13768          5 VFFL-GTAGSGKTTLVGALSDWLEEQGYDVAIVNLDPAVE---YLP---YKPDIDVREYV----SAREIMRKYGLGPNGA   73 (253)
T ss_pred             EEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCC---CCC---CCCCCCHHHHC----CHHHHHHHHCCCCCHH
T ss_conf             9998-99999889999999999997699759997898665---899---99886378617----8999998819896468


Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCH--------HHHHHHCCCCCCCCCHH
Q ss_conf             0148874577500012322221023332247651027820331013332222101--------12331001111123113
Q gi|254780806|r   88 IIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNA--------MAAADSILVPLQCEFFA  159 (265)
Q Consensus        88 iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~a--------l~aad~viip~~p~~~s  159 (265)
                      ++      .-++. +   .....++.+.+..   .+-||+|||||+.+...+...        |......+++.--|..-
T Consensus        74 li------~~~e~-l---~~~~d~l~~~i~~---~~~dY~i~D~PGQiElft~~~~~~~i~~~L~~~~~~~~v~l~D~~~  140 (253)
T PRK13768         74 LI------ASVDL-L---LTKAEEIKEEIER---LDADYVLVDTPGQMELFAFRESGRYLVEKLSSGSKSLSVYLIDAVL  140 (253)
T ss_pred             HH------HHHHH-H---HHHHHHHHHHHHH---CCCCEEEEECCCCEEEEECCHHHHHHHHHHHCCCCEEEEEEECHHH
T ss_conf             99------99999-9---9989999999851---5887599826874432223407999999986368628999845056


Q ss_pred             HHHHHHHHH-HHHHHHHHHHCCCCCCCCCCCEEECC
Q ss_conf             788875335-77765543202677431002023125
Q gi|254780806|r  160 LEGLSQLLE-TVEEVRRTVNSALDIQGIILTMFDSR  194 (265)
Q Consensus       160 ~~~~~~~~~-~i~~~~~~~~~~~~~~~iv~N~~~~~  194 (265)
                      ......++. .+-.....+.-.++.. .|+|+.|--
T Consensus       141 ~~~~~~fiS~~L~a~s~m~~l~lP~i-nVlsK~Dll  175 (253)
T PRK13768        141 AKDPSDFVSLLLLALSVQLRLGLPQI-PVLNKIDLL  175 (253)
T ss_pred             HCCHHHHHHHHHHHHHHHHHCCCCEE-EEEEHHHCC
T ss_conf             37887999999999999997399979-986768627


No 89 
>COG1797 CobB Cobyrinic acid a,c-diamide synthase [Coenzyme metabolism]
Probab=98.47  E-value=4.2e-07  Score=60.93  Aligned_cols=171  Identities=18%  Similarity=0.252  Sum_probs=85.6

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCEE
Q ss_conf             99998088988889999999999998799599998787768011212463334541167630257712102444444200
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLS   87 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l~   87 (265)
                      -|.+....-|+||||+|..|..+|.++|++|--.-.-|-          .-|+  +.+....+          ....|||
T Consensus         2 ~vvIAg~~SG~GKTTvT~glm~aL~~rg~~VqpfKvGPD----------YIDP--~~H~~atG----------~~srNLD   59 (451)
T COG1797           2 AVVIAGTSSGSGKTTVTLGLMRALRRRGLKVQPFKVGPD----------YIDP--GYHTAATG----------RPSRNLD   59 (451)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCC----------CCCC--HHHHHHHC----------CCCCCCC
T ss_conf             359954888885899999999999866872166556878----------6381--35667638----------8567776


Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCC--------CCCCCHHHHHH--HCCCCCCCCC
Q ss_conf             0148874577500012322221023332247651027820331013332--------22210112331--0011111231
Q gi|254780806|r   88 IIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFN--------LLTMNAMAAAD--SILVPLQCEF  157 (265)
Q Consensus        88 iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~--------~~~~~al~aad--~viip~~p~~  157 (265)
                      ..            +...    ..++... ..-..+.|+.||----|+=        .-+..-++..-  =||.|+..+-
T Consensus        60 ~~------------mm~~----~~v~~~f-~~~~~~adi~vIEGVMGLfDG~~~~~~~gSTA~lAk~l~~PVvLVid~~~  122 (451)
T COG1797          60 SW------------MMGE----EGVRALF-ARAAADADIAVIEGVMGLFDGRGSATDTGSTADLAKLLGAPVVLVVDASG  122 (451)
T ss_pred             HH------------HCCH----HHHHHHH-HHHCCCCCEEEEEECCCCCCCCCCCCCCCCHHHHHHHHCCCEEEEEECCC
T ss_conf             54------------4699----8999999-98627898799961230236887776777799999985999899995752


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHH-HHHHHCCCCCCCCCCCCHHHH
Q ss_conf             13788875335777655432026774310020231253100112689-998808520156267868898
Q gi|254780806|r  158 FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSD-VRKNLGGKVYNTVIPRNVRIS  225 (265)
Q Consensus       158 ~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~-l~~~~~~~v~~~~Ip~~~~i~  225 (265)
                      .|-. +..++.-+    +.+.++.++.|+|+||+-+  ..|.+.+.+ +.+..+.++++ +||+++.+.
T Consensus       123 ~s~S-~AAiv~G~----~~fdp~v~iaGVIlNrVgs--erH~~llr~Ale~~~gv~vlG-~lpr~~~l~  183 (451)
T COG1797         123 LSRS-VAAIVKGF----KHFDPDVNIAGVILNRVGS--ERHYELLRDALEEYTGVPVLG-YLPRDDDLE  183 (451)
T ss_pred             HHHH-HHHHHHHH----HHCCCCCCEEEEEEECCCC--HHHHHHHHHHHHHCCCCCEEE-EECCCCCCC
T ss_conf             2578-99999889----8619988257899724777--889999998755327985798-742785567


No 90 
>PRK13886 conjugal transfer protein TraL; Provisional
Probab=98.46  E-value=2.6e-07  Score=62.13  Aligned_cols=41  Identities=37%  Similarity=0.545  Sum_probs=37.6

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             74999980889888899999999999987995999987877
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      ++|=-|..+|||||||.+|..||.++...+..+.+||.||-
T Consensus         2 a~IH~vlqgKGGVGKS~va~~LaQY~~~~~~~~~~iDTDpv   42 (241)
T PRK13886          2 AKIHMVLQGKGGVGKSMIAATIAQYKAGKGQKPLCIDTDPV   42 (241)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEECCCC
T ss_conf             75999855888630999999999999835999855608999


No 91 
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=98.46  E-value=1.1e-06  Score=58.41  Aligned_cols=43  Identities=33%  Similarity=0.418  Sum_probs=34.6

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHC----CCCEEEEECCCC
Q ss_conf             76874999980889888899999999999987----995999987877
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAI----GENVLLIDLDPQ   46 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~----g~rVllID~D~q   46 (265)
                      ..+.|||++. +==||||||+.+-||..++..    |++|.+|=+|..
T Consensus       171 ~~k~~vi~lV-GPTGvGKTTTiAKLAa~~~l~~~~k~~~V~lit~Dty  217 (388)
T PRK12723        171 NLKKRIFILV-GPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNY  217 (388)
T ss_pred             CCCCEEEEEE-CCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCC
T ss_conf             5576289998-9988757879999999999862676773799980787


No 92 
>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=98.43  E-value=8e-07  Score=59.33  Aligned_cols=92  Identities=17%  Similarity=0.233  Sum_probs=61.3

Q ss_pred             HCCCCCCEEEECCCCCC--CCCCHHHHHHHCCCCCCCCCHHHH-HHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHH
Q ss_conf             10278203310133322--221011233100111112311378-887533577765543202677431002023125310
Q gi|254780806|r  121 TSDFSYIFLDCPPSFNL--LTMNAMAAADSILVPLQCEFFALE-GLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSL  197 (265)
Q Consensus       121 ~~~yD~IiiD~pp~~~~--~~~~al~aad~viip~~p~~~s~~-~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~  197 (265)
                      |+++.+=|||||+..+.  .+..+|.++|.+++|+.+.. .++ ++.+   .|+..++.   +++.+ +++|+.|....-
T Consensus        68 w~~~kinliDTPG~~DF~~e~~~al~v~D~AviVv~a~~-GVe~~T~~---~w~~a~~~---~iP~i-ifINKmDr~~ad  139 (267)
T cd04169          68 YRDCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAK-GVEPQTRK---LFEVCRLR---GIPII-TFINKLDREGRD  139 (267)
T ss_pred             ECCEEEEEEECCCCHHHHHHHHHHHHHHHCEEEEEECCC-CCCHHHHH---HHHHHHHC---CCCEE-EEEECCCCCCCC
T ss_conf             899899999796977899999999988645479952566-65355899---99999972---99979-998534567898


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             01126899988085201562678
Q gi|254780806|r  198 SQQVVSDVRKNLGGKVYNTVIPR  220 (265)
Q Consensus       198 ~~~~~~~l~~~~~~~v~~~~Ip~  220 (265)
                      ..+.++++++.||..+++-.+|.
T Consensus       140 f~~~l~~i~~~lg~~~vpi~lPi  162 (267)
T cd04169         140 PLELLDEIEEELGIDCTPLTWPI  162 (267)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEEE
T ss_conf             78999999998687751168775


No 93 
>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]
Probab=98.41  E-value=1.5e-06  Score=57.67  Aligned_cols=172  Identities=20%  Similarity=0.302  Sum_probs=85.2

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHH--HCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCC
Q ss_conf             68749999808898888999999999999--8799599998787768011212463334541167630257712102444
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALA--AIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQT   81 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la--~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~   81 (265)
                      ++.|||++. +--||||||+.+-||+.+.  ...+||.+|-+|... +.....+..+             +++-      
T Consensus       201 ~~~~vi~LV-GPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYR-IGA~EQLk~Y-------------a~im------  259 (407)
T COG1419         201 EQKRVIALV-GPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYR-IGAVEQLKTY-------------ADIM------  259 (407)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCH-HHHHHHHHHH-------------HHHH------
T ss_conf             468579998-998875887999999999753257606899714411-5289999999-------------9986------


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCC--CCCCCCCHHH----HH--HHCCCCC
Q ss_conf             44420001488745775000123222210233322476510278203310133--3222210112----33--1001111
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPS--FNLLTMNAMA----AA--DSILVPL  153 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~--~~~~~~~al~----aa--d~viip~  153 (265)
                         |+.+.            ....+   .-|...+.  .-.+||+|+|||.+-  .+.....-|.    ++  ..+.+++
T Consensus       260 ---~vp~~------------vv~~~---~el~~ai~--~l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvl  319 (407)
T COG1419         260 ---GVPLE------------VVYSP---KELAEAIE--ALRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVL  319 (407)
T ss_pred             ---CCCEE------------EECCH---HHHHHHHH--HHHCCCEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEE
T ss_conf             ---99559------------96399---99999999--853188899968998833789999999997035662179998


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHH-HHCCC--CCCCCCCCCHHHHH
Q ss_conf             123113788875335777655432026774310020231253100112689998-80852--01562678688987
Q gi|254780806|r  154 QCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRK-NLGGK--VYNTVIPRNVRISE  226 (265)
Q Consensus       154 ~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~-~~~~~--v~~~~Ip~~~~i~~  226 (265)
                      ... .-.+++.   ..++.++     .+++-++|+|+.|..+....- ++-+.+ .++..  -.++.||+|..+.+
T Consensus       320 sat-~K~~dlk---ei~~~f~-----~~~i~~~I~TKlDET~s~G~~-~s~~~e~~~PV~YvT~GQ~VPeDI~va~  385 (407)
T COG1419         320 SAT-TKYEDLK---EIIKQFS-----LFPIDGLIFTKLDETTSLGNL-FSLMYETRLPVSYVTNGQRVPEDIVVAN  385 (407)
T ss_pred             ECC-CCHHHHH---HHHHHHC-----CCCCCEEEEECCCCCCCHHHH-HHHHHHHCCCEEEEECCCCCCCHHHHCC
T ss_conf             457-6468899---9999724-----588661689713356763389-9999996897499717987870355358


No 94 
>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=98.36  E-value=1.9e-07  Score=62.93  Aligned_cols=62  Identities=18%  Similarity=0.320  Sum_probs=49.4

Q ss_pred             CCCCEEEECCCCCCCCCCHH--HHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEE
Q ss_conf             78203310133322221011--233100111112311378887533577765543202677431002023
Q gi|254780806|r  124 FSYIFLDCPPSFNLLTMNAM--AAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMF  191 (265)
Q Consensus       124 yD~IiiD~pp~~~~~~~~al--~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~  191 (265)
                      .||++||+|||.|+..+..+  ...+.+++|++|+..|+..+.|..+++++.      +.+++|+|.||.
T Consensus         1 LDyLiiD~PPGTgD~~ltl~~~~~~~~~ivVTTP~~ls~~dv~r~i~~~~~~------~i~ilGiVENMs   64 (81)
T pfam10609         1 LDYLIIDMPPGTGDEHLTLAQSLPVDGAVIVTTPQDVALLDVRKAIDMFKKL------NVPILGIVENMS   64 (81)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHHC------CCCEEEEEECCC
T ss_conf             9899994899967899999974885776998098599999999999999984------996189997797


No 95 
>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=98.34  E-value=1e-06  Score=58.71  Aligned_cols=91  Identities=14%  Similarity=0.197  Sum_probs=62.8

Q ss_pred             HCCCCCCEEEECCCCCC--CCCCHHHHHHHCCCCCCCCCHHHH-HHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHH
Q ss_conf             10278203310133322--221011233100111112311378-887533577765543202677431002023125310
Q gi|254780806|r  121 TSDFSYIFLDCPPSFNL--LTMNAMAAADSILVPLQCEFFALE-GLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSL  197 (265)
Q Consensus       121 ~~~yD~IiiD~pp~~~~--~~~~al~aad~viip~~p~~~s~~-~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~  197 (265)
                      |+++.+=|||||+..+.  .+..+|.++|.+++|+.... .++ ++.+   .++..++.   +++.+ +++|+.|....-
T Consensus        61 w~~~~inliDTPG~~DF~~e~~~aL~~~D~AviVv~a~~-GVe~~T~~---~w~~~~~~---~lP~i-~fINKmDre~ad  132 (270)
T cd01886          61 WKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVA-GVEPQTET---VWRQADRY---NVPRI-AFVNKMDRTGAD  132 (270)
T ss_pred             ECCEEEEEEECCCCHHHHHHHHHHHHHHCEEEEEEECCC-CHHHHHHH---HHHHHHHC---CCCEE-EEEECCCCCCCC
T ss_conf             899899998696967889999999877555999984676-44263699---99889984---99989-999887877887


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             0112689998808520156267
Q gi|254780806|r  198 SQQVVSDVRKNLGGKVYNTVIP  219 (265)
Q Consensus       198 ~~~~~~~l~~~~~~~v~~~~Ip  219 (265)
                      ..+.++++++.|+.++.+-.+|
T Consensus       133 ~~~~l~~i~~~lg~~~vp~~~P  154 (270)
T cd01886         133 FFRVVEQIREKLGANPVPLQLP  154 (270)
T ss_pred             CHHHHHHHHHHHCCCEEEEEEE
T ss_conf             1668999999858973889856


No 96 
>PRK12727 flagellar biosynthesis regulator FlhF; Provisional
Probab=98.32  E-value=9e-07  Score=59.03  Aligned_cols=168  Identities=21%  Similarity=0.284  Sum_probs=83.4

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CC-CCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCC
Q ss_conf             687499998088988889999999999998-79-9599998787768011212463334541167630257712102444
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAA-IG-ENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQT   81 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g-~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~   81 (265)
                      +++-|++++ +--||||||+.+-||..++. .| ++|.+|-+|...     .|-...  -.+..          . |   
T Consensus       346 ~~gGv~Alv-GpTGvGKTTT~aKlAa~~~~~~g~~~valit~DtyR-----iga~eQ--L~~y~----------~-i---  403 (557)
T PRK12727        346 ERGGVIALV-GPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQR-----VGGREQ--LHSYG----------R-Q---  403 (557)
T ss_pred             HCCCEEEEE-CCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCC-----HHHHHH--HHHHH----------H-H---
T ss_conf             407647874-377767311799999999997399818999726640-----879999--99999----------9-8---


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCC------CCCHHHHH---HH-CCC
Q ss_conf             444200014887457750001232222102333224765102782033101333222------21011233---10-011
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLL------TMNAMAAA---DS-ILV  151 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~------~~~al~aa---d~-vii  151 (265)
                        =|+-+            ....+.   .-|...|..  -.++|+|||||.+- ++-      ....|...   +. +++
T Consensus       404 --lgvpv------------~~~~~~---~~l~~~l~~--l~~~~lvliDTaG~-~~rd~~~~~~~~~l~~~~~~~~~Lvl  463 (557)
T PRK12727        404 --LGIAV------------HEADSA---ESLLDLLER--LRDYKLVLIDTAGM-GQRDRALAAQLNWLRAARQVTSLLVL  463 (557)
T ss_pred             --HCCEE------------EEECCH---HHHHHHHHH--HCCCCEEEEECCCC-CCCCHHHHHHHHHHHCCCCCCEEEEE
T ss_conf             --39757------------982899---999999998--36999899949998-84699999999987514776359999


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC----CCCCCCCCHHHHH
Q ss_conf             11123113788875335777655432026774310020231253100112689998808520----1562678688987
Q gi|254780806|r  152 PLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV----YNTVIPRNVRISE  226 (265)
Q Consensus       152 p~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v----~~~~Ip~~~~i~~  226 (265)
                      ..+..   .+.+..   .++.++     .+.+-|+|+|+.|....... +++.+.++ +.++    -+..||+|..+.+
T Consensus       464 ~a~~~---~~~l~~---~~~~~~-----~~~~~~~i~TKlDE~~~~G~-~l~~~~~~-~lp~~y~t~GQ~VPeDi~~a~  529 (557)
T PRK12727        464 PANAH---FSDLDE---VVRRFA-----HAKPQGVVLTKLDETGRFGS-ALSVVVDH-QMPITWVTDGQRVPDDLHRAN  529 (557)
T ss_pred             ECCCC---HHHHHH---HHHHHC-----CCCCCEEEEEECCCCCCCCH-HHHHHHHH-CCCEEEECCCCCCCCCHHHCC
T ss_conf             68899---899999---999853-----79987489961436787039-99999996-898289758982852364389


No 97 
>KOG0781 consensus
Probab=98.32  E-value=9.6e-07  Score=58.85  Aligned_cols=156  Identities=21%  Similarity=0.262  Sum_probs=82.3

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC-HHHCCCCCCCCCCEEEEEECCCCHHHCCCCC
Q ss_conf             768749999808898888999999999999879959999878776801-1212463334541167630257712102444
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS-TGLGIELYDRKYSSYDLLIEEKNINQILIQT   81 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~-~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~   81 (265)
                      .++..||+|+ +=-||||||.-+-+|+.|.+.+.||++.-||+..+-. --|.                          +
T Consensus       375 ~krPYvi~fv-GVNGVGKSTNLAKIayWLlqNkfrVlIAACDTFRsGAvEQLr--------------------------t  427 (587)
T KOG0781         375 RKRPYVISFV-GVNGVGKSTNLAKIAYWLLQNKFRVLIAACDTFRSGAVEQLR--------------------------T  427 (587)
T ss_pred             CCCCEEEEEE-EECCCCCCCHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHH--------------------------H
T ss_conf             6897599998-214766513299999999857836999862431244789999--------------------------9


Q ss_pred             CCCCEE-ECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCC--CCCCCCHHHHHHHCCCCCCCCC-
Q ss_conf             444200-014887457750001232222102333224765102782033101333--2222101123310011111231-
Q gi|254780806|r   82 AIPNLS-IIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSF--NLLTMNAMAAADSILVPLQCEF-  157 (265)
Q Consensus        82 ~~~~l~-iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~--~~~~~~al~aad~viip~~p~~-  157 (265)
                      +.++|. +.+....+  |+.-  -..+.....++++...-.+.||+|+|||.+-.  ++-.+.+|   ..++-+..||. 
T Consensus       428 Hv~rl~~l~~~~v~l--fekG--Ygkd~a~vak~AI~~a~~~gfDvvLiDTAGRmhn~~~LM~~L---~kl~~~n~pD~i  500 (587)
T KOG0781         428 HVERLSALHGTMVEL--FEKG--YGKDAAGVAKEAIQEARNQGFDVVLIDTAGRMHNNAPLMTSL---AKLIKVNKPDLI  500 (587)
T ss_pred             HHHHHHHHCCCHHHH--HHHH--CCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHH---HHHHHCCCCCEE
T ss_conf             999998745520488--8610--477828999999999986698789983544334780678999---999744798659


Q ss_pred             -------HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEC
Q ss_conf             -------137888753357776554320267743100202312
Q gi|254780806|r  158 -------FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDS  193 (265)
Q Consensus       158 -------~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~  193 (265)
                             ..-..+.++.++=+.+...-.+. .+-+|+++++|.
T Consensus       501 ~~VgEALVG~dsvdq~~~Fn~al~d~~~~r-~iDgilltK~DT  542 (587)
T KOG0781         501 LFVGEALVGNDSVDQLKKFNRALADHSTPR-LIDGILLTKFDT  542 (587)
T ss_pred             EEEHHHHHCCHHHHHHHHHHHHHHCCCCCC-CCCEEEEEECCH
T ss_conf             985055527558999999999874489744-234378871250


No 98 
>KOG0780 consensus
Probab=98.30  E-value=3.2e-06  Score=55.78  Aligned_cols=43  Identities=30%  Similarity=0.315  Sum_probs=37.2

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             76874999980889888899999999999987995999987877
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      +.++-||-|. +=-|+||||++.-||+++.+.|+++++|=+|..
T Consensus        98 K~kpsVimfV-GLqG~GKTTtc~KlA~y~kkkG~K~~LvcaDTF  140 (483)
T KOG0780          98 KGKPSVIMFV-GLQGSGKTTTCTKLAYYYKKKGYKVALVCADTF  140 (483)
T ss_pred             CCCCCEEEEE-ECCCCCCCEEHHHHHHHHHHCCCCEEEEEECCC
T ss_conf             6897089998-305788630089999999846872457760224


No 99 
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=98.28  E-value=1.9e-06  Score=57.12  Aligned_cols=165  Identities=24%  Similarity=0.302  Sum_probs=87.7

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC
Q ss_conf             76874999980889888899999999999987995999987877680112124633345411676302577121024444
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA   82 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~   82 (265)
                      +++.-||.|. +=-||||||+.+-||+.|.+.|++|++.=+|.......    +                .+..   ...
T Consensus       136 ~~~p~Vil~v-GVNG~GKTTTIaKLA~~l~~~g~~VllaA~DTFRAaAi----E----------------QL~~---w~e  191 (340)
T COG0552         136 EKKPFVILFV-GVNGVGKTTTIAKLAKYLKQQGKSVLLAAGDTFRAAAI----E----------------QLEV---WGE  191 (340)
T ss_pred             CCCCEEEEEE-ECCCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHH----H----------------HHHH---HHH
T ss_conf             8986799999-34888637179999999997898699982334789999----9----------------9999---999


Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCC--CCCCHHHH------------HHH
Q ss_conf             4420001488745775000123222210233322476510278203310133322--22101123------------310
Q gi|254780806|r   83 IPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNL--LTMNAMAA------------ADS  148 (265)
Q Consensus        83 ~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~--~~~~al~a------------ad~  148 (265)
                      .-|+++|...   .        ..+......+++....+.+||++||||.+-+--  -.++-|.-            -++
T Consensus       192 r~gv~vI~~~---~--------G~DpAaVafDAi~~Akar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e  260 (340)
T COG0552         192 RLGVPVISGK---E--------GADPAAVAFDAIQAAKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHE  260 (340)
T ss_pred             HHCCEEECCC---C--------CCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCE
T ss_conf             9599278259---9--------9980899999999999769999999675544573668999999999846456899842


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             01111123113788875335777655432026774310020231253100112689998808520
Q gi|254780806|r  149 ILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV  213 (265)
Q Consensus       149 viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v  213 (265)
                      ++++....    .|    .+.+.+.+ .++....+-|+|+|++|...+-. - +=.+...++.|+
T Consensus       261 ~llvlDAt----tG----qnal~QAk-~F~eav~l~GiIlTKlDgtAKGG-~-il~I~~~l~~PI  314 (340)
T COG0552         261 ILLVLDAT----TG----QNALSQAK-IFNEAVGLDGIILTKLDGTAKGG-I-ILSIAYELGIPI  314 (340)
T ss_pred             EEEEEECC----CC----HHHHHHHH-HHHHHCCCCEEEEEECCCCCCCC-E-EEEHHHHHCCCE
T ss_conf             89997756----47----56899999-99875288669997024677762-4-350888869997


No 100
>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=98.27  E-value=1.5e-06  Score=57.70  Aligned_cols=92  Identities=17%  Similarity=0.179  Sum_probs=63.4

Q ss_pred             CCCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHH
Q ss_conf             027820331013332--222101123310011111231137888753357776554320267743100202312531001
Q gi|254780806|r  122 SDFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQ  199 (265)
Q Consensus       122 ~~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~  199 (265)
                      +++.+=|||||+..+  ..+..+|.++|.+|+|+.+.. .++.  +....++..++.   +++.+ +++|+.|....-..
T Consensus        62 ~~~~inliDTPG~~DF~~e~~~aL~v~D~Av~Vida~~-GVe~--~T~~~w~~~~~~---~iP~i-~fINKmDr~~ad~~  134 (268)
T cd04170          62 KGHKINLIDTPGYADFVGETRAALRAADAALVVVSAQS-GVEV--GTEKLWEFADEA---GIPRI-IFINKMDRERADFD  134 (268)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHCCCCEEEEEECCCC-CHHH--HHHHHHHHHHHC---CCCEE-EEEECCCCCCCCHH
T ss_conf             99799998698975799999998404783999941875-4768--799999999985---99989-99978787899647


Q ss_pred             HHHHHHHHHHCCCCCCCCCCC
Q ss_conf             126899988085201562678
Q gi|254780806|r  200 QVVSDVRKNLGGKVYNTVIPR  220 (265)
Q Consensus       200 ~~~~~l~~~~~~~v~~~~Ip~  220 (265)
                      +.++++++.|+.+++.-.+|-
T Consensus       135 ~~l~~i~~~lg~~~vp~~~Pi  155 (268)
T cd04170         135 KTLAALQEAFGRPVVPLQLPI  155 (268)
T ss_pred             HHHHHHHHHHCCCEEEEEEEE
T ss_conf             799999998689849999665


No 101
>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=98.25  E-value=8e-06  Score=53.49  Aligned_cols=63  Identities=14%  Similarity=0.280  Sum_probs=40.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             1111123113788875335777655432026774310020231253100112689998808520156267
Q gi|254780806|r  150 LVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIP  219 (265)
Q Consensus       150 iip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip  219 (265)
                      |+|+....-++-.   .+-+++.++.   ..+++.|+|+|++++....+++..+.+++..+.++++ +||
T Consensus        72 IlV~~~~LG~INh---tlLt~eal~~---~gi~v~G~i~N~~~~~~~~~~~N~~~I~~~t~vPvLG-~vP  134 (134)
T cd03109          72 ILVTSAGLGSINH---AFLTIEAARI---KGIILNGVLGNVIVEKEGLATLNVETIERLTGIPVLG-IVP  134 (134)
T ss_pred             EEEECCCCCHHHH---HHHHHHHHHH---CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEE-ECC
T ss_conf             9997788785899---9999999998---7992889999467997106787599999974999778-288


No 102
>COG0132 BioD Dethiobiotin synthetase [Coenzyme metabolism]
Probab=98.24  E-value=1.7e-05  Score=51.62  Aligned_cols=194  Identities=20%  Similarity=0.241  Sum_probs=100.9

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECC----CCHHHCCCCC
Q ss_conf             749999808898888999999999999879959999878776801121246333454116763025----7712102444
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEE----KNINQILIQT   81 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~----~~l~~~i~~~   81 (265)
                      .|.|-|...-=|||||..+..|+.+|..+|++|...-- .|......=.  ..|.  -++.-+.+.    ..+....++.
T Consensus         2 ~~~~fVtGTDT~VGKTv~S~aL~~~l~~~g~~~~~~KP-VqsG~~~~~~--~~D~--~~l~~~~~~~~~~~~~~py~f~~   76 (223)
T COG0132           2 MKRFFVTGTDTGVGKTVVSAALAQALKQQGYSVAGYKP-VQTGSEETAE--NSDA--LVLQRLSGLDLSYELINPYRFKE   76 (223)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECC-EEECCCCCCC--CCHH--HHHHHHCCCCCCCCCCCCEECCC
T ss_conf             73699982799964999999999999968970598775-2217877899--7459--99998519986633543353078


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CCCCCHHHHHH-------HCCCCC
Q ss_conf             4442000148874577500012322221023332247651027820331013332-22210112331-------001111
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFN-LLTMNAMAAAD-------SILVPL  153 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~-~~~~~al~aad-------~viip~  153 (265)
                              |.++-++ ++.+  +..-....+...+. .+.+.||+|+|--.+|+- +++.. ...+|       -+|+|+
T Consensus        77 --------P~sPhlA-a~~e--g~~I~~~~l~~~l~-~l~~~~d~vlVEGAGGl~vPl~~~-~~~~D~~~~~~lpvILV~  143 (223)
T COG0132          77 --------PLSPHLA-AELE--GRTIDLEKLSQGLR-QLLKKYDLVLVEGAGGLLVPLTEE-YTFADLAVQLQLPVILVV  143 (223)
T ss_pred             --------CCCCHHH-HHHC--CCCCCHHHHHHHHH-HHHCCCCEEEEECCCCEEEECCCC-CCHHHHHHHCCCCEEEEE
T ss_conf             --------8884777-8764--89356999987888-540546789996787333325786-529999998099999996


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHH
Q ss_conf             12311378887533577765543202677431002023125310011268999880852015626786889
Q gi|254780806|r  154 QCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRI  224 (265)
Q Consensus       154 ~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i  224 (265)
                      ....-++   ...+-+++-++.   ..+++.|+|+|++++......+....+.+..+.+++. .+|+....
T Consensus       144 ~~~LGtI---NHtlLt~eal~~---~gl~l~G~I~n~~~~~~~~~~~~~~~l~~~~~~p~~g-~~p~~~~~  207 (223)
T COG0132         144 GIKLGTI---NHTLLTVEALRA---RGLPLAGWVANGINPELDHYAEINATLLKRIGAPLLG-IIPYLPES  207 (223)
T ss_pred             CCCCCHH---HHHHHHHHHHHH---CCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCC-CCCCCCCC
T ss_conf             6775778---799999999997---7998789997267885557888899999742897434-05577663


No 103
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=98.23  E-value=3.9e-06  Score=55.30  Aligned_cols=90  Identities=20%  Similarity=0.246  Sum_probs=58.4

Q ss_pred             CCCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHH-HHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHH
Q ss_conf             027820331013332--2221011233100111112311378887-5335777655432026774310020231253100
Q gi|254780806|r  122 SDFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLS-QLLETVEEVRRTVNSALDIQGIILTMFDSRNSLS  198 (265)
Q Consensus       122 ~~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~-~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~  198 (265)
                      ++|-+=|||||+..+  .-+..+|.++|.+|+|+...    .|++ +....++..+.+   +++++ +++|+.|......
T Consensus        77 ~~~~iNliDTPGh~DF~~e~~raL~a~D~Av~Vida~----~GVe~qTe~~w~~~~~~---~iP~i-~FINKmDR~~ad~  148 (526)
T PRK00741         77 RDCLINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAA----KGVEPQTRKLMEVCRLR---DTPIF-TFINKLDRDGREP  148 (526)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHHCEEEEEEECC----CCCCHHHHHHHHHHHHC---CCCEE-EEEECCCCCCCCH
T ss_conf             8989999909894677899999998737599999777----55233368999998863---99889-9996567678987


Q ss_pred             HHHHHHHHHHHCCCCCCCCCC
Q ss_conf             112689998808520156267
Q gi|254780806|r  199 QQVVSDVRKNLGGKVYNTVIP  219 (265)
Q Consensus       199 ~~~~~~l~~~~~~~v~~~~Ip  219 (265)
                      .+.++++++.||..+.+-.+|
T Consensus       149 ~~~l~ei~~~lg~~~~p~~~P  169 (526)
T PRK00741        149 LELLDEIEEVLGIACAPITWP  169 (526)
T ss_pred             HHHHHHHHHHHCCCCEEEEEE
T ss_conf             898877888747873688830


No 104
>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=98.20  E-value=2.6e-06  Score=56.32  Aligned_cols=87  Identities=10%  Similarity=0.152  Sum_probs=58.5

Q ss_pred             CCCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHH
Q ss_conf             027820331013332--222101123310011111231137888753357776554320267743100202312531001
Q gi|254780806|r  122 SDFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQ  199 (265)
Q Consensus       122 ~~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~  199 (265)
                      +++.+-|||||+..+  ..+..+|.++|.+++|+.+..---.++.+   .|+..++.   +++.+ +++|+.|....-..
T Consensus        62 ~~~~~n~iDtPG~~dF~~e~~~al~~~D~av~Vv~a~~Gv~~~t~~---~~~~~~~~---~~P~i-ifiNKmDre~adf~  134 (237)
T cd04168          62 EDTKVNLIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRI---LWRLLRKL---NIPTI-IFVNKIDRAGADLE  134 (237)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCHHH---HHHHHHHC---CCCEE-EEEECCCCCCCCHH
T ss_conf             9987999889884656668988976348169999658882234499---99999985---99859-98624457899999


Q ss_pred             HHHHHHHHHHCCCCCC
Q ss_conf             1268999880852015
Q gi|254780806|r  200 QVVSDVRKNLGGKVYN  215 (265)
Q Consensus       200 ~~~~~l~~~~~~~v~~  215 (265)
                      +.++++++.|+..++.
T Consensus       135 ~~l~~i~~~l~~~~~p  150 (237)
T cd04168         135 KVYQEIKEKLSSDIVP  150 (237)
T ss_pred             HHHHHHHHHHCCCEEE
T ss_conf             9999999997897476


No 105
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=98.16  E-value=1.9e-06  Score=57.11  Aligned_cols=41  Identities=34%  Similarity=0.483  Sum_probs=20.4

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHH-CC-CCEEEEECCCC
Q ss_conf             87499998088988889999999999998-79-95999987877
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAA-IG-ENVLLIDLDPQ   46 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g-~rVllID~D~q   46 (265)
                      +.|||+|+ +==||||||+.+=||..++. .| ++|.+|=+|..
T Consensus       193 ~~~vi~lv-GPTGVGKTTTiAKLAa~~~l~~~~~~V~lIT~Dty  235 (282)
T TIGR03499       193 QGGVIALV-GPTGVGKTTTLAKLAARFVLEHGKKKVALITTDTY  235 (282)
T ss_pred             CCCEEEEE-CCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf             67279997-78887578899999999999738996799980777


No 106
>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=98.15  E-value=4.6e-06  Score=54.91  Aligned_cols=166  Identities=24%  Similarity=0.314  Sum_probs=98.2

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCC
Q ss_conf             87687499998088988889999999999998799599998787768011212463334541167630257712102444
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQT   81 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~   81 (265)
                      ++++.-||-|+ +==|+||||+-+=||..|.++||+|++.=+|...-...                    +.|...   .
T Consensus        78 ~~~kp~Vil~V-GVNG~GKTTTIaKLA~~l~~~Gk~V~laAgDTFRAAA~--------------------EQL~~W---a  133 (284)
T TIGR00064        78 EEKKPNVILFV-GVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTFRAAAI--------------------EQLEVW---A  133 (284)
T ss_pred             CCCCCEEEEEE-EEECCCHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHH--------------------HHHHHH---H
T ss_conf             47897799998-44088601028899999987499089982752479999--------------------999998---9


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCH-------H---------HH
Q ss_conf             4442000148874577500012322221023332247651027820331013332222101-------1---------23
Q gi|254780806|r   82 AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNA-------M---------AA  145 (265)
Q Consensus        82 ~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~a-------l---------~a  145 (265)
                      ..-|++||.....          ..+......+++....+.+||++||||.+=+- .-.|-       .         .+
T Consensus       134 ~R~gv~vi~~~~g----------n~DPAaV~fDAi~~Ak~~niDvvliDTAGRLq-nk~NLm~EL~KI~RV~~k~~~~~a  202 (284)
T TIGR00064       134 KRLGVDVIKQKEG----------NADPAAVIFDAIQAAKARNIDVVLIDTAGRLQ-NKVNLMDELKKIKRVIKKVDPVDA  202 (284)
T ss_pred             HHHCCEEEECCCC----------CCCCHHHHHHHHHHHHHCCCCEEEEECCCCCC-CCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             8838755407889----------88717899998999987499789973475454-662039999999998732102578


Q ss_pred             HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             31001111123113788875335777655432026774310020231253100112689998808520
Q gi|254780806|r  146 ADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV  213 (265)
Q Consensus       146 ad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v  213 (265)
                      -|++++|.....        -.+.+.+. +.++....+-|||+|+.|...+=.  +.=.+.+.++.||
T Consensus       203 P~e~lLVlDAt~--------Gqna~~QA-~~F~eav~ltGiiLTKLDg~AKGG--~~l~i~~~l~~Pv  259 (284)
T TIGR00064       203 PDEVLLVLDATT--------GQNALEQA-KVFNEAVGLTGIILTKLDGTAKGG--IILAIAYELKLPV  259 (284)
T ss_pred             CCEEEEEEHHHH--------HHHHHHHH-HHHHHHCCCCEEEEECCCCCCHHH--HHHHHHHHHCCCE
T ss_conf             755754220222--------03089999-998654068858996346880378--9998899857976


No 107
>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=98.14  E-value=1.4e-05  Score=52.06  Aligned_cols=123  Identities=23%  Similarity=0.245  Sum_probs=72.3

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCEE
Q ss_conf             99998088988889999999999998799599998787768011212463334541167630257712102444444200
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLS   87 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l~   87 (265)
                      ||.+. +-.|+||||+.-.|...+.++|+||.+|=.||...-+-.          .+   +.++....+.   ...+++.
T Consensus         1 viGit-G~pGaGKStLi~~l~~~~~~~g~~VaVlavDPsS~~sgG----------al---LGDRiRm~~~---~~~~~vf   63 (148)
T cd03114           1 VIGIT-GVPGAGKSTLIDALITALRARGKRVAVLAIDPSSPFSGG----------AI---LGDRIRMERH---ASDPGVF   63 (148)
T ss_pred             CEEEC-CCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCC----------CC---HHHHHHHHHH---CCCCCEE
T ss_conf             97625-899787899999999999978983799996888786686----------20---3235453441---5799836


Q ss_pred             EC--CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCCH
Q ss_conf             01--488745775000123222210233322476510278203310133322221011233100111112311
Q gi|254780806|r   88 II--PSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFF  158 (265)
Q Consensus        88 ii--pa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~~  158 (265)
                      +-  |+...+.+..          ....+.+...-...||+|||.|-+ .+..-......+|..+++..|..-
T Consensus        64 iRs~atrg~~ggla----------~~~~~~i~~l~~~g~D~IiIETvG-vGQse~~i~~~aD~~i~v~~p~~G  125 (148)
T cd03114          64 IRSLATRGFLGGLS----------RATPEVIRVLDAAGFDVIIVETVG-VGQSEVDIASMADTTVVVMAPGAG  125 (148)
T ss_pred             EEECCCCCCCCCHH----------HHHHHHHHHHHHCCCCEEEEECCC-CCCCHHHHHHHCCEEEEEECCCCC
T ss_conf             86346666542046----------889999999997599989997487-775602655435669999636887


No 108
>KOG1532 consensus
Probab=98.14  E-value=5.6e-06  Score=54.38  Aligned_cols=115  Identities=26%  Similarity=0.389  Sum_probs=64.3

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC-
Q ss_conf             874999980889888899999999999987995999987877-680112124633345411676302577121024444-
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA-   82 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~-   82 (265)
                      +..+|.|. +=.|+||||+.--|-..+...+.+--+|-+||- .++....+++       |.|..    .-.+.+.+-. 
T Consensus        18 ~p~~ilVv-GMAGSGKTTF~QrL~~hl~~~~~ppYviNLDPAv~~vpy~aniD-------IRDtV----kYkEvMkqY~L   85 (366)
T KOG1532          18 RPVIILVV-GMAGSGKTTFMQRLNSHLHAKKTPPYVINLDPAVRNVPYPANID-------IRDTV----KYKEVMKQYQL   85 (366)
T ss_pred             CCCEEEEE-ECCCCCCHHHHHHHHHHHHHCCCCCEEEECCHHHHCCCCCCCCC-------HHHHH----HHHHHHHHHCC
T ss_conf             87079999-44778841399999999862369980886788885488866775-------66543----09999998388


Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCH
Q ss_conf             442000148874577500012322221023332247651027820331013332222101
Q gi|254780806|r   83 IPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNA  142 (265)
Q Consensus        83 ~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~a  142 (265)
                      .||=-|+.+   +    ..+....+.   ..+.+ ....+++||||||||+.+..++.++
T Consensus        86 GPNGgI~Ts---L----NLF~tk~dq---v~~~i-ek~~~~~~~~liDTPGQIE~FtWSA  134 (366)
T KOG1532          86 GPNGGIVTS---L----NLFATKFDQ---VIELI-EKRAEEFDYVLIDTPGQIEAFTWSA  134 (366)
T ss_pred             CCCCCHHHH---H----HHHHHHHHH---HHHHH-HHHHCCCCEEEECCCCCEEEEEECC
T ss_conf             998640335---8----999987899---99999-9742204779974888068998427


No 109
>PRK05632 phosphate acetyltransferase; Reviewed
Probab=98.11  E-value=4.6e-05  Score=49.07  Aligned_cols=164  Identities=21%  Similarity=0.248  Sum_probs=81.1

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCC
Q ss_conf             74999980889888899999999999987995999987877680112124633345411676302577121024444442
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPN   85 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~   85 (265)
                      +|.|=+.+.-+|+|||+++..|..+|.++|.||...=  |-+.....     .....++ +++....+++      +.+ 
T Consensus         1 arsIyIa~te~~sGKTsVaLGL~~aL~r~g~KVGfFK--PI~q~~~~-----~~~D~~i-~Li~~~~~L~------~~~-   65 (702)
T PRK05632          1 SRTIYLAPTGTGVGLTSVSLGLVRALERKGVKVGFFK--PIAQPRPD-----DGPDRST-ELLRARLGLP------YEE-   65 (702)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEC--CCCCCCCC-----CCCCCHH-HHHHHHCCCC------CCC-
T ss_conf             9369996279998799999999999983688479983--35547888-----9976079-9999855989------533-


Q ss_pred             EEECCCCCCCCCCCCCCCCCCCCCHHHHHHHH--HHHHCCCCCCEEEECCCCC----CCCCCHHHHH---HHCCCCCCCC
Q ss_conf             00014887457750001232222102333224--7651027820331013332----2221011233---1001111123
Q gi|254780806|r   86 LSIIPSTMDLLGIEMILGGEKDRLFRLDKALS--VQLTSDFSYIFLDCPPSFN----LLTMNAMAAA---DSILVPLQCE  156 (265)
Q Consensus        86 l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~--~~l~~~yD~IiiD~pp~~~----~~~~~al~aa---d~viip~~p~  156 (265)
                            ...+...+..+.+ ......+.+.+.  ..+..+||+|||.-....+    ....|+-.+.   -.+|+|+.+.
T Consensus        66 ------~i~~s~a~~ll~~-g~~D~LlE~IV~~y~~l~~~~DvVLVEGs~~~~~~~~~~~lNa~IAknLgA~VILV~~~~  138 (702)
T PRK05632         66 ------PLSLSYAEELLAS-GQLDVLLEEIVARYHALAKDCDVVLVEGLVPTRKHPFALSLNAEIAKNLGAEVILVSSGG  138 (702)
T ss_pred             ------CCCHHHHHHHHHC-CCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             ------6078899999868-998999999999999975389989994888788986044335999997699889996389


Q ss_pred             CHHHHHHHHHHHHHHHHHHHH--HCCCCCCCCCCCEEECC
Q ss_conf             113788875335777655432--02677431002023125
Q gi|254780806|r  157 FFALEGLSQLLETVEEVRRTV--NSALDIQGIILTMFDSR  194 (265)
Q Consensus       157 ~~s~~~~~~~~~~i~~~~~~~--~~~~~~~~iv~N~~~~~  194 (265)
                      ..+...+..   .++.....+  ..+.+++|+|+|++++.
T Consensus       139 ~~s~~el~d---~i~ia~~~f~~~k~~~vlGvIiNrv~~~  175 (702)
T PRK05632        139 NDTPEELAE---RIELAARSFGGAKNANILGVIINKVNAD  175 (702)
T ss_pred             CCCHHHHHH---HHHHHHHHHHHCCCCCEEEEEEECCCCH
T ss_conf             999999999---9999999852306997899998479823


No 110
>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=97.98  E-value=1.8e-05  Score=51.42  Aligned_cols=146  Identities=21%  Similarity=0.282  Sum_probs=76.1

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC
Q ss_conf             76874999980889888899999999999987995999987877680112124633345411676302577121024444
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA   82 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~   82 (265)
                      +.++.||=|. +==|+||||++.=||+|+.++|+|+.||=+|...              -+-+|=|..  +...|-+|  
T Consensus       118 Kgk~~ViMfV-GLQGaGKTTtctKLA~YYk~rGfK~~lvCADTFR--------------AGAFdQLkq--NA~kA~iP--  178 (453)
T TIGR01425       118 KGKSSVIMFV-GLQGAGKTTTCTKLAYYYKRRGFKPALVCADTFR--------------AGAFDQLKQ--NATKAKIP--  178 (453)
T ss_pred             CCCCEEEEEE-ECCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCC--------------CCHHHHHHH--HHHHCCCC--
T ss_conf             6882158886-2148871566878777763266432565177542--------------324899987--47644897--


Q ss_pred             CCCEEECCCCCCCCCCC-CCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCC---CCCCCCHHHH-----HHHCCCCC
Q ss_conf             44200014887457750-001232222102333224765102782033101333---2222101123-----31001111
Q gi|254780806|r   83 IPNLSIIPSTMDLLGIE-MILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSF---NLLTMNAMAA-----ADSILVPL  153 (265)
Q Consensus        83 ~~~l~iipa~~~~~~~~-~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~---~~~~~~al~a-----ad~viip~  153 (265)
                      +-|.+        .+.| +..+.+  ...+++       .+++|+|||||.+-=   ..+...-...     =|.+|.|.
T Consensus       179 FYGsy--------~E~DPVkiA~E--Gv~~Fk-------~E~~diIivDTSGRHkQe~~LF~Em~qv~~Ai~Pd~iifVM  241 (453)
T TIGR01425       179 FYGSY--------LESDPVKIASE--GVEKFK-------KEKFDIIIVDTSGRHKQEEELFEEMVQVAEAIKPDSIIFVM  241 (453)
T ss_pred             CCCCC--------CCCCCEEEECC--CHHHHH-------CCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCEEEEE
T ss_conf             12010--------48987078002--011322-------12784799837987322588889987686334998369980


Q ss_pred             CCCC--HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCC
Q ss_conf             1231--13788875335777655432026774310020231253
Q gi|254780806|r  154 QCEF--FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRN  195 (265)
Q Consensus       154 ~p~~--~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~  195 (265)
                      .-+.  .+...+           +.+...-++-.||+|+.|-..
T Consensus       242 DGsIGQAA~~QA-----------kAFK~~~~vGSvIiTKLDGHA  274 (453)
T TIGR01425       242 DGSIGQAAFSQA-----------KAFKDSVEVGSVIITKLDGHA  274 (453)
T ss_pred             CCCHHHHHHHHH-----------HHHHHCCCCEEEEEECCCCCC
T ss_conf             661667889999-----------986300350038875156776


No 111
>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=97.93  E-value=3.3e-05  Score=49.85  Aligned_cols=174  Identities=22%  Similarity=0.305  Sum_probs=82.3

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCE-----EEEEC-CCCC-CCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCC
Q ss_conf             999808898888999999999999879959-----99987-8776-8011212463334541167630257712102444
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENV-----LLIDL-DPQG-NASTGLGIELYDRKYSSYDLLIEEKNINQILIQT   81 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rV-----llID~-D~q~-~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~   81 (265)
                      +.++...-+|||||+|..|=.+|++++++|     .= |. ||.= ++.+.     .. -.++=..+..+..+.++..+.
T Consensus         2 VviAGt~S~vGKT~I~~g~m~~L~~~~~~VQ~fKVGP-DYIDP~fH~~aTG-----r~-sRNLDsF~~~~~~i~~~F~~~   74 (464)
T TIGR00379         2 VVIAGTSSKVGKTTISTGIMKALSRRKLEVQPFKVGP-DYIDPSFHTLATG-----RK-SRNLDSFFMSEAQIKELFIRH   74 (464)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCEEECC-CCCCCCCCCCCCC-----CC-CCCCCHHHHHHHHHHHHHHHH
T ss_conf             7883056875478999999999861863246544258-7437884541147-----86-667685330289999999986


Q ss_pred             C-CC--CEEECCCCCCCCCCC-CCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCCCC
Q ss_conf             4-44--200014887457750-0012322221023332247651027820331013332222101123310011111231
Q gi|254780806|r   82 A-IP--NLSIIPSTMDLLGIE-MILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEF  157 (265)
Q Consensus        82 ~-~~--~l~iipa~~~~~~~~-~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip~~p~~  157 (265)
                      . ..  .+.||-|-..|-+-- ..--.+.....-..++|..      -                       +|+++....
T Consensus        75 ~~~~Gs~~s~IEGv~GLYdg~Py~a~~d~gStA~vAk~L~~------P-----------------------vvLv~n~~~  125 (464)
T TIGR00379        75 SKGAGSDVSIIEGVRGLYDGIPYSAISDKGSTASVAKALDA------P-----------------------VVLVVNAKR  125 (464)
T ss_pred             HCCCCCCEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHCC------C-----------------------EEEEEECCH
T ss_conf             13478965797274134367688776877518899998659------8-----------------------899995640


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHH-CCCCCCCCCCCCHHHH
Q ss_conf             1378887533577765543202677431002023125310011268999880-8520156267868898
Q gi|254780806|r  158 FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNL-GGKVYNTVIPRNVRIS  225 (265)
Q Consensus       158 ~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~-~~~v~~~~Ip~~~~i~  225 (265)
                      ++ +++..++.-.    +.+.++..+.|||+|+|.. .++...+...+.+.. |.+|++ +||+.+.+.
T Consensus       126 L~-~saaAiv~Gy----~~fdp~V~l~GVILN~V~~-~rH~~k~k~A~e~L~Pgi~vlG-~~pR~~~l~  187 (464)
T TIGR00379       126 LS-RSAAAIVLGY----RSFDPDVKLKGVILNRVGS-ERHLEKLKTAVEKLAPGIEVLG-VIPRKEDLK  187 (464)
T ss_pred             HH-HHHHHHHHHH----HHCCCCCEEEEEEEEEECC-HHHHHHHHHHHHHHCCCCEEEE-EEECCCCCC
T ss_conf             33-5786776413----4308983178788731077-4468999999886368945887-773675321


No 112
>COG1341 Predicted GTPase or GTP-binding protein [General function prediction only]
Probab=97.88  E-value=9.7e-05  Score=47.17  Aligned_cols=40  Identities=30%  Similarity=0.412  Sum_probs=32.8

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC-CCC
Q ss_conf             99998088988889999999999998799599998787-768
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP-QGN   48 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~-q~~   48 (265)
                      ++.++ +==++||||+|.-||-.+-++|++|.+||+|+ |.+
T Consensus        75 ~vmvv-G~vDSGKSTLt~~LaN~~l~rG~~v~iiDaDvGQ~e  115 (398)
T COG1341          75 VVMVV-GPVDSGKSTLTTYLANKLLARGRKVAIIDADVGQSE  115 (398)
T ss_pred             EEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCC
T ss_conf             89998-986767889999999887644741899968999766


No 113
>KOG1533 consensus
Probab=97.81  E-value=1.3e-05  Score=52.33  Aligned_cols=105  Identities=25%  Similarity=0.416  Sum_probs=57.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCEEECCCCC
Q ss_conf             88988889999999999998799599998787768011212463334541167630257712102444444200014887
Q gi|254780806|r   14 QKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLSIIPSTM   93 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l~iipa~~   93 (265)
                      +--|+||||-+..+-..|...|++|.+|-+||- |-..     +++...++.+++    ++.+..-+     +.+=|-+ 
T Consensus         9 GPPgSGKsTYc~g~~~fls~~gr~~~vVNLDPa-Nd~~-----~Y~~~v~I~eli----t~edvm~~-----~~LGPNg-   72 (290)
T KOG1533           9 GPPGSGKSTYCNGMSQFLSAIGRPVAVVNLDPA-NDNL-----PYECAVDIRELI----TVEDVMEE-----LGLGPNG-   72 (290)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHCCCEEEEECCCC-CCCC-----CCCCCCCHHHHC----CHHHHHHH-----HCCCCCH-
T ss_conf             699998531132099999974896279956876-5678-----887765199971----39999998-----5879961-


Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCC
Q ss_conf             45775000123222210233322476510278203310133322221
Q gi|254780806|r   94 DLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTM  140 (265)
Q Consensus        94 ~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~  140 (265)
                         +.-..+..-.....||...|..   .++-|++||||+.....+.
T Consensus        73 ---~l~yc~E~l~~~idwl~~~l~~---~~~~Y~lFDcPGQVELft~  113 (290)
T KOG1533          73 ---ALKYCMEYLEANIDWLLEKLKP---LTDHYVLFDCPGQVELFTH  113 (290)
T ss_pred             ---HHHHHHHHHHHHHHHHHHHHHH---CCCCEEEEECCCCEEEEEC
T ss_conf             ---2799999998544999997452---3474899957982798742


