Query         gi|254780680|ref|YP_003065093.1| seryl-tRNA synthetase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 430
No_of_seqs    246 out of 2490
Neff          6.6 
Searched_HMMs 39220
Date          Sun May 29 23:50:13 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780680.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK05431 seryl-tRNA synthetase 100.0       0       0 1283.1  33.1  421    1-425     1-422 (422)
  2 COG0172 SerS Seryl-tRNA synthe 100.0       0       0 1155.8  31.6  424    1-426     1-428 (429)
  3 KOG2509 consensus              100.0       0       0 1032.2  22.3  423    1-427     2-443 (455)
  4 cd00770 SerRS_core Seryl-tRNA  100.0       0       0  908.3  18.6  296  121-417     1-297 (297)
  5 TIGR00414 serS seryl-tRNA synt 100.0       0       0  765.4  24.2  417    1-417     1-460 (460)
  6 cd00670 Gly_His_Pro_Ser_Thr_tR 100.0       0       0  506.4  14.0  219  171-397     1-235 (235)
  7 cd00768 class_II_aaRS-like_cor 100.0       0       0  391.4  10.7  205  176-392     3-211 (211)
  8 cd00779 ProRS_core_prok Prolyl 100.0       0       0  363.4  14.3  245  140-399     6-255 (255)
  9 pfam00587 tRNA-synt_2b tRNA sy 100.0 9.6E-38 2.4E-42  301.2   8.1  166  174-344     1-170 (170)
 10 cd00771 ThrRS_core Threonyl-tR 100.0 5.5E-31 1.4E-35  251.0   7.1  246  140-401     1-289 (298)
 11 cd00772 ProRS_core Prolyl-tRNA  99.9 5.7E-26 1.5E-30  213.7  10.7  247  141-399     6-264 (264)
 12 cd00778 ProRS_core_arch_euk Pr  99.9 1.3E-22 3.3E-27  188.8  11.9  241  143-398     8-260 (261)
 13 PRK12325 prolyl-tRNA synthetas  99.9 7.3E-23 1.9E-27  190.6  10.3  266  143-424    24-351 (438)
 14 PRK12305 thrS threonyl-tRNA sy  99.9 2.7E-22 6.8E-27  186.4  11.1  264  138-416   177-482 (576)
 15 PRK12444 threonyl-tRNA synthet  99.9 7.1E-22 1.8E-26  183.3   9.9  260  138-416   244-542 (639)
 16 PRK03772 threonyl-tRNA synthet  99.9 1.3E-21 3.3E-26  181.4  10.9  256  138-415   241-539 (642)
 17 PRK00413 thrS threonyl-tRNA sy  99.9 5.7E-22 1.5E-26  184.0   6.8  258  138-416   238-538 (639)
 18 PRK04483 threonyl-tRNA synthet  99.9 2.1E-21 5.3E-26  179.8   9.2  260  138-416   241-540 (634)
 19 PRK03991 threonyl-tRNA synthet  99.9 3.6E-21 9.2E-26  178.0   9.6  277  129-415   188-499 (613)
 20 PRK12304 thrS threonyl-tRNA sy  99.8 1.8E-21 4.5E-26  180.3   7.2  257  138-415   208-506 (604)
 21 TIGR00418 thrS threonyl-tRNA s  99.8 1.5E-20 3.7E-25  173.5   6.6  355   36-401    38-480 (595)
 22 pfam02403 Seryl_tRNA_N Seryl-t  99.8 5.2E-19 1.3E-23  162.0  13.4  107    1-109     1-108 (108)
 23 PRK09194 prolyl-tRNA synthetas  99.8 1.3E-18 3.3E-23  159.0  12.2  193  130-335    13-210 (570)
 24 COG0441 ThrS Threonyl-tRNA syn  99.7 1.4E-17 3.7E-22  151.3   8.4  265  137-416   188-488 (589)
 25 PRK08661 prolyl-tRNA synthetas  99.7 2.7E-16 6.9E-21  141.8  12.6  260  142-417    20-290 (478)
 26 COG0442 ProS Prolyl-tRNA synth  99.7 8.9E-17 2.3E-21  145.4   8.2  262  135-414    17-284 (500)
 27 KOG2324 consensus               99.6 6.7E-15 1.7E-19  131.4  10.5  269  143-427    29-338 (457)
 28 PRK00960 seryl-tRNA synthetase  99.6 3.8E-14 9.6E-19  125.9  13.0  281  124-424   181-510 (516)
 29 KOG1637 consensus               99.5   3E-14 7.6E-19  126.6   9.1  246  138-403   162-452 (560)
 30 PRK04173 glycyl-tRNA synthetas  99.4 5.8E-12 1.5E-16  109.7  11.1  255  156-417    22-365 (460)
 31 TIGR00408 proS_fam_I prolyl-tR  99.3 1.4E-11 3.5E-16  106.9   8.0  258  143-413    14-305 (533)
 32 TIGR00409 proS_fam_II prolyl-t  99.1 2.2E-10 5.6E-15   97.9   5.6  230  159-403    35-283 (620)
 33 COG0423 GRS1 Glycyl-tRNA synth  99.0 5.1E-09 1.3E-13   87.7  11.6  249  162-416    30-458 (558)
 34 TIGR00415 serS_MJ seryl-tRNA s  99.0 3.7E-09 9.4E-14   88.8   9.1  265  125-405   182-494 (520)
 35 PRK00037 hisS histidyl-tRNA sy  98.7 1.4E-07 3.6E-12   77.1   8.1  155  163-330     9-171 (417)
 36 cd00774 GlyRS-like_core Glycyl  98.4 6.2E-07 1.6E-11   72.3   6.1  190  162-363    22-216 (254)
 37 TIGR02367 PylS pyrrolysyl-tRNA  98.4 5.4E-07 1.4E-11   72.7   5.5  135  170-323   241-379 (453)
 38 PRK09537 pylS pyrolysyl-tRNA s  98.3 8.7E-07 2.2E-11   71.2   3.9  189  171-402   209-402 (420)
 39 PRK12420 histidyl-tRNA synthet  98.0 3.4E-05 8.6E-10   59.4   7.7  140  166-318    12-157 (421)
 40 COG0016 PheS Phenylalanyl-tRNA  98.0 0.00022 5.5E-09   53.4  11.7  186  178-393   116-313 (335)
 41 COG0124 HisS Histidyl-tRNA syn  97.9  0.0001 2.6E-09   55.8   8.0  146  169-326    15-168 (429)
 42 TIGR00389 glyS_dimeric glycyl-  97.8   1E-04 2.5E-09   55.9   7.0  196  162-362    27-367 (606)
 43 CHL00201 syh histidine-tRNA sy  97.7 0.00021 5.5E-09   53.4   8.3  145  159-316     7-158 (424)
 44 PRK12292 hisZ ATP phosphoribos  97.7  0.0002   5E-09   53.7   7.9  140  164-316     9-154 (388)
 45 KOG4163 consensus               97.7 3.8E-05 9.7E-10   59.0   3.8  255  143-412    74-342 (551)
 46 PRK12293 hisZ ATP phosphoribos  97.5 0.00035 8.9E-09   51.8   6.4  136  166-329    13-152 (281)
 47 cd00773 HisRS-like_core Class   97.5 0.00066 1.7E-08   49.8   7.7  132  172-316     2-138 (261)
 48 PRK12295 hisZ ATP phosphoribos  97.4 0.00074 1.9E-08   49.4   7.0  125  176-319     8-140 (373)
 49 pfam01409 tRNA-synt_2d tRNA sy  97.4  0.0013 3.4E-08   47.5   8.0  188  179-395    23-222 (243)
 50 PRK00488 pheS phenylalanyl-tRN  97.3   0.027   7E-07   37.8  15.8  185  179-394   113-316 (338)
 51 cd00496 PheRS_alpha_core Pheny  97.2   0.002 5.1E-08   46.2   7.7  186  178-395     6-202 (218)
 52 PRK00476 aspS aspartyl-tRNA sy  97.2  0.0009 2.3E-08   48.8   5.6  147  129-312   105-258 (587)
 53 PRK07080 hypothetical protein;  97.1   0.014 3.7E-07   39.8  11.1  233  169-418    42-316 (318)
 54 PRK05159 aspC aspartyl-tRNA sy  97.1 0.00069 1.8E-08   49.6   4.4  117  170-313   135-253 (434)
 55 PRK03932 asnC asparaginyl-tRNA  97.1  0.0018 4.5E-08   46.6   6.4  121  171-313   134-269 (462)
 56 PRK09350 lysyl-tRNA synthetase  96.9  0.0011 2.8E-08   48.1   3.5  118  173-313    17-138 (325)
 57 cd00775 LysRS_core Lys_tRNA sy  96.8  0.0015 3.9E-08   47.0   3.8  116  172-312     8-124 (329)
 58 PRK04172 pheS phenylalanyl-tRN  96.8    0.01 2.6E-07   40.9   7.9  188  176-394   248-478 (501)
 59 PRK12421 ATP phosphoribosyltra  96.7  0.0066 1.7E-07   42.4   6.5  142  167-323    16-164 (391)
 60 PRK00484 lysS lysyl-tRNA synth  96.6  0.0031 7.8E-08   44.8   4.4  117  173-313   172-288 (491)
 61 cd00776 AsxRS_core Asx tRNA sy  96.6  0.0039   1E-07   44.0   4.6  114  171-312    23-139 (322)
 62 COG0017 AsnS Aspartyl/asparagi  96.5  0.0032 8.1E-08   44.7   4.1  139  133-304   103-247 (435)
 63 PRK06462 asparagine synthetase  96.4   0.004   1E-07   44.0   3.7  122  170-312    27-148 (332)
 64 cd00777 AspRS_core Asp tRNA sy  96.3  0.0029 7.4E-08   45.0   2.8  113  175-311     4-116 (280)
 65 PRK06253 O-phosphoseryl-tRNA s  96.3  0.0079   2E-07   41.8   4.7   97  243-357   198-303 (527)
 66 cd00669 Asp_Lys_Asn_RS_core As  96.2  0.0042 1.1E-07   43.8   3.2   95  176-288     5-99  (269)
 67 TIGR00442 hisS histidyl-tRNA s  96.2   0.032 8.1E-07   37.3   7.7  156  166-331    13-177 (446)
 68 COG0173 AspS Aspartyl-tRNA syn  96.0   0.034 8.7E-07   37.0   7.1  179  106-316    81-268 (585)
 69 PTZ00326 phenylalanyl-tRNA syn  96.0   0.026 6.6E-07   38.0   6.3  201  168-394   238-487 (505)
 70 PRK12820 bifunctional aspartyl  95.9   0.098 2.5E-06   33.6   8.9  112  173-305   157-272 (706)
 71 TIGR00457 asnS asparaginyl-tRN  95.7   0.016 4.2E-07   39.4   4.2  145  168-330   142-308 (495)
 72 TIGR00019 prfA peptide chain r  95.6    0.26 6.6E-06   30.5  10.5  106    4-126    10-119 (373)
 73 KOG0555 consensus               95.3   0.032   8E-07   37.3   4.5  102  162-286   229-337 (545)
 74 PRK12445 lysyl-tRNA synthetase  95.2   0.015 3.8E-07   39.7   2.8  117  173-313   185-301 (505)
 75 pfam00152 tRNA-synt_2 tRNA syn  95.2   0.022 5.7E-07   38.4   3.6  117  173-313    23-139 (341)
 76 PRK02983 lysS lysyl-tRNA synth  95.1   0.018 4.5E-07   39.2   2.9  117  173-313   777-893 (1099)
 77 KOG2298 consensus               95.0   0.035   9E-07   36.9   4.2   46  245-294   203-248 (599)
 78 PRK00226 greA transcription el  93.6    0.78   2E-05   27.0   8.6  101   35-143    10-112 (157)
 79 TIGR03185 DNA_S_dndD DNA sulfu  93.4    0.82 2.1E-05   26.8  10.2   97    6-102   186-289 (650)
 80 pfam07106 TBPIP Tat binding pr  93.0    0.94 2.4E-05   26.3  10.1   68   25-95     69-136 (169)
 81 TIGR00468 pheS phenylalanyl-tR  93.0    0.25 6.3E-06   30.7   5.1  107  248-367   202-318 (362)
 82 PRK00591 prfA peptide chain re  92.9    0.98 2.5E-05   26.2  11.2  106    4-126     9-117 (360)
 83 COG3883 Uncharacterized protei  92.3     1.1 2.9E-05   25.7  10.4   72   29-105    39-110 (265)
 84 pfam03961 DUF342 Protein of un  92.1     1.2   3E-05   25.7   7.6   28  192-220   174-201 (450)
 85 TIGR02231 TIGR02231 conserved   92.1     1.2 3.1E-05   25.5   8.6   93   17-109    60-187 (558)
 86 COG3705 HisZ ATP phosphoribosy  92.0    0.66 1.7E-05   27.5   6.4  139  159-316     6-151 (390)
 87 TIGR00409 proS_fam_II prolyl-t  91.3    0.52 1.3E-05   28.2   5.2   70  345-417   449-519 (620)
 88 PRK11637 hypothetical protein;  90.3     1.8 4.5E-05   24.3  10.6   34   28-61     23-56  (404)
 89 PRK10884 putative signal trans  89.8     1.9 4.9E-05   24.1  10.2   71   27-98     92-162 (206)
 90 KOG0554 consensus               89.8    0.25 6.4E-06   30.6   2.5  189  123-346    91-286 (446)
 91 TIGR01462 greA transcription e  89.8     1.5 3.8E-05   24.9   6.4   98   35-143     5-109 (155)
 92 PRK01885 greB transcription el  89.8     1.9   5E-05   24.0   7.6  109   35-152    12-122 (159)
 93 PRK13363 protocatechuate 4,5-d  89.6    0.19 4.8E-06   31.5   1.7   42  224-268   280-323 (335)
 94 PRK05729 valS valyl-tRNA synth  89.0     1.2 3.1E-05   25.5   5.5   12   13-24     63-74  (877)
 95 pfam02994 Transposase_22 L1 tr  88.9     2.2 5.6E-05   23.6   7.4  108   25-132    95-217 (370)
 96 COG1579 Zn-ribbon protein, pos  88.3     2.4 6.2E-05   23.3  10.8   69   29-100    53-121 (239)
 97 KOG2411 consensus               88.1    0.68 1.7E-05   27.4   3.7  109  173-306   179-296 (628)
 98 COG1340 Uncharacterized archae  87.6     2.7 6.8E-05   23.0  10.5   73   28-105    20-92  (294)
 99 TIGR01061 parC_Gpos DNA topois  86.9     2.9 7.3E-05   22.7   7.1  113    4-130   386-508 (745)
100 KOG0804 consensus               86.9     2.9 7.4E-05   22.7  11.3   73   34-107   381-453 (493)
101 TIGR02169 SMC_prok_A chromosom  85.8     3.3 8.3E-05   22.3   7.9   27   28-54    436-462 (1202)
102 TIGR00470 sepS O-phosphoseryl-  85.3    0.48 1.2E-05   28.5   1.7  162  136-315    13-271 (558)
103 pfam12325 TMF_TATA_bd TATA ele  84.7     3.6 9.3E-05   22.0   9.1   63   28-92     24-86  (121)
104 TIGR00459 aspS_bact aspartyl-t  84.3     1.4 3.7E-05   25.0   3.8  110  177-312   156-278 (653)
105 COG0216 PrfA Protein chain rel  83.9     3.9   1E-04   21.7  12.2  105    5-126    10-117 (363)
106 pfam04420 CHD5 CHD5-like prote  83.7       4  0.0001   21.7   6.8   73   33-107    36-110 (159)
107 KOG0250 consensus               83.4     4.1  0.0001   21.6   9.7   33   31-63    354-386 (1074)
108 KOG1936 consensus               81.6     4.7 0.00012   21.1   6.2  125  176-315    74-208 (518)
109 COG4026 Uncharacterized protei  81.1     4.9 0.00013   21.0   9.8   18    2-19    103-122 (290)
110 COG2024 Phenylalanyl-tRNA synt  80.8    0.88 2.2E-05   26.6   1.6   38  241-281   197-234 (536)
111 pfam03449 GreA_GreB_N domain.   80.8       5 0.00013   20.9   7.7   59   35-93      6-68  (71)
112 TIGR00020 prfB peptide chain r  80.2     5.3 0.00013   20.8  11.4  124    1-138    24-171 (373)
113 cd07366 3MGA_Dioxygenase Subun  79.5     1.1 2.9E-05   25.8   1.8   41  225-268   277-319 (328)
114 PRK05561 DNA topoisomerase IV   79.4     5.5 0.00014   20.6   9.3   58    4-64    400-460 (745)
115 PRK05560 DNA gyrase subunit A;  79.3     5.6 0.00014   20.6   9.9   59    4-64    394-457 (822)
116 pfam03357 Snf7 Snf7. This fami  78.6     5.8 0.00015   20.5  10.3   62   29-90      2-63  (169)
117 PRK09616 pheT phenylalanyl-tRN  77.4     6.3 0.00016   20.2   6.4  184  130-346   315-505 (546)
118 pfam03962 Mnd1 Mnd1 family. Th  77.2     6.4 0.00016   20.2  10.3   67   28-94     62-129 (188)
119 pfam11932 DUF3450 Protein of u  77.0     6.4 0.00016   20.1   7.8   77   31-119    53-129 (250)
120 PRK05892 nucleoside diphosphat  75.6       7 0.00018   19.9   7.0   74   35-117    13-90  (161)
121 TIGR00458 aspS_arch aspartyl-t  75.5     1.3 3.4E-05   25.2   1.2  136   97-267    95-237 (466)
122 pfam07246 Phlebovirus_NSM Phle  75.2     7.1 0.00018   19.8   9.1   36   69-104   203-238 (264)
123 pfam05622 HOOK HOOK protein. T  75.0     7.2 0.00018   19.8   9.6   29   28-56    284-312 (713)
124 pfam06447 consensus             74.1     7.6 0.00019   19.6   7.3   29   75-103    83-111 (407)
125 COG2269 Truncated, possibly in  74.0     3.1   8E-05   22.5   2.8  114  173-303    16-139 (322)
126 pfam06508 ExsB ExsB. This fami  73.9       3 7.8E-05   22.6   2.7   55  280-338    22-77  (137)
127 TIGR00570 cdk7 CDK-activating   73.1       8  0.0002   19.4   7.5  124    6-139   134-264 (322)
128 PRK13979 DNA topoisomerase IV   72.8     8.1 0.00021   19.4  10.1   59    4-64    406-469 (959)
129 KOG0979 consensus               72.7     8.1 0.00021   19.4   8.9   57   69-125   319-375 (1072)
130 TIGR02894 DNA_bind_RsfA transc  72.1     8.4 0.00021   19.3   9.6   67   24-102    81-147 (163)
131 pfam07851 TMPIT TMPIT-like pro  69.9     9.3 0.00024   18.9   9.1   75   28-107    11-93  (330)
132 pfam08317 Spc7 Spc7 kinetochor  69.5     9.5 0.00024   18.9  10.5   62   44-105   178-245 (322)
133 COG1190 LysU Lysyl-tRNA synthe  68.6     6.1 0.00016   20.3   3.3  174  179-400   187-376 (502)
134 COG1196 Smc Chromosome segrega  68.0      10 0.00026   18.7   9.4  103  153-264   531-648 (1163)
135 TIGR03545 conserved hypothetic  67.7      10 0.00026   18.6   8.4   42   68-109   219-260 (554)
136 PRK09343 prefoldin subunit bet  66.8      11 0.00027   18.5   9.7   89   28-116    14-119 (122)
137 pfam10168 Nup88 Nuclear pore c  66.5      11 0.00028   18.5   9.5   16  348-363   463-478 (717)
138 COG1382 GimC Prefoldin, chaper  65.2      11 0.00029   18.3   9.7   60   56-115    57-117 (119)
139 pfam12127 YdfA_immunity SigmaW  64.8     5.9 0.00015   20.4   2.6   59    4-66    188-252 (321)
140 COG4915 XpaC 5-bromo-4-chloroi  64.1      12  0.0003   18.1   7.2   18    3-20     69-86  (204)
141 PRK11020 hypothetical protein;  63.9      12 0.00031   18.1   8.8   50   59-111    22-71  (118)
142 TIGR02865 spore_II_E stage II   63.6      12 0.00031   18.1   7.0  244    7-273   418-750 (794)
143 KOG0996 consensus               63.4      12 0.00031   18.1   8.9  141   34-182   499-661 (1293)
144 PRK10636 putative ABC transpor  62.7      13 0.00032   18.0   9.5   34  304-337   408-441 (638)
145 KOG0995 consensus               61.8      13 0.00033   17.9  12.7   29   76-104   295-323 (581)
146 KOG0933 consensus               61.6      13 0.00033   17.8   8.2   22  309-330   713-734 (1174)
147 cd01279 HTH_HspR-like Helix-Tu  61.2      13 0.00034   17.8   5.9   45   14-58     50-95  (98)
148 pfam04645 DUF603 Protein of un  60.6      14 0.00035   17.7   7.2   50   34-83    104-153 (181)
149 TIGR01843 type_I_hlyD type I s  60.4      14 0.00035   17.7  10.3  142   15-174   191-359 (434)
150 pfam11853 DUF3373 Protein of u  60.0      14 0.00036   17.6   4.1   13  112-124    95-107 (485)
151 KOG4673 consensus               59.1      14 0.00037   17.5   9.5   59   28-86    409-471 (961)
152 PRK00578 prfB peptide chain re  57.9      15 0.00038   17.4  11.1   53    2-54     23-75  (367)
153 pfam04111 APG6 Autophagy prote  57.3      15 0.00039   17.3   9.8  141   28-195    70-219 (356)
154 PRK13665 hypothetical protein;  57.1     6.8 0.00017   20.0   1.8   22    4-25    189-210 (327)
155 PRK09039 hypothetical protein;  57.0      16  0.0004   17.3   9.6   21  191-211   212-232 (343)
156 COG5185 HEC1 Protein involved   56.6      16  0.0004   17.3   7.8   19   30-48    297-315 (622)
157 COG0072 PheT Phenylalanyl-tRNA  55.8      16 0.00041   17.2   4.8  176  130-322   308-496 (650)
158 pfam10018 Med4 Vitamin-D-recep  55.6      16 0.00042   17.1   9.0   60   27-102     4-63  (175)
159 pfam08614 ATG16 Autophagy prot  55.5      16 0.00042   17.1   9.8   31   73-103   128-158 (194)
160 pfam05529 Bap31 B-cell recepto  55.4      16 0.00042   17.1   8.4   32   70-101   149-180 (192)
161 smart00787 Spc7 Spc7 kinetocho  54.4      17 0.00043   17.0  10.9   40   66-105   202-241 (312)
162 PRK12704 phosphodiesterase; Pr  54.1      17 0.00044   17.0   9.7   30   31-60     45-74  (455)
163 TIGR03007 pepcterm_ChnLen poly  53.8      17 0.00044   16.9   5.4   90   16-105   141-234 (510)
164 KOG0964 consensus               53.8      17 0.00044   16.9  10.3   48   11-58    687-736 (1200)
165 PRK10240 undecaprenyl pyrophos  52.8     7.3 0.00019   19.7   1.4   95   74-193   128-222 (229)
166 COG0603 Predicted PP-loop supe  52.7      10 0.00026   18.6   2.2   10  162-171   129-138 (222)
167 pfam06419 COG6 Conserved oligo  52.1      18 0.00047   16.7   9.4   86   14-104    21-109 (615)
168 pfam09730 BicD Microtubule-ass  52.1      18 0.00047   16.7   9.8   31  296-330   437-467 (711)
169 pfam03194 LUC7 LUC7 N_terminus  51.8      19 0.00047   16.7   8.0   48   43-90    124-171 (252)
170 PHA00727 hypothetical protein   51.3      19 0.00048   16.7   6.0   60   29-88      5-70  (276)
171 pfam12329 TMF_DNA_bd TATA elem  51.2      19 0.00048   16.7   9.5   66   29-99      6-71  (74)
172 KOG2391 consensus               51.0      19 0.00049   16.6   9.9   80   34-118   217-296 (365)
173 pfam06810 Phage_GP20 Phage min  50.7      19 0.00049   16.6   9.6   54   36-91     21-74  (156)
174 COG3914 Spy Predicted O-linked  50.7     6.1 0.00016   20.3   0.7   61  252-314   260-321 (620)
175 cd00475 CIS_IPPS Cis (Z)-Isopr  50.0      10 0.00026   18.6   1.8   53   76-138   137-189 (221)
176 KOG2629 consensus               48.7      21 0.00053   16.4   9.1   98   13-115   103-204 (300)
177 KOG0999 consensus               48.4      21 0.00053   16.3   9.4   20  311-330   492-511 (772)
178 COG4985 ABC-type phosphate tra  47.9      21 0.00054   16.3   8.1   43   67-109   213-255 (289)
179 pfam06632 XRCC4 DNA double-str  46.7      22 0.00056   16.2   7.8   73   24-96    128-203 (331)
180 KOG0977 consensus               46.2      22 0.00057   16.1   9.0   24   27-50     55-78  (546)
181 cd01368 KISc_KIF23_like Kinesi  45.7      15 0.00038   17.5   2.1   43  379-421   267-316 (345)
182 COG2433 Uncharacterized conser  45.6      23 0.00058   16.0  10.8   28  174-204   504-531 (652)
183 pfam10146 zf-C4H2 Zinc finger-  45.6      23 0.00058   16.0  10.2   60   33-104    44-103 (220)
184 KOG1029 consensus               45.3      23 0.00059   16.0   8.7   11  135-145   701-711 (1118)
185 KOG3229 consensus               45.2      23 0.00059   16.0   9.9   72   32-107    22-93  (227)
186 TIGR01063 gyrA DNA gyrase, A s  45.0      23  0.0006   16.0  10.1  111    4-125   389-527 (864)
187 pfam04880 NUDE_C NUDE protein,  44.9      23  0.0006   16.0   8.1   49   68-116    24-77  (166)
188 PRK11147 ABC transporter ATPas  44.1      24 0.00061   15.9   6.9   11  136-146   181-191 (632)
189 pfam10498 IFT57 Intra-flagella  44.1      24 0.00061   15.9   8.9   11  124-134    79-89  (355)
190 KOG4657 consensus               43.7      24 0.00062   15.8   8.9   46   11-56     31-76  (246)
191 COG4942 Membrane-bound metallo  43.6      24 0.00062   15.8   9.9   19  403-423   338-356 (420)
192 TIGR00958 3a01208 antigen pept  43.2      17 0.00044   16.9   2.1   53   93-149   501-553 (770)
193 KOG4674 consensus               42.9      25 0.00064   15.8  12.2   21  298-318  1663-1683(1822)
194 pfam11622 DUF3251 Protein of u  42.8     8.5 0.00022   19.3   0.5   42  230-282   105-155 (156)
195 pfam10482 CtIP_N Tumour-suppre  42.5      25 0.00065   15.7   7.4   54   34-92     13-66  (120)
196 KOG0728 consensus               42.5      25 0.00065   15.7   5.0  168   28-211    24-228 (404)
197 pfam07888 CALCOCO1 Calcium bin  42.4      25 0.00065   15.7   9.9   69  237-314   384-455 (546)
198 KOG4302 consensus               42.1      26 0.00066   15.7  10.1   81   28-108    54-143 (660)
199 PRK05771 V-type ATP synthase s  42.0      26 0.00066   15.7   7.3  100    8-108    10-132 (640)
200 COG3879 Uncharacterized protei  41.2      27 0.00068   15.6   9.4   43   20-62     42-84  (247)
201 TIGR00998 8a0101 efflux pump m  40.9      27 0.00068   15.5   5.3   94   10-105   142-242 (379)
202 KOG2077 consensus               40.9      27 0.00068   15.5   9.0   25  317-343   642-666 (832)
203 KOG2911 consensus               40.5      27 0.00069   15.5  10.3   43   29-71    234-276 (439)
204 pfam01920 Prefoldin_2 Prefoldi  40.3      27  0.0007   15.5  10.9   75   28-102     5-96  (104)
205 KOG0837 consensus               39.9      28  0.0007   15.4   4.9   15  167-181    65-79  (279)
206 PRK11106 queuosine biosynthesi  39.6      16  0.0004   17.3   1.4   13  234-246   158-170 (231)
207 COG3352 FlaC Putative archaeal  39.6      28 0.00071   15.4   6.2   69   43-111    45-115 (157)
208 pfam04156 IncA IncA protein. C  38.4      29 0.00074   15.3   9.2   69   29-102    80-148 (186)
209 TIGR02997 Sig70-cyanoRpoD RNA   37.9      30 0.00075   15.2   4.3   53   68-120   194-253 (336)
210 TIGR00364 TIGR00364 exsB prote  37.8      29 0.00073   15.3   2.5   97  277-385    18-152 (227)
211 KOG2784 consensus               37.7      24 0.00061   15.9   2.1  104  233-358   317-426 (483)
212 pfam10458 Val_tRNA-synt_C Valy  37.5      30 0.00076   15.2   7.4   61   33-100     2-64  (66)
213 TIGR02168 SMC_prok_B chromosom  37.2      30 0.00077   15.1   9.8   19  190-208   575-593 (1191)
214 KOG1656 consensus               37.1      30 0.00078   15.1   7.1   18   87-104   162-180 (221)
215 PRK04863 mukB cell division pr  36.9      31 0.00078   15.1  11.8   93    8-105  1032-1124(1486)
216 KOG0432 consensus               36.5      31 0.00079   15.1   6.0   28  175-204   742-769 (995)
217 pfam03629 DUF303 Domain of unk  36.5      14 0.00036   17.6   0.8   32  304-343     6-37  (72)
218 COG0782 Uncharacterized conser  36.4      31 0.00079   15.1   6.4   79   35-117     4-83  (151)
219 COG3236 Uncharacterized protei  36.4     3.2 8.1E-05   22.4  -2.6   97  210-328    27-125 (162)
220 pfam05103 DivIVA DivIVA protei  35.9      32 0.00081   15.0   9.9   42   20-61     15-58  (131)
221 pfam01496 V_ATPase_I V-type AT  35.8      32 0.00081   15.0   4.0   15  186-200   202-216 (707)
222 COG0525 ValS Valyl-tRNA synthe  35.6      32 0.00081   15.0   7.7   12   27-38    106-117 (877)
223 pfam03999 MAP65_ASE1 Microtubu  35.0      33 0.00083   14.9   8.3   33   27-59     18-50  (619)
224 PRK09239 chorismate mutase; Pr  34.9      33 0.00084   14.9   8.7   38   29-66     11-48  (104)
225 pfam05531 NPV_P10 Nucleopolyhe  34.8      33 0.00084   14.9   6.5   23   28-50     11-33  (75)
226 pfam05565 Sipho_Gp157 Siphovir  34.7      33 0.00084   14.9   7.3  116   44-165    31-154 (162)
227 KOG2264 consensus               34.4      33 0.00085   14.8  11.5  113   41-170    92-204 (907)
228 pfam05266 DUF724 Protein of un  34.1      34 0.00086   14.8   9.1   26   16-41     79-109 (190)
229 pfam01255 Prenyltransf Putativ  33.6      34 0.00087   14.7   3.7   85   76-183   131-215 (222)
230 cd00733 GlyRS_alpha_core Class  33.3      35 0.00088   14.7   4.3   80  250-344    45-133 (279)
231 PRK06665 flgK flagellar hook-a  33.3      35 0.00088   14.7   7.9   80   35-114   139-227 (628)
232 cd00584 Prefoldin_alpha Prefol  32.8      35  0.0009   14.7   9.6   58  112-178    52-110 (129)
233 cd00769 PheRS_beta_core Phenyl  32.7      35  0.0009   14.6   6.1  125  173-318     4-142 (198)
234 pfam06673 L_lactis_ph-MCP Lact  32.4      36 0.00091   14.6   5.7   59   30-90     13-71  (347)
235 PRK13923 putative spore coat p  32.3      36 0.00091   14.6   7.7   65   37-101    57-144 (162)
236 PRK06945 flgK flagellar hook-a  32.3      36 0.00091   14.6   7.5   80   36-115   129-218 (649)
237 KOG1962 consensus               32.3      36 0.00091   14.6   8.6   36   70-105   153-188 (216)
238 pfam02991 MAP1_LC3 Microtubule  32.0      36 0.00092   14.6   2.3   56  345-407    35-93  (104)
239 cd00890 Prefoldin Prefoldin is  32.0      36 0.00092   14.6   9.7   28  151-178    83-110 (129)
240 pfam07926 TPR_MLP1_2 TPR/MLP1/  31.8      37 0.00093   14.5   9.2   19   44-62     61-79  (132)
241 TIGR03319 YmdA_YtgF conserved   31.6      37 0.00094   14.5   9.6   24  386-409   478-501 (514)
242 pfam06273 eIF-4B Plant specifi  31.5      37 0.00094   14.5   4.2   10  102-111    89-98  (430)
243 PRK11530 hypothetical protein;  31.0      17 0.00043   17.0   0.4   43  229-282   121-172 (176)
244 COG1422 Predicted membrane pro  30.9      38 0.00096   14.4   8.8   49   31-79     61-109 (201)
245 COG4573 GatZ Predicted tagatos  30.6      17 0.00045   16.9   0.5   57  355-421   334-391 (426)
246 pfam02091 tRNA-synt_2e Glycyl-  30.5      38 0.00098   14.4   4.2   79  251-344    45-132 (284)
247 COG3167 PilO Tfp pilus assembl  30.4      38 0.00098   14.4   4.9   26   84-109    75-100 (211)
248 pfam05667 DUF812 Protein of un  30.3      39 0.00098   14.4   9.8   20  203-222   433-452 (536)
249 pfam03954 Lectin_N Hepatic lec  30.2      39 0.00098   14.4   5.6   59   34-100    54-112 (138)
250 KOG4797 consensus               30.0      39 0.00099   14.3   4.7   26   72-97     64-89  (123)
251 TIGR02249 integrase_gron integ  29.9      33 0.00083   14.9   1.8   53  150-204   146-209 (320)
252 pfam10359 Fmp27_WPPW RNA pol I  29.9      39   0.001   14.3   8.3   63   35-101   161-223 (470)
253 KOG0556 consensus               29.7      19 0.00048   16.7   0.5   77  173-265   229-308 (533)
254 COG4864 Uncharacterized protei  29.7      19 0.00047   16.7   0.5   33  138-170   185-219 (328)
255 pfam09798 LCD1 DNA damage chec  29.5      40   0.001   14.3  11.5   40   67-106    32-71  (648)
256 PRK13729 conjugal transfer pil  29.4      40   0.001   14.3   8.1   35  248-283   251-288 (474)
257 KOG3433 consensus               29.2      40   0.001   14.2   9.2   39   25-63     71-109 (203)
258 pfam01841 Transglut_core Trans  28.9      38 0.00096   14.4   1.9   49  300-349    55-105 (108)
259 PRK06746 peptide chain release  28.5      41   0.001   14.2  10.1   19    1-20      1-19  (326)
260 pfam07889 DUF1664 Protein of u  28.5      41  0.0011   14.1   9.0   61   33-101    59-122 (126)
261 PRK00106 hypothetical protein;  28.4      41  0.0011   14.1   9.6   50  353-409   473-522 (535)
262 TIGR01320 mal_quin_oxido malat  28.1      25 0.00064   15.8   0.9   65  191-257   289-371 (487)
263 TIGR03414 ABC_choline_bnd chol  28.1      29 0.00074   15.3   1.2   35  225-261   149-183 (290)
264 pfam04582 Reo_sigmaC Reovirus   27.9      42  0.0011   14.1   8.8   59    3-61     29-89  (326)
265 pfam11382 DUF3186 Protein of u  27.9      42  0.0011   14.1   7.6   59    1-59      1-63  (307)
266 pfam05008 V-SNARE Vesicle tran  27.8      42  0.0011   14.1   8.0   57   35-91     22-78  (79)
267 TIGR01710 typeII_sec_gspG gene  27.8      24  0.0006   15.9   0.7   23  218-242    50-72  (137)
268 TIGR02905 spore_yutH spore coa  27.7      38 0.00096   14.4   1.8  124  163-306   165-315 (325)
269 KOG4196 consensus               27.4      43  0.0011   14.0  10.4   79   19-105    40-118 (135)
270 COG3175 COX11 Cytochrome oxida  27.4      26 0.00067   15.6   0.9   12  280-291   125-136 (195)
271 PRK11546 zraP zinc resistance   27.2      43  0.0011   14.0   9.8   71   27-102    42-112 (139)
272 PRK11281 potassium efflux prot  27.2      43  0.0011   14.0   6.5   31   77-107   122-152 (1107)
273 KOG3033 consensus               27.1      21 0.00053   16.4   0.4  165  226-424    67-279 (286)
274 pfam08286 Spc24 Spc24 subunit   27.0      44  0.0011   14.0   4.8   31   31-61      2-32  (117)
275 TIGR01503 MthylAspMut_E methyl  27.0      44  0.0011   14.0   2.5  174  176-378   265-462 (481)
276 pfam08581 Tup_N Tup N-terminal  26.9      44  0.0011   14.0   7.5   63   44-106     6-70  (79)
277 PRK08871 flgK flagellar hook-a  26.8      44  0.0011   13.9   6.8   78   36-113   131-214 (626)
278 PRK12999 pyruvate carboxylase;  26.6      13 0.00034   17.8  -0.7  100  296-397   651-758 (1147)
279 COG1305 Transglutaminase-like   26.6      44  0.0011   13.9   2.8   55  303-358   201-264 (319)
280 PRK08187 pyruvate kinase; Vali  26.5      44  0.0011   13.9   2.6   44  319-362   409-454 (606)
281 pfam06910 MEA1 Male enhanced a  26.0      40   0.001   14.3   1.6   55   87-147    78-132 (174)
282 pfam09016 Pas_Saposin Pas fact  26.0      38 0.00097   14.4   1.5   34  302-335    20-54  (76)
283 KOG0161 consensus               25.9      46  0.0012   13.8  10.1   41  377-420   649-690 (1930)
284 pfam07665 consensus             25.8      46  0.0012   13.8   5.6   33   69-101    13-45  (57)
285 pfam04089 BRICHOS BRICHOS doma  25.8      46  0.0012   13.8   2.1   46  356-404    10-55  (97)
286 cd04914 ACT_AKi-DapG-BS_1 ACT   25.4      46  0.0012   13.8   1.9   37  284-320    30-66  (67)
287 TIGR01880 Ac-peptdase-euk N-ac  25.3      28 0.00072   15.4   0.8   26  119-145   375-408 (433)
288 KOG1234 consensus               25.2     7.6 0.00019   19.6  -2.2   16  289-304   320-336 (363)
289 pfam10573 UPF0561 Uncharacteri  25.1      21 0.00054   16.3   0.1   33  121-155    82-114 (126)
290 pfam06156 DUF972 Protein of un  25.1      47  0.0012   13.7   8.3   54   37-95      3-56  (106)
291 PRK04778 septation ring format  25.0      47  0.0012   13.7   7.8   29   33-61    117-145 (569)
292 PRK07245 consensus              25.0      47  0.0012   13.7   9.6   38   12-49      6-43  (337)
293 cd01107 HTH_BmrR Helix-Turn-He  24.8      47  0.0012   13.7   6.2   30   71-100    78-107 (108)
294 PRK03947 prefoldin subunit alp  24.7      48  0.0012   13.7  10.8   28   28-55      7-34  (141)
295 COG0188 GyrA Type IIA topoisom  24.5      48  0.0012   13.6   8.9   60    4-64    393-456 (804)
296 PRK00396 rnpA ribonuclease P;   24.4      46  0.0012   13.8   1.7   44  272-315    70-115 (134)
297 pfam02381 MraZ MraZ protein. T  24.3      30 0.00076   15.2   0.7   18  402-419    11-28  (72)
298 PRK13169 DNA replication intia  24.3      48  0.0012   13.6   8.3   52   37-93      3-54  (107)
299 pfam07050 consensus             24.3      49  0.0012   13.6   8.3   45   69-113    69-115 (145)
300 PRK10696 C32 tRNA thiolase; Pr  24.2      49  0.0012   13.6   1.8   23  170-196   124-146 (311)
301 pfam10502 Peptidase_S26 Peptid  24.1      49  0.0012   13.6   2.0   27  272-298    10-39  (138)
302 TIGR02977 phageshock_pspA phag  24.0      49  0.0013   13.6   9.1   65   35-99     52-130 (222)
303 TIGR00433 bioB biotin synthase  24.0      43  0.0011   14.0   1.5  138   37-180   134-322 (350)
304 pfam06160 EzrA Septation ring   23.9      49  0.0013   13.6   7.8   30   33-62    113-142 (559)
305 pfam09457 RBD-FIP FIP domain.   23.3      51  0.0013   13.5   4.3   35   71-105     3-37  (48)
306 pfam01544 CorA CorA-like Mg2+   22.3      53  0.0013   13.3   8.9   83   12-101    92-177 (291)
307 pfam09738 DUF2051 Double stran  22.1      53  0.0014   13.3   8.4   35   28-62     83-117 (294)
308 pfam08590 DUF1771 Domain of un  22.1      53  0.0014   13.3   8.0   56   37-92      2-57  (66)
309 PTZ00327 eukaryotic translatio  21.9      22 0.00055   16.2  -0.4   16  269-286   273-288 (460)
310 smart00129 KISc Kinesin motor,  21.9      54  0.0014   13.3   1.9   40  379-420   252-296 (335)
311 COG3933 Transcriptional antite  21.6      45  0.0011   13.9   1.2   55  160-221   164-221 (470)
312 cd00632 Prefoldin_beta Prefold  21.6      54  0.0014   13.2  11.0   50   56-105    50-100 (105)
313 pfam12186 AcylCoA_dehyd_C Acyl  21.6      29 0.00075   15.2   0.2   22   37-58     21-42  (114)
314 PRK05257 malate:quinone oxidor  21.4      23 0.00058   16.1  -0.3   33  235-268   300-335 (499)
315 pfam09389 consensus             21.3      55  0.0014   13.2   9.3   67   28-94    121-194 (209)
316 cd01106 HTH_TipAL-Mta Helix-Tu  21.1      55  0.0014   13.2   5.2   29   69-97     74-102 (103)
317 pfam11285 DUF3086 Protein of u  21.1      56  0.0014   13.2   8.9   53   28-84      4-56  (283)
318 TIGR02770 nickel_nikD nickel i  21.1      52  0.0013   13.4   1.4   12  320-331   186-197 (239)
319 pfam06039 Mqo Malate:quinone o  21.0      27 0.00068   15.6  -0.1   33  235-268   295-330 (489)
320 PRK13339 malate:quinone oxidor  20.9      28 0.00072   15.4   0.0   34  234-268   296-332 (497)
321 pfam11607 DUF3247 Protein of u  20.7      27 0.00069   15.5  -0.1   38  259-305    52-89  (101)
322 KOG0612 consensus               20.5      57  0.0015   13.1   9.8   35  358-394  1236-1271(1317)
323 pfam03210 Paramyx_P_V Paramyxo  20.5      57  0.0015   13.1   8.1   85   44-131   264-352 (435)
324 PRK08471 flgK flagellar hook-a  20.5      57  0.0015   13.1   7.4   79   35-113   132-221 (612)
325 pfam10758 DUF2586 Protein of u  20.4      57  0.0015   13.1   2.8   28  331-361   227-260 (363)

No 1  
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=100.00  E-value=0  Score=1283.05  Aligned_cols=421  Identities=55%  Similarity=0.894  Sum_probs=412.5

Q ss_pred             CCCHHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             98844785199999999984698958899999999999999999999999999999999986449987999999999999
Q gi|254780680|r    1 MLDIQWIRQNPEHLDIALKKRHLEPQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTL   80 (430)
Q Consensus         1 MLDik~IRen~e~v~~~l~~R~~~~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~L   80 (430)
                      |||||+||+||+.|++++++||.+.++|+++++|++||++++++|+||+++|++||+||+++++++  +.+++++++++|
T Consensus         1 MLDik~IReNpe~v~~~lkkR~~~~~id~il~lD~~rr~l~~e~e~Lr~erN~iSK~Ig~~kk~g~--~~~~l~~~~~~l   78 (422)
T PRK05431          1 MLDIKLIRENPDAVKEKLAKRGDPLDVDELLELDEERRELQTETEELQAERNALSKEIGQAKAKGE--DAEELIAEVKEL   78 (422)
T ss_pred             CCCHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CHHHHHHHHHHH
T ss_conf             988789874999999999865984519999999999999999999999999999999999874897--799999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHC
Q ss_conf             98864446666677888774431002258811221135554024200015656656662112202211731000112221
Q gi|254780680|r   81 KEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILIRSVGKKPSAIHLSREHFEIGEALGLMDFDRATKLS  160 (430)
Q Consensus        81 k~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~~~G~~~~f~f~~k~H~elge~l~liDfe~a~kvs  160 (430)
                      +++|+.+++++++++++++++++.|||+||++||+|.||++|++|+.||++|.|+|+||+|||||+.+|++||++|+|||
T Consensus        79 k~~i~~le~~~~~~~~~l~~~ll~IPNi~~~~VP~G~dE~dNv~I~~~G~~~~f~f~~k~H~elge~l~liDfe~aaKiS  158 (422)
T PRK05431         79 KEEIKALEAELKELEAELEELLLSIPNLPHDSVPVGKDEDDNVEVRRWGEPREFDFEPKDHWELGEKLGILDFERAAKVS  158 (422)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHC
T ss_conf             99999999999999999999998489988865788998302255420377444567887788998764761046677550


Q ss_pred             CCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHH-HCCEECCCCCCHHHHH
Q ss_conf             675301056488999999999998622320320212356202788986551422476776431-0002313454114544
Q gi|254780680|r  161 GARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTT-DGRWLIPTSEVSLTNL  239 (430)
Q Consensus       161 GsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~-d~l~Li~TaEvpL~~~  239 (430)
                      |||||||+|+||+|||||+|||||+|+ ++||++|+||+|||+++|+||||||+|++|+|+++ +|+||||||||||+||
T Consensus       159 GsRF~~Lkg~~A~LerALi~f~ld~~~-~~Gy~~v~~P~lv~~~~~~gtGqlPkfe~~~Y~i~~~dl~Li~TAEvpL~~~  237 (422)
T PRK05431        159 GSRFYVLKGDGARLERALIQFMLDLHT-EEGYTEVIPPYLVNEESMYGTGQLPKFEEDLFKIEDDDLYLIPTAEVPLTNL  237 (422)
T ss_pred             CCCEEEEHHHHHHHHHHHHHHHHHHHH-HCCCEEEECHHHHHHHHHHHHCCCCCCHHHHHHHCCCCEEEECCCCCCHHHH
T ss_conf             787046004899999999999999999-8799799673763678874453797448775410588717605653212334


Q ss_pred             HHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             53420595550420885322107884335543432122221020021212786501457898999999999984106753
Q gi|254780680|r  240 YSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRV  319 (430)
Q Consensus       240 ~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRv  319 (430)
                      |+|++|+.++||+||||+|||||+||||||||||||||||||+|||||+||+||+|+++|++|+.++++||+.|+|||||
T Consensus       238 ~~~eil~~~~LPik~~~~S~CFR~EAGs~GkdtrGl~RvHQF~KVE~f~~~~pe~S~~~~e~~~~~~e~i~~~L~lpyrv  317 (422)
T PRK05431        238 HRDEILDEEELPIKYTAYSPCFRSEAGSAGRDTRGLIRQHQFDKVELVKFTKPEDSYAELEELTGNAEEILQKLELPYRV  317 (422)
T ss_pred             HHCCCCCHHHCCHHHEEECCHHHHCCCCCCCCCCCCEEEEEECEEEEEEECCHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             40113365439844527883653031336755676124430000343353586779999999999999999875985023


Q ss_pred             CCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             03780117844340241011010048332375310210076453268473389984101042004322899999999883
Q gi|254780680|r  320 VSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAILEN  399 (430)
Q Consensus       320 v~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ailEn  399 (430)
                      |+|||||||++|+||||||||||||++|||||||||||||||||||||||+.+|+ ++||||||||||||||+|+|||||
T Consensus       318 v~~~sgdlg~~a~~~yDiE~W~P~~~~y~EvsS~Snc~d~QsrRl~iry~~~~~~-~~~~htlNgt~~A~~R~l~ailEn  396 (422)
T PRK05431        318 VLLCTGDMGFSAAKTYDLEVWLPGQNTYREISSCSNCTDFQARRANIRYRDEDGK-PELVHTLNGSGLAVGRTLVAILEN  396 (422)
T ss_pred             CCCCCCCCCHHHHHHEEEEEEECCCCCEEEEEEECCCCHHHHHHCCCEEECCCCC-EEEEEECCCCHHHHHHHHHHHHHH
T ss_conf             5678765576656545457871566854524000150148875302655179998-664043115121887899999884


Q ss_pred             CCCCCCCEECCCCCCCCCCCEEEECC
Q ss_conf             46899838658222310188013073
Q gi|254780680|r  400 YLNADGSVTIPTVLRPYMNNLAVIKK  425 (430)
Q Consensus       400 ~q~~dg~i~iP~~L~pym~g~~~i~~  425 (430)
                      |||+||+|+||+||||||||+++|++
T Consensus       397 ~q~~dg~i~iP~~L~~y~~~~~~i~~  422 (422)
T PRK05431        397 YQQADGSVTIPEVLRPYMGGLEIIPK  422 (422)
T ss_pred             CCCCCCCEECCHHHHHHCCCCEECCC
T ss_conf             64899888478131201698830889


No 2  
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=1155.78  Aligned_cols=424  Identities=53%  Similarity=0.872  Sum_probs=410.5

Q ss_pred             CCCHHHHHCCHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             988447851999999999846989-5889999999999999999999999999999999998644998799999999999
Q gi|254780680|r    1 MLDIQWIRQNPEHLDIALKKRHLE-PQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETST   79 (430)
Q Consensus         1 MLDik~IRen~e~v~~~l~~R~~~-~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~   79 (430)
                      |||+|+||+|||.+++++.+|+.+ .++|++++||++||+++.+.++|+++||.+||+||+.++.+.+ .+..++++++.
T Consensus         1 mld~k~ir~n~d~v~~~l~~r~~~~~~~~~~~~ld~~~r~~~~~~e~l~~~rn~~sk~ig~~~~~~~~-~~~~l~~e~~~   79 (429)
T COG0172           1 MLDLKLIRENPDAVREKLKKRGGDALDVDKLLELDEERRKLLRELEELQAERNELSKEIGRALKRGED-DAEELIAEVKE   79 (429)
T ss_pred             CCHHHHHHHCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH-HHHHHHHHHHH
T ss_conf             96487765099999998763488376789999999999999999999999988999999987632621-48999998898


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEEEECCCCC--CCCCCCCCCCHHHHCCCCCHHHHH
Q ss_conf             998864446666677888774431002258811221135554024200015656--656662112202211731000112
Q gi|254780680|r   80 LKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILIRSVGKKPS--AIHLSREHFEIGEALGLMDFDRAT  157 (430)
Q Consensus        80 Lk~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~~~G~~~~--f~f~~k~H~elge~l~liDfe~a~  157 (430)
                      ++++++.++.++++++.+++.+++.|||+||++||+|.||++|++|++||+++.  |+|.||+||+||+.+|++||++|+
T Consensus        80 l~~~l~~~e~~~~~~~~el~~~ll~ipNi~~~~VPvg~de~~n~~vr~~g~~~~~~~~f~pk~H~~lge~l~~~Df~~aa  159 (429)
T COG0172          80 LKEKLKELEAALDELEAELDTLLLTIPNIPHESVPVGKDEDDNVEVRRWGEPPVFVFDFEPKDHVELGEKLGLLDFERAA  159 (429)
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCHHHHHHHHCCCCHHHHHC
T ss_conf             88998724377999999999999709999865668688865654889973376544467853099876542762456650


Q ss_pred             HHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHH-CCEECCCCCCHH
Q ss_conf             2216753010564889999999999986223203202123562027889865514224767764310-002313454114
Q gi|254780680|r  158 KLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTD-GRWLIPTSEVSL  236 (430)
Q Consensus       158 kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d-~l~Li~TaEvpL  236 (430)
                      |+||||||||+|+||+|+|||+|||||+|+ ++||+++.||+|||.++|.||||||+|++++|++.+ ++||||||||||
T Consensus       160 KvsGsrf~~~~~~~a~L~rAL~~f~ld~~~-~~Gf~e~~~P~lv~~e~m~gtgqlpkf~e~~y~v~~~~~~LipTaEvpl  238 (429)
T COG0172         160 KVSGSRFYFYKGKGARLERALIQFMLDLHT-KHGFTEVLPPYLVNLESMFGTGQLPKFEEDLYKVEDPDLYLIPTAEVPL  238 (429)
T ss_pred             CCCCCCEEEECCHHHHHHHHHHHHHHHHHH-HCCCEEEECCEEECHHHHHCCCCCCCCCCCCEEECCCCEEEEECCHHHH
T ss_conf             207874389807789999999999999998-7696586576060598862237898880121584589879970202156


Q ss_pred             HHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf             54453420595550420885322107884335543432122221020021212786501457898999999999984106
Q gi|254780680|r  237 TNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLH  316 (430)
Q Consensus       237 ~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lp  316 (430)
                      +|||+++|++.++||++|+|+|||||+||||||||||||+|||||+|||||+||+||+|+++||+|+.++|++++.|+||
T Consensus       239 ~~l~~~Eil~~~~LP~k~~~~S~cFR~EAGs~GrdtrGliRvHQF~KVE~v~~~~Pe~S~~~~E~m~~~ae~il~~LeLP  318 (429)
T COG0172         239 TNLHRDEILDEEDLPIKYTAYSPCFRSEAGSAGKDTRGLIRVHQFDKVELVVITKPEESEEELEEMLGNAEEVLQELELP  318 (429)
T ss_pred             HHHHCCCCCCCCCCCEEEEEECHHHHCCCCCCCCCCCCEEEEEEEEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             78651620152127802678772542145656643553014664355899997070116999999999999999970898


Q ss_pred             HHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             75303780117844340241011010048332375310210076453268473389984101042004322899999999
Q gi|254780680|r  317 YRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAI  396 (430)
Q Consensus       317 yRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ai  396 (430)
                      ||||.+|||||||+|+||||||||||+|++||||||||||+||||||++||||+...++.+|||||||||||++|+++||
T Consensus       319 yRvv~lctGDlgf~a~kkYDlEvWlP~q~~yrEisScSnc~DfQaRR~~~Ryr~~~~~k~~~vhTLNGsglA~~R~l~Ai  398 (429)
T COG0172         319 YRVVNLCTGDLGFSAAKKYDLEVWLPGQNKYREISSCSNCTDFQARRLNIRYRDKEEGKREFVHTLNGSGLAVGRTLVAI  398 (429)
T ss_pred             CEEEEECCCCCCCCCCCCEEEEEEECCCCCCEEEEEEECCCCHHHHHHHCCCCCCCCCCCEEEEECCCHHHHHHHHHHHH
T ss_conf             36843256776886467323799853778740212443454288898754056365799669995464277999999999


Q ss_pred             HHHCCCCCCCEECCCCCCCCCCCEEEECCC
Q ss_conf             883468998386582223101880130733
Q gi|254780680|r  397 LENYLNADGSVTIPTVLRPYMNNLAVIKKE  426 (430)
Q Consensus       397 lEn~q~~dg~i~iP~~L~pym~g~~~i~~~  426 (430)
                      |||||++||+|+||+||||||||.++|++.
T Consensus       399 lENyq~~dG~v~IPevL~~y~gg~~~i~~~  428 (429)
T COG0172         399 LENYQQEDGSVKIPEVLRPYMGGLEIIPKP  428 (429)
T ss_pred             HHCCCCCCCCEECCHHHHHHCCCCEECCCC
T ss_conf             971537899863447887327853005899


No 3  
>KOG2509 consensus
Probab=100.00  E-value=0  Score=1032.24  Aligned_cols=423  Identities=36%  Similarity=0.598  Sum_probs=388.7

Q ss_pred             CCCHHHHHC----CHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH--
Q ss_conf             988447851----99999999984698958-89999999999999999999999999999999998644998799999--
Q gi|254780680|r    1 MLDIQWIRQ----NPEHLDIALKKRHLEPQ-SEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDAL--   73 (430)
Q Consensus         1 MLDik~IRe----n~e~v~~~l~~R~~~~~-id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~L--   73 (430)
                      |||++++|.    ||+.++++.++|+.+.. +++++++|.+|+....++++|+.+.|.++|+||.++-+. ++...++  
T Consensus         2 ~L~~~lf~~~~g~~p~~ir~~q~~r~~d~~~v~~~i~~d~~w~~~~~~ldeln~~~n~l~k~i~~~k~kk-ke~~~~l~~   80 (455)
T KOG2509           2 MLDIRLFRTRKGGNPELIRESQKKRFQDVEAVDEVIELDKEWIETRFELDELNKEKNKLNKEIGDLKLKK-KEDIGQLEE   80 (455)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCHHHHHHH
T ss_conf             3000030346799867899989875047888998875036776566878888888877666766788764-021257777


Q ss_pred             -------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCHHH
Q ss_conf             -------9999999988644466666778887744310022588112211355540242000156566566621122022
Q gi|254780680|r   74 -------KNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILIRSVGKKPSAIHLSREHFEIGE  146 (430)
Q Consensus        74 -------k~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~~~G~~~~f~f~~k~H~elge  146 (430)
                             .++.+.|+++...+++...+++++++..+.+|||++||+||+|.+|.+|++ .+||.++.+.+.++.|.+|+.
T Consensus        81 ~~~~~~~~~~~~~l~e~~~~~~~~~~~l~~el~~~~~~ipN~~hpsVpv~~ee~~~~v-~~~~~~~~~~~~~~~~~~l~~  159 (455)
T KOG2509          81 SKAKNTEGAERKLLKEEAVELEEDESKLEDELYEVLLQIPNITHPSVPVSNEEQANVV-QRVGGPLEFEFKLSHHDELVR  159 (455)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHH-HHHCCCCCCCCCCCCHHHHHH
T ss_conf             6667655666554578877667899999999999998687767899777832352688-886387530246653889998


Q ss_pred             HCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHH--
Q ss_conf             117310001122216753010564889999999999986223203202123562027889865514224767764310--
Q gi|254780680|r  147 ALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTD--  224 (430)
Q Consensus       147 ~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d--  224 (430)
                      .+|++|+++|++|||+|||||+|+||+||+||+||+|++ +.++||+|++||+|||.++|.+|||+|+|++++|++.|  
T Consensus       160 ~~~~~~~~~~a~vsG~r~Yyl~g~~a~LeqALi~yal~~-l~~kGy~pl~~P~i~rkeVm~~cg~~~~~d~~~~y~ld~~  238 (455)
T KOG2509         160 ALGFIDLERGAKVSGHRGYYLKGAGAFLEQALINYALDF-LNAKGYTPLTTPDILRKEVMQKCGQLPRFDEEQYYVLDGG  238 (455)
T ss_pred             HCCCCCCCCHHHCCCCCCEEECCHHHHHHHHHHHHHHHH-HHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCEEEEECCC
T ss_conf             606634000100146651587577999999999999999-9976982466814536999998565767883217860688


Q ss_pred             -CCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             -0023134541145445342059555042088532210788433554343212222102002121278650145789899
Q gi|254780680|r  225 -GRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERML  303 (430)
Q Consensus       225 -~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~  303 (430)
                       ++|||||||+||+|||+|++|.+++||+||+|+|+|||+||||||+|||||||||||+|||||++|+|++||++||||+
T Consensus       239 ~~~~LiaTaE~plAa~~~~e~~~~~~lPiK~vg~S~CfR~EaGs~G~d~~GlyRVHqF~KVE~Fvit~Pe~S~~~~eEmi  318 (455)
T KOG2509         239 DEKYLIATAEQPLAAYHRDEWLEEDQLPIKYVGVSRCFRAEAGSHGKDTKGLYRVHQFEKVEQFVITGPEDSWEMLEEMI  318 (455)
T ss_pred             CCCEEEEECCCHHHHHHCCCCCCCCCCCEEEEEHHHHHHHHHHHCCCCCCCCEEEEEEEEEEEEEECCCCHHHHHHHHHH
T ss_conf             64226762111066650364036112760134303788877600465455514665200257888658535699999999


Q ss_pred             HHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEEC--CCCCCCCEEEE
Q ss_conf             9999999984106753037801178443402410110100483323753102100764532684733--89984101042
Q gi|254780680|r  304 SCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRD--PNSKSLKFTHT  381 (430)
Q Consensus       304 ~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~--~~~~~~~~~ht  381 (430)
                      .+++++|++||||||||+|+||+||.+|+|||||||||||++.||||||||||||||||||+|||+.  .+.+..+||||
T Consensus       319 ~~~eef~qsLgip~rvl~m~S~eLg~aAakKyDiEAWmPgrg~ygEl~ScSNCTDyQSRRL~IRy~~~k~~~~~~~yvHt  398 (455)
T KOG2509         319 NNQEEFYQSLGLPYRVLNMPSGELGAAAAKKYDIEAWMPGRGAYGELVSCSNCTDYQSRRLGIRYGQKKTNDGEKKYVHT  398 (455)
T ss_pred             HHHHHHHHHHCCCEEEECCCCHHHCCHHHHHCCHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEE
T ss_conf             99999999809960673477423376777512666526765532330101465257776542020523246775415543


Q ss_pred             ECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCCCCEEEECCCC
Q ss_conf             0043228999999998834689983865822231018801307334
Q gi|254780680|r  382 LNGSGVAVGRCLIAILENYLNADGSVTIPTVLRPYMNNLAVIKKEH  427 (430)
Q Consensus       382 lNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~pym~g~~~i~~~~  427 (430)
                      ||||+|||||+|||||||||++|| |.||++|||||||++.|+...
T Consensus       399 LN~TacA~~R~l~aiLEnyQ~edG-i~VPe~Lr~ym~~~~~ip~~k  443 (455)
T KOG2509         399 LNGTACATPRALCAILENYQTEDG-IEVPEVLRPYMGGQEFIPFVK  443 (455)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCC-CCCCHHHHHHCCCCCCCCCCC
T ss_conf             040667646788776753467788-167776774068864021246


No 4  
>cd00770 SerRS_core Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate.  Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. SerRS synthetase is a homodimer.
Probab=100.00  E-value=0  Score=908.35  Aligned_cols=296  Identities=51%  Similarity=0.878  Sum_probs=291.0

Q ss_pred             CCEEEEEECCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHH
Q ss_conf             40242000156566566621122022117310001122216753010564889999999999986223203202123562
Q gi|254780680|r  121 ENILIRSVGKKPSAIHLSREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLL  200 (430)
Q Consensus       121 dNv~i~~~G~~~~f~f~~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~l  200 (430)
                      ||++|++||++|.|+|+||||++||+++|++||++++|+||+|||||+|+||+|++||++||+|++. ++||++|.||+|
T Consensus         1 ~n~~v~~~G~~~~f~f~~rdH~~Lg~~L~L~dfe~~akvsG~rf~~l~g~ga~Le~AL~~f~~d~~~-~~Gy~eV~tP~i   79 (297)
T cd00770           1 DNVEIRRWGEPRVFDFKPKDHVELGEKLDILDFERGAKVSGSRFYYLKGDGALLERALINFALDFLT-KRGFTPVIPPFL   79 (297)
T ss_pred             CCEEEEEECCCCCCCCCCCCHHHHHHHCCCEECCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHH-HCCCEEEECCCC
T ss_conf             9787997548899999988999999977881023224689877799888899999999999999999-879989988530


Q ss_pred             CCHHHHHHHHHCHHHHHHHHHHH-HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEE
Q ss_conf             02788986551422476776431-00023134541145445342059555042088532210788433554343212222
Q gi|254780680|r  201 VRDEAMYGTGQIPKFADDMFCTT-DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQH  279 (430)
Q Consensus       201 v~~~~~~gtG~lp~f~~~~y~~~-d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvH  279 (430)
                      ||+++++||||+|+|++++|+++ +++|||||||+||+++|+++++++++||+||+++|+|||+||||||+|++||||||
T Consensus        80 v~~~~~~~sG~~~~~~e~~y~i~~~~~~Li~tae~~l~~~~~~~~~~~~dLPlr~~~~s~cfR~Eags~G~d~~GL~Rvh  159 (297)
T cd00770          80 VRKEVMEGTGQLPKFDEQLYKVEGEDLYLIATAEVPLAALHRDEILEEEELPLKYAGYSPCFRKEAGSAGRDTRGLFRVH  159 (297)
T ss_pred             CHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHCCCCCEEEEEEEEECCHHHCCCCEEECCCHHHHCCCCCCCCCCCEEEEE
T ss_conf             13899854357876356521035505555440566622344200317755886502246341320377775555457887


Q ss_pred             EEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCH
Q ss_conf             10200212127865014578989999999999841067530378011784434024101101004833237531021007
Q gi|254780680|r  280 QFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNF  359 (430)
Q Consensus       280 QF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~  359 (430)
                      ||+|||||+||+||+|+++|++|++++++||++||||||||++||||||++|+|||||||||||+++|+||||||||+||
T Consensus       160 qF~kvE~~~~c~pe~s~~~~e~~~~~~e~~l~~L~lpyrvv~~~tgdlg~~a~~~~DiE~W~P~~~~y~EvsS~Snc~Df  239 (297)
T cd00770         160 QFEKVEQFVFTKPEESWEELEELISNAEEILQELGLPYRVVNICTGDLGFAAAKKYDIEAWMPGQGKYREISSCSNCTDF  239 (297)
T ss_pred             ECCEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCHHHEEEEEEEEHHHCCEEEEEECCCCHHH
T ss_conf             21100377616878899999999999999999815501450124655573222207656310541976886131540006


Q ss_pred             HHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCC
Q ss_conf             6453268473389984101042004322899999999883468998386582223101
Q gi|254780680|r  360 QSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAILENYLNADGSVTIPTVLRPYM  417 (430)
Q Consensus       360 QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~pym  417 (430)
                      |||||||||+++++++.+||||||||++|+||+|+||||||||+||+|.||+||||||
T Consensus       240 QarRl~iry~~~~~~~~~~~htlngt~~A~~R~l~allEn~q~~dg~v~iP~~L~~ym  297 (297)
T cd00770         240 QARRLNIRYRDKKDGKKQYVHTLNGTALATPRTIVAILENYQTEDGSVVIPEVLRPYM  297 (297)
T ss_pred             HHHHCCCEEECCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCEECCCCCCCCC
T ss_conf             6652367773489995265488136320888899999972738998786880031319


No 5  
>TIGR00414 serS seryl-tRNA synthetase; InterPro: IPR002317   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa .; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=765.36  Aligned_cols=417  Identities=49%  Similarity=0.835  Sum_probs=401.1

Q ss_pred             CCCH---HHHHCCHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH--HHHCCCHHHHH
Q ss_conf             9884---478519999999998469895--88999999999999999999999--999999999999--86449987999
Q gi|254780680|r    1 MLDI---QWIRQNPEHLDIALKKRHLEP--QSEYILSLDEKNRILIKKIEDIR--ARRNSNSAQIGQ--AIAEGNLSLVD   71 (430)
Q Consensus         1 MLDi---k~IRen~e~v~~~l~~R~~~~--~id~il~Ld~~rr~l~~e~e~Lr--aerN~lSKeIg~--~k~~~~~~~~~   71 (430)
                      |+|+   +.+|+|++.++..+..|+...  +++.+..++.+++....+++.++  +++|.++++++.  .+..+.+...+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (460)
T TIGR00414         1 MLDLRLLKLLRNNPDLVKESLKARGLSLDIDLEKLIALDDKRKKLLSELEELNLLAKRNELSKEIGKKLKKGEKKDKLIE   80 (460)
T ss_pred             CCCHHHHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             95446788741367888988875111124457788888889998887777888888776668888888764210111124


Q ss_pred             H---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC------CCCHHHHCCCCCCCE--------EEEEECCC--C
Q ss_conf             9---999999999886444666667788877443100225------881122113555402--------42000156--5
Q gi|254780680|r   72 A---LKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNV------PLEEVPIGTSANENI--------LIRSVGKK--P  132 (430)
Q Consensus        72 ~---Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi------~~~~VP~G~de~dNv--------~i~~~G~~--~  132 (430)
                      .   ++.+++.++.++..++..++.++.+++..++.+||+      +|++||+|.++++|+        .+..||.+  +
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~p~g~~~~~~~~~~~w~~~~~~~~~~~~~~  160 (460)
T TIGR00414        81 EGKALKKELKELKEELTELEAALKALEEELEDLLLSIPNLKKKILEPHESVPVGKDEEDNLPVKYWYDEEVKKWGTPPLP  160 (460)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCCCCEEHHHHHHHHHHHHCCCCC
T ss_conf             67899998876778888876778889999888875234024555301444567887544520001001356664100122


Q ss_pred             CCCCCCC--CCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHH
Q ss_conf             6656662--11220221173100011222167530105648899999999999862232032021235620278898655
Q gi|254780680|r  133 SAIHLSR--EHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTG  210 (430)
Q Consensus       133 ~f~f~~k--~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG  210 (430)
                      .|+|.|+  +||++++.++++||++|++++|+||||++|.+|+|++||++|++|++..++||.++.||++++...+.|||
T Consensus       161 ~~~~~~~~~~h~~~~~~~~~~d~~~~~~~~g~~~~~~~~~~~~~~~al~~~~l~~~~~~~g~~~~~~p~~~~~~~~~~~g  240 (460)
T TIGR00414       161 SFDFKPKDLPHWELGEKLGLLDFERAVKLAGSRFYYLKGDGAKLERALINFMLDLLREKNGYSELYPPYLVNEELLDGTG  240 (460)
T ss_pred             CCCCCCCCCHHHHHHHHCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECCCHHHHHHHHHHCC
T ss_conf             00133111215678877065101333344101012132136789999999999864432264010140354234431024


Q ss_pred             ---HCHHHHHHHHHHHH-C---CEECCCCCCHHHHHHHHHCCCH--HHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             ---14224767764310-0---0231345411454453420595--5504208853221078843355434321222210
Q gi|254780680|r  211 ---QIPKFADDMFCTTD-G---RWLIPTSEVSLTNLYSHEIIES--KSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQF  281 (430)
Q Consensus       211 ---~lp~f~~~~y~~~d-~---l~Li~TaEvpL~~~~~~~~l~~--~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF  281 (430)
                         ++|+|++++|++.+ +   +||+||+|+|++++|++++++.  .+||++|+|+|+|||+|||+||+||+|++|+|||
T Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~l~~t~e~~~~~~~~~~~~~~~~~~lp~~~~~~~~cfr~eag~~g~~~~g~~r~h~f  320 (460)
T TIGR00414       241 FNPQLPKFEEDLFKLEDTDDEKLYLIPTAEVPLTNLHRDEILDLPSEELPIKYTGYSPCFRSEAGSYGKDTKGLIRVHQF  320 (460)
T ss_pred             CCCCCCCHHHHHHHHCCCCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCEEHCCCCHHHHHHCCCCCCCCHHHHHHHHC
T ss_conf             56556530234432126777504652010001222220001026521034000002202333213455410001211100


Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCC--CEEEEEEECCCCCH
Q ss_conf             2002121278650145789899999999998410675303780117844340241011010048--33237531021007
Q gi|254780680|r  282 WKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQN--LYREISSCSTCGNF  359 (430)
Q Consensus       282 ~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~--~y~Ev~S~Snc~D~  359 (430)
                      +|||+|.||.|++|+.+|++|+..++.+++.|++|||++.+|+||||++++++||+|+|+|+++  .|+|++|||||+||
T Consensus       321 ~k~e~~~~~~p~~~~~~~~~~~~~~~~~~~~l~~p~~~~~~~~gd~g~~~~~~yd~e~W~p~~~gg~y~e~~~~~~~~d~  400 (460)
T TIGR00414       321 NKVELVKFCKPEESWEELEELLSDAEKILQELELPYRVLNLCTGDLGFGAAKKYDLEVWLPGQNGGTYREISSCSNCTDF  400 (460)
T ss_pred             CCEEEEEEECCHHHHHHHHHHHHHHHHHHHHHCCCHHHHEECCCCCCCCCCCCEEEEEEEECCCCCCCCEECCCCCCHHH
T ss_conf             31024566354014899999987899999974375111000124346420110100134104678741100012331145


Q ss_pred             HHHHCCCEEECCCCCC--CCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCC
Q ss_conf             6453268473389984--101042004322899999999883468998386582223101
Q gi|254780680|r  360 QSRRMNSRYRDPNSKS--LKFTHTLNGSGVAVGRCLIAILENYLNADGSVTIPTVLRPYM  417 (430)
Q Consensus       360 QsrRl~iry~~~~~~~--~~~~htlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~pym  417 (430)
                      ||||++|||++..+++  .+|+||||||++|++|+++||+||||++||.|.||++|++||
T Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~lng~~~~~~r~~~~~~en~~~~~g~~~~p~~l~~~~  460 (460)
T TIGR00414       401 QARRLNIRYKDKGGGKRENEYVHTLNGTALAVGRTLVAILENYQDEDGSVEVPEVLRKYL  460 (460)
T ss_pred             HHHHHHHHHHHCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCCEECHHHHHCCC
T ss_conf             666544333220366532100010033123456788877764105577454125541139


No 6  
>cd00670 Gly_His_Pro_Ser_Thr_tRS_core Gly_His_Pro_Ser_Thr_tRNA synthetase class II core domain. This domain is the core catalytic domain of tRNA synthetases of the subgroup containing glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. These enzymes belong to class II aminoacyl-tRNA synthetases (aaRS) based upon their structure and the presence of three characteristic sequence motifs in the core domain. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ and the accessory subunit of mitochondrial polymerase gamma (Pol gamma b) . Most class II tRNA synthetases are dimers, with this subgroup consisting of mostly homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=100.00  E-value=0  Score=506.43  Aligned_cols=219  Identities=26%  Similarity=0.366  Sum_probs=208.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHH--------HCCEECCCCCCHHHHHHHH
Q ss_conf             88999999999998622320320212356202788986551422476776431--------0002313454114544534
Q gi|254780680|r  171 LAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTT--------DGRWLIPTSEVSLTNLYSH  242 (430)
Q Consensus       171 ~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~--------d~l~Li~TaEvpL~~~~~~  242 (430)
                      ||+|++||++|++|.+ .++||++|.+|.||++++++++||+|+|++++|+++        +++||+||||+|++++|++
T Consensus         1 Ga~L~~aL~~~~~~~~-~~~G~~~v~~P~l~~~~~~~~sg~~~~f~~~~y~v~~~~~~~~~~~~~L~PTsE~~~~~~~~~   79 (235)
T cd00670           1 GTALWRALERFLDDRM-AEYGYQEILFPFLAPTVLFFKGGHLDGYRKEMYTFEDKGRELRDTDLVLRPAACEPIYQIFSG   79 (235)
T ss_pred             CHHHHHHHHHHHHHHH-HHCCCEEEECCCCCCHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCEEEEECCCHHHHHHHHC
T ss_conf             9889999999999999-986998998985578999922386754520528982377666787389930786999999948


Q ss_pred             HCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCC
Q ss_conf             20595550420885322107884335543432122221020021212786501457898999999999984106753037
Q gi|254780680|r  243 EIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVSL  322 (430)
Q Consensus       243 ~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~  322 (430)
                      +++++.+||+||+++|+|||+|+|+    ++||+|||||+|||+++||+||+|.+++++|++++++|++.|+|||||+.+
T Consensus        80 ~i~s~~dLPlr~~~~s~~fR~E~~~----~~Gl~Rv~eF~k~E~~~~~~~e~~~~~~~~~~~~~~~i~~~L~l~y~v~~~  155 (235)
T cd00670          80 EILSYRALPLRLDQIGPCFRHEPSG----RRGLMRVREFRQVEYVVFGEPEEAEEERREWLELAEEIARELGLPVRVVVA  155 (235)
T ss_pred             CCCCHHHCCEEEEEECCEECCCCCC----CCCCEEEEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             3287687995454456533367899----999836789998507999688999999999999999999986997799975


Q ss_pred             CCHHCCCHHH--------EEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHH
Q ss_conf             8011784434--------02410110100483323753102100764532684733899841010420043228999999
Q gi|254780680|r  323 CTGDLGFSAC--------KTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLI  394 (430)
Q Consensus       323 ~sgdlg~~a~--------~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~  394 (430)
                      |+||+|+++.        +|||||+|||++++|+||+|||||+||||||++|||++.++   +++||+|||++|+||+|+
T Consensus       156 ~~~d~g~~~~~~~~~~a~~~~d~E~~~p~~~~~~e~~s~S~~~~~q~r~~~~~~~~~~~---~~~ht~~~s~~a~~R~l~  232 (235)
T cd00670         156 DDPFFGRGGKRGLDAGRETVVEFELLLPLPGRAKETAVGSANVHLDHFGASFKIDEDGG---GRAHTGCGGAGGEERLVL  232 (235)
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEEECCCHHHCCCCCEEECCCC---CEEEEECCCCCHHHHHHH
T ss_conf             86133766410002565556469999778994678999302578444302530146999---689997263288999999


Q ss_pred             HHH
Q ss_conf             998
Q gi|254780680|r  395 AIL  397 (430)
Q Consensus       395 ail  397 (430)
                      |||
T Consensus       233 All  235 (235)
T cd00670         233 ALL  235 (235)
T ss_pred             HHC
T ss_conf             869


No 7  
>cd00768 class_II_aaRS-like_core Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ.
Probab=100.00  E-value=0  Score=391.43  Aligned_cols=205  Identities=25%  Similarity=0.399  Sum_probs=187.2

Q ss_pred             HHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHH-HCCEECCCCCCHHHHHHHHHCCCHHHHCCEE
Q ss_conf             999999998622320320212356202788986551422476776431-0002313454114544534205955504208
Q gi|254780680|r  176 RALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTT-DGRWLIPTSEVSLTNLYSHEIIESKSLPLRF  254 (430)
Q Consensus       176 ~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~-d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~  254 (430)
                      +.+.++.-+ +..++||++|.+|.|++.+.+.+||++|++...++... +++||+||+|++++.+|++++   .+||+||
T Consensus         3 ~~ie~~~r~-~~~~~G~~ev~~P~l~~~~~~~~sg~~~~~~~~~~~~~~~~~~L~pt~e~~~~~~~~~~~---~dLP~r~   78 (211)
T cd00768           3 SKIEQKLRR-FMAELGFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEEDLYLRPTLEPGLVRLFVSHI---RKLPLRL   78 (211)
T ss_pred             HHHHHHHHH-HHHHCCCEEEECCEECCHHHHHHCCCCHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHH---HHCCHHH
T ss_conf             899999999-999869989999834279999750676222301104679769995168499999975247---6577786


Q ss_pred             EEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCH--HHHCCCCCHHCCCH-H
Q ss_conf             85322107884335543432122221020021212786501457898999999999984106--75303780117844-3
Q gi|254780680|r  255 TTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLH--YRVVSLCTGDLGFS-A  331 (430)
Q Consensus       255 ~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lp--yRvv~~~sgdlg~~-a  331 (430)
                      +++|+|||.|+|+     +||+|||||+|+|+++||+|++|++++++|+..+++||+.|||+  ++++..|+|+++++ +
T Consensus        79 ~~~~~~fR~E~~~-----~Gl~RvreF~~~e~~~f~~~~~~~~~~~~~~~~~~~i~~~lgl~~~~~~~~~~~~~~~~~~a  153 (211)
T cd00768          79 AEIGPAFRNEGGR-----RGLRRVREFTQLEGEVFGEDGEEASEFEELIELTEELLRALGIKLDIVFVEKTPGEFSPGGA  153 (211)
T ss_pred             HEECCEECCCCCC-----CCCCCCCCEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCC
T ss_conf             4320056057888-----88446046889847999884888999999999999999974998886999977867666452


Q ss_pred             HEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHH
Q ss_conf             4024101101004833237531021007645326847338998410104200432289999
Q gi|254780680|r  332 CKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRC  392 (430)
Q Consensus       332 ~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~  392 (430)
                      .+||||||||| .++|+||+|||||+||||||++|||++++|+ .+||||+ |+|++++|+
T Consensus       154 ~~~~Die~~~p-~~~~~Ev~s~~~~~d~qsr~~~i~y~~~dg~-~~~~~~~-~~gl~v~Rl  211 (211)
T cd00768         154 GPGFEIEVDHP-EGRGLEIGSGGYRQDEQARAADLYFLDEALE-YRYPPTI-GFGLGLERL  211 (211)
T ss_pred             EEEEEEEEECC-CCCEEEEECEECCCCHHHHHCCCEEECCCCC-EEEEEEE-ECEECCCCC
T ss_conf             35455789837-8979999354616778788469899999999-9875563-032413669


No 8  
>cd00779 ProRS_core_prok Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from prokaryotes and from the mitochondria of eukaryotes.
Probab=100.00  E-value=0  Score=363.36  Aligned_cols=245  Identities=22%  Similarity=0.278  Sum_probs=224.1

Q ss_pred             CCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHH
Q ss_conf             11220221173100011222167530105648899999999999862232032021235620278898655142247677
Q gi|254780680|r  140 EHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDM  219 (430)
Q Consensus       140 ~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~  219 (430)
                      +| +|.-+-|+|.      =+++|+|++...|+++.++|++|+.+. ..+.||++|.+|.|++.+.+.+||++++|.+++
T Consensus         6 s~-~ll~~ag~i~------~~~~G~~~~lP~G~~i~~~i~~~i~~~-~~~~G~~ev~~P~l~~~~l~~~sg~~~~f~~em   77 (255)
T cd00779           6 SH-KLLLRAGFIR------QTSSGLYSWLPLGLRVLKKIENIIREE-MNKIGAQEILMPILQPAELWKESGRWDAYGPEL   77 (255)
T ss_pred             HH-HHHHHCCCCC------CCCCCCEEECCHHHHHHHHHHHHHHHH-HHHCCCEEEECCCCCCHHHHHHHCCCCCCCCCE
T ss_conf             79-9998758876------578862788502999999999999999-998599899765347388874425301368731


Q ss_pred             HHHH----HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECC-CCCC
Q ss_conf             6431----0002313454114544534205955504208853221078843355434321222210200212127-8650
Q gi|254780680|r  220 FCTT----DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSIT-REED  294 (430)
Q Consensus       220 y~~~----d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~-~pe~  294 (430)
                      |++.    ++++|.||+|.+++++|++++.++.+||++++.+++|||.|+.    .++||+|+|||.+.|++.|+ ++++
T Consensus        78 f~v~d~~~~~~~L~PT~E~~~~~~~~~~i~SyrdLPl~~~q~~~~fR~E~r----~~~GllR~rEF~~~d~hsf~~~~e~  153 (255)
T cd00779          78 LRLKDRHGKEFLLGPTHEEVITDLVANEIKSYKQLPLNLYQIQTKFRDEIR----PRFGLMRGREFLMKDAYSFDIDEES  153 (255)
T ss_pred             EEEECCCCCEEEECCCCHHHHHHHHHHHCCCHHHCCEEEECCCCEECCCCC----CCCCCCEEEEEEEEHHHCCCCCHHH
T ss_conf             544537887773168874889999986503612257454135335425667----8866324313770022035699899


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECCCCC
Q ss_conf             14578989999999999841067530378011784434024101101004833237531021007645326847338998
Q gi|254780680|r  295 SFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDPNSK  374 (430)
Q Consensus       295 S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~  374 (430)
                      +.+.++.+++..+.||+.|+|||++|..|+||+|++++..|++++|+|.. ++.||++|+||+|+||||++|+|.+++|+
T Consensus       154 a~~~~~~~~~~y~~i~~~Lglp~~~v~~~~g~~g~~~s~ef~~~~~l~~~-~~lEvg~~~~lG~~~s~~~~i~y~d~dg~  232 (255)
T cd00779         154 LEETYEKMYQAYSRIFKRLGLPFVKVEADSGAIGGSLSHEFHVLSPLKIT-KGIEVGHIFQLGTKYSKALGATFLDENGK  232 (255)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCEEEEEEECCCCC-CEEEEEEEECCCCHHHHHCCCEEECCCCC
T ss_conf             99999999999999999839987998547667788745799998247777-56899745505625578559999999999


Q ss_pred             CCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             4101042004322899999999883
Q gi|254780680|r  375 SLKFTHTLNGSGVAVGRCLIAILEN  399 (430)
Q Consensus       375 ~~~~~htlNgt~~A~~R~l~ailEn  399 (430)
                       .+++|+ |+.|++++|+|+||+|.
T Consensus       233 -~~~~~m-~s~Gi~i~R~i~AliEq  255 (255)
T cd00779         233 -PKPLEM-GCYGIGVSRLLAAIIEQ  255 (255)
T ss_pred             -EEEEEE-ECCCCHHHHHHHHHCCC
T ss_conf             -884697-06504898888884049


No 9  
>pfam00587 tRNA-synt_2b tRNA synthetase class II core domain (G, H, P, S and T). Other tRNA synthetase sub-families are too dissimilar to be included. This domain is the core catalytic domain of tRNA synthetases and includes glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases.
Probab=100.00  E-value=9.6e-38  Score=301.20  Aligned_cols=166  Identities=40%  Similarity=0.618  Sum_probs=158.8

