Query         gi|254780191|ref|YP_003064604.1| alanyl-tRNA synthetase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 898
No_of_seqs    260 out of 2790
Neff          6.2 
Searched_HMMs 39220
Date          Mon May 23 09:17:57 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780191.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK00252 alaS alanyl-tRNA synt 100.0       0       0 2394.1  83.7  856    1-898     1-862 (864)
  2 COG0013 AlaS Alanyl-tRNA synth 100.0       0       0 2376.4  81.5  860    1-898     5-877 (879)
  3 PRK13902 alaS lanyl-tRNA synth 100.0       0       0 2077.1  70.8  782    2-896    58-898 (898)
  4 KOG0188 consensus              100.0       0       0 1942.2  64.2  847    1-896     1-891 (895)
  5 PRK01584 alanyl-tRNA synthetas 100.0       0       0 1817.3  47.0  580    2-729     1-593 (593)
  6 pfam01411 tRNA-synt_2c tRNA sy 100.0       0       0 1548.9  44.7  542    6-579     1-545 (545)
  7 TIGR00344 alaS alanyl-tRNA syn 100.0       0       0 1282.4  48.5  848    6-879     1-914 (914)
  8 cd00673 AlaRS_core Alanyl-tRNA 100.0       0       0  838.7  18.2  232    4-240     1-232 (232)
  9 COG2872 Predicted metal-depend 100.0 8.5E-43       0  354.0  16.9  222  488-733    15-240 (241)
 10 KOG2105 consensus              100.0 1.5E-37 3.9E-42  312.9  28.6  357  509-896    42-408 (415)
 11 PRK00413 thrS threonyl-tRNA sy  99.1 4.9E-09 1.2E-13   89.6  15.2  149  583-739    67-234 (639)
 12 PRK03772 threonyl-tRNA synthet  99.1 5.8E-09 1.5E-13   89.0  14.9  161  565-739    51-237 (642)
 13 PRK12304 thrS threonyl-tRNA sy  99.1 1.1E-09 2.9E-14   94.6  10.8  162  564-739    20-204 (604)
 14 PRK12444 threonyl-tRNA synthet  99.1 2.5E-09 6.4E-14   91.9  11.8  168  565-740    55-241 (639)
 15 PRK04483 threonyl-tRNA synthet  99.1 1.4E-08 3.5E-13   86.1  15.0  152  581-739    67-237 (634)
 16 pfam07973 tRNA_SAD Threonyl an  99.1 7.2E-11 1.8E-15  103.9   2.6   44  676-724     1-44  (44)
 17 smart00863 tRNA_SAD Threonyl a  98.9 7.1E-10 1.8E-14   96.2   2.0   44  676-724     1-44  (44)
 18 PRK12305 thrS threonyl-tRNA sy  98.9 1.7E-08 4.4E-13   85.3   9.1  156  583-740     5-174 (576)
 19 COG0441 ThrS Threonyl-tRNA syn  98.5   9E-07 2.3E-11   71.9   8.0  134  584-728    28-171 (589)
 20 pfam02272 DHHA1 DHHA1 domain.   98.4 1.2E-06   3E-11   70.9   7.9   67  823-893     2-68  (69)
 21 cd00733 GlyRS_alpha_core Class  98.3  0.0002 5.2E-09   53.4  15.8  169    3-247     1-177 (279)
 22 PRK09348 glyQ glycyl-tRNA synt  98.2 0.00022 5.7E-09   53.1  15.9  167    1-247     1-179 (291)
 23 COG0752 GlyQ Glycyl-tRNA synth  98.1 0.00042 1.1E-08   51.0  15.5  175    1-246     4-181 (298)
 24 TIGR00418 thrS threonyl-tRNA s  98.1 7.4E-06 1.9E-10   64.7   6.3  148  586-744     1-176 (595)
 25 pfam02091 tRNA-synt_2e Glycyl-  98.1 0.00035   9E-09   51.6  14.1  166    6-247     3-176 (284)
 26 pfam01411 tRNA-synt_2c tRNA sy  97.7   9E-06 2.3E-10   64.0   0.4  107  130-263    93-205 (545)
 27 cd00768 class_II_aaRS-like_cor  97.0 0.00068 1.7E-08   49.3   3.5  175    5-233     3-211 (211)
 28 pfam00152 tRNA-synt_2 tRNA syn  95.2    0.26 6.7E-06   29.0   9.0  100    5-115    26-137 (341)
 29 pfam01409 tRNA-synt_2d tRNA sy  94.9    0.19 4.8E-06   30.2   7.6  180    4-244    19-230 (243)
 30 TIGR00344 alaS alanyl-tRNA syn  94.1   0.057 1.4E-06   34.3   3.5  100  145-266   126-239 (914)
 31 cd00669 Asp_Lys_Asn_RS_core As  94.0    0.27   7E-06   28.9   6.8  215    3-249     3-264 (269)
 32 cd00496 PheRS_alpha_core Pheny  93.6    0.62 1.6E-05   26.1   9.5  182    4-243     3-209 (218)
 33 PRK06462 asparagine synthetase  93.3    0.71 1.8E-05   25.7   8.4   99    5-113    33-152 (332)
 34 TIGR00644 recJ single-stranded  92.7    0.83 2.1E-05   25.1  14.3  139  753-897   428-570 (705)
 35 COG0016 PheS Phenylalanyl-tRNA  92.7    0.21 5.3E-06   29.8   4.5   14  694-707   282-295 (335)
 36 cd00777 AspRS_core Asp tRNA sy  92.2    0.96 2.5E-05   24.6  10.1  102    2-115     2-116 (280)
 37 PRK00488 pheS phenylalanyl-tRN  91.9    0.36 9.2E-06   28.0   4.9   13  694-706   284-296 (338)
 38 TIGR00470 sepS O-phosphoseryl-  91.9    0.29 7.4E-06   28.7   4.5   29  216-246   107-135 (558)
 39 KOG1501 consensus               91.2    0.17 4.3E-06   30.5   2.6   73  223-295    72-158 (636)
 40 cd00776 AsxRS_core Asx tRNA sy  90.7     1.3 3.3E-05   23.7   6.7   94    5-112    28-142 (322)
 41 COG2024 Phenylalanyl-tRNA synt  88.9     0.9 2.3E-05   24.9   4.8   55  669-729   406-473 (536)
 42 PTZ00326 phenylalanyl-tRNA syn  88.0     1.1 2.7E-05   24.3   4.7   14  694-707   456-469 (505)
 43 PRK04172 pheS phenylalanyl-tRN  87.4     1.4 3.5E-05   23.5   4.9   19  601-620   261-279 (501)
 44 PRK07562 ribonucleotide-diphos  87.1     2.2 5.7E-05   21.8   8.6   30  731-760  1017-1046(1177)
 45 TIGR00706 SppA_dom signal pept  86.6     1.2 3.1E-05   23.8   4.3   91  311-404   124-219 (224)
 46 KOG1637 consensus               86.5    0.23 5.9E-06   29.5   0.6   25  512-536   259-284 (560)
 47 TIGR00457 asnS asparaginyl-tRN  86.0       2 5.1E-05   22.2   5.2   31  825-856   380-410 (495)
 48 COG0104 PurA Adenylosuccinate   81.4     3.8 9.6E-05   20.0   6.0  168  210-396    54-235 (430)
 49 KOG1759 consensus               80.8     1.8 4.6E-05   22.5   3.2   28  106-133    76-103 (115)
 50 PRK06253 O-phosphoseryl-tRNA s  78.1     1.3 3.4E-05   23.5   1.8   26  669-698   397-422 (527)
 51 pfam01187 MIF Macrophage migra  75.7       2 5.2E-05   22.1   2.2   28  106-133    75-102 (114)
 52 KOG2783 consensus               75.1       3 7.5E-05   20.8   2.9   14  803-816   361-374 (436)
 53 TIGR00469 pheS_mito phenylalan  70.4     2.5 6.4E-05   21.4   1.7   40  803-842   386-427 (460)
 54 COG0017 AsnS Aspartyl/asparagi  69.9     4.2 0.00011   19.7   2.7   39  802-844   303-341 (435)
 55 smart00788 Adenylsucc_synt Ade  69.8     5.6 0.00014   18.6   3.3  173  209-402    51-238 (421)
 56 TIGR01677 pln_FAD_oxido plant-  69.1     4.3 0.00011   19.6   2.6   34  608-641   436-476 (577)
 57 COG1244 Predicted Fe-S oxidore  69.1     7.5 0.00019   17.7   6.7  104  218-334   159-279 (358)
 58 PRK00484 lysS lysyl-tRNA synth  68.8       1 2.6E-05   24.5  -0.7   20    5-24      7-26  (491)
 59 TIGR00016 ackA acetate kinase;  68.3     4.3 0.00011   19.5   2.5   34  712-750   246-283 (416)
 60 PRK09982 universal stress prot  68.0       7 0.00018   17.9   3.5   56  302-362    17-73  (142)
 61 PRK11649 hypothetical protein;  66.4     8.4 0.00021   17.3   3.8  108  516-644   301-413 (418)
 62 pfam00587 tRNA-synt_2b tRNA sy  64.9     6.6 0.00017   18.1   2.9  104    5-121     3-142 (170)
 63 PRK09275 aspartate aminotransf  64.2     9.1 0.00023   17.0   4.2   98  275-395    61-173 (531)
 64 pfam05882 consensus             62.2     1.9 4.8E-05   22.4  -0.3   45  322-366     8-58  (90)
 65 pfam01343 Peptidase_S49 Peptid  62.0     7.1 0.00018   17.9   2.6   47  341-387    82-128 (154)
 66 TIGR01343 hacA_fam homoaconita  61.7      10 0.00026   16.7   6.2   56  551-622    97-163 (432)
 67 KOG0121 consensus               57.8      11 0.00028   16.3   3.0   19   93-116    41-59  (153)
 68 TIGR00392 ileS isoleucyl-tRNA   57.1     5.5 0.00014   18.7   1.3   19  575-593   628-646 (938)
 69 COG3981 Predicted acetyltransf  56.2     9.5 0.00024   16.8   2.5   25  575-599   101-125 (174)
 70 pfam04536 DUF477 Domain of unk  55.2      13 0.00032   15.9  13.5   94  792-897    22-122 (124)
 71 TIGR02088 LEU3_arch isopropylm  55.0      13 0.00032   15.9   3.1   14  624-637    48-61  (350)
 72 cd03578 NTR_netrin-4_like NTR   54.2      11 0.00027   16.5   2.4   12  513-524    44-55  (111)
 73 pfam04199 Cyclase Putative cyc  54.1     8.3 0.00021   17.3   1.9   61  583-646    41-110 (162)
 74 TIGR00388 glyQ glycyl-tRNA syn  53.6      13 0.00034   15.7   5.0  173    3-247     2-178 (295)
 75 pfam06557 DUF1122 Protein of u  52.7      14 0.00035   15.6   4.1   44  102-149    60-103 (170)
 76 cd07215 Pat17_PNPLA8_PNPLA9_li  52.2      14 0.00036   15.5   6.2   70  573-648   245-320 (329)
 77 PRK06153 hypothetical protein;  52.2     2.6 6.7E-05   21.2  -0.9   35  787-824   260-294 (393)
 78 TIGR02156 PA_CoA_Oxy1 phenylac  51.6     9.8 0.00025   16.7   1.9   10  625-634   216-225 (297)
 79 TIGR02952 Sig70_famx2 RNA poly  51.3      14 0.00035   15.6   2.6   39  247-285    40-86  (171)
 80 COG2509 Uncharacterized FAD-de  51.3     4.2 0.00011   19.6  -0.0   86  667-764   277-367 (486)
 81 KOG4215 consensus               51.0      11 0.00027   16.5   2.0   82  575-669   183-268 (432)
 82 PRK09537 pylS pyrolysyl-tRNA s  51.0     8.9 0.00023   17.1   1.6   10  673-682   283-292 (420)
 83 KOG1159 consensus               50.2     6.9 0.00018   17.9   1.0   38  275-319    83-120 (574)
 84 cd00773 HisRS-like_core Class   50.2      15 0.00038   15.3   4.3   24    5-28      6-29  (261)
 85 COG3494 Uncharacterized protei  50.1      14 0.00036   15.6   2.5   35  691-729    42-78  (279)
 86 cd01017 AdcA Metal binding pro  50.0      15 0.00038   15.3   3.3  200  588-819     8-219 (282)
 87 pfam00709 Adenylsucc_synt Aden  49.4      15 0.00039   15.2   4.0  170  208-402    50-238 (420)
 88 pfam10440 WIYLD WIYLD domain.   49.1      15 0.00039   15.2   4.5   40  303-342     9-48  (65)
 89 PTZ00068 60S ribosomal protein  48.7      16  0.0004   15.1   2.9   24  739-762   134-157 (201)
 90 TIGR01283 nifE nitrogenase MoF  46.9      17 0.00042   15.0   7.3  162  694-882   203-418 (470)
 91 cd01140 FatB Siderophore bindi  46.4      11 0.00028   16.4   1.4   16  512-527   243-258 (270)
 92 TIGR00170 leuC 3-isopropylmala  46.2      17 0.00043   14.9   3.6   46  541-597   101-146 (472)
 93 cd03698 eRF3_II_like eRF3_II_l  46.2      17 0.00043   14.9   3.0   14  558-571    20-33  (83)
 94 TIGR00468 pheS phenylalanyl-tR  46.0      17 0.00044   14.9   3.0   32  627-658   240-274 (362)
 95 pfam04931 DNA_pol_phi DNA poly  45.9     8.3 0.00021   17.3   0.8   11  133-143   151-161 (784)
 96 pfam04336 DUF479 Protein of un  45.8      17 0.00044   14.8   3.5   31  279-309    40-73  (106)
 97 cd07213 Pat17_PNPLA8_PNPLA9_li  45.3      18 0.00045   14.8   3.9   57  573-640   223-279 (288)
 98 PRK01346 hypothetical protein;  45.2      18 0.00045   14.8   2.4   47  822-879   335-383 (411)
 99 COG1480 Predicted membrane-ass  44.2      18 0.00046   14.7   2.3   71  581-658   577-670 (700)
100 TIGR02364 dha_pts dihydroxyace  44.0      18 0.00047   14.6   2.8   14  879-892    45-58  (128)
101 PRK12421 ATP phosphoribosyltra  43.9      18 0.00047   14.6   6.3   36    4-42     24-59  (391)
102 PRK01117 adenylosuccinate synt  43.6      19 0.00047   14.6   4.7  173  208-402    52-241 (431)
103 KOG1035 consensus               42.5      19 0.00049   14.5   7.1   11  587-597   863-873 (1351)
104 COG1512 Beta-propeller domains  42.2      19 0.00049   14.4  10.3   53  620-674    38-94  (271)
105 COG0060 IleS Isoleucyl-tRNA sy  41.9      20  0.0005   14.4   4.5   97  101-202   124-234 (933)
106 KOG0554 consensus               41.1      11 0.00029   16.2   0.9   30  509-544    50-79  (446)
107 PRK10528 multifunctional acyl-  40.7      20 0.00052   14.3   4.1   14  225-238    55-68  (191)
108 KOG2384 consensus               40.7      20 0.00052   14.3   4.3   20  288-307   144-163 (223)
109 PRK11118 hypothetical protein;  40.4      21 0.00052   14.2   3.2   54  617-670     5-58  (100)
110 COG3957 Phosphoketolase [Carbo  38.9      17 0.00042   15.0   1.5   30  146-176    74-103 (793)
111 KOG0556 consensus               38.6      19 0.00048   14.5   1.7   28  800-827   396-423 (533)
112 TIGR02155 PA_CoA_ligase phenyl  38.5      22 0.00056   14.0   6.5   19  805-823   383-401 (431)
113 PRK09819 alpha-mannosidase; Pr  38.2      22 0.00056   14.0   8.4   53  347-399   345-397 (874)
114 PRK12336 translation initiatio  37.9      22 0.00057   14.0   6.3   48  584-644    49-96  (201)
115 PRK07757 acetyltransferase; Pr  37.8      22 0.00057   14.0   2.7   23  628-650     8-30  (152)
116 TIGR02915 PEP_resp_reg putativ  37.8      22 0.00057   13.9   3.1   38  363-400    59-107 (451)
117 PRK02983 lysS lysyl-tRNA synth  37.6     7.7  0.0002   17.6  -0.4   10  593-602   782-791 (1099)
118 COG5405 HslV ATP-dependent pro  37.5      23 0.00057   13.9   3.5   42  723-769    47-88  (178)
119 PRK13137 consensus              37.3      23 0.00058   13.9   4.0   42  361-406     4-46  (266)
120 PRK01233 glyS glycyl-tRNA synt  37.2      23 0.00058   13.9   9.6   15    5-19     23-37  (687)
121 pfam08803 ydhR Putative mono-o  37.0      23 0.00059   13.9   3.1   54  617-670     2-55  (97)
122 COG3673 Uncharacterized conser  36.8      21 0.00054   14.1   1.7  121  270-402   109-232 (423)
123 cd01138 FeuA Periplasmic bindi  36.6      16 0.00042   15.0   1.1   14  512-525   235-248 (248)
124 COG1730 GIM5 Predicted prefold  36.3      24  0.0006   13.8   7.0   55  715-771    81-135 (145)
125 TIGR01068 thioredoxin thioredo  35.8      12 0.00031   16.1   0.3   17  786-802    39-55  (101)
126 pfam08318 COG4 COG4 transport   35.8      24 0.00061   13.7   3.9   22  273-294    54-75  (330)
127 PTZ00072 40S ribosomal protein  35.6      24 0.00061   13.7   6.3   60  369-429    30-96  (148)
128 PRK13787 adenylosuccinate synt  35.0      25 0.00063   13.6   4.3  171  209-402    53-240 (423)
129 KOG0434 consensus               34.9      14 0.00037   15.5   0.6   51  317-367   404-455 (1070)
130 pfam11079 YqhG Bacterial prote  34.5      25 0.00064   13.6   3.3   11  815-825   238-248 (260)
131 PRK11805 N5-glutamine S-adenos  34.4      25 0.00064   13.6   4.8   27  624-650    65-91  (307)
132 TIGR01428 HAD_type_II haloacid  33.6      26 0.00066   13.5   2.6   13  397-409   125-137 (207)
133 PRK10045 acyl carrier protein   33.6      26 0.00066   13.5   2.9   59  273-337    20-84  (193)
134 pfam00853 Runt Runt domain.     33.5      11 0.00027   16.4  -0.2   17   72-88     81-97  (134)
135 COG2826 Tra8 Transposase and i  33.2      26 0.00065   13.5   1.7   51  595-648   237-302 (318)
136 TIGR02707 butyr_kinase butyrat  33.0      24  0.0006   13.8   1.5   19  399-417   132-150 (353)
137 PRK12570 N-acetylmuramic acid-  32.6      27 0.00068   13.4   1.9   58  346-403    21-93  (296)
138 PRK08561 rps15p 30S ribosomal   32.6      27 0.00068   13.4   5.9   60  369-429    33-99  (151)
139 COG2012 RPB5 DNA-directed RNA   32.5      21 0.00054   14.1   1.1   47  626-681    20-66  (80)
140 TIGR03443 alpha_am_amid L-amin  32.0      23 0.00059   13.8   1.3   11  848-858  1148-1158(1389)
141 cd06008 NF-X1-zinc-finger Pres  31.9      17 0.00042   15.0   0.5   11  166-176    22-32  (49)
142 COG0282 ackA Acetate kinase [E  31.9     8.6 0.00022   17.2  -0.9   54  790-845   316-381 (396)
143 COG0430 RCL1 RNA 3'-terminal p  31.8      27  0.0007   13.3   1.6   18  509-526   146-163 (341)
144 TIGR03533 L3_gln_methyl protei  31.6      28  0.0007   13.2   5.0   27  624-650    53-79  (284)
145 COG0751 GlyS Glycyl-tRNA synth  31.4      28 0.00071   13.2  10.3   44  246-293   130-177 (691)
146 PRK11619 lytic murein transgly  31.4      28 0.00071   13.2   2.0   42  707-752   498-539 (645)
147 COG3316 Transposase and inacti  31.2      28 0.00071   13.2   1.9   38  386-424    16-53  (215)
148 cd06815 PLPDE_III_AR_like_1 Ty  31.2      28 0.00071   13.2   2.5   21  564-584   323-343 (353)
149 pfam02031 Peptidase_M7 Strepto  31.0      20 0.00051   14.3   0.8   19  584-602    72-90  (132)
150 TIGR02639 ClpA ATP-dependent C  31.0      28 0.00072   13.2   3.3  114  300-420     4-145 (774)
151 TIGR00871 zwf glucose-6-phosph  31.0      28 0.00072   13.2   5.0  326  216-605    59-440 (498)
152 PRK11411 fecB iron-dicitrate t  30.9      28 0.00072   13.2   2.1   23  385-411   186-208 (297)
153 PRK11070 ssDNA exonuclease Rec  30.9      28 0.00072   13.2  16.2   91  797-895   355-449 (574)
154 CHL00130 rbcS ribulose-1,5-bis  30.9      28 0.00072   13.1   5.7   91  621-718     8-119 (138)
155 cd01553 EPT_RTPC-like This dom  30.8      27 0.00069   13.3   1.5   21  508-528   141-161 (211)
156 smart00022 PLAc Cytoplasmic ph  30.6      29 0.00073   13.1   2.2   11  588-598   301-311 (549)
157 CHL00176 ftsH cell division pr  30.6      29 0.00073   13.1   1.6   15  575-589   347-361 (631)
158 KOG0037 consensus               30.3     7.6 0.00019   17.6  -1.4   30  394-424   155-188 (221)
159 TIGR00458 aspS_arch aspartyl-t  30.2      23  0.0006   13.8   1.1  206  625-840   147-366 (466)
160 TIGR01181 dTDP_gluc_dehyt dTDP  29.9      29 0.00075   13.0   3.1   17  583-599    97-113 (340)
161 pfam11867 DUF3387 Domain of un  29.7      29 0.00075   13.0   6.7  162  214-377    29-209 (333)
162 cd05007 SIS_Etherase N-acetylm  29.7      29 0.00075   13.0   2.4   59  346-404    12-85  (257)
163 pfam09637 Med18 Med18 protein.  29.6      19 0.00047   14.6   0.5   13  513-525   163-175 (239)
164 TIGR03076 near_not_gcvH Chlamy  29.5      18 0.00046   14.7   0.4   36  613-651   432-467 (686)
165 KOG1576 consensus               29.2      30 0.00077   12.9   1.8   12  513-524    69-80  (342)
166 TIGR02873 spore_ylxY probable   29.1      30 0.00077   12.9   3.0   43  599-654   139-181 (269)
167 pfam01113 DapB_N Dihydrodipico  29.1      26 0.00067   13.4   1.2   17  625-641    97-113 (122)
168 TIGR01099 galU UTP-glucose-1-p  28.9      30 0.00077   12.9   2.2  121  712-839    39-175 (270)
169 COG1482 ManA Phosphomannose is  28.8      30 0.00077   12.9   1.7   25  113-138    79-103 (312)
170 KOG0673 consensus               28.6      31 0.00078   12.9   3.3   15  333-347    47-61  (293)
171 KOG0414 consensus               28.3      24 0.00062   13.7   0.9   20  390-409   386-405 (1251)
172 pfam01297 SBP_bac_9 Periplasmi  28.3      31 0.00079   12.8   3.4   81  739-819   121-213 (272)
173 TIGR02367 PylS pyrrolysyl-tRNA  28.2      31 0.00079   12.8   1.5   59  565-654    39-97  (453)
174 PRK10628 hypothetical protein;  27.9      24  0.0006   13.8   0.7   15  388-402    47-61  (246)
175 pfam03473 MOSC MOSC domain. Th  27.4      32 0.00082   12.7   2.0   13  560-572   111-123 (124)
176 COG0124 HisS Histidyl-tRNA syn  27.4      29 0.00073   13.1   1.1   14   98-111    10-23  (429)
177 pfam00413 Peptidase_M10 Matrix  26.7      33 0.00084   12.6   4.0   49  589-638   104-156 (158)
178 PRK05441 murQ N-acetylmuramic   26.6      33 0.00084   12.6   2.6   59  346-404    21-94  (273)
179 pfam00634 BRCA2 BRCA2 repeat.   26.6      23 0.00059   13.8   0.5   26  873-898     7-32  (35)
180 cd00375 Urease_alpha Urease al  26.5      31 0.00079   12.8   1.2  128  114-266    69-221 (567)
181 KOG4445 consensus               26.4      33 0.00085   12.6   3.4   32  617-648    62-93  (368)
182 TIGR01840 esterase_phb esteras  26.4      29 0.00074   13.1   1.0   11  118-128   106-116 (231)
183 KOG2021 consensus               26.3      33 0.00085   12.6   7.0   51  321-376   379-429 (980)
184 LOAD_rna_Cyc consensus          26.3      33 0.00085   12.6   1.5   18  511-528   144-161 (329)
185 KOG2805 consensus               26.1      17 0.00043   14.9  -0.3   22  198-220    77-99  (377)
186 TIGR02966 phoR_proteo phosphat  26.0      33 0.00083   12.7   1.2   12  805-816   232-243 (339)
187 TIGR01204 bioW 6-carboxyhexano  25.8      34 0.00087   12.5   1.8   37  702-739   192-231 (238)
188 PHA02103 hypothetical protein   25.8      25 0.00064   13.6   0.6   15  129-143    84-98  (135)
189 COG5127 Vacuolar H+-ATPase V1   25.8      34 0.00087   12.5   8.7   26  575-600   131-156 (383)
190 pfam11554 DUF3232 Protein of u  25.7      25 0.00063   13.6   0.5   11  806-816    70-80  (149)
191 COG0572 Udk Uridine kinase [Nu  25.2      35 0.00089   12.4   3.0   12  620-631    61-72  (218)
192 cd00775 LysRS_core Lys_tRNA sy  25.0      35  0.0009   12.4   6.3   87    5-101    12-111 (329)
193 TIGR00459 aspS_bact aspartyl-t  24.8      23 0.00059   13.8   0.2   25  743-767   559-584 (653)
194 pfam10503 Esterase_phd Esteras  24.6      36 0.00091   12.4   1.8   77   32-130    32-110 (226)
195 PRK03947 prefoldin subunit alp  24.6      36 0.00091   12.3   6.5   53  716-770    83-135 (141)
196 cd00477 FTHFS Formyltetrahydro  24.5      21 0.00053   14.2  -0.0   34  703-736   287-322 (524)
197 cd03695 CysN_NodQ_II CysN_NodQ  24.4      36 0.00092   12.3   4.3   34  484-517    36-69  (81)
198 pfam05634 DUF794 Arabidopsis t  24.4      29 0.00074   13.1   0.7   10  386-395   149-158 (378)
199 pfam06925 MGDG_synth Monogalac  24.4      36 0.00092   12.3   2.9   35  367-410    79-113 (169)
200 KOG2484 consensus               24.3      36 0.00092   12.3   1.5   12  509-520   178-189 (435)
201 PRK05963 3-oxoacyl-(acyl carri  24.0      37 0.00093   12.3   3.5   13  671-683   304-316 (327)
202 PRK05771 V-type ATP synthase s  24.0      37 0.00093   12.3  12.1   15  627-641   281-295 (640)
203 pfam09292 Neil1-DNA_bind Endon  23.9      37 0.00093   12.3   2.2   37  135-171     3-39  (39)
204 cd04162 Arl9_Arfrp2_like Arl9/  23.9      37 0.00094   12.3   7.6   95  792-898    66-160 (164)
205 COG1210 GalU UDP-glucose pyrop  23.9      37 0.00094   12.2   3.2  112  711-830    41-162 (291)
206 PRK10707 hypothetical protein;  23.8      37 0.00094   12.2   2.4   10  591-600    75-84  (190)
207 smart00762 Cog4 COG4 transport  23.7      37 0.00094   12.2   3.9   13  413-425   173-185 (324)
208 PRK13308 ureC urease subunit a  23.4      37 0.00096   12.2   1.5  131  114-266    72-221 (569)
209 PRK10957 iron-enterobactin tra  23.4      28 0.00071   13.2   0.4   27  211-237    35-63  (319)
210 PTZ00179 60S ribosomal protein  23.1      23 0.00058   13.9  -0.1   44  571-625    53-98  (189)
211 cd02948 TRX_NDPK TRX domain, T  23.1      26 0.00066   13.4   0.2   14  807-820    33-46  (102)
212 PRK09258 3-oxoacyl-(acyl carri  23.1      38 0.00097   12.1   4.8   90  333-426    24-129 (339)
213 TIGR02924 ICDH_alpha isocitrat  23.1      38 0.00097   12.1   2.4   23  808-830   389-411 (481)
214 PRK13985 UreB urease subunit b  23.1      24 0.00062   13.7   0.1   50  114-177    69-121 (568)
215 cd03527 RuBisCO_small Ribulose  23.0      38 0.00097   12.1   5.2   48  621-671     6-57  (99)
216 TIGR00113 queA S-adenosylmethi  22.9      38 0.00098   12.1   1.6   60  512-576    56-116 (364)
217 TIGR03257 met_CoM_red_bet meth  22.9      30 0.00075   13.0   0.5   79  216-307   109-194 (433)
218 COG4402 Uncharacterized protei  22.8      32 0.00081   12.8   0.6   14   86-99     95-108 (457)
219 TIGR01803 CM-like chorismate m  22.6      39 0.00099   12.1   2.4   25  308-332    53-77  (82)
220 COG1944 Uncharacterized conser  22.5      34 0.00086   12.6   0.7   22  806-827   336-357 (398)
221 PRK02948 cysteine desulfurase;  22.5      39 0.00099   12.1   1.7   22  877-898   353-374 (381)
222 pfam10075 PCI_Csn8 COP9 signal  22.5      39 0.00099   12.1   1.7   24  319-342    38-61  (144)
223 KOG1227 consensus               22.5      32 0.00082   12.7   0.6   42  694-737   193-236 (351)
224 TIGR00434 cysH phosophoadenyly  22.4      39   0.001   12.0   3.7   23  385-409    73-95  (226)
225 pfam01268 FTHFS Formate--tetra  22.3      23 0.00059   13.8  -0.2   34  703-736   303-338 (555)
226 cd07211 Pat_PNPLA8 Patatin-lik  22.1      39   0.001   12.0   5.9   56  581-646   248-308 (308)
227 pfam03455 dDENN dDENN domain.   22.0      40   0.001   12.0   2.1   13    5-17      3-15  (68)
228 TIGR02959 SigZ RNA polymerase   21.9      40   0.001   12.0   1.3   60  354-426    82-141 (170)
229 PRK10252 entF enterobactin syn  21.9      40   0.001   12.0   1.8   25  616-640   715-739 (1293)
230 TIGR01508 rib_reduct_arch diam  21.8      28 0.00072   13.1   0.2   66  802-879   131-196 (224)
231 COG0467 RAD55 RecA-superfamily  21.7      40   0.001   11.9   4.1   35  273-316   127-161 (260)
232 TIGR02706 P_butyryltrans phosp  21.6      40   0.001   11.9   1.7   16  336-351   142-157 (295)
233 cd07363 45_DOPA_Dioxygenase Th  21.5      38 0.00098   12.1   0.8   15  388-402    57-71  (253)
234 PRK08332 ribonucleotide-diphos  21.5      41   0.001   11.9   8.1  256   10-293   240-531 (1748)
235 pfam06623 MHC_I_C MHC_I C-term  21.3      38 0.00096   12.2   0.8   17  865-884     3-19  (29)
236 PRK03147 thiol-disulfide oxido  21.2      27 0.00068   13.3  -0.0   14  388-401    45-58  (176)
237 pfam05631 DUF791 Protein of un  21.1      20  0.0005   14.4  -0.7   27  271-297    72-98  (354)
238 PRK12292 hisZ ATP phosphoribos  21.0      41  0.0011   11.8   7.2   34  628-661   334-367 (388)
239 COG3235 Predicted membrane pro  21.0      38 0.00098   12.1   0.8   14  281-294    94-107 (223)
240 TIGR03400 18S_RNA_Rcl1p 18S rR  20.9      42  0.0011   11.8   1.3   18  511-528   143-160 (360)
241 pfam04526 DUF568 Protein of un  20.9      31 0.00078   12.9   0.2   13  603-615    69-81  (101)
242 PRK07956 ligA NAD-dependent DN  20.9      19 0.00047   14.6  -0.9   18  798-815   602-619 (668)
243 PRK06052 5-methyltetrahydropte  20.7      42  0.0011   11.8   3.1   39  303-356    38-76  (343)
244 CHL00201 syh histidine-tRNA sy  20.7      36 0.00093   12.3   0.6   30  627-656   333-362 (424)
245 KOG0128 consensus               20.4      23 0.00058   13.9  -0.5   18  219-237   258-275 (881)
246 pfam09404 DUF2003 Eukaryotic p  20.3      43  0.0011   11.7   0.9   14   86-99     18-31  (447)
247 COG4043 Preprotein translocase  20.3      31 0.00079   12.8   0.1   60  358-424    11-85  (111)
248 pfam02906 Fe_hyd_lg_C Iron onl  20.2      42  0.0011   11.8   0.8   60  287-347    50-109 (286)
249 PRK13309 ureC urease subunit a  20.2      43  0.0011   11.7   1.2   51  114-177    72-125 (572)
250 KOG2250 consensus               20.2      43  0.0011   11.7   0.8   20  390-409   287-306 (514)
251 PRK06720 hypothetical protein;  20.1      40   0.001   12.0   0.7   26  796-821    67-92  (169)
252 KOG1372 consensus               20.1      36 0.00091   12.3   0.4   47  296-348    50-100 (376)
253 pfam07897 DUF1675 Protein of u  20.1      43  0.0011   11.7   1.8   46  639-700   214-262 (283)
254 cd04278 ZnMc_MMP Zinc-dependen  20.0      43  0.0011   11.7   4.3   46  587-638   109-155 (157)