No 114
>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=97.74  E-value=3.3e-05  Score=49.90  Aligned_cols=57  Identities=28%  Similarity=0.316  Sum_probs=46.7

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCCEE
Q ss_conf             999980889888899999999999987995999987877-6801121246333454116
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYSSY   65 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~ti~   65 (265)
                      ||=+ .+=-|+||||+|.-|.-.|.++|+++-++|.|.= -+|..-||....++..++.
T Consensus        21 vlWl-TGLSGsGKsTiA~Al~~~L~~~G~~~~~LDGDnvR~gL~~dLGFS~~DR~eNIR   78 (187)
T TIGR00455        21 VLWL-TGLSGSGKSTIANALEKKLEKKGYRVYVLDGDNVRHGLNKDLGFSEEDRKENIR   78 (187)
T ss_pred             EEEE-ECCCCCHHHHHHHHHHHHHHHCCCEEEEECCCEEECCCCCCCCCCHHHHCCCCC
T ss_conf             9851-168856357999999999996697499975863424778888888567056883


No 115
>PRK00007 elongation factor G; Reviewed
Probab=97.63  E-value=0.00029  Score=44.34  Aligned_cols=89  Identities=10%  Similarity=0.159  Sum_probs=55.8

Q ss_pred             CCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHH-HHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHH
Q ss_conf             27820331013332--222101123310011111231137-888753357776554320267743100202312531001
Q gi|254780806|r  123 DFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFAL-EGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQ  199 (265)
Q Consensus       123 ~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~-~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~  199 (265)
                      .|-+=|||||+..+  ..+..+|.++|.+++++..-. .+ .++.++   |+...   ..+++.. +++|+.|.-.....
T Consensus        75 ~~~iNlIDTPGHvDF~~Ev~~aLrv~DgAvlVvDav~-GV~~qT~~v---~r~a~---~~~lp~i-~fINK~Dr~~ad~~  146 (693)
T PRK00007         75 GHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFCAVG-GVEPQSETV---WRQAD---KYKVPRI-VFVNKMDRTGADFL  146 (693)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHCEEEEEEECCC-CCCHHHHHH---HHHHH---HCCCCEE-EEEECCCCCCCCHH
T ss_conf             7389999197975248999999998586899998898-877779999---99998---7598969-99979778999989


Q ss_pred             HHHHHHHHHHCCCCCCCCCC
Q ss_conf             12689998808520156267
Q gi|254780806|r  200 QVVSDVRKNLGGKVYNTVIP  219 (265)
Q Consensus       200 ~~~~~l~~~~~~~v~~~~Ip  219 (265)
                      ..++++++.++..++..-+|
T Consensus       147 ~~l~~i~~~l~~~~~~~~~p  166 (693)
T PRK00007        147 RVVEQIKDRLGANPVPIQLP  166 (693)
T ss_pred             HHHHHHHHHHCCCEEEEEEE
T ss_conf             99999999859976899840


No 116
>PRK07667 uridine kinase; Provisional
Probab=97.37  E-value=0.00036  Score=43.85  Aligned_cols=44  Identities=27%  Similarity=0.375  Sum_probs=35.6

Q ss_pred             CCCCCCE--EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             9876874--99998088988889999999999998799599998787
Q gi|254780806|r    1 MEEKKSR--IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         1 ~~~~~~k--vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      |++++..  +|+| ++-+|+||||+|-.|+..|...|..|.++-.|-
T Consensus         7 ~~~~~~~r~iIgI-aG~sgSGKTTla~~L~~~l~~~~~~v~v~~~Dd   52 (190)
T PRK07667          7 MKKHKENRFILGI-DGLSRSGKTTFVANLKENMKQEGIPFHIFHIDD   52 (190)
T ss_pred             HHHCCCCEEEEEE-ECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             9857598699997-798978899999999999866598379996662


No 117
>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=97.36  E-value=0.0019  Score=39.65  Aligned_cols=170  Identities=19%  Similarity=0.285  Sum_probs=97.2

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCC
Q ss_conf             87499998088988889999999999998799599998787768011212463334541167630257712102444444
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIP   84 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~   84 (265)
                      ++++|.+...-.-+||=|++..|..++.++|.++..+=....|=+-..         +.+        .           
T Consensus       112 ~~~rvl~vGTDcavGK~tTal~l~~~l~~~Gi~a~fiaTGQTGili~g---------~Gv--------~-----------  163 (302)
T pfam07755       112 KAKRVLTVGTDCAVGKMTTALELERALRERGLNAAFVATGQTGILIAG---------YGV--------P-----------  163 (302)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCEEEEEC---------CEE--------E-----------
T ss_conf             987899960573340789999999999977998479972761368815---------247--------8-----------


Q ss_pred             CEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCC-----CCCCCCHHHHH--HHCCCCCCCCC
Q ss_conf             200014887457750001232222102333224765102782033101333-----22221011233--10011111231
Q gi|254780806|r   85 NLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSF-----NLLTMNAMAAA--DSILVPLQCEF  157 (265)
Q Consensus        85 ~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~-----~~~~~~al~aa--d~viip~~p~~  157 (265)
                       +|-+|++.--...|              ... ....++.|+|+|--.+++     +..+...|..|  |.+|+.-.|..
T Consensus       164 -iDav~~DFvaGavE--------------~~v-~~~~~~~d~iiIEGQgSL~hP~y~gvsl~lL~Gs~Pd~lIL~H~p~R  227 (302)
T pfam07755       164 -LDAVPADFVAGAVE--------------ALV-LDAAEEDDWIVIEGQGSLSHPAYSGVTLGLLHGSQPDALVLCHRPGR  227 (302)
T ss_pred             -ECCCHHHHHHHHHH--------------HHH-HHHCCCCCEEEEECCCCCCCCCCCCCCHHHHCCCCCCEEEEECCCCC
T ss_conf             -43224766767899--------------999-86454678799916543236656654598860789986999637898


Q ss_pred             HH--------HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             13--------7888753357776554320267743100202312531001126899988085201562678
Q gi|254780806|r  158 FA--------LEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPR  220 (265)
Q Consensus       158 ~s--------~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~  220 (265)
                      ..        +..+...++.++.+.... ++.++.||-+|-..-.....++..+++.+.++.++... +++
T Consensus       228 ~~~~~~~~~~iP~l~~~i~l~e~~a~~~-~~~kvvgIslNt~~l~~~ea~~~~~~~~~~~glPv~Dp-~r~  296 (302)
T pfam07755       228 KHRRGFPHYPLPPLEEEIELIEALAGTT-PPAKVVGISLNTRGLSEAEAREAIERIEEELGLPVTDP-VRF  296 (302)
T ss_pred             CEECCCCCCCCCCHHHHHHHHHHHHCCC-CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEC-CCC
T ss_conf             6227876688999899999999973647-99739999955787999999999999999989974712-123


No 118
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=97.25  E-value=0.00039  Score=43.65  Aligned_cols=60  Identities=32%  Similarity=0.329  Sum_probs=45.8

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCCC
Q ss_conf             76874999980889888899999999999987995999987877-68011212463334541
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKYS   63 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~t   63 (265)
                      ..++.||=|. +=-|+||||+|.-|+..|..+|++|-++|.|.- -++...||.+..++..+
T Consensus        20 ~~~~~viW~T-GLSGsGKSTiA~ale~~L~~~G~~~y~LDGDnvR~gL~~dLgFs~edR~en   80 (197)
T COG0529          20 GQKGAVIWFT-GLSGSGKSTIANALEEKLFAKGYHVYLLDGDNVRHGLNRDLGFSREDRIEN   80 (197)
T ss_pred             CCCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEECCHHHHHCCCCCCCCCHHHHHHH
T ss_conf             7998599964-688887879999999999975975898557467650057889786789999


No 119
>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=97.14  E-value=0.00095  Score=41.38  Aligned_cols=41  Identities=34%  Similarity=0.384  Sum_probs=36.0

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             749999808898888999999999999879959999878776
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG   47 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~   47 (265)
                      .|+|+|+ +.-|+||||+...|...|..+|+||..|==|..+
T Consensus         1 mkii~iv-G~snSGKTTLi~kli~~l~~~G~~V~~iKH~~H~   41 (159)
T cd03116           1 MKVIGFV-GYSGSGKTTLLEKLIPALSARGLRVAVIKHDHHD   41 (159)
T ss_pred             CEEEEEE-ECCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCC
T ss_conf             9299999-6799999999999999999779859899734767


No 120
>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=97.14  E-value=0.0012  Score=40.79  Aligned_cols=79  Identities=11%  Similarity=0.193  Sum_probs=43.0

Q ss_pred             CCCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHH-H
Q ss_conf             027820331013332--2221011233100111112311378887533577765543202677431002023125310-0
Q gi|254780806|r  122 SDFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSL-S  198 (265)
Q Consensus       122 ~~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~-~  198 (265)
                      +.+.+.|||||+...  ..+..++..+|.+++++.+..--.....+   .++.+.. .+  .++. +++|++|.-... .
T Consensus        65 ~~~~i~~iDtPGh~~f~~~~~~~l~~aD~~vlVvda~~G~~~qt~~---~~~~~~~-~~--~p~i-v~vNKiD~v~~~~~  137 (185)
T pfam00009        65 KKRHINIIDTPGHVDFTKEMIRGAAQADGAILVVDAVEGVMPQTRE---HLLLAKQ-LG--VPII-VFINKMDRVDDAEL  137 (185)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCCCHH---HHHHHHH-HC--CCEE-EEEECCCCCCHHHH
T ss_conf             8936899989987143999999986465642999867685323099---9999998-28--9879-99977327776769


Q ss_pred             HHHHHHHHH
Q ss_conf             112689998
Q gi|254780806|r  199 QQVVSDVRK  207 (265)
Q Consensus       199 ~~~~~~l~~  207 (265)
                      .+..+++.+
T Consensus       138 ~~~~~e~~~  146 (185)
T pfam00009       138 DEVVEEISR  146 (185)
T ss_pred             HHHHHHHHH
T ss_conf             999999999


No 121
>KOG1534 consensus
Probab=97.13  E-value=0.00068  Score=42.22  Aligned_cols=107  Identities=21%  Similarity=0.431  Sum_probs=58.7

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCEEEC
Q ss_conf             99808898888999999999999879959999878776801121246333454116763025771210244444420001
Q gi|254780806|r   10 TIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLSII   89 (265)
Q Consensus        10 ~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l~ii   89 (265)
                      .+.-+-.|+||||.+.++-......|+++-+|-+||-+   -.|+++..   -.+.|++    .++++     -+.+++=
T Consensus         6 ~lV~GpAgSGKSTyC~~~~~h~e~~gRs~~vVNLDPAa---e~f~y~~~---iDiRdlI----svdDV-----mEdl~~G   70 (273)
T KOG1534           6 QLVMGPAGSGKSTYCSSMYEHCETVGRSVHVVNLDPAA---EHFNYPVT---IDIRDLI----SVDDV-----MEDLDLG   70 (273)
T ss_pred             EEEECCCCCCCCHHHHHHHHHHHHHCCEEEEEECCHHH---HHHCCCCC---CCHHHHC----CHHHH-----HHHHCCC
T ss_conf             89874678884307899999998628545886268788---86089620---0288752----18888-----8886349


Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHC-CCCCCEEEECCCCCCCC
Q ss_conf             488745775000123222210233322476510-27820331013332222
Q gi|254780806|r   90 PSTMDLLGIEMILGGEKDRLFRLDKALSVQLTS-DFSYIFLDCPPSFNLLT  139 (265)
Q Consensus        90 pa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~-~yD~IiiD~pp~~~~~~  139 (265)
                      |-+.-+--+|..+.    ...||.    ..+.+ +-||+++|||+.+...|
T Consensus        71 PNGgLv~cmEyl~~----NldwL~----~~~Gd~eddylifDcPGQIELyt  113 (273)
T KOG1534          71 PNGGLVYCMEYLLE----NLDWLE----EEIGDVEDDYLIFDCPGQIELYT  113 (273)
T ss_pred             CCCCCHHHHHHHHH----HHHHHH----HHCCCCCCCEEEEECCCEEEEEE
T ss_conf             98652038999997----788877----54067567779984798167754


No 122
>COG1492 CobQ Cobyric acid synthase [Coenzyme metabolism]
Probab=97.08  E-value=0.0014  Score=40.37  Aligned_cols=203  Identities=17%  Similarity=0.155  Sum_probs=96.0

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCCCC---CEEEEEE-C---CCCHHHCCC
Q ss_conf             999980889888899999999999987995999987877-6801121246333454---1167630-2---577121024
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDRKY---SSYDLLI-E---EKNINQILI   79 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~~~---ti~~~l~-~---~~~l~~~i~   79 (265)
                      .|-|...--.+|||++++.|-..++++|++|.=.-  +| .++..+  +.+....-   .+.+.+. +   ....++.+.
T Consensus         3 ~iMv~GT~S~~GKS~~~aglcRi~~~~G~~V~PFK--~QNMsLNs~--it~~G~EIgraQ~~QA~Aa~i~p~v~mNPvLL   78 (486)
T COG1492           3 AIMVQGTTSDAGKSFLVAGLCRILARRGYRVAPFK--SQNMSLNSA--ITPGGGEIGRAQALQALAAGIEPSVHMNPVLL   78 (486)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCH--HHHCCCCCE--ECCCCCEEEHHHHHHHHHCCCCCCCCCCCEEE
T ss_conf             53787214776546752453488873577547870--654346607--87799687550667898739987434287787


Q ss_pred             CCCC-CCEEECCCCCCCCCCCCCC-CCCCCCCHHHHHHHH---HHHHCCCCCCEEEECCCCCCCCC-----CHHH---HH
Q ss_conf             4444-4200014887457750001-232222102333224---76510278203310133322221-----0112---33
Q gi|254780806|r   80 QTAI-PNLSIIPSTMDLLGIEMIL-GGEKDRLFRLDKALS---VQLTSDFSYIFLDCPPSFNLLTM-----NAMA---AA  146 (265)
Q Consensus        80 ~~~~-~~l~iipa~~~~~~~~~~l-~~~~~~~~~l~~~l~---~~l~~~yD~IiiD~pp~~~~~~~-----~al~---aa  146 (265)
                      +... -+..+|--+.........- ...  ....+...+.   ..+.+.||+|++--.++......     ..+.   .+
T Consensus        79 KP~sd~~sQVIv~G~~~G~~s~~~yy~~--~~~~l~~~v~~s~~~l~~~~d~Vv~EGAGSpaEiNlr~~Di~Nm~~a~~~  156 (486)
T COG1492          79 KPCSDTGSQVIVMGKDIGRKSAVEYYQE--GKGLLWVAVKESLERLDREYDVVVIEGAGSPAEINLRDRDIANMGVAEIA  156 (486)
T ss_pred             EECCCCCEEEEEECCCCCCCCHHHHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHCCCCCCCCCCEEEEHHC
T ss_conf             0358884479994634466571788999--88999999999998754105589996379823227663661100220233


Q ss_pred             HH-CCCCCCCCC----HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             10-011111231----1378887533577765543202677431002023125310011268999880852015626786
Q gi|254780806|r  147 DS-ILVPLQCEF----FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRN  221 (265)
Q Consensus       147 d~-viip~~p~~----~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~  221 (265)
                      |. +|+|..=+.    .|+.|...      .+.....  -.+.|+++|++.-...+-...++.|.+..|.++++ ++|+.
T Consensus       157 dapvILV~DIdRGGvfAsl~GT~~------lL~~~~r--~~VkG~iINkFRGd~~ll~~gik~Le~~tg~~vlG-v~P~~  227 (486)
T COG1492         157 DAPVILVGDIDRGGVFASLYGTLA------LLPESDR--ALVKGFIINKFRGDESLLDPGLKWLEELTGVPVLG-VLPYL  227 (486)
T ss_pred             CCCEEEEEEECCCCEEEEEEEHHE------ECCHHHH--CCEEEEEEEEECCCHHHHHHHHHHHHHHHCCEEEE-ECCCC
T ss_conf             898899995115645417302122------3687676--00147999631798788745999999861974675-65255


Q ss_pred             HHHH
Q ss_conf             8898
Q gi|254780806|r  222 VRIS  225 (265)
Q Consensus       222 ~~i~  225 (265)
                      ....
T Consensus       228 ~~~~  231 (486)
T COG1492         228 KDAL  231 (486)
T ss_pred             CCCC
T ss_conf             5455


No 123
>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=97.08  E-value=0.0013  Score=40.50  Aligned_cols=43  Identities=35%  Similarity=0.433  Sum_probs=36.3

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             749999808898888999999999999879959999878776801
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS   50 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~   50 (265)
                      ..||+=+=+-||+||||+|..+|...+.+|++|.=||.-  |.+|
T Consensus        11 ~G~iTQiYGp~G~GKTn~c~~~a~~a~~~Gk~v~YiDTE--GGLS   53 (223)
T TIGR02237        11 RGIITQIYGPPGSGKTNICLILAVNAARQGKKVVYIDTE--GGLS   53 (223)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECC--CCCH
T ss_conf             035889875899867899999999998618958999628--9832


No 124
>PRK05541 adenylylsulfate kinase; Provisional
Probab=97.07  E-value=0.0015  Score=40.26  Aligned_cols=43  Identities=33%  Similarity=0.304  Sum_probs=36.3

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             76874999980889888899999999999987995999987877
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      +.++-||=+. +=-|+||||+|-.|...|...|.+|.++|.|-.
T Consensus         4 ~~kg~viW~T-GLsGSGKTTiA~~l~~~L~~~g~~~~~LDGD~l   46 (176)
T PRK05541          4 KPNGYVIWIT-GLAGSGKTTIAKALYERLKLKYSNVIYLDGDEL   46 (176)
T ss_pred             CCCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEECCHHH
T ss_conf             8886799978-999998999999999999975997799886899


No 125
>pfam03205 MobB Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
Probab=97.04  E-value=0.0021  Score=39.40  Aligned_cols=41  Identities=32%  Similarity=0.333  Sum_probs=33.3

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEE-EEECCC-CCCC
Q ss_conf             99998088988889999999999998799599-998787-7680
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVL-LIDLDP-QGNA   49 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVl-lID~D~-q~~~   49 (265)
                      ++.|+ +.-++||||++-.|...+.++|+++. ++|+|+ |+..
T Consensus         2 ~v~i~-G~~~sGKttl~~~L~~~~~~~g~~~~~~~~~d~gq~~~   44 (122)
T pfam03205         2 IVLVV-GPKDSGKTTLIRKLLNYLKRRGYRVAVVKHLDHGQGEI   44 (122)
T ss_pred             EEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCC
T ss_conf             79999-48999899999999999998799448999899998776


No 126
>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=97.02  E-value=0.0025  Score=38.96  Aligned_cols=28  Identities=32%  Similarity=0.343  Sum_probs=25.6

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             9888899999999999987995999987
Q gi|254780806|r   16 GGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus        16 GGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      =|||||-++.+||..+-++|++|...=.
T Consensus         7 T~VGKT~~ss~La~~lk~~G~~~g~~Kp   34 (187)
T TIGR00347         7 TGVGKTVVSSALAKKLKKAGYSVGYYKP   34 (187)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEECC
T ss_conf             5861789989999999975985251120


No 127
>PRK12740 elongation factor G; Reviewed
Probab=96.86  E-value=0.00084  Score=41.67  Aligned_cols=91  Identities=12%  Similarity=0.110  Sum_probs=59.0

Q ss_pred             CCCCCCEEEECCCCCC--CCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHH
Q ss_conf             0278203310133322--22101123310011111231137888753357776554320267743100202312531001
Q gi|254780806|r  122 SDFSYIFLDCPPSFNL--LTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQ  199 (265)
Q Consensus       122 ~~yD~IiiD~pp~~~~--~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~  199 (265)
                      ++|-+=|||||+..+.  .+..+|.++|.+++++..-.-=-.++.++   |+..   ...+++.+ +++|++|......+
T Consensus        58 ~~~~iNlIDTPGHvDF~~EV~~aLrv~DgAvlvVDaveGV~~qT~~v---~r~a---~~~~lp~i-lvINKiDr~~a~~~  130 (670)
T PRK12740         58 KGHKINIIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEVQTETV---WRYA---EEYGVPRI-AFVNKLDRAGADFR  130 (670)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHCEEEEEEECCCCCCHHHHHH---HHHH---HHCCCCEE-EEEECCCCCCCCHH
T ss_conf             99899999297975148999999998686899997899973789999---9999---98799969-99979789999989


Q ss_pred             HHHHHHHHHHCCCCCCCCCC
Q ss_conf             12689998808520156267
Q gi|254780806|r  200 QVVSDVRKNLGGKVYNTVIP  219 (265)
Q Consensus       200 ~~~~~l~~~~~~~v~~~~Ip  219 (265)
                      +.++++++.|+..++.-.+|
T Consensus       131 ~~l~~i~~~l~~~~~~~~~P  150 (670)
T PRK12740        131 RVLAQLQEALGAPVVPLQLP  150 (670)
T ss_pred             HHHHHHHHHHCCCCEEEEEE
T ss_conf             99999999848983579855


No 128
>PRK03846 adenylylsulfate kinase; Provisional
Probab=96.84  E-value=0.0022  Score=39.26  Aligned_cols=54  Identities=28%  Similarity=0.342  Sum_probs=41.1

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHCCCC
Q ss_conf             768749999808898888999999999999879959999878776-8011212463
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIEL   57 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~-~~~~~l~~~~   57 (265)
                      ..++.||=+. +--|+||||+|-.|...|...|.++.++|.|-.. .++.-+|++.
T Consensus        21 ~~kg~viWlT-GLSGSGKTTlA~~L~~~L~~~~~~~~~LDGD~lR~~l~~dlgfs~   75 (198)
T PRK03846         21 GHKGVVLWFT-GLSGSGKSTVAGALEEALHELGVHTYLLDGDNVRHGLCSDLGFSD   75 (198)
T ss_pred             CCCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEECHHHHHHHHCCCCCCCH
T ss_conf             8998699987-999998899999999999975997599777999874366789899


No 129
>PRK00652 lpxK tetraacyldisaccharide 4'-kinase; Reviewed
Probab=96.83  E-value=0.0022  Score=39.28  Aligned_cols=40  Identities=33%  Similarity=0.422  Sum_probs=35.3

Q ss_pred             CCEEEEEECC-CCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             8749999808-898888999999999999879959999878
Q gi|254780806|r    5 KSRIITIANQ-KGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         5 ~~kvI~v~s~-KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ...||+|.|- =||+|||-++.-||..|..+|++|.+|-=.
T Consensus        48 ~vpVI~VGNitvGGtGKTP~v~~la~~l~~~g~~~~IlSRG   88 (334)
T PRK00652         48 PVPVISVGNLTVGGNGKTPVVIWLAEQLQARGVKVGVVSRG   88 (334)
T ss_pred             CCCEEEEECEEECCCCHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             99899990888788777999999999999769936787346


No 130
>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=96.82  E-value=0.0025  Score=38.90  Aligned_cols=52  Identities=27%  Similarity=0.299  Sum_probs=38.9

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHCCCC
Q ss_conf             8749999808898888999999999999879959999878776-8011212463
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIEL   57 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~-~~~~~l~~~~   57 (265)
                      ++-||=+. +--|+||||+|-.|...|...|..|.++|.|-.. .+..-+|++.
T Consensus         1 kG~viW~T-GLsGsGKTTlA~~l~~~L~~~~~~~~~LDGD~~R~~l~~dlgys~   53 (157)
T pfam01583         1 RGCTVWFT-GLSGSGKSTIANALERKLFAQGISVYVLDGDNVRHGLNKDLGFSE   53 (157)
T ss_pred             CCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEECCHHHHCCCCCCCCCCH
T ss_conf             98899988-989999999999999999975997799768877501257779898


No 131
>PRK06696 uridine kinase; Validated
Probab=96.80  E-value=0.0031  Score=38.39  Aligned_cols=37  Identities=27%  Similarity=0.336  Sum_probs=32.8

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             99998088988889999999999998799599998787
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +|+| .+-.|+||||+|-.|+..|..+|..|++|-.|-
T Consensus        28 ~VgI-dG~~gSGKTTlA~~La~~L~~~G~~V~~v~~Dd   64 (227)
T PRK06696         28 RVAI-DGITASGKTTFANELAEEIKKRGRPVIRASIDD   64 (227)
T ss_pred             EEEE-ECCCCCCHHHHHHHHHHHHHHCCCCEEEECCCC
T ss_conf             9997-789987879999999999974699489971544


No 132
>PRK13351 elongation factor G; Reviewed
Probab=96.80  E-value=0.001  Score=41.14  Aligned_cols=90  Identities=12%  Similarity=0.188  Sum_probs=58.1

Q ss_pred             CCCCCEEEECCCCCC--CCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             278203310133322--221011233100111112311378887533577765543202677431002023125310011
Q gi|254780806|r  123 DFSYIFLDCPPSFNL--LTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       123 ~yD~IiiD~pp~~~~--~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      .|-+=|||||+..+.  .+..+|.++|.+++++....---..+.++++   ..   ...+++.. +++|++|.....-+.
T Consensus        72 ~~~iNlIDTPGHvDF~~Ev~~aLr~~DgallVVDaveGv~~qT~~v~r---~a---~~~~lp~i-l~iNK~DR~~~d~~~  144 (687)
T PRK13351         72 NHRINLIDTPGHIDFTGEVERSLRVLDGAVVVIDAVTGVQPQTETVWE---QA---DKYKIPRL-IFINKMDRVGADLFD  144 (687)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHCEEEEEEECCCCCCHHHHHHHH---HH---HHCCCCEE-EEEECCCCCCCCHHH
T ss_conf             989999809797430999999999878689999789998688999999---99---98799859-999797789987667


Q ss_pred             HHHHHHHHHCCCCCCCCCC
Q ss_conf             2689998808520156267
Q gi|254780806|r  201 VVSDVRKNLGGKVYNTVIP  219 (265)
Q Consensus       201 ~~~~l~~~~~~~v~~~~Ip  219 (265)
                      .++++++.|+...+...+|
T Consensus       145 ~l~~i~~~l~~~~~~~~~p  163 (687)
T PRK13351        145 VLEDIEEKFGKRPLPLQLP  163 (687)
T ss_pred             HHHHHHHHHCCCEEEEEEC
T ss_conf             7889999848964778600


No 133
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=96.78  E-value=0.0035  Score=38.07  Aligned_cols=100  Identities=20%  Similarity=0.247  Sum_probs=57.7

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCEEE
Q ss_conf             99980889888899999999999987995999987877680112124633345411676302577121024444442000
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLSI   88 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l~i   88 (265)
                      +....+-=|+|||+++..+++...+.|++|+.|-..-  +...++. +-..-++          ++.+.+.   .+.+.+
T Consensus        26 ~~li~G~~GtGKsi~~~~~~~~~l~~g~~~~yis~e~--t~~~~i~-qm~s~g~----------di~~~~~---~G~l~~   89 (230)
T PRK08533         26 IILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSSQL--TTTEFIK-QMMSLGY----------DINKKLI---SGKLLY   89 (230)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEECC--CHHHHHH-HHHHCCC----------CCHHHHH---CCCEEE
T ss_conf             8999868998789999999999987898699999438--9999999-9998699----------8179975---796799


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             1488745775000123222210233322476510278203310
Q gi|254780806|r   89 IPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDC  131 (265)
Q Consensus        89 ipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~  131 (265)
                      +|..+-..       ....+...|.+.+...-..+.|+|+||+
T Consensus        90 i~~~~~~~-------~~~~~~~~L~~ll~~~~~~~~dvIIIDS  125 (230)
T PRK08533         90 IPVYPLLS-------GNSEKRDFLDKLMNTRRFYEKDVVIIDS  125 (230)
T ss_pred             EECCCCCC-------CHHHHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             96134335-------4045789999997326643798999905


No 134
>COG0480 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]
Probab=96.78  E-value=0.002  Score=39.55  Aligned_cols=84  Identities=12%  Similarity=0.167  Sum_probs=53.8

Q ss_pred             CCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             27820331013332--2221011233100111112311378887533577765543202677431002023125310011
Q gi|254780806|r  123 DFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       123 ~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      +|.+-+||||+..+  ..+..+|.++|.+++|+.+..-=-...+.+   |++..+   .+.+.. +++|++|.-...-..
T Consensus        75 ~~~iNlIDTPGHVDFt~EV~rslrvlDgavvVvdaveGV~~QTEtv---~rqa~~---~~vp~i-~fiNKmDR~~a~~~~  147 (697)
T COG0480          75 DYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETV---WRQADK---YGVPRI-LFVNKMDRLGADFYL  147 (697)
T ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHCCEEEEEECCCCEEECHHHH---HHHHHH---CCCCEE-EEEECCCCCCCCHHH
T ss_conf             6589995799735347787998886165099998878830037999---999865---599759-999784335567335


Q ss_pred             HHHHHHHHHCCCC
Q ss_conf             2689998808520
Q gi|254780806|r  201 VVSDVRKNLGGKV  213 (265)
Q Consensus       201 ~~~~l~~~~~~~v  213 (265)
                      ..+++.+.++..+
T Consensus       148 ~~~~l~~~l~~~~  160 (697)
T COG0480         148 VVEQLKERLGANP  160 (697)
T ss_pred             HHHHHHHHHCCCC
T ss_conf             0999999867983


No 135
>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=96.78  E-value=0.0018  Score=39.80  Aligned_cols=39  Identities=36%  Similarity=0.371  Sum_probs=34.0

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             9999808898888999999999999879959999878776
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG   47 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~   47 (265)
                      ||+|+ +.=++||||+...|+-.|..+||||.+|==+|.|
T Consensus         1 v~~i~-G~k~SGKTtL~~~l~~~L~~~Gy~V~~IKH~ghG   39 (165)
T TIGR00176         1 VLQIV-GYKNSGKTTLIERLVKALKARGYRVATIKHDGHG   39 (165)
T ss_pred             CEEEE-EECCCCHHHHHHHHHHHHHCCCCCEEEEEECCCC
T ss_conf             93789-6258867899999999997079950898608988


No 136
>PRK00313 lpxK tetraacyldisaccharide 4'-kinase; Provisional
Probab=96.74  E-value=0.0024  Score=38.98  Aligned_cols=39  Identities=26%  Similarity=0.295  Sum_probs=34.8

Q ss_pred             CEEEEEECC-CCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             749999808-898888999999999999879959999878
Q gi|254780806|r    6 SRIITIANQ-KGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         6 ~kvI~v~s~-KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ..||+|.|- =||+|||-++.-||..|.++|++|.+|-=.
T Consensus        51 vPVI~VGNitvGGTGKTP~v~~La~~L~~~G~~~~IiSRG   90 (332)
T PRK00313         51 VPVIVVGNITVGGTGKTPLILWLIEHCRRRGLRVGVVSRG   90 (332)
T ss_pred             CCEEEECCEEECCCCHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             9899987873588777799999999999779965898646


No 137
>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional
Probab=96.73  E-value=0.0034  Score=38.16  Aligned_cols=40  Identities=35%  Similarity=0.335  Sum_probs=35.3

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             49999808898888999999999999879959999878776
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG   47 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~   47 (265)
                      .||+|+ +.-|+||||+...|-..|..+|+||..|==|..+
T Consensus         3 Pii~iv-G~s~SGKTTLi~kli~~l~~~G~rV~~IKH~~H~   42 (170)
T PRK10751          3 PLLAIA-AWSGTGKTTLLKKLIPALCARGIRPGLIKHTHHD   42 (170)
T ss_pred             CEEEEE-ECCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCC
T ss_conf             779999-4699999999999999999879849999457778


No 138
>PRK00889 adenylylsulfate kinase; Provisional
Probab=96.69  E-value=0.0046  Score=37.38  Aligned_cols=54  Identities=31%  Similarity=0.339  Sum_probs=41.0

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHCCCCC
Q ss_conf             68749999808898888999999999999879959999878776-80112124633
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIELY   58 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~-~~~~~l~~~~~   58 (265)
                      +++-||=+. +--|+||||++-.|...|...|..+.++|.|--. .+..-+|++..
T Consensus         2 ~kg~viWlt-GlsgSGKTTia~~l~~~L~~~~~~~~~LDGD~lR~~l~~~lgfs~~   56 (175)
T PRK00889          2 QRGVTVWFT-GLSGAGKTTISHALAEKLRARGYPVEVLDGDIVRTNLSKGLGFSKE   56 (175)
T ss_pred             CCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEECCHHHHHHHCCCCCCCHH
T ss_conf             988899988-9899999999999999999869967997768888753678898989


No 139
>pfam02606 LpxK Tetraacyldisaccharide-1-P 4'-kinase. This family consists of tetraacyldisaccharide-1-P 4'-kinase also known as Lipid-A 4'-kinase or Lipid A biosynthesis protein LpxK, EC:2.7.1.130. This enzyme catalyses the reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D -glucosaminyl-(beta-D-1,6)-2,3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl beta-phosphate <= ADP + 2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D- glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate. This enzyme is involved in the synthesis of lipid A portion of the bacterial lipopolysaccharide layer (LPS). The family contains a P-loop motif at the N terminus.
Probab=96.65  E-value=0.0031  Score=38.40  Aligned_cols=39  Identities=31%  Similarity=0.382  Sum_probs=34.3

Q ss_pred             CCEEEEEECC-CCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             8749999808-89888899999999999987995999987
Q gi|254780806|r    5 KSRIITIANQ-KGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         5 ~~kvI~v~s~-KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      ...||+|.|- =||+|||-++.-||..|..+|++|.+|-=
T Consensus        34 ~vpVI~VGNit~GGtGKTP~v~~l~~~l~~~g~~~~ilSR   73 (318)
T pfam02606        34 PVPVIVVGNITVGGTGKTPLVIALAELLRARGLRPGVLSR   73 (318)
T ss_pred             CCCEEEECCEEECCCCHHHHHHHHHHHHHHCCCCEEEECC
T ss_conf             9999999898458878589999999999976994478326


No 140
>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=96.63  E-value=0.036  Score=32.15  Aligned_cols=26  Identities=27%  Similarity=0.427  Sum_probs=22.8

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             99998088988889999999999998
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAA   33 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~   33 (265)
                      .+++.-+-||+|||+++..||.+.|.
T Consensus         2 ~v~~l~g~gG~GKS~lal~lAl~vA~   27 (239)
T cd01125           2 YVSALVAPGGTGKSSLLLVLALAMAL   27 (239)
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHHHC
T ss_conf             38999808998889999999999975


No 141
>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
Probab=96.62  E-value=0.0024  Score=39.04  Aligned_cols=79  Identities=14%  Similarity=0.114  Sum_probs=40.2

Q ss_pred             CCCCCCEEEECCCCCCCCCCH---HHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHH
Q ss_conf             027820331013332222101---12331001111123113788875335777655432026774310020231253100
Q gi|254780806|r  122 SDFSYIFLDCPPSFNLLTMNA---MAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLS  198 (265)
Q Consensus       122 ~~yD~IiiD~pp~~~~~~~~a---l~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~  198 (265)
                      +.+.|||+|+|+.- ..+.|.   ...||..|+++....--+....+   +. .+-..++.  +.+-+.+|++|- -...
T Consensus        85 ~~r~~~i~DaPGH~-~y~rNMitgAs~ad~AilliDa~~G~~~QTrr---H~-~i~~llGI--~~iivaVNKMDl-V~y~  156 (613)
T PRK05506         85 PKRKFIVADTPGHE-QYTRNMATGASTADLAIILVDARKGVLTQTRR---HS-FIASLLGI--RHIVLAVNKMDL-VDYD  156 (613)
T ss_pred             CCEEEEEECCCCHH-HHHHHHHHHHHHCCEEEEEEECCCCCHHHHHH---HH-HHHHHCCC--CEEEEEEECCCC-CCCH
T ss_conf             87059994289679-89989998786538799999888795155189---99-99987298--759999852012-4781


Q ss_pred             HHHHHHHHHH
Q ss_conf             1126899988
Q gi|254780806|r  199 QQVVSDVRKN  208 (265)
Q Consensus       199 ~~~~~~l~~~  208 (265)
                      ++..+++.+.
T Consensus       157 ~~~f~~I~~~  166 (613)
T PRK05506        157 QEVFDRIVAD  166 (613)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 142
>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=96.54  E-value=0.0052  Score=37.04  Aligned_cols=31  Identities=32%  Similarity=0.404  Sum_probs=26.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             8898888999999999999879959999878776
Q gi|254780806|r   14 QKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG   47 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~   47 (265)
                      +=-|+||||+|.|+|   .++++.|++|-.|-+=
T Consensus        28 GPaG~GKT~LA~hvA---~~r~RPV~l~~Gd~eL   58 (265)
T TIGR02640        28 GPAGTGKTTLAMHVA---RKRDRPVVLINGDAEL   58 (265)
T ss_pred             CCCCCCHHHHHHHHH---HHCCCCEEEEECCCCC
T ss_conf             788855689999999---7368968998658232


No 143
>PRK07560 elongation factor EF-2; Reviewed
Probab=96.53  E-value=0.0033  Score=38.23  Aligned_cols=63  Identities=13%  Similarity=0.184  Sum_probs=37.3

Q ss_pred             CCCCEEEECCCCCC--CCCCHHHHHHHCCCCCCCCCHHHH-HHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECC
Q ss_conf             78203310133322--221011233100111112311378-887533577765543202677431002023125
Q gi|254780806|r  124 FSYIFLDCPPSFNL--LTMNAMAAADSILVPLQCEFFALE-GLSQLLETVEEVRRTVNSALDIQGIILTMFDSR  194 (265)
Q Consensus       124 yD~IiiD~pp~~~~--~~~~al~aad~viip~~p~~~s~~-~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~  194 (265)
                      |-+=|||||+..+.  .+..+|.++|.+|+++.... ++. ++.+   .|+...+   ..++.. +++|++|.-
T Consensus        87 ~~INlIDTPGh~DF~~Ev~~aLrv~DgAvvVvdav~-GV~~qTe~---v~rqa~~---~~~p~i-lfINKmDR~  152 (730)
T PRK07560         87 YLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDAVE-GVMPQTET---VLRQALE---ERVRPV-LFINKVDRL  152 (730)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHCEEEEEEECCC-CCCCHHHH---HHHHHHH---CCCCEE-EEEECCCCC
T ss_conf             789998196973059999999988587899997898-87731899---9999987---799979-998686623


No 144
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=96.50  E-value=0.0068  Score=36.39  Aligned_cols=38  Identities=34%  Similarity=0.434  Sum_probs=33.7

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             49999808898888999999999999879959999878
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ..|+...+--|+||||++.++|...+..|++|+-||+.
T Consensus        23 G~itei~G~pG~GKTtl~lq~a~~~~~~g~~vlYidtE   60 (224)
T PRK09361         23 GTITQIYGPPGSGKTNICIQLAVEAARQGKKVIYIDTE   60 (224)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECCC
T ss_conf             87999989999859999999999999749909996787


No 145
>PRK01906 tetraacyldisaccharide 4'-kinase; Provisional
Probab=96.48  E-value=0.0045  Score=37.41  Aligned_cols=39  Identities=33%  Similarity=0.428  Sum_probs=34.6

Q ss_pred             CCEEEEEECC-CCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             8749999808-89888899999999999987995999987
Q gi|254780806|r    5 KSRIITIANQ-KGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         5 ~~kvI~v~s~-KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      ...||+|.|- =||+|||-++.-||-.|.++|++|.+|-=
T Consensus        55 ~vPVI~VGNitvGGTGKTP~vi~L~~~L~~~G~k~~IlSR   94 (339)
T PRK01906         55 GVPVVVVGNVTVGGTGKTPTVIALVDALRAAGFTPGVVSR   94 (339)
T ss_pred             CCCEEEECCEEECCCCHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             9999998688768875779999999999976995599854


No 146
>PRK05480 uridine kinase; Provisional
Probab=96.47  E-value=0.0074  Score=36.18  Aligned_cols=41  Identities=39%  Similarity=0.467  Sum_probs=35.0

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             98768749999808898888999999999999879959999878
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      |-.|++=+|+++ +-.|+||||+|-.|+..|.  +..|.+|.+|
T Consensus         1 ~~~k~P~iIgIa-G~SgSGKTT~a~~L~~~l~--~~~v~vi~~D   41 (209)
T PRK05480          1 MMMKQPIIIGIA-GGSGSGKTTVASTIYEELG--DESIAVISQD   41 (209)
T ss_pred             CCCCCCEEEEEE-CCCCCCHHHHHHHHHHHCC--CCCEEEEECC
T ss_conf             998898899998-9997789999999999808--6875999554


No 147
>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated
Probab=96.35  E-value=0.0043  Score=37.52  Aligned_cols=58  Identities=31%  Similarity=0.377  Sum_probs=38.8

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHC-CCCEEEEECCCC-CCCCHHHCCCCCCCC
Q ss_conf             76874999980889888899999999999987-995999987877-680112124633345
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAI-GENVLLIDLDPQ-GNASTGLGIELYDRK   61 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~-g~rVllID~D~q-~~~~~~l~~~~~~~~   61 (265)
                      .+++-+|=+. +=-|+||||+|-.|...|.+. |+.|-++|.|.- .+++.-||.+..++.
T Consensus       389 ~~~G~tiwlT-GLsgsGKsTiA~al~~~L~~~~~~~v~lLDGD~~R~~l~~dLgfs~~dR~  448 (568)
T PRK05537        389 HKQGFTVFFT-GLSGAGKSTIAKALMAKLMEMRGRPVTLLDGDVVRKHLSSELGFSKEDRD  448 (568)
T ss_pred             CCCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHCCCCCCCHHHHH
T ss_conf             4586499984-57888776999999999997189279995468887421557898988999


No 148
>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=96.35  E-value=0.0057  Score=36.83  Aligned_cols=36  Identities=31%  Similarity=0.305  Sum_probs=31.8

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             980889888899999999999987995999987877
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      -..+--|+||||++-.|...|...|.++.++|.|--
T Consensus         3 W~tGLsgsGKTTlA~~l~~~L~~~~~~~~~lDGD~i   38 (149)
T cd02027           3 WLTGLSGSGKSTIARALEEKLFQRGRPVYVLDGDNV   38 (149)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCCEEEECCHHH
T ss_conf             987999999999999999999986997599774889


No 149
>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=96.33  E-value=0.01  Score=35.32  Aligned_cols=37  Identities=30%  Similarity=0.495  Sum_probs=31.6

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECC
Q ss_conf             99998088988889999999999998-79959999878
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLD   44 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~D   44 (265)
                      -+.+..+.=|+||||++.|+|..+|. +|++|+.+=+.
T Consensus        14 ~L~vi~a~~g~GKS~~~~~la~~~a~~~g~~V~~~SlE   51 (242)
T cd00984          14 DLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLE   51 (242)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             18999968999999999999999999779959999333


No 150
>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=96.31  E-value=0.0083  Score=35.88  Aligned_cols=37  Identities=41%  Similarity=0.500  Sum_probs=32.6

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             99998088988889999999999998799599998787
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +|+|+ +=-|+||||+|-.|+..|...|.+|.+|-+|-
T Consensus         1 iIgIa-G~SgSGKTT~a~~L~~~l~~~~~~~~vis~D~   37 (179)
T cd02028           1 VVGIA-GPSGSGKTTFAKKLSNQLRVNGIGPVVISLDD   37 (179)
T ss_pred             CEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             98998-98977899999999999846488539995466


No 151
>PRK12739 elongation factor G; Reviewed
Probab=96.30  E-value=0.0034  Score=38.12  Aligned_cols=90  Identities=11%  Similarity=0.163  Sum_probs=56.0

Q ss_pred             CCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             27820331013332--2221011233100111112311378887533577765543202677431002023125310011
Q gi|254780806|r  123 DFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       123 ~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      .|-+=|||||+..+  ..+..+|.++|.+++++..-.-=-..+..++   ++..   ..+++.. +++|+.|.-......
T Consensus        74 ~~~iNLIDTPGHvDF~~EV~~alrv~DgalvvVDaveGV~~qT~~v~---rqa~---~~~lp~i-l~iNKiDR~~ad~~~  146 (693)
T PRK12739         74 DHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQSETVW---RQAD---KYGVPRI-VFVNKMDRIGADFFR  146 (693)
T ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHHCEEEEEEECCCCCCHHHHHHH---HHHH---HCCCCEE-EEEECCCCCCCCHHH
T ss_conf             98999994969740589999999984879999978988767799999---9999---8698969-999797889999899


Q ss_pred             HHHHHHHHHCCCCCCCCCC
Q ss_conf             2689998808520156267
Q gi|254780806|r  201 VVSDVRKNLGGKVYNTVIP  219 (265)
Q Consensus       201 ~~~~l~~~~~~~v~~~~Ip  219 (265)
                      .++++.+.++.....-.+|
T Consensus       147 ~~~~i~~~l~~~~~~~~~p  165 (693)
T PRK12739        147 VVEQIKDRLGANAVPIQLP  165 (693)
T ss_pred             HHHHHHHHHCCCEEEEECC
T ss_conf             9999999858977999742


No 152
>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=96.28  E-value=0.0096  Score=35.51  Aligned_cols=37  Identities=35%  Similarity=0.453  Sum_probs=32.8

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             9999808898888999999999999879959999878
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      -|+-..+--|+||||++..+|...++.|.+|+-||.-
T Consensus        20 ~it~i~G~pG~GKStl~lq~a~~~~~~g~~v~YidtE   56 (218)
T cd01394          20 TVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTE   56 (218)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             7999989999849999999999986369869999665


No 153
>COG3367 Uncharacterized conserved protein [Function unknown]
Probab=96.23  E-value=0.043  Score=31.70  Aligned_cols=178  Identities=15%  Similarity=0.197  Sum_probs=94.6

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC
Q ss_conf             76874999980889888899999999999987995999987877680112124633345411676302577121024444
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA   82 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~   82 (265)
                      ..+++++.+...---+||-|++..|...+-..|.++..+-.++-+    .|.   .+  .++        .+ +++    
T Consensus       145 k~~a~~V~vvGTd~~vGKrTTa~~L~~~~~e~G~~a~fvaTgqtg----il~---~~--~gv--------vv-dav----  202 (339)
T COG3367         145 KVDAKVVLVVGTDCAVGKRTTALELREAAREEGIKAGFVATGQTG----ILI---AD--DGV--------VV-DAV----  202 (339)
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCEEECCCEE----EEE---EC--CCE--------EE-CCH----
T ss_conf             467768999335632104388999999999709863157607604----688---52--746--------75-303----


Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHC-CCCCCEEEECCCCC----CCCCCHHHH--HHHCCCCCCC
Q ss_conf             4420001488745775000123222210233322476510-27820331013332----222101123--3100111112
Q gi|254780806|r   83 IPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTS-DFSYIFLDCPPSFN----LLTMNAMAA--ADSILVPLQC  155 (265)
Q Consensus        83 ~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~-~yD~IiiD~pp~~~----~~~~~al~a--ad~viip~~p  155 (265)
                        -.|+..+                    ..+.+.-.+++ ++|||+|--..++.    ..+...|..  .|.++++-.|
T Consensus       203 --~~DfaAG--------------------ave~~v~~~~e~~~Dii~VEGQgsl~HP~y~vtl~il~gs~PDavvL~H~P  260 (339)
T COG3367         203 --VMDFAAG--------------------AVESAVYEAEEKNPDIIFVEGQGSLTHPAYGVTLGILHGSAPDAVVLCHDP  260 (339)
T ss_pred             --HHHHHHH--------------------HHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCHHHHCCCCCCEEEEEECC
T ss_conf             --6888988--------------------888888876522898799906534347776521433047789769997469


Q ss_pred             CCHHHHHHHHHHHHHHHHHHH--HHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf             311378887533577765543--2026774310020231253100112689998808520156267868898
Q gi|254780806|r  156 EFFALEGLSQLLETVEEVRRT--VNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRIS  225 (265)
Q Consensus       156 ~~~s~~~~~~~~~~i~~~~~~--~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~~~i~  225 (265)
                      ......+-...+.-++.+...  .-.+.++.++.+|--+-.....++..+++...||.+++++ +.+...+.
T Consensus       261 ~r~~~~g~P~~ip~leevi~l~e~l~~a~Vvgi~lNtr~~dE~~are~~a~l~~efglP~~Dp-~~~~~d~~  331 (339)
T COG3367         261 NRKYRDGFPEPIPPLEEVIALYELLSNAKVVGIALNTRNLDEEEARELCAKLEAEFGLPVTDP-LRFGEDVL  331 (339)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCC-CCCCHHHH
T ss_conf             975236798768988998899987167857999924444686889999999864039742263-00214899


No 154
>PRK00089 era GTP-binding protein Era; Reviewed
Probab=96.21  E-value=0.035  Score=32.22  Aligned_cols=38  Identities=32%  Similarity=0.482  Sum_probs=27.1

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             876874999980889888899999999999987995999987877
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      ++.++=.|++. +|=-|||||+.=.|.      |.++.++--=||
T Consensus         4 ~~~ksG~Vaiv-G~PNvGKSTL~N~l~------~~k~siVS~k~~   41 (296)
T PRK00089          4 EKFKSGFVAIV-GRPNVGKSTLLNALV------GQKISIVSPKPQ   41 (296)
T ss_pred             CCCCEEEEEEE-CCCCCCHHHHHHHHH------CCCEEEECCCCC
T ss_conf             89837999999-899988899999996------896176149599


No 155
>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=96.20  E-value=0.0033  Score=38.19  Aligned_cols=106  Identities=22%  Similarity=0.186  Sum_probs=54.4

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCEE
Q ss_conf             99998088988889999999999998799599998787768011212463334541167630257712102444444200
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLS   87 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l~   87 (265)
                      .|-+. +|||.||||++=+|-      | |+|++|+|.-   |..|               .            +.+|+|
T Consensus        15 ~~lIY-G~~G~GKTS~~K~l~------G-ktL~l~~D~S---SkVL---------------~------------G~~nvd   56 (229)
T TIGR01618        15 RYLIY-GKPGLGKTSTIKYLP------G-KTLVLSLDKS---SKVL---------------A------------GDENVD   56 (229)
T ss_pred             EEEEE-CCCCCCCCCEEEECC------C-CEEEEECCCC---CCCC---------------C------------CCCCCE
T ss_conf             68887-589887230566458------8-7898836786---4434---------------6------------899833


Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCHHHHHHH---HHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHCCCC-CCCCCHHHHHH
Q ss_conf             01488745775000123222210233322---476510278203310133322221011233100111-11231137888
Q gi|254780806|r   88 IIPSTMDLLGIEMILGGEKDRLFRLDKAL---SVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVP-LQCEFFALEGL  163 (265)
Q Consensus        88 iipa~~~~~~~~~~l~~~~~~~~~l~~~l---~~~l~~~yD~IiiD~pp~~~~~~~~al~aad~viip-~~p~~~s~~~~  163 (265)
                      |+-+..+....          ...+.+++   ......+||-|+||-   +|.+....|.--+.-=== ..|+...+.-.
T Consensus        57 iim~~~d~~~~----------~~~~~e~~~~~~~~~~~~Y~niViDN---is~lq~~~L~~~gr~~K~~~~p~~q~Y~~~  123 (229)
T TIGR01618        57 IIMADLDDEKP----------IQEMVEFYKELQNIQAEEYDNIVIDN---ISELQKLWLINLGREAKNGRSPELQHYQKL  123 (229)
T ss_pred             EEEEEECCCCC----------HHHHHHHHHHHHCCHHHCCCEEEEEC---HHHHHHHHHHHCCCCCCCCCCCCCCCHHHH
T ss_conf             89986069984----------78999999997322534576589814---278999999846844245788650003688


Q ss_pred             H
Q ss_conf             7
Q gi|254780806|r  164 S  164 (265)
Q Consensus       164 ~  164 (265)
                      .
T Consensus       124 ~  124 (229)
T TIGR01618       124 D  124 (229)
T ss_pred             H
T ss_conf             8


No 156
>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=96.18  E-value=0.01  Score=35.36  Aligned_cols=36  Identities=28%  Similarity=0.438  Sum_probs=31.4

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECC
Q ss_conf             9998088988889999999999998-79959999878
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLD   44 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~D   44 (265)
                      +.+..+.=|+||||++.|+|..+|. .|++|+.+.+.
T Consensus        21 l~vi~g~pg~GKS~~~~~~a~~~a~~~g~~Vl~~slE   57 (186)
T pfam03796        21 LIIIAARPSMGKTAFALNIARNAALKQDKPVLFFSLE   57 (186)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCC
T ss_conf             7999967999879999999999999709966875475


No 157
>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=96.14  E-value=0.0057  Score=36.81  Aligned_cols=84  Identities=17%  Similarity=0.225  Sum_probs=51.8

Q ss_pred             CCCCCEEEECCCCCC--CCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             278203310133322--221011233100111112311378887533577765543202677431002023125310011
Q gi|254780806|r  123 DFSYIFLDCPPSFNL--LTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       123 ~yD~IiiD~pp~~~~--~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      .|-+-|||||+..+.  .+..++.++|.+++++....- ++  .+..+.++.... .  ++++. +++|+.|..+....+
T Consensus        66 ~~~in~iDtPGh~dF~~~~~~al~~~D~allVVda~~G-v~--~qT~~~~~~a~~-~--~~p~i-vviNKiD~~~ad~~~  138 (179)
T cd01890          66 EYLLNLIDTPGHVDFSYEVSRSLAACEGALLLVDATQG-VE--AQTLANFYLALE-N--NLEII-PVINKIDLPSADPER  138 (179)
T ss_pred             CEEEEEEECCCCCCCHHHHHHHHHHHCEEEEEEECCCC-CC--HHHHHHHHHHHH-C--CCCEE-EEEECCCCCCCCHHH
T ss_conf             14899998998645177898899754427899864778-73--748999999987-6--99889-998655567789999


