Query         gi|254780316|ref|YP_003064729.1| phenylalanyl-tRNA synthetase subunit beta [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 805
No_of_seqs    256 out of 2999
Neff          7.5 
Searched_HMMs 39220
Date          Sun May 29 15:46:56 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780316.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK00629 pheT phenylalanyl-tRN 100.0       0       0 1889.9  67.6  783    1-804     1-786 (786)
  2 TIGR00472 pheT_bact phenylalan 100.0       0       0 1800.5  61.7  797    1-803     1-848 (848)
  3 CHL00192 syfB phenylalanyl-tRN 100.0       0       0 1456.7  49.7  676    1-803     1-701 (702)
  4 COG0072 PheT Phenylalanyl-tRNA 100.0       0       0 1199.6  44.1  643  142-803     1-650 (650)
  5 PRK09616 pheT phenylalanyl-tRN 100.0       0       0  910.9  37.1  505    3-695     6-545 (546)
  6 TIGR00471 pheT_arch phenylalan 100.0       0       0  556.4  22.1  497  143-694    37-604 (605)
  7 pfam03483 B3_4 B3/4 domain. Th 100.0       0       0  448.4  10.7  173  213-385     1-174 (174)
  8 KOG2472 consensus              100.0       0       0  429.0  20.8  474  153-694    59-577 (578)
  9 smart00873 B3_4 B3/4 domain. T 100.0       0       0  362.8  11.0  172  214-385     1-174 (174)
 10 cd00769 PheRS_beta_core Phenyl 100.0 9.9E-44       0  329.5  12.3  195  491-694     2-198 (198)
 11 cd02796 tRNA_bind_bactPheRS tR 100.0 3.4E-32 8.8E-37  247.6  10.1  102   44-146     1-103 (103)
 12 COG0073 ARC1 EMAP domain [Gene  99.9 5.2E-28 1.3E-32  218.0   8.2  120   25-146     1-123 (123)
 13 pfam03147 FDX-ACB Ferredoxin-f  99.9 1.8E-24 4.6E-29  192.9  13.4   93  711-803     1-94  (94)
 14 cd02153 tRNA_bindingDomain The  99.9 3.1E-24   8E-29  191.2   8.6   93   44-146     1-99  (99)
 15 pfam01588 tRNA_bind Putative t  99.8 2.3E-21 5.8E-26  170.9   6.2   93   44-145     1-94  (94)
 16 TIGR00469 pheS_mito phenylalan  99.8 1.5E-18 3.7E-23  150.9  12.1  163  637-802   264-460 (460)
 17 KOG2783 consensus               99.8 8.1E-19 2.1E-23  152.7  10.4  182  619-803   228-436 (436)
 18 pfam03484 B5 tRNA synthetase B  99.7 7.2E-18 1.8E-22  146.0   4.4   69  401-469     1-69  (69)
 19 cd02799 tRNA_bind_EMAP-II_like  99.7 4.3E-17 1.1E-21  140.5   5.5   95   43-146     7-104 (105)
 20 smart00874 B5 tRNA synthetase   99.7 5.8E-17 1.5E-21  139.6   4.3   69  401-469     1-71  (71)
 21 cd02800 tRNA_bind_EcMetRS_like  99.4 2.3E-13   6E-18  114.0   4.1   92   43-146    10-104 (105)
 22 PRK12267 methionyl-tRNA synthe  99.3 2.3E-12 5.9E-17  106.9   6.5   22  404-425   293-314 (644)
 23 COG3382 Solo B3/4 domain (OB-f  99.3 1.1E-11 2.9E-16  102.0   9.6  141  227-390    80-222 (229)
 24 PRK00133 metG methionyl-tRNA s  99.3 4.7E-12 1.2E-16  104.8   7.3   16  373-388   388-403 (666)
 25 cd02798 tRNA_bind_CsaA tRNA-bi  99.2   3E-11 7.6E-16   99.1   6.6   87   43-145    10-106 (107)
 26 PRK10089 hypothetical protein;  99.2 9.9E-12 2.5E-16  102.5   3.8   88   43-146    13-109 (110)
 27 PRK04172 pheS phenylalanyl-tRN  99.1 3.7E-09 9.5E-14   84.2  11.6  191  484-698   240-480 (501)
 28 pfam01409 tRNA-synt_2d tRNA sy  99.0 9.7E-09 2.5E-13   81.2  12.4  191  485-697    13-222 (243)
 29 COG2517 Predicted RNA-binding   99.0 1.3E-09 3.2E-14   87.5   6.6   68   42-121   120-188 (219)
 30 PTZ00326 phenylalanyl-tRNA syn  98.9 5.3E-08 1.4E-12   76.0  13.7  192  484-697   237-488 (505)
 31 PRK06253 O-phosphoseryl-tRNA s  98.9   5E-09 1.3E-13   83.3   8.1  209  534-758   175-400 (527)
 32 KOG2241 consensus               98.8 7.7E-09   2E-13   81.9   5.1   91   41-146    96-195 (255)
 33 COG0016 PheS Phenylalanyl-tRNA  98.8 3.7E-07 9.5E-12   70.0  13.3  192  485-697   107-315 (335)
 34 TIGR00399 metG_C_term methiony  98.7 1.4E-08 3.5E-13   80.2   4.1   95   43-146    47-148 (149)
 35 cd00496 PheRS_alpha_core Pheny  98.6 5.8E-07 1.5E-11   68.6  10.6  181  492-698     4-203 (218)
 36 PRK08655 prephenate dehydrogen  98.5   4E-06   1E-10   62.6  12.2  131  659-803   310-440 (441)
 37 pfam09513 consensus             98.5 5.3E-07 1.4E-11   68.9   7.7   97   44-151     4-122 (356)
 38 PHA02142 putative RNA ligase    98.5 8.7E-07 2.2E-11   67.4   8.0   96   44-151    10-124 (366)
 39 PRK00488 pheS phenylalanyl-tRN  98.3 1.4E-05 3.6E-10   58.8  11.7  186  486-697   104-317 (338)
 40 TIGR02306 RNA_lig_DRB0094 RNA   97.9 4.6E-06 1.2E-10   62.2   1.3  217   45-381     4-246 (374)
 41 COG4937 Predicted regulatory d  97.7 0.00047 1.2E-08   48.0  10.0   61  713-774    80-141 (171)
 42 PRK09537 pylS pyrolysyl-tRNA s  97.7 1.3E-05 3.4E-10   59.0   1.5  182  492-698   210-397 (420)
 43 COG2024 Phenylalanyl-tRNA synt  97.5 7.8E-05   2E-09   53.5   3.6  179  531-725   173-368 (536)
 44 TIGR00468 pheS phenylalanyl-tR  97.5  0.0007 1.8E-08   46.7   8.5  146  538-698   174-338 (362)
 45 cd00768 class_II_aaRS-like_cor  97.5 0.00071 1.8E-08   46.7   7.9  178  492-681     3-188 (211)
 46 TIGR00470 sepS O-phosphoseryl-  97.5 0.00031   8E-09   49.2   6.0  213  531-761   183-424 (558)
 47 KOG2784 consensus               97.4  0.0021 5.4E-08   43.4   9.1  222  447-691   166-445 (483)
 48 TIGR02367 PylS pyrrolysyl-tRNA  97.3  0.0002   5E-09   50.7   2.9  180  492-699   243-431 (453)
 49 cd00773 HisRS-like_core Class   96.4    0.03 7.7E-07   35.2   8.5   90  491-581     5-97  (261)
 50 PRK09616 pheT phenylalanyl-tRN  94.7   0.043 1.1E-06   34.1   4.0   53  236-288   132-185 (546)
 51 PRK12292 hisZ ATP phosphoribos  94.2   0.039 9.9E-07   34.4   2.8   62  668-741   289-352 (388)
 52 PRK12295 hisZ ATP phosphoribos  93.9   0.049 1.3E-06   33.7   2.8   22  674-695   345-368 (373)
 53 pfam00587 tRNA-synt_2b tRNA sy  93.0   0.096 2.4E-06   31.6   3.1   88  492-580     3-95  (170)
 54 PRK00037 hisS histidyl-tRNA sy  92.9   0.088 2.3E-06   31.8   2.8   32  668-700   286-318 (417)
 55 TIGR02222 chap_CsaA export-rel  92.7   0.096 2.4E-06   31.6   2.8   75   43-146     8-106 (107)
 56 cd00779 ProRS_core_prok Prolyl  92.1    0.95 2.4E-05   24.5   8.3   92  488-580    31-127 (255)
 57 PRK12421 ATP phosphoribosyltra  91.5    0.15 3.9E-06   30.2   2.6   80  648-744   277-360 (391)
 58 CHL00192 syfB phenylalanyl-tRN  91.1    0.23   6E-06   28.8   3.3   68  652-740   615-688 (702)
 59 CHL00201 syh histidine-tRNA sy  90.1     0.3 7.5E-06   28.1   3.1   64  668-741   285-352 (424)
 60 PRK12420 histidyl-tRNA synthet  90.0    0.27   7E-06   28.4   2.8   27  673-699   301-330 (421)
 61 cd00778 ProRS_core_arch_euk Pr  89.7    0.49 1.2E-05   26.6   3.9  122  448-581     4-134 (261)
 62 PRK12293 hisZ ATP phosphoribos  89.0    0.21 5.2E-06   29.3   1.5   88  491-580    22-109 (281)
 63 PRK03932 asnC asparaginyl-tRNA  88.9    0.29 7.3E-06   28.2   2.2   33   45-80     22-54  (462)
 64 pfam00152 tRNA-synt_2 tRNA syn  87.8    0.55 1.4E-05   26.2   3.1  115  492-633    26-140 (341)
 65 PRK12325 prolyl-tRNA synthetas  87.6    0.59 1.5E-05   26.0   3.2   26  231-261    40-65  (438)
 66 cd00776 AsxRS_core Asx tRNA sy  87.5    0.44 1.1E-05   26.9   2.5   79  491-582    27-105 (322)
 67 PRK11342 mhpD 2-keto-4-penteno  86.6     2.4 6.1E-05   21.7   7.0   23  664-686    57-80  (262)
 68 TIGR02865 spore_II_E stage II   86.6     1.2   3E-05   23.8   4.2   96  685-786   662-769 (794)
 69 cd00771 ThrRS_core Threonyl-tR  86.4    0.64 1.6E-05   25.7   2.8   93  486-581    28-126 (298)
 70 COG0124 HisS Histidyl-tRNA syn  86.2    0.82 2.1E-05   25.0   3.3   65  668-741   293-362 (429)
 71 PRK12305 thrS threonyl-tRNA sy  86.1    0.92 2.3E-05   24.6   3.5  150  409-581   149-305 (576)
 72 PRK12445 lysyl-tRNA synthetase  85.1    0.91 2.3E-05   24.7   3.1  112  492-632   188-301 (505)
 73 TIGR01393 lepA GTP-binding pro  84.7     2.9 7.5E-05   21.1   7.0  158  546-738   250-425 (598)
 74 cd00770 SerRS_core Seryl-tRNA   84.2    0.77   2E-05   25.2   2.4  129  446-581    11-146 (297)
 75 PRK05159 aspC aspartyl-tRNA sy  83.3     1.5 3.7E-05   23.2   3.5   34   45-81     21-54  (434)
 76 PRK08526 threonine dehydratase  82.9     1.5 3.8E-05   23.1   3.4  297  111-437    77-401 (403)
 77 PRK12304 thrS threonyl-tRNA sy  82.3     2.4 6.2E-05   21.6   4.3  146  410-581   181-335 (604)
 78 PRK06382 threonine dehydratase  79.7     2.5 6.3E-05   21.6   3.6  296  110-436    75-398 (400)
 79 PRK02983 lysS lysyl-tRNA synth  79.1     1.5 3.9E-05   23.1   2.3   76  492-580   780-858 (1099)
 80 cd00775 LysRS_core Lys_tRNA sy  78.0     2.9 7.5E-05   21.1   3.6   25  493-517    13-37  (329)
 81 PRK03772 threonyl-tRNA synthet  76.7     2.5 6.4E-05   21.5   2.9  239  410-681   214-496 (642)
 82 PRK00413 thrS threonyl-tRNA sy  76.4     2.7   7E-05   21.3   3.0  149  410-582   211-366 (639)
 83 cd00669 Asp_Lys_Asn_RS_core As  76.2     3.3 8.4E-05   20.7   3.4  115  492-633     5-119 (269)
 84 PRK04483 threonyl-tRNA synthet  75.8     2.9 7.3E-05   21.1   3.0  147  409-581   213-367 (634)
 85 KOG0556 consensus               75.7     1.9 4.9E-05   22.4   2.1   88  489-588   229-316 (533)
 86 TIGR01127 ilvA_1Cterm threonin  75.5     5.7 0.00015   19.0   5.4  282  111-436    57-380 (381)
 87 PRK09350 lysyl-tRNA synthetase  75.0     2.2 5.6E-05   21.9   2.3  116  490-633    18-139 (325)
 88 pfam09840 DUF2067 Uncharacteri  74.8     2.6 6.7E-05   21.4   2.6   62  402-468    69-130 (190)
 89 PRK08198 threonine dehydratase  74.2     2.4 6.1E-05   21.7   2.3  292  111-436    81-403 (406)
 90 COG1190 LysU Lysyl-tRNA synthe  73.2     2.9 7.5E-05   21.1   2.5  108  493-632   185-297 (502)
 91 PRK00484 lysS lysyl-tRNA synth  71.1     5.7 0.00015   19.0   3.6   59   16-82     33-92  (491)
 92 PRK12444 threonyl-tRNA synthet  70.5     5.8 0.00015   19.0   3.5  146  410-581   217-370 (639)
 93 TIGR03220 catechol_dmpE 2-oxop  69.6     7.8  0.0002   18.1   7.2   23  664-686    53-76  (255)
 94 PRK03991 threonyl-tRNA synthet  69.3       6 0.00015   18.8   3.4  114  462-580   201-323 (613)
 95 cd00772 ProRS_core Prolyl-tRNA  68.5     6.3 0.00016   18.7   3.4   93  488-580    32-133 (264)
 96 cd00777 AspRS_core Asp tRNA sy  66.2     7.6 0.00019   18.1   3.4  113  492-632     5-118 (280)
 97 PRK06462 asparagine synthetase  66.0     4.6 0.00012   19.7   2.3  117  490-632    31-149 (332)
 98 TIGR00308 TRM1 N2,N2-dimethylg  65.9       6 0.00015   18.8   2.8   23  442-465   342-364 (462)
 99 cd00670 Gly_His_Pro_Ser_Thr_tR  64.4     6.7 0.00017   18.5   2.8   92  490-581     4-103 (235)
100 TIGR00802 nico transition meta  63.8     1.7 4.3E-05   22.7  -0.3   41  265-331    11-51  (290)
101 TIGR00458 aspS_arch aspartyl-t  62.5     5.2 0.00013   19.3   2.0   54  292-345   206-263 (466)
102 pfam11148 DUF2922 Protein of u  62.1      11 0.00027   17.1   4.0   36  752-793     6-41  (69)
103 TIGR01703 hybrid_clust hydroxy  61.1     7.4 0.00019   18.2   2.6   24  504-527   211-234 (567)
104 pfam02005 TRM N2,N2-dimethylgu  61.0     6.4 0.00016   18.7   2.2   21  254-274   111-131 (375)
105 PRK12820 bifunctional aspartyl  59.1     7.3 0.00019   18.3   2.3   82  651-736   488-596 (706)
106 TIGR02902 spore_lonB ATP-depen  58.4     3.4 8.7E-05   20.6   0.5   60  280-340   117-213 (532)
107 TIGR00418 thrS threonyl-tRNA s  55.4      12 0.00031   16.7   2.9  148  409-580   147-309 (595)
108 PRK04140 hypothetical protein;  55.1      14 0.00035   16.3   3.8   83  346-438   144-227 (319)
109 pfam08853 DUF1823 Domain of un  53.9       8  0.0002   18.0   1.8   57  406-462     2-62  (116)
110 COG0441 ThrS Threonyl-tRNA syn  52.4      15 0.00039   16.0   4.6  147  410-581   162-316 (589)
111 TIGR00501 met_pdase_II methion  51.0     8.9 0.00023   17.6   1.6   42  241-303   172-213 (327)
112 TIGR00442 hisS histidyl-tRNA s  50.9      15 0.00039   16.0   2.8   28  670-697   307-335 (446)
113 PRK07334 threonine dehydratase  50.3      14 0.00036   16.2   2.6  124  303-436   270-397 (399)
114 KOG1936 consensus               50.1      16 0.00042   15.7   3.1   22  681-702   389-410 (518)
115 TIGR00268 TIGR00268 conserved   46.9      18 0.00047   15.4   3.0  180  327-511    42-253 (263)
116 PRK07522 acetylornithine deace  46.2      19 0.00048   15.3   4.1   45    4-48      7-59  (387)
117 pfam08501 Shikimate_dh_N Shiki  45.3     9.9 0.00025   17.3   1.1   48  418-469    32-79  (83)
118 PRK12310 hydroxylamine reducta  45.2      19  0.0005   15.2   3.9   12  749-760   386-397 (429)
119 TIGR01278 DPOR_BchB light-inde  44.2     5.3 0.00014   19.2  -0.4   82  414-509   173-270 (562)
120 PRK05290 hydroxylamine reducta  43.9      19  0.0005   15.2   2.4   14  747-760   495-508 (540)
121 COG4079 Uncharacterized protei  43.1      21 0.00053   15.0   4.4   40   16-55     44-87  (293)
122 TIGR01047 nspC carboxynorsperm  42.3     8.5 0.00022   17.8   0.4   72  440-537    77-152 (403)
123 cd01914 HCP Hybrid cluster pro  42.3      21 0.00055   14.9   2.5   10  169-178    74-83  (423)
124 TIGR01362 KDO8P_synth 3-deoxy-  42.2      16 0.00041   15.8   1.8   25  163-187    46-70  (279)
125 COG0849 ftsA Cell division ATP  42.1      22 0.00055   14.9   3.8   12   61-72      7-18  (418)
126 TIGR01371 met_syn_B12ind 5-met  41.9      14 0.00035   16.3   1.4   93  415-514   278-381 (778)
127 TIGR01995 PTS-II-ABC-beta PTS   41.7      12 0.00031   16.7   1.1   15  337-351   161-176 (660)
128 KOG1885 consensus               39.6      12  0.0003   16.7   0.8   74  493-580   230-307 (560)
129 COG2877 KdsA 3-deoxy-D-manno-o  39.5      18 0.00046   15.4   1.7   33  155-187    51-84  (279)
130 cd01982 Chlide_reductase_Z Chl  38.3      12  0.0003   16.8   0.6   23  415-437   166-190 (412)
131 TIGR01059 gyrB DNA gyrase, B s  37.6      25 0.00064   14.4   2.2  115  383-513   441-582 (818)
132 KOG0578 consensus               37.3      25 0.00065   14.4   2.5   11  458-468   316-326 (550)
133 pfam05919 Mitovir_RNA_pol Mito  37.1    0.75 1.9E-05   25.2  -5.6   72  256-329   200-274 (495)
134 KOG2713 consensus               36.0      27 0.00068   14.3   2.9   16  617-632   283-299 (347)
135 TIGR02628 fuculo_kin_coli L-fu  35.3      19 0.00048   15.3   1.3   17  213-230   105-121 (473)
136 PRK06133 glutamate carboxypept  35.2      27  0.0007   14.2   5.2   44    5-48     48-101 (418)
137 cd04750 Commd2 COMM_Domain con  35.0      24 0.00061   14.6   1.8   96  339-456    15-111 (166)
138 COG3971 2-keto-4-pentenoate hy  34.6      28 0.00071   14.1   3.9   13  224-236    59-71  (264)
139 KOG0736 consensus               34.1      11 0.00028   17.0  -0.1   24  413-436   500-523 (953)
140 pfam02027 RolB_RolC RolB/RolC   33.7      29 0.00073   14.0   2.0   40  417-456    77-116 (189)
141 PRK08639 threonine dehydratase  32.8      30 0.00076   13.9   4.0  293  111-437    82-406 (418)
142 COG1724 Predicted RNA binding   32.6      30 0.00077   13.9   2.5   33  418-450     6-47  (66)
143 COG0381 WecB UDP-N-acetylgluco  32.2      27 0.00069   14.2   1.7   22  444-466   207-231 (383)
144 cd01990 Alpha_ANH_like_I This   32.0      31 0.00078   13.8   3.3   55  418-472   131-190 (202)
145 PRK03634 rhamnulose-1-phosphat  32.0      31 0.00078   13.8   3.9   32   49-81     79-110 (274)
146 TIGR02700 flavo_MJ0208 archaeo  32.0      16  0.0004   15.9   0.4   10  460-469    40-49  (237)
147 smart00842 FtsA Cell division   31.3      32  0.0008   13.7   5.2   91  360-453    37-130 (187)
148 pfam08536 Whirly Whirly transc  30.5      32 0.00083   13.6   3.5   68   15-91     56-127 (139)
149 PRK04338 N(2),N(2)-dimethylgua  30.2      33 0.00083   13.6   2.3   43  232-274    89-131 (376)
150 COG3705 HisZ ATP phosphoribosy  30.0      33 0.00084   13.6   3.4   79  646-739   266-347 (390)
151 TIGR01124 ilvA_2Cterm threonin  30.0      27 0.00069   14.2   1.4  155  110-308    75-257 (508)
152 pfam08676 MutL_C MutL C termin  29.7      33 0.00085   13.6   3.7   59  398-464    52-112 (142)
153 PTZ00031 ribosomal protein L2;  29.2      34 0.00087   13.5   8.5   43   45-88    119-161 (330)
154 pfam09866 DUF2093 Uncharacteri  28.7      35 0.00088   13.4   2.0   19   82-100     2-20  (42)
155 TIGR02045 P_fruct_ADP ADP-spec  28.6      20 0.00052   15.1   0.5   27  498-524    96-123 (466)
156 pfam05339 DUF739 Protein of un  28.6      12  0.0003   16.8  -0.7   19  337-355    42-60  (69)
157 TIGR01792 urease_alph urease,   27.8      36 0.00091   13.3   1.7   79  664-751   500-594 (605)
158 TIGR02342 chap_CCT_delta T-com  27.7      17 0.00043   15.6  -0.0  122  405-543   296-429 (526)
159 pfam02311 AraC_binding AraC-li  27.7      36 0.00092   13.3   4.9  107  260-380     9-115 (134)
160 PRK09310 aroDE bifunctional 3-  27.7      36 0.00092   13.3   1.7   51  417-471   250-300 (477)
161 COG1606 ATP-utilizing enzymes   27.6      36 0.00092   13.3   4.9  176  326-508    43-246 (269)
162 TIGR01686 FkbH FkbH domain; In  27.4      27 0.00069   14.2   1.0   38  332-373    84-123 (337)
163 TIGR02280 PaaB1 phenylacetate   27.3      36 0.00091   13.4   1.6   25  160-184    11-37  (259)
164 PRK10296 DNA-binding transcrip  26.8      37 0.00094   13.2   1.6   45  259-309    26-70  (271)
165 TIGR01241 FtsH_fam ATP-depende  26.1      35  0.0009   13.4   1.4   39  130-169   151-211 (505)
166 PRK12271 rps10p 30S ribosomal   26.1      38 0.00098   13.1   4.3   10  373-382    16-25  (102)
167 KOG0456 consensus               25.9      39 0.00098   13.1   2.3   23  707-730   502-524 (559)
168 COG3376 HoxN High-affinity nic  25.7      19 0.00047   15.4  -0.1   44  264-333    61-104 (342)
169 PRK10119 hypothetical protein;  25.3      40   0.001   13.0   1.6   13  455-467    92-104 (231)
170 KOG0358 consensus               25.2      40   0.001   13.0   2.0   39  418-463   322-360 (534)
171 PRK02910 light-independent pro  25.1      28 0.00073   14.1   0.8   24  414-437   168-193 (524)
172 PRK00095 mutL DNA mismatch rep  25.0      40   0.001   13.0   3.2   21  246-268   167-187 (612)
173 COG1171 IlvA Threonine dehydra  24.9      40   0.001   13.0   1.9  217  110-347    82-324 (347)
174 CHL00076 chlB photochlorophyll  24.9      30 0.00077   13.8   0.9   23  414-436   173-197 (510)
175 PHA02512 minor structural prot  24.7      18 0.00046   15.5  -0.3   42  721-762   773-819 (844)
176 TIGR02939 RpoE_Sigma70 RNA pol  24.7      29 0.00074   14.0   0.7   56  496-555    82-137 (192)
177 TIGR01458 HAD-SF-IIA-hyp3 HAD-  24.6      36 0.00093   13.3   1.2   21  228-248   180-200 (258)
178 cd00153 RalGDS_RA This CD repr  24.5      41   0.001   12.9   2.8   35  327-361    17-51  (87)
179 pfam11548 Receptor_IA-2 Protei  24.3      41  0.0011   12.9   5.0   69  727-803    13-83  (91)
180 pfam11829 DUF3349 Protein of u  24.0      42  0.0011   12.9   2.5   63  411-507    28-90  (97)
181 TIGR01647 ATPase-IIIA_H plasma  24.0      28 0.00073   14.0   0.6  268  204-511   186-566 (835)
182 PRK09295 selenocysteine lyase;  24.0      42  0.0011   12.9   4.4   30  766-799   377-406 (406)
183 TIGR00003 TIGR00003 copper ion  22.9      44  0.0011   12.7   1.8   13   18-30     51-63  (66)
184 PRK11161 fumarate/nitrate redu  22.9      44  0.0011   12.7   2.6   55  370-433   154-210 (235)
185 PRK12354 carbamate kinase; Rev  22.8      44  0.0011   12.7   3.8   56  410-465   119-174 (302)
186 KOG0971 consensus               22.2      45  0.0011   12.6   3.6   54   73-126    22-75  (1243)
187 COG1458 Predicted DNA-binding   22.1      45  0.0012   12.6   2.9   43  422-464    57-101 (221)
188 TIGR02824 quinone_pig3 putativ  21.8      34 0.00086   13.5   0.6   17  153-169    28-45  (334)
189 TIGR03676 aRF1/eRF1 peptide ch  21.8      46  0.0012   12.6   1.6   85  302-402   136-223 (403)
190 TIGR00658 orni_carb_tr ornithi  21.1      47  0.0012   12.5   2.7   91  216-325    95-195 (341)
191 TIGR01246 dapE_proteo succinyl  21.0      48  0.0012   12.5   2.4  132    5-162     2-164 (383)
192 COG1867 TRM1 N2,N2-dimethylgua  20.8      48  0.0012   12.4   3.0   25  251-275   109-133 (380)
193 TIGR01490 HAD-SF-IB-hyp1 HAD-s  20.8      48  0.0012   12.5   1.2   61  455-515   114-181 (204)
194 PRK04011 peptide chain release  20.6      48  0.0012   12.4   1.5   84  302-401   143-229 (409)
195 PRK00029 hypothetical protein;  20.4      11 0.00028   17.0  -2.1   63  313-384   246-312 (487)
196 PRK12342 putative electron tra  20.3      49  0.0013   12.4   4.4  126  665-799   122-254 (254)
197 PHA02241 hypothetical protein   20.1      50  0.0013   12.3   3.3  133  662-804    30-170 (182)
198 COG1904 UxaC Glucuronate isome  20.0      37 0.00096   13.2   0.5   13  414-426   258-270 (463)

No 1  
>PRK00629 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=100.00  E-value=0  Score=1889.88  Aligned_cols=783  Identities=41%  Similarity=0.685  Sum_probs=737.6

Q ss_pred             CCCCHHHHHHHCCCCCCHHHHHHHHHHCCCEEEEEECC-CCCCCEEEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECC
Q ss_conf             97786799884789998899999987458604211124-656874899999975657998-7089997599957989754
Q gi|254780316|r    1 MKFTLSWLKDHLDTDVSLEKICDTLTSIGLEVEKVDNR-EALSPFTIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCG   78 (805)
Q Consensus         1 M~is~~WL~~~v~~~~~~~~l~~~lt~~G~EVe~i~~~-~~~~~vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~Ivcg   78 (805)
                      ||||++||+||+|+++|+++|+++||++|+|||+++.. ..+++||||+|++|+|||||| |++|+||+|+ +.+|||||
T Consensus         1 M~vs~~WL~e~v~~~~~~~~l~~~Lt~~G~EVE~v~~~~~~~~~vvvg~Vl~~~~HP~adkL~vc~Vd~G~-~~~qIVcG   79 (786)
T PRK00629          1 MKFSLSWLKELVDTDISPDELAEALTMIGLEVEGVEPLAPGLSGVVVGKVLECEKHPNADKLRVCQVDVGD-ELLQIVCG   79 (786)
T ss_pred             CCCCHHHHHHHCCCCCCHHHHHHHHHHCCEEEEEEEECCCCCCCEEEEEEEEEEECCCCCCEEEEEEEECC-EEEEEECC
T ss_conf             94787999977299999999999986543621267725667787699999997667998712799998399-68889879


Q ss_pred             CCCCCCCCEEEEECCCCEECCCCEEEEEEHHCCCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCCCCHHHHHCCCCEEEE
Q ss_conf             83455897898966877925898398331205865054541188769985477507816888888455887088855999
Q gi|254780316|r   79 APNVRVGLLGVWAPPGSCIPENNMIVNVRKIRGIESTGMMCSEKELMLSDDSASIMELPIDAPVGGRLSDYLELSDPIID  158 (805)
Q Consensus        79 A~Nv~~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G~~~~~~l~l~D~i~e  158 (805)
                      ||||++|++||||+|||+|| ||++||++||||++|+|||||++||||+++|+|||+||+++++|+++.+|++++|+|||
T Consensus        80 A~Nv~~G~~V~vA~~Ga~lp-~~~~Ik~~kirGv~S~GMlCS~~ELGl~~~~~GI~~l~~~~~~G~~~~~~l~l~D~iie  158 (786)
T PRK00629         80 APNVRAGLKVPVALPGAVLP-GGFKIKKAKLRGVESEGMLCSASELGLSDDHDGIIELPEDAPLGTDIREYLGLDDPVIE  158 (786)
T ss_pred             CCCCCCCCEEEEECCCCCCC-CCCEEEEEEECCEEECCEECCHHHCCCCCCCCCEEECCCCCCCCCCHHHHHCCCCEEEE
T ss_conf             86225899999977798968-99789764457703365564987849997779859858999888488997289975999


Q ss_pred             EEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf             87087857665557899987764115666655456677777774158984073111233201123224556637787888
Q gi|254780316|r  159 VSLTPNRSDCIGVRGIALDLVAAGLGKLKEINISCPLSSESIPLEIKFDLDDSSLCKGFAMCCVKGVRNNVAPNWMRQRL  238 (805)
Q Consensus       159 i~iTpNR~D~ls~~GiARElaa~~~~~l~~~~~~~~~~~~~~~~~i~v~i~~~~~c~~y~~~~i~~v~~~~SP~wl~~rL  238 (805)
                      ++|||||||||||+|+|||+||+++.+++.|......   .....++++++++++||+|.+++|+||++++||+|||.||
T Consensus       159 i~iTpNR~D~ls~~GiARElaa~~~~~l~~~~~~~~~---~~~~~~~v~i~~~~~c~~y~~~~i~~v~~~~SP~wl~~rL  235 (786)
T PRK00629        159 ISLTPNRADCLSVRGIARELAAAYGLPLKLPEIEPVP---ATSDDLPVEVEDPEACPRYAGRVIKGVKNAPSPLWLQERL  235 (786)
T ss_pred             EEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC---CCCCCCEEEEECCCCCCCEEEEEEECCCCCCCHHHHHHHH
T ss_conf             8737974777788999999999859987786656566---6667744898566788737589997853478959999999


Q ss_pred             HHHCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEEECCCCCCHHHHHHHCCCCCCCCEEEECCCCCCCCHHHCC
Q ss_conf             86401321039999989998608700000102233326886235543114554201124543200002567631001113
Q gi|254780316|r  239 KAVGLRSISALVDITNYVSLDRGYPSHVFDASRISDVLTVRRACSGEKILALDNQEYDLSPDNVVIASDGRIQSIAGIIG  318 (805)
Q Consensus       239 ~~~Gir~inniVDitNyvmle~GqPlHafD~dki~~~i~vr~a~~~E~~~~Ld~~e~~L~~~~lvI~d~~~~ialaGImG  318 (805)
                      .++|+|||||+||||||||||+||||||||+|||+++|+||+|++||+|+||||++|+|++++|||||+++|+|||||||
T Consensus       236 ~~~Gir~iNniVDitNyvmle~GqPlHafD~dki~~~i~Vr~a~~~E~~~tLd~~e~~L~~~~lvI~d~~~~ialAGVmG  315 (786)
T PRK00629        236 RRAGIRPINNLVDITNYVMLELGQPLHAFDLDKIKGGIVVRRAKEGEKLVTLDGKERTLDEDDLVIADDDKPLALAGVMG  315 (786)
T ss_pred             HHCCCCCCCHHHHHHHHHHHHHCCCCEEECCHHCCCCEEEEECCCCCEEEEECCCEEECCCCCEEEEECCCCCEEEEEEC
T ss_conf             97598551258889999999849413588723348978999768994578644845752788589993898534635706


Q ss_pred             CCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECC
Q ss_conf             55312013672699997157878887788761654015544134553013588999888752123345556525874135
Q gi|254780316|r  319 GKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLILSLCGGTASDICIARNIT  398 (805)
Q Consensus       319 g~~s~v~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li~e~~gg~~~~~~~~~~~~  398 (805)
                      |.+|+|+++||+||||||||+|.+||+|||+|+|+||||||||||+||+++..|++||++||.++|||++++..+.+..+
T Consensus       316 g~~s~v~~~T~~illEsA~F~p~~Ir~tsr~l~l~TdaS~RfERGvdp~~~~~al~ra~~Li~e~~gg~~~~~~~~~~~~  395 (786)
T PRK00629        316 GEDSEVTEDTTNVLLEAAYFDPLAIRKTARRLGLHTDASYRFERGVDPALTVEALERATALILELCGGEVSPVVDAGSEP  395 (786)
T ss_pred             CCCCEEECCCCEEEEEECEECHHHHHHHHHHHCCCCHHEEEEECCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCC
T ss_conf             77633414750599995669979999999984999601578735899899999999999999987398140027704678


Q ss_pred             CCCCCEECCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             54310000431133331134587899999998402221034562366403454334402567676765352334667655
Q gi|254780316|r  399 YKPRKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQIKSEPLP  478 (805)
Q Consensus       399 ~~~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGYdnIp~~~l~  478 (805)
                      .++++|.++.++++++||++|+.++|.++|++|||+++.++++|.|+||+||+||++|+||||||+|+|||||||++++.
T Consensus       396 ~~~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~~~~~~v~vPs~R~DI~~e~DLiEEIaRiyGYdnIp~~~~~  475 (786)
T PRK00629        396 TLPATITLRLERINRLLGTEIPKEEVERILTRLGFKVDGDGESLTVTVPSYRFDIEIEADLVEEVARIYGYDNIPSTPPE  475 (786)
T ss_pred             CCCCEEEECHHHHHHHHCCCCCHHHHHHHHHHCCCEEEECCCCEEEECCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCC
T ss_conf             88816995899999872887799999999997499998348518998589776668886399999988180437775776


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHH
Q ss_conf             44345767899889546789887877877402321004825765520000000024677643210151221106776432
Q gi|254780316|r  479 LTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPISADMSNMRTSLLPGLLKATGR  558 (805)
Q Consensus       479 ~~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~  558 (805)
                      .+.  ..+..+..+.+.+++|+.|+++||+|++||||++++.++.|+..++.++|.||+|+|+++||+||+||||+++++
T Consensus       476 ~~~--~~~~~~~~~~~~~~ir~~L~~~Gf~EvitySf~s~~~~~~~~~~~~~v~l~NPls~e~s~lR~SLlp~LL~~~~~  553 (786)
T PRK00629        476 AKL--PAGELTEAQKRRRRVRRALAARGYQEAITYSFVSPEVADLFGLGEDALKLLNPISSELSVMRTSLLPGLLEALAY  553 (786)
T ss_pred             CCC--CCCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHCCCCCCEEECCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             555--788899899999999999997898424136667979998627887756853754212688888779999998998


Q ss_pred             HCCCCCCHHHHHHHCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCE
Q ss_conf             10158611345430244447775443100022103543101246202345443333146888753111111101453330
Q gi|254780316|r  559 NVDRAIADFAIFEVSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVSLDSL  638 (805)
Q Consensus       559 N~~r~~~~i~lFEiG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~~~~~~  638 (805)
                      |++|+++++++||+|+||.++.  .|...++++        .+|..+...|..+.+.+|||++||++++++..++....+
T Consensus       554 N~~r~~~~i~lFEiG~vf~~~~--~E~~~La~~--------~~G~~~~~~w~~~~~~~dffdlKg~ve~ll~~lgi~~~~  623 (786)
T PRK00629        554 NQNRKNKDVALFEIGLVFLPGP--REPLHLAGV--------LTGLRLNESWGGKGRPVDFFDAKGDLEALLGALGLLADV  623 (786)
T ss_pred             HHHCCCCCEEEEEEEEEECCCC--CHHEEEEEE--------EECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCE
T ss_conf             8627998767998754389998--446599999--------989877666566676468999999999999973998435


Q ss_pred             EEECCCCCCCCCCCEEEEEECCEEEEEEEEEECHHHHHHCCCCCCEEEEEEEHHHHHHHHHCCCCCCCCCCCCCCCCCEE
Q ss_conf             33058865678981699998792999998547789999668799789999878762354520245663136898887200
Q gi|254780316|r  639 RFESGAPSWYHPGRSGIIKTSAEIVLGYFGEFHPNILDFFGLSNPICGFEVYLDSIPISQKKRTKTKKVVHLSSLHPVKR  718 (805)
Q Consensus       639 ~~~~~~~~~~hPgrsa~I~~~gk~iiG~iG~ihP~i~~~~~i~~~v~~~EI~ld~L~~~~~~~~~~~~~~~~s~fP~v~R  718 (805)
                      ++...++++|||||||.|+++|+.+ |++|+|||.++++|+|+.+||+|||+|+.|....   ...++|+++|+||+++|
T Consensus       624 ~~~~~~~~~~hPgrsA~I~~~~~~I-G~iG~lhP~i~~~~~i~~~v~~~Ei~l~~l~~~~---~~~~~~~~~skfP~v~R  699 (786)
T PRK00629        624 EFVPAEHPALHPGRSAAIYLGGKVI-GFIGQLHPEVLKKYDLPGRTYVFELDLDALLERK---KKKPPAKPISKFPAVRR  699 (786)
T ss_pred             EEECCCCCCCCCCCEEEEEECCEEE-EEEEEECHHHHHHCCCCCCEEEEEEEHHHHHHHH---HCCCCCCCCCCCCCCCE
T ss_conf             8811788776787579999999899-9999998999997397998899999989944313---04776788898997024


Q ss_pred             EEEEEECCCCCHHHHHHHHHHCC-CCEEEEEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             18999668879999999997111-00357698987636779988426999999847798889999999999999999999
Q gi|254780316|r  719 DLAFIVDQHIPAGTLVNIIKNVD-RLIDDVTVFDVFQGKSLGEGKKSVAIQVLIQPLKDTFRDDDIRILMDRIVENVVKK  797 (805)
Q Consensus       719 Dls~iv~~~v~~~~I~~~i~~~~-~ll~~v~lfDvY~g~~i~~gkkSla~rl~fqs~~kTLtd~EI~~i~~~ii~~l~~k  797 (805)
                      ||||++|+++++++|+++|++++ ++|+++++||+|+|+++++||||+||||+||+.+|||||+||++++++|++.|+++
T Consensus       700 Dla~vvd~~v~~~~I~~~I~~~~~~ll~~v~lfDvY~g~~i~~gkKSla~rl~fq~~~kTLtd~EI~~~~~~ii~~l~~~  779 (786)
T PRK00629        700 DIALVVDEDVPAAEIVKAIKKAGGKLLESVRLFDVYEGKGLPEGKKSLAISLTLQDPERTLTDEEINAAVDKIVAALEEK  779 (786)
T ss_pred             EEEEEECCCCCHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             69999889998999999998629332628879998679998999658999999999899979999999999999999997


Q ss_pred             HCCEECC
Q ss_conf             5119816
Q gi|254780316|r  798 TNAVLRS  804 (805)
Q Consensus       798 ~ga~LRs  804 (805)
                      |||+||.
T Consensus       780 ~~a~LRg  786 (786)
T PRK00629        780 FGATLRG  786 (786)
T ss_pred             HCCEECC
T ss_conf             4928379


No 2  
>TIGR00472 pheT_bact phenylalanyl-tRNA synthetase, beta subunit; InterPro: IPR004532   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 (see IPR002319 from INTERPRO). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta. 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 beta subunit. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps (see also IPR004531 from INTERPRO). This family represents the subfamily that includes the beta subunit from bacteria other than spirochetes, as well as a chloroplast-encoded form from Porphyra purpurea. The chloroplast-derived sequence is considerably shorter at the N-terminal.; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=1800.46  Aligned_cols=797  Identities=37%  Similarity=0.602  Sum_probs=729.5

Q ss_pred             CCCCHHHHHHHCCC-CC-CHHHHHHHHHHCC-CEEEEEECCC-CCCC--EEEEEEEEEEECCCCC-CCEEEEECCCC-CE
Q ss_conf             97786799884789-99-8899999987458-6042111246-5687--4899999975657998-70899975999-57
Q gi|254780316|r    1 MKFTLSWLKDHLDT-DV-SLEKICDTLTSIG-LEVEKVDNRE-ALSP--FTIVKVLSVERNPDLD-CAILRIDTGKH-QE   72 (805)
Q Consensus         1 M~is~~WL~~~v~~-~~-~~~~l~~~lt~~G-~EVe~i~~~~-~~~~--vvvg~v~~~~~hP~ad-l~v~~Vd~g~~-~~   72 (805)
                      |+||++||++|+++ ++ |+++||++||++| +|||.|..+. ..++  ||||+|++++|||||| |+|||||+|++ +.
T Consensus         1 M~~S~~WL~~~~~~~~~~s~~ei~~~L~~~G~~EVE~v~~~~~~~~~~~vvvG~v~~~~~HP~adkL~vc~V~~G~~e~~   80 (848)
T TIGR00472         1 MKISLKWLREYVPLSEIDSLEEIAEKLTSIGVLEVEEVEPFKKSLKGRYVVVGKVLEVEPHPNADKLKVCKVDIGEKEEP   80 (848)
T ss_pred             CCCCHHHHHHHCCCCCCCCHHHHHHHHHHCCEEEEEEEEECCCCCCCCEEEEEEEEEEECCCCCCCCEEEEEEECCCEEE
T ss_conf             95656889974275567898999999862770566200103655478558999999861388888856899887796067


Q ss_pred             EEEECCCCCCCCCCEEEEECCCCEECCCC---EEEEEEHHCCCCCCCHHHHHHHCCCCCC-----CCCEEEEC--CCCCC
Q ss_conf             98975483455897898966877925898---3983312058650545411887699854-----77507816--88888
Q gi|254780316|r   73 IQVVCGAPNVRVGLLGVWAPPGSCIPENN---MIVNVRKIRGIESTGMMCSEKELMLSDD-----SASIMELP--IDAPV  142 (805)
Q Consensus        73 ~~IvcgA~Nv~~g~~V~~A~~Ga~lp~g~---~~i~~~~irGv~S~GMlCS~~ELgl~~~-----~~gI~~l~--~~~~~  142 (805)
                      +||||||+||++|++||||++||+|| ++   ++||++||||++|+|||||+.||||+++     ++|||+||  +++++
T Consensus        81 ~qIVcGA~Nv~~g~~V~VA~~GA~L~-~~~~~~~Ik~~klRG~~S~GMlCS~~ELGl~~~~~~e~~dgi~~L~~~~~~~~  159 (848)
T TIGR00472        81 LQIVCGAPNVEAGDKVAVALPGAKLP-NGEEELKIKKSKLRGVESEGMLCSESELGLEEESLTEDSDGIIVLDEAEDAPL  159 (848)
T ss_pred             EEEEECCCCCCCCCEEEEECCCCEEE-CCCCEEEEEHHHCCCCCCCCCEECHHHCCCCCCCCCCCCCCEEEECCCCCCCC
T ss_conf             88862765401478859960485740-89721578543437535665042464628631023222564688177688865


Q ss_pred             CCCHHHHHCCCCE-EEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC--CCCCCCEEEEEEECCCHHHHHHH
Q ss_conf             8455887088855-99987087857665557899987764115666655456677--77777415898407311123320
Q gi|254780316|r  143 GGRLSDYLELSDP-IIDVSLTPNRSDCIGVRGIALDLVAAGLGKLKEINISCPLS--SESIPLEIKFDLDDSSLCKGFAM  219 (805)
Q Consensus       143 G~~~~~~l~l~D~-i~ei~iTpNR~D~ls~~GiARElaa~~~~~l~~~~~~~~~~--~~~~~~~i~v~i~~~~~c~~y~~  219 (805)
                      |+++.+||++||. +|||+|||||||||||+||||||||++++ |+.|....+..  .........+.+++.+.||+|.+
T Consensus       160 G~~~~~~L~ldd~~~~e~~iTpNR~DclS~~G~ARElAa~~~~-l~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~  238 (848)
T TIGR00472       160 GTDIAEYLGLDDDTVIEISITPNRGDCLSILGIARELAALFDL-LKTPVPFEPETTETETIDEGFKVEIEDEEACPRYLG  238 (848)
T ss_pred             CCCHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHCC-CCCCCCCCCCCCHHEECCCCCCEEECCCCCCCCEEE
T ss_conf             6777887146880799964389835776488999999987242-565543354410000025544212135010781468


Q ss_pred             CCCCCCCCCC-CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCC-E-EEEEECCCCCCHHHHHHHCCC
Q ss_conf             1123224556-637787888864013210399999899986087000001022333-2-688623554311455420112
Q gi|254780316|r  220 CCVKGVRNNV-APNWMRQRLKAVGLRSISALVDITNYVSLDRGYPSHVFDASRISD-V-LTVRRACSGEKILALDNQEYD  296 (805)
Q Consensus       220 ~~i~~v~~~~-SP~wl~~rL~~~Gir~inniVDitNyvmle~GqPlHafD~dki~~-~-i~vr~a~~~E~~~~Ld~~e~~  296 (805)
                      ++|+||++++ ||+|||.||+++|+|||||||||||||||++||||||||+|||+| . |+||.|++||+|++|||++|.
T Consensus       239 ~~i~~v~~~~~sP~w~~~rL~~~G~r~~N~~VDitNYv~~~~GQPlHafD~~~~~g~~si~Vr~ak~~e~~~~Ld~~e~~  318 (848)
T TIGR00472       239 RVIKGVKVKPQSPLWLKERLRASGIRPINNIVDITNYVMLELGQPLHAFDADKIEGSNSIVVRSAKEGESFTTLDGKERE  318 (848)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHCCHHHHCCCCEEEEEEECCCCEEEECCCEEEE
T ss_conf             99743531568988999999964898332335267899998568222212456338845999983367143304653466


Q ss_pred             CCCCCEEEECCC-CCCCCHHHCCCCCCCCCCCC-CEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCC-CCCCHHHHHHH
Q ss_conf             454320000256-76310011135531201367-2699997157878887788761654015544134-55301358899
Q gi|254780316|r  297 LSPDNVVIASDG-RIQSIAGIIGGKHAGCDDNT-TDVLVEVALWDPINIARSGKNLGIITDSRYRFER-GVDLQGMIPVL  373 (805)
Q Consensus       297 L~~~~lvI~d~~-~~ialaGImGg~~s~v~~~T-~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfER-gvd~~~~~~al  373 (805)
                      |+++++||+|++ +|+||||||||.+|+|+++| ++|+||||||+|..||+|||+|||+||||||||| |+||+.+..|+
T Consensus       319 L~~~~lvi~d~~~~~~aiaGv~Gg~~s~v~~~tT~~i~lE~A~F~p~~Irk~~~~l~i~t~~s~Rfer~g~D~~~~~~a~  398 (848)
T TIGR00472       319 LKKGDLVIADDEDKPLAIAGVMGGKESGVTDETTTNIFLESAYFNPESIRKTARRLGISTDSSYRFERTGVDPELTELAL  398 (848)
T ss_pred             ECCCCEEEECCCCCEEEEEEECCCCCCCCCCCCCEEEEEEEEECCHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHH
T ss_conf             53786799828997799985114656532266650699998605778999899883787125233113798888999999


Q ss_pred             HHHHHHHCCCCCCC--CCCCEEEEECCCCCCCEECCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCC-
Q ss_conf             98887521233455--565258741355431000043113333113458789999999840222103456236640345-
Q gi|254780316|r  374 KHIVSLILSLCGGT--ASDICIARNITYKPRKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWR-  450 (805)
Q Consensus       374 ~r~~~Li~e~~gg~--~~~~~~~~~~~~~~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R-  450 (805)
                      +||++||.++|||+  .+.....+..+.++++|.++.++++++||.+++.+++.++|++|||+++..+++|+|+||||| 
T Consensus       399 ~~A~~li~~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~lG~~~~~~~~~~iL~~Lg~~~~~~~~~~~v~vPs~R~  478 (848)
T TIGR00472       399 DRALNLILELAGGEDVISVVSDVYKEKKKEKKISLRLEKLNKILGTSLSDEEVRDILKRLGFKVEKQKEGLEVTVPSYRF  478 (848)
T ss_pred             HHHHHHHHHHCCCCCCCCEEEECCCCCCCCCEEEEEHHHHHHHHCCCCCHHHHHHHHHHCCCEEEECCCEEEEECCCCCC
T ss_conf             99999998505844344015641444565537874189999870855578899999986596243436656984286356


Q ss_pred             CCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH---HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
Q ss_conf             4334402567676765352334667655443457678998895467---8988787787740232100482576552000
Q gi|254780316|r  451 QDVEEKADLVEEILRIYGVDQIKSEPLPLTQVEDKRNLSLQQSRTR---YVKRVLASRAMMEVVNWSFISKEQSVLFGGG  527 (805)
Q Consensus       451 ~DI~~e~DLiEEIaRiyGYdnIp~~~l~~~~~~~~~~~~~~~~~~~---~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~  527 (805)
                      +||++++||||||+|+||||||+++|+.........+  ..+...+   ++|.+|+++||+|++||||++++.++.|+..
T Consensus       479 ~Di~~~~Dl~EEi~R~yGyd~i~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~G~~E~itYsl~~~~~~~~~~~~  556 (848)
T TIGR00472       479 HDIEIEEDLIEEIARIYGYDNIEAEPLSVSSKNNKNN--ENQLLLKFLKKLRKLLVGLGLNEVITYSLVSKEKLEKFNFP  556 (848)
T ss_pred             CCCCCCCCHHEEHHHHCCCCCCCCCCCCCCCCCCCCC--CHHHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHCCC
T ss_conf             6756252121001324130001034532110244442--04578899999999998489857773013887999871687


Q ss_pred             H-H----HCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCC-CCCCEEHHHHCCCCCCCCCC
Q ss_conf             0-0----0002467764321015122110677643210158611345430244447775-44310002210354310124
Q gi|254780316|r  528 Q-R----ELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFEVSHVYENDTP-EGQKYMAAGIRKGSSGIEGS  601 (805)
Q Consensus       528 ~-~----~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lFEiG~Vf~~~~~-~~~~~~~~~~~~~~~~~~~~  601 (805)
                      . .    .++|.||+|+|+++||+||+||||++++||++|++++++|||+|+||.++.. .++ ......+...++...+
T Consensus       557 ~~~~~~~~~~i~NP~s~e~~~lR~sL~~sLL~~~~~N~~r~~~~~~lFE~G~~f~~~~~AR~e-~~~~~~e~~~La~~~~  635 (848)
T TIGR00472       557 KLENLDELVEIKNPLSEERSVLRTSLLPSLLEVLAYNQNRKNKDVKLFEIGKVFAKDGKARGE-EDEAVKEQLRLAILIS  635 (848)
T ss_pred             CCCCCHHEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCC-HHHHHHHHHHHEEEEE
T ss_conf             778610104515898354788766446889999999986389715899887642688533575-0121234431100240


Q ss_pred             CCCCCCCCCC--CCCCCCHHHHHHHHHHHHHHCCCC-C-CE----EEECCCCCCCCCCCEEEEEEC-CEEEEEEEEEECH
Q ss_conf             6202345443--333146888753111111101453-3-30----330588656789816999987-9299999854778
Q gi|254780316|r  602 GRLWSDKSEE--RCRFVDLFDAKADALSVIEPFVSL-D-SL----RFESGAPSWYHPGRSGIIKTS-AEIVLGYFGEFHP  672 (805)
Q Consensus       602 g~~~~~~~~~--~~~~~df~dlKg~v~~ll~~l~~~-~-~~----~~~~~~~~~~hPgrsa~I~~~-gk~iiG~iG~ihP  672 (805)
                      |......|..  +...+|||++||+++++|..++.. . .+    .+....++.||||++|.|+++ ++.+ |+||+|||
T Consensus       636 G~~~~~~w~~~~~~~~~df~~~Kg~ve~~L~~l~~~~~~~~~~~~~~~~~~~~~~hP~~~a~i~~~~~~~~-G~iG~~hp  714 (848)
T TIGR00472       636 GEKEPSSWNSKKKEEKVDFYDLKGIVESLLELLGLSESAAYEVLDFKEAAENEELHPGQSAEIYLKSGKLI-GFIGEVHP  714 (848)
T ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCEEEEEEECCEEE-EEEEEECH
T ss_conf             44566666001576656788999999999997086555302222113330565568873279998268289-99998855


Q ss_pred             HHHHHCCCCCCEEEEEEEHHHHHHHHHCCCC-CCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHCC-CCEEEEEEE
Q ss_conf             9999668799789999878762354520245-66313689888720018999668879999999997111-003576989
Q gi|254780316|r  673 NILDFFGLSNPICGFEVYLDSIPISQKKRTK-TKKVVHLSSLHPVKRDLAFIVDQHIPAGTLVNIIKNVD-RLIDDVTVF  750 (805)
Q Consensus       673 ~i~~~~~i~~~v~~~EI~ld~L~~~~~~~~~-~~~~~~~s~fP~v~RDls~iv~~~v~~~~I~~~i~~~~-~ll~~v~lf  750 (805)
                      +++++|+|+.++|+|||+|+.|........+ .++|+++|+||+++|||||++|+++++++|++.+++.+ ++|++|+||
T Consensus       715 ~~~~~~~l~~~~~~~El~l~~l~~~~~~~~~~~~~~~~~s~~P~~~RDi~~~~~~~~~~~~i~~~~kk~~~~~l~~v~lf  794 (848)
T TIGR00472       715 EIAKEYDLKEPTFVAELDLDRLLESLKKSRKLVPKYRPISKFPAVTRDISFLVPKDVPVNEIIKLIKKSGLELLEEVELF  794 (848)
T ss_pred             HHHHHHCCCCCEEEEEEEHHHHHHHHHHHCCEEEEEECCCCCCCCCCCEEEEECCCCCHHHHHHHHHHCCCCEEEEEEEE
T ss_conf             89975079863599987278888652242211456532677885202288994587778999999974686689999999


Q ss_pred             EEEECCCCC-CCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCEEC
Q ss_conf             876367799-88426999999847798889999999999999999999511981
Q gi|254780316|r  751 DVFQGKSLG-EGKKSVAIQVLIQPLKDTFRDDDIRILMDRIVENVVKKTNAVLR  803 (805)
Q Consensus       751 DvY~g~~i~-~gkkSla~rl~fqs~~kTLtd~EI~~i~~~ii~~l~~k~ga~LR  803 (805)
                      |+|+|++++ +|+||+||||+|||.+|||+|+||++++++|++.|+++|||+||
T Consensus       795 DvY~g~~~~~~~~~S~~~~~~l~~~~~TL~~~~i~~~~~k~~~~L~~~~~~~lR  848 (848)
T TIGR00472       795 DVYEGKNIGKEGKKSLALRLVLRDKERTLTDEEINKIVEKVLNLLKEKLGAELR  848 (848)
T ss_pred             EEEECCCCCCCCEEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCEEC
T ss_conf             998468768887058999999986888888789999999999999998184609


No 3  
>CHL00192 syfB phenylalanyl-tRNA synthetase beta chain; Provisional
Probab=100.00  E-value=0  Score=1456.71  Aligned_cols=676  Identities=28%  Similarity=0.464  Sum_probs=601.3

Q ss_pred             CCCCHHHHHHHCCCC-CCHHHHHHHHHHCCCEEEEEECCCCCCCEEEEEEEEEEECCCCCCCEEEEECCCCCEEEEECCC
Q ss_conf             977867998847899-9889999998745860421112465687489999997565799870899975999579897548
Q gi|254780316|r    1 MKFTLSWLKDHLDTD-VSLEKICDTLTSIGLEVEKVDNREALSPFTIVKVLSVERNPDLDCAILRIDTGKHQEIQVVCGA   79 (805)
Q Consensus         1 M~is~~WL~~~v~~~-~~~~~l~~~lt~~G~EVe~i~~~~~~~~vvvg~v~~~~~hP~adl~v~~Vd~g~~~~~~IvcgA   79 (805)
                      |+||+||||+|++++ +++++|+++||++|+|||++++..                                        
T Consensus         1 m~~~~~wl~~~~~~~~~~~~~l~~~lt~~g~~~e~~~~~~----------------------------------------   40 (702)
T CHL00192          1 MKVSLNWLKELVDIENIDFDTLVDKLSLAGFEVEDIERLS----------------------------------------   40 (702)
T ss_pred             CCCCHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCHHHHC----------------------------------------
T ss_conf             9476899998638779998999998744476533102221----------------------------------------


Q ss_pred             CCCCCCCEEEEECCCCEECCCCEEEEEEHHCCCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCCCCHHHHHCCCCEEEEE
Q ss_conf             34558978989668779258983983312058650545411887699854775078168888884558870888559998
Q gi|254780316|r   80 PNVRVGLLGVWAPPGSCIPENNMIVNVRKIRGIESTGMMCSEKELMLSDDSASIMELPIDAPVGGRLSDYLELSDPIIDV  159 (805)
Q Consensus        80 ~Nv~~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G~~~~~~l~l~D~i~ei  159 (805)
                                                                                           .||+||+||||
T Consensus        41 ---------------------------------------------------------------------~lgldD~vlei   51 (702)
T CHL00192         41 ---------------------------------------------------------------------ILGEKDMILDV   51 (702)
T ss_pred             ---------------------------------------------------------------------CCCCCCEEEEE
T ss_conf             ---------------------------------------------------------------------06899868997


Q ss_pred             EECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHCCCCCCCCCCCCHHHHHHHH
Q ss_conf             70878576655578999877641156666554566777777741589840731112332011232245566377878888
Q gi|254780316|r  160 SLTPNRSDCIGVRGIALDLVAAGLGKLKEINISCPLSSESIPLEIKFDLDDSSLCKGFAMCCVKGVRNNVAPNWMRQRLK  239 (805)
Q Consensus       160 ~iTpNR~D~ls~~GiARElaa~~~~~l~~~~~~~~~~~~~~~~~i~v~i~~~~~c~~y~~~~i~~v~~~~SP~wl~~rL~  239 (805)
                      ++||||||||||+|+|||+||+++.+++.|...........+. ..+...+...||+|.+++|+||++++||+|||.||.
T Consensus        52 ~iTPNR~DclS~~GiARElaa~~~~~l~~p~~~~~~~~~~~~~-~~~~~~~~~~c~~y~~~~i~~v~v~~SP~wl~~rL~  130 (702)
T CHL00192         52 TSTANRSDSLSIIGLSREISALTNRDLKYKAYKPSIAIFTHKI-TILSSHSLLNCGIYSIVIIDNLRVNDSPLWLQNRLS  130 (702)
T ss_pred             EECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC-EEECCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHH
T ss_conf             5598778988889999999997598988856577643346761-230245545787388999878736899799999999


Q ss_pred             HHCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCC-------EEEEEECCCCCCHHHHHHHCCCCCCCCEEEECCCCCCC
Q ss_conf             64013210399999899986087000001022333-------26886235543114554201124543200002567631
Q gi|254780316|r  240 AVGLRSISALVDITNYVSLDRGYPSHVFDASRISD-------VLTVRRACSGEKILALDNQEYDLSPDNVVIASDGRIQS  312 (805)
Q Consensus       240 ~~Gir~inniVDitNyvmle~GqPlHafD~dki~~-------~i~vr~a~~~E~~~~Ld~~e~~L~~~~lvI~d~~~~ia  312 (805)
                      ++|+|||||+||||||||||+||||||||+|||++       .|++|.|.+||++++|||++|+|++++|||+|+++|+|
T Consensus       131 ~~Gir~inniVDitNYvmle~GqPlHAfD~dki~~~~~~~~~~i~vr~a~~~e~~~~Ld~~e~~L~~~~lvI~d~~~~ia  210 (702)
T CHL00192        131 SSGIKPLNLLVDISNYIMLKWGQPINIFDLDKISSVPIQPSLLILSNFNLGKSSHFILDNPNIKLSSEILLVQYNDNPIS  210 (702)
T ss_pred             HCCCCCCCCCCCHHHHHHHHCCCCCEEECHHHHCCCCCCCCEEEEEEECCCCCEEEECCCCEEECCCCCEEEEECCEEEE
T ss_conf             86998654334666633343088618973889368766664048997057985588238867854888779981992588


Q ss_pred             CHHHCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCE
Q ss_conf             00111355312013672699997157878887788761654015544134553013588999888752123345556525
Q gi|254780316|r  313 IAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLILSLCGGTASDIC  392 (805)
Q Consensus       313 laGImGg~~s~v~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li~e~~gg~~~~~~  392 (805)
                      |||||||.+|+|+++||+||||||+|+|.+||+|||+|||+||||||||||+||+.+..|+.||++||.++|||++.+..
T Consensus       211 lAGVmGG~~s~V~~~T~~IllEsA~F~p~~Ir~tar~l~l~tdaS~RfERGvdp~~~~~al~ra~~Li~e~~~g~~~~~~  290 (702)
T CHL00192        211 IAGIGLNSEIDCDANTKSILIEGAIFSKQVVRKSSRKLGIRTESSIRQEKGLNRDNFLNALYEAISLLGELTFGKIGKTF  290 (702)
T ss_pred             ECCEECCCCCEEECCHHHHHHHHEECCHHHHHHHHHHHCCCCHHHEEECCCCCHHHHHHHHHHHHHHHHHHCCCEECCCE
T ss_conf             72060786533505604614544215779989999983677514233246899789999999999999987398442203


Q ss_pred             EEEECCCCCCCEECCCCHHHHHHC--------CCCCHHHHHHHHHHHHHHHHCC-CCCCEEEECCCCC-CCCCHHHHHHH
Q ss_conf             874135543100004311333311--------3458789999999840222103-4562366403454-33440256767
Q gi|254780316|r  393 IARNITYKPRKIVFMNSEVKRLSG--------IDVPIEDSLRILERLGFSVIGE-YDKFEVSVPSWRQ-DVEEKADLVEE  462 (805)
Q Consensus       393 ~~~~~~~~~~~I~l~~~~i~~ilG--------~~i~~~ei~~iL~~Lgf~v~~~-~~~~~V~vPs~R~-DI~~e~DLiEE  462 (805)
                      .....+..++.|.++.++++++||        .+|+.++|.++|++|||++..+ .++|.|+||+||+ ||.+|+|||||
T Consensus       291 ~~~~~~~~~~~i~~~~~~i~~~lG~~~~~~~~~~i~~~~i~~iL~~Lgf~v~~~~~~~~~V~vPs~R~~DI~~e~DLiEE  370 (702)
T CHL00192        291 GYHKLTNISKPINLSKKKIQDILGPIKINGSTRYLSFEEIENILKSLNFKLIYDSLKNWEVIIPSYRQDDIFREIDLIEE  370 (702)
T ss_pred             ECCCCCCCCCEEECCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCEEEECCCCCEEEECCCCCHHHHCCCCHHHHH
T ss_conf             12556777850775899999973976445655568999999999977998995478868998897566664771059999


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             67653523346676554434576789988954678988787787740232100482576552000000002467764321
Q gi|254780316|r  463 ILRIYGVDQIKSEPLPLTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPISADMS  542 (805)
Q Consensus       463 IaRiyGYdnIp~~~l~~~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s  542 (805)
                      |||+|||||||++ +|...  ..+..+..+.+.+++|+.|+++||+|++||||++++..     .++.++|+||||+|++
T Consensus       371 VaRiyGydnI~~~-~p~~~--~~~~~~~~~~~~~~lr~~L~~~Gf~E~itysf~s~~~~-----~~~~v~l~NPis~e~s  442 (702)
T CHL00192        371 IARLYGFDNFISK-LPLIQ--FDGRLSFLRNFIDKIRSLLRNLGLTELVHYSLVKSYTY-----YKGEIKLYNPLLQDYS  442 (702)
T ss_pred             HHHHHCCCCCCCC-CCCCC--CCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHC-----CCCCEEECCCCCHHHH
T ss_conf             9998080336555-78754--67888988999999999999689834775314684445-----6772897087524378


Q ss_pred             CCCCHHHCHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCC--CCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             0151221106776432101586113454302444477754--43100022103543101246202345443333146888
Q gi|254780316|r  543 NMRTSLLPGLLKATGRNVDRAIADFAIFEVSHVYENDTPE--GQKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFD  620 (805)
Q Consensus       543 ~lR~SLlp~LL~~~~~N~~r~~~~i~lFEiG~Vf~~~~~~--~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~d  620 (805)
                      +||+||+||||+++++|++|++++++|||+|+||..+...  ++..+.+++.        .|......|..+.+.+|||+
T Consensus       443 ~LR~sLlpgLL~~~~~N~~r~~~~i~lFEiG~vf~~~~~~~~e~~~l~~~~~--------~g~~~~~~w~~~~~~~dFfd  514 (702)
T CHL00192        443 TLRSSLLPGLILAQQYNLKQSNQTIEGFEIGHVFRDNTEKIFETLHLAGGIG--------GGLDIRSSWSEKAQSLNWYE  514 (702)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCCHHEEEEEEE--------CCCCCCCCCCCCCCCCCHHH
T ss_conf             8888779999999986153599774289764552688788621122999998--------18866544456677678999


