Query         gi|254780979|ref|YP_003065392.1| aspartyl/glutamyl-tRNA amidotransferase subunit B [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 500
No_of_seqs    209 out of 1752
Neff          6.3 
Searched_HMMs 39220
Date          Mon May 30 02:51:55 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780979.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK05477 gatB aspartyl/glutamy 100.0       0       0 1383.7  47.7  474   19-497     2-478 (479)
  2 COG0064 GatB Asp-tRNAAsn/Glu-t 100.0       0       0 1327.4  46.7  475   19-498     3-482 (483)
  3 PRK04028 glutamyl-tRNA(Gln) am 100.0       0       0 1152.6  42.3  447   19-498     2-628 (631)
  4 KOG2438 consensus              100.0       0       0 1148.9  35.6  480   16-498    17-505 (505)
  5 pfam02934 GatB_N GatB/GatE cat 100.0       0       0  961.2  26.7  286   23-314     1-287 (287)
  6 TIGR00133 gatB glutamyl-tRNA(G 100.0       0       0  823.7  34.4  477   20-497     2-523 (523)
  7 COG2511 GatE Archaeal Glu-tRNA 100.0       0       0  712.2  38.1  444   21-497     5-626 (631)
  8 TIGR00134 gatE_arch glutamyl-t 100.0       0       0  423.0  25.3  446   21-498     3-629 (631)
  9 pfam02637 GatB_Yqey GatB domai 100.0 1.2E-34 3.1E-39  275.6  16.6  146  351-496     1-148 (148)
 10 smart00845 GatB_Yqey GatB doma 100.0 4.1E-34   1E-38  271.7  16.0  145  352-496     1-147 (147)
 11 pfam01162 consensus             99.8 1.6E-21   4E-26  179.0   5.6   69  281-349     1-69  (69)
 12 pfam09424 YqeY Yqey-like prote  97.8 0.00025 6.4E-09   52.3   9.4  113  365-496    22-143 (143)
 13 pfam04558 tRNA_synt_1c_R1 Glut  97.3   0.027 6.8E-07   37.4  13.7  152  323-486     4-164 (164)
 14 KOG1148 consensus               96.8   0.066 1.7E-06   34.5  14.1   19  188-206   294-312 (764)
 15 COG1610 Uncharacterized conser  96.0   0.024 6.1E-07   37.8   6.3   97  387-497    43-148 (148)
 16 TIGR00838 argH argininosuccina  88.1     1.3 3.3E-05   25.0   5.1  119  359-481   158-311 (469)
 17 COG3937 Uncharacterized conser  75.4     6.8 0.00017   19.7   5.6   64  386-449    18-94  (108)
 18 cd07363 45_DOPA_Dioxygenase Th  71.5     4.5 0.00012   21.0   3.2   43  256-308    85-129 (253)
 19 TIGR02407 ectoine_ectB diamino  69.0     9.3 0.00024   18.7   4.7   68  408-493   300-368 (413)
 20 TIGR01398 FlhA flagellar biosy  68.1     7.1 0.00018   19.5   3.6   59  363-421   472-531 (713)
 21 PRK10628 hypothetical protein;  65.7     4.1 0.00011   21.3   2.0   41  258-308    77-118 (246)
 22 pfam06576 DUF1133 Protein of u  65.3      11 0.00028   18.1   6.6   61  399-459    48-120 (176)
 23 TIGR02653 Lon_rel_chp conserve  64.7     7.4 0.00019   19.4   3.1  123  294-434   333-458 (677)
 24 pfam12570 DUF3750 Protein of u  64.0     5.1 0.00013   20.6   2.2   29  289-323    90-118 (129)
 25 PRK00116 ruvA Holliday junctio  63.9      12  0.0003   18.0  10.7  105  324-428    70-187 (198)
 26 COG3384 Aromatic ring-opening   63.5     8.2 0.00021   19.1   3.2  100  188-308    26-140 (268)
 27 PRK11913 phhA phenylalanine 4-  63.4     5.8 0.00015   20.2   2.4   45  279-335   104-148 (272)
 28 PHA01082 putative transcriptio  62.7       3 7.7E-05   22.3   0.8   56  138-201    78-133 (133)
 29 cd03346 eu_TrpOH Eukaryotic tr  61.8      11 0.00029   18.1   3.6  111  185-335    80-190 (287)
 30 cd03348 pro_PheOH Prokaryotic   59.7     7.9  0.0002   19.2   2.5   45  279-335    92-136 (228)
 31 TIGR01011 rpsB_bact ribosomal   58.6     5.2 0.00013   20.5   1.4  122  258-416     5-136 (227)
 32 KOG2305 consensus               58.5      11 0.00028   18.2   3.1   37  186-224    35-71  (313)
 33 pfam11212 DUF2999 Protein of u  50.0      19 0.00049   16.4   5.3   18  469-492    47-64  (82)
 34 pfam11867 DUF3387 Domain of un  49.8      19 0.00049   16.3   6.3   18  391-408   198-215 (333)
 35 cd00361 arom_aa_hydroxylase Bi  49.6      14 0.00036   17.4   2.4   45  279-335    86-130 (221)
 36 cd04775 HTH_Cfa-like Helix-Tur  48.0     5.4 0.00014   20.4   0.1   59  269-350    15-73  (102)
 37 COG4901 Ribosomal protein S25   47.6      21 0.00053   16.1   3.2   42  304-345    40-81  (107)
 38 pfam04262 Glu_cys_ligase Gluta  46.7      16  0.0004   17.0   2.3   50  166-220    56-105 (377)
 39 pfam06519 TolA TolA C-terminal  43.9      23 0.00059   15.8   2.8   48  186-235     9-56  (96)
 40 COG1490 Dtd D-Tyr-tRNAtyr deac  43.6      24  0.0006   15.7   3.7   47  180-229    89-138 (145)
 41 pfam05606 DUF777 Borrelia burg  43.1     9.2 0.00023   18.7   0.7   23   89-112    88-113 (180)
 42 KOG1795 consensus               41.5      25 0.00065   15.5   4.8   10  255-264   783-792 (2321)
 43 COG0105 Ndk Nucleoside diphosp  40.5      13 0.00034   17.6   1.1   77  139-226    32-112 (135)
 44 KOG2181 consensus               40.2      16  0.0004   17.0   1.5  128  194-342   119-255 (415)
 45 cd03345 eu_TyrOH Eukaryotic ty  39.9      21 0.00053   16.1   2.1   46  279-336   145-190 (298)
 46 PRK02107 glutamate--cysteine l  39.5      26 0.00066   15.4   2.5   33  393-427   430-462 (523)
 47 TIGR01083 nth endonuclease III  38.7      28 0.00071   15.2   6.7   24  428-451   142-165 (192)
 48 KOG2243 consensus               38.5      24 0.00062   15.6   2.2   27  235-261  1824-1855(5019)
 49 PRK09849 putative oxidoreducta  38.3      12 0.00032   17.7   0.7   14   67-80    210-224 (702)
 50 PRK13979 DNA topoisomerase IV   37.2      29 0.00075   15.0   7.5   37  307-345   402-438 (959)
 51 cd04789 HTH_Cfa Helix-Turn-Hel  37.1     9.9 0.00025   18.5   0.1   55  269-346    15-69  (102)
 52 cd04770 HTH_HMRTR Helix-Turn-H  37.0      15 0.00038   17.1   1.0   50  272-345    18-68  (123)
 53 PRK09514 zntR zinc-responsive   36.7      14 0.00035   17.4   0.7   54  269-345    15-69  (140)
 54 CHL00139 rpl18 ribosomal prote  35.4      31 0.00079   14.8   2.9   62   29-103    26-92  (109)
 55 TIGR01059 gyrB DNA gyrase, B s  35.3      26 0.00067   15.3   2.0   29  439-467   729-761 (818)
 56 cd04766 HTH_HspR Helix-Turn-He  35.3      10 0.00027   18.3  -0.0   53  271-346    18-70  (91)
 57 TIGR03575 selen_PSTK_euk L-ser  35.1      29 0.00073   15.1   2.2   14  468-481   262-275 (340)
 58 PRK05560 DNA gyrase subunit A;  35.1      32  0.0008   14.8   7.3   76  304-381   387-480 (822)
 59 COG2326 Uncharacterized conser  35.0      32 0.00081   14.8   3.2   30  255-284   122-151 (270)
 60 TIGR00676 fadh2 5,10-methylene  34.9      24 0.00062   15.6   1.8   18  200-221    96-113 (302)
 61 pfam11181 YflT Heat induced st  34.9      32 0.00081   14.7   5.0   45  300-345    47-92  (103)
 62 cd01110 HTH_SoxR Helix-Turn-He  34.4     9.7 0.00025   18.5  -0.3   56  267-345    13-68  (139)
 63 COG4050 Uncharacterized protei  34.3      32 0.00083   14.7   3.7   38  166-206   112-149 (152)
 64 pfam11950 DUF3467 Protein of u  34.2      32 0.00083   14.7   4.3   58  145-203    15-80  (90)
 65 cd03347 eu_PheOH Eukaryotic ph  32.8      33 0.00084   14.6   2.2  109  187-335    82-190 (306)
 66 KOG4168 consensus               32.5      34 0.00088   14.5   4.4   80  369-452    50-129 (149)
 67 COG5418 Predicted secreted pro  32.4      18 0.00045   16.6   0.8   16  102-117    38-53  (164)
 68 cd05298 GH4_GlvA_pagL_like Gly  32.3      34 0.00086   14.6   2.2   86  369-462   351-437 (437)
 69 COG3495 Uncharacterized protei  32.0      17 0.00043   16.8   0.6   29  100-128   113-141 (166)
 70 TIGR00034 aroFGH phospho-2-deh  31.8      35  0.0009   14.4   3.2   72  178-250    54-155 (348)
 71 cd01199 INT_Tn1545_C Tn1545-re  31.6      36 0.00091   14.4   2.3   40  207-246    46-85  (205)
 72 PRK11814 cysteine desulfurase   31.0      35 0.00088   14.5   2.0   38  317-355   425-462 (484)
 73 PRK06740 histidinol-phosphatas  30.8      34 0.00086   14.5   2.0   47  308-357   155-208 (338)
 74 TIGR02614 ftsW cell division p  30.3      15 0.00038   17.2   0.1   32   99-130   214-252 (370)
 75 KOG2050 consensus               30.1      38 0.00096   14.2  11.7   13  292-304   275-287 (652)
 76 CHL00085 ycf24 putative ABC tr  30.1      23 0.00058   15.8   1.0   36  317-357   426-461 (485)
 77 KOG0823 consensus               30.0      12  0.0003   17.9  -0.5   46   19-64     45-94  (230)
 78 KOG3591 consensus               29.6      38 0.00098   14.1   3.4   24  105-128   123-146 (173)
 79 PRK02471 bifunctional glutamat  29.3      39 0.00099   14.1   2.3   41  363-407   349-389 (753)
 80 pfam07028 DUF1319 Protein of u  28.9      33 0.00084   14.6   1.6   20  440-460    84-103 (119)
 81 cd04767 HTH_HspR-like_MBC Heli  28.6      12  0.0003   17.9  -0.7   57  267-346    13-69  (120)
 82 TIGR00954 3a01203 Peroxysomal   28.5      40   0.001   14.0   3.2   73  278-354   592-664 (788)
 83 TIGR01204 bioW 6-carboxyhexano  28.4      40   0.001   14.0   2.4   49  141-207    38-86  (238)
 84 KOG3666 consensus               28.4      40   0.001   14.0   6.2   46  295-341   790-835 (1141)
 85 pfam00351 Biopterin_H Biopteri  28.3      40   0.001   14.0   2.0  111  185-335    80-190 (309)
 86 KOG1261 consensus               27.5      41  0.0011   13.9   3.0   78  141-224   175-261 (552)
 87 KOG2599 consensus               27.3      42  0.0011   13.9   2.1  108  140-305    30-137 (308)
 88 pfam09043 Lys-AminoMut_A D-Lys  26.8      43  0.0011   13.8   8.4   52  401-462   414-465 (509)
 89 PRK13335 superantigen-like pro  26.6      43  0.0011   13.8   2.2   70  256-336   239-308 (356)
 90 cd04790 HTH_Cfa-like_unk Helix  26.5      18 0.00047   16.5  -0.0   56  270-347    16-71  (172)
 91 PRK12559 transcriptional regul  26.5      43  0.0011   13.8   3.6   85  360-470    11-105 (131)
 92 PRK05561 DNA topoisomerase IV   26.5      43  0.0011   13.8   6.7   34  307-345   396-429 (745)
 93 TIGR00577 fpg formamidopyrimid  26.5      43  0.0011   13.8   2.0   57  366-433   184-243 (292)
 94 pfam12224 Amidoligase_2 Putati  26.3      43  0.0011   13.7   5.0   69  166-251    65-135 (250)
 95 TIGR01801 CM_A chorismate muta  26.3      22 0.00055   16.0   0.3   33  393-426    56-88  (104)
 96 TIGR01846 type_I_sec_HlyB type  26.2      40   0.001   14.0   1.7   52  294-346    91-145 (703)
 97 COG1978 Uncharacterized protei  26.1      27 0.00068   15.3   0.7   70  323-396    73-143 (152)
 98 PRK06108 aspartate aminotransf  25.6      45  0.0011   13.6   2.2   42  231-275    78-119 (382)
 99 smart00422 HTH_MERR helix_turn  25.4      22 0.00056   15.9   0.2   50  272-345    18-68  (70)
100 PRK13901 ruvA Holliday junctio  25.3      45  0.0012   13.6  10.8  115  324-452    69-192 (196)
101 cd01018 ZntC Metal binding pro  25.2      34 0.00087   14.5   1.2   47  387-438   199-245 (266)
102 PRK07531 bifunctional 3-hydrox  24.7      46  0.0012   13.5   1.8   29  173-206   144-172 (489)
103 PRK01966 ddl D-alanyl-alanine   24.4      47  0.0012   13.5   2.7   37  168-210   112-149 (344)
104 TIGR00707 argD acetylornithine  24.4      42  0.0011   13.8   1.5  282  146-477    12-349 (402)
105 KOG2164 consensus               24.1      36 0.00093   14.3   1.1   45   16-66    147-198 (513)
106 TIGR02698 CopY_TcrY copper tra  23.5      49  0.0012   13.4   2.3   41  408-449    74-116 (130)
107 cd02977 ArsC_family Arsenate R  23.4      49  0.0012   13.4   4.0   77  376-470    18-105 (105)
108 pfam11829 DUF3349 Protein of u  23.0      50  0.0013   13.3   6.4   84  370-470     5-90  (97)
109 cd04779 HTH_MerR-like_sg4 Heli  23.0      19 0.00047   16.5  -0.5   54  270-346    15-68  (134)
110 COG3608 Predicted deacylase [G  22.8      50  0.0013   13.3   5.2   55  168-223   198-255 (331)
111 PRK13344 spxA transcriptional   22.8      50  0.0013   13.3   1.8   91  360-470    11-105 (132)
112 PRK09261 phospho-2-dehydro-3-d  22.6      50  0.0013   13.3   3.3   26  178-203    56-82  (351)
113 TIGR02051 MerR Hg(II)-responsi  22.6      48  0.0012   13.4   1.5   62  261-345     5-67  (126)
114 TIGR01267 Phe4hydrox_mono phen  22.5      45  0.0012   13.6   1.4   62  280-353    93-154 (251)
115 COG2905 Predicted signal-trans  22.3      36 0.00092   14.3   0.8   48  141-190   160-207 (610)
116 cd04165 GTPBP1_like GTPBP1-lik  22.3      51  0.0013   13.2   4.3   40  169-208   135-174 (224)
117 pfam08777 RRM_3 RNA binding mo  22.0      52  0.0013   13.2   2.1   40  178-219     6-45  (102)
118 pfam02885 Glycos_trans_3N Glyc  21.9      52  0.0013   13.2   5.6   42  388-429    14-55  (66)
119 KOG1280 consensus               21.7      29 0.00074   15.0   0.2   56  263-327   247-302 (381)
120 PRK13752 putative transcriptio  21.7      50  0.0013   13.3   1.5   56  267-345    19-75  (144)
121 pfam10228 DUF2228 Uncharacteri  21.7      53  0.0013   13.1   6.1   21  279-300   150-170 (253)
122 TIGR00591 phr2 deoxyribodipyri  21.6      49  0.0013   13.3   1.4   31  142-181    90-121 (471)
123 pfam11202 DUF2983 Protein of u  21.6      38 0.00096   14.2   0.8   17  159-175    79-95  (353)
124 PRK13515 carboxylate-amine lig  21.6      53  0.0013   13.1   3.7   29  175-204    52-80  (381)
125 PRK08136 glycosyl transferase   21.5      53  0.0013   13.1   4.6   11   78-88     44-54  (316)
126 TIGR02333 2met_isocit_dHY 2-me  21.5      53  0.0014   13.1   1.8   90  189-287   250-350 (864)
127 KOG0979 consensus               21.4      53  0.0014   13.1   1.6   47   25-71     22-74  (1072)
128 cd04782 HTH_BltR Helix-Turn-He  21.3      53  0.0014   13.1   2.3   59  271-352    17-75  (97)
129 PRK01372 ddl D-alanine--D-alan  21.3      53  0.0014   13.1   2.5   13  198-210   103-115 (304)
130 PRK04182 cytidylate kinase; Pr  21.2      54  0.0014   13.1   4.7   72  321-405   100-173 (178)
131 pfam07830 PP2C_C Protein serin  20.9      54  0.0014   13.0   1.6   10  443-452    28-37  (81)
132 KOG1147 consensus               20.8      47  0.0012   13.5   1.2   28  289-318   370-397 (712)
133 TIGR02365 dha_L_ycgS dihydroxy  20.6      33 0.00084   14.6   0.4   99  308-420     2-109 (200)
134 PRK09071 hypothetical protein;  20.3      56  0.0014   12.9   6.6   69  168-248   128-206 (323)
135 KOG0479 consensus               20.0      47  0.0012   13.5   1.1   53  363-415   578-639 (818)
136 COG2160 AraA L-arabinose isome  20.0      57  0.0014   12.9   2.9   33  230-262   201-234 (497)

No 1  
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=100.00  E-value=0  Score=1383.66  Aligned_cols=474  Identities=58%  Similarity=0.944  Sum_probs=462.5

Q ss_pred             CCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEEECC
Q ss_conf             47803389899978886898655588424689876520613026898887378999999999877829762442013113
Q gi|254780979|r   19 TGDWEVVIGIEVHAQLSVVSKLFSGASVNFGAEPNTQVSFFDAAMPGMLPILNGRCVQQAVMTGLGLNAHINKYSVFARK   98 (500)
Q Consensus        19 ~~~~e~vIGLEiH~qL~t~tKlFc~c~~~~~~~pNt~v~~~~~g~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~fdRK   98 (500)
                      ..||++||||||||||+|+|||||+|+++|+++|||+|||||+|+|||||++|++||++|+++|+||||+|+++++||||
T Consensus         2 ~~~~~~viGlEiH~qL~t~tKlF~~~~~~~~~~pNt~v~~v~~~~PG~lP~lN~~av~~ai~~a~al~~~i~~~~~f~RK   81 (479)
T PRK05477          2 MMNFEVVIGLEVHVQLNTKSKIFSGCSTEFGAEPNTNVCPVCLGLPGALPVLNKEAVEKAIKAGLALNCEIAKRSVFDRK   81 (479)
T ss_pred             CCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEECCC
T ss_conf             87653168899987707996857899987899976663842006898877669999999999999839864633155023


Q ss_pred             CEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEE
Q ss_conf             21237678882014454420153389997067777741037984236665202310011567871488661578612576
Q gi|254780979|r   99 NYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRTIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEI  178 (500)
Q Consensus        99 ~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEI  178 (500)
                      ||||||||||||||||+.|||.||+|++...++.     .++|+|+||||||||||++|+..+++|||||||||+|||||
T Consensus        82 ~YfYpDlp~gyQiTq~~~Pi~~~G~l~~~~~~g~-----~k~i~I~~i~lEeD~gk~~h~~~~~~~~vD~NRaG~PLiEI  156 (479)
T PRK05477         82 NYFYPDLPKGYQISQYDEPIVENGYLEIEVEDGE-----EKRIGIERIHLEEDAGKSVHDGGAGYSLVDYNRAGVPLIEI  156 (479)
T ss_pred             CCCCCCCCCCCCCCCCCCCEECCCEEEEEECCCC-----EEEEEEEEEEECCCHHHHCCCCCCCCEEEECCCCCCCEEEE
T ss_conf             4668989877521667556306618999807896-----45762278886001001024679982476224579733788


Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             30365277899999999999998642045676432201125754321376-66788622235402465999999999999
Q gi|254780979|r  179 VTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPG-EAWGTRCEVKNVNSIRFLGLAIEYEARRQ  257 (500)
Q Consensus       179 VT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~-~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ  257 (500)
                      ||+|||+||+||++|+++||+||||+|+|||+||+||||||||||||+.| ..|||||||||||||++|++||+||+.||
T Consensus       157 vT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~me~GslR~DvNVSi~~~g~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ  236 (479)
T PRK05477        157 VSEPDMRSPEEAVAYLKKLRSILRYLGISDGNMEEGSLRCDANVSVRPKGQEEFGTRVEIKNLNSFRFVEKAIEYEIQRQ  236 (479)
T ss_pred             ECCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHH
T ss_conf             54799899999999999999999861878666334512056624424788655563588627787889999999999999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCH
Q ss_conf             99731398003443233755433665303566777783327787731269999999885302483689886432026889
Q gi|254780979|r  258 IAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISL  337 (500)
Q Consensus       258 ~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~  337 (500)
                      +++|++|++|.||||+||+.+|+|++||+||+++||||||||||||+.|+++||++++.+|||||+++++||+++||||+
T Consensus       237 ~~ll~~G~~v~qETR~~d~~~g~T~~mR~Ke~a~DYRyfPEpDLppi~i~~e~i~~ik~~lPelP~~~~~rl~~~ygLs~  316 (479)
T PRK05477        237 IEILESGGEVVQETRLFDEDKGETRSMRSKEEAHDYRYFPEPDLPPLEISDEWIEEIRATLPELPDAKRARFVEEYGLSE  316 (479)
T ss_pred             HHHHHCCCCCCCCEEEECCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCH
T ss_conf             99997599823321215378996754445777656440678887773589999999997489989999999998619999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             998887641136789886402-4302457777654578876433874000648989999999888638731478999999
Q gi|254780979|r  338 YDASVLVSDKSIADYFEKLAV-NRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFN  416 (500)
Q Consensus       338 ~dA~~L~~~~~la~~FE~v~~-~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~  416 (500)
                      ++|++|++++.+++|||.++. ..+||.+||||+++++++||+.+.++++++++|++|++|+.|+++|+||.++||+||+
T Consensus       317 ~~a~~L~~~~~l~~~Fe~v~~~~~~pk~aanwi~~el~~~Ln~~~~~i~~~~i~~~~laeLi~li~~g~Is~~~AK~il~  396 (479)
T PRK05477        317 YDARVLTSDKELADYFEAVVAGGADAKLAANWLMGELLGRLNKEGLEIEESPVTPEQLAELIKLIDDGTISGKIAKKVFE  396 (479)
T ss_pred             HHHHHHHHCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             99999984679999999999857887775457666789987452798663788999999999999859856899999999


Q ss_pred             HHHHCCCCHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHH-CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             9981799988999963987618988999999999983999899752-721322658999999728977889999999997
Q gi|254780979|r  417 ILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIA-TKPNLVSWFVGQVMKNTGGKANPSIVQKMLKEK  495 (500)
Q Consensus       417 ~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~k-gk~ka~gfLvGqVMK~tkGkAdpk~v~~lL~e~  495 (500)
                      .|+.++++|+++|+++||.++||+++|+++|++||++||++|++|+ ||++++|||||||||+|||||||+.|+++|+++
T Consensus       397 ~m~~~~~sp~~ii~~~gL~~isD~~eLe~ii~eVI~~np~~Ve~yk~Gk~ka~gfLmGqVMK~tkGkAdPk~v~elL~e~  476 (479)
T PRK05477        397 EMLEGGGDPDEIVEEKGLKQISDEGALEAIVDEVLAANPKAVEDYKAGKEKALGFLVGQVMKATKGKANPKLVNELLKEK  476 (479)
T ss_pred             HHHHCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             99966999999999739824489999999999999979999999976438778789999999857997999999999998


Q ss_pred             HC
Q ss_conf             07
Q gi|254780979|r  496 LG  497 (500)
Q Consensus       496 L~  497 (500)
                      ||
T Consensus       477 L~  478 (479)
T PRK05477        477 LG  478 (479)
T ss_pred             HC
T ss_conf             67


No 2  
>COG0064 GatB Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit (PET112 homolog) [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=1327.39  Aligned_cols=475  Identities=56%  Similarity=0.914  Sum_probs=459.5

Q ss_pred             CCCCCEEEEEEEEEEECCCCCCCCCCCCCCC-CCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEEEC
Q ss_conf             4780338989997888689865558842468-987652061302689888737899999999987782976244201311
Q gi|254780979|r   19 TGDWEVVIGIEVHAQLSVVSKLFSGASVNFG-AEPNTQVSFFDAAMPGMLPILNGRCVQQAVMTGLGLNAHINKYSVFAR   97 (500)
Q Consensus        19 ~~~~e~vIGLEiH~qL~t~tKlFc~c~~~~~-~~pNt~v~~~~~g~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~fdR   97 (500)
                      ..+|++|||||||+||+|+|||||+|+++|+ ++|||||||||+||||+||+||++||+.|+++|+||||+|+..++|||
T Consensus         3 ~~~~e~vIGLEvHvqL~T~tKlFs~~~~~f~~a~PNtnv~pv~lglPGaLPvlN~~av~~ai~~~lAL~~~i~~~~~FdR   82 (483)
T COG0064           3 MMNFEVVIGLEVHVQLNTKTKLFSGCSTDFGGAEPNTNVCPVCLGLPGALPVLNKEAVEKAIKAGLALNCEINEKSVFDR   82 (483)
T ss_pred             CCCCEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCEECCC
T ss_conf             65520576557877861576646788521267899777885002689876656899999999964531656256503166


Q ss_pred             CCEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEE
Q ss_conf             32123767888201445442015338999706777774103798423666520231001156787148866157861257
Q gi|254780979|r   98 KNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRTIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALME  177 (500)
Q Consensus        98 K~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiE  177 (500)
                      |||||||||||||||||+.|||.||++++...++     ..++|+|+|+||||||||++|.+++++|+||||||||||||
T Consensus        83 K~YFYPDlPkgyQIsQ~d~Pi~~~G~i~i~~~~~-----~~k~i~I~r~HlEEDaGK~~h~~~~~~s~vD~NRaGvPLiE  157 (483)
T COG0064          83 KNYFYPDLPKGYQISQFDKPIAENGYLEIELEDG-----EEKRIGIERIHLEEDAGKLTHEGSAGYSLVDYNRAGVPLIE  157 (483)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCC-----CCEEECCCEEECCCCCCCCCCCCCCCCEEEECCCCCCCEEE
T ss_conf             7889998888865013556656685799864788-----60253452343023687650058998404541326874046


Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             630365277899999999999998642045676432201125754321376-6678862223540246599999999999
Q gi|254780979|r  178 IVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPG-EAWGTRCEVKNVNSIRFLGLAIEYEARR  256 (500)
Q Consensus       178 IVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~-~~~GtRvEIKNlnS~~~i~~AI~yEi~R  256 (500)
                      |||+||||||+||++|+.+||.|+||+|||||+||+||||||||||||+.| .+|||||||||+|||++|++||+||+.|
T Consensus       158 IVtePdirs~~eA~ayl~~Lr~ilrylgisd~~meeGsmR~DaNvSvr~~g~~~~GtrvEiKNiNS~~~v~kAi~yE~~R  237 (483)
T COG0064         158 IVTEPDIRSPEEARAYLKKLRSILRYLGISDGNMEEGSMRCDANVSVRPKGQEEFGTRVEIKNLNSFRNVEKAIEYEIQR  237 (483)
T ss_pred             EECCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHH
T ss_conf             54146789999999999999999998088988756675676410330246654557635452586499999999999999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf             99973139800344323375543366530356677778332778773126999999988530248368988643202688
Q gi|254780979|r  257 QIAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGIS  336 (500)
Q Consensus       257 Q~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs  336 (500)
                      |.+++++|+.|.||||+||+.+|.|++||+||++.||||||||||||+.||++|+++++..|||||+++++||+.+||||
T Consensus       238 Q~~~l~~g~~i~qeTR~~d~~~g~T~~mR~KE~a~DYRYfpePDl~p~~is~~~i~~~~~~lPelP~~~~~r~~~~~gls  317 (483)
T COG0064         238 QIELLESGGEIEQETRRFDEATGKTVSMRSKEEAEDYRYFPEPDLPPLEISDEWIEEVRATLPELPDEKRERYIKEYGLS  317 (483)
T ss_pred             HHHHHHCCCCEEEHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
T ss_conf             99999738966502005056788076410346644456579998487237999999999757789899999999974999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHH-
Q ss_conf             999888764113678988640-243024577776545788764338740006489899999998886387314789999-
Q gi|254780979|r  337 LYDASVLVSDKSIADYFEKLA-VNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDI-  414 (500)
Q Consensus       337 ~~dA~~L~~~~~la~~FE~v~-~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~i-  414 (500)
                      ++||++|++++.+++|||+++ .+.+||.+|||+++||++.||+.++++.+++++|++|++|++++++|+||+++||++ 
T Consensus       318 ~~dA~~L~~d~~la~~fe~~~~~~~~~k~~anW~~~el~~~Ln~~~~~i~~~~~~p~~la~Li~li~~g~IS~k~AK~~v  397 (483)
T COG0064         318 EYDARVLTSDKELADYFEEAVKAGADAKLAANWLTNELLGLLNKAGITLEESPLTPEQLAELIKLIDEGTISGKIAKELV  397 (483)
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             88999997689999999999745888899888999999999986599755358998999999999970873199999999


Q ss_pred             HHHHHHCCCCHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHH-CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             999981799988999963987618988999999999983999899752-7213226589999997289778899999999
Q gi|254780979|r  415 FNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIA-TKPNLVSWFVGQVMKNTGGKANPSIVQKMLK  493 (500)
Q Consensus       415 l~~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~k-gk~ka~gfLvGqVMK~tkGkAdpk~v~~lL~  493 (500)
                      +..|+..+++|.+||+++||.|++|+++|+++|++||++||++|++|+ ||++++|||||||||+|+|||||+.|+++|+
T Consensus       398 ~~~~~~~~~~p~~iie~~gL~qisD~~~l~~~V~evia~Np~~ve~yk~GK~~~~~f~vGQVMk~T~GkAnP~~v~~ll~  477 (483)
T COG0064         398 FEILANGGKDPEEIIEEKGLVQISDEGELEKIVDEVLAENPKAVEDYKSGKEKALGFLVGQVMKATKGKANPQQVNELLK  477 (483)
T ss_pred             HHHHHCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             99997379998999986496324899999999999999798999998646898988899999998469999899999999


Q ss_pred             HHHCC
Q ss_conf             97078
Q gi|254780979|r  494 EKLGI  498 (500)
Q Consensus       494 e~L~~  498 (500)
                      ++|+.
T Consensus       478 ~~L~~  482 (483)
T COG0064         478 EKLGK  482 (483)
T ss_pred             HHHCC
T ss_conf             98624


No 3  
>PRK04028 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated
Probab=100.00  E-value=0  Score=1152.57  Aligned_cols=447  Identities=32%  Similarity=0.497  Sum_probs=409.0

Q ss_pred             CCCCCEE---EEEEEEEEECCCCCCCCCCCCCCCC-C-------------------------------------CCCCCC
Q ss_conf             4780338---9899978886898655588424689-8-------------------------------------765206
Q gi|254780979|r   19 TGDWEVV---IGIEVHAQLSVVSKLFSGASVNFGA-E-------------------------------------PNTQVS   57 (500)
Q Consensus        19 ~~~~e~v---IGLEiH~qL~t~tKlFc~c~~~~~~-~-------------------------------------pNt~v~   57 (500)
                      +-|||.+   ||||||+||+|+|||||+|+++|++ +                                     ||+++|
T Consensus         2 ~~~~e~~gl~IGLEiH~QL~T~tKlFc~c~t~~~~~~pn~~~~~~~~~~~~~lg~~d~aa~~e~~~~~~f~y~~~~~~~C   81 (631)
T PRK04028          2 KMDYEELGLKVGLEIHQQLDTKRKLFCRCPTELRDDEPHFEFERYLRPTQSELGEIDPAALEESKKGRKFIYEAYRDTTC   81 (631)
T ss_pred             CCCHHHHCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf             98859969876689987748998737899986567886531000245431111323265554321133334458899857


Q ss_pred             HH-HCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEEECCCEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCC
Q ss_conf             13-02689888737899999999987782976244201311321237678882014454420153389997067777741
Q gi|254780979|r   58 FF-DAAMPGMLPILNGRCVQQAVMTGLGLNAHINKYSVFARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQF  136 (500)
Q Consensus        58 ~~-~~g~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~fdRK~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~  136 (500)
                      || |.|+||++|  |++||++|+++|+||||+|+++++|||||||||||||||||||+   ||.||+|+++         
T Consensus        82 ~v~~~~~Pp~~~--N~~av~~ai~~~~alnc~I~~~~~f~RK~yfypd~pkgyQiTq~---i~~~G~le~~---------  147 (631)
T PRK04028         82 LVELDEEPPHEL--NEEALEIALAVAKLLNMKPVDEIHVMRKIVIDGSNTSGFQRTAL---VALGGYIETS---------  147 (631)
T ss_pred             CCCCCCCCCCCC--CHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE---ECCCCEEECC---------
T ss_conf             223678998777--99999999999998498136465003666668876631345635---5389679656---------