Q ss_pred             HHHHHHHHHCCCC
Q ss_conf             2689998808520
Q gi|254780806|r  201 VVSDVRKNLGGKV  213 (265)
Q Consensus       201 ~~~~l~~~~~~~v  213 (265)
                      +.+++++.+|...
T Consensus       139 v~~~i~~~~g~~~  151 (179)
T cd01890         139 VKQQIEDVLGLDP  151 (179)
T ss_pred             HHHHHHHHHCCCC
T ss_conf             9999999868897


No 158
>KOG2749 consensus
Probab=96.09  E-value=0.017  Score=34.04  Aligned_cols=45  Identities=24%  Similarity=0.307  Sum_probs=34.2

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC-CCCCC
Q ss_conf             87499998088988889999999999998799599998787-76801
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP-QGNAS   50 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~-q~~~~   50 (265)
                      ++..+.+. +---+||||++--|-.+..++|+|.+.+|+|| |++.+
T Consensus       102 ~GPrv~vV-Gp~d~GKsTl~r~L~nyavk~gr~Plfv~LDvgQ~sit  147 (415)
T KOG2749         102 YGPRVMVV-GPTDVGKSTLCRILLNYAVKQGRRPLFVELDVGQGSIT  147 (415)
T ss_pred             CCCEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCCCCEE
T ss_conf             59779998-98765667899999999987178653897479997244


No 159
>PRK12377 putative replication protein; Provisional
Probab=96.08  E-value=0.012  Score=34.95  Aligned_cols=33  Identities=27%  Similarity=0.465  Sum_probs=29.8

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             980889888899999999999987995999987
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      |..+.=|+|||-+|+.||..+.+.|++|+.+-+
T Consensus       105 If~G~pGtGKTHLA~AIg~~a~~~G~sVlF~t~  137 (248)
T PRK12377        105 VFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTV  137 (248)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEH
T ss_conf             998999987889999999999987996999889


No 160
>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]
Probab=96.05  E-value=0.011  Score=35.10  Aligned_cols=40  Identities=28%  Similarity=0.249  Sum_probs=34.7

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             74999980889888899999999999987995999987877
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      .+|+.|+ +.-++||||+.-.|...|..+|+||.+|=-+..
T Consensus         2 ~~Il~iv-G~k~SGKTTLie~lv~~L~~~G~rVa~iKH~hh   41 (161)
T COG1763           2 MKILGIV-GYKNSGKTTLIEKLVRKLKARGYRVATVKHAHH   41 (161)
T ss_pred             CCEEEEE-ECCCCCHHHHHHHHHHHHHHCCCEEEEEEECCC
T ss_conf             7289999-627997342899999999757937999986587


No 161
>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=96.02  E-value=0.013  Score=34.78  Aligned_cols=38  Identities=24%  Similarity=0.365  Sum_probs=29.3

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             6874999980889888899999999999987995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      .++.|.... + =|=||||.|..+|.-.+-+|+||++|-+
T Consensus         2 ~~G~i~iyt-G-~GKGKTTAAlGlalRA~G~G~rV~ivQF   39 (172)
T pfam02572         2 EKGLLIVYT-G-NGKGKSTAAFGMALRALGHGMRVGVVQF   39 (172)
T ss_pred             CCCEEEEEE-C-CCCCHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             763799995-7-9997188999999998259988999999


No 162
>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=95.95  E-value=0.035  Score=32.24  Aligned_cols=107  Identities=14%  Similarity=0.216  Sum_probs=57.6

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCEEE
Q ss_conf             99980889888899999999999987995999987877680112124633345411676302577121024444442000
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLSI   88 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l~i   88 (265)
                      +..+-+--|+|||-++..++|.+...|++|..+-.  |-..--++ .+-....++          +.+.+.   .+.+.+
T Consensus        30 L~lIEGd~~tGKSvLsqr~~YG~L~~g~~v~yvsT--e~T~refi-~qm~sl~yd----------v~~~~l---~G~l~~   93 (235)
T COG2874          30 LILIEGDNGTGKSVLSQRFAYGFLMNGYRVTYVST--ELTVREFI-KQMESLSYD----------VSDFLL---SGRLLF   93 (235)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEE--CHHHHHHH-HHHHHCCCC----------CHHHHH---CCEEEE
T ss_conf             99998889854889999999988708954899984--03599999-988863887----------168775---062689


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCC
Q ss_conf             148874577500012322221023332247651027820331013332222
Q gi|254780806|r   89 IPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLT  139 (265)
Q Consensus        89 ipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~  139 (265)
                      +|.+....     .++...+...|...+...-.-++|+||||+   +++..
T Consensus        94 ~~~~~~~~-----~~~~~~~~~~L~~l~~~~k~~~~dViIIDS---ls~~~  136 (235)
T COG2874          94 FPVNLEPV-----NWGRRSARKLLDLLLEFIKRWEKDVIIIDS---LSAFA  136 (235)
T ss_pred             EEECCCCC-----CCCHHHHHHHHHHHHHHHHHHCCCEEEEEC---CCHHH
T ss_conf             99324542-----257377899999997557752377899953---43776


No 163
>TIGR01166 cbiO cobalt ABC transporter, ATP-binding protein; InterPro: IPR005876   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This entry represents the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. This superfamily includes two groups, one which catalyses the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drives both the process of uptake and efflux.; GO: 0006824 cobalt ion transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=95.94  E-value=0.046  Score=31.52  Aligned_cols=158  Identities=19%  Similarity=0.214  Sum_probs=87.8

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCC
Q ss_conf             98768749999808898888999999999999-87995999987877680112124633345411676302577121024
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILI   79 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~   79 (265)
                      |+=.++++++.. +.=|+||||+=.||+-.|. +.|  -+++|.-|-.-.-..    ..+.+..+.=+|+++.  ++.+.
T Consensus        13 ~~~~~G~~~aLl-G~NGaGKsTLl~~LnG~LrP~~G--~v~~dG~~l~Ysrkg----L~~~R~~V~~VfQdPD--DQlF~   83 (190)
T TIGR01166        13 FAVERGEVLALL-GANGAGKSTLLLHLNGLLRPQSG--KVLLDGEPLDYSRKG----LLEVRQRVGLVFQDPD--DQLFA   83 (190)
T ss_pred             EEECCCCEEEEE-CCCCCCHHHHHHHHCCCCCCCCC--EEEECCEECCCCCHH----HHHHCCEEEEEEECHH--HHCCC
T ss_conf             022057168987-28998578998874367779755--587678540357244----6752503003762634--42026


Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHH-----HHHCCCCCC
Q ss_conf             444442000148874577500012322221023332247651027820331013332222101123-----310011111
Q gi|254780806|r   80 QTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAA-----ADSILVPLQ  154 (265)
Q Consensus        80 ~~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~a-----ad~viip~~  154 (265)
                      .+..+.+.+=|=+..+.+.|..        .+..++|...-..+|.-=-+-|= |.|.-=+-|++.     .|++|+ =+
T Consensus        84 a~V~~DVaFGPlNLGL~e~Ev~--------~RV~eAL~~vg~~~~~~rp~h~L-S~GekkRvAIAGAvAM~Pd~l~L-DE  153 (190)
T TIGR01166        84 ADVDQDVAFGPLNLGLSEAEVE--------RRVREALTAVGISGLEERPTHLL-SGGEKKRVAIAGAVAMRPDVLLL-DE  153 (190)
T ss_pred             CCCCCCCCCCCCCCCCCHHHHH--------HHHHHHHHHCCHHHHHHCCHHHC-CCCCHHHHHHHHHHHHCCCEEEE-EC
T ss_conf             7622100335456733715767--------87899998606322441224115-58613577777588616634664-27


Q ss_pred             CC-CHHHHHHHHHHHHHHHHHHHH
Q ss_conf             23-113788875335777655432
Q gi|254780806|r  155 CE-FFALEGLSQLLETVEEVRRTV  177 (265)
Q Consensus       155 p~-~~s~~~~~~~~~~i~~~~~~~  177 (265)
                      |+ -.+-.|..+++..|+.+++..
T Consensus       154 PTAGLDp~G~~q~~~~l~~L~~~G  177 (190)
T TIGR01166       154 PTAGLDPAGAEQLLAILRRLRAEG  177 (190)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             888978747999999988787239


No 164
>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=95.90  E-value=0.0067  Score=36.43  Aligned_cols=80  Identities=13%  Similarity=0.171  Sum_probs=47.8

Q ss_pred             CCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             27820331013332--2221011233100111112311378887533577765543202677431002023125310011
Q gi|254780806|r  123 DFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       123 ~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      .+-|-+||||+..+  ..+..++.++|.+|+++....--..++.   ..+....+ .  +++.. +++|++|.......+
T Consensus        64 ~~~~n~IDtPGH~dF~~~~~~~~~~~D~ailVVdA~~Gv~~QT~---~~l~~a~~-~--~~~~i-v~iNK~D~~~a~~~~  136 (194)
T cd01891          64 DTKINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTR---FVLKKALE-L--GLKPI-VVINKIDRPDARPEE  136 (194)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHH---HHHHHHHH-C--CCCEE-EEEECCCCCCCCHHH
T ss_conf             98899998998477777898776434467898653789758999---99999987-2--99749-988564589888999


Q ss_pred             HHHHHHHHH
Q ss_conf             268999880
Q gi|254780806|r  201 VVSDVRKNL  209 (265)
Q Consensus       201 ~~~~l~~~~  209 (265)
                      +.+++++.|
T Consensus       137 v~~ei~~~~  145 (194)
T cd01891         137 VVDEVFDLF  145 (194)
T ss_pred             HHHHHHHHH
T ss_conf             999999999


No 165
>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=95.90  E-value=0.022  Score=33.46  Aligned_cols=39  Identities=36%  Similarity=0.399  Sum_probs=32.0

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECC
Q ss_conf             87499998088988889999999999998-79959999878
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLD   44 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~D   44 (265)
                      .+..+ |..+.=|+||||++.++|..++. .|++|+.+-+.
T Consensus        29 ~GeL~-viaarpg~GKT~f~~~~a~~~~~~~g~~vl~~SlE   68 (271)
T cd01122          29 KGELI-ILTAGTGVGKTTFLREYALDLITQHGVRVGTISLE   68 (271)
T ss_pred             CCCEE-EEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             98089-99968998699999999999999769908999704


No 166
>PRK06526 transposase; Provisional
Probab=95.89  E-value=0.017  Score=33.99  Aligned_cols=32  Identities=31%  Similarity=0.353  Sum_probs=29.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             08898888999999999999879959999878
Q gi|254780806|r   13 NQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus        13 s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      -++-|+|||-+++.||+...++|++|.-+-++
T Consensus       104 ~G~~GtGKThLA~Alg~~A~~~G~~v~f~~~~  135 (254)
T PRK06526        104 LGPPGTGKTHLAIGLGIRACQAGHRVLFATAA  135 (254)
T ss_pred             ECCCCCCHHHHHHHHHHHHHHCCCCEEEEEHH
T ss_conf             89999868999999999999869967998779


No 167
>COG1663 LpxK Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]
Probab=95.89  E-value=0.0093  Score=35.58  Aligned_cols=42  Identities=36%  Similarity=0.445  Sum_probs=36.4

Q ss_pred             CEEEEEECC-CCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             749999808-898888999999999999879959999878776
Q gi|254780806|r    6 SRIITIANQ-KGGVGKTTTAINLSTALAAIGENVLLIDLDPQG   47 (265)
Q Consensus         6 ~kvI~v~s~-KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~   47 (265)
                      .-||+|.|. =||+|||-++.-||..|.++|.++.++-=.--|
T Consensus        47 vPVI~VGNltvGGtGKTP~vi~la~~l~~rG~~~gvvSRGYgg   89 (336)
T COG1663          47 VPVICVGNLTVGGTGKTPVVIWLAEALQARGVRVGVVSRGYGG   89 (336)
T ss_pred             CCEEEECCEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCCCC
T ss_conf             8789985577778996889999999998669736798057688


No 168
>PRK06749 replicative DNA helicase; Provisional
Probab=95.85  E-value=0.027  Score=32.91  Aligned_cols=40  Identities=25%  Similarity=0.380  Sum_probs=33.7

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             87499998088988889999999999998799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      .+..|.+ .++=|+|||+++.|+|...++.|++|++.-+..
T Consensus       185 ~g~Livi-aaRPsmGKTa~alnia~~~a~~g~~v~~fSlEM  224 (428)
T PRK06749        185 EGDFVVL-GARPSMGKTAFALNVGLHAAKSGAAVGLFSLEM  224 (428)
T ss_pred             CCCEEEE-ECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             8868999-627989768999999999996499279983789


No 169
>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=95.82  E-value=0.018  Score=33.93  Aligned_cols=35  Identities=40%  Similarity=0.472  Sum_probs=28.4

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             99998088988889999999999998799599998787
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +|+++ +-.|+||||+|-.|+..|  .+.+|.+|.+|.
T Consensus         1 iIgI~-G~sgsGKTT~a~~L~~~l--~~~~v~~i~~D~   35 (198)
T cd02023           1 IIGIA-GGSGSGKTTVAEEIIEQL--GNPKVVIISQDS   35 (198)
T ss_pred             CEEEE-CCCCCCHHHHHHHHHHHH--CCCCEEEEECCC
T ss_conf             98988-999885999999999980--999858997888


No 170
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=95.82  E-value=0.018  Score=33.88  Aligned_cols=37  Identities=32%  Similarity=0.420  Sum_probs=31.3

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             74999980889888899999999999987995999987
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      .+=+.+ .++-|||||-+++-+|..+.+.|.+|+.+-.
T Consensus       105 ~~nl~l-~G~~G~GKthLa~Ai~~~l~~~g~sv~f~~~  141 (254)
T COG1484         105 GENLVL-LGPPGVGKTHLAIAIGNELLKAGISVLFITA  141 (254)
T ss_pred             CCCEEE-ECCCCCCHHHHHHHHHHHHHHCCCEEEEEEH
T ss_conf             882899-8999987999999999999983984999885


No 171
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=95.81  E-value=0.02  Score=33.62  Aligned_cols=38  Identities=21%  Similarity=0.318  Sum_probs=29.1

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHC-CCCEEEEECC
Q ss_conf             74999980889888899999999999987-9959999878
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAI-GENVLLIDLD   44 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~-g~rVllID~D   44 (265)
                      .+++ ..++-=|+||||++.++.+.-++. |.+++-|=++
T Consensus        24 g~~~-LV~G~pGsGKTtla~QfL~~Ga~~~GE~~lyitl~   62 (501)
T PRK09302         24 GRPT-LVSGTAGTGKTLFALQFLHNGIKSFGEPGVFVTFE   62 (501)
T ss_pred             CCEE-EEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             9779-99838999999999999999988559978999857


No 172
>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=95.77  E-value=0.019  Score=33.75  Aligned_cols=35  Identities=37%  Similarity=0.392  Sum_probs=31.3

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             99808898888999999999999879959999878
Q gi|254780806|r   10 TIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus        10 ~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      +...+-=|+||||++.++++..++.|.+|+-|-++
T Consensus         2 tLi~G~pGsGKT~~a~qfl~~~a~~ge~~lyis~e   36 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLE   36 (187)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf             15876899999999999999998769978999950


No 173
>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=95.73  E-value=0.0061  Score=36.64  Aligned_cols=126  Identities=12%  Similarity=0.112  Sum_probs=81.6

Q ss_pred             CCCCEEEECCC--CCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHH
Q ss_conf             78203310133--3222210112331001111123113788875335777655432026774310020231253100112
Q gi|254780806|r  124 FSYIFLDCPPS--FNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQV  201 (265)
Q Consensus       124 yD~IiiD~pp~--~~~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~  201 (265)
                      +.+=|||||+.  +|=...-+|-+.|.+++.+.+..=-+-.+.    ++  +++.+...|+++ +|+|++|....-..++
T Consensus        70 ~~INIvDTPGHADFGGEVERvL~MVDGvlLlVDA~EGPMPQTr----FV--L~KAL~~gLkPI-VViNKiDrp~ARP~eV  142 (609)
T TIGR01394        70 TKINIVDTPGHADFGGEVERVLGMVDGVLLLVDASEGPMPQTR----FV--LKKALELGLKPI-VVINKIDRPSARPDEV  142 (609)
T ss_pred             EEEEEEECCCCCCCCCEEEEECEEEEEEEEEEECCCCCCCCCH----HH--HHHHHHCCCCEE-EEECCCCCCCCCHHHH
T ss_conf             8997781689887886588733024058999857888988534----78--999995689369-9971347887883788


Q ss_pred             HHHHHHHHCCCCCCCC--CCCCHHHHHHHHCCCCEEEECC--CCHHHHHHHHHHHHHHHHH
Q ss_conf             6899988085201562--6786889877737985799979--9989999999999999999
Q gi|254780806|r  202 VSDVRKNLGGKVYNTV--IPRNVRISEAPSYGKPAIIYDL--KCAGSQAYLKLASELIQQE  258 (265)
Q Consensus       202 ~~~l~~~~~~~v~~~~--Ip~~~~i~~a~~~g~pv~~~~p--~s~~a~~~~~la~el~~~~  258 (265)
                      .++.-+.|-. + ++-  ==.=+.+..|...|..-..+..  ...-++++..|.+-|++..
T Consensus       143 ~d~vFDLF~~-L-gA~deQLDFP~vYASa~~G~A~l~~~~dg~~~~~~~m~PLFd~I~~hv  201 (609)
T TIGR01394       143 VDEVFDLFIE-L-GADDEQLDFPIVYASARAGWASLDKDKDGLDDDSEDMAPLFDAILRHV  201 (609)
T ss_pred             HHHHHHHHHH-C-CCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf             7578788885-3-888001012567665236720144665778872201789998986406


No 174
>cd00561 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 (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer,  which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.
Probab=95.67  E-value=0.021  Score=33.58  Aligned_cols=37  Identities=30%  Similarity=0.345  Sum_probs=29.0

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             874999980889888899999999999987995999987
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      ++.|...  .=-|=||||.|..+|.-.+-+|+||+++-+
T Consensus         2 ~Gli~vy--tG~GKGKTTAAlG~alRA~G~G~rV~ivQF   38 (159)
T cd00561           2 KGLIQVY--TGNGKGKTTAALGLALRALGHGYRVGVVQF   38 (159)
T ss_pred             CCEEEEE--ECCCCCHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             8479999--579997089999999998449998999998


No 175
>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=95.67  E-value=0.028  Score=32.84  Aligned_cols=40  Identities=33%  Similarity=0.540  Sum_probs=32.4

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCC
Q ss_conf             8749999808898888999999999999-8799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~   45 (265)
                      ++..| |..++=|+|||+++.|+|...| +.|++|+.+-+..
T Consensus       193 ~g~Li-IiaARPsmGKTafalnia~n~A~~~g~~Vl~fSLEM  233 (421)
T TIGR03600       193 KGDLI-VIGARPSMGKTTLALNIAENVALREGKPVLFFSLEM  233 (421)
T ss_pred             CCCEE-EEEEECCCCHHHHHHHHHHHHHHHCCCEEEEEECCC
T ss_conf             88689-998546787459999999999986698389992579


No 176
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.    Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=95.59  E-value=0.013  Score=34.65  Aligned_cols=35  Identities=34%  Similarity=0.388  Sum_probs=28.5

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHC-CCCEEEEE
Q ss_conf             4999980889888899999999999987-99599998
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAI-GENVLLID   42 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~-g~rVllID   42 (265)
                      +-+|++ .==||||||+-.-+|..||.. |+|+++|=
T Consensus       100 ~SFai~-APTGVGKttFG~~mslflA~kKGkR~y~il  135 (1843)
T TIGR01054       100 DSFAIV-APTGVGKTTFGLVMSLFLAKKKGKRSYIIL  135 (1843)
T ss_pred             CCEEEE-CCCCCCHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             964898-058876779999999998654298789994


No 177
>PRK08181 transposase; Validated
Probab=95.58  E-value=0.025  Score=33.06  Aligned_cols=32  Identities=28%  Similarity=0.236  Sum_probs=29.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             08898888999999999999879959999878
Q gi|254780806|r   13 NQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus        13 s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      -+.-|+|||-+++.||....++|++|.-+.++
T Consensus       112 ~Gp~GtGKThLA~Alg~~A~~~G~~V~f~~~~  143 (269)
T PRK08181        112 FGPPGGGKSHLAAAIGLALIENGWRVLFTRTT  143 (269)
T ss_pred             ECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHH
T ss_conf             89999878899999999999879939997899


No 178
>PRK06547 hypothetical protein; Provisional
Probab=95.57  E-value=0.022  Score=33.41  Aligned_cols=37  Identities=32%  Similarity=0.410  Sum_probs=26.8

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             768749999808898888999999999999879959999878
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ...+++|+|= +.+|+||||+|..|+..+.  +  +-+|-+|
T Consensus        12 ~g~~~iVaID-G~sGaGKTTLA~~La~~~~--~--~~vvHmD   48 (184)
T PRK06547         12 GGDMITVLID-GRSGSGKTTLAGELAACWE--G--SQLVHLD   48 (184)
T ss_pred             CCCEEEEEEE-CCCCCCHHHHHHHHHHHCC--C--CCEEEEC
T ss_conf             9976999986-8998888999999997457--9--8289705


No 179
>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=95.57  E-value=0.012  Score=35.04  Aligned_cols=36  Identities=33%  Similarity=0.373  Sum_probs=30.7

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             9999808898888999999999999879959999878
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      +|+|+ +-.|+||||+|-.|+..|...|.++..+++|
T Consensus         1 iIgIa-G~SgSGKTT~a~~L~~~l~~~~~~~~~~~~d   36 (196)
T pfam00485         1 IIGVA-GSSGAGKTTVARTFVSIFGREGVPAAGIEGD   36 (196)
T ss_pred             CEEEE-CCCCCCHHHHHHHHHHHHCCCCCCCCCCCCE
T ss_conf             98998-9985719999999999966058776412431


No 180
>PRK09183 transposase/IS protein; Provisional
Probab=95.54  E-value=0.026  Score=32.97  Aligned_cols=31  Identities=32%  Similarity=0.310  Sum_probs=29.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             0889888899999999999987995999987
Q gi|254780806|r   13 NQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus        13 s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      -+.-|||||-+|+.||....++|++|+-+.+
T Consensus       107 ~G~~GtGKThLA~Alg~~A~~~G~~v~f~~~  137 (258)
T PRK09183        107 LGPSGVGKTHLAIALGYEAVRAGIKVRFTTA  137 (258)
T ss_pred             ECCCCCCHHHHHHHHHHHHHHCCCEEEEEEH
T ss_conf             8999986899999999999987993999789


No 181
>PRK05595 replicative DNA helicase; Provisional
Probab=95.53  E-value=0.038  Score=32.04  Aligned_cols=40  Identities=33%  Similarity=0.490  Sum_probs=32.8

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCC
Q ss_conf             8749999808898888999999999999-8799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~   45 (265)
                      .+..|.+ .++=|+|||+++.|+|...| +.|++|+..-+..
T Consensus       200 ~GdLiii-aaRP~mGKTa~alnia~~~a~~~g~~V~~fSlEM  240 (444)
T PRK05595        200 KGDMILI-AARPSMGKTTFALNIAEYAALREGKSVVIFSLEM  240 (444)
T ss_pred             CCCEEEE-EECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             5777999-8579898079999999999986699379995889


No 182
>PRK07952 DNA replication protein DnaC; Validated
Probab=95.52  E-value=0.025  Score=33.07  Aligned_cols=33  Identities=33%  Similarity=0.477  Sum_probs=29.6

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             980889888899999999999987995999987
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      +.++.=|+|||.+|+-+|..|..+|+.|+.+-.
T Consensus       100 lF~G~~GTGKThLA~aIan~Li~~G~sVlf~t~  132 (242)
T PRK07952        100 IFSGKPGTGKNHLAAAICNELLLRGKSVLIITV  132 (242)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEH
T ss_conf             997899997899999999999987994999779


No 183
>COG1159 Era GTPase [General function prediction only]
Probab=95.51  E-value=0.092  Score=29.78  Aligned_cols=40  Identities=28%  Similarity=0.409  Sum_probs=29.5

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             98768749999808898888999999999999879959999878776
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG   47 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~   47 (265)
                      |+..++=-+++. ++=-|||||+.=+|      .|.++.++--=||.
T Consensus         1 ~~~~ksGfVaIi-GrPNvGKSTLlN~l------~G~KisIvS~k~QT   40 (298)
T COG1159           1 PMKFKSGFVAII-GRPNVGKSTLLNAL------VGQKISIVSPKPQT   40 (298)
T ss_pred             CCCCEEEEEEEE-CCCCCCHHHHHHHH------HCCCEEEECCCCCH
T ss_conf             997368999998-69987689999898------56825751598531


No 184
>PRK05748 replicative DNA helicase; Provisional
Probab=95.48  E-value=0.04  Score=31.88  Aligned_cols=40  Identities=28%  Similarity=0.468  Sum_probs=32.8

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCC
Q ss_conf             8749999808898888999999999999-8799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~   45 (265)
                      ++..|.+ .++=|+|||+++.|+|...| +.|++|+.+-+..
T Consensus       202 ~g~Livi-aaRP~mGKTa~alnia~~~a~~~~~~v~~fSlEM  242 (448)
T PRK05748        202 PNDLIIV-AARPSVGKTAFALNIAQNVATKTDKNVAIFSLEM  242 (448)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHHCCCEEEEEECCC
T ss_conf             6737999-8479987689999999999985698089981778


No 185
>PRK08506 replicative DNA helicase; Provisional
Probab=95.46  E-value=0.042  Score=31.76  Aligned_cols=40  Identities=28%  Similarity=0.416  Sum_probs=33.4

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             87499998088988889999999999998799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      ++..| |..++=|+|||+++.|+|...+..|+.|++.-+..
T Consensus       192 ~gdLi-IIAARPsmGKTAfAlniA~~~a~~~~~V~~FSLEM  231 (473)
T PRK08506        192 KGDLI-IIAARPSMGKTTLVLNMVLKALNQGKGVAFFSLEM  231 (473)
T ss_pred             CCCEE-EEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             56279-99507998678999999999996599658982247


No 186
>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=95.46  E-value=0.03  Score=32.60  Aligned_cols=35  Identities=31%  Similarity=0.514  Sum_probs=30.6

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             98088988889999999999998799599998787
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      ...+--|+||||++.++|...+..|.+|+.+|..-
T Consensus         3 li~g~~g~GKttl~~~~~~~~~~~~~~~~~~~~ee   37 (165)
T cd01120           3 LVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEE   37 (165)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCC
T ss_conf             99989999899999999999876399799998666


No 187
>PRK07004 replicative DNA helicase; Provisional
Probab=95.43  E-value=0.036  Score=32.16  Aligned_cols=40  Identities=20%  Similarity=0.375  Sum_probs=32.9

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCC
Q ss_conf             8749999808898888999999999999-8799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~   45 (265)
                      .+..|.+ .++=|+|||+++.|+|...| +.|++|+++-+..
T Consensus       212 ~gdLiII-AARPsmGKTafAlniA~n~A~~~g~~V~~FSLEM  252 (460)
T PRK07004        212 GGELIIV-AGRPSMGKTAFSMNIGEYVAVEYGLPVAVFSMEM  252 (460)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCC
T ss_conf             7757999-7368764269999999999872588669984779


No 188
>TIGR01393 lepA GTP-binding protein LepA; InterPro: IPR006297   LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function of the proteins in this family are unknown. ; GO: 0005525 GTP binding.
Probab=95.37  E-value=0.014  Score=34.53  Aligned_cols=85  Identities=15%  Similarity=0.324  Sum_probs=59.5

Q ss_pred             CCCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHH
Q ss_conf             027820331013332--222101123310011111231137888753357776554320267743100202312531001
Q gi|254780806|r  122 SDFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQ  199 (265)
Q Consensus       122 ~~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~  199 (265)
                      +.|-+=|||||+..+  -...-+|+||..+|+++.++    +|++.  +++.++=-.++.+|+++- |+|+.|=.+..-.
T Consensus        69 e~Y~LNLIDTPGHVDFsYEVSRSLAACEGALL~VDA~----QGvEA--QT~aN~YlAlE~dLeIIP-ViNKIDLP~Adpe  141 (598)
T TIGR01393        69 ETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAA----QGVEA--QTLANVYLALENDLEIIP-VINKIDLPSADPE  141 (598)
T ss_pred             CEEEEEEECCCCCCCCCHHHHHHHHHHCCEEEEEECC----CCHHH--HHHHHHHHHHHCCCEEEE-EECCCCCCCCCHH
T ss_conf             7889964528897212737888888716403561410----32358--889999887561875847-7825368888858


Q ss_pred             HHHHHHHHHHCCCC
Q ss_conf             12689998808520
Q gi|254780806|r  200 QVVSDVRKNLGGKV  213 (265)
Q Consensus       200 ~~~~~l~~~~~~~v  213 (265)
                      ++.+++++.+|..-
T Consensus       142 ~v~~eIe~~iGld~  155 (598)
T TIGR01393       142 RVKKEIEEVIGLDA  155 (598)
T ss_pred             HHHHHHHHHCCCCC
T ss_conf             99998765418896


No 189
>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=95.36  E-value=0.025  Score=33.07  Aligned_cols=53  Identities=28%  Similarity=0.367  Sum_probs=38.8

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCC--CCHHHCCCCC
Q ss_conf             87499998088988889999999999998799599998787768--0112124633
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGN--ASTGLGIELY   58 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~--~~~~l~~~~~   58 (265)
                      .+|++.+. +-=++||||++.++....++.|..++.||..---+  ....+|++..
T Consensus        51 ~GRi~ei~-G~essGKTtlal~~ia~aQk~gg~~~~iD~E~a~d~~~a~~lGVD~~  105 (322)
T pfam00154        51 KGRIIEIY-GPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDID  105 (322)
T ss_pred             CCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHCCHHHHHHCCCCHH
T ss_conf             87089998-89877789999999999973499389985366059889998098802


No 190
>pfam00931 NB-ARC NB-ARC domain.
Probab=95.33  E-value=0.02  Score=33.62  Aligned_cols=26  Identities=35%  Similarity=0.493  Sum_probs=21.8

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHH
Q ss_conf             768749999808898888999999999
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLST   29 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~   29 (265)
                      ...-+||+|. +-||+||||+|-.+-.
T Consensus        16 ~~~~~vI~I~-G~gGiGKTtLA~~v~~   41 (285)
T pfam00931        16 SENLGVVGIV-GMGGVGKTTLAKQIYN   41 (285)
T ss_pred             CCCCEEEEEE-CCCCCCHHHHHHHHHC
T ss_conf             9895399988-9995639999999971


No 191
>PRK05433 GTP-binding protein LepA; Provisional
Probab=95.25  E-value=0.019  Score=33.74  Aligned_cols=82  Identities=17%  Similarity=0.314  Sum_probs=45.6

Q ss_pred             CCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             27820331013332--2221011233100111112311378887533577765543202677431002023125310011
Q gi|254780806|r  123 DFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       123 ~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      .|-+=|||||+..+  -....+|.++|.+++++....    |+..  .++..+......+++++ .|+|++|-......+
T Consensus        73 ~y~lNLIDTPGHVDF~~EVsRSL~aceGalLlVDa~q----GVqa--QT~an~~~A~~~~L~iI-pviNKIDlp~Ad~e~  145 (601)
T PRK05433         73 TYQLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQ----GVEA--QTLANVYLALENDLEII-PVLNKIDLPAADPER  145 (601)
T ss_pred             EEEEEEECCCCCCCCCEEEEEEHHHCCCEEEEEECCC----CCCC--HHHHHHHHHHHCCCCEE-EEEECCCCCCCCHHH
T ss_conf             7999985489856645045560334072599997687----8560--06999999998799657-778614688899899


Q ss_pred             HHHHHHHHHCC
Q ss_conf             26899988085
Q gi|254780806|r  201 VVSDVRKNLGG  211 (265)
Q Consensus       201 ~~~~l~~~~~~  211 (265)
                      +.+++.+.+|.
T Consensus       146 v~~qi~~~igl  156 (601)
T PRK05433        146 VKQEIEDIIGI  156 (601)
T ss_pred             HHHHHHHHHCC
T ss_conf             99999988689


No 192
>PRK13506 formate--tetrahydrofolate ligase; Provisional
Probab=95.24  E-value=0.033  Score=32.39  Aligned_cols=40  Identities=30%  Similarity=0.463  Sum_probs=32.6

Q ss_pred             CCCCEEEEEEC---CCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             76874999980---88988889999999999998799599998
Q gi|254780806|r    3 EKKSRIITIAN---QKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         3 ~~~~kvI~v~s---~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      ++++|.|.|..   ..-|-||||+++.|+-+|++.|+++.+-=
T Consensus        51 ~~~gklilVTaitPTP~GEGKTTttIGL~~aL~~lgk~~~~~l   93 (577)
T PRK13506         51 QPKGKLVIVTAVTPTPLGEGKTVTTIGLTQGLNALGQKVCACI   93 (577)
T ss_pred             CCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEEE
T ss_conf             8996499998568988989841109879999987198458997


No 193
>pfam01695 IstB IstB-like ATP binding protein. This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function.
Probab=95.24  E-value=0.044  Score=31.67  Aligned_cols=36  Identities=28%  Similarity=0.290  Sum_probs=30.6

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             4999980889888899999999999987995999987
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      +-|.+ .+.-|+|||-+++.+|..+.++|++|+-+-+
T Consensus        48 ~Nlll-~G~~GtGKThLA~Ai~~~~~~~g~~v~f~~~   83 (178)
T pfam01695        48 ENLLL-LGPPGVGKTHLACALGHQACRAGYSVLFTRT   83 (178)
T ss_pred             CCEEE-ECCCCCCHHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf             76899-8999987899999999999986985999961


No 194
>PRK04328 hypothetical protein; Provisional
Probab=95.21  E-value=0.046  Score=31.56  Aligned_cols=36  Identities=17%  Similarity=0.261  Sum_probs=32.3

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             999808898888999999999999879959999878
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      +...++--|+||||++.++++.-++.|.+++.|-++
T Consensus        26 ~~Lv~G~pGtGKT~la~qFl~~g~~~GE~~lyis~e   61 (250)
T PRK04328         26 VVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVALE   61 (250)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             999982899998999999999998769977999972


No 195
>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]
Probab=95.19  E-value=0.038  Score=32.01  Aligned_cols=36  Identities=44%  Similarity=0.629  Sum_probs=26.1

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHH----CCC------CEEEEEC
Q ss_conf             99998088988889999999999998----799------5999987
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAA----IGE------NVLLIDL   43 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~----~g~------rVllID~   43 (265)
                      +.++.-+-||+||||+..-|..+++.    .|+      +|+.|-|
T Consensus        90 ~~~~~~gdsg~GKttllL~l~IalaaG~~lfG~~v~epGkvlyvsl  135 (402)
T COG3598          90 YVSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSL  135 (402)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEE
T ss_conf             0589844886237689999999998647774533558880799982


No 196
>PRK07263 consensus
Probab=95.18  E-value=0.059  Score=30.92  Aligned_cols=40  Identities=20%  Similarity=0.395  Sum_probs=32.8

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCC
Q ss_conf             8749999808898888999999999999-8799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~   45 (265)
                      .+..|.+ .++=|+|||+++.|+|...| +.|++|+.+-+..
T Consensus       202 ~GdLivi-aaRPsmGKTa~alnia~~iA~~~~~~V~~fSlEM  242 (453)
T PRK07263        202 PDQLIIL-AARPAVGKTAFVLNIAQNVGTKQKKTVAIFSLEM  242 (453)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHHCCCEEEEEECCC
T ss_conf             7868999-7278884789999999999985598289992469


No 197
>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=95.05  E-value=0.038  Score=31.99  Aligned_cols=31  Identities=32%  Similarity=0.436  Sum_probs=26.7

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             9999808898888999999999999879959999
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      ||+|.   ||=||||+-..||..+..+|+||++-
T Consensus         1 VIs~V---GaGGKTS~m~~LA~e~~~~G~~VlvT   31 (232)
T TIGR03172         1 VIAFV---GAGGKTSTMFWLAAEYRKEGYRVLVT   31 (232)
T ss_pred             CEEEE---CCCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             98998---89879999999999998769909998


No 198
>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated
Probab=95.03  E-value=0.058  Score=30.94  Aligned_cols=37  Identities=14%  Similarity=0.214  Sum_probs=29.0

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             874999980889888899999999999987995999987
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      ++.|...  .=-|=||||.|..+|.-.+-+|+||+++-+
T Consensus        21 kGlI~VY--TGdGKGKTTAAlGlalRA~G~G~rV~ivQF   57 (178)
T PRK07414         21 EGLVQVF--TSSQRNFFTSVMAQALRIAGQGTPVLIVQF   57 (178)
T ss_pred             CCEEEEE--ECCCCCHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             4179999--579998089999999999539987999997


No 199
>PRK08082 consensus
Probab=95.02  E-value=0.065  Score=30.66  Aligned_cols=40  Identities=30%  Similarity=0.516  Sum_probs=32.6

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCC
Q ss_conf             8749999808898888999999999999-8799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~   45 (265)
                      .+..|.+ .++=|+|||+++.|+|...| +.|++|++.-+..
T Consensus       202 ~g~Livi-aaRPsmGKTa~alnia~~~a~~~~~~V~~fSlEM  242 (453)
T PRK08082        202 RNDLIIV-AARPSVGKTAFALNIAQNVATKTDENVAIFSLEM  242 (453)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             5857999-8678875789999999999985599489973138


No 200
>PRK05636 replicative DNA helicase; Provisional
Probab=94.98  E-value=0.069  Score=30.52  Aligned_cols=40  Identities=20%  Similarity=0.417  Sum_probs=32.9

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCC
Q ss_conf             8749999808898888999999999999-8799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~   45 (265)
                      .+..|.+ .++=|+|||+++.|+|...| +.|++|++.-+..
T Consensus       266 ~G~LiIi-AARPsmGKTalAlnia~n~A~~~g~~v~~fSLEM  306 (507)
T PRK05636        266 GGQMIIV-AARPGVGKSTIALDFMRSASIKNNKASVIFSLEM  306 (507)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             3567999-7378786689999999999987699379971569


No 201
>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]
Probab=94.97  E-value=0.064  Score=30.69  Aligned_cols=40  Identities=28%  Similarity=0.376  Sum_probs=34.3

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             87499998088988889999999999998799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +.+++.| ++-=|+|||+++.++++..++.|.+|+.|-+|-
T Consensus        22 ~g~~~lI-~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~e   61 (260)
T COG0467          22 RGSVVLI-TGPPGTGKTIFALQFLYEGAREGEPVLYVSTEE   61 (260)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHCCCEEEEEEEEC
T ss_conf             9978999-938998689999999997762698589999206


No 202
>COG0523 Putative GTPases (G3E family) [General function prediction only]
Probab=94.95  E-value=0.26  Score=27.12  Aligned_cols=34  Identities=26%  Similarity=0.284  Sum_probs=25.5

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             999808898888999999999999879959999878
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      +++.++==|+||||+--||.....  |+|+++|=-+
T Consensus         3 VtvitGFLGsGKTTlL~~lL~~~~--g~kiAVIVNE   36 (323)
T COG0523           3 VTVITGFLGSGKTTLLNHLLANRD--GKKIAVIVNE   36 (323)
T ss_pred             EEEEEECCCCCHHHHHHHHHHCCC--CCEEEEEEEC
T ss_conf             799811677998999999985458--9807999855


No 203
>COG2403 Predicted GTPase [General function prediction only]
Probab=94.92  E-value=0.05  Score=31.34  Aligned_cols=37  Identities=22%  Similarity=0.382  Sum_probs=34.6

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             4999980889888899999999999987995999987
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      -+|+|....-|+|||+++.-+|..|..+|+||++|-.
T Consensus       127 PviaV~atrtg~GKsaVS~~v~r~l~ergyrv~vVrh  163 (449)
T COG2403         127 PVIAVTATRTGVGKSAVSRYVARLLRERGYRVCVVRH  163 (449)
T ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             5599997236655678889999999866982379955


No 204
>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=94.92  E-value=0.078  Score=30.18  Aligned_cols=53  Identities=32%  Similarity=0.418  Sum_probs=38.8

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCC--CCHHHCCCCC
Q ss_conf             87499998088988889999999999998799599998787768--0112124633
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGN--ASTGLGIELY   58 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~--~~~~l~~~~~   58 (265)
                      .+|++.+. +.=++||||++.++....++.|..|+.||..---+  .-..+|++..
T Consensus        54 ~GRivei~-G~essGKTtlal~~ia~aQk~gg~~~~iDaE~a~d~~~a~~lGVD~~  108 (325)
T cd00983          54 KGRIIEIY-GPESSGKTTLALHAIAEAQKLGGTVAFIDAEHALDPVYAKKLGVDLD  108 (325)
T ss_pred             CCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHCCCHHHHHHCCCCHH
T ss_conf             88089998-89877799999999999873598399996254259899998099846


No 205
>TIGR01085 murE UDP-N-acetylmuramyl-tripeptide synthetases; InterPro: IPR005761   The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:    (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.    Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC)  and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .    This entry represents DP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligases (MurE; 6.3.2.13 from EC). An exception is found with Staphylococcus aureus, in which diaminopimelate is replaced by lysine in the peptidoglycan and MurE is (6.3.2.7 from EC). The Mycobacteria, part of the closest neighbouring branch outside of the low-GC Gram-positive bacteria, use diaminopimelate.; GO: 0005524 ATP binding, 0016881 acid-amino acid ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=94.91  E-value=0.056  Score=31.02  Aligned_cols=39  Identities=33%  Similarity=0.446  Sum_probs=32.6

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             876874999980889888899999999999987995999987
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      |.++=+||.|.   |==||||+|.-++..|.+.|+|+.+|-.
T Consensus        84 Ps~~l~viGvT---GTNGKTtt~~li~~~l~~~G~~tgliGT  122 (494)
T TIGR01085        84 PSKKLKVIGVT---GTNGKTTTTSLIAQLLELLGKKTGLIGT  122 (494)
T ss_pred             CCCCEEEEEEE---ECCCCHHHHHHHHHHHHHCCCEEEEEEE
T ss_conf             55251689997---1287448999999999867970899865


No 206
>PRK13505 formate--tetrahydrofolate ligase; Provisional
Probab=94.89  E-value=0.044  Score=31.64  Aligned_cols=51  Identities=27%  Similarity=0.460  Sum_probs=35.9

Q ss_pred             CCCCEEEEEEC---CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCC
Q ss_conf             76874999980---889888899999999999987995999987877680112124
Q gi|254780806|r    3 EKKSRIITIAN---QKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGI   55 (265)
Q Consensus         3 ~~~~kvI~v~s---~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~   55 (265)
                      ++.+|.|-|..   ..-|-||||+++.|+-+|.+.|+++.+-==  |.|+.-.||+
T Consensus        51 ~~~gklIlVTaitPTP~GEGKTTttIGL~~aL~~lgk~~~~~lR--ePSlGP~FGi  104 (556)
T PRK13505         51 KKDGKLILVTAINPTPAGEGKTTVTVGLGDALNKIGKKTVIALR--EPSLGPVFGI  104 (556)
T ss_pred             CCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEEEE--CCCCCCCCCC
T ss_conf             89963999984588888888630179899999871874379973--5887873166


No 207
>PRK04308 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=94.87  E-value=0.054  Score=31.13  Aligned_cols=38  Identities=21%  Similarity=0.344  Sum_probs=30.7

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             87687499998088988889999999999998799599998
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      .++..|+|+|.   |--||||+|..+++.|...|+++.+.-
T Consensus       106 ~~~~~~~IaVT---GTnGKTTTtsli~~iL~~~g~~~~~~G  143 (445)
T PRK04308        106 NRRGDKVIAIT---GSNGKTTVTSLVGYLCIKCGLDTVIAG  143 (445)
T ss_pred             HCCCCCEEEEE---CCCCCHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             41699579994---899837799999999997599629985


No 208
>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=94.83  E-value=0.045  Score=31.56  Aligned_cols=40  Identities=33%  Similarity=0.466  Sum_probs=32.1

Q ss_pred             CCCCEEEEEEC---CCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             76874999980---88988889999999999998799599998
Q gi|254780806|r    3 EKKSRIITIAN---QKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         3 ~~~~kvI~v~s---~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      +..+|.|.|.+   ..-|-||||+++.|+-+|.+.|+++.+-=
T Consensus        35 ~~~gklilVTaitPTP~GEGKTTttIGL~~aL~~~gk~~~~~l   77 (524)
T cd00477          35 RPDGKLILVTAITPTPAGEGKTTTTIGLAQALNAHGKKAIACL   77 (524)
T ss_pred             CCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEEE
T ss_conf             8995599998468888888853109989999987366314886


No 209
>PRK08939 primosomal protein DnaI; Reviewed
Probab=94.78  E-value=0.096  Score=29.67  Aligned_cols=37  Identities=24%  Similarity=0.251  Sum_probs=28.2

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             74999980889888899999999999987995999987
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      .|=+= ..+.-|||||-+++-+|-.|+++|+.|+++-.
T Consensus       157 ~kGly-l~G~~G~GKTyL~~aian~La~~g~~v~~v~~  193 (306)
T PRK08939        157 VKGLY-LYGDFGVGKTYLLAAIANELAKKGVSSTLVHF  193 (306)
T ss_pred             CCEEE-EECCCCCCHHHHHHHHHHHHHHCCCEEEEEEH
T ss_conf             87788-98999998999999999999986992999875


No 210
>pfam01268 FTHFS Formate--tetrahydrofolate ligase.
Probab=94.74  E-value=0.04  Score=31.86  Aligned_cols=40  Identities=30%  Similarity=0.479  Sum_probs=32.3

Q ss_pred             CCCCEEEEEEC---CCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             76874999980---88988889999999999998799599998
Q gi|254780806|r    3 EKKSRIITIAN---QKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         3 ~~~~kvI~v~s---~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      +.++|-|.|.+   ..-|-||||+++.|+-+|++.|+++.+-=
T Consensus        51 ~~~gklilVTaitPTP~GEGKTTttIGL~~aL~~lgk~~~~~l   93 (555)
T pfam01268        51 RPDGKLILVTAITPTPAGEGKTTTTIGLGQALNRLGKKAIAAL   93 (555)
T ss_pred             CCCCEEEEEEECCCCCCCCCCCEEHHHHHHHHHHHCCCEEEEE
T ss_conf             8985399998457888888863023659999986287436897


No 211
>PRK08694 consensus
Probab=94.70  E-value=0.077  Score=30.23  Aligned_cols=40  Identities=23%  Similarity=0.420  Sum_probs=32.6

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCC-CEEEEECCC
Q ss_conf             87499998088988889999999999998799-599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGE-NVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~-rVllID~D~   45 (265)
                      .+..|.+ .++=|+|||+++.|+|...|..|+ +|++.-+..
T Consensus       217 ~G~LiVI-aaRPsmGKTalalnia~~~a~~~~~~V~~fSLEM  257 (468)
T PRK08694        217 PGDLIIV-AGRPSMGKTAFSINIAEHVAVEGKLPVAVFSMEM  257 (468)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCC
T ss_conf             7847999-6178653789999999999984798479977889


No 212
>PRK08840 replicative DNA helicase; Provisional
Probab=94.69  E-value=0.087  Score=29.91  Aligned_cols=40  Identities=33%  Similarity=0.444  Sum_probs=32.6

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCC
Q ss_conf             8749999808898888999999999999-8799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~   45 (265)
                      .+..|.+ .++=|+|||+++.|+|...| ..|++|++.-+..
T Consensus       216 ~G~Livi-aaRPsmGKTalalnia~n~a~~~~~~v~~fSlEM  256 (464)
T PRK08840        216 GSDLIIV-AARPSMGKTTFAMNLCENAAMDQDKPVLIFSLEM  256 (464)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCC
T ss_conf             5767999-8379873689999999999996599679976779


No 213
>PRK09270 frcK putative fructose transport system kinase; Reviewed
Probab=94.67  E-value=0.11  Score=29.22  Aligned_cols=38  Identities=29%  Similarity=0.381  Sum_probs=30.2

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCC--CCEEEEECCC
Q ss_conf             49999808898888999999999999879--9599998787
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIG--ENVLLIDLDP   45 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g--~rVllID~D~   45 (265)
                      .+|++ .+-.|+||||+|-.|+..|.+.+  ..+.++-+|.
T Consensus        35 ~lIgI-aG~pGSGKSTlA~~l~~~L~~~~~~~~~~~vpmDG   74 (230)
T PRK09270         35 TVVGI-AGPPGAGKSTLAETLWEALSQQGPELPAIQVPMDG   74 (230)
T ss_pred             EEEEE-ECCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCC
T ss_conf             89999-89998899999999999986237998579973653


No 214
>KOG0635 consensus
Probab=94.62  E-value=0.083  Score=30.03  Aligned_cols=55  Identities=35%  Similarity=0.398  Sum_probs=39.0

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHCCCCCCC
Q ss_conf             8749999808898888999999999999879959999878776-8011212463334
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIELYDR   60 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~-~~~~~l~~~~~~~   60 (265)
                      ++=||=+. +=.|+||||+++.|..+|.++|+-...+|.|.-. .+..-|+....++
T Consensus        30 kGcviWiT-GLSgSGKStlACaL~q~L~qrgkl~Y~LDGDNvRhGLN~DL~F~a~dR   85 (207)
T KOG0635          30 KGCVIWIT-GLSGSGKSTLACALSQALLQRGKLTYILDGDNVRHGLNKDLGFKAEDR   85 (207)
T ss_pred             CCCEEEEE-CCCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCCCHHHH
T ss_conf             99689974-257788025999999999865865898548540104344567650334


No 215
>PRK13507 formate--tetrahydrofolate ligase; Provisional
Probab=94.62  E-value=0.054  Score=31.13  Aligned_cols=40  Identities=25%  Similarity=0.280  Sum_probs=32.4

Q ss_pred             CCCCEEEEEEC---CCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             76874999980---88988889999999999998799599998
Q gi|254780806|r    3 EKKSRIITIAN---QKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         3 ~~~~kvI~v~s---~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      +..+|-|.|.+   ..-|-||||+++.|+-+|.+.|+++.+-=
T Consensus        60 ~~~gklILVTaitPTP~GEGKTTttIGL~~aL~~lgkk~~~~l  102 (587)
T PRK13507         60 RPDGKYIDVTAITPTPLGEGKSTTTMGLVQGLGKRGKKVGGAI  102 (587)
T ss_pred             CCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEEE
T ss_conf             8996399998468888889862105629999986088258997


No 216
>PRK09401 reverse gyrase; Reviewed
Probab=94.61  E-value=0.045  Score=31.62  Aligned_cols=36  Identities=31%  Similarity=0.370  Sum_probs=30.0

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             7499998088988889999999999998799599998
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      ++-+++. .=-|+||||+-.-+|.++|+.|+|+++|=
T Consensus        93 g~SFaii-APTG~GKTtfgl~~sly~a~kgkks~~i~  128 (1176)
T PRK09401         93 GESFAII-APTGVGKTTFGLVMALYLAKKGKKSYIIF  128 (1176)
T ss_pred             CCCEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             8974898-88998888999999999986598399996


No 217
>PRK10218 GTP-binding protein; Provisional
Probab=94.49  E-value=0.029  Score=32.68  Aligned_cols=81  Identities=15%  Similarity=0.148  Sum_probs=48.6

Q ss_pred             CCCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHH
Q ss_conf             027820331013332--222101123310011111231137888753357776554320267743100202312531001
Q gi|254780806|r  122 SDFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQ  199 (265)
Q Consensus       122 ~~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~  199 (265)
                      ++|-+=|||||+..+  -.+..+|.++|.+++++....--..+..      ..+++....+++++ +++|++|.......
T Consensus        66 ~~~~iNiIDTPGH~DF~gEVeR~L~~~DGalLvVDA~eGv~pQT~------~V~~~Al~~~l~~I-vvINKiDr~~A~~~  138 (607)
T PRK10218         66 NDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTR------FVTKKAFAYGLKPI-VVINKVDRPGARPD  138 (607)
T ss_pred             CCEEEEEECCCCCCCCHHHHHHHHHHCCEEEEEEECCCCCCHHHH------HHHHHHHHCCCCEE-EEECCCCCCCCCHH
T ss_conf             878997865998543014889789766848999978878624589------99999998799759-97216676655357


Q ss_pred             HHHHHHHHHH
Q ss_conf             1268999880
Q gi|254780806|r  200 QVVSDVRKNL  209 (265)
Q Consensus       200 ~~~~~l~~~~  209 (265)
                      ++.+++.+.|
T Consensus       139 ~V~~ei~dlf  148 (607)
T PRK10218        139 WVVDQVFDLF  148 (607)
T ss_pred             HHHHHHHHHH
T ss_conf             8999999887


No 218
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=94.48  E-value=0.095  Score=29.69  Aligned_cols=36  Identities=14%  Similarity=0.207  Sum_probs=32.1

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             999808898888999999999999879959999878
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      +...++-=|+|||+++..+++..+++|.+++.|-++
T Consensus        34 ~~li~G~~G~GKt~~~~~f~~~~~~~g~~~~~~~~e   69 (241)
T PRK06067         34 LILIEGENDTGKSVLSQQFVWGALNQGKRGLAITTE   69 (241)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEEC
T ss_conf             899980799887999999999998679829999942


No 219
>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]
Probab=94.47  E-value=0.096  Score=29.67  Aligned_cols=38  Identities=32%  Similarity=0.379  Sum_probs=32.1

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             749999808898888999999999999879959999878
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ++|+=|+ +=.|+||||+|.+++...+..|.+++.||.-
T Consensus        60 g~ItEiy-G~~gsGKT~lal~~~~~aq~~g~~a~fIDtE   97 (279)
T COG0468          60 GRITEIY-GPESSGKTTLALQLVANAQKPGGKAAFIDTE   97 (279)
T ss_pred             CEEEEEE-CCCCCCHHHHHHHHHHHHHCCCCEEEEEECC
T ss_conf             3589984-6887654668999988865379808999589


No 220
>PRK09165 replicative DNA helicase; Provisional
Probab=94.44  E-value=0.12  Score=29.04  Aligned_cols=40  Identities=28%  Similarity=0.327  Sum_probs=31.1