No 1  
>PRK00252 alaS alanyl-tRNA synthetase; Reviewed
Probab=100.00  E-value=0  Score=2394.14  Aligned_cols=856  Identities=51%  Similarity=0.847  Sum_probs=821.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCHHHC
Q ss_conf             97878999999999997898891166756677871002301434755400588799999851115432248987863434
Q gi|254780191|r    1 MSNVSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNIFTGQEKPVYQAVTTVQKCVRAGGKHNDLDNV   80 (898)
Q Consensus         1 m~s~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~f~G~~~p~~~r~~~~QkCiR~ggkhnDld~V   80 (898)
                      |||++|||++||+||++|||+++|||||||+||||||||||||+||||||+|+++||++|+|+||||||+    ||||||
T Consensus         1 ~m~~~eiR~~fl~fF~~k~H~~v~s~~lvp~~DptllftnAGm~~fk~~f~G~~~p~~~r~~~~QkCiR~----nDld~V   76 (864)
T PRK00252          1 MMTTAEIRQAFLDFFESKGHTVVPSSSLVPKNDPTLLFTNAGMVQFKDYFLGLEKPPYPRATTSQKCIRT----NDLENV   76 (864)
T ss_pred             CCCHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCEEEEECCCCCCHHHHCCCCCCCCCCCCCCCCCEEC----CCHHHC
T ss_conf             9977999999999998789888078772558998046750364016223258878999973454034003----648763


Q ss_pred             CCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHCCCCHHHEEECCCCCCC
Q ss_conf             64885001788854223147537889998998613341898123799971882899997566349998997535786665
Q gi|254780191|r   81 GRTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKLWKKISGLSADKIIRITTNDNF  160 (898)
Q Consensus        81 G~t~rH~TfFEMlGn~SfgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~iW~~~~gi~~~~i~~~~~~dNf  160 (898)
                      |+|+|||||||||||||||||||+|||.|||||||++|+|||+|||||||++|+||++||++.+|||++||++++.+|||
T Consensus        77 G~t~rH~TfFEMlGN~SfGdYfK~eai~~awe~lt~~~~l~~~~l~vTv~~~D~e~~~iW~~~~gi~~~~I~~~~~~dNf  156 (864)
T PRK00252         77 GYTARHHTFFEMLGNFSFGDYFKKEAIEFAWELLTSVLGLPKEKLYVTVYEDDDEAYDIWKKEIGVPPERIIRIGASDNF  156 (864)
T ss_pred             CCCCCCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHEEEEEECCCHHHHHHHHHCCCCCHHHEEECCCCCCC
T ss_conf             88877525442376566551058899999999987541897799599993787899999987029988993536754563


Q ss_pred             CCCCCCCCCCCCEEEEEECCCCCCCCCCCC-CCCCCCEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCC
Q ss_conf             457999998770467885385568988877-7889826896001123443047887565766531017579999999887
Q gi|254780191|r  161 WSMAETGPCGPCSEIFFDQGECIPGGLPGS-SEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLERMATVLQE  239 (898)
Q Consensus       161 W~~g~~GpcGPcsEi~~d~g~~~~~~~~~~-~~~~~r~lEiwNlVFmq~~~~~~g~~~~Lp~~~IDTGmGLERl~~vlqg  239 (898)
                      |+||+|||||||||||||||++++++.++. .+||||||||||||||||||+.+|+|.|||+||||||||||||+|++||
T Consensus       157 W~mG~~GpcGPcsEI~yD~g~~~~~~~~~~~~~d~~r~lEiwNlVFmQynr~~~g~~~~Lp~k~IDTGmGLERl~~vlQg  236 (864)
T PRK00252        157 WSMGDTGPCGPCSEIFYDRGEEYWGGPPGSPEEDGDRYIEIWNLVFMQFNRDADGNLTPLPKKNIDTGMGLERIAAILQG  236 (864)
T ss_pred             CCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCC
T ss_conf             11489869987657898506523789988776677645665210101540288997444888874467679999999849


Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             98530057699999999973067854335024899999898999987403333444641257788999999999848743
Q gi|254780191|r  240 KTNNYDIDLFKHLIQASEQVTGMKYEGNNIVNHRVIVDHLRSSSFLIADGILPANEGRGYVLRRIMRRAMCYARLLGYTE  319 (898)
Q Consensus       240 ~~s~ydtD~f~pii~~i~~~~g~~y~~~~~~~~rvIaDH~Ra~~f~I~DGv~PsN~GrGYvlRrilRRa~r~~~~lg~~~  319 (898)
                      ++||||||+|.|||++|+++||++|..+.++||||||||+||++|||+|||+|||+|||||||||||||+||+++||++.
T Consensus       237 ~~snYdtDlF~pii~~i~~~s~~~~~~~~~~a~RVIADH~R~~~f~I~DGv~PsN~grGYVLRRilRRA~r~~~~Lg~~~  316 (864)
T PRK00252        237 VHSNYETDLFRPLIKAIEELTGVKYDEDDDVSFRVIADHIRSVAFLIADGVLPSNEGRGYVLRRILRRAVRHGRLLGIKE  316 (864)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf             98760203089999999998589976566501234577776655123257644668884499999999999999838995


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHH
Q ss_conf             31045689999986455555576467889999874898999999899999999861154642457437998524588889
Q gi|254780191|r  320 PLMMHLLPALCTEMGSAYPELIQAKLLIEETLRSEDERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLD  399 (898)
Q Consensus       320 ~fl~~lv~~v~~~m~~~ypeL~~~~~~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsg~~af~LyDTyGfP~d  399 (898)
                      |||++||+.+++.|++.||||.++++.|.+||+.||++|.+||++|+++|++.+++++ ++.|||++||+||||||||+|
T Consensus       317 ~fl~~Lv~~v~~~m~~~ypeL~~~~~~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~~k-~~~lsge~aF~LYDTyGfP~d  395 (864)
T PRK00252        317 PFLYKLVPVLIDVMGDAYPELKEKQELIEKVLKAEEERFLKTLERGLKLLEEELAKLK-GKVLSGEDAFKLYDTYGFPLD  395 (864)
T ss_pred             CHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHCCCCCHH
T ss_conf             3388889999999745451667779999999999999999999988999999998656-895688999988860599889


Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99987665077443588899999999976444331100120135678887304886264344444321112221113444
Q gi|254780191|r  400 IMQDILCARGLAGIDIISFNQALEEQRSRARAHSLGLGSGTTEKIWFSLKEKYGATQFIGYDLLRGSKFMKEDRKVLCQK  479 (898)
Q Consensus       400 lt~eia~e~gi~~vD~~~f~~~m~~qk~~sr~~~~~~~~~~~~~~~~~~~~~~~~t~F~GYe~~~~~~~~~~~~~~~~~~  479 (898)
                      ||++||+|+|+. ||+++|+++|++||++||++++..+.      ..++.....+|+|+||+.++               
T Consensus       396 Lt~~ia~e~gi~-vD~~~F~~~m~~qk~~sr~~~~~~~~------~~~~~~~~~~teF~GYe~~~---------------  453 (864)
T PRK00252        396 LTAEIARERGLK-VDEEGFEAAMEEQRERARAAAKFGSG------FNDLLEVDGATEFVGYDTLE---------------  453 (864)
T ss_pred             HHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHCCCCCCC------HHHHHHCCCCCEEECCCCCC---------------
T ss_conf             999999986996-67788999999999998750023542------57686447985240466454---------------


Q ss_pred             CCCCCCCCCCEEEEEEEECCCEEEECCCCCEEEEEECCCCEEECCCCCCCCCCEEEECCEEEEEECCCCCCCEEEEEEEC
Q ss_conf             54455565534899997478132000479769999737520003687656651454042489852245655338998510
Q gi|254780191|r  480 PPIDLTNGVSSIVKAIVQQGEIVEEAVSGQKVEVVFDQTPFYAEAGGQLGDTGCAIGDGIRLQITDVQKKAEGIFVHHAI  559 (898)
Q Consensus       480 ~~~~~~~~~~s~v~~i~~~~~~v~~~~~g~~~~ivLd~T~FY~E~GGQ~~D~G~i~~~~~~~~V~dv~k~~~g~i~H~~~  559 (898)
                              ++++|++++.+++.|+++++|+.++||||+||||||||||++|+|+|.+++..+.|.||||..+|+++|++.
T Consensus       454 --------~~akVl~i~~~~~~v~~~~~~~~~~vVLd~T~FY~E~GGQ~~D~G~i~~~~~~~~V~dv~k~~~~~i~H~~~  525 (864)
T PRK00252        454 --------AEAKVLALFKDGESVDSASAGEEVVVVLDQTPFYAESGGQVGDTGLIKGDGGRFEVTDTQKPPGGLIVHIGK  525 (864)
T ss_pred             --------EEEEEEEEEECCEEEEEECCCCEEEEEECCCCCEECCCCCCCCCEEEEECCCEEEEEEEEEECCCEEEEEEE
T ss_conf             --------169999998788662130579558999468753015789678741796089648986207705986999998


Q ss_pred             CCCCCCCCCCEEEEEEHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHH
Q ss_conf             46787556733888421255677752013688999997521254444455300243000002476789999999999999
Q gi|254780191|r  560 VERGILRTEMSLVLTIDYQNRRQLSINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNV  639 (898)
Q Consensus       560 ~~~g~l~~g~~V~~~VD~~rR~~~~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~v  639 (898)
                      +.+|++++|++|.+.|||+||..+|+|||||||||+|||++||+||+|+||+|+++++||||||+++||++||.+||++|
T Consensus       526 ~~~g~l~~g~~V~~~iD~~rR~~~~~nHTatHlL~~alr~vlG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~iE~~v  605 (864)
T PRK00252        526 VESGSLKVGDTVTAEVDEARRRAIARNHSATHLLHAALRQVLGEHVTQKGSLVAPDRLRFDFSHFEALTPEELRQVEDLV  605 (864)
T ss_pred             ECCCCCCCCCEEEEEECHHHHHHHHHHCHHHHHHHHHHHHHHCCCEEECCCCCCCCEEEEEECCCCCCCHHHHHHHHHHH
T ss_conf             22686456998999986999999986357999999999998487708666335776079973168889999999999999


Q ss_pred             HHHHHHCCCCEEEEECCCCCCCCHHHHHHHHCCCCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCCCCCC
Q ss_conf             89887304530466123222100035544315556248998447677855310156222588646011001101212688
Q gi|254780191|r  640 NDIIAQNLPVVTRIMNREDAIASGAAALLGTKYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESSIRAG  719 (898)
Q Consensus       640 N~~I~~n~~V~~~~~~~~eA~~~ga~alfgekygd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~si~sG  719 (898)
                      |++|++|+||++.+|++++|++.||+|+|||||||+||||+|+     +||+||||||||.|||+||.|||++++++++|
T Consensus       606 N~~I~~n~~V~~~~~~~~eA~~~ga~alfgekY~d~VRVV~ig-----~~s~ElCGGTHv~~TgeIg~~kI~~e~~i~~G  680 (864)
T PRK00252        606 NEQIRENLPVETEEMDIEEAKKMGAMALFGEKYGDEVRVVSMG-----DFSIELCGGTHVSNTGDIGLFKIVSESGVAAG  680 (864)
T ss_pred             HHHHHHCCCEEEEECCHHHHHHHCHHHHCCCCCCCEEEEEEEC-----CEEEECCCCCCCCCCCEEEEEEEEEECCCCCC
T ss_conf             9999967965898569899975231210142148806999989-----92685678988997052354999984563588


Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHCCC
Q ss_conf             2899997168999999999999999999839998899999999999999999999999999876365-----35553695
Q gi|254780191|r  720 IRRIEAITGQRARSHLMGQDEKLKSLASFLKVSQGNVVGRVEEIWEEYRKLQLIHAKRKLQLNVEDL-----SCHKIADV  794 (898)
Q Consensus       720 vRRIeavtG~~A~~~~~~~~~~l~~la~~L~~~~~~i~~ki~~L~~e~K~l~k~~~k~k~~~~~~~~-----~~~~i~~~  794 (898)
                      ||||||+||.+|++|+++.++.+++++..|+++.+++++++++|++++|++++++.+++.+......     .+..++++
T Consensus       681 vrRIeavtG~~A~~~~~~~~~~l~~l~~~l~~~~~~l~~~v~~l~~e~k~l~k~l~~l~~~~~~~~~~~l~~~~~~i~~~  760 (864)
T PRK00252        681 VRRIEAVTGEAALEYLNEQEALLKEIAALLKAPPDELPERVAALLEELKELEKELEQLKKKLAAAAAGDLLAQAEEINGV  760 (864)
T ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEECCE
T ss_conf             17999971589999999999999999998689988999999999999999999999999999999898888656142886


Q ss_pred             CEEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCEEEEEEEECHHHHCCCCHHHHHHHHHHHHCCCCCCCCCHH
Q ss_conf             27999957999789999999999754997899999538981799998677897267989999999988349999998101
Q gi|254780191|r  795 NFMSHIISEVDSKELKSVMDALQKKIQSGIIMLVGISKEKKASVLIVVTEDLLDRFNAVDLARLSAKVLGGGGGGGRPHM  874 (898)
Q Consensus       795 ~~i~~~~~~~d~~~Lr~l~d~l~~k~~~~vvvL~~~~~~~k~~ivv~vs~~~~~~~~A~~lik~ia~~l~GGgGGGkpd~  874 (898)
                      +++...+++.|+++||.+++.++++.++.+++|++ ..++|+.+++++++++.++++|++|+|++++.+ ||||||||+|
T Consensus       761 ~~i~~~~~~~d~k~Lr~l~~~l~~k~~~~vvil~s-~~~~K~~~vv~vs~~~~~~i~A~~lvk~i~~~~-gGkGGGkp~~  838 (864)
T PRK00252        761 KVLAAQLDGVDAKDLRTLADDLKNKLGSGVVVLAS-VADGKVSLVVGVTKDLTKGLKAGDLVKELAAIV-GGKGGGRPDM  838 (864)
T ss_pred             EEEEEEECCCCHHHHHHHHHHHHHHCCCEEEEEEE-ECCCEEEEEEEECHHHCCCCCHHHHHHHHHHHC-CCCCCCCHHH
T ss_conf             99999906999999999999999656996999998-039908999998978727988899999999865-9965793574


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             145899987889999999998619
Q gi|254780191|r  875 AQSGGPNGNKADQAIAGVASFLKK  898 (898)
Q Consensus       875 AQgGG~~~~~l~eal~~vk~~Lke  898 (898)
                      |||||++++++++||+.++++|++
T Consensus       839 AQgGG~~~~~l~~al~~a~~~l~~  862 (864)
T PRK00252        839 AQAGGKDPAKLDEALAAVKEWLKA  862 (864)
T ss_pred             EECCCCCHHHHHHHHHHHHHHHHH
T ss_conf             663899878999999999999983


No 2  
>COG0013 AlaS Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=2376.44  Aligned_cols=860  Identities=50%  Similarity=0.838  Sum_probs=820.8

Q ss_pred             CCCHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCHHHC
Q ss_conf             97878999999999997898891166756677871002301434755400588799999851115432248987863434
Q gi|254780191|r    1 MSNVSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNIFTGQEKPVYQAVTTVQKCVRAGGKHNDLDNV   80 (898)
Q Consensus         1 m~s~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~f~G~~~p~~~r~~~~QkCiR~ggkhnDld~V   80 (898)
                      |||++|||++||+||++|||+++|||||||+||||||||||||+||||||+|.++||++|+|+|||||||    ||||||
T Consensus         5 ~~t~~EiR~~FL~FF~~kgH~~v~s~slVP~nDptLLftnAGm~~FK~~f~g~v~p~~~r~~~sQkcIR~----NDieNV   80 (879)
T COG0013           5 KLTTNEIRQKFLDFFEKKGHTVVPSSPLVPRNDPTLLFTNAGMVQFKPYFTGGVTPPANRAVTSQKCIRT----NDIDNV   80 (879)
T ss_pred             CCCHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCEEEEECCCCCCHHHHCCCCCCCCCCEECCCCCCCC----CCHHHC
T ss_conf             5779999999999998779734578886789999768960463014113217888999970010212014----766543


Q ss_pred             CCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHCCCCHHHEEECCCCCCC
Q ss_conf             64885001788854223147537889998998613341898123799971882899997566349998997535786665
Q gi|254780191|r   81 GRTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKLWKKISGLSADKIIRITTNDNF  160 (898)
Q Consensus        81 G~t~rH~TfFEMlGn~SfgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~iW~~~~gi~~~~i~~~~~~dNf  160 (898)
                      |+|+|||||||||||||||||||+|||.|||||||+||||||+|||||||++||||+++|++.+|+|++||++++.+|||
T Consensus        81 G~T~RHhTfFEMLGNfSFGdYFKeeAI~~AwEflT~~lgl~~ekL~vtvy~~Ddea~~~W~~~~gip~~rIir~~~~dNf  160 (879)
T COG0013          81 GYTARHHTFFEMLGNFSFGDYFKEEAIEFAWEFLTKVLGLPKEKLYVTVYEDDDEAYNEWEKIIGIPPERIIRIGASDNF  160 (879)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHEEEEEECCCHHHHHHHHHHCCCCHHHEEECCCCCCC
T ss_conf             76654106777650570667788999999999987450898789799994586678888876329988984535767887