Q ss_pred             EEEEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEE
Q ss_conf             03798423666520231001156787148866157861257630365277899999999999998642045676432201
Q gi|254780979|r  137 RTIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSM  216 (500)
Q Consensus       137 ~~~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGsl  216 (500)
                       .++|+|+||||||||||++|+. ++++.+||||||||||||||+|||+||+||++|+++|++||||+|.|+++  +|||
T Consensus       148 -~~~V~I~rihLEEDagK~i~~~-~~~~~ydlNRaGvPLiEIVTePDi~s~eeA~~~~~~l~~ilr~~g~~~~~--~Gsl  223 (631)
T PRK04028        148 -GGKVGIETICLEEDAARKIEEK-GDYVVYSLDRLGIPLIEISTEPDIHSPEQAKEVALRIGMILRSTGKVKRG--LGTI  223 (631)
T ss_pred             -CCEEEEEEEEECCCCCCCCCCC-CCCEEEECCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC--CCCE
T ss_conf             -8434037998512457643468-98337744557985388843788899999999999999999986412456--7754


Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH----------------------------------
Q ss_conf             1257543213766678862223540246599999999999999731----------------------------------
Q gi|254780979|r  217 RADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILE----------------------------------  262 (500)
Q Consensus       217 R~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~----------------------------------  262 (500)
                      |||||||||     +||||||||||||++|++||+||+.||+++|+                                  
T Consensus       224 R~DvNVSvr-----~GtRvEIKNlnS~~~i~~AieyEi~RQ~~ll~~~~ei~~~g~~~~~~~~~~~d~t~~~~~t~s~ii  298 (631)
T PRK04028        224 RQDVNVSIA-----GGARVEIKGVQDLDLIPKVVEYEVQRQLNLLKIRDELRRRGASREEVVDEIVDVTELFKNTKSKVI  298 (631)
T ss_pred             EEEEEEEEC-----CCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCHHH
T ss_conf             566676414-----785256407754889999999999999999875777753144311134320013555313530788


Q ss_pred             -----CCCC-----------------------------------------------------------------------
Q ss_conf             -----3980-----------------------------------------------------------------------
Q gi|254780979|r  263 -----DGGH-----------------------------------------------------------------------  266 (500)
Q Consensus       263 -----~G~~-----------------------------------------------------------------------  266 (500)
                           .||.                                                                       
T Consensus       299 ~~~l~~gg~v~a~~~~~~~g~lg~e~q~~rR~g~E~~d~~k~~g~~Gi~HsDElp~Ygi~~~e~~~~~~~l~~~~~Da~~  378 (631)
T PRK04028        299 KRALKKGGKVLAVKLPGFKGLLGREIQPGRRLGTELADYAKWAGVGGIFHSDELPGYGITEEEVEALRDALGAGENDAVI  378 (631)
T ss_pred             HHHHHCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCEE
T ss_conf             76550487378775156344336566754200056766765415565334543434465266778888752467554135


Q ss_pred             --------------------------CCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCC
Q ss_conf             --------------------------034432337554336653035667777833277877312699999998853024
Q gi|254780979|r  267 --------------------------IRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPE  320 (500)
Q Consensus       267 --------------------------v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPe  320 (500)
                                                |.||||+|+++ |.|.+||+||+++  ||||||||||+.|+++||++++++|||
T Consensus       379 l~~~~~~~~~~~~~~v~~R~~~~~~~vp~EtR~~~~d-g~T~~mR~k~ga~--RyfPEPDLPPi~Is~e~Ie~Ik~~LPE  455 (631)
T PRK04028        379 LVADEEEKAKKALEAVIERAKEALEGVPEETRKALPD-GTTRYLRPLPGAA--RMYPETDIPPIRITEELLEKIKKNLPE  455 (631)
T ss_pred             EECCCHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCCC-CCEEECCCCCCCC--CCCCCCCCCCEECCHHHHHHHHHHCCC
T ss_conf             5327377788899999999987540685554156778-9874235567532--207798877464699999999971899


Q ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf             836898864320268899988876411367898864-0243024577776545788764338740006489899999998
Q gi|254780979|r  321 LPDAKRERFIGEFGISLYDASVLVSDKSIADYFEKL-AVNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELID  399 (500)
Q Consensus       321 lP~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v-~~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~  399 (500)
                      ||+++++||+++||||++||.+|++++.+ +|||++ ..+.+|+.+|||+++.+ +.||+.+.++.  .++|++|++|+.
T Consensus       456 LP~~kr~Rl~~eygLs~~dA~~L~~~~~l-~~FE~~v~~~~~pk~~An~l~~~l-~~L~~~~~~i~--~I~pe~La~Li~  531 (631)
T PRK04028        456 LPEEKLERLVKEYGLSEELAEQLANSERL-DLFEELVKKGVKPTLIARTLVNTL-KELKREGVDIE--NITDEHIEEVFD  531 (631)
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHCCCHH-HHHHHHHHCCCCHHHHHHHHHHHH-HHHHHCCCCCC--CCCHHHHHHHHH
T ss_conf             99999999999709899999999747389-999999971699999999999999-99997689813--399999999999


Q ss_pred             HHHCCCCCHHHHHHHHHHHHHC-CCCHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             8863873147899999999817-999889999639876189889999999999839998997527213226589999997
Q gi|254780979|r  400 LIIDGTISGKIAKDIFNILWEK-GGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIATKPNLVSWFVGQVMKN  478 (500)
Q Consensus       400 li~~g~Is~~~aK~il~~l~~~-~~~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~kgk~ka~gfLvGqVMK~  478 (500)
                      |+++|+||.++||+||+.|+.+ +.+|++||++.||.|+||+ +|+++|++||++||++|++  ||++++|||||||||+
T Consensus       532 Li~~G~IS~~~aK~V~~~m~~~~g~~p~~Iiee~gL~qisd~-eLe~iV~eVI~eN~~~Vk~--gK~kaigfLvGQVMK~  608 (631)
T PRK04028        532 LVSEGKIAKEAIEEILKALAENPGKSVEEAAEELGLTRLSEE-EVEKIIEEIVEENIDFVKE--KGMGAFGPLMGEVMAE  608 (631)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHH-HHHHHHHHHHHHCHHHHHH--CCCCCCHHHHHHHHHH
T ss_conf             998698538999999999985799899999997699768999-9999999999978999985--4423201099999998


Q ss_pred             HCCCCCHHHHHHHHHHHHCC
Q ss_conf             28977889999999997078
Q gi|254780979|r  479 TGGKANPSIVQKMLKEKLGI  498 (500)
Q Consensus       479 tkGkAdpk~v~~lL~e~L~~  498 (500)
                      |||||||+.|+++|+++|..
T Consensus       609 tkGKAnPk~VnelLkekLke  628 (631)
T PRK04028        609 LRGKADGKIVSEILREKLKE  628 (631)
T ss_pred             HCCCCCHHHHHHHHHHHHHH
T ss_conf             57997999999999999999


No 4  
>KOG2438 consensus
Probab=100.00  E-value=0  Score=1148.93  Aligned_cols=480  Identities=43%  Similarity=0.742  Sum_probs=462.0

Q ss_pred             CCCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEE
Q ss_conf             24547803389899978886898655588424689876520613026898887378999999999877829762442013
Q gi|254780979|r   16 SGTTGDWEVVIGIEVHAQLSVVSKLFSGASVNFGAEPNTQVSFFDAAMPGMLPILNGRCVQQAVMTGLGLNAHINKYSVF   95 (500)
Q Consensus        16 ~~~~~~~e~vIGLEiH~qL~t~tKlFc~c~~~~~~~pNt~v~~~~~g~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~f   95 (500)
                      ..-..+|.+|||||||+||+|.+||||+|.++|++.|||+||+||+++||||||||++||++|++.||||||+++..|.|
T Consensus        17 ~~~~r~waaviGlEiH~Ql~t~~KlFs~s~~~~~a~pNt~v~yfd~slPGtlPVLN~~~vefavk~~LALnc~vn~~s~F   96 (505)
T KOG2438          17 GMPFRKWAAVIGLEIHAQLATVSKLFSGSKVNFGAPPNTSVSYFDASLPGTLPVLNREAVEFAVKLSLALNCEVNNVSKF   96 (505)
T ss_pred             CCCHHHHHHHHCCEEHHHHHHHHHHHCCCCCCCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHC
T ss_conf             87256566631111014576656551566787788997620255235887644357999999988776434611033320


Q ss_pred             ECCCEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCE
Q ss_conf             11321237678882014454420153389997067777741037984236665202310011567871488661578612
Q gi|254780979|r   96 ARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRTIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVAL  175 (500)
Q Consensus        96 dRK~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPL  175 (500)
                      |||||||||||+||||||++.||+.||.+.+..+.+.   ...++|+|.|||||||||||+|+....+|||||||||+||
T Consensus        97 DRKhYFY~DlP~GYQitQ~~~pia~~G~~~l~~~~~~---v~~k~~~i~qiqlEqDtgKst~~d~~~~sLvDlNRAGvpL  173 (505)
T KOG2438          97 DRKHYFYPDLPAGYQITQQRIPIARNGFIPLSAGLDN---VPDKTIGILQIQLEQDTGKSTHDDAPSRSLVDLNRAGVPL  173 (505)
T ss_pred             CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCC---CCCCEECEEEEEEECCCCCCCCCCCCCCEEEECCCCCCCE
T ss_conf             2100446788887344432223035885335656678---8763102389986123564531258873366213369852


Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             57630365277899999999999998642045676432201125754321376667886222354024659999999999
Q gi|254780979|r  176 MEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEAR  255 (500)
Q Consensus       176 iEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~  255 (500)
                      +||||+|||++.+||.+|+.+||.|+|++|+|+|+||+|+|||||||||+++|++||||||||||||+|+|.+||+|||.
T Consensus       174 lEiVt~Pdf~~~~eaa~fv~elqlIlr~lgis~g~meeG~lRvDvNiSI~~~g~~lG~RvElKNLnsirsI~~AI~yEi~  253 (505)
T KOG2438         174 LEIVTKPDFSDGIEAAAFVKELQLILRHLGISSGNMEEGALRVDVNISIAPDGSELGTRVELKNLNSIRSISNAIDYEIQ  253 (505)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHCCCEEEEEEEEECCCCCCCEEEEEECCCHHHHHHHHHHHHHHH
T ss_conf             78762766212899999999999999996436442203845775446766777623234553155138899998879999


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             99997313980034432337554336653035667777833277877312699999998853024836898864320268
Q gi|254780979|r  256 RQIAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI  335 (500)
Q Consensus       256 RQ~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL  335 (500)
                      ||+++++.|+.|..|||+||...|.|++||.||+.+||||||||||||+.++.+||+.++.+||+||++.+++|.++||+
T Consensus       254 RQvel~~nGg~i~nETR~wd~~~~rTvsmRdKEt~~DYRfmPEPnLPpl~L~~~~v~~Vre~LPeLP~~~~~~L~e~~gl  333 (505)
T KOG2438         254 RQVELLNNGGAIQNETRGWDSEGGRTVSMRDKETLQDYRFMPEPNLPPLILHGKYVDSVREELPELPDATREKLVEQYGL  333 (505)
T ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCCCEECCCCCCCCCEEECHHHHHHHHHHCCCCCHHHHHHHHHHHCC
T ss_conf             99999965882555244543567725861354431011016899998766448899999975523768899999886266


Q ss_pred             CHHHHHHHHHHHHHHHHH-HHH-H----CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHH
Q ss_conf             899988876411367898-864-0----2430245777765457887643387400064898999999988863873147
Q gi|254780979|r  336 SLYDASVLVSDKSIADYF-EKL-A----VNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGK  409 (500)
Q Consensus       336 s~~dA~~L~~~~~la~~F-E~v-~----~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~  409 (500)
                      +.++|.+|+++.++.+|| +.+ .    ....||.+++||+++++++++.......++.++|.+||+|+.++++++||..
T Consensus       334 ~~k~a~~L~~~~~~~~~~~d~v~i~k~~ae~~~k~~~~Wi~~~~~g~lrq~~ls~~~~~~~p~~la~ll~ll~~~~Is~~  413 (505)
T KOG2438         334 SAKDAVTLANEVELLEFYKDSVRIIKYKAETTPKLITYWIKEEFLGYLRQIALSPNQSIVTPRQLADLLKLLSEETISAL  413 (505)
T ss_pred             CHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             54553455435568888765466653025455321178999999888751467865343686999999998534012577


Q ss_pred             HHHHHHHHHHHCCC--CHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHH-CCCCCHHHHHHHHHHHHCCCCCHH
Q ss_conf             89999999981799--988999963987618988999999999983999899752-721322658999999728977889
Q gi|254780979|r  410 IAKDIFNILWEKGG--TPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIA-TKPNLVSWFVGQVMKNTGGKANPS  486 (500)
Q Consensus       410 ~aK~il~~l~~~~~--~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~k-gk~ka~gfLvGqVMK~tkGkAdpk  486 (500)
                      +||++|.+++++++  ++..+|+++.|++|.|.+||+++|.+||++|||.|++++ ||.|+++||+|+|||.|+|+|||+
T Consensus       414 ~ak~ll~~l~~~~~~~~~s~LIeek~l~~I~dp~eIe~lv~~vm~~h~k~ve~~rsGk~k~~~~l~G~vmk~s~g~a~p~  493 (505)
T KOG2438         414 SAKQLLRHLLKNPGVMTVSILIEEKRLWQIRDPAEIEELVRSVMEKHPKQVEQLRSGKTKSIKRLIGLVMKSSQGRANPK  493 (505)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             89999999984878688899976643541179999999999999877899999875568899999999999751679989


Q ss_pred             HHHHHHHHHHCC
Q ss_conf             999999997078
Q gi|254780979|r  487 IVQKMLKEKLGI  498 (500)
Q Consensus       487 ~v~~lL~e~L~~  498 (500)
                      .+.+.|+++|+.
T Consensus       494 ~le~~l~~~L~~  505 (505)
T KOG2438         494 DLEKILEELLNR  505 (505)
T ss_pred             HHHHHHHHHHCC
T ss_conf             999999987369


No 5  
>pfam02934 GatB_N GatB/GatE catalytic domain. This domain is found in the GatB and GatE proteins.
Probab=100.00  E-value=0  Score=961.25  Aligned_cols=286  Identities=57%  Similarity=0.924  Sum_probs=278.2

Q ss_pred             CEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEEECCCEEC
Q ss_conf             33898999788868986555884246898765206130268988873789999999998778297624420131132123
Q gi|254780979|r   23 EVVIGIEVHAQLSVVSKLFSGASVNFGAEPNTQVSFFDAAMPGMLPILNGRCVQQAVMTGLGLNAHINKYSVFARKNYFY  102 (500)
Q Consensus        23 e~vIGLEiH~qL~t~tKlFc~c~~~~~~~pNt~v~~~~~g~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~fdRK~YfY  102 (500)
                      |+|||||||+||+|+|||||+|+++|+++|||+|||+|+|+||+||++|++||++|+++|+||||+|++.++||||||||
T Consensus         1 e~vIGLEiH~qL~T~tKlFc~c~~~~~~~PNt~v~p~~lg~PG~LPvlN~~av~~Ai~~~laL~c~I~~~s~fdRK~YfY   80 (287)
T pfam02934         1 ELVIGLEIHVQLNTKTKLFCGCPTEFGAEPNTNVCPVCLGLPGALPVLNKEAVELAIKAGLALNCEINDESRFDRKNYFY   80 (287)
T ss_pred             CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEECCEEEEC
T ss_conf             98899999988179977668999867899756578043069878764699999999999998298636221761202676


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECC
Q ss_conf             76788820144544201533899970677777410379842366652023100115678714886615786125763036
Q gi|254780979|r  103 PDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRTIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKP  182 (500)
Q Consensus       103 pDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~P  182 (500)
                      |||||||||||++.|||.||++++..++      ..++|+|+||||||||||++|+..+++|+|||||||+|||||||+|
T Consensus        81 pDlPkgYQITQ~~~Pi~~~G~l~i~~~~------~~k~i~I~rihlEEDagK~~h~~~~~~slvD~NRaGvPLiEIVTeP  154 (287)
T pfam02934        81 PDLPKGYQITQYDLPIATNGYLEIEVDG------EEKRIGIERIHLEEDAGKLIHEGGGDYSLVDLNRAGVPLIEIVTEP  154 (287)
T ss_pred             CCCCCCCCEECCCCCEECCCEEEEECCC------CCEEEEEEEEEECCCCCCCCCCCCCCEEEEECCCCCCCEEEEEECC
T ss_conf             9888564300564677301389860289------6205714798870023424546899736884045798248998358


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5277899999999999998642045676432201125754321376-667886222354024659999999999999973
Q gi|254780979|r  183 DMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPG-EAWGTRCEVKNVNSIRFLGLAIEYEARRQIAIL  261 (500)
Q Consensus       183 d~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~-~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll  261 (500)
                      ||+||+||++|+++|++||||+|+|||+||+|+||||||||||+.| ..||+||||||||||++|++||+||+.||+++|
T Consensus       155 d~~s~eeA~~~~~~L~~il~~lgisd~~me~GslR~DvNVSv~~~g~~~~g~rvEIKNlNS~~~v~~Ai~~Ei~RQ~~~l  234 (287)
T pfam02934       155 DIRSPEEARAYLKKLRQILRYLGVSDGNMEEGSLRCDANVSVRPKGSEEFGTRVEIKNLNSFRFVEKAIEYEIERQIELL  234 (287)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             88999999999999999999747555674556345420377535788765315886347679999999999999999999


Q ss_pred             HCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             13980034432337554336653035667777833277877312699999998
Q gi|254780979|r  262 EDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAI  314 (500)
Q Consensus       262 ~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i  314 (500)
                      ++|+.|.||||+||+.+++|++||+||+|+||||||||||||+.|+++||++|
T Consensus       235 ~~G~~v~qETR~~d~~~~~T~~mR~Ke~a~DYRyfPePDLppi~i~~~~i~~i  287 (287)
T pfam02934       235 EEGGKVPQETRLWDEDKGETVSMRSKEGAADYRYFPEPDLPPIVISDEWIEEI  287 (287)
T ss_pred             HCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCEECCHHHHHHC
T ss_conf             85998432116797898958106268863365757899978767699999349


No 6  
>TIGR00133 gatB glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit; InterPro: IPR004413 In many species, Gln-tRNA ligase is missing. tRNA(Gln) is misacylated with Glu after which a heterotrimeric amidotransferase converts Glu to Gln. This group represents the chain of the heterotrimer, encoded by the gatB gene called glutamyl-tRNA(Gln) amidotransferase, B subunit 6.3.5 from EC. This enzyme functions as an alternative to a direct Gln-tRNA synthetase (Gln-tRNA ligase) in mitochondria, chloroplasts, Gram-positive bacteria, cyanobacteria, and the archaea.   The archaea have an Asp-tRNA(Asn) amidotransferase instead of an Asp-tRNA ligase. In the archaea a paralog of gatB is found, here designated gatB_rel, that is a candidate B subunit of the Asp-tRNA(Asn) amidotransferase. The gatA-encoded subunit may be shared by gatB and gatB_rel. ; GO: 0016884 carbon-nitrogen ligase activity with glutamine as amido-N-donor, 0006412 translation.
Probab=100.00  E-value=0  Score=823.72  Aligned_cols=477  Identities=48%  Similarity=0.806  Sum_probs=454.8

Q ss_pred             CCCCEEEEEEEEEEECCCCCCCCCCCCCCCC-CC--CCCCCHHHCCCCCCCCC-CCHHHHHHHHHHHHHHCCE-EC-CCC
Q ss_conf             7803389899978886898655588424689-87--65206130268988873-7899999999987782976-24-420
Q gi|254780979|r   20 GDWEVVIGIEVHAQLSVVSKLFSGASVNFGA-EP--NTQVSFFDAAMPGMLPI-LNGRCVQQAVMTGLGLNAH-IN-KYS   93 (500)
Q Consensus        20 ~~~e~vIGLEiH~qL~t~tKlFc~c~~~~~~-~p--Nt~v~~~~~g~PG~lP~-lN~~av~~ai~~~~al~~~-i~-~~~   93 (500)
                      -+|+.+||||+|+||+|++|+||+|+++|+. .|  |+++||+|+|+||++|+ +|.+++..|++++.|++|+ +. +.+
T Consensus         2 ~~~~~~~gle~h~~l~~~~k~f~~~~~~~~~~~p~pn~~~~p~~lg~pg~~p~p~n~~~~~~~~~~~~~~~~~~~~~~~~   81 (523)
T TIGR00133         2 IEYEAVIGLEVHVQLNTKTKLFCSCPNDFGSAPPAPNTNVCPVCLGLPGALPVPLNKEAVKKALKLGLALNAKIVSPPVS   81 (523)
T ss_pred             CCCCEEEEEEEEEEECCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf             75200211235555323201100475333456778765445000157876566644889999998877631200254112


Q ss_pred             EEECCCEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEEECCCCCCCCCC--CCCEEEEECCC
Q ss_conf             1311321237678882014454420153389997067777741037984236665202310011567--87148866157
Q gi|254780979|r   94 VFARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRTIEVGIERIHLEQDAGKSIHDQY--SAVSCIDLNRS  171 (500)
Q Consensus        94 ~fdRK~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~~~v~I~~i~lEED~gk~~h~~~--~~~slvD~NRa  171 (500)
                      .||||||||||+|+|||+||++.|++.+|++.+....+..... .+.|+|.++|+|||+||+.|...  +.++++||||+
T Consensus        82 ~f~~k~y~y~d~p~g~~~~~~~~p~~~~g~~~~~~~~~~~~~~-~~~~~~~~~~~e~d~g~~~~~~~~~~~~~~~d~n~~  160 (523)
T TIGR00133        82 VFDRKHYFYPDLPKGYQITQFDRPIAEGGKLEIELDGGETDES-AKRIGIERLHLEEDPGKLQHKGSDKPSQSLVDFNRS  160 (523)
T ss_pred             HHHHHHCCCCCCCCCCEECCCCCCEECCCEEEEEECCCHHHHH-HHHHHHEEEEECCCCCHHHHCCCCCCCEEEEECCCC
T ss_conf             2211003466676543000024540016526884065302344-444311002101132101102355432034422445


Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             861257630365277899999999999998642045676432201125754321376-6678862223540246599999
Q gi|254780979|r  172 GVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPG-EAWGTRCEVKNVNSIRFLGLAI  250 (500)
Q Consensus       172 GvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~-~~~GtRvEIKNlnS~~~i~~AI  250 (500)
                      |+||+||||+||++++++|++|+++++.+++|+|+++|+|++|++|||+|||++..| ..+|+|+||||+|||+++.+|+
T Consensus       161 g~pl~e~~~~p~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~g~~~~d~n~~~~~~g~~~~~~~~e~kn~~~~~~~~~~~  240 (523)
T TIGR00133       161 GAPLLEIVTKPDLNSPKEARAFLKKLRQLLRYLGISDGNLEEGSLRCDVNVSIRPKGQEEGGTRVEIKNLNSFKGVEKAI  240 (523)
T ss_pred             CCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEECEEEEEECCCCCCCCEEEEECCCCHHHHHHHH
T ss_conf             76332110144557778999999999999987311235534464121000235541432244314541253046788888


Q ss_pred             HHHHHHHHHHHHCC---CCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHH-HHHHCCCCHHHHH
Q ss_conf             99999999973139---8003443233755433665303566777783327787731269999999-8853024836898
Q gi|254780979|r  251 EYEARRQIAILEDG---GHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRA-IKKQIPELPDAKR  326 (500)
Q Consensus       251 ~yEi~RQ~~ll~~G---~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~-i~~~lPelP~~~~  326 (500)
                      +||+.||.+++..|   ..+.++||+|++..+.|++||.||++.||||||||||||+.+++.++.. +...+|++|..++
T Consensus       241 ~~e~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~dy~y~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~  320 (523)
T TIGR00133       241 EYEIERQKKLLIRGKYDEEVLQETRLFDESSGITVSLRSKETSSDYRYFPEPDLPPINIDEELVKGPVAGKLPELPSAKR  320 (523)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHCCHHHHH
T ss_conf             88888889998602100123443321001244123320222200000025776430002466753234442002336888


Q ss_pred             HHHHHHCCCCHHHHHHHHHHHH------------HHHHHHHHHC-CCCH---HHHHHHHHHHHHHHHHHCCCCCCCC--C
Q ss_conf             8643202688999888764113------------6789886402-4302---4577776545788764338740006--4
Q gi|254780979|r  327 ERFIGEFGISLYDASVLVSDKS------------IADYFEKLAV-NRDK---KIVANWVINDLLGVLNRSGKSIEDT--P  388 (500)
Q Consensus       327 ~rl~~~yGLs~~dA~~L~~~~~------------la~~FE~v~~-~~~p---k~~Anwi~~el~~~ln~~~~~~~~~--~  388 (500)
                      .|+..+||++++++.+|+.+..            +++||+++.. ..+|   +.+++|++.++.+.++..+..+..+  .
T Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~W~~~~~~~~l~~~~~~~~~~~~~  400 (523)
T TIGR00133       321 IRLKKEYGLSEEDAKLLTSDLDQNDLYNHEALRYLADYFEEVVKLGGPPSNAKLAANWLCDELLGELNKLKISLAECWEG  400 (523)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             87766406763342332103310100246899999999999986125400246788999999998864215634565420


Q ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHC--------CCCHHHHHHH--CCCEECCCHHHHHHHHHHHHHHCHHHH
Q ss_conf             898999999988863873147899999999817--------9998899996--398761898899999999998399989
Q gi|254780979|r  389 ISPNQLGELIDLIIDGTISGKIAKDIFNILWEK--------GGTPKEIVEE--LGLRQVTDLSAIEKVVDEVINSNPNNV  458 (500)
Q Consensus       389 i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~--------~~~p~~iie~--~gL~~isD~~eL~~iv~eVI~~np~~V  458 (500)
                      +.|.++++++.++..|+|+.+.+|+++..++..        +++|..++++  .|+.++.|..++..+|.+++.+||+.+
T Consensus       401 ~~p~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~d~~~~~~~~~~~~~~~l~~~~d~~~~~~~~~~~~~~~~~~~  480 (523)
T TIGR00133       401 LKPSDLAELLKLIKEGKISGKSAKELLDELLENFGQNCQDLGGDPDKLIEEFELGLEQISDPDELVKIIEEVIKENPKEV  480 (523)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCHHHH
T ss_conf             26478999999875432114678899998875202212331455889999975001015777899999999973173457


Q ss_pred             HHHH---C-CCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHC
Q ss_conf             9752---7-2132265899999972897788999999999707
Q gi|254780979|r  459 ARIA---T-KPNLVSWFVGQVMKNTGGKANPSIVQKMLKEKLG  497 (500)
Q Consensus       459 ~~~k---g-k~ka~gfLvGqVMK~tkGkAdpk~v~~lL~e~L~  497 (500)
                      .+|.   + +..+++|++||+|+.++|+|+|..+.+++++.|+
T Consensus       481 ~~~~~~~~g~~~~~~~~~g~~~~~~~g~~~p~~~~~~~~~~l~  523 (523)
T TIGR00133       481 EDYLLVTSGKERALKFLVGQVMKKTRGRANPKLVNELLKELLS  523 (523)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCC
T ss_conf             7776542015678888887777651354457899999987419


No 7  
>COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=712.19  Aligned_cols=444  Identities=33%  Similarity=0.532  Sum_probs=397.2

Q ss_pred             CCC---EEEEEEEEEEECCCCCCCCCCCCCCCC-C-------------------------------------CCCCCCHH
Q ss_conf             803---389899978886898655588424689-8-------------------------------------76520613
Q gi|254780979|r   21 DWE---VVIGIEVHAQLSVVSKLFSGASVNFGA-E-------------------------------------PNTQVSFF   59 (500)
Q Consensus        21 ~~e---~vIGLEiH~qL~t~tKlFc~c~~~~~~-~-------------------------------------pNt~v~~~   59 (500)
                      ||+   +.+|||||+||+|++||||+||+...+ +                                     ++.++|.|
T Consensus         5 dy~~lgLKvGLEIHqQLdT~~KLFC~Cpt~~~~~E~~~~f~R~Lrpt~SElGevD~AA~~E~~r~R~f~Y~~~~d~tCLV   84 (631)
T COG2511           5 DYEELGLKVGLEIHQQLDTKRKLFCRCPTELRDGEPDFEFERYLRPTRSELGEVDPAALEESKRGRKFIYEAYYDTTCLV   84 (631)
T ss_pred             CHHHHCCEECEEEHHHHCCCCCEECCCCCCCCCCCCCCEEEEEECCCHHHHCCCCHHHHHHHHHCCEEEEEECCCCCEEE
T ss_conf             76774640000201001677643336986445687674167763453666355478889998756668998137863565


Q ss_pred             HCC-CCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEEECCCEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEE
Q ss_conf             026-8988873789999999998778297624420131132123767888201445442015338999706777774103
Q gi|254780979|r   60 DAA-MPGMLPILNGRCVQQAVMTGLGLNAHINKYSVFARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRT  138 (500)
Q Consensus        60 ~~g-~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~fdRK~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~  138 (500)
                      -+- .|-  .-+|++|+..|+.+|++|||+|.++++.|||.+.+++|+.|||+|..   |+.||+++++.|         
T Consensus        85 E~DEEPP--h~~neeAl~iAl~Va~lln~~iVDei~vMRKiVIDGSNTsGFQRTai---va~~G~iets~g---------  150 (631)
T COG2511          85 EADEEPP--HEPNEEALAIALAVAKLLNMDIVDEIHVMRKIVIDGSNTSGFQRTAI---VAIGGYIETSEG---------  150 (631)
T ss_pred             ECCCCCC--CCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCCCCCEEEEE---EEECCEEECCCC---------
T ss_conf             5478999--99898999999999998389740104677788861687755112578---851765535888---------


Q ss_pred             EEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEC
Q ss_conf             79842366652023100115678714886615786125763036527789999999999999864204567643220112
Q gi|254780979|r  139 IEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRA  218 (500)
Q Consensus       139 ~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~  218 (500)
                       +|+|..+|||||||+.+.+.++.. .+.++|+|+|||||.|+||++||++|++.++.|+.+||.+|.+..++  |++||
T Consensus       151 -~V~I~tlclEEDAARKIee~~~~V-vYsLDRLGIPLiEIsT~PdI~sp~~A~evA~~IG~~lrsTGkvKrgl--gTIRQ  226 (631)
T COG2511         151 -PVGIETLCLEEDAARKIEEKGDTV-VYSLDRLGIPLIEISTEPDIRSPEQAREVAERIGYILRSTGKVKRGL--GTIRQ  226 (631)
T ss_pred             -CCCCEEEEECHHHHHHHHCCCCEE-EEEECCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC--CCEEE
T ss_conf             -756413662377766654058738-99721368744884268888997999999999879999835512367--64000


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH------------------------------------
Q ss_conf             57543213766678862223540246599999999999999731------------------------------------
Q gi|254780979|r  219 DVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILE------------------------------------  262 (500)
Q Consensus       219 DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~------------------------------------  262 (500)
                      ||||||     .+|+|||||+++++..|++.|+||+.||.+||+                                    
T Consensus       227 DvNvSI-----~~GarvEIKGVq~LdlI~~vv~yEv~RQ~nLlkirdeL~~RG~~~~~~~~~DVTdlF~~TkSkiI~~~l  301 (631)
T COG2511         227 DVNVSI-----KGGARVEIKGVQDLDLIPDVVEYEVERQLNLLKIRDELKERGGADVSEEVFDVTDLFANTKSKIIRSGL  301 (631)
T ss_pred             EEEEEE-----CCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHCCCCHHHHHHHH
T ss_conf             002553-----387168862740566678999999999988999999999735530014445289886557318888754


Q ss_pred             -CCC----------------------------------------------------------------------------
Q ss_conf             -398----------------------------------------------------------------------------
Q gi|254780979|r  263 -DGG----------------------------------------------------------------------------  265 (500)
Q Consensus       263 -~G~----------------------------------------------------------------------------  265 (500)
                       +||                                                                            
T Consensus       302 ~~gG~V~A~~l~~f~GlvG~EiqpGrRlGtE~AD~ar~~GvgGlfHsDELP~YGITeeEV~~v~~~lga~~~Davvlva~  381 (631)
T COG2511         302 KKGGKVYAVLLPGFAGLVGREIQPGRRLGTEFADYARAYGVGGLFHSDELPGYGITEEEVEAVRDALGAGEEDAVVLVAG  381 (631)
T ss_pred             CCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEC
T ss_conf             24876999974775652230025774103578999998277751005667567879999999999847997774899707


Q ss_pred             ---------------------CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHH
Q ss_conf             ---------------------00344323375543366530356677778332778773126999999988530248368
Q gi|254780979|r  266 ---------------------HIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDA  324 (500)
Q Consensus       266 ---------------------~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~  324 (500)
                                           -|..|||+-.++ |+|.+||+.++++  ||||||||||+.|++++++.++..+||+|++
T Consensus       382 ~~~~~~~a~~~V~~Ra~~ai~gvpeETR~a~~D-GtT~yLRPlPGaa--RMYPETDIPpi~i~~~~l~~~~~~~Pe~~~e  458 (631)
T COG2511         382 EEERAKRALEAVIERAKEAIEGVPEETRGALPD-GTTVYLRPLPGAA--RMYPETDIPPIRIDEELLEKIKENLPELPEE  458 (631)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCHHHCCCCCC-CCCEEECCCCCCC--CCCCCCCCCCEECCHHHHHHHHHHCCCCHHH
T ss_conf             788999999999999999871797766357889-8703515799854--5687678997205889987766437878799


Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHC
Q ss_conf             9886432026889998887641136789886402-430245777765457887643387400064898999999988863
Q gi|254780979|r  325 KRERFIGEFGISLYDASVLVSDKSIADYFEKLAV-NRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIID  403 (500)
Q Consensus       325 ~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~~-~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~  403 (500)
                      +.+||+.+||||.+.|++++++..+ +.||++.. +.+|+.+|..+++.+. .|.+.+..++  +++-+|+.+++.++.+
T Consensus       459 k~~r~~~eygLs~~LA~~~~~~~~~-~~FEel~e~~v~p~~~A~~L~~~~~-~L~reg~~i~--~l~~~~i~~~~~~~~~  534 (631)
T COG2511         459 KVERYVKEYGLSKELAEQLASDPRV-DLFEELVEKGVDPTLIASTLVNTLP-ELRREGVEID--NLDDEHIEELLRLVSE  534 (631)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHCHHH-HHHHHHHHCCCCHHHHHHHHHHHHH-HHHHCCCCCC--CCCHHHHHHHHHHHHC
T ss_conf             9999999849779999999742048-9999999747877899999998779-9985687466--6667999999999862


Q ss_pred             CCCCHHHHHHHHHHHHHC-CCCHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHHHHCCC
Q ss_conf             873147899999999817-9998899996398761898899999999998399989975272132265899999972897
Q gi|254780979|r  404 GTISGKIAKDIFNILWEK-GGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIATKPNLVSWFVGQVMKNTGGK  482 (500)
Q Consensus       404 g~Is~~~aK~il~~l~~~-~~~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~kgk~ka~gfLvGqVMK~tkGk  482 (500)
                      |+|+..++.++|..|..+ +.++.+++++.||...+ .+|++.+|++++..|-+.+.+.+  ++++|++||+||++++|+
T Consensus       535 g~iake~iee~l~~l~~~p~~~~~~~~~~~gL~~ls-~eEve~iI~eii~~~~d~i~~rg--~~a~g~lmg~~M~~~rg~  611 (631)
T COG2511         535 GKIAKEAIEEILKALAENPGKDAAEIAEKLGLKELS-EEEVEKIIDEIIESNLDVIKERG--MGAMGLLMGRVMAKLRGR  611 (631)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHHHHHHC--HHHHHHHHHHHHHHHHCC
T ss_conf             520099999999999848898999999872633279-99999999999974378998712--226899999999986065


Q ss_pred             CCHHHHHHHHHHHHC
Q ss_conf             788999999999707
Q gi|254780979|r  483 ANPSIVQKMLKEKLG  497 (500)
Q Consensus       483 Adpk~v~~lL~e~L~  497 (500)
                      |||++|+++|+++|.
T Consensus       612 aDgk~v~e~l~~~i~  626 (631)
T COG2511         612 ADGKLVSEILREKLQ  626 (631)
T ss_pred             CCCHHHHHHHHHHHH
T ss_conf             780899999999999


No 8  
>TIGR00134 gatE_arch glutamyl-tRNA(Gln) amidotransferase, subunit E; InterPro: IPR004414   The aspartyl-tRNA(Asn) amidotransferase, B subunit or designated here gatB_rel, is found only in the archaea. It is paralogous to the gatB-encoded subunit of Glu-tRNA(Gln) amidotransferase. The GatABC system operates in many bacteria to convert Glu-tRNA(Gln) into Gln-tRNA(Gln). However, the homologous system in archaea instead converts Asp-tRNA(Asn) to Asn-tRNA(Asn). Glu-tRNA(Gln) is converted to Gln-tRNA(Gln) by a heterodimeric amidotransferase of GatE (this protein) and GatD. The Archaea have an Asp-tRNA(Asn) amidotransferase instead of an Asp--tRNA ligase, but the genes have not been identified. It is likely that this protein replaces gatB in Asp-tRNA(Asn) amidotransferase but that both enzymes share gatA . ; GO: 0016884 carbon-nitrogen ligase activity with glutamine as amido-N-donor, 0006412 translation.
Probab=100.00  E-value=0  Score=422.98  Aligned_cols=446  Identities=28%  Similarity=0.418  Sum_probs=384.2

Q ss_pred             CCCEE---EEEEEEEEECCCCCCCCCCCCCC-CCCC-CC-------------------------------------CCCH
Q ss_conf             80338---98999788868986555884246-8987-65-------------------------------------2061
Q gi|254780979|r   21 DWEVV---IGIEVHAQLSVVSKLFSGASVNF-GAEP-NT-------------------------------------QVSF   58 (500)
Q Consensus        21 ~~e~v---IGLEiH~qL~t~tKlFc~c~~~~-~~~p-Nt-------------------------------------~v~~   58 (500)
                      +|+.+   +|+|||.||+|++|+||.|++.. ..+| |.                                     .+|.
T Consensus         3 ~~~~~gl~~g~~~~~~l~~~~~l~c~c~~~~~~~~~~~~~~~~~l~~~~~~~g~~d~~~~~~~~~~~~~~~~~~~~~~cl   82 (631)
T TIGR00134         3 DYEKVGLKVGLEIHQQLDTKHKLFCPCPTLLRDDEPSDGEIVRYLRPSLSELGEFDRAALEEAERGKKFIYEFYNDTTCL   82 (631)
T ss_pred             CHHHHCHHHCHHHHHHHCCCCHHEECCCHHHCCCCCCCCHHHHHHCHHHHHHCHHHHHHHHHHHHHHHHHHHCCCCCEEE
T ss_conf             50221102011344330311000001302212455444300101000034401134678888774212221002542024


Q ss_pred             HHCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEEECCCEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEE
Q ss_conf             30268988873789999999998778297624420131132123767888201445442015338999706777774103
Q gi|254780979|r   59 FDAAMPGMLPILNGRCVQQAVMTGLGLNAHINKYSVFARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRT  138 (500)
Q Consensus        59 ~~~g~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~fdRK~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~  138 (500)
                      +.+...-.. -+|++|+..|+.+++.+|+++.+..+.+||..+.++++.|||.|.+   ++.+|++++..          
T Consensus        83 ~~~d~~pp~-~~~~~~l~~~~~~~~~~~~~~~d~~~~~~~~~~dg~~~~g~~~~~~---~~~~g~~~~~~----------  148 (631)
T TIGR00134        83 VEADEEPPH-PPNPEALLIALEVALLLNMEVVDEAHTMRKIVIDGSNTGGFQRTGL---VAFDGYLETPG----------  148 (631)
T ss_pred             EECCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHEEE---EEECCEEECCC----------
T ss_conf             432556888-7666788899999988512456667665543112666543100021---23065222476----------


Q ss_pred             EEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEC
Q ss_conf             79842366652023100115678714886615786125763036527789999999999999864204567643220112
Q gi|254780979|r  139 IEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRA  218 (500)
Q Consensus       139 ~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~  218 (500)
                      .+++|..+|||||+++.+.+. ++...+.++|.|+||+||.|+|++.+|+.++..+..++.++|.+|....++  |++|+
T Consensus       149 ~~~~~~~lcl~~~~~~~~~~~-~~~~~~~ld~lg~pl~~~~~~p~~~~p~~~~~~~~~~g~~l~~~g~~~~gl--g~~~~  225 (631)
T TIGR00134       149 GKVGIASLCLEEDAARKIEDG-GDGVVYNLDRLGIPLVEIGTDPDIDDPELAKEVAARLGEILRSTGKVKRGL--GTIRQ  225 (631)
T ss_pred             CCEEHHHHHHHHHHHHHHHCC-CCEEEEEECCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH
T ss_conf             520012222203555432025-770466400016530220467776666789999998878876310123200--01222


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC---------------------------------
Q ss_conf             57543213766678862223540246599999999999999731398---------------------------------
Q gi|254780979|r  219 DVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDGG---------------------------------  265 (500)
Q Consensus       219 DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G~---------------------------------  265 (500)
                      |+|+|++.     |.|+|+|+++.+..+.+.+++|+.||.++++...                                 
T Consensus       226 d~~~~~~d-----g~~~~~~g~~~ld~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~  300 (631)
T TIGR00134       226 DLNISIRD-----GARVEVKGVQDLDLLPKIVENEVLRQLNLLKIRDELKERGAEVEEKIFDVTEVFADTKSKIIRNALK  300 (631)
T ss_pred             CCCEEECC-----CCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             02201126-----7513322530234567887778876666778778887415413455543577753235666643332


Q ss_pred             --------------------------------------------------------------------------------
Q ss_conf             --------------------------------------------------------------------------------
Q gi|254780979|r  266 --------------------------------------------------------------------------------  265 (500)
Q Consensus       266 --------------------------------------------------------------------------------  265 (500)
                                                                                                      
T Consensus       301 ~~~g~~~~~~l~g~~g~~g~~~~pg~~lg~~~~d~~~~~~g~~g~~~~d~lp~~g~~~~~~~~l~~~~~~~~~d~~~~~~  380 (631)
T TIGR00134       301 KKNGKVKAVLLRGFGGLVGKEIQPGRRLGTEFADYAKTYAGVGGLFHTDELPAYGITEEEVKGLRDAVGAEEGDAVVLVA  380 (631)
T ss_pred             HCCCCEEEEEECCCCCCCCCCCCCCCHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEC
T ss_conf             01453212211022320133126630101035555555420243111222443467678887777750666676268851


Q ss_pred             ----------------------CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHH
Q ss_conf             ----------------------0034432337554336653035667777833277877312699999998853024836
Q gi|254780979|r  266 ----------------------HIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPD  323 (500)
Q Consensus       266 ----------------------~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~  323 (500)
                                            .+..+||... ..|.|..+|+-+++.  |+|||+|+||+.+.+++++.++.++|++|.
T Consensus       381 ~~~~~~~~~l~~~~~~~~~~~~g~p~~~~~~~-~dg~~~~l~plp~~~--~~~~~~d~p~~~~~~~~~~~~~~~~p~l~~  457 (631)
T TIGR00134       381 GEEVKVERALREVIERAKEALVGVPEETRKAL-EDGNTAYLRPLPGAA--RMYPETDIPPVVIEEELLEGIRANLPELPE  457 (631)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCHHHHHCC-CCCCCHHHCCCCCCH--HHCCCCCCCCEEEHHHHHHHHHHHCCCCHH
T ss_conf             50345778999999876676505852454215-576510102476300--002123666202107787677642010036


Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCC---CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             898864320268899988876411367898864024---30245777765457887643387400064898999999988
Q gi|254780979|r  324 AKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVN---RDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDL  400 (500)
Q Consensus       324 ~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~~~---~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~l  400 (500)
                      ++.+|+..+|+++.+.+..++. ..+.+.|+.++..   .+|..++..+... +..+++.+.+++.  +...++...+.+
T Consensus       458 ~~~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~g~~~~~--l~~~~~~~~~~~  533 (631)
T TIGR00134       458 EKAERFKKEYGLPDDLAWELVD-SPYVDLFEDLCEKFKNVDPTVIATLLEGT-LKELRREGYDIDG--LEDRHLRDALKL  533 (631)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHH-HHHHHHHHHHHHHHHCCCHHHHHHHHHHH-HHHHHHCCCCCCC--CCHHHHHHHHHH
T ss_conf             7888888761473567888875-46788899998874044336778888876-8987531552000--214678999988


Q ss_pred             HHCCCCCHHHHHHHHHHHHHCCCCH-HHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             8638731478999999998179998-899996398761898899999999998399989975272132265899999972
Q gi|254780979|r  401 IIDGTISGKIAKDIFNILWEKGGTP-KEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIATKPNLVSWFVGQVMKNT  479 (500)
Q Consensus       401 i~~g~Is~~~aK~il~~l~~~~~~p-~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~kgk~ka~gfLvGqVMK~t  479 (500)
                      +..|+|+...+.+++..+...+... ....+-.|+...+ .++++.++.+++.++.+.+.+.+  .+++|++||++|+..
T Consensus       534 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~-~~~~~~~~~~~~~~~~~~~~~~g--~~~~~~l~g~~~~~~  610 (631)
T TIGR00134       534 LLEGKIAKEGLEEVLKGLCEEPDKAEDAAGELKGLKLLA-EEEIEGIIEGLIEENLDLIAERG--EGAFGPLMGLAMGKL  610 (631)
T ss_pred             HHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHH
T ss_conf             862011256799999986216613567777643233100-56788999998654555655403--202467888888874


Q ss_pred             CCCCCHHHHHHHHHHHHCC
Q ss_conf             8977889999999997078
Q gi|254780979|r  480 GGKANPSIVQKMLKEKLGI  498 (500)
Q Consensus       480 kGkAdpk~v~~lL~e~L~~  498 (500)
                      +|++|++.++++|+++|..
T Consensus       611 ~g~~dg~~~~~~l~~~~~~  629 (631)
T TIGR00134       611 RGKADGKVVNDILRKKLKE  629 (631)
T ss_pred             HCCCCHHHHHHHHHHHHHH
T ss_conf             0211046889999998762


No 9  
>pfam02637 GatB_Yqey GatB domain. This domain is found in GatB. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB, which transamidates Glu-tRNA to Gln-tRNA.
Probab=100.00  E-value=1.2e-34  Score=275.62  Aligned_cols=146  Identities=50%  Similarity=0.853  Sum_probs=141.2

Q ss_pred             HHHHHHH-CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHH
Q ss_conf             8988640-243024577776545788764338740006489899999998886387314789999999981799988999
Q gi|254780979|r  351 DYFEKLA-VNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIV  429 (500)
Q Consensus       351 ~~FE~v~-~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~ii  429 (500)
                      +|||+++ ...+|+.+|||+++|++++||+.+.++++++++|++|++|+.++++|+||.++||+||+.|+.++++|.+++
T Consensus         1 d~FE~~~~~~~~~k~aanwi~~el~~~l~~~~~~~~~~~i~~~~la~li~lv~~g~Is~~~ak~vl~~~~~~~~~~~~ii   80 (148)
T pfam02637         1 DFFEEAVKAGADPKLAANWLLGELLGYLNKEGLDIDESPLTPEHLAELIKLIDEGTISGKIAKEVLEELLENGKSPEEIV   80 (148)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHH
T ss_conf             97899988079899999999999999997779986637989999999999998699768999999999987699879999


Q ss_pred             HHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHH-CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             963987618988999999999983999899752-7213226589999997289778899999999970
Q gi|254780979|r  430 EELGLRQVTDLSAIEKVVDEVINSNPNNVARIA-TKPNLVSWFVGQVMKNTGGKANPSIVQKMLKEKL  496 (500)
Q Consensus       430 e~~gL~~isD~~eL~~iv~eVI~~np~~V~~~k-gk~ka~gfLvGqVMK~tkGkAdpk~v~~lL~e~L  496 (500)
                      +++||.+++|+++|+.+|++||++||++|++|+ ||++++|||||||||+|||||||+.|+++|+++|
T Consensus        81 ~~~gl~~i~d~~~l~~iv~~vi~~np~~v~~yk~Gk~k~~~~lvGqvMK~tkGkadp~~v~~~l~e~L  148 (148)
T pfam02637        81 EEKGLVQISDEEELEKIVDEVIAENPKAVEDYKSGKEKALGFLVGQVMKKTRGKADPKLVNELLKEKL  148 (148)
T ss_pred             HHCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHC
T ss_conf             88197646888999999999999899999999837677899999999998579989999999999659


No 10 
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=100.00  E-value=4.1e-34  Score=271.72  Aligned_cols=145  Identities=51%  Similarity=0.866  Sum_probs=139.9

Q ss_pred             HHHHHH-CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf             988640-2430245777765457887643387400064898999999988863873147899999999817999889999
Q gi|254780979|r  352 YFEKLA-VNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVE  430 (500)
Q Consensus       352 ~FE~v~-~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie  430 (500)
                      |||+++ .+.+|+.+|||+++|++++||+.+.++++++++|++|++|+.++++|+||.++||+||..|+.++++|.++++
T Consensus         1 ~Fe~~~~~~~~~k~~anwi~~el~~~ln~~~~~i~~~~i~~~~la~li~lv~~g~Is~~~ak~il~~~~~~~~~~~~ii~   80 (147)
T smart00845        1 YFEEVVKAGADPKLAANWLLGELLGELNKEGLEIEESPITPEHLAELLKLIEDGTISGKIAKEVLEELLESGKSPEEIVE   80 (147)
T ss_pred             CHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             96889770799999999999999999847799856378799999999999986997589899999999873688899998


Q ss_pred             HCCCEECCCHHHHHHHHHHHHHHCHHHHHHHH-CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             63987618988999999999983999899752-7213226589999997289778899999999970
Q gi|254780979|r  431 ELGLRQVTDLSAIEKVVDEVINSNPNNVARIA-TKPNLVSWFVGQVMKNTGGKANPSIVQKMLKEKL  496 (500)
Q Consensus       431 ~~gL~~isD~~eL~~iv~eVI~~np~~V~~~k-gk~ka~gfLvGqVMK~tkGkAdpk~v~~lL~e~L  496 (500)
                      ++||.++||+++|+.+|++||++||++|++|+ ||++++|||||||||+|||||||+.|+++|+++|
T Consensus        81 ~~gl~~isd~~~l~~lv~~ii~~n~~~v~~~~~Gk~k~~~~lvGqvMK~tkGkadp~~v~~ll~e~L  147 (147)
T smart00845       81 EKGLKQISDEGELEAIVDEVIAENPKAVEDYRAGKKKALGFLVGQVMKATRGKADPKLVNELLKEKL  147 (147)
T ss_pred             HCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHC
T ss_conf             8297546883899999999999899999999877488899999999998679989999999999659


No 11 
>pfam01162 consensus
Probab=99.84  E-value=1.6e-21  Score=179.01  Aligned_cols=69  Identities=55%  Similarity=0.935  Sum_probs=66.9

Q ss_pred             EEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             665303566777783327787731269999999885302483689886432026889998887641136
Q gi|254780979|r  281 TRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDKSI  349 (500)
Q Consensus       281 T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~l  349 (500)
                      |++||+||+++||||||||||||+.|+++||+.++.+|||||+++++||+++|||+.++|.+|++++.+
T Consensus         1 T~~mR~KE~a~DYRyfPePDLppi~i~~~~i~~ik~~lPElP~~~~~r~~~~ygL~~~dA~~L~~~~~l   69 (69)
T pfam01162         1 TVIMRAKEEAEDYRYFPEPDLPPLNITDELIEEIRATLPELPDEKRERLVKEYGLSEEDAQTLVSDKEL   69 (69)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCC
T ss_conf             976656576446580789987886689999999999489999999999999939699999999726669


No 12 
>pfam09424 YqeY Yqey-like protein. The function of this domain found in the YqeY protein is uncertain.
Probab=97.81  E-value=0.00025  Score=52.34  Aligned_cols=113  Identities=19%  Similarity=0.219  Sum_probs=73.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHH-HHHHCCCCCHHHHHHHHHHHHHCCC--------CHHHHHHHCCCE
Q ss_conf             7777654578876433874000648989999999-8886387314789999999981799--------988999963987
Q gi|254780979|r  365 VANWVINDLLGVLNRSGKSIEDTPISPNQLGELI-DLIIDGTISGKIAKDIFNILWEKGG--------TPKEIVEELGLR  435 (500)
Q Consensus       365 ~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi-~li~~g~Is~~~aK~il~~l~~~~~--------~p~~iie~~gL~  435 (500)
                      +...+.+++...-...+     ..++.+.+..+| .++.+.       ++-++.+-..|-        .=-+|+++.=..
T Consensus        22 ~lR~i~saik~~ei~~~-----~~l~D~~v~~ii~k~vKqr-------kes~e~y~~agR~dlae~e~~Ei~il~~yLP~   89 (143)
T pfam09424        22 TLRMLKAAIKQEEVDER-----IELSDEEVLTVLAKEVKQR-------RESIEQFEKAGRQDLAEKEKAEIAILEEYLPQ   89 (143)
T ss_pred             HHHHHHHHHHHHHHHCC-----CCCCHHHHHHHHHHHHHHH-------HHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999999989986579-----9999999999999999978-------99999998869866899999999999974633


Q ss_pred             ECCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             6189889999999999839998997527213226589999997289778899999999970
Q gi|254780979|r  436 QVTDLSAIEKVVDEVINSNPNNVARIATKPNLVSWFVGQVMKNTGGKANPSIVQKMLKEKL  496 (500)
Q Consensus       436 ~isD~~eL~~iv~eVI~~np~~V~~~kgk~ka~gfLvGqVMK~tkGkAdpk~v~~lL~e~L  496 (500)
                      |+| +++++.+|.++|+++.-      ...+-+|..||.+|+..+|+||++.|++++++.|
T Consensus        90 qls-eeEl~~~i~~~i~e~ga------~~~kdmGkVM~~l~~~~~G~~Dg~~vs~iVk~~L  143 (143)
T pfam09424        90 QLS-DEEIEALVDEAIAEVGA------TSMKDMGKVMGALMPKVAGRADGKLVSALVKELL  143 (143)
T ss_pred             CCC-HHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHC
T ss_conf             699-99999999999998389------9858899999999987588687799999998629


No 13 
>pfam04558 tRNA_synt_1c_R1 Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1. This is a region found N terminal to the catalytic domain of glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes but not in Escherichia coli. This region is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function.
Probab=97.25  E-value=0.027  Score=37.38  Aligned_cols=152  Identities=16%  Similarity=0.187  Sum_probs=97.8

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCC-----CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHH
Q ss_conf             6898864320268899988876411367898864024-----30245777765457887643387400064898999999
Q gi|254780979|r  323 DAKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVN-----RDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGEL  397 (500)
Q Consensus       323 ~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~~~-----~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeL  397 (500)
                      ++..+.| .+.||++.-|.-++.++.++.-+..+...     .-++...+.+ ..+...++.         -...+..-|
T Consensus         4 eel~~lF-~~iGL~e~kAketlKN~k~t~~L~~ii~ea~~~~~~dk~~g~LL-y~lAtk~k~---------~~~~~~~~i   72 (164)
T pfam04558         4 EELLKLF-SKIGLDEKKAKETLKNKKVSASLLAIIAEAGATSGCDKKTGALL-YNLATKLKG---------NEVPHRPLI   72 (164)
T ss_pred             HHHHHHH-HHCCCCHHHHHHHHHCHHHHHHHHHHHHHCCCCCCCCHHHHHHH-HHHHHHCCC---------CCCHHHHHH
T ss_conf             9999999-98598714599998389999999999997565567887899999-999986565---------321207999


Q ss_pred             HHHHHCCCCCH-HHHHHHHHHHHHCCC---CHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHH
Q ss_conf             98886387314-789999999981799---98899996398761898899999999998399989975272132265899
Q gi|254780979|r  398 IDLIIDGTISG-KIAKDIFNILWEKGG---TPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIATKPNLVSWFVG  473 (500)
Q Consensus       398 i~li~~g~Is~-~~aK~il~~l~~~~~---~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~kgk~ka~gfLvG  473 (500)
                      +..|-+|+|.. .+.-..|.-+...+.   +..++-++.|-..+-..++++..|+++|++|.+.+..-|-+.=-+|.++|
T Consensus        73 v~yI~~~kikT~~Qv~aA~~Yl~~~~~~~id~~~fe~~cGVGV~VT~eqI~~~V~~~i~~~k~~i~~~RY~~~n~g~~~~  152 (164)
T pfam04558        73 VSYIVDGKLKTTLQVDAALKYLKSNGSEAFDVAEFEEACGVGVVVTPEDVERAVADYIEENKEEILEKRYKLFNVGLLLV  152 (164)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCEEECHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             99998566897999999999999779988888999997799868889999999999999969999986223565167888


Q ss_pred             HHHHHHCCCCCHH
Q ss_conf             9999728977889
Q gi|254780979|r  474 QVMKNTGGKANPS  486 (500)
Q Consensus       474 qVMK~tkGkAdpk  486 (500)
                      ++....|= |||+
T Consensus       153 ~~r~~LkW-Ad~k  164 (164)
T pfam04558       153 KARPELKW-ADPK  164 (164)
T ss_pred             HHHCCCCC-CCCC
T ss_conf             76115899-8989


No 14 
>KOG1148 consensus
Probab=96.79  E-value=0.066  Score=34.48  Aligned_cols=19  Identities=16%  Similarity=0.557  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999999864204
Q gi|254780979|r  188 LEAKAFLTKLRSILRYLGT  206 (500)
Q Consensus       188 ~ea~~~~~~l~~ilr~~gi  206 (500)
                      .|...|...|..++..+|-
T Consensus       294 kEee~yf~sI~e~V~WLG~  312 (764)
T KOG1148         294 KEEEEYFESIKEMVAWLGF  312 (764)
T ss_pred             HHHHHHHHHHHHHHHHHCC
T ss_conf             3368999999999987187


No 15 
>COG1610 Uncharacterized conserved protein [Function unknown]
Probab=96.05  E-value=0.024  Score=37.75  Aligned_cols=97  Identities=19%  Similarity=0.217  Sum_probs=64.0

Q ss_pred             CCCCHHHHHHHH-HHHHCCCCCHHHHHHHHHHHHHCCC-C-------HHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHH
Q ss_conf             648989999999-8886387314789999999981799-9-------889999639876189889999999999839998
Q gi|254780979|r  387 TPISPNQLGELI-DLIIDGTISGKIAKDIFNILWEKGG-T-------PKEIVEELGLRQVTDLSAIEKVVDEVINSNPNN  457 (500)
Q Consensus       387 ~~i~p~~laeLi-~li~~g~Is~~~aK~il~~l~~~~~-~-------p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~  457 (500)
                      .+++.+.+-.++ +++.+       -++.+..+-+.+- +       --.|+++.-..|.+ +++|..+|+++|++--. 
T Consensus        43 ~~l~d~~il~vl~k~iKQ-------RrdS~~~y~~agR~dLa~kE~~Ei~Ii~~ylP~qLs-d~e~~~~v~~aIae~Ga-  113 (148)
T COG1610          43 DELDDEEILKVLAKEIKQ-------RRDSAEEYEKAGRQDLAAKERAEIAIIEEYLPQQLS-EDELRALVDAAIAEVGA-  113 (148)
T ss_pred             CCCCHHHHHHHHHHHHHH-------HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHH-
T ss_conf             889869999999999998-------789999998768487999999499999986764689-89999999999999877-


Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHC
Q ss_conf             9975272132265899999972897788999999999707
Q gi|254780979|r  458 VARIATKPNLVSWFVGQVMKNTGGKANPSIVQKMLKEKLG  497 (500)
Q Consensus       458 V~~~kgk~ka~gfLvGqVMK~tkGkAdpk~v~~lL~e~L~  497 (500)
                           ...+-+|..||..|-..+|+||++.|+.++++.|.
T Consensus       114 -----s~~~dMGkvM~al~~k~~GkaD~~~vs~~VK~~L~  148 (148)
T COG1610         114 -----SSMKDMGKVMKALKPKVAGKADGGRVSKLVKELLS  148 (148)
T ss_pred             -----HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf             -----21888999999881885266838899999998729


No 16 
>TIGR00838 argH argininosuccinate lyase; InterPro: IPR009049   This entry represents argininosuccinate lyase, but may include examples of avian delta crystallins, in which argininosuccinate lyase activity may or may not be present and the biological role is to provide the optically clear cellular protein of the eye lens. ; GO: 0004056 argininosuccinate lyase activity, 0042450 arginine biosynthetic process via ornithine.
Probab=88.09  E-value=1.3  Score=25.00  Aligned_cols=119  Identities=15%  Similarity=0.235  Sum_probs=77.1

Q ss_pred             CCCHHHHHHHHHHHHHHHH----------HHCCC--------CCCCCCCCHHHHHHHHH--HHHCCCCCHHHHHH-HHHH
Q ss_conf             4302457777654578876----------43387--------40006489899999998--88638731478999-9999
Q gi|254780979|r  359 NRDKKIVANWVINDLLGVL----------NRSGK--------SIEDTPISPNQLGELID--LIIDGTISGKIAKD-IFNI  417 (500)
Q Consensus       359 ~~~pk~~Anwi~~el~~~l----------n~~~~--------~~~~~~i~p~~laeLi~--li~~g~Is~~~aK~-il~~  417 (500)
                      .+.|-..|.|++...--+.          ++-+.        .-...+|..+.+|+++.  .+-++.+-+.++++ |++.
T Consensus       158 rAQPi~lAHhLLAY~~~l~RD~~RL~d~~kR~n~SPLGsGAlAGt~f~iDR~~~A~lLGF~~~~~NSlDaVSdRDFi~E~  237 (469)
T TIGR00838       158 RAQPITLAHHLLAYAEMLERDYERLQDALKRVNVSPLGSGALAGTSFPIDREYTAELLGFDAVTENSLDAVSDRDFIIEL  237 (469)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCCCHHHHHHHCCHHHHHHCCHHHHHHHHHHHHH
T ss_conf             50105699999999989998899999999885048865503206898768888976318678875204665207899999


Q ss_pred             HHHC---CCCH----HHHH----HHCCCEECCCHHHHHHHHHHHH--HHCHHHHHHHHCCC-CCHHHHHHHHHHHHCC
Q ss_conf             9817---9998----8999----9639876189889999999999--83999899752721-3226589999997289
Q gi|254780979|r  418 LWEK---GGTP----KEIV----EELGLRQVTDLSAIEKVVDEVI--NSNPNNVARIATKP-NLVSWFVGQVMKNTGG  481 (500)
Q Consensus       418 l~~~---~~~p----~~ii----e~~gL~~isD~~eL~~iv~eVI--~~np~~V~~~kgk~-ka~gfLvGqVMK~tkG  481 (500)
                      |+..   ..+.    +++|    .|.|+..++|+=.   -=-+++  .+|||..|-+|||. +++|=|+|..| -.||
T Consensus       238 l~~~a~~m~hLSR~aEelIlw~s~EFgfieL~D~~s---tGSSiMPQKKNPD~aELiRGK~Grv~G~L~g~L~-~lKa  311 (469)
T TIGR00838       238 LFVAALIMVHLSRLAEELILWSSQEFGFIELPDEFS---TGSSIMPQKKNPDVAELIRGKTGRVIGNLTGLLT-ILKA  311 (469)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCEE---ECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH-HHHH
T ss_conf             999999974176898999998446876067457320---0576888877720799998755268999999999-9711


No 17 
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=75.37  E-value=6.8  Score=19.66  Aligned_cols=64  Identities=19%  Similarity=0.406  Sum_probs=43.3

Q ss_pred             CCCCCHHHHHHHHH-HHHCCCCCHHHHHHHHHHHHHCCCC---------H---HHHHHHCCCEECCCHHHHHHHHHH
Q ss_conf             06489899999998-8863873147899999999817999---------8---899996398761898899999999
Q gi|254780979|r  386 DTPISPNQLGELID-LIIDGTISGKIAKDIFNILWEKGGT---------P---KEIVEELGLRQVTDLSAIEKVVDE  449 (500)
Q Consensus       386 ~~~i~p~~laeLi~-li~~g~Is~~~aK~il~~l~~~~~~---------p---~~iie~~gL~~isD~~eL~~iv~e  449 (500)
                      ....+.+++.+|++ ||..|+||...||.++..++...+.         |   ..++.+.++.+-|+-.++..=|+.
T Consensus        18 ~~a~~~ek~~klvDelVkkGeln~eEak~~vddl~~q~k~~~~e~e~K~~r~i~~ml~~~~~~r~~~~~~l~~rvd~   94 (108)
T COG3937          18 LAAETAEKVQKLVDELVKKGELNAEEAKRFVDDLLRQAKEAQGELEEKIPRKIEEMLSDLEVARQSEMDELTERVDA   94 (108)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
T ss_conf             89999999999999999827878999999999999998987602777636899999845020000248888989999


No 18 
>cd07363 45_DOPA_Dioxygenase The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine. This subfamily is composed of plant 4,5-DOPA Dioxygenase, the uncharacterized Escherichia coli protein Jw3007, and similar proteins. 4,5-DOPA Dioxygenase catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine (4,5-DOPA). The reaction results in the opening of the cyclic ring  between carbons 4 and 5 and producing an unstable seco-DOPA that rearranges to betalamic acid. 4,5-DOPA Dioxygenase is a key enzyme in the biosynthetic pathway of the plant pigment betalain. Homologs of DODA are present not only in betalain-producing plants but also in bacteria and archaea. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated ca
Probab=71.50  E-value=4.5  Score=20.96  Aligned_cols=43  Identities=19%  Similarity=0.280  Sum_probs=30.1

Q ss_pred             HHHHHHHC-CCCCCC-CCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             99997313-980034-432337554336653035667777833277877312699
Q gi|254780979|r  256 RQIAILED-GGHIRQ-ETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDE  308 (500)
Q Consensus       256 RQ~~ll~~-G~~v~q-ETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~  308 (500)
                      |=.++|.. |-.+.. .+|+||  -|..++|+        .||||.|+|-|.||-
T Consensus        85 ~i~~~L~~~gi~~~~d~~rGlD--HG~wvpL~--------~m~P~adiPVvqlSl  129 (253)
T cd07363          85 RVAELLKAAGIPARLDPERGLD--HGAWVPLK--------LMYPDADIPVVQLSL  129 (253)
T ss_pred             HHHHHHHHCCCCEEECCCCCCC--CCCEEEEE--------EECCCCCCCEEEEEC
T ss_conf             9999998649871305766766--55225788--------627899997799755