Q ss_pred             HHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHH----HCCEECCCCCCHHHHHHHHHCCCHHH
Q ss_conf             99999999998622320320212356202788986551422476776431----00023134541145445342059555
Q gi|254780680|r  174 LERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTT----DGRWLIPTSEVSLTNLYSHEIIESKS  249 (430)
Q Consensus       174 Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~----d~l~Li~TaEvpL~~~~~~~~l~~~~  249 (430)
                      |++||++|+.+.+ .++||++|.+|.|++.+++.+||+++++.++||...    ++++|.||+|+|++.+|++.++...+
T Consensus         1 l~~~l~~~~~~~~-~~~G~~~i~tP~l~~~~~~~~sg~~~~~~~~my~~~d~~~~~l~Lrp~~~~~~~~~~~~~~~~~~~   79 (170)
T pfam00587         1 LRNALENFIRDLF-KRYGYQEVDTPILEPKELWEGSGHWDDYFDEMYRFKDRGGEELYLRPTAEVGITRLFKNEILSYRD   79 (170)
T ss_pred             CHHHHHHHHHHHH-HHCCCEEEECCEEEEHHHHHHCCCCCCCHHHEEEEECCCCCEEEEECCCCHHHHHHHHHHCCCCCC
T ss_conf             9799999999999-985998999991756789834477655753125673589976887325745888998862003235


Q ss_pred             HCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCC
Q ss_conf             04208853221078843355434321222210200212127865014578989999999999841067530378011784
Q gi|254780680|r  250 LPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGF  329 (430)
Q Consensus       250 LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~  329 (430)
                      ||+|++++++|||.|+|    +++||+|+|||+++|+++||+||+|.+++.+++.++.++|+.||||||++..|+||||+
T Consensus        80 lP~r~~~~~~~fR~E~~----~~~Gl~R~reF~q~d~~~~~~~e~s~~~~~e~~~~~~~~~~~lgl~~~i~~~~~g~l~~  155 (170)
T pfam00587        80 LPLKLYQIGPCFRYEAR----PRRGLGRVREFTQVDAEIFGTPEQSEEEDEELLKLAEEILQDLGLPYRVVLNTRGDLGG  155 (170)
T ss_pred             CCCEEECCCCCCCCCCC----CCCCCCEEEEEEEECEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
T ss_conf             86013306530067777----66677436788980479996700429999999999999999879967999726777898


Q ss_pred             HHHEEEEEEEECCCC
Q ss_conf             434024101101004
Q gi|254780680|r  330 SACKTYDLEVWLAGQ  344 (430)
Q Consensus       330 ~a~~~~DiE~w~P~~  344 (430)
                      +++++||+|+|+|++
T Consensus       156 ~~~~~~d~E~w~~~~  170 (170)
T pfam00587       156 YASKTGDLEAWLPAE  170 (170)
T ss_pred             HHHHCCCCCEECCCC
T ss_conf             678607852057889


No 10 
>cd00771 ThrRS_core Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=99.97  E-value=5.5e-31  Score=250.97  Aligned_cols=246  Identities=21%  Similarity=0.323  Sum_probs=208.1

Q ss_pred             CCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHH
Q ss_conf             11220221173100011222167530105648899999999999862232032021235620278898655142247677
Q gi|254780680|r  140 EHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDM  219 (430)
Q Consensus       140 ~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~  219 (430)
                      ||..||..++++.|...   .|+|.++..-.|+++-++|.+|+.+.+ .++||++|.+|.|++.+.++.+|++++|.++|
T Consensus         1 dHrklg~el~lf~~~~~---~g~G~~~w~P~G~~i~~~L~~~ir~~~-~~~Gy~eV~tP~i~~~~Lw~~SGH~~~y~e~m   76 (298)
T cd00771           1 DHRRLGGELELFFFFDE---AGPGLPFWLPKGAIIRNELEDFLRELQ-RKRGYQEVETPIIYNKELWETSGHWDHYRENM   76 (298)
T ss_pred             CHHHHCCCCCCCCCCCC---CCCCCEEECCCHHHHHHHHHHHHHHHH-HHCCCEEEECCCCCCHHHHHHCCCCCCCCCCE
T ss_conf             94574401157511777---667657883888999999999999999-98699899886126655675477631136856


Q ss_pred             HHH---HHCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHH
Q ss_conf             643---10002313454114544534205955504208853221078843355434321222210200212127865014
Q gi|254780680|r  220 FCT---TDGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSF  296 (430)
Q Consensus       220 y~~---~d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~  296 (430)
                      |.+   +++++|.|++..+-+.+|++.+.++.+||+|++.+++|||.|+.  | ...||.||++|+..+..+||++||..
T Consensus        77 f~~~~~~~~~~LkPmnCp~h~~i~~~~~~SYrdLPlR~~E~g~~~R~E~s--G-~L~GL~RvR~FtqdDaHiFc~~eQ~~  153 (298)
T cd00771          77 FPFEEEDEEYGLKPMNCPGHCLIFKSKPRSYRDLPLRLAEFGTVHRYEQS--G-ALHGLTRVRGFTQDDAHIFCTPDQIK  153 (298)
T ss_pred             EEEEECCCCEEEECCCCHHHHHHHHCCCCCHHHCCHHHHCCCCEECCCCC--C-CCCCCCCCCCCCCCCCEEECCHHHHH
T ss_conf             88886254168850686889999863556734346765207505547677--6-75574455567457632441688999


Q ss_pred             HHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCC------------------------------
Q ss_conf             57898999999999984106753037801178443402410110100483------------------------------
Q gi|254780680|r  297 TEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNL------------------------------  346 (430)
Q Consensus       297 ~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~------------------------------  346 (430)
                      +++..+++...++|+.+|+...-+.+++.+-++-.    |.|.|-.+++.                              
T Consensus       154 ~E~~~~~~~~~~vy~~fG~~~~~~~ls~r~ek~~g----~~e~W~~ae~~l~~~l~~~~~~~~~~~ge~AFyGPKiD~~~  229 (298)
T cd00771         154 EEIKGVLDLIKEVYSDFGFFDYKVELSTRPEKFIG----SDEVWEKAEAALREALEEIGLPYEINEGEGAFYGPKIDFHV  229 (298)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCC----CHHHHHHHHHHHHHHHHHCCCCCEECCCCCEEEEEEEEEEE
T ss_conf             99999999999999982887324899647876779----98999999999999999759985757886001300589998


Q ss_pred             ------EEEEEEECCCCCHH-HHHCCCEEECCCCCCC--CEEE-EECCCHHHHHHHHHHHHHHCC
Q ss_conf             ------32375310210076-4532684733899841--0104-200432289999999988346
Q gi|254780680|r  347 ------YREISSCSTCGNFQ-SRRMNSRYRDPNSKSL--KFTH-TLNGSGVAVGRCLIAILENYL  401 (430)
Q Consensus       347 ------y~Ev~S~Snc~D~Q-srRl~iry~~~~~~~~--~~~h-tlNgt~~A~~R~l~ailEn~q  401 (430)
                            .-+++.+  =.||+ ++|.++.|.+++|++.  -.+| ++.||   +-|.|++|||+|.
T Consensus       230 ~D~lgR~~q~~Ti--QlDf~lp~rF~l~Y~~~dg~~~~Pv~iHrai~GS---~ERfia~LiE~~~  289 (298)
T cd00771         230 KDALGREWQCSTI--QLDFNLPERFDLTYIGEDGEKKRPVMIHRAILGS---IERFIGILIEHYA  289 (298)
T ss_pred             EECCCCEEEEEEE--EEEECCHHHCCCEEECCCCCCCCCEEEEECCCCH---HHHHHHHHHHHCC
T ss_conf             6068976870146--8850674326988998999864898999557670---9999999998607


No 11 
>cd00772 ProRS_core Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=99.93  E-value=5.7e-26  Score=213.72  Aligned_cols=247  Identities=20%  Similarity=0.235  Sum_probs=222.8

Q ss_pred             CCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHH-HHHHH
Q ss_conf             12202211731000112221675301056488999999999998622320320212356202788986551422-47677
Q gi|254780680|r  141 HFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPK-FADDM  219 (430)
Q Consensus       141 H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~-f~~~~  219 (430)
                      -+++..+-+|+|.     -.|+|.|++.-.|.+.-+.+.+++-+. ..+.|+.+|..|.|+..+.+..+|.+.+ |++++
T Consensus         6 ~~~v~~~a~l~d~-----~~~~G~~~~lP~G~~i~~ki~~~i~~e-~~~~G~qev~~P~l~p~~lw~ksgr~~~~~~~e~   79 (264)
T cd00772           6 SLEHIGKAELADQ-----GPGRGIINFLPLAKAILDKIENVLDKM-FKEHGAQNALFPFFILASFLEKEAEHDEGFSKEL   79 (264)
T ss_pred             HHHHHHHHCCEEC-----CCCCCEEEECHHHHHHHHHHHHHHHHH-HHHCCCEEEECCCCCCHHHHHHCCCHHHCCCCCE
T ss_conf             8478676354204-----898875888905999999999999999-9982994981256799899997698444378523


Q ss_pred             HHHH--------HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEEC-C
Q ss_conf             6431--------000231345411454453420595550420885322107884335543432122221020021212-7
Q gi|254780680|r  220 FCTT--------DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSI-T  290 (430)
Q Consensus       220 y~~~--------d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~-~  290 (430)
                      +.+.        ++++|-||+|..++.++++.+-.+.+||+++.-++++||-|.    |.+.||+|+.+|..-|.+.| +
T Consensus        80 ~~~~~~~~~~~e~~~~L~PT~Ee~~~~~~~~~i~SyrdLPl~lyQ~~~~fR~E~----r~r~GllR~REFlmkDahsf~~  155 (264)
T cd00772          80 AVFKDAGDEELEEDFALRPTLEENIGEIAAKFIKSWKDLPQHLNQIGNKFRDEI----RPRFGFLRAREFIMKDGHSAHA  155 (264)
T ss_pred             EEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHCCHHHHHHHHHHHCCC----CCCCCCHHHEEEEEEEEEECCC
T ss_conf             799734874212352016778689999998640766557977876557860578----8554332320434110353259


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHC-CHHHHCCCCCHHCCCHHHEEEEEEEECC-CCCCEEEEEEECCCCCHHHHHCCCEE
Q ss_conf             865014578989999999999841-0675303780117844340241011010-04833237531021007645326847
Q gi|254780680|r  291 REEDSFTEHERMLSCAEEILKRLD-LHYRVVSLCTGDLGFSACKTYDLEVWLA-GQNLYREISSCSTCGNFQSRRMNSRY  368 (430)
Q Consensus       291 ~pe~S~~~~e~~~~~~~~i~~~L~-lpyRvv~~~sgdlg~~a~~~~DiE~w~P-~~~~y~Ev~S~Snc~D~QsrRl~iry  368 (430)
                      +.+++.+..+.|+.....|++.|+ |||.++.-++|+--+.+..++.+|++|| |+..-.||+.+-.+++-.|.-++++|
T Consensus       156 t~e~a~~~y~~~~~~Y~~if~~lg~lp~~~~~~~~g~kf~Ga~~s~ef~~~~~~G~~~~~ev~H~f~~g~~~s~~~~~~f  235 (264)
T cd00772         156 DAEEADEEFLNMLSAYAEIARDLAAIDFIEGEADEGAKFAGASKSREFEALMEDGKAKQAETGHIFGEGFARAFDLKAKF  235 (264)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEECCCCCCEECCCCCEE
T ss_conf             99999999999999999999996698516764477885688501689999878887136446888157850122566578


Q ss_pred             ECCCCCCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             3389984101042004322899999999883
Q gi|254780680|r  369 RDPNSKSLKFTHTLNGSGVAVGRCLIAILEN  399 (430)
Q Consensus       369 ~~~~~~~~~~~htlNgt~~A~~R~l~ailEn  399 (430)
                      .+++|+. ++||+ |+=|+.+.|+|+||+|.
T Consensus       236 ~~~dg~~-~~v~m-~syGIgitRligaiIeq  264 (264)
T cd00772         236 LDKDGKE-KFFEM-GCWGIGISRFIGAIIEQ  264 (264)
T ss_pred             ECCCCCE-EEEEE-CCCCCHHHHHHHEEECC
T ss_conf             8899998-22580-36778177444405529


No 12 
>cd00778 ProRS_core_arch_euk Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria.
Probab=99.89  E-value=1.3e-22  Score=188.82  Aligned_cols=241  Identities=22%  Similarity=0.243  Sum_probs=209.6

Q ss_pred             CHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHH-HHHCHHHHHHHHH
Q ss_conf             202211731000112221675301056488999999999998622320320212356202788986-5514224767764
Q gi|254780680|r  143 EIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYG-TGQIPKFADDMFC  221 (430)
Q Consensus       143 elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~g-tG~lp~f~~~~y~  221 (430)
                      +|.++-+++|. .  -|+  |.|++.-.|.++-+.|.+|+-+. ..+.||.+|.+|.|+..+.++. +|+++.|.++||.
T Consensus         8 ~~~~~~~l~d~-~--pv~--G~~~~lP~G~~i~~~l~~~~r~~-~~~~G~~ev~~P~l~~~~~~~k~sgh~~~y~~emf~   81 (261)
T cd00778           8 EVITKAELIDY-G--PVK--GCMVFRPYGYAIWENIQKILDKE-IKETGHENVYFPLLIPESELEKEKEHIEGFAPEVAW   81 (261)
T ss_pred             HHHHHHCCCCC-C--CCC--CEEEECCCHHHHHHHHHHHHHHH-HHHCCCEEEECCCCCCHHHHHHHHCHHHCCCCCCEE
T ss_conf             99998177224-7--998--30888632899999999999999-998699699883327889999742814305765335


Q ss_pred             HH--------HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEE-ECCCC
Q ss_conf             31--------0002313454114544534205955504208853221078843355434321222210200212-12786
Q gi|254780680|r  222 TT--------DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELV-SITRE  292 (430)
Q Consensus       222 ~~--------d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~-~~~~p  292 (430)
                      +.        +.++|-||+|-..+.++++.+-.+.+||+|+.-+++|||-|..  |  +.||+||-+|.--+.. .+|++
T Consensus        82 v~~~g~~~~d~~y~LkPmne~~~~~i~~~~~~SYRdLPlrl~q~g~~~R~E~s--~--~~gL~RvReF~~dDahs~~~t~  157 (261)
T cd00778          82 VTHGGLEELEEPLALRPTSETAIYPMFSKWIRSYRDLPLKINQWVNVFRWETK--T--TRPFLRTREFLWQEGHTAHATE  157 (261)
T ss_pred             EECCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHCCCEECCCCC--C--CCCCCEEEEEEEECCCCCCCCH
T ss_conf             52168520135603478886999999973505402278255530422437788--8--8765325425234233655899


Q ss_pred             CCHHHHHHHHHHHHHHHHHH-HCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECC
Q ss_conf             50145789899999999998-41067530378011784434024101101004833237531021007645326847338
Q gi|254780680|r  293 EDSFTEHERMLSCAEEILKR-LDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDP  371 (430)
Q Consensus       293 e~S~~~~e~~~~~~~~i~~~-L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~  371 (430)
                      |+..++...+++....+|.. +++|+.+..-+..|-...|.....||+-+|. ++..|++.+-+..+--|+|+++.|.++
T Consensus       158 eq~~~e~~~~~~~y~~i~~~l~~~~~~~~~~~~~dk~~Ga~y~~~id~~~~d-gr~~q~gti~~l~~~~s~~f~l~y~~~  236 (261)
T cd00778         158 EEAEEEVLQILDLYKEFYEDLLAIPVVKGRKTEWEKFAGADYTYTIEAMMPD-GRALQSGTSHNLGQNFSKAFDIKYQDK  236 (261)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCEEEEEECCCHHCCCCCCCCCEEEEEECCC-CCEEEEEHHHHCCCCHHHHCCCEEECC
T ss_conf             9999999999999999999847815786056521116785100014787478-870467510202765356379899999


Q ss_pred             CCCCCCEEEE-ECCCHHHHHHHHHHHHH
Q ss_conf             9984101042-00432289999999988
Q gi|254780680|r  372 NSKSLKFTHT-LNGSGVAVGRCLIAILE  398 (430)
Q Consensus       372 ~~~~~~~~ht-lNgt~~A~~R~l~ailE  398 (430)
                      +|++ +++|. +-|++   .|.|+||+|
T Consensus       237 dg~~-~~phr~~~G~~---eR~ig~lI~  260 (261)
T cd00778         237 DGQK-EYVHQTSWGIS---TRLIGAIIM  260 (261)
T ss_pred             CCCC-CCCEEEEEEHH---HHHHHHHHC
T ss_conf             9998-08557412499---899889734


No 13 
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=99.89  E-value=7.3e-23  Score=190.64  Aligned_cols=266  Identities=20%  Similarity=0.270  Sum_probs=205.4

Q ss_pred             CHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHH
Q ss_conf             20221173100011222167530105648899999999999862232032021235620278898655142247677643
Q gi|254780680|r  143 EIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCT  222 (430)
Q Consensus       143 elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~  222 (430)
                      .|.-+-|+|.      -+|+|+|++.-.|+++-+.|.+|+-+. ..+.||.+|.+|.|.+.+....+|+++.+.++||.+
T Consensus        24 ~ll~~~g~i~------~~~~Gl~~wlP~G~~i~~~le~~ir~e-~~~~G~~eV~tP~l~~~~Lw~~SGh~~~y~~~mf~~   96 (438)
T PRK12325         24 RLMLRAGMIR------QQAAGIYSWLPLGLKVLKKIENIVREE-QNRAGAIEILMPTIQPADLWRESGRYDAYGKEMLRI   96 (438)
T ss_pred             HHHHHCCCCC------CCCCCCCEECCCHHHHHHHHHHHHHHH-HHHCCCEEEECCCCCCHHHHHHHCCHHHHHHHHCEE
T ss_conf             9999707756------346873221605899999999999999-997499799877658778998628764555742121


Q ss_pred             H----HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEEC-CCCCCHHH
Q ss_conf             1----000231345411454453420595550420885322107884335543432122221020021212-78650145
Q gi|254780680|r  223 T----DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSI-TREEDSFT  297 (430)
Q Consensus       223 ~----d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~-~~pe~S~~  297 (430)
                      .    .+++|-||.|-..+.+|+.++-++.+||+|++-++++||.|..  |+  .||+||-+|+.-+..+| ++.++..+
T Consensus        97 ~d~~~~~~~l~Pmnc~~~~~i~~~~~~SYRdLPlrl~q~g~~~R~E~s--p~--~GLlRvReF~m~Dah~F~~~~e~~~~  172 (438)
T PRK12325         97 KDRHDREMLYGPTNEEMITDIFRSYVKSYKDLPLNLYHIQWKFRDEIR--PR--FGVMRGREFLMKDAYSFDLDEEGARK  172 (438)
T ss_pred             ECCCCCEECCCCCCCHHHHHHHHHCCCCHHHCCHHHHHHHHEECCCCC--CC--CCCCEEEEEECCCHHHCCCCHHHHHH
T ss_conf             347777431389984999999974034265425788764440112026--76--44101223330415432468899999


Q ss_pred             HHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEE-------------EEEEE-----CCCC---------------
Q ss_conf             78989999999999841067530378011784434024-------------10110-----1004---------------
Q gi|254780680|r  298 EHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTY-------------DLEVW-----LAGQ---------------  344 (430)
Q Consensus       298 ~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~-------------DiE~w-----~P~~---------------  344 (430)
                      .++.+......+|+.|||++..|...+|.+|...+.-|             |-+.|     -++.               
T Consensus       173 ~~~~v~~~y~~if~~lgl~~~~v~ad~g~igg~~s~Ef~~~~~~ged~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  252 (438)
T PRK12325        173 SYNRMFVAYLRTFKRLGLKAIPMRADTGPIGGDLSHEFHILAETGESTVFYDKDFLDLPVPGEDIDYDADLQDIVDEWTS  252 (438)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHHHCCCHHEEECHHHHHCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             99999999999999809944899823676677512674766522650246613334225676554623566789988876


Q ss_pred             -----------C-------------CEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHC
Q ss_conf             -----------8-------------3323753102100764532684733899841010420043228999999998834
Q gi|254780680|r  345 -----------N-------------LYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAILENY  400 (430)
Q Consensus       345 -----------~-------------~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ailEn~  400 (430)
                                 .             +=.||+.+=++++=-|..++..|.+++|++ ..+|+- .-|+.+.|.|++|+|++
T Consensus       253 ~~~~~~~~~~~~~~~~~~~~~~~~~~~iEvG~if~lg~~ys~~~~~~~~~~dg~~-~~~~m~-~~GIgieR~ia~liE~~  330 (438)
T PRK12325        253 LYAATDEMHDEAKFAAVPEERRLSARGIEVGHIFYFGTKYSEPMNAKVQGPDGKE-VPVHMG-SYGIGVSRLVAAIIEAS  330 (438)
T ss_pred             HHHHHHHHCCHHHCCCCCHHHHEECCCEEEEEEEECCCCCCHHCCCCCCCCCCCC-CCEEEE-CCCCCHHHHHHHHHHHH
T ss_conf             5034664346755376675663011330331243045301522067444877773-222554-13342878999999983


Q ss_pred             CCCCCCEECCCCCCCCCCCEEEEC
Q ss_conf             689983865822231018801307
Q gi|254780680|r  401 LNADGSVTIPTVLRPYMNNLAVIK  424 (430)
Q Consensus       401 q~~dg~i~iP~~L~pym~g~~~i~  424 (430)
                      ..+.| ++.|-.|-||=  ..+|+
T Consensus       331 ~d~~G-~~wP~wlAP~Q--V~Iip  351 (438)
T PRK12325        331 HDDKG-IIWPESVAPFK--VGIIN  351 (438)
T ss_pred             CCCCC-CCCCCCCCCEE--EEEEE
T ss_conf             64688-54676748657--99997


No 14 
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=99.88  E-value=2.7e-22  Score=186.42  Aligned_cols=264  Identities=23%  Similarity=0.370  Sum_probs=211.6

Q ss_pred             CCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHH
Q ss_conf             62112202211731000112221675301056488999999999998622320320212356202788986551422476
Q gi|254780680|r  138 SREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFAD  217 (430)
Q Consensus       138 ~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~  217 (430)
                      -+||--||..++|+.|.   ..+|.|.++..-.|+++-+.|.+|+-+.+ .++||.+|.+|.|.+.+..+.+|+++++.+
T Consensus       177 kRDHRklGkel~LF~f~---~~~gpG~~~wlP~G~~i~~~le~~~r~~~-~~~Gy~eV~TP~i~~~~Lw~~SGH~~~Y~e  252 (576)
T PRK12305        177 ERDHRKIGKDLKLFTFS---SLAGQGFPIWLENGMIIKNAIRKFILELD-RKYGFDEVLTPHFGEKKLYKTSGHLDHYKD  252 (576)
T ss_pred             HCCHHHHHHHCCEEEEC---CCCCCCCEEECCCHHHHHHHHHHHHHHHH-HHCCCEEEECCCCCCHHHHHHCCCHHHHHH
T ss_conf             65778764215658723---44688764674767899999999999999-986998984642142889976664655664


Q ss_pred             HHHHH----HHCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCC
Q ss_conf             77643----10002313454114544534205955504208853221078843355434321222210200212127865
Q gi|254780680|r  218 DMFCT----TDGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREE  293 (430)
Q Consensus       218 ~~y~~----~d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe  293 (430)
                      +||..    ++++.|=|+..-.-+-+|+...-++.+||+|++-++.|||-|.  .| ...||+||.+|+.-...+||+||
T Consensus       253 ~Mf~~~~~~~e~~~lKPMNCP~H~~if~~~~rSYRdLPlR~aEfg~~~R~E~--SG-~L~GL~RvR~FtqDDAHIFct~d  329 (576)
T PRK12305        253 DMFKPLKIENEELIPRPMTCPHHIILYSNELRSYRDLPIRLSEQSRLYRYEK--SG-ALTGLERVRAMDLTEGHIFVRKD  329 (576)
T ss_pred             HCCCCEECCCCEEEECCCCCHHHHHHHHCCCCCHHHCCHHHHCCCCEECCCC--CC-CCCCCCCCCCCCCCCCCEEECHH
T ss_conf             2573063156416535778632677764277544432422000443544788--86-55575546688768712120899


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEE--------------------CCCCCCE------
Q ss_conf             01457898999999999984106753037801178443402410110--------------------1004833------
Q gi|254780680|r  294 DSFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVW--------------------LAGQNLY------  347 (430)
Q Consensus       294 ~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w--------------------~P~~~~y------  347 (430)
                      +-.++...+++...++|..+|+..-.+.+++-|-+.+...-=|.|.|                    .||.+.|      
T Consensus       330 Qi~~Ei~~~l~~i~~vy~~fGf~~~~~~lS~r~~~~~ek~~g~de~W~~Ae~~L~~al~~~g~~y~~~~GegAFYGPKID  409 (576)
T PRK12305        330 QIESEVKHLFKMIQEALSIFKIKIFYISLSLRDPNDKEKFFDDDQMWEQAEADLKKMLKDNKINYKEMIGEAAFYGPKID  409 (576)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEECCCCCCEECCCCC
T ss_conf             99999999999999999853987315899943898875345972769999999999999749971423065010567634


Q ss_pred             -------EEEEEECCC-CCHH-HHHCCCEEECCCCCCCC--EEE-EECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCC
Q ss_conf             -------237531021-0076-45326847338998410--104-20043228999999998834689983865822231
Q gi|254780680|r  348 -------REISSCSTC-GNFQ-SRRMNSRYRDPNSKSLK--FTH-TLNGSGVAVGRCLIAILENYLNADGSVTIPTVLRP  415 (430)
Q Consensus       348 -------~Ev~S~Snc-~D~Q-srRl~iry~~~~~~~~~--~~h-tlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~p  415 (430)
                             +-.-.||.. .||+ ..|.++.|.+++|.+..  .+| .+-||   +-|.++.|+|+|.-     ..|-=|-|
T Consensus       410 ~~v~DalgR~wq~~TIQlDf~lPeRF~l~Y~~~dg~~~rPVmIHRAilGS---~ERfigiLiEh~~G-----~~P~WLaP  481 (576)
T PRK12305        410 FQVKTVLNKEITVSTIQLDFLLPEKFNISYINENNEKETPVLIHRGLIGT---YERFIAILLEQTKG-----NLPFWLSP  481 (576)
T ss_pred             EEEECCCCCEEEEEEEEEEECCHHHCCCEEECCCCCCCCCEEEEECCCCC---HHHHHHHHHHHCCC-----CCCCCCCC
T ss_conf             69850678678742456663458557988877888767875987335474---89999999997079-----99836273


Q ss_pred             C
Q ss_conf             0
Q gi|254780680|r  416 Y  416 (430)
Q Consensus       416 y  416 (430)
                      .
T Consensus       482 ~  482 (576)
T PRK12305        482 K  482 (576)
T ss_pred             C
T ss_conf             0


No 15 
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=99.87  E-value=7.1e-22  Score=183.29  Aligned_cols=260  Identities=19%  Similarity=0.363  Sum_probs=207.2

Q ss_pred             CCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHH
Q ss_conf             62112202211731000112221675301056488999999999998622320320212356202788986551422476
Q gi|254780680|r  138 SREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFAD  217 (430)
Q Consensus       138 ~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~  217 (430)
                      -+||--||..++|+.|.--    |.|.+++.-.|+.+-+.|.+|+-+.+ .++||.+|.+|.+.+.+..+.+|+++.+.+
T Consensus       244 kRDHRklGkel~LF~f~~~----~pG~~fwlP~G~~i~~~le~~~r~~~-~~~GY~eV~TP~i~~~~Lw~~SGH~~~Y~e  318 (639)
T PRK12444        244 KRNHRKLGNELELFMFSEE----APGMPFYLPKGQIIRNELEAFLREIQ-KEYNYQEVRTPFMMNQELWERSGHWGHYKD  318 (639)
T ss_pred             HCCHHHHHHHCCEEEECCC----CCCCEEEECCHHHHHHHHHHHHHHHH-HHCCCEEECCCEEEHHHHHHHCCHHHHHHH
T ss_conf             6478876532272882277----89744784678699999999999999-983987822866621568761660433330


Q ss_pred             HHHHHH---HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCC
Q ss_conf             776431---00023134541145445342059555042088532210788433554343212222102002121278650
Q gi|254780680|r  218 DMFCTT---DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREED  294 (430)
Q Consensus       218 ~~y~~~---d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~  294 (430)
                      +||..+   +++.|=|.-.-.-+-+|+...-++.+||+||+-++.|||-|.  .| ...||.||.+|+.=...+||+||+
T Consensus       319 ~Mf~~~~d~~~~~lKPMNCP~H~~if~~~~rSYRdLPlR~aEfg~vhR~E~--SG-~L~GL~RVR~FtqDDAHIFct~dQ  395 (639)
T PRK12444        319 NMYFSEVDNKSFALKPMNCPGHMLMFKNKLHSYRELPIRMCEFGQVHRHEF--SG-ALNGLLRVRTFCQDDAHLFVTPEQ  395 (639)
T ss_pred             CCCCCCCCCCEEECCCCCCHHHHHHHHCCCCCHHHCCHHHHHCCCEECCCC--CC-CCCCCCCCCCCCCCCCEEECCHHH
T ss_conf             275545454033126768588999986056214436522243364633778--76-645767788998798246538899


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEEC--------------------CCCCCE-------
Q ss_conf             14578989999999999841067530378011784434024101101--------------------004833-------
Q gi|254780680|r  295 SFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWL--------------------AGQNLY-------  347 (430)
Q Consensus       295 S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~--------------------P~~~~y-------  347 (430)
                      -.++...+++...++|+.+|+.|+ +.+++..    .-.-=|.|.|-                    ||.+.|       
T Consensus       396 i~~Ei~~~~~~~~~vy~~fGf~~~-~~LStrp----ek~~G~de~W~~Ae~~L~~aL~~~g~~y~~~~GegAFYGPKiD~  470 (639)
T PRK12444        396 IEDEIKSVMAQIDYVYKTFGFEYE-VELSTRP----EDSMGDDKLWEQAEAALENVLQSLNYKYRLNEGDGAFYGPKIDF  470 (639)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEE-EEECCCC----CCCCCCHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCEEEE
T ss_conf             999999999999999974797299-9816786----33458889999999999999997499758676863640326568


Q ss_pred             ------EEEEEECC-CCCHH-HHHCCCEEECCCCCCCCEEEEECCCHH-HHHHHHHHHHHHCCCCCCCEECCCCCCCC
Q ss_conf             ------23753102-10076-453268473389984101042004322-89999999988346899838658222310
Q gi|254780680|r  348 ------REISSCST-CGNFQ-SRRMNSRYRDPNSKSLKFTHTLNGSGV-AVGRCLIAILENYLNADGSVTIPTVLRPY  416 (430)
Q Consensus       348 ------~Ev~S~Sn-c~D~Q-srRl~iry~~~~~~~~~~~htlNgt~~-A~~R~l~ailEn~q~~dg~i~iP~~L~py  416 (430)
                            +---.||. =.||+ ..|.++.|.+++|.+ +-+-++.-..+ .+-|.++.|+|+|.-     ..|--|-|.
T Consensus       471 ~v~DalgR~wq~~TIQlDF~lPeRF~l~Y~~~dg~~-~rPVmIHRAilGS~ERFigiLiEh~~G-----~fP~WLaP~  542 (639)
T PRK12444        471 HIKDALNRSHQCGTIQLDFQMPEKFDLNYIDEKNEK-VRPVVIHRAVLGSLDRFLAILIEHFGG-----AFPAWVAPV  542 (639)
T ss_pred             EEEECCCCEEECCEEEEEECCHHHCCCEEECCCCCC-CCCEEEEECCCCCHHHHHHHHHHHCCC-----CCCCCCCCC
T ss_conf             998078872451234552056633587778789982-598899957877789999999997279-----898565720


No 16 
>PRK03772 threonyl-tRNA synthetase; Validated
Probab=99.87  E-value=1.3e-21  Score=181.36  Aligned_cols=256  Identities=21%  Similarity=0.340  Sum_probs=204.4

Q ss_pred             CCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHH
Q ss_conf             62112202211731000112221675301056488999999999998622320320212356202788986551422476
Q gi|254780680|r  138 SREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFAD  217 (430)
Q Consensus       138 ~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~  217 (430)
                      -+||--||..++|+.|.-   . |.|.+++.-.|+.+-+.|..|+-+.+ .++||.+|.+|.+.+.+....+|+++++.+
T Consensus       241 kRDHRklGkel~LF~f~~---~-~pG~~fwlP~G~~i~~~le~~~r~~~-~~~Gy~eV~TP~i~~~~Lw~~SGH~~~Y~e  315 (642)
T PRK03772        241 KRDHRKIGKQLDLYHMQE---E-APGMVFWHNDGWTIFRELEVFVRSKL-KEYQYQEVKGPFMMDRVLWEKTGHWDNYAD  315 (642)
T ss_pred             HCCHHHHHHHCCCEEECC---C-CCCCEEECCCHHHHHHHHHHHHHHHH-HHCCCEEEECCHHCCHHHHHHCCHHHHHHC
T ss_conf             658888877522047546---5-88763665858899999999999999-986985985543213778873444766410


Q ss_pred             HHHHHH---HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCC
Q ss_conf             776431---00023134541145445342059555042088532210788433554343212222102002121278650
Q gi|254780680|r  218 DMFCTT---DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREED  294 (430)
Q Consensus       218 ~~y~~~---d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~  294 (430)
                      +||.+.   +++.|=|..--.-+-+|+...-++.+||+|++-+++|||-|..  |. ..||+||.+|+.-...+||+||+
T Consensus       316 ~Mf~~~~e~~ey~lKPMNCP~H~~iy~~~~rSYRdLPlR~aEfg~~~R~E~S--G~-L~GL~RVR~FtqdDaHIFC~~dQ  392 (642)
T PRK03772        316 AMFTTSSENREYAIKPMNCPGHVQIFNQGLKSYRDLPLRMAEFGSCHRNEPS--GS-LHGLMRVRGFTQDDAHIFCTEEQ  392 (642)
T ss_pred             CCCCCCCCHHHHCCCCCCCHHHHHHHHCCCCCHHHCCHHHHHHHHHHCCCCC--CC-CCCCCCCCCCCCCCCEEECCHHH
T ss_conf             3422342014430467787348899861664344365455541134316666--55-34745688998788435537899


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCH-HHHCCCCCHHCCCHHHEEEEEEEE--------------------CCCCCCE------
Q ss_conf             1457898999999999984106-753037801178443402410110--------------------1004833------
Q gi|254780680|r  295 SFTEHERMLSCAEEILKRLDLH-YRVVSLCTGDLGFSACKTYDLEVW--------------------LAGQNLY------  347 (430)
Q Consensus       295 S~~~~e~~~~~~~~i~~~L~lp-yRvv~~~sgdlg~~a~~~~DiE~w--------------------~P~~~~y------  347 (430)
                      -.++...+++...++|+.+|+. |+ +.+++.    +..+--|.|.|                    .||.+.|      
T Consensus       393 i~~Ei~~~l~~~~~vy~~fGf~~~~-~~LStr----pek~~G~~e~W~~AE~~L~~aL~~~g~~y~~~~GegAFYGPKID  467 (642)
T PRK03772        393 IRDEVNSCIKMVYDMYSTFGFEKIV-VKLSTR----PEKRIGSDEMWDRAEADLAVALEENNIPFEYQPGEGAFYGPKIE  467 (642)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEE-EEECCC----CHHCCCCHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCC
T ss_conf             9999999999999999973986389-996268----22025888899999999999999739970455676344455302


Q ss_pred             --------EEEEEECCCCCHH-HHHCCCEEECCCCCCCCEEEE----ECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCC
Q ss_conf             --------2375310210076-453268473389984101042----004322899999999883468998386582223
Q gi|254780680|r  348 --------REISSCSTCGNFQ-SRRMNSRYRDPNSKSLKFTHT----LNGSGVAVGRCLIAILENYLNADGSVTIPTVLR  414 (430)
Q Consensus       348 --------~Ev~S~Snc~D~Q-srRl~iry~~~~~~~~~~~ht----lNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~  414 (430)
                              ||-.-...-.||+ ..|.++.|.+++|.+ +-+-.    +-||   +-|.++.|+|+|.-     ..|--|-
T Consensus       468 ~~v~DalgR~wq~~TiQlDF~lP~RF~l~Y~~~dg~~-~~PVmIHRAilGS---~ERfiaiLiEh~~G-----~~P~WLa  538 (642)
T PRK03772        468 FTLYDCLDRAWQCGTVQLDFSLPGRLSASYVGEDNER-KVPVMIHRAILGS---MERFIGILTEEYAG-----FFPTWLA  538 (642)
T ss_pred             EEEECCCCCEEEECCCEEECCCHHHCCCEEECCCCCC-CCCEEEEECCCCC---HHHHHHHHHHHCCC-----CCCCCCC
T ss_conf             5997078976880232430013544288888789985-7858999246477---89999999998079-----9985647


Q ss_pred             C
Q ss_conf             1
Q gi|254780680|r  415 P  415 (430)
Q Consensus       415 p  415 (430)
                      |
T Consensus       539 P  539 (642)
T PRK03772        539 P  539 (642)
T ss_pred             C
T ss_conf             6


No 17 
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=99.86  E-value=5.7e-22  Score=183.99  Aligned_cols=258  Identities=22%  Similarity=0.387  Sum_probs=203.0

Q ss_pred             CCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHH
Q ss_conf             62112202211731000112221675301056488999999999998622320320212356202788986551422476
Q gi|254780680|r  138 SREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFAD  217 (430)
Q Consensus       138 ~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~  217 (430)
                      -+||--||..|+|+.|.-   . |.|.+++.-.|+.+-+.|.+|+-+.+ .++||.+|.+|.|.+.+..+.+|+++.+.+
T Consensus       238 kRDHRklGkel~LF~f~~---~-~pGl~~w~P~G~~i~~~le~~~r~~~-~~~Gy~eV~TP~i~~~~Lw~~SGHw~~Y~e  312 (639)
T PRK00413        238 KRDHRKLGKELDLFSFQE---E-GPGLPFWHPKGWIIRNELEDYMRRRH-LKAGYQEVNTPHILDRSLWETSGHWDHYRE  312 (639)
T ss_pred             HCCHHHHHHHCCCEEECC---C-CCCCEEECCCHHHHHHHHHHHHHHHH-HHCCCEEEECCCCCCHHHHHHCCCHHHHCC
T ss_conf             528888877435157036---6-88764663768999999999999999-986985983641346889965474223225


Q ss_pred             HHHHH----HHCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCC
Q ss_conf             77643----10002313454114544534205955504208853221078843355434321222210200212127865
Q gi|254780680|r  218 DMFCT----TDGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREE  293 (430)
Q Consensus       218 ~~y~~----~d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe  293 (430)
                      +||..    +++++|=|..--.-+-+|+...-++.+||+||+-+++|||-|.  .| ...||+||.+|+.=...+||+||
T Consensus       313 ~Mf~~~~~~~~~~~lKPMNCP~H~~if~~~~~SYRdLPlR~aEfg~~~R~E~--SG-~L~GL~RvR~FtqdDaHIFc~~d  389 (639)
T PRK00413        313 NMFPTMSDDGEDYALKPMNCPGHILIFKSGLRSYRELPLRLAEFGTVHRYEK--SG-ALHGLMRVRGFTQDDAHIFCTPE  389 (639)
T ss_pred             CCCCCEECCCCEEEECCCCCCCHHHHHHCCCCCHHHCCHHHHHHHHHHCCCC--CC-CCCCEEEEEEEECCCCEEECCHH
T ss_conf             4223240152103204668700335644355355547556664113205677--87-44564233000015841324789


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCH-HHHCCCCCHHCCCHHHEEEEEEEEC--------------------CCCCCE----E
Q ss_conf             01457898999999999984106-7530378011784434024101101--------------------004833----2
Q gi|254780680|r  294 DSFTEHERMLSCAEEILKRLDLH-YRVVSLCTGDLGFSACKTYDLEVWL--------------------AGQNLY----R  348 (430)
Q Consensus       294 ~S~~~~e~~~~~~~~i~~~L~lp-yRvv~~~sgdlg~~a~~~~DiE~w~--------------------P~~~~y----~  348 (430)
                      |-.++...+++...++|+.+|+. |+ +.+++-+    ...-=|.|.|-                    ||.+.|    .
T Consensus       390 Qi~~Ei~~~l~~~~~vy~~fGf~~~~-~~lStrp----ek~~g~~e~W~~Ae~~L~~al~~~g~~y~~~~GegAFYGPKI  464 (639)
T PRK00413        390 QIKDELLSVLDLILSVYKDFGLTDYY-LELSTRP----EKRVGSDELWEKATEALREALEESGLEYVENPGEGAFYGPKI  464 (639)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCEEE-EEEECCC----CCCCCCHHHHHHHHHHHHHHHHHCCCCEEECCCCCCEECCEE
T ss_conf             99999999999999999974998038-9996475----113588899999999999999974998087888611110166


Q ss_pred             E---------EEEECCC-CCHH-HHHCCCEEECCCCCCCC--EEE-EECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCC
Q ss_conf             3---------7531021-0076-45326847338998410--104-2004322899999999883468998386582223
Q gi|254780680|r  349 E---------ISSCSTC-GNFQ-SRRMNSRYRDPNSKSLK--FTH-TLNGSGVAVGRCLIAILENYLNADGSVTIPTVLR  414 (430)
Q Consensus       349 E---------v~S~Snc-~D~Q-srRl~iry~~~~~~~~~--~~h-tlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~  414 (430)
                      +         ---||.. .||+ ..|.++.|.+++|.+..  .+| .+-||   +-|.++.|+|+|.   |  ..|--|-
T Consensus       465 D~~~~DalgR~wq~~TiQlDf~lPerF~l~Y~~~dg~~~~PVmIHRAi~GS---~ERfiaiLiEh~~---G--~~P~WLa  536 (639)
T PRK00413        465 DVQLKDAIGRTWQCGTIQLDFNLPERFDLEYIAADGEKHRPVMIHRAIFGS---IERFIGILIEHYA---G--AFPLWLA  536 (639)
T ss_pred             EEEEECCCCCEEECCHHHHHHCCHHHCCCEEECCCCCCCCEEEEEECCCCC---HHHHHHHHHHHHC---C--CCCCCCC
T ss_conf             778514468713200233222245424888998889816308999525565---8999999999808---9--8873657


Q ss_pred             CC
Q ss_conf             10
Q gi|254780680|r  415 PY  416 (430)
Q Consensus       415 py  416 (430)
                      |-
T Consensus       537 P~  538 (639)
T PRK00413        537 PV  538 (639)
T ss_pred             CC
T ss_conf             61


No 18 
>PRK04483 threonyl-tRNA synthetase; Validated
Probab=99.86  E-value=2.1e-21  Score=179.79  Aligned_cols=260  Identities=19%  Similarity=0.300  Sum_probs=207.6

Q ss_pred             CCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHH
Q ss_conf             62112202211731000112221675301056488999999999998622320320212356202788986551422476
Q gi|254780680|r  138 SREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFAD  217 (430)
Q Consensus       138 ~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~  217 (430)
                      -+||--||..++|+.|.-    .|.|.++..-.|+++-+.|.+|+-+.+ .++||.+|.+|.|.+.+..+.+|+++.+.+
T Consensus       241 kRDHRklGkel~LF~f~~----~~pG~~~wlP~G~~i~~~le~~~r~~~-~~~Gy~eV~tP~i~~~~Lw~~SGH~~~Y~e  315 (634)
T PRK04483        241 KRDHRKIGKAQDLFHLQE----EAPGLVFWHPKGWSLWQVVEQYMRKVY-RDSGYGEVRCPQILDVSLWQKSGHWDNYQD  315 (634)
T ss_pred             HCCHHHHHHHCCEEEECC----CCCCCEEECCCHHHHHHHHHHHHHHHH-HHCCCEEEECCEECCHHHHHHCCCHHHHHH
T ss_conf             658888754211067337----788643881668999999999999999-982995998862513778762561645530


Q ss_pred             HHHHHH---HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCC
Q ss_conf             776431---00023134541145445342059555042088532210788433554343212222102002121278650
Q gi|254780680|r  218 DMFCTT---DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREED  294 (430)
Q Consensus       218 ~~y~~~---d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~  294 (430)
                      +||.++   +++.|=|...-.-+-+|+...-++.+||+|++-+++|||-|..  | ...||.||.+|+.=...+||+||+
T Consensus       316 ~Mf~~~~~~~~~~lKPMNCP~H~~if~~~~rSYRdLPlR~aE~g~~~R~E~S--G-~L~GL~RvR~FtqdDaHIFc~~dQ  392 (634)
T PRK04483        316 AMFFTESEKRTYAVKPMNCPGHVQVFNQGLHSYRDLPIRYGEFGACHRNEPS--G-ALHGILRVRGFTQDDGHVFCLESQ  392 (634)
T ss_pred             CCCEECCCCCEEEECCCCCHHHHHHHHCCCCCHHHCCHHHHHCCCEEECCCC--C-CCCCCCCCCCCCCCCCEEECCHHH
T ss_conf             3713425540355157685648799871774444343665543302205677--6-545745688998898335638999


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCH-HHHCCCCCHHCCCHHHEEEEEEEEC--------------------CCCCCE------
Q ss_conf             1457898999999999984106-7530378011784434024101101--------------------004833------
Q gi|254780680|r  295 SFTEHERMLSCAEEILKRLDLH-YRVVSLCTGDLGFSACKTYDLEVWL--------------------AGQNLY------  347 (430)
Q Consensus       295 S~~~~e~~~~~~~~i~~~L~lp-yRvv~~~sgdlg~~a~~~~DiE~w~--------------------P~~~~y------  347 (430)
                      -.++...+++...++|+.+|+- |++ .+++..    ..+-=|.|.|-                    ||.+.|      
T Consensus       393 i~~Ei~~~l~~~~~vy~~fGf~~~~~-~lStrp----ek~~G~~~~W~~AE~~L~~al~~~g~~y~~~~GegAFYGPKID  467 (634)
T PRK04483        393 IEAEVTAFHQQALAVYTAFGFDDIQI-KIALRP----EKRLGDDATWDKAEAALRSALGVCGVEWQELPGEGAFYGPKIE  467 (634)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEEE-EECCCC----CCCCCCHHHHHHHHHHHHHHHHHCCCCCEECCCCCCEECCCEE
T ss_conf             99999999999999998639953899-963576----2345875568899999999999749870776797010566228


Q ss_pred             -------EEEEEEC-CCCCHH-HHHCCCEEECCCCCCCCEEEEECCCHH-HHHHHHHHHHHHCCCCCCCEECCCCCCCC
Q ss_conf             -------2375310-210076-453268473389984101042004322-89999999988346899838658222310
Q gi|254780680|r  348 -------REISSCS-TCGNFQ-SRRMNSRYRDPNSKSLKFTHTLNGSGV-AVGRCLIAILENYLNADGSVTIPTVLRPY  416 (430)
Q Consensus       348 -------~Ev~S~S-nc~D~Q-srRl~iry~~~~~~~~~~~htlNgt~~-A~~R~l~ailEn~q~~dg~i~iP~~L~py  416 (430)
                             +-.-.|| .-.||| ..|.++.|.+++|++ +.+.++.-..+ .+-|.++.|+|+|.-     ..|-=|-|.
T Consensus       468 ~~v~DalgR~~q~~TiQlDf~lP~rF~l~Y~~~dg~~-~rPvmIHRAilGS~ERfi~iLiEh~~G-----~fP~WLaP~  540 (634)
T PRK04483        468 YHLKDAIGRTWQLGTMQVDFMMPGRLGAEYVDENSQK-KHPVMLHRAIVGSMERFIGILIEHHAG-----AFPAWLAPV  540 (634)
T ss_pred             EEEEECCCCEEECCEEEEECCCCCCCCCEEECCCCCC-CCEEEEEECCCCCHHHHHHHHHHHCCC-----CCCCCCCCC
T ss_conf             9999279986741145762145343677898568983-860899945767789999999997379-----898576873


No 19 
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=99.85  E-value=3.6e-21  Score=178.03  Aligned_cols=277  Identities=21%  Similarity=0.261  Sum_probs=211.6

Q ss_pred             CCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHH
Q ss_conf             15656656662112202211731000112221675301056488999999999998622320320212356202788986
Q gi|254780680|r  129 GKKPSAIHLSREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYG  208 (430)
Q Consensus       129 G~~~~f~f~~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~g  208 (430)
                      |....-+-+ .+|++++.++++.|+|-++-   +|...+--.|.+.-++|.+|+.+. +...||.+|.+|.|++.+...-
T Consensus       188 ~~~~~~~~e-pphv~~mr~~~~~dyEp~Sd---~G~~rw~PkG~~i~~lle~Yv~~~-~~~~G~~eV~TP~m~d~~~~~~  262 (613)
T PRK03991        188 FKKELVGGE-PPHVELMRKKELADYEPGSD---VGHMRYYPKGRLMKDLLEDYVYNL-VKELGAMPVETPNMYDLSHPAI  262 (613)
T ss_pred             CCCCCCCCC-CCHHHHHHHCCCCCCCCCCC---CCCEEECCCHHHHHHHHHHHHHHH-HHHCCCEEEECCCEEECCCCHH
T ss_conf             134457789-83889998717655574787---775123554789999999999999-9863966845761640554025


Q ss_pred             HHHCHHHHHHHHHHH---HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECC-CCCCCCCCCCCCCCEEEEEEEEEE
Q ss_conf             551422476776431---0002313454114544534205955504208853221-078843355434321222210200
Q gi|254780680|r  209 TGQIPKFADDMFCTT---DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPS-FRSEAGSAGRDTRGMLRQHQFWKC  284 (430)
Q Consensus       209 tG~lp~f~~~~y~~~---d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~c-fR~EaGs~GkdtrGl~RvHQF~KV  284 (430)
                      .|++.+|.+.||.++   .++.|=|-+=-.-.-++.+..+.+.+||+|++.+++| ||.|..  | ...||.||..|+.=
T Consensus       263 sgH~~~f~e~my~~~~d~~~~~LrpmnCpgh~~i~~~~~~SYRdLPlRl~E~g~~syR~E~S--G-~L~GL~RVR~FTqd  339 (613)
T PRK03991        263 REHADKFGERQYRVKSDKKDLMLRFAACFGQFAMLKDMTISYKNLPLKMYELSDYSFRLEQR--G-ELVGLKRLRAFTMP  339 (613)
T ss_pred             HHHHHHHCCCCEEEECCCHHHCCCCCCCCCCEEEECCCCCCHHHCCHHHHHHCCCEEECCCC--C-CEECEEEEECCCCC
T ss_conf             56887611134256327633230445786312351024457432646776522420212567--7-44440133235668


Q ss_pred             EEEECCCC-CCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCC-------HHHEE----EEEEEECCCCCCE-----
Q ss_conf             21212786-5014578989999999999841067530378011784-------43402----4101101004833-----
Q gi|254780680|r  285 ELVSITRE-EDSFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGF-------SACKT----YDLEVWLAGQNLY-----  347 (430)
Q Consensus       285 E~~~~~~p-e~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~-------~a~~~----~DiE~w~P~~~~y-----  347 (430)
                      .+.+||++ ++..+++..+++...+.+..+|+.|.+....|.|.=.       .+.++    +-+|+| |+...|     
T Consensus       340 DaHIFC~~~dQi~~E~~~~~~li~~v~~~fG~~y~~~~r~t~e~w~~ae~~l~~~~~~~g~~~~~e~~-~g~~~fyGPKI  418 (613)
T PRK03991        340 DMHTLCKDMDEAMEEFEKQHKLILETGRDLGRDYEVAFRFTEDFYEENKDWIVELAKREGKPVLVEIL-PERKHYWVLKV  418 (613)
T ss_pred             CCEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEC-CCCCCEECCCE
T ss_conf             61131687789999999999999999986397637997078888889999999999972997147665-87631431416


Q ss_pred             ---------EEEEEECCCCCHH-HHHCCCEEECCCCCCCCEEEEECCCH-HHHHHHHHHHHHHCC--CCCCCE-ECCCCC
Q ss_conf             ---------2375310210076-45326847338998410104200432-289999999988346--899838-658222
Q gi|254780680|r  348 ---------REISSCSTCGNFQ-SRRMNSRYRDPNSKSLKFTHTLNGSG-VAVGRCLIAILENYL--NADGSV-TIPTVL  413 (430)
Q Consensus       348 ---------~Ev~S~Snc~D~Q-srRl~iry~~~~~~~~~~~htlNgt~-~A~~R~l~ailEn~q--~~dg~i-~iP~~L  413 (430)
                               |+..-...=.||| +.|.++.|.+.+|++ +.+-.|.-+- =.+-|.+++|||+|-  ..+|.. ..|-=|
T Consensus       419 Df~v~DalGR~wq~~TiQlDf~lp~RF~l~Yv~edg~~-~~PvmiHrAi~GS~ERfi~~LiE~~ag~~~~Gk~p~~P~WL  497 (613)
T PRK03991        419 EFAIIDSLGRPIENPTVQIDVENAERFGIKYVDENGKE-KYPVILHCSPTGSIERVIYALLEKAAKEEKEGKVPMLPTWL  497 (613)
T ss_pred             EEEEEECCCCCEEEEEEEEECCCHHHCCCEEECCCCCC-CCCEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             89998468972450158983278322687899899989-58858972665639999999999850101247878888787


Q ss_pred             CC
Q ss_conf             31
Q gi|254780680|r  414 RP  415 (430)
Q Consensus       414 ~p  415 (430)
                      -|
T Consensus       498 aP  499 (613)
T PRK03991        498 SP  499 (613)
T ss_pred             CC
T ss_conf             86


No 20 
>PRK12304 thrS threonyl-tRNA synthetase; Reviewed
Probab=99.85  E-value=1.8e-21  Score=180.32  Aligned_cols=257  Identities=23%  Similarity=0.407  Sum_probs=204.4

Q ss_pred             CCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHH
Q ss_conf             62112202211731000112221675301056488999999999998622320320212356202788986551422476
Q gi|254780680|r  138 SREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFAD  217 (430)
Q Consensus       138 ~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~  217 (430)
                      -+||--||..++|+.|.-   -.|.+++++.-.|+.+-+.|.+|+-+.+ .++||.+|.+|.|.+.+..+.+|+++++.+
T Consensus       208 kRDHRklGkel~LF~f~~---~~g~G~~~wlP~G~~i~~~le~~~r~~~-~~~Gy~eV~TP~i~~~~Lw~~SGH~~~Y~e  283 (604)
T PRK12304        208 KRDHRKLGVEMKLFTFDD---EIGAGLPIWLPKGARLRSKLEHLLYKAH-RLRGYEPVRGPEILKSDVWKISGHYANYKE  283 (604)
T ss_pred             HCCHHHHHHHCCCEECCC---CCCCCCEEECCCHHHHHHHHHHHHHHHH-HHCCCEEECCCCCCCHHHHHCCCHHHHHCC
T ss_conf             667888877455156255---4588753683775499999999999999-982996803865455888730551532105


Q ss_pred             HHHHHH---HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCC
Q ss_conf             776431---00023134541145445342059555042088532210788433554343212222102002121278650
Q gi|254780680|r  218 DMFCTT---DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREED  294 (430)
Q Consensus       218 ~~y~~~---d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~  294 (430)
                      +||.++   +++.|=|..--.-+-+|+...-++.+||+|++-++.|||-|+  .| ...||.||.+|+.=...+||+|||
T Consensus       284 ~Mf~~~~d~~~y~lKPMNCP~H~~if~~~~rSYRdLPlR~aEfg~~hR~E~--SG-~L~GL~RvR~FtqDDaHIFc~~dQ  360 (604)
T PRK12304        284 NMYFTTIDEQEYGIKPMNCVGHIKVYQSDLRSYRDLPLKFFEYGVVHRHEK--SG-VLHGLFRVREFTQDDAHIFCMPSQ  360 (604)
T ss_pred             CCCEEECCCCEEECCCCCCHHHHHHHHCCCCCHHHCCHHHHHCCCEECCCC--CC-CCCCCCCCCCCCCCCCEEECCHHH
T ss_conf             764450577433036779574999986277444435555454353202677--76-634645577897788446548999


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCC--------------------CCE-E---E-
Q ss_conf             14578989999999999841067530378011784434024101101004--------------------833-2---3-
Q gi|254780680|r  295 SFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQ--------------------NLY-R---E-  349 (430)
Q Consensus       295 S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~--------------------~~y-~---E-  349 (430)
                      -.++...+++...++|..+|+.|++ .+++..    ...-=|-|.|--+.                    +.| |   + 
T Consensus       361 i~~Ei~~~l~~~~~vy~~fGf~~~~-~lstrp----ek~~G~de~W~~Ae~~L~~aL~~~g~~y~~~~GegAFYGPKID~  435 (604)
T PRK12304        361 IKEEVLEILDFVDKIMKAFDFSYEM-EISTKP----AKAIGDDEVWEKATKALKEALDENGLKYGIDEGGGAFYGPKIDI  435 (604)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEE-EECCCC----CCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCEEE
T ss_conf             9999999999999999745961999-976886----33479889999999999999996499866574855203211017


Q ss_pred             -E-------EEECC-CCCHH-HHHCCCEEECCCCCCCCEEEEE----CCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCC
Q ss_conf             -7-------53102-10076-4532684733899841010420----043228999999998834689983865822231
Q gi|254780680|r  350 -I-------SSCST-CGNFQ-SRRMNSRYRDPNSKSLKFTHTL----NGSGVAVGRCLIAILENYLNADGSVTIPTVLRP  415 (430)
Q Consensus       350 -v-------~S~Sn-c~D~Q-srRl~iry~~~~~~~~~~~htl----Ngt~~A~~R~l~ailEn~q~~dg~i~iP~~L~p  415 (430)
                       |       -.||. =.||| ..|.++.|.+++|.+ +-+-.+    -||   +-|.++.|+|+|.-.     .|-=|-|
T Consensus       436 ~v~DalgR~wq~~TIQlDf~lPeRF~l~Y~~~dg~~-~rPVmIHRAilGS---~ERfiaiLiEh~~G~-----~P~WLaP  506 (604)
T PRK12304        436 KITDALKRKWQCGTIQVDFNLPERFKLEYTDENNEK-KQPVMIHRAILGS---FERFIGILTEHFAGE-----FPFFIAP  506 (604)
T ss_pred             EEECCCCCHHHHHHHHHHHHCHHHCCCEEECCCCCC-CCCEEEEEECCCC---HHHHHHHHHHHCCCC-----CCCCCCC
T ss_conf             986224889887788887636431573898889983-6778997203577---899999999980899-----9857576


No 21 
>TIGR00418 thrS threonyl-tRNA synthetase; InterPro: IPR002320   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Threonyl-tRNA synthetase (6.1.1.3 from EC) exists as a monomer and belongs to class IIa. The enzyme from Escherichia coli represses the translation of its own mRNA. The crystal structure of the complex between tRNA(Thr) and ThrRS show structural features that reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination . The zinc ion may act to ensure that only amino acids that possess a hydroxyl group attached to the beta-position are activated .; GO: 0004829 threonine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006435 threonyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=99.82  E-value=1.5e-20  Score=173.53  Aligned_cols=355  Identities=19%  Similarity=0.258  Sum_probs=244.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHH-HHHHHHHHHHHH---HHHHHHH--HHH-HHHHH--HHC
Q ss_conf             99999999999999999999999998644-99879999999-999999886444---6666677--888-77443--100
Q gi|254780680|r   36 KNRILIKKIEDIRARRNSNSAQIGQAIAE-GNLSLVDALKN-ETSTLKEQLPIL---EKEEHEV--CSS-LKKLI--SCI  105 (430)
Q Consensus        36 ~rr~l~~e~e~LraerN~lSKeIg~~k~~-~~~~~~~~Lk~-e~~~Lk~eik~l---e~~~~~l--e~e-l~~ll--l~I  105 (430)
                      ...-.+.+++.+.++-|++.+++-.-.++ -..+++.+..+ ....+|..|..-   ......+  +.+ +..++  -.|
T Consensus        38 ~~~~~~~dl~~ie~~m~~~~~~~~~~~~~~~s~~~A~~~f~~~~~~~k~~l~~~~~~~~~~~~~y~~~~~f~dlC~GpHl  117 (595)
T TIGR00418        38 DKSITEEDLEKIEKEMKEIIKKNYPIARLSVSLEEALEAFKEVGEPLKLELLDEIIPNGEAVTVYGQGEAFVDLCRGPHL  117 (595)
T ss_pred             CHHCCHHHHHHHHHHHHHHHHHHCCEEEEEECHHHHHHHHHHHCCHHHHHHHHHCCCCCCCEEEECCCCEEEECCCCCCC
T ss_conf             00027789999999999998640570257724789999998621312267785104566642042252134561579768


Q ss_pred             CCCCCCHHHH-------------CCCCCCCEEEEEEC--CCCCCC--------------CCCC--CCCCHHHHCCCCCHH
Q ss_conf             2258811221-------------13555402420001--565665--------------6662--112202211731000
Q gi|254780680|r  106 PNVPLEEVPI-------------GTSANENILIRSVG--KKPSAI--------------HLSR--EHFEIGEALGLMDFD  154 (430)
Q Consensus       106 PNi~~~~VP~-------------G~de~dNv~i~~~G--~~~~f~--------------f~~k--~H~elge~l~liDfe  154 (430)
                      ||.---.+|.             ..|++....+|-.|  ..-.|.              -.-+  ||..||+.|+|++|+
T Consensus       118 p~~~~~~~~~~~fkL~~~~gaYw~Gd~~n~~LqRiyGn~~~~~~~~k~~L~~yl~~~eEa~~r~PDHRklGKeL~Lf~f~  197 (595)
T TIGR00418       118 PNTSRIKPAQKAFKLEKVAGAYWRGDSKNEMLQRIYGNIDITAFADKKQLAEYLKRLEEAKKREPDHRKLGKELELFSFE  197 (595)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCCEEEECCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCC
T ss_conf             32356676403456654323310268898537888572545014587899999999999742685725675453123458


Q ss_pred             HHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHH-HH---HCCEECC
Q ss_conf             1122216753010564889999999999986223203202123562027889865514224767764-31---0002313
Q gi|254780680|r  155 RATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFC-TT---DGRWLIP  230 (430)
Q Consensus       155 ~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~-~~---d~l~Li~  230 (430)
                      -.   .|+|.+++-.+|+++-.-|.+|.-+.+ .+.||.+|.+|.|.+.+...-+||+.+|.|.||. .+   ..++|=|
T Consensus       198 ~~---~gpG~~~WlPkG~~ir~~ledf~~~~~-~~~Gy~~V~TP~m~~~~l~~~sGH~~~Y~e~Mf~~~~~~~~~~~LkP  273 (595)
T TIGR00418       198 PE---IGPGLPFWLPKGALIRNLLEDFVREKQ-IKRGYEEVETPIMYDSELWEISGHWDHYKERMFPFTEEDNQEFMLKP  273 (595)
T ss_pred             CC---CCCCCEEECCCHHHHHHHHHHHHHHHH-HHCCCCCCCCCEECCCCCHHHHHHHHHCCCCCCCCEEECCCCCCCCC
T ss_conf             32---048741465764678999999999999-87588641574121565424530545034235401010353033456


Q ss_pred             CCCCHHHHHHHHHCCCHHHHCCEEEEEE-CCCCCCC-CCCCCCCCCEEEEEEEEEEEEEECCC-CCCHHHHHHHHHHHHH
Q ss_conf             4541145445342059555042088532-2107884-33554343212222102002121278-6501457898999999
Q gi|254780680|r  231 TSEVSLTNLYSHEIIESKSLPLRFTTLA-PSFRSEA-GSAGRDTRGMLRQHQFWKCELVSITR-EEDSFTEHERMLSCAE  307 (430)
Q Consensus       231 TaEvpL~~~~~~~~l~~~~LPik~~~~s-~cfR~Ea-Gs~GkdtrGl~RvHQF~KVE~~~~~~-pe~S~~~~e~~~~~~~  307 (430)
                      =+=..=.-+|.+....+.+||+|++-+| .|||-|+ |+    ..||-||--||-=.+..||+ +||..+++.+.+....
T Consensus       274 MnCpgH~~i~k~~~~SYR~LP~R~aE~g~~~hR~E~sG~----L~GL~RvR~FT~dDaHifc~d~dQi~~E~~~~~~l~~  349 (595)
T TIGR00418       274 MNCPGHILIFKSSLRSYRDLPLRIAELGTTVHRYEKSGA----LHGLKRVRGFTQDDAHIFCTDEDQIKSEIKNQFRLIQ  349 (595)
T ss_pred             CCCHHHHHHHCCCCCCHHHCCCHHHHCCCEEEEEECCCC----CCHHHHHHHCCCCCCCEEECCHHHHHHHHHHHHHHHH
T ss_conf             775445330017777732335034331860478842542----1010164430699852453786779999999999999


Q ss_pred             HHHHHHCCHHHHCCCCCHHCCCHHHEEE--EEEEECCCC--------------------CCE--------------EEEE
Q ss_conf             9999841067530378011784434024--101101004--------------------833--------------2375
Q gi|254780680|r  308 EILKRLDLHYRVVSLCTGDLGFSACKTY--DLEVWLAGQ--------------------NLY--------------REIS  351 (430)
Q Consensus       308 ~i~~~L~lpyRvv~~~sgdlg~~a~~~~--DiE~w~P~~--------------------~~y--------------~Ev~  351 (430)
                      ++++.+|+-.-.+.+++-|--.  .+||  |-+.|--++                    +.|              |+..
T Consensus       350 ~v~~~fgf~~~~~~LS~R~Pe~--~~Ky~g~d~~W~~~~~~l~~~l~~~~~~yei~~G~~AFYGPKiDf~~~DaL~R~~q  427 (595)
T TIGR00418       350 KVYSKFGFSNYKYELSTRDPEN--DKKYIGEDELWEKAESALEEALKELGVDYEIDEGEGAFYGPKIDFQIKDALGREWQ  427 (595)
T ss_pred             HHHHHHCCCCCEEEEEECCCCC--CCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEECCEEEEEEEECCCCHHH
T ss_conf             9988728842168998717775--45545887899999999999985079840550788113022268887510176425


Q ss_pred             EECCCCCHHH-HHCCCEEECCC--CCCCCEEEEECCCHH-HHHHHHHHHHHHCC
Q ss_conf             3102100764-53268473389--984101042004322-89999999988346
Q gi|254780680|r  352 SCSTCGNFQS-RRMNSRYRDPN--SKSLKFTHTLNGSGV-AVGRCLIAILENYL  401 (430)
Q Consensus       352 S~Snc~D~Qs-rRl~iry~~~~--~~~~~~~htlNgt~~-A~~R~l~ailEn~q  401 (430)
                      -..-=.||+. -|.++.|.+++  ++. +.+-.|.-+-+ ++-|.+++|+|-|-
T Consensus       428 ~~TvQlDf~lPeRF~l~Y~~~dqd~~~-~~Pv~IHra~~GS~ERfi~iL~E~~~  480 (595)
T TIGR00418       428 CATVQLDFELPERFDLTYINEDQDNKE-KRPVMIHRAILGSIERFIAILLEKYA  480 (595)
T ss_pred             CCCEEEECCCCCCCCCEEEEECCCCCC-CCCEEEECCCCHHHHHHHHHHHHHHH
T ss_conf             881488715887203148420367870-06778980440058999999998752


No 22 
>pfam02403 Seryl_tRNA_N Seryl-tRNA synthetase N-terminal domain. This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.
Probab=99.82  E-value=5.2e-19  Score=162.03  Aligned_cols=107  Identities=40%  Similarity=0.596  Sum_probs=102.4

Q ss_pred             CCCHHHHHCCHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             988447851999999999846989-5889999999999999999999999999999999998644998799999999999
Q gi|254780680|r    1 MLDIQWIRQNPEHLDIALKKRHLE-PQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETST   79 (430)
Q Consensus         1 MLDik~IRen~e~v~~~l~~R~~~-~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~   79 (430)
                      |||+++||+||+.|+++|++||.+ .+++.|+++|.+||.+++++++||+++|.+||+||.++++|+  ++++++++++.
T Consensus         1 MlDik~ir~n~~~v~~~l~~R~~~~~~~~~i~~ld~~~r~~~~~~e~L~~~~N~~sk~ig~~~~~~~--~~~~l~~~~~~   78 (108)
T pfam02403         1 MLDIKLIRENPEAVKEKLRKRGVDVLDVDELLELDEERRELQVELEELQAERNELSKEIGKAKKKKE--DAEALIAEVKE   78 (108)
T ss_pred             CCCHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CHHHHHHHHHH
T ss_conf             9888998809999999998829988789999999999999999999999998598999999875774--16889999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             998864446666677888774431002258
Q gi|254780680|r   80 LKEQLPILEKEEHEVCSSLKKLISCIPNVP  109 (430)
Q Consensus        80 Lk~eik~le~~~~~le~el~~lll~IPNi~  109 (430)
                      ++++++.+++++..++++++.+++.|||+|
T Consensus        79 lk~~i~~le~~~~~~e~~l~~~l~~iPNiP  108 (108)
T pfam02403        79 LKDELKALEAELRELEAELDKLLLSIPNIP  108 (108)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             999999999999999999999988389999


No 23 
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=99.80  E-value=1.3e-18  Score=159.03  Aligned_cols=193  Identities=23%  Similarity=0.298  Sum_probs=163.4

Q ss_pred             CCCCCCCCCCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHH
Q ss_conf             56566566621122022117310001122216753010564889999999999986223203202123562027889865
Q gi|254780680|r  130 KKPSAIHLSREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGT  209 (430)
Q Consensus       130 ~~~~f~f~~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gt  209 (430)
                      +.|+ +-+..+| .|.-+-|+|.-      ..||-|.+.--|-+--+-+.+-.-. ++.+-|..++..|.+...+.+..|
T Consensus        13 e~P~-dae~~Sh-~Ll~raG~Ir~------~~sGiy~~LPlg~rvl~Kie~IIr~-em~~iGa~Ev~mp~l~p~elW~~s   83 (570)
T PRK09194         13 ETPA-DAEVISH-QLMLRAGYIRK------LASGIYTYLPLGLRVLRKIENIVRE-EMNKIGAQEVLMPALQPAELWQES   83 (570)
T ss_pred             CCCC-CCCHHHH-HHHHHCCCCCC------CCCCHHHHHHHHHHHHHHHHHHHHH-HHHHCCCEEEECCCCCCHHHHHHC
T ss_conf             7974-3245669-99987067341------4377255424369999999999999-998649879853567977898761


Q ss_pred             HHCHHHHHHHHHHHH----CCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEE
Q ss_conf             514224767764310----0023134541145445342059555042088532210788433554343212222102002
Q gi|254780680|r  210 GQIPKFADDMFCTTD----GRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCE  285 (430)
Q Consensus       210 G~lp~f~~~~y~~~d----~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE  285 (430)
                      |-+..+.+++|+..|    +++|-||.|-.+|.+.++++-.+.+||+++.-+.+-||.|+=.    --||+|..+|-.-.
T Consensus        84 gR~~~~g~el~r~kDR~~~~~~L~PThEE~it~lv~~~i~SYkqLP~~lYQIqtKfRDE~RP----R~GllR~REF~MKD  159 (570)
T PRK09194         84 GRWEKYGPELLRLKDRHGRDFVLGPTHEEVITDLVRNEIKSYKQLPLNLYQIQTKFRDEIRP----RFGLMRGREFIMKD  159 (570)
T ss_pred             CCHHHCCHHHEEEECCCCCEEEECCCCHHHHHHHHHHHHCCHHHCCHHEECCCCEECCCCCC----CCCCHHHHHHHHHC
T ss_conf             88212361346985278985653787389999999985113764680200132333477887----67623456534512


Q ss_pred             EEECCCC-CCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEE
Q ss_conf             1212786-5014578989999999999841067530378011784434024
Q gi|254780680|r  286 LVSITRE-EDSFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTY  335 (430)
Q Consensus       286 ~~~~~~p-e~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~  335 (430)
                      +++|... +...+.++.|..-...||+.|||||++|.--||.||.+.|--|
T Consensus       160 aYSFd~~~e~l~~tY~~~~~AY~~IF~rlgL~~~~v~ADsG~iGG~~ShEF  210 (570)
T PRK09194        160 AYSFHADEESLDETYDAMYQAYSRIFTRLGLDFRAVEADSGAIGGSASHEF  210 (570)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCEEE
T ss_conf             456669989999999999999999999809862999914667588665237


No 24 
>COG0441 ThrS Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=99.73  E-value=1.4e-17  Score=151.30  Aligned_cols=265  Identities=23%  Similarity=0.340  Sum_probs=207.0

Q ss_pred             CCCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHH
Q ss_conf             66211220221173100011222167530105648899999999999862232032021235620278898655142247
Q gi|254780680|r  137 LSREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFA  216 (430)
Q Consensus       137 ~~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~  216 (430)
                      +.+||..||+.++++.|+-   -.|.+++++...|+.+...|.+|+.+.+ .+.||.+|.+|.|++.+...-+|+++++.
T Consensus       188 ~krdHrklg~el~LF~~~~---~~~~G~~~~~pkG~~ir~~le~y~~~~~-~~~Gy~~V~TP~~~~~~l~~~SGH~~~y~  263 (589)
T COG0441         188 KKRDHRKLGKELDLFSFSP---EEGPGLPFWHPKGATIRNLLEDYVRTKL-RSYGYQEVKTPVLADLELWELSGHWDNYK  263 (589)
T ss_pred             CCCCHHHHHHHHCCEEECC---CCCCCCEEECCCCCCHHHHHHHHHHHHH-HHCCCEEECCCEEEECCCCHHCCCHHHCC
T ss_conf             2786476877621434144---4588506987884669999999999898-75585271287363000010112045513


Q ss_pred             HHHHHHH---HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCC-CCCCCCCCCEEEEEEEEEEEEEECCCC
Q ss_conf             6776431---000231345411454453420595550420885322107884-335543432122221020021212786
Q gi|254780680|r  217 DDMFCTT---DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEA-GSAGRDTRGMLRQHQFWKCELVSITRE  292 (430)
Q Consensus       217 ~~~y~~~---d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~Ea-Gs~GkdtrGl~RvHQF~KVE~~~~~~p  292 (430)
                      ++||...   .++.|=|.+=-.-.-+|.+....+.+||+|++.+|.|||-|. |+    ..||.||--|+.=..-.||++
T Consensus       264 e~mf~~~~~~~~~~lKpmNCpgh~~ifk~~~~SYR~LP~r~~E~g~v~R~E~SGa----l~GL~RvR~ftqdD~Hifc~~  339 (589)
T COG0441         264 EDMFLTESDDREYALKPMNCPGHILIFKSGLRSYRELPLRLAEFGYVYRYEKSGA----LHGLMRVRGFTQDDAHIFCTP  339 (589)
T ss_pred             CCCEEECCCCHHHEEEECCCHHHHHHHHCCCCCEECCCHHHHHCCEEECCCCCCH----HHCCCCCCCEEECCCCEECCH
T ss_conf             6606621377233064107876899985378611004404331442211567642----222400113224562014046


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCH-HHHCCCCCHH--CC-------C-----HHHEEEEEEEECC-CCCCEE--------
Q ss_conf             501457898999999999984106-7530378011--78-------4-----4340241011010-048332--------
Q gi|254780680|r  293 EDSFTEHERMLSCAEEILKRLDLH-YRVVSLCTGD--LG-------F-----SACKTYDLEVWLA-GQNLYR--------  348 (430)
Q Consensus       293 e~S~~~~e~~~~~~~~i~~~L~lp-yRvv~~~sgd--lg-------~-----~a~~~~DiE~w~P-~~~~y~--------  348 (430)
                      ++..++....+.....+++.+|+. |++ .+++.+  .|       +     .|.+.+.++.|.. |.+.|-        
T Consensus       340 dQi~~E~~~~~~~i~~v~~~fg~~~y~~-~ls~r~k~ig~d~~W~~a~~~l~~al~~~~~~~~~~~G~gaFyGPKid~~v  418 (589)
T COG0441         340 DQIKDEFKGILELILEVYKDFGFTDYEV-KLSTRPKFIGSDEMWDKAEAALREALKEIGVEYVEEPGEGAFYGPKIDFQV  418 (589)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCEEEE-EEECCCCCCCCHHHHHHHHHHHHHHHHHHCCEEEECCCCEEEECCCCCEEE
T ss_conf             7889999999999999998469753799-996477646873556778899998887608603646873579776642488


Q ss_pred             -----EEEEECC-CCCHHHH-HCCCEEECCCCCCCCEEEEE-CCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCCC
Q ss_conf             -----3753102-1007645-32684733899841010420-0432289999999988346899838658222310
Q gi|254780680|r  349 -----EISSCST-CGNFQSR-RMNSRYRDPNSKSLKFTHTL-NGSGVAVGRCLIAILENYLNADGSVTIPTVLRPY  416 (430)
Q Consensus       349 -----Ev~S~Sn-c~D~Qsr-Rl~iry~~~~~~~~~~~htl-Ngt~~A~~R~l~ailEn~q~~dg~i~iP~~L~py  416 (430)
                           ..--||. -.||+.- |+++.|.++++++ +.+-++ -+..-++-|.+++++|++.   |  ..|.-|-|-
T Consensus       419 ~Dalgr~~q~~TIQlDf~lpeRF~l~Yv~~d~~~-~~PvmiHrai~GSiERfi~iLiE~~~---G--~~P~WLaPv  488 (589)
T COG0441         419 KDALGREWQLGTIQLDFNLPERFDLEYVDEDGEK-KRPVIIHRAILGSIERFIGILLEHYA---G--ALPTWLAPV  488 (589)
T ss_pred             EECCCCCEECCEEEEECCCHHHCEEEEECCCCCC-CCCEEEEECCCHHHHHHHHHHHHHCC---C--CCCCCCCCC
T ss_conf             7356861005617870377242147998577875-38789992464148999999998646---9--887657851


No 25 
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=99.71  E-value=2.7e-16  Score=141.81  Aligned_cols=260  Identities=20%  Similarity=0.256  Sum_probs=219.0

Q ss_pred             CCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHH-HHHHCHHHHHHHH
Q ss_conf             220221173100011222167530105648899999999999862232032021235620278898-6551422476776
Q gi|254780680|r  142 FEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMY-GTGQIPKFADDMF  220 (430)
Q Consensus       142 ~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~-gtG~lp~f~~~~y  220 (430)
                      .++..+-+|+|.   .-|  +|+|+++-.|-.+-+...+++-+ .+.+.|-.++.-|.++-.+.++ ..++.--|...+|
T Consensus        20 ~~vi~~a~l~d~---~~V--kG~~v~~P~g~~iw~~i~~~~~~-~~~~~g~~~~~fP~liP~~~l~kE~~hvegF~pE~~   93 (478)
T PRK08661         20 TDVVKKAELADY---SPV--KGCMVIRPYGYAIWENIQKILDE-MFKETGHENVYFPLLIPESLLQKEAEHIEGFAPEVA   93 (478)
T ss_pred             HHHHHHHCCCCC---CCC--CEEEEECCCHHHHHHHHHHHHHH-HHHHCCCEEEEECCCCCHHHHHHHHHHHCCCCCEEE
T ss_conf             999997187323---688--72799787489999999999999-998639808730240668999866656615674048


Q ss_pred             HH--------HHCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECC-C
Q ss_conf             43--------10002313454114544534205955504208853221078843355434321222210200212127-8
Q gi|254780680|r  221 CT--------TDGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSIT-R  291 (430)
Q Consensus       221 ~~--------~d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~-~  291 (430)
                      .+        ++.++|=||||..++.||+..|-++.|||+++--+..-||-|.     .||-++|..+|---|-..+- +
T Consensus        94 ~VT~~G~~~l~~~l~lrPTsEt~i~~~~~~wI~SyrdLPl~l~Qw~~v~R~E~-----r~r~flR~rEFl~qe~ht~h~t  168 (478)
T PRK08661         94 WVTHGGGEKLEEPLALRPTSETIIYPMFKKWIQSYRDLPLLYNQWVNVVRWEK-----KTRPFLRTREFLWQEGHTAHAT  168 (478)
T ss_pred             EEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCC-----CCCCHHHHHHHHHHCCCCCCCC
T ss_conf             99547875556763108887999999999985236526900020044586578-----8963143426354212011399


Q ss_pred             CCCHHHHHHHHHHHHHHHHH-HHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEEC
Q ss_conf             65014578989999999999-84106753037801178443402410110100483323753102100764532684733
Q gi|254780680|r  292 EEDSFTEHERMLSCAEEILK-RLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRD  370 (430)
Q Consensus       292 pe~S~~~~e~~~~~~~~i~~-~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~  370 (430)
                      .+++.++...|++....|++ .|.||+-+-.=+..|-=+.|..+|.||+.||. ++-.+++.+-+.++=-|+.++|+|.+
T Consensus       169 ~eea~~~~~~~~~~Y~~~~e~~LaiPvi~g~k~~~ekFaGa~~T~~iea~m~d-GkaLQ~gtsH~LGq~fskaf~i~f~d  247 (478)
T PRK08661        169 EEEAEEETLEMLEIYKEFAEDYLAIPVIIGKKTEWEKFAGADYTYTIEAMMPD-GKALQIGTSHYLGQNFAKAFDIKFQD  247 (478)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCEECCCCCCCCCCCCCCCCCEEEEECCC-CCEEECCCEECCCHHHHHHCCCEEEC
T ss_conf             99999999999999999999837875563777830217898654205887268-86311431421622356754969988


Q ss_pred             CCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCC
Q ss_conf             89984101042004322899999999883468998386582223101
Q gi|254780680|r  371 PNSKSLKFTHTLNGSGVAVGRCLIAILENYLNADGSVTIPTVLRPYM  417 (430)
Q Consensus       371 ~~~~~~~~~htlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~pym  417 (430)
                      .+|+ .+|+|+= .=|+- .|+|.|+++.|-+.+| +++|..+-||=
T Consensus       248 ~~g~-~~~~~~t-s~Gis-tR~iga~Im~H~Dd~G-lvlPp~iAP~q  290 (478)
T PRK08661        248 KDGK-LEYVHQT-SWGVS-TRLIGALIMVHGDDKG-LVLPPKIAPIQ  290 (478)
T ss_pred             CCCC-EEEEEEE-CCCHH-HHHHHHHHHHHCCCCC-CCCCHHHCCCC
T ss_conf             9998-8678875-34542-7899999998479986-51784559830


No 26 
>COG0442 ProS Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=99.69  E-value=8.9e-17  Score=145.41  Aligned_cols=262  Identities=23%  Similarity=0.281  Sum_probs=208.5

Q ss_pred             CCCCCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHH
Q ss_conf             56662112202211731000112221675301056488999999999998622320320212356202788986551422
Q gi|254780680|r  135 IHLSREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPK  214 (430)
Q Consensus       135 ~f~~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~  214 (430)
                      +|..-.|. |..+-+++|.      ..+|.|.+.--|-+.-+...+..-. .+.+.|..++.-|.++-.+...-+|++-.
T Consensus        17 da~~~sh~-ll~rAg~i~~------~~~G~y~~lP~g~rv~~kI~~iir~-em~~~G~~Evl~P~L~p~eLwkEs~r~~~   88 (500)
T COG0442          17 DASEWSHQ-LLLRAGMIRK------PVKGLYVWLPLGLRVLEKIENIIRE-EMDKIGAQEVLFPTLIPAELWKESGRWEG   88 (500)
T ss_pred             HHHHHHHH-HHHHCCCEEE------CCCCEEEECCCHHHHHHHHHHHHHH-HHHHCCCEEEECHHCCHHHHHHHHCHHHC
T ss_conf             23799999-9986686020------2571699776589999999999999-99860850883110587899987485630


Q ss_pred             HHHHHHHHHH----CCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECC
Q ss_conf             4767764310----002313454114544534205955504208853221078843355434321222210200212127
Q gi|254780680|r  215 FADDMFCTTD----GRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSIT  290 (430)
Q Consensus       215 f~~~~y~~~d----~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~  290 (430)
                      |..++|++.|    +++|-||+|..++.|+++.+-++.|||+++.-+.+-||.|.    |-++|++|..+|.--|-+.|-
T Consensus        89 f~~El~~v~drg~~~l~L~PTsEe~it~~~~~~i~SYkdLPl~lYQi~~kfRdE~----rpr~gllR~REF~mkdaySfh  164 (500)
T COG0442          89 FGPELFRVKDRGDRPLALRPTSEEVITDMFRKWIRSYKDLPLKLYQIQSKFRDEK----RPRFGLLRGREFLMKDAYSFH  164 (500)
T ss_pred             CCHHHEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCC----CCCCCCCCHHEEEECCCCCCC
T ss_conf             3644489971699634357886899999999986556518812101345884334----688773000203301112102