Q ss_pred             HHHHHHHHHHHCCCCCC---EEEECCCCCCCCCCCEEEEEECCEEEEEEEEEECHHHHHHCCCCCCEEEEEEEHHHHHHH
Q ss_conf             75311111110145333---033058865678981699998792999998547789999668799789999878762354
Q gi|254780316|r  621 AKADALSVIEPFVSLDS---LRFESGAPSWYHPGRSGIIKTSAEIVLGYFGEFHPNILDFFGLSNPICGFEVYLDSIPIS  697 (805)
Q Consensus       621 lKg~v~~ll~~l~~~~~---~~~~~~~~~~~hPgrsa~I~~~gk~iiG~iG~ihP~i~~~~~i~~~v~~~EI~ld~L~~~  697 (805)
                      +||++++++..++....   .......+++|||||||.|+++|+.+ |++|+|||.++++|+|+.+||+|||+|+.|...
T Consensus       515 ~Kg~ve~ll~~l~~~~~~~~~~~~~~~~~~~hPg~sA~I~~~~~~i-G~iG~lhP~v~~~~~l~~~v~~~Eidl~~l~~~  593 (702)
T CHL00192        515 AKGIVEEFFQRLNLPIVWKKIDSLDQRNKFLHPGRSAEIIYNNENI-GIFGQLHPLLASNLGLNTSTYLFEFDLEKLQAS  593 (702)
T ss_pred             HHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCEEEEEECCEEE-EEEEEECHHHHHHCCCCCCEEEEEEEHHHHHHH
T ss_conf             9999999999818984200201455542334877548999999799-999998799998739999779999997994323


Q ss_pred             HHCCCC-CCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHCC-CCEEEEEEEEEEECCCCCCCCEEEEEEEEEECCC
Q ss_conf             520245-66313689888720018999668879999999997111-0035769898763677998842699999984779
Q gi|254780316|r  698 QKKRTK-TKKVVHLSSLHPVKRDLAFIVDQHIPAGTLVNIIKNVD-RLIDDVTVFDVFQGKSLGEGKKSVAIQVLIQPLK  775 (805)
Q Consensus       698 ~~~~~~-~~~~~~~s~fP~v~RDls~iv~~~v~~~~I~~~i~~~~-~ll~~v~lfDvY~g~~i~~gkkSla~rl~fqs~~  775 (805)
                      ...... ...|+|+|+||+++|||||++|+++++++|+++|++++ ++|++|++||+|+|+++|+||||+||||+||+.+
T Consensus       594 ~~~~~~~~~~~~~~skfP~v~RDlalvv~~~v~~~~I~~~I~~~~~~ll~~v~lfDvY~g~~i~~gkKSla~~l~fq~~~  673 (702)
T CHL00192        594 IEQLNYLNYIIQPYSKYPSITRDLSLIIPKNMTISFLLKLILQFGNNLLESITLFDQYKGKSIGEGKKSLGLRLTYRSNK  673 (702)
T ss_pred             HHHCCCCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCEEEEEEEEEECCC
T ss_conf             44304466656778999970068999989999799999999862924171788999857999899966999999998989


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCEEC
Q ss_conf             8889999999999999999999511981
Q gi|254780316|r  776 DTFRDDDIRILMDRIVENVVKKTNAVLR  803 (805)
Q Consensus       776 kTLtd~EI~~i~~~ii~~l~~k~ga~LR  803 (805)
                      |||||+||++++++|++.|+++|||+||
T Consensus       674 rTLtd~eV~~~~~kIi~~l~~k~~a~LR  701 (702)
T CHL00192        674 KTLTNKEIDRIQNELQKNLLKQLQLVLR  701 (702)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCEEC
T ss_conf             9969999999999999999998593867


No 4  
>COG0072 PheT Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=1199.64  Aligned_cols=643  Identities=38%  Similarity=0.626  Sum_probs=587.6

Q ss_pred             CCCCHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEEC-CCHHHHHHHC
Q ss_conf             884558870888559998708785766555789998776411566665545667777777415898407-3111233201
Q gi|254780316|r  142 VGGRLSDYLELSDPIIDVSLTPNRSDCIGVRGIALDLVAAGLGKLKEINISCPLSSESIPLEIKFDLDD-SSLCKGFAMC  220 (805)
Q Consensus       142 ~G~~~~~~l~l~D~i~ei~iTpNR~D~ls~~GiARElaa~~~~~l~~~~~~~~~~~~~~~~~i~v~i~~-~~~c~~y~~~  220 (805)
                      +|++..+|++|+|.++|+++||||+||||++|+|||+||.++.+++.++.............+.+.+++ ...||+|.++
T Consensus         1 ~g~~~~~~~~L~d~i~e~~~tpnr~D~ls~~GiarE~aa~~~~~~~~~~~~d~~~~~~~~~~~~v~ie~~~~~~~~~~~~   80 (650)
T COG0072           1 MPTIVREYLDLDDLIIEISITPNRADCLSMLGIARELAAEYDLKLEFPKIRDLESAEGLARKIFLEIEAGKYACPRYAGR   80 (650)
T ss_pred             CCCCHHHHHHHCCCCEECCCCCCHHHHHCCCCEEEEHHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCEE
T ss_conf             98522545553453112336778788612255253304541761225776643344455614787334550117765359


Q ss_pred             CCCCCC-CCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEEECCCCCCHHHHHHHCCCCCC
Q ss_conf             123224-5566377878888640132103999998999860870000010223332688623554311455420112454
Q gi|254780316|r  221 CVKGVR-NNVAPNWMRQRLKAVGLRSISALVDITNYVSLDRGYPSHVFDASRISDVLTVRRACSGEKILALDNQEYDLSP  299 (805)
Q Consensus       221 ~i~~v~-~~~SP~wl~~rL~~~Gir~inniVDitNyvmle~GqPlHafD~dki~~~i~vr~a~~~E~~~~Ld~~e~~L~~  299 (805)
                      +++|++ +++||+|||.+|..+|+||||++||+|||||+++|||+|+||++++.+++.||.|+.+|++++||+.++.|..
T Consensus        81 ~i~~v~~~~~sP~~~~~~l~~~gir~in~lVDitnyv~l~~Gqp~h~~d~~~~~~~i~vr~a~~~e~~~~ld~~~~~l~~  160 (650)
T COG0072          81 VIKGVKVNAPSPLWLQARLRGVGIRPINNLVDITNYVHLELGQPRHAFDIGKIDGKIPVRYAKEGETLVFLDGKERELLT  160 (650)
T ss_pred             EEECCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCEEEECCCCCCEEECCCCCEEECC
T ss_conf             99856568899889999998779970779999999999996897146446443787368973578735863885335368


Q ss_pred             CCEEEECCCCCCCCHHHCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             32000025676310011135531201367269999715787888778876165401554413455301358899988875
Q gi|254780316|r  300 DNVVIASDGRIQSIAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSL  379 (805)
Q Consensus       300 ~~lvI~d~~~~ialaGImGg~~s~v~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~L  379 (805)
                      +++||+|.++++||||||||++|+|+++|+|+++|+|+|+|..||+++||++++|+||||||||+||..+..|++++++|
T Consensus       161 ~~~vi~d~~~~~alagv~g~~~s~~~~~t~d~~~E~a~f~Pi~i~~~~r~l~~~T~~~~r~~rGvD~~~v~~al~~~~~l  240 (650)
T COG0072         161 GDLVIADHEKGLALAGVMGGADSEVDPNTTDVLLEVASFPPIIISKTSRRLGLDTEASFRFERGVDPELVEKALNRATTL  240 (650)
T ss_pred             CCEEEEECCCCEEEEEEECCCCCCCCCCEEEEEEEEEECCHHHHHHHCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHH
T ss_conf             87899837974455346413556878440230336785476888751451257850268871279989999999999999


Q ss_pred             HCCCCCCCCCCCEEEEEC--CCCCCCEECCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHH
Q ss_conf             212334555652587413--554310000431133331134587899999998402221034562366403454334402
Q gi|254780316|r  380 ILSLCGGTASDICIARNI--TYKPRKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKA  457 (805)
Q Consensus       380 i~e~~gg~~~~~~~~~~~--~~~~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~  457 (805)
                      +.++|||+++++.+.+..  ..+++++.++.++++++||.+++.+++.++|++|||.++..+++|.|++|+||+||.+++
T Consensus       241 l~e~~gg~v~~~~~~~~~~~~~~~~~i~~~~~~i~~llG~~ls~eei~~iL~rLg~~~~~~~~~~~V~vPs~R~DI~~e~  320 (650)
T COG0072         241 LAEICGGEVSSVVIVGGDEKLTPPRKIELRLERINRLLGLELSAEEIEKILKRLGFKVEVKGDGLTVTVPSYRVDILIEA  320 (650)
T ss_pred             HHHHCCCEEEEEEEECCCCCCCCCCEEECCHHHHHHHHCCCCCHHHHHHHHHHCCCCEECCCCCEEEECCCCCCCCCCCC
T ss_conf             99862985514899457766788844871899999986898899999999997699034168746997688721356532


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH-HCCCCCC
Q ss_conf             567676765352334667655443457678998895467898878778774023210048257655200000-0002467
Q gi|254780316|r  458 DLVEEILRIYGVDQIKSEPLPLTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQR-ELEILNP  536 (805)
Q Consensus       458 DLiEEIaRiyGYdnIp~~~l~~~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~-~i~l~NP  536 (805)
                      ||||||+|+|||||||++++........ ..+..+.+.+.+|+.|+++||+|++||+|++++.+..|+.... .++|+||
T Consensus       321 DliEEv~r~yGy~ni~~~~p~~~~~~~~-~~~~~~~~~r~vr~~l~~~G~~Evitysl~s~e~~~~~~~~~~~~~~l~NP  399 (650)
T COG0072         321 DLIEEVARIYGYNNIPPELPSAFTIGRG-GLTPLQKFRRKVRRALVGLGFQEVITYSLTSPEEAKLFGLENDEALELANP  399 (650)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHCCCCCCCEEECCC
T ss_conf             7888999985714488758765445666-656678999999999985897599861258989999742377752685686


Q ss_pred             CCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCC-CCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             7643210151221106776432101586113454302444477754-431000221035431012462023454433331
Q gi|254780316|r  537 ISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFEVSHVYENDTPE-GQKYMAAGIRKGSSGIEGSGRLWSDKSEERCRF  615 (805)
Q Consensus       537 lS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lFEiG~Vf~~~~~~-~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  615 (805)
                      +|+|+++||+||+||||+++++|++|+++++++||+|+||..+... .+....+++.++..        +...|... +.
T Consensus       400 iS~e~s~mR~sLlp~LL~~~~~N~~r~~~~~~iFEiG~v~~~~~~~~~~~~~~~~l~~g~~--------~~~~w~~~-~~  470 (650)
T COG0072         400 ISEEYSVLRTSLLPGLLEALSYNKNRKNPDVRIFEIGDVFVKDEEAERETRHLAGLAAGLA--------GEESWQGK-RP  470 (650)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCCCCCHHHHHHHHHHCCC--------CCCCCCCC-CC
T ss_conf             7623888887778889999998753368864688667457058865320278999874446--------43334556-76


Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCEEEEEECCEEEEEEEEEECHHHHHHCCCCCCEEEEEEEHHHHH
Q ss_conf             46888753111111101453330330588656789816999987929999985477899996687997899998787623
Q gi|254780316|r  616 VDLFDAKADALSVIEPFVSLDSLRFESGAPSWYHPGRSGIIKTSAEIVLGYFGEFHPNILDFFGLSNPICGFEVYLDSIP  695 (805)
Q Consensus       616 ~df~dlKg~v~~ll~~l~~~~~~~~~~~~~~~~hPgrsa~I~~~gk~iiG~iG~ihP~i~~~~~i~~~v~~~EI~ld~L~  695 (805)
                      +|||++||++++++..++.  .+++.+..+++|||||||.|++++ ..+|++|++||.++++|+|+.++|+|||+++.+.
T Consensus       471 v~f~d~Kg~ve~ll~~lg~--~~~~~~~~~~~~hpgrsA~I~~~~-~~iG~iGeiHP~vl~~~dl~~~~~~fEi~l~~l~  547 (650)
T COG0072         471 VDFYDAKGDLEALLEALGV--EYEFEPAEHPAFHPGRSAAIYLNK-EVIGFIGELHPEVLKEFDLPGPVYVFEIDLDALL  547 (650)
T ss_pred             CCHHHHHHHHHHHHHHCCC--CCEEEECCCCCCCCCCCEEEEECC-EEEEEEEEECHHHHHHCCCCCCCEEEEEEHHHHC
T ss_conf             4699999999999997299--727840556751368607999999-8889988876999987599888189997134424


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHCC-CCEEEEEEEEEEECCCCCCCCEEEEEEEEEECC
Q ss_conf             5452024566313689888720018999668879999999997111-003576989876367799884269999998477
Q gi|254780316|r  696 ISQKKRTKTKKVVHLSSLHPVKRDLAFIVDQHIPAGTLVNIIKNVD-RLIDDVTVFDVFQGKSLGEGKKSVAIQVLIQPL  774 (805)
Q Consensus       696 ~~~~~~~~~~~~~~~s~fP~v~RDls~iv~~~v~~~~I~~~i~~~~-~ll~~v~lfDvY~g~~i~~gkkSla~rl~fqs~  774 (805)
                           ......|.++|+||++.|||||++|+++++++|.++|++++ +++++|.+||+|+ +++++|+||+|||++||+.
T Consensus       548 -----~~~~~~~~~~s~~pa~~RDia~~v~~~v~~~~i~~~i~~~~~~~l~~v~lfDvy~-~~~~~~~ks~a~~~~~~~~  621 (650)
T COG0072         548 -----KRKKPAYKPISKFPAVRRDIALVVDEDVPAGDIVKAIKKAGGKLLESVNLFDVYQ-KGLGEGKKSLAIRLTFQDP  621 (650)
T ss_pred             -----CCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCEEEEEEEEEEEE-CCCCCCCEEEEEEEEEECC
T ss_conf             -----4446567888989854330699968999989999999983636689999999850-2578996689999999889


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCEEC
Q ss_conf             98889999999999999999999511981
Q gi|254780316|r  775 KDTFRDDDIRILMDRIVENVVKKTNAVLR  803 (805)
Q Consensus       775 ~kTLtd~EI~~i~~~ii~~l~~k~ga~LR  803 (805)
                      +|||||+||+.++++++++++++|||+||
T Consensus       622 ~rTLtdeev~~~~~~~~~~l~~~~~~~lr  650 (650)
T COG0072         622 ERTLTDEEVNALVNKIVEALKEKFGAELR  650 (650)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCEEC
T ss_conf             88888799999999999999998484709


No 5  
>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=100.00  E-value=0  Score=910.92  Aligned_cols=505  Identities=23%  Similarity=0.320  Sum_probs=425.2

Q ss_pred             CCHHHHHHHCCCCCCHHHHHHHHHHCCCEEEEEECCCCCCCEEEEEEEEEEECCCCCCCEEEEECCCCCEEEEECCCCCC
Q ss_conf             78679988478999889999998745860421112465687489999997565799870899975999579897548345
Q gi|254780316|r    3 FTLSWLKDHLDTDVSLEKICDTLTSIGLEVEKVDNREALSPFTIVKVLSVERNPDLDCAILRIDTGKHQEIQVVCGAPNV   82 (805)
Q Consensus         3 is~~WL~~~v~~~~~~~~l~~~lt~~G~EVe~i~~~~~~~~vvvg~v~~~~~hP~adl~v~~Vd~g~~~~~~IvcgA~Nv   82 (805)
                      |+++||++|++.++|.+++++.||++|+|||.                                                
T Consensus         6 ~~~~~~~~~~~~~~s~~~~~~~l~~~g~e~~~------------------------------------------------   37 (546)
T PRK09616          6 VNKSDLERLTGIDLSDELLEDLLPMLKAEVEE------------------------------------------------   37 (546)
T ss_pred             ECHHHHHHHHCCCCCHHHHHHHHHHCCCCCCC------------------------------------------------
T ss_conf             74999999868999999999988874971236------------------------------------------------


Q ss_pred             CCCCEEEEECCCCEECCCCEEEEEEHHCCCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCCCCHHHHHCCCCEEEEEEEC
Q ss_conf             58978989668779258983983312058650545411887699854775078168888884558870888559998708
Q gi|254780316|r   83 RVGLLGVWAPPGSCIPENNMIVNVRKIRGIESTGMMCSEKELMLSDDSASIMELPIDAPVGGRLSDYLELSDPIIDVSLT  162 (805)
Q Consensus        83 ~~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G~~~~~~l~l~D~i~ei~iT  162 (805)
                                                                                           +||+|||++||
T Consensus        38 ---------------------------------------------------------------------ldD~iieieiT   48 (546)
T PRK09616         38 ---------------------------------------------------------------------IDEDEIKIEFN   48 (546)
T ss_pred             ---------------------------------------------------------------------CCCCEEEEEEC
T ss_conf             ---------------------------------------------------------------------78867999758


Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             78576655578999877641156666554566777777741589840731112332011232245566377878888640
Q gi|254780316|r  163 PNRSDCIGVRGIALDLVAAGLGKLKEINISCPLSSESIPLEIKFDLDDSSLCKGFAMCCVKGVRNNVAPNWMRQRLKAVG  242 (805)
Q Consensus       163 pNR~D~ls~~GiARElaa~~~~~l~~~~~~~~~~~~~~~~~i~v~i~~~~~c~~y~~~~i~~v~~~~SP~wl~~rL~~~G  242 (805)
                      |||||||||+|||||+||+++.+++.|.+.....    ...+++++++.+.||+|.+++|+||++++||.|.        
T Consensus        49 PNR~DcLSv~GiARElaA~~~~~l~~p~~~~~~~----~~~i~v~~~~~~~~p~~~~~vi~~Vki~~s~~~~--------  116 (546)
T PRK09616         49 PDRPDLFSVEGLARALKGFLGIETGLPKYEVKDS----DVKIKVDEEVIEIRPYIAGAVVRGVKLDDEALES--------  116 (546)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC----CCEEEEEECCCCCCCEEEEEEEECCCCCCCHHHH--------
T ss_conf             8768884889999999997598879997523788----8338993056566865889999896617604677--------


Q ss_pred             CCCCHHHHHHHHHHHHHHCC-----CEEEECCCCCCCEEEEEECCCCCCHHHHHHHC-CCC-------------------
Q ss_conf             13210399999899986087-----00000102233326886235543114554201-124-------------------
Q gi|254780316|r  243 LRSISALVDITNYVSLDRGY-----PSHVFDASRISDVLTVRRACSGEKILALDNQE-YDL-------------------  297 (805)
Q Consensus       243 ir~inniVDitNyvmle~Gq-----PlHafD~dki~~~i~vr~a~~~E~~~~Ld~~e-~~L-------------------  297 (805)
                            ++|+.|++|..+||     |+|+||+|||.+.|.||.++.||+|.+||+.+ .++                   
T Consensus       117 ------~i~l~~~l~~~~G~~r~~~~ig~~d~~kI~~~i~~~~~~~ge~~~~Ld~~~~~~~~~i~~~~~~g~~~~~ll~~  190 (546)
T PRK09616        117 ------LIQLQEKLHWTYGRKRKKVAIGIHDLDKIKPPIYYKAVSPDEKFVPLGYDEEMTLREILEKHPKGREYGHLLKD  190 (546)
T ss_pred             ------HHHHHHHHHHHHCCCCCCCCCCCCCHHHCCCCEEEEECCCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHCC
T ss_conf             ------99898999987565442134565048874895799987899758737874226899998740034100001116


Q ss_pred             CCCCEEEECCC-CCCCCHHHCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             54320000256-76310011135531201367269999715787888778876165401554413455301358899988
Q gi|254780316|r  298 SPDNVVIASDG-RIQSIAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHI  376 (805)
Q Consensus       298 ~~~~lvI~d~~-~~ialaGImGg~~s~v~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~  376 (805)
                      ...+.||+|++ +++||||||||++|+|+++|++||||||+|||..++++                          ++++
T Consensus       191 ~~~~~vI~d~~~~v~alAGVmGG~~S~vt~~T~~IllEsAg~Dp~~v~~a--------------------------l~~~  244 (546)
T PRK09616        191 FDKYPLIVDSEGNVLSFPPIINSELTRVTEGTRNLFIDVTGTDLEAVLLA--------------------------LNII  244 (546)
T ss_pred             CCCCEEEEECCCCEEEECCCCCCCCEEECCCCCEEEEEEECCCHHHHHHH--------------------------HHHH
T ss_conf             88631799279964641431266414662786548998515898999999--------------------------9999


Q ss_pred             HHHHCCCCCCCCCCCEEEEE---CCCCCCCEECCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCC
Q ss_conf             87521233455565258741---355431000043113333113458789999999840222103456236640345433
Q gi|254780316|r  377 VSLILSLCGGTASDICIARN---ITYKPRKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDV  453 (805)
Q Consensus       377 ~~Li~e~~gg~~~~~~~~~~---~~~~~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI  453 (805)
                      +.++.+ +||++..+...+.   +..++++|.++.++++++||++++.++|.++|++|||+++.+++.|.|+|||||+||
T Consensus       245 ~~~l~e-~gg~~~~v~~~~~~~~p~~~~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~Di  323 (546)
T PRK09616        245 VTALAE-RGGEIESVKVIGPDGTPDLTPRTREVSVDEINKLLGLDLSAEEIIELLEKMRFDAEVEDDEVKVLVPPYRVDI  323 (546)
T ss_pred             HHHHHH-CCCCEEEEEEEECCCCCCCCCEEEEECHHHHHHHHCCCCCHHHHHHHHHHCCCEEEECCCCEEEECCCCCCCC
T ss_conf             999997-5895546899815877677764899489999987488679999999999879979956885799888732333


Q ss_pred             CCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH--HHHHHHC
Q ss_conf             44025676767653523346676554434576789988954678988787787740232100482576552--0000000
Q gi|254780316|r  454 EEKADLVEEILRIYGVDQIKSEPLPLTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLF--GGGQREL  531 (805)
Q Consensus       454 ~~e~DLiEEIaRiyGYdnIp~~~l~~~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~--~~~~~~i  531 (805)
                      .+++||||||||+|||||||++.+. .  ...+..+..+++.+++|+.|+++||+|++||||++++++..+  .+.++++
T Consensus       324 ~~e~DLiEEVaRiyGYd~Ip~~~p~-~--~~~~~~~~~~~~~~~ir~~L~~~G~~Evitysf~s~~~~~~~~~~~~~~~v  400 (546)
T PRK09616        324 LHEVDVIEDVAIAYGYNNLEPELPK-I--FTIGRLHPIEELSRAIRDLMVGLGFQEVMNFTLTSEEVLFEKMNLEEDDPV  400 (546)
T ss_pred             CCHHHHHHHHHHHHCCCCCCCCCCC-C--CCCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHCCCCCCEE
T ss_conf             5501389999998182228754676-5--457889989999999999999689612762256898999876168868748


Q ss_pred             CCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCC----CCEEHHHHCCCCCCCCCCCCCCCC
Q ss_conf             0246776432101512211067764321015861134543024444777544----310002210354310124620234
Q gi|254780316|r  532 EILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFEVSHVYENDTPEG----QKYMAAGIRKGSSGIEGSGRLWSD  607 (805)
Q Consensus       532 ~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lFEiG~Vf~~~~~~~----~~~~~~~~~~~~~~~~~~g~~~~~  607 (805)
                      +|.||||+|+++|||||+||||+++++|++|+. +++|||+|+||..+....    +...++++.        .|     
T Consensus       401 ~l~NPis~e~s~mRtsLlp~LL~~~~~N~~r~~-~~~lFEiG~Vf~~~~~~~~~~~e~~~la~~~--------~g-----  466 (546)
T PRK09616        401 EVLNPISEDYTVLRTSLLPSLLEFLSINKHREY-PQKIFEIGDVVLIDESTETGTKTERKLAAAI--------AH-----  466 (546)
T ss_pred             EECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCC-CEEEEEEECEEECCCCCCCCCCCCCEEEEEE--------EC-----
T ss_conf             964887456777775538999999998466899-8459974055804886555640023799999--------79-----


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCEEEEEECCEEEEEEEEEECHHHHHHCCCCCCEEEE
Q ss_conf             54433331468887531111111014533303305886567898169999879299999854778999966879978999
Q gi|254780316|r  608 KSEERCRFVDLFDAKADALSVIEPFVSLDSLRFESGAPSWYHPGRSGIIKTSAEIVLGYFGEFHPNILDFFGLSNPICGF  687 (805)
Q Consensus       608 ~~~~~~~~~df~dlKg~v~~ll~~l~~~~~~~~~~~~~~~~hPgrsa~I~~~gk~iiG~iG~ihP~i~~~~~i~~~v~~~  687 (805)
                            ..+|||++||.+++++..++.  .+++.+.++++|||||||.|+++|+.+ |++|+|||.++++|+|+.++|+|
T Consensus       467 ------~~~dF~d~Kg~ve~ll~~l~~--~~~~~~~~~~~~hPgrsA~I~~~g~~i-G~iG~LHP~v~~~~~i~~~v~~f  537 (546)
T PRK09616        467 ------SGATFTEIKSVVKALLRELGI--EYEVEESEHPSFIPGRCADILVNGKEI-GVIGEIHPEVLENFGLEVPVVAF  537 (546)
T ss_pred             ------CCCCHHHHHHHHHHHHHHCCC--CEEEEECCCCCCCCCCEEEEEECCEEE-EEEEEECHHHHHHCCCCCCEEEE
T ss_conf             ------977999999999999998499--559942788877899769999999799-99999999999975979986999


Q ss_pred             EEEHHHHH
Q ss_conf             98787623
Q gi|254780316|r  688 EVYLDSIP  695 (805)
Q Consensus       688 EI~ld~L~  695 (805)
                      |||||.|.
T Consensus       538 Eldld~L~  545 (546)
T PRK09616        538 EIDLEALL  545 (546)
T ss_pred             EEEHHHHC
T ss_conf             99957840


No 6  
>TIGR00471 pheT_arch phenylalanyl-tRNA synthetase, beta subunit; InterPro: IPR004531   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 (see IPR002319 from INTERPRO). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta. 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 beta subunit. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps (see also IPR004532 from INTERPRO). This family represents the subfamily that includes the beta subunit from eukaryotic cytosol, the archaea, and spirochetes.; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=556.42  Aligned_cols=497  Identities=21%  Similarity=0.306  Sum_probs=382.5

Q ss_pred             CCCHHHHHCCC-CEEEEEEEC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEEC--CCHHHHHH
Q ss_conf             84558870888-559998708-785766555789998776411566665545667777777415898407--31112332
Q gi|254780316|r  143 GGRLSDYLELS-DPIIDVSLT-PNRSDCIGVRGIALDLVAAGLGKLKEINISCPLSSESIPLEIKFDLDD--SSLCKGFA  218 (805)
Q Consensus       143 G~~~~~~l~l~-D~i~ei~iT-pNR~D~ls~~GiARElaa~~~~~l~~~~~~~~~~~~~~~~~i~v~i~~--~~~c~~y~  218 (805)
                      |.++-++..-+ +..+++++. |||||+||+.|+||-|-.+++.+-....+..... +.....+++.|+.  .+..||.+
T Consensus        37 ~~~~E~~~~~~~E~~ik~ef~dpNRPDLlS~EG~AR~lrg~lg~e~g~~~y~~~~~-dfkkf~~k~~Vd~s~~~~RP~i~  115 (605)
T TIGR00471        37 GAEIEGFDEESEEKKIKVEFNDPNRPDLLSVEGVARSLRGYLGIEKGLKSYDSKKG-DFKKFEVKITVDESVLQIRPFIT  115 (605)
T ss_pred             CCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-CCEEEEEEEEEECCHHHHHHHHE
T ss_conf             64113420378985588973489850578899999986665124568864443355-32365328998072133324411


Q ss_pred             HCCCCCCCCCC----CCHHHHHHHHHH-CC-CCCHHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEEECCCC-CCHHHHH
Q ss_conf             01123224556----637787888864-01-32103999998999860870000010223332688623554-3114554
Q gi|254780316|r  219 MCCVKGVRNNV----APNWMRQRLKAV-GL-RSISALVDITNYVSLDRGYPSHVFDASRISDVLTVRRACSG-EKILALD  291 (805)
Q Consensus       219 ~~~i~~v~~~~----SP~wl~~rL~~~-Gi-r~inniVDitNyvmle~GqPlHafD~dki~~~i~vr~a~~~-E~~~~Ld  291 (805)
                      +++++||++.+    |-..+|++||+. |- |..           ...|  +|  |+|+|++++.++..... -+|++||
T Consensus       116 ~av~kg~~~~Dk~l~s~i~~QEkLH~~~GR~Rrk-----------vAiG--~H--Dld~v~~Pf~Y~av~p~g~kFVPL~  180 (605)
T TIGR00471       116 GAVVKGIILNDKVLESLIELQEKLHWNIGRNRRK-----------VAIG--IH--DLDKVKFPFSYKAVSPNGIKFVPLN  180 (605)
T ss_pred             EHHHCCCEECHHHHHHHHHHHHHHHHHHCCCCCE-----------EEEE--EC--CCCCCCCCEEEECCCCCCEEECCCC
T ss_conf             1111244024799999999888888862778525-----------7772--00--1234358653641289880533478


Q ss_pred             H---------------------H-CCC--CCC--CCEEEECCC-CCCCCHHHCCCCCCC-CCCCCCEEEEEEECCCHHHH
Q ss_conf             2---------------------0-112--454--320000256-763100111355312-01367269999715787888
Q gi|254780316|r  292 N---------------------Q-EYD--LSP--DNVVIASDG-RIQSIAGIIGGKHAG-CDDNTTDVLVEVALWDPINI  343 (805)
Q Consensus       292 ~---------------------~-e~~--L~~--~~lvI~d~~-~~ialaGImGg~~s~-v~~~T~~illEsA~F~p~~I  343 (805)
                      -                     . +|.  |..  .-.+|.|++ .++|+++||+|++|+ |+.+|||||+++.-+     
T Consensus       181 ~d~EmT~~eilEfyksPeh~KG~G~YaHii~d~D~fP~I~Ds~~~V~S~PPiIN~E~t~s~~v~Tr~lliDVTG~-----  255 (605)
T TIGR00471       181 SDQEMTPDEILEFYKSPEHPKGIGEYAHIIKDSDKFPLILDSKDDVLSMPPIINSELTKSVTVNTRDLLIDVTGT-----  255 (605)
T ss_pred             CCCCCCHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCEEEECCCCEEECCCCCCCCCCCEEEECCEEEEEEEECC-----
T ss_conf             832457778876433888768864158885288976547636888773587103255300232670677885211-----


Q ss_pred             HHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEE------CCCCC----CCEECCCCHHHH
Q ss_conf             77887616540155441345530135889998887521233455565258741------35543----100004311333
Q gi|254780316|r  344 ARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLILSLCGGTASDICIARN------ITYKP----RKIVFMNSEVKR  413 (805)
Q Consensus       344 r~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li~e~~gg~~~~~~~~~~------~~~~~----~~I~l~~~~i~~  413 (805)
                                           |-..+..+|.-++..+.+.|-|......+.+.      ....+    +.+.++.+.||+
T Consensus       256 ---------------------D~~a~~~~LnI~~t~fa~~g~g~i~~~~V~~~~~~~~~~~L~~~~~~~~mev~v~~iN~  314 (605)
T TIGR00471       256 ---------------------DKEAVELTLNIICTDFADRGFGRIEVVEVVRPDEELLLPNLAPRFYDRIMEVSVEEINR  314 (605)
T ss_pred             ---------------------CHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEEHHHHHH
T ss_conf             ---------------------76999999999999998707873311676656732378777764024265541766654


Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHHCCCC---CCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             311345878999999984022210345---62366403454334402567676765352334667655443457678998
Q gi|254780316|r  414 LSGIDVPIEDSLRILERLGFSVIGEYD---KFEVSVPSWRQDVEEKADLVEEILRIYGVDQIKSEPLPLTQVEDKRNLSL  490 (805)
Q Consensus       414 ilG~~i~~~ei~~iL~~Lgf~v~~~~~---~~~V~vPs~R~DI~~e~DLiEEIaRiyGYdnIp~~~l~~~~~~~~~~~~~  490 (805)
                      +||.++|.++|...|+++++.....++   .+.|.+|.||.||.||+|+|||||--|||+||++..+.........++ +
T Consensus       315 ~LGl~Lsa~~I~~~L~Kmr~~a~~~~~DkDk~~v~IP~YR~DIlHE~D~~EdvAigyG~~~~~pE~P~~~t~g~~~Pl-p  393 (605)
T TIGR00471       315 LLGLNLSADEIAESLKKMRLDAESKDEDKDKLKVVIPAYRVDILHEVDVIEDVAIGYGYNNIEPELPKILTIGRLKPL-P  393 (605)
T ss_pred             HHCCCCCHHHHHHHHHHCCCCEEECCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHCCCCC-C
T ss_conf             425678989999897417731144267752468717897640210031777778873221068777712222104888-7


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH-HH-HH---HHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCC
Q ss_conf             8954678988787787740232100482576552-00-00---0000246776432101512211067764321015861
Q gi|254780316|r  491 QQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLF-GG-GQ---RELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIA  565 (805)
Q Consensus       491 ~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~-~~-~~---~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~  565 (805)
                      ..+..+.+|..|+|+||+|++++.|+|++..... .. ++   ..|+++||+|.||+++|+||||+||++++.|.|+..|
T Consensus       394 ~~~~~~~~R~~mvG~GF~EVi~l~L~s~~~~~~~mR~~d~~~k~~v~V~~P~t~e~~~~R~SlLP~LLe~~~~Nk~~~lP  473 (605)
T TIGR00471       394 LEKVSDIIREIMVGLGFQEVISLTLTSEEVLFKRMRIEDNNFKLAVKVANPLTLEYTIVRTSLLPGLLETLSENKHHELP  473 (605)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             77887576542204704342410047806999980757887200333117876233377656223678888651489988


Q ss_pred             HHHHHHHCCCCCCCCCC----CCCE---EHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCE
Q ss_conf             13454302444477754----4310---0022103543101246202345443333146888753111111101453330
Q gi|254780316|r  566 DFAIFEVSHVYENDTPE----GQKY---MAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVSLDSL  638 (805)
Q Consensus       566 ~i~lFEiG~Vf~~~~~~----~~~~---~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~~~~~~  638 (805)
                       .++||+|+|..++...    .+..   .+++...+..       ..-+.  -..+.++|..++..+++++..++.  .+
T Consensus       474 -~KiFE~GDVV~~d~~~erk~~~~r~~~~lA~~~~~~~-------eiiqG--llGki~~F~eI~S~v~~~~~~L~~--e~  541 (605)
T TIGR00471       474 -QKIFEIGDVVVKDDDSERKETRSRVVTKLAVLITHSE-------EIIQG--LLGKIANFNEIKSIVAALLRELGI--EY  541 (605)
T ss_pred             -CEEEEEEEEEEECCCHHHHHHCCEEEEEEEEEEECCH-------HHHHH--HHHHHCCCHHHHHHHHHHHHHCCC--CE
T ss_conf             -2078874388828720122305625556787762761-------43343--553201302478899999996398--37


Q ss_pred             EEECC-CCCCCCCCCEEEEEECCE-----EEEE-EEEEECHHHHHHCCCCCCEEEEEEEHHHH
Q ss_conf             33058-865678981699998792-----9999-98547789999668799789999878762
Q gi|254780316|r  639 RFESG-APSWYHPGRSGIIKTSAE-----IVLG-YFGEFHPNILDFFGLSNPICGFEVYLDSI  694 (805)
Q Consensus       639 ~~~~~-~~~~~hPgrsa~I~~~gk-----~iiG-~iG~ihP~i~~~~~i~~~v~~~EI~ld~L  694 (805)
                      +..+. +++.|.+||||+|..+||     ..|| +||+|||.|+.+|+|.-||.+|||+++.+
T Consensus       542 ~~~e~D~~~~fi~GR~A~I~~~GK~GaeP~~IGG~FGe~HPEV~~NF~l~~Pvs~fE~~~~~f  604 (605)
T TIGR00471       542 EIEESDEHPSFIEGRGAKIVIEGKEGAEPKAIGGVFGEIHPEVLTNFELEFPVSAFEVNIEVF  604 (605)
T ss_pred             EEECCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCEECCEECCCCCCEEEEEEEEEEHHC
T ss_conf             983178861311671048984165788833257402314220562788320169999850120


No 7  
>pfam03483 B3_4 B3/4 domain. This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins.
Probab=100.00  E-value=0  Score=448.35  Aligned_cols=173  Identities=40%  Similarity=0.771  Sum_probs=170.7

Q ss_pred             HHHHHHHCCCCCCC-CCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEEECCCCCCHHHHH
Q ss_conf             11233201123224-55663778788886401321039999989998608700000102233326886235543114554
Q gi|254780316|r  213 LCKGFAMCCVKGVR-NNVAPNWMRQRLKAVGLRSISALVDITNYVSLDRGYPSHVFDASRISDVLTVRRACSGEKILALD  291 (805)
Q Consensus       213 ~c~~y~~~~i~~v~-~~~SP~wl~~rL~~~Gir~inniVDitNyvmle~GqPlHafD~dki~~~i~vr~a~~~E~~~~Ld  291 (805)
                      .|++|.++.++||+ +.+||+|||+||.++|+||||++||||||||||+|||+||||+|||.|.|.||.|++||+|.+||
T Consensus         1 ~c~~~~~~~i~~i~~~~~SP~wl~~rL~~~G~~pIN~iVDitNyv~le~GqP~hafD~dki~g~i~vr~a~~~E~~~~L~   80 (174)
T pfam03483         1 ACPRYFGRVIRGVKKNRPSPEWLQRRLRRAGIRPINNVVDITNYVMLELGQPLHAFDLDKIEGDIVVRLAKGGEKFTTLD   80 (174)
T ss_pred             CCCCEEEEEEECCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCEEEEECCCCCEEEECC
T ss_conf             99875079998987789998999999998599872175609999999958974454688748977999889996036226


Q ss_pred             HHCCCCCCCCEEEECCCCCCCCHHHCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHH
Q ss_conf             20112454320000256763100111355312013672699997157878887788761654015544134553013588
Q gi|254780316|r  292 NQEYDLSPDNVVIASDGRIQSIAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIP  371 (805)
Q Consensus       292 ~~e~~L~~~~lvI~d~~~~ialaGImGg~~s~v~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~  371 (805)
                      +++|+|+++++||+|+++|+||||||||.+|+|+++||+||||+|+|+|..||+|||+|+|+||||+|||||+||+.+..
T Consensus        81 ~~~~~l~~~~lVi~D~~~~i~laGi~gg~~s~v~~~Tk~I~lE~a~f~p~~i~~~~r~~~l~tdas~rfergvd~~~~~~  160 (174)
T pfam03483        81 GKERELDPGDLVIADDDGPVALAGIMGGEESEVTEDTTNIFLESAYFDPVAIRKTSRKLGLRTDASYRFERGVDPELLEA  160 (174)
T ss_pred             CCCCCCCCHHEEEEECCCCEEEEEEECCCCCCCCCCCEEEEEEEEEECHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHH
T ss_conf             86052784122888678760551010675333344730799995388689999999981898688887756899899999


Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             99988875212334
Q gi|254780316|r  372 VLKHIVSLILSLCG  385 (805)
Q Consensus       372 al~r~~~Li~e~~g  385 (805)
                      |++|+++||.++||
T Consensus       161 al~~~~~Li~~~~g  174 (174)
T pfam03483       161 ALDRATALLLELCG  174 (174)
T ss_pred             HHHHHHHHHHHHCC
T ss_conf             99999999999749


No 8  
>KOG2472 consensus
Probab=100.00  E-value=0  Score=429.04  Aligned_cols=474  Identities=20%  Similarity=0.279  Sum_probs=359.6

Q ss_pred             CCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHCCCCCCCCCC---
Q ss_conf             85599987087857665557899987764115666655456677777774158984073111233201123224556---
Q gi|254780316|r  153 SDPIIDVSLTPNRSDCIGVRGIALDLVAAGLGKLKEINISCPLSSESIPLEIKFDLDDSSLCKGFAMCCVKGVRNNV---  229 (805)
Q Consensus       153 ~D~i~ei~iTpNR~D~ls~~GiARElaa~~~~~l~~~~~~~~~~~~~~~~~i~v~i~~~~~c~~y~~~~i~~v~~~~---  229 (805)
                      +.....+++.+||.|+++..|+|+-+-+ |..+...|.++........-..+.+..+..+..|++.+++++||+..+   
T Consensus        59 e~~~ykidipANrydllC~egl~qalrv-f~~~~~~p~yk~~~~s~t~~~k~~v~~~t~qIRP~~v~aVir~v~l~~~ds  137 (578)
T KOG2472          59 EEVRYKIDIPANRYDLLCLEGLAQALRV-FPRETEFPSYKLQDFSSTKRQKLIVKPETSQIRPFAVCAVIRNVSLDPPDS  137 (578)
T ss_pred             CCEEEEHHCCCCCCCCCCHHHHHHHHHH-CCCCCCCCCCEEECCCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCCCHHH
T ss_conf             5512301055544562006889888774-445578876300024666414899866401011378888873575685256


Q ss_pred             --CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEEECCCCC-CHHHHHHHCCCCCCCC-----
Q ss_conf             --63778788886401321039999989998608700000102233326886235543-1145542011245432-----
Q gi|254780316|r  230 --APNWMRQRLKAVGLRSISALVDITNYVSLDRGYPSHVFDASRISDVLTVRRACSGE-KILALDNQEYDLSPDN-----  301 (805)
Q Consensus       230 --SP~wl~~rL~~~Gir~inniVDitNyvmle~GqPlHafD~dki~~~i~vr~a~~~E-~~~~Ld~~e~~L~~~~-----  301 (805)
                        |-.-+|.+|++.=.|-         =.+-..|  +|  |+|++.|++.++.-...| +|.+|+ +++.++...     
T Consensus       138 y~sFIdlQdKLHqnicrn---------RtLvAiG--TH--DLDt~qgPf~Y~Al~peei~f~PLN-qtre~~~~eL~~~y  203 (578)
T KOG2472         138 YKSFIDLQDKLHQNICRN---------RTLVAIG--TH--DLDTIQGPFEYEALPPEEIKFKPLN-QTREVTASELMSFY  203 (578)
T ss_pred             HHHHHHHHHHHHHHHHHH---------CCCCCCC--CC--CCHHCCCCEEEEEECHHHCCCCCCH-HHHCCCCCCCCCCC
T ss_conf             676776899999988764---------2034565--55--5311048705652073441743035-54113520002634


Q ss_pred             -------------------EEEECCCC-CCCCHHHCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHC
Q ss_conf             -------------------00002567-6310011135531201367269999715787888778876165401554413
Q gi|254780316|r  302 -------------------VVIASDGR-IQSIAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFE  361 (805)
Q Consensus       302 -------------------lvI~d~~~-~ialaGImGg~~s~v~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfE  361 (805)
                                         .||.|.++ +.++++|++|++|+++-+|+|||+|+          ||              
T Consensus       204 ~~d~~l~rYlhII~~sPvypvi~Ds~~~V~SlPPIiNsd~Skitl~TknIfiev----------Ta--------------  259 (578)
T KOG2472         204 KRDMHLKRYLHIIENSPVYPVIYDSKGVVCSLPPIINSDHSKITLNTKNIFIEV----------TA--------------  259 (578)
T ss_pred             CCCCCHHHHEHHHCCCCCCCEEECCCCCEEECCCCCCCCCCEEEECCCEEEEEE----------EE--------------
T ss_conf             676546440221248986420217887657169945765432430451178885----------31--------------


Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCC--CCCCEEEEE-------CCCCCCCEECCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             45530135889998887521233455--565258741-------355431000043113333113458789999999840
Q gi|254780316|r  362 RGVDLQGMIPVLKHIVSLILSLCGGT--ASDICIARN-------ITYKPRKIVFMNSEVKRLSGIDVPIEDSLRILERLG  432 (805)
Q Consensus       362 Rgvd~~~~~~al~r~~~Li~e~~gg~--~~~~~~~~~-------~~~~~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lg  432 (805)
                        .|...+..++.-.+.|..+.|+-+  ++++-+...       +....+....+.+.++.-+|.+++.+++..+|+||-
T Consensus       260 --Td~~ka~ivl~~~v~lfS~~c~~~ftiepveIv~~~G~~~l~P~l~~r~~~~~~~~in~~~g~~l~~~~~~~~l~RM~  337 (578)
T KOG2472         260 --TDFTKAKIVLNTIVTLFSQQCFLKFTIEPVEIVCGEGGSILYPQLANRSMTMSIQAINFAIGLNLTIEEQAYYLTRMY  337 (578)
T ss_pred             --CCCHHHHCCCCEEEEHHHHHHCCCCCCCCEEEECCCCCEEECCCCCCCCEEEEHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             --321100000012641235653467622414888589947977222675326305566653155888899998876431


Q ss_pred             HHHHCCCC-CCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             22210345-62366403454334402567676765352334667655443457678998895467898878778774023
Q gi|254780316|r  433 FSVIGEYD-KFEVSVPSWRQDVEEKADLVEEILRIYGVDQIKSEPLPLTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVV  511 (805)
Q Consensus       433 f~v~~~~~-~~~V~vPs~R~DI~~e~DLiEEIaRiyGYdnIp~~~l~~~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~  511 (805)
                      .+.+..++ +++|.||.-|.||.|.+|++|++|-.||||||+.+ +|....  ....-+..++.+.+|..++.+||.|++
T Consensus       338 L~a~v~~~~~l~v~iPptraDIlHaCDI~ED~aIAyGyNNi~~~-lP~~~~--~~~~~plNkl~d~lR~e~a~ag~~E~l  414 (578)
T KOG2472         338 LKAKVIGNGNLEVKIPPTRADILHACDIVEDAAIAYGYNNIQMT-LPASNT--IAKPFPLNKLTDILRIEVAAAGFTEAL  414 (578)
T ss_pred             EEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCC-CCCHHC--CCCCCCHHHHHHHHHHHHHHHHHHHHE
T ss_conf             24474489843786698603310021256677777241540114-750320--147445478889999999885156531


Q ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCC----CCEE
Q ss_conf             210048257655200000000246776432101512211067764321015861134543024444777544----3100
Q gi|254780316|r  512 NWSFISKEQSVLFGGGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFEVSHVYENDTPEG----QKYM  587 (805)
Q Consensus       512 tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lFEiG~Vf~~~~~~~----~~~~  587 (805)
                      |+.|+|.++.  -.....+|.|.||.|-|+.++|+||+||||++++.|.++..+ +++||+++|...+...+    .+..
T Consensus       415 ~~~LcS~de~--~~d~~~AV~l~NPkt~efqv~RtsLlPGllKTv~~N~~~~lP-~klFEisDvv~~D~~~e~ga~N~R~  491 (578)
T KOG2472         415 TFTLCSRDEN--VIDGDKAVHLGNPKTLEFQVVRTSLLPGLLKTVASNRKMPLP-IKLFEISDVVFKDSSTEVGARNERH  491 (578)
T ss_pred             EEEEECCCCC--CCCCCCCEEECCCCCEEEEEEHHHHCHHHHHHHHHCCCCCCC-EEEEEEEEEEEECCCCCCCCCCHHE
T ss_conf             0013336557--766443058459873454320243023889988860479876-3588751079851654014424000


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCEEEEEECCEEEEEEE
Q ss_conf             02210354310124620234544333314688875311111110145333033058865678981699998792999998
Q gi|254780316|r  588 AAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVSLDSLRFESGAPSWYHPGRSGIIKTSAEIVLGYF  667 (805)
Q Consensus       588 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~~~~~~~~~~~~~~~~hPgrsa~I~~~gk~iiG~i  667 (805)
                      ++++-+|.                   ...|--+.|.+..+++.-...+.+..+.++.+ |.|||||.|++.|+.+ |.+
T Consensus       492 l~A~y~g~-------------------~~gfE~i~Glld~~l~~~~~~~~Y~i~~~~~~-yfpgr~A~v~~~g~~i-G~~  550 (578)
T KOG2472         492 LAAVYCGK-------------------TSGFEIIHGLLDQLLNVPPIRDSYYIEADEDP-YFPGRCAKVIVEGKVI-GKI  550 (578)
T ss_pred             EEEEECCC-------------------CCCHHHHHHHHHHHHCCCCCCCCEEEECCCCC-CCCCCCEEEEECCCEE-EEE
T ss_conf             00000278-------------------86489998799998447765550578447687-6788613789727155-321


Q ss_pred             EEECHHHHHHCCCCCCEEEEEEEHHHH
Q ss_conf             547789999668799789999878762
Q gi|254780316|r  668 GEFHPNILDFFGLSNPICGFEVYLDSI  694 (805)
Q Consensus       668 G~ihP~i~~~~~i~~~v~~~EI~ld~L  694 (805)
                      |.+||.++++|++..|+.++|||++.+
T Consensus       551 GvlhPev~~~F~l~~~~s~~Ei~ie~~  577 (578)
T KOG2472         551 GVLHPEVLTKFELTYPCSAVEIDIEPF  577 (578)
T ss_pred             CCCCHHHHHHCCCCCCCCEEEEEEEEC
T ss_conf             014899985258887541379620735


No 9  
>smart00873 B3_4 B3/4 domain. This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins.
Probab=100.00  E-value=0  Score=362.80  Aligned_cols=172  Identities=38%  Similarity=0.732  Sum_probs=168.1

Q ss_pred             HHHHHHCCCCCCCCC-CCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCE-EEEEECCCCCCHHHHH
Q ss_conf             123320112322455-66377878888640132103999998999860870000010223332-6886235543114554
Q gi|254780316|r  214 CKGFAMCCVKGVRNN-VAPNWMRQRLKAVGLRSISALVDITNYVSLDRGYPSHVFDASRISDV-LTVRRACSGEKILALD  291 (805)
Q Consensus       214 c~~y~~~~i~~v~~~-~SP~wl~~rL~~~Gir~inniVDitNyvmle~GqPlHafD~dki~~~-i~vr~a~~~E~~~~Ld  291 (805)
                      ||+|.++++++++.. +||+|||+||+++|+||||++|||+|||||++|||+||||+|||.+. |.+|.|+++|+|.+||
T Consensus         1 ~~~~~~~~~~~v~~~~~Sp~~l~~rL~~~g~~~in~iVDi~Nyv~l~~g~P~h~~D~dki~~~~i~l~~a~~~e~~~~l~   80 (174)
T smart00873        1 CPRYLGRVIRGVKNTRPSPEWLQERLHRAGIRPINNVVDITNYVSLETGQPLHAFDLDKIKGKDIPLRRAKEGETFETLD   80 (174)
T ss_pred             CCCEEEEEEECCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCEEEEEECCCCCEEEECC
T ss_conf             99772899989977999859999999985998731767099999999389753433542679838999779997256048


Q ss_pred             HHCCCCCCCCEEEECCCCCCCCHHHCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHH
Q ss_conf             20112454320000256763100111355312013672699997157878887788761654015544134553013588
Q gi|254780316|r  292 NQEYDLSPDNVVIASDGRIQSIAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIP  371 (805)
Q Consensus       292 ~~e~~L~~~~lvI~d~~~~ialaGImGg~~s~v~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~  371 (805)
                      ++++.|.++++||+|+++|+++||||||.+|+|+++|++|++|+|+|+|..||+|++++++.||+|+|||||+||+.+..
T Consensus        81 ~~~~~l~~~~~vi~d~~~~~~iagi~G~~~~~v~~~t~~i~le~a~~~~~~ir~t~~~~~l~~d~s~r~e~gvd~~~~~~  160 (174)
T smart00873       81 GKEYELDEGDLVIADDEGPLALAGVMGGEESEVTENTTNIFLEPAIFSPRTIRITARTLNLFTDASGRFERGVDPELVEL  160 (174)
T ss_pred             CCEEECCCCCEEEEECCCCCEEEEECCCCCCCCCCCCCEEEEEEEEECHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHH
T ss_conf             84797687532788636671541120676431000510499997587689999999984898688876636899899999


Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             99988875212334
Q gi|254780316|r  372 VLKHIVSLILSLCG  385 (805)
Q Consensus       372 al~r~~~Li~e~~g  385 (805)
                      |++++++||.++||
T Consensus       161 al~~~~~ll~~~~g  174 (174)
T smart00873      161 ALDRAAALLLEICG  174 (174)
T ss_pred             HHHHHHHHHHHHCC
T ss_conf             99999999999749


No 10 
>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=100.00  E-value=9.9e-44  Score=329.53  Aligned_cols=195  Identities=33%  Similarity=0.562  Sum_probs=171.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH-HHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHH
Q ss_conf             895467898878778774023210048257655200-0000002467764321015122110677643210158611345
Q gi|254780316|r  491 QQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGG-GQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAI  569 (805)
Q Consensus       491 ~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~-~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~l  569 (805)
                      .+++++++|+.|+++||+|++||||+++++++.+.. .+++++|+||+|+|+++||+||+||||+++++|++|++.++++
T Consensus         2 ~~~l~~~ir~~L~~~Gf~Ev~t~s~~~~~~~~~~~~~~~~~i~l~NPls~e~~~lR~sLlp~LL~~~~~N~~r~~~~~~l   81 (198)
T cd00769           2 LQKLERKLRRLLAGLGFQEVITYSLTSPEEAELFDGGLDEAVELSNPLSEEYSVLRTSLLPGLLDALARNLNRKNKPLRL   81 (198)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf             67999999999997897141306768989998724887873897088656688988877999999998650567777328


Q ss_pred             HHHCCCCCCCCCC-CCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCC
Q ss_conf             4302444477754-431000221035431012462023454433331468887531111111014533303305886567
Q gi|254780316|r  570 FEVSHVYENDTPE-GQKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVSLDSLRFESGAPSWY  648 (805)
Q Consensus       570 FEiG~Vf~~~~~~-~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~~~~~~~~~~~~~~~~  648 (805)
                      ||+|+||.++... .|+..++++        .+|......|..+.+..|||++||++++++..++....+.+.+..+++|
T Consensus        82 FEiG~vy~~~~~~~~E~~~l~~~--------~~g~~~~~~~~~~~~~~df~~lKg~v~~ll~~l~~~~~~~~~~~~~~~~  153 (198)
T cd00769          82 FEIGRVFLKDEDGPEEEEHLAAL--------LSGNREPESWQGKGRPVDFYDAKGILEALLRALGIIVEFELEELDADLF  153 (198)
T ss_pred             EEEEEEEECCCCCCCCCEEEEEE--------EECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC
T ss_conf             99763896688876423057888--------8667775564557776799999999999999809985189920787665


Q ss_pred             CCCCEEEEEECCEEEEEEEEEECHHHHHHCCCCCCEEEEEEEHHHH
Q ss_conf             8981699998792999998547789999668799789999878762
Q gi|254780316|r  649 HPGRSGIIKTSAEIVLGYFGEFHPNILDFFGLSNPICGFEVYLDSI  694 (805)
Q Consensus       649 hPgrsa~I~~~gk~iiG~iG~ihP~i~~~~~i~~~v~~~EI~ld~L  694 (805)
                      ||||||+|+++|+.+ |++|+|||.++++|||+.+|++||||||.|
T Consensus       154 hpg~sa~I~~~~~~i-G~iG~l~p~il~~~~i~~~v~~~Ei~ld~L  198 (198)
T cd00769         154 HPGRSAKIYVNGEVI-GFIGELHPEVLKEFDLKEPVYAFELDLDAL  198 (198)
T ss_pred             CCCCEEEEEECCEEE-EEEEEECHHHHHHCCCCCCEEEEEEECCCC
T ss_conf             568669999999899-999999999999759899779999973359


No 11 
>cd02796 tRNA_bind_bactPheRS tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain.  PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe).  PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate the 2'OH of the terminal ribose of tRNA they belong functionally to class 1 aaRSs.  This domain has general tRNA binding properties and is believed to direct tRNAphe to the active site of the enzyme.
Probab=99.98  E-value=3.4e-32  Score=247.62  Aligned_cols=102  Identities=48%  Similarity=0.834  Sum_probs=98.9

Q ss_pred             EEEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECCCCCCCCCCEEEEECCCCEECCCCEEEEEEHHCCCCCCCHHHHHH
Q ss_conf             4899999975657998-708999759995798975483455897898966877925898398331205865054541188
Q gi|254780316|r   44 FTIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCGAPNVRVGLLGVWAPPGSCIPENNMIVNVRKIRGIESTGMMCSEK  122 (805)
Q Consensus        44 vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~IvcgA~Nv~~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S~GMlCS~~  122 (805)
                      +|||+|++++|||+|| |++|+||+|+++.+||||||+|+++|++|++|++||+|| ++.+|+++++||++|+|||||++
T Consensus         1 vvvgkI~~~~~hP~adkL~~~~Vd~g~~~~~~Iv~ga~n~~~g~~vvva~~Gs~l~-~g~~i~~~~i~Gv~S~GMlcS~~   79 (103)
T cd02796           1 VVVGKVLEVEPHPNADKLNVCKVDIGENKPLQIVCGAPNVRAGDKVVVALPGAVLP-GGLKIKKRKLRGVESEGMLCSAK   79 (103)
T ss_pred             CEEEEEEEEEECCCCCEEEEEEEECCCCEEEEEECCCCHHHCCCEEEEECCCCEEC-CCCCCCCCEECCEECCCEECCHH
T ss_conf             98999999785899998899999858956999854998577798999972687942-77620320105721270786788


Q ss_pred             HCCCCCCCCCEEEECCCCCCCCCH
Q ss_conf             769985477507816888888455
Q gi|254780316|r  123 ELMLSDDSASIMELPIDAPVGGRL  146 (805)
Q Consensus       123 ELgl~~~~~gI~~l~~~~~~G~~~  146 (805)
                      |||++++++||++||+++++|+|+
T Consensus        80 ELGl~~~~~gi~~l~~~~~~G~~~  103 (103)
T cd02796          80 ELGLGEDSDGIIELPEDAPVGTDI  103 (103)
T ss_pred             HCCCCCCCCCEEECCCCCCCCCCC
T ss_conf             979998898779999999898979


No 12 
>COG0073 ARC1 EMAP domain [General function prediction only]
Probab=99.95  E-value=5.2e-28  Score=217.96  Aligned_cols=120  Identities=38%  Similarity=0.591  Sum_probs=110.5

Q ss_pred             HHHCCCEEEEEECCC-CCCCEEEEEEEEEEECCCCC-CCEEEEECCCCC-EEEEECCCCCCCCCCEEEEECCCCEECCCC
Q ss_conf             874586042111246-56874899999975657998-708999759995-798975483455897898966877925898
Q gi|254780316|r   25 LTSIGLEVEKVDNRE-ALSPFTIVKVLSVERNPDLD-CAILRIDTGKHQ-EIQVVCGAPNVRVGLLGVWAPPGSCIPENN  101 (805)
Q Consensus        25 lt~~G~EVe~i~~~~-~~~~vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~-~~~IvcgA~Nv~~g~~V~~A~~Ga~lp~g~  101 (805)
                      ++..|.|+|.+.... ....++||+|++++|||+|| |++|+||+|+++ .+||||||+|+++|+.|++|++|+++| ++
T Consensus         1 ~~~~~~e~e~i~~~~~~~~~l~vg~V~~~~~~p~adkL~~~~Vd~G~~~~~~qiv~G~~n~~~~~~vv~a~v~~v~~-~~   79 (123)
T COG0073           1 LTRIGLEVEEIEIDDFAKVDLRVGKVVEAEPHPNADKLLVLKVDLGDEKEPRQIVCGAPNFYAGEKLVGAKVGAVLN-GG   79 (123)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCEEEEEEEEEEEC-CC
T ss_conf             96322234411115444378189999981258997835799998089883789983362203761235377999976-77


Q ss_pred             EEEEEEHHCCCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCCCCH
Q ss_conf             398331205865054541188769985477507816888888455
Q gi|254780316|r  102 MIVNVRKIRGIESTGMMCSEKELMLSDDSASIMELPIDAPVGGRL  146 (805)
Q Consensus       102 ~~i~~~~irGv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G~~~  146 (805)
                       +||++|+||++|+|||||+.|+|+++.+.||+.+|++++.|.++
T Consensus        80 -~ikp~klrG~~S~GMics~~e~~~~~~~~~il~~~~~~~~g~~~  123 (123)
T COG0073          80 -KLKPAKLRGVESEGMLLSAEELGLSDENVGILTLDEGVPPGTKV  123 (123)
T ss_pred             -CCCCCEECCCEECEEEEECCCCCCCCCCCEEEECCCCCCCCCCC
T ss_conf             -41632036830021798652388864456369678777888889


No 13 
>pfam03147 FDX-ACB Ferredoxin-fold anticodon binding domain. This is the anticodon binding domain found in some phenylalanyl tRNA synthetases. The domain has a ferredoxin fold.
Probab=99.92  E-value=1.8e-24  Score=192.86  Aligned_cols=93  Identities=39%  Similarity=0.735  Sum_probs=90.7

Q ss_pred             CCCCCCEEEEEEEECCCCCHHHHHHHHHHCC-CCEEEEEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHH
Q ss_conf             9888720018999668879999999997111-003576989876367799884269999998477988899999999999
Q gi|254780316|r  711 SSLHPVKRDLAFIVDQHIPAGTLVNIIKNVD-RLIDDVTVFDVFQGKSLGEGKKSVAIQVLIQPLKDTFRDDDIRILMDR  789 (805)
Q Consensus       711 s~fP~v~RDls~iv~~~v~~~~I~~~i~~~~-~ll~~v~lfDvY~g~~i~~gkkSla~rl~fqs~~kTLtd~EI~~i~~~  789 (805)
                      |+||++.|||||++|+++++++|.++|++.+ +++++|.+||+|+|+++++|+||+||||+||+.+|||||+||+.++++
T Consensus         1 SkfP~v~RDlS~~v~~~~~~~~i~~~i~~~~~~~l~~v~lfDvy~~~~i~~~kkSl~~r~~~qs~~kTLtd~eI~~~~~~   80 (94)
T pfam03147         1 SKFPAVRRDLAFVVDEDVPAADILDVIRKAGGELLEDVELFDVYRGKKIPEGKKSLAFRLTFQSAERTLTDEEVNAIHEK   80 (94)
T ss_pred             CCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHH
T ss_conf             95988223089998898989999999986093707899999896399989997899999999999988799999999999


Q ss_pred             HHHHHHHHHCCEEC
Q ss_conf             99999999511981
Q gi|254780316|r  790 IVENVVKKTNAVLR  803 (805)
Q Consensus       790 ii~~l~~k~ga~LR  803 (805)
                      |++.|+++|||+||
T Consensus        81 ii~~l~~k~~~~lR   94 (94)
T pfam03147        81 IVKALEKKFGAELR   94 (94)
T ss_pred             HHHHHHHHHCCEEC
T ss_conf             99999998591869


No 14 
>cd02153 tRNA_bindingDomain The tRNA binding domain is also known as the Myf domain in literature. This domain is found in a diverse collection of tRNA binding proteins, including prokaryotic phenylalanyl tRNA synthetases (PheRS), methionyl-tRNA synthetases (MetRS), human tyrosyl-tRNA synthetase(hTyrRS), Saccharomyces cerevisiae Arc1p, Thermus thermophilus CsaA, Aquifex aeolicus Trbp111, human p43 and human EMAP-II. PheRS, MetRS and hTyrRS aminoacylate their cognate tRNAs.  Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases.  The molecular chaperones Trbp111 and CsaA also contain this domain.  CsaA has export related activities; Trbp111 is structure-specific recognizing the L-shape of the tRNA fold. This domain has general tRNA binding properties.  In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multi
Probab=99.91  E-value=3.1e-24  Score=191.15  Aligned_cols=93  Identities=42%  Similarity=0.667  Sum_probs=85.3

Q ss_pred             EEEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECCCCCC-----CCCCEEEEECCCCEECCCCEEEEEEHHCCCCCCCH
Q ss_conf             4899999975657998-70899975999579897548345-----58978989668779258983983312058650545
Q gi|254780316|r   44 FTIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCGAPNV-----RVGLLGVWAPPGSCIPENNMIVNVRKIRGIESTGM  117 (805)
Q Consensus        44 vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~IvcgA~Nv-----~~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S~GM  117 (805)
                      ++||+|++++|||+|| |++|+||+|+++.+||||||+|+     ..|.+|+++          ..|+++++||++|+||
T Consensus         1 l~Vg~I~~~~~hp~adkL~~~~Vd~G~~~~~~iv~g~~n~~~~~~l~g~~v~~~----------~ni~~~ki~Gv~S~GM   70 (99)
T cd02153           1 LRVGKIVEAEPHPNADKLYVLKVDIGEEKPRQIVSGAANVYPPEELVGKKVVVA----------VNLKPKKLRGVESEGM   70 (99)
T ss_pred             CEEEEEEEEEECCCCCEEEEEEEECCCCCEEEEEECCCCCCCHHHHCCCEEEEE----------EEEEECEEECCCCCEE
T ss_conf             979999998858999877899999589948999955512068356159899999----------8230010405446549


Q ss_pred             HHHHHHCCCCCCCCCEEEECCCCCCCCCH
Q ss_conf             41188769985477507816888888455
Q gi|254780316|r  118 MCSEKELMLSDDSASIMELPIDAPVGGRL  146 (805)
Q Consensus       118 lCS~~ELgl~~~~~gI~~l~~~~~~G~~~  146 (805)
                      |||+.|||+++++.||+++|+++++|+++
T Consensus        71 l~s~~elg~~~~~~~il~~~~~~~~G~~v   99 (99)
T cd02153          71 LLSAEELGLEEGSVGILELPEDAPVGDRI   99 (99)
T ss_pred             EEECHHCCCCCCCEEEEECCCCCCCCCCC
T ss_conf             98953348888977999899997788929


No 15 
>pfam01588 tRNA_bind Putative tRNA binding domain. This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1), human tyrosyl-tRNA synthetase, and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme. This domain may perform a common function in tRNA aminoacylation.
Probab=99.84  E-value=2.3e-21  Score=170.87  Aligned_cols=93  Identities=35%  Similarity=0.519  Sum_probs=83.0

Q ss_pred             EEEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECCCCCCCCCCEEEEECCCCEECCCCEEEEEEHHCCCCCCCHHHHHH
Q ss_conf             4899999975657998-708999759995798975483455897898966877925898398331205865054541188
Q gi|254780316|r   44 FTIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCGAPNVRVGLLGVWAPPGSCIPENNMIVNVRKIRGIESTGMMCSEK  122 (805)
Q Consensus        44 vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~IvcgA~Nv~~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S~GMlCS~~  122 (805)
                      ++||+|+++++||+|| |++|+||+|+ +.+||||||+|+.++..+ ++..++.++ +   ++++||||++|+|||||+.
T Consensus         1 irVg~I~~~~~hp~adkL~~~~Vd~G~-~~~~ivsg~~~~~~~~~l-vg~~v~~~~-n---lk~~ki~Gv~S~GMlls~~   74 (94)
T pfam01588         1 LRVGKVLEAEKHPNADKLLVLKVDVGE-EERQIVSGAVNVYPPEEL-VGKLVVVVA-N---LKPAKLRGVESEGMILSAE   74 (94)
T ss_pred             CEEEEEEEEEECCCCCEEEEEEEECCC-CEEEEEECCCCEEEEEEE-EEEEEEEEC-C---CCCCCCCCCCCCEEEEEEE
T ss_conf             979999999989999878999999079-769999747543614136-610799940-7---7851497836888999888