No 19 
>TIGR02407 ectoine_ectB diaminobutyrate--2-oxoglutarate aminotransferase; InterPro: IPR012773    Members of this family of class III pyridoxal-phosphate-dependent aminotransferases are diaminobutyrate--2-oxoglutarate aminotransferase (2.6.1.76 from EC) that catalyze the first step in ectoine biosynthesis from L-aspartate beta-semialdehyde. This family is readily separated phylogenetically from enzymes with the same substrate and product but involved in other process such as siderophore (Q9Z3R2 from SWISSPROT) or 1,3-diaminopropane (P44951 from SWISSPROT) biosynthesis. Ectoine is a compatible solute particularly effective in conferring salt tolerance.; GO: 0030170 pyridoxal phosphate binding, 0047307 diaminobutyrate-pyruvate transaminase activity, 0019491 ectoine biosynthetic process.
Probab=68.98  E-value=9.3  Score=18.65  Aligned_cols=68  Identities=15%  Similarity=0.262  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHH-HHHHCCCCCHHHHHHHHHHHHCCCCCHH
Q ss_conf             478999999998179998899996398761898899999999998399989-9752721322658999999728977889
Q gi|254780979|r  408 GKIAKDIFNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNV-ARIATKPNLVSWFVGQVMKNTGGKANPS  486 (500)
Q Consensus       408 ~~~aK~il~~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V-~~~kgk~ka~gfLvGqVMK~tkGkAdpk  486 (500)
                      --+|++.|+.+|. +.+.++-|+++       ...|++..++++++||+.. .+.||+    ||+.|-.+      .++.
T Consensus       300 FVtA~aAL~~yW~-Dd~f~~~v~~~-------s~~~~~~l~~~~~~~~~~~~~~~RGR----Glm~Gl~~------~~~~  361 (413)
T TIGR02407       300 FVTATAALEYYWS-DDAFEKAVQRK-------SEIIQERLDEIVAEFPELIEKSVRGR----GLMQGLEC------GDGD  361 (413)
T ss_pred             HHHHHHHHHHHCC-CHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHCCCCCCCC----CEEEECCC------CCHH
T ss_conf             9999999998489-62689999999-------99999999999987455213110452----01420004------7724


Q ss_pred             HHHHHHH
Q ss_conf             9999999
Q gi|254780979|r  487 IVQKMLK  493 (500)
Q Consensus       487 ~v~~lL~  493 (500)
                      .+.++.+
T Consensus       362 ~A~~i~~  368 (413)
T TIGR02407       362 LAGKIAK  368 (413)
T ss_pred             HHHHHHH
T ss_conf             6899999


No 20 
>TIGR01398 FlhA flagellar biosynthesis protein FlhA; InterPro: IPR006301   These sequences describe the flagellar biosynthesis protein FlhA, one of a large number of genes associated with the biosynthesis of functional bacterial flagella. Homologs of many such proteins, including FlhA, function in type III protein secretion systems. ; GO: 0015031 protein transport, 0016021 integral to membrane, 0019861 flagellum.
Probab=68.06  E-value=7.1  Score=19.52  Aligned_cols=59  Identities=15%  Similarity=0.269  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCC-CCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHC
Q ss_conf             4577776545788764338740-0064898999999988863873147899999999817
Q gi|254780979|r  363 KIVANWVINDLLGVLNRSGKSI-EDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEK  421 (500)
Q Consensus       363 k~~Anwi~~el~~~ln~~~~~~-~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~  421 (500)
                      ..-|-||.....-.....|-++ +...+=+-||.|+|+--...-+|.+.++.+|+.+-++
T Consensus       472 Gl~A~WI~e~~~e~A~~~GYTVVDp~tVlaTHL~E~ik~na~~LL~r~ev~~LLd~l~~~  531 (713)
T TIGR01398       472 GLPAYWIEEKNKEEAERLGYTVVDPATVLATHLSEVIKNNAAELLTRQEVQNLLDRLKEE  531 (713)
T ss_pred             CCCCEECCHHHHHHHHHCCCEEECCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_conf             986121381348999864985870179999999999999898851589999999860132


No 21 
>PRK10628 hypothetical protein; Provisional
Probab=65.73  E-value=4.1  Score=21.27  Aligned_cols=41  Identities=15%  Similarity=0.271  Sum_probs=27.8

Q ss_pred             HHHHHCCC-CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             99731398-0034432337554336653035667777833277877312699
Q gi|254780979|r  258 IAILEDGG-HIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDE  308 (500)
Q Consensus       258 ~~ll~~G~-~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~  308 (500)
                      .++|...+ ....+.|+||  -|..++|+        +||||.|+|-|.+|=
T Consensus        77 ~~lL~~~~~~~~~~~~GlD--HG~W~pL~--------~myP~AdiPVVqlSl  118 (246)
T PRK10628         77 VELLAPVPVTLDKEAWGFD--HGSWGVLI--------KMYPDADIPMVQLSI  118 (246)
T ss_pred             HHHHHCCCCCCCCCCCCCC--CCCCHHHH--------HHCCCCCCCEEEEEC
T ss_conf             9985146865576556877--54216678--------638899997799756


No 22 
>pfam06576 DUF1133 Protein of unknown function (DUF1133). This family consists of a number of hypothetical proteins from Escherichia coli O157:H7 and Salmonella typhi. The function of this family is unknown.
Probab=65.28  E-value=11  Score=18.14  Aligned_cols=61  Identities=20%  Similarity=0.338  Sum_probs=44.5

Q ss_pred             HHHHCCCCCHHHHHHHHHHHHHCCCCH---HHHHHH-------CCCEECCCHHH--HHHHHHHHHHHCHHHHH
Q ss_conf             888638731478999999998179998---899996-------39876189889--99999999983999899
Q gi|254780979|r  399 DLIIDGTISGKIAKDIFNILWEKGGTP---KEIVEE-------LGLRQVTDLSA--IEKVVDEVINSNPNNVA  459 (500)
Q Consensus       399 ~li~~g~Is~~~aK~il~~l~~~~~~p---~~iie~-------~gL~~isD~~e--L~~iv~eVI~~np~~V~  459 (500)
                      .|+.+++||.+..+++|..|-++|-+-   +++..+       -+|.--+|.+.  ++.+|-+|++++|..+.
T Consensus        48 ~LLas~klTKtAinealrrmKksGl~k~eLeaflrem~n~K~kS~La~CtD~E~l~iD~VI~~vl~~~pgL~~  120 (176)
T pfam06576        48 QLLASKKLTKTAVNEALRRMKKSGIEKPELEAFFREMLNGKQKSWLAHCTDTEALKIDRVISEVLGEYPGLIS  120 (176)
T ss_pred             HHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHHHHHHHCCCHHH
T ss_conf             9984043139999999999998379808999999998574321364021451567889999999985830999


No 23 
>TIGR02653 Lon_rel_chp conserved hypothetical protein; InterPro: IPR013473    This entry describes a protein family of unknown function, about 690 residues in length, in which some members show C-terminal sequence similarity to IPR008269 from INTERPRO, which is the Lon protease C-terminal proteolytic domain, from MEROPS family S16. However, the annotated catalytic sites of Escherichia coli Lon protease are not conserved in members of this family. Members have a motif GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif GxxGxGK[ST]..
Probab=64.68  E-value=7.4  Score=19.38  Aligned_cols=123  Identities=21%  Similarity=0.384  Sum_probs=78.2

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHCC--CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             83327787731269999999885302--4836898864320268899988876411367898864024302457777654
Q gi|254780979|r  294 RYFSEPDLLPLEIDEDFIRAIKKQIP--ELPDAKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVNRDKKIVANWVIN  371 (500)
Q Consensus       294 RyfPEPDLPpi~is~e~i~~i~~~lP--elP~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~~~~~pk~~Anwi~~  371 (500)
                      -+.|=|++  +..+-.|++.+..-+|  |.|-=|-+-|...||+=-         ..||+||-++-...-+..+-+++  
T Consensus       333 Lf~PfP~a--~~~DtAFfDR~H~YiPGWEIPKmRpEyFT~~YGfiv---------DYlAE~~REmRkrsf~d~idrfF--  399 (677)
T TIGR02653       333 LFAPFPEA--MREDTAFFDRIHYYIPGWEIPKMRPEYFTNRYGFIV---------DYLAEYLREMRKRSFADAIDRFF--  399 (677)
T ss_pred             HCCCCHHH--HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHH---------HHHHHHHHHHHCCCHHHHHHHHH--
T ss_conf             30440688--741025675563058887688876442017776035---------67899999852011124555666--


Q ss_pred             HHHHHHHHCCCCCCCCCCCHHHHHHHHHHHH-CCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCC
Q ss_conf             5788764338740006489899999998886-38731478999999998179998899996398
Q gi|254780979|r  372 DLLGVLNRSGKSIEDTPISPNQLGELIDLII-DGTISGKIAKDIFNILWEKGGTPKEIVEELGL  434 (500)
Q Consensus       372 el~~~ln~~~~~~~~~~i~p~~laeLi~li~-~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL  434 (500)
                      .|-..||.++.--    + -.-++-|++|+. ++.+|+..++++|+.-+++--.++|=.++.|-
T Consensus       400 klGnnLNqRDViA----V-rkTvSGL~KLlyP~~~~tk~~~~~~l~yalegRRRVKEQLKK~Gg  458 (677)
T TIGR02653       400 KLGNNLNQRDVIA----V-RKTVSGLLKLLYPDGEYTKDDVREILDYALEGRRRVKEQLKKLGG  458 (677)
T ss_pred             HHCCCCCCCCHHH----H-HHHHCEEEEEECCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCC
T ss_conf             5123233231321----2-110010000126885568799999988762356203666643067


No 24 
>pfam12570 DUF3750 Protein of unknown function (DUF3750). This family of proteins is found in bacteria. Proteins in this family are typically between 175 and 265 amino acids in length.
Probab=63.98  E-value=5.1  Score=20.58  Aligned_cols=29  Identities=28%  Similarity=0.550  Sum_probs=24.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHH
Q ss_conf             67777833277877312699999998853024836
Q gi|254780979|r  289 DALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPD  323 (500)
Q Consensus       289 ~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~  323 (500)
                      -..+||+||-||      |+.|++-|-...|||--
T Consensus        90 ~~~~Yr~wPGPN------SNTFvawv~r~vpel~~  118 (129)
T pfam12570        90 YPNEYRAWPGPN------SNTFVAWVLRQVPELDL  118 (129)
T ss_pred             CCCCCEECCCCC------HHHHHHHHHHHCHHCCC
T ss_conf             889721778997------07799999865810146


No 25 
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=63.87  E-value=12  Score=17.96  Aligned_cols=105  Identities=15%  Similarity=0.136  Sum_probs=56.8

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCC---------HHHHHHHHHHHHHHHHHHCCCC----CCCCCCC
Q ss_conf             89886432026889998887641136789886402430---------2457777654578876433874----0006489
Q gi|254780979|r  324 AKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVNRD---------KKIVANWVINDLLGVLNRSGKS----IEDTPIS  390 (500)
Q Consensus       324 ~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~~~~~---------pk~~Anwi~~el~~~ln~~~~~----~~~~~i~  390 (500)
                      +.+..|++--|+-+..|-.+++.....++.+++..+..         .+..|.-|+.||.+-+.+....    .......
T Consensus        70 ~~F~~Li~V~GIGpK~AL~ILs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~  149 (198)
T PRK00116         70 ELFRLLISVSGVGPKLALAILSGLSPEELAQAIANGDIKALTKVPGVGKKTAERIVLELKDKLAALADAGAAAAAAASAA  149 (198)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             99999856688578999988702999999999985899997068897889999999999988874212455454566777


Q ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHH
Q ss_conf             89999999888638731478999999998179998899
Q gi|254780979|r  391 PNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEI  428 (500)
Q Consensus       391 p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~i  428 (500)
                      ...+.+++..+.+=-.+...++.++..+...+.+.+++
T Consensus       150 ~~~~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~eel  187 (198)
T PRK00116        150 NDALEEAVSALVALGYKPKEAQKAVAAILKEGASVEEL  187 (198)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHH
T ss_conf             52599999999985999999999999864369999999


No 26 
>COG3384 Aromatic ring-opening dioxygenase, catalytic LigB subunit related    enzyme [Amino acid transport and metabolism]
Probab=63.46  E-value=8.2  Score=19.06  Aligned_cols=100  Identities=17%  Similarity=0.168  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCC-CC----CCCCCCCHHHHHHH---HHHHH------
Q ss_conf             999999999999986420456764322011257543213766678-86----22235402465999---99999------
Q gi|254780979|r  188 LEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWG-TR----CEVKNVNSIRFLGL---AIEYE------  253 (500)
Q Consensus       188 ~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~G-tR----vEIKNlnS~~~i~~---AI~yE------  253 (500)
                      ..+....++|++-++-            +|.|+=|=+..+=...| +.    -.-+.+..|-..+.   ++.|.      
T Consensus        26 n~~~~~l~~lG~~~~e------------~rp~tIiV~SaHw~t~~~~~v~~~e~~~~i~DfygFP~~ly~~~Y~a~G~pe   93 (268)
T COG3384          26 NAATRGLRELGRELPE------------LRPDTIIVFSAHWETRGAYHVTASEHPETIHDFYGFPDELYDVKYPAPGSPE   93 (268)
T ss_pred             CHHHHHHHHHHHHHHH------------CCCCEEEEEECEEEECCCEEEECCCCCCEEECCCCCCHHHHHCCCCCCCCHH
T ss_conf             0789999999776566------------0898799983507862743687066766122158898899843379999989


Q ss_pred             H-HHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             9-999997313980034432337554336653035667777833277877312699
Q gi|254780979|r  254 A-RRQIAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDE  308 (500)
Q Consensus       254 i-~RQ~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~  308 (500)
                      . +|=++++...+-..| +-.|.-+-|+.++||        -||||-|+|-|.||-
T Consensus        94 La~~i~~~l~~~~v~a~-~~~~gLDHGtwvpL~--------~M~PdadipVV~iSi  140 (268)
T COG3384          94 LAQRIVELLAKLGVPAD-APSWGLDHGTWVPLR--------YMFPDADIPVVQISI  140 (268)
T ss_pred             HHHHHHHHHCCCCCCCC-CCCCCCCCCCEEEEH--------HHCCCCCCCEEEEEC
T ss_conf             99999997412586666-876687764333303--------227756896799963


No 27 
>PRK11913 phhA phenylalanine 4-monooxygenase; Reviewed
Probab=63.38  E-value=5.8  Score=20.20  Aligned_cols=45  Identities=24%  Similarity=0.466  Sum_probs=35.7

Q ss_pred             CEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             336653035667777833277877312699999998853024836898864320268
Q gi|254780979|r  279 NETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI  335 (500)
Q Consensus       279 ~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL  335 (500)
                      -.|..+|+.+.-.   |-||||+         +-++---.|.|-+.....|...||.
T Consensus       104 p~t~~iR~~~~~~---YtpEPDi---------fHe~fGHvP~L~~p~fA~f~~~~G~  148 (272)
T PRK11913        104 PVATFIRTPEELD---YLQEPDI---------FHDVFGHVPLLTNPVFADFMQAYGQ  148 (272)
T ss_pred             CEEEEECCCCCCC---CCCCCHH---------HHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             2253435776556---6888437---------8876256742079889999999999


No 28 
>PHA01082 putative transcription regulator
Probab=62.66  E-value=3  Score=22.26  Aligned_cols=56  Identities=18%  Similarity=0.256  Sum_probs=37.2

Q ss_pred             EEEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             3798423666520231001156787148866157861257630365277899999999999998
Q gi|254780979|r  138 TIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSIL  201 (500)
Q Consensus       138 ~~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~il  201 (500)
                      +...++..=.||=-+|.++-   +...+     .|+.|+||-.++|+......-.|++.|..++
T Consensus        78 W~~f~m~~~rLelPTG~lVt---pQqIL-----tGiALLEIGAe~D~~~~~kiLKyAR~L~~~~  133 (133)
T PHA01082         78 WENFVMRHDRLELPTGDLVT---AQQVL-----IGVALLELGASNDIKVAHQILKYARALKRFI  133 (133)
T ss_pred             HHHHEEECCEEECCCCCCCC---HHHHH-----HHHHHHCCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             45452157768768877136---99998-----7766520167610789999999999998639


No 29 
>cd03346 eu_TrpOH Eukaryotic tryptophan hydroxylase (TrpOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH) and eukaryotic tyrosine hydroxylase (TyrOH). TrpOH oxidizes L-tryptophan to 5-hydroxy-L-tryptophan, the rate-limiting step in the biosynthesis of serotonin (5-hydroxytryptamine), a widely distributed hormone and neurotransmitter.
Probab=61.75  E-value=11  Score=18.07  Aligned_cols=111  Identities=22%  Similarity=0.320  Sum_probs=62.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             77899999999999998642045676432201125754321376667886222354024659999999999999973139
Q gi|254780979|r  185 RSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDG  264 (500)
Q Consensus       185 ~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G  264 (500)
                      ....-+++|+.-+..+-+++|...-++  =+++ |||-=+++. +.|. -+-+-++=|.|.--..+.+            
T Consensus        80 ~~~~AC~eyl~~~~~L~~~~g~~~d~I--PQl~-dvs~~L~~~-TGf~-l~pV~Gll~~r~F~~~LA~------------  142 (287)
T cd03346          80 YPTHACREYLKNLPLLEKHCGYREDNI--PQLE-DVSRFLKER-TGFT-IRPVAGYLSPRDFLAGLAF------------  142 (287)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCC--CCHH-HHHHHHHHH-CCCE-EEECCCCCCHHHHHHHHHH------------
T ss_conf             530638999999999998449997789--9779-999999874-1988-9854665788899998731------------


Q ss_pred             CCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             80034432337554336653035667777833277877312699999998853024836898864320268
Q gi|254780979|r  265 GHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI  335 (500)
Q Consensus       265 ~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL  335 (500)
                             |.|    -.|..+|..+.-   -|-||||+         +-++---+|.|-+.....|..++|+
T Consensus       143 -------r~F----~~TqyIRh~~~p---~YtpEPDi---------~HEl~GHvPlLadp~fA~f~q~iG~  190 (287)
T cd03346         143 -------RVF----HCTQYVRHSSDP---FYTPEPDT---------CHELLGHVPLLADPSFAQFSQEIGL  190 (287)
T ss_pred             -------CCC----CCEEEECCCCCC---CCCCCCCH---------HHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             -------637----621345258887---77899962---------6566445633379889999999999


No 30 
>cd03348 pro_PheOH Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH), tyrosine hydroxylase (TyrOH) and tryptophan hydroxylase (TrpOH). PheOH catalyzes the hydroxylation of L-Phe to L-tyrosine (L-Tyr). It uses (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) as the physiological electron donor.
Probab=59.74  E-value=7.9  Score=19.19  Aligned_cols=45  Identities=27%  Similarity=0.475  Sum_probs=36.2

Q ss_pred             CEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             336653035667777833277877312699999998853024836898864320268
Q gi|254780979|r  279 NETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI  335 (500)
Q Consensus       279 ~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL  335 (500)
                      -.|..+|+.+.-.   |-||||+         +-++---+|.|-+.....|...||.
T Consensus        92 p~t~~iR~~~~~~---YtpEPDi---------fHe~~GH~P~L~np~fA~f~q~~G~  136 (228)
T cd03348          92 PVTNFIRRPEELD---YLQEPDI---------FHDIFGHVPMLTNPVFADFMQAYGK  136 (228)
T ss_pred             CEEEEECCCCCCC---CCCCCCH---------HHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             3352445865356---6889428---------9998365620088899999999999


No 31 
>TIGR01011 rpsB_bact ribosomal protein S2; InterPro: IPR005706   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    This family describes the bacterial, mitochondrial and chloroplast forms of ribosomal protein S2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=58.58  E-value=5.2  Score=20.55  Aligned_cols=122  Identities=19%  Similarity=0.256  Sum_probs=60.2

Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCC-C-CCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHC--
Q ss_conf             997313980034432337554336653035667777833277-8-773126999999988530248368988643202--
Q gi|254780979|r  258 IAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEP-D-LLPLEIDEDFIRAIKKQIPELPDAKRERFIGEF--  333 (500)
Q Consensus       258 ~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEP-D-LPpi~is~e~i~~i~~~lPelP~~~~~rl~~~y--  333 (500)
                      .+|||+|-..--+||+|||..+.=.             |+|- | +=-+.|. ..+..++..+..     ..+.+++-  
T Consensus         5 k~LleaGvHFGHqtRRWNPkMk~fI-------------f~eRKngihIIDL~-kT~~~~~~Ay~~-----v~~~~~~gg~   65 (227)
T TIGR01011         5 KDLLEAGVHFGHQTRRWNPKMKPFI-------------FGERKNGIHIIDLQ-KTLQLLEEAYNF-----VREVVANGGK   65 (227)
T ss_pred             HHHHHCCCCCCCEECCCCCCCCCCC-------------CCCCCCCCEEECHH-HHHHHHHHHHHH-----HHHHHHCCCE
T ss_conf             7686388543754223688898855-------------32012785122578-999999999999-----9999981995


Q ss_pred             ----CCCH-HHHHHHHHHHHHHHHHHHHHCCCCHHHHH-HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCC
Q ss_conf             ----6889-99888764113678988640243024577-77654578876433874000648989999999888638731
Q gi|254780979|r  334 ----GISL-YDASVLVSDKSIADYFEKLAVNRDKKIVA-NWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTIS  407 (500)
Q Consensus       334 ----GLs~-~dA~~L~~~~~la~~FE~v~~~~~pk~~A-nwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is  407 (500)
                          | +. .+|+.++.         +.+..++.-.+. .||=|-|.        +|....-+-+.|-+|-.+.++|...
T Consensus        66 iLFVG-TKNkQA~~~i~---------~~A~r~g~~YVn~RWLGGMLT--------Nf~TirkSi~kL~~lE~~~~~g~~~  127 (227)
T TIGR01011        66 ILFVG-TKNKQAKEIIK---------EEAERCGMFYVNQRWLGGMLT--------NFKTIRKSIKKLKKLEKMEEDGTFD  127 (227)
T ss_pred             EEEEE-CHHHHHHHHHH---------HHHHHCCCCEECCCCCCCCCH--------HHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             88851-65889999999---------999874896211333464002--------4799999999999999877613312


Q ss_pred             HHHHHHHHH
Q ss_conf             478999999
Q gi|254780979|r  408 GKIAKDIFN  416 (500)
Q Consensus       408 ~~~aK~il~  416 (500)
                      .-+=||++.
T Consensus       128 ~LtKKE~~~  136 (227)
T TIGR01011       128 VLTKKEILM  136 (227)
T ss_pred             CCCCCCHHH
T ss_conf             477000776


No 32 
>KOG2305 consensus
Probab=58.51  E-value=11  Score=18.18  Aligned_cols=37  Identities=19%  Similarity=0.276  Sum_probs=20.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCC
Q ss_conf             789999999999999864204567643220112575432
Q gi|254780979|r  186 SSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSV  224 (500)
Q Consensus       186 s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi  224 (500)
                      .+++....++.++.=|+-+.-  .+.-.|++++|--.+.
T Consensus        35 ~e~Ql~~ALen~~Kel~~Lee--~g~lrGnlsa~eqla~   71 (313)
T KOG2305          35 LEKQLQTALENVEKELRKLEE--HGLLRGNLSADEQLAL   71 (313)
T ss_pred             CHHHHHHHHHHHHHHHHHHHH--HHHHCCCCCHHHHHHH
T ss_conf             599999999999999999997--2101267648888888


No 33 
>pfam11212 DUF2999 Protein of unknown function (DUF2999). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=50.00  E-value=19  Score=16.36  Aligned_cols=18  Identities=22%  Similarity=0.477  Sum_probs=7.8

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             658999999728977889999999
Q gi|254780979|r  469 SWFVGQVMKNTGGKANPSIVQKML  492 (500)
Q Consensus       469 gfLvGqVMK~tkGkAdpk~v~~lL  492 (500)
                      ..|||+||      .||..+++-.
T Consensus        47 Q~lm~~VM------~nP~LIkeAv   64 (82)
T pfam11212        47 QQLMMLVM------QNPALIKEAV   64 (82)
T ss_pred             HHHHHHHH------CCHHHHHHHH
T ss_conf             99999997------1928899999


No 34 
>pfam11867 DUF3387 Domain of unknown function (DUF3387). This domain is functionally uncharacterized. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with pfam04851, pfam04313.
Probab=49.75  E-value=19  Score=16.34  Aligned_cols=18  Identities=22%  Similarity=0.294  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHHHCCCCCH
Q ss_conf             899999998886387314
Q gi|254780979|r  391 PNQLGELIDLIIDGTISG  408 (500)
Q Consensus       391 p~~laeLi~li~~g~Is~  408 (500)
                      .+.|.++++-..++.|+.
T Consensus       198 sE~Le~~i~~Y~nr~it~  215 (333)
T pfam11867       198 SERLEEAINKYHNRAITT  215 (333)
T ss_pred             HHHHHHHHHHHHCCCCCH
T ss_conf             999999999998077749


No 35 
>cd00361 arom_aa_hydroxylase Biopterin-dependent aromatic amino acid hydroxylase; a family of non-heme, iron(II)-dependent enzymes that includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH converts L-phenylalanine to L-tyrosine, an important step in phenylalanine catabolism and neurotransmitter biosynthesis, and is linked to a severe variant of phenylketonuria in humans. TyrOH and TrpOH are involved in the biosynthesis of catecholamine and serotonin, respectively. The eukaryotic enzymes are all homotetramers.
Probab=49.56  E-value=14  Score=17.37  Aligned_cols=45  Identities=29%  Similarity=0.523  Sum_probs=35.0

Q ss_pred             CEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             336653035667777833277877312699999998853024836898864320268
Q gi|254780979|r  279 NETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI  335 (500)
Q Consensus       279 ~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL  335 (500)
                      -.|..+|..+.-.   |-||||+         +-++---+|.|-+.....|...||.
T Consensus        86 p~t~~iR~~~~~~---YtpEPDi---------fHe~~GH~P~L~~p~fA~f~q~~G~  130 (221)
T cd00361          86 PVTQYIRHPEEPD---YTPEPDI---------FHELFGHVPLLADPSFADFSQEYGL  130 (221)
T ss_pred             CEEEEECCCCCCC---CCCCCCH---------HHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             3253445787677---7899943---------8776167731179889999999999


No 36 
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=47.98  E-value=5.4  Score=20.43  Aligned_cols=59  Identities=27%  Similarity=0.312  Sum_probs=35.6

Q ss_pred             CCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             44323375543366530356677778332778773126999999988530248368988643202688999888764113
Q gi|254780979|r  269 QETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDKS  348 (500)
Q Consensus       269 qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~  348 (500)
                      ..|-+|=+..|.-.+.|   ++..||+|.+.|+.-+.                   ...++ .+.|+|.+++..+++.+.
T Consensus        15 ~~tlRyYe~~GLl~~~r---~~~gyR~Y~~~~i~~l~-------------------~I~~l-r~~G~sL~eIk~lL~~~~   71 (102)
T cd04775          15 RSTLLYYESIGLIPSAR---SEANYRLYSEADLSRLE-------------------KIVFL-QAGGLPLEEIAGCLAQPH   71 (102)
T ss_pred             HHHHHHHHHCCCCCCCC---CCCCCEECCHHHHHHHH-------------------HHHHH-HHCCCCHHHHHHHHCCCC
T ss_conf             99999999879999873---99999637899999999-------------------99999-996999999999985995


Q ss_pred             HH
Q ss_conf             67
Q gi|254780979|r  349 IA  350 (500)
Q Consensus       349 la  350 (500)
                      ..
T Consensus        72 ~~   73 (102)
T cd04775          72 VQ   73 (102)
T ss_pred             HH
T ss_conf             79


No 37 
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=47.58  E-value=21  Score=16.10  Aligned_cols=42  Identities=19%  Similarity=0.388  Sum_probs=32.2

Q ss_pred             CCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             126999999988530248368988643202688999888764
Q gi|254780979|r  304 LEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS  345 (500)
Q Consensus       304 i~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~  345 (500)
                      +.++++.++.|++++|-.-....--+.+.||++-..|...+.
T Consensus        40 v~vdee~~~ki~KEV~~~r~VTpy~la~r~gI~~SvAr~vLR   81 (107)
T COG4901          40 VTVDEELLDKIRKEVPRERVVTPYVLASRYGINGSVARIVLR   81 (107)
T ss_pred             HHCCHHHHHHHHHHCCCCEEECHHHHHHHHCCCHHHHHHHHH
T ss_conf             120599999999862545155499988885552589999999


No 38 
>pfam04262 Glu_cys_ligase Glutamate-cysteine ligase. Family of bacterial f glutamate-cysteine ligases (EC:6.3.2.2) that carry out the first step of the glutathione biosynthesis pathway.
Probab=46.71  E-value=16  Score=16.97  Aligned_cols=50  Identities=20%  Similarity=0.271  Sum_probs=33.7

Q ss_pred             EEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCC
Q ss_conf             8661578612576303652778999999999999986420456764322011257
Q gi|254780979|r  166 IDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADV  220 (500)
Q Consensus       166 vD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~Dv  220 (500)
                      -||--   .|+|+|| |...++++|..|+..|+.++...= -|--+=-.||=|-.
T Consensus        56 TDFSE---sqlE~IT-P~~~s~~~~~~~L~~lh~~v~~~l-~dE~LWP~SMP~~l  105 (377)
T pfam04262        56 TDFAE---SLLEFIT-PPSKDIEDTLAFLSDIHRFVQSKL-KGEYLWPLSMPCRL  105 (377)
T ss_pred             CCCCH---HHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCCC
T ss_conf             75578---8766178-998999999999999999999618-98643567788889


No 39 
>pfam06519 TolA TolA C-terminal. This family consists of several bacterial TolA proteins as well as two eukaryotic proteins of unknown function. Tol proteins are involved in the translocation of group A colicins. Colicins are bacterial protein toxins, which are active against Escherichia coli and other related species (See pfam01024). TolA is anchored to the cytoplasmic membrane by a single membrane spanning segment near the N-terminus, leaving most of the protein exposed to the periplasm.
Probab=43.85  E-value=23  Score=15.77  Aligned_cols=48  Identities=13%  Similarity=0.230  Sum_probs=33.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCC
Q ss_conf             78999999999999986420456764322011257543213766678862
Q gi|254780979|r  186 SSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRC  235 (500)
Q Consensus       186 s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRv  235 (500)
                      +..|+-.|...+++.++.-=.-+..| .|- .|.++|.+.+.|.-.+.++
T Consensus         9 ~~sev~~Y~a~I~~~Iq~~~~~~~~~-~GK-~C~v~I~LapdG~v~~v~~   56 (96)
T pfam06519         9 SGAEVDRYAGQIKQAIQSRFLDDDSF-AGK-TCRVRIKLAPDGTLISVKV   56 (96)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCC-CCC-EEEEEEEECCCCEEEEEEE
T ss_conf             47689999999999999844886134-999-7899999869956987440


No 40 
>COG1490 Dtd D-Tyr-tRNAtyr deacylase [Translation, ribosomal structure and biogenesis]
Probab=43.60  E-value=24  Score=15.68  Aligned_cols=47  Identities=28%  Similarity=0.483  Sum_probs=38.5

Q ss_pred             ECCCCCC---HHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCC
Q ss_conf             0365277---8999999999999986420456764322011257543213766
Q gi|254780979|r  180 TKPDMRS---SLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGE  229 (500)
Q Consensus       180 T~Pd~~s---~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~  229 (500)
                      +.|.++.   |++|.+.-+++-..+|-.|+   .-|.|-+..|-+||+-..|.
T Consensus        89 ~RPsFs~aa~p~~A~~lYe~f~~~lr~~~~---~V~tG~FgA~M~V~LvNdGP  138 (145)
T COG1490          89 RRPSFSKAAKPDQAEELYEYFVELLRELGI---KVETGRFGADMQVSLVNDGP  138 (145)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHCCC---CEEEEEEECEEEEEEECCCC
T ss_conf             998866658857889999999999986288---40210220000789861897


No 41 
>pfam05606 DUF777 Borrelia burgdorferi protein of unknown function (DUF777). This family consists of several hypothetical proteins of unknown function from Borrelia burgdorferi (Lyme disease spirochete).
Probab=43.09  E-value=9.2  Score=18.71  Aligned_cols=23  Identities=35%  Similarity=0.456  Sum_probs=14.3

Q ss_pred             ECCCCEEECCCEECCC---CCCCCCCC
Q ss_conf             2442013113212376---78882014
Q gi|254780979|r   89 INKYSVFARKNYFYPD---LPQGYQIS  112 (500)
Q Consensus        89 i~~~~~fdRK~YfYpD---lpkgyQiT  112 (500)
                      .++..+|| |||||-=   .||.--|-
T Consensus        88 ~nDnnhFD-K~yFYILs~i~pk~l~i~  113 (180)
T pfam05606        88 ESDNNHFD-KNYFYILSVLNPKKIGII  113 (180)
T ss_pred             CCCCCCCC-CCEEEEEECCCCCEEEEE
T ss_conf             46665544-426899972585300058


No 42 
>KOG1795 consensus
Probab=41.52  E-value=25  Score=15.46  Aligned_cols=10  Identities=50%  Similarity=0.704  Sum_probs=3.2