Q ss_pred             -CCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHC-CCEE
Q ss_conf             -86501457898999999999984106753037801178443402410110100483323753102100764532-6847
Q gi|254780680|r  291 -REEDSFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRM-NSRY  368 (430)
Q Consensus       291 -~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl-~iry  368 (430)
                       +.+++.+..++|++....||..|++.|+.+.--+|-+|...+  +-++|-||.- +=..+..|-++.+.-++-- .+.|
T Consensus       165 ~~~e~a~~~y~~~~~~Y~~if~~i~l~~~~~~ad~g~~Gg~~S--~eF~~l~pd~-ge~qi~ts~~y~aN~e~a~~~~~~  241 (500)
T COG0442         165 ADEEDAEETYEKMLDAYSRIFLRLPLIFGPVPADEGFIGGSYS--HEFEALMPDG-GEDQIATSHHYGANFEKAFIDIKF  241 (500)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCC--EEEEEECCCC-CCCEEEEECCHHHHHHHHCCCCCC
T ss_conf             8989999999999999999998589538862566778887653--6999985689-854799806266668774467775


Q ss_pred             ECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCC
Q ss_conf             3389984101042004322899999999883468998386582223
Q gi|254780680|r  369 RDPNSKSLKFTHTLNGSGVAVGRCLIAILENYLNADGSVTIPTVLR  414 (430)
Q Consensus       369 ~~~~~~~~~~~htlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~  414 (430)
                      +++.+....|+||=  |.....|.+.+++=-+-..+|.| .|..+-
T Consensus       242 ~~~~~~~~~~v~t~--s~~~s~r~~~~~i~i~GDn~G~v-~Pp~vA  284 (500)
T COG0442         242 EDEEEGELEYVHTT--SYGISTRIIGAAILIHGDNEGLV-LPPIVA  284 (500)
T ss_pred             CCCCCCCCEEECCC--CEEEEEEEEEEEEEEECCCCCCC-CCCHHC
T ss_conf             56665541475146--26887400158999714887764-875004


No 27 
>KOG2324 consensus
Probab=99.61  E-value=6.7e-15  Score=131.44  Aligned_cols=269  Identities=24%  Similarity=0.353  Sum_probs=208.4

Q ss_pred             CHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHH
Q ss_conf             20221173100011222167530105648899999999999862232032021235620278898655142247677643
Q gi|254780680|r  143 EIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCT  222 (430)
Q Consensus       143 elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~  222 (430)
                      ++....|++-      -|-.++|-+.--|.|----|++. +|...+.-|-..|..|.+-..+..+.||-|.....++|+.
T Consensus        29 ~LL~e~GfI~------ps~~G~yq~LPlg~R~~~K~~~~-l~~~mqs~Ga~kIslp~ls~~~LWekTgRw~~~gsEl~rl  101 (457)
T KOG2324          29 ELLQEVGFIR------PSSPGLYQLLPLGLRVLNKLCRL-LDNEMQSGGAQKISLPILSSKELWEKTGRWDAMGSELFRL  101 (457)
T ss_pred             HHHHHHCCCC------CCCCCCEEECCCHHHHHHHHHHH-HHHHHHHCCCEEEEECCCCHHHHHHHCCCCCCCCHHHEEE
T ss_conf             9999707101------48987012130037999999999-9999872367057404468689987618511246045375


Q ss_pred             HH----CCEECCCCCCHHHHHHHHHCC-CHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCC-CCCHH
Q ss_conf             10----002313454114544534205-9555042088532210788433554343212222102002121278-65014
Q gi|254780680|r  223 TD----GRWLIPTSEVSLTNLYSHEII-ESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITR-EEDSF  296 (430)
Q Consensus       223 ~d----~l~Li~TaEvpL~~~~~~~~l-~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~-pe~S~  296 (430)
                      .|    ..||.||.|-.+|++.+..+= .+++|||++.-+++-||.|--..|    ||.|-.||-.-.|+.|.. +|.+.
T Consensus       102 ~Dr~gkq~cL~pThEE~iT~lmat~~~lsykqlPi~vYQigrKfRDElrpRf----GLlRgREFlMKDmYsFd~~~etA~  177 (457)
T KOG2324         102 HDRKGKQMCLTPTHEEDITALMATYIPLSYKQLPIRVYQIGRKFRDELRPRF----GLLRGREFLMKDMYSFDSDEETAQ  177 (457)
T ss_pred             ECCCCCEECCCCCHHHHHHHHHHHCCCCCCCCCCEEEEEECHHHHHCCCCCC----CCHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             1047877305775489999999862743220286776650545441347542----301247888765330258888999


Q ss_pred             HHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEE--------CCCC-----CC---EEEEEEECCCCC--
Q ss_conf             57898999999999984106753037801178443402410110--------1004-----83---323753102100--
Q gi|254780680|r  297 TEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVW--------LAGQ-----NL---YREISSCSTCGN--  358 (430)
Q Consensus       297 ~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w--------~P~~-----~~---y~Ev~S~Snc~D--  358 (430)
                      +.++.+.+....||++|++||=-|...+|++|-.-+.-|-+-.=        -|+=     ..   .--+.||-+|-+  
T Consensus       178 qTy~~v~~aY~~iFkqL~~pfVkv~AdsG~iGG~vShEfhl~~~vgED~l~~C~~C~~s~n~e~~~~sk~~~Cp~C~~~~  257 (457)
T KOG2324         178 QTYQLVDQAYDRIFKQLGLPFVKVWADSGDIGGEVSHEFHLIHPVGEDTLMSCPSCGYSKNSEDLDLSKIASCPKCNEGR  257 (457)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCEEEEEEECCCCCCCCCEEECCCCCCCCCHHHHCCCCCCCCCCCCCCC
T ss_conf             99999999999999973997699860356647610125752576675003446767755760121377656687656777


Q ss_pred             -----------------HHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCCCCEE
Q ss_conf             -----------------764532684733899841010420043228999999998834689983865822231018801
Q gi|254780680|r  359 -----------------FQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAILENYLNADGSVTIPTVLRPYMNNLA  421 (430)
Q Consensus       359 -----------------~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~pym~g~~  421 (430)
                                       =-|.-||.+|-+..|| .+++|+- .-|+-|.|+|+|++|---.++| ++-|..+-||=  .-
T Consensus       258 L~~~~~IEVgHtF~LG~kYS~~lna~f~~~~gK-pe~l~Mg-CyGIGVtRllaAa~evls~~~~-lrwP~~iAPy~--vc  332 (457)
T KOG2324         258 LTKTKSIEVGHTFLLGTKYSKPLNAKFVNVEGK-PEFLHMG-CYGIGVTRLLAAAAEVLSDDKG-LRWPSLIAPYK--VC  332 (457)
T ss_pred             CCCCCCEEEEEEEEECCCCCCCCCCEEEEECCC-CCEEEEC-CEECCHHHHHHHHHHHHCCCCC-CCCCCCCCCCE--EE
T ss_conf             511243477778871430154347655440598-4068740-2000489899999998156554-31500027513--47


Q ss_pred             EECCCC
Q ss_conf             307334
Q gi|254780680|r  422 VIKKEH  427 (430)
Q Consensus       422 ~i~~~~  427 (430)
                      .|.|+.
T Consensus       333 li~pk~  338 (457)
T KOG2324         333 LIGPKK  338 (457)
T ss_pred             EECCCC
T ss_conf             853688


No 28 
>PRK00960 seryl-tRNA synthetase; Provisional
Probab=99.59  E-value=3.8e-14  Score=125.88  Aligned_cols=281  Identities=21%  Similarity=0.338  Sum_probs=213.5

Q ss_pred             EEEEECCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCH
Q ss_conf             42000156566566621122022117310001122216753010564889999999999986223203202123562027
Q gi|254780680|r  124 LIRSVGKKPSAIHLSREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRD  203 (430)
Q Consensus       124 ~i~~~G~~~~f~f~~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~  203 (430)
                      +|.. ..++.+.|. .|--+.++++||+-     +-+|-+=.++.-..|.|.||+-++.++..+.+-||.++.-|-+|-=
T Consensus       181 iv~e-s~~re~~F~-~DPTeea~k~GWvK-----~f~gRGQW~y~P~~t~LFRafE~ii~Ee~i~~lGf~e~lFPKLipl  253 (516)
T PRK00960        181 IVSE-SAPREITFD-GDPTEEAEKLGWVK-----RFPGRGQWFYTPPMAKLFRAFEEIILEECIEKLGFDECLFPKLIPL  253 (516)
T ss_pred             CCCC-CCCCCCCCC-CCHHHHHHHCCCHH-----CCCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCHH
T ss_conf             1035-677433578-98279998626042-----1888874243775889999999999999743237610001345529


Q ss_pred             HHHHHHHHCHHHHHHHHHHH----H-------CCEECCCCCCHH----------------------HHHHHHHCCCHHHH
Q ss_conf             88986551422476776431----0-------002313454114----------------------54453420595550
Q gi|254780680|r  204 EAMYGTGQIPKFADDMFCTT----D-------GRWLIPTSEVSL----------------------TNLYSHEIIESKSL  250 (430)
Q Consensus       204 ~~~~gtG~lp~f~~~~y~~~----d-------~l~Li~TaEvpL----------------------~~~~~~~~l~~~~L  250 (430)
                      ++|...|++----+.||++-    |       --++.=|-|||+                      =-++.+++++.+.|
T Consensus       254 evm~kmryleGlp~gmYYVCpPKRDPe~feef~~e~~i~~EiPi~~lKe~l~~P~yvlapAQCePFy~fl~~e~v~~d~l  333 (516)
T PRK00960        254 DVMYKMRYLEGLPEGMYYVCPPKRDPEMFEEFVNEMMIKKEIPIDLLKEKLRDPGYVLAPAQCEPFYQFLDHELVDVDEL  333 (516)
T ss_pred             HHHHHHCCCCCCCCCCEEECCCCCCHHHHHHHHHHHEEECCCCHHHHHHHHCCCCCEEEECCCCCHHHHHCCCCCCCCCC
T ss_conf             99977330126998727866998986899999777334053668999986128861351024993788736772565558


Q ss_pred             CCEEEEEE-CCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCH-HHHCCCC-----
Q ss_conf             42088532-2107884335543432122221020021212786501457898999999999984106-7530378-----
Q gi|254780680|r  251 PLRFTTLA-PSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLH-YRVVSLC-----  323 (430)
Q Consensus       251 Pik~~~~s-~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lp-yRvv~~~-----  323 (430)
                      |+|++--| ..||=|.|.    .+||=|||.|..||++.+-+||--...-+..+..++.+-+.|+|- +|.|-.-     
T Consensus       334 Pik~FDrSGwtyRwE~GG----~~GleRV~EF~RiE~VW~gtpe~ve~~r~~~~~y~~~~ae~LdLE~w~ev~ddPfyle  409 (516)
T PRK00960        334 PIKFFDKSGWTYRWEGGG----AKGLDRVNEFLRIECVWMGTPEFVEEVRDDTLKYAHILAEKLDLEYWTEVGDDPFYLE  409 (516)
T ss_pred             CEEEEECCCCEEEECCCC----CCCHHHHHHHHEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHCHHHHEEECCCCHHHC
T ss_conf             657885588626404787----4323555010147778846889999998889999999887743244223056750322


Q ss_pred             -----CHHCCCHHHEEEEEEEECCC---CCCEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             -----01178443402410110100---4833237531021007645326847338998410104200432289999999
Q gi|254780680|r  324 -----TGDLGFSACKTYDLEVWLAG---QNLYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIA  395 (430)
Q Consensus       324 -----sgdlg~~a~~~~DiE~w~P~---~~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~a  395 (430)
                           ..+.-++..-|||.|+|+|.   .++|.|++|+|--+|---.--||  |+..|.+   +.| ..||+-+.|..++
T Consensus       410 gr~~e~r~iE~p~vp~ye~~~~LP~~~~e~k~v~v~s~nVhG~hf~eGF~V--K~~~g~~---~Wt-GCtG~GL~RWv~g  483 (516)
T PRK00960        410 GRKLEDRGIEFPDVPKYEMRLWLPHIKEERKGVAVTSANIHGTHFVEGFNV--KDYKGRK---LWT-GCTGVGLTRWVIG  483 (516)
T ss_pred             CCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEECCCCCCCCCCC--EECCCCE---EEC-CCCCCCHHHHHHH
T ss_conf             565445564368888546799657647767726888863147535676522--0035873---113-7764457899999


Q ss_pred             HHHHCCC-CCCCEECCCCCCCCCCCEEEEC
Q ss_conf             9883468-9983865822231018801307
Q gi|254780680|r  396 ILENYLN-ADGSVTIPTVLRPYMNNLAVIK  424 (430)
Q Consensus       396 ilEn~q~-~dg~i~iP~~L~pym~g~~~i~  424 (430)
                      .|-+|-- .|.   -|+-.+.-.|++..+.
T Consensus       484 FLAQ~Gfd~~~---WPe~i~~rvge~pe~~  510 (516)
T PRK00960        484 FLAQKGFDPDN---WPEEIRKRVGELPEIP  510 (516)
T ss_pred             HHHHCCCCCCC---CCHHHHHHHHCCCCCC
T ss_conf             99870798121---6499998862567665


No 29 
>KOG1637 consensus
Probab=99.55  E-value=3e-14  Score=126.65  Aligned_cols=246  Identities=23%  Similarity=0.366  Sum_probs=186.4

Q ss_pred             CCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHH
Q ss_conf             62112202211731000112221675301056488999999999998622320320212356202788986551422476
Q gi|254780680|r  138 SREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFAD  217 (430)
Q Consensus       138 ~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~  217 (430)
                      -+||--||....|+=|..-+  .||  +|..-.||+.--+|+.|+-.. -+++||++|++|.|-|....+.+|++...++
T Consensus       162 ~rdHRkig~~qeLfff~~lS--PGS--~FflP~G~~iyN~Lv~fir~e-y~~rGf~EVitPniy~~~LWe~SGHwqnY~e  236 (560)
T KOG1637         162 KRDHRKIGKEQELFFFHELS--PGS--CFFLPHGTRIYNTLVDFIRAE-YRKRGFTEVITPNIYNKKLWETSGHWQNYSE  236 (560)
T ss_pred             HHHHHHHHHHHHHEEECCCC--CCC--EEECCCCCHHHHHHHHHHHHH-HHHCCCCEECCCCHHHHHHHHHCCCHHHHHH
T ss_conf             10055540222202413579--862--453148642788999999999-8753874322722121566653252555443


Q ss_pred             HHHHHH---HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCC-CCCCCCCCCEEEEEEEEEEEEEECCCCC
Q ss_conf             776431---000231345411454453420595550420885322107884-3355434321222210200212127865
Q gi|254780680|r  218 DMFCTT---DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEA-GSAGRDTRGMLRQHQFWKCELVSITREE  293 (430)
Q Consensus       218 ~~y~~~---d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~Ea-Gs~GkdtrGl~RvHQF~KVE~~~~~~pe  293 (430)
                      +||..+   |.+-|-|--=-..+-|++.+-....+||+|++.+++--|.|+ |+    ..||-||.-|..=.-..||+|+
T Consensus       237 nmF~~e~eke~~~LKPMNCPgHcLmf~~r~rS~reLPlR~aDFg~LHRnE~SGa----LsGLTRvRrFqQDDaHIFCt~~  312 (560)
T KOG1637         237 NMFKFEVEKEEFALKPMNCPGHCLMFAHRDRSYRELPLRFADFGVLHRNEASGA----LSGLTRVRRFQQDDAHIFCTPD  312 (560)
T ss_pred             HCEEEEECHHHHCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCC----CCCCCEEEEECCCCCEEEECCC
T ss_conf             101231010332258668975301336677427447842267522530545642----3221011011015715885576


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCHHHHCCCCC---HHCCCHHHEEEEEEEECC--------------------CCCC-EEE
Q ss_conf             0145789899999999998410675303780---117844340241011010--------------------0483-323
Q gi|254780680|r  294 DSFTEHERMLSCAEEILKRLDLHYRVVSLCT---GDLGFSACKTYDLEVWLA--------------------GQNL-YRE  349 (430)
Q Consensus       294 ~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~s---gdlg~~a~~~~DiE~w~P--------------------~~~~-y~E  349 (430)
                      +-+.+....++..+..|.-+|.-|++. ++|   +=+|       |+|+|--                    |-+. |+-
T Consensus       313 Qi~~Eik~~l~fl~~vY~~fgf~f~l~-lSTRPe~~lG-------~l~~Wd~AE~~L~~al~e~g~pw~lN~GDGAFYGP  384 (560)
T KOG1637         313 QVKEEIKGCLDFLDYVYGVFGFTFKLN-LSTRPEKFLG-------DLETWDEAEFKLEEALNESGEPWVLNPGDGAFYGP  384 (560)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCEEE-ECCCHHHHCC-------CHHHHHHHHHHHHHHHHHHCCCCEECCCCCCEECC
T ss_conf             379999879999999986125420257-4167587665-------78889999999999999709971422898530264


Q ss_pred             -------------EEEECCCCCHHHH-HCCCEEECCCCCC--CCEEEE-ECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             -------------7531021007645-3268473389984--101042-0043228999999998834689
Q gi|254780680|r  350 -------------ISSCSTCGNFQSR-RMNSRYRDPNSKS--LKFTHT-LNGSGVAVGRCLIAILENYLNA  403 (430)
Q Consensus       350 -------------v~S~Snc~D~Qsr-Rl~iry~~~~~~~--~~~~ht-lNgt~~A~~R~l~ailEn~q~~  403 (430)
                                   ---+|--.|||.- |-+..|++.+|..  .-.+|- +-||   +-|+++-|+|+|-+.
T Consensus       385 KIDi~l~Dal~r~hQcaTIQLDFqLP~rFdL~y~~~~g~~erPVmIHRAIlGS---vERmiaiL~E~~~gk  452 (560)
T KOG1637         385 KIDITLDDALGRKHQCATIQLDFQLPIRFDLEYETEDGDLERPVMIHRAILGS---VERMIAILLESYGGK  452 (560)
T ss_pred             EEEEEHHHHCCCCCCEEEEEECCCCHHHCCCEEECCCCCCCCHHHHHHHHHHH---HHHHHHHHHHHHCCC
T ss_conf             33257243327610102566313673331751104666523123589987521---999999999970799


No 30 
>PRK04173 glycyl-tRNA synthetase; Provisional
Probab=99.39  E-value=5.8e-12  Score=109.66  Aligned_cols=255  Identities=18%  Similarity=0.272  Sum_probs=188.1

Q ss_pred             HHHHCC--CCCEEECCHHHHHHHHHHHHHHHHHHHHC-CCCEEHHHHHCCHHHHHHHHHCHHHHHHHH---------HH-
Q ss_conf             122216--75301056488999999999998622320-320212356202788986551422476776---------43-
Q gi|254780680|r  156 ATKLSG--ARFSVLTGHLAHLERALGQFMIDLHTSEH-GYTEVSAPLLVRDEAMYGTGQIPKFADDMF---------CT-  222 (430)
Q Consensus       156 a~kvsG--srF~~Lkg~~A~Le~ALi~y~ld~~~~~~-Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y---------~~-  222 (430)
                      ++.|-|  ++||=|=--|+.|-+.+++..-+..+.++ +..++-.|.|+++.++.++||+..|.|-|-         +. 
T Consensus        22 ssEIYGG~ag~~DyGPlG~~LK~Ni~~~W~~~fv~~~~~~~~id~~ii~~~~V~~ASGHv~~F~D~~v~c~~~~~r~RaD  101 (460)
T PRK04173         22 SSEIYGGLAGFWDYGPLGVELKNNIKKAWWKSFVQERPDVVGIDSPIIMPPEVWKASGHVDNFSDPLVECKKCKKRYRAD  101 (460)
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHCCCCCCCCCCCEEECCCCCCEECHH
T ss_conf             73003781236155853599999999999999865258778861444489878544677465676234757678363016


Q ss_pred             ---HH-------------------------------CC------EE-----C-CCCCCHHHHHHHHH-------------
Q ss_conf             ---10-------------------------------00------23-----1-34541145445342-------------
Q gi|254780680|r  223 ---TD-------------------------------GR------WL-----I-PTSEVSLTNLYSHE-------------  243 (430)
Q Consensus       223 ---~d-------------------------------~l------~L-----i-~TaEvpL~~~~~~~-------------  243 (430)
                         ++                               ++      .|     | |++.-...+|.|-|             
T Consensus       102 ~Lie~~~~~~~~~~~~~~l~~~i~~~~i~cP~cg~~~lt~~~~FNLMF~T~iG~~~~~~~~~YLRPETAQGiFvnFk~v~  181 (460)
T PRK04173        102 HLIEEYLGIDAEGLSNEELEELIEENNIKCPECGGENWTEVRQFNLMFKTFIGPVEDSSSLGYLRPETAQGIFVNFKNVL  181 (460)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEECHHHHHHHHHHHHHHH
T ss_conf             77666532012335899999999970887999999677544312055575135566777502316044104566119999


Q ss_pred             CCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCH---HHHC
Q ss_conf             0595550420885322107884335543432122221020021212786501457898999999999984106---7530
Q gi|254780680|r  244 IIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLH---YRVV  320 (430)
Q Consensus       244 ~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lp---yRvv  320 (430)
                      -..-..||.-.+-++.+||-|....    .||||+.+|+..|+=.||+|+++.++++..+.....++.+||++   .|.-
T Consensus       182 ~~~r~KlPFgiaQIGKaFRNEIsPr----~~lfR~REFeQmEiE~F~~P~~~~e~~~yw~~~~~~fl~~lGi~~~~lR~r  257 (460)
T PRK04173        182 RTARKKLPFGIAQIGKSFRNEITPR----NFIFRTREFEQMELEFFVKPGTDEEWFAYWIALRKNFLLDLGIDPENLRFR  257 (460)
T ss_pred             HHCCCCCCEEEEECCCCCCCCCCCC----CCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHEEEE
T ss_conf             9717788804310040012430655----451223455552433105867458999999999999999839988994786


Q ss_pred             CCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHH------CCCEEECCCCCCCCEEEEECCCHHHHHHHHH
Q ss_conf             3780117844340241011010048332375310210076453------2684733899841010420043228999999
Q gi|254780680|r  321 SLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRR------MNSRYRDPNSKSLKFTHTLNGSGVAVGRCLI  394 (430)
Q Consensus       321 ~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrR------l~iry~~~~~~~~~~~htlNgt~~A~~R~l~  394 (430)
                      .-...+|..=|..++|+|.-+|.  .|.|+.-++|=|||-=.+      -+..|.+...+..-.+|-+- +..-+.|++-
T Consensus       258 ~h~~~elAHYa~~~~D~E~~~~~--Gw~E~~Gia~RtdyDL~~H~~~Sg~~L~~~d~~~~~k~iPhVIE-pS~GvdR~~l  334 (460)
T PRK04173        258 EHLPEELAHYSKATWDIEYKFPF--GWGELEGIANRTDYDLSRHSKHSGEDLSYFDQETGEKYIPYVIE-PSFGLDRLFL  334 (460)
T ss_pred             ECCCHHHCCCCHHHEEEEEECCC--CEEEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCCEECCEEEE-ECCCCCHHHH
T ss_conf             30613420002200558994589--82887664064210278898744887179822558561340564-0467108999


Q ss_pred             HHHHHCCCCC----C----CEECCCCCCCCC
Q ss_conf             9988346899----8----386582223101
Q gi|254780680|r  395 AILENYLNAD----G----SVTIPTVLRPYM  417 (430)
Q Consensus       395 ailEn~q~~d----g----~i~iP~~L~pym  417 (430)
                      |+|++--.++    +    ..++|..|-||-
T Consensus       335 a~L~~ay~ee~~~~~e~R~vL~l~p~lAPik  365 (460)
T PRK04173        335 AFLEDAYTEEELGDGDKRTVLRLPPALAPVK  365 (460)
T ss_pred             HHHHHHHHHHCCCCCCEEEEEECCCCCCCEE
T ss_conf             9998765200047875058996266457716


No 31 
>TIGR00408 proS_fam_I prolyl-tRNA synthetase; InterPro: IPR004499   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by IPR002314 from INTERPRO, which recognises tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi (Lyme desease spirochete). The other family, IPR004500 from INTERPRO, includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis sp.  (strain PCC6803), and one of the two prolyl-tRNA synthetases of Saccharomyces cerevisiae (Baker's yeast).; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=99.29  E-value=1.4e-11  Score=106.90  Aligned_cols=258  Identities=20%  Similarity=0.285  Sum_probs=208.1

Q ss_pred             CHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHC-------------------CCCEEHHHHHCCH
Q ss_conf             202211731000112221675301056488999999999998622320-------------------3202123562027
Q gi|254780680|r  143 EIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEH-------------------GYTEVSAPLLVRD  203 (430)
Q Consensus       143 elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~-------------------Gy~~v~~P~lv~~  203 (430)
                      +|.++=.|+|..--+  .|  .+++..-|=.+-+...+. +|..+...                   |..+++-|.||-.
T Consensus        14 ~il~kAel~d~RypV--KG--~~v~~P~g~~iw~~iq~~-~~~~~~~~~~~~~~~L~~F~P~~~~~Y~h~~v~fP~L~p~   88 (533)
T TIGR00408        14 QILQKAELIDYRYPV--KG--CYVFLPYGFKIWENIQKI-LRDKLDEIKLKDKVILKKFIPIESLPYGHEEVYFPMLIPE   88 (533)
T ss_pred             HHHHCCEEEEECCCC--CC--EEEECCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHEECCCCCCH
T ss_conf             987305576641760--10--378459877899999999-9999987643546766405677777777001005644525


Q ss_pred             HHHHHHH-HCHHHHHHHHHHH--------HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCC
Q ss_conf             8898655-1422476776431--------000231345411454453420595550420885322107884335543432
Q gi|254780680|r  204 EAMYGTG-QIPKFADDMFCTT--------DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRG  274 (430)
Q Consensus       204 ~~~~gtG-~lp~f~~~~y~~~--------d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrG  274 (430)
                      +.+.-=+ |--=|++++|.++        +-|-|=||||.++.+||+..+..+.|||||+--+..-||-|.    |.||=
T Consensus        89 ~~L~KEk~HikGF~pEv~wi~~~G~~~L~~pLaLRPTSEt~~y~m~~kWv~sy~DLPlk~nQw~~vfR~E~----kHTRP  164 (533)
T TIGR00408        89 SELEKEKDHIKGFEPEVYWITHGGLKKLDEPLALRPTSETAMYNMYKKWVKSYRDLPLKINQWVNVFRYEK----KHTRP  164 (533)
T ss_pred             HHHHHHCCCCCCCCCHHHHEECCCCCCCCCCCEECCCCHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCC----CCCCC
T ss_conf             57863213568858400210103777246750125861788876578785121588768984358898021----78786


Q ss_pred             EEEEEEEE-EEEEE-ECCCCCCHHHHHHHHHHHHHHHHH-HHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEE
Q ss_conf             12222102-00212-127865014578989999999999-8410675303780117844340241011010048332375
Q gi|254780680|r  275 MLRQHQFW-KCELV-SITREEDSFTEHERMLSCAEEILK-RLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREIS  351 (430)
Q Consensus       275 l~RvHQF~-KVE~~-~~~~pe~S~~~~e~~~~~~~~i~~-~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~  351 (430)
                      ++|+-+|. =-|-. ++.+.++|.+.-..++++..++|. .|+|||=|-.=|--|==+.|.-|+-+|+.||--++=.=++
T Consensus       165 flR~rEf~twqE~HT~H~t~~eAee~v~~~~~~Yk~f~~~~LaIP~~~g~k~E~eKFaGA~~T~~~e~imPDgG~~LQ~A  244 (533)
T TIGR00408       165 FLRTREFLTWQEAHTAHATAEEAEEEVLKALDLYKEFIENLLAIPYFVGRKSEKEKFAGAEYTWTFETIMPDGGRTLQIA  244 (533)
T ss_pred             CHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCEEEEEECCCCCEEHHHH
T ss_conf             10233321010001314377788999999999889997502886468714887554788762235675247765001221


Q ss_pred             EECCCCCHHHHHCCCEEECCCC---CCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEECCCCC
Q ss_conf             3102100764532684733899---8410104200432289999999988346899838658222
Q gi|254780680|r  352 SCSTCGNFQSRRMNSRYRDPNS---KSLKFTHTLNGSGVAVGRCLIAILENYLNADGSVTIPTVL  413 (430)
Q Consensus       352 S~Snc~D~QsrRl~iry~~~~~---~~~~~~htlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L  413 (430)
                      -.=|.+|=-||-=+|.|.++.|   .+ .|+|-- .=|+ ..|+|+||+=-|=++-|-| +|=-+
T Consensus       245 TsH~LGqnF~K~F~i~fe~p~Gs~~~~-~~ayq~-s~G~-StR~igali~~HsD~~GLV-LPp~v  305 (533)
T TIGR00408       245 TSHDLGQNFAKTFDIKFENPTGSDMDK-VYAYQT-SYGI-STRVIGALILIHSDEKGLV-LPPRV  305 (533)
T ss_pred             HHHHHHCCCEEEEEEEEECCCCCCCCC-CCCEEC-CCCH-HHHHHHHEEEEECCCCCCC-CCCCC
T ss_conf             211330354020367887788897641-010010-1335-7887545000122677751-67012


No 32 
>TIGR00409 proS_fam_II prolyl-tRNA synthetase; InterPro: IPR004500   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Prolyl-tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form, is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa.    This family includes the enzyme from Escherichia coli that contains all three of the conserved consensus motifs characteristic of class II aminoacyl-tRNA synthetases  and the enzyme from the spirochete Borrelia burgdorferi.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=99.07  E-value=2.2e-10  Score=97.93  Aligned_cols=230  Identities=21%  Similarity=0.253  Sum_probs=181.0

Q ss_pred             HCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC-CCEEHHHHHCC-HHHHHHHHHCHHHHH---HHHHHHH----CCEEC
Q ss_conf             216753010564889999999999986223203-20212356202-788986551422476---7764310----00231
Q gi|254780680|r  159 LSGARFSVLTGHLAHLERALGQFMIDLHTSEHG-YTEVSAPLLVR-DEAMYGTGQIPKFAD---DMFCTTD----GRWLI  229 (430)
Q Consensus       159 vsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~G-y~~v~~P~lv~-~~~~~gtG~lp~f~~---~~y~~~d----~l~Li  229 (430)
                      =.|||-|-+.--|.+-=.-.-|-.-.. ..+.| -.+++-|.+.. .+.+..+|-|.+...   .+++..|    +++|-
T Consensus        35 ~~~SGlY~~LPL~~rVL~Kv~~ivree-M~~~GGA~E~~lp~~~~la~LW~~SGRW~~YG~seGELl~lkDR~~r~f~Lg  113 (620)
T TIGR00409        35 RLGSGLYNWLPLGLRVLKKVENIVREE-MNKDGGAIEVLLPALQPLAELWQESGRWDTYGPSEGELLRLKDRKGREFVLG  113 (620)
T ss_pred             ECCCCHHHHHHHHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEECCCCCCCCC
T ss_conf             243414456578999999889999986-2267853346676677899987540753246865433667652688873567


Q ss_pred             CCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCC-CHHHHHHHHHHHHHH
Q ss_conf             3454114544534205955504208853221078843355434321222210200212127865-014578989999999
Q gi|254780680|r  230 PTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREE-DSFTEHERMLSCAEE  308 (430)
Q Consensus       230 ~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe-~S~~~~e~~~~~~~~  308 (430)
                      ||-|=-+|.+.+++|=.+.+||+.+.-..+=||-|.==.+    ||.|--+|=.=.-++|-+.+ .-.+.+..|=+-..+
T Consensus       114 pT~EEvIT~l~~~~i~SYKqLP~~lYQI~tKFRDEiRPRF----Gl~RgREFiMKDAYSFH~~~ESL~~ty~~m~~aY~~  189 (620)
T TIGR00409       114 PTHEEVITDLVRNEIKSYKQLPLNLYQIQTKFRDEIRPRF----GLLRGREFIMKDAYSFHSDEESLDATYQKMDQAYSN  189 (620)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCEECCCCCCCCCCCCCC----CCCCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             8665568999999875453068301004512144204887----600012323024255447876799998899999999


Q ss_pred             HHHHHCCHHH-HCCCCCHH-CCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEE-------CCCCCCCCEE
Q ss_conf             9998410675-30378011-7844340241011010048332375310210076453268473-------3899841010
Q gi|254780680|r  309 ILKRLDLHYR-VVSLCTGD-LGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYR-------DPNSKSLKFT  379 (430)
Q Consensus       309 i~~~L~lpyR-vv~~~sgd-lg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~-------~~~~~~~~~~  379 (430)
                      ||+.|||+|| +|.-=||| +|-++|+=|-+=+    +-.==+|.+|..|+||=|--..+.+.       +........+
T Consensus       190 IF~rlGldFR~iV~ADSGdaIGG~~S~EF~vL~----~~GEDti~~~~h~~dyaAlNiE~A~~~~~~~P~~~~~~~~~~~  265 (620)
T TIGR00409       190 IFSRLGLDFRPIVQADSGDAIGGSASHEFMVLA----ESGEDTIVYSDHESDYAALNIELAEALKPGEPRNAPTAELKKV  265 (620)
T ss_pred             HHHHCCCCCCEEEEECCCCCCCCCCCHHHHHHH----HCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCHHHCCCCC
T ss_conf             998658982106871578757888625678866----4589617886257651232367776425788750113314454


Q ss_pred             EEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             420043228999999998834689
Q gi|254780680|r  380 HTLNGSGVAVGRCLIAILENYLNA  403 (430)
Q Consensus       380 htlNgt~~A~~R~l~ailEn~q~~  403 (430)
                      ||=|-|-      +.-++|-.+.+
T Consensus       266 ~tPN~~t------i~~~~~~f~~~  283 (620)
T TIGR00409       266 DTPNTKT------IAELVEFFNLP  283 (620)
T ss_pred             CCCCCHH------HHHHHHHHCCC
T ss_conf             7744111------89999986788


No 33 
>COG0423 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=99.04  E-value=5.1e-09  Score=87.74  Aligned_cols=249  Identities=18%  Similarity=0.306  Sum_probs=174.2

Q ss_pred             CCCEEECCHHHHHHHHHHHHHHHHHHHH-CCCCEEHHHHHCCHHHHHHHHHCHHHHHHH---------HH----HHH---
Q ss_conf             7530105648899999999999862232-032021235620278898655142247677---------64----310---
Q gi|254780680|r  162 ARFSVLTGHLAHLERALGQFMIDLHTSE-HGYTEVSAPLLVRDEAMYGTGQIPKFADDM---------FC----TTD---  224 (430)
Q Consensus       162 srF~~Lkg~~A~Le~ALi~y~ld~~~~~-~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~---------y~----~~d---  224 (430)
                      ++||=|=--|+.|-+-+++-.-...+.+ -+..++-+|.|+..+++.++||+.+|.|-|         |+    +++   
T Consensus        30 ~GfyDYGPlG~~LK~nI~~~Wrk~fV~~~e~~~eIdtpii~p~~V~kASGHvd~FsDplv~c~~c~~~yRADHLiEe~l~  109 (558)
T COG0423          30 AGFYDYGPLGVELKNNIKEAWRKSFVTEREDVVEIDTPIILPEEVWKASGHVDKFSDPLVECKKCGERYRADHLIEEYLG  109 (558)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHEECCCCEEEECCCCCCCHHHHHHCCCCCCCCCCEEECCCCCHHHHHHHHHHHHHH
T ss_conf             46532577518999999999999866246876784255448688864347613465620434624534533688898764


Q ss_pred             -C-C-----------------------------------E--ECCCCCC------------HHHHHHHHHCCCHHHHCCE
Q ss_conf             -0-0-----------------------------------2--3134541------------1454453420595550420
Q gi|254780680|r  225 -G-R-----------------------------------W--LIPTSEV------------SLTNLYSHEIIESKSLPLR  253 (430)
Q Consensus       225 -~-l-----------------------------------~--Li~TaEv------------pL~~~~~~~~l~~~~LPik  253 (430)
                       + .                                   |  -||..+-            -..|+-+=.-+.-..||.-
T Consensus       110 ~~~~~~~~~~e~~~ii~~~~ir~p~~g~~l~~v~~FNLMF~T~IGp~~~~~~YLRPETAQGiFvnFk~l~~~~r~klPFg  189 (558)
T COG0423         110 KDGHGNMSPEELTEIIREYDIRCPECGGELNEVREFNLMFKTTIGPVEDSLGYLRPETAQGIFVNFKNLLEFARNKLPFG  189 (558)
T ss_pred             HCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCCCEEECCCCCCHHHHHHHHHHHHHCCCCCEE
T ss_conf             10345578788888888617758876886687503446667314577886324565100212153699999753689848


Q ss_pred             EEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCC-------------------H--HH----------HHH--
Q ss_conf             88532210788433554343212222102002121278650-------------------1--45----------789--
Q gi|254780680|r  254 FTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREED-------------------S--FT----------EHE--  300 (430)
Q Consensus       254 ~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~-------------------S--~~----------~~e--  300 (430)
                      .+.++..||-|..-.    .||+|+.+|+..|+=.||+|++                   .  .+          +++  
T Consensus       190 iaQIGKsfRNEISPr----~gl~R~REF~QaEiE~Fv~P~~k~~p~f~~v~~~~l~l~~~~~q~~~~~~EAv~~g~~~n~  265 (558)
T COG0423         190 IAQIGKSFRNEISPR----NGLFRTREFEQAEIEFFVDPEEKEHPKFNEVKDEKLPLLPREAQEEGTEEEAVEEGIVENE  265 (558)
T ss_pred             EEEECHHHCCCCCCC----CCEEEHHHHHHHEEEEEECCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHCCEECCH
T ss_conf             886231014652766----5366512343120135887775568633333210024664777641003455441545044


Q ss_pred             ---HHHHHHHHHHHHHCCH---HHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCC--------
Q ss_conf             ---8999999999984106---75303780117844340241011010048332375310210076453268--------
Q gi|254780680|r  301 ---RMLSCAEEILKRLDLH---YRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNS--------  366 (430)
Q Consensus       301 ---~~~~~~~~i~~~L~lp---yRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~i--------  366 (430)
                         -.+.....++..||++   .|.-.-...+|..=|+.|+|+|+.+|.-+ |+|+.-|+|=|||-=+|-.=        
T Consensus       266 ~~~y~~~~~~~fl~~lGI~~e~lRfrqh~~~E~AHYa~~twD~E~~~~~~g-WiE~~GiAdRtdYDL~~H~k~s~~~l~v  344 (558)
T COG0423         266 TLAYFIARTKFFLEDLGIDPEKLRFRQHLPEELAHYSKDTWDAEYKFPFGG-WIELVGIADRTDYDLSRHSKFSGEDLTV  344 (558)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHCCEEEEEECCCCC-EEEEEEEECCCCCCHHHHHHHCCCCCEE
T ss_conf             389999999999998099989806652390877665440232799637886-6999986135544556565403666223


Q ss_pred             --EE-----------------ECCCC---------------------C-------------------CCCEEEEECCCHH
Q ss_conf             --47-----------------33899---------------------8-------------------4101042004322
Q gi|254780680|r  367 --RY-----------------RDPNS---------------------K-------------------SLKFTHTLNGSGV  387 (430)
Q Consensus       367 --ry-----------------~~~~~---------------------~-------------------~~~~~htlNgt~~  387 (430)
                        +|                 -++.-                     +                   ..-.+|-+-- +.
T Consensus       345 ~~~~~ePk~v~~~~~~~~~~~~gp~~k~~a~~v~~~~se~~~~~~~~~~~~~~~~~~~i~~~~~~~~e~~iP~VIEP-Sf  423 (558)
T COG0423         345 FREYDEPKEVERWHSKVDLKFLGPEFKKDAKKVAEALSELEELEKELNGYEVSKDLVIIEEVEKVTGEKYIPHVIEP-SF  423 (558)
T ss_pred             EECCCCCCEEEEEECCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHEEEEECCCCEECCCEECC-CC
T ss_conf             32147762233100146621038144556677765445666665304762135310010011002475506715656-77


Q ss_pred             HHHHHHHHHHH-HCCCCCC-----CEECCCCCCCC
Q ss_conf             89999999988-3468998-----38658222310
Q gi|254780680|r  388 AVGRCLIAILE-NYLNADG-----SVTIPTVLRPY  416 (430)
Q Consensus       388 A~~R~l~ailE-n~q~~dg-----~i~iP~~L~py  416 (430)
                      -+.|++-|+|| .|+.+.+     ..++|..|-|+
T Consensus       424 GidRi~y~~l~~ay~~ee~~e~R~vLrl~p~lAPi  458 (558)
T COG0423         424 GIDRIFYALLEHAYTEEEVEEKRIVLRLPPDLAPI  458 (558)
T ss_pred             CCHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCE
T ss_conf             71189999998762011356650599558655852


No 34 
>TIGR00415 serS_MJ seryl-tRNA synthetase; InterPro: IPR004503   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa . The seryl-tRNA synthetases from a few of the archaea that belong to this group are different from the set of mutually more closely related seryl-tRNA synthetases from eubacteria, eukaryotes, and other archaea (IPR002317 from INTERPRO).; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=98.99  E-value=3.7e-09  Score=88.81  Aligned_cols=265  Identities=20%  Similarity=0.337  Sum_probs=205.7

Q ss_pred             EEEECCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHH
Q ss_conf             20001565665666211220221173100011222167530105648899999999999862232032021235620278
Q gi|254780680|r  125 IRSVGKKPSAIHLSREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDE  204 (430)
Q Consensus       125 i~~~G~~~~f~f~~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~  204 (430)
                      +...-.++.+.|. +|-.+.+.+++|+.     +..|.+-+++.-....|++||-.++++..+..-||.++.-|-++--+
T Consensus       182 ~~~~~~~~~~~~~-~dp~~~~~~~gw~~-----~~pg~g~w~~~p~~~~~~~~~~~~~~~~~~~~~g~~~c~~p~~~p~~  255 (520)
T TIGR00415       182 VAEYKAKRDFFFD-GDPTDEAEKLGWVK-----KFPGRGQWFYGPPITALFRALEELFVEEVVKPLGFVECLFPKLIPLD  255 (520)
T ss_pred             HHHHHHCCCEEEC-CCCHHHHHHHCCHH-----CCCCCCCEECCCCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_conf             3321100120005-77345676611011-----26887620016506788888998889887654011345310010267


Q ss_pred             HHHHHHHCHHHHHHHHHH--------------------------------HH-CCEECCCCCCHHHHHHHHHCCCHHHHC
Q ss_conf             898655142247677643--------------------------------10-002313454114544534205955504
Q gi|254780680|r  205 AMYGTGQIPKFADDMFCT--------------------------------TD-GRWLIPTSEVSLTNLYSHEIIESKSLP  251 (430)
Q Consensus       205 ~~~gtG~lp~f~~~~y~~--------------------------------~d-~l~Li~TaEvpL~~~~~~~~l~~~~LP  251 (430)
                      ++...-++.-..+.+|..                                .| ++.+.|..=-|.-.++..++++..++|
T Consensus       256 ~~~~~~~~~g~p~g~~~~~~p~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~dpg~~~~p~~c~p~~~~~~~~~~~~~d~p  335 (520)
T TIGR00415       256 ILYKLRYLEGLPEGLYYCCPPKRDPELFEEFKNELLINKEVPLDLLKNGLKDPGYVLAPAQCEPFYQFLEGEVVDAEDLP  335 (520)
T ss_pred             HHHHHHHHHCCCCCCEEECCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCEECCCCCCHHHHHHCCCCCCCCCCC
T ss_conf             77776764136545255227755635789876655420035578987530487704303110035675412110000143


Q ss_pred             CEEEEE-ECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHC---------C
Q ss_conf             208853-221078843355434321222210200212127865014578989999999999841067530---------3
Q gi|254780680|r  252 LRFTTL-APSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVV---------S  321 (430)
Q Consensus       252 ik~~~~-s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv---------~  321 (430)
                      +++..- +-.||-|+|.    .+||-|+|+|.+||++.+..|+...+..+..+..++.+-+.|++.|-+-         -
T Consensus       336 ~~~~d~~gw~~~w~~gg----~~g~d~~~~~~~~~~~w~~~p~~~~~~~d~~~~~~~~~~~~~~~~~~~~~gddp~~~~g  411 (520)
T TIGR00415       336 VKFFDRSGWTYRWEGGG----AKGLDRVNEFLRVELVWLGEPGFTEETRDKTLELAEDLADELDLEWWTEVGDDPFYLEG  411 (520)
T ss_pred             EEEECCCCCEEEECCCC----CCCHHHHHHHHHEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHEEECCCCCEEECC
T ss_conf             11220577424423766----32124554533111355147520123334456655555554100110011786301036


Q ss_pred             C--CCHHCCCHHHEEEEEEEECCCCC---CEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             7--80117844340241011010048---332375310210076453268473389984101042004322899999999
Q gi|254780680|r  322 L--CTGDLGFSACKTYDLEVWLAGQN---LYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAI  396 (430)
Q Consensus       322 ~--~sgdlg~~a~~~~DiE~w~P~~~---~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ai  396 (430)
                      -  -..-+.++..-+|++..|+|+..   +-.-++|+.--+..-..-  .+.++..+..   +.| ..|+..+.|.+...
T Consensus       412 ~~~~~~g~~~pd~p~~~~~~~~p~~~d~~~g~~~~~~~~~g~~~~~g--~~~~~~~~~~---~w~-gc~g~g~~~w~~g~  485 (520)
T TIGR00415       412 RKKEDRGIEFPDVPKYELRLWLPGREDERKGVAVTSANVHGTHFVEG--FRIKDYKGLN---VWT-GCTGYGLTRWVYGF  485 (520)
T ss_pred             CCCCCCCCCCCCCCCHHHEEECCCCCCCCCCEEEEECCCCCCEEECC--CEEHHCCCCE---EEC-CCCCCCHHHHHHHH
T ss_conf             42000256577775201101057743111340455303344100012--1000003650---110-33322046787777


Q ss_pred             HHHCCCCCC
Q ss_conf             883468998
Q gi|254780680|r  397 LENYLNADG  405 (430)
Q Consensus       397 lEn~q~~dg  405 (430)
                      |-.+--.-|
T Consensus       486 ~~~~g~~~~  494 (520)
T TIGR00415       486 LAQYGFEFG  494 (520)
T ss_pred             HHHHCCCCC
T ss_conf             765056667


No 35 
>PRK00037 hisS histidyl-tRNA synthetase; Reviewed
Probab=98.66  E-value=1.4e-07  Score=77.05  Aligned_cols=155  Identities=17%  Similarity=0.246  Sum_probs=109.0

Q ss_pred             CCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHH-HHHCH-HHHHHHHHHH----HCCEECCCCCCHH
Q ss_conf             5301056488999999999998622320320212356202788986-55142-2476776431----0002313454114
Q gi|254780680|r  163 RFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYG-TGQIP-KFADDMFCTT----DGRWLIPTSEVSL  236 (430)
Q Consensus       163 rF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~g-tG~lp-~f~~~~y~~~----d~l~Li~TaEvpL  236 (430)
                      |+.=+-.+.+..-+.+.+.+.+. ...+||.+|.||.|-..+++.. .|... .-..+||...    ..+.|-|--=+|+
T Consensus         9 G~rD~lP~~~~~~~~i~~~i~~~-~~~~Gy~~I~tP~lE~~d~~~~~~g~~~d~~~k~~y~f~D~~g~~l~LRpD~T~~i   87 (417)
T PRK00037          9 GTRDILPEESAKWQYVEDTIREV-FERYGFSEIRTPIFEYTELFKRKIGESTDIVEKEMYTFQDKGGRSLTLRPEGTAPV   87 (417)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHH-HHHCCCEEEECCCCCHHHHHCCCCCCCCCHHHHHEEEEECCCCCEEEECCCCCHHH
T ss_conf             87767988999999999999999-99859958577521509886245776322013320567759998898567767299


Q ss_pred             HHHHHHHC-CCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCC-CHHHHHHHHHHHHHHHHHHHC
Q ss_conf             54453420-5955504208853221078843355434321222210200212127865-014578989999999999841
Q gi|254780680|r  237 TNLYSHEI-IESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREE-DSFTEHERMLSCAEEILKRLD  314 (430)
Q Consensus       237 ~~~~~~~~-l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe-~S~~~~e~~~~~~~~i~~~L~  314 (430)
                      +-++...- .....+|+|++-+++|||.|--.     +|  |+.||.-+-.=.|+.++ .++   -|++..+.++++.||
T Consensus        88 aR~~~~~~~~~~~~~P~r~~y~g~vfR~e~p~-----~G--R~REf~Q~g~eiiG~~~~~aD---aEvi~l~~~~l~~lG  157 (417)
T PRK00037         88 VRAVIENKLYNELPKPFKLYYIGPMFRYERPQ-----KG--RYRQFHQFGVEVIGSDSPAAD---AEVIALAADLLKALG  157 (417)
T ss_pred             HHHHHHHHHHCCCCCCEEEEEECCEEECCCCC-----CC--CCCCEEECCHHHHCCCCHHHH---HHHHHHHHHHHHHCC
T ss_conf             99999721010688765899872466047898-----87--635245635277466417888---999999999999839


Q ss_pred             CHHHHCCCCCHHCCCH
Q ss_conf             0675303780117844
Q gi|254780680|r  315 LHYRVVSLCTGDLGFS  330 (430)
Q Consensus       315 lpyRvv~~~sgdlg~~  330 (430)
                      ++...+.+  |.+|..
T Consensus       158 l~~~~i~i--~~~g~~  171 (417)
T PRK00037        158 LKGLVLLL--NSLGDF  171 (417)
T ss_pred             CCCCCCCC--CCCCCH
T ss_conf             96520010--567768


No 36 
>cd00774 GlyRS-like_core Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP binding and hydrolysis. This alignment contains only sequences from the GlyRS form which homodimerizes. The heterotetramer glyQ is in a different family of class II aaRS. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the N-terminus of the accessory subunit of mitochondrial polymerase gamma (Pol gamma b). Pol gamma b stimulates processive DNA synthesis and is functional as a homodimer, which can associate with the catalytic subunit Pol gamma alpha to form a heterotrimer. Despite significant both structural and sequence similarity with Gly
Probab=98.42  E-value=6.2e-07  Score=72.28  Aligned_cols=190  Identities=17%  Similarity=0.203  Sum_probs=145.3

Q ss_pred             CCCEEECCHHHHHHHHHHHHHHHHHHHHC-CCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECC-CCCCHHHHH
Q ss_conf             75301056488999999999998622320-3202123562027889865514224767764310002313-454114544
Q gi|254780680|r  162 ARFSVLTGHLAHLERALGQFMIDLHTSEH-GYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIP-TSEVSLTNL  239 (430)
Q Consensus       162 srF~~Lkg~~A~Le~ALi~y~ld~~~~~~-Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~-TaEvpL~~~  239 (430)
                      ++||=+=--|+.|-+.+++.--+..+..+ +..++-.|.++.+ .|+.|-.=|...     ....-||=| ||-=.++|+
T Consensus        22 ag~yDyGPlG~~LK~Ni~~~W~~~fv~~~~~~~~id~~ii~p~-LmF~T~iG~~~~-----~~~~~yLRPETAQGifvnF   95 (254)
T cd00774          22 AGFYDYGPLGVELKNNIKSAWRKSFVLEEEDMLEIDSPIITPE-LMFKTSIGPVES-----GGNLGYLRPETAQGIFVNF   95 (254)
T ss_pred             HCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCC-CCEECCCCCCCC-----CCCCEEECHHHHHHHHHHH
T ss_conf             1061548237999999999999998743798799541003663-220012156558-----9860353634534779878


Q ss_pred             HHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCC---H
Q ss_conf             5342059555042088532210788433554343212222102002121278650145789899999999998410---6
Q gi|254780680|r  240 YSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDL---H  316 (430)
Q Consensus       240 ~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~l---p  316 (430)
                      -.=--..-..||.-.+-++.|||-|....    .||+|+-+|+..|+-.||+|+++..+++...+..-.++..+++   .
T Consensus        96 k~~~~~~r~kLPFGiaQIGk~FRNEIsPr----~~l~R~REF~q~EiE~F~~P~~~~~~~~~w~~~~l~~~~~~~~~~~~  171 (254)
T cd00774          96 KNLLEFNRRKLPFGVAQIGKSFRNEISPR----NGLFRVREFTQAEIEFFVDPEKSHPWFDYWADQRLKWLPKFAQSPEN  171 (254)
T ss_pred             HHHHHHCCCCCCEEEEEEEECCCCCCCCC----CCCCCHHCHHHHEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             99999648888844565420226734777----67540000021257888579864257899999998663873899665


Q ss_pred             HHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHH
Q ss_conf             75303780117844340241011010048332375310210076453
Q gi|254780680|r  317 YRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRR  363 (430)
Q Consensus       317 yRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrR  363 (430)
                      .|+-.-.+.++|.-+.+++|++.=+|  ..|.|.--+.|-+||-=..
T Consensus       172 ~~~~~~~a~e~~~~~~~~~~~~~~~~--~g~~e~~Gi~~~~~r~~~~  216 (254)
T cd00774         172 LRLTDHEKEELAHYANETLDYFYAFP--HGFLELEGIANRGDRFLQH  216 (254)
T ss_pred             EEEECCCHHHHCEECCCCEEEEEEHH--HHHHHHHCCCCCCCHHHHC
T ss_conf             36730463674333222178786334--4167861828672578762


No 37 
>TIGR02367 PylS pyrrolysyl-tRNA synthetase; InterPro: IPR012739    PylS is the archaeal enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, e.g. trimethylamine methyltransferase. .
Probab=98.40  E-value=5.4e-07  Score=72.70  Aligned_cols=135  Identities=23%  Similarity=0.438  Sum_probs=109.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHH--HHHHHHHHHCCEECCCCCCHHHHHHH--HHCC
Q ss_conf             4889999999999986223203202123562027889865514224--76776431000231345411454453--4205
Q gi|254780680|r  170 HLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKF--ADDMFCTTDGRWLIPTSEVSLTNLYS--HEII  245 (430)
Q Consensus       170 ~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f--~~~~y~~~d~l~Li~TaEvpL~~~~~--~~~l  245 (430)
                      -+.+|||.+..|++|     +||.++..|.++--+-++..|-.-+-  ..|+|+++.++||-|----.|-||.+  |.++
T Consensus       241 ylGkler~it~ffvd-----rGfleiksPiliP~ey~ermGi~ndtelskqifrvdkn~ClrPmlaP~lynylrkldr~l  315 (453)
T TIGR02367       241 YLGKLEREITKFFVD-----RGFLEIKSPILIPLEYVERMGIDNDTELSKQIFRVDKNLCLRPMLAPTLYNYLRKLDRIL  315 (453)
T ss_pred             HHHHHHHHHHHHHHH-----CCEEEECCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHC
T ss_conf             754676667666531-----240232363101056886507764025666666441001012100056899999987537


Q ss_pred             CHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCCC
Q ss_conf             955504208853221078843355434321222210200212127865014578989999999999841067530378
Q gi|254780680|r  246 ESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVSLC  323 (430)
Q Consensus       246 ~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~  323 (430)
                      +.   |||...++||||+|  |-||+     .+-+|+   |+.||.-- |--.-|.+-.+..+++.-|++-|.+|-=+
T Consensus       316 P~---Pik~fe~GPCyrke--sdGke-----hleeft---m~nfCqmG-sGCtrenle~~i~~fl~~l~idf~ivGds  379 (453)
T TIGR02367       316 PD---PIKVFEVGPCYRKE--SDGKE-----HLEEFT---MLNFCQMG-SGCTRENLEALIKEFLDYLEIDFKIVGDS  379 (453)
T ss_pred             CC---CEEEEEECCCCCCC--CCCHH-----HHHHHH---HHHHHHCC-CCCCHHHHHHHHHHHHHHHCCCEEEECCE
T ss_conf             89---64798606752435--65335-----666666---55543147-87326779999999887615424785242


No 38 
>PRK09537 pylS pyrolysyl-tRNA synthetase; Reviewed
Probab=98.26  E-value=8.7e-07  Score=71.19  Aligned_cols=189  Identities=21%  Similarity=0.365  Sum_probs=121.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHH--HHHHHHHHHCCEECCCCCCHHHHHHH--HHCCC
Q ss_conf             889999999999986223203202123562027889865514224--76776431000231345411454453--42059
Q gi|254780680|r  171 LAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKF--ADDMFCTTDGRWLIPTSEVSLTNLYS--HEIIE  246 (430)
Q Consensus       171 ~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f--~~~~y~~~d~l~Li~TaEvpL~~~~~--~~~l~  246 (430)
                      +.+|||-...|+.|     +||.++..|.|+--+-.+..|-.-+.  ..|+|.+++++||-|-----|-++.+  +..++
T Consensus       209 lgkler~it~ffvd-----rgfleikspilip~eyiermgid~d~elskQiFrvd~n~CLRPMLAPnLYnylrkL~R~lp  283 (420)
T PRK09537        209 LGKLERDITKFFVD-----RGFLEIKSPILIPAEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALP  283 (420)
T ss_pred             HHHHHHHHHHHHHC-----CCCEEECCCEECCHHHHHHHCCCCHHHHHHHHEEECCCCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf             76778888998541-----4513514850421999998578860565545167434533241014269999999986168


Q ss_pred             HHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHH
Q ss_conf             55504208853221078843355434321222210200212127865014578989999999999841067530378011
Q gi|254780680|r  247 SKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVSLCTGD  326 (430)
Q Consensus       247 ~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgd  326 (430)
                      .   |||.+.++||||+|.  -|+.     .+.+|+.+-...+-.+    -.-|.+-..+.+++..|||.|.++--.+--
T Consensus       284 d---PIrIFEIGpCyRKES--dG~~-----HLeEFTMlNfcqmgsg----ctrenle~~i~efl~~lgIdfeiv~dscmV  349 (420)
T PRK09537        284 D---PIKIFEIGPCYRKES--DGKE-----HLEEFTMVNFCQMGSG----CTRENLEALITEFLNHLGIDFEIVGDSCMV  349 (420)
T ss_pred             C---CEEEEEECCCCCCCC--CCHH-----HHHHHHHHHHHHHCCC----CCHHHHHHHHHHHHHHCCCEEEEECCCEEE
T ss_conf             8---715886204303444--1067-----8877777768864489----867889999999998619727984252068


Q ss_pred             CCCH-HHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCC
Q ss_conf             7844-340241011010048332375310210076453268473389984101042004322899999999883468
Q gi|254780680|r  327 LGFS-ACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAILENYLN  402 (430)
Q Consensus       327 lg~~-a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ailEn~q~  402 (430)
                      -|.+ ..+.=|+|           ++|+-----|--|+-+|            +----|-|...-|+|. +.+++|+
T Consensus       350 YGdT~DvMhgDlE-----------LsSavvGP~pLDr~Wgi------------~kPWiGaGFGLERLLk-V~hg~~n  402 (420)
T PRK09537        350 YGDTLDIMHGDLE-----------LSSAVVGPIPLDREWGI------------DKPWIGAGFGLERLLK-VMHGFKN  402 (420)
T ss_pred             ECCHHHHHCCCHH-----------HCCCCCCCCCCCCCCCC------------CCCCCCCCHHHHHHHH-HHHCCHH
T ss_conf             5322565426401-----------10354477445655576------------6762023330999999-9835366


No 39 
>PRK12420 histidyl-tRNA synthetase; Provisional
Probab=98.00  E-value=3.4e-05  Score=59.37  Aligned_cols=140  Identities=16%  Similarity=0.183  Sum_probs=101.1

Q ss_pred             EECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHH-HHCHHHHHHHHHHH----HCCEECCCCCCHHHHHH
Q ss_conf             10564889999999999986223203202123562027889865-51422476776431----00023134541145445
Q gi|254780680|r  166 VLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGT-GQIPKFADDMFCTT----DGRWLIPTSEVSLTNLY  240 (430)
Q Consensus       166 ~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gt-G~lp~f~~~~y~~~----d~l~Li~TaEvpL~~~~  240 (430)
                      =+-++-+...+.+.+-+.+. ...+||.++.||.+=..+++... |.-+.-..+||.-.    ..+.|=|---+|++-++
T Consensus        12 D~lp~e~~~~~~i~~~~~~~-~~~~Gy~~I~tP~~E~~elf~~~~g~~~~i~kemy~f~D~~gr~l~LRPe~Ta~iaR~~   90 (421)
T PRK12420         12 DYLPEEQVLRNKIKRACEDT-FERYGCKPLETPTLNMYELMSYKYGGGDEILKEIYTLQDQGKRDLALRYDLTIPFAKVV   90 (421)
T ss_pred             CCCHHHHHHHHHHHHHHHHH-HHHCCCEEEECCCCCHHHHHCCCCCCCCHHHHHEEEEECCCCCEEEECCCCCHHHHHHH
T ss_conf             78999999999999999999-99859947247650118764244788442241107888189987985677658999999


Q ss_pred             HHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEE-EEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHH
Q ss_conf             34205955504208853221078843355434321222-2102002121278650145789899999999998410675
Q gi|254780680|r  241 SHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQ-HQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYR  318 (430)
Q Consensus       241 ~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~Rv-HQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyR  318 (430)
                      ...  ..-.+|+|++.++||||.|---     +|=+|. |||. ||+|....|    ..=-|++..+-++++.|||.+.
T Consensus        91 a~~--~~~~~P~k~~y~g~vfR~erpq-----~GR~ReF~Q~G-vEiiG~~~~----~aDaEiI~la~~~l~~lgl~~~  157 (421)
T PRK12420         91 AMN--PNIRLPFKRYEIGKVFRDGPIK-----QGRFREFIQCD-VDIVGVESV----MAEAELMSMAFELFRTLNLEVT  157 (421)
T ss_pred             HHC--CCCCCCEEEEEECCEEECCCCC-----CCCCCEEEECC-EEEECCCCH----HHHHHHHHHHHHHHHHCCCCEE
T ss_conf             977--5777874588876778538987-----88555134357-542078877----8899999999999996598659


No 40 
>COG0016 PheS Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]
Probab=97.99  E-value=0.00022  Score=53.36  Aligned_cols=186  Identities=19%  Similarity=0.269  Sum_probs=116.5

Q ss_pred             HHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHH-----HHHHHHHHHC--CEECCCCCCHHHHHHHHHCCCHHHH
Q ss_conf             99999986223203202123562027889865514224-----7677643100--0231345411454453420595550
Q gi|254780680|r  178 LGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKF-----ADDMFCTTDG--RWLIPTSEVSLTNLYSHEIIESKSL  250 (430)
Q Consensus       178 Li~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f-----~~~~y~~~d~--l~Li~TaEvpL~~~~~~~~l~~~~L  250 (430)
                      .+.-..++- .+-||+++.-|.+-...-=+-+=++|.+     ..|.|+++++  ..|.=|---|+.+-++.+--+.   
T Consensus       116 ~~e~i~~iF-~~mGF~~~~gp~IE~d~~NFDaLn~P~dHPARdmqDTFy~~~~~~~~lLRTHTs~vq~R~l~~~~~~---  191 (335)
T COG0016         116 TIEEIEDIF-LGMGFTEVEGPEIETDFYNFDALNIPQDHPARDMQDTFYLKDDREKLLLRTHTSPVQARTLAENAKI---  191 (335)
T ss_pred             HHHHHHHHH-HHCCCEECCCCCCCCCCCCHHHHCCCCCCCCCCCCCEEEECCCCCCEEECCCCCHHHHHHHHHCCCC---
T ss_conf             999999999-9749666458821320225243249999984124443787688773002366827659999847999---


Q ss_pred             CCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHC-----CHHHHCCCCCH
Q ss_conf             4208853221078843355434321222210200212127865014578989999999999841-----06753037801
Q gi|254780680|r  251 PLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLD-----LHYRVVSLCTG  325 (430)
Q Consensus       251 Pik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~-----lpyRvv~~~sg  325 (430)
                      |+|+.+...|||+++-.+   |.    .|||+.||-+++.+.-.    +..|...-++++..+.     +-||--.-|=-
T Consensus       192 P~k~~~~grvyR~D~~Da---TH----s~~FhQiEGlvvd~~~s----~~~Lkg~L~~f~~~~fg~~~~vRfrpsyFPFT  260 (335)
T COG0016         192 PIKIFSPGRVYRNDTVDA---TH----SPEFHQIEGLVVDKNIS----FADLKGTLEEFAKKFFGEDVKVRFRPSYFPFT  260 (335)
T ss_pred             CCEEECCCCEECCCCCCC---CC----CHHEEEEEEEEEECCCC----HHHHHHHHHHHHHHHCCCCCCEEEECCCCCCC
T ss_conf             915845663411788776---42----61013367899958956----99999999999999637776357606878989


Q ss_pred             HCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHH
Q ss_conf             17844340241011010048332375310210076453268473389984101042004322899999
Q gi|254780680|r  326 DLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCL  393 (430)
Q Consensus       326 dlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l  393 (430)
                      +-      ...+++|.|+-++|.||.-|.-.-.=--+.++|   +++. -..|+.     |+.+.|+-
T Consensus       261 EP------S~Evdv~~~~~~~WlEi~G~Gmv~P~VL~~~G~---~~~~-~~GfAf-----GlGlERlA  313 (335)
T COG0016         261 EP------SAEVDVYCPGCGGWLEILGCGMVHPNVLEAVGI---DPEE-YSGFAF-----GLGLERLA  313 (335)
T ss_pred             CC------EEEEEEEECCCCCEEEEECCCCCCHHHHHHCCC---CCCC-CEEEEE-----EECHHHHH
T ss_conf             97------178999976878689983565457888974599---9876-058887-----40488999


No 41 
>COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=97.85  E-value=0.0001  Score=55.76  Aligned_cols=146  Identities=19%  Similarity=0.312  Sum_probs=104.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHH-HHHHCHH-HHHHHHHHHH----CCEECCCCCCHHHHHHHH
Q ss_conf             648899999999999862232032021235620278898-6551422-4767764310----002313454114544534
Q gi|254780680|r  169 GHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMY-GTGQIPK-FADDMFCTTD----GRWLIPTSEVSLTNLYSH  242 (430)
Q Consensus       169 g~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~-gtG~lp~-f~~~~y~~~d----~l~Li~TaEvpL~~~~~~  242 (430)
                      .+=+.+.+.+.+.+.+. ....||.|+.+|.+=..+++. +.|.-.+ -..+||.-.|    .+-|-|-.-+|++-++..
T Consensus        15 p~d~~~~~~i~~~~~~v-~~~yGf~eI~TPifE~telf~r~~Ge~td~v~kemY~F~Dkggr~laLRpe~Tapv~R~~~e   93 (429)
T COG0124          15 PEDMALREYIESTIRKV-FESYGFSEIRTPIFEYTELFARKSGEETDVVEKEMYTFKDKGGRSLALRPELTAPVARAVAE   93 (429)
T ss_pred             HHHHHHHHHHHHHHHHH-HHHCCCEECCCCCCCCHHHHHHCCCCCCCCCCCCEEEEEECCCCEEEECCCCCHHHHHHHHH
T ss_conf             67789999999999999-99809976557551116676201697433332102899948998898446674999999995


Q ss_pred             HCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEE-EEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCH-HHHC
Q ss_conf             205955504208853221078843355434321222-21020021212786501457898999999999984106-7530
Q gi|254780680|r  243 EIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQ-HQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLH-YRVV  320 (430)
Q Consensus       243 ~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~Rv-HQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lp-yRvv  320 (430)
                      .-+... .|+|+....||||-|--.     +|=||+ |||+ ||.|....|.-    --|++..+-++|+.|||. |++-
T Consensus        94 n~~~~~-~p~k~yy~g~vfRyErPQ-----~GR~RqF~Q~g-~E~iG~~~~~~----DAEvi~l~~~~l~~lGi~~~~l~  162 (429)
T COG0124          94 NKLDLP-KPLKLYYFGPVFRYERPQ-----KGRYRQFYQFG-VEVIGSDSPDA----DAEVIALAVEILEALGIGGFTLE  162 (429)
T ss_pred             CCCCCC-CCEEEEEECCEECCCCCC-----CCCCEEEEECC-EEEECCCCCCC----CHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             622036-872599833562378888-----88750368767-67767998653----89999999999997499867999


Q ss_pred             CCCCHH
Q ss_conf             378011
Q gi|254780680|r  321 SLCTGD  326 (430)
Q Consensus       321 ~~~sgd  326 (430)
                      .-.-|.
T Consensus       163 iN~~g~  168 (429)
T COG0124         163 INSRGI  168 (429)
T ss_pred             ECCCCC
T ss_conf             817644


No 42 
>TIGR00389 glyS_dimeric glycyl-tRNA synthetase; InterPro: IPR002315   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   In eubacteria, glycyl-tRNA synthetase (6.1.1.14 from EC) is an alpha2/beta2 tetramer composed of 2 different subunits , , . In some eubacteria, in archaea and eukaryota, glycyl-tRNA synthetase is an alpha2 dimer, this family. It belongs to class IIc and is one of the most complex synthetases. What is most interesting is the lack of similarity between the two types: divergence at the sequence level is so great that it is impossible to infer descent from common genes. The alpha (see IPR002310 from INTERPRO) and beta subunits (see IPR002311 from INTERPRO) also lack significant sequence similarity. However, they are translated from a single mRNA , and a single chain glycyl-tRNA synthetase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain .   The sequence and crystal structure of the homodimeric glycyl-tRNA synthetase from Thermus thermophilus, shows that each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C-terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C-terminal domain has a novel five-stranded parallel-antiparallel beta-sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl-tRNA synthetase due to the conserved nature of the class II active site , .; GO: 0000166 nucleotide binding, 0004820 glycine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006426 glycyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=97.78  E-value=1e-04  Score=55.88  Aligned_cols=196  Identities=17%  Similarity=0.270  Sum_probs=137.6

Q ss_pred             CCCEEECCHHHHHHHHHHHHHHHHHHHHCC-CCEEHHHHHCCHHHHHHHHHCHHHHHHH---------HHHH--------
Q ss_conf             753010564889999999999986223203-2021235620278898655142247677---------6431--------
Q gi|254780680|r  162 ARFSVLTGHLAHLERALGQFMIDLHTSEHG-YTEVSAPLLVRDEAMYGTGQIPKFADDM---------FCTT--------  223 (430)
Q Consensus       162 srF~~Lkg~~A~Le~ALi~y~ld~~~~~~G-y~~v~~P~lv~~~~~~gtG~lp~f~~~~---------y~~~--------  223 (430)
                      |+|+=|=--||.|.+-+++-.-.+.+.+++ +.+|-+|.+++++++.++||..+|-|-|         |+.+        
T Consensus        27 aG~~DyGPLG~~Lk~~I~~~wr~~fi~~e~d~~~id~P~i~~~evlKASGHvd~F~D~~v~Ck~C~~~fRADHl~e~~~~  106 (606)
T TIGR00389        27 AGFWDYGPLGAVLKNNIKNAWRKFFIINERDVLEIDSPIITPEEVLKASGHVDNFTDPMVDCKKCKERFRADHLIEEKLG  106 (606)
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCHHHHHHCCCCCCCCCCEEECCCCCCEECHHHHHHHHHH
T ss_conf             20010157247899999998887511103653464245337257997528645673122673788804010123256651


Q ss_pred             ---HC-------------------------------------------------C-----------EECCCCC-CHHHHH
Q ss_conf             ---00-------------------------------------------------0-----------2313454-114544
Q gi|254780680|r  224 ---DG-------------------------------------------------R-----------WLIPTSE-VSLTNL  239 (430)
Q Consensus       224 ---d~-------------------------------------------------l-----------~Li~TaE-vpL~~~  239 (430)
                         ++                                                 |           -.||-++ -...+|
T Consensus       107 ~~~~~dqqiK~V~~~D~K~~E~iL~~iDG~~~~eL~E~m~~~~i~CP~C~g~~nl~~v~~FNLMF~T~IG~~~~~~~~gY  186 (606)
T TIGR00389       107 KDVEGDQQIKDVKLDDVKEYEKILAKIDGETGPELKEVMEKYDINCPNCGGENNLTEVRSFNLMFQTEIGVVGDSKRKGY  186 (606)
T ss_pred             HHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHCCCCCEEEECCCCCCCCEEE
T ss_conf             00047610012685457779989755078711567877634278898223545613501204541102113347762241


Q ss_pred             HHHH-----------CC--CHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCC-CCHHHHHHHHHHH
Q ss_conf             5342-----------05--95550420885322107884335543432122221020021212786-5014578989999
Q gi|254780680|r  240 YSHE-----------II--ESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITRE-EDSFTEHERMLSC  305 (430)
Q Consensus       240 ~~~~-----------~l--~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~p-e~S~~~~e~~~~~  305 (430)
                      -|=|           ++  ....||-=.|.++.+||-|....    .||+||-+|+..||=.||+| ++|...|++.-+.
T Consensus       187 LRPETAQG~FinFk~LL~~~r~klPFgvAQiGKSfRNEIsPr----~gl~R~REF~QaE~E~FV~P~~k~h~~F~~~~~~  262 (606)
T TIGR00389       187 LRPETAQGIFINFKRLLQFFRNKLPFGVAQIGKSFRNEISPR----QGLIRLREFEQAEIEFFVDPEDKSHPKFEEVKQE  262 (606)
T ss_pred             CCCHHCCCCCHHHHHHHHHHCCCCCEEEEEECCEEECCCCCC----CCEEEECHHHHHHHHHCCCCCCCCCCCHHHHHHC
T ss_conf             476010475121689999745899648997441360400389----8757103154466874259600167200145405


Q ss_pred             H---------------------------------------------HHHHHHHC-CH---HHHCCCCCHHCCCHHHEEEE
Q ss_conf             9---------------------------------------------99999841-06---75303780117844340241
Q gi|254780680|r  306 A---------------------------------------------EEILKRLD-LH---YRVVSLCTGDLGFSACKTYD  336 (430)
Q Consensus       306 ~---------------------------------------------~~i~~~L~-lp---yRvv~~~sgdlg~~a~~~~D  336 (430)
                      .                                             ..+|...| |+   .|-=.=-..+|..=|..|+|
T Consensus       263 ~~~Llp~~R~~~E~g~~~~~v~~t~gEAVe~G~i~ne~L~YFia~~~~FL~~igkI~~dklRFrqH~~~E~AHYA~dcwD  342 (606)
T TIGR00389       263 VVPLLPAERQMQESGESEKPVKMTIGEAVEKGIIENETLAYFIALVKRFLLEIGKINPDKLRFRQHLKNEMAHYAKDCWD  342 (606)
T ss_pred             CCCCCCCCCCCHHCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHEE
T ss_conf             00136764540001576405444178886346521006899999999999865278878852331360045565553623


Q ss_pred             EEEECCCCCCEEEEEEECCCCCHHHH
Q ss_conf             01101004833237531021007645
Q gi|254780680|r  337 LEVWLAGQNLYREISSCSTCGNFQSR  362 (430)
Q Consensus       337 iE~w~P~~~~y~Ev~S~Snc~D~Qsr  362 (430)
                      +|+-.|+- .|+||.=|.|=|||==+
T Consensus       343 ~E~~t~~y-GwiE~~GiADR~~yDL~  367 (606)
T TIGR00389       343 AEILTSRY-GWIEVVGIADRTDYDLT  367 (606)
T ss_pred             EEEECCCC-CCEEEEEEECCCCCCHH
T ss_conf             55665798-73899874067722168


No 43 
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=97.75  E-value=0.00021  Score=53.40  Aligned_cols=145  Identities=19%  Similarity=0.280  Sum_probs=102.2

Q ss_pred             HCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHH-HHCHH-HHHHHHHHHH----CCEECCCC
Q ss_conf             216753010564889999999999986223203202123562027889865-51422-4767764310----00231345
Q gi|254780680|r  159 LSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGT-GQIPK-FADDMFCTTD----GRWLIPTS  232 (430)
Q Consensus       159 vsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gt-G~lp~-f~~~~y~~~d----~l~Li~Ta  232 (430)
                      +.|.|  =+..+-+...+.+.+-..+. ...+||.++.||.+=..+++... |.-.+ -..++|+..|    .+.|-|--
T Consensus         7 ~kG~r--D~lp~e~~~~~~i~~~i~~~-f~~~Gf~~I~TP~lE~~e~~~~~~g~~~d~i~k~~y~f~D~~g~~l~LRpD~   83 (424)
T CHL00201          7 LRGTK--DILPDEIEYWQFIHEKAATL-LKLANYQEIRTPIFENTELFDRGIGEETDIVNKEMYRFFDRGNRSITLRPEG   83 (424)
T ss_pred             CCCCC--CCCHHHHHHHHHHHHHHHHH-HHHCCCEEEECCCCCCHHHHCCCCCCCCHHHHHHHEEEECCCCCEEEECCCC
T ss_conf             99998--78999999999999999999-9985992504754041988623578742056665325455999888867877


Q ss_pred             CCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEE-EEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             4114544534205955504208853221078843355434321222-210200212127865014578989999999999
Q gi|254780680|r  233 EVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQ-HQFWKCELVSITREEDSFTEHERMLSCAEEILK  311 (430)
Q Consensus       233 EvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~Rv-HQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~  311 (430)
                      -+|++=++...-+.....|+|++-.+||||.|-...     |=+|. ||+ =||+|....|.    .=-|++..+.++++
T Consensus        84 T~piaR~~~~~~~~~~~~P~r~~y~g~vfR~e~pq~-----GR~REF~Q~-gvEiiG~~~~~----aDaEvi~l~~~~l~  153 (424)
T CHL00201         84 TASIVRAFIENRMAYHMRPQRLWYSGPMFRYERPQS-----GRQRQFHQL-GIEFIGSSDPR----ADMEVIHLAMTLFN  153 (424)
T ss_pred             HHHHHHHHHHCCCCCCCCCEEEEEECCEEECCCCCC-----CCCCHHHHC-CEEEECCCCHH----HHHHHHHHHHHHHH
T ss_conf             099999999747655799878998754780589878-----864210414-62000689828----78999999999998


Q ss_pred             HHCCH
Q ss_conf             84106
Q gi|254780680|r  312 RLDLH  316 (430)
Q Consensus       312 ~L~lp  316 (430)
                      .|||+
T Consensus       154 ~lgl~  158 (424)
T CHL00201        154 ELPVH  158 (424)
T ss_pred             HCCCC
T ss_conf             65965


No 44 
>PRK12292 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=97.73  E-value=0.0002  Score=53.68  Aligned_cols=140  Identities=21%  Similarity=0.239  Sum_probs=99.1

Q ss_pred             CEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHH-----CCEECCCCCCHHHH
Q ss_conf             3010564889999999999986223203202123562027889865514224767764310-----00231345411454
Q gi|254780680|r  164 FSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTD-----GRWLIPTSEVSLTN  238 (430)
Q Consensus       164 F~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d-----~l~Li~TaEvpL~~  238 (430)
                      +-=+.++-|...+.+.+-+.+. ...+||.+|.||.+=..+++...+- +.-+.++|+..|     .+.|=|---+|++-
T Consensus         9 ~~D~lp~e~~~~~~i~~~~~~~-f~~~Gy~~I~tP~lE~~e~f~~~~g-~~~~~~~~~f~D~~~Gr~l~LRpD~T~~iaR   86 (388)
T PRK12292          9 IRDLLPEEARKIEEIRRRLLDV-FRLWGYEEVITPTLEYLDTLLTGGG-ADLDLRTFKLVDQLSGRTLGLRPDMTPQIAR   86 (388)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHH-HHHCCCEEEECCCCCCHHHHCCCCC-CCCCHHEEEEEECCCCCEEEECCCCCHHHHH
T ss_conf             8667999999999999999999-9987996735766062988544577-5021104899826999789856877199999


Q ss_pred             HHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEE-EEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf             4534205955504208853221078843355434321222-21020021212786501457898999999999984106
Q gi|254780680|r  239 LYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQ-HQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLH  316 (430)
Q Consensus       239 ~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~Rv-HQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lp  316 (430)
                      ++... +.....|+|++-.++|||.|.-.     +|-+|. ||+ =||+|....|    ..=-|++..+-++++.||++
T Consensus        87 ~~~~~-~~~~~~p~r~~Y~g~vfR~e~pq-----~Gr~REf~Q~-G~EiiG~~~~----~aDaEvI~l~~~~l~~lgl~  154 (388)
T PRK12292         87 IAATR-LANRPGPLRLCYAGNVFRAQPRG-----LGRSREFLQS-GVELIGDAGI----EADAEVLSLLLDALKALGLP  154 (388)
T ss_pred             HHHHH-HHCCCCCEEEEEEEEEEEECCCC-----CCCCCEEEEC-CEEEECCCCH----HHHHHHHHHHHHHHHHCCCC
T ss_conf             99973-10467876899852268705898-----9961023425-7553178888----99999999999999976998


No 45 
>KOG4163 consensus
Probab=97.70  E-value=3.8e-05  Score=59.00  Aligned_cols=255  Identities=16%  Similarity=0.200  Sum_probs=180.2

Q ss_pred             CHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHH-HCHHHHHHHHH
Q ss_conf             20221173100011222167530105648899999999999862232032021235620278898655-14224767764
Q gi|254780680|r  143 EIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTG-QIPKFADDMFC  221 (430)
Q Consensus       143 elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG-~lp~f~~~~y~  221 (430)
                      ++..+-.++|+-.   |  |+.|+|+-.+--.--|...|+-. .+.+-|-..++-|.+|...+++.-- |...|.-++-.
T Consensus        74 qVitk~emieYyd---v--sGcyilRP~s~aIWe~Iq~wfd~-~ik~lGv~ncYFPmfVs~~~LEkEk~Hve~FaPEvAw  147 (551)
T KOG4163          74 QVITKGEMIEYYD---V--SGCYILRPWSYAIWEAIQDWFDA-EIKKLGVKNCYFPMFVSKSVLEKEKDHVEGFAPEVAW  147 (551)
T ss_pred             HHHHHHHHHEEEC---C--CCEEEECCHHHHHHHHHHHHHHH-HHHHHCCCCCEEEEECCHHHHHHHHHHHCCCCCCEEE
T ss_conf             9854341100233---5--41489553478999999999987-8887364340103324788876556554157853279


Q ss_pred             --------HHHCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEE-EEECCCC
Q ss_conf             --------3100023134541145445342059555042088532210788433554343212222102002-1212786
Q gi|254780680|r  222 --------TTDGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCE-LVSITRE  292 (430)
Q Consensus       222 --------~~d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE-~~~~~~p  292 (430)
                              .++-.-.-||||--+--+|+.=|-.+.|||||+--+-.--|=|-    |.+.-.+|..+|-=-| --+|.+|
T Consensus       148 VTr~G~seLeepiaiRPTSETvmyp~yakWi~ShRDLPlkLNQW~nVvRWEf----k~p~PFlRtrEFLWQEGHTAfat~  223 (551)
T KOG4163         148 VTRAGNSELEEPIAIRPTSETVMYPYYAKWIQSHRDLPLKLNQWCNVVRWEF----KHPQPFLRTREFLWQEGHTAFATP  223 (551)
T ss_pred             EEECCCCCCCCCEEECCCCCCEECHHHHHHHHHHCCCCHHHHHHHHHEEEEC----CCCCCCHHHHHHHHHCCCCHHCCH
T ss_conf             9703884114642234675211038889988760467546654322235302----489751235577774573010797


Q ss_pred             CCHHHHHHHHHHHHHHHHHHH-CCH---HHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEE
Q ss_conf             501457898999999999984-106---7530378011784434024101101004833237531021007645326847
Q gi|254780680|r  293 EDSFTEHERMLSCAEEILKRL-DLH---YRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRY  368 (430)
Q Consensus       293 e~S~~~~e~~~~~~~~i~~~L-~lp---yRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry  368 (430)
                      +++.++--.|+++...+|..| -+|   -|--.   .+-=+.+--++-+|+++|..++=.-=...-+.+-.-||-.+|.|
T Consensus       224 ~eA~eEvlqiLdlYa~vy~ellAiPVvkGrKse---~EkFaGgd~TttvEa~i~~~GrgiQgaTSH~LGQNFSkmF~i~~  300 (551)
T KOG4163         224 EEAEEEVLQILDLYARVYEELLAIPVVKGRKSE---KEKFAGGDYTTTVEAFIPCSGRGIQGATSHHLGQNFSKMFEIVF  300 (551)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCH---HHHCCCCCCEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHCEEE
T ss_conf             677899999999999998762034301476345---33025775047776652466655554320256677998623441


Q ss_pred             ECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEECCCC
Q ss_conf             33899841010420043228999999998834689983865822
Q gi|254780680|r  369 RDPNSKSLKFTHTLNGSGVAVGRCLIAILENYLNADGSVTIPTV  412 (430)
Q Consensus       369 ~~~~~~~~~~~htlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~  412 (430)
                      -+.......||.- |.=|+ +.|+|.+++=.|-+.-|-|.=|.|
T Consensus       301 ed~~~g~~~fv~Q-nSWg~-sTRtiGvmiM~HgDdkGLvLPPrV  342 (551)
T KOG4163         301 EDPGEGEKEFVWQ-NSWGL-STRTIGVMIMTHGDDKGLVLPPRV  342 (551)
T ss_pred             CCCCCCCHHHEEE-CCCCC-CCCEEEEEEEEECCCCCCCCCCCC
T ss_conf             5887411220331-25553-421134799983178653048752


No 46 
>PRK12293 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=97.50  E-value=0.00035  Score=51.85  Aligned_cols=136  Identities=15%  Similarity=0.288  Sum_probs=96.1