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHH---------------CCCCEEEEECCC
Q ss_conf             87499998088988889999999999998---------------799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAA---------------IGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~---------------~g~rVllID~D~   45 (265)
                      .+..|.+ .++=|+|||+++.|+|...|+               .|+.|+++-+..
T Consensus       204 ~GdLiII-AARPsmGKTafaLniA~n~A~~~~~~~~~~~~~~~~~g~~V~~FSLEM  258 (484)
T PRK09165        204 PSDLIIL-AGRPSMGKTALATNIAFNAAKAYLREAQPDGSKKAVNGGVVGFFSLEM  258 (484)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCC
T ss_conf             7737999-607999778999999999998741022223321136898489994779


No 221
>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=94.42  E-value=0.066  Score=30.62  Aligned_cols=39  Identities=36%  Similarity=0.407  Sum_probs=31.5

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             4999980889888899999999999987995999987877
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      +.+.+ .+.-|+||||++..+|..+...++.|..++++..
T Consensus         3 ~~ill-~G~~GsGKTtl~~~la~~~~~~~~~v~~~~~~~~   41 (148)
T smart00382        3 EVILI-VGPPGSGKTTLARALARELGPPGGGVIYIDGEDI   41 (148)
T ss_pred             CEEEE-ECCCCHHHHHHHHHHHHHHCCCCCCEEEEEHHHH
T ss_conf             78999-9999702999999999872668996899875998


No 222
>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=94.41  E-value=0.11  Score=29.44  Aligned_cols=36  Identities=22%  Similarity=0.206  Sum_probs=25.6

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHH----CCCC-EEEEECCCC
Q ss_conf             98088988889999999999998----7995-999987877
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAA----IGEN-VLLIDLDPQ   46 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~----~g~r-VllID~D~q   46 (265)
                      |.-+|=|||||.+|-++.-.|..    .|-+ |..+-.+.|
T Consensus        47 ~iYGkTGtGKT~vt~~v~~~l~~~~~~~d~~D~~~~~~NC~   87 (383)
T TIGR02928        47 FIYGKTGTGKTAVTKYVMKELEEAAEDRDVRDVSTVYINCQ   87 (383)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCC
T ss_conf             88788898788999999999999862269971589997785


No 223
>PRK08116 hypothetical protein; Validated
Probab=94.34  E-value=0.081  Score=30.09  Aligned_cols=33  Identities=24%  Similarity=0.344  Sum_probs=29.3

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             980889888899999999999987995999987
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      +..+.=|+|||-+++.+|..|...|+.|+.+..
T Consensus       112 ll~G~~GtGKThLa~aIa~~l~~~g~~V~~~~~  144 (262)
T PRK08116        112 LLWGSPGNGKTYLAAAIANELIEKGVPVVFVNV  144 (262)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEH
T ss_conf             998989998999999999999987993999889


No 224
>PRK08760 replicative DNA helicase; Provisional
Probab=94.14  E-value=0.14  Score=28.68  Aligned_cols=40  Identities=23%  Similarity=0.365  Sum_probs=32.3

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCC
Q ss_conf             8749999808898888999999999999-8799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~   45 (265)
                      .+..|.+ .++=|+|||+++.|+|...| +.|+.|+++-+..
T Consensus       228 ~G~LiVi-aaRPsmGKTalalnia~~~A~~~~~~V~~fSLEM  268 (476)
T PRK08760        228 PTDLIIL-AARPAMGKTTFALNIAEYAAIKSKKGVAVFSMEM  268 (476)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             7777999-8778874789999999999983799789970369


No 225
>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=94.14  E-value=0.018  Score=33.97  Aligned_cols=31  Identities=29%  Similarity=0.343  Sum_probs=24.8

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHH-HCC
Q ss_conf             68749999808898888999999999999-879
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALA-AIG   35 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g   35 (265)
                      +.++.+++. ++-|+||||+..-|+-.++ ..|
T Consensus       345 ~~g~~talv-G~SGaGKSTLl~lL~G~~~~~~G  376 (559)
T COG4988         345 KAGQLTALV-GASGAGKSTLLNLLLGFLAPTQG  376 (559)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHCCCCCCCC
T ss_conf             489679998-89999789999998475777784


No 226
>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=94.11  E-value=0.036  Score=32.19  Aligned_cols=37  Identities=22%  Similarity=0.240  Sum_probs=24.6

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             6874999980889888899999999999987995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      ++++++++. ++-|+||||+.--|....-..| ++ .||.
T Consensus       374 ~~Ge~vaIV-G~SGsGKSTl~~LL~g~~p~~G-~I-~i~g  410 (588)
T PRK11174        374 PAGQRVALV-GPSGAGKTSLLNALLGFLPYQG-SL-KING  410 (588)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHHHCCCCC-EE-EECC
T ss_conf             499789998-9998649999999987289883-89-9999


No 227
>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=94.07  E-value=0.12  Score=29.07  Aligned_cols=37  Identities=30%  Similarity=0.316  Sum_probs=29.9

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCC------CCEEEEECC
Q ss_conf             9999808898888999999999999879------959999878
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIG------ENVLLIDLD   44 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g------~rVllID~D   44 (265)
                      .|+-..+-.|+|||+++.++|...+..|      .+|+-||..
T Consensus        20 ~ItEi~G~~gsGKT~l~lqla~~~q~~~~~~~~~g~vvyIDtE   62 (226)
T cd01393          20 RITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTE   62 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECC
T ss_conf             3999999999989999999999985422116999619999557


No 228
>PRK04690 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=94.04  E-value=0.14  Score=28.76  Aligned_cols=35  Identities=29%  Similarity=0.401  Sum_probs=29.6

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             87499998088988889999999999998799599998
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      .+|+|+|.   |--||||+|..+++.|...|+++.+.-
T Consensus       114 ~~k~IaVT---GTNGKTTTt~ll~~iL~~~g~~~~~~G  148 (468)
T PRK04690        114 VPGAVCVT---GTKGKSTTTALLAHLLRAAGHRTALVG  148 (468)
T ss_pred             CCCEEEEE---CCCCHHHHHHHHHHHHHHCCCCEEEEC
T ss_conf             78789996---998589999999999985799828986


No 229
>KOG0462 consensus
Probab=94.02  E-value=0.064  Score=30.69  Aligned_cols=84  Identities=15%  Similarity=0.171  Sum_probs=57.1

Q ss_pred             CCCCCEEEECCCC--CCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             2782033101333--22221011233100111112311378887533577765543202677431002023125310011
Q gi|254780806|r  123 DFSYIFLDCPPSF--NLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       123 ~yD~IiiD~pp~~--~~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      .|-.=+||||+..  +-...-.|.++|.+++++....- ++  .   .++..+...+..++.+. .|+|++|-.+....+
T Consensus       124 ~ylLNLIDTPGHvDFs~EVsRslaac~G~lLvVDA~qG-vq--A---QT~anf~lAfe~~L~iI-pVlNKIDlp~adpe~  196 (650)
T KOG0462         124 SYLLNLIDTPGHVDFSGEVSRSLAACDGALLVVDASQG-VQ--A---QTVANFYLAFEAGLAII-PVLNKIDLPSADPER  196 (650)
T ss_pred             CEEEEEECCCCCCCCCCEEHEHHHHCCCEEEEEECCCC-CH--H---HHHHHHHHHHHCCCEEE-EEEECCCCCCCCHHH
T ss_conf             32887505898555541000126535715999976768-12--8---89999999998597488-865315789889899


Q ss_pred             HHHHHHHHHCCCC
Q ss_conf             2689998808520
Q gi|254780806|r  201 VVSDVRKNLGGKV  213 (265)
Q Consensus       201 ~~~~l~~~~~~~v  213 (265)
                      +...+.+.|+.+.
T Consensus       197 V~~q~~~lF~~~~  209 (650)
T KOG0462         197 VENQLFELFDIPP  209 (650)
T ss_pred             HHHHHHHHHCCCC
T ss_conf             9999999866896


No 230
>PRK08006 replicative DNA helicase; Provisional
Probab=93.97  E-value=0.17  Score=28.20  Aligned_cols=40  Identities=33%  Similarity=0.444  Sum_probs=32.5

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCC
Q ss_conf             87499998088988889999999999998-799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~D~   45 (265)
                      .+..|.+ .++=|+|||+++.|+|...|. .|++|+++-+..
T Consensus       223 ~G~Livi-aaRPsmGKTalalnia~~~a~~~~~~V~~fSlEM  263 (471)
T PRK08006        223 PSDLIIV-AARPSMGKTTFAMNLCENAAMLQDKPVLIFSLEM  263 (471)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             1738999-9469987699999999999986699579981679


No 231
>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=93.90  E-value=0.033  Score=32.39  Aligned_cols=82  Identities=13%  Similarity=0.175  Sum_probs=47.7

Q ss_pred             CCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCH-HHH
Q ss_conf             27820331013332--222101123310011111231137888753357776554320267743100202312531-001
Q gi|254780806|r  123 DFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNS-LSQ  199 (265)
Q Consensus       123 ~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~-~~~  199 (265)
                      .+.+.+||||+...  ..+..++..+|.+++++....---....+   .++..+. .+.  ++. +++|++|.-.. ...
T Consensus        61 ~~~i~~iDTPGh~~f~~~~~~~l~~aD~ailvVda~~G~~~qt~~---~~~~~~~-~~~--p~i-v~iNKiD~~~~~~~~  133 (189)
T cd00881          61 DRRVNFIDTPGHEDFSSEVIRGLSVSDGAILVVDANEGVQPQTRE---HLRIARE-GGL--PII-VAINKIDRVGEEDLE  133 (189)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHH---HHHHHHH-CCC--CEE-EEEECCCCCCHHHHH
T ss_conf             989999969981889999999986468569999879899878999---9999997-699--879-999897187756299


Q ss_pred             HHHHHHHHHHCC
Q ss_conf             126899988085
Q gi|254780806|r  200 QVVSDVRKNLGG  211 (265)
Q Consensus       200 ~~~~~l~~~~~~  211 (265)
                      +..+++++.+..
T Consensus       134 ~~~~ei~~~l~~  145 (189)
T cd00881         134 EVLREIKELLGL  145 (189)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999875


No 232
>PRK04220 2-phosphoglycerate kinase; Provisional
Probab=93.90  E-value=0.081  Score=30.09  Aligned_cols=26  Identities=35%  Similarity=0.549  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             49999808898888999999999999
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALA   32 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la   32 (265)
                      -+|...++-.||||||+|..||..|.
T Consensus        92 pliILigGtsGvGKSTlA~~LA~rLg  117 (306)
T PRK04220         92 PIIILIGGASGVGTSTIAFELASRLG  117 (306)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             87999858998878999999999709


No 233
>PRK08233 hypothetical protein; Provisional
Probab=93.89  E-value=0.14  Score=28.71  Aligned_cols=37  Identities=43%  Similarity=0.527  Sum_probs=26.9

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             6874999980889888899999999999987995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      |++.||+|+ +=-|+||||++-.|...+-  +..++..|.
T Consensus         1 kkp~IIgIa-GgSgSGKTtla~~l~~~l~--~~~~~~~D~   37 (182)
T PRK08233          1 KKTKIITIA-AVSGGGKTTLTERLTHKLK--NSKALYFDR   37 (182)
T ss_pred             CCCEEEEEE-CCCCCCHHHHHHHHHHHCC--CCEEEEECC
T ss_conf             998899996-8886789999999999746--775899666


No 234
>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.
Probab=93.85  E-value=0.11  Score=29.22  Aligned_cols=36  Identities=28%  Similarity=0.332  Sum_probs=31.8

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             998088988889999999999998799599998787
Q gi|254780806|r   10 TIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus        10 ~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      .+++|-=|+||||.|-.|+..+.+.|.+|.++..|.
T Consensus         2 ivl~GlP~SGKSt~a~~L~~~l~~~~~~~i~~~~d~   37 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELSKKLSEKNIDNIILGTDL   37 (249)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCEEEECCCC
T ss_conf             789678999899999999999998299659965520


No 235
>PTZ00301 uridine kinase; Provisional
Probab=93.77  E-value=0.21  Score=27.63  Aligned_cols=40  Identities=28%  Similarity=0.356  Sum_probs=30.2

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHC-C-CCEEEEECCC
Q ss_conf             874999980889888899999999999987-9-9599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAI-G-ENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~-g-~rVllID~D~   45 (265)
                      .+-||+|+ +=-|+||||+|-+|+..|... | .+|.++-.|-
T Consensus         2 ~~~iIgIa-GgSgSGKTT~a~~i~~~l~~~~~~~~v~ii~~D~   43 (210)
T PTZ00301          2 PCTVIGIS-GASGSGKSSLSTNIVSELMAHCGPVSIGVICEDF   43 (210)
T ss_pred             CCEEEEEE-CCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCC
T ss_conf             98899996-8876789999999999987614998079983676


No 236
>PRK09354 recA recombinase A; Provisional
Probab=93.77  E-value=0.21  Score=27.73  Aligned_cols=51  Identities=29%  Similarity=0.438  Sum_probs=38.2

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC----CCCCCCHHHCCCCC
Q ss_conf             8749999808898888999999999999879959999878----77680112124633
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD----PQGNASTGLGIELY   58 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D----~q~~~~~~l~~~~~   58 (265)
                      ++|++-+. +.=++||||++.|.....++.|.-++.||+.    |.  -...+|++..
T Consensus        59 ~GRivEi~-G~esSGKTtlal~~iaeaQk~Gg~~a~iDaE~ald~~--~a~~lGVd~d  113 (350)
T PRK09354         59 KGRIVEIY-GPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV--YAKKLGVDID  113 (350)
T ss_pred             CCCEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCHH--HHHHCCCCHH
T ss_conf             87089998-8987779999999999999759947999600027988--9998497715


No 237
>pfam08433 KTI12 Chromatin associated protein KTI12. This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II. The Elongator complex has histone acetyltransferase activity.
Probab=93.75  E-value=0.11  Score=29.27  Aligned_cols=36  Identities=28%  Similarity=0.324  Sum_probs=32.1

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             998088988889999999999998799599998787
Q gi|254780806|r   10 TIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus        10 ~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      .|+++-=++||||.|..|+..|.+.|++|.+|+-|.
T Consensus         2 ivl~G~P~SGKSt~A~~L~~~l~~~~~~v~vi~d~~   37 (266)
T pfam08433         2 IILTGLPSSGKSTRAKELAKYLEEKGYDVIVISDES   37 (266)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCEEEEECCCC
T ss_conf             798579999688999999999997599389978001


No 238
>pfam01935 DUF87 Domain of unknown function DUF87. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.
Probab=93.60  E-value=0.13  Score=28.93  Aligned_cols=40  Identities=38%  Similarity=0.547  Sum_probs=32.2

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCCCCC
Q ss_conf             749999808898888999999999999-8799599998787768
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDPQGN   48 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~q~~   48 (265)
                      +|-++|. ++=|+|||.++.-|...+. ..+..++++|  |+|-
T Consensus        23 ~rH~aIl-g~TGsGKS~tv~vLl~~l~~~~~~~vlVfD--pHgE   63 (218)
T pfam01935        23 SRHFAIL-GSTGSGKSNTVAVLLEELLEKKGATVLIFD--PHGE   63 (218)
T ss_pred             HHHEEEE-CCCCCCHHHHHHHHHHHHHHCCCCCEEEEC--CCCC
T ss_conf             4214787-269997699999999999854799789982--8863


No 239
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=93.56  E-value=0.18  Score=28.03  Aligned_cols=34  Identities=29%  Similarity=0.407  Sum_probs=28.8

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             8749999808898888999999999999879959999
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      ..|+|+|.   |=-||||+|..+++.|...|+++.+.
T Consensus       113 ~~~iIaVT---GTnGKTTTtsli~~iL~~~g~~~~~g  146 (457)
T PRK01390        113 DAPFIAIT---GTNGKSTTTALIAHLLRQAGRDVQMG  146 (457)
T ss_pred             CCCEEEEE---CCCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             89889992---89964989999999999739986996


No 240
>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=93.56  E-value=0.069  Score=30.51  Aligned_cols=81  Identities=14%  Similarity=0.237  Sum_probs=45.6

Q ss_pred             CCCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCC-HHH
Q ss_conf             027820331013332--22210112331001111123113788875335777655432026774310020231253-100
Q gi|254780806|r  122 SDFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRN-SLS  198 (265)
Q Consensus       122 ~~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~-~~~  198 (265)
                      ..|.+-|||||+...  ..+..++..+|.+++++..+.- ++  .+..+.+... ..++.  ++. +++|++|.-. ...
T Consensus        66 ~~~~i~~IDtPGH~df~~~~~~g~~~~D~ailvVda~~G-~~--~QT~eh~~~~-~~~~~--~~i-v~iNK~D~v~~~~~  138 (192)
T cd01889          66 ENLQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDATKG-IQ--TQTAECLVIG-EILCK--KLI-VVLNKIDLIPEEER  138 (192)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEECCCC-CC--HHHHHHHHHH-HHCCC--CEE-EEEECCCCCCHHHH
T ss_conf             745899987798388998888887432652799987888-87--8999999999-98589--979-99974127881577


Q ss_pred             HHHHHHHHHHH
Q ss_conf             11268999880
Q gi|254780806|r  199 QQVVSDVRKNL  209 (265)
Q Consensus       199 ~~~~~~l~~~~  209 (265)
                      ++..+++++.+
T Consensus       139 ~~~~~~i~~~l  149 (192)
T cd01889         139 ERKIEKMKKKL  149 (192)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 241
>PRK05973 replicative DNA helicase; Provisional
Probab=93.46  E-value=0.2  Score=27.85  Aligned_cols=36  Identities=19%  Similarity=0.330  Sum_probs=31.7

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             998088988889999999999998799599998787
Q gi|254780806|r   10 TIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus        10 ~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      .+..++=|.|||+++.|+|...++.|+.|++.-+..
T Consensus        67 IIlAARPsMGKTafaLnla~~A~k~g~~v~fFSLEM  102 (237)
T PRK05973         67 VLLGARPGQGKTLLGLELAVEAMKSGRTGVFFTLEY  102 (237)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             999428988789999999999999599669996159


No 242
>PRK11545 gntK gluconate kinase 1; Provisional
Probab=93.43  E-value=0.088  Score=29.90  Aligned_cols=36  Identities=22%  Similarity=0.343  Sum_probs=27.9

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             768749999808898888999999999999879959999878
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      +....+|.|+ +=-|+||||++.-||..|   |.  -.+|.|
T Consensus         5 ~~~~~iiVVM-GVsGsGKSTig~~LA~~l---~~--~fiegD   40 (177)
T PRK11545          5 NHDHHIYVLM-GVSGSGKSAVASAVAHQL---HA--AFLDGD   40 (177)
T ss_pred             CCCCEEEEEE-CCCCCCHHHHHHHHHHHH---CC--CEECCC
T ss_conf             7887599998-479899999999999981---99--855365


No 243
>PRK06321 replicative DNA helicase; Provisional
Probab=93.42  E-value=0.22  Score=27.51  Aligned_cols=40  Identities=23%  Similarity=0.318  Sum_probs=31.0

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHC-CCCEEEEECCC
Q ss_conf             874999980889888899999999999987-99599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAI-GENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~-g~rVllID~D~   45 (265)
                      ++..| |..++=|+|||+++.|+|...|.. ++.|++.-+..
T Consensus       225 ~Gdli-viaaRPsmGKTalalnia~~~a~~~~~~v~~fSLEM  265 (472)
T PRK06321        225 PSNLM-ILAARPAMGKTALALNIAENFCFQNRLPVGIFSLEM  265 (472)
T ss_pred             CCCEE-EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCC
T ss_conf             67579-985389997799999999999985699469975779


No 244
>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=93.35  E-value=0.2  Score=27.77  Aligned_cols=36  Identities=22%  Similarity=0.322  Sum_probs=29.8

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECC
Q ss_conf             999808898888999999999999-879959999878
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLD   44 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D   44 (265)
                      +....+--|+|||+++.++++.-+ +.|.+|+-|-++
T Consensus        21 ~~LI~G~pGsGKT~la~qfl~~ga~~~ge~~lYis~e   57 (231)
T pfam06745        21 VVLITGGPGTGKTIFGLQFLYNGALEYGEPGVYVTLE   57 (231)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf             9999858972599999999999998658968999813


No 245
>PRK00139 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional
Probab=93.22  E-value=0.15  Score=28.57  Aligned_cols=38  Identities=34%  Similarity=0.489  Sum_probs=31.4

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             76874999980889888899999999999987995999987
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      .++-+||+|.   |=.||||++--++..|...|+++.++-.
T Consensus        97 ~~~l~vIgIT---GTnGKTTt~~~l~~iL~~~g~~~~~igT  134 (481)
T PRK00139         97 SDKLKLIGVT---GTNGKTTTAYLIAQILRLLGKKAALIGT  134 (481)
T ss_pred             HHCCCEEEEE---CCCCCHHHHHHHHHHHHHCCCCCEEECC
T ss_conf             4318089995---8998434999999999874986314302


No 246
>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=93.21  E-value=0.27  Score=27.07  Aligned_cols=39  Identities=23%  Similarity=0.226  Sum_probs=30.3

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHH------CCCCEEEEECCC
Q ss_conf             499998088988889999999999998------799599998787
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAA------IGENVLLIDLDP   45 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~------~g~rVllID~D~   45 (265)
                      ..|+-..+--|+|||+++..+|...+.      .+.+|+-||...
T Consensus        19 G~itEi~G~~GsGKTql~lqla~~~~~~~~~~g~~~~vvyIdtE~   63 (235)
T cd01123          19 GSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEG   63 (235)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf             879999999998499999999999842475367896299995367


No 247
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=93.20  E-value=0.18  Score=28.06  Aligned_cols=37  Identities=35%  Similarity=0.457  Sum_probs=31.1

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             87499998088988889999999999998799599998
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      +++-+++. .--|+||||+-.-++.++|..|+|+++|=
T Consensus        96 rg~SFaii-APTGvGKTTfg~~~sl~~a~kgkr~yii~  132 (1187)
T COG1110          96 RGKSFAII-APTGVGKTTFGLLMSLYLAKKGKRVYIIV  132 (1187)
T ss_pred             CCCCEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             37844898-27887654799999999875587499996


No 248
>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=93.20  E-value=0.23  Score=27.46  Aligned_cols=109  Identities=19%  Similarity=0.231  Sum_probs=53.1

Q ss_pred             CCCCEEEECCC--CCCCCCCHHHHHHHCCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             78203310133--3222210112331001111123-11378887533577765543202677431002023125310011
Q gi|254780806|r  124 FSYIFLDCPPS--FNLLTMNAMAAADSILVPLQCE-FFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       124 yD~IiiD~pp~--~~~~~~~al~aad~viip~~p~-~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      |.+.|.|+++.  +..+....+..||.++++...+ ..|+..+...++   .+.+....++++. +|-|+.|-...  + 
T Consensus        48 ~~~~i~Dt~G~e~~~~~~~~~~~~ad~~iivfd~~~~~S~~~i~~~~~---~i~~~~~~~~pii-lvgnK~Dl~~~--~-  120 (162)
T pfam00071        48 VKLQIWDTAGQERFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLE---EILRHADDNVPIV-LVGNKCDLEDQ--R-  120 (162)
T ss_pred             EEEEEEECCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHH---HHHHHCCCCCEEE-EEEECCCHHHC--C-
T ss_conf             999999789872046788998625765504234898899999999999---9998579886288-99752474651--8-


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHH
Q ss_conf             26899988085201562678688987773798579997999--89999999999999
Q gi|254780806|r  201 VVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELI  255 (265)
Q Consensus       201 ~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~  255 (265)
                                      .|+..+.-.-|...+.|.++-+.++  ..-+.|..|+++++
T Consensus       121 ----------------~i~~~e~~~~a~~~~~~y~e~Sak~g~gI~~~F~~i~~~il  161 (162)
T pfam00071       121 ----------------VVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREIL  161 (162)
T ss_pred             ----------------CCCHHHHHHHHHHHCCEEEEECCCCCCCHHHHHHHHHHHHC
T ss_conf             ----------------89999999999980997999737888299999999999967


No 249
>PRK07261 topology modulation protein; Provisional
Probab=93.18  E-value=0.17  Score=28.28  Aligned_cols=32  Identities=34%  Similarity=0.337  Sum_probs=22.4

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             4999980889888899999999999987995999987
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      ||. |+ +-+|+||||+|-.||.   ..|..+.-+|.
T Consensus         2 rI~-Ii-G~sGsGKSTlAr~L~~---~~~ip~~~LD~   33 (171)
T PRK07261          2 KIA-II-GYSGSGKSTLARFLGQ---HYNCPVLHLDQ   33 (171)
T ss_pred             EEE-EE-CCCCCCHHHHHHHHHH---HHCCCEEEECC
T ss_conf             899-98-8999868999999999---87979797022


No 250
>PRK06904 replicative DNA helicase; Validated
Probab=93.13  E-value=0.23  Score=27.43  Aligned_cols=40  Identities=33%  Similarity=0.438  Sum_probs=31.6

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHC-CCCEEEEECCC
Q ss_conf             874999980889888899999999999987-99599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAI-GENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~-g~rVllID~D~   45 (265)
                      .+..|.+ .++=|+|||+++.|+|...|.. +++|+++-+..
T Consensus       220 ~g~LiVi-AaRPsmGKTa~alnia~n~A~~~~~~V~~fSLEM  260 (472)
T PRK06904        220 PSDLIIV-AARPSMGKTTFAMNLCENAAMASEKPVLVFSLEM  260 (472)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCC
T ss_conf             5757999-7379875689999999999995599579977879


No 251
>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=93.10  E-value=0.4  Score=26.08  Aligned_cols=111  Identities=16%  Similarity=0.127  Sum_probs=59.5

Q ss_pred             CCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             7820331013332--2221011233100111112-311378887533577765543202677431002023125310011
Q gi|254780806|r  124 FSYIFLDCPPSFN--LLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       124 yD~IiiD~pp~~~--~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      +.+-|.||++.-.  .+....+..||.++++... +..|+..+..   .++.++...+++..+ -+|-|+.|-..  .+ 
T Consensus        53 ~~l~iwDt~G~e~~~~l~~~~~~~a~~~ilvydit~~~Sf~~l~~---w~~~i~~~~~~~~~i-iLVGNK~DL~~--~r-  125 (168)
T cd01866          53 IKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTS---WLEDARQHSNSNMTI-MLIGNKCDLES--RR-  125 (168)
T ss_pred             EEEEEEECCCCCCCCCCHHHHHHHHCEEEEECCCCCHHHHHHHHH---HHHHHHHHCCCCCEE-EEEEECCCHHH--CC-
T ss_conf             999999799973346255888664368999344587799999999---999999867999659-98434235454--07-


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHHH
Q ss_conf             26899988085201562678688987773798579997999--8999999999999999
Q gi|254780806|r  201 VVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQQ  257 (265)
Q Consensus       201 ~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~~  257 (265)
                                      .|+..+.-.-|...|.+.++-+.+.  ...+.|..+++++++|
T Consensus       126 ----------------~V~~~e~~~~a~~~~~~~~E~SAk~~~nV~~~F~~l~~~i~~k  168 (168)
T cd01866         126 ----------------EVSYEEGEAFAKEHGLIFMETSAKTASNVEEAFINTAKEIYEK  168 (168)
T ss_pred             ----------------CCCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHC
T ss_conf             ----------------7899999999998699999976788808899999999999739


No 252
>pfam04851 ResIII Type III restriction enzyme, res subunit.
Probab=93.05  E-value=0.23  Score=27.43  Aligned_cols=34  Identities=32%  Similarity=0.372  Sum_probs=26.0

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             749999808898888999999999999879959999
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      .+.+.+  .=-|+|||.+++.++..+...++|++++
T Consensus        19 ~~~~i~--~pTGsGKT~~~~~~i~~~~~~~~~~lvl   52 (103)
T pfam04851        19 KRGLIV--MATGSGKTLTAAKLIARLLKGKKKVLFL   52 (103)
T ss_pred             CCEEEE--ECCCCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             986999--5899987999999999998469929999


No 253
>PRK02006 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=92.98  E-value=0.24  Score=27.37  Aligned_cols=34  Identities=26%  Similarity=0.351  Sum_probs=28.3

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             8749999808898888999999999999879959999
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      ..|+|+|.   |--||||+|..+++.|...|+++.+.
T Consensus       121 ~~~iIaVT---GTnGKTTTt~li~~iL~~~g~~~~~~  154 (501)
T PRK02006        121 APKVLAIT---GTNGKTTTTSLTGLLCERAGKKVAVA  154 (501)
T ss_pred             CCCEEEEE---CCCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             87489993---89966879999999999769974652


No 254
>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=92.96  E-value=0.24  Score=27.38  Aligned_cols=35  Identities=26%  Similarity=0.445  Sum_probs=31.1

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             99808898888999999999999879959999878
Q gi|254780806|r   10 TIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus        10 ~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ...++-=|+||||+...+|..+++.|++||-|-..
T Consensus        85 vLlgGePGIGKSTLLLQia~~la~~~~~vLYvSGE  119 (372)
T cd01121          85 ILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGE  119 (372)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECH
T ss_conf             99825998868899999999998639938998245


No 255
>PRK03333 coaE dephospho-CoA kinase/unknown domain fusion protein; Provisional
Probab=92.94  E-value=0.28  Score=26.94  Aligned_cols=31  Identities=29%  Similarity=0.461  Sum_probs=21.5

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             99998088988889999999999998799599998787
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +|.+. +-=|+||||++.-|+    .+|.  .+||+|-
T Consensus         3 ~IGLT-GGIgsGKStv~~~l~----~~G~--~viDaD~   33 (394)
T PRK03333          3 RIGLT-GGIGAGKSTVSATLA----QLGA--VVVDGDV   33 (394)
T ss_pred             EEEEE-CCCCCCHHHHHHHHH----HCCC--EEEEHHH
T ss_conf             99830-675557999999999----8799--4998579


No 256
>PRK06835 DNA replication protein DnaC; Validated
Probab=92.93  E-value=0.2  Score=27.76  Aligned_cols=30  Identities=23%  Similarity=0.276  Sum_probs=18.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             889888899999999999987995999987
Q gi|254780806|r   14 QKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      +.=|+|||-++.-+|..|.++|+.|+-+-+
T Consensus       190 G~~G~GKTfLa~~IA~ell~~g~sViy~ta  219 (330)
T PRK06835        190 GNTGTGKTFLSNCIAKELLDRGKTVIYRTS  219 (330)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCEEEEEEH
T ss_conf             999998899999999999987994999629


No 257
>PRK03803 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=92.90  E-value=0.21  Score=27.73  Aligned_cols=35  Identities=26%  Similarity=0.323  Sum_probs=29.2

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             68749999808898888999999999999879959999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      -++++|+|.   |--||||+|..+++.|...|+++.+.
T Consensus       107 ~~~~~IaVT---GTnGKTTTtsli~~iL~~~g~~~~~g  141 (448)
T PRK03803        107 AKAPIVAIT---GSNAKSTVTTLVGEMAKAAGKRVAVG  141 (448)
T ss_pred             CCCCEEEEC---CCCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             789889985---89983889999999998659837994


No 258
>PRK08118 topology modulation protein; Reviewed
Probab=92.85  E-value=0.18  Score=28.13  Aligned_cols=32  Identities=31%  Similarity=0.429  Sum_probs=21.9

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             499998088988889999999999998799599998
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      |-|.|+ +-.|+||||+|-.||.   ..|..+.-+|
T Consensus         2 ~rI~Ii-G~~GsGKSTlAr~L~~---~~~ip~~~LD   33 (167)
T PRK08118          2 KKIILI-GSGGSGKSTLARQLGE---KLNIPVHHLD   33 (167)
T ss_pred             CEEEEE-CCCCCCHHHHHHHHHH---HHCCCEEECC
T ss_conf             679998-8999879999999999---8896979644


No 259
>PRK03369 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=92.84  E-value=0.27  Score=27.03  Aligned_cols=35  Identities=34%  Similarity=0.435  Sum_probs=29.1

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             87499998088988889999999999998799599998
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      ..|+|+|.   |--||||+|..+++.|...|.++.+.-
T Consensus       116 ~~~~IaVT---GTnGKTTttsli~~iL~~~g~~~~~~G  150 (487)
T PRK03369        116 PRRWLVVT---GTNGKTTTTSMLHAMLRAAGRRSVLCG  150 (487)
T ss_pred             CCCEEEEE---CCCCHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             66559997---988727899999999985899859981


No 260
>KOG1805 consensus
Probab=92.80  E-value=0.12  Score=29.16  Aligned_cols=34  Identities=38%  Similarity=0.438  Sum_probs=29.1

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             9980889888899999999999987995999987
Q gi|254780806|r   10 TIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus        10 ~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      +.+-+=-|+||||+-+.|-..|...|++||+.-.
T Consensus       688 ~LI~GMPGTGKTTtI~~LIkiL~~~gkkVLLtsy  721 (1100)
T KOG1805         688 ALILGMPGTGKTTTISLLIKILVALGKKVLLTSY  721 (1100)
T ss_pred             HEEECCCCCCCHHHHHHHHHHHHHCCCEEEEEEH
T ss_conf             2032699898122599999999973881899850


No 261
>pfam02223 Thymidylate_kin Thymidylate kinase.
Probab=92.76  E-value=0.16  Score=28.42  Aligned_cols=30  Identities=40%  Similarity=0.488  Sum_probs=25.0

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             9888899999999999987995999987877
Q gi|254780806|r   16 GGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus        16 GGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      -|+||||.+-.|+-.|...|++|... .-|.
T Consensus         5 DGsGKsTq~~~L~~~L~~~g~~v~~~-~ep~   34 (186)
T pfam02223         5 DGAGKTTQAELLKERLKEQGIKVVLT-REPG   34 (186)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCEEEEE-ECCC
T ss_conf             99899999999999999879908997-4999


No 262
>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=92.72  E-value=0.2  Score=27.84  Aligned_cols=38  Identities=24%  Similarity=0.325  Sum_probs=31.3

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             749999808898888999999999999879959999878
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      .+-+ +..+-=|+||||++-.+|..+...+..++.+++.
T Consensus        19 ~~~i-ll~GppGtGKT~la~~ia~~~~~~~~~~~~~~~~   56 (151)
T cd00009          19 PKNL-LLYGPPGTGKTTLARAIANELFRPGAPFLYLNAS   56 (151)
T ss_pred             CCEE-EEECCCCCCHHHHHHHHHHHHCCCCCCEEEEEHH
T ss_conf             9808-9989999886599999999712137982785477


No 263
>PRK01710 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=92.72  E-value=0.24  Score=27.37  Aligned_cols=35  Identities=26%  Similarity=0.275  Sum_probs=29.1

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             68749999808898888999999999999879959999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      .++|+|+|.   |==||||+|..+++.|...|+++.+.
T Consensus       115 ~~~~~IaVT---GTnGKTTTtsmi~~iL~~~g~~~~~g  149 (458)
T PRK01710        115 CPAKVFGIT---GSDGKTTTTTLIYEMLKEEGYKTWVG  149 (458)
T ss_pred             CCCCEEEEE---CCCCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             758779993---68984789999999999849975851


No 264
>COG0857 Pta BioD-like N-terminal domain of phosphotransacetylase [General function prediction only]
Probab=92.69  E-value=0.28  Score=26.99  Aligned_cols=37  Identities=32%  Similarity=0.457  Sum_probs=33.6

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             7499998088988889999999999998799599998
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      .+.+-+++.-.|+|||+++.+|+..|.++|.+|...=
T Consensus         2 ~~~l~l~p~~~~~G~tsi~lgLl~~l~~k~~kva~~k   38 (354)
T COG0857           2 SRTLLLIPTETGVGKTSISLGLLRALEQKGLKVAYFK   38 (354)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             6149984268886288999999999997073269984


No 265
>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=92.68  E-value=0.27  Score=27.06  Aligned_cols=37  Identities=46%  Similarity=0.413  Sum_probs=29.7

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHC--CCCEEEEECCC
Q ss_conf             999980889888899999999999987--99599998787
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAI--GENVLLIDLDP   45 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~--g~rVllID~D~   45 (265)
                      +|.|+ +--|+||||+|-.|...|.+.  +.+|.+|-.|.
T Consensus         1 IIGIa-G~sgSGKST~a~~l~~~l~~~~~~~~v~ii~~D~   39 (220)
T cd02025           1 IIGIA-GSVAVGKSTTARVLQALLSRWPDHPNVELITTDG   39 (220)
T ss_pred             CEEEE-CCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCC
T ss_conf             98978-8998779999999999860026999489997878


No 266
>COG4240 Predicted kinase [General function prediction only]
Probab=92.68  E-value=0.23  Score=27.48  Aligned_cols=37  Identities=32%  Similarity=0.382  Sum_probs=31.9

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCC-CCEEEEECC
Q ss_conf             9999808898888999999999999879-959999878
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIG-ENVLLIDLD   44 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g-~rVllID~D   44 (265)
                      -|..+|+--|+||||+++-|-..|+..| +||+-.-+|
T Consensus        51 li~gisGpQGSGKStls~~i~~~L~~kg~ert~~lSLD   88 (300)
T COG4240          51 LIVGISGPQGSGKSTLSALIVRLLAAKGLERTATLSLD   88 (300)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEHH
T ss_conf             39985268887653599999999997365306886645


No 267
>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]
Probab=92.65  E-value=0.24  Score=27.30  Aligned_cols=38  Identities=50%  Similarity=0.592  Sum_probs=28.3

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             87499998088988889999999999998799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +..+|.++ +=.|+||||++-.|...|..  .++.+|-.|-
T Consensus         7 ~~iiIgIa-G~SgSGKTTv~~~l~~~~~~--~~~~~I~~D~   44 (218)
T COG0572           7 KVIIIGIA-GGSGSGKTTVAKELSEQLGV--EKVVVISLDD   44 (218)
T ss_pred             CEEEEEEE-CCCCCCHHHHHHHHHHHHCC--CCCEEEECCC
T ss_conf             66999986-79877889999999998286--7524765223


No 268
>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=92.64  E-value=0.26  Score=27.18  Aligned_cols=36  Identities=31%  Similarity=0.362  Sum_probs=27.6

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             768749999808898888999999999999879959999
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      +.+.++|+|.   |=-||||+|..+++.|...|+++.+.
T Consensus       102 ~~~~~iIaVT---GTnGKTTTt~li~~iL~~~g~~~~~g  137 (438)
T PRK03806        102 EAQAPIVAIT---GSNGKSTVTTLVGEMAKAAGVNVGVG  137 (438)
T ss_pred             CCCCCEEEEE---CCCCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             2799889994---89984899999999998659975677


No 269
>KOG4658 consensus
Probab=92.57  E-value=0.13  Score=28.87  Aligned_cols=25  Identities=40%  Similarity=0.494  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             49999808898888999999999999
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALA   32 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la   32 (265)
                      .++++. +-||+||||++..+=-...
T Consensus       180 ~ivgi~-GMGGvGKTTL~~qi~N~~~  204 (889)
T KOG4658         180 GIVGIY-GMGGVGKTTLARQIFNKFD  204 (889)
T ss_pred             CEEEEE-CCCCCCHHHHHHHHHHCCH
T ss_conf             689998-8970349999999841331


No 270
>PRK06278 cobyrinic acid a,c-diamide synthase; Validated
Probab=92.52  E-value=0.77  Score=24.39  Aligned_cols=168  Identities=16%  Similarity=0.215  Sum_probs=81.4

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCC
Q ss_conf             87499998088988889999999999998799599998787768011212463334541167630257712102444444
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIP   84 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~   84 (265)
                      ..|-|...+.-.-+|||.++..|+..|..   ||.+.-.-|.          .++..++++=  . ++++.      .+.
T Consensus       243 ~kkgiiLl~TgS~SGKTFl~T~i~~kL~~---kvfv~KiGpD----------vRDIVPsLYl--l-rE~M~------ky~  300 (482)
T PRK06278        243 VKKGIILLATGSESGKTFLSTSIVSKLRG---KTFVSKIGPD----------VRDIVPSLYL--L-REPME------KYS  300 (482)
T ss_pred             CCCEEEEEECCCCCCCEEHHHHHHHHHCC---CEEEEECCCC----------HHHCCHHHHH--C-CCHHH------HCC
T ss_conf             99659998437877743116778887506---4899860886----------6652524631--0-42122------046


Q ss_pred             CEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEC--CCCCCCC----CCHHHHH---H-HCCCCCC
Q ss_conf             200014887457750001232222102333224765102782033101--3332222----1011233---1-0011111
Q gi|254780806|r   85 NLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCP--PSFNLLT----MNAMAAA---D-SILVPLQ  154 (265)
Q Consensus        85 ~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~p--p~~~~~~----~~al~aa---d-~viip~~  154 (265)
                      .+.+  ++.              ...-+.+++...-..+|||+||.--  ...+.+.    .++-..|   . -+++|+.
T Consensus       301 SIkI--~~r--------------GW~~~~efle~vk~sdYd~~iiEGVMgafTg~Ln~k~~YS~aeIak~lg~PvyivS~  364 (482)
T PRK06278        301 SIKI--SDR--------------GWMEPSEFLEFVKNSDYDNYIIEGVMGAFTGALNKKNPYSGAEIAKALGFPVYIVSS  364 (482)
T ss_pred             CEEE--CCC--------------CCCCHHHHHHHHHCCCCCEEEEEHHHHHHHHHHCCCCCCCHHHHHHHCCCCEEEEEC
T ss_conf             1685--467--------------876899999997347987899850478888875057887689999855998899942


Q ss_pred             CCCHHHHHHHHH-HHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf             231137888753-3577765543202677431002023125310011268999880852015
Q gi|254780806|r  155 CEFFALEGLSQL-LETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYN  215 (265)
Q Consensus       155 p~~~s~~~~~~~-~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~  215 (265)
                      .+...++++.-- +.....+ +  .....+.|+++|++=. ... -+-...+.+.++..+++
T Consensus       365 cnksGIEgAfve~~ay~slL-k--~~Gv~v~giILNKvYn-~~i-fekvk~~~~~~~i~~~~  421 (482)
T PRK06278        365 CSKGGIEGAFVELMAYYSLL-K--EMGVNVAGIILNKVYN-MEI-FEKVKKIASNLNINVIG  421 (482)
T ss_pred             CCCCCCHHHHHHHHHHHHHH-H--HCCCCEEEEEEEEECC-HHH-HHHHHHHHHHCCCEEEE
T ss_conf             55566047899999999999-8--6697358899741125-889-99999999865952986


No 271
>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family; InterPro: IPR006001    This family of proteins includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases (IPR000577 from INTERPRO).; GO: 0016301 kinase activity, 0005975 carbohydrate metabolic process.
Probab=92.50  E-value=0.081  Score=30.11  Aligned_cols=39  Identities=31%  Similarity=0.341  Sum_probs=27.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEEEECC---CCCCCCHH
Q ss_conf             8898888999999999999879959999878---77680112
Q gi|254780806|r   14 QKGGVGKTTTAINLSTALAAIGENVLLIDLD---PQGNASTG   52 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA~~la~~g~rVllID~D---~q~~~~~~   52 (265)
                      +=-|+||||++..|+..|.+-=-..--||.|   |++|...|
T Consensus         5 GvaG~GKs~~a~~l~~~lg~iyPd~~yieGDdLHP~~Ni~KM   46 (175)
T TIGR01313         5 GVAGSGKSTIASALAHRLGDIYPDAKYIEGDDLHPAANIEKM   46 (175)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHH
T ss_conf             027862889999999985431578875688666787779873


No 272
>COG1072 CoaA Panthothenate kinase [Coenzyme metabolism]
Probab=92.49  E-value=0.41  Score=25.98  Aligned_cols=43  Identities=30%  Similarity=0.284  Sum_probs=33.4

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCC--EEEEECCC
Q ss_conf             76874999980889888899999999999987995--99998787
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGEN--VLLIDLDP   45 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~r--VllID~D~   45 (265)
                      +.+++.|.-..+-=||||||++-.|+..+++.+..  |-+|=+|.
T Consensus        78 ~~~~pfIIgiaGsvavGKST~ar~L~~ll~~~~~~~~v~lvpmDG  122 (283)
T COG1072          78 NQQRPFIIGIAGSVAVGKSTTARILQALLSRWPESPKVDLVTMDG  122 (283)
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCC
T ss_conf             888887999605766557789999999996388987337871454


No 273
>TIGR00437 feoB ferrous iron transport protein B; InterPro: IPR003373 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 and may play a role in the transport of ferrous iron. 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 .; GO: 0005525 GTP binding, 0015093 ferrous iron transmembrane transporter activity, 0015684 ferrous iron transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=92.46  E-value=0.063  Score=30.74  Aligned_cols=85  Identities=16%  Similarity=0.210  Sum_probs=47.3

Q ss_pred             CCCCEEEECCCCCCCCCCH-----------HHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEE
Q ss_conf             7820331013332222101-----------12331001111123113788875335777655432026774310020231
Q gi|254780806|r  124 FSYIFLDCPPSFNLLTMNA-----------MAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFD  192 (265)
Q Consensus       124 yD~IiiD~pp~~~~~~~~a-----------l~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~  192 (265)
                      .|+=|||+|+-+|--+.+.           -+.+|.+|.|+..+... |++.-.++.++     .+.  +.+ +++|++|
T Consensus        41 ~~i~ivDLPG~YSL~~~S~~dE~v~~dyl~~e~~DLv~nVVDA~nLE-RnL~LTLQL~E-----~G~--p~i-~~LN~~D  111 (733)
T TIGR00437        41 EDIEIVDLPGIYSLTTFSGLDEKVARDYLLNEKPDLVVNVVDASNLE-RNLYLTLQLLE-----LGI--PMI-LALNLVD  111 (733)
T ss_pred             EEEEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEEEECHHHHH-HHHHHHHHHHH-----HCC--HHH-HHHHHHH
T ss_conf             27899844873005899874279998997538996799972566777-89999999997-----162--585-6872678


Q ss_pred             CCCHHH-HHHHHHHHHHHCCCCCCCC
Q ss_conf             253100-1126899988085201562
Q gi|254780806|r  193 SRNSLS-QQVVSDVRKNLGGKVYNTV  217 (265)
Q Consensus       193 ~~~~~~-~~~~~~l~~~~~~~v~~~~  217 (265)
                      ...+.. +--.+.|.+.+|.+|.++.
T Consensus       112 eA~k~GI~Id~~~Lee~LGvPVv~~~  137 (733)
T TIGR00437       112 EAEKKGIRIDEEKLEERLGVPVVPTS  137 (733)
T ss_pred             HHHHCCCEECHHHHHHHCCCCEEEEE
T ss_conf             99772963125777543386525653


No 274
>PRK00698 tmk thymidylate kinase; Validated
Probab=92.41  E-value=0.47  Score=25.67  Aligned_cols=37  Identities=30%  Similarity=0.415  Sum_probs=32.2

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             87499998088988889999999999998799599998
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      +++-|+|- +=-|+||||.+--|+-.|...|++|.+..
T Consensus         2 kG~fIviE-GiDGsGKsTq~~~L~~~L~~~g~~v~~t~   38 (204)
T PRK00698          2 RGMFITIE-GIDGAGKSTQIELLAERLEEQGRDVVFTR   38 (204)
T ss_pred             CCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             83199998-89999899999999999996799789986


No 275
>PRK00683 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=92.27  E-value=0.19  Score=27.92  Aligned_cols=35  Identities=29%  Similarity=0.430  Sum_probs=29.8

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             68749999808898888999999999999879959999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      .+.++|+|.   |--||||+|..++..|...|+++.+.
T Consensus       100 ~~~~~IaIT---GTNGKTTTt~ll~~iL~~~g~~~~~~  134 (418)
T PRK00683        100 QRYPSLGIT---GSTGKTTTILFLEHLLRTLGIPAFAM  134 (418)
T ss_pred             CCCCEEEEE---CCCCCEEHHHHHHHHHHHCCCCCEEE
T ss_conf             479879997---68986609999999998679981888


No 276
>PRK13764 ATPase; Provisional
Probab=92.27  E-value=0.19  Score=27.92  Aligned_cols=39  Identities=26%  Similarity=0.322  Sum_probs=29.6

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             6874999980889888899999999999987995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      .+++=| ++++.-|+||||++.+||-+++.+|+=|=-+..
T Consensus       257 ~~a~Gi-lIaG~PGaGKsTfaqalA~~~~~~g~iVKTmEs  295 (605)
T PRK13764        257 ERAEGI-LIAGAPGAGKSTFAQALAEFYADMGKIVKTMES  295 (605)
T ss_pred             HCCCEE-EEECCCCCCHHHHHHHHHHHHHHCCCEEEECCC
T ss_conf             336649-997799997789999999999847978983248


No 277
>PRK04663 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=92.18  E-value=0.29  Score=26.85  Aligned_cols=35  Identities=26%  Similarity=0.250  Sum_probs=28.8

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             68749999808898888999999999999879959999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      ...++|+|.   |--||||+|..+++.|...|.++.+.
T Consensus       106 ~~~~iIaVT---GTnGKTTTtsli~~iL~~~g~~~~~g  140 (438)
T PRK04663        106 VDKPVIAIT---GSNGKSTVTDLTGVMAKAAGVKVAVG  140 (438)
T ss_pred             CCCCEEEEE---CCCCHHHHHHHHHHHHHHCCCCCEEE
T ss_conf             589789994---89982899999999998289970687


No 278
>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=92.17  E-value=0.54  Score=25.29  Aligned_cols=111  Identities=16%  Similarity=0.160  Sum_probs=54.9

Q ss_pred             EEEECCCCC--CCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHH
Q ss_conf             331013332--2221011233100111112-3113788875335777655432026774310020231253100112689
Q gi|254780806|r  128 FLDCPPSFN--LLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSD  204 (265)
Q Consensus       128 iiD~pp~~~--~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~  204 (265)
                      |.||++.-.  .+....+..||.+|++... +..|+..+....+.+..++.....++++ -+|-|+.|-..  .++    
T Consensus        51 iwDtaG~e~~~~l~~~~~r~a~~~ilVydvtd~~SF~~l~~w~~~i~~~~~~~~~~~pi-iLVGNK~Dl~~--~r~----  123 (190)
T cd04144          51 VLDTAGQEEYTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPI-MIVGNKCDKVY--ERE----  123 (190)
T ss_pred             EEECCCCCCHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCEE-EECCCCCCHHH--CCC----
T ss_conf             99899973116788998236765899972797789999999999999985337999528-95145535033--057----


Q ss_pred             HHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHHHH
Q ss_conf             9988085201562678688987773798579997999--89999999999999999
Q gi|254780806|r  205 VRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQQE  258 (265)
Q Consensus       205 l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~~~  258 (265)
                                   |+..+.-.-|...|.+.++-+-+.  ..-+.|..|+++|.++.
T Consensus       124 -------------V~~~e~~~~a~~~~~~~~E~SAk~~~nV~e~F~~l~~~i~~~~  166 (190)
T cd04144         124 -------------VSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLVRALRQQR  166 (190)
T ss_pred             -------------CCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             -------------8999999999980998999735888097999999999999877


No 279
>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=92.11  E-value=0.36  Score=26.35  Aligned_cols=39  Identities=31%  Similarity=0.280  Sum_probs=31.0

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             6874999980889888899999999999987995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      +.+.-|.+ ++.=||||||++.-+|-.|...|++|.=+=+
T Consensus         3 ~~~mki~I-TG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t   41 (179)
T COG1618           3 KMAMKIFI-TGRPGVGKTTLVLKIAEKLREKGYKVGGFIT   41 (179)
T ss_pred             CCCEEEEE-ECCCCCCHHHHHHHHHHHHHHCCCEEEEEEE
T ss_conf             75459998-6799845899999999999855966513983


No 280
>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=92.05  E-value=0.11  Score=29.22  Aligned_cols=78  Identities=13%  Similarity=0.153  Sum_probs=39.9

Q ss_pred             CCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             27820331013332--2221011233100111112311378887533577765543202677431002023125310011
Q gi|254780806|r  123 DFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       123 ~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      .+.+.++|||+.-.  .+...++..+|.+++++..+..-.....   +.++.++. .+.  ++ -+++|++|.......+
T Consensus        49 ~~~i~~iDTPGh~~f~~~~~~~~~~aD~~ilvvda~~g~~~~~~---~~~~~l~~-~~~--p~-ivviNKiD~~~~~~~~  121 (168)
T cd01887          49 IPGITFIDTPGHEAFTNMRARGASLTDIAILVVAADDGVMPQTI---EAIKLAKA-ANV--PF-IVALNKIDKPNANPER  121 (168)
T ss_pred             CCEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHH---HHHHHHHH-CCC--CE-EEEEECCCCCCCCHHH
T ss_conf             87189998998167799999998626889999864667545899---99999987-699--78-9999893089879899


Q ss_pred             HHHHHHH
Q ss_conf             2689998
Q gi|254780806|r  201 VVSDVRK  207 (265)
Q Consensus       201 ~~~~l~~  207 (265)
                      +..++.+
T Consensus       122 v~~~l~~  128 (168)
T cd01887         122 VKNELSE  128 (168)
T ss_pred             HHHHHHH
T ss_conf             9999999


No 281
>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=92.04  E-value=0.2  Score=27.84  Aligned_cols=26  Identities=31%  Similarity=0.408  Sum_probs=21.2

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             499998088988889999999999998
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAA   33 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~   33 (265)
                      ++|.+ .+.-|+||||+.-.+|...++
T Consensus         1 r~i~i-~G~aG~GKTtll~kl~~~wa~   26 (165)
T pfam05729         1 RTVIL-QGEAGSGKTTLLQKLALLWAQ   26 (165)
T ss_pred             CEEEE-ECCCCCCHHHHHHHHHHHHHC
T ss_conf             98999-827989899999999999986