Q ss_pred             HHHHHHHHCC
Q ss_conf             9999973139
Q gi|254780979|r  255 RRQIAILEDG  264 (500)
Q Consensus       255 ~RQ~~ll~~G  264 (500)
                      .||.+.+..|
T Consensus       783 Erq~n~~k~G  792 (2321)
T KOG1795         783 ERQHNYLKDG  792 (2321)
T ss_pred             HHHHHHHHCC
T ss_conf             8876566228


No 43 
>COG0105 Ndk Nucleoside diphosphate kinase [Nucleotide transport and metabolism]
Probab=40.50  E-value=13  Score=17.56  Aligned_cols=77  Identities=16%  Similarity=0.303  Sum_probs=50.1

Q ss_pred             EEEEEEEEEEEECCCCCCCCCCCCC----EEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             7984236665202310011567871----488661578612576303652778999999999999986420456764322
Q gi|254780979|r  139 IEVGIERIHLEQDAGKSIHDQYSAV----SCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEG  214 (500)
Q Consensus       139 ~~v~I~~i~lEED~gk~~h~~~~~~----slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeG  214 (500)
                      +-+..+.+|+.++.+..-+....+.    .||+|         |++.|.+----|-...+...|.++-.+.-.++  +.|
T Consensus        32 kiva~K~~~~~~e~Ae~~Y~~h~~kpFf~~Lv~f---------itSgPvv~~VleGe~ai~~~R~l~GaTnp~~A--~pG  100 (135)
T COG0105          32 KIVALKMVQLSRELAENHYAEHKGKPFFGELVEF---------ITSGPVVAMVLEGENAISVVRKLMGATNPANA--APG  100 (135)
T ss_pred             EEEEEEEECCCHHHHHHHHHHHCCCCCCHHHHHH---------EECCCEEEEEEECHHHHHHHHHHHCCCCCCCC--CCC
T ss_conf             8876440204799997778987678752877862---------31265899998527699999999779981217--998


Q ss_pred             EEECCCCCCCCC
Q ss_conf             011257543213
Q gi|254780979|r  215 SMRADVNVSVCR  226 (500)
Q Consensus       215 slR~DvNVSi~~  226 (500)
                      +||.|-++|+..
T Consensus       101 TIRgdfa~~~~~  112 (135)
T COG0105         101 TIRGDFALSVGE  112 (135)
T ss_pred             EEEEEHHCCCCC
T ss_conf             276232014676


No 44 
>KOG2181 consensus
Probab=40.20  E-value=16  Score=17.00  Aligned_cols=128  Identities=16%  Similarity=0.186  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCE--EECCCCCCCCCCCCCCCCC--CCCCCCCHH--HHH--HHHHHHHHHHHHHHHHCCC
Q ss_conf             9999999864204567643220--1125754321376667886--222354024--659--9999999999999731398
Q gi|254780979|r  194 LTKLRSILRYLGTCDGNMEEGS--MRADVNVSVCRPGEAWGTR--CEVKNVNSI--RFL--GLAIEYEARRQIAILEDGG  265 (500)
Q Consensus       194 ~~~l~~ilr~~gisd~~meeGs--lR~DvNVSi~~~~~~~GtR--vEIKNlnS~--~~i--~~AI~yEi~RQ~~ll~~G~  265 (500)
                      +.+|+-+|++-   .+....||  +-||--.-|-.+|..+=|+  +|-|=+=.|  ..+  -|+-.+||+|..+++-+  
T Consensus       119 ~~eLyyvLkh~---ket~hn~s~~~dcdq~~~iTqhgkp~ft~VctegrL~lEF~fDd~MRIK~Wh~~ik~~rElvpr--  193 (415)
T KOG2181         119 MRELYYVLKHP---KETLHNGSQAYDCDQVLQITQHGKPSFTEVCTEGRLYLEFAFDDVMRIKAWHLEIKRSRELVPR--  193 (415)
T ss_pred             HHHHHHHHCCC---HHHHCCCCEEEECCCEEEEEECCCCCCEEEECCCEEEEEEEHHHHHHHHHEEEEEECCCCCCCH--
T ss_conf             24316555185---5553277356513533577534874013561365388874112455121103662201001404--


Q ss_pred             CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCH-HHHHHHHHHHCCCCHHHHHH
Q ss_conf             003443233755433665303566777783327787731269999999885302483-68988643202688999888
Q gi|254780979|r  266 HIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELP-DAKRERFIGEFGISLYDASV  342 (500)
Q Consensus       266 ~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP-~~~~~rl~~~yGLs~~dA~~  342 (500)
                      .|.|-|--||+.---      -+         --+++-.-++...++-++-..---| .+...|- +.|.||+.|.-.
T Consensus       194 sil~~~a~~dp~~ld------q~---------~kNitR~G~~nsTlNylrlcvILePMQelMSrh-KayalsPRdclK  255 (415)
T KOG2181         194 SILQNTADYDPEALD------QE---------QKNITRMGFFNSTLNYLRLCVILEPMQELMSRH-KAYALSPRDCLK  255 (415)
T ss_pred             HHHHCCCCCCHHHHC------HH---------HCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCHHHHHH
T ss_conf             565304798845637------45---------506632101110488999999875899998753-566788899999


No 45 
>cd03345 eu_TyrOH Eukaryotic tyrosine hydroxylase (TyrOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH) and eukaryotic tryptophan hydroxylase (TrpOH). TyrOH catalyzes the conversion of tyrosine to L-dihydroxyphenylalanine (L-DOPA), the rate-limiting step in the biosynthesis of the catecholamines dopamine, noradrenaline, and adrenaline.
Probab=39.92  E-value=21  Score=16.06  Aligned_cols=46  Identities=22%  Similarity=0.369  Sum_probs=34.1

Q ss_pred             CEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf             3366530356677778332778773126999999988530248368988643202688
Q gi|254780979|r  279 NETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGIS  336 (500)
Q Consensus       279 ~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs  336 (500)
                      -.|..+|..+.-   -|-||||+         +-++---+|.|-+.....|..++|+.
T Consensus       145 ~~TqyIRh~~~p---~YtpEPDi---------~Hel~GH~Plladp~fA~f~q~iG~a  190 (298)
T cd03345         145 QCTQYIRHASSP---MHSPEPDC---------CHELLGHVPMLADPTFAQFSQDIGLA  190 (298)
T ss_pred             CCEEEECCCCCC---CCCCCCCH---------HHHHHCCCCCCCCHHHHHHHHHHHHH
T ss_conf             530024267777---77899953---------66664456122798999999999998


No 46 
>PRK02107 glutamate--cysteine ligase; Provisional
Probab=39.49  E-value=26  Score=15.38  Aligned_cols=33  Identities=12%  Similarity=0.108  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHH
Q ss_conf             99999988863873147899999999817999889
Q gi|254780979|r  393 QLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKE  427 (500)
Q Consensus       393 ~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~  427 (500)
                      .+......+.+-..|-+  -.+|.+|.+.+.+-.+
T Consensus       430 Al~~~~~ki~dp~lTPS--ariL~em~~~g~sf~e  462 (523)
T PRK02107        430 ACDALRAKFDDPELTPS--ARVLRSMRENGQSFGG  462 (523)
T ss_pred             HHHHHHHHHCCCCCCHH--HHHHHHHHHCCCCHHH
T ss_conf             99999998449888948--9999999873998999


No 47 
>TIGR01083 nth endonuclease III; InterPro: IPR005759    The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases. Among these modified bases, 7,8-dihydro-8-oxoguanine (8-oxoG) is an important mutagenic lesion. Base excision repair is a critical mechanism for preventing mutations by removing the oxidative lesion from the DNA. Escherichia coli Nth protein (endonuclease III) has an 8-oxoG DNA glycosylase/AP lyase activity which removes 8-oxoG preferentially from 8-oxoG/G mispairs. Human hNTH1 protein, a homolog of E. coli Nth protein, has similar DNA glycosylase/AP lyase activity that removes 8-oxoG from 8-oxoG/G mispairs . ; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0006284 base-excision repair, 0005622 intracellular.
Probab=38.68  E-value=28  Score=15.16  Aligned_cols=24  Identities=25%  Similarity=0.410  Sum_probs=8.6

Q ss_pred             HHHHCCCEECCCHHHHHHHHHHHH
Q ss_conf             999639876189889999999999
Q gi|254780979|r  428 IVEELGLRQVTDLSAIEKVVDEVI  451 (500)
Q Consensus       428 iie~~gL~~isD~~eL~~iv~eVI  451 (500)
                      +.++.||..-.|..++|+-..+++
T Consensus       142 v~~Rlgl~~~~dp~~vE~~L~~l~  165 (192)
T TIGR01083       142 VSNRLGLSKGKDPDKVEEELLKLI  165 (192)
T ss_pred             HHHHHCCCCCCCHHHHHHHHHHHC
T ss_conf             543313577789899999998744


No 48 
>KOG2243 consensus
Probab=38.49  E-value=24  Score=15.62  Aligned_cols=27  Identities=22%  Similarity=0.349  Sum_probs=11.9

Q ss_pred             CCCCCCCHHHHHHH-----HHHHHHHHHHHHH
Q ss_conf             22235402465999-----9999999999973
Q gi|254780979|r  235 CEVKNVNSIRFLGL-----AIEYEARRQIAIL  261 (500)
Q Consensus       235 vEIKNlnS~~~i~~-----AI~yEi~RQ~~ll  261 (500)
                      +|.-=+.-++.+..     ...-+-.||+-+|
T Consensus      1824 ~ef~fvp~ikl~~tllimgif~~dd~k~il~l 1855 (5019)
T KOG2243        1824 TEFLFVPLIKLFGTLLIMGIFDDDDLKHILLL 1855 (5019)
T ss_pred             EEEEEEHHHHHHHHHHHEEECCCHHHHHHHHH
T ss_conf             47863049999988872310251668889996


No 49 
>PRK09849 putative oxidoreductase; Provisional
Probab=38.34  E-value=12  Score=17.75  Aligned_cols=14  Identities=7%  Similarity=0.040  Sum_probs=8.1

Q ss_pred             CCCC-CHHHHHHHHH
Q ss_conf             8737-8999999999
Q gi|254780979|r   67 LPIL-NGRCVQQAVM   80 (500)
Q Consensus        67 lP~l-N~~av~~ai~   80 (500)
                      +|+. +++.++...+
T Consensus       210 v~va~d~e~~~~~~~  224 (702)
T PRK09849        210 VNIAGDRQEMKRLND  224 (702)
T ss_pred             CCCCCCHHHHHHHHH
T ss_conf             767789999999999


No 50 
>PRK13979 DNA topoisomerase IV subunit A; Provisional,Validated
Probab=37.22  E-value=29  Score=15.00  Aligned_cols=37  Identities=19%  Similarity=0.392  Sum_probs=31.4

Q ss_pred             CHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             999999988530248368988643202688999888764
Q gi|254780979|r  307 DEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS  345 (500)
Q Consensus       307 s~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~  345 (500)
                      =++.|+-||++  ..|.+-+++|++.|+||+.+|+.++.
T Consensus       402 IDevI~iIR~S--~~~~~Ak~~L~~~f~lse~QA~AILd  438 (959)
T PRK13979        402 MDEIIKTIRAS--KSKKDASENLIEKFGFTDEQAEAILE  438 (959)
T ss_pred             HHHHHHHHHCC--CCHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             99999999818--98379999898761999999999999


No 51 
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=37.06  E-value=9.9  Score=18.46  Aligned_cols=55  Identities=22%  Similarity=0.273  Sum_probs=34.4

Q ss_pred             CCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             443233755433665303566777783327787731269999999885302483689886432026889998887641
Q gi|254780979|r  269 QETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSD  346 (500)
Q Consensus       269 qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~  346 (500)
                      ..|-+|=+..|.-.+.|+   +.-||+|++-|+--+.                   ...++ ..+|+|..++..+++.
T Consensus        15 ~~TlRyYe~~GLl~~~R~---~ngyR~Y~~~~l~~l~-------------------~I~~l-r~~G~sL~eI~~~l~~   69 (102)
T cd04789          15 RSTLLYYEKLGLITGTRN---ANGYRLYPDSDLQRLL-------------------LIQQL-QAGGLSLKECLACLQG   69 (102)
T ss_pred             HHHHHHHHHCCCCCCCCC---CCCCCCCCHHHHHHHH-------------------HHHHH-HHCCCCHHHHHHHHCC
T ss_conf             999999998699898819---9999506999999999-------------------99999-9979989999999859


No 52 
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper),  CadR (cadmium),  PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.98  E-value=15  Score=17.15  Aligned_cols=50  Identities=28%  Similarity=0.389  Sum_probs=26.2

Q ss_pred             CCCCCCCCEE-EEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             2337554336-6530356677778332778773126999999988530248368988643202688999888764
Q gi|254780979|r  272 RLFDPSKNET-RSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS  345 (500)
Q Consensus       272 R~~d~~~~~T-~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~  345 (500)
                      |.|+ ..|.- .+-|   ++..||||.+-|+.-+.       -            ..++ .+.|+|..++..++.
T Consensus        18 R~Ye-~~GLl~~~~R---~~~gyR~Y~~~~l~~l~-------~------------I~~l-r~~G~sL~eI~~ll~   68 (123)
T cd04770          18 RYYE-RIGLLPPPQR---SENGYRLYGEADLARLR-------F------------IRRA-QALGFSLAEIRELLS   68 (123)
T ss_pred             HHHH-HCCCCCCCEE---CCCCCEEEHHHHHHHHH-------H------------HHHH-HHCCCCHHHHHHHHH
T ss_conf             9999-8189875146---79995621377878899-------9------------9999-986999999999985


No 53 
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=36.66  E-value=14  Score=17.45  Aligned_cols=54  Identities=30%  Similarity=0.399  Sum_probs=32.5

Q ss_pred             CCCCCCCCCCCEEE-EEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             44323375543366-530356677778332778773126999999988530248368988643202688999888764
Q gi|254780979|r  269 QETRLFDPSKNETR-SLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS  345 (500)
Q Consensus       269 qETR~~d~~~~~T~-~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~  345 (500)
                      .+|-+|=+..|.-. +.|   ++..||+|++.|+.-+.       -|            .++ .++|+|..++..|+.
T Consensus        15 ~~tiRyYE~~GLl~~~~R---~~~gyR~Y~~~~v~rL~-------fI------------~~~-r~lGfsL~eI~~ll~   69 (140)
T PRK09514         15 PDTLRFYEKQGLMDPSVR---TESGYRLYTEQDLQRLR-------FI------------LRA-KQLGFTLEEIRELLS   69 (140)
T ss_pred             HHHHHHHHHCCCCCCCCC---CCCCEECCCCCHHHHHH-------HH------------HHH-HHCCCCHHHHHHHHH
T ss_conf             999999998699986511---89980206710999999-------99------------999-993999999999981


No 54 
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=35.39  E-value=31  Score=14.80  Aligned_cols=62  Identities=19%  Similarity=0.134  Sum_probs=32.7

Q ss_pred             EEEEEE--CCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCC-CCHH-HHHHH-HHHHHHHCCEECCCCEEECCCEECC
Q ss_conf             997888--68986555884246898765206130268988873-7899-99999-9987782976244201311321237
Q gi|254780979|r   29 EVHAQL--SVVSKLFSGASVNFGAEPNTQVSFFDAAMPGMLPI-LNGR-CVQQA-VMTGLGLNAHINKYSVFARKNYFYP  103 (500)
Q Consensus        29 EiH~qL--~t~tKlFc~c~~~~~~~pNt~v~~~~~g~PG~lP~-lN~~-av~~a-i~~~~al~~~i~~~~~fdRK~YfYp  103 (500)
                      -|++|+  ++..+-.|+++|---+-.            ..+.. -|.+ |-..+ +.+-.|+...|. ...|||--|-|.
T Consensus        26 hiyaQiIDD~~g~tl~saST~~k~~~------------~~~~~~~n~e~A~~vG~~ia~~a~~~gI~-~VvFDRggy~YH   92 (109)
T CHL00139         26 HIYAQIIDDTNGKTLVSCSTLDPDVK------------SNLSIGSTCDASKLVGQKLAKKSLKKGIT-KVVFDRGGKLYH   92 (109)
T ss_pred             EEEEEEEECCCCCEEEEEECCHHHHH------------HHHCCCCHHHHHHHHHHHHHHHHHHCCCC-EEEECCCCCCCH
T ss_conf             18999998799989999623367776------------55147866999999999999999987999-999858998422


No 55 
>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=35.31  E-value=26  Score=15.33  Aligned_cols=29  Identities=14%  Similarity=0.393  Sum_probs=20.0

Q ss_pred             CHHHHHHHHHHHHHHCHHHH--HHHH--CCCCC
Q ss_conf             98899999999998399989--9752--72132
Q gi|254780979|r  439 DLSAIEKVVDEVINSNPNNV--ARIA--TKPNL  467 (500)
Q Consensus       439 D~~eL~~iv~eVI~~np~~V--~~~k--gk~ka  467 (500)
                      +...++++++..+..+++.+  .+||  |.+.+
T Consensus       729 ~~~~~~~~~~~l~~~~~~g~~iQRYKGLGEMna  761 (818)
T TIGR01059       729 EINSLEEALDKLVELGRKGIEIQRYKGLGEMNA  761 (818)
T ss_pred             CCCCHHHHHHHHHHCCCCCCEEEEECCCCCCCH
T ss_conf             002589999999840789860454316666782


No 56 
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain  with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.  A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=35.28  E-value=10  Score=18.29  Aligned_cols=53  Identities=25%  Similarity=0.351  Sum_probs=34.3

Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             3233755433665303566777783327787731269999999885302483689886432026889998887641
Q gi|254780979|r  271 TRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSD  346 (500)
Q Consensus       271 TR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~  346 (500)
                      -|.|+ ..|.-.|.|+   ..-||+|.+-||.-+          +         ...+|..+.|+|..++..++..
T Consensus        18 LR~yE-~~GLl~P~R~---~~g~R~Ys~~di~~l----------~---------~I~~L~~~~G~sl~~I~~~L~l   70 (91)
T cd04766          18 LRLYE-RLGLLSPSRT---DGGTRRYSERDIERL----------R---------RIQRLTQELGVNLAGVKRILEL   70 (91)
T ss_pred             HHHHH-HCCCCCCCCC---CCCCEECCHHHHHHH----------H---------HHHHHHHHCCCCHHHHHHHHHH
T ss_conf             99999-8599798839---999974479999999----------9---------9999999869989999999980


No 57 
>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.
Probab=35.08  E-value=29  Score=15.06  Aligned_cols=14  Identities=14%  Similarity=0.352  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHHHCC
Q ss_conf             26589999997289
Q gi|254780979|r  468 VSWFVGQVMKNTGG  481 (500)
Q Consensus       468 ~gfLvGqVMK~tkG  481 (500)
                      +--+|+|.||+.||
T Consensus       262 ~Rr~is~tmk~ak~  275 (340)
T TIGR03575       262 LRRIISQTMREAKD  275 (340)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999999850


No 58 
>PRK05560 DNA gyrase subunit A; Validated
Probab=35.06  E-value=32  Score=14.76  Aligned_cols=76  Identities=16%  Similarity=0.341  Sum_probs=46.4

Q ss_pred             CCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHH--HHHHH--------HHHHH--------CCCCHHHH
Q ss_conf             12699999998853024836898864320268899988876411--36789--------88640--------24302457
Q gi|254780979|r  304 LEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDK--SIADY--------FEKLA--------VNRDKKIV  365 (500)
Q Consensus       304 i~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~--~la~~--------FE~v~--------~~~~pk~~  365 (500)
                      +..-++.|+-||++  .-|.+-++.|++.|+||+.+|+.++.=+  .|..+        ++++.        .-.+.+..
T Consensus       387 ~~~iDeVI~iIR~S--~~~~~Ak~~L~~~f~lse~QA~AIL~mrL~rLt~Le~~kl~~E~~eL~~~I~~l~~IL~s~~~l  464 (822)
T PRK05560        387 LDNIDEVIALIRAS--PTPAEAREGLMERYGLSEIQAQAILDMRLQRLTGLEREKIEDEYKELLAEIADLLDILASPERL  464 (822)
T ss_pred             HHCHHHHHHHHHCC--CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
T ss_conf             95879999999718--9878999989887588999999999989999876789999999999999999999886599999


Q ss_pred             HHHHHHHHHHHHHHCC
Q ss_conf             7776545788764338
Q gi|254780979|r  366 ANWVINDLLGVLNRSG  381 (500)
Q Consensus       366 Anwi~~el~~~ln~~~  381 (500)
                      .+.|..||....++-+
T Consensus       465 ~~iI~~EL~eik~kyg  480 (822)
T PRK05560        465 MEIIREELEEIKEKFG  480 (822)
T ss_pred             HHHHHHHHHHHHHHHC
T ss_conf             9999999999999829


No 59 
>COG2326 Uncharacterized conserved protein [Function unknown]
Probab=34.98  E-value=32  Score=14.75  Aligned_cols=30  Identities=23%  Similarity=0.241  Sum_probs=15.8

Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf             999997313980034432337554336653
Q gi|254780979|r  255 RRQIAILEDGGHIRQETRLFDPSKNETRSL  284 (500)
Q Consensus       255 ~RQ~~ll~~G~~v~qETR~~d~~~~~T~~m  284 (500)
                      .|=+.-+-.+|+|.==-|.|=..-|++..|
T Consensus       122 qRy~~~lPa~GeiviFdRSwYnr~gVeRVm  151 (270)
T COG2326         122 QRYVAHLPAAGEIVIFDRSWYNRAGVERVM  151 (270)
T ss_pred             HHHHHHCCCCCEEEEECHHHCCCCCEEECC
T ss_conf             999986788873898651221332714402


No 60 
>TIGR00676 fadh2 5,10-methylenetetrahydrofolate reductase; InterPro: IPR004620 The enzyme activities methylenetetrahydrofolate reductase (1.5.1.20 from EC) and 5,10-methylenetetrahydrofolate reductase (FADH) (1.7.99.5 from EC) differ in that the former (assigned in many eukaryotes) is defined to use NADP+ as an acceptor, while the latter (assigned in many bacteria) is flexible with respect to the acceptor. Both convert 5-methyltetrahydrofolate to 5,10-methylenetetrahydrofolate. From a larger set of proteins assigned as one or the other, this family describes the subset of proteins found in bacteria, and currently designated 5,10-methylenetetrahydrofolate reductase. This protein is an FAD-containing flavoprotein.; GO: 0009086 methionine biosynthetic process.
Probab=34.95  E-value=24  Score=15.59  Aligned_cols=18  Identities=28%  Similarity=0.348  Sum_probs=7.5

Q ss_pred             HHHHHCCCCCCCCCCEEECCCC
Q ss_conf             9864204567643220112575
Q gi|254780979|r  200 ILRYLGTCDGNMEEGSMRADVN  221 (500)
Q Consensus       200 ilr~~gisd~~meeGslR~DvN  221 (500)
                      -++.+||.+= |   .||-|.-
T Consensus        96 ~y~~~Gi~~i-l---ALRGD~p  113 (302)
T TIGR00676        96 EYRELGIRNI-L---ALRGDPP  113 (302)
T ss_pred             HHHHCCCCEE-E---EECCCCC
T ss_conf             9987488679-8---7437688


No 61 
>pfam11181 YflT Heat induced stress protein YflT. YflT is a heat induced protein.
Probab=34.92  E-value=32  Score=14.75  Aligned_cols=45  Identities=16%  Similarity=0.208  Sum_probs=31.6

Q ss_pred             CCCCCCCC-HHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             87731269-99999988530248368988643202688999888764
Q gi|254780979|r  300 DLLPLEID-EDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS  345 (500)
Q Consensus       300 DLPpi~is-~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~  345 (500)
                      |--++.++ ..|++.++.....--++.+.++ .+|||+++.|..+-.
T Consensus        47 ~~~~~~~~e~g~~~~v~n~F~~~gDElr~~l-~~lGl~~~ea~~ye~   92 (103)
T pfam11181        47 DTNTIGAKEQGLGDSVMNTFRKKGDELRNKM-SELGLSDDEAEQYEE   92 (103)
T ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCHHHHHHH-HHCCCCHHHHHHHHH
T ss_conf             8763455447589999998655758889999-985999999999999


No 62 
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=34.38  E-value=9.7  Score=18.52  Aligned_cols=56  Identities=18%  Similarity=0.151  Sum_probs=34.5

Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             0344323375543366530356677778332778773126999999988530248368988643202688999888764
Q gi|254780979|r  267 IRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS  345 (500)
Q Consensus       267 v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~  345 (500)
                      |.-.|-+|=+..|.-.+.|+   ..-||+|++.||--+.       -            ..++ .+.|+|.+++..|+.
T Consensus        13 vs~~tiRyYE~~GLl~p~R~---~~gyR~Y~~~~l~rl~-------~------------I~~~-r~lGfsL~eI~~lL~   68 (139)
T cd01110          13 VAVSALHFYEQKGLIASWRN---AGNQRRYPRDVLRRIA-------F------------IKVA-QRLGLSLAEIAEALA   68 (139)
T ss_pred             CCHHHHHHHHHCCCCCCCCC---CCCCCEECHHHHHHHH-------H------------HHHH-HHCCCCHHHHHHHHH
T ss_conf             78899999998788466678---9887704989999999-------9------------9999-985998999999998


No 63 
>COG4050 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.29  E-value=32  Score=14.68  Aligned_cols=38  Identities=32%  Similarity=0.538  Sum_probs=30.5

Q ss_pred             EEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             86615786125763036527789999999999999864204
Q gi|254780979|r  166 IDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGT  206 (500)
Q Consensus       166 vD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gi  206 (500)
                      +-.-|-|+|.+|.-- |  +|-|||+.|+.++...|..+-.
T Consensus       112 ylvR~k~iPiLelkY-P--~s~Eea~~~VnkI~~FL~sLe~  149 (152)
T COG4050         112 YLVRRKGIPILELKY-P--RSEEEAIDFVNKIANFLKSLEA  149 (152)
T ss_pred             HHHHHCCCCEEEEEC-C--CCHHHHHHHHHHHHHHHHHHHH
T ss_conf             876426984388757-8--8679999999999999986666


No 64 
>pfam11950 DUF3467 Protein of unknown function (DUF3467). This family of proteins are functionally uncharacterized. This protein is found in bacteria, archaea and viruses. Proteins in this family are typically between 101 to 118 amino acids in length.
Probab=34.20  E-value=32  Score=14.67  Aligned_cols=58  Identities=17%  Similarity=0.208  Sum_probs=38.6

Q ss_pred             EEEEEECCCCCCCC------CCCCCEEEEECCC--CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             66652023100115------6787148866157--86125763036527789999999999999864
Q gi|254780979|r  145 RIHLEQDAGKSIHD------QYSAVSCIDLNRS--GVALMEIVTKPDMRSSLEAKAFLTKLRSILRY  203 (500)
Q Consensus       145 ~i~lEED~gk~~h~------~~~~~slvD~NRa--GvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~  203 (500)
                      +|.+.+|.++.++.      .+...-.+||.+.  |+|=..+. .-.+.||..|+.++..|+.-+.-
T Consensus        15 ~iel~~~~~~g~YsN~~~v~~S~~Ef~idF~~~~pg~~~~~v~-sRVilsP~hAKrL~~aL~~ni~~   80 (90)
T pfam11950        15 NIELDEDNARGTYSNLAQVSHSPEEFILDFLWLMPGEPEAKVK-SRVILSPQHAKRLLAALQNNIKK   80 (90)
T ss_pred             EEECCHHHHEEEEEEEEEECCCCHHEEEEEEECCCCCCCCCEE-EEEEECHHHHHHHHHHHHHHHHH
T ss_conf             7880856701564216896268216468713027999866269-99982999999999999999999


No 65 
>cd03347 eu_PheOH Eukaryotic phenylalanine-4-hydroxylase (eu_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic phenylalanine-4-hydroxylase (pro_PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH).  PheOH catalyzes the first and rate-limiting step in the metabolism of the amino acid L-phenylalanine (L-Phe), the hydroxylation of L-Phe to L-tyrosine (L-Tyr). It uses (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) as the physiological electron donor. The catalytic activity of the tetrameric enzyme is tightly regulated by the binding of L-Phe and BH4 as well as by phosphorylation. Mutations in the human enzyme are linked to a severe variant of phenylketonuria.
Probab=32.84  E-value=33  Score=14.60  Aligned_cols=109  Identities=19%  Similarity=0.285  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             89999999999999864204567643220112575432137666788622235402465999999999999997313980
Q gi|254780979|r  187 SLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDGGH  266 (500)
Q Consensus       187 ~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G~~  266 (500)
                      -.-+++|+..+..+-+++|...-++  -+++ |||-=+++. +.|-- .-+-++=|.|.--..           |.    
T Consensus        82 ~~Ac~ey~~~~~~l~~~~g~~~d~I--PQl~-dvs~~L~~~-TGf~l-~pv~Glls~rdF~~~-----------LA----  141 (306)
T cd03347          82 THACYEYNHVFPLLEKNCGFSEDNI--PQLE-DVSNFLQTC-TGFRL-RPVAGLLSSRDFLAG-----------LA----  141 (306)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCC--CCHH-HHHHHHHHH-HCCEE-EECCCCCCHHHHHHH-----------HH----
T ss_conf             7778999999999999549998889--9769-999998862-09889-743664788999999-----------74----


Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             034432337554336653035667777833277877312699999998853024836898864320268
Q gi|254780979|r  267 IRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI  335 (500)
Q Consensus       267 v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL  335 (500)
                          -|.|    -.|..+|..+.-   -|-||||+         +-++---+|.|-+.....|..++|+
T Consensus       142 ----~rvF----~~TqyiRh~~~p---~YtpEPDi---------~He~~GH~p~ladp~fA~f~q~iG~  190 (306)
T cd03347         142 ----FRVF----HSTQYIRHPSKP---MYTPEPDI---------CHELLGHVPLFADPSFAQFSQEIGL  190 (306)
T ss_pred             ----CCCC----CCEEEECCCCCC---CCCCCCCH---------HHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             ----1835----410134267777---77899962---------6566445744478889999999999


No 66 
>KOG4168 consensus
Probab=32.48  E-value=34  Score=14.47  Aligned_cols=80  Identities=18%  Similarity=0.176  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCEECCCHHHHHHHHH
Q ss_conf             65457887643387400064898999999988863873147899999999817999889999639876189889999999
Q gi|254780979|r  369 VINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVD  448 (500)
Q Consensus       369 i~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~  448 (500)
                      +.-++..+|+...-   -+..+.+.|.+++.....++++..-+++++..--.+-....-+|++-.= ...|++.|+++|.
T Consensus        50 i~~et~kYls~~~n---~~~qt~E~i~el~~k~~~fkLtKAE~LqiiN~rPss~vel~~~iE~~ee-Rf~~ee~i~elv~  125 (149)
T KOG4168          50 ITYETLKYLSDNKN---ASTQTNESIIELITKLKSFKLTKAEILQIINLRPSSSVELYLIIEEVEE-RFQDEEDIEELVE  125 (149)
T ss_pred             HHHHHHHHHHCCCC---CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHH-HCCCHHCHHHHHH
T ss_conf             69999999844733---2313688999999986232203899998850286148999999988887-3003105999987


Q ss_pred             HHHH
Q ss_conf             9998
Q gi|254780979|r  449 EVIN  452 (500)
Q Consensus       449 eVI~  452 (500)
                      .|-.
T Consensus       126 ~i~~  129 (149)
T KOG4168         126 TISK  129 (149)
T ss_pred             HCCC
T ss_conf             6015


No 67 
>COG5418 Predicted secreted protein [Function unknown]
Probab=32.42  E-value=18  Score=16.59  Aligned_cols=16  Identities=31%  Similarity=0.546  Sum_probs=9.8

Q ss_pred             CCCCCCCCCCCCCCCC
Q ss_conf             3767888201445442
Q gi|254780979|r  102 YPDLPQGYQISQHDKP  117 (500)
Q Consensus       102 YpDlpkgyQiTQ~~~P  117 (500)
                      -|.|||||||-|+--|
T Consensus        38 l~~npk~~~IiqlPCP   53 (164)
T COG5418          38 LPSNPKDWNIIQLPCP   53 (164)
T ss_pred             HCCCCCCCCEEECCCC
T ss_conf             4059777855762583


No 68 
>cd05298 GH4_GlvA_pagL_like Glycoside Hydrolases Family 4; GlvA- and pagL-like glycosidases. Bacillus subtilis GlvA and Clostridium acetobutylicum pagL are 6-phospho-alpha-glucosidase, catalyzing the hydrolysis of alpha-glucopyranoside bonds to release glucose from oligosaccharides. The substrate specificities of other members of this subgroup are unknown. Some bacteria simultaneously translocate and phosphorylate disaccharides via the phosphoenolpyruvate-dependent phosphotransferase system (PEP_PTS).  After translocation, these phospho-disaccharides may be hydrolyzed by the GH4 glycoside hydrolases, which include 6-phospho-beta-glucosidases, 6-phospho-alpha-glucosidases, alpha-glucosidases/alpha-glucuronidases (only from Thermotoga), and alpha-galactosidases. Members of this subfamily are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductas
Probab=32.31  E-value=34  Score=14.56  Aligned_cols=86  Identities=15%  Similarity=0.231  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCC-EECCCHHHHHHHH
Q ss_conf             654578876433874000648989999999888638731478999999998179998899996398-7618988999999
Q gi|254780979|r  369 VINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGL-RQVTDLSAIEKVV  447 (500)
Q Consensus       369 i~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL-~~isD~~eL~~iv  447 (500)
                      .+.|+...+++.|.......--|.+++.|+.....-      -+-.++..++  +|.+.+....-+ -.+.+.+..++++
T Consensus       351 ~vVEvp~~Vd~~Gi~P~~vg~lP~~~~~L~~~~~~~------e~LtveAal~--g~~~~a~~Al~~dPlv~s~~~a~~l~  422 (437)
T cd05298         351 AMVEVPAYIGSNGPEPLVVGKIPTFYKGLMEQQVAY------EKLLVEAYLE--GSYQKALQAFTLNRTVPSAKVAKEVL  422 (437)
T ss_pred             CEEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHH------HHHHHHHHHH--CCHHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf             679988897699853141698998999999999999------9999999996--89999999997298999989999999