Q ss_pred             CCCCCCCCCCCCEEEEEECCCCCCCCCCC-CCCCCCCEEEEEEHHHHHHHCC-CCCCCCCCCCCCCCCCCCHHHHHHHHC
Q ss_conf             45799999877046788538556898887-7788982689600112344304-788756576653101757999999988
Q gi|254780191|r  161 WSMAETGPCGPCSEIFFDQGECIPGGLPG-SSEEGERYIEIWNLVFMQFEQQ-NKQERFILPKMSIDTGMGLERMATVLQ  238 (898)
Q Consensus       161 W~~g~~GpcGPcsEi~~d~g~~~~~~~~~-~~~~~~r~lEiwNlVFmq~~~~-~~g~~~~Lp~~~IDTGmGLERl~~vlq  238 (898)
                      |+||+ ||||||||||||||++++++.+. .+.|+||||||||||||||||+ .+|+|.|||+||||||||||||+||||
T Consensus       161 W~~G~-GPcGPcsEI~yD~G~~~~~~~~~~~~~d~dR~lEiwNLVFmQfnr~~~~g~~~~Lp~k~IDTGmGLERi~~vlQ  239 (879)
T COG0013         161 WEMGD-GPCGPCSEIFYDRGEEIGGGPPGSPDEDGDRYLEIWNLVFMQYNRDPGDGNYTPLPKKNIDTGMGLERIAAVLQ  239 (879)
T ss_pred             CCCCC-CCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEEEEEEHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHC
T ss_conf             77888-68888558997677666888778867778826897564301101379998755188877156866999999984


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCCCCCCC---CHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             798530057699999999973067854335---02489999989899998740333344464125778899999999984
Q gi|254780191|r  239 EKTNNYDIDLFKHLIQASEQVTGMKYEGNN---IVNHRVIVDHLRSSSFLIADGILPANEGRGYVLRRIMRRAMCYARLL  315 (898)
Q Consensus       239 g~~s~ydtD~f~pii~~i~~~~g~~y~~~~---~~~~rvIaDH~Ra~~f~I~DGv~PsN~GrGYvlRrilRRa~r~~~~l  315 (898)
                      |+|||||||+|.|||+.+++++|.+|..+.   ++++||||||+||++|||+|||+|||+|||||||||||||+||+++|
T Consensus       240 ~~~tnyd~dlf~~ii~~~e~~~g~~~~~~~~~~~~s~rVIADH~Rs~~f~iaDGv~PSNegrGYvlRriiRRa~R~~~~L  319 (879)
T COG0013         240 GVPTNYDTDLFRPIIKAIEKLTGKKYGEDEEDPDVSFRVIADHIRSLAFMIADGVLPSNEGRGYVLRRIIRRALRHGKLL  319 (879)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             99962144406899999999709767766544432589864578889999837776687773099999999999999974


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCC
Q ss_conf             87433104568999998645555557646788999987489899999989999999986115464245743799852458
Q gi|254780191|r  316 GYTEPLMMHLLPALCTEMGSAYPELIQAKLLIEETLRSEDERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHG  395 (898)
Q Consensus       316 g~~~~fl~~lv~~v~~~m~~~ypeL~~~~~~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsg~~af~LyDTyG  395 (898)
                      |++.|||++||+.+++.|+++||||++++++|+++|+.||++|.+||++|+++|++.++++++++.|||++||+||||||
T Consensus       320 G~~~~fl~~LV~~~~~~m~~~ypel~~~~~~I~~vl~~EEe~F~~TL~~G~~l~~~~~~~~~~~~~l~ge~afkLYDTyG  399 (879)
T COG0013         320 GIKEPFLYKLVDTVIDEMGDAYPELKEKEDFIKEVLKLEEERFAKTLERGLKLLEKELAKLKKSKTLDGEDAFKLYDTYG  399 (879)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHEEEHHCCC
T ss_conf             99936899999999999865667777778999999999999999999999999999998621477357677402310579


Q ss_pred             CCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCC
Q ss_conf             88899998766507744358889999999997644433110012013567888730488626434444432111222111
Q gi|254780191|r  396 LPLDIMQDILCARGLAGIDIISFNQALEEQRSRARAHSLGLGSGTTEKIWFSLKEKYGATQFIGYDLLRGSKFMKEDRKV  475 (898)
Q Consensus       396 fP~dlt~eia~e~gi~~vD~~~f~~~m~~qk~~sr~~~~~~~~~~~~~~~~~~~~~~~~t~F~GYe~~~~~~~~~~~~~~  475 (898)
                      ||+|||++||+|+|++ ||+++|+++|++||++||+++ ..+....+..+..+....++|+|+|||.+++          
T Consensus       400 fP~eLt~eia~e~g~~-VD~~~f~~~m~~qr~~ar~~~-~~~~~~~~~~~~~~~~~~~~tef~gY~~~~~----------  467 (879)
T COG0013         400 FPVELTEEIAEERGLK-VDEPGFEYAMEAQRERARASA-GSGEGAKESEDLELIDKLPETEFLGYDDLEM----------  467 (879)
T ss_pred             CCHHHHHHHHHHCCCE-ECCCCHHHHHHHHHHHHHHCC-CCCCCCCHHHHHHHHCCCCCCEEEECCCCCC----------
T ss_conf             9989999999984985-354467999999999866300-2354310134456540478843651156641----------


Q ss_pred             CCCCCCCCCCCCCCEEEEEEEECCCEEEECCCCCEEEEEECCCCEEECCCCCCCCCCEEEEC-CEEEEEECCCCCCCEEE
Q ss_conf             34445445556553489999747813200047976999973752000368765665145404-24898522456553389
Q gi|254780191|r  476 LCQKPPIDLTNGVSSIVKAIVQQGEIVEEAVSGQKVEVVFDQTPFYAEAGGQLGDTGCAIGD-GIRLQITDVQKKAEGIF  554 (898)
Q Consensus       476 ~~~~~~~~~~~~~~s~v~~i~~~~~~v~~~~~g~~~~ivLd~T~FY~E~GGQ~~D~G~i~~~-~~~~~V~dv~k~~~g~i  554 (898)
                                   .+++.+|+.+++.|+++.+|++++||||+||||||||||++|+|+|.++ +..+.|.||||.++|++
T Consensus       468 -------------~~~i~~l~~~~~~v~~~~~g~~~~vVld~TpFYaEsGGQ~~D~G~i~~~~~~~~~V~dvqK~~~~~~  534 (879)
T COG0013         468 -------------EFKVLVLFVDGKEVSELNEGQEVYVVLDQTPFYAESGGQVGDTGYIFGDGGGRFEVTDVQKVGNGVI  534 (879)
T ss_pred             -------------EEEEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEECCCCEE
T ss_conf             -------------2799999955844022367853799984687557889967765899955882899988787179669


Q ss_pred             EEEECCCCCCCCCCCEEEEEEHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCCHHHHHH
Q ss_conf             98510467875567338884212556777520136889999975212544444553002430000024767899999999
Q gi|254780191|r  555 VHHAIVERGILRTEMSLVLTIDYQNRRQLSINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKS  634 (898)
Q Consensus       555 ~H~~~~~~g~l~~g~~V~~~VD~~rR~~~~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~  634 (898)
                      +|.+.+.+|.+++|+.|.++|||+||..+|+|||||||||+|||+|||+||||+||+|++++|||||||+++||+|||++
T Consensus       535 vH~~~~~~G~l~~gd~V~~~vD~~rR~~~~~nHTATHLLh~ALr~VLG~hV~QaGSlv~~~~lRfDfsH~~~it~Eel~~  614 (879)
T COG0013         535 VHKGKVESGELKVGDEVTAEVDEERRRRLMRNHTATHLLHAALRKVLGDHVWQAGSLVDPEKLRFDFSHYKALTAEELKE  614 (879)
T ss_pred             EEEEEECCCCCCCCCEEEEEECHHHHHHHHHHCHHHHHHHHHHHHHHCCCCEECCCCCCCCEEEEEECCCCCCCHHHHHH
T ss_conf             99985046766889889999889999999862769999999999973732120676467770688531788899999999


Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHCCCCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCC
Q ss_conf             99999898873045304661232221000355443155562489984476778553101562225886460110011012
Q gi|254780191|r  635 IEDNVNDIIAQNLPVVTRIMNREDAIASGAAALLGTKYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSES  714 (898)
Q Consensus       635 IE~~vN~~I~~n~~V~~~~~~~~eA~~~ga~alfgekygd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~  714 (898)
                      ||++||++|++|+||++.+|++++|+++||+||||||||+.||||+|+     +||+||||||||+|||+||+|||+||+
T Consensus       615 IE~~vNe~I~~n~~V~~~~m~~~eAk~~Ga~alfGekY~~~VRVV~ig-----~~SvElCGGTHv~~Tg~IG~fkI~~e~  689 (879)
T COG0013         615 IERLVNEIIRENLPVKTEEMDLDEAKAKGAMALFGEKYGDEVRVVEIG-----DFSVELCGGTHVSNTGDIGLFKIISEE  689 (879)
T ss_pred             HHHHHHHHHHCCCCEEEEECCHHHHHHHCHHHHCCCCCCCEEEEEEEC-----CCEEECCCCCCCCCCCCEEEEEEEEEC
T ss_conf             999999999828941489736999997192965288679868999989-----915661377456775650117998764


Q ss_pred             CCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----H--
Q ss_conf             126882899997168999999999999999999839998899999999999999999999999999876365-----3--
Q gi|254780191|r  715 SIRAGIRRIEAITGQRARSHLMGQDEKLKSLASFLKVSQGNVVGRVEEIWEEYRKLQLIHAKRKLQLNVEDL-----S--  787 (898)
Q Consensus       715 si~sGvRRIeavtG~~A~~~~~~~~~~l~~la~~L~~~~~~i~~ki~~L~~e~K~l~k~~~k~k~~~~~~~~-----~--  787 (898)
                      +|++|||||||+||..|++|++++++.+++++..|++ +.+++.++++|++++|++++++.+++.+++....     .  
T Consensus       690 ~i~aGVrRIeavtG~~a~~~~~~~~~~l~~~a~~lk~-~~~~~~kv~~l~~~~k~lekel~~lk~~~~~~~~~~~~~~~~  768 (879)
T COG0013         690 GIAAGVRRIEAVTGEAALEYLQEQEDLLKEIASLLKV-PPELLPKVERLLEELKELEKELERLKKKLAAAELADLLSNAK  768 (879)
T ss_pred             CCCCCEEEEEEECCHHHHHHHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             1306758999982789999999999999999998689-866788999999999999999999999998888776530110


Q ss_pred             HHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCEEEEEEEECHHHHCCCCHHHHHHHHHHHHCCCC
Q ss_conf             55536952799995799978999999999975499789999953898179999867789726798999999998834999
Q gi|254780191|r  788 CHKIADVNFMSHIISEVDSKELKSVMDALQKKIQSGIIMLVGISKEKKASVLIVVTEDLLDRFNAVDLARLSAKVLGGGG  867 (898)
Q Consensus       788 ~~~i~~~~~i~~~~~~~d~~~Lr~l~d~l~~k~~~~vvvL~~~~~~~k~~ivv~vs~~~~~~~~A~~lik~ia~~l~GGg  867 (898)
                      ..++++++++...+++.|+++||.+++.++++.++.+++|++.. ++|+.++++++++++.+++|++|+++++..+ ||+
T Consensus       769 ~~~i~g~~~~~~~~~~~d~~~Lr~~a~~lk~k~~~~vivl~~~~-~~Kv~~~~~v~~~~~~~~~a~~lvk~la~~~-gG~  846 (879)
T COG0013         769 AEEIGGVKVLAKEVDGADMKELREIADDLKKKLGSAVIVLASVA-DGKVSLVVAVSKDLTDKVKAGELVKELAAIV-GGK  846 (879)
T ss_pred             CEEECCEEEEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEEEC-CCEEEEEEEECHHHHCCCCHHHHHHHHHHHC-CCC
T ss_conf             03328879999994478989999999999750478379999852-7708999996514413548999999999862-998


Q ss_pred             CCCCCHHCCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             9998101145899987889999999998619
Q gi|254780191|r  868 GGGRPHMAQSGGPNGNKADQAIAGVASFLKK  898 (898)
Q Consensus       868 GGGkpd~AQgGG~~~~~l~eal~~vk~~Lke  898 (898)
                      |||||+||||||+++.++++|++.+.++|++
T Consensus       847 GGGr~d~Aqggg~d~~~~~~al~~~~~~~~~  877 (879)
T COG0013         847 GGGRPDMAQGGGKDPEKLDEALELVIEWVKE  877 (879)
T ss_pred             CCCCHHHHEECCCCCCCHHHHHHHHHHHHHH
T ss_conf             8896255211789833289999999999984


No 3  
>PRK13902 alaS lanyl-tRNA synthetase; Provisional
Probab=100.00  E-value=0  Score=2077.07  Aligned_cols=782  Identities=30%  Similarity=0.507  Sum_probs=719.4

Q ss_pred             CCHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCCCC-CCCCCCCCCCCCCCCCEECCCCCCCHHHC
Q ss_conf             78789999999999978988911667566778710023014347554005-88799999851115432248987863434
Q gi|254780191|r    2 SNVSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNIFT-GQEKPVYQAVTTVQKCVRAGGKHNDLDNV   80 (898)
Q Consensus         2 ~s~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~f~-G~~~p~~~r~~~~QkCiR~ggkhnDld~V   80 (898)
                      .|++|||++||+||++|||++||||||||+||||||||||||+||||||+ |.++||++|+|+||||||+    ||||||
T Consensus        58 ~~~~eiR~~Fl~fF~~~gH~~v~s~plvp~~~ddllftnAgm~~Fkp~~~~G~~~pp~~~~~~sQkCiR~----nDlenV  133 (898)
T PRK13902         58 YSLDEMREKFLSFFEKRGHTRIKRYPVVARWRDDVYLTIASIYDFQPWVTSGIVPPPANPLVISQPCIRL----NDIDNV  133 (898)
T ss_pred             CCHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCEEEEECCCHHCHHHHCCCCCCCCCCCCCCCCCCEEC----CCHHHC
T ss_conf             7899999999999976899891785637899998057603513240443388758999972565223004----767543


Q ss_pred             CCCCCCHHHHHHHHHHHHCC-----CCHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHCCCCHHHEEECC
Q ss_conf             64885001788854223147-----5378899989986133418981237999718828999975663499989975357
Q gi|254780191|r   81 GRTNRHHTFFEMLGNFSFGG-----YFKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKLWKKISGLSADKIIRIT  155 (898)
Q Consensus        81 G~t~rH~TfFEMlGn~Sfgd-----YfK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~iW~~~~gi~~~~i~~~~  155 (898)
                      |+|+||||||||||||||||     |||+|||+|||||||++|||||+||.                             
T Consensus       134 G~t~rHhTfFEMlGn~SFg~~d~~~YfK~eaI~~awe~lt~~lgi~~~~i~-----------------------------  184 (898)
T PRK13902        134 GRTGRHLTSFEMMAHHAFNYPDKEVYWKDETVELCFEFFTKELGIDPEEIT-----------------------------  184 (898)
T ss_pred             CCCCCCCHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHEE-----------------------------
T ss_conf             888774354523765414899756470789999999998701287879945-----------------------------


Q ss_pred             CCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             86665457999998770467885385568988877788982689600112344304788756576653101757999999
Q gi|254780191|r  156 TNDNFWSMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLERMAT  235 (898)
Q Consensus       156 ~~dNfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNlVFmq~~~~~~g~~~~Lp~~~IDTGmGLERl~~  235 (898)
                      .+||||+||  |||||||||||                  |+|||||||||||||+++|+|.|||+||||||||||||||
T Consensus       185 ~ken~W~~g--GpcGPcsEi~~------------------~GlEiwNlVFmq~~~~~~g~~~~Lp~k~IDTGmGLERia~  244 (898)
T PRK13902        185 FKESPWEGG--GNAGPCFEVLV------------------RGLELATLVFMQYKKDKGGKYVEMPLKIVDTGYGLERIAW  244 (898)
T ss_pred             EECCCCCCC--CCCCCCEEEEE------------------CCEEEEEEECCCCEECCCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf             624574789--99988635651------------------9797442202341136999733087776346856999999


Q ss_pred             HHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCC--------------------------------------------CHH
Q ss_conf             988798530057699999999973067854335--------------------------------------------024
Q gi|254780191|r  236 VLQEKTNNYDIDLFKHLIQASEQVTGMKYEGNN--------------------------------------------IVN  271 (898)
Q Consensus       236 vlqg~~s~ydtD~f~pii~~i~~~~g~~y~~~~--------------------------------------------~~~  271 (898)
                      ++||+|||||| +|.|||+.+++++|++|..++                                            ..+
T Consensus       245 vlQg~~tnydt-~F~pii~~~~~~~g~~~~~~~~~~~~~~~~g~~d~~~~~~~~~~~~~va~~~~~~~~~~~~~~~~~~~  323 (898)
T PRK13902        245 ASQGTPTAYDA-VFGEIVDKLKKLAGVEEPDEEILAEAARLAGLMDIEEIGDLRELRQKVAEKIGIDVEELEELIEPLEA  323 (898)
T ss_pred             HHCCCCCHHHH-HHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHCCCCCCC
T ss_conf             99099953776-42899999999738986503677776654045662100258899988766406651332200243223


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999989899998740333344464125778899999999984874331045689999986455555576467889999
Q gi|254780191|r  272 HRVIVDHLRSSSFLIADGILPANEGRGYVLRRIMRRAMCYARLLGYTEPLMMHLLPALCTEMGSAYPELIQAKLLIEETL  351 (898)
Q Consensus       272 ~rvIaDH~Ra~~f~I~DGv~PsN~GrGYvlRrilRRa~r~~~~lg~~~~fl~~lv~~v~~~m~~~ypeL~~~~~~I~~ii  351 (898)
                      +||||||+||++|||+|||+|||+|||||||||||||+||+++||++.| |++||+.+++.|++.||||.++++.|.+||
T Consensus       324 ~~vIaDH~R~~~f~i~DGv~PsN~grGYvlRrilRRa~r~~~~Lg~~~~-L~~Lv~~~~~~m~~~ypel~~~~~~I~~ii  402 (898)
T PRK13902        324 VYAIADHTRTLAFMLGDGIVPSNVGEGYLARLVIRRTLRLLKDLGLDVP-LSELVDMQIEYLKEDYPELKENRDYILDIV  402 (898)
T ss_pred             CCEECCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHH-HHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_conf             3021318999999996588778788744999999999999999397132-999999999987415768898699999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCH-HHHHHHHHHHHHHHH
Q ss_conf             8748989999998999999998611546424574379985245888899998766507744358-889999999997644
Q gi|254780191|r  352 RSEDERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLDIMQDILCARGLAGIDI-ISFNQALEEQRSRAR  430 (898)
Q Consensus       352 ~~EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsg~~af~LyDTyGfP~dlt~eia~e~gi~~vD~-~~f~~~m~~qk~~sr  430 (898)
                      +.||++|.+||++|+++|++.+++   ++.|||++||+||||||||+|||++||+|+|+. ||+ ++|++.|++|+++++
T Consensus       403 ~~EEe~F~~TL~~G~~~l~~~~~~---~~~i~g~~af~LYDTyGfP~Dlt~eia~e~gi~-vD~~~~F~~~~~~~~~~~~  478 (898)
T PRK13902        403 DLEEEKYRETLERGRRIVERLAKK---KKEIPLDDLIELYDSHGIPPEIVKEIAKKKGVE-VEIPDNFYSLVAARHEKAE  478 (898)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHC---CCCCCHHHHHHHHHCCCCCHHHHHHHHHHCCCC-CCCCCHHHHHHHHHHHHHH
T ss_conf             999999999999999999999851---898888999999870498989999999982980-1464429999999999876


Q ss_pred             HHHHHCCCCCHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCEEEECCCCCE
Q ss_conf             43311001201356788873048862643444443211122211134445445556553489999747813200047976
Q gi|254780191|r  431 AHSLGLGSGTTEKIWFSLKEKYGATQFIGYDLLRGSKFMKEDRKVLCQKPPIDLTNGVSSIVKAIVQQGEIVEEAVSGQK  510 (898)
Q Consensus       431 ~~~~~~~~~~~~~~~~~~~~~~~~t~F~GYe~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~i~~~~~~v~~~~~g~~  510 (898)
                      +..+...      .........++|+|+||+.....                    +.+++|+.++.+            
T Consensus       479 ~~~~~~~------~~~~~~~~~~~T~~~~Y~~~~~~--------------------e~~a~Vl~i~~~------------  520 (898)
T PRK13902        479 KKEEEVL------PLADRLKDLPETRLLFYEDPYMR--------------------EFEAKVLGVIDN------------  520 (898)
T ss_pred             HHHCCCC------CHHHHHHCCCCCEEEEECCCCEE--------------------EEEEEEEEEECC------------
T ss_conf             4103121------00457753798503430246502--------------------578999998435------------


Q ss_pred             EEEEECCCCEEECCCCCCCCCCEEEECCEEEEEECCCCCCCEEEEEEECCCCCCCCCCCEEEEEEHHHHHHHHHHCCCHH
Q ss_conf             99997375200036876566514540424898522456553389985104678755673388842125567775201368
Q gi|254780191|r  511 VEVVFDQTPFYAEAGGQLGDTGCAIGDGIRLQITDVQKKAEGIFVHHAIVERGILRTEMSLVLTIDYQNRRQLSINHSAT  590 (898)
Q Consensus       511 ~~ivLd~T~FY~E~GGQ~~D~G~i~~~~~~~~V~dv~k~~~g~i~H~~~~~~g~l~~g~~V~~~VD~~rR~~~~~~HTat  590 (898)
                       +||||+||||||||||++|+|+|..++..+.|.||||. +|+|+|.  +..+.+++|++|.+.|||+||.++|+|||||
T Consensus       521 -~vVLd~T~FY~E~GGQ~~D~G~i~~~~~~~~V~dv~k~-~g~i~H~--v~~~~~~~g~~V~~~VD~~rR~~~~~nHTaT  596 (898)
T PRK13902        521 -YVVLDQTAFYPEGGGQPADTGVLVVNGKEIKVVDVQKV-GGVIVHV--VEGEPPPKGDEVKGEIDWERRYRLMRHHTAT  596 (898)
T ss_pred             -EEEEECCCCCCCCCCCCCCEEEEEECCCEEEEEEEEEE-CCEEEEE--ECCCCCCCCCEEEEEECHHHHHHHHHHHHHH
T ss_conf             -49961575445678977880279968937999732774-8989999--5788888899899999989998887600388


Q ss_pred             HHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHH--
Q ss_conf             899999752125444445530024300000247678999999999999989887304530466123222100035544--
Q gi|254780191|r  591 HLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIASGAAALL--  668 (898)
Q Consensus       591 HlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~~ga~alf--  668 (898)
                      ||||+|||+|||+||+|+||+|+++++||||||+++||+|||.+||++||++|++|+||++.+|+++||++.|+++||  
T Consensus       597 HlL~~alr~vLG~hv~Q~Gs~v~~~~lRfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~~~a~alf~g  676 (898)
T PRK13902        597 HILLAAARKVLGDHVWQAGAQKDTDKARLDITHYKRITREEVKEIERLANRIVMENRPVKVEWMDRNEAEQKYGFRLYQG  676 (898)
T ss_pred             HHHHHHHHHHHCCCEEECCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECHHHHHHHCCHHHHCC
T ss_conf             88779999872775684032337980899624888789899999999999999848962799947899976154033227


Q ss_pred             HHCCCCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCCCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHH
Q ss_conf             31555624899844767785531015622258864601100110121268828999971689999999999999999998
Q gi|254780191|r  669 GTKYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESSIRAGIRRIEAITGQRARSHLMGQDEKLKSLASF  748 (898)
Q Consensus       669 gekygd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~si~sGvRRIeavtG~~A~~~~~~~~~~l~~la~~  748 (898)
                      |+||+|.||||+|+     +||+||||||||.||||||+|||+|+++|++|||||||+||.+|++|+++.++.++++++.
T Consensus       677 G~kygd~VRVV~ig-----~~s~ElCGGTHV~nTgeIG~fkIise~si~~GVRRIEavtG~~A~~~~~~~~~~l~~~a~~  751 (898)
T PRK13902        677 GVVPGKEIRVVEIE-----GWDVEACGGTHVKNTGEIGPIKILKTERIQDGVERLEFAAGDAAVEYIQELEDILREAAEI  751 (898)
T ss_pred             CCCCCCCEEEEEEC-----CCEEECCCCCCCCCCCCEEEEEEEEECCEECCCEEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_conf             87888735898657-----8036523798778703134389998552637816999980789999999999999999998


Q ss_pred             HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             39998899999999999999999999999999876365-----3555369527999957999789999999999754997
Q gi|254780191|r  749 LKVSQGNVVGRVEEIWEEYRKLQLIHAKRKLQLNVEDL-----SCHKIADVNFMSHIISEVDSKELKSVMDALQKKIQSG  823 (898)
Q Consensus       749 L~~~~~~i~~ki~~L~~e~K~l~k~~~k~k~~~~~~~~-----~~~~i~~~~~i~~~~~~~d~~~Lr~l~d~l~~k~~~~  823 (898)
                      |+++++++++++++|++++|++++++.+++.+++....     .+..+++++++...+ +.|+++||.+++.++++  +.
T Consensus       752 L~~~~~~l~~~v~~l~~e~k~l~kei~~lk~~l~~~~~~~l~~~~~~i~g~~v~~~~~-~~d~~~lr~~~~~l~~k--~~  828 (898)
T PRK13902        752 LGVPPEQLPETVKRFFEEWKEQKKEIEKLRKELAELLIYELLAEAEEVGGVKVVVEEV-DADDDELQKIANKLSKK--GG  828 (898)
T ss_pred             HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEECCEEEEEEEC-CCCHHHHHHHHHHHHCC--CC
T ss_conf             5899889999999999999999999999999999998888775451638879999983-79999999999986357--95