Q ss_pred             HCCCCCCCCCEEEECCCCCCCCC
Q ss_conf             76998547750781688888845
Q gi|254780316|r  123 ELMLSDDSASIMELPIDAPVGGR  145 (805)
Q Consensus       123 ELgl~~~~~gI~~l~~~~~~G~~  145 (805)
                      |   ++++.||+.+|+++++|+.
T Consensus        75 e---~~~~~~ll~~~~~~~~G~r   94 (94)
T pfam01588        75 E---DGGSVGLLEPPGDVPPGTR   94 (94)
T ss_pred             C---CCCCEEEEECCCCCCCCCC
T ss_conf             5---7996899989999746989


No 16 
>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=99.79  E-value=1.5e-18  Score=150.91  Aligned_cols=163  Identities=22%  Similarity=0.356  Sum_probs=140.0

Q ss_pred             CEEEECCCCCCCCCCCEEEEEECCE--EEEEEEEEECHHHHHHCCCCCC--E-EEEEEEHHHHH----------------
Q ss_conf             3033058865678981699998792--9999985477899996687997--8-99998787623----------------
Q gi|254780316|r  637 SLRFESGAPSWYHPGRSGIIKTSAE--IVLGYFGEFHPNILDFFGLSNP--I-CGFEVYLDSIP----------------  695 (805)
Q Consensus       637 ~~~~~~~~~~~~hPgrsa~I~~~gk--~iiG~iG~ihP~i~~~~~i~~~--v-~~~EI~ld~L~----------------  695 (805)
                      ++++..+=.||-.|.---+|+..|+  .++| ||.+--.|+.+-|.+..  + |+|-+-||.|.                
T Consensus       264 K~RW~~~YFP~T~PSWE~E~y~~~~WLE~~G-CG~~R~~~L~R~G~~~SetIGyAFG~GL~R~AM~LF~IPDIRLlWS~D  342 (460)
T TIGR00469       264 KVRWVDAYFPFTAPSWELEVYFKDEWLELLG-CGLIRQDVLLRAGVKQSETIGYAFGLGLDRLAMLLFDIPDIRLLWSRD  342 (460)
T ss_pred             EEEEEECCCCCCCCCCEEEEEECCCEEEEEC-CCHHHHHHHHHCCCCCCCCCCEEECCCHHHHHHHHHCCCCEEEEEECC
T ss_conf             1557503388988840589888376556515-514677898845897333220000100889998873488615662045


Q ss_pred             ------HHHHCCCCCCCCCCCCCCCCCEEEEEEEECCCC------CHHHHHHHHHH-CCCCEEEEEEEEEEECCCCCCCC
Q ss_conf             ------545202456631368988872001899966887------99999999971-11003576989876367799884
Q gi|254780316|r  696 ------ISQKKRTKTKKVVHLSSLHPVKRDLAFIVDQHI------PAGTLVNIIKN-VDRLIDDVTVFDVFQGKSLGEGK  762 (805)
Q Consensus       696 ------~~~~~~~~~~~~~~~s~fP~v~RDls~iv~~~v------~~~~I~~~i~~-~~~ll~~v~lfDvY~g~~i~~gk  762 (805)
                            .++...-..++|+|+|+||.+.||+||++|++.      .-.++.+.||+ ||.++++|.|+|-|+..+  .|+
T Consensus       343 ~~F~~QFS~~dlh~~~~yKP~S~~P~~~~D~~FWLP~D~~~~~~~~~NDl~~~~R~~AGDlVE~~~LVD~F~HPK--TG~  420 (460)
T TIGR00469       343 ERFLRQFSKKDLHLLTKYKPISKYPQSFRDLAFWLPEDKEVIAQVSENDLYDLVRSVAGDLVESVKLVDKFKHPK--TGK  420 (460)
T ss_pred             CCHHHHHCCHHHHCCCCCCCCCCCCCCCCHHHHCCCCCCHHHCCCCCCHHHHHHHHHHCCEEEEEEEEECCCCCC--CCC
T ss_conf             302333111023215676864578874020533188985434468833489999875134033567764135888--887


Q ss_pred             EEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCEE
Q ss_conf             2699999984779888999999999999999999951198
Q gi|254780316|r  763 KSVAIQVLIQPLKDTFRDDDIRILMDRIVENVVKKTNAVL  802 (805)
Q Consensus       763 kSla~rl~fqs~~kTLtd~EI~~i~~~ii~~l~~k~ga~L  802 (805)
                      +|+.||+.||++|||||.+|||++++.|-+++.++|+++|
T Consensus       421 ~S~CyRI~Y~~M~R~LT~AEVN~~~~~~~S~~V~~y~V~~  460 (460)
T TIGR00469       421 KSVCYRIVYRSMDRTLTNAEVNELQDQVASKLVDEYSVEL  460 (460)
T ss_pred             CCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHEEECC
T ss_conf             3135886310223311056788898888642010101039


No 17 
>KOG2783 consensus
Probab=99.79  E-value=8.1e-19  Score=152.74  Aligned_cols=182  Identities=21%  Similarity=0.331  Sum_probs=148.6

Q ss_pred             HHHHHHHHHHHHHCC-CCCCEEEECCCCCCCCCCCEEEEEECCE--EEEEEEEEECHHHHHHCCCCCCE-EEEEEEHHHH
Q ss_conf             887531111111014-5333033058865678981699998792--99999854778999966879978-9999878762
Q gi|254780316|r  619 FDAKADALSVIEPFV-SLDSLRFESGAPSWYHPGRSGIIKTSAE--IVLGYFGEFHPNILDFFGLSNPI-CGFEVYLDSI  694 (805)
Q Consensus       619 ~dlKg~v~~ll~~l~-~~~~~~~~~~~~~~~hPgrsa~I~~~gk--~iiG~iG~ihP~i~~~~~i~~~v-~~~EI~ld~L  694 (805)
                      .++|-.++.+...+. ....+++...-.++-||.---+|+..|+  .++| +|.+-..+++.-++.+.+ ++|-+.||.|
T Consensus       228 ~~lk~~l~~L~~~Lf~~~~~~rwV~~yfpft~ps~eleI~~~~~wlevlg-cgvi~~~il~~ag~~~~igwafglgLerL  306 (436)
T KOG2783         228 QHLKQTLEGLCDELFGKEVEYRWVDAYFPFTHPSWELEIYFKGEWLEVLG-CGVMRQRLLKRAGLNNYIGWAFGLGLERL  306 (436)
T ss_pred             HHHHHHHHHHHHHHCCCHHHEEHEEEECCCCCCCEEEEEEECCCCHHHHC-CCHHHHHHHHHCCCCCEEEEEEECCHHHH
T ss_conf             99999998899986260441101105766689875899996587676515-50567788752041100345650467888


Q ss_pred             HHH-------------------HHCCCCC-CCCCCCCCCCCCEEEEEEEECC--CCCHHHHHHHHHHC-CCCEEEEEEEE
Q ss_conf             354-------------------5202456-6313689888720018999668--87999999999711-10035769898
Q gi|254780316|r  695 PIS-------------------QKKRTKT-KKVVHLSSLHPVKRDLAFIVDQ--HIPAGTLVNIIKNV-DRLIDDVTVFD  751 (805)
Q Consensus       695 ~~~-------------------~~~~~~~-~~~~~~s~fP~v~RDls~iv~~--~v~~~~I~~~i~~~-~~ll~~v~lfD  751 (805)
                      ...                   +-...+. ++|+|+|+||+..+|+||++|+  +..-.+..+++|.+ |.++++|.+.|
T Consensus       307 AMll~~IpDiRlfWs~DeRFlkqF~~g~I~~~FKp~SkYP~c~~DiSFWl~~~~~f~endf~~viR~V~gDlVesV~lid  386 (436)
T KOG2783         307 AMLLFDIPDIRLFWSFDERFLKQFSPGKIEPKFKPYSKYPPCYKDISFWLPQDKGFDENDFYDVIRTVAGDLVESVKLID  386 (436)
T ss_pred             HHHHHCCCCHHEEECCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88873676221011222677873185546646565455897524416860665588825899999987351645532565


Q ss_pred             EEECCCCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCEEC
Q ss_conf             7636779988426999999847798889999999999999999999511981
Q gi|254780316|r  752 VFQGKSLGEGKKSVAIQVLIQPLKDTFRDDDIRILMDRIVENVVKKTNAVLR  803 (805)
Q Consensus       752 vY~g~~i~~gkkSla~rl~fqs~~kTLtd~EI~~i~~~ii~~l~~k~ga~LR  803 (805)
                      .|+.++  .||+|+.||++||+.|||||.+|||.+++++-+.+.+.|+.++|
T Consensus       387 ~F~hpK--tgk~S~CYRi~YrsmeR~LTq~EVn~iq~q~r~~~~~~l~VelR  436 (436)
T KOG2783         387 QFTHPK--TGKTSLCYRIVYRSMERALTQEEVNSIQSQIRSELVQSLGVELR  436 (436)
T ss_pred             HCCCCC--CCCEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEECC
T ss_conf             404776--67422589876576665542999999999999999886270119


No 18 
>pfam03484 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=99.71  E-value=7.2e-18  Score=146.03  Aligned_cols=69  Identities=42%  Similarity=0.749  Sum_probs=66.9

Q ss_pred             CCCEECCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             310000431133331134587899999998402221034562366403454334402567676765352
Q gi|254780316|r  401 PRKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGV  469 (805)
Q Consensus       401 ~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGY  469 (805)
                      |++|.++.++++++||++++.+++.++|++|||+++.+++.|.|++|+||+||.+++||+|||||+|||
T Consensus         1 ~~~i~~~~~~i~~~lG~~i~~~~i~~~L~~lg~~~~~~~~~~~v~vPs~R~Di~~~~DliEEi~R~~Gy   69 (69)
T pfam03484         1 PRVITLDLEKINRLLGIELSPEEIKKILKRLGFKVEEDEDTLKVTVPSYRPDILHEVDLIEEVARLYGY   69 (69)
T ss_pred             CEEEEECHHHHHHHHCCCCCHHHHHHHHHHCCCEEEECCCEEEEECCCCCCCCCCCCHHHHHHHHHHCC
T ss_conf             958998799999971888799999999998699899479869998999857668625699999998089


No 19 
>cd02799 tRNA_bind_EMAP-II_like tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of tRNA binding proteins, including Caenorhabditis elegans methionyl-tRNA synthetase (CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS), Saccharomyces cerevisiae Arc1p, human p43 and EMAP2.  CeMetRS and hTyrRS aminoacylate their cognate tRNAs.  Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases.  This domain has general tRNA binding properties.  In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. A EMAP-II-like cytokine also is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain.
Probab=99.68  E-value=4.3e-17  Score=140.47  Aligned_cols=95  Identities=25%  Similarity=0.381  Sum_probs=72.0

Q ss_pred             CEEEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECCCCCCCCCCEEEEECCCCEECCCCEEEEEEHHCCCCCCCHHHHH
Q ss_conf             74899999975657998-70899975999579897548345589789896687792589839833120586505454118
Q gi|254780316|r   43 PFTIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCGAPNVRVGLLGVWAPPGSCIPENNMIVNVRKIRGIESTGMMCSE  121 (805)
Q Consensus        43 ~vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~IvcgA~Nv~~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S~GMlCS~  121 (805)
                      .++||+|+++++||||| |++|+||+|+++.+|||||+.|...    +-.++|.+.. .-..+|++||||++|+||||++
T Consensus         7 dirVG~I~~~e~hp~adkL~~~~VD~G~~~~r~ivsg~~~~y~----~e~L~gk~v~-~v~Nlkp~kirG~~SegMiL~a   81 (105)
T cd02799           7 DIRVGKILKVRKHPDADSLYVEEIDLGEEEPRTIVSGLVKFVP----LEQMQNRLVV-VLCNLKPRKMRGVKSQGMVLCA   81 (105)
T ss_pred             EEEEEEEEEEEECCCCCEEEEEEEECCCCCEEEEEEECCCCCC----HHHHCCCEEE-EEEEECCCCCCCCCCEEEEEEE
T ss_conf             9999999999989998854799998289723899970034249----8893787589-9963166207892650699997


Q ss_pred             HHCCCCCCCCCE--EEECCCCCCCCCH
Q ss_conf             876998547750--7816888888455
Q gi|254780316|r  122 KELMLSDDSASI--MELPIDAPVGGRL  146 (805)
Q Consensus       122 ~ELgl~~~~~gI--~~l~~~~~~G~~~  146 (805)
                      .    .++++++  +..|+++++|+.+
T Consensus        82 ~----~~d~~~v~ll~p~~~~~~G~rI  104 (105)
T cd02799          82 S----NADHEKVELLEPPEGAKPGERV  104 (105)
T ss_pred             E----CCCCCEEEEECCCCCCCCCCCC
T ss_conf             8----4999879996389998898856


No 20 
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=99.66  E-value=5.8e-17  Score=139.58  Aligned_cols=69  Identities=46%  Similarity=0.752  Sum_probs=64.6

Q ss_pred             CCCEECCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHCC--CCCCEEEECCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             31000043113333113458789999999840222103--4562366403454334402567676765352
Q gi|254780316|r  401 PRKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSVIGE--YDKFEVSVPSWRQDVEEKADLVEEILRIYGV  469 (805)
Q Consensus       401 ~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~--~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGY  469 (805)
                      +++|.++.++++++||++++.+++.++|++|||+++..  ++.|.|++|+||+||.+++||+|||||+|||
T Consensus         1 ~~~i~~~~~~i~~~lG~~i~~~~i~~~L~~lg~~~~~~~~~~~~~v~~Ps~R~Di~~~~DliEEi~R~~Gy   71 (71)
T smart00874        1 PRTITLRRERINRLLGLDLSAEEIEEILKRLGFEVEVSGDDDTLEVTVPSYRFDILIEADLIEEVARIYGY   71 (71)
T ss_pred             CEEEEECHHHHHHHHCCCCCHHHHHHHHHHCCCEEEECCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHCC
T ss_conf             96899879999987088879999999999869989965789759997899706559734699988898079


No 21 
>cd02800 tRNA_bind_EcMetRS_like tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins.  This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties.  MetRS aminoacylates methionine transfer RNAs (tRNAmet). AaTrbp111 is structure-specific molecular chaperone recognizing the L-shape of the tRNA fold. AaTrbp111 plays a role in nuclear trafficking of tRNAs. The functional unit of EcMetRs and AaTrbp111 is a homodimer, this domain acts as the dimerization domain.
Probab=99.39  E-value=2.3e-13  Score=113.98  Aligned_cols=92  Identities=26%  Similarity=0.369  Sum_probs=68.2

Q ss_pred             CEEEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECCCCCCCCCCEEEEECCCCEECCCCEEEEEEHHCCCCCCCHHHHH
Q ss_conf             74899999975657998-70899975999579897548345589789896687792589839833120586505454118
Q gi|254780316|r   43 PFTIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCGAPNVRVGLLGVWAPPGSCIPENNMIVNVRKIRGIESTGMMCSE  121 (805)
Q Consensus        43 ~vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~IvcgA~Nv~~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S~GMlCS~  121 (805)
                      .+.||+|+++++||+|| |++++||+|+ +.+|||||..+.    |-|-.++|.++. .-..++++||||++|+||+|++
T Consensus        10 DirVG~I~~ve~~p~a~kL~~~~VD~G~-~~r~ivsgi~~~----y~~eeLiGk~v~-~v~Nlkp~ki~G~~SegmiL~a   83 (105)
T cd02800          10 DLRVGKVLEAERVEGSDKLLKLTVDLGE-EERQIVSGIAKF----YPPEELVGKKVV-VVANLKPRKLRGVESQGMILAA   83 (105)
T ss_pred             EEEEEEEEEEEECCCCCEEEEEEEEECC-CCEEEEECCCCC----CCHHHHCCCEEE-EEEEECCCCCCCCCCCEEEEEE
T ss_conf             1899999999977885303999998478-527999846551----298995899899-9982158338991276899988


Q ss_pred             HHCCCCCCCCC--EEEECCCCCCCCCH
Q ss_conf             87699854775--07816888888455
Q gi|254780316|r  122 KELMLSDDSAS--IMELPIDAPVGGRL  146 (805)
Q Consensus       122 ~ELgl~~~~~g--I~~l~~~~~~G~~~  146 (805)
                      .+      ..+  ++..|+++++|+.+
T Consensus        84 ~~------~~~v~ll~p~~~~~~G~~v  104 (105)
T cd02800          84 ED------GGKLKLLTPDEEVEPGSRV  104 (105)
T ss_pred             EC------CCEEEEEECCCCCCCCCCC
T ss_conf             07------9999999379998898756


No 22 
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=99.34  E-value=2.3e-12  Score=106.93  Aligned_cols=22  Identities=14%  Similarity=0.205  Sum_probs=10.9

Q ss_pred             EECCCCHHHHHHCCCCCHHHHH
Q ss_conf             0004311333311345878999
Q gi|254780316|r  404 IVFMNSEVKRLSGIDVPIEDSL  425 (805)
Q Consensus       404 I~l~~~~i~~ilG~~i~~~ei~  425 (805)
                      +.++-.+..+=+|.-+...++.
T Consensus       293 ~~~~g~KmSKS~Gn~i~~~~~~  314 (644)
T PRK12267        293 WLMKDGKMSKSKGNVVDPEELV  314 (644)
T ss_pred             EECCCCEECCCCCCEECHHHHH
T ss_conf             8717860055368422379998


No 23 
>COG3382 Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]
Probab=99.33  E-value=1.1e-11  Score=102.00  Aligned_cols=141  Identities=21%  Similarity=0.233  Sum_probs=116.9

Q ss_pred             CCCCCHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEEECCCCCCHHHHHHHCCCCCCCCEEEE
Q ss_conf             5566377878888640-132103999998999860870000010223332688623554311455420112454320000
Q gi|254780316|r  227 NNVAPNWMRQRLKAVG-LRSISALVDITNYVSLDRGYPSHVFDASRISDVLTVRRACSGEKILALDNQEYDLSPDNVVIA  305 (805)
Q Consensus       227 ~~~SP~wl~~rL~~~G-ir~inniVDitNyvmle~GqPlHafD~dki~~~i~vr~a~~~E~~~~Ld~~e~~L~~~~lvI~  305 (805)
                      ..+|-.-|..|..+=+ +-.||++||+-|.+-|+++.|+-+||+||+.|++.++.|.-||.|.+|.++.....++.+|.+
T Consensus        80 ~r~S~EALlrRv~kg~~lp~InpvVD~yNa~Sl~y~vPig~~D~d~~~g~lrL~~a~ggE~f~~lg~~~~~~~~geiv~~  159 (229)
T COG3382          80 TRPSAEALLRRVLKGNSLPRINPVVDIYNAASLKYAVPIGGYDADKIVGDLRLTLADGGETFDTLGAKNEPPLEGEIVLV  159 (229)
T ss_pred             CCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHCCCCEEEECCCCCEEECCCCCCCCCCCCCEEEE
T ss_conf             89729999999874898666562554105777762487441138770798169863687254324677878999947997


Q ss_pred             CCCCCCC-CHHHCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             2567631-001113553120136726999971578788877887616540155441345530135889998887521233
Q gi|254780316|r  306 SDGRIQS-IAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLILSLC  384 (805)
Q Consensus       306 d~~~~ia-laGImGg~~s~v~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li~e~~  384 (805)
                      |++++.+ .=..-.|..|.||++|+|+|+=.+.-+.                       +.-+....|++.++.++.+++
T Consensus       160 Dd~G~~~r~~~~Rds~rT~vt~~Tk~~l~I~e~vp~-----------------------~~~~~l~~a~~~l~~~l~~~~  216 (229)
T COG3382         160 DDEGAFCRRWNWRDSVRTMVTESTKNVLLIAEGVPG-----------------------VEVEDLVEALDSLADLLEKLL  216 (229)
T ss_pred             CCCCCEEEECCCCCCEEEEHHHCCCEEEEEEECCCC-----------------------CCHHHHHHHHHHHHHHHHHHC
T ss_conf             489880410454245055511056627898865898-----------------------568999999999999999865


Q ss_pred             CCCCCC
Q ss_conf             455565
Q gi|254780316|r  385 GGTASD  390 (805)
Q Consensus       385 gg~~~~  390 (805)
                      ||+...
T Consensus       217 gG~~~~  222 (229)
T COG3382         217 GGTRAV  222 (229)
T ss_pred             CCCCCC
T ss_conf             886552


No 24 
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=99.32  E-value=4.7e-12  Score=104.75  Aligned_cols=16  Identities=13%  Similarity=0.104  Sum_probs=8.0

Q ss_pred             HHHHHHHHCCCCCCCC
Q ss_conf             9988875212334555
Q gi|254780316|r  373 LKHIVSLILSLCGGTA  388 (805)
Q Consensus       373 l~r~~~Li~e~~gg~~  388 (805)
                      +.|.+.++...++|.+
T Consensus       388 ~~R~~~~~~k~~~g~v  403 (666)
T PRK00133        388 ASRAAGFINKRFDGKL  403 (666)
T ss_pred             HHHHHHHHHHHCCCCC
T ss_conf             9999999998659978


No 25 
>cd02798 tRNA_bind_CsaA tRNA-binding-domain-containing CsaA-like proteins.  CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain.
Probab=99.21  E-value=3e-11  Score=99.06  Aligned_cols=87  Identities=17%  Similarity=0.244  Sum_probs=68.4

Q ss_pred             CEEEEEEEEEEECCCC-C-CCEEEEECCCCCEEEEECCCCCC-----CCCCEEEEECCCCEECCCCEEEEEEHHCCCCCC
Q ss_conf             7489999997565799-8-70899975999579897548345-----589789896687792589839833120586505
Q gi|254780316|r   43 PFTIVKVLSVERNPDL-D-CAILRIDTGKHQEIQVVCGAPNV-----RVGLLGVWAPPGSCIPENNMIVNVRKIRGIEST  115 (805)
Q Consensus        43 ~vvvg~v~~~~~hP~a-d-l~v~~Vd~g~~~~~~IvcgA~Nv-----~~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S~  115 (805)
                      .+.||+|+++++||+| | |.+++||+|+.+.+|||+|....     =.|.+|++.          .-+|++|+||++|+
T Consensus        10 DiRVg~I~~~e~~p~a~dkL~~l~vD~G~~~~r~ivsgi~~~y~~eeL~Gk~Vvvv----------~NLkp~ki~G~~Se   79 (107)
T cd02798          10 DLRVGTIVEVEDFPEARKPAYKLKVDFGEIGVKQSSAQITKYYKPEELIGRQVVAV----------VNFPPKQIAGVLSE   79 (107)
T ss_pred             EEEEEEEEEEEECCCCCCCEEEEEEECCCCEEEEEEEHHHHCCCHHHHCCCEEEEE----------ECCCCCEECCCCCC
T ss_conf             27999999999878877613899996189708999990100279899689989999----------95688237990255


Q ss_pred             CHHHHHHHCCCCCCCCC---EEEECCCCCCCCC
Q ss_conf             45411887699854775---0781688888845
Q gi|254780316|r  116 GMMCSEKELMLSDDSAS---IMELPIDAPVGGR  145 (805)
Q Consensus       116 GMlCS~~ELgl~~~~~g---I~~l~~~~~~G~~  145 (805)
                      ||+.++.      +.+|   ++.-++++++|+.
T Consensus        80 gMiL~a~------~~~~~~~ll~p~~~~~~G~r  106 (107)
T cd02798          80 VLVLGAD------DEGGEVVLLVPDREVPNGAK  106 (107)
T ss_pred             EEEEEEE------CCCCEEEEEECCCCCCCCCC
T ss_conf             8999888------79981999818999879886


No 26 
>PRK10089 hypothetical protein; Provisional
Probab=99.21  E-value=9.9e-12  Score=102.46  Aligned_cols=88  Identities=26%  Similarity=0.411  Sum_probs=63.9

Q ss_pred             CEEEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECCCCCC-----CCCCEEEEECCCCEECCCCEEEEEEHHCCCCCCC
Q ss_conf             74899999975657998-70899975999579897548345-----5897898966877925898398331205865054
Q gi|254780316|r   43 PFTIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCGAPNV-----RVGLLGVWAPPGSCIPENNMIVNVRKIRGIESTG  116 (805)
Q Consensus        43 ~vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~IvcgA~Nv-----~~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S~G  116 (805)
                      .+.||+|+++++||+|| |.+++||+|+ +.+|+|||....     -.|.+|++.          .-++++|+||+.|+|
T Consensus        13 DiRVG~I~~~e~~~~a~kL~~~~VD~G~-~~~~ivsgi~~~y~~eeLvGk~v~~v----------~NLkp~ki~G~~Seg   81 (110)
T PRK10089         13 EMRVGKIVEVKRHENADKLYIVQVDVGE-KTLQTVTSLVPYYSEEELMGKTVVVL----------CNLQKAKMRGETSEC   81 (110)
T ss_pred             EEEEEEEEEEEECCCCCCCEEEEEECCC-CCCEEEEECCCCCCHHHHCCCEEEEE----------ECCCCCCCCCCCCCE
T ss_conf             2799999998888998710899998189-75189998300379899289989999----------876753218931525


Q ss_pred             H-HHHHHHCCCCCCCCCE-EEEC-CCCCCCCCH
Q ss_conf             5-4118876998547750-7816-888888455
Q gi|254780316|r  117 M-MCSEKELMLSDDSASI-MELP-IDAPVGGRL  146 (805)
Q Consensus       117 M-lCS~~ELgl~~~~~gI-~~l~-~~~~~G~~~  146 (805)
                      | ||+..|     +...+ +.-| +++++|+.+
T Consensus        82 MiL~a~~~-----dg~~~~ll~p~~~v~~G~ri  109 (110)
T PRK10089         82 MLLCAETD-----DGSESVLLTPERMMPAGVRI  109 (110)
T ss_pred             EEEEEECC-----CCCEEEEECCCCCCCCCCCC
T ss_conf             99998869-----99869996799999898851


No 27 
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=99.06  E-value=3.7e-09  Score=84.16  Aligned_cols=191  Identities=15%  Similarity=0.171  Sum_probs=136.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH---HHHHHHH-------HHCCCCCCCCCC-------------
Q ss_conf             76789988954678988787787740232100482576---5520000-------000024677643-------------
Q gi|254780316|r  484 DKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQS---VLFGGGQ-------RELEILNPISAD-------------  540 (805)
Q Consensus       484 ~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~---~~~~~~~-------~~i~l~NPlS~e-------------  540 (805)
                      ..+.+.+..++.+.+|++++++||.|+ +-+++..+.-   .+|.+.+       +..-|.||-..+             
T Consensus       240 ~~g~~Hp~~~~~~~~r~i~~~mGF~e~-~g~~ve~~fwNfdaLf~Pq~HPARd~~Dtf~l~~~~~~~lp~~~~~~Vk~~H  318 (501)
T PRK04172        240 YPGKKHPYREFIEEVRDILVEMGFEEV-KGPIVETEFWNFDALFQPQDHPAREMQDTFYLKYPSKGELPEELVERVKEVH  318 (501)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCEEE-ECCCEECCCCCHHHHCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHH
T ss_conf             988748899999999999997897685-3661010000334305898998555445378657654557378898899987


Q ss_pred             ---------------------CCCCCCHHHCHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCC----CEEHHHHCCCC
Q ss_conf             ---------------------21015122110677643210158611345430244447775443----10002210354
Q gi|254780316|r  541 ---------------------MSNMRTSLLPGLLKATGRNVDRAIADFAIFEVSHVYENDTPEGQ----KYMAAGIRKGS  595 (805)
Q Consensus       541 ---------------------~s~lR~SLlp~LL~~~~~N~~r~~~~i~lFEiG~Vf~~~~~~~~----~~~~~~~~~~~  595 (805)
                                           ..+|||.--+--.+.++.   +..+.+++|=+|+||+++.....    -+.+-|+.   
T Consensus       319 E~Gg~~gS~Gw~y~w~~~~~~~~~lRthtt~~~~r~l~~---~~~~p~~~f~~~rvfR~e~~d~tH~~~F~Q~eg~v---  392 (501)
T PRK04172        319 EHGGDTGSRGWGYKWDEDIAKRLVLRTHTTALSARYLAE---RPEPPGKYFSIGRVFRPETIDATHLPEFYQLEGIV---  392 (501)
T ss_pred             HCCCCCCCCCCCCCCCHHHHHHHCCCCCCCHHHHHHHHH---CCCCCEEEECCCCEEECCCCCCCCCCEEEEEEEEE---
T ss_conf             427767887767777855664301043674667999974---68998357356505426888865441332224899---


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCEEEEEECCE--EEEEEEEEECHH
Q ss_conf             310124620234544333314688875311111110145333033058865678981699998792--999998547789
Q gi|254780316|r  596 SGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVSLDSLRFESGAPSWYHPGRSGIIKTSAE--IVLGYFGEFHPN  673 (805)
Q Consensus       596 ~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~~~~~~~~~~~~~~~~hPgrsa~I~~~gk--~iiG~iG~ihP~  673 (805)
                                      -...+.|-++||.+..++..+|. ..++|.++=.||-.|..-..++..+.  .-+|-.|.+||+
T Consensus       393 ----------------~~~~~~~~~L~g~l~~f~~~~g~-~~~rfrp~yfPftEPs~E~~~~~~~~~WiE~~g~G~~~pe  455 (501)
T PRK04172        393 ----------------MGEDVSFRHLLGILKEFYKRLGF-EEVKFRPAYFPFTEPSVEVEVYHPGLGWVELGGAGIFRPE  455 (501)
T ss_pred             ----------------ECCCCCHHHHHHHHHHHHHHHCC-CCEEECCCCCCCCCCCEEEEEEECCCCEEEEECCCCCCHH
T ss_conf             ----------------84888799999999999998588-6078679989989982789999579986998267578889


Q ss_pred             HHHHCCCCCCEEEEEEEHHHHHHHH
Q ss_conf             9996687997899998787623545
Q gi|254780316|r  674 ILDFFGLSNPICGFEVYLDSIPISQ  698 (805)
Q Consensus       674 i~~~~~i~~~v~~~EI~ld~L~~~~  698 (805)
                      +++.+|++.++++|-+-++.+....
T Consensus       456 vl~~~g~~~~~~a~G~g~eR~am~~  480 (501)
T PRK04172        456 VTEPLGIDVPVLAWGIGIDRLAMLR  480 (501)
T ss_pred             HHHHCCCCCCEEEEEECHHHHHHHH
T ss_conf             9975599987478751599999998


No 28 
>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=99.02  E-value=9.7e-09  Score=81.22  Aligned_cols=191  Identities=17%  Similarity=0.206  Sum_probs=134.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH-HHHH-HH-------HHHCCCCCCCCCCCCCCCCHHHCHHHHH
Q ss_conf             6789988954678988787787740232100482576-5520-00-------0000024677643210151221106776
Q gi|254780316|r  485 KRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQS-VLFG-GG-------QRELEILNPISADMSNMRTSLLPGLLKA  555 (805)
Q Consensus       485 ~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~-~~~~-~~-------~~~i~l~NPlS~e~s~lR~SLlp~LL~~  555 (805)
                      .+...+.....+++++.+.++||.++-.--..+..++ +.++ +.       .+..=+.+|......+|||.--+.-.+.
T Consensus        13 ~G~~HPi~~~~~~i~~~f~~~GF~~~~g~eves~~~NFDaLn~P~dHPaR~~~DTfy~~~~~~~~~~vLRtHTS~~q~r~   92 (243)
T pfam01409        13 PGGLHPLTRVLEEIRDIFLSMGFEEVEGPEVESDFYNFDALNIPQDHPARDMQDTFYLKKPLKARRLLLRTHTTPVQART   92 (243)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCEEECCCCCHHHHHH
T ss_conf             99858599999999999987798687698356427777755789889876767603433666676865768798899999


Q ss_pred             HHHHCCCCCCHHHHHHHCCCCCCCCCCCCC----EEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             432101586113454302444477754431----0002210354310124620234544333314688875311111110
Q gi|254780316|r  556 TGRNVDRAIADFAIFEVSHVYENDTPEGQK----YMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEP  631 (805)
Q Consensus       556 ~~~N~~r~~~~i~lFEiG~Vf~~~~~~~~~----~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~  631 (805)
                      ++.|   ..+.+|+|-+|+||+++.....-    +.+.|+.                   -.+.+.|-++||.++.++..
T Consensus        93 l~~~---~~~p~r~~~~grvyR~d~~DatH~~~FhQ~Eg~v-------------------vd~~it~~~Lk~~l~~~~~~  150 (243)
T pfam01409        93 LAEK---NKPPIKIFSIGRVFRRDQVDATHLPEFHQVEGLV-------------------VDENVSFADLKGVLEEFLRK  150 (243)
T ss_pred             HHHC---CCCCEEEECCCEEEECCCCCCCCCCEEEEEEEEE-------------------ECCCCCHHHHHHHHHHHHHH
T ss_conf             9742---7998489814313325889843153105755789-------------------65777899999999999999


Q ss_pred             CC-CCCCEEEECCCCCCCCCCCEEEEEE--CCE-EEEEEEEEECHHHHHHCCCC--CCEEEEEEEHHHHHHH
Q ss_conf             14-5333033058865678981699998--792-99999854778999966879--9789999878762354
Q gi|254780316|r  632 FV-SLDSLRFESGAPSWYHPGRSGIIKT--SAE-IVLGYFGEFHPNILDFFGLS--NPICGFEVYLDSIPIS  697 (805)
Q Consensus       632 l~-~~~~~~~~~~~~~~~hPgrsa~I~~--~gk-~iiG~iG~ihP~i~~~~~i~--~~v~~~EI~ld~L~~~  697 (805)
                      ++ ..-++++.++-.|+-.|+--.+++.  +++ .-+|-+|.+||+++++.|+.  .+.++|-+-+|.|...
T Consensus       151 lfg~~~~~R~rp~yFPFTePS~Evdv~~~~~~~WlEi~G~Gmv~p~vl~~~gid~~~~g~AfG~GlERlaMl  222 (243)
T pfam01409       151 FFGFEVKVRFRPSYFPFTEPSAEVDVYCCKGGGWIEIGGAGMVHPNVLEAVGIDEDYPGFAFGLGVERLAML  222 (243)
T ss_pred             HCCCCCEEEECCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCHHHHHHCCCCCCCEEEEEEECHHHHHHH
T ss_conf             739973798678869999986179999964997258750366678899866989897699985348899999


No 29 
>COG2517 Predicted RNA-binding protein containing a C-terminal EMAP domain [General function prediction only]
Probab=98.98  E-value=1.3e-09  Score=87.52  Aligned_cols=68  Identities=26%  Similarity=0.397  Sum_probs=61.6

Q ss_pred             CCEEEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECCCCCCCCCCEEEEECCCCEECCCCEEEEEEHHCCCCCCCHHHH
Q ss_conf             874899999975657998-7089997599957989754834558978989668779258983983312058650545411
Q gi|254780316|r   42 SPFTIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCGAPNVRVGLLGVWAPPGSCIPENNMIVNVRKIRGIESTGMMCS  120 (805)
Q Consensus        42 ~~vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~IvcgA~Nv~~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S~GMlCS  120 (805)
                      -.+++|+|.++.+||+|| |++|-||+|. ..++|||..--|++|.+|+||+    ||       ++.+-|+.|+||+|-
T Consensus       120 V~~vvGEV~Sv~~hp~aD~L~v~vvn~G~-r~~tVVTN~~~vreg~~vaVAl----LP-------Pr~F~gvvSeGMFlg  187 (219)
T COG2517         120 VDIVVGEVMSVGKHPNADKLLVTVVNIGG-RAVTVVTNDLDVREGDRVAVAL----LP-------PRNFFGVVSEGMFLG  187 (219)
T ss_pred             EEEEEEEEEECCCCCCCCCEEEEEEECCC-EEEEEEECCCCCCCCCEEEEEE----CC-------HHHHCCCCCCCEEEC
T ss_conf             88876323422568987715999982188-4789970652211388779996----38-------067445013525631


Q ss_pred             H
Q ss_conf             8
Q gi|254780316|r  121 E  121 (805)
Q Consensus       121 ~  121 (805)
                      .
T Consensus       188 ~  188 (219)
T COG2517         188 A  188 (219)
T ss_pred             C
T ss_conf             1


No 30 
>PTZ00326 phenylalanyl-tRNA synthetase; Provisional
Probab=98.95  E-value=5.3e-08  Score=75.99  Aligned_cols=192  Identities=16%  Similarity=0.194  Sum_probs=128.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH---HHHHHH-------HHHCCCCCCCCCC-------------
Q ss_conf             76789988954678988787787740232100482576---552000-------0000024677643-------------
Q gi|254780316|r  484 DKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQS---VLFGGG-------QRELEILNPISAD-------------  540 (805)
Q Consensus       484 ~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~---~~~~~~-------~~~i~l~NPlS~e-------------  540 (805)
                      ..+...+..++.+.+|++++++||.|+-+-.++..+.-   .+|.+.       .+..-|.+|-..+             
T Consensus       237 ~~g~~hp~~~~~~~~r~if~~mGF~E~~~~~~ves~fwNfDaLf~Pq~HPARd~~DTF~l~~p~~~~~~~~~~~~~Vk~v  316 (505)
T PTZ00326        237 SMGNLHPLLKVRQEFREIFMEMGFEEMPTNRWVESSFWNFDALFIPQQHPARDLQDTFFLSKPETSKFLDAEYVERVKAV  316 (505)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCEECCCCCEEEECCCCCHHHCCCCCCCCCCCCCEEEECCCCCCCCCCHHHHHHHHHH
T ss_conf             87766889999999999999779767668971331321311104898998665233477447542456878999988888


Q ss_pred             ---------------------CCCCCCHHHCHHHHHHHH---HC--CCCCCHHHHHHHCCCCCCCCCCCC----CEEHHH
Q ss_conf             ---------------------210151221106776432---10--158611345430244447775443----100022
Q gi|254780316|r  541 ---------------------MSNMRTSLLPGLLKATGR---NV--DRAIADFAIFEVSHVYENDTPEGQ----KYMAAG  590 (805)
Q Consensus       541 ---------------------~s~lR~SLlp~LL~~~~~---N~--~r~~~~i~lFEiG~Vf~~~~~~~~----~~~~~~  590 (805)
                                           ..+|||.--+--.+.+.+   +.  .+.....++|-+|+||+++.....    -+.+-|
T Consensus       317 He~G~~gs~Gw~y~W~~~~a~~~~LRthTt~vs~r~l~~~~~~~~~~~~~~P~k~fsi~rv~R~e~~d~th~~~f~Q~eg  396 (505)
T PTZ00326        317 HSGGGYGSIGWQYNWKLEEARKNVLRTHTTAVSARMLYKLAQQYQKGKGFKPKKYFSIDRVFRNETLDATHLAEFHQVEG  396 (505)
T ss_pred             HCCCCCCCCCCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEECCCEEECCCCCCCCCCEEEEEEE
T ss_conf             50688788876778797787520636577537699999875404655688981475237264157777653404554357


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCEEEEEE--CC--E-EEEE
Q ss_conf             10354310124620234544333314688875311111110145333033058865678981699998--79--2-9999
Q gi|254780316|r  591 IRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVSLDSLRFESGAPSWYHPGRSGIIKT--SA--E-IVLG  665 (805)
Q Consensus       591 ~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~~~~~~~~~~~~~~~~hPgrsa~I~~--~g--k-~iiG  665 (805)
                      +.                   -.+.++|-++||.+..++..++. ..++|.++=.||-.|  |+++..  .+  + .-+|
T Consensus       397 ~~-------------------~~~~~~~~~l~~~l~~f~~~~g~-~~~rfrp~yfpfteP--s~e~~~~~~~~~~w~Ei~  454 (505)
T PTZ00326        397 VV-------------------IDRNLSLGDLMGTLREFFRRIGI-SKLRFKPAFNPYTEP--SMEIFGYHPQLKKWVEVG  454 (505)
T ss_pred             EE-------------------ECCCCCHHHHHHHHHHHHHHHCC-CCEEECCCCCCCCCC--CEEEEEEECCCCCEEEEE
T ss_conf             89-------------------64888899999999999998498-757868888898998--278999707888479982


Q ss_pred             EEEEECHHHHHHCCCCC--CEEEEEEEHHHHHHH
Q ss_conf             98547789999668799--789999878762354
Q gi|254780316|r  666 YFGEFHPNILDFFGLSN--PICGFEVYLDSIPIS  697 (805)
Q Consensus       666 ~iG~ihP~i~~~~~i~~--~v~~~EI~ld~L~~~  697 (805)
                      -+|.+||++++..|++.  ++++|-+-++.+...
T Consensus       455 g~Gm~~p~vl~~~g~~~~~~~~a~G~g~eR~am~  488 (505)
T PTZ00326        455 NSGLFRPEMLRPMGFPEDVTVIAWGLSLERPTMI  488 (505)
T ss_pred             CCCCCCHHHHHHCCCCCCCEEEEEEECHHHHHHH
T ss_conf             6657587887325959998489986238899999


No 31 
>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed
Probab=98.93  E-value=5e-09  Score=83.28  Aligned_cols=209  Identities=15%  Similarity=0.254  Sum_probs=135.4

Q ss_pred             CCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             46776432101512211067764321015861134543024444777544310002210354310124620234544333
Q gi|254780316|r  534 LNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFEVSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSEERC  613 (805)
Q Consensus       534 ~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lFEiG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  613 (805)
                      +-|.| ...+||+.+..|-.-+++.=.++....+++|-|.+||+++......++......              ...-..
T Consensus       175 L~p~s-~~~tLRSHmTsgwfitL~~l~~k~~~P~klFSIDRcFRrEq~eD~~hL~~yhsa--------------scvv~~  239 (527)
T PRK06253        175 LKPES-SRLTLRSHMTSGWFITLSALWERKPLPFKLFSIDRCFRREQKEDASRLMTYHSA--------------SCVVAG  239 (527)
T ss_pred             CCCCC-CCCEEHHCCCCHHHHHHHHHHHCCCCCEEEEEEEHEEECHHHCCHHHHHHHHEE--------------EEEEEC
T ss_conf             25544-453410010302788799997267998368741010220000245563454432--------------269975


Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCEEEECC--CCCCCCCCCEEEEEE-----CCEEEEEEEEEECHHHHHHCCCCCCEEE
Q ss_conf             314688875311111110145333033058--865678981699998-----7929999985477899996687997899
Q gi|254780316|r  614 RFVDLFDAKADALSVIEPFVSLDSLRFESG--APSWYHPGRSGIIKT-----SAEIVLGYFGEFHPNILDFFGLSNPICG  686 (805)
Q Consensus       614 ~~~df~dlKg~v~~ll~~l~~~~~~~~~~~--~~~~~hPgrsa~I~~-----~gk~iiG~iG~ihP~i~~~~~i~~~v~~  686 (805)
                      ..+++-++|++++.++..+|.. +++|.++  ...||.|+-+.+++.     +|=.-+|.+|.-.|.++..|||+.||..
T Consensus       240 edVn~d~gkav~~~lL~~fGF~-~frFrPdek~skYY~P~TqtEVy~yhp~~~gWvEvatfGIysP~aL~~ygI~~PVmn  318 (527)
T PRK06253        240 EDVTVDDGKAVAEGLLSQFGFT-NFRFRPDEKRSKYYTPDTQTEVYAYHPKLDGWVEVATFGIYSPTALAEYGIDVPVMN  318 (527)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCC-EEEECCCCCCCCCCCCCCCEEEEEECCCCCCEEEEECCCCCCHHHHHHCCCCCCEEE
T ss_conf             9866777799999999970975-378434423566537886327999636678628973142567544543199974220


Q ss_pred             EEEEHHHHHHHHHCCCCCC--CCCCCCCCCCCEEEEEEEEC-----CCCCHHHHHHHH-HHC--CCCEEEEEEEEEEECC
Q ss_conf             9987876235452024566--31368988872001899966-----887999999999-711--1003576989876367
Q gi|254780316|r  687 FEVYLDSIPISQKKRTKTK--KVVHLSSLHPVKRDLAFIVD-----QHIPAGTLVNII-KNV--DRLIDDVTVFDVFQGK  756 (805)
Q Consensus       687 ~EI~ld~L~~~~~~~~~~~--~~~~~s~fP~v~RDls~iv~-----~~v~~~~I~~~i-~~~--~~ll~~v~lfDvY~g~  756 (805)
                      +-+-++.|...........  .|..+...-.+.||||=.+.     ....-.++...| +.+  ..--.+=.=|..|+|+
T Consensus       319 lGlGvERLAMI~~~~~DiR~l~ypQf~~~~lsD~eiA~~i~~~~~P~t~eg~~~a~~ii~~~~~~~~e~sPC~f~~~~g~  398 (527)
T PRK06253        319 LGLGVERLAMILHNAEDVREMVYPQFYEWELSDREIARMIKVDKVPVTDEGKDLAREIVETCVKHADEPSPCEFEAWEGE  398 (527)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECC
T ss_conf             01118999999818277887633456775668699986514046767578999999999999981899999468874031


Q ss_pred             CC
Q ss_conf             79
Q gi|254780316|r  757 SL  758 (805)
Q Consensus       757 ~i  758 (805)
                      -.
T Consensus       399 ~~  400 (527)
T PRK06253        399 IF  400 (527)
T ss_pred             CC
T ss_conf             04


No 32 
>KOG2241 consensus
Probab=98.79  E-value=7.7e-09  Score=81.95  Aligned_cols=91  Identities=27%  Similarity=0.432  Sum_probs=70.0

Q ss_pred             CCCEEEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECCCCCCC-----CCCEEEEECCCCEECCCCEEEEEEHHCCCCC
Q ss_conf             6874899999975657998-708999759995798975483455-----8978989668779258983983312058650
Q gi|254780316|r   41 LSPFTIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCGAPNVR-----VGLLGVWAPPGSCIPENNMIVNVRKIRGIES  114 (805)
Q Consensus        41 ~~~vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~IvcgA~Nv~-----~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S  114 (805)
                      .-.+.||+|+++.+||+|| |++-+||+|+.+++|||.|=-...     .|-+|+|      |  .  .+|++|+||+.|
T Consensus        96 ~LDiRvG~Ivka~kHpdADsLYve~IdvgE~~PRTVvSGLvk~vpleemq~R~Vvv------l--c--NLKPakmRgv~S  165 (255)
T KOG2241          96 LLDIRVGKIVKAGKHPDADSLYVEEIDVGEAEPRTVVSGLVKHVPLEEMQNRLVVV------L--C--NLKPAKMRGVKS  165 (255)
T ss_pred             EEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCCEEEHHHHHHCCHHHHHCCEEEE------E--E--CCCCCCCCCCCC
T ss_conf             14678768988303688662578886306556631003467548898972884999------9--3--355432466223


Q ss_pred             CCHH-HHHHHCCCCCCCC--CEEEECCCCCCCCCH
Q ss_conf             5454-1188769985477--507816888888455
Q gi|254780316|r  115 TGMM-CSEKELMLSDDSA--SIMELPIDAPVGGRL  146 (805)
Q Consensus       115 ~GMl-CS~~ELgl~~~~~--gI~~l~~~~~~G~~~  146 (805)
                      +||+ |..     +.|+.  -++..|.++.+|..+
T Consensus       166 ~gMvlcaS-----s~d~~~VE~l~pP~gs~pGdRv  195 (255)
T KOG2241         166 QGMVLCAS-----SPDKSVVEPLAPPAGSKPGDRV  195 (255)
T ss_pred             CEEEEECC-----CCCCCEEEECCCCCCCCCCCEE
T ss_conf             14688637-----8665504651599989998746


No 33 
>COG0016 PheS Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]
Probab=98.78  E-value=3.7e-07  Score=69.98  Aligned_cols=192  Identities=16%  Similarity=0.195  Sum_probs=129.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH--HHH-HHH-------HHCCCCCCCCCCCCCCCCHHHCHHHH
Q ss_conf             67899889546789887877877402321004825765--520-000-------00002467764321015122110677
Q gi|254780316|r  485 KRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSV--LFG-GGQ-------RELEILNPISADMSNMRTSLLPGLLK  554 (805)
Q Consensus       485 ~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~--~~~-~~~-------~~i~l~NPlS~e~s~lR~SLlp~LL~  554 (805)
                      .+...+.....+++++.+.++||+|+-.. .+..+..+  .++ +.+       +..-+ |+ +.+..+|||.--|--.+
T Consensus       107 ~G~~Hpl~~~~e~i~~iF~~mGF~~~~gp-~IE~d~~NFDaLn~P~dHPARdmqDTFy~-~~-~~~~~lLRTHTs~vq~R  183 (335)
T COG0016         107 PGSLHPLTQTIEEIEDIFLGMGFTEVEGP-EIETDFYNFDALNIPQDHPARDMQDTFYL-KD-DREKLLLRTHTSPVQAR  183 (335)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCEECCCC-CCCCCCCCHHHHCCCCCCCCCCCCCEEEE-CC-CCCCEEECCCCCHHHHH
T ss_conf             89867089999999999997496664588-21320225243249999984124443787-68-87730023668276599


Q ss_pred             HHHHHCCCCCCHHHHHHHCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             64321015861134543024444777544310002210354310124620234544333314688875311111110145
Q gi|254780316|r  555 ATGRNVDRAIADFAIFEVSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVS  634 (805)
Q Consensus       555 ~~~~N~~r~~~~i~lFEiG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~~  634 (805)
                      .+..|..   +.+++|=+|+||+++..... +..-.-+.       .|..       -.+.++|-++||.++.++..++.
T Consensus       184 ~l~~~~~---~P~k~~~~grvyR~D~~DaT-Hs~~FhQi-------EGlv-------vd~~~s~~~Lkg~L~~f~~~~fg  245 (335)
T COG0016         184 TLAENAK---IPIKIFSPGRVYRNDTVDAT-HSPEFHQI-------EGLV-------VDKNISFADLKGTLEEFAKKFFG  245 (335)
T ss_pred             HHHHCCC---CCCEEECCCCEECCCCCCCC-CCHHEEEE-------EEEE-------EECCCCHHHHHHHHHHHHHHHCC
T ss_conf             9984799---99158456634117887764-26101336-------7899-------95895699999999999999637


Q ss_pred             CC-CEEEECCCCCCCCCCCEEEEEECCE---EEEEEEEEECHHHHHHCCC-CCCEE--EEEEEHHHHHHH
Q ss_conf             33-3033058865678981699998792---9999985477899996687-99789--999878762354
Q gi|254780316|r  635 LD-SLRFESGAPSWYHPGRSGIIKTSAE---IVLGYFGEFHPNILDFFGL-SNPIC--GFEVYLDSIPIS  697 (805)
Q Consensus       635 ~~-~~~~~~~~~~~~hPgrsa~I~~~gk---~iiG~iG~ihP~i~~~~~i-~~~v~--~~EI~ld~L~~~  697 (805)
                      .. .++|.++=.||--|.--.+++..+.   .-+|=+|.+||+|++..|+ +.++.  +|-+-+|.|...
T Consensus       246 ~~~~vRfrpsyFPFTEPS~Evdv~~~~~~~WlEi~G~Gmv~P~VL~~~G~~~~~~~GfAfGlGlERlAML  315 (335)
T COG0016         246 EDVKVRFRPSYFPFTEPSAEVDVYCPGCGGWLEILGCGMVHPNVLEAVGIDPEEYSGFAFGLGLERLAML  315 (335)
T ss_pred             CCCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEECCCCCCHHHHHHCCCCCCCCEEEEEEECHHHHHHH
T ss_conf             7763576068789899717899997687868998356545788897459998760588874048899999


No 34 
>TIGR00399 metG_C_term methionyl-tRNA synthetase, beta subunit; InterPro: IPR004495   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 . The methionyl-tRNA synthetase (metG) (6.1.1.10 from EC) is a class I amino acyl-tRNA ligase. This family describes a region of the methionyl-tRNA synthetase that is present at the C-terminus of MetG in some species (Escherichia coli, Bacillus subtilis, Thermotoga maritima, Methanobacterium thermoautotrophicum), and as a separate beta chain in Aquifex aeolicus. It is absent in a number of other species (e.g. Mycoplasma genitalium, Mycobacterium tuberculosis), while Pyrococcus horikoshii has both a full length MetG and a second protein homologous to the beta chain only.; GO: 0000166 nucleotide binding, 0004825 methionine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006431 methionyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=98.70  E-value=1.4e-08  Score=80.17  Aligned_cols=95  Identities=22%  Similarity=0.298  Sum_probs=70.1

Q ss_pred             CEEEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECCCCCCCCCCEE-EEECCCCEEC--CCCEEEEEEHH-CCCCCCCH
Q ss_conf             74899999975657998-70899975999579897548345589789-8966877925--89839833120-58650545
Q gi|254780316|r   43 PFTIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCGAPNVRVGLLG-VWAPPGSCIP--ENNMIVNVRKI-RGIESTGM  117 (805)
Q Consensus        43 ~vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~IvcgA~Nv~~g~~V-~~A~~Ga~lp--~g~~~i~~~~i-rGv~S~GM  117 (805)
                      .+.||+|.++|+.|.|| |...+||.|+++.+|||.|=.    +.|- |=.++|=.+=  .|   +|++|| +||.|+||
T Consensus        47 dlRVg~i~~AE~v~kS~KLLkL~lDlG~~~~RQivSGI~----~~Y~~PEeLvGk~vivv~N---LKPaKl~~Gv~SeGM  119 (149)
T TIGR00399        47 DLRVGKILEAERVEKSDKLLKLKLDLGDEKDRQIVSGIA----EDYTDPEELVGKKVIVVAN---LKPAKLKFGVKSEGM  119 (149)
T ss_pred             EEEEEEEEEECCCCCCCCEEEEEEECCCCEECCEEEECH----HCCCCCHHHCCCEEEEEEC---CCCHHHCCCCCCCCC
T ss_conf             245577553205846566256887538970002352002----4178704743977999704---876012377343351


Q ss_pred             HHHHHHCCCCCCCCCEEEECC--CCCCCCCH
Q ss_conf             411887699854775078168--88888455
Q gi|254780316|r  118 MCSEKELMLSDDSASIMELPI--DAPVGGRL  146 (805)
Q Consensus       118 lCS~~ELgl~~~~~gI~~l~~--~~~~G~~~  146 (805)
                      |-++.+=|=.-  .-|.+|+.  +++.|+-+
T Consensus       120 iLAae~~g~nf--k~l~lls~~~~~~aG~ri  148 (149)
T TIGR00399       120 ILAAEDDGKNF--KNLFLLSPDKEVEAGERI  148 (149)
T ss_pred             EEEEECCCCCE--EEEEEECCCCCCCCCCCC
T ss_conf             78852699724--578886667888998435


No 35 
>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=98.63  E-value=5.8e-07  Score=68.61  Aligned_cols=181  Identities=14%  Similarity=0.172  Sum_probs=124.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCHHHH-HHHH-HHH-------HHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCC
Q ss_conf             954678988787787740232100482576-5520-000-------0000246776432101512211067764321015
Q gi|254780316|r  492 QSRTRYVKRVLASRAMMEVVNWSFISKEQS-VLFG-GGQ-------RELEILNPISADMSNMRTSLLPGLLKATGRNVDR  562 (805)
Q Consensus       492 ~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~-~~~~-~~~-------~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r  562 (805)
                      ....+++++.+.++||.|+-.--..+..++ +.++ +.+       +..=+.++   +..+|||..-+.-.+.+..+   
T Consensus         4 ~~~~~~i~~~f~~~GF~~~~gp~ie~~~~NFD~Ln~P~dHPaR~~~DTfy~~~~---~~~lLRtHTS~~q~r~l~~~---   77 (218)
T cd00496           4 NKVIEEIEDIFVSMGFTEVEGPEVETDFYNFDALNIPQDHPARDMQDTFYINDP---ARLLLRTHTSAVQARALAKL---   77 (218)
T ss_pred             HHHHHHHHHHHHHCCCEEECCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCC---CCCEECCCCCHHHHHHHHHC---
T ss_conf             899999999998779868228951231030453385988755372432786377---66021578756679999745---


Q ss_pred             CCCHHHHHHHCCCCCCCCCCCCC----EEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC-CCC
Q ss_conf             86113454302444477754431----0002210354310124620234544333314688875311111110145-333
Q gi|254780316|r  563 AIADFAIFEVSHVYENDTPEGQK----YMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVS-LDS  637 (805)
Q Consensus       563 ~~~~i~lFEiG~Vf~~~~~~~~~----~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~~-~~~  637 (805)
                       .+.+++|.+|+||+++.....-    +.+.|+.                   -...+.+-++|+.++.++..++. ...
T Consensus        78 -~~p~~~~~~G~VyR~D~iDatH~~~FhQ~Eg~~-------------------v~~~~~~~~Lk~~l~~~~~~lfg~~~~  137 (218)
T cd00496          78 -KPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLV-------------------VDKGLTFADLKGTLEEFAKELFGPITK  137 (218)
T ss_pred             -CCCCEEEECCCEEECCCCCCCCCCEEEEEEEEE-------------------EECCCCHHHHHHHHHHHHHHHCCCCCE
T ss_conf             -898179942504653889843153125763799-------------------956511999999999999997387664


Q ss_pred             EEEECCCCCCCCCCCEEEEEECC--E-EEEEEEEEECHHHHHHCCCCC--CEEEEEEEHHHHHHHH
Q ss_conf             03305886567898169999879--2-999998547789999668799--7899998787623545
Q gi|254780316|r  638 LRFESGAPSWYHPGRSGIIKTSA--E-IVLGYFGEFHPNILDFFGLSN--PICGFEVYLDSIPISQ  698 (805)
Q Consensus       638 ~~~~~~~~~~~hPgrsa~I~~~g--k-~iiG~iG~ihP~i~~~~~i~~--~v~~~EI~ld~L~~~~  698 (805)
                      +++.++-.|+-+|+.-.++...+  + .-+|-+|.+||+++++.|++.  ..++|-+-+|.|....
T Consensus       138 ~r~rp~yFPFTePS~Evdv~~~~~~~WlEv~G~G~v~p~vL~~~G~d~~~~g~AfG~GlERlaMl~  203 (218)
T cd00496         138 VRFRPSYFPFTEPSFEVDVYCPGCLGWLEILGCGMVRPEVLENAGIDEEYSGFAFGIGLERLAMLK  203 (218)
T ss_pred             EEECCCCCCCCCCCEEEEEEECCCCCCEEEECCCCCCHHHHHHCCCCCCCEEEEEEECHHHHHHHH
T ss_conf             536778899999826999996587871488504654889998669799988999852588999998


No 36 
>PRK08655 prephenate dehydrogenase; Provisional
Probab=98.51  E-value=4e-06  Score=62.65  Aligned_cols=131  Identities=18%  Similarity=0.356  Sum_probs=88.8

Q ss_pred             CCEEEEEEEEEECHHHHHHCCCCCCEEEEEEEHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHH
Q ss_conf             79299999854778999966879978999987876235452024566313689888720018999668879999999997
Q gi|254780316|r  659 SAEIVLGYFGEFHPNILDFFGLSNPICGFEVYLDSIPISQKKRTKTKKVVHLSSLHPVKRDLAFIVDQHIPAGTLVNIIK  738 (805)
Q Consensus       659 ~gk~iiG~iG~ihP~i~~~~~i~~~v~~~EI~ld~L~~~~~~~~~~~~~~~~s~fP~v~RDls~iv~~~v~~~~I~~~i~  738 (805)
                      .|+.-+|.+.++.|...- ++-++....+-+  +++.......-...+-   -.+|...||+|+++|.++.-+-|..++.
T Consensus       310 s~~vh~G~lk~v~~~~~~-l~~~~~~~~l~~--~ni~~~~~~el~~wk~---~nl~~~~~disv~~~~~~d~~ii~~~~~  383 (441)
T PRK08655        310 SGKVHVGILKKVYPDEII-LKKGNKEIKLKI--SNIRLLSEKELREWKV---ENLEKYVRDISVLFPKGADPEVILELLD  383 (441)
T ss_pred             CCCEEEEEEEEECCCEEE-EECCCCEEEEEE--ECCCCCCHHHHHHHHH---CCCCCCEEEEEEEECCCCCHHHHHHHHH
T ss_conf             880798788774386589-813993799986--3010389889999886---4576313568999269999799999985


Q ss_pred             HCCCCEEEEEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCEEC
Q ss_conf             11100357698987636779988426999999847798889999999999999999999511981
Q gi|254780316|r  739 NVDRLIDDVTVFDVFQGKSLGEGKKSVAIQVLIQPLKDTFRDDDIRILMDRIVENVVKKTNAVLR  803 (805)
Q Consensus       739 ~~~~ll~~v~lfDvY~g~~i~~gkkSla~rl~fqs~~kTLtd~EI~~i~~~ii~~l~~k~ga~LR  803 (805)
                      ... -+-++++.|+|+|++++++.+|+|||++.      +.+++.+.+.......+. .+|..+|
T Consensus       384 ~~~-~~~~~~i~d~y~g~~i~~~~~s~tfri~~------~~~~~~~~~~~~~~~~l~-~~g~~~r  440 (441)
T PRK08655        384 NLK-HKFDIEIIDVYSGPQIDEGRLSVTFRITS------FGKEDLENLEEEFTKLLE-GIGGKIR  440 (441)
T ss_pred             CCC-CEEEEEEEEECCCCCCCCCCEEEEEEEEE------ECHHHHHHHHHHHHHHHH-CCCCEEC
T ss_conf             235-13457888803687467773279999998------457778889999999985-4687625


No 37 
>pfam09513 consensus
Probab=98.51  E-value=5.3e-07  Score=68.89  Aligned_cols=97  Identities=29%  Similarity=0.416  Sum_probs=76.2

Q ss_pred             EEEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECCCCCCCCCCEEEEECCCCEECC---------------------CC
Q ss_conf             4899999975657998-7089997599957989754834558978989668779258---------------------98
Q gi|254780316|r   44 FTIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCGAPNVRVGLLGVWAPPGSCIPE---------------------NN  101 (805)
Q Consensus        44 vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~IvcgA~Nv~~g~~V~~A~~Ga~lp~---------------------g~  101 (805)
                      +-|.+|.+++|||||| +-+++||-     -++|----..++|+.|+++.+-+.||.                     .+
T Consensus         4 a~v~~I~~i~pi~~AD~ie~a~V~G-----W~vVV~Kge~k~GD~~Vy~EiDS~lP~~~~~~~~~~~~~~~~~~~~g~~g   78 (356)
T pfam09513         4 ATVRRILKLEPHPGADAIELATIDG-----WRVVVKKGEYRVGDPAVYIEEDSLLPVDDLKAHTLLNADGGAGRLYGKDG   78 (356)
T ss_pred             EEEEEEEECCCCCCCCEEEEEEECC-----EEEEEECCCCCCCCEEEEEECCCCCCCCCHHHHHHHCCCCCCCCCCCCCC
T ss_conf             5899975312048986488999888-----68999878613699799982421488653345555403566542267767


Q ss_pred             EEEEEEHHCCCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCCCCHHHHHC
Q ss_conf             39833120586505454118876998547750781688888845588708
Q gi|254780316|r  102 MIVNVRKIRGIESTGMMCSEKELMLSDDSASIMELPIDAPVGGRLSDYLE  151 (805)
Q Consensus       102 ~~i~~~~irGv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G~~~~~~l~  151 (805)
                      +-|+..||||..|+||+|-.+++-...+      +..+.++|+|+.+.|+
T Consensus        79 ~RikT~kLRG~~SQGl~lpl~~~~~~~~------~~~~~~~g~d~te~LG  122 (356)
T pfam09513        79 FRVKTIKLRGEVSQGLVLPLKALAYEGE------LISDQEVGDDFAELLG  122 (356)
T ss_pred             CEEEEEEECCEEEEEEEEEHHHCCCCCC------CCCCCCCCCCHHHHCC
T ss_conf             3687999652885249971678464322------3552004855577528


No 38 
>PHA02142 putative RNA ligase
Probab=98.47  E-value=8.7e-07  Score=67.36  Aligned_cols=96  Identities=22%  Similarity=0.265  Sum_probs=74.8

Q ss_pred             EEEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECCCCCCCCCCEEEEECCCCEECC------------------CCEEE
Q ss_conf             4899999975657998-7089997599957989754834558978989668779258------------------98398
Q gi|254780316|r   44 FTIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCGAPNVRVGLLGVWAPPGSCIPE------------------NNMIV  104 (805)
Q Consensus        44 vvvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~IvcgA~Nv~~g~~V~~A~~Ga~lp~------------------g~~~i  104 (805)
                      +-|-+|.+++|||+|| +-+|+|| |    -++|----.++.|+.|++..+-+.||.                  .++-|
T Consensus        10 atir~i~~i~pi~~aD~ie~a~Vd-g----W~vVV~kgefk~GD~~Vy~EiDS~lP~~~~~fefl~~~~~~~~G~~~~Ri   84 (366)
T PHA02142         10 ASMRKIADLQPIPGADAIEVATID-G----WEVVVKKGEFRVGDDCVYFEIDSLLPTDNPAFRFLETRARIYDGKMRARI   84 (366)
T ss_pred             EEEEEEEEEEECCCCCEEEEEEEC-C----EEEEEECCCCCCCCEEEEEECCCCCCCCCHHHHHHCCCCCCCCCCCCCEE
T ss_conf             999997520004899758899988-8----79999878623599799984211477886133343047642478656467


Q ss_pred             EEEHHCCCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCCCCHHHHHC
Q ss_conf             33120586505454118876998547750781688888845588708
Q gi|254780316|r  105 NVRKIRGIESTGMMCSEKELMLSDDSASIMELPIDAPVGGRLSDYLE  151 (805)
Q Consensus       105 ~~~~irGv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G~~~~~~l~  151 (805)
                      +..+|||..|+||+|..+++-..+.       ..+.++|+++.+.||
T Consensus        85 kT~kLRG~~SQGl~~pl~~~~~~~~-------~~~~~~g~d~te~LG  124 (366)
T PHA02142         85 KTIKLRGQISQGIALPTGAFTVGEL-------LGGQEMDKTLDQMLG  124 (366)
T ss_pred             EEEEEEEEEEEEEEEEHHHCCCCCC-------CCCCCCCCCHHHHHC
T ss_conf             8999825972238870456576322-------454113867778608


No 39 
>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated
Probab=98.35  E-value=1.4e-05  Score=58.76  Aligned_cols=186  Identities=15%  Similarity=0.191  Sum_probs=120.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH--HHH-HHHHH-------CCCCCCCCCCCCCCCCHHHCHHHHH
Q ss_conf             7899889546789887877877402321004825765--520-00000-------0024677643210151221106776
Q gi|254780316|r  486 RNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSV--LFG-GGQRE-------LEILNPISADMSNMRTSLLPGLLKA  555 (805)
Q Consensus       486 ~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~--~~~-~~~~~-------i~l~NPlS~e~s~lR~SLlp~LL~~  555 (805)
                      +...+.....+.+++++.++||.+ ..-+-+..++.+  .++ +.+.+       .-+     ++..+|||.--|.-+++
T Consensus       104 G~~HPit~~~~ei~~iF~~~Gf~v-~~GpeiE~~~~NFdaLn~P~~HPAR~~~DTFy~-----~~~~lLRTHTS~~qir~  177 (338)
T PRK00488        104 GGLHPLTRTIERIEDIFVGLGFEV-AEGPEIEDDYYNFEALNIPKDHPARDMQDTFYI-----DDRLLLRTHTSPVQIRT  177 (338)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCEE-ECCCCEEEHHHHHHHHCCCCCCCCCCCCCEEEE-----CCCCEECCCCCHHHHHH
T ss_conf             664769999999999999869769-618831004546887569978854364662897-----68713435687888999