Q ss_pred             HHHHHHCHHHHHHHH
Q ss_conf             999983999899752
Q gi|254780979|r  448 DEVINSNPNNVARIA  462 (500)
Q Consensus       448 ~eVI~~np~~V~~~k  462 (500)
                      ++.|++|.+-.-+||
T Consensus       423 deml~a~~~~LP~fk  437 (437)
T cd05298         423 DDLIEANKGYWPELK  437 (437)
T ss_pred             HHHHHHHHHHCCCCC
T ss_conf             999999787665669


No 69 
>COG3495 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.05  E-value=17  Score=16.76  Aligned_cols=29  Identities=21%  Similarity=0.374  Sum_probs=24.3

Q ss_pred             EECCCCCCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf             12376788820144544201533899970
Q gi|254780979|r  100 YFYPDLPQGYQISQHDKPIVGEGKVSVSI  128 (500)
Q Consensus       100 YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~  128 (500)
                      -.|---|||||+++.+.|+...|.+.++.
T Consensus       113 IV~Vk~~kg~km~elyqp~wV~GtlK~e~  141 (166)
T COG3495         113 IVLVKPAKGYKMSELYQPVWVTGTLKPEI  141 (166)
T ss_pred             EEEEECCCCCCHHHHHCEEEEEEEECHHH
T ss_conf             89985698861767302147863202102


No 70 
>TIGR00034 aroFGH phospho-2-dehydro-3-deoxyheptonate aldolase; InterPro: IPR006219   Members of this group catalyze the first enzymatic reaction of the shikimate pathway. The common (shikimate) pathway links metabolism of carbohydrates to biosynthesis of aromatic amino acids phenylalanine, tyrosine, tryptophan, and derivatives in microorganisms and in plants. In a sequence of seven enzymatic reactions, D-erythrose 4-phosphate (E4P), an intermediate of the pentose phosphate pathway, and phosphoenol pyruvate (PEP), a glycolytic intermediate, are converted to chorismate. The pathway begins with the stereospecific condensation of E4P and PEP to yield 7-phospho 2-dehydro 3-deoxy-D-arabino-heptulosonate (DAHP), catalyzed by 3-deoxy-7-phosphoheptulonate synthase (DAHPS) (EC 2.5.1.54, formerly EC 4.1.2.15). The divalent metal cation requirement of this enzyme can be satisfied by a broad range of metals . A Cys residue in a Cys-X-X-His motif has been identified as part of a metal binding site . In Escherichia coli, the enzyme exists in three isoforms, each specifically inhibited by one of the three aromatic amino acids.   DAHP synthetases fall into two classes, class I (represented by this entry) and class II (represented by PIRSF015573 from PIRSF). Class I was believed to be limited to microorganisms and class II to plants. However, a more recent study showed that class II also contains enzymes from a microbial eukaryote and several bacteria . Brick and Woodard  proposed that the difference between the two classes lies in their metal ion requirement for activity. Whereas class I requires no metal cation, class II is dependent on a metal cation for activity. However, recently a class I DAHP synthase from Thermotoga maritima has been purified, characterised, and shown to be a metalloenzyme .   The three-dimentional structures of DAHP synthases have been determined , , , , . The DAHPS(Phe) monomer is a (beta/alpha)8 barrel with an additional N-terminal beta strand and helices and an extra beta sheet near the C terminus . The active site is located in a cleft at the carboxyl end of the barrel . The allosteric feedback inhibition binding site of DAHPS(Phe) is composed of residues from two adjacent subunits of a tight dimer and is at least 20 angstroms away from the closest active site .   The absence of the shikimate pathway in animals makes it an attractive target for nontoxic herbicidal, antimicrobial, and antifungal agents. The nontoxic herbicide glyphosphate competitively inhibits 3-phosphoshikimate 1-carboxyvinyltransferase, the sixth enzymatic reaction of the pathway.; GO: 0003849 3-deoxy-7-phosphoheptulonate synthase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=31.80  E-value=35  Score=14.40  Aligned_cols=72  Identities=21%  Similarity=0.330  Sum_probs=38.0

Q ss_pred             EEECCC-CCCHHHHHHHHHHHHHHHHHH----------------------C-CCCCCCCCCEEECCCCCCCCCC-----C
Q ss_conf             630365-277899999999999998642----------------------0-4567643220112575432137-----6
Q gi|254780979|r  178 IVTKPD-MRSSLEAKAFLTKLRSILRYL----------------------G-TCDGNMEEGSMRADVNVSVCRP-----G  228 (500)
Q Consensus       178 IVT~Pd-~~s~~ea~~~~~~l~~ilr~~----------------------g-isd~~meeGslR~DvNVSi~~~-----~  228 (500)
                      +|-.|| +|+|+-|.+|+..|..|-.-+                      | |+|..| .||+|..-=.-|.++     .
T Consensus        54 VViGPCSiHDP~AA~eYA~RL~~L~~~l~~~L~IvMRvYfEKPRTtVGWKGLINDP~l-n~sf~in~GL~iARkLL~~~~  132 (348)
T TIGR00034        54 VVIGPCSIHDPEAAIEYATRLKKLREKLKDDLEIVMRVYFEKPRTTVGWKGLINDPDL-NGSFRINKGLRIARKLLLDLN  132 (348)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCCCC-CCCCCHHHHHHHHHHHHHHHH
T ss_conf             9975888574689999999999999875037607876431698701034444588888-885220256899999998886


Q ss_pred             -CCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             -6678862223540246599999
Q gi|254780979|r  229 -EAWGTRCEVKNVNSIRFLGLAI  250 (500)
Q Consensus       229 -~~~GtRvEIKNlnS~~~i~~AI  250 (500)
                       -.+-.-+|.=-++|=-++.+.+
T Consensus       133 ~~GlP~a~EfLD~~sPQylADl~  155 (348)
T TIGR00034       133 NLGLPIAGEFLDMISPQYLADLV  155 (348)
T ss_pred             HCCCCCCCCCCCCCCHHHHHHHH
T ss_conf             31576344312466637899999


No 71 
>cd01199 INT_Tn1545_C Tn1545-related conjugative transposon integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes bacterial (gram positive) and phage integrases, including those similar to Tn1545, Tn5252, and Tn5276 conjugative transposon integrases and Lactobacillus phage phi adh integrase.
Probab=31.63  E-value=36  Score=14.38  Aligned_cols=40  Identities=23%  Similarity=0.170  Sum_probs=17.8

Q ss_pred             CCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             5676432201125754321376667886222354024659
Q gi|254780979|r  207 CDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFL  246 (500)
Q Consensus       207 sd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i  246 (500)
                      +|-+++++.++++-++.-.......+.+...|+-+|.|.|
T Consensus        46 ~did~~~~~i~i~~~~~~~~~~~~~~~~~~~Kt~~~~R~v   85 (205)
T cd01199          46 KDIDFENKLINIDGTLDSHTGKEENGYKDTPKTKSSIRTI   85 (205)
T ss_pred             HHCCCCCCEEEEEEEEEEECCCCCCCEECCCCCCCCEEEE
T ss_conf             8806558989997788641256666243457788863686


No 72 
>PRK11814 cysteine desulfurase activator complex subunit SufB; Provisional
Probab=31.03  E-value=35  Score=14.46  Aligned_cols=38  Identities=18%  Similarity=0.181  Sum_probs=22.4

Q ss_pred             HCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             302483689886432026889998887641136789886
Q gi|254780979|r  317 QIPELPDAKRERFIGEFGISLYDASVLVSDKSIADYFEK  355 (500)
Q Consensus       317 ~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~  355 (500)
                      +...+-.+..--|++ =||++++|..|+-..-+...+++
T Consensus       425 tvg~I~eeqlfYLmS-RGl~e~eA~~lIV~GF~~~v~~~  462 (484)
T PRK11814        425 TTSKISEDQLFYCRQ-RGISEEDAVSMIVNGFCKDVFQE  462 (484)
T ss_pred             ECCCCCHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             445679899999986-79999999999999978999876


No 73 
>PRK06740 histidinol-phosphatase; Validated
Probab=30.78  E-value=34  Score=14.53  Aligned_cols=47  Identities=11%  Similarity=0.188  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHCCCCHHHHH---HHHHHHCCCCHHHHHHHHHHHH----HHHHHHHHH
Q ss_conf             9999998853024836898---8643202688999888764113----678988640
Q gi|254780979|r  308 EDFIRAIKKQIPELPDAKR---ERFIGEFGISLYDASVLVSDKS----IADYFEKLA  357 (500)
Q Consensus       308 ~e~i~~i~~~lPelP~~~~---~rl~~~yGLs~~dA~~L~~~~~----la~~FE~v~  357 (500)
                      ++.+.++-+.   -|++..   --|+..||+.......--....    ..+||+.+.
T Consensus       155 E~~l~~lL~~---YpfDYvIGSVHFl~gWgFDnPe~~~~~~~~Dl~~iy~~YF~~ve  208 (338)
T PRK06740        155 EQELQSLLAL---GDFDYVIGSVHFLNGWGFDNPDTKEYFEEHDLYALYDTFFKTVE  208 (338)
T ss_pred             HHHHHHHHHC---CCCCEEEEEEEEECCCCCCCHHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf             9999999744---99755998888607878889789988850899999999999999


No 74 
>TIGR02614 ftsW cell division protein FtsW; InterPro: IPR013437    FtsW is an integral membrane protein with ten transmembrane segments . In general, it is one of two paralogs involved in peptidoglycan biosynthesis, the other being RodA, and is essential for cell division. The FtsW designation is not used in endospore-forming bacteria (e.g. Bacillus subtilis), where these proteins are designated SpoVE, and three or more RodA/FtsW/SpoVE family paralogs are present. SpoVE acts in spore cortex formation and is dispensable for growth. Biological roles for FtsW in cell division include recruitment of penicillin-binding protein 3 to the division site.; GO: 0009252 peptidoglycan biosynthetic process, 0051301 cell division, 0016021 integral to membrane.
Probab=30.28  E-value=15  Score=17.15  Aligned_cols=32  Identities=25%  Similarity=0.398  Sum_probs=25.9

Q ss_pred             CEECCCC-------CCCCCCCCCCCCCCCCEEEEEECCC
Q ss_conf             2123767-------8882014454420153389997067
Q gi|254780979|r   99 NYFYPDL-------PQGYQISQHDKPIVGEGKVSVSIGP  130 (500)
Q Consensus        99 ~YfYpDl-------pkgyQiTQ~~~Pi~~~G~l~~~~~~  130 (500)
                      .|..|+.       -+|||+||--..++++|..=...|.
T Consensus       214 ~Fl~P~~Dp~~~~~g~gyQl~qsl~A~g~GG~~G~GLG~  252 (370)
T TIGR02614       214 SFLDPWADPFLADQGSGYQLTQSLIALGRGGLFGVGLGN  252 (370)
T ss_pred             HHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEECCCC
T ss_conf             873777664010478960499999998679856741687


No 75 
>KOG2050 consensus
Probab=30.09  E-value=38  Score=14.20  Aligned_cols=13  Identities=15%  Similarity=0.506  Sum_probs=6.4

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             7783327787731
Q gi|254780979|r  292 DYRYFSEPDLLPL  304 (500)
Q Consensus       292 DYRyfPEPDLPpi  304 (500)
                      .|+-|-|.|.+.+
T Consensus       275 efqlfK~sn~~Tl  287 (652)
T KOG2050         275 EFQLFKDSNDKTL  287 (652)
T ss_pred             HHHHHHCCCCCCH
T ss_conf             9898761685519


No 76 
>CHL00085 ycf24 putative ABC transporter
Probab=30.08  E-value=23  Score=15.81  Aligned_cols=36  Identities=17%  Similarity=0.265  Sum_probs=22.0

Q ss_pred             HCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             30248368988643202688999888764113678988640
Q gi|254780979|r  317 QIPELPDAKRERFIGEFGISLYDASVLVSDKSIADYFEKLA  357 (500)
Q Consensus       317 ~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~  357 (500)
                      +...+-.+..--|++ =||++++|..|+-..    |++.+.
T Consensus       426 tvgkI~eeqlfYLmS-RGl~e~eA~~lIV~G----F~~~v~  461 (485)
T CHL00085        426 STSKIGEEQIFYFLQ-RGINLEEAISLMISG----FCQDVF  461 (485)
T ss_pred             ECCCCCHHHHHHHHH-CCCCHHHHHHHHHHH----HHHHHH
T ss_conf             435679999999986-699999999999998----479888


No 77 
>KOG0823 consensus
Probab=29.99  E-value=12  Score=17.95  Aligned_cols=46  Identities=15%  Similarity=0.239  Sum_probs=28.1

Q ss_pred             CCCCCEEEEEEEEEE-ECCC-CCCCC-CCCCCC-CCCCCCCCCHHHCCCC
Q ss_conf             478033898999788-8689-86555-884246-8987652061302689
Q gi|254780979|r   19 TGDWEVVIGIEVHAQ-LSVV-SKLFS-GASVNF-GAEPNTQVSFFDAAMP   64 (500)
Q Consensus        19 ~~~~e~vIGLEiH~q-L~t~-tKlFc-~c~~~~-~~~pNt~v~~~~~g~P   64 (500)
                      -++|+-=|-||.-.. .-|- --||| +|-..+ ..-+|+..||||-+--
T Consensus        45 ~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~V   94 (230)
T KOG0823          45 GGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEV   94 (230)
T ss_pred             CCCEEEEEECCCCCCCEEEECCCCEEHHHHHHHHHHCCCCEECCCCCCCC
T ss_conf             88222365312357877741454303488888776347870488624323


No 78 
>KOG3591 consensus
Probab=29.55  E-value=38  Score=14.13  Aligned_cols=24  Identities=13%  Similarity=0.364  Sum_probs=17.3

Q ss_pred             CCCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf             788820144544201533899970
Q gi|254780979|r  105 LPQGYQISQHDKPIVGEGKVSVSI  128 (500)
Q Consensus       105 lpkgyQiTQ~~~Pi~~~G~l~~~~  128 (500)
                      ||+||-.++-.--+..+|.|.|..
T Consensus       123 LP~~vdp~~V~S~LS~dGvLtI~a  146 (173)
T KOG3591         123 LPEDVDPTSVTSTLSSDGVLTIEA  146 (173)
T ss_pred             CCCCCCHHHEEEEECCCCEEEEEC
T ss_conf             999989506278637994089973


No 79 
>PRK02471 bifunctional glutamate--cysteine ligase/glutathione synthetase; Provisional
Probab=29.31  E-value=39  Score=14.11  Aligned_cols=41  Identities=10%  Similarity=0.170  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCC
Q ss_conf             457777654578876433874000648989999999888638731
Q gi|254780979|r  363 KIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTIS  407 (500)
Q Consensus       363 k~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is  407 (500)
                      +..|.+++.++...++.-+.+-.    -.+-+.++...+.+-+.|
T Consensus       349 ~~~a~~il~~l~~~~~~l~l~~~----y~~~~~~~~~~v~~P~~T  389 (753)
T PRK02471        349 AAEGELILDAMEDFVQHLGLPDE----FQDLIEQLKEQVTDPKKT  389 (753)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCHH----HHHHHHHHHHHHHCCCCC
T ss_conf             78999999999999997199889----999999999987391139


No 80 
>pfam07028 DUF1319 Protein of unknown function (DUF1319). This family contains a number of viral proteins of unknown function approximately 200 residues long. Family members seem to be restricted to badnaviruses.
Probab=28.87  E-value=33  Score=14.63  Aligned_cols=20  Identities=20%  Similarity=0.406  Sum_probs=12.1

Q ss_pred             HHHHHHHHHHHHHHCHHHHHH
Q ss_conf             889999999999839998997
Q gi|254780979|r  440 LSAIEKVVDEVINSNPNNVAR  460 (500)
Q Consensus       440 ~~eL~~iv~eVI~~np~~V~~  460 (500)
                      ..+++++|.+ |++.|+.|++
T Consensus        84 k~dV~eLV~~-IseQPK~IEq  103 (119)
T pfam07028        84 KEDVEELVLR-ISEQPKLIEK  103 (119)
T ss_pred             HHHHHHHHHH-HHHCCHHHHH
T ss_conf             8999999999-9868588999


No 81 
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=28.63  E-value=12  Score=17.88  Aligned_cols=57  Identities=21%  Similarity=0.278  Sum_probs=38.5

Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             03443233755433665303566777783327787731269999999885302483689886432026889998887641
Q gi|254780979|r  267 IRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSD  346 (500)
Q Consensus       267 v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~  346 (500)
                      |...|-+|=+..|.-.+-|.    .-||+|.+-|+          +.++         ..+||+++.|++...+..|++=
T Consensus        13 v~~~TLR~YEr~GLi~P~R~----~G~RlYs~~Di----------~rLr---------fIkrL~~e~G~nlagI~~iLsl   69 (120)
T cd04767          13 IHPETLRIWERHGLIKPARR----NGQRLYSNNDL----------KRLR---------FIKKLINEKGLNIAGVKQILSM   69 (120)
T ss_pred             CCHHHHHHHHHCCCCCCCCC----CCCCCCCHHHH----------HHHH---------HHHHHHHHCCCCHHHHHHHHHC
T ss_conf             68899999998589688888----98227799999----------9999---------9999999759689999999806


No 82 
>TIGR00954 3a01203 Peroxysomal long chain fatty acyl transporter; InterPro: IPR005283   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     The members of this family are integral membrane proteins and they are involved in the import of activated long-chain fatty acids from the cytosol to the peroxisomal matrix. ; GO: 0005524 ATP binding, 0006810 transport, 0016021 integral to membrane.
Probab=28.51  E-value=40  Score=14.01  Aligned_cols=73  Identities=15%  Similarity=0.252  Sum_probs=46.4

Q ss_pred             CCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             43366530356677778332778773126999999988530248368988643202688999888764113678988
Q gi|254780979|r  278 KNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDKSIADYFE  354 (500)
Q Consensus       278 ~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE  354 (500)
                      .......++|+...  ++|==|==|-+-.-..+=+.|=  =|..+++..+||-++||+++.|=..++..-.|.+..+
T Consensus       592 sklimG~Lt~P~~~--~lFY~PQRPYM~~G~TLRDQiI--YPDs~~d~~~ryhndyG~sD~dL~~iL~~V~L~~iL~  664 (788)
T TIGR00954       592 SKLIMGRLTKPAKG--KLFYVPQRPYMTLGSTLRDQII--YPDSSEDMKRRYHNDYGLSDKDLEQILDNVQLEHILE  664 (788)
T ss_pred             CEEECCEECCCCCC--CEEECCCCCCCCCCCCCCCCCC--CCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCHHHHHH
T ss_conf             20344410558888--7641357764588885334103--5889799998630258998899999975413223422


No 83 
>TIGR01204 bioW 6-carboxyhexanoate--CoA ligase; InterPro: IPR005499 This family contains the enzyme 6-carboxyhexanoate--CoA ligase 6.2.1.14 from EC. This enzyme is involved in the first step of biotin synthesis, where it converts pimelate into pimeloyl-CoA . The enzyme requires magnesium as a cofactor and forms a homodimer .; GO: 0009102 biotin biosynthetic process.
Probab=28.41  E-value=40  Score=14.00  Aligned_cols=49  Identities=20%  Similarity=0.321  Sum_probs=26.8

Q ss_pred             EEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             8423666520231001156787148866157861257630365277899999999999998642045
Q gi|254780979|r  141 VGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTC  207 (500)
Q Consensus       141 v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gis  207 (500)
                      ..-.+|++|+=.+-+|         +-+     |=++|.|- ++.|||+|..++.   .+|..-|||
T Consensus        38 ~DF~qi~vEkv~~~~i---------~~~-----~PL~i~T~-~~~spEea~k~Ar---~~Lt~eGv~   86 (238)
T TIGR01204        38 ADFMQIKVEKVKDEEI---------VKI-----NPLKISTI-EVSSPEEARKLAR---KLLTKEGVS   86 (238)
T ss_pred             CCEEEEEEEEEECCEE---------EEE-----CCCEEEEE-ECCCHHHHHHHHH---HHHHHCCCH
T ss_conf             6535678998707566---------752-----48612331-0158467899999---876514742


No 84 
>KOG3666 consensus
Probab=28.37  E-value=40  Score=13.99  Aligned_cols=46  Identities=24%  Similarity=0.366  Sum_probs=18.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHH
Q ss_conf             33277877312699999998853024836898864320268899988
Q gi|254780979|r  295 YFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDAS  341 (500)
Q Consensus       295 yfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~  341 (500)
                      ..|=|+.||+..|..+|.++-.++-...+-+..+|.. ...+=+|.+
T Consensus       790 ~ipip~f~p~d~s~~fIgrL~~eilriTdPK~t~F~d-~~~tWyd~K  835 (1141)
T KOG3666         790 HIPIPKFTPVDESVTFIGRLCREILRITDPKMTCFID-QLNTWYDMK  835 (1141)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHH-HHHHHHHHH
T ss_conf             5678889998815679999999888238823678887-441488787


No 85 
>pfam00351 Biopterin_H Biopterin-dependent aromatic amino acid hydroxylase. This family includes phenylalanine-4-hydroxylase, the phenylketonuria disease protein.
Probab=28.30  E-value=40  Score=14.02  Aligned_cols=111  Identities=22%  Similarity=0.334  Sum_probs=57.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             77899999999999998642045676432201125754321376667886222354024659999999999999973139
Q gi|254780979|r  185 RSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDG  264 (500)
Q Consensus       185 ~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G  264 (500)
                      ..-.-+++|+..+..+-+++|...-++  -+++ |||-=+++. +.|.- .=+-++=|.|.--..           |.  
T Consensus        80 ~~~~AC~eyl~~~~~L~~~~g~~~d~I--PQL~-dvs~~L~~~-TGf~l-rpv~Glls~rdFl~~-----------LA--  141 (309)
T pfam00351        80 YPTHACREYLHAFPLLEKYCGFREDNI--PQLE-DVSNFLKER-TGFSL-RPVAGLLSARDFLAG-----------LA--  141 (309)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCC--CCHH-HHHHHHHHC-CCCEE-EECCCCCCHHHHHHH-----------HH--
T ss_conf             776758999999999998459998888--9769-999988750-39878-632553688999999-----------74--


Q ss_pred             CCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             80034432337554336653035667777833277877312699999998853024836898864320268
Q gi|254780979|r  265 GHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI  335 (500)
Q Consensus       265 ~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL  335 (500)
                            -|.|    -.|-.+|.-+.-   -|-||||+         +-++---+|.|-+.....|..++|+
T Consensus       142 ------~rvF----~~TqyIRh~s~p---~YtpEPD~---------~Hel~GH~p~l~dp~fA~f~q~~G~  190 (309)
T pfam00351       142 ------FRVF----HCTQYIRHASSP---MYTPEPDC---------CHELLGHVPLLADPSFAQFSQEIGL  190 (309)
T ss_pred             ------HCCC----CCCCEECCCCCC---CCCCCCCH---------HHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             ------1836----521114158887---77899962---------6566445734378789999999999


No 86 
>KOG1261 consensus
Probab=27.53  E-value=41  Score=13.89  Aligned_cols=78  Identities=23%  Similarity=0.231  Sum_probs=51.5

Q ss_pred             EEEEEEEEEECCCCCCCCCCCCCEEEEEC----CCCCCEEEEEECC-----CCCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             84236665202310011567871488661----5786125763036-----52778999999999999986420456764
Q gi|254780979|r  141 VGIERIHLEQDAGKSIHDQYSAVSCIDLN----RSGVALMEIVTKP-----DMRSSLEAKAFLTKLRSILRYLGTCDGNM  211 (500)
Q Consensus       141 v~I~~i~lEED~gk~~h~~~~~~slvD~N----RaGvPLiEIVT~P-----d~~s~~ea~~~~~~l~~ilr~~gisd~~m  211 (500)
                      ||=.--||-|--- .+|+...+-|++||-    ----.||-+.+.|     -|.+.+||+-+-.-+...-.++|+..   
T Consensus       175 VRPRGWHl~EkH~-~Id~eP~sgslfDFGLyffHNAK~li~~GsGPyFYLPKmeh~~EaklWndvF~~aed~~Gi~R---  250 (552)
T KOG1261         175 VRPRGWHLPEKHL-LIDDEPISGSLFDFGLYFFHNAKELIKQGSGPYFYLPKMEHHEEAKLWNDVFCVAEDKIGIPR---  250 (552)
T ss_pred             ECCCCCCCCHHEE-EECCCCCCCEEEEEEEEEEECHHHHHHCCCCCEEECCCCCCHHHHHHHHHHHHHHHHHCCCCC---
T ss_conf             7167656750026-652874541366434567712799985489873656321106788888989998888608876---


Q ss_pred             CCCEEECCCCCCC
Q ss_conf             3220112575432
Q gi|254780979|r  212 EEGSMRADVNVSV  224 (500)
Q Consensus       212 eeGslR~DvNVSi  224 (500)
                        |++||-|=|--
T Consensus       251 --GtIraTVLIEt  261 (552)
T KOG1261         251 --GTIRATVLIET  261 (552)
T ss_pred             --CCEEEEEEHHH
T ss_conf             --73578874863


No 87 
>KOG2599 consensus
Probab=27.28  E-value=42  Score=13.86  Aligned_cols=108  Identities=15%  Similarity=0.200  Sum_probs=49.4

Q ss_pred             EEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECC
Q ss_conf             98423666520231001156787148866157861257630365277899999999999998642045676432201125
Q gi|254780979|r  140 EVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRAD  219 (500)
Q Consensus       140 ~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~D  219 (500)
                      ....+-.--|=|+--+++=         =|-+|   -..++.+. .+++|.....+.         ....++    .--|
T Consensus        30 tFPLQllGwdVD~insVqF---------SNHtG---Y~~~kG~~-~~~~eL~dL~eg---------l~~nn~----~~Y~   83 (308)
T KOG2599          30 TFPLQLLGWDVDVINSVQF---------SNHTG---YAHVKGQV-LNEEELEDLYEG---------LLLNNL----NKYD   83 (308)
T ss_pred             CCCHHHHCCCCCCCCCEEE---------CCCCC---CCCCCCCC-CCHHHHHHHHHH---------HHHCCC----CCCC
T ss_conf             3421220632343441564---------26668---74111631-689999999998---------764366----3322


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCC
Q ss_conf             75432137666788622235402465999999999999997313980034432337554336653035667777833277
Q gi|254780979|r  220 VNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEP  299 (500)
Q Consensus       220 vNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEP  299 (500)
                      +=.+           ==+-|.++++.|...+.     +  +-+....   -+-..|+..|-       ++    |||-+.
T Consensus        84 ~vLT-----------GY~~n~~~l~~i~~iv~-----~--lk~~np~---~~wv~DPVmGD-------nG----~lYV~e  131 (308)
T KOG2599          84 AVLT-----------GYLPNVSFLQKIADIVK-----K--LKKKNPN---LTWVCDPVMGD-------NG----RLYVPE  131 (308)
T ss_pred             EEEE-----------ECCCCHHHHHHHHHHHH-----H--HHHCCCC---EEEEECCCCCC-------CC----CEECCH
T ss_conf             4553-----------05688269999999999-----9--9842998---49996763467-------85----174458


Q ss_pred             CCCCCC
Q ss_conf             877312
Q gi|254780979|r  300 DLLPLE  305 (500)
Q Consensus       300 DLPpi~  305 (500)
                      |+-|+.
T Consensus       132 elipvY  137 (308)
T KOG2599         132 ELIPVY  137 (308)
T ss_pred             HHHHHH
T ss_conf             777999


No 88 
>pfam09043 Lys-AminoMut_A D-Lysine 5,6-aminomutase alpha subunit. Members of his family are involved in the 1,2 rearrangement of the terminal amino group of DL-lysine and of L-beta-lysine, using adenosylcobalamin (AdoCbl) and pyridoxal-5'-phosphate as cofactors. The structure is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl cofactor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state.
Probab=26.75  E-value=43  Score=13.79  Aligned_cols=52  Identities=25%  Similarity=0.321  Sum_probs=26.6

Q ss_pred             HHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHH
Q ss_conf             86387314789999999981799988999963987618988999999999983999899752
Q gi|254780979|r  401 IIDGTISGKIAKDIFNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIA  462 (500)
Q Consensus       401 i~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~k  462 (500)
                      +.+.-++-..||-||..+-.-+       ++.   .....+-++.-..+|+.+--+..+++.
T Consensus       414 l~DR~laiena~Yifn~~~~l~-------~ei---~fk~~G~i~~RA~eVL~~a~~LLe~i~  465 (509)
T pfam09043       414 MSDRALAIENAKYIFNNMKDIG-------EEI---EFKEGGIIQSRAQEVLEKALALLEEIE  465 (509)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCC-------CCE---EECCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             4457888634699998776425-------323---368987289999999999999999998


No 89 
>PRK13335 superantigen-like protein; Reviewed
Probab=26.63  E-value=43  Score=13.78  Aligned_cols=70  Identities=16%  Similarity=0.227  Sum_probs=38.0

Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             99997313980034432337554336653035667777833277877312699999998853024836898864320268
Q gi|254780979|r  256 RQIAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI  335 (500)
Q Consensus       256 RQ~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL  335 (500)
                      ||..-+.-||--.---..+|..-+..+.--.+++..      ++|.-++.|..|.|     +|-||-...|++|+++|||
T Consensus       239 ~q~~kYSIGGITKtNsk~vd~~~~~~i~k~d~~g~~------~~d~s~y~I~KEeI-----SLKELDFKLRK~LIe~~gL  307 (356)
T PRK13335        239 YQLKKYSVGGITKTNSKKVDHKVELSITKKDNQGMI------SRDVSEYMITKEEI-----SLKELDFKLRKQLIEKHNL  307 (356)
T ss_pred             CCCCEEEECCEECCCCHHHHEECCCEEEEECCCCCC------CCCCCCEEECHHHC-----CHHHHHHHHHHHHHHHCCC
T ss_conf             333200125673157300100046404662247740------45554113115234-----3766426999999986064


Q ss_pred             C
Q ss_conf             8
Q gi|254780979|r  336 S  336 (500)
Q Consensus       336 s  336 (500)
                      =
T Consensus       308 Y  308 (356)
T PRK13335        308 Y  308 (356)
T ss_pred             C
T ss_conf             2


No 90 
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=26.54  E-value=18  Score=16.50  Aligned_cols=56  Identities=25%  Similarity=0.310  Sum_probs=33.7

Q ss_pred             CCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             432337554336653035667777833277877312699999998853024836898864320268899988876411
Q gi|254780979|r  270 ETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDK  347 (500)
Q Consensus       270 ETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~  347 (500)
                      .|-+|=+..|.-.+-+  -+..-||||.+-|+.-+.                   ....| .++|+|..++..++.++
T Consensus        16 ~TLRyYe~~GLl~P~~--r~~nGYR~Ys~~dl~rL~-------------------~I~~l-r~lG~sL~eIk~~L~~~   71 (172)
T cd04790          16 STLLYYERIGLLSPSA--RSESNYRLYGERDLERLE-------------------QICAY-RSAGVSLEDIRSLLQQP   71 (172)
T ss_pred             HHHHHHHHCCCCCCCC--CCCCCCCCCCHHHHHHHH-------------------HHHHH-HHCCCCHHHHHHHHCCC
T ss_conf             8999999887989988--499987077999999999-------------------99999-98799999999998399


No 91 
>PRK12559 transcriptional regulator Spx; Provisional
Probab=26.51  E-value=43  Score=13.77  Aligned_cols=85  Identities=15%  Similarity=0.354  Sum_probs=46.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCC-----CCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCC
Q ss_conf             302457777654578876433874-----000648989999999888638731478999999998179998899996398
Q gi|254780979|r  360 RDKKIVANWVINDLLGVLNRSGKS-----IEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGL  434 (500)
Q Consensus       360 ~~pk~~Anwi~~el~~~ln~~~~~-----~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL  434 (500)
                      ...+.|-.|+-        +.+++     +.+.+++.+.|..++.+.+.|.      .+++.   ..+....    +.++
T Consensus        11 stcRKA~~wL~--------~~~I~y~~~d~~~~~~t~~el~~ll~~~~~g~------~~lin---trs~~~k----~L~~   69 (131)
T PRK12559         11 ASCRKAKAWLE--------ENQIDYTEKNIVSNSMTVDELKSILRLTEEGA------TEIIS---TRSKTFQ----DLNI   69 (131)
T ss_pred             HHHHHHHHHHH--------HCCCCCEEECCCCCCCCHHHHHHHHHHHCCCH------HHHHH---CCCHHHH----HCCC
T ss_conf             77999999999--------87998187210028989999999999836789------99873---4436688----7489


