Query         gi|254781066|ref|YP_003065479.1| putative lysyl-tRNA synthetase protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 355
No_of_seqs    141 out of 3606
Neff          7.6 
Searched_HMMs 39220
Date          Mon May 30 04:07:58 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781066.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK00484 lysS lysyl-tRNA synth 100.0       0       0  743.2  27.7  340    1-352   137-491 (491)
  2 COG1190 LysU Lysyl-tRNA synthe 100.0       0       0  728.1  21.7  340    1-352   146-502 (502)
  3 PRK02983 lysS lysyl-tRNA synth 100.0       0       0  712.2  24.5  338    1-351   742-1099(1099)
  4 PRK12445 lysyl-tRNA synthetase 100.0       0       0  708.1  23.0  340    1-352   150-505 (505)
  5 KOG1885 consensus              100.0       0       0  684.4  21.6  348    1-354   191-560 (560)
  6 PRK09350 lysyl-tRNA synthetase 100.0       0       0  655.9  22.0  317    8-350     5-325 (325)
  7 cd00775 LysRS_core Lys_tRNA sy 100.0       0       0  655.3  22.1  325   17-350     3-329 (329)
  8 pfam00152 tRNA-synt_2 tRNA syn 100.0       0       0  622.8  17.9  317   18-350    18-341 (341)
  9 COG2269 Truncated, possibly in 100.0       0       0  605.2  24.7  321    4-350     1-322 (322)
 10 PRK05159 aspC aspartyl-tRNA sy 100.0       0       0  587.7  17.8  291   19-352   134-432 (434)
 11 PRK00476 aspS aspartyl-tRNA sy 100.0       0       0  564.2  20.0  327    3-353   111-563 (587)
 12 cd00776 AsxRS_core Asx tRNA sy 100.0       0       0  570.0  11.9  289   18-348    20-320 (322)
 13 PRK03932 asnC asparaginyl-tRNA 100.0       0       0  560.4  17.9  311   20-352   133-460 (462)
 14 cd00669 Asp_Lys_Asn_RS_core As 100.0       0       0  563.4  15.0  265   22-349     1-268 (269)
 15 PRK12820 bifunctional aspartyl 100.0       0       0  555.5  21.3  315   12-353   136-579 (706)
 16 PRK06462 asparagine synthetase 100.0       0       0  546.2  16.1  294   18-352    25-329 (332)
 17 TIGR00459 aspS_bact aspartyl-t 100.0       0       0  535.9  13.5  316   21-350   150-622 (653)
 18 TIGR00457 asnS asparaginyl-tRN 100.0       0       0  532.3  15.2  304   14-348   133-489 (495)
 19 TIGR00462 genX lysyl-tRNA synt 100.0       0       0  527.7  18.5  321    4-350     6-330 (330)
 20 cd00777 AspRS_core Asp tRNA sy 100.0       0       0  509.7  12.2  276   22-350     1-280 (280)
 21 COG0017 AsnS Aspartyl/asparagi 100.0       0       0  506.6  14.3  288   20-351   132-432 (435)
 22 COG0173 AspS Aspartyl-tRNA syn 100.0       0       0  493.5  22.9  308   21-352   140-560 (585)
 23 TIGR00458 aspS_arch aspartyl-t 100.0       0       0  469.1  12.5  295   19-352   152-464 (466)
 24 TIGR00499 lysS_bact lysyl-tRNA 100.0       0       0  447.5  20.1  345    1-351   156-537 (538)
 25 KOG2411 consensus              100.0       0       0  439.1  21.5  313   19-353   175-602 (628)
 26 KOG0554 consensus              100.0       0       0  430.1  11.4  294   14-348   119-440 (446)
 27 KOG0556 consensus              100.0       0       0  415.0  12.9  297   20-349   226-528 (533)
 28 KOG0555 consensus              100.0       0       0  346.1  12.3  287   20-347   241-538 (545)
 29 cd00496 PheRS_alpha_core Pheny  99.6 2.8E-14 7.1E-19  104.0  10.2  112   26-143     4-131 (218)
 30 pfam01409 tRNA-synt_2d tRNA sy  99.5 1.8E-13 4.5E-18   99.3  11.1  114   26-142    20-150 (243)
 31 PRK04172 pheS phenylalanyl-tRN  99.5 3.1E-13   8E-18   97.8  11.8  115   26-142   248-412 (501)
 32 PTZ00326 phenylalanyl-tRNA syn  99.5 3.2E-13 8.1E-18   97.7  11.2   48   95-142   369-418 (505)
 33 cd00768 class_II_aaRS-like_cor  99.5 1.8E-13 4.5E-18   99.2   7.2  116   24-142     1-124 (211)
 34 PRK09537 pylS pyrolysyl-tRNA s  99.4   3E-14 7.6E-19  103.8   2.1   93   26-126   210-317 (420)
 35 COG0016 PheS Phenylalanyl-tRNA  99.4 4.8E-12 1.2E-16   90.8  10.9  115   26-143   114-243 (335)
 36 PRK00488 pheS phenylalanyl-tRN  99.2 2.5E-10 6.5E-15   80.6   9.8  112   26-144   110-236 (338)
 37 CHL00201 syh histidine-tRNA sy  99.2 9.9E-11 2.5E-15   83.0   6.8  112    8-128     7-136 (424)
 38 PRK12292 hisZ ATP phosphoribos  99.1 1.4E-09 3.7E-14   76.1  12.4  103   21-128    16-132 (388)
 39 PRK12293 hisZ ATP phosphoribos  99.1   4E-10   1E-14   79.4   9.1  126    1-143     4-139 (281)
 40 PRK00037 hisS histidyl-tRNA sy  99.1 2.6E-09 6.5E-14   74.6  12.8  111    7-128     6-137 (417)
 41 PRK12325 prolyl-tRNA synthetas  99.1 2.1E-09 5.4E-14   75.1  10.8  118   22-142    47-180 (438)
 42 cd00773 HisRS-like_core Class   99.1 9.9E-09 2.5E-13   71.1  14.2  100   23-128     3-116 (261)
 43 COG0124 HisS Histidyl-tRNA syn  99.0 7.8E-09   2E-13   71.8  10.2  134    8-150     7-157 (429)
 44 PRK12420 histidyl-tRNA synthet  99.0 3.8E-09 9.8E-14   73.6   8.4  117   21-148    17-153 (421)
 45 TIGR02367 PylS pyrrolysyl-tRNA  98.9   3E-10 7.6E-15   80.1   0.4  115   26-141   243-367 (453)
 46 PRK12295 hisZ ATP phosphoribos  98.8 1.4E-07 3.6E-12   64.3  13.0   97   22-127     4-112 (373)
 47 pfam00587 tRNA-synt_2b tRNA sy  98.8 1.6E-08 4.2E-13   69.9   7.6  119   24-143     1-132 (170)
 48 cd00779 ProRS_core_prok Prolyl  98.8 3.2E-08 8.2E-13   68.1   7.2  122   22-143    31-165 (255)
 49 cd00771 ThrRS_core Threonyl-tR  98.7 3.9E-08 9.8E-13   67.6   7.5  133    5-146    20-166 (298)
 50 PRK12421 ATP phosphoribosyltra  98.7   4E-07   1E-11   61.7  11.8  122   20-148    19-155 (391)
 51 cd00778 ProRS_core_arch_euk Pr  98.6 3.6E-07 9.3E-12   61.9   9.6  130    4-143    21-171 (261)
 52 cd00670 Gly_His_Pro_Ser_Thr_tR  98.6 2.2E-07 5.6E-12   63.2   6.8  121   23-144     3-140 (235)
 53 cd00772 ProRS_core Prolyl-tRNA  98.5 1.9E-06 4.9E-11   57.6  11.3  122   22-143    32-171 (264)
 54 PRK05425 asparagine synthetase  98.5 1.5E-05 3.8E-10   52.4  15.1  267   22-344     8-308 (327)
 55 cd00774 GlyRS-like_core Glycyl  98.4 5.1E-07 1.3E-11   61.0   5.8   99   22-130    32-145 (254)
 56 cd00645 AsnA Asparagine synthe  98.4 2.6E-05 6.6E-10   50.9  13.2  262   28-344     3-298 (309)
 57 PRK12305 thrS threonyl-tRNA sy  98.3 5.6E-06 1.4E-10   54.8   9.1  130    5-145   198-344 (576)
 58 PRK03772 threonyl-tRNA synthet  98.2 1.9E-05 4.9E-10   51.7   9.9  130    5-145   261-406 (642)
 59 PRK06253 O-phosphoseryl-tRNA s  98.2 9.5E-07 2.4E-11   59.4   2.6   48   96-143   208-258 (527)
 60 cd00770 SerRS_core Seryl-tRNA   98.1 3.3E-06 8.3E-11   56.2   4.8  122   21-145    51-188 (297)
 61 PRK12304 thrS threonyl-tRNA sy  98.1 4.9E-05 1.3E-09   49.3  10.1  132    5-147   229-376 (604)
 62 PTZ00213 asparagine synthetase  98.1 9.8E-05 2.5E-09   47.5  11.3  294   22-344     8-336 (350)
 63 PRK04483 threonyl-tRNA synthet  98.1 2.5E-05 6.3E-10   51.1   8.0  133    5-148   261-412 (634)
 64 PRK00413 thrS threonyl-tRNA sy  98.0 4.3E-05 1.1E-09   49.6   8.8  130    5-145   258-404 (639)
 65 PRK12444 threonyl-tRNA synthet  98.0 8.8E-05 2.3E-09   47.8   9.8  130    5-145   264-409 (639)
 66 COG0442 ProS Prolyl-tRNA synth  97.9 2.8E-05 7.2E-10   50.7   6.2  123   22-145    47-183 (500)
 67 TIGR00469 pheS_mito phenylalan  97.9 7.3E-05 1.8E-09   48.3   7.6  129    9-147    31-194 (460)
 68 PRK03991 threonyl-tRNA synthet  97.8 3.8E-05 9.7E-10   49.9   5.7  123   23-147   228-366 (613)
 69 COG0441 ThrS Threonyl-tRNA syn  97.8 7.2E-05 1.8E-09   48.3   6.2  114   23-147   221-357 (589)
 70 PRK08661 prolyl-tRNA synthetas  97.7  0.0002 5.1E-09   45.7   7.7  122   22-143    45-183 (478)
 71 KOG2784 consensus               97.7 5.7E-05 1.4E-09   48.9   4.6   59   83-143   322-384 (483)
 72 PRK04173 glycyl-tRNA synthetas  97.6 0.00018 4.5E-09   46.0   6.5   33   97-131   192-228 (460)
 73 COG2502 AsnA Asparagine synthe  97.6   0.002   5E-08   39.8  11.5  106   22-130     5-127 (330)
 74 TIGR00418 thrS threonyl-tRNA s  97.5 0.00012 3.2E-09   46.9   4.6  133    7-147   204-352 (595)
 75 COG0423 GRS1 Glycyl-tRNA synth  97.4 0.00017 4.3E-09   46.1   4.2   31   22-52     40-72  (558)
 76 PRK09194 prolyl-tRNA synthetas  97.4 0.00085 2.2E-08   42.0   7.1  123   22-148    47-189 (570)
 77 PRK05431 seryl-tRNA synthetase  97.3 0.00059 1.5E-08   42.9   5.4  122   23-147   171-308 (422)
 78 KOG2324 consensus               97.1  0.0018 4.5E-08   40.0   6.5  125   22-150    52-197 (457)
 79 COG0172 SerS Seryl-tRNA synthe  96.8  0.0016   4E-08   40.4   3.8  113   29-144   181-309 (429)
 80 TIGR00442 hisS histidyl-tRNA s  96.3  0.0081 2.1E-07   36.1   4.8  128   21-149    17-159 (446)
 81 TIGR00389 glyS_dimeric glycyl-  95.7  0.0013 3.3E-08   40.8  -1.4   30   23-52     38-69  (606)
 82 KOG1035 consensus               95.3   0.073 1.9E-06   30.5   6.5  110   24-144   934-1056(1351)
 83 COG3705 HisZ ATP phosphoribosy  95.3    0.02 5.1E-07   33.8   3.5  100   21-127    16-128 (390)
 84 cd00673 AlaRS_core Alanyl-tRNA  94.6    0.34 8.7E-06   26.5  11.3   95   27-147     3-107 (232)
 85 TIGR00468 pheS phenylalanyl-tR  94.3   0.018 4.5E-07   34.1   1.2  119   25-143    83-256 (362)
 86 KOG1936 consensus               94.2   0.018 4.7E-07   34.0   1.0  108   21-137    73-194 (518)
 87 PRK00252 alaS alanyl-tRNA synt  94.1    0.43 1.1E-05   25.9   8.6   99   26-145     5-108 (864)
 88 KOG2783 consensus               93.9   0.031   8E-07   32.7   1.9   98   28-127    77-184 (436)
 89 KOG2509 consensus               93.9   0.038 9.6E-07   32.2   2.3  122   21-143   184-328 (455)
 90 PRK13902 alaS lanyl-tRNA synth  93.8   0.033 8.4E-07   32.5   1.7   32   96-128   117-153 (898)
 91 cd00769 PheRS_beta_core Phenyl  93.6    0.08   2E-06   30.3   3.4   81   25-109     2-93  (198)
 92 PRK09348 glyQ glycyl-tRNA synt  93.4   0.058 1.5E-06   31.1   2.5   20   26-45      5-24  (291)
 93 TIGR00408 proS_fam_I prolyl-tR  93.3    0.11 2.9E-06   29.3   3.9  214   22-260    39-301 (533)
 94 PRK09616 pheT phenylalanyl-tRN  93.3    0.29 7.3E-06   27.0   5.9   13  123-135   228-240 (546)
 95 COG0013 AlaS Alanyl-tRNA synth  92.9     0.7 1.8E-05   24.7   7.4   45   96-146    64-113 (879)
 96 COG0752 GlyQ Glycyl-tRNA synth  90.2    0.24 6.1E-06   27.4   2.7   20   26-45      8-27  (298)
 97 TIGR00389 glyS_dimeric glycyl-  90.0    0.28 7.2E-06   27.0   2.8   64   62-129   171-248 (606)
 98 TIGR00470 sepS O-phosphoseryl-  89.8    0.14 3.7E-06   28.8   1.2   33  314-347   329-362 (558)
 99 COG2024 Phenylalanyl-tRNA synt  89.2    0.26 6.6E-06   27.3   2.2   32  314-346   319-351 (536)
100 KOG0188 consensus               86.8     2.3 5.8E-05   21.6  10.9  102   26-144     5-117 (895)
101 pfam02091 tRNA-synt_2e Glycyl-  86.8    0.42 1.1E-05   26.0   2.0   21   26-46      2-22  (284)
102 KOG2298 consensus               85.8     0.2 5.1E-06   27.9  -0.0   30   24-53     48-78  (599)
103 cd00733 GlyRS_alpha_core Class  85.0    0.55 1.4E-05   25.3   1.9   29  316-344   150-178 (279)
104 CHL00192 syfB phenylalanyl-tRN  83.3     3.1   8E-05   20.8   5.2  113   25-143   396-526 (702)
105 TIGR00468 pheS phenylalanyl-tR  81.8    0.58 1.5E-05   25.2   1.0   27  318-344   323-349 (362)
106 TIGR00669 asnA aspartate--ammo  77.1     3.3 8.4E-05   20.7   3.6   47  297-344   268-315 (330)
107 COG2160 AraA L-arabinose isome  71.6     7.5 0.00019   18.6   5.1   53   94-147   175-233 (497)
108 cd00768 class_II_aaRS-like_cor  69.7    0.32 8.2E-06   26.7  -3.0   52  258-329   153-211 (211)
109 pfam10026 DUF2268 Predicted Zn  68.7       3 7.8E-05   20.9   1.8   88  257-346    99-189 (195)
110 PRK02929 L-arabinose isomerase  68.5     8.8 0.00022   18.2   4.3   14  259-272   399-412 (499)
111 pfam02610 Arabinose_Isome L-ar  66.5     9.6 0.00024   18.0   4.5   50    1-50      1-55  (359)
112 PRK00629 pheT phenylalanyl-tRN  64.5     7.5 0.00019   18.6   3.1  115   25-143   486-617 (786)
113 PRK01584 alanyl-tRNA synthetas  63.5     4.6 0.00012   19.9   1.9  101   27-148     5-109 (593)
114 PRK07080 hypothetical protein;  62.9     5.9 0.00015   19.2   2.3   42  101-143   160-202 (318)
115 KOG0903 consensus               60.9       5 0.00013   19.6   1.7   14   37-50    312-325 (847)
116 pfam01411 tRNA-synt_2c tRNA sy  58.2     8.7 0.00022   18.2   2.5   91   30-140     4-106 (545)
117 PRK13384 delta-aminolevulinic   44.9      11 0.00029   17.6   1.3   15   87-101    69-83  (323)
118 TIGR02151 IPP_isom_2 isopenten  44.6      12 0.00031   17.4   1.5   19  328-346   326-344 (349)
119 PRK09283 delta-aminolevulinic   37.8      23 0.00059   15.7   2.1   11   87-97     66-76  (321)
120 pfam05830 NodZ Nodulation prot  37.5      11 0.00027   17.7   0.3   21  304-324   267-290 (322)
121 cd04823 ALAD_PBGS_aspartate_ri  37.0      21 0.00053   16.0   1.7   11   87-97     61-71  (320)
122 pfam03590 AsnA Aspartate-ammon  35.5      32 0.00081   14.9   7.3  120   22-144     3-139 (244)
123 TIGR00614 recQ_fam ATP-depende  34.8      12 0.00032   17.3   0.3   20   80-99    110-130 (497)
124 TIGR00409 proS_fam_II prolyl-t  34.6      33 0.00083   14.8   2.8  123   22-150    48-197 (620)
125 TIGR00414 serS seryl-tRNA synt  34.0      34 0.00085   14.7   4.2  119   24-143   204-345 (460)
126 cd00384 ALAD_PBGS Porphobilino  33.7      24  0.0006   15.6   1.6   11   87-97     58-68  (314)
127 TIGR01226 phe_am_lyase phenyla  33.2      14 0.00035   17.1   0.3   14   72-85    340-354 (714)
128 COG4302 EutC Ethanolamine ammo  32.2      36 0.00091   14.6   3.5   13   28-40      6-18  (294)
129 pfam00490 ALAD Delta-aminolevu  30.6      31  0.0008   14.9   1.8   10   30-39     13-22  (322)
130 KOG1637 consensus               29.9      39   0.001   14.3   3.1  120   23-148   193-333 (560)
131 TIGR02400 trehalose_OtsA alpha  29.4      40   0.001   14.3   3.0   23  116-138   239-261 (476)
132 TIGR02764 spore_ybaN_pdaB poly  28.7      13 0.00034   17.1  -0.4   10  264-273    58-67  (198)
133 cd03557 L-arabinose_isomerase   28.7      41  0.0011   14.2   5.0   16  259-274   393-408 (484)
134 pfam09743 DUF2042 Uncharacteri  28.5      29 0.00074   15.1   1.3   17   88-104    63-80  (272)
135 TIGR01184 ntrCD nitrate ABC tr  28.5      17 0.00044   16.5   0.1   38  302-353   172-210 (230)
136 TIGR01733 AA-adenyl-dom amino   28.0      33 0.00084   14.8   1.5   26  263-290   357-382 (452)
137 PRK05776 DNA topoisomerase III  25.7      47  0.0012   13.9   3.8   23  276-299   538-560 (675)
138 TIGR02676 cas_provis_2 CRISPR-  25.4      47  0.0012   13.9   3.1   93   28-124    87-193 (1104)
139 COG1304 idi Isopentenyl diphos  21.7      52  0.0013   13.6   1.6   20  328-347   329-348 (360)
140 TIGR02708 L_lactate_ox L-lacta  21.1      46  0.0012   13.9   1.2   21  328-348   340-360 (368)
141 TIGR02653 Lon_rel_chp conserve  21.1      50  0.0013   13.7   1.3   17  255-271   344-360 (677)
142 pfam12109 CXCR4_N CXCR4 Chemok  21.0      31 0.00078   15.0   0.2   10  101-110    21-30  (33)
143 COG0113 HemB Delta-aminolevuli  20.4      60  0.0015   13.3   1.9   15  128-142    98-112 (330)
144 COG3919 Predicted ATP-grasp en  20.1      61  0.0015   13.2   3.0   40   89-138    76-115 (415)

No 1  
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=100.00  E-value=0  Score=743.15  Aligned_cols=340  Identities=31%  Similarity=0.513  Sum_probs=313.1

Q ss_pred             CCCCCCCCCC--CHHHCCCHH-----------HHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC
Q ss_conf             9988987478--831261548-----------999999999999999999879889847821056898544541241024
Q gi|254781066|r    1 MHQIPSQPWW--NRDFHYRRR-----------PFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI   67 (355)
Q Consensus         1 ~~~~p~~~~~--~~~~~~r~R-----------~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~   67 (355)
                      ++|||..+.+  +.+.|+|+|           .+++.||+|+++||+||+++||+||+||+|++++||++ |+||.|+  
T Consensus       137 l~plP~k~~g~~d~e~r~r~RyLDLi~n~~~~~~f~~Rs~ii~~iR~~l~~~gF~EVeTPiL~~~~gGA~-ArpF~t~--  213 (491)
T PRK00484        137 LRPLPDKFHGLSDQETRYRQRYLDLIVNEESRETFRKRSKIISAIRRFLDNRGFLEVETPMLQPIPGGAA-ARPFITH--  213 (491)
T ss_pred             CCCCCCCCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCCCC-CCCCCCC--
T ss_conf             8899854445567556311330210279999999999999999999999867689986787766688756-6765564--


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             78867832000028589999898744688999886424567775448430020001157765787775578887766641
Q gi|254781066|r   68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA  147 (355)
Q Consensus        68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~  147 (355)
                       +|++++++||+||||||||+||+||++||||||||||||+++++|+||||||||||||+|++|+|+++|+||+++++.+
T Consensus       214 -~n~l~~~~yL~~SPqLylk~l~vgG~ervfeI~r~FR~E~~~~rH~pEFT~lE~e~af~d~~dvm~l~E~li~~v~~~v  292 (491)
T PRK00484        214 -HNALDIDLYLRIAPELYLKRLIVGGFERVFEIGRNFRNEGIDTRHNPEFTMIEFYQAYADYNDMMDLTEELIRHLAKEV  292 (491)
T ss_pred             -CCCCCCCEEECCCHHHHHHHHHHCCCHHHEEHHHHHHCCCCCCCCCCCEEEEEEEEECCCHHHHHHHHHHHHHHHHHHH
T ss_conf             -4566855442068789877787627202222487662575543418401021367724799999999999999999996


Q ss_pred             -CCCEECCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEE
Q ss_conf             -8830002234332467732078888656660876532345556232799999999768877876534789876643003
Q gi|254781066|r  148 -NQKIFSFQNVNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKI  226 (355)
Q Consensus       148 -~~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~i  226 (355)
                       ++..+.+.+..++...+|++++|.+++++++++++....      ....+...+++.+.++...++|+++++.++++++
T Consensus       293 ~g~~~~~~~~~~idl~~pf~rit~~eai~~~~g~d~~~~~------~~~~l~~~~~~~g~~~~~~~~~g~l~~~lfe~~v  366 (491)
T PRK00484        293 LGTTKITYGGTEIDFGKPFKRLTMVDAIKEYTGVDFTPQD------EEEEARAIAKELGVEVEKSWGLGKLINELFEEFV  366 (491)
T ss_pred             CCCCEEEECCEEECCCCCCEECCHHHHHHHHCCCCCCCCC------CHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             1995673287763378995022399999997099876556------7899999999869987887787899999888776


Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHH
Q ss_conf             62237675443257688886413678778363302202236712256402106999999999999999972888530101
Q gi|254781066|r  227 EPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPID  306 (355)
Q Consensus       227 e~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D  306 (355)
                      ++++  ..|+||+|||.++|||||.+++||++++|||||++|+||||||+|||||.+|++||++|+..|+.+++|++++|
T Consensus       367 e~~l--~~PtFV~d~P~e~sPlak~~~~dp~~~erfdL~i~G~Ei~ng~~el~Dp~~Q~~rf~~q~~~k~~gd~ea~~~D  444 (491)
T PRK00484        367 EPKL--IQPTFITDYPVEISPLAKRHRSNPGFTERFELFIGGRELANAFSELNDPIDQRERFEAQVEAKEAGDDEAMFYD  444 (491)
T ss_pred             HHHC--CCCEECCCCCCCCCCCCCCCCCCCCCEEEECEEECCEEECCCCHHHCCHHHHHHHHHHHHHHHHCCCCHHHHCC
T ss_conf             5411--46400136722158755668889670367564348899736503317999999999999999864883233240


Q ss_pred             HHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCC
Q ss_conf             8999986-188963245315999989981559713111585648743
Q gi|254781066|r  307 EDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQ  352 (355)
Q Consensus       307 ~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~  352 (355)
                      ++||+|| +|||||||||||||||||+|||++|||||||||.|||++
T Consensus       445 edfl~Al~yG~PPhgG~GlGiDRLvMlLtg~~sIRdVI~FP~~kp~~  491 (491)
T PRK00484        445 EDFLRALEYGMPPTGGLGIGIDRLVMLLTNSPSIRDVILFPAMRPEK  491 (491)
T ss_pred             HHHHHHHHCCCCCCCEEEEHHHHHHHHHCCCCCHHHCCCCCCCCCCC
T ss_conf             99999977799998526556999999983999577501688889999


No 2  
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=728.12  Aligned_cols=340  Identities=31%  Similarity=0.518  Sum_probs=316.4

Q ss_pred             CCCCCCCCCC--CHHHCCCHHH-----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC
Q ss_conf             9988987478--8312615489-----------99999999999999999879889847821056898544541241024
Q gi|254781066|r    1 MHQIPSQPWW--NRDFHYRRRP-----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI   67 (355)
Q Consensus         1 ~~~~p~~~~~--~~~~~~r~R~-----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~   67 (355)
                      |+|||..+.|  +++.|+|+|.           .++.||+|+++||+||+++||+||+||+|++.+||++ |+||.|+  
T Consensus       146 L~pLPeK~hgL~D~E~RyR~RylDLi~N~e~r~~f~~Rs~ii~~iR~fl~~~gFlEVETP~lq~i~GGA~-ArPF~Th--  222 (502)
T COG1190         146 LRPLPEKFHGLTDKEIRYRQRYLDLIVNPESRQTFIKRSKIIRAIREFLDDRGFLEVETPMLQPIPGGAA-ARPFITH--  222 (502)
T ss_pred             CCCCCHHHCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCC-CCCCEEE--
T ss_conf             7779745437863888999888898659999999999999999999999877975841600035578732-2650122--


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             78867832000028589999898744688999886424567775448430020001157765787775578887766641
Q gi|254781066|r   68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA  147 (355)
Q Consensus        68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~  147 (355)
                       ||.++.++||++|||||||+|+++|++|||+||++||||+.|++|||||||||+|+||+|++|+|+++|++|+++++.+
T Consensus       223 -hNald~dlyLRIApELyLKRliVGG~erVfEIgr~FRNEGid~tHNPEFTmlE~Y~AYaDy~D~m~ltE~Li~~~a~~v  301 (502)
T COG1190         223 -HNALDMDLYLRIAPELYLKRLIVGGFERVFEIGRNFRNEGIDTTHNPEFTMLEFYQAYADYEDLMDLTEELIKELAKEV  301 (502)
T ss_pred             -ECCCCCCEEEEECCHHHHHHHHHCCCHHHEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             -0236775687624189999887537214223055200378766648423568999998579999999999999999995


Q ss_pred             C-CCEECCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCC--CCHHHHHHHHHHC
Q ss_conf             8-830002234332467732078888656660876532345556232799999999768877876--5347898766430
Q gi|254781066|r  148 N-QKIFSFQNVNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHD--DTWSDIFSRILIE  224 (355)
Q Consensus       148 ~-~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~l~~~  224 (355)
                      . +..+.|.+..+++.++|+++++.+++++++++++.      ...+...+...+++.++++...  +++|.++.++|++
T Consensus       302 ~gt~~v~y~~~~id~~~pf~ri~m~dal~e~~g~~~~------~~~~~e~~~~~ak~~~i~~~~~~~~~~g~ll~~lFe~  375 (502)
T COG1190         302 NGTTKVTYGGQEIDFSKPFKRITMVDALKEYLGVDFD------DLFDDEEAKELAKKHGIEVEKYGTWGLGHLLNELFEE  375 (502)
T ss_pred             CCCEEEEECCEEEECCCCEEEEEHHHHHHHHHCCCCC------CCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             4973787899767548972256648999987186655------4588799999999808975765553678999999987


Q ss_pred             EECCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCH
Q ss_conf             03622376754432576888864136787783633022022367122564021069999999999999999728885301
Q gi|254781066|r  225 KIEPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYP  304 (355)
Q Consensus       225 ~ie~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~  304 (355)
                      .+|++|  .+|+||+|||.++|||||.++++|++++||||||+|.||||||+|||||.+|++||++|...++.|++|++.
T Consensus       376 ~vE~~l--iqPTFv~d~P~eiSPLak~~~~~p~~teRFElfi~g~EiaNaysELNDP~dQ~~RF~~Q~~~k~~Gddea~~  453 (502)
T COG1190         376 LVEAKL--IQPTFVTDHPVEISPLAKRHRSNPGLTERFELFIGGKEIANAYSELNDPVDQRERFEAQVEEKEAGDDEAME  453 (502)
T ss_pred             HHHHHH--CCCCEEECCCCCCCCCCCCCCCCCCHHHHHEEEECCEEEEECCCHHCCHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             765641--488246168543686656798886513221013545876311222069999999999999998729930011


Q ss_pred             HHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCC
Q ss_conf             0189999861-88963245315999989981559713111585648743
Q gi|254781066|r  305 IDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQ  352 (355)
Q Consensus       305 ~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~  352 (355)
                      +|++|++||+ ||||+||+|||||||||+|||+.||||||+||.||+.+
T Consensus       454 ~Dedfv~ALeyGmPPTgG~GiGIDRLvMllT~~~sIRdVilFP~mr~~~  502 (502)
T COG1190         454 LDEDFVEALEYGMPPTGGLGIGIDRLVMLLTNSPSIRDVILFPAMRPEK  502 (502)
T ss_pred             CCHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCHHHEECCCCCCCCC
T ss_conf             5799999986699998875125777777773998554222156557889


No 3  
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=100.00  E-value=0  Score=712.22  Aligned_cols=338  Identities=29%  Similarity=0.414  Sum_probs=305.4

Q ss_pred             CCCCCCCCCC--CHHHCCCHHH-----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC
Q ss_conf             9988987478--8312615489-----------99999999999999999879889847821056898544541241024
Q gi|254781066|r    1 MHQIPSQPWW--NRDFHYRRRP-----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI   67 (355)
Q Consensus         1 ~~~~p~~~~~--~~~~~~r~R~-----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~   67 (355)
                      |+|||..+.+  +.+.|+|+|.           +++.||+|+++||+||+++||+|||||||++.+||+. |+||.|+. 
T Consensus       742 L~PLP~k~~gl~d~E~RlR~RYLDLr~npe~r~~~~~RS~Vi~aiR~~L~~~GFlEVETPiLq~~~GGA~-ARPFlThs-  819 (1099)
T PRK02983        742 LRPLPDKWKGLTDPEARVRARYLDLAVNPEARDLIRARSAVLRAVRETLVAKGFLEVETPILQQIHGGAN-ARPFLTHI-  819 (1099)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCC-CCCCCCCC-
T ss_conf             6799976779887767556455651589899999999999999999999878988955754677888756-78530103-


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             78867832000028589999898744688999886424567775448430020001157765787775578887766641
Q gi|254781066|r   68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA  147 (355)
Q Consensus        68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~  147 (355)
                        |.++.++||+||||||||+||++|++||||||||||||+.+.+||||||||||||||+|++++|+++|+|++.+++.+
T Consensus       820 --na~d~~~YLriAPELflKRLmVGGfeRVFEI~RcFRNEglradHnPEFTmLE~Y~Ay~Dyedmm~ltEeLi~~~a~~~  897 (1099)
T PRK02983        820 --NAYDLDLYLRIAPELYLKRLCVGGVERVFELGRAFRNEGVDFSHNPEFTLLEAYQAHADYLVMRDLCRELIQNAAQAA  897 (1099)
T ss_pred             --CCCCCCCEEECCHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             --367866145148089999998648631134325446799998749407999999984789999999999999999995


Q ss_pred             CC-CEEC-----CCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHH
Q ss_conf             88-3000-----22343324677320788886566608765323455562327999999997688778765347898766
Q gi|254781066|r  148 NQ-KIFS-----FQNVNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRI  221 (355)
Q Consensus       148 ~~-~~~~-----~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  221 (355)
                      .. .++.     +....+|...+|+++++.+++++.++.++...      .....+...+++.++.....+++|+++.++
T Consensus       898 ~G~~v~~~pd~~~~~~~iDls~~w~~~t~~eai~e~~G~di~~~------~~~e~L~~~a~~~gi~~~~~~~~G~lv~eL  971 (1099)
T PRK02983        898 NGEPVVMRPGTDGVLEPVDISGEWPVKTVHEAVSEALGEEIDAD------TPLETLRRLCDAAGIPYLTHWDAGAVVLEL  971 (1099)
T ss_pred             HCCEEEECCCCCCCCEEEECCCCCEEEEHHHHHHHHHCCCCCCC------CCHHHHHHHHHHCCCCCCCCCCHHHHHHHH
T ss_conf             19657861687788768656999526539999999838878999------999999999997799778999977999999


Q ss_pred             HHCEECCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             43003622376754432576888864136787783633022022367122564021069999999999999999728885
Q gi|254781066|r  222 LIEKIEPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNE  301 (355)
Q Consensus       222 ~~~~ie~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e  301 (355)
                      +++.+++++  ..|+||+|||.+++||+|++++||++++|||||+||+||+|||+|||||.+|++||++|+.++.+++.|
T Consensus       972 ~e~lVE~~l--~~PtFV~DfP~e~sPLarp~~~dp~lAeRfDLvinG~ELgnGysELnDP~eQR~Rf~eQ~~~~~ggD~E 1049 (1099)
T PRK02983        972 YEHLVEDRT--TEPTFYTDFPTSVSPLTRPHRSDPGVAERWDLVAWGVELGTAYSELTDPVEQRRRLTEQSLLAAGGDPE 1049 (1099)
T ss_pred             HHHHCCCCC--CCCEEEECCCCCCCCCCCCCCCCCCEEEEEEEEECCEEEECCHHHHCCHHHHHHHHHHHHHHHHCCCCH
T ss_conf             998527376--677899899722390417789996827877255558997021035169999999999999998679900


Q ss_pred             CCHHHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCC
Q ss_conf             3010189999861-8896324531599998998155971311158564874
Q gi|254781066|r  302 TYPIDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSN  351 (355)
Q Consensus       302 ~~~~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~  351 (355)
                      ++++|++||+||+ |||||||+|+|||||||+|||. ||||||+||++||.
T Consensus      1050 am~~DEdFL~ALeYGmPPhGGialGIDRLVMLLTG~-SIREVIaFPl~kP~ 1099 (1099)
T PRK02983       1050 AMELDEDFLQALEYAMPPTGGLGMGVDRLVMLITGR-SIRETLPFPLAKPR 1099 (1099)
T ss_pred             HHHCHHHHHHHHCCCCCCCCCEEEHHHHHHHHHCCC-CHHHHCCCCCCCCC
T ss_conf             233217899984318997364754499999996299-75987438787998


No 4  
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=100.00  E-value=0  Score=708.05  Aligned_cols=340  Identities=27%  Similarity=0.457  Sum_probs=304.7

Q ss_pred             CCCCCCCCCC--CHHHCCCHHH-----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC
Q ss_conf             9988987478--8312615489-----------99999999999999999879889847821056898544541241024
Q gi|254781066|r    1 MHQIPSQPWW--NRDFHYRRRP-----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI   67 (355)
Q Consensus         1 ~~~~p~~~~~--~~~~~~r~R~-----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~   67 (355)
                      ++|||..+.+  +.+.|+|+|.           +++.||+|+++||+||+++||+||+||+|+++|||++ |+||.|+  
T Consensus       150 l~plP~k~~g~~d~e~R~r~RyLDLir~~~~~~~~~~Rs~ii~~iR~~l~~~gF~EVeTPil~~~~gGa~-Arpf~t~--  226 (505)
T PRK12445        150 LRPLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGAS-ARPFITH--  226 (505)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCC-CCEEEEC--
T ss_conf             7898974557878877634111143659999999999999999999999977938997887555458766-6103304--


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             78867832000028589999898744688999886424567775448430020001157765787775578887766641
Q gi|254781066|r   68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA  147 (355)
Q Consensus        68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~  147 (355)
                       +++++.++||+||||||||+||+|||+||||||||||||+++++|+||||||||||||+|++|+|+++|+||+++++.+
T Consensus       227 -~~~~~~~~yL~qSPQLykk~LmvgGfdRvfeI~r~FRnE~~~~~H~PEFT~lE~e~af~d~~dvm~l~E~li~~i~~~v  305 (505)
T PRK12445        227 -HNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEV  305 (505)
T ss_pred             -CCCCCCCEEECCCCHHHHHHHHHCCCCCEEEHHHHHHCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             -6678867434169399999998579744576278760788886654445435687632789899999999999999984


Q ss_pred             -CCCEECCCCCCCCCCCCCCCCCHHHHHHHHCC-CCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCE
Q ss_conf             -88300022343324677320788886566608-7653234555623279999999976887787653478987664300
Q gi|254781066|r  148 -NQKIFSFQNVNCNPFSEPEYITVAEAFARYAN-IDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEK  225 (355)
Q Consensus       148 -~~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~-~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  225 (355)
                       +...++|.+...+...+|+++++.++++++.. .+...      ..........+.+.+......+.++.++..++.+.
T Consensus       306 ~g~~~i~y~~~~~d~~~pf~rlt~~eai~~~~~~~~~~~------~~~~~~~~~~~~~~g~~~~~~~~~g~l~~~~~~e~  379 (505)
T PRK12445        306 LGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMAD------LDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEV  379 (505)
T ss_pred             CCCCEEEECCCHHCCCCCCCCCCHHHHHHHHCCCCCHHH------CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             488358665201201698410349999998568887453------34469999999985985344434427999998877


Q ss_pred             ECCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHH
Q ss_conf             36223767544325768888641367877836330220223671225640210699999999999999997288853010
Q gi|254781066|r  226 IEPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPI  305 (355)
Q Consensus       226 ie~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~  305 (355)
                      +++++  ..|+||+|||.+++||||.++++|.+++|||||++|.||||||+|||||.+|++||++|...+..++++++.+
T Consensus       380 ~e~~l--~~P~fv~d~P~e~splak~~~~~p~~t~rfdl~i~G~Ei~nG~~el~Dp~~Q~~rf~~q~~~k~~g~~e~~~~  457 (505)
T PRK12445        380 AEAHL--IQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFY  457 (505)
T ss_pred             HHHCC--CCCCCCCCCCCCCCCHHCCCCCCHHHHHEEEEEECCEEEEECEECCCCHHHHHHHHHHHHHHHHCCCCCHHHC
T ss_conf             77505--5554244775445830016799841401453511899987460226899999999999887775476600012


Q ss_pred             HHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCC
Q ss_conf             189999861-88963245315999989981559713111585648743
Q gi|254781066|r  306 DEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQ  352 (355)
Q Consensus       306 D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~  352 (355)
                      |++||+||+ |||||||||||||||||+|||++||||||+||.|||++
T Consensus       458 de~fl~Al~yG~PPhgG~glGiDRLvMlLtg~~sIRdVI~FP~~rp~~  505 (505)
T PRK12445        458 DEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRPQK  505 (505)
T ss_pred             HHHHHHHHHCCCCCHHCCHHHHHHHHHHHCCCCCHHEECCCCCCCCCC
T ss_conf             288999965699850034379999999981999564071699989999


No 5  
>KOG1885 consensus
Probab=100.00  E-value=0  Score=684.38  Aligned_cols=348  Identities=27%  Similarity=0.445  Sum_probs=323.4

Q ss_pred             CCCCCCCCCC--CHHHCCCHHH-----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC
Q ss_conf             9988987478--8312615489-----------99999999999999999879889847821056898544541241024
Q gi|254781066|r    1 MHQIPSQPWW--NRDFHYRRRP-----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI   67 (355)
Q Consensus         1 ~~~~p~~~~~--~~~~~~r~R~-----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~   67 (355)
                      |||||+.|++  +.+.|+|+|.           .|++||+|++.||.||+++||+||+||+|+..+||++ |+||+|+  
T Consensus       191 Lh~lP~~~~gLkD~EtRyrqRylDlilN~~~r~~f~~RakII~~iRkfld~rgFlEVETPmmn~iaGGA~-AkPFIT~--  267 (560)
T KOG1885         191 LHMLPHEHFGLKDKETRYRKRYLDLILNPEVRDRFRIRAKIISYIRKFLDSRGFLEVETPMMNMIAGGAT-AKPFITH--  267 (560)
T ss_pred             HCCCCHHHCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCHHHCCCCCCCC-CCCEEEC--
T ss_conf             1348766517776888999888998708889999999999999999986544956844465525468632-5760431--


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             78867832000028589999898744688999886424567775448430020001157765787775578887766641
Q gi|254781066|r   68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA  147 (355)
Q Consensus        68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~  147 (355)
                       ||.++.++||+++||||+|+|+++|++|||+||+.||||++|.+||||||.+|+||||+|++|+|+.+|+|++.+++.+
T Consensus       268 -hndldm~LylRiAPEL~lK~LvVGGldrVYEIGr~FRNEGIDlTHNPEFTTcEfY~AYady~dlm~~TE~l~s~mv~~i  346 (560)
T KOG1885         268 -HNDLDMDLYLRIAPELYLKMLVVGGLDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYEDLMDMTEELLSGMVKNI  346 (560)
T ss_pred             -CCCCCCCEEEEECHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             -4556755145636599999898601789999878763057665458774218999987538889999999999999960


Q ss_pred             CC-CEECCCC-------CCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHH
Q ss_conf             88-3000223-------433246773207888865666087653234555623279999999976887787653478987
Q gi|254781066|r  148 NQ-KIFSFQN-------VNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFS  219 (355)
Q Consensus       148 ~~-~~~~~~~-------~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  219 (355)
                      .. ..++|+.       ..+++..+|+++++.+.+++.+++++..............+...+.+.+++++...+.+.+++
T Consensus       347 ~G~~~i~y~p~~~~~~~~eldf~~pfrri~mi~~L~k~lgi~l~~~~~l~~~e~~~~L~~~~~~~~v~~p~p~t~arlLd  426 (560)
T KOG1885         347 TGSYKITYHPNGPEEPELELDFTRPFRRIEMIEELEKELGIKLPPGSTLHTEETRELLKSLCVDEAVECPPPRTTARLLD  426 (560)
T ss_pred             CCCEEEEECCCCCCCCCEEEECCCCEEEEEHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHH
T ss_conf             37436752688988874366236872545078999999588789833357531689999987753667898310899999


Q ss_pred             HHHHCEECCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCC
Q ss_conf             66430036223767544325768888641367877836330220223671225640210699999999999999997288
Q gi|254781066|r  220 RILIEKIEPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIY  299 (355)
Q Consensus       220 ~l~~~~ie~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~  299 (355)
                      +++++++|++|.  .|+||.++|..+|||||.+++++|+++||||||+|.||||+|+|||||..||+||++|.+.+..|+
T Consensus       427 KLvg~flE~~cv--nPTFi~~hP~imSPLAK~hrs~~glteRFElFi~~kEicNAYtElNdP~~Qr~rFe~Q~~~k~~GD  504 (560)
T KOG1885         427 KLVGEFLEPTCV--NPTFIIDHPQIMSPLAKYHRSKAGLTERFELFIAGKEICNAYTELNDPVDQRQRFEQQARDKDAGD  504 (560)
T ss_pred             HHHHHHHCCCCC--CCEEECCCCHHCCCCCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCC
T ss_conf             987676410357--970672781331842224565400456778754108875466660688999999999987764498


Q ss_pred             CCCCHHHHHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCCCC
Q ss_conf             85301018999986-18896324531599998998155971311158564874334
Q gi|254781066|r  300 NETYPIDEDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQEE  354 (355)
Q Consensus       300 ~e~~~~D~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~~~  354 (355)
                      +|++.+|++|++|| ||+||+||||||||||+|+||+++|||||++||.||+++.+
T Consensus       505 DEa~~~De~Fc~ALEYGlPPtgGwGmGIDRL~MllTds~~I~EVL~Fp~mkp~~~~  560 (560)
T KOG1885         505 DEAQMVDEDFCTALEYGLPPTGGWGMGIDRLVMLLTDSNNIREVLLFPAMKPEDRQ  560 (560)
T ss_pred             CCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCHHHEEECCCCCHHCCC
T ss_conf             31136528788897707999776653664653321377653223524656711049


No 6  
>PRK09350 lysyl-tRNA synthetase; Provisional
Probab=100.00  E-value=0  Score=655.93  Aligned_cols=317  Identities=33%  Similarity=0.567  Sum_probs=286.2

Q ss_pred             CCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCC-CCCCCCCCCCCCHHHHH
Q ss_conf             47883126154899999999999999999987988984782105689854454124102478-86783200002858999
Q gi|254781066|r    8 PWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQ-DHIRKPLYLQTSPEFSC   86 (355)
Q Consensus         8 ~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~-~~~~~~~yL~~SPql~l   86 (355)
                      --|.|++   ++..|++||+|+++||+||+++||+||+||+|+.++.+++++.||.|.+... +..++++||+||||+||
T Consensus         5 ~~w~~~a---s~~~l~~Rs~i~~~iR~ff~~~gFlEVeTP~L~~~t~~~~~~~~f~~~~~~~~~~~~~~~yL~~SPql~~   81 (325)
T PRK09350          5 ASWQPSA---SIKNLLKRAAIIAEIRRFFADRGVLEVETPAMSQATVTDIHLVPFETRFVGPGHSQGKTLWLMTSPEYHM   81 (325)
T ss_pred             CCCCCHH---HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEECCHHHHH
T ss_conf             8777714---7999999999999999999988968977984257788764676222102565545676645507919999


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCC
Q ss_conf             98987446889998864245677754484300200011577657877755788877666418830002234332467732
Q gi|254781066|r   87 KKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSEPE  166 (355)
Q Consensus        87 K~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (355)
                      |+||++|++||||||||||||+++++|+|||||||||++|+|++|+|+++|++++.+++                ..+|+
T Consensus        82 k~l~~~G~~rvfqI~~~FR~E~~~~~H~pEFtmlE~~~~~~d~~d~m~~~e~ll~~~~~----------------~~~~~  145 (325)
T PRK09350         82 KRLLAAGSGPIFQLCRSFRNEEAGRYHNPEFTMLEWYRPHYDMYRLMNEVDDLLQQVLD----------------CPPAE  145 (325)
T ss_pred             HHHHHCCCCCEEEEEHHHCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC----------------CCCCC
T ss_conf             99986678855896113228999876573778889998154899999999999999974----------------89852


Q ss_pred             CCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCC--CCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHH
Q ss_conf             07888865666087653234555623279999999976887--7876534789876643003622376754432576888
Q gi|254781066|r  167 YITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIR--VAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAP  244 (355)
Q Consensus       167 ~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~  244 (355)
                      ++++.+++.++++++....       ....+...+++.+..  .....+|+.+++.++...|+++++.+.|+||+|||++
T Consensus       146 ~~~~~~~~~~~~~~~~~~~-------~~~~l~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~ve~~l~~~~P~fv~d~P~~  218 (325)
T PRK09350        146 SLSYQQAFLRYLGIDPLSA-------DKTQLREVAAKLDLSNIADTEEDRDTLLQLLFTFGVEPNIGKEKPTFVYHFPAS  218 (325)
T ss_pred             EEEHHHHHHHHHCCCCCCC-------CHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCC
T ss_conf             6419999999819996548-------889999999974997566753478799999999988875076587699558433


Q ss_pred             HHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCCCEEE
Q ss_conf             864136787783633022022367122564021069999999999999999728885301018999986-1889632453
Q gi|254781066|r  245 ESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-TEMPQSSGIA  323 (355)
Q Consensus       245 ~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~G~PPhgG~g  323 (355)
                      ++|||+.+++|+++|+|||||++|+||+|||+|++||.+|++||+.++..++..+.+..++|++||+|| +|+|||||||
T Consensus       219 ~~~~~~~~~~d~~~a~rfdl~~~G~El~~G~~el~d~~~~~~r~~~~~~~~~~~g~~~~~~d~~~l~a~~yG~PPhgG~g  298 (325)
T PRK09350        219 QAALAQISTEDHRVAERFEVYFKGIELANGFHELTDAREQLQRFEQDNRKRAARGLPQQPIDQNLIAALKAGLPDCSGVA  298 (325)
T ss_pred             CCHHHCCCCCCCCHHHHHHCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCEEE
T ss_conf             37032358789852232101048789667645668999999999999999985799800558999999667999983576


Q ss_pred             CCHHHHHHHHHCCCCHHHHCCCCCCCC
Q ss_conf             159999899815597131115856487
Q gi|254781066|r  324 MGFDRLVMLVTGANNINEVIWTPFSQS  350 (355)
Q Consensus       324 lGidRLvm~l~g~~~Irdvi~FP~~r~  350 (355)
                      ||||||||++||.+|||||||||++||
T Consensus       299 lGlDRLvm~l~g~~~IRdvi~FP~dR~  325 (325)
T PRK09350        299 LGVDRLIMLALGAESIAEVIAFPVDRA  325 (325)
T ss_pred             EHHHHHHHHHHCCCCHHHEECCCCCCC
T ss_conf             559999999818993887107885549


No 7  
>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=100.00  E-value=0  Score=655.32  Aligned_cols=325  Identities=29%  Similarity=0.478  Sum_probs=291.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             54899999999999999999987988984782105689854454124102478867832000028589999898744688
Q gi|254781066|r   17 RRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEK   96 (355)
Q Consensus        17 r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~r   96 (355)
                      +.|.++++||+|+++||+||.++||+||+||||++++||+ .++||.|++   ++++.++||+||||+|||+||++|++|
T Consensus         3 ~~~~~~~~Rs~i~~~iR~ff~~~gF~Ev~TPiL~~~~~g~-~~~~f~~~~---~~~~~~~yL~qSpQl~~q~l~~~g~~r   78 (329)
T cd00775           3 EVRQTFIVRSKIISYIRKFLDDRGFLEVETPMLQPIAGGA-AARPFITHH---NALDMDLYLRIAPELYLKRLIVGGFER   78 (329)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCC-CCCCEEECC---CCCCCCCCCCCCHHHHHHHHHHCCCCC
T ss_conf             8999999999999999999998898899798655668875-675313224---467867230689899999998567776