Q ss_pred             HHHHCCCCCCHHHHHHHCCCCCCCCCCC-CCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             4321015861134543024444777544-310002210354310124620234544333314688875311111110145
Q gi|254780316|r  556 TGRNVDRAIADFAIFEVSHVYENDTPEG-QKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVS  634 (805)
Q Consensus       556 ~~~N~~r~~~~i~lFEiG~Vf~~~~~~~-~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~~  634 (805)
                      +..    +.+.+++|=.|+||+++.... .......++         |..       -.+.++|.++||.++.++..++.
T Consensus       178 m~~----~~pp~~~i~~GrvyR~d~~DatH~~~FhQ~E---------gl~-------vd~~it~~~Lk~~l~~f~~~~fg  237 (338)
T PRK00488        178 MEK----QKPPIRIIAPGRVYRNDSDDATHSPMFHQVE---------GLV-------VDKNISFADLKGTLEDFLKAFFG  237 (338)
T ss_pred             HHH----CCCCEEEEECCCCCCCCCCCCCCCEEEEEEE---------EEE-------EECCCCHHHHHHHHHHHHHHHCC
T ss_conf             972----6998699952663158999875350466400---------589-------71788799999999999999728


Q ss_pred             -CCCEEEECCCCCCCCCCCEEEEEE------------CCE-EEEEEEEEECHHHHHHCCCCCC---EEEEEEEHHHHHHH
Q ss_conf             -333033058865678981699998------------792-9999985477899996687997---89999878762354
Q gi|254780316|r  635 -LDSLRFESGAPSWYHPGRSGIIKT------------SAE-IVLGYFGEFHPNILDFFGLSNP---ICGFEVYLDSIPIS  697 (805)
Q Consensus       635 -~~~~~~~~~~~~~~hPgrsa~I~~------------~gk-~iiG~iG~ihP~i~~~~~i~~~---v~~~EI~ld~L~~~  697 (805)
                       .-.++|.++=.|+-.|+--.+|..            +++ .-+|=+|.+||+|++..++..+   -|+|-+-+|.+...
T Consensus       238 ~~~~~R~rpsyFPFtEPs~Evdi~~~~~~g~gc~~~~~~~WlEi~G~Gmv~p~Vl~~~gid~~~~~G~AfG~GieR~aMl  317 (338)
T PRK00488        238 EDLKIRFRPSYFPFTEPSAEVDVSCFNCKGKGCRVCKNTGWLEVLGCGMVHPNVLRNVGIDPEEYSGFAFGMGIERLAML  317 (338)
T ss_pred             CCCEEEECCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEECCCCCCCHHHHHHCCCCCCCCEEEEEEECHHHHHHH
T ss_conf             76647754788999998534788731457766544789963897376667889998669995527599875158899999


No 40 
>TIGR02306 RNA_lig_DRB0094 RNA ligase, DRB0094 family; InterPro: IPR012646   RNA repair, though not as well characterised as DNA repair, is an important component of many biological systems. These include the kinteoplastid RNA-editing process and the defence of bacteriophage T4 against tRNA damage caused by host nucleases. RNA ligase is an essential enzyme in the process of RNA repair . It is part of the broader nucleotidyl transferase superfamily which includes DNA ligase and RNA capping enzymes, and has the same basic mechanism as other memebers of this family. The RNA ligase family is divided into two distinct branches: the Rnl-1 like proteins, found only in viruses and fungi so far, and the Rnl2-like proteins which have been found in all three kingdoms of life.   This entry represents a small group of known and predicted RNA ligases found in some bacterial and phage species. The best characterised memeber is found in Deinococcus radiodurans, a bacterium capable of withstanding a variety of adverse environmental conditions including extreme amounts of radiation. Ligase activity is apparently specific to nicks within either duplex RNA or an RNA:DNA hybrid and is dependenton divalent cations such as manganese . These proteins have a distinctive domain structure, lacking the C-terminal domain observed in other Rnl2-like ligases, and possesing a distinctive N-terminal domain not found in other ligases but which is important for catalytic activity..
Probab=97.87  E-value=4.6e-06  Score=62.25  Aligned_cols=217  Identities=17%  Similarity=0.235  Sum_probs=130.9

Q ss_pred             EEEEEEEEEECCCCC-CCEEEEECCCCCEEEEECCCCCCCCCCEEEEECCCCEECC--CC-----------------EEE
Q ss_conf             899999975657998-7089997599957989754834558978989668779258--98-----------------398
Q gi|254780316|r   45 TIVKVLSVERNPDLD-CAILRIDTGKHQEIQVVCGAPNVRVGLLGVWAPPGSCIPE--NN-----------------MIV  104 (805)
Q Consensus        45 vvg~v~~~~~hP~ad-l~v~~Vd~g~~~~~~IvcgA~Nv~~g~~V~~A~~Ga~lp~--g~-----------------~~i  104 (805)
                      |+.+|.+..|||||| |=+|+|+.     .++|----..|.|.-.+++..-|+||.  .+                 --|
T Consensus         4 v~~~~a~l~P~PnAdalEla~vg~-----~~~VV~KGeyR~G~~~Vy~p~~svLPP~~agl~~~l~t~a~~l~G~~~~Rv   78 (374)
T TIGR02306         4 VIREIADLFPHPNADALELAKVGG-----YEVVVKKGEYRVGEDIVYIPEDSVLPPTDAGLFRELETRAKILDGKEKDRV   78 (374)
T ss_pred             HHHHHHHHCCCCCCCEEEEEECCC-----EEEEEEECCCCCCCCEEEEEHHHCCCCCCCHHHHHHCCCCEEECCCCCCCE
T ss_conf             566798718898856033243273-----899993067557885588433315986434046631355001147443642


Q ss_pred             EEEHHCCCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCCCCHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             33120586505454118876998547750781688888845588708885599987087857665557899987764115
Q gi|254780316|r  105 NVRKIRGIESTGMMCSEKELMLSDDSASIMELPIDAPVGGRLSDYLELSDPIIDVSLTPNRSDCIGVRGIALDLVAAGLG  184 (805)
Q Consensus       105 ~~~~irGv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G~~~~~~l~l~D~i~ei~iTpNR~D~ls~~GiARElaa~~~~  184 (805)
                      |.-+|||..|+|.+|-..-|--.+-..       ...-|+++.+.|+         ||                      
T Consensus        79 k~vrLRGe~SQGi~lp~~al~d~~l~~-------~~~~~~d~ae~Lg---------I~----------------------  120 (374)
T TIGR02306        79 KTVRLRGEISQGIVLPTDALEDAELLG-------GVEDDKDLAELLG---------IT----------------------  120 (374)
T ss_pred             EEEEECCEEECCEEECCCCCEECCCCC-------CCCCCCCHHHHCC---------CE----------------------
T ss_conf             468862434212476677630120236-------5234231886559---------35----------------------


Q ss_pred             CCCCCCCCCCC--CCCCCCCEEEEEEECCCHHHHHHHCCCC---CCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             66665545667--7777774158984073111233201123---224556637787888864013210399999899986
Q gi|254780316|r  185 KLKEINISCPL--SSESIPLEIKFDLDDSSLCKGFAMCCVK---GVRNNVAPNWMRQRLKAVGLRSISALVDITNYVSLD  259 (805)
Q Consensus       185 ~l~~~~~~~~~--~~~~~~~~i~v~i~~~~~c~~y~~~~i~---~v~~~~SP~wl~~rL~~~Gir~inniVDitNyvmle  259 (805)
                       .-.|+.+..-  ..+..|-..-+...|.+.|.+|.-+.-.   ++++                                
T Consensus       121 -kwePP~p~tm~ge~e~~PPa~~~~~~D~E~~q~y~~~f~~kyag~~v--------------------------------  167 (374)
T TIGR02306       121 -KWEPPVPGTMAGEVETVPPADFLKKTDVERIQRYVDRFKEKYAGEKV--------------------------------  167 (374)
T ss_pred             -EECCCCCCCCCCCCCCCCCHHHCCCCCHHHHCCCHHHCCHHHCCCCE--------------------------------
T ss_conf             -87277468888888888806753556734514201100300078627--------------------------------


Q ss_pred             HCCCEEEECCCCCCCE-EEEEECCCCCCHHHHHHHCCCCCCCCEEEECCCCCCCCHHHCCCCCCCCCCCCCEEEEEEECC
Q ss_conf             0870000010223332-688623554311455420112454320000256763100111355312013672699997157
Q gi|254780316|r  260 RGYPSHVFDASRISDV-LTVRRACSGEKILALDNQEYDLSPDNVVIASDGRIQSIAGIIGGKHAGCDDNTTDVLVEVALW  338 (805)
Q Consensus       260 ~GqPlHafD~dki~~~-i~vr~a~~~E~~~~Ld~~e~~L~~~~lvI~d~~~~ialaGImGg~~s~v~~~T~~illEsA~F  338 (805)
                             -=-.||+|+ +.|-+..+.+.+.              |.+-++.|-|           -+-+-...++     
T Consensus       168 -------~~teKLhGt~~~v~~~tde~r~l--------------v~skgeePya-----------hdyddaqfi~-----  210 (374)
T TIGR02306       168 -------VLTEKLHGTSILVAYVTDEERFL--------------VLSKGEEPYA-----------HDYDDAQFIL-----  210 (374)
T ss_pred             -------EEEECCCCCEEEEEEEECCCCEE--------------ECCCCCCCCC-----------CCCCCCEEEE-----
T ss_conf             -------88742467627899975686077--------------5166788753-----------4644313565-----


Q ss_pred             CHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             8788877887616540155441345530135889998887521
Q gi|254780316|r  339 DPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLIL  381 (805)
Q Consensus       339 ~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li~  381 (805)
                             ++|.+-|+-+|+..|=|++.-......++|+++-+.
T Consensus       211 -------~~~~l~Lre~a~n~yW~av~n~~~~~~a~rla~~~~  246 (374)
T TIGR02306       211 -------ASRNLVLREDADNLYWKAVENYQIVDRAKRLAEALL  246 (374)
T ss_pred             -------ECCCCCEEECCCCCCHHHHCHHHHHHHHHHHHHHHH
T ss_conf             -------237620111334310000010268999999999872


No 41 
>COG4937 Predicted regulatory domain of prephenate dehydrogenase [Translation, ribosomal structure and biogenesis]
Probab=97.75  E-value=0.00047  Score=48.00  Aligned_cols=61  Identities=18%  Similarity=0.394  Sum_probs=50.6

Q ss_pred             CCCCEEEEEEEECCCCCHHHHHHHHHHCCCCEEEEEEEEEEECCCCCCCC-EEEEEEEEEECC
Q ss_conf             88720018999668879999999997111003576989876367799884-269999998477
Q gi|254780316|r  713 LHPVKRDLAFIVDQHIPAGTLVNIIKNVDRLIDDVTVFDVFQGKSLGEGK-KSVAIQVLIQPL  774 (805)
Q Consensus       713 fP~v~RDls~iv~~~v~~~~I~~~i~~~~~ll~~v~lfDvY~g~~i~~gk-kSla~rl~fqs~  774 (805)
                      .-...||+|.++++++.-+-|..+++-. +-+.++++.|+|+|++++++. +|+|||++--+.
T Consensus        80 L~~~v~DvSvlf~~~vDpEvil~avkll-k~~vd~~I~DvY~G~~i~ede~~siT~Ri~~f~~  141 (171)
T COG4937          80 LEKKVIDVSVLFKKDVDPEVILNAVKLL-KKMVDIEIIDVYEGEKIEEDEYKSITFRIYGFNK  141 (171)
T ss_pred             HHEEEEEEEEEECCCCCHHHHHHHHHHH-HHEEEEEEEEEECCCCCCCCCEEEEEEEEEEECH
T ss_conf             3007888999834899989987278765-3136789987202775798854358999999571


No 42 
>PRK09537 pylS pyrolysyl-tRNA synthetase; Reviewed
Probab=97.70  E-value=1.3e-05  Score=58.97  Aligned_cols=182  Identities=18%  Similarity=0.163  Sum_probs=108.6

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH-HCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHH
Q ss_conf             95467898878778774023210048257655200000-00024677643210151221106776432101586113454
Q gi|254780316|r  492 QSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQR-ELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIF  570 (805)
Q Consensus       492 ~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~-~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lF  570 (805)
                      -+++|.+..+++..||-|+.+--++..++.+..+.+.+ .+.-.=---.+.-.||+-|.|+|-.-+..=.+---..+++|
T Consensus       210 gkler~it~ffvdrgfleikspilip~eyiermgid~d~elskQiFrvd~n~CLRPMLAPnLYnylrkL~R~lpdPIrIF  289 (420)
T PRK09537        210 GKLERDITKFFVDRGFLEIKSPILIPAEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIF  289 (420)
T ss_pred             HHHHHHHHHHHHCCCCEEECCCEECCHHHHHHHCCCCHHHHHHHHEEECCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             67788889985414513514850421999998578860565545167434533241014269999999986168871588


Q ss_pred             HHCCCCCCCCCCCC---C-EEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCC
Q ss_conf             30244447775443---1-0002210354310124620234544333314688875311111110145333033058865
Q gi|254780316|r  571 EVSHVYENDTPEGQ---K-YMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVSLDSLRFESGAPS  646 (805)
Q Consensus       571 EiG~Vf~~~~~~~~---~-~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~~~~~~~~~~~~~~  646 (805)
                      |||.+|.+++.+.+   + +++...+.|      +|-.             =-.+-..+..+++.+|.  .+++...+.-
T Consensus       290 EIGpCyRKESdG~~HLeEFTMlNfcqmg------sgct-------------renle~~i~efl~~lgI--dfeiv~dscm  348 (420)
T PRK09537        290 EIGPCYRKESDGKEHLEEFTMVNFCQMG------SGCT-------------RENLEALITEFLNHLGI--DFEIVGDSCM  348 (420)
T ss_pred             EECCCCCCCCCCHHHHHHHHHHHHHHHC------CCCC-------------HHHHHHHHHHHHHHCCC--EEEEECCCEE
T ss_conf             6204303444106788777777688644------8986-------------78899999999986197--2798425206


Q ss_pred             CCCCCCEEEEEECCEEEEEEEEEECHHHHH-HCCCCCCEEEEEEEHHHHHHHH
Q ss_conf             678981699998792999998547789999-6687997899998787623545
Q gi|254780316|r  647 WYHPGRSGIIKTSAEIVLGYFGEFHPNILD-FFGLSNPICGFEVYLDSIPISQ  698 (805)
Q Consensus       647 ~~hPgrsa~I~~~gk~iiG~iG~ihP~i~~-~~~i~~~v~~~EI~ld~L~~~~  698 (805)
                      .|  |.+.+++- |..-++. |.+-|.-++ +|++..|..++-+-|+.|+...
T Consensus       349 VY--GdT~DvMh-gDlELsS-avvGP~pLDr~Wgi~kPWiGaGFGLERLLkV~  397 (420)
T PRK09537        349 VY--GDTLDIMH-GDLELSS-AVVGPIPLDREWGIDKPWIGAGFGLERLLKVM  397 (420)
T ss_pred             EE--CCHHHHHC-CCHHHCC-CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             85--32256542-6401103-54477445655576676202333099999998


No 43 
>COG2024 Phenylalanyl-tRNA synthetase alpha subunit (archaeal type) [Translation, ribosomal structure and biogenesis]
Probab=97.55  E-value=7.8e-05  Score=53.52  Aligned_cols=179  Identities=17%  Similarity=0.272  Sum_probs=121.4

Q ss_pred             CCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             00246776432101512211067764321015861134543024444777544310002210354310124620234544
Q gi|254780316|r  531 LEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFEVSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSE  610 (805)
Q Consensus       531 i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lFEiG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~  610 (805)
                      ++=+-|.|+ .-+||+.+..|..-+++.=++|.-+.++||-|-++|+....+...++....              +.+..
T Consensus       173 fk~Lkp~s~-tlTLRSHMTsGWFItLs~i~~r~~~PlklFSIDRCFRREQ~ED~shLmtYh--------------SASCV  237 (536)
T COG2024         173 FKDLKPESS-TLTLRSHMTSGWFITLSEILKREDPPLKLFSIDRCFRREQREDASHLMTYH--------------SASCV  237 (536)
T ss_pred             HHHCCCCCC-CEEHHHHCCCCEEEEHHHHHHCCCCCCEEEEHHHHHHHHHHCCHHHHHHHC--------------CCEEE
T ss_conf             763577777-505666334310135798872348984164256776655310156664320--------------34079


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECC--CCCCCCCCCEEEEEEC-------------CEEEEEEEEEECHHHH
Q ss_conf             333314688875311111110145333033058--8656789816999987-------------9299999854778999
Q gi|254780316|r  611 ERCRFVDLFDAKADALSVIEPFVSLDSLRFESG--APSWYHPGRSGIIKTS-------------AEIVLGYFGEFHPNIL  675 (805)
Q Consensus       611 ~~~~~~df~dlKg~v~~ll~~l~~~~~~~~~~~--~~~~~hPgrsa~I~~~-------------gk~iiG~iG~ihP~i~  675 (805)
                      --...+..-+-|+..+.++..+|.. +++|.+.  ...||.||-+-+++--             |=.-+..||.-+|.-+
T Consensus       238 vvde~vtvD~GKaVAEglL~qfGFe-~F~FrpDEK~SKYYvP~TQTEVyAyHPkL~gs~~kysdgWiEiATFGlYSP~AL  316 (536)
T COG2024         238 VVDEDVTVDDGKAVAEGLLRQFGFE-KFRFRPDEKKSKYYVPGTQTEVYAYHPKLVGSIEKYSDGWIEIATFGLYSPIAL  316 (536)
T ss_pred             EECCCCCCCCCHHHHHHHHHHHCCC-CEEECCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEEEECCCCHHHH
T ss_conf             9758644354389999999971940-035466200355347996304777454003652125887089996035672779


Q ss_pred             HHCCCCCCEEEEEEEHHHHHHHHHCC--CCCCCCCCCCCCCCCEEEEEEEEC
Q ss_conf             96687997899998787623545202--456631368988872001899966
Q gi|254780316|r  676 DFFGLSNPICGFEVYLDSIPISQKKR--TKTKKVVHLSSLHPVKRDLAFIVD  725 (805)
Q Consensus       676 ~~~~i~~~v~~~EI~ld~L~~~~~~~--~~~~~~~~~s~fP~v~RDls~iv~  725 (805)
                      .+|+|+.||.-.-+-.+.|.......  ...-.|..+..+-.+.||||=.+.
T Consensus       317 aeY~Id~pVMNLGlGVERlaMIl~g~~DVR~mvYpqi~ew~lSD~diA~mi~  368 (536)
T COG2024         317 AEYGIDYPVMNLGLGVERLAMILHGADDVRSMVYPQIYEWRLSDRDIARMIR  368 (536)
T ss_pred             HHCCCCCCEEECCHHHHHHHHHHHCCHHHHHHHCCCCCCCCCCHHHHHHHHH
T ss_conf             8729997012032208999999817447766513453445666588886640


No 44 
>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=97.54  E-value=0.0007  Score=46.74  Aligned_cols=146  Identities=15%  Similarity=0.167  Sum_probs=106.0

Q ss_pred             CCCCCCCCCHHHC---HHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             6432101512211---0677643210158611345430244447775443100022103543101246202345443333
Q gi|254780316|r  538 SADMSNMRTSLLP---GLLKATGRNVDRAIADFAIFEVSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSEERCR  614 (805)
Q Consensus       538 S~e~s~lR~SLlp---~LL~~~~~N~~r~~~~i~lFEiG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  614 (805)
                      .....+||+.-.+   -.+..++.+.+.+.+.+++|-+|+||.++...... .....+              ........
T Consensus       174 ~~~~~~lrt~~~~~~~~~~~~~~~~~~~~~pp~~~~~~~~~~r~~~~d~~h-~~~f~~--------------~~g~~~~~  238 (362)
T TIGR00468       174 LARRLLLRTHTTASSAVQLRTLEENPKAKNPPIRIFCPGRVFRRDTVDATH-LPEFHQ--------------LEGLVVDK  238 (362)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHCCCCCCCCC-CCHHHH--------------EEEEEEEC
T ss_conf             665555431132135666666654101378862576410111023333101-410221--------------00235415


Q ss_pred             CCCHHHHHHHHHHHHHHCCCC-CCEEEECCCCCCCCCCCEEEEEE-C-CE----------EEEEEEEEECHHHHHHCCCC
Q ss_conf             146888753111111101453-33033058865678981699998-7-92----------99999854778999966879
Q gi|254780316|r  615 FVDLFDAKADALSVIEPFVSL-DSLRFESGAPSWYHPGRSGIIKT-S-AE----------IVLGYFGEFHPNILDFFGLS  681 (805)
Q Consensus       615 ~~df~dlKg~v~~ll~~l~~~-~~~~~~~~~~~~~hPgrsa~I~~-~-gk----------~iiG~iG~ihP~i~~~~~i~  681 (805)
                      .+.|-+++|.++.++..++.. ..++|.+.-.++-.|....++.. . ++          .-+|-.|.+||.+++..++.
T Consensus       239 ~~~~~~l~g~~~~~~~~~~~~~~~~~~~p~~fp~t~p~~e~~~~~~~c~~gc~~c~~~~W~e~~g~g~~~p~~~~~~g~~  318 (362)
T TIGR00468       239 NVSFTNLKGLLEEFLKKLFGEDTEVRFRPSYFPFTEPSAEVDVYCPECGKGCSVCKGTGWLELLGAGIFRPEVLEPLGID  318 (362)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCCEEEEEHHHCCCCHHHCCCCEEEEECCCCCCHHHHHHCCCC
T ss_conf             66467889999999997413221202310336655555302442000013100101465035404553242355423787


Q ss_pred             C---CEEEEEEEHHHHHHHH
Q ss_conf             9---7899998787623545
Q gi|254780316|r  682 N---PICGFEVYLDSIPISQ  698 (805)
Q Consensus       682 ~---~v~~~EI~ld~L~~~~  698 (805)
                      .   +++.+-+-++.+....
T Consensus       319 ~~~~~~~~~g~g~~r~~~~~  338 (362)
T TIGR00468       319 PEEYPGLAWGLGIERLAMLK  338 (362)
T ss_pred             CCCCEEEEECCCHHHHHHHH
T ss_conf             31011343212401244545


No 45 
>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=97.49  E-value=0.00071  Score=46.71  Aligned_cols=178  Identities=13%  Similarity=0.110  Sum_probs=105.3

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             95467898878778774023210048257655200000000246776432101512211067764321015861134543
Q gi|254780316|r  492 QSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFE  571 (805)
Q Consensus       492 ~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lFE  571 (805)
                      ++..+.+|+.+...||+|+.+..|++.+....-+...+...-.+....+.=+||++.-|++........ +.. .+++++
T Consensus         3 ~~ie~~~r~~~~~~G~~ev~~P~l~~~~~~~~sg~~~~~~~~~~~~~~~~~~L~pt~e~~~~~~~~~~~-~dL-P~r~~~   80 (211)
T cd00768           3 SKIEQKLRRFMAELGFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEEDLYLRPTLEPGLVRLFVSHI-RKL-PLRLAE   80 (211)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCEECCHHHHHHCCCCHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHH-HHC-CHHHHE
T ss_conf             899999999999869989999834279999750676222301104679769995168499999975247-657-778643


Q ss_pred             HCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCC-EEEECCCCCC--C
Q ss_conf             024444777544310002210354310124620234544333314688875311111110145333-0330588656--7
Q gi|254780316|r  572 VSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVSLDS-LRFESGAPSW--Y  648 (805)
Q Consensus       572 iG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~~~~~-~~~~~~~~~~--~  648 (805)
                      +|++|+.+...      .|+...+--....+-.+...   ....--+..+....+.++..++.... +.........  -
T Consensus        81 ~~~~fR~E~~~------~Gl~RvreF~~~e~~~f~~~---~~~~~~~~~~~~~~~~i~~~lgl~~~~~~~~~~~~~~~~~  151 (211)
T cd00768          81 IGPAFRNEGGR------RGLRRVREFTQLEGEVFGED---GEEASEFEELIELTEELLRALGIKLDIVFVEKTPGEFSPG  151 (211)
T ss_pred             ECCEECCCCCC------CCCCCCCCEEEEEEEEEECC---HHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCC
T ss_conf             20056057888------88446046889847999884---8889999999999999999749988869999778676664


Q ss_pred             CCCCEEEEEEC-----CEEEEEEEEEECHHHHHHCCCC
Q ss_conf             89816999987-----9299999854778999966879
Q gi|254780316|r  649 HPGRSGIIKTS-----AEIVLGYFGEFHPNILDFFGLS  681 (805)
Q Consensus       649 hPgrsa~I~~~-----gk~iiG~iG~ihP~i~~~~~i~  681 (805)
                      +.+.+.+|.+.     +.. +|.++-....-++.++++
T Consensus       152 ~a~~~~Die~~~p~~~~~E-v~s~~~~~d~qsr~~~i~  188 (211)
T cd00768         152 GAGPGFEIEVDHPEGRGLE-IGSGGYRQDEQARAADLY  188 (211)
T ss_pred             CCEEEEEEEEECCCCCEEE-EECEECCCCHHHHHCCCE
T ss_conf             5235455789837897999-935461677878846989


No 46 
>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=97.48  E-value=0.00031  Score=49.24  Aligned_cols=213  Identities=19%  Similarity=0.330  Sum_probs=135.1

Q ss_pred             CCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             00246776432101512211067764321015861134543024444777544310002210354310124620234544
Q gi|254780316|r  531 LEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFEVSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSE  610 (805)
Q Consensus       531 i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lFEiG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~  610 (805)
                      ++=+-|+|.. .+||+.+..|-.=+++.=..+..=.++||=|-|+|+.+..+...++.+.. +..+.+.           
T Consensus       183 fkdLKP~S~t-lTLRSHMTsGWFItLs~i~dk~~lPlKLFSIDRCFRREQ~ED~shLmtYh-SASCVvV-----------  249 (558)
T TIGR00470       183 FKDLKPVSST-LTLRSHMTSGWFITLSSIADKLKLPLKLFSIDRCFRREQKEDASHLMTYH-SASCVVV-----------  249 (558)
T ss_pred             HHCCCCCCCC-CCCHHHCCCHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCCCCCCEE-EEEEEEE-----------
T ss_conf             0016886554-32001010027888987875158971122003231446643531001134-5466785-----------


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCC--CCCCCCCCEEEEEE------------CCE-EEEEEEEEECHHHH
Q ss_conf             3333146888753111111101453330330588--65678981699998------------792-99999854778999
Q gi|254780316|r  611 ERCRFVDLFDAKADALSVIEPFVSLDSLRFESGA--PSWYHPGRSGIIKT------------SAE-IVLGYFGEFHPNIL  675 (805)
Q Consensus       611 ~~~~~~df~dlKg~v~~ll~~l~~~~~~~~~~~~--~~~~hPgrsa~I~~------------~gk-~iiG~iG~ihP~i~  675 (805)
                        ...+..=+-|...|+||+++|.. +++|.+++  ..||.|+-+-+++-            ..+ .-++.||.-+|.-+
T Consensus       250 --deevsvDdGKaVAEgLL~qfGF~-~FrFrpDEKkSKYYiP~TQTEVyAyHPkL~GsstkysdeWiEvATFG~YSPiAL  326 (558)
T TIGR00470       250 --DEEVSVDDGKAVAEGLLEQFGFE-KFRFRPDEKKSKYYIPDTQTEVYAYHPKLKGSSTKYSDEWIEVATFGVYSPIAL  326 (558)
T ss_pred             --CCCCCCCCCHHHHHHHHHHHCCC-CCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEEECCCCHHHHH
T ss_conf             --77124364268899999870854-475057646454357888505677626456664410476479874343104677


Q ss_pred             HHCCCCCCEEEEEEEHHHHHHHHHCCCCCCCCCCCCC----CCCCEEEEEEEEC-CCCC--------HHHHHHHHHHCCC
Q ss_conf             9668799789999878762354520245663136898----8872001899966-8879--------9999999971110
Q gi|254780316|r  676 DFFGLSNPICGFEVYLDSIPISQKKRTKTKKVVHLSS----LHPVKRDLAFIVD-QHIP--------AGTLVNIIKNVDR  742 (805)
Q Consensus       676 ~~~~i~~~v~~~EI~ld~L~~~~~~~~~~~~~~~~s~----fP~v~RDls~iv~-~~v~--------~~~I~~~i~~~~~  742 (805)
                      .+|+|+.||.=.-+=.+.|...-.......+.. +|+    |--+.||||=.+- +.+|        +++|+++.+. ++
T Consensus       327 a~Y~Id~pVMNLGlGVERlAMIlygy~DVR~MV-YPQiyGE~rLSDrDIA~~irv~~vP~t~~g~~~a~~iv~~~~a-ha  404 (558)
T TIGR00470       327 AKYDIDVPVMNLGLGVERLAMILYGYEDVRKMV-YPQIYGEYRLSDRDIAEMIRVDKVPVTAEGLKLAEEIVETAEA-HA  404 (558)
T ss_pred             HHCCCCCCEEECCCHHHHHHHHHHCHHHHHHCC-CCCCCCEEECCHHHHHHHHEECCCCCCHHHHHHHHHHHHHHHH-CC
T ss_conf             416849652225631876787781403343226-8842122312336667450104675228899999999999996-07


Q ss_pred             CEEEEEEEEEE-ECCCCCCC
Q ss_conf             03576989876-36779988
Q gi|254780316|r  743 LIDDVTVFDVF-QGKSLGEG  761 (805)
Q Consensus       743 ll~~v~lfDvY-~g~~i~~g  761 (805)
                      =-.+=.=|.+| +|+=+|..
T Consensus       405 d~pSPCSfev~regef~Grr  424 (558)
T TIGR00470       405 DEPSPCSFEVYREGEFLGRR  424 (558)
T ss_pred             CCCCCCEEEEEECCCCCCCC
T ss_conf             78889418998422003661


No 47 
>KOG2784 consensus
Probab=97.37  E-value=0.0021  Score=43.36  Aligned_cols=222  Identities=15%  Similarity=0.215  Sum_probs=129.5

Q ss_pred             CCCCCCCC-CHHHHHHHHHHHCCCCCCCCCCCC---CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHH-H
Q ss_conf             03454334-402567676765352334667655---443457678998895467898878778774023210048257-6
Q gi|254780316|r  447 PSWRQDVE-EKADLVEEILRIYGVDQIKSEPLP---LTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQ-S  521 (805)
Q Consensus       447 Ps~R~DI~-~e~DLiEEIaRiyGYdnIp~~~l~---~~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~-~  521 (805)
                      |.|-.+++ .+.||--|..----|...+-++..   ....+..+.+.+.-+.+..+|+++..+||.|.-|+.++...- +
T Consensus       166 p~Fst~l~k~eTdLT~emi~~gsw~dl~FK~YNF~a~G~~p~~G~lHPLmKvR~eFRqiF~emGFsEMptn~yVEssFWN  245 (483)
T KOG2784         166 PNFSTSLTKLETDLTSEMIASGSWKDLKFKPYNFNAEGVPPSSGHLHPLMKVREEFRQIFFEMGFSEMPTNNYVESSFWN  245 (483)
T ss_pred             CCCCCHHHHHHHHCCHHHHCCCCHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCCCC
T ss_conf             76543377776432598860585331567646754678999777655488889999999998062306654401102445


Q ss_pred             --HHHHH-------HHHHCCCCCCCCCCC----------------------------------CCCCCH---HHCHHHHH
Q ss_conf             --55200-------000000246776432----------------------------------101512---21106776
Q gi|254780316|r  522 --VLFGG-------GQRELEILNPISADM----------------------------------SNMRTS---LLPGLLKA  555 (805)
Q Consensus       522 --~~~~~-------~~~~i~l~NPlS~e~----------------------------------s~lR~S---Llp~LL~~  555 (805)
                        .+|.+       ..+..=|.+|.+++.                                  .+|||.   .-..+|-.
T Consensus       246 FDALfqPQqHpARDahDTFfl~~Pa~s~~~p~dY~~rVk~vH~~G~ygs~GY~y~wk~eEaqKnvLRTHTTavSArmLy~  325 (483)
T KOG2784         246 FDALFQPQQHPARDAHDTFFLKDPATSTKFPEDYLERVKAVHEQGGYGSIGYRYNWKLEEAQKNVLRTHTTAVSARMLYR  325 (483)
T ss_pred             CHHHCCCCCCCCCCCCCCEEECCHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             30004755587533345247637133036989999999988716886776567888989998777765047764999999


Q ss_pred             HHHHCCCCCCHHHHHHHCCCCCCCCCCC----CCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             4321015861134543024444777544----310002210354310124620234544333314688875311111110
Q gi|254780316|r  556 TGRNVDRAIADFAIFEVSHVYENDTPEG----QKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEP  631 (805)
Q Consensus       556 ~~~N~~r~~~~i~lFEiG~Vf~~~~~~~----~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~  631 (805)
                      ++   +.+++..++|-|-+||+++.-..    +-+.+.|++.                   .+....-++.|.++.++..
T Consensus       326 LA---k~~f~p~K~FSIDrVFRNEtvDaTHLAEFHQVEGvia-------------------d~gltLgdLig~l~~ff~~  383 (483)
T KOG2784         326 LA---KKGFKPAKYFSIDRVFRNETVDATHLAEFHQVEGVIA-------------------DKGLTLGDLIGILMEFFTK  383 (483)
T ss_pred             HH---HCCCCCCCCCCHHHHHHCCCCCHHHHHHHHHHCEEEE-------------------CCCCCHHHHHHHHHHHHHC
T ss_conf             97---4799851101041344034320577877763203651-------------------3787699999999999732


Q ss_pred             CCCCCCEEEECCCCCCCCCCCEEEEEECC---EEEEEEEEEECHHHHHHCCCCCCEEEEEEEH
Q ss_conf             14533303305886567898169999879---2999998547789999668799789999878
Q gi|254780316|r  632 FVSLDSLRFESGAPSWYHPGRSGIIKTSA---EIVLGYFGEFHPNILDFFGLSNPICGFEVYL  691 (805)
Q Consensus       632 l~~~~~~~~~~~~~~~~hPgrsa~I~~~g---k~iiG~iG~ihP~i~~~~~i~~~v~~~EI~l  691 (805)
                      ++. .+++|++.-.+|-||..---.+-.|   -.-+|--|..||..+..+|++..+.+..-.|
T Consensus       384 lg~-tnlrfKPaynpYtepsmeif~yh~gl~kwvEvgnSg~frPeml~pMGLp~Dv~vl~~gl  445 (483)
T KOG2784         384 LGA-TNLRFKPAYNPYTEPSMEIFSYHHGLFKWVEVGNSGMFRPEMLLPMGLPMDVVVLAWGL  445 (483)
T ss_pred             CCC-CCCCCCCCCCCCCCCEEEEEEECCCCCEEEEECCCCCCCHHHHHCCCCCCCCEEEEECC
T ss_conf             687-66422699898888635787740565148997688887876760568986532333044


No 48 
>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=97.27  E-value=0.0002  Score=50.65  Aligned_cols=180  Identities=17%  Similarity=0.213  Sum_probs=110.4

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCC--CCCCCCCCCHHHCHHHHHHHHHCCCCCC-HHH
Q ss_conf             9546789887877877402321004825765520000000024677--6432101512211067764321015861-134
Q gi|254780316|r  492 QSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPI--SADMSNMRTSLLPGLLKATGRNVDRAIA-DFA  568 (805)
Q Consensus       492 ~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPl--S~e~s~lR~SLlp~LL~~~~~N~~r~~~-~i~  568 (805)
                      -+++|.+..+++..||-|+.+--|+..++.+..+.+.+ .+|..-+  -...=.||+-|.|.|.+-+.. +.|-.+ .++
T Consensus       243 Gkler~it~ffvdrGfleiksPiliP~ey~ermGi~nd-telskqifrvdkn~ClrPmlaP~lynylrk-ldr~lP~Pik  320 (453)
T TIGR02367       243 GKLEREITKFFVDRGFLEIKSPILIPLEYVERMGIDND-TELSKQIFRVDKNLCLRPMLAPTLYNYLRK-LDRILPDPIK  320 (453)
T ss_pred             HHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHCCCCCC-HHHHHHHHHHHHHHHCCCCHHHHHHHHHHH-HHHHCCCCEE
T ss_conf             46766676665312402323631010568865077640-256666664410010121000568999999-8753789647


Q ss_pred             HHHHCCCCCCCCCCCC---C-EEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf             5430244447775443---1-00022103543101246202345443333146888753111111101453330330588
Q gi|254780316|r  569 IFEVSHVYENDTPEGQ---K-YMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVSLDSLRFESGA  644 (805)
Q Consensus       569 lFEiG~Vf~~~~~~~~---~-~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~~~~~~~~~~~~  644 (805)
                      +||+|.+|.++..+.+   + .++...+.|      +|-.             --.+.+++..+++.+.    +.|+--.
T Consensus       321 ~fe~GPCyrkesdGkehleeftm~nfCqmG------sGCt-------------renle~~i~~fl~~l~----idf~ivG  377 (453)
T TIGR02367       321 VFEVGPCYRKESDGKEHLEEFTMLNFCQMG------SGCT-------------RENLEALIKEFLDYLE----IDFKIVG  377 (453)
T ss_pred             EEEECCCCCCCCCCHHHHHHHHHHHHHHCC------CCCC-------------HHHHHHHHHHHHHHHC----CCEEEEC
T ss_conf             986067524356533566666655543147------8732-------------6779999999887615----4247852


Q ss_pred             CCCCCCCCEEEEEECCEEE--EEEEEEECHHHHHHCCCCCCEEEEEEEHHHHHHHHH
Q ss_conf             6567898169999879299--999854778999966879978999987876235452
Q gi|254780316|r  645 PSWYHPGRSGIIKTSAEIV--LGYFGEFHPNILDFFGLSNPICGFEVYLDSIPISQK  699 (805)
Q Consensus       645 ~~~~hPgrsa~I~~~gk~i--iG~iG~ihP~i~~~~~i~~~v~~~EI~ld~L~~~~~  699 (805)
                      ..-+--|-+-+|+- |+.-  -.++|-+.  +-.+|||..|..++-+-|+.|+....
T Consensus       378 dsCmvyGdtld~mh-GdlelssavvGP~~--ldreWGidkPWiGaGfGlerllkv~h  431 (453)
T TIGR02367       378 DSCMVYGDTLDVMH-GDLELSSAVVGPVS--LDREWGIDKPWIGAGFGLERLLKVKH  431 (453)
T ss_pred             CEEEEECCHHEEEE-CCHHHCCEEECCCC--CCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             42465335010001-32000000223632--23013788872125323678887763


No 49 
>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=96.44  E-value=0.03  Score=35.15  Aligned_cols=90  Identities=12%  Similarity=0.141  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH-H--HHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHH
Q ss_conf             8954678988787787740232100482576552-0--000000024677643210151221106776432101586113
Q gi|254780316|r  491 QQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLF-G--GGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADF  567 (805)
Q Consensus       491 ~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~-~--~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i  567 (805)
                      .+...+++++.+...||.|+.|-.|-..+..... +  ..+...++..+ +-+.=.||+-+.++..+.++.|.......+
T Consensus         5 r~~i~~~l~~~f~~~Gy~~I~~P~lE~~d~~~~~~~~~~~~~~~~f~D~-~g~~l~LRpD~T~~iaR~~~~~~~~~~~p~   83 (261)
T cd00773           5 RRYIEDTLREVFERYGYEEIDTPVFEYTELFLRKSGDEVSKEMYRFKDK-GGRDLALRPDLTAPVARAVAENLLSLPLPL   83 (261)
T ss_pred             HHHHHHHHHHHHHHCCCEEEECCCCCCHHHHCCCCCCCCHHCEEEEECC-CCCEEEECCCCCHHHHHHHHHHHCCCCCCE
T ss_conf             9999999999999869978667764527675244653102116999979-999897678662799999997415378885


Q ss_pred             HHHHHCCCCCCCCC
Q ss_conf             45430244447775
Q gi|254780316|r  568 AIFEVSHVYENDTP  581 (805)
Q Consensus       568 ~lFEiG~Vf~~~~~  581 (805)
                      |+|-+|+||+.+.+
T Consensus        84 r~~Y~g~VfR~~~~   97 (261)
T cd00773          84 KLYYIGPVFRYERP   97 (261)
T ss_pred             EEEEECCEEEECCC
T ss_conf             89997318997689


No 50 
>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=94.75  E-value=0.043  Score=34.09  Aligned_cols=53  Identities=8%  Similarity=0.055  Sum_probs=37.7

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHCCCEEEECCCCC-CCEEEEEECCCCCCHH
Q ss_conf             8888640132103999998999860870000010223-3326886235543114
Q gi|254780316|r  236 QRLKAVGLRSISALVDITNYVSLDRGYPSHVFDASRI-SDVLTVRRACSGEKIL  288 (805)
Q Consensus       236 ~rL~~~Gir~inniVDitNyvmle~GqPlHafD~dki-~~~i~vr~a~~~E~~~  288 (805)
                      .|+.++|++++|+|+|.+||+|.+.|||+|++|.++- ...-+++...+|+.+.
T Consensus       132 r~~~~ig~~d~~kI~~~i~~~~~~~ge~~~~Ld~~~~~~~~~i~~~~~~g~~~~  185 (546)
T PRK09616        132 RKKVAIGIHDLDKIKPPIYYKAVSPDEKFVPLGYDEEMTLREILEKHPKGREYG  185 (546)
T ss_pred             CCCCCCCCCCHHHCCCCEEEEECCCCCEEEECCCCCCCCHHHHHHHHCCCCHHH
T ss_conf             421345650488748957999878997587378742268999987400341000


No 51 
>PRK12292 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=94.21  E-value=0.039  Score=34.38  Aligned_cols=62  Identities=18%  Similarity=0.295  Sum_probs=34.6

Q ss_pred             EEECHHHHHHCCCCCCEEEEEEEHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCC--HHHHHHHHHHCC
Q ss_conf             54778999966879978999987876235452024566313689888720018999668879--999999997111
Q gi|254780316|r  668 GEFHPNILDFFGLSNPICGFEVYLDSIPISQKKRTKTKKVVHLSSLHPVKRDLAFIVDQHIP--AGTLVNIIKNVD  741 (805)
Q Consensus       668 G~ihP~i~~~~~i~~~v~~~EI~ld~L~~~~~~~~~~~~~~~~s~fP~v~RDls~iv~~~v~--~~~I~~~i~~~~  741 (805)
                      |.-+ .+.+.|+-+.|..+|-+.+|.|........           +.-.+++-+..+++..  +-.+.+.+|+.|
T Consensus       289 GRYD-~L~~~fG~~~PAvGfa~g~eRl~~~l~~~~-----------~~~~~~~~v~~~~~~~~~a~~~a~~LR~~G  352 (388)
T PRK12292        289 GRYD-DLGGRFGRARPATGFSLDLDRLRELLPEEE-----------ERKQKDLLILAPWERLEAALAAAQALRKKG  352 (388)
T ss_pred             CCHH-HHHHHHCCCCCEEEEEECHHHHHHHHHHCC-----------CCCCCEEEEECCHHHHHHHHHHHHHHHHCC
T ss_conf             5664-799983899971589963999999864205-----------678867999858676999999999999779


No 52 
>PRK12295 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=93.91  E-value=0.049  Score=33.66  Aligned_cols=22  Identities=32%  Similarity=0.727  Sum_probs=10.5

Q ss_pred             HHHHCCCC--CCEEEEEEEHHHHH
Q ss_conf             99966879--97899998787623
Q gi|254780316|r  674 ILDFFGLS--NPICGFEVYLDSIP  695 (805)
Q Consensus       674 i~~~~~i~--~~v~~~EI~ld~L~  695 (805)
                      ++..|+-+  .|.++|-+.+|.|.
T Consensus       345 L~~~fG~~~~~PAvGfaigidRl~  368 (373)
T PRK12295        345 LLTRLGAGEPIPAVGFSIWLDRLA  368 (373)
T ss_pred             HHHHHCCCCCCCEEEEEEEHHHHH
T ss_conf             999858999986369997099985


No 53 
>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=93.01  E-value=0.096  Score=31.61  Aligned_cols=88  Identities=8%  Similarity=0.087  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH----HHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCC-CCCH
Q ss_conf             95467898878778774023210048257655200----000000246776432101512211067764321015-8611
Q gi|254780316|r  492 QSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGG----GQRELEILNPISADMSNMRTSLLPGLLKATGRNVDR-AIAD  566 (805)
Q Consensus       492 ~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~----~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r-~~~~  566 (805)
                      +...+.+++.+...||.|+.|-.|...+....-+.    .++..++.+ ...+.=+||++.-+++...++.+..- ..-.
T Consensus         3 ~~l~~~~~~~~~~~G~~~i~tP~l~~~~~~~~sg~~~~~~~~my~~~d-~~~~~l~Lrp~~~~~~~~~~~~~~~~~~~lP   81 (170)
T pfam00587         3 NALENFIRDLFKRYGYQEVDTPILEPKELWEGSGHWDDYFDEMYRFKD-RGGEELYLRPTAEVGITRLFKNEILSYRDLP   81 (170)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCEEEEHHHHHHCCCCCCCHHHEEEEEC-CCCCEEEEECCCCHHHHHHHHHHCCCCCCCC
T ss_conf             999999999999859989999917567898344776557531256735-8997688732574588899886200323586


Q ss_pred             HHHHHHCCCCCCCC
Q ss_conf             34543024444777
Q gi|254780316|r  567 FAIFEVSHVYENDT  580 (805)
Q Consensus       567 i~lFEiG~Vf~~~~  580 (805)
                      +++|++|+||+.+.
T Consensus        82 ~r~~~~~~~fR~E~   95 (170)
T pfam00587        82 LKLYQIGPCFRYEA   95 (170)
T ss_pred             CEEECCCCCCCCCC
T ss_conf             01330653006777


No 54 
>PRK00037 hisS histidyl-tRNA synthetase; Reviewed
Probab=92.93  E-value=0.088  Score=31.84  Aligned_cols=32  Identities=19%  Similarity=0.590  Sum_probs=21.0

Q ss_pred             EEECHHHHHHCC-CCCCEEEEEEEHHHHHHHHHC
Q ss_conf             547789999668-799789999878762354520
Q gi|254780316|r  668 GEFHPNILDFFG-LSNPICGFEVYLDSIPISQKK  700 (805)
Q Consensus       668 G~ihP~i~~~~~-i~~~v~~~EI~ld~L~~~~~~  700 (805)
                      |.-+ .+...|+ -+.|..+|-+.++.+......
T Consensus       286 GRYD-~L~~~fgg~~~PAvGfa~gieRi~~~l~~  318 (417)
T PRK00037        286 GRYD-GLVEQFGGPPTPAVGFAIGIERLLLLLEE  318 (417)
T ss_pred             CCHH-HHHHHHCCCCCCEEEEEECHHHHHHHHHH
T ss_conf             7315-78998489978747898639999999996


No 55 
>TIGR02222 chap_CsaA export-related chaperone CsaA; InterPro: IPR008231 The CsaA protein is required for SecA-mediated translocation of a subset of proteins , . CsaA and its relatives are typified by the presence of little more than a tRNA-binding motif that adopts an OB-fold. The Aquifex aeolicus member, Trbp111, has been demonstrated to bind tRNA, likely in a structure-specific manner .; GO: 0000049 tRNA binding, 0008565 protein transporter activity, 0015031 protein transport.
Probab=92.71  E-value=0.096  Score=31.60  Aligned_cols=75  Identities=21%  Similarity=0.389  Sum_probs=50.5

Q ss_pred             CEEEEEEEEEEECCCCC--CCEEEEECCCCCE--------------------EEEECCCCCCCCCCEEEEECCCCEECCC
Q ss_conf             74899999975657998--7089997599957--------------------9897548345589789896687792589
Q gi|254780316|r   43 PFTIVKVLSVERNPDLD--CAILRIDTGKHQE--------------------IQVVCGAPNVRVGLLGVWAPPGSCIPEN  100 (805)
Q Consensus        43 ~vvvg~v~~~~~hP~ad--l~v~~Vd~g~~~~--------------------~~IvcgA~Nv~~g~~V~~A~~Ga~lp~g  100 (805)
                      .+.||+|++++|||.|-  -....||+|+ +.                    ++||| +-|                   
T Consensus         8 dlRVGrIv~a~~fPeARKPAY~L~vDfG~-elG~k~SSAQiT~lY~~E~L~gr~Vva-VVN-------------------   66 (107)
T TIGR02222         8 DLRVGRIVKAEPFPEARKPAYKLEVDFGE-ELGVKTSSAQITKLYKPEDLVGRLVVA-VVN-------------------   66 (107)
T ss_pred             EECCCCEEEECCCCCCCCCEEEEEEECCC-CCCCCCCHHHHHCCCCCCCCCCCEEEE-EEC-------------------
T ss_conf             30226378616898557871799970179-777414405641237833001977899-981-------------------


Q ss_pred             CEEEEEEHHCCCCCCCHHHHHHHCCCCCCCCCEEEE--CCCCCCCCCH
Q ss_conf             839833120586505454118876998547750781--6888888455
Q gi|254780316|r  101 NMIVNVRKIRGIESTGMMCSEKELMLSDDSASIMEL--PIDAPVGGRL  146 (805)
Q Consensus       101 ~~~i~~~~irGv~S~GMlCS~~ELgl~~~~~gI~~l--~~~~~~G~~~  146 (805)
                         .-+++|-|+.||=.-     ||..++.+-+.-+  |.+.|+|+-+
T Consensus        67 ---FppKqiA~f~SEVLV-----lG~~~~~g~VvL~~pD~~vp~G~k~  106 (107)
T TIGR02222        67 ---FPPKQIAGFKSEVLV-----LGVIDEEGEVVLLQPDREVPLGTKI  106 (107)
T ss_pred             ---CCCCEECCCEEEEEE-----CCCCCCCCCEEEEECCCCCCCCCCC
T ss_conf             ---887305692404886-----1833787877986348668898504


No 56 
>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=92.15  E-value=0.95  Score=24.54  Aligned_cols=92  Identities=7%  Similarity=0.082  Sum_probs=56.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH----HHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCC-C
Q ss_conf             99889546789887877877402321004825765520----000000024677643210151221106776432101-5
Q gi|254780316|r  488 LSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFG----GGQRELEILNPISADMSNMRTSLLPGLLKATGRNVD-R  562 (805)
Q Consensus       488 ~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~----~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~-r  562 (805)
                      ....++..+.+++.+...|++|+.+-.|++.+..+.-+    +.++...+.+--.++ =+|||+==+.+....+.-.+ +
T Consensus        31 ~~i~~~i~~~i~~~~~~~G~~ev~~P~l~~~~l~~~sg~~~~f~~emf~v~d~~~~~-~~L~PT~E~~~~~~~~~~i~Sy  109 (255)
T cd00779          31 LRVLKKIENIIREEMNKIGAQEILMPILQPAELWKESGRWDAYGPELLRLKDRHGKE-FLLGPTHEEVITDLVANEIKSY  109 (255)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHCCCCCCCCCEEEEECCCCCE-EEECCCCHHHHHHHHHHHCCCH
T ss_conf             999999999999999985998997653473888744253013687315445378877-7316887488999998650361


Q ss_pred             CCCHHHHHHHCCCCCCCC
Q ss_conf             861134543024444777
Q gi|254780316|r  563 AIADFAIFEVSHVYENDT  580 (805)
Q Consensus       563 ~~~~i~lFEiG~Vf~~~~  580 (805)
                      +.-.++++++|.+|+.+.
T Consensus       110 rdLPl~~~q~~~~fR~E~  127 (255)
T cd00779         110 KQLPLNLYQIQTKFRDEI  127 (255)
T ss_pred             HHCCEEEECCCCEECCCC
T ss_conf             225745413533542566


No 57 
>PRK12421 ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=91.45  E-value=0.15  Score=30.17  Aligned_cols=80  Identities=15%  Similarity=0.222  Sum_probs=44.6

Q ss_pred             CCCCCEEEEEECC--EEEEEEEEEECHHHHHHCCCCCCEEEEEEEHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEEEC
Q ss_conf             7898169999879--29999985477899996687997899998787623545202456631368988872001899966
Q gi|254780316|r  648 YHPGRSGIIKTSA--EIVLGYFGEFHPNILDFFGLSNPICGFEVYLDSIPISQKKRTKTKKVVHLSSLHPVKRDLAFIVD  725 (805)
Q Consensus       648 ~hPgrsa~I~~~g--k~iiG~iG~ihP~i~~~~~i~~~v~~~EI~ld~L~~~~~~~~~~~~~~~~s~fP~v~RDls~iv~  725 (805)
                      ||.|-..+++..|  +.+ +-=|.-+ .+.+.||-..|..+|-++++.|.....            ..|.  .+ .+.+|
T Consensus       277 YyTG~vFe~y~~g~~~~I-a~GGRYD-~L~~~fG~~~PA~GFsl~l~rL~~~~~------------~~~~--~~-~i~~p  339 (391)
T PRK12421        277 YHTGLVFAAYAPGRGAPL-ARGGRYD-GIGEAFGRARPATGFSMDLRALLALLT------------QFAE--PE-AVLAP  339 (391)
T ss_pred             CCCEEEEEEEECCCCCEE-ECCCCCC-CHHHHCCCCCCEEEEEECHHHHHHHCC------------CCCC--CC-EEEEE
T ss_conf             454489999948988835-4166637-177753999980489966999997265------------6688--88-79976


Q ss_pred             CCCCHH--HHHHHHHHCCCCE
Q ss_conf             887999--9999997111003
Q gi|254780316|r  726 QHIPAG--TLVNIIKNVDRLI  744 (805)
Q Consensus       726 ~~v~~~--~I~~~i~~~~~ll  744 (805)
                      ..-..+  ..++.+|..|..+
T Consensus       340 ~~~~~~~~~~i~~LR~~G~~V  360 (391)
T PRK12421        340 WGDDPDLLAAIAELRQQGERV  360 (391)
T ss_pred             CCCCHHHHHHHHHHHHCCCEE
T ss_conf             799799999999999679799


No 58 
>CHL00192 syfB phenylalanyl-tRNA synthetase beta chain; Provisional
Probab=91.13  E-value=0.23  Score=28.85  Aligned_cols=68  Identities=18%  Similarity=0.225  Sum_probs=32.0

Q ss_pred             CEEEEEECCEEEEEEEEEECHHHHHH-CCCCCCEEEEEEEHHHHHHHHHCCCCCCCCCCCCCCCCCEEE----EEEEE-C
Q ss_conf             16999987929999985477899996-687997899998787623545202456631368988872001----89996-6
Q gi|254780316|r  652 RSGIIKTSAEIVLGYFGEFHPNILDF-FGLSNPICGFEVYLDSIPISQKKRTKTKKVVHLSSLHPVKRD----LAFIV-D  725 (805)
Q Consensus       652 rsa~I~~~gk~iiG~iG~ihP~i~~~-~~i~~~v~~~EI~ld~L~~~~~~~~~~~~~~~~s~fP~v~RD----ls~iv-~  725 (805)
                      |=-.+.++.+.   -.++|--.+.+. -++-..+.+|.++-.+                  ..|.-++-    +.|-- +
T Consensus       615 RDlalvv~~~v---~~~~I~~~I~~~~~~ll~~v~lfDvY~g~------------------~i~~gkKSla~~l~fq~~~  673 (702)
T CHL00192        615 RDLSLIIPKNM---TISFLLKLILQFGNNLLESITLFDQYKGK------------------SIGEGKKSLGLRLTYRSNK  673 (702)
T ss_pred             EEEEEEECCCC---CHHHHHHHHHHCCCCCEEEEEEEEEECCC------------------CCCCCCEEEEEEEEEECCC
T ss_conf             68999989999---79999999986292417178899985799------------------9899966999999998989


Q ss_pred             CCCCHHHHHHHHHHC
Q ss_conf             887999999999711
Q gi|254780316|r  726 QHIPAGTLVNIIKNV  740 (805)
Q Consensus       726 ~~v~~~~I~~~i~~~  740 (805)
                      +..+-++|.+++.+.
T Consensus       674 rTLtd~eV~~~~~kI  688 (702)
T CHL00192        674 KTLTNKEIDRIQNEL  688 (702)
T ss_pred             CCCCHHHHHHHHHHH
T ss_conf             996999999999999


No 59 
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=90.13  E-value=0.3  Score=28.12  Aligned_cols=64  Identities=14%  Similarity=0.321  Sum_probs=35.2

Q ss_pred             EEECHHHHHHCCCC-CCEEEEEEEHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCC---HHHHHHHHHHCC
Q ss_conf             54778999966879-978999987876235452024566313689888720018999668879---999999997111
Q gi|254780316|r  668 GEFHPNILDFFGLS-NPICGFEVYLDSIPISQKKRTKTKKVVHLSSLHPVKRDLAFIVDQHIP---AGTLVNIIKNVD  741 (805)
Q Consensus       668 G~ihP~i~~~~~i~-~~v~~~EI~ld~L~~~~~~~~~~~~~~~~s~fP~v~RDls~iv~~~v~---~~~I~~~i~~~~  741 (805)
                      |.-+ .+...|+-+ .|..+|-+-+|.|.........         +|...-|+-++...+..   +-+|.+.++++|
T Consensus       285 GRYD-~Lv~~fgg~~~PavGfaiGieRl~~~l~~~~~---------~~~~~~~~~v~~~~~~~~~~~~~ia~~LR~~g  352 (424)
T CHL00201        285 GRYD-SLVEQLGGPKTPAVGWAIGIERLLLIAKDNIL---------LPKPSIDFYIATKGNVAIKIAFSIQRFLHNQG  352 (424)
T ss_pred             CCCH-HHHHHCCCCCCCEEEEEECHHHHHHHHHHCCC---------CCCCCCCEEEEECCHHHHHHHHHHHHHHHHCC
T ss_conf             7707-78997299999857788439999999973377---------77778858999778499999999999999889


No 60 
>PRK12420 histidyl-tRNA synthetase; Provisional
Probab=89.97  E-value=0.27  Score=28.36  Aligned_cols=27  Identities=30%  Similarity=0.436  Sum_probs=17.9

Q ss_pred             HHHHHCC---CCCCEEEEEEEHHHHHHHHH
Q ss_conf             9999668---79978999987876235452
Q gi|254780316|r  673 NILDFFG---LSNPICGFEVYLDSIPISQK  699 (805)
Q Consensus       673 ~i~~~~~---i~~~v~~~EI~ld~L~~~~~  699 (805)
                      .+.+.|+   ++.|..+|-+-+|.|...-.
T Consensus       301 ~Li~~fgg~~~~~PavGfa~Gierl~~~L~  330 (421)
T PRK12420        301 NIIGAFRGDNMNYPTVGISFGLDVIYTALS  330 (421)
T ss_pred             HHHHHHCCCCCCCCEEEEEEHHHHHHHHHH
T ss_conf             489881899899974799851999999985


No 61 
>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=89.65  E-value=0.49  Score=26.58  Aligned_cols=122  Identities=11%  Similarity=0.101  Sum_probs=70.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH----
Q ss_conf             3454334402567676765352334667655443457678998895467898878778774023210048257655----
Q gi|254780316|r  448 SWRQDVEEKADLVEEILRIYGVDQIKSEPLPLTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVL----  523 (805)
Q Consensus       448 s~R~DI~~e~DLiEEIaRiyGYdnIp~~~l~~~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~----  523 (805)
                      .|=.+|....+|+|     | | .+|-.+.     -.+......+...+.+|+.+...||+||.+-.+++......    
T Consensus         4 ~wy~~~~~~~~l~d-----~-~-pv~G~~~-----~lP~G~~i~~~l~~~~r~~~~~~G~~ev~~P~l~~~~~~~k~sgh   71 (261)
T cd00778           4 EWYTEVITKAELID-----Y-G-PVKGCMV-----FRPYGYAIWENIQKILDKEIKETGHENVYFPLLIPESELEKEKEH   71 (261)
T ss_pred             HHHHHHHHHHCCCC-----C-C-CCCCEEE-----ECCCHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHCH
T ss_conf             99999999817722-----4-7-9983088-----863289999999999999999869969988332788999974281


Q ss_pred             HH-HHHHHCCCCCC-C--CCCCCCCCCHHHCHHHHHHHHHCC-CCCCHHHHHHHCCCCCCCCC
Q ss_conf             20-00000002467-7--643210151221106776432101-58611345430244447775
Q gi|254780316|r  524 FG-GGQRELEILNP-I--SADMSNMRTSLLPGLLKATGRNVD-RAIADFAIFEVSHVYENDTP  581 (805)
Q Consensus       524 ~~-~~~~~i~l~NP-l--S~e~s~lR~SLlp~LL~~~~~N~~-r~~~~i~lFEiG~Vf~~~~~  581 (805)
                      +. ..++...+... .  .++.=.|||+-=|.+....+...+ ++.-.+++||+|.+|+.+..
T Consensus        72 ~~~y~~emf~v~~~g~~~~d~~y~LkPmne~~~~~i~~~~~~SYRdLPlrl~q~g~~~R~E~s  134 (261)
T cd00778          72 IEGFAPEVAWVTHGGLEELEEPLALRPTSETAIYPMFSKWIRSYRDLPLKINQWVNVFRWETK  134 (261)
T ss_pred             HHCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHCCCEECCCCC
T ss_conf             430576533552168520135603478886999999973505402278255530422437788


No 62 
>PRK12293 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=88.97  E-value=0.21  Score=29.25  Aligned_cols=88  Identities=13%  Similarity=0.190  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHH
Q ss_conf             89546789887877877402321004825765520000000024677643210151221106776432101586113454
Q gi|254780316|r  491 QQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIF  570 (805)
Q Consensus       491 ~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lF  570 (805)
                      .+...+++++.+...||.|+.|-.|--.+... -...++..+...+-... =+|||-+.+++.+.++.++.+.....|+|
T Consensus        22 ~~~Ie~~~~~~f~~~Gy~eI~TP~~E~~e~~~-~~~~kemy~f~D~~gr~-l~LRPd~Ta~iaR~v~~~l~~~~~p~rl~   99 (281)
T PRK12293         22 KRDIENVASEILYKEGFEEIVTPSFSYHQHLS-VADEKELLRFSDEKNHE-ISLRADSTVDVVRIITKRLGRSTEHKKWF   99 (281)
T ss_pred             HHHHHHHHHHHHHHCCCEEEECCCEEEEECCC-CCCCCEEEEEECCCCCE-EEECCCCCHHHHHHHHHCCCCCCCCEEEE
T ss_conf             99999999999998599485378568644346-65630179998799987-99778887899999996554468975799


Q ss_pred             HHCCCCCCCC
Q ss_conf             3024444777
Q gi|254780316|r  571 EVSHVYENDT  580 (805)
Q Consensus       571 EiG~Vf~~~~  580 (805)
                      =+|+||+...
T Consensus       100 Y~g~vFRye~  109 (281)
T PRK12293        100 YIQPVFRYPT  109 (281)
T ss_pred             EECCEEECCC
T ss_conf             8756353467


No 63 
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=88.87  E-value=0.29  Score=28.23  Aligned_cols=33  Identities=12%  Similarity=0.009  Sum_probs=19.2

Q ss_pred             EEEEEEEEEECCCCCCCEEEEECCCCCEEEEECCCC
Q ss_conf             899999975657998708999759995798975483
Q gi|254780316|r   45 TIVKVLSVERNPDLDCAILRIDTGKHQEIQVVCGAP   80 (805)
Q Consensus        45 vvg~v~~~~~hP~adl~v~~Vd~g~~~~~~IvcgA~   80 (805)
                      +.|.|..+..+-+  +....+..|++ ..||+|-.+
T Consensus        22 v~Grv~~~R~~Gk--l~Fi~LrD~tg-~~qiq~~~~   54 (462)
T PRK03932         22 IRGWVRTKRDSGK--ISFLELNDGSC-FKQIQVVKN   54 (462)
T ss_pred             EEEEEEEEECCCC--CEEEEEECCCC-CEEEEEEEC
T ss_conf             9897782781798--38999982898-789999967


No 64 
>pfam00152 tRNA-synt_2 tRNA synthetases class II (D, K and N).
Probab=87.82  E-value=0.55  Score=26.19  Aligned_cols=115  Identities=17%  Similarity=0.221  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             95467898878778774023210048257655200000000246776432101512211067764321015861134543
Q gi|254780316|r  492 QSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFE  571 (805)
Q Consensus       492 ~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lFE  571 (805)
                      ....+.+|++|...||.||-|-.+++..--    ...++..+.+. ..+..+||+|  |-|-.-..  +.-|..  ++||
T Consensus        26 s~i~~~iR~ff~~~~f~EV~TP~L~~~~~e----~~a~~F~~~~~-~~~~~yL~~S--pel~~k~l--l~~g~~--rVfe   94 (341)
T pfam00152        26 SKIIRAIREFLDERGFLEVETPILTKSTPE----GGARDFLVPKF-YAKEAYLPQS--PQLYKQLL--MVAGFD--RVFQ   94 (341)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCCCCC----CCCCEEEECCC-CCCCEEECCC--HHHHHHHH--HHCCCC--CCEE
T ss_conf             999999999999889899879820055898----77766450267-8982340548--89999999--865887--6379


Q ss_pred             HCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             02444477754431000221035431012462023454433331468887531111111014
Q gi|254780316|r  572 VSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFV  633 (805)
Q Consensus       572 iG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~  633 (805)
                      ||++|+++......+..-              +|.-.|..  ...|+.++...++.++..+.
T Consensus        95 i~~~FR~E~~~t~rH~~E--------------FtmlE~y~--a~~d~~d~m~~~E~li~~i~  140 (341)
T pfam00152        95 IAPCFRDEDLRTDRHPPE--------------FTQLDLEM--SFVDYEDVMDLTEDLIKYVF  140 (341)
T ss_pred             EECHHCCCCCCCCCCCHH--------------HHHHHHHH--HCCCHHHHHHHHHHHHHHHH
T ss_conf             723202798988655077--------------88776755--35999999999999999999


No 65 
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=87.62  E-value=0.59  Score=26.02  Aligned_cols=26  Identities=19%  Similarity=0.465  Sum_probs=14.4