Q ss_pred             EEEEEEECCCCEEEEEEEECHHHHCCCCHHHHHHHHHHHHCCCCCCCCCHHCCCCC-CCHHHHHHHHHHHHHHH
Q ss_conf             89999953898179999867789726798999999998834999999810114589-99878899999999986
Q gi|254780191|r  824 IIMLVGISKEKKASVLIVVTEDLLDRFNAVDLARLSAKVLGGGGGGGRPHMAQSGG-PNGNKADQAIAGVASFL  896 (898)
Q Consensus       824 vvvL~~~~~~~k~~ivv~vs~~~~~~~~A~~lik~ia~~l~GGgGGGkpd~AQgGG-~~~~~l~eal~~vk~~L  896 (898)
                      +++|++ ..+++..+++++++++  +++|++|++++++.+ ||||||||+|||||| +|++++++||+.|+++|
T Consensus       829 vvvl~~-~~~~~~~~v~~~~~~~--~i~A~~ivk~v~~~~-gGkGGGrp~~AQgGG~~d~~kl~eAL~~a~~~i  898 (898)
T PRK13902        829 VVVLIN-SGGYGRVIVASGGEKA--GVNAGEIVRELAREL-GGKGGGKPTLAQGGGSPDVEKIDEALSRALSLI  898 (898)
T ss_pred             EEEEEE-ECCCCEEEEEEECCCC--CCCHHHHHHHHHHHC-CCCCCCCHHHEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             899998-0599389999975658--979899999999855-997679388760589998789999999999759


No 4  
>KOG0188 consensus
Probab=100.00  E-value=0  Score=1942.18  Aligned_cols=847  Identities=37%  Similarity=0.619  Sum_probs=743.8

Q ss_pred             CCCHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCHHHC
Q ss_conf             97878999999999997898891166756677871002301434755400588799999851115432248987863434
Q gi|254780191|r    1 MSNVSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNIFTGQEKPVYQAVTTVQKCVRAGGKHNDLDNV   80 (898)
Q Consensus         1 m~s~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~f~G~~~p~~~r~~~~QkCiR~ggkhnDld~V   80 (898)
                      |.|.+|||++||+||++|.|++|+||||||.+||||||+|||||||||+|||. ..+.+|++|||||||+||||||||+|
T Consensus         1 ~~ta~evR~tFldfF~~k~H~~V~SSsViP~dDpTLLFaNAGMNQFKpifLgt-~a~lkRa~NsQKCIRAGGKHNDLdDV   79 (895)
T KOG0188           1 MLTASEVRKTFLDFFKSKHHKIVHSSSVIPFDDPTLLFANAGMNQFKPIFLGT-MAKLKRAANSQKCIRAGGKHNDLDDV   79 (895)
T ss_pred             CCCHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCEEEEECCCHHHCCHHHHHC-HHHHHHHHHHHHHHHCCCCCCCHHHC
T ss_conf             96378999999999985484684468744589980477326544321365422-14567665046677626876766662


Q ss_pred             CCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEEC--------CCHHHHHHHHHHHCCCCHHHEE
Q ss_conf             64885001788854223147537889998998613341898123799971--------8828999975663499989975
Q gi|254780191|r   81 GRTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRLYITVY--------DEDEEAFKLWKKISGLSADKII  152 (898)
Q Consensus        81 G~t~rH~TfFEMlGn~SfgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~--------~~D~e~~~iW~~~~gi~~~~i~  152 (898)
                      |++.|||||||||||||||||||||||.|||||||++||||+||||||||        +.|-||++||+++ |+|++||+
T Consensus        80 GkD~yHHTfFEMLGNWSFGdYFKeEac~~AwElLt~vygi~~dRLYVTYF~Gde~~Gle~DlE~r~iW~~l-Gvp~srIL  158 (895)
T KOG0188          80 GKDFYHHTFFEMLGNWSFGDYFKEEACAWAWELLTFVYGIPTDRLYVTYFGGDEKLGLEPDLECREIWNEL-GVPDSRIL  158 (895)
T ss_pred             CCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHC-CCCHHHCC
T ss_conf             66521567999863763887889999999999987763798350799983584103799566899999982-99788806


Q ss_pred             ECCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCC---CCCCCCCEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             3578666545799999877046788538556898887---7788982689600112344304788756576653101757
Q gi|254780191|r  153 RITTNDNFWSMAETGPCGPCSEIFFDQGECIPGGLPG---SSEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMG  229 (898)
Q Consensus       153 ~~~~~dNfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~---~~~~~~r~lEiwNlVFmq~~~~~~g~~~~Lp~~~IDTGmG  229 (898)
                      +++.|||||+||+||||||||||||||    .|++..   +|.|+|.++||||||||||||..||++.|||++|||||||
T Consensus       159 p~~~kDNFWEMGdtGPCGPCtEIHyDr----iGgr~a~~LVN~ddp~v~EiWNlVFIq~NRe~dGsL~pLp~khIDTGMG  234 (895)
T KOG0188         159 PFGMKDNFWEMGDTGPCGPCTEIHYDR----IGGRDAVKLVNHDDPDVLEIWNIVFIQYNREADGSLKPLPKKHIDTGMG  234 (895)
T ss_pred             CCCCHHHHHHCCCCCCCCCCHHHHHHH----HCCCCHHHHHCCCCCCHHHEEEEEEEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf             786102156505887887840210143----0686658772688965554000125774135687656674114544657


Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCC----CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHH
Q ss_conf             99999998879853005769999999997306785433----50248999998989999874033334446412577889
Q gi|254780191|r  230 LERMATVLQEKTNNYDIDLFKHLIQASEQVTGMKYEGN----NIVNHRVIVDHLRSSSFLIADGILPANEGRGYVLRRIM  305 (898)
Q Consensus       230 LERl~~vlqg~~s~ydtD~f~pii~~i~~~~g~~y~~~----~~~~~rvIaDH~Ra~~f~I~DGv~PsN~GrGYvlRril  305 (898)
                      ||||++|||++.||||||+|.||+++|++.++.+|.++    .++||||+|||+|++++|||||.+|+|+||||||||||
T Consensus       235 fERLvsVlQnk~SNYDTDlFtPif~aiq~~~~~~YtG~d~d~~D~AyRVvADH~RtlTvalsDG~~Pdn~GrgyvLRRIL  314 (895)
T KOG0188         235 FERLVSVLQNKTSNYDTDLFTPIFEAIQEGTGARYTGEDADGIDTAYRVVADHARTLTVALSDGGVPDNTGRGYVLRRIL  314 (895)
T ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHEEECCCCCCCCCCHHHHHHHH
T ss_conf             99999999565556641243799999998608875577543421368898877656210100487778888706899999


Q ss_pred             HHHHHHHH-HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             99999999-84874331045689999986455555576467889999874898999999899999999861154642457
Q gi|254780191|r  306 RRAMCYAR-LLGYTEPLMMHLLPALCTEMGSAYPELIQAKLLIEETLRSEDERFGKTLDRGLVLLDGVLSHLGKDEILNG  384 (898)
Q Consensus       306 RRa~r~~~-~lg~~~~fl~~lv~~v~~~m~~~ypeL~~~~~~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsg  384 (898)
                      |||+||++ +||.+..||.+|||+|++.||++||||.++...|.++|..||..|.+||++|.++|++.+..++++++|||
T Consensus       315 RRavrya~e~l~~~~g~~~~LVpvvv~~lgd~fPEl~~~~~~v~diineEE~~F~ktl~rg~~~f~r~~~~~~~s~tipG  394 (895)
T KOG0188         315 RRAVRYAHEKLNAPPGFFSTLVPVVVETLGDAFPELKRDPQHVIDIINEEEAQFLKTLDRGRKLFDRVARELGSSKTIPG  394 (895)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCH
T ss_conf             99999999985799631333269999987554544422878999874679999999998889999999986688886761


Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHH-HHHCCCCEEECCCCC
Q ss_conf             4379985245888899998766507744358889999999997644433110012013567888-730488626434444
Q gi|254780191|r  385 DVAFKLYDTHGLPLDIMQDILCARGLAGIDIISFNQALEEQRSRARAHSLGLGSGTTEKIWFSL-KEKYGATQFIGYDLL  463 (898)
Q Consensus       385 ~~af~LyDTyGfP~dlt~eia~e~gi~~vD~~~f~~~m~~qk~~sr~~~~~~~~~~~~~~~~~~-~~~~~~t~F~GYe~~  463 (898)
                      ++||+||||||||+|||++||+|+|++ +|+++|+++..+.+++|+.+......     ++.++ .+..++|.    |  
T Consensus       395 d~~w~LydTyGfPvdlt~lmAee~gl~-iD~~~fE~ar~~A~~~Sk~~~~~~~~-----i~ldvl~el~p~Td----D--  462 (895)
T KOG0188         395 DVAWRLYDTYGFPVDLTELMAEEKGLK-IDETGFEAARQEAQEKSKGAGGGKLS-----IDLDVLSELVPPTD----D--  462 (895)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHHCCCCCCCC-----CCHHHHHHHCCCCC----C--
T ss_conf             787777761288488999999972975-57256899999999987515787876-----32777774289989----8--


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCEEEECCCCCEEEEEECCCCEEECCCCCCCCCCEEEECCE---E
Q ss_conf             4321112221113444544555655348999974781320004797699997375200036876566514540424---8
Q gi|254780191|r  464 RGSKFMKEDRKVLCQKPPIDLTNGVSSIVKAIVQQGEIVEEAVSGQKVEVVFDQTPFYAEAGGQLGDTGCAIGDGI---R  540 (898)
Q Consensus       464 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~i~~~~~~v~~~~~g~~~~ivLd~T~FY~E~GGQ~~D~G~i~~~~~---~  540 (898)
                                     ...+..+..+.++|+++..++..++++..|+++.||||+|.||||+|||.+|+|.|..++.   .
T Consensus       463 ---------------s~KY~~~~~~~~~il~l~~e~~~v~~~~~g~~~givldkTnFYaEqGGQ~~D~G~lv~~~~~~~~  527 (895)
T KOG0188         463 ---------------SFKYNEFGVCKTRILALYREDQFVESIPKGQECGIVLDKTNFYAEQGGQIYDTGKLVIDGDEDFV  527 (895)
T ss_pred             ---------------CCCCCCCCCCHHHHHHHHCCCCEEEECCCCCEEEEEEECCEEEHHCCCCCCCCCEEEEECCCCCE
T ss_conf             ---------------40003576303212100017855631378856789951331202138813466049982675422


Q ss_pred             EEEECCCCCCCEEEEEEECCCCCCCCCCCEEEEEEHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEE
Q ss_conf             98522456553389985104678755673388842125567775201368899999752125444445530024300000
Q gi|254780191|r  541 LQITDVQKKAEGIFVHHAIVERGILRTEMSLVLTIDYQNRRQLSINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFD  620 (898)
Q Consensus       541 ~~V~dv~k~~~g~i~H~~~~~~g~l~~g~~V~~~VD~~rR~~~~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfD  620 (898)
                      +.|.++|-  +|+++|+|.+ .|.+++|++|.+.+|..||+.+|+||||||||++|||++| ....|+||+|+||+||||
T Consensus       528 fnV~~~~~--gg~vvh~g~l-~~~l~vgdqv~~~~De~rR~~im~nHTaTHlLN~aLr~~l-~~t~QkGSlV~pdklRfD  603 (895)
T KOG0188         528 FNVKRVQV--GGYVVHIGVL-EGDLSVGDQVELHVDEERRQLIMRNHTATHLLNFALRQVL-KGTDQKGSLVAPDKLRFD  603 (895)
T ss_pred             EEHHHCCC--CCEEEEEEEE-CCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC-CCCCCCCCCCCHHHEEEE
T ss_conf             33000014--7789998641-3665335358877559998777631409999999999862-652456664575670564


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC-CHHHHHHHHCCCCCEEEEEECCCCCCCCCEECCCCCCC
Q ss_conf             24767899999999999998988730453046612322210-00355443155562489984476778553101562225
Q gi|254780191|r  621 VTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIA-SGAAALLGTKYNDRVRVVSVEYEDGGVHSSALCGGTHV  699 (898)
Q Consensus       621 fsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~-~ga~alfgekygd~VRVV~I~~~d~~~~S~ElCGGTHV  699 (898)
                      |++..++|.|||+++|+.+|+.|.+|.+|...+.|+.+|++ .|.++.|+|.|||.||||+|+  ++..+|+|+|||||+
T Consensus       604 f~~k~~lt~eql~~vE~~~ne~I~~~~~V~~~e~~l~~ak~i~glr~v~~E~YPdpVRVVsvg--~~~~~svE~CgGTH~  681 (895)
T KOG0188         604 FSTKGALTKEQLKKVEDKINEFIQKNAPVYAKELPLAEAKKIPGLRAVFDEVYPDPVRVVSVG--AGQLTSVEFCGGTHL  681 (895)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHCCCCCCCCCCCCCCCCEEEEEEC--CCCCCCEEECCCCCC
T ss_conf             236777899999999999999986388569886578887327771002577458864899833--665431010277444


Q ss_pred             CCHHHHHHHHEECCCCCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHCCCH--------------------HHHHHH
Q ss_conf             886460110011012126882899997168999999999999999999839998--------------------899999
Q gi|254780191|r  700 SSTGEIMLLYIVSESSIRAGIRRIEAITGQRARSHLMGQDEKLKSLASFLKVSQ--------------------GNVVGR  759 (898)
Q Consensus       700 ~nTgeIG~fkIise~si~sGvRRIeavtG~~A~~~~~~~~~~l~~la~~L~~~~--------------------~~i~~k  759 (898)
                      .|||+||.|.|+++++|++|+|||.||||.+|.+..+..+.+.+.++..-++.+                    .++.++
T Consensus       682 ~~t~~i~~fvI~se~~iakgirRivavTG~eA~~a~~~a~~~~~~~~~~~~~~~kei~~l~~~~~~a~iP~~~k~~~~~~  761 (895)
T KOG0188         682 TNTSHIGDFVIVSEEGIAKGIRRIVAVTGKEAQEALRLAEDLDKDLRKTDKALEKEIQELGENLDHAVIPYWQKDEIREL  761 (895)
T ss_pred             CCCCCCCEEEEECHHHHHHCEEEEEEECCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             66555442899630444105067878336889999998887876540265256899999998631453507759999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCEEE
Q ss_conf             999999999999999999999876365--355536952799995799978999999999975499789999953898179
Q gi|254780191|r  760 VEEIWEEYRKLQLIHAKRKLQLNVEDL--SCHKIADVNFMSHIISEVDSKELKSVMDALQKKIQSGIIMLVGISKEKKAS  837 (898)
Q Consensus       760 i~~L~~e~K~l~k~~~k~k~~~~~~~~--~~~~i~~~~~i~~~~~~~d~~~Lr~l~d~l~~k~~~~vvvL~~~~~~~k~~  837 (898)
                      +++++...+.+.+...+...+......  ..+...+..+++..++-.         ..+++..+...+.|++....+|+.
T Consensus       762 ~k~~~K~~~d~~ra~~~~~~k~~l~~~~~~~~~~~~~~~~v~~~~~~---------~~~k~~~~~~~i~lls~~~~gkv~  832 (895)
T KOG0188         762 LKKLQKRMDDLSRALKAAVQKEVLEEAKQLKESNPNQPLLVHYIESS---------KLLKKQAPDKSIMLLSDDESGKVT  832 (895)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCC---------HHHHHCCCCCEEEEEECCCCCEEE
T ss_conf             99999887788999988879999999999874289998799995430---------777636998737997338777278


Q ss_pred             EEEEECHHHHC-CCCHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             99986778972-679899999999883499999981011458999878899999999986
Q gi|254780191|r  838 VLIVVTEDLLD-RFNAVDLARLSAKVLGGGGGGGRPHMAQSGGPNGNKADQAIAGVASFL  896 (898)
Q Consensus       838 ivv~vs~~~~~-~~~A~~lik~ia~~l~GGgGGGkpd~AQgGG~~~~~l~eal~~vk~~L  896 (898)
                      +.|.|++.+.. +++|.+|++.++..+ ||+||||+..|||-|.++.+|++|++.+..+-
T Consensus       833 ~~c~V~~~a~~~~l~a~~w~~~v~~~~-ggk~~gK~~~~q~~g~~~~~l~~av~~a~~~a  891 (895)
T KOG0188         833 CLCQVPQNAANKGLKASEWVQSVSGTM-GGKGGGKGVLAQATGNNVGCLDEAVSLATEFA  891 (895)
T ss_pred             EEEEECHHHHHCCCCHHHHHHHHHHHH-CCCCCCCCCCHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             988605778644577899999988872-68767876420221886767999999999998


No 5  
>PRK01584 alanyl-tRNA synthetase; Provisional
Probab=100.00  E-value=0  Score=1817.34  Aligned_cols=580  Identities=38%  Similarity=0.694  Sum_probs=549.2

Q ss_pred             CCHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCHHHCC
Q ss_conf             78789999999999978988911667566778710023014347554005887999998511154322489878634346
Q gi|254780191|r    2 SNVSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNIFTGQEKPVYQAVTTVQKCVRAGGKHNDLDNVG   81 (898)
Q Consensus         2 ~s~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~f~G~~~p~~~r~~~~QkCiR~ggkhnDld~VG   81 (898)
                      ||++|||++||+||++|||+++|||||||+||||||||||||+||||||+|.++||++|+|+||||||+    |||||||
T Consensus         1 mt~~eiR~~Fl~fF~~kgH~~v~ssslvp~~dptllftnAGm~~Fk~~f~G~~~p~~~r~~~~QkCiR~----~DldnVG   76 (593)
T PRK01584          1 MTLDELRKKYIDFFKSKGHVEIAGKSLVPENDPTVLFNTAGMQPLVPYLLGEPHPSGDMLVNVQKCLRT----GDIDEVG   76 (593)
T ss_pred             CCHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCEEEEECCCCCCCHHHCCCCCCCCCCCCCCCCEEEC----CCHHHCC
T ss_conf             988999999999998789888378771779999835740451017123258889999974567531333----7563368


Q ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHH--HHCCCCHHHEEEEECCC------HHHHHHHHHHHCCCCHHHEEE
Q ss_conf             4885001788854223147537889998998613--34189812379997188------289999756634999899753
Q gi|254780191|r   82 RTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLT--KEFDLDQRRLYITVYDE------DEEAFKLWKKISGLSADKIIR  153 (898)
Q Consensus        82 ~t~rH~TfFEMlGn~SfgdYfK~eai~~awe~lt--~~~~l~~~~l~vtv~~~------D~e~~~iW~~~~gi~~~~i~~  153 (898)
                       |+|||||||||||||||||||+|||+|||||||  ++|+|||+|||||||++      |+||++||+++ |||++||++
T Consensus        77 -~~~H~TfFEMLGn~SFgdYfK~eaI~~awe~lt~~~~l~l~~~rl~vtv~~~D~~~~~D~E~~~iW~~~-Gi~~~~I~~  154 (593)
T PRK01584         77 -DLSHLTFFEMLGNWSLGAYFKEESVKYSFEFLTSPDYLNIPKDKLYVSVFEGDEDIPRDEETAKIWESL-GISKDRIFY  154 (593)
T ss_pred             -CCCCCHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHEEEEEEECCCCCCCCHHHHHHHHHC-CCCHHHEEE
T ss_conf             -887527775054452331148999999999806632048883247999960587665448899999981-998999464


Q ss_pred             CCCCCCCC-CCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             57866654-57999998770467885385568988877788982689600112344304788756576653101757999
Q gi|254780191|r  154 ITTNDNFW-SMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLER  232 (898)
Q Consensus       154 ~~~~dNfW-~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNlVFmq~~~~~~g~~~~Lp~~~IDTGmGLER  232 (898)
                      ++.+|||| +||++||||||||||||+|+...+..+..++||+|||||||||||||||++||+|.|||+|||||||||||
T Consensus       155 ~~~~dNfW~~~G~~GPCGPcsEi~~d~g~~~~~~~~~~~~d~~r~lEIWNlVFmqy~r~~~G~~~pLp~k~VDTGmGLER  234 (593)
T PRK01584        155 LSREHNFWGPVGETGPCGPDTEIFVDTGKPKCSVNCRITCSCGKYFEIWNNVFMQYNKDEDGNYEELKRKCVDTGMGIER  234 (593)
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEECEEECCCCCEEECCCCCCCCCCCHHH
T ss_conf             57667710038998899875789974677766778898788887699865411352126999721688774036868999


Q ss_pred             HHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCC--CCHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCHHHHHHHHHH
Q ss_conf             99998879853005769999999997306785433--5024899999898999987403--3334446412577889999
Q gi|254780191|r  233 MATVLQEKTNNYDIDLFKHLIQASEQVTGMKYEGN--NIVNHRVIVDHLRSSSFLIADG--ILPANEGRGYVLRRIMRRA  308 (898)
Q Consensus       233 l~~vlqg~~s~ydtD~f~pii~~i~~~~g~~y~~~--~~~~~rvIaDH~Ra~~f~I~DG--v~PsN~GrGYvlRrilRRa  308 (898)
                      |||+|||++||||||+|.|||+.+++++|++|..+  +++++||||||+||++||||||  |+|||+|||||||||||||
T Consensus       235 i~~vlQg~~snYdtD~F~pii~~i~~~s~~~y~~~~~~~~a~rvIADH~Rs~~f~IaDG~~v~PsN~grGYvLRriiRRa  314 (593)
T PRK01584        235 TIAFLQGKSSVYDTDAFTPIIKRIEKISGKIYGQNEEDDRSIRIIADHIKAACFILADPKVVLPSNVGQGYVLRRLIRRS  314 (593)
T ss_pred             HHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCEEEEHHHHHEEEEEECCCCEECCCCCCCCCHHHHHHHHH
T ss_conf             99998299974203110689999999858866776666431543112123046895369743577788870489999999


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEE
Q ss_conf             99999848743310456899999864555555764678899998748989999998999999998611546424574379
Q gi|254780191|r  309 MCYARLLGYTEPLMMHLLPALCTEMGSAYPELIQAKLLIEETLRSEDERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAF  388 (898)
Q Consensus       309 ~r~~~~lg~~~~fl~~lv~~v~~~m~~~ypeL~~~~~~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsg~~af  388 (898)
                      +||+++||++.|||++||+.+++.|++.||||.++++.|+++|..||++|.+||++|+++|++.+++++ ++.|||++||
T Consensus       315 ~r~~~~Lg~~~~fL~~lv~~vi~~~~~~ypeL~~~~~~I~~ii~~EEe~F~~TL~~G~~~~~~~i~~~~-~~~l~g~~af  393 (593)
T PRK01584        315 IRYAKKLGIESHFLADLVDSVEEIYASFYKELTEKKDFIKKELNKEEEKFFKTLRKGEQEFIKMIPQLS-SKIIPGDIAF  393 (593)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCCEEE
T ss_conf             999987388711599999999999877788888899999999999999999999999999999998655-7867875237


Q ss_pred             EEECCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCEEECCCCCCCCCC
Q ss_conf             98524588889999876650774435888999999999764443311001201356788873048862643444443211
Q gi|254780191|r  389 KLYDTHGLPLDIMQDILCARGLAGIDIISFNQALEEQRSRARAHSLGLGSGTTEKIWFSLKEKYGATQFIGYDLLRGSKF  468 (898)
Q Consensus       389 ~LyDTyGfP~dlt~eia~e~gi~~vD~~~f~~~m~~qk~~sr~~~~~~~~~~~~~~~~~~~~~~~~t~F~GYe~~~~~~~  468 (898)
                      +||||||||+|||++||+|+|+. ||.++|+++|++||++||+...                                  
T Consensus       394 ~LYDTyGfP~dlt~eia~e~Gl~-vD~~~F~~~~~~~~~~sr~g~~----------------------------------  438 (593)
T PRK01584        394 KLYDTYGFPYELTEELASEYGFT-VDREGFDEHFKKHQKVSKKGGD----------------------------------  438 (593)
T ss_pred             EEECCCCCCHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHCCC----------------------------------
T ss_conf             86305697999999999984972-1588999999999998873797----------------------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCEEEECCCCCEEEEEECCCCEEECCCCCCCCCCEEEECCEEEEEECCCC
Q ss_conf             12221113444544555655348999974781320004797699997375200036876566514540424898522456
Q gi|254780191|r  469 MKEDRKVLCQKPPIDLTNGVSSIVKAIVQQGEIVEEAVSGQKVEVVFDQTPFYAEAGGQLGDTGCAIGDGIRLQITDVQK  548 (898)
Q Consensus       469 ~~~~~~~~~~~~~~~~~~~~~s~v~~i~~~~~~v~~~~~g~~~~ivLd~T~FY~E~GGQ~~D~G~i~~~~~~~~V~dv~k  548 (898)
                                                                  .++         .||.+|++                
T Consensus       439 --------------------------------------------~~~---------kG~l~d~~----------------  449 (593)
T PRK01584        439 --------------------------------------------KVF---------KGGLADHS----------------  449 (593)
T ss_pred             --------------------------------------------EEE---------ECCCCCCC----------------
T ss_conf             --------------------------------------------067---------61520254----------------


Q ss_pred             CCCEEEEEEECCCCCCCCCCCEEEEEEHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCC
Q ss_conf             55338998510467875567338884212556777520136889999975212544444553002430000024767899
Q gi|254780191|r  549 KAEGIFVHHAIVERGILRTEMSLVLTIDYQNRRQLSINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPIT  628 (898)
Q Consensus       549 ~~~g~i~H~~~~~~g~l~~g~~V~~~VD~~rR~~~~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt  628 (898)
                                                      ..+|+|||||||||+|||+|||+||+|+||+|++++|||||||+++||
T Consensus       450 --------------------------------~~~~~~HTATHLLh~ALR~VLG~hV~Q~GS~v~~~~lRfDfth~~~lt  497 (593)
T PRK01584        450 --------------------------------YETTKLHTATHLLHKALQLVLGDHVRQKGSNITAERLRFDFSHPRKMT  497 (593)
T ss_pred             --------------------------------CCCCCCCHHHHHHHHHHHHHCCCCEEECCCCCCCCEEEEEEECCCCCC
T ss_conf             --------------------------------001351548999999999862875598785457981799962799999