Q ss_pred             EECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHH----CCEECCCCCCHHHHHHH
Q ss_conf             10564889999999999986223203202123562027889865514224767764310----00231345411454453
Q gi|254780680|r  166 VLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTD----GRWLIPTSEVSLTNLYS  241 (430)
Q Consensus       166 ~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d----~l~Li~TaEvpL~~~~~  241 (430)
                      =+-++-|.+.+.+.+-+.+. ...+||.+|.||.+=..+..   +  ...+.+||.-.|    .+.|=|-.-.|++=++.
T Consensus        13 D~~p~~~~~~~~Ie~~~~~~-f~~~Gy~eI~TP~~E~~e~~---~--~~~~kemy~f~D~~gr~l~LRPd~Ta~iaR~v~   86 (281)
T PRK12293         13 LYFGKSAKLKRDIENVASEI-LYKEGFEEIVTPSFSYHQHL---S--VADEKELLRFSDEKNHEISLRADSTVDVVRIIT   86 (281)
T ss_pred             CCCHHHHHHHHHHHHHHHHH-HHHCCCEEEECCCEEEEECC---C--CCCCCEEEEEECCCCCEEEECCCCCHHHHHHHH
T ss_conf             66819999999999999999-99859948537856864434---6--656301799987999879977888789999999


Q ss_pred             HHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCC
Q ss_conf             42059555042088532210788433554343212222102002121278650145789899999999998410675303
Q gi|254780680|r  242 HEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVS  321 (430)
Q Consensus       242 ~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~  321 (430)
                      ... .....|+|++-++||||.|.       |   -.||+. ||++....|       .+++..+.++++.||+..- +.
T Consensus        87 ~~l-~~~~~p~rl~Y~g~vFRye~-------r---Ef~Q~G-vEliG~~s~-------~Evi~la~~~l~~lgl~~~-l~  146 (281)
T PRK12293         87 KRL-GRSTEHKKWFYIQPVFRYPT-------T---EIYQIG-AEIIGESDL-------SKVLNIAAEIFNELEIEPV-LQ  146 (281)
T ss_pred             HCC-CCCCCCEEEEEECCEEECCC-------C---CCEEEC-EEEECCCCH-------HHHHHHHHHHHHHCCCCCE-EE
T ss_conf             655-44689757998756353467-------7---746847-488779999-------9999999999997699624-99


Q ss_pred             CCCHHCCC
Q ss_conf             78011784
Q gi|254780680|r  322 LCTGDLGF  329 (430)
Q Consensus       322 ~~sgdlg~  329 (430)
                      +  ++++.
T Consensus       147 i--~~~~~  152 (281)
T PRK12293        147 I--SNIKI  152 (281)
T ss_pred             E--CCCCC
T ss_conf             8--56562


No 47 
>cd00773 HisRS-like_core Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain.
Probab=97.48  E-value=0.00066  Score=49.78  Aligned_cols=132  Identities=23%  Similarity=0.351  Sum_probs=94.3

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHH----HCCEECCCCCCHHHHHHHHHCCCH
Q ss_conf             8999999999998622320320212356202788986551422476776431----000231345411454453420595
Q gi|254780680|r  172 AHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTT----DGRWLIPTSEVSLTNLYSHEIIES  247 (430)
Q Consensus       172 A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~----d~l~Li~TaEvpL~~~~~~~~l~~  247 (430)
                      |.+.+.+.+=..+. ..++||.++.||.+-..+++.+.. -+...+++|+..    ..++|=|---+|++-+++.... .
T Consensus         2 ~~~r~~i~~~l~~~-f~~~Gy~~I~~P~lE~~d~~~~~~-~~~~~~~~~~f~D~~g~~l~LRpD~T~~iaR~~~~~~~-~   78 (261)
T cd00773           2 AALRRYIEDTLREV-FERYGYEEIDTPVFEYTELFLRKS-GDEVSKEMYRFKDKGGRDLALRPDLTAPVARAVAENLL-S   78 (261)
T ss_pred             HHHHHHHHHHHHHH-HHHCCCEEEECCCCCCHHHHCCCC-CCCCHHCEEEEECCCCCEEEECCCCCHHHHHHHHHHHC-C
T ss_conf             68999999999999-998699786677645276752446-53102116999979999897678662799999997415-3


Q ss_pred             HHHCCEEEEEECCCCCCCCCCCCCCCCEEEEE-EEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf             55042088532210788433554343212222-1020021212786501457898999999999984106
Q gi|254780680|r  248 KSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQH-QFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLH  316 (430)
Q Consensus       248 ~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvH-QF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lp  316 (430)
                      ..+|+|++-.+++||.+....|     -+|.+ | -=+|+|.-.    |...--|++..+.++++.|+++
T Consensus        79 ~~~p~r~~Y~g~VfR~~~~~~g-----~~rE~~Q-~G~EiiG~~----~~~ad~Eii~l~~~~l~~lg~~  138 (261)
T cd00773          79 LPLPLKLYYIGPVFRYERPQKG-----RYREFYQ-VGVEIIGSD----SPLADAEVIALAVEILEALGLK  138 (261)
T ss_pred             CCCCEEEEEECCEEEECCCCCC-----CCCCCCC-EEEEEECCC----CHHHHHHHHHHHHHHHHHCCCC
T ss_conf             7888589997318997689999-----8443221-469997289----7588999999999999976998


No 48 
>PRK12295 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=97.39  E-value=0.00074  Score=49.40  Aligned_cols=125  Identities=20%  Similarity=0.265  Sum_probs=88.4

Q ss_pred             HHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHH-HHHHCHHHHHHHHHHHH----CCEECCCCCCHHHHHHHHHCCCHHHH
Q ss_conf             99999999862232032021235620278898-65514224767764310----00231345411454453420595550
Q gi|254780680|r  176 RALGQFMIDLHTSEHGYTEVSAPLLVRDEAMY-GTGQIPKFADDMFCTTD----GRWLIPTSEVSLTNLYSHEIIESKSL  250 (430)
Q Consensus       176 ~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~-gtG~lp~f~~~~y~~~d----~l~Li~TaEvpL~~~~~~~~l~~~~L  250 (430)
                      +||..=.++. -..+||++|.||.+-..+++. ++|-  .-..++|...|    +++|=|---+|++=+|...-   ...
T Consensus         8 ~~~~~~i~~~-f~~~Gy~~I~tP~lE~~d~~~~~~Ge--~~~~~~y~f~D~~g~~l~LRpDlT~piaR~~~~~~---~~~   81 (373)
T PRK12295          8 AALAEALLAS-FEAAGAVRVDPPILQPAEPFLDLSGE--DIRRRIFVTSDENGEELCLRPDFTIPVCRRHLASN---AGE   81 (373)
T ss_pred             HHHHHHHHHH-HHHCCCEEECCCCCCCHHHHCCCCCC--HHHEEEEEEECCCCCEEEEECCCCHHHHHHHHHHC---CCC
T ss_conf             9999999999-99869968568760417764143563--31100488998998989981788899999999838---999


Q ss_pred             CCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEE--EEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCH-HHH
Q ss_conf             420885322107884335543432122221020--021212786501457898999999999984106-753
Q gi|254780680|r  251 PLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWK--CELVSITREEDSFTEHERMLSCAEEILKRLDLH-YRV  319 (430)
Q Consensus       251 Pik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~K--VE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lp-yRv  319 (430)
                      |.||+-.+++||...|        -+|  ||..  ||+|.-..+..++.   |++..+.++++.|++. |+|
T Consensus        82 p~R~~Y~G~VfR~q~g--------r~r--Ef~Q~GvEiiG~~~~~~aDa---Evi~la~~~l~~lgl~~~~i  140 (373)
T PRK12295         82 PARYSYLGEVFRQRRD--------RAS--EFLQAGIESFGRADPAAADA---EVLALALEALAALGPADLEI  140 (373)
T ss_pred             CEEEEEECCEEECCCC--------CCC--CEEEEEEEEECCCCCCCCCH---HHHHHHHHHHHHCCCCCEEE
T ss_conf             8007877332245799--------988--51670157857898210649---99999999999759976399


No 49 
>pfam01409 tRNA-synt_2d tRNA synthetases class II core domain (F). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain.
Probab=97.37  E-value=0.0013  Score=47.52  Aligned_cols=188  Identities=19%  Similarity=0.260  Sum_probs=111.5

Q ss_pred             HHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHH-----HHHHHHHHH----CCEEC--CCCCCHHHHHHHHHCCCH
Q ss_conf             9999986223203202123562027889865514224-----767764310----00231--345411454453420595
Q gi|254780680|r  179 GQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKF-----ADDMFCTTD----GRWLI--PTSEVSLTNLYSHEIIES  247 (430)
Q Consensus       179 i~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f-----~~~~y~~~d----~l~Li--~TaEvpL~~~~~~~~l~~  247 (430)
                      ++...++. ..-||+.+.-|.++...=-+.+=..|.+     ..|.|.++.    ...|-  =||-+..-.|.     ..
T Consensus        23 ~~~i~~~f-~~~GF~~~~g~eves~~~NFDaLn~P~dHPaR~~~DTfy~~~~~~~~~~vLRtHTS~~q~r~l~-----~~   96 (243)
T pfam01409        23 LEEIRDIF-LSMGFEEVEGPEVESDFYNFDALNIPQDHPARDMQDTFYLKKPLKARRLLLRTHTTPVQARTLA-----EK   96 (243)
T ss_pred             HHHHHHHH-HHCCCEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCEEECCCCCHHHHHHHH-----HC
T ss_conf             99999999-8779868769835642777775578988987676760343366667686576879889999997-----42


Q ss_pred             HHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH-CCHHHHCCCCCHH
Q ss_conf             550420885322107884335543432122221020021212786501457898999999999984-1067530378011
Q gi|254780680|r  248 KSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRL-DLHYRVVSLCTGD  326 (430)
Q Consensus       248 ~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L-~lpyRvv~~~sgd  326 (430)
                      ...|+|+.+.++|||+|+=.+   |.    .++|+.+|-+++-+    .--+..+....+.+++.| |...++---|+ =
T Consensus        97 ~~~p~r~~~~grvyR~d~~Da---tH----~~~FhQ~Eg~vvd~----~it~~~Lk~~l~~~~~~lfg~~~~~R~rp~-y  164 (243)
T pfam01409        97 NKPPIKIFSIGRVFRRDQVDA---TH----LPEFHQVEGLVVDE----NVSFADLKGVLEEFLRKFFGFEVKVRFRPS-Y  164 (243)
T ss_pred             CCCCEEEECCCEEEECCCCCC---CC----CCEEEEEEEEEECC----CCCHHHHHHHHHHHHHHHCCCCCEEEECCC-C
T ss_conf             799848981431332588984---31----53105755789657----778999999999999997399737986788-6


Q ss_pred             CCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             784434024101101004833237531021007645326847338998410104200432289999999
Q gi|254780680|r  327 LGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIA  395 (430)
Q Consensus       327 lg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~a  395 (430)
                      -.|+. -...+++|.|..++|.||..|.-.--=--+.++|-     .+-..++.     |+-+-|+..-
T Consensus       165 FPFTe-PS~Evdv~~~~~~~WlEi~G~Gmv~p~vl~~~gid-----~~~~g~Af-----G~GlERlaMl  222 (243)
T pfam01409       165 FPFTE-PSAEVDVYCCKGGGWIEIGGAGMVHPNVLEAVGID-----EDYPGFAF-----GLGVERLAML  222 (243)
T ss_pred             CCCCC-CCCEEEEEEECCCCEEEEEECCCCCHHHHHHCCCC-----CCCEEEEE-----EECHHHHHHH
T ss_conf             99999-86179999964997258750366678899866989-----89769998-----5348899999


No 50 
>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated
Probab=97.27  E-value=0.027  Score=37.75  Aligned_cols=185  Identities=18%  Similarity=0.275  Sum_probs=113.8

Q ss_pred             HHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHH-----HHHHHHHHHCCE-ECCCCCCHHHHHHHHHCCCHHHHCC
Q ss_conf             9999986223203202123562027889865514224-----767764310002-3134541145445342059555042
Q gi|254780680|r  179 GQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKF-----ADDMFCTTDGRW-LIPTSEVSLTNLYSHEIIESKSLPL  252 (430)
Q Consensus       179 i~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f-----~~~~y~~~d~l~-Li~TaEvpL~~~~~~~~l~~~~LPi  252 (430)
                      ++-..|+- ..-||+.+.-|.+-...--+..=..|..     ..|.|+++++.. -.-||-|.+-.|..      ...|+
T Consensus       113 ~~ei~~iF-~~~Gf~v~~GpeiE~~~~NFdaLn~P~~HPAR~~~DTFy~~~~~lLRTHTS~~qir~m~~------~~pp~  185 (338)
T PRK00488        113 IERIEDIF-VGLGFEVAEGPEIEDDYYNFEALNIPKDHPARDMQDTFYIDDRLLLRTHTSPVQIRTMEK------QKPPI  185 (338)
T ss_pred             HHHHHHHH-HHCCCEEECCCCEEEHHHHHHHHCCCCCCCCCCCCCEEEECCCCEECCCCCHHHHHHHHH------CCCCE
T ss_conf             99999999-986976961883100454688756997885436466289768713435687888999972------69986


Q ss_pred             EEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH-----CCHHHHCCCCCHHC
Q ss_conf             0885322107884335543432122221020021212786501457898999999999984-----10675303780117
Q gi|254780680|r  253 RFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRL-----DLHYRVVSLCTGDL  327 (430)
Q Consensus       253 k~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L-----~lpyRvv~~~sgdl  327 (430)
                      |+++.++|||+++-.+   |+    -|+|+.+|-+++-+ +-|   +-.+....+.+++.+     .+-||--.-|=.+=
T Consensus       186 ~~i~~GrvyR~d~~Da---tH----~~~FhQ~Egl~vd~-~it---~~~Lk~~l~~f~~~~fg~~~~~R~rpsyFPFtEP  254 (338)
T PRK00488        186 RIIAPGRVYRNDSDDA---TH----SPMFHQVEGLVVDK-NIS---FADLKGTLEDFLKAFFGEDLKIRFRPSYFPFTEP  254 (338)
T ss_pred             EEEECCCCCCCCCCCC---CC----CEEEEEEEEEEEEC-CCC---HHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCC
T ss_conf             9995266315899987---53----50466400589717-887---9999999999999972876647754788999998


Q ss_pred             CCHHHEEEEEEEECCC--------CCCEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHH
Q ss_conf             8443402410110100--------483323753102100764532684733899841010420043228999999
Q gi|254780680|r  328 GFSACKTYDLEVWLAG--------QNLYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLI  394 (430)
Q Consensus       328 g~~a~~~~DiE~w~P~--------~~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~  394 (430)
                          |--+||..|..+        ...|.||.-|.-.---.=+..+|   |++. -+.|+.     |+-+-|+..
T Consensus       255 ----s~Evdi~~~~~~g~gc~~~~~~~WlEi~G~Gmv~p~Vl~~~gi---d~~~-~~G~Af-----G~GieR~aM  316 (338)
T PRK00488        255 ----SAEVDVSCFNCKGKGCRVCKNTGWLEVLGCGMVHPNVLRNVGI---DPEE-YSGFAF-----GMGIERLAM  316 (338)
T ss_pred             ----CEEEEEEECCCCCCCCCCCCCCCEEEECCCCCCCHHHHHHCCC---CCCC-CEEEEE-----EECHHHHHH
T ss_conf             ----5347887314577665447899638973766678899986699---9552-759987-----515889999


No 51 
>cd00496 PheRS_alpha_core Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA,  PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs.  PheRS is an alpha-2/ beta-2 tetramer.
Probab=97.23  E-value=0.002  Score=46.20  Aligned_cols=186  Identities=21%  Similarity=0.260  Sum_probs=114.8

Q ss_pred             HHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHH-----HHHHHHHHHC--CEE-CCCCCCHHHHHHHHHCCCHHH
Q ss_conf             99999986223203202123562027889865514224-----7677643100--023-134541145445342059555
Q gi|254780680|r  178 LGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKF-----ADDMFCTTDG--RWL-IPTSEVSLTNLYSHEIIESKS  249 (430)
Q Consensus       178 Li~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f-----~~~~y~~~d~--l~L-i~TaEvpL~~~~~~~~l~~~~  249 (430)
                      +++-..|+. ..-||+++.-|.+....--+..=..|.+     ..|.|.+++.  +.| .=||-+..-.|.+.      .
T Consensus         6 ~~~~i~~~f-~~~GF~~~~gp~ie~~~~NFD~Ln~P~dHPaR~~~DTfy~~~~~~~lLRtHTS~~q~r~l~~~------~   78 (218)
T cd00496           6 VIEEIEDIF-VSMGFTEVEGPEVETDFYNFDALNIPQDHPARDMQDTFYINDPARLLLRTHTSAVQARALAKL------K   78 (218)
T ss_pred             HHHHHHHHH-HHCCCEEECCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCCEECCCCCHHHHHHHHHC------C
T ss_conf             999999999-877986822895123103045338598875537243278637766021578756679999745------8


Q ss_pred             HCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCC---HHHHCCCCCHH
Q ss_conf             042088532210788433554343212222102002121278650145789899999999998410---67530378011
Q gi|254780680|r  250 LPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDL---HYRVVSLCTGD  326 (430)
Q Consensus       250 LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~l---pyRvv~~~sgd  326 (430)
                      -|+|+++.+.|||+|+=.+   |.    .++|+.+|-+++-.    .--+..+....+++++.|.=   .+|..  |+ =
T Consensus        79 ~p~~~~~~G~VyR~D~iDa---tH----~~~FhQ~Eg~~v~~----~~~~~~Lk~~l~~~~~~lfg~~~~~r~r--p~-y  144 (218)
T cd00496          79 PPIRIFSIGRVYRNDEIDA---TH----LPEFHQIEGLVVDK----GLTFADLKGTLEEFAKELFGPITKVRFR--PS-Y  144 (218)
T ss_pred             CCCEEEECCCEEECCCCCC---CC----CCEEEEEEEEEEEC----CCCHHHHHHHHHHHHHHHCCCCCEEEEC--CC-C
T ss_conf             9817994250465388984---31----53125763799956----5119999999999999973876645367--78-8


Q ss_pred             CCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             784434024101101004833237531021007645326847338998410104200432289999999
Q gi|254780680|r  327 LGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIA  395 (430)
Q Consensus       327 lg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~a  395 (430)
                      -.|+ --.+.+++|.|..+.|.||..|.-..----+.+++   +  .+-+.|+.     |+-+-|+..-
T Consensus       145 FPFT-ePS~Evdv~~~~~~~WlEv~G~G~v~p~vL~~~G~---d--~~~~g~Af-----G~GlERlaMl  202 (218)
T cd00496         145 FPFT-EPSFEVDVYCPGCLGWLEILGCGMVRPEVLENAGI---D--EEYSGFAF-----GIGLERLAML  202 (218)
T ss_pred             CCCC-CCCEEEEEEECCCCCCEEEECCCCCCHHHHHHCCC---C--CCCEEEEE-----EECHHHHHHH
T ss_conf             9999-98269999965878714885046548899986697---9--99889998-----5258899999


No 52 
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=97.20  E-value=0.0009  Score=48.79  Aligned_cols=147  Identities=19%  Similarity=0.365  Sum_probs=69.4

Q ss_pred             CCCCCCCCCCCCCCCHHHHC----CCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHH
Q ss_conf             15656656662112202211----73100011222167530105648899999999999862232032021235620278
Q gi|254780680|r  129 GKKPSAIHLSREHFEIGEAL----GLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDE  204 (430)
Q Consensus       129 G~~~~f~f~~k~H~elge~l----~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~  204 (430)
                      +......+.+++|....+.+    --+|. |. ....        +.-++--++++.+-++ +.++||++|-+|.|..+.
T Consensus       105 ska~~lP~~~~~~~~~~e~~Rl~~RyLDL-r~-~~~~--------~~fr~Rs~i~~~iR~f-l~~~gFiEVeTPiL~~s~  173 (587)
T PRK00476        105 NKSKTLPFQIDDETNVSEELRLKYRYLDL-RR-PEMQ--------NNLKLRSKVTSAIRNF-LDDNGFLEIETPILTKST  173 (587)
T ss_pred             ECCCCCCCCCCCCCCCCHHHHHHHHHHHH-CC-HHHH--------HHHHHHHHHHHHHHHH-HHHCCCCEECCCCCCCCC
T ss_conf             76889998865566777888655478887-21-7788--------9999999999999999-997597400475432568


Q ss_pred             HHHHHHHC--HHHHHHHHHHHHCCE-ECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             89865514--224767764310002-313454114544534205955504208853221078843355434321222210
Q gi|254780680|r  205 AMYGTGQI--PKFADDMFCTTDGRW-LIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQF  281 (430)
Q Consensus       205 ~~~gtG~l--p~f~~~~y~~~d~l~-Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF  281 (430)
                       -+|.+-+  |.   .+|+  +..| | +-|-    -+|. +.+--.-+ =|+..++||||.| |+   +|.   |.-+|
T Consensus       174 -~eGA~~F~vps---r~~~--~~fyaL-~qSP----QLyk-q~L~vgG~-erVyeig~~FRnE-~~---~t~---r~pEF  233 (587)
T PRK00476        174 -PEGARDYLVPS---RVHP--GKFYAL-PQSP----QLFK-QLLMVAGF-DRYYQIARCFRDE-DL---RAD---RQPEF  233 (587)
T ss_pred             -CCCCCCCCCCC---CCCC--CCEECC-CCCH----HHHH-HHHHHCCC-CEEEEECCCCCCC-CC---CCC---CCCHH
T ss_conf             -66664430131---0578--855135-6797----9999-99885175-5279964312388-88---766---68234


Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             2002121278650145789899999999998
Q gi|254780680|r  282 WKCELVSITREEDSFTEHERMLSCAEEILKR  312 (430)
Q Consensus       282 ~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~  312 (430)
                      +.+|+..      |+.-++.+.+.+|++++.
T Consensus       234 t~lE~E~------af~d~~dvm~~~E~li~~  258 (587)
T PRK00476        234 TQIDIEM------SFVTQEDVMDLMEGLIRH  258 (587)
T ss_pred             HEEEHHH------HCCCHHHHHHHHHHHHHH
T ss_conf             2311111------116899999999999999


No 53 
>PRK07080 hypothetical protein; Validated
Probab=97.11  E-value=0.014  Score=39.84  Aligned_cols=233  Identities=16%  Similarity=0.179  Sum_probs=149.2

Q ss_pred             CHHHHHHH---HHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHH-----HH------------HH-----
Q ss_conf             64889999---9999999862232032021235620278898655142247677-----64------------31-----
Q gi|254780680|r  169 GHLAHLER---ALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDM-----FC------------TT-----  223 (430)
Q Consensus       169 g~~A~Le~---ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~-----y~------------~~-----  223 (430)
                      |-.+..|.   +|-.+..... ...|-+-+--|-.++...++.+|++-.|.+-.     |+            .+     
T Consensus        42 gRs~~fE~vv~~l~a~i~~~g-~~~~~evlrFPPvm~r~~fE~s~YlkSFP~L~GtV~~f~G~e~~h~~ll~~~~~g~dW  120 (318)
T PRK07080         42 GRSGLFERVVDALDALITRLG-ADQGAEVLRFPPAMSRAEFERSGYLKSFPQLAGTVHSFCGNEREHRRLLACLDRGEDW  120 (318)
T ss_pred             CCCHHHHHHHHHHHHHHHHHC-CCCCCCEEECCCCCCHHHHHHCCHHHHCCHHHCCEECCCCCCHHHHHHHHHHHCCCCC
T ss_conf             361549999999999998736-4458715766998865553330465525002010010468968999999998718984


Q ss_pred             ------HCCEECCCCCCHHHHHHHH-HCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHH
Q ss_conf             ------0002313454114544534-205955504208853221078843355434321222210200212127865014
Q gi|254780680|r  224 ------DGRWLIPTSEVSLTNLYSH-EIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSF  296 (430)
Q Consensus       224 ------d~l~Li~TaEvpL~~~~~~-~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~  296 (430)
                            .|.-|+|-|=.|+--+.+. -.++.+  ...+--.|-|||.|-.   +   -+-|+.-|..-|.+.+-+||+..
T Consensus       121 t~~~~ptdvvLtPAACyPvYP~~a~rG~LP~~--G~~~dv~~yCFRhEPS---~---dp~Rmq~FRMrEyV~iGt~e~v~  192 (318)
T PRK07080        121 TESQKPTDVVLTPAACYPVYPVVASRGPLPAG--GRIVDVFSYCFRHEPS---L---DPARMQLFRMREYVRIGTPEQIL  192 (318)
T ss_pred             CCCCCCCCEEECCCCCCCCCHHHCCCCCCCCC--CEEEEEEEEHHCCCCC---C---CHHHHHHHHCEEEEEECCHHHHH
T ss_conf             22357664575040114253766027889888--7489876421017898---8---85888864404457717999999


Q ss_pred             HHHHHHHHHHHHHHHHHCCHHHHCCCCC------HHCCCH----HHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCC
Q ss_conf             5789899999999998410675303780------117844----340241011010048332375310210076453268
Q gi|254780680|r  297 TEHERMLSCAEEILKRLDLHYRVVSLCT------GDLGFS----ACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNS  366 (430)
Q Consensus       297 ~~~e~~~~~~~~i~~~L~lpyRvv~~~s------gdlg~~----a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~i  366 (430)
                      +.-+.-+.-+..+.+.|+||+++.--+-      |-|-+.    ...||.|-+-+.|...=--+.|+-+-.|+-..+-+|
T Consensus       193 a~R~~W~~r~~~~~~~L~L~~~vd~AnDPFFGr~Gk~~a~~Qreq~LKfEllipi~~~~~ptAc~S~NyH~dhFG~~~~i  272 (318)
T PRK07080        193 AFRQRWIERGTRMADALGLPVEIDVANDPFFGRGGKIVADSQREQNLKFELLIPIESDARPTACMSFNYHMDHFGLTWGI  272 (318)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCHHHHHHHHHHHHHCCEEEEEECCCCCCCEEEEEECHHHHHCCCCCCC
T ss_conf             99999999999999975998523115787546307777557776421347999736899971589621145550366674


Q ss_pred             EEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCCC
Q ss_conf             4733899841010420043228999999998834689983865822231018
Q gi|254780680|r  367 RYRDPNSKSLKFTHTLNGSGVAVGRCLIAILENYLNADGSVTIPTVLRPYMN  418 (430)
Q Consensus       367 ry~~~~~~~~~~~htlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~pym~  418 (430)
                      +--  +|   ..+||- .-|.-+-|+-.|++-.|--.-  -.-|+..|.-|+
T Consensus       273 ~~a--dg---~~AHT~-CVgFGlERlalAL~~~HGlD~--~~WP~~VR~~L~  316 (318)
T PRK07080        273 RTA--DG---AVAHTG-CVGFGLERLALALFRHHGLDP--AAWPAAVRDVLW  316 (318)
T ss_pred             CCC--CC---CEEEHH-HHHCCHHHHHHHHHHHCCCCH--HHCCHHHHHHHC
T ss_conf             047--88---710010-211159999999998719981--437788999855


No 54 
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=97.11  E-value=0.00069  Score=49.62  Aligned_cols=117  Identities=20%  Similarity=0.391  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECCCCCCHHHHHHHHHCCCHHH
Q ss_conf             48899999999999862232032021235620278898655142247677643100023134541145445342059555
Q gi|254780680|r  170 HLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIPTSEVSLTNLYSHEIIESKS  249 (430)
Q Consensus       170 ~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~  249 (430)
                      +.-++--++++++-++ +.++||++|.||.|+...+-.|.--+|-   . | .+.+.||-=..|.     |....+- .-
T Consensus       135 ~~~r~Rs~i~~~iR~f-l~~~gF~EVeTP~l~~~~~eGga~~f~~---~-~-~~~~~yL~~Spql-----y~q~li~-~G  202 (434)
T PRK05159        135 AIFKIRSEVLRAFREF-LYEEGFTEIFTPKIVATGTEGGTELFPV---K-Y-FEKEAFLAQSPQL-----YKQMMMA-AG  202 (434)
T ss_pred             HHHHHHHHHHHHHHHH-HHHCCCEEEECCCCCCCCCCCCCCCCCE---E-E-CCCEEEECCCCHH-----HHHHHHH-CC
T ss_conf             9999999999999999-9877919997874325678875565861---3-1-2753341468379-----9999876-35


Q ss_pred             HCCEEEEEECCCCCCCCCCCCCCCCEEEEE--EEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             042088532210788433554343212222--1020021212786501457898999999999984
Q gi|254780680|r  250 LPLRFTTLAPSFRSEAGSAGRDTRGMLRQH--QFWKCELVSITREEDSFTEHERMLSCAEEILKRL  313 (430)
Q Consensus       250 LPik~~~~s~cfR~EaGs~GkdtrGl~RvH--QF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L  313 (430)
                      + =|+..++||||.|-.    +|.    -|  +|+.+|...      ++.-+++|.+..|+++..+
T Consensus       203 ~-~rvfeI~~~FR~E~~----~t~----RH~pEFT~lE~e~------af~d~~d~m~~~E~li~~i  253 (434)
T PRK05159        203 F-ERVFEIGPAFRAEEH----NTT----RHLNEAISIDVEM------GFIDEEDVMDLLENLLKYV  253 (434)
T ss_pred             C-CCEEEECCCEECCCC----CCC----CCHHHHHHHHHHH------CCCCHHHHHHHHHHHHHHH
T ss_conf             6-855996601023658----754----4535676566663------1068999999999999999


No 55 
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=97.10  E-value=0.0018  Score=46.59  Aligned_cols=121  Identities=25%  Similarity=0.474  Sum_probs=64.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHH-CHHHHHHH-----------HHH---HHCCEECCCCCCH
Q ss_conf             88999999999998622320320212356202788986551-42247677-----------643---1000231345411
Q gi|254780680|r  171 LAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQ-IPKFADDM-----------FCT---TDGRWLIPTSEVS  235 (430)
Q Consensus       171 ~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~-lp~f~~~~-----------y~~---~d~l~Li~TaEvp  235 (430)
                      ..++.-.+++.+-++ +.++||+||-||.|+.... +|.+. +.-..-++           |+.   +.+.||.=..|  
T Consensus       134 ifr~RS~i~~~iR~~-l~~~~F~EVeTP~L~~~~~-eGaa~~F~v~~~~~~~~~~~~~~~~~~~~yf~~~~yL~~Spq--  209 (462)
T PRK03932        134 VMRVRNTLAQAIHEF-FQENGFVWVHTPIITASDC-EGAGELFRVTTLDLENLPRTDGKVDFSKDFFGKEAFLTVSGQ--  209 (462)
T ss_pred             HHHHHHHHHHHHHHH-HHHCCCEEEECCCCCCCCC-CCCCCCEEECCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHH--
T ss_conf             999999999999999-9767967997886535687-645574042145434454334443311454277620265768--


Q ss_pred             HHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             454453420595550420885322107884335543432122221020021212786501457898999999999984
Q gi|254780680|r  236 LTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRL  313 (430)
Q Consensus       236 L~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L  313 (430)
                         +|....+.  -+. |+..++||||.|-.    ||.  -..-+|+.+|+..-      +.-+++|.+..|++++.+
T Consensus       210 ---Lylq~li~--G~e-rVfeIg~~FRnE~~----~t~--RH~pEFT~lE~e~a------~~d~~d~m~l~E~li~~i  269 (462)
T PRK03932        210 ---LYAEAYAM--ALS-KVYTFGPTFRAENS----NTR--RHLAEFWMIEPEMA------FADLEDNMDLAEDMLKYV  269 (462)
T ss_pred             ---HHHHHHHH--HCC-CEEEEEHHHHHCCC----CCC--CCCCCCEEEEEEEE------CCCHHHHHHHHHHHHHHH
T ss_conf             ---99999875--206-48997332320567----754--45430025553110------068999999999999999


No 56 
>PRK09350 lysyl-tRNA synthetase; Provisional
Probab=96.85  E-value=0.0011  Score=48.15  Aligned_cols=118  Identities=17%  Similarity=0.293  Sum_probs=65.9

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHH----HHHHHCCEECCCCCCHHHHHHHHHCCCHH
Q ss_conf             99999999999862232032021235620278898655142247677----64310002313454114544534205955
Q gi|254780680|r  173 HLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDM----FCTTDGRWLIPTSEVSLTNLYSHEIIESK  248 (430)
Q Consensus       173 ~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~----y~~~d~l~Li~TaEvpL~~~~~~~~l~~~  248 (430)
                      ++--++++..-++ ..++||++|.||.|++... .|++-.| |+-+.    .......||.-..|     +|+...+.. 
T Consensus        17 ~~Rs~i~~~iR~f-f~~~gFlEVeTP~L~~~t~-~~~~~~~-f~~~~~~~~~~~~~~~yL~~SPq-----l~~k~l~~~-   87 (325)
T PRK09350         17 LKRAAIIAEIRRF-FADRGVLEVETPAMSQATV-TDIHLVP-FETRFVGPGHSQGKTLWLMTSPE-----YHMKRLLAA-   87 (325)
T ss_pred             HHHHHHHHHHHHH-HHHCCCEEEECCCCCCCCC-CCCCCCC-EEEECCCCCCCCCCCEEEECCHH-----HHHHHHHHC-
T ss_conf             9999999999999-9988968977984257788-7646762-22102565545676645507919-----999999866-


Q ss_pred             HHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             50420885322107884335543432122221020021212786501457898999999999984
Q gi|254780680|r  249 SLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRL  313 (430)
Q Consensus       249 ~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L  313 (430)
                       .==|+..++||||.|- + +  +   -|+-+|+.+|..      .|..-++.+.+..+++++.+
T Consensus        88 -G~~rvfqI~~~FR~E~-~-~--~---~H~pEFtmlE~~------~~~~d~~d~m~~~e~ll~~~  138 (325)
T PRK09350         88 -GSGPIFQLCRSFRNEE-A-G--R---YHNPEFTMLEWY------RPHYDMYRLMNEVDDLLQQV  138 (325)
T ss_pred             -CCCCEEEEEHHHCCCC-C-C--C---CCCCHHHHHHHH------HHCCCHHHHHHHHHHHHHHH
T ss_conf             -7885589611322899-9-8--7---657377888999------81548999999999999999


No 57 
>cd00775 LysRS_core Lys_tRNA synthetase (LysRS) class II core domain.  Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three characteristic sequence motifs in the core domain. It is found in eukaryotes as well as some prokaryotes and archaea.  However, LysRS belongs to class I aaRS's  in some prokaryotes and archaea. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.
Probab=96.78  E-value=0.0015  Score=47.03  Aligned_cols=116  Identities=19%  Similarity=0.356  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHH-HHHCCEECCCCCCHHHHHHHHHCCCHHHH
Q ss_conf             89999999999986223203202123562027889865514224767764-31000231345411454453420595550
Q gi|254780680|r  172 AHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFC-TTDGRWLIPTSEVSLTNLYSHEIIESKSL  250 (430)
Q Consensus       172 A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~-~~d~l~Li~TaEvpL~~~~~~~~l~~~~L  250 (430)
                      -++--.+++.+-++ ..++||++|.||.| . .+-.|.+-.| |.- -|. -+.+.||.-..+     +|+...+-. .+
T Consensus         8 ~~~Rs~i~~~iR~f-f~~~gF~Ev~TPiL-~-~~~~g~~~~~-f~~-~~~~~~~~~yL~qSpQ-----l~~q~l~~~-g~   76 (329)
T cd00775           8 FIVRSKIISYIRKF-LDDRGFLEVETPML-Q-PIAGGAAARP-FIT-HHNALDMDLYLRIAPE-----LYLKRLIVG-GF   76 (329)
T ss_pred             HHHHHHHHHHHHHH-HHHCCCEEEECCCC-C-CCCCCCCCCC-EEE-CCCCCCCCCCCCCCHH-----HHHHHHHHC-CC
T ss_conf             99999999999999-99889889979865-5-6688756753-132-2446786723068989-----999999856-77


Q ss_pred             CCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             42088532210788433554343212222102002121278650145789899999999998
Q gi|254780680|r  251 PLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKR  312 (430)
Q Consensus       251 Pik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~  312 (430)
                       =|+..++||||.| ++ +  +   -|.-+|+.+|+..      +..-++++.+.+|+++..
T Consensus        77 -~rvfqI~p~FR~E-~~-~--~---rHl~EFtmle~E~------~f~d~~dvm~~~E~li~~  124 (329)
T cd00775          77 -ERVYEIGRNFRNE-GI-D--L---THNPEFTMIEFYE------AYADYNDMMDLTEDLFSG  124 (329)
T ss_pred             -CCEEEEEECCCCC-CC-C--C---CCCCHHHHHHHHH------HCCCHHHHHHHHHHHHHH
T ss_conf             -7679981022479-99-9--7---7473456345777------447999999999999999


No 58 
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=96.77  E-value=0.01  Score=40.94  Aligned_cols=188  Identities=19%  Similarity=0.282  Sum_probs=111.9

Q ss_pred             HHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHH-----HHHHHHHHHC-------------------------
Q ss_conf             9999999986223203202123562027889865514224-----7677643100-------------------------
Q gi|254780680|r  176 RALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKF-----ADDMFCTTDG-------------------------  225 (430)
Q Consensus       176 ~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f-----~~~~y~~~d~-------------------------  225 (430)
                      +-.++.+-+..+ .=||+++.-|++-.+-==+-+=+.|.+     ..|.|.+.+.                         
T Consensus       248 ~~~~~~~r~i~~-~mGF~e~~g~~ve~~fwNfdaLf~Pq~HPARd~~Dtf~l~~~~~~~lp~~~~~~Vk~~HE~Gg~~gS  326 (501)
T PRK04172        248 REFIEEVRDILV-EMGFEEVKGPIVETEFWNFDALFQPQDHPAREMQDTFYLKYPSKGELPEELVERVKEVHEHGGDTGS  326 (501)
T ss_pred             HHHHHHHHHHHH-HCCCEEEECCCEECCCCCHHHHCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCC
T ss_conf             999999999999-7897685366101000033430589899855544537865765455737889889998742776788


Q ss_pred             -------------CEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCC
Q ss_conf             -------------0231345411454453420595550420885322107884335543432122221020021212786
Q gi|254780680|r  226 -------------RWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITRE  292 (430)
Q Consensus       226 -------------l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~p  292 (430)
                                   ..+.-|---++.+-+.   ....+-|+|+.+..+|||.|+=.+   |+    .++|+.||=+++-. 
T Consensus       327 ~Gw~y~w~~~~~~~~~lRthtt~~~~r~l---~~~~~~p~~~f~~~rvfR~e~~d~---tH----~~~F~Q~eg~v~~~-  395 (501)
T PRK04172        327 RGWGYKWDEDIAKRLVLRTHTTALSARYL---AERPEPPGKYFSIGRVFRPETIDA---TH----LPEFYQLEGIVMGE-  395 (501)
T ss_pred             CCCCCCCCHHHHHHHCCCCCCCHHHHHHH---HHCCCCCEEEECCCCEEECCCCCC---CC----CCEEEEEEEEEECC-
T ss_conf             77677778556643010436746679999---746899835735650542688886---54----41332224899848-


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECCC
Q ss_conf             50145789899999999998410675303780117844340241011010048332375310210076453268473389
Q gi|254780680|r  293 EDSFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDPN  372 (430)
Q Consensus       293 e~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~~  372 (430)
                         .--+-.++...+++++.||.. .|-.-|+ =-.|+. -...+.+|.|+.+ |.||.-|.-+-----+-++|.|    
T Consensus       396 ---~~~~~~L~g~l~~f~~~~g~~-~~rfrp~-yfPftE-Ps~E~~~~~~~~~-WiE~~g~G~~~pevl~~~g~~~----  464 (501)
T PRK04172        396 ---DVSFRHLLGILKEFYKRLGFE-EVKFRPA-YFPFTE-PSVEVEVYHPGLG-WVELGGAGIFRPEVTEPLGIDV----  464 (501)
T ss_pred             ---CCCHHHHHHHHHHHHHHHCCC-CEEECCC-CCCCCC-CCEEEEEEECCCC-EEEEECCCCCCHHHHHHCCCCC----
T ss_conf             ---887999999999999985886-0786799-899899-8278999957998-6998267578889997559998----


Q ss_pred             CCCCCEEEEECCCHHHHHHHHH
Q ss_conf             9841010420043228999999
Q gi|254780680|r  373 SKSLKFTHTLNGSGVAVGRCLI  394 (430)
Q Consensus       373 ~~~~~~~htlNgt~~A~~R~l~  394 (430)
                         ..++.     |+.+.|+-.
T Consensus       465 ---~~~a~-----G~g~eR~am  478 (501)
T PRK04172        465 ---PVLAW-----GIGIDRLAM  478 (501)
T ss_pred             ---CEEEE-----EECHHHHHH
T ss_conf             ---74787-----515999999


No 59 
>PRK12421 ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=96.69  E-value=0.0066  Score=42.37  Aligned_cols=142  Identities=16%  Similarity=0.169  Sum_probs=93.6

Q ss_pred             ECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHH-HHHHCHHHHHHHHHHHHC-----CEECCCCCCHHHHHH
Q ss_conf             05648899999999999862232032021235620278898-655142247677643100-----023134541145445
Q gi|254780680|r  167 LTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMY-GTGQIPKFADDMFCTTDG-----RWLIPTSEVSLTNLY  240 (430)
Q Consensus       167 Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~-gtG~lp~f~~~~y~~~d~-----l~Li~TaEvpL~~~~  240 (430)
                      +-.+-|.-...|.+-.+|. ...+||.+|.||.+=..+++. |.|.  .-+.++|+..|.     +.|-|---.|++=+.
T Consensus        16 ~lP~ea~~~~~l~~~l~~~-f~~~Gy~~V~tP~lE~~e~l~~~~g~--~~~~~~f~~~D~~sGr~l~LRpD~T~~vARi~   92 (391)
T PRK12421         16 LLPEEAQKIERLRRRLLDL-FASRGYQLVMPPFIEYLESLLTGAGQ--DLDLQTFKLIDQLSGRLMGVRADITPQVARID   92 (391)
T ss_pred             CCHHHHHHHHHHHHHHHHH-HHHCCCEEEECCCCCCHHHHCCCCCC--CCCEEEEEEEECCCCCEEEECCCCCHHHHHHH
T ss_conf             8999999999999999999-99869976216760728785656687--34147999961799978655653206889999


Q ss_pred             HHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEE-EEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             34205955504208853221078843355434321222-21020021212786501457898999999999984106753
Q gi|254780680|r  241 SHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQ-HQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRV  319 (430)
Q Consensus       241 ~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~Rv-HQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRv  319 (430)
                      + .. ...+.|.|++-.+++||.+.-..     |=+|. ||+ =||+|....++    .=-|++..+-+.++.||++--.
T Consensus        93 a-~~-~~~~~p~Rl~Y~G~V~R~~~~~~-----gr~Ref~Q~-G~EliG~~~~~----aD~EvI~l~~~~L~~lGl~~~~  160 (391)
T PRK12421         93 A-HL-LNREGVARYCYAGSVLHTLPQGL-----NASRAPLQL-GAELYGHAGIE----ADIEIIDLMLGLLRNAGVEGLH  160 (391)
T ss_pred             H-HH-CCCCCCEEEEEECEEEECCCCCC-----CCCCCCEEC-CEEEECCCCHH----HHHHHHHHHHHHHHHCCCCCEE
T ss_conf             8-74-04688657999651775168888-----876652150-58985699879----8999999999999976998069


Q ss_pred             CCCC
Q ss_conf             0378
Q gi|254780680|r  320 VSLC  323 (430)
Q Consensus       320 v~~~  323 (430)
                      +++.
T Consensus       161 l~lg  164 (391)
T PRK12421        161 LDLG  164 (391)
T ss_pred             EEEC
T ss_conf             9968


No 60 
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=96.62  E-value=0.0031  Score=44.82  Aligned_cols=117  Identities=22%  Similarity=0.384  Sum_probs=64.5

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECCCCCCHHHHHHHHHCCCHHHHCC
Q ss_conf             99999999999862232032021235620278898655142247677643100023134541145445342059555042
Q gi|254780680|r  173 HLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIPTSEVSLTNLYSHEIIESKSLPL  252 (430)
Q Consensus       173 ~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~LPi  252 (430)
                      ++--.+++.+-++ +.++||.+|-+|.|  ..+..|+.-.| |..-....+.++|| +.|-    =+|....+- .-+ =
T Consensus       172 ~~Rs~ii~~iR~~-l~~~gF~EVeTPiL--~~~~gGA~Arp-F~t~~n~l~~~~yL-~~SP----qLylk~l~v-gG~-e  240 (491)
T PRK00484        172 RKRSKIISAIRRF-LDNRGFLEVETPML--QPIPGGAAARP-FITHHNALDIDLYL-RIAP----ELYLKRLIV-GGF-E  240 (491)
T ss_pred             HHHHHHHHHHHHH-HHHCCEEEEECCCC--CCCCCCCCCCC-CCCCCCCCCCCEEE-CCCH----HHHHHHHHH-CCC-H
T ss_conf             9999999999999-98676899867877--66688756676-55644566855442-0687----898777876-272-0


Q ss_pred             EEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             0885322107884335543432122221020021212786501457898999999999984
Q gi|254780680|r  253 RFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRL  313 (430)
Q Consensus       253 k~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L  313 (430)
                      ||..++||||.| |+   +++   |.-+|+.+|...      |+.-++.|.+..|++++.+
T Consensus       241 rvfeI~r~FR~E-~~---~~r---H~pEFT~lE~e~------af~d~~dvm~l~E~li~~v  288 (491)
T PRK00484        241 RVFEIGRNFRNE-GI---DTR---HNPEFTMIEFYQ------AYADYNDMMDLTEELIRHL  288 (491)
T ss_pred             HHEEHHHHHHCC-CC---CCC---CCCCEEEEEEEE------ECCCHHHHHHHHHHHHHHH
T ss_conf             222248766257-55---434---184010213677------2479999999999999999


No 61 
>cd00776 AsxRS_core Asx tRNA synthetase (AspRS/AsnRS) class II core domain.  Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS.  AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the appropriate tRNA.  While archaea lack asnRS, they possess a non-discriminating aspRS, which can mischarge Asp-tRNA with Asn. Subsequently, a tRNA-dependent aspartate amidotransferase converts the bound aspartate to asparagine. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.
Probab=96.55  E-value=0.0039  Score=44.01  Aligned_cols=114  Identities=25%  Similarity=0.512  Sum_probs=64.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECCCCCCHHHHHHHHHCCCHHHH
Q ss_conf             88999999999998622320320212356202788986551422476776431000231345411454453420595550
Q gi|254780680|r  171 LAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIPTSEVSLTNLYSHEIIESKSL  250 (430)
Q Consensus       171 ~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~L  250 (430)
                      .-++--.+++.+-++ +.++||++|-||.|+...+ +|.+..  |.-.  .-+.+.||.=..|     +| .+.+-. -+
T Consensus        23 ~l~~Rs~i~~~iR~f-l~~~gF~EVeTP~L~~~~~-eg~a~~--f~~~--~~~~~~yL~~Spe-----l~-Kqlli~-G~   89 (322)
T cd00776          23 IFRIRSEVLRAFREF-LRENGFTEVHTPKITSTDT-EGGAEL--FKVS--YFGKPAYLAQSPQ-----LY-KEMLIA-AL   89 (322)
T ss_pred             HHHHHHHHHHHHHHH-HHHCCCEEEECCCCCCCCC-CCCCCC--CCCC--CCCCCEEECCCHH-----HH-HHHHHC-CC
T ss_conf             999999999999999-9988999997984007889-865466--7621--0587600154858-----89-999753-42


Q ss_pred             CCEEEEEECCCCCCCCCCCCCCCCEEEEE--EEEEEEEEECCCCCCHHH-HHHHHHHHHHHHHHH
Q ss_conf             42088532210788433554343212222--102002121278650145-789899999999998
Q gi|254780680|r  251 PLRFTTLAPSFRSEAGSAGRDTRGMLRQH--QFWKCELVSITREEDSFT-EHERMLSCAEEILKR  312 (430)
Q Consensus       251 Pik~~~~s~cfR~EaGs~GkdtrGl~RvH--QF~KVE~~~~~~pe~S~~-~~e~~~~~~~~i~~~  312 (430)
                      . |+..+++|||.|-+ .   |    +-|  +|+.+|.      +.++. -+++|.+.+|++++.
T Consensus        90 ~-rVfei~~~FR~E~~-~---t----~rH~pEFTmlE~------e~af~~d~~d~m~~~E~li~~  139 (322)
T cd00776          90 E-RVYEIGPVFRAEKS-N---T----RRHLSEFWMLEA------EMAFIEDYNEVMDLIEELIKY  139 (322)
T ss_pred             C-CEEEECCEEECCCC-C---C----CCCHHHHHHHHH------HHHHHCCHHHHHHHHHHHHHH
T ss_conf             4-43887261407999-8---7----534788876525------552332899999999999999


No 62 
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=96.54  E-value=0.0032  Score=44.70  Aligned_cols=139  Identities=20%  Similarity=0.337  Sum_probs=76.4

Q ss_pred             CCCCCCCCCCCHHHHCC--CCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHH
Q ss_conf             66566621122022117--3100011222167530105648899999999999862232032021235620278898655
Q gi|254780680|r  133 SAIHLSREHFEIGEALG--LMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTG  210 (430)
Q Consensus       133 ~f~f~~k~H~elge~l~--liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG  210 (430)
                      .+...++.|.++-..++  .+|..+.          ..+...+..-++...+-++ ..++||++|.||.|+-..+--|+-
T Consensus       103 ~~Pi~~~~~~~~e~lld~rhL~lR~~----------~~~Av~kirs~i~~a~~ef-f~~~gF~eV~tP~i~~~~~EGg~e  171 (435)
T COG0017         103 PYPIDKKEHSELETLLDNRHLDLRTP----------KIQAVFKIRSSILRAIREF-FYENGFTEVHTPIITASATEGGGE  171 (435)
T ss_pred             CCCCCCCCCCCHHHHHHCHHEECCCC----------CHHHHHHHHHHHHHHHHHH-HHHCCCEEECCCEEECCCCCCCCE
T ss_conf             77768645557888874403020462----------0377894999999999999-975895896594685347899850


Q ss_pred             HCH--HHHHHHHHHHH-CCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEE-
Q ss_conf             142--24767764310-00231345411454453420595550420885322107884335543432122221020021-
Q gi|254780680|r  211 QIP--KFADDMFCTTD-GRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCEL-  286 (430)
Q Consensus       211 ~lp--~f~~~~y~~~d-~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~-  286 (430)
                      .++  .|+.+.|.... -||+    |.-.++           | -|...++|+||+|..    +|+=  .+-+|..+|. 
T Consensus       172 lF~v~yf~~~a~LtqS~QLyk----e~~~~a-----------l-~rVf~igP~FRAE~s----~T~R--HL~EF~~ld~E  229 (435)
T COG0017         172 LFKVDYFDKEAYLTQSPQLYK----EALAAA-----------L-ERVFTIGPTFRAEKS----NTRR--HLSEFWMLDPE  229 (435)
T ss_pred             EEEEEECCCCEEEECCHHHHH----HHHHHH-----------H-CCEEEECCCEECCCC----CCCC--HHHHHHEECCE
T ss_conf             577750685667714788999----999998-----------5-764895672554778----9700--36667330211


Q ss_pred             EECCCCCCHHHHHHHHHH
Q ss_conf             212786501457898999
Q gi|254780680|r  287 VSITREEDSFTEHERMLS  304 (430)
Q Consensus       287 ~~~~~pe~S~~~~e~~~~  304 (430)
                      ..|++-++.....|+|+.
T Consensus       230 maf~~~~d~m~l~E~~i~  247 (435)
T COG0017         230 MAFADLNDVMDLAEELIK  247 (435)
T ss_pred             ECCCCHHHHHHHHHHHHH
T ss_conf             136768889999999999


No 63 
>PRK06462 asparagine synthetase A; Reviewed
Probab=96.37  E-value=0.004  Score=43.97  Aligned_cols=122  Identities=16%  Similarity=0.193  Sum_probs=65.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECCCCCCHHHHHHHHHCCCHHH
Q ss_conf             48899999999999862232032021235620278898655142247677643100023134541145445342059555
Q gi|254780680|r  170 HLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIPTSEVSLTNLYSHEIIESKS  249 (430)
Q Consensus       170 ~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~  249 (430)
                      +.-++.-++++.+-++ ..++||++|.||.|.....--+.+.++ |.-+  .-+.+.||.-..|     +|....+... 
T Consensus        27 ~ifriRs~i~~~iR~f-~~~~gF~EV~TPiL~~~~~~~~~~~~~-~~~~--~~~~~~~L~~Spq-----l~lk~li~~g-   96 (332)
T PRK06462         27 LVLKIQSSILRYTREF-LDGRGFVEVLPPIISPSTDPLMGDAKP-ASID--FYGVEYYLADSMI-----FHKQLMLRLL-   96 (332)
T ss_pred             HHHHHHHHHHHHHHHH-HHHCCCEEEECCCCCCCCCCCCCCCCC-CEEE--CCCCCEEECCCHH-----HHHHHHHHCC-
T ss_conf             9999999999999999-988899998797236778876677601-0584--4898633145869-----9999998638-


Q ss_pred             HCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             042088532210788433554343212222102002121278650145789899999999998
Q gi|254780680|r  250 LPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKR  312 (430)
Q Consensus       250 LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~  312 (430)
                      + =|+..++||||.|--    |...--..-+|+.+|...      ++.-++.|.+.+|++++.
T Consensus        97 ~-~rVfeIg~~FR~E~~----d~~t~rHlpEFt~lE~y~------a~~d~~d~m~~~E~li~~  148 (332)
T PRK06462         97 K-GKVFYLSPNFRLEPV----DKDTGRHLYEFTQLDIEI------EGADLEEVMSLAEDLIKY  148 (332)
T ss_pred             C-CCEEEECCHHHCCCC----CCCCCCCCHHHHHHHHHH------HHCCHHHHHHHHHHHHHH
T ss_conf             9-977997452316877----767776545777655878------738999999999999999


No 64 
>cd00777 AspRS_core Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. AspRS in this family differ from those found in the AsxRS family by a GAD insert in the core domain.
Probab=96.33  E-value=0.0029  Score=45.02  Aligned_cols=113  Identities=23%  Similarity=0.396  Sum_probs=57.1

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECCCCCCHHHHHHHHHCCCHHHHCCEE
Q ss_conf             99999999986223203202123562027889865514224767764310002313454114544534205955504208
Q gi|254780680|r  175 ERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIPTSEVSLTNLYSHEIIESKSLPLRF  254 (430)
Q Consensus       175 e~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~  254 (430)
                      .-.+++.+-++ ..++||.+|.||.|.... -+|++.   |..-...-.+..|..+||-.    +|+...+.. .+ =|+
T Consensus         4 Rs~i~~~iR~f-f~~~gflEV~TPiL~~~~-~ega~~---f~~~~~~~~~~~~~L~~Spe----l~~k~l~~~-g~-~rv   72 (280)
T cd00777           4 RSRVIKAIRNF-LDEQGFVEIETPILTKST-PEGARD---FLVPSRLHPGKFYALPQSPQ----LFKQLLMVS-GF-DRY   72 (280)
T ss_pred             HHHHHHHHHHH-HHHCCCEEEECCCCCCCC-CCCCCC---CEECCCCCCCCCCCCCCCHH----HHHHHHHHC-CC-CCC
T ss_conf             99999999999-998898998798106878-776766---44244168876036887989----999999856-87-775


Q ss_pred             EEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             853221078843355434321222210200212127865014578989999999999
Q gi|254780680|r  255 TTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILK  311 (430)
Q Consensus       255 ~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~  311 (430)
                      ..++||||.|- +   +++   |--+|+.+|...      ++..++++.+.+|++++
T Consensus        73 f~i~~~FR~E~-~---~~~---h~~EFtmLE~e~------~~~~~~d~m~~~E~li~  116 (280)
T cd00777          73 FQIARCFRDED-L---RAD---RQPEFTQIDIEM------SFVDQEDIMSLIEGLLK  116 (280)
T ss_pred             EEEECEECCCC-C---CCC---CCHHHHHHHHHC------CCCCHHHHHHHHHHHHH
T ss_conf             79845174788-8---876---634776234422------68889999999999999


No 65 
>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed
Probab=96.25  E-value=0.0079  Score=41.77  Aligned_cols=97  Identities=16%  Similarity=0.270  Sum_probs=64.6

Q ss_pred             HCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCH-HHHCC
Q ss_conf             20595550420885322107884335543432122221020021212786501457898999999999984106-75303
Q gi|254780680|r  243 EIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLH-YRVVS  321 (430)
Q Consensus       243 ~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lp-yRvv~  321 (430)
                      .+.+...+|+|+.++-+|||+|-.-   |-.-|.--||   ++.++. .+   +--++.....++.+|+++|.. +|..-
T Consensus       198 ~l~~k~~~P~klFSIDRcFRrEq~e---D~~hL~~yhs---ascvv~-~e---dVn~d~gkav~~~lL~~fGF~~frFrP  267 (527)
T PRK06253        198 ALWERKPLPFKLFSIDRCFRREQKE---DASRLMTYHS---ASCVVA-GE---DVTVDDGKAVAEGLLSQFGFTNFRFRP  267 (527)
T ss_pred             HHHHCCCCCEEEEEEEHEEECHHHC---CHHHHHHHHE---EEEEEE-CC---CCCHHHHHHHHHHHHHHHCCCEEEECC
T ss_conf             9972679983687410102200002---4556345443---226997-59---866777799999999970975378434


Q ss_pred             --------CCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCC
Q ss_conf             --------780117844340241011010048332375310210
Q gi|254780680|r  322 --------LCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCG  357 (430)
Q Consensus       322 --------~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~  357 (430)
                              +|.-        +-.+.++-|..+.|.||.-+.-+.
T Consensus       268 dek~skYY~P~T--------qtEVy~yhp~~~gWvEvatfGIys  303 (527)
T PRK06253        268 DEKRSKYYTPDT--------QTEVYAYHPKLDGWVEVATFGIYS  303 (527)
T ss_pred             CCCCCCCCCCCC--------CEEEEEECCCCCCEEEEECCCCCC
T ss_conf             423566537886--------327999636678628973142567


No 66 
>cd00669 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=96.23  E-value=0.0042  Score=43.83  Aligned_cols=95  Identities=19%  Similarity=0.242  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECCCCCCHHHHHHHHHCCCHHHHCCEEE
Q ss_conf             99999999862232032021235620278898655142247677643100023134541145445342059555042088
Q gi|254780680|r  176 RALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIPTSEVSLTNLYSHEIIESKSLPLRFT  255 (430)
Q Consensus       176 ~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~  255 (430)
                      -++++..-++. .++||++|.||.|+....-.+   -..|.-..+..+.+.||.-..|..+     ...+.. -+ =|+.
T Consensus         5 s~i~~~iR~ff-~~~~f~EV~TP~l~~~~~~~~---~~~f~~~~~~~~~~~~L~~Spel~~-----k~ll~~-g~-~~if   73 (269)
T cd00669           5 SKIIKAIRDFM-DDRGFLEVETPMLQKITGGAG---ARPFLVKYNALGLDYYLRISPQLFK-----KRLMVG-GL-DRVF   73 (269)
T ss_pred             HHHHHHHHHHH-HHCCCEEEECCEEECCCCCCC---CCEEEEECCCCCCEEEECCCHHHHH-----HHHHHC-CC-CCEE
T ss_conf             99999999999-988989987985305789876---7425731378994077343889999-----999865-88-8679


Q ss_pred             EEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEE
Q ss_conf             532210788433554343212222102002121
Q gi|254780680|r  256 TLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVS  288 (430)
Q Consensus       256 ~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~  288 (430)
                      .++||||.| ++ |  +|   ..-+|+.+|...
T Consensus        74 ~i~~~FR~e-~~-~--~r---H~~EFtmlE~y~   99 (269)
T cd00669          74 EINRNFRNE-DL-R--AR---HQPEFTMMDLEM   99 (269)
T ss_pred             EEECCCCCC-CC-C--CC---CCHHHHHHHHHC
T ss_conf             984621078-98-6--55---434877578751


No 67 
>TIGR00442 hisS histidyl-tRNA synthetase; InterPro: IPR015807   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Histidyl-tRNA synthetase (6.1.1.21 from EC) is an alpha2 dimer that belongs to class IIa. Every completed genome includes a histidyl-tRNA synthetase. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and not demonstrated to act as histidyl-tRNA synthetases (see IPR004517 from INTERPRO). The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation, but these regulatory proteins are not orthologous.; GO: 0000166 nucleotide binding, 0004821 histidine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006427 histidyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=96.23  E-value=0.032  Score=37.29  Aligned_cols=156  Identities=21%  Similarity=0.276  Sum_probs=109.9

Q ss_pred             EECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHH-HHHCHH-HHHHHHHHH----HCCEECCCCCCHHHHH
Q ss_conf             1056488999999999998622320320212356202788986-551422-476776431----0002313454114544
Q gi|254780680|r  166 VLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYG-TGQIPK-FADDMFCTT----DGRWLIPTSEVSLTNL  239 (430)
Q Consensus       166 ~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~g-tG~lp~-f~~~~y~~~----d~l~Li~TaEvpL~~~  239 (430)
                      ++-++. ...+.+..-+-+. ....||.++.+|.+-..+.+.. +|.-.+ -..++|...    .++-|-|-.-+|++-+
T Consensus        13 ~~p~~~-~~~~~~~~~~~~~-~~~~g~~~~~~P~~e~~~~~~~~~~~~~~~~~~~~y~f~d~~~~~~~lrp~~t~~~~r~   90 (446)
T TIGR00442        13 WLPGEL-VYRQWIEAKLRSV-LESYGYSEIRTPIFEYTELFARGIGKSGDEVEKELYTFKDKGGRDLALRPELTAPVVRL   90 (446)
T ss_pred             CCCHHH-HHHHHHHHHHHHH-HHHCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHEEEECCCCCEEEECCCHHHHHHHH
T ss_conf             254157-8999999999999-97517720012114445666530253013344443012127884144222003689999


Q ss_pred             HHHHCCCH-HHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHH-
Q ss_conf             53420595-5504208853221078843355434321222210200212127865014578989999999999841067-
Q gi|254780680|r  240 YSHEIIES-KSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHY-  317 (430)
Q Consensus       240 ~~~~~l~~-~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpy-  317 (430)
                      +..+.+.. ...|+|+..+++|||.|-..    .+|-||.|----+|.+....|    ..--+++..+..+++.|++.. 
T Consensus        91 ~~~~~~~~~~~~p~~~~~~g~~~r~e~p~----~~gr~r~f~~~~~~~~G~~~~----~~~~~~~~~~~~~~~~~g~~~~  162 (446)
T TIGR00442        91 VAENKLLLPANKPLRLYYIGPVFRYERPQ----LKGRYREFWQFGCEVIGSESP----LADAEVLSLAVEGLKALGLEGH  162 (446)
T ss_pred             HHHHHHHCCCCCCEEEEEEECHHHCCCHH----HHCCHHHHHHCCEEEECCCCC----HHHHHHHHHHHHHHHHHCCCCE
T ss_conf             98754310467642432320101022412----301011332115046436652----0368999999998986076632


Q ss_pred             -HHCCCCCHHCCCHH
Q ss_conf             -53037801178443
Q gi|254780680|r  318 -RVVSLCTGDLGFSA  331 (430)
Q Consensus       318 -Rvv~~~sgdlg~~a  331 (430)
                       .+..-.-|.+....
T Consensus       163 ~~~~~~~~g~~~~~~  177 (446)
T TIGR00442       163 FKLKLNHLGILEGIL  177 (446)
T ss_pred             EEEEECCCHHHHHHH
T ss_conf             788741300145666


No 68 
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=96.04  E-value=0.034  Score=37.05  Aligned_cols=179  Identities=20%  Similarity=0.306  Sum_probs=103.7

Q ss_pred             CCCCCCHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCHHHH----CCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHH
Q ss_conf             225881122113555402420001565665666211220221----1731000112221675301056488999999999
Q gi|254780680|r  106 PNVPLEEVPIGTSANENILIRSVGKKPSAIHLSREHFEIGEA----LGLMDFDRATKLSGARFSVLTGHLAHLERALGQF  181 (430)
Q Consensus       106 PNi~~~~VP~G~de~dNv~i~~~G~~~~f~f~~k~H~elge~----l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y  181 (430)
                      +....+..|-|.-|--...|.-.+......|.+.+..+..|.    +--+|..|..         +...+ +|-...+..
T Consensus        81 e~~~N~~l~TGeiEv~a~~i~vln~s~~lPf~i~d~~~~~Ee~RLkYRyLDLRR~~---------m~~~l-~lR~kv~~~  150 (585)
T COG0173          81 EGTINPNLPTGEIEVLAEEIEVLNASKTLPFQIEDETNASEEIRLKYRYLDLRRPE---------MQKNL-KLRSKVTKA  150 (585)
T ss_pred             CCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHCCHH---------HHHHH-HHHHHHHHH
T ss_conf             55668888861499996268998647889947788888652220244555636888---------99999-999999999


Q ss_pred             HHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHH---HHHH-CCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEE
Q ss_conf             998622320320212356202788986551422476776---4310-002313454114544534205955504208853
Q gi|254780680|r  182 MIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMF---CTTD-GRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTL  257 (430)
Q Consensus       182 ~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y---~~~d-~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~  257 (430)
                      +-++ +..+||+++.+|.|.++.        |..+-|-.   ++.. ..|-.|-|-+-.-     +.|--+- ==||.-+
T Consensus       151 iR~~-ld~~gF~EiETPiLtkST--------PEGARDfLVPSRv~~G~FYALPQSPQlfK-----QLLMvsG-fdRYyQI  215 (585)
T COG0173         151 IRNF-LDDQGFLEIETPILTKST--------PEGARDFLVPSRVHPGKFYALPQSPQLFK-----QLLMVAG-FDRYYQI  215 (585)
T ss_pred             HHHH-HHHCCCEEEECCCCCCCC--------CCCCCCCCCCCCCCCCCEEECCCCHHHHH-----HHHHHHC-CCCEEEE
T ss_conf             9997-765498573467414679--------86554430134558996530688879999-----9998805-3300235


Q ss_pred             ECCCCCCCCCCCCCCCCEEEEEEEEEEEE-EECCCCCCHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf             22107884335543432122221020021-212786501457898999999999984106
Q gi|254780680|r  258 APSFRSEAGSAGRDTRGMLRQHQFWKCEL-VSITREEDSFTEHERMLSCAEEILKRLDLH  316 (430)
Q Consensus       258 s~cfR~EaGs~GkdtrGl~RvHQF~KVE~-~~~~~pe~S~~~~e~~~~~~~~i~~~L~lp  316 (430)
                      .+|||.|-      .| ==|+-+|+.+.| .+|++.++-....|+|+..+-.-....+|+
T Consensus       216 arCFRDED------lR-aDRQPEFTQiD~EmSF~~~edv~~~~E~l~~~vf~~~~~i~l~  268 (585)
T COG0173         216 ARCFRDED------LR-ADRQPEFTQIDLEMSFVDEEDVMELIEKLLRYVFKEVKGIELK  268 (585)
T ss_pred             EEEECCCC------CC-CCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             65404664------44-4468753367677643889999999999999999985097548


No 69 
>PTZ00326 phenylalanyl-tRNA synthetase; Provisional
Probab=96.00  E-value=0.026  Score=37.96  Aligned_cols=201  Identities=18%  Similarity=0.240  Sum_probs=113.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCC-----HHHHHHHHHCH-HHHHHHHHHHH-C---------------
Q ss_conf             56488999999999998622320320212356202-----78898655142-24767764310-0---------------
Q gi|254780680|r  168 TGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVR-----DEAMYGTGQIP-KFADDMFCTTD-G---------------  225 (430)
Q Consensus       168 kg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~-----~~~~~gtG~lp-~f~~~~y~~~d-~---------------  225 (430)
                      .|..--|- -.+..+-+..+ .=||+++-+|.+|-     -++++---+-| +...|.|.+.+ .               
T Consensus       238 ~g~~hp~~-~~~~~~r~if~-~mGF~E~~~~~~ves~fwNfDaLf~Pq~HPARd~~DTF~l~~p~~~~~~~~~~~~~Vk~  315 (505)
T PTZ00326        238 MGNLHPLL-KVRQEFREIFM-EMGFEEMPTNRWVESSFWNFDALFIPQQHPARDLQDTFFLSKPETSKFLDAEYVERVKA  315 (505)
T ss_pred             CCCCCHHH-HHHHHHHHHHH-HCCCEECCCCCEEEECCCCCHHHCCCCCCCCCCCCCEEEECCCCCCCCCCHHHHHHHHH
T ss_conf             77668899-99999999999-77976766897133132131110489899866523347744754245687899998888


Q ss_pred             ----------------------CEEC--CCCCCHHHHHHH--HHCCC-HHHHCCEEEEEECCCCCCCCCCCCCCCCEEEE
Q ss_conf             ----------------------0231--345411454453--42059-55504208853221078843355434321222
Q gi|254780680|r  226 ----------------------RWLI--PTSEVSLTNLYS--HEIIE-SKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQ  278 (430)
Q Consensus       226 ----------------------l~Li--~TaEvpL~~~~~--~~~l~-~~~LPik~~~~s~cfR~EaGs~GkdtrGl~Rv  278 (430)
                                            ..+.  -|+-|+.-.||.  ++..+ ...-|.||+++.+|||.|+=.+   |+    .
T Consensus       316 vHe~G~~gs~Gw~y~W~~~~a~~~~LRthTt~vs~r~l~~~~~~~~~~~~~~P~k~fsi~rv~R~e~~d~---th----~  388 (505)
T PTZ00326        316 VHSGGGYGSIGWQYNWKLEEARKNVLRTHTTAVSARMLYKLAQQYQKGKGFKPKKYFSIDRVFRNETLDA---TH----L  388 (505)
T ss_pred             HHCCCCCCCCCCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEECCCEEECCCCCC---CC----C
T ss_conf             8506887888767787977875206365775376999998754046556889814752372641577776---53----4


Q ss_pred             EEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCC
Q ss_conf             21020021212786501457898999999999984106753037801178443402410110100483323753102100
Q gi|254780680|r  279 HQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGN  358 (430)
Q Consensus       279 HQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D  358 (430)
                      ++|+.||=+++-.    .--+-.+...-+++++.||.. ++---|+-- .|+.- ...+.+|.|+.++|.||.-|.-+--
T Consensus       389 ~~f~Q~eg~~~~~----~~~~~~l~~~l~~f~~~~g~~-~~rfrp~yf-pfteP-s~e~~~~~~~~~~w~Ei~g~Gm~~p  461 (505)
T PTZ00326        389 AEFHQVEGVVIDR----NLSLGDLMGTLREFFRRIGIS-KLRFKPAFN-PYTEP-SMEIFGYHPQLKKWVEVGNSGLFRP  461 (505)
T ss_pred             CEEEEEEEEEECC----CCCHHHHHHHHHHHHHHHCCC-CEEECCCCC-CCCCC-CEEEEEEECCCCCEEEEECCCCCCH
T ss_conf             0455435789648----888999999999999984987-578688888-98998-2789997078884799826657587


Q ss_pred             HHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHH
Q ss_conf             764532684733899841010420043228999999
Q gi|254780680|r  359 FQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLI  394 (430)
Q Consensus       359 ~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~  394 (430)
                      -.-+-++|   +.+  -+.|+.     |+-+.|+..
T Consensus       462 ~vl~~~g~---~~~--~~~~a~-----G~g~eR~am  487 (505)
T PTZ00326        462 EMLRPMGF---PED--VTVIAW-----GLSLERPTM  487 (505)
T ss_pred             HHHHHCCC---CCC--CEEEEE-----EECHHHHHH
T ss_conf             88732595---999--848998-----623889999


No 70 
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=95.90  E-value=0.098  Score=33.65  Aligned_cols=112  Identities=21%  Similarity=0.332  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHC--HH-HHHHHHHHHHCCEECCCCCCHHHHHHHHHCCCHHH
Q ss_conf             9999999999986223203202123562027889865514--22-47677643100023134541145445342059555
Q gi|254780680|r  173 HLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQI--PK-FADDMFCTTDGRWLIPTSEVSLTNLYSHEIIESKS  249 (430)
Q Consensus       173 ~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~l--p~-f~~~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~  249 (430)
                      ++--.+++.+-++ +.++||++|-+|.|+++ +-+|...+  |. +.      ..+.|-.|-|-+    +| .+.+--.-
T Consensus       157 ~~Rskv~~~iR~~-l~~~gF~EVETP~L~~s-tpEGArdflvPsr~~------~~~fyaLpQSPQ----ly-KQlLMvgG  223 (706)
T PRK12820        157 AKRHRIIKCARDF-LDSRGFLEIETPILTKS-TPEGARDYLVPSRIH------PKEFYALPQSPQ----LF-KQLLMIAG  223 (706)
T ss_pred             HHHHHHHHHHHHH-HHHCCCEEEECCEECCC-CCCCCCCCCCCEECC------CCCEECCCCCHH----HH-HHHHHHCC
T ss_conf             9999999999999-98779889668704456-753245750024458------876500566829----99-99998628


Q ss_pred             HCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEE-ECCCCCCHHHHHHHHHHH
Q ss_conf             04208853221078843355434321222210200212-127865014578989999
Q gi|254780680|r  250 LPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELV-SITREEDSFTEHERMLSC  305 (430)
Q Consensus       250 LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~-~~~~pe~S~~~~e~~~~~  305 (430)
                      + =||.-+.||||.|-..       --|+-+|+-+++- +|.+.++-.+..|+|+..
T Consensus       224 ~-dRyFqIarcFRdEd~r-------~dRqPEFTqlDiEmSF~d~edvm~l~E~li~~  272 (706)
T PRK12820        224 F-ERYFQLARCFRDEDLR-------PNRQPEFTQLDIEASFIDEEFIFELIEELTAR  272 (706)
T ss_pred             C-CEEEEEEEEECCCCCC-------CCCCCCEEEEEEEHHCCCHHHHHHHHHHHHHH
T ss_conf             6-6179960011289999-------88798340687421348999999999999999


No 71 
>TIGR00457 asnS asparaginyl-tRNA synthetase; InterPro: IPR004522   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   AsparaginyltRNA synthetase (6.1.1.22 from EC) is an alpha2 dimer that belongs to class IIb. There is a striking similarity between asparaginyl-tRNA synthetases and archaeal/eukaryotic type aspartyl-tRNA synthetases (IPR004523 from INTERPRO) and a striking divergence of bacterial type aspartyl-tRNA synthetases (IPR004524 from INTERPRO). This family, AsnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.; GO: 0000166 nucleotide binding, 0004816 asparagine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006421 asparaginyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=95.67  E-value=0.016  Score=39.43  Aligned_cols=145  Identities=23%  Similarity=0.412  Sum_probs=76.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHH-HHHHHH--------------HCCEECCCC
Q ss_conf             56488999999999998622320320212356202788986551422476-776431--------------000231345
Q gi|254780680|r  168 TGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFAD-DMFCTT--------------DGRWLIPTS  232 (430)
Q Consensus       168 kg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~-~~y~~~--------------d~l~Li~Ta  232 (430)
                      .|+.+++=-+|.+-..++- .++||+.|.||.|+-++ -||+|-+=+-.. ++=++.              .+=||.   
T Consensus       142 ~~AvmrvR~~l~~ai~~yF-~~~gF~~V~~PilT~~d-~EGAGElF~v~TLdl~~lp~~~g~~df~~~fFgk~ayLT---  216 (495)
T TIGR00457       142 LGAVMRVRNALSQAIHEYF-QKNGFVKVSPPILTSND-CEGAGELFKVSTLDLEKLPRNDGKIDFSKDFFGKEAYLT---  216 (495)
T ss_pred             HHHHHHHHHHHHHHHHHHH-HCCCCEEECCCEEECCC-CCCCCCCCEEEEHHHHCCCCCCCCCCCCCCCCCCEEEEE---
T ss_conf             7789999999999999876-04786786886311368-888754332200324215332688876302488601233---


Q ss_pred             CCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEE-EEECCCCCCHHHHHHHHHHHH-HHHH
Q ss_conf             41145445342059555042088532210788433554343212222102002-121278650145789899999-9999
Q gi|254780680|r  233 EVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCE-LVSITREEDSFTEHERMLSCA-EEIL  310 (430)
Q Consensus       233 EvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE-~~~~~~pe~S~~~~e~~~~~~-~~i~  310 (430)
                         ..+-...|+.... | -|...++||||+|- |+  .+|   .+-+|..|| =++|++=++-.++-|.||... +.++
T Consensus       217 ---VSGQL~~E~~A~A-L-~kvyTfGPTFRAEk-S~--T~R---HLsEFWMiEPE~AF~~l~d~~~~~E~~~k~~~k~VL  285 (495)
T TIGR00457       217 ---VSGQLYAEAYALA-L-SKVYTFGPTFRAEK-SN--TSR---HLSEFWMIEPEMAFANLNDLLQLIETLIKYIIKAVL  285 (495)
T ss_pred             ---ECCHHHHHHHHHH-H-CCCEECCCCEECCC-CC--CCC---CHHHHHHHHHHEEECCHHHHHHHHHHHHHHHHHHHH
T ss_conf             ---0227899999997-4-78144587400428-64--870---111221011200000133338999999999999983


Q ss_pred             HH--HCCHHHHCCCCCHH---CCCH
Q ss_conf             98--41067530378011---7844
Q gi|254780680|r  311 KR--LDLHYRVVSLCTGD---LGFS  330 (430)
Q Consensus       311 ~~--L~lpyRvv~~~sgd---lg~~  330 (430)
                      +.  ==||-+  -+|+.|   |.+=
T Consensus       286 ~~~qellPkq--fi~~~enn~~~~L  308 (495)
T TIGR00457       286 ENQQELLPKQ--FICSQENNLLKFL  308 (495)
T ss_pred             CCHHHHCCHH--HCCCCHHHHHHHH
T ss_conf             0524504201--0377713799986


No 72 
>TIGR00019 prfA peptide chain release factor 1; InterPro: IPR004373 This family describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognise and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cut-off for this model. RF-1 does not have a translational frameshift.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=95.64  E-value=0.26  Score=30.49  Aligned_cols=106  Identities=21%  Similarity=0.289  Sum_probs=66.0

Q ss_pred             HHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---H-CCCHHHHHHHHHHHHH
Q ss_conf             44785199999999984698958899999999999999999999999999999999986---4-4998799999999999
Q gi|254780680|r    4 IQWIRQNPEHLDIALKKRHLEPQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAI---A-EGNLSLVDALKNETST   79 (430)
Q Consensus         4 ik~IRen~e~v~~~l~~R~~~~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k---~-~~~~~~~~~Lk~e~~~   79 (430)
                      ++.|.+..+.+.+.|.+=++-.|.+++.++..++..|. ++...-.+-..+.++|..++   . ++++.++.+      .
T Consensus        10 L~~~~~~~~eL~~~L~dp~v~~d~~k~~~~~ke~~~l~-~i~~~~~~~~~~~~~~~~A~~~l~E~~~D~El~e------l   82 (373)
T TIGR00019        10 LESLEERYEELEELLSDPEVISDQDKLRKLSKEYSQLE-EIVDKYEEYKKAQEDLKEAKELLEEKGDDKELRE------L   82 (373)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH------H
T ss_conf             99999999999985068631136799999988620656-8999999999999999999999974258865899------9


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEE
Q ss_conf             99886444666667788877443100225881122113555402420
Q gi|254780680|r   80 LKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILIR  126 (430)
Q Consensus        80 Lk~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~  126 (430)
                      .+++|..++.+..+++++|.-+|  |        |.-++++.|+++.
T Consensus        83 ak~El~~l~~~~~~LE~~Lk~LL--l--------PkDPND~kNv~lE  119 (373)
T TIGR00019        83 AKEELEELEKEIEELEEQLKILL--L--------PKDPNDEKNVILE  119 (373)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHC--C--------CCCCCCCCCEEEE
T ss_conf             99999999988888999999726--8--------8697669534888


No 73 
>KOG0555 consensus
Probab=95.26  E-value=0.032  Score=37.30  Aligned_cols=102  Identities=28%  Similarity=0.389  Sum_probs=67.3

Q ss_pred             CCCEEECCHHHHHH----HHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHC--HHHHHHHHHHHH-CCEECCCCCC
Q ss_conf             75301056488999----9999999986223203202123562027889865514--224767764310-0023134541
Q gi|254780680|r  162 ARFSVLTGHLAHLE----RALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQI--PKFADDMFCTTD-GRWLIPTSEV  234 (430)
Q Consensus       162 srF~~Lkg~~A~Le----~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~l--p~f~~~~y~~~d-~l~Li~TaEv  234 (430)
                      .|.-.++|+-+-.-    -+|.+-|-| |--+.||++|.||.||-..+--|+--+  .-|.++.|.++. .|||    |-
T Consensus       229 nrHl~iRge~~s~vLK~Ra~~lr~~Rd-~y~~~~ytEVtPPtmVQTQVEGGsTLFkldYyGEeAyLTQSSQLYL----Et  303 (545)
T KOG0555         229 NRHLVIRGENASKVLKARAALLRAMRD-HYFERGYTEVTPPTMVQTQVEGGSTLFKLDYYGEEAYLTQSSQLYL----ET  303 (545)
T ss_pred             CCEEEEECHHHHHHHHHHHHHHHHHHH-HHHHCCCEECCCCCEEEEEECCCCEEEEECCCCCHHHCCCHHHHHH----HH
T ss_conf             552688410478999999999999998-8874484245797157887517604873113574033022358889----87


Q ss_pred             HHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEE
Q ss_conf             1454453420595550420885322107884335543432122221020021
Q gi|254780680|r  235 SLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCEL  286 (430)
Q Consensus       235 pL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~  286 (430)
                      .|.+++            ...++++.||+|.. +   ||-  .+.+|+-||-
T Consensus       304 clpAlg------------dvy~I~~SyRAEkS-r---TRR--HLsEytHVEa  337 (545)
T KOG0555         304 CLPALG------------DVYCIQQSYRAEKS-R---TRR--HLSEYTHVEA  337 (545)
T ss_pred             HHHHCC------------CEEEECHHHHHHHH-H---HHH--HHHHHEEEEE
T ss_conf             655207------------62673275665566-6---666--5533111023


No 74 
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=95.23  E-value=0.015  Score=39.71  Aligned_cols=117  Identities=19%  Similarity=0.330  Sum_probs=65.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECCCCCCHHHHHHHHHCCCHHHHCC
Q ss_conf             99999999999862232032021235620278898655142247677643100023134541145445342059555042
Q gi|254780680|r  173 HLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIPTSEVSLTNLYSHEIIESKSLPL  252 (430)
Q Consensus       173 ~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~LPi  252 (430)
                      ++--.+++.+-++ +.++||.+|-+|.|  ..+..|++-.| |.--.-..+.++||-=.-|     +|....+- .-+ =
T Consensus       185 ~~Rs~ii~~iR~~-l~~~gF~EVeTPil--~~~~gGa~Arp-f~t~~~~~~~~~yL~qSPQ-----Lykk~Lmv-gGf-d  253 (505)
T PRK12445        185 VVRSKILAAIRQF-MVARGFMEVETPMM--QVIPGGASARP-FITHHNALDLDMYLRIAPE-----LYLKRLVV-GGF-E  253 (505)
T ss_pred             HHHHHHHHHHHHH-HHHCCCEEEECCCC--CCCCCCCCCCE-EEECCCCCCCCEEECCCCH-----HHHHHHHH-CCC-C
T ss_conf             9999999999999-99779389978875--55458766610-3304667886743416939-----99999985-797-4


Q ss_pred             EEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             0885322107884335543432122221020021212786501457898999999999984
Q gi|254780680|r  253 RFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRL  313 (430)
Q Consensus       253 k~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L  313 (430)
                      ||..++||||.|    |.+++   |.-+|+-+|+.      .|+.-++.|.+..|++++.+
T Consensus       254 RvfeI~r~FRnE----~~~~~---H~PEFT~lE~e------~af~d~~dvm~l~E~li~~i  301 (505)
T PRK12445        254 RVFEINRNFRNE----GISVR---HNPEFTMMELY------MAYADYHDLIELTESLFRTL  301 (505)
T ss_pred             CEEEHHHHHHCC----CCCCC---CCHHHHHHHHH------HHCCCHHHHHHHHHHHHHHH
T ss_conf             457627876078----88866---54445435687------63278989999999999999