Q ss_pred             HHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHC-CCEECCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             9998864245677754484300200011577657877755788877666418-830002234332467732078888656
Q gi|254781066|r   97 IFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVAN-QKIFSFQNVNCNPFSEPEYITVAEAFA  175 (355)
Q Consensus        97 vyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~-~~~~~~~~~~~~~~~~~~~i~~~e~~~  175 (355)
                      |||||||||||+++++|+||||||||||+|+|++|+|+++|+||+++++.+. .....+.....+...+|+++++.++++
T Consensus        79 vfqI~p~FR~E~~~~rHl~EFtmle~E~~f~d~~dvm~~~E~li~~i~~~~~~~~~~~~~~~~~d~~~pf~rit~~ea~~  158 (329)
T cd00775          79 VYEIGRNFRNEGIDLTHNPEFTMIEFYEAYADYNDMMDLTEDLFSGLVKKINGKTKIEYGGKELDFTPPFKRVTMVDALK  158 (329)
T ss_pred             EEEEEECCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf             79981022479999774734563457774479999999999999999999838875314661235689974376999999


Q ss_pred             HHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHCCCCCCC
Q ss_conf             66087653234555623279999999976887787653478987664300362237675443257688886413678778
Q gi|254781066|r  176 RYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALANIYPAD  255 (355)
Q Consensus       176 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~plak~~~~~  255 (355)
                      +++++++......   .............+.....+..|++++++++++++++++  ..|+||+|||.+++|||+.++++
T Consensus       159 ~~~g~~~~~~~~~---~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ie~~~--~~p~fi~dyP~~~~pf~~~~~~~  233 (329)
T cd00775         159 EKTGIDFPELDLE---QPEELAKLLAKLIKEKIEKPRTLGKLLDKLFEEFVEPTL--IQPTFIIDHPVEISPLAKRHRSN  233 (329)
T ss_pred             HHHCCCCCCCCCC---CHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHC--CCCEEEECCHHHCCCHHHCCCCC
T ss_conf             9858998766732---389999998775686656787789999999999997513--79689947701118443129999


Q ss_pred             CCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC-CCCCCCEEECCHHHHHHHHH
Q ss_conf             36330220223671225640210699999999999999997288853010189999861-88963245315999989981
Q gi|254781066|r  256 PRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLT-EMPQSSGIAMGFDRLVMLVT  334 (355)
Q Consensus       256 ~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~-G~PPhgG~glGidRLvm~l~  334 (355)
                      +++++|||||++|+||||||+|++||.+|++||++|++.++.++.+...+|++||+|++ |+|||||||||+|||||++|
T Consensus       234 ~~~~~~fdl~~~G~Ei~~G~~el~d~~~q~~r~~~~~~~~~~~~~~~~~~de~yl~a~k~G~pPhgG~glGldRLvm~l~  313 (329)
T cd00775         234 PGLTERFELFICGKEIANAYTELNDPFDQRERFEEQAKQKEAGDDEAMMMDEDFVTALEYGMPPTGGLGIGIDRLVMLLT  313 (329)
T ss_pred             CCEEEECCCCCCCEEEECCEEEECCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHH
T ss_conf             77010012456877984153311799999999999999985467511242399999966799986114099999999993


Q ss_pred             CCCCHHHHCCCCCCCC
Q ss_conf             5597131115856487
Q gi|254781066|r  335 GANNINEVIWTPFSQS  350 (355)
Q Consensus       335 g~~~Irdvi~FP~~r~  350 (355)
                      |++|||||||||.+||
T Consensus       314 g~~nIRdvi~FP~~r~  329 (329)
T cd00775         314 DSNSIRDVILFPAMRP  329 (329)
T ss_pred             CCCHHHHCCCCCCCCC
T ss_conf             8981875137999897


No 8  
>pfam00152 tRNA-synt_2 tRNA synthetases class II (D, K and N).
Probab=100.00  E-value=0  Score=622.84  Aligned_cols=317  Identities=26%  Similarity=0.299  Sum_probs=261.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             48999999999999999999879889847821056898544541241024788678320000285899998987446889
Q gi|254781066|r   18 RRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKI   97 (355)
Q Consensus        18 ~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rv   97 (355)
                      .+.++++||+|+++||+||.++||+||+||+|+++++++ .+++|.|+    .++++++||+||||+|||+||++|++||
T Consensus        18 ~~~~l~~Rs~i~~~iR~ff~~~~f~EV~TP~L~~~~~e~-~a~~F~~~----~~~~~~~yL~~Spel~~k~ll~~g~~rV   92 (341)
T pfam00152        18 MQANLKLRSKIIRAIREFLDERGFLEVETPILTKSTPEG-GARDFLVP----KFYAKEAYLPQSPQLYKQLLMVAGFDRV   92 (341)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCC-CCCEEEEC----CCCCCCEEECCCHHHHHHHHHHCCCCCC
T ss_conf             899999999999999999998898998798200558987-77664502----6789823405488999999986588763


Q ss_pred             HHHHHHHCCCCC-CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCC-EECCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             998864245677-75448430020001157765787775578887766641883-0002234332467732078888656
Q gi|254781066|r   98 FCFAHAWRNGEQ-GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQK-IFSFQNVNCNPFSEPEYITVAEAFA  175 (355)
Q Consensus        98 yqig~~FRaE~~-~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~-~~~~~~~~~~~~~~~~~i~~~e~~~  175 (355)
                      ||||||||||++ ++||+||||||||||+|+|++++|+++|+||+++++.+... .........+...+|++++|.++++
T Consensus        93 fei~~~FR~E~~~t~rH~~EFtmlE~y~a~~d~~d~m~~~E~li~~i~~~v~~~~~~~~~~~~~~~~~~f~rity~ea~~  172 (341)
T pfam00152        93 FQIAPCFRDEDLRTDRHPPEFTQLDLEMSFVDYEDVMDLTEDLIKYVFKEVKGKTEKGELLLGIELPEPFPRITYAEAIE  172 (341)
T ss_pred             EEEECHHCCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCEEEEHHHHHH
T ss_conf             79723202798988655077887767553599999999999999999999863440244124554789844742999999


Q ss_pred             HHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCC---CCCCCCCCCCCHHHHHHCCCC
Q ss_conf             66087653234555623279999999976887787653478987664300362237---675443257688886413678
Q gi|254781066|r  176 RYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLG---INCCTILDRYPAPESALANIY  252 (355)
Q Consensus       176 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~---~~~pvfi~~yP~~~~plak~~  252 (355)
                      ++.+++.....       ...+.....+..........+...++.++.+.+++.++   .+.||||+|||.+++|||+..
T Consensus       173 ~~~~~~~~~~~-------~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~~~~~~p~fv~dyP~~~~pf~~~~  245 (341)
T pfam00152       173 RYGSDKPDLRF-------GLELKDVTEIKFEDAALNGGSNKLLGALRSELGERLLGDENLDNPVFVTDFPLFKRPFYMPK  245 (341)
T ss_pred             HHCCCCCCCCC-------HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCC
T ss_conf             97199988688-------79999999984422333455244899999999888755303786199988884438666867


Q ss_pred             -CCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC-CCCCCCEEECCHHHHH
Q ss_conf             -77836330220223671225640210699999999999999997288853010189999861-8896324531599998
Q gi|254781066|r  253 -PADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLT-EMPQSSGIAMGFDRLV  330 (355)
Q Consensus       253 -~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~-G~PPhgG~glGidRLv  330 (355)
                       ++++++|+|||||++|+||||||+|+|||++|++||++|..    ..+++++.|++||+|++ |+|||||||||||||+
T Consensus       246 ~~~~~~~a~rFel~~~G~Ei~nG~~el~d~~~~~~rf~~~~~----~~~~~~~~d~~yl~a~~~G~PP~~G~glGidRL~  321 (341)
T pfam00152       246 DEDPPGLAERFDLVLNGGEIGGGSIRIHDPEEQRKRFEELGL----DPEEAEEKFGFYLDALKYGMPPHGGIGLGLDRLV  321 (341)
T ss_pred             CCCCCCCHHEEEECCCCEEEECCCCCCCCHHHHHHHHHHHCC----CHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHH
T ss_conf             877765012157526974982575345999999999998198----9023356589999998669799705657899999


Q ss_pred             HHHHCCCCHHHHCCCCCCCC
Q ss_conf             99815597131115856487
Q gi|254781066|r  331 MLVTGANNINEVIWTPFSQS  350 (355)
Q Consensus       331 m~l~g~~~Irdvi~FP~~r~  350 (355)
                      |++||.+||||||+||.+|.
T Consensus       322 m~l~g~~~Irdv~~FPr~~~  341 (341)
T pfam00152       322 MLLTGLESIREVIAFPKTRK  341 (341)
T ss_pred             HHHCCCCCHHHCCCCCCCCC
T ss_conf             99808994887267899999


No 9  
>COG2269 Truncated, possibly inactive, lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=605.23  Aligned_cols=321  Identities=42%  Similarity=0.732  Sum_probs=304.3

Q ss_pred             CCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCC-CCCCCCCCCH
Q ss_conf             898747883126154899999999999999999987988984782105689854454124102478867-8320000285
Q gi|254781066|r    4 IPSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHI-RKPLYLQTSP   82 (355)
Q Consensus         4 ~p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~-~~~~yL~~SP   82 (355)
                      ++..+||.|+++..+   +..|++|+++||.||.++||+||+||+|+.+++++.|+.+|.|++..+.+- .+++||+|||
T Consensus         1 ~~~~~~W~p~~~~~~---ll~Ra~i~~~iR~FF~erg~lEVeTp~Ls~a~vtd~hL~~F~Te~~~~~~~~~~~l~L~TSP   77 (322)
T COG2269           1 MSETPWWQPSASIDN---LLKRAAIIAAIRRFFAERGVLEVETPALSVAPVTDIHLHPFETEFLGPGGAKGKPLWLHTSP   77 (322)
T ss_pred             CCCCCCCCCCCCHHH---HHHHHHHHHHHHHHHHHCCCEEECCHHHHCCCCCCCCEEEEEEEEECCCCCCCCEEEEECCC
T ss_conf             998876888888899---99899999999999987692585336765078986423445667654676665303665680


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCC
Q ss_conf             89999898744688999886424567775448430020001157765787775578887766641883000223433246
Q gi|254781066|r   83 EFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPF  162 (355)
Q Consensus        83 ql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~  162 (355)
                      |++||+|||+|.++|||||+||||++.+++|+|||||||||+++.|++.+|+.+-++++.+++.                
T Consensus        78 Ey~mKrLLAag~~~ifql~kvfRN~E~G~~H~PEFTMLEWYrv~~d~~~lm~e~~~Ll~~vl~~----------------  141 (322)
T COG2269          78 EYHMKRLLAAGSGPIFQLGKVFRNEEMGRLHNPEFTMLEWYRVGCDYYRLMNEVDDLLQLVLEC----------------  141 (322)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHC----------------
T ss_conf             7778999975488601454777263325667984367651006785999999999999999703----------------


Q ss_pred             CCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCC
Q ss_conf             77320788886566608765323455562327999999997688778765347898766430036223767544325768
Q gi|254781066|r  163 SEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYP  242 (355)
Q Consensus       163 ~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP  242 (355)
                      .+++++||.++|++|+|+|+..       ++...+...+.+.++....+++|.+++..++.+.|||++|.+.|+||+|||
T Consensus       142 ~~~E~ls~~eaF~r~~gid~l~-------~~~~~L~~~~~~~~l~~~~~~~~d~L~~~lf~~~VEP~lg~~rpt~ly~fP  214 (322)
T COG2269         142 VEAERLSYQEAFLRYLGIDPLS-------ADKTELREAAAKLGLSAATDEDWDTLLQLLFVEGVEPNLGKERPTFLYHFP  214 (322)
T ss_pred             CCCCEEEHHHHHHHHHCCCCCC-------CCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECC
T ss_conf             7853555999999983889452-------429999999985587777755899999998886407566888844887272


Q ss_pred             HHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCEE
Q ss_conf             88864136787783633022022367122564021069999999999999999728885301018999986188963245
Q gi|254781066|r  243 APESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLTEMPQSSGI  322 (355)
Q Consensus       243 ~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~G~PPhgG~  322 (355)
                      +++++||+++++||+|++|||||++|+||+|||+||+|+.+|++||+.+|+.|.+.+.+.+++|++||.||+.||||+|+
T Consensus       215 ~~qaaLA~i~~~D~rVAERFElY~kGiELaNgf~EltDa~EqrrRfe~dn~~r~~~~l~~~piDe~fl~Al~~mP~cSGv  294 (322)
T COG2269         215 ASQAALAQISTGDPRVAERFELYYKGIELANGFHELTDAAEQRRRFEQDNKERARRGLPQYPIDEDFLAALARMPPCSGV  294 (322)
T ss_pred             HHHHHHHCCCCCCCCHHHHHHHEEEEEEECCCCHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCC
T ss_conf             77887604677896256664320100221024000178899999999988999863788777887899999858986541


Q ss_pred             ECCHHHHHHHHHCCCCHHHHCCCCCCCC
Q ss_conf             3159999899815597131115856487
Q gi|254781066|r  323 AMGFDRLVMLVTGANNINEVIWTPFSQS  350 (355)
Q Consensus       323 glGidRLvm~l~g~~~Irdvi~FP~~r~  350 (355)
                      |||||||||+++|.++|.|||+||+.++
T Consensus       295 ALG~DRLvmLalg~~~i~~Vi~f~v~~a  322 (322)
T COG2269         295 ALGFDRLVMLALGAESIDDVIAFPVARA  322 (322)
T ss_pred             EECHHHHHHHHCCCCHHHHHHHCCCCCC
T ss_conf             3238899999818214877761311469


No 10 
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=100.00  E-value=0  Score=587.74  Aligned_cols=291  Identities=20%  Similarity=0.323  Sum_probs=231.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEC-CCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             899999999999999999987988984782105-6898544541241024788678320000285899998987446889
Q gi|254781066|r   19 RPFLLKRNMIQSSLREYFVENQFIEIDSMSLQY-SPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKI   97 (355)
Q Consensus        19 R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~-~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rv   97 (355)
                      +.+++.||+++++||+||.++||+||+||+|++ +++|+  ++.|.+     +++++++||+||||||||+||++|++||
T Consensus       134 ~~~~r~Rs~i~~~iR~fl~~~gF~EVeTP~l~~~~~eGg--a~~f~~-----~~~~~~~yL~~Spqly~q~li~~G~~rv  206 (434)
T PRK05159        134 QAIFKIRSEVLRAFREFLYEEGFTEIFTPKIVATGTEGG--TELFPV-----KYFEKEAFLAQSPQLYKQMMMAAGFERV  206 (434)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCC--CCCCCE-----EECCCEEEECCCCHHHHHHHHHCCCCCE
T ss_conf             999999999999999999877919997874325678875--565861-----3127533414683799999876356855


Q ss_pred             HHHHHHHCCCCCC-CCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCE---ECCCCCCC-CCCCCCCCCCHHH
Q ss_conf             9988642456777-54484300200011577657877755788877666418830---00223433-2467732078888
Q gi|254781066|r   98 FCFAHAWRNGEQG-CLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKI---FSFQNVNC-NPFSEPEYITVAE  172 (355)
Q Consensus        98 yqig~~FRaE~~~-~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~---~~~~~~~~-~~~~~~~~i~~~e  172 (355)
                      ||||||||||+++ +|||||||||||||||+|++|+|+++|+||+++++.+....   +...+.+. ....+|+++++.|
T Consensus       207 feI~~~FR~E~~~t~RH~pEFT~lE~e~af~d~~d~m~~~E~li~~i~~~v~~~~~~~~~~~~~~~~~~~~~~~rit~~e  286 (434)
T PRK05159        207 FEIGPAFRAEEHNTTRHLNEAISIDVEMGFIDEEDVMDLLENLLKYVYEDVAENCEKELELLGIELPVPETPIPRITYDE  286 (434)
T ss_pred             EEECCCEECCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCCCCCCCCEEEHHH
T ss_conf             99660102365875445356765666631068999999999999999999986564778635865566799864778999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHH-CCC
Q ss_conf             6566608765323455562327999999997688778765347898766430036223767544325768888641-367
Q gi|254781066|r  173 AFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESAL-ANI  251 (355)
Q Consensus       173 ~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~pl-ak~  251 (355)
                      +++..                        .+.+.+.    .|++.+....++.+.+.+....|+||+|||++++|| ++.
T Consensus       287 ai~~l------------------------~~~~~~~----~~g~dl~~~~e~~l~~~~~~~~~~fI~d~P~~~~pfy~~~  338 (434)
T PRK05159        287 AIEIL------------------------KSKGVEI----SWGDDLDTEGERLLGKYVKESDFYFITDWPTEIRPFYTMP  338 (434)
T ss_pred             HHHHH------------------------HHCCCCC----CCCCCCCHHHHHHHHHHHCCCCCEEEECCCHHCCCCCCCC
T ss_conf             99999------------------------8519987----8555537899999999847589889989970008654677


Q ss_pred             CCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC-CCCCCCEEECCHHHHH
Q ss_conf             877836330220223671225640210699999999999999997288853010189999861-8896324531599998
Q gi|254781066|r  252 YPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLT-EMPQSSGIAMGFDRLV  330 (355)
Q Consensus       252 ~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~-G~PPhgG~glGidRLv  330 (355)
                      ++++|++++|||||++|+||||||+|+|||++|+++|+++     +.+.+.+   ++||+||+ |+|||||||||||||+
T Consensus       339 ~~~~~~~~~~fdl~~~G~Ei~~G~~r~~d~~~l~~~~~~~-----g~~~~~~---~~yl~al~yG~PP~gG~glGiDRLv  410 (434)
T PRK05159        339 YEDDPEITKSFDLMYRGLEITSGAQRIHDYDMLVESIKEK-----GLNPESF---EFYLEAFKYGMPPHAGWGLGLERLT  410 (434)
T ss_pred             CCCCCCEEEEEEEEECCEEEEEEEEECCCHHHHHHHHHHC-----CCCHHHH---HHHHHHHHCCCCCCCEEEEHHHHHH
T ss_conf             7888320014326776699843101117899999999974-----9898999---9999996679998755878799999


Q ss_pred             HHHHCCCCHHHHCCCCCCCCCC
Q ss_conf             9981559713111585648743
Q gi|254781066|r  331 MLVTGANNINEVIWTPFSQSNQ  352 (355)
Q Consensus       331 m~l~g~~~Irdvi~FP~~r~~~  352 (355)
                      |++||++|||||||||.++.+-
T Consensus       411 m~l~g~~sIrdvi~FPr~~~rl  432 (434)
T PRK05159        411 MKLLGLENVREAVLFPRDRTRL  432 (434)
T ss_pred             HHHCCCCCHHEEECCCCCCCCC
T ss_conf             9981999665481488998989


No 11 
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=100.00  E-value=0  Score=564.20  Aligned_cols=327  Identities=23%  Similarity=0.294  Sum_probs=231.1

Q ss_pred             CCCCCCCC--CHHHCCCHH----------HHHHHHHHHHHHHHHHHHHCCCEEEECCCEE-CCCCCCCCCCCEEEECCCC
Q ss_conf             88987478--831261548----------9999999999999999998798898478210-5689854454124102478
Q gi|254781066|r    3 QIPSQPWW--NRDFHYRRR----------PFLLKRNMIQSSLREYFVENQFIEIDSMSLQ-YSPGNETHIRAFSTELIIQ   69 (355)
Q Consensus         3 ~~p~~~~~--~~~~~~r~R----------~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~-~~~~g~~~~~~f~t~~~~~   69 (355)
                      |+|....+  ..+.|+|.|          .++++||+++++||+||+++||+||+||+|+ ++++|   |++|.|+...+
T Consensus       111 P~~~~~~~~~~e~~Rl~~RyLDLr~~~~~~~fr~Rs~i~~~iR~fl~~~gFiEVeTPiL~~s~~eG---A~~F~vpsr~~  187 (587)
T PRK00476        111 PFQIDDETNVSEELRLKYRYLDLRRPEMQNNLKLRSKVTSAIRNFLDDNGFLEIETPILTKSTPEG---ARDYLVPSRVH  187 (587)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEECCCCCCCCCCCC---CCCCCCCCCCC
T ss_conf             988655667778886554788872177889999999999999999997597400475432568666---64430131057


Q ss_pred             CCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             86783200-00285899998987446889998864245677754484300200011577657877755788877666418
Q gi|254781066|r   70 DHIRKPLY-LQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVAN  148 (355)
Q Consensus        70 ~~~~~~~y-L~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~  148 (355)
                         ..++| |+||||||||+|||||++||||||||||||++++.|+|||||||+||||+|++|+|+++|+||+++++.+.
T Consensus       188 ---~~~fyaL~qSPQLykq~L~vgG~erVyeig~~FRnE~~~t~r~pEFt~lE~E~af~d~~dvm~~~E~li~~v~~~v~  264 (587)
T PRK00476        188 ---PGKFYALPQSPQLFKQLLMVAGFDRYYQIARCFRDEDLRADRQPEFTQIDIEMSFVTQEDVMDLMEGLIRHVFKEVL  264 (587)
T ss_pred             ---CCCEECCCCCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCHHHEEEHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             ---88551356797999999885175527996431238888766682342311111116899999999999999999971


Q ss_pred             CCEECCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC--------CC-------------------------CCC-----C
Q ss_conf             830002234332467732078888656660876532--------34-------------------------555-----6
Q gi|254781066|r  149 QKIFSFQNVNCNPFSEPEYITVAEAFARYANIDLGT--------TL-------------------------DNP-----D  190 (355)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~--------~~-------------------------~~~-----~  190 (355)
                      .         .+...+|++++|.|++++|.......        ..                         ..+     .
T Consensus       265 ~---------~~l~~pf~rit~~eai~~yG~DKPDlR~~~~l~d~~~~~~~~~~~~f~~~~~~~~~~v~~i~~p~~~~~~  335 (587)
T PRK00476        265 G---------VDLTKPFPRMTYAEAMRRYGSDKPDLRFPLELVDVTDLFKDSGFKVFAGAANDPGGRVKAIRVPGGASLS  335 (587)
T ss_pred             C---------CCCCCCCCEEEHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHCCCCEEEEEECCCCCCCC
T ss_conf             9---------7478884245699999985799965457621546688761564167899986058869999746867666


Q ss_pred             CCCHHHHHHHHHHCCCC------CCCCCC--------------------------------------H---HHHHHHHHH
Q ss_conf             23279999999976887------787653--------------------------------------4---789876643
Q gi|254781066|r  191 QPDRHLLYLQAQQAGIR------VAHDDT--------------------------------------W---SDIFSRILI  223 (355)
Q Consensus       191 ~~~~~~~~~~~~~~~~~------~~~~~~--------------------------------------~---~~~~~~l~~  223 (355)
                      ......+...+++.+.+      ......                                      +   |.+..++..
T Consensus       336 r~~id~l~~~~~~~~~~~l~~i~~~~~~~~spi~k~~~~~~~~~l~~~~~~~~gd~~~f~~~~~~~~~~~lg~~r~~~~~  415 (587)
T PRK00476        336 RKQIDELTEFAKIYGAKGLAYIKVNEDGLKGPIAKFLSEEELEALLERTGAKDGDLIFFGADKKKVVNDALGALRLKLGK  415 (587)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHCCHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHCHHHHHHHH
T ss_conf             66799999999981887733799805556560776469999999999848877877999359607888763317999988


Q ss_pred             --CEECCCCCCCCCCCCCCCCH-----H-------HHHHCCCCCCC-------CC--CCCCCEEEECCEECCCCCHHCCC
Q ss_conf             --00362237675443257688-----8-------86413678778-------36--33022022367122564021069
Q gi|254781066|r  224 --EKIEPNLGINCCTILDRYPA-----P-------ESALANIYPAD-------PR--FTKRFELYACNIELCNACDELLD  280 (355)
Q Consensus       224 --~~ie~~l~~~~pvfi~~yP~-----~-------~~plak~~~~~-------~~--va~rfdl~i~G~El~ng~~El~d  280 (355)
                        ..++++.  ..|+||+|||.     +       ..||+++++++       |+  .+++|||+++|+||+|||+|+||
T Consensus       416 ~~~li~~~~--~~p~fV~dfPlfe~~~~~~~~~a~hhPFt~P~~~~~~~~~~dp~~~~~~~yDLv~~G~El~~Gs~Ri~d  493 (587)
T PRK00476        416 ELGLIDEDK--FAFLWVVDFPMFEYDEEEGRYVAAHHPFTMPKDEDLELLETDPGKALAYAYDLVLNGYELGGGSIRIHR  493 (587)
T ss_pred             HHCCCCCCC--CCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCHHHHHEEEEEEEECCEEECCCEEECCC
T ss_conf             846666666--642689814531144202563102177458885378877538123234674053077895135032279


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHH---HHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCCC
Q ss_conf             99999999999999972888530101---8999986-1889632453159999899815597131115856487433
Q gi|254781066|r  281 PIEQRHRFEKEMQEKKKIYNETYPID---EDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQE  353 (355)
Q Consensus       281 ~~~q~~rf~~q~~~k~~~~~e~~~~D---~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~~  353 (355)
                      |++|+++|+.      .+.++. .++   .+||+|| +|||||||||||||||||+|||++|||||||||.+...++
T Consensus       494 ~~~q~~~~~~------~gl~~~-~~~~~F~~yl~al~yG~PPhgG~GlGiDRLvmlltg~~nIRDVI~FPkt~~g~d  563 (587)
T PRK00476        494 PEIQEKVFEI------LGISEE-EAEEKFGFLLDALKYGAPPHGGIAFGLDRLVMLLAGADSIRDVIAFPKTQSAAD  563 (587)
T ss_pred             HHHHHHHHHH------CCCCHH-HHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHCCCCCHHEEEECCCCCCCCC
T ss_conf             9999999998------599989-998888899999767999976376149999999759995530650789999877


No 12 
>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=100.00  E-value=0  Score=569.96  Aligned_cols=289  Identities=22%  Similarity=0.324  Sum_probs=228.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             48999999999999999999879889847821056898544541241024788678320000285899998987446889
Q gi|254781066|r   18 RRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKI   97 (355)
Q Consensus        18 ~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rv   97 (355)
                      .+.+++.||+|+++||+||+++||+||+||+|+++++ +.++++|.++     ++++++||+|||||| ||||++|++||
T Consensus        20 ~~~~l~~Rs~i~~~iR~fl~~~gF~EVeTP~L~~~~~-eg~a~~f~~~-----~~~~~~yL~~Spel~-Kqlli~G~~rV   92 (322)
T cd00776          20 VQAIFRIRSEVLRAFREFLRENGFTEVHTPKITSTDT-EGGAELFKVS-----YFGKPAYLAQSPQLY-KEMLIAALERV   92 (322)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCC-CCCCCCCCCC-----CCCCCEEECCCHHHH-HHHHHCCCCCE
T ss_conf             9999999999999999999988999997984007889-8654667621-----058760015485889-99975342443


Q ss_pred             HHHHHHHCCCCCC-CCCCCCEEEECEEECCC-CHHHHHHHHHHHHHHHHHHHCCCEEC-------CCCCCCCCCCCCCCC
Q ss_conf             9988642456777-54484300200011577-65787775578887766641883000-------223433246773207
Q gi|254781066|r   98 FCFAHAWRNGEQG-CLHQPEFTMLEWYRAHE-SYEQLMKDCMNIIRCAAEVANQKIFS-------FQNVNCNPFSEPEYI  168 (355)
Q Consensus        98 yqig~~FRaE~~~-~rHlpEFtmLE~e~af~-d~~dlm~~~E~li~~~~~~~~~~~~~-------~~~~~~~~~~~~~~i  168 (355)
                      ||||||||||+++ +|||||||||||||||+ |++++|+++|++|+++++.+......       +.........+|.++
T Consensus        93 fei~~~FR~E~~~t~rH~pEFTmlE~e~af~~d~~d~m~~~E~li~~i~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~r~  172 (322)
T cd00776          93 YEIGPVFRAEKSNTRRHLSEFWMLEAEMAFIEDYNEVMDLIEELIKYIFKRVLERCAKELELVNQLNRELLKPLEPFPRI  172 (322)
T ss_pred             EEECCEEECCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf             88726140799987534788876525552332899999999999999999998652678899875121100247996424


Q ss_pred             CHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             88886566608765323455562327999999997688778765347898766430036223767544325768888641
Q gi|254781066|r  169 TVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESAL  248 (355)
Q Consensus       169 ~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~pl  248 (355)
                      ++.+++..                        ..+.+..  .+..|+..+....+..+.+.+. +.||||+|||.+++||
T Consensus       173 ~~~ea~~~------------------------l~~~~~~--~~~~~~~dl~~~~e~~l~~~~~-~~p~fv~d~P~~~~pf  225 (322)
T cd00776         173 TYDEAIEL------------------------LREKGVE--EEVKWGEDLSTEHERLLGEIVK-GDPVFVTDYPKEIKPF  225 (322)
T ss_pred             CHHHHHHH------------------------HHHCCCC--CCCCCCCCCCHHHHHHHHHHHC-CCCEEEECCHHHCCCC
T ss_conf             19999999------------------------9856996--6877666337699999999965-8988997974421976


Q ss_pred             -CCCCCCCCCCCCCCEEEECCE-ECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC-CCCCCCEEECC
Q ss_conf             -367877836330220223671-225640210699999999999999997288853010189999861-88963245315
Q gi|254781066|r  249 -ANIYPADPRFTKRFELYACNI-ELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLT-EMPQSSGIAMG  325 (355)
Q Consensus       249 -ak~~~~~~~va~rfdl~i~G~-El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~-G~PPhgG~glG  325 (355)
                       ++.++++|++++|||||++|+ ||+|||+|++||++|++||+++      +.++.  .+++|++|++ |+|||||||||
T Consensus       226 y~~~~~~~~~~~~rfel~~~G~~El~~g~~r~~d~~~l~~r~~~~------g~~~~--~~~~yl~al~~G~PP~gG~glG  297 (322)
T cd00776         226 YMKPDDDNPETVESFDLLMPGVGEIVGGSQRIHDYDELEERIKEH------GLDPE--SFEWYLDLRKYGMPPHGGFGLG  297 (322)
T ss_pred             CCCCCCCCHHHHHHHHEECCCCEEECCHHHHHCCHHHHHHHHHHC------CCCHH--HHHHHHHHHHCCCCCCCEEEEH
T ss_conf             588668854554542001289278677666408999999999985------99978--9999999976699997245438


Q ss_pred             HHHHHHHHHCCCCHHHHCCCCCC
Q ss_conf             99998998155971311158564
Q gi|254781066|r  326 FDRLVMLVTGANNINEVIWTPFS  348 (355)
Q Consensus       326 idRLvm~l~g~~~Irdvi~FP~~  348 (355)
                      ||||+|++||++||||||+||.+
T Consensus       298 iDRLvmll~g~~~Irdvi~FPr~  320 (322)
T cd00776         298 LERLVMWLLGLDNIREAILFPRD  320 (322)
T ss_pred             HHHHHHHHCCCCCHHHEECCCCC
T ss_conf             99999998299727605138999


No 13 
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=100.00  E-value=0  Score=560.37  Aligned_cols=311  Identities=18%  Similarity=0.198  Sum_probs=239.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEEC--------------CCCCCCCCCCCCCCCHHHH
Q ss_conf             99999999999999999987988984782105689854454124102--------------4788678320000285899
Q gi|254781066|r   20 PFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTEL--------------IIQDHIRKPLYLQTSPEFS   85 (355)
Q Consensus        20 ~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~--------------~~~~~~~~~~yL~~SPql~   85 (355)
                      .+++.||+|+++||+||+++||+||+||+|++++++++ +++|.|..              ...+|+++++||+||||||
T Consensus       133 ~ifr~RS~i~~~iR~~l~~~~F~EVeTP~L~~~~~eGa-a~~F~v~~~~~~~~~~~~~~~~~~~~yf~~~~yL~~SpqLy  211 (462)
T PRK03932        133 AVMRVRNTLAQAIHEFFQENGFVWVHTPIITASDCEGA-GELFRVTTLDLENLPRTDGKVDFSKDFFGKEAFLTVSGQLY  211 (462)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCC-CCCEEECCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHHH
T ss_conf             99999999999999999767967997886535687645-57404214543445433444331145427762026576899


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCC-CCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCC
Q ss_conf             9989874468899988642456777-544843002000115776578777557888776664188300022343324677
Q gi|254781066|r   86 CKKLLAAGEEKIFCFAHAWRNGEQG-CLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSE  164 (355)
Q Consensus        86 lK~ll~~G~~rvyqig~~FRaE~~~-~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~  164 (355)
                      || +|++|++||||||||||||+++ +||||||||||+||||+|++|+|+++|+|++++++.+.+    .....++..++
T Consensus       212 lq-~li~G~erVfeIg~~FRnE~~~t~RH~pEFT~lE~e~a~~d~~d~m~l~E~li~~i~~~v~~----~~~~el~~~~~  286 (462)
T PRK03932        212 AE-AYAMALSKVYTFGPTFRAENSNTRRHLAEFWMIEPEMAFADLEDNMDLAEDMLKYVIKAVLE----ECPDDLEFLNR  286 (462)
T ss_pred             HH-HHHHHCCCEEEEEHHHHHCCCCCCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHH----HCHHHHHHHCC
T ss_conf             99-98752064899733232056775445430025553110068999999999999999999987----58677876245


Q ss_pred             CCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHH
Q ss_conf             32078888656660876532345556232799999999768877876534789876643003622376754432576888
Q gi|254781066|r  165 PEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAP  244 (355)
Q Consensus       165 ~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~  244 (355)
                      +......+.++..++.++...       .........++.+.+......||+.+....+.++.+.. .+.|+||+|||++
T Consensus       287 ~~~~~~~~~l~~~~~~~~~~i-------t~~eai~~l~~~~~~~~~~~~~g~dl~~~~E~~l~e~~-~~~P~fi~d~P~~  358 (462)
T PRK03932        287 DVDKGLIERLENFIESPFPRI-------TYTEAIEILQKSGKKFEFPVEWGDDLGSEHERYLTEEH-FKKPVFVTNYPKD  358 (462)
T ss_pred             CCCHHHHHHHHHHCCCCCCEE-------EHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHH-CCCCEEEECCCCC
T ss_conf             478368899998628997264-------69999999996496456772111203548888888886-5878899776201


Q ss_pred             HHHHCCCCCCCCCCCCCCEEEECCE-ECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCCCEE
Q ss_conf             8641367877836330220223671-22564021069999999999999999728885301018999986-188963245
Q gi|254781066|r  245 ESALANIYPADPRFTKRFELYACNI-ELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-TEMPQSSGI  322 (355)
Q Consensus       245 ~~plak~~~~~~~va~rfdl~i~G~-El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~G~PPhgG~  322 (355)
                      ++|||+..++++..+.+|||+++|+ ||+||+.++++++++.+++.      +.+.++. .+ ++||+|+ +||||||||
T Consensus       359 ~~Pfy~~~~~d~~~~~~~dll~~G~~Ei~~G~~R~~~~~~l~~~~~------~~g~~~e-~~-~~yl~~~~yG~PP~gG~  430 (462)
T PRK03932        359 IKAFYMRLNPDGKTVAAMDLLAPGIGEIIGGSQREERLDVLDARMK------ELGLDKE-DY-WWYLDLRRYGSVPHSGF  430 (462)
T ss_pred             CCCCCCCCCCCCCEEEEEEEEECCCEEEECHHHHCCCHHHHHHHHH------HCCCCHH-HH-HHHHHHHHCCCCCCCEE
T ss_conf             3853356588977467776773586476065553379999999999------8699989-99-99999976799987737


Q ss_pred             ECCHHHHHHHHHCCCCHHHHCCCCCCCCCC
Q ss_conf             315999989981559713111585648743
Q gi|254781066|r  323 AMGFDRLVMLVTGANNINEVIWTPFSQSNQ  352 (355)
Q Consensus       323 glGidRLvm~l~g~~~Irdvi~FP~~r~~~  352 (355)
                      |||||||||++||++||||||+||.+..+-
T Consensus       431 GiGiDRLvm~l~~~~sIRdvi~FPr~~~r~  460 (462)
T PRK03932        431 GLGFERLVAYVTGLENIRDVIPFPRTPGRA  460 (462)
T ss_pred             EEHHHHHHHHHCCCCCHHEEECCCCCCCCC
T ss_conf             677999999982999654586488987757


No 14 
>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=100.00  E-value=0  Score=563.40  Aligned_cols=265  Identities=27%  Similarity=0.408  Sum_probs=228.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998798898478210568985445412410247886783200002858999989874468899988
Q gi|254781066|r   22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFA  101 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig  101 (355)
                      |++||+++++||+||.++||+||+||+|+++++++ ++++|.++++   +.++++||+||||+|||+||++|++||||||
T Consensus         1 lr~Rs~i~~~iR~ff~~~~f~EV~TP~l~~~~~~~-~~~~f~~~~~---~~~~~~~L~~Spel~~k~ll~~g~~~if~i~   76 (269)
T cd00669           1 FKVRSKIIKAIRDFMDDRGFLEVETPMLQKITGGA-GARPFLVKYN---ALGLDYYLRISPQLFKKRLMVGGLDRVFEIN   76 (269)
T ss_pred             CCHHHHHHHHHHHHHHHCCCEEEECCEEECCCCCC-CCCEEEEECC---CCCCEEEECCCHHHHHHHHHHCCCCCEEEEE
T ss_conf             91699999999999998898998798530578987-6742573137---8994077343889999999865888679984


Q ss_pred             HHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCC-EECCCCCCCCCCCCCCCCCHHHHHHHHCCC
Q ss_conf             6424567775448430020001157765787775578887766641883-000223433246773207888865666087
Q gi|254781066|r  102 HAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQK-IFSFQNVNCNPFSEPEYITVAEAFARYANI  180 (355)
Q Consensus       102 ~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~-~~~~~~~~~~~~~~~~~i~~~e~~~~~~~~  180 (355)
                      ||||||++++||+|||||||||++|+|++++|+++|++|+++++.+... .........++..+|+++++.++++++   
T Consensus        77 ~~FR~e~~~~rH~~EFtmlE~y~~~~d~~~~m~~~e~li~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ea~e~~---  153 (269)
T cd00669          77 RNFRNEDLRARHQPEFTMMDLEMAFADYEDVIELTERLVRHLAREVLGVTAVTYGFELEDFGLPFPRLTYREALERY---  153 (269)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCCCEEEHHHHHHHH---
T ss_conf             62107898655434877578751489999999999999999999996555245355444458998785799999984---


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHH-HCCCCCCCCCCC
Q ss_conf             6532345556232799999999768877876534789876643003622376754432576888864-136787783633
Q gi|254781066|r  181 DLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESA-LANIYPADPRFT  259 (355)
Q Consensus       181 d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~p-lak~~~~~~~va  259 (355)
                                                                          ..|+||+|||++++| +++.++++++++
T Consensus       154 ----------------------------------------------------~~p~fi~dyP~~~~~~~~~~~~~~~~~a  181 (269)
T cd00669         154 ----------------------------------------------------GQPLFLTDYPAEMHSPLASPHDVNPEIA  181 (269)
T ss_pred             ----------------------------------------------------CCCEEEECCCHHCCCCCCCCCCCCCCHH
T ss_conf             ----------------------------------------------------9978998985010780209079996676


Q ss_pred             CCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCC
Q ss_conf             0220223671225640210699999999999999997288853010189999861-889632453159999899815597
Q gi|254781066|r  260 KRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANN  338 (355)
Q Consensus       260 ~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~  338 (355)
                      +|||||++|+||||||+|++||++|++||+++...++    +....|++||+|++ |+|||||+|||+|||+|+++|++|
T Consensus       182 ~rfdl~~~G~El~nG~~r~~d~~~~~~r~~~~~~~~~----~~~~~~~~yl~a~~~G~pp~~G~glG~dRL~m~~~g~~~  257 (269)
T cd00669         182 DAFDLFINGVEVGNGSSRLHDPDIQAEVFQEQGINKE----AGMEYFEFYLKALEYGLPPHGGLGIGIDRLIMLMTNSPT  257 (269)
T ss_pred             HHCCCCCCCEEECCCCCCCCCHHHHHHHHHHHCCCHH----HHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHCCCC
T ss_conf             6502467860670325204888999999998560744----556658999999877999971663479999999808996


Q ss_pred             HHHHCCCCCCC
Q ss_conf             13111585648
Q gi|254781066|r  339 INEVIWTPFSQ  349 (355)
Q Consensus       339 Irdvi~FP~~r  349 (355)
                      |||||+||++|
T Consensus       258 Irdv~~FPr~r  268 (269)
T cd00669         258 IREVIAFPKMR  268 (269)
T ss_pred             HHHCCCCCCCC
T ss_conf             88624789988


No 15 
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=100.00  E-value=0  Score=555.49  Aligned_cols=315  Identities=22%  Similarity=0.243  Sum_probs=226.7

Q ss_pred             HHHCCCHHH----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEE-CCCCCCCCCCCEEEECCCCCCCCCCCC-CC
Q ss_conf             312615489----------999999999999999998798898478210-568985445412410247886783200-00
Q gi|254781066|r   12 RDFHYRRRP----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQ-YSPGNETHIRAFSTELIIQDHIRKPLY-LQ   79 (355)
Q Consensus        12 ~~~~~r~R~----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~-~~~~g~~~~~~f~t~~~~~~~~~~~~y-L~   79 (355)
                      .+.|+|.|.          +++.||+++++||+||+++||+||+||+|+ ++|+|   |++|.|+...+   +..+| |+
T Consensus       136 ee~RLkyRyLDLRr~~~~~~~~~Rskv~~~iR~~l~~~gF~EVETP~L~~stpEG---ArdflvPsr~~---~~~fyaLp  209 (706)
T PRK12820        136 EDLRLQYRYLDIRRPAMQDHLAKRHRIIKCARDFLDSRGFLEIETPILTKSTPEG---ARDYLVPSRIH---PKEFYALP  209 (706)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCEECCCCCCC---CCCCCCCEECC---CCCEECCC
T ss_conf             8887665677647998999999999999999999987798896687044567532---45750024458---87650056


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCC
Q ss_conf             28589999898744688999886424567775448430020001157765787775578887766641883000223433
Q gi|254781066|r   80 TSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNC  159 (355)
Q Consensus        80 ~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~  159 (355)
                      ||||+|||+||+||++||||||||||||++++.|+|||||||+||||+|++|+|+++|+|++++++..+          .
T Consensus       210 QSPQlyKQlLMvgG~dRyFqIarcFRdEd~r~dRqPEFTqlDiEmSF~d~edvm~l~E~li~~~~~~~~----------~  279 (706)
T PRK12820        210 QSPQLFKQLLMIAGFERYFQLARCFRDEDLRPNRQPEFTQLDIEASFIDEEFIFELIEELTARMFAIGG----------I  279 (706)
T ss_pred             CCHHHHHHHHHHCCCCEEEEEEEEECCCCCCCCCCCCEEEEEEEHHCCCHHHHHHHHHHHHHHHHHHCC----------C
T ss_conf             682999999986286617996001128999988798340687421348999999999999999998538----------4


Q ss_pred             CCCCCCCCCCHHHHHHHHCCCCCCCC--------CCCCCCCCHHH--------------------------------HHH
Q ss_conf             24677320788886566608765323--------45556232799--------------------------------999
Q gi|254781066|r  160 NPFSEPEYITVAEAFARYANIDLGTT--------LDNPDQPDRHL--------------------------------LYL  199 (355)
Q Consensus       160 ~~~~~~~~i~~~e~~~~~~~~d~~~~--------~~~~~~~~~~~--------------------------------~~~  199 (355)
                      +...+|++++|.+++.+|........        ...........                                ...
T Consensus       280 ~l~~pFprmtY~eAm~~YGsDKPDlRf~lel~d~t~if~~~~f~vF~~~l~~gg~Vk~I~v~~~~~~~s~~~i~~e~~~e  359 (706)
T PRK12820        280 ALPRPFPRMPYAEAMDTTGSDRPDLRFDLKFADATDIFENTRYGIFKQILQRGGRIKGINIKGQSEKLSKNVLQNEYAKE  359 (706)
T ss_pred             CCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHCCCCHHHCCCCCHHHHHHHHHCCEEEEEECCCCHHHHHHHHHHHHHHHH
T ss_conf             54687453419999998689874310230102330122155405899988508868899768835665666656699998


Q ss_pred             HHHHCCCCCCCCCCH------------HH-----HHHHHH------------------------------------HCEE
Q ss_conf             999768877876534------------78-----987664------------------------------------3003
Q gi|254781066|r  200 QAQQAGIRVAHDDTW------------SD-----IFSRIL------------------------------------IEKI  226 (355)
Q Consensus       200 ~~~~~~~~~~~~~~~------------~~-----~~~~l~------------------------------------~~~i  226 (355)
                      .+.+.+.+   +..|            .+     ....+.                                    ...+
T Consensus       360 ia~~~gak---Gl~w~k~~~~~l~~~i~kf~see~~~~l~~~~~~~~GD~i~~~ad~~~~~v~~~LG~lR~~la~~l~Li  436 (706)
T PRK12820        360 IAPSFGAK---GMTWMRAEAGGLDSNIVQFFSADEKEALKRRFHAEDGDVIIMIADASCAIVLSALGQLRLHLADRLGLI  436 (706)
T ss_pred             HHHHCCCC---CCEEEEEECCCCCCHHHHCCCHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             62430656---625898616864631443079999999999848788988999727506689988626789999984887


Q ss_pred             CCCCCCCCCCCCCCCC-----------HHHHHHCCCCCCC--CC--------CCCCCEEEECCEECCCCCHHCCCHHHHH
Q ss_conf             6223767544325768-----------8886413678778--36--------3302202236712256402106999999
Q gi|254781066|r  227 EPNLGINCCTILDRYP-----------APESALANIYPAD--PR--------FTKRFELYACNIELCNACDELLDPIEQR  285 (355)
Q Consensus       227 e~~l~~~~pvfi~~yP-----------~~~~plak~~~~~--~~--------va~rfdl~i~G~El~ng~~El~d~~~q~  285 (355)
                      .++.  ..|+||+|||           ....||++++.++  +.        .+.+|||++||.||+||+.|+|||+.|+
T Consensus       437 ~~~~--~~flWVtDFPLFE~~ee~~~~s~HHPFT~P~~ed~d~~~~~~~~~v~a~aYDLVlNG~ElggGSiRIHd~~iQ~  514 (706)
T PRK12820        437 PEGV--FHPLWITDFPLFEATDDGGVTSSHHPFTAPDREDFDPGDIEELLDLRSRAYDLVVNGEELGGGSIRINDKDIQL  514 (706)
T ss_pred             CCCC--CEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCEEEEEECCEEEEEEEEECCCHHHHH
T ss_conf             8786--31688516742234544465335489778882336832245532000364606899999614022038999999


Q ss_pred             HHHHHHHHHHHCCCCCC-C-HHHHHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCCC
Q ss_conf             99999999997288853-0-1018999986-1889632453159999899815597131115856487433
Q gi|254781066|r  286 HRFEKEMQEKKKIYNET-Y-PIDEDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQE  353 (355)
Q Consensus       286 ~rf~~q~~~k~~~~~e~-~-~~D~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~~  353 (355)
                      ++|+.      .|..+. . .-..+||+|| ||+|||||+|||||||||+|||.+|||||||||.+.+.++
T Consensus       515 ~if~~------lGl~~ee~~~kFgf~LeAf~YGaPPHGGialGlDRLvMlLtg~~sIRDVIaFPKt~~g~d  579 (706)
T PRK12820        515 RIFAA------LGLSEEDIEDKFGFFLRAFDFAAPPHGGIALGLDRVVSMILQTPSIREVIAFPKNRSAAC  579 (706)
T ss_pred             HHHHH------CCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEHHHHHHHHHCCCCCHHHEECCCCCCCCCC
T ss_conf             99997------599978988899999999866999867031039999999769982650522789988786


No 16 
>PRK06462 asparagine synthetase A; Reviewed
Probab=100.00  E-value=0  Score=546.21  Aligned_cols=294  Identities=16%  Similarity=0.136  Sum_probs=220.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             48999999999999999999879889847821056898544541241024788678320000285899998987446889
Q gi|254781066|r   18 RRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKI   97 (355)
Q Consensus        18 ~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rv   97 (355)
                      .|.++++||+|+++||+||+++||+||+||+|+++.+++. +.+|.++   .+++++++||+||||||||+|+++|++||
T Consensus        25 ~~~ifriRs~i~~~iR~f~~~~gF~EV~TPiL~~~~~~~~-~~~~~~~---~~~~~~~~~L~~Spql~lk~li~~g~~rV  100 (332)
T PRK06462         25 YSLVLKIQSSILRYTREFLDGRGFVEVLPPIISPSTDPLM-GDAKPAS---IDFYGVEYYLADSMIFHKQLMLRLLKGKV  100 (332)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCC-CCCCCCE---EECCCCCEEECCCHHHHHHHHHHCCCCCE
T ss_conf             9999999999999999999888999987972367788766-7760105---84489863314586999999986389977


Q ss_pred             HHHHHHHCCCCCC---CCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCE---E-CCCC-CCCCCCCCCCCCC
Q ss_conf             9988642456777---54484300200011577657877755788877666418830---0-0223-4332467732078
Q gi|254781066|r   98 FCFAHAWRNGEQG---CLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKI---F-SFQN-VNCNPFSEPEYIT  169 (355)
Q Consensus        98 yqig~~FRaE~~~---~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~---~-~~~~-~~~~~~~~~~~i~  169 (355)
                      ||||||||||++|   +|||||||||||||||+|++|+|+++|++|+++++.+....   + ...+ ...+...+|++++
T Consensus       101 feIg~~FR~E~~d~~t~rHlpEFt~lE~y~a~~d~~d~m~~~E~li~~i~~~v~~~~~~~~~~~~~~~~~~~~~~~~ri~  180 (332)
T PRK06462        101 FYLSPNFRLEPVDKDTGRHLYEFTQLDIEIEGADLEEVMSLAEDLIKYLVKELLREHSAELEFFLGRDLPEIKRPFKRIT  180 (332)
T ss_pred             EEECCHHHCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCC
T ss_conf             99745231687776777654577765587873899999999999999999999986679999870777523598114546


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHC
Q ss_conf             88865666087653234555623279999999976887787653478987664300362237675443257688886413
Q gi|254781066|r  170 VAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALA  249 (355)
Q Consensus       170 ~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~pla  249 (355)
                      +.++++....                        .+........++...+    ..+++++  ..||||+|||++++|||
T Consensus       181 ~~eai~~l~~------------------------~~~~~~~~~~~~~~~e----~~l~~~~--~~P~fv~d~P~~~~Pfy  230 (332)
T PRK06462        181 HKEAIEILNE------------------------EGCSGEELEEIGSEGE----KSLSEHF--EEPVWIINIPKGSREFY  230 (332)
T ss_pred             HHHHHHHHHH------------------------CCCCCCHHHHHHHHHH----HHHHHHH--CCCEEEECCHHHHCHHH
T ss_conf             9999999986------------------------2765660767545999----9999980--89789975625529586