No 282
>cd04111 Rab39 Rab39 subfamily.  Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines.  It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.   Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
Probab=91.95  E-value=0.91  Score=23.98  Aligned_cols=112  Identities=13%  Similarity=0.119  Sum_probs=58.3

Q ss_pred             EEEECCCC--CCCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHH
Q ss_conf             33101333--22221011233100111112-3113788875335777655432026774310020231253100112689
Q gi|254780806|r  128 FLDCPPSF--NLLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSD  204 (265)
Q Consensus       128 iiD~pp~~--~~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~  204 (265)
                      |.||++.-  ..++..-...|+.+|++..- +..|+..+..   .+++++...++...+.-+|-|+.|-..  .|     
T Consensus        56 IwDTaGqe~~~si~~~yyr~a~g~ilVyDvt~~~SF~~l~~---W~~ei~~~~~~~~~~iiLVGNK~DL~~--~R-----  125 (211)
T cd04111          56 LWDTAGQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHD---WLEEARSHIQPHRPVFILVGHKCDLES--QR-----  125 (211)
T ss_pred             EEECCCCCCCCCCHHHHHHHCCEEEEEECCCCHHHHHHHHH---HHHHHHHHCCCCCCEEEEEEECCCHHH--HC-----
T ss_conf             99798863456442877421244689714777799999999---999999974988853898874231285--67-----


Q ss_pred             HHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHHHHHHH
Q ss_conf             9988085201562678688987773798579997999--89999999999999999867
Q gi|254780806|r  205 VRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQQERHR  261 (265)
Q Consensus       205 l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~~~~~~  261 (265)
                                  .|...+.-.-|...|.+.++-+-++  ..-+.|..||++|+++.+.+
T Consensus       126 ------------~Vs~ee~~~~A~~~~~~f~EtSAK~g~nV~e~F~~la~~i~~~~~~~  172 (211)
T cd04111         126 ------------QVTREEAEKLAKDLGMKYIETSARTGDNVEEAFELLTQEIYERIKRG  172 (211)
T ss_pred             ------------CCCHHHHHHHHHHHCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             ------------88999999999983997999759998198999999999999998738


No 283
>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=91.87  E-value=0.068  Score=30.56  Aligned_cols=64  Identities=13%  Similarity=0.187  Sum_probs=39.0

Q ss_pred             CCCCCEEEECCCC--CCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEC
Q ss_conf             2782033101333--2222101123310011111231137888753357776554320267743100202312
Q gi|254780806|r  123 DFSYIFLDCPPSF--NLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDS  193 (265)
Q Consensus       123 ~yD~IiiD~pp~~--~~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~  193 (265)
                      .|-+=+||||+..  +..+..++.++|.+++++....--..+++..++   .   ....++++. +++|++|.
T Consensus        72 ~~~inlIDTPGH~dF~~ev~~al~~~DgailVVDa~eGv~~qT~~vl~---~---a~~~~l~~i-l~iNKiDR  137 (222)
T cd01885          72 EYLINLIDSPGHVDFSSEVTAALRLCDGALVVVDAVEGVCVQTETVLR---Q---ALKERVKPV-LVINKIDR  137 (222)
T ss_pred             CEEEEEEECCCHHHHHHHHHHHHHHCCEEEEEECCCCCCCHHHHHHHH---H---HHHCCCCEE-EEEECCCC
T ss_conf             638999728856989999999998568179961045785778999999---9---998599979-99989036


No 284
>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=91.79  E-value=0.35  Score=26.39  Aligned_cols=37  Identities=22%  Similarity=0.351  Sum_probs=33.2

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             99998088988889999999999998799599998787
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      ||+|. +--|+||||+.-.+...+.+.|-+..+|.+|-
T Consensus         1 IIaVt-GsSGAGtsTv~r~f~~IF~re~v~a~vIegD~   37 (277)
T cd02029           1 VIAVT-GSSGAGTTTVKRAFEHIFAREGIHPAVVEGDS   37 (277)
T ss_pred             CEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             98993-38888478799999998720588528996786


No 285
>PRK12339 2-phosphoglycerate kinase; Provisional
Probab=91.66  E-value=0.2  Score=27.75  Aligned_cols=25  Identities=28%  Similarity=0.252  Sum_probs=19.7

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             74999980889888899999999999
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTAL   31 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~l   31 (265)
                      +++| +..+--||||||++..||..|
T Consensus         3 ~~ii-ligG~sGvGKStla~~lA~rl   27 (197)
T PRK12339          3 STIH-FIGGIPGVGKTSISGYIARHR   27 (197)
T ss_pred             CEEE-EEECCCCCCHHHHHHHHHHHC
T ss_conf             4799-985799887899999999974


No 286
>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).
Probab=91.59  E-value=0.48  Score=25.61  Aligned_cols=34  Identities=35%  Similarity=0.339  Sum_probs=29.2

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             99980889888899999999999987995999987
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      |+|- +=-|+||||.+-.|+-.|...|++|.+..-
T Consensus         3 IviE-G~dGsGKsT~~~~L~~~L~~~g~~v~~~~e   36 (200)
T cd01672           3 IVFE-GIDGAGKTTLIELLAERLEARGYEVVLTRE   36 (200)
T ss_pred             EEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             9998-998999999999999999977993899869


No 287
>PRK01438 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=91.58  E-value=0.43  Score=25.88  Aligned_cols=35  Identities=29%  Similarity=0.357  Sum_probs=28.3

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             68749999808898888999999999999879959999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      +.+++|+|.   |=-||||+|..+++.|...|+++.++
T Consensus       120 ~~~~~IaVT---GTnGKTTTtsli~~iL~~~g~~~~~~  154 (481)
T PRK01438        120 TPAPWLAVT---GTNGKTTTVQMLASILRAAGLRAAAV  154 (481)
T ss_pred             CCCCEEEEE---CCCCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             888789993---89974609999999999669970799


No 288
>PRK01368 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=91.54  E-value=0.42  Score=25.93  Aligned_cols=35  Identities=31%  Similarity=0.389  Sum_probs=29.0

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             68749999808898888999999999999879959999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      +..|+|+|.   |=-||||+|..+++.|...|+++.+.
T Consensus       102 ~~~~~IaIT---GTnGKTTTt~li~~iL~~~g~~~~~~  136 (450)
T PRK01368        102 KNLKFIAIT---GTNGKSTTTALISHILNSNGLDYPVA  136 (450)
T ss_pred             CCCCEEEEE---CCCCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             799779996---89997489999999999759962896


No 289
>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=91.50  E-value=0.23  Score=27.51  Aligned_cols=37  Identities=30%  Similarity=0.242  Sum_probs=31.0

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             9998088988889999999999998799599998787
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +.+.++=-|+||||.+-+||..|.+.+.+|..+-.|-
T Consensus         3 LiIlTGyPgsGKTtfakeLak~L~~~i~~vi~l~kdy   39 (261)
T COG4088           3 LIILTGYPGSGKTTFAKELAKELRQEIWRVIHLEKDY   39 (261)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf             6998269998801789999999997200112132014


No 290
>PRK06217 hypothetical protein; Validated
Probab=91.48  E-value=0.27  Score=27.01  Aligned_cols=31  Identities=35%  Similarity=0.400  Sum_probs=21.7

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             9999808898888999999999999879959999878
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      .|-|+ +-+|+||||++..||..+   |..  .+|+|
T Consensus         3 rI~i~-G~sGsGkSTla~~La~~l---~~~--~~~lD   33 (185)
T PRK06217          3 RIHIT-GASGSGTTTLGAALAEAL---DLP--HLDTD   33 (185)
T ss_pred             EEEEE-CCCCCCHHHHHHHHHHHH---CCC--EEECC
T ss_conf             79997-899887899999999975---989--68645


No 291
>PRK13721 conjugal transfer ATP-binding protein TraC; Provisional
Probab=91.47  E-value=0.44  Score=25.83  Aligned_cols=34  Identities=21%  Similarity=0.263  Sum_probs=30.1

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             9808898888999999999999879959999878
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ++.++-|+|||.++-.|+...-.+|-+|.+||..
T Consensus       478 ~I~g~SGsGKSf~~q~l~~~~~~~G~~V~IID~G  511 (864)
T PRK13721        478 AVCGTSGAGKTGLIQPLIRSVLDSGGFAVVFDMG  511 (864)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             9982899868999999999998579979999699


No 292
>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=91.46  E-value=0.12  Score=29.19  Aligned_cols=70  Identities=17%  Similarity=0.189  Sum_probs=40.2

Q ss_pred             CCCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHH-H---HHHHHHHHHHHHHHHHCCCCCCCCCCCEEECC
Q ss_conf             027820331013332--2221011233100111112311378-8---87533577765543202677431002023125
Q gi|254780806|r  122 SDFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALE-G---LSQLLETVEEVRRTVNSALDIQGIILTMFDSR  194 (265)
Q Consensus       122 ~~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~-~---~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~  194 (265)
                      +.+.|.|||+|+.-.  ..+..++..+|..|+++....-.++ +   -.+..+++... ..++.  +.+=+.+|++|.-
T Consensus        75 ~~~~~~iiDtPGH~df~~~mi~g~~~ad~ailvvda~~g~~e~g~~~~~QTreH~~l~-~~lGi--k~iIVavNKMD~v  150 (219)
T cd01883          75 EKYRFTILDAPGHRDFVPNMITGASQADVAVLVVDARKGEFEAGFEKGGQTREHALLA-RTLGV--KQLIVAVNKMDDV  150 (219)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCCCHHHHHHHHH-HHCCC--CEEEEEEECCCCC
T ss_conf             9936999878972667889998775316689999857675103667776599999999-98499--7489999875368


No 293
>PRK02472 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=91.43  E-value=0.36  Score=26.32  Aligned_cols=35  Identities=40%  Similarity=0.479  Sum_probs=26.6

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             68749999808898888999999999999879959999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      .++++|+|.   |=-||||+|..+++.|...|+++.+.
T Consensus       110 ~~~~~IaVT---GTnGKTTTt~ll~~iL~~~g~~~~~~  144 (450)
T PRK02472        110 SEAPIIGIT---GSNGKTTTTTLIAEMLNAGGQHGLLA  144 (450)
T ss_pred             CCCCEEEEE---CCCCCCHHHHHHHHHHHHCCCCEEEE
T ss_conf             159789982---79997319999999999749973999


No 294
>TIGR00041 DTMP_kinase thymidylate kinase; InterPro: IPR000062   Thymidylate kinase (2.7.4.9 from EC; dTMP kinase) catalyzes the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium:   ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate    Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages. ; GO: 0004798 thymidylate kinase activity, 0005524 ATP binding, 0006233 dTDP biosynthetic process, 0006235 dTTP biosynthetic process.
Probab=91.40  E-value=0.22  Score=27.56  Aligned_cols=28  Identities=36%  Similarity=0.345  Sum_probs=24.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHH-CCCCEEEE
Q ss_conf             88988889999999999998-79959999
Q gi|254780806|r   14 QKGGVGKTTTAINLSTALAA-IGENVLLI   41 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA~~la~-~g~rVllI   41 (265)
                      +==|+||||.+--|+..|.. .|++|+..
T Consensus         9 GiDGaGKTT~~~~l~~~l~~l~g~~~~~t   37 (211)
T TIGR00041         9 GIDGAGKTTQLNLLKKLLKELEGYKVLFT   37 (211)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             11587589999999999775138347887


No 295
>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=91.39  E-value=0.18  Score=28.08  Aligned_cols=66  Identities=14%  Similarity=0.086  Sum_probs=38.8

Q ss_pred             CCCCCCEEEECCCCCC--CCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEC
Q ss_conf             0278203310133322--22101123310011111231137888753357776554320267743100202312
Q gi|254780806|r  122 SDFSYIFLDCPPSFNL--LTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDS  193 (265)
Q Consensus       122 ~~yD~IiiD~pp~~~~--~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~  193 (265)
                      +.+.|+|||+|+...-  .+..+...+|.+++++....--..   +..+++..++ .++.  +.+=+++|++|.
T Consensus        75 ~~~~~~iiDtPGH~dfi~nmi~gas~aD~ailVVda~~G~~~---QT~eh~~~~~-~lgi--~~iIv~vNKmD~  142 (208)
T cd04166          75 PKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGVLE---QTRRHSYILS-LLGI--RHVVVAVNKMDL  142 (208)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCH---HHHHHHHHHH-HCCC--CEEEEEEECCCC
T ss_conf             992699987896288999999998637747999975888727---8999999999-7499--839999988576


No 296
>PRK09554 feoB ferrous iron transport protein B; Reviewed
Probab=91.34  E-value=0.11  Score=29.22  Aligned_cols=20  Identities=30%  Similarity=0.277  Sum_probs=9.9

Q ss_pred             EEEEECCCCCCCHHHHHHHHH
Q ss_conf             999980889888899999999
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLS   28 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA   28 (265)
                      +|+.. +-=-|||||+=-.|.
T Consensus         5 ~IALv-GNPN~GKSTLFN~LT   24 (772)
T PRK09554          5 TIGLI-GNPNSGKTTLFNQLT   24 (772)
T ss_pred             EEEEE-CCCCCCHHHHHHHHH
T ss_conf             69988-899878999999986


No 297
>TIGR01082 murC UDP-N-acetylmuramate--alanine ligase; InterPro: IPR005758   The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:    (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.    Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC)  and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .    This entry represents UDP-N-acetylmuramate-alanine ligase (MurC). MurC is an essential, cytoplasmic peptidoglycan biosynthetic enzyme, catalyzes the ATP-dependent ligation of L-alanine (Ala) and UDP-N-acetylmuramic acid (UNAM) to form UDP-N-acetylmuramyl-L-alanine (UNAM-Ala). The enzyme is a nonribosomal peptide ligase which utilises ATP to form an amide bond between L-alanine and UNAM.1 Mechanistic studies on the Escherichia coli MurC enzyme using oxygen isotope analyses demonstrated that the enzyme-catalyzed reaction proceeds through an acyl phosphate UNAM intermediate prior to L-alanine addition.; GO: 0005524 ATP binding, 0008763 UDP-N-acetylmuramate-L-alanine ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=91.29  E-value=0.29  Score=26.83  Aligned_cols=40  Identities=30%  Similarity=0.449  Sum_probs=31.2

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCC-CEEEEECC
Q ss_conf             987687499998088988889999999999998799-59999878
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGE-NVLLIDLD   44 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~-rVllID~D   44 (265)
                      |..|+ ..|+|+   |==||||+|+.||..+...|. .+.+|-.-
T Consensus       104 ~~~~k-~~iaVa---GtHGKTTTTamia~~~~~aGLdPt~~~GG~  144 (491)
T TIGR01082       104 MRKRK-ESIAVA---GTHGKTTTTAMIAVILKEAGLDPTVIVGGE  144 (491)
T ss_pred             HHHHC-CEEEEE---CCCCCHHHHHHHHHHHHHCCCCCCEEECCC
T ss_conf             86208-707998---368725689999999984499976898664


No 298
>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=91.27  E-value=0.095  Score=29.70  Aligned_cols=63  Identities=14%  Similarity=0.261  Sum_probs=39.1

Q ss_pred             CCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEC
Q ss_conf             7820331013332--222101123310011111231137888753357776554320267743100202312
Q gi|254780806|r  124 FSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDS  193 (265)
Q Consensus       124 yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~  193 (265)
                      |-+-+||||+..+  ..+..++.++|.+++++....--...+++.   ++..   ...++++. +++|++|.
T Consensus        71 ~~inlIDTPGH~dF~~ev~~al~~~DgailVVDa~eGv~~qT~~~---l~~a---~~~~l~~i-lviNKiDR  135 (213)
T cd04167          71 YLFNIIDTPGHVNFMDEVAAALRLSDGVVLVVDVVEGVTSNTERL---IRHA---ILEGLPIV-LVINKIDR  135 (213)
T ss_pred             EEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHH---HHHH---HHCCCCEE-EEEECCCC
T ss_conf             578778898724179999988863776799998788875779999---9999---98699989-99988234


No 299
>COG2759 MIS1 Formyltetrahydrofolate synthetase [Nucleotide transport and metabolism]
Probab=91.15  E-value=0.18  Score=28.10  Aligned_cols=51  Identities=27%  Similarity=0.448  Sum_probs=35.6

Q ss_pred             CCCCEEEEEEC---CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCC
Q ss_conf             76874999980---889888899999999999987995999987877680112124
Q gi|254780806|r    3 EKKSRIITIAN---QKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGI   55 (265)
Q Consensus         3 ~~~~kvI~v~s---~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~   55 (265)
                      ++.+|-|.|..   .--|-||||+|+.|+-+|.+.||++.+-==  |.|+.-.||+
T Consensus        49 k~~gKlILVTaitPTPaGEGKsTttiGL~~al~~lgK~~i~alR--ePSlGP~fGi  102 (554)
T COG2759          49 KPDGKLILVTAITPTPAGEGKTTTTIGLVDALNKLGKKAIIALR--EPSLGPVFGI  102 (554)
T ss_pred             CCCCEEEEEEECCCCCCCCCCCEEEEHHHHHHHHCCCHHEEEEC--CCCCCCCCCC
T ss_conf             88860899982578888888612542489999861860058860--5776873144


No 300
>PRK07933 thymidylate kinase; Validated
Probab=91.04  E-value=0.32  Score=26.61  Aligned_cols=34  Identities=35%  Similarity=0.469  Sum_probs=28.8

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             99980889888899999999999987995999987
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      |+| -+==|+||||-+-.|+-.|...|++|.+...
T Consensus         3 I~f-EGiDGsGKSTq~~~L~~~L~~~g~~v~~~re   36 (213)
T PRK07933          3 IAI-EGVDGAGKRTLTEALRAALEAAGRSVATLAF   36 (213)
T ss_pred             EEE-ECCCCCCHHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf             999-8899998999999999999977990799846


No 301
>PRK05986 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated
Probab=91.04  E-value=0.24  Score=27.31  Aligned_cols=39  Identities=26%  Similarity=0.415  Sum_probs=31.1

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             76874999980889888899999999999987995999987
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      ++++-|...+  =-|=||||.|..+|.-.+-+|+||++|-+
T Consensus        20 ~~kGli~Vyt--G~GKGKTTAAlGlalRA~G~G~rV~ivQF   58 (190)
T PRK05986         20 EEKGLLIVHT--GNGKGKSTAAFGMALRAVGHGKKVGVVQF   58 (190)
T ss_pred             CCCCEEEEEE--CCCCCHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             4686799980--69987188999999998369988999999


No 302
>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=91.03  E-value=0.27  Score=27.07  Aligned_cols=88  Identities=20%  Similarity=0.376  Sum_probs=53.0

Q ss_pred             CCCCE-EEEEECCCCCCCHHHHHHHHHHHHHH----------------CCCC-----------------------EEEEE
Q ss_conf             76874-99998088988889999999999998----------------7995-----------------------99998
Q gi|254780806|r    3 EKKSR-IITIANQKGGVGKTTTAINLSTALAA----------------IGEN-----------------------VLLID   42 (265)
Q Consensus         3 ~~~~k-vI~v~s~KGGvGKTT~a~nlA~~la~----------------~g~r-----------------------VllID   42 (265)
                      .-+++ |+||. +==|||||+++-.+|.+|-+                +|+|                       |.|||
T Consensus       446 ~~~GpqIlClv-GPPGVGKTSlg~SIA~ALnRkFvR~SlGG~~DeAEIrGHRRTYvGAMPGriiQ~lk~~~t~NPl~LlD  524 (941)
T TIGR00763       446 KMKGPQILCLV-GPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTKNPLILLD  524 (941)
T ss_pred             CCCCCEEEEEE-CCCCCCHHHHHHHHHHHHCCEEEEEEECCCEEHHHCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEE
T ss_conf             88887678720-72695422278999999688049995267220311278643203467257899987604158806862


Q ss_pred             -C-------CCCCCCCHHHC--CCCCCCCCCEEEEEE-CCCCHHHCC--CCCCCCCEEECCCC
Q ss_conf             -7-------87768011212--463334541167630-257712102--44444420001488
Q gi|254780806|r   43 -L-------DPQGNASTGLG--IELYDRKYSSYDLLI-EEKNINQIL--IQTAIPNLSIIPST   92 (265)
Q Consensus        43 -~-------D~q~~~~~~l~--~~~~~~~~ti~~~l~-~~~~l~~~i--~~~~~~~l~iipa~   92 (265)
                       -       |-||+.+..|.  +||.. ...+.|... -+.||++++  +=...-.+|=||..
T Consensus       525 EIDK~~~~~~~~GDPaSALLEvLDPEQ-N~~F~DHYldvp~DLS~V~CyFi~TAN~~d~IP~P  586 (941)
T TIGR00763       525 EIDKIGLKSSFRGDPASALLEVLDPEQ-NNAFSDHYLDVPFDLSKVLCYFIATANSIDTIPRP  586 (941)
T ss_pred             EEEEECCCCCCCCCHHHHHHHHCCHHH-CCCCCCCCCCCCCCHHHHHHHEEECCCCCCCCCCC
T ss_conf             022001678865563788864128643-60425530023400420021000244757677722


No 303
>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]
Probab=91.01  E-value=0.25  Score=27.20  Aligned_cols=38  Identities=32%  Similarity=0.316  Sum_probs=27.5

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             6874999980889888899999999999987995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      .+++++++. +.-|+||||+--.|+..+.-.+=.|. +|.
T Consensus        26 ~~G~i~~ii-GpNG~GKSTLLk~l~~~l~p~~G~V~-l~g   63 (258)
T COG1120          26 PKGEITGIL-GPNGSGKSTLLKCLAGLLKPKSGEVL-LDG   63 (258)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHCCCCCCCCEEE-ECC
T ss_conf             599799998-99888999999998656788887799-999


No 304
>PRK13973 thymidylate kinase; Provisional
Probab=91.00  E-value=0.74  Score=24.51  Aligned_cols=39  Identities=36%  Similarity=0.482  Sum_probs=32.1

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             87499998088988889999999999998799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +++-|+|= +=-|+||||.+-.|+-.|...|.+|.+.-- |
T Consensus         2 kG~fIv~E-GiDGsGKsTq~~~L~~~L~~~g~~v~~tre-P   40 (216)
T PRK13973          2 RGRFITFE-GGEGAGKSTQIRLLAERLRAAGYDVLVTRE-P   40 (216)
T ss_pred             CCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEEC-C
T ss_conf             82499988-999998999999999999977995799409-8


No 305
>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=90.95  E-value=1.1  Score=23.40  Aligned_cols=109  Identities=17%  Similarity=0.066  Sum_probs=55.4

Q ss_pred             CCCEEEECCCC--CCCCCCHHHHHHHCCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHH
Q ss_conf             82033101333--222210112331001111123-113788875335777655432026774310020231253100112
Q gi|254780806|r  125 SYIFLDCPPSF--NLLTMNAMAAADSILVPLQCE-FFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQV  201 (265)
Q Consensus       125 D~IiiD~pp~~--~~~~~~al~aad~viip~~p~-~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~  201 (265)
                      .+-|.||++.-  ..+....+..++.+|++...+ ..|+..+..   .++.++...+++..+ -+|-|+.|-..  .+  
T Consensus        52 ~l~iwDtaG~e~~~~~~~~~~~~a~~~ilvydvt~~~Sf~~l~~---w~~~~~~~~~~~~~i-ilVGNK~DL~~--~r--  123 (166)
T cd04122          52 KLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSS---WLTDARNLTNPNTVI-FLIGNKADLEA--QR--  123 (166)
T ss_pred             EEEEEECCCCCCCCCCCHHHEECCCEEEEEECCCCHHHHHHHHH---HHHHHHHHCCCCCEE-EECCCCCCHHH--CC--
T ss_conf             99999899985444252111431546599725874767999999---999999856999758-70340157444--38--


Q ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHH
Q ss_conf             6899988085201562678688987773798579997999--899999999999999
Q gi|254780806|r  202 VSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQ  256 (265)
Q Consensus       202 ~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~  256 (265)
                                     .|+..+.-.-|...|.+.++-+.+.  ...+.|..||++|.+
T Consensus       124 ---------------~V~~~e~~~~a~~~~~~~~E~SAk~g~nV~e~F~~l~~~i~~  165 (166)
T cd04122         124 ---------------DVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKKIYQ  165 (166)
T ss_pred             ---------------CCCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHH
T ss_conf             ---------------999999999999869989998658780889999999999974


No 306
>PRK05876 short chain dehydrogenase; Provisional
Probab=90.94  E-value=0.34  Score=26.48  Aligned_cols=41  Identities=29%  Similarity=0.374  Sum_probs=35.8

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             9876874999980889888899999999999987995999987877
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      |..-++|++.|..+-+|.|+.     +|..|++.|.+|.+.|.|..
T Consensus         1 M~~~~gKvavITGaasGIG~a-----~A~~la~~Ga~Vvi~d~~~~   41 (275)
T PRK05876          1 MDGFPGRGAVITGGASGIGLA-----TGTEFARRGARVVLGDVDKP   41 (275)
T ss_pred             CCCCCCCEEEEECCCCHHHHH-----HHHHHHHCCCEEEEEECCHH
T ss_conf             959899879992826699999-----99999987998999979889


No 307
>COG0771 MurD UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]
Probab=90.93  E-value=0.47  Score=25.66  Aligned_cols=33  Identities=39%  Similarity=0.524  Sum_probs=26.7

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             874999980889888899999999999987995999
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLL   40 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVll   40 (265)
                      .+++|+|.   |=-||||+|..+++.|...|.++.+
T Consensus       109 ~~p~vaIT---GTNGKTTTTsli~~~l~~~G~~~~l  141 (448)
T COG0771         109 EAPIVAIT---GTNGKTTTTSLIAHLLKAAGLDALL  141 (448)
T ss_pred             CCCEEEEE---CCCCHHHHHHHHHHHHHHCCCCCEE
T ss_conf             99989997---9996288999999999855998321


No 308
>PRK06194 hypothetical protein; Provisional
Probab=90.92  E-value=0.35  Score=26.38  Aligned_cols=41  Identities=20%  Similarity=0.434  Sum_probs=36.1

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             9876874999980889888899999999999987995999987877
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      |.+-+.||+.|..+-+|.|+.     +|..|++.|.+|.++|.+..
T Consensus         1 M~~l~gKvavITGassGIG~a-----~A~~la~~Ga~Vvl~d~~~~   41 (301)
T PRK06194          1 MKDFAGKVAVITGAASGFGRE-----FARIGARLGMKLVLADVQQD   41 (301)
T ss_pred             CCCCCCCEEEEECCCCHHHHH-----HHHHHHHCCCEEEEEECCHH
T ss_conf             989899989992737799999-----99999987998999979889


No 309
>TIGR02475 CobW cobalamin biosynthesis protein CobW; InterPro: IPR012824   Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase .    There are at least two distinct cobalamin biosynthetic pathways in bacteria :  Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii.     Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.   This entry represents CobW proteins, which are generally found proximal to the trimeric cobaltochelatase subunit CobN, an essential protein for vitamin B12 (cobalamin) biosynthesis . They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids.; GO: 0009236 cobalamin biosynthetic process.
Probab=90.88  E-value=0.2  Score=27.87  Aligned_cols=31  Identities=32%  Similarity=0.396  Sum_probs=23.9

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEE
Q ss_conf             9998088988889999999999998-799599998
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAA-IGENVLLID   42 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID   42 (265)
                      .||+.+==|+||||+.=||   |.. .|||..+|=
T Consensus         6 vTvvTGFLGaGKTTLiRhl---L~NA~GkRiAvIV   37 (349)
T TIGR02475         6 VTVVTGFLGAGKTTLIRHL---LENAEGKRIAVIV   37 (349)
T ss_pred             EEEEECCCCCCHHHHHHHH---HHCCCCCEEEEEE
T ss_conf             2787375676158999999---7174787699998


No 310
>PRK09825 idnK D-gluconate kinase; Provisional
Probab=90.84  E-value=0.26  Score=27.16  Aligned_cols=34  Identities=18%  Similarity=0.260  Sum_probs=26.0

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             8749999808898888999999999999879959999878
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ++|-|.|+ +=-|+||||++--||..|   |  .-.||.|
T Consensus         2 ~~~a~VVm-GVsGsGKSTvg~~LA~~L---~--~~fiegD   35 (176)
T PRK09825          2 AGESYILM-GVSGSGKSLIGSKIAALF---S--AKFIDGD   35 (176)
T ss_pred             CCCEEEEE-ECCCCCHHHHHHHHHHHH---C--CCEECCC
T ss_conf             98579998-289899899999999995---9--8776234


No 311
>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=90.82  E-value=0.44  Score=25.80  Aligned_cols=35  Identities=34%  Similarity=0.343  Sum_probs=28.5

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             68749999808898888999999999999879959999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      +..++|+|.   |=-||||+|..+++.|...|+++.+.
T Consensus       107 ~~~~~IaVT---GTnGKTTTt~ll~~iL~~~g~~~~~~  141 (459)
T PRK02705        107 KHIPWVGIT---GTNGKTTVTHLLAHILQAAGLNAPMC  141 (459)
T ss_pred             CCCCEEEEE---CCCCCHHHHHHHHHHHHHCCCCCEEE
T ss_conf             049757771---78972789999999999839985364


No 312
>cd01897 NOG NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans.  NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes.  Thus, defects in NOG1 can lead to defects in 60S biogenesis.  The S. cerevisiae NOG1 gene is essential for cell viability, and mutations in the predicted G motifs abrogate function.  It is a member of the ODN family of GTP-binding proteins that also includes the bacterial Obg and DRG proteins.
Probab=90.80  E-value=0.16  Score=28.31  Aligned_cols=28  Identities=21%  Similarity=0.195  Sum_probs=18.1

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             99998088988889999999999998799599998
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      +|++. ++==|||||+--.|      .|.++.+-+
T Consensus         2 ~Vaiv-G~pNvGKStL~N~L------~g~~~~v~~   29 (168)
T cd01897           2 TLVIA-GYPNVGKSSLVNKL------TRAKPEVAP   29 (168)
T ss_pred             EEEEE-CCCCCCHHHHHHHH------HCCCCEECC
T ss_conf             79998-89998899999999------589860237


No 313
>PRK00141 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=90.74  E-value=0.59  Score=25.05  Aligned_cols=34  Identities=26%  Similarity=0.337  Sum_probs=27.7

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             8749999808898888999999999999879959999
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      ..++|+|.   |=-||||+|..+++.|...|+++.++
T Consensus       122 ~~~~IaVT---GTnGKTTTtsli~~iL~~~g~~~~~~  155 (476)
T PRK00141        122 PRTWLAVT---GTNGKTTTTAMLAAMMQAGGFAAVAV  155 (476)
T ss_pred             CCCEEEEE---CCCCHHHHHHHHHHHHHHCCCCCEEE
T ss_conf             77638896---89967989999999998379972899


No 314
>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=90.73  E-value=0.21  Score=27.70  Aligned_cols=25  Identities=36%  Similarity=0.349  Sum_probs=20.1

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             9998088988889999999999998
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAA   33 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~   33 (265)
                      |.++|+-=|+||||+|-.||-.|..
T Consensus         2 ~I~ISGpPGSGktTvA~~lA~~Lsl   26 (173)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKLSL   26 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCC
T ss_conf             7887358968647899999986398


No 315
>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=90.72  E-value=0.42  Score=25.93  Aligned_cols=36  Identities=28%  Similarity=0.401  Sum_probs=25.5

Q ss_pred             EEEEEECCCCCCCHHHHHHH-HHHHHHH-----CCCCEEEEE
Q ss_conf             49999808898888999999-9999998-----799599998
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAIN-LSTALAA-----IGENVLLID   42 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~n-lA~~la~-----~g~rVllID   42 (265)
                      ..|.|.++--|+||||++.| +||.|..     +++.|+++-
T Consensus       226 ~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~  267 (747)
T COG3973         226 NKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLG  267 (747)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEC
T ss_conf             874899558888713588999999985356624668659982


No 316
>cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily.  Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics.   These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains.  Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42.  Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells.  Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42.  This ternary complex is proposed to have physiological function in processes such as tumorigenesis.  Activated Ric is likely to sign
Probab=90.70  E-value=0.94  Score=23.88  Aligned_cols=112  Identities=12%  Similarity=0.153  Sum_probs=57.7

Q ss_pred             CCCEEEECCCC--CCCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHH
Q ss_conf             82033101333--22221011233100111112-3113788875335777655432026774310020231253100112
Q gi|254780806|r  125 SYIFLDCPPSF--NLLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQV  201 (265)
Q Consensus       125 D~IiiD~pp~~--~~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~  201 (265)
                      .+-|.||++.-  ..+....+..||.+|++... +..|+..+....+.+...+  ...+.++. +|-|+.|-..  .+  
T Consensus        51 ~l~iwDtaGqe~~~~l~~~~~r~a~~~ilvydvt~~~Sf~~~~~w~~~i~~~~--~~~~~pii-lvGNK~DL~~--~r--  123 (172)
T cd04141          51 LLDILDTAGQAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKKLITRVR--LTEDIPLV-LVGNKVDLES--QR--  123 (172)
T ss_pred             EEEEEECCCCCCCCCCHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHH--CCCCCCEE-EEEECCCHHH--HC--
T ss_conf             99999788851357451556427865688731688889999999999999972--88998689-9850456676--18--


Q ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHHHH
Q ss_conf             6899988085201562678688987773798579997999--89999999999999999
Q gi|254780806|r  202 VSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQQE  258 (265)
Q Consensus       202 ~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~~~  258 (265)
                                     .|...+.-.-|...|.+.++-+-+.  ..-+.|..|+++|.+++
T Consensus       124 ---------------~Vs~~e~~~~a~~~~~~f~EtSAk~~~nV~e~F~~l~~~i~~k~  167 (172)
T cd04141         124 ---------------QVTTEEGRNLAREFNCPFFETSAALRHYIDDAFHGLVREIRRKE  167 (172)
T ss_pred             ---------------CCCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             ---------------88999999999985997999747888288999999999998635


No 317
>pfam02562 PhoH PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.
Probab=90.45  E-value=0.58  Score=25.10  Aligned_cols=35  Identities=23%  Similarity=0.276  Sum_probs=26.3

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCC--CEEEEE
Q ss_conf             99998088988889999999999998799--599998
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGE--NVLLID   42 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~--rVllID   42 (265)
                      -|+++.+.-|+|||.+|+..|..+-..|+  |+.++=
T Consensus        20 ~iv~~~GpAGtGKT~la~~~al~~l~~~~~~kiii~R   56 (205)
T pfam02562        20 DIVFGIGPAGTGKTYLAVAAAVDALKDGKVKRIILTR   56 (205)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             8079989998609999999999999718943799975


No 318
>TIGR02770 nickel_nikD nickel import ATP-binding protein NikD; InterPro: IPR014138   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are related families..
Probab=90.38  E-value=0.29  Score=26.85  Aligned_cols=27  Identities=22%  Similarity=0.497  Sum_probs=22.8

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             6874999980889888899999999999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTAL   31 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~l   31 (265)
                      |+++|++.. ++-|+|||++|..+=-.|
T Consensus        10 k~G~~~aLv-G~SGSGKS~tc~A~Lg~L   36 (239)
T TIGR02770        10 KRGEVLALV-GESGSGKSLTCLAILGLL   36 (239)
T ss_pred             ECCEEEEEE-CCCCCCHHHHHHHHHCCC
T ss_conf             324378887-487875899999985035


No 319
>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=90.37  E-value=1.1  Score=23.58  Aligned_cols=110  Identities=13%  Similarity=0.187  Sum_probs=54.0

Q ss_pred             CCCEEEECCCC--CCCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHH
Q ss_conf             82033101333--22221011233100111112-3113788875335777655432026774310020231253100112
Q gi|254780806|r  125 SYIFLDCPPSF--NLLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQV  201 (265)
Q Consensus       125 D~IiiD~pp~~--~~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~  201 (265)
                      .+-|.||++.-  ..+....+..||.+|++..- +..|+..+...   ++.+.+..+.+.++. +|-|+.|-...  +  
T Consensus        53 ~l~iwDt~G~e~~~~~~~~y~~~a~~~ilvfdit~~~Sf~~~~~w---~~~i~~~~~~~~~~i-lVgNK~Dl~~~--r--  124 (167)
T cd01867          53 KLQIWDTAGQERFRTITTAYYRGAMGIILVYDITDEKSFENIRNW---MRNIEEHASEDVERM-LVGNKCDMEEK--R--  124 (167)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHHH---HHHHHHHCCCCCCEE-EECCCCCCHHC--C--
T ss_conf             999998999700116679985650588995568987999999999---999998669997057-64212450230--7--


Q ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHHH
Q ss_conf             6899988085201562678688987773798579997999--8999999999999999
Q gi|254780806|r  202 VSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQQ  257 (265)
Q Consensus       202 ~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~~  257 (265)
                                     .|+..+.-.-|...|.|.++-+-++  ..-+.|..|++++.++
T Consensus       125 ---------------~v~~~e~~~~a~~~~~~~~e~SAktg~nI~e~F~~l~~~i~~k  167 (167)
T cd01867         125 ---------------VVSKEEGEALADEYGIKFLETSAKANINVEEAFFTLAKDIKKK  167 (167)
T ss_pred             ---------------CCCHHHHHHHHHHHCCEEEEECCCCCCCHHHHHHHHHHHHHHC
T ss_conf             ---------------7999999999998099699982257907899999999999709


No 320
>PRK12297 obgE GTPase ObgE; Reviewed
Probab=90.34  E-value=0.31  Score=26.68  Aligned_cols=85  Identities=11%  Similarity=0.178  Sum_probs=49.0

Q ss_pred             CCCCCCEEEECC---------CCCCCCCCHHHHHHHCCCCCCCCC----HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             027820331013---------332222101123310011111231----1378887533577765543202677431002
Q gi|254780806|r  122 SDFSYIFLDCPP---------SFNLLTMNAMAAADSILVPLQCEF----FALEGLSQLLETVEEVRRTVNSALDIQGIIL  188 (265)
Q Consensus       122 ~~yD~IiiD~pp---------~~~~~~~~al~aad~viip~~p~~----~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~  188 (265)
                      +.+.+++.|.|+         |++.-.+.-+..+..++-++..+.    -.+++...+.+.++.+...+.....+  +|+
T Consensus       204 ~~~~~~iADiPGLIeGA~~g~GLG~~FLrHieR~~~L~hviD~s~~~~~dp~~d~~~i~~EL~~y~~~L~~kp~i--vv~  281 (429)
T PRK12297        204 DGRSFVMADLPGLIEGASEGVGLGHQFLRHIERTRVIVHVIDMSGSEGRDPIEDYETINKELKKYNLRLLERPQI--IVA  281 (429)
T ss_pred             CCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHCHHHHCCCEE--EEE
T ss_conf             986699962674567744688866888887662467999997878777798999999999999868987269669--999


Q ss_pred             CEEECCCHHHHHHHHHHHHHHC
Q ss_conf             0231253100112689998808
Q gi|254780806|r  189 TMFDSRNSLSQQVVSDVRKNLG  210 (265)
Q Consensus       189 N~~~~~~~~~~~~~~~l~~~~~  210 (265)
                      |+.|-.  ..++.++.+++.+.
T Consensus       282 NK~Dl~--~~~~~~~~~~~~~~  301 (429)
T PRK12297        282 NKMDLP--EAEENLEEFKEKLA  301 (429)
T ss_pred             ECCCCC--CHHHHHHHHHHHHH
T ss_conf             764585--76999999999753


No 321
>PRK12299 obgE GTPase ObgE; Reviewed
Probab=90.32  E-value=0.44  Score=25.79  Aligned_cols=86  Identities=13%  Similarity=0.189  Sum_probs=45.2

Q ss_pred             CCCCCEEEECC---------CCCCCCCCHHHHHHHCCCCCCCCCHH-HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEE
Q ss_conf             27820331013---------33222210112331001111123113-788875335777655432026774310020231
Q gi|254780806|r  123 DFSYIFLDCPP---------SFNLLTMNAMAAADSILVPLQCEFFA-LEGLSQLLETVEEVRRTVNSALDIQGIILTMFD  192 (265)
Q Consensus       123 ~yD~IiiD~pp---------~~~~~~~~al~aad~viip~~p~~~s-~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~  192 (265)
                      ..++++.|.|+         |++.-.+.-++.+..++.++..+..+ +.....+.+.++.+...+.....  -+|+|++|
T Consensus       205 ~~~~~iaDiPGlIegA~~g~GLG~~FLrHieR~~~L~~viD~s~~d~~~~~~~l~~EL~~y~~~L~~Kp~--ivvlNK~D  282 (334)
T PRK12299        205 YKSFVIADIPGLIEGASEGAGLGHRFLKHIERTRLLLHLVDASSEDPVEDYKTIRNELEKYSPELADKPR--ILVLNKID  282 (334)
T ss_pred             CCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCE--EEEEECCC
T ss_conf             8678998667433552347774789987665343699999799889899999999999985065536987--99998810


Q ss_pred             CCCHHH-HHHHHHHHHHHC
Q ss_conf             253100-112689998808
Q gi|254780806|r  193 SRNSLS-QQVVSDVRKNLG  210 (265)
Q Consensus       193 ~~~~~~-~~~~~~l~~~~~  210 (265)
                      --.... .+..+.+.+.++
T Consensus       283 l~~~~~~~~~~~~~~~~~~  301 (334)
T PRK12299        283 LLDEEERKEKIKELIKALG  301 (334)
T ss_pred             CCCHHHHHHHHHHHHHHCC
T ss_conf             6885678999999998709


No 322
>pfam05970 DUF889 PIF1 helicase. The PIF1 helicase inhibits telomerase activity and is cell cycle regulated.
Probab=90.27  E-value=0.46  Score=25.71  Aligned_cols=28  Identities=36%  Similarity=0.380  Sum_probs=23.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             8898888999999999999879959999
Q gi|254780806|r   14 QKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      +.||+|||++--.+...+...++.|++.
T Consensus         1 G~AGTGKS~ll~~i~~~l~~~~~~v~vt   28 (418)
T pfam05970         1 GYGGTGKTFLWNALSARIRSRGKIVLNV   28 (418)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             9798879999999999997689889998


No 323
>PRK12298 obgE GTPase ObgE; Reviewed
Probab=90.26  E-value=0.29  Score=26.89  Aligned_cols=87  Identities=10%  Similarity=0.226  Sum_probs=50.0

Q ss_pred             CCCCCEEEECC---------CCCCCCCCHHHHHHHCCCCCCCCCH----HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             27820331013---------3322221011233100111112311----3788875335777655432026774310020
Q gi|254780806|r  123 DFSYIFLDCPP---------SFNLLTMNAMAAADSILVPLQCEFF----ALEGLSQLLETVEEVRRTVNSALDIQGIILT  189 (265)
Q Consensus       123 ~yD~IiiD~pp---------~~~~~~~~al~aad~viip~~p~~~----s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N  189 (265)
                      ...|+|-|.|+         |++.-.+.-+..+..++-++..+..    .+.....+.+.++.+...+....++  ||+|
T Consensus       206 ~~~fviADIPGLIeGAs~G~GLG~~FLrHieRt~~LlhviD~s~~~~~dp~~~~~~i~~EL~~Y~~~L~~kp~i--iv~N  283 (380)
T PRK12298        206 ERSFVIADIPGLIEGAAEGAGLGIRFLKHLERCRVLLHLIDIAPIDGSDPVENARIIVNELEKYSPKLAEKPRW--LVFN  283 (380)
T ss_pred             CCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHCHHHCCCCEE--EEEE
T ss_conf             86699987775557755587728999999875358999996887775199999999999999859766059879--9998


Q ss_pred             EEECCCH-HHHHHHHHHHHHHCC
Q ss_conf             2312531-001126899988085
Q gi|254780806|r  190 MFDSRNS-LSQQVVSDVRKNLGG  211 (265)
Q Consensus       190 ~~~~~~~-~~~~~~~~l~~~~~~  211 (265)
                      ++|--.. ...+..+++.+.++.
T Consensus       284 K~Dl~~~~e~~~~~~~~~~~~~~  306 (380)
T PRK12298        284 KIDLLDEEEAEERAKEIVEALGW  306 (380)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             85489979999999999997088


No 324
>pfam00437 GSPII_E Type II/IV secretion system protein. This family contains both type II and type IV pathway secretion proteins from bacteria. VirB11 ATPase is a subunit of the Agrobacterium tumefaciens transfer DNA (T-DNA) transfer system, a type IV secretion pathway required for delivery of T-DNA and effector proteins to plant cells during infection.
Probab=90.16  E-value=0.35  Score=26.41  Aligned_cols=43  Identities=16%  Similarity=0.157  Sum_probs=20.3

Q ss_pred             CCCCCCCCCCCCHH--HHHHHHCCCCEEEE-CCCCHHHHHHHHHHH
Q ss_conf             85201562678688--98777379857999-799989999999999
Q gi|254780806|r  210 GGKVYNTVIPRNVR--ISEAPSYGKPAIIY-DLKCAGSQAYLKLAS  252 (265)
Q Consensus       210 ~~~v~~~~Ip~~~~--i~~a~~~g~pv~~~-~p~s~~a~~~~~la~  252 (265)
                      +..++-.-|+..+.  +.+|.+.|-++..- -..+.+..++.+|..
T Consensus       210 PD~IivGEiR~~Ea~~~l~a~~TGH~g~ltTiHA~sa~~ai~RL~~  255 (283)
T pfam00437       210 PDRIMVGEIRDGETADILRAANTGHPGSLSTLHANSAAGALTRLEQ  255 (283)
T ss_pred             CCEEEECCCCCHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHH
T ss_conf             9989757869989999999997599840785714998999999998


No 325
>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=90.11  E-value=0.27  Score=27.09  Aligned_cols=81  Identities=15%  Similarity=0.139  Sum_probs=44.0

Q ss_pred             CCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHH-HHH
Q ss_conf             7820331013332--2221011233100111112311378887533577765543202677431002023125310-011
Q gi|254780806|r  124 FSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSL-SQQ  200 (265)
Q Consensus       124 yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~-~~~  200 (265)
                      +.|.|||||+.-.  ..+..+...||.+++++..+.-..+  .+..+++..++ .++.  +.+=+++|++|.-... ..+
T Consensus        83 r~~tiiD~PGH~df~~nmi~Gas~aD~aiLvVdA~eG~~~--~QT~eH~~l~~-~lgv--~~iIV~vNKmDlv~~~~~~~  157 (203)
T cd01888          83 RHVSFVDCPGHEILMATMLSGAAVMDGALLLIAANEPCPQ--PQTSEHLAALE-IMGL--KHIIIVQNKIDLVKEEQALE  157 (203)
T ss_pred             EEEEEEECCCHHHHHHHHHHHHHHCCEEEEEEECCCCCCH--HHHHHHHHHHH-HCCC--CCEEEEEECCCCCCHHHHHH
T ss_conf             4799986898799999999766434766898643667750--77999999999-8499--86367750777788678999


Q ss_pred             HHHHHHHHH
Q ss_conf             268999880
Q gi|254780806|r  201 VVSDVRKNL  209 (265)
Q Consensus       201 ~~~~l~~~~  209 (265)
                      ..+++++.+
T Consensus       158 ~~~ei~~~l  166 (203)
T cd01888         158 NYEQIKKFV  166 (203)
T ss_pred             HHHHHHHHH
T ss_conf             999999985


No 326
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=90.04  E-value=0.97  Score=23.80  Aligned_cols=38  Identities=37%  Similarity=0.364  Sum_probs=31.6

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             874999980889888899999999999987995999987
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      +++-|+|= +==|+||||.+--|+..|...|++|.+.=-
T Consensus         2 ~g~fI~iE-GiDGaGKTT~~~~L~~~l~~~g~~v~~trE   39 (208)
T COG0125           2 KGMFIVIE-GIDGAGKTTQAELLKERLEERGIKVVLTRE   39 (208)
T ss_pred             CCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf             96299997-888898899999999999982980799868


No 327
>cd04109 Rab28 Rab28 subfamily.  First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA).  In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos.  Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus.  The two human isoforms are presumbly the result of alternative splicing.  Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations.  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 
Probab=89.93  E-value=0.82  Score=24.23  Aligned_cols=113  Identities=12%  Similarity=0.110  Sum_probs=58.6

Q ss_pred             CCEEEECCCC--CCCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHH
Q ss_conf             2033101333--22221011233100111112-31137888753357776554320267743100202312531001126
Q gi|254780806|r  126 YIFLDCPPSF--NLLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVV  202 (265)
Q Consensus       126 ~IiiD~pp~~--~~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~  202 (265)
                      +-|.||++.-  ..++...+..||.+|++..- +..|+..+...++.+++........+. .-+|-|+.|-.  ..|   
T Consensus        52 l~iwDtaGqe~~~~~~~~y~~~a~~~ilVYDitn~~SF~~l~~W~~~i~~~~~~~~~~~~-iiLVGNK~DL~--~~R---  125 (215)
T cd04109          52 LQVWDIGGQSIGGKMLDKYIYGAHAVFLVYDVTNSQSFENLEDWYSMVRKVLKSSETQPL-VVLVGNKTDLE--HNR---  125 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCE-EEEEEECCCHH--HHC---
T ss_conf             999969985002378999997515137741478678999899999999998504577852-99997545428--647---


Q ss_pred             HHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHHHH
Q ss_conf             899988085201562678688987773798579997999--89999999999999999
Q gi|254780806|r  203 SDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQQE  258 (265)
Q Consensus       203 ~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~~~  258 (265)
                                    .|+..+.-.-|...|.+.++-+.++  ...+.|..||++|++-.
T Consensus       126 --------------~Vs~ee~~~~A~~~g~~f~E~SAktg~nV~e~F~~la~~i~~~~  169 (215)
T cd04109         126 --------------TVKDDKHARFAQANGMESCLVSAKTGDRVNLLFQQLAAELLGVD  169 (215)
T ss_pred             --------------CCCHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHCCC
T ss_conf             --------------76999999999982998999838999498999999999997683


No 328
>PRK06398 aldose dehydrogenase; Validated
Probab=89.90  E-value=0.52  Score=25.39  Aligned_cols=41  Identities=15%  Similarity=0.406  Sum_probs=35.7

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             9876874999980889888899999999999987995999987877
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      |.+-+.|++.|..+-+|.|+.     +|..|++.|.+|.++|.+..
T Consensus         1 M~~L~gKvalVTGgs~GIG~a-----ia~~la~~Ga~V~~~~~~~~   41 (256)
T PRK06398          1 MRDLRDKVVIVTGGSSGIGLA-----IVSRFVDEGSKVVSISRSEP   41 (256)
T ss_pred             CCCCCCCEEEEECCCCHHHHH-----HHHHHHHCCCEEEEEECCCC
T ss_conf             989998989996878789999-----99999986999999948751


No 329
>PRK13695 putative NTPase; Provisional
Probab=89.84  E-value=0.68  Score=24.72  Aligned_cols=30  Identities=33%  Similarity=0.326  Sum_probs=25.4

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCE
Q ss_conf             999808898888999999999999879959
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENV   38 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rV   38 (265)
                      -.+.+++=|+||||+.-.+...|...|++|
T Consensus         5 kI~iTG~PGvGKTTli~Kv~~~L~~~g~~v   34 (174)
T PRK13695          5 RIGITGMPGVGKTTLVLKIAELLAREGYKV   34 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             999878999889999999999986369617


No 330
>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=89.83  E-value=0.93  Score=23.92  Aligned_cols=110  Identities=9%  Similarity=0.161  Sum_probs=60.5

Q ss_pred             CCCEEEECCC--CCCCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHH
Q ss_conf             8203310133--322221011233100111112-3113788875335777655432026774310020231253100112
Q gi|254780806|r  125 SYIFLDCPPS--FNLLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQV  201 (265)
Q Consensus       125 D~IiiD~pp~--~~~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~  201 (265)
                      .+-|.||++.  +..+...-+..|+.++++..- +..|+..+.+.++.+   ++. .+++++. +|-|+.|-..  .+  
T Consensus        56 ~l~iwDtaGqe~f~~l~~~y~r~a~~~ilvyDvt~~~Sf~~l~~w~~~i---~~~-~~~~p~i-LVGNK~DL~~--~r--  126 (189)
T cd04121          56 KLQLWDTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEI---DEH-APGVPKI-LVGNRLHLAF--KR--  126 (189)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHH---HHH-CCCCCEE-EEEECCCHHH--CC--
T ss_conf             9999817886221167898866337048982279889999999999999---997-6898789-9613255033--08--


Q ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHHHH
Q ss_conf             6899988085201562678688987773798579997999--89999999999999999
Q gi|254780806|r  202 VSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQQE  258 (265)
Q Consensus       202 ~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~~~  258 (265)
                                     .|+..+...-|...|.+.++-+.+.  ...+.|..|++.++.+.
T Consensus       127 ---------------~V~~ee~~~~A~~~~~~f~EtSAk~g~nV~e~F~~l~~~il~~~  170 (189)
T cd04121         127 ---------------QVATEQAQAYAERNGMTFFEVSPLCNFNITESFTELARIVLMRH  170 (189)
T ss_pred             ---------------CCCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             ---------------89999999999988999999600679398999999999999865


No 331
>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=89.81  E-value=1.4  Score=22.90  Aligned_cols=109  Identities=15%  Similarity=0.166  Sum_probs=52.8