Q ss_pred             CHHHHHHHHHHCCCCCHHHHHHHHHHHHHHC
Q ss_conf             3778788886401321039999989998608
Q gi|254780316|r  231 PNWMRQRLKAVGLRSISALVDITNYVSLDRG  261 (805)
Q Consensus       231 P~wl~~rL~~~Gir~inniVDitNyvmle~G  261 (805)
                      |.||=     -|.|-.|++.++.-=.|...|
T Consensus        40 ~~wlP-----~G~~i~~~le~~ir~e~~~~G   65 (438)
T PRK12325         40 YSWLP-----LGLKVLKKIENIVREEQNRAG   65 (438)
T ss_pred             CEECC-----CHHHHHHHHHHHHHHHHHHCC
T ss_conf             22160-----589999999999999999749


No 66 
>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=87.52  E-value=0.44  Score=26.89  Aligned_cols=79  Identities=18%  Similarity=0.298  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHH
Q ss_conf             89546789887877877402321004825765520000000024677643210151221106776432101586113454
Q gi|254780316|r  491 QQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIF  570 (805)
Q Consensus       491 ~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lF  570 (805)
                      .....+.+|++|...||.||-|-.|++..--    +..++..+ +-. ....+||+|  |.|-+-+.   --|..  ++|
T Consensus        27 Rs~i~~~iR~fl~~~gF~EVeTP~L~~~~~e----g~a~~f~~-~~~-~~~~yL~~S--pel~Kqll---i~G~~--rVf   93 (322)
T cd00776          27 RSEVLRAFREFLRENGFTEVHTPKITSTDTE----GGAELFKV-SYF-GKPAYLAQS--PQLYKEML---IAALE--RVY   93 (322)
T ss_pred             HHHHHHHHHHHHHHCCCEEEECCCCCCCCCC----CCCCCCCC-CCC-CCCEEECCC--HHHHHHHH---HCCCC--CEE
T ss_conf             9999999999999889999979840078898----65466762-105-876001548--58899997---53424--438


Q ss_pred             HHCCCCCCCCCC
Q ss_conf             302444477754
Q gi|254780316|r  571 EVSHVYENDTPE  582 (805)
Q Consensus       571 EiG~Vf~~~~~~  582 (805)
                      |||++|+++...
T Consensus        94 ei~~~FR~E~~~  105 (322)
T cd00776          94 EIGPVFRAEKSN  105 (322)
T ss_pred             EECCEEECCCCC
T ss_conf             872614079998


No 67 
>PRK11342 mhpD 2-keto-4-pentenoate hydratase; Provisional
Probab=86.65  E-value=2.4  Score=21.68  Aligned_cols=23  Identities=30%  Similarity=0.634  Sum_probs=10.2

Q ss_pred             EEE-EEEECHHHHHHCCCCCCEEE
Q ss_conf             999-85477899996687997899
Q gi|254780316|r  664 LGY-FGEFHPNILDFFGLSNPICG  686 (805)
Q Consensus       664 iG~-iG~ihP~i~~~~~i~~~v~~  686 (805)
                      +|| +|--+|.+.+.+++..|+|+
T Consensus        57 vG~KiG~Ts~~~q~~~gv~~P~~G   80 (262)
T PRK11342         57 VGRKVGLTHPKVQQQLGVDQPDFG   80 (262)
T ss_pred             EEEEEECCCHHHHHHCCCCCCCEE
T ss_conf             899983389999997098998267


No 68 
>TIGR02865 spore_II_E stage II sporulation protein E; InterPro: IPR014221   This entry contains the stage II sporulation protein E (SpoIIE), which is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation and it has phosphatase activity, located in the C-terminal region, which is required to activate sigma-F. All members of this entry are found in endospore-forming Gram-positive bacteria. A homologous protein, not a member of this entry, is found in the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis..
Probab=86.55  E-value=1.2  Score=23.85  Aligned_cols=96  Identities=21%  Similarity=0.286  Sum_probs=49.5

Q ss_pred             EEEEEEHHHHHHHHHCCCCCCCCCCCCCCCC-CEE--EEEEEECCCCCHHHHHHH-H---H-H--CCCCE--EEEEEEEE
Q ss_conf             9999878762354520245663136898887-200--189996688799999999-9---7-1--11003--57698987
Q gi|254780316|r  685 CGFEVYLDSIPISQKKRTKTKKVVHLSSLHP-VKR--DLAFIVDQHIPAGTLVNI-I---K-N--VDRLI--DDVTVFDV  752 (805)
Q Consensus       685 ~~~EI~ld~L~~~~~~~~~~~~~~~~s~fP~-v~R--Dls~iv~~~v~~~~I~~~-i---~-~--~~~ll--~~v~lfDv  752 (805)
                      -+.=+||..|.+..    ....|..+---|+ ++|  ++..+-.++.|.+-+.+. +   + +  .|.++  -+=-+..-
T Consensus       662 ~FsTlDL~~iDL~~----g~~~F~KvGavpSFiKRG~~V~vI~~~~LPiG~~~~vd~e~~~~~L~~GD~ivm~SDGvLE~  737 (794)
T TIGR02865       662 KFSTLDLSVIDLYT----GQAEFVKVGAVPSFIKRGAKVEVIRSSNLPIGILDEVDVELVRKKLKNGDLIVMVSDGVLEA  737 (794)
T ss_pred             HHHHHHHHHHCCCC----CEEEEEEECCCCCEEEECCEEEEEEECCCCCCCCCCCCCCCEEEECCCCCEEEEECCCHHHC
T ss_conf             05776788744776----32789996161251666788999862789846545323430012337998799812313330


Q ss_pred             EECCCCCCCCEEEEEEEEEECCCCCCCHHHHHHH
Q ss_conf             6367799884269999998477988899999999
Q gi|254780316|r  753 FQGKSLGEGKKSVAIQVLIQPLKDTFRDDDIRIL  786 (805)
Q Consensus       753 Y~g~~i~~gkkSla~rl~fqs~~kTLtd~EI~~i  786 (805)
                      ++|++-.+||-..-+|+.  ..+.+..=+||-+.
T Consensus       738 l~g~~~~e~k~~W~~~~l--~e~~~~~P~E~Ae~  769 (794)
T TIGR02865       738 LEGEKEVEGKVLWLVRFL--KETDTNDPEEIAEY  769 (794)
T ss_pred             CCCCHHHCCHHHHHHHHH--CCCCCCCHHHHHHH
T ss_conf             587300116288999996--13677895889999


No 69 
>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=86.36  E-value=0.64  Score=25.73  Aligned_cols=93  Identities=12%  Similarity=0.095  Sum_probs=62.2

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH----HHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCC
Q ss_conf             7899889546789887877877402321004825765520----000000024677643210151221106776432101
Q gi|254780316|r  486 RNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFG----GGQRELEILNPISADMSNMRTSLLPGLLKATGRNVD  561 (805)
Q Consensus       486 ~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~----~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~  561 (805)
                      +.....+.+.+.+|+.....||+||.|-.+.+.+.-+.-+    +.++...+.  ...+.=+||+.--|+.....+.-. 
T Consensus        28 ~G~~i~~~L~~~ir~~~~~~Gy~eV~tP~i~~~~Lw~~SGH~~~y~e~mf~~~--~~~~~~~LkPmnCp~h~~i~~~~~-  104 (298)
T cd00771          28 KGAIIRNELEDFLRELQRKRGYQEVETPIIYNKELWETSGHWDHYRENMFPFE--EEDEEYGLKPMNCPGHCLIFKSKP-  104 (298)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCCCCCCCCEEEEE--ECCCCEEEECCCCHHHHHHHHCCC-
T ss_conf             88999999999999999986998998861266556754776311368568888--625416885068688999986355-


Q ss_pred             CCCC--HHHHHHHCCCCCCCCC
Q ss_conf             5861--1345430244447775
Q gi|254780316|r  562 RAIA--DFAIFEVSHVYENDTP  581 (805)
Q Consensus       562 r~~~--~i~lFEiG~Vf~~~~~  581 (805)
                      |..+  .+|++|+|.||+.+.+
T Consensus       105 ~SYrdLPlR~~E~g~~~R~E~s  126 (298)
T cd00771         105 RSYRDLPLRLAEFGTVHRYEQS  126 (298)
T ss_pred             CCHHHCCHHHHCCCCEECCCCC
T ss_conf             6734346765207505547677


No 70 
>COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=86.22  E-value=0.82  Score=24.97  Aligned_cols=65  Identities=15%  Similarity=0.358  Sum_probs=31.3

Q ss_pred             EEECHHHHHHCC-CCCCEEEEEEEHHHHHHHHHCCCCCCCCCCCCCCC-CCEEEEEEE-ECCCC--CHHHHHHHHHHCC
Q ss_conf             547789999668-79978999987876235452024566313689888-720018999-66887--9999999997111
Q gi|254780316|r  668 GEFHPNILDFFG-LSNPICGFEVYLDSIPISQKKRTKTKKVVHLSSLH-PVKRDLAFI-VDQHI--PAGTLVNIIKNVD  741 (805)
Q Consensus       668 G~ihP~i~~~~~-i~~~v~~~EI~ld~L~~~~~~~~~~~~~~~~s~fP-~v~RDls~i-v~~~v--~~~~I~~~i~~~~  741 (805)
                      |.-+. +.+.|+ -+.|..+|-+-++.|.........        ..| ...-|+-++ ++++.  .+-.+.+.+++++
T Consensus       293 GRYD~-Lv~~~gG~~~pavGFaiGveRl~~~l~~~~~--------~~~~~~~~~v~v~~~~~~~~~~a~~la~~LR~~g  362 (429)
T COG0124         293 GRYDG-LVEEFGGKPTPAVGFAIGVERLILALEEEGK--------EDPVETRVDVYVVPLGEDAEPEALKLAQKLRAAG  362 (429)
T ss_pred             CCCHH-HHHHHCCCCCCCEEEEHHHHHHHHHHHHCCC--------CCCCCCCCCEEEEECCCHHHHHHHHHHHHHHHCC
T ss_conf             66158-9998489988713675179999999997188--------7776777888999848615999999999999759


No 71 
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=86.15  E-value=0.92  Score=24.63  Aligned_cols=150  Identities=14%  Similarity=0.084  Sum_probs=84.7

Q ss_pred             CHHHHHHCCCCC-HHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             113333113458-7899999998402221034562366403454334402567676765352334667655443457678
Q gi|254780316|r  409 SEVKRLSGIDVP-IEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQIKSEPLPLTQVEDKRN  487 (805)
Q Consensus       409 ~~i~~ilG~~i~-~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGYdnIp~~~l~~~~~~~~~~  487 (805)
                      ..+.|+-|+.++ .++....|+++.=--..+          +|.           +++-.+.=.|....-|-...=.++.
T Consensus       149 ~~LqRIYG~af~~k~~L~~yl~~~eEakkRD----------HRk-----------lGkel~LF~f~~~~gpG~~~wlP~G  207 (576)
T PRK12305        149 KQLTRIYGTSWESKEELDKYLAILQERKERD----------HRK-----------IGKDLKLFTFSSLAGQGFPIWLENG  207 (576)
T ss_pred             CEEEEEEEEEECCHHHHHHHHHHHHHHHHCC----------HHH-----------HHHHCCEEEECCCCCCCCEEECCCH
T ss_conf             1008999997179889999999999998657----------787-----------6421565872344688764674767


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH----HHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCC
Q ss_conf             99889546789887877877402321004825765520----00000002467764321015122110677643210158
Q gi|254780316|r  488 LSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFG----GGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRA  563 (805)
Q Consensus       488 ~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~----~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~  563 (805)
                      ....+.+.+.+|+.....||+||.|-.+.+.+.-+.-|    +.++...... +..+.=.|+|.--|+.....+.-. |.
T Consensus       208 ~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SGH~~~Y~e~Mf~~~~-~~~e~~~lKPMNCP~H~~if~~~~-rS  285 (576)
T PRK12305        208 MIIKNAIRKFILELDRKYGFDEVLTPHFGEKKLYKTSGHLDHYKDDMFKPLK-IENEELIPRPMTCPHHIILYSNEL-RS  285 (576)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCHHHHHHHCCCCEE-CCCCEEEECCCCCHHHHHHHHCCC-CC
T ss_conf             8999999999999999869989846421428899766646556642573063-156416535778632677764277-54


Q ss_pred             CC--HHHHHHHCCCCCCCCC
Q ss_conf             61--1345430244447775
Q gi|254780316|r  564 IA--DFAIFEVSHVYENDTP  581 (805)
Q Consensus       564 ~~--~i~lFEiG~Vf~~~~~  581 (805)
                      .+  .+|+||+|.||+.+.+
T Consensus       286 YRdLPlR~aEfg~~~R~E~S  305 (576)
T PRK12305        286 YRDLPIRLSEQSRLYRYEKS  305 (576)
T ss_pred             HHHCCHHHHCCCCEECCCCC
T ss_conf             44324220004435447888


No 72 
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=85.09  E-value=0.91  Score=24.66  Aligned_cols=112  Identities=17%  Similarity=0.213  Sum_probs=57.1

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH-HHHH-CCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHH
Q ss_conf             95467898878778774023210048257655200-0000-002467764321015122110677643210158611345
Q gi|254780316|r  492 QSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGG-GQRE-LEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAI  569 (805)
Q Consensus       492 ~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~-~~~~-i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~l  569 (805)
                      .+..+.+|++|...||.||-|--|.+-.     ++ ...+ +.=.|.+..++ +||.|  |.|-+-..-  --|..  |+
T Consensus       188 s~ii~~iR~~l~~~gF~EVeTPil~~~~-----gGa~Arpf~t~~~~~~~~~-yL~qS--PQLykk~Lm--vgGfd--Rv  255 (505)
T PRK12445        188 SKILAAIRQFMVARGFMEVETPMMQVIP-----GGASARPFITHHNALDLDM-YLRIA--PELYLKRLV--VGGFE--RV  255 (505)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCCC-----CCCCCCEEEECCCCCCCCE-EECCC--CHHHHHHHH--HCCCC--CE
T ss_conf             9999999999997793899788755545-----8766610330466788674-34169--399999998--57974--45


Q ss_pred             HHHCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             430244447775443100022103543101246202345443333146888753111111101
Q gi|254780316|r  570 FEVSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPF  632 (805)
Q Consensus       570 FEiG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l  632 (805)
                      ||||++|+++... ..+..              .+|.-.|..  ...|+.|+...++.++..+
T Consensus       256 feI~r~FRnE~~~-~~H~P--------------EFT~lE~e~--af~d~~dvm~l~E~li~~i  301 (505)
T PRK12445        256 FEINRNFRNEGIS-VRHNP--------------EFTMMELYM--AYADYHDLIELTESLFRTL  301 (505)
T ss_pred             EEHHHHHHCCCCC-CCCCH--------------HHHHHHHHH--HCCCHHHHHHHHHHHHHHH
T ss_conf             7627876078888-66544--------------454356876--3278989999999999999


No 73 
>TIGR01393 lepA GTP-binding protein LepA; InterPro: IPR006297   LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function of the proteins in this family are unknown. ; GO: 0005525 GTP binding.
Probab=84.74  E-value=2.9  Score=21.05  Aligned_cols=158  Identities=16%  Similarity=0.214  Sum_probs=87.7

Q ss_pred             CHHHCHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             12211067764321015861134543024444777544310002210354310124620234544333314688875311
Q gi|254780316|r  546 TSLLPGLLKATGRNVDRAIADFAIFEVSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADA  625 (805)
Q Consensus       546 ~SLlp~LL~~~~~N~~r~~~~i~lFEiG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v  625 (805)
                      ++|-.|=.--+.-|++. ..+++   +|++-+.-...-.+.+.++-.-.+..+  +|.. .      -..-||-+||-.+
T Consensus       250 ~~L~aGeVGy~~AgIK~-v~D~~---VGDTiT~~~~Pa~eplpGF~~~KP~VF--aGlY-P------id~~~Ye~LrdAL  316 (598)
T TIGR01393       250 QELSAGEVGYIIAGIKD-VSDVK---VGDTITSVKNPAKEPLPGFKEVKPMVF--AGLY-P------IDTEDYEDLRDAL  316 (598)
T ss_pred             CCEECCCEEEEEEEEEE-CCCEE---CCCEEECCCCCCCCCCCCCCCCCCEEE--ECCC-C------CCCHHHHHHHHHH
T ss_conf             62001630599986531-04112---054452567873767888612576586--0125-8------8803468999997


Q ss_pred             HHHHHHCCCCCCEEEECCCCCCCCCCCEEEEEECCEEEEEEEEEECHHHHHH-----CCCC----CCEEEEEEEHHHHHH
Q ss_conf             1111101453330330588656789816999987929999985477899996-----6879----978999987876235
Q gi|254780316|r  626 LSVIEPFVSLDSLRFESGAPSWYHPGRSGIIKTSAEIVLGYFGEFHPNILDF-----FGLS----NPICGFEVYLDSIPI  696 (805)
Q Consensus       626 ~~ll~~l~~~~~~~~~~~~~~~~hPgrsa~I~~~gk~iiG~iG~ihP~i~~~-----~~i~----~~v~~~EI~ld~L~~  696 (805)
                      +.|-   ..-..++|++.+...+  |       -|-.+ ||+|.||=+|.++     |||.    -|.+.-++.+.    
T Consensus       317 eKL~---LNDAsL~yE~E~S~AL--G-------FGFRC-GFLGLLHmEiiqERLeREFnldlI~TAP~V~Y~V~~~----  379 (598)
T TIGR01393       317 EKLK---LNDASLTYEPESSPAL--G-------FGFRC-GFLGLLHMEIIQERLEREFNLDLITTAPSVVYKVYLT----  379 (598)
T ss_pred             HHHH---HHHHHHHCCCCCCCCC--C-------CCEEE-CCCCCHHHHHHHHHHHHHCCCEEEEECCCEEEEEEEE----
T ss_conf             5554---4025421022363003--7-------40433-2666336899987654430870687278159999970----


Q ss_pred             HHHCCCCCCCCCCCCCCCCCEE---------EEEEEECCCCCHHHHHHHHH
Q ss_conf             4520245663136898887200---------18999668879999999997
Q gi|254780316|r  697 SQKKRTKTKKVVHLSSLHPVKR---------DLAFIVDQHIPAGTLVNIIK  738 (805)
Q Consensus       697 ~~~~~~~~~~~~~~s~fP~v~R---------Dls~iv~~~v~~~~I~~~i~  738 (805)
                          .........||.||.-..         .+++++|++. .+.|++.+.
T Consensus       380 ----~G~~~~v~nP~~~P~~~~I~~v~EPyv~~~IitP~ey-~G~iM~LC~  425 (598)
T TIGR01393       380 ----DGEVIEVDNPSDLPDPNKIEHVEEPYVKATIITPSEY-LGAIMELCQ  425 (598)
T ss_pred             ----CCCEEEEECCHHCCCCCCCCEEECCEEEEEEECCCCH-HHHHHHHHH
T ss_conf             ----7818997183006850157778447499994358301-246888763


No 74 
>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=84.20  E-value=0.77  Score=25.18  Aligned_cols=129  Identities=10%  Similarity=0.043  Sum_probs=71.0

Q ss_pred             ECCCCCCCCCHHHHHHHHHHHCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf             4034543344025676767653523346676-554434576789988954678988787787740232100482576552
Q gi|254780316|r  446 VPSWRQDVEEKADLVEEILRIYGVDQIKSEP-LPLTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLF  524 (805)
Q Consensus       446 vPs~R~DI~~e~DLiEEIaRiyGYdnIp~~~-l~~~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~  524 (805)
                      +|.+-.....-.+|.|+.. ++-|++-...+ ..+.. .........+.+.+..++.+...||.|+.|-.+++.+....-
T Consensus        11 ~~~f~f~~rdH~~Lg~~L~-L~dfe~~akvsG~rf~~-l~g~ga~Le~AL~~f~~d~~~~~Gy~eV~tP~iv~~~~~~~s   88 (297)
T cd00770          11 PRVFDFKPKDHVELGEKLD-ILDFERGAKVSGSRFYY-LKGDGALLERALINFALDFLTKRGFTPVIPPFLVRKEVMEGT   88 (297)
T ss_pred             CCCCCCCCCCHHHHHHHCC-CEECCCCCCCCCCEEEE-ECCHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHH
T ss_conf             8999999889999999778-81023224689877799-888899999999999999999879989988530138998543


Q ss_pred             HH----HHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCC--HHHHHHHCCCCCCCCC
Q ss_conf             00----000000246776432101512211067764321015861--1345430244447775
Q gi|254780316|r  525 GG----GQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIA--DFAIFEVSHVYENDTP  581 (805)
Q Consensus       525 ~~----~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~--~i~lFEiG~Vf~~~~~  581 (805)
                      +.    .++..++.+    +.-+|.++-=++|.. +-.|.-+...  .+|++++|++|+.+..
T Consensus        89 G~~~~~~e~~y~i~~----~~~~Li~tae~~l~~-~~~~~~~~~~dLPlr~~~~s~cfR~Eag  146 (297)
T cd00770          89 GQLPKFDEQLYKVEG----EDLYLIATAEVPLAA-LHRDEILEEEELPLKYAGYSPCFRKEAG  146 (297)
T ss_pred             CCCCCCHHHHHCCCC----HHHHHHHCCCCCEEE-EEEEEECCHHHCCCCEEECCCHHHHCCC
T ss_conf             578763565210355----055554405666223-4420031775588650224634132037


No 75 
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=83.34  E-value=1.5  Score=23.19  Aligned_cols=34  Identities=18%  Similarity=0.022  Sum_probs=22.7

Q ss_pred             EEEEEEEEEECCCCCCCEEEEECCCCCEEEEECCCCC
Q ss_conf             8999999756579987089997599957989754834
Q gi|254780316|r   45 TIVKVLSVERNPDLDCAILRIDTGKHQEIQVVCGAPN   81 (805)
Q Consensus        45 vvg~v~~~~~hP~adl~v~~Vd~g~~~~~~IvcgA~N   81 (805)
                      +-|.|.++..|-  .+....+..+.+ .+|||+-..+
T Consensus        21 v~G~v~~~R~~G--kl~Fi~LrD~~g-~iQ~~~~~~~   54 (434)
T PRK05159         21 LAGWVHEIRDLG--GIKFLLLRDRTG-IIQVVVPKKK   54 (434)
T ss_pred             EEEEEEEEECCC--CCEEEEEEECCC-CEEEEEECCC
T ss_conf             989887288179--859999996980-2899997998


No 76 
>PRK08526 threonine dehydratase; Provisional
Probab=82.89  E-value=1.5  Score=23.12  Aligned_cols=297  Identities=14%  Similarity=0.114  Sum_probs=148.5

Q ss_pred             CCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCC-CCHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             865054541188769985477507816888888-4558870888559998708785766555789998776411566665
Q gi|254780316|r  111 GIESTGMMCSEKELMLSDDSASIMELPIDAPVG-GRLSDYLELSDPIIDVSLTPNRSDCIGVRGIALDLVAAGLGKLKEI  189 (805)
Q Consensus       111 Gv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G-~~~~~~l~l~D~i~ei~iTpNR~D~ls~~GiARElaa~~~~~l~~~  189 (805)
                      |-..+|+-++++.||+.    ..++.|+.+|.. .+..+.+|  -.++-..  +|-.|+   +-.|++++.-.+..+-+|
T Consensus        77 GNHaqgvA~aa~~lgi~----a~IvmP~~ap~~Kv~~~r~~G--A~Vil~g--~~~~ea---~~~A~~~a~~~g~~~ihp  145 (403)
T PRK08526         77 GNHAQGVAISAKHFGIK----AVIVMPESTPLLKVSGTKALG--AEVILKG--DNFDEA---YAFALEYAKENNLTFIHP  145 (403)
T ss_pred             CHHHHHHHHHHHHHCCC----EEEEECCCCCHHHHHHHHHCC--CEEEEEC--CCHHHH---HHHHHHHHHHHCCCCCCC
T ss_conf             62899999999970998----899956668699999998269--8899978--985899---999999998604305483


Q ss_pred             CCCCCCC---CCCCCCEEEEEEE--CCCHHHHHHHCCCCCCCCCCCCHHHHHH---HHHHCCCCCHHHHHHHHHHHHHHC
Q ss_conf             5456677---7777741589840--7311123320112322455663778788---886401321039999989998608
Q gi|254780316|r  190 NISCPLS---SESIPLEIKFDLD--DSSLCKGFAMCCVKGVRNNVAPNWMRQR---LKAVGLRSISALVDITNYVSLDRG  261 (805)
Q Consensus       190 ~~~~~~~---~~~~~~~i~v~i~--~~~~c~~y~~~~i~~v~~~~SP~wl~~r---L~~~Gir~inniVDitNyvmle~G  261 (805)
                       +..+..   ......++--...  |.-.+|.=.|-.+.|+-     .|++..   ..-+|+-|.+.-   +-|-.+..|
T Consensus       146 -fdd~~vIaGqGTiglEileq~~d~D~vvvpvGGGGLisGia-----~a~K~~~P~ikViGVEpe~a~---~m~~Sl~~g  216 (403)
T PRK08526        146 -FEDEEVMAGQGTIALEMLDEISDLDMIVVPVGGGGLISGIA-----SAAKQINPNIKIIGVGAKGAP---AMKESFHAK  216 (403)
T ss_pred             -CCCHHHHCCCCCHHHHHHHHCCCCCEEEECCCCCCHHHHHH-----HHHHHHCCCCCEEEECCCCCH---HHHHHHHCC
T ss_conf             -57865762532389999975568998998588861689999-----999862998838996647876---899998769


Q ss_pred             CCEEEECCCCCCCEEEEEECCCCCCHHHH----------HHHCC-----CCCCCCEEEECCCCCCCCHHHCCCCCCCCCC
Q ss_conf             70000010223332688623554311455----------42011-----2454320000256763100111355312013
Q gi|254780316|r  262 YPSHVFDASRISDVLTVRRACSGEKILAL----------DNQEY-----DLSPDNVVIASDGRIQSIAGIIGGKHAGCDD  326 (805)
Q Consensus       262 qPlHafD~dki~~~i~vr~a~~~E~~~~L----------d~~e~-----~L~~~~lvI~d~~~~ialaGImGg~~s~v~~  326 (805)
                      +|...-..+.+.+.+-++...+ .+|-.+          ++.+.     .|-+..=+|+.+..++++|+++.+.......
T Consensus       217 ~~v~~~~~~tiaDGlav~~~g~-~tf~i~~~~vD~iv~V~e~eI~~A~~~l~e~~k~vvEpaGA~~lAAll~~~~~~~~g  295 (403)
T PRK08526        217 KIKNSKSVRTIADGIAVRDASP-ITLAIILECVDDFVQVDDEEIANAILFLLEKQKIVVEGAGAAGVAALLHQKINLQKG  295 (403)
T ss_pred             CCEECCCCCCEECCCCCCCCCH-HHHHHHHHCCCCEEEECHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCC
T ss_conf             9453488782403423576662-569999970896799799999999999998566442574379999997276201169


Q ss_pred             CCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCEEC
Q ss_conf             67269999715787888778876165401554413455301358899988875212334555652587413554310000
Q gi|254780316|r  327 NTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLILSLCGGTASDICIARNITYKPRKIVF  406 (805)
Q Consensus       327 ~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li~e~~gg~~~~~~~~~~~~~~~~~I~l  406 (805)
                      .+--++|=-++.|+..+++-..|--....-.+||.=-+  .-..-+|.+++.+|.+. ++.+..+........      +
T Consensus       296 k~Vv~ilsGGNiD~~~l~~ii~r~l~~~gr~~~~~v~~--~d~pG~l~~~~~~i~~~-~~ni~~~~~~r~~~~------~  366 (403)
T PRK08526        296 AKIGVVLSGGNIDVQMLNVIIEKGLIKSYRKMKLHVTL--VDKPGALMGLTDILKIA-NANIVKIDYDRFSTK------L  366 (403)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEEC--CCCCCHHHHHHHHHCCC-CCCEEEEEEEECCCC------C
T ss_conf             97999971588898899999999888559989999986--88996799999997258-995799998862577------8


Q ss_pred             CCCHHHHHHCCCCC----HHHHHHHHHHHHHHHHC
Q ss_conf             43113333113458----78999999984022210
Q gi|254780316|r  407 MNSEVKRLSGIDVP----IEDSLRILERLGFSVIG  437 (805)
Q Consensus       407 ~~~~i~~ilG~~i~----~~ei~~iL~~Lgf~v~~  437 (805)
                      +.....=.++++..    .+++.+.|+.-||.+..
T Consensus       367 ~~~~~~v~~~~Et~~~~h~~~l~~~l~~~G~~~~~  401 (403)
T PRK08526        367 DYGDANISITLETKGKEHQEEIRKILTEKGFNFYE  401 (403)
T ss_pred             CCCCEEEEEEEEECCHHHHHHHHHHHHHCCCCEEE
T ss_conf             87736999999949999999999999987998784


No 77 
>PRK12304 thrS threonyl-tRNA synthetase; Reviewed
Probab=82.33  E-value=2.4  Score=21.64  Aligned_cols=146  Identities=14%  Similarity=0.132  Sum_probs=86.2

Q ss_pred             HHHHHHCCCCC-HHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCC-C-CCCCCCCCCCCCCC
Q ss_conf             13333113458-789999999840222103456236640345433440256767676535233-4-66765544345767
Q gi|254780316|r  410 EVKRLSGIDVP-IEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQ-I-KSEPLPLTQVEDKR  486 (805)
Q Consensus       410 ~i~~ilG~~i~-~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGYdn-I-p~~~l~~~~~~~~~  486 (805)
                      .+.|+-|+.++ +++....|+++.=--+.+          +|. |-.+-|       ++-++. + |..|    -. .++
T Consensus       181 ~LqRIYG~af~~k~~L~~~l~~~eEakkRD----------HRk-lGkel~-------LF~f~~~~g~G~~----~w-lP~  237 (604)
T PRK12304        181 MLTRIYGIAFADKESLKDYLFIIEEAKKRD----------HRK-LGVEMK-------LFTFDDEIGAGLP----IW-LPK  237 (604)
T ss_pred             CEEEEEEEECCCHHHHHHHHHHHHHHHHCC----------HHH-HHHHCC-------CEECCCCCCCCCE----EE-CCC
T ss_conf             038999984199999999999999998667----------888-877455-------1562554588753----68-377


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH----HHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCC
Q ss_conf             899889546789887877877402321004825765520----0000000246776432101512211067764321015
Q gi|254780316|r  487 NLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFG----GGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDR  562 (805)
Q Consensus       487 ~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~----~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r  562 (805)
                      .....+.+.+.+|+.....||+||.|-.+.+.+.-+.-|    +.++... . -+..+.=.|+|.--|+.....+... |
T Consensus       238 G~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SGH~~~Y~e~Mf~-~-~~d~~~y~lKPMNCP~H~~if~~~~-r  314 (604)
T PRK12304        238 GARLRSKLEHLLYKAHRLRGYEPVRGPEILKSDVWKISGHYANYKENMYF-T-TIDEQEYGIKPMNCVGHIKVYQSDL-R  314 (604)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEECCCCCCCHHHHHCCCHHHHHCCCCCE-E-ECCCCEEECCCCCCHHHHHHHHCCC-C
T ss_conf             54999999999999999829968038654558887305515321057644-5-0577433036779574999986277-4


Q ss_pred             CCC--HHHHHHHCCCCCCCCC
Q ss_conf             861--1345430244447775
Q gi|254780316|r  563 AIA--DFAIFEVSHVYENDTP  581 (805)
Q Consensus       563 ~~~--~i~lFEiG~Vf~~~~~  581 (805)
                      ..+  .+|++|+|.||+.+.+
T Consensus       315 SYRdLPlR~aEfg~~hR~E~S  335 (604)
T PRK12304        315 SYRDLPLKFFEYGVVHRHEKS  335 (604)
T ss_pred             CHHHCCHHHHHCCCEECCCCC
T ss_conf             444355554543532026777


No 78 
>PRK06382 threonine dehydratase; Provisional
Probab=79.68  E-value=2.5  Score=21.57  Aligned_cols=296  Identities=15%  Similarity=0.101  Sum_probs=142.6

Q ss_pred             CCCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCCC-CHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             58650545411887699854775078168888884-55887088855999870878576655578999877641156666
Q gi|254780316|r  110 RGIESTGMMCSEKELMLSDDSASIMELPIDAPVGG-RLSDYLELSDPIIDVSLTPNRSDCIGVRGIALDLVAAGLGKLKE  188 (805)
Q Consensus       110 rGv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G~-~~~~~l~l~D~i~ei~iTpNR~D~ls~~GiARElaa~~~~~l~~  188 (805)
                      .|...+|+-++++.||+.-    .+++|+.+|... +..+.+|  -.++-..  .+-.|+   +-.|++++.-.+..+-+
T Consensus        75 aGNHaqgvA~aa~~lgi~a----~IvmP~~tp~~Kv~~~r~~G--A~Vil~g--~~~dea---~~~A~~~a~e~g~~~Ih  143 (400)
T PRK06382         75 AGNHAQGVAYAASINGIDA----KIVMPEYTIPQKVNAVEAYG--AHVILTG--RDYDEA---HRYADKIAMDENRTFIE  143 (400)
T ss_pred             CCCHHHHHHHHHHHHCCCE----EEEECCCCCHHHHHHHHHCC--CEEEEEC--CCCHHH---HHHHHHHHHHHCCEECC
T ss_conf             9946999999999839988----99917889999999998559--7899977--764699---99999999983976258


Q ss_pred             CCCCCCCCCC---CCCCEEEEEEE--CCCHHHHHHHCCCCCCCCCCCCHHHHHH---HHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             5545667777---77741589840--7311123320112322455663778788---88640132103999998999860
Q gi|254780316|r  189 INISCPLSSE---SIPLEIKFDLD--DSSLCKGFAMCCVKGVRNNVAPNWMRQR---LKAVGLRSISALVDITNYVSLDR  260 (805)
Q Consensus       189 ~~~~~~~~~~---~~~~~i~v~i~--~~~~c~~y~~~~i~~v~~~~SP~wl~~r---L~~~Gir~inniVDitNyvmle~  260 (805)
                      | +..+....   ....++--...  |.-.+|.=.|-.+.|+..     +++..   ..-+|+-|.+.   -+-|--+.-
T Consensus       144 p-fdd~~vIaGqGTiglEIleq~pd~D~vvvpvGGGGLisGia~-----a~K~~~P~ikViGVEpe~a---~~~~~sl~~  214 (400)
T PRK06382        144 A-FNDRWVISGQGTIGLEIMEDLPDLDQIIVPVGGGGLISGIAL-----AAKHINPNVKIIGIESELS---DSMKASLRE  214 (400)
T ss_pred             C-CCCHHHHHCCHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH-----HHHHHCCCCEEEEECCCCC---HHHHHHHHC
T ss_conf             8-898468707305999999866899989993687158899999-----9998599975999796898---789999877


Q ss_pred             CCCEEEECCCCCCCEEEEEECCCCCCHHHH----------HHHC-----CCCCCCCEEEECCCCCCCCHHHCCCCCCCCC
Q ss_conf             870000010223332688623554311455----------4201-----1245432000025676310011135531201
Q gi|254780316|r  261 GYPSHVFDASRISDVLTVRRACSGEKILAL----------DNQE-----YDLSPDNVVIASDGRIQSIAGIIGGKHAGCD  325 (805)
Q Consensus       261 GqPlHafD~dki~~~i~vr~a~~~E~~~~L----------d~~e-----~~L~~~~lvI~d~~~~ialaGImGg~~s~v~  325 (805)
                      |+|...-..+.+.+.+-++...+ .+|-.+          ++.+     +.|-+..=+++.+..++++|++|-+.. .+.
T Consensus       215 g~~v~~~~~~tiaDGiav~~~G~-~tf~i~~~~vD~vv~V~e~eI~~A~~~l~e~~k~vvEpaGA~~lAAll~~~~-~~~  292 (400)
T PRK06382        215 GKIVAHTSGVSICDGISVKYPGD-LTFDIAKNYVDDIVTVTEESVSKAIYKLFEREKIVAEPSGAVGLAAIMEGKV-DVK  292 (400)
T ss_pred             CCCCCCCCCCEEECCCCCCCCCC-CCHHHHHHCCCCEEEECHHHHHHHHHHHHHHCCEEEECHHHHHHHHHHHCCH-HHC
T ss_conf             99620588773642403565551-1599998408977998999999999999996395882679999999984906-537


Q ss_pred             CCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCEE
Q ss_conf             36726999971578788877887616540155441345530135889998887521233455565258741355431000
Q gi|254780316|r  326 DNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLILSLCGGTASDICIARNITYKPRKIV  405 (805)
Q Consensus       326 ~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li~e~~gg~~~~~~~~~~~~~~~~~I~  405 (805)
                      ..+.-++|=-++.|+...++-..|--....-..||.=-+  .-..-+|.+++++|.+. ++.+..+..+....      .
T Consensus       293 gk~Vv~vlsGGNiD~~~l~~ii~r~l~~~gr~~~~~v~i--~d~pG~L~~~~~~i~~~-~~ni~~i~~~r~~~------~  363 (400)
T PRK06382        293 GKKVAIVVSGGNINPLLMSKIIYKELENLGQLVRIECNI--PDRPGNLYRIANAIASN-GGNIYHAEVDNLRK------E  363 (400)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEEC--CCCCCHHHHHHHHHHCC-CCCEEEEEEEEECC------C
T ss_conf             984999963788797899999999888639979999986--88997799999997068-99579999876025------5


Q ss_pred             CCCCHHHHHHCCCCC----HHHHHHHHHHHHHHHH
Q ss_conf             043113333113458----7899999998402221
Q gi|254780316|r  406 FMNSEVKRLSGIDVP----IEDSLRILERLGFSVI  436 (805)
Q Consensus       406 l~~~~i~~ilG~~i~----~~ei~~iL~~Lgf~v~  436 (805)
                      ++.....=.++++..    .+++.+-|+..||+++
T Consensus       364 ~~~~~~~v~~~iEt~~~~h~~~i~~~l~~~G~~~~  398 (400)
T PRK06382        364 TPPGFQSVTFTVNVRGQDHLDRILNALREMGYKFN  398 (400)
T ss_pred             CCCCEEEEEEEEEECCHHHHHHHHHHHHHCCCEEE
T ss_conf             78762689999980999999999999998789683


No 79 
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=79.10  E-value=1.5  Score=23.10  Aligned_cols=76  Identities=18%  Similarity=0.268  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCH---HHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHH
Q ss_conf             954678988787787740232100482---57655200000000246776432101512211067764321015861134
Q gi|254780316|r  492 QSRTRYVKRVLASRAMMEVVNWSFISK---EQSVLFGGGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFA  568 (805)
Q Consensus       492 ~~~~~~ir~~L~~~Gf~Ev~tysl~s~---~~~~~~~~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~  568 (805)
                      .+..+.+|++|...||.|+-|-.|...   +.+.      ..+.=.|-+..++- ||.|  |.|....--  --|..  |
T Consensus       780 S~Vi~aiR~~L~~~GFlEVETPiLq~~~GGA~AR------PFlThsna~d~~~Y-LriA--PELflKRLm--VGGfe--R  846 (1099)
T PRK02983        780 SAVLRAVRETLVAKGFLEVETPILQQIHGGANAR------PFLTHINAYDLDLY-LRIA--PELYLKRLC--VGGVE--R  846 (1099)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCC------CCCCCCCCCCCCCE-EECC--HHHHHHHHH--HCCCC--C
T ss_conf             9999999999987898895575467788875678------53010336786614-5148--089999998--64863--1


Q ss_pred             HHHHCCCCCCCC
Q ss_conf             543024444777
Q gi|254780316|r  569 IFEVSHVYENDT  580 (805)
Q Consensus       569 lFEiG~Vf~~~~  580 (805)
                      +||||++|.++.
T Consensus       847 VFEI~RcFRNEg  858 (1099)
T PRK02983        847 VFELGRAFRNEG  858 (1099)
T ss_pred             CEEECCCCCCCC
T ss_conf             134325446799


No 80 
>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=78.00  E-value=2.9  Score=21.05  Aligned_cols=25  Identities=20%  Similarity=0.359  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             5467898878778774023210048
Q gi|254780316|r  493 SRTRYVKRVLASRAMMEVVNWSFIS  517 (805)
Q Consensus       493 ~~~~~ir~~L~~~Gf~Ev~tysl~s  517 (805)
                      +..+.+|++|...||.|+-|=.+++
T Consensus        13 ~i~~~iR~ff~~~gF~Ev~TPiL~~   37 (329)
T cd00775          13 KIISYIRKFLDDRGFLEVETPMLQP   37 (329)
T ss_pred             HHHHHHHHHHHHCCCEEEECCCCCC
T ss_conf             9999999999988988997986556


No 81 
>PRK03772 threonyl-tRNA synthetase; Validated
Probab=76.74  E-value=2.5  Score=21.53  Aligned_cols=239  Identities=13%  Similarity=0.104  Sum_probs=117.9

Q ss_pred             HHHHHHCCCCCH-HHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCC-CCCCCCCCCCCCCCC
Q ss_conf             133331134587-899999998402221034562366403454334402567676765352334-667655443457678
Q gi|254780316|r  410 EVKRLSGIDVPI-EDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQI-KSEPLPLTQVEDKRN  487 (805)
Q Consensus       410 ~i~~ilG~~i~~-~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGYdnI-p~~~l~~~~~~~~~~  487 (805)
                      .+.|+-|+.++. ++....|+++.=--..+          +|. |-.+       .-++-++.. |..    +-. .++.
T Consensus       214 ~LqRIYG~af~~k~~L~~~l~~~eEakkRD----------HRk-lGke-------l~LF~f~~~~pG~----~fw-lP~G  270 (642)
T PRK03772        214 MLQRIYGTAWADKKALNAYLQRLEEAAKRD----------HRK-IGKQ-------LDLYHMQEEAPGM----VFW-HNDG  270 (642)
T ss_pred             HHEEEEEEECCCHHHHHHHHHHHHHHHHCC----------HHH-HHHH-------CCCEEECCCCCCC----EEE-CCCH
T ss_conf             007999986189899999999999998658----------888-8775-------2204754658876----366-5858


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH----HHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCC
Q ss_conf             99889546789887877877402321004825765520----00000002467764321015122110677643210158
Q gi|254780316|r  488 LSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFG----GGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRA  563 (805)
Q Consensus       488 ~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~----~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~  563 (805)
                      ....+.+.+.+|+.....||+||.|-.+.+.+.-+.-+    +.++...+.  ...+.=.|||.--|+.....+... |.
T Consensus       271 ~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SGH~~~Y~e~Mf~~~--~e~~ey~lKPMNCP~H~~iy~~~~-rS  347 (642)
T PRK03772        271 WTIFRELEVFVRSKLKEYQYQEVKGPFMMDRVLWEKTGHWDNYADAMFTTS--SENREYAIKPMNCPGHVQIFNQGL-KS  347 (642)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCHHCCHHHHHHCCHHHHHHCCCCCCC--CCHHHHCCCCCCCHHHHHHHHCCC-CC
T ss_conf             899999999999999986985985543213778873444766410342234--201443046778734889986166-43


Q ss_pred             CC--HHHHHHHCCCCCCCCCCCCCEEHHHHC---------------------------------CCCCCCCCCCCCCCC-
Q ss_conf             61--134543024444777544310002210---------------------------------354310124620234-
Q gi|254780316|r  564 IA--DFAIFEVSHVYENDTPEGQKYMAAGIR---------------------------------KGSSGIEGSGRLWSD-  607 (805)
Q Consensus       564 ~~--~i~lFEiG~Vf~~~~~~~~~~~~~~~~---------------------------------~~~~~~~~~g~~~~~-  607 (805)
                      ..  .+|++|.|.||+.+.++.    +.|+.                                 ....++....-..+. 
T Consensus       348 YRdLPlR~aEfg~~~R~E~SG~----L~GL~RVR~FtqdDaHIFC~~dQi~~Ei~~~l~~~~~vy~~fGf~~~~~~LStr  423 (642)
T PRK03772        348 YRDLPLRMAEFGSCHRNEPSGS----LHGLMRVRGFTQDDAHIFCTEEQIRDEVNSCIKMVYDMYSTFGFEKIVVKLSTR  423 (642)
T ss_pred             HHHCCHHHHHHHHHHCCCCCCC----CCCCCCCCCCCCCCCEEECCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCC
T ss_conf             4436545554113431666655----347456889987884355378999999999999999999973986389996268


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCEEEEEE--CCEEEEEEEEEECHHHHHHCCCC
Q ss_conf             544333314688875311111110145333033058865678981699998--79299999854778999966879
Q gi|254780316|r  608 KSEERCRFVDLFDAKADALSVIEPFVSLDSLRFESGAPSWYHPGRSGIIKT--SAEIVLGYFGEFHPNILDFFGLS  681 (805)
Q Consensus       608 ~~~~~~~~~df~dlKg~v~~ll~~l~~~~~~~~~~~~~~~~hPgrsa~I~~--~gk~iiG~iG~ihP~i~~~~~i~  681 (805)
                      ....-.....|-.+-+.+...++..+.  .+...+.+..+|=|.---.+..  +.+.-+|.+ +++-.+-++|++.
T Consensus       424 pek~~G~~e~W~~AE~~L~~aL~~~g~--~y~~~~GegAFYGPKID~~v~DalgR~wq~~Ti-QlDF~lP~RF~l~  496 (642)
T PRK03772        424 PEKRIGSDEMWDRAEADLAVALEENNI--PFEYQPGEGAFYGPKIEFTLYDCLDRAWQCGTV-QLDFSLPGRLSAS  496 (642)
T ss_pred             CHHCCCCHHHHHHHHHHHHHHHHHCCC--CEEECCCCCCCCCCCCCEEEECCCCCEEEECCC-EEECCCHHHCCCE
T ss_conf             220258888999999999999997399--704556763444553025997078976880232-4300135442888


No 82 
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=76.38  E-value=2.7  Score=21.27  Aligned_cols=149  Identities=13%  Similarity=0.158  Sum_probs=85.6

Q ss_pred             HHHHHHCCCCC-HHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             13333113458-78999999984022210345623664034543344025676767653523346676554434576789
Q gi|254780316|r  410 EVKRLSGIDVP-IEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQIKSEPLPLTQVEDKRNL  488 (805)
Q Consensus       410 ~i~~ilG~~i~-~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGYdnIp~~~l~~~~~~~~~~~  488 (805)
                      .+.|+-|+.++ .++....|+++.=--+.+          +|. |-.+-       -++-++.. +.-+|  -. .++..
T Consensus       211 ~LqRIYG~af~~k~~L~~~l~~~eEakkRD----------HRk-lGkel-------~LF~f~~~-~pGl~--~w-~P~G~  268 (639)
T PRK00413        211 MLQRIYGTAWADKEDLDAYLHRLEEAEKRD----------HRK-LGKEL-------DLFSFQEE-GPGLP--FW-HPKGW  268 (639)
T ss_pred             CEEEEEEEECCCHHHHHHHHHHHHHHHHCC----------HHH-HHHHC-------CCEEECCC-CCCCE--EE-CCCHH
T ss_conf             038999985199899999999999988528----------888-87743-------51570366-88764--66-37689


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH----HHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCC
Q ss_conf             9889546789887877877402321004825765520----000000024677643210151221106776432101586
Q gi|254780316|r  489 SLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFG----GGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAI  564 (805)
Q Consensus       489 ~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~----~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~  564 (805)
                      ...+.+.+.+|+.....||+||.|-.+.+.+.-+.-|    +.++..... -...+.=.|||---|+......... |..
T Consensus       269 ~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SGHw~~Y~e~Mf~~~-~~~~~~~~lKPMNCP~H~~if~~~~-~SY  346 (639)
T PRK00413        269 IIRNELEDYMRRRHLKAGYQEVNTPHILDRSLWETSGHWDHYRENMFPTM-SDDGEDYALKPMNCPGHILIFKSGL-RSY  346 (639)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCHHHHCCCCCCCE-ECCCCEEEECCCCCCCHHHHHHCCC-CCH
T ss_conf             99999999999999986985983641346889965474223225422324-0152103204668700335644355-355


Q ss_pred             C--HHHHHHHCCCCCCCCCC
Q ss_conf             1--13454302444477754
Q gi|254780316|r  565 A--DFAIFEVSHVYENDTPE  582 (805)
Q Consensus       565 ~--~i~lFEiG~Vf~~~~~~  582 (805)
                      .  .+|++|.|.+|+.+.++
T Consensus       347 RdLPlR~aEfg~~~R~E~SG  366 (639)
T PRK00413        347 RELPLRLAEFGTVHRYEKSG  366 (639)
T ss_pred             HHCCHHHHHHHHHHCCCCCC
T ss_conf             54755666411320567787


No 83 
>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=76.20  E-value=3.3  Score=20.70  Aligned_cols=115  Identities=12%  Similarity=0.090  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             95467898878778774023210048257655200000000246776432101512211067764321015861134543
Q gi|254780316|r  492 QSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFE  571 (805)
Q Consensus       492 ~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lFE  571 (805)
                      ....+.+|+++...||.||-|-.+++..-.    .......+.-.-.....+|++|=---+=..++    -+..  ++||
T Consensus         5 s~i~~~iR~ff~~~~f~EV~TP~l~~~~~~----~~~~~f~~~~~~~~~~~~L~~Spel~~k~ll~----~g~~--~if~   74 (269)
T cd00669           5 SKIIKAIRDFMDDRGFLEVETPMLQKITGG----AGARPFLVKYNALGLDYYLRISPQLFKKRLMV----GGLD--RVFE   74 (269)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCEEECCCCC----CCCCEEEEECCCCCCEEEECCCHHHHHHHHHH----CCCC--CEEE
T ss_conf             999999999999889899879853057898----76742573137899407734388999999986----5888--6799


Q ss_pred             HCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             02444477754431000221035431012462023454433331468887531111111014
Q gi|254780316|r  572 VSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFV  633 (805)
Q Consensus       572 iG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~  633 (805)
                      ||++|+.+.. ...+..              .+|.-.|...  ..|+-++...++.++..+.
T Consensus        75 i~~~FR~e~~-~~rH~~--------------EFtmlE~y~~--~~d~~~~m~~~e~li~~~~  119 (269)
T cd00669          75 INRNFRNEDL-RARHQP--------------EFTMMDLEMA--FADYEDVIELTERLVRHLA  119 (269)
T ss_pred             EECCCCCCCC-CCCCCH--------------HHHHHHHHCC--CCCHHHHHHHHHHHHHHHH
T ss_conf             8462107898-655434--------------8775787514--8999999999999999999


No 84 
>PRK04483 threonyl-tRNA synthetase; Validated
Probab=75.84  E-value=2.9  Score=21.11  Aligned_cols=147  Identities=12%  Similarity=0.109  Sum_probs=83.7

Q ss_pred             CHHHHHHCCCCCH-HHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCC-CCCCCCCCCCCCCC
Q ss_conf             1133331134587-899999998402221034562366403454334402567676765352334-66765544345767
Q gi|254780316|r  409 SEVKRLSGIDVPI-EDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQI-KSEPLPLTQVEDKR  486 (805)
Q Consensus       409 ~~i~~ilG~~i~~-~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGYdnI-p~~~l~~~~~~~~~  486 (805)
                      ..++|+-|+.+++ ++..+.|+++.=--+.+          +|. |-.+-       -++-++.. |.  +|  -. .++
T Consensus       213 ~~LqRIYG~af~~k~~L~~yl~~~eEakkRD----------HRk-lGkel-------~LF~f~~~~pG--~~--~w-lP~  269 (634)
T PRK04483        213 EQLQRIYGTAWADKKQLDAYILRMEEADKRD----------HRK-IGKAQ-------DLFHLQEEAPG--LV--FW-HPK  269 (634)
T ss_pred             CCEEEEEEEEECCHHHHHHHHHHHHHHHHCC----------HHH-HHHHC-------CEEEECCCCCC--CE--EE-CCC
T ss_conf             1028999995089899999999999988658----------888-75421-------10673377886--43--88-166


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH----HHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCC
Q ss_conf             899889546789887877877402321004825765520----0000000246776432101512211067764321015
Q gi|254780316|r  487 NLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFG----GGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDR  562 (805)
Q Consensus       487 ~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~----~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r  562 (805)
                      .....+.+.+.+|+.....||+||.|-.+.+.+.-+.-|    +.++...  -....+.=.|||.--|+......... |
T Consensus       270 G~~i~~~le~~~r~~~~~~Gy~eV~tP~i~~~~Lw~~SGH~~~Y~e~Mf~--~~~~~~~~~lKPMNCP~H~~if~~~~-r  346 (634)
T PRK04483        270 GWSLWQVVEQYMRKVYRDSGYGEVRCPQILDVSLWQKSGHWDNYQDAMFF--TESEKRTYAVKPMNCPGHVQVFNQGL-H  346 (634)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCEECCHHHHHHCCCHHHHHHCCCE--ECCCCCEEEECCCCCHHHHHHHHCCC-C
T ss_conf             89999999999999999829959988625137787625616455303713--42554035515768564879987177-4


Q ss_pred             CCCH--HHHHHHCCCCCCCCC
Q ss_conf             8611--345430244447775
Q gi|254780316|r  563 AIAD--FAIFEVSHVYENDTP  581 (805)
Q Consensus       563 ~~~~--i~lFEiG~Vf~~~~~  581 (805)
                      ..++  +|++|+|.+|+.+.+
T Consensus       347 SYRdLPlR~aE~g~~~R~E~S  367 (634)
T PRK04483        347 SYRDLPIRYGEFGACHRNEPS  367 (634)
T ss_pred             CHHHCCHHHHHCCCEEECCCC
T ss_conf             444343665543302205677


No 85 
>KOG0556 consensus
Probab=75.70  E-value=1.9  Score=22.37  Aligned_cols=88  Identities=15%  Similarity=0.269  Sum_probs=49.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHH
Q ss_conf             98895467898878778774023210048257655200000000246776432101512211067764321015861134
Q gi|254780316|r  489 SLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFA  568 (805)
Q Consensus       489 ~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~  568 (805)
                      ..+.-.-..+|++|...||.|+.|--+++....    +..+..++.--  ..-.+|-+|  |.|-+..+--  -..+  |
T Consensus       229 riq~gvc~~FRe~L~~kgF~EIhTpKli~asSE----GGanvF~v~Yf--k~~A~LAQS--PQLyKQMaI~--gdf~--r  296 (533)
T KOG0556         229 RIQAGVCFAFREYLRSKGFVEIHTPKLIGASSE----GGANVFRVSYF--KQKAYLAQS--PQLYKQMAIC--GDFE--R  296 (533)
T ss_pred             EHHHHHHHHHHHHHHHCCCCEECCCCCCCCCCC----CCCEEEEEEEC--CCCCHHHCC--HHHHHHHHHH--CCHH--H
T ss_conf             068889999999997568604326320146677----77226899860--675032058--5888778876--0611--0


Q ss_pred             HHHHCCCCCCCCCCCCCEEH
Q ss_conf             54302444477754431000
Q gi|254780316|r  569 IFEVSHVYENDTPEGQKYMA  588 (805)
Q Consensus       569 lFEiG~Vf~~~~~~~~~~~~  588 (805)
                      +||||.||+.+.+....++.
T Consensus       297 VyeIGpVfRAEdSnthRhlt  316 (533)
T KOG0556         297 VYEIGPVFRAEDSNTHRHLT  316 (533)
T ss_pred             EEEECCEEECCCCCHHHHHH
T ss_conf             46523556604464166667


No 86 
>TIGR01127 ilvA_1Cterm threonine dehydratase; InterPro: IPR005789    Serine and threonine dehydratases ,  are functionally and structurally related pyridoxal-phosphate dependent enzymes. L-serine dehydratase () and D-serine dehydratase () catalyze the dehydratation of L-serine (respectively D-serine) into ammonia and pyruvate. Threonine dehydratase () (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism. Threonine synthase () is also a pyridoxal-phosphate enzyme, it catalyzes the transformation of homoserine-phosphate into threonine. It has been shown  that threonine synthase is distantly related to the serine/threonine dehydratases. In all these enzymes, the pyridoxal-phosphate group is attached to a lysine residue.    A form of threonine dehydratase with two copies of the C-terminal domain  is described by . This model describes a phylogenetically distinct which branches with the catabolic threonine dehydratase of E. coli; many members are designated as catabolic for this reason. However, the catabolic form lacks any  domain. Many members of this model are found in species with other isoleucine biosynthetic enzymes.; GO: 0004794 L-threonine ammonia-lyase activity.
Probab=75.54  E-value=5.7  Score=18.98  Aligned_cols=282  Identities=19%  Similarity=0.195  Sum_probs=150.9

Q ss_pred             CCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCCC-CHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             8650545411887699854775078168888884-558870888559998708785766555789998776411566665
Q gi|254780316|r  111 GIESTGMMCSEKELMLSDDSASIMELPIDAPVGG-RLSDYLELSDPIIDVSLTPNRSDCIGVRGIALDLVAAGLGKLKEI  189 (805)
Q Consensus       111 Gv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G~-~~~~~l~l~D~i~ei~iTpNR~D~ls~~GiARElaa~~~~~l~~~  189 (805)
                      |-.-+|-=-|++--|+..    .++.|+.+|+-+ ...+-|| .+.||.=.      |.=-.+-.|.+++...+.-+-+|
T Consensus        57 GNHAQGVA~AA~~~Gi~a----~IVMPE~aP~~Kv~AT~~yG-AEViL~G~------~~DEA~~~A~~~~~~~g~~fvHp  125 (381)
T TIGR01127        57 GNHAQGVALAAKVFGIKA----KIVMPEYAPLSKVKATKSYG-AEVILHGA------DYDEAYALAEELAEEEGRVFVHP  125 (381)
T ss_pred             CCHHHHHHHHHHHCCCCC----EEECCCCCHHHHHHHHHHCC-CEEEECCC------CHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             543789999987618774----68788767357899976269-61898088------70789999999998609878740


Q ss_pred             CCCCCCC---CCCCCCEEEEEEE--CCCHHHHHHHCCCCCCC----------------CCCCCHHHHHHHHHHCCCCCHH
Q ss_conf             5456677---7777741589840--73111233201123224----------------5566377878888640132103
Q gi|254780316|r  190 NISCPLS---SESIPLEIKFDLD--DSSLCKGFAMCCVKGVR----------------NNVAPNWMRQRLKAVGLRSISA  248 (805)
Q Consensus       190 ~~~~~~~---~~~~~~~i~v~i~--~~~~c~~y~~~~i~~v~----------------~~~SP~wl~~rL~~~Gir~inn  248 (805)
                       ++.+.-   ..++.+++-=+..  |.=..|-=.|-.|.||.                -.-+|. |.+            
T Consensus       126 -F~D~~vmAGQGTigLEi~ed~pd~D~viVPVGGGGLISGv~~a~K~~~P~VkvIGV~aE~ap~-m~~------------  191 (381)
T TIGR01127       126 -FDDEYVMAGQGTIGLEIMEDLPDVDTVIVPVGGGGLISGVASAAKKLNPEVKVIGVEAEGAPS-MVE------------  191 (381)
T ss_pred             -CCCCEEEECCCHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHHCCCCEEEEEECCCCHH-HHH------------
T ss_conf             -588778616748999999647981379984178712879999998728994799860278558-999------------


Q ss_pred             HHHHHHHHHHHHCCCEEEECCCCCCCEEEEEECCCCC---------CHHHHHHHCCC-----CCCCCEEEECCCCCCCCH
Q ss_conf             9999989998608700000102233326886235543---------11455420112-----454320000256763100
Q gi|254780316|r  249 LVDITNYVSLDRGYPSHVFDASRISDVLTVRRACSGE---------KILALDNQEYD-----LSPDNVVIASDGRIQSIA  314 (805)
Q Consensus       249 iVDitNyvmle~GqPlHafD~dki~~~i~vr~a~~~E---------~~~~Ld~~e~~-----L~~~~lvI~d~~~~iala  314 (805)
                              -|.-|||-.+=--+.|.+.|.||.+..-.         .+++-|+.|..     |-+..=+++-+.++.++|
T Consensus       192 --------Sl~~Gk~~~v~~~~tiADGIaVk~pG~lTF~i~k~~VD~~V~V~eeEIA~A~~~LLEr~Ki~aEGAGA~gvA  263 (381)
T TIGR01127       192 --------SLREGKIKAVESVDTIADGIAVKKPGDLTFNIVKEYVDEVVAVDEEEIAKAILLLLERAKIVAEGAGAVGVA  263 (381)
T ss_pred             --------HHHCCCEEEECCCCEEECCCEECCCCCCCHHHHHHHCCCEEEECHHHHHHHHHHHHCCCCEEECCCHHHHHH
T ss_conf             --------985199056045641415211637887674789974797088473779999999860774788274589999


Q ss_pred             HHCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCC--CC--CCHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             111355312013672699997157878887788761654015544134--55--30135889998887521233455565
Q gi|254780316|r  315 GIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFER--GV--DLQGMIPVLKHIVSLILSLCGGTASD  390 (805)
Q Consensus       315 GImGg~~s~v~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfER--gv--d~~~~~~al~r~~~Li~e~~gg~~~~  390 (805)
                      =||..+---++-.+.-|++=-.+-|+..+.+=-.| ||  .-++|.=|  ++  |--.   +|.++...+.+. ++.+..
T Consensus       264 A~L~~K~~~~kG~K~~~v~SGGNID~~~l~~iI~k-GL--~~~GR~v~I~~~~~D~PG---~L~~ll~~~A~~-~aNi~~  336 (381)
T TIGR01127       264 AVLEDKVDYVKGKKVAVVVSGGNIDLNLLEKIILK-GL--VKSGRKVRIETVIPDRPG---ALYKLLEVIAEE-RANIVK  336 (381)
T ss_pred             HHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHH-HH--HCCCCEEEEEEEEECCCC---CHHHHHHHHHHH-CCCEEE
T ss_conf             99975403689828999985477686677788655-22--205836999999823898---669999999981-697899


Q ss_pred             CEEEEECCCCCCCEECCCCHHHHHHCCC--CCHHHHHHHHHHHHHHHH
Q ss_conf             2587413554310000431133331134--587899999998402221
Q gi|254780316|r  391 ICIARNITYKPRKIVFMNSEVKRLSGID--VPIEDSLRILERLGFSVI  436 (805)
Q Consensus       391 ~~~~~~~~~~~~~I~l~~~~i~~ilG~~--i~~~ei~~iL~~Lgf~v~  436 (805)
                      +..+..    .+.|..-..+|.=-|=+.  --.+++.+.|..+||++.
T Consensus       337 i~hDR~----~~~~~~G~a~v~~~LEt~g~~H~~ei~~~L~~~Gy~f~  380 (381)
T TIGR01127       337 IEHDRL----SKEIPPGFAKVELELETRGKEHLDEILKVLRDKGYEFK  380 (381)
T ss_pred             EEECCC----CCCCCCCCEEEEEEEEECCHHHHHHHHHHHHHCCCEEC
T ss_conf             997375----77778675389999840886899999999976375442


No 87 
>PRK09350 lysyl-tRNA synthetase; Provisional
Probab=75.01  E-value=2.2  Score=21.93  Aligned_cols=116  Identities=12%  Similarity=0.143  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCHH--HHHHHHHHHHHCC--CCCCC--CCCCCCCCCHHHCHHHHHHHHHCCCC
Q ss_conf             889546789887877877402321004825--7655200000000--24677--64321015122110677643210158
Q gi|254780316|r  490 LQQSRTRYVKRVLASRAMMEVVNWSFISKE--QSVLFGGGQRELE--ILNPI--SADMSNMRTSLLPGLLKATGRNVDRA  563 (805)
Q Consensus       490 ~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~--~~~~~~~~~~~i~--l~NPl--S~e~s~lR~SLlp~LL~~~~~N~~r~  563 (805)
                      ...+..+.+|++|...||.||-|=.|+...  ...     ..+.+  ..-|-  ....-+|++|  |.|-.-..  +.-|
T Consensus        18 ~Rs~i~~~iR~ff~~~gFlEVeTP~L~~~t~~~~~-----~~~f~~~~~~~~~~~~~~~yL~~S--Pql~~k~l--~~~G   88 (325)
T PRK09350         18 KRAAIIAEIRRFFADRGVLEVETPAMSQATVTDIH-----LVPFETRFVGPGHSQGKTLWLMTS--PEYHMKRL--LAAG   88 (325)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCC-----CCCEEEECCCCCCCCCCCEEEECC--HHHHHHHH--HHCC
T ss_conf             99999999999999889689779842577887646-----762221025655456766455079--19999999--8667


Q ss_pred             CCHHHHHHHCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             6113454302444477754431000221035431012462023454433331468887531111111014
Q gi|254780316|r  564 IADFAIFEVSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFV  633 (805)
Q Consensus       564 ~~~i~lFEiG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l~  633 (805)
                      ..  ++||||++|+.+... ..+..-              +|...|..  ...|+.++-..++.++....
T Consensus        89 ~~--rvfqI~~~FR~E~~~-~~H~pE--------------FtmlE~~~--~~~d~~d~m~~~e~ll~~~~  139 (325)
T PRK09350         89 SG--PIFQLCRSFRNEEAG-RYHNPE--------------FTMLEWYR--PHYDMYRLMNEVDDLLQQVL  139 (325)
T ss_pred             CC--CEEEEEHHHCCCCCC-CCCCCH--------------HHHHHHHH--HCCCHHHHHHHHHHHHHHHH
T ss_conf             88--558961132289998-765737--------------78889998--15489999999999999997


No 88 
>pfam09840 DUF2067 Uncharacterized protein conserved in archaea (DUF2067). This domain, found in various archaeal proteins, has no known function.
Probab=74.76  E-value=2.6  Score=21.38  Aligned_cols=62  Identities=26%  Similarity=0.301  Sum_probs=49.2

Q ss_pred             CCEECCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCC
Q ss_conf             1000043113333113458789999999840222103456236640345433440256767676535
Q gi|254780316|r  402 RKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYG  468 (805)
Q Consensus       402 ~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyG  468 (805)
                      ....+..+.+.+-+|..++.+-+.+.|+.||+++...++.+...+| |    ..-.++++++.++|-
T Consensus        69 gl~~y~l~~l~re~~~pvp~~~L~~aL~llG~~~e~~~~~i~T~ap-~----eev~e~~~~L~eiy~  130 (190)
T pfam09840        69 GLFEYPLSDLFRELGRPVPPDLLADALRLLGYRVEVRGDVIKTNAP-L----EEVVEVARELSEIYK  130 (190)
T ss_pred             CCEEECHHHHHHHHCCCCCHHHHHHHHHHCCCEEEEECCEEEECCC-H----HHHHHHHHHHHHHHH
T ss_conf             8479719999997079999899999999679568976775673697-9----999999999999999


No 89 
>PRK08198 threonine dehydratase; Provisional
Probab=74.18  E-value=2.4  Score=21.68  Aligned_cols=292  Identities=16%  Similarity=0.186  Sum_probs=143.0