Q ss_pred             CCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHH-HHHHCCCCCCCHHHHHHHHHH-CCCC-CCCEEECCH
Q ss_conf             6787783633022022367122564021069999999999999-999728885301018999986-1889-632453159
Q gi|254781066|r  250 NIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEM-QEKKKIYNETYPIDEDFLACL-TEMP-QSSGIAMGF  326 (355)
Q Consensus       250 k~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~-~~k~~~~~e~~~~D~~fl~al-~G~P-PhgG~glGi  326 (355)
                      +.+++++++++||||++     +|||+|++|+.+|+++++++. ++++.+.++...  +|||+|+ +|+| |||||||||
T Consensus       231 ~~~~~~~~~~~~fdl~~-----~~g~~El~~g~~r~~~~~~l~~~~~~~g~~~~~~--~~yl~~~~~G~P~P~gG~GiGi  303 (332)
T PRK06462        231 DREDERPGVLRDYDLLL-----PEGIGEAVSGGEREYEYEEIVERIREHGVDPENY--KWYLEMAKEGYPLPTAGFGIGV  303 (332)
T ss_pred             HCCCCCCCEEEECCHHH-----HCCCEEECCHHHHHHHHHHHHHHHHHCCCCHHHH--HHHHHHHHHCCCCCCCEEEEHH
T ss_conf             64899988487536033-----0666222251767855999999999769997899--9999999828999987761489


Q ss_pred             HHHHHHHHCCCCHHHHCCCCCCCCCC
Q ss_conf             99989981559713111585648743
Q gi|254781066|r  327 DRLVMLVTGANNINEVIWTPFSQSNQ  352 (355)
Q Consensus       327 dRLvm~l~g~~~Irdvi~FP~~r~~~  352 (355)
                      |||||++||.+||||||+||++....
T Consensus       304 DRLvm~l~~~~~Irdvi~FPR~pg~~  329 (332)
T PRK06462        304 ERLTRYICGLRDIREVQPFPRVPGIV  329 (332)
T ss_pred             HHHHHHHHCCCCHHEEEECCCCCCCC
T ss_conf             99999980898576174179998988


No 17 
>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=100.00  E-value=0  Score=535.94  Aligned_cols=316  Identities=21%  Similarity=0.277  Sum_probs=225.5

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCEE-CCCCCCCCCCCEEEECCCC-CCCCCCCC-CCCCHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999998798898478210-5689854454124102478-86783200-00285899998987446889
Q gi|254781066|r   21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQ-YSPGNETHIRAFSTELIIQ-DHIRKPLY-LQTSPEFSCKKLLAAGEEKI   97 (355)
Q Consensus        21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~-~~~~g~~~~~~f~t~~~~~-~~~~~~~y-L~~SPql~lK~ll~~G~~rv   97 (355)
                      .|..||+|..+||+||+++||+|||||||+ +||+|   |+.|.|+.+.+ .....+|| |+||||||||.||+||++||
T Consensus       150 ~L~lR~~v~~~~Rn~l~~~gFleiETP~LtKsTPEG---ARDyLVPsRv~rsdG~g~FYALpQSPQlfKQLLMvsG~drY  226 (653)
T TIGR00459       150 RLKLRHKVTKAVRNFLDQQGFLEIETPILTKSTPEG---ARDYLVPSRVHRSDGKGEFYALPQSPQLFKQLLMVSGVDRY  226 (653)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCC---HHHCCCCCCCCCCCCCCCEECCCCCHHHHHHHHHHCCCCCC
T ss_conf             986688989999866642787065067777888431---10157755300368588451468975689998751255531


Q ss_pred             HHHHHHHCCCCC--CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCC---CCC-----
Q ss_conf             998864245677--7544843002000115776578777557888776664188300022343324677---320-----
Q gi|254781066|r   98 FCFAHAWRNGEQ--GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSE---PEY-----  167 (355)
Q Consensus        98 yqig~~FRaE~~--~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~---~~~-----  167 (355)
                      |||++||||||+  |||  |||||+|+||||++.++||+++|+|+.+|++.+...     ...++...+   |++     
T Consensus       227 yQIArCFRDEDLRADRQ--PEFTQiD~E~SF~~~~~vm~l~E~l~~~vf~~v~~k-----rGl~~L~~~GtlfP~kkenG  299 (653)
T TIGR00459       227 YQIARCFRDEDLRADRQ--PEFTQIDMEMSFMTQEDVMDLIEKLVSGVFKEVKGK-----RGLIDLKKPGTLFPVKKENG  299 (653)
T ss_pred             EEEEEEECCCCCCCCCC--CCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC-----CCEEEECCCCCEEEEECCCC
T ss_conf             35788976625666577--873244263112893568999999999999997078-----51375078852411221676


Q ss_pred             ------CCHHHHHHHHCCCCCCCCCCCCC--------------------------------------------CCCHHHH
Q ss_conf             ------78888656660876532345556--------------------------------------------2327999
Q gi|254781066|r  168 ------ITVAEAFARYANIDLGTTLDNPD--------------------------------------------QPDRHLL  197 (355)
Q Consensus       168 ------i~~~e~~~~~~~~d~~~~~~~~~--------------------------------------------~~~~~~~  197 (355)
                            +||.||+.+|....++.....+.                                            ......+
T Consensus       300 tvsifrmty~EAm~~yGsDKPDLR~~~el~dv~d~f~afshld~~F~vF~~~~~~P~g~v~~i~v~~~~~~ls~~~i~~l  379 (653)
T TIGR00459       300 TVSIFRMTYQEAMERYGSDKPDLRFGLELIDVSDLFKAFSHLDSEFKVFSNLINAPGGRVKAIRVKGGDAELSRKSIKEL  379 (653)
T ss_pred             EEEEEECCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEECCCCCCCCCHHHHHHH
T ss_conf             07998556799986167768778888346777667777664067534579998488855775772786422550212220


Q ss_pred             H---HHHHHCCCCC-----------------------------------------------CCCCC-HHHHHHHHHH---
Q ss_conf             9---9999768877-----------------------------------------------87653-4789876643---
Q gi|254781066|r  198 Y---LQAQQAGIRV-----------------------------------------------AHDDT-WSDIFSRILI---  223 (355)
Q Consensus       198 ~---~~~~~~~~~~-----------------------------------------------~~~~~-~~~~~~~l~~---  223 (355)
                      .   ..+...|.+-                                               -.... +......+-+   
T Consensus       380 ~~~~~~a~~~GakGlAy~~v~~~~~~~~~~~~~i~kfL~~~~~~~~~~~t~a~~gdillnPfg~~~l~~~v~~~lgGkal  459 (653)
T TIGR00459       380 RVLIKFAKEYGAKGLAYLKVNEDAEGLEEVKSPIKKFLDEKKLKKLLERTDAQEGDILLNPFGAGDLKKIVLDALGGKAL  459 (653)
T ss_pred             CHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCHHHHCCCHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHCCHHH
T ss_conf             11445676658631566565216741024531012024735778899874212687865577860589999985041688


Q ss_pred             -CEECCCCC--C-----CCCCCCCC---------CCHH------------HHHHCCCCCCCC---------CCCCCCEEE
Q ss_conf             -00362237--6-----75443257---------6888------------864136787783---------633022022
Q gi|254781066|r  224 -EKIEPNLG--I-----NCCTILDR---------YPAP------------ESALANIYPADP---------RFTKRFELY  265 (355)
Q Consensus       224 -~~ie~~l~--~-----~~pvfi~~---------yP~~------------~~plak~~~~~~---------~va~rfdl~  265 (355)
                       ..+..+++  .     -.|+||+|         ||.-            --||+++.+.+.         -.|+.|||+
T Consensus       460 Rl~l~~~l~sWL~d~~~~~flWv~DksGkkeklaFP~fE~d~~E~~~~a~HHpFT~Pk~~~~~~lE~~p~~a~a~aYDlV  539 (653)
T TIGR00459       460 RLKLGKDLGSWLVDPDAFSFLWVVDKSGKKEKLAFPLFEKDEEEGRLVAAHHPFTMPKPEDLEDLETAPEEALAEAYDLV  539 (653)
T ss_pred             HHHHHHHHHCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCHHHHHCCHHHHHHHCCCEE
T ss_conf             99987653000235231471789837887023427656677652755840578898751227877407455412028768


Q ss_pred             ECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHC
Q ss_conf             367122564021069999999999999999728885-301018999986-188963245315999989981559713111
Q gi|254781066|r  266 ACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNE-TYPIDEDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVI  343 (355)
Q Consensus       266 i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e-~~~~D~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi  343 (355)
                      +||+||++|+.+++||..|...|+.-.    +.+++ +.+-=-++|+|+ +|+|||||+|+|||||+|+||+.+||||||
T Consensus       540 lNG~ElGGGSiRIh~~~~Q~~~F~d~L----gid~eea~EkFGFLLeA~~yGaPPHgG~A~GlDRL~Mll~~~~nIRDVI  615 (653)
T TIGR00459       540 LNGVELGGGSIRIHDPEVQEKVFEDIL----GIDPEEAREKFGFLLEAFKYGAPPHGGLALGLDRLVMLLTGTDNIRDVI  615 (653)
T ss_pred             EEEEEECCCEEEECCHHHHHHHHHHHH----CCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCEEC
T ss_conf             830698871046428789999998762----8898998776356875873576851015555899999980899722001


Q ss_pred             CCCCCCC
Q ss_conf             5856487
Q gi|254781066|r  344 WTPFSQS  350 (355)
Q Consensus       344 ~FP~~r~  350 (355)
                      |||.+..
T Consensus       616 AFPKt~~  622 (653)
T TIGR00459       616 AFPKTAQ  622 (653)
T ss_pred             CCCCCCC
T ss_conf             7887601


No 18 
>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=100.00  E-value=0  Score=532.32  Aligned_cols=304  Identities=20%  Similarity=0.242  Sum_probs=243.5

Q ss_pred             HCCCHHH-----HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC-CCCCCCCCEEEEC--------------CCCCCCC
Q ss_conf             2615489-----999999999999999998798898478210568-9854454124102--------------4788678
Q gi|254781066|r   14 FHYRRRP-----FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP-GNETHIRAFSTEL--------------IIQDHIR   73 (355)
Q Consensus        14 ~~~r~R~-----~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-~g~~~~~~f~t~~--------------~~~~~~~   73 (355)
                      +|||-|+     ++++||.+.++||+||+++||+.|+||||+++. +|+.  +-|.|..              +..+||+
T Consensus       133 ~HLr~Rt~~~~AvmrvR~~l~~ai~~yF~~~gF~~V~~PilT~~d~EGAG--ElF~v~TLdl~~lp~~~g~~df~~~fFg  210 (495)
T TIGR00457       133 AHLRLRTNTLGAVMRVRNALSQAIHEYFQKNGFVKVSPPILTSNDCEGAG--ELFKVSTLDLEKLPRNDGKIDFSKDFFG  210 (495)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCEEECCCCCCCC--CCCEEEEHHHHCCCCCCCCCCCCCCCCC
T ss_conf             63777898877899999999999998760478678688631136888875--4332200324215332688876302488


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCE-
Q ss_conf             3200002858999989874468899988642456777-54484300200011577657877755788877666418830-
Q gi|254781066|r   74 KPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQG-CLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKI-  151 (355)
Q Consensus        74 ~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~-~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~-  151 (355)
                      +++||+||.||++ +.+|..|+|||+||||||||.|+ +|||+||||||.||||++++|+++++|++|+++++.+-... 
T Consensus       211 k~ayLTVSGQL~~-E~~A~AL~kvyTfGPTFRAEkS~T~RHLsEFWMiEPE~AF~~l~d~~~~~E~~~k~~~k~VL~~~q  289 (495)
T TIGR00457       211 KEAYLTVSGQLYA-EAYALALSKVYTFGPTFRAEKSNTSRHLSEFWMIEPEMAFANLNDLLQLIETLIKYIIKAVLENQQ  289 (495)
T ss_pred             CEEEEEECCHHHH-HHHHHHHCCCEECCCCEECCCCCCCCCHHHHHHHHHHEEECCHHHHHHHHHHHHHHHHHHHHCCHH
T ss_conf             6012330227899-999997478144587400428648701112210112000001333389999999999999830524


Q ss_pred             --ECCC---CCC---CC-----------------CCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCC
Q ss_conf             --0022---343---32-----------------4677320788886566608765323455562327999999997688
Q gi|254781066|r  152 --FSFQ---NVN---CN-----------------PFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGI  206 (355)
Q Consensus       152 --~~~~---~~~---~~-----------------~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~  206 (355)
                        +.-+   ..+   .+                 ..++|.+|+|.+|+.                    +|.....+...
T Consensus       290 ellPkqfi~~~enn~~~~L~~~~~~~~~~~l~~~i~~~F~~i~Y~~Ai~--------------------iL~~~~~~~~~  349 (495)
T TIGR00457       290 ELLPKQFICSQENNLLKFLEKNFDKDLIKKLENIINNKFARITYTDAIE--------------------ILKESDNKEKK  349 (495)
T ss_pred             HHCCHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHCCCCEECHHHHHH--------------------HHHHHHHCCCC
T ss_conf             5042010377713799986641275677522566622676004789999--------------------98742111464


Q ss_pred             CCCCCCC-HHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHCCCCC-CCCCCCCCCEEEECC-E-ECCCCCHHCCCHH
Q ss_conf             7787653-4789876643003622376754432576888864136787-783633022022367-1-2256402106999
Q gi|254781066|r  207 RVAHDDT-WSDIFSRILIEKIEPNLGINCCTILDRYPAPESALANIYP-ADPRFTKRFELYACN-I-ELCNACDELLDPI  282 (355)
Q Consensus       207 ~~~~~~~-~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~plak~~~-~~~~va~rfdl~i~G-~-El~ng~~El~d~~  282 (355)
                      +++.++. ||..+...+|.++.++....+||||+|||+++|||||... +|++++.++||++.+ + ||++|+.|+.|-+
T Consensus       350 ~Fe~~d~~wG~DL~~eHER~LaE~~Fk~qPvfV~~YPk~~KaFYMk~NS~D~~tV~a~DlL~P~GiGEIiGGS~Re~dld  429 (495)
T TIGR00457       350 NFEYEDFEWGIDLQTEHERFLAEEYFKPQPVFVTDYPKDIKAFYMKLNSDDGKTVAAVDLLAPKGIGEIIGGSEREDDLD  429 (495)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHCCCCCCCEEEECCCCCCCCHHCCCCCCCCCEEEEEEEECCCCEEEEECCCCCHHHHH
T ss_conf             35888613488863368998763158988889973885558010536678887478999837896266516754322689


Q ss_pred             HHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCC
Q ss_conf             99999999999997288853-01018999986-18896324531599998998155971311158564
Q gi|254781066|r  283 EQRHRFEKEMQEKKKIYNET-YPIDEDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFS  348 (355)
Q Consensus       283 ~q~~rf~~q~~~k~~~~~e~-~~~D~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~  348 (355)
                      ++.+|+.+      .|-+.. ..  +||++-. +|..||||||||+||||+|+||..|||||||||++
T Consensus       430 ~L~~r~k~------~g~d~~G~l--~WY~DlRKyGs~PH~GFGLGfERl~ay~~G~~niRD~IPFPR~  489 (495)
T TIGR00457       430 KLEERMKE------MGLDTDGAL--NWYLDLRKYGSVPHSGFGLGFERLVAYITGLENIRDAIPFPRT  489 (495)
T ss_pred             HHHHHHHH------CCCCCCCCC--HHHHHHCCEECCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             99999996------486887750--4326415120566466432489999998178744416677877


No 19 
>TIGR00462 genX lysyl-tRNA synthetase homolog GenX; InterPro: IPR004525   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 .   This entry represents lysyl-tRNA synthetases from bacteria, as well as other related proteins. Escherichia coli, Haemophilus influenzae, and Aquifex aeolicus each have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS, so they appear to be orthologous. The protein is termed PoxA or GenX after its designation in E. coli. Its function is unknown.; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=527.68  Aligned_cols=321  Identities=36%  Similarity=0.593  Sum_probs=296.4

Q ss_pred             CCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCC-CCCCCCCCCCCH
Q ss_conf             8987478831261548999999999999999999879889847821056898544541241024788-678320000285
Q gi|254781066|r    4 IPSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQD-HIRKPLYLQTSP   82 (355)
Q Consensus         4 ~p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~-~~~~~~yL~~SP   82 (355)
                      |-.-.-|+|++-.   ....+|++|+..||.||.++|++||+||+|...+..+.++.||.|...... .-++..+|.|||
T Consensus         6 M~~l~~W~Psa~i---~n~LkRa~~i~~iR~FF~e~G~~EV~TP~l~~~~~~D~~l~p~~~~~l~~g~~~~~~~WL~TSP   82 (330)
T TIGR00462         6 MDLLDAWQPSADI---KNLLKRAKIIAEIRKFFKERGLLEVETPLLSDFPVTDLHLEPFKTEFLEPGGEQNKVLWLSTSP   82 (330)
T ss_pred             CHHHHCCCCCCCH---HHHHHHHHHHHHHHHHHHHCCCEEECCCCHHCCCCCCEEEEEEEEEEECCCCCCCCEECCCCCC
T ss_conf             1033357865224---6778899999999998861784253263010156443022136888842665333312114587


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCC
Q ss_conf             89999898744688999886424567775448430020001157765787775578887766641883000223433246
Q gi|254781066|r   83 EFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPF  162 (355)
Q Consensus        83 ql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~  162 (355)
                      |++||+||++|.+.||||+++||||+.+++|+|||||||||++..|+.-+|+.+.++++.++.                +
T Consensus        83 EY~MK~LL~~~~~~iFQi~k~FRN~E~G~~H~~EF~MLEWY~~~~d~~~Li~E~~~LL~~~ld----------------~  146 (330)
T TIGR00462        83 EYHMKRLLSAGKGPIFQITKVFRNEEAGRLHNPEFTMLEWYRPHYDMLRLINEVDDLLQQLLD----------------C  146 (330)
T ss_pred             CHHHHHHHHHCCCCEEEEEEHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC----------------C
T ss_conf             278999986217862310000100024675775310011121102389999999999999728----------------8


Q ss_pred             CCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCC--CCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCC
Q ss_conf             773207888865666087653234555623279999999976887--787653478987664300362237675443257
Q gi|254781066|r  163 SEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIR--VAHDDTWSDIFSRILIEKIEPNLGINCCTILDR  240 (355)
Q Consensus       163 ~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~  240 (355)
                      .+++.+||.++|++|.++|+..       .++..+...+.+.++.  ...+.+|..++..+|.+.||+++|.+.|+||+|
T Consensus       147 ~~~E~l~~~~~F~~y~g~d~l~-------~e~s~l~E~~~k~~~~~~~~~~ED~~TLl~~~F~~~VE~~~G~~rP~~~~~  219 (330)
T TIGR00462       147 PEAESLSYQEAFKRYLGLDPLS-------AEKSELKELAEKKDLDNVAEEDEDRDTLLQLLFIEVVEPQIGKERPTFVYH  219 (330)
T ss_pred             CCCCEECHHHHHHHHHCCCCCC-------HHHHHHHHHHHHCCCHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEE
T ss_conf             6300001899999984479873-------025789999985473233203444799999999876401037778757880


Q ss_pred             CCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC-CCCCC
Q ss_conf             68888641367877836330220223671225640210699999999999999997288853010189999861-88963
Q gi|254781066|r  241 YPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLT-EMPQS  319 (355)
Q Consensus       241 yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~-G~PPh  319 (355)
                      ||..+++||+..++|.++|+|||+|+.|+||||||+|++||.+|++||+.+++.|.+.+.+..++|++|+.|++ |||.|
T Consensus       220 FP~~~aaLA~v~~eD~~~AERFE~y~KGiELANGf~E~t~a~E~r~R~E~~~~kR~~~~~P~~~~D~~~i~A~~~GMP~c  299 (330)
T TIGR00462       220 FPERQAALAQVSTEDNRVAERFELYYKGIELANGFHELTDAEEQRKRFERDNKKRAKRELPTLPIDEDFIKALEDGMPDC  299 (330)
T ss_pred             CCHHHHHHHCCCCCCCCCCHHEEHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCC
T ss_conf             70455555204513363200100100100002775322584889988768877788625898514599999985478741


Q ss_pred             CEEECCHHHHHHHHHCCCCHHHHCCCCCCCC
Q ss_conf             2453159999899815597131115856487
Q gi|254781066|r  320 SGIAMGFDRLVMLVTGANNINEVIWTPFSQS  350 (355)
Q Consensus       320 gG~glGidRLvm~l~g~~~Irdvi~FP~~r~  350 (355)
                      +|++||||||+|+.+|++.|-+||.|-.++|
T Consensus       300 sGvaLGiDRL~~l~Lg~E~l~~~~~~avD~a  330 (330)
T TIGR00462       300 SGVALGIDRLVMLALGKEELVEVIAFAVDRA  330 (330)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHHHHCCC
T ss_conf             4402557899998707326888998863159


No 20 
>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=100.00  E-value=0  Score=509.74  Aligned_cols=276  Identities=25%  Similarity=0.315  Sum_probs=204.6

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCEECC-CCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999879889847821056-898544541241024788678320000285899998987446889998
Q gi|254781066|r   22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYS-PGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCF  100 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqi  100 (355)
                      |++||+|+++||+||+++||+||+||+|+++ ++|   +.+|.+...  .+.+..+||+||||+|||+||++|++|||||
T Consensus         1 lr~Rs~i~~~iR~ff~~~gflEV~TPiL~~~~~eg---a~~f~~~~~--~~~~~~~~L~~Spel~~k~l~~~g~~rvf~i   75 (280)
T cd00777           1 LRLRSRVIKAIRNFLDEQGFVEIETPILTKSTPEG---ARDFLVPSR--LHPGKFYALPQSPQLFKQLLMVSGFDRYFQI   75 (280)
T ss_pred             CCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCC---CCCCEECCC--CCCCCCCCCCCCHHHHHHHHHHCCCCCCEEE
T ss_conf             96699999999999998898998798106878776---766442441--6887603688798999999985687775798


Q ss_pred             HHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCHHHHHHHHCCC
Q ss_conf             86424567775448430020001157765787775578887766641883000223433246773207888865666087
Q gi|254781066|r  101 AHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSEPEYITVAEAFARYANI  180 (355)
Q Consensus       101 g~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~~  180 (355)
                      |||||||+++++|+||||||||||+|+|++|+|+++|+||+++++.+..         .+...+|++++|.++++++ +.
T Consensus        76 ~~~FR~E~~~~~h~~EFtmLE~e~~~~~~~d~m~~~E~li~~i~~~~~~---------~~~~~~~~rity~ea~~~~-g~  145 (280)
T cd00777          76 ARCFRDEDLRADRQPEFTQIDIEMSFVDQEDIMSLIEGLLKYVFKEVLG---------VELTTPFPRMTYAEAMERY-GF  145 (280)
T ss_pred             ECEECCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHC---------CCCCCCCCEEEHHHHHHHH-CC
T ss_conf             4517478888766347762344226888999999999999999999819---------8779997577688999986-89


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHH-CCCCCCCCCCC
Q ss_conf             65323455562327999999997688778765347898766430036223767544325768888641-36787783633
Q gi|254781066|r  181 DLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESAL-ANIYPADPRFT  259 (355)
Q Consensus       181 d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~pl-ak~~~~~~~va  259 (355)
                      +.....+.+.                     ..+.....    ..+..    ..| |.  .|....+. ...++ +..++
T Consensus       146 ~~~~~~d~~~---------------------~~~~~~~~----~~~~~----~~p-f~--~p~~~~~~~~~~~p-~~~~~  192 (280)
T cd00777         146 KFLWIVDFPL---------------------FEWDEEEG----RLVSA----HHP-FT--APKEEDLDLLEKDP-EDARA  192 (280)
T ss_pred             CCCCCCCCCC---------------------CCCCHHHC----CCCCC----CCC-CC--CCCHHHHHHHHCCC-HHHHH
T ss_conf             7331135753---------------------34624425----52222----077-34--78244167763380-24567


Q ss_pred             CCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCC
Q ss_conf             0220223671225640210699999999999999997288853-010189999861-88963245315999989981559
Q gi|254781066|r  260 KRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNET-YPIDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGAN  337 (355)
Q Consensus       260 ~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~-~~~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~  337 (355)
                      +|||||++|+||||||+|++||++|++||+...     .+.+. ..-+++||+|++ |+|||||||||||||||++||++
T Consensus       193 ~~fdl~~~G~El~nG~~r~~d~~~~~~~~~~~~-----~~~~~~~~~~~~~l~a~~~G~pP~~G~glGiDRLvm~l~g~~  267 (280)
T cd00777         193 QAYDLVLNGVELGGGSIRIHDPDIQEKVFEILG-----LSEEEAEEKFGFLLEAFKYGAPPHGGIALGLDRLVMLLTGSE  267 (280)
T ss_pred             HHHCCCCCCEEECCCCCEECCHHHHHHHHHHCC-----CCHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHCCC
T ss_conf             774135686442353102279999999999859-----896677888999999976699987435158999999992898


Q ss_pred             CHHHHCCCCCCCC
Q ss_conf             7131115856487
Q gi|254781066|r  338 NINEVIWTPFSQS  350 (355)
Q Consensus       338 ~Irdvi~FP~~r~  350 (355)
                      |||||||||+++.
T Consensus       268 ~Irdvi~FPR~~n  280 (280)
T cd00777         268 SIRDVIAFPKTQN  280 (280)
T ss_pred             CHHEEECCCCCCC
T ss_conf             2870734799998


No 21 
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=506.62  Aligned_cols=288  Identities=24%  Similarity=0.285  Sum_probs=230.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC-CCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999998798898478210568-985445412410247886783200002858999989874468899
Q gi|254781066|r   20 PFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP-GNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIF   98 (355)
Q Consensus        20 ~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvy   98 (355)
                      .++++||.+++++|+||.++||+||+||+|++++ +|+  ..+|.+     +|++.++||+||||||+ ++++++++|||
T Consensus       132 Av~kirs~i~~a~~eff~~~gF~eV~tP~i~~~~~EGg--~elF~v-----~yf~~~a~LtqS~QLyk-e~~~~al~rVf  203 (435)
T COG0017         132 AVFKIRSSILRAIREFFYENGFTEVHTPIITASATEGG--GELFKV-----DYFDKEAYLTQSPQLYK-EALAAALERVF  203 (435)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEECCCEEECCCCCCC--CEEEEE-----EECCCCEEEECCHHHHH-HHHHHHHCCEE
T ss_conf             78949999999999999758958965946853478998--505777-----50685667714788999-99999857648


Q ss_pred             HHHHHHCCCCCC-CCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCC---EECCC---CCCCCC--CCCCCCCC
Q ss_conf             988642456777-5448430020001157765787775578887766641883---00022---343324--67732078
Q gi|254781066|r   99 CFAHAWRNGEQG-CLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQK---IFSFQ---NVNCNP--FSEPEYIT  169 (355)
Q Consensus        99 qig~~FRaE~~~-~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~---~~~~~---~~~~~~--~~~~~~i~  169 (355)
                      +|||+||||+++ +|||+||||+|+||||+|++|+|+++|+||+++++.+...   .+...   +.....  ..+|+|++
T Consensus       204 ~igP~FRAE~s~T~RHL~EF~~ld~Emaf~~~~d~m~l~E~~i~~i~~~v~e~~~~el~~l~~~~~~l~~~~~~pf~rit  283 (435)
T COG0017         204 TIGPTFRAEKSNTRRHLSEFWMLDPEMAFADLNDVMDLAEELIKYLFKKVLEECADELEFLGRDNSELKRPESAPFPRIT  283 (435)
T ss_pred             EECCCEECCCCCCCCHHHHHHEECCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCEEE
T ss_conf             95672554778970036667330211136768889999999999999999997189888761461110344468963777


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHC
Q ss_conf             88865666087653234555623279999999976887787653478987664300362237675443257688886413
Q gi|254781066|r  170 VAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALA  249 (355)
Q Consensus       170 ~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~pla  249 (355)
                      |.||++-.                        .+.+.+.   ..||+.+....+.++.++... +||||+|||++++|||
T Consensus       284 Y~eAieiL------------------------~~~~~e~---~~~GdDl~~e~Er~l~e~~~~-~~vfv~~yP~~~kpFY  335 (435)
T COG0017         284 YKEAIEIL------------------------EEKGFEK---VEWGDDLGTEHERYLGEEYFK-PPVFVTNYPKEIKPFY  335 (435)
T ss_pred             HHHHHHHH------------------------HHCCCCC---CCCCCCCCCHHHHHHHHHHCC-CCEEEEECCCCCCCCC
T ss_conf             99999999------------------------8647765---677775688999999987579-9499981764446650


Q ss_pred             C-CCCCCCCCCCCCEEEECC-EECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCCCEEECCH
Q ss_conf             6-787783633022022367-122564021069999999999999999728885301018999986-1889632453159
Q gi|254781066|r  250 N-IYPADPRFTKRFELYACN-IELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-TEMPQSSGIAMGF  326 (355)
Q Consensus       250 k-~~~~~~~va~rfdl~i~G-~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~G~PPhgG~glGi  326 (355)
                      + .++++|+++.+|||++.| .||++|+++++|.+.+.+|+      ++.|-++...  +|||+++ +|+|||||||||+
T Consensus       336 m~~~~d~p~~~~~~Dll~p~~gEIigGsqRe~~~d~L~~ri------~~~gl~~e~~--~wYld~~kyG~~PHaGfGlG~  407 (435)
T COG0017         336 MRPDPDNPGTVASFDLLAPGGGEIIGGSQREHDYDLLVERI------KEKGLDPESY--EWYLDLRKYGMPPHAGFGLGL  407 (435)
T ss_pred             CCCCCCCCCEEEEEEEECCCCEEEECCEECCCCHHHHHHHH------HHCCCCHHHH--HHHHHHHHCCCCCCCCCCCCH
T ss_conf             33379988769987652478705603623043099999999------9809996881--899999873899986003379


Q ss_pred             HHHHHHHHCCCCHHHHCCCCCCCCC
Q ss_conf             9998998155971311158564874
Q gi|254781066|r  327 DRLVMLVTGANNINEVIWTPFSQSN  351 (355)
Q Consensus       327 dRLvm~l~g~~~Irdvi~FP~~r~~  351 (355)
                      |||+|++||++|||||||||+++..
T Consensus       408 ERlv~~i~gl~nIRea~pFPR~~~r  432 (435)
T COG0017         408 ERLVMYILGLDNIREAIPFPRDPGR  432 (435)
T ss_pred             HHHHHHHHCCCCCEECCCCCCCCCC
T ss_conf             9999999488832012447777787


No 22 
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=493.48  Aligned_cols=308  Identities=23%  Similarity=0.304  Sum_probs=224.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCEE-CCCCCCCCCCCEEEECCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999998798898478210-568985445412410247886783200-002858999989874468899
Q gi|254781066|r   21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQ-YSPGNETHIRAFSTELIIQDHIRKPLY-LQTSPEFSCKKLLAAGEEKIF   98 (355)
Q Consensus        21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~-~~~~g~~~~~~f~t~~~~~~~~~~~~y-L~~SPql~lK~ll~~G~~rvy   98 (355)
                      .++.||++.++||+||+++||+||+||+|+ ++|+|   |+.|.|++..+..   +|| |+||||+|||.||++||+|||
T Consensus       140 ~l~lR~kv~~~iR~~ld~~gF~EiETPiLtkSTPEG---ARDfLVPSRv~~G---~FYALPQSPQlfKQLLMvsGfdRYy  213 (585)
T COG0173         140 NLKLRSKVTKAIRNFLDDQGFLEIETPILTKSTPEG---ARDFLVPSRVHPG---KFYALPQSPQLFKQLLMVAGFDRYY  213 (585)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCC---CCCCCCCCCCCCC---CEEECCCCHHHHHHHHHHHCCCCEE
T ss_conf             999999999999997765498573467414679865---5443013455899---6530688879999999880533002


Q ss_pred             HHHHHHCCCCC--CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             98864245677--7544843002000115776578777557888776664188300022343324677320788886566
Q gi|254781066|r   99 CFAHAWRNGEQ--GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSEPEYITVAEAFAR  176 (355)
Q Consensus        99 qig~~FRaE~~--~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~e~~~~  176 (355)
                      ||+||||||++  ||+  |||||||+||||+|.+|+|+++|+|++++++.+..         ++...+|++|+|.+|+.+
T Consensus       214 QIarCFRDEDlRaDRQ--PEFTQiD~EmSF~~~edv~~~~E~l~~~vf~~~~~---------i~l~~pFprmtY~eAm~~  282 (585)
T COG0173         214 QIARCFRDEDLRADRQ--PEFTQIDLEMSFVDEEDVMELIEKLLRYVFKEVKG---------IELKTPFPRMTYAEAMRR  282 (585)
T ss_pred             EEEEEECCCCCCCCCC--CCCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHCC---------CCCCCCCCCCCHHHHHHH
T ss_conf             3565404664444468--75336767764388999999999999999998509---------754898561059999997


Q ss_pred             HCCCCCCCCCC--------------------------------CCC-----CCCHHHHHHHHHHCCCCCC------CCC-
Q ss_conf             60876532345--------------------------------556-----2327999999997688778------765-
Q gi|254781066|r  177 YANIDLGTTLD--------------------------------NPD-----QPDRHLLYLQAQQAGIRVA------HDD-  212 (355)
Q Consensus       177 ~~~~d~~~~~~--------------------------------~~~-----~~~~~~~~~~~~~~~~~~~------~~~-  212 (355)
                      |..........                                .+.     ......+...++..|.+.-      .+. 
T Consensus       283 YGSDKPDlRf~lel~dvt~~~~~~~F~vF~~~~~~~~~v~ai~vp~~~~~sRk~id~~~~~ak~~gakGLa~ikv~~~~~  362 (585)
T COG0173         283 YGSDKPDLRFPLELIDVTDLFKDSEFKVFSNALANGGRVKAIVVPGGASLSRKQIDELTEFAKIYGAKGLAYIKVEEDGL  362 (585)
T ss_pred             HCCCCCCCCCCCEEHHHHHHHCCCCCCEEHHHHHCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEECCCC
T ss_conf             38999855688352127987447885130314506982799984786646889999999999974987438999716876


Q ss_pred             --CHH-----HHHHHHHH-----------------------------------CEECCCCCCCCCCCCCCCCHH------
Q ss_conf             --347-----89876643-----------------------------------003622376754432576888------
Q gi|254781066|r  213 --TWS-----DIFSRILI-----------------------------------EKIEPNLGINCCTILDRYPAP------  244 (355)
Q Consensus       213 --~~~-----~~~~~l~~-----------------------------------~~ie~~l~~~~pvfi~~yP~~------  244 (355)
                        ...     ..+..+..                                   ..+.+..  -.++||+|||.-      
T Consensus       363 ~gpi~kfl~e~~~~~l~~~~~~~~gD~iff~A~~~~~~~~~lGalR~~l~~~l~li~~~~--~~f~WVvDFPlfE~~ee~  440 (585)
T COG0173         363 KGPIAKFLSEEILEELIERLGAEDGDIIFFVADKKKVVNKALGALRLKLGKELGLIDKDQ--FKFLWVVDFPLFEWDEEE  440 (585)
T ss_pred             CCHHHHHCCHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCC--CEEEEEEECCCCCCCCCC
T ss_conf             661776447899999999828777888999669488999988999999888738778343--248999706766775345


Q ss_pred             ------HHHHCCCCCCCCC---------CCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCC-CCHHHHH
Q ss_conf             ------8641367877836---------33022022367122564021069999999999999999728885-3010189
Q gi|254781066|r  245 ------ESALANIYPADPR---------FTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNE-TYPIDED  308 (355)
Q Consensus       245 ------~~plak~~~~~~~---------va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e-~~~~D~~  308 (355)
                            --||+++.+++..         .+..|||++||.||++|+.++|+|+.|...|+.-     +.+.+ +..-=-.
T Consensus       441 ~~~~a~HHPFT~P~~~~~~~l~~~p~~~~a~aYDlVlNG~ElggGSiRIh~~eiQ~~vF~~l-----g~~~eea~ekFGF  515 (585)
T COG0173         441 GRYVAAHHPFTMPKPEDLELLEADPESVRARAYDLVLNGYELGGGSIRIHDPEIQEKVFEIL-----GISPEEAEEKFGF  515 (585)
T ss_pred             CCEECCCCCCCCCCCCCHHHHHCCHHHHHHHHCCEEECCEEECCCEEEECCHHHHHHHHHHC-----CCCHHHHHHHHHH
T ss_conf             86740448878998442445416977764532567760275135436407889999999981-----9998999988778


Q ss_pred             HHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCC
Q ss_conf             99986-188963245315999989981559713111585648743
Q gi|254781066|r  309 FLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQ  352 (355)
Q Consensus       309 fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~  352 (355)
                      +|+|| +|+|||||+|+|+|||||+|+|.+|||||||||.+...+
T Consensus       516 ll~Af~yGaPPHgGiA~GlDRlvmll~g~~sIReVIAFPKt~~a~  560 (585)
T COG0173         516 LLEAFKYGAPPHGGIAFGLDRLVMLLTGAESIRDVIAFPKTQQAA  560 (585)
T ss_pred             HHHHHHCCCCCCCCEECCHHHHHHHHCCCCCHHHEEECCCCCCCC
T ss_conf             999976589997624245999999982897444213147886555


No 23 
>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=100.00  E-value=0  Score=469.12  Aligned_cols=295  Identities=22%  Similarity=0.290  Sum_probs=239.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-CCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             8999999999999999999879889847821056-898544541241024788678320000285899998987446889
Q gi|254781066|r   19 RPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-PGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKI   97 (355)
Q Consensus        19 R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rv   97 (355)
                      ..++++|+++++++|+||.++||+||+||.|.++ .+|++       ++|...||.+++||.||||||||.||++||+||
T Consensus       152 ~AIF~I~~~~~~~vR~~L~~~~F~Ev~TPKlv~~~tEGGt-------~lF~i~YF~~~AfL~QSPQlyKQ~l~~~g~~rV  224 (466)
T TIGR00458       152 QAIFRIRSEVLESVREFLAEEGFIEVHTPKLVASATEGGT-------ELFPITYFEREAFLGQSPQLYKQVLMAAGLERV  224 (466)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEECCCCCCC-------CCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCE
T ss_conf             2125568999999999873088256307621421668885-------332012212300013570356687765265203


Q ss_pred             HHHHHHHCCCCCCC-CCCCCEEEECEEECCCCH-HHHHHHHHHHHHHHHHHHCCC----------EECCCCCCC-CCCCC
Q ss_conf             99886424567775-448430020001157765-787775578887766641883----------000223433-24677
Q gi|254781066|r   98 FCFAHAWRNGEQGC-LHQPEFTMLEWYRAHESY-EQLMKDCMNIIRCAAEVANQK----------IFSFQNVNC-NPFSE  164 (355)
Q Consensus        98 yqig~~FRaE~~~~-rHlpEFtmLE~e~af~d~-~dlm~~~E~li~~~~~~~~~~----------~~~~~~~~~-~~~~~  164 (355)
                      |+|||+||||+++| ||+.|++.||+||||.|. +++|+..|+++..++..+...          .+...+... .+..+
T Consensus       225 yEI~PiFRAE~~nT~RHl~E~~siDiE~~F~dhy~~v~d~L~~lv~~~~~dv~~~~~~e~el~r~~~~~~~~~le~P~~~  304 (466)
T TIGR00458       225 YEIGPIFRAEEHNTRRHLNEAISIDIEMAFEDHYEDVMDILEELVVRVFEDVAEKCAKEIELVRKELETLEVKLEVPEEK  304 (466)
T ss_pred             EEECCEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCC
T ss_conf             55055220566652145544444224444275378999999999999999999887888999987521023132488875


Q ss_pred             CCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCC-CCH
Q ss_conf             3207888865666087653234555623279999999976887787653478987664300362237675443257-688
Q gi|254781066|r  165 PEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDR-YPA  243 (355)
Q Consensus       165 ~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~-yP~  243 (355)
                      +.|++|.|++                        ..+...|..+....+.+..-.+.+++.+.+..  +..+||++ ||.
T Consensus       305 ~~Rl~Y~Ea~------------------------e~~~~~G~ei~~gEDLs~~a~K~~G~l~re~~--~g~yfI~d~wP~  358 (466)
T TIGR00458       305 FERLTYDEAI------------------------EIANAKGKEIKWGEDLSTEAEKALGKLVREEM--DGLYFITDKWPT  358 (466)
T ss_pred             CCCCCCHHHH------------------------HHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHH--CCCEEEEECCCC
T ss_conf             5532207789------------------------99986597155546654357887647887742--761687405876


Q ss_pred             HHHHHC-CCC-CCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCCC
Q ss_conf             886413-678-7783633022022367122564021069999999999999999728885301018999986-1889632
Q gi|254781066|r  244 PESALA-NIY-PADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-TEMPQSS  320 (355)
Q Consensus       244 ~~~pla-k~~-~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~G~PPhg  320 (355)
                      +++||| |++ .++|..+++|||+.++.||.+|-+++|+.+.+.++      +|+.|-++.-+-=..||+|+ |||||||
T Consensus       359 ei~PFY~MPd~E~~P~~s~~fDl~~~~~Ei~SGA~RiH~~dlL~E~------iK~~Gl~P~dp~~~~Yl~aF~YG~PPHA  432 (466)
T TIGR00458       359 EIRPFYTMPDDEDNPEISKSFDLMYRDLEISSGAQRIHLYDLLVEK------IKAKGLNPEDPGFKDYLEAFKYGMPPHA  432 (466)
T ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHCCCHHCCHHHHHHHHHHHHHH------HHHCCCCCCCCCHHHHHHHCCCCCCCCC
T ss_conf             4676213888656786001444333110110003454458888999------9845889885336878733047847888


Q ss_pred             EEECCHHHHHHHHHCCCCHHHHCCCCCCCCCC
Q ss_conf             45315999989981559713111585648743
Q gi|254781066|r  321 GIAMGFDRLVMLVTGANNINEVIWTPFSQSNQ  352 (355)
Q Consensus       321 G~glGidRLvm~l~g~~~Irdvi~FP~~r~~~  352 (355)
                      |||||.||++|.+++++|||++++||++|.+.
T Consensus       433 GwGlG~eR~~M~~~~lkNiR~~~LFPRDr~RL  464 (466)
T TIGR00458       433 GWGLGAERLVMVLLGLKNIREAVLFPRDRKRL  464 (466)
T ss_pred             CCCCHHHHHHHHHHCCHHHHHHCCCCCCCCCC
T ss_conf             76410678888774010112200488886568


No 24 
>TIGR00499 lysS_bact lysyl-tRNA synthetase; InterPro: IPR002313   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 .   Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and some eubacteria . Moreover in some eubacteria there is a gene X, which is similar to a part of lysyl-tRNA synthetase from class II. Lysyl-tRNA synthetase is duplicated in some species with, for example in E. coli, as a constitutive gene (lysS) and an induced one (lysU). No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. Lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. The refined crystal structures give "snapshots" of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding .; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=447.54  Aligned_cols=345  Identities=31%  Similarity=0.514  Sum_probs=298.0

Q ss_pred             CCCCCCCCCC--CHHHCCCHHH-----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC
Q ss_conf             9988987478--8312615489-----------99999999999999999879889847821056898544541241024
Q gi|254781066|r    1 MHQIPSQPWW--NRDFHYRRRP-----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI   67 (355)
Q Consensus         1 ~~~~p~~~~~--~~~~~~r~R~-----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~   67 (355)
                      ++++|..+.+  +.+.++|+|.           .++.|+++++++|.|++.+||+||+||++...+||+. ++||.|+  
T Consensus       156 ~~~~p~~~~gl~d~e~~~~~~~~d~~~n~~~~~~~~~~~~~~~~~~~~~~~~g~~e~e~p~~~~~~gg~~-~~pf~~~--  232 (538)
T TIGR00499       156 LRPLPDKWHGLTDQETRYRQRYLDLIVNPDSRDTFLKRSKIIAAIRRFLDDRGFLEVETPLLQVIPGGAN-ARPFITH--  232 (538)
T ss_pred             HHCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCHHHCCCCCCC-CCCCEEC--
T ss_conf             4226510046651567777655433105024667788999999999987624842211310101267654-4650100--


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             78867832000028589999898744688999886424567775448430020001157765787775578887766641
Q gi|254781066|r   68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA  147 (355)
Q Consensus        68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~  147 (355)
                       ++.++.++||+++||+|+|+|+++|+++||++|+.||+|+.+.+|+||||++|+|++|+|++++|+.+|.+++.+++.+
T Consensus       233 -~n~~~~~~~~~~~~e~~l~~l~~gg~~~~~e~g~~f~neg~~~~hnpef~~~e~y~~~~~~~~~~~~~~~l~~~~~~~~  311 (538)
T TIGR00499       233 -HNALDLDLYLRIAPELYLKRLVVGGLEKVYEIGRNFRNEGVDTTHNPEFTSLEFYQAYADYEDLLDLTENLFKFLAKEL  311 (538)
T ss_pred             -CCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             -2322442121122577887776401367787643331046654457530245567765108899998999999999875


Q ss_pred             C-CCEE------------CCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCC---CC-CC
Q ss_conf             8-8300------------022343324677320788886566608765323455562327999999997688---77-87
Q gi|254781066|r  148 N-QKIF------------SFQNVNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGI---RV-AH  210 (355)
Q Consensus       148 ~-~~~~------------~~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~  210 (355)
                      . ...+            .+.....+...+|+++++.+++.++........  .....+.......+.+.+.   .. ..
T Consensus       312 ~~~~~~~~~p~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~  389 (538)
T TIGR00499       312 LGTTKITRLPVPKTFPELTYGDLELDLKKPWKRITMLDALKKYDLLETGID--FDDLKDDETAKALAKELGIKYFEVAED  389 (538)
T ss_pred             HHHHHEEECCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCC--CHHCCHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             321100112566543112203210023554002245677765200004654--001002578888888754332022345


Q ss_pred             C--CCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHH
Q ss_conf             6--53478987664300362237675443257688886413678778363302202236712256402106999999999
Q gi|254781066|r  211 D--DTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRF  288 (355)
Q Consensus       211 ~--~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf  288 (355)
                      .  +..+.++..++++.++.++....|+|+++||..++|+++.++.+|++++||++|++|.|++|||+|++||..|++||
T Consensus       390 ~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~p~~~~pl~~~~~~~p~~~~~fe~f~~g~e~~n~~~e~~~p~~~~~~~  469 (538)
T TIGR00499       390 SGPLTLGHILNELFEEFLEHTLIQTLPTFITGYPAEISPLAKRNPSNPELTDRFELFIGGKEIANAFSELNDPLDQRERF  469 (538)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCHHCCCCCCCCHHHHHHHEECCHHHHCCHHHHCCHHHHHHHH
T ss_conf             77420688999988887755666532143404641222100057777530111110010112201012204627889999


Q ss_pred             HHHHHHHHCC----CCCCCHHHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCC
Q ss_conf             9999999728----8853010189999861-8896324531599998998155971311158564874
Q gi|254781066|r  289 EKEMQEKKKI----YNETYPIDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSN  351 (355)
Q Consensus       289 ~~q~~~k~~~----~~e~~~~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~  351 (355)
                      +.|...++.+    ++++..+|++|+.|++ |+||.||+|+|+|||+|++|++++||||++||.+|+.
T Consensus       470 ~~~~~~~~~gg~~~~~~~~~~d~~~~~~l~~g~pp~~g~g~g~d~l~~l~~~~~~~~~~~~fp~~~~~  537 (538)
T TIGR00499       470 EAQLAEKEAGGNKTDDEAPLLDEDFVEALEYGLPPTGGLGIGIDRLVMLLTDSPSIRDVLLFPALRPD  537 (538)
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHCCCCCCC
T ss_conf             99888875067754103444336788888716886565443277787766167510133202531357


No 25 
>KOG2411 consensus
Probab=100.00  E-value=0  Score=439.15  Aligned_cols=313  Identities=23%  Similarity=0.347  Sum_probs=224.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHC-CCEEEECCCE-ECCCCCCCCCCCEEEECCCCCCCCCCCC-CCCCHHHHHHHHHHHHHH
Q ss_conf             899999999999999999987-9889847821-0568985445412410247886783200-002858999989874468
Q gi|254781066|r   19 RPFLLKRNMIQSSLREYFVEN-QFIEIDSMSL-QYSPGNETHIRAFSTELIIQDHIRKPLY-LQTSPEFSCKKLLAAGEE   95 (355)
Q Consensus        19 R~~l~~Rs~i~~~iR~ff~~~-gF~EV~TPiL-~~~~~g~~~~~~f~t~~~~~~~~~~~~y-L~~SPql~lK~ll~~G~~   95 (355)
                      +..++.||.+...||+||.++ ||+||+||.| ..+|||   |+.|.|+....+   ..|| |+||||+|+|.||++|++
T Consensus       175 q~nLrlRS~~v~~iR~yl~n~~GFvevETPtLFkrTPgG---A~EFvVPtr~~~---g~FYaLpQSPQQfKQlLMvsGid  248 (628)
T KOG2411         175 QNNLRLRSNVVKKIRRYLNNRHGFVEVETPTLFKRTPGG---AREFVVPTRTPR---GKFYALPQSPQQFKQLLMVSGID  248 (628)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCEEECCCCCHHCCCCCC---CCEEECCCCCCC---CCEEECCCCHHHHHHHHHHHCHH
T ss_conf             878999999999999998610473551572020148886---412322367898---85553688989999999872303


Q ss_pred             HHHHHHHHHCCCCC--CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             89998864245677--7544843002000115776578777557888776664188300022343324677320788886
Q gi|254781066|r   96 KIFCFAHAWRNGEQ--GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSEPEYITVAEA  173 (355)
Q Consensus        96 rvyqig~~FRaE~~--~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~e~  173 (355)
                      ||||||+|||+|++  ||+  |||||+|+||||+|.+|+|+++|+++++++.....         +..-.+|++|||.+|
T Consensus       249 rYyQiARCfRDEdlR~DRQ--PEFTQvD~EMsF~~~~dim~liEdll~~~ws~~k~---------~~l~~PF~riTY~~A  317 (628)
T KOG2411         249 RYYQIARCFRDEDLRADRQ--PEFTQVDMEMSFTDQEDIMKLIEDLLRYVWSEDKG---------IQLPVPFPRITYADA  317 (628)
T ss_pred             HHHHHHHHHCCCCCCCCCC--CCCEEEEEEEECCCHHHHHHHHHHHHHHHCHHHCC---------CCCCCCCCCCCHHHH
T ss_conf             6776776641345676568--76435444785367787899999999973624219---------988888664239999