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHCCCCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHH
Q ss_conf             99999999999898873045304661232221000355443155562489984476778553101562225886460110
Q gi|254780191|r  629 SAELKSIEDNVNDIIAQNLPVVTRIMNREDAIASGAAALLGTKYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLL  708 (898)
Q Consensus       629 ~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~~ga~alfgekygd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~f  708 (898)
                      +|||++||++||++|++|+||++.+|+++||++.||++||||||||.||||+|+     .||+||||||||.|||+||.|
T Consensus       498 ~eei~~IE~~vN~~I~~~~~V~~~~~~~~eA~~~ga~alfgekY~d~VRVv~i~-----~~S~ElCGGTHv~~TgeIg~f  572 (593)
T PRK01584        498 DDEIKKVEDIVNLQIKNDLSVKKEVMSLEEAKEKGAMALFGEKYEDVVSVYEID-----GFSIEVCGGPHVENTSELGTF  572 (593)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEECHHHHHHCCCEEECCCCCCCEEEEEEEC-----CEEEECCCCCCCCCHHHCCCE
T ss_conf             999999999999999838962599824999997499262289999866899889-----967865786133877334467


Q ss_pred             HEECCCCCCCCCEEEEEEECH
Q ss_conf             011012126882899997168
Q gi|254780191|r  709 YIVSESSIRAGIRRIEAITGQ  729 (898)
Q Consensus       709 kIise~si~sGvRRIeavtG~  729 (898)
                      ||++|++|++||||||||||+
T Consensus       573 kI~~e~si~~GvrRIeAvtGd  593 (593)
T PRK01584        573 KIQKEQSSSSGVRRIKAILID  593 (593)
T ss_pred             EEEEECCCCCCCEEEEEEECC
T ss_conf             999767660784789998178


No 6  
>pfam01411 tRNA-synt_2c tRNA synthetases class II (A). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only alanyl-tRNA synthetases.
Probab=100.00  E-value=0  Score=1548.88  Aligned_cols=542  Identities=51%  Similarity=0.877  Sum_probs=519.7

Q ss_pred             HHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCCCCCC-CCCCCCCCCCCCCCEECCCCCCCHHHCCCCC
Q ss_conf             999999999997898891166756677871002301434755400588-7999998511154322489878634346488
Q gi|254780191|r    6 SIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNIFTGQ-EKPVYQAVTTVQKCVRAGGKHNDLDNVGRTN   84 (898)
Q Consensus         6 eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~f~G~-~~p~~~r~~~~QkCiR~ggkhnDld~VG~t~   84 (898)
                      |||++||+||++|||+++|||||||+||||||||||||+||||||+|. .+||++|+|+||||||+    |||||||+|+
T Consensus         1 eiR~~fl~fF~~~gH~~i~s~~lvp~~d~~llft~Agm~~fkp~~~g~~~~pp~~~l~~~Q~CiR~----~DidnVG~t~   76 (545)
T pfam01411         1 EIRQTFLDFFEKKGHTRVPSSPVVPRNDPTLLFTNAGMNQFKPIFLGGEDKPPYNRAVNSQKCIRA----GDLDNVGRTA   76 (545)
T ss_pred             CHHHHHHHHHHHCCCEEECCCCCCCCCCCCEEEECCCCHHCHHHHCCCCCCCCCCCCCCCCCCEEC----CCHHHCCCCC
T ss_conf             968999999987898880786706799998146404601173765498758998872443332443----7654336777


Q ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHCCCCHHHEEECCCCCCCCCCC
Q ss_conf             50017888542231475378899989986133418981237999718828999975663499989975357866654579
Q gi|254780191|r   85 RHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKLWKKISGLSADKIIRITTNDNFWSMA  164 (898)
Q Consensus        85 rH~TfFEMlGn~SfgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~iW~~~~gi~~~~i~~~~~~dNfW~~g  164 (898)
                      |||||||||||||||||||+|||+|||||||++|||||+|||||||+.|+||++||.+++|+|++||++++.+||||+||
T Consensus        77 rH~T~FEMlGn~SFg~YfK~eai~~a~e~lt~~l~i~~~~l~~t~~~~d~ea~~~w~~~~g~~~~~i~~~~~~~nfw~~g  156 (545)
T pfam01411        77 RHHTFFEMLGNFSFGDYFKEEAIEFAWELLTKELGLDPERLYVTVYEWDDEAGPIWEKIVGGPEERILRFGDKDNFWEMG  156 (545)
T ss_pred             CCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCHHHEEEEECCCCCCHHHHHHHHCCCCHHHCEECCCCCCEEECC
T ss_conf             75323220334515624378999999999765617886676999888863366768886299999906267777605778


Q ss_pred             CCCCCCCCEEEEEECCCCCCCCCCC--CCCCCCCEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf             9999877046788538556898887--77889826896001123443047887565766531017579999999887985
Q gi|254780191|r  165 ETGPCGPCSEIFFDQGECIPGGLPG--SSEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLERMATVLQEKTN  242 (898)
Q Consensus       165 ~~GpcGPcsEi~~d~g~~~~~~~~~--~~~~~~r~lEiwNlVFmq~~~~~~g~~~~Lp~~~IDTGmGLERl~~vlqg~~s  242 (898)
                      ++||||||||||||+|+++.+..+.  ++++++||+||||+|||||+|+.+|++.|||++||||||||||++++||+++|
T Consensus       157 ~~gpcgPcseI~~d~G~e~~~~~~~~~~~~~~~~~~EiwNlVF~q~~~~~~g~~~~Lp~~~iDtGmGlER~~~vlq~~~~  236 (545)
T pfam01411       157 DTGPCGPCSEIDYDRGEEIGGWPSGGTPTADDDRFLEIWNLVFMQFNRESDGTLKPLPKKSIDTGMGLERLVAVLQNVRS  236 (545)
T ss_pred             CCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEHHHHHHHHHHHCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHCCHH
T ss_conf             98899776899976672026888889988888782889999999958766787440662023306753778999837388


Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCH
Q ss_conf             30057699999999973067854335024899999898999987403333444641257788999999999848743310
Q gi|254780191|r  243 NYDIDLFKHLIQASEQVTGMKYEGNNIVNHRVIVDHLRSSSFLIADGILPANEGRGYVLRRIMRRAMCYARLLGYTEPLM  322 (898)
Q Consensus       243 ~ydtD~f~pii~~i~~~~g~~y~~~~~~~~rvIaDH~Ra~~f~I~DGv~PsN~GrGYvlRrilRRa~r~~~~lg~~~~fl  322 (898)
                      ||+||+|.||++.++++++++|.+..+.|+||||||+||++|||+|||+|||+|||||||||||||+||+++||++.|||
T Consensus       237 ~y~tdlf~~i~~~~~~~~~~~y~~~~~~a~riIaDH~Ra~~f~I~DGv~PSN~grGYvlRrllRRa~r~~~~lg~~~~~L  316 (545)
T pfam01411       237 NYDTDVFIPLIELIEAISGAKYYDETDEAYRVIADHTRALTFAIADGVVPSNEGRGYVLRRILRRALRHAKKLGLKEPFL  316 (545)
T ss_pred             HHHHHHCHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCHH
T ss_conf             87777555899999998399866665522665177788899986467546777776147899999999998745764209


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHH
Q ss_conf             45689999986455555576467889999874898999999899999999861154642457437998524588889999
Q gi|254780191|r  323 MHLLPALCTEMGSAYPELIQAKLLIEETLRSEDERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLDIMQ  402 (898)
Q Consensus       323 ~~lv~~v~~~m~~~ypeL~~~~~~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsg~~af~LyDTyGfP~dlt~  402 (898)
                      ++||+.+++.|++.||||.++++.|.+||+.||++|.+||++|+++|+++++++++++.|||++||+||||||||+|||+
T Consensus       317 ~~Lv~~vi~~m~~~YpEL~~~~~~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~~~~~~~l~g~~af~LYDTyGfP~dlt~  396 (545)
T pfam01411       317 YDLVPTVIEEMGDAYPELKEKEDTIQEILELEEERFAKTLERGLRLLERLIKSLKKKKTLPGEDAFKLYDTYGFPVDLTK  396 (545)
T ss_pred             HHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEHHCCCCCHHHHH
T ss_conf             99999999987525868898689999999999999999999899999999985426870350210230453698989999


Q ss_pred             HHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             87665077443588899999999976444331100120135678887304886264344444321112221113444544
Q gi|254780191|r  403 DILCARGLAGIDIISFNQALEEQRSRARAHSLGLGSGTTEKIWFSLKEKYGATQFIGYDLLRGSKFMKEDRKVLCQKPPI  482 (898)
Q Consensus       403 eia~e~gi~~vD~~~f~~~m~~qk~~sr~~~~~~~~~~~~~~~~~~~~~~~~t~F~GYe~~~~~~~~~~~~~~~~~~~~~  482 (898)
                      +||+|+|++ ||+++|+++|++||++||++++.....   ..+..+.+...+|+|+||+.++                  
T Consensus       397 eia~e~gi~-vD~~~f~~~m~~qr~~sr~~~~~~~~~---~~~~~~~~~~~~t~f~gYe~~~------------------  454 (545)
T pfam01411       397 EIAEERGLT-VDMPGFEYAMVEQRERSKQAKKEKGEE---LDNSALKELPATTEFLGYDDLE------------------  454 (545)
T ss_pred             HHHHHCCCC-CCCCCHHHHHHHHHHHHHHHHCCCCCC---HHHHHHHCCCCCCCCCCCCCCC------------------
T ss_conf             999985992-164037999999999978603135632---0178874468997677767677------------------


Q ss_pred             CCCCCCCEEEEEEEECCCEEEECCCCCEEEEEECCCCEEECCCCCCCCCCEEEECCEEEEEECCCCCCCEEEEEEECCCC
Q ss_conf             55565534899997478132000479769999737520003687656651454042489852245655338998510467
Q gi|254780191|r  483 DLTNGVSSIVKAIVQQGEIVEEAVSGQKVEVVFDQTPFYAEAGGQLGDTGCAIGDGIRLQITDVQKKAEGIFVHHAIVER  562 (898)
Q Consensus       483 ~~~~~~~s~v~~i~~~~~~v~~~~~g~~~~ivLd~T~FY~E~GGQ~~D~G~i~~~~~~~~V~dv~k~~~g~i~H~~~~~~  562 (898)
                           ++++|++|+.+++.++++..++.+.||||+||||||||||++|+|+|.++++.+.|+||||. +|+|+|++.+.+
T Consensus       455 -----~~~~V~~i~~~~~~v~~~~~~~~~~VVLDkTpFYaEsGGQvgD~G~I~~~~~~~~V~DvqK~-gg~ilH~~~~~~  528 (545)
T pfam01411       455 -----AEAKIIALPDDGEFVAEVLAGQEGGVILDRTPFYAESGGQIGDTGYIIGNGGEFRVTDVQKY-GGVVVHKGKLES  528 (545)
T ss_pred             -----CCEEEEEEEECCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCEEEEEECCEEEEEEEEEEE-CCEEEEEEEECC
T ss_conf             -----42799999869867124337882799970897777568988787999649979999864999-999999999635


Q ss_pred             CCCCCCCEEEEEEHHHH
Q ss_conf             87556733888421255
Q gi|254780191|r  563 GILRTEMSLVLTIDYQN  579 (898)
Q Consensus       563 g~l~~g~~V~~~VD~~r  579 (898)
                      |.+++|++|.++|||+|
T Consensus       529 G~l~~Gd~V~~~VD~~R  545 (545)
T pfam01411       529 GSLKVGDTVIAVVDEDR  545 (545)
T ss_pred             CCCCCCCEEEEEECCCC
T ss_conf             85178999999967889


No 7  
>TIGR00344 alaS alanyl-tRNA synthetase; InterPro: IPR002318   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Alanyl-tRNA synthetase (6.1.1.7 from EC) is an alpha4 tetramer that belongs to class IIc. ; GO: 0004813 alanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006419 alanyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=1282.41  Aligned_cols=848  Identities=46%  Similarity=0.779  Sum_probs=782.9

Q ss_pred             HHHHHHHHHHHHCCCEECCCCCCCCC-CCCCHHEEECCCCCCCCCCCCCCCCC----CCCCCCCCCCEECCCCCCCHHHC
Q ss_conf             99999999999789889116675667-78710023014347554005887999----99851115432248987863434
Q gi|254780191|r    6 SIRTTFLEFFQKNGHELLPSSSLIPC-NDPTLMFTNSGMVPFKNIFTGQEKPV----YQAVTTVQKCVRAGGKHNDLDNV   80 (898)
Q Consensus         6 eiR~~fl~fF~~~~H~~~~s~slvp~-~d~~llft~Agm~~fk~~f~G~~~p~----~~r~~~~QkCiR~ggkhnDld~V   80 (898)
                      ++|+.||+||+++||.++|++|++|+ |||+++|++|||++|||+|+|...||    ++|++++|+|+|+||||||++||
T Consensus         1 ~~~~~~~~~f~~~gh~~~~~~~~~p~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gg~~~d~~~~   80 (914)
T TIGR00344         1 EVRQTFLDFFKEKGHEVLPSAPLVPRRWDPTLLLTNAGVATFKPYFLGGVVPPPDFYAPRLTNAQPCIRLGGKHNDLENV   80 (914)
T ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCCCHHCCHHHHHHHHHHCCCCCCCHHHC
T ss_conf             91457889876215410112444323467624554222234324442255665200011023323454337753321230


Q ss_pred             CCCCCCHHHHHHHHHHHHC-----CCCHHHHHHHHHHHHH--HHCCCCHHHEEEEECCCHHHHHHHHHHHCC-CCHHHEE
Q ss_conf             6488500178885422314-----7537889998998613--341898123799971882899997566349-9989975
Q gi|254780191|r   81 GRTNRHHTFFEMLGNFSFG-----GYFKERAIQLAWDLLT--KEFDLDQRRLYITVYDEDEEAFKLWKKISG-LSADKII  152 (898)
Q Consensus        81 G~t~rH~TfFEMlGn~Sfg-----dYfK~eai~~awe~lt--~~~~l~~~~l~vtv~~~D~e~~~iW~~~~g-i~~~~i~  152 (898)
                      |+|+||||||||+||||||     ||||+|+|.|+|+|+|  .++++|++++|+|+|++|++++++|.+..| +|.++|+
T Consensus        81 g~~~~h~~~f~~~g~~~~g~~~~~~y~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~d~~~~~~w~~~~~~~p~~~~~  160 (914)
T TIGR00344        81 GRTGRHHTLFEMLGNFSFGYEDDEDYFKEEAIAFAWELLTSELGLGLPKERLYVTVYEEDDEAYELWEKGGGAGPCERII  160 (914)
T ss_pred             CCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHHCCCCCCCHHHHH
T ss_conf             44201345666530112578764024456788888887530110344320168887537325677653145545313443


Q ss_pred             ECCC------CCCCCCCCCCCCCCCCEEEEEECCCCCCC---CCCC-CC--CCCCCEEEEEEHHHHHHHCCCCCC-CCCC
Q ss_conf             3578------66654579999987704678853855689---8887-77--889826896001123443047887-5657
Q gi|254780191|r  153 RITT------NDNFWSMAETGPCGPCSEIFFDQGECIPG---GLPG-SS--EEGERYIEIWNLVFMQFEQQNKQE-RFIL  219 (898)
Q Consensus       153 ~~~~------~dNfW~~g~~GpcGPcsEi~~d~g~~~~~---~~~~-~~--~~~~r~lEiwNlVFmq~~~~~~g~-~~~L  219 (898)
                      +.+.      .+|||.+|++||||||+|+|||+|+.+.+   +... ..  .+.+||+|+||+||+||++..+|+ +.||
T Consensus       161 ~~g~~~gp~~~~~~w~~~~~~p~gp~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (914)
T TIGR00344       161 RGGDELGPYAADNFWDLGDTGPCGPCTEIYYDRGEKIGDTGYGPEKLFWESGEPDRYLEIWNLVFSQFNRDGDGNDLTPL  240 (914)
T ss_pred             HCCCCCCCCCCHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCHH
T ss_conf             13542364200012320356777641013221143114544674312346677621356777788865203576400011


Q ss_pred             CCCCCCCCCCHHHHHHHHC-CCCCCCHHHHHHHHHHHHHHHCCCCCCCC---------CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             6653101757999999988-79853005769999999997306785433---------5024899999898999987403
Q gi|254780191|r  220 PKMSIDTGMGLERMATVLQ-EKTNNYDIDLFKHLIQASEQVTGMKYEGN---------NIVNHRVIVDHLRSSSFLIADG  289 (898)
Q Consensus       220 p~~~IDTGmGLERl~~vlq-g~~s~ydtD~f~pii~~i~~~~g~~y~~~---------~~~~~rvIaDH~Ra~~f~I~DG  289 (898)
                      |+++||||||+||++.++| +.+++|++|+|.|++..++++++..|..+         ...++|+|+||+|+++|+++||
T Consensus       241 ~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~dh~~~~~~~~~~g  320 (914)
T TIGR00344       241 PKKNIDTGAGLERLVAVLQGDVPNNFDTDLFLPLIESVEELTGLTYPSENYKTFDKDGADTSLRVIADHTRALAFLLADG  320 (914)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             13333321026778887752000012467888887877865200011001100000010113444555678888876426


Q ss_pred             CCCC-CCCCCHHHHHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3334-4464125778899999999984874331--045689999986455555576467889999874898999999899
Q gi|254780191|r  290 ILPA-NEGRGYVLRRIMRRAMCYARLLGYTEPL--MMHLLPALCTEMGSAYPELIQAKLLIEETLRSEDERFGKTLDRGL  366 (898)
Q Consensus       290 v~Ps-N~GrGYvlRrilRRa~r~~~~lg~~~~f--l~~lv~~v~~~m~~~ypeL~~~~~~I~~ii~~EE~~F~~TL~~G~  366 (898)
                      ++|+ |+||||++||++||++|+++.+++..+|  ++++++.+++.+++.||++....+.|.+++..|+++|.+|+++|.
T Consensus       321 ~~p~p~~~~gy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~  400 (914)
T TIGR00344       321 VLPSPNEGRGYVLRRLLRRALRHGKLLGLKEPFNFLYKLVPTLIEVLGDLYPELKEKQELVEEILELEEERFAKTLERGL  400 (914)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             66687653138899999999887777404431036788889999986433455410378999999878888888887668


Q ss_pred             HHHHHHHHHCC--CCCCCCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             99999986115--4642457437998524588889999876650774435888999999999764443311001201356
Q gi|254780191|r  367 VLLDGVLSHLG--KDEILNGDVAFKLYDTHGLPLDIMQDILCARGLAGIDIISFNQALEEQRSRARAHSLGLGSGTTEKI  444 (898)
Q Consensus       367 ~~l~~~i~~~~--~~~~lsg~~af~LyDTyGfP~dlt~eia~e~gi~~vD~~~f~~~m~~qk~~sr~~~~~~~~~~~~~~  444 (898)
                      .++++.++..+  .+..++++++|+||||||||+|++.+++.++|+. +|.++|+.+|.+++.+++..+...... ....
T Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~g~p~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~  478 (914)
T TIGR00344       401 RLLEKLLKKLKKDGNKELDGEDAFKLYDTYGFPVELTEELAEEKGLT-VDWPGFEYALEEQRERSKAAKKTLGDL-FEED  478 (914)
T ss_pred             HHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHH-HHHH
T ss_conf             99999987520024210123565543420377678899888640760-121256889888877643211013444-4433


Q ss_pred             HHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEE-CCCEEEECCCCCEEEEEECCCCEEEC
Q ss_conf             78887304886264344444321112221113444544555655348999974-78132000479769999737520003
Q gi|254780191|r  445 WFSLKEKYGATQFIGYDLLRGSKFMKEDRKVLCQKPPIDLTNGVSSIVKAIVQ-QGEIVEEAVSGQKVEVVFDQTPFYAE  523 (898)
Q Consensus       445 ~~~~~~~~~~t~F~GYe~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~i~~-~~~~v~~~~~g~~~~ivLd~T~FY~E  523 (898)
                      ...+.....+++|.||+..+.                       .+.+..++. ++..++.+..++..+++||+||||||
T Consensus       479 ~~~~~~~~~~~~~~~y~~~~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~  535 (914)
T TIGR00344       479 LEALANVYPATEFLGYDDPEL-----------------------LAKVLGLLDGDGKLVEEANPGQSGGVILDRTPFYAE  535 (914)
T ss_pred             HHHHHHCCCCHHHCCCCCCHH-----------------------HHHHHHHHCCCCCHHHHHCCCCCCEEEEECCCCCCC
T ss_conf             223321122012100232002-----------------------345555430454001221034431377604302345


Q ss_pred             CCCCCCCCCEEEECC-EEEEEECCCCCCCEEEEEEECCCCCCCCCCCEEEEEEHHHHHHHHHHCCCHHHHHHHHHHHCCC
Q ss_conf             687656651454042-4898522456553389985104678755673388842125567775201368899999752125
Q gi|254780191|r  524 AGGQLGDTGCAIGDG-IRLQITDVQKKAEGIFVHHAIVERGILRTEMSLVLTIDYQNRRQLSINHSATHLLHHALSTILG  602 (898)
Q Consensus       524 ~GGQ~~D~G~i~~~~-~~~~V~dv~k~~~g~i~H~~~~~~g~l~~g~~V~~~VD~~rR~~~~~~HTatHlL~~alr~vLG  602 (898)
                      +|||++|+|++..++ ..+.|.++++..++.+.|.+....+.+..|+.+.+.+|+.+|..+++|||+||+||+++++++|
T Consensus       536 ~gg~~~d~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~h~~~h~~~~~~~~~~g  615 (914)
T TIGR00344       536 SGGQIGDTGYLNGDNGAKFRVEDVQKFKGGVVLHFGELLEGSLKVGDKVTAVVDEKRRLRLKRNHTATHLLHAALKKVLG  615 (914)
T ss_pred             CCCCCCCCCEEECCCCCEEEEEHHHHCCCCCEEEEEHHCCCCCCCCCEEEEEECHHHHHHHHHCCHHHHHHHHHHHHHHH
T ss_conf             67753444204406653243101122256411221000012113474145531045666555200378999999998641


Q ss_pred             CCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHCCC--CCEEEEE
Q ss_conf             44444553002430000024767899999999999998988730453046612322210003554431555--6248998
Q gi|254780191|r  603 SHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIASGAAALLGTKYN--DRVRVVS  680 (898)
Q Consensus       603 ~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~~ga~alfgekyg--d~VRVV~  680 (898)
                      .|++|+|+++...++||||+|++.++.+++.++|+++|+.|+.++|+.+.+++++.|+..+++++|+++|+  +.+|||.
T Consensus       616 ~~~~~~g~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  695 (914)
T TIGR00344       616 PHVWQAGSLVSAKKLRFDFSHPRALTKEELEEVEDLVNEQILANLPVKVEFLDLDEAKAKGALALFGEGYGPGEKVRVVS  695 (914)
T ss_pred             HHHHHCCCCCCHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHCHHHHHHHHHHHHCCCCCCCCCEEEEEE
T ss_conf             12221012000013210010000267778999999999998752250121201344554300110024457764057885


Q ss_pred             ECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCCCCCCCEEEEEEEC-HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf             447677855310156222588646011001101212688289999716-8999999999999999999839998899999
Q gi|254780191|r  681 VEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESSIRAGIRRIEAITG-QRARSHLMGQDEKLKSLASFLKVSQGNVVGR  759 (898)
Q Consensus       681 I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~si~sGvRRIeavtG-~~A~~~~~~~~~~l~~la~~L~~~~~~i~~k  759 (898)
                      +++.....+|+|+|||||+.+||+||.|+|+.++++++|++||++++| ..+..+++.....+.+.+..++..+.+++.+
T Consensus       696 ~~~~~~~~~~~~~cgg~h~~~~g~~g~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  775 (914)
T TIGR00344       696 VGDPNGELYSVELCGGTHVENTGDIGLFKILKESGIGAGVRRIEAVTGNEAALEYLNEEEDLLKEAADLLKVDPNELPKK  775 (914)
T ss_pred             CCCCCCCEEEEEECCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHEECCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             07754210121001563112322200023321000121023211002526889998877777876677621334555678


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHCCCCEEEEEECCCCHHH-HHHHHHHHHHHCCCCE----EEEEE
Q ss_conf             99999999999999999999987636-----53555369527999957999789-9999999997549978----99999
Q gi|254780191|r  760 VEEIWEEYRKLQLIHAKRKLQLNVED-----LSCHKIADVNFMSHIISEVDSKE-LKSVMDALQKKIQSGI----IMLVG  829 (898)
Q Consensus       760 i~~L~~e~K~l~k~~~k~k~~~~~~~-----~~~~~i~~~~~i~~~~~~~d~~~-Lr~l~d~l~~k~~~~v----vvL~~  829 (898)
                      +.++..+++.++++...++.+.....     .....+++++++...+...+.+. ++.+++.++.++...+    ++++.
T Consensus       776 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  855 (914)
T TIGR00344       776 VERLFEEWKELRKELEKLKEKLAPLKSTELLEKAETLDGLKVLVEELKTVDAKPNLKTLLDKLKEKLGSLVDKDKAVLLA  855 (914)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHEEEE
T ss_conf             89888889899999999988776677887766666641134335453011355037899999998764321100110122


Q ss_pred             ECCCCEEEEEEEECHHHHC--CCCHHHHHHHHHH-----HHCCCCCC---CCCHHCCCCC
Q ss_conf             5389817999986778972--6798999999998-----83499999---9810114589
Q gi|254780191|r  830 ISKEKKASVLIVVTEDLLD--RFNAVDLARLSAK-----VLGGGGGG---GRPHMAQSGG  879 (898)
Q Consensus       830 ~~~~~k~~ivv~vs~~~~~--~~~A~~lik~ia~-----~l~GGgGG---Gkpd~AQgGG  879 (898)
                      ...+.+..+++++..++..  +++++.+++.++.     .+ ||+||   |+|+++|+||
T Consensus       856 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-gg~gg~~~g~~~~~~~~g  914 (914)
T TIGR00344       856 LLNDGKGKLLAGVSEDLVKAKGLKAGELLNEVAEVPSFLIL-GGGGGCIEGRPDLAQGGG  914 (914)
T ss_pred             ECCCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCEEEE-CCCCCEECCCCCHHHCCC
T ss_conf             11455531442001345554100378899876316652775-476431114300210379