Q ss_pred             CCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCCC-CHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             8650545411887699854775078168888884-558870888559998708785766555789998776411566665
Q gi|254780316|r  111 GIESTGMMCSEKELMLSDDSASIMELPIDAPVGG-RLSDYLELSDPIIDVSLTPNRSDCIGVRGIALDLVAAGLGKLKEI  189 (805)
Q Consensus       111 Gv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G~-~~~~~l~l~D~i~ei~iTpNR~D~ls~~GiARElaa~~~~~l~~~  189 (805)
                      |...+|+-++++.+|+.    ..+++|+.+|.-. ...+.||  -.++-..  ++--|   .+-.|++++.-.+..+-+|
T Consensus        81 GNHaqgvA~aa~~~gi~----a~IvmP~~ap~~Ki~~~r~~G--A~Vil~G--~~~~e---a~~~A~~~a~e~g~~~ihp  149 (406)
T PRK08198         81 GNHAQGVAYAASLLGIK----ATIVMPETAPLSKVQATKSYG--AEVVLHG--DVYDE---ALAAALELAEETGATFVHP  149 (406)
T ss_pred             CHHHHHHHHHHHHCCCC----EEEEECCCCCHHHHHHHHHCC--CEEEEEC--CCHHH---HHHHHHHHHHHCCCEEECC
T ss_conf             76999999999981998----899936778899999998479--8899969--98689---9999999997438675389


Q ss_pred             CCCCCCCCC---CCCCEEEEEEE--CCCHHHHHHHCCCCCCCCCCCCHHHHHH---HHHHCCCCCHHHHHHHHHHHHHHC
Q ss_conf             545667777---77741589840--7311123320112322455663778788---886401321039999989998608
Q gi|254780316|r  190 NISCPLSSE---SIPLEIKFDLD--DSSLCKGFAMCCVKGVRNNVAPNWMRQR---LKAVGLRSISALVDITNYVSLDRG  261 (805)
Q Consensus       190 ~~~~~~~~~---~~~~~i~v~i~--~~~~c~~y~~~~i~~v~~~~SP~wl~~r---L~~~Gir~inniVDitNyvmle~G  261 (805)
                       +..+....   ....++--...  |.-.+|.=.|-.+.|+.     .|++..   ..-+|.-|.+.   -+-|.-+..|
T Consensus       150 -fdd~~viaGqGTiglEileq~p~~D~vvvpvGGGGLiaGia-----~a~K~~~P~ikViGVEpe~a---~~~~~Sl~ag  220 (406)
T PRK08198        150 -FDDPDVIAGQGTIGLEILEDLPDVDTVVVPIGGGGLISGVA-----TAVKALRPNVRVIGVQAEGA---PAMPLSLAAG  220 (406)
T ss_pred             -CCCHHHHCCHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHH-----HHHHHHCCCCCEEEEEECCC---HHHHHHHHCC
T ss_conf             -89954660101499999986777787886378626889999-----99998689970899965787---6899999849


Q ss_pred             CCEEEECCCCCCCEEEEEECCCCCCHHHHHH---HCCCCCC------------CCEEEECCCCCCCCHHHCCCCCCCCCC
Q ss_conf             7000001022333268862355431145542---0112454------------320000256763100111355312013
Q gi|254780316|r  262 YPSHVFDASRISDVLTVRRACSGEKILALDN---QEYDLSP------------DNVVIASDGRIQSIAGIIGGKHAGCDD  326 (805)
Q Consensus       262 qPlHafD~dki~~~i~vr~a~~~E~~~~Ld~---~e~~L~~------------~~lvI~d~~~~ialaGImGg~~s~v~~  326 (805)
                      +|...=..+.+.+.+.|+...+ .+|..+..   .-...++            ..=+++.+..++++|+++-+.. .+..
T Consensus       221 ~~v~~~~~~tiADGiav~~~G~-~tf~i~~~~vD~vv~V~e~eI~~A~~~l~e~~k~vvEpaGA~~lAAll~~~~-~~~g  298 (406)
T PRK08198        221 RPVELESVDTIADGIAVKRPGD-LTFPIIRELVDDVVTVSDEEIARAILLLLERAKLVVEGAGAVSVAALLSGKV-KVRG  298 (406)
T ss_pred             CCEECCCCCEEECCCCCCCCCH-HHHHHHHHCCCCEEEECHHHHHHHHHHHHHHCCEEEECHHHHHHHHHHHCCC-CCCC
T ss_conf             9565599997971144687778-8999999629978998999999999999997491774289999999984773-3479


Q ss_pred             CCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECC---CCCCC
Q ss_conf             672699997157878887788761654015544134553013588999888752123345556525874135---54310
Q gi|254780316|r  327 NTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLILSLCGGTASDICIARNIT---YKPRK  403 (805)
Q Consensus       327 ~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li~e~~gg~~~~~~~~~~~~---~~~~~  403 (805)
                      .+--+++=-++.|+...++-..|--+...-..||.=-+  .-..=+|.+++.+|.+. ++.+.++.......   .....
T Consensus       299 k~Vv~ilsGGNiD~~~l~~i~er~l~~~gr~~~~~v~i--~d~PG~l~~~~~~i~~~-~anI~~i~h~R~~~~~~~~~~~  375 (406)
T PRK08198        299 KKVVAVLSGGNIDVLLLSRVIERGLVAAGRYLKLRVEL--PDRPGQLAKLLSIIAEL-RANVIDVDHDRFSPGLRLGEVE  375 (406)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEEC--CCCCCHHHHHHHHHHHC-CCCEEEEEEEECCCCCCCCEEE
T ss_conf             84999972578798999999999877659979999982--78996799999999757-9937999988725778866489


Q ss_pred             EECCCCHHHHHHCCCCC----HHHHHHHHHHHHHHHH
Q ss_conf             00043113333113458----7899999998402221
Q gi|254780316|r  404 IVFMNSEVKRLSGIDVP----IEDSLRILERLGFSVI  436 (805)
Q Consensus       404 I~l~~~~i~~ilG~~i~----~~ei~~iL~~Lgf~v~  436 (805)
                      +.         ++++..    .+++.+-|+.-||.++
T Consensus       376 v~---------~~iEt~~~~h~~~i~~~L~~~Gy~~~  403 (406)
T PRK08198        376 VE---------LTLETRGPEHIDEILAALRDAGYEVK  403 (406)
T ss_pred             EE---------EEEEECCHHHHHHHHHHHHHCCCCEE
T ss_conf             99---------99992999999999999997899459


No 90 
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=73.16  E-value=2.9  Score=21.06  Aligned_cols=108  Identities=16%  Similarity=0.199  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH--HHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHHH
Q ss_conf             54678988787787740232100482576552000--0000024677643210151221106776432101586113454
Q gi|254780316|r  493 SRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGG--QRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIF  570 (805)
Q Consensus       493 ~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~--~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~lF  570 (805)
                      +..+.+|++|-..||-||-|--+..-     .++.  ..-+.-.|.+..|+ +||-+.=--|=+.+    --|.+  |+|
T Consensus       185 ~ii~~iR~fl~~~gFlEVETP~lq~i-----~GGA~ArPF~ThhNald~dl-yLRIApELyLKRli----VGG~e--rVf  252 (502)
T COG1190         185 KIIRAIREFLDDRGFLEVETPMLQPI-----PGGAAARPFITHHNALDMDL-YLRIAPELYLKRLI----VGGFE--RVF  252 (502)
T ss_pred             HHHHHHHHHHHHCCCEEECCCCCCCC-----CCCCCCCCCEEEECCCCCCE-EEEECCHHHHHHHH----HCCCH--HHE
T ss_conf             99999999998779758416000355-----78732265012202367756-87624189999887----53721--422


Q ss_pred             HHCCCCCCCCCCC---CCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             3024444777544---3100022103543101246202345443333146888753111111101
Q gi|254780316|r  571 EVSHVYENDTPEG---QKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPF  632 (805)
Q Consensus       571 EiG~Vf~~~~~~~---~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l  632 (805)
                      |||++|+++.-..   -+.....            ..|        .-.|+.|+....+.++..+
T Consensus       253 EIgr~FRNEGid~tHNPEFTmlE------------~Y~--------AYaDy~D~m~ltE~Li~~~  297 (502)
T COG1190         253 EIGRNFRNEGIDTTHNPEFTMLE------------FYQ--------AYADYEDLMDLTEELIKEL  297 (502)
T ss_pred             EECCCCCCCCCCCCCCCCHHHHH------------HHH--------HHHHHHHHHHHHHHHHHHH
T ss_conf             30552003787666484235689------------999--------9857999999999999999


No 91 
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=71.14  E-value=5.7  Score=19.00  Aligned_cols=59  Identities=17%  Similarity=0.196  Sum_probs=30.7

Q ss_pred             CCHHHHHHHHHHCCCEEEEEECCCCCCCE-EEEEEEEEEECCCCCCCEEEEECCCCCEEEEECCCCCC
Q ss_conf             98899999987458604211124656874-89999997565799870899975999579897548345
Q gi|254780316|r   16 VSLEKICDTLTSIGLEVEKVDNREALSPF-TIVKVLSVERNPDLDCAILRIDTGKHQEIQVVCGAPNV   82 (805)
Q Consensus        16 ~~~~~l~~~lt~~G~EVe~i~~~~~~~~v-vvg~v~~~~~hP~adl~v~~Vd~g~~~~~~IvcgA~Nv   82 (805)
                      .+..++.+....+--  ++.   ..-..| +.|.|.....|-  .+....+..+++ .+|||+...++
T Consensus        33 ~~~~~~~~~~~~~~~--~~~---~~~~~V~vaGrv~~~R~~G--k~~F~~lrD~~g-~iQ~~~~~~~~   92 (491)
T PRK00484         33 HTSAELQAKYADLEK--EEL---EALIEVSVAGRVMLKRVMG--KASFATIQDGSG-RIQLYVSKDDV   92 (491)
T ss_pred             CCHHHHHHHHHHCCC--CCC---CCCCEEEEEEEEEEEECCC--CEEEEEEEECCC-CEEEEEECCCC
T ss_conf             669999998751385--334---6798899998784050569--819999996994-58999966758


No 92 
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=70.49  E-value=5.8  Score=18.96  Aligned_cols=146  Identities=9%  Similarity=0.116  Sum_probs=84.4

Q ss_pred             HHHHHHCCCCC-HHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCC-CCCCCCCCCCCCCCC
Q ss_conf             13333113458-7899999998402221034562366403454334402567676765352334-667655443457678
Q gi|254780316|r  410 EVKRLSGIDVP-IEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQI-KSEPLPLTQVEDKRN  487 (805)
Q Consensus       410 ~i~~ilG~~i~-~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGYdnI-p~~~l~~~~~~~~~~  487 (805)
                      .+.|+-|+.++ +++..+.|++|.=--..+          +|. |-.+-       -++-++.. |..|    .. .++.
T Consensus       217 ~LqRIYG~af~~k~~L~~yl~~leEakkRD----------HRk-lGkel-------~LF~f~~~~pG~~----fw-lP~G  273 (639)
T PRK12444        217 VLQRIYGVAFSSQKELEEYLHFVEEAAKRN----------HRK-LGNEL-------ELFMFSEEAPGMP----FY-LPKG  273 (639)
T ss_pred             CEEEEEEEEECCHHHHHHHHHHHHHHHHCC----------HHH-HHHHC-------CEEEECCCCCCCE----EE-ECCH
T ss_conf             216899998588577999999999988647----------887-65322-------7288227789744----78-4678


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH----HHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCC
Q ss_conf             99889546789887877877402321004825765520----00000002467764321015122110677643210158
Q gi|254780316|r  488 LSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFG----GGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRA  563 (805)
Q Consensus       488 ~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~----~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~  563 (805)
                      ....+.+.+.+|+.....||+||.|-.+.+.+.-+.-|    +.++.. .. -+..+.=.|||---|+......... |.
T Consensus       274 ~~i~~~le~~~r~~~~~~GY~eV~TP~i~~~~Lw~~SGH~~~Y~e~Mf-~~-~~d~~~~~lKPMNCP~H~~if~~~~-rS  350 (639)
T PRK12444        274 QIIRNELEAFLREIQKEYNYQEVRTPFMMNQELWERSGHWGHYKDNMY-FS-EVDNKSFALKPMNCPGHMLMFKNKL-HS  350 (639)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEECCCEEEHHHHHHHCCHHHHHHHCCC-CC-CCCCCEEECCCCCCHHHHHHHHCCC-CC
T ss_conf             699999999999999983987822866621568761660433330275-54-5454033126768588999986056-21


Q ss_pred             CCH--HHHHHHCCCCCCCCC
Q ss_conf             611--345430244447775
Q gi|254780316|r  564 IAD--FAIFEVSHVYENDTP  581 (805)
Q Consensus       564 ~~~--i~lFEiG~Vf~~~~~  581 (805)
                      .++  +|++|+|.||+.+.+
T Consensus       351 YRdLPlR~aEfg~vhR~E~S  370 (639)
T PRK12444        351 YRELPIRMCEFGQVHRHEFS  370 (639)
T ss_pred             HHHCCHHHHHCCCEECCCCC
T ss_conf             44365222433646337787


No 93 
>TIGR03220 catechol_dmpE 2-oxopent-4-enoate hydratase. Members of this protein family are 2-oxopent-4-enoate hydratase, which is also called 2-hydroxypent-2,4-dienoate hydratase. It is closely related to another gene found in the same operon, 4-oxalocrotonate decarboxylase, with which it interacts closely.
Probab=69.63  E-value=7.8  Score=18.05  Aligned_cols=23  Identities=22%  Similarity=0.554  Sum_probs=10.2

Q ss_pred             EEE-EEEECHHHHHHCCCCCCEEE
Q ss_conf             999-85477899996687997899
Q gi|254780316|r  664 LGY-FGEFHPNILDFFGLSNPICG  686 (805)
Q Consensus       664 iG~-iG~ihP~i~~~~~i~~~v~~  686 (805)
                      +|| +|--++...+.+++..|+|+
T Consensus        53 vG~KiG~Ts~~~q~~~gv~~P~~G   76 (255)
T TIGR03220        53 IGKKIGVTSKAVMNMLGVYQPDFG   76 (255)
T ss_pred             EEEEEECCCHHHHHHHCCCCCCEE
T ss_conf             899983289999997197999468


No 94 
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=69.26  E-value=6  Score=18.83  Aligned_cols=114  Identities=11%  Similarity=0.121  Sum_probs=66.5

Q ss_pred             HHHHHCCCCCC-CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHH------HHHHHHHHHHCCCC
Q ss_conf             76765352334-667655443457678998895467898878778774023210048257------65520000000024
Q gi|254780316|r  462 EILRIYGVDQI-KSEPLPLTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQ------SVLFGGGQRELEIL  534 (805)
Q Consensus       462 EIaRiyGYdnI-p~~~l~~~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~------~~~~~~~~~~i~l~  534 (805)
                      +++|-.|+-.. |....--.... ++.....+.+.+.+++.....|+.||.|-.+.+.+.      ...|+  ++...+.
T Consensus       201 ~~mr~~~~~dyEp~Sd~G~~rw~-PkG~~i~~lle~Yv~~~~~~~G~~eV~TP~m~d~~~~~~sgH~~~f~--e~my~~~  277 (613)
T PRK03991        201 ELMRKKELADYEPGSDVGHMRYY-PKGRLMKDLLEDYVYNLVKELGAMPVETPNMYDLSHPAIREHADKFG--ERQYRVK  277 (613)
T ss_pred             HHHHHCCCCCCCCCCCCCCEEEC-CCHHHHHHHHHHHHHHHHHHCCCEEEECCCEEECCCCHHHHHHHHHC--CCCEEEE
T ss_conf             99987176555747877751235-54789999999999999986396684576164055402556887611--1342563


Q ss_pred             CCCCCCCCCCCCHHHCHHHHHHHHHCCC-CCCHHHHHHHCCC-CCCCC
Q ss_conf             6776432101512211067764321015-8611345430244-44777
Q gi|254780316|r  535 NPISADMSNMRTSLLPGLLKATGRNVDR-AIADFAIFEVSHV-YENDT  580 (805)
Q Consensus       535 NPlS~e~s~lR~SLlp~LL~~~~~N~~r-~~~~i~lFEiG~V-f~~~~  580 (805)
                        ...+.=.||+--=||..........- +.-.+|+||+|++ |+.+.
T Consensus       278 --~d~~~~~LrpmnCpgh~~i~~~~~~SYRdLPlRl~E~g~~syR~E~  323 (613)
T PRK03991        278 --SDKKDLMLRFAACFGQFAMLKDMTISYKNLPLKMYELSDYSFRLEQ  323 (613)
T ss_pred             --CCCHHHCCCCCCCCCCEEEECCCCCCHHHCCHHHHHHCCCEEECCC
T ss_conf             --2763323044578631235102445743264677652242021256


No 95 
>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=68.48  E-value=6.3  Score=18.68  Aligned_cols=93  Identities=4%  Similarity=0.003  Sum_probs=58.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH-----HHHHCCCCCCCC---CCCCCCCCHHHCHHHHHHHHH
Q ss_conf             998895467898878778774023210048257655200-----000000246776---432101512211067764321
Q gi|254780316|r  488 LSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGG-----GQRELEILNPIS---ADMSNMRTSLLPGLLKATGRN  559 (805)
Q Consensus       488 ~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~-----~~~~i~l~NPlS---~e~s~lR~SLlp~LL~~~~~N  559 (805)
                      ....++..+.+|+.|...|++|+.+-.|++.+..+.-+-     ..+...+..--.   ++.=.|||+-=+..-...+..
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             CC-CCCCHHHHHHHCCCCCCCC
Q ss_conf             01-5861134543024444777
Q gi|254780316|r  560 VD-RAIADFAIFEVSHVYENDT  580 (805)
Q Consensus       560 ~~-r~~~~i~lFEiG~Vf~~~~  580 (805)
                      .+ ++.-.+++|++|.+|+.+.
T Consensus       112 i~SyrdLPl~lyQ~~~~fR~E~  133 (264)
T cd00772         112 IKSWKDLPQHLNQIGNKFRDEI  133 (264)
T ss_pred             CCCHHHCCHHHHHHHHHHHCCC
T ss_conf             0766557977876557860578


No 96 
>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=66.17  E-value=7.6  Score=18.10  Aligned_cols=113  Identities=9%  Similarity=0.106  Sum_probs=54.5

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCC-CCCCHHHCHHHHHHHHHCCCCCCHHHHH
Q ss_conf             954678988787787740232100482576552000000002467764321-0151221106776432101586113454
Q gi|254780316|r  492 QSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPISADMS-NMRTSLLPGLLKATGRNVDRAIADFAIF  570 (805)
Q Consensus       492 ~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s-~lR~SLlp~LL~~~~~N~~r~~~~i~lF  570 (805)
                      ....+.+|+++...||.||-|-.+++..--    .... ..+......... .|++|--- .++.+.   .-|..  ++|
T Consensus         5 s~i~~~iR~ff~~~gflEV~TPiL~~~~~e----ga~~-f~~~~~~~~~~~~~L~~Spel-~~k~l~---~~g~~--rvf   73 (280)
T cd00777           5 SRVIKAIRNFLDEQGFVEIETPILTKSTPE----GARD-FLVPSRLHPGKFYALPQSPQL-FKQLLM---VSGFD--RYF   73 (280)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCCCCC----CCCC-CEECCCCCCCCCCCCCCCHHH-HHHHHH---HCCCC--CCE
T ss_conf             999999999999889899879810687877----6766-442441688760368879899-999998---56877--757


Q ss_pred             HHCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             30244447775443100022103543101246202345443333146888753111111101
Q gi|254780316|r  571 EVSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPF  632 (805)
Q Consensus       571 EiG~Vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l  632 (805)
                      |||++|+++..... +..              .+|...|...  ..|+.++...++.++..+
T Consensus        74 ~i~~~FR~E~~~~~-h~~--------------EFtmLE~e~~--~~~~~d~m~~~E~li~~i  118 (280)
T cd00777          74 QIARCFRDEDLRAD-RQP--------------EFTQIDIEMS--FVDQEDIMSLIEGLLKYV  118 (280)
T ss_pred             EEECEECCCCCCCC-CCH--------------HHHHHHHHCC--CCCHHHHHHHHHHHHHHH
T ss_conf             98451747888876-634--------------7762344226--888999999999999999


No 97 
>PRK06462 asparagine synthetase A; Reviewed
Probab=66.00  E-value=4.6  Score=19.67  Aligned_cols=117  Identities=15%  Similarity=0.123  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCCCHHHH
Q ss_conf             88954678988787787740232100482576552000000002467764321015122110677643210158611345
Q gi|254780316|r  490 LQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAI  569 (805)
Q Consensus       490 ~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~~~~N~~r~~~~i~l  569 (805)
                      ......+.+|++|...||.||-|-.+++...-..  ....... .|-. ...-+||.|----|=..+.    -|..  |+
T Consensus        31 iRs~i~~~iR~f~~~~gF~EV~TPiL~~~~~~~~--~~~~~~~-~~~~-~~~~~L~~Spql~lk~li~----~g~~--rV  100 (332)
T PRK06462         31 IQSSILRYTREFLDGRGFVEVLPPIISPSTDPLM--GDAKPAS-IDFY-GVEYYLADSMIFHKQLMLR----LLKG--KV  100 (332)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCC--CCCCCCE-EECC-CCCEEECCCHHHHHHHHHH----CCCC--CE
T ss_conf             9999999999999888999987972367788766--7760105-8448-9863314586999999986----3899--77


Q ss_pred             HHHCCCCCCCCCCC--CCEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             43024444777544--3100022103543101246202345443333146888753111111101
Q gi|254780316|r  570 FEVSHVYENDTPEG--QKYMAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPF  632 (805)
Q Consensus       570 FEiG~Vf~~~~~~~--~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~df~dlKg~v~~ll~~l  632 (805)
                      ||||++|+++....  ..++.-              +|.-.|..  ...|+.++...++.++...
T Consensus       101 feIg~~FR~E~~d~~t~rHlpE--------------Ft~lE~y~--a~~d~~d~m~~~E~li~~i  149 (332)
T PRK06462        101 FYLSPNFRLEPVDKDTGRHLYE--------------FTQLDIEI--EGADLEEVMSLAEDLIKYL  149 (332)
T ss_pred             EEECCHHHCCCCCCCCCCCCHH--------------HHHHHHHH--HHCCHHHHHHHHHHHHHHH
T ss_conf             9974523168777677765457--------------77655878--7389999999999999999


No 98 
>TIGR00308 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA:  S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs . The enzyme is found in both eukaryotes and archaea .; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing.
Probab=65.85  E-value=6  Score=18.82  Aligned_cols=23  Identities=17%  Similarity=0.678  Sum_probs=10.8

Q ss_pred             CEEEECCCCCCCCCHHHHHHHHHH
Q ss_conf             236640345433440256767676
Q gi|254780316|r  442 FEVSVPSWRQDVEEKADLVEEILR  465 (805)
Q Consensus       442 ~~V~vPs~R~DI~~e~DLiEEIaR  465 (805)
                      +.+.=|-|=-||.. -++|||+++
T Consensus       342 ~~laGPly~G~L~~-~~fiEe~~~  364 (462)
T TIGR00308       342 YDLAGPLYVGELKD-KEFIEEVLK  364 (462)
T ss_pred             CCCCCCEECCCCCC-HHHHHHHHH
T ss_conf             02115510055334-689999999


No 99 
>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=64.41  E-value=6.7  Score=18.51  Aligned_cols=92  Identities=7%  Similarity=0.016  Sum_probs=61.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH----HHHHHCCCCCCCC---CCCCCCCCHHHCHHHHHHHHHCCC
Q ss_conf             889546789887877877402321004825765520----0000000246776---432101512211067764321015
Q gi|254780316|r  490 LQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFG----GGQRELEILNPIS---ADMSNMRTSLLPGLLKATGRNVDR  562 (805)
Q Consensus       490 ~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~----~~~~~i~l~NPlS---~e~s~lR~SLlp~LL~~~~~N~~r  562 (805)
                      ..+.+.+.+++.+...||.|+.+-.|++.+....-+    +.++...+..+-.   .+-=+||++-=+.+....+.-...
T Consensus         4 L~~aL~~~~~~~~~~~G~~~v~~P~l~~~~~~~~sg~~~~f~~~~y~v~~~~~~~~~~~~~L~PTsE~~~~~~~~~~i~s   83 (235)
T cd00670           4 LWRALERFLDDRMAEYGYQEILFPFLAPTVLFFKGGHLDGYRKEMYTFEDKGRELRDTDLVLRPAACEPIYQIFSGEILS   83 (235)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCEEEEECCCHHHHHHHHCCCCC
T ss_conf             99999999999999869989989855789999223867545205289823776667873899307869999999483287


Q ss_pred             -CCCHHHHHHHCCCCCCCCC
Q ss_conf             -8611345430244447775
Q gi|254780316|r  563 -AIADFAIFEVSHVYENDTP  581 (805)
Q Consensus       563 -~~~~i~lFEiG~Vf~~~~~  581 (805)
                       ..-.++++++|++|+.+..
T Consensus        84 ~~dLPlr~~~~s~~fR~E~~  103 (235)
T cd00670          84 YRALPLRLDQIGPCFRHEPS  103 (235)
T ss_pred             HHHCCEEEEEECCEECCCCC
T ss_conf             68799545445653336789


No 100
>TIGR00802 nico transition metal uptake transporter, Ni2+-Co2+ transporter (NiCoT) family; InterPro: IPR004688 This family is found in both Gram-negative and Gram-positive bacteria. The functionally characterised members of the family catalyze uptake of either Ni2+ or Co2+ in a proton motive force-dependent process. Topological analyses with the HoxN Ni2+ transporter of Ralstonia eutropha suggest that it possesses 8 TMSs with its N- and C-termini in the cytoplasm.; GO: 0015099 nickel ion transmembrane transporter activity, 0015675 nickel ion transport, 0016021 integral to membrane.
Probab=63.75  E-value=1.7  Score=22.75  Aligned_cols=41  Identities=32%  Similarity=0.396  Sum_probs=30.6

Q ss_pred             EEECCCCCCCEEEEEECCCCCCHHHHHHHCCCCCCCCEEEECCCCCCCCHHHCCCCCCCCCCCCCEE
Q ss_conf             0001022333268862355431145542011245432000025676310011135531201367269
Q gi|254780316|r  265 HVFDASRISDVLTVRRACSGEKILALDNQEYDLSPDNVVIASDGRIQSIAGIIGGKHAGCDDNTTDV  331 (805)
Q Consensus       265 HafD~dki~~~i~vr~a~~~E~~~~Ld~~e~~L~~~~lvI~d~~~~ialaGImGg~~s~v~~~T~~i  331 (805)
                      ||||+|.|.               +.|+..|+|-      .||++|++.     |...+--++|=-|
T Consensus        11 HAfDADHIA---------------AIDnttRkLm------q~G~~P~gv-----G~fFslGHStVVv   51 (290)
T TIGR00802        11 HAFDADHIA---------------AIDNTTRKLM------QQGKRPLGV-----GFFFSLGHSTVVV   51 (290)
T ss_pred             HHHCHHHHH---------------HHHHHHHHHH------HCCCCCHHH-----HHHHHHCCCHHHH
T ss_conf             331334564---------------1468899976------276971113-----4546404108899


No 101
>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=62.53  E-value=5.2  Score=19.27  Aligned_cols=54  Identities=17%  Similarity=0.179  Sum_probs=31.5

Q ss_pred             HHCCCCCCCCEEEECCCCCCCCHHHCCCCCCCC---CCCCCEEEEEEECCCH-HHHHH
Q ss_conf             201124543200002567631001113553120---1367269999715787-88877
Q gi|254780316|r  292 NQEYDLSPDNVVIASDGRIQSIAGIIGGKHAGC---DDNTTDVLVEVALWDP-INIAR  345 (805)
Q Consensus       292 ~~e~~L~~~~lvI~d~~~~ialaGImGg~~s~v---~~~T~~illEsA~F~p-~~Ir~  345 (805)
                      +|.-+|.+..|+.++=+++--||+|-=.+++.-   -++.+.|=+|+|+-|. ..+..
T Consensus       206 ~QSPQlyKQ~l~~~g~~rVyEI~PiFRAE~~nT~RHl~E~~siDiE~~F~dhy~~v~d  263 (466)
T TIGR00458       206 GQSPQLYKQVLMAAGLERVYEIGPIFRAEEHNTRRHLNEAISIDIEMAFEDHYEDVMD  263 (466)
T ss_pred             CCCCHHHHHHHHHCCCCCEEEECCEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             3570356687765265203550552205666521455444442244442753789999


No 102
>pfam11148 DUF2922 Protein of unknown function (DUF2922). This bacterial family of proteins has no known function.
Probab=62.06  E-value=11  Score=17.06  Aligned_cols=36  Identities=22%  Similarity=0.534  Sum_probs=27.9

Q ss_pred             EEECCCCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             763677998842699999984779888999999999999999
Q gi|254780316|r  752 VFQGKSLGEGKKSVAIQVLIQPLKDTFRDDDIRILMDRIVEN  793 (805)
Q Consensus       752 vY~g~~i~~gkkSla~rl~fqs~~kTLtd~EI~~i~~~ii~~  793 (805)
                      +|..   .+||   +++++...+...|+++||.++|+.|++.
T Consensus         6 ~F~~---~~gK---~~~l~i~~p~~~lt~~~V~~aM~~Ii~~   41 (69)
T pfam11148         6 TFKT---AEGK---TVTLSLPDPKEDLTEAEVKAAMDTIIAK   41 (69)
T ss_pred             EEEC---CCCC---EEEEECCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             9976---8998---8999769987778999999999999986


No 103
>TIGR01703 hybrid_clust hydroxylamine reductase; InterPro: IPR010048   Hybrid cluster proteins (HCP, or Prismane) have been identified in bacteria, archaea and eukaryotic protozoa. No specific function has yet been assigned to these proteins, but it may involve oxidoreductase enzymatic activity. These proteins contain one 4Fe-4S cluster, and one hybrid 4Fe-2O-2S cluster, the latter being similar to the Ni-Fe-S cluster found in carbon monoxide dehydrogenase enzymes (IPR010047 from INTERPRO) , .    This subfamily is heterogeneous with respect to the presence or absence of a region of about 100 amino acids not far from the N terminus of the protein. Members have been described as monomeric. ; GO: 0016661 oxidoreductase activity acting on other nitrogenous compounds as donors, 0051536 iron-sulfur cluster binding, 0006118 electron transport, 0005737 cytoplasm.
Probab=61.07  E-value=7.4  Score=18.19  Aligned_cols=24  Identities=13%  Similarity=0.238  Sum_probs=14.2

Q ss_pred             HHHHHHCCCCCCCCHHHHHHHHHH
Q ss_conf             787740232100482576552000
Q gi|254780316|r  504 SRAMMEVVNWSFISKEQSVLFGGG  527 (805)
Q Consensus       504 ~~Gf~Ev~tysl~s~~~~~~~~~~  527 (805)
                      ..|=.-+-+.-|.++...+.||.+
T Consensus       211 E~Gk~~l~~M~LLDkAnT~tyG~P  234 (567)
T TIGR01703       211 EVGKMNLEAMKLLDKANTDTYGEP  234 (567)
T ss_pred             CCCEECHHHHHHHHHHHHHCCCCC
T ss_conf             037000247656423524247895


No 104
>pfam02005 TRM N2,N2-dimethylguanosine tRNA methyltransferase. This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The enzyme is found in both eukaryotes and archaebacteria
Probab=61.02  E-value=6.4  Score=18.65  Aligned_cols=21  Identities=14%  Similarity=0.124  Sum_probs=14.1

Q ss_pred             HHHHHHHCCCEEEECCCCCCC
Q ss_conf             899986087000001022333
Q gi|254780316|r  254 NYVSLDRGYPSHVFDASRISD  274 (805)
Q Consensus       254 Nyvmle~GqPlHafD~dki~~  274 (805)
                      |-+|.+..+..+.-|+|-...
T Consensus       111 n~lm~~~~~~fD~IDlDPfGS  131 (375)
T pfam02005       111 NMLMRENHRRFDVIDLDPFGS  131 (375)
T ss_pred             HHHHHHCCCCCCEEEECCCCC
T ss_conf             999985588675686789999


No 105
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=59.13  E-value=7.3  Score=18.25  Aligned_cols=82  Identities=12%  Similarity=0.066  Sum_probs=48.7

Q ss_pred             CCEEEEEECCEEEEEEEEEEC-HHHH----------------------HH--CCCCCCEEEEEEEHHHHHHHHHCCCCCC
Q ss_conf             816999987929999985477-8999----------------------96--6879978999987876235452024566
Q gi|254780316|r  651 GRSGIIKTSAEIVLGYFGEFH-PNIL----------------------DF--FGLSNPICGFEVYLDSIPISQKKRTKTK  705 (805)
Q Consensus       651 grsa~I~~~gk~iiG~iG~ih-P~i~----------------------~~--~~i~~~v~~~EI~ld~L~~~~~~~~~~~  705 (805)
                      .++.+++++|..+.|=-=.+| |.++                      +.  ||. -|.-++-+=+|.|...-...   .
T Consensus       488 a~aYDLVlNG~ElggGSiRIHd~~iQ~~if~~lGl~~ee~~~kFgf~LeAf~YGa-PPHGGialGlDRLvMlLtg~---~  563 (706)
T PRK12820        488 SRAYDLVVNGEELGGGSIRINDKDIQLRIFAALGLSEEDIEDKFGFFLRAFDFAA-PPHGGIALGLDRVVSMILQT---P  563 (706)
T ss_pred             CCEEEEEECCEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCC-CCCCCEEEHHHHHHHHHCCC---C
T ss_conf             3646068999996140220389999999999759997898889999999986699-98670310399999997699---8


Q ss_pred             CCCCCCCCCCCE--EEEEEEECCCCCHHHHHHH
Q ss_conf             313689888720--0189996688799999999
Q gi|254780316|r  706 KVVHLSSLHPVK--RDLAFIVDQHIPAGTLVNI  736 (805)
Q Consensus       706 ~~~~~s~fP~v~--RDls~iv~~~v~~~~I~~~  736 (805)
                      .+.+..-||...  +|+=.-.|..++-.++.+.
T Consensus       564 sIRDVIaFPKt~~g~dlm~~aPs~v~~~QL~El  596 (706)
T PRK12820        564 SIREVIAFPKNRSAACPLTGAPSEVAQEQLAEL  596 (706)
T ss_pred             CHHHEECCCCCCCCCCCCCCCCCCCCHHHHHHC
T ss_conf             265052278998878600279886899999763


No 106
>TIGR02902 spore_lonB ATP-dependent protease LonB; InterPro: IPR014251   This entry represents LonB, a paralog of the ATP-dependent protease La (LonA, IPR004815 from INTERPRO). LonB proteins are unassigned peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ) and are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore during sporulation, under control of sigmaF . The lonB gene, despite being located immediately upstream of lonA, was shown to be monocistronic. LonB appears to be involved in the post-translation control of sigmaH, but lonB mutation did not produce an obvious sporulation defect under the conditions tested . Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and these are excluded from this entry. .
Probab=58.42  E-value=3.4  Score=20.60  Aligned_cols=60  Identities=13%  Similarity=0.199  Sum_probs=40.7

Q ss_pred             ECCCCCCHHHHHHHCCCCCCC----CEE------EECCCCCCCCHHHCCCCCCCC-------------------------
Q ss_conf             235543114554201124543----200------002567631001113553120-------------------------
Q gi|254780316|r  280 RACSGEKILALDNQEYDLSPD----NVV------IASDGRIQSIAGIIGGKHAGC-------------------------  324 (805)
Q Consensus       280 ~a~~~E~~~~Ld~~e~~L~~~----~lv------I~d~~~~ialaGImGg~~s~v-------------------------  324 (805)
                      ..+++-+|+-+|-.+..-|+.    .|+      |+-|-+|+++|||=.=+--+|                         
T Consensus       117 PFke~A~FVEiDATT~RFDERGIADPLIGSVHDPIYQGAGplG~AGIPQPK~GAVT~AHGGvLFIDEIGELHP~~MNKLL  196 (532)
T TIGR02902       117 PFKEEAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGVAGIPQPKPGAVTKAHGGVLFIDEIGELHPVQMNKLL  196 (532)
T ss_pred             CCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCHHHHHHHH
T ss_conf             78988668985051036021466665677615853337654578855758777632025865512124665824353141


Q ss_pred             --CCCCCEEEEEEECCCH
Q ss_conf             --1367269999715787
Q gi|254780316|r  325 --DDNTTDVLVEVALWDP  340 (805)
Q Consensus       325 --~~~T~~illEsA~F~p  340 (805)
                        =|+ +-||||||||++
T Consensus       197 KVLED-RKVFLdSAYY~s  213 (532)
T TIGR02902       197 KVLED-RKVFLDSAYYSS  213 (532)
T ss_pred             HHHHC-CCCHHHCCCCCC
T ss_conf             13302-220000123587


No 107
>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=55.43  E-value=12  Score=16.72  Aligned_cols=148  Identities=16%  Similarity=0.187  Sum_probs=89.0

Q ss_pred             CHHHHHHC----CCCC-HHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHH---HCCCC-CCCCCCCCC
Q ss_conf             11333311----3458-789999999840222103456236640345433440256767676---53523-346676554
Q gi|254780316|r  409 SEVKRLSG----IDVP-IEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILR---IYGVD-QIKSEPLPL  479 (805)
Q Consensus       409 ~~i~~ilG----~~i~-~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaR---iyGYd-nIp~~~l~~  479 (805)
                      ..+.|+-|    +... .++..++|..+.=....        -|-||.           ++|   ++-|+ .+-+= +| 
T Consensus       147 ~~LqRiyGn~~~~~~~~k~~L~~yl~~~eEa~~r--------~PDHRk-----------lGKeL~Lf~f~~~~gpG-~~-  205 (595)
T TIGR00418       147 EMLQRIYGNIDITAFADKKQLAEYLKRLEEAKKR--------EPDHRK-----------LGKELELFSFEPEIGPG-LP-  205 (595)
T ss_pred             CEEEEECCCEEEECCCCHHHHHHHHHHHHHHHCC--------CCCHHH-----------HHHHHCCCCCCCCCCCC-CE-
T ss_conf             5378885725450145878999999999997426--------857256-----------75453123458320487-41-


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCC---CCCCCCCCCHHHCHHHHHH
Q ss_conf             4345767899889546789887877877402321004825765520000000024677---6432101512211067764
Q gi|254780316|r  480 TQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPI---SADMSNMRTSLLPGLLKAT  556 (805)
Q Consensus       480 ~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPl---S~e~s~lR~SLlp~LL~~~  556 (805)
                       -..+ ++......+.+.+++.+...||.||.|=-+.+.+.-+.-+-.++.=.-+-|.   .+..=+||+--=||.....
T Consensus       206 -~WlP-kG~~ir~~ledf~~~~~~~~Gy~~V~TP~m~~~~l~~~sGH~~~Y~e~Mf~~~~~~~~~~~LkPMnCpgH~~i~  283 (595)
T TIGR00418       206 -FWLP-KGALIRNLLEDFVREKQIKRGYEEVETPIMYDSELWEISGHWDHYKERMFPFTEEDNQEFMLKPMNCPGHILIF  283 (595)
T ss_pred             -EECC-CHHHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHCCCCCCCCEEECCCCCCCCCCCCHHHHHHH
T ss_conf             -4657-64678999999999999875886415741215654245305450342354010103530334567754453300


Q ss_pred             HHHCCCCCCH--HHHHHHC-CCCCCCC
Q ss_conf             3210158611--3454302-4444777
Q gi|254780316|r  557 GRNVDRAIAD--FAIFEVS-HVYENDT  580 (805)
Q Consensus       557 ~~N~~r~~~~--i~lFEiG-~Vf~~~~  580 (805)
                      +.-.+ ...+  +|++|.| .+|+.+.
T Consensus       284 k~~~~-SYR~LP~R~aE~g~~~hR~E~  309 (595)
T TIGR00418       284 KSSLR-SYRDLPLRIAELGTTVHRYEK  309 (595)
T ss_pred             CCCCC-CHHHCCCHHHHCCCEEEEEEC
T ss_conf             17777-732335034331860478842


No 108
>PRK04140 hypothetical protein; Provisional
Probab=55.13  E-value=14  Score=16.27  Aligned_cols=83  Identities=16%  Similarity=0.169  Sum_probs=41.5

Q ss_pred             HHHHHCCCCHHHHHHCC-CCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCEECCCCHHHHHHCCCCCHHHH
Q ss_conf             88761654015544134-55301358899988875212334555652587413554310000431133331134587899
Q gi|254780316|r  346 SGKNLGIITDSRYRFER-GVDLQGMIPVLKHIVSLILSLCGGTASDICIARNITYKPRKIVFMNSEVKRLSGIDVPIEDS  424 (805)
Q Consensus       346 tar~l~l~TdaS~RfER-gvd~~~~~~al~r~~~Li~e~~gg~~~~~~~~~~~~~~~~~I~l~~~~i~~ilG~~i~~~ei  424 (805)
                      =|..||.+-.+-|+||+ |.+...     +.|.. +.++-|..+.+.++.-............... .   =.+-...++
T Consensus       144 LA~~LGVSRrtv~~YE~g~~~~si-----evA~k-Leeif~~~i~~~Idil~~~~~~~~~~~~~~~-~---~~~~~e~~i  213 (319)
T PRK04140        144 LASELGVSRRTISKYENGGMNASI-----EVAIK-LEEILDEPLTKPIDILDSAERVEDDEKTLEE-P---EDDPFEKEV  213 (319)
T ss_pred             HHHHHCCCHHHHHHHHHCCCCCCH-----HHHHH-HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC-C---CCCHHHHHH
T ss_conf             999849869999999706886649-----99999-9998387323552022320125433457678-7---654156799


Q ss_pred             HHHHHHHHHHHHCC
Q ss_conf             99999840222103
Q gi|254780316|r  425 LRILERLGFSVIGE  438 (805)
Q Consensus       425 ~~iL~~Lgf~v~~~  438 (805)
                      ...|++|||.+...
T Consensus       214 ~~~L~~iG~~v~~~  227 (319)
T PRK04140        214 IEILSRLGFDVLPT  227 (319)
T ss_pred             HHHHHHCCCEEEEE
T ss_conf             99999649646773


No 109
>pfam08853 DUF1823 Domain of unknown function (DUF1823). This presumed domain is functionally uncharacterized.
Probab=53.91  E-value=8  Score=17.96  Aligned_cols=57  Identities=19%  Similarity=0.365  Sum_probs=44.1

Q ss_pred             CCCCHHHHHHCCCCCHHHHHHHH-HHHHHHHHCCCCCCEEEE--CC-CCCCCCCHHHHHHH
Q ss_conf             04311333311345878999999-984022210345623664--03-45433440256767
Q gi|254780316|r  406 FMNSEVKRLSGIDVPIEDSLRIL-ERLGFSVIGEYDKFEVSV--PS-WRQDVEEKADLVEE  462 (805)
Q Consensus       406 l~~~~i~~ilG~~i~~~ei~~iL-~~Lgf~v~~~~~~~~V~v--Ps-~R~DI~~e~DLiEE  462 (805)
                      ++.+-+-++|--++++.++.+.. ++||+......+.|....  |. ||.+--.+-|+|++
T Consensus         2 Ls~~~l~~Il~d~isD~~V~eLVW~~LgYr~~~~~~~W~~~~vtp~~W~e~ype~P~~I~~   62 (116)
T pfam08853         2 LSRDLLWAILEDRISDRFVNELVWERLGYRYDASSDKWDAGPVTPSYWREEYPEPPEFIAS   62 (116)
T ss_pred             CCHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCCHHHHC
T ss_conf             8789999999633589999999999978713776566778988869999867998358762


No 110
>COG0441 ThrS Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=52.43  E-value=15  Score=15.98  Aligned_cols=147  Identities=16%  Similarity=0.122  Sum_probs=80.9

Q ss_pred             HHHHHHCCCCCH-HHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             133331134587-8999999984022210345623664034543344025676767653523346676554434576789
Q gi|254780316|r  410 EVKRLSGIDVPI-EDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQIKSEPLPLTQVEDKRNL  488 (805)
Q Consensus       410 ~i~~ilG~~i~~-~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGYdnIp~~~l~~~~~~~~~~~  488 (805)
                      .+.++-|+...+ ++....|+++.....          |-+|.           +++--+.-.++...-+-...-.++..
T Consensus       162 ~l~riygta~~~~~~l~~~l~~~eea~k----------rdHrk-----------lg~el~LF~~~~~~~~G~~~~~pkG~  220 (589)
T COG0441         162 MLQRIYGTAFADKKELEAYLKRLEEAKK----------RDHRK-----------LGKELDLFSFSPEEGPGLPFWHPKGA  220 (589)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHCCC----------CCHHH-----------HHHHHCCEEECCCCCCCCEEECCCCC
T ss_conf             1067733355788999999766665027----------86476-----------87762143414445885069878846


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH----HHHHHCCCCCCCCC-CCCCCCCHHHCHHHHHHHHHCCCC
Q ss_conf             9889546789887877877402321004825765520----00000002467764-321015122110677643210158
Q gi|254780316|r  489 SLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFG----GGQRELEILNPISA-DMSNMRTSLLPGLLKATGRNVDRA  563 (805)
Q Consensus       489 ~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~----~~~~~i~l~NPlS~-e~s~lR~SLlp~LL~~~~~N~~r~  563 (805)
                      ...+.+.+.++..+...||+|+.|-.+.+.+.-+.-+    +.++..   -+.+. +.=.+|+---||.+.....-.+ .
T Consensus       221 ~ir~~le~y~~~~~~~~Gy~~V~TP~~~~~~l~~~SGH~~~y~e~mf---~~~~~~~~~~lKpmNCpgh~~ifk~~~~-S  296 (589)
T COG0441         221 TIRNLLEDYVRTKLRSYGYQEVKTPVLADLELWELSGHWDNYKEDMF---LTESDDREYALKPMNCPGHILIFKSGLR-S  296 (589)
T ss_pred             CHHHHHHHHHHHHHHHCCCEEECCCEEEECCCCHHCCCHHHCCCCCE---EECCCCHHHEEEECCCHHHHHHHHCCCC-C
T ss_conf             69999999999898755852712873630000101120455136606---6213772330641078768999853786-1


Q ss_pred             CCH--HHHHHHCCCCCCCCC
Q ss_conf             611--345430244447775
Q gi|254780316|r  564 IAD--FAIFEVSHVYENDTP  581 (805)
Q Consensus       564 ~~~--i~lFEiG~Vf~~~~~  581 (805)
                      ..+  +|++|.|.||....+
T Consensus       297 YR~LP~r~~E~g~v~R~E~S  316 (589)
T COG0441         297 YRELPLRLAEFGYVYRYEKS  316 (589)
T ss_pred             EECCCHHHHHCCEEECCCCC
T ss_conf             10044043314422115676


No 111
>TIGR00501 met_pdase_II methionine aminopeptidase, type II; InterPro: IPR002468   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of metallopeptidases belong to MEROPS peptidase family M24 (clan MG), subfamily M24A.   Methionine aminopeptidase (3.4.11.18 from EC) (MAP) is responsible for the removal of the amino-terminal (initiator) methionine from nascent eukaryotic cytosolic and cytoplasmic prokaryotic proteins if the penultimate amino acid is small and uncharged. All MAP studied to date are monomeric proteins that require cobalt ions for activity. Two subfamilies of MAP enzymes are known to exist , . While being evolutionary related, they only share a limited amount of sequence similarity mostly clustered around the residues shown, in the Escherichia coli MAP , to be involved in cobalt-binding. The first family consists of enzymes from prokaryotes as well as eukaryotic MAP-1, while the second group (IPR002467 from INTERPRO) is made up of archaeal MAP and eukaryotic MAP-2 and includes proteins which do not seem to be MAP, but that are clearly evolutionary related such as mouse proliferation-associated protein 1 and fission yeast curved DNA-binding protein. ; GO: 0004239 methionyl aminopeptidase activity, 0006508 proteolysis.
Probab=51.03  E-value=8.9  Score=17.63  Aligned_cols=42  Identities=21%  Similarity=0.313  Sum_probs=26.2

Q ss_pred             HCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEEECCCCCCHHHHHHHCCCCCCCCEE
Q ss_conf             401321039999989998608700000102233326886235543114554201124543200
Q gi|254780316|r  241 VGLRSISALVDITNYVSLDRGYPSHVFDASRISDVLTVRRACSGEKILALDNQEYDLSPDNVV  303 (805)
Q Consensus       241 ~Gir~inniVDitNyvmle~GqPlHafD~dki~~~i~vr~a~~~E~~~~Ld~~e~~L~~~~lv  303 (805)
                      -|++||+|+          +|+-||=|   .+++++.|=..+++        +..+|+.+++|
T Consensus       172 Yg~kP~~NL----------~GHs~~rY---~~H~G~SiPn~~~~--------~~~~leeG~~~  213 (327)
T TIGR00501       172 YGVKPISNL----------TGHSMARY---LLHAGLSIPNVKER--------DTTKLEEGDVV  213 (327)
T ss_pred             CCCCCCCCC----------CCCCCCHH---HHCCCCCCEEEECC--------CCCEEECCCEE
T ss_conf             143342227----------35640015---43589500034279--------87451025788


No 112
>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=50.91  E-value=15  Score=15.96  Aligned_cols=28  Identities=25%  Similarity=0.352  Sum_probs=15.3

Q ss_pred             ECHHHHHHCCCC-CCEEEEEEEHHHHHHH
Q ss_conf             778999966879-9789999878762354
Q gi|254780316|r  670 FHPNILDFFGLS-NPICGFEVYLDSIPIS  697 (805)
Q Consensus       670 ihP~i~~~~~i~-~~v~~~EI~ld~L~~~  697 (805)
                      -...+.+.|+=. .|..+|.+-++.+...
T Consensus       307 ~yd~l~~~~~~~~~~~~G~~~g~~r~~~~  335 (446)
T TIGR00442       307 RYDNLVEEFGGPPTPAVGFAFGLERLINL  335 (446)
T ss_pred             CHHHHHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             10125665067545410023308999998


No 113
>PRK07334 threonine dehydratase; Provisional
Probab=50.28  E-value=14  Score=16.19  Aligned_cols=124  Identities=12%  Similarity=0.093  Sum_probs=66.7

Q ss_pred             EEECCCCCCCCHHHCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             00025676310011135531201367269999715787888778876165401554413455301358899988875212
Q gi|254780316|r  303 VIASDGRIQSIAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLILS  382 (805)
Q Consensus       303 vI~d~~~~ialaGImGg~~s~v~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li~e  382 (805)
                      +++.+..++++|+++.+. ..+...+--++|=-++.|+..+++-..|--....-..||.=-+  .-..-+|.+++.++.+
T Consensus       270 ~vvEpaGA~~lAAll~~~-~~~~gk~Vv~vlsGGNiD~~~l~~ii~r~l~~~gr~~~~~v~i--pd~PG~l~~~~~~i~~  346 (399)
T PRK07334        270 TVVEGAGAAGLAALLAHP-ERFRGRKVGLVLCGGNIDTRLLANVLLRGLVRAGRLARLRVDI--RDRPGALAKVTALIGE  346 (399)
T ss_pred             CCCCCCHHHHHHHHHHCH-HHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEEC--CCCCCHHHHHHHHHHH
T ss_conf             865771799999997381-6646981999968688698899999999888559989999988--8899679999999821


Q ss_pred             CCCCCCCCCEEEEECCCCCCCEECCCCHHHHHHCCCCC----HHHHHHHHHHHHHHHH
Q ss_conf             33455565258741355431000043113333113458----7899999998402221
Q gi|254780316|r  383 LCGGTASDICIARNITYKPRKIVFMNSEVKRLSGIDVP----IEDSLRILERLGFSVI  436 (805)
Q Consensus       383 ~~gg~~~~~~~~~~~~~~~~~I~l~~~~i~~ilG~~i~----~~ei~~iL~~Lgf~v~  436 (805)
                      . ++.+.++........      .+.....=.++++..    .+++.+-|+.-||.+.
T Consensus       347 ~-~ani~~i~h~r~~~~------~~~~~~~v~~~~Et~~~~h~~~l~~~L~~~Gy~~~  397 (399)
T PRK07334        347 A-GANIIEVHHQRLFTT------LPAKGAELELVIETRDAAHIQEVMAALRAAGFVAR  397 (399)
T ss_pred             C-CCCEEEEEEEECCCC------CCCCEEEEEEEEEECCHHHHHHHHHHHHHCCCCEE
T ss_conf             7-997699998871577------88773899999993999999999999997799856


No 114
>KOG1936 consensus
Probab=50.11  E-value=16  Score=15.73  Aligned_cols=22  Identities=23%  Similarity=0.234  Sum_probs=15.2

Q ss_pred             CCCEEEEEEEHHHHHHHHHCCC
Q ss_conf             9978999987876235452024
Q gi|254780316|r  681 SNPICGFEVYLDSIPISQKKRT  702 (805)
Q Consensus       681 ~~~v~~~EI~ld~L~~~~~~~~  702 (805)
                      .-|+.++++-++.|...-..+.
T Consensus       389 ~vPcvG~S~GVeRiFsile~r~  410 (518)
T KOG1936         389 KVPCVGQSVGVERIFSILEQRA  410 (518)
T ss_pred             CCCCCCEEEHHHHHHHHHHHHH
T ss_conf             4874540400768999999988


No 115
>TIGR00268 TIGR00268 conserved hypothetical protein TIGR00268; InterPro: IPR005232   This family of conserved hypothetical proteins has no known function but is predicted to be part of the wider PP-loop superfamily ..
Probab=46.86  E-value=18  Score=15.39  Aligned_cols=180  Identities=19%  Similarity=0.256  Sum_probs=90.5

Q ss_pred             CCCEEEEEEECCCH-HHH---HHHHHHHCCCC-----HHHH--HHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEE
Q ss_conf             67269999715787-888---77887616540-----1554--4134553013588999888752123345556525874
Q gi|254780316|r  327 NTTDVLVEVALWDP-INI---ARSGKNLGIIT-----DSRY--RFERGVDLQGMIPVLKHIVSLILSLCGGTASDICIAR  395 (805)
Q Consensus       327 ~T~~illEsA~F~p-~~I---r~tar~l~l~T-----daS~--RfERgvd~~~~~~al~r~~~Li~e~~gg~~~~~~~~~  395 (805)
                      +|=-|++-|-+.-| ..+   .+.|+.+|++-     |.-.  -|.+. +++.|-..=.++...+.+.+-..--.++.+|
T Consensus        42 ~~lait~~sP~~sp~~el~~A~~~A~~~g~~he~~~~d~~~n~~f~~N-~~~RCY~CK~~~~~~L~~~a~~~gy~~V~dG  120 (263)
T TIGR00268        42 EVLAITVVSPSISPRRELEDAKAIAKEIGVKHELVKIDKMANPNFRAN-VEERCYFCKKKVLSILVKLAEKRGYDVVVDG  120 (263)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCC-CCCCCHHHHHHHHHHHHHHHHHCCCCEEEEC
T ss_conf             113578762775735448999999988083012110012368500168-8544415488899998999986399579823


Q ss_pred             EC-----CCCC-----CCEECCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHCC--CCCCEEEECCCC-CCCC--CHHHHH
Q ss_conf             13-----5543-----1000043113333113458789999999840222103--456236640345-4334--402567
Q gi|254780316|r  396 NI-----TYKP-----RKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSVIGE--YDKFEVSVPSWR-QDVE--EKADLV  460 (805)
Q Consensus       396 ~~-----~~~~-----~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~--~~~~~V~vPs~R-~DI~--~e~DLi  460 (805)
                      ..     .+-|     +...-.   -.=+.-+.|++.+|..|=+.||+.+-.+  ...+.-.+|+-+ -|+.  ..+|=+
T Consensus       121 tN~dDL~~~RPG~~A~~E~~g~---~SP~aef~I~K~eir~ia~~lg~~~~DKP~~~CL~sR~p~g~EI~~ekL~~v~ea  197 (263)
T TIGR00268       121 TNADDLEDHRPGLRAVKELNGV---YSPWAEFGITKKEIREIAKSLGLSFYDKPSEACLASRFPFGEEIDVEKLKKVDEA  197 (263)
T ss_pred             CCCCCCCCCCCHHHHHHHCCCC---CCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHCCCCCCCCCCHHHHHHHHHH
T ss_conf             4620002367513567660788---6872002568799999999748898888662102104768751048987769999


Q ss_pred             H-HHHHHCCCCCCCCCC---CCCCCCCCCCCCC-HHHHHHH-HHHHHHHHHHHHHCC
Q ss_conf             6-767653523346676---5544345767899-8895467-898878778774023
Q gi|254780316|r  461 E-EILRIYGVDQIKSEP---LPLTQVEDKRNLS-LQQSRTR-YVKRVLASRAMMEVV  511 (805)
Q Consensus       461 E-EIaRiyGYdnIp~~~---l~~~~~~~~~~~~-~~~~~~~-~ir~~L~~~Gf~Ev~  511 (805)
                      | ++.|.+|+..+--.-   +..-.++. ..+. ..+.... .+++.|...||..|.
T Consensus       198 E~~~l~~~g~~qvRVR~y~nlAviE~~~-~~l~kl~~~~~~Ge~~~~~k~~GF~~V~  253 (263)
T TIGR00268       198 EEIVLRRAGVKQVRVRNYDNLAVIEVAE-DELSKLLNEAEEGEVVDKLKDIGFRKVL  253 (263)
T ss_pred             HHHHHHHHCCCCEEEECCCCEEEEEECH-HHHHHHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             9999998356605765267657996285-8899998631321799999744731577


No 116
>PRK07522 acetylornithine deacetylase; Provisional
Probab=46.17  E-value=19  Score=15.32  Aligned_cols=45  Identities=27%  Similarity=0.299  Sum_probs=28.8

Q ss_pred             CHHHHHHHCCCC-CCH-------HHHHHHHHHCCCEEEEEECCCCCCCEEEEE
Q ss_conf             867998847899-988-------999999874586042111246568748999
Q gi|254780316|r    4 TLSWLKDHLDTD-VSL-------EKICDTLTSIGLEVEKVDNREALSPFTIVK   48 (805)
Q Consensus         4 s~~WL~~~v~~~-~~~-------~~l~~~lt~~G~EVe~i~~~~~~~~vvvg~   48 (805)
                      ++.+|+++|.++ .|.       +-|++.|...|||+|.++.......-+++.
T Consensus         7 ~v~ll~~LV~i~Svs~~~~~~~~~~l~~~l~~~G~~~~~~~~~~g~~~nlia~   59 (387)
T PRK07522          7 SLDILERLVAFDTVSRDSNLALIEWVRDYLAAHGIESELIHDPEGTKANLFAT   59 (387)
T ss_pred             HHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCEEEEEEE
T ss_conf             99999998099895998459999999999997799189997689983379999


No 117
>pfam08501 Shikimate_dh_N Shikimate dehydrogenase substrate binding domain. This domain is the substrate binding domain of shikimate dehydrogenase.
Probab=45.33  E-value=9.9  Score=17.29  Aligned_cols=48  Identities=17%  Similarity=0.275  Sum_probs=31.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             4587899999998402221034562366403454334402567676765352
Q gi|254780316|r  418 DVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGV  469 (805)
Q Consensus       418 ~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGY  469 (805)
                      +++.++..+.+..|.   ..+-.++.||+| |..++..-+|-+.|-||..|=
T Consensus        32 ~v~~~~l~~~~~~l~---~~~~~G~nVT~P-~K~~v~~~~d~~~~~A~~iGA   79 (83)
T pfam08501        32 EVPPDNLPEFVEGLR---ALGFRGLNVTIP-HKEAAIPLLDELSPEAKRIGA   79 (83)
T ss_pred             ECCHHHHHHHHHHHH---CCCCCEEEECHH-HHHHHHHHHCCCCHHHHHHCC
T ss_conf             068889999999985---489987998889-999999984417999998588


No 118
>PRK12310 hydroxylamine reductase; Provisional
Probab=45.23  E-value=19  Score=15.22  Aligned_cols=12  Identities=25%  Similarity=0.567  Sum_probs=5.3

Q ss_pred             EEEEEECCCCCC
Q ss_conf             898763677998
Q gi|254780316|r  749 VFDVFQGKSLGE  760 (805)
Q Consensus       749 lfDvY~g~~i~~  760 (805)
                      +-++|-|..+|.
T Consensus       386 vknI~lGPtlPa  397 (429)
T PRK12310        386 IKNIYIGPKLPE  397 (429)
T ss_pred             CCCEECCCCCCC
T ss_conf             775000898742


No 119
>TIGR01278 DPOR_BchB light-independent protochlorophyllide reductase, B subunit; InterPro: IPR005969    Synonym: dark protochlorophyllide reductase    Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite .; GO: 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction.
Probab=44.22  E-value=5.3  Score=19.20  Aligned_cols=82  Identities=16%  Similarity=0.279  Sum_probs=47.6

Q ss_pred             HHCCCC--CHHHHHHHHHHHHHHHHCC---CC----------CCEEEECCCCC-CCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             311345--8789999999840222103---45----------62366403454-33440256767676535233466765
Q gi|254780316|r  414 LSGIDV--PIEDSLRILERLGFSVIGE---YD----------KFEVSVPSWRQ-DVEEKADLVEEILRIYGVDQIKSEPL  477 (805)
Q Consensus       414 ilG~~i--~~~ei~~iL~~Lgf~v~~~---~~----------~~~V~vPs~R~-DI~~e~DLiEEIaRiyGYdnIp~~~l  477 (805)
                      -||++-  +-.++++.|+.||.+|..-   +.          -| +.+=.||= =..--    +=..+-.|.+-|-.+|+
T Consensus       173 ~LGFH~r~D~~elrrlL~~LG~evN~v~P~GA~i~dL~~lp~Aw-~NI~pYrE~G~~aA----~YL~E~Fg~p~i~~~Pi  247 (562)
T TIGR01278       173 SLGFHHRHDLIELRRLLKTLGIEVNVVAPWGASIADLARLPAAW-LNIAPYREIGLMAA----EYLKEKFGIPYITETPI  247 (562)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCEEEEEECCCCCCHHHHHHHHHHH-CCCCCCHHHHHHHH----HHHHHHCCCCHHHCCCC
T ss_conf             33423210338999999658947989737998858898866621-22355255899999----99987458850121777


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             54434576789988954678988787787740
Q gi|254780316|r  478 PLTQVEDKRNLSLQQSRTRYVKRVLASRAMME  509 (805)
Q Consensus       478 ~~~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~E  509 (805)
                               .+....++.++|+..+...|+..
T Consensus       248 ---------Gv~~T~~f~~~i~~~l~~~G~d~  270 (562)
T TIGR01278       248 ---------GVNATRRFIREIAALLNQAGADK  270 (562)
T ss_pred             ---------CHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             ---------66889999999999998648875


No 120
>PRK05290 hydroxylamine reductase; Provisional
Probab=43.87  E-value=19  Score=15.22  Aligned_cols=14  Identities=21%  Similarity=0.268  Sum_probs=7.5

Q ss_pred             EEEEEEEECCCCCC
Q ss_conf             69898763677998
Q gi|254780316|r  747 VTVFDVFQGKSLGE  760 (805)
Q Consensus       747 v~lfDvY~g~~i~~  760 (805)
                      .-+-++|-|..+|.
T Consensus       495 LGiknI~lGPtlPa  508 (540)
T PRK05290        495 LGVKNIRLGPTLPA  508 (540)
T ss_pred             CCCCCEEECCCCCC
T ss_conf             38774244898853


No 121
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=43.14  E-value=21  Score=15.01  Aligned_cols=40  Identities=23%  Similarity=0.354  Sum_probs=29.3

Q ss_pred             CCHHHHHHHHHHCCCEEEEEECC----CCCCCEEEEEEEEEEEC
Q ss_conf             98899999987458604211124----65687489999997565
Q gi|254780316|r   16 VSLEKICDTLTSIGLEVEKVDNR----EALSPFTIVKVLSVERN   55 (805)
Q Consensus        16 ~~~~~l~~~lt~~G~EVe~i~~~----~~~~~vvvg~v~~~~~h   55 (805)
                      .+-++|+.....+|.+.+-....    +..++||+|+|-+.++.
T Consensus        44 kteEEL~r~aeel~Vki~vtDdr~KVrk~~d~VvvGEV~s~~~~   87 (293)
T COG4079          44 KTEEELARKAEELGVKITVTDDRNKVRKRNDGVVVGEVSSVERG   87 (293)
T ss_pred             CCHHHHHHHHHHCCCEEEEECCHHHHHCCCCCEEEEEEECCCCC
T ss_conf             65899999999769779997164765223686799875203565


No 122
>TIGR01047 nspC carboxynorspermidine decarboxylase; InterPro: IPR005730    Carboxynorspermidine synthase, mediates the nicotinamide-nucleotide-linked reduction of the Schiff base H2N(CH2)3N = CHCH2CH(NH2)COOH. This is formed from L-aspartic beta-semialdehyde (ASA) and 1,3-diaminopropane (DAP) and is reduced to carboxynorspermidine [H2N(CH2)3NH(CH2)2CH(NH2)COOH], an intermediate in the novel pathway for norspermidine biosynthesis shown in Vibrio alginolyticus.; GO: 0016830 carbon-carbon lyase activity, 0045312 nor-spermidine biosynthetic process.
Probab=42.34  E-value=8.5  Score=17.77  Aligned_cols=72  Identities=25%  Similarity=0.331  Sum_probs=39.6

Q ss_pred             CCCEEEECCCCC-CCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH--HHH-HHHHHHHHCCCCCC
Q ss_conf             562366403454-33440256767676535233466765544345767899889546789--887-87787740232100
Q gi|254780316|r  440 DKFEVSVPSWRQ-DVEEKADLVEEILRIYGVDQIKSEPLPLTQVEDKRNLSLQQSRTRYV--KRV-LASRAMMEVVNWSF  515 (805)
Q Consensus       440 ~~~~V~vPs~R~-DI~~e~DLiEEIaRiyGYdnIp~~~l~~~~~~~~~~~~~~~~~~~~i--r~~-L~~~Gf~Ev~tysl  515 (805)
                      ....|..|.||. |+..-+||+.-|.    ||.+       .+.         .+++.++  |+. |-.+|..++.-===
T Consensus        77 kE~HvYsPay~e~d~~~I~~La~~i~----FNS~-------~Q~---------~~yr~~~~~K~~qlenlG~~~~k~GLR  136 (403)
T TIGR01047        77 KEVHVYSPAYKEEDLPEIIPLADHII----FNSL-------AQW---------ARYREKVEDKNSQLENLGLREVKLGLR  136 (403)
T ss_pred             CCEEEECCCCCHHHHHHHHHHHHHHH----HCCH-------HHH---------HHHHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             66687158888645888987741334----1037-------899---------999999999999888559750224123


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCC
Q ss_conf             4825765520000000024677
Q gi|254780316|r  516 ISKEQSVLFGGGQRELEILNPI  537 (805)
Q Consensus       516 ~s~~~~~~~~~~~~~i~l~NPl  537 (805)
                      ++++..      .-.-.|.||=
T Consensus       137 INPeyS------~v~~dLYNPc  152 (403)
T TIGR01047       137 INPEYS------EVETDLYNPC  152 (403)
T ss_pred             ECCCCC------CCCHHHCCCC
T ss_conf             467446------5661320878