Q ss_pred             HHHHCCCCCCCCCCCCCC---------------------------------C---CHHHHHHHHHHC---CC----CCCC
Q ss_conf             566608765323455562---------------------------------3---279999999976---88----7787
Q gi|254781066|r  174 FARYANIDLGTTLDNPDQ---------------------------------P---DRHLLYLQAQQA---GI----RVAH  210 (355)
Q Consensus       174 ~~~~~~~d~~~~~~~~~~---------------------------------~---~~~~~~~~~~~~---~~----~~~~  210 (355)
                      +.+|..............                                 .   ..........+.   +.    ....
T Consensus       318 m~~YG~DKPD~Rf~l~l~dv~~~~~~~~~~~~~~d~l~~~~~vv~~~~~~~~s~~~~rk~~e~~~~~~~~~~~f~~~~~~  397 (628)
T KOG2411         318 MDKYGSDKPDTRFPLKLKDVSESISKSFEEALLSDGLISVEIVVLGAKKYSNSNYKKRKIYESLGKSGFVGLPFPIEHDA  397 (628)
T ss_pred             HHHHCCCCCCCCCCCEECCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCC
T ss_conf             99738999866577673226776566555554148854058999514344412567767999875434666300153262


Q ss_pred             CCCHHHHHHHHHHCEE--------------------CC---------------------CC---CCCCCCCCCCCCHHH-
Q ss_conf             6534789876643003--------------------62---------------------23---767544325768888-
Q gi|254781066|r  211 DDTWSDIFSRILIEKI--------------------EP---------------------NL---GINCCTILDRYPAPE-  245 (355)
Q Consensus       211 ~~~~~~~~~~l~~~~i--------------------e~---------------------~l---~~~~pvfi~~yP~~~-  245 (355)
                      ...|-+.+..+..+.+                    .+                     ++   ......||+|||.-. 
T Consensus       398 ~~~w~~~~~~l~~e~~~~el~~~~~l~~~Div~~~~g~~~~~~~~LgrlRL~l~~l~~~~l~d~~~~~~lWVvDFPLF~p  477 (628)
T KOG2411         398 NKNWFKKFSSLTDEAVAIELIKQLGLAEGDIVLLCVGPKVSVNTPLGRLRLVLQDLLVKNLRDKSKFSFLWVVDFPLFSP  477 (628)
T ss_pred             HHHHHHHCHHHCCCHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCC
T ss_conf             01154413242242378999998588878889993268766777237789999998751643666534899983355676


Q ss_pred             ------------HHHCCCCCCCCC---------CCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCH
Q ss_conf             ------------641367877836---------33022022367122564021069999999999999999728885301
Q gi|254781066|r  246 ------------SALANIYPADPR---------FTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYP  304 (355)
Q Consensus       246 ------------~plak~~~~~~~---------va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~  304 (355)
                                  -||+.++++|-.         ....|||++||+||++|+.+++||+.|+..++.-.  |.-   +.+.
T Consensus       478 ~~E~~q~L~StHHPFTaP~~~Di~~L~s~p~~~rgqhYDlV~NGvElGGGSiRIhn~diQr~vLe~iL--k~p---~~~~  552 (628)
T KOG2411         478 WEEKNQRLESTHHPFTAPHPKDIDLLESAPEKIRGQHYDLVVNGVELGGGSIRIHNPDIQRYVLEDIL--KIP---EDAE  552 (628)
T ss_pred             CCCCCCEECCCCCCCCCCCHHHHHHHHCCCHHHHCCEEEEEECCEEECCCEEEECCHHHHHHHHHHHH--CCC---HHHH
T ss_conf             56677530002588778885566676518166524300167714762473467528889999999985--596---6666


Q ss_pred             HHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCCC
Q ss_conf             0189999861-889632453159999899815597131115856487433
Q gi|254781066|r  305 IDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQE  353 (355)
Q Consensus       305 ~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~~  353 (355)
                      .-..+|+||. |+|||||||+|+|||||++||..|||||||||.+...++
T Consensus       553 s~gHLL~ALd~GaPPHGGiAlGlDRlvaml~~a~sIRDVIAFPKt~~G~D  602 (628)
T KOG2411         553 SKGHLLNALDMGAPPHGGIALGLDRLVAMLTGAPSIRDVIAFPKTTTGAD  602 (628)
T ss_pred             HHHHHHHHHHCCCCCCCCEEECHHHHHHHHCCCCCHHEEEECCCCCCCCC
T ss_conf             67789988626999987444127889999808975222564466577543


No 26 
>KOG0554 consensus
Probab=100.00  E-value=0  Score=430.09  Aligned_cols=294  Identities=20%  Similarity=0.246  Sum_probs=229.9

Q ss_pred             HCCCHHH-----HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC-CCCCCCCCEEEEC---CCCCCCCCCCCCCCCHHH
Q ss_conf             2615489-----999999999999999998798898478210568-9854454124102---478867832000028589
Q gi|254781066|r   14 FHYRRRP-----FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP-GNETHIRAFSTEL---IIQDHIRKPLYLQTSPEF   84 (355)
Q Consensus        14 ~~~r~R~-----~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-~g~~~~~~f~t~~---~~~~~~~~~~yL~~SPql   84 (355)
                      .|+|.|+     ++|.||.+..++|.||++++|++|+||||+++. +|+  -+.|.|..   ...+++++++||++|.||
T Consensus       119 ~HLR~Rt~~~~av~RvRs~~~~a~h~ffq~~~F~~i~tPiiTtnDCEGa--GE~F~Vtt~~d~~~~fFgrp~fLTVSgQL  196 (446)
T KOG0554         119 LHLRSRTAKVGAVLRVRSALAFATHSFFQSHDFTYINTPIITTNDCEGA--GEVFQVTTLTDYSKDFFGRPAFLTVSGQL  196 (446)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCEEECCCCCCC--CCEEEEEECCCCCCCCCCCCEEEEEECEE
T ss_conf             3321002578999999989999999999875946733867634577787--40589874686543314885079971321


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCCCEEEECEEECCCC-HHHHHHHHHHHHHHHHHHHCCCE---ECCCCCCC
Q ss_conf             9998987446889998864245677-7544843002000115776-57877755788877666418830---00223433
Q gi|254781066|r   85 SCKKLLAAGEEKIFCFAHAWRNGEQ-GCLHQPEFTMLEWYRAHES-YEQLMKDCMNIIRCAAEVANQKI---FSFQNVNC  159 (355)
Q Consensus        85 ~lK~ll~~G~~rvyqig~~FRaE~~-~~rHlpEFtmLE~e~af~d-~~dlm~~~E~li~~~~~~~~~~~---~~~~~~~~  159 (355)
                      ++ ..|++++.|||++||+||||++ ++|||+||||+|.|+||++ ++|+|..+|.+++++++.+.+.-   .+......
T Consensus       197 hl-Ea~a~aLsrvyt~gP~FRAE~s~t~rHLaEFwmlE~E~af~~sl~d~~~~~e~~~k~m~k~~le~~~Edm~l~~~~~  275 (446)
T KOG0554         197 HL-EAMACALSRVYTFGPTFRAENSHTSRHLAEFWMLEAELAFAESLDDLMSCAEAYIKHMIKYLLEKCIEDMELMHKNE  275 (446)
T ss_pred             HH-HHHHHHHCCEEEECCCEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHEEECCCC
T ss_conf             59-98875523237616613226787546776565242788788888888899999999999999860511010100114


Q ss_pred             CC----------CCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCC-CCCCCCCCHHHHHHHHHHCEECC
Q ss_conf             24----------67732078888656660876532345556232799999999768-87787653478987664300362
Q gi|254781066|r  160 NP----------FSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAG-IRVAHDDTWSDIFSRILIEKIEP  228 (355)
Q Consensus       160 ~~----------~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~ie~  228 (355)
                      +.          ..+|.+++|.+|+..                        .++.. .++.....||..+...++.++.+
T Consensus       276 ~~~~~~rl~~~~~~~~~~itYteAie~------------------------L~~a~t~~fk~~~kwG~~lstehe~yL~~  331 (446)
T KOG0554         276 DPGSIDRLELVAKENLLRITYTEAIEL------------------------LQKAVTKKFKTPPKWGIDLSTEHEKYLVE  331 (446)
T ss_pred             CCCCCCHHHHHHHHHHHHEEHHHHHHH------------------------HHHHCCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             777531577720102332028999999------------------------99840244356720154400456878999


Q ss_pred             CCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCE-ECCCCCHHCCCHHHHHHHHHHHHHHHHCC-CCCCCHHH
Q ss_conf             23767544325768888641367877836330220223671-22564021069999999999999999728-88530101
Q gi|254781066|r  229 NLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNI-ELCNACDELLDPIEQRHRFEKEMQEKKKI-YNETYPID  306 (355)
Q Consensus       229 ~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~-El~ng~~El~d~~~q~~rf~~q~~~k~~~-~~e~~~~D  306 (355)
                      .+. +.||||+|||+.++||||..++++..+.+|||+|.|+ ||++|+.++-++          .++++.+ ..+..   
T Consensus       332 ~~~-~~PVfV~dYP~~iKpFYMr~n~~~~tVaa~DlLVP~vGELiGGSlREe~~----------~~l~e~g~~~~~~---  397 (446)
T KOG0554         332 ECF-KKPVFVTDYPKGIKPFYMRLNDDGKTVAAFDLLVPGVGELIGGSLREERK----------ARLKERGLTREEL---  397 (446)
T ss_pred             HHC-CCCEEEEECCCCCCCEEEEECCCCCEEEEEEEECCCCHHHCCCCCCHHHH----------HHHHHCCCCCCCC---
T ss_conf             856-89779970644466448885599972689986136631122765312358----------9998659995121---


Q ss_pred             HHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCC
Q ss_conf             8999986-18896324531599998998155971311158564
Q gi|254781066|r  307 EDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFS  348 (355)
Q Consensus       307 ~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~  348 (355)
                      +|||+-. +|.+|||||||||||++.+++|.+|||||||||+.
T Consensus       398 eWYldLRryG~vphgGFGlGfERmlq~~tG~~nIkd~IPFpR~  440 (446)
T KOG0554         398 EWYLDLRRYGSVPHGGFGLGFERMLQYLTGNDNIKDVIPFPRY  440 (446)
T ss_pred             CEEHHHHHCCCCCCCCCCCCHHHHHHHHHCCCCHHHCEECCCC
T ss_conf             0001155438999873140599999998577654220005788


No 27 
>KOG0556 consensus
Probab=100.00  E-value=0  Score=414.98  Aligned_cols=297  Identities=19%  Similarity=0.298  Sum_probs=235.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-CCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999879889847821056-8985445412410247886783200002858999989874468899
Q gi|254781066|r   20 PFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-PGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIF   98 (355)
Q Consensus        20 ~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvy   98 (355)
                      .++++.+.+..+.|+||..+||+||+||.|.++ .+|  ++..|.+.     |+++++||.||||||+|++++++|+|||
T Consensus       226 AiFriq~gvc~~FRe~L~~kgF~EIhTpKli~asSEG--GanvF~v~-----Yfk~~A~LAQSPQLyKQMaI~gdf~rVy  298 (533)
T KOG0556         226 AIFRIQAGVCFAFREYLRSKGFVEIHTPKLIGASSEG--GANVFRVS-----YFKQKAYLAQSPQLYKQMAICGDFERVY  298 (533)
T ss_pred             HEEEHHHHHHHHHHHHHHHCCCCEECCCCCCCCCCCC--CCEEEEEE-----ECCCCCHHHCCHHHHHHHHHHCCHHHEE
T ss_conf             1000688899999999975686043263201466777--72268998-----6067503205858887788760611046


Q ss_pred             HHHHHHCCCCCCC-CCCCCEEEECEEECCC-CHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCHHHHHH-
Q ss_conf             9886424567775-4484300200011577-657877755788877666418830002234332467732078888656-
Q gi|254781066|r   99 CFAHAWRNGEQGC-LHQPEFTMLEWYRAHE-SYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSEPEYITVAEAFA-  175 (355)
Q Consensus        99 qig~~FRaE~~~~-rHlpEFtmLE~e~af~-d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~e~~~-  175 (355)
                      +|||+||||++++ ||++||+-||+||+|- +|+++|+.+.+++-++++.+....-..                .+++. 
T Consensus       299 eIGpVfRAEdSnthRhltEFvGLD~EMaf~~hYhEVm~~i~~lfv~IF~~l~ery~~E----------------ie~Vr~  362 (533)
T KOG0556         299 EIGPVFRAEDSNTHRHLTEFVGLDLEMAFNEHYHEVMDTIGELFVFIFKGLRERYAKE----------------IETVRK  362 (533)
T ss_pred             EECCEEECCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------HHHHHH
T ss_conf             5235566044641666677617422547777799999999999999998788888999----------------999861


Q ss_pred             HHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHC-CCCCC
Q ss_conf             66087653234555623279999999976887787653478987664300362237675443257688886413-67877
Q gi|254781066|r  176 RYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALA-NIYPA  254 (355)
Q Consensus       176 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~pla-k~~~~  254 (355)
                      +|...++ .....+............++.|++.+...+....-++.++..|.++++.+ ..++..||.+++||| |++++
T Consensus       363 qyp~e~f-kf~~~~lrl~~~e~v~mLreaGvE~g~~dDlsTe~Ek~LG~lV~eky~td-fyildkyP~avRPFYTmpd~~  440 (533)
T KOG0556         363 QYPFEPF-KFLEPPLRLTFKEGVAMLREAGVEMGDEDDLSTESEKKLGQLVREKYDTD-FYILDKYPLAVRPFYTMPDPE  440 (533)
T ss_pred             CCCCCCC-CCCCCCEEEEHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC-EEEECCCCCCCCCCCCCCCCC
T ss_conf             0888633-35787557655889999997286358722358865889999999871784-799714754446643367888


Q ss_pred             CCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCCCEEECCHHHHHHHH
Q ss_conf             83633022022367122564021069999999999999999728885301018999986-18896324531599998998
Q gi|254781066|r  255 DPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-TEMPQSSGIAMGFDRLVMLV  333 (355)
Q Consensus       255 ~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~G~PPhgG~glGidRLvm~l  333 (355)
                      ||.++++||+|++|.||.+|-++++||+.+.+|.      ++-|-+. ..+ ..|++++ +|+|||||+|+|+||++|+.
T Consensus       441 ~p~ySnSyD~fmRGeEIlSGAQRIhdpe~L~era------~~hGid~-~~i-~~YidsFryG~PPHaGgGIGLERvvmly  512 (533)
T KOG0556         441 NPRYSNSYDFFMRGEEILSGAQRIHDPELLVERA------KEHGIDP-SKI-STYIDSFRYGAPPHAGGGIGLERVVMLY  512 (533)
T ss_pred             CCCCCCCHHHEECHHHHHCCCCCCCCHHHHHHHH------HHCCCCH-HHH-HHHHHHHCCCCCCCCCCCCCHHHHHHHH
T ss_conf             8773441432234666634430037889999999------9739887-899-9888874058998778751599999998


Q ss_pred             HCCCCHHHHCCCCCCC
Q ss_conf             1559713111585648
Q gi|254781066|r  334 TGANNINEVIWTPFSQ  349 (355)
Q Consensus       334 ~g~~~Irdvi~FP~~r  349 (355)
                      +|++|||-+.+||++-
T Consensus       513 l~L~nIR~~SlFPRDP  528 (533)
T KOG0556         513 LGLNNIRKTSLFPRDP  528 (533)
T ss_pred             HCCCCCHHHCCCCCCC
T ss_conf             1677500102578882


No 28 
>KOG0555 consensus
Probab=100.00  E-value=0  Score=346.07  Aligned_cols=287  Identities=17%  Similarity=0.263  Sum_probs=223.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEEECCCEEC--CCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999987988984782105--6898544541241024788678320000285899998987446889
Q gi|254781066|r   20 PFLLKRNMIQSSLREYFVENQFIEIDSMSLQY--SPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKI   97 (355)
Q Consensus        20 ~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~--~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rv   97 (355)
                      .+++.|+.+.+++|++|.++|++||.+|+|..  ..||.+        +|..||+++++||+||.|||+..++++ +++|
T Consensus       241 ~vLK~Ra~~lr~~Rd~y~~~~ytEVtPPtmVQTQVEGGsT--------LFkldYyGEeAyLTQSSQLYLEtclpA-lgdv  311 (545)
T KOG0555         241 KVLKARAALLRAMRDHYFERGYTEVTPPTMVQTQVEGGST--------LFKLDYYGEEAYLTQSSQLYLETCLPA-LGDV  311 (545)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCEECCCCCEEEEEECCCCE--------EEEECCCCCHHHCCCHHHHHHHHHHHH-CCCE
T ss_conf             9999999999999988874484245797157887517604--------873113574033022358889876552-0762


Q ss_pred             HHHHHHHCCCC-CCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECC-----CCCCCCCCCCCCCCCHH
Q ss_conf             99886424567-7754484300200011577657877755788877666418830002-----23433246773207888
Q gi|254781066|r   98 FCFAHAWRNGE-QGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSF-----QNVNCNPFSEPEYITVA  171 (355)
Q Consensus        98 yqig~~FRaE~-~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~-----~~~~~~~~~~~~~i~~~  171 (355)
                      |+|.++||||. .+||||+|||++|+|++|.+++++|+.+|++|...++.+....+..     +..-..+..||.|++|.
T Consensus       312 y~I~~SyRAEkSrTRRHLsEytHVEaE~afltfd~ll~~iE~lvc~~vdr~l~dp~~~li~~lnP~f~~P~~PFkRm~Y~  391 (545)
T KOG0555         312 YCIQQSYRAEKSRTRRHLSEYTHVEAECAFLTFDDLLDRIEALVCDSVDRLLEDPIAPLIKQLNPDFKAPKRPFKRMNYS  391 (545)
T ss_pred             EEECHHHHHHHHHHHHHHHHHEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCCCCCCCHHCCCHH
T ss_conf             67327566556666665533111023246364889999999999999999986701566887498988888812107889


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHCCC
Q ss_conf             86566608765323455562327999999997688778765347898766430036223767544325768888641367
Q gi|254781066|r  172 EAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALANI  251 (355)
Q Consensus       172 e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~plak~  251 (355)
                      +|++-....++.                  ++.|-+...+++..+.-++.+.+    ..  +.|+|+++||.++++|||.
T Consensus       392 dAI~wLke~~vk------------------~edg~~fefGdDI~eAaER~mtd----tI--g~PIfLtrFpveiKsFYM~  447 (545)
T KOG0555         392 DAIEWLKEHDVK------------------KEDGTDFEFGDDIPEAAERKMTD----TI--GVPIFLTRFPVEIKSFYMK  447 (545)
T ss_pred             HHHHHHHHCCCC------------------CCCCCCCCCCCCHHHHHHHHHHH----HC--CCCEEEEECCCCCCCEEEE
T ss_conf             999999863976------------------76676020466425678876555----22--8814786333334451331


Q ss_pred             -CCCCCCCCCCCEEEECCE-ECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCCCEEECCHHH
Q ss_conf             -877836330220223671-22564021069999999999999999728885301018999986-188963245315999
Q gi|254781066|r  252 -YPADPRFTKRFELYACNI-ELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-TEMPQSSGIAMGFDR  328 (355)
Q Consensus       252 -~~~~~~va~rfdl~i~G~-El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~G~PPhgG~glGidR  328 (355)
                       ..+|++++++.|+.+.|+ ||++|+-++-|.++...-|     .|++.+...+   .||++.. +|..||||+|||+||
T Consensus       448 rc~dd~~lTESvD~LmPnVGEIvGGSMRi~d~eeLlagf-----kRegId~~pY---YWy~DqrkyGt~pHGGyGLGlER  519 (545)
T KOG0555         448 RCEDDPRLTESVDVLMPNVGEIVGGSMRIDDSEELLAGF-----KREGIDPDPY---YWYTDQRKYGTCPHGGYGLGLER  519 (545)
T ss_pred             CCCCCCCCCEEEEEECCCCCCCCCCEEEECCHHHHHHHH-----HHCCCCCCCC---EEEEECCCCCCCCCCCCCCCHHH
T ss_conf             166765543001111478610036604516599999888-----6558998870---47740100266898851314999


Q ss_pred             HHHHHHCCCCHHHHCCCCC
Q ss_conf             9899815597131115856
Q gi|254781066|r  329 LVMLVTGANNINEVIWTPF  347 (355)
Q Consensus       329 Lvm~l~g~~~Irdvi~FP~  347 (355)
                      ++||||+..+||||-+||+
T Consensus       520 fL~wL~~r~~vre~cLyPR  538 (545)
T KOG0555         520 FLAWLCDRYHVREVCLYPR  538 (545)
T ss_pred             HHHHHHCCCCHHHEEECCH
T ss_conf             9998722231523121231


No 29 
>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=99.57  E-value=2.8e-14  Score=104.01  Aligned_cols=112  Identities=24%  Similarity=0.381  Sum_probs=69.3

Q ss_pred             HHHHHHHHHHHHHCCCEEEECCCEECCCCC-CC------C-CCCEEEECCCCCCCCCC--CCC--CCCHHHHHHHHHHH-
Q ss_conf             999999999999879889847821056898-54------4-54124102478867832--000--02858999989874-
Q gi|254781066|r   26 NMIQSSLREYFVENQFIEIDSMSLQYSPGN-ET------H-IRAFSTELIIQDHIRKP--LYL--QTSPEFSCKKLLAA-   92 (355)
Q Consensus        26 s~i~~~iR~ff~~~gF~EV~TPiL~~~~~g-~~------~-~~~f~t~~~~~~~~~~~--~yL--~~SPql~lK~ll~~-   92 (355)
                      ++++..|+++|.+.||.+++.|.+.+.--. ++      | ++... +.+   |.+.+  .-|  +|||=..  +.|.. 
T Consensus         4 ~~~~~~i~~~f~~~GF~~~~gp~ie~~~~NFD~Ln~P~dHPaR~~~-DTf---y~~~~~~~lLRtHTS~~q~--r~l~~~   77 (218)
T cd00496           4 NKVIEEIEDIFVSMGFTEVEGPEVETDFYNFDALNIPQDHPARDMQ-DTF---YINDPARLLLRTHTSAVQA--RALAKL   77 (218)
T ss_pred             HHHHHHHHHHHHHCCCEEECCCCCCCCHHHHHHHCCCCCCCCCCCC-CEE---EECCCCCCEECCCCCHHHH--HHHHHC
T ss_conf             8999999999987798682289512310304533859887553724-327---8637766021578756679--999745


Q ss_pred             -HHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCC--CHHHHHHHHHHHHHHH
Q ss_conf             -46889998864245677754484300200011577--6578777557888776
Q gi|254781066|r   93 -GEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHE--SYEQLMKDCMNIIRCA  143 (355)
Q Consensus        93 -G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~--d~~dlm~~~E~li~~~  143 (355)
                       .--|++.+|+|||+|..|.+|.|+|.|+|.-..+-  +..++...++.+++.+
T Consensus        78 ~~p~~~~~~G~VyR~D~iDatH~~~FhQ~Eg~~v~~~~~~~~Lk~~l~~~~~~l  131 (218)
T cd00496          78 KPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGTLEEFAKEL  131 (218)
T ss_pred             CCCCEEEECCCEEECCCCCCCCCCEEEEEEEEEEECCCCHHHHHHHHHHHHHHH
T ss_conf             898179942504653889843153125763799956511999999999999997


No 30 
>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=99.52  E-value=1.8e-13  Score=99.26  Aligned_cols=114  Identities=22%  Similarity=0.358  Sum_probs=67.7

Q ss_pred             HHHHHHHHHHHHHCCCEEEECCCEECC---------CCCCCCCCCEE-EECCCCCCCCCCCCC--CCCHHHHHHHHHHHH
Q ss_conf             999999999999879889847821056---------89854454124-102478867832000--028589999898744
Q gi|254781066|r   26 NMIQSSLREYFVENQFIEIDSMSLQYS---------PGNETHIRAFS-TELIIQDHIRKPLYL--QTSPEFSCKKLLAAG   93 (355)
Q Consensus        26 s~i~~~iR~ff~~~gF~EV~TPiL~~~---------~~g~~~~~~f~-t~~~~~~~~~~~~yL--~~SPql~lK~ll~~G   93 (355)
                      ++++..|+++|.+.||.+++.|.+.+.         |..-+ |+... |-+......++..-|  ++|+=..  +.|...
T Consensus        20 ~~~~~~i~~~f~~~GF~~~~g~eves~~~NFDaLn~P~dHP-aR~~~DTfy~~~~~~~~~~vLRtHTS~~q~--r~l~~~   96 (243)
T pfam01409        20 TRVLEEIRDIFLSMGFEEVEGPEVESDFYNFDALNIPQDHP-ARDMQDTFYLKKPLKARRLLLRTHTTPVQA--RTLAEK   96 (243)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHCCCCCCC-CCCCCCEEEECCCCCCCCEEECCCCCHHHH--HHHHHC
T ss_conf             99999999999877986876983564277777557898898-767676034336666768657687988999--999742


Q ss_pred             HH---HHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHHH
Q ss_conf             68---8999886424567775448430020001157--7657877755788877
Q gi|254781066|r   94 EE---KIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIRC  142 (355)
Q Consensus        94 ~~---rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~~  142 (355)
                      -+   |++.+|+|||+|..|.+|+|+|.|+|.-...  +++.+++..++.+++.
T Consensus        97 ~~~p~r~~~~grvyR~d~~DatH~~~FhQ~Eg~vvd~~it~~~Lk~~l~~~~~~  150 (243)
T pfam01409        97 NKPPIKIFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVSFADLKGVLEEFLRK  150 (243)
T ss_pred             CCCCEEEECCCEEEECCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHH
T ss_conf             799848981431332588984315310575578965777899999999999999


No 31 
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=99.51  E-value=3.1e-13  Score=97.78  Aligned_cols=115  Identities=21%  Similarity=0.235  Sum_probs=68.4

Q ss_pred             HHHHHHHHHHHHHCCCEEEECCCEECC---------CC--CCC-CCCCEEEECCCC------------------------
Q ss_conf             999999999999879889847821056---------89--854-454124102478------------------------
Q gi|254781066|r   26 NMIQSSLREYFVENQFIEIDSMSLQYS---------PG--NET-HIRAFSTELIIQ------------------------   69 (355)
Q Consensus        26 s~i~~~iR~ff~~~gF~EV~TPiL~~~---------~~--g~~-~~~~f~t~~~~~------------------------   69 (355)
                      .+++..||+.|-+-||.|++.|.+.++         |-  ++. .-+.|-+.....                        
T Consensus       248 ~~~~~~~r~i~~~mGF~e~~g~~ve~~fwNfdaLf~Pq~HPARd~~Dtf~l~~~~~~~lp~~~~~~Vk~~HE~Gg~~gS~  327 (501)
T PRK04172        248 REFIEEVRDILVEMGFEEVKGPIVETEFWNFDALFQPQDHPAREMQDTFYLKYPSKGELPEELVERVKEVHEHGGDTGSR  327 (501)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCEECCCCCHHHHCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCC
T ss_conf             99999999999978976853661010000334305898998555445378657654557378898899987427767887


Q ss_pred             --CC-CC----CCCCC--CCCHHHHHHHHHHH---HHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHH
Q ss_conf             --86-78----32000--02858999989874---4688999886424567775448430020001157--765787775
Q gi|254781066|r   70 --DH-IR----KPLYL--QTSPEFSCKKLLAA---GEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKD  135 (355)
Q Consensus        70 --~~-~~----~~~yL--~~SPql~lK~ll~~---G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~  135 (355)
                        +| .+    +..-|  +||+=..  +.|+.   .=-|||.||+|||+|..|.+|+|||.|+|--.+.  +++.+++..
T Consensus       328 Gw~y~w~~~~~~~~~lRthtt~~~~--r~l~~~~~~p~~~f~~~rvfR~e~~d~tH~~~F~Q~eg~v~~~~~~~~~L~g~  405 (501)
T PRK04172        328 GWGYKWDEDIAKRLVLRTHTTALSA--RYLAERPEPPGKYFSIGRVFRPETIDATHLPEFYQLEGIVMGEDVSFRHLLGI  405 (501)
T ss_pred             CCCCCCCHHHHHHHCCCCCCCHHHH--HHHHHCCCCCEEEECCCCEEECCCCCCCCCCEEEEEEEEEECCCCCHHHHHHH
T ss_conf             7677778556643010436746679--99974689983573565054268888654413322248998488879999999


Q ss_pred             HHHHHHH
Q ss_conf             5788877
Q gi|254781066|r  136 CMNIIRC  142 (355)
Q Consensus       136 ~E~li~~  142 (355)
                      .+.+.+.
T Consensus       406 l~~f~~~  412 (501)
T PRK04172        406 LKEFYKR  412 (501)
T ss_pred             HHHHHHH
T ss_conf             9999998


No 32 
>PTZ00326 phenylalanyl-tRNA synthetase; Provisional
Probab=99.50  E-value=3.2e-13  Score=97.72  Aligned_cols=48  Identities=25%  Similarity=0.292  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHHH
Q ss_conf             88999886424567775448430020001157--7657877755788877
Q gi|254781066|r   95 EKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIRC  142 (355)
Q Consensus        95 ~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~~  142 (355)
                      .|||.||+|||+|..|.+|+|||.|+|--.+.  +++.+++...+.+++.
T Consensus       369 ~k~fsi~rv~R~e~~d~th~~~f~Q~eg~~~~~~~~~~~l~~~l~~f~~~  418 (505)
T PTZ00326        369 KKYFSIDRVFRNETLDATHLAEFHQVEGVVIDRNLSLGDLMGTLREFFRR  418 (505)
T ss_pred             CEEEECCCEEECCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHH
T ss_conf             14752372641577776534045543578964888899999999999998


No 33 
>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=99.46  E-value=1.8e-13  Score=99.24  Aligned_cols=116  Identities=22%  Similarity=0.223  Sum_probs=81.9

Q ss_pred             HHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHH----HHH
Q ss_conf             999999999999998798898478210568--98544541241024788678320000285899998987446----889
Q gi|254781066|r   24 KRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGE----EKI   97 (355)
Q Consensus        24 ~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~----~rv   97 (355)
                      .|++|.+.+|+++.++||.||.||+|....  .+..+...+.  ....+..+.++||+.+.+..+..+++...    -|+
T Consensus         1 ~r~~ie~~~r~~~~~~G~~ev~~P~l~~~~~~~~sg~~~~~~--~~~~~~~~~~~~L~pt~e~~~~~~~~~~~~dLP~r~   78 (211)
T cd00768           1 IRSKIEQKLRRFMAELGFQEVETPIVEREPLLEKAGHEPKDL--LPVGAENEEDLYLRPTLEPGLVRLFVSHIRKLPLRL   78 (211)
T ss_pred             CHHHHHHHHHHHHHHCCCEEEECCEECCHHHHHHCCCCHHHH--HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHCCHHH
T ss_conf             978999999999998699899998342799997506762223--011046797699951684999999752476577786


Q ss_pred             HHHHHHHCCCCCCC--CCCCCEEEECEEECCCCHHHHHHHHHHHHHH
Q ss_conf             99886424567775--4484300200011577657877755788877
Q gi|254781066|r   98 FCFAHAWRNGEQGC--LHQPEFTMLEWYRAHESYEQLMKDCMNIIRC  142 (355)
Q Consensus        98 yqig~~FRaE~~~~--rHlpEFtmLE~e~af~d~~dlm~~~E~li~~  142 (355)
                      |++++|||+|..++  .|.-||+|.|.+....+.+ .-+..++++..
T Consensus        79 ~~~~~~fR~E~~~~Gl~RvreF~~~e~~~f~~~~~-~~~~~~~~~~~  124 (211)
T cd00768          79 AEIGPAFRNEGGRRGLRRVREFTQLEGEVFGEDGE-EASEFEELIEL  124 (211)
T ss_pred             HEECCEECCCCCCCCCCCCCCEEEEEEEEEECCHH-HHHHHHHHHHH
T ss_conf             43200560578888844604688984799988488-89999999999


No 34 
>PRK09537 pylS pyrolysyl-tRNA synthetase; Reviewed
Probab=99.44  E-value=3e-14  Score=103.81  Aligned_cols=93  Identities=29%  Similarity=0.491  Sum_probs=61.9

Q ss_pred             HHHHHHHHHHHHHCCCEEEECCCEECCC-----C--CCCCC--CCEEEECCCCCCCCCCCCCC--CCHHHH--HHHHHHH
Q ss_conf             9999999999998798898478210568-----9--85445--41241024788678320000--285899--9989874
Q gi|254781066|r   26 NMIQSSLREYFVENQFIEIDSMSLQYSP-----G--NETHI--RAFSTELIIQDHIRKPLYLQ--TSPEFS--CKKLLAA   92 (355)
Q Consensus        26 s~i~~~iR~ff~~~gF~EV~TPiL~~~~-----~--g~~~~--~~f~t~~~~~~~~~~~~yL~--~SPql~--lK~ll~~   92 (355)
                      .++-+.|-+||-.+||+||..|||.+..     |  .++.+  .-|.+        ++.+.|+  -+|-||  ++.|.-.
T Consensus       210 gkler~it~ffvdrgfleikspilip~eyiermgid~d~elskQiFrv--------d~n~CLRPMLAPnLYnylrkL~R~  281 (420)
T PRK09537        210 GKLERDITKFFVDRGFLEIKSPILIPAEYIERMGIDNDTELSKQIFRV--------DKNFCLRPMLAPNLYNYLRKLDRA  281 (420)
T ss_pred             HHHHHHHHHHHHCCCCEEECCCEECCHHHHHHHCCCCHHHHHHHHEEE--------CCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             677888899854145135148504219999985788605655451674--------345332410142699999999861


Q ss_pred             --HHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECC
Q ss_conf             --4688999886424567775448430020001157
Q gi|254781066|r   93 --GEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH  126 (355)
Q Consensus        93 --G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af  126 (355)
                        .==|||+||||||-|+-+..|+.|||||-+-+-+
T Consensus       282 lpdPIrIFEIGpCyRKESdG~~HLeEFTMlNfcqmg  317 (420)
T PRK09537        282 LPDPIKIFEIGPCYRKESDGKEHLEEFTMVNFCQMG  317 (420)
T ss_pred             CCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             688715886204303444106788777777688644


No 35 
>COG0016 PheS Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]
Probab=99.39  E-value=4.8e-12  Score=90.76  Aligned_cols=115  Identities=21%  Similarity=0.299  Sum_probs=67.8

Q ss_pred             HHHHHHHHHHHHHCCCEEEECCCEECC-CCCCC-C------CCCEEEECCCCCCCCCCCCC--CCCHHHHHHHHHHHH--
Q ss_conf             999999999999879889847821056-89854-4------54124102478867832000--028589999898744--
Q gi|254781066|r   26 NMIQSSLREYFVENQFIEIDSMSLQYS-PGNET-H------IRAFSTELIIQDHIRKPLYL--QTSPEFSCKKLLAAG--   93 (355)
Q Consensus        26 s~i~~~iR~ff~~~gF~EV~TPiL~~~-~~g~~-~------~~~f~t~~~~~~~~~~~~yL--~~SPql~lK~ll~~G--   93 (355)
                      .+++..|+++|-+-||.+++.|.+.+. -.=++ +      |+... +.+..+.-....-|  ++||=..  +.|...  
T Consensus       114 ~~~~e~i~~iF~~mGF~~~~gp~IE~d~~NFDaLn~P~dHPARdmq-DTFy~~~~~~~~lLRTHTs~vq~--R~l~~~~~  190 (335)
T COG0016         114 TQTIEEIEDIFLGMGFTEVEGPEIETDFYNFDALNIPQDHPARDMQ-DTFYLKDDREKLLLRTHTSPVQA--RTLAENAK  190 (335)
T ss_pred             HHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHCCCCCCCCCCCC-CEEEECCCCCCEEECCCCCHHHH--HHHHHCCC
T ss_conf             9999999999997496664588213202252432499999841244-43787688773002366827659--99984799


Q ss_pred             -HHHHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHHHH
Q ss_conf             -688999886424567775448430020001157--76578777557888776
Q gi|254781066|r   94 -EEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIRCA  143 (355)
Q Consensus        94 -~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~~~  143 (355)
                       =-|++.+|+|||++..|.+|+|||.|+|-=.+.  .+..++.-..+++++.+
T Consensus       191 ~P~k~~~~grvyR~D~~DaTHs~~FhQiEGlvvd~~~s~~~Lkg~L~~f~~~~  243 (335)
T COG0016         191 IPIKIFSPGRVYRNDTVDATHSPEFHQIEGLVVDKNISFADLKGTLEEFAKKF  243 (335)
T ss_pred             CCCEEECCCCEECCCCCCCCCCHHEEEEEEEEEECCCCHHHHHHHHHHHHHHH
T ss_conf             99158456634117887764261013367899958956999999999999996


No 36 
>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated
Probab=99.18  E-value=2.5e-10  Score=80.56  Aligned_cols=112  Identities=18%  Similarity=0.271  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHHHHCCCEEEECCCEECC---------CCCCCCCCCEEEECCCCCCCCCCCCC--CCCHHHHHHHHHHHHH
Q ss_conf             999999999999879889847821056---------89854454124102478867832000--0285899998987446
Q gi|254781066|r   26 NMIQSSLREYFVENQFIEIDSMSLQYS---------PGNETHIRAFSTELIIQDHIRKPLYL--QTSPEFSCKKLLAAGE   94 (355)
Q Consensus        26 s~i~~~iR~ff~~~gF~EV~TPiL~~~---------~~g~~~~~~f~t~~~~~~~~~~~~yL--~~SPql~lK~ll~~G~   94 (355)
                      ++++..|+++|.+-||..++-|-+-+.         |..-+ |+.-. +.+   |++...-|  +|||=.-  +.|..+-
T Consensus       110 t~~~~ei~~iF~~~Gf~v~~GpeiE~~~~NFdaLn~P~~HP-AR~~~-DTF---y~~~~~lLRTHTS~~qi--r~m~~~~  182 (338)
T PRK00488        110 TRTIERIEDIFVGLGFEVAEGPEIEDDYYNFEALNIPKDHP-ARDMQ-DTF---YIDDRLLLRTHTSPVQI--RTMEKQK  182 (338)
T ss_pred             HHHHHHHHHHHHHCCCEEECCCCEEEHHHHHHHHCCCCCCC-CCCCC-CEE---EECCCCEECCCCCHHHH--HHHHHCC
T ss_conf             99999999999986976961883100454688756997885-43646-628---97687134356878889--9997269


Q ss_pred             --HHHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHHHHH
Q ss_conf             --88999886424567775448430020001157--765787775578887766
Q gi|254781066|r   95 --EKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIRCAA  144 (355)
Q Consensus        95 --~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~~~~  144 (355)
                        =||+..|+|||+|..|.+|.|+|.|+|--+..  +++.++....+.+++.++
T Consensus       183 pp~~~i~~GrvyR~d~~DatH~~~FhQ~Egl~vd~~it~~~Lk~~l~~f~~~~f  236 (338)
T PRK00488        183 PPIRIIAPGRVYRNDSDDATHSPMFHQVEGLVVDKNISFADLKGTLEDFLKAFF  236 (338)
T ss_pred             CCEEEEECCCCCCCCCCCCCCCEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHC
T ss_conf             986999526631589998753504664005897178879999999999999972


No 37 
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=99.15  E-value=9.9e-11  Score=82.99  Aligned_cols=112  Identities=12%  Similarity=0.110  Sum_probs=67.6

Q ss_pred             CCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-----CCCCC-CC---CCEEEECCCCCCCCCCCCC
Q ss_conf             478831261548999999999999999999879889847821056-----89854-45---4124102478867832000
Q gi|254781066|r    8 PWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-----PGNET-HI---RAFSTELIIQDHIRKPLYL   78 (355)
Q Consensus         8 ~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-----~~g~~-~~---~~f~t~~~~~~~~~~~~yL   78 (355)
                      +.|.+|...   +-...|..+...+++.|...||-+|+||++-..     .+|+. .+   ..|.    ..+..++.+-|
T Consensus         7 ~kG~rD~lp---~e~~~~~~i~~~i~~~f~~~Gf~~I~TP~lE~~e~~~~~~g~~~d~i~k~~y~----f~D~~g~~l~L   79 (424)
T CHL00201          7 LRGTKDILP---DEIEYWQFIHEKAATLLKLANYQEIRTPIFENTELFDRGIGEETDIVNKEMYR----FFDRGNRSITL   79 (424)
T ss_pred             CCCCCCCCH---HHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHCCCCCCCCHHHHHHHEE----EECCCCCEEEE
T ss_conf             999987899---99999999999999999985992504754041988623578742056665325----45599988886


Q ss_pred             CC--CHHHHHHHHHHHH-------HHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCC
Q ss_conf             02--8589999898744-------68899988642456777544843002000115776
Q gi|254781066|r   79 QT--SPEFSCKKLLAAG-------EEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHES  128 (355)
Q Consensus        79 ~~--SPql~lK~ll~~G-------~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d  128 (355)
                      +-  .+.+.  |.+++.       --|.|++|||||+|...+-..-||||+.+|..+.+
T Consensus        80 RpD~T~pia--R~~~~~~~~~~~~P~r~~y~g~vfR~e~pq~GR~REF~Q~gvEiiG~~  136 (424)
T CHL00201         80 RPEGTASIV--RAFIENRMAYHMRPQRLWYSGPMFRYERPQSGRQRQFHQLGIEFIGSS  136 (424)
T ss_pred             CCCCHHHHH--HHHHHCCCCCCCCCEEEEEECCEEECCCCCCCCCCHHHHCCEEEECCC
T ss_conf             787709999--999974765579987899875478058987886421041462000689


No 38 
>PRK12292 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=99.14  E-value=1.4e-09  Score=76.09  Aligned_cols=103  Identities=17%  Similarity=0.220  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-----CCCC-CCCCCEEEECCCCCCCCCCCCCC--CCHHHHHHHHHHH
Q ss_conf             99999999999999999879889847821056-----8985-44541241024788678320000--2858999989874
Q gi|254781066|r   21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-----PGNE-THIRAFSTELIIQDHIRKPLYLQ--TSPEFSCKKLLAA   92 (355)
Q Consensus        21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-----~~g~-~~~~~f~t~~~~~~~~~~~~yL~--~SPql~lK~ll~~   92 (355)
                      -...|..+.+.+++.|.+.||-||+||++-.+     ..|+ .....|..   ....-++.+-|+  ..++..  |+++.
T Consensus        16 e~~~~~~i~~~~~~~f~~~Gy~~I~tP~lE~~e~f~~~~g~~~~~~~~~f---~D~~~Gr~l~LRpD~T~~ia--R~~~~   90 (388)
T PRK12292         16 EARKIEEIRRRLLDVFRLWGYEEVITPTLEYLDTLLTGGGADLDLRTFKL---VDQLSGRTLGLRPDMTPQIA--RIAAT   90 (388)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHCCCCCCCCCHHEEEE---EECCCCCEEEECCCCCHHHH--HHHHH
T ss_conf             99999999999999999879967357660629885445775021104899---82699978985687719999--99997


Q ss_pred             HH------HHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCC
Q ss_conf             46------8899988642456777544843002000115776
Q gi|254781066|r   93 GE------EKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHES  128 (355)
Q Consensus        93 G~------~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d  128 (355)
                      .+      -|+|.+|+|||.|....-..-||||+.+|.-+.+
T Consensus        91 ~~~~~~~p~r~~Y~g~vfR~e~pq~Gr~REf~Q~G~EiiG~~  132 (388)
T PRK12292         91 RLANRPGPLRLCYAGNVFRAQPRGLGRSREFLQSGVELIGDA  132 (388)
T ss_pred             HHHCCCCCEEEEEEEEEEEECCCCCCCCCEEEECCEEEECCC
T ss_conf             310467876899852268705898996102342575531788


No 39 
>PRK12293 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=99.13  E-value=4e-10  Score=79.41  Aligned_cols=126  Identities=16%  Similarity=0.187  Sum_probs=75.5

Q ss_pred             CCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC-CCCCCCCCEEEECCCCCCCCCCCCCC
Q ss_conf             99889874788312615489999999999999999998798898478210568-98544541241024788678320000
Q gi|254781066|r    1 MHQIPSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP-GNETHIRAFSTELIIQDHIRKPLYLQ   79 (355)
Q Consensus         1 ~~~~p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-~g~~~~~~f~t~~~~~~~~~~~~yL~   79 (355)
                      +||+|   .|.+|.-.   +-...+..|...+|+.|.+.||-||.||++--.. .++..-+..   +.-.|..++.+-|+
T Consensus         4 ~~~lP---~GtrD~~p---~~~~~~~~Ie~~~~~~f~~~Gy~eI~TP~~E~~e~~~~~~~kem---y~f~D~~gr~l~LR   74 (281)
T PRK12293          4 EHEIP---QGSRLYFG---KSAKLKRDIENVASEILYKEGFEEIVTPSFSYHQHLSVADEKEL---LRFSDEKNHEISLR   74 (281)
T ss_pred             CCCCC---CCCCCCCH---HHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEECCCCCCCCEE---EEEECCCCCEEEEC
T ss_conf             67899---97816681---99999999999999999985994853785686443466563017---99987999879977


Q ss_pred             C--CHHHHHHHHHHHH------HHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCC-CHHHHHHHHHHHHHHH
Q ss_conf             2--8589999898744------6889998864245677754484300200011577-6578777557888776
Q gi|254781066|r   80 T--SPEFSCKKLLAAG------EEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHE-SYEQLMKDCMNIIRCA  143 (355)
Q Consensus        80 ~--SPql~lK~ll~~G------~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~-d~~dlm~~~E~li~~~  143 (355)
                      .  .++..  |+++..      --|+|.+|||||.|.      .||+|+-+|.-+. +..+++.++-++++.+
T Consensus        75 Pd~Ta~ia--R~v~~~l~~~~~p~rl~Y~g~vFRye~------rEf~Q~GvEliG~~s~~Evi~la~~~l~~l  139 (281)
T PRK12293         75 ADSTVDVV--RIITKRLGRSTEHKKWFYIQPVFRYPT------TEIYQIGAEIIGESDLSKVLNIAAEIFNEL  139 (281)
T ss_pred             CCCCHHHH--HHHHHCCCCCCCCEEEEEECCEEECCC------CCCEEECEEEECCCCHHHHHHHHHHHHHHC
T ss_conf             88878999--999965544689757998756353467------774684748877999999999999999976


No 40 
>PRK00037 hisS histidyl-tRNA synthetase; Reviewed
Probab=99.12  E-value=2.6e-09  Score=74.61  Aligned_cols=111  Identities=18%  Similarity=0.257  Sum_probs=66.7

Q ss_pred             CCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-----CCCCC-C-CC--CEEEECCCCCCCCCCCC
Q ss_conf             7478831261548999999999999999999879889847821056-----89854-4-54--12410247886783200
Q gi|254781066|r    7 QPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-----PGNET-H-IR--AFSTELIIQDHIRKPLY   77 (355)
Q Consensus         7 ~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-----~~g~~-~-~~--~f~t~~~~~~~~~~~~y   77 (355)
                      .+.|.+|.-.   +-.+.|..+...+|+-|.+.||-||+||+|...     ..|+. . +.  .|..    .+.-++.+-
T Consensus         6 ~p~G~rD~lP---~~~~~~~~i~~~i~~~~~~~Gy~~I~tP~lE~~d~~~~~~g~~~d~~~k~~y~f----~D~~g~~l~   78 (417)
T PRK00037          6 APRGTRDILP---EESAKWQYVEDTIREVFERYGFSEIRTPIFEYTELFKRKIGESTDIVEKEMYTF----QDKGGRSLT   78 (417)
T ss_pred             CCCCCCCCCH---HHHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHCCCCCCCCCHHHHHEEEE----ECCCCCEEE
T ss_conf             9998776798---899999999999999999859958577521509886245776322013320567----759998898


Q ss_pred             CCC--CHHHHHHHHHHHHH--------HHHHHHHHHHCCCCC--CCCCCCCEEEECEEECCCC
Q ss_conf             002--85899998987446--------889998864245677--7544843002000115776
Q gi|254781066|r   78 LQT--SPEFSCKKLLAAGE--------EKIFCFAHAWRNGEQ--GCLHQPEFTMLEWYRAHES  128 (355)
Q Consensus        78 L~~--SPql~lK~ll~~G~--------~rvyqig~~FRaE~~--~~rHlpEFtmLE~e~af~d  128 (355)
                      |+-  .|+..  |.++...        =|.|++|+|||+|..  +|  .-||||+++|..+.+
T Consensus        79 LRpD~T~~ia--R~~~~~~~~~~~~~P~r~~y~g~vfR~e~p~~GR--~REf~Q~g~eiiG~~  137 (417)
T PRK00037         79 LRPEGTAPVV--RAVIENKLYNELPKPFKLYYIGPMFRYERPQKGR--YRQFHQFGVEVIGSD  137 (417)
T ss_pred             ECCCCCHHHH--HHHHHHHHHCCCCCCEEEEEECCEEECCCCCCCC--CCCEEECCHHHHCCC
T ss_conf             5677672999--9999721010688765899872466047898876--352456352774664


No 41 
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=99.07  E-value=2.1e-09  Score=75.11  Aligned_cols=118  Identities=15%  Similarity=0.192  Sum_probs=74.1

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCCCCCCCEEEECCC-CCCCCCCCCCCC-CH----HHHHHHHHH
Q ss_conf             99999999999999998798898478210568----985445412410247-886783200002-85----899998987
Q gi|254781066|r   22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNETHIRAFSTELII-QDHIRKPLYLQT-SP----EFSCKKLLA   91 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~~~~~~f~t~~~~-~~~~~~~~yL~~-SP----ql~lK~ll~   91 (355)
                      .+++.+|...+|+-+.+.||-||.||.|.+..    +|  |.+-|.-+.+. .+--++++.|.. .-    ++| |.-+-
T Consensus        47 ~~i~~~le~~ir~e~~~~G~~eV~tP~l~~~~Lw~~SG--h~~~y~~~mf~~~d~~~~~~~l~Pmnc~~~~~i~-~~~~~  123 (438)
T PRK12325         47 LKVLKKIENIVREEQNRAGAIEILMPTIQPADLWRESG--RYDAYGKEMLRIKDRHDREMLYGPTNEEMITDIF-RSYVK  123 (438)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHC--CHHHHHHHHCEEECCCCCEECCCCCCCHHHHHHH-HHCCC
T ss_conf             99999999999999997499799877658778998628--7645557421213477774313899849999999-74034