No 75 
>pfam00152 tRNA-synt_2 tRNA synthetases class II (D, K and N).
Probab=95.20  E-value=0.022  Score=38.41  Aligned_cols=117  Identities=22%  Similarity=0.402  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECCCCCCHHHHHHHHHCCCHHHHCC
Q ss_conf             99999999999862232032021235620278898655142247677643100023134541145445342059555042
Q gi|254780680|r  173 HLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIPTSEVSLTNLYSHEIIESKSLPL  252 (430)
Q Consensus       173 ~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~LPi  252 (430)
                      ++--++++..-++ ..++||++|.||.|+...+ +|.+.  -|.-..|. .+..||.-..|     +|+...+...  -=
T Consensus        23 ~~Rs~i~~~iR~f-f~~~~f~EV~TP~L~~~~~-e~~a~--~F~~~~~~-~~~~yL~~Spe-----l~~k~ll~~g--~~   90 (341)
T pfam00152        23 KLRSKIIRAIREF-LDERGFLEVETPILTKSTP-EGGAR--DFLVPKFY-AKEAYLPQSPQ-----LYKQLLMVAG--FD   90 (341)
T ss_pred             HHHHHHHHHHHHH-HHHCCCEEEECCCCCCCCC-CCCCC--EEEECCCC-CCCEEECCCHH-----HHHHHHHHCC--CC
T ss_conf             9999999999999-9988989987982005589-87776--64502678-98234054889-----9999998658--87


Q ss_pred             EEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             0885322107884335543432122221020021212786501457898999999999984
Q gi|254780680|r  253 RFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRL  313 (430)
Q Consensus       253 k~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L  313 (430)
                      |+..++||||.|- +.+.  |   ...+|+.+|....      ..-+++|.+.+|+++..+
T Consensus        91 rVfei~~~FR~E~-~~t~--r---H~~EFtmlE~y~a------~~d~~d~m~~~E~li~~i  139 (341)
T pfam00152        91 RVFQIAPCFRDED-LRTD--R---HPPEFTQLDLEMS------FVDYEDVMDLTEDLIKYV  139 (341)
T ss_pred             CCEEEECHHCCCC-CCCC--C---CCHHHHHHHHHHH------CCCHHHHHHHHHHHHHHH
T ss_conf             6379723202798-9886--5---5077887767553------599999999999999999


No 76 
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=95.11  E-value=0.018  Score=39.16  Aligned_cols=117  Identities=19%  Similarity=0.255  Sum_probs=67.5

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECCCCCCHHHHHHHHHCCCHHHHCC
Q ss_conf             99999999999862232032021235620278898655142247677643100023134541145445342059555042
Q gi|254780680|r  173 HLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIPTSEVSLTNLYSHEIIESKSLPL  252 (430)
Q Consensus       173 ~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~LPi  252 (430)
                      ++--..++.+-++ +.++||.||.+|.|-.  +-.|.|--| |.--.=..+-++|| +.|-    =+|.+..+-.. + =
T Consensus       777 ~~RS~Vi~aiR~~-L~~~GFlEVETPiLq~--~~GGA~ARP-FlThsna~d~~~YL-riAP----ELflKRLmVGG-f-e  845 (1099)
T PRK02983        777 RARSAVLRAVRET-LVAKGFLEVETPILQQ--IHGGANARP-FLTHINAYDLDLYL-RIAP----ELYLKRLCVGG-V-E  845 (1099)
T ss_pred             HHHHHHHHHHHHH-HHHCCCEEEECCCCCC--CCCCCCCCC-CCCCCCCCCCCCEE-ECCH----HHHHHHHHHCC-C-C
T ss_conf             9999999999999-9878988955754677--888756785-30103367866145-1480----89999998648-6-3


Q ss_pred             EEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             0885322107884335543432122221020021212786501457898999999999984
Q gi|254780680|r  253 RFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRL  313 (430)
Q Consensus       253 k~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L  313 (430)
                      ||.-+.+|||.|-    -|.+   |.-+|+.+|.+      .|+.-++.|.+..|++++.+
T Consensus       846 RVFEI~RcFRNEg----lrad---HnPEFTmLE~Y------~Ay~Dyedmm~ltEeLi~~~  893 (1099)
T PRK02983        846 RVFELGRAFRNEG----VDFS---HNPEFTLLEAY------QAHADYLVMRDLCRELIQNA  893 (1099)
T ss_pred             CCEEECCCCCCCC----CCCC---CCCCHHHHHHH------HHHCCHHHHHHHHHHHHHHH
T ss_conf             1134325446799----9987---49407999999------98478999999999999999


No 77 
>KOG2298 consensus
Probab=95.03  E-value=0.035  Score=36.93  Aligned_cols=46  Identities=24%  Similarity=0.377  Sum_probs=37.7

Q ss_pred             CCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCC
Q ss_conf             59555042088532210788433554343212222102002121278650
Q gi|254780680|r  245 IESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREED  294 (430)
Q Consensus       245 l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~  294 (430)
                      ++...||.--+.++..||-|..-    -.||+||.+|+..|+-.|++|++
T Consensus       203 ~N~~KlPFA~AqiG~~fRNEISp----RsGLlRvrEF~maEIEHFvdP~~  248 (599)
T KOG2298         203 FNQGKLPFASAQIGKSFRNEISP----RSGLLRVREFTMAEIEHFVDPLL  248 (599)
T ss_pred             HCCCCCCCHHHHHCHHHHHCCCC----CCCCEEEEEEEHHHHHCCCCCCC
T ss_conf             52887763488746576513375----55743678754677653489777


No 78 
>PRK00226 greA transcription elongation factor GreA; Reviewed
Probab=93.57  E-value=0.78  Score=26.96  Aligned_cols=101  Identities=18%  Similarity=0.177  Sum_probs=62.0

Q ss_pred             HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCCCCCH
Q ss_conf             999999999999999-9999999999986449987999999999999988644466666778887744-31002258811
Q gi|254780680|r   35 EKNRILIKKIEDIRA-RRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKL-ISCIPNVPLEE  112 (430)
Q Consensus        35 ~~rr~l~~e~e~Lra-erN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~l-ll~IPNi~~~~  112 (430)
                      +-+..|+.+++.|+. +|.+++++|+.+...|+-.+-.+.    ..-|++...++.....++..|... ...-++++.+.
T Consensus        10 eg~~~L~~El~~L~~~~r~~i~~~i~~Ar~~GDlsENaeY----~aAke~q~~~e~rI~~Le~~L~~A~iid~~~~~~~~   85 (157)
T PRK00226         10 EGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEY----HAAKEEQGFIEGRIRELEDKLSNAEVIDPTKPSSGK   85 (157)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCHHH----HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             9999999999999872368999999999986996405769----999999999999999999999850145866577884


Q ss_pred             HHHCCCCCCCEEEEEECCCCCCCCCCCCCCC
Q ss_conf             2211355540242000156566566621122
Q gi|254780680|r  113 VPIGTSANENILIRSVGKKPSAIHLSREHFE  143 (430)
Q Consensus       113 VP~G~de~dNv~i~~~G~~~~f~f~~k~H~e  143 (430)
                      |=.|..    |.++..+......|....-+|
T Consensus        86 V~~Gs~----V~l~d~~~g~~~~y~iVG~~E  112 (157)
T PRK00226         86 VKFGAT----VTIYDLDTDEEETYQIVGDDE  112 (157)
T ss_pred             EECCCE----EEEEECCCCCEEEEEEECCCC
T ss_conf             206758----999985899679999913322


No 79 
>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
Probab=93.41  E-value=0.82  Score=26.78  Aligned_cols=97  Identities=19%  Similarity=0.141  Sum_probs=50.1

Q ss_pred             HHHCCHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH------HHHHHHHHHH
Q ss_conf             785199999999984698958-899999999999999999999999999999999986449987------9999999999
Q gi|254780680|r    6 WIRQNPEHLDIALKKRHLEPQ-SEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLS------LVDALKNETS   78 (430)
Q Consensus         6 ~IRen~e~v~~~l~~R~~~~~-id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~------~~~~Lk~e~~   78 (430)
                      .++.+.+.+.....++..+.+ ..++.++..+..++..+++.+..++..+.+++..+...-+.-      .-..+..+-.
T Consensus       186 ~l~~dL~~~~~r~~~~~~~~~~~~~l~~l~~~~~~~~~~~e~~~~~~~~~~~el~~~~~~~~~~~~~~~~~g~~l~~~r~  265 (650)
T TIGR03185       186 QLAGDLTNYLRRRKKEELPSSILSEIEALEAELKEQSSKYEDLEQDIAHARQEIEEAQRSLESLKKKFEDEGGDIAEERE  265 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999987501014579999999999999999999999999999999999999999999999985347799999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999886444666667788877443
Q gi|254780680|r   79 TLKEQLPILEKEEHEVCSSLKKLI  102 (430)
Q Consensus        79 ~Lk~eik~le~~~~~le~el~~ll  102 (430)
                      .+..+++.++.++..+..++..++
T Consensus       266 ~le~~~~~l~~~~~~~~~~l~~~~  289 (650)
T TIGR03185       266 QLERQLKEIEAKRKANRAELRELI  289 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999998


No 80 
>pfam07106 TBPIP Tat binding protein 1(TBP-1)-interacting protein (TBPIP). This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation.
Probab=92.99  E-value=0.94  Score=26.33  Aligned_cols=68  Identities=15%  Similarity=0.220  Sum_probs=50.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             58899999999999999999999999999999999986449987999999999999988644466666778
Q gi|254780680|r   25 PQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVC   95 (430)
Q Consensus        25 ~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le   95 (430)
                      ++-+++-.+|.+...++.++..++.+.+.++.++..+.+.-..   +++..+..+|+.++..+++.+..+.
T Consensus        69 ~~~eel~~~d~~i~~L~~~l~~l~~~~~~l~~el~~L~s~~t~---eel~~~i~~L~~e~~~l~~kL~~l~  136 (169)
T pfam07106        69 PSDEELNKLDMEIEELREEVQLLKQDCSTLEIELKSLTSDLTT---EELQEEIQELKKEVREIEEKLESLE  136 (169)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCH---HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9988998769999999999999999999999999998758999---9999999999999999999999988


No 81 
>TIGR00468 pheS phenylalanyl-tRNA synthetase, alpha subunit; InterPro: IPR004529   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases .   This family describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this family. ; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=92.95  E-value=0.25  Score=30.67  Aligned_cols=107  Identities=10%  Similarity=0.124  Sum_probs=75.2

Q ss_pred             HHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHH-HCCHHHHCCCCCHH
Q ss_conf             55042088532210788433554343212222102002121278650145789899999999998-41067530378011
Q gi|254780680|r  248 KSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKR-LDLHYRVVSLCTGD  326 (430)
Q Consensus       248 ~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~-L~lpyRvv~~~sgd  326 (430)
                      ..-|+|+++.++|||+++-.+       -..|+|+.+|.+++...-.-....--+-.....++.+ +++-||--..|-.+
T Consensus       202 ~~pp~~~~~~~~~~r~~~~d~-------~h~~~f~~~~g~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~~~p~~fp~t~  274 (362)
T TIGR00468       202 KNPPIRIFCPGRVFRRDTVDA-------THLPEFHQLEGLVVDKNVSFTNLKGLLEEFLKKLFGEDTEVRFRPSYFPFTE  274 (362)
T ss_pred             CCCCEEEEECCHHHCCCCCCC-------CCCCHHHHEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCC
T ss_conf             788625764101110233331-------0141022100235415664678899999999974132212023103366555


Q ss_pred             CCCHHHEEEEEEEECCC-CC--------CEEEEEEECCCCCHHHHHCCCE
Q ss_conf             78443402410110100-48--------3323753102100764532684
Q gi|254780680|r  327 LGFSACKTYDLEVWLAG-QN--------LYREISSCSTCGNFQSRRMNSR  367 (430)
Q Consensus       327 lg~~a~~~~DiE~w~P~-~~--------~y~Ev~S~Snc~D~QsrRl~ir  367 (430)
                      -.      ..+++|.|. ..        .|.|+..|.-..--..+.+++.
T Consensus       275 p~------~e~~~~~~~c~~gc~~c~~~~W~e~~g~g~~~p~~~~~~g~~  318 (362)
T TIGR00468       275 PS------AEVDVYCPECGKGCSVCKGTGWLELLGAGIFRPEVLEPLGID  318 (362)
T ss_pred             CC------CCEEEEEHHHCCCCHHHCCCCEEEEECCCCCCHHHHHHCCCC
T ss_conf             55------302442000013100101465035404553242355423787


No 82 
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=92.86  E-value=0.98  Score=26.21  Aligned_cols=106  Identities=18%  Similarity=0.243  Sum_probs=52.7

Q ss_pred             HHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             447851999999999846989588999999999999999999999---99999999999986449987999999999999
Q gi|254780680|r    4 IQWIRQNPEHLDIALKKRHLEPQSEYILSLDEKNRILIKKIEDIR---ARRNSNSAQIGQAIAEGNLSLVDALKNETSTL   80 (430)
Q Consensus         4 ik~IRen~e~v~~~l~~R~~~~~id~il~Ld~~rr~l~~e~e~Lr---aerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~L   80 (430)
                      +..+.+..+.+.+.+..-++=.|.++..++-.+...+...++..+   ...+.+..-. .+....++++   ++   ..+
T Consensus         9 Le~l~~rl~eLe~~ls~p~fW~D~~~a~kl~kE~~~L~~~v~~~~~l~~~~~dl~el~-eLl~ee~D~e---l~---e~a   81 (360)
T PRK00591          9 LEALEERYEELEALLSDPEVISDQKRFRKLSKEYAELEPIVEAYREYKQAEEDLEDAK-ELLKEESDPE---MR---EMA   81 (360)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHCCCCHH---HH---HHH
T ss_conf             9999999999999872985212999999999999999999999999999999899999-9986279978---99---999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEE
Q ss_conf             9886444666667788877443100225881122113555402420
Q gi|254780680|r   81 KEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILIR  126 (430)
Q Consensus        81 k~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~  126 (430)
                      ++++..+++++..++.++..+|+  |        .|+.+..|.++.
T Consensus        82 ~~El~~l~~~l~~lE~eL~~lLl--p--------~d~~D~~nailE  117 (360)
T PRK00591         82 KEELKELEERLEELEEELKILLL--P--------KDPNDDKNVILE  117 (360)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHC--C--------CCCCCCCCEEEE
T ss_conf             99999999999999999999837--9--------997756785899


No 83 
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.34  E-value=1.1  Score=25.74  Aligned_cols=72  Identities=18%  Similarity=0.238  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999999999999999999999999864499879999999999999886444666667788877443100
Q gi|254780680|r   29 YILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCI  105 (430)
Q Consensus        29 ~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~I  105 (430)
                      .+-.+......++.+++.|..+...+++++...     .++++++..+++.++.+|+.+++...+-++.+..-+-.+
T Consensus        39 ~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~-----~~~i~~~~~eik~l~~eI~~~~~~I~~r~~~l~~raRAm  110 (265)
T COG3883          39 KLSELQKEKKNIQNEIESLDNQIEEIQSKIDEL-----QKEIDQSKAEIKKLQKEIAELKENIVERQELLKKRARAM  110 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999989999999999999999988878-----988888999999999899999988999999999999999


No 84 
>pfam03961 DUF342 Protein of unknown function (DUF342). This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=92.06  E-value=1.2  Score=25.67  Aligned_cols=28  Identities=21%  Similarity=0.344  Sum_probs=16.8

Q ss_pred             CCEEHHHHHCCHHHHHHHHHCHHHHHHHH
Q ss_conf             20212356202788986551422476776
Q gi|254780680|r  192 YTEVSAPLLVRDEAMYGTGQIPKFADDMF  220 (430)
Q Consensus       192 y~~v~~P~lv~~~~~~gtG~lp~f~~~~y  220 (430)
                      -.-|.|=+.|+.++=..||.. +|..++.
T Consensus       174 ~i~V~~vl~v~gdVd~~TGNI-~F~G~V~  201 (450)
T pfam03961       174 GISVDDVLEIKGDVDLSTGNI-DFKGSVI  201 (450)
T ss_pred             EEEEEEEEEECCCCCCCCCCE-EEEEEEE
T ss_conf             899999899768778773446-7777799


No 85 
>TIGR02231 TIGR02231 conserved hypothetical protein; InterPro: IPR011935    This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown..
Probab=92.05  E-value=1.2  Score=25.50  Aligned_cols=93  Identities=19%  Similarity=0.233  Sum_probs=61.2

Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------C------------------
Q ss_conf             99846989588999999999999999999999999999999999864--------------4------------------
Q gi|254780680|r   17 ALKKRHLEPQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIA--------------E------------------   64 (430)
Q Consensus        17 ~l~~R~~~~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~--------------~------------------   64 (430)
                      ....+....+-.++.+|+.+.+.+..++..++++.+.++++.+.+-|              +                  
T Consensus        60 ~~~~~~~~~~~~~~~~L~~~i~~~~~~~~~~~~~~~~l~~~~~~L~K~~~~~~~~~~~~~~~sg~~~~~~~~~~~~~~~f  139 (558)
T TIGR02231        60 TIRERTSRADPERLAELDKQIRELEAELRDLEDRGDALKALKSNLDKFLEDIREGLTEPIKDSGVLKRNEPDLKELKQLF  139 (558)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCEEEECCCCHHHHHHHH
T ss_conf             32114774642368999999999999998777788899985301025677774201467321523561576568999999


Q ss_pred             -CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HCCCCC
Q ss_conf             -998799999999999998864446666677888774431--002258
Q gi|254780680|r   65 -GNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLIS--CIPNVP  109 (430)
Q Consensus        65 -~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll--~IPNi~  109 (430)
                       .....++.+..+.++...+++++++++.+++.+++.++-  ..++.-
T Consensus       140 ~~~~~~~~~~~~~~r~~~~~~~el~~~~~~L~~el~~~~~~s~~~~~~  187 (558)
T TIGR02231       140 DFVGSEIERLLTEDREVERRIRELEKQLSELENELRALLTLSGKEQRS  187 (558)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEE
T ss_conf             988999999988877899999999999999999998741104786604


No 86 
>COG3705 HisZ ATP phosphoribosyltransferase involved in histidine biosynthesis [Amino acid transport and metabolism]
Probab=92.03  E-value=0.66  Score=27.50  Aligned_cols=139  Identities=24%  Similarity=0.355  Sum_probs=93.7

Q ss_pred             HCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHH-HHCHHHHHHHHHHHH----CCEECCCCC
Q ss_conf             216753010564889999999999986223203202123562027889865-514224767764310----002313454
Q gi|254780680|r  159 LSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGT-GQIPKFADDMFCTTD----GRWLIPTSE  233 (430)
Q Consensus       159 vsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gt-G~lp~f~~~~y~~~d----~l~Li~TaE  233 (430)
                      -+|+|. +|..+..+.+.+--+ +++. ....||..|.+|+|=--+++.-. |.  .-...+|+..|    .++|=|-=-
T Consensus         6 p~g~rd-~Lp~e~~~~~~i~~~-l~~~-f~~~Gy~~v~tP~lE~~d~~l~~~g~--~l~~~~f~l~d~~g~~l~LRpD~T   80 (390)
T COG3705           6 PEGIRD-VLPLEARRKEEIRDQ-LLAL-FRAWGYERVETPTLEPADPLLDGAGE--DLRRRLFKLEDETGGRLGLRPDFT   80 (390)
T ss_pred             CCCCHH-CCHHHHHHHHHHHHH-HHHH-HHHHCCCCCCCCCCCHHHHHHHCCCH--HHHHHHEEEECCCCCEEEECCCCC
T ss_conf             875201-063677647999999-9999-99808740466313402665402225--555220687657897688354330


Q ss_pred             CHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEE--EEEEECCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             11454453420595550420885322107884335543432122221020--0212127865014578989999999999
Q gi|254780680|r  234 VSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWK--CELVSITREEDSFTEHERMLSCAEEILK  311 (430)
Q Consensus       234 vpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~K--VE~~~~~~pe~S~~~~e~~~~~~~~i~~  311 (430)
                      .|++=.|.-.--.   .|.||+=.+.-||..-|.+|+       .-+|..  ||++...    |.+.=-|++..+-..++
T Consensus        81 ~pVaR~~~~~~~~---~P~Rl~Y~G~Vfr~~~~~~g~-------~~Ef~QaGiEllG~~----~~~ADaEvi~la~~~L~  146 (390)
T COG3705          81 IPVARIHATLLAG---TPLRLSYAGKVFRAREGRHGR-------RAEFLQAGIELLGDD----SAAADAEVIALALAALK  146 (390)
T ss_pred             HHHHHHHHHHCCC---CCCEEEECCHHHHCCHHCCCC-------CCCHHHHHHHHHCCC----CCHHHHHHHHHHHHHHH
T ss_conf             8999999982378---871466401454020102676-------420455336773787----20002899999999999


Q ss_pred             HHCCH
Q ss_conf             84106
Q gi|254780680|r  312 RLDLH  316 (430)
Q Consensus       312 ~L~lp  316 (430)
                      .+|++
T Consensus       147 ~~gl~  151 (390)
T COG3705         147 ALGLA  151 (390)
T ss_pred             HCCCC
T ss_conf             74886


No 87 
>TIGR00409 proS_fam_II prolyl-tRNA synthetase; InterPro: IPR004500   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Prolyl-tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form, is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa.    This family includes the enzyme from Escherichia coli that contains all three of the conserved consensus motifs characteristic of class II aminoacyl-tRNA synthetases  and the enzyme from the spirochete Borrelia burgdorferi.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=91.27  E-value=0.52  Score=28.25  Aligned_cols=70  Identities=24%  Similarity=0.369  Sum_probs=60.1

Q ss_pred             CCEEEEEEECCCCCHHHHHCCCEEECCCCCCCC-EEEEECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCC
Q ss_conf             833237531021007645326847338998410-1042004322899999999883468998386582223101
Q gi|254780680|r  345 NLYREISSCSTCGNFQSRRMNSRYRDPNSKSLK-FTHTLNGSGVAVGRCLIAILENYLNADGSVTIPTVLRPYM  417 (430)
Q Consensus       345 ~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~-~~htlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~pym  417 (430)
                      .+=.||+.+=-.+.==|.-||..|-+++|+. + +.|+ -.=|+=|+|++.||+|.+..++| ++=|+..=||-
T Consensus       449 ~~gIEVGHIF~LG~kYS~al~A~f~de~Gk~-~t~~~M-GCYGIGVSRl~~Ai~Eq~~D~~G-~~WP~~~APy~  519 (620)
T TIGR00409       449 AKGIEVGHIFKLGTKYSKALKATFLDENGKE-QTFLTM-GCYGIGVSRLVSAIAEQHYDERG-IIWPKAIAPYD  519 (620)
T ss_pred             CCCCEEEEEECCCHHHHHHHCCEEECCCCCC-CCEEEC-CCCCCHHHHHHHHHHHHCCCCCC-CCCCCCCCCCE
T ss_conf             0562341133022033333065564668850-252560-55571389999999985058786-36764538814


No 88 
>PRK11637 hypothetical protein; Provisional
Probab=90.29  E-value=1.8  Score=24.30  Aligned_cols=34  Identities=15%  Similarity=0.162  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999998
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQA   61 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~   61 (430)
                      ++|-.+.++....+.++++++.+++.+.+++.++
T Consensus        23 ~~L~~i~~~I~~~~~~l~~~~~~~~~l~~~L~~~   56 (404)
T PRK11637         23 DQLKSIQADIAAKERAVRQQQQQRASLLAQLKKQ   56 (404)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999999999999


No 89 
>PRK10884 putative signal transduction protein; Provisional
Probab=89.84  E-value=1.9  Score=24.05  Aligned_cols=71  Identities=24%  Similarity=0.377  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             899999999999999999999999999999999986449987999999999999988644466666778887
Q gi|254780680|r   27 SEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSL   98 (430)
Q Consensus        27 id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el   98 (430)
                      -..+-+|..+...+..++.+++++.|+.+.+..+.... .++.+.+|.++-..+++++..++++.+.+..++
T Consensus        92 r~rl~~Le~ql~~l~~~L~~l~~~~~q~~~el~~~~~~-~~~~i~~L~~en~~L~~eL~~~~~~~~~~~~~l  162 (206)
T PRK10884         92 RTRVPDLENQVKTLTDKLANIDNTWNQRTAEMQQKVAQ-SDSVINGLKEENQKLKNELIVAQKKVDAANLQL  162 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88999999999999999999999999999999999998-999999999999999999999999999999999


No 90 
>KOG0554 consensus
Probab=89.78  E-value=0.25  Score=30.63  Aligned_cols=189  Identities=21%  Similarity=0.380  Sum_probs=101.1

Q ss_pred             EEEEEECCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCC
Q ss_conf             24200015656656662112202211731000112221675301056488999999999998622320320212356202
Q gi|254780680|r  123 ILIRSVGKKPSAIHLSREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVR  202 (430)
Q Consensus       123 v~i~~~G~~~~f~f~~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~  202 (430)
                      +.|+-+|.....-+-+|.|...----+...+.       +| .-..|..+|+.-||.--.-++ .++++|+.+.||.|-.
T Consensus        91 eki~~vG~v~~~ypl~Kk~lt~e~LR~~~HLR-------~R-t~~~~av~RvRs~~~~a~h~f-fq~~~F~~i~tPiiTt  161 (446)
T KOG0554          91 EKIKVVGTVDESYPLQKKKLTPEMLRDKLHLR-------SR-TAKVGAVLRVRSALAFATHSF-FQSHDFTYINTPIITT  161 (446)
T ss_pred             EEEEEEEECCCCCCCCCCCCCHHHHHHCCCCC-------CH-HHHHHHHHHHHHHHHHHHHHH-HHHCCCEEECCCEEEC
T ss_conf             57899853489987742338988985323321-------00-257899999998999999999-9875946733867634


Q ss_pred             HHHHHHHHHCH------HHHHHHHHHHHCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEE
Q ss_conf             78898655142------247677643100023134541145445342059555042088532210788433554343212
Q gi|254780680|r  203 DEAMYGTGQIP------KFADDMFCTTDGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGML  276 (430)
Q Consensus       203 ~~~~~gtG~lp------~f~~~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~  276 (430)
                      .++ +|.|..=      +++.+.|  +..-||.-.+---|-+|-       ..| -|...+|||||+|-.--.+.     
T Consensus       162 nDC-EGaGE~F~Vtt~~d~~~~fF--grp~fLTVSgQLhlEa~a-------~aL-srvyt~gP~FRAE~s~t~rH-----  225 (446)
T KOG0554         162 NDC-EGAGEVFQVTTLTDYSKDFF--GRPAFLTVSGQLHLEAMA-------CAL-SRVYTFGPTFRAENSHTSRH-----  225 (446)
T ss_pred             CCC-CCCCCEEEEEECCCCCCCCC--CCCEEEEEECEEHHHHHH-------HHH-CCEEEECCCEECCCCCCHHH-----
T ss_conf             577-78740589874686543314--885079971321599887-------552-32376166132267875467-----


Q ss_pred             EEEEEEEEEEEECCCCCCHHHH-HHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCC
Q ss_conf             2221020021212786501457-898999999999984106753037801178443402410110100483
Q gi|254780680|r  277 RQHQFWKCELVSITREEDSFTE-HERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNL  346 (430)
Q Consensus       277 RvHQF~KVE~~~~~~pe~S~~~-~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~  346 (430)
                       +-+|..+|      +|-+-.. ++++..++++.++.+  --.+++-|-.||.+. .+.+|.-.|-|-...
T Consensus       226 -LaEFwmlE------~E~af~~sl~d~~~~~e~~~k~m--~k~~le~~~Edm~l~-~~~~~~~~~~rl~~~  286 (446)
T KOG0554         226 -LAEFWMLE------AELAFAESLDDLMSCAEAYIKHM--IKYLLEKCIEDMELM-HKNEDPGSIDRLELV  286 (446)
T ss_pred             -HHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHCCCHHEEE-CCCCCCCCCCHHHHH
T ss_conf             -76565242------78878888888889999999999--999986051101010-011477753157772


No 91 
>TIGR01462 greA transcription elongation factor GreA; InterPro: IPR006359   Bacterial GreA and GreB IPR006358 from INTERPRO promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase (RNAP) , allowing RNA transcription to continue past template-encoded arresting sites. GreA and GreB are sequence homologues and have homologues in every known bacterial genome. GreA and GreB stimulate transcript cleavage in different ways; GreA induces cleavage of 3'-RNA fragments 23 nt in length and can only prevent the formation of arrested complexes, whereas GreB induces cleavage of fragments up to 18 nt in length and can rescue pre-existing arrested complexes.    The 2.2  resolution crystal structure of Escherichia coli GreA comprises an N-terminal antiparallel alpha-helical coiled coil, and a C-terminal globular domain. While the C-terminal domain binds RNAP, the N-terminal coiled coil interacts with the transcript 3' end and is responsible for stimulating the transcript cleavage reaction . Functional differences between GreA and GreB correlate with the distribution of positively charged residues on one face of the N-terminal coiled coil.  Because members of the family outside the Proteobacteria resemble GreA more closely than GreB, the GreB clade (IPR006358 from INTERPRO) forms a plausible outgroup and the remainder of the GreA/B family, included in this family, is designated GreA. In the Chlamydias and some spirochetes, the conserved region of these proteins is found as the C-terminal region of a much larger protein.  ; GO: 0003677 DNA binding, 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=89.76  E-value=1.5  Score=24.89  Aligned_cols=98  Identities=19%  Similarity=0.256  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHCCCCC
Q ss_conf             99999999999999-9999999999998644998---799999999999998864446666677888774-431002258
Q gi|254780680|r   35 EKNRILIKKIEDIR-ARRNSNSAQIGQAIAEGNL---SLVDALKNETSTLKEQLPILEKEEHEVCSSLKK-LISCIPNVP  109 (430)
Q Consensus        35 ~~rr~l~~e~e~Lr-aerN~lSKeIg~~k~~~~~---~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~-lll~IPNi~  109 (430)
                      +-..+|+.|++.|. -+|-+++++|+.+...||-   ++-++.|++-..+..+|..|+       +.|.. ....-+-+-
T Consensus         5 ~g~~kL~~EL~~Lk~v~RpeI~~~I~~AR~~GDLsENAEY~AAKe~Q~~~E~RI~~le-------~~l~~A~vi~~~~~~   77 (155)
T TIGR01462         5 EGYEKLKEELEYLKTVKRPEISEEIKEAREHGDLSENAEYHAAKEEQGFIEGRIAELE-------DLLANAEVIDDSKLS   77 (155)
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHH-------HHHHCEEECCHHHCC
T ss_conf             8999999999885026118999999999851886556003899999999988999999-------887620623601004


Q ss_pred             CC--HHHHCCCCCCCEEEEEECCCCCCCCCCCCCCC
Q ss_conf             81--12211355540242000156566566621122
Q gi|254780680|r  110 LE--EVPIGTSANENILIRSVGKKPSAIHLSREHFE  143 (430)
Q Consensus       110 ~~--~VP~G~de~dNv~i~~~G~~~~f~f~~k~H~e  143 (430)
                      ++  .|-.|..    |.|.....-....+.+..-||
T Consensus        78 ~~gd~V~~G~~----V~~~~~~~~e~~~y~IVG~~E  109 (155)
T TIGR01462        78 TDGDKVSFGST----VTIKDEDTGEEETYTIVGSWE  109 (155)
T ss_pred             CCCCEEECCCE----EEEEECCCCCEEEEEEECCCC
T ss_conf             78837715758----999983899648999834520


No 92 
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=89.75  E-value=1.9  Score=24.00  Aligned_cols=109  Identities=16%  Similarity=0.097  Sum_probs=59.8

Q ss_pred             HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCCCCH
Q ss_conf             9999999999999-99999999999998644998799999999999998864446666677888774431-002258811
Q gi|254780680|r   35 EKNRILIKKIEDI-RARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLIS-CIPNVPLEE  112 (430)
Q Consensus        35 ~~rr~l~~e~e~L-raerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll-~IPNi~~~~  112 (430)
                      +-+..|+.+++.| +.+|-+++++|+.+...|+-.+-.+.    ..-|++...++..+..++..|...-. .-.+++.+.
T Consensus        12 eg~~kL~~El~~L~~~~r~~~~~~i~~Ar~~GDlsENaeY----~aAke~q~~le~rI~~Le~~L~~A~iid~~~~~~~~   87 (159)
T PRK01885         12 EGYERLKQELDYLWREERPEVTQKVSWAASLGDRSENADY----IYGKKRLREIDRRVRFLTKRLENLKVVDYSPQQEGK   87 (159)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHH----HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCE
T ss_conf             9999999999998745304589999999985994302638----999999999999999999998733035766677881


Q ss_pred             HHHCCCCCCCEEEEEECCCCCCCCCCCCCCCHHHHCCCCC
Q ss_conf             2211355540242000156566566621122022117310
Q gi|254780680|r  113 VPIGTSANENILIRSVGKKPSAIHLSREHFEIGEALGLMD  152 (430)
Q Consensus       113 VP~G~de~dNv~i~~~G~~~~f~f~~k~H~elge~l~liD  152 (430)
                      |=.|..    |.++. ..-....|.....+|.--..|.|.
T Consensus        88 V~~Gs~----V~l~~-~~g~~~~y~iVG~~Ead~~~g~IS  122 (159)
T PRK01885         88 VFFGAW----VEIEN-EDGEEKRFRIVGPDEIDGRKGYIS  122 (159)
T ss_pred             EECCCE----EEEEE-CCCCEEEEEEECHHHCCCCCCCCC
T ss_conf             562408----99986-689769999948244266678222


No 93 
>PRK13363 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=89.61  E-value=0.19  Score=31.52  Aligned_cols=42  Identities=29%  Similarity=0.442  Sum_probs=26.8

Q ss_pred             HCCEECCCCCCHHHHHHHHHCCCHHHHCC--EEEEEECCCCCCCCCC
Q ss_conf             00023134541145445342059555042--0885322107884335
Q gi|254780680|r  224 DGRWLIPTSEVSLTNLYSHEIIESKSLPL--RFTTLAPSFRSEAGSA  268 (430)
Q Consensus       224 d~l~Li~TaEvpL~~~~~~~~l~~~~LPi--k~~~~s~cfR~EaGs~  268 (430)
                      ++.+..||+|+-.=.-.++- +  .++|+  ..+.|-||||+|||+.
T Consensus       280 ~~~l~~GtsEirnWi~~~ga-~--~~~~~~~~~~dYvP~yRt~AgTG  323 (335)
T PRK13363        280 ERQLQAGTSEIKNWIIAAGA-V--RDLDLSGEWTDYVPCYRSEAGTG  323 (335)
T ss_pred             HHHHHCCCHHHHHHHHHHHH-H--HCCCCCCCEEEEEEECCCCCCCC
T ss_conf             88885773999999999877-6--32798753576423101567666


No 94 
>PRK05729 valS valyl-tRNA synthetase; Reviewed
Probab=89.04  E-value=1.2  Score=25.51  Aligned_cols=12  Identities=8%  Similarity=-0.175  Sum_probs=4.1

Q ss_pred             HHHHHHHHCCCC
Q ss_conf             999999846989
Q gi|254780680|r   13 HLDIALKKRHLE   24 (430)
Q Consensus        13 ~v~~~l~~R~~~   24 (430)
                      .+..--..+|++
T Consensus        63 ~i~Ry~rm~G~~   74 (877)
T PRK05729         63 ILIRYKRMQGYN   74 (877)
T ss_pred             HHHHHHHCCCCC
T ss_conf             999998727996


No 95 
>pfam02994 Transposase_22 L1 transposable element.
Probab=88.92  E-value=2.2  Score=23.59  Aligned_cols=108  Identities=14%  Similarity=0.137  Sum_probs=70.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CC------------HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5889999999999999999999999999999999998644-99------------8799999999999998864446666
Q gi|254780680|r   25 PQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAE-GN------------LSLVDALKNETSTLKEQLPILEKEE   91 (430)
Q Consensus        25 ~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~-~~------------~~~~~~Lk~e~~~Lk~eik~le~~~   91 (430)
                      -.+.++.++...-++|..+++.++.++++..=+|-...+. |.            .+-++.+.....+++..++..++..
T Consensus        95 k~lKe~mEl~kti~eLk~ev~~ikK~q~E~tL~IEn~~Krsg~id~S~snRi~~mEERis~~ED~I~ei~~~~k~~eK~~  174 (370)
T pfam02994        95 KCLKELMELKKKARELKEECRSIKKEHMETTLDIENQKKRQGVVDTSFTNRIQEMEERISGAEDSIEEIKRTGKFNEKRK  174 (370)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             31999999988889999740466665555542034430234542100546889999875457778998657888889999


Q ss_pred             HHHHHHHHHHH--HHCCCCCCCHHHHCCCCCCCEEEEEECCCC
Q ss_conf             67788877443--100225881122113555402420001565
Q gi|254780680|r   92 HEVCSSLKKLI--SCIPNVPLEEVPIGTSANENILIRSVGKKP  132 (430)
Q Consensus        92 ~~le~el~~ll--l~IPNi~~~~VP~G~de~dNv~i~~~G~~~  132 (430)
                      +.++..++++.  +.-||+---.||.+.++..+..-..+.++-
T Consensus       175 K~l~qniqei~D~~rr~NlriIGipE~e~~~~kg~enIf~~II  217 (370)
T pfam02994       175 KRLEQNIQEIQDYVRRPNLRIIGVPESEDEQLKGPENIFQKII  217 (370)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCHHHHHHHHH
T ss_conf             9988759999987317885274478654433245889999999


No 96 
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=88.27  E-value=2.4  Score=23.29  Aligned_cols=69  Identities=23%  Similarity=0.291  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999998644998799999999999998864446666677888774
Q gi|254780680|r   29 YILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKK  100 (430)
Q Consensus        29 ~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~  100 (430)
                      .+-+++.+.+.+..++..++.+.+......+..+   +..+..+|..+...++.++..++.++..+.+++..
T Consensus        53 e~e~le~qv~~~e~ei~~~r~r~~~~e~kl~~v~---~~~e~~aL~~E~~~ak~r~~~le~el~~l~~~~~~  121 (239)
T COG1579          53 ELEDLENQVSQLESEIQEIRERIKRAEEKLSAVK---DERELRALNIEIQIAKERINSLEDELAELMEEIEK  121 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999998999888899999999987899886125---69999987889999999999999999999999998


No 97 
>KOG2411 consensus
Probab=88.11  E-value=0.68  Score=27.39  Aligned_cols=109  Identities=24%  Similarity=0.387  Sum_probs=63.7

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECCCCCCHHHHHHH--------HHC
Q ss_conf             999999999998622320320212356202788986551422476776431000231345411454453--------420
Q gi|254780680|r  173 HLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIPTSEVSLTNLYS--------HEI  244 (430)
Q Consensus       173 ~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~TaEvpL~~~~~--------~~~  244 (430)
                      +|--+++.-+-.+....+||++|-+|.+.+..        |-.+        .-|++||-+-+ .-+|+        .++
T Consensus       179 rlRS~~v~~iR~yl~n~~GFvevETPtLFkrT--------PgGA--------~EFvVPtr~~~-g~FYaLpQSPQQfKQl  241 (628)
T KOG2411         179 RLRSNVVKKIRRYLNNRHGFVEVETPTLFKRT--------PGGA--------REFVVPTRTPR-GKFYALPQSPQQFKQL  241 (628)
T ss_pred             HHHHHHHHHHHHHHHHHCCEEECCCCCHHCCC--------CCCC--------CEEECCCCCCC-CCEEECCCCHHHHHHH
T ss_conf             99999999999998610473551572020148--------8864--------12322367898-8555368898999999


Q ss_pred             CCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEE-EECCCCCCHHHHHHHHHHHH
Q ss_conf             595550420885322107884335543432122221020021-21278650145789899999
Q gi|254780680|r  245 IESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCEL-VSITREEDSFTEHERMLSCA  306 (430)
Q Consensus       245 l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~-~~~~~pe~S~~~~e~~~~~~  306 (430)
                      |-.+- ==||.-+.+|||.|.--       -=|+-+|+.|.| .+|++.++-.+..|.++.-+
T Consensus       242 LMvsG-idrYyQiARCfRDEdlR-------~DRQPEFTQvD~EMsF~~~~dim~liEdll~~~  296 (628)
T KOG2411         242 LMVSG-IDRYYQIARCFRDEDLR-------ADRQPEFTQVDMEMSFTDQEDIMKLIEDLLRYV  296 (628)
T ss_pred             HHHHC-HHHHHHHHHHHCCCCCC-------CCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHH
T ss_conf             98723-03677677664134567-------656876435444785367787899999999973


No 98 
>COG1340 Uncharacterized archaeal coiled-coil protein [Function unknown]
Probab=87.57  E-value=2.7  Score=22.99  Aligned_cols=73  Identities=22%  Similarity=0.323  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999999999999999999999999999999999864499879999999999999886444666667788877443100
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCI  105 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~I  105 (430)
                      ..+..+-++|..+.+++..++++|..+++++....     +.+.+++.+-.++.++++.+.+...++-.+++.+.-.+
T Consensus        20 ~~~~e~~ekR~El~~~~~~~~ekRdeln~kvrE~~-----e~~~elr~~rdeineev~elK~kR~ein~kl~eL~~~~   92 (294)
T COG1340          20 EEIEELKEKRDELRKEASELAEKRDELNAKVRELR-----EKAQELREERDEINEEVQELKEKRDEINAKLQELRKEY   92 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98999999899999999999998999889999999-----99999999999999999999998988999999999999


No 99 
>TIGR01061 parC_Gpos DNA topoisomerase IV, A subunit; InterPro: IPR005741   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit A (parC) of topoisomerase IV from Gram positive bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=86.92  E-value=2.9  Score=22.74  Aligned_cols=113  Identities=20%  Similarity=0.252  Sum_probs=73.8

Q ss_pred             HHHHH--CCHHHHHHHHHHCCCCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             44785--19999999998469895---88999999999999999999999999999999999864499879999999999
Q gi|254780680|r    4 IQWIR--QNPEHLDIALKKRHLEP---QSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETS   78 (430)
Q Consensus         4 ik~IR--en~e~v~~~l~~R~~~~---~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~   78 (430)
                      |+.||  +|...-+++|... +++   ..+.|+.| ..+|-..+.+=.|+.|.++|.++|..+.     +-+.+.+..-+
T Consensus       386 I~~IRas~~k~DAk~~Li~~-f~FT~~QAEAIv~L-rLY~LTnTDi~~L~~E~~eL~~~~~~l~-----~~i~~~k~~~~  458 (745)
T TIGR01061       386 IKLIRASEDKSDAKENLIDK-FEFTENQAEAIVSL-RLYRLTNTDIFELKEEEEELEKKIKSLE-----EIIASEKARKK  458 (745)
T ss_pred             HHHHHCCCCCCCHHHHHCCC-CCCCHHHHHHHHHH-HHHCCCCHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHH
T ss_conf             88773024533603431011-37772579999998-8603732037777878999999999999-----98765789999


Q ss_pred             HHHHHHHHHHHHH-----HHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEEEECC
Q ss_conf             9998864446666-----677888774431002258811221135554024200015
Q gi|254780680|r   79 TLKEQLPILEKEE-----HEVCSSLKKLISCIPNVPLEEVPIGTSANENILIRSVGK  130 (430)
Q Consensus        79 ~Lk~eik~le~~~-----~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~~~G~  130 (430)
                      -||+++.+++++.     ..+++++.+.=...      +.=+ ..++-+|.|-+-|+
T Consensus       459 ~lk~~l~~~KK~F~~~R~s~l~~~~~~~~i~~------~~li-~~~~~~v~itk~Gn  508 (745)
T TIGR01061       459 LLKKKLKELKKKFAQERRSKLEDEIEKIKINE------DELI-EKEDLYVVITKDGN  508 (745)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHEECCH------HHHH-HHCCCEEEEEECCC
T ss_conf             98999998723105750456751165301046------7853-21464079984476


No 100
>KOG0804 consensus
Probab=86.89  E-value=2.9  Score=22.72  Aligned_cols=73  Identities=14%  Similarity=0.156  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99999999999999999999999999986449987999999999999988644466666778887744310022
Q gi|254780680|r   34 DEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPN  107 (430)
Q Consensus        34 d~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPN  107 (430)
                      ..+..+++.+++.++.+.+..- ++.+...++.+.-..++++.-...++.+...+++..++++++.+++..|-+
T Consensus       381 e~k~~q~q~k~~k~~kel~~~~-E~n~~l~knq~vw~~kl~~~~e~~~~~~~s~d~~I~dLqEQlrDlmf~le~  453 (493)
T KOG0804         381 ERKLQQLQTKLKKCQKELKEER-EENKKLIKNQDVWRGKLKELEEREKEALGSKDEKITDLQEQLRDLMFFLEA  453 (493)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEHHH
T ss_conf             9999999999999999988889-999998762798888999999999999877888888899999768603101


No 101
>TIGR02169 SMC_prok_A chromosome segregation protein SMC; InterPro: IPR011891   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression .    This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by IPR011890 from INTERPRO. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent ..
Probab=85.77  E-value=3.3  Score=22.33  Aligned_cols=27  Identities=22%  Similarity=0.155  Sum_probs=10.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSN   54 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~l   54 (430)
                      |....++.+...+..++..+.++.+++
T Consensus       436 e~~~~~~~~~~~~~~~l~~~~~~~~el  462 (1202)
T TIGR02169       436 EELRRLSEELADLKAELARIEAKIAEL  462 (1202)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999999999999999999998888


No 102
>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase; InterPro: IPR005246   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   All known phenylalanyl-tRNA synthetases, excepting a monomeric mitochondrial form, have an alpha 2 beta 2 heterotetrameric structure. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains but is longer and of unknown function; more generally, it resembles class 2 aminoacyl tRNA ligases. .
Probab=85.34  E-value=0.48  Score=28.50  Aligned_cols=162  Identities=22%  Similarity=0.317  Sum_probs=91.7

Q ss_pred             CCCCCCCCHHHHCCCCCHHHHHHHCCC--------------CCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHC
Q ss_conf             666211220221173100011222167--------------530105648899999999999862232032021235620
Q gi|254780680|r  136 HLSREHFEIGEALGLMDFDRATKLSGA--------------RFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLV  201 (430)
Q Consensus       136 f~~k~H~elge~l~liDfe~a~kvsGs--------------rF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv  201 (430)
                      |.+|--++|++    =|||+|++-|+.              ||.|=|..-  | .+-|+-.-+=-++ =||.||..|.||
T Consensus        13 fdikK~~eLae----kDFE~AW~e~~~~l~~~h~d~~YPRl~f~~GK~Hp--l-~~TI~rlReAYLr-~GFsE~vNPliv   84 (558)
T TIGR00470        13 FDIKKVLELAE----KDFEAAWKESKELLKEKHIDEKYPRLKFEFGKEHP--L-FETIERLREAYLR-LGFSEMVNPLIV   84 (558)
T ss_pred             HHHHHHHHHHH----HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC--H-HHHHHHHHHHHHH-CCCEECCCCEEE
T ss_conf             46799999756----56899989867876227866568724554588875--6-8999999999864-683130077465


Q ss_pred             CHH------------HHHHHHH---CHHH-----HH---------------------HH---HH----HHHCC-EECCCC
Q ss_conf             278------------8986551---4224-----76---------------------77---64----31000-231345
Q gi|254780680|r  202 RDE------------AMYGTGQ---IPKF-----AD---------------------DM---FC----TTDGR-WLIPTS  232 (430)
Q Consensus       202 ~~~------------~~~gtG~---lp~f-----~~---------------------~~---y~----~~d~l-~Li~Ta  232 (430)
                      -+.            ++--|=+   ||+=     .+                     ++   |+    .+||| |+|+.|
T Consensus        85 de~hiykQFGpEA~AVLDRCFYLagLPrPdvGlg~eki~~Ie~~gid~~deK~E~L~Evfh~YKKG~idGDDLv~eia~a  164 (558)
T TIGR00470        85 DEVHIYKQFGPEALAVLDRCFYLAGLPRPDVGLGAEKIRIIEDLGIDVSDEKKERLKEVFHRYKKGEIDGDDLVYEIAEA  164 (558)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHH
T ss_conf             35135203786035775366662578788635560277888870774210134035788631467666754188888766


Q ss_pred             -CCH-H------------------------------HHHH--HHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEE
Q ss_conf             -411-4------------------------------5445--34205955504208853221078843355434321222
Q gi|254780680|r  233 -EVS-L------------------------------TNLY--SHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQ  278 (430)
Q Consensus       233 -Evp-L------------------------------~~~~--~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~Rv  278 (430)
                       +|. .                              +|+|  -..+.+.-.||||+.++-+|||||=+   =|..-|+-=
T Consensus       165 L~V~~~~glkvLe~vFPEfkdLKP~S~tlTLRSHMTsGWFItLs~i~dk~~lPlKLFSIDRCFRREQ~---ED~shLmtY  241 (558)
T TIGR00470       165 LDVEDETGLKVLEEVFPEFKDLKPVSSTLTLRSHMTSGWFITLSSIADKLKLPLKLFSIDRCFRREQK---EDASHLMTY  241 (558)
T ss_pred             HCCCCCCHHHHHHHHCCCHHCCCCCCCCCCCHHHCCCHHHHHHHHHHHHCCCCCEEECCCCCCCCCCC---CCCCCCCCE
T ss_conf             25675110213333086400168865543200101002788898787515897112200323144664---353100113


Q ss_pred             EEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             2102002121278650145789899999999998410
Q gi|254780680|r  279 HQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDL  315 (430)
Q Consensus       279 HQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~l  315 (430)
                      |==..    +++..|=|-   +.=-..||.||.+||.
T Consensus       242 hSASC----VvVdeevsv---DdGKaVAEgLL~qfGF  271 (558)
T TIGR00470       242 HSASC----VVVDEEVSV---DDGKAVAEGLLEQFGF  271 (558)
T ss_pred             EEEEE----EEECCCCCC---CCCHHHHHHHHHHHCC
T ss_conf             45466----785771243---6426889999987085


No 103
>pfam12325 TMF_TATA_bd TATA element modulatory factor 1 TATA binding. This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family.
Probab=84.70  E-value=3.6  Score=21.98  Aligned_cols=63  Identities=21%  Similarity=0.260  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999986449987999999999999988644466666
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEH   92 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~   92 (430)
                      ..|-.++.+...++.++..|.++|..++.+|-++....  ++......+...++.++..++....
T Consensus        24 s~lr~lE~E~~~lk~el~~l~~~r~~~~~Eiv~l~~~~--ee~~~~~~~~~~l~~~l~~l~~r~~   86 (121)
T pfam12325        24 STLRRLEGELASLKDELARLEAERDEARQEIVKLTEEN--EELRELKKEIEELEAELEDLEQRYE   86 (121)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99986998999999999999999999999999999999--9998888689999999999999999


No 104
>TIGR00459 aspS_bact aspartyl-tRNA synthetase; InterPro: IPR004524   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Aspartyl tRNA synthetase 6.1.1.12 from EC is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module .     This family represents aspartyl-tRNA synthetases from the bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). ; GO: 0000166 nucleotide binding, 0004815 aspartate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006422 aspartyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=84.27  E-value=1.4  Score=24.96  Aligned_cols=110  Identities=25%  Similarity=0.430  Sum_probs=67.6

Q ss_pred             HHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECCCCCC---HHHHHHH----HHCCCHHH
Q ss_conf             9999999862232032021235620278898655142247677643100023134541---1454453----42059555
Q gi|254780680|r  177 ALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIPTSEV---SLTNLYS----HEIIESKS  249 (430)
Q Consensus       177 ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~TaEv---pL~~~~~----~~~l~~~~  249 (430)
                      ..+..+-++ +.++||++|-||.|-++.        |.++-|        ||+||==+   .=..+|+    =++  .+|
T Consensus       156 ~v~~~~Rn~-l~~~gFleiETP~LtKsT--------PEGARD--------yLVPsRv~rsdG~g~FYALpQSPQl--fKQ  216 (653)
T TIGR00459       156 KVTKAVRNF-LDQQGFLEIETPILTKST--------PEGARD--------YLVPSRVHRSDGKGEFYALPQSPQL--FKQ  216 (653)
T ss_pred             HHHHHHHHH-HHHCCCCEEECCCCCCCC--------CCCHHH--------CCCCCCCCCCCCCCCEECCCCCHHH--HHH
T ss_conf             989999866-642787065067777888--------431101--------5775530036858845146897568--999


Q ss_pred             H-----CCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEE-EECCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             0-----420885322107884335543432122221020021-21278650145789899999999998
Q gi|254780680|r  250 L-----PLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCEL-VSITREEDSFTEHERMLSCAEEILKR  312 (430)
Q Consensus       250 L-----Pik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~-~~~~~pe~S~~~~e~~~~~~~~i~~~  312 (430)
                      |     ==||.-.-+|||-|=      .| ==|+=+||-|.+ .+||+.++-....|+|+..+=.-+..
T Consensus       217 LLMvsG~drYyQIArCFRDED------LR-ADRQPEFTQiD~E~SF~~~~~vm~l~E~l~~~vf~~v~~  278 (653)
T TIGR00459       217 LLMVSGVDRYYQIARCFRDED------LR-ADRQPEFTQIDMEMSFMTQEDVMDLIEKLVSGVFKEVKG  278 (653)
T ss_pred             HHHHCCCCCCEEEEEEECCCC------CC-CCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             875125553135788976625------66-657787324426311289356899999999999999707


No 105
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=83.90  E-value=3.9  Score=21.74  Aligned_cols=105  Identities=19%  Similarity=0.241  Sum_probs=56.6

Q ss_pred             HHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HCCCHHHHHHHHHHHHHHH
Q ss_conf             4785199999999984698958899999999999999999999999999999999986---4499879999999999999
Q gi|254780680|r    5 QWIRQNPEHLDIALKKRHLEPQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAI---AEGNLSLVDALKNETSTLK   81 (430)
Q Consensus         5 k~IRen~e~v~~~l~~R~~~~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k---~~~~~~~~~~Lk~e~~~Lk   81 (430)
                      ..+.+-.+.+..-|..-..-.+.+++.++..+...+..-++..+.- +.+.+++..++   ....+.+   ++   ...+
T Consensus        10 ~~~~~r~~el~~~L~~p~v~~d~~~~~~lske~a~l~~iv~~~~~~-~~~~~~l~~a~~~l~~~~D~e---m~---ema~   82 (363)
T COG0216          10 ESLLERYEELEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREY-KKAQEDLEDAKEMLAEEKDPE---MR---EMAE   82 (363)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCCHH---HH---HHHH
T ss_conf             9999999999998539633369999999999998888999999999-999999999999983568878---99---9999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEE
Q ss_conf             886444666667788877443100225881122113555402420
Q gi|254780680|r   82 EQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILIR  126 (430)
Q Consensus        82 ~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~  126 (430)
                      ++|..+++++..++++|..+|+  |        ..++++.|+++.
T Consensus        83 ~Ei~~~~~~~~~le~~L~~lLl--P--------kDpnd~knvilE  117 (363)
T COG0216          83 EEIKELEAKIEELEEELKILLL--P--------KDPNDDKNIILE  117 (363)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCC--C--------CCCCCCCCEEEE
T ss_conf             9999999989999999998628--9--------998877776899


No 106
>pfam04420 CHD5 CHD5-like protein. Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. In Saccharomyces cerevisiae this protein localizes to the ER and is thought to play a homeostatic role.
Probab=83.66  E-value=4  Score=21.68  Aligned_cols=73  Identities=19%  Similarity=0.183  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             9999999999999999999999999--99986449987999999999999988644466666778887744310022
Q gi|254780680|r   33 LDEKNRILIKKIEDIRARRNSNSAQ--IGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPN  107 (430)
Q Consensus        33 Ld~~rr~l~~e~e~LraerN~lSKe--Ig~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPN  107 (430)
                      -..+.++++.|+.+++.|.|.+|-+  .++-.+-  .-..+++.++.+++++.+...+...+..-.-..-++...|-
T Consensus        36 ~~~~~~~l~~E~~~~k~E~~~iS~qDefAKwaKl--~Rk~dKl~~el~~~~~~~~~~~~~~~~~~~~~~~v~t~~~~  110 (159)
T pfam04420        36 DAREQQKLRKEILELKRELSAISAQDEFAKWAKL--NRKIDKLTDELEKLKKELTSQKAKFKRLLKLARLLLTTGPM  110 (159)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             1999999999999999998558818889999999--99899999999999989999999999999999999998789


No 107
>KOG0250 consensus
Probab=83.41  E-value=4.1  Score=21.60  Aligned_cols=33  Identities=18%  Similarity=0.184  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999864
Q gi|254780680|r   31 LSLDEKNRILIKKIEDIRARRNSNSAQIGQAIA   63 (430)
Q Consensus        31 l~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~   63 (430)
                      .+++.+.+..+..++.++.+...+-|+|+.+.+
T Consensus       354 ~~~~~~~~~~~n~i~~~k~~~d~l~k~I~~~~~  386 (1074)
T KOG0250         354 NDLKEEIREIENSIRKLKKEVDRLEKQIADLEK  386 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             888999999998999988999999999999999


No 108
>KOG1936 consensus
Probab=81.60  E-value=4.7  Score=21.13  Aligned_cols=125  Identities=19%  Similarity=0.211  Sum_probs=76.8

Q ss_pred             HHHHHHHHHHH---HHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHH---CC-EECCCCCCHHHHHHHHHCCCHH
Q ss_conf             99999999862---23203202123562027889865514224767764310---00-2313454114544534205955
Q gi|254780680|r  176 RALGQFMIDLH---TSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTD---GR-WLIPTSEVSLTNLYSHEIIESK  248 (430)
Q Consensus       176 ~ALi~y~ld~~---~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d---~l-~Li~TaEvpL~~~~~~~~l~~~  248 (430)
                      ++|-+..+++.   -..||++++-+|.+=-++++.|-  -......+|...|   .+ .|-.---||+|-|.+..-+  .
T Consensus        74 m~lRe~if~~i~~vFkrhGa~~iDTPVFElkeiL~gK--YGEdskLiYdlkDQGGEl~SLRYDLTVPfARylAmNki--~  149 (518)
T KOG1936          74 MALREKIFSTIKEVFKRHGAETIDTPVFELKEILTGK--YGEDSKLIYDLKDQGGELCSLRYDLTVPFARYLAMNKI--T  149 (518)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEECCCCCHHHHHHHHHH--CCCCCCEEEEHHHCCCCEEEEECCCCCHHHHHHHHCCC--C
T ss_conf             8999999999999999719744466004599998664--05532306752324885887413566479999987145--5


Q ss_pred             HHCCEEEEEECCCCCCCCCCCCCCCCEEEEE---EEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             5042088532210788433554343212222---102002121278650145789899999999998410
Q gi|254780680|r  249 SLPLRFTTLAPSFRSEAGSAGRDTRGMLRQH---QFWKCELVSITREEDSFTEHERMLSCAEEILKRLDL  315 (430)
Q Consensus       249 ~LPik~~~~s~cfR~EaGs~GkdtrGl~RvH---QF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~l  315 (430)
                      .+|....|  .-||+.--+   =|||=||-|   -|+=.-+|--..||      -|.+.+..++++.|+|
T Consensus       150 sikRy~iA--kVyRRd~P~---mtrGR~REFYQcDFDIAG~~d~M~pd------aE~lkiv~e~L~~l~I  208 (518)
T KOG1936         150 SIKRYHIA--KVYRRDQPA---MTRGRYREFYQCDFDIAGQFDPMIPD------AECLKIVVEILSRLGI  208 (518)
T ss_pred             CCEEEEEE--EEEECCCCH---HHCHHHHHHHCCCCCCCCCCCCCCCH------HHHHHHHHHHHHHCCC
T ss_conf             21104678--787506814---42302455650675212667777860------9999999999865275


No 109
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=81.08  E-value=4.9  Score=21.01  Aligned_cols=18  Identities=22%  Similarity=0.505  Sum_probs=8.3

Q ss_pred             CCHHHHHCCHH--HHHHHHH
Q ss_conf             88447851999--9999998
Q gi|254780680|r    2 LDIQWIRQNPE--HLDIALK   19 (430)
Q Consensus         2 LDik~IRen~e--~v~~~l~   19 (430)
                      +|+.++|+...  .|+..|+
T Consensus       103 iD~elvrkEl~nAlvRAGLk  122 (290)
T COG4026         103 IDVELVRKELKNALVRAGLK  122 (290)
T ss_pred             CCHHHHHHHHHHHHHHHHHH
T ss_conf             58999999999999998888


No 110
>COG2024 Phenylalanyl-tRNA synthetase alpha subunit (archaeal type) [Translation, ribosomal structure and biogenesis]
Probab=80.79  E-value=0.88  Score=26.55  Aligned_cols=38  Identities=24%  Similarity=0.450  Sum_probs=26.4

Q ss_pred             HHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             34205955504208853221078843355434321222210
Q gi|254780680|r  241 SHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQF  281 (430)
Q Consensus       241 ~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF  281 (430)
                      ..++++..++|+|+.++-+|||+|-+-   |..-|+.-|--
T Consensus       197 Ls~i~~r~~~PlklFSIDRCFRREQ~E---D~shLmtYhSA  234 (536)
T COG2024         197 LSEILKREDPPLKLFSIDRCFRREQRE---DASHLMTYHSA  234 (536)
T ss_pred             HHHHHHCCCCCCEEEEHHHHHHHHHHC---CHHHHHHHCCC
T ss_conf             798872348984164256776655310---15666432034


No 111
>pfam03449 GreA_GreB_N domain. This domain adopts a long alpha-hairpin structure.
Probab=80.78  E-value=5  Score=20.93  Aligned_cols=59  Identities=22%  Similarity=0.284  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCCH---HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999-999999999998644998---79999999999999886444666667
Q gi|254780680|r   35 EKNRILIKKIEDIRA-RRNSNSAQIGQAIAEGNL---SLVDALKNETSTLKEQLPILEKEEHE   93 (430)
Q Consensus        35 ~~rr~l~~e~e~Lra-erN~lSKeIg~~k~~~~~---~~~~~Lk~e~~~Lk~eik~le~~~~~   93 (430)
                      +-+..++.+++.|.. ++-++++.|+.+...|+-   .+-+..+.+...+...|..|+..+..
T Consensus         6 eg~~~L~~EL~~L~~v~rp~i~~~i~~Ar~~GDlsENaeY~aAke~q~~le~RI~eLe~~L~~   68 (71)
T pfam03449         6 EGYEKLQEELERLKNVERPEIIKAIAEAREHGDLSENAEYHAAKEEQREIEARIRELEDRLAR   68 (71)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999987538999999999988599042067899999999999999999999961


No 112
>TIGR00020 prfB peptide chain release factor 2; InterPro: IPR004374 In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a superfamily IPR000352 from INTERPRO of RF-1, RF-2, mitochondrial, RF-H, etc proteins.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=80.17  E-value=5.3  Score=20.79  Aligned_cols=124  Identities=15%  Similarity=0.140  Sum_probs=75.4

Q ss_pred             CCCHHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             98844785199999999984698958899999999999999999999999999999--9999864499879999999999
Q gi|254780680|r    1 MLDIQWIRQNPEHLDIALKKRHLEPQSEYILSLDEKNRILIKKIEDIRARRNSNSA--QIGQAIAEGNLSLVDALKNETS   78 (430)
Q Consensus         1 MLDik~IRen~e~v~~~l~~R~~~~~id~il~Ld~~rr~l~~e~e~LraerN~lSK--eIg~~k~~~~~~~~~~Lk~e~~   78 (430)
                      .||..-|+...+.+.+.+...++=-|..+-..+-+++..++..++.++.-+|.+-.  ..-.+..+.+++.+.+-+.-..
T Consensus        24 ~Ld~e~~~~rle~le~e~~dP~fW~D~~rAq~v~~e~~~l~~~l~~~~~l~~~~~dl~~L~Ela~ee~d~aaasGm~~~~  103 (373)
T TIGR00020        24 ILDPEKLKARLEELEKEMEDPNFWNDQERAQKVIKERSSLEEELDTLEELKNSLDDLSELLELAKEEDDEAAASGMETFA  103 (373)
T ss_pred             HCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             13866899999999877507866612589999999999999863279998755325788998743760357778999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEE----------------------EEECCCCCCCC
Q ss_conf             99988644466666778887744310022588112211355540242----------------------00015656656
Q gi|254780680|r   79 TLKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILI----------------------RSVGKKPSAIH  136 (430)
Q Consensus        79 ~Lk~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i----------------------~~~G~~~~f~f  136 (430)
                      ++-.+++.|++++++++-+..-   +           |.-|..|..+                      .+|+|.+.|.-
T Consensus       104 el~~El~~Le~~~~~lE~~~~L---S-----------gE~D~~nA~ltI~~GAGGTEa~DWa~ML~RMY~RWAE~rgykv  169 (373)
T TIGR00020       104 ELEEELKALEKELEELELRTLL---S-----------GEYDANNAILTIQSGAGGTEAQDWASMLYRMYLRWAERRGYKV  169 (373)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHC---C-----------CCCCHHCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE
T ss_conf             9999999999999999999970---6-----------7577210633523877985166699999875357641057513


Q ss_pred             CC
Q ss_conf             66
Q gi|254780680|r  137 LS  138 (430)
Q Consensus       137 ~~  138 (430)
                      +.
T Consensus       170 E~  171 (373)
T TIGR00020       170 EI  171 (373)
T ss_pred             EE
T ss_conf             56


No 113
>cd07366 3MGA_Dioxygenase Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 3-O-Methylgallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate. 3-O-Methylgallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate (3MGA) between carbons 2 and 3. 3-O-Methylgallate Dioxygenase is a key enzyme in the syringate degradation pathway, in which the syringate is first converted to 3-O-Methylgallate by O-demethylase. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B.
Probab=79.49  E-value=1.1  Score=25.77  Aligned_cols=41  Identities=24%  Similarity=0.268  Sum_probs=24.1

Q ss_pred             CCEECCCCCCHHHHHHHHHCCCHHHHCC--EEEEEECCCCCCCCCC
Q ss_conf             0023134541145445342059555042--0885322107884335
Q gi|254780680|r  225 GRWLIPTSEVSLTNLYSHEIIESKSLPL--RFTTLAPSFRSEAGSA  268 (430)
Q Consensus       225 ~l~Li~TaEvpL~~~~~~~~l~~~~LPi--k~~~~s~cfR~EaGs~  268 (430)
                      +....||+|+--=.-.++ .+  .++|+  -.+.|-||||+|||+.
T Consensus       277 ~~~~aGt~EIrnWi~~~G-Am--~~~g~~~~~~dY~P~yRt~AgtG  319 (328)
T cd07366         277 AHLQSGTSELKNWIAAAG-AL--DDLGLKMTSVDYVPCYRTEAGTG  319 (328)
T ss_pred             HHHHCCHHHHHHHHHHHH-HH--HCCCCCCCEEEEEEECCCCCCCC
T ss_conf             877376499999999997-87--51799864687655102566666


No 114
>PRK05561 DNA topoisomerase IV subunit A; Validated
Probab=79.44  E-value=5.5  Score=20.63  Aligned_cols=58  Identities=26%  Similarity=0.275  Sum_probs=38.6

Q ss_pred             HHHHHCCHHHHHHHHHHCCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             44785199999999984698958---89999999999999999999999999999999998644
Q gi|254780680|r    4 IQWIRQNPEHLDIALKKRHLEPQ---SEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAE   64 (430)
Q Consensus         4 ik~IRen~e~v~~~l~~R~~~~~---id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~   64 (430)
                      |+.||+..+ .+++|-.| +.++   .+.|+++ ..+|-...+.+.|+.|..++.++|..+..-
T Consensus       400 I~iIR~S~d-ak~~L~~~-f~lse~QA~AIL~m-rL~rLt~LE~~kl~~E~~eL~~~I~~l~~I  460 (745)
T PRK05561        400 IEIIRESDE-PKANLMAR-FGLTEIQAEAILEL-RLRRLAKLEEIEIRKEQDELRKEIAELEAI  460 (745)
T ss_pred             HHHHHCCCH-HHHHHHHH-HCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999970632-66777555-08799999999999-999987667999999999999999999999


No 115
>PRK05560 DNA gyrase subunit A; Validated
Probab=79.32  E-value=5.6  Score=20.61  Aligned_cols=59  Identities=22%  Similarity=0.240  Sum_probs=42.5

Q ss_pred             HHHHHC--CHHHHHHHHHHCCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             447851--99999999984698958---89999999999999999999999999999999998644
Q gi|254780680|r    4 IQWIRQ--NPEHLDIALKKRHLEPQ---SEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAE   64 (430)
Q Consensus         4 ik~IRe--n~e~v~~~l~~R~~~~~---id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~   64 (430)
                      |+.||+  |++..+.+|..+ +.++   .+.|+++ ..+|-...+.+.|+.|..++.++|..+..-
T Consensus       394 I~iIR~S~~~~~Ak~~L~~~-f~lse~QA~AIL~m-rL~rLt~Le~~kl~~E~~eL~~~I~~l~~I  457 (822)
T PRK05560        394 IALIRASPTPAEAREGLMER-YGLSEIQAQAILDM-RLQRLTGLEREKIEDEYKELLAEIADLLDI  457 (822)
T ss_pred             HHHHHCCCCHHHHHHHHHHH-HCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99997189878999989887-58899999999998-999987678999999999999999999988


No 116
>pfam03357 Snf7 Snf7. This family of proteins are involved in protein sorting and transport from the endosome to the vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes play an important role in the degradation of both lipids and cellular proteins. In order to perform this degradative function, vacuoles/lysosomes contain numerous hydrolases which have been transported in the form of inactive precursors via the biosynthetic pathway and are proteolytically activated upon delivery to the vacuole/lysosome. The delivery of transmembrane proteins, such as activated cell surface receptors to the lumen of the vacuole/lysosome, either for degradation/downregulation, or in the case of hydrolases, for proper localisation, requires the formation of multivesicular bodies (MVBs). These late endosomal structures are formed by invaginating and budding of the limiting membrane into the lumen of the compartment. During this process, a subset of the endosomal membrane proteins is sorted into the form
Probab=78.57  E-value=5.8  Score=20.45  Aligned_cols=62  Identities=27%  Similarity=0.271  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999864499879999999999999886444666
Q gi|254780680|r   29 YILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKE   90 (430)
Q Consensus        29 ~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~   90 (430)
                      .|++|-...+.+..+...|..+...+..++.++.++|+...+-.+..+.+.+...+..+...
T Consensus         2 aI~~Lk~~~~~L~k~~~~Le~~~~~~~~~aK~~~~~g~k~~A~~~lk~kk~~ek~~~~~~~~   63 (169)
T pfam03357         2 AILSLRKAIRELDKKQESLEKKIKKLEAEIKKLAKKGNKDAALILLKQKKRYEKQLDQLDGQ   63 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             78899999999999999999999999999999988463999999999999999999999999


No 117
>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=77.38  E-value=6.3  Score=20.21  Aligned_cols=184  Identities=15%  Similarity=0.161  Sum_probs=94.9

Q ss_pred             CCCCCCCCCCCCCCHHHHC-CCCCHHHH-HHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHH
Q ss_conf             5656656662112202211-73100011-222167530105648899999999999862232032021235620278898
Q gi|254780680|r  130 KKPSAIHLSREHFEIGEAL-GLMDFDRA-TKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMY  207 (430)
Q Consensus       130 ~~~~f~f~~k~H~elge~l-~liDfe~a-~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~  207 (430)
                      .+|.+.+....-.||.|.. -+.-+++- +++...-..--...--.+.+.+-    ++. ...||.|+.+-.|+.++...
T Consensus       315 ~vPs~R~Di~~e~DLiEEVaRiyGYd~Ip~~~p~~~~~~~~~~~~~~~~~ir----~~L-~~~G~~Evitysf~s~~~~~  389 (546)
T PRK09616        315 LVPPYRVDILHEVDVIEDVAIAYGYNNLEPELPKIFTIGRLHPIEELSRAIR----DLM-VGLGFQEVMNFTLTSEEVLF  389 (546)
T ss_pred             ECCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHH----HHH-HHCCCCEEEECCCCCHHHHH
T ss_conf             8887323335501389999998182228754676545788998999999999----999-96896127622568989998


Q ss_pred             HHHHCHHHHHHHHHH---HHCCEECCCCCCH--HHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEE
Q ss_conf             655142247677643---1000231345411--45445342059555042088532210788433554343212222102
Q gi|254780680|r  208 GTGQIPKFADDMFCT---TDGRWLIPTSEVS--LTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFW  282 (430)
Q Consensus       208 gtG~lp~f~~~~y~~---~d~l~Li~TaEvp--L~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~  282 (430)
                      .-+++|... .+-..   .+++-..=|+=+|  |.++..|.  . .+.+++++.++++|....+..   +.    ..|..
T Consensus       390 ~~~~~~~~~-~v~l~NPis~e~s~mRtsLlp~LL~~~~~N~--~-r~~~~~lFEiG~Vf~~~~~~~---~~----~~e~~  458 (546)
T PRK09616        390 EKMNLEEDD-PVEVLNPISEDYTVLRTSLLPSLLEFLSINK--H-REYPQKIFEIGDVVLIDESTE---TG----TKTER  458 (546)
T ss_pred             HHHCCCCCC-EEEECCCCCHHHHHHHHHHHHHHHHHHHHHH--C-CCCCEEEEEEECEEECCCCCC---CC----CCCCC
T ss_conf             761688687-4896488745677777553899999999846--6-899845997405580488655---56----40023


Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCC
Q ss_conf             0021212786501457898999999999984106753037801178443402410110100483
Q gi|254780680|r  283 KCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNL  346 (430)
Q Consensus       283 KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~  346 (430)
                      ++-. .++..   ..-|..+....+.++..|++.|.+.             .-+...|.|||..
T Consensus       459 ~la~-~~~g~---~~dF~d~Kg~ve~ll~~l~~~~~~~-------------~~~~~~~hPgrsA  505 (546)
T PRK09616        459 KLAA-AIAHS---GATFTEIKSVVKALLRELGIEYEVE-------------ESEHPSFIPGRCA  505 (546)
T ss_pred             EEEE-EEECC---CCCHHHHHHHHHHHHHHCCCCEEEE-------------ECCCCCCCCCCEE
T ss_conf             7999-99799---7799999999999999849955994-------------2788877899769


No 118
>pfam03962 Mnd1 Mnd1 family. This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.
Probab=77.18  E-value=6.4  Score=20.17  Aligned_cols=67  Identities=21%  Similarity=0.188  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999999864499-8799999999999998864446666677
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGN-LSLVDALKNETSTLKEQLPILEKEEHEV   94 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~-~~~~~~Lk~e~~~Lk~eik~le~~~~~l   94 (430)
                      +....+......+..+++.++++...+..+|..++.... .++...+..+...|+.+++.|.+++...
T Consensus        62 ~~~~~~~~~~~~L~~~~~~~~~~i~~l~~~i~~~k~~r~~~~er~~ll~~l~~l~~~~~~L~~el~~~  129 (188)
T pfam03962        62 QAKNKLKTRLEKLKKELEELKQRIAELQAQIEKLKVGREETEERTELLEELKQLEKELKKLKAELEKY  129 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999999998658551669999999999999999999999998


No 119
>pfam11932 DUF3450 Protein of unknown function (DUF3450). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are about 260 amino acids in length.
Probab=76.99  E-value=6.4  Score=20.14  Aligned_cols=77  Identities=18%  Similarity=0.302  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             99999999999999999999999999999986449987999999999999988644466666778887744310022588
Q gi|254780680|r   31 LSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPL  110 (430)
Q Consensus        31 l~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~  110 (430)
                      ..+-.++|.+..+++.|+....++.+.|.            +...++..|..+|..++.....+.--+...+-.|-.++.
T Consensus        53 ~~l~~e~~~~~~e~e~L~~yn~ql~~~i~------------~Q~~ei~~l~~qi~~i~~~~~~i~Plm~~Mi~~Le~fV~  120 (250)
T pfam11932        53 QELLAEIRQLLKEIENLRVYNDQLQRLVA------------NQQQEIASLQQQIEQIEKTRQGLVPLMYRMIDGLEQFVA  120 (250)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999------------999999999999999999996475699999999999987


Q ss_pred             CHHHHCCCC
Q ss_conf             112211355
Q gi|254780680|r  111 EEVPIGTSA  119 (430)
Q Consensus       111 ~~VP~G~de  119 (430)
                      -|+|.=.+|
T Consensus       121 ~D~PFl~~E  129 (250)
T pfam11932       121 LDLPFLKEE  129 (250)
T ss_pred             CCCCCCHHH
T ss_conf             689988899


No 120
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=75.58  E-value=7  Score=19.87  Aligned_cols=74  Identities=18%  Similarity=0.196  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             99999999999999999999999999-8644998---7999999999999988644466666778887744310022588
Q gi|254780680|r   35 EKNRILIKKIEDIRARRNSNSAQIGQ-AIAEGNL---SLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPL  110 (430)
Q Consensus        35 ~~rr~l~~e~e~LraerN~lSKeIg~-~k~~~~~---~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~  110 (430)
                      +-+..|..+++.|++++-.+..++.. +..-|+-   ++-..-|++...|-..|..|++.+...         ..+....
T Consensus        13 eG~~~L~~EL~~Lk~~rr~~v~~~~~~a~~~GDlSENaEY~~aK~eq~~ie~RI~~Le~~L~~a---------~~~~~~~   83 (161)
T PRK05892         13 AARDHLAAELARLRQRRDRLEVEVKNDRGMIGDHGDAAEAIQRADELAILGDRINELDRRLRTG---------PTPWSGS   83 (161)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC---------CCCCCCC
T ss_conf             9999999999999882639999999999977994566739999999999999999999999728---------8877888


Q ss_pred             CHHHHCC
Q ss_conf             1122113
Q gi|254780680|r  111 EEVPIGT  117 (430)
Q Consensus       111 ~~VP~G~  117 (430)
                      ..|+.|.
T Consensus        84 ~~v~~G~   90 (161)
T PRK05892         84 ETLPGGT   90 (161)
T ss_pred             CEEECCE
T ss_conf             8784666


No 121
>TIGR00458 aspS_arch aspartyl-tRNA synthetase; InterPro: IPR004523   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Aspartyl tRNA synthetase 6.1.1.12 from EC is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module .     This family represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). ; GO: 0000166 nucleotide binding, 0004815 aspartate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006422 aspartyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=75.48  E-value=1.3  Score=25.24  Aligned_cols=136  Identities=18%  Similarity=0.318  Sum_probs=81.8

Q ss_pred             HHHHHHHHCCCCCCCHHHHCCCCCC--CEEEEEECCCCCCCCCCCCCCCHHHHCC--CCCHHHHHHHCCCCCEEECCHHH
Q ss_conf             8774431002258811221135554--0242000156566566621122022117--31000112221675301056488
Q gi|254780680|r   97 SLKKLISCIPNVPLEEVPIGTSANE--NILIRSVGKKPSAIHLSREHFEIGEALG--LMDFDRATKLSGARFSVLTGHLA  172 (430)
Q Consensus        97 el~~lll~IPNi~~~~VP~G~de~d--Nv~i~~~G~~~~f~f~~k~H~elge~l~--liDfe~a~kvsGsrF~~Lkg~~A  172 (430)
                      ++.-.-+.+=|......|+-..|..  .-++...|-         +-+.+-.+|+  .+|..+...          .+.=
T Consensus        95 EI~~~~~~v~~~~~~pLPl~~~ea~k~~AE~daagl---------p~~~ldTRLd~R~~DLR~~~~----------~AIF  155 (466)
T TIGR00458        95 EIIPTKLEVLNEAKEPLPLDLTEASKVEAELDAAGL---------PVVNLDTRLDARFLDLRRPKV----------QAIF  155 (466)
T ss_pred             EEEEEHHHHHHCCCCCCCCCHHHCCCCHHHHHHCCC---------CEEEECCCHHHHHHHCCCCCH----------HHHH
T ss_conf             563100011122776788761110234033431375---------234300111000110256540----------2125


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCH--HHHHHHHHHHH-CCEECCCCCCHHHHHHHHHCCCHHH
Q ss_conf             99999999999862232032021235620278898655142--24767764310-0023134541145445342059555
Q gi|254780680|r  173 HLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIP--KFADDMFCTTD-GRWLIPTSEVSLTNLYSHEIIESKS  249 (430)
Q Consensus       173 ~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp--~f~~~~y~~~d-~l~Li~TaEvpL~~~~~~~~l~~~~  249 (430)
                      +....+++-+-.+ +.+.||++|.+|-||-+.+=-||--+|  -|+...|..+. .+|              ++++-..+
T Consensus       156 ~I~~~~~~~vR~~-L~~~~F~Ev~TPKlv~~~tEGGt~lF~i~YF~~~AfL~QSPQly--------------KQ~l~~~g  220 (466)
T TIGR00458       156 RIRSEVLESVREF-LAEEGFIEVHTPKLVASATEGGTELFPITYFEREAFLGQSPQLY--------------KQVLMAAG  220 (466)
T ss_pred             HHHHHHHHHHHHH-HHHCCCEEEECCCEEECCCCCCCCCCEEEEECCCCCCCCCCHHH--------------HHHHHHCC
T ss_conf             5689999999998-73088256307621421668885332012212300013570356--------------68776526


Q ss_pred             HCCEEEEEECCCCCCCCC
Q ss_conf             042088532210788433
Q gi|254780680|r  250 LPLRFTTLAPSFRSEAGS  267 (430)
Q Consensus       250 LPik~~~~s~cfR~EaGs  267 (430)
                      | =|...++|.||+|-..
T Consensus       221 ~-~rVyEI~PiFRAE~~n  237 (466)
T TIGR00458       221 L-ERVYEIGPIFRAEEHN  237 (466)
T ss_pred             C-CCEEEECCEEECCCCC
T ss_conf             5-2035505522056665


No 122
>pfam07246 Phlebovirus_NSM Phlebovirus nonstructural protein NS-M. This family consists of several Phlebovirus nonstructural NS-M proteins which represent the N-terminal region of the M polyprotein precursor. The function of this family is unknown.
Probab=75.19  E-value=7.1  Score=19.80  Aligned_cols=36  Identities=25%  Similarity=0.218  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999988644466666778887744310
Q gi|254780680|r   69 LVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISC  104 (430)
Q Consensus        69 ~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~  104 (430)
                      ..+++++..+.|+++.+.|..++..+..++..+--.
T Consensus       203 ~~~e~MAr~~~l~~~~~~ltde~~~~k~~~~~~r~~  238 (264)
T pfam07246       203 RVEESMARVKGLKEELKQLTDELQHAKSEMQSLRKK  238 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999874427888788879999998889999874


No 123
>pfam05622 HOOK HOOK protein. This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagel
Probab=75.02  E-value=7.2  Score=19.77  Aligned_cols=29  Identities=17%  Similarity=0.305  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSA   56 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSK   56 (430)
                      +.+.....+.+.++-++|.||.+...++|
T Consensus       284 ~eL~~~A~ea~~LrDElD~LRe~adk~~k  312 (713)
T pfam05622       284 DELTSLAAESQALKDEIDVLRESSDKAKK  312 (713)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999889999977889999998899999


No 124
>pfam06447 consensus
Probab=74.14  E-value=7.6  Score=19.62  Aligned_cols=29  Identities=17%  Similarity=0.250  Sum_probs=15.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999998864446666677888774431
Q gi|254780680|r   75 NETSTLKEQLPILEKEEHEVCSSLKKLIS  103 (430)
Q Consensus        75 ~e~~~Lk~eik~le~~~~~le~el~~lll  103 (430)
                      .+..+.+++|..++.+..++.++++++..
T Consensus        83 ~~~~~~q~~l~~l~qe~~~L~~q~~~~~~  111 (407)
T pfam06447        83 RDLDQNQERIASLEQENQQLREQLAAGQA  111 (407)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             87888899999999999999999998872


No 125
>COG2269 Truncated, possibly inactive, lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=74.00  E-value=3.1  Score=22.45  Aligned_cols=114  Identities=21%  Similarity=0.238  Sum_probs=64.5

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHH----HHCCEECCCCCCHHHHHHHHHCCCHH
Q ss_conf             99999999999862232032021235620278898655142247677643----10002313454114544534205955
Q gi|254780680|r  173 HLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCT----TDGRWLIPTSEVSLTNLYSHEIIESK  248 (430)
Q Consensus       173 ~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~----~d~l~Li~TaEvpL~~~~~~~~l~~~  248 (430)
                      +|-||-|.-++-.--.++||.+|-+|.|-..-+-+.  ++-.|+.+..-.    .-.|||...-|.     |++..|...
T Consensus        16 ll~Ra~i~~~iR~FF~erg~lEVeTp~Ls~a~vtd~--hL~~F~Te~~~~~~~~~~~l~L~TSPEy-----~mKrLLAag   88 (322)
T COG2269          16 LLKRAAIIAAIRRFFAERGVLEVETPALSVAPVTDI--HLHPFETEFLGPGGAKGKPLWLHTSPEY-----HMKRLLAAG   88 (322)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEECCHHHHCCCCCCC--CEEEEEEEEECCCCCCCCEEEEECCCHH-----HHHHHHHCC
T ss_conf             998999999999999876925853367650789864--2344566765467666530366568077-----789999754