Q ss_pred             CCCEEEECCCC--CCCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCC--HHHH
Q ss_conf             82033101333--22221011233100111112-3113788875335777655432026774310020231253--1001
Q gi|254780806|r  125 SYIFLDCPPSF--NLLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRN--SLSQ  199 (265)
Q Consensus       125 D~IiiD~pp~~--~~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~--~~~~  199 (265)
                      .+-|.||++.-  ..+....+..||.+|++... +..|+..+...   ++.++.....++.+ -+|-|+.|-..  ....
T Consensus        51 ~l~iwDtaG~e~~~~l~~~~~~~a~~~ilvydit~~~Sf~~l~~w---~~~i~~~~~~~~~i-ilVGNK~DL~~~r~V~~  126 (191)
T cd04112          51 KLQIWDTAGQERFRSVTHAYYRDAHALLLLYDITNKASFDNIRAW---LTEIKEYAQEDVVI-MLLGNKADMSGERVVKR  126 (191)
T ss_pred             EEEEEECCCCCCCCCCHHHHHHCCCEEEEEEECCCHHHHHHHHHH---HHHHHHHCCCCCEE-EEECCCCCCCCCCCCCH
T ss_conf             999997998633464647771177778999727988999999999---99999866678538-98612465530267999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHHHH
Q ss_conf             126899988085201562678688987773798579997999--89999999999999999
Q gi|254780806|r  200 QVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQQE  258 (265)
Q Consensus       200 ~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~~~  258 (265)
                      +-.+.+                     |...|.+.++-+-++  ..-+.|..|+++|..+.
T Consensus       127 ~e~~~~---------------------a~~~~~~f~EtSAkt~~nI~e~F~~i~~~i~~~~  166 (191)
T cd04112         127 EDGERL---------------------AKEYGVPFMETSAKTGLNVELAFTAVAKELKHRK  166 (191)
T ss_pred             HHHHHH---------------------HHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             999999---------------------9982997999854898097999999999998742


No 332
>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=89.76  E-value=1  Score=23.64  Aligned_cols=39  Identities=33%  Similarity=0.408  Sum_probs=34.0

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             8749999808898888999999999999879959999878
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ++|||=|. +-=-+||||++.|.-...++.|--+..||+.
T Consensus        54 ~GRi~EiY-GpESsGKTTLal~~iA~~Qk~Gg~~afiDAE   92 (322)
T TIGR02012        54 KGRIIEIY-GPESSGKTTLALHVIAEAQKAGGVAAFIDAE   92 (322)
T ss_pred             CCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEECH
T ss_conf             75079985-4898847899999999997439838998451


No 333
>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]
Probab=89.74  E-value=0.92  Score=23.95  Aligned_cols=39  Identities=31%  Similarity=0.460  Sum_probs=31.0

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECC
Q ss_conf             87499998088988889999999999998-79959999878
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLD   44 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~D   44 (265)
                      ++..| +..++=|.|||+++.|+|..+|. .++.|++.-+-
T Consensus       195 ~~dLi-ilAaRP~mGKTafalnia~n~a~~~~~~v~iFSLE  234 (435)
T COG0305         195 PGDLI-IVAARPGMGKTALALNIALNAAADGRKPVAIFSLE  234 (435)
T ss_pred             CCCEE-EECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             67779-97168999758999999999998558975999826


No 334
>PRK12338 hypothetical protein; Provisional
Probab=89.74  E-value=0.38  Score=26.19  Aligned_cols=36  Identities=28%  Similarity=0.502  Sum_probs=24.1

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             68749999808898888999999999999879959999878
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      |++=|| ..++--|+||||+|.-||.   +.|-+.+ |-.|
T Consensus         2 r~PliI-LiGGtSGvGKSTlAseLAs---RLgI~tv-IsTD   37 (320)
T PRK12338          2 RKPYVI-LIGSASGIGKSTIASEVAR---RLNIKHL-IETD   37 (320)
T ss_pred             CCCEEE-EEECCCCCCHHHHHHHHHH---HCCCCEE-ECCH
T ss_conf             976799-9706888768889999998---5198711-0334


No 335
>KOG2004 consensus
Probab=89.74  E-value=0.25  Score=27.20  Aligned_cols=30  Identities=30%  Similarity=0.455  Sum_probs=25.6

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             7687499998088988889999999999998
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAA   33 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~   33 (265)
                      .-++||+||. +--|||||+++-.+|.+|-+
T Consensus       435 s~qGkIlCf~-GPPGVGKTSI~kSIA~ALnR  464 (906)
T KOG2004         435 SVQGKILCFV-GPPGVGKTSIAKSIARALNR  464 (906)
T ss_pred             CCCCCEEEEE-CCCCCCCCCHHHHHHHHHCC
T ss_conf             6788379986-89987732189999998487


No 336
>cd04140 ARHI_like ARHI subfamily.  ARHI (A Ras homolog member I) is a member of the Ras family with several unique structural and functional properties.  ARHI is expressed in normal human ovarian and breast tissue, but its expression is decreased or eliminated in breast and ovarian cancer.  ARHI contains an N-terminal extension of 34 residues (human) that is required to retain its tumor suppressive activity.   Unlike most other Ras family members, ARHI is maintained in the constitutively active (GTP-bound) state in resting cells and has modest GTPase activity.  ARHI inhibits STAT3 (signal transducers and activators of transcription 3), a latent transcription factor whose abnormal activation plays a critical role in oncogenesis.  Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid.  Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.  Due to
Probab=89.71  E-value=0.67  Score=24.73  Aligned_cols=68  Identities=13%  Similarity=0.162  Sum_probs=36.5

Q ss_pred             CCCEEEECCCC--CCCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEC
Q ss_conf             82033101333--22221011233100111112-31137888753357776554320267743100202312
Q gi|254780806|r  125 SYIFLDCPPSF--NLLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDS  193 (265)
Q Consensus       125 D~IiiD~pp~~--~~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~  193 (265)
                      .+-|.||++.-  ..+....+..||.+|++... +..|+..+....+.+..++.....+.++ -+|-|+.|-
T Consensus        50 ~l~iwDtaG~e~~~~l~~~~~~~a~~~ilvydit~~~Sf~~~~~~~~~i~~~~~~~~~~~pi-ilVgNK~Dl  120 (165)
T cd04140          50 TLQITDTTGSHQFPAMQRLSISKGHAFILVYSVTSKQSLEELKPIYELICEIKGNNIEKIPI-MLVGNKCDE  120 (165)
T ss_pred             EEEEEECCCCCCCCCCHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCCCCE-EEEEECCCC
T ss_conf             99999899984654232445068857999813898789999999999999996158888878-998642464


No 337
>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=89.68  E-value=1.5  Score=22.72  Aligned_cols=110  Identities=16%  Similarity=0.204  Sum_probs=53.3

Q ss_pred             CCCCEEEECCCC--CCCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             782033101333--22221011233100111112-311378887533577765543202677431002023125310011
Q gi|254780806|r  124 FSYIFLDCPPSF--NLLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       124 yD~IiiD~pp~~--~~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      +.+-|.||++.-  ..+....+..||.+|++... +..|+..+...+.   .+.+....+..+. +|-|+.|-...  + 
T Consensus        51 ~~l~iwDtaG~e~~~~~~~~~~~~a~~~ilvfdit~~~Sf~~i~~w~~---~i~~~~~~~~~~i-lvgNK~DL~~~--r-  123 (166)
T cd01869          51 IKLQIWDTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQ---EIDRYASENVNKL-LVGNKCDLTDK--R-  123 (166)
T ss_pred             EEEEEEECCCCCCCCCCHHHHHHHCCEEEEEECCCCHHHHHHHHHHHH---HHHHHCCCCCCEE-EEEEEECCCCC--C-
T ss_conf             999999899982346267888563267799711799899999999999---9998678777448-86132011314--6-


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHH
Q ss_conf             26899988085201562678688987773798579997999--899999999999999
Q gi|254780806|r  201 VVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQ  256 (265)
Q Consensus       201 ~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~  256 (265)
                                      .|...+.-.-|...|.+.++-+-++  ...+.|..|++++.+
T Consensus       124 ----------------~v~~~~~~~~a~~~~~~~~E~SAk~g~nI~e~F~~l~~~i~k  165 (166)
T cd01869         124 ----------------VVDYSEAQEFADELGIPFLETSAKNATNVEQAFMTMAREIKK  165 (166)
T ss_pred             ----------------CCCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHH
T ss_conf             ----------------679999999999839969998768780689999999999971


No 338
>COG3903 Predicted ATPase [General function prediction only]
Probab=89.60  E-value=0.41  Score=25.97  Aligned_cols=44  Identities=30%  Similarity=0.431  Sum_probs=31.9

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCCCCCCCHH
Q ss_conf             9999808898888999999999999-87995999987877680112
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDPQGNASTG   52 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~q~~~~~~   52 (265)
                      ...-..+-|||||||++.+.|. ++ ...+-|..+|+-|-++.+.+
T Consensus        15 RlvtL~g~ggvgkttl~~~~a~-~~~~~~~~v~~vdl~pitD~~~v   59 (414)
T COG3903          15 RLVTLTGAGGVGKTTLALQAAH-AASEYADGVAFVDLAPITDPALV   59 (414)
T ss_pred             HEEEEECCCCCCEEHHHHHHHH-HHHHCCCCEEEEECCCCCCHHHH
T ss_conf             0124651573000001655676-76533454444212404746676


No 339
>COG4108 PrfC Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]
Probab=89.59  E-value=0.41  Score=26.01  Aligned_cols=91  Identities=20%  Similarity=0.281  Sum_probs=58.2

Q ss_pred             CEEEECCC--CCCCCCCHHHHHHHCCCCCCCCCHHHHHHH-HHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHH
Q ss_conf             03310133--322221011233100111112311378887-533577765543202677431002023125310011268
Q gi|254780806|r  127 IFLDCPPS--FNLLTMNAMAAADSILVPLQCEFFALEGLS-QLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVS  203 (265)
Q Consensus       127 IiiD~pp~--~~~~~~~al~aad~viip~~p~~~s~~~~~-~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~  203 (265)
                      =|+|||+.  +|.-|.-.|.|+|..+.|+..-    +|++ +.++.++--+-   ++++++ -.+|+.|...+..-++++
T Consensus        84 NLLDTPGHeDFSEDTYRtLtAvDsAvMVIDaA----KGiE~qT~KLfeVcrl---R~iPI~-TFiNKlDR~~rdP~ELLd  155 (528)
T COG4108          84 NLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAA----KGIEPQTLKLFEVCRL---RDIPIF-TFINKLDREGRDPLELLD  155 (528)
T ss_pred             ECCCCCCCCCCCHHHHHHHHHHHEEEEEEECC----CCCCHHHHHHHHHHHH---CCCCEE-EEEECCCCCCCCHHHHHH
T ss_conf             61479986543236789998641046898603----5866889999999850---598469-975023656688689999


Q ss_pred             HHHHHHCCCCCC--CCCCCCHHHH
Q ss_conf             999880852015--6267868898
Q gi|254780806|r  204 DVRKNLGGKVYN--TVIPRNVRIS  225 (265)
Q Consensus       204 ~l~~~~~~~v~~--~~Ip~~~~i~  225 (265)
                      ++++.++....+  +.|.....+.
T Consensus       156 EiE~~L~i~~~PitWPIG~gk~F~  179 (528)
T COG4108         156 EIEEELGIQCAPITWPIGMGKDFK  179 (528)
T ss_pred             HHHHHHCCCEECCCCCCCCCCCCC
T ss_conf             999985775035524456885643


No 340
>cd01898 Obg Obg subfamily.  The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation.  Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans.  The E. coli homolog, ObgE is believed to function in ribosomal biogenesis.  Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain.
Probab=89.50  E-value=0.39  Score=26.10  Aligned_cols=27  Identities=15%  Similarity=0.142  Sum_probs=18.0

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9998088988889999999999998799599998
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      |++. ++--|||||+--.      ..|.++.+-|
T Consensus         3 VAii-G~pNvGKSTLlN~------l~~~~~~V~~   29 (170)
T cd01898           3 VGLV-GLPNAGKSTLLSA------ISNAKPKIAD   29 (170)
T ss_pred             EEEE-CCCCCCHHHHHHH------HHCCCCEEEC
T ss_conf             8998-9999989999999------9678760325


No 341
>pfam03266 DUF265 Protein of unknown function, DUF265.
Probab=89.41  E-value=0.55  Score=25.25  Aligned_cols=28  Identities=32%  Similarity=0.351  Sum_probs=24.4

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHCCCCE
Q ss_conf             9808898888999999999999879959
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAAIGENV   38 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~~g~rV   38 (265)
                      +.++.=|+||||+.-.++..|...|.+|
T Consensus         3 ~ITG~pGvGKTTli~kv~~~l~~~~~~v   30 (168)
T pfam03266         3 FITGPPGVGKTTLVKKVIELLKSEGVKV   30 (168)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             9978999889999999999998679707


No 342
>COG3451 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]
Probab=89.31  E-value=0.84  Score=24.17  Aligned_cols=46  Identities=24%  Similarity=0.161  Sum_probs=34.2

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCC-CCEEEEECCCC-CCCCHHHCC
Q ss_conf             99808898888999999999999879-95999987877-680112124
Q gi|254780806|r   10 TIANQKGGVGKTTTAINLSTALAAIG-ENVLLIDLDPQ-GNASTGLGI   55 (265)
Q Consensus        10 ~v~s~KGGvGKTT~a~nlA~~la~~g-~rVllID~D~q-~~~~~~l~~   55 (265)
                      +++.+..|.||||+-.-|+..+.+.+ -+++++|-|-- -..+..+|-
T Consensus       439 T~I~G~tGaGKTvLl~~lla~~~k~~~~~iv~fDk~~g~~~~~~a~gG  486 (796)
T COG3451         439 TLIIGPTGAGKTVLLSFLLAQALKYGNPQIVAFDKDNGAYIFIEALGG  486 (796)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHCC
T ss_conf             499889888789999999999987459818998489735778887498


No 343
>TIGR00503 prfC peptide chain release factor 3; InterPro: IPR004548   Peptide chain release factor 3 increases the formation of ribosomal termination complexes and stimulates activity of RF-1 and RF-2. It binds to guanine nucleotides and has a strong preference for UGA stop codons. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis sp. (strain PCC 6803), and in Staphylococcus aureus.; GO: 0005525 GTP binding, 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=89.27  E-value=0.35  Score=26.42  Aligned_cols=103  Identities=17%  Similarity=0.212  Sum_probs=64.8

Q ss_pred             EEEECCC--CCCCCCCHHHHHHHCCCCCCCCCHHHHHHHH-HHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHH
Q ss_conf             3310133--3222210112331001111123113788875-335777655432026774310020231253100112689
Q gi|254780806|r  128 FLDCPPS--FNLLTMNAMAAADSILVPLQCEFFALEGLSQ-LLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSD  204 (265)
Q Consensus       128 iiD~pp~--~~~~~~~al~aad~viip~~p~~~s~~~~~~-~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~  204 (265)
                      |+|||+.  +|.-|.-.|.|+|.++.++..-    +|++. ..+.++-.+-+   +++++ -.+|+.|......-|.+++
T Consensus        84 LLDTPGH~DFSEDTYRTL~A~D~~~M~IDaA----KG~E~~T~KL~EV~RLR---~~PI~-TF~NKLDR~~~~P~ELlDE  155 (530)
T TIGR00503        84 LLDTPGHEDFSEDTYRTLTAVDNCLMVIDAA----KGVETRTRKLMEVTRLR---DLPIL-TFINKLDRDIRDPLELLDE  155 (530)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHEEEHHCC----CCHHHHHHHHHHHHHHC---CCCHH-HHHHHCCCCCCCHHHHHHH
T ss_conf             0368588876404679999851230011112----56123424454201000---47443-3523206543553788888


Q ss_pred             HHHHHCCCCCCCC--CCCCHHHH-HHHHCCCCEEEEC
Q ss_conf             9988085201562--67868898-7773798579997
Q gi|254780806|r  205 VRKNLGGKVYNTV--IPRNVRIS-EAPSYGKPAIIYD  238 (265)
Q Consensus       205 l~~~~~~~v~~~~--Ip~~~~i~-~a~~~g~pv~~~~  238 (265)
                      +++.++.......  |---..|. -.......++.|.
T Consensus       156 vE~~L~~~~~~~~~PIG~G~~F~GVY~~~~~~~yLy~  192 (530)
T TIGR00503       156 VENELKINCAPITYPIGCGKLFKGVYHLLKDEIYLYQ  192 (530)
T ss_pred             HHHHHCCCEEEEECCCCCCCCCHHHHHHHCCEEEEEE
T ss_conf             8877064113430565788431135543014066763


No 344
>PRK09519 recA recombinase A; Reviewed
Probab=89.25  E-value=1.2  Score=23.23  Aligned_cols=39  Identities=31%  Similarity=0.410  Sum_probs=34.0

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             8749999808898888999999999999879959999878
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ++||+-+. +.-.+||||++.|.....++.|-.+..||+.
T Consensus        59 rGRIvEIy-GpESSGKTTLALH~IAeaQK~GG~aAfIDAE   97 (790)
T PRK09519         59 RGRVIEIY-GPESSGKTTVALHAVANAQAAGGVAAFIDAE   97 (790)
T ss_pred             CEEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             60499987-8977658999999999998539979999520


No 345
>PRK06761 hypothetical protein; Provisional
Probab=89.24  E-value=0.94  Score=23.88  Aligned_cols=39  Identities=33%  Similarity=0.396  Sum_probs=30.1

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE-ECCC
Q ss_conf             749999808898888999999999999879959999-8787
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI-DLDP   45 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI-D~D~   45 (265)
                      +|.| |+-+=-|+||||++--|+-.|..+|..|-+. .+|+
T Consensus         2 ~kLI-iIEGlPGsGKSTta~~l~d~L~~~g~~v~~~~Egd~   41 (281)
T PRK06761          2 TKLI-IIEGLPGFGKSTTAHLLNDKLSQLKIEVELFVEGDL   41 (281)
T ss_pred             CCEE-EEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCC
T ss_conf             6179-996689998014999999999866985389950789


No 346
>PRK13898 type IV secretion system ATPase VirB4; Provisional
Probab=89.20  E-value=0.96  Score=23.84  Aligned_cols=32  Identities=22%  Similarity=0.260  Sum_probs=29.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             88988889999999999998799599998787
Q gi|254780806|r   14 QKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +.=|+||||+..-|+..+.+.+-++.++|-|-
T Consensus       453 G~TGsGKTtl~~fL~aq~~ky~~~~f~fDkd~  484 (800)
T PRK13898        453 GPTGAGKTVLMNFLCAQAMKFSPRMFFFDKDR  484 (800)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHCCEEEEEECCC
T ss_conf             99999899999999999875488799997999


No 347
>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional
Probab=89.10  E-value=0.34  Score=26.44  Aligned_cols=79  Identities=14%  Similarity=0.163  Sum_probs=43.0

Q ss_pred             CCCCCCEEEECCCCCCCCCC---HHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHH
Q ss_conf             02782033101333222210---112331001111123113788875335777655432026774310020231253100
Q gi|254780806|r  122 SDFSYIFLDCPPSFNLLTMN---AMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLS  198 (265)
Q Consensus       122 ~~yD~IiiD~pp~~~~~~~~---al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~  198 (265)
                      +.+.|+|+|+|+.- .++.|   +...||..|+++..+.--+..+.   +++. +...++.  +..=+++|++|.- ...
T Consensus       105 ~~r~~~i~DaPGH~-~f~~NMitGas~aD~aiLvVdA~~G~~~QTr---eH~~-i~~llGI--~~iIVaVNKMDlV-~~~  176 (475)
T PRK05124        105 EKRKFIIADTPGHE-QYTRNMATGASTCDLAILLIDARKGVLDQTR---RHSF-IATLLGI--KHLVVAVNKMDLV-DYS  176 (475)
T ss_pred             CCEEEEEEECCCHH-HHHHHHHHHHHHCCEEEEEEECCCCCHHHHH---HHHH-HHHHCCC--CEEEEEEECHHCC-CCC
T ss_conf             87689997379638-7788898888767889999989889478889---9999-9986599--8599998504313-543


Q ss_pred             HHHHHHHHHH
Q ss_conf             1126899988
Q gi|254780806|r  199 QQVVSDVRKN  208 (265)
Q Consensus       199 ~~~~~~l~~~  208 (265)
                      ++.++++++.
T Consensus       177 ~~~f~~I~~e  186 (475)
T PRK05124        177 EEVFERIRED  186 (475)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 348
>TIGR01087 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase; InterPro: IPR005762   The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:    (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.    Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC)  and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .    This entry represents UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD). MurD catalyses the addition of d-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-l-alanine. ; GO: 0005524 ATP binding, 0008764 UDP-N-acetylmuramoylalanine-D-glutamate ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=89.05  E-value=0.92  Score=23.94  Aligned_cols=33  Identities=36%  Similarity=0.479  Sum_probs=27.0

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             874999980889888899999999999987995999
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLL   40 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVll   40 (265)
                      ..|+|+|+   |=-||||+|.-+.+.|...|.++.+
T Consensus       109 ~~~~~aIT---GTnGKtTTT~L~~~~L~~~G~~a~~  141 (476)
T TIGR01087       109 PAKVVAIT---GTNGKTTTTSLLYHLLKAAGLKAVL  141 (476)
T ss_pred             CCCEEEEE---CCCCHHHHHHHHHHHHHHCCCCEEE
T ss_conf             87379997---2686079999999999846997786


No 349
>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.
Probab=89.03  E-value=0.56  Score=25.21  Aligned_cols=31  Identities=42%  Similarity=0.483  Sum_probs=22.5

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             99998088988889999999999998799599998787
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +|+++ +.=|+||||++--|    ...|.+|  +|+|-
T Consensus         1 iigiT-G~igSGKStv~~~l----~~~g~~v--~~aD~   31 (179)
T cd02022           1 IIGLT-GGIGSGKSTVAKLL----KELGIPV--IDADK   31 (179)
T ss_pred             CEEEE-CCCCCCHHHHHHHH----HHCCCEE--EECHH
T ss_conf             98863-78757899999999----9879909--96359


No 350
>TIGR00682 lpxK tetraacyldisaccharide 4'-kinase; InterPro: IPR003758   Tetraacyldisaccharide 4'-kinase 2.7.1.130 from EC phosphorylates the 4'-position of a tetraacyldisaccharide 1-phosphate precursor (DS-1-P) of lipid A, but the enzyme has not yet been purified because of instability . This enzyme is involved in the synthesis of lipid A portion of the bacterial lipopolysaccharide layer (LPS). ; GO: 0009029 tetraacyldisaccharide 4'-kinase activity, 0009245 lipid A biosynthetic process.
Probab=88.99  E-value=0.65  Score=24.83  Aligned_cols=40  Identities=28%  Similarity=0.377  Sum_probs=33.7

Q ss_pred             CCEEEEEECC-CCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             8749999808-898888999999999999879959999878
Q gi|254780806|r    5 KSRIITIANQ-KGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         5 ~~kvI~v~s~-KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      .+.|++|.|. -||.|||.+.+-||-.|..+|.++.++.--
T Consensus        31 ~~~~~~vGn~~~GG~Gktp~v~wl~~~l~~~g~~~~~~~~g   71 (342)
T TIGR00682        31 VPVVISVGNLSVGGTGKTPVVLWLAELLKDRGLRVGVLSRG   71 (342)
T ss_pred             CCEEEEECCEEECCCCCCHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             41367623244257875148787899998569818998535


No 351
>TIGR01137 cysta_beta cystathionine beta-synthase; InterPro: IPR005857    This model discriminates cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain from cysteine synthases. Cysteine synthase (O-acetylserine (thiol)-lyase) is the enzyme responsible for the formation of cysteine from O-acetyl-serine and hydrogen sulphide with the concomitant release of acetic acid - the function of many of these enzymes is unproven.; GO: 0004122 cystathionine beta-synthase activity, 0019343 cysteine biosynthetic process via cystathionine, 0005737 cytoplasm.
Probab=88.97  E-value=0.77  Score=24.38  Aligned_cols=112  Identities=15%  Similarity=0.266  Sum_probs=66.4

Q ss_pred             HHHHHHHHH-HCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCC-CCCCC--CEEECCCCCCCCCCC
Q ss_conf             999999999-87995999987877680112124633345411676302577121024-44444--200014887457750
Q gi|254780806|r   24 AINLSTALA-AIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILI-QTAIP--NLSIIPSTMDLLGIE   99 (265)
Q Consensus        24 a~nlA~~la-~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~-~~~~~--~l~iipa~~~~~~~~   99 (265)
                      ...+|.+|- .+.-+|-+|-.||.||+=.                  +++.|+++-. +-..|  |-|++|.-.+..-.|
T Consensus       193 ItGi~ryLK~~~~~~~~ivGaDP~GSila------------------~pE~LN~t~~t~Y~VEGiGyDF~P~vlDR~v~D  254 (527)
T TIGR01137       193 ITGIARYLKDESNPKVRIVGADPEGSILA------------------QPEELNKTGRTPYKVEGIGYDFIPTVLDRKVVD  254 (527)
T ss_pred             HHHHHHHHHHCCCCCEEEEEECCCCCEEC------------------CCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCC
T ss_conf             55455654321389338998769853321------------------764655578983148762147768523765254


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHH--------HHCCCCCCCCCHHHHH
Q ss_conf             00123222210233322476510278203310133322221011233--------1001111123113788
Q gi|254780806|r  100 MILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAA--------DSILVPLQCEFFALEG  162 (265)
Q Consensus       100 ~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~aa--------d~viip~~p~~~s~~~  162 (265)
                      .....+-...|.+.|-|..   +  +=+|  |+++-|--...||.+|        |.++||+-||  |+|+
T Consensus       255 ~w~k~~D~~SF~maRrLi~---e--EGlL--vGGS~GsAvvaal~~A~~hP~l~~~~~~VvlLPD--S~R~  316 (527)
T TIGR01137       255 EWIKTDDKESFKMARRLIK---E--EGLL--VGGSSGSAVVAALKVAEDHPELKEDQVIVVLLPD--SIRN  316 (527)
T ss_pred             EEEEECCHHHHHHHHHHHH---H--CCEE--EECCHHHHHHHHHHHHHHCCCCCCCCEEEEEECC--CCCH
T ss_conf             4688088168999999987---4--4726--4043035899999998726788888789998468--7300


No 352
>COG0481 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]
Probab=88.93  E-value=0.45  Score=25.77  Aligned_cols=22  Identities=18%  Similarity=0.419  Sum_probs=15.5

Q ss_pred             HHHHHHHHCCCCCCEEEECCCC
Q ss_conf             3224765102782033101333
Q gi|254780806|r  114 KALSVQLTSDFSYIFLDCPPSF  135 (265)
Q Consensus       114 ~~l~~~l~~~yD~IiiD~pp~~  135 (265)
                      +.+...+..+||.=+|=|+|+.
T Consensus       354 eiiqERLeREf~ldlI~TaPsV  375 (603)
T COG0481         354 EIIQERLEREFDLDLITTAPSV  375 (603)
T ss_pred             HHHHHHHHHHHCCCEEECCCCE
T ss_conf             9999999876086348438946


No 353
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=88.92  E-value=0.42  Score=25.92  Aligned_cols=28  Identities=39%  Similarity=0.552  Sum_probs=20.4

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEE
Q ss_conf             99998088988889999999999998799599
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVL   39 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVl   39 (265)
                      +|++ |++-|+||||++.-||-.   .|++..
T Consensus         2 ~ItI-sG~pGsG~TTva~~lAe~---~gl~~v   29 (179)
T COG1102           2 VITI-SGLPGSGKTTVARELAEH---LGLKLV   29 (179)
T ss_pred             EEEE-CCCCCCCCHHHHHHHHHH---HCCCEE
T ss_conf             7996-179999702799999998---297156


No 354
>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=88.91  E-value=0.8  Score=24.28  Aligned_cols=36  Identities=28%  Similarity=0.194  Sum_probs=29.1

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             9998088988889999999999998799599998787
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +.+.++==|+||||+--++... ...|+|+++|=.|.
T Consensus         2 v~iitGFLGsGKTTll~~ll~~-~~~~~~~avI~Ne~   37 (174)
T pfam02492         2 VTVLTGFLGSGKTTLLEHLLRD-NREGLKIAVIVNDF   37 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH-CCCCCCEEEEEECC
T ss_conf             6999348878899999999984-44898479999336


No 355
>PRK07429 phosphoribulokinase; Provisional
Probab=88.87  E-value=1.1  Score=23.39  Aligned_cols=38  Identities=34%  Similarity=0.422  Sum_probs=29.2

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             87499998088988889999999999998799599998787
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +.=+|.|+ +--|+||||++-.|...|..  .+|.+|-.|-
T Consensus         7 rP~IIGIA-GgSGSGKTTv~r~I~~~fg~--~~VtvI~~Dd   44 (331)
T PRK07429          7 RPVIIGVA-GDSGCGKSTFLRRLADLFGE--ELVTVICLDD   44 (331)
T ss_pred             CCEEEEEE-CCCCCCHHHHHHHHHHHHCC--CCEEEEECCC
T ss_conf             99899985-78877899999999998388--8779994786


No 356
>PRK04195 replication factor C large subunit; Provisional
Probab=88.82  E-value=0.9  Score=23.99  Aligned_cols=32  Identities=28%  Similarity=0.338  Sum_probs=23.7

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             99980889888899999999999987995999987
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      ..+.++--|+||||++--||-.   .|+.|+=+.+
T Consensus        42 ~lLL~GPpGvGKTT~a~~lAk~---~g~~viElNA   73 (403)
T PRK04195         42 ALLLYGPPGVGKTSLAHALAND---YGWEVIELNA   73 (403)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---HCCCEEEECC
T ss_conf             6998893998799999999998---4998599771


No 357
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=88.71  E-value=1.5  Score=22.62  Aligned_cols=110  Identities=18%  Similarity=0.181  Sum_probs=53.1

Q ss_pred             CCCEEEECCCCC--CCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHH
Q ss_conf             820331013332--2221011233100111112-3113788875335777655432026774310020231253100112
Q gi|254780806|r  125 SYIFLDCPPSFN--LLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQV  201 (265)
Q Consensus       125 D~IiiD~pp~~~--~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~  201 (265)
                      .+-|.||++.-.  .+....+..||.+|++... +..|+..+...+   +.++...+++.++. +|-|+.|-...  +  
T Consensus        50 ~l~iwDt~G~e~~~~l~~~~~~~~~~~ilvfdi~~~~Sf~~i~~w~---~~i~~~~~~~~pii-lvgnK~Dl~~~--r--  121 (164)
T smart00175       50 KLQIWDTAGQERFRSITSSYYRGAVGALLVYDITNRESFENLKNWL---KELREYADPNVVIM-LVGNKSDLEDQ--R--  121 (164)
T ss_pred             EEEEEECCCCHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHH---HHHHHHCCCCCCEE-ECCCCCCHHHH--C--
T ss_conf             9999967994466477998833665368843689989999999999---99998679998255-11645685651--8--


Q ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHHH
Q ss_conf             6899988085201562678688987773798579997999--8999999999999999
Q gi|254780806|r  202 VSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQQ  257 (265)
Q Consensus       202 ~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~~  257 (265)
                                     .|+..+.-.-|...|.+.++-+-++  ...+.|..|+++++++
T Consensus       122 ---------------~V~~~e~~~~a~~~~~~~~e~SAk~~~~v~e~F~~l~~~i~k~  164 (164)
T smart00175      122 ---------------QVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELAREILKR  164 (164)
T ss_pred             ---------------CCCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHCC
T ss_conf             ---------------7999999999998499799983166908899999999999719


No 358
>PRK03839 putative kinase; Provisional
Probab=88.70  E-value=0.8  Score=24.30  Aligned_cols=28  Identities=39%  Similarity=0.521  Sum_probs=19.5

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEE
Q ss_conf             99998088988889999999999998799599
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVL   39 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVl   39 (265)
                      +|++ ++-=||||||++-.||..   .|++++
T Consensus         2 ~I~I-TGTPGtGKTTva~~La~~---lg~~~i   29 (180)
T PRK03839          2 IIAI-TGTPGVGKTTISKLLAEK---LGYEYV   29 (180)
T ss_pred             EEEE-ECCCCCCHHHHHHHHHHH---HCCEEE
T ss_conf             8999-789999989999999997---698798


No 359
>pfam07726 AAA_3 ATPase family associated with various cellular activities (AAA). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
Probab=88.69  E-value=1  Score=23.66  Aligned_cols=32  Identities=28%  Similarity=0.366  Sum_probs=21.4

Q ss_pred             ECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             80889888899999999999987995999987877
Q gi|254780806|r   12 ANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus        12 ~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      .-+-=|+|||+++-.+|..+   |.+..-|.+.++
T Consensus         4 L~GppG~GKT~l~~~lA~~~---~~~~~~i~~~~~   35 (131)
T pfam07726         4 LEGVPGLAKTLLARTLARSL---GLDFRRIQFTPD   35 (131)
T ss_pred             EECCCCCHHHHHHHHHHHHH---CCCCEEEEECCC
T ss_conf             89899876999999999995---998168883377


No 360
>KOG1969 consensus
Probab=88.61  E-value=0.84  Score=24.18  Aligned_cols=37  Identities=27%  Similarity=0.339  Sum_probs=30.3

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             6874999980889888899999999999987995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      |..|-|...++--|.||||+|.-+|.   +.||+|+=|-+
T Consensus       323 RP~kKilLL~GppGlGKTTLAHViAk---qaGYsVvEINA  359 (877)
T KOG1969         323 RPPKKILLLCGPPGLGKTTLAHVIAK---QAGYSVVEINA  359 (877)
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHH---HCCCEEEEECC
T ss_conf             98400687536887872479999998---62854887325


No 361
>TIGR00631 uvrb excinuclease ABC, B subunit; InterPro: IPR004807 All proteins in this family for which functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0005737 cytoplasm, 0009380 excinuclease repair complex.
Probab=88.53  E-value=0.45  Score=25.75  Aligned_cols=26  Identities=31%  Similarity=0.429  Sum_probs=22.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             88988889999999999998799599998
Q gi|254780806|r   14 QKGGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      |==|+|||-+.+|+   .|+.++.+|+|=
T Consensus        36 GvTGsGKTFT~AnV---Ia~~~rPTLV~a   61 (667)
T TIGR00631        36 GVTGSGKTFTMANV---IAQVQRPTLVLA   61 (667)
T ss_pred             EEECCCHHHHHHHH---HHHHCCCEEEEC
T ss_conf             32148627889899---998479849985


No 362
>cd01862 Rab7 Rab7 subfamily.  Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway.  The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion.  Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-
Probab=88.50  E-value=1.7  Score=22.34  Aligned_cols=116  Identities=15%  Similarity=0.128  Sum_probs=53.2

Q ss_pred             CCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCC-CHHHHHHHHHHHHHH-HHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             820331013332--22210112331001111123-113788875335777-65543202677431002023125310011
Q gi|254780806|r  125 SYIFLDCPPSFN--LLTMNAMAAADSILVPLQCE-FFALEGLSQLLETVE-EVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       125 D~IiiD~pp~~~--~~~~~al~aad~viip~~p~-~~s~~~~~~~~~~i~-~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      .+-|.||++.-.  .+....+..||.++++...+ ..|+..+....+.+. .........+++. +|-|+.|-..  .+.
T Consensus        50 ~l~iwDtaG~e~~~~l~~~~~~~a~~~ilvydvt~~~Sf~~l~~w~~~~~~~~~~~~~~~~pii-lvgNK~Dl~~--~r~  126 (172)
T cd01862          50 TLQIWDTAGQERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPSDPENFPFV-VLGNKIDLEE--KRQ  126 (172)
T ss_pred             EEEEEECCCCHHHHHHHHHHHHHCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEE-EEEECCCHHH--CCC
T ss_conf             9999969998311068899865275799993389989999999999999997276776576389-9963368364--189


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCC-CCEEEECCCC--HHHHHHHHHHHHHHHHHHH
Q ss_conf             2689998808520156267868898777379-8579997999--8999999999999999986
Q gi|254780806|r  201 VVSDVRKNLGGKVYNTVIPRNVRISEAPSYG-KPAIIYDLKC--AGSQAYLKLASELIQQERH  260 (265)
Q Consensus       201 ~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g-~pv~~~~p~s--~~a~~~~~la~el~~~~~~  260 (265)
                                       |...+.-.-|...| .+.++-+.+.  ..-+.|..|++.+++++|+
T Consensus       127 -----------------V~~~e~~~~a~~~~~~~~~E~SAk~~~nV~e~F~~l~~~~l~~~k~  172 (172)
T cd01862         127 -----------------VSTKKAQQWCQSNGNIPYFETSAKEAINVEQAFETIARKALEQEKE  172 (172)
T ss_pred             -----------------CCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             -----------------9999999999976997899975267919899999999999986329


No 363
>pfam06418 CTP_synth_N CTP synthase N-terminus. This family consists of the N-terminal region of the CTP synthase protein (EC:6.3.4.2). This family is found in conjunction with pfam00117 located in the C-terminal region of the protein. CTP synthase catalyses the synthesis of CTP from UTP by amination of the pyrimidine ring at the 4-position.
Probab=88.48  E-value=1.4  Score=22.96  Aligned_cols=45  Identities=27%  Similarity=0.362  Sum_probs=35.2

Q ss_pred             CEEEEEEC-CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             74999980-8898888999999999999879959999878776801
Q gi|254780806|r    6 SRIITIAN-QKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS   50 (265)
Q Consensus         6 ~kvI~v~s-~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~   50 (265)
                      +|-|.|.. -=-|.||-.+++.+|..|..+|++|-.+-+||.=|.+
T Consensus         1 tkyi~vtGGV~SglGKGi~~aSig~ll~~~g~~v~~~K~DpYlNvD   46 (275)
T pfam06418         1 TKYIFVTGGVVSSLGKGITAASLGRLLKSRGLKVTIQKIDPYLNVD   46 (275)
T ss_pred             CEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCEECC
T ss_conf             9399995985025631899999999999679636787415631238


No 364
>PRK09112 DNA polymerase III subunit delta'; Validated
Probab=88.47  E-value=0.54  Score=25.29  Aligned_cols=22  Identities=27%  Similarity=0.449  Sum_probs=18.0

Q ss_pred             ECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             8088988889999999999998
Q gi|254780806|r   12 ANQKGGVGKTTTAINLSTALAA   33 (265)
Q Consensus        12 ~s~KGGvGKTT~a~nlA~~la~   33 (265)
                      .++--|+||||++-.+|..|-.
T Consensus        50 f~GP~GiGKaTlA~~~A~~Ll~   71 (352)
T PRK09112         50 FEGPEGIGKATLAFHLANHILS   71 (352)
T ss_pred             EECCCCCCHHHHHHHHHHHHHC
T ss_conf             3589980899999999999866


No 365
>cd04139 RalA_RalB RalA/RalB subfamily.  The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB.  Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics.  Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration.  In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it.  A Ral-specific set of GEFs has been identified that are activated by Ras binding.  This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K).   Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis.  In rat kidney cells, RalB is required for functional assembly of the exo
Probab=88.45  E-value=1.6  Score=22.60  Aligned_cols=112  Identities=14%  Similarity=0.196  Sum_probs=54.3

Q ss_pred             CCCCEEEECCCC--CCCCCCHHHHHHHCCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             782033101333--222210112331001111123-11378887533577765543202677431002023125310011
Q gi|254780806|r  124 FSYIFLDCPPSF--NLLTMNAMAAADSILVPLQCE-FFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       124 yD~IiiD~pp~~--~~~~~~al~aad~viip~~p~-~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      +.+-|.||++.-  ..+....+..||.++++...+ ..|+..+......+....  .+..+++ -+|-|+.|-..  .++
T Consensus        48 v~l~iwDtaG~e~~~~l~~~~~~~a~~~ilvydvt~~~Sf~~~~~~~~~~~~~~--~~~~~pi-ilVgNK~DL~~--~r~  122 (164)
T cd04139          48 VQLNILDTAGQEDYAAIRDNYHRSGEGFLLVFSITDMESFTATAEFREQILRVK--DDDNVPL-LLVGNKCDLED--KRQ  122 (164)
T ss_pred             EEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEECCCHHHHHHHHHHHHHHHHHH--CCCCCCE-EEEEEEHHHHH--CCC
T ss_conf             999999898866248899998863768899997797788999999999999860--8788636-98733032334--177


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHHH
Q ss_conf             26899988085201562678688987773798579997999--8999999999999999
Q gi|254780806|r  201 VVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQQ  257 (265)
Q Consensus       201 ~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~~  257 (265)
                                       |+..+.-.-|...|.+.++-+-+.  ..-+.|..|+++|.+|
T Consensus       123 -----------------v~~~e~~~~a~~~~~~~~E~SAk~g~nV~~~F~~l~~~i~~~  164 (164)
T cd04139         123 -----------------VSSEEAANLARQWGVPYVETSAKTRQNVEKAFYDLVREIRQR  164 (164)
T ss_pred             -----------------CCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHC
T ss_conf             -----------------899999999998399899982687908899999999999729


No 366
>COG5623 CLP1 Predicted GTPase subunit of the pre-mRNA cleavage complex [Translation, ribosomal structure and biogenesis]
Probab=88.44  E-value=0.97  Score=23.79  Aligned_cols=40  Identities=23%  Similarity=0.382  Sum_probs=32.4

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             74999980889888899999999999987995999987877
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      ++.+.+. +---.|||+++--|-.+.-++|++++.+.+|||
T Consensus        99 gp~v~vv-Ggsq~Gkts~~~tL~syalk~~~~pl~~nlDP~  138 (424)
T COG5623          99 GPTVMVV-GGSQNGKTSFCFTLISYALKLGKKPLFTNLDPS  138 (424)
T ss_pred             CCEEEEE-CCCCCCCEEHHHHHHHHHHHHCCCCEEEECCCC
T ss_conf             9779998-887678310899999999971677507854888


No 367
>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional
Probab=88.34  E-value=1.5  Score=22.66  Aligned_cols=39  Identities=23%  Similarity=0.325  Sum_probs=29.2

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             876874999980889888899999999999987995999987
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      +.++-++|.|.   |=-||||++.-++..|...|+++.+|-.
T Consensus       107 ps~~l~vigVT---GTNGKTTt~~~i~~il~~~g~~~~~iGT  145 (953)
T PRK11929        107 PSQDLSVVAVT---GTNGKTSCAQWLAQMLTRLGKPCGSIGT  145 (953)
T ss_pred             CCCCCCEEEEE---CCCCHHHHHHHHHHHHHHCCCCEEEECC
T ss_conf             67588789997---9997999999999999867998899832


No 368
>TIGR00337 PyrG CTP synthase; InterPro: IPR004468 CTP synthase is involved in pyrimidine ribonucleotide/ribonucleoside metabolism. The enzyme catalyzes the reaction L-glutamine + H2O + UTP + ATP = CTP + phosphate + ADP + L-glutamate. The enzyme exists as a dimer of identical chains that aggregates as a tetramer. This gene has been found circa 500 bp 5 upstream of enolase in both beta (Nitrosomonas europaea) and gamma (Escherichia coli) subdivisions of Proteobacterium .; GO: 0003883 CTP synthase activity, 0006221 pyrimidine nucleotide biosynthetic process.
Probab=88.22  E-value=1.4  Score=22.95  Aligned_cols=47  Identities=32%  Similarity=0.386  Sum_probs=37.7

Q ss_pred             CCCEEEEEECC-CCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             68749999808-898888999999999999879959999878776801
Q gi|254780806|r    4 KKSRIITIANQ-KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS   50 (265)
Q Consensus         4 ~~~kvI~v~s~-KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~   50 (265)
                      +.+|-|.|+.+ =-|-||=-+|+.||..|..+|++|-.|=+||.-|.+
T Consensus         2 ~~~KyifVTGGV~SslGKGI~AAS~grLL~~~gl~Vt~iKiDPYiN~D   49 (571)
T TIGR00337         2 KMMKYIFVTGGVVSSLGKGITAASLGRLLKARGLKVTIIKIDPYINID   49 (571)
T ss_pred             CCCEEEEEECCEECCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCC
T ss_conf             861179994438504026789999999998558806576307755668


No 369
>cd00755 YgdL_like Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like substrate, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of the substrate. The exact function of this family is unknown.
Probab=88.22  E-value=0.57  Score=25.16  Aligned_cols=36  Identities=33%  Similarity=0.516  Sum_probs=27.0

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCC-CEEEEECCCC
Q ss_conf             687499998088988889999999999998799-5999987877
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGE-NVLLIDLDPQ   46 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~-rVllID~D~q   46 (265)
                      ++++|+.|  +=||+|-.     .|.+|++.|- +..+||.|.-
T Consensus        10 ~~s~V~v~--G~GGvGs~-----~a~~LarsGVG~l~lvD~D~v   46 (231)
T cd00755          10 RNAHVAVV--GLGGVGSW-----AAEALARSGVGKLTLIDFDVV   46 (231)
T ss_pred             HCCCEEEE--CCCHHHHH-----HHHHHHHCCCCEEEEEECCEE
T ss_conf             54978998--88636899-----999999809975999719990


No 370
>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=88.17  E-value=0.29  Score=26.86  Aligned_cols=28  Identities=25%  Similarity=0.464  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             49999808898888999999999999879959999
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      =.|+++ ++=.|||||+-=.|.      |.++..+
T Consensus         4 ~~V~iv-G~pN~GKSsL~N~L~------~~~~a~v   31 (168)
T cd04163           4 GFVAIV-GRPNVGKSTLLNALV------GQKISIV   31 (168)
T ss_pred             CEEEEE-CCCCCCHHHHHHHHH------CCCEEEE
T ss_conf             689999-999999999999995------8970332


No 371
>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=88.13  E-value=0.41  Score=25.97  Aligned_cols=44  Identities=18%  Similarity=0.244  Sum_probs=32.8

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCCCCCCC
Q ss_conf             68749999808898888999999999999-879959999878776801
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDPQGNAS   50 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~q~~~~   50 (265)
                      +.+++||.. ++-|+||||++--|-...- ..|  =.|+|.++-.+.+
T Consensus       386 ~~G~~vALV-GRSGSGKsTlv~LlPRFy~p~~G--~IllDG~~l~d~~  430 (603)
T TIGR02203       386 EPGETVALV-GRSGSGKSTLVNLLPRFYEPDSG--QILLDGVDLQDYT  430 (603)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHCCCCCCCCCC--CEEECCCHHHHCC
T ss_conf             587359987-06885389998552366045888--5652784044302


No 372
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=87.93  E-value=0.7  Score=24.63  Aligned_cols=36  Identities=31%  Similarity=0.311  Sum_probs=27.6

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             8749999808898888999999999999879959999
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      +++=|-+ ++--|.||||++..||-.++.+|+=|=-+
T Consensus       262 raeGILI-AG~PGaGKsTFaqAlAefy~~~GkiVKTm  297 (604)
T COG1855         262 RAEGILI-AGAPGAGKSTFAQALAEFYASQGKIVKTM  297 (604)
T ss_pred             HHCCEEE-ECCCCCCHHHHHHHHHHHHHHCCCEEEEC
T ss_conf             4164699-56999974689999999998669688632


No 373
>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional
Probab=87.89  E-value=0.85  Score=24.14  Aligned_cols=57  Identities=19%  Similarity=0.146  Sum_probs=42.5

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHH--CCCCEEEEECCCC-CCCCHHHCCCCCC
Q ss_conf             7687499998088988889999999999998--7995999987877-6801121246333
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAA--IGENVLLIDLDPQ-GNASTGLGIELYD   59 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~--~g~rVllID~D~q-~~~~~~l~~~~~~   59 (265)
                      .-++|-..+..+--|+|||-+|--||.+|.-  ...|+-+|..-|. +.-+...|+.+..
T Consensus       190 sLktKknvIL~G~pGtGKT~lAk~lA~~l~g~~~~~rv~~VqfhpsysYEDfi~Gyrp~~  249 (459)
T PRK11331        190 RLTIKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNG  249 (459)
T ss_pred             HHCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCHHHHHCCCCCCC
T ss_conf             854588279658999887899999999970788778468998358866178764605688


No 374
>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=87.89  E-value=0.47  Score=25.66  Aligned_cols=67  Identities=18%  Similarity=0.207  Sum_probs=37.6

Q ss_pred             CCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCC
Q ss_conf             27820331013332--22210112331001111123113788875335777655432026774310020231253
Q gi|254780806|r  123 DFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRN  195 (265)
Q Consensus       123 ~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~  195 (265)
                      .+.|-+||||+...  ..+..++..+|.+++++....--..   +..+.+...+ .++  ++.+=+++|++|...
T Consensus        64 ~~~~~~IDtPGH~dF~~~~i~g~~~~D~aiLVVdA~eGv~~---QT~eh~~la~-~lg--i~~iiV~iNK~D~~~  132 (195)
T cd01884          64 NRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMP---QTREHLLLAR-QVG--VPYIVVFLNKADMVD  132 (195)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHCCEEEEEEECCCCCCH---HHHHHHHHHH-HHC--CCCEEEEEECCCCCC
T ss_conf             81699626896077888998635113626899852778747---8999999999-809--996279996877898


No 375
>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=87.89  E-value=2  Score=21.99  Aligned_cols=108  Identities=12%  Similarity=0.107  Sum_probs=53.1

Q ss_pred             CCCEEEECCCC--CCCCCCHHHHHHHCCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHH
Q ss_conf             82033101333--222210112331001111123-113788875335777655432026774310020231253100112
Q gi|254780806|r  125 SYIFLDCPPSF--NLLTMNAMAAADSILVPLQCE-FFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQV  201 (265)
Q Consensus       125 D~IiiD~pp~~--~~~~~~al~aad~viip~~p~-~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~  201 (265)
                      .+-|.||++.-  ..++...+..||.++++...+ ..|+..+...   ++.+++..+....+ -+|-|+.|-..  .++ 
T Consensus        57 ~l~iwDtaG~e~~~~l~~~~~~~a~~~ilvydvt~~~Sf~~l~~w---~~~i~~~~~~~~~~-ilVGNK~DL~~--~r~-  129 (169)
T cd04114          57 KLQIWDTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEW---LREIEQYANNKVIT-ILVGNKIDLAE--RRE-  129 (169)
T ss_pred             EEEEEECCCCCCCCCCHHHHHHCCCEEEEEECCCCHHHHHHHHHH---HHHHHHHCCCCCEE-EEECCCCCHHH--CCC-
T ss_conf             999998999844451557774236645998148988899999999---99999868988638-97311343454--178-


Q ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHH
Q ss_conf             6899988085201562678688987773798579997999--89999999999999
Q gi|254780806|r  202 VSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELI  255 (265)
Q Consensus       202 ~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~  255 (265)
                                      |+..+.-.-|...|.|.++-+.+.  ..-+.|..||++|+
T Consensus       130 ----------------v~~~~~~~~a~~~~~~~~E~SAktg~nV~e~F~~la~~li  169 (169)
T cd04114         130 ----------------VSQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDLACRLI  169 (169)
T ss_pred             ----------------CCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHC
T ss_conf             ----------------8999999999988999999868988088999999999879


No 376
>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=87.88  E-value=0.34  Score=26.43  Aligned_cols=27  Identities=30%  Similarity=0.512  Sum_probs=18.2

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             9999808898888999999999999879959999
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      .|++. ++=-|||||+-=.|      .|+++..+
T Consensus         4 ~V~iv-G~pN~GKSTL~N~l------~g~~~~~v   30 (174)
T cd01895           4 RIAII-GRPNVGKSSLVNAL------LGEERVIV   30 (174)
T ss_pred             EEEEE-CCCCCCHHHHHHHH------HCCCCEEE
T ss_conf             99999-89999899999998------38984443


No 377
>pfam08423 Rad51 Rad51. Rad51 is a DNA repair and recombination protein and is a homologue of the bacterial ATPase RecA protein.
Probab=87.82  E-value=1.4  Score=22.85  Aligned_cols=40  Identities=23%  Similarity=0.120  Sum_probs=29.8

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHH------HCCCCEEEEECCC
Q ss_conf             749999808898888999999999999------8799599998787
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALA------AIGENVLLIDLDP   45 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la------~~g~rVllID~D~   45 (265)
                      +..|+=+.+--|+|||.++..||...+      ..+.+|+-||...
T Consensus        42 ~g~ITEi~G~~gsGKTQlc~qlav~~qlp~~~gg~~g~vvyIDTEg   87 (261)
T pfam08423        42 TGSITEVFGEFRTGKTQLCHTLCVTCQLPLEMGGGEGKALYIDTEG   87 (261)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHCHHHHCCCCCEEEEEECCC
T ss_conf             7729999899888789999999999407096569997289993688


No 378
>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
Probab=87.66  E-value=0.25  Score=27.23  Aligned_cols=56  Identities=27%  Similarity=0.335  Sum_probs=38.4

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCCCCCCC
Q ss_conf             6874999980889888899999999999987995999987877-68011212463334
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGIELYDR   60 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~~~~~~   60 (265)
                      .++++|-|. +--|+||||+|-.|...|.+.|+++.++|.|-- ..++.-||.+..++
T Consensus       441 ~~~~~iw~t-GlsgsGKstiA~~le~~L~~~g~~~~~LDGd~lR~gl~~dlgf~~~dR  497 (613)
T PRK05506        441 QKPATVWFT-GLSGSGKSTIANLVERRLHALGRHTYVLDGDNVRHGLNRDLGFTDADR  497 (613)
T ss_pred             CCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEECCHHHHHHHCCCCCCCHHHH
T ss_conf             997699997-789897479999999999977998799880898741045779798999


No 379
>PRK11823 DNA repair protein RadA; Provisional
Probab=87.65  E-value=1.3  Score=23.03  Aligned_cols=35  Identities=29%  Similarity=0.527  Sum_probs=28.8

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             999808898888999999999999879959999878
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      +...++-=|+||||+...+|..+| .|++||-|-..
T Consensus        92 ~iLlgGePGIGKSTLlLQ~a~~la-~~~~vLYvSGE  126 (454)
T PRK11823         92 VVLIGGDPGIGKSTLLLQVAAALA-AGGKVLYVSGE  126 (454)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHH-CCCCEEEECCC
T ss_conf             899507998889999999999985-59957998150


No 380
>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=87.61  E-value=1.1  Score=23.48  Aligned_cols=38  Identities=29%  Similarity=0.524  Sum_probs=32.2

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             6874999980889888899999999999987995999987877
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      --.||+.|..+=||.||-|     |..|+..|..|+|.|+|..
T Consensus       422 LA~~Va~VtGGasGIG~~~-----A~rL~~eGAhvV~aD~d~~  459 (709)
T TIGR02632       422 LARRVAFVTGGASGIGRET-----ARRLVDEGAHVVLADLDAE  459 (709)
T ss_pred             CCCEEEEEECCCCCHHHHH-----HHHHHHCCCEEEEECCCHH
T ss_conf             1570688973886526899-----9999736977999623657