Q ss_pred             HHHH---HHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHH
Q ss_conf             4468---8999886424567775---4484300200011577657877755788877
Q gi|254781066|r   92 AGEE---KIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRC  142 (355)
Q Consensus        92 ~G~~---rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~  142 (355)
                      |.-+   |+||||.+||+|-+.+   .-.-||||-|.|.-..+.++..+..+.+...
T Consensus       124 SYRdLPlrl~q~g~~~R~E~sp~~GLlRvReF~m~Dah~F~~~~e~~~~~~~~v~~~  180 (438)
T PRK12325        124 SYKDLPLNLYHIQWKFRDEIRPRFGVMRGREFLMKDAYSFDLDEEGARKSYNRMFVA  180 (438)
T ss_pred             CHHHCCHHHHHHHHEECCCCCCCCCCCEEEEEECCCHHHCCCCHHHHHHHHHHHHHH
T ss_conf             265425788764440112026764410122333041543246889999999999999


No 42 
>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=99.07  E-value=9.9e-09  Score=71.14  Aligned_cols=100  Identities=18%  Similarity=0.238  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEECCCEECCC-----CCCC-CCCCEEEECCCCCCCCCCCCCC--CCHHHHHHHHHHHHH
Q ss_conf             9999999999999998798898478210568-----9854-4541241024788678320000--285899998987446
Q gi|254781066|r   23 LKRNMIQSSLREYFVENQFIEIDSMSLQYSP-----GNET-HIRAFSTELIIQDHIRKPLYLQ--TSPEFSCKKLLAAGE   94 (355)
Q Consensus        23 ~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-----~g~~-~~~~f~t~~~~~~~~~~~~yL~--~SPql~lK~ll~~G~   94 (355)
                      +.|..|.+.+++.|.+.||-+|+||++-...     .|+. .-..|...    +.-++.+-|+  ..++..  |.++...
T Consensus         3 ~~r~~i~~~l~~~f~~~Gy~~I~~P~lE~~d~~~~~~~~~~~~~~~~f~----D~~g~~l~LRpD~T~~ia--R~~~~~~   76 (261)
T cd00773           3 ALRRYIEDTLREVFERYGYEEIDTPVFEYTELFLRKSGDEVSKEMYRFK----DKGGRDLALRPDLTAPVA--RAVAENL   76 (261)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHCCCCCCCCHHCEEEEE----CCCCCEEEECCCCCHHHH--HHHHHHH
T ss_conf             8999999999999998699786677645276752446531021169999----799998976786627999--9999741


Q ss_pred             ------HHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCC
Q ss_conf             ------8899988642456777544843002000115776
Q gi|254781066|r   95 ------EKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHES  128 (355)
Q Consensus        95 ------~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d  128 (355)
                            -|+|.+|+|||.+....-..-||+|+.+|.-+.+
T Consensus        77 ~~~~~p~r~~Y~g~VfR~~~~~~g~~rE~~Q~G~EiiG~~  116 (261)
T cd00773          77 LSLPLPLKLYYIGPVFRYERPQKGRYREFYQVGVEIIGSD  116 (261)
T ss_pred             CCCCCCEEEEEECCEEEECCCCCCCCCCCCCEEEEEECCC
T ss_conf             5378885899973189976899998443221469997289


No 43 
>COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=98.97  E-value=7.8e-09  Score=71.77  Aligned_cols=134  Identities=19%  Similarity=0.248  Sum_probs=76.5

Q ss_pred             CCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC-----CCCC-CCCCEEEECCCCCCCCCCCCCC--
Q ss_conf             4788312615489999999999999999998798898478210568-----9854-4541241024788678320000--
Q gi|254781066|r    8 PWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP-----GNET-HIRAFSTELIIQDHIRKPLYLQ--   79 (355)
Q Consensus         8 ~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-----~g~~-~~~~f~t~~~~~~~~~~~~yL~--   79 (355)
                      +.|.+|.-.   .-...|..|...+|+-+.+-||.||+||++-.+.     .|+. ..-.-....+ .|..++..-|+  
T Consensus         7 prG~~D~lp---~d~~~~~~i~~~~~~v~~~yGf~eI~TPifE~telf~r~~Ge~td~v~kemY~F-~Dkggr~laLRpe   82 (429)
T COG0124           7 PRGTRDFLP---EDMALREYIESTIRKVFESYGFSEIRTPIFEYTELFARKSGEETDVVEKEMYTF-KDKGGRSLALRPE   82 (429)
T ss_pred             CCCCCCCCH---HHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCHHHHHHCCCCCCCCCCCCEEEE-EECCCCEEEECCC
T ss_conf             998665586---778999999999999999809976557551116676201697433332102899-9489988984466


Q ss_pred             -CCHHHHHHHHHHHH------HHHHHHHHHHHCCCCC--CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             -28589999898744------6889998864245677--75448430020001157765787775578887766641883
Q gi|254781066|r   80 -TSPEFSCKKLLAAG------EEKIFCFAHAWRNGEQ--GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQK  150 (355)
Q Consensus        80 -~SPql~lK~ll~~G------~~rvyqig~~FRaE~~--~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~  150 (355)
                       |+|   .=|..+..      --|.|.+|||||.|..  +|.  -||||+++|..+.+--..=..+-.|+...++.++-.
T Consensus        83 ~Tap---v~R~~~en~~~~~~p~k~yy~g~vfRyErPQ~GR~--RqF~Q~g~E~iG~~~~~~DAEvi~l~~~~l~~lGi~  157 (429)
T COG0124          83 LTAP---VARAVAENKLDLPKPLKLYYFGPVFRYERPQKGRY--RQFYQFGVEVIGSDSPDADAEVIALAVEILEALGIG  157 (429)
T ss_pred             CCHH---HHHHHHHCCCCCCCCEEEEEECCEECCCCCCCCCC--EEEEECCEEEECCCCCCCCHHHHHHHHHHHHHCCCC
T ss_conf             7499---99999956220368725998335623788888875--036876767767998653899999999999974998


No 44 
>PRK12420 histidyl-tRNA synthetase; Provisional
Probab=98.96  E-value=3.8e-09  Score=73.58  Aligned_cols=117  Identities=21%  Similarity=0.255  Sum_probs=69.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCEECC------CCCCCCC--CCEEEECCCCCCCCCCCCCC---CCHHHHHHHH
Q ss_conf             99999999999999999879889847821056------8985445--41241024788678320000---2858999989
Q gi|254781066|r   21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQYS------PGNETHI--RAFSTELIIQDHIRKPLYLQ---TSPEFSCKKL   89 (355)
Q Consensus        21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~------~~g~~~~--~~f~t~~~~~~~~~~~~yL~---~SPql~lK~l   89 (355)
                      -...|..+.+.+|+.|...||-||+||++-.+      .|+++.+  ..|.    -.+..+..+-|+   |+| +.  |.
T Consensus        17 e~~~~~~i~~~~~~~~~~~Gy~~I~tP~~E~~elf~~~~g~~~~i~kemy~----f~D~~gr~l~LRPe~Ta~-ia--R~   89 (421)
T PRK12420         17 EQVLRNKIKRACEDTFERYGCKPLETPTLNMYELMSYKYGGGDEILKEIYT----LQDQGKRDLALRYDLTIP-FA--KV   89 (421)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHCCCCCCCCHHHHHEEE----EECCCCCEEEECCCCCHH-HH--HH
T ss_conf             999999999999999998599472476501187642447884422411078----881899879856776589-99--99


Q ss_pred             HHHH--H---HHHHHHHHHHCCCCC--CCCCCCCEEEECEEECCCCHHHHHHHHH--HHHHHHHHHHC
Q ss_conf             8744--6---889998864245677--7544843002000115776578777557--88877666418
Q gi|254781066|r   90 LAAG--E---EKIFCFAHAWRNGEQ--GCLHQPEFTMLEWYRAHESYEQLMKDCM--NIIRCAAEVAN  148 (355)
Q Consensus        90 l~~G--~---~rvyqig~~FRaE~~--~~rHlpEFtmLE~e~af~d~~dlm~~~E--~li~~~~~~~~  148 (355)
                      ++..  .   -|.|.+|||||.|.-  +|.  -||||+.+|.-+.+--  ..++|  .+...+++.++
T Consensus        90 ~a~~~~~~~P~k~~y~g~vfR~erpq~GR~--ReF~Q~GvEiiG~~~~--~aDaEiI~la~~~l~~lg  153 (421)
T PRK12420         90 VAMNPNIRLPFKRYEIGKVFRDGPIKQGRF--REFIQCDVDIVGVESV--MAEAELMSMAFELFRTLN  153 (421)
T ss_pred             HHHCCCCCCCEEEEEECCEEECCCCCCCCC--CEEEECCEEEECCCCH--HHHHHHHHHHHHHHHHCC
T ss_conf             997757778745888767785389878855--5134357542078877--889999999999999659


No 45 
>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=98.88  E-value=3e-10  Score=80.15  Aligned_cols=115  Identities=27%  Similarity=0.346  Sum_probs=70.3

Q ss_pred             HHHHHHHHHHHHHCCCEEEECCCEECCCCCCC-CCCCEEEECCCCC-CCCCCCCCC--CCHHHH--HHHH--HHHHHHHH
Q ss_conf             99999999999987988984782105689854-4541241024788-678320000--285899--9989--87446889
Q gi|254781066|r   26 NMIQSSLREYFVENQFIEIDSMSLQYSPGNET-HIRAFSTELIIQD-HIRKPLYLQ--TSPEFS--CKKL--LAAGEEKI   97 (355)
Q Consensus        26 s~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~-~~~~f~t~~~~~~-~~~~~~yL~--~SPql~--lK~l--l~~G~~rv   97 (355)
                      .++-+.|-.||-.+||+||..|||.+..--+. +++ -.|++...- -.++.+.|+  -+|.||  +.+|  +..+==||
T Consensus       243 Gkler~it~ffvdrGfleiksPiliP~ey~ermGi~-ndtelskqifrvdkn~ClrPmlaP~lynylrkldr~lP~Pik~  321 (453)
T TIGR02367       243 GKLEREITKFFVDRGFLEIKSPILIPLEYVERMGID-NDTELSKQIFRVDKNLCLRPMLAPTLYNYLRKLDRILPDPIKV  321 (453)
T ss_pred             HHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHCCCC-CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCEEE
T ss_conf             467666766653124023236310105688650776-4025666666441001012100056899999987537896479


Q ss_pred             HHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHH
Q ss_conf             99886424567775448430020001157--765787775578887
Q gi|254781066|r   98 FCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIR  141 (355)
Q Consensus        98 yqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~  141 (355)
                      |+||||||.|+-+..|+-||||+.+=+.+  .+-+.+-.++.+++.
T Consensus       322 fe~GPCyrkesdGkehleeftm~nfCqmGsGCtrenle~~i~~fl~  367 (453)
T TIGR02367       322 FEVGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLEALIKEFLD  367 (453)
T ss_pred             EEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             8606752435653356666665554314787326779999999887


No 46 
>PRK12295 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=98.84  E-value=1.4e-07  Score=64.32  Aligned_cols=97  Identities=19%  Similarity=0.193  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCEECC-----CCCCC-CCCCEEEECCCCCCCCCCCCCC--CCHHHHHHHH-HHH
Q ss_conf             9999999999999999879889847821056-----89854-4541241024788678320000--2858999989-874
Q gi|254781066|r   22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYS-----PGNET-HIRAFSTELIIQDHIRKPLYLQ--TSPEFSCKKL-LAA   92 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-----~~g~~-~~~~f~t~~~~~~~~~~~~yL~--~SPql~lK~l-l~~   92 (355)
                      +.+|-.+...|++-|.+.||-+|+||++-..     ..|+. -...|..    .+..++..-|+  -.+++.  |. +..
T Consensus         4 ~~r~~~~~~~i~~~f~~~Gy~~I~tP~lE~~d~~~~~~Ge~~~~~~y~f----~D~~g~~l~LRpDlT~pia--R~~~~~   77 (373)
T PRK12295          4 LSRSAALAEALLASFEAAGAVRVDPPILQPAEPFLDLSGEDIRRRIFVT----SDENGEELCLRPDFTIPVC--RRHLAS   77 (373)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEECCCCCCCHHHHCCCCCCHHHEEEEEE----ECCCCCEEEEECCCCHHHH--HHHHHH
T ss_conf             6779999999999999869968568760417764143563311004889----9899898998178889999--999983


Q ss_pred             H---HHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCC
Q ss_conf             4---6889998864245677754484300200011577
Q gi|254781066|r   93 G---EEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHE  127 (355)
Q Consensus        93 G---~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~  127 (355)
                      +   --|+|.+|+|||.. .++.  -||||+.+|.-+.
T Consensus        78 ~~~~p~R~~Y~G~VfR~q-~gr~--rEf~Q~GvEiiG~  112 (373)
T PRK12295         78 NAGEPARYSYLGEVFRQR-RDRA--SEFLQAGIESFGR  112 (373)
T ss_pred             CCCCCEEEEEECCEEECC-CCCC--CCEEEEEEEEECC
T ss_conf             899980078773322457-9998--8516701578578


No 47 
>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=98.82  E-value=1.6e-08  Score=69.86  Aligned_cols=119  Identities=19%  Similarity=0.282  Sum_probs=69.0

Q ss_pred             HHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEEEECCC-CCCCCCCCCCCCCHHHHHHHHHHH----HHH-
Q ss_conf             999999999999998798898478210568--985445412410247-886783200002858999989874----468-
Q gi|254781066|r   24 KRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFSTELII-QDHIRKPLYLQTSPEFSCKKLLAA----GEE-   95 (355)
Q Consensus        24 ~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~t~~~~-~~~~~~~~yL~~SPql~lK~ll~~----G~~-   95 (355)
                      .|.+|.+.+|+.+.+.||.||.||+|....  .+..+...|.-+.+. .+..+...+|+-.-+..+-++.+.    .-+ 
T Consensus         1 l~~~l~~~~~~~~~~~G~~~i~tP~l~~~~~~~~sg~~~~~~~~my~~~d~~~~~l~Lrp~~~~~~~~~~~~~~~~~~~l   80 (170)
T pfam00587         1 LRNALENFIRDLFKRYGYQEVDTPILEPKELWEGSGHWDDYFDEMYRFKDRGGEELYLRPTAEVGITRLFKNEILSYRDL   80 (170)
T ss_pred             CHHHHHHHHHHHHHHCCCEEEECCEEEEHHHHHHCCCCCCCHHHEEEEECCCCCEEEEECCCCHHHHHHHHHHCCCCCCC
T ss_conf             97999999999999859989999917567898344776557531256735899768873257458889988620032358


Q ss_pred             --HHHHHHHHHCCCCCCCC---CCCCEEEECEEECCCCHHHHHHHHHHHHHHH
Q ss_conf             --89998864245677754---4843002000115776578777557888776
Q gi|254781066|r   96 --KIFCFAHAWRNGEQGCL---HQPEFTMLEWYRAHESYEQLMKDCMNIIRCA  143 (355)
Q Consensus        96 --rvyqig~~FRaE~~~~r---HlpEFtmLE~e~af~d~~dlm~~~E~li~~~  143 (355)
                        |+|++|+|||+|-..++   -.-||||.|++....+ ++..+..++++..+
T Consensus        81 P~r~~~~~~~fR~E~~~~~Gl~R~reF~q~d~~~~~~~-e~s~~~~~e~~~~~  132 (170)
T pfam00587        81 PLKLYQIGPCFRYEARPRRGLGRVREFTQVDAEIFGTP-EQSEEEDEELLKLA  132 (170)
T ss_pred             CCEEECCCCCCCCCCCCCCCCCEEEEEEEECEEEEECC-CHHHHHHHHHHHHH
T ss_conf             60133065300677776667743678898047999670-04299999999999


No 48 
>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=98.75  E-value=3.2e-08  Score=68.13  Aligned_cols=122  Identities=20%  Similarity=0.178  Sum_probs=80.6

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCEECCCC--CCCCCCCEEEECCC-CCCCCCCCCCCCCHHHHHHHHHH----HHH
Q ss_conf             999999999999999987988984782105689--85445412410247-88678320000285899998987----446
Q gi|254781066|r   22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSPG--NETHIRAFSTELII-QDHIRKPLYLQTSPEFSCKKLLA----AGE   94 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~--g~~~~~~f~t~~~~-~~~~~~~~yL~~SPql~lK~ll~----~G~   94 (355)
                      .+.+.+|.+.||+-+++.|+-||.||+|++..-  ...+.+-|..+.+. .+..+.+++|+...|-.+-.+..    +--
T Consensus        31 ~~i~~~i~~~i~~~~~~~G~~ev~~P~l~~~~l~~~sg~~~~f~~emf~v~d~~~~~~~L~PT~E~~~~~~~~~~i~Syr  110 (255)
T cd00779          31 LRVLKKIENIIREEMNKIGAQEILMPILQPAELWKESGRWDAYGPELLRLKDRHGKEFLLGPTHEEVITDLVANEIKSYK  110 (255)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHCCCCCCCCCEEEEECCCCCEEEECCCCHHHHHHHHHHHCCCHH
T ss_conf             99999999999999998599899765347388874425301368731544537887773168874889999986503612


Q ss_pred             H---HHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHHH
Q ss_conf             8---8999886424567775---44843002000115776578777557888776
Q gi|254781066|r   95 E---KIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCA  143 (355)
Q Consensus        95 ~---rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~  143 (355)
                      +   ++||+++|||+|-+++   .-.-||+|-|.|....|.++..+..+.+....
T Consensus       111 dLPl~~~q~~~~fR~E~r~~~GllR~rEF~~~d~hsf~~~~e~a~~~~~~~~~~y  165 (255)
T cd00779         111 QLPLNLYQIQTKFRDEIRPRFGLMRGREFLMKDAYSFDIDEESLEETYEKMYQAY  165 (255)
T ss_pred             HCCEEEECCCCEECCCCCCCCCCCEEEEEEEEHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf             2574541353354256678866324313770022035699899999999999999


No 49 
>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=98.75  E-value=3.9e-08  Score=67.65  Aligned_cols=133  Identities=14%  Similarity=0.178  Sum_probs=85.7

Q ss_pred             CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEEEECCCCCCCCCCCCCCCCH
Q ss_conf             9874788312615489999999999999999998798898478210568--98544541241024788678320000285
Q gi|254781066|r    5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFSTELIIQDHIRKPLYLQTSP   82 (355)
Q Consensus         5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~t~~~~~~~~~~~~yL~~SP   82 (355)
                      |-.++|+|.       =.++|..+...+|+-..++||.||.||.|....  ....|.+-|.-..+....-+++++|.-..
T Consensus        20 ~G~~~w~P~-------G~~i~~~L~~~ir~~~~~~Gy~eV~tP~i~~~~Lw~~SGH~~~y~e~mf~~~~~~~~~~LkPmn   92 (298)
T cd00771          20 PGLPFWLPK-------GAIIRNELEDFLRELQRKRGYQEVETPIIYNKELWETSGHWDHYRENMFPFEEEDEEYGLKPMN   92 (298)
T ss_pred             CCCEEECCC-------HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCCCCCCCCEEEEEECCCCEEEECCC
T ss_conf             765788388-------8999999999999999986998998861266556754776311368568888625416885068


Q ss_pred             -----HHHHHHHHHHHHH---HHHHHHHHHCCCCCCC----CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             -----8999989874468---8999886424567775----44843002000115776578777557888776664
Q gi|254781066|r   83 -----EFSCKKLLAAGEE---KIFCFAHAWRNGEQGC----LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEV  146 (355)
Q Consensus        83 -----ql~lK~ll~~G~~---rvyqig~~FRaE~~~~----rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~  146 (355)
                           ++|. .-+-|.-+   |++++|.|||+|-++.    .-+-+|||-|... |...+++.+.+.++++.+.+.
T Consensus        93 Cp~h~~i~~-~~~~SYrdLPlR~~E~g~~~R~E~sG~L~GL~RvR~FtqdDaHi-Fc~~eQ~~~E~~~~~~~~~~v  166 (298)
T cd00771          93 CPGHCLIFK-SKPRSYRDLPLRLAEFGTVHRYEQSGALHGLTRVRGFTQDDAHI-FCTPDQIKEEIKGVLDLIKEV  166 (298)
T ss_pred             CHHHHHHHH-CCCCCHHHCCHHHHCCCCEECCCCCCCCCCCCCCCCCCCCCCEE-ECCHHHHHHHHHHHHHHHHHH
T ss_conf             688999986-35567343467652075055476776755744555674576324-416889999999999999999


No 50 
>PRK12421 ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=98.71  E-value=4e-07  Score=61.67  Aligned_cols=122  Identities=11%  Similarity=0.092  Sum_probs=71.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-----CCC-CCCCCCEEEECCCCCC-CCCCCCCC--CCHHHHHHHHH
Q ss_conf             999999999999999999879889847821056-----898-5445412410247886-78320000--28589999898
Q gi|254781066|r   20 PFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-----PGN-ETHIRAFSTELIIQDH-IRKPLYLQ--TSPEFSCKKLL   90 (355)
Q Consensus        20 ~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-----~~g-~~~~~~f~t~~~~~~~-~~~~~yL~--~SPql~lK~ll   90 (355)
                      +-...+..+.+.+.+.|.+.||-+|.||++-..     ..| +.....|+.    .+. -++.+-|+  ..||..  |+.
T Consensus        19 ~ea~~~~~l~~~l~~~f~~~Gy~~V~tP~lE~~e~l~~~~g~~~~~~~f~~----~D~~sGr~l~LRpD~T~~vA--Ri~   92 (391)
T PRK12421         19 EEAQKIERLRRRLLDLFASRGYQLVMPPFIEYLESLLTGAGQDLDLQTFKL----IDQLSGRLMGVRADITPQVA--RID   92 (391)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHCCCCCCCCCEEEEEE----EECCCCCEEEECCCCCHHHH--HHH
T ss_conf             999999999999999999869976216760728785656687341479999----61799978655653206889--999


Q ss_pred             H-----HHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCC-HHHHHHHHHHHHHHHHHHHC
Q ss_conf             7-----4468899988642456777544843002000115776-57877755788877666418
Q gi|254781066|r   91 A-----AGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHES-YEQLMKDCMNIIRCAAEVAN  148 (355)
Q Consensus        91 ~-----~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d-~~dlm~~~E~li~~~~~~~~  148 (355)
                      +     .+--|+|.+|++||.+....--.-||+|+.+|.-+.+ .+.=.+++ .++..+.+.++
T Consensus        93 a~~~~~~~p~Rl~Y~G~V~R~~~~~~gr~Ref~Q~G~EliG~~~~~aD~EvI-~l~~~~L~~lG  155 (391)
T PRK12421         93 AHLLNREGVARYCYAGSVLHTLPQGLNASRAPLQLGAELYGHAGIEADIEII-DLMLGLLRNAG  155 (391)
T ss_pred             HHHCCCCCCEEEEEECEEEECCCCCCCCCCCCEECCEEEECCCCHHHHHHHH-HHHHHHHHHCC
T ss_conf             8740468865799965177516888887665215058985699879899999-99999999769


No 51 
>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=98.63  E-value=3.6e-07  Score=61.87  Aligned_cols=130  Identities=17%  Similarity=0.108  Sum_probs=82.9

Q ss_pred             CCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-----CCCCCCCCC-----EEEECCCCCCCC
Q ss_conf             8987478831261548999999999999999999879889847821056-----898544541-----241024788678
Q gi|254781066|r    4 IPSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-----PGNETHIRA-----FSTELIIQDHIR   73 (355)
Q Consensus         4 ~p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-----~~g~~~~~~-----f~t~~~~~~~~~   73 (355)
                      .|-.+.|+|-       =.+.+.+|.+.+|+-+.+.|+-||.||+|.+.     .+|  |.+-     |.+........+
T Consensus        21 v~G~~~~lP~-------G~~i~~~l~~~~r~~~~~~G~~ev~~P~l~~~~~~~k~sg--h~~~y~~emf~v~~~g~~~~d   91 (261)
T cd00778          21 VKGCMVFRPY-------GYAIWENIQKILDKEIKETGHENVYFPLLIPESELEKEKE--HIEGFAPEVAWVTHGGLEELE   91 (261)
T ss_pred             CCCEEEECCC-------HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHC--HHHCCCCCCEEEECCCCCCCC
T ss_conf             9830888632-------8999999999999999986996998833278899997428--143057653355216852013


Q ss_pred             CCCCCCCCH-----HHHHHHHHHHHHH---HHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHH
Q ss_conf             320000285-----8999989874468---8999886424567775---4484300200011577657877755788877
Q gi|254781066|r   74 KPLYLQTSP-----EFSCKKLLAAGEE---KIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRC  142 (355)
Q Consensus        74 ~~~yL~~SP-----ql~lK~ll~~G~~---rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~  142 (355)
                      .++.|...-     ++|. .-+-|.-+   |+||+|.+||+|-+++   .-.-||+|-|.|..|.+.+++.+.+..++..
T Consensus        92 ~~y~LkPmne~~~~~i~~-~~~~SYRdLPlrl~q~g~~~R~E~s~~~gL~RvReF~~dDahs~~~t~eq~~~e~~~~~~~  170 (261)
T cd00778          92 EPLALRPTSETAIYPMFS-KWIRSYRDLPLKINQWVNVFRWETKTTRPFLRTREFLWQEGHTAHATEEEAEEEVLQILDL  170 (261)
T ss_pred             CCCCCCCCCHHHHHHHHH-HHHCCCCCCCHHHHHCCCEECCCCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHH
T ss_conf             560347888699999997-3505402278255530422437788887653254252342336558999999999999999


Q ss_pred             H
Q ss_conf             6
Q gi|254781066|r  143 A  143 (355)
Q Consensus       143 ~  143 (355)
                      .
T Consensus       171 y  171 (261)
T cd00778         171 Y  171 (261)
T ss_pred             H
T ss_conf             9


No 52 
>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=98.56  E-value=2.2e-07  Score=63.17  Aligned_cols=121  Identities=14%  Similarity=0.104  Sum_probs=76.7

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEE-----EECCCCCCCCCCCCCCCCHH-----HHHHHHH
Q ss_conf             9999999999999998798898478210568--9854454124-----10247886783200002858-----9999898
Q gi|254781066|r   23 LKRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFS-----TELIIQDHIRKPLYLQTSPE-----FSCKKLL   90 (355)
Q Consensus        23 ~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~-----t~~~~~~~~~~~~yL~~SPq-----l~lK~ll   90 (355)
                      +++.++.+.+++.+.+.||.||.||.|.+..  .+..+..-|.     +........+.++||.-..|     +|.+..+
T Consensus         3 ~L~~aL~~~~~~~~~~~G~~~v~~P~l~~~~~~~~sg~~~~f~~~~y~v~~~~~~~~~~~~~L~PTsE~~~~~~~~~~i~   82 (235)
T cd00670           3 ALWRALERFLDDRMAEYGYQEILFPFLAPTVLFFKGGHLDGYRKEMYTFEDKGRELRDTDLVLRPAACEPIYQIFSGEIL   82 (235)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCEEEEECCCHHHHHHHHCCCC
T ss_conf             89999999999999986998998985578999922386754520528982377666787389930786999999948328


Q ss_pred             HH-HH-HHHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf             74-46-88999886424567775---448430020001157765787775578887766
Q gi|254781066|r   91 AA-GE-EKIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAA  144 (355)
Q Consensus        91 ~~-G~-~rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~  144 (355)
                      .. -+ =|++++++|||+|-.++   .-.-||+|.|.+. |.+-++..+..+.++....
T Consensus        83 s~~dLPlr~~~~s~~fR~E~~~~~Gl~Rv~eF~k~E~~~-~~~~e~~~~~~~~~~~~~~  140 (235)
T cd00670          83 SYRALPLRLDQIGPCFRHEPSGRRGLMRVREFRQVEYVV-FGEPEEAEEERREWLELAE  140 (235)
T ss_pred             CHHHCCEEEEEECCEECCCCCCCCCCEEEEEEEEEEEEE-EECHHHHHHHHHHHHHHHH
T ss_conf             768799545445653336789999983678999850799-9688999999999999999


No 53 
>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=98.54  E-value=1.9e-06  Score=57.63  Aligned_cols=122  Identities=13%  Similarity=0.116  Sum_probs=79.7

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCC--CCC--CCEEEECCCCCCCCCCCCCCCCHHHHHHHH----
Q ss_conf             99999999999999998798898478210568----985--445--412410247886783200002858999989----
Q gi|254781066|r   22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNE--THI--RAFSTELIIQDHIRKPLYLQTSPEFSCKKL----   89 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~--~~~--~~f~t~~~~~~~~~~~~yL~~SPql~lK~l----   89 (355)
                      ++++.+|...||+-+++.|+-||-+|+|++..    +|.  .+.  .-|.+..........++.|+...|-.+-.+    
T Consensus        32 ~~i~~ki~~~i~~e~~~~G~qev~~P~l~p~~lw~ksgr~~~~~~~e~~~~~~~~~~~~e~~~~L~PT~Ee~~~~~~~~~  111 (264)
T cd00772          32 KAILDKIENVLDKMFKEHGAQNALFPFFILASFLEKEAEHDEGFSKELAVFKDAGDEELEEDFALRPTLEENIGEIAAKF  111 (264)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCHHHCCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             99999999999999998299498125679989999769844437852379973487421235201677868999999864


Q ss_pred             HHHHHH---HHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHHH
Q ss_conf             874468---8999886424567775---44843002000115776578777557888776
Q gi|254781066|r   90 LAAGEE---KIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCA  143 (355)
Q Consensus        90 l~~G~~---rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~  143 (355)
                      +-|--+   ++|||+.+||+|-+.+   --.-||+|-|.|..++|.++..+..+.++..-
T Consensus       112 i~SyrdLPl~lyQ~~~~fR~E~r~r~GllR~REFlmkDahsf~~t~e~a~~~y~~~~~~Y  171 (264)
T cd00772         112 IKSWKDLPQHLNQIGNKFRDEIRPRFGFLRAREFIMKDGHSAHADAEEADEEFLNMLSAY  171 (264)
T ss_pred             CCCHHHCCHHHHHHHHHHHCCCCCCCCCHHHEEEEEEEEEECCCCHHHHHHHHHHHHHHH
T ss_conf             076655797787655786057885543323204341103532599999999999999999


No 54 
>PRK05425 asparagine synthetase AsnA; Provisional
Probab=98.51  E-value=1.5e-05  Score=52.36  Aligned_cols=267  Identities=14%  Similarity=0.145  Sum_probs=122.6

Q ss_pred             HHHHHHHHHHHHHHHH-----HCCCEEEECCCEECC-CCCCCCC----CCEEEECCCCCCCCCCCCCCCCHHHHHHHH-H
Q ss_conf             9999999999999999-----879889847821056-8985445----412410247886783200002858999989-8
Q gi|254781066|r   22 LLKRNMIQSSLREYFV-----ENQFIEIDSMSLQYS-PGNETHI----RAFSTELIIQDHIRKPLYLQTSPEFSCKKL-L   90 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~-----~~gF~EV~TPiL~~~-~~g~~~~----~~f~t~~~~~~~~~~~~yL~~SPql~lK~l-l   90 (355)
                      ++.....++.|+++|.     +-+.+.|..|+++.. .|---++    +|....  ..+.-+..+--.+|--=| ||. |
T Consensus         8 ~~etq~aI~~iK~~F~~~L~~~LnL~rVsAPLfv~~~sGlNDnLnG~ErpV~F~--vk~~~~~~~EiVhSLAKW-KR~aL   84 (327)
T PRK05425          8 FIETQQAISFVKNFFERQLAKKLNLIRVSAPLFVRVGSGLNDNLNGVEKPVSFK--VKDLPDATFEVVHSLAKW-KRLAL   84 (327)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCEEECCCEEECCCCCCCCCCCCEEEEEEEE--CCCCCCCEEEEEEEHHHH-HHHHH
T ss_conf             999999999999999999999709079557858737888667777726336986--568888706886106889-99999


Q ss_pred             H-HHHH---HHHHHHHHHC-CCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCC---E-ECCCCCCCCC
Q ss_conf             7-4468---8999886424-567775448430020001157765787775578887766641883---0-0022343324
Q gi|254781066|r   91 A-AGEE---KIFCFAHAWR-NGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQK---I-FSFQNVNCNP  161 (355)
Q Consensus        91 ~-~G~~---rvyqig~~FR-aE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~---~-~~~~~~~~~~  161 (355)
                      . -||.   -+|+=-.+.| +|+.|..|+-=.-|.|||..-...+-.++...+.++.+.+.+...   + ..|.... ..
T Consensus        85 ~~y~f~~geGlyTdMnAiR~DE~ldn~HSiyVDQWDWEkvI~~edRnl~~LK~tV~~Iy~~ik~tE~~v~~~yp~~~-~L  163 (327)
T PRK05425         85 KRYGFSAGEGLYTDMNAIRPDEDLDNTHSVYVDQWDWEKVIDKEERNLDFLKETVNKIYKAIKATELAVSEKYPLAK-FL  163 (327)
T ss_pred             HHCCCCCCCEECCCCCCCCCCCCCCCCEEEEECCCCHHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CC
T ss_conf             96599989532016762546755687601898400364536853267899999999999999999999999686311-48


Q ss_pred             CCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCC
Q ss_conf             67732078888656660876532345556232799999999768877876534789876643003622376754432576
Q gi|254781066|r  162 FSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRY  241 (355)
Q Consensus       162 ~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~y  241 (355)
                      -.+.-.++-.+....|...+           ...-....+++.                             +.|||++-
T Consensus       164 p~~I~FitsqeL~~~YP~Ls-----------~keRE~~i~ke~-----------------------------gAVFl~~I  203 (327)
T PRK05425        164 PEKITFIHSQELEDRYPDLT-----------PKEREDAIAKEY-----------------------------GAVFLIGI  203 (327)
T ss_pred             CCCCEEECHHHHHHHCCCCC-----------HHHHHHHHHHHH-----------------------------CCEEEEEC
T ss_conf             76116864899997675899-----------789999999983-----------------------------94999944


Q ss_pred             CHHHHHHC--CCCC----CCCCCCCCCEEEE------CCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHH
Q ss_conf             88886413--6787----7836330220223------6712256402106999999999999999972888530101899
Q gi|254781066|r  242 PAPESALA--NIYP----ADPRFTKRFELYA------CNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDF  309 (355)
Q Consensus       242 P~~~~pla--k~~~----~~~~va~rfdl~i------~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~f  309 (355)
                      =-   +|+  ++++    +-......=|+++      ...||++-+.+.+     +..+..|.......+....+    |
T Consensus       204 G~---~L~~g~~Hd~RApDYDDW~LNGDilvw~~vl~~a~ElSSMGIRVd-----~~sL~~QL~~~~~~dr~~l~----~  271 (327)
T PRK05425        204 GG---KLSDGKPHDGRAPDYDDWGLNGDILVWNPVLDRAFELSSMGIRVD-----EEALKKQLKLTGDEDRLELE----W  271 (327)
T ss_pred             CC---CCCCCCCCCCCCCCCCCCCCCCEEEEEEHHCCCEEEEECCEEEEC-----HHHHHHHHHHCCCHHHHCCH----H
T ss_conf             88---689989677779998676667549996023073246623547888-----99999999973973543498----9


Q ss_pred             HHHH-CC-CCCCCEEECCHHHHHHHHHCCCCHHHHCC
Q ss_conf             9986-18-89632453159999899815597131115
Q gi|254781066|r  310 LACL-TE-MPQSSGIAMGFDRLVMLVTGANNINEVIW  344 (355)
Q Consensus       310 l~al-~G-~PPhgG~glGidRLvm~l~g~~~Irdvi~  344 (355)
                      -.++ .| +|-+=|.|||=.||||+|++...|-||.+
T Consensus       272 H~~ll~~~LP~TIGGGIGQSRlcM~lL~KaHIGEVQ~  308 (327)
T PRK05425        272 HQALLNGELPLTIGGGIGQSRLCMLLLRKAHIGEVQA  308 (327)
T ss_pred             HHHHHCCCCCCCCCCCCCHHHHHHHHHCCCCCCCEEE
T ss_conf             9999749998431276239999999973252211576


No 55 
>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=5.1e-07  Score=60.99  Aligned_cols=99  Identities=28%  Similarity=0.267  Sum_probs=64.3

Q ss_pred             HHHHHHHHHHHHHHHH--HCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHH----H--HHHHHHH
Q ss_conf             9999999999999999--879889847821056898544541241024788678320000285899----9--9898744
Q gi|254781066|r   22 LLKRNMIQSSLREYFV--ENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFS----C--KKLLAAG   93 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~--~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~----l--K~ll~~G   93 (355)
                      ...+..|.++-|+.|-  +.+++|||||++.+.       -.|.|.....+..+..+||+  ||..    .  |.++-..
T Consensus        32 ~~LK~Ni~~~W~~~fv~~~~~~~~id~~ii~p~-------LmF~T~iG~~~~~~~~~yLR--PETAQGifvnFk~~~~~~  102 (254)
T cd00774          32 VELKNNIKSAWRKSFVLEEEDMLEIDSPIITPE-------LMFKTSIGPVESGGNLGYLR--PETAQGIFVNFKNLLEFN  102 (254)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCC-------CCEECCCCCCCCCCCCEEEC--HHHHHHHHHHHHHHHHHC
T ss_conf             999999999999998743798799541003663-------22001215655898603536--345347798789999964


Q ss_pred             HHH----HHHHHHHHCCCCCCCCCC---CCEEEECEEECCCCHH
Q ss_conf             688----999886424567775448---4300200011577657
Q gi|254781066|r   94 EEK----IFCFAHAWRNGEQGCLHQ---PEFTMLEWYRAHESYE  130 (355)
Q Consensus        94 ~~r----vyqig~~FRaE~~~~rHl---pEFtmLE~e~af~d~~  130 (355)
                      -.|    |-|||+|||||=+-++.+   -||||+|+|. |++-+
T Consensus       103 r~kLPFGiaQIGk~FRNEIsPr~~l~R~REF~q~EiE~-F~~P~  145 (254)
T cd00774         103 RRKLPFGVAQIGKSFRNEISPRNGLFRVREFTQAEIEF-FVDPE  145 (254)
T ss_pred             CCCCCEEEEEEEECCCCCCCCCCCCCCHHCHHHHEEEE-EECCC
T ss_conf             88888445654202267347776754000002125788-85798


No 56 
>cd00645 AsnA Asparagine synthetase (aspartate-ammonia ligase) (AsnA) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia.  AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II aminoacyl-tRNA synthetases. Ammonia-dependent AsnA is not homologous to the glutamine-dependent asparagine synthetase AsnB.
Probab=98.35  E-value=2.6e-05  Score=50.91  Aligned_cols=262  Identities=16%  Similarity=0.170  Sum_probs=122.1

Q ss_pred             HHHHHHHHHH-----HCCCEEEECCCEECC-CC-CCC---CCCCEEEECCCCCCCCCCCCCCCCHHHHHHHH-HH-HHHH
Q ss_conf             9999999999-----879889847821056-89-854---45412410247886783200002858999989-87-4468
Q gi|254781066|r   28 IQSSLREYFV-----ENQFIEIDSMSLQYS-PG-NET---HIRAFSTELIIQDHIRKPLYLQTSPEFSCKKL-LA-AGEE   95 (355)
Q Consensus        28 i~~~iR~ff~-----~~gF~EV~TPiL~~~-~~-g~~---~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~l-l~-~G~~   95 (355)
                      .|+.|+++|.     +-+.+.|..|+++.. .| .+-   .-+|.....  .+.-+..+=-.+|--=+ ||+ |. -||.
T Consensus         3 aI~~iK~~F~~~L~~~LnL~rVsAPLfv~~~sGlND~LnG~ErpV~F~i--k~~~~~~~EIVhSLAKW-KR~aL~~y~f~   79 (309)
T cd00645           3 AIKFIKDFFQDNLAKELNLIRVSAPLFVEKGSGLNDNLNGVEKPVSFKV--KALPDATLEVVHSLAKW-KRLALARYGFS   79 (309)
T ss_pred             HHHHHHHHHHHHHHHHHCCEEECCCEEECCCCCCCCCCCCEEECEEEEC--CCCCCCEEEEEEEHHHH-HHHHHHHCCCC
T ss_conf             4999999999999997392796666177079887768787460228635--78899726997135888-99999966998


Q ss_pred             ---HHHHHHHHHCC-CCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCE----ECCCCCCCCCCCCCCC
Q ss_conf             ---89998864245-677754484300200011577657877755788877666418830----0022343324677320
Q gi|254781066|r   96 ---KIFCFAHAWRN-GEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKI----FSFQNVNCNPFSEPEY  167 (355)
Q Consensus        96 ---rvyqig~~FRa-E~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~----~~~~~~~~~~~~~~~~  167 (355)
                         -+|+=-.+-|- |+.|..|+-=.-|-|||..-...+-.++...+.++.+.+.+...-    ..|.......-.+.-.
T Consensus        80 ~geGlytdMnAiR~DE~ldn~HSiyVDQWDWEkvI~~~dRnl~~Lk~tV~~Iy~~ik~tE~~v~~~yp~l~~~Lp~~I~F  159 (309)
T cd00645          80 LGEGLYTDMNAIRPDEDLDNIHSIYVDQWDWEKVISKGERNLETLKETVNKIYKAIKETELEVNEKYPQLEPILPEEITF  159 (309)
T ss_pred             CCCEECCCCCCCCCCCCCCCCCEEEECCCCHHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCEEE
T ss_conf             99430127762557755687612898500353427852258999999999999999999999999762034408886089


Q ss_pred             CCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHH
Q ss_conf             78888656660876532345556232799999999768877876534789876643003622376754432576888864
Q gi|254781066|r  168 ITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESA  247 (355)
Q Consensus       168 i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~p  247 (355)
                      ++-.+....|....           ...-....+++.                             +.|||++-=.   +
T Consensus       160 itsqeL~~~YP~Lt-----------~keRE~~i~ke~-----------------------------gaVFi~~IG~---~  196 (309)
T cd00645         160 ITSQELEDRYPDLT-----------PKEREDAICKEH-----------------------------GAVFIIGIGG---K  196 (309)
T ss_pred             ECHHHHHHHCCCCC-----------HHHHHHHHHHHH-----------------------------CCEEEEECCC---C
T ss_conf             62899997777999-----------789999999972-----------------------------9399994488---5


Q ss_pred             HC--CCCC----CCCCCCCCCEEEE------CCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-C
Q ss_conf             13--6787----7836330220223------67122564021069999999999999999728885301018999986-1
Q gi|254781066|r  248 LA--NIYP----ADPRFTKRFELYA------CNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-T  314 (355)
Q Consensus       248 la--k~~~----~~~~va~rfdl~i------~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~  314 (355)
                      |+  ++++    +-......=|+++      ...||++-+.+.+     +..+..|.......+....+    |-.++ .
T Consensus       197 L~~g~~Hd~RApDYDDW~LNGDilvw~~vl~~a~ElSSMGIRVd-----~~~L~~QL~~~~~~dr~~l~----~Hk~ll~  267 (309)
T cd00645         197 LSDGKKHDGRAPDYDDWTLNGDILVWNPVLQRAFELSSMGIRVD-----EESLQKQLKLAGDEDRLELP----FHKMLLN  267 (309)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEECHHCCCEEEEECCEEEEC-----HHHHHHHHHHCCCHHHHCCH----HHHHHHC
T ss_conf             78989566779998675447648997023073225634646888-----99999999975983543598----9999974


Q ss_pred             C-CCCCCEEECCHHHHHHHHHCCCCHHHHCC
Q ss_conf             8-89632453159999899815597131115
Q gi|254781066|r  315 E-MPQSSGIAMGFDRLVMLVTGANNINEVIW  344 (355)
Q Consensus       315 G-~PPhgG~glGidRLvm~l~g~~~Irdvi~  344 (355)
                      | +|-+=|.|||=.||||+|+....|-||.+
T Consensus       268 ~~LP~TIGGGIGQSRlcM~lL~KaHIGEVQ~  298 (309)
T cd00645         268 GELPQTIGGGIGQSRLCMFLLQKAHIGEVQA  298 (309)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCCCCCEEE
T ss_conf             9998452376039999999975373223675


No 57 
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=98.32  E-value=5.6e-06  Score=54.83  Aligned_cols=130  Identities=12%  Similarity=0.165  Sum_probs=80.3

Q ss_pred             CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCCCCCCCEEEECCCC-CCCCCCCCCC
Q ss_conf             9874788312615489999999999999999998798898478210568----9854454124102478-8678320000
Q gi|254781066|r    5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNETHIRAFSTELIIQ-DHIRKPLYLQ   79 (355)
Q Consensus         5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~~~~~~f~t~~~~~-~~~~~~~yL~   79 (355)
                      |-.++|+|.       =.++|..+...+|+-..+.||.||.||.+....    +|  |.+-+.-..+.. ..-++.+.|.
T Consensus       198 pG~~~wlP~-------G~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SG--H~~~Y~e~Mf~~~~~~~e~~~lK  268 (576)
T PRK12305        198 QGFPIWLEN-------GMIIKNAIRKFILELDRKYGFDEVLTPHFGEKKLYKTSG--HLDHYKDDMFKPLKIENEELIPR  268 (576)
T ss_pred             CCCEEECCC-------HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCC--CHHHHHHHCCCCEECCCCEEEEC
T ss_conf             876467476-------789999999999999998699898464214288997666--46556642573063156416535


Q ss_pred             -----CCHHHHHHHHHHHHHH---HHHHHHHHHCCCCCCCC----CCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             -----2858999989874468---89998864245677754----484300200011577657877755788877666
Q gi|254781066|r   80 -----TSPEFSCKKLLAAGEE---KIFCFAHAWRNGEQGCL----HQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE  145 (355)
Q Consensus        80 -----~SPql~lK~ll~~G~~---rvyqig~~FRaE~~~~r----HlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~  145 (355)
                           ..-++|. .-.-|.-+   |++++|.|||+|-++.-    -.-.|||=|.. .|.+.+++.+.+.++++.+..
T Consensus       269 PMNCP~H~~if~-~~~rSYRdLPlR~aEfg~~~R~E~SG~L~GL~RvR~FtqDDAH-IFct~dQi~~Ei~~~l~~i~~  344 (576)
T PRK12305        269 PMTCPHHIILYS-NELRSYRDLPIRLSEQSRLYRYEKSGALTGLERVRAMDLTEGH-IFVRKDQIESEVKHLFKMIQE  344 (576)
T ss_pred             CCCCHHHHHHHH-CCCCCHHHCCHHHHCCCCEECCCCCCCCCCCCCCCCCCCCCCC-EEECHHHHHHHHHHHHHHHHH
T ss_conf             778632677764-2775444324220004435447888655575546688768712-120899999999999999999


No 58 
>PRK03772 threonyl-tRNA synthetase; Validated
Probab=98.21  E-value=1.9e-05  Score=51.70  Aligned_cols=130  Identities=14%  Similarity=0.189  Sum_probs=79.3

Q ss_pred             CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC----CCCCCCCCCEEEECCCCCCCCCCCCCCC
Q ss_conf             987478831261548999999999999999999879889847821056----8985445412410247886783200002
Q gi|254781066|r    5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS----PGNETHIRAFSTELIIQDHIRKPLYLQT   80 (355)
Q Consensus         5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~----~~g~~~~~~f~t~~~~~~~~~~~~yL~~   80 (355)
                      |-.++|+|.-       .++|..+...+|+-..++||.||.||.+...    .+|  |.+-+.-..+....-+++++|..
T Consensus       261 pG~~fwlP~G-------~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SG--H~~~Y~e~Mf~~~~e~~ey~lKP  331 (642)
T PRK03772        261 PGMVFWHNDG-------WTIFRELEVFVRSKLKEYQYQEVKGPFMMDRVLWEKTG--HWDNYADAMFTTSSENREYAIKP  331 (642)
T ss_pred             CCCEEECCCH-------HHHHHHHHHHHHHHHHHCCCEEEECCHHCCHHHHHHCC--HHHHHHCCCCCCCCCHHHHCCCC
T ss_conf             8763665858-------89999999999999998698598554321377887344--47664103422342014430467


Q ss_pred             -----CHHHHHHHHHHHHHH---HHHHHHHHHCCCCCCC----CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             -----858999989874468---8999886424567775----4484300200011577657877755788877666
Q gi|254781066|r   81 -----SPEFSCKKLLAAGEE---KIFCFAHAWRNGEQGC----LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE  145 (355)
Q Consensus        81 -----SPql~lK~ll~~G~~---rvyqig~~FRaE~~~~----rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~  145 (355)
                           .-++|+ .-.-|.-+   |++++|.|+|+|-++.    .-.-.|||=|.. .|...+++-+.+.++++.+.+
T Consensus       332 MNCP~H~~iy~-~~~rSYRdLPlR~aEfg~~~R~E~SG~L~GL~RVR~FtqdDaH-IFC~~dQi~~Ei~~~l~~~~~  406 (642)
T PRK03772        332 MNCPGHVQIFN-QGLKSYRDLPLRMAEFGSCHRNEPSGSLHGLMRVRGFTQDDAH-IFCTEEQIRDEVNSCIKMVYD  406 (642)
T ss_pred             CCCHHHHHHHH-CCCCCHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCE-EECCHHHHHHHHHHHHHHHHH
T ss_conf             78734889986-1664344365455541134316666553474568899878843-553789999999999999999


No 59 
>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed
Probab=98.18  E-value=9.5e-07  Score=59.42  Aligned_cols=48  Identities=8%  Similarity=0.089  Sum_probs=30.6

Q ss_pred             HHHHHHHHHCCC-CCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHHHH
Q ss_conf             899988642456-7775448430020001157--76578777557888776
Q gi|254781066|r   96 KIFCFAHAWRNG-EQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIRCA  143 (355)
Q Consensus        96 rvyqig~~FRaE-~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~~~  143 (355)
                      |+|.|.+|||.| ..|..||+||.+.+.=.+.  +++++.....+.+++..
T Consensus       208 klFSIDRcFRrEq~eD~~hL~~yhsascvv~~edVn~d~gkav~~~lL~~f  258 (527)
T PRK06253        208 KLFSIDRCFRREQKEDASRLMTYHSASCVVAGEDVTVDDGKAVAEGLLSQF  258 (527)
T ss_pred             EEEEEEHEEECHHHCCHHHHHHHHEEEEEEECCCCCHHHHHHHHHHHHHHH
T ss_conf             687410102200002455634544322699759866777799999999970


No 60 
>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=98.14  E-value=3.3e-06  Score=56.24  Aligned_cols=122  Identities=15%  Similarity=0.202  Sum_probs=70.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEEEECCCCCCCCCCCCCCCCHH-----HHHHHHHHH-
Q ss_conf             999999999999999998798898478210568--985445412410247886783200002858-----999989874-
Q gi|254781066|r   21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFSTELIIQDHIRKPLYLQTSPE-----FSCKKLLAA-   92 (355)
Q Consensus        21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~t~~~~~~~~~~~~yL~~SPq-----l~lK~ll~~-   92 (355)
                      ..+....+++.+++++.++||.||.||.|....  .|..+..-|.-..+...  +.+.||.-.-|     +|..+.+.. 
T Consensus        51 ga~Le~AL~~f~~d~~~~~Gy~eV~tP~iv~~~~~~~sG~~~~~~e~~y~i~--~~~~~Li~tae~~l~~~~~~~~~~~~  128 (297)
T cd00770          51 GALLERALINFALDFLTKRGFTPVIPPFLVRKEVMEGTGQLPKFDEQLYKVE--GEDLYLIATAEVPLAALHRDEILEEE  128 (297)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHCCCCCCHHHHHCCC--CHHHHHHHCCCCCEEEEEEEEECCHH
T ss_conf             9999999999999999987998998853013899854357876356521035--50555544056662234420031775