No 8  
>cd00673 AlaRS_core Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its predicted structure and the presence of three characteristic sequence motifs.
Probab=100.00  E-value=0  Score=838.71  Aligned_cols=232  Identities=53%  Similarity=0.957  Sum_probs=225.8

Q ss_pred             HHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCHHHCCCC
Q ss_conf             78999999999997898891166756677871002301434755400588799999851115432248987863434648
Q gi|254780191|r    4 VSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNIFTGQEKPVYQAVTTVQKCVRAGGKHNDLDNVGRT   83 (898)
Q Consensus         4 ~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~f~G~~~p~~~r~~~~QkCiR~ggkhnDld~VG~t   83 (898)
                      ++|||++||+||++|||+++|||||||++|||||||||||+||||||+|.++||++|+|+||||||+    +||+|||+|
T Consensus         1 s~eiR~~Fl~fF~~~gH~~vpssslvp~~DptllFtnAGM~~Fkp~flG~~~p~~~r~~~~QkCiR~----~di~nvG~t   76 (232)
T cd00673           1 ASEIRETFLSFFEKKGHTRVPSSPVVPRDDPTLLFTNAGMNQFKPIFLGEVPPPANRLVNSQKCIRA----GDIDNVGKT   76 (232)
T ss_pred             CHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCEEEEECCHHHHHHHHCCCCCCCCCCCEEEEECCCC----CCCCCCCCC
T ss_conf             9689999999998789888278772238999501441146888998677889998751000012365----783246777


Q ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHCCCCHHHEEECCCCCCCCCC
Q ss_conf             85001788854223147537889998998613341898123799971882899997566349998997535786665457
Q gi|254780191|r   84 NRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKLWKKISGLSADKIIRITTNDNFWSM  163 (898)
Q Consensus        84 ~rH~TfFEMlGn~SfgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~iW~~~~gi~~~~i~~~~~~dNfW~~  163 (898)
                      +|||||||||||||||||||+|||.|||||||++|+||++|||||||.+|||++++|.+.+|+|++||++++.+||||+|
T Consensus        77 ~rH~TfFEMLGnfSFGdYfK~eaI~~awe~lt~~~~l~~~rlyvTv~~~Dde~~~~~~~~~gi~~~~i~~~~~~dNfW~~  156 (232)
T cd00673          77 GRHHTFFEMLGNFSFGDYFKEEAIAFAWELLTEVLGLPKDRLYVSVFEGDDEEEAIWWWKIGLPGIRIERIGFKDNFWEM  156 (232)
T ss_pred             CCCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCHHHHHHHHHHCCCCHHHEEECCCCCCCCCC
T ss_conf             76402333044420314589999999999875123768562426674697799999997419988983466776667869


Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCC
Q ss_conf             99999877046788538556898887778898268960011234430478875657665310175799999998879
Q gi|254780191|r  164 AETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLERMATVLQEK  240 (898)
Q Consensus       164 g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNlVFmq~~~~~~g~~~~Lp~~~IDTGmGLERl~~vlqg~  240 (898)
                      |++||||||||||||+|+++++ ....+++|+|||||||||||||+|++||++.|||+||||||||||||||||||+
T Consensus       157 G~~GPcGPcsEI~yd~g~~~~~-~~~~~~~~~r~lEiwNlVFmqy~r~~dg~l~~Lp~k~IDTGmGlERl~~vlQgv  232 (232)
T cd00673         157 GGNGPCGPCSEIFYDRGEERDA-ASLPNEDDDRYLEIWNLVFMQYNRDADGTYRPLPKKIVDTGMGLERLVWVLQGV  232 (232)
T ss_pred             CCCCCCCCCEEEEECCCCCCCC-CCCCCCCCCCEEEEEEEEEEEEEECCCCCCCCCCCCEECCCCCHHHHHHHHCCC
T ss_conf             9987998767789757777788-657788899889986731375200699976508998141683799999998379


No 9  
>COG2872 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]
Probab=100.00  E-value=8.5e-43  Score=354.00  Aligned_cols=222  Identities=32%  Similarity=0.442  Sum_probs=192.0

Q ss_pred             CCEEEEEEEECCCEEEECCCCCEEEEEECCCCEEECCCCCCCCCCEEEECCEEEEEECCCCCCCEEEEEEECCCCCCCCC
Q ss_conf             53489999747813200047976999973752000368765665145404248985224565533899851046787556
Q gi|254780191|r  488 VSSIVKAIVQQGEIVEEAVSGQKVEVVFDQTPFYAEAGGQLGDTGCAIGDGIRLQITDVQKKAEGIFVHHAIVERGILRT  567 (898)
Q Consensus       488 ~~s~v~~i~~~~~~v~~~~~g~~~~ivLd~T~FY~E~GGQ~~D~G~i~~~~~~~~V~dv~k~~~g~i~H~~~~~~g~l~~  567 (898)
                      +++.|..+..+             .|+||+|+|||+|||||+|+|+|.+.+++..|.++.+.+ ..|+|+.... ..+++
T Consensus        15 ~~~~v~~v~~~-------------~i~ld~T~Fyp~~GGQp~D~G~l~~~~~~~~~~~~~~~~-~~I~H~~~~~-~~~~v   79 (241)
T COG2872          15 FEATVVDVEDN-------------EIVLDRTIFYPTGGGQPGDTGTLIWAGGEYVVEDVTKDG-EEIVHVLAEH-AKLKV   79 (241)
T ss_pred             CEEEEEEEECC-------------EEEEEECCCCCCCCCCCCCCEEEEECCCEEEEEEEEECC-EEEEEEECCC-CCCCC
T ss_conf             24899998287-------------389871222479899868866898289469999887616-1999981676-66789


Q ss_pred             CCEEEEEEHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             73388842125567775201368899999752125444445530024300000247678999999999999989887304
Q gi|254780191|r  568 EMSLVLTIDYQNRRQLSINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNL  647 (898)
Q Consensus       568 g~~V~~~VD~~rR~~~~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~  647 (898)
                      |++|.++|||+||+++||+|||+|||.++|.+.++  ++-.|..+.+++.|+||.-..  +++.+.+++.++|+.|.+|+
T Consensus        80 G~~V~~~IDW~rRy~~mr~HTa~Hlls~~~~~~~~--~~~~g~~i~~d~~~iD~~~e~--~~~~~~~v~~~~ne~v~~~~  155 (241)
T COG2872          80 GDKVKLKIDWERRYRHMRMHTALHLLSAVLYKVYG--ALTTGFEIGEDYARIDFDGED--TEDEIEEVEALANELVKENL  155 (241)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHHHHHHHHHCCCC--CEEECCEECCCCCCCCCCCCC--CHHHHHHHHHHHHHHHHCCC
T ss_conf             97899997908988887560799999987501246--313112003663020246663--05569999999989987597


Q ss_pred             CCEEEEECCCCCCCCHHH-HHHHHCCC---CCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCCCCCCCEEE
Q ss_conf             530466123222100035-54431555---62489984476778553101562225886460110011012126882899
Q gi|254780191|r  648 PVVTRIMNREDAIASGAA-ALLGTKYN---DRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESSIRAGIRRI  723 (898)
Q Consensus       648 ~V~~~~~~~~eA~~~ga~-alfgekyg---d~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~si~sGvRRI  723 (898)
                      ||.+.+++.+||.+...+ ++-..-++   ..+|+|.|++.|     +..||||||+||+|||.|+|++.+++++|.+||
T Consensus       156 ~v~~~~i~~EE~~~~p~~~~~~~~~~~~~~g~iRiV~I~did-----~qpCgGtHVk~T~EIG~Iki~k~e~k~k~~~Rv  230 (241)
T COG2872         156 PVIIYFIPREEAEKLPGLVKLKNKVPPDVEGKIRIVEIGDID-----VQPCGGTHVKNTGEIGEIKILKTEKKGKGNRRV  230 (241)
T ss_pred             EEEEEECCHHHHHHCCCHHHHCCCCCCCCCCEEEEEEECCEE-----CCCCCCCCCCCCCEEEEEEEEEEEEECCCEEEE
T ss_conf             302455278998648471023245886556518999989903-----167888522886206779999999805724899


Q ss_pred             EEEECHHHHH
Q ss_conf             9971689999
Q gi|254780191|r  724 EAITGQRARS  733 (898)
Q Consensus       724 eavtG~~A~~  733 (898)
                      +|.+|.+|..
T Consensus       231 ~f~~~~~~~~  240 (241)
T COG2872         231 YFTLGERASA  240 (241)
T ss_pred             EEEECCCCCC
T ss_conf             9993663447


No 10 
>KOG2105 consensus
Probab=100.00  E-value=1.5e-37  Score=312.86  Aligned_cols=357  Identities=21%  Similarity=0.283  Sum_probs=265.3

Q ss_pred             CEEEEEECCCCEEECCCCCCCCCCEEEECCEEEEEECCCCCCCEEEEEEECCCCCCCCCCCEEEEEEHHHHHHHHHHCCC
Q ss_conf             76999973752000368765665145404248985224565533899851046787556733888421255677752013
Q gi|254780191|r  509 QKVEVVFDQTPFYAEAGGQLGDTGCAIGDGIRLQITDVQKKAEGIFVHHAIVERGILRTEMSLVLTIDYQNRRQLSINHS  588 (898)
Q Consensus       509 ~~~~ivLd~T~FY~E~GGQ~~D~G~i~~~~~~~~V~dv~k~~~g~i~H~~~~~~g~l~~g~~V~~~VD~~rR~~~~~~HT  588 (898)
                      +.+.+.|..|..||||||||.|.|++..    +.|..|.+.+. .--|+   ....+..|.+|...|||+||+++|||||
T Consensus        42 eg~~i~lqdtiLfpegggqp~d~gf~~~----v~V~~VsR~G~-~A~H~---~~~~iePGt~V~V~VD~qkR~D~MQQHs  113 (415)
T KOG2105          42 EGYEIELQDTILFPEGGGQPSDSGFLKI----VEVSHVSRFGL-HAKHH---VNDYIEPGTTVEVAVDEQKRMDYMQQHS  113 (415)
T ss_pred             ECCEEEEEEEEECCCCCCCCCCCCCCCC----EEEEEEECCCC-CHHHC---CCCCCCCCCEEEEEECHHHHHHHHHHHC
T ss_conf             1004530036862677998775565131----15788630320-21431---3787799976999855787748988713


Q ss_pred             HHHHHHHHHHHCC--CCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCC--CCHH
Q ss_conf             6889999975212--54444455300243000002476789999999999999898873045304661232221--0003
Q gi|254780191|r  589 ATHLLHHALSTIL--GSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAI--ASGA  664 (898)
Q Consensus       589 atHlL~~alr~vL--G~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~--~~ga  664 (898)
                      +|||+.|.+.+.+  -..-|-.|-+.+.-.+  |   ..++|.||+..||+.+|+.|+.-.||.+.+..+++-.  ..-.
T Consensus       114 GQHLitAvad~~fKlkTtSWelG~~~sa~e~--~---~~~mTaeqvaaieqsvNe~I~d~~~~~v~E~sl~d~eVeqVS~  188 (415)
T KOG2105         114 GQHLITAVADHLFKLKTTSWELGRFRSAIEL--D---TPSMTAEQVAAIEQSVNEKIRDRLPVNVRELSLDDPEVEQVSG  188 (415)
T ss_pred             CHHHHHHHHHHHHCCCEEEEECCCEEECCCC--C---CCCCCHHHHHHHHHHHHHHHHHCCCHHEEECCCCCCCHHHCCC
T ss_conf             2269999997640322003541451440236--8---8874699998789998899873243020101159842200268


Q ss_pred             HHHHHHCCCCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCCCCCCCEEEEEEECHHHHHHHHHHHHHHHH
Q ss_conf             55443155562489984476778553101562225886460110011012126882899997168999999999999999
Q gi|254780191|r  665 AALLGTKYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESSIRAGIRRIEAITGQRARSHLMGQDEKLKS  744 (898)
Q Consensus       665 ~alfgekygd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~si~sGvRRIeavtG~~A~~~~~~~~~~l~~  744 (898)
                      ..++.+-- .++|||.|+++|.++     ||||||+||++||.|+|++.++-.+|-.-..|+.|.|...|+...+.+++.
T Consensus       189 ~~~~D~ha-G~iRvvnI~~vDSN~-----CCGTHvs~~Sdl~vI~ILgtekg~k~rtN~~f~~GnRV~~~mersh~t~~a  262 (415)
T KOG2105         189 RGLPDDHA-GPIRVVNIEGVDSNM-----CCGTHVSNLSDLQVIKILGTEKGKKNRTNLIFLSGNRVLKWMERSHGTEKA  262 (415)
T ss_pred             CCCCCCCC-CCEEEEEECCCCCCC-----CCCCCCCCHHHCCEEEEEECCCCCCCCCCEEEEECCHHHHHHHHHCCHHHH
T ss_conf             99854466-864898535755776-----400124433115358984043134676322897450799999870025888


Q ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HH--HHHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHC
Q ss_conf             9998399988999999999999999999999999998763--65--3555369527999957999789999999999754
Q gi|254780191|r  745 LASFLKVSQGNVVGRVEEIWEEYRKLQLIHAKRKLQLNVE--DL--SCHKIADVNFMSHIISEVDSKELKSVMDALQKKI  820 (898)
Q Consensus       745 la~~L~~~~~~i~~ki~~L~~e~K~l~k~~~k~k~~~~~~--~~--~~~~i~~~~~i~~~~~~~d~~~Lr~l~d~l~~k~  820 (898)
                      +..+|+|..+++.++|++++++.|.|+|....+...++..  ..  ..-+.++  ++..+....+..    +.+.+++..
T Consensus       263 ~taLLkCgaed~vEavkk~qnstk~LqKnn~~~lr~LA~~iahsL~Ns~d~gG--~vi~~~~e~~sE----~~N~ianei  336 (415)
T KOG2105         263 LTALLKCGAEDHVEAVKKLQNSTKILQKNNLNLLRDLAVHIAHSLRNSPDWGG--VVILHRKEGDSE----FMNIIANEI  336 (415)
T ss_pred             HHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--EEEEEHHHCCHH----HHHHHHHCC
T ss_conf             99887546277999999888789998666489999999999999733867675--078651321089----999876324


Q ss_pred             CCCEEEEEEECCC--CEEEEEEEECHHHHCCCCHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             9978999995389--817999986778972679899999999883499999981011458999878899999999986
Q gi|254780191|r  821 QSGIIMLVGISKE--KKASVLIVVTEDLLDRFNAVDLARLSAKVLGGGGGGGRPHMAQSGGPNGNKADQAIAGVASFL  896 (898)
Q Consensus       821 ~~~vvvL~~~~~~--~k~~ivv~vs~~~~~~~~A~~lik~ia~~l~GGgGGGkpd~AQgGG~~~~~l~eal~~vk~~L  896 (898)
                      ++--++|+....+  +...++.+-+.....     .+.-.+++.+. ||||||.--.||..++.+.--+|.+...++|
T Consensus       337 ~s~EtlL~~~~~dek~GgLflLa~~~asve-----tLg~rvae~Le-G~Ga~K~Gr~QGKaTkmSrrmea~AlLqDYi  408 (415)
T KOG2105         337 GSEETLLFLTVGDEKGGGLFLLAGPPASVE-----TLGPRVAEVLE-GKGAGKKGRFQGKATKMSRRMEAQALLQDYI  408 (415)
T ss_pred             CCEEEEEEEEEECCCCCEEEEECCCCHHHH-----HHHHHHHHHHH-CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             771689999961257852799638924665-----54378999860-6788767601330345667789999998875


No 11 
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=99.14  E-value=4.9e-09  Score=89.62  Aligned_cols=149  Identities=25%  Similarity=0.405  Sum_probs=98.4

Q ss_pred             HHHCCCHHHHHHHHHHHCCCC-CCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC
Q ss_conf             752013688999997521254-4444553002430000024767899999999999998988730453046612322210
Q gi|254780191|r  583 LSINHSATHLLHHALSTILGS-HVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIA  661 (898)
Q Consensus       583 ~~~~HTatHlL~~alr~vLG~-hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~  661 (898)
                      -.-.||+.|||.+|+.+..+. .+. -|-- ..+-+=.||....++|++++.+||+.++++|.+|.|+...++++++|++
T Consensus        67 ~v~rHS~AHvla~Av~~l~p~~kl~-iGP~-ie~GFYYDf~~~~~it~~Dl~~IEk~M~~iik~~~~~~r~~vs~~eA~~  144 (639)
T PRK00413         67 EIIRHSAAHVLAQAVQRLFPDAKLG-IGPV-IENGFYYDFDVEEPFTPEDLPAIEKEMKKIIKENLPFTREVVSREEALE  144 (639)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEE-ECCC-CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHH
T ss_conf             9988889999999999977997787-7897-5770367212699899899999999999998479984999918999999


Q ss_pred             CHH-------HHHHHHCC-CCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCCC-------CCCCEEEEEE
Q ss_conf             003-------55443155-56248998447677855310156222588646011001101212-------6882899997
Q gi|254780191|r  662 SGA-------AALLGTKY-NDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESSI-------RAGIRRIEAI  726 (898)
Q Consensus       662 ~ga-------~alfgeky-gd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~si-------~sGvRRIeav  726 (898)
                      ...       +.+-.+.. ++.|-+-.-|     + =+.||-|.||.|||.|+.||+++.++-       ..-..||..+
T Consensus       145 ~F~~~~~~yK~eli~~~~~~~~is~Y~~g-----~-f~DLCrGPHv~~t~~ikafKL~~vsgaYWrGd~~n~~LqRIYG~  218 (639)
T PRK00413        145 LFADIGEPYKLELIEDIPEGEEITIYRQG-----E-FVDLCRGPHVPSTGKIKAFKLLKVAGAYWRGDSKNEMLQRIYGT  218 (639)
T ss_pred             HHHHCCCHHHHHHHHHCCCCCCEEEEEEC-----C-EEEECCCCCCCCCCCCCEEEEEECCHHHCCCCCCCCCEEEEEEE
T ss_conf             99861866899998636799857999915-----5-78966888776522044578753141110788667303899998


Q ss_pred             EC---HHHHHHHHHHH
Q ss_conf             16---89999999999
Q gi|254780191|r  727 TG---QRARSHLMGQD  739 (898)
Q Consensus       727 tG---~~A~~~~~~~~  739 (898)
                      +=   ....+|+...+
T Consensus       219 af~~k~~L~~~l~~~e  234 (639)
T PRK00413        219 AWADKEDLDAYLHRLE  234 (639)
T ss_pred             ECCCHHHHHHHHHHHH
T ss_conf             5199899999999999


No 12 
>PRK03772 threonyl-tRNA synthetase; Validated
Probab=99.13  E-value=5.8e-09  Score=89.05  Aligned_cols=161  Identities=19%  Similarity=0.305  Sum_probs=103.1

Q ss_pred             CCCCCEEEEEEHHHHHHHHHHCCCHHHHHHHHHHHCC-------CCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHH
Q ss_conf             5567338884212556777520136889999975212-------544444553002430000024767899999999999
Q gi|254780191|r  565 LRTEMSLVLTIDYQNRRQLSINHSATHLLHHALSTIL-------GSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIED  637 (898)
Q Consensus       565 l~~g~~V~~~VD~~rR~~~~~~HTatHlL~~alr~vL-------G~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~  637 (898)
                      +..+.++...-..+-.-...-.||+.|||-+|+.+..       |+-+ ..|.+-       ||.-..++|++++.+||+
T Consensus        51 i~~d~~le~it~~d~eg~~v~rHS~AHvla~Av~~l~p~~kl~iGP~i-e~GFYY-------Df~~~~~~t~~Dl~~IE~  122 (642)
T PRK03772         51 IENDAQLSIITAKDEEGLEIIRHSCAHLLGHAIKQLWPHTKMAIGPVI-DNGFYY-------DVDLDRTLTQEDLEALEK  122 (642)
T ss_pred             CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCC-CCEEEE-------EECCCCCCCHHHHHHHHH
T ss_conf             579977999358997899999888999999999997699678457865-771577-------224799999899999999


Q ss_pred             HHHHHHHHCCCCEEEEECCCCCCCCHH-------HHHHHHC--CCCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHH
Q ss_conf             998988730453046612322210003-------5544315--5562489984476778553101562225886460110
Q gi|254780191|r  638 NVNDIIAQNLPVVTRIMNREDAIASGA-------AALLGTK--YNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLL  708 (898)
Q Consensus       638 ~vN~~I~~n~~V~~~~~~~~eA~~~ga-------~alfgek--ygd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~f  708 (898)
                      .++++|.+|.|+...++++++|++...       +.+-.++  -++.|-+..-     |+| +.||-|.||.||+.|+.|
T Consensus       123 ~M~~iik~~~~~~r~~~s~~eA~~~f~~~~~~yK~eli~e~~~~~~~is~Y~~-----g~f-~DLCrGPHvp~t~~ikaf  196 (642)
T PRK03772        123 RMHELAKTNYDVIKKKVSWQEARDTFAARGESYKVAILDENISHDDKPGLYHH-----EEY-VDMCRGPHVPNMRFCHHF  196 (642)
T ss_pred             HHHHHHHCCCCEEEEEECHHHHHHHHHHCCCHHHHHHHHHCCCCCCCEEEEEC-----CCE-EEECCCCCCCCCCCCCEE
T ss_conf             99999846998499996889999999852863554555422778882679935-----987-895588877875555325


Q ss_pred             HEECCCCC-------CCCCEEEEEEECH---HHHHHHHHHH
Q ss_conf             01101212-------6882899997168---9999999999
Q gi|254780191|r  709 YIVSESSI-------RAGIRRIEAITGQ---RARSHLMGQD  739 (898)
Q Consensus       709 kIise~si-------~sGvRRIeavtG~---~A~~~~~~~~  739 (898)
                      |+++.++-       ..-..||..++=+   ...+|+...+
T Consensus       197 kl~~vagAYWrGd~~n~~LqRIYG~af~~k~~L~~~l~~~e  237 (642)
T PRK03772        197 KLMKTAGAYWRGDSNNKMLQRIYGTAWADKKALNAYLQRLE  237 (642)
T ss_pred             EEEECCHHEECCCCCCCHHEEEEEEECCCHHHHHHHHHHHH
T ss_conf             77312321147776570007999986189899999999999


No 13 
>PRK12304 thrS threonyl-tRNA synthetase; Reviewed
Probab=99.11  E-value=1.1e-09  Score=94.61  Aligned_cols=162  Identities=19%  Similarity=0.243  Sum_probs=109.7

Q ss_pred             CCCCCCEEEEEE-HHHHHHHHHHCCCHHHHHHHHHHHCC-------CCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHH
Q ss_conf             755673388842-12556777520136889999975212-------5444445530024300000247678999999999
Q gi|254780191|r  564 ILRTEMSLVLTI-DYQNRRQLSINHSATHLLHHALSTIL-------GSHVSQNGSCITPDGLRFDVTHSKPITSAELKSI  635 (898)
Q Consensus       564 ~l~~g~~V~~~V-D~~rR~~~~~~HTatHlL~~alr~vL-------G~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~I  635 (898)
                      ++..+..+...+ |-.-.-...-.||+.|||.+|..+..       |+-+. .|.+-       ||....++|++++.+|
T Consensus        20 ~~~~d~~~~~i~~~~s~eg~~v~rHS~AHvla~Av~~l~p~~k~~iGP~ie-~GFYY-------Df~~~~~~t~~Dl~~I   91 (604)
T PRK12304         20 AKVLGNGGEPIYFDNSPEALEVIRHSCAHLMAQAIKSLYPDAKFFVGPVVE-EGFYY-------DFRVESKIGEEDLPKI   91 (604)
T ss_pred             CCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCC-CEEEE-------EECCCCCCCHHHHHHH
T ss_conf             667896489982699978999999879999999999977997698789758-81158-------5156998998999999


Q ss_pred             HHHHHHHHHHCCCCEEEEECCCCCCCCHH-----HHHHHHCCCCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHE
Q ss_conf             99998988730453046612322210003-----5544315556248998447677855310156222588646011001
Q gi|254780191|r  636 EDNVNDIIAQNLPVVTRIMNREDAIASGA-----AALLGTKYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYI  710 (898)
Q Consensus       636 E~~vN~~I~~n~~V~~~~~~~~eA~~~ga-----~alfgekygd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkI  710 (898)
                      |+.+.++|.+|.|++...+++++|++...     ..+..+..++.|-+-..|     +| +.||-|.||.||+.|+.||+
T Consensus        92 E~~M~~iik~~~~f~r~~~~~~eA~~~f~~~~yK~eli~~~~~~~is~Y~~g-----~f-~DLCrGPHv~~T~~ikafKL  165 (604)
T PRK12304         92 EKKMKELAKAKLEITKYEITKEEALEKFKNDDLKQAVLSRIPDDAVSIYKQG-----EF-EDLCRGPHLPNTKFLRFFKL  165 (604)
T ss_pred             HHHHHHHHHCCCCEEEEEECHHHHHHHHCCCCCCHHHHHCCCCCCEEEEEEC-----CE-EEECCCCCCCCCCCCCEEEE
T ss_conf             9999999968998599997799999986058404588843678856999848-----96-68658876677222626798