No 381
>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=87.56  E-value=0.68  Score=24.71  Aligned_cols=25  Identities=32%  Similarity=0.494  Sum_probs=20.6

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHH
Q ss_conf             987687499998088988889999999
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINL   27 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nl   27 (265)
                      |.+|+-||+.+  +-.||||||+.-.+
T Consensus        10 ~~~~~~Kilil--G~~~sGKTsll~~l   34 (173)
T cd04154          10 LKEREMRILIL--GLDNAGKTTILKKL   34 (173)
T ss_pred             CCCCCEEEEEE--CCCCCCHHHHHHHH
T ss_conf             44573189999--89997889999998


No 382
>PRK07471 DNA polymerase III subunit delta'; Validated
Probab=87.48  E-value=1.2  Score=23.33  Aligned_cols=27  Identities=30%  Similarity=0.345  Sum_probs=19.8

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             4999980889888899999999999987
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAI   34 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~   34 (265)
                      --.-| ++--|+||+|++..+|.+|-..
T Consensus        40 HA~Lf-~Gp~GiGK~tlA~~~A~~ll~~   66 (363)
T PRK07471         40 HAWLI-GGPQGIGKATLAYRMARFLLAT   66 (363)
T ss_pred             CEEEE-ECCCCCCHHHHHHHHHHHHHCC
T ss_conf             45876-7999818899999999998579


No 383
>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=87.47  E-value=1.1  Score=23.41  Aligned_cols=109  Identities=14%  Similarity=0.156  Sum_probs=51.8

Q ss_pred             CCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             7820331013332--22210112331001111123-11378887533577765543202677431002023125310011
Q gi|254780806|r  124 FSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCE-FFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       124 yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~-~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      +.+.+.|+++.-.  .+....+..||.++++...+ ..|+..+....   +.++...+.+.++. +|-|+.|-..  .++
T Consensus        49 ~~l~iwDt~G~~~~~~~~~~~~~~a~~~ilv~d~t~~~Sf~~i~~~~---~~i~~~~~~~~~ii-lvgnK~Dl~~--~r~  122 (162)
T cd04123          49 IDLAIWDTAGQERYHALGPIYYRDADGAILVYDITDADSFQKVKKWI---KELKQMRGNNISLV-IVGNKIDLER--QRV  122 (162)
T ss_pred             EEEEEEECCCCCCCCCCCHHHEECCCEEEEEEECCCHHHHHHHHHHH---HHHHHHCCCCCCEE-EECCCCCCHH--HCC
T ss_conf             99999958997303556313301144579996389989999999999---99998769997468-6633213254--088


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHH
Q ss_conf             26899988085201562678688987773798579997999--89999999999999
Q gi|254780806|r  201 VVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELI  255 (265)
Q Consensus       201 ~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~  255 (265)
                                       |...+.-.-|...|.+.++-+-+.  ...+.|..|+++|+
T Consensus       123 -----------------v~~~e~~~~a~~~~~~y~e~Sak~g~nV~e~F~~l~~~il  162 (162)
T cd04123         123 -----------------VSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRMI  162 (162)
T ss_pred             -----------------CCHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             -----------------8999999999982998999812788198999999999869


No 384
>cd02026 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=87.43  E-value=0.62  Score=24.95  Aligned_cols=35  Identities=34%  Similarity=0.406  Sum_probs=27.1

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             99998088988889999999999998799599998787
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      ||+|+ +--|+||||++-.+...+...  +|.+|-.|-
T Consensus         1 IIgVa-G~SGSGKTTv~~~i~~ifg~~--~v~vI~~D~   35 (273)
T cd02026           1 IIGVA-GDSGCGKSTFLRRLTSLFGSD--LVTVICLDD   35 (273)
T ss_pred             CEEEE-CCCCCCHHHHHHHHHHHHCCC--CEEEEECCC
T ss_conf             98997-888786999999999985848--769996577


No 385
>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=87.39  E-value=2.1  Score=21.82  Aligned_cols=107  Identities=16%  Similarity=0.127  Sum_probs=51.7

Q ss_pred             CCCCEEEECCCC--CCCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             782033101333--22221011233100111112-311378887533577765543202677431002023125310011
Q gi|254780806|r  124 FSYIFLDCPPSF--NLLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       124 yD~IiiD~pp~~--~~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      |.+-|.|+++.-  ..+....+..||.++++... +..|+..+...++.+.....  +.++.+ -+|-|+.|...   + 
T Consensus        49 ~~l~iwDt~g~~~~~~~~~~~~~~a~~~ilvfd~~~~~Sf~~i~~~~~~i~~~~~--~~~~~~-ilVgnK~D~~~---~-  121 (161)
T cd01863          49 VKLAIWDTAGQERFRTLTSSYYRGAQGVILVYDVTRRDTFTNLETWLNELETYST--NNDIVK-MLVGNKIDKEN---R-  121 (161)
T ss_pred             EEEEEEECCCCCCCCCCHHHHHHHCCEEEEEEECCCHHHHHHHHHHHHHHHHHCC--CCCCEE-EEEEECCCCCC---C-
T ss_conf             9999999999842353422441321534899767826569999999999998568--888737-88731044000---6-


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHH
Q ss_conf             26899988085201562678688987773798579997999--899999999999
Q gi|254780806|r  201 VVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASE  253 (265)
Q Consensus       201 ~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~e  253 (265)
                                      .++..+...-|...|.+.++-+-+.  ..-+.|..|+++
T Consensus       122 ----------------~v~~~~~~~~a~~~~~~y~e~Sak~g~nV~~~F~~l~~~  160 (161)
T cd01863         122 ----------------EVTREEGLKFARKHNMLFIETSAKTRDGVQQAFEELVEK  160 (161)
T ss_pred             ----------------CCCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHH
T ss_conf             ----------------899999999999869999997158681599999999970


No 386
>PRK05380 pyrG CTP synthetase; Validated
Probab=87.37  E-value=1.9  Score=22.10  Aligned_cols=45  Identities=31%  Similarity=0.390  Sum_probs=36.0

Q ss_pred             CEEEEEECC-CCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             749999808-898888999999999999879959999878776801
Q gi|254780806|r    6 SRIITIANQ-KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS   50 (265)
Q Consensus         6 ~kvI~v~s~-KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~   50 (265)
                      +|-|.|..+ =-|.||-.+++.|+..|..+|++|-++-+||.=|.+
T Consensus         2 tKyIfVTGGVvS~lGKGi~aaSig~lLk~~G~~V~~~K~DPYlNvD   47 (534)
T PRK05380          2 TKYIFVTGGVVSSLGKGITAASLGALLKARGLKVTIQKLDPYLNVD   47 (534)
T ss_pred             CEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCC
T ss_conf             6099996983015740899999999999789658898414652258


No 387
>PRK13873 conjugal transfer ATPase TrbE; Provisional
Probab=87.33  E-value=1.6  Score=22.56  Aligned_cols=32  Identities=19%  Similarity=0.308  Sum_probs=28.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHC-CCCEEEEECCC
Q ss_conf             889888899999999999987-99599998787
Q gi|254780806|r   14 QKGGVGKTTTAINLSTALAAI-GENVLLIDLDP   45 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA~~la~~-g~rVllID~D~   45 (265)
                      +.-|+||||+-.-|+..+.+. +.+|.+.|-|-
T Consensus       448 GpTGsGKTvll~~l~~q~~ry~~~~vf~FDkd~  480 (815)
T PRK13873        448 GPTGAGKSVLLALMALQFRRYPGSQVFAFDFGG  480 (815)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCC
T ss_conf             889998999999999998644898489997898


No 388
>cd03113 CTGs CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent ammonia to the acceptor substrate at the synthetase domain to form an aminated product. Glutaminase domains have evolved from the same ancestor, whereas the synthetase domains are evolutionarily unrelated and have different functions. This protein family is classified based on the N-terminal synthetase domain.
Probab=87.31  E-value=1.4  Score=22.91  Aligned_cols=39  Identities=33%  Similarity=0.332  Sum_probs=32.9

Q ss_pred             ECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             808898888999999999999879959999878776801
Q gi|254780806|r   12 ANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS   50 (265)
Q Consensus        12 ~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~   50 (265)
                      ..-=-|.||-.+++.+|..|..+|++|-.+-+||.=|.+
T Consensus         7 GGV~SglGKGi~~aSig~ll~~~g~~V~~~K~DPYlNvD   45 (255)
T cd03113           7 GGVVSSLGKGITAASLGRLLKARGLKVTAQKLDPYLNVD   45 (255)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCEECC
T ss_conf             882015730899999999999789758898425650138


No 389
>PRK12337 2-phosphoglycerate kinase; Provisional
Probab=87.29  E-value=0.73  Score=24.51  Aligned_cols=25  Identities=24%  Similarity=0.336  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             4999980889888899999999999
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTAL   31 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~l   31 (265)
                      -+|..+.+--||||||++.-||+-|
T Consensus       262 PiiILIGGaSGvGKSTlAseLA~RL  286 (492)
T PRK12337        262 PLHVLLGGVSGTGKSVLAAELAYRL  286 (492)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             7699960788866888999999960


No 390
>cd01127 TrwB Bacterial conjugation protein TrwB,  ATP binding domain. TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.
Probab=87.24  E-value=1.8  Score=22.28  Aligned_cols=47  Identities=26%  Similarity=0.379  Sum_probs=35.1

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHC
Q ss_conf             87499998088988889999999999998799599998787768011212
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLG   54 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~   54 (265)
                      ..+-+.|+ +-=|+|||+.-.++...+..+|.++++.|  |.|.....|.
T Consensus        41 e~~H~lv~-G~tGsGKT~~i~~li~~~~~rg~~~II~D--pkGe~~~~fy   87 (410)
T cd01127          41 EEAHTMII-GTTGTGKTTQIRELLASIRARGDRAIIYD--PNGGFVSKFY   87 (410)
T ss_pred             HHCCEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEE--CCCHHHHHHH
T ss_conf             02747998-89999889999999999998699099995--8854999975


No 391
>TIGR00618 sbcc exonuclease SbcC; InterPro: IPR004592 All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. SbcC may have nuclease activity that is functionally related to one of the nuclease activities of the RecBCD enzyme (IPR004586 from INTERPRO).; GO: 0004527 exonuclease activity, 0006259 DNA metabolic process.
Probab=87.15  E-value=0.66  Score=24.79  Aligned_cols=29  Identities=31%  Similarity=0.374  Sum_probs=21.1

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCE
Q ss_conf             9999808898888999999999999879959
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENV   38 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rV   38 (265)
                      -+.++.||-|+||||+-=-++|+|  .|+++
T Consensus        31 ~~f~i~G~tGAGKtsLldAI~yAL--YGkP~   59 (1063)
T TIGR00618        31 KLFVICGKTGAGKTSLLDAITYAL--YGKPV   59 (1063)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH--CCCCC
T ss_conf             736777889983545999999987--28887


No 392
>TIGR02528 EutP ethanolamine utilization protein, EutP; InterPro: IPR012381   Members of this family function in ethanolamine  and propanediol  degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively.  The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems.  Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose , . More than 10f the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect , . The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella , , . Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 biogenic amine metabolic process.
Probab=87.12  E-value=0.37  Score=26.27  Aligned_cols=37  Identities=19%  Similarity=0.150  Sum_probs=23.4

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             499998088988889999999999998799599998787
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      |.|.|+ ++-|+||||++-.|--.- -.=||+=.|.+-+
T Consensus         1 Kr~~f~-G~~gCGKTTL~q~L~g~~-~~YKKTQAvE~~~   37 (144)
T TIGR02528         1 KRIMFI-GSVGCGKTTLTQALQGEE-IKYKKTQAVEYKD   37 (144)
T ss_pred             CEEEEE-ECCCCCHHHHHHHCCCCC-CCEEEEEEEEECC
T ss_conf             917887-158887443543116873-2102334454258


No 393
>PRK10773 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed
Probab=87.05  E-value=0.85  Score=24.14  Aligned_cols=35  Identities=20%  Similarity=0.399  Sum_probs=28.5

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             76874999980889888899999999999987995999
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLL   40 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVll   40 (265)
                      +...|+|+|.   |-.||||++-.++..|...|+.+..
T Consensus        97 ~~~~~vIgIT---GSnGKTTtk~~i~~iL~~~g~~~~t  131 (452)
T PRK10773         97 QVPARVVALT---GSSGKTSVKEMTAAILSQCGNTLYT  131 (452)
T ss_pred             CCCCCEEEEE---ECCCCCHHHHHHHHHHHHHCCCCCC
T ss_conf             5997589999---1699625999999999972884124


No 394
>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.
Probab=86.93  E-value=1.1  Score=23.51  Aligned_cols=37  Identities=30%  Similarity=0.303  Sum_probs=32.3

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECCC
Q ss_conf             9998088988889999999999998-799599998787
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLDP   45 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~D~   45 (265)
                      |+|.++==|+||||++--|...+.+ +|-+|.+|-.|-
T Consensus         1 lCVLcGLPaAGKTTLar~L~~~l~~~~gw~v~vI~YDd   38 (340)
T TIGR03575         1 LCVLCGLPAAGKSTLARSLSATLRRERGWAVAVITYDD   38 (340)
T ss_pred             CEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEHHH
T ss_conf             90432698787368999999998644476058986212


No 395
>PRK12826 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed
Probab=86.89  E-value=1.1  Score=23.46  Aligned_cols=41  Identities=24%  Similarity=0.519  Sum_probs=35.7

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             9876874999980889888899999999999987995999987877
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      |++-+.|++.|..+-+|.|+.     +|..|++.|.+|.+.|.+..
T Consensus         1 M~~L~gK~alITGgs~GIG~a-----ia~~la~~G~~V~~~~r~~~   41 (253)
T PRK12826          1 MRDLMGRVALVTGAARGIGRA-----IAVRFAADGADVIVVDICGQ   41 (253)
T ss_pred             CCCCCCCEEEEECCCCHHHHH-----HHHHHHHCCCEEEEEECCHH
T ss_conf             998899889994897789999-----99999987998999989889


No 396
>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=86.88  E-value=0.61  Score=24.97  Aligned_cols=122  Identities=19%  Similarity=0.175  Sum_probs=58.1

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEEC-CC-CCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCC
Q ss_conf             68749999808898888999999999999-87995999987-87-76801121246333454116763025771210244
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDL-DP-QGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQ   80 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~-D~-q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~   80 (265)
                      |.+.+|-|. +.-|+||||+|=-+=...- +.| |||+ |. |. |.+        |..-+..+-=+|++.. +   ...
T Consensus       489 ~~Ge~IGIv-GpSGSGKSTLTKL~QRLYtP~~G-qVLV-DG~DLA~~D--------P~wLRRQ~gVVLQEn~-L---Fsr  553 (703)
T TIGR01846       489 KPGEVIGIV-GPSGSGKSTLTKLLQRLYTPEHG-QVLV-DGVDLAIAD--------PAWLRRQVGVVLQENV-L---FSR  553 (703)
T ss_pred             CCCEEEEEE-CCCCCCHHHHHHHHHHHCCCCCC-EEEE-CCCCCCCCC--------CCHHHHCCEEEEECCH-H---HCC
T ss_conf             786579987-27898678999998861488887-4777-030001018--------5201022302340002-1---012


Q ss_pred             CCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCC--CCHHHHH
Q ss_conf             44442000148874577500012322221023332247651027820331013332222--1011233
Q gi|254780806|r   81 TAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLT--MNAMAAA  146 (265)
Q Consensus        81 ~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~--~~al~aa  146 (265)
                      +..||+.+-  ++.. ..|...+.  .+..--.+|+. .+.+.||-.+--=++++|--.  +-||+-|
T Consensus       554 SirdNI~l~--~P~~-~~E~Vi~A--A~LAGA~dFI~-~Lp~GY~T~vgE~G~~LSGGQRQRIAiARA  615 (703)
T TIGR01846       554 SIRDNIALC--NPGA-SVEHVIAA--AKLAGAHDFIS-ELPQGYNTEVGEKGANLSGGQRQRIAIARA  615 (703)
T ss_pred             CHHHHHHHC--CCCC-CHHHHHHH--HHHCCHHHHHH-HCCCCCCCCCEEECCCCCCHHHHHHHHHHH
T ss_conf             278898517--7776-98999999--86218589997-363767740012415667337899999999


No 397
>PTZ00265 multidrug resistance protein (mdr1); Provisional
Probab=86.87  E-value=1.5  Score=22.73  Aligned_cols=41  Identities=17%  Similarity=0.326  Sum_probs=27.2

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEEC-CCC
Q ss_conf             68749999808898888999999999999-87995999987-877
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDL-DPQ   46 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~-D~q   46 (265)
                      +.+|++++. ++-|+||||+..-|-...- ..| .|++-|. |.+
T Consensus       409 ~~G~t~AlV-G~SGsGKSTii~LL~RfYdP~~G-~I~i~Dg~di~  451 (1467)
T PTZ00265        409 KEGKTYAFV-GESGCGKSTILKLIERLYDPTEG-DIIINDSHNLK  451 (1467)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHCCCCCCCC-EEEECCCCCCH
T ss_conf             389779986-68887566799999632688998-69978997802


No 398
>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=86.82  E-value=1  Score=23.74  Aligned_cols=65  Identities=12%  Similarity=0.133  Sum_probs=30.6

Q ss_pred             CCCEEEECCCC--CCCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEC
Q ss_conf             82033101333--22221011233100111112-31137888753357776554320267743100202312
Q gi|254780806|r  125 SYIFLDCPPSF--NLLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDS  193 (265)
Q Consensus       125 D~IiiD~pp~~--~~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~  193 (265)
                      .+.|.||++.-  ..+....+.-||.++++... +..|+..+...   ++.+++....+.++. +|-|+.|-
T Consensus        50 ~l~iwDt~G~e~~~~l~~~~~~~~d~~ilv~d~~~~~Sf~~~~~~---~~~i~~~~~~~~~ii-lvgnK~DL  117 (159)
T cd00154          50 KLQIWDTAGQERFRSITPSYYRGAHGAILVYDITNRESFENLDKW---LKELKEYAPENIPII-LVGNKIDL  117 (159)
T ss_pred             EEEEEECCCCHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHHH---HHHHHHHCCCCCCEE-EEEECCCC
T ss_conf             999997898265778899997541275672448988999999999---999998689888269-99974563


No 399
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=86.75  E-value=1.3  Score=23.05  Aligned_cols=38  Identities=18%  Similarity=0.280  Sum_probs=30.9

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             749999808898888999999999999879959999878
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      .+.+ +..+..|+|||.+.--++..+...++++.-+++.
T Consensus        38 ~~~l-~i~G~~GsGKTHLl~a~~~~~~~~~~~~~yl~~~   75 (226)
T TIGR03420        38 DRFL-YLWGESGSGKSHLLQAACAAAEERGKSAIYLPLA   75 (226)
T ss_pred             CCEE-EEECCCCCCHHHHHHHHHHHHHCCCCCEEEECHH
T ss_conf             8869-9989999988999999999986269957995299


No 400
>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]
Probab=86.65  E-value=0.92  Score=23.95  Aligned_cols=32  Identities=34%  Similarity=0.409  Sum_probs=22.9

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEE
Q ss_conf             687499998088988889999999999998799599
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVL   39 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVl   39 (265)
                      +...+|+|. +-=|+||||+|-.||-.|   |.+|.
T Consensus         2 ~~~~~IvI~-G~IG~GKSTLa~~La~~l---~~~~~   33 (216)
T COG1428           2 NVAMVIVIE-GMIGAGKSTLAQALAEHL---GFKVF   33 (216)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHHHH---CCCEE
T ss_conf             866089984-464468789999999883---88502


No 401
>cd01868 Rab11_like Rab11-like.  Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP
Probab=86.63  E-value=2.3  Score=21.57  Aligned_cols=107  Identities=17%  Similarity=0.126  Sum_probs=50.3

Q ss_pred             CCCEEEECCCCC--CCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHH
Q ss_conf             820331013332--2221011233100111112-3113788875335777655432026774310020231253100112
Q gi|254780806|r  125 SYIFLDCPPSFN--LLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQV  201 (265)
Q Consensus       125 D~IiiD~pp~~~--~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~  201 (265)
                      .+-|.||++.-.  .+....+..||.++++... +..|+..+..   .++.++.....+.++ -+|-|+.|-..  .+  
T Consensus        53 ~l~iwDtaG~e~~~~~~~~~~~~a~~~ilvydit~~~Sf~~i~~---w~~~i~~~~~~~~~i-ilVgnK~DL~~--~r--  124 (165)
T cd01868          53 KAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKKQTFENVER---WLKELRDHADSNIVI-MLVGNKSDLRH--LR--  124 (165)
T ss_pred             EEEEEECCCCHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHH---HHHHHHHHCCCCCEE-EEECCCCCHHH--HC--
T ss_conf             99999899972126789987332051489862698899999999---999999855577359-87023478688--57--


Q ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHH
Q ss_conf             6899988085201562678688987773798579997999--8999999999999
Q gi|254780806|r  202 VSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASEL  254 (265)
Q Consensus       202 ~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el  254 (265)
                                     .|+..+.-.-|...|.+.++-+-++  ..-+.|..|+++|
T Consensus       125 ---------------~Vs~~e~~~~a~~~~~~~~E~SAk~g~nV~e~F~~l~~~i  164 (165)
T cd01868         125 ---------------AVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQLLTEI  164 (165)
T ss_pred             ---------------CCCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             ---------------8889999999998599799967888929899999999986


No 402
>PRK05872 short chain dehydrogenase; Provisional
Probab=86.63  E-value=1.1  Score=23.59  Aligned_cols=41  Identities=29%  Similarity=0.516  Sum_probs=35.0

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             9876874999980889888899999999999987995999987877
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      |..-+.|++.|..+-+|.|+-     +|..|++.|.+|.++|.|.+
T Consensus         4 M~~L~gKvalITGassGIG~a-----iA~~la~~Ga~Vvl~dr~~~   44 (296)
T PRK05872          4 MTSLDGKVVFVTGAARGVGAE-----LARRLHARGAKVALVDLEEA   44 (296)
T ss_pred             CCCCCCCEEEEECCCCHHHHH-----HHHHHHHCCCEEEEEECCHH
T ss_conf             988599879992710589999-----99999987998999989999


No 403
>pfam06414 Zeta_toxin Zeta toxin. This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid.
Probab=86.53  E-value=1.5  Score=22.75  Aligned_cols=39  Identities=33%  Similarity=0.467  Sum_probs=27.9

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             768749999808898888999999999999879959999878
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ..+.|.| |+.+=-|+|||+++-.+...+.  +..+..||.|
T Consensus         9 ~~~Pkai-~laG~pGAGKS~~~~~~~~~~~--~~~~v~In~D   47 (191)
T pfam06414         9 QERPVAV-LLGGQPGAGKTELARALLEELG--GGNVVRIDPD   47 (191)
T ss_pred             CCCCEEE-EEECCCCCCHHHHHHHHHHHCC--CCCCEEECCH
T ss_conf             7698799-9957998888999999987537--8993897135


No 404
>PRK07773 replicative DNA helicase; Validated
Probab=86.45  E-value=2.2  Score=21.71  Aligned_cols=39  Identities=18%  Similarity=0.405  Sum_probs=30.8

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEECC
Q ss_conf             87499998088988889999999999998-79959999878
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLD   44 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~D   44 (265)
                      ++..|.+ .++=|.|||+++.|+|...|. .+..|++.-+.
T Consensus       202 ~~~l~i~-a~rp~~GKt~~~~~~a~~~a~~~~~~v~~FSLE  241 (868)
T PRK07773        202 PGQMIIV-AARPGVGKSTLGLDFARSCSIRHRLASVIFSLE  241 (868)
T ss_pred             CCCEEEE-EECCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf             7767999-828977777899999999998659965897305


No 405
>PRK13640 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=86.42  E-value=0.98  Score=23.77  Aligned_cols=29  Identities=17%  Similarity=0.252  Sum_probs=24.4

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             687499998088988889999999999998
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAA   33 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~   33 (265)
                      ++++++++. +.-|+||||+.-.|+-.+.-
T Consensus        32 ~~Ge~vaii-G~nGsGKSTL~~~l~Gll~P   60 (283)
T PRK13640         32 PRGSWTALI-GHNGSGKSTISKLINGLLLP   60 (283)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCCC
T ss_conf             899999999-99998799999999640378


No 406
>COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]
Probab=86.36  E-value=0.57  Score=25.14  Aligned_cols=81  Identities=12%  Similarity=0.190  Sum_probs=39.3

Q ss_pred             CCCCCCEEEECCC--CCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHH
Q ss_conf             0278203310133--32222101123310011111231137888753357776554320267743100202312531001
Q gi|254780806|r  122 SDFSYIFLDCPPS--FNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQ  199 (265)
Q Consensus       122 ~~yD~IiiD~pp~--~~~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~  199 (265)
                      .+|-+=|+|||+.  +|-...-.|.+.|.+++++....-.+-...=      -+++.+...++.+ +|+|+.|.......
T Consensus        66 ~~~~INIvDTPGHADFGGEVERvl~MVDgvlLlVDA~EGpMPQTrF------VlkKAl~~gL~PI-VVvNKiDrp~Arp~  138 (603)
T COG1217          66 NGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRF------VLKKALALGLKPI-VVINKIDRPDARPD  138 (603)
T ss_pred             CCEEEEEECCCCCCCCCCHHHHHHHHCCEEEEEEECCCCCCCCHHH------HHHHHHHCCCCCE-EEEECCCCCCCCHH
T ss_conf             8838987658986776625451143233489999755588873144------4899997499848-99967789998878


Q ss_pred             HHHHHHHHHH
Q ss_conf             1268999880
Q gi|254780806|r  200 QVVSDVRKNL  209 (265)
Q Consensus       200 ~~~~~l~~~~  209 (265)
                      ++.+++.+.|
T Consensus       139 ~Vvd~vfDLf  148 (603)
T COG1217         139 EVVDEVFDLF  148 (603)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 407
>PRK13644 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=86.22  E-value=0.85  Score=24.13  Aligned_cols=35  Identities=43%  Similarity=0.577  Sum_probs=27.0

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEE
Q ss_conf             687499998088988889999999999998-7995999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLL   40 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVll   40 (265)
                      +++++++++ +.-|+||||+.-.|+-.+.- .| +|.+
T Consensus        26 ~~Ge~vaii-G~nGsGKSTL~~~l~Gll~P~~G-~I~v   61 (274)
T PRK13644         26 KKGEYIGII-GKNGSGKSTLALHLNGLLRPQKG-KVLV   61 (274)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCCCCCC-EEEE
T ss_conf             489999999-99998099999999706858887-2999


No 408
>PRK13830 conjugal transfer protein TrbE; Provisional
Probab=86.21  E-value=1.7  Score=22.38  Aligned_cols=33  Identities=18%  Similarity=0.261  Sum_probs=28.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHC-CCCEEEEECCC
Q ss_conf             0889888899999999999987-99599998787
Q gi|254780806|r   13 NQKGGVGKTTTAINLSTALAAI-GENVLLIDLDP   45 (265)
Q Consensus        13 s~KGGvGKTT~a~nlA~~la~~-g~rVllID~D~   45 (265)
                      -+.-|+||||+-.-|+..+.+. |.+|.+.|-|-
T Consensus       462 iGpTGsGKTvll~fl~aq~~ky~~~~vf~FDKd~  495 (818)
T PRK13830        462 FGPTGSGKSTLLALIAAQFRRYAGAQIFAFDKGR  495 (818)
T ss_pred             ECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf             8999998899999999998642798389974887


No 409
>COG0370 FeoB Fe2+ transport system protein B [Inorganic ion transport and metabolism]
Probab=86.18  E-value=0.64  Score=24.84  Aligned_cols=32  Identities=28%  Similarity=0.330  Sum_probs=15.6

Q ss_pred             CCCCEEECCCHHH-HHHHHHHHHHHCCCCCCCC
Q ss_conf             0020231253100-1126899988085201562
Q gi|254780806|r  186 IILTMFDSRNSLS-QQVVSDVRKNLGGKVYNTV  217 (265)
Q Consensus       186 iv~N~~~~~~~~~-~~~~~~l~~~~~~~v~~~~  217 (265)
                      +.+||+|...+.. +--.+.+.+.+|.++.+++
T Consensus       113 laLNm~D~A~~~Gi~Id~~~L~~~LGvPVv~tv  145 (653)
T COG0370         113 LALNMIDEAKKRGIRIDIEKLSKLLGVPVVPTV  145 (653)
T ss_pred             EEECCHHHHHHCCCCCCHHHHHHHHCCCEEEEE
T ss_conf             996127568864971269999998689889987


No 410
>PRK08589 short chain dehydrogenase; Validated
Probab=86.15  E-value=1.1  Score=23.51  Aligned_cols=41  Identities=27%  Similarity=0.505  Sum_probs=35.0

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             9876874999980889888899999999999987995999987877
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      |..-+.||+.|..+-+|.|+.+     |..|++.|.+|++.|.+..
T Consensus         1 M~rL~gKvalVTGas~GIG~ai-----A~~la~~Ga~Vv~~d~~~~   41 (272)
T PRK08589          1 MKRLENKVAVITGASTGIGQAS-----AIALAQEGAYVLAVDIAEA   41 (272)
T ss_pred             CCCCCCCEEEEECCCCHHHHHH-----HHHHHHCCCEEEEEECCHH
T ss_conf             9999979899978256999999-----9999986999999838278


No 411
>PRK00421 murC UDP-N-acetylmuramate--L-alanine ligase; Provisional
Probab=85.86  E-value=1.3  Score=23.09  Aligned_cols=36  Identities=36%  Similarity=0.452  Sum_probs=27.6

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCE-EEEE
Q ss_conf             68749999808898888999999999999879959-9998
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENV-LLID   42 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rV-llID   42 (265)
                      +..++|+|.   |==||||+|..+++.|...|+++ .+|-
T Consensus       106 ~~~~~IaVt---GTnGKTTtT~ll~~il~~~g~~~~~~iG  142 (459)
T PRK00421        106 RLRTSIAVA---GTHGKTTTTSLLAHVLAEAGLDPTFIIG  142 (459)
T ss_pred             HCCCEEEEE---CCCCCCHHHHHHHHHHHHCCCCCEEEEC
T ss_conf             259649997---7888611899999999976998748857


No 412
>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]
Probab=85.85  E-value=0.85  Score=24.12  Aligned_cols=26  Identities=38%  Similarity=0.521  Sum_probs=20.3

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             874999980889888899999999999
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTAL   31 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~l   31 (265)
                      ++.+| +..+--||||||+|.-+|.-|
T Consensus        88 ~p~II-LIGGasGVGkStIA~ElA~rL  113 (299)
T COG2074          88 RPLII-LIGGASGVGKSTIAGELARRL  113 (299)
T ss_pred             CCEEE-EECCCCCCCHHHHHHHHHHHC
T ss_conf             87599-961788777257999999972


No 413
>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=85.84  E-value=2.6  Score=21.33  Aligned_cols=110  Identities=13%  Similarity=0.094  Sum_probs=57.9

Q ss_pred             CCCEEEECCCC--CCCCCCHHHHHHHCCCCCCCC-CHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCCCCEEECCCHHHHH
Q ss_conf             82033101333--222210112331001111123-113788875335777655432-02677431002023125310011
Q gi|254780806|r  125 SYIFLDCPPSF--NLLTMNAMAAADSILVPLQCE-FFALEGLSQLLETVEEVRRTV-NSALDIQGIILTMFDSRNSLSQQ  200 (265)
Q Consensus       125 D~IiiD~pp~~--~~~~~~al~aad~viip~~p~-~~s~~~~~~~~~~i~~~~~~~-~~~~~~~~iv~N~~~~~~~~~~~  200 (265)
                      .+-|.||++.-  ..+....+..|+.+|++...+ ..|+..+...+   +.++... ...+.+ -+|-|+.|-...  + 
T Consensus        64 ~l~iwDtaGqe~~~~l~~~~~~~a~~~ilvydit~~~Sf~~l~~w~---~~i~~~~~~~~~~i-ilVGNK~DL~~~--r-  136 (180)
T cd04127          64 HLQLWDTAGQERFRSLTTAFFRDAMGFLLIFDLTNEQSFLNVRNWM---SQLQTHAYCENPDI-VLCGNKADLEDQ--R-  136 (180)
T ss_pred             EEEEEECCCCHHHHHHHHHHHHHHCEEEEEEECCCHHHHHHHHHHH---HHHHHHCCCCCCCE-EEECCCCCHHHC--C-
T ss_conf             9999989886304788899987543658999689889999899999---99998546689857-875032366750--8-


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHHH
Q ss_conf             26899988085201562678688987773798579997999--8999999999999999
Q gi|254780806|r  201 VVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQQ  257 (265)
Q Consensus       201 ~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~~  257 (265)
                                      .|+..+.-.-|...|.|.++-+.++  ...+.|..|++.+++|
T Consensus       137 ----------------~V~~~e~~~~a~~~~~~~~E~SAk~g~nV~e~F~~l~~~i~~~  179 (180)
T cd04127         137 ----------------QVSEEQAKALADKYGIPYFETSAATGTNVEKAVERLLDLVMKR  179 (180)
T ss_pred             ----------------CCCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHH
T ss_conf             ----------------8899999999998499799980377919899999999999972


No 414
>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=85.80  E-value=0.7  Score=24.63  Aligned_cols=19  Identities=37%  Similarity=0.370  Sum_probs=14.2

Q ss_pred             EEEEECCCCCCCHHHHHHHH
Q ss_conf             99998088988889999999
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINL   27 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nl   27 (265)
                      +|++. ++=-|||||+-=.|
T Consensus         1 tVaIv-G~PNvGKSTLlN~L   19 (188)
T pfam02421         1 TIALV-GNPNVGKTTLFNAL   19 (188)
T ss_pred             CEEEE-CCCCCCHHHHHHHH
T ss_conf             98998-89998999999999


No 415
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=85.71  E-value=2.1  Score=21.89  Aligned_cols=27  Identities=41%  Similarity=0.485  Sum_probs=21.2

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             499998088988889999999999998
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAA   33 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~   33 (265)
                      +-++|+|+=-|+||||+.+.|-..|.+
T Consensus       162 ~~~~vIsGGPGTGKTttV~~lLa~l~~  188 (607)
T PRK10875        162 RRISVISGGPGTGKTTTVAKLLAALIQ  188 (607)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             577899679998778899999999999


No 416
>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=85.67  E-value=0.75  Score=24.46  Aligned_cols=80  Identities=16%  Similarity=0.127  Sum_probs=38.1

Q ss_pred             CCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHH-HH
Q ss_conf             7820331013332--22210112331001111123113788875335777655432026774310020231253100-11
Q gi|254780806|r  124 FSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLS-QQ  200 (265)
Q Consensus       124 yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~-~~  200 (265)
                      ..+.+||||+.-.  ..+..++..+|.+++++..+.---....   +.+..++ ..+.+ .+. +++|++|.-.... ..
T Consensus        51 ~~i~~iDtPGh~~~~~~~~~~~~~aD~~llVvda~~g~~~q~~---e~~~~~~-~~~i~-~~i-vvlNK~D~v~~~~~~~  124 (164)
T cd04171          51 KRLGFIDVPGHEKFIKNMLAGAGGIDLVLLVVAADEGIMPQTR---EHLEILE-LLGIK-RGL-VVLTKADLVDEDWLEL  124 (164)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHH---HHHHHHH-HCCCC-CEE-EEEECCCCCCHHHHHH
T ss_conf             8999994878799999999987426725899861778888899---9999998-73887-278-7346342579789999


Q ss_pred             HHHHHHHHH
Q ss_conf             268999880
Q gi|254780806|r  201 VVSDVRKNL  209 (265)
Q Consensus       201 ~~~~l~~~~  209 (265)
                      ..+++++.+
T Consensus       125 ~~~~i~~~l  133 (164)
T cd04171         125 VEEEIRELL  133 (164)
T ss_pred             HHHHHHHHH
T ss_conf             999999999


No 417
>pfam01121 CoaE Dephospho-CoA kinase. This family catalyses the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form Coenzyme A EC:2.7.1.24. This enzyme uses ATP in its reaction.
Probab=85.60  E-value=1.5  Score=22.62  Aligned_cols=31  Identities=32%  Similarity=0.440  Sum_probs=23.3

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             99998088988889999999999998799599998787
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      ||+++ +.=|+||||++--|    ...|.+|.  |+|-
T Consensus         2 iIgiT-G~IgsGKStv~~~l----~~~G~~vi--daD~   32 (179)
T pfam01121         2 IVGLT-GGIGSGKSTVANLF----ADLGVPIV--DADV   32 (179)
T ss_pred             EEEEE-CCCCCCHHHHHHHH----HHCCCCEE--ECHH
T ss_conf             89985-78647899999999----98799199--1809


No 418
>TIGR02729 Obg_CgtA GTP-binding protein Obg/CgtA; InterPro: IPR014100   This entry describes a universal, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure..
Probab=85.56  E-value=0.5  Score=25.48  Aligned_cols=67  Identities=16%  Similarity=0.252  Sum_probs=48.3

Q ss_pred             CCCEEEECC---------CCCCCCCCHHHHHHHCCCCCCCCCH---------HHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             820331013---------3322221011233100111112311---------3788875335777655432026774310
Q gi|254780806|r  125 SYIFLDCPP---------SFNLLTMNAMAAADSILVPLQCEFF---------ALEGLSQLLETVEEVRRTVNSALDIQGI  186 (265)
Q Consensus       125 D~IiiD~pp---------~~~~~~~~al~aad~viip~~p~~~---------s~~~~~~~~~~i~~~~~~~~~~~~~~~i  186 (265)
                      +|||=|-|+         |+++-.+--++-+..++-++..+..         .+++...+.++++.+...+-...++  |
T Consensus       210 ~fviADIPGLIEGAs~G~GLG~~FLKHIERt~~L~hviD~~~~qlSkh~~~~p~~~y~~l~~EL~~Y~~~L~~k~~~--i  287 (296)
T TIGR02729       210 SFVIADIPGLIEGASEGKGLGHKFLKHIERTRLLLHVIDASGIQLSKHDGRDPIEDYETLRNELELYSPELADKPQI--I  287 (296)
T ss_pred             EEEEEECCCCHHHHHCCCCCCHHHHHHHHHEEEEEEEEECCCCEEEECCCCCHHHHHHHHHHHHHHCCHHHCCCCEE--E
T ss_conf             89998568615666268875335545752026688798068753424289888999999999997508736278079--9


Q ss_pred             CCCEEEC
Q ss_conf             0202312
Q gi|254780806|r  187 ILTMFDS  193 (265)
Q Consensus       187 v~N~~~~  193 (265)
                      |+|++|-
T Consensus       288 v~NK~Dl  294 (296)
T TIGR02729       288 VLNKIDL  294 (296)
T ss_pred             EEEECCC
T ss_conf             9860677


No 419
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=85.52  E-value=1.9  Score=22.08  Aligned_cols=34  Identities=26%  Similarity=0.466  Sum_probs=29.9

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             99808898888999999999999879959999878
Q gi|254780806|r   10 TIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus        10 ~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ..+++-=|+||||+-..++..+|+++ +||-|-..
T Consensus        96 iLIgGdPGIGKSTLLLQva~~lA~~~-~vLYVsGE  129 (456)
T COG1066          96 ILIGGDPGIGKSTLLLQVAARLAKRG-KVLYVSGE  129 (456)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCC-CEEEEECC
T ss_conf             99736898779899999999987059-57999677


No 420
>TIGR00073 hypB hydrogenase accessory protein HypB; InterPro: IPR004392 The hydrogenase accessory protein HypB is a GTP hydrolase for assembly of nickel metallocentre of hydrogenase. A similar protein, ureG, is an accessory protein for urease, which also uses nickel.; GO: 0016151 nickel ion binding, 0006461 protein complex assembly.
Probab=85.47  E-value=0.97  Score=23.79  Aligned_cols=41  Identities=24%  Similarity=0.268  Sum_probs=29.5

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             9999808898888999999999999879959999878776801
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS   50 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~   50 (265)
                      ++=|+ +-=|+||||+--++.-.+ +..+|+++|-.|.|...+
T Consensus        36 ~lNfm-sspGSGKT~LiEk~~~~~-~~~~K~Avi~GD~~t~~D   76 (225)
T TIGR00073        36 VLNFM-SSPGSGKTTLIEKLIERL-DDEVKIAVIEGDVQTKND   76 (225)
T ss_pred             EEEEC-CCCCCCHHHHHHHHHHHH-CCCCCEEEEECCHHHHHH
T ss_conf             99802-588611589999999984-578978999755322556


No 421
>smart00487 DEXDc DEAD-like helicases superfamily.
Probab=85.36  E-value=1.8  Score=22.27  Aligned_cols=32  Identities=28%  Similarity=0.309  Sum_probs=24.9

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHCC--CCEEEEE
Q ss_conf             9808898888999999999999879--9599998
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAAIG--ENVLLID   42 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~~g--~rVllID   42 (265)
                      +...--|.|||+.+..++..+...+  .+|+++=
T Consensus        28 ~i~~~tGsGKT~~~~~~~~~~~~~~~~~~~li~~   61 (201)
T smart00487       28 ILAAPTGSGKTLAALLPALEALKRGKGKRVLVLV   61 (201)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEE
T ss_conf             9989999609999999999986338997599990


No 422
>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]
Probab=85.34  E-value=0.71  Score=24.59  Aligned_cols=16  Identities=44%  Similarity=0.391  Sum_probs=6.3

Q ss_pred             CCCCCCCHHHHHHHHH
Q ss_conf             0889888899999999
Q gi|254780806|r   13 NQKGGVGKTTTAINLS   28 (265)
Q Consensus        13 s~KGGvGKTT~a~nlA   28 (265)
                      |+..|+||||+.--|.
T Consensus       179 sGGTGSGKTTlLNal~  194 (355)
T COG4962         179 SGGTGSGKTTLLNALS  194 (355)
T ss_pred             ECCCCCCHHHHHHHHH
T ss_conf             6787887999999997


No 423
>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.
Probab=85.33  E-value=0.9  Score=24.01  Aligned_cols=23  Identities=43%  Similarity=0.569  Sum_probs=18.8

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             999980889888899999999999
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTAL   31 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~l   31 (265)
                      ||++ ++.-|+||||++-.||-.|
T Consensus         1 iIaI-dGpagsGKsT~ak~lA~~l   23 (147)
T cd02020           1 IIAI-DGPAGSGKSTVAKLLAKKL   23 (147)
T ss_pred             CEEE-ECCCCCCHHHHHHHHHHHH
T ss_conf             9888-6899789899999999990


No 424
>PRK10536 hypothetical protein; Provisional
Probab=85.33  E-value=1.1  Score=23.48  Aligned_cols=30  Identities=20%  Similarity=0.199  Sum_probs=24.4

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             749999808898888999999999999879
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIG   35 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g   35 (265)
                      .+-|+|+.+.-|+|||-+|+..|..+-..+
T Consensus        73 ~~~ivf~~GpAGTGKT~lA~a~Al~~l~~~  102 (262)
T PRK10536         73 SKQLIFATGEAGCGKTWISAAKAAEALIHK  102 (262)
T ss_pred             HCCEEEEECCCCCCHHHHHHHHHHHHHHHC
T ss_conf             198399989998758999999999999858


No 425
>PRK13632 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=85.24  E-value=0.87  Score=24.09  Aligned_cols=38  Identities=21%  Similarity=0.225  Sum_probs=27.1

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             6874999980889888899999999999987995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      +++++++++ +.-|+||||+.-.|+-.+--.+=+| .+|.
T Consensus        34 ~~Ge~vaiv-G~nGsGKSTLlk~l~Gll~p~~G~I-~v~G   71 (273)
T PRK13632         34 NEGEYVAIL-GHNGSGKSTISKILTGLLKPQSGEI-KIFG   71 (273)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCCCCCCEE-EECC
T ss_conf             499899999-9999869999999973877888759-9999


No 426
>PRK06912 acoL dihydrolipoamide dehydrogenase; Validated
Probab=85.13  E-value=0.77  Score=24.39  Aligned_cols=38  Identities=26%  Similarity=0.363  Sum_probs=26.7

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             749999808898888999999999999879959999878776801
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS   50 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~   50 (265)
                      +|||.+.++-||.       ..|..+++.|++|++||-++-|...
T Consensus         1 ~~vvVIG~GpaG~-------~aA~~aa~~G~kV~lIEk~~~GGtC   38 (458)
T PRK06912          1 SKLVIIGGGPAGY-------VAAITAAQNGKEVTLIDEADLGGTC   38 (458)
T ss_pred             CEEEEEEECHHHH-------HHHHHHHHCCCEEEEEECCCCCCEE
T ss_conf             9499990088999-------9999999785959999589978740


No 427
>PRK12829 short chain dehydrogenase; Provisional
Probab=85.09  E-value=1.3  Score=22.99  Aligned_cols=41  Identities=17%  Similarity=0.359  Sum_probs=35.0

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             9876874999980889888899999999999987995999987877
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      |..-++||+.|..+-+|.|+.+     |..|++.|.+|.+.|.++.
T Consensus         6 m~~L~GKvalVTGgs~GIG~ai-----A~~la~~Ga~V~i~~r~~~   46 (264)
T PRK12829          6 LKPLDGLRVLVTGGASGIGRAI-----AEAFAEAGARVHVCDVSEA   46 (264)
T ss_pred             CCCCCCCEEEEECCCCHHHHHH-----HHHHHHCCCEEEEEECCHH
T ss_conf             7689999799947376899999-----9999987998999979989


No 428
>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=85.04  E-value=1  Score=23.61  Aligned_cols=28  Identities=29%  Similarity=0.378  Sum_probs=22.8

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             68749999808898888999999999999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALA   32 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la   32 (265)
                      +++.++++. +.-|+||||+.-.++-.+.
T Consensus        29 ~~Ge~~~ii-G~sGsGKSTLl~~i~Gl~~   56 (228)
T cd03257          29 KKGETLGLV-GESGSGKSTLARAILGLLK   56 (228)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCC
T ss_conf             699899999-9999869999999972898


No 429
>PRK08862 short chain dehydrogenase; Provisional
Probab=84.99  E-value=0.94  Score=23.89  Aligned_cols=39  Identities=31%  Similarity=0.485  Sum_probs=32.3

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             68749999808898888999999999999879959999878776
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG   47 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~   47 (265)
                      -+.||+.|..+-+|.|+.     +|..||+.|.+|.+.|-|++.
T Consensus         3 lk~Kv~lITGas~GIG~a-----iA~~~A~~Ga~Vii~~r~~~~   41 (227)
T PRK08862          3 IKNSIILITSAGSVLGRT-----ISCHFARLGATLILCDQDQSA   41 (227)
T ss_pred             CCCCEEEEECCCCHHHHH-----HHHHHHHCCCEEEEEECCHHH
T ss_conf             999999997988799999-----999999879999999699999


No 430
>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.
Probab=84.98  E-value=0.85  Score=24.14  Aligned_cols=30  Identities=30%  Similarity=0.425  Sum_probs=22.1

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             98088988889999999999998799599998787
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      |..+--|+||||++..||..   .|  ...||.|-
T Consensus         3 iv~GvsGsGKSTia~~La~~---lg--~~~i~~D~   32 (150)
T cd02021           3 VVMGVSGSGKSTVGKALAER---LG--APFIDGDD   32 (150)
T ss_pred             EEECCCCCCHHHHHHHHHHH---HC--CCEECCCC
T ss_conf             99918999999999999997---19--95641543


No 431
>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]
Probab=84.97  E-value=2.5  Score=21.36  Aligned_cols=39  Identities=23%  Similarity=0.116  Sum_probs=32.5

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             49999808898888999999999999879959999878776
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG   47 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~   47 (265)
                      +.|.|. +-=|+|||++.-.+-..|... +++.+|-.|.+.
T Consensus        14 ~~i~v~-Gp~GSGKTaLie~~~~~L~~~-~~~aVI~~Di~t   52 (202)
T COG0378          14 LRIGVG-GPPGSGKTALIEKTLRALKDE-YKIAVITGDIYT   52 (202)
T ss_pred             EEEEEC-CCCCCCHHHHHHHHHHHHHHH-CCEEEEECEEEC
T ss_conf             899961-799867899999999999752-776899640400


No 432
>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=84.97  E-value=1  Score=23.62  Aligned_cols=41  Identities=24%  Similarity=0.261  Sum_probs=31.0

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCCC
Q ss_conf             68749999808898888999999999999-87995999987877
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDPQ   46 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~q   46 (265)
                      +.+|.|+|. +--|+||||+..-|+-.+- +.| .|.+=|.+++
T Consensus       385 ~~G~r~Ai~-G~SG~GKsTLL~~L~G~l~P~~G-~vtl~G~~~~  426 (566)
T TIGR02868       385 PPGERVAIL-GPSGSGKSTLLATLAGLLDPLQG-EVTLDGVPVS  426 (566)
T ss_pred             CCCCCEEEE-CCCCCCHHHHHHHHHHHCCCCCC-CEEECCCCHH
T ss_conf             388608986-68876578999999840289999-1787773243


No 433
>PRK00300 gmk guanylate kinase; Provisional
Probab=84.89  E-value=1.2  Score=23.20  Aligned_cols=27  Identities=26%  Similarity=0.405  Sum_probs=21.8

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHH
Q ss_conf             9876874999980889888899999999
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLS   28 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA   28 (265)
                      |-.+++++|+++ +=-||||||+.-.|.
T Consensus         2 ~~~~~g~livis-GPSG~GK~tl~~~L~   28 (208)
T PRK00300          2 MMMRRGLLIVLS-APSGAGKSTLVRALL   28 (208)
T ss_pred             CCCCCCCEEEEE-CCCCCCHHHHHHHHH
T ss_conf             624188389999-999889999999999


No 434
>PRK08324 short chain dehydrogenase; Validated
Probab=84.84  E-value=2  Score=21.95  Aligned_cols=40  Identities=30%  Similarity=0.520  Sum_probs=33.6

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             768749999808898888999999999999879959999878776
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG   47 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~   47 (265)
                      +-.+||..|..+-||.|+.+     |..|+..|.+|++.|.|+..
T Consensus       418 ~L~GKVALVTGga~GIG~A~-----A~~fa~eGA~Vvl~D~~~~~  457 (676)
T PRK08324        418 PLAGKVALVTGAAGGIGLAT-----AKRLAAEGACVVLADIDEEA  457 (676)
T ss_pred             CCCCCEEEEECCCCCHHHHH-----HHHHHHCCCEEEEEECCHHH
T ss_conf             88998799947988162999-----99999879989999588899


No 435
>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]
Probab=84.80  E-value=1.3  Score=23.08  Aligned_cols=23  Identities=35%  Similarity=0.476  Sum_probs=18.3

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHH
Q ss_conf             874999980889888899999999
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLS   28 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA   28 (265)
                      +++.|++ |+.-||||||+.-.|=
T Consensus         3 ~G~l~vl-sgPSG~GKsTl~k~L~   25 (191)
T COG0194           3 KGLLIVL-SGPSGVGKSTLVKALL   25 (191)
T ss_pred             CCEEEEE-ECCCCCCHHHHHHHHH
T ss_conf             8639999-8998888899999998


No 436
>pfam10412 TrwB_AAD_bind Type IV secretion-system coupling protein DNA-binding domain. The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export.
Probab=84.72  E-value=2.9  Score=21.01  Aligned_cols=47  Identities=26%  Similarity=0.410  Sum_probs=32.8

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHH
Q ss_conf             76874999980889888899999999999987995999987877680112
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTG   52 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~   52 (265)
                      +...|-+-|+ +-=|+|||+.-.++-..+..+|..++++|  |.|.+...
T Consensus        12 ~~~~~H~lvi-G~tGsGKT~~i~~~i~~~~~~~~s~iv~D--pKGe~~~~   58 (386)
T pfam10412        12 RSETQHILIV-GTTGTGKTQALRELLDQIRARGDRAIIYD--PTGTFVER   58 (386)
T ss_pred             CCCCCEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEEE--CCCHHHHH
T ss_conf             8776758998-89999888799999999997799199995--87368898


No 437
>TIGR02880 cbbX_cfxQ CbbX protein; InterPro: IPR000470 Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. The Cfx genes in Alcaligenes eutrophus encode a number of Calvin cycle enzymes . The observed sizes of two of the gene products, CfxX and CfxY, are 35 kDa and 27 kDa respectively . No functions could be assigned to CfxX and CfxY. These proteins show a high degree of similarity to the Bacillus subtilis stage V sporulation protein K . ; GO: 0005524 ATP binding.
Probab=84.62  E-value=1.3  Score=23.12  Aligned_cols=37  Identities=24%  Similarity=0.425  Sum_probs=27.8

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCC----CEEEEECC
Q ss_conf             499998088988889999999999998799----59999878
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGE----NVLLIDLD   44 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~----rVllID~D   44 (265)
                      =..+|. +.-|+||||++..+|..|.+.|+    .++-+--|
T Consensus        59 lhm~ft-G~PGtGkttva~~m~~~l~~lGy~r~G~~~~~trd   99 (284)
T TIGR02880        59 LHMSFT-GNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRD   99 (284)
T ss_pred             EEEEEC-CCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEHH
T ss_conf             267751-68987248999999999987154003626785300


No 438
>PRK13648 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=84.60  E-value=1.2  Score=23.20  Aligned_cols=27  Identities=26%  Similarity=0.250  Sum_probs=22.1

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             6874999980889888899999999999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTAL   31 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~l   31 (265)
                      +++++++++ +.-|+||||+.-.|+-.+
T Consensus        33 ~~Ge~vaii-G~sGsGKSTLl~ll~Gl~   59 (269)
T PRK13648         33 PKGQWTSIV-GHNGSGKSTIAKLMIGIE   59 (269)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHCCC
T ss_conf             599899999-999997999999996497