Q ss_pred             HH-HHHHHHHHHHCCC-CC---CC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             46-8899988642456-77---75---4484300200011577657877755788877666
Q gi|254781066|r   93 GE-EKIFCFAHAWRNG-EQ---GC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE  145 (355)
Q Consensus        93 G~-~rvyqig~~FRaE-~~---~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~  145 (355)
                      -+ =|++.+++|||+| ++   ++   ...-.|+++|.. ++.+-++..+..|+|+..+.+
T Consensus       129 dLPlr~~~~s~cfR~Eags~G~d~~GL~RvhqF~kvE~~-~~c~pe~s~~~~e~~~~~~e~  188 (297)
T cd00770         129 ELPLKYAGYSPCFRKEAGSAGRDTRGLFRVHQFEKVEQF-VFTKPEESWEELEELISNAEE  188 (297)
T ss_pred             HCCCCEEECCCHHHHCCCCCCCCCCCEEEEEECCEEEEE-EECCHHHHHHHHHHHHHHHHH
T ss_conf             588650224634132037777555545788721100377-616878899999999999999


No 61 
>PRK12304 thrS threonyl-tRNA synthetase; Reviewed
Probab=98.10  E-value=4.9e-05  Score=49.26  Aligned_cols=132  Identities=16%  Similarity=0.151  Sum_probs=80.2

Q ss_pred             CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCCCCCCC-----EEEECCCCCCCCCC
Q ss_conf             9874788312615489999999999999999998798898478210568----98544541-----24102478867832
Q gi|254781066|r    5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNETHIRA-----FSTELIIQDHIRKP   75 (355)
Q Consensus         5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~~~~~~-----f~t~~~~~~~~~~~   75 (355)
                      |-.++|+|.=       .++|..+...+|+-..+.||.||.||.+....    +|  |.+-     |.+......+.=+|
T Consensus       229 ~G~~~wlP~G-------~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SG--H~~~Y~e~Mf~~~~d~~~y~lKP  299 (604)
T PRK12304        229 AGLPIWLPKG-------ARLRSKLEHLLYKAHRLRGYEPVRGPEILKSDVWKISG--HYANYKENMYFTTIDEQEYGIKP  299 (604)
T ss_pred             CCCEEECCCH-------HHHHHHHHHHHHHHHHHCCCEEECCCCCCCHHHHHCCC--HHHHHCCCCCEEECCCCEEECCC
T ss_conf             8753683775-------49999999999999998299680386545588873055--15321057644505774330367


Q ss_pred             CCCCCCHHHHHHHHHHHHHH---HHHHHHHHHCCCCCCCC----CCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             00002858999989874468---89998864245677754----48430020001157765787775578887766641
Q gi|254781066|r   76 LYLQTSPEFSCKKLLAAGEE---KIFCFAHAWRNGEQGCL----HQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA  147 (355)
Q Consensus        76 ~yL~~SPql~lK~ll~~G~~---rvyqig~~FRaE~~~~r----HlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~  147 (355)
                      +--+..-++|+ .-.-|.-+   |++++|.|||+|.++.-    -.-.|||=|.. .|...+++-+.+.++++.+.+..
T Consensus       300 MNCP~H~~if~-~~~rSYRdLPlR~aEfg~~hR~E~SG~L~GL~RvR~FtqDDaH-IFc~~dQi~~Ei~~~l~~~~~vy  376 (604)
T PRK12304        300 MNCVGHIKVYQ-SDLRSYRDLPLKFFEYGVVHRHEKSGVLHGLFRVREFTQDDAH-IFCMPSQIKEEVLEILDFVDKIM  376 (604)
T ss_pred             CCCHHHHHHHH-CCCCCHHHCCHHHHHCCCEECCCCCCCCCCCCCCCCCCCCCCE-EECCHHHHHHHHHHHHHHHHHHH
T ss_conf             79574999986-2774444355554543532026777663464557789778844-65489999999999999999999


No 62 
>PTZ00213 asparagine synthetase A; Provisional
Probab=98.08  E-value=9.8e-05  Score=47.50  Aligned_cols=294  Identities=12%  Similarity=0.125  Sum_probs=131.9

Q ss_pred             HHHHHHHHHHHHHHHH-----HCCCEEEECCCEECCCCC--CC---CCCCEEEECCCCCCCCCCCCCCCCHHHHHHHH-H
Q ss_conf             9999999999999999-----879889847821056898--54---45412410247886783200002858999989-8
Q gi|254781066|r   22 LLKRNMIQSSLREYFV-----ENQFIEIDSMSLQYSPGN--ET---HIRAFSTELIIQDHIRKPLYLQTSPEFSCKKL-L   90 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~-----~~gF~EV~TPiL~~~~~g--~~---~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~l-l   90 (355)
                      ++...+.|+.|+++|.     +-+.++|..|+++....|  +-   .-+|...+...  --+..+=-.+|--=| ||. |
T Consensus         8 ~~~tq~aI~~iK~~F~~~L~~~LnL~rVsAPLfv~~~sGlND~LnG~ErpV~f~ik~--~p~~~~EIVhSLAKW-KR~aL   84 (350)
T PTZ00213          8 YIDLQEQILTVKQIFSEALAKELNLVEVEAPILARVGDGTQDNLSGVEKAVQVHVKE--IPDAKFEVVHSLAKW-KRQTL   84 (350)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCEEECCCEEEECCCCCCCCCCCEECCEEEECCC--CCCCCEEEEEEHHHH-HHHHH
T ss_conf             999999999999999999999739179645638707988766878725131654477--899715997133888-99999


Q ss_pred             H-HHH---HHHHHHHHHHCCC-CCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCC---E-ECCCCCCCCC
Q ss_conf             7-446---8899988642456-7775448430020001157765787775578887766641883---0-0022343324
Q gi|254781066|r   91 A-AGE---EKIFCFAHAWRNG-EQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQK---I-FSFQNVNCNP  161 (355)
Q Consensus        91 ~-~G~---~rvyqig~~FRaE-~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~---~-~~~~~~~~~~  161 (355)
                      . -||   +-+|+=-.+-|.+ +.|..|+-=.-|-|||..-...+-.++...+.|+.+.+.+...   + ..|. .....
T Consensus        85 ~~y~f~~geGlyTdMnAIR~De~lDn~HSiYVDQWDWEkvI~~e~R~l~~LK~tV~~Iy~~ik~tE~~v~~~y~-~~~~L  163 (350)
T PTZ00213         85 GNHKFPVGQGIYTHMKALRVEETLDNIHSVYVDQWDWERVMAPADRNLEFLKATVRSLYAAIRQTEEALCSKYD-IDPIL  163 (350)
T ss_pred             HHCCCCCCCEEEECCCCCCCCCCCCCCCCEEECCCCHHCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCC
T ss_conf             96599899555424440257655687631898520420006842268999999999999999999999998668-65668


Q ss_pred             CCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCC----CHHHHHHHHHHCEECCCCCCCC-CC
Q ss_conf             677320788886566608765323455562327999999997688778765----3478987664300362237675-44
Q gi|254781066|r  162 FSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDD----TWSDIFSRILIEKIEPNLGINC-CT  236 (355)
Q Consensus       162 ~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~l~~~~ie~~l~~~~-pv  236 (355)
                      -.+.-.++-.|....|...           +...-....+++.|.-+-.+.    .-|+..+.     =.|.+.... |+
T Consensus       164 P~~I~FitsqeL~~~YP~L-----------t~keRE~~i~ke~gAVFl~gIG~~L~~G~~HD~-----RAPDYDDW~t~~  227 (350)
T PTZ00213        164 PESIQFVHAEHLLKRYPEL-----------DPKEREREIVKKYGAVFLIGIGCKLSSGDPHDA-----RAPDYDDWSSPV  227 (350)
T ss_pred             CCCCEEECHHHHHHHCCCC-----------CHHHHHHHHHHHHCCEEEEECCCCCCCCCCCCC-----CCCCCCCCCCCC
T ss_conf             8752686289999777799-----------878899999998395999943786789895777-----799876454655


Q ss_pred             --CCCCCCHHHHHHCCCCCCCCCCCCCCEEEE------CCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHH
Q ss_conf             --325768888641367877836330220223------671225640210699999999999999997288853010189
Q gi|254781066|r  237 --ILDRYPAPESALANIYPADPRFTKRFELYA------CNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDED  308 (355)
Q Consensus       237 --fi~~yP~~~~plak~~~~~~~va~rfdl~i------~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~  308 (355)
                        --..||..-.+--..|.-+.--...=|+++      +..||.+-+.+.+     +..+..|.......+....+    
T Consensus       228 ~~~~~g~~~~~~~~~~~~~~~~~~GLNGDIlvw~pvL~~a~ElSSMGIRVd-----~~sL~~QL~~~~~~dr~~l~----  298 (350)
T PTZ00213        228 SASKIGFPTADDEKPTMNSLMSLQGLNGDILVYNPVLDDVLELSSMGIRVD-----AEALRRQLELTGNEDRLKCV----  298 (350)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHCCCEEEEECCEEEEC-----HHHHHHHHHHCCCHHHHCCH----
T ss_conf             444344444333333332222345666618996113075125634647888-----99999999875983554498----


Q ss_pred             HHHHH-CC-CCCCCEEECCHHHHHHHHHCCCCHHHHCC
Q ss_conf             99986-18-89632453159999899815597131115
Q gi|254781066|r  309 FLACL-TE-MPQSSGIAMGFDRLVMLVTGANNINEVIW  344 (355)
Q Consensus       309 fl~al-~G-~PPhgG~glGidRLvm~l~g~~~Irdvi~  344 (355)
                      |-.++ .| +|-+=|.|||--||||+|+....|-||.+
T Consensus       299 ~Hk~ll~geLP~TIGGGIGQSRlcM~lL~KaHIGEVQa  336 (350)
T PTZ00213        299 WHQCLLNGEFPQTIGGGIGQSRMVMFMLRKKHIGEVQC  336 (350)
T ss_pred             HHHHHHCCCCCCCCCCCCCHHHHHHHHHCCCCCCCEEE
T ss_conf             99999759998432276219999999973262222664


No 63 
>PRK04483 threonyl-tRNA synthetase; Validated
Probab=98.07  E-value=2.5e-05  Score=51.05  Aligned_cols=133  Identities=11%  Similarity=0.154  Sum_probs=78.8

Q ss_pred             CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCCCCCCCEEEECCCCCCCCCCCCCCC
Q ss_conf             9874788312615489999999999999999998798898478210568----985445412410247886783200002
Q gi|254781066|r    5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNETHIRAFSTELIIQDHIRKPLYLQT   80 (355)
Q Consensus         5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~~~~~~f~t~~~~~~~~~~~~yL~~   80 (355)
                      |-.++|+|.=       .++|..+...+|+-..++||.||.||.+....    +|  |.+-+.-..+....-++.+.|..
T Consensus       261 pG~~~wlP~G-------~~i~~~le~~~r~~~~~~Gy~eV~tP~i~~~~Lw~~SG--H~~~Y~e~Mf~~~~~~~~~~lKP  331 (634)
T PRK04483        261 PGLVFWHPKG-------WSLWQVVEQYMRKVYRDSGYGEVRCPQILDVSLWQKSG--HWDNYQDAMFFTESEKRTYAVKP  331 (634)
T ss_pred             CCCEEECCCH-------HHHHHHHHHHHHHHHHHCCCEEEECCEECCHHHHHHCC--CHHHHHHCCCEECCCCCEEEECC
T ss_conf             8643881668-------99999999999999998299599886251377876256--16455303713425540355157


Q ss_pred             -----CHHHHHHHHHHHHHH---HHHHHHHHHCCCCCCCC----CCCCEEEECEEECCCCHHHHHHHHHHHHH---HHHH
Q ss_conf             -----858999989874468---89998864245677754----48430020001157765787775578887---7666
Q gi|254781066|r   81 -----SPEFSCKKLLAAGEE---KIFCFAHAWRNGEQGCL----HQPEFTMLEWYRAHESYEQLMKDCMNIIR---CAAE  145 (355)
Q Consensus        81 -----SPql~lK~ll~~G~~---rvyqig~~FRaE~~~~r----HlpEFtmLE~e~af~d~~dlm~~~E~li~---~~~~  145 (355)
                           --++|. .-.-|.-+   |++++|.|||+|-++.-    -.-.|||=|.. .|...+++-+.+.++++   .+.+
T Consensus       332 MNCP~H~~if~-~~~rSYRdLPlR~aE~g~~~R~E~SG~L~GL~RvR~FtqdDaH-IFc~~dQi~~Ei~~~l~~~~~vy~  409 (634)
T PRK04483        332 MNCPGHVQVFN-QGLHSYRDLPIRYGEFGACHRNEPSGALHGILRVRGFTQDDGH-VFCLESQIEAEVTAFHQQALAVYT  409 (634)
T ss_pred             CCCHHHHHHHH-CCCCCHHHCCHHHHHCCCEEECCCCCCCCCCCCCCCCCCCCCE-EECCHHHHHHHHHHHHHHHHHHHH
T ss_conf             68564879987-1774444343665543302205677654574568899889833-563899999999999999999998


Q ss_pred             HHC
Q ss_conf             418
Q gi|254781066|r  146 VAN  148 (355)
Q Consensus       146 ~~~  148 (355)
                      .++
T Consensus       410 ~fG  412 (634)
T PRK04483        410 AFG  412 (634)
T ss_pred             HCC
T ss_conf             639


No 64 
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=98.04  E-value=4.3e-05  Score=49.61  Aligned_cols=130  Identities=15%  Similarity=0.207  Sum_probs=79.4

Q ss_pred             CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCCCCCCCEEEECCCCCCC-CCCCCCC
Q ss_conf             9874788312615489999999999999999998798898478210568----9854454124102478867-8320000
Q gi|254781066|r    5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNETHIRAFSTELIIQDHI-RKPLYLQ   79 (355)
Q Consensus         5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~~~~~~f~t~~~~~~~~-~~~~yL~   79 (355)
                      |-.++|+|.=       .++|..+...+|+-..++||-||.||.+....    +|  |.+-+.-..+..... +..++|.
T Consensus       258 pGl~~w~P~G-------~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SG--Hw~~Y~e~Mf~~~~~~~~~~~lK  328 (639)
T PRK00413        258 PGLPFWHPKG-------WIIRNELEDYMRRRHLKAGYQEVNTPHILDRSLWETSG--HWDHYRENMFPTMSDDGEDYALK  328 (639)
T ss_pred             CCCEEECCCH-------HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCC--CHHHHCCCCCCCEECCCCEEEEC
T ss_conf             8764663768-------99999999999999998698598364134688996547--42232254223240152103204


Q ss_pred             -----CCHHHHHHHHHHHHHH---HHHHHHHHHCCCCCCCC----CCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             -----2858999989874468---89998864245677754----484300200011577657877755788877666
Q gi|254781066|r   80 -----TSPEFSCKKLLAAGEE---KIFCFAHAWRNGEQGCL----HQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE  145 (355)
Q Consensus        80 -----~SPql~lK~ll~~G~~---rvyqig~~FRaE~~~~r----HlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~  145 (355)
                           .--++|. .-.-|.-+   |++++|.|+|+|.++.-    -.-.|||=|.. .|...+++.+.+.++++.+.+
T Consensus       329 PMNCP~H~~if~-~~~~SYRdLPlR~aEfg~~~R~E~SG~L~GL~RvR~FtqdDaH-IFc~~dQi~~Ei~~~l~~~~~  404 (639)
T PRK00413        329 PMNCPGHILIFK-SGLRSYRELPLRLAEFGTVHRYEKSGALHGLMRVRGFTQDDAH-IFCTPEQIKDELLSVLDLILS  404 (639)
T ss_pred             CCCCCCHHHHHH-CCCCCHHHCCHHHHHHHHHHCCCCCCCCCCEEEEEEEECCCCE-EECCHHHHHHHHHHHHHHHHH
T ss_conf             668700335644-3553555475566641132056778744564233000015841-324789999999999999999


No 65 
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=98.00  E-value=8.8e-05  Score=47.76  Aligned_cols=130  Identities=16%  Similarity=0.186  Sum_probs=77.2

Q ss_pred             CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCCCCCCCEEEECCCCCCCCCCCCCCC
Q ss_conf             9874788312615489999999999999999998798898478210568----985445412410247886783200002
Q gi|254781066|r    5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNETHIRAFSTELIIQDHIRKPLYLQT   80 (355)
Q Consensus         5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~~~~~~f~t~~~~~~~~~~~~yL~~   80 (355)
                      |-.++|+|.       =.++|..+...+|+-..++||.||-||.+....    +|  |.+-+.-..+...--++.+.|..
T Consensus       264 pG~~fwlP~-------G~~i~~~le~~~r~~~~~~GY~eV~TP~i~~~~Lw~~SG--H~~~Y~e~Mf~~~~d~~~~~lKP  334 (639)
T PRK12444        264 PGMPFYLPK-------GQIIRNELEAFLREIQKEYNYQEVRTPFMMNQELWERSG--HWGHYKDNMYFSEVDNKSFALKP  334 (639)
T ss_pred             CCCEEEECC-------HHHHHHHHHHHHHHHHHHCCCEEECCCEEEHHHHHHHCC--HHHHHHHCCCCCCCCCCEEECCC
T ss_conf             974478467-------869999999999999998398782286662156876166--04333302755454540331267


Q ss_pred             -----CHHHHHHHHHHHHHH---HHHHHHHHHCCCCCCCC----CCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             -----858999989874468---89998864245677754----484300200011577657877755788877666
Q gi|254781066|r   81 -----SPEFSCKKLLAAGEE---KIFCFAHAWRNGEQGCL----HQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE  145 (355)
Q Consensus        81 -----SPql~lK~ll~~G~~---rvyqig~~FRaE~~~~r----HlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~  145 (355)
                           --+.|. .-.-|.-+   |++++|.|||+|-++..    -.-.|||=|.. .|.+.+++-+.+.+++..+..
T Consensus       335 MNCP~H~~if~-~~~rSYRdLPlR~aEfg~vhR~E~SG~L~GL~RVR~FtqDDAH-IFct~dQi~~Ei~~~~~~~~~  409 (639)
T PRK12444        335 MNCPGHMLMFK-NKLHSYRELPIRMCEFGQVHRHEFSGALNGLLRVRTFCQDDAH-LFVTPEQIEDEIKSVMAQIDY  409 (639)
T ss_pred             CCCHHHHHHHH-CCCCCHHHCCHHHHHCCCEECCCCCCCCCCCCCCCCCCCCCCE-EECCHHHHHHHHHHHHHHHHH
T ss_conf             68588999986-0562144365222433646337787664576778899879824-653889999999999999999


No 66 
>COG0442 ProS Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=97.92  E-value=2.8e-05  Score=50.68  Aligned_cols=123  Identities=20%  Similarity=0.237  Sum_probs=82.6

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCEECCC---CCCCCCCCEEEECCC-CCCCCCCCCCCCCHHHHH----HHHHHHH
Q ss_conf             99999999999999998798898478210568---985445412410247-886783200002858999----9898744
Q gi|254781066|r   22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSP---GNETHIRAFSTELII-QDHIRKPLYLQTSPEFSC----KKLLAAG   93 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~---~g~~~~~~f~t~~~~-~~~~~~~~yL~~SPql~l----K~ll~~G   93 (355)
                      ++.+.+|.+-||+.|++-|..||-=|+|+++-   +.+ +.+-|.-+++. .+-.+.++.|+...|--+    +.-+-|.
T Consensus        47 ~rv~~kI~~iir~em~~~G~~Evl~P~L~p~eLwkEs~-r~~~f~~El~~v~drg~~~l~L~PTsEe~it~~~~~~i~SY  125 (500)
T COG0442          47 LRVLEKIENIIREEMDKIGAQEVLFPTLIPAELWKESG-RWEGFGPELFRVKDRGDRPLALRPTSEEVITDMFRKWIRSY  125 (500)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECHHCCHHHHHHHHC-HHHCCCHHHEEEECCCCCEEEECCCCHHHHHHHHHHHHHHH
T ss_conf             99999999999999986085088311058789998748-56303644489971699634357886899999999986556


Q ss_pred             HH---HHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             68---8999886424567775---4484300200011577657877755788877666
Q gi|254781066|r   94 EE---KIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE  145 (355)
Q Consensus        94 ~~---rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~  145 (355)
                      -+   ++|||+..||+|-.-|   --.-||+|=|.|.+++|.+++.+..+.|...-.+
T Consensus       126 kdLPl~lYQi~~kfRdE~rpr~gllR~REF~mkdaySfh~~~e~a~~~y~~~~~~Y~~  183 (500)
T COG0442         126 KDLPLKLYQIQSKFRDEKRPRFGLLRGREFLMKDAYSFHADEEDAEETYEKMLDAYSR  183 (500)
T ss_pred             HHCCCCEEEEEEEEECCCCCCCCCCCHHEEEECCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             5188121013458843346887730002033011121028989999999999999999


No 67 
>TIGR00469 pheS_mito phenylalanyl-tRNA synthetase; InterPro: IPR004530   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 mitochondrial phenylalanyl-tRNA synthetases. Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases.; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=97.88  E-value=7.3e-05  Score=48.27  Aligned_cols=129  Identities=16%  Similarity=0.197  Sum_probs=67.0

Q ss_pred             CCCHHHCCCH-HHHHHHHHHHHHHHHHHHH-HCCCE-----EEECCCEECCCCCCCCCCCEEEECCCCC----------C
Q ss_conf             7883126154-8999999999999999999-87988-----9847821056898544541241024788----------6
Q gi|254781066|r    9 WWNRDFHYRR-RPFLLKRNMIQSSLREYFV-ENQFI-----EIDSMSLQYSPGNETHIRAFSTELIIQD----------H   71 (355)
Q Consensus         9 ~~~~~~~~r~-R~~l~~Rs~i~~~iR~ff~-~~gF~-----EV~TPiL~~~~~g~~~~~~f~t~~~~~~----------~   71 (355)
                      +-+++.||+. .|+=++|..|...+-.--. .+|==     .=--|+.+....    .+..   .++.+          |
T Consensus        31 ~~~~~~HL~~~HP~~I~R~~I~~~l~~~~~nqrGnP~F~~y~~~~PVVT~~~N----FD~L---~~P~DH~~R~KSD~YY  103 (460)
T TIGR00469        31 LVDASKHLKEDHPLSILRDLIVKKLYSVDRNQRGNPLFKVYDNFKPVVTVQEN----FDSL---LIPKDHVSRSKSDTYY  103 (460)
T ss_pred             HHCCHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEHCCCCCCEEEECCC----CCCC---CCCCCCCCCCCCCEEE
T ss_conf             62100011235764677889998763221035688511110057974732013----3112---7888778875454133


Q ss_pred             CCCCCCCC---CCHHHHHHHHHHHHHHH-------HHHHHHHHCCCCCCCCCCCCEEEECEEECC-CCHHHH-------H
Q ss_conf             78320000---28589999898744688-------999886424567775448430020001157-765787-------7
Q gi|254781066|r   72 IRKPLYLQ---TSPEFSCKKLLAAGEEK-------IFCFAHAWRNGEQGCLHQPEFTMLEWYRAH-ESYEQL-------M  133 (355)
Q Consensus        72 ~~~~~yL~---~SPql~lK~ll~~G~~r-------vyqig~~FRaE~~~~rHlpEFtmLE~e~af-~d~~dl-------m  133 (355)
                      .++.--|+   ++.|+-   |+.+|.+.       --=.|-+||-.++|.+|=|=|-|+|--..+ .+-.++       +
T Consensus       104 IN~~HLLR~HT~AH~~E---~~~~~~~~sdniksGFL~~~~VYRRDEID~THYPVFHQ~~Ga~~~~~TK~~~~~~~P~y~  180 (460)
T TIGR00469       104 INETHLLRAHTSAHELE---LISKILDDSDNIKSGFLVVADVYRRDEIDKTHYPVFHQADGAAVRKVTKDDLFVKEPGYL  180 (460)
T ss_pred             ECCCHHHHHCCCHHHHH---HHHCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEECCCCCEEHHHHHHHHCCCCCCHH
T ss_conf             03300333302134545---442223532111212068743441234568788701426762121002344304687401


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             75578887766641
Q gi|254781066|r  134 KDCMNIIRCAAEVA  147 (355)
Q Consensus       134 ~~~E~li~~~~~~~  147 (355)
                      +.+++-++.+....
T Consensus       181 E~~~E~~~~~~~~~  194 (460)
T TIGR00469       181 EKIREDIRQVLALL  194 (460)
T ss_pred             HHHHHHHHHHHHCC
T ss_conf             24566678885100


No 68 
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=97.84  E-value=3.8e-05  Score=49.94  Aligned_cols=123  Identities=13%  Similarity=0.167  Sum_probs=75.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEECCCEECC--CCCCCCCCCEEEECCCCCCCCCCCCCCCC--H---HHHHHHHHHHHHH
Q ss_conf             999999999999999879889847821056--89854454124102478867832000028--5---8999989874468
Q gi|254781066|r   23 LKRNMIQSSLREYFVENQFIEIDSMSLQYS--PGNETHIRAFSTELIIQDHIRKPLYLQTS--P---EFSCKKLLAAGEE   95 (355)
Q Consensus        23 ~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~--~~g~~~~~~f~t~~~~~~~~~~~~yL~~S--P---ql~lK~ll~~G~~   95 (355)
                      ..|+.+.+.+|+-..+.|+.||.||+|-..  ..-..|++-|.-..+....-++.+.|+-.  |   +.|+ .-+.|.-+
T Consensus       228 ~i~~lle~Yv~~~~~~~G~~eV~TP~m~d~~~~~~sgH~~~f~e~my~~~~d~~~~~LrpmnCpgh~~i~~-~~~~SYRd  306 (613)
T PRK03991        228 LMKDLLEDYVYNLVKELGAMPVETPNMYDLSHPAIREHADKFGERQYRVKSDKKDLMLRFAACFGQFAMLK-DMTISYKN  306 (613)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEECCCEEECCCCHHHHHHHHHCCCCEEEECCCHHHCCCCCCCCCCEEEEC-CCCCCHHH
T ss_conf             99999999999999863966845761640554025568876111342563276332304457863123510-24457432


Q ss_pred             ---HHHHHHHH-HCCCCCCC----CCCCCEEEECEEECCC-CHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---89998864-24567775----4484300200011577-65787775578887766641
Q gi|254781066|r   96 ---KIFCFAHA-WRNGEQGC----LHQPEFTMLEWYRAHE-SYEQLMKDCMNIIRCAAEVA  147 (355)
Q Consensus        96 ---rvyqig~~-FRaE~~~~----rHlpEFtmLE~e~af~-d~~dlm~~~E~li~~~~~~~  147 (355)
                         |+|++|.| ||+|.++.    .-+-.|||=|.= .|+ +.+++++.+.+++..+.+..
T Consensus       307 LPlRl~E~g~~syR~E~SG~L~GL~RVR~FTqdDaH-IFC~~~dQi~~E~~~~~~li~~v~  366 (613)
T PRK03991        307 LPLKMYELSDYSFRLEQRGELVGLKRLRAFTMPDMH-TLCKDMDEAMEEFEKQHKLILETG  366 (613)
T ss_pred             CCHHHHHHCCCEEECCCCCCEECEEEEECCCCCCCE-ECCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             646776522420212567744440133235668611-316877899999999999999999


No 69 
>COG0441 ThrS Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=97.78  E-value=7.2e-05  Score=48.27  Aligned_cols=114  Identities=18%  Similarity=0.240  Sum_probs=72.5

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEECCCEECCCC--CCCCCCCEEEECCCCCCCCCCCCCCCCH--HHHHHHHHHHH-----
Q ss_conf             99999999999999987988984782105689--8544541241024788678320000285--89999898744-----
Q gi|254781066|r   23 LKRNMIQSSLREYFVENQFIEIDSMSLQYSPG--NETHIRAFSTELIIQDHIRKPLYLQTSP--EFSCKKLLAAG-----   93 (355)
Q Consensus        23 ~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~--g~~~~~~f~t~~~~~~~~~~~~yL~~SP--ql~lK~ll~~G-----   93 (355)
                      +.|+.+.+.+|.-..+.||-||.||+|....-  ...|.+          .+...+|+..|.  ++.+|.+=+-|     
T Consensus       221 ~ir~~le~y~~~~~~~~Gy~~V~TP~~~~~~l~~~SGH~~----------~y~e~mf~~~~~~~~~~lKpmNCpgh~~if  290 (589)
T COG0441         221 TIRNLLEDYVRTKLRSYGYQEVKTPVLADLELWELSGHWD----------NYKEDMFLTESDDREYALKPMNCPGHILIF  290 (589)
T ss_pred             CHHHHHHHHHHHHHHHCCCEEECCCEEEECCCCHHCCCHH----------HCCCCCEEECCCCHHHEEEECCCHHHHHHH
T ss_conf             6999999999989875585271287363000010112045----------513660662137723306410787689998


Q ss_pred             ------H----HHHHHHHHHHCCCCCCC----CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             ------6----88999886424567775----448430020001157765787775578887766641
Q gi|254781066|r   94 ------E----EKIFCFAHAWRNGEQGC----LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA  147 (355)
Q Consensus        94 ------~----~rvyqig~~FRaE~~~~----rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~  147 (355)
                            +    -|++++|.|+|.|.++-    +-+-+|||=|. --|...+++.+.+.+.+..+....
T Consensus       291 k~~~~SYR~LP~r~~E~g~v~R~E~SGal~GL~RvR~ftqdD~-Hifc~~dQi~~E~~~~~~~i~~v~  357 (589)
T COG0441         291 KSGLRSYRELPLRLAEFGYVYRYEKSGALHGLMRVRGFTQDDA-HIFCTPDQIKDEFKGILELILEVY  357 (589)
T ss_pred             HCCCCCEECCCHHHHHCCEEECCCCCCHHHCCCCCCCEEECCC-CEECCHHHHHHHHHHHHHHHHHHH
T ss_conf             5378611004404331442211567642222400113224562-014046788999999999999999


No 70 
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=97.71  E-value=0.0002  Score=45.65  Aligned_cols=122  Identities=20%  Similarity=0.150  Sum_probs=83.1

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCC-CCCC-----EEEECCCCCCCCCCCCCCCCHHHHH----HHH
Q ss_conf             99999999999999998798898478210568--9854-4541-----2410247886783200002858999----989
Q gi|254781066|r   22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNET-HIRA-----FSTELIIQDHIRKPLYLQTSPEFSC----KKL   89 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~-~~~~-----f~t~~~~~~~~~~~~yL~~SPql~l----K~l   89 (355)
                      +.+.-+|.+.+|+-|++.|--|+-=|+|++..  .-+. |.+-     |.|.-.....++.++.|+...|--+    +.-
T Consensus        45 ~~iw~~i~~~~~~~~~~~g~~~~~fP~liP~~~l~kE~~hvegF~pE~~~VT~~G~~~l~~~l~lrPTsEt~i~~~~~~w  124 (478)
T PRK08661         45 YAIWENIQKILDEMFKETGHENVYFPLLIPESLLQKEAEHIEGFAPEVAWVTHGGGEKLEEPLALRPTSETIIYPMFKKW  124 (478)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             99999999999999986398087302406689998666566156740489954787555676310888799999999998


Q ss_pred             HHHHHH---HHHHHHHHHCCCCCCC--CCCCCEEEECEEECCCCHHHHHHHHHHHHHHH
Q ss_conf             874468---8999886424567775--44843002000115776578777557888776
Q gi|254781066|r   90 LAAGEE---KIFCFAHAWRNGEQGC--LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCA  143 (355)
Q Consensus        90 l~~G~~---rvyqig~~FRaE~~~~--rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~  143 (355)
                      +-|.-+   ++||++-+||+|-..|  --..||.|=|.|.+++|.++..+.+..|+..-
T Consensus       125 I~SyrdLPl~l~Qw~~v~R~E~r~r~flR~rEFl~qe~ht~h~t~eea~~~~~~~~~~Y  183 (478)
T PRK08661        125 IQSYRDLPLLYNQWVNVVRWEKKTRPFLRTREFLWQEGHTAHATEEEAEEETLEMLEIY  183 (478)
T ss_pred             HHHHHHCCCEEEEEEEEEECCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             52365269000200445865788963143426354212011399999999999999999


No 71 
>KOG2784 consensus
Probab=97.69  E-value=5.7e-05  Score=48.91  Aligned_cols=59  Identities=22%  Similarity=0.246  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHH--HHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHHHH
Q ss_conf             8999989874468--8999886424567775448430020001157--76578777557888776
Q gi|254781066|r   83 EFSCKKLLAAGEE--KIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIRCA  143 (355)
Q Consensus        83 ql~lK~ll~~G~~--rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~~~  143 (355)
                      .||  +|--.||.  |+|.|-++||||-+|..|++||-|+|--.+.  .++-++|.+.++++..+
T Consensus       322 mLy--~LAk~~f~p~K~FSIDrVFRNEtvDaTHLAEFHQVEGviad~gltLgdLig~l~~ff~~l  384 (483)
T KOG2784         322 MLY--RLAKKGFKPAKYFSIDRVFRNETVDATHLAEFHQVEGVIADKGLTLGDLIGILMEFFTKL  384 (483)
T ss_pred             HHH--HHHHCCCCCCCCCCHHHHHHCCCCCHHHHHHHHHHCEEEECCCCCHHHHHHHHHHHHHCC
T ss_conf             999--997479985110104134403432057787776320365137876999999999997326


No 72 
>PRK04173 glycyl-tRNA synthetase; Provisional
Probab=97.64  E-value=0.00018  Score=45.98  Aligned_cols=33  Identities=18%  Similarity=0.096  Sum_probs=24.2

Q ss_pred             HHHHHHHHCCCCCCCCC----CCCEEEECEEECCCCHHH
Q ss_conf             99988642456777544----843002000115776578
Q gi|254781066|r   97 IFCFAHAWRNGEQGCLH----QPEFTMLEWYRAHESYEQ  131 (355)
Q Consensus        97 vyqig~~FRaE~~~~rH----lpEFtmLE~e~af~d~~d  131 (355)
                      |-|||++|||| +++|+    +-||+|+|+|. |.+-++
T Consensus       192 iaQIGKaFRNE-IsPr~~lfR~REFeQmEiE~-F~~P~~  228 (460)
T PRK04173        192 IAQIGKSFRNE-ITPRNFIFRTREFEQMELEF-FVKPGT  228 (460)
T ss_pred             EEECCCCCCCC-CCCCCCCHHHHHHHHHHHHH-HCCCCC
T ss_conf             31004001243-06554512234555524331-058674


No 73 
>COG2502 AsnA Asparagine synthetase A [Amino acid transport and metabolism]
Probab=97.61  E-value=0.002  Score=39.79  Aligned_cols=106  Identities=15%  Similarity=0.172  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHHHHH-----HHCCCEEEECCCEECCCCCCC-C----CCCEEEECCCCCCCCCCCC-CCCCHHHHHHHHH
Q ss_conf             999999999999999-----987988984782105689854-4----5412410247886783200-0028589999898
Q gi|254781066|r   22 LLKRNMIQSSLREYF-----VENQFIEIDSMSLQYSPGNET-H----IRAFSTELIIQDHIRKPLY-LQTSPEFSCKKLL   90 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff-----~~~gF~EV~TPiL~~~~~g~~-~----~~~f~t~~~~~~~~~~~~y-L~~SPql~lK~ll   90 (355)
                      ++...+-++.+.++|     ++.|.+||..|+|+....|-- +    -++..+....   .+...| ...|---++...|
T Consensus         5 fI~qq~~IsfvKn~Ft~~l~~~L~lieVq~Pils~vg~G~qDnLsg~ekaVsv~vk~---~p~a~fEvVhSLAKWKR~tL   81 (330)
T COG2502           5 FILQQQAISFVKNTFTQHLEERLGLIEVQAPILSRVGDGLQDNLSGTEKAVSVKVKK---LPDATFEVVHSLAKWKRHTL   81 (330)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCEEEEECCEEECCCCCCCCCCCCCCCCEEEEEEE---CCCCHHHHHHHHHHHHHHHH
T ss_conf             777888899999999999998649688614517505775445555751435888753---68734467688899988889


Q ss_pred             H-HHH---HHHHHHHHHHCCC-C-CCCCCCCCEEEECEEECCCCHH
Q ss_conf             7-446---8899988642456-7-7754484300200011577657
Q gi|254781066|r   91 A-AGE---EKIFCFAHAWRNG-E-QGCLHQPEFTMLEWYRAHESYE  130 (355)
Q Consensus        91 ~-~G~---~rvyqig~~FRaE-~-~~~rHlpEFtmLE~e~af~d~~  130 (355)
                      + -||   +-+|+=-++.|.. + .|..|+-=--|-|||..-.+.+
T Consensus        82 ~r~~f~~~eGlythM~AlRpDeD~ld~~HSvYVDQWDWEkvi~~g~  127 (330)
T COG2502          82 ARYGFSAGEGLYTHMKALRPDEDRLDPIHSVYVDQWDWEKVIPDGD  127 (330)
T ss_pred             HHCCCCCCCCEEEECCCCCCCCCCCCCHHEEEECCCCHHHHCCCCC
T ss_conf             8638767872465211037873344530227852113644258754


No 74 
>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=97.54  E-value=0.00012  Score=46.88  Aligned_cols=133  Identities=16%  Similarity=0.164  Sum_probs=81.3

Q ss_pred             CCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEEEECCCCCCCC-CCCCCCCCH-
Q ss_conf             74788312615489999999999999999998798898478210568--98544541241024788678-320000285-
Q gi|254781066|r    7 QPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFSTELIIQDHIR-KPLYLQTSP-   82 (355)
Q Consensus         7 ~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~t~~~~~~~~~-~~~yL~~SP-   82 (355)
                      .++|.|.=       -++|..|-..+|.-..+.||-+|.||+|....  ....|.+-|.=..+.....+ +.++|+-.- 
T Consensus       204 ~~~WlPkG-------~~ir~~ledf~~~~~~~~Gy~~V~TP~m~~~~l~~~sGH~~~Y~e~Mf~~~~~~~~~~~LkPMnC  276 (595)
T TIGR00418       204 LPFWLPKG-------ALIRNLLEDFVREKQIKRGYEEVETPIMYDSELWEISGHWDHYKERMFPFTEEDNQEFMLKPMNC  276 (595)
T ss_pred             CEEECCCH-------HHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHCCCCCCCCEEECCCCCCCCCCCC
T ss_conf             41465764-------67899999999999987588641574121565424530545034235401010353033456775


Q ss_pred             ----HHHHHHHHHHHHH---HHHHHH-HHHCCCCCCC----CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             ----8999989874468---899988-6424567775----448430020001157765787775578887766641
Q gi|254781066|r   83 ----EFSCKKLLAAGEE---KIFCFA-HAWRNGEQGC----LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA  147 (355)
Q Consensus        83 ----ql~lK~ll~~G~~---rvyqig-~~FRaE~~~~----rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~  147 (355)
                          +.|+ .-+-|--+   |+|++| -|||.|-+|.    +=+=.|||.|.=.--.|.+++.+.+.+.++-+.+..
T Consensus       277 pgH~~i~k-~~~~SYR~LP~R~aE~g~~~hR~E~sG~L~GL~RvR~FT~dDaHifc~d~dQi~~E~~~~~~l~~~v~  352 (595)
T TIGR00418       277 PGHILIFK-SSLRSYRDLPLRIAELGTTVHRYEKSGALHGLKRVRGFTQDDAHIFCTDEDQIKSEIKNQFRLIQKVY  352 (595)
T ss_pred             HHHHHHHC-CCCCCHHHCCCHHHHCCCEEEEEECCCCCCHHHHHHHCCCCCCCEEECCHHHHHHHHHHHHHHHHHHH
T ss_conf             44533001-77777323350343318604788425421010164430699852453786779999999999999998


No 75 
>COG0423 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=97.44  E-value=0.00017  Score=46.12  Aligned_cols=31  Identities=26%  Similarity=0.372  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHHHH--CCCEEEECCCEECC
Q ss_conf             99999999999999998--79889847821056
Q gi|254781066|r   22 LLKRNMIQSSLREYFVE--NQFIEIDSMSLQYS   52 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~--~gF~EV~TPiL~~~   52 (355)
                      ...+..|.++-|++|-.  .+++|||||+|.+.
T Consensus        40 ~~LK~nI~~~Wrk~fV~~~e~~~eIdtpii~p~   72 (558)
T COG0423          40 VELKNNIKEAWRKSFVTEREDVVEIDTPIILPE   72 (558)
T ss_pred             HHHHHHHHHHHHHHHEECCCCEEEECCCCCCCH
T ss_conf             899999999999986624687678425544868


No 76 
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=97.38  E-value=0.00085  Score=41.96  Aligned_cols=123  Identities=15%  Similarity=0.127  Sum_probs=76.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CC--CC-CCCCEEEECCCCCCCCCCCCCCCCH-HHHH---HHHH
Q ss_conf             99999999999999998798898478210568----98--54-4541241024788678320000285-8999---9898
Q gi|254781066|r   22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GN--ET-HIRAFSTELIIQDHIRKPLYLQTSP-EFSC---KKLL   90 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g--~~-~~~~f~t~~~~~~~~~~~~yL~~SP-ql~l---K~ll   90 (355)
                      +|...+|.+-||+-|++-|..||..|+|++..    .|  +. +-+-|+..    |-.+.++.|.... |..-   +..+
T Consensus        47 ~rvl~Kie~IIr~em~~iGa~Ev~mp~l~p~elW~~sgR~~~~g~el~r~k----DR~~~~~~L~PThEE~it~lv~~~i  122 (570)
T PRK09194         47 LRVLRKIENIVREEMNKIGAQEVLMPALQPAELWQESGRWEKYGPELLRLK----DRHGRDFVLGPTHEEVITDLVRNEI  122 (570)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCHHHCCHHHEEEE----CCCCCEEEECCCCHHHHHHHHHHHH
T ss_conf             999999999999999864987985356797789876188212361346985----2789856537873899999999851


Q ss_pred             HHHH---HHHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHH---HHHHHHC
Q ss_conf             7446---88999886424567775---448430020001157765787775578887---7666418
Q gi|254781066|r   91 AAGE---EKIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIR---CAAEVAN  148 (355)
Q Consensus        91 ~~G~---~rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~---~~~~~~~  148 (355)
                      .|.-   =++|||+.-||||-.-|   --.-||+|-|.|--..|.+++.+.-+.+..   .+++.++
T Consensus       123 ~SYkqLP~~lYQIqtKfRDE~RPR~GllR~REF~MKDaYSFd~~~e~l~~tY~~~~~AY~~IF~rlg  189 (570)
T PRK09194        123 KSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFIMKDAYSFHADEESLDETYDAMYQAYSRIFTRLG  189 (570)
T ss_pred             CCHHHCCHHEECCCCEECCCCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             1376468020013233347788767623456534512456669989999999999999999999809


No 77 
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=97.27  E-value=0.00059  Score=42.88  Aligned_cols=122  Identities=15%  Similarity=0.183  Sum_probs=66.8

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEECCCEECC-C-CCCCCCCCEEEECCCCCCCCCCCCCCCCHHH-----HHHHHHHH-HH
Q ss_conf             999999999999999879889847821056-8-9854454124102478867832000028589-----99989874-46
Q gi|254781066|r   23 LKRNMIQSSLREYFVENQFIEIDSMSLQYS-P-GNETHIRAFSTELIIQDHIRKPLYLQTSPEF-----SCKKLLAA-GE   94 (355)
Q Consensus        23 ~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-~-~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql-----~lK~ll~~-G~   94 (355)
                      +.--.+++.+-+++.++||.+|.||.|... . .|...+--|....+...  +.++||.-..|.     |....+-. -+
T Consensus       171 ~LerALi~f~ld~~~~~Gy~~v~~P~lv~~~~~~gtGqlPkfe~~~Y~i~--~~dl~Li~TAEvpL~~~~~~eil~~~~L  248 (422)
T PRK05431        171 RLERALIQFMLDLHTEEGYTEVIPPYLVNEESMYGTGQLPKFEEDLFKIE--DDDLYLIPTAEVPLTNLHRDEILDEEEL  248 (422)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEECHHHHHHHHHHHHCCCCCCHHHHHHHC--CCCEEEECCCCCCHHHHHHCCCCCHHHC
T ss_conf             99999999999999987997996737636788744537974487754105--8871760565321233440113365439


Q ss_pred             -HHHHHHHHHHCCC-CC---CCC---CCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             -8899988642456-77---754---48430020001157765787775578887766641
Q gi|254781066|r   95 -EKIFCFAHAWRNG-EQ---GCL---HQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA  147 (355)
Q Consensus        95 -~rvyqig~~FRaE-~~---~~r---HlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~  147 (355)
                       =||.-++||||.| ++   |+|   ..-+|+=+|.. +++.-++..+.-|.|+..+.+.+
T Consensus       249 Pik~~~~S~CFR~EAGs~GkdtrGl~RvHQF~KVE~f-~~~~pe~S~~~~e~~~~~~e~i~  308 (422)
T PRK05431        249 PIKYTAYSPCFRSEAGSAGRDTRGLIRQHQFDKVELV-KFTKPEDSYAELEELTGNAEEIL  308 (422)
T ss_pred             CHHHEEECCHHHHCCCCCCCCCCCCEEEEEECEEEEE-EECCHHHHHHHHHHHHHHHHHHH
T ss_conf             8445278836530313367556761244300003433-53586779999999999999999


No 78 
>KOG2324 consensus
Probab=97.12  E-value=0.0018  Score=40.05  Aligned_cols=125  Identities=15%  Similarity=0.100  Sum_probs=80.7

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCEECCC---CCC----CCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             99999999999999998798898478210568---985----44541241024788678320000285899998987446
Q gi|254781066|r   22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSP---GNE----THIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGE   94 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~---~g~----~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~   94 (355)
                      +|.-.++.+.|+.-|++-|=.+|.-|+|++..   .++    .+-+-|..+    +--++.+.|...-|=-.-.||+.-.
T Consensus        52 ~R~~~K~~~~l~~~mqs~Ga~kIslp~ls~~~LWekTgRw~~~gsEl~rl~----Dr~gkq~cL~pThEE~iT~lmat~~  127 (457)
T KOG2324          52 LRVLNKLCRLLDNEMQSGGAQKISLPILSSKELWEKTGRWDAMGSELFRLH----DRKGKQMCLTPTHEEDITALMATYI  127 (457)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHCCCCCCCCHHHEEEE----CCCCCEECCCCCHHHHHHHHHHHCC
T ss_conf             799999999999998723670574044686899876185112460453751----0478773057754899999998627


Q ss_pred             H--------HHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHH---HHHHHHHHCCC
Q ss_conf             8--------8999886424567775---4484300200011577657877755788---87766641883
Q gi|254781066|r   95 E--------KIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNI---IRCAAEVANQK  150 (355)
Q Consensus        95 ~--------rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~l---i~~~~~~~~~~  150 (355)
                      .        +|||||+-||||-..|   -.--||.|=|+|.-..|-++.|+.-+.+   ...+++.++..
T Consensus       128 ~lsykqlPi~vYQigrKfRDElrpRfGLlRgREFlMKDmYsFd~~~etA~qTy~~v~~aY~~iFkqL~~p  197 (457)
T KOG2324         128 PLSYKQLPIRVYQIGRKFRDELRPRFGLLRGREFLMKDMYSFDSDEETAQQTYQLVDQAYDRIFKQLGLP  197 (457)
T ss_pred             CCCCCCCCEEEEEECHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             4322028677665054544134754230124788876533025888899999999999999999973997


No 79 
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=96.78  E-value=0.0016  Score=40.38  Aligned_cols=113  Identities=14%  Similarity=0.170  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEEEECCCCCCCCCCCCCCCCHH-----HHHHHHHHHH--HHHHHH
Q ss_conf             9999999998798898478210568--985445412410247886783200002858-----9999898744--688999
Q gi|254781066|r   29 QSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFSTELIIQDHIRKPLYLQTSPE-----FSCKKLLAAG--EEKIFC   99 (355)
Q Consensus        29 ~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~t~~~~~~~~~~~~yL~~SPq-----l~lK~ll~~G--~~rvyq   99 (355)
                      ++.+=++..++||.||.+|.|....  -|...+.-|.-..+...  +...||.-.-|     +|-++.+...  =-++.-
T Consensus       181 ~~f~ld~~~~~Gf~e~~~P~lv~~e~m~gtgqlpkf~e~~y~v~--~~~~~LipTaEvpl~~l~~~Eil~~~~LP~k~~~  258 (429)
T COG0172         181 IQFMLDLHTKHGFTEVLPPYLVNLESMFGTGQLPKFEEDLYKVE--DPDLYLIPTAEVPLTNLHRDEILDEEDLPIKYTA  258 (429)
T ss_pred             HHHHHHHHHHCCCEEEECCEEECHHHHHCCCCCCCCCCCCEEEC--CCCEEEEECCHHHHHHHHCCCCCCCCCCCEEEEE
T ss_conf             99999999876965865760605988622378988801215845--8987997020215678651620152127802678


Q ss_pred             HHHHHCCC-CC---CCC---CCCCEEEECEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf             88642456-77---754---48430020001157765787775578887766
Q gi|254781066|r  100 FAHAWRNG-EQ---GCL---HQPEFTMLEWYRAHESYEQLMKDCMNIIRCAA  144 (355)
Q Consensus       100 ig~~FRaE-~~---~~r---HlpEFtmLE~e~af~d~~dlm~~~E~li~~~~  144 (355)
                      .+||||.| ++   |+|   -.-+|..+|.- +++.-++..+.-|.|+.+.-
T Consensus       259 ~S~cFR~EAGs~GrdtrGliRvHQF~KVE~v-~~~~Pe~S~~~~E~m~~~ae  309 (429)
T COG0172         259 YSPCFRSEAGSAGKDTRGLIRVHQFDKVELV-VITKPEESEEELEEMLGNAE  309 (429)
T ss_pred             ECHHHHCCCCCCCCCCCCEEEEEEEEEEEEE-EEECCCHHHHHHHHHHHHHH
T ss_conf             7725421456566435530146643558999-97070116999999999999