Q ss_pred             --EECCCHHHHHHHHHHHHHHCHHHHHH-H--HCCCCCHHH
Q ss_conf             --76189889999999999839998997-5--272132265
Q gi|254780979|r  435 --RQVTDLSAIEKVVDEVINSNPNNVAR-I--ATKPNLVSW  470 (500)
Q Consensus       435 --~~isD~~eL~~iv~eVI~~np~~V~~-~--kgk~ka~gf  470 (500)
                        ...+    ..+++ ++|.+||..+++ +  .++.-.+||
T Consensus        70 ~~~~ls----~~e~i-~ll~~~P~LiKRPIl~~~~~~~vGf  105 (131)
T PRK12559         70 NIEELS----LNEFY-KLIIEHPLMLRRPIMLDEKRLQIGF  105 (131)
T ss_pred             CCHHCC----HHHHH-HHHHHCHHHEECCEEEECCEEEECC
T ss_conf             710189----99999-9999594351285696299888579


No 92 
>PRK05561 DNA topoisomerase IV subunit A; Validated
Probab=26.49  E-value=43  Score=13.76  Aligned_cols=34  Identities=18%  Similarity=0.478  Sum_probs=27.0

Q ss_pred             CHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             999999988530248368988643202688999888764
Q gi|254780979|r  307 DEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS  345 (500)
Q Consensus       307 s~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~  345 (500)
                      -++.|+-||++     ++-++.|++.|+||+.+|+.++.
T Consensus       396 iD~VI~iIR~S-----~dak~~L~~~f~lse~QA~AIL~  429 (745)
T PRK05561        396 IDEVIEIIRES-----DEPKANLMARFGLTEIQAEAILE  429 (745)
T ss_pred             HHHHHHHHHCC-----CHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             68999999706-----32667775550879999999999


No 93 
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase; InterPro: IPR000191   Formamidopyrimidine-DNA glycosylase (3.2.2.23 from EC)  (Fapy-DNA glycosylase) (gene fpg) is a bacterial enzyme involved in DNA repair and which excise oxidized purine bases to release 2,6-diamino-4-hydroxy-5N-methylformamido- pyrimidine (Fapy) and 7,8-dihydro-8-oxoguanine (8-OxoG) residues. In addition to its glycosylase activity, FPG can also nick DNA at apurinic/apyrimidinic sites (AP sites). FPG is a monomeric protein of about 32 Kd which binds and require zinc for its activity.   The C-terminal region is the zinc binding site in the enzyme where four conserved and essential cysteines are located ..
Probab=26.47  E-value=43  Score=13.76  Aligned_cols=57  Identities=21%  Similarity=0.255  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC-CCHHH--HHHHCC
Q ss_conf             777654578876433874000648989999999888638731478999999998179-99889--999639
Q gi|254780979|r  366 ANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKG-GTPKE--IVEELG  433 (500)
Q Consensus       366 Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~-~~p~~--iie~~g  433 (500)
                      =||.+.|.+=.          ++|.|++.|.=+..-+=..| ...+++||++-++.| .+..+  +....|
T Consensus       184 GNIYADE~LF~----------A~ihP~~~A~~L~~~~~~~L-~~~i~~vL~~Aie~GGtt~~~q~f~~~~G  243 (292)
T TIGR00577       184 GNIYADEVLFR----------AGIHPERLANQLSKEECELL-HKAIKEVLRKAIEAGGTTIRDQLFVQSDG  243 (292)
T ss_pred             HHHHHHHHHHH----------HCCCCCHHHHCCCHHHHHHH-HHHHHHHHHHHHHCCCCCCCCEEEEECCC
T ss_conf             01066689987----------36881010001588899999-99999999999864897000200230478


No 94 
>pfam12224 Amidoligase_2 Putative amidoligase enzyme. This family of proteins are likely to act as amidoligase enzymes Protein in this family are found in conserved gene neighborhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes).
Probab=26.27  E-value=43  Score=13.74  Aligned_cols=69  Identities=30%  Similarity=0.299  Sum_probs=39.6

Q ss_pred             EEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCC--CCHH
Q ss_conf             86615786125763036527789999999999999864204567643220112575432137666788622235--4024
Q gi|254780979|r  166 IDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKN--VNSI  243 (500)
Q Consensus       166 vD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEIKN--lnS~  243 (500)
                      -|+..+++| +||||-|.--+  +...-++++-..||..|..-.+-   |  |..-|-|.         .|.-+  .+++
T Consensus        65 ~~~~~~~~p-~EiVSPpl~~~--~~l~~l~~l~~~Lr~~ga~~tn~---s--cG~hVHin---------~~~~~~~~~~l  127 (250)
T pfam12224        65 RDLADADVP-VEIVSPPLPYS--EDLEQLQELVRALRRAGAKGTNA---S--CGFHVHIN---------AEPPDLTAQTL  127 (250)
T ss_pred             HHHHCCCCC-EEEECCCCCCH--HHHHHHHHHHHHHHHCCCCCCCC---C--EEEEEECC---------CCCCCCCHHHH
T ss_conf             231025787-46888986770--67899999999999828834677---5--47778715---------75678898999


Q ss_pred             HHHHHHHH
Q ss_conf             65999999
Q gi|254780979|r  244 RFLGLAIE  251 (500)
Q Consensus       244 ~~i~~AI~  251 (500)
                      +.+-+|+-
T Consensus       128 ~~~~~~~~  135 (250)
T pfam12224       128 RNLLQAYA  135 (250)
T ss_pred             HHHHHHHH
T ss_conf             99999999


No 95 
>TIGR01801 CM_A chorismate mutase; InterPro: IPR010954   This entry represents chorismate mutase (CM) domains N-terminally fused to the first enzyme in the chorismate pathway, 2-dehydro-3-deoxyphosphoheptanoate aldolase (DAHP synthetase, AroA) which are found in some Gram-positive species and Deinococcus. Only in Deinococcus, where this domain is the sole CM domain in the genome can a trusted assignment of function be made. In the other species there is at least one other CM domain present. The similarity between the Deinococcus gene and the others in this clade is sufficiently strong (~44 0dentity), that the whole clade can be trusted to be functional. The possibility exists, however, that in the Gram-positive species the fusion to the first enzyme in the pathway has evolved a separate, regulatory role..
Probab=26.27  E-value=22  Score=15.96  Aligned_cols=33  Identities=27%  Similarity=0.400  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHH
Q ss_conf             9999998886387314789999999981799988
Q gi|254780979|r  393 QLGELIDLIIDGTISGKIAKDIFNILWEKGGTPK  426 (500)
Q Consensus       393 ~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~  426 (500)
                      .|-+|++ ...|-...++.|.||.++|.-+.+.+
T Consensus        56 ~L~~li~-~N~GPF~~~Tik~iFKEIFkAsl~L~   88 (104)
T TIGR01801        56 MLNELIE-SNDGPFEDATIKQIFKEIFKASLELQ   88 (104)
T ss_pred             HHHHHHH-CCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9999986-07876884047788899987504543


No 96 
>TIGR01846 type_I_sec_HlyB type I secretion system ATPase; InterPro: IPR010132   Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This entry contains one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane.
Probab=26.18  E-value=40  Score=13.98  Aligned_cols=52  Identities=23%  Similarity=0.272  Sum_probs=26.9

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHH---HHHCCCCHHHHHHHHHH
Q ss_conf             833277877312699999998853024836898864---32026889998887641
Q gi|254780979|r  294 RYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERF---IGEFGISLYDASVLVSD  346 (500)
Q Consensus       294 RyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl---~~~yGLs~~dA~~L~~~  346 (500)
                      =|+|+.|= |-.++.+-+++.-..-=-|-..|-+-.   ..++|+|=--+.++=+-
T Consensus        91 ~~d~~~~~-p~~~~~e~~~~lw~g~viL~A~r~~~~~~k~~kFgfsWFiP~~~ryR  145 (703)
T TIGR01846        91 IYDPEEDK-PRVLDREVLEALWSGKVILLATRSEVLGVKKLKFGFSWFIPAVIRYR  145 (703)
T ss_pred             EEECCCCC-CCCCCHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             98078788-65127788998748827999826877343001467512689999879


No 97 
>COG1978 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.10  E-value=27  Score=15.31  Aligned_cols=70  Identities=21%  Similarity=0.321  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHH
Q ss_conf             689886432026889998887641136789886-40243024577776545788764338740006489899999
Q gi|254780979|r  323 DAKRERFIGEFGISLYDASVLVSDKSIADYFEK-LAVNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGE  396 (500)
Q Consensus       323 ~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~-v~~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~lae  396 (500)
                      ...|+|+..+-.+|.+.|..+..--... -||- +..+.|.+-+..-+++|..|++.-.|....   |.|+.+|.
T Consensus        73 ~slrqrI~~Eta~Sle~A~~v~ha~d~~-~feVHlDIg~~~kglTk~Lv~e~tGyvtg~G~~~q---IKPdSyaA  143 (152)
T COG1978          73 NSLRQRIMEETARSLEHALMVMHAVDGR-HFEVHLDIGPDEKGLTKDLVKEATGYVTGQGYTYQ---IKPDSYAA  143 (152)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCC-CEEEEEECCCCCCCCHHHHHHHHHHHEECCCCCCE---ECCCHHHH
T ss_conf             4699999999998999999999986357-63899833777454417889987530414765411---27407888


No 98 
>PRK06108 aspartate aminotransferase; Provisional
Probab=25.58  E-value=45  Score=13.65  Aligned_cols=42  Identities=14%  Similarity=0.101  Sum_probs=19.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             788622235402465999999999999997313980034432337
Q gi|254780979|r  231 WGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDGGHIRQETRLFD  275 (500)
Q Consensus       231 ~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G~~v~qETR~~d  275 (500)
                      +|..++-.|+--......|+..=+   ..+++.|..|.-+|=.|.
T Consensus        78 ~g~~v~~d~I~it~G~~~al~~~~---~~~~~pGD~Vlv~~P~Y~  119 (382)
T PRK06108         78 HGATTPPERIAVTSSGVQALMLAA---QALVGPGDEVVAVTPAWP  119 (382)
T ss_pred             HCCCCCHHHEEECCCHHHHHHHHH---HHHCCCCCEEEECCCCCC
T ss_conf             788986684998078999999999---996699998998168786


No 99 
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=25.37  E-value=22  Score=15.92  Aligned_cols=50  Identities=28%  Similarity=0.435  Sum_probs=28.1

Q ss_pred             CCCCCCCCEEEE-EECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             233755433665-30356677778332778773126999999988530248368988643202688999888764
Q gi|254780979|r  272 RLFDPSKNETRS-LRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS  345 (500)
Q Consensus       272 R~~d~~~~~T~~-mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~  345 (500)
                      |.|+.. |.-.+ -|   ++..||||.+-|+.-+.       .            ...| .+.|+|..++..++.
T Consensus        18 R~ye~~-Gll~p~~r---~~~g~R~Y~~~di~~l~-------~------------I~~l-r~~G~~l~~Ik~~l~   68 (70)
T smart00422       18 RYYERI-GLLPPPIR---TEGGYRLYSDEDLERLR-------F------------IKRL-KELGFSLEEIKELLE   68 (70)
T ss_pred             HHHHHC-CCCCCCCC---CCCCCEECCHHHHHHHH-------H------------HHHH-HHCCCCHHHHHHHHH
T ss_conf             999985-89899844---89997443999999999-------9------------9999-997899999999996


No 100
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional
Probab=25.25  E-value=45  Score=13.61  Aligned_cols=115  Identities=17%  Similarity=0.145  Sum_probs=61.2

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCC---------HHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHH
Q ss_conf             89886432026889998887641136789886402430---------245777765457887643387400064898999
Q gi|254780979|r  324 AKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVNRD---------KKIVANWVINDLLGVLNRSGKSIEDTPISPNQL  394 (500)
Q Consensus       324 ~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~~~~~---------pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~l  394 (500)
                      +.++.|++--|+-+..|-.+++.-...++.+++..+..         .+..|.-|+.||.+-+.+.... .   -....+
T Consensus        69 ~~F~~LisVsGIGpk~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~ELk~Kl~~~~~~-~---~~~~~~  144 (196)
T PRK13901         69 EVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRGKLVKNDEL-E---SSLFKF  144 (196)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCC-C---CCCCCH
T ss_conf             999998765882689999997579999999999928999983199958999999999997653156655-6---553448


Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCEECCCHHHHHHHHHHHHH
Q ss_conf             9999888638731478999999998179998899996398761898899999999998
Q gi|254780979|r  395 GELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDEVIN  452 (500)
Q Consensus       395 aeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~eVI~  452 (500)
                      .++...+..=-.+.+.++.++.++..          ......+.|.+..+.+|++++.
T Consensus       145 ~e~~~AL~~LGy~~~~a~~al~~i~~----------~~~~~~~~~~~~~e~likeaLK  192 (196)
T PRK13901        145 KELEQSIVNMGFDRKLVNSAIKEIML----------LDEFLNLKDSEQEQFLFKEVLK  192 (196)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHH----------HCCCCCCCCCHHHHHHHHHHHH
T ss_conf             99999999849998999999999985----------0845677850428999999999


No 101
>cd01018 ZntC Metal binding protein ZntC.  These proteins are predicted to function as initial receptors in ABC transport of metal ions.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains.  In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=25.18  E-value=34  Score=14.52  Aligned_cols=47  Identities=28%  Similarity=0.331  Sum_probs=32.6

Q ss_pred             CCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCEECC
Q ss_conf             6489899999998886387314789999999981799988999963987618
Q gi|254780979|r  387 TPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGLRQVT  438 (500)
Q Consensus       387 ~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL~~is  438 (500)
                      ...+|.++++|++.+.+..|.     -||.+--.+.+..+.|+++.|...+.
T Consensus       199 ~eps~~~l~~l~~~ik~~~v~-----~If~E~~~~~k~~~~ia~etg~kv~~  245 (266)
T cd01018         199 KEPSPADLKRLIDLAKEKGVR-----VVFVQPQFSTKSAEAIAREIGAKVVT  245 (266)
T ss_pred             CCCCHHHHHHHHHHHHHCCCC-----EEEEECCCCCHHHHHHHHHHCCCEEE
T ss_conf             898999999999999983998-----99970899909999999970993799


No 102
>PRK07531 bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase; Validated
Probab=24.72  E-value=46  Score=13.55  Aligned_cols=29  Identities=28%  Similarity=0.429  Sum_probs=16.4

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             6125763036527789999999999999864204
Q gi|254780979|r  173 VALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGT  206 (500)
Q Consensus       173 vPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gi  206 (500)
                      +||+|||-.|.-  ..   +.+.....+++.+|.
T Consensus       144 ~PLVEvV~g~~T--~~---~~v~~a~~~~~~iG~  172 (489)
T PRK07531        144 LPLVELVGGGKT--SP---ETIERAKEILREIGM  172 (489)
T ss_pred             CCEEEEECCCCC--CH---HHHHHHHHHHHHCCC
T ss_conf             762798168888--99---999999999998298


No 103
>PRK01966 ddl D-alanyl-alanine synthetase A; Reviewed
Probab=24.42  E-value=47  Score=13.50  Aligned_cols=37  Identities=16%  Similarity=0.120  Sum_probs=18.9

Q ss_pred             ECCCCCCEEEEEECCCCCCHHHHHHHHHHH-HHHHHHHCCCCCC
Q ss_conf             615786125763036527789999999999-9998642045676
Q gi|254780979|r  168 LNRSGVALMEIVTKPDMRSSLEAKAFLTKL-RSILRYLGTCDGN  210 (500)
Q Consensus       168 ~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l-~~ilr~~gisd~~  210 (500)
                      |+-+|+|-    |.++..+.  |.++=+.+ ..+++..|+...+
T Consensus       112 Le~l~IPY----tGs~~~as--al~mDK~~tK~i~~~~gI~tp~  149 (344)
T PRK01966        112 LELLNIPY----VGCGVLAS--AVSMDKILTKRLLAAAGIPQAP  149 (344)
T ss_pred             HHHCCCCC----CCCCHHHH--HHHHHHHHHHHHHHHCCCCCCC
T ss_conf             99759993----68848999--9876699999999987999898


No 104
>TIGR00707 argD acetylornithine and succinylornithine aminotransferases; InterPro: IPR004636   This family of proteins, for which ornithine aminotransferases form an outgroup, consists mostly of proteins designated acetylornithine aminotransferase. However, the two very closely related members from Escherichia coli are assigned different enzymatic activities. One is acetylornithine aminotransferase (2.6.1.11 from EC), ArgD, an enzyme of arginine biosynthesis, while another is succinylornithine aminotransferase, an enzyme of the arginine succinyltransferase pathway, an ammonia-generating pathway of arginine catabolism . Members of this family may also act on ornithine, like ornithine aminotransferase (2.6.1.13 from EC)  and on succinyldiaminopimelate, like N-succinyldiaminopmelate-aminotransferase (2.6.1.17 from EC, DapC, an enzyme of lysine biosynthesis) . ; GO: 0008483 transaminase activity, 0006525 arginine metabolic process.
Probab=24.39  E-value=42  Score=13.82  Aligned_cols=282  Identities=20%  Similarity=0.237  Sum_probs=136.0

Q ss_pred             EEEEECCCCCCCCCCCCCEEEEECCCCCC----------EEEEEEC---------CCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             66520231001156787148866157861----------2576303---------6527789999999999999864204
Q gi|254780979|r  146 IHLEQDAGKSIHDQYSAVSCIDLNRSGVA----------LMEIVTK---------PDMRSSLEAKAFLTKLRSILRYLGT  206 (500)
Q Consensus       146 i~lEED~gk~~h~~~~~~slvD~NRaGvP----------LiEIVT~---------Pd~~s~~ea~~~~~~l~~ilr~~gi  206 (500)
                      |.+..=-|-.++|+.++.+|||| =+||.          |+|.|++         +-..++ +-.+.++||-.+.-.   
T Consensus        12 ~~i~rG~G~~v~Dd~~GK~YlDf-~aGIAV~~LGH~hP~l~Ea~~~Q~~kL~H~SNlY~~~-~~~~LA~kLv~~~~~---   86 (402)
T TIGR00707        12 IVIVRGKGAYVYDDVNGKEYLDF-VAGIAVNALGHAHPKLVEALKEQLEKLVHVSNLYYTE-PQEELAEKLVEHSGA---   86 (402)
T ss_pred             EEEECCCCCEEEECCCCCEEEEE-CCCHHHHCCCCCCHHHHHHHHHHHHHHEEECCCCCCC-HHHHHHHHHHHHHHC---
T ss_conf             01631664089876789465201-0022440113578899999998662406607765580-899999999999704---


Q ss_pred             CCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf             56764322011257543213766678862223540246599999999999999731398003443233755433665303
Q gi|254780979|r  207 CDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDGGHIRQETRLFDPSKNETRSLRT  286 (500)
Q Consensus       207 sd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G~~v~qETR~~d~~~~~T~~mR~  286 (500)
                       |+    |+              .--+||=.=| .---++|-|+.+=.+--..--....+|+-=+-.|+-.|--|.+.=.
T Consensus        87 -dg----Gq--------------hd~~rvFFCN-SGaEAnEAAlKlARk~~~~~g~~k~~ivaf~naFHGRT~g~LsaTg  146 (402)
T TIGR00707        87 -DG----GQ--------------HDASRVFFCN-SGAEANEAALKLARKYTGDKGKEKKKIVAFENAFHGRTMGALSATG  146 (402)
T ss_pred             -CC----CC--------------CCCCEEEEEC-CHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHCCC
T ss_conf             -68----83--------------0232667514-7478999999998986402278865388887077630045430047


Q ss_pred             CCCCCCCCCCCCCCCCCCC-CCHHH-HHHHHHHCCCC-----HHHHH-HHHHHHCCCCHHHHHHHHHHHHHHHH------
Q ss_conf             5667777833277877312-69999-99988530248-----36898-86432026889998887641136789------
Q gi|254780979|r  287 KEDALDYRYFSEPDLLPLE-IDEDF-IRAIKKQIPEL-----PDAKR-ERFIGEFGISLYDASVLVSDKSIADY------  352 (500)
Q Consensus       287 KE~a~DYRyfPEPDLPpi~-is~e~-i~~i~~~lPel-----P~~~~-~rl~~~yGLs~~dA~~L~~~~~la~~------  352 (500)
                      |+   =||=.-+|=+|++. +.=.- |+++++.+-+.     -.+.. +=.+.|=|+.+-+.+.|..=+++.+=      
T Consensus       147 qp---Ky~~~F~PLvpgf~y~~yNDe~~~l~~~i~~~~eg~rtAAvivEpiQGEgGV~pa~~~fL~a~r~lc~~~~~LLI  223 (402)
T TIGR00707       147 QP---KYQKPFEPLVPGFKYVPYNDEIEALKEAIDDEKEGDRTAAVIVEPIQGEGGVVPADKEFLKALRELCEDKDALLI  223 (402)
T ss_pred             CC---CCCCCCCCCCCCCEEECCCCCHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHCCEEEE
T ss_conf             76---456857884238124448897899999850257787188999853217865334877899999999864891899


Q ss_pred             HHHHHC--CCCHHHHHHHHHHHHHHHHHHCCCCCCCCC--CCHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHC------
Q ss_conf             886402--430245777765457887643387400064--8989999999888638-73147899999999817------
Q gi|254780979|r  353 FEKLAV--NRDKKIVANWVINDLLGVLNRSGKSIEDTP--ISPNQLGELIDLIIDG-TISGKIAKDIFNILWEK------  421 (500)
Q Consensus       353 FE~v~~--~~~pk~~Anwi~~el~~~ln~~~~~~~~~~--i~p~~laeLi~li~~g-~Is~~~aK~il~~l~~~------  421 (500)
                      |++|=.  +...|..|.                 +-..  ++|+ +..+-+-+-.| =|-...+|+=+...+.-      
T Consensus       224 ~DEVQtG~GRTG~~fA~-----------------~Hygse~~PD-i~T~AKgLGgG~PiGA~~~~e~~a~~~~~G~HGsT  285 (402)
T TIGR00707       224 FDEVQTGLGRTGKLFAY-----------------EHYGSEVEPD-IITLAKGLGGGVPIGAVLAKEEVAEALTPGDHGST  285 (402)
T ss_pred             EEEEEECCCCCHHHHHH-----------------HCCCCCCCCH-HHHHHHHHHCCCHHHHHEEHHHHHHHCCCCCCCCC
T ss_conf             94475287743322331-----------------2068845523-87540555278202232023678731589898666


Q ss_pred             -CCCHH---------HHHHHCCCE-ECCCHH-HHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             -99988---------999963987-618988-999999999983999899752721322658999999
Q gi|254780979|r  422 -GGTPK---------EIVEELGLR-QVTDLS-AIEKVVDEVINSNPNNVARIATKPNLVSWFVGQVMK  477 (500)
Q Consensus       422 -~~~p~---------~iie~~gL~-~isD~~-eL~~iv~eVI~~np~~V~~~kgk~ka~gfLvGqVMK  477 (500)
                       |++|-         ++|++..|. ++++.+ -+.+-.++.+....+.+.++||+    |-++|-+..
T Consensus       286 FGGNPLAc~Aa~~vl~~i~~~~~l~~v~~~G~~f~~~L~~~~~~~~~l~k~VRG~----GLmlG~e~~  349 (402)
T TIGR00707       286 FGGNPLACAAALAVLEVIEKERLLEKVKEKGDYFKERLEELIKKYIDLIKEVRGK----GLMLGIELE  349 (402)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECC----EEEEEEEEC
T ss_conf             7873899999877666550510478999988999999998617766740153231----234655642


No 105
>KOG2164 consensus
Probab=24.15  E-value=36  Score=14.30  Aligned_cols=45  Identities=9%  Similarity=0.104  Sum_probs=29.1

Q ss_pred             CCCCCCCCEEEEEEEEEEECCC-C------CCCCCCCCCCCCCCCCCCCHHHCCCCCC
Q ss_conf             2454780338989997888689-8------6555884246898765206130268988
Q gi|254780979|r   16 SGTTGDWEVVIGIEVHAQLSVV-S------KLFSGASVNFGAEPNTQVSFFDAAMPGM   66 (500)
Q Consensus        16 ~~~~~~~e~vIGLEiH~qL~t~-t------KlFc~c~~~~~~~pNt~v~~~~~g~PG~   66 (500)
                      ..-..||..||-.+=|++.++. .      ++||-    +++.  ...||||++.|-+
T Consensus       147 ~f~~any~fvv~~gd~~~qn~dpD~p~~~e~i~qv----~~~t--~~~CPICL~~~~~  198 (513)
T KOG2164         147 TFLNANYRFVVDEGDYVLQNTDPDAPVDWEDIFQV----YGST--DMQCPICLEPPSV  198 (513)
T ss_pred             HHHCCCCEEEECCCCHHHHCCCCCCCCCHHHHHHH----HCCC--CCCCCCCCCCCCC
T ss_conf             20102200122233102330697643067877664----0476--7768700478885


No 106
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family; InterPro: IPR014071   This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferable copper resistance) of an Enterococcus faecium (Streptococcus faecium) plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this entry are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI..
Probab=23.48  E-value=49  Score=13.37  Aligned_cols=41  Identities=32%  Similarity=0.559  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHHC--CCCHHHHHHHCCCEECCCHHHHHHHHHH
Q ss_conf             47899999999817--9998899996398761898899999999
Q gi|254780979|r  408 GKIAKDIFNILWEK--GGTPKEIVEELGLRQVTDLSAIEKVVDE  449 (500)
Q Consensus       408 ~~~aK~il~~l~~~--~~~p~~iie~~gL~~isD~~eL~~iv~e  449 (500)
                      ...|+++|+++...  |.-...||++.-|.+ +|-+.|++++.+
T Consensus        74 ~~~~~~lf~~~C~~k~g~~i~~Liee~~ls~-~Di~~L~~~L~~  116 (130)
T TIGR02698        74 ENAAEDLFSRICSKKVGNVIADLIEESTLSQ-DDIEKLEKLLSE  116 (130)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHCCCCCH-HHHHHHHHHHHH
T ss_conf             9999999987602138999999884066787-689999999987


No 107
>cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase.
Probab=23.42  E-value=49  Score=13.37  Aligned_cols=77  Identities=27%  Similarity=0.439  Sum_probs=38.4

Q ss_pred             HHHHCCCCCC-----CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCE---ECCCHHHHHHHH
Q ss_conf             7643387400-----06489899999998886387314789999999981799988999963987---618988999999
Q gi|254780979|r  376 VLNRSGKSIE-----DTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGLR---QVTDLSAIEKVV  447 (500)
Q Consensus       376 ~ln~~~~~~~-----~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL~---~isD~~eL~~iv  447 (500)
                      +|++.+++++     ..+++.+.|.+++.....+      ..+    ++...+   ..-++.++.   ..++ ++    +
T Consensus        18 ~L~~~~i~~~~~d~~k~~~s~~eL~~~l~~~~~~------~~~----li~~~~---~~~k~l~~~~~~~ls~-~e----~   79 (105)
T cd02977          18 WLEEHGIEYEFIDYLKEPPTKEELKELLAKLGLG------VED----LFNTRG---TPYRKLGLADKDELSD-EE----A   79 (105)
T ss_pred             HHHHCCCCCEEEHHHHCCCCHHHHHHHHHHCCCC------HHH----HHHHCC---HHHHHCCCCCCCCCCH-HH----H
T ss_conf             9985799738860432269999999999975998------999----986332---4598849834013999-99----9


Q ss_pred             HHHHHHCHHHHHH-H--HCCCCCHHH
Q ss_conf             9999839998997-5--272132265
Q gi|254780979|r  448 DEVINSNPNNVAR-I--ATKPNLVSW  470 (500)
Q Consensus       448 ~eVI~~np~~V~~-~--kgk~ka~gf  470 (500)
                      -+.|.+||..+++ +  .|+.-.+||
T Consensus        80 ~~ll~~~P~LlkRPIi~~~~~~~iGf  105 (105)
T cd02977          80 LELMAEHPKLIKRPIVVDGDRLLVGF  105 (105)
T ss_pred             HHHHHHCHHHHCCCEEEECCEEEECC
T ss_conf             99999696783397698699888259


No 108
>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=23.04  E-value=50  Score=13.31  Aligned_cols=84  Identities=15%  Similarity=0.326  Sum_probs=55.2

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCEECCCHHHHHHHHHH
Q ss_conf             54578876433874000648989999999888638731478999999998179998899996398761898899999999
Q gi|254780979|r  370 INDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDE  449 (500)
Q Consensus       370 ~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~e  449 (500)
                      +..++++|+. |-   ...+++.+..-|+.|+.. .+|....++|...+...+..+           + |..+|...|.+
T Consensus         5 l~~iv~WLRa-GY---P~GvP~~Dy~pLLALL~r-~Ltddev~~Va~~L~~~~~~~-----------i-~~~dI~~~I~~   67 (97)
T pfam11829         5 LASIVAWLRA-GY---PEGVPGPDYVPLLALLRR-RLTDDEVAEVAAELTRRGEPA-----------I-DDDDIGVLITA   67 (97)
T ss_pred             HHHHHHHHHC-CC---CCCCCCCCCHHHHHHHHC-CCCHHHHHHHHHHHHHCCCCC-----------C-CHHHHHHHHHH
T ss_conf             9999999986-89---999898870899999814-288999999999998647899-----------9-99999999999


Q ss_pred             HHHH--CHHHHHHHHCCCCCHHH
Q ss_conf             9983--99989975272132265
Q gi|254780979|r  450 VINS--NPNNVARIATKPNLVSW  470 (500)
Q Consensus       450 VI~~--np~~V~~~kgk~ka~gf  470 (500)
                      |..+  .|+.|++...+-.+-||
T Consensus        68 vt~~~P~p~di~RV~arLaa~Gw   90 (97)
T pfam11829        68 VTDELPSPEDVERVRARLAAHGW   90 (97)
T ss_pred             HHCCCCCHHHHHHHHHHHHHCCC
T ss_conf             87479898999999999986799


No 109
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.97  E-value=19  Score=16.45  Aligned_cols=54  Identities=20%  Similarity=0.222  Sum_probs=33.6

Q ss_pred             CCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             43233755433665303566777783327787731269999999885302483689886432026889998887641
Q gi|254780979|r  270 ETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSD  346 (500)
Q Consensus       270 ETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~  346 (500)
                      .|-+|=+..|.-.+.|   ....||||.+.|+.-+.                   ...++ .++|+|..++..++..
T Consensus        15 ~TlRyYe~~GLl~p~R---~~~gyR~Y~~~~~~rL~-------------------~I~~l-r~lg~sL~eIk~lL~~   68 (134)
T cd04779          15 RTIDYYTNLGLLTPER---SDSNYRYYDETALDRLQ-------------------LIEHL-KGQRLSLAEIKDQLEE   68 (134)
T ss_pred             HHHHHHHHCCCCCCCC---CCCCCCCCCHHHHHHHH-------------------HHHHH-HHCCCCHHHHHHHHHC
T ss_conf             9999999779979996---99998206999999999-------------------99999-9979989999999847


No 110
>COG3608 Predicted deacylase [General function prediction only]
Probab=22.83  E-value=50  Score=13.28  Aligned_cols=55  Identities=16%  Similarity=0.228  Sum_probs=34.9

Q ss_pred             ECCCCCCEE--EEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEE-CCCCCC
Q ss_conf             615786125--76303652778999999999999986420456764322011-257543
Q gi|254780979|r  168 LNRSGVALM--EIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMR-ADVNVS  223 (500)
Q Consensus       168 ~NRaGvPLi--EIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR-~DvNVS  223 (500)
                      .+|+|+|-+  |+... -=-+|+.+..++..+...|++.|+..+.++..-.+ .+.+-|
T Consensus       198 ~~~~gi~~iT~E~gg~-g~v~~~~i~~~~~gi~n~L~~~Gil~g~~~~~p~~~~~~~~~  255 (331)
T COG3608         198 AERAGIPVITVELGGA-GDVDAESIEIAAEGILNFLRHRGILAGEVEKTPTKGLALPSS  255 (331)
T ss_pred             HHHCCCCEEEEEECCC-CCCCHHHHHHHHHHHHHHHHHHCEECCCCCCCCCCEEECCCC
T ss_conf             8873996797651686-434788888899999999997184448867888523540365


No 111
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=22.81  E-value=50  Score=13.28  Aligned_cols=91  Identities=14%  Similarity=0.280  Sum_probs=50.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHC-CCCHHHHHHHCCCEECC
Q ss_conf             30245777765457887643387400064898999999988863873147899999999817-99988999963987618
Q gi|254780979|r  360 RDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEK-GGTPKEIVEELGLRQVT  438 (500)
Q Consensus       360 ~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~-~~~p~~iie~~gL~~is  438 (500)
                      ...+.|-.|+-.-   -+.....++.+.+++.+.|..++.+.+.|.      +    .++.+ +.+..++-.  .+..+|
T Consensus        11 ~TcrKA~kWL~~~---~I~y~~~di~k~p~s~~el~~~L~~~~~g~------~----~lintrs~~~r~L~~--~~~~ls   75 (132)
T PRK13344         11 TSCKKAKTWLNAH---QLAYKEQNLGKEPLTKEEILAILSKTENGV------E----SIVSSKNRYAKALDC--DIEELS   75 (132)
T ss_pred             HHHHHHHHHHHHC---CCCEEEEEEECCCCCHHHHHHHHHHCCCCH------H----HHEECCCCHHHHCCC--CHHHCC
T ss_conf             6789999999987---996388541227969999999999815589------9----913788821664275--644399