No 439
>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional
Probab=84.54  E-value=1.3  Score=23.07  Aligned_cols=39  Identities=23%  Similarity=0.233  Sum_probs=28.3

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCC
Q ss_conf             99998088988889999999999998799599998787768
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGN   48 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~   48 (265)
                      ++-++ .-=|+||||+-......|... +++.+|..|.|.+
T Consensus       106 ~lNl~-sSPGSGKTtLLe~ti~~L~~~-~~~aVIeGD~~T~  144 (290)
T PRK10463        106 VLNLV-SSPGSGKTTLLTETLMRLKDS-VPCAVIEGDQQTV  144 (290)
T ss_pred             EEEEC-CCCCCCHHHHHHHHHHHHHCC-CCEEEEEECCCCH
T ss_conf             99930-699878899999999987336-7579996042356


No 440
>pfam08245 Mur_ligase_M Mur ligase middle domain.
Probab=84.43  E-value=1.5  Score=22.73  Aligned_cols=27  Identities=37%  Similarity=0.278  Sum_probs=24.0

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             988889999999999998799599998
Q gi|254780806|r   16 GGVGKTTTAINLSTALAAIGENVLLID   42 (265)
Q Consensus        16 GGvGKTT~a~nlA~~la~~g~rVllID   42 (265)
                      |=.||||++..|+..|...|+++..+-
T Consensus         3 GT~GKTTt~~ml~~iL~~~g~~~~~~g   29 (188)
T pfam08245         3 GTNGKTTTTELIAALLSAAGGVVGTGG   29 (188)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEEC
T ss_conf             758689999999999983899899838


No 441
>PRK05057 aroK shikimate kinase I; Reviewed
Probab=84.23  E-value=1.9  Score=22.09  Aligned_cols=37  Identities=32%  Similarity=0.414  Sum_probs=25.5

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             987687499998088988889999999999998799599998787
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      |.+|+  -|.++ +==|+||||+.-.||..|   |  .-.||+|-
T Consensus         1 M~~kk--nI~Li-G~mGsGKstvgk~LA~~l---~--~~fiD~D~   37 (172)
T PRK05057          1 MAEKR--NIFLV-GPMGAGKSTIGRQLAQQL---N--MEFYDSDQ   37 (172)
T ss_pred             CCCCC--CEEEE-CCCCCCHHHHHHHHHHHH---C--CCEEECHH
T ss_conf             99888--28988-999998899999999996---9--99687809


No 442
>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein; InterPro: IPR011924   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 LolD, a member of the ABC transporter family. LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on the residue immediately following the modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. Excluded from this entry are homologs from the archaeal genus Methanosarcina .; GO: 0005524 ATP binding, 0006810 transport, 0016020 membrane.
Probab=84.22  E-value=0.76  Score=24.41  Aligned_cols=24  Identities=33%  Similarity=0.422  Sum_probs=19.9

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHH
Q ss_conf             6874999980889888899999999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLS   28 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA   28 (265)
                      .++.+++|+ ++-|+||||+=.-|+
T Consensus        29 ~~GE~~~Iv-G~SGSGKSTLLHlLG   52 (221)
T TIGR02211        29 GKGEIVAIV-GSSGSGKSTLLHLLG   52 (221)
T ss_pred             ECCCEEEEE-CCCCCCHHHHHHHHH
T ss_conf             066337987-367871689999873


No 443
>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=84.17  E-value=1.2  Score=23.22  Aligned_cols=36  Identities=14%  Similarity=0.273  Sum_probs=24.7

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             6874999980889888899999999999987995999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLL   40 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVll   40 (265)
                      +++++++++ ++-|+||||+.--|+-.+....-++.+
T Consensus        25 ~~Ge~~~Iv-G~sGsGKSTLl~~l~g~~~~~~G~I~~   60 (218)
T cd03290          25 PTGQLTMIV-GQVGCGKSSLLLAILGEMQTLEGKVHW   60 (218)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHCCCCCCCCEEEE
T ss_conf             699999999-999980999999985556567764998


No 444
>TIGR02746 TraC-F-type type-IV secretion system protein TraC; InterPro: IPR014117   The proteins in this entry are found in the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The proteins contain the Walker A and B motifs and so are putative nucleotide triphosphatases..
Probab=84.03  E-value=2.4  Score=21.47  Aligned_cols=46  Identities=24%  Similarity=0.307  Sum_probs=35.6

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC-CCCCCCHHHCC
Q ss_conf             999808898888999999999999879959999878-77680112124
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD-PQGNASTGLGI   55 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D-~q~~~~~~l~~   55 (265)
                      |+|+ +.-|.|||.+.=.++...-..|.+|-+||.- .---|+..||-
T Consensus       492 ~~~~-g~sG~GKSf~~Q~~~~~~L~~G~kv~viDvG~Sy~KLC~~lgG  538 (900)
T TIGR02746       492 IAVV-GGSGAGKSFFMQELIVSVLSRGGKVWVIDVGRSYKKLCEMLGG  538 (900)
T ss_pred             EEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHHHHCC
T ss_conf             8997-2889871687989999985179848999607884888765187


No 445
>pfam07693 KAP_NTPase KAP family P-loop domain. The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side.
Probab=84.02  E-value=3.1  Score=20.83  Aligned_cols=42  Identities=24%  Similarity=0.257  Sum_probs=33.9

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             6874999980889888899999999999987995999987877
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      ..+=||++. ++=|+||||+--.+...|.+...++.+|..||-
T Consensus        18 ~~~~vIgl~-G~WGsGKTs~l~~~~~~L~~~~~~~~~v~fn~W   59 (301)
T pfam07693        18 APGFVIGLY-GAWGSGKTSFLNLLEDELKEFPEEFHIVYFDPW   59 (301)
T ss_pred             CCCEEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECC
T ss_conf             999799998-989999999999999998613688269998123


No 446
>PRK10789 putative multidrug transporter membrane\ATP-binding components; Provisional
Probab=84.02  E-value=2.7  Score=21.25  Aligned_cols=37  Identities=19%  Similarity=0.279  Sum_probs=26.9

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEEC
Q ss_conf             687499998088988889999999999998-7995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~   43 (265)
                      ++++.+++. ++-|+||||+.--|...+.- .| ++. ||.
T Consensus       339 ~~Ge~vaIV-G~SGsGKSTLl~LL~g~y~p~~G-~I~-idg  376 (569)
T PRK10789        339 KPGQMLGIC-GPTGSGKSTLLSLIQRHFDVSEG-DIR-FHD  376 (569)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHHHHHCCCC-CEE-EEC
T ss_conf             899789987-99999879999999977642678-746-501


No 447
>PRK13394 3-hydroxybutyrate dehydrogenase; Provisional
Probab=84.02  E-value=1.8  Score=22.25  Aligned_cols=40  Identities=25%  Similarity=0.483  Sum_probs=34.3

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             987687499998088988889999999999998799599998787
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      |.+-+.|++.|..+-+|.|+.     +|..|++.|.+|++.|.+.
T Consensus         2 m~~l~gKvalVTGgs~GIG~a-----~A~~la~~Ga~V~i~~~~~   41 (262)
T PRK13394          2 MSNLNGKTAVVTGAASGIGKE-----IALELARAGAAVAIADLNQ   41 (262)
T ss_pred             CCCCCCCEEEEECCCCHHHHH-----HHHHHHHCCCEEEEEECCH
T ss_conf             978899989995857789999-----9999998799999997988


No 448
>PRK13631 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=83.98  E-value=1.3  Score=23.02  Aligned_cols=36  Identities=19%  Similarity=0.301  Sum_probs=26.5

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             6874999980889888899999999999987995999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLL   40 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVll   40 (265)
                      +++++++++ +.-|+||||+.-.|+-.+.-..-++.+
T Consensus        50 ~~Ge~vaII-G~nGsGKSTL~~~l~Gll~p~~G~I~i   85 (320)
T PRK13631         50 EKNKIYFII-GNSGSGKSTLVTHFNGLIKSKYGTIQV   85 (320)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHCCCCCCCCEEEE
T ss_conf             599899999-499984999999997588899835998


No 449
>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=83.94  E-value=1.3  Score=23.09  Aligned_cols=28  Identities=25%  Similarity=0.402  Sum_probs=22.7

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             68749999808898888999999999999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALA   32 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la   32 (265)
                      ++++.++++ ++-|+||||+.--|+-.+.
T Consensus        61 ~~Ge~vaIV-G~sGSGKSTLl~lL~gl~~   88 (282)
T cd03291          61 EKGEMLAIT-GSTGSGKTSLLMLILGELE   88 (282)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCC
T ss_conf             499999999-9999819999999957872


No 450
>PRK10846 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional
Probab=83.88  E-value=2.5  Score=21.44  Aligned_cols=37  Identities=32%  Similarity=0.329  Sum_probs=31.0

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             8768749999808898888999999999999879959999
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLI   41 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllI   41 (265)
                      +++.-|+|-|.   |==||.+++..|+..|...|+||.+-
T Consensus        45 p~~~~~~IhVa---GTNGKGSt~~~l~~il~~~G~~vG~f   81 (416)
T PRK10846         45 LKPAPFVFTVA---GTNGKGTTCRTLESILMAAGYRVGVY   81 (416)
T ss_pred             CCCCCCEEEEE---CCCCHHHHHHHHHHHHHHCCCCCCEE
T ss_conf             86579989996---88557999999999999879973077


No 451
>cd04174 Rnd1_Rho6 Rnd1/Rho6 subfamily.  Rnd1/Rho6 is a member of the novel Rho subfamily Rnd, together with Rnd2/Rho7 and Rnd3/RhoE/Rho8.  Rnd1/Rho6 binds GTP but does not hydrolyze it to GDP, indicating that it is constitutively active.  In rat, Rnd1/Rho6 is highly expressed in the cerebral cortex and hippocampus during synapse formation, and plays a role in spine formation.  Rnd1/Rho6 is also expressed in the liver and in endothelial cells, and is upregulated in uterine myometrial cells during pregnancy.  Like Rnd3/RhoE/Rho8, Rnd1/Rho6 is believed to function as an antagonist to RhoA.  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.  Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=83.77  E-value=1.6  Score=22.47  Aligned_cols=104  Identities=11%  Similarity=0.075  Sum_probs=44.5

Q ss_pred             HHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             1233100111112-311378887533577765543202677431002023125310011268999880852015626786
Q gi|254780806|r  143 MAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRN  221 (265)
Q Consensus       143 l~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v~~~~Ip~~  221 (265)
                      ...||.++++..- ++.|++.+  +...+.+++. +.++.+++ +|-|+.|-++.  ...+.+|.+. +    ...|-+.
T Consensus        82 Y~~a~~~ll~Fdvt~~~Sfe~~--~~~Wi~Ei~~-~~p~~pii-LVGnK~DLr~d--~~~l~~L~~~-~----~~pVt~e  150 (232)
T cd04174          82 YSDSDAVLLCFDISRPETVDSA--LKKWKAEIMD-YCPSTRIL-LIGCKTDLRTD--LSTLMELSNQ-K----QAPISYE  150 (232)
T ss_pred             HCCCCEEEEEEECCCHHHHHHH--HHHHHHHHHH-HCCCCCEE-EEEECHHCCCC--HHHHHHHHHC-C----CCCCCHH
T ss_conf             4068789999968987999989--9999999998-68999789-99876021547--5778899756-8----8875799


Q ss_pred             HHHHHHHHCCCC-EEEECCCC--HHHH-HHHHHHHHHHHH
Q ss_conf             889877737985-79997999--8999-999999999999
Q gi|254780806|r  222 VRISEAPSYGKP-AIIYDLKC--AGSQ-AYLKLASELIQQ  257 (265)
Q Consensus       222 ~~i~~a~~~g~p-v~~~~p~s--~~a~-~~~~la~el~~~  257 (265)
                      +...-|...|-+ .+|-+-..  ...+ .|+..+..++++
T Consensus       151 eg~~~Ak~iga~~Y~E~SA~tge~~v~~vF~~a~~~~~~~  190 (232)
T cd04174         151 QGCALAKQLGAEVYLECSAFTSEKSIHSIFRSASLLCLNK  190 (232)
T ss_pred             HHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             9999999749978998756866625999999999999854


No 452
>cd01853 Toc34_like Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts).  This family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90.  The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex.  The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle.  Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein.  Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic.  Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon.
Probab=83.74  E-value=0.93  Score=23.92  Aligned_cols=29  Identities=31%  Similarity=0.381  Sum_probs=20.4

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             999980889888899999999999987995999987
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      .|-|. +|||||||.+.=+      -.|.++..+++
T Consensus        33 tILvl-GKtGVGKSsTINS------ifgE~~~~~~a   61 (249)
T cd01853          33 TILVL-GKTGVGKSSTINS------IFGERKAATSA   61 (249)
T ss_pred             EEEEE-ECCCCCHHHHHHH------HCCCCCCCCCC
T ss_conf             99998-0687645776776------50854134477


No 453
>PRK12296 obgE GTPase ObgE; Reviewed
Probab=83.70  E-value=0.87  Score=24.07  Aligned_cols=81  Identities=14%  Similarity=0.253  Sum_probs=38.4

Q ss_pred             CCCCCEEEECC---------CCCCCCCCHHHHHHHCCCCCCCCC-----HHHHHHHHHHHHHHHHHHH---------HHC
Q ss_conf             27820331013---------332222101123310011111231-----1378887533577765543---------202
Q gi|254780806|r  123 DFSYIFLDCPP---------SFNLLTMNAMAAADSILVPLQCEF-----FALEGLSQLLETVEEVRRT---------VNS  179 (265)
Q Consensus       123 ~yD~IiiD~pp---------~~~~~~~~al~aad~viip~~p~~-----~s~~~~~~~~~~i~~~~~~---------~~~  179 (265)
                      +..|++-|.|+         |++.-.+--+..+-.++-++..+.     -.+.+...+...++.+...         +..
T Consensus       205 d~~f~iADiPGLIeGAs~g~GLG~~FLRHieR~~vL~hviD~~~~e~~rDP~~d~~~I~~EL~~Y~~~l~~~~~~~~L~e  284 (495)
T PRK12296        205 DHTFTVADVPGLIPGASEGRGLGLDFLRHIERCAVLVHVVDCATLEPGRDPISDIDALEAELAAYTPTLQGDAGLGDLAE  284 (495)
T ss_pred             CCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHCCHHHHCCCCCCCCCC
T ss_conf             95289985664346500389843999998752547999996887666789699999999999971914304433232101


Q ss_pred             CCCCCCCCCCEEECCCHHHHHHHHHHHH
Q ss_conf             6774310020231253100112689998
Q gi|254780806|r  180 ALDIQGIILTMFDSRNSLSQQVVSDVRK  207 (265)
Q Consensus       180 ~~~~~~iv~N~~~~~~~~~~~~~~~l~~  207 (265)
                      .++  =||+|++|--.  .++..+.+++
T Consensus       285 rpq--IVvlNKiDlp~--a~e~~e~~~~  308 (495)
T PRK12296        285 RPR--LVVLNKIDVPD--ARELAEFVRP  308 (495)
T ss_pred             CCE--EEEEECCCCCC--HHHHHHHHHH
T ss_conf             965--99996656757--6999999999


No 454
>PRK13642 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=83.61  E-value=1.2  Score=23.18  Aligned_cols=38  Identities=29%  Similarity=0.309  Sum_probs=26.7

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             6874999980889888899999999999987995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      +++++++++ +.-|+||||++-.|+..+....=+| .+|.
T Consensus        31 ~~Ge~~aii-G~sGsGKSTL~~~l~Gl~~~~~G~I-~~~G   68 (277)
T PRK13642         31 TKGEWVSII-GQNGSGKSTTARLIDGLFEEFEGIV-KIDG   68 (277)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCCCCCCEE-EECC
T ss_conf             899899999-9999689999999963899888489-9999


No 455
>PRK13645 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=83.56  E-value=0.81  Score=24.25  Aligned_cols=35  Identities=20%  Similarity=0.355  Sum_probs=25.8

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEE
Q ss_conf             687499998088988889999999999998-7995999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLL   40 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVll   40 (265)
                      +++++++++ +.-|+||||+.-.++-.+.- .| +|.+
T Consensus        35 ~~Ge~~aIi-G~nGsGKSTL~~~l~Gll~p~~G-~v~~   70 (289)
T PRK13645         35 KKNKVTCVI-GTTGSGKSTMIQLTNGLIISETG-QTIV   70 (289)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCCCCCC-EEEE
T ss_conf             899899999-99995799999999659889998-5999


No 456
>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]
Probab=83.45  E-value=0.49  Score=25.51  Aligned_cols=32  Identities=34%  Similarity=0.476  Sum_probs=21.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCEEEEECC---CCCCCCH
Q ss_conf             898888999999999999879959999878---7768011
Q gi|254780806|r   15 KGGVGKTTTAINLSTALAAIGENVLLIDLD---PQGNAST   51 (265)
Q Consensus        15 KGGvGKTT~a~nlA~~la~~g~rVllID~D---~q~~~~~   51 (265)
                      =-|+||||++..||..|.     ---||.|   |++|...
T Consensus         3 VsG~GKStvg~~lA~~lg-----~~fidGDdlHp~aNi~K   37 (161)
T COG3265           3 VSGSGKSTVGSALAERLG-----AKFIDGDDLHPPANIEK   37 (161)
T ss_pred             CCCCCHHHHHHHHHHHCC-----CCEECCCCCCCHHHHHH
T ss_conf             776577799999999809-----82333565699889998


No 457
>PRK12898 secA preprotein translocase subunit SecA; Reviewed
Probab=83.43  E-value=0.52  Score=25.38  Aligned_cols=33  Identities=33%  Similarity=0.357  Sum_probs=26.1

Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             980889888899999999999987995999987
Q gi|254780806|r   11 IANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus        11 v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      ++-.|-|-|||-++.--|+.-|..|+.|-+|-.
T Consensus       135 IaEM~TGEGKTL~atlpaylnAL~G~gVHvvTv  167 (673)
T PRK12898        135 LAEMQTGEGKTLTATLPAGTAALAGRPVHVITV  167 (673)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             357507885899999999999736997089804


No 458
>COG4167 SapF ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
Probab=83.40  E-value=0.93  Score=23.91  Aligned_cols=36  Identities=22%  Similarity=0.416  Sum_probs=27.7

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             6874999980889888899999999999987995999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLL   40 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVll   40 (265)
                      +++.+++|+ ++-|+||||++-.||-...-.+-+.++
T Consensus        37 ~~~QTlaiI-G~NGSGKSTLakMlaGmi~PTsG~il~   72 (267)
T COG4167          37 REGQTLAII-GENGSGKSTLAKMLAGMIEPTSGEILI   72 (267)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHCCCCCCCCEEEE
T ss_conf             079679998-269974758999983555898854878


No 459
>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=83.31  E-value=1.6  Score=22.58  Aligned_cols=25  Identities=28%  Similarity=0.383  Sum_probs=19.5

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHH
Q ss_conf             987687499998088988889999999
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINL   27 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nl   27 (265)
                      +.+|+.||+.+  +-.|+||||+.-.+
T Consensus        10 ~~~~~~Ki~il--G~~~sGKTsll~~l   34 (173)
T cd04155          10 KSSEEPRILIL--GLDNAGKTTILKQL   34 (173)
T ss_pred             CCCCCCEEEEE--CCCCCCHHHHHHHH
T ss_conf             56877589999--79999889999998


No 460
>PRK06484 short chain dehydrogenase; Validated
Probab=83.29  E-value=1.8  Score=22.24  Aligned_cols=40  Identities=25%  Similarity=0.561  Sum_probs=32.9

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             876874999980889888899999999999987995999987877
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      .|.++|++.|..+-+|.|+.     +|..|++.|.+|++.|-+..
T Consensus         1 ~~~eGKvalVTGas~GIG~a-----iA~~la~~Ga~V~~~dr~~~   40 (530)
T PRK06484          1 REGQARVVLVTGAAGGIGRA-----CCQRFARAGDRVVMADRDLA   40 (530)
T ss_pred             CCCCCCEEEEECCCCHHHHH-----HHHHHHHCCCEEEEEECCHH
T ss_conf             99999899997836689999-----99999987999999968889


No 461
>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=83.26  E-value=1.5  Score=22.76  Aligned_cols=37  Identities=22%  Similarity=0.343  Sum_probs=25.6

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEEC
Q ss_conf             68749999808898888999999999999-87995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~   43 (265)
                      ++++.++++ ++-|+||||+.--|...+. ..|  ...||.
T Consensus        27 ~~G~~iaIv-G~sGsGKSTLl~ll~gl~~p~~G--~I~idg   64 (238)
T cd03249          27 PPGKTVALV-GSSGCGKSTVVSLLERFYDPTSG--EILLDG   64 (238)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHHCCCCCCC--EEEECC
T ss_conf             699999999-99999899999998238618851--899999


No 462
>PRK13633 cobalt transporter ATP-binding subunit; Provisional
Probab=83.21  E-value=1.4  Score=22.81  Aligned_cols=36  Identities=28%  Similarity=0.398  Sum_probs=25.3

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             6874999980889888899999999999987995999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLL   40 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVll   40 (265)
                      +++++++++ +.-|+||||+.-.++..+.-.+=+|.+
T Consensus        35 ~~GE~v~ii-G~nGsGKSTL~r~l~gl~~P~~G~I~i   70 (281)
T PRK13633         35 KKGEFLVIL-GHNGSGKSTIAKHMNALLLPSEGKVYV   70 (281)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             799899999-999984999999997588788856999


No 463
>PRK13650 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=83.20  E-value=1.4  Score=22.91  Aligned_cols=37  Identities=32%  Similarity=0.459  Sum_probs=26.7

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEEC
Q ss_conf             687499998088988889999999999998-7995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~   43 (265)
                      ++++++++. +.-|+||||+.-.|+-.+.- .| + +.+|.
T Consensus        28 ~~GE~vaiv-G~nGsGKSTL~~~l~Gll~p~~G-~-I~i~G   65 (276)
T PRK13650         28 KQGEWLSII-GHNGSGKSTTVRLIDGLLEAESG-S-IIIDG   65 (276)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCCCCCE-E-EEECC
T ss_conf             899899999-99998799999999738898860-8-99999


No 464
>PRK12814 putative NADPH-dependent glutamate synthase small subunit; Provisional
Probab=83.13  E-value=2.7  Score=21.19  Aligned_cols=50  Identities=22%  Similarity=0.320  Sum_probs=34.8

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCC
Q ss_conf             87687499998088988889999999999998799599998787768011212463
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIEL   57 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~   57 (265)
                      ..+.+|.|+|+    |.|=.-+|+  |+.|+++|++|-+.|..|+..-=+.+|+..
T Consensus       189 ~~~tGKkVAII----GaGPAGLsa--Ay~L~~~Gh~VTVfE~~~~~GGmlryGIP~  238 (652)
T PRK12814        189 APKSGKKVAII----GAGPAGLTA--AYYLLRKGHDVTIFDANEQAGGMMRYGIPR  238 (652)
T ss_pred             CCCCCCEEEEE----CCCHHHHHH--HHHHHHCCCEEEEEECCCCCCCEEEECCCC
T ss_conf             78889979996----837899999--999997799069981588889867644863


No 465
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=83.08  E-value=1.9  Score=22.14  Aligned_cols=42  Identities=19%  Similarity=0.135  Sum_probs=27.9

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             8749999808898888999999999999879959999878776
Q gi|254780806|r    5 KSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG   47 (265)
Q Consensus         5 ~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~   47 (265)
                      ..+=+++..+-=|+||||+.-.+...+......+..| .+|+.
T Consensus        41 ~~~g~~lltGe~GtGKTtllr~l~~~l~~~~~~~~~i-~~~~l   82 (269)
T TIGR03015        41 QREGFILITGEVGAGKTTLIRNLLKRLDQERVVAAKL-VNTRV   82 (269)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHCCCCCEEEEEE-CCCCC
T ss_conf             4896599972998988999999998459345489997-69999


No 466
>PRK07454 short chain dehydrogenase; Provisional
Probab=83.03  E-value=2  Score=21.99  Aligned_cols=41  Identities=22%  Similarity=0.299  Sum_probs=35.2

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             9876874999980889888899999999999987995999987877
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      |.-..-||..|...-+|.|+.     +|..|++.|++|.++|-|..
T Consensus         1 m~~~~mKvalITGas~GIG~a-----~A~~la~~G~~V~l~~R~~~   41 (241)
T PRK07454          1 MSLNSMPTALITGASRGIGKA-----TALAFAKAGWDLALVARSQD   41 (241)
T ss_pred             CCCCCCCEEEECCCCCHHHHH-----HHHHHHHCCCEEEEEECCHH
T ss_conf             998999889991758789999-----99999987998999989999


No 467
>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=82.97  E-value=1.5  Score=22.68  Aligned_cols=26  Identities=23%  Similarity=0.342  Sum_probs=20.8

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHH
Q ss_conf             687499998088988889999999999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTA   30 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~   30 (265)
                      +++++++++ +..|+||||+.-.++-.
T Consensus        24 ~~Ge~~~ii-G~SGsGKSTll~~i~gL   49 (235)
T cd03261          24 RRGEILAII-GPSGSGKSTLLRLIVGL   49 (235)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCC
T ss_conf             799899999-99997299999999759


No 468
>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]
Probab=82.94  E-value=2.4  Score=21.46  Aligned_cols=32  Identities=38%  Similarity=0.452  Sum_probs=23.8

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             749999808898888999999999999879959999878
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ..+|.+. ++=|+||||++=-++    +.|  +-+||+|
T Consensus         2 ~~iIglT-G~igsGKStva~~~~----~~G--~~vidaD   33 (201)
T COG0237           2 MLIIGLT-GGIGSGKSTVAKILA----ELG--FPVIDAD   33 (201)
T ss_pred             CEEEEEE-CCCCCCHHHHHHHHH----HCC--CEEEECC
T ss_conf             6499995-788778899999999----779--9399886


No 469
>PRK10787 DNA-binding ATP-dependent protease La; Provisional
Probab=82.91  E-value=1.3  Score=23.09  Aligned_cols=29  Identities=28%  Similarity=0.408  Sum_probs=24.6

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             768749999808898888999999999999
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALA   32 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la   32 (265)
                      +.++.|+|+. +==|||||+++-.+|.+|.
T Consensus       346 ~~kg~Ilclv-GpPGvGKTSl~~sIA~al~  374 (784)
T PRK10787        346 KIKGPILCLV-GPPGVGKTSLGQSIAKATG  374 (784)
T ss_pred             CCCCCEEEEE-CCCCCCHHHHHHHHHHHHC
T ss_conf             6778779964-6998772469999999858


No 470
>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]
Probab=82.90  E-value=1.5  Score=22.64  Aligned_cols=37  Identities=24%  Similarity=0.284  Sum_probs=25.5

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEEC
Q ss_conf             687499998088988889999999999998-7995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~   43 (265)
                      +.++.|++. ++-|+||||++=.|.-.+.- .|  -..+|.
T Consensus       497 ~~Ge~vaIv-G~SGsGKSTL~KLL~gly~p~~G--~I~~dg  534 (709)
T COG2274         497 PPGEKVAIV-GRSGSGKSTLLKLLLGLYKPQQG--RILLDG  534 (709)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHCCCCCCCC--EEEECC
T ss_conf             799889998-79999889999998367888885--599998


No 471
>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=82.77  E-value=1.5  Score=22.76  Aligned_cols=37  Identities=22%  Similarity=0.297  Sum_probs=26.2

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEEC
Q ss_conf             68749999808898888999999999999-87995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~   43 (265)
                      +++++++++ +.-|+||||+.--|...+. ..|  ...+|-
T Consensus        38 ~~Ge~vaIv-G~sGsGKSTL~~ll~gl~~p~~G--~I~idg   75 (226)
T cd03248          38 HPGEVTALV-GPSGSGKSTVVALLENFYQPQGG--QVLLDG   75 (226)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCCCCCC--EEEECC
T ss_conf             299999999-99998499999999645467887--899999


No 472
>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=82.77  E-value=1.3  Score=23.05  Aligned_cols=37  Identities=22%  Similarity=0.298  Sum_probs=26.2

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             6874999980889888899999999999987995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      +++++++++ ++-|+||||+.-.|...+...|.  +.||.
T Consensus        28 ~~Ge~vaIv-G~sGsGKSTLl~lL~gl~~~~G~--I~idg   64 (275)
T cd03289          28 SPGQRVGLL-GRTGSGKSTLLSAFLRLLNTEGD--IQIDG   64 (275)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHHHCCCCCE--EEECC
T ss_conf             799999999-99999799999999603578953--99998


No 473
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=82.77  E-value=1.6  Score=22.58  Aligned_cols=32  Identities=31%  Similarity=0.426  Sum_probs=27.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHH-------HCCCCEEEEECC
Q ss_conf             08898888999999999999-------879959999878
Q gi|254780806|r   13 NQKGGVGKTTTAINLSTALA-------AIGENVLLIDLD   44 (265)
Q Consensus        13 s~KGGvGKTT~a~nlA~~la-------~~g~rVllID~D   44 (265)
                      =+-.|||||.++-.||..++       .+|+++.-+|+-
T Consensus       214 VGepGVGKTAIvEGLA~rI~~g~VP~~L~~~~i~sLDlg  252 (852)
T TIGR03345       214 TGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLG  252 (852)
T ss_pred             ECCCCCCHHHHHHHHHHHHHCCCCCHHHHCCEEEEEEHH
T ss_conf             579998799999999999976999867743856786788


No 474
>KOG2859 consensus
Probab=82.74  E-value=2.2  Score=21.68  Aligned_cols=46  Identities=28%  Similarity=0.372  Sum_probs=32.5

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHH------HCCCCEEEEECCCCCC
Q ss_conf             8768749999808898888999999999999------8799599998787768
Q gi|254780806|r    2 EEKKSRIITIANQKGGVGKTTTAINLSTALA------AIGENVLLIDLDPQGN   48 (265)
Q Consensus         2 ~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la------~~g~rVllID~D~q~~   48 (265)
                      +++.+.++-| ++-||+|||-+-.+++...-      -++.-|+.||+|-.-+
T Consensus        34 ~~daG~~vEi-~Gp~~sgKt~vL~ql~a~CilPk~~GGl~~~VLfidld~~fd   85 (293)
T KOG2859          34 EADAGTLVEI-SGPGNSGKTLVLQQLVAHCILPKKFGGLQWSVLFIDLDHKFD   85 (293)
T ss_pred             CCCCCCEEEE-ECCCCCCHHHHHHHHHHHEECCCCCCCCEEEEEEEECCCCCC
T ss_conf             6556867998-689986188999999888354534488506999996444112


No 475
>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]
Probab=82.71  E-value=1.3  Score=23.07  Aligned_cols=38  Identities=34%  Similarity=0.401  Sum_probs=23.6

Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             7499998088988889999999999998799599998787
Q gi|254780806|r    6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         6 ~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      -|++ +. +=||+||||+...+....-..++..-+...++
T Consensus         6 ~kiv-v~-G~~g~GKTtl~~~l~~~~~~~~~~~t~~~~~~   43 (219)
T COG1100           6 FKIV-VL-GDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDP   43 (219)
T ss_pred             EEEE-EE-CCCCCCHHHHHHHHHCCCCCCCCCCCEEECCC
T ss_conf             7999-99-99999889999999647676556761454043


No 476
>PRK13646 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=82.59  E-value=1.6  Score=22.53  Aligned_cols=40  Identities=23%  Similarity=0.337  Sum_probs=27.7

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             68749999808898888999999999999879959999878
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      +++++++++ +.-|+||||+.-.++-.+.-..=+|.+=+.|
T Consensus        31 ~~Ge~~aii-G~nGsGKSTLl~~l~GLl~p~~G~I~~~g~~   70 (286)
T PRK13646         31 EQGKYYAIV-GQTGSGKSTLIQNINALLKPTTGTVTVDDIT   70 (286)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCCCCCCEEEECCEE
T ss_conf             699899999-9999819999999970788888759999898


No 477
>cd03808 GT1_cap1E_like This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides.
Probab=82.55  E-value=2.4  Score=21.55  Aligned_cols=35  Identities=29%  Similarity=0.428  Sum_probs=29.3

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             4999980889888899999999999987995999987
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDL   43 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~   43 (265)
                      ||+-|+|.-||+  -+...+||.+|+++|+.|-++=.
T Consensus         1 kil~i~~~~GG~--e~~~~~La~~L~~~Gh~V~vit~   35 (359)
T cd03808           1 KILHIVTVDGGL--YSFRLPLIKALRAAGYEVHVVAP   35 (359)
T ss_pred             CEEEEECCCCHH--HHHHHHHHHHHHHCCCEEEEEEE
T ss_conf             989997587659--99999999999976999999970


No 478
>pfam07728 AAA_5 AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
Probab=82.53  E-value=0.85  Score=24.13  Aligned_cols=33  Identities=27%  Similarity=0.369  Sum_probs=22.4

Q ss_pred             ECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             80889888899999999999987995999987877
Q gi|254780806|r   12 ANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus        12 ~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      .-+-=|+|||+++-.+|..+.  |.+...|-+..+
T Consensus         4 l~Gp~G~GKT~la~~la~~l~--~~~~~~i~~~~~   36 (139)
T pfam07728         4 LVGPPGTGKSELAERLAAALS--NRPVFYVQLTRD   36 (139)
T ss_pred             EECCCCCHHHHHHHHHHHHCC--CCCCHHHCCCCC
T ss_conf             998997569999999999807--983111214655


No 479
>pfam00910 RNA_helicase RNA helicase. This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.
Probab=82.39  E-value=1.7  Score=22.45  Aligned_cols=23  Identities=35%  Similarity=0.289  Sum_probs=19.5

Q ss_pred             ECCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             80889888899999999999987
Q gi|254780806|r   12 ANQKGGVGKTTTAINLSTALAAI   34 (265)
Q Consensus        12 ~s~KGGvGKTT~a~nlA~~la~~   34 (265)
                      ..+.-|+|||+++-.||..+++.
T Consensus         3 l~G~~G~GKS~~a~~la~~~~~~   25 (105)
T pfam00910         3 LYGPPGCGKSTLAKYLARALLDH   25 (105)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHH
T ss_conf             97999898899999999999998


No 480
>PRK06500 short chain dehydrogenase; Provisional
Probab=82.38  E-value=1.8  Score=22.19  Aligned_cols=41  Identities=22%  Similarity=0.333  Sum_probs=35.6

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             9876874999980889888899999999999987995999987877
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      |..-+.|++.|..+-+|.|+.     +|..|++.|.+|.+.|-|.+
T Consensus         1 M~rl~gK~~lITGas~GIG~a-----iA~~la~~Ga~V~i~~r~~~   41 (249)
T PRK06500          1 MSRLQGKTALITGGTSGIGLE-----TARQFAAEGARVAITGRDAA   41 (249)
T ss_pred             CCCCCCCEEEEECCCCHHHHH-----HHHHHHHCCCEEEEEECCHH
T ss_conf             989899889993768789999-----99999987999999969989


No 481
>PRK06172 short chain dehydrogenase; Provisional
Probab=82.35  E-value=1.7  Score=22.36  Aligned_cols=38  Identities=24%  Similarity=0.439  Sum_probs=32.2

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             6874999980889888899999999999987995999987877
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ   46 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q   46 (265)
                      -+.||+.|..+-+|.|+.+     |..|++.|.+|.+.|.++.
T Consensus         5 L~gKvalVTGas~GIG~ai-----A~~la~~Ga~V~i~~~~~~   42 (253)
T PRK06172          5 FSGQVALVTGGAAGIGRAT-----AIAFAREGAKVVVADRDAA   42 (253)
T ss_pred             CCCCEEEEECCCCHHHHHH-----HHHHHHCCCEEEEEECCHH
T ss_conf             6999899937576899999-----9999987998999979889


No 482
>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=82.31  E-value=1.1  Score=23.59  Aligned_cols=15  Identities=40%  Similarity=0.348  Sum_probs=10.4

Q ss_pred             CCCCCCHHHHHHHHH
Q ss_conf             889888899999999
Q gi|254780806|r   14 QKGGVGKTTTAINLS   28 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA   28 (265)
                      ++=-|||||+--.|.
T Consensus         3 G~pNvGKSTL~N~L~   17 (158)
T cd01879           3 GNPNVGKTTLFNALT   17 (158)
T ss_pred             CCCCCCHHHHHHHHH
T ss_conf             989888999999995


No 483
>PRK13700 conjugal transfer protein TraD; Provisional
Probab=82.29  E-value=3.7  Score=20.42  Aligned_cols=40  Identities=18%  Similarity=0.234  Sum_probs=33.3

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             68749999808898888999999999999879959999878
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      -.++-+.+. +.=|+||||.--.|-...-.+|.|+.+.|.-
T Consensus       183 sE~qH~li~-GTtGtGKS~~ir~LL~qIR~RGdrAIIyD~~  222 (732)
T PRK13700        183 SEIQNFCLH-GTVGAGKSEVIRRLANYARQRGDMVVIYDRS  222 (732)
T ss_pred             CHHHEEEEE-CCCCCCHHHHHHHHHHHHHHCCCCEEEECCC
T ss_conf             203126774-6888889999999999999729958999399


No 484
>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=82.24  E-value=2.3  Score=21.57  Aligned_cols=107  Identities=13%  Similarity=0.080  Sum_probs=49.2

Q ss_pred             CCCEEEECCCC--CCCCCCHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHH
Q ss_conf             82033101333--22221011233100111112-3113788875335777655432026774310020231253100112
Q gi|254780806|r  125 SYIFLDCPPSF--NLLTMNAMAAADSILVPLQC-EFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQV  201 (265)
Q Consensus       125 D~IiiD~pp~~--~~~~~~al~aad~viip~~p-~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~  201 (265)
                      .+-|.||++.-  ..+....+..||.++++... +..|+..+...   ++.++...+++..+. +|-|+.|-..  .++ 
T Consensus        50 ~l~iwDtaG~e~~~~~~~~~~~~a~~~ilvydit~~~Sf~~~~~w---~~~i~~~~~~~~~ii-lVgNK~Dl~~--~r~-  122 (161)
T cd04113          50 KLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITNRTSFEALPTW---LSDARALASPNIVVI-LVGNKSDLAD--QRE-  122 (161)
T ss_pred             EEEEEECCCCHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHH---HHHHHHHCCCCCEEE-EECCCCCCHH--CCC-
T ss_conf             999998999701226789984057778995368988999999999---999998679996498-6034344000--378-


Q ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHH
Q ss_conf             6899988085201562678688987773798579997999--8999999999999
Q gi|254780806|r  202 VSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASEL  254 (265)
Q Consensus       202 ~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el  254 (265)
                                      |+..+.-.-|...+.+.++-+-++  ..-+.|..||++|
T Consensus       123 ----------------V~~~e~~~~a~~~~~~~~E~SAk~~~nV~e~F~~la~~i  161 (161)
T cd04113         123 ----------------VTFLEASRFAQENGLLFLETSALTGENVEEAFLKCARSI  161 (161)
T ss_pred             ----------------CCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHC
T ss_conf             ----------------899999999998599799974156905899999999709


No 485
>PRK13651 cobalt transporter ATP-binding subunit; Provisional
Probab=82.22  E-value=1.4  Score=22.79  Aligned_cols=41  Identities=27%  Similarity=0.297  Sum_probs=28.6

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             687499998088988889999999999998799599998787
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      +++.+++++ +.-|+||||+.-.|+..+.-..=+|.+.-.|.
T Consensus        31 ~~GE~v~Ii-G~nGsGKSTL~k~l~Gll~P~~G~V~~~g~d~   71 (304)
T PRK13651         31 NQGEFIAII-GQTGSGKTTFIEHLNALLLPDTGTIEWIYFDE   71 (304)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHCCCCCCCCEEEEECCCC
T ss_conf             599899998-79998599999999669998871699942454


No 486
>COG0770 MurF UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]
Probab=82.20  E-value=1.9  Score=22.06  Aligned_cols=30  Identities=37%  Similarity=0.520  Sum_probs=25.3

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             768749999808898888999999999999879
Q gi|254780806|r    3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIG   35 (265)
Q Consensus         3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g   35 (265)
                      +.+.|||+|.   |=+||||+.-.+++.|+..|
T Consensus       100 ~~~~kvIaIT---GS~GKTTTKe~la~iL~~~~  129 (451)
T COG0770         100 KFNAKVIAIT---GSNGKTTTKEMLAAILSTKG  129 (451)
T ss_pred             HCCCCEEEEE---CCCCCHHHHHHHHHHHHHCC
T ss_conf             3699689995---89970769999999986368


No 487
>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+). This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.
Probab=82.10  E-value=1.8  Score=22.19  Aligned_cols=32  Identities=38%  Similarity=0.363  Sum_probs=23.0

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             9999808898888999999999999879959999878
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD   44 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D   44 (265)
                      ||+++ +=-|+||||+|-.|...+   + .+.+|=.|
T Consensus         1 iIgIa-G~S~SGKTTla~~L~~~l---~-~~~iI~qD   32 (187)
T cd02024           1 IVGIS-GVTNSGKTTLAKLLQRIL---P-NCCVIHQD   32 (187)
T ss_pred             CEEEE-CCCCCCHHHHHHHHHHHC---C-CCEEECCC
T ss_conf             98996-888875999999999987---9-98897154


No 488
>PRK06921 hypothetical protein; Provisional
Probab=82.09  E-value=3.3  Score=20.73  Aligned_cols=28  Identities=29%  Similarity=0.315  Sum_probs=11.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHC-CCCEEEE
Q ss_conf             889888899999999999987-9959999
Q gi|254780806|r   14 QKGGVGKTTTAINLSTALAAI-GENVLLI   41 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA~~la~~-g~rVllI   41 (265)
                      +.=|+|||-+++-+|-.|-.. |..|+-+
T Consensus       123 G~~G~GKThLa~aIa~~Ll~~~~~~Vly~  151 (265)
T PRK06921        123 GQPGSGKTHLLTAAANELMRKKGVPVLYF  151 (265)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             28989889999999999999629719998


No 489
>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=82.08  E-value=1.8  Score=22.19  Aligned_cols=36  Identities=22%  Similarity=0.405  Sum_probs=25.3

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEE
Q ss_conf             687499998088988889999999999998-799599998
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLID   42 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID   42 (265)
                      ++++.|+++ ++-|+||||+.-.|...+.- .|  -+++|
T Consensus        45 ~~Ge~vaIv-G~sGsGKSTL~~ll~gl~~p~~G--~I~id   81 (257)
T cd03288          45 KPGQKVGIC-GRTGSGKSSLSLAFFRMVDIFDG--KIVID   81 (257)
T ss_pred             CCCCEEEEE-CCCCCCHHHHHHHHHHCCCCCCC--EEEEC
T ss_conf             799999999-99998199999999605667888--89999


No 490
>CHL00181 cbbX CbbX; Provisional
Probab=82.04  E-value=2.1  Score=21.89  Aligned_cols=29  Identities=28%  Similarity=0.426  Sum_probs=23.7

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             499998088988889999999999998799
Q gi|254780806|r    7 RIITIANQKGGVGKTTTAINLSTALAAIGE   36 (265)
Q Consensus         7 kvI~v~s~KGGvGKTT~a~nlA~~la~~g~   36 (265)
                      .-.+| .+-=|+||||+|--+|..|...|.
T Consensus        60 ~h~vF-~GnPGTGKTTVARl~a~il~~lG~   88 (287)
T CHL00181         60 LHMSF-TGSPGTGKTTVALKMADILYRLGY   88 (287)
T ss_pred             CEEEE-ECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             53888-789986799999999999998699


No 491
>TIGR01966 RNasePH ribonuclease PH; InterPro: IPR002381   Prokaryotic ribonuclease PH (2.7.7.56 from EC) (RNase PH) is a phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates . There is a similar protein in Caenorhabditis elegans that belongs to this group.   More information about these proteins can be found at Protein of the Month: RNA Exosomes .; GO: 0000049 tRNA binding, 0004549 tRNA-specific ribonuclease activity, 0008033 tRNA processing.
Probab=81.97  E-value=0.94  Score=23.87  Aligned_cols=21  Identities=38%  Similarity=0.564  Sum_probs=14.1

Q ss_pred             HHHHHHCCCCEEEEECC-CCCC
Q ss_conf             99999879959999878-7768
Q gi|254780806|r   28 STALAAIGENVLLIDLD-PQGN   48 (265)
Q Consensus        28 A~~la~~g~rVllID~D-~q~~   48 (265)
                      +.-|..+|.|++.|||| .|++
T Consensus       100 vvDl~aLGErTI~iDCDVlQAD  121 (237)
T TIGR01966       100 VVDLEALGERTIWIDCDVLQAD  121 (237)
T ss_pred             HHHHHHCCCEEEEEECCEEECC
T ss_conf             7346234850279853343388


No 492
>PRK13853 type IV secretion system protein VirB4; Provisional
Probab=81.94  E-value=3.7  Score=20.42  Aligned_cols=32  Identities=28%  Similarity=0.254  Sum_probs=25.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHC----CCCEEEEECCC
Q ss_conf             889888899999999999987----99599998787
Q gi|254780806|r   14 QKGGVGKTTTAINLSTALAAI----GENVLLIDLDP   45 (265)
Q Consensus        14 ~KGGvGKTT~a~nlA~~la~~----g~rVllID~D~   45 (265)
                      +.=|+||||+..-|+..+.+.    +.++..+|-|-
T Consensus       433 G~TGsGKTtll~fL~aq~~ky~~~~~~~~~~fDkd~  468 (789)
T PRK13853        433 GPIGRGKTTLMTFILAMLEQSMVDRAGAVVFFDKDR  468 (789)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf             899998899999999999974223577089995886


No 493
>TIGR02982 heterocyst_DevA ABC exporter ATP-binding subunit, DevA family; InterPro: IPR014324   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    This entry represents the ATP-binding subunit DevA, found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The ABC transporter encoded by the devBCA operon is induced by nitrogen deficiency and is necessary for the formation of the laminated layer which envelops heterocysts , . It is thought to be involved in the export of either the heterocyst-specific glycolipids found in the laminated layer, or an enzyme essential for their formation..
Probab=81.91  E-value=0.94  Score=23.88  Aligned_cols=21  Identities=33%  Similarity=0.359  Sum_probs=16.9

Q ss_pred             EEEECCCCCCCHHHHHHHHHH
Q ss_conf             999808898888999999999
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLST   29 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~   29 (265)
                      |++..+--|+||||+=.-++.
T Consensus        33 iViltGPSGSGKTTLLtLiG~   53 (220)
T TIGR02982        33 IVILTGPSGSGKTTLLTLIGG   53 (220)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
T ss_conf             798437889846889998876


No 494
>PRK12825 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=81.88  E-value=2.1  Score=21.86  Aligned_cols=40  Identities=23%  Similarity=0.429  Sum_probs=33.9

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             987687499998088988889999999999998799599998787
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      |..-+.|++.|..+-+|.|+.     +|..|++.|++|.++|-..
T Consensus         2 m~~LkgK~~lITGas~GIG~a-----ia~~la~~G~~V~~~~~~~   41 (250)
T PRK12825          2 MGSLSGRVALVTGAARGIGRA-----IALRLAAAGADVIVHPPSD   41 (250)
T ss_pred             CCCCCCCEEEEECCCCHHHHH-----HHHHHHHCCCEEEEEECCC
T ss_conf             866097889993895589999-----9999998799899997988


No 495
>pfam00996 GDI GDP dissociation inhibitor.
Probab=81.87  E-value=0.75  Score=24.46  Aligned_cols=37  Identities=35%  Similarity=0.454  Sum_probs=24.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCEEEEECCCC-CCCCHHHCC
Q ss_conf             888899999999999987995999987877-680112124
Q gi|254780806|r   17 GVGKTTTAINLSTALAAIGENVLLIDLDPQ-GNASTGLGI   55 (265)
Q Consensus        17 GvGKTT~a~nlA~~la~~g~rVllID~D~q-~~~~~~l~~   55 (265)
                      |+|=+-  +-||.+|+..|+|||-+|-... |+....|.+
T Consensus        11 GTGL~E--sILaaaLS~~GKkVLHiDrN~yYGg~~ASl~l   48 (439)
T pfam00996        11 GTGLKE--CILSGLLSVDGKKVLHIDRNDYYGGESASLSL   48 (439)
T ss_pred             CCCHHH--HHHHHHHHHCCCEEEEECCCCCCCCCCCCCCH
T ss_conf             998799--99999997369989997799877863015289


No 496
>cd03112 CobW_like The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.
Probab=81.80  E-value=2  Score=21.94  Aligned_cols=35  Identities=26%  Similarity=0.302  Sum_probs=26.4

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             9998088988889999999999998799599998787
Q gi|254780806|r    9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDP   45 (265)
Q Consensus         9 I~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~   45 (265)
                      |++.++==|+||||+--++..  +..|+|+.+|=-|-
T Consensus         2 v~iitGFLGaGKTTll~~lL~--~~~~~~~avIvNEf   36 (158)
T cd03112           2 VTVLTGFLGAGKTTLLNHILT--EQHGRKIAVIENEF   36 (158)
T ss_pred             EEEEEECCCCCHHHHHHHHHH--CCCCCCEEEEEECC
T ss_conf             089984888999999999984--78899779997076


No 497
>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=81.79  E-value=1.8  Score=22.29  Aligned_cols=37  Identities=22%  Similarity=0.284  Sum_probs=25.6

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCEEEEEC
Q ss_conf             687499998088988889999999999998-7995999987
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDL   43 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la~-~g~rVllID~   43 (265)
                      ++++.+++. ++-|+||||+.--|...+.- .|  -+.||.
T Consensus        26 ~~Ge~i~Iv-G~sGsGKSTLl~ll~gl~~p~~G--~I~i~g   63 (234)
T cd03251          26 PAGETVALV-GPSGSGKSTLVNLIPRFYDVDSG--RILIDG   63 (234)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCCCCCC--EEEECC
T ss_conf             799999999-89998299999999667667886--899999


No 498
>PRK13635 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=81.77  E-value=1.7  Score=22.35  Aligned_cols=28  Identities=29%  Similarity=0.319  Sum_probs=22.8

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             68749999808898888999999999999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLSTALA   32 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA~~la   32 (265)
                      +++.+++++ +.-|+||||+.-.|+-.+.
T Consensus        31 ~~GE~vaiv-G~nGsGKSTL~k~l~Gl~~   58 (279)
T PRK13635         31 YEGEWVAIV-GHNGSGKSTLAKLLNGLLL   58 (279)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHHCCCC
T ss_conf             799899999-9999659999999972888


No 499
>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=81.74  E-value=2.8  Score=21.09  Aligned_cols=112  Identities=11%  Similarity=0.151  Sum_probs=53.9

Q ss_pred             CCCCEEEECCC--CCCCCCCHHHHHHHCCCCCCCC-CHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCCCCEEECCCHHHH
Q ss_conf             78203310133--3222210112331001111123-113788875335777655432-0267743100202312531001
Q gi|254780806|r  124 FSYIFLDCPPS--FNLLTMNAMAAADSILVPLQCE-FFALEGLSQLLETVEEVRRTV-NSALDIQGIILTMFDSRNSLSQ  199 (265)
Q Consensus       124 yD~IiiD~pp~--~~~~~~~al~aad~viip~~p~-~~s~~~~~~~~~~i~~~~~~~-~~~~~~~~iv~N~~~~~~~~~~  199 (265)
                      |++-|.||++.  +..+...-+..++.+|++...+ ..|+..+....   +.+.... ..++++. +|-|+.|-...  +
T Consensus        49 ~~l~iwDtaG~e~~~~~~~~~~~~a~~~ilvydvt~~~Sf~~~~~~~---~~~~~~~~~~~~pii-lVgNK~DL~~~--r  122 (180)
T cd04137          49 YHLEIVDTAGQDEYSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIY---DKILDMLGKESVPIV-LVGNKSDLHTQ--R  122 (180)
T ss_pred             EEEEEEECCCCCCCCHHHHHHHHHCCEEEEEEECCCHHHHHHHHHHH---HHHHHHHCCCCCCEE-EEEECCCCHHH--C
T ss_conf             99999989987010066799986355789997438878899999999---999997588888679-77653462440--7


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCC--HHHHHHHHHHHHHHHHH
Q ss_conf             126899988085201562678688987773798579997999--89999999999999999
Q gi|254780806|r  200 QVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKC--AGSQAYLKLASELIQQE  258 (265)
Q Consensus       200 ~~~~~l~~~~~~~v~~~~Ip~~~~i~~a~~~g~pv~~~~p~s--~~a~~~~~la~el~~~~  258 (265)
                                       .|...+.-.-|...|.+.++-+-+.  ...+.|..|+++|.+.+
T Consensus       123 -----------------~V~~~e~~~~a~~~~~~f~EtSAk~g~nV~e~F~~l~~~i~k~~  166 (180)
T cd04137         123 -----------------QVSTEEGKELAESWGAAFLESSARENENVEEAFELLIEEIEKVE  166 (180)
T ss_pred             -----------------CCCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             -----------------88999999999983998999776889198999999999998863


No 500
>PRK13643 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=81.69  E-value=1.7  Score=22.44  Aligned_cols=24  Identities=29%  Similarity=0.383  Sum_probs=0.0

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHH
Q ss_conf             6874999980889888899999999
Q gi|254780806|r    4 KKSRIITIANQKGGVGKTTTAINLS   28 (265)
Q Consensus         4 ~~~kvI~v~s~KGGvGKTT~a~nlA   28 (265)
                      ++++.++++ +.-|+||||+.-.++
T Consensus        30 ~~Ge~vaii-G~nGsGKSTLl~~l~   53 (288)
T PRK13643         30 KKGSYTALI-GHTGSGKSTLLQHLN   53 (288)
T ss_pred             CCCCEEEEE-CCCCCHHHHHHHHHH
T ss_conf             599899999-999947999999997


Done!