No 80 
>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=96.25  E-value=0.0081  Score=36.14  Aligned_cols=128  Identities=14%  Similarity=0.149  Sum_probs=73.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC-----CCCCCCCCEEEE-CCCCCCCCCCCCCC---CCH--HHHHHHH
Q ss_conf             999999999999999998798898478210568-----985445412410-24788678320000---285--8999989
Q gi|254781066|r   21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP-----GNETHIRAFSTE-LIIQDHIRKPLYLQ---TSP--EFSCKKL   89 (355)
Q Consensus        21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-----~g~~~~~~f~t~-~~~~~~~~~~~yL~---~SP--ql~lK~l   89 (355)
                      -...|..+...+|+.+.+-||.||.||++..+.     .|+. .+..... +...+..++..-|+   ++|  .++....
T Consensus        17 ~~~~~~~~~~~~~~~~~~~g~~~~~~P~~e~~~~~~~~~~~~-~~~~~~~~y~f~d~~~~~~~lrp~~t~~~~r~~~~~~   95 (446)
T TIGR00442        17 ELVYRQWIEAKLRSVLESYGYSEIRTPIFEYTELFARGIGKS-GDEVEKELYTFKDKGGRDLALRPELTAPVVRLVAENK   95 (446)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCC-HHHHHHHHEEEECCCCCEEEECCCHHHHHHHHHHHHH
T ss_conf             578999999999999975177200121144456665302530-1334444301212788414422200368999998754


Q ss_pred             H-H--HHHHHHHHHHHHHCCCCCC-CCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             8-7--4468899988642456777-544843002000115776578777557888776664188
Q gi|254781066|r   90 L-A--AGEEKIFCFAHAWRNGEQG-CLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQ  149 (355)
Q Consensus        90 l-~--~G~~rvyqig~~FRaE~~~-~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~  149 (355)
                      + .  ..--|.|.+|+|||-|... .-..-|||++.++..+..-...-..+-.+....++.++-
T Consensus        96 ~~~~~~~p~~~~~~g~~~r~e~p~~~gr~r~f~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~g~  159 (446)
T TIGR00442        96 LLLPANKPLRLYYIGPVFRYERPQLKGRYREFWQFGCEVIGSESPLADAEVLSLAVEGLKALGL  159 (446)
T ss_pred             HHCCCCCCEEEEEEECHHHCCCHHHHCCHHHHHHCCEEEECCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             3104676424323201010224123010113321150464366520368999999998986076


No 81 
>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=95.69  E-value=0.0013  Score=40.84  Aligned_cols=30  Identities=27%  Similarity=0.497  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHHHHH-CC-CEEEECCCEECC
Q ss_conf             9999999999999998-79-889847821056
Q gi|254781066|r   23 LKRNMIQSSLREYFVE-NQ-FIEIDSMSLQYS   52 (355)
Q Consensus        23 ~~Rs~i~~~iR~ff~~-~g-F~EV~TPiL~~~   52 (355)
                      ..+.+|+++-|+||-- ++ ++|||||++++.
T Consensus        38 ~Lk~~I~~~wr~~fi~~e~d~~~id~P~i~~~   69 (606)
T TIGR00389        38 VLKNNIKNAWRKFFIINERDVLEIDSPIITPE   69 (606)
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEECCCCCCCH
T ss_conf             89999999888751110365346424533725


No 82 
>KOG1035 consensus
Probab=95.31  E-value=0.073  Score=30.49  Aligned_cols=110  Identities=15%  Similarity=0.178  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHHHHCCCEEEECCCEEC-C--CCCCCCCCCEEEECCCCC----CCCCCC--CCCCCHHHHHHHHHHHHH
Q ss_conf             9999999999999987988984782105-6--898544541241024788----678320--000285899998987446
Q gi|254781066|r   24 KRNMIQSSLREYFVENQFIEIDSMSLQY-S--PGNETHIRAFSTELIIQD----HIRKPL--YLQTSPEFSCKKLLAAGE   94 (355)
Q Consensus        24 ~Rs~i~~~iR~ff~~~gF~EV~TPiL~~-~--~~g~~~~~~f~t~~~~~~----~~~~~~--yL~~SPql~lK~ll~~G~   94 (355)
                      .|..+.--+-+-|..+|++|++||.|.. .  +-+-+.+..+.++.+..-    .+..+|  |+.--+=+         .
T Consensus       934 l~~~v~e~~~~ifr~Hga~~l~tpp~~~~~~~~~~~~~~v~~ld~sG~~v~Lp~DLr~pfar~vs~N~~~---------~ 1004 (1351)
T KOG1035         934 LREYVVEEVVKIFRKHGAIELETPPLSLRNACAYFSRKAVELLDHSGDVVELPYDLRLPFARYVSRNSVL---------S 1004 (1351)
T ss_pred             HHHHHHHHHHHHHHHHCCEECCCCCCCCCCCCCHHCCCEEEEECCCCCEEEEECCCCCHHHHHHHHCHHH---------H
T ss_conf             9999999999999982430216786553345420015403544279978996300124677886605288---------8


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCC----HHHHHHHHHHHHHHHH
Q ss_conf             8899988642456777544843002000115776----5787775578887766
Q gi|254781066|r   95 EKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHES----YEQLMKDCMNIIRCAA  144 (355)
Q Consensus        95 ~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d----~~dlm~~~E~li~~~~  144 (355)
                      -|=|+|+++||-+. .+ |=-|++.+++-...-+    --+++.++-+++..++
T Consensus      1005 ~Kry~i~rVyr~~~-~~-hP~~~~ec~fDii~~t~sl~~AE~L~vi~Ei~~~~l 1056 (1351)
T KOG1035        1005 FKRYCISRVYRPAI-HN-HPKECLECDFDIIGPTTSLTEAELLKVIVEITTEIL 1056 (1351)
T ss_pred             HHHHHHHEEECCCC-CC-CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             77762320344634-58-984010015667558777407899999999999986


No 83 
>COG3705 HisZ ATP phosphoribosyltransferase involved in histidine biosynthesis [Amino acid transport and metabolism]
Probab=95.25  E-value=0.02  Score=33.82  Aligned_cols=100  Identities=16%  Similarity=0.178  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----C-CCC-CCCCEEEECCCCCCCCCCCCCCC--CHHHHHHHHH--
Q ss_conf             999999999999999998798898478210568----9-854-45412410247886783200002--8589999898--
Q gi|254781066|r   21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----G-NET-HIRAFSTELIIQDHIRKPLYLQT--SPEFSCKKLL--   90 (355)
Q Consensus        21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~-g~~-~~~~f~t~~~~~~~~~~~~yL~~--SPql~lK~ll--   90 (355)
                      -......|.+.+++.|...||-.|+||+|....    + |+- -.+-|++.    +..++.+-|+-  .++..  ++.  
T Consensus        16 e~~~~~~i~~~l~~~f~~~Gy~~v~tP~lE~~d~~l~~~g~~l~~~~f~l~----d~~g~~l~LRpD~T~pVa--R~~~~   89 (390)
T COG3705          16 EARRKEEIRDQLLALFRAWGYERVETPTLEPADPLLDGAGEDLRRRLFKLE----DETGGRLGLRPDFTIPVA--RIHAT   89 (390)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCHHHHHHHEEEE----CCCCCEEEECCCCCHHHH--HHHHH
T ss_conf             776479999999999998087404663134026654022255552206876----578976883543308999--99998


Q ss_pred             --HHHHHHHHHHHHHHCCC-CCCCCCCCCEEEECEEECCC
Q ss_conf             --74468899988642456-77754484300200011577
Q gi|254781066|r   91 --AAGEEKIFCFAHAWRNG-EQGCLHQPEFTMLEWYRAHE  127 (355)
Q Consensus        91 --~~G~~rvyqig~~FRaE-~~~~rHlpEFtmLE~e~af~  127 (355)
                        .++-.|++..|++||+. +.+.+ ..||+|+=+|.-+.
T Consensus        90 ~~~~~P~Rl~Y~G~Vfr~~~~~~g~-~~Ef~QaGiEllG~  128 (390)
T COG3705          90 LLAGTPLRLSYAGKVFRAREGRHGR-RAEFLQAGIELLGD  128 (390)
T ss_pred             HCCCCCCEEEECCHHHHCCHHCCCC-CCCHHHHHHHHHCC
T ss_conf             2378871466401454020102676-42045533677378


No 84 
>cd00673 AlaRS_core Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine 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 predicted structure and the presence of three characteristic sequence motifs.
Probab=94.56  E-value=0.34  Score=26.52  Aligned_cols=95  Identities=17%  Similarity=0.220  Sum_probs=55.7

Q ss_pred             HHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCH-HHHHHHHHH----HHHHHHHHHH
Q ss_conf             99999999999879889847821056898544541241024788678320000285-899998987----4468899988
Q gi|254781066|r   27 MIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSP-EFSCKKLLA----AGEEKIFCFA  101 (355)
Q Consensus        27 ~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SP-ql~lK~ll~----~G~~rvyqig  101 (355)
                      +|-+..=+||.++|-..|..--|.  |..++                 .++++.|. +.+ |..+.    ....|+-...
T Consensus         3 eiR~~Fl~fF~~~gH~~vpssslv--p~~Dp-----------------tllFtnAGM~~F-kp~flG~~~p~~~r~~~~Q   62 (232)
T cd00673           3 EIRETFLSFFEKKGHTRVPSSPVV--PRDDP-----------------TLLFTNAGMNQF-KPIFLGEVPPPANRLVNSQ   62 (232)
T ss_pred             HHHHHHHHHHHHCCCEECCCCCCC--CCCCC-----------------CEEEEECCHHHH-HHHHCCCCCCCCCCCEEEE
T ss_conf             899999999987898882787722--38999-----------------501441146888-9986778899987510000


Q ss_pred             HHHCCCCC-----CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             64245677-----75448430020001157765787775578887766641
Q gi|254781066|r  102 HAWRNGEQ-----GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA  147 (355)
Q Consensus       102 ~~FRaE~~-----~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~  147 (355)
                      ||.|..+.     |.||++=|-||-= .||.||-     -++.|..+.+.+
T Consensus        63 kCiR~~di~nvG~t~rH~TfFEMLGn-fSFGdYf-----K~eaI~~awe~l  107 (232)
T cd00673          63 KCIRAGDIDNVGKTGRHHTFFEMLGN-FSFGDYF-----KEEAIAFAWELL  107 (232)
T ss_pred             ECCCCCCCCCCCCCCCCCHHHHCCCC-CCHHHHH-----HHHHHHHHHHHH
T ss_conf             12365783246777764023330444-2031458-----999999999987


No 85 
>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=94.31  E-value=0.018  Score=34.12  Aligned_cols=119  Identities=17%  Similarity=0.180  Sum_probs=66.8

Q ss_pred             HHHHHHHHHHHHHHCCCEEEECCC-EECCC-CCCCC-------C----CCEEEEC-------------------------
Q ss_conf             999999999999987988984782-10568-98544-------5----4124102-------------------------
Q gi|254781066|r   25 RNMIQSSLREYFVENQFIEIDSMS-LQYSP-GNETH-------I----RAFSTEL-------------------------   66 (355)
Q Consensus        25 Rs~i~~~iR~ff~~~gF~EV~TPi-L~~~~-~g~~~-------~----~~f~t~~-------------------------   66 (355)
                      -.+++..++++|...||.+..-|. +...- .-++-       +    +.|-...                         
T Consensus        83 ~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~f~~l~~p~~hp~r~~~d~f~~~~p~~~~~~~~~~~~~~~~~~~~~~~g  162 (362)
T TIGR00468        83 LTRVIDEIRDIFLGLGFTEEKGPEYVETDFWNFDALNLPQDHPARDLQDTFYLKDPLTGDLPPELVSDVKDAHETGGATG  162 (362)
T ss_pred             HHHHHHHHHHHHHHHCCEEECCCCEECCCCCCCHHHCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCCC
T ss_conf             78999999998765033010473101111001011127754543112330331374200032246776777665202122


Q ss_pred             -CCCCC-C----CCCCCC--CCCH----HHHHHHHHH---HHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCH
Q ss_conf             -47886-7----832000--0285----899998987---44688999886424567775448430020001157--765
Q gi|254781066|r   67 -IIQDH-I----RKPLYL--QTSP----EFSCKKLLA---AGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESY  129 (355)
Q Consensus        67 -~~~~~-~----~~~~yL--~~SP----ql~lK~ll~---~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~  129 (355)
                       ....+ .    .+..-|  ++++    ++.-....-   ..--|++.++++||++..|..|+++|.++|.-...  .++
T Consensus       163 ~~gw~~~~~~~~~~~~~lrt~~~~~~~~~~~~~~~~~~~~~pp~~~~~~~~~~r~~~~d~~h~~~f~~~~g~~~~~~~~~  242 (362)
T TIGR00468       163 SRGWRYEWDEDLARRLLLRTHTTASSAVQLRTLEENPKAKNPPIRIFCPGRVFRRDTVDATHLPEFHQLEGLVVDKNVSF  242 (362)
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHCCCCCCCCCCCHHHHEEEEEEECCCCH
T ss_conf             32445444555665555431132135666666654101378862576410111023333101410221002354156646


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             78777557888776
Q gi|254781066|r  130 EQLMKDCMNIIRCA  143 (355)
Q Consensus       130 ~dlm~~~E~li~~~  143 (355)
                      .++...++++++.+
T Consensus       243 ~~l~g~~~~~~~~~  256 (362)
T TIGR00468       243 TNLKGLLEEFLKKL  256 (362)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             78899999999974


No 86 
>KOG1936 consensus
Probab=94.16  E-value=0.018  Score=34.05  Aligned_cols=108  Identities=19%  Similarity=0.198  Sum_probs=63.2

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCEE--CC---CCCCCCCCCEEEECCCCCCCCCCC---C-CCCCHHHHHHHHHH
Q ss_conf             999999999999999998798898478210--56---898544541241024788678320---0-00285899998987
Q gi|254781066|r   21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQ--YS---PGNETHIRAFSTELIIQDHIRKPL---Y-LQTSPEFSCKKLLA   91 (355)
Q Consensus        21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~--~~---~~g~~~~~~f~t~~~~~~~~~~~~---y-L~~SPql~lK~ll~   91 (355)
                      -+..|.++++.|.+-|..+|...|+||++-  .+   .-|+- .+   .-+...+..++-.   | |+++=    -|.+|
T Consensus        73 qm~lRe~if~~i~~vFkrhGa~~iDTPVFElkeiL~gKYGEd-sk---LiYdlkDQGGEl~SLRYDLTVPf----ARylA  144 (518)
T KOG1936          73 QMALREKIFSTIKEVFKRHGAETIDTPVFELKEILTGKYGED-SK---LIYDLKDQGGELCSLRYDLTVPF----ARYLA  144 (518)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEECCCCCHHHHHHHHHHCCCC-CC---EEEEHHHCCCCEEEEECCCCCHH----HHHHH
T ss_conf             889999999999999997197444660045999986640553-23---06752324885887413566479----99998


Q ss_pred             HH---HHHHHHHHHHHCCCC-C-CCCCCCCEEEECEEECCCCHHHHHHHHH
Q ss_conf             44---688999886424567-7-7544843002000115776578777557
Q gi|254781066|r   92 AG---EEKIFCFAHAWRNGE-Q-GCLHQPEFTMLEWYRAHESYEQLMKDCM  137 (355)
Q Consensus        92 ~G---~~rvyqig~~FRaE~-~-~~rHlpEFtmLE~e~af~d~~dlm~~~E  137 (355)
                      ..   .=+-|+||+++|-+. . ++=..-||.|+|+-.|+ +++.++-..|
T Consensus       145 mNki~sikRy~iAkVyRRd~P~mtrGR~REFYQcDFDIAG-~~d~M~pdaE  194 (518)
T KOG1936         145 MNKITSIKRYHIAKVYRRDQPAMTRGRYREFYQCDFDIAG-QFDPMIPDAE  194 (518)
T ss_pred             HCCCCCCEEEEEEEEEECCCCHHHCHHHHHHHCCCCCCCC-CCCCCCCHHH
T ss_conf             7145521104678787506814423024556506752126-6777786099


No 87 
>PRK00252 alaS alanyl-tRNA synthetase; Reviewed
Probab=94.11  E-value=0.43  Score=25.95  Aligned_cols=99  Identities=20%  Similarity=0.198  Sum_probs=51.8

Q ss_pred             HHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999987988984782105689854454124102478867832000028589999898744688999886424
Q gi|254781066|r   26 NMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWR  105 (355)
Q Consensus        26 s~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FR  105 (355)
                      ++|-+..-+||.++|=..|..--|.  |-.++-+ .| |.-. .+.| ++.||-+.+--         ..|+-...||.|
T Consensus         5 ~eiR~~fl~fF~~k~H~~v~s~~lv--p~~Dptl-lf-tnAG-m~~f-k~~f~G~~~p~---------~~r~~~~QkCiR   69 (864)
T PRK00252          5 AEIRQAFLDFFESKGHTVVPSSSLV--PKNDPTL-LF-TNAG-MVQF-KDYFLGLEKPP---------YPRATTSQKCIR   69 (864)
T ss_pred             HHHHHHHHHHHHHCCCEEECCCCCC--CCCCCCE-EE-EECC-CCCC-HHHHCCCCCCC---------CCCCCCCCCCEE
T ss_conf             9999999999987898880787725--5899804-67-5036-4016-22325887899---------997345403400


Q ss_pred             CCCC-----CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             5677-----754484300200011577657877755788877666
Q gi|254781066|r  106 NGEQ-----GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE  145 (355)
Q Consensus       106 aE~~-----~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~  145 (355)
                      +.|+     |.||.+=|-||-= +||.||-     =++-|.+.++
T Consensus        70 ~nDld~VG~t~rH~TfFEMlGN-~SfGdYf-----K~eai~~awe  108 (864)
T PRK00252         70 TNDLENVGYTARHHTFFEMLGN-FSFGDYF-----KKEAIEFAWE  108 (864)
T ss_pred             CCCHHHCCCCCCCCHHHHCCCC-CCCCCCH-----HHHHHHHHHH
T ss_conf             3648763888775254423765-6655105-----8899999999


No 88 
>KOG2783 consensus
Probab=93.94  E-value=0.031  Score=32.68  Aligned_cols=98  Identities=16%  Similarity=0.218  Sum_probs=53.3

Q ss_pred             HHHHHHHHHHHCCC-----EEEECCCEECCCCCCCCCCCE--EEECCCC-CCCCCCCCC--CCCHHHHHHHHHHHHHHHH
Q ss_conf             99999999998798-----898478210568985445412--4102478-867832000--0285899998987446889
Q gi|254781066|r   28 IQSSLREYFVENQF-----IEIDSMSLQYSPGNETHIRAF--STELIIQ-DHIRKPLYL--QTSPEFSCKKLLAAGEEKI   97 (355)
Q Consensus        28 i~~~iR~ff~~~gF-----~EV~TPiL~~~~~g~~~~~~f--~t~~~~~-~~~~~~~yL--~~SPql~lK~ll~~G~~rv   97 (355)
                      +-+.|-++|...+-     .+..+|+.+....=+..+-|=  ...+... .|.+...-|  ++|--.  -.++..|.+.-
T Consensus        77 lr~~i~~~f~~~~~~~fs~~~~~spvvt~~qnfdsl~~p~dh~sr~ksdtyy~n~~~~lr~htsahq--~e~~~~~~~~f  154 (436)
T KOG2783          77 LRQRIEDYFYKTYRNLFSIFENESPVVTTYQNFDSLLFPADHVSRSKSDTYYVNHTHCLRAHTSAHQ--HELFQKGLDGF  154 (436)
T ss_pred             HHHHHHHHHHHHHCCCCHHCCCCCCEEEHHHHCCCCCCCCCCCCCCCCCCEEECCEEEEHHCCHHHH--HHHHHHCCCCC
T ss_conf             9998777898862353100467886023554144445742355567677414212332111350537--99997315466


Q ss_pred             HHHHHHHCCCCCCCCCCCCEEEECEEECCC
Q ss_conf             998864245677754484300200011577
Q gi|254781066|r   98 FCFAHAWRNGEQGCLHQPEFTMLEWYRAHE  127 (355)
Q Consensus        98 yqig~~FRaE~~~~rHlpEFtmLE~e~af~  127 (355)
                      -..|-++|-.++|+.|-|=|-++|--..+.
T Consensus       155 lv~~DVyrrdeidsthypvfhq~eg~~~~s  184 (436)
T KOG2783         155 LVTGDVYRRDEIDSTHYPVFHQMEGVRLWS  184 (436)
T ss_pred             CEEEEEEEECCCCCCCCCEECCCCCEEEEE
T ss_conf             234334530000230251003553305773


No 89 
>KOG2509 consensus
Probab=93.92  E-value=0.038  Score=32.20  Aligned_cols=122  Identities=11%  Similarity=0.123  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCC--CCCEEEE-CCCCCCCCCCCCCCCCHHHH-----HHHHHHH
Q ss_conf             99999999999999999879889847821056898544--5412410-24788678320000285899-----9989874
Q gi|254781066|r   21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETH--IRAFSTE-LIIQDHIRKPLYLQTSPEFS-----CKKLLAA   92 (355)
Q Consensus        21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~--~~~f~t~-~~~~~~~~~~~yL~~SPql~-----lK~ll~~   92 (355)
                      ....-..+++..-+|+.++||+-+.||.+......+..  ..-|.-+ +...+.. .+.||.-..|..     +...+..
T Consensus       184 ~a~LeqALi~yal~~l~~kGy~pl~~P~i~rkeVm~~cg~~~~~d~~~~y~ld~~-~~~~LiaTaE~plAa~~~~e~~~~  262 (455)
T KOG2509         184 GAFLEQALINYALDFLNAKGYTPLTTPDILRKEVMQKCGQLPRFDEEQYYVLDGG-DEKYLIATAEQPLAAYHRDEWLEE  262 (455)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCEEEEECCC-CCCEEEEECCCHHHHHHCCCCCCC
T ss_conf             9999999999999999976982466814536999998565767883217860688-642267621110666503640361


Q ss_pred             H-H-HHHHHHHHHHCCC-CC---CCC---CCCCEEEECE------EECCCCHHHHHHHHHHHHHHH
Q ss_conf             4-6-8899988642456-77---754---4843002000------115776578777557888776
Q gi|254781066|r   93 G-E-EKIFCFAHAWRNG-EQ---GCL---HQPEFTMLEW------YRAHESYEQLMKDCMNIIRCA  143 (355)
Q Consensus        93 G-~-~rvyqig~~FRaE-~~---~~r---HlpEFtmLE~------e~af~d~~dlm~~~E~li~~~  143 (355)
                      + + -||--.++|||+| ++   +++   -.-+|+-+|.      +.|+.-++++++..|++++.+
T Consensus       263 ~~lPiK~vg~S~CfR~EaGs~G~d~~GlyRVHqF~KVE~Fvit~Pe~S~~~~eEmi~~~eef~qsL  328 (455)
T KOG2509         263 DQLPIKYVGVSRCFRAEAGSHGKDTKGLYRVHQFEKVEQFVITGPEDSWEMLEEMINNQEEFYQSL  328 (455)
T ss_pred             CCCCEEEEEHHHHHHHHHHHCCCCCCCCEEEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             127601343037888776004654555146652002578886585356999999999999999980


No 90 
>PRK13902 alaS lanyl-tRNA synthetase; Provisional
Probab=93.76  E-value=0.033  Score=32.53  Aligned_cols=32  Identities=16%  Similarity=0.140  Sum_probs=22.9

Q ss_pred             HHHHHHHHHCCCCC-----CCCCCCCEEEECEEECCCC
Q ss_conf             89998864245677-----7544843002000115776
Q gi|254781066|r   96 KIFCFAHAWRNGEQ-----GCLHQPEFTMLEWYRAHES  128 (355)
Q Consensus        96 rvyqig~~FRaE~~-----~~rHlpEFtmLE~e~af~d  128 (355)
                      ++=...||.|+.|+     +.||.+=|-||== .||.|
T Consensus       117 ~~~~sQkCiR~nDlenVG~t~rHhTfFEMlGn-~SFg~  153 (898)
T PRK13902        117 PLVISQPCIRLNDIDNVGRTGRHLTSFEMMAH-HAFNY  153 (898)
T ss_pred             CCCCCCCCEECCCHHHCCCCCCCCHHHHCCCC-CCCCC
T ss_conf             72565223004767543888774354523765-41489


No 91 
>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=93.55  E-value=0.08  Score=30.28  Aligned_cols=81  Identities=17%  Similarity=0.144  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHHHHHCCCEEEECCCEECCCCC----CCCCCCEEEECCCCCCCCCC-CCCCCCHHHHHHHHHHH----HH-
Q ss_conf             9999999999999879889847821056898----54454124102478867832-00002858999989874----46-
Q gi|254781066|r   25 RNMIQSSLREYFVENQFIEIDSMSLQYSPGN----ETHIRAFSTELIIQDHIRKP-LYLQTSPEFSCKKLLAA----GE-   94 (355)
Q Consensus        25 Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g----~~~~~~f~t~~~~~~~~~~~-~yL~~SPql~lK~ll~~----G~-   94 (355)
                      +.++.+.||++|-+.||.||-|-.+++...-    ....++..+    .|-...+ -+||+|-=--+=..++.    |. 
T Consensus         2 ~~~l~~~ir~~L~~~Gf~Ev~t~s~~~~~~~~~~~~~~~~~i~l----~NPls~e~~~lR~sLlp~LL~~~~~N~~r~~~   77 (198)
T cd00769           2 LQKLERKLRRLLAGLGFQEVITYSLTSPEEAELFDGGLDEAVEL----SNPLSEEYSVLRTSLLPGLLDALARNLNRKNK   77 (198)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHCCCCCCEEEE----ECCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             67999999999997897141306768989998724887873897----08865668898887799999999865056777


Q ss_pred             -HHHHHHHHHHCCCCC
Q ss_conf             -889998864245677
Q gi|254781066|r   95 -EKIFCFAHAWRNGEQ  109 (355)
Q Consensus        95 -~rvyqig~~FRaE~~  109 (355)
                       -++|+||+||..++.
T Consensus        78 ~~~lFEiG~vy~~~~~   93 (198)
T cd00769          78 PLRLFEIGRVFLKDED   93 (198)
T ss_pred             CCEEEEEEEEEECCCC
T ss_conf             7328997638966888


No 92 
>PRK09348 glyQ glycyl-tRNA synthetase subunit alpha; Validated
Probab=93.41  E-value=0.058  Score=31.09  Aligned_cols=20  Identities=15%  Similarity=0.346  Sum_probs=15.7

Q ss_pred             HHHHHHHHHHHHHCCCEEEE
Q ss_conf             99999999999987988984
Q gi|254781066|r   26 NMIQSSLREYFVENQFIEID   45 (355)
Q Consensus        26 s~i~~~iR~ff~~~gF~EV~   45 (355)
                      ..|+..+.+|..++|-+=++
T Consensus         5 q~~I~~Lq~~W~~~GC~i~q   24 (291)
T PRK09348          5 QDIILTLQDYWADQGCAILQ   24 (291)
T ss_pred             HHHHHHHHHHHHHCCCEEEC
T ss_conf             99999999999767978865


No 93 
>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=93.31  E-value=0.11  Score=29.34  Aligned_cols=214  Identities=20%  Similarity=0.179  Sum_probs=119.4

Q ss_pred             HHHHHHHHHHHHHHHHHC-------------------CCEEEECCCEECCCCC---CCCCCCEE-----EECCCCCCCCC
Q ss_conf             999999999999999987-------------------9889847821056898---54454124-----10247886783
Q gi|254781066|r   22 LLKRNMIQSSLREYFVEN-------------------QFIEIDSMSLQYSPGN---ETHIRAFS-----TELIIQDHIRK   74 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~~-------------------gF~EV~TPiL~~~~~g---~~~~~~f~-----t~~~~~~~~~~   74 (355)
                      +.+|+.|.+.+|+-+++.                   |.-||-=|+|.+...-   ..|++=|.     +.-.....+..
T Consensus        39 ~~iw~~iq~~~~~~~~~~~~~~~~~L~~F~P~~~~~Y~h~~v~fP~L~p~~~L~KEk~HikGF~pEv~wi~~~G~~~L~~  118 (533)
T TIGR00408        39 FKIWENIQKILRDKLDEIKLKDKVILKKFIPIESLPYGHEEVYFPMLIPESELEKEKDHIKGFEPEVYWITHGGLKKLDE  118 (533)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHEECCCCCCHHHHHHHCCCCCCCCCHHHHEECCCCCCCCC
T ss_conf             78999999999999987643546766405677777777001005644525578632135688584002101037772467


Q ss_pred             CCCCCCCHHH-----HHHHHHHHHHH---HHHHHHHHHCCCC-CCC--CCCCCEE-EECEEECCCCHHHHHHHHHHHH--
Q ss_conf             2000028589-----99989874468---8999886424567-775--4484300-2000115776578777557888--
Q gi|254781066|r   75 PLYLQTSPEF-----SCKKLLAAGEE---KIFCFAHAWRNGE-QGC--LHQPEFT-MLEWYRAHESYEQLMKDCMNII--  140 (355)
Q Consensus        75 ~~yL~~SPql-----~lK~ll~~G~~---rvyqig~~FRaE~-~~~--rHlpEFt-mLE~e~af~d~~dlm~~~E~li--  140 (355)
                      |+-||-..|.     |.|..- +.-|   ||||+.-+||.|- ++|  --+.||+ ==|.=-+|.|.++--+.+...+  
T Consensus       119 pLaLRPTSEt~~y~m~~kWv~-sy~DLPlk~nQw~~vfR~E~kHTRPflR~rEf~twqE~HT~H~t~~eAee~v~~~~~~  197 (533)
T TIGR00408       119 PLALRPTSETAMYNMYKKWVK-SYRDLPLKINQWVNVFRYEKKHTRPFLRTREFLTWQEAHTAHATAEEAEEEVLKALDL  197 (533)
T ss_pred             CCEECCCCHHHHHHHHHHHHH-HCCCCCEEEEEEEEEEECCCCCCCCCHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             501258617888765787851-2158876898435889802178786102333210100013143777889999999998


Q ss_pred             -HHHHH-HHCCCEECCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHH
Q ss_conf             -77666-4188300022343324677320788886566608765323455562327999999997688778765347898
Q gi|254781066|r  141 -RCAAE-VANQKIFSFQNVNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIF  218 (355)
Q Consensus       141 -~~~~~-~~~~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (355)
                       +.+++ .++-+.+--.      -.+|         .+++|.+...+.+.. -+|.        -.++.+.-.-..|+-|
T Consensus       198 Yk~f~~~~LaIP~~~g~------k~E~---------eKFaGA~~T~~~e~i-mPDg--------G~~LQ~ATsH~LGqnF  253 (533)
T TIGR00408       198 YKEFIENLLAIPYFVGR------KSEK---------EKFAGAEYTWTFETI-MPDG--------GRTLQIATSHDLGQNF  253 (533)
T ss_pred             HHHHHHHCCCCCEEEEC------CCCC---------CCCCCCCCCEEEEEE-CCCC--------CEEHHHHHHHHHHCCC
T ss_conf             89997502886468714------8875---------547887622356752-4776--------5001221211330354


Q ss_pred             HHHHHCEECCCCCCCC-CCCCCC--CCHH---HHHHCCCCCCCCCCCC
Q ss_conf             7664300362237675-443257--6888---8641367877836330
Q gi|254781066|r  219 SRILIEKIEPNLGINC-CTILDR--YPAP---ESALANIYPADPRFTK  260 (355)
Q Consensus       219 ~~l~~~~ie~~l~~~~-pvfi~~--yP~~---~~plak~~~~~~~va~  260 (355)
                      .+-|+=..+...|++. =.|.+.  |=.+   ++++=+.|-||.|++.
T Consensus       254 ~K~F~i~fe~p~Gs~~~~~~ayq~s~G~StR~igali~~HsD~~GLVL  301 (533)
T TIGR00408       254 AKTFDIKFENPTGSDMDKVYAYQTSYGISTRVIGALILIHSDEKGLVL  301 (533)
T ss_pred             EEEEEEEEECCCCCCCCCCCCEECCCCHHHHHHHHEEEEECCCCCCCC
T ss_conf             020367887788897641010010133578875450001226777516


No 94 
>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=93.29  E-value=0.29  Score=27.00  Aligned_cols=13  Identities=8%  Similarity=0.013  Sum_probs=6.2

Q ss_pred             EECCCCHHHHHHH
Q ss_conf             1157765787775
Q gi|254781066|r  123 YRAHESYEQLMKD  135 (355)
Q Consensus       123 e~af~d~~dlm~~  135 (355)
                      |.|+.|...+...
T Consensus       228 EsAg~Dp~~v~~a  240 (546)
T PRK09616        228 DVTGTDLEAVLLA  240 (546)
T ss_pred             EEECCCHHHHHHH
T ss_conf             8515898999999


No 95 
>COG0013 AlaS Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=92.87  E-value=0.7  Score=24.71  Aligned_cols=45  Identities=20%  Similarity=0.138  Sum_probs=29.8

Q ss_pred             HHHHHHHHHCCCCC-----CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             89998864245677-----7544843002000115776578777557888776664
Q gi|254781066|r   96 KIFCFAHAWRNGEQ-----GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEV  146 (355)
Q Consensus        96 rvyqig~~FRaE~~-----~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~  146 (355)
                      |+-...||-|+.|+     +.||++=|-||== .||.||-     -|+-|.++++.
T Consensus        64 r~~~sQkcIR~NDieNVG~T~RHhTfFEMLGN-fSFGdYF-----KeeAI~~AwEf  113 (879)
T COG0013          64 RAVTSQKCIRTNDIDNVGYTARHHTFFEMLGN-FSFGDYF-----KEEAIEFAWEF  113 (879)
T ss_pred             CEECCCCCCCCCCHHHCCCCCCCHHHHHHHHC-CCHHHHH-----HHHHHHHHHHH
T ss_conf             70010212014766543766541067776505-7066778-----89999999999


No 96 
>COG0752 GlyQ Glycyl-tRNA synthetase, alpha subunit [Translation, ribosomal structure and biogenesis]
Probab=90.25  E-value=0.24  Score=27.44  Aligned_cols=20  Identities=15%  Similarity=0.306  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHCCCEEEE
Q ss_conf             99999999999987988984
Q gi|254781066|r   26 NMIQSSLREYFVENQFIEID   45 (355)
Q Consensus        26 s~i~~~iR~ff~~~gF~EV~   45 (355)
                      +.+|..+.+|..++|-+=++
T Consensus         8 Q~~IltLq~yW~~qGC~i~Q   27 (298)
T COG0752           8 QGLILTLQNYWAEQGCTILQ   27 (298)
T ss_pred             HHHHHHHHHHHHHCCCEEEC
T ss_conf             99999999999876978614


No 97 
>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=89.95  E-value=0.28  Score=27.04  Aligned_cols=64  Identities=25%  Similarity=0.260  Sum_probs=43.2

Q ss_pred             EEEECCCCCCCCCCCCCCCCHHH-------HHHHHHHHHHHH----HHHHHHHHCCCCCCC---CCCCCEEEECEEECCC
Q ss_conf             24102478867832000028589-------999898744688----999886424567775---4484300200011577
Q gi|254781066|r   62 FSTELIIQDHIRKPLYLQTSPEF-------SCKKLLAAGEEK----IFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHE  127 (355)
Q Consensus        62 f~t~~~~~~~~~~~~yL~~SPql-------~lK~ll~~G~~r----vyqig~~FRaE~~~~---rHlpEFtmLE~e~af~  127 (355)
                      |.|+.+..+.-.+..|||  ||.       | |+||-.--.|    |=||||+||||=+-+   --+-||+|.|+|. |+
T Consensus       171 F~T~IG~~~~~~~~gYLR--PETAQG~FinF-k~LL~~~r~klPFgvAQiGKSfRNEIsPr~gl~R~REF~QaE~E~-FV  246 (606)
T TIGR00389       171 FQTEIGVVGDSKRKGYLR--PETAQGIFINF-KRLLQFFRNKLPFGVAQIGKSFRNEISPRQGLIRLREFEQAEIEF-FV  246 (606)
T ss_pred             CEEEECCCCCCCCEEECC--CHHCCCCCHHH-HHHHHHHCCCCCEEEEEECCEEECCCCCCCCEEEECHHHHHHHHH-CC
T ss_conf             110211334776224147--60104751216-899997458996489974413604003898757103154466874-25


Q ss_pred             CH
Q ss_conf             65
Q gi|254781066|r  128 SY  129 (355)
Q Consensus       128 d~  129 (355)
                      |-
T Consensus       247 ~P  248 (606)
T TIGR00389       247 DP  248 (606)
T ss_pred             CC
T ss_conf             96


No 98 
>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=89.77  E-value=0.14  Score=28.77  Aligned_cols=33  Identities=18%  Similarity=0.522  Sum_probs=27.3

Q ss_pred             CCCC-CCCEEECCHHHHHHHHHCCCCHHHHCCCCC
Q ss_conf             1889-632453159999899815597131115856
Q gi|254781066|r  314 TEMP-QSSGIAMGFDRLVMLVTGANNINEVIWTPF  347 (355)
Q Consensus       314 ~G~P-PhgG~glGidRLvm~l~g~~~Irdvi~FP~  347 (355)
                      ||.| |-=-.|+|+|||.|+|-|.+.+|+-+ +|.
T Consensus       329 Y~Id~pVMNLGlGVERlAMIlygy~DVR~MV-YPQ  362 (558)
T TIGR00470       329 YDIDVPVMNLGLGVERLAMILYGYEDVRKMV-YPQ  362 (558)
T ss_pred             CCCCCCEEECCCHHHHHHHHHHCHHHHHHCC-CCC
T ss_conf             6849652225631876787781403343226-884


No 99 
>COG2024 Phenylalanyl-tRNA synthetase alpha subunit (archaeal type) [Translation, ribosomal structure and biogenesis]
Probab=89.23  E-value=0.26  Score=27.26  Aligned_cols=32  Identities=22%  Similarity=0.596  Sum_probs=26.5

Q ss_pred             CCCC-CCCEEECCHHHHHHHHHCCCCHHHHCCCC
Q ss_conf             1889-63245315999989981559713111585
Q gi|254781066|r  314 TEMP-QSSGIAMGFDRLVMLVTGANNINEVIWTP  346 (355)
Q Consensus       314 ~G~P-PhgG~glGidRLvm~l~g~~~Irdvi~FP  346 (355)
                      ||.| |---.|+|+|||+|+|-|.+.+|..+ +|
T Consensus       319 Y~Id~pVMNLGlGVERlaMIl~g~~DVR~mv-Yp  351 (536)
T COG2024         319 YGIDYPVMNLGLGVERLAMILHGADDVRSMV-YP  351 (536)
T ss_pred             CCCCCCEEECCHHHHHHHHHHHCCHHHHHHH-CC
T ss_conf             2999701203220899999981744776651-34


No 100
>KOG0188 consensus
Probab=86.85  E-value=2.3  Score=21.65  Aligned_cols=102  Identities=17%  Similarity=0.250  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999987988984782105689854454124102478867832000028589999898744688999886424
Q gi|254781066|r   26 NMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWR  105 (355)
Q Consensus        26 s~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FR  105 (355)
                      |.+-++.=+||.++.-.-|+.--.  .|-.++-+ .|.  .-..|.| +|.||-+          .+.+.|+.-..+|-|
T Consensus         5 ~evR~tFldfF~~k~H~~V~SSsV--iP~dDpTL-LFa--NAGMNQF-KpifLgt----------~a~lkRa~NsQKCIR   68 (895)
T KOG0188           5 SEVRKTFLDFFKSKHHKIVHSSSV--IPFDDPTL-LFA--NAGMNQF-KPIFLGT----------MAKLKRAANSQKCIR   68 (895)
T ss_pred             HHHHHHHHHHHHHCCCEEECCCCC--CCCCCCEE-EEE--CCCHHHC-CHHHHHC----------HHHHHHHHHHHHHHH
T ss_conf             899999999998548468446874--45899804-773--2654432-1365422----------145676650466776


Q ss_pred             CCCC---------CCCCCCCEEEECEEECCCCHH--HHHHHHHHHHHHHH
Q ss_conf             5677---------754484300200011577657--87775578887766
Q gi|254781066|r  106 NGEQ---------GCLHQPEFTMLEWYRAHESYE--QLMKDCMNIIRCAA  144 (355)
Q Consensus       106 aE~~---------~~rHlpEFtmLE~e~af~d~~--dlm~~~E~li~~~~  144 (355)
                      |.+.         |.-|-+=|-||-= |||.||-  +.+...=+++..+.
T Consensus        69 AGGKHNDLdDVGkD~yHHTfFEMLGN-WSFGdYFKeEac~~AwElLt~vy  117 (895)
T KOG0188          69 AGGKHNDLDDVGKDFYHHTFFEMLGN-WSFGDYFKEEACAWAWELLTFVY  117 (895)
T ss_pred             CCCCCCCHHHCCCCCHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             26876766662665215679998637-63887889999999999987763


No 101
>pfam02091 tRNA-synt_2e Glycyl-tRNA synthetase alpha subunit.
Probab=86.76  E-value=0.42  Score=25.99  Aligned_cols=21  Identities=14%  Similarity=0.370  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHHHHCCCEEEEC
Q ss_conf             999999999999879889847
Q gi|254781066|r   26 NMIQSSLREYFVENQFIEIDS   46 (355)
Q Consensus        26 s~i~~~iR~ff~~~gF~EV~T   46 (355)
                      ..|+..+.+|..++|.+=+++
T Consensus         2 q~ii~~L~~fW~~~GC~i~qp   22 (284)
T pfam02091         2 QSMILTLQEYWASQGCVIMQP   22 (284)
T ss_pred             HHHHHHHHHHHHHCCCEEECC
T ss_conf             589999999998779688777


No 102
>KOG2298 consensus
Probab=85.85  E-value=0.2  Score=27.90  Aligned_cols=30  Identities=30%  Similarity=0.463  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHH-HHCCCEEEECCCEECCC
Q ss_conf             9999999999999-98798898478210568
Q gi|254781066|r   24 KRNMIQSSLREYF-VENQFIEIDSMSLQYSP   53 (355)
Q Consensus        24 ~Rs~i~~~iR~ff-~~~gF~EV~TPiL~~~~   53 (355)
                      ..+-|++.-|+.| .+++.+||++|+|++.+
T Consensus        48 lk~Nil~~WRkhFilEE~MlEvdct~ltP~~   78 (599)
T KOG2298          48 LKSNILSLWRKHFILEEDMLEVDCTMLTPEP   78 (599)
T ss_pred             HHHHHHHHHHHHHHHHHCCEEECCCCCCCHH
T ss_conf             6776999999987413020440167578088


No 103
>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=85.04  E-value=0.55  Score=25.32  Aligned_cols=29  Identities=31%  Similarity=0.756  Sum_probs=22.1

Q ss_pred             CCCCCEEECCHHHHHHHHHCCCCHHHHCC
Q ss_conf             89632453159999899815597131115
Q gi|254781066|r  316 MPQSSGIAMGFDRLVMLVTGANNINEVIW  344 (355)
Q Consensus       316 ~PPhgG~glGidRLvm~l~g~~~Irdvi~  344 (355)
                      .|..+-+.-|+|||.|++-|.+||-|++.
T Consensus       150 ~pv~~EiTYGLERiaMylQ~vd~v~dl~w  178 (279)
T cd00733         150 KPISVEITYGLERIAMYLQGVDNVYDIEW  178 (279)
T ss_pred             CCCCEEEEHHHHHHHHHHHCCCHHEEEEC
T ss_conf             45323310119999999857542314123


No 104
>CHL00192 syfB phenylalanyl-tRNA synthetase beta chain; Provisional
Probab=83.34  E-value=3.1  Score=20.84  Aligned_cols=113  Identities=12%  Similarity=0.041  Sum_probs=53.9

Q ss_pred             HHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCC-CCCCCCCHHHHHHHHHHH----HHH--HH
Q ss_conf             99999999999998798898478210568985445412410247886783-200002858999989874----468--89
Q gi|254781066|r   25 RNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRK-PLYLQTSPEFSCKKLLAA----GEE--KI   97 (355)
Q Consensus        25 Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~-~~yL~~SPql~lK~ll~~----G~~--rv   97 (355)
                      ..++.+.+|++|.+.||.|+-|=.+++....+.  ...  .  ..|-... --+|++|-=--|=..++-    |..  ++
T Consensus       396 ~~~~~~~lr~~L~~~Gf~E~itysf~s~~~~~~--~~v--~--l~NPis~e~s~LR~sLlpgLL~~~~~N~~r~~~~i~l  469 (702)
T CHL00192        396 LRNFIDKIRSLLRNLGLTELVHYSLVKSYTYYK--GEI--K--LYNPLLQDYSTLRSSLLPGLILAQQYNLKQSNQTIEG  469 (702)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEECCCCHHHCCC--CCE--E--ECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEE
T ss_conf             899999999999968983477531468444567--728--9--7087524378888877999999998615359977428


Q ss_pred             HHHHHHHCCCCCC---CCCCCCEEE------ECEEEC--CCCHHHHHHHHHHHHHHH
Q ss_conf             9988642456777---544843002------000115--776578777557888776
Q gi|254781066|r   98 FCFAHAWRNGEQG---CLHQPEFTM------LEWYRA--HESYEQLMKDCMNIIRCA  143 (355)
Q Consensus        98 yqig~~FRaE~~~---~rHlpEFtm------LE~e~a--f~d~~dlm~~~E~li~~~  143 (355)
                      |+||++|......   ..|+.=..+      -.|-..  -.|+.++-..+|.++..+
T Consensus       470 FEiG~vf~~~~~~~~e~~~l~~~~~~g~~~~~~w~~~~~~~dFfd~Kg~ve~ll~~l  526 (702)
T CHL00192        470 FEIGHVFRDNTEKIFETLHLAGGIGGGLDIRSSWSEKAQSLNWYEAKGIVEEFFQRL  526 (702)
T ss_pred             EEEECCCCCCCCCCCCHHEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             976455268878862112299999818866544456677678999999999999981


No 105
>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=81.85  E-value=0.58  Score=25.17  Aligned_cols=27  Identities=22%  Similarity=0.449  Sum_probs=24.1

Q ss_pred             CCCEEECCHHHHHHHHHCCCCHHHHCC
Q ss_conf             632453159999899815597131115
Q gi|254781066|r  318 QSSGIAMGFDRLVMLVTGANNINEVIW  344 (355)
Q Consensus       318 PhgG~glGidRLvm~l~g~~~Irdvi~  344 (355)
                      +--+||+|++|+.|+-.|.++||+..-
T Consensus       323 ~~~~~g~g~~r~~~~~~~~~d~r~~~~  349 (362)
T TIGR00468       323 PGLAWGLGIERLAMLKYGLDDLRDLYE  349 (362)
T ss_pred             EEEEECCCHHHHHHHHHCHHHHHHHHC
T ss_conf             134321240124454513356888640


No 106
>TIGR00669 asnA aspartate--ammonia ligase; InterPro: IPR004618   Aspartate--ammonia ligase (asparagine synthetase) 6.3.1.1 from EC catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. This family represents one of two non-homologous forms of aspartate--ammonia ligase found in Escherichia coli. This type is also found in Haemophilus influenzae, Treponema pallidum and Lactobacillus delbrueckii, but appears to have a very limited distribution. The fact that the protein from the H. influenzae is more than 70 0dentical to that from the spirochete T. pallidum, but less than 65 0dentical to that from the closely related E. coli, strongly suggests lateral transfer.; GO: 0004071 aspartate-ammonia ligase activity, 0006529 asparagine biosynthetic process, 0005737 cytoplasm.
Probab=77.12  E-value=3.3  Score=20.70  Aligned_cols=47  Identities=26%  Similarity=0.311  Sum_probs=34.2

Q ss_pred             CCCCCCCHHHHHHHHHHCC-CCCCCEEECCHHHHHHHHHCCCCHHHHCC
Q ss_conf             2888530101899998618-89632453159999899815597131115
Q gi|254781066|r  297 KIYNETYPIDEDFLACLTE-MPQSSGIAMGFDRLVMLVTGANNINEVIW  344 (355)
Q Consensus       297 ~~~~e~~~~D~~fl~al~G-~PPhgG~glGidRLvm~l~g~~~Irdvi~  344 (355)
                      .|+.....+++ .-+-+.| +|-+-|-|+|--||.|+|+..+.|-+|-.
T Consensus       268 tGded~l~~~W-hq~l~~G~lP~~iGGGiGqsrl~mlll~~~hiG~vq~  315 (330)
T TIGR00669       268 TGDEDRLELEW-HQDLLNGKLPQTIGGGIGQSRLAMLLLQKKHIGEVQA  315 (330)
T ss_pred             CCCCCHHHHHH-HHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHC
T ss_conf             47610123477-8997448776201565307899999862001452000


No 107
>COG2160 AraA L-arabinose isomerase [Carbohydrate transport and metabolism]
Probab=71.64  E-value=7.5  Score=18.60  Aligned_cols=53  Identities=8%  Similarity=-0.039  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHCCCC---CCC--CCCCCEEEECEEECCCCHHHHHHH-HHHHHHHHHHHH
Q ss_conf             688999886424567---775--448430020001157765787775-578887766641
Q gi|254781066|r   94 EEKIFCFAHAWRNGE---QGC--LHQPEFTMLEWYRAHESYEQLMKD-CMNIIRCAAEVA  147 (355)
Q Consensus        94 ~~rvyqig~~FRaE~---~~~--rHlpEFtmLE~e~af~d~~dlm~~-~E~li~~~~~~~  147 (355)
                      .-||=-+|...|.=-   .|.  .+-.==|.++.+-. .|+-.+|+. +|+=|..+.+..
T Consensus       175 h~kvarfGdnmr~vavtegDkv~aqiqFGwsv~~~gI-gdLv~~~~~vse~eV~~l~eey  233 (497)
T COG2160         175 HLKVARFGDNMREVAVTEGDKVAAQIQFGWSVNTWGI-GDLVEVVNEVSEGEVEALLEEY  233 (497)
T ss_pred             HHHHHHHCCHHHHHCCCCCHHHHHHHHHCCEEEEEEH-HHHHHHHHHCCHHHHHHHHHHH
T ss_conf             2014122201331201022788998863625767744-6899999751687899999998


No 108
>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=69.72  E-value=0.32  Score=26.69  Aligned_cols=52  Identities=25%  Similarity=0.328  Sum_probs=29.4

Q ss_pred             CCCCCEEEEC-----CEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH-H-CCCCCCCEEECCHHHH
Q ss_conf             3302202236-----712256402106999999999999999972888530101899998-6-1889632453159999
Q gi|254781066|r  258 FTKRFELYAC-----NIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLAC-L-TEMPQSSGIAMGFDRL  329 (355)
Q Consensus       258 va~rfdl~i~-----G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~a-l-~G~PPhgG~glGidRL  329 (355)
                      .+..||+.+.     +.|+++++.-.   ..|..||..                 .|.+. - ...|++.|+|||++||
T Consensus       153 a~~~~Die~~~p~~~~~Ev~s~~~~~---d~qsr~~~i-----------------~y~~~dg~~~~~~~~~~gl~v~Rl  211 (211)
T cd00768         153 AGPGFEIEVDHPEGRGLEIGSGGYRQ---DEQARAADL-----------------YFLDEALEYRYPPTIGFGLGLERL  211 (211)
T ss_pred             CEEEEEEEEECCCCCEEEEECEECCC---CHHHHHCCC-----------------EEECCCCCEEEEEEEECEECCCCC
T ss_conf             23545578983789799993546167---787884698-----------------999999999875563032413669