Q ss_pred             CHHHHHHHHHHHHHHCHHHHHH-H--HCCCCCHHH
Q ss_conf             9889999999999839998997-5--272132265
Q gi|254780979|r  439 DLSAIEKVVDEVINSNPNNVAR-I--ATKPNLVSW  470 (500)
Q Consensus       439 D~~eL~~iv~eVI~~np~~V~~-~--kgk~ka~gf  470 (500)
                      ..    +++ ++|.+||..+.+ +  .|+.-.+||
T Consensus        76 ~~----E~i-~ll~~~p~LiKRPil~~~~~~~vGF  105 (132)
T PRK13344         76 VS----EVI-DLIQENPRILKSPILIDDKRLQVGY  105 (132)
T ss_pred             HH----HHH-HHHHHCCCCEECCEEEECCEEEECC
T ss_conf             99----999-9999590103274795199889625


No 112
>PRK09261 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated
Probab=22.61  E-value=50  Score=13.26  Aligned_cols=26  Identities=15%  Similarity=0.261  Sum_probs=17.5

Q ss_pred             EEECCC-CCCHHHHHHHHHHHHHHHHH
Q ss_conf             630365-27789999999999999864
Q gi|254780979|r  178 IVTKPD-MRSSLEAKAFLTKLRSILRY  203 (500)
Q Consensus       178 IVT~Pd-~~s~~ea~~~~~~l~~ilr~  203 (500)
                      +|..|| +|+|+.|.+|+++|..+-.-
T Consensus        56 vivGPCSiHD~~aaleYA~rL~~l~~~   82 (351)
T PRK09261         56 VVVGPCSIHDPKAALEYARRLAKLREE   82 (351)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             997178668989999999999999998


No 113
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator; InterPro: IPR011794    This entry represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix .; GO: 0003677 DNA binding, 0045340 mercury ion binding, 0045449 regulation of transcription, 0046689 response to mercury ion.
Probab=22.59  E-value=48  Score=13.44  Aligned_cols=62  Identities=21%  Similarity=0.247  Sum_probs=36.7

Q ss_pred             HHCCCCCCCCCCCCCCCCCEE-EEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHH
Q ss_conf             313980034432337554336-6530356677778332778773126999999988530248368988643202688999
Q gi|254780979|r  261 LEDGGHIRQETRLFDPSKNET-RSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYD  339 (500)
Q Consensus       261 l~~G~~v~qETR~~d~~~~~T-~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~d  339 (500)
                      |.+--.|-.||=+|=+.+|-- -|-|   ...-||.||+.|+-=|+                 .-  +| +.++|+|.+.
T Consensus         5 LA~~~GVNvETiRyYeRkGLl~eP~k---~~~GyR~Y~~~~v~R~r-----------------FI--KR-~QeLGFsL~E   61 (126)
T TIGR02051         5 LAKAAGVNVETIRYYERKGLLPEPDK---PEGGYRRYPEETVKRVR-----------------FI--KR-AQELGFSLEE   61 (126)
T ss_pred             HHHHCCCCEEEEEHHHHCCCCCCCCC---CCCCCCCCCHHHHHHHH-----------------HH--HH-HHHCCCCHHH
T ss_conf             36666897012210010077888899---88771407865443645-----------------54--42-0003797889


Q ss_pred             HHHHHH
Q ss_conf             888764
Q gi|254780979|r  340 ASVLVS  345 (500)
Q Consensus       340 A~~L~~  345 (500)
                      +..|+.
T Consensus        62 I~~LL~   67 (126)
T TIGR02051        62 IGKLLG   67 (126)
T ss_pred             HHHHCC
T ss_conf             998706


No 114
>TIGR01267 Phe4hydrox_mono phenylalanine-4-hydroxylase; InterPro: IPR005960    This entry represents the small, monomeric form of phenylalanine-4-hydroxylase (PAH; 1.14.16.1 from EC), as found in a certain Gram-negative bacteria. The enzyme is biopterin and metal dependent, and acts to irreversibly convert phenylalanine to tyrosine, the rate-limiting step in phenylalanine catabolism in some systems:    L-phenylalanine + tetrahydrobiopterin + O2 = L-tyrosine + dihydrobiopterin + H2O     The structure of PAH from Colwellia psychrerythraea (strain 34H / ATCC BAA-681), which binds tetrahydrobiopterin (BH4) as cofactor, is a cold-active form of the enzyme that has increased stability and flexibility around the active site .   More information about these proteins can be found at Protein of the Month: Phenylalanine Hydroxylase .; GO: 0004505 phenylalanine 4-monooxygenase activity, 0006559 L-phenylalanine catabolic process.
Probab=22.46  E-value=45  Score=13.59  Aligned_cols=62  Identities=26%  Similarity=0.398  Sum_probs=47.3

Q ss_pred             EEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             36653035667777833277877312699999998853024836898864320268899988876411367898
Q gi|254780979|r  280 ETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDKSIADYF  353 (500)
Q Consensus       280 ~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~la~~F  353 (500)
                      +|..+|+.++-+   |.-|||+-         -++=--.|-|-.-....|+..||=.--+|..+=.+..++.+|
T Consensus        93 Vt~wlRtp~eLD---Yl~EPD~F---------Hd~FGHvPlL~nPvFAdf~~~YGK~g~ka~alg~~e~laRLY  154 (251)
T TIGR01267        93 VTTWLRTPEELD---YLQEPDVF---------HDLFGHVPLLTNPVFADFLEAYGKKGVKAKALGAAEFLARLY  154 (251)
T ss_pred             CCCCCCCHHHCC---CCCCCCCC---------CCCCCCCCCCCCCCHHHHHHHHCCCCCCHHHHCCHHHHHHHH
T ss_conf             422136720056---14387421---------000376653457404688875164200001111125677777


No 115
>COG2905 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]
Probab=22.31  E-value=36  Score=14.33  Aligned_cols=48  Identities=35%  Similarity=0.456  Sum_probs=34.7

Q ss_pred             EEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHH
Q ss_conf             84236665202310011567871488661578612576303652778999
Q gi|254780979|r  141 VGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEA  190 (500)
Q Consensus       141 v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea  190 (500)
                      +.+.-...=+|+++.+-+.+.+ |++-++++| |+.-|||+-||++.--|
T Consensus       160 ~~v~~~~~i~~aa~km~~~gv~-s~v~l~~~~-~~~GIvT~~dl~~~v~~  207 (610)
T COG2905         160 VTVSPQASIQDAARKMKDEGVS-SLVVLDDSG-PLLGIVTRKDLRSRVIA  207 (610)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCC-EEEEECCCC-CCCCEEEHHHHHHHHHH
T ss_conf             5268657679999999960887-289983798-74332422777899986


No 116
>cd04165 GTPBP1_like GTPBP1-like.  Mammalian GTP binding protein 1 (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1 are GTPases whose specific functions remain unknown.  In mouse, GTPBP1 is expressed in macrophages, in smooth muscle cells of various tissues and in some neurons of the cerebral cortex; GTPBP2 tissue distribution appears to overlap that of GTPBP1.  In human leukemia and macrophage cell lines, expression of both GTPBP1 and GTPBP2 is enhanced by interferon-gamma (IFN-gamma).  The chromosomal location of both genes has been identified in humans, with GTPBP1 located in chromosome 22q12-13.1 and GTPBP2 located in chromosome 6p21-12.  Human glioblastoma multiforme (GBM), a highly-malignant astrocytic glioma and the most common cancer in the central nervous system, has been linked to chromosomal deletions and a translocation on chromosome 6.  The GBM translocation results in a fusion of GTPBP2 and PTPRZ1, a protein involved in oligodendrocyte differentiation, recovery, and
Probab=22.29  E-value=51  Score=13.21  Aligned_cols=40  Identities=23%  Similarity=0.279  Sum_probs=32.3

Q ss_pred             CCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             1578612576303652778999999999999986420456
Q gi|254780979|r  169 NRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCD  208 (500)
Q Consensus       169 NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd  208 (500)
                      ...|+|.+=+||.=|+.+++.....+.+|..+++..|+..
T Consensus       135 ~~l~ip~~vvitKiDl~~~~~l~~~~~~i~~~lk~p~~~k  174 (224)
T cd04165         135 LALNIPVFVVVTKIDLAPANILQETLKDLKRILKVPGVRK  174 (224)
T ss_pred             HHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             9839998999989776898999999999999970447556


No 117
>pfam08777 RRM_3 RNA binding motif. This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif.
Probab=21.99  E-value=52  Score=13.17  Aligned_cols=40  Identities=18%  Similarity=0.264  Sum_probs=17.2

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECC
Q ss_conf             630365277899999999999998642045676432201125
Q gi|254780979|r  178 IVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRAD  219 (500)
Q Consensus       178 IVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~D  219 (500)
                      +..-+...|-++.++.+.++.. +.|++.+.|.. +|.+|++
T Consensus         6 ~~~~~~~~sRediK~~f~~~g~-V~yVD~~~Gd~-eg~vRf~   45 (102)
T pfam08777         6 FSGLNKPTSREDIKEAFSQHGE-VKYVDFLEGDK-EGYVRFK   45 (102)
T ss_pred             EECCCCCCCHHHHHHHHHHCCC-EEEEEECCCCC-EEEEEEC
T ss_conf             9568988899999999983597-56898427883-6999967


No 118
>pfam02885 Glycos_trans_3N Glycosyl transferase family, helical bundle domain. This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate.
Probab=21.90  E-value=52  Score=13.16  Aligned_cols=42  Identities=31%  Similarity=0.421  Sum_probs=26.6

Q ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHH
Q ss_conf             489899999998886387314789999999981799988999
Q gi|254780979|r  388 PISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIV  429 (500)
Q Consensus       388 ~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~ii  429 (500)
                      .++.++...++..+-+|+++..+.-..|-.+...|.++++++
T Consensus        14 ~Ls~~e~~~~~~~i~~g~~s~~qi~afL~al~~kget~~Ei~   55 (66)
T pfam02885        14 DLSREEAEALMDAIMSGEASDAQIAAFLMALRIKGETPEEIA   55 (66)
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHH
T ss_conf             979999999999998699999999999999998399999999


No 119
>KOG1280 consensus
Probab=21.75  E-value=29  Score=15.03  Aligned_cols=56  Identities=13%  Similarity=0.105  Sum_probs=36.8

Q ss_pred             CCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH
Q ss_conf             39800344323375543366530356677778332778773126999999988530248368988
Q gi|254780979|r  263 DGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRE  327 (500)
Q Consensus       263 ~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~  327 (500)
                      .+..-...|+.-+...-.|..+         +++-+++|-+..-|...|..-+..+|.+|+.+..
T Consensus       247 ~~~t~~naa~~~~T~~~~~~~~---------ef~~t~~i~~tess~~~l~~t~~~~~~~~~~~~~  302 (381)
T KOG1280         247 QLETPRNAAPRTNTSDVTTTIT---------EFTATTNIANTESSQQTLQNTQFLLTRLNDPKMS  302 (381)
T ss_pred             HCCCCCCCCCCCCCCCCHHHHH---------HHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             2137544678765672012324---------3331105556767899999877643037875446


No 120
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=21.69  E-value=50  Score=13.25  Aligned_cols=56  Identities=21%  Similarity=0.237  Sum_probs=32.9

Q ss_pred             CCCCCCCCCCCCCEE-EEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             034432337554336-6530356677778332778773126999999988530248368988643202688999888764
Q gi|254780979|r  267 IRQETRLFDPSKNET-RSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS  345 (500)
Q Consensus       267 v~qETR~~d~~~~~T-~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~  345 (500)
                      |--+|-+|=+..|.- .+.|   .+..||+|++.|+--+.       -|          +  + ..++|+|.+++..|+.
T Consensus        19 vs~~tIRyYE~~GLl~~~~R---~~~gyR~Y~~~~v~rL~-------fI----------~--~-~r~lGfsL~eI~~LL~   75 (144)
T PRK13752         19 VNVETIRFYQRKGLLPEPDK---PYGSIRRYGEADVTRVR-------FV----------K--S-AQRLGFSLDEIAELLR   75 (144)
T ss_pred             CCHHHHHHHHHCCCCCCCCC---CCCCCCCCCHHHHHHHH-------HH----------H--H-HHHCCCCHHHHHHHHC
T ss_conf             98456679872599798777---99998247999999999-------99----------9--9-9987998999999977


No 121
>pfam10228 DUF2228 Uncharacterized conserved protein (DUF2228). This is a family of conserved proteins of approximately 700 residues found from worms to humans.
Probab=21.66  E-value=53  Score=13.12  Aligned_cols=21  Identities=24%  Similarity=0.377  Sum_probs=9.2

Q ss_pred             CEEEEEECCCCCCCCCCCCCCC
Q ss_conf             3366530356677778332778
Q gi|254780979|r  279 NETRSLRTKEDALDYRYFSEPD  300 (500)
Q Consensus       279 ~~T~~mR~KE~a~DYRyfPEPD  300 (500)
                      |..++- .+.+..-||=-|+.|
T Consensus       150 GiVVP~-d~k~~vGYR~L~~sd  170 (253)
T pfam10228       150 GLVVPV-DNKTDVGYRPLSESD  170 (253)
T ss_pred             EEEEEC-CCCCCCCCCCCCCCH
T ss_conf             489711-687875551078573


No 122
>TIGR00591 phr2 deoxyribodipyrimidine photolyase; InterPro: IPR008148   Deoxyribodipyrimidine photolyase (DNA photolyase)  is a DNA repair enzyme. It binds to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), breaks the cyclobutane ring joining the two pyrimidines of the dimer. DNA photolyase is an enzyme that requires two choromophore-cofactors for its activity: a reduced FADH2 and either 5,10-methenyltetrahydrofolate (5,10-MTFH) or an oxidized 8-hydroxy-5- deazaflavin (8-HDF) derivative (F420). The folate or deazaflavin chromophore appears to function as an antenna, while the FADH2 chromophore is thought to be responsible for electron transfer. On the basis of sequence similarities  DNA photolyases can be grouped into two classes.     The second class contains enzymes from Myxococcus xanthus, methanogenic archaebacteria, insects, fish and marsupial mammals. It is not yet known what second cofactor is bound to class 2 enzymes. There are a number of conserved sequence regions in all known class 2 DNA photolyases, especially in the C-terminal part. ; GO: 0003904 deoxyribodipyrimidine photo-lyase activity, 0006281 DNA repair.
Probab=21.64  E-value=49  Score=13.33  Aligned_cols=31  Identities=19%  Similarity=0.190  Sum_probs=17.5

Q ss_pred             EEEEEEEEEC-CCCCCCCCCCCCEEEEECCCCCCEEEEEEC
Q ss_conf             4236665202-310011567871488661578612576303
Q gi|254780979|r  142 GIERIHLEQD-AGKSIHDQYSAVSCIDLNRSGVALMEIVTK  181 (500)
Q Consensus       142 ~I~~i~lEED-~gk~~h~~~~~~slvD~NRaGvPLiEIVT~  181 (500)
                      +=.+-|||.+ +++.+-.     .+++--++|.    |||+
T Consensus        90 l~Ipf~Ll~gr~~~~~lP-----~f~~~~~~~a----~VtD  121 (471)
T TIGR00591        90 LGIPFHLLLGRSAKEVLP-----KFVQERDAGA----VVTD  121 (471)
T ss_pred             CCCCEEEECCCCCHHHHH-----HHHHHCCCCE----EECC
T ss_conf             489879757898666558-----8885417752----6536


No 123
>pfam11202 DUF2983 Protein of unknown function (DUF2983). This bacterial family of proteins has no known function.
Probab=21.62  E-value=38  Score=14.18  Aligned_cols=17  Identities=18%  Similarity=0.421  Sum_probs=14.0

Q ss_pred             CCCCCEEEEECCCCCCE
Q ss_conf             67871488661578612
Q gi|254780979|r  159 QYSAVSCIDLNRSGVAL  175 (500)
Q Consensus       159 ~~~~~slvD~NRaGvPL  175 (500)
                      .+...+||.+-|||+|+
T Consensus        79 ~~~~ivLVSLaRAGtPi   95 (353)
T pfam11202        79 RGEPIVLVSLARAGTPI   95 (353)
T ss_pred             CCCCCEEEEEECCCCCH
T ss_conf             18996799853258738


No 124
>PRK13515 carboxylate-amine ligase; Provisional
Probab=21.60  E-value=53  Score=13.11  Aligned_cols=29  Identities=31%  Similarity=0.250  Sum_probs=19.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             257630365277899999999999998642
Q gi|254780979|r  175 LMEIVTKPDMRSSLEAKAFLTKLRSILRYL  204 (500)
Q Consensus       175 LiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~  204 (500)
                      -|||+|. ..++..|+++.+..++..+...
T Consensus        52 qiEi~T~-v~~~~~e~~~~L~~~r~~l~~a   80 (381)
T PRK13515         52 QIEVGTP-VCATLAEAREELGRLRQRLAEL   80 (381)
T ss_pred             EEEECCC-CCCCHHHHHHHHHHHHHHHHHH
T ss_conf             7994687-7799999999999999999999


No 125
>PRK08136 glycosyl transferase family protein; Provisional
Probab=21.51  E-value=53  Score=13.10  Aligned_cols=11  Identities=18%  Similarity=0.477  Sum_probs=3.9

Q ss_pred             HHHHHHHHCCE
Q ss_conf             99987782976
Q gi|254780979|r   78 AVMTGLGLNAH   88 (500)
Q Consensus        78 ai~~~~al~~~   88 (500)
                      |+.+++....+
T Consensus        44 afL~alr~KGE   54 (316)
T PRK08136         44 AILIALRIKGE   54 (316)
T ss_pred             HHHHHHHCCCC
T ss_conf             99999972289


No 126
>TIGR02333 2met_isocit_dHY 2-methylisocitrate dehydratase, Fe/S-dependent; InterPro: IPR012708    This entry represents Fe/S-dependent 2-methylisocitrate dehydratase (AcnD; 4.2.1.99 from EC), which is part of the 2-methylcitrate (2-MC) cycle that occurs in certain fungi and bacteria. The 2-MC cycle is involved in the degradation of propionyl-CoA via 2-methylcitrate, with AcnD functioning after PrpD and before PrpB. AcnD acts to catalyse the dehydration of 2-methylcitrate and citrate to 2-methyl-cis-aconitate and cis-aconitate, respectively, as well as to catalyse the hydration of cis-aconitate. However, 2-methylisocitrate and isocitrate were not substrates for AcnD, indicating that AcnD only catalyses the first half of the aconitase-like dehydration reactions . The enzyme from the fungus Yarrowia lipolytica (Candida lipolytica) does not act on isocitrate. AcnD is homologous to aconitases A and B. In Escherichia coli, which lacks a member of this family, 2-methylisocitrate dehydratase activity was traced to aconitase B (IPR004406 from INTERPRO) .   Information about related proteins can be found at Protein of the Month: Aconitase ..
Probab=21.46  E-value=53  Score=13.09  Aligned_cols=90  Identities=18%  Similarity=0.195  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH-HHHHHCCCCC
Q ss_conf             999999999999864204567643220112575432137666788622235402465999999999999-9973139800
Q gi|254780979|r  189 EAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQ-IAILEDGGHI  267 (500)
Q Consensus       189 ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ-~~ll~~G~~v  267 (500)
                      .|...+..|-..||.-.+..+-+|-   -..---++     ..|.|.-|.||.- .+=..|--|-|..| ++.|.--|.-
T Consensus       250 tatd~vlalteflr~~~vv~~y~ef---~GeGa~~l-----~~Gdratisnm~P-e~Gata~mf~id~qt~~yl~ltGr~  320 (864)
T TIGR02333       250 TATDIVLALTEFLRKEKVVSAYLEF---FGEGARAL-----TLGDRATISNMTP-EYGATAAMFAIDEQTIDYLKLTGRE  320 (864)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH---HCCCCCEE-----ECCCCHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             2788999999987642466555665---05651012-----1143001101574-2001466777667778777523885


Q ss_pred             ----------CCCCCCCCCCCCEEEEEECC
Q ss_conf             ----------34432337554336653035
Q gi|254780979|r  268 ----------RQETRLFDPSKNETRSLRTK  287 (500)
Q Consensus       268 ----------~qETR~~d~~~~~T~~mR~K  287 (500)
                                -+.+-.|.+.-.....-|.-
T Consensus       321 ~~qv~lve~yak~~GlW~d~l~~a~y~r~l  350 (864)
T TIGR02333       321 EEQVKLVETYAKAAGLWADSLKQAVYERVL  350 (864)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHCCHHHHHHE
T ss_conf             688888877765402105544000000110


No 127
>KOG0979 consensus
Probab=21.36  E-value=53  Score=13.08  Aligned_cols=47  Identities=23%  Similarity=0.277  Sum_probs=31.2

Q ss_pred             EEEEEEEEEECCCCCCCCCCCC-CCCCCCC-----CCCCHHHCCCCCCCCCCC
Q ss_conf             8989997888689865558842-4689876-----520613026898887378
Q gi|254780979|r   25 VIGIEVHAQLSVVSKLFSGASV-NFGAEPN-----TQVSFFDAAMPGMLPILN   71 (500)
Q Consensus        25 vIGLEiH~qL~t~tKlFc~c~~-~~~~~pN-----t~v~~~~~g~PG~lP~lN   71 (500)
                      +|-+|.|-=+.-+.=-|.+||. ++-.-||     |-||.+|+|+-|..-++-
T Consensus        22 IvrI~l~NF~Ty~~~e~~pgpsLNmIiGpNGSGKSSiVcAIcLglgG~Pk~lG   74 (1072)
T KOG0979          22 IVRIELHNFLTYDHTEFLPGPSLNMIIGPNGSGKSSIVCAICLGLGGKPKLLG   74 (1072)
T ss_pred             EEEEEEEEEEEEEEEEECCCCCEEEEECCCCCCCHHHHHHHHHHCCCCHHHCC
T ss_conf             69999740044433344378861268778989704889999997279744314


No 128
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.30  E-value=53  Score=13.07  Aligned_cols=59  Identities=15%  Similarity=0.215  Sum_probs=34.0

Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Q ss_conf             32337554336653035667777833277877312699999998853024836898864320268899988876411367
Q gi|254780979|r  271 TRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDKSIA  350 (500)
Q Consensus       271 TR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~la  350 (500)
                      -|.|+ ..|.-.|-+.  +..-||||-+-|+.          .+.         ....| ..+|+|..++..++++....
T Consensus        17 LRyYe-~~GLl~p~~~--~~ngYR~Y~~~~~~----------~l~---------~I~~~-r~lG~sL~eI~~~~~~~~~~   73 (97)
T cd04782          17 LFHYD-KIGLFKPEIV--KENGYRYYTLEQFE----------QLD---------IILLL-KELGISLKEIKDYLDNRNPD   73 (97)
T ss_pred             HHHHH-HCCCCCCCCC--CCCCCCCCCHHHHH----------HHH---------HHHHH-HHCCCCHHHHHHHHHCCCHH
T ss_conf             99999-6699898613--99998427999999----------999---------99999-99699999999998279989


Q ss_pred             HH
Q ss_conf             89
Q gi|254780979|r  351 DY  352 (500)
Q Consensus       351 ~~  352 (500)
                      ++
T Consensus        74 ~~   75 (97)
T cd04782          74 EL   75 (97)
T ss_pred             HH
T ss_conf             99


No 129
>PRK01372 ddl D-alanine--D-alanine ligase; Reviewed
Probab=21.29  E-value=53  Score=13.07  Aligned_cols=13  Identities=8%  Similarity=0.077  Sum_probs=8.2

Q ss_pred             HHHHHHHCCCCCC
Q ss_conf             9998642045676
Q gi|254780979|r  198 RSILRYLGTCDGN  210 (500)
Q Consensus       198 ~~ilr~~gisd~~  210 (500)
                      .++++..|+....
T Consensus       103 K~i~~~~gI~tp~  115 (304)
T PRK01372        103 KLVWQAAGLPTAP  115 (304)
T ss_pred             HHHHHHCCCCCCC
T ss_conf             9999986999898


No 130
>PRK04182 cytidylate kinase; Provisional
Probab=21.16  E-value=54  Score=13.05  Aligned_cols=72  Identities=21%  Similarity=0.153  Sum_probs=40.0

Q ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHH--HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHH
Q ss_conf             8368988643202688999888764--11367898864024302457777654578876433874000648989999999
Q gi|254780979|r  321 LPDAKRERFIGEFGISLYDASVLVS--DKSIADYFEKLAVNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELI  398 (500)
Q Consensus       321 lP~~~~~rl~~~yGLs~~dA~~L~~--~~~la~~FE~v~~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi  398 (500)
                      .++.|.+|.+..++++..+|...+.  +..-..+|...- +.++...            ...++-++.+.++++..+++|
T Consensus       100 ~~e~R~~Ri~~r~~~~~~~a~~~i~~rd~~~~~r~~~~y-~~~~~d~------------~~ydl~Idts~l~~d~vv~~I  166 (178)
T PRK04182        100 PLEVRAKRIAEREGISVEEALEETIEREESEAKRYLEYY-GIDIDDL------------SIYDLVINTSKWSPEEVFEII  166 (178)
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCC------------CCCCEEEECCCCCHHHHHHHH
T ss_conf             999999999973299999999999998999999999860-8997753------------107489989999999999999


Q ss_pred             HHHHCCC
Q ss_conf             8886387
Q gi|254780979|r  399 DLIIDGT  405 (500)
Q Consensus       399 ~li~~g~  405 (500)
                      .-.-+..
T Consensus       167 ~~~i~k~  173 (178)
T PRK04182        167 LAAIDKL  173 (178)
T ss_pred             HHHHHHH
T ss_conf             9999999


No 131
>pfam07830 PP2C_C Protein serine/threonine phosphatase 2C, C-terminal domain. Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain.
Probab=20.87  E-value=54  Score=13.01  Aligned_cols=10  Identities=40%  Similarity=0.787  Sum_probs=3.8

Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999998
Q gi|254780979|r  443 IEKVVDEVIN  452 (500)
Q Consensus       443 L~~iv~eVI~  452 (500)
                      |+..|+++++
T Consensus        28 le~~v~Eii~   37 (81)
T pfam07830        28 LEQRVEEIIE   37 (81)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 132
>KOG1147 consensus
Probab=20.82  E-value=47  Score=13.48  Aligned_cols=28  Identities=11%  Similarity=0.290  Sum_probs=14.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             677778332778773126999999988530
Q gi|254780979|r  289 DALDYRYFSEPDLLPLEIDEDFIRAIKKQI  318 (500)
Q Consensus       289 ~a~DYRyfPEPDLPpi~is~e~i~~i~~~l  318 (500)
                      +..-|+-||-=|...=.++.  |+.+...|
T Consensus       370 TG~KYkvYPTYDFaCPIVDs--lEGVThaL  397 (712)
T KOG1147         370 TGDKYKVYPTYDFACPIVDS--LEGVTHAL  397 (712)
T ss_pred             CCCCEEEECCCCCCCCCCHH--HHHHHHHH
T ss_conf             78730330454424522002--43245665


No 133
>TIGR02365 dha_L_ycgS dihydroxyacetone kinase, L subunit; InterPro: IPR012737    Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated 2.7.1.29 from EC. By contract, Escherichia coli and many other bacterial species have a multisubunit form (2.7.1 from EC) with a phosphoprotein donor related to PTS transport proteins. The sequences in this entry represent the subunit homologous to the E. coli YcgS subunit..
Probab=20.60  E-value=33  Score=14.60  Aligned_cols=99  Identities=14%  Similarity=0.173  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH-HHHHHHHHHHHHCC--CCH----HHHHHHHHHHHHHHHHHC
Q ss_conf             99999988530248368988643202688999888764-11367898864024--302----457777654578876433
Q gi|254780979|r  308 EDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS-DKSIADYFEKLAVN--RDK----KIVANWVINDLLGVLNRS  380 (500)
Q Consensus       308 ~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~-~~~la~~FE~v~~~--~~p----k~~Anwi~~el~~~ln~~  380 (500)
                      .+||..+...+    .+-+++| .++.-.--|+..=++ ++-+..+-+.+...  .++    |.++-.|++.+-|     
T Consensus         2 ~~wl~~~~~~~----~~~~~yL-TeLD~aIGDgDHG~Nm~RGF~~v~~kL~~~~~~~~~~~LK~~gM~LiS~VGG-----   71 (200)
T TIGR02365         2 LEWLKNLGDLV----IENKEYL-TELDRAIGDGDHGINMARGFSEVKEKLDDFKDKTIQEILKKTGMALISKVGG-----   71 (200)
T ss_pred             HHHHHHHHHHH----HHHHHHH-HHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCC-----
T ss_conf             67899999999----8623420-0105433565455147888999999974258999878999988888522032-----


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHC-CCC-CHHHHHHHHHHHHH
Q ss_conf             87400064898999999988863-873-14789999999981
Q gi|254780979|r  381 GKSIEDTPISPNQLGELIDLIID-GTI-SGKIAKDIFNILWE  420 (500)
Q Consensus       381 ~~~~~~~~i~p~~laeLi~li~~-g~I-s~~~aK~il~~l~~  420 (500)
                          -+=||==-.|.+.=..+.+ ..+ +.....++|+.+++
T Consensus        72 ----ASGPLYGT~Fl~as~a~~~~~~~~~~~~l~~~l~~g~~  109 (200)
T TIGR02365        72 ----ASGPLYGTAFLKASKALKDKEEILDAEDLAEILEAGLE  109 (200)
T ss_pred             ----HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf             ----01577999999999986230126898899999999999


No 134
>PRK09071 hypothetical protein; Validated
Probab=20.30  E-value=56  Score=12.93  Aligned_cols=69  Identities=17%  Similarity=0.238  Sum_probs=33.0

Q ss_pred             ECCCCCCEEEEEECCCCCCHHHHHHHHHHH----------HHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCC
Q ss_conf             615786125763036527789999999999----------9998642045676432201125754321376667886222
Q gi|254780979|r  168 LNRSGVALMEIVTKPDMRSSLEAKAFLTKL----------RSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEV  237 (500)
Q Consensus       168 ~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l----------~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEI  237 (500)
                      +..+|+|+        -.+|+++...+.+.          .--++++.-.+..|   .+|-=.|+-- |--.+.+.+.-+
T Consensus       128 LeaLGi~i--------~~~~~~~~~~l~~~gi~Fl~ap~fhP~~~~v~~~R~~L---G~rTifN~lg-pL~NPa~~~~ql  195 (323)
T PRK09071        128 LEALGIPI--------ARSWAEAEQALEEHGIAYLPLEDFAPQLQRMIDLRNTL---GLRSPINTLA-RLLNPLNAKASL  195 (323)
T ss_pred             HHHCCCCC--------CCCHHHHHHHHHHCCCEEEEHHHHCHHHHHHHHHHHHH---CCCCHHHHHH-HHCCCCCCCCEE
T ss_conf             99769976--------68999999999971955723778699999999999995---8897999888-612877887649


Q ss_pred             CCCCHHHHHHH
Q ss_conf             35402465999
Q gi|254780979|r  238 KNVNSIRFLGL  248 (500)
Q Consensus       238 KNlnS~~~i~~  248 (500)
                      =++-+-..+..
T Consensus       196 ~GV~~~~~~~~  206 (323)
T PRK09071        196 QGIFHPGYQQL  206 (323)
T ss_pred             EEEECHHHHHH
T ss_conf             97758889999


No 135
>KOG0479 consensus
Probab=20.05  E-value=47  Score=13.46  Aligned_cols=53  Identities=17%  Similarity=0.280  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHHHHCCC--CCCCCCCCHHHHHHHHHHHHC-------CCCCHHHHHHHH
Q ss_conf             45777765457887643387--400064898999999988863-------873147899999
Q gi|254780979|r  363 KIVANWVINDLLGVLNRSGK--SIEDTPISPNQLGELIDLIID-------GTISGKIAKDIF  415 (500)
Q Consensus       363 k~~Anwi~~el~~~ln~~~~--~~~~~~i~p~~laeLi~li~~-------g~Is~~~aK~il  415 (500)
                      ..++.+|..+..++-|....  .-..+||++..|-.||.|--.       ..++...|+..+
T Consensus       578 ~ea~e~Ia~~Y~~LR~~d~~~d~~rt~PiTARtLETlIRLaTAhAKaRlSk~V~~~DAe~A~  639 (818)
T KOG0479         578 QEAAEYIAEEYTDLRNDDSRKDQERTSPITARTLETLIRLATAHAKARLSKVVEKDDAEAAV  639 (818)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHH
T ss_conf             99999999997643023443333454677189999999998877776631412454189999


No 136
>COG2160 AraA L-arabinose isomerase [Carbohydrate transport and metabolism]
Probab=20.04  E-value=57  Score=12.89  Aligned_cols=33  Identities=9%  Similarity=0.059  Sum_probs=16.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHH-HHHHHHHHHHHH
Q ss_conf             678862223540246599999-999999999731
Q gi|254780979|r  230 AWGTRCEVKNVNSIRFLGLAI-EYEARRQIAILE  262 (500)
Q Consensus       230 ~~GtRvEIKNlnS~~~i~~AI-~yEi~RQ~~ll~  262 (500)
                      .||+-|++=.+..+-.+.+++ +-|+.+-.+-++
T Consensus       201 qFGwsv~~~gIgdLv~~~~~vse~eV~~l~eey~  234 (497)
T COG2160         201 QFGWSVNTWGIGDLVEVVNEVSEGEVEALLEEYR  234 (497)
T ss_pred             HHCCEEEEEEHHHHHHHHHHCCHHHHHHHHHHHH
T ss_conf             6362576774468999997516878999999988


Done!