Q ss_pred             HHCCEEEEEECCCCCC-CCCCCCCCCCEEEEEEEEEEEEEECCCC-----CCHHHHHHHHH
Q ss_conf             5042088532210788-4335543432122221020021212786-----50145789899
Q gi|254780680|r  249 SLPLRFTTLAPSFRSE-AGSAGRDTRGMLRQHQFWKCELVSITRE-----EDSFTEHERML  303 (430)
Q Consensus       249 ~LPik~~~~s~cfR~E-aGs~GkdtrGl~RvHQF~KVE~~~~~~p-----e~S~~~~e~~~  303 (430)
                      +-|  ...++.|||-+ +|.+        .--+|+.+|-+.+--.     +++.+.+..++
T Consensus        89 ~~~--ifql~kvfRN~E~G~~--------H~PEFTMLEWYrv~~d~~~lm~e~~~Ll~~vl  139 (322)
T COG2269          89 SGP--IFQLGKVFRNEEMGRL--------HNPEFTMLEWYRVGCDYYRLMNEVDDLLQLVL  139 (322)
T ss_pred             CCC--CHHHHHHHHCCCCCCC--------CCCCEEEEEEECCCCCHHHHHHHHHHHHHHHH
T ss_conf             886--0145477726332566--------79843676510067859999999999999997


No 126
>pfam06508 ExsB ExsB. This family includes putative transcriptional regulators from Bacteria and Archaea.
Probab=73.91  E-value=3  Score=22.56  Aligned_cols=55  Identities=24%  Similarity=0.350  Sum_probs=35.2

Q ss_pred             EEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCC-HHCCCHHHEEEEEE
Q ss_conf             102002121278650145789899999999998410675303780-11784434024101
Q gi|254780680|r  280 QFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVSLCT-GDLGFSACKTYDLE  338 (430)
Q Consensus       280 QF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~s-gdlg~~a~~~~DiE  338 (430)
                      ++..|..+.|--...    |..=++.++.+.+.|+++++++++.. ++++.++-..-+++
T Consensus        22 ~~~~v~ait~dYGQ~----~~~Ei~~A~~ia~~l~i~h~vidl~~l~~~~~saL~~~~~~   77 (137)
T pfam06508        22 EGYEVYALTFDYGQR----HSKELECAKKIAKALGVEHKIVDLDFLKQIGGSALTDDSIE   77 (137)
T ss_pred             CCCEEEEEEECCCCC----HHHHHHHHHHHHHHCCCCCEEECCCHHHHHCCCCCCCCCCC
T ss_conf             699689998147887----39999999999998299750303302444165522368855


No 127
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1; InterPro: IPR004575   MAT1 (menage a trois 1) is a RING finger protein with a characteristic C3HC4 motif located in the N-terminal domain. MAT1 stabilises the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex which then goes on to activate many of the CDK enzymes intimately involved in the cell cycle . CDK7 forms a stable complex with cyclin H and MAT1 in vivo only when phosphorylated on either one of two residues (Ser164 or Thr170) in its T-loop. The requirement for MAT1 for the activation of CAK can be by-passed by the phosphorylation of CDK7 on the T-loop. The two mechanisms for CDK7 complex stabilisation and activation (MAT1 addition and T-loop phosphorylation), which can operate independently in vitro, actually cooperate under physiological conditions to maintain complex integrity. With prolonged exposure to elevated temperature, dissociation to monomeric subunits occurs in vivo when CDK7 is dephosphorylated, even in the presence of MAT1 .    The Cyclin H-MAT1-CDK7 complex also forms part of TFIIH, a multiprotein complex required for both transcription and DNA repair.; GO: 0007049 cell cycle, 0005634 nucleus.
Probab=73.10  E-value=8  Score=19.45  Aligned_cols=124  Identities=20%  Similarity=0.223  Sum_probs=73.3

Q ss_pred             HHHCCHHHHHHHHHHCCCCCC-HHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             785199999999984698958-8999999----99999999999999999999999999986449987999999999999
Q gi|254780680|r    6 WIRQNPEHLDIALKKRHLEPQ-SEYILSL----DEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTL   80 (430)
Q Consensus         6 ~IRen~e~v~~~l~~R~~~~~-id~il~L----d~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~L   80 (430)
                      |=++|.+.|.+|..+-.-+.. +++.+++    .+++|...+++|+.+...+.-.|          .+.+++|......+
T Consensus       134 Y~~~Nk~~I~~Nk~k~~~e~~~LE~~l~~Ek~~~e~rr~~l~~~E~~~~~~K~~~K----------~al~d~L~~s~~p~  203 (322)
T TIGR00570       134 YQKENKEVIQKNKEKSTREQEELEEALELEKEEEEKRRLLLQKLEEEEKMKKRRDK----------QALIDELETSTLPA  203 (322)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHCCCCCH
T ss_conf             98850799874110152348999999987678899999999999999987567569----------99999752268348


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCHHHHCCCC-CCCEEEEEECCCCCCCCCCC
Q ss_conf             988644466666778887744310022-588112211355-54024200015656656662
Q gi|254780680|r   81 KEQLPILEKEEHEVCSSLKKLISCIPN-VPLEEVPIGTSA-NENILIRSVGKKPSAIHLSR  139 (430)
Q Consensus        81 k~eik~le~~~~~le~el~~lll~IPN-i~~~~VP~G~de-~dNv~i~~~G~~~~f~f~~k  139 (430)
                      ..-|....+....++.+....-+.=|+ ..+-.+-.|..- ..++-|...-+.+-|.|.|.
T Consensus       204 ~~~~~~h~~~~~~~~~~~~k~~~~k~~~~fstgIK~G~g~~~s~~pv~k~ee~~l~~Y~P~  264 (322)
T TIGR00570       204 AELIAQHKKNSVKLEKQVEKLKLEKPNRTFSTGIKVGFGYQISLVPVPKSEEKALFEYEPL  264 (322)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCCCCCC
T ss_conf             9999999988999887764278654222001563337776524267653000355011565


No 128
>PRK13979 DNA topoisomerase IV subunit A; Provisional,Validated
Probab=72.84  E-value=8.1  Score=19.41  Aligned_cols=59  Identities=19%  Similarity=0.089  Sum_probs=42.7

Q ss_pred             HHHHHC--CHHHHHHHHHHCCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             447851--99999999984698958---89999999999999999999999999999999998644
Q gi|254780680|r    4 IQWIRQ--NPEHLDIALKKRHLEPQ---SEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAE   64 (430)
Q Consensus         4 ik~IRe--n~e~v~~~l~~R~~~~~---id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~   64 (430)
                      |+.||.  +++..+++|-.|. .++   .+.|+++ ..+|-..-+.+.++.|.+++.++|..+..-
T Consensus       406 I~iIR~S~~~~~Ak~~L~~~f-~lse~QA~AILdm-rL~rLT~LE~~ki~~E~~eL~~~I~~l~~I  469 (959)
T PRK13979        406 IKTIRASKSKKDASENLIEKF-GFTDEQAEAILEL-MLYRLTGLEIKVFEKEYKELEKLIKKLEKI  469 (959)
T ss_pred             HHHHHCCCCHHHHHHHHHHHC-CCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999981898379999898761-9999999999998-999987889999999999999999999999


No 129
>KOG0979 consensus
Probab=72.70  E-value=8.1  Score=19.38  Aligned_cols=57  Identities=14%  Similarity=0.076  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEE
Q ss_conf             999999999999988644466666778887744310022588112211355540242
Q gi|254780680|r   69 LVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILI  125 (430)
Q Consensus        69 ~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i  125 (430)
                      .+..++++...++.+-....+......+.+.+..-.+|+.+.+.=|.+++++-+..+
T Consensus       319 ~v~~~~~~le~lk~~~~~rq~~i~~~~k~i~~~q~el~~~~~~e~~~~~~~ei~~~~  375 (1072)
T KOG0979         319 EVEEKKNKLESLKKAAEKRQKRIEKAKKMILDAQAELQETEDPENPVEEDQEIMKEV  375 (1072)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf             999999889999877899999999999999998866520678656505579999999


No 130
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family; InterPro: IPR014243    This entry represents a set of transcription factors found in some endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria). In some species these proteins are encoded multiple times. The best characterised protein in this entry is the prespore-specific transcription factor RsfA from Bacillus subtilis, previously known as YwfN. Expression of RsfA is controlled by sigma factor F, and it seems to improve the efficiency of sporulation by fine-tuning the expression of genes in the sigma F regulon, particularly the timing of their expression . It also negatively regulates spoIIR and its own synthesis. A paralog in B. subtilis is designated YlbO, though its function is not known. A highly variable linker region separates two very strongly conserved sequence regions within the protein. .
Probab=72.07  E-value=8.4  Score=19.28  Aligned_cols=67  Identities=13%  Similarity=0.209  Sum_probs=50.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9588999999999999999999999999999999999864499879999999999999886444666667788877443
Q gi|254780680|r   24 EPQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLI  102 (430)
Q Consensus        24 ~~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~ll  102 (430)
                      ++-+..+|.-=+..+..+.+...||.++..|.+++.            .|..+..+|..+++.|+++...++++...++
T Consensus        81 ~lTl~~VI~FLq~~~~~~~~~~~l~~E~~~L~~~~~------------~Lq~~ne~L~~el~~L~~~~~~~eEDY~~L~  147 (163)
T TIGR02894        81 SLTLQDVISFLQNLKTTNPSDQALQKENERLKKELE------------SLQKRNEELEKELEKLEKRQSTIEEDYETLI  147 (163)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             268788999999988877999999989999999999------------9999999999999999998467899999999


No 131
>pfam07851 TMPIT TMPIT-like protein. A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this.
Probab=69.85  E-value=9.3  Score=18.94  Aligned_cols=75  Identities=17%  Similarity=0.237  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999999864499879999999999--------999886444666667788877
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETS--------TLKEQLPILEKEEHEVCSSLK   99 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~--------~Lk~eik~le~~~~~le~el~   99 (430)
                      ++..++.+..+..+++++++...++..++.|..-++.     ..++++..+        +.++.++++++++.+....+.
T Consensus        11 ~e~~~Lee~hk~Y~~Kleel~~~Q~~c~~~i~~q~kr-----l~~l~~slk~l~~~~~~E~~~~~~~l~~~i~~r~~~l~   85 (330)
T pfam07851        11 KEFQQLQETHRLYKQKLEEVEKLQEQCTSAIARQRKR-----LKQLIVSLKKLKKSLTPEDSELVEQLEEQIKERKNQFF   85 (330)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999999899999999-----99999999973647997789999999999999999999


Q ss_pred             HHHHHCCC
Q ss_conf             44310022
Q gi|254780680|r  100 KLISCIPN  107 (430)
Q Consensus       100 ~lll~IPN  107 (430)
                      +.-..+|+
T Consensus        86 dme~~LP~   93 (330)
T pfam07851        86 DMESFLPK   93 (330)
T ss_pred             HHHHHCCC
T ss_conf             99864886


No 132
>pfam08317 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=69.54  E-value=9.5  Score=18.90  Aligned_cols=62  Identities=15%  Similarity=0.157  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHH------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999999999864------499879999999999999886444666667788877443100
Q gi|254780680|r   44 IEDIRARRNSNSAQIGQAIA------EGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCI  105 (430)
Q Consensus        44 ~e~LraerN~lSKeIg~~k~------~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~I  105 (430)
                      +..++.+.+.+..++..+..      .-+.++..+++.+..+...+|.....++.++++++..+-..|
T Consensus       178 ~p~l~~~~~~L~~e~~~l~~~~~e~~~~D~~eL~~~r~eL~~~~~~i~~~~~~l~el~~el~~l~~~i  245 (322)
T pfam08317       178 KPKLRKKLQALKEEIANLRQLADELNLCDPLELEKARQELRSLSVKISEKRKQLEELQQELQELTIAI  245 (322)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999997365552179999999999999999999999989999999999999999


No 133
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=68.57  E-value=6.1  Score=20.32  Aligned_cols=174  Identities=18%  Similarity=0.319  Sum_probs=86.9

Q ss_pred             HHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHH------HHHHHH-HHHHCCEECCCCCCHHHHHHHHHCCCHHHHC
Q ss_conf             999998622320320212356202788986551422------476776-4310002313454114544534205955504
Q gi|254780680|r  179 GQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPK------FADDMF-CTTDGRWLIPTSEVSLTNLYSHEIIESKSLP  251 (430)
Q Consensus       179 i~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~------f~~~~y-~~~d~l~Li~TaEvpL~~~~~~~~l~~~~LP  251 (430)
                      |+..-.+ +..+||.||-+|.|  ..+.-|..-.|.      ..-++| ++...|||            +.-++.--   
T Consensus       187 i~~iR~f-l~~~gFlEVETP~l--q~i~GGA~ArPF~ThhNald~dlyLRIApELyL------------KRliVGG~---  248 (502)
T COG1190         187 IRAIREF-LDDRGFLEVETPML--QPIPGGAAARPFITHHNALDMDLYLRIAPELYL------------KRLIVGGF---  248 (502)
T ss_pred             HHHHHHH-HHHCCCEEECCCCC--CCCCCCCCCCCCEEEECCCCCCEEEEECCHHHH------------HHHHHCCC---
T ss_conf             9999999-98779758416000--355787322650122023677568762418999------------98875372---


Q ss_pred             CEEEEEECCCCCCCCCCCCCCCCEEEEE--EEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCC
Q ss_conf             2088532210788433554343212222--10200212127865014578989999999999841067530378011784
Q gi|254780680|r  252 LRFTTLAPSFRSEAGSAGRDTRGMLRQH--QFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGF  329 (430)
Q Consensus       252 ik~~~~s~cfR~EaGs~GkdtrGl~RvH--QF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~  329 (430)
                      =|..-.+++||-|    |-|+     -|  +|+.+|.+.      .+.-++.|....|++++.+-.----    +..+-.
T Consensus       249 erVfEIgr~FRNE----Gid~-----tHNPEFTmlE~Y~------AYaDy~D~m~ltE~Li~~~a~~v~g----t~~v~y  309 (502)
T COG1190         249 ERVFEIGRNFRNE----GIDT-----THNPEFTMLEFYQ------AYADYEDLMDLTEELIKELAKEVNG----TTKVTY  309 (502)
T ss_pred             HHHEEECCCCCCC----CCCC-----CCCCCHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHCC----CEEEEE
T ss_conf             1422305520037----8766-----6484235689999------9857999999999999999999549----737878


Q ss_pred             HHHEEEEEEE-E-----CCCCCCEEEEEEECCCCC-HHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHC
Q ss_conf             4340241011-0-----100483323753102100-764532684733899841010420043228999999998834
Q gi|254780680|r  330 SACKTYDLEV-W-----LAGQNLYREISSCSTCGN-FQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAILENY  400 (430)
Q Consensus       330 ~a~~~~DiE~-w-----~P~~~~y~Ev~S~Snc~D-~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ailEn~  400 (430)
                       ...++|+.- |     .++-..|.-+. .+...| -++|-+--+..-.-.   +++     + .-.++++.++-|..
T Consensus       310 -~~~~id~~~pf~ri~m~dal~e~~g~~-~~~~~~~e~~~~~ak~~~i~~~---~~~-----~-~~~g~ll~~lFe~~  376 (502)
T COG1190         310 -GGQEIDFSKPFKRITMVDALKEYLGVD-FDDLFDDEEAKELAKKHGIEVE---KYG-----T-WGLGHLLNELFEEL  376 (502)
T ss_pred             -CCEEEECCCCEEEEEHHHHHHHHHCCC-CCCCCCHHHHHHHHHHCCCCCC---CCC-----C-CCHHHHHHHHHHHH
T ss_conf             -997675489722566489999871866-5545887999999998089757---655-----5-36789999999877


No 134
>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]
Probab=67.98  E-value=10  Score=18.67  Aligned_cols=103  Identities=11%  Similarity=0.087  Sum_probs=49.1

Q ss_pred             HHHHHHH-CCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHH--------------HHHHCHHHHH
Q ss_conf             0011222-167530105648899999999999862232032021235620278898--------------6551422476
Q gi|254780680|r  153 FDRATKL-SGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMY--------------GTGQIPKFAD  217 (430)
Q Consensus       153 fe~a~kv-sGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~--------------gtG~lp~f~~  217 (430)
                      ++.|..+ .|++.....-+--.--...++|+-..   ..|..-+.|+.-++.....              -+-+.|+|..
T Consensus       531 y~~Aie~alG~~l~~vVV~~~~~a~~~i~~lk~~---~~gr~tflpl~~i~~~~~~~~~~~~g~~~~a~dli~~d~~~~~  607 (1163)
T COG1196         531 YETALEAALGNRLQAVVVENEEVAKKAIEFLKEN---KAGRATFLPLDRIKPLRSLKSDAAPGFLGLASDLIDFDPKYEP  607 (1163)
T ss_pred             HHHHHHHHHCCCCCCEEECCHHHHHHHHHHHHHC---CCCCCEECCCHHCCCCCCCCCCCCCCCHHHHHHHHCCCHHHHH
T ss_conf             9999999956344747878778899999999854---8997431141210345455543334403778888618777899


Q ss_pred             HHHHHHHCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCC
Q ss_conf             77643100023134541145445342059555042088532210788
Q gi|254780680|r  218 DMFCTTDGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSE  264 (430)
Q Consensus       218 ~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~E  264 (430)
                      .++.+-.+...+.+-|.+..-.+.      .....|.|...-++-.=
T Consensus       608 ~~~~~l~~t~Iv~~l~~A~~l~~~------~~~~~riVTl~G~~~~~  648 (1163)
T COG1196         608 AVRFVLGDTLVVDDLEQARRLARK------LRIKYRIVTLDGDLVEP  648 (1163)
T ss_pred             HHHHHHCCEEEECCHHHHHHHHHH------CCCCEEEEECCCCEEEC
T ss_conf             999994895885787899999874------14570489679858827


No 135
>TIGR03545 conserved hypothetical protein TIGR03545. This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair.
Probab=67.65  E-value=10  Score=18.63  Aligned_cols=42  Identities=21%  Similarity=0.244  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             799999999999998864446666677888774431002258
Q gi|254780680|r   68 SLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVP  109 (430)
Q Consensus        68 ~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~  109 (430)
                      +++++++.+++..+++|+.+.+++....+++.+.+-.|-+.|
T Consensus       219 ~~~d~lk~e~~adk~~i~~~k~~l~~~~~~l~~~~~~lk~Ap  260 (554)
T TIGR03545       219 EEFDKLKKEGKADKQQIISAKNDLQNDLKQLKAQLAELKKAP  260 (554)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999999999999999999999999985999999999998533


No 136
>PRK09343 prefoldin subunit beta; Provisional
Probab=66.81  E-value=11  Score=18.51  Aligned_cols=89  Identities=17%  Similarity=0.182  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-----------------CCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999998644-----------------99879999999999999886444666
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAE-----------------GNLSLVDALKNETSTLKEQLPILEKE   90 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~-----------------~~~~~~~~Lk~e~~~Lk~eik~le~~   90 (430)
                      +.+..+-.+...+..+...+.++.+++-+.+..+.+-                 .+++.+.+|.++...|.-.++.++++
T Consensus        14 ~qlQqlQqqlQ~v~~Qkqq~e~el~E~e~aLeELek~~dda~vYK~VG~vLik~~k~~~~~eL~ekkE~Lelr~ktLekQ   93 (122)
T PRK09343         14 GQLQQLQQQLERVAQQKYQIDLELREANKTLEELEKLPDDTPVYKTVGNLLVKVDKNKVIKELKEQKELLELRSNTLEKQ   93 (122)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCHHHEECCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999999987287544799983566402349999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHC
Q ss_conf             66778887744310022588112211
Q gi|254780680|r   91 EHEVCSSLKKLISCIPNVPLEEVPIG  116 (430)
Q Consensus        91 ~~~le~el~~lll~IPNi~~~~VP~G  116 (430)
                      .+.+.+++.++--.|=-.....-|-|
T Consensus        94 Ee~l~~~~eeLq~~iq~~l~k~~~~~  119 (122)
T PRK09343         94 EKKLREKLKELQKKIQEALRKYYPQG  119 (122)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99999999999999999986428998


No 137
>pfam10168 Nup88 Nuclear pore component. Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumour cells.
Probab=66.50  E-value=11  Score=18.47  Aligned_cols=16  Identities=19%  Similarity=-0.137  Sum_probs=8.1

Q ss_pred             EEEEEECCCCCHHHHH
Q ss_conf             2375310210076453
Q gi|254780680|r  348 REISSCSTCGNFQSRR  363 (430)
Q Consensus       348 ~Ev~S~Snc~D~QsrR  363 (430)
                      +++.+.+...|+|--+
T Consensus       463 g~visl~Ll~~~~~~~  478 (717)
T pfam10168       463 YECISLPLLIDAQPLS  478 (717)
T ss_pred             CCEEEEECCCCCCCCC
T ss_conf             8389733001455678


No 138
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=65.20  E-value=11  Score=18.30  Aligned_cols=60  Identities=23%  Similarity=0.287  Sum_probs=41.2

Q ss_pred             HHHHHHH-HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH
Q ss_conf             9999986-44998799999999999998864446666677888774431002258811221
Q gi|254780680|r   56 AQIGQAI-AEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPI  115 (430)
Q Consensus        56 KeIg~~k-~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~~VP~  115 (430)
                      |.+|.+. +..++...++|..+...|..+++.|+.+.+.+++++.++-..|=...++..+-
T Consensus        57 k~VG~llvk~~k~~~~~eL~er~E~Le~ri~tLekQe~~l~e~l~eLq~~i~~~l~~~~~~  117 (119)
T COG1382          57 KKVGNLLVKVSKEEAVDELEERKETLELRIKTLEKQEEKLQERLEELQSEIQKALGDAANG  117 (119)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             9851377520089899999989999999999999889999999999999999986002468


No 139
>pfam12127 YdfA_immunity SigmaW regulon antibacterial. This protein is found in bacteria. Proteins in this family are about 330 amino acids in length. The operon from which this protein is derived confers immunity for the host species to a broad range of antibacterial compounds, unlike the specific immunity proteins that are linked to and co-regulated with their antibiotic-synthesis proteins.
Probab=64.75  E-value=5.9  Score=20.40  Aligned_cols=59  Identities=17%  Similarity=0.250  Sum_probs=28.9

Q ss_pred             HHHHHCCHHHHHHHHHHCCCCCCHH-H-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             4478519999999998469895889-9-----9999999999999999999999999999999864499
Q gi|254780680|r    4 IQWIRQNPEHLDIALKKRHLEPQSE-Y-----ILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGN   66 (430)
Q Consensus         4 ik~IRen~e~v~~~l~~R~~~~~id-~-----il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~   66 (430)
                      -|...||||.+.+....||.|..-- +     |-+.|-- +.+   --.||+.+-+.-|.|++++.+..
T Consensus       188 hk~VLEnPd~ISk~VL~kgLDagTAFeIlSIDIADvdVG-~NI---GA~Lq~dQAeADk~vAqAkAE~R  252 (321)
T pfam12127       188 HKEVLENPDSISKTVLEKGLDAGTAFEILSIDIADIDVG-ENI---GARLQTDQAEADKRIAQAKAEER  252 (321)
T ss_pred             HHHHHCCHHHHHHHHHHCCCCCCCEEEEEEEEEECCCHH-HHH---CHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             879972987879999853678685169998754234122-222---54551778878789998778889


No 140
>COG4915 XpaC 5-bromo-4-chloroindolyl phosphate hydrolysis protein [General function prediction only]
Probab=64.08  E-value=12  Score=18.15  Aligned_cols=18  Identities=33%  Similarity=0.564  Sum_probs=15.5

Q ss_pred             CHHHHHCCHHHHHHHHHH
Q ss_conf             844785199999999984
Q gi|254780680|r    3 DIQWIRQNPEHLDIALKK   20 (430)
Q Consensus         3 Dik~IRen~e~v~~~l~~   20 (430)
                      |+++||+|.++.++++++
T Consensus        69 dykyiR~nLeearqki~~   86 (204)
T COG4915          69 DYKYIRENLEEARQKIKR   86 (204)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             499999769999999999


No 141
>PRK11020 hypothetical protein; Provisional
Probab=63.89  E-value=12  Score=18.13  Aligned_cols=50  Identities=18%  Similarity=0.338  Sum_probs=22.9

Q ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             99864499879999999999999886444666667788877443100225881
Q gi|254780680|r   59 GQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLE  111 (430)
Q Consensus        59 g~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~  111 (430)
                      ..+...++.+.+.+...+...+..+|..+......   ++....-.|-++|..
T Consensus        22 aaa~~rgd~~~i~qf~~E~~~l~k~I~~lk~~q~~---~lske~~~l~~lpF~   71 (118)
T PRK11020         22 AAASLRGDADKIAQFEKEKATLEKEIARLKEVQSQ---KLSKEAQKLMKLPFS   71 (118)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHCCCCC
T ss_conf             99997478899999999999999999999889999---988989998738731


No 142
>TIGR02865 spore_II_E stage II sporulation protein E; InterPro: IPR014221   This entry contains the stage II sporulation protein E (SpoIIE), which is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation and it has phosphatase activity, located in the C-terminal region, which is required to activate sigma-F. All members of this entry are found in endospore-forming Gram-positive bacteria. A homologous protein, not a member of this entry, is found in the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis..
Probab=63.60  E-value=12  Score=18.09  Aligned_cols=244  Identities=17%  Similarity=0.190  Sum_probs=127.1

Q ss_pred             HHCCHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             85199999999984698958-89999999999999999999999999999999998644998799999999999998864
Q gi|254780680|r    7 IRQNPEHLDIALKKRHLEPQ-SEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLP   85 (430)
Q Consensus         7 IRen~e~v~~~l~~R~~~~~-id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik   85 (430)
                      -|..|+.+.+.|-||..=.+ .+.++..+...+.+++++++   .|+-++.||..        -.+    -+.++.++++
T Consensus       418 ~s~~p~~~e~kC~k~~~l~~~~~~~~~~y~~~~~w~~rl~e---~r~l~a~Ql~g--------v~~----~~~~~~~ei~  482 (794)
T TIGR02865       418 NSKLPDELERKCIKRKELVKTTEEILNNYKINEMWRKRLEE---GRELVAEQLKG--------VAE----SVEDIAKEIN  482 (794)
T ss_pred             CCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHH--------HHH----HHHHHHHHHH
T ss_conf             65564588851475899999999998768888999999889---89999999751--------999----9999999863


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEEEE-----CCCCC-------------------------CC
Q ss_conf             4466666778887744310022588112211355540242000-----15656-------------------------65
Q gi|254780680|r   86 ILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILIRSV-----GKKPS-------------------------AI  135 (430)
Q Consensus        86 ~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~~~-----G~~~~-------------------------f~  135 (430)
                      .--.--...|+++-..|.. -||+-.+|-+=.+|..|..|+-.     |..+-                         .+
T Consensus       483 ~~~~f~~~~E~~I~~~L~k-~gI~~~~v~~y~~~~g~~~v~~~~~~c~g~~~~~k~I~p~i~~~~g~~~~v~~~~c~~~~  561 (794)
T TIGR02865       483 KEISFNQLLEEKIIRALNK-NGIEVEDVLIYNTEGGRIIVELTIAACGGKGECEKKIAPIISEVTGELMVVKDERCSIDP  561 (794)
T ss_pred             HHHHCCHHHHHHHHHHHHH-CCCCEEEEEEEECCCCCEEEEEEECCCCCCCCCCCCCCCHHHHHCCCEEEEECCCCCCCC
T ss_conf             0122016679999999844-389055798887599825899873378898765102541324511434565223358689


Q ss_pred             CCCCCCCCHHHHCCC---CC----HHHHHHHCCCCCEEEC----------------CHHHHHH-HHHHHHHHHHHHHHCC
Q ss_conf             666211220221173---10----0011222167530105----------------6488999-9999999986223203
Q gi|254780680|r  136 HLSREHFEIGEALGL---MD----FDRATKLSGARFSVLT----------------GHLAHLE-RALGQFMIDLHTSEHG  191 (430)
Q Consensus       136 f~~k~H~elge~l~l---iD----fe~a~kvsGsrF~~Lk----------------g~~A~Le-~ALi~y~ld~~~~~~G  191 (430)
                      ..-..|+..++.-..   ..    -..|-+|||=.+.+.+                |.-|.-| .|-++ +|... -+.|
T Consensus       562 ~ng~C~~~F~~~~~y~v~t~~~~~~K~Ge~vSGDSY~~~~L~~Gky~~~iSDGMG~G~~A~~ES~a~~~-LlEk~-l~~G  639 (794)
T TIGR02865       562 KNGRCHLTFEETPKYHVSTGVAKAAKDGELVSGDSYSFGKLSAGKYAVAISDGMGSGPEAAQESSACVR-LLEKF-LESG  639 (794)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCEEEEEECCCCEEEEEEECCCCCHHHHHHHHHHHHH-HHHHH-HHCC
T ss_conf             987136750578023655565533789994016556776317970799985479981889999999999-99999-9707


Q ss_pred             CCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHH----CC-----------------------EECCCCCCHHHHHH----
Q ss_conf             202123562027889865514224767764310----00-----------------------23134541145445----
Q gi|254780680|r  192 YTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTD----GR-----------------------WLIPTSEVSLTNLY----  240 (430)
Q Consensus       192 y~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d----~l-----------------------~Li~TaEvpL~~~~----  240 (430)
                      |-+-..=-.||+-....=+.     |++|-+=|    ||                       .-|--+--|+..+-    
T Consensus       640 f~~~~AI~tvNSil~LrF~~-----~E~FsTlDL~~iDL~~g~~~F~KvGavpSFiKRG~~V~vI~~~~LPiG~~~~vd~  714 (794)
T TIGR02865       640 FDREVAIKTVNSILSLRFSE-----DEKFSTLDLSVIDLYTGQAEFVKVGAVPSFIKRGAKVEVIRSSNLPIGILDEVDV  714 (794)
T ss_pred             CCHHHHHHHHHHHHHCCCCC-----CCHHHHHHHHHHCCCCCEEEEEEECCCCCEEEECCEEEEEEECCCCCCCCCCCCC
T ss_conf             88768999988997314899-----8405776788744776327899961612516667889998627898465453234


Q ss_pred             --HHHCCCHHHHCCEEE-EEECCCCCCCCCCCCCCC
Q ss_conf             --342059555042088-532210788433554343
Q gi|254780680|r  241 --SHEIIESKSLPLRFT-TLAPSFRSEAGSAGRDTR  273 (430)
Q Consensus       241 --~~~~l~~~~LPik~~-~~s~cfR~EaGs~Gkdtr  273 (430)
                        ..+.|.+.||=+.+. |+=-||=-|--..|||.+
T Consensus       715 e~~~~~L~~GD~ivm~SDGvLE~l~g~~~~e~k~~W  750 (794)
T TIGR02865       715 ELVRKKLKNGDLIVMVSDGVLEALEGEKEVEGKVLW  750 (794)
T ss_pred             CCEEEECCCCCEEEEECCCHHHCCCCCHHHCCHHHH
T ss_conf             300123379987998123133305873001162889


No 143
>KOG0996 consensus
Probab=63.44  E-value=12  Score=18.07  Aligned_cols=141  Identities=20%  Similarity=0.257  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999986449---------987999999999999988644466666778887744310
Q gi|254780680|r   34 DEKNRILIKKIEDIRARRNSNSAQIGQAIAEG---------NLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISC  104 (430)
Q Consensus        34 d~~rr~l~~e~e~LraerN~lSKeIg~~k~~~---------~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~  104 (430)
                      -.+.+..+.+++-|....|...+.+-.++++-         +...+.+++.+...++.+++..++.+..+..+...+-..
T Consensus       499 ~~e~~vaesel~~L~~~~~~~~~~~e~lk~~L~~~~~~~~e~~~~l~~~k~~l~~~k~e~~~~~k~l~~~~~e~~~~~~~  578 (1293)
T KOG0996         499 RSELDVAESELDILLSRHETGLKKVEELKGKLLASSESLKEKKTELDDLKEELPSLKQELKEKEKELPKLRKEERNLKSQ  578 (1293)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88877789899999999999988899999999998987887777888788765467789999987678999999988888


Q ss_pred             CCCCCCCHHHHC-----CCCCCCEEE------EEECCCCCCCCCCCCCCCHHHHCCCCC--HHHHHHHCCCCCEEECCHH
Q ss_conf             022588112211-----355540242------000156566566621122022117310--0011222167530105648
Q gi|254780680|r  105 IPNVPLEEVPIG-----TSANENILI------RSVGKKPSAIHLSREHFEIGEALGLMD--FDRATKLSGARFSVLTGHL  171 (430)
Q Consensus       105 IPNi~~~~VP~G-----~de~dNv~i------~~~G~~~~f~f~~k~H~elge~l~liD--fe~a~kvsGsrF~~Lkg~~  171 (430)
                      + |-....|-.-     ..-+.|.|+      +.-|.+|.|      |=-|| .||.||  |+.|.-++|+|.-|..=+-
T Consensus       579 ~-~~~rqrveE~ks~~~~~~s~~kVl~al~r~kesG~i~Gf------~GRLG-DLg~Id~kYDvAIsTac~~LdyiVVdt  650 (1293)
T KOG0996         579 L-NKLRQRVEEAKSSLSSSRSRNKVLDALMRLKESGRIPGF------YGRLG-DLGAIDEKYDVAISTACARLDYIVVDT  650 (1293)
T ss_pred             H-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC------CCCCC-CCCCCCHHHHHHHHHHCCCCCEEEECC
T ss_conf             9-999999999998887544453999999999876997764------35444-334662577789988603445377362


Q ss_pred             HHHHHHHHHHH
Q ss_conf             89999999999
Q gi|254780680|r  172 AHLERALGQFM  182 (430)
Q Consensus       172 A~Le~ALi~y~  182 (430)
                      .---++-|+|-
T Consensus       651 ~e~aq~cI~fl  661 (1293)
T KOG0996         651 IETAQECINFL  661 (1293)
T ss_pred             HHHHHHHHHHH
T ss_conf             78899999999


No 144
>PRK10636 putative ABC transporter ATP-binding protein; Provisional
Probab=62.73  E-value=13  Score=17.98  Aligned_cols=34  Identities=12%  Similarity=-0.042  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEE
Q ss_conf             9999999984106753037801178443402410
Q gi|254780680|r  304 SCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDL  337 (430)
Q Consensus       304 ~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~Di  337 (430)
                      ..+..++..++++---+.-+.+.|+...-.+.-|
T Consensus       408 ~~~r~~L~~f~f~~~~~~~~v~~LSGGEk~Rl~L  441 (638)
T PRK10636        408 QKLRDYLGGFGFQGDKVTEETRRFSGGEKARLVL  441 (638)
T ss_pred             HHHHHHHHHCCCCHHHHCCCCCCCCHHHHHHHHH
T ss_conf             9999999866889778639113399999999999


No 145
>KOG0995 consensus
Probab=61.77  E-value=13  Score=17.86  Aligned_cols=29  Identities=17%  Similarity=0.133  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999988644466666778887744310
Q gi|254780680|r   76 ETSTLKEQLPILEKEEHEVCSSLKKLISC  104 (430)
Q Consensus        76 e~~~Lk~eik~le~~~~~le~el~~lll~  104 (430)
                      .+..++.+|...|++...++.+...+-..
T Consensus       295 ~l~~l~~Eie~kEeE~e~lq~~~d~Lk~~  323 (581)
T KOG0995         295 KLEMLKSEIEEKEEEIEKLQKENDELKKQ  323 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999988999999


No 146
>KOG0933 consensus
Probab=61.60  E-value=13  Score=17.84  Aligned_cols=22  Identities=18%  Similarity=0.291  Sum_probs=9.3

Q ss_pred             HHHHHCCHHHHCCCCCHHCCCH
Q ss_conf             9998410675303780117844
Q gi|254780680|r  309 ILKRLDLHYRVVSLCTGDLGFS  330 (430)
Q Consensus       309 i~~~L~lpyRvv~~~sgdlg~~  330 (430)
                      +.++|++--|-+.++-..+..+
T Consensus       713 l~~ql~l~~~~l~l~~~r~~~~  734 (1174)
T KOG0933         713 LKQQLELKLHELALLEKRLEQN  734 (1174)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9999999988889999887538


No 147
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=61.16  E-value=13  Score=17.79  Aligned_cols=45  Identities=7%  Similarity=-0.037  Sum_probs=33.8

Q ss_pred             HHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999984698958-89999999999999999999999999999999
Q gi|254780680|r   14 LDIALKKRHLEPQ-SEYILSLDEKNRILIKKIEDIRARRNSNSAQI   58 (430)
Q Consensus        14 v~~~l~~R~~~~~-id~il~Ld~~rr~l~~e~e~LraerN~lSKeI   58 (430)
                      |+.-++..|+++. +..|++|..++..++.+..+|+++....++..
T Consensus        50 I~~L~~~~G~~l~gik~iL~l~~q~~~l~~~~~~l~~el~~~~~~~   95 (98)
T cd01279          50 VQRLSQDEGFNLAGIKRIIELYPQVLLLQCRSCEHATELIGCAKPC   95 (98)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999995898899999999989999999999999999999876665


No 148
>pfam04645 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
Probab=60.61  E-value=14  Score=17.72  Aligned_cols=50  Identities=20%  Similarity=0.190  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999986449987999999999999988
Q gi|254780680|r   34 DEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQ   83 (430)
Q Consensus        34 d~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~e   83 (430)
                      +-+......+++.|+.+...+.++|....++.-+.++++|+.+..++..+
T Consensus       104 ~leL~s~~~ei~~L~~kI~~L~~~~~~~n~~~~n~~i~slk~EL~elike  153 (181)
T pfam04645       104 SLELKSMNHKIEVLRSKIDSLNKKINKKNLSHVNEEINSLKLELDELIKE  153 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             61599999799999999999997732213302530278899899999999


No 149
>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family; InterPro: IPR010129   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).    Type I secretion is an ABC transporter that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C terminus of the transported protein. This entry represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This entry selects a group of sequences closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.; GO: 0015031 protein transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=60.41  E-value=14  Score=17.70  Aligned_cols=142  Identities=18%  Similarity=0.287  Sum_probs=84.3

Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999984698958899999999999999999999999999999999986449---98799999999999998864446666
Q gi|254780680|r   15 DIALKKRHLEPQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEG---NLSLVDALKNETSTLKEQLPILEKEE   91 (430)
Q Consensus        15 ~~~l~~R~~~~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~---~~~~~~~Lk~e~~~Lk~eik~le~~~   91 (430)
                      ..+|..+++-.- -.++++..++.+++.++...+++++.+..++..+..+-   ...-.++..++..+-..++..+++++
T Consensus       191 ~~~L~~~g~~~~-~~~L~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~A~~~l~~~~~~l  269 (434)
T TIGR01843       191 LRKLKEKGLVSR-LELLELERERAELQGELARLEAELEVLKAQIDELQLKLQQLEQTFREEVLEELTEAQARLAELREEL  269 (434)
T ss_pred             HHHHHHCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             630663343216-7899999999999999998799999999999999999988999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEEEECCC-----------CC---------CCCCCCCCCCHHH----H
Q ss_conf             6778887744310022588112211355540242000156-----------56---------6566621122022----1
Q gi|254780680|r   92 HEVCSSLKKLISCIPNVPLEEVPIGTSANENILIRSVGKK-----------PS---------AIHLSREHFEIGE----A  147 (430)
Q Consensus        92 ~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~~~G~~-----------~~---------f~f~~k~H~elge----~  147 (430)
                      ..+.+.+.....+=|        +-. ==.|..+.+.|--           |.         +..+--+|+..|.    +
T Consensus       270 ~~a~~~~~~~~irsP--------vdG-~v~~l~~~T~GgVv~pG~~lm~IVP~~~~l~iEa~~~~~Dig~v~~Gq~a~ik  340 (434)
T TIGR01843       270 SKARDRLQRLIIRSP--------VDG-TVQSLKVHTVGGVVQPGETLMEIVPEDDPLEIEAKLSNKDIGFVHVGQPAEIK  340 (434)
T ss_pred             HHHHHHHHHHEEECC--------CCE-EEEEEEEEEECCEECCCCCEEEEECCCCCEEEEEEECCCCCCEEECCCEEEEE
T ss_conf             999987532114425--------451-99999998405443278617898339996589999735465345558716999


Q ss_pred             CCCCCHHHHHHHCCCCCEEECCHHHHH
Q ss_conf             173100011222167530105648899
Q gi|254780680|r  148 LGLMDFDRATKLSGARFSVLTGHLAHL  174 (430)
Q Consensus       148 l~liDfe~a~kvsGsrF~~Lkg~~A~L  174 (430)
                      +.-||+        +|+.++.|....+
T Consensus       341 ~~AF~~--------~ryG~~~G~V~~i  359 (434)
T TIGR01843       341 FSAFPY--------TRYGLLNGKVKSI  359 (434)
T ss_pred             EECCCC--------CCCCCEEEEEEEE
T ss_conf             963686--------0335189999986


No 150
>pfam11853 DUF3373 Protein of unknown function (DUF3373). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=59.95  E-value=14  Score=17.64  Aligned_cols=13  Identities=23%  Similarity=0.266  Sum_probs=6.1

Q ss_pred             HHHHCCCCCCCEE
Q ss_conf             1221135554024
Q gi|254780680|r  112 EVPIGTSANENIL  124 (430)
Q Consensus       112 ~VP~G~de~dNv~  124 (430)
                      .||-.+-++++..
T Consensus        95 ~v~~~~~~Nd~l~  107 (485)
T pfam11853        95 MVPGQKYKNDALY  107 (485)
T ss_pred             CCCCCCCCCCHHH
T ss_conf             7776676542230


No 151
>KOG4673 consensus
Probab=59.08  E-value=14  Score=17.54  Aligned_cols=59  Identities=17%  Similarity=0.287  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999998644----9987999999999999988644
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAE----GNLSLVDALKNETSTLKEQLPI   86 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~----~~~~~~~~Lk~e~~~Lk~eik~   86 (430)
                      .+|-.+..+...+..+.|.||.+.|.+-++.+....+    .+++-+..|+.++.+|++++-.
T Consensus       409 QRva~lEkKvqa~~kERDalr~e~kslk~ela~~l~~DeLaEkdE~I~~lm~EGEkLSK~ql~  471 (961)
T KOG4673         409 QRVATLEKKVQALTKERDALRREQKSLKKELAAALLKDELAEKDEIINQLMAEGEKLSKKQLA  471 (961)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999987678999999877899998650677777799999999877886799987


No 152
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=57.89  E-value=15  Score=17.40  Aligned_cols=53  Identities=15%  Similarity=0.216  Sum_probs=26.2

Q ss_pred             CCHHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             88447851999999999846989588999999999999999999999999999
Q gi|254780680|r    2 LDIQWIRQNPEHLDIALKKRHLEPQSEYILSLDEKNRILIKKIEDIRARRNSN   54 (430)
Q Consensus         2 LDik~IRen~e~v~~~l~~R~~~~~id~il~Ld~~rr~l~~e~e~LraerN~l   54 (430)
                      +|+.-+++..+.+...+..-++=.|-++..++-.+...+...++.++.-++.+
T Consensus        23 ldle~l~~rl~ELe~~lsdP~~W~D~~~a~kl~kE~~~L~~~v~~~~~l~~~~   75 (367)
T PRK00578         23 LDVDALKERLEELEAEAEDPDFWNDQERAQKVGKELSSLKAKLDTLENLRQRL   75 (367)
T ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             79999999999999986397054499999999999999999999999999999


No 153
>pfam04111 APG6 Autophagy protein Apg6. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.
Probab=57.30  E-value=15  Score=17.33  Aligned_cols=141  Identities=13%  Similarity=0.068  Sum_probs=75.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999999999999999999999999999998644998--79999999999999886444666667788877443100
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNL--SLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCI  105 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~--~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~I  105 (430)
                      +++.++.++...+.++++.|.+++..+.++|..+..+...  .+-++...+-...+-++-..+++.+.++.++......+
T Consensus        70 ~el~~l~~ee~~l~~eL~~le~e~~~l~~el~~le~e~~~l~~ee~~~w~~~n~~~~~l~~~~~e~~sl~~q~~~~~~qL  149 (356)
T pfam04111        70 SELDELKKEEERLLDELEELEKEDDDLDGELVELQEEKEQLENEELQYLREYNLFDRNNLQLEDNLQSLELQYEYSLNQL  149 (356)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999999999999999999999999977879999999999999999999999999


Q ss_pred             -----CCCCCCHHHHCCCCCCCEEEEEECCCCCCCCCCC--CCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHH
Q ss_conf             -----2258811221135554024200015656656662--112202211731000112221675301056488999999
Q gi|254780680|r  106 -----PNVPLEEVPIGTSANENILIRSVGKKPSAIHLSR--EHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERAL  178 (430)
Q Consensus       106 -----PNi~~~~VP~G~de~dNv~i~~~G~~~~f~f~~k--~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~AL  178 (430)
                           -|+..+.-.|+.|.       .+|.+-.|.--..  .-|+.-|-       .||          .|..|+|-..|
T Consensus       150 dkLrktNV~NdtF~I~hdG-------~fGTINglRLGrlp~~~V~W~EI-------NAA----------wGQ~~LLL~tl  205 (356)
T pfam04111       150 DKLRKTNIFNATFHISHSG-------PFATINGLRLGRLPSVVVPWKEI-------NAA----------WGQTVLLLAAL  205 (356)
T ss_pred             HHHHHCCCCCCEEEEEECC-------CCEEECCCCCCCCCCCCCCHHHH-------HHH----------HHHHHHHHHHH
T ss_conf             9987516460306887548-------83546464027999999893888-------789----------99999999999


Q ss_pred             HHHHHHHHHHHCCCCEE
Q ss_conf             99999862232032021
Q gi|254780680|r  179 GQFMIDLHTSEHGYTEV  195 (430)
Q Consensus       179 i~y~ld~~~~~~Gy~~v  195 (430)
                      .+. +.+..  .||..+
T Consensus       206 a~k-l~~~f--~~Y~Lv  219 (356)
T pfam04111       206 AKK-LGLNF--VRYRLV  219 (356)
T ss_pred             HHH-HCCCC--CCEEEE
T ss_conf             998-19884--523787


No 154
>PRK13665 hypothetical protein; Provisional
Probab=57.14  E-value=6.8  Score=19.98  Aligned_cols=22  Identities=14%  Similarity=0.326  Sum_probs=15.1

Q ss_pred             HHHHHCCHHHHHHHHHHCCCCC
Q ss_conf             4478519999999998469895
Q gi|254780680|r    4 IQWIRQNPEHLDIALKKRHLEP   25 (430)
Q Consensus         4 ik~IRen~e~v~~~l~~R~~~~   25 (430)
                      -|...||||.+.+....||.+.
T Consensus       189 hk~VLEnPd~ISk~VL~kgLDa  210 (327)
T PRK13665        189 HKEVLENPDSISKTVLSKGLDA  210 (327)
T ss_pred             HHHHHCCHHHHHHHHHHCCCCC
T ss_conf             8888629878799999636786


No 155
>PRK09039 hypothetical protein; Validated
Probab=57.03  E-value=16  Score=17.30  Aligned_cols=21  Identities=24%  Similarity=0.490  Sum_probs=10.0

Q ss_pred             CCCEEHHHHHCCHHHHHHHHH
Q ss_conf             320212356202788986551
Q gi|254780680|r  191 GYTEVSAPLLVRDEAMYGTGQ  211 (430)
Q Consensus       191 Gy~~v~~P~lv~~~~~~gtG~  211 (430)
                      |-..+---+..-+++++.+|.
T Consensus       212 ~I~i~gdrfvf~SevLF~~gs  232 (343)
T PRK09039        212 GIRIVGDRFVFQSEVLFPTGS  232 (343)
T ss_pred             CCCCCCCEEEECCCCCCCCCC
T ss_conf             741025547740332316884


No 156
>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]
Probab=56.62  E-value=16  Score=17.25  Aligned_cols=19  Identities=32%  Similarity=0.282  Sum_probs=7.3

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999
Q gi|254780680|r   30 ILSLDEKNRILIKKIEDIR   48 (430)
Q Consensus        30 il~Ld~~rr~l~~e~e~Lr   48 (430)
                      +..|+++||.++.....++
T Consensus       297 i~~l~ek~r~l~~D~nk~~  315 (622)
T COG5185         297 IKTLREKWRALKSDSNKYE  315 (622)
T ss_pred             HHHHHHHHHHHHHHHHHHH
T ss_conf             9999999998752689999


No 157
>COG0072 PheT Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis]
Probab=55.85  E-value=16  Score=17.16  Aligned_cols=176  Identities=15%  Similarity=0.082  Sum_probs=89.4

Q ss_pred             CCCCCCCCCCCCCCHHHHC----CCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHH
Q ss_conf             5656656662112202211----731000112221675301056488999999999998622320320212356202788
Q gi|254780680|r  130 KKPSAIHLSREHFEIGEAL----GLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEA  205 (430)
Q Consensus       130 ~~~~f~f~~k~H~elge~l----~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~  205 (430)
                      ..|.+.+.+...+||.|..    |.=.+..-...+..   .-.|....+. -+-.-+-+. +...||+++.+-.|+.++.
T Consensus       308 ~vPs~R~DI~~e~DliEEv~r~yGy~ni~~~~p~~~~---~~~~~~~~~~-~~~r~vr~~-l~~~G~~Evitysl~s~e~  382 (650)
T COG0072         308 TVPSYRVDILIEADLIEEVARIYGYNNIPPELPSAFT---IGRGGLTPLQ-KFRRKVRRA-LVGLGFQEVITYSLTSPEE  382 (650)
T ss_pred             ECCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC---CCCCCCCHHH-HHHHHHHHH-HHHCCCEEEEEECCCCHHH
T ss_conf             7688721356532788899998571448875876544---5666656678-999999999-9858975998612589899


Q ss_pred             HHHHHHCHHHHHHHHHHH----HCCEECCCCCC-HHH-HHHHHHCCCHHHHC-CEEEEEECCCCCCCCCCCC--CCCCEE
Q ss_conf             986551422476776431----00023134541-145-44534205955504-2088532210788433554--343212
Q gi|254780680|r  206 MYGTGQIPKFADDMFCTT----DGRWLIPTSEV-SLT-NLYSHEIIESKSLP-LRFTTLAPSFRSEAGSAGR--DTRGML  276 (430)
Q Consensus       206 ~~gtG~lp~f~~~~y~~~----d~l~Li~TaEv-pL~-~~~~~~~l~~~~LP-ik~~~~s~cfR~EaGs~Gk--dtrGl~  276 (430)
                      ....+..+..   ...+.    .++.-+=|+=. .|. +.-.+.   ..+.| ++...++.+|......-..  ..+|+.
T Consensus       383 ~~~~~~~~~~---~~~l~NPiS~e~s~mR~sLlp~LL~~~~~N~---~r~~~~~~iFEiG~v~~~~~~~~~~~~~~~~l~  456 (650)
T COG0072         383 AKLFGLENDE---ALELANPISEEYSVLRTSLLPGLLEALSYNK---NRKNPDVRIFEIGDVFVKDEEAERETRHLAGLA  456 (650)
T ss_pred             HHHHCCCCCC---CEEECCCCCCCHHHHHHHHHHHHHHHHHHHH---CCCCCCEEEEEEEEEEECCCCCCCHHHHHHHHH
T ss_conf             9974237775---2685686762388888777888999999875---336886468866745705886532027899987


Q ss_pred             EEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCC
Q ss_conf             2221020021212786501457898999999999984106753037
Q gi|254780680|r  277 RQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVSL  322 (430)
Q Consensus       277 RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~  322 (430)
                      ...+.  -+.  |...  ...-+..+-..++.++..|++.|.+...
T Consensus       457 ~g~~~--~~~--w~~~--~~v~f~d~Kg~ve~ll~~lg~~~~~~~~  496 (650)
T COG0072         457 AGLAG--EES--WQGK--RPVDFYDAKGDLEALLEALGVEYEFEPA  496 (650)
T ss_pred             HCCCC--CCC--CCCC--CCCCHHHHHHHHHHHHHHCCCCCEEEEC
T ss_conf             44464--333--4556--7646999999999999972997278405


No 158
>pfam10018 Med4 Vitamin-D-receptor interacting Mediator subunit 17t. Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter.
Probab=55.57  E-value=16  Score=17.13  Aligned_cols=60  Identities=23%  Similarity=0.346  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999999999999999999999999999999864499879999999999999886444666667788877443
Q gi|254780680|r   27 SEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLI  102 (430)
Q Consensus        27 id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~ll  102 (430)
                      ++.++..|++..+.+.++..-+...                ..+..|.++++.+-++++.+-+++.++..+|..+.
T Consensus         4 ~~~Li~~d~~L~~~L~~l~~hq~~~----------------~~I~~L~~e~~~lD~~ik~i~~~L~~~~~eL~~~~   63 (175)
T pfam10018         4 AEDLISADDELKSALKELEEHQENQ----------------ARILQLRAEVESLDEKIKDILKELKEAEKELRALP   63 (175)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999998999999999999999999----------------99999999999999999999999999999999714


No 159
>pfam08614 ATG16 Autophagy protein 16 (ATG16). Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. ATG16 (also known as Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway.
Probab=55.52  E-value=16  Score=17.13  Aligned_cols=31  Identities=29%  Similarity=0.342  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999998864446666677888774431
Q gi|254780680|r   73 LKNETSTLKEQLPILEKEEHEVCSSLKKLIS  103 (430)
Q Consensus        73 Lk~e~~~Lk~eik~le~~~~~le~el~~lll  103 (430)
                      +..+.+.+..+++...+....+.+++..+-+
T Consensus       128 L~~~~~~l~~el~ek~k~~e~l~DE~~aL~l  158 (194)
T pfam08614       128 LETEIRDLREELQEKEKDNETLQDELISLNI  158 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999988899999999999


No 160
>pfam05529 Bap31 B-cell receptor-associated protein 31-like. Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31.
Probab=55.38  E-value=16  Score=17.11  Aligned_cols=32  Identities=25%  Similarity=0.249  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999988644466666778887744
Q gi|254780680|r   70 VDALKNETSTLKEQLPILEKEEHEVCSSLKKL  101 (430)
Q Consensus        70 ~~~Lk~e~~~Lk~eik~le~~~~~le~el~~l  101 (430)
                      .+.+.++.+.++++++.+++++++.+.++..+
T Consensus       149 ~~~~~~e~~~l~~el~~lk~el~~~~~d~eal  180 (192)
T pfam05529       149 AKKKMAEEDGLAKEIEKLKKELEEKDKDLEAL  180 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99888777757999999999999888779999


No 161
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=54.40  E-value=17  Score=17.00  Aligned_cols=40  Identities=25%  Similarity=0.247  Sum_probs=18.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9879999999999999886444666667788877443100
Q gi|254780680|r   66 NLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCI  105 (430)
Q Consensus        66 ~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~I  105 (430)
                      ++++..+++++.++...++.....++.++++++..+-..|
T Consensus       202 d~~eL~~lk~~L~~~~~ei~~~~~~l~e~~~~l~~l~~~I  241 (312)
T smart00787      202 DPTELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKI  241 (312)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999999999999999999


No 162
>PRK12704 phosphodiesterase; Provisional
Probab=54.10  E-value=17  Score=16.97  Aligned_cols=30  Identities=17%  Similarity=0.286  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999
Q gi|254780680|r   31 LSLDEKNRILIKKIEDIRARRNSNSAQIGQ   60 (430)
Q Consensus        31 l~Ld~~rr~l~~e~e~LraerN~lSKeIg~   60 (430)
                      ..|+++...+..+.+.+...++++.+.+.+
T Consensus        45 ~~Le~~e~~L~~~~~~l~~~~~el~~~~~~   74 (455)
T PRK12704         45 EELEKKEESLEQKQQEVEKKESELEELIAE   74 (455)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999999999


No 163
>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; InterPro: IPR014345   Members of this entry belong to the family of polysaccharide chain length determinant proteins. They are found in species that encode the PEP-CTERM/exosortase system and are predicted to act in protein sorting in a number of Gram-negative bacteria, they are also found near the epsH homologue that is the putative exosortase gene..
Probab=53.83  E-value=17  Score=16.94  Aligned_cols=90  Identities=14%  Similarity=0.106  Sum_probs=40.7

Q ss_pred             HHHHHCCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99984698958-8999999999999999999999999999999999864499---8799999999999998864446666
Q gi|254780680|r   16 IALKKRHLEPQ-SEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGN---LSLVDALKNETSTLKEQLPILEKEE   91 (430)
Q Consensus        16 ~~l~~R~~~~~-id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~---~~~~~~Lk~e~~~Lk~eik~le~~~   91 (430)
                      .+|-++.++-. .++=.+.+.-.|=+-.+++.-+.+-.+.-+.+...|.+.-   +..-..+..+.+...+++...+-++
T Consensus       141 ~~L~~~FvE~~~~~kR~dS~~A~rFi~~Qik~Y~~kL~~aE~~L~~FK~~~~~~lp~~~~~y~~~l~~~~~~L~~~~l~~  220 (510)
T TIGR03007       141 QTLLTIFVEETLGSKRQDSDSAQRFIDEQIKEYEKKLEAAENRLKAFKQENGGILPDQEGDYYSELSEAQEELEAARLEL  220 (510)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98875435426650356546999999999999999999999999987687345377973789999999999999999999


Q ss_pred             HHHHHHHHHHHHHC
Q ss_conf             67788877443100
Q gi|254780680|r   92 HEVCSSLKKLISCI  105 (430)
Q Consensus        92 ~~le~el~~lll~I  105 (430)
                      .++...++.+--+|
T Consensus       221 ~e~~~~Rd~l~rQL  234 (510)
T TIGR03007       221 NEAKAQRDALKRQL  234 (510)
T ss_pred             HHHHHHHHHHHHCC
T ss_conf             98887678875145


No 164
>KOG0964 consensus
Probab=53.82  E-value=17  Score=16.93  Aligned_cols=48  Identities=4%  Similarity=0.131  Sum_probs=20.8

Q ss_pred             HHHHHHHHHHCCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999984698958--89999999999999999999999999999999
Q gi|254780680|r   11 PEHLDIALKKRHLEPQ--SEYILSLDEKNRILIKKIEDIRARRNSNSAQI   58 (430)
Q Consensus        11 ~e~v~~~l~~R~~~~~--id~il~Ld~~rr~l~~e~e~LraerN~lSKeI   58 (430)
                      .+.++..+..+...++  .+.+..+..+|+....+.+.|+.+.|.++.++
T Consensus       687 L~~~r~~i~~~~~~i~q~~~~~qk~e~~~~~~~~~~~~l~~e~~~~k~e~  736 (1200)
T KOG0964         687 LDEVRNEIEDIDQKIDQLNNNMQKVENDRNAFKREHEKLKRELNTIKGEK  736 (1200)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999888777778999988999988689999998999999999865179


No 165
>PRK10240 undecaprenyl pyrophosphate synthase; Provisional
Probab=52.85  E-value=7.3  Score=19.73  Aligned_cols=95  Identities=17%  Similarity=0.233  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCHHHHCCCCCH
Q ss_conf             99999999886444666667788877443100225881122113555402420001565665666211220221173100
Q gi|254780680|r   74 KNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILIRSVGKKPSAIHLSREHFEIGEALGLMDF  153 (430)
Q Consensus        74 k~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~~~G~~~~f~f~~k~H~elge~l~liDf  153 (430)
                      ..-++.+.++++.-.-....+.++.-..-+..|.+|+||          .+||+-|+.+-.+|-+   |+++-.  -+-|
T Consensus       128 ~~A~~~i~~~~~~~~~~~~~i~~~~~~~~l~~~~~p~pD----------LlIRTsGe~RLSnFLL---wQ~aya--El~F  192 (229)
T PRK10240        128 VQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVD----------LVIRTGGEHRISNFLL---WQIAYA--ELYF  192 (229)
T ss_pred             HHHHHHHHHHHHCCCCCHHHCCHHHHHHCCCCCCCCCCC----------EEEECCCCEECCCHHH---HCCCCE--EEEE
T ss_conf             999999999998378991331788876314667899967----------5885488631243133---223450--4887


Q ss_pred             HHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             0112221675301056488999999999998622320320
Q gi|254780680|r  154 DRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYT  193 (430)
Q Consensus       154 e~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~  193 (430)
                            +..=||=+.  -.-|..||..|.--  -+..|=+
T Consensus       193 ------~~~lWPdF~--~~dl~~al~~y~~R--~RrfGg~  222 (229)
T PRK10240        193 ------TDVLWPDFD--EQDFEGALNAFANR--ERRFGGT  222 (229)
T ss_pred             ------CCCCCCCCC--HHHHHHHHHHHHCC--CCCCCCC
T ss_conf             ------788887799--99999999998543--4768999


No 166
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=52.70  E-value=10  Score=18.63  Aligned_cols=10  Identities=0%  Similarity=0.062  Sum_probs=3.5

Q ss_pred             CCCEEECCHH
Q ss_conf             7530105648
Q gi|254780680|r  162 ARFSVLTGHL  171 (430)
Q Consensus       162 srF~~Lkg~~  171 (430)
                      ++|+--+-+-
T Consensus       129 sgYPDcrpef  138 (222)
T COG0603         129 SGYPDCRPEF  138 (222)
T ss_pred             CCCCCCCHHH
T ss_conf             7899888899


No 167
>pfam06419 COG6 Conserved oligomeric complex COG6. COG6 is a component of the conserved oligomeric golgi complex, which is composed of eight different subunits and is required for normal golgi morphology and localisation.
Probab=52.11  E-value=18  Score=16.75  Aligned_cols=86  Identities=17%  Similarity=0.182  Sum_probs=49.1

Q ss_pred             HHHHHHHCCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999984698958---8999999999999999999999999999999999864499879999999999999886444666
Q gi|254780680|r   14 LDIALKKRHLEPQ---SEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKE   90 (430)
Q Consensus        14 v~~~l~~R~~~~~---id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~   90 (430)
                      .+..+++|..+.+   ++.+-.+.++.+.+...++++..--..+.+++...+     .....+..++..|+++.+.++.+
T Consensus        21 LR~~iEk~~l~~n~~~L~~f~~v~~~L~~i~~~v~~ln~~c~~m~~~l~~~~-----~~T~~ll~~~~~L~~~~~~ie~k   95 (615)
T pfam06419        21 LRLDIEKELLKSNGEILKEFGPVAEQLKRIGEDLSKLNNTCEEMKSQLNNAK-----QDTKDLLEEASTLMEQKRQIELK   95 (615)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7889999999988999999999999999999999999999999999998755-----41799999999999999999999


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             66778887744310
Q gi|254780680|r   91 EHEVCSSLKKLISC  104 (430)
Q Consensus        91 ~~~le~el~~lll~  104 (430)
                      .+-+..=+....++
T Consensus        96 ~~ll~aF~~~F~Ls  109 (615)
T pfam06419        96 KKLLKAFLSRFTLS  109 (615)
T ss_pred             HHHHHHHHHHCCCC
T ss_conf             99999999847888


No 168
>pfam09730 BicD Microtubule-associated protein Bicaudal-D. BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER). For full functioning they bind with GSK-3beta pfam05350 to maintain the anchoring of microtubules to the centromere. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells.
Probab=52.08  E-value=18  Score=16.74  Aligned_cols=31  Identities=16%  Similarity=0.412  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCH
Q ss_conf             45789899999999998410675303780117844
Q gi|254780680|r  296 FTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFS  330 (430)
Q Consensus       296 ~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~  330 (430)
                      ....++|+.+.+++.+    -|.-|.+|.|+....
T Consensus       437 ~~aqdeL~~~seeLaq----lYhhvc~~n~etP~r  467 (711)
T pfam09730       437 NAAQDELVTFSEELAQ----LYHHVCMCNNETPNR  467 (711)
T ss_pred             HHHHHHHHHHHHHHHH----HHHHHHHHCCCCCCH
T ss_conf             8899999999999999----988998736878839


No 169
>pfam03194 LUC7 LUC7 N_terminus. This family contains the N terminal region of several LUC7 protein homologues and only contains eukaryotic proteins. LUC7 has been shown to be a U1 snRNA associated protein with a role in splice site recognition. The family also contains human and mouse LUC7 like (LUC7L) proteins and human cisplatin resistance-associated overexpressed protein (CROP).
Probab=51.79  E-value=19  Score=16.71  Aligned_cols=48  Identities=19%  Similarity=0.176  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999864499879999999999999886444666
Q gi|254780680|r   43 KIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKE   90 (430)
Q Consensus        43 e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~   90 (430)
                      +++.|..+.+.+-+++-++-.+|+-+++.++..++..|+.+...++++
T Consensus       124 ~i~~l~~~I~~ll~e~E~LGe~G~VdeA~~~~~~~e~Lk~er~~l~~~  171 (252)
T pfam03194       124 ELAELDEEIGKLLAEAEALGEEGKVDEAMKLMKEVEELKAKKKELEDS  171 (252)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999986799999999999999999999999866


No 170
>PHA00727 hypothetical protein
Probab=51.27  E-value=19  Score=16.66  Aligned_cols=60  Identities=13%  Similarity=0.120  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999986449------98799999999999998864446
Q gi|254780680|r   29 YILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEG------NLSLVDALKNETSTLKEQLPILE   88 (430)
Q Consensus        29 ~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~------~~~~~~~Lk~e~~~Lk~eik~le   88 (430)
                      +++..+++.-.--+.+|+|+..-++..|+|+.-+.-+      +.-+.+-.+++-++||.++....
T Consensus         5 kl~s~~eeelrkaqsleelkqkyee~qkqi~d~k~lkrlykvyekrefelk~~qf~qlkaelskkk   70 (276)
T PHA00727          5 KLVSAYEEELRKAQSLEELKQKYEEVQKQIADGKTLKRLYKVYEKREFELKLQQFRQLKAELSKKK   70 (276)
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             057888999874055999999999999976232889999999988889999999999999998877


No 171
>pfam12329 TMF_DNA_bd TATA element modulatory factor 1 DNA binding. This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures.. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells.
Probab=51.23  E-value=19  Score=16.65  Aligned_cols=66  Identities=26%  Similarity=0.308  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999864499879999999999999886444666667788877
Q gi|254780680|r   29 YILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLK   99 (430)
Q Consensus        29 ~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~   99 (430)
                      .|-+-|++-..|+.+.+.|.......+..|.++..+.+     .+-.....++.++..++.++..++..+.
T Consensus         6 ~l~eKDe~I~~L~~EgekLsk~el~~~~~IkkLr~~~~-----e~e~~~~~l~~k~~~~e~e~~~l~~~l~   71 (74)
T pfam12329         6 KLAEKDEQIAQLMEEGEKLSKKELKHNNTIKKLRAKNK-----ELEKEIAELKKKLEKLEKELENLEERLK   71 (74)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98846899999999988822888887899999999888-----6589999999999989999999999876


No 172
>KOG2391 consensus
Probab=50.96  E-value=19  Score=16.62  Aligned_cols=80  Identities=18%  Similarity=0.208  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHH
Q ss_conf             99999999999999999999999999986449987999999999999988644466666778887744310022588112
Q gi|254780680|r   34 DEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEV  113 (430)
Q Consensus        34 d~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~~V  113 (430)
                      ++-|+....++++++++++.+..- .+..++|    .++|.+....|..+...+.+..+-+..+..+-+-..-|+-..++
T Consensus       217 eklR~r~eeeme~~~aeq~slkRt-~EeL~~G----~~kL~~~~etLEqq~~~L~~niDIL~~k~~eal~~~~n~~~~~~  291 (365)
T KOG2391         217 EKLRRRREEEMERLQAEQESLKRT-EEELNIG----KQKLVAMKETLEQQLQSLQKNIDILKSKVREALEKAENLEALDI  291 (365)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             999999999998899999998856-9999866----99999999999999999986458988999997765416767981


Q ss_pred             HHCCC
Q ss_conf             21135
Q gi|254780680|r  114 PIGTS  118 (430)
Q Consensus       114 P~G~d  118 (430)
                      -.+.+
T Consensus       292 D~~~~  296 (365)
T KOG2391         292 DEAIE  296 (365)
T ss_pred             HHHHH
T ss_conf             03332


No 173
>pfam06810 Phage_GP20 Phage minor structural protein GP20. This family consists of several phage minor structural protein GP20 sequences of around 180 residues in length. The function of this family is unknown.
Probab=50.72  E-value=19  Score=16.60  Aligned_cols=54  Identities=15%  Similarity=0.116  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999998644998799999999999998864446666
Q gi|254780680|r   36 KNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEE   91 (430)
Q Consensus        36 ~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~   91 (430)
                      +.-.+..+.+.++.+.....++|..+++...+  .++|+.++.++..+.+..+++.
T Consensus        21 ~~~~~~~e~~~lk~Ql~~rd~ql~~Lk~~~~d--~e~L~~~ie~lq~~~~~~~~e~   74 (156)
T pfam06810        21 KLDKANEERDSLKKQLKNRDKQIEDLKKKVKD--NEELQKKIEKLKQQNKTAKEEY   74 (156)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC--HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999999999999999889998871588--8999999999999999889999


No 174
>COG3914 Spy Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]
Probab=50.67  E-value=6.1  Score=20.32  Aligned_cols=61  Identities=23%  Similarity=0.183  Sum_probs=49.2

Q ss_pred             CEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECC-CCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             208853221078843355434321222210200212127-865014578989999999999841
Q gi|254780680|r  252 LRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSIT-REEDSFTEHERMLSCAEEILKRLD  314 (430)
Q Consensus       252 ik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~-~pe~S~~~~e~~~~~~~~i~~~L~  314 (430)
                      +|..=+|.|+|.-|  -|--.+++|-.|-=+|.|.|++. .|+.++..++.+...++..+..-+
T Consensus       260 lRvGylS~dlr~Ha--vg~l~~~v~e~hDRdkfEvfay~~g~~~~dal~~rI~a~~~~~~~~~~  321 (620)
T COG3914         260 LRVGYLSSDLRSHA--VGFLLRWVFEYHDRDKFEVFAYSLGPPHTDALQERISAAVEKWYPIGR  321 (620)
T ss_pred             EEEEEECCCCCCCH--HHHHHHHHHHHHCHHHEEEEEEECCCCCCHHHHHHHHHHHHHEECCCC
T ss_conf             16788525464113--899999999873500158999965887731678888876531410588


No 175
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.
Probab=50.03  E-value=10  Score=18.60  Aligned_cols=53  Identities=15%  Similarity=0.161  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEEEECCCCCCCCCC
Q ss_conf             999999886444666667788877443100225881122113555402420001565665666
Q gi|254780680|r   76 ETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILIRSVGKKPSAIHLS  138 (430)
Q Consensus        76 e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~~~G~~~~f~f~~  138 (430)
                      -++.+.++.+.-.-....+.++.-...+..|++|+||          .+||+-|+.+-.+|-+
T Consensus       137 A~k~i~~~~~~~~~~~~~i~~~~~~~~L~~~~~p~pD----------LlIRTsGe~RLSnFLl  189 (221)
T cd00475         137 AVREIAEKVKAGKLTPEDIDESTLNKHLYTHDSPDPD----------LLIRTSGEQRLSNFLL  189 (221)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC----------EEEECCCCCCCCCHHH
T ss_conf             9999999998089996786788877407789999767----------7885489611124056


No 176
>KOG2629 consensus
Probab=48.68  E-value=21  Score=16.37  Aligned_cols=98  Identities=17%  Similarity=0.155  Sum_probs=52.7

Q ss_pred             HHHHHHHHCCCCCC----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999984698958----89999999999999999999999999999999998644998799999999999998864446
Q gi|254780680|r   13 HLDIALKKRHLEPQ----SEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILE   88 (430)
Q Consensus        13 ~v~~~l~~R~~~~~----id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le   88 (430)
                      .++.-+..+-+...    -+..-.||++-.++.+.++.|..+.-++++++.+-..+- ......++.....++..+..++
T Consensus       103 ~~K~YV~P~~l~~~~~k~e~~k~~Ld~~~~~~~~~~~~l~~~va~v~q~~~~qq~El-s~~L~~l~~~~~~~s~~~~k~e  181 (300)
T KOG2629         103 FVKSYVLPRFLGESKDKLEADKRQLDDQFDKAAKSLNALMDEVAQVSQLLATQQSEL-SRALASLKNTLVQLSRNIEKLE  181 (300)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999988887607651167777888889999999999999999999999999999999-9999999977777530198888


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHHH
Q ss_conf             666677888774431002258811221
Q gi|254780680|r   89 KEEHEVCSSLKKLISCIPNVPLEEVPI  115 (430)
Q Consensus        89 ~~~~~le~el~~lll~IPNi~~~~VP~  115 (430)
                      .+.+.+.    .+++.--|++.|.+|.
T Consensus       182 sei~~Ik----~lvln~~~f~~p~~p~  204 (300)
T KOG2629         182 SEINTIK----QLVLNMSNFAPPVAPS  204 (300)
T ss_pred             HHHHHHH----HHHHCCCCCCCCCCCC
T ss_conf             7888888----9985343357887833


No 177
>KOG0999 consensus
Probab=48.38  E-value=21  Score=16.34  Aligned_cols=20  Identities=20%  Similarity=0.287  Sum_probs=11.6

Q ss_pred             HHHCCHHHHCCCCCHHCCCH
Q ss_conf             98410675303780117844
Q gi|254780680|r  311 KRLDLHYRVVSLCTGDLGFS  330 (430)
Q Consensus       311 ~~L~lpyRvv~~~sgdlg~~  330 (430)
                      ..|-.-|..|.+|-+.+..-
T Consensus       492 d~La~lyh~vc~~n~etp~r  511 (772)
T KOG0999         492 DELAQLYHHVCECNNETPNR  511 (772)
T ss_pred             HHHHHHHHHHHHHCCCCCCH
T ss_conf             98999999999981778750


No 178
>COG4985 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]
Probab=47.94  E-value=21  Score=16.30  Aligned_cols=43  Identities=16%  Similarity=0.222  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             8799999999999998864446666677888774431002258
Q gi|254780680|r   67 LSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVP  109 (430)
Q Consensus        67 ~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~  109 (430)
                      ++--+.+-++-.+|-.+.+.++++++.+..+++...+-+-..-
T Consensus       213 ~~~q~~~~ae~seLq~r~~~l~~~L~~L~~e~~r~~l~~~Dm~  255 (289)
T COG4985         213 DEFQQHYVAEKSELQKRLAQLQTELDALRAELERQFLYLVDMQ  255 (289)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEECCC
T ss_conf             8899999988899999999999999987536653458888167


No 179
>pfam06632 XRCC4 DNA double-strand break repair and V(D)J recombination protein XRCC4. This family consists of several mammalian specific DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalysed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks.
Probab=46.68  E-value=22  Score=16.16  Aligned_cols=73  Identities=16%  Similarity=0.051  Sum_probs=45.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9588999999999999999999999999999999999864499879---999999999999886444666667788
Q gi|254780680|r   24 EPQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSL---VDALKNETSTLKEQLPILEKEEHEVCS   96 (430)
Q Consensus        24 ~~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~---~~~Lk~e~~~Lk~eik~le~~~~~le~   96 (430)
                      +..++.|-.|....-.|+.+-+.|..++|.+-++.-+....+..-+   .....--.++-|.+|..|.+.+.++++
T Consensus       128 ~~~L~~ia~L~a~n~hLqkENeRL~~e~~~i~~rLEk~V~~KEeLE~DLY~rFvlVLNEKKAKIRsLq~~L~e~qe  203 (331)
T pfam06632       128 CYCLDTIAELQAKNEHLQKENERLLRDWNDIQGRFEKCVSGKEALETDLYKRFILVLNEKKAKIRSLHKLLSEAQE  203 (331)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             9999999998887888887878988899999999999974499999999875452011268889999999999987


No 180
>KOG0977 consensus
Probab=46.15  E-value=22  Score=16.10  Aligned_cols=24  Identities=29%  Similarity=0.303  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             899999999999999999999999
Q gi|254780680|r   27 SEYILSLDEKNRILIKKIEDIRAR   50 (430)
Q Consensus        27 id~il~Ld~~rr~l~~e~e~Lrae   50 (430)
                      +|++-.|..+.+.|..+++.||..
T Consensus        55 IekVR~LEaqN~~L~~di~~lr~~   78 (546)
T KOG0977          55 IEKVRFLEAQNRKLEHDINLLRGV   78 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999998998878899999999864


No 181
>cd01368 KISc_KIF23_like Kinesin motor domain, KIF23-like subgroup. Members of this group may play a role in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, a
Probab=45.71  E-value=15  Score=17.47  Aligned_cols=43  Identities=21%  Similarity=0.483  Sum_probs=34.5

Q ss_pred             EEEECCCHHHHHHHHHHHHHHCCCCCCCEECC-------CCCCCCCCCEE
Q ss_conf             04200432289999999988346899838658-------22231018801
Q gi|254780680|r  379 THTLNGSGVAVGRCLIAILENYLNADGSVTIP-------TVLRPYMNNLA  421 (430)
Q Consensus       379 ~htlNgt~~A~~R~l~ailEn~q~~dg~i~iP-------~~L~pym~g~~  421 (430)
                      .-.+|-|.+|.+++|.||-++.....++..||       ..|+.++||--
T Consensus       267 ~~~IN~SL~~L~~vI~aL~~~~~~~~~~~hVPYRdSkLT~lL~dsLgGns  316 (345)
T cd01368         267 AGNINTSLMTLGKCIEVLRENQLSGSTNKMVPYRDSKLTHLFQNYFDGEG  316 (345)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCC
T ss_conf             32006128999999999974200357899788757888998687569986


No 182
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=45.64  E-value=23  Score=16.05  Aligned_cols=28  Identities=21%  Similarity=0.157  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHHHHHHCCCCEEHHHHHCCHH
Q ss_conf             9999999999862232032021235620278
Q gi|254780680|r  174 LERALGQFMIDLHTSEHGYTEVSAPLLVRDE  204 (430)
Q Consensus       174 Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~  204 (430)
                      |++..-.++|+. .. .| +||.+=....-+
T Consensus       504 l~~l~k~~~lE~-sG-~g-~pvk~ve~~t~~  531 (652)
T COG2433         504 LAELRKMRKLEL-SG-KG-TPVKVVEKLTLE  531 (652)
T ss_pred             HHHHHHHHHHHH-CC-CC-CCEEHHHHHHHH
T ss_conf             999988776662-38-87-510114354388


No 183
>pfam10146 zf-C4H2 Zinc finger-containing protein. This is a family of proteins which appears to have a highly conserved zinc finger domain at the C terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members are annotated as being tumour-associated antigen HCA127 in humans but this could not confirmed.
Probab=45.56  E-value=23  Score=16.04  Aligned_cols=60  Identities=17%  Similarity=0.129  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999986449987999999999999988644466666778887744310
Q gi|254780680|r   33 LDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISC  104 (430)
Q Consensus        33 Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~  104 (430)
                      |.+++..--.++..+-+..|.+-.-|.++.            .+-....+.+..+.+++..+...++.++..
T Consensus        44 L~qEKmaHvEELRqIhaDIN~mE~iIKqse------------~e~~~~~~~i~r~~~ey~~Lk~~id~~r~e  103 (220)
T pfam10146        44 LLMEKMSHVEELRQIHADINDMENIIKQSE------------SELEKRKEKIRRAHEEYKRLKEFINEMREE  103 (220)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999899999999999711999999999889------------999999999999999999899999999996


No 184
>KOG1029 consensus
Probab=45.26  E-value=23  Score=16.01  Aligned_cols=11  Identities=36%  Similarity=0.305  Sum_probs=5.0

Q ss_pred             CCCCCCCCCHH
Q ss_conf             56662112202
Q gi|254780680|r  135 IHLSREHFEIG  145 (430)
Q Consensus       135 ~f~~k~H~elg  145 (430)
                      .|+.++|-||.
T Consensus       701 ~FeaRs~dEis  711 (1118)
T KOG1029         701 PFEARSHDEIS  711 (1118)
T ss_pred             CCCCCCCCCCC
T ss_conf             33357764101


No 185
>KOG3229 consensus
Probab=45.19  E-value=23  Score=16.00  Aligned_cols=72  Identities=17%  Similarity=0.205  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             9999999999999999999999999999986449987999999999999988644466666778887744310022
Q gi|254780680|r   32 SLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPN  107 (430)
Q Consensus        32 ~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPN  107 (430)
                      .+-++-|.+..++-.++.+.+++.+.|.++.++++....--|-+++-..+..++.+.+    -...++.+.+.+-|
T Consensus        22 kiRke~r~ldrqir~iqree~kv~~~iK~aAKknD~~t~~iLAKEiv~srk~v~Rly~----sKAqlnSv~M~l~e   93 (227)
T KOG3229          22 KIRKEGRQLDRQIRDIQREEEKVQKSIKQAAKKNDKDTCRILAKEIVQSRKAVKRLYE----SKAQLNSVSMQLKE   93 (227)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHH
T ss_conf             9999997799999999999999999999998713479999999999999899999987----39877259989989


No 186
>TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.   This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=45.02  E-value=23  Score=15.98  Aligned_cols=111  Identities=18%  Similarity=0.110  Sum_probs=62.6

Q ss_pred             HHHHH--CCHHHHHHHHHHC---------------------CCCCCHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             44785--1999999999846---------------------9895889-----999999999999999999999999999
Q gi|254780680|r    4 IQWIR--QNPEHLDIALKKR---------------------HLEPQSE-----YILSLDEKNRILIKKIEDIRARRNSNS   55 (430)
Q Consensus         4 ik~IR--en~e~v~~~l~~R---------------------~~~~~id-----~il~Ld~~rr~l~~e~e~LraerN~lS   55 (430)
                      |++||  +|++..++.|-.+                     +..++++     .|+++ .-+|-.=-|.|.|+.|.++|.
T Consensus       389 I~lIr~S~~~~~Ak~~L~e~~W~l~di~~ll~~~~~~~l~~~g~F~l~E~QA~AILdM-rL~rLTgLE~~Kl~~E~~~L~  467 (864)
T TIGR01063       389 IALIRASQNTEEAKTRLVERQWELLDILPLLKLVLEVELGERGTFSLSEIQAQAILDM-RLQRLTGLEREKLEEEYKELL  467 (864)
T ss_pred             HHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHH
T ss_conf             9997427898899988421686078999999887675328888654488999999998-876778888999999999999


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEE
Q ss_conf             9999986449987999999999999988644466666778887744310022588112211355540242
Q gi|254780680|r   56 AQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILI  125 (430)
Q Consensus        56 KeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i  125 (430)
                      .+|+.+..--.++     .....-+|+|+.++.++..  ...+.++...--+..+.+==+   ..+|+||
T Consensus       468 ~~I~~l~~iL~~~-----~r~~~iireEL~~i~~~Fg--d~RRT~I~~~~~~~~D~EDLI---~~E~vVv  527 (864)
T TIGR01063       468 ELIADLEDILASE-----ERVLEIIREELEEIKEQFG--DPRRTEIVAEESEDIDIEDLI---ARENVVV  527 (864)
T ss_pred             HHHHHHHHHCCCH-----HHHHHHHHHHHHHHHHHHC--CCCCCHHHHCCCCCCCCHHHH---CCCCEEE
T ss_conf             9999999750377-----6899999999999999738--853212220243224503441---4787899


No 187
>pfam04880 NUDE_C NUDE protein, C-terminal conserved region. This family represents the C-terminal conserved region of the NUDE proteins. NUDE proteins are involved in nuclear migration.
Probab=44.89  E-value=23  Score=15.97  Aligned_cols=49  Identities=18%  Similarity=0.139  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CCC-CCHHHHC
Q ss_conf             799999999999998864446666677888774431002----258-8112211
Q gi|254780680|r   68 SLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIP----NVP-LEEVPIG  116 (430)
Q Consensus        68 ~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IP----Ni~-~~~VP~G  116 (430)
                      ++.+.|+.+.+.|++++..|..++..+++++..-..+-|    |.. .|++|.+
T Consensus        24 ~Eke~L~i~~QRLkDE~rDLk~E~~v~q~~~~~~~~~~~~~~~~~~s~P~tP~~   77 (166)
T pfam04880        24 DEKESLRIENQRLRDELRDLKQELIVQERLRNNNRKSRPAPVVNLGSSPSTPHT   77 (166)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf             689999999999999999999999999999862344067765445668888988


No 188
>PRK11147 ABC transporter ATPase component; Reviewed
Probab=44.08  E-value=24  Score=15.88  Aligned_cols=11  Identities=18%  Similarity=0.380  Sum_probs=6.2

Q ss_pred             CCCCCCCCHHH
Q ss_conf             66621122022
Q gi|254780680|r  136 HLSREHFEIGE  146 (430)
Q Consensus       136 f~~k~H~elge  146 (430)
                      .+|-+|+|+-.
T Consensus       181 DEPTn~LD~~~  191 (632)
T PRK11147        181 DEPTNHLDIET  191 (632)
T ss_pred             ECCCCCCCHHH
T ss_conf             48876589999


No 189
>pfam10498 IFT57 Intra-flagellar transport protein 57. Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.
Probab=44.07  E-value=24  Score=15.88  Aligned_cols=11  Identities=9%  Similarity=0.220  Sum_probs=5.6

Q ss_pred             EEEEECCCCCC
Q ss_conf             42000156566
Q gi|254780680|r  124 LIRSVGKKPSA  134 (430)
Q Consensus       124 ~i~~~G~~~~f  134 (430)
                      +++.||-++.|
T Consensus        79 ~lk~~g~~~dF   89 (355)
T pfam10498        79 ELKAIGIPVDF   89 (355)
T ss_pred             HHHHCCCCCCC
T ss_conf             99963999998