No 123
>cd01914 HCP Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a central beta-sheet flanked by alpha-helices. HCP contains two iron-sulfur clusters, one of which is a [Fe4-S4] cubane cluster similar to that of carbon monoxide dehydrogenase (CODH).  The second cluster, referred to as the hybrid cluster, is a hybrid [Fe4-S2-O2] center located at the interface of the three domains. Although the hybrid cluster is buried within the protein, it is accessible through a large hydrophobic cavity.
Probab=42.26  E-value=21  Score=14.92  Aligned_cols=10  Identities=20%  Similarity=0.205  Sum_probs=3.4

Q ss_pred             HHHHHHHHHH
Q ss_conf             5557899987
Q gi|254780316|r  169 IGVRGIALDL  178 (805)
Q Consensus       169 ls~~GiAREl  178 (805)
                      -.+++++-|.
T Consensus        74 ~~ll~l~l~~   83 (423)
T cd01914          74 DELLALALET   83 (423)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999997


No 124
>TIGR01362 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase; InterPro: IPR006269   These sequences describe 2-dehydro-3-deoxyphosphooctonate aldolase. Alternate names include 3-deoxy-d-manno-octulosonic acid 8-phosphate and KDO-8 phosphate synthetase. It catalyzes the aldol condensation of phosphoenolpyruvate with D-arabinose 5-phosphate.   phosphoenolpyruvate + D-arabinose 5-phosphate + H_2O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate    In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide. ; GO: 0008676 3-deoxy-8-phosphooctulonate synthase activity, 0008152 metabolic process, 0005737 cytoplasm.
Probab=42.23  E-value=16  Score=15.84  Aligned_cols=25  Identities=32%  Similarity=0.299  Sum_probs=14.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             7857665557899987764115666
Q gi|254780316|r  163 PNRSDCIGVRGIALDLVAAGLGKLK  187 (805)
Q Consensus       163 pNR~D~ls~~GiARElaa~~~~~l~  187 (805)
                      +||.=.-|.+|.--|=+-...+++|
T Consensus        46 ANRtS~~SfRGpGle~GL~iL~kvK   70 (279)
T TIGR01362        46 ANRTSINSFRGPGLEEGLKILQKVK   70 (279)
T ss_pred             HHHCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             2321102436888789999999865


No 125
>COG0849 ftsA Cell division ATPase FtsA [Cell division and chromosome partitioning]
Probab=42.08  E-value=22  Score=14.90  Aligned_cols=12  Identities=25%  Similarity=0.462  Sum_probs=8.3

Q ss_pred             CEEEEECCCCCE
Q ss_conf             089997599957
Q gi|254780316|r   61 AILRIDTGKHQE   72 (805)
Q Consensus        61 ~v~~Vd~g~~~~   72 (805)
                      .+.-+|+|+.+.
T Consensus         7 ~iv~LDIGTskV   18 (418)
T COG0849           7 LIVGLDIGTSKV   18 (418)
T ss_pred             EEEEEECCCCEE
T ss_conf             499997267479


No 126
>TIGR01371 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; InterPro: IPR006276   This group represents cobalamin-independent methionine synthase. A family of uncharacterised archaeal proteins having substantial homology to the C-terminal region of this family, are not included in this group, though they are contained in a larger family of vitamin-B12 independent methionine synthase.; GO: 0003871 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity, 0009086 methionine biosynthetic process.
Probab=41.91  E-value=14  Score=16.27  Aligned_cols=93  Identities=24%  Similarity=0.322  Sum_probs=58.1

Q ss_pred             HCCCCCHHHHH--HHHHHHHHHHHCCCCCCEEEE----CCCCCCCCCHHHHHHHHHHHCCCCCC---CCCCCCCCCCCCC
Q ss_conf             11345878999--999984022210345623664----03454334402567676765352334---6676554434576
Q gi|254780316|r  415 SGIDVPIEDSL--RILERLGFSVIGEYDKFEVSV----PSWRQDVEEKADLVEEILRIYGVDQI---KSEPLPLTQVEDK  485 (805)
Q Consensus       415 lG~~i~~~ei~--~iL~~Lgf~v~~~~~~~~V~v----Ps~R~DI~~e~DLiEEIaRiyGYdnI---p~~~l~~~~~~~~  485 (805)
                      ||+|+-...-.  .-+..-||.-.   ..+..-|    =-||.|+.-.-++++.+.-..|-|+|   ||++|    .+.+
T Consensus       278 iglDfV~~~~~NL~~~~~~~~~~d---k~L~aGvIDGRNiW~~DL~a~l~~~~~l~~~~~~~~l~~~~SCSL----LHvP  350 (778)
T TIGR01371       278 IGLDFVHGKAQNLLELAKAGFPED---KVLSAGVIDGRNIWRADLEASLALLKKLLAHLGKDRLVVSTSCSL----LHVP  350 (778)
T ss_pred             EEEEEECCCCCCHHHHHHCCCCCC---CEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCC----CCCC
T ss_conf             543552371013698975257656---568876775731317889999999999998640886898268751----0676


Q ss_pred             CCCCHHHHHHHHHHHHHH--HHHHHHCCCCC
Q ss_conf             789988954678988787--78774023210
Q gi|254780316|r  486 RNLSLQQSRTRYVKRVLA--SRAMMEVVNWS  514 (805)
Q Consensus       486 ~~~~~~~~~~~~ir~~L~--~~Gf~Ev~tys  514 (805)
                      -.+..+.++...+|+.|+  ..-..|+....
T Consensus       351 v~L~~E~~LD~~~~~~LAFA~eKl~El~~L~  381 (778)
T TIGR01371       351 VDLELETKLDPELKSWLAFAKEKLEELKVLK  381 (778)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             2444443587678755436888999999999


No 127
>TIGR01995 PTS-II-ABC-beta PTS system, beta-glucoside-specific IIABC component; InterPro: IPR011297   The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) ,  is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.   The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).    The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site.    An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , .    This entry represents a family of PTS enzyme II proteins in which all three domains are found in the same polypeptide chain and which appear to have a broad specificity for beta-glucosides including salicin (beta-D-glucose-1-salicylate) and arbutin (hydroquinone-O-beta-D-glucopyranoside) . These are distinct from the closely related sucrose-specific and trehalose-specific PTS transporters.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system.
Probab=41.72  E-value=12  Score=16.65  Aligned_cols=15  Identities=33%  Similarity=0.403  Sum_probs=7.0

Q ss_pred             CCCHHHHHHH-HHHHC
Q ss_conf             5787888778-87616
Q gi|254780316|r  337 LWDPINIARS-GKNLG  351 (805)
Q Consensus       337 ~F~p~~Ir~t-ar~l~  351 (805)
                      ||-|..+.-| |||++
T Consensus       161 YFlPi~la~saAk~Fk  176 (660)
T TIGR01995       161 YFLPILLAISAAKRFK  176 (660)
T ss_pred             HHHHHHHHHHHHHHHC
T ss_conf             9889999976557727


No 128
>KOG1885 consensus
Probab=39.57  E-value=12  Score=16.73  Aligned_cols=74  Identities=23%  Similarity=0.360  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH--HHHCCCCCCCCCCC-CCCCCHHHCHHH-HHHHHHCCCCCCHHH
Q ss_conf             54678988787787740232100482576552000--00000246776432-101512211067-764321015861134
Q gi|254780316|r  493 SRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGG--QRELEILNPISADM-SNMRTSLLPGLL-KATGRNVDRAIADFA  568 (805)
Q Consensus       493 ~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~--~~~i~l~NPlS~e~-s~lR~SLlp~LL-~~~~~N~~r~~~~i~  568 (805)
                      +....||.+|-+.||-||-|--+...     .++.  +..|.--|-+  ++ =+||-  .|-|. +-+.   =-|..  |
T Consensus       230 kII~~iRkfld~rgFlEVETPmmn~i-----aGGA~AkPFIT~hndl--dm~LylRi--APEL~lK~Lv---VGGld--r  295 (560)
T KOG1885         230 KIISYIRKFLDSRGFLEVETPMMNMI-----AGGATAKPFITHHNDL--DMDLYLRI--APELYLKMLV---VGGLD--R  295 (560)
T ss_pred             HHHHHHHHHHHHCCCEEECCHHHCCC-----CCCCCCCCEEECCCCC--CCCEEEEE--CHHHHHHHHH---HCCHH--H
T ss_conf             99999999865449568444655254-----6863257604314556--75514563--6599999898---60178--9


Q ss_pred             HHHHCCCCCCCC
Q ss_conf             543024444777
Q gi|254780316|r  569 IFEVSHVYENDT  580 (805)
Q Consensus       569 lFEiG~Vf~~~~  580 (805)
                      +||||++|+++.
T Consensus       296 VYEIGr~FRNEG  307 (560)
T KOG1885         296 VYEIGRQFRNEG  307 (560)
T ss_pred             HHHHHHHHHHCC
T ss_conf             999878763057


No 129
>COG2877 KdsA 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]
Probab=39.51  E-value=18  Score=15.45  Aligned_cols=33  Identities=27%  Similarity=0.196  Sum_probs=19.9

Q ss_pred             EEEEEE-ECCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             599987-087857665557899987764115666
Q gi|254780316|r  155 PIIDVS-LTPNRSDCIGVRGIALDLVAAGLGKLK  187 (805)
Q Consensus       155 ~i~ei~-iTpNR~D~ls~~GiARElaa~~~~~l~  187 (805)
                      ++|.-+ =-+||.-.-|++|.--|-+--...++|
T Consensus        51 ~vfKsSfDKANRsSi~s~RGpGLeeglki~~~vK   84 (279)
T COG2877          51 YVFKSSFDKANRSSIHSYRGPGLEEGLKILQEVK   84 (279)
T ss_pred             EEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             6986243423333211246877888999999999


No 130
>cd01982 Chlide_reductase_Z Chlide_reductase_Z : Z subunit of chlorophyllide (chlide) reductase (BchZ).  Chlide reductase participates in photosynthetic pigment synthesis playing a role in the conversion of chlorophylls(Chl) into bacteriochlorophylls (BChl). Chlide reductase catalyzes the reduction of the B-ring of the tetrapyrolle. Chlide reductase is a three subunit enzyme (subunits are designated BchX, BchY and BchZ). The similarity between these three subunits and the subunits for nitrogenase suggests that BchX serves as an electron donor for the BchY-BchY catalytic subunits.
Probab=38.29  E-value=12  Score=16.78  Aligned_cols=23  Identities=17%  Similarity=0.368  Sum_probs=16.5

Q ss_pred             HCCCCC--HHHHHHHHHHHHHHHHC
Q ss_conf             113458--78999999984022210
Q gi|254780316|r  415 SGIDVP--IEDSLRILERLGFSVIG  437 (805)
Q Consensus       415 lG~~i~--~~ei~~iL~~Lgf~v~~  437 (805)
                      ||++-.  -.|++++|+.||.++..
T Consensus       166 lgF~~r~D~~EikRLL~~lGi~VN~  190 (412)
T cd01982         166 GCFNSPSDLAEVKRLVTGIGAEVNH  190 (412)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf             7778878899999999976984789


No 131
>TIGR01059 gyrB DNA gyrase, B subunit; InterPro: IPR011557   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .    Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.   This entry represents the B subunit (gyrB) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrB has two functional domains: an N-terminal ATPase and a C-terminal responsible for subunit interactions, the latter differing between subunit B and single polypeptide topoisomerase II .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=37.61  E-value=25  Score=14.44  Aligned_cols=115  Identities=16%  Similarity=0.220  Sum_probs=70.6

Q ss_pred             CCCC-CCCCCEEEE---ECCCCCCCEECCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHCC-CC--CCE---EEE------
Q ss_conf             3345-556525874---1355431000043113333113458789999999840222103-45--623---664------
Q gi|254780316|r  383 LCGG-TASDICIAR---NITYKPRKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSVIGE-YD--KFE---VSV------  446 (805)
Q Consensus       383 ~~gg-~~~~~~~~~---~~~~~~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~-~~--~~~---V~v------  446 (805)
                      -||| .+...-+-.   -.|..-|.+.+-.+++.|+|.    .+||..+...|||.+..+ -+  .+.   |.+      
T Consensus       441 SAGGcSAKqGRDR~fQAILPLrGKILNVEKaR~dK~l~----N~Ei~~~ItALG~GI~~d~Fdl~KLRYHKIIIMTDADV  516 (818)
T TIGR01059       441 SAGGCSAKQGRDRKFQAILPLRGKILNVEKARLDKILS----NDEIQAIITALGCGIGKDEFDLEKLRYHKIIIMTDADV  516 (818)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCEECEECCCHHHHHH----HHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEECCCC
T ss_conf             27776544467865434233245521000120455321----25338889973688676678723246443688406787


Q ss_pred             -----------CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             -----------0345433440256767676535233466765544345767899889546789887877877402321
Q gi|254780316|r  447 -----------PSWRQDVEEKADLVEEILRIYGVDQIKSEPLPLTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNW  513 (805)
Q Consensus       447 -----------Ps~R~DI~~e~DLiEEIaRiyGYdnIp~~~l~~~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~ty  513 (805)
                                 =.||+    --+|||.     ||==|. . ||+-.+...+.. ..-+-.+.+-++|...|.+++.=.
T Consensus       517 DGSHIRTLLLTFFYR~----M~~LIE~-----GyvYIA-q-PPLYKvk~gk~~-~Yikdd~e~d~yll~~~~~~~~l~  582 (818)
T TIGR01059       517 DGSHIRTLLLTFFYRY----MRPLIEN-----GYVYIA-Q-PPLYKVKKGKKE-RYIKDDKELDHYLLNLGINEAELV  582 (818)
T ss_pred             CHHHHHHHHHHHHHHH----HHHHHHC-----CCEEEE-C-CCCHHHHCCCCC-CCCCCHHHHHHHHHHHHCCCEEEE
T ss_conf             8368999999988740----1588745-----872650-7-860212046551-122277899889887532420265


No 132
>KOG0578 consensus
Probab=37.28  E-value=25  Score=14.39  Aligned_cols=11  Identities=36%  Similarity=0.398  Sum_probs=3.7

Q ss_pred             HHHHHHHHHCC
Q ss_conf             56767676535
Q gi|254780316|r  458 DLVEEILRIYG  468 (805)
Q Consensus       458 DLiEEIaRiyG  468 (805)
                      =|+.||.++-|
T Consensus       316 LilnEi~Vm~~  326 (550)
T KOG0578         316 LLLNEILVMRD  326 (550)
T ss_pred             HHHHHHHHHHH
T ss_conf             35779999874


No 133
>pfam05919 Mitovir_RNA_pol Mitovirus RNA-dependent RNA polymerase. This family consists of several Mitovirus RNA-dependent RNA polymerase proteins. The family also contains fragment matches in the mitochondria of Arabidopsis thaliana.
Probab=37.12  E-value=0.75  Score=25.25  Aligned_cols=72  Identities=17%  Similarity=0.174  Sum_probs=39.9

Q ss_pred             HHHHHCCCEEEECC---CCCCCEEEEEECCCCCCHHHHHHHCCCCCCCCEEEECCCCCCCCHHHCCCCCCCCCCCCC
Q ss_conf             99860870000010---223332688623554311455420112454320000256763100111355312013672
Q gi|254780316|r  256 VSLDRGYPSHVFDA---SRISDVLTVRRACSGEKILALDNQEYDLSPDNVVIASDGRIQSIAGIIGGKHAGCDDNTT  329 (805)
Q Consensus       256 vmle~GqPlHafD~---dki~~~i~vr~a~~~E~~~~Ld~~e~~L~~~~lvI~d~~~~ialaGImGg~~s~v~~~T~  329 (805)
                      |.+..||||-||--   =.+.-.++|..|..--  ..-.-..|.+-.+|+||+|++-+..--.||.-..-+|+.+-+
T Consensus       200 ~~y~~GQPmGa~sSwa~~aLtHH~iV~~~a~~~--~~~~f~~Y~iLGDDIvi~~~~vA~~Y~~iM~~LGVeIS~sKS  274 (495)
T pfam05919       200 LRYSVGQPMGAYSSWAMLALTHHLIVQVAAFRA--GKSRFTDYIILGDDIVIANDKVAKKYLEIMTDLGVEISLSKS  274 (495)
T ss_pred             EEEECCCCCHHHCCHHHHHHHHHHHHHHHHHHH--CCCCCCCEEEECCCEEECCHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             588468856001127999877899999999984--578777638853848984869999999999982811224754


No 134
>KOG2713 consensus
Probab=36.00  E-value=27  Score=14.26  Aligned_cols=16  Identities=31%  Similarity=0.308  Sum_probs=5.8

Q ss_pred             CHHHHHHHH-HHHHHHC
Q ss_conf             688875311-1111101
Q gi|254780316|r  617 DLFDAKADA-LSVIEPF  632 (805)
Q Consensus       617 df~dlKg~v-~~ll~~l  632 (805)
                      +..+.|-.+ +++++.+
T Consensus       283 ~~~~fK~~vaeAvie~L  299 (347)
T KOG2713         283 STADFKDNVAEAVIEHL  299 (347)
T ss_pred             CHHHHHHHHHHHHHHHH
T ss_conf             77777888999999974


No 135
>TIGR02628 fuculo_kin_coli L-fuculokinase; InterPro: IPR013450    Proteins in this entry are L-fuculokinases from the clade that includes the Escherichia coli enzyme P11553 from SWISSPROT. They catalyze the second step in fucose catabolism and belong to the FGGY family of carbohydrate kinases. These enzymes are encoded by the kinase (K) gene of the fucose (fuc) operon.; GO: 0008737 L-fuculokinase activity, 0005975 carbohydrate metabolic process.
Probab=35.29  E-value=19  Score=15.34  Aligned_cols=17  Identities=12%  Similarity=0.327  Sum_probs=12.4

Q ss_pred             HHHHHHHCCCCCCCCCCC
Q ss_conf             112332011232245566
Q gi|254780316|r  213 LCKGFAMCCVKGVRNNVA  230 (805)
Q Consensus       213 ~c~~y~~~~i~~v~~~~S  230 (805)
                      +||| +..|++||...-+
T Consensus       105 KCPR-T~pVM~n~e~~ld  121 (473)
T TIGR02628       105 KCPR-TVPVMENVERELD  121 (473)
T ss_pred             CCCC-CCHHHHHHHHHHH
T ss_conf             6888-6256888898865


No 136
>PRK06133 glutamate carboxypeptidase; Reviewed
Probab=35.18  E-value=27  Score=14.17  Aligned_cols=44  Identities=20%  Similarity=0.351  Sum_probs=29.3

Q ss_pred             HHHHHHHCCCCC-C-----H----HHHHHHHHHCCCEEEEEECCCCCCCEEEEE
Q ss_conf             679988478999-8-----8----999999874586042111246568748999
Q gi|254780316|r    5 LSWLKDHLDTDV-S-----L----EKICDTLTSIGLEVEKVDNREALSPFTIVK   48 (805)
Q Consensus         5 ~~WL~~~v~~~~-~-----~----~~l~~~lt~~G~EVe~i~~~~~~~~vvvg~   48 (805)
                      +.||+++|+++- |     +    +-++++|..+|++||-+.......+.+++.
T Consensus        48 l~~l~~lVni~Sgt~~~~gv~~v~~~~~~~l~~~G~~v~~~~~~~~~g~~l~a~  101 (418)
T PRK06133         48 LDTLRELVSIESGSGDAEGLKQVAALLAERLKALGATVELVPATPSAGDMVVAT  101 (418)
T ss_pred             HHHHHHHEECCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEE
T ss_conf             999998735078999768999999999999997799589964788868879999


No 137
>cd04750 Commd2 COMM_Domain containing protein 2. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=34.96  E-value=24  Score=14.58  Aligned_cols=96  Identities=15%  Similarity=0.128  Sum_probs=50.9

Q ss_pred             CHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCEECCCCHHHHHHCCC
Q ss_conf             87888778876165401554413455301358899988875212334555652587413554310000431133331134
Q gi|254780316|r  339 DPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLILSLCGGTASDICIARNITYKPRKIVFMNSEVKRLSGID  418 (805)
Q Consensus       339 ~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li~e~~gg~~~~~~~~~~~~~~~~~I~l~~~~i~~ilG~~  418 (805)
                      ||......|++|+            |+++.+..+..-++.|+.+-|--.+++....    ..-..+.|+.+...-++..-
T Consensus        15 n~k~y~~aA~kl~------------v~~~~Vq~aVe~L~~Ll~es~K~~l~e~df~----~sl~~lgf~ee~~~~L~q~y   78 (166)
T cd04750          15 NQKKYEGAARKLE------------VEVETVQHGVEALVYLLIESTKLKLSERDFQ----DSIEFLGFSDDLNEILLQLY   78 (166)
T ss_pred             CHHHHHHHHHHHC------------CCHHHHHHHHHHHHHHHHHHHHHHCCHHHHH----HHHHHCCCCHHHHHHHHHHH
T ss_conf             7679999999939------------9989999999999999999998717788899----88872688879999999999


Q ss_pred             C-CHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCH
Q ss_conf             5-8789999999840222103456236640345433440
Q gi|254780316|r  419 V-PIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEK  456 (805)
Q Consensus       419 i-~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e  456 (805)
                      - ...++..+|..++...- .     ..==-||.|++.-
T Consensus        79 ~~~r~~i~~~L~~~~~~lp-~-----y~nLeWRlDvqva  111 (166)
T cd04750          79 ESNRKEIRNILKELSPDLP-H-----YHNLEWRLDVQIA  111 (166)
T ss_pred             HHHHHHHHHHHHHCCCCCC-C-----CCCCCEEEEHHHH
T ss_conf             9989999999997598852-0-----0355401110105


No 138
>COG3971 2-keto-4-pentenoate hydratase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=34.56  E-value=28  Score=14.10  Aligned_cols=13  Identities=23%  Similarity=0.317  Sum_probs=4.3

Q ss_pred             CCCCCCCCHHHHH
Q ss_conf             2245566377878
Q gi|254780316|r  224 GVRNNVAPNWMRQ  236 (805)
Q Consensus       224 ~v~~~~SP~wl~~  236 (805)
                      |.|++.++.|||.
T Consensus        59 G~Kvglts~a~q~   71 (264)
T COG3971          59 GHKVGLTSPAMQQ   71 (264)
T ss_pred             EEEECCCCHHHHH
T ss_conf             2560568999998


No 139
>KOG0736 consensus
Probab=34.12  E-value=11  Score=17.02  Aligned_cols=24  Identities=21%  Similarity=0.272  Sum_probs=13.9

Q ss_pred             HHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             331134587899999998402221
Q gi|254780316|r  413 RLSGIDVPIEDSLRILERLGFSVI  436 (805)
Q Consensus       413 ~ilG~~i~~~ei~~iL~~Lgf~v~  436 (805)
                      .++|++=...+..++++.+.+.++
T Consensus       500 dvl~id~dgged~rl~~~i~~~ls  523 (953)
T KOG0736         500 DVLGIDQDGGEDARLLKVIRHLLS  523 (953)
T ss_pred             CEEEECCCCCHHHHHHHHHHHHHH
T ss_conf             245533777442779999999972


No 140
>pfam02027 RolB_RolC RolB/RolC glucosidase family. This family of proteins includes RolB and RolC. RolC releases cytokinins from glucoside conjugates. Whereas RolB hydrolyses indole glucosides.
Probab=33.66  E-value=29  Score=14.02  Aligned_cols=40  Identities=18%  Similarity=0.232  Sum_probs=25.1

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCH
Q ss_conf             3458789999999840222103456236640345433440
Q gi|254780316|r  417 IDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEK  456 (805)
Q Consensus       417 ~~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e  456 (805)
                      +-.+.+++..++++--+......+-+-+++|+||.|++..
T Consensus        77 VY~s~~~~~~~~~~~~l~~~~~~g~vattlpPY~~dvs~~  116 (189)
T pfam02027        77 VYVSRETMQQCVEGRSLPSNSSSGLVATTLPPYREDVSLA  116 (189)
T ss_pred             EEECHHHHHHHHHCCCCCCCCCCCEEEECCCCCCCCCCHH
T ss_conf             9918999999985897300477887898569755675699


No 141
>PRK08639 threonine dehydratase; Validated
Probab=32.79  E-value=30  Score=13.91  Aligned_cols=293  Identities=16%  Similarity=0.171  Sum_probs=132.8

Q ss_pred             CCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCC-CCHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             865054541188769985477507816888888-4558870888559998708785766555789998776411566665
Q gi|254780316|r  111 GIESTGMMCSEKELMLSDDSASIMELPIDAPVG-GRLSDYLELSDPIIDVSLTPNRSDCIGVRGIALDLVAAGLGKLKEI  189 (805)
Q Consensus       111 Gv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G-~~~~~~l~l~D~i~ei~iTpNR~D~ls~~GiARElaa~~~~~l~~~  189 (805)
                      |-.-+|+-.+++.||+.    ..+++|+.+|.- ....+.+|  -.++|+-+..+-  .--.+-.|++++.-.+..+-+|
T Consensus        82 GNHaqgvA~aa~~lgi~----a~IvmP~~tp~~Ki~~~r~~G--a~~veV~l~G~~--~dea~~~A~~~a~~~g~~~i~p  153 (418)
T PRK08639         82 GNHAQGVAYACRHLGIP----GVIFMPVTTPKQKIDQVRFFG--GEFVEIVLVGDT--FDDSAAAAQEYAEETGATFIPP  153 (418)
T ss_pred             CHHHHHHHHHHHHHCCC----EEEEECCCCHHHHHHHHHHCC--CCEEEEEECCCC--HHHHHHHHHHHHHHCCCCCCCC
T ss_conf             58999999999983996----899936667599999999629--966999971898--7999999999999709714587


Q ss_pred             CCCCCCCCCC---CCCEEEEEEE---CCCHHHHHHHCCCCCCCCCCCCHHHHHH---HHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             5456677777---7741589840---7311123320112322455663778788---88640132103999998999860
Q gi|254780316|r  190 NISCPLSSES---IPLEIKFDLD---DSSLCKGFAMCCVKGVRNNVAPNWMRQR---LKAVGLRSISALVDITNYVSLDR  260 (805)
Q Consensus       190 ~~~~~~~~~~---~~~~i~v~i~---~~~~c~~y~~~~i~~v~~~~SP~wl~~r---L~~~Gir~inniVDitNyvmle~  260 (805)
                       +..+....+   ...++--...   |.-.||.=.|..+.|+-     .|++..   ..-+|+-|-+.   -+=+--++.
T Consensus       154 -fdd~~vIaGqGTiglEI~eq~~~~~D~vvvpvGGGGLiaGia-----~~lK~~~P~ikIiGVEp~~a---~~m~~Sl~~  224 (418)
T PRK08639        154 -FDDPDVIAGQGTVAVEILEQLEEEPDYVFVPVGGGGLISGVT-----TYLKEVSPKTKVIGVEPAGA---ASMKAALEA  224 (418)
T ss_pred             -CCCCCHHHCCHHHHHHHHHHCCCCCCEEEEEECCCHHHHHHH-----HHHHHHCCCCEEEEEEECCC---HHHHHHHHC
T ss_conf             -788344632146999999856887888999618736899999-----99985099971899815897---689999985


Q ss_pred             CCCEEEECCCCCCCEEEEEECCCCC-CHHHH----------HHHCC-----CCCCCCEEEECCCCCCCCHHHCCCCCCCC
Q ss_conf             8700000102233326886235543-11455----------42011-----24543200002567631001113553120
Q gi|254780316|r  261 GYPSHVFDASRISDVLTVRRACSGE-KILAL----------DNQEY-----DLSPDNVVIASDGRIQSIAGIIGGKHAGC  324 (805)
Q Consensus       261 GqPlHafD~dki~~~i~vr~a~~~E-~~~~L----------d~~e~-----~L~~~~lvI~d~~~~ialaGImGg~~s~v  324 (805)
                      |.|...-..+++.+.+.|+..  |+ +|..+          ++.+.     .|-+..=+|+...+++++|+++... ..+
T Consensus       225 g~~v~~~~~~t~aDG~av~~~--G~~tf~i~~~~vd~iv~V~e~eI~~Am~~l~e~~k~vvEpaGA~~lAal~~~~-~~~  301 (418)
T PRK08639        225 GKPVTLEKIDKFVDGAAVARV--GDLTFEILKDVVDDVILVPEGAVCTTILELYNKEGIVAEPAGALSIAALDEYK-DEI  301 (418)
T ss_pred             CCCCCCCCCCCCCCCCCCCCC--CHHHHHHHHHHCCCCEEECHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCH-HHH
T ss_conf             996006876761133433545--56789999862897077289999999999999659822452899999998461-552


Q ss_pred             CCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCC--CCCCEEEEECCCCCC
Q ss_conf             136726999971578788877887616540155441345530135889998887521233455--565258741355431
Q gi|254780316|r  325 DDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLILSLCGGT--ASDICIARNITYKPR  402 (805)
Q Consensus       325 ~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li~e~~gg~--~~~~~~~~~~~~~~~  402 (805)
                      ...+--+++=-++.|....+.-..|--+...--++|-  +...-..=+|.+++..+   .|..  +..+  .|.... .+
T Consensus       302 ~gk~Vv~ilsGgNiD~~~l~~i~er~l~~~gr~~~~~--v~~pd~PG~l~~f~~~~---lg~~~~It~f--~y~r~~-~~  373 (418)
T PRK08639        302 KGKTVVCVISGGNNDIERMPEIKERSLRYEGLKHYFI--VNFPQRPGALREFLDDV---LGPDDDITRF--EYLKKN-NR  373 (418)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEE--EECCCCCCHHHHHHHHH---CCCCCCEEEE--EEEECC-CC
T ss_conf             6980999981588898899999999878629869999--97899997699999997---2999856899--878626-88


Q ss_pred             CEECCCCHHHHHHCCCCCH----HHHHHHHHHHHHHHHC
Q ss_conf             0000431133331134587----8999999984022210
Q gi|254780316|r  403 KIVFMNSEVKRLSGIDVPI----EDSLRILERLGFSVIG  437 (805)
Q Consensus       403 ~I~l~~~~i~~ilG~~i~~----~ei~~iL~~Lgf~v~~  437 (805)
                            +.-.-+.|+++..    +++.+.|+..||++..
T Consensus       374 ------~~~~v~vgie~~~~~~~~~l~~~l~~~g~~~~~  406 (418)
T PRK08639        374 ------ETGPVLIGIELKDAEDYDGLLARMEAFGPSYID  406 (418)
T ss_pred             ------CCEEEEEEEEECCHHHHHHHHHHHHHCCCCEEE
T ss_conf             ------704599999959877899999999977997698


No 142
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family    [General function prediction only]
Probab=32.55  E-value=30  Score=13.88  Aligned_cols=33  Identities=24%  Similarity=0.418  Sum_probs=19.5

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCC---------CCCEEEECCCC
Q ss_conf             4587899999998402221034---------56236640345
Q gi|254780316|r  418 DVPIEDSLRILERLGFSVIGEY---------DKFEVSVPSWR  450 (805)
Q Consensus       418 ~i~~~ei~~iL~~Lgf~v~~~~---------~~~~V~vPs~R  450 (805)
                      .++..++++.|+.+||......         ++-.|+||.+-
T Consensus         6 ~~~~ke~ik~Le~~Gf~~vrqkGSH~q~kHp~~~~vtVP~Hp   47 (66)
T COG1724           6 RMKAKEVIKALEKDGFQLVRQKGSHRQYKHPDGGRVTVPFHP   47 (66)
T ss_pred             CCCHHHHHHHHHHCCCEEEEEECCEEEEECCCCCEEEECCCC
T ss_conf             678899999998578489886233058875999879951788


No 143
>COG0381 WecB UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]
Probab=32.22  E-value=27  Score=14.21  Aligned_cols=22  Identities=23%  Similarity=0.353  Sum_probs=11.4

Q ss_pred             EEECCCC---CCCCCHHHHHHHHHHH
Q ss_conf             6640345---4334402567676765
Q gi|254780316|r  444 VSVPSWR---QDVEEKADLVEEILRI  466 (805)
Q Consensus       444 V~vPs~R---~DI~~e~DLiEEIaRi  466 (805)
                      +.+-.+|   .| ..-.++++.+.++
T Consensus       207 iLvT~HRreN~~-~~~~~i~~al~~i  231 (383)
T COG0381         207 ILVTAHRRENVG-EPLEEICEALREI  231 (383)
T ss_pred             EEEECCHHHCCC-CCHHHHHHHHHHH
T ss_conf             999705554036-4299999999999


No 144
>cd01990 Alpha_ANH_like_I This is a subfamily of Adenine nucleotide alpha hydrolases superfamily. Adenine nucleotide alpha hydrolases superfamily  includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which  binds to Adenosine group.  This subfamily   of proteins probably binds ATP. This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N terminus.
Probab=32.04  E-value=31  Score=13.82  Aligned_cols=55  Identities=16%  Similarity=0.282  Sum_probs=34.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHCC--CCCCEEEECCCC---CCCCCHHHHHHHHHHHCCCCCC
Q ss_conf             458789999999840222103--456236640345---4334402567676765352334
Q gi|254780316|r  418 DVPIEDSLRILERLGFSVIGE--YDKFEVSVPSWR---QDVEEKADLVEEILRIYGVDQI  472 (805)
Q Consensus       418 ~i~~~ei~~iL~~Lgf~v~~~--~~~~~V~vPs~R---~DI~~e~DLiEEIaRiyGYdnI  472 (805)
                      .+++++|.++-+.||+.+-.+  ...+...+|..-   .+-...++-.|++.|-+||..+
T Consensus       131 gl~K~eVR~la~~lgLp~~~kp~~~CLasRip~g~~it~e~L~~v~~aE~~L~~~G~~~~  190 (202)
T cd01990         131 GLGKAEIRELARELGLPTWDKPAMACLASRIPYGTEITEERLKKVEAAEEFLRSLGFREV  190 (202)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCE
T ss_conf             978899999999839985668998754666578884899999999999999998199827


No 145
>PRK03634 rhamnulose-1-phosphate aldolase; Provisional
Probab=32.00  E-value=31  Score=13.82  Aligned_cols=32  Identities=16%  Similarity=0.426  Sum_probs=17.6

Q ss_pred             EEEEEECCCCCCCEEEEECCCCCEEEEECCCCC
Q ss_conf             999756579987089997599957989754834
Q gi|254780316|r   49 VLSVERNPDLDCAILRIDTGKHQEIQVVCGAPN   81 (805)
Q Consensus        49 v~~~~~hP~adl~v~~Vd~g~~~~~~IvcgA~N   81 (805)
                      ...+...|..++-+++||.+. +-++|+-|+.+
T Consensus        79 fR~v~~~P~~~~~ii~I~~~G-~~y~i~wG~~~  110 (274)
T PRK03634         79 FRNVQLDPAANLGVIKVDSDG-AGYHILWGLTN  110 (274)
T ss_pred             HHHCCCCHHHCCEEEEECCCC-CEEEEEECCCC
T ss_conf             654002822335089996898-67898750577


No 146
>TIGR02700 flavo_MJ0208 archaeoflavoprotein, MJ0208 family; InterPro: IPR014073   This entry describes one of two paralogous families of archaeal flavoprotein. The other, described by IPR014072 from INTERPRO and typified by the partially characterised AF1518 of ArchaArchaeoglobus fulgidus, is a homodimeric FMN-containing flavoprotein that accepts electrons from ferredoxin and can transfer them to various oxidoreductases. The function of this protein family is unknown..
Probab=32.00  E-value=16  Score=15.86  Aligned_cols=10  Identities=50%  Similarity=1.072  Sum_probs=5.3

Q ss_pred             HHHHHHHCCC
Q ss_conf             7676765352
Q gi|254780316|r  460 VEEILRIYGV  469 (805)
Q Consensus       460 iEEIaRiyGY  469 (805)
                      .|||.||||.
T Consensus        40 gEEVvrMyGL   49 (237)
T TIGR02700        40 GEEVVRMYGL   49 (237)
T ss_pred             HHHHHHHHCC
T ss_conf             2233541131


No 147
>smart00842 FtsA Cell division protein FtsA. FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. It has been suggested that the interaction of FtsA-FtsZ has arisen through coevolution in different bacterial strains PUBMED:9352931.
Probab=31.26  E-value=32  Score=13.74  Aligned_cols=91  Identities=14%  Similarity=0.196  Sum_probs=58.0

Q ss_pred             HCCC--CCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCEECCCCHHHHHHCCCCCHHHHHHHHHHHHHHHH-
Q ss_conf             1345--5301358899988875212334555652587413554310000431133331134587899999998402221-
Q gi|254780316|r  360 FERG--VDLQGMIPVLKHIVSLILSLCGGTASDICIARNITYKPRKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSVI-  436 (805)
Q Consensus       360 fERg--vd~~~~~~al~r~~~Li~e~~gg~~~~~~~~~~~~~~~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~-  436 (805)
                      ..+|  +|.+.+..++.++++-..+.+|.++..+.+..+-.. .+......  --.+-|-.++.+++.+.++..-.... 
T Consensus        37 i~~G~I~d~~~~~~~I~~ai~~aE~~ag~~I~~V~v~isg~~-~~s~~~~~--~~~i~~~~It~~DI~~~~~~a~~~~~~  113 (187)
T smart00842       37 IRKGVIVDIEAAARAIREAVEEAERMAGVKIDSVYVGISGRH-LKSVNVSG--VVAIPDKEITQEDIDRVLEAAKAVALP  113 (187)
T ss_pred             EECCEEECHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCC-EEEEEEEE--EEECCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             078999828999999999999998743874257999966885-79999899--998898792899999999985632469


Q ss_pred             CCCCCCEEEECCCCCCC
Q ss_conf             03456236640345433
Q gi|254780316|r  437 GEYDKFEVSVPSWRQDV  453 (805)
Q Consensus       437 ~~~~~~~V~vPs~R~DI  453 (805)
                      .+.+-+.+.+..|+.|=
T Consensus       114 ~~~~ilh~~p~~y~iD~  130 (187)
T smart00842      114 PDREILHVLPQEYILDG  130 (187)
T ss_pred             CCCEEEEEEEEEEEECC
T ss_conf             88469999832679958


No 148
>pfam08536 Whirly Whirly transcription factor. This family contains the plant whirly transcription factors.
Probab=30.48  E-value=32  Score=13.65  Aligned_cols=68  Identities=13%  Similarity=0.035  Sum_probs=32.0

Q ss_pred             CCCHHHHHHHHHHCCCE--EEEEEC-CC-CCCCEEEEEEEEEEECCCCCCCEEEEECCCCCEEEEECCCCCCCCCCEEEE
Q ss_conf             99889999998745860--421112-46-568748999999756579987089997599957989754834558978989
Q gi|254780316|r   15 DVSLEKICDTLTSIGLE--VEKVDN-RE-ALSPFTIVKVLSVERNPDLDCAILRIDTGKHQEIQVVCGAPNVRVGLLGVW   90 (805)
Q Consensus        15 ~~~~~~l~~~lt~~G~E--Ve~i~~-~~-~~~~vvvg~v~~~~~hP~adl~v~~Vd~g~~~~~~IvcgA~Nv~~g~~V~~   90 (805)
                      .+|+.|+.+-++ +|..  +|-+|+ .. .-..=.|.|+++++||||-.-..        --++|+.+..|+.+...|||
T Consensus        56 ~LS~tEvG~l~s-l~~~~sceFfHDP~~~~s~~G~v~K~Lkvep~pdGsG~F--------~nlsV~n~~~~~~e~~~ipV  126 (139)
T pfam08536        56 MLSATEAGELAS-MAPNGSCEFFHDPSAGGSNAGQVRKALKVEPMPDGSGYF--------VNLSVTNSINKGNERFSVPV  126 (139)
T ss_pred             EECHHHHHHHHH-HCCCCCEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEE--------EEEEEECCCCCCCCEEEEEE
T ss_conf             857999645663-447997047727665788876256667755769996589--------99998726635676599863


Q ss_pred             E
Q ss_conf             6
Q gi|254780316|r   91 A   91 (805)
Q Consensus        91 A   91 (805)
                      -
T Consensus       127 t  127 (139)
T pfam08536       127 T  127 (139)
T ss_pred             E
T ss_conf             2


No 149
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=30.23  E-value=33  Score=13.62  Aligned_cols=43  Identities=14%  Similarity=0.207  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCC
Q ss_conf             7787888864013210399999899986087000001022333
Q gi|254780316|r  232 NWMRQRLKAVGLRSISALVDITNYVSLDRGYPSHVFDASRISD  274 (805)
Q Consensus       232 ~wl~~rL~~~Gir~inniVDitNyvmle~GqPlHafD~dki~~  274 (805)
                      .++++=|...|+..+.-.-+=.|-+|.+..+..|.-|+|-...
T Consensus        89 ~~i~~N~~~N~~~~~~v~~~dAn~lm~~~~~~fD~IDlDPfGS  131 (376)
T PRK04338         89 ELIKKNLELNGLENAEVFNEDANVLLHENERKFDVVDIDPFGS  131 (376)
T ss_pred             HHHHHHHHHHCCCCEEEECCCHHHHHHHCCCCCCEEEECCCCC
T ss_conf             9999999982998269813248999983787587786789999


No 150
>COG3705 HisZ ATP phosphoribosyltransferase involved in histidine biosynthesis [Amino acid transport and metabolism]
Probab=30.05  E-value=33  Score=13.60  Aligned_cols=79  Identities=20%  Similarity=0.308  Sum_probs=39.0

Q ss_pred             CCCCCCCEEEEEECCE-EEEEEEEEECHHHHHHCCCCCCEEEEEEEHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEEE
Q ss_conf             5678981699998792-999998547789999668799789999878762354520245663136898887200189996
Q gi|254780316|r  646 SWYHPGRSGIIKTSAE-IVLGYFGEFHPNILDFFGLSNPICGFEVYLDSIPISQKKRTKTKKVVHLSSLHPVKRDLAFIV  724 (805)
Q Consensus       646 ~~~hPgrsa~I~~~gk-~iiG~iG~ihP~i~~~~~i~~~v~~~EI~ld~L~~~~~~~~~~~~~~~~s~fP~v~RDls~iv  724 (805)
                      ..||.|+....+.++- ..++--|... ..+..|+=..|...|+++++.|...              .-|.-++.....+
T Consensus       266 ~~YyTg~~F~ay~~~~~~al~~GGRYd-~l~~~f~~~~patGf~~~l~~l~~~--------------~~~~~~~~~~~~f  330 (390)
T COG3705         266 FDYYTGLVFLAYADGLGDALASGGRYD-GLLGLFGRAAPATGFALRLDALAQG--------------GLPLEERRYAALF  330 (390)
T ss_pred             CCHHHCEEEEEEECCCCCHHHCCCCHH-HHHHHCCCCCCCHHHHHHHHHHHHC--------------CCCCCCCHHHHCC
T ss_conf             431220023465256564332142200-0233227666640167319999834--------------7885443022203


Q ss_pred             CCCCC--HHHHHHHHHH
Q ss_conf             68879--9999999971
Q gi|254780316|r  725 DQHIP--AGTLVNIIKN  739 (805)
Q Consensus       725 ~~~v~--~~~I~~~i~~  739 (805)
                      +....  .+.+.+.+.+
T Consensus       331 ~~~~~~~~~~~~e~~~~  347 (390)
T COG3705         331 GRELDYYTGAAFEAAQA  347 (390)
T ss_pred             CCCCHHHHHHHHHHHHH
T ss_conf             75401567799999997


No 151
>TIGR01124 ilvA_2Cterm threonine ammonia-lyase, biosynthetic; InterPro: IPR005787    Serine and threonine dehydratases ,  are functionally and structurally related pyridoxal-phosphate dependent enzymes. L-serine dehydratase () and D-serine dehydratase () catalyze the dehydratation of L-serine (respectively D-serine) into ammonia and pyruvate. Threonine dehydratase () (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism. Threonine synthase () is also a pyridoxal-phosphate enzyme, it catalyzes the transformation of homoserine-phosphate into threonine. It has been shown  that threonine synthase is distantly related to the serine/threonine dehydratases. In all these enzymes, the pyridoxal-phosphate group is attached to a lysine residue.    This family describes a form of threonine dehydratase, with two copies of the threonine dehydratase C-terminal domain IPR001721 from INTERPRO. Members with known function participate in isoleucine biosynthesis and are inhibited by isoleucine.; GO: 0004794 L-threonine ammonia-lyase activity, 0009097 isoleucine biosynthetic process.
Probab=29.98  E-value=27  Score=14.21  Aligned_cols=155  Identities=18%  Similarity=0.250  Sum_probs=76.3

Q ss_pred             CCCCCCCHHHHHHHCCCCCCCCCEEEECCCCC-CCCCHHHHHCCCCEEEEEEECCCHHHHHHH-HHHHHHHHHHHCCCCC
Q ss_conf             58650545411887699854775078168888-884558870888559998708785766555-7899987764115666
Q gi|254780316|r  110 RGIESTGMMCSEKELMLSDDSASIMELPIDAP-VGGRLSDYLELSDPIIDVSLTPNRSDCIGV-RGIALDLVAAGLGKLK  187 (805)
Q Consensus       110 rGv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~-~G~~~~~~l~l~D~i~ei~iTpNR~D~ls~-~GiARElaa~~~~~l~  187 (805)
                      -|-.-+|-=-|++-||+.    -++|.|+.+| +=.+..+-+| ...|+       +||-+|- .+-|+||+---+..+-
T Consensus        75 AGNHAQGVAlsa~~LG~~----A~IVMP~tTP~IKV~AVk~~G-geVvL-------hG~~y~~A~~~A~eL~q~~GlTfi  142 (508)
T TIGR01124        75 AGNHAQGVALSAEKLGLK----AVIVMPETTPDIKVDAVKAFG-GEVVL-------HGDNYDDAKDHAIELAQEKGLTFI  142 (508)
T ss_pred             CCCHHHHHHHHHHHCCCC----EEEECCCCCCCCCHHHEECCC-CEEEE-------ECCCHHHHHHHHHHHHHHCCCEEE
T ss_conf             454578998766317972----698788888220012031269-87997-------379857999999999973688652


Q ss_pred             CCCCCCCCCCCC--------------CCCEEEEEEECCCHHHHHHHCCCCCC---------CCCCCCHHHHHHHHHHCCC
Q ss_conf             655456677777--------------77415898407311123320112322---------4556637787888864013
Q gi|254780316|r  188 EINISCPLSSES--------------IPLEIKFDLDDSSLCKGFAMCCVKGV---------RNNVAPNWMRQRLKAVGLR  244 (805)
Q Consensus       188 ~~~~~~~~~~~~--------------~~~~i~v~i~~~~~c~~y~~~~i~~v---------~~~~SP~wl~~rL~~~Gir  244 (805)
                      +| +..|....+              .-..|=|.|--..+.-- ++..||.+         .-.+| .=|+.-       
T Consensus       143 ~P-FDdPlVIAGQGT~alEil~Q~~~~~davFVpvGGGGLiAG-VA~~~K~l~P~IkvIGVEp~DS-~am~~s-------  212 (508)
T TIGR01124       143 HP-FDDPLVIAGQGTVALEILRQVAEDLDAVFVPVGGGGLIAG-VAALVKQLMPEIKVIGVEPTDS-DAMKQS-------  212 (508)
T ss_pred             CC-CCCCCEECCCHHHHHHHHHCCCCCCCEEEEECCCCHHHHH-HHHHHHHCCCCEEEEEECCCHH-HHHHHH-------
T ss_conf             78-8886403251066687650576847688871177368999-9999972289618997478659-999999-------


Q ss_pred             CCHHHHHHHHHHHHHHCCCEEEECCCCC---CCEEEEEECCCCCCHHHHHHHCCCCCCCCEEEECCC
Q ss_conf             2103999998999860870000010223---332688623554311455420112454320000256
Q gi|254780316|r  245 SISALVDITNYVSLDRGYPSHVFDASRI---SDVLTVRRACSGEKILALDNQEYDLSPDNVVIASDG  308 (805)
Q Consensus       245 ~inniVDitNyvmle~GqPlHafD~dki---~~~i~vr~a~~~E~~~~Ld~~e~~L~~~~lvI~d~~  308 (805)
                                   |+-|.|.   +++.+   .+.+-||...+ |||-+ - ++| |  +|+|-.|.+
T Consensus       213 -------------L~AG~~V---~L~~VGlFaDGVAVk~vG~-~TF~L-C-~~Y-v--Dd~v~VdtD  257 (508)
T TIGR01124       213 -------------LEAGERV---DLDQVGLFADGVAVKEVGD-ETFRL-C-QQY-V--DDIVRVDTD  257 (508)
T ss_pred             -------------HHCCCCC---CCCCCCEEECCEEEHHHHH-HHHHH-H-HHH-C--CCEEEECCH
T ss_conf             -------------8568811---3771103426735400434-45899-9-974-4--554862644


No 152
>pfam08676 MutL_C MutL C terminal dimerization domain. MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognizes mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerization.
Probab=29.70  E-value=33  Score=13.56  Aligned_cols=59  Identities=27%  Similarity=0.392  Sum_probs=38.4

Q ss_pred             CCCCCCEECCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCC-CCEE-EECCCCCCCCCHHHHHHHHH
Q ss_conf             5543100004311333311345878999999984022210345-6236-64034543344025676767
Q gi|254780316|r  398 TYKPRKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSVIGEYD-KFEV-SVPSWRQDVEEKADLVEEIL  464 (805)
Q Consensus       398 ~~~~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~~~-~~~V-~vPs~R~DI~~e~DLiEEIa  464 (805)
                      -..|..+.++......+       .+....|+++||.++.-++ .+.| .+|+|=.. ....++++|++
T Consensus        52 Ll~P~~i~l~~~e~~~l-------~~~~~~l~~lGf~~e~~g~~~~~i~~vP~~l~~-~~~~~~i~~il  112 (142)
T pfam08676        52 LLIPLTLELSPEEAALL-------EEHKELLARLGFELEEFGPNSLIVRSVPALLRQ-QNLEELIRELL  112 (142)
T ss_pred             CCCCCEECCCHHHHHHH-------HHHHHHHHHCCEEEEECCCCEEEEEEECCCCCC-CCHHHHHHHHH
T ss_conf             57896331699999999-------999999997793999558999999984855577-58999999999


No 153
>PTZ00031 ribosomal protein L2; Provisional
Probab=29.22  E-value=34  Score=13.50  Aligned_cols=43  Identities=21%  Similarity=0.240  Sum_probs=16.9

Q ss_pred             EEEEEEEEEECCCCCCCEEEEECCCCCEEEEECCCCCCCCCCEE
Q ss_conf             89999997565799870899975999579897548345589789
Q gi|254780316|r   45 TIVKVLSVERNPDLDCAILRIDTGKHQEIQVVCGAPNVRVGLLG   88 (805)
Q Consensus        45 vvg~v~~~~~hP~adl~v~~Vd~g~~~~~~IvcgA~Nv~~g~~V   88 (805)
                      +.|+|..+|=-||---+|+-|...+++..-|++ ..++++|+.|
T Consensus       119 i~a~V~~IEYDPNRSA~IALv~y~DGek~YILA-P~glkvGD~I  161 (330)
T PTZ00031        119 IYSTVLRIEYDPTRSAHVALIQYEDGVLSYILC-PAGVRPGDKL  161 (330)
T ss_pred             CCEEEEEEEECCCCCEEEEEEECCCCCEEEEEC-CCCCCCCCEE
T ss_conf             977999987899998068999847996889977-4898789989


No 154
>pfam09866 DUF2093 Uncharacterized protein conserved in bacteria (DUF2093). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=28.70  E-value=35  Score=13.44  Aligned_cols=19  Identities=26%  Similarity=0.338  Sum_probs=14.9

Q ss_pred             CCCCCEEEEECCCCEECCC
Q ss_conf             5589789896687792589
Q gi|254780316|r   82 VRVGLLGVWAPPGSCIPEN  100 (805)
Q Consensus        82 v~~g~~V~~A~~Ga~lp~g  100 (805)
                      +++|.+|.+|.-|.++|-.
T Consensus         2 i~~G~~V~CAVsgk~IpL~   20 (42)
T pfam09866         2 LSPGSFVLCAVTGEPIPLD   20 (42)
T ss_pred             CCCCCEEEEEEECCEECHH
T ss_conf             4579998997409800264


No 155
>TIGR02045 P_fruct_ADP ADP-specific phosphofructokinase; InterPro: IPR011790   Phosphofructokinase is a key enzyme of glycolysis. The phosphate group donor for different subtypes of phosphofructokinase can be ATP, ADP, or pyrophosphate. This family consists of ADP-dependent phosphofructokinases found in archaea. Members are more similar to ADP-dependent glucokinases (excluded from this family) than to other phosphofructokinases .; GO: 0008443 phosphofructokinase activity, 0006000 fructose metabolic process, 0006096 glycolysis, 0005737 cytoplasm.
Probab=28.61  E-value=20  Score=15.07  Aligned_cols=27  Identities=30%  Similarity=0.604  Sum_probs=11.2

Q ss_pred             HHHHHHHHHHHHCCCCC-CCCHHHHHHH
Q ss_conf             98878778774023210-0482576552
Q gi|254780316|r  498 VKRVLASRAMMEVVNWS-FISKEQSVLF  524 (805)
Q Consensus       498 ir~~L~~~Gf~Ev~tys-l~s~~~~~~~  524 (805)
                      +.+.|+.+++.+|+-|+ |.|++.++.|
T Consensus        96 isNLL~~L~~~kvi~YtPfLsk~qAE~F  123 (466)
T TIGR02045        96 ISNLLARLQLKKVIVYTPFLSKRQAEMF  123 (466)
T ss_pred             HHHHHCCCCEEEEEEECCCCHHHHHHHH
T ss_conf             9987503870079986787616788764


No 156
>pfam05339 DUF739 Protein of unknown function (DUF739). This family contains several bacteriophage proteins. Some of the proteins in this family have been labeled putative cro repressor proteins.
Probab=28.57  E-value=12  Score=16.77  Aligned_cols=19  Identities=32%  Similarity=0.529  Sum_probs=15.3

Q ss_pred             CCCHHHHHHHHHHHCCCCH
Q ss_conf             5787888778876165401
Q gi|254780316|r  337 LWDPINIARSGKNLGIITD  355 (805)
Q Consensus       337 ~F~p~~Ir~tar~l~l~Td  355 (805)
                      .|....|.++..-|++.+|
T Consensus        42 ~w~q~ei~kai~lL~i~~d   60 (69)
T pfam05339        42 IWVANEIEKAIDLLGIPKD   60 (69)
T ss_pred             CCCHHHHHHHHHHHCCCHH
T ss_conf             7539999999999689988


No 157
>TIGR01792 urease_alph urease, alpha subunit; InterPro: IPR005848    Urease (urea amidohydrolase, 3.5.1.5 from EC) catalyses the hydrolysis of urea to form ammonia and carbamate. The subunit composition of urease from different sources varies , but each holoenzyme consists of four structural domains : three structural domains and a nickel-binding catalytic domain common to amidohydrolases . Urease is unique among nickel metalloenzymes in that it catalyses a hydrolysis rather than a redox reaction. In Helicobacter pylori, the gamma and beta domains are fused and called the alpha subunit (IPR008223 from INTERPRO). The catalytic subunit (called beta or B) has the same organization as the Klebsiella alpha subunit. Jack bean (Canavalia ensiformis) urease has a fused gamma-beta-alpha organization (IPR008221 from INTERPRO). This entry describes the urease alpha subunit UreC (designated beta or B chain, UreB in Helicobacter species).    Urease (3.5.1.5 from EC) belongs to MEROPS peptidase family M38 (clan MJ). ; GO: 0009039 urease activity, 0016151 nickel ion binding, 0006807 nitrogen compound metabolic process.
Probab=27.83  E-value=36  Score=13.34  Aligned_cols=79  Identities=19%  Similarity=0.220  Sum_probs=45.4

Q ss_pred             EEEEEE--ECHHHHHHCCCCCCEEEEEEEHH-HHHHHHHCCCCCCCCCCCCCCCC-CEEE---EEEEECC-------CCC
Q ss_conf             999854--77899996687997899998787-62354520245663136898887-2001---8999668-------879
Q gi|254780316|r  664 LGYFGE--FHPNILDFFGLSNPICGFEVYLD-SIPISQKKRTKTKKVVHLSSLHP-VKRD---LAFIVDQ-------HIP  729 (805)
Q Consensus       664 iG~iG~--ihP~i~~~~~i~~~v~~~EI~ld-~L~~~~~~~~~~~~~~~~s~fP~-v~RD---ls~iv~~-------~v~  729 (805)
                      +-|+-+  +.--+.++|+|+..+. .--|.- .|-...        -+--|-.|. ++=|   ..+-||=       +.+
T Consensus       500 ~TFVS~~a~d~gi~e~~gL~k~~~-pV~N~RG~igK~~--------Mk~N~~~P~tieVDPqTydV~vDGndlenWleqP  570 (605)
T TIGR01792       500 VTFVSQAAYDKGIKERLGLEKKLL-PVKNTRGSIGKAD--------MKLNSATPKTIEVDPQTYDVKVDGNDLENWLEQP  570 (605)
T ss_pred             EEHEEHHHHHHCHHHHHCCCEEEE-EECCCCCCCCCCC--------CCCCCCCCCCEEECCCCEEEEECHHHHHHHHCCH
T ss_conf             401025345512376608320688-5315478777434--------4322678860111786115774213677664051


Q ss_pred             HHHHHHHHHH-C-CCCEEEEEEEE
Q ss_conf             9999999971-1-10035769898
Q gi|254780316|r  730 AGTLVNIIKN-V-DRLIDDVTVFD  751 (805)
Q Consensus       730 ~~~I~~~i~~-~-~~ll~~v~lfD  751 (805)
                      +.++.+.+|+ + ++.+-.+++.|
T Consensus       571 aaelakklkktanGk~~~t~~P~~  594 (605)
T TIGR01792       571 AAELAKKLKKTANGKELITVEPAD  594 (605)
T ss_pred             HHHHHHHHHHHCCCCEEECCCCCC
T ss_conf             789999875421787675257757


No 158
>TIGR02342 chap_CCT_delta T-complex protein 1, delta subunit; InterPro: IPR012717    Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT delta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=27.68  E-value=17  Score=15.65  Aligned_cols=122  Identities=24%  Similarity=0.305  Sum_probs=66.9

Q ss_pred             ECCCCHHHHHHC---CCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHH--------HHHCCCCC-C
Q ss_conf             004311333311---34587899999998402221034562366403454334402567676--------76535233-4
Q gi|254780316|r  405 VFMNSEVKRLSG---IDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEI--------LRIYGVDQ-I  472 (805)
Q Consensus       405 ~l~~~~i~~ilG---~~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEI--------aRiyGYdn-I  472 (805)
                      ++.+.+++|.-=   -+|+.++|.-+=+.|||....+       |-.|-.|-...+||+|||        .|+-|..| -
T Consensus       296 dlaLHfL~K~~I~vvKDIeRe~veF~~k~lGc~PiA~-------id~f~~d~LG~A~lvEev~~~~~~k~~kitG~~~~~  368 (526)
T TIGR02342       296 DLALHFLAKMKIMVVKDIEREEVEFISKTLGCKPIAS-------IDHFTADKLGKAELVEEVKTSDDSKIIKITGVQNNN  368 (526)
T ss_pred             HHHHHHHHHCCEEEEEECCCCCHHHHHHHCCCCCEEC-------CCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCC
T ss_conf             8999998428817986056131455643218840202-------114482006874114532238981389985224688


Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             66765544345767899889546789887877877402321004825765520000000024677643210
Q gi|254780316|r  473 KSEPLPLTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPISADMSN  543 (805)
Q Consensus       473 p~~~l~~~~~~~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s~  543 (805)
                      +.++.. --....+.+ .-..-+|.+-+.|+=       ==+|+.++.+ .-|++...++|.--|++.-..
T Consensus       369 ~~~tV~-v~~RGSN~L-vi~EAeRSlHDALCV-------iRsLVk~r~L-~~GGGaPE~E~a~~L~~~a~~  429 (526)
T TIGR02342       369 AGKTVT-VLVRGSNKL-VIDEAERSLHDALCV-------IRSLVKKRAL-IAGGGAPEIEIALKLSKLART  429 (526)
T ss_pred             CCCEEE-EEEECCCCH-HHHHHHHHHHHHHHH-------HHHHHHCCCC-CCCCCCCHHHHHHHHHHHHHH
T ss_conf             886278-998068602-242332215678999-------9988750651-388695289999999986654


No 159
>pfam02311 AraC_binding AraC-like ligand binding domain. This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.
Probab=27.67  E-value=36  Score=13.32  Aligned_cols=107  Identities=17%  Similarity=0.277  Sum_probs=63.4

Q ss_pred             HCCCEEEECCCCCCCEEEEEECCCCCCHHHHHHHCCCCCCCCEEEECCCCCCCCHHHCCCCCCCCCCCCCEEEEEEECCC
Q ss_conf             08700000102233326886235543114554201124543200002567631001113553120136726999971578
Q gi|254780316|r  260 RGYPSHVFDASRISDVLTVRRACSGEKILALDNQEYDLSPDNVVIASDGRIQSIAGIIGGKHAGCDDNTTDVLVEVALWD  339 (805)
Q Consensus       260 ~GqPlHafD~dki~~~i~vr~a~~~E~~~~Ld~~e~~L~~~~lvI~d~~~~ialaGImGg~~s~v~~~T~~illEsA~F~  339 (805)
                      .+.|-|.|.. ...+...+-...+|+.....+|+++.+.++++++..-+.+-          +...+.+...-.=+-+|+
T Consensus         9 a~~~~~~f~~-H~H~~~~i~~i~~G~~~~~~~~~~~~~~~G~~~li~P~~~H----------~~~~~~~~~~~y~~l~~~   77 (134)
T pfam02311         9 ARYPGHRFPP-HVHDFYVIGYIERGVGRLRLNGRTYHLGPGDLFLLPPGEPH----------DYEPESEDGWRYRWLYFE   77 (134)
T ss_pred             EEECCCCCCC-CCCCCEEEEEEECCCEEEEECCEEEEECCCEEEEECCCCCE----------EEEECCCCCCEEEEEEEC
T ss_conf             9868964199-47697899999898499999999999689949998999969----------888689999699999999


Q ss_pred             HHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             78887788761654015544134553013588999888752
Q gi|254780316|r  340 PINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLI  380 (805)
Q Consensus       340 p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li  380 (805)
                      |..++...+..+.......+.-  -|+.+ ...+.++..++
T Consensus        78 ~~~l~~~~~~~~~~~~~~~~~~--~d~~l-~~~l~~l~~~l  115 (134)
T pfam02311        78 PELLERILADISILAGGPGLLL--RDPEL-AALLRALFRLL  115 (134)
T ss_pred             HHHHHHHHHHCCCCCCCCCCEE--CCHHH-HHHHHHHHHHH
T ss_conf             9999999987048988985636--48889-99999999988


No 160
>PRK09310 aroDE bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase protein; Reviewed
Probab=27.66  E-value=36  Score=13.32  Aligned_cols=51  Identities=10%  Similarity=0.181  Sum_probs=37.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             3458789999999840222103456236640345433440256767676535233
Q gi|254780316|r  417 IDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQ  471 (805)
Q Consensus       417 ~~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGYdn  471 (805)
                      ++++.+++.+.++.+.   ..+-.++.||+| |..|+..-.|=+.|.|+..|==|
T Consensus       250 ~~v~~~~l~~f~~~~~---~~~f~G~sVTiP-~K~~i~~~lDeld~~A~~iGAVN  300 (477)
T PRK09310        250 LPLTPQELPEFFSLIR---DLPFLGLSVTMP-LKTAVLDFLDKLDPSVKLCGSCN  300 (477)
T ss_pred             EECCHHHHHHHHHHHH---HCCCCEEEECCC-CHHHHHHHHCCCCHHHHHHCCEE
T ss_conf             8568889999999875---379988998807-79999987152898899737665


No 161
>COG1606 ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]
Probab=27.59  E-value=36  Score=13.31  Aligned_cols=176  Identities=17%  Similarity=0.219  Sum_probs=80.9

Q ss_pred             CCCCEEEEEEECCCHHHH---HHHHHHHCCCCH--HHHHHC---CCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEC
Q ss_conf             367269999715787888---778876165401--554413---455301358899988875212334555652587413
Q gi|254780316|r  326 DNTTDVLVEVALWDPINI---ARSGKNLGIITD--SRYRFE---RGVDLQGMIPVLKHIVSLILSLCGGTASDICIARNI  397 (805)
Q Consensus       326 ~~T~~illEsA~F~p~~I---r~tar~l~l~Td--aS~RfE---Rgvd~~~~~~al~r~~~Li~e~~gg~~~~~~~~~~~  397 (805)
                      ++.--+.+-+-|+.+-.+   +..|+.+|++-+  -+.|-.   +-=+++.+-..=...-..|.+.+...-..++.++..
T Consensus        43 ~~v~AvTv~sP~~p~~e~e~A~~~A~~iGi~H~~i~~~~~~~~~~~n~~~rCY~CK~~v~~~l~~~a~~~Gyd~V~dGtN  122 (269)
T COG1606          43 DNVVAVTVDSPYIPRREIEEAKNIAKEIGIRHEFIKMNRMDPEFKENPENRCYLCKRAVYSTLVEEAEKRGYDVVADGTN  122 (269)
T ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEHHHCCHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCC
T ss_conf             64699997168777666067899999948762465500025233049987355778999999999999739988974775


Q ss_pred             -----CCCCCCEECCCCHHHHHHC-------CCCCHHHHHHHHHHHHHHHHC--CCCCCEEEECCCCC-CC--CCHHHHH
Q ss_conf             -----5543100004311333311-------345878999999984022210--34562366403454-33--4402567
Q gi|254780316|r  398 -----TYKPRKIVFMNSEVKRLSG-------IDVPIEDSLRILERLGFSVIG--EYDKFEVSVPSWRQ-DV--EEKADLV  460 (805)
Q Consensus       398 -----~~~~~~I~l~~~~i~~ilG-------~~i~~~ei~~iL~~Lgf~v~~--~~~~~~V~vPs~R~-DI--~~e~DLi  460 (805)
                           .+.|-      =+..+-+|       +.|++++|..+.++||+..-.  ....+...+|.|.. ++  ...++=.
T Consensus       123 asDl~~~RPG------~rA~kE~gi~sPl~e~gitk~eIre~a~~lgl~~~~kp~~aCl~sr~p~g~ei~~e~l~kv~~a  196 (269)
T COG1606         123 ASDLFDYRPG------LRALKELGIRSPLAEFGITKKEIREIAKSLGLPTWDKPSMACLASRIPYGEEITVEDLKKVEEA  196 (269)
T ss_pred             HHHHCCCCCC------HHHHHHCCCCCHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             7873378830------2357760777718883975999999999759984558654332000677765668889988999