Q ss_pred             ECCCCC-------CCCCEEEEEEECH---HHHHHHHHHH
Q ss_conf             101212-------6882899997168---9999999999
Q gi|254780191|r  711 VSESSI-------RAGIRRIEAITGQ---RARSHLMGQD  739 (898)
Q Consensus       711 ise~si-------~sGvRRIeavtG~---~A~~~~~~~~  739 (898)
                      ++.++-       ..-+.||..++=.   ...+|+...+
T Consensus       166 ~~vsgaYWrGd~~n~~LqRIYG~af~~k~~L~~~l~~~e  204 (604)
T PRK12304        166 TRVAGAYLGGDEKNEMLTRIYGIAFADKESLKDYLFIIE  204 (604)
T ss_pred             EECCCEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHH
T ss_conf             533751775788671038999984199999999999999


No 14 
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=99.09  E-value=2.5e-09  Score=91.86  Aligned_cols=168  Identities=22%  Similarity=0.344  Sum_probs=106.5

Q ss_pred             CCCCCEEEEE-EHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             5567338884-212556777520136889999975212544444553002430000024767899999999999998988
Q gi|254780191|r  565 LRTEMSLVLT-IDYQNRRQLSINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDII  643 (898)
Q Consensus       565 l~~g~~V~~~-VD~~rR~~~~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I  643 (898)
                      +..+.++... .|...=..++ .||+.|||.+|+.+..+.-----|--+ .+-+=.||....++|++++.+||+.++++|
T Consensus        55 i~~d~~le~it~~~~eg~~v~-rHS~AHvla~Av~~l~p~~kl~iGP~i-e~GFYYDf~~~~~~t~~Dl~~IE~~M~~ii  132 (639)
T PRK12444         55 IEENAEVEIITIDSNEGVEIA-RHSAAHILAQAVKRLYGDVNLGVGPVI-ENGFYYDMDLPSSVNVEDLRKIEKEMKKII  132 (639)
T ss_pred             CCCCCEEEEECCCCHHHHHHH-HHHHHHHHHHHHHHHCCCCEEEECCCC-CCEEEEEECCCCCCCHHHHHHHHHHHHHHH
T ss_conf             689978999558997789999-888999999999997799638878988-883247534699999899999999999987


Q ss_pred             HHCCCCEEEEECCCCCCCCHH-------HHHHHH-CCCCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCC
Q ss_conf             730453046612322210003-------554431-555624899844767785531015622258864601100110121
Q gi|254780191|r  644 AQNLPVVTRIMNREDAIASGA-------AALLGT-KYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESS  715 (898)
Q Consensus       644 ~~n~~V~~~~~~~~eA~~~ga-------~alfge-kygd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~s  715 (898)
                      .+|.|++..+++++||++...       +.+-.+ +-++.|-+-.-|     +| +.||-|.||.|||.|+.||+++.++
T Consensus       133 k~~~~f~r~~~s~~eA~~~f~~~~~~yK~eli~~~~~~~~is~Y~~g-----~f-~DLCrGPHv~~t~~ikafkL~~vsg  206 (639)
T PRK12444        133 NENIKIERVEVSREEAAKLFQEMNDRLKLELLEAIPSGESVTLYKQG-----EF-VDLCRGPHLPSTGYLKAFQLTHVSG  206 (639)
T ss_pred             HCCCCEEEEEECHHHHHHHHHHCCCHHHHHHHHCCCCCCCEEEEEEC-----CE-EEECCCCCCCCCCCCEEEEEEEEEC
T ss_conf             37897499985899999999863847777887517899843289948-----98-8966887778745440789734002


Q ss_pred             C-------CCCCEEEEEEEC---HHHHHHHHHHHH
Q ss_conf             2-------688289999716---899999999999
Q gi|254780191|r  716 I-------RAGIRRIEAITG---QRARSHLMGQDE  740 (898)
Q Consensus       716 i-------~sGvRRIeavtG---~~A~~~~~~~~~  740 (898)
                      -       ..-..||..++=   ....+|+...++
T Consensus       207 AYWrGd~~n~~LqRIYG~af~~k~~L~~yl~~leE  241 (639)
T PRK12444        207 AYWRGDSNNQVLQRIYGVAFSSQKELEEYLHFVEE  241 (639)
T ss_pred             CEECCCCCCCCEEEEEEEEECCHHHHHHHHHHHHH
T ss_conf             14278876822168999985885779999999999


No 15 
>PRK04483 threonyl-tRNA synthetase; Validated
Probab=99.08  E-value=1.4e-08  Score=86.14  Aligned_cols=152  Identities=23%  Similarity=0.422  Sum_probs=98.9

Q ss_pred             HHHHHCCCHHHHHHHHHHHCCCCCCCC-CCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             777520136889999975212544444-5530024300000247678999999999999989887304530466123222
Q gi|254780191|r  581 RQLSINHSATHLLHHALSTILGSHVSQ-NGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDA  659 (898)
Q Consensus       581 ~~~~~~HTatHlL~~alr~vLG~hv~Q-~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA  659 (898)
                      -.-.-.||+.|||-+|+.+.... +.= -|--+ .+-+=.||-...++|+++|.+||+.++++|.+|.|+...+++++||
T Consensus        67 gl~v~rHS~AHvla~Av~~l~p~-~kl~iGP~i-e~GFYYDf~~~~~~t~~Dl~~IE~~M~~iik~~~~~~r~~~s~~eA  144 (634)
T PRK04483         67 GVEIIRHSCAHLVGHAVKQLYPE-VKMVIGPVI-AEGFYYDIYSERPFTPEDMAAIEQRMQELIAQDYDVIKKVTPRAEV  144 (634)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCC-CEEEECCCC-CCEEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECHHHH
T ss_conf             99999999999999999997799-758878977-8844573268998998899999999999860778759998079999


Q ss_pred             CCCHHHHHHHHCCC--------CCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCCC-------CCCCEEEE
Q ss_conf             10003554431555--------6248998447677855310156222588646011001101212-------68828999
Q gi|254780191|r  660 IASGAAALLGTKYN--------DRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESSI-------RAGIRRIE  724 (898)
Q Consensus       660 ~~~ga~alfgekyg--------d~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~si-------~sGvRRIe  724 (898)
                      ++...-  .|++|.        +..-.+++=.  .|+ =+.||-|.||.|||.|+.||+++.++-       ..-..||.
T Consensus       145 ~~~f~~--~~~~yK~eli~~~~~~~~~is~Y~--~g~-f~DLCrGPHv~~T~~ikafkL~~vsgaYWrGd~~n~~LqRIY  219 (634)
T PRK04483        145 IEVFAQ--RGEEYKLRLIEDMSDDITAMGLYY--HQE-YVDMCRGPHVPNTRFLKAFKLTRISGAYWRGDAKNEQLQRIY  219 (634)
T ss_pred             HHHHHH--CCCHHHHHHHHHCCCCCCEEEEEE--CCC-EEEECCCCCCCCCCCCCHHEEEEHHHHEECCCCCCCCEEEEE
T ss_conf             999987--697787879864488873588997--388-758379998897111311123011021126887571028999


Q ss_pred             EEEC---HHHHHHHHHHH
Q ss_conf             9716---89999999999
Q gi|254780191|r  725 AITG---QRARSHLMGQD  739 (898)
Q Consensus       725 avtG---~~A~~~~~~~~  739 (898)
                      .++=   ....+|+...+
T Consensus       220 G~af~~k~~L~~yl~~~e  237 (634)
T PRK04483        220 GTAWADKKQLDAYILRME  237 (634)
T ss_pred             EEEECCHHHHHHHHHHHH
T ss_conf             995089899999999999


No 16 
>pfam07973 tRNA_SAD Threonyl and Alanyl tRNA synthetase second additional domain. The catalytically active from of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this domain (the second additional domain). The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain.
Probab=99.05  E-value=7.2e-11  Score=103.94  Aligned_cols=44  Identities=45%  Similarity=0.678  Sum_probs=41.6

Q ss_pred             EEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCCCCCCCEEEE
Q ss_conf             4899844767785531015622258864601100110121268828999
Q gi|254780191|r  676 VRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESSIRAGIRRIE  724 (898)
Q Consensus       676 VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~si~sGvRRIe  724 (898)
                      ||||+|+     +||.||||||||.||++||.|+|++.+++++|++||+
T Consensus         1 vrvv~ig-----~~~~~~C~GtHV~nT~~I~~fki~k~~~~~~g~~RI~   44 (44)
T pfam07973         1 VRVVRIG-----DFDVDLCGGTHVPNTGEIGAFKILKGDSKNKGLQRIY   44 (44)
T ss_pred             CEEEEEC-----CEEEECCCCCCCCCCCCCCEEEEEECCCCCCCCEECC
T ss_conf             9799989-----9198787795878825201299997144828759629


No 17 
>smart00863 tRNA_SAD Threonyl and Alanyl tRNA synthetase second additional domain. The catalytically active form of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this SAD domain (the second additional domain). The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain.
Probab=98.87  E-value=7.1e-10  Score=96.16  Aligned_cols=44  Identities=50%  Similarity=0.675  Sum_probs=41.4

Q ss_pred             EEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCCCCCCCEEEE
Q ss_conf             4899844767785531015622258864601100110121268828999
Q gi|254780191|r  676 VRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESSIRAGIRRIE  724 (898)
Q Consensus       676 VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~si~sGvRRIe  724 (898)
                      ||||.|+     ++|.++||||||.||++||.|||++.+++..|++||+
T Consensus         1 vrvv~i~-----~~~~~~C~GtHv~~T~~ig~~ki~~~~~~~~~~~RI~   44 (44)
T smart00863        1 VRVVSIG-----DFDVELCGGTHVPNTGEIGAFKILSVSGAYWGLQRIY   44 (44)
T ss_pred             CEEEEEC-----CEEEECCCCCCCCCCCEEEEEEEEEECHHCCCCEECC
T ss_conf             9799999-----9798787896636706243699999562132859249


No 18 
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=98.87  E-value=1.7e-08  Score=85.28  Aligned_cols=156  Identities=22%  Similarity=0.274  Sum_probs=96.4

Q ss_pred             HHHCCCHHHHHHHHHHHCCC-CCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC
Q ss_conf             75201368899999752125-44444553002430000024767899999999999998988730453046612322210
Q gi|254780191|r  583 LSINHSATHLLHHALSTILG-SHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIA  661 (898)
Q Consensus       583 ~~~~HTatHlL~~alr~vLG-~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~  661 (898)
                      .+-.||+.|||.+|+.+... .++.. |- +..+-+=.||....++|++++.+||+.+.++|.++.|+......++.++.
T Consensus         5 ~~lRHS~AHila~Av~~l~p~~kl~i-GP-~ie~GFYYDf~~~~~~t~~Dl~~IE~~m~~iik~~~~~~r~~~~~~~f~~   82 (576)
T PRK12305          5 KKLNHSTSHLLAAAILKLYPNVKLGI-GP-AIDEGFYYDFDFEDPLSESDLLKIEKLMKKLASQNLKMVKVDGANYDFKN   82 (576)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEE-CC-CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEHHHHHHHCC
T ss_conf             20033599999999999779976997-89-86886668624699999899999999999998589987983350786758


Q ss_pred             C-HHHHHHHHCC--CCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCCC-------CCCCEEEEEEEC---
Q ss_conf             0-0355443155--56248998447677855310156222588646011001101212-------688289999716---
Q gi|254780191|r  662 S-GAAALLGTKY--NDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESSI-------RAGIRRIEAITG---  728 (898)
Q Consensus       662 ~-ga~alfgeky--gd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~si-------~sGvRRIeavtG---  728 (898)
                      . +-+.+-.+..  ++.+-+...+....+.-=+.||-|.||.|||.|+.||+++.++-       ..-..||..++=   
T Consensus        83 ~~yK~eli~~~~~~~~~i~~y~~~~~~~~~~f~DLCrGpHv~~t~~ikafkL~~vsgaYWrGd~~n~~LqRIYG~af~~k  162 (576)
T PRK12305         83 QPYKKELYEELKKKGEEITFYSIVDPKNKELFFDLCAGNHVESTKEIKNFKLLSIAGAYWRGDSKNKQLTRIYGTSWESK  162 (576)
T ss_pred             CCHHHHHHHHCCCCCCEEEEEECCCCCCCCCEEECCCCCCCCCCCCCCEEEEEECCCCEECCCCCCCEEEEEEEEEECCH
T ss_conf             90799998527346964889963676667726587899888972324246886436630357875810089999971798


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             899999999999
Q gi|254780191|r  729 QRARSHLMGQDE  740 (898)
Q Consensus       729 ~~A~~~~~~~~~  740 (898)
                      ....+|+...++
T Consensus       163 ~~L~~yl~~~eE  174 (576)
T PRK12305        163 EELDKYLAILQE  174 (576)
T ss_pred             HHHHHHHHHHHH
T ss_conf             899999999999


No 19 
>COG0441 ThrS Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=98.47  E-value=9e-07  Score=71.87  Aligned_cols=134  Identities=28%  Similarity=0.436  Sum_probs=92.0

Q ss_pred             HHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCH
Q ss_conf             52013688999997521254444455300243000002476789999999999999898873045304661232221000
Q gi|254780191|r  584 SINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIASG  663 (898)
Q Consensus       584 ~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~~g  663 (898)
                      .-.||+.|||..|+.+...+  -.-| -+-.+-.-.||....++|++++.+||...+++|.+|++++-...++++|++..
T Consensus        28 ~~rhs~ah~l~~av~~l~p~--~~~g-p~ie~gfyyd~~~~~~~~~~dl~~ie~~m~~i~~~~~~~~~~~~~~e~a~~~f  104 (589)
T COG0441          28 IIRHSCAHVLAQAVKRLYPD--VTIG-PVIEEGFYYDFDVKEPITPEDLLKIEKEMKEIAKENLPIEREVVSREEARAPF  104 (589)
T ss_pred             HEEHHHHHHHHHHHHHHCCC--CCCC-CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECHHHHHHHH
T ss_conf             30066889999999975888--6546-76134058840258888988999999999999983577289980499998776


Q ss_pred             H---HHHHHHCCCCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCCC-----CC--CCEEEEEEEC
Q ss_conf             3---5544315556248998447677855310156222588646011001101212-----68--8289999716
Q gi|254780191|r  664 A---AALLGTKYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESSI-----RA--GIRRIEAITG  728 (898)
Q Consensus       664 a---~alfgekygd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~si-----~s--GvRRIeavtG  728 (898)
                      +   ..+-.++ ++.+-+.+-+     . =.+||-|.||.+|+.| .||+++.++-     +.  -..||...+=
T Consensus       105 ~~yK~~~i~~~-~~~~s~y~~~-----~-~~dlc~gph~~~t~~i-~fkl~~~~~ayw~gd~~~~~l~riygta~  171 (589)
T COG0441         105 GPYKAELIDCK-GHPLSEYSQG-----E-FVDLCRGPHVPSTGKI-AFKLLKLAGAYWRGDENNEMLQRIYGTAF  171 (589)
T ss_pred             HHHHHHHHHCC-CCCCCEEECC-----C-CCCCCCCCCCCCCCEE-EEEEEEECCHHHCCCCCCCCEEEEECCCC
T ss_conf             66579998627-9875067357-----6-0003678888765337-88988812453336877721067733355


No 20 
>pfam02272 DHHA1 DHHA1 domain. This domain is often found adjacent to the DHH domain pfam01368 and is called DHHA1 for DHH associated domain. This domain is diagnostic of DHH subfamily 1 members. This domains is also found in alanyl tRNA synthetase, suggesting that this domain may have an RNA binding function. The domain is about 60 residues long and contains a conserved GG motif.
Probab=98.43  E-value=1.2e-06  Score=70.91  Aligned_cols=67  Identities=28%  Similarity=0.486  Sum_probs=56.1

Q ss_pred             CEEEEEEECCCCEEEEEEEECHHHHCCCCHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCHHHHHHHHHHHH
Q ss_conf             78999995389817999986778972679899999999883499999981011458999878899999999
Q gi|254780191|r  823 GIIMLVGISKEKKASVLIVVTEDLLDRFNAVDLARLSAKVLGGGGGGGRPHMAQSGGPNGNKADQAIAGVA  893 (898)
Q Consensus       823 ~vvvL~~~~~~~k~~ivv~vs~~~~~~~~A~~lik~ia~~l~GGgGGGkpd~AQgGG~~~~~l~eal~~vk  893 (898)
                      .++++++ ..++++.+.+.+++++...  +++|++.+++.+ ||+|||+|++||+++++..+++++++.+.
T Consensus         2 ~~vi~~~-~~~~k~~~s~rs~~~~~~~--~~~i~~~~~~~~-gG~GGGh~~aAg~~~~~~~~~~~~~~~~~   68 (69)
T pfam02272         2 KPVVLFA-EEDGKVKVSARSSKGLDVK--GGELLKEVAEIL-GGGGGGHPDAAGAGGKDPSKLEEALELLE   68 (69)
T ss_pred             CEEEEEE-ECCCEEEEEEEECHHHHHH--HHHHHHHHHHHH-CCCCCCCHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             5599998-1499599999965788878--999999999993-89889975676158998788999999834


No 21 
>cd00733 GlyRS_alpha_core Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. This alignment contains only sequences from the GlyRS form which heterotetramerizes. The homodimer form of GlyRS is in a different family of class II aaRS. Class II assignment is based upon structure and the presence of three characteristic sequence motifs.
Probab=98.25  E-value=0.0002  Score=53.42  Aligned_cols=169  Identities=24%  Similarity=0.372  Sum_probs=101.0

Q ss_pred             CHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCEECCCCCCCH---H
Q ss_conf             87899999999999789889116675667787100230143475540-0588799999851115432248987863---4
Q gi|254780191|r    3 NVSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNI-FTGQEKPVYQAVTTVQKCVRAGGKHNDL---D   78 (898)
Q Consensus         3 s~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~-f~G~~~p~~~r~~~~QkCiR~ggkhnDl---d   78 (898)
                      |..+|-.+--+|+.++|+.+..++.+=         +.||  .|-|- |+..--|.--+++=+|||.|-    .|=   +
T Consensus         1 tfq~ii~~L~~fW~~~GC~i~qpyd~e---------~GAg--T~hp~T~lr~lg~~pw~~aYvqPsrRP----~DgRYG~   65 (279)
T cd00733           1 TFQDLILKLQKFWASQGCLIIQPYDME---------VGAG--TFHPATFLRALGPEPWNVAYVEPSRRP----TDGRYGE   65 (279)
T ss_pred             CHHHHHHHHHHHHHHCCCEEECCCCCC---------CCCC--CCCHHHHHHHCCCCCCEEEEECCCCCC----CCCCCCC
T ss_conf             978999999999987796887676542---------4646--588899886319986315542467799----9987778


Q ss_pred             HCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHH---HHHCCC-CHHHEEEC
Q ss_conf             34648850017888542231475378899989986133418981237999718828999975---663499-98997535
Q gi|254780191|r   79 NVGRTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKLW---KKISGL-SADKIIRI  154 (898)
Q Consensus        79 ~VG~t~rH~TfFEMlGn~SfgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~iW---~~~~gi-~~~~i~~~  154 (898)
                      |--+ -.||.=|..+=-=|.                                   +..-++.   ++.+|| |.+|=++|
T Consensus        66 NPNR-lq~y~QfQVilKPsp-----------------------------------~n~q~lYL~SL~~igid~~~hDIrF  109 (279)
T cd00733          66 NPNR-LQHYYQFQVIIKPSP-----------------------------------DNIQELYLESLEALGINPKEHDIRF  109 (279)
T ss_pred             CCCH-HCEEEEEEEEECCCC-----------------------------------HHHHHHHHHHHHHCCCCCCCCCEEE
T ss_conf             9323-100034579987895-----------------------------------6589999998998497954362478


Q ss_pred             CCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             78666545799999877046788538556898887778898268960011234430478875657665310175799999
Q gi|254780191|r  155 TTNDNFWSMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLERMA  234 (898)
Q Consensus       155 ~~~dNfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNlVFmq~~~~~~g~~~~Lp~~~IDTGmGLERl~  234 (898)
                      - +|| |+..--|.-|--=||-.|                  ++||--.-.+|   +-.|  .++..-.+.--+||||||
T Consensus       110 v-eDn-WEsPtLGAwGlGWEVwld------------------GMEItQFTYFQ---QvGG--i~c~pv~~EiTYGLERia  164 (279)
T cd00733         110 V-EDN-WESPTLGAWGLGWEVWLD------------------GMEVTQFTYFQ---QVGG--IPCKPISVEITYGLERIA  164 (279)
T ss_pred             E-ECC-CCCCCCCCCCCCEEEEEC------------------CEEEEEEEEEE---EECC--EECCCCCEEEEHHHHHHH
T ss_conf             6-147-878753102343499987------------------75776435121---1378--214453233101199999


Q ss_pred             HHHCCCCCCCHHH
Q ss_conf             9988798530057
Q gi|254780191|r  235 TVLQEKTNNYDID  247 (898)
Q Consensus       235 ~vlqg~~s~ydtD  247 (898)
                      +.+|++.|+||..
T Consensus       165 MylQ~vd~v~dl~  177 (279)
T cd00733         165 MYLQGVDNVYDIE  177 (279)
T ss_pred             HHHHCCCHHEEEE
T ss_conf             9985754231412


No 22 
>PRK09348 glyQ glycyl-tRNA synthetase subunit alpha; Validated
Probab=98.25  E-value=0.00022  Score=53.12  Aligned_cols=167  Identities=23%  Similarity=0.354  Sum_probs=104.5

Q ss_pred             CCCHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCEECCCCCCCHHH
Q ss_conf             9787899999999999789889116675667787100230143475540-058879999985111543224898786343
Q gi|254780191|r    1 MSNVSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNI-FTGQEKPVYQAVTTVQKCVRAGGKHNDLDN   79 (898)
Q Consensus         1 m~s~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~-f~G~~~p~~~r~~~~QkCiR~ggkhnDld~   79 (898)
                      |||..+|-.+--+|+.++|+.++.++.+=         +.|  -.|-|. |+..--|.--+++-+|||.|-    .|   
T Consensus         1 ~~~fq~~I~~Lq~~W~~~GC~i~qpyd~e---------vGA--gT~~p~Tflr~lgp~pw~~aYvqPsrRP----~D---   62 (291)
T PRK09348          1 KMTFQDIILTLQDYWADQGCAILQPYDME---------VGA--GTFHPATFLRALGPEPWNAAYVQPSRRP----TD---   62 (291)
T ss_pred             CCCHHHHHHHHHHHHHHCCCEEECCCCCC---------CCC--CCCCHHHHHHCCCCCCCCEEEECCCCCC----CC---
T ss_conf             97589999999999976797886575443---------454--6588398885028876405421345788----87---


Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEEC-------CCHHHHHHHH---HHHCCC-CH
Q ss_conf             464885001788854223147537889998998613341898123799971-------8828999975---663499-98
Q gi|254780191|r   80 VGRTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRLYITVY-------DEDEEAFKLW---KKISGL-SA  148 (898)
Q Consensus        80 VG~t~rH~TfFEMlGn~SfgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~-------~~D~e~~~iW---~~~~gi-~~  148 (898)
                          +|                                ||-.|.||+- ||       +.-+..-++.   ++.+|| |.
T Consensus        63 ----gR--------------------------------YGeNPNRlq~-y~QfQVilKPsP~n~q~lyL~SL~~lgid~~  105 (291)
T PRK09348         63 ----GR--------------------------------YGENPNRLQH-YYQFQVILKPSPDNIQELYLGSLEALGIDPL  105 (291)
T ss_pred             ----CC--------------------------------CCCCCHHHHH-EEEEEEEECCCCCCHHHHHHHHHHHHCCCCC
T ss_conf             ----75--------------------------------4689124201-0556899778971399999999998088975


Q ss_pred             HHEEECCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             99753578666545799999877046788538556898887778898268960011234430478875657665310175
Q gi|254780191|r  149 DKIIRITTNDNFWSMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGM  228 (898)
Q Consensus       149 ~~i~~~~~~dNfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNlVFmq~~~~~~g~~~~Lp~~~IDTGm  228 (898)
                      +|=+||- +|| |+--.-|.-|--=||..|                  ++||--.-+.|   +-.|  .++.--.+.--+
T Consensus       106 ~hDirFv-ED~-WEsPtlGAwGlGWEVWld------------------GMEitQFTYFQ---QvGG--i~c~pvs~EiTY  160 (291)
T PRK09348        106 EHDIRFV-EDN-WESPTLGAWGLGWEVWLD------------------GMEVTQFTYFQ---QVGG--IECKPVTGEITY  160 (291)
T ss_pred             CCCEEEE-ECC-CCCCCCCCCCCCEEEEEC------------------CEEEEEEEHHH---HCCC--CCCCCCCEEEEH
T ss_conf             3543786-337-778762342343499987------------------66765223201---1078--015664344213


Q ss_pred             CHHHHHHHHCCCCCCCHHH
Q ss_conf             7999999988798530057
Q gi|254780191|r  229 GLERMATVLQEKTNNYDID  247 (898)
Q Consensus       229 GLERl~~vlqg~~s~ydtD  247 (898)
                      ||||||+.+||+.|+||++
T Consensus       161 GLERiAMylQ~vdnVyDl~  179 (291)
T PRK09348        161 GLERLAMYLQGVDNVYDLV  179 (291)
T ss_pred             HHHHHHHHHHCCCEEEEEE
T ss_conf             1999999982888048855