No 190
>KOG4657 consensus
Probab=43.70  E-value=24  Score=15.84  Aligned_cols=46  Identities=15%  Similarity=0.186  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999984698958899999999999999999999999999999
Q gi|254780680|r   11 PEHLDIALKKRHLEPQSEYILSLDEKNRILIKKIEDIRARRNSNSA   56 (430)
Q Consensus        11 ~e~v~~~l~~R~~~~~id~il~Ld~~rr~l~~e~e~LraerN~lSK   56 (430)
                      .|.+-....+|-++..+.-+..+-....+...-...|+.-.|++++
T Consensus        31 ~D~f~q~~r~~~~nS~~efar~lS~~~~e~e~l~~~l~etene~~~   76 (246)
T KOG4657          31 IDSFIQSPRRRSMNSLVEFARALSQSQVELENLKADLRETENELVK   76 (246)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999987999999999999999888789999999999999999999


No 191
>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]
Probab=43.61  E-value=24  Score=15.83  Aligned_cols=19  Identities=53%  Similarity=0.714  Sum_probs=10.0

Q ss_pred             CCCCEECCCCCCCCCCCEEEE
Q ss_conf             998386582223101880130
Q gi|254780680|r  403 ADGSVTIPTVLRPYMNNLAVI  423 (430)
Q Consensus       403 ~dg~i~iP~~L~pym~g~~~i  423 (430)
                      .||.|..-..|+-|  |+-+|
T Consensus       338 AdG~VvyA~~l~GY--G~vvI  356 (420)
T COG4942         338 ADGRVVYADWLRGY--GLVVI  356 (420)
T ss_pred             CCCEEEECHHHCCC--CEEEE
T ss_conf             69569954332567--56999


No 192
>TIGR00958 3a01208 antigen peptide transporter 2; InterPro: IPR005293   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     Proteins of this family are involved in the transport of antigens from the cytoplasm to a membrane-bound compartment for association with MHC class I molecules.; GO: 0005215 transporter activity, 0006810 transport.
Probab=43.23  E-value=17  Score=16.93  Aligned_cols=53  Identities=13%  Similarity=0.133  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCHHHHCC
Q ss_conf             778887744310022588112211355540242000156566566621122022117
Q gi|254780680|r   93 EVCSSLKKLISCIPNVPLEEVPIGTSANENILIRSVGKKPSAIHLSREHFEIGEALG  149 (430)
Q Consensus        93 ~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~~~G~~~~f~f~~k~H~elge~l~  149 (430)
                      -+.+++-+++-+=||++++..=.=..-+.+++-+.    -.|..+.++...|.+.|.
T Consensus       501 GAs~KvFey~DR~P~~~~~G~~~P~~~~G~ieF~d----VsFsYP~RP~~pvLk~Lt  553 (770)
T TIGR00958       501 GASEKVFEYLDRKPQIPLTGTLAPKNLEGKIEFQD----VSFSYPNRPDVPVLKGLT  553 (770)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEEE----EEECCCCCCCCCCCCCCC
T ss_conf             24777544427889988797514576322588753----223178988976112774


No 193
>KOG4674 consensus
Probab=42.94  E-value=25  Score=15.76  Aligned_cols=21  Identities=14%  Similarity=0.082  Sum_probs=9.4

Q ss_pred             HHHHHHHHHHHHHHHHCCHHH
Q ss_conf             789899999999998410675
Q gi|254780680|r  298 EHERMLSCAEEILKRLDLHYR  318 (430)
Q Consensus       298 ~~e~~~~~~~~i~~~L~lpyR  318 (430)
                      .+.......+.++..|..|=-
T Consensus      1663 ~l~~~~k~~~~l~~~~~~~s~ 1683 (1822)
T KOG4674        1663 FLSELEKSLESLVKPLVASSK 1683 (1822)
T ss_pred             HHHHHHHHHHHHHHHHCCCCC
T ss_conf             200678889987523116876


No 194
>pfam11622 DUF3251 Protein of unknown function (DUF3251). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. Some members if this family are annotated as putative lipoprotein YajI however this cannot be confirmed.
Probab=42.77  E-value=8.5  Score=19.26  Aligned_cols=42  Identities=24%  Similarity=0.364  Sum_probs=27.1

Q ss_pred             CCCCCHHHHHHHHHCCC---------HHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEE
Q ss_conf             34541145445342059---------555042088532210788433554343212222102
Q gi|254780680|r  230 PTSEVSLTNLYSHEIIE---------SKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFW  282 (430)
Q Consensus       230 ~TaEvpL~~~~~~~~l~---------~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~  282 (430)
                      ||++-|+++-..++.|.         +.+.|+++.|++|           |--|-.|||.|.
T Consensus       105 ~~s~~~~~~~~qsq~~~ap~sl~p~S~~~i~l~L~G~tP-----------~QLGfVRvHdiq  155 (156)
T pfam11622       105 GTTGNYQEVNTQSQLFVAPASLLPPSDVSIPLRLSGVTP-----------DQLGFVRVHDIQ  155 (156)
T ss_pred             CCCCCCCCCCCCCCEEECCCCCCCCCCCEEEEEECCCCH-----------HHCCEEEEEECC
T ss_conf             777883302100202506777589764436888678996-----------771259873058


No 195
>pfam10482 CtIP_N Tumour-suppressor protein CtIP N-terminal domain. CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control. This N-terminal domain carries a coiled-coil region and is essential for homodimerization of the protein. The C-terminal domain is family pfam08573.
Probab=42.54  E-value=25  Score=15.72  Aligned_cols=54  Identities=17%  Similarity=0.355  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999986449987999999999999988644466666
Q gi|254780680|r   34 DEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEH   92 (430)
Q Consensus        34 d~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~   92 (430)
                      |.+...++.++-.|..+|+.-+.-+..+.++.     ..|+++-+.+++.|+.+|..++
T Consensus        13 d~ev~glQ~Kl~~L~~erc~DaqRleEl~sKN-----~qLREQQk~l~enikvLEnRLR   66 (120)
T pfam10482        13 DKEVQGLQAKLAKLKKERCLDAQRLEEFFSKN-----QQLREQQKVLQENIRVLEDRLR   66 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999998798824299999998701-----8899999999988999999987


No 196
>KOG0728 consensus
Probab=42.53  E-value=25  Score=15.72  Aligned_cols=168  Identities=23%  Similarity=0.219  Sum_probs=78.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH----------------
Q ss_conf             9999999999999999999999999999999998644998799999999999998864446666----------------
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEE----------------   91 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~----------------   91 (430)
                      .+|.++..+.++-.+.+..|+++||++...+.-++     ++++-+.+.++-+.+-++.+.+..                
T Consensus        24 ~ki~~~~~~v~~kt~nlrrleaqrneln~kvr~lr-----eel~~lqe~gsyvgev~k~m~k~kVLVKvhpegKyvvdv~   98 (404)
T KOG0728          24 QKIEELQLQVAEKTQNLRRLEAQRNELNAKVRLLR-----EELQLLQEPGSYVGEVVKAMGKKKVLVKVHPEGKYVVDVD   98 (404)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCEEEECC
T ss_conf             88999999999988789999999988768899999-----9999873676268899986066548999768885788626


Q ss_pred             -------------HHHHHHHHHHHHHCCCCCCCHH--------HHCCCCCCCEEEEEECCCCCCCCCCCCCCCHHHHCCC
Q ss_conf             -------------6778887744310022588112--------2113555402420001565665666211220221173
Q gi|254780680|r   92 -------------HEVCSSLKKLISCIPNVPLEEV--------PIGTSANENILIRSVGKKPSAIHLSREHFEIGEALGL  150 (430)
Q Consensus        92 -------------~~le~el~~lll~IPNi~~~~V--------P~G~de~dNv~i~~~G~~~~f~f~~k~H~elge~l~l  150 (430)
                                   -.+..+-+.+-.-+||-.+|-|        |+..-|----.-+..-++++--.-|.-|-||-+.||+
T Consensus        99 k~i~i~~~~~~~rVaLR~dsY~lhkiLpnKvDpLVsLMmVeKvPDStYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLGI  178 (404)
T KOG0728          99 KNIDISDVTPSSRVALRNDSYTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI  178 (404)
T ss_pred             CCCCHHHCCCCCEEEEECCCHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHCCC
T ss_conf             88767445866468881553689886444533466777453078308887503888999999998265668789985187


Q ss_pred             CCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHH
Q ss_conf             1000112221675301056488999999999998622320320212356202788986551
Q gi|254780680|r  151 MDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQ  211 (430)
Q Consensus       151 iDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~  211 (430)
                      .. .+|.-+-|.-+.   |. -+|-||..     .|+ .--|..|+-..+|-.-+-+|+-.
T Consensus       179 aQ-PKGvlLygppgt---Gk-tLlaraVa-----hht-~c~firvsgselvqk~igegsrm  228 (404)
T KOG0728         179 AQ-PKGVLLYGPPGT---GK-TLLARAVA-----HHT-DCTFIRVSGSELVQKYIGEGSRM  228 (404)
T ss_pred             CC-CCCEEEECCCCC---CH-HHHHHHHH-----HHC-CEEEEEECHHHHHHHHHHHHHHH
T ss_conf             88-760488469997---56-29999987-----541-40799964499999985013899


No 197
>pfam07888 CALCOCO1 Calcium binding and coiled-coil domain (CALCOCO1) like. Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.
Probab=42.36  E-value=25  Score=15.70  Aligned_cols=69  Identities=22%  Similarity=0.168  Sum_probs=38.6

Q ss_pred             HHHHHHHCCCHHHHCCEEEEEECCCCC---CCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             544534205955504208853221078---84335543432122221020021212786501457898999999999984
Q gi|254780680|r  237 TNLYSHEIIESKSLPLRFTTLAPSFRS---EAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRL  313 (430)
Q Consensus       237 ~~~~~~~~l~~~~LPik~~~~s~cfR~---EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L  313 (430)
                      -.....+--....|-+.+..-.-|+|-   |++--=+..|.=+||-|=+|         |+--.+..+++..+..+=..|
T Consensus       384 E~~lQEer~ere~l~~eL~~EkDc~rvQLsE~rREl~ELks~lrv~qkEK---------EqlqeE~Qel~~y~~~le~rl  454 (546)
T pfam07888       384 EEWLQEERSQREKLEVELGIEKDCNRVQLSENRRELSELRSALRVLQKEK---------EQLQEEKQELLDYIRVLELRL  454 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999888878888744521348887777779999999999999889---------999999999999999999998


Q ss_pred             C
Q ss_conf             1
Q gi|254780680|r  314 D  314 (430)
Q Consensus       314 ~  314 (430)
                      +
T Consensus       455 ~  455 (546)
T pfam07888       455 D  455 (546)
T ss_pred             H
T ss_conf             6


No 198
>KOG4302 consensus
Probab=42.06  E-value=26  Score=15.67  Aligned_cols=81  Identities=20%  Similarity=0.207  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999999864499---------87999999999999988644466666778887
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGN---------LSLVDALKNETSTLKEQLPILEKEEHEVCSSL   98 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~---------~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el   98 (430)
                      ..+-+....++.+.+++..++++-|.+...+|....-+.         .+....+......|+.+-.+--.++.++..++
T Consensus        54 ~kve~a~~~~~~L~~~ia~~eael~~l~s~l~~~~~~~~~~~k~e~tLke~l~~l~~~le~lr~qk~eR~~ef~el~~qi  133 (660)
T KOG4302          54 RKVEEASESKARLLQEIAVIEAELNDLCSALGEPSIIGEISDKIEGTLKEQLESLKPYLEGLRKQKDERRAEFKELYHQI  133 (660)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999889999999999999999999999847752224432446765999999999989999999999999999999999


Q ss_pred             HHHHHHCCCC
Q ss_conf             7443100225
Q gi|254780680|r   99 KKLISCIPNV  108 (430)
Q Consensus        99 ~~lll~IPNi  108 (430)
                      ..+...|..-
T Consensus       134 e~l~~~l~g~  143 (660)
T KOG4302         134 EKLCEELGGP  143 (660)
T ss_pred             HHHHHHHCCC
T ss_conf             9999996687


No 199
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=42.00  E-value=26  Score=15.66  Aligned_cols=100  Identities=18%  Similarity=0.137  Sum_probs=50.3

Q ss_pred             HCCHHHHHHHHHHCCCC----C--------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHC
Q ss_conf             51999999999846989----5--------88999999999999999999999999999999999-----------8644
Q gi|254780680|r    8 RQNPEHLDIALKKRHLE----P--------QSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQ-----------AIAE   64 (430)
Q Consensus         8 Ren~e~v~~~l~~R~~~----~--------~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~-----------~k~~   64 (430)
                      +++.+.+-+.|...|.-    .        .-+.+.+..++.+++...++.|+....+.......           ...+
T Consensus        10 ~~~~~~vl~~L~elG~v~i~dl~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (640)
T PRK05771         10 KSYKDEVLEALQELGVVEIEDLKEEKKPDISSESLRKLLELLSKLSEALDLLKSYVPKEGKPKALRKKKKSLSSEEEELK   89 (640)
T ss_pred             HHHHHHHHHHHHHCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHH
T ss_conf             88899999999838978998277532433200678779999999999999999987650776544456567883078888


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99879999999999999886444666667788877443100225
Q gi|254780680|r   65 GNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNV  108 (430)
Q Consensus        65 ~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi  108 (430)
                      ....+.+++.++++++.+++.+++++.+++++++..+- .+-|+
T Consensus        90 ~~e~~l~~l~~~v~~L~~~~~~l~~~~~~L~~~~~~l~-~~~~~  132 (640)
T PRK05771         90 SVEEELEEIEEEISELEEELSELENEIKELEEEIEELE-PWGNF  132 (640)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCC
T ss_conf             89989999999999999999999999999999999999-78548


No 200
>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.18  E-value=27  Score=15.57  Aligned_cols=43  Identities=16%  Similarity=0.132  Sum_probs=29.7

Q ss_pred             HCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4698958899999999999999999999999999999999986
Q gi|254780680|r   20 KRHLEPQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAI   62 (430)
Q Consensus        20 ~R~~~~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k   62 (430)
                      .++.+..-.+...|-++.+++|.+..+|+++++.+.+.+....
T Consensus        42 ~k~~~~~~~r~~~L~~e~~s~Q~~~~~L~~ev~~~~~~~~s~~   84 (247)
T COG3879          42 SKGESVRRARDLDLVKELRSLQKKVNTLAAEVEDLENKLDSVR   84 (247)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             2685032235668999989999999999999999999998877


No 201
>TIGR00998 8a0101 efflux pump membrane protein; InterPro: IPR005694    emrA and emrB confer resistance to carbonylcyanide m-chlorophenylhydrazone, nalidixic acid, and a number of other toxic compounds. EmrB encodes a highly hydrophobic 56.2-kDa peptide, with 14 potential alpha-helices to span the inner membrane. EmrA encodes a putative 42.7-kDa peptide containing a single hydrophobic domain and a large C-terminal hydrophilic domain.; GO: 0015238 drug transporter activity, 0006855 multidrug transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=40.90  E-value=27  Score=15.54  Aligned_cols=94  Identities=21%  Similarity=0.234  Sum_probs=60.1

Q ss_pred             CHHHHHHHHHHCCCC---CCHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             999999999846989---5889--999999999999999999999999999--999998644998799999999999998
Q gi|254780680|r   10 NPEHLDIALKKRHLE---PQSE--YILSLDEKNRILIKKIEDIRARRNSNS--AQIGQAIAEGNLSLVDALKNETSTLKE   82 (430)
Q Consensus        10 n~e~v~~~l~~R~~~---~~id--~il~Ld~~rr~l~~e~e~LraerN~lS--KeIg~~k~~~~~~~~~~Lk~e~~~Lk~   82 (430)
                      ..+.++-.+.||--=   --++  ++-++|..|..+...-.+|.+-++++|  -+|... ++|... +.+-......|++
T Consensus       142 ~~~~~~~dl~Rr~~L~~~G~I~~RkFE~l~~ar~a~~~a~A~L~aa~~~I~evT~~~R~-~~G~~~-An~Al~~~~~L~~  219 (379)
T TIGR00998       142 KIKLVKLDLRRRVPLLKKGLISRRKFEELDHARKALLSAKAALNAAIQEINEVTEIKRA-KKGQLN-ANQALVRGTPLKK  219 (379)
T ss_pred             HHHHHHCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH-HHHHHHCCCCHHH
T ss_conf             65653215353488984789987544434768999999998788998543345678999-999999-9874112442043


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             86444666667788877443100
Q gi|254780680|r   83 QLPILEKEEHEVCSSLKKLISCI  105 (430)
Q Consensus        83 eik~le~~~~~le~el~~lll~I  105 (430)
                      +.+.||++..++.+.+.+-+|.|
T Consensus       220 qpasLeeev~~A~~~~~~A~L~L  242 (379)
T TIGR00998       220 QPASLEEEVQEAKERLKKAWLAL  242 (379)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             34107899999999999998740


No 202
>KOG2077 consensus
Probab=40.85  E-value=27  Score=15.54  Aligned_cols=25  Identities=20%  Similarity=0.263  Sum_probs=14.5

Q ss_pred             HHHCCCCCHHCCCHHHEEEEEEEECCC
Q ss_conf             753037801178443402410110100
Q gi|254780680|r  317 YRVVSLCTGDLGFSACKTYDLEVWLAG  343 (430)
Q Consensus       317 yRvv~~~sgdlg~~a~~~~DiE~w~P~  343 (430)
                      --+|-+||..++.+-.--  |.|--||
T Consensus       642 SSlVWi~tSt~~~skv~i--iDAnqPg  666 (832)
T KOG2077         642 SSLVWICTSTHSASKVLI--IDANQPG  666 (832)
T ss_pred             CCEEEEEECCCCCCEEEE--EECCCCC
T ss_conf             515999942777405899--8368998


No 203
>KOG2911 consensus
Probab=40.51  E-value=27  Score=15.50  Aligned_cols=43  Identities=21%  Similarity=0.254  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH
Q ss_conf             9999999999999999999999999999999986449987999
Q gi|254780680|r   29 YILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVD   71 (430)
Q Consensus        29 ~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~   71 (430)
                      .|..|-..+.++..+++.|..+.++.+++.-+..++|+..-+.
T Consensus       234 ~V~~L~~~~~~L~kqie~L~qeie~~~~~~r~~~k~g~K~iA~  276 (439)
T KOG2911         234 SVADLIQARAKLAKQIEFLEQEIEKSKEKLRQALKEGKKQIAI  276 (439)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH
T ss_conf             5999999999999999999999999799999999706268899


No 204
>pfam01920 Prefoldin_2 Prefoldin subunit. This family includes prefoldin subunits that are not detected by pfam02996.
Probab=40.31  E-value=27  Score=15.48  Aligned_cols=75  Identities=17%  Similarity=0.329  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------HHHHHHHCCC-HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999----------------9999864499-879999999999999886444666
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSA----------------QIGQAIAEGN-LSLVDALKNETSTLKEQLPILEKE   90 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSK----------------eIg~~k~~~~-~~~~~~Lk~e~~~Lk~eik~le~~   90 (430)
                      ..+..+..+...+..++..+..+.+....                .||...-..+ .+..+.+......+..+|+.++++
T Consensus         5 ~~f~~l~~~~~~l~~~~~~le~~~~e~~~v~~EL~~ld~d~~vy~~VG~vlv~~~~~e~~~~L~~~~e~i~~~i~~le~q   84 (104)
T pfam01920         5 NKFQQLQQQLQLLAQQIKQLETQLKEIELVLEELELLDEDTKVYKLIGDVLVKQDKEEVKEELEERKETLEKEIKTLEKQ   84 (104)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCHHEECCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999999997189876178982512402159999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             667788877443
Q gi|254780680|r   91 EHEVCSSLKKLI  102 (430)
Q Consensus        91 ~~~le~el~~ll  102 (430)
                      ...++.++.++-
T Consensus        85 ~~~~~~~~~~lk   96 (104)
T pfam01920        85 LEKLEKELEELK   96 (104)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 205
>KOG0837 consensus
Probab=39.94  E-value=28  Score=15.44  Aligned_cols=15  Identities=33%  Similarity=0.233  Sum_probs=8.7

Q ss_pred             ECCHHHHHHHHHHHH
Q ss_conf             056488999999999
Q gi|254780680|r  167 LTGHLAHLERALGQF  181 (430)
Q Consensus       167 Lkg~~A~Le~ALi~y  181 (430)
                      ++..---||+|+++-
T Consensus        65 l~l~speLe~aiv~s   79 (279)
T KOG0837          65 LKLASPELERAIVRS   79 (279)
T ss_pred             CCCCCHHHHHHHHHC
T ss_conf             214767788888631


No 206
>PRK11106 queuosine biosynthesis protein QueC; Provisional
Probab=39.63  E-value=16  Score=17.28  Aligned_cols=13  Identities=23%  Similarity=0.051  Sum_probs=7.5

Q ss_pred             CHHHHHHHHHCCC
Q ss_conf             1145445342059
Q gi|254780680|r  234 VSLTNLYSHEIIE  246 (430)
Q Consensus       234 vpL~~~~~~~~l~  246 (430)
                      -||..|-+.+|+.
T Consensus       158 aPl~~l~K~eiv~  170 (231)
T PRK11106        158 TPLMWLDKAETWA  170 (231)
T ss_pred             ECCCCCCHHHHHH
T ss_conf             3777788889999


No 207
>COG3352 FlaC Putative archaeal flagellar protein C [Cell motility and secretion]
Probab=39.61  E-value=28  Score=15.40  Aligned_cols=69  Identities=20%  Similarity=0.250  Sum_probs=42.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             999999999999999999864--499879999999999999886444666667788877443100225881
Q gi|254780680|r   43 KIEDIRARRNSNSAQIGQAIA--EGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLE  111 (430)
Q Consensus        43 e~e~LraerN~lSKeIg~~k~--~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~  111 (430)
                      .++..-..-+.++.++|+.+.  .|.+..++..+.+...|.+.++.+......+..+++-+....|-...-
T Consensus        45 ~id~imer~~~ieNdlg~~~~~~~g~kk~~~~~~eelerLe~~iKdl~~lye~Vs~d~Npf~s~~~qes~~  115 (157)
T COG3352          45 VIDAIMERMTDIENDLGKVKIEIEGQKKQLQDIKEELERLEENIKDLVSLYELVSRDFNPFMSKTPQESRG  115 (157)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999998886424454212444566887999999999999999999999997612677644888887


No 208
>pfam04156 IncA IncA protein. Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA.
Probab=38.36  E-value=29  Score=15.27  Aligned_cols=69  Identities=20%  Similarity=0.313  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999864499879999999999999886444666667788877443
Q gi|254780680|r   29 YILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLI  102 (430)
Q Consensus        29 ~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~ll  102 (430)
                      ++.+.......+..++++++.....+.+++...+..     ........+..++++..++.......+++.++.
T Consensus        80 e~~~~~~~l~~l~~el~~~~~~~~~~~~~l~~~~~~-----~~~~~~~~~~~~~~l~~l~~~~~~~~~e~~~l~  148 (186)
T pfam04156        80 ELSELKQQLSELQEELEDLEERIAELESELEDLKED-----LQLLRELLKSLEERLESLEESIKELAKELRELR  148 (186)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999899999999998998987688874475978878-----999899878888889999989998999999999


No 209
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=37.94  E-value=30  Score=15.22  Aligned_cols=53  Identities=9%  Similarity=0.155  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH-CCCCC
Q ss_conf             79999999999999886------4446666677888774431002258811221-13555
Q gi|254780680|r   68 SLVDALKNETSTLKEQL------PILEKEEHEVCSSLKKLISCIPNVPLEEVPI-GTSAN  120 (430)
Q Consensus        68 ~~~~~Lk~e~~~Lk~ei------k~le~~~~~le~el~~lll~IPNi~~~~VP~-G~de~  120 (430)
                      +...++|+-.++|..++      .++.+.+.---+++.+++...+-..+=|+|+ |.+++
T Consensus       194 EKLnkiKK~qReL~q~lGR~Ps~~EiAe~lel~~~qvR~~l~~~~~p~SLd~~VrG~e~d  253 (336)
T TIGR02997       194 EKLNKIKKVQRELSQKLGRRPSEAEIAEALELEPEQVRELLQRARQPVSLDTRVRGDEED  253 (336)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             666899899899999838897868999883889889999999707874457732688854


No 210
>TIGR00364 TIGR00364 exsB protein; InterPro: IPR004479   This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome.    In Sinorhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA , .    In Arthrobacter viscosus, the homologous gene is designated alu1 and is associated with an aluminum tolerance phenotype. When expressed in Escherichia coli, it conferred aliminium tolerance .   The entry also contains the gene queC, which is responsible for the conversion of GTP to 7-cyano-7-deazaguanine (preQ0). The biosynthesis of hypermodified tRNA nucleoside queuosine only occurs in eubacteria. It occupies the wobble position for all known tRNAs that are specific for Asp, Asn, His or Tyr ..
Probab=37.82  E-value=29  Score=15.32  Aligned_cols=97  Identities=22%  Similarity=0.320  Sum_probs=65.2

Q ss_pred             EEEEE--EEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHH-HCCCCC-HHCCC-HHHEEEEE--------------
Q ss_conf             22210--2002121278650145789899999999998410675-303780-11784-43402410--------------
Q gi|254780680|r  277 RQHQF--WKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYR-VVSLCT-GDLGF-SACKTYDL--------------  337 (430)
Q Consensus       277 RvHQF--~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyR-vv~~~s-gdlg~-~a~~~~Di--------------  337 (430)
                      =..+|  .+|+.+.|-   ---..|..=++.|++|-+.||+|+. +|+|.. +++|. +|=.+=+.              
T Consensus        18 a~~~~GkyeV~a~TF~---YGQR~H~~Ele~A~~ia~~Lgi~~~~~~Dl~~l~~l~~YsaLt~~~~~~~~~~~e~d~~~~   94 (227)
T TIGR00364        18 ALDEGGKYEVHAITFD---YGQRAHSRELESARKIAEALGIRHHFVIDLSLLKQLGKYSALTDEQEIPEQKSNEEDKEKA   94 (227)
T ss_pred             HHHCCCCEEEEEECCC---CHHHHHHHHHHHHHHHHHHHCCCCEEEECHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf             9961795079985465---0137899999999999998089707861779998554045235787567666653202356


Q ss_pred             -----EEECCCCCC--------------EEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCC
Q ss_conf             -----110100483--------------323753102100764532684733899841010420043
Q gi|254780680|r  338 -----EVWLAGQNL--------------YREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGS  385 (430)
Q Consensus       338 -----E~w~P~~~~--------------y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt  385 (430)
                           -+|.||||.              =.+|---=|-+||      --|-  +-+ .+|+-++|-+
T Consensus        95 ~E~~p~tfVPgRN~~fl~~a~~yA~~~gA~~v~~G~~~~Df------SgYP--DCr-~EFvka~n~~  152 (227)
T TIGR00364        95 LETLPNTFVPGRNLIFLSLAASYAEALGAEAVITGVCETDF------SGYP--DCR-DEFVKALNHA  152 (227)
T ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHCCCCCCC------CCCC--CCC-HHHHHHHHHH
T ss_conf             53113333780479999999998886184252200100036------5798--886-8899999999


No 211
>KOG2784 consensus
Probab=37.69  E-value=24  Score=15.92  Aligned_cols=104  Identities=20%  Similarity=0.277  Sum_probs=65.7

Q ss_pred             CCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             41145445342059555042088532210788433554343212222102002121278650145789899999999998
Q gi|254780680|r  233 EVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKR  312 (430)
Q Consensus       233 EvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~  312 (430)
                      -|+--.+|+=-  ...=-|-||.++-+.||-|+=.+   |.    +-+|+.||=++...    .--+-.++.+-.+++..
T Consensus       317 avSArmLy~LA--k~~f~p~K~FSIDrVFRNEtvDa---TH----LAEFHQVEGviad~----gltLgdLig~l~~ff~~  383 (483)
T KOG2784         317 AVSARMLYRLA--KKGFKPAKYFSIDRVFRNETVDA---TH----LAEFHQVEGVIADK----GLTLGDLIGILMEFFTK  383 (483)
T ss_pred             HHHHHHHHHHH--HCCCCCCCCCCHHHHHHCCCCCH---HH----HHHHHHHCEEEECC----CCCHHHHHHHHHHHHHC
T ss_conf             76499999997--47998511010413440343205---77----87776320365137----87699999999999732


Q ss_pred             HCCHHHHCCCCCHHCCC-HHHEEE-----EEEEECCCCCCEEEEEEECCCCC
Q ss_conf             41067530378011784-434024-----10110100483323753102100
Q gi|254780680|r  313 LDLHYRVVSLCTGDLGF-SACKTY-----DLEVWLAGQNLYREISSCSTCGN  358 (430)
Q Consensus       313 L~lpyRvv~~~sgdlg~-~a~~~~-----DiE~w~P~~~~y~Ev~S~Snc~D  358 (430)
                      |++         .++-+ |+++.|     -+=.|-++..+|.||+...|+.-
T Consensus       384 lg~---------tnlrfKPaynpYtepsmeif~yh~gl~kwvEvgnSg~frP  426 (483)
T KOG2784         384 LGA---------TNLRFKPAYNPYTEPSMEIFSYHHGLFKWVEVGNSGMFRP  426 (483)
T ss_pred             CCC---------CCCCCCCCCCCCCCCEEEEEEECCCCCEEEEECCCCCCCH
T ss_conf             687---------6642269989888863578774056514899768888787


No 212
>pfam10458 Val_tRNA-synt_C Valyl tRNA synthetase tRNA binding arm. This domain is found at the C-terminus of Valyl tRNA synthetases.
Probab=37.54  E-value=30  Score=15.18  Aligned_cols=61  Identities=13%  Similarity=0.206  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999986--44998799999999999998864446666677888774
Q gi|254780680|r   33 LDEKNRILIKKIEDIRARRNSNSAQIGQAI--AEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKK  100 (430)
Q Consensus        33 Ld~~rr~l~~e~e~LraerN~lSKeIg~~k--~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~  100 (430)
                      ++.+...|..+++.+..+...+++..+...  .+.-.+.++.       -++++..++.++..+++.+..
T Consensus         2 ~~~E~~RL~Kel~kl~~~i~~~~~kL~N~~Fv~kAP~~VV~~-------er~kl~~~~~~~~~l~~~L~~   64 (66)
T pfam10458         2 VEKERARLEKELAKLQKEIERLQKKLSNPGFVAKAPAEVVEE-------EKAKLAEYEEQLEKLKERLSQ   64 (66)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHH-------HHHHHHHHHHHHHHHHHHHHH
T ss_conf             798999899999999999999998778767777098999999-------999999999999999999987


No 213
>TIGR02168 SMC_prok_B chromosome segregation protein SMC; InterPro: IPR011890   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . The smc gene is often associated with scpB (IPR005234 from INTERPRO) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle , , .; GO: 0005515 protein binding, 0005524 ATP binding, 0005694 chromosome.
Probab=37.20  E-value=30  Score=15.14  Aligned_cols=19  Identities=11%  Similarity=0.176  Sum_probs=7.9

Q ss_pred             CCCCEEHHHHHCCHHHHHH
Q ss_conf             0320212356202788986
Q gi|254780680|r  190 HGYTEVSAPLLVRDEAMYG  208 (430)
Q Consensus       190 ~Gy~~v~~P~lv~~~~~~g  208 (430)
                      .|-.-+.|.++++.....+
T Consensus       575 ~Gr~~fl~l~~~~~~~~~~  593 (1191)
T TIGR02168       575 LGRVTFLPLDVIKGAEIQG  593 (1191)
T ss_pred             CCEEEEEECCCCCCCCCCC
T ss_conf             8827763025567766777


No 214
>KOG1656 consensus
Probab=37.06  E-value=30  Score=15.13  Aligned_cols=18  Identities=28%  Similarity=0.150  Sum_probs=8.1

Q ss_pred             HHHHHHHHH-HHHHHHHHH
Q ss_conf             466666778-887744310
Q gi|254780680|r   87 LEKEEHEVC-SSLKKLISC  104 (430)
Q Consensus        87 le~~~~~le-~el~~lll~  104 (430)
                      |..++.+++ ++++..++.
T Consensus       162 L~~ELdeLeqeeld~~ll~  180 (221)
T KOG1656         162 LMAELDELEQEELDKELLD  180 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHC
T ss_conf             9999999999988898854


No 215
>PRK04863 mukB cell division protein MukB; Provisional
Probab=36.89  E-value=31  Score=15.11  Aligned_cols=93  Identities=14%  Similarity=0.095  Sum_probs=45.1

Q ss_pred             HCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             51999999999846989588999999999999999999999999999999999864499879999999999999886444
Q gi|254780680|r    8 RQNPEHLDIALKKRHLEPQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPIL   87 (430)
Q Consensus         8 Ren~e~v~~~l~~R~~~~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~l   87 (430)
                      ++....++..+..=|++.+.+.-..+...+.++..++..-|.+++++.|+++...     .+.+.+....++...+....
T Consensus      1032 ~q~l~e~~~el~~lGv~~~~gaE~~a~~~rdeL~~~L~~~r~rr~~le~~l~~~e-----~e~~~l~k~~~k~e~~y~~~ 1106 (1486)
T PRK04863       1032 RELLAELKRELQDLGVPADSGAEERARARRDELHAQLSANRSRRNQLEKQLTFCE-----AEMDNLTKRLRKLERDYTEQ 1106 (1486)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999997599899027989774478899999987889999999999999-----99999999999988778999


Q ss_pred             HHHHHHHHHHHHHHHHHC
Q ss_conf             666667788877443100
Q gi|254780680|r   88 EKEEHEVCSSLKKLISCI  105 (430)
Q Consensus        88 e~~~~~le~el~~lll~I  105 (430)
                      .+........+...+-.+
T Consensus      1107 r~~v~~ak~~w~~Vl~~~ 1124 (1486)
T PRK04863       1107 REQVVAAKAGWCAVLRLA 1124 (1486)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             999998875799999999


No 216
>KOG0432 consensus
Probab=36.51  E-value=31  Score=15.07  Aligned_cols=28  Identities=32%  Similarity=0.355  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEHHHHHCCHH
Q ss_conf             999999999862232032021235620278
Q gi|254780680|r  175 ERALGQFMIDLHTSEHGYTEVSAPLLVRDE  204 (430)
Q Consensus       175 e~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~  204 (430)
                      -.||-+|.+.-. .. =|.+..-|.+-...
T Consensus       742 t~a~~~Fwl~~l-CD-VYlE~~Kp~l~~~~  769 (995)
T KOG0432         742 TSALYAFWLYDL-CD-VYLEATKPLLWGDS  769 (995)
T ss_pred             HHHHHHHHHHHH-HH-HHHHHHHHHHCCCC
T ss_conf             999999999999-89-99998558762893


No 217
>pfam03629 DUF303 Domain of unknown function (DUF303). Distribution of this domain seems limited to prokaryotes and viruses.
Probab=36.48  E-value=14  Score=17.64  Aligned_cols=32  Identities=19%  Similarity=0.456  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCC
Q ss_conf             9999999984106753037801178443402410110100
Q gi|254780680|r  304 SCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAG  343 (430)
Q Consensus       304 ~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~  343 (430)
                      -.+.++.+.|++|-=+|..+-|-..        ||+|+|+
T Consensus         6 ~Fa~~l~~~l~vpIGlI~~a~GGt~--------ie~W~~~   37 (72)
T pfam03629         6 FFARKLQQELNVPIGLIPCAWGGTP--------IEAWMPG   37 (72)
T ss_pred             HHHHHHHHHHCCCEEEEECCCCCCC--------HHHCCCC
T ss_conf             9999999983999899864889966--------7542588


No 218
>COG0782 Uncharacterized conserved protein, YhbC family [Function unknown]
Probab=36.43  E-value=31  Score=15.06  Aligned_cols=79  Identities=22%  Similarity=0.225  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHH
Q ss_conf             99999999999999-99999999999986449987999999999999988644466666778887744310022588112
Q gi|254780680|r   35 EKNRILIKKIEDIR-ARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEV  113 (430)
Q Consensus        35 ~~rr~l~~e~e~Lr-aerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~~V  113 (430)
                      .-++.+..+++.|+ .++..+++.|..+..-|+..+...    -..-|++...++.....+++.+....+-=+-.+..-|
T Consensus         4 ~g~~~l~~el~~l~~~~rp~i~~~i~~ar~~gdl~enae----y~aak~~q~~~e~ri~~le~~l~~a~vi~~~~~~~~V   79 (151)
T COG0782           4 EGFRKLKEELEYLKPVERPEIVEEIADARELGDLSENAE----YRAAKEEQAFIERRIRLLEELLRNAQVIDDEKPPDVV   79 (151)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCHHHCHH----HHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCEE
T ss_conf             277899999997655352269999999997155010835----4789987510177999999886075415877778978


Q ss_pred             HHCC
Q ss_conf             2113
Q gi|254780680|r  114 PIGT  117 (430)
Q Consensus       114 P~G~  117 (430)
                      ..|.
T Consensus        80 ~~Gs   83 (151)
T COG0782          80 TFGS   83 (151)
T ss_pred             ECCC
T ss_conf             4698


No 219
>COG3236 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.37  E-value=3.2  Score=22.43  Aligned_cols=97  Identities=26%  Similarity=0.347  Sum_probs=65.7

Q ss_pred             HHCHHHHHHHHHHHHCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEEC
Q ss_conf             51422476776431000231345411454453420595550420885322107884335543432122221020021212
Q gi|254780680|r  210 GQIPKFADDMFCTTDGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSI  289 (430)
Q Consensus       210 G~lp~f~~~~y~~~d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~  289 (430)
                      |-+..|..--+++....|  ||||+-+.+.-.-+.+++...|--+++-||   .||-+-||++.|-.|.|          
T Consensus        27 gcFSnf~~~~~k~~G~~~--~taEhY~~a~K~~~~~D~~~~~aIlaarsP---~EAkaLGR~vs~~lr~~----------   91 (162)
T COG3236          27 GCFSNFAPWPIKVDGKTW--PTAEHYFQAQKFLEFLDPAYREAILAARSP---MEAKALGRDVSGFLRKN----------   91 (162)
T ss_pred             CCCCCCCCCCEEECCEEC--CCHHHHHHHHHHHHCCCHHHHHHHHHCCCH---HHHHHHCCCCCCCCHHC----------
T ss_conf             521136877554367354--649999999999840798899999960796---89998662002332124----------


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCH--HHHCCCCCHHCC
Q ss_conf             786501457898999999999984106--753037801178
Q gi|254780680|r  290 TREEDSFTEHERMLSCAEEILKRLDLH--YRVVSLCTGDLG  328 (430)
Q Consensus       290 ~~pe~S~~~~e~~~~~~~~i~~~L~lp--yRvv~~~sgdlg  328 (430)
                            |..... .-..+.++....-|  -|-.++.|||.-
T Consensus        92 ------W~~vr~-~V~~ea~~~KF~q~~~LRe~LL~Tgd~v  125 (162)
T COG3236          92 ------WESVRV-QVMREALLAKFLQHADLRELLLATGDAV  125 (162)
T ss_pred             ------HHHHHH-HHHHHHHHHHHCCCHHHHHHHHHCCCEE
T ss_conf             ------677889-9999999999717088999987248726


No 220
>pfam05103 DivIVA DivIVA protein. The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate mini-cells. Inactivation of divIVA produces a mini-cell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype. These proteins appear to contain coiled-coils.
Probab=35.92  E-value=32  Score=15.00  Aligned_cols=42  Identities=14%  Similarity=0.249  Sum_probs=25.4

Q ss_pred             HCCCCCC-HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4698958-899999-99999999999999999999999999998
Q gi|254780680|r   20 KRHLEPQ-SEYILS-LDEKNRILIKKIEDIRARRNSNSAQIGQA   61 (430)
Q Consensus        20 ~R~~~~~-id~il~-Ld~~rr~l~~e~e~LraerN~lSKeIg~~   61 (430)
                      .||++.+ ||.++. +-..+..+..+...|+.+...+..++...
T Consensus        15 ~rGYd~~EVD~FLd~va~e~e~l~~en~~L~~~~~~l~~~l~~~   58 (131)
T pfam05103        15 MRGYDPDEVDEFLDQVIKDYEALYKENEELKEEIERLEEKLEEY   58 (131)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             68999999999999999999999999999999999999999998


No 221
>pfam01496 V_ATPase_I V-type ATPase 116kDa subunit family. This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.
Probab=35.78  E-value=32  Score=14.99  Aligned_cols=15  Identities=13%  Similarity=0.200  Sum_probs=9.1

Q ss_pred             HHHHCCCCEEHHHHH
Q ss_conf             223203202123562
Q gi|254780680|r  186 HTSEHGYTEVSAPLL  200 (430)
Q Consensus       186 ~~~~~Gy~~v~~P~l  200 (430)
                      .+++.||+.+..|..
T Consensus       202 i~~~~~~~~~~~p~~  216 (707)
T pfam01496       202 ILDSFGFELYDVPET  216 (707)
T ss_pred             HHHHCCCEEECCCCC
T ss_conf             999869989448998


No 222
>COG0525 ValS Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=35.65  E-value=32  Score=14.97  Aligned_cols=12  Identities=17%  Similarity=-0.094  Sum_probs=4.9

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             899999999999
Q gi|254780680|r   27 SEYILSLDEKNR   38 (430)
Q Consensus        27 id~il~Ld~~rr   38 (430)
                      -+++++.--+|+
T Consensus       106 Re~Fl~~~weWk  117 (877)
T COG0525         106 REEFLKKCWEWK  117 (877)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 223
>pfam03999 MAP65_ASE1 Microtubule associated protein (MAP65/ASE1 family).
Probab=34.97  E-value=33  Score=14.90  Aligned_cols=33  Identities=24%  Similarity=0.275  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             899999999999999999999999999999999
Q gi|254780680|r   27 SEYILSLDEKNRILIKKIEDIRARRNSNSAQIG   59 (430)
Q Consensus        27 id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg   59 (430)
                      .|.+-+-...+..+...++.+|++.+.++...|
T Consensus        18 ~~~~~es~~~~~~i~~~i~~~~~E~~~L~~~~g   50 (619)
T pfam03999        18 KDLKEESSTKKQAILKDIAVLRAEIKRLSAENG   50 (619)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999999888999999999999999999876304


No 224
>PRK09239 chorismate mutase; Provisional
Probab=34.88  E-value=33  Score=14.89  Aligned_cols=38  Identities=16%  Similarity=0.110  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99999999999999999999999999999999864499
Q gi|254780680|r   29 YILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGN   66 (430)
Q Consensus        29 ~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~   66 (430)
                      ++.+|-.+--.+-.++=.|-++|..++++||.+|++.+
T Consensus        11 ~L~~lR~~ID~iD~~iv~LLa~R~~~~~~Ig~~K~~~~   48 (104)
T PRK09239         11 ELAALRQSIDNIDAALIHMLAERFKCTQAVGVLKAEHG   48 (104)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99999999999999999999999999999999998759


No 225
>pfam05531 NPV_P10 Nucleopolyhedrovirus P10 protein. This family consists of several nucleopolyhedrovirus P10 proteins which are thought to be involved in the morphogenesis of the polyhedra.
Probab=34.77  E-value=33  Score=14.88  Aligned_cols=23  Identities=30%  Similarity=0.489  Sum_probs=10.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRAR   50 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~Lrae   50 (430)
                      +.|.+++.+.-.+|++++.+++.
T Consensus        11 ~dIkavd~KVdalQ~~V~dl~~n   33 (75)
T pfam05531        11 ADIKAVDDKVDALQTQVDDLRAN   33 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             99999987889999999999864


No 226
>pfam05565 Sipho_Gp157 Siphovirus Gp157. This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophages. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage.
Probab=34.69  E-value=33  Score=14.87  Aligned_cols=116  Identities=16%  Similarity=0.266  Sum_probs=62.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCHHHHCCCCC-
Q ss_conf             99999999999999999864499879999999999999886444666667788877443100--225881122113555-
Q gi|254780680|r   44 IEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCI--PNVPLEEVPIGTSAN-  120 (430)
Q Consensus        44 ~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~I--PNi~~~~VP~G~de~-  120 (430)
                      +|.++.+.+.-...|+...+. -..+++.++++.+.+.+..+..+.+...+.+-+...|...  .-+-.+..-++.--+ 
T Consensus        31 Le~i~~~~~~K~~~i~~~ikn-lea~~~~~k~e~krl~erkk~~enk~~~LK~yl~~~m~~~g~~kikt~~~tis~rk~~  109 (162)
T pfam05565        31 LESIEEEFEDKVENIAKVIKN-LEADIEAIKAEIKRLAERKKSIENKVKRLKDYLEEAMEATGIKKIKTPLFTVSIRKSK  109 (162)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCEEEEEECCC
T ss_conf             999999999999999999983-2978999999999999999999989999999999999980986776376799973789


Q ss_pred             CCEEEEEECCCCCCCCC----CC-CCCCHHHHCCCCCHHHHHHHCCCCCE
Q ss_conf             40242000156566566----62-11220221173100011222167530
Q gi|254780680|r  121 ENILIRSVGKKPSAIHL----SR-EHFEIGEALGLMDFDRATKLSGARFS  165 (430)
Q Consensus       121 dNv~i~~~G~~~~f~f~----~k-~H~elge~l~liDfe~a~kvsGsrF~  165 (430)
                      ..|+|..-...|..-+.    |+ |--.|.+.     ...|-.|.|++..
T Consensus       110 ~sv~I~de~~iP~ey~~~~~~~k~DK~~Ik~a-----LK~G~~V~GA~L~  154 (162)
T pfam05565       110 PSVEIEDEAKIPAEYFVEPQTPKPDKKAIKEA-----LKAGEEVPGAELK  154 (162)
T ss_pred             CCEECCCHHHCCHHHHCCCCCCCCCHHHHHHH-----HHCCCCCCCEEEE
T ss_conf             91324895668899850667687899999999-----9879988993885


No 227
>KOG2264 consensus
Probab=34.39  E-value=33  Score=14.83  Aligned_cols=113  Identities=18%  Similarity=0.205  Sum_probs=52.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCC
Q ss_conf             99999999999999999999864499879999999999999886444666667788877443100225881122113555
Q gi|254780680|r   41 IKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSAN  120 (430)
Q Consensus        41 ~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~  120 (430)
                      ..|+-+|+++|-++..+|.+...     .+++++...-.-+.++..|+.+....+-.+.++..  -|-|.-..|..--. 
T Consensus        92 s~EL~ele~krqel~seI~~~n~-----kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~El~~--~n~pkl~LP~sllP-  163 (907)
T KOG2264          92 SLELTELEVKRQELNSEIEEINT-----KIEELKRLIPQKQLELSALKGEIEQAQRQLEELRE--TNNPKLFLPFSLLP-  163 (907)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HCCCCEEECCCCCC-
T ss_conf             79999889888887747999999-----99999988777677899877079999999999986--06984660211275-


Q ss_pred             CCEEEEEECCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCH
Q ss_conf             40242000156566566621122022117310001122216753010564
Q gi|254780680|r  121 ENILIRSVGKKPSAIHLSREHFEIGEALGLMDFDRATKLSGARFSVLTGH  170 (430)
Q Consensus       121 dNv~i~~~G~~~~f~f~~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~  170 (430)
                       ++ +-+--++|+       -..=.+..+.+|..|-+-.||---|++-.|
T Consensus       164 -~~-~pr~l~pp~-------~~~~c~lhncfdySRCsltSgfPVYvyd~D  204 (907)
T KOG2264         164 -LQ-IPRELEPPS-------QISPCQLHNCFDYSRCSLTSGFPVYVYDSD  204 (907)
T ss_pred             -CC-CCCCCCCCC-------CCCCCCCHHCCCCCCCCCCCCCEEEEECCC
T ss_conf             -55-765689844-------557653010025255654578606996565


No 228
>pfam05266 DUF724 Protein of unknown function (DUF724). This family contains several uncharacterized proteins found in Arabidopsis thaliana and other plants. This region is often found associated with Agenet domains and may contain coiled-coil.
Probab=34.08  E-value=34  Score=14.80  Aligned_cols=26  Identities=23%  Similarity=0.285  Sum_probs=10.7

Q ss_pred             HHHHHCCCCCC-----HHHHHHHHHHHHHHH
Q ss_conf             99984698958-----899999999999999
Q gi|254780680|r   16 IALKKRHLEPQ-----SEYILSLDEKNRILI   41 (430)
Q Consensus        16 ~~l~~R~~~~~-----id~il~Ld~~rr~l~   41 (430)
                      ..|..-|+++.     +.+++.+-..+..++
T Consensus        79 ~~LE~hGFdV~~~~sRl~kLL~iK~~~~~~~  109 (190)
T pfam05266        79 SELEKHGFNVQALQSRLNKLLSLKDDQTKKL  109 (190)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999839871759999999998877689999


No 229
>pfam01255 Prenyltransf Putative undecaprenyl diphosphate synthase. Previously known as uncharacterized protein family UPF0015, a single member of this family has been identified as an undecaprenyl diphosphate synthase.
Probab=33.64  E-value=34  Score=14.75  Aligned_cols=85  Identities=18%  Similarity=0.221  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCHHHHCCCCCHHH
Q ss_conf             99999988644466666778887744310022588112211355540242000156566566621122022117310001
Q gi|254780680|r   76 ETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILIRSVGKKPSAIHLSREHFEIGEALGLMDFDR  155 (430)
Q Consensus        76 e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~~~G~~~~f~f~~k~H~elge~l~liDfe~  155 (430)
                      -++.+.++.+.-.-..+++.++.-...+..|++|+||          .+||+-|+.+-.+|-+   |++...-  +-|. 
T Consensus       131 Av~~i~~~~~~~~~~~~~i~~~~i~~~l~~~~~p~~D----------LlIRTsGe~RLSnFll---wQ~ayse--l~F~-  194 (222)
T pfam01255       131 AVKRLAEDVKDGKLSPEDIDEEVIEKYLYTSDLPDPD----------LLIRTSGEKRLSNFLL---WQSAYAE--LYFT-  194 (222)
T ss_pred             HHHHHHHHHHCCCCCHHHCCHHHHHHCCCCCCCCCCC----------EEEECCCCHHCCCCHH---HHHCCCE--EEEC-
T ss_conf             9999999998189992121489998707678999977----------6885488401235202---3104725--9977-


Q ss_pred             HHHHCCCCCEEECCHHHHHHHHHHHHHH
Q ss_conf             1222167530105648899999999999
Q gi|254780680|r  156 ATKLSGARFSVLTGHLAHLERALGQFMI  183 (430)
Q Consensus       156 a~kvsGsrF~~Lkg~~A~Le~ALi~y~l  183 (430)
                           ..=|+=+.  ...|..||..|..
T Consensus       195 -----~~lWPdf~--~~dl~~ai~~y~~  215 (222)
T pfam01255       195 -----DTLWPDFT--KEDLLRAIRDYQS  215 (222)
T ss_pred             -----CCCCCCCC--HHHHHHHHHHHHH
T ss_conf             -----88887699--9999999999975


No 230
>cd00733 GlyRS_alpha_core Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. This alignment contains only sequences from the GlyRS form which heterotetramerizes. The homodimer form of GlyRS is in a different family of class II aaRS. Class II assignment is based upon structure and the presence of three characteristic sequence motifs.
Probab=33.34  E-value=35  Score=14.71  Aligned_cols=80  Identities=24%  Similarity=0.315  Sum_probs=50.4

Q ss_pred             HCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCC--CHHHHHHHHHHHHHHHHHHHCCHHHHCCCC----
Q ss_conf             04208853221078843355434321222210200212127865--014578989999999999841067530378----
Q gi|254780680|r  250 LPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREE--DSFTEHERMLSCAEEILKRLDLHYRVVSLC----  323 (430)
Q Consensus       250 LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe--~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~----  323 (430)
                      -|.+.+=+-||.|.--|-||..---|.+-|||.     ++.+|.  ++-+.       .-+=++.|||..+.-++-    
T Consensus        45 ~pw~~aYvqPsrRP~DgRYG~NPNRlq~y~QfQ-----VilKPsp~n~q~l-------YL~SL~~igid~~~hDIrFveD  112 (279)
T cd00733          45 EPWNVAYVEPSRRPTDGRYGENPNRLQHYYQFQ-----VIIKPSPDNIQEL-------YLESLEALGINPKEHDIRFVED  112 (279)
T ss_pred             CCCEEEEECCCCCCCCCCCCCCCCHHCEEEEEE-----EEECCCCHHHHHH-------HHHHHHHCCCCCCCCCEEEEEC
T ss_conf             863155424677999987778932310003457-----9987895658999-------9998998497954362478614


Q ss_pred             ---CHHCCCHHHEEEEEEEECCCC
Q ss_conf             ---011784434024101101004
Q gi|254780680|r  324 ---TGDLGFSACKTYDLEVWLAGQ  344 (430)
Q Consensus       324 ---sgdlg~~a~~~~DiE~w~P~~  344 (430)
                         |--||+-.   .--|||+-|-
T Consensus       113 nWEsPtLGAwG---lGWEVwldGM  133 (279)
T cd00733         113 NWESPTLGAWG---LGWEVWLDGM  133 (279)
T ss_pred             CCCCCCCCCCC---CCEEEEECCE
T ss_conf             78787531023---4349998775


No 231
>PRK06665 flgK flagellar hook-associated protein FlgK; Validated
Probab=33.33  E-value=35  Score=14.71  Aligned_cols=80  Identities=10%  Similarity=0.172  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC------HHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHC
Q ss_conf             99999999999999999999999999864499------87999999999999988644466---6667788877443100
Q gi|254780680|r   35 EKNRILIKKIEDIRARRNSNSAQIGQAIAEGN------LSLVDALKNETSTLKEQLPILEK---EEHEVCSSLKKLISCI  105 (430)
Q Consensus        35 ~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~------~~~~~~Lk~e~~~Lk~eik~le~---~~~~le~el~~lll~I  105 (430)
                      ..|..+..+.+.|-.+-|.++.++..+...-+      -.++..+.+++.+|.++|...+.   .-..+.++.+.++-.|
T Consensus       139 ~~R~~vl~~a~~L~~~~n~~~~~L~~~~~~~n~~i~~~V~~iN~l~~~Ia~LN~qI~~~~~~g~~~NdLlDqRD~ll~eL  218 (628)
T PRK06665        139 AERQVVLERAQALGERIEDRYRSLERIRDMANDEIEITTEEVNNYLRNIADLNEQIVKSQAMGDNPNDLMDKRDLLVEKL  218 (628)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999999999999999999999999999999972057999247789999999999


Q ss_pred             CCCCCCHHH
Q ss_conf             225881122
Q gi|254780680|r  106 PNVPLEEVP  114 (430)
Q Consensus       106 PNi~~~~VP  114 (430)
                      --+.+=.|-
T Consensus       219 S~~v~i~v~  227 (628)
T PRK06665        219 SNLIDVSIE  227 (628)
T ss_pred             HHHCCEEEE
T ss_conf             866392899


No 232
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=32.82  E-value=35  Score=14.66  Aligned_cols=58  Identities=19%  Similarity=0.319  Sum_probs=26.5

Q ss_pred             HHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCHHHHC-CCCCHHHHHHHCCCCCEEECCHHHHHHHHH
Q ss_conf             1221135554024200015656656662112202211-731000112221675301056488999999
Q gi|254780680|r  112 EVPIGTSANENILIRSVGKKPSAIHLSREHFEIGEAL-GLMDFDRATKLSGARFSVLTGHLAHLERAL  178 (430)
Q Consensus       112 ~VP~G~de~dNv~i~~~G~~~~f~f~~k~H~elge~l-~liDfe~a~kvsGsrF~~Lkg~~A~Le~AL  178 (430)
                      -||+|.+      +...|..+..+   +-=++||... --.+++.|.+.-..|--.|......|+..+
T Consensus        52 lVplg~~------~~v~~~i~~~~---~vlV~iG~g~~vE~~~~~A~~~l~~r~~~l~~~~~~l~~~l  110 (129)
T cd00584          52 LVPLGAG------VFVKAKVKDTD---KVLVDLGTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKEL  110 (129)
T ss_pred             EEECCCC------EEEEEEECCCC---EEEEEECCCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9974897------59999975888---48998679668993499999999999999999999999999


No 233
>cd00769 PheRS_beta_core Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA,  PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer. While the alpha chain contains a catalytic core domain, the beta chain has a non-catalytic core domain.
Probab=32.72  E-value=35  Score=14.64  Aligned_cols=125  Identities=18%  Similarity=0.197  Sum_probs=67.1

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHH----HCCEECCCCCC-HH-HHHHHHHCCC
Q ss_conf             999999999998622320320212356202788986551422476776431----00023134541-14-5445342059
Q gi|254780680|r  173 HLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTT----DGRWLIPTSEV-SL-TNLYSHEIIE  246 (430)
Q Consensus       173 ~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~----d~l~Li~TaEv-pL-~~~~~~~~l~  246 (430)
                      .|++.+-+++    + ..||.|+.+-.|+..+.+...+.-+   ++...+.    +++-..=|+=+ +| -++-.+  +.
T Consensus         4 ~l~~~ir~~L----~-~~Gf~Ev~t~s~~~~~~~~~~~~~~---~~~i~l~NPls~e~~~lR~sLlp~LL~~~~~N--~~   73 (198)
T cd00769           4 KLERKLRRLL----A-GLGFQEVITYSLTSPEEAELFDGGL---DEAVELSNPLSEEYSVLRTSLLPGLLDALARN--LN   73 (198)
T ss_pred             HHHHHHHHHH----H-HCCCCEEEECCCCCHHHHHHHCCCC---CCEEEEECCCCHHHHHHHHHHHHHHHHHHHHH--CC
T ss_conf             9999999999----9-7897141306768989998724887---87389708865668898887799999999865--05


Q ss_pred             HHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCC--------CHHHHHHHHHHHHHHHHHHHCCHHH
Q ss_conf             55504208853221078843355434321222210200212127865--------0145789899999999998410675
Q gi|254780680|r  247 SKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREE--------DSFTEHERMLSCAEEILKRLDLHYR  318 (430)
Q Consensus       247 ~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe--------~S~~~~e~~~~~~~~i~~~L~lpyR  318 (430)
                      ....++++..++++|.++...+          .|-..+-.+ +|...        ....-+..+-...+.+++.|+++..
T Consensus        74 r~~~~~~lFEiG~vy~~~~~~~----------~E~~~l~~~-~~g~~~~~~~~~~~~~~df~~lKg~v~~ll~~l~~~~~  142 (198)
T cd00769          74 RKNKPLRLFEIGRVFLKDEDGP----------EEEEHLAAL-LSGNREPESWQGKGRPVDFYDAKGILEALLRALGIIVE  142 (198)
T ss_pred             CCCCCCEEEEEEEEEECCCCCC----------CCCEEEEEE-EECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCE
T ss_conf             6777732899763896688876----------423057888-86677755645577767999999999999998099851


No 234
>pfam06673 L_lactis_ph-MCP Lactococcus lactis bacteriophage major capsid protein. This family consists of several Lactococcus lactis bacteriophage major capsid proteins.
Probab=32.36  E-value=36  Score=14.60  Aligned_cols=59  Identities=14%  Similarity=0.182  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999864499879999999999999886444666
Q gi|254780680|r   30 ILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKE   90 (430)
Q Consensus        30 il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~   90 (430)
                      .++.--+.|++..++++|..+|.++.|+-..-....++++++  ++=+++|.++..++-++
T Consensus        13 aieagvkvreleakveelnkereelkkereanipsekpedae--rkfmrelgdkmaempeq   71 (347)
T pfam06673        13 AIEAGVKVRELEAKVEELNKEREELKKEREANIPSEKPEDAE--RKFMRELGDKMAEMPEQ   71 (347)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHH--HHHHHHHHHHHHHCCHH
T ss_conf             997162067889889998777999877664389988942689--99999986887637234


No 235
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=32.32  E-value=36  Score=14.60  Aligned_cols=65  Identities=17%  Similarity=0.147  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-----------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999986449-----------------------9879999999999999886444666667
Q gi|254780680|r   37 NRILIKKIEDIRARRNSNSAQIGQAIAEG-----------------------NLSLVDALKNETSTLKEQLPILEKEEHE   93 (430)
Q Consensus        37 rr~l~~e~e~LraerN~lSKeIg~~k~~~-----------------------~~~~~~~Lk~e~~~Lk~eik~le~~~~~   93 (430)
                      |++-..+++.++.+|++.-++.+...+..                       ...+..++..+...+..+...|..+...
T Consensus        57 RkqY~e~I~~AKk~Rke~kr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~L~~e~~~L~~~~~~  136 (162)
T PRK13923         57 RKQYYEQIKLAKKERKELRKQLGQHPSNLEDNLKTGDEIITSGISDLTLEDVLSEQLGKLQEELEKLSWENQTLKQELSM  136 (162)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999987521353233442234300012220011688999999999999999999999999999999


Q ss_pred             HHHHHHHH
Q ss_conf             78887744
Q gi|254780680|r   94 VCSSLKKL  101 (430)
Q Consensus        94 le~el~~l  101 (430)
                      ++++...+
T Consensus       137 ~~edy~~L  144 (162)
T PRK13923        137 TEEDYRAL  144 (162)
T ss_pred             HHHHHHHH
T ss_conf             99999999


No 236
>PRK06945 flgK flagellar hook-associated protein FlgK; Validated
Probab=32.30  E-value=36  Score=14.60  Aligned_cols=80  Identities=11%  Similarity=0.157  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC------HHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHC
Q ss_conf             9999999999999999999999999864499------879999999999999886444666----667788877443100
Q gi|254780680|r   36 KNRILIKKIEDIRARRNSNSAQIGQAIAEGN------LSLVDALKNETSTLKEQLPILEKE----EHEVCSSLKKLISCI  105 (430)
Q Consensus        36 ~rr~l~~e~e~LraerN~lSKeIg~~k~~~~------~~~~~~Lk~e~~~Lk~eik~le~~----~~~le~el~~lll~I  105 (430)
                      .|..+....+.|-..-|.++.++..+...-+      -.++..+..++..|..+|...+..    -..+.++.+.++-.|
T Consensus       129 ~R~~~~~~a~~L~~~~~~~~~~l~~~~~~~~~~i~~~V~~iN~l~~~Ia~LN~qI~~~~~~~g~~~NdL~DqRD~ll~eL  208 (649)
T PRK06945        129 ARQTALSNAQALASQFNAAGQQYDQLRQGVNTQLTSTVTQINSYTKQIAQLNQQIAKAESSQGQPPNDLLDQRDLAVSNL  208 (649)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999999999999999999999999999999975568999268999999999999


Q ss_pred             CCCCCCHHHH
Q ss_conf             2258811221
Q gi|254780680|r  106 PNVPLEEVPI  115 (430)
Q Consensus       106 PNi~~~~VP~  115 (430)
                      -.+.+=.|=.
T Consensus       209 S~~i~i~v~~  218 (649)
T PRK06945        209 SKLVGVQVVQ  218 (649)
T ss_pred             HHHCCEEEEE
T ss_conf             8661959997


No 237
>KOG1962 consensus
Probab=32.29  E-value=36  Score=14.60  Aligned_cols=36  Identities=19%  Similarity=0.181  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999999999999886444666667788877443100
Q gi|254780680|r   70 VDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCI  105 (430)
Q Consensus        70 ~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~I  105 (430)
                      .++++++...+++++.+...+++..+++..++.-..
T Consensus       153 ~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~  188 (216)
T KOG1962         153 NDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQS  188 (216)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             788776678899999987778888877799999999


No 238
>pfam02991 MAP1_LC3 Microtubule associated protein 1A/1B, light chain 3. Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity.
Probab=32.01  E-value=36  Score=14.56  Aligned_cols=56  Identities=20%  Similarity=0.281  Sum_probs=34.4

Q ss_pred             CCEEEEEEECCCCCHH---HHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCE
Q ss_conf             8332375310210076---45326847338998410104200432289999999988346899838
Q gi|254780680|r  345 NLYREISSCSTCGNFQ---SRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAILENYLNADGSV  407 (430)
Q Consensus       345 ~~y~Ev~S~Snc~D~Q---srRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ailEn~q~~dg~i  407 (430)
                      ++|. |.+-...+.|+   -+||++    ... +.=|.. +|++...+..+|..|-|.|.++||=.
T Consensus        35 ~KfL-VP~dlt~~qf~~vIRkrl~l----~~~-~alflf-v~~~lp~~s~~i~~lY~~~KdeDGFL   93 (104)
T pfam02991        35 KKYL-VPADLTVGQFIYIIRKRIQL----RPE-KAIFLF-VNNTLPPTSATMSALYEEEKDEDGFL   93 (104)
T ss_pred             CEEE-ECCCCCHHHHHHHHHHHCCC----CCC-CEEEEE-ECCCCCCCCCHHHHHHHHCCCCCCEE
T ss_conf             4687-25986788999999986079----967-449999-98875774047999999807999679


No 239
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=31.98  E-value=36  Score=14.56  Aligned_cols=28  Identities=21%  Similarity=0.406  Sum_probs=11.9

Q ss_pred             CCHHHHHHHCCCCCEEECCHHHHHHHHH
Q ss_conf             1000112221675301056488999999
Q gi|254780680|r  151 MDFDRATKLSGARFSVLTGHLAHLERAL  178 (430)
Q Consensus       151 iDfe~a~kvsGsrF~~Lkg~~A~Le~AL  178 (430)
                      .+.+.|.+.--.|--.|......|+..+
T Consensus        83 ~~~~eA~~~~~~r~~~l~~~~~~l~~~~  110 (129)
T cd00890          83 KSLEEAIEFLKKRLETLEKQIEKLEKQL  110 (129)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             5799999999999999999999999999


No 240
>pfam07926 TPR_MLP1_2 TPR/MLP1/MLP2-like protein. The sequences featured in this family are similar to a region of human TPR protein and to yeast myosin-like proteins 1 (MLP1) and 2 (MLP2). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores. TPR is thought to be a component of nuclear pore complex- attached intra-nuclear filaments, and is implicated in nuclear protein import. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerization of kinase domains or by targeting these kinases to the nuclear pore complex. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity.
Probab=31.79  E-value=37  Score=14.54  Aligned_cols=19  Identities=21%  Similarity=0.298  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999986
Q gi|254780680|r   44 IEDIRARRNSNSAQIGQAI   62 (430)
Q Consensus        44 ~e~LraerN~lSKeIg~~k   62 (430)
                      +..+|.+.+.+.+++..++
T Consensus        61 L~~lr~e~~~~~~e~~~Lk   79 (132)
T pfam07926        61 LQALRKQLNELKKEIAQLK   79 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999


No 241
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=31.56  E-value=37  Score=14.51  Aligned_cols=24  Identities=21%  Similarity=0.376  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCEEC
Q ss_conf             228999999998834689983865
Q gi|254780680|r  386 GVAVGRCLIAILENYLNADGSVTI  409 (430)
Q Consensus       386 ~~A~~R~l~ailEn~q~~dg~i~i  409 (430)
                      +.-..|-|+-=+|.--+--|.|+|
T Consensus       478 ~~~la~~Ia~~Ie~el~yPG~Ikv  501 (514)
T TIGR03319       478 AVVLARDIAKKIEEELEYPGQIKV  501 (514)
T ss_pred             HHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             999999999999974859981699


No 242
>pfam06273 eIF-4B Plant specific eukaryotic initiation factor 4B. This family consists of several plant specific eukaryotic initiation factor 4B proteins.
Probab=31.46  E-value=37  Score=14.50  Aligned_cols=10  Identities=20%  Similarity=0.458  Sum_probs=4.0

Q ss_pred             HHHCCCCCCC
Q ss_conf             3100225881
Q gi|254780680|r  102 ISCIPNVPLE  111 (430)
Q Consensus       102 ll~IPNi~~~  111 (430)
                      |+.||-=|-.
T Consensus        89 m~~LPTGPRe   98 (430)
T pfam06273        89 LMQLPTGPRQ   98 (430)
T ss_pred             HCCCCCCCCC
T ss_conf             5037888633


No 243
>PRK11530 hypothetical protein; Provisional
Probab=30.99  E-value=17  Score=17.04  Aligned_cols=43  Identities=21%  Similarity=0.366  Sum_probs=28.6

Q ss_pred             CCCCCCHHHHHHHHHCCC---------HHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEE
Q ss_conf             134541145445342059---------555042088532210788433554343212222102
Q gi|254780680|r  229 IPTSEVSLTNLYSHEIIE---------SKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFW  282 (430)
Q Consensus       229 i~TaEvpL~~~~~~~~l~---------~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~  282 (430)
                      -||++-|+++-..++.|.         +-+.|+++.|++|           |--|-.|||+-.
T Consensus       121 d~tsg~pl~~~~qsq~i~ap~sllp~S~~~i~L~L~GitP-----------~qLGfVRvHdiq  172 (176)
T PRK11530        121 QGTTGNPQEVNVQSQLINAPASLLAPSDVDIPLQLKGITP-----------DQLGFVRIHDIQ  172 (176)
T ss_pred             CCCCCCCCCCCCCCEEECCCCCCCCCCCCEEEEEECCCCH-----------HHEEEEEEECCE
T ss_conf             6777884312001202506777599765425889778895-----------660159974114


No 244
>COG1422 Predicted membrane protein [Function unknown]
Probab=30.88  E-value=38  Score=14.43  Aligned_cols=49  Identities=12%  Similarity=0.217  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999998644998799999999999
Q gi|254780680|r   31 LSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETST   79 (430)
Q Consensus        31 l~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~   79 (430)
                      +.+-.+.---+.+.+++|.+-.+..+++.++.++++....++|.++-.+
T Consensus        61 ~~i~~~~liD~ekm~~~qk~m~efq~e~~eA~~~~d~~~lkkLq~~qme  109 (201)
T COG1422          61 ITILQKLLIDQEKMKELQKMMKEFQKEFREAQESGDMKKLKKLQEKQME  109 (201)
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf             9999999602999999999999999999999980889999999999999


No 245
>COG4573 GatZ Predicted tagatose 6-phosphate kinase [Carbohydrate transport and metabolism]
Probab=30.56  E-value=17  Score=16.92  Aligned_cols=57  Identities=23%  Similarity=0.322  Sum_probs=37.2

Q ss_pred             CCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCC-CCCCEE
Q ss_conf             2100764532684733899841010420043228999999998834689983865822231-018801
Q gi|254780680|r  355 TCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAILENYLNADGSVTIPTVLRP-YMNNLA  421 (430)
Q Consensus       355 nc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~p-ym~g~~  421 (430)
                      .-+|+-.+||.++|..++--  .|-++-       ||+..|.=.-.++-|| +.||+.|.. ||+.+-
T Consensus       334 Y~g~~~~~rl~r~ySySDRi--RYYWp~-------p~~~~ave~L~~nL~~-~~IPl~LisQylp~~~  391 (426)
T COG4573         334 YHGDANAQRLARHYSYSDRI--RYYWPH-------PRIAAAVETLMANLDG-VDIPLPLISQYLPRQY  391 (426)
T ss_pred             CCCCHHHHHHHHHCCHHCCC--EEECCC-------HHHHHHHHHHHHHCCC-CCCCHHHHHHHHHHHH
T ss_conf             58868999998742620020--000787-------7899999999986479-9787678998841678


No 246
>pfam02091 tRNA-synt_2e Glycyl-tRNA synthetase alpha subunit.
Probab=30.50  E-value=38  Score=14.39  Aligned_cols=79  Identities=24%  Similarity=0.286  Sum_probs=49.5

Q ss_pred             CCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCC--CHHHHHHHHHHHHHHHHHHHCCHHHHCCC------
Q ss_conf             4208853221078843355434321222210200212127865--01457898999999999984106753037------
Q gi|254780680|r  251 PLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREE--DSFTEHERMLSCAEEILKRLDLHYRVVSL------  322 (430)
Q Consensus       251 Pik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe--~S~~~~e~~~~~~~~i~~~L~lpyRvv~~------  322 (430)
                      |.+.+=+-||.|.--|-||..---|.+-|||.     ++.+|.  ++-+.       .-+=++.|||....-++      
T Consensus        45 pw~~aYvqPsrRP~DgRYGenPnRlq~y~QfQ-----Vi~KPsp~n~q~l-------YL~SL~~lgid~~~hDIrFveDn  112 (284)
T pfam02091        45 PWNVAYVEPSRRPTDGRYGENPNRLQHYYQFQ-----VILKPSPDNIQEL-------YLGSLKALGIDPLDHDIRFVEDN  112 (284)
T ss_pred             CCEEEEECCCCCCCCCCCCCCCCHHHHHEEEE-----EEECCCCHHHHHH-------HHHHHHHCCCCCCCCCEEEEECC
T ss_conf             64155424677999987778920420022357-----8977894668999-------99989983979543624786147


Q ss_pred             -CCHHCCCHHHEEEEEEEECCCC
Q ss_conf             -8011784434024101101004
Q gi|254780680|r  323 -CTGDLGFSACKTYDLEVWLAGQ  344 (430)
Q Consensus       323 -~sgdlg~~a~~~~DiE~w~P~~  344 (430)
                       -|--||+-.   .--|||+-|-
T Consensus       113 WEsPtLGAwG---lGWEVwldGM  132 (284)
T pfam02091       113 WESPTLGAWG---LGWEVWLDGM  132 (284)
T ss_pred             CCCCCCCCCC---CCEEEEECCE
T ss_conf             8787531023---4339998775


No 247
>COG3167 PilO Tfp pilus assembly protein PilO [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=30.38  E-value=38  Score=14.37  Aligned_cols=26  Identities=19%  Similarity=0.259  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             64446666677888774431002258
Q gi|254780680|r   84 LPILEKEEHEVCSSLKKLISCIPNVP  109 (430)
Q Consensus        84 ik~le~~~~~le~el~~lll~IPNi~  109 (430)
                      +..+.+++.++++.+..++.++||-.
T Consensus        75 L~~lr~Ql~emee~~~~llrQLPs~t  100 (211)
T COG3167          75 LEALRAQLAEMEERFDILLRQLPSDT  100 (211)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             59999999999999999998588621


No 248
>pfam05667 DUF812 Protein of unknown function (DUF812). This family consists of several eukaryotic proteins of unknown function.
Probab=30.31  E-value=39  Score=14.37  Aligned_cols=20  Identities=15%  Similarity=-0.006  Sum_probs=10.3

Q ss_pred             HHHHHHHHHCHHHHHHHHHH
Q ss_conf             78898655142247677643
Q gi|254780680|r  203 DEAMYGTGQIPKFADDMFCT  222 (430)
Q Consensus       203 ~~~~~gtG~lp~f~~~~y~~  222 (430)
                      .-+++=+|..-|-+++++++
T Consensus       433 ~RIlEIikNIrKQk~dI~KI  452 (536)
T pfam05667       433 RRILEIIKNIKKQKEDIDKI  452 (536)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             99999998899879999999


No 249
>pfam03954 Lectin_N Hepatic lectin, N-terminal domain.
Probab=30.24  E-value=39  Score=14.36  Aligned_cols=59  Identities=19%  Similarity=0.275  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999998644998799999999999998864446666677888774
Q gi|254780680|r   34 DEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKK  100 (430)
Q Consensus        34 d~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~  100 (430)
                      -.++-+++.++..||..--..|..        -..++..+...+..+.++++.+|.++++.+.++.+
T Consensus        54 gSQnsqlq~dL~tLretfsNfts~--------t~~evqaL~sqGgs~~~kv~sleaklEk~qqdl~a  112 (138)
T pfam03954        54 GSQNSQLQEELRTLRETFSNFTSS--------TLAEVQALSTQGGSVGRKMTSLESKLEKQQQDLKA  112 (138)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCHH--------HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             373299999999999987314398--------99999999972552888999999999999999851


No 250
>KOG4797 consensus
Probab=29.96  E-value=39  Score=14.33  Aligned_cols=26  Identities=31%  Similarity=0.424  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998864446666677888
Q gi|254780680|r   72 ALKNETSTLKEQLPILEKEEHEVCSS   97 (430)
Q Consensus        72 ~Lk~e~~~Lk~eik~le~~~~~le~e   97 (430)
                      ..++++..||++|.+|++....++.+
T Consensus        64 AVREEVe~Lk~qI~eL~er~~~Le~E   89 (123)
T KOG4797          64 AVREEVEVLKEQIRELEERNSALERE   89 (123)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999998


No 251
>TIGR02249 integrase_gron integron integrase; InterPro: IPR011946    Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family that also includes recombinases XerC (IPR011931 from INTERPRO) and XerD (IPR011932 from INTERPRO), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration.
Probab=29.92  E-value=33  Score=14.90  Aligned_cols=53  Identities=34%  Similarity=0.385  Sum_probs=33.8

Q ss_pred             CCCHHHHH------HHCCCCCEEECCHHH-----HHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHH
Q ss_conf             31000112------221675301056488-----99999999999862232032021235620278
Q gi|254780680|r  150 LMDFDRAT------KLSGARFSVLTGHLA-----HLERALGQFMIDLHTSEHGYTEVSAPLLVRDE  204 (430)
Q Consensus       150 liDfe~a~------kvsGsrF~~Lkg~~A-----~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~  204 (430)
                      -|||+++.      |=.-.|-+.|=.+++     .+++|..=|.-|. .. .||--|.-|+-..+.
T Consensus       146 DiDF~~~~I~vr~GKG~KdR~v~Lp~~L~~~L~~q~~~~~~~h~~Dl-~~-~G~g~V~LP~AL~rK  209 (320)
T TIGR02249       146 DIDFDYGEIRVRDGKGGKDRVVTLPKSLAPPLREQLERARALHEKDL-LA-EGYGGVYLPHALARK  209 (320)
T ss_pred             EEEECCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH-HC-CCCCCEEHHHHHHCC
T ss_conf             03433766899736689886126817557999999999999999864-05-885301004554215


No 252
>pfam10359 Fmp27_WPPW RNA pol II promoter Fmp27 protein domain. Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.
Probab=29.90  E-value=39  Score=14.32  Aligned_cols=63  Identities=13%  Similarity=0.303  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999986449987999999999999988644466666778887744
Q gi|254780680|r   35 EKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKL  101 (430)
Q Consensus        35 ~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~l  101 (430)
                      -+.+-+...+..|+++.+.....|+.+.....    +.++.+.+.+..++..|.+.+.-++..+..+
T Consensus       161 vQ~~Li~~Rl~~L~~qi~~~~~~i~~~~~~~~----~~~~~~~~~~~~~~~~L~~~~~~l~~~l~~l  223 (470)
T pfam10359       161 VQRELLRERLKQLEEQIKKLEEKLGDLELNDD----EELQSDLEELEKELSVLKERLEFLEKLLEDL  223 (470)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999998865433303676----6788999999999999999999999999975


No 253
>KOG0556 consensus
Probab=29.69  E-value=19  Score=16.70  Aligned_cols=77  Identities=17%  Similarity=0.329  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCH--HHHHHHHHHHH-CCEECCCCCCHHHHHHHHHCCCHHH
Q ss_conf             99999999999862232032021235620278898655142--24767764310-0023134541145445342059555
Q gi|254780680|r  173 HLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIP--KFADDMFCTTD-GRWLIPTSEVSLTNLYSHEIIESKS  249 (430)
Q Consensus       173 ~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp--~f~~~~y~~~d-~l~Li~TaEvpL~~~~~~~~l~~~~  249 (430)
                      +++-...+++-++ +..+||+++.+|-|+-..+--|+.-+.  -|+...|.... .|             |....|-. +
T Consensus       229 riq~gvc~~FRe~-L~~kgF~EIhTpKli~asSEGGanvF~v~Yfk~~A~LAQSPQL-------------yKQMaI~g-d  293 (533)
T KOG0556         229 RIQAGVCFAFREY-LRSKGFVEIHTPKLIGASSEGGANVFRVSYFKQKAYLAQSPQL-------------YKQMAICG-D  293 (533)
T ss_pred             EHHHHHHHHHHHH-HHHCCCCEECCCCCCCCCCCCCCEEEEEEECCCCCHHHCCHHH-------------HHHHHHHC-C
T ss_conf             0688899999999-9756860432632014667777226899860675032058588-------------87788760-6


Q ss_pred             HCCEEEEEECCCCCCC
Q ss_conf             0420885322107884
Q gi|254780680|r  250 LPLRFTTLAPSFRSEA  265 (430)
Q Consensus       250 LPik~~~~s~cfR~Ea  265 (430)
                      + -|...++|-||+|-
T Consensus       294 f-~rVyeIGpVfRAEd  308 (533)
T KOG0556         294 F-ERVYEIGPVFRAED  308 (533)
T ss_pred             H-HHEEEECCEEECCC
T ss_conf             1-10465235566044


No 254
>COG4864 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.67  E-value=19  Score=16.73  Aligned_cols=33  Identities=27%  Similarity=0.247  Sum_probs=15.4

Q ss_pred             CCCCCCHHHHCCCCCHHHHHH--HCCCCCEEECCH
Q ss_conf             621122022117310001122--216753010564
Q gi|254780680|r  138 SREHFEIGEALGLMDFDRATK--LSGARFSVLTGH  170 (430)
Q Consensus       138 ~k~H~elge~l~liDfe~a~k--vsGsrF~~Lkg~  170 (430)
                      .++|-+..|.-+.+.-.--.|  -+|.-|-.|.=+
T Consensus       185 s~~h~~vlenpd~isktvl~kgld~gtafeilsid  219 (328)
T COG4864         185 SDEHTKVLENPDSISKTVLEKGLDSGTAFEILSID  219 (328)
T ss_pred             CCCHHHHHCCCCHHHHHHHHCCCCCCCEEEEEEEE
T ss_conf             74144675092277799997067878416999864


No 255
>pfam09798 LCD1 DNA damage checkpoint protein. This is a family of proteins which regulate checkpoint kinases. In Schizosaccharomyces pombe this protein is called Rad26 and in Saccharomyces cerevisiae it is called LCD1.
Probab=29.53  E-value=40  Score=14.27  Aligned_cols=40  Identities=18%  Similarity=0.169  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             8799999999999998864446666677888774431002
Q gi|254780680|r   67 LSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIP  106 (430)
Q Consensus        67 ~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IP  106 (430)
                      +.+.+.|+.++..+.++-|=+..+.+.+...-.......|
T Consensus        32 ~~el~~Lk~~vq~LEDEkKFL~nE~r~ls~~~~r~~~~~~   71 (648)
T pfam09798        32 DQELQKLKQELQSLEDERKFLVLEQRGLSANDLRTELSPP   71 (648)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             9999999999999888899998899875346542015664


No 256
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=29.42  E-value=40  Score=14.26  Aligned_cols=35  Identities=20%  Similarity=0.243  Sum_probs=14.5

Q ss_pred             HHHCCEEE-EEECCCCCCCCCCC--CCCCCEEEEEEEEE
Q ss_conf             55042088-53221078843355--43432122221020
Q gi|254780680|r  248 KSLPLRFT-TLAPSFRSEAGSAG--RDTRGMLRQHQFWK  283 (430)
Q Consensus       248 ~~LPik~~-~~s~cfR~EaGs~G--kdtrGl~RvHQF~K  283 (430)
                      ..||=++- -+.-||=--+ +||  ...|+.+|..-.+.
T Consensus       251 a~LPN~~~~dlkgC~V~gs-ayGDlSSER~~vRte~lSC  288 (474)
T PRK13729        251 VEMPNSKTYDLTGCFVGLE-AWGDVSSERAIVRTRNISC  288 (474)
T ss_pred             CCCCCCCCCCCCCCEEEEE-EECCCCCCEEEEEEEEEEE
T ss_conf             4079875056676389888-8614432010466424786


No 257
>KOG3433 consensus
Probab=29.17  E-value=40  Score=14.23  Aligned_cols=39  Identities=15%  Similarity=0.035  Sum_probs=25.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             588999999999999999999999999999999999864
Q gi|254780680|r   25 PQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIA   63 (430)
Q Consensus        25 ~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~   63 (430)
                      +-.+.+.+.-..+.+|..+++..+.+...+.+.|-+.+.
T Consensus        71 fps~a~~~~ks~~qeLe~~L~~~~qk~~tl~e~~en~K~  109 (203)
T KOG3433          71 FPSEAICDRKSVLQELESQLATGSQKKATLGESIENRKA  109 (203)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             632778779999999999998742667689989999986


No 258
>pfam01841 Transglut_core Transglutaminase-like superfamily. This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease.
Probab=28.95  E-value=38  Score=14.44  Aligned_cols=49  Identities=20%  Similarity=0.096  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHHHCCHHHHCCC--CCHHCCCHHHEEEEEEEECCCCCCEEE
Q ss_conf             98999999999984106753037--801178443402410110100483323
Q gi|254780680|r  300 ERMLSCAEEILKRLDLHYRVVSL--CTGDLGFSACKTYDLEVWLAGQNLYRE  349 (430)
Q Consensus       300 e~~~~~~~~i~~~L~lpyRvv~~--~sgdlg~~a~~~~DiE~w~P~~~~y~E  349 (430)
                      +++-.....++..+|||.|+|.=  ++.+-+....---=.|+|+|+. .|.-
T Consensus        55 ~~~A~l~~~l~R~~GIpaR~v~G~~~~~~~~~~~~~HaW~ev~~~~~-gW~~  105 (108)
T pfam01841        55 GDFASLFVALLRALGIPARYVTGYLRGPDTVRNGDAHAWVEVYLPGY-GWVP  105 (108)
T ss_pred             CCCHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCEEEEEEEECCC-CEEE
T ss_conf             23387999999986997699997726998788897179999997899-4897