No 109
>pfam10026 DUF2268 Predicted Zn-dependent protease (DUF2268). This domain, found in various hypothetical bacterial proteins, as well as predicted zinc dependent proteases, has no known function.
Probab=68.71  E-value=3  Score=20.91  Aligned_cols=88  Identities=15%  Similarity=0.166  Sum_probs=41.2

Q ss_pred             CCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCC-CCHHHHHH-HHHHCCCCCCCEEECCHHHHHHHHH
Q ss_conf             633022022367122564021069999999999999999728885-30101899-9986188963245315999989981
Q gi|254781066|r  257 RFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNE-TYPIDEDF-LACLTEMPQSSGIAMGFDRLVMLVT  334 (355)
Q Consensus       257 ~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e-~~~~D~~f-l~al~G~PPhgG~glGidRLvm~l~  334 (355)
                      |+|+.|.--+.|.+...-+..-.|....++...+ . .+...+.. ....+..+ .+...++|+.+|.++|..=+--+|.
T Consensus        99 GLAe~f~~e~~G~~~~~pw~~~~~~~~l~~~~~~-~-~~~~l~~~~~~~~~~~l~G~~~~~~P~~~GYa~Gy~iV~~yL~  176 (195)
T pfam10026        99 GLAEHFVAELYGEEYLGPWTTPYDEEQLEHLWKQ-V-IKPNLDLKGFSEHDPYLYGDDIGRLPKWAGYAVGYYIVKKYLE  176 (195)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHH-H-HHHHCCCCCCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             2399999998198778773324899999999999-9-8764146663221405557876789860037989999999999


Q ss_pred             C-CCCHHHHCCCC
Q ss_conf             5-59713111585
Q gi|254781066|r  335 G-ANNINEVIWTP  346 (355)
Q Consensus       335 g-~~~Irdvi~FP  346 (355)
                      . -.+|.+...-|
T Consensus       177 ~~~~s~~e~t~~~  189 (195)
T pfam10026       177 KNGKSIAEATLLP  189 (195)
T ss_pred             HCCCCHHHHHCCC
T ss_conf             8799889986399


No 110
>PRK02929 L-arabinose isomerase; Provisional
Probab=68.50  E-value=8.8  Score=18.20  Aligned_cols=14  Identities=21%  Similarity=0.458  Sum_probs=10.0

Q ss_pred             CCCCEEEECCEECC
Q ss_conf             30220223671225
Q gi|254781066|r  259 TKRFELYACNIELC  272 (355)
Q Consensus       259 a~rfdl~i~G~El~  272 (355)
                      ..||-|++|-++.+
T Consensus       399 G~rFRli~n~V~~v  412 (499)
T PRK02929        399 GDRFRLLVNEVDTV  412 (499)
T ss_pred             CCCEEEEEEEEEEE
T ss_conf             77568997567776


No 111
>pfam02610 Arabinose_Isome L-arabinose isomerase. This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose <= L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme.
Probab=66.54  E-value=9.6  Score=17.96  Aligned_cols=50  Identities=10%  Similarity=0.060  Sum_probs=26.0

Q ss_pred             CCCCCCCCCCCH--HHCCCHHHHHHHHHHHHHHHHHHHHHCCCEE---EECCCEE
Q ss_conf             998898747883--1261548999999999999999999879889---8478210
Q gi|254781066|r    1 MHQIPSQPWWNR--DFHYRRRPFLLKRNMIQSSLREYFVENQFIE---IDSMSLQ   50 (355)
Q Consensus         1 ~~~~p~~~~~~~--~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~E---V~TPiL~   50 (355)
                      |..++...+|+-  |.||=--+.|..=++=.+.|-+.|++.+-+-   |--|+++
T Consensus         1 M~~~~~~e~WFvtGSQ~LYG~e~L~qVa~~s~~i~~~Ln~s~~lp~~iv~Kpv~~   55 (359)
T pfam02610         1 MLDFKQYEFWFVTGSQHLYGEETLKQVAAHSQEIVEGLNASGKLPVKIVLKPVVT   55 (359)
T ss_pred             CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCC
T ss_conf             9878883599994786556889999999999999998700689854899704437


No 112
>PRK00629 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=64.46  E-value=7.5  Score=18.58  Aligned_cols=115  Identities=14%  Similarity=0.115  Sum_probs=58.3

Q ss_pred             HHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEE---ECCCCCCCCCC-CCCCCCHHHHHHHHHH----HHHH-
Q ss_conf             9999999999999879889847821056898544541241---02478867832-0000285899998987----4468-
Q gi|254781066|r   25 RNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFST---ELIIQDHIRKP-LYLQTSPEFSCKKLLA----AGEE-   95 (355)
Q Consensus        25 Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t---~~~~~~~~~~~-~yL~~SPql~lK~ll~----~G~~-   95 (355)
                      ..+..+.+|++|.+.||.||-|=.+++..    .++.|..   .....|-...+ -+||+|-=.-|=..+.    -|.. 
T Consensus       486 ~~~~~~~ir~~L~~~Gf~EvitySf~s~~----~~~~~~~~~~~v~l~NPls~e~s~lR~SLlp~LL~~~~~N~~r~~~~  561 (786)
T PRK00629        486 AQKRRRRVRRALAARGYQEAITYSFVSPE----VADLFGLGEDALKLLNPISSELSVMRTSLLPGLLEALAYNQNRKNKD  561 (786)
T ss_pred             HHHHHHHHHHHHHHCCCEEEECCCCCCHH----HHHHHCCCCCCEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99999999999997898424136667979----99862788775685375421268888877999999899886279987


Q ss_pred             -HHHHHHHHHCCCCCCCCCCCCEE-----EECEEE--CCCCHHHHHHHHHHHHHHH
Q ss_conf             -89998864245677754484300-----200011--5776578777557888776
Q gi|254781066|r   96 -KIFCFAHAWRNGEQGCLHQPEFT-----MLEWYR--AHESYEQLMKDCMNIIRCA  143 (355)
Q Consensus        96 -rvyqig~~FRaE~~~~rHlpEFt-----mLE~e~--af~d~~dlm~~~E~li~~~  143 (355)
                       ++|+||++|.....-..|+.=-.     .-.|..  .-.|+.++-..+|.++..+
T Consensus       562 i~lFEiG~vf~~~~~E~~~La~~~~G~~~~~~w~~~~~~~dffdlKg~ve~ll~~l  617 (786)
T PRK00629        562 VALFEIGLVFLPGPREPLHLAGVLTGLRLNESWGGKGRPVDFFDAKGDLEALLGAL  617 (786)
T ss_pred             EEEEEEEEEECCCCCHHEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             67998754389998446599999989877666566676468999999999999973


No 113
>PRK01584 alanyl-tRNA synthetase; Provisional
Probab=63.55  E-value=4.6  Score=19.88  Aligned_cols=101  Identities=17%  Similarity=0.217  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             99999999999879889847821056898544541241024788678320000285899998987446889998864245
Q gi|254781066|r   27 MIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRN  106 (355)
Q Consensus        27 ~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRa  106 (355)
                      .|-+..-+||.++|-..|..--|.+  -+++-+ -| |... .+.| ++.||-+.+--         ..|+=...||.|+
T Consensus         5 eiR~~Fl~fF~~kgH~~v~ssslvp--~~dptl-lf-tnAG-m~~F-k~~f~G~~~p~---------~~r~~~~QkCiR~   69 (593)
T PRK01584          5 ELRKKYIDFFKSKGHVEIAGKSLVP--ENDPTV-LF-NTAG-MQPL-VPYLLGEPHPS---------GDMLVNVQKCLRT   69 (593)
T ss_pred             HHHHHHHHHHHHCCCEECCCCCCCC--CCCCCE-EE-EECC-CCCC-CHHHCCCCCCC---------CCCCCCCCCEEEC
T ss_conf             9999999999878988837877177--999983-57-4045-1017-12325888999---------9974567531333


Q ss_pred             CCC----CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             677----754484300200011577657877755788877666418
Q gi|254781066|r  107 GEQ----GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVAN  148 (355)
Q Consensus       107 E~~----~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~  148 (355)
                      .++    +++|.+=|-||== .||.||-     -++-|.++++.+.
T Consensus        70 ~DldnVG~~~H~TfFEMLGn-~SFgdYf-----K~eaI~~awe~lt  109 (593)
T PRK01584         70 GDIDEVGDLSHLTFFEMLGN-WSLGAYF-----KEESVKYSFEFLT  109 (593)
T ss_pred             CCHHHCCCCCCCHHHHHCCC-CCCCCHH-----HHHHHHHHHHHHC
T ss_conf             75633688875277750544-5233114-----8999999999806


No 114
>PRK07080 hypothetical protein; Validated
Probab=62.88  E-value=5.9  Score=19.21  Aligned_cols=42  Identities=19%  Similarity=0.178  Sum_probs=29.2

Q ss_pred             HHHHCCCCC-CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHH
Q ss_conf             864245677-7544843002000115776578777557888776
Q gi|254781066|r  101 AHAWRNGEQ-GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCA  143 (355)
Q Consensus       101 g~~FRaE~~-~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~  143 (355)
                      +-|||.|.+ |+.-+.+|.|-|+=.. .+-+++++.-|..+.-.
T Consensus       160 ~yCFRhEPS~dp~Rmq~FRMrEyV~i-Gt~e~v~a~R~~W~~r~  202 (318)
T PRK07080        160 SYCFRHEPSLDPARMQLFRMREYVRI-GTPEQILAFRQRWIERG  202 (318)
T ss_pred             EEHHCCCCCCCHHHHHHHHCEEEEEE-CCHHHHHHHHHHHHHHH
T ss_conf             42101789888588886440445771-79999999999999999


No 115
>KOG0903 consensus
Probab=60.93  E-value=5  Score=19.64  Aligned_cols=14  Identities=14%  Similarity=0.057  Sum_probs=5.3

Q ss_pred             HHCCCEEEECCCEE
Q ss_conf             98798898478210
Q gi|254781066|r   37 VENQFIEIDSMSLQ   50 (355)
Q Consensus        37 ~~~gF~EV~TPiL~   50 (355)
                      .+.++-+++.|.+.
T Consensus       312 ~n~~la~~~i~~~~  325 (847)
T KOG0903         312 RNCDLAEAEITLLI  325 (847)
T ss_pred             HCCCHHHHEECCCC
T ss_conf             50334551200145


No 116
>pfam01411 tRNA-synt_2c tRNA synthetases class II (A). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only alanyl-tRNA synthetases.
Probab=58.16  E-value=8.7  Score=18.23  Aligned_cols=91  Identities=14%  Similarity=0.223  Sum_probs=48.1

Q ss_pred             HHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHH-----HHHHHHHHHHH
Q ss_conf             9999999987988984782105689854454124102478867832000028589999898744-----68899988642
Q gi|254781066|r   30 SSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAG-----EEKIFCFAHAW  104 (355)
Q Consensus        30 ~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G-----~~rvyqig~~F  104 (355)
                      +..-+||.++|-..|..--|.+  -.+.                 +.++..|.=.-.|....+|     ..|+=...||+
T Consensus         4 ~~fl~fF~~~gH~~i~s~~lvp--~~d~-----------------~llft~Agm~~fkp~~~g~~~~pp~~~l~~~Q~Ci   64 (545)
T pfam01411         4 QTFLDFFEKKGHTRVPSSPVVP--RNDP-----------------TLLFTNAGMNQFKPIFLGGEDKPPYNRAVNSQKCI   64 (545)
T ss_pred             HHHHHHHHHCCCEEECCCCCCC--CCCC-----------------CEEEECCCCHHCHHHHCCCCCCCCCCCCCCCCCCE
T ss_conf             9999999878988807867067--9999-----------------81464046011737654987589988724433324


Q ss_pred             CCCCC-----CCCCCCCEEEECEEECCCCHH--HHHHHHHHHH
Q ss_conf             45677-----754484300200011577657--8777557888
Q gi|254781066|r  105 RNGEQ-----GCLHQPEFTMLEWYRAHESYE--QLMKDCMNII  140 (355)
Q Consensus       105 RaE~~-----~~rHlpEFtmLE~e~af~d~~--dlm~~~E~li  140 (355)
                      |..++     |.||++=|-||-= .||.||-  +.++.+-+++
T Consensus        65 R~~DidnVG~t~rH~T~FEMlGn-~SFg~YfK~eai~~a~e~l  106 (545)
T pfam01411        65 RAGDLDNVGRTARHHTFFEMLGN-FSFGDYFKEEAIEFAWELL  106 (545)
T ss_pred             ECCCHHHCCCCCCCCHHHHCCCC-CCCCCCHHHHHHHHHHHHH
T ss_conf             43765433677775323220334-5156243789999999997


No 117
>PRK13384 delta-aminolevulinic acid dehydratase; Provisional
Probab=44.88  E-value=11  Score=17.56  Aligned_cols=15  Identities=27%  Similarity=0.454  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             989874468899988
Q gi|254781066|r   87 KKLLAAGEEKIFCFA  101 (355)
Q Consensus        87 K~ll~~G~~rvyqig  101 (355)
                      +.++..|...|.=+|
T Consensus        69 e~~~~lGI~av~LFg   83 (323)
T PRK13384         69 ERLYALGIRYVMPFG   83 (323)
T ss_pred             HHHHHCCCCEEEECC
T ss_conf             999978996898369


No 118
>TIGR02151 IPP_isom_2 isopentenyl-diphosphate delta-isomerase, type 2; InterPro: IPR011179   This group represents the bacterial and archaeal isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP isomerase catalyses the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), and is a key enzyme in the biosynthesis of isoprenoids via the mevalonate pathway. The bacterial and archaeal IPP isomerase (type 2 enzyme) differs from that found in eukaryotes (type 1 enzyme), and requires NADPH, magnesium, and FMN for activity , .; GO: 0004452 isopentenyl-diphosphate delta-isomerase activity, 0010181 FMN binding, 0008299 isoprenoid biosynthetic process, 0005737 cytoplasm.
Probab=44.61  E-value=12  Score=17.36  Aligned_cols=19  Identities=42%  Similarity=0.719  Sum_probs=15.3

Q ss_pred             HHHHHHHCCCCHHHHCCCC
Q ss_conf             9989981559713111585
Q gi|254781066|r  328 RLVMLVTGANNINEVIWTP  346 (355)
Q Consensus       328 RLvm~l~g~~~Irdvi~FP  346 (355)
                      |.+|+++|+.||+|.--=|
T Consensus       326 k~~mfl~G~~~i~EL~~~~  344 (349)
T TIGR02151       326 KVAMFLTGAKNIKELKKVP  344 (349)
T ss_pred             HHHHHHHCCCCHHHHCCCC
T ss_conf             9999871798879861787


No 119
>PRK09283 delta-aminolevulinic acid dehydratase; Validated
Probab=37.83  E-value=23  Score=15.71  Aligned_cols=11  Identities=9%  Similarity=0.232  Sum_probs=5.4

Q ss_pred             HHHHHHHHHHH
Q ss_conf             98987446889
Q gi|254781066|r   87 KKLLAAGEEKI   97 (355)
Q Consensus        87 K~ll~~G~~rv   97 (355)
                      ++++..|...|
T Consensus        66 e~~~~lGI~av   76 (321)
T PRK09283         66 EEAVDLGIPAV   76 (321)
T ss_pred             HHHHHCCCCEE
T ss_conf             99998799989


No 120
>pfam05830 NodZ Nodulation protein Z (NodZ). The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal.
Probab=37.50  E-value=11  Score=17.70  Aligned_cols=21  Identities=19%  Similarity=0.270  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHC---CCCCCCEEEC
Q ss_conf             10189999861---8896324531
Q gi|254781066|r  304 PIDEDFLACLT---EMPQSSGIAM  324 (355)
Q Consensus       304 ~~D~~fl~al~---G~PPhgG~gl  324 (355)
                      -+|-+.|..+.   ..||++-|+.
T Consensus       267 LidM~lLarCD~lIrf~~~SaFsr  290 (322)
T pfam05830       267 LVEMYLLARCDTVIRFPPTSAFTR  290 (322)
T ss_pred             HHHHHHHHHCCEEEECCCCCHHHH
T ss_conf             999999873754353488426778


No 121
>cd04823 ALAD_PBGS_aspartate_rich Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. All of PBGS_aspartate_rich contain an aspartate rich metal binding site with the general sequence DXALDX(Y/F)X3G(H/Q)DG. They also contain an allosteric magnesiu
Probab=36.95  E-value=21  Score=15.98  Aligned_cols=11  Identities=9%  Similarity=0.232  Sum_probs=4.8

Q ss_pred             HHHHHHHHHHH
Q ss_conf             98987446889
Q gi|254781066|r   87 KKLLAAGEEKI   97 (355)
Q Consensus        87 K~ll~~G~~rv   97 (355)
                      ++++..|...|
T Consensus        61 ~~~~~lGI~av   71 (320)
T cd04823          61 EEAVDLGIPAV   71 (320)
T ss_pred             HHHHHCCCCEE
T ss_conf             99998899789


No 122
>pfam03590 AsnA Aspartate-ammonia ligase.
Probab=35.52  E-value=32  Score=14.90  Aligned_cols=120  Identities=16%  Similarity=0.156  Sum_probs=66.9

Q ss_pred             HHHHHHHHHHHHHHHHH-----CCCEEEECCCEECC-CC-CCC---CCCCEEEECCCCCCCCCCCCCCCCHHHHHHHH-H
Q ss_conf             99999999999999998-----79889847821056-89-854---45412410247886783200002858999989-8
Q gi|254781066|r   22 LLKRNMIQSSLREYFVE-----NQFIEIDSMSLQYS-PG-NET---HIRAFSTELIIQDHIRKPLYLQTSPEFSCKKL-L   90 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~-----~gF~EV~TPiL~~~-~~-g~~---~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~l-l   90 (355)
                      ++.+.+.|+.|+++|..     -+.+.|..|+++.. .| .+-   .-+|...+..  +.-+..+=-.+|--=+ ||+ |
T Consensus         3 ~i~~Q~AI~~iK~~F~~~L~~~LnL~rVsAPLfv~~~sGlND~LnG~ErpV~F~ik--~~~~~~~EIVhSLAKW-KR~aL   79 (244)
T pfam03590         3 FILQQQEISFVKNTFTQKLAEHLGLIEVQGPILSQVGDGIQDNLSGAEKAVSVKVK--QIPDATFEVVHSLAKW-KRHTL   79 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCEEECCCEEEECCCCCCCCCCCEEEEEEEECC--CCCCCCEEEEEEHHHH-HHHHH
T ss_conf             88999999999999999999973917966662871798877687873611386457--8899716997214888-99999


Q ss_pred             H-HHH---HHHHHHHHHHC-CCC-CCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf             7-446---88999886424-567-775448430020001157765787775578887766
Q gi|254781066|r   91 A-AGE---EKIFCFAHAWR-NGE-QGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAA  144 (355)
Q Consensus        91 ~-~G~---~rvyqig~~FR-aE~-~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~  144 (355)
                      . -||   +-+|+=-.+-| +|+ +|..|+-=.-|-|||..-...+-.++...+.++.+.
T Consensus        80 ~~Y~f~~geGlyTdMnAIR~DEe~Ldn~HSiYVDQWDWEkvI~~~dR~~~~LK~tV~~Iy  139 (244)
T pfam03590        80 ARFGFSEGEGLFVHMKALRPDEDSLDPTHSVYVDQWDWEKVIPNGDRNLAYLKSTVNKIY  139 (244)
T ss_pred             HHCCCCCCCEEEECCCCCCCCCCCCCCCCEEEECCCCHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf             965998995455245600167545787600898510221226801167899999999999


No 123
>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family; InterPro: IPR004589   The ATP-dependent DNA helicase RecQ (3.6.1 from EC) is involved in genome maintenance . All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novo synthesis DNA, such as the replication fork, and protein levels peak during S-phase.    A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that is necessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and the RecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response. ; GO: 0008026 ATP-dependent helicase activity, 0006310 DNA recombination.
Probab=34.81  E-value=12  Score=17.30  Aligned_cols=20  Identities=30%  Similarity=0.323  Sum_probs=8.0

Q ss_pred             CCHHHHHHH-HHHHHHHHHHH
Q ss_conf             285899998-98744688999
Q gi|254781066|r   80 TSPEFSCKK-LLAAGEEKIFC   99 (355)
Q Consensus        80 ~SPql~lK~-ll~~G~~rvyq   99 (355)
                      ++||.=++- -+.+-+++.|+
T Consensus       110 vtPE~~~~~~~ll~~Le~~Y~  130 (497)
T TIGR00614       110 VTPEKISKSKSLLQTLEKLYE  130 (497)
T ss_pred             ECHHHHHCCHHHHHHHHHHHH
T ss_conf             163465346478999999886


No 124
>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=34.62  E-value=33  Score=14.81  Aligned_cols=123  Identities=15%  Similarity=0.162  Sum_probs=75.6

Q ss_pred             HHHHHHHHHHHHHHHHHCC-CEEEECCCEEC-CC---CCCC---C----CCCEEEECCCCCCCCCCCCCCCCHH-----H
Q ss_conf             9999999999999999879-88984782105-68---9854---4----5412410247886783200002858-----9
Q gi|254781066|r   22 LLKRNMIQSSLREYFVENQ-FIEIDSMSLQY-SP---GNET---H----IRAFSTELIIQDHIRKPLYLQTSPE-----F   84 (355)
Q Consensus        22 l~~Rs~i~~~iR~ff~~~g-F~EV~TPiL~~-~~---~g~~---~----~~~f~t~~~~~~~~~~~~yL~~SPq-----l   84 (355)
                      +|.=.+|-+.||+-|++.| =+||-=|.+++ +.   ..++   |    -.-|.-    .|-.+++|-|.-.-|     |
T Consensus        48 ~rVL~Kv~~ivreeM~~~GGA~E~~lp~~~~la~LW~~SGRW~~YG~seGELl~l----kDR~~r~f~LgpT~EEvIT~l  123 (620)
T TIGR00409        48 LRVLKKVENIVREEMNKDGGAIEVLLPALQPLAELWQESGRWDTYGPSEGELLRL----KDRKGREFVLGPTHEEVITDL  123 (620)
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEE----EECCCCCCCCCCCCHHHHHHH
T ss_conf             9999988999998622678533466766778999875407532468654336676----526888735678665568999


Q ss_pred             HHHHHHHHHHH---HHHHHHHHHCCCC--C-CC-CCCCCEEEECEEECCCCHHHHHHHHHHH---HHHHHHHHCCC
Q ss_conf             99989874468---8999886424567--7-75-4484300200011577657877755788---87766641883
Q gi|254781066|r   85 SCKKLLAAGEE---KIFCFAHAWRNGE--Q-GC-LHQPEFTMLEWYRAHESYEQLMKDCMNI---IRCAAEVANQK  150 (355)
Q Consensus        85 ~lK~ll~~G~~---rvyqig~~FRaE~--~-~~-rHlpEFtmLE~e~af~d~~dlm~~~E~l---i~~~~~~~~~~  150 (355)
                      - |..+.|.-.   ..|||..=||||=  . += | .=||.|=|.|-=..|.+++-+.=..|   .+.++..++-.
T Consensus       124 ~-~~~i~SYKqLP~~lYQI~tKFRDEiRPRFGl~R-gREFiMKDAYSFH~~~ESL~~ty~~m~~aY~~IF~rlGld  197 (620)
T TIGR00409       124 V-RNEIKSYKQLPLNLYQIQTKFRDEIRPRFGLLR-GREFIMKDAYSFHSDEESLDATYQKMDQAYSNIFSRLGLD  197 (620)
T ss_pred             H-HHHHHHHHHCCCCEECCCCCCCCCCCCCCCCCC-CHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             9-998754530683010045121442048876000-1232302425544787679999889999999999865898


No 125
>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=33.97  E-value=34  Score=14.75  Aligned_cols=119  Identities=14%  Similarity=0.207  Sum_probs=60.1

Q ss_pred             HHHHHHHHHHHHH-HHCCCEEEECCCEECC---CCCC--CCCCCEEEECCCCCCCCCC-CCCCCCHHH-----HHHHHHH
Q ss_conf             9999999999999-9879889847821056---8985--4454124102478867832-000028589-----9998987
Q gi|254781066|r   24 KRNMIQSSLREYF-VENQFIEIDSMSLQYS---PGNE--THIRAFSTELIIQDHIRKP-LYLQTSPEF-----SCKKLLA   91 (355)
Q Consensus        24 ~Rs~i~~~iR~ff-~~~gF~EV~TPiL~~~---~~g~--~~~~~f~t~~~~~~~~~~~-~yL~~SPql-----~lK~ll~   91 (355)
                      ....++...-++. .++||.++.+|.+...   .|.+  .....|.-..+.....+.+ .||....|.     +....+.
T Consensus       204 ~~~al~~~~l~~~~~~~g~~~~~~p~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~l~~t~e~~~~~~~~~~~~~  283 (460)
T TIGR00414       204 LERALINFMLDLLREKNGYSELYPPYLVNEELLDGTGFNPQLPKFEEDLFKLEDTDDEKLYLIPTAEVPLTNLHRDEILD  283 (460)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEECCCHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCEEEEEECCHHHHHHHHHHHHCC
T ss_conf             99999999998644322640101403542344310245655653023443212677750465201000122222000102


Q ss_pred             H--H-H-HHHHHHHHHHCCC-CC---CC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHHH
Q ss_conf             4--4-6-8899988642456-77---75---44843002000115776578777557888776
Q gi|254781066|r   92 A--G-E-EKIFCFAHAWRNG-EQ---GC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCA  143 (355)
Q Consensus        92 ~--G-~-~rvyqig~~FRaE-~~---~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~  143 (355)
                      .  + + -++--.++|||.| ++   ++   -..-+|..+|.. .+..-++.....|.++...
T Consensus       284 ~~~~~lp~~~~~~~~cfr~eag~~g~~~~g~~r~h~f~k~e~~-~~~~p~~~~~~~~~~~~~~  345 (460)
T TIGR00414       284 LPSEELPIKYTGYSPCFRSEAGSYGKDTKGLIRVHQFNKVELV-KFCKPEESWEELEELLSDA  345 (460)
T ss_pred             CCCCCCCEEHCCCCHHHHHHCCCCCCCCHHHHHHHHCCCEEEE-EEECCHHHHHHHHHHHHHH
T ss_conf             6521034000002202333213455410001211100310245-6635401489999998789


No 126
>cd00384 ALAD_PBGS Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. They either contain a cysteine-rich zinc binding site (consensus DXCXCX(Y/F)X3G(H/Q)CG) or an aspartate-rich magnesium binding site (consensus DXALDX(Y/F)X3G(H/Q)DG). The cyste
Probab=33.75  E-value=24  Score=15.64  Aligned_cols=11  Identities=18%  Similarity=0.326  Sum_probs=5.0

Q ss_pred             HHHHHHHHHHH
Q ss_conf             98987446889
Q gi|254781066|r   87 KKLLAAGEEKI   97 (355)
Q Consensus        87 K~ll~~G~~rv   97 (355)
                      +.++..|...|
T Consensus        58 ~~~~~lGI~av   68 (314)
T cd00384          58 EELADLGIRAV   68 (314)
T ss_pred             HHHHHCCCCEE
T ss_conf             99998799889


No 127
>TIGR01226 phe_am_lyase phenylalanine ammonia-lyase; InterPro: IPR005922    The ubiquitous higher plant enzyme phenylalanine ammonia-lyase (PAL; 4.3.1.5 from EC) is a key biosynthetic catalyst in phenylpropanoid assembly. PAL catalyses the non-oxidative deamination of L-phenylalanine to trans-cinnamic acid. PAL contains a catalytic Ala-Ser-Gly triad that is post-translationally cyclised. PAL is structurally similar to the mechanistically related histidine ammonia lyase (HAL; 4.3.1.3 from EC), with PAL having an additional approximately 160 residues extending from the common fold . Catalysis in PAL may be governed by the dipole moments of seven alpha helices associated with the PAL active site. The cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) resides atop the positive poles of three helices, for increasing its electrophilicity. Plant and fungal PAL enzymes contain aa approximately 100-residue long C-terminal multi-helix domain, which might play a role in the rapid response of PAL in the regulation of phenylpropanoid biosynthesis by destabilising the enzyme . ; GO: 0016841 ammonia-lyase activity, 0006559 L-phenylalanine catabolic process, 0005737 cytoplasm.
Probab=33.18  E-value=14  Score=17.08  Aligned_cols=14  Identities=36%  Similarity=0.655  Sum_probs=8.4

Q ss_pred             CCCCCC-CCCCHHHH
Q ss_conf             783200-00285899
Q gi|254781066|r   72 IRKPLY-LQTSPEFS   85 (355)
Q Consensus        72 ~~~~~y-L~~SPql~   85 (355)
                      ..|+.| ||+|||.-
T Consensus       340 ~kQDRY~LRtSPQwL  354 (714)
T TIGR01226       340 PKQDRYALRTSPQWL  354 (714)
T ss_pred             CCCCCCCCCCCCCCC
T ss_conf             675644235775212


No 128
>COG4302 EutC Ethanolamine ammonia-lyase, small subunit [Amino acid transport and metabolism]
Probab=32.24  E-value=36  Score=14.58  Aligned_cols=13  Identities=15%  Similarity=0.217  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHHCC
Q ss_conf             9999999999879
Q gi|254781066|r   28 IQSSLREYFVENQ   40 (355)
Q Consensus        28 i~~~iR~ff~~~g   40 (355)
                      +-.-||.-+.+-+
T Consensus         6 ~~eii~~v~~~m~   18 (294)
T COG4302           6 IEEIVRSVMASMG   18 (294)
T ss_pred             HHHHHHHHHHHHC
T ss_conf             9999999999954


No 129
>pfam00490 ALAD Delta-aminolevulinic acid dehydratase.
Probab=30.61  E-value=31  Score=14.92  Aligned_cols=10  Identities=30%  Similarity=0.428  Sum_probs=4.3

Q ss_pred             HHHHHHHHHC
Q ss_conf             9999999987
Q gi|254781066|r   30 SSLREYFVEN   39 (355)
Q Consensus        30 ~~iR~ff~~~   39 (355)
                      ..+|+...++
T Consensus        13 ~~iR~lv~Et   22 (322)
T pfam00490        13 PALRRLVRET   22 (322)
T ss_pred             HHHHHHHHCC
T ss_conf             7899998527


No 130
>KOG1637 consensus
Probab=29.91  E-value=39  Score=14.34  Aligned_cols=120  Identities=16%  Similarity=0.161  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEECCCEECC----CCCCC--CC-CCEEEECCCCCCCCCCCC-----C--CCCHHHHHHH
Q ss_conf             999999999999999879889847821056----89854--45-412410247886783200-----0--0285899998
Q gi|254781066|r   23 LKRNMIQSSLREYFVENQFIEIDSMSLQYS----PGNET--HI-RAFSTELIIQDHIRKPLY-----L--QTSPEFSCKK   88 (355)
Q Consensus        23 ~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~----~~g~~--~~-~~f~t~~~~~~~~~~~~y-----L--~~SPql~lK~   88 (355)
                      ++=.+++..||.-...+||.||-||-+-..    .+|--  |. +-|.++.....+.-+|+-     |  ..-+--| +.
T Consensus       193 ~iyN~Lv~fir~ey~~rGf~EVitPniy~~~LWe~SGHwqnY~enmF~~e~eke~~~LKPMNCPgHcLmf~~r~rS~-re  271 (560)
T KOG1637         193 RIYNTLVDFIRAEYRKRGFTEVITPNIYNKKLWETSGHWQNYSENMFKFEVEKEEFALKPMNCPGHCLMFAHRDRSY-RE  271 (560)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEECCCCHHHHHHHHHCCCHHHHHHHCEEEEECHHHHCCCCCCCCCCCCCCCCCCCCH-HH
T ss_conf             27889999999998753874322722121566653252555443101231010332258668975301336677427-44


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCC----CCCCCCEEEECEEECCCCHHH---HHHHHHHHHHHHHHHHC
Q ss_conf             9874468899988642456777----544843002000115776578---77755788877666418
Q gi|254781066|r   89 LLAAGEEKIFCFAHAWRNGEQG----CLHQPEFTMLEWYRAHESYEQ---LMKDCMNIIRCAAEVAN  148 (355)
Q Consensus        89 ll~~G~~rvyqig~~FRaE~~~----~rHlpEFtmLE~e~af~d~~d---lm~~~E~li~~~~~~~~  148 (355)
                      |=    =|.=.+|..-|||-|+    -.|+-+|.|=|.-. |.+.++   -++-+-++++++...++
T Consensus       272 LP----lR~aDFg~LHRnE~SGaLsGLTRvRrFqQDDaHI-FCt~~Qi~~Eik~~l~fl~~vY~~fg  333 (560)
T KOG1637         272 LP----LRFADFGVLHRNEASGALSGLTRVRRFQQDDAHI-FCTPDQVKEEIKGCLDFLDYVYGVFG  333 (560)
T ss_pred             CC----CCCCCCCEEEECCCCCCCCCCCEEEEECCCCCEE-EECCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             78----4226752253054564232210110110157158-85576379999879999999986125


No 131
>TIGR02400 trehalose_OtsA alpha,alpha-trehalose-phosphate synthase [UDP-forming]; InterPro: IPR012766    This enzyme catalyzes the key, penultimate step in biosynthesis of trehalose, a compatible solute made as an osmoprotectant in some species in all three domains of life. The gene symbol OtsA stands for osmotically regulated trehalose synthesis A. Trehalose helps protect against both osmotic and thermal stresses, and is made from two glucose subunits. This entry excludes glucosylglycerol-phosphate synthase, an enzyme of an analogous osmoprotectant system in many cyanobacterial strains. This entry does not identify archaeal examples, as they are more divergent than glucosylglycerol-phosphate synthase. Sequences that score in the gray zone between the trusted and noise cut offs include a number of yeast multidomain proteins in which the N-terminal domain may be functionally equivalent to this family. The gray zone also includes the OtsA of Cornyebacterium glutamicum (and related species), shown to be responsible for synthesis of only trace amounts of trehalose while the majority is synthesized by the TreYZ pathway; the significance of OtsA in this species is unclear (see ).; GO: 0003825 alphaalpha-trehalose-phosphate synthase (UDP-forming) activity, 0005992 trehalose biosynthetic process.
Probab=29.38  E-value=40  Score=14.29  Aligned_cols=23  Identities=0%  Similarity=0.004  Sum_probs=18.7

Q ss_pred             CEEEECEEECCCCHHHHHHHHHH
Q ss_conf             30020001157765787775578
Q gi|254781066|r  116 EFTMLEWYRAHESYEQLMKDCMN  138 (355)
Q Consensus       116 EFtmLE~e~af~d~~dlm~~~E~  138 (355)
                      =.+.++.|=-++|-+...+.+.+
T Consensus       239 R~~~v~aFPIGID~~~f~~~a~~  261 (476)
T TIGR02400       239 RTVRVGAFPIGIDVDRFAEQAKK  261 (476)
T ss_pred             CEEEEEEEEECCCHHHHHHHHHC
T ss_conf             36999887420077999987314


No 132
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB; InterPro: IPR014132   This entry describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reduced sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterised polysaccharide deacetylase; the exact function this protein family is unknown..
Probab=28.74  E-value=13  Score=17.10  Aligned_cols=10  Identities=10%  Similarity=0.056  Sum_probs=4.0

Q ss_pred             EEECCEECCC
Q ss_conf             2236712256
Q gi|254781066|r  264 LYACNIELCN  273 (355)
Q Consensus       264 l~i~G~El~n  273 (355)
                      ++=+|-||+|
T Consensus        58 I~~~GHEIGs   67 (198)
T TIGR02764        58 IVKDGHEIGS   67 (198)
T ss_pred             HHHCCCCCCC
T ss_conf             9844843033


No 133
>cd03557 L-arabinose_isomerase L-Arabinose isomerase (AI) catalyzes the isomerization of L-arabinose to L-ribulose, the first reaction in its conversion into D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon source. AI can also convert D-galactose to D-tagatose at elevated temperatures in the presence of divalent metal ions. D-tagatose, rarely found in nature, is of commercial interest as a low-calorie sugar substitute.
Probab=28.73  E-value=41  Score=14.22  Aligned_cols=16  Identities=19%  Similarity=0.412  Sum_probs=11.1

Q ss_pred             CCCCEEEECCEECCCC
Q ss_conf             3022022367122564
Q gi|254781066|r  259 TKRFELYACNIELCNA  274 (355)
Q Consensus       259 a~rfdl~i~G~El~ng  274 (355)
                      .+||-|+++-.|.+..
T Consensus       393 G~rFRLivneve~v~p  408 (484)
T cd03557         393 GNRFRLVVNEVDAVEP  408 (484)
T ss_pred             CCCEEEEEEEEEEECC
T ss_conf             8847999975777468


No 134
>pfam09743 DUF2042 Uncharacterized conserved protein (DUF2042). This entry is the conserved N-terminal 300 residues of a group of proteins found from protozoa to Humans. The function is unknown.
Probab=28.54  E-value=29  Score=15.11  Aligned_cols=17  Identities=29%  Similarity=0.407  Sum_probs=8.3

Q ss_pred             HHHH-HHHHHHHHHHHHH
Q ss_conf             8987-4468899988642
Q gi|254781066|r   88 KLLA-AGEEKIFCFAHAW  104 (355)
Q Consensus        88 ~ll~-~G~~rvyqig~~F  104 (355)
                      +|.+ +|-=.+.++++.-
T Consensus        63 El~~~gGRinl~dL~~~L   80 (272)
T pfam09743        63 ELLANGGRINVVDLAKIL   80 (272)
T ss_pred             HHHHCCCCEEHHHHHHHC
T ss_conf             999829955699988761


No 135
>TIGR01184 ntrCD nitrate ABC transporter, ATP-binding proteins C and D; InterPro: IPR005890   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 model describes the ATP binding subunits of nitrate transport in bacteria and archaea. This protein belongs to the ATP-binding cassette (ABC) superfamily. It is thought that the two subunits encoded by ntrC and ntrD form the binding surface for interaction with ATP. This model is restricted in identifying ATP binding subunit associated with the nitrate transport. Nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA - a regulatory protein; ntrB - a hydropbobic transmembrane permease and narB - a reductase. ; GO: 0015112 nitrate transmembrane transporter activity, 0015706 nitrate transport, 0016020 membrane.
Probab=28.51  E-value=17  Score=16.48  Aligned_cols=38  Identities=37%  Similarity=0.656  Sum_probs=26.2

Q ss_pred             CCHHHHHHHHHHCCCCCCCEEECCHHHHHHHHHC-CCCHHHHCCCCCCCCCCC
Q ss_conf             3010189999861889632453159999899815-597131115856487433
Q gi|254781066|r  302 TYPIDEDFLACLTEMPQSSGIAMGFDRLVMLVTG-ANNINEVIWTPFSQSNQE  353 (355)
Q Consensus       302 ~~~~D~~fl~al~G~PPhgG~glGidRLvm~l~g-~~~Irdvi~FP~~r~~~~  353 (355)
                      ++-+||.++=|              ||+||+-.| ..+|=+++--|+.||++-
T Consensus       172 THDvDEAllLs--------------DR~VMlTnGP~a~IG~il~v~~~RPR~R  210 (230)
T TIGR01184       172 THDVDEALLLS--------------DRVVMLTNGPAAKIGQILEVPFPRPRDR  210 (230)
T ss_pred             ECCHHHHHHHH--------------CCEEEEECCCCCCCCCEEEECCCCCHHH
T ss_conf             52445788873--------------5102430777422575776278886007


No 136
>TIGR01733 AA-adenyl-dom amino acid adenylation domain; InterPro: IPR010071   This entry represents a domain responsible for the specific recognition of amino acids and activation as adenylyl amino acids. The reaction catalysed is aa + ATP to aa-AMP + PPi. These domains are usually found as components of multi-domain non-ribosomal peptide synthetases and are usually called 'A-domains' in that context (for a review, see ). A-domains are almost invariably followed by 'T-domains' (thiolation domains, IPR006163 from INTERPRO) to which the amino acid adenylate is transferred as a thiol-ester to a bound pantetheine cofactor with the release of AMP (these are also called peptide carrier proteins, or PCPs. When the A-domain does not represent the first module (corresponding to the first amino acid in the product molecule) it is usually preceded by a 'C-domain' (condensation domain, IPR001242 from INTERPRO) which catalyses the ligation of two amino acid thiol-esters from neighbouring modules. This domain is a subset of the AMP-binding domain, which also hits substrate--CoA ligases and luciferases.; GO: 0016874 ligase activity.
Probab=27.96  E-value=33  Score=14.78  Aligned_cols=26  Identities=27%  Similarity=0.309  Sum_probs=21.9

Q ss_pred             EEEECCEECCCCCHHCCCHHHHHHHHHH
Q ss_conf             0223671225640210699999999999
Q gi|254781066|r  263 ELYACNIELCNACDELLDPIEQRHRFEK  290 (355)
Q Consensus       263 dl~i~G~El~ng~~El~d~~~q~~rf~~  290 (355)
                      ||||.|.=+|-||  +|+|+.=.+||-.
T Consensus       357 ELyi~G~gvArGY--lnrp~lTaerFv~  382 (452)
T TIGR01733       357 ELYIGGPGVARGY--LNRPELTAERFVP  382 (452)
T ss_pred             EEEECCCCEECCC--CCCHHHHHHHCCC
T ss_conf             2786165010245--7875331654157


No 137
>PRK05776 DNA topoisomerase III; Provisional
Probab=25.73  E-value=47  Score=13.89  Aligned_cols=23  Identities=17%  Similarity=0.231  Sum_probs=10.9

Q ss_pred             HHCCCHHHHHHHHHHHHHHHHCCC
Q ss_conf             210699999999999999997288
Q gi|254781066|r  276 DELLDPIEQRHRFEKEMQEKKKIY  299 (355)
Q Consensus       276 ~El~d~~~q~~rf~~q~~~k~~~~  299 (355)
                      .++.+|+. ...+|+++..-+.|.
T Consensus       538 ~~l~~p~~-Ta~~E~~L~~I~~Gk  560 (675)
T PRK05776        538 PDLTSVEL-TRRFEEKLEKIRSGK  560 (675)
T ss_pred             HHHCCHHH-HHHHHHHHHHHHCCC
T ss_conf             65259148-999999989998799


No 138
>TIGR02676 cas_provis_2 CRISPR-associated large protein (provisional); InterPro: IPR013492    Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognizable features . This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins..
Probab=25.43  E-value=47  Score=13.86  Aligned_cols=93  Identities=16%  Similarity=0.143  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHCCCEEEECCC----EECCCCC--CCCCCCEEEECCCCCCCCCCCCCCCCH-------HHHHHHHHHHHH
Q ss_conf             999999999987988984782----1056898--544541241024788678320000285-------899998987446
Q gi|254781066|r   28 IQSSLREYFVENQFIEIDSMS----LQYSPGN--ETHIRAFSTELIIQDHIRKPLYLQTSP-------EFSCKKLLAAGE   94 (355)
Q Consensus        28 i~~~iR~ff~~~gF~EV~TPi----L~~~~~g--~~~~~~f~t~~~~~~~~~~~~yL~~SP-------ql~lK~ll~~G~   94 (355)
                      --++|+-+|++|||+.|++-.    |.-.|+-  +.-.+-|. ++...+  +.+-||.-+.       |.| -.||-.-+
T Consensus        87 ~~~ai~~lfN~RGyty~~~~ldteylnivPeqvkailmdifd-dynGed--dldsylklateqeskiseiy-nklmqkil  162 (1104)
T TIGR02676        87 EEQAISFLFNKRGYTYVDDDLDTEYLNIVPEQVKAILMDIFD-DYNGED--DLDSYLKLATEQESKISEIY-NKLMQKIL  162 (1104)
T ss_pred             HHHHHHHHHHCCCCCEECCCCCHHHHHHCHHHHHHHHHHHHH-CCCCCC--HHHHHHHHHHHHHHHHHHHH-HHHHHHHH
T ss_conf             037999987178752332775514665036889999988764-037741--16788876532124689999-99999999


Q ss_pred             H-HHHHHHHHHCCCCCCCCCCCCEEEECEEE
Q ss_conf             8-89998864245677754484300200011
Q gi|254781066|r   95 E-KIFCFAHAWRNGEQGCLHQPEFTMLEWYR  124 (355)
Q Consensus        95 ~-rvyqig~~FRaE~~~~rHlpEFtmLE~e~  124 (355)
                      + +.=.++-=......++.-|-||+.-|.+.
T Consensus       163 efklrklCte~kkD~~~~~tLKE~ls~e~e~  193 (1104)
T TIGR02676       163 EFKLRKLCTEIKKDKVETDTLKELLSEELEL  193 (1104)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             8888886101220102366775420367764


No 139
>COG1304 idi Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]
Probab=21.75  E-value=52  Score=13.61  Aligned_cols=20  Identities=40%  Similarity=0.714  Sum_probs=17.0

Q ss_pred             HHHHHHHCCCCHHHHCCCCC
Q ss_conf             99899815597131115856
Q gi|254781066|r  328 RLVMLVTGANNINEVIWTPF  347 (355)
Q Consensus       328 RLvm~l~g~~~Irdvi~FP~  347 (355)
                      +..|.|||+.||.|+-..|.
T Consensus       329 ~~~M~L~G~~~i~el~~~~l  348 (360)
T COG1304         329 KIAMALTGAKNIEELKRVPL  348 (360)
T ss_pred             HHHHHHCCCCCHHHHCCCCE
T ss_conf             99997428881999655736


No 140
>TIGR02708 L_lactate_ox L-lactate oxidase; InterPro: IPR014080   Members of this entry oxidize L-lactate to pyruvate, reducing molecular oxygen to hydrogen peroxide. The enzyme is known in Aerococcus viridans, Streptococcus iniae, and some strains of Streptococcus pyogenes where it appears to contribute to virulence..
Probab=21.11  E-value=46  Score=13.93  Aligned_cols=21  Identities=29%  Similarity=0.382  Sum_probs=17.2

Q ss_pred             HHHHHHHCCCCHHHHCCCCCC
Q ss_conf             998998155971311158564
Q gi|254781066|r  328 RLVMLVTGANNINEVIWTPFS  348 (355)
Q Consensus       328 RLvm~l~g~~~Irdvi~FP~~  348 (355)
                      ..||-|+|++||.||=.|-+-
T Consensus       340 ~~VMQL~G~Q~i~D~K~~~L~  360 (368)
T TIGR02708       340 KRVMQLTGTQTIEDVKGLDLR  360 (368)
T ss_pred             HHHHHHCCCCCHHHHHCCCCC
T ss_conf             777641387515653214133


No 141
>TIGR02653 Lon_rel_chp conserved hypothetical protein; InterPro: IPR013473    This entry describes a protein family of unknown function, about 690 residues in length, in which some members show C-terminal sequence similarity to IPR008269 from INTERPRO, which is the Lon protease C-terminal proteolytic domain, from MEROPS family S16. However, the annotated catalytic sites of Escherichia coli Lon protease are not conserved in members of this family. Members have a motif GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif GxxGxGK[ST]..
Probab=21.08  E-value=50  Score=13.73  Aligned_cols=17  Identities=29%  Similarity=0.481  Sum_probs=8.4

Q ss_pred             CCCCCCCCEEEECCEEC
Q ss_conf             83633022022367122
Q gi|254781066|r  255 DPRFTKRFELYACNIEL  271 (355)
Q Consensus       255 ~~~va~rfdl~i~G~El  271 (355)
                      |.-+-+|+--|+.|+||
T Consensus       344 DtAFfDR~H~YiPGWEI  360 (677)
T TIGR02653       344 DTAFFDRIHYYIPGWEI  360 (677)
T ss_pred             HHHHHHHHHCCCCCCCC
T ss_conf             02567556305888768


No 142
>pfam12109 CXCR4_N CXCR4 Chemokine receptor N terminal. CXCR4 and its ligand stromal cell-derived factor-1 (a.k.a. CXCL12) are essential for proper fetal development. CXCR4 is also the major coreceptor for T-tropic strains of human immunodeficiency virus 1 (HIV-1), and SDF-1 inhibits HIV-1 infection. Additionally, SDF-1 and CXCR4 mediate cancer cell migration and metastasis. The N terminal domain of most chemokine receptors is the ligand binding domain and so the N terminal domain of CXCR4 is the binding site for SDF-1.
Probab=20.96  E-value=31  Score=14.99  Aligned_cols=10  Identities=10%  Similarity=0.298  Sum_probs=6.3

Q ss_pred             HHHHCCCCCC
Q ss_conf             8642456777
Q gi|254781066|r  101 AHAWRNGEQG  110 (355)
Q Consensus       101 g~~FRaE~~~  110 (355)
                      -||||.|+.+
T Consensus        21 EPCf~~eNa~   30 (33)
T pfam12109        21 EPCFRHENAD   30 (33)
T ss_pred             CCCCCCCCCC
T ss_conf             7410113454


No 143
>COG0113 HemB Delta-aminolevulinic acid dehydratase [Coenzyme metabolism]
Probab=20.43  E-value=60  Score=13.26  Aligned_cols=15  Identities=7%  Similarity=0.224  Sum_probs=5.8

Q ss_pred             CHHHHHHHHHHHHHH
Q ss_conf             657877755788877
Q gi|254781066|r  128 SYEQLMKDCMNIIRC  142 (355)
Q Consensus       128 d~~dlm~~~E~li~~  142 (355)
                      |-+.+..-+-..||.
T Consensus        98 ~~~givqravr~ik~  112 (330)
T COG0113          98 DPDGIVQRAVRAIKE  112 (330)
T ss_pred             CCCCHHHHHHHHHHH
T ss_conf             877809999999998


No 144
>COG3919 Predicted ATP-grasp enzyme [General function prediction only]
Probab=20.07  E-value=61  Score=13.22  Aligned_cols=40  Identities=18%  Similarity=0.223  Sum_probs=17.4

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHH
Q ss_conf             98744688999886424567775448430020001157765787775578
Q gi|254781066|r   89 LLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMN  138 (355)
Q Consensus        89 ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~  138 (355)
                      ||+++-+-.-++.-..|.|      +++|    ++....++..+--++|+
T Consensus        76 LLva~GDgev~lvSq~ree------LSa~----f~v~lp~w~~l~wlceK  115 (415)
T COG3919          76 LLVACGDGEVLLVSQYREE------LSAF----FEVPLPDWALLRWLCEK  115 (415)
T ss_pred             EEEECCCCEEEEHHHHHHH------HHHH----HCCCCCCHHHHHHHHHC
T ss_conf             9996388306625756999------9887----65778738999998608


Done!