Q ss_pred             HHHHHHCCCCCCCCCCC-CCCCCCCCCCCCHHH--HHHHHHHHHHHHHHHH
Q ss_conf             67676535233466765-544345767899889--5467898878778774
Q gi|254780316|r  461 EEILRIYGVDQIKSEPL-PLTQVEDKRNLSLQQ--SRTRYVKRVLASRAMM  508 (805)
Q Consensus       461 EEIaRiyGYdnIp~~~l-~~~~~~~~~~~~~~~--~~~~~ir~~L~~~Gf~  508 (805)
                      |+..|-+|+.+|-...- .+..+ ...+.....  .....+.+.+...||-
T Consensus       197 e~~l~~l~~~~irvr~~~~~A~i-Ev~~ee~~k~~~~~~~i~~~lk~~Gf~  246 (269)
T COG1606         197 EEFLRELGVRQIRVRSEDNLAVI-EVGPEEPEKLLNEVEEIDDKLKKVGFR  246 (269)
T ss_pred             HHHHHHHHHCEEEEEECCCEEEE-ECCCCCHHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999864211444204753688-538557999964089999999983601


No 162
>TIGR01686 FkbH FkbH domain; InterPro: IPR010037   This entry describes a domain of unknown function. One of proteins with this domain is a modular polyketide synthase, which is 4800 amino acids in length from Streptomyces avermilitis, where the domain is the C-terminal segment. By contrast, the FkbH protein from Streptomyces hygroscopicus (Q84G18 from SWISSPROT) apparently contains only this domain. The remaining members of the family all contain an additional N-terminal domain of between 200 and 275 amino acids, which show less than 20 0dentity to one another. It seems likely then that these proteins are involved in disparate functions, probably the biosynthesis of different natural products. For instance, the FkbH gene is found in a gene cluster believed to be responsible for the biosynthesis of unusual 'PKS extender units' in the ascomycin pathway . This domain is composed of two parts, the first of which is a member of subfamily IIIC of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. All of the characterised enzymes within subfamily III are phosphatases, and all of the active site residues characteristic of HAD-superfamily phosphatases  are present in this domain. The C-terminal portion of this domain is unique to this family (by BLAST)..
Probab=27.42  E-value=27  Score=14.20  Aligned_cols=38  Identities=24%  Similarity=0.300  Sum_probs=24.2

Q ss_pred             EEEEECCCHH--HHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHH
Q ss_conf             9997157878--88778876165401554413455301358899
Q gi|254780316|r  332 LVEVALWDPI--NIARSGKNLGIITDSRYRFERGVDLQGMIPVL  373 (805)
Q Consensus       332 llEsA~F~p~--~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al  373 (805)
                      -.-++.|+|.  +||+-||+|||.|||=. |   +|=+.++.+.
T Consensus        84 ~~~~~~W~PKs~~~~~~A~~LNl~~~s~~-F---~DD~p~E~~~  123 (337)
T TIGR01686        84 SLLSIAWGPKSESLRKIAKKLNLGTDSFL-F---IDDNPAERAE  123 (337)
T ss_pred             HHHHHCCCCCCHHHHHHHHHHCCCCCHHE-E---ECCCHHHHHH
T ss_conf             77864379971689999998488523110-0---0788754876


No 163
>TIGR02280 PaaB1 phenylacetate degradation probable enoyl-CoA hydratase paaB; InterPro: IPR011968    This family of proteins are found within apparent operons for the degradation of phenylacetic acid . These proteins contain the enoyl-CoA hydratase domain. This activity is consistent with current hypotheses for the degradation pathway  which involve the ligation of phenylacetate with coenzyme A (paaF), hydroxylation (paaGHIJK), ring-opening (paaN) and degradation of the resulting fatty acid-like compound to a Krebs cycle intermediate (paaABCDE)..
Probab=27.27  E-value=36  Score=13.35  Aligned_cols=25  Identities=28%  Similarity=0.167  Sum_probs=20.2

Q ss_pred             EECCCHHHHHHHH--HHHHHHHHHHCC
Q ss_conf             7087857665557--899987764115
Q gi|254780316|r  160 SLTPNRSDCIGVR--GIALDLVAAGLG  184 (805)
Q Consensus       160 ~iTpNR~D~ls~~--GiARElaa~~~~  184 (805)
                      .+|-||||=|.-+  +|=+||+..+.+
T Consensus        11 ~LTLNRPd~LNSF~~~MH~~l~~aL~~   37 (259)
T TIGR02280        11 RLTLNRPDKLNSFTAEMHAELREALER   37 (259)
T ss_pred             EEECCCCCHHCCHHHHHHHHHHHHHHH
T ss_conf             431377001024008899999999866


No 164
>PRK10296 DNA-binding transcriptional regulator ChbR; Provisional
Probab=26.83  E-value=37  Score=13.24  Aligned_cols=45  Identities=13%  Similarity=0.104  Sum_probs=30.6

Q ss_pred             HHCCCEEEECCCCCCCEEEEEECCCCCCHHHHHHHCCCCCCCCEEEECCCC
Q ss_conf             608700000102233326886235543114554201124543200002567
Q gi|254780316|r  259 DRGYPSHVFDASRISDVLTVRRACSGEKILALDNQEYDLSPDNVVIASDGR  309 (805)
Q Consensus       259 e~GqPlHafD~dki~~~i~vr~a~~~E~~~~Ld~~e~~L~~~~lvI~d~~~  309 (805)
                      |.+-|+|-.|.--      +-...+|+-....||+++.|.++|+++-....
T Consensus        26 ~~~~~lH~Hd~~E------i~yv~~G~~~~~in~~~~~l~~Gdli~I~~~~   70 (271)
T PRK10296         26 ESVSGLHQHDYYE------FTLVLTGRYYQEINGKRVLLERGDFVFIPLGS   70 (271)
T ss_pred             CCCCCCEECCCEE------EEEEECCEEEEEECCEEEEEECCEEEEECCCC
T ss_conf             7899886668689------99997674899999999997089899982997


No 165
>TIGR01241 FtsH_fam ATP-dependent metallopeptidase HflB; InterPro: IPR005936   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH.    FtsH is a membrane-anchored ATP-dependent protease that degrades misfolded or misassembled membrane proteins as well as a subset of cytoplasmic regulatory proteins. FtsH is a 647-residue protein of 70 kDa, with two putative transmembrane segments towards its N terminus which anchor the protein to the membrane, giving rise to a periplasmic domain of 70 residues and a cytoplasmic segment of 520 residues containing the ATPase and protease domains . ; GO: 0004222 metalloendopeptidase activity, 0030163 protein catabolic process, 0016020 membrane.
Probab=26.15  E-value=35  Score=13.38  Aligned_cols=39  Identities=31%  Similarity=0.525  Sum_probs=28.6

Q ss_pred             CCCEEEECC-CC--------CCCC-------CHHHHH----CC--CCEEEEEEECCCHHHHH
Q ss_conf             775078168-88--------8884-------558870----88--85599987087857665
Q gi|254780316|r  130 SASIMELPI-DA--------PVGG-------RLSDYL----EL--SDPIIDVSLTPNRSDCI  169 (805)
Q Consensus       130 ~~gI~~l~~-~~--------~~G~-------~~~~~l----~l--~D~i~ei~iTpNR~D~l  169 (805)
                      .=+|+-.|+ ||        ++|.       ++++.|    |+  +|-||=|.=| ||||.|
T Consensus       151 APCIIFIDEIDAVGr~RGaG~lGGGnDEREQTLNQLLVEMDGF~~~~gvIv~AAT-NRPDvL  211 (505)
T TIGR01241       151 APCIIFIDEIDAVGRQRGAGELGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAAT-NRPDVL  211 (505)
T ss_pred             CCCEEEEECHHHCCCCCCCCCCCCCCCHHHHHHHHHHEECCCCCCCCCEEEEEEC-CCCCCC
T ss_conf             8970564010000333564366765413554332331331785898857998504-884116


No 166
>PRK12271 rps10p 30S ribosomal protein S10P; Reviewed
Probab=26.06  E-value=38  Score=13.12  Aligned_cols=10  Identities=20%  Similarity=0.255  Sum_probs=3.6

Q ss_pred             HHHHHHHHCC
Q ss_conf             9988875212
Q gi|254780316|r  373 LKHIVSLILS  382 (805)
Q Consensus       373 l~r~~~Li~e  382 (805)
                      ++.++.-|.+
T Consensus        16 Ld~~~~~I~~   25 (102)
T PRK12271         16 LDGVCNQIKE   25 (102)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 167
>KOG0456 consensus
Probab=25.95  E-value=39  Score=13.11  Aligned_cols=23  Identities=22%  Similarity=0.261  Sum_probs=12.9

Q ss_pred             CCCCCCCCCCEEEEEEEECCCCCH
Q ss_conf             136898887200189996688799
Q gi|254780316|r  707 VVHLSSLHPVKRDLAFIVDQHIPA  730 (805)
Q Consensus       707 ~~~~s~fP~v~RDls~iv~~~v~~  730 (805)
                      .+-+| .-+++-.||++++++...
T Consensus       502 vqMIS-QGAskvNIS~ivne~ea~  524 (559)
T KOG0456         502 VQMIS-QGASKVNISCIVNEKEAE  524 (559)
T ss_pred             EEEEC-CCCCCCEEEEEECHHHHH
T ss_conf             26410-565521079997738889


No 168
>COG3376 HoxN High-affinity nickel permease [Inorganic ion transport and metabolism]
Probab=25.70  E-value=19  Score=15.37  Aligned_cols=44  Identities=27%  Similarity=0.347  Sum_probs=31.7

Q ss_pred             EEEECCCCCCCEEEEEECCCCCCHHHHHHHCCCCCCCCEEEECCCCCCCCHHHCCCCCCCCCCCCCEEEE
Q ss_conf             0000102233326886235543114554201124543200002567631001113553120136726999
Q gi|254780316|r  264 SHVFDASRISDVLTVRRACSGEKILALDNQEYDLSPDNVVIASDGRIQSIAGIIGGKHAGCDDNTTDVLV  333 (805)
Q Consensus       264 lHafD~dki~~~i~vr~a~~~E~~~~Ld~~e~~L~~~~lvI~d~~~~ialaGImGg~~s~v~~~T~~ill  333 (805)
                      =||||+|.|               .+.|+..|+|-.      ++++|.+.     |...++..+|--|++
T Consensus        61 RHA~DADHI---------------AAIDN~tRKLmQ------qgK~p~~V-----G~fFSlGHStVViL~  104 (342)
T COG3376          61 RHAFDADHI---------------AAIDNVTRKLMQ------QGKNPLGV-----GFFFSLGHSTVVILL  104 (342)
T ss_pred             CCCCCHHHH---------------HHHHHHHHHHHH------CCCCCCEE-----EEEEECCCHHHHHHH
T ss_conf             211563889---------------998789999996------79998526-----678854730899999


No 169
>PRK10119 hypothetical protein; Provisional
Probab=25.31  E-value=40  Score=13.03  Aligned_cols=13  Identities=15%  Similarity=0.153  Sum_probs=6.5

Q ss_pred             CHHHHHHHHHHHC
Q ss_conf             4025676767653
Q gi|254780316|r  455 EKADLVEEILRIY  467 (805)
Q Consensus       455 ~e~DLiEEIaRiy  467 (805)
                      .+.+.|+.|.++.
T Consensus        92 ~~~~~I~~I~~~I  104 (231)
T PRK10119         92 FPAEKIEAVCHAI  104 (231)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             7389999999999


No 170
>KOG0358 consensus
Probab=25.21  E-value=40  Score=13.02  Aligned_cols=39  Identities=36%  Similarity=0.430  Sum_probs=16.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHH
Q ss_conf             4587899999998402221034562366403454334402567676
Q gi|254780316|r  418 DVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEI  463 (805)
Q Consensus       418 ~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEI  463 (805)
                      +++.++|.-+-+.|||+...+       +-.|+.|-...+||+||+
T Consensus       322 dieRediefick~l~c~Pia~-------id~f~~d~Lg~adlveE~  360 (534)
T KOG0358         322 DIEREDIEFICKTLGCKPIAD-------IDHFTADKLGSADLVEET  360 (534)
T ss_pred             CCCHHHHHHHHHHCCCEECCH-------HHHCCHHHCCCCHHHHHC
T ss_conf             443766789885149701310-------432496443750244412


No 171
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=25.13  E-value=28  Score=14.05  Aligned_cols=24  Identities=25%  Similarity=0.326  Sum_probs=16.4

Q ss_pred             HHCCCCC--HHHHHHHHHHHHHHHHC
Q ss_conf             3113458--78999999984022210
Q gi|254780316|r  414 LSGIDVP--IEDSLRILERLGFSVIG  437 (805)
Q Consensus       414 ilG~~i~--~~ei~~iL~~Lgf~v~~  437 (805)
                      .||++-.  -.|++++|+.||.+|..
T Consensus       168 ~LGF~~r~D~~Ei~RLl~~lGi~VNv  193 (524)
T PRK02910        168 ALGFHNRDDLTELRRLLATLGIDVNV  193 (524)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf             56768778899999999875966889


No 172
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=25.05  E-value=40  Score=13.00  Aligned_cols=21  Identities=19%  Similarity=0.344  Sum_probs=10.0

Q ss_pred             CHHHHHHHHHHHHHHCCCEEEEC
Q ss_conf             10399999899986087000001
Q gi|254780316|r  246 ISALVDITNYVSLDRGYPSHVFD  268 (805)
Q Consensus       246 inniVDitNyvmle~GqPlHafD  268 (805)
                      .+.++|+-.-  +.+.+|-=.|-
T Consensus       167 ~~~I~~~v~~--~AL~~P~I~f~  187 (612)
T PRK00095        167 LGHIDDVVRR--LALAHPDVAFT  187 (612)
T ss_pred             HHHHHHHHHH--HHHHCCCEEEE
T ss_conf             9999999999--97517975899


No 173
>COG1171 IlvA Threonine dehydratase [Amino acid transport and metabolism]
Probab=24.94  E-value=40  Score=12.98  Aligned_cols=217  Identities=20%  Similarity=0.182  Sum_probs=105.4

Q ss_pred             CCCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCC-CCHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             5865054541188769985477507816888888-455887088855999870878576655578999877641156666
Q gi|254780316|r  110 RGIESTGMMCSEKELMLSDDSASIMELPIDAPVG-GRLSDYLELSDPIIDVSLTPNRSDCIGVRGIALDLVAAGLGKLKE  188 (805)
Q Consensus       110 rGv~S~GMlCS~~ELgl~~~~~gI~~l~~~~~~G-~~~~~~l~l~D~i~ei~iTpNR~D~ls~~GiARElaa~~~~~l~~  188 (805)
                      .|..-+|.--|.+-||+.    +.++.|.++|.= .+-...+|  -.++-..  .|--|+   +-.|+|++.--+..+-+
T Consensus        82 aGNHaQGvA~aa~~lGi~----a~IvMP~~tp~~Kv~a~r~~G--aeVil~g--~~~dda---~~~a~~~a~~~G~~~i~  150 (347)
T COG1171          82 AGNHAQGVAYAAKRLGIK----ATIVMPETTPKIKVDATRGYG--AEVILHG--DNFDDA---YAAAEELAEEEGLTFVP  150 (347)
T ss_pred             CCCHHHHHHHHHHHHCCC----EEEEECCCCCHHHHHHHHHCC--CEEEEEC--CCHHHH---HHHHHHHHHHCCCEEEC
T ss_conf             873799999999980998----799956998299999998569--8899979--977999---99999999973978858


Q ss_pred             CCCCCCCCCCCCC---CEEEEEE---ECCCHHHHHHHCCCCCCCCCCCCHHHHHH---HHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             5545667777777---4158984---07311123320112322455663778788---8864013210399999899986
Q gi|254780316|r  189 INISCPLSSESIP---LEIKFDL---DDSSLCKGFAMCCVKGVRNNVAPNWMRQR---LKAVGLRSISALVDITNYVSLD  259 (805)
Q Consensus       189 ~~~~~~~~~~~~~---~~i~v~i---~~~~~c~~y~~~~i~~v~~~~SP~wl~~r---L~~~Gir~inniVDitNyvmle  259 (805)
                      | +..+....+..   .++--..   .|.-.||.=.|-.+.||..     +++.+   ..-+|+-|-+.-   +=|--++
T Consensus       151 p-fD~p~viAGQGTi~lEileq~~~~~d~v~vpvGGGGLisGia~-----~~k~~~p~~~vIGVEp~~a~---~~~~Sl~  221 (347)
T COG1171         151 P-FDDPDVIAGQGTIALEILEQLPDLPDAVFVPVGGGGLISGIAT-----ALKALSPEIKVIGVEPEGAP---SMYASLK  221 (347)
T ss_pred             C-CCCCCEEECCCHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHH-----HHHHHCCCCEEEEEEECCCH---HHHHHHH
T ss_conf             9-9994525342589999998464568989995386479999999-----99983999729998148885---8999997


Q ss_pred             HC-CCEEEECCCCCCCEEEEEECCCCCCHHH----------HHHHC-----CCCCCCCEEEECCCCCCCCHHHCCCCCCC
Q ss_conf             08-7000001022333268862355431145----------54201-----12454320000256763100111355312
Q gi|254780316|r  260 RG-YPSHVFDASRISDVLTVRRACSGEKILA----------LDNQE-----YDLSPDNVVIASDGRIQSIAGIIGGKHAG  323 (805)
Q Consensus       260 ~G-qPlHafD~dki~~~i~vr~a~~~E~~~~----------Ld~~e-----~~L~~~~lvI~d~~~~ialaGImGg~~s~  323 (805)
                      -| +|.+.-+-+++.+.+-++...+ ++|..          .|+.+     +.|-...-+|+-..+.+++|+...+....
T Consensus       222 ~G~~~~~~~~~~tiaDG~av~~~g~-~tf~i~~~~vd~~v~V~e~ei~~am~~l~~~~~iI~EpaGAlalAal~~~~~~~  300 (347)
T COG1171         222 AGKIVVVLPDVGTIADGLAVKRPGD-LTFEILRELVDDIVLVDEDEICAAMRDLFERTKIIAEPAGALALAALLAGKIEP  300 (347)
T ss_pred             CCCCEEECCCCCCCCCCCCCCCCCH-HHHHHHHHCCCCEEEECHHHHHHHHHHHHHCCCEECCCCHHHHHHHHHHHHHHH
T ss_conf             5994353698780025420488877-789999970996899888999999999973277113660799999999600211


Q ss_pred             CCCCCCEEEEEEECCCHHHHHHHH
Q ss_conf             013672699997157878887788
Q gi|254780316|r  324 CDDNTTDVLVEVALWDPINIARSG  347 (805)
Q Consensus       324 v~~~T~~illEsA~F~p~~Ir~ta  347 (805)
                      ....|--+++=-+++|+...+...
T Consensus       301 ~~g~~v~~ilSGgN~d~~~~~~v~  324 (347)
T COG1171         301 LQGKTVVVILSGGNIDFERLAEVL  324 (347)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHH
T ss_conf             379759999607887989999998


No 174
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=24.91  E-value=30  Score=13.85  Aligned_cols=23  Identities=22%  Similarity=0.364  Sum_probs=15.9

Q ss_pred             HHCCCCC--HHHHHHHHHHHHHHHH
Q ss_conf             3113458--7899999998402221
Q gi|254780316|r  414 LSGIDVP--IEDSLRILERLGFSVI  436 (805)
Q Consensus       414 ilG~~i~--~~ei~~iL~~Lgf~v~  436 (805)
                      .+|++-.  -.|++++|+.||.+|.
T Consensus       173 ~lgF~~~~Dl~Ei~RLl~~~Gi~VN  197 (510)
T CHL00076        173 TLGFHNQHDCRELKRLLQDLGIEIN  197 (510)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCEEE
T ss_conf             5667887889999999997597788


No 175
>PHA02512 minor structural protein; Provisional
Probab=24.67  E-value=18  Score=15.46  Aligned_cols=42  Identities=10%  Similarity=0.258  Sum_probs=21.3

Q ss_pred             EEEECCCCCHHHHHHHHHHC-CCCEEEE----EEEEEEECCCCCCCC
Q ss_conf             99966887999999999711-1003576----989876367799884
Q gi|254780316|r  721 AFIVDQHIPAGTLVNIIKNV-DRLIDDV----TVFDVFQGKSLGEGK  762 (805)
Q Consensus       721 s~iv~~~v~~~~I~~~i~~~-~~ll~~v----~lfDvY~g~~i~~gk  762 (805)
                      .+++|-.+..+...+.+..+ .+-+.+.    -..+.|--.++++..
T Consensus       773 ~VllPwGM~~~qF~kqv~~a~~~~~~~~Gik~~~vg~~glqs~GdsQ  819 (844)
T PHA02512        773 DVLLPFGMDAEQFDDQVNAAANEALKDAGIKTNAVGNFGLQNIGDNQ  819 (844)
T ss_pred             CEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCE
T ss_conf             45521578888998999999987551556677996531510347742


No 176
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE; InterPro: IPR014286   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    This entry represents the clade of sigma factors called RpoE. These proteins are variously annotated as sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=24.66  E-value=29  Score=13.98  Aligned_cols=56  Identities=16%  Similarity=0.090  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCHHHHH
Q ss_conf             789887877877402321004825765520000000024677643210151221106776
Q gi|254780316|r  496 RYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEILNPISADMSNMRTSLLPGLLKA  555 (805)
Q Consensus       496 ~~ir~~L~~~Gf~Ev~tysl~s~~~~~~~~~~~~~i~l~NPlS~e~s~lR~SLlp~LL~~  555 (805)
                      +.-|++|++.|=.=- +-.=++.++++.|...+..=.+.||   |...|+.-|---.-++
T Consensus        82 NTAKNyLVaq~Rr~p-~~dg~~~edAE~F~~a~~Lr~~~tP---E~~ll~~el~~~v~~a  137 (192)
T TIGR02939        82 NTAKNYLVAQGRRPP-TSDGVEAEDAEQFEEADALRDIDTP---ERLLLSRELEQTVNKA  137 (192)
T ss_pred             HHHHHHHHHCCCCCC-CCCCCCCHHHHCCCCCCCCCCCCCH---HHHHHHHHHHHHHHHH
T ss_conf             887776642479887-4456760433120026766556661---6799999999999999


No 177
>TIGR01458 HAD-SF-IIA-hyp3 HAD-superfamily subfamily IIA hydrolase, TIGR01458; InterPro: IPR006355   These sequences are all members of the IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. .
Probab=24.57  E-value=36  Score=13.29  Aligned_cols=21  Identities=19%  Similarity=0.468  Sum_probs=13.3

Q ss_pred             CCCCHHHHHHHHHHCCCCCHH
Q ss_conf             566377878888640132103
Q gi|254780316|r  228 NVAPNWMRQRLKAVGLRSISA  248 (805)
Q Consensus       228 ~~SP~wl~~rL~~~Gir~inn  248 (805)
                      +|||.+.++-|.+.|+.|...
T Consensus       180 KPs~~fF~~al~a~G~epeea  200 (258)
T TIGR01458       180 KPSKEFFKEALRALGVEPEEA  200 (258)
T ss_pred             CCCHHHHHHHHHHCCCCCCEE
T ss_conf             888589988866258881026


No 178
>cd00153 RalGDS_RA This CD represents the C-terminal Ras-associating (RA) domain of three closely related guanine-nucleotide exchange factors (GEF's),  Ral guanine nucleotide dissociation stimulator (RalGDS), RalGDS-like (RGL), and RalGDS-like factor (RLF).  The RalGDS proteins are downstream effectors of the Ras-related protein Ral, providing a mechanism for Ral activation by extracellular signals.  The RA domain is structurally similar to ubiquitin and exists in a number of other signalling proteins including AF6, rasfadin, SNX27, CYR1, and STE50.
Probab=24.45  E-value=41  Score=12.92  Aligned_cols=35  Identities=14%  Similarity=0.132  Sum_probs=25.0

Q ss_pred             CCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHC
Q ss_conf             67269999715787888778876165401554413
Q gi|254780316|r  327 NTTDVLVEVALWDPINIARSGKNLGIITDSRYRFE  361 (805)
Q Consensus       327 ~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfE  361 (805)
                      --|.|+|++--=-|..||+.-.+|++..|...+||
T Consensus        17 ~YKSIllt~qDktP~VI~~Am~Kh~l~~~~~~~y~   51 (87)
T cd00153          17 LYKSILLTSQDKAPQVIRRAMEKHNLESEVAEDYE   51 (87)
T ss_pred             EEEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCEE
T ss_conf             79999985288677999999998488878701208


No 179
>pfam11548 Receptor_IA-2 Protein-tyrosine phosphatase receptor IA-2. IA-2 is a protein-tyrosine phosphatase receptor that upon exocytosis, the cytoplasmic domain is cleaved and moves to the nucleus where it enhances transcription of the insulin gene. The mature exodomain of IA-2 participates in adhesion to the extracellular matrix and is self-proteolyzed in vitro by reactive oxygen species which may be a new shedding mechanism.
Probab=24.34  E-value=41  Score=12.91  Aligned_cols=69  Identities=10%  Similarity=0.140  Sum_probs=43.9

Q ss_pred             CCCHHHHHHHHHHCCCCE--EEEEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCEEC
Q ss_conf             879999999997111003--57698987636779988426999999847798889999999999999999999511981
Q gi|254780316|r  727 HIPAGTLVNIIKNVDRLI--DDVTVFDVFQGKSLGEGKKSVAIQVLIQPLKDTFRDDDIRILMDRIVENVVKKTNAVLR  803 (805)
Q Consensus       727 ~v~~~~I~~~i~~~~~ll--~~v~lfDvY~g~~i~~gkkSla~rl~fqs~~kTLtd~EI~~i~~~ii~~l~~k~ga~LR  803 (805)
                      -.++++=.+.++....++  ..-...|+-    + . --.+|||+  ++..+-++-.||-+.....-+.|++.-|.++=
T Consensus        13 ~ls~~~G~~Ll~~lA~ll~l~~s~F~~i~----V-~-gpaVTFrV--~~N~qN~t~adVa~~a~~~K~~Le~~tGl~Il   83 (91)
T pfam11548        13 PLSLDEGVRLMEILAERVHLPSSSFANIS----V-V-GPAVTFRV--RPNEQNVSTADVAKAAVDNKDQLEKQTGLRIL   83 (91)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCEEEEE----E-E-CCCEEEEE--CCCCCCCCHHHHHHHHHHHHHHHHHHHCEEEE
T ss_conf             88788999999999999579711236789----8-5-78179996--46713587999999999868888774182986


No 180
>pfam11829 DUF3349 Protein of unknown function (DUF3349). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length.
Probab=24.00  E-value=42  Score=12.86  Aligned_cols=63  Identities=14%  Similarity=0.084  Sum_probs=35.5

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             33331134587899999998402221034562366403454334402567676765352334667655443457678998
Q gi|254780316|r  411 VKRLSGIDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQIKSEPLPLTQVEDKRNLSL  490 (805)
Q Consensus       411 i~~ilG~~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaRiyGYdnIp~~~l~~~~~~~~~~~~~  490 (805)
                      +-.+|.-.++.+|+..+-..|-    ..++ +    |      ....||-+.|.++-+..       |          +.
T Consensus        28 LLALL~r~Ltddev~~Va~~L~----~~~~-~----~------i~~~dI~~~I~~vt~~~-------P----------~p   75 (97)
T pfam11829        28 LLALLRRRLTDDEVAEVAAELT----RRGE-P----A------IDDDDIGVLITAVTDEL-------P----------SP   75 (97)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHH----HCCC-C----C------CCHHHHHHHHHHHHCCC-------C----------CH
T ss_conf             9999814288999999999998----6478-9----9------99999999999987479-------8----------98


Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             89546789887877877
Q gi|254780316|r  491 QQSRTRYVKRVLASRAM  507 (805)
Q Consensus       491 ~~~~~~~ir~~L~~~Gf  507 (805)
                       +. ..+++..|.+.|+
T Consensus        76 -~d-i~RV~arLaa~Gw   90 (97)
T pfam11829        76 -ED-VERVRARLAAHGW   90 (97)
T ss_pred             -HH-HHHHHHHHHHCCC
T ss_conf             -99-9999999986799


No 181
>TIGR01647 ATPase-IIIA_H plasma-membrane proton-efflux P-type ATPase; InterPro: IPR006534   These sequences represent the plasma membrane proton efflux P-type ATPase found in plants, fungi, protozoa, slime molds and archaea. The best studied representative is from yeast . ; GO: 0016887 ATPase activity, 0015992 proton transport, 0016021 integral to membrane.
Probab=23.99  E-value=28  Score=14.05  Aligned_cols=268  Identities=17%  Similarity=0.167  Sum_probs=117.8

Q ss_pred             EEEEEECCCHHHHHHHCCCCCCCCCC-CCHHHHHHHHHHCCCCCHH---HHHHHHHHHHH-HCCCEEEECCCCCCCEEEE
Q ss_conf             58984073111233201123224556-6377878888640132103---99999899986-0870000010223332688
Q gi|254780316|r  204 IKFDLDDSSLCKGFAMCCVKGVRNNV-APNWMRQRLKAVGLRSISA---LVDITNYVSLD-RGYPSHVFDASRISDVLTV  278 (805)
Q Consensus       204 i~v~i~~~~~c~~y~~~~i~~v~~~~-SP~wl~~rL~~~Gir~inn---iVDitNyvmle-~GqPlHafD~dki~~~i~v  278 (805)
                      +.--|-.+ .-.-|.|+.-.=|+-.. .--.+|.-|.++|.=.|-.   .|=|+=.+++- .+..+|     ..+     
T Consensus       186 ~~a~V~AT-G~NTFFGkaA~Lv~~~~~~~GHlQ~il~~IG~~liv~~~~~v~i~~~~~~~~~~~~~~-----~~~-----  254 (835)
T TIGR01647       186 AEAVVTAT-GMNTFFGKAAALVQSTETGSGHLQKILSKIGLFLIVLIGVLVLIELVVLFFGRGESFR-----EGE-----  254 (835)
T ss_pred             EEEEEEEC-CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEE-----ECC-----
T ss_conf             05899972-7886077899988887521422989999864899999999999999998551064502-----347-----


Q ss_pred             EECCCCCCHHHHHHHCCCCCCCCEEEECCCCCCCCHHHC---------------------------CCCCCCCCCCCCE-
Q ss_conf             623554311455420112454320000256763100111---------------------------3553120136726-
Q gi|254780316|r  279 RRACSGEKILALDNQEYDLSPDNVVIASDGRIQSIAGII---------------------------GGKHAGCDDNTTD-  330 (805)
Q Consensus       279 r~a~~~E~~~~Ld~~e~~L~~~~lvI~d~~~~ialaGIm---------------------------Gg~~s~v~~~T~~-  330 (805)
                          +|  =.+       |+ ..||+.=+.=|+|++=|+                           -|.+==|||.|-+ 
T Consensus       255 ----~G--C~~-------l~-f~LVLLvggIPiAmP~VlSvTmAvGA~~LAk~~AIV~rL~AIEElAGmdILCSDKTGTL  320 (835)
T TIGR01647       255 ----EG--CLT-------LQ-FALVLLVGGIPIAMPAVLSVTMAVGAAELAKKKAIVTRLTAIEELAGMDILCSDKTGTL  320 (835)
T ss_pred             ----CC--CCC-------HH-CEEEEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             ----77--622-------13-01554564000013145567788999998653775014888888764862133773432


Q ss_pred             ----------EEEEE--ECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHH--CCCCCCCCCCCEEEEE
Q ss_conf             ----------99997--157878887788761654015544134553013588999888752--1233455565258741
Q gi|254780316|r  331 ----------VLVEV--ALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLI--LSLCGGTASDICIARN  396 (805)
Q Consensus       331 ----------illEs--A~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li--~e~~gg~~~~~~~~~~  396 (805)
                                .+.+.  -.|++.+|-..|      .=||.|=|.+-|+--.. .+..+..+=  .+.|.    +......
T Consensus       321 TlNKL~i~~~~~~~~~G~~~~~~Dv~l~A------aLAskwree~~DaID~~-~l~~~~~~~~~~~~~~----~y~~~~F  389 (835)
T TIGR01647       321 TLNKLSIDEILPFFGGGPGFDKDDVLLYA------ALASKWREENQDAIDTA-VLGSLKDLKRLKEARA----GYKVLEF  389 (835)
T ss_pred             CCCEEEECCEEEEECCCCCCCHHHHHHHH------HHHHCCCCCCCCHHHHH-HHHHCCCHHHHHHHHH----CCEEEEE
T ss_conf             14445751112440657320488899988------77731687668743499-8741289689999972----9726786


Q ss_pred             CCCC----------------CCCEECCCCHHHHHHCCC-----CCHH---HHHHH--------HHHHHHHHH--------
Q ss_conf             3554----------------310000431133331134-----5878---99999--------998402221--------
Q gi|254780316|r  397 ITYK----------------PRKIVFMNSEVKRLSGID-----VPIE---DSLRI--------LERLGFSVI--------  436 (805)
Q Consensus       397 ~~~~----------------~~~I~l~~~~i~~ilG~~-----i~~~---ei~~i--------L~~Lgf~v~--------  436 (805)
                      .|..                .+...+..--=+-+|+.-     +.++   ++.+.        +..||--.+        
T Consensus       390 ~PFdhPv~KrT~a~~~~~~~G~~f~~~KGAP~~il~~~~~~~~~~~~v~~~Ve~~v~~lA~RG~RaLGVA~~evP~g~~~  469 (835)
T TIGR01647       390 VPFDHPVDKRTEATVEDPETGKKFKVTKGAPQVILDLCDNKKEIEEEVREKVEEKVEELASRGYRALGVARTEVPSGEKA  469 (835)
T ss_pred             ECCCCCCCCEEEEEEEECCCCCEEEEECCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCC
T ss_conf             55887955448999975588868998159848999963143427889998889999999707871421432017786555


Q ss_pred             CCCCCCEEE--ECCC---CCCCCCHHHHH------------------HHHHHHCCCC-CC-CCCCCCCCCCCCCCCCCHH
Q ss_conf             034562366--4034---54334402567------------------6767653523-34-6676554434576789988
Q gi|254780316|r  437 GEYDKFEVS--VPSW---RQDVEEKADLV------------------EEILRIYGVD-QI-KSEPLPLTQVEDKRNLSLQ  491 (805)
Q Consensus       437 ~~~~~~~V~--vPs~---R~DI~~e~DLi------------------EEIaRiyGYd-nI-p~~~l~~~~~~~~~~~~~~  491 (805)
                      .+.+.|+..  .|-|   |+|=..-++=+                  =|+||..|.. || +++.|+........   . 
T Consensus       470 ~~~g~W~~~GllplfDPPR~DT~eTI~~A~~~GV~VKMvTGDhlaIAKEtaR~LGlGtni~~~~~L~~~~~~~~~---~-  545 (835)
T TIGR01647       470 DEKGRWHFLGLLPLFDPPRHDTKETIERARELGVEVKMVTGDHLAIAKETARRLGLGTNIYNADVLLKKDNRDKL---P-  545 (835)
T ss_pred             CCCCCEEEEEECCCCCCCCCCHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC---C-
T ss_conf             788735888720027836987389999998769769897002678776653215798753474100467776656---6-


Q ss_pred             HHHHHHHHHHHH-HHHHHHCC
Q ss_conf             954678988787-78774023
Q gi|254780316|r  492 QSRTRYVKRVLA-SRAMMEVV  511 (805)
Q Consensus       492 ~~~~~~ir~~L~-~~Gf~Ev~  511 (805)
                      ....+++.+... +-||-||.
T Consensus       546 ~~~~~~~~E~ve~aDGFA~VF  566 (835)
T TIGR01647       546 SGAEEDLGELVESADGFAEVF  566 (835)
T ss_pred             CCCCCCHHHHEEECCCCCCCC
T ss_conf             664222011111058830267


No 182
>PRK09295 selenocysteine lyase; Validated
Probab=23.97  E-value=42  Score=12.86  Aligned_cols=30  Identities=3%  Similarity=0.087  Sum_probs=19.0

Q ss_pred             EEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999984779888999999999999999999951
Q gi|254780316|r  766 AIQVLIQPLKDTFRDDDIRILMDRIVENVVKKTN  799 (805)
Q Consensus       766 a~rl~fqs~~kTLtd~EI~~i~~~ii~~l~~k~g  799 (805)
                      ++|+.|.-.   =|.+||+...+.+-+ +.+-||
T Consensus       377 ~iRvS~~~y---nT~eeId~lv~aL~~-I~k~l~  406 (406)
T PRK09295        377 MCRASLAMY---NTHEEVDRLVAGLQR-IHRLLG  406 (406)
T ss_pred             EEEEECCCC---CCHHHHHHHHHHHHH-HHHHHC
T ss_conf             799978899---999999999999999-999729


No 183
>TIGR00003 TIGR00003 copper ion binding protein; InterPro: IPR006122    Proteins that transport heavy metals in micro-organisms and eukaryotes share similarities in their sequences and structures.    These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases .    A conserved 30-residue domain has been found in a number of these heavy metal transport or detoxification proteins . The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. This sub-domain is found in copper-binding proteins. ; GO: 0005507 copper ion binding, 0006825 copper ion transport.
Probab=22.92  E-value=44  Score=12.72  Aligned_cols=13  Identities=15%  Similarity=0.348  Sum_probs=4.2

Q ss_pred             HHHHHHHHHHCCC
Q ss_conf             8999999874586
Q gi|254780316|r   18 LEKICDTLTSIGL   30 (805)
Q Consensus        18 ~~~l~~~lt~~G~   30 (805)
                      .++|+++|...|.
T Consensus        51 ~~~I~~Ai~d~GY   63 (66)
T TIGR00003        51 AKEIKEAILDAGY   63 (66)
T ss_pred             HHHHHHHHHHCCC
T ss_conf             6778889873665


No 184
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=22.86  E-value=44  Score=12.71  Aligned_cols=55  Identities=13%  Similarity=0.237  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHCCCCC--CCCCCCEEEEECCCCCCCEECCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             8899988875212334--555652587413554310000431133331134587899999998402
Q gi|254780316|r  370 IPVLKHIVSLILSLCG--GTASDICIARNITYKPRKIVFMNSEVKRLSGIDVPIEDSLRILERLGF  433 (805)
Q Consensus       370 ~~al~r~~~Li~e~~g--g~~~~~~~~~~~~~~~~~I~l~~~~i~~ilG~~i~~~ei~~iL~~Lgf  433 (805)
                      ..+-.|.+.++.+++.  |....       ....-.+.++.+.+-..+|+  +.+.+.+.|++|.=
T Consensus       154 ~~~~~Rla~~Ll~L~~~~g~~~~-------~~~~i~l~lt~~dLA~~lG~--trEtVsR~L~~L~~  210 (235)
T PRK11161        154 KNAEERLAAFIYNLSRRFAQRGF-------SPREFRLTMTRGDIGNYLGL--TVETISRLLGRFQK  210 (235)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCC-------CCCEEEECCCHHHHHHHHCC--CHHHHHHHHHHHHH
T ss_conf             89999999999999998387788-------88779823789999988789--89999999999997


No 185
>PRK12354 carbamate kinase; Reviewed
Probab=22.76  E-value=44  Score=12.70  Aligned_cols=56  Identities=20%  Similarity=0.210  Sum_probs=47.6

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHH
Q ss_conf             13333113458789999999840222103456236640345433440256767676
Q gi|254780316|r  410 EVKRLSGIDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILR  465 (805)
Q Consensus       410 ~i~~ilG~~i~~~ei~~iL~~Lgf~v~~~~~~~~V~vPs~R~DI~~e~DLiEEIaR  465 (805)
                      .-.|.+|--++.+|..+.-+..|+.+..++.+|.-.|||=++-=..|.|.|.....
T Consensus       119 ~PtKpIGpfy~~eeA~~l~~~~gw~~~edgrG~RRVVpSP~P~~IvE~~~Ik~L~~  174 (302)
T PRK12354        119 NPTKPIGPVYSEEEAERLAAEKGWVIKPDGDKFRRVVPSPKPKRIVEIRAIKWLLE  174 (302)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHCCCEEECCCCEEEEEECCCCCCEEECHHHHHHHHH
T ss_conf             89986078869999999999749887115880368637999855564999999997


No 186
>KOG0971 consensus
Probab=22.24  E-value=45  Score=12.63  Aligned_cols=54  Identities=11%  Similarity=0.016  Sum_probs=37.6

Q ss_pred             EEEECCCCCCCCCCEEEEECCCCEECCCCEEEEEEHHCCCCCCCHHHHHHHCCC
Q ss_conf             989754834558978989668779258983983312058650545411887699
Q gi|254780316|r   73 IQVVCGAPNVRVGLLGVWAPPGSCIPENNMIVNVRKIRGIESTGMMCSEKELML  126 (805)
Q Consensus        73 ~~IvcgA~Nv~~g~~V~~A~~Ga~lp~g~~~i~~~~irGv~S~GMlCS~~ELgl  126 (805)
                      .-.-||+.|+++|.||-|-+.-++=-++|.+-+..-+.--+-+||+.-..-+-+
T Consensus        22 ~VayvG~T~FA~G~WvGVvLDep~GKNnGsVqg~qYF~Cd~ncG~FVr~sq~r~   75 (1243)
T KOG0971          22 TVAYVGQTQFAEGKWVGVVLDEPKGKNNGSVQGVQYFECDENCGVFVRSSQVRE   75 (1243)
T ss_pred             EEEEECCCCCCCCCEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEHHHHHH
T ss_conf             479842320034735899833666787872144156753888625741435687


No 187
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=22.08  E-value=45  Score=12.61  Aligned_cols=43  Identities=23%  Similarity=0.334  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHH--HHCCCCCCEEEECCCCCCCCCHHHHHHHHH
Q ss_conf             8999999984022--210345623664034543344025676767
Q gi|254780316|r  422 EDSLRILERLGFS--VIGEYDKFEVSVPSWRQDVEEKADLVEEIL  464 (805)
Q Consensus       422 ~ei~~iL~~Lgf~--v~~~~~~~~V~vPs~R~DI~~e~DLiEEIa  464 (805)
                      .|+...+++-||.  +..+-+.|-|.-|+-|+|+.++.++.=|..
T Consensus        57 ~El~~fm~r~gc~~e~~~ki~twivkKtPnryevkiPa~ifyeyV  101 (221)
T COG1458          57 RELMGFMERNGCPEEVIAKIETWIVKKTPNRYEVKIPAAIFYEYV  101 (221)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHEEEEECCCCCEEECCCHHHHHHHH
T ss_conf             999999974799688888666036755998223217099999999


No 188
>TIGR02824 quinone_pig3 putative NAD(P)H quinone oxidoreductase, PIG3 family; InterPro: IPR014189   Members of this family are putative quinone oxidoreductases that belong to the broader superfamily of zinc-dependent alcohol (of medium chain length) dehydrogenases and quinone oxidoreductases. An alignment shows no motif of conserved Cys residues as are found in zinc-binding members of the superfamily, consequently members of this entry are likely to be quinone oxidoreductases. A member of this family in Homo sapiens (Human), PIG3, is induced by p53 but is otherwise uncharacterised..
Probab=21.79  E-value=34  Score=13.51  Aligned_cols=17  Identities=29%  Similarity=0.483  Sum_probs=9.9

Q ss_pred             CCEEEEEE-ECCCHHHHH
Q ss_conf             85599987-087857665
Q gi|254780316|r  153 SDPIIDVS-LTPNRSDCI  169 (805)
Q Consensus       153 ~D~i~ei~-iTpNR~D~l  169 (805)
                      +..+++|. .==||||||
T Consensus        28 GEVLi~V~AAGVNRPD~l   45 (334)
T TIGR02824        28 GEVLIRVAAAGVNRPDVL   45 (334)
T ss_pred             CEEEEEEEEECCCHHHHH
T ss_conf             625899998426827998


No 189
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=21.75  E-value=46  Score=12.56  Aligned_cols=85  Identities=20%  Similarity=0.189  Sum_probs=45.1

Q ss_pred             EEEECCCCCCCCHHHCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHH---HHHHHHHHHH
Q ss_conf             0000256763100111355312013672699997157878887788761654015544134553013---5889998887
Q gi|254780316|r  302 VVIASDGRIQSIAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQG---MIPVLKHIVS  378 (805)
Q Consensus       302 lvI~d~~~~ialaGImGg~~s~v~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~---~~~al~r~~~  378 (805)
                      ++|-|++.  |+-|..-|       ++..|+=+...+-|.       +|+----|+.||+|=..-..   ...+..+|.+
T Consensus       136 ~ivid~~~--a~~g~l~G-------~~~evl~~~~~~vP~-------Kh~~GGQSa~RF~Rlre~~~h~~~kkvae~a~~  199 (403)
T TIGR03676       136 LIVLDRRE--ATIGLLKG-------KRIEVLKELTSGVPG-------KHRAGGQSARRFERLIEIAAHEFYKRVGEAANE  199 (403)
T ss_pred             EEEEECCC--CEEEEECC-------CEEEEEEEEECCCCC-------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99995797--56999809-------879997898524774-------334563027789999999999999999999998


Q ss_pred             HHCCCCCCCCCCCEEEEECCCCCC
Q ss_conf             521233455565258741355431
Q gi|254780316|r  379 LILSLCGGTASDICIARNITYKPR  402 (805)
Q Consensus       379 Li~e~~gg~~~~~~~~~~~~~~~~  402 (805)
                      .+.....-.+.++...++.+.++.
T Consensus       200 ~Fl~~~~~~v~GiilgGp~~~K~~  223 (403)
T TIGR03676       200 AFLPLKDKKLKGILIGGPGPTKEE  223 (403)
T ss_pred             HHHCCCCCCEEEEEECCCCHHHHH
T ss_conf             730368755379993378417677


No 190
>TIGR00658 orni_carb_tr ornithine carbamoyltransferase; InterPro: IPR002292 The ornithine carbamoyltransferases are a family of enzymes that catalyse the production of citrulline from carbamoyl-phosphate and ornithine . This reaction is part of the arginine biosynthetic pathway, and in some organisms the reaction is also part of the arginine deaminase pathway . In most prokaryotes, and some lower eukaryotes, the enzyme is found in the cytoplasm, but in higher eukaryotes, such as mammals, the enzyme is found in the mitochondrial matrix and functions as part of the urea cycle. In most organisms analysed to date, the enzyme has been shown to consist of a trimer of identical or nonidentical subunits . Extensive similarity has been found within the ornithine carbamoyltransferase family, some of the conserved areas being important in catalysis .   The C-terminal region of these enzymes shows a degree of similarity to the aspartate carbamoyltransferases, which are also known to bind carbamoyl- phosphate . This region contains a highly conserved Cys residue (in a His-Cys-Lys-Pro motif) implicated in ornithine binding . ; GO: 0004585 ornithine carbamoyltransferase activity, 0006520 amino acid metabolic process, 0009348 ornithine carbamoyltransferase complex.
Probab=21.10  E-value=47  Score=12.47  Aligned_cols=91  Identities=15%  Similarity=0.143  Sum_probs=40.0

Q ss_pred             HHHHCCCCCCCCC-CCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCEEEE-CCCCCCCEEEEEECCCCCCHH--HHH
Q ss_conf             3320112322455-663778788886401321039999989998608700000-102233326886235543114--554
Q gi|254780316|r  216 GFAMCCVKGVRNN-VAPNWMRQRLKAVGLRSISALVDITNYVSLDRGYPSHVF-DASRISDVLTVRRACSGEKIL--ALD  291 (805)
Q Consensus       216 ~y~~~~i~~v~~~-~SP~wl~~rL~~~Gir~inniVDitNyvmle~GqPlHaf-D~dki~~~i~vr~a~~~E~~~--~Ld  291 (805)
                      |..+|.|.+|-.. -+=.|+++.=.-+++=-||.+-|.        =||+=+- |+=+|.           |.+=  .|+
T Consensus        95 RVLsRyVD~I~~R~~~h~~v~~lA~yasVPVINgLtD~--------~HPcQ~LADllTI~-----------E~~g~~~l~  155 (341)
T TIGR00658        95 RVLSRYVDGIMARVYKHEDVEELAKYASVPVINGLTDL--------FHPCQALADLLTIK-----------EHFGEKKLK  155 (341)
T ss_pred             HHHCCEEEEEEEECCCHHHHHHHHHHCCCCEECCCCCC--------CCHHHHHHHHHHHH-----------HHCCCCCCC
T ss_conf             02031565677732553789999854898546055685--------52379999988898-----------746795600


Q ss_pred             HHCCCCCC--CCEEEECC-CCC---CCCHHHCCCCCCCCC
Q ss_conf             20112454--32000025-676---310011135531201
Q gi|254780316|r  292 NQEYDLSP--DNVVIASD-GRI---QSIAGIIGGKHAGCD  325 (805)
Q Consensus       292 ~~e~~L~~--~~lvI~d~-~~~---ialaGImGg~~s~v~  325 (805)
                      |-..-+++  ..--|=|+ +++   +-|||.|=|.+..|.
T Consensus       156 g~nkGinsklk~vy~GDgRNNVcnSL~la~a~~Gm~~~v~  195 (341)
T TIGR00658       156 GVNKGINSKLKVVYVGDGRNNVCNSLLLAAAKLGMDVVVA  195 (341)
T ss_pred             HHCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHCCEEEEE
T ss_conf             0003524421689973785126889999999728547887


No 191
>TIGR01246 dapE_proteo succinyl-diaminopimelate desuccinylase; InterPro: IPR005941   The lysine/diaminopimelic acid branch of the aspartate pathway produces the essential amino acid lysine via the intermediate meso-diaminopimelic acid (meso-DAP), which is also a vital cell wall component in Gram-negative bacteria . The production of dihydropicolinate from aspartate-semialdehyde controls flux into the lysine/diaminopimelic acid pathway. Three variants of this pathway exist, differing in how tetrahydropicolinate (formed by reduction of dihydropicolinate) is metabolised to meso-DAP. One variant, the most commonly found one in archaea and bacteria, uses primarily succinyl intermediates, while a second variant, found only in Bacillus, utilises primarily acetyl intermediates. In the third variant, found in some Gram-positive bacteria, a dehydrogenase converts tetrahydropicolinate directly to meso-DAP. In all variants meso-DAP is subsequently converted to lysine by a decarboxylase, or, in Gram-negative bacteria, assimilated into the cell wall. Evidence exists that a fourth, currently unknown, variant of this pathway may function in plants .    Succinyl-diaminopimelate desuccinylase (3.5.1.18 from EC) hydrolyses N-succinyl-L,L-diaminopimelic acid which is required for the bacterial synthesis of lysine and meso-diaminopimelic acid.    This group of bacterial sequences belong to the MEROPS peptidase family M20 (clan MH), subfamily M20A (non-peptidase homologs).  ; GO: 0009014 succinyl-diaminopimelate desuccinylase activity, 0009089 lysine biosynthetic process via diaminopimelate.
Probab=20.96  E-value=48  Score=12.46  Aligned_cols=132  Identities=20%  Similarity=0.212  Sum_probs=65.2

Q ss_pred             HHHHHHHCCC-CCCHH------HHHHHHHHCCCEEEEEECCCCCCCEEEEEEEEEEECCCCC-CCEEEEE--CCCCCEEE
Q ss_conf             6799884789-99889------9999987458604211124656874899999975657998-7089997--59995798
Q gi|254780316|r    5 LSWLKDHLDT-DVSLE------KICDTLTSIGLEVEKVDNREALSPFTIVKVLSVERNPDLD-CAILRID--TGKHQEIQ   74 (805)
Q Consensus         5 ~~WL~~~v~~-~~~~~------~l~~~lt~~G~EVe~i~~~~~~~~vvvg~v~~~~~hP~ad-l~v~~Vd--~g~~~~~~   74 (805)
                      ...++|+|.. ++||+      =|+++|..+||+.|.++..                  |.. |++..--  +|+     
T Consensus         2 ~~lak~Lis~pSVTP~D~Gcq~~Ia~rL~~~gF~~e~~~f~------------------d~kN~wa~~g~aif~~-----   58 (383)
T TIGR01246         2 TELAKELISRPSVTPNDAGCQDLIAERLKKIGFEIEILHFG------------------DTKNLWATRGTAIFKD-----   58 (383)
T ss_pred             HHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEECC------------------CCHHHHHHCCEEEECC-----
T ss_conf             12466330378889984778999999984539758998508------------------7344454557146508-----


Q ss_pred             EECCCCCCCCCCEEEEECCC--CEECC-CCE--EEEEEHHCCCCCCCHH------HHHHH--CCCCCCCCC-EE-EE---
Q ss_conf             97548345589789896687--79258-983--9833120586505454------11887--699854775-07-81---
Q gi|254780316|r   75 VVCGAPNVRVGLLGVWAPPG--SCIPE-NNM--IVNVRKIRGIESTGMM------CSEKE--LMLSDDSAS-IM-EL---  136 (805)
Q Consensus        75 IvcgA~Nv~~g~~V~~A~~G--a~lp~-g~~--~i~~~~irGv~S~GMl------CS~~E--Lgl~~~~~g-I~-~l---  136 (805)
                         ++|++.=+-||=|-+.|  -.+.+ +-|  .++..+|-|==+-=|=      .-+.|  +----||.| =+ .|   
T Consensus        59 ---~~P~l~F~GHtDVVP~G~~e~W~~s~PF~p~~~dG~lYGRGAaDMKGs~Aafv~AaerFv~~~pdhkGa~islLiTS  135 (383)
T TIGR01246        59 ---GEPVLAFAGHTDVVPAGPLEQWSSSPPFEPVERDGKLYGRGAADMKGSLAAFVVAAERFVKKNPDHKGASISLLITS  135 (383)
T ss_pred             ---CCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf             ---87658874621211388887788876966346212176265621467899999999999984777784053443330


Q ss_pred             CC--CCCCCC-CHHHHHCCCCEEEEEEEC
Q ss_conf             68--888884-558870888559998708
Q gi|254780316|r  137 PI--DAPVGG-RLSDYLELSDPIIDVSLT  162 (805)
Q Consensus       137 ~~--~~~~G~-~~~~~l~l~D~i~ei~iT  162 (805)
                      ||  ++.-|+ .+.+||.--|..||.-|+
T Consensus       136 DEEG~A~dGT~~vve~L~~r~~~IDyc~V  164 (383)
T TIGR01246       136 DEEGEAIDGTKKVVETLMARDELIDYCIV  164 (383)
T ss_pred             HCCCCCHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             00133113688999999972589978986


No 192
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=20.82  E-value=48  Score=12.44  Aligned_cols=25  Identities=12%  Similarity=0.001  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHCCCEEEECCCCCCCE
Q ss_conf             9998999860870000010223332
Q gi|254780316|r  251 DITNYVSLDRGYPSHVFDASRISDV  275 (805)
Q Consensus       251 DitNyvmle~GqPlHafD~dki~~~  275 (805)
                      +=.|-+|++.-+..|.-|.|-...+
T Consensus       109 ~DAN~lm~~~~~~fd~IDiDPFGSP  133 (380)
T COG1867         109 KDANALLHELHRAFDVIDIDPFGSP  133 (380)
T ss_pred             CHHHHHHHHCCCCCCEEECCCCCCC
T ss_conf             4289998725887637813899997


No 193
>TIGR01490 HAD-SF-IB-hyp1 HAD-superfamily subfamily IB hydrolase, TIGR01490; InterPro: IPR006385   This group of sequences belong to the IB subfamily of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The sequences are all bacterial. The IB subfamily includes the enzyme phosphoserine phosphatase. Due to this relationship, several of these sequences have been annotated as "phosphoserine phosphatase related proteins," or "phosphoserine phosphatase-family enzymes." There is presently no evidence that any of the proteins in this family possess PSPase activity. .
Probab=20.76  E-value=48  Score=12.46  Aligned_cols=61  Identities=16%  Similarity=0.128  Sum_probs=36.4

Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCC-CCCCCC----CCCCHHHHHHHHHHHHHHHHHHH--HCCCCCC
Q ss_conf             4025676767653523346676554-434576----78998895467898878778774--0232100
Q gi|254780316|r  455 EKADLVEEILRIYGVDQIKSEPLPL-TQVEDK----RNLSLQQSRTRYVKRVLASRAMM--EVVNWSF  515 (805)
Q Consensus       455 ~e~DLiEEIaRiyGYdnIp~~~l~~-~~~~~~----~~~~~~~~~~~~ir~~L~~~Gf~--Ev~tysl  515 (805)
                      ...=+|+++||.+|.|++=.+-++. ....-.    +..........+|++.+....+.  ++.-||=
T Consensus       114 S~~~~v~~~A~~~G~~~~~g~~~~~~~dG~~tG~~~G~~~~~~~K~~al~~~~~~~~~~L~~syaY~D  181 (204)
T TIGR01490       114 SLEILVKPLARKLGIDNAIGTRLEEAEDGIYTGEIIGNNCKGEGKVHALAELLAEEQIDLKDSYAYSD  181 (204)
T ss_pred             CHHHHHHHHHHHCCCCEEEEEEEEEECCCEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEEEECC
T ss_conf             78899999998718660301200210277055235053235868999999983203788200245318


No 194
>PRK04011 peptide chain release factor 1; Provisional
Probab=20.64  E-value=48  Score=12.41  Aligned_cols=84  Identities=23%  Similarity=0.266  Sum_probs=46.2

Q ss_pred             EEEECCCCCCCCHHHCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHH---HHHHHHHHHH
Q ss_conf             0000256763100111355312013672699997157878887788761654015544134553013---5889998887
Q gi|254780316|r  302 VVIASDGRIQSIAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQG---MIPVLKHIVS  378 (805)
Q Consensus       302 lvI~d~~~~ialaGImGg~~s~v~~~T~~illEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~---~~~al~r~~~  378 (805)
                      ++|.|++.  |+-|..-|..-       .|+=+.-.+-|.       +|+----|+.||+|=..-..   ......+|.+
T Consensus       143 ~iviD~~~--a~~g~l~G~~~-------evl~~~~~~vP~-------Kh~~GGQSa~RF~Rlree~~~~f~kkvaE~a~~  206 (409)
T PRK04011        143 LIVVDRRE--ATIGLLKGKRI-------EVLKELTSFVPG-------KHRAGGQSARRFERLIEIAAHEFYKRVGEHANE  206 (409)
T ss_pred             EEEEECCC--CEEEEECCCEE-------EEEEEEEECCCC-------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99994796--26999859789-------998898504774-------235552668999999999999999999999998


Q ss_pred             HHCCCCCCCCCCCEEEEECCCCC
Q ss_conf             52123345556525874135543
Q gi|254780316|r  379 LILSLCGGTASDICIARNITYKP  401 (805)
Q Consensus       379 Li~e~~gg~~~~~~~~~~~~~~~  401 (805)
                      ++.....-.+.++...++.+.+.
T Consensus       207 ~Fl~~~~~~v~GiilgGp~~~K~  229 (409)
T PRK04011        207 AFLPLLEKKLKGILIGGPGPTKE  229 (409)
T ss_pred             HHHCCCCCCEEEEEECCCCHHHH
T ss_conf             74147876437899516835878


No 195
>PRK00029 hypothetical protein; Validated
Probab=20.43  E-value=11  Score=16.97  Aligned_cols=63  Identities=17%  Similarity=0.249  Sum_probs=48.2

Q ss_pred             CHHHCCCCCCCCCCCCCEE----EEEEECCCHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             0011135531201367269----99971578788877887616540155441345530135889998887521233
Q gi|254780316|r  313 IAGIIGGKHAGCDDNTTDV----LVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLILSLC  384 (805)
Q Consensus       313 laGImGg~~s~v~~~T~~i----llEsA~F~p~~Ir~tar~l~l~TdaS~RfERgvd~~~~~~al~r~~~Li~e~~  384 (805)
                      +-|||+.++..|+-.|=+-    |++.  |||..|-.       ++|..=||.=|--|..+.+.+.|+++-+..+-
T Consensus       246 vHGVmNTDNmsI~GeTiDYGP~aFmd~--ydp~~v~n-------~~D~~GRYaf~nQP~i~~WNL~~LaeaL~pLi  312 (487)
T PRK00029        246 VHGVMNTDNMSILGETFDYGPYGFLDD--YDPGFTCN-------HSDHQGRYAFGNQPAIALWNLQRLAQALLPLI  312 (487)
T ss_pred             CCCCCCCCCCEEEEEECCCCCCHHHHH--CCCCCCCC-------CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             045123688600134236776012543--58666665-------63898774357775999999999999878761


No 196
>PRK12342 putative electron transfer flavoprotein YdiQ; Provisional
Probab=20.30  E-value=49  Score=12.36  Aligned_cols=126  Identities=14%  Similarity=0.194  Sum_probs=55.1

Q ss_pred             EEEEEECHHHHHHCCCCCCEEEEEEEHHH--HHHHHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCC-HHHHHHHHHHCC
Q ss_conf             99854778999966879978999987876--235452024566313689888720018999668879-999999997111
Q gi|254780316|r  665 GYFGEFHPNILDFFGLSNPICGFEVYLDS--IPISQKKRTKTKKVVHLSSLHPVKRDLAFIVDQHIP-AGTLVNIIKNVD  741 (805)
Q Consensus       665 G~iG~ihP~i~~~~~i~~~v~~~EI~ld~--L~~~~~~~~~~~~~~~~s~fP~v~RDls~iv~~~v~-~~~I~~~i~~~~  741 (805)
                      |.-|++-|.++..++++.-.++-++.++.  +............++  .++|++   +|+.-.-+.+ +-.+...++...
T Consensus       122 ~~tgqvg~~lAe~Lg~P~vt~v~~i~~~~~~~~v~R~~e~g~e~ve--~~lPav---vtv~~~~n~PR~psl~~im~Akk  196 (254)
T PRK12342        122 LYAQQVGLLLGELLQLPVINAVSKIQRQGNKLVVERTLEDDVEVIE--LSLPAV---LCVTSDINVPRIPSMKAILGAGK  196 (254)
T ss_pred             CCCCCHHHHHHHHCCCCCEEEEEEEEEECCEEEEEEECCCCEEEEE--ECCCEE---EEEECCCCCCCCCCHHHHHHHCC
T ss_conf             8988578999987099716679999971998999999179679999--779989---99989988557799789998669


Q ss_pred             CCEEEEEEEEEEECCCCCCCC-EEEEEEEEEEC---CCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             003576989876367799884-26999999847---79888999999999999999999951
Q gi|254780316|r  742 RLIDDVTVFDVFQGKSLGEGK-KSVAIQVLIQP---LKDTFRDDDIRILMDRIVENVVKKTN  799 (805)
Q Consensus       742 ~ll~~v~lfDvY~g~~i~~gk-kSla~rl~fqs---~~kTLtd~EI~~i~~~ii~~l~~k~g  799 (805)
                      +-++.+.+-|+    ++.... ..-..++.+-.   ..+..-+.+.++..+++++.|++++|
T Consensus       197 K~i~~~~~~dl----g~~~~~~~~~v~~~~~Pp~~~~~~~i~egd~~e~v~~Lv~~Lkee~~  254 (254)
T PRK12342        197 KPVNQWQASDI----GWSQSAPLAELVSILVPPQTERKHIILDNDSPEAIAELAEHLKKALN  254 (254)
T ss_pred             CCCEEECHHHC----CCCCCCCCEEEEEEECCCCCCCCCEEECCCHHHHHHHHHHHHHHHHC
T ss_conf             98508589994----97767786389997479976677668249989999999999988659


No 197
>PHA02241 hypothetical protein
Probab=20.05  E-value=50  Score=12.33  Aligned_cols=133  Identities=21%  Similarity=0.270  Sum_probs=71.5

Q ss_pred             EEEEEEEEECH--HHHHHCCCCCCEEEEEEEHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEE-EEECCCCCHHHHHHH--
Q ss_conf             99999854778--9999668799789999878762354520245663136898887200189-996688799999999--
Q gi|254780316|r  662 IVLGYFGEFHP--NILDFFGLSNPICGFEVYLDSIPISQKKRTKTKKVVHLSSLHPVKRDLA-FIVDQHIPAGTLVNI--  736 (805)
Q Consensus       662 ~iiG~iG~ihP--~i~~~~~i~~~v~~~EI~ld~L~~~~~~~~~~~~~~~~s~fP~v~RDls-~iv~~~v~~~~I~~~--  736 (805)
                      .++||-.-|.-  -+..+||+.+|+|+-|++--.    +....+.++|..++.+-..+|-=- |+.+ ++.-.++...  
T Consensus        30 eilgys~~le~~eyi~~ny~~~~~~fi~e~~~it----ke~~i~eqry~~y~s~ielkr~ng~f~~~-~i~~~~~~e~fs  104 (182)
T PHA02241         30 EILGYTDSLEDAEYIRDNYGTSNPIFINEYPYIT----KEKLIEEQRYFRYNSYIELKRVNGYFEIS-EINDLQVTEDFS  104 (182)
T ss_pred             EEECCCCCHHHHHHHHHCCCCCCCHHHHHCCHHH----HHHHHHHHHHEECCCEEEEEECCCEEEEE-CHHCCCCCEEEE
T ss_conf             6651347477889998525887722323140131----88887675511201147887316758850-000477515465


Q ss_pred             HHHCCCCEEEEEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCH---HHHHHHHHHHHHHHHHHHCCEECC
Q ss_conf             97111003576989876367799884269999998477988899---999999999999999995119816
Q gi|254780316|r  737 IKNVDRLIDDVTVFDVFQGKSLGEGKKSVAIQVLIQPLKDTFRD---DDIRILMDRIVENVVKKTNAVLRS  804 (805)
Q Consensus       737 i~~~~~ll~~v~lfDvY~g~~i~~gkkSla~rl~fqs~~kTLtd---~EI~~i~~~ii~~l~~k~ga~LRs  804 (805)
                      +.+..+.+.+-...|++.     .+.-|+++-+.++|.-.-..|   ++++....++--.|+..-+|.+||
T Consensus       105 i~k~~~~~dsp~~i~~~~-----~~rnsi~i~~~m~sey~d~edi~~~~~~s~~~kl~~ll~~~k~adirs  170 (182)
T PHA02241        105 INKDDKNFDSPFSINMFS-----HNRNSIGIEFIMFSEYDDKEDIIEKEKNSFLMKLKYLLKHSKEADIRS  170 (182)
T ss_pred             ECCCCCCCCCCEEEEEEE-----CCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf             547865567867999885-----278736899998301263778999878999999999984044111366


No 198
>COG1904 UxaC Glucuronate isomerase [Carbohydrate transport and metabolism]
Probab=20.03  E-value=37  Score=13.20  Aligned_cols=13  Identities=23%  Similarity=0.422  Sum_probs=5.7

Q ss_pred             HHCCCCCHHHHHH
Q ss_conf             3113458789999
Q gi|254780316|r  414 LSGIDVPIEDSLR  426 (805)
Q Consensus       414 ilG~~i~~~ei~~  426 (805)
                      +.|..++.+|+..
T Consensus       258 l~G~~lt~~E~~~  270 (463)
T COG1904         258 LAGEALSTEEAEQ  270 (463)
T ss_pred             HCCCCCCHHHHHH
T ss_conf             6478788899999


Done!