No 259
>PRK06746 peptide chain release factor 2; Provisional
Probab=28.51  E-value=41  Score=14.15  Aligned_cols=19  Identities=5%  Similarity=0.251  Sum_probs=11.8

Q ss_pred             CCCHHHHHCCHHHHHHHHHH
Q ss_conf             98844785199999999984
Q gi|254780680|r    1 MLDIQWIRQNPEHLDIALKK   20 (430)
Q Consensus         1 MLDik~IRen~e~v~~~l~~   20 (430)
                      |+|..|. +||+..++-++.
T Consensus         1 M~~p~fW-dD~~~A~~i~kE   19 (326)
T PRK06746          1 MMGAGFW-DDQQGAQAVINE   19 (326)
T ss_pred             CCCCCCC-CCHHHHHHHHHH
T ss_conf             9897778-699999999999


No 260
>pfam07889 DUF1664 Protein of unknown function (DUF1664). The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=28.47  E-value=41  Score=14.15  Aligned_cols=61  Identities=11%  Similarity=0.269  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999---9999999999986449987999999999999988644466666778887744
Q gi|254780680|r   33 LDEKNRILIKKIEDIRA---RRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKL  101 (430)
Q Consensus        33 Ld~~rr~l~~e~e~Lra---erN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~l  101 (430)
                      +...+|.|-++++.+-.   +.+++|+.|.        +++.+++.....+..+++.+......++.++..+
T Consensus        59 l~~tKrhLsqRI~~vd~kld~~~eis~~i~--------~eV~e~~~~~~~i~~D~~~v~~~v~~Le~Ki~~i  122 (126)
T pfam07889        59 IAATKKHLSQRIDNLDDKLDEQKEISESTR--------DEVTEIREDLSNIGEDVKSVQQAVEGLEGKLDSI  122 (126)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999988735321999999999999--------9999999649988769999999999899999888


No 261
>PRK00106 hypothetical protein; Provisional
Probab=28.37  E-value=41  Score=14.14  Aligned_cols=50  Identities=16%  Similarity=0.151  Sum_probs=25.0

Q ss_pred             ECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEEC
Q ss_conf             102100764532684733899841010420043228999999998834689983865
Q gi|254780680|r  353 CSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAILENYLNADGSVTI  409 (430)
Q Consensus       353 ~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ailEn~q~~dg~i~i  409 (430)
                      ++.|--.||-|= +|.--...+-    .  ..-+.-..|-|+.=+|+--+--|.|+|
T Consensus       473 V~kayAiQAGRE-iRViV~p~~v----~--D~~~~~la~~Ia~kIe~el~yPG~IkV  522 (535)
T PRK00106        473 VQNSFALQAGRE-IRIMVQPEKI----S--DDQVTILSHKVREKIENNLDYPGNIKV  522 (535)
T ss_pred             HHHHHHHHCCCE-EEEEECCCCC----C--HHHHHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             788888744976-9998687867----8--688999999999999974859981599


No 262
>TIGR01320 mal_quin_oxido malate:quinone-oxidoreductase; InterPro: IPR006231   The membrane-associated enzyme, malate:quinone-oxidoreductase, is an alternative to the better-known NAD-dependent malate dehydrogenase as part of the TCA cycle. The reduction of a quinone rather than NAD+ makes the reaction essentially irreversible in the direction of malate oxidation to oxaloacetate. Both forms of malate dehydrogenase are active in E. coli; disruption of this form causes less phenotypic change. In some bacteria, this form is the only or the more important malate dehydrogenase . ; GO: 0008924 malate dehydrogenase (acceptor) activity, 0006099 tricarboxylic acid cycle.
Probab=28.10  E-value=25  Score=15.76  Aligned_cols=65  Identities=31%  Similarity=0.454  Sum_probs=32.3

Q ss_pred             CCCEEHHHHHC------CHHHHHH--HHHCHHHH-----HHHHHH--HHCCE--E-CCCCCCHHHHHHHHHCCCHHHHCC
Q ss_conf             32021235620------2788986--55142247-----677643--10002--3-134541145445342059555042
Q gi|254780680|r  191 GYTEVSAPLLV------RDEAMYG--TGQIPKFA-----DDMFCT--TDGRW--L-IPTSEVSLTNLYSHEIIESKSLPL  252 (430)
Q Consensus       191 Gy~~v~~P~lv------~~~~~~g--tG~lp~f~-----~~~y~~--~d~l~--L-i~TaEvpL~~~~~~~~l~~~~LPi  252 (430)
                      |==|+++|+|=      ++..|+|  .|+-|||=     -|+++.  .|+++  | +|..|.+||.|--.++....  |-
T Consensus       289 GAPPmSvpHLDtR~v~Gk~~LlFGPYAGf~~kFLk~Gs~~DLP~SirpDNl~s~L~va~~~~~Lt~YLi~~l~~~~--~~  366 (487)
T TIGR01320       289 GAPPMSVPHLDTRVVDGKKSLLFGPYAGFSPKFLKHGSLLDLPLSIRPDNLLSMLGVALAEMDLTKYLIGELRKSK--EE  366 (487)
T ss_pred             CCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCHHCCCCHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCH--HH
T ss_conf             6488875400010255711210157788883120176312065432676512378887752047888998760693--57


Q ss_pred             EEEEE
Q ss_conf             08853
Q gi|254780680|r  253 RFTTL  257 (430)
Q Consensus       253 k~~~~  257 (430)
                      |+.|.
T Consensus       367 R~~AL  371 (487)
T TIGR01320       367 RLEAL  371 (487)
T ss_pred             HHHHH
T ss_conf             89999


No 263
>TIGR03414 ABC_choline_bnd choline ABC transporter, periplasmic binding protein. Partial phylogenetic profiling (PMID:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins.
Probab=28.07  E-value=29  Score=15.26  Aligned_cols=35  Identities=20%  Similarity=0.233  Sum_probs=17.9

Q ss_pred             CCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCC
Q ss_conf             0023134541145445342059555042088532210
Q gi|254780680|r  225 GRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSF  261 (430)
Q Consensus       225 ~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cf  261 (430)
                      ++.|+..|+-.+.+=....+ ...+ |+-+.+++|.+
T Consensus       149 ~~~l~~~S~aam~a~l~~A~-~~~e-piv~~~W~Phw  183 (290)
T TIGR03414       149 GFKLVESSEAGMLAQVARAV-KRKE-WVVFLGWEPHP  183 (290)
T ss_pred             CCEECCCCHHHHHHHHHHHH-HCCC-CEEEEECCCCH
T ss_conf             70213688899999999999-8699-98998237754


No 264
>pfam04582 Reo_sigmaC Reovirus sigma C capsid protein.
Probab=27.91  E-value=42  Score=14.08  Aligned_cols=59  Identities=15%  Similarity=0.111  Sum_probs=27.9

Q ss_pred             CHHHHHCCHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             84478519999999998469895--889999999999999999999999999999999998
Q gi|254780680|r    3 DIQWIRQNPEHLDIALKKRHLEP--QSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQA   61 (430)
Q Consensus         3 Dik~IRen~e~v~~~l~~R~~~~--~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~   61 (430)
                      |+--||+....++.....=...+  -...+-.|......+...+.++..+-+.++..+..+
T Consensus        29 DL~~i~erL~aLes~~~sL~~sv~~lss~~S~Lss~L~dl~~sl~~~t~~L~slss~v~~l   89 (326)
T pfam04582        29 DLTPIYERLTNLESATASLSESVSTISSRLSDLSADLQDMTTSLDDAKATLNGLITTVQAL   89 (326)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             4099999999999988889989999988999988778999999998888999999999998


No 265
>pfam11382 DUF3186 Protein of unknown function (DUF3186). This bacterial family of proteins has no known function.
Probab=27.89  E-value=42  Score=14.08  Aligned_cols=59  Identities=17%  Similarity=0.159  Sum_probs=26.1

Q ss_pred             CCCHHHHHCCHHHHHHHHHH---CCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98844785199999999984---698958899-999999999999999999999999999999
Q gi|254780680|r    1 MLDIQWIRQNPEHLDIALKK---RHLEPQSEY-ILSLDEKNRILIKKIEDIRARRNSNSAQIG   59 (430)
Q Consensus         1 MLDik~IRen~e~v~~~l~~---R~~~~~id~-il~Ld~~rr~l~~e~e~LraerN~lSKeIg   59 (430)
                      |||++|--=-.-.|--.|.-   =|.-+.-+. +-.|..+..++..+.++|+++++.+.+++.
T Consensus         1 MIdfRYHiVSlvAVFLALavGIvlG~~~l~~~l~~~l~~~~~~Lr~e~~~l~~~~~~l~~~~~   63 (307)
T pfam11382         1 MISLRYHIVSIAAVFLALAIGIVLGSGLLQENLLSGLEDEFSDLRTENDRLRAEREALNEQAS   63 (307)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             964689999999999999999993631111567878888999999999999999999999999


No 266
>pfam05008 V-SNARE Vesicle transport v-SNARE protein N-terminus. V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this. This domain is the N-terminal half of the V-Snare proteins.
Probab=27.82  E-value=42  Score=14.07  Aligned_cols=57  Identities=16%  Similarity=0.134  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999998644998799999999999998864446666
Q gi|254780680|r   35 EKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEE   91 (430)
Q Consensus        35 ~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~   91 (430)
                      ++++.+..+++.--.+-..+=+++.-....-.......+..+++..+.+++.+..++
T Consensus        22 e~rk~~i~~ie~~l~ea~ell~qMelEv~~~p~s~R~~~~~klr~Yk~el~~lk~el   78 (79)
T pfam05008        22 EERKAALREIERALDEAEELLDQMELEVRNLPSSERAKYNAKLREYKSELDKLKREL   78 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             788999999998799999999999999881987779999999999999999998762


No 267
>TIGR01710 typeII_sec_gspG general secretion pathway protein G; InterPro: IPR010054   This entry represents GspG, protein G of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=27.80  E-value=24  Score=15.94  Aligned_cols=23  Identities=39%  Similarity=0.709  Sum_probs=15.4

Q ss_pred             HHHHHHHCCEECCCCCCHHHHHHHH
Q ss_conf             7764310002313454114544534
Q gi|254780680|r  218 DMFCTTDGRWLIPTSEVSLTNLYSH  242 (430)
Q Consensus       218 ~~y~~~d~l~Li~TaEvpL~~~~~~  242 (430)
                      ++|+.++..|  ||.|..|+++...
T Consensus        50 d~yrLDng~y--Pt~eQGL~ALV~k   72 (137)
T TIGR01710        50 DMYRLDNGRY--PTEEQGLAALVKK   72 (137)
T ss_pred             HHHHHHHCCC--CCCHHHHHHHCCC
T ss_conf             7665662589--8815789982779


No 268
>TIGR02905 spore_yutH spore coat protein YutH; InterPro: IPR014254    This entry, represented by the Bacillus subtilis protein YutH, is found only in the family Bacillaceae, part of the endospore-forming group within the Firmicutes. YutH has been shown to be involved in spore coat assmebly . Proteins in this entry are homologous to CotS (IPR014255 from INTERPRO)..
Probab=27.75  E-value=38  Score=14.43  Aligned_cols=124  Identities=20%  Similarity=0.217  Sum_probs=59.6

Q ss_pred             CCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHH-H--HHHCCEECCCCC---CH-
Q ss_conf             5301056488999999999998622320320212356202788986551422476776-4--310002313454---11-
Q gi|254780680|r  163 RFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMF-C--TTDGRWLIPTSE---VS-  235 (430)
Q Consensus       163 rF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y-~--~~d~l~Li~TaE---vp-  235 (430)
                      .|||+.|-   =|-| |||+.|+++.+. =.+.--|.+=.          -+|.++.. .  ..+.+-=+||.=   || 
T Consensus       165 tFPYYlGl---tENA-IQy~aDtelD~~-p~~~D~gTiCH----------~Rf~~~~W~~ms~~~~~~K~P~~wVyDH~a  229 (325)
T TIGR02905       165 TFPYYLGL---TENA-IQYLADTELDEE-PGEADSGTICH----------ERFTEETWLRMSERGGLIKVPTEWVYDHAA  229 (325)
T ss_pred             CCCCHHHH---HHHH-HHHHHHHHCCCC-CCCCCCCCCCC----------CCCCCCHHEEECCCCCEECCCHHHHCCCCC
T ss_conf             26602124---7889-999986331468-87656764244----------435421002210478751267032236730


Q ss_pred             --HHHHHHH-----HCCCHHH-HCCEE--EEE------ECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCC----CH
Q ss_conf             --4544534-----2059555-04208--853------221078843355434321222210200212127865----01
Q gi|254780680|r  236 --LTNLYSH-----EIIESKS-LPLRF--TTL------APSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREE----DS  295 (430)
Q Consensus       236 --L~~~~~~-----~~l~~~~-LPik~--~~~------s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe----~S  295 (430)
                        ||=+.|.     .+..... |-|.-  -+|      ||-=++=  =|   .|=||=+|=|+-||-+=.|.-|    .+
T Consensus       230 RDLAEW~R~n~~~~~~r~~~~al~i~~Fl~~Ye~~~PLt~f~wRl--~Y---ARLLFPLHYFE~iE~YY~~~~E~er~~~  304 (325)
T TIGR02905       230 RDLAEWVRENRYLKEIRKNQRALAIASFLQEYEQAAPLTSFSWRL--MY---ARLLFPLHYFETIENYYIAQLESERREL  304 (325)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHH--HH---HHHHCCCHHHHHHHHHCCCCCHHHHHHH
T ss_conf             457998740023444114304889999984012237664578999--99---8850311156766521168870677665


Q ss_pred             HHHHHHHHHHH
Q ss_conf             45789899999
Q gi|254780680|r  296 FTEHERMLSCA  306 (430)
Q Consensus       296 ~~~~e~~~~~~  306 (430)
                      ...+..+++..
T Consensus       305 E~~l~~LL~~~  315 (325)
T TIGR02905       305 EKELQRLLDRE  315 (325)
T ss_pred             HHHHHHHHHCC
T ss_conf             78999886017


No 269
>KOG4196 consensus
Probab=27.42  E-value=43  Score=14.02  Aligned_cols=79  Identities=18%  Similarity=0.143  Sum_probs=47.1

Q ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             84698958899999999999999999999999999999999986449987999999999999988644466666778887
Q gi|254780680|r   19 KKRHLEPQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSL   98 (430)
Q Consensus        19 ~~R~~~~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el   98 (430)
                      +.||  .+-++++.|-++||-|...--..-.+.+.+..+..-.      .+...|..++..|+.+...+.-+++....++
T Consensus        40 ~LrG--~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE------~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~  111 (135)
T KOG4196          40 HLRG--LSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELE------KEKAELQQQVEKLKEENSRLRRELDAYKSKY  111 (135)
T ss_pred             HHCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8608--9899999999999888510479888899998899999------9999999999999999999999999999999


Q ss_pred             HHHHHHC
Q ss_conf             7443100
Q gi|254780680|r   99 KKLISCI  105 (430)
Q Consensus        99 ~~lll~I  105 (430)
                      +.+.-..
T Consensus       112 e~l~~~~  118 (135)
T KOG4196         112 EALQNSA  118 (135)
T ss_pred             HHHHHHH
T ss_conf             9997535


No 270
>COG3175 COX11 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=27.39  E-value=26  Score=15.58  Aligned_cols=12  Identities=33%  Similarity=0.310  Sum_probs=10.4

Q ss_pred             EEEEEEEEECCC
Q ss_conf             102002121278
Q gi|254780680|r  280 QFWKCELVSITR  291 (430)
Q Consensus       280 QF~KVE~~~~~~  291 (430)
                      =|+|||+|+|+.
T Consensus       125 YF~KveCFCFte  136 (195)
T COG3175         125 YFNKVECFCFTE  136 (195)
T ss_pred             HEEEEEEEEEEE
T ss_conf             242156897312


No 271
>PRK11546 zraP zinc resistance protein; Provisional
Probab=27.17  E-value=43  Score=13.99  Aligned_cols=71  Identities=7%  Similarity=0.066  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999999999999999999999999999999864499879999999999999886444666667788877443
Q gi|254780680|r   27 SEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLI  102 (430)
Q Consensus        27 id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~ll  102 (430)
                      -++=..++.-..+...+..+||.+...-.-++..+....+++ .+    +++.+.++|..|..++.+..-+++-.+
T Consensus        42 ~EQQa~~qkL~~eF~~eTa~LRqqL~aKr~ElNALL~at~PD-~~----kI~avakEis~LR~kl~e~rv~~dv~~  112 (139)
T PRK11546         42 TEQQAAAQKIHNDFYAQTSALRQQLVSKRYEYNALLTANPPD-SS----KINAVAKEMETLRQSLDEQRVKRDIAM  112 (139)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-HH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999999899999998069977-99----999999999999999999999999999


No 272
>PRK11281 potassium efflux protein KefA; Provisional
Probab=27.17  E-value=43  Score=13.99  Aligned_cols=31  Identities=13%  Similarity=0.086  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             9999988644466666778887744310022
Q gi|254780680|r   77 TSTLKEQLPILEKEEHEVCSSLKKLISCIPN  107 (430)
Q Consensus        77 ~~~Lk~eik~le~~~~~le~el~~lll~IPN  107 (430)
                      ..++..++.+..+++...++++.+.-..+.+
T Consensus       122 l~~LE~~L~~~~~qlq~~Q~~L~~~ns~L~~  152 (1107)
T PRK11281        122 LRQLEQRLAERLDQLQNAQNDLAEYNSQLVS  152 (1107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999988887


No 273
>KOG3033 consensus
Probab=27.09  E-value=21  Score=16.36  Aligned_cols=165  Identities=22%  Similarity=0.300  Sum_probs=71.6

Q ss_pred             CEECCCCCCHHHHH--------HHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCC---C
Q ss_conf             02313454114544--------534205955504208853221078843355434321222210200212127865---0
Q gi|254780680|r  226 RWLIPTSEVSLTNL--------YSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREE---D  294 (430)
Q Consensus       226 l~Li~TaEvpL~~~--------~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe---~  294 (430)
                      .|-.|||||||+|-        .-+++.+.++ -+++...|---+     +-+|..|.        |||   --|+   .
T Consensus        67 RwFTp~aEvplcGHaTLasahvlf~~~~n~n~-~l~f~t~sG~l~-----akrd~~~~--------iel---n~P~y~~~  129 (286)
T KOG3033          67 RWFTPTAEVPLCGHATLASAHVLFNEIGNVNK-ELKFDTLSGILT-----AKRDELGS--------IEL---NFPEYDTT  129 (286)
T ss_pred             EEECCCCCCCCCCCCHHHHHHHHHHHCCCCCC-EEEEEEECCEEE-----EEECCCCC--------EEE---CCCCCCCC
T ss_conf             87334333764676136677888875267751-599984113699-----98525651--------687---16754431


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCE-------
Q ss_conf             1457898999999999984106753037801178443402410110100483323753102100764532684-------
Q gi|254780680|r  295 SFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSR-------  367 (430)
Q Consensus       295 S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~ir-------  367 (430)
                      |-    ++..-.+.+++...=|.=+.+++.---+.             .++--.=+++.-+|.++|..|.++-       
T Consensus       130 si----~~~~~~~~~fska~~~~~i~dv~~~~~~~-------------p~~liVvl~~~~t~~elep~~~d~~di~~~p~  192 (286)
T KOG3033         130 SI----NISNELEGIFSKAEGPAFIFDVIKCVTPT-------------PRKLIVVLDPWETVFELEPNRIDISDISTCPN  192 (286)
T ss_pred             CC----CCCCHHHHHHHHHHCCCEECCCHHCCCCC-------------CCEEEEEECCCCEEEECCHHHHHHHHHHCCCC
T ss_conf             44----33506799999862875551511046898-------------74599995783204634702422346542898


Q ss_pred             ------EECCCCCCCCEEE------------EECCCH-HHHHHHHHHHHHH-----CC---CCCCCEEC---CCCCCCCC
Q ss_conf             ------7338998410104------------200432-2899999999883-----46---89983865---82223101
Q gi|254780680|r  368 ------YRDPNSKSLKFTH------------TLNGSG-VAVGRCLIAILEN-----YL---NADGSVTI---PTVLRPYM  417 (430)
Q Consensus       368 ------y~~~~~~~~~~~h------------tlNgt~-~A~~R~l~ailEn-----~q---~~dg~i~i---P~~L~pym  417 (430)
                            +.++.|.+..|+-            -.+||| ||.++-+.-++--     +|   +..|.++|   +++-|=|+
T Consensus       193 ~~~~v~~~g~~g~~~dy~~RyFAP~~GVnEDPvtGSa~caL~~yws~~~~k~~~~afqas~~Rgg~~rv~l~~ea~rV~l  272 (286)
T KOG3033         193 NGMIVTFAGSSGSPYDYESRYFAPWVGVNEDPVTGSAHCALGPYWSLILGKKDFYAFQASPTRGGLFRVSLKKEAQRVIL  272 (286)
T ss_pred             CCEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCEEEEHHHHHHHHCCCCCEEEEEECCCCCCEEEEEECCCCEEEEE
T ss_conf             72489976699998766765124400456788887145633777998728423000100246783799998477608995


Q ss_pred             CCEEEEC
Q ss_conf             8801307
Q gi|254780680|r  418 NNLAVIK  424 (430)
Q Consensus       418 ~g~~~i~  424 (430)
                      +|.-+..
T Consensus       273 ~G~avtV  279 (286)
T KOG3033         273 NGGAVTV  279 (286)
T ss_pred             CCCCEEE
T ss_conf             4981899


No 274
>pfam08286 Spc24 Spc24 subunit of Ndc80. Spc24 is a component of the evolutionarily conserved kinetochore-associated Ndc80 complex and is involved in chromosome segregation.
Probab=27.04  E-value=44  Score=13.97  Aligned_cols=31  Identities=16%  Similarity=0.306  Sum_probs=16.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999998
Q gi|254780680|r   31 LSLDEKNRILIKKIEDIRARRNSNSAQIGQA   61 (430)
Q Consensus        31 l~Ld~~rr~l~~e~e~LraerN~lSKeIg~~   61 (430)
                      .+||.++-.+..++..|.++.|.+..+...+
T Consensus         2 ~~Ld~~k~~laK~l~dlE~~l~~L~~el~~l   32 (117)
T pfam08286         2 QELENEKFRLAKELNDLESELNNLQSELEEL   32 (117)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             0788999999998579999999999999999


No 275
>TIGR01503 MthylAspMut_E methylaspartate mutase, E subunit; InterPro: IPR006396   Glutamate mutase (methylaspartate mutase) catalyses the reversible interconversion of L-glutamate and L-threo-3-methylaspartate, the first step in the pathway of glutamate fermentation . Catalysis is initiated using the cobalamin cofactor. The E subunit is the catalytic subunit (MutE) . ; GO: 0016866 intramolecular transferase activity, 0031419 cobalamin binding, 0019670 anaerobic glutamate catabolic process.
Probab=26.96  E-value=44  Score=13.96  Aligned_cols=174  Identities=22%  Similarity=0.366  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHHHHHHHHHHHCCEECCCCCCHHHHHH-HHHCCCHHHHCCEE
Q ss_conf             99999999862232032021235620278898655142247677643100023134541145445-34205955504208
Q gi|254780680|r  176 RALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKFADDMFCTTDGRWLIPTSEVSLTNLY-SHEIIESKSLPLRF  254 (430)
Q Consensus       176 ~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f~~~~y~~~d~l~Li~TaEvpL~~~~-~~~~l~~~~LPik~  254 (430)
                      |||--..-.+ +...||+-|.+-...+..    .|=||..|.-.|-      +|++|= .+|+|- ..++|-.+  |-=+
T Consensus       265 ~aL~e~~~eY-L~~ygy~D~~vsTVfhQW----mGGFP~dE~kAf~------vIs~at-aiA~l~~~tkvivK~--p~Ea  330 (481)
T TIGR01503       265 RALKELIQEY-LDTYGYKDVEVSTVFHQW----MGGFPEDESKAFG------VISLAT-AIAALSGATKVIVKS--PHEA  330 (481)
T ss_pred             HHHHHHHHHH-HHHCCCCCEEEEEEEECC----CCCCCHHHHHHHH------HHHHHH-HHHHHHCCCEEEEEC--CHHH
T ss_conf             9999999864-020183211687566427----7996256788877------899999-999873786488607--2211


Q ss_pred             EEEECCCCCCCCCCC-CCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHE
Q ss_conf             853221078843355-4343212222102002121278650145789899999999998410675303780117844340
Q gi|254780680|r  255 TTLAPSFRSEAGSAG-RDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACK  333 (430)
Q Consensus       255 ~~~s~cfR~EaGs~G-kdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~  333 (430)
                      +|+++   +||-+.| |-|+-++++-.=.|     +..-++-.-+.+-+-.-+..|+.      .|=++|-|||.-.-.+
T Consensus       331 ~g~pt---~~~n~~gL~~t~~~L~m~~~Q~-----~~~~~~v~~E~~~Ik~e~~~il~------kvFe~G~GDla~gtv~  396 (481)
T TIGR01503       331 VGIPT---AEANIAGLKATKQVLNMLNEQK-----IPLSEEVELEKELIKKEVRSILD------KVFELGDGDLARGTVK  396 (481)
T ss_pred             CCCCH---HHHHHHHHHHHHHHHHHHCCCC-----CCCCHHHHHHHHHHHHHHHHHHH------HHHHCCCCHHHHHHHH
T ss_conf             06886---8999999999999998643685-----78746667789999999999999------9861178706778888


Q ss_pred             EEEEEEE--------------CCCCCC-----EEEEEEECCCC---CHHHHHCCCEEECCCCCCCCE
Q ss_conf             2410110--------------100483-----32375310210---076453268473389984101
Q gi|254780680|r  334 TYDLEVW--------------LAGQNL-----YREISSCSTCG---NFQSRRMNSRYRDPNSKSLKF  378 (430)
Q Consensus       334 ~~DiE~w--------------~P~~~~-----y~Ev~S~Snc~---D~QsrRl~iry~~~~~~~~~~  378 (430)
                      -||-=|-              ||.|..     |.|++.+.-|.   +|--.|+.=|=+ ..|+...|
T Consensus       397 AFe~GvLDvPFaPS~~naGk~lP~RD~~G~vR~L~~G~vpl~~~i~~~h~~~~~eRa~-~EgR~~~F  462 (481)
T TIGR01503       397 AFEAGVLDVPFAPSKYNAGKMLPARDNEGAVRYLEFGAVPLDEEIKELHRKRLKERAK-KEGREISF  462 (481)
T ss_pred             HHCCCCCCCCCCHHHHHHCCCCCEECCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHH-HCCCCCCE
T ss_conf             7616615788860565307822002488746501047898988899987899998851-13799840


No 276
>pfam08581 Tup_N Tup N-terminal. The N-terminal domain of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor.
Probab=26.88  E-value=44  Score=13.95  Aligned_cols=63  Identities=14%  Similarity=0.171  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999999999999999998644998--799999999999998864446666677888774431002
Q gi|254780680|r   44 IEDIRARRNSNSAQIGQAIAEGNL--SLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIP  106 (430)
Q Consensus        44 ~e~LraerN~lSKeIg~~k~~~~~--~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IP  106 (430)
                      +|.+|++-..+|.+....+...++  ..+.+=..++..++..+-.||.....+.+...+-+.+|-
T Consensus         6 Ld~ir~Efe~~~~e~~~~k~~~~dyE~ki~~Qi~Emq~IR~~vyeLE~~h~k~Kq~YEeEI~rLk   70 (79)
T pfam08581         6 LDAIRAEFEALSREASSYKAQQDDYEHKIQQQIQEMQMIRQTVYELEQAHRKMKQKYEEEIARLK   70 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999878888887688899999999999999999999999989999999999999999


No 277
>PRK08871 flgK flagellar hook-associated protein FlgK; Validated
Probab=26.78  E-value=44  Score=13.94  Aligned_cols=78  Identities=13%  Similarity=0.139  Sum_probs=44.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             99999999999999999999999998644998------799999999999998864446666677888774431002258
Q gi|254780680|r   36 KNRILIKKIEDIRARRNSNSAQIGQAIAEGNL------SLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVP  109 (430)
Q Consensus        36 ~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~------~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~  109 (430)
                      .|..+..+.+.|-.+.|.++.++.++...-+.      .++..+.++..+|..+|...+..-..+.++.+.++-.|--+.
T Consensus       131 ~R~~~l~~a~~L~~~~n~~~~~l~~~~~~~~~~i~~~V~~iN~l~~~Ia~lN~~I~~~~~~~ndL~DqRD~ll~eLS~~~  210 (626)
T PRK08871        131 ARKVVLEKAKLISQTLNDFHETVRQQKDVTNKKLDMGIERINQIALEIRDIHRLMMRTPGPHNDLMDQHEKLIKELSQYT  210 (626)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             89999999999999999999999999999999999999999999999999999998548998526889999999997514


Q ss_pred             CCHH
Q ss_conf             8112
Q gi|254780680|r  110 LEEV  113 (430)
Q Consensus       110 ~~~V  113 (430)
                      +-+|
T Consensus       211 ~v~v  214 (626)
T PRK08871        211 KVTV  214 (626)
T ss_pred             CEEE
T ss_conf             9699


No 278
>PRK12999 pyruvate carboxylase; Reviewed
Probab=26.61  E-value=13  Score=17.76  Aligned_cols=100  Identities=16%  Similarity=0.108  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCC--------CCHHHHHCCCE
Q ss_conf             4578989999999999841067530378011784434024101101004833237531021--------00764532684
Q gi|254780680|r  296 FTEHERMLSCAEEILKRLDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTC--------GNFQSRRMNSR  367 (430)
Q Consensus       296 ~~~~e~~~~~~~~i~~~L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc--------~D~QsrRl~ir  367 (430)
                      -.+.+.|..-.+...+. |-+..---+-|||+-.+.+.+|+++-|+---..--+.+.-|-|        .-|-|+.|=-.
T Consensus       651 LN~~~nm~~~i~~v~~~-g~~~e~aicyTGdi~dp~~~~~~l~yy~~~a~~l~~~G~~~l~IKDMAGLl~P~aa~~LV~a  729 (1147)
T PRK12999        651 LNWVENMRVAIDAVRET-GKVAEAAICYTGDILDPARAKYDLDYYVDLAKELEAAGAHILAIKDMAGLLKPAAAYKLVSA  729 (1147)
T ss_pred             CCCHHHHHHHHHHHHHC-CCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHH
T ss_conf             44667789999999970-98899998742577787888766999999999999768988997144546887999999999


Q ss_pred             EECCCCCCCCEEEEECCCHHHHHHHHHHHH
Q ss_conf             733899841010420043228999999998
Q gi|254780680|r  368 YRDPNSKSLKFTHTLNGSGVAVGRCLIAIL  397 (430)
Q Consensus       368 y~~~~~~~~~~~htlNgt~~A~~R~l~ail  397 (430)
                      .|..-+= +-+.||=+-||+++...+.|+=
T Consensus       730 Lk~~~~l-PIhlHtHdTsG~~~at~laA~e  758 (1147)
T PRK12999        730 LKEEVDL-PIHLHTHDTSGNGLATYLAAAE  758 (1147)
T ss_pred             HHHHCCC-CEEEECCCCCCHHHHHHHHHHH
T ss_conf             9861698-4598436788558999999998


No 279
>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]
Probab=26.59  E-value=44  Score=13.91  Aligned_cols=55  Identities=18%  Similarity=0.078  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHCCHHHHCC--CCCHH-------CCCHHHEEEEEEEECCCCCCEEEEEEECCCCC
Q ss_conf             9999999998410675303--78011-------78443402410110100483323753102100
Q gi|254780680|r  303 LSCAEEILKRLDLHYRVVS--LCTGD-------LGFSACKTYDLEVWLAGQNLYREISSCSTCGN  358 (430)
Q Consensus       303 ~~~~~~i~~~L~lpyRvv~--~~sgd-------lg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D  358 (430)
                      -..-..++..+|||.|.|.  +++..       +.....-..-.|+|+|++ .|.-+-..++..-
T Consensus       201 a~l~val~Ra~GIpAR~V~Gy~~~~~~~~~~~~~~~~~~~Haw~ev~~~~~-gW~~~Dpt~~~~~  264 (319)
T COG1305         201 AHLLVALLRAAGIPARYVSGYLGAEVEPLSGRPLVRNDDAHAWAEVYLPGR-GWVPLDPTNGLLA  264 (319)
T ss_pred             HHHHHHHHHHCCCCEEEECCEECCCCCCCCCCCCCCCCCCEEEEEEECCCC-CEEEECCCCCCCC
T ss_conf             999999999759860986220237765444543345676426689883886-0597368788666


No 280
>PRK08187 pyruvate kinase; Validated
Probab=26.50  E-value=44  Score=13.90  Aligned_cols=44  Identities=18%  Similarity=0.148  Sum_probs=19.7

Q ss_pred             HCCCCCHHCCCHHHEEEEEE--EECCCCCCEEEEEEECCCCCHHHH
Q ss_conf             30378011784434024101--101004833237531021007645
Q gi|254780680|r  319 VVSLCTGDLGFSACKTYDLE--VWLAGQNLYREISSCSTCGNFQSR  362 (430)
Q Consensus       319 vv~~~sgdlg~~a~~~~DiE--~w~P~~~~y~Ev~S~Snc~D~Qsr  362 (430)
                      =|++|..+++.++--.-|.+  .|.-....|.-+|=+-+..|-..=
T Consensus       409 GiN~P~~~l~lp~lT~kD~~dl~f~~~~~D~va~SFVr~~~Dv~~l  454 (606)
T PRK08187        409 GINLPDTELPLPALTDKDLEDLAFVAKHADIVGLSFVQSPEDVEYL  454 (606)
T ss_pred             CEECCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEECCCCHHHHHHH
T ss_conf             6458999889988987799999999856998998515889999999


No 281
>pfam06910 MEA1 Male enhanced antigen 1 (MEA1). This family consists of several mammalian male enhanced antigen 1 (MEA1) proteins. The Mea-1 gene is found to be localized in primary and secondary spermatocytes and spermatids, but the protein products are detected only in spermatids. Intensive transcription of Mea-1 gene and specific localisation of the gene product suggest that Mea-1 may play a important role in the late stage of spermatogenesis.
Probab=26.04  E-value=40  Score=14.25  Aligned_cols=55  Identities=18%  Similarity=0.259  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCHHHH
Q ss_conf             4666667788877443100225881122113555402420001565665666211220221
Q gi|254780680|r   87 LEKEEHEVCSSLKKLISCIPNVPLEEVPIGTSANENILIRSVGKKPSAIHLSREHFEIGEA  147 (430)
Q Consensus        87 le~~~~~le~el~~lll~IPNi~~~~VP~G~de~dNv~i~~~G~~~~f~f~~k~H~elge~  147 (430)
                      -+..+..+++.++.+-|.||.-|-++  .+.++......+....+|-.    -+|+||-++
T Consensus        78 ~~~~~~diQeRiqamgLHLP~PP~~s--edEd~EgAaa~~s~~SIPMD----~~HVELVKR  132 (174)
T pfam06910        78 GEDGAADIQDRIQALGLHLPDPPLES--EDEDEEGAAALNNHSSIPMD----PEHVELVKR  132 (174)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCCCCCC--CCCCHHHHHHHHCCCCCCCC----HHHHHHHHH
T ss_conf             62377899999998426689989884--44460133454056777788----899999999


No 282
>pfam09016 Pas_Saposin Pas factor saposin fold. Members of this family adopt a compact structure comprising five alpha helices. Charged and polar residues are exposed mostly on the surface, while most of the hydrophobic residues are buried inside the hydrophobic core of the helical bundle. The precise function of this domain is unknown, but it is has been shown to induce secretion of periplasmic proteins, especially collagenase.
Probab=26.00  E-value=38  Score=14.40  Aligned_cols=34  Identities=18%  Similarity=0.329  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHCCHHH-HCCCCCHHCCCHHHEEE
Q ss_conf             99999999998410675-30378011784434024
Q gi|254780680|r  302 MLSCAEEILKRLDLHYR-VVSLCTGDLGFSACKTY  335 (430)
Q Consensus       302 ~~~~~~~i~~~L~lpyR-vv~~~sgdlg~~a~~~~  335 (430)
                      --.+-..+|.+|+|||- .+-+-|.-||+.++-|.
T Consensus        20 hAqiRQ~LYeqLdL~FdKqlaLYs~vLGPassGkl   54 (76)
T pfam09016        20 HAQIRQNLYEQLDLSFDKQLALYSSVLGPASSGKL   54 (76)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCC
T ss_conf             99999999998088578999999980286445766


No 283
>KOG0161 consensus
Probab=25.85  E-value=46  Score=13.82  Aligned_cols=41  Identities=24%  Similarity=0.312  Sum_probs=26.7

Q ss_pred             CEEEEECCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCC-CCCCE
Q ss_conf             010420043228999999998834689983865822231-01880
Q gi|254780680|r  377 KFTHTLNGSGVAVGRCLIAILENYLNADGSVTIPTVLRP-YMNNL  420 (430)
Q Consensus       377 ~~~htlNgt~~A~~R~l~ailEn~q~~dg~i~iP~~L~p-ym~g~  420 (430)
                      +.-+|||.|   -|+-+-||+=|+-..-|.+-.|-||.. -|||.
T Consensus       649 ~Lm~~l~~T---~phFvRCiIPn~~K~~g~ld~~lvl~QLrcngV  690 (1930)
T KOG0161         649 KLMTTLRST---HPHFVRCIIPNEEKKPGKLDAPLVLNQLRCNGV  690 (1930)
T ss_pred             HHHHHHHCC---CCCEEEEECCCCCCCCCCCCHHHHHHHHHCCCC
T ss_conf             999975058---976147853176446555678889877551671


No 284
>pfam07665 consensus
Probab=25.81  E-value=46  Score=13.82  Aligned_cols=33  Identities=21%  Similarity=0.327  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999988644466666778887744
Q gi|254780680|r   69 LVDALKNETSTLKEQLPILEKEEHEVCSSLKKL  101 (430)
Q Consensus        69 ~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~l  101 (430)
                      ++..|+..+.++|+.++.|.+....+++..-.+
T Consensus        13 Dv~~LK~Dmv~vK~Di~~LK~dV~~Lk~Dvs~i   45 (57)
T pfam07665        13 DVAVLKTDMVEVKSDIKILKEDVAVLKKDVSKI   45 (57)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999999999999999999999999989998


No 285
>pfam04089 BRICHOS BRICHOS domain. The BRICHOS domain is about 100 amino acids long. It is found in a variety of proteins implicated in dementia, respiratory distress and cancer. Its exact function is unknown; roles that have been proposed for it include (a) in targeting of the protein to the secretory pathway, (b) intramolecular chaperone-like function, and (c) assisting the specialized intracellular protease processing system. This C-terminal domain is embedded in the endoplasmic reticulum lumen, and binds to the N-terminal, transmembrane, SP_C, pfam08999, provided that it is in non-helical conformation. Thus the Brichos domain of proSP-C is a chaperone that induces alpha-helix formation of an aggregation-prone TM region.
Probab=25.78  E-value=46  Score=13.81  Aligned_cols=46  Identities=13%  Similarity=0.191  Sum_probs=37.0

Q ss_pred             CCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             1007645326847338998410104200432289999999988346899
Q gi|254780680|r  356 CGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAILENYLNAD  404 (430)
Q Consensus       356 c~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ailEn~q~~d  404 (430)
                      -.|||..=  +-||+..++ .=|++.+|-+.+..++.|.-++.|.|...
T Consensus        10 v~Df~~g~--~a~~~~~~~-~C~i~~m~~~~ip~l~~l~~~~~~~~~~~   55 (97)
T pfam04089        10 VHDFKNGL--TAIRDAGGT-KCYIMKMDKEVIPSLQALTELLKNKQLGG   55 (97)
T ss_pred             EEECCCCC--EEEEECCCC-EEEEEECCHHHCCCHHHHHHHHHHHHCCC
T ss_conf             98756790--899978998-68999757310789899999998764278


No 286
>cd04914 ACT_AKi-DapG-BS_1 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI. This CD includes the N-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria, bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive aspartokinase isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The B. subtilis AKI is tetrameric consisting of two alpha and 
Probab=25.44  E-value=46  Score=13.77  Aligned_cols=37  Identities=27%  Similarity=0.387  Sum_probs=25.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHC
Q ss_conf             0212127865014578989999999999841067530
Q gi|254780680|r  284 CELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVV  320 (430)
Q Consensus       284 VE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv  320 (430)
                      |.++.+...+...-.-+++.+.++++++.||+-|.|.
T Consensus        30 vDfINI~P~~~vfTV~~~~~~ka~~iL~~lg~~p~v~   66 (67)
T cd04914          30 VDLINVSPEEVIFTVDGEVAEKAVDILEKMGLDPSVR   66 (67)
T ss_pred             EEEEEECCCCEEEEECHHHHHHHHHHHHHCCCCCEEE
T ss_conf             7899866774799807788999999999869983750


No 287
>TIGR01880 Ac-peptdase-euk N-acyl-L-amino-acid amidohydrolase; InterPro: IPR010159   This entry represents a family of eukaryotic N-acyl-L-amino-acid amidohydrolase (3.5.1.14 from EC) is a homodimeric zinc-binding mammalian enzyme that catalyzes the hydrolysis of N-alpha-acylated amino acids except L-aspartic acid. , . These enzymes are listed as being members of MEROPS peptidase family S20A (clan MH).; GO: 0004046 aminoacylase activity, 0006520 amino acid metabolic process, 0005737 cytoplasm.
Probab=25.34  E-value=28  Score=15.39  Aligned_cols=26  Identities=27%  Similarity=0.367  Sum_probs=17.1

Q ss_pred             CCCCEEEEEECCCCCCCCCC--------CCCCCHH
Q ss_conf             55402420001565665666--------2112202
Q gi|254780680|r  119 ANENILIRSVGKKPSAIHLS--------REHFEIG  145 (430)
Q Consensus       119 e~dNv~i~~~G~~~~f~f~~--------k~H~elg  145 (430)
                      .+|+..||..| +|.+.|.|        .||-|-.
T Consensus       375 ~TDsRyiR~~G-vPAlGFSPm~NTP~LLHDHnEfL  408 (433)
T TIGR01880       375 STDSRYIRAVG-VPALGFSPMNNTPVLLHDHNEFL  408 (433)
T ss_pred             CCCHHHHHHCC-CCCCCCCCCCCCHHHHHHHHHHC
T ss_conf             64314475227-75426776200113440010220


No 288
>KOG1234 consensus
Probab=25.23  E-value=7.6  Score=19.61  Aligned_cols=16  Identities=13%  Similarity=0.474  Sum_probs=9.3

Q ss_pred             CC-CCCCHHHHHHHHHH
Q ss_conf             27-86501457898999
Q gi|254780680|r  289 IT-REEDSFTEHERMLS  304 (430)
Q Consensus       289 ~~-~pe~S~~~~e~~~~  304 (430)
                      .| .||+.+..|-+|-.
T Consensus       320 L~pPPeEtYsLHRklsG  336 (363)
T KOG1234         320 LCPPPEETYSLHRKLSG  336 (363)
T ss_pred             CCCCCHHHHHHHHHHHH
T ss_conf             78994888999998423


No 289
>pfam10573 UPF0561 Uncharacterized protein family UPF0561. This family of proteins has no known function.
Probab=25.15  E-value=21  Score=16.32  Aligned_cols=33  Identities=18%  Similarity=0.131  Sum_probs=13.6

Q ss_pred             CCEEEEEECCCCCCCCCCCCCCCHHHHCCCCCHHH
Q ss_conf             40242000156566566621122022117310001
Q gi|254780680|r  121 ENILIRSVGKKPSAIHLSREHFEIGEALGLMDFDR  155 (430)
Q Consensus       121 dNv~i~~~G~~~~f~f~~k~H~elge~l~liDfe~  155 (430)
                      .|.+-..|++.-++...  .--.-|..|=++||++
T Consensus        82 ~~~~~ee~~es~s~~~~--e~e~~g~~Lf~ldyeA  114 (126)
T pfam10573        82 SNAEAEEKNESGSSEET--EPESPGTQLFCLDYEA  114 (126)
T ss_pred             CCCCHHHHCCCCCCCCC--CCCCCCCEEEEEEEEC
T ss_conf             87003443135665556--6589863789988643


No 290
>pfam06156 DUF972 Protein of unknown function (DUF972). This family consists of several hypothetical bacterial sequences. The function of this family is unknown.
Probab=25.13  E-value=47  Score=13.73  Aligned_cols=54  Identities=15%  Similarity=0.217  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999986449987999999999999988644466666778
Q gi|254780680|r   37 NRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVC   95 (430)
Q Consensus        37 rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le   95 (430)
                      ++.+-..+.++..+.+.+..+++.+|.     .+.++.++-..|+-+-..|.+.+.+.+
T Consensus         3 k~elfd~l~~le~ql~~l~~el~~LK~-----~~~~l~EEN~~L~iEN~~Lr~~l~~~~   56 (106)
T pfam06156         3 KKELFDALSELEQQLGQLLAELGELKQ-----QLAELLEENAELRIENEHLRERLEELE   56 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             789999999999999999999999999-----999999988999999999999999887


No 291
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=25.05  E-value=47  Score=13.72  Aligned_cols=29  Identities=10%  Similarity=0.362  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999998
Q gi|254780680|r   33 LDEKNRILIKKIEDIRARRNSNSAQIGQA   61 (430)
Q Consensus        33 Ld~~rr~l~~e~e~LraerN~lSKeIg~~   61 (430)
                      .+++.+.+...++.|...-.+-+.+|..+
T Consensus       117 ~e~~i~~i~~~l~~L~~~e~~nr~~v~~l  145 (569)
T PRK04778        117 IEEDIEQILEELQELLESEEKNREEVEQL  145 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999998689989999999


No 292
>PRK07245 consensus
Probab=25.01  E-value=47  Score=13.71  Aligned_cols=38  Identities=8%  Similarity=0.004  Sum_probs=17.0

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999998469895889999999999999999999999
Q gi|254780680|r   12 EHLDIALKKRHLEPQSEYILSLDEKNRILIKKIEDIRA   49 (430)
Q Consensus        12 e~v~~~l~~R~~~~~id~il~Ld~~rr~l~~e~e~Lra   49 (430)
                      +.+.+.+..-++=.|.++..++-.+...+...++..+.
T Consensus         6 ~eLe~~~s~Pd~w~D~~ka~kl~ke~~~L~~~v~~~~~   43 (337)
T PRK07245          6 ALLENHMTEPDFWNDNIAAQKTSQELNELKGKYDTFHN   43 (337)
T ss_pred             HHHHHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999862970330999999999999999999999999


No 293
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif  that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=24.82  E-value=47  Score=13.69  Aligned_cols=30  Identities=17%  Similarity=0.255  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999998864446666677888774
Q gi|254780680|r   71 DALKNETSTLKEQLPILEKEEHEVCSSLKK  100 (430)
Q Consensus        71 ~~Lk~e~~~Lk~eik~le~~~~~le~el~~  100 (430)
                      +-+.++...|.++|..++...+.++..+.+
T Consensus        78 ~~l~~~~~~l~~~i~~L~~~~~~l~~~l~~  107 (108)
T cd01107          78 KLLREKLAELEAEIEELQRILRLLEDRLKQ  107 (108)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999999973


No 294
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=24.65  E-value=48  Score=13.67  Aligned_cols=28  Identities=14%  Similarity=0.150  Sum_probs=12.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNS   55 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lS   55 (430)
                      .++..|....+.+..+++.|+.+.+.+.
T Consensus         7 ~elq~L~~~~~~l~~~ie~L~~~l~~l~   34 (141)
T PRK03947          7 QELEELAAQYQALQAQIEALQQQLALLQ   34 (141)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999999


No 295
>COG0188 GyrA Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair]
Probab=24.49  E-value=48  Score=13.65  Aligned_cols=60  Identities=25%  Similarity=0.225  Sum_probs=35.3

Q ss_pred             HHHHHCC--HHHHHHHHHHCC-CC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             4478519--999999998469-89-5889999999999999999999999999999999998644
Q gi|254780680|r    4 IQWIRQN--PEHLDIALKKRH-LE-PQSEYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAE   64 (430)
Q Consensus         4 ik~IRen--~e~v~~~l~~R~-~~-~~id~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~   64 (430)
                      |..||+.  +...+..|..|. ++ ...+.|+++ ..+|-...+.+.++.+.+.+.++|..+..-
T Consensus       393 I~iIr~s~~~~~a~~~L~~~f~lse~Qa~aIl~m-rL~rLt~le~~~i~~E~~~L~~~i~~l~~i  456 (804)
T COG0188         393 IEIIRESKDKPEAKEELMARFGLSEKQAEAILDL-RLRRLTGLEEEKIEKELKELEKEIADLEKI  456 (804)
T ss_pred             HHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHH-HHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9888708981678999998738967889999862-677764040878888999999999999987


No 296
>PRK00396 rnpA ribonuclease P; Reviewed
Probab=24.35  E-value=46  Score=13.80  Aligned_cols=44  Identities=20%  Similarity=0.162  Sum_probs=29.6

Q ss_pred             CCCEEEEEEEE--EEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             43212222102--002121278650145789899999999998410
Q gi|254780680|r  272 TRGMLRQHQFW--KCELVSITREEDSFTEHERMLSCAEEILKRLDL  315 (430)
Q Consensus       272 trGl~RvHQF~--KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~l  315 (430)
                      .|-.||.||..  -+.+++++...-...-..++...-..+|+.|.=
T Consensus        70 iRE~FR~~~~~L~~~DiVViar~~~~~l~n~el~~~L~~lw~rL~r  115 (134)
T PRK00396         70 MRESFRLNQDSLAGWDIVIVARKGLGELENPELHQQFGKLWKRLAR  115 (134)
T ss_pred             HHHHHHHCCCCCCCCCEEEEECCCHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             9999995730079989899937770024999999999999999985


No 297
>pfam02381 MraZ MraZ protein. This small 70 amino acid domain is found duplicated in a family of bacterial proteins. These proteins may be DNA-binding transcription factors (Pers. comm. A Andreeva & A Murzin).
Probab=24.35  E-value=30  Score=15.18  Aligned_cols=18  Identities=28%  Similarity=0.643  Sum_probs=11.0

Q ss_pred             CCCCCEECCCCCCCCCCC
Q ss_conf             899838658222310188
Q gi|254780680|r  402 NADGSVTIPTVLRPYMNN  419 (430)
Q Consensus       402 ~~dg~i~iP~~L~pym~g  419 (430)
                      ...|.|.||..||.|.++
T Consensus        11 D~kGRi~iP~~lR~~~~~   28 (72)
T pfam02381        11 DSKGRIILPAKLREYAGL   28 (72)
T ss_pred             CCCCCEECCHHHHHHHCC
T ss_conf             878737279999998679


No 298
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=24.34  E-value=48  Score=13.63  Aligned_cols=52  Identities=15%  Similarity=0.239  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999864499879999999999999886444666667
Q gi|254780680|r   37 NRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHE   93 (430)
Q Consensus        37 rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~   93 (430)
                      ++.+-..+.++..+.+.+.++++.++.     .+.++.++-..|+-+-..|.+.+.+
T Consensus         3 k~elfd~l~~le~ql~~l~~e~~~LK~-----~~~~l~EEN~~L~iEN~~Lre~l~~   54 (107)
T PRK13169          3 KKEIFDKLDDLEQNLGVLLKELGALKQ-----QLAELLEENTALRLENEKLRERLEE   54 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             789999999999999999999999999-----9999999889999999999999998


No 299
>pfam07050 consensus
Probab=24.29  E-value=49  Score=13.62  Aligned_cols=45  Identities=18%  Similarity=0.177  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHCCCCCCCHH
Q ss_conf             99999999999998864446--6666778887744310022588112
Q gi|254780680|r   69 LVDALKNETSTLKEQLPILE--KEEHEVCSSLKKLISCIPNVPLEEV  113 (430)
Q Consensus        69 ~~~~Lk~e~~~Lk~eik~le--~~~~~le~el~~lll~IPNi~~~~V  113 (430)
                      +..++..++++++.++...+  ..++..+.+++.+|-.|-.++...|
T Consensus        69 d~k~v~~ei~~~krelD~~p~V~~Fk~Ae~~lq~LL~eVs~~Ia~~V  115 (145)
T pfam07050        69 DYKDVMREIRELKRELDLNEVVAAFKRAETDLQSLLDEVSSKIANSV  115 (145)
T ss_pred             CHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             49999999999999876684999999999999999999999999975


No 300
>PRK10696 C32 tRNA thiolase; Provisional
Probab=24.24  E-value=49  Score=13.61  Aligned_cols=23  Identities=22%  Similarity=0.391  Sum_probs=11.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCEEH
Q ss_conf             488999999999998622320320212
Q gi|254780680|r  170 HLAHLERALGQFMIDLHTSEHGYTEVS  196 (430)
Q Consensus       170 ~~A~Le~ALi~y~ld~~~~~~Gy~~v~  196 (430)
                      -.++|-|..+ |  . .+.+.|++-+.
T Consensus       124 lCsRlRRg~L-y--~-~A~e~G~nKIA  146 (311)
T PRK10696        124 LCSRLRRGIL-Y--R-TATELGATKIA  146 (311)
T ss_pred             HHHHHHHHHH-H--H-HHHHCCCCEEE
T ss_conf             9999999999-9--9-99986998798


No 301
>pfam10502 Peptidase_S26 Peptidase S26. This is a family of serine endopeptidases which function in the processing of newly-synthesized secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes.
Probab=24.13  E-value=49  Score=13.60  Aligned_cols=27  Identities=22%  Similarity=0.197  Sum_probs=19.4

Q ss_pred             CCCEEEEEEEEEEE---EEECCCCCCHHHH
Q ss_conf             43212222102002---1212786501457
Q gi|254780680|r  272 TRGMLRQHQFWKCE---LVSITREEDSFTE  298 (430)
Q Consensus       272 trGl~RvHQF~KVE---~~~~~~pe~S~~~  298 (430)
                      -.|+|+++.+.+.+   +++||-|+++..+
T Consensus        10 P~G~Y~v~~~~~~~rGD~V~f~~P~~~~~~   39 (138)
T pfam10502        10 PVGLYRIEPLDRPEVGDLVAVCPPEPAAFF   39 (138)
T ss_pred             EEEEEEEEECCCCCCCCEEEEECCHHHHHH
T ss_conf             235699965898742889999798488777


No 302
>TIGR02977 phageshock_pspA phage shock protein A; InterPro: IPR014319   Members of this protein are the phage shock protein PspA, from the phage shock operon. PspA appears to maintain the proton motive force under stress conditions that include over expression of certain phage secretins, heat shock, ethanol and protein export defects..
Probab=23.98  E-value=49  Score=13.58  Aligned_cols=65  Identities=18%  Similarity=0.326  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999998644998--------------79999999999999886444666667788877
Q gi|254780680|r   35 EKNRILIKKIEDIRARRNSNSAQIGQAIAEGNL--------------SLVDALKNETSTLKEQLPILEKEEHEVCSSLK   99 (430)
Q Consensus        35 ~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~--------------~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~   99 (430)
                      .++++|..+++.++++.+.=+.+=.-+..+|..              +.++.|..+...+.+.|..+..++..++.+|.
T Consensus        52 Ad~KeL~R~~~~~e~~~~~W~~KAeLAL~KgREDLARAAL~EK~K~~~~~~~L~~E~~~~~e~l~~~~~di~~Lq~KL~  130 (222)
T TIGR02977        52 ADKKELERRVSRLEAQVEDWQDKAELALSKGREDLARAALIEKQKAAELAEALEQELAAVEETLAKLQEDIAKLQAKLA  130 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999998998888652069716899999999999999999999999999999998989999999988


No 303
>TIGR00433 bioB biotin synthase; InterPro: IPR002684   Biotin synthase 2.8.1.6 from EC works with flavodoxin, S-adenosylmethionine, and possibly cysteine to catalyze the last step of the biotin biosynthetic pathway. The reaction consists of the introduction of a sulphur atom into dethiobiotin, thus requiring activation of C-H bonds . Biotin (vitamin H) is a prosthetic group in enzymes catalysing carboxylation and transcarboxylation reactions .    Biotin synthase from Escherichia coli is a homodimer of 76 kDa, with each polypeptide chain carrying an oxygen-sensitive (4Fe-4S) cluster, probably ligated by three cysteines of a CXXXCXXC box conserved among all known BioB sequences and a fourth still not identified ligand. BioB displays a pyridoxal phosphate-dependent cysteine desulphurase activity, which allows mobilization of the sulphur atom from free cysteine .  ; GO: 0004076 biotin synthase activity, 0009102 biotin biosynthetic process.
Probab=23.97  E-value=43  Score=13.99  Aligned_cols=138  Identities=15%  Similarity=0.121  Sum_probs=83.1

Q ss_pred             HHHHHHHHHHHHHHHHH--HHHHHHHHHHCCCHHHHHHHHH----------------------HHHHHHHHHHHHHHHH-
Q ss_conf             99999999999999999--9999999864499879999999----------------------9999998864446666-
Q gi|254780680|r   37 NRILIKKIEDIRARRNS--NSAQIGQAIAEGNLSLVDALKN----------------------ETSTLKEQLPILEKEE-   91 (430)
Q Consensus        37 rr~l~~e~e~LraerN~--lSKeIg~~k~~~~~~~~~~Lk~----------------------e~~~Lk~eik~le~~~-   91 (430)
                      -|+..+.+++++.-.|+  +.=++=.....-+.+.+++||+                      -.+..-++++.+++-. 
T Consensus       134 dref~~~v~~~~~~~~~ee~GL~~C~~LG~l~~eqa~~LKdAGld~YNHNl~~TS~~~y~~I~sThty~DR~~T~~~~k~  213 (350)
T TIGR00433       134 DREFIEIVEAVVKIVEEEELGLKTCATLGLLDPEQAKQLKDAGLDRYNHNLDETSQEYYSKIISTHTYDDRVDTVKNAKE  213 (350)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCEECCCHHHHHHHHHHHHH
T ss_conf             20288999999999752003712232037768899998886388611167367878766873432307767999999997


Q ss_pred             -------------HHHHHHHHHHHHHCCCC--CCCHHHHCCCCCCCEEEEEECCC----CCC-CCCCCCCCCHHHH---C
Q ss_conf             -------------67788877443100225--88112211355540242000156----566-5666211220221---1
Q gi|254780680|r   92 -------------HEVCSSLKKLISCIPNV--PLEEVPIGTSANENILIRSVGKK----PSA-IHLSREHFEIGEA---L  148 (430)
Q Consensus        92 -------------~~le~el~~lll~IPNi--~~~~VP~G~de~dNv~i~~~G~~----~~f-~f~~k~H~elge~---l  148 (430)
                                   .+-.++.-.++..|-|+  .-++||+      |..+..-|.|    -.- ..+..+-.|..+.   .
T Consensus       214 aGl~~CsGGI~GlgEt~~DrI~l~~~L~~L~p~peSvPi------N~L~~~~GTP~~E~L~~~~~~~L~~~~~Lk~iA~a  287 (350)
T TIGR00433       214 AGLKVCSGGILGLGETWEDRIGLALALANLSPEPESVPI------NFLVKIEGTPAYEKLADGEVKKLSADDALKTIALA  287 (350)
T ss_pred             CCCCCCCCCEECCCCCHHHHHHHHHHHHCCCCCCCEECC------CCEECCCCCCCHHHHCCCCCCCCCHHHHHHHHHHH
T ss_conf             388724462345898889999999997527767870111------32026888853443158886733889999999998


Q ss_pred             CCCCHHHHHHHCCCCCEEECCHHH---HHHHHHHH
Q ss_conf             731000112221675301056488---99999999
Q gi|254780680|r  149 GLMDFDRATKLSGARFSVLTGHLA---HLERALGQ  180 (430)
Q Consensus       149 ~liDfe~a~kvsGsrF~~Lkg~~A---~Le~ALi~  180 (430)
                      .++--..-.++||-|-|.|+..--   ++-.|=+|
T Consensus       288 ri~mP~~~iRlagGR~~~m~e~~~kea~~~~ag~N  322 (350)
T TIGR00433       288 RIIMPKAEIRLAGGREVNMKELQQKEAMCFMAGAN  322 (350)
T ss_pred             HHHCCCCEEEEECCEEEECCCCCHHHHHHHHHHHH
T ss_conf             86543110010025145047675489999998421


No 304
>pfam06160 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.
Probab=23.93  E-value=49  Score=13.57  Aligned_cols=30  Identities=7%  Similarity=0.357  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999986
Q gi|254780680|r   33 LDEKNRILIKKIEDIRARRNSNSAQIGQAI   62 (430)
Q Consensus        33 Ld~~rr~l~~e~e~LraerN~lSKeIg~~k   62 (430)
                      .+++.+.+...++.|...-.+-+.+|.+++
T Consensus       113 ~e~~i~~i~~~l~~L~~~e~~nr~~v~~lk  142 (559)
T pfam06160       113 IEEDIEQILEELNELKESEEKNRKEVEELK  142 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999987898899999999


No 305
>pfam09457 RBD-FIP FIP domain. The FIP domain is the Rab11-binding domain (RBD) at the C-terminus of a family of Rab11-interacting proteins (FIPs). The Rab proteins constitute the largest family of small GTPases (60 members in mammals). Among them Rab11 is a well characterized regulator of endocytic and recycling pathways. Rab11 associates with a broad range of post-Golgi organelles, including recycling endosomes.
Probab=23.30  E-value=51  Score=13.49  Aligned_cols=35  Identities=20%  Similarity=0.193  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999886444666667788877443100
Q gi|254780680|r   71 DALKNETSTLKEQLPILEKEEHEVCSSLKKLISCI  105 (430)
Q Consensus        71 ~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~I  105 (430)
                      +++.....+.+.+++..+...+++++-++.++++|
T Consensus         3 ~eLi~~l~k~e~e~~~k~~~v~eLedYiD~LLvrV   37 (48)
T pfam09457         3 DELIQELLKQEEENRRKDQHVRELEDYIDNLLVRI   37 (48)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88999999999999988989989999999999999


No 306
>pfam01544 CorA CorA-like Mg2+ transporter protein. The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli. CorA is virtually ubiquitous in the Bacteria and Archaea. There are also eukaryotic relatives of this protein. The family includes the MRS2 protein from yeast, which is thought to be an RNA splicing protein. However its membership of this family suggests that its effect on splicing is due to altered magnesium levels in the cell.
Probab=22.28  E-value=53  Score=13.35  Aligned_cols=83  Identities=17%  Similarity=0.187  Sum_probs=41.5

Q ss_pred             HHHHHHHHHCCC-CCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999984698-958899999--99999999999999999999999999998644998799999999999998864446
Q gi|254780680|r   12 EHLDIALKKRHL-EPQSEYILS--LDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILE   88 (430)
Q Consensus        12 e~v~~~l~~R~~-~~~id~il~--Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le   88 (430)
                      +.+++.+.+... ..+...++-  ++.-.......++.+..+...+..++-   ...+++    ...+.-.++.++-.+.
T Consensus        92 ~~~~~~~~~~~~~~~~~~~ll~~ll~~i~~~~~~~l~~i~~~~~~le~~l~---~~~~~~----~l~~i~~lr~~l~~l~  164 (291)
T pfam01544        92 DEIRKRLENLGLGPKSPGDLLYLLLDSIVDRYFEILEKLEEELDELEDELE---DETTNE----LLRELLRLRRSLVRLR  164 (291)
T ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---CCCCHH----HHHHHHHHHHHHHHHH
T ss_conf             999999970788999999999999999999999999999999999999975---388769----9999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             6666778887744
Q gi|254780680|r   89 KEEHEVCSSLKKL  101 (430)
Q Consensus        89 ~~~~~le~el~~l  101 (430)
                      ..+.....-+..+
T Consensus       165 ~~l~~~~~~l~~l  177 (291)
T pfam01544       165 RSLAPLREVLNRL  177 (291)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9998789999999


No 307
>pfam09738 DUF2051 Double stranded RNA binding protein (DUF2051). This is a novel protein identified as interacting with the leucine-rich repeat domain of human flightless-I, FliI protein.
Probab=22.15  E-value=53  Score=13.33  Aligned_cols=35  Identities=6%  Similarity=0.137  Sum_probs=20.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999986
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAI   62 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k   62 (430)
                      +.+.++.+++|+....--+|-.+++.+.=+|-.+|
T Consensus        83 ~~L~EvEEK~rKAMvsNAQLDNEKs~l~YqVdlLK  117 (294)
T pfam09738        83 DSLIEVEEKVKKAMVSNAQLDNEKTNLMYEVDLLK  117 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf             99999999999999987502108889999999999


No 308
>pfam08590 DUF1771 Domain of unknown function (DUF1771). This domain is always found adjacent to pfam01713.
Probab=22.10  E-value=53  Score=13.32  Aligned_cols=56  Identities=14%  Similarity=0.151  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999986449987999999999999988644466666
Q gi|254780680|r   37 NRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEH   92 (430)
Q Consensus        37 rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~   92 (430)
                      +..+..+.......+|+...+-.++-..|+...+..|..+++....+.+....+-.
T Consensus         2 Y~~lR~~A~~~~~~r~~~~~~A~~Ay~~Gd~~~A~~lS~~gk~~~~~~~~~n~~Aa   57 (66)
T pfam08590         2 YQRLRAEADKHGQKRNELFQKAAEAYKRGDKAAAKELSEEGKKHGEKAEEANRQAA   57 (66)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             68799999999999999999999998828888899999998999999999979999


No 309
>PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional
Probab=21.95  E-value=22  Score=16.23  Aligned_cols=16  Identities=25%  Similarity=0.360  Sum_probs=10.1

Q ss_pred             CCCCCCEEEEEEEEEEEE
Q ss_conf             543432122221020021
Q gi|254780680|r  269 GRDTRGMLRQHQFWKCEL  286 (430)
Q Consensus       269 GkdtrGl~RvHQF~KVE~  286 (430)
                      |+=.+|.++|-  ++||.
T Consensus       273 Gti~~G~lkvG--DeIEI  288 (460)
T PTZ00327        273 GSILQGVLKVG--DEVEI  288 (460)
T ss_pred             EEEEEEEEECC--CEEEE
T ss_conf             89988179369--98998


No 310
>smart00129 KISc Kinesin motor, catalytic domain. ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.
Probab=21.91  E-value=54  Score=13.30  Aligned_cols=40  Identities=15%  Similarity=0.229  Sum_probs=28.4

Q ss_pred             EEEECCCHHHHHHHHHHHHHHCCCCCCCE-----ECCCCCCCCCCCE
Q ss_conf             04200432289999999988346899838-----6582223101880
Q gi|254780680|r  379 THTLNGSGVAVGRCLIAILENYLNADGSV-----TIPTVLRPYMNNL  420 (430)
Q Consensus       379 ~htlNgt~~A~~R~l~ailEn~q~~dg~i-----~iP~~L~pym~g~  420 (430)
                      ...+|.|.+|..++|.||-++..+  ..|     ++-..|++++||-
T Consensus       252 ~~~IN~SL~aL~~vi~~L~~~~~~--~~iPyR~SkLT~lL~d~l~g~  296 (335)
T smart00129      252 AGNINKSLSALGNVINALADGQKS--RHIPYRDSKLTRLLQDSLGGN  296 (335)
T ss_pred             HHHHCHHHHHHHHHHHHHHHCCCC--CCCCCCCCHHHHHHHHHCCCC
T ss_conf             877465689999999999834899--968875687899878755999


No 311
>COG3933 Transcriptional antiterminator [Transcription]
Probab=21.64  E-value=45  Score=13.88  Aligned_cols=55  Identities=13%  Similarity=0.056  Sum_probs=29.2

Q ss_pred             CCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHH---CHHHHHHHHH
Q ss_conf             1675301056488999999999998622320320212356202788986551---4224767764
Q gi|254780680|r  160 SGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQ---IPKFADDMFC  221 (430)
Q Consensus       160 sGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~---lp~f~~~~y~  221 (430)
                      .|+|--.|...|.     |..|.-- ..++. -.||.+=.+|...++.-.|-   +..+=+++|.
T Consensus       164 ~~~GlllLVDMGS-----L~~f~~~-i~~~~-~ipv~~i~nVST~~vLea~rk~~l~~~le~I~~  221 (470)
T COG3933         164 YRSGLLLLVDMGS-----LTSFGSI-ISEEF-GIPVKVIPNVSTSMVLEAGRKISLGLNLEQIYQ  221 (470)
T ss_pred             CCCCEEEEEECCH-----HHHHHHH-HHHHH-CCCEEEEECCCHHHHHHHHHHHHHHCCHHHHHH
T ss_conf             5674599982530-----8789999-99986-896499705418999999999873458999999


No 312
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea.  Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=21.58  E-value=54  Score=13.25  Aligned_cols=50  Identities=22%  Similarity=0.335  Sum_probs=30.4

Q ss_pred             HHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999864-499879999999999999886444666667788877443100
Q gi|254780680|r   56 AQIGQAIA-EGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCI  105 (430)
Q Consensus        56 KeIg~~k~-~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~I  105 (430)
                      |.||...- ....+..+.+..+..-|..+|+.+++....++.++..+--.|
T Consensus        50 K~vG~vLvkq~~~ea~~~v~~R~E~i~~eik~lekq~~~l~~k~~e~~~~i  100 (105)
T cd00632          50 KLVGNVLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQEKI  100 (105)
T ss_pred             HHHCCHHHEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             983433401319999999999999999999999999999999999999999


No 313
>pfam12186 AcylCoA_dehyd_C Acyl-CoA dehydrogenase C terminal. This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam02770, pfam00441, pfam02771. There is a conserved ARRL sequence motif. The C terminal domain is an alpha helical domain. The flavin ring of Acyl-CoA dehydrogenase is buried in the crevice between the two alpha helical domains and the beta-sheet domain of one subunit, and the adenosine pyrophosphate moiety is stretched into the subunit junction of a neighbouring subunit, composed of two C terminal domains.
Probab=21.55  E-value=29  Score=15.24  Aligned_cols=22  Identities=5%  Similarity=0.077  Sum_probs=7.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999
Q gi|254780680|r   37 NRILIKKIEDIRARRNSNSAQI   58 (430)
Q Consensus        37 rr~l~~e~e~LraerN~lSKeI   58 (430)
                      +..++..+..+..+..+.-+.+
T Consensus        21 l~~lk~rl~~m~~~~ee~v~~V   42 (114)
T pfam12186        21 LEPLKDRLKKMADKFEACVNFV   42 (114)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999999999999


No 314
>PRK05257 malate:quinone oxidoreductase; Validated
Probab=21.39  E-value=23  Score=16.05  Aligned_cols=33  Identities=18%  Similarity=0.206  Sum_probs=17.9

Q ss_pred             HHHHHHHHHCC-CHHH--HCCEEEEEECCCCCCCCCC
Q ss_conf             14544534205-9555--0420885322107884335
Q gi|254780680|r  235 SLTNLYSHEII-ESKS--LPLRFTTLAPSFRSEAGSA  268 (430)
Q Consensus       235 pL~~~~~~~~l-~~~~--LPik~~~~s~cfR~EaGs~  268 (430)
                      |+.--|-|.-+ +-+.  |===|+|+||-|=+ -||+
T Consensus       300 PMSVPHLDtR~IdGk~~LLFGPfAgfs~KFLK-~GS~  335 (499)
T PRK05257        300 PMSVPHLDTRVIDGKKSLLFGPFAGFSTKFLK-NGSL  335 (499)
T ss_pred             CCCCCCCCCEEECCCEEEEECCCCCCCHHHHC-CCCH
T ss_conf             96677677503689166764375455647644-8841


No 315
>pfam09389 consensus
Probab=21.26  E-value=55  Score=13.20  Aligned_cols=67  Identities=18%  Similarity=0.198  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999986-------44998799999999999998864446666677
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAI-------AEGNLSLVDALKNETSTLKEQLPILEKEEHEV   94 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k-------~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~l   94 (430)
                      .-+..|.+.|++.|.++..-..-.|+-|.++-.-.       ...-...+--|+.-...|+.+|+.||+.....
T Consensus       121 ~Y~~~l~~~~~~rQkq~~dN~~vv~eYs~elE~q~~yIketvd~~iP~nlRvLr~VLe~lR~KIQKLE~aI~tQ  194 (209)
T pfam09389       121 QYVTLLKNKWKKRQKQVKDNENVVNEYSSELEEQHLYIKETVDTNIPSNLRVLRSVLENLRSKIQKLESAISTQ  194 (209)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999997012348989889999999999988614574058999999999999999999999999


No 316
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an  N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=21.14  E-value=55  Score=13.19  Aligned_cols=29  Identities=24%  Similarity=0.353  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999998864446666677888
Q gi|254780680|r   69 LVDALKNETSTLKEQLPILEKEEHEVCSS   97 (430)
Q Consensus        69 ~~~~Lk~e~~~Lk~eik~le~~~~~le~e   97 (430)
                      ..+.+...-..+.++++.++.....++..
T Consensus        74 ~~~~L~~~~~~l~~~i~~L~~~~~~l~~~  102 (103)
T cd01106          74 LLEALREQKELLEEKKERLDKLIKTIDRT  102 (103)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999875


No 317
>pfam11285 DUF3086 Protein of unknown function (DUF3086). This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=21.10  E-value=56  Score=13.18  Aligned_cols=53  Identities=17%  Similarity=0.352  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999999864499879999999999999886
Q gi|254780680|r   28 EYILSLDEKNRILIKKIEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQL   84 (430)
Q Consensus        28 d~il~Ld~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~ei   84 (430)
                      ..+.+|.+++..|+.++++|..+|+.+-+++..-. .|..+   .+-.+++-.++=+
T Consensus         4 ~aL~eL~qrr~aL~~eIe~LErRk~rie~EmrtsF-aGqSd---~iA~RVkGFqdYL   56 (283)
T pfam11285         4 EALKDLEQRRQALEIEIEKLERRKEQIEQELRTSF-AGQSD---AIARRVKGFQDYL   56 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCH---HHHHHHHHHHHHH
T ss_conf             89999999999999999999999999999997224-65308---9999985289999


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=21.09  E-value=52  Score=13.39  Aligned_cols=12  Identities=50%  Similarity=0.606  Sum_probs=4.3

Q ss_pred             CCCCCHHCCCHH
Q ss_conf             037801178443
Q gi|254780680|r  320 VSLCTGDLGFSA  331 (430)
Q Consensus       320 v~~~sgdlg~~a  331 (430)
                      +.+-|+|||--|
T Consensus       186 iLLiTHDlgVvA  197 (239)
T TIGR02770       186 ILLITHDLGVVA  197 (239)
T ss_pred             EEEEEHHHHHHH
T ss_conf             265200078999


No 319
>pfam06039 Mqo Malate:quinone oxidoreductase (Mqo). This family consists of several bacterial Malate:quinone oxidoreductase (Mqo) proteins (EC:1.1.99.16). Mqo takes part in the citric acid cycle. It oxidizes L-malate to oxaloacetate and donates electrons to ubiquinone-1 and other artificial acceptors or, via the electron transfer chain, to oxygen. NAD is not an acceptor and the natural direct acceptor for the enzyme is most likely a quinone. The enzyme is therefore called malate:quinone oxidoreductase, abbreviated to Mqo. Mqo is a peripheral membrane protein and can be released from the membrane by addition of chelators.
Probab=21.00  E-value=27  Score=15.55  Aligned_cols=33  Identities=18%  Similarity=0.239  Sum_probs=19.8

Q ss_pred             HHHHHHHHHCCCHHHHCCE---EEEEECCCCCCCCCC
Q ss_conf             1454453420595550420---885322107884335
Q gi|254780680|r  235 SLTNLYSHEIIESKSLPLR---FTTLAPSFRSEAGSA  268 (430)
Q Consensus       235 pL~~~~~~~~l~~~~LPik---~~~~s~cfR~EaGs~  268 (430)
                      |++..|-|--+-..+=.++   |+++||-|=+. ||+
T Consensus       295 PmSvPHlDtr~idGk~~llFGP~AgfspkfLK~-GS~  330 (489)
T pfam06039       295 PMSVPHLDTRVIDGKKSLLFGPFAGFSPKFLKN-GSY  330 (489)
T ss_pred             CCCCCCCCCEEECCCEEEEECCCCCCCHHHHCC-CCH
T ss_conf             865767885045796105656754547787617-977


No 320
>PRK13339 malate:quinone oxidoreductase; Reviewed
Probab=20.87  E-value=28  Score=15.38  Aligned_cols=34  Identities=18%  Similarity=0.191  Sum_probs=21.5

Q ss_pred             CHHHHHHHHHCCCHHHHCCE---EEEEECCCCCCCCCC
Q ss_conf             11454453420595550420---885322107884335
Q gi|254780680|r  234 VSLTNLYSHEIIESKSLPLR---FTTLAPSFRSEAGSA  268 (430)
Q Consensus       234 vpL~~~~~~~~l~~~~LPik---~~~~s~cfR~EaGs~  268 (430)
                      -|+..-|-|.-+-...=.+.   |+|+||-|=+. ||+
T Consensus       296 PPMSVPHLDtR~idGk~~llFGP~Agfs~KFLK~-GS~  332 (497)
T PRK13339        296 PPMTVPHLDTRYIDGKRSLLFGPYANFGPKFLKH-GSN  332 (497)
T ss_pred             CCCCCCCCCCEEECCCEEEEECCCCCCCHHHHHC-CCH
T ss_conf             9866776763034796647644754656287627-861


No 321
>pfam11607 DUF3247 Protein of unknown function (DUF3247). This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions.
Probab=20.72  E-value=27  Score=15.52  Aligned_cols=38  Identities=26%  Similarity=0.485  Sum_probs=26.2

Q ss_pred             CCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             21078843355434321222210200212127865014578989999
Q gi|254780680|r  259 PSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSC  305 (430)
Q Consensus       259 ~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~  305 (430)
                      .-||.|+|.-|.  -|-.|+.|++.       .-+.-+-|+++++.+
T Consensus        52 q~yr~~~gdegs--ngqlrld~~d~-------~~~~~~iw~d~i~av   89 (101)
T pfam11607        52 QTYRDEHGDEGS--NGQLRLDQLDA-------SQEPQWIWMDRIVAV   89 (101)
T ss_pred             HHHHHCCCCCCC--CCCEEEHHCCC-------CCCCCEEEHHHEEEC
T ss_conf             876431166676--86276112277-------546422501220112


No 322
>KOG0612 consensus
Probab=20.54  E-value=57  Score=13.10  Aligned_cols=35  Identities=17%  Similarity=0.232  Sum_probs=14.2

Q ss_pred             CHHHHHCCCEE-ECCCCCCCCEEEEECCCHHHHHHHHH
Q ss_conf             07645326847-33899841010420043228999999
Q gi|254780680|r  358 NFQSRRMNSRY-RDPNSKSLKFTHTLNGSGVAVGRCLI  394 (430)
Q Consensus       358 D~QsrRl~iry-~~~~~~~~~~~htlNgt~~A~~R~l~  394 (430)
                      -|+.+|.++.. ++.-++ .-++-- --|..|.++++-
T Consensus      1236 ~ye~~~~~~~~~~d~~~k-~m~p~k-y~~~~a~~l~l~ 1271 (1317)
T KOG0612        1236 AYECRRCHIKCHKDHMDK-IMAPCK-YDTSSARHLLLL 1271 (1317)
T ss_pred             HHHHHHHHCCCCCCCCCC-CCCCCC-CCCCCCCCCEEC
T ss_conf             899998512302065545-567654-565677432210


No 323
>pfam03210 Paramyx_P_V Paramyxovirus P/V phosphoprotein. Paramyxoviral P genes are able to generate more than one product, using alternative reading frames and RNA editing. The P gene encodes the structural phosphoprotein P. In addition, it encodes several non-structural proteins present in the infected cell but not in the virus particle. This family includes phosphoprotein P and the non-structural phosphoprotein V from different paramyxoviruses. Phosphoprotein P is essential for the activity of the RNA polymerase complex which it forms with another subunit, L pfam00946. Although all the catalytic activities of the polymerase are associated with the L subunit, its function requires specific interactions with phosphoprotein P. The P and V phosphoproteins are amino co-terminal, but diverge at their C-termini. This difference is generated by an RNA-editing mechanism in which one or two non-templated G residues are inserted into P-gene-derived mRNA. In measles virus and Sendai virus, one G 
Probab=20.54  E-value=57  Score=13.10  Aligned_cols=85  Identities=20%  Similarity=0.321  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC----HHHHCCCC
Q ss_conf             99999999999999999864499879999999999999886444666667788877443100225881----12211355
Q gi|254780680|r   44 IEDIRARRNSNSAQIGQAIAEGNLSLVDALKNETSTLKEQLPILEKEEHEVCSSLKKLISCIPNVPLE----EVPIGTSA  119 (430)
Q Consensus        44 ~e~LraerN~lSKeIg~~k~~~~~~~~~~Lk~e~~~Lk~eik~le~~~~~le~el~~lll~IPNi~~~----~VP~G~de  119 (430)
                      ++.+..+.|+|-.+.-...+.  .+-+..++.++..||.++.+.-..+..+|..+..+...+|=.+..    ++=... +
T Consensus       264 i~~i~~rl~kLe~~~d~Il~~--~~~I~~ik~Ei~~iK~~~~k~~~slAtiEg~l~s~~I~dPG~~~~~s~~~~~~~~-~  340 (435)
T pfam03210       264 IQSIDERLDKLEEKVDKILSK--LETILLIKNEIESIKKQISKQNISLATIEGHLSSVMIAIPGFGKDVSDADVRINP-D  340 (435)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHEEEEECCCCCCCCCHHHHHHCC-C
T ss_conf             999999999999999999986--4028999999999876530355239987502423477468999987788886265-5


Q ss_pred             CCCEEEEEECCC
Q ss_conf             540242000156
Q gi|254780680|r  120 NENILIRSVGKK  131 (430)
Q Consensus       120 ~dNv~i~~~G~~  131 (430)
                      ..-|+++--|..
T Consensus       341 ~~pVi~~gpg~~  352 (435)
T pfam03210       341 LRPIIGRGPGRA  352 (435)
T ss_pred             CCCEEECCCCCC
T ss_conf             685785189997


No 324
>PRK08471 flgK flagellar hook-associated protein FlgK; Validated
Probab=20.48  E-value=57  Score=13.09  Aligned_cols=79  Identities=18%  Similarity=0.226  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC------HHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999864499------87999999999999988644466-----66677888774431
Q gi|254780680|r   35 EKNRILIKKIEDIRARRNSNSAQIGQAIAEGN------LSLVDALKNETSTLKEQLPILEK-----EEHEVCSSLKKLIS  103 (430)
Q Consensus        35 ~~rr~l~~e~e~LraerN~lSKeIg~~k~~~~------~~~~~~Lk~e~~~Lk~eik~le~-----~~~~le~el~~lll  103 (430)
                      ..|..+..+.+.|-.+-|.++.++.+....-+      -.++..+..++.+|.++|...+.     .-.++.++.+.++.
T Consensus       132 ~~R~~vl~~a~~L~~~~n~~~~~l~~~~~~~n~~i~~~V~~iN~l~~~Ia~LN~qI~~~~~~~~~~~andLlDqRD~ll~  211 (612)
T PRK08471        132 AQKQALAKKTETLTNNINDTRARLYTLQKKVNEELKVTVDEVNSLGKQIAEINKQIQEVEAGKTLKHANELRDKRDELEL  211 (612)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999999999999999999999999999999985457888982567889999999


Q ss_pred             HCCCCCCCHH
Q ss_conf             0022588112
Q gi|254780680|r  104 CIPNVPLEEV  113 (430)
Q Consensus       104 ~IPNi~~~~V  113 (430)
                      .|--+.+-.|
T Consensus       212 ~LS~lv~i~v  221 (612)
T PRK08471        212 TLSKLVGANV  221 (612)
T ss_pred             HHHHHHCEEE
T ss_conf             9987629478


No 325
>pfam10758 DUF2586 Protein of unknown function (DUF2586). This bacterial family of proteins has no known function.
Probab=20.45  E-value=57  Score=13.09  Aligned_cols=28  Identities=18%  Similarity=0.433  Sum_probs=15.5

Q ss_pred             HHEEEEEEEECCCCCC-EEEEEEECC-----CCCHHH
Q ss_conf             3402410110100483-323753102-----100764
Q gi|254780680|r  331 ACKTYDLEVWLAGQNL-YREISSCST-----CGNFQS  361 (430)
Q Consensus       331 a~~~~DiE~w~P~~~~-y~Ev~S~Sn-----c~D~Qs  361 (430)
                      +.-.|.+-.|.|-... |-   |-.|     -+|||.
T Consensus       227 ~~~R~SVP~wYpDYdG~YW---~DG~tLDv~GGDyQ~  260 (363)
T pfam10758       227 DAARYSVPQWYPDYDGVYW---GDGNTLDAEGGDYQV  260 (363)
T ss_pred             HHCCCCCCCCCCCCCCCEE---CCCCEEECCCCCHHE
T ss_conf             8637466523489997550---478165058875020


Done!