No 23 
>COG0752 GlyQ Glycyl-tRNA synthetase, alpha subunit [Translation, ribosomal structure and biogenesis]
Probab=98.14  E-value=0.00042  Score=50.97  Aligned_cols=175  Identities=22%  Similarity=0.335  Sum_probs=102.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCC-CCCC-CCCCCCCCCCCCCCEECCCCCCCHH
Q ss_conf             9787899999999999789889116675667787100230143475540-0588-7999998511154322489878634
Q gi|254780191|r    1 MSNVSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNI-FTGQ-EKPVYQAVTTVQKCVRAGGKHNDLD   78 (898)
Q Consensus         1 m~s~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~-f~G~-~~p~~~r~~~~QkCiR~ggkhnDld   78 (898)
                      |||...|--+-.+|+.++|+.++.++-+=         +.||  .|-|. ||.. -+-|++ ++-+|||=|-    .|  
T Consensus         4 ~~~fQ~~IltLq~yW~~qGC~i~QpyD~e---------vGAG--T~hPaTfLralGpePw~-aAYVqPSRRP----~D--   65 (298)
T COG0752           4 KLTFQGLILTLQNYWAEQGCTILQPYDME---------VGAG--TFHPATFLRALGPEPWN-AAYVQPSRRP----TD--   65 (298)
T ss_pred             CCCHHHHHHHHHHHHHHCCCEEECCCCCC---------CCCC--CCCHHHHHHHCCCCCCC-EEEECCCCCC----CC--
T ss_conf             43399999999999987697861455344---------5667--67768899760997641-0010567799----88--


Q ss_pred             HCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHCCC-CHHHEEECCCC
Q ss_conf             34648850017888542231475378899989986133418981237999718828999975663499-98997535786
Q gi|254780191|r   79 NVGRTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKLWKKISGL-SADKIIRITTN  157 (898)
Q Consensus        79 ~VG~t~rH~TfFEMlGn~SfgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~iW~~~~gi-~~~~i~~~~~~  157 (898)
                        |+-+-|--   -|.     -|+-=          --.++-.|+.+        +|-|--=++.+|| |.+|=+||-+ 
T Consensus        66 --GRYGenPN---Rlq-----~yyQf----------QVilKPsP~Ni--------QeLYL~SL~~lGid~~~HDIRFVE-  116 (298)
T COG0752          66 --GRYGENPN---RLQ-----HYYQF----------QVIIKPSPDNI--------QELYLGSLEALGIDPLEHDIRFVE-  116 (298)
T ss_pred             --CCCCCCCH---HHH-----HHEEE----------EEEECCCCCCH--------HHHHHHHHHHCCCCHHHCCEEEEC-
T ss_conf             --87788926---652-----33157----------89955897118--------999998899809990123613411-


Q ss_pred             CCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             66545799999877046788538556898887778898268960011234430478875657665310175799999998
Q gi|254780191|r  158 DNFWSMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLERMATVL  237 (898)
Q Consensus       158 dNfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNlVFmq~~~~~~g~~~~Lp~~~IDTGmGLERl~~vl  237 (898)
                      || |+--..|..|--=|+..|                  ++||--.-++|   +-.| + ++.--.+.--+||||||+.+
T Consensus       117 Dn-WE~PTlGawGlGWEVWld------------------GMEvTQFTYFQ---QvGG-i-ec~pV~~EITYGlERlAmYi  172 (298)
T COG0752         117 DN-WENPTLGAWGLGWEVWLD------------------GMEVTQFTYFQ---QVGG-L-ECKPVSGEITYGLERLAMYI  172 (298)
T ss_pred             CC-CCCCCCCCCCCCEEEEEC------------------CEEEEEEEHHH---HHCC-E-ECCCEEEEEEHHHHHHHHHH
T ss_conf             68-878863202344067776------------------62653000646---5078-2-04531145422299999999


Q ss_pred             CCCCCCCHH
Q ss_conf             879853005
Q gi|254780191|r  238 QEKTNNYDI  246 (898)
Q Consensus       238 qg~~s~ydt  246 (898)
                      |++.++||.
T Consensus       173 Q~vdnVydl  181 (298)
T COG0752         173 QGVDNVYDL  181 (298)
T ss_pred             HCCCCEEEE
T ss_conf             576611576


No 24 
>TIGR00418 thrS threonyl-tRNA synthetase; InterPro: IPR002320   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Threonyl-tRNA synthetase (6.1.1.3 from EC) exists as a monomer and belongs to class IIa. The enzyme from Escherichia coli represses the translation of its own mRNA. The crystal structure of the complex between tRNA(Thr) and ThrRS show structural features that reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination . The zinc ion may act to ensure that only amino acids that possess a hydroxyl group attached to the beta-position are activated .; GO: 0004829 threonine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006435 threonyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=98.13  E-value=7.4e-06  Score=64.68  Aligned_cols=148  Identities=25%  Similarity=0.365  Sum_probs=95.1

Q ss_pred             CCCHHHHHHHHHHHCC-------CCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             0136889999975212-------544444553002430000024767899999999999998988730453046612322
Q gi|254780191|r  586 NHSATHLLHHALSTIL-------GSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNRED  658 (898)
Q Consensus       586 ~HTatHlL~~alr~vL-------G~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~e  658 (898)
                      -||+.|+|..|+.+..       |+-| -.|.+-       ||...+.+|.++|.+||+.+|+++..+.||.-..+++++
T Consensus         1 rh~~Ah~l~~a~k~~~~~~~~~~gp~~-e~GFyy-------D~~~~~~~~~~dl~~ie~~m~~~~~~~~~~~~~~~s~~~   72 (595)
T TIGR00418         1 RHSIAHLLAEAVKQLYPDVKLAVGPVI-EDGFYY-------DFEVDKSITEEDLEKIEKEMKEIIKKNYPIARLSVSLEE   72 (595)
T ss_pred             CCCHHHHHHHHHHHCCCCCEEEEECCC-CCCCCC-------CCCCCHHCCHHHHHHHHHHHHHHHHHHCCEEEEEECHHH
T ss_conf             950124638999704787189982554-787545-------520000027789999999999998640570257724789


Q ss_pred             CCCCHH-------HHHHHHCCCCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHH----HHHEECCCC-------CCCCC
Q ss_conf             210003-------554431555624899844767785531015622258864601----100110121-------26882
Q gi|254780191|r  659 AIASGA-------AALLGTKYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIM----LLYIVSESS-------IRAGI  720 (898)
Q Consensus       659 A~~~ga-------~alfgekygd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG----~fkIise~s-------i~sGv  720 (898)
                      |++.-.       .+|-.+.-+..+-+.-.+   .+.+=+.+|=|+||.+||.|.    .||.++.++       -..-+
T Consensus        73 A~~~f~~~~~~~k~~l~~~~~~~~~~~~~y~---~~~~f~dlC~GpHlp~~~~~~~~~~~fkL~~~~gaYw~Gd~~n~~L  149 (595)
T TIGR00418        73 ALEAFKEVGEPLKLELLDEIIPNGEAVTVYG---QGEAFVDLCRGPHLPNTSRIKPAQKAFKLEKVAGAYWRGDSKNEML  149 (595)
T ss_pred             HHHHHHHHCCHHHHHHHHHCCCCCCCEEEEC---CCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEE
T ss_conf             9999986213122677851045666420422---5213456157976832356676403456654323310268898537


Q ss_pred             EEEEE---EECHHHHHHHHHHHHHHHH
Q ss_conf             89999---7168999999999999999
Q gi|254780191|r  721 RRIEA---ITGQRARSHLMGQDEKLKS  744 (898)
Q Consensus       721 RRIea---vtG~~A~~~~~~~~~~l~~  744 (898)
                      -||+-   .+..+-.+.|.+....+.+
T Consensus       150 qRiyGn~~~~~~~~k~~L~~yl~~~eE  176 (595)
T TIGR00418       150 QRIYGNIDITAFADKKQLAEYLKRLEE  176 (595)
T ss_pred             EEECCCEEEECCCCHHHHHHHHHHHHH
T ss_conf             888572545014587899999999999


No 25 
>pfam02091 tRNA-synt_2e Glycyl-tRNA synthetase alpha subunit.
Probab=98.08  E-value=0.00035  Score=51.56  Aligned_cols=166  Identities=27%  Similarity=0.361  Sum_probs=97.9

Q ss_pred             HHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCEECCCCCCCH---HHCC
Q ss_conf             99999999999789889116675667787100230143475540-0588799999851115432248987863---4346
Q gi|254780191|r    6 SIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNI-FTGQEKPVYQAVTTVQKCVRAGGKHNDL---DNVG   81 (898)
Q Consensus         6 eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~-f~G~~~p~~~r~~~~QkCiR~ggkhnDl---d~VG   81 (898)
                      +|-.+--+|+.++|+.++.++.+=         +.||  .|-|- |+..--|.--+++=+|||.|-    .|=   +|--
T Consensus         3 ~ii~~L~~fW~~~GC~i~qpyd~e---------~GAg--T~~p~T~lr~lgp~pw~~aYvqPsrRP----~DgRYGenPn   67 (284)
T pfam02091         3 SMILTLQEYWASQGCVIMQPYDME---------VGAG--TFNPATFLRALGPEPWNVAYVEPSRRP----TDGRYGENPN   67 (284)
T ss_pred             HHHHHHHHHHHHCCCEEECCCCCC---------CCCC--CCCHHHHHHHCCCCCCEEEEECCCCCC----CCCCCCCCCC
T ss_conf             899999999987796887776542---------4646--588899886319986415542467799----9987778920


Q ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHH---HHHCCC-CHHHEEECCCC
Q ss_conf             48850017888542231475378899989986133418981237999718828999975---663499-98997535786
Q gi|254780191|r   82 RTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKLW---KKISGL-SADKIIRITTN  157 (898)
Q Consensus        82 ~t~rH~TfFEMlGn~SfgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~iW---~~~~gi-~~~~i~~~~~~  157 (898)
                      + -.||.=|..+=-=|..                                   ..-++.   ++.+|| |.+|=++|- +
T Consensus        68 R-lq~y~QfQVi~KPsp~-----------------------------------n~q~lYL~SL~~lgid~~~hDIrFv-e  110 (284)
T pfam02091        68 R-LQHYYQFQVILKPSPD-----------------------------------NIQELYLGSLKALGIDPLDHDIRFV-E  110 (284)
T ss_pred             H-HHHHEEEEEEECCCCH-----------------------------------HHHHHHHHHHHHCCCCCCCCCEEEE-E
T ss_conf             4-2002235789778946-----------------------------------6899999989983979543624786-1


Q ss_pred             CCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             66545799999877046788538556898887778898268960011234430478875657665310175799999998
Q gi|254780191|r  158 DNFWSMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLERMATVL  237 (898)
Q Consensus       158 dNfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNlVFmq~~~~~~g~~~~Lp~~~IDTGmGLERl~~vl  237 (898)
                      || |+.-.-|.-|--=||-.|                  ++||--.-.+|   +-.|  .++..-.+.--+||||||+.+
T Consensus       111 Dn-WEsPtLGAwGlGWEVwld------------------GMEITQFTYFQ---QvGG--i~c~pv~~EiTYGLERiAMyl  166 (284)
T pfam02091       111 DN-WESPTLGAWGLGWEVWLD------------------GMEITQFTYFQ---QVGG--LECKPVSGEITYGLERLAMYL  166 (284)
T ss_pred             CC-CCCCCCCCCCCCEEEEEC------------------CEEEEEEEEEE---EECC--EECCCCCEEEEHHHHHHHHHH
T ss_conf             47-878753102343399987------------------75776435120---1378--214453233101199999999


Q ss_pred             CCCCCCCHHH
Q ss_conf             8798530057
Q gi|254780191|r  238 QEKTNNYDID  247 (898)
Q Consensus       238 qg~~s~ydtD  247 (898)
                      ||+.++||+.
T Consensus       167 Q~vdnv~Dl~  176 (284)
T pfam02091       167 QKVDSVYDLV  176 (284)
T ss_pred             HCCCHHHEEE
T ss_conf             5762241301


No 26 
>pfam01411 tRNA-synt_2c tRNA synthetases class II (A). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only alanyl-tRNA synthetases.
Probab=97.68  E-value=9e-06  Score=64.02  Aligned_cols=107  Identities=21%  Similarity=0.149  Sum_probs=80.5

Q ss_pred             CCCHHH---HHHHHHHHCCCCHHHEEECCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHH-
Q ss_conf             188289---9997566349998997535786665457999998770467885385568988877788982689600112-
Q gi|254780191|r  130 YDEDEE---AFKLWKKISGLSADKIIRITTNDNFWSMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNLVF-  205 (898)
Q Consensus       130 ~~~D~e---~~~iW~~~~gi~~~~i~~~~~~dNfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNlVF-  205 (898)
                      |..++-   |++.-.+..|||++||...   ...|.    |.||||-|.++                  ++.|..++|| 
T Consensus        93 YfK~eai~~a~e~lt~~l~i~~~~l~~t---~~~~d----~ea~~~w~~~~------------------g~~~~~i~~~~  147 (545)
T pfam01411        93 YFKEEAIEFAWELLTKELGLDPERLYVT---VYEWD----DEAGPIWEKIV------------------GGPEERILRFG  147 (545)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCHHHEEEE---ECCCC----CCHHHHHHHHC------------------CCCHHHCEECC
T ss_conf             4378999999999765617886676999---88886----33667688862------------------99999906267


Q ss_pred             --HHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             --3443047887565766531017579999999887985300576999999999730678
Q gi|254780191|r  206 --MQFEQQNKQERFILPKMSIDTGMGLERMATVLQEKTNNYDIDLFKHLIQASEQVTGMK  263 (898)
Q Consensus       206 --mq~~~~~~g~~~~Lp~~~IDTGmGLERl~~vlqg~~s~ydtD~f~pii~~i~~~~g~~  263 (898)
                        |+|-...+ +....|-.-||+|+|+||.+|..+++|+.|+ |.|..|.+-+-.-.+..
T Consensus       148 ~~~nfw~~g~-~gpcgPcseI~~d~G~e~~~~~~~~~~~~~~-~~~~EiwNlVF~q~~~~  205 (545)
T pfam01411       148 DKDNFWEMGD-TGPCGPCSEIDYDRGEEIGGWPSGGTPTADD-DRFLEIWNLVFMQFNRE  205 (545)
T ss_pred             CCCCEEECCC-CCCCCCCEEEEECCCCCCCCCCCCCCCCCCC-CEEHHHHHHHHHHHCCC
T ss_conf             7776057789-8899776899976672026888889988888-78288999999995876


No 27 
>cd00768 class_II_aaRS-like_core Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ.
Probab=97.00  E-value=0.00068  Score=49.31  Aligned_cols=175  Identities=23%  Similarity=0.250  Sum_probs=99.1

Q ss_pred             HHHHHHHHHHHHHCCCEECCCCCCCCC-------------------CCCCHHEEECCCCCCCCCCCCC-CCCCCCCCCCC
Q ss_conf             899999999999789889116675667-------------------7871002301434755400588-79999985111
Q gi|254780191|r    5 SSIRTTFLEFFQKNGHELLPSSSLIPC-------------------NDPTLMFTNSGMVPFKNIFTGQ-EKPVYQAVTTV   64 (898)
Q Consensus         5 ~eiR~~fl~fF~~~~H~~~~s~slvp~-------------------~d~~llft~Agm~~fk~~f~G~-~~p~~~r~~~~   64 (898)
                      +.|-+..-+|+.++|++.|-.-.+++.                   .|.++++....-.....+|-.. .+.| .|++..
T Consensus         3 ~~ie~~~r~~~~~~G~~ev~~P~l~~~~~~~~sg~~~~~~~~~~~~~~~~~~L~pt~e~~~~~~~~~~~~dLP-~r~~~~   81 (211)
T cd00768           3 SKIEQKLRRFMAELGFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEEDLYLRPTLEPGLVRLFVSHIRKLP-LRLAEI   81 (211)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCEECCHHHHHHCCCCHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHCC-HHHHEE
T ss_conf             8999999999998699899998342799997506762223011046797699951684999999752476577-786432


Q ss_pred             CCCEECCCCCCCHHHCCCCCCCHHHHHHHHHHHHCCC-----CHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHH
Q ss_conf             5432248987863434648850017888542231475-----37889998998613341898123799971882899997
Q gi|254780191|r   65 QKCVRAGGKHNDLDNVGRTNRHHTFFEMLGNFSFGGY-----FKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKL  139 (898)
Q Consensus        65 QkCiR~ggkhnDld~VG~t~rH~TfFEMlGn~SfgdY-----fK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~i  139 (898)
                      ++|.|-.     .-.-|.  .|.--|+|.-.|+|...     ..++.+..+++++.. |+|+-..               
T Consensus        82 ~~~fR~E-----~~~~Gl--~RvreF~~~e~~~f~~~~~~~~~~~~~~~~~~~i~~~-lgl~~~~---------------  138 (211)
T cd00768          82 GPAFRNE-----GGRRGL--RRVREFTQLEGEVFGEDGEEASEFEELIELTEELLRA-LGIKLDI---------------  138 (211)
T ss_pred             CCEECCC-----CCCCCC--CCCCCEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHH-CCCCCCE---------------
T ss_conf             0056057-----888884--4604688984799988488899999999999999997-4998886---------------


Q ss_pred             HHHHCCCCHHHEEECCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHC---------
Q ss_conf             56634999899753578666545799999877046788538556898887778898268960011234430---------
Q gi|254780191|r  140 WKKISGLSADKIIRITTNDNFWSMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNLVFMQFEQ---------  210 (898)
Q Consensus       140 W~~~~gi~~~~i~~~~~~dNfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNlVFmq~~~---------  210 (898)
                                 +........++    .+.++|+.+|.++..             +.|++||++.-+..-++         
T Consensus       139 -----------~~~~~~~~~~~----~~~a~~~~Die~~~p-------------~~~~~Ev~s~~~~~d~qsr~~~i~y~  190 (211)
T cd00768         139 -----------VFVEKTPGEFS----PGGAGPGFEIEVDHP-------------EGRGLEIGSGGYRQDEQARAADLYFL  190 (211)
T ss_pred             -----------EEEEECCCCCC----CCCCEEEEEEEEECC-------------CCCEEEEECEECCCCHHHHHCCCEEE
T ss_conf             -----------99997786766----645235455789837-------------89799993546167787884698999


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             47887565766531017579999
Q gi|254780191|r  211 QNKQERFILPKMSIDTGMGLERM  233 (898)
Q Consensus       211 ~~~g~~~~Lp~~~IDTGmGLERl  233 (898)
                      +.||+....++-  -.|+|+|||
T Consensus       191 ~~dg~~~~~~~~--~~gl~v~Rl  211 (211)
T cd00768         191 DEALEYRYPPTI--GFGLGLERL  211 (211)
T ss_pred             CCCCCEEEEEEE--ECEECCCCC
T ss_conf             999999875563--032413669


No 28 
>pfam00152 tRNA-synt_2 tRNA synthetases class II (D, K and N).
Probab=95.17  E-value=0.26  Score=29.04  Aligned_cols=100  Identities=25%  Similarity=0.361  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHHHHCCCEECCCCCCCCC--CCCCHHEEECCCCCCCCCCCCCCCC---------CCCCCCCCCCCEECCCC
Q ss_conf             899999999999789889116675667--7871002301434755400588799---------99985111543224898
Q gi|254780191|r    5 SSIRTTFLEFFQKNGHELLPSSSLIPC--NDPTLMFTNSGMVPFKNIFTGQEKP---------VYQAVTTVQKCVRAGGK   73 (898)
Q Consensus         5 ~eiR~~fl~fF~~~~H~~~~s~slvp~--~d~~llft~Agm~~fk~~f~G~~~p---------~~~r~~~~QkCiR~ggk   73 (898)
                      ++|-+.+-+||.++|-.-|..--|++.  ....-+|..- .+--++.||-+.+-         -..|+=..-||.|+.  
T Consensus        26 s~i~~~iR~ff~~~~f~EV~TP~L~~~~~e~~a~~F~~~-~~~~~~~yL~~Spel~~k~ll~~g~~rVfei~~~FR~E--  102 (341)
T pfam00152        26 SKIIRAIREFLDERGFLEVETPILTKSTPEGGARDFLVP-KFYAKEAYLPQSPQLYKQLLMVAGFDRVFQIAPCFRDE--  102 (341)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCEEEEC-CCCCCCEEECCCHHHHHHHHHHCCCCCCEEEECHHCCC--
T ss_conf             999999999999889899879820055898777664502-67898234054889999999865887637972320279--


Q ss_pred             CCCHHHCCCCCCCHHHHHHHH-HHHHCCCCHHHHHHHHHHHHH
Q ss_conf             786343464885001788854-223147537889998998613
Q gi|254780191|r   74 HNDLDNVGRTNRHHTFFEMLG-NFSFGGYFKERAIQLAWDLLT  115 (898)
Q Consensus        74 hnDld~VG~t~rH~TfFEMlG-n~SfgdYfK~eai~~awe~lt  115 (898)
                           ++ .|.||++=|-||- =++|.||  ++.+...=+++.
T Consensus       103 -----~~-~t~rH~~EFtmlE~y~a~~d~--~d~m~~~E~li~  137 (341)
T pfam00152       103 -----DL-RTDRHPPEFTQLDLEMSFVDY--EDVMDLTEDLIK  137 (341)
T ss_pred             -----CC-CCCCCCHHHHHHHHHHHCCCH--HHHHHHHHHHHH
T ss_conf             -----89-886550778877675535999--999999999999


No 29 
>pfam01409 tRNA-synt_2d tRNA synthetases class II core domain (F). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain.
Probab=94.91  E-value=0.19  Score=30.20  Aligned_cols=180  Identities=15%  Similarity=0.190  Sum_probs=86.0

Q ss_pred             HHHHHHHHHHHHHHCCCEECCCCCCC-----------CCCCC-----CHHEE-------------ECCCCCCCCCCCCCC
Q ss_conf             78999999999997898891166756-----------67787-----10023-------------014347554005887
Q gi|254780191|r    4 VSSIRTTFLEFFQKNGHELLPSSSLI-----------PCNDP-----TLMFT-------------NSGMVPFKNIFTGQE   54 (898)
Q Consensus         4 ~~eiR~~fl~fF~~~~H~~~~s~slv-----------p~~d~-----~llft-------------~Agm~~fk~~f~G~~   54 (898)
                      ++++++...++|.+-|.+++.+..+.           |.+.|     +.++.             -.+-+|..-.. -..
T Consensus        19 i~~~~~~i~~~f~~~GF~~~~g~eves~~~NFDaLn~P~dHPaR~~~DTfy~~~~~~~~~~vLRtHTS~~q~r~l~-~~~   97 (243)
T pfam01409        19 LTRVLEEIRDIFLSMGFEEVEGPEVESDFYNFDALNIPQDHPARDMQDTFYLKKPLKARRLLLRTHTTPVQARTLA-EKN   97 (243)
T ss_pred             HHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCEEECCCCCHHHHHHHH-HCC
T ss_conf             9999999999998779868769835642777775578988987676760343366667686576879889999997-427


Q ss_pred             CCCCCCCCCCCCCEECCCCCCCHHHCCCCCCCHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHCCCCHH-HEEEEECCC
Q ss_conf             9999985111543224898786343464885001788854223147-53788999899861334189812-379997188
Q gi|254780191|r   55 KPVYQAVTTVQKCVRAGGKHNDLDNVGRTNRHHTFFEMLGNFSFGG-YFKERAIQLAWDLLTKEFDLDQR-RLYITVYDE  132 (898)
Q Consensus        55 ~p~~~r~~~~QkCiR~ggkhnDld~VG~t~rH~TfFEMlGn~Sfgd-YfK~eai~~awe~lt~~~~l~~~-~l~vtv~~~  132 (898)
                      +|| -|+.+.-+|-|     ||=.    ++.|+-.|-.+--+-.+. .=-.+-...--+|+.+.+|.+-+ |+--+||  
T Consensus        98 ~~p-~r~~~~grvyR-----~d~~----DatH~~~FhQ~Eg~vvd~~it~~~Lk~~l~~~~~~lfg~~~~~R~rp~yF--  165 (243)
T pfam01409        98 KPP-IKIFSIGRVFR-----RDQV----DATHLPEFHQVEGLVVDENVSFADLKGVLEEFLRKFFGFEVKVRFRPSYF--  165 (243)
T ss_pred             CCC-EEEECCCEEEE-----CCCC----CCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCC--
T ss_conf             998-48981431332-----5889----84315310575578965777899999999999999739973798678869--


Q ss_pred             HHHHHHHHHHHCCCCHHHEEECCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEH-HHHHHHCC
Q ss_conf             28999975663499989975357866654579999987704678853855689888777889826896001-12344304
Q gi|254780191|r  133 DEEAFKLWKKISGLSADKIIRITTNDNFWSMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNL-VFMQFEQQ  211 (898)
Q Consensus       133 D~e~~~iW~~~~gi~~~~i~~~~~~dNfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNl-VFmq~~~~  211 (898)
                                                 .+       --|+.|+.+-.            |....+|||... +|-+---.
T Consensus       166 ---------------------------PF-------TePS~Evdv~~------------~~~~~WlEi~G~Gmv~p~vl~  199 (243)
T pfam01409       166 ---------------------------PF-------TEPSAEVDVYC------------CKGGGWIEIGGAGMVHPNVLE  199 (243)
T ss_pred             ---------------------------CC-------CCCCCEEEEEE------------ECCCCEEEEEECCCCCHHHHH
T ss_conf             ---------------------------99-------99861799999------------649972587503666788998


Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             788756576653101757999999988798530
Q gi|254780191|r  212 NKQERFILPKMSIDTGMGLERMATVLQEKTNNY  244 (898)
Q Consensus       212 ~~g~~~~Lp~~~IDTGmGLERl~~vlqg~~s~y  244 (898)
                      .-| +- =.....--||||||||++.-|.+..=
T Consensus       200 ~~g-id-~~~~g~AfG~GlERlaMl~~gi~DIR  230 (243)
T pfam01409       200 AVG-ID-EDYPGFAFGLGVERLAMLKYGIDDIR  230 (243)
T ss_pred             HCC-CC-CCCEEEEEEECHHHHHHHHCCCCHHH
T ss_conf             669-89-89769998534889999982997789


No 30 
>TIGR00344 alaS alanyl-tRNA synthetase; InterPro: IPR002318   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Alanyl-tRNA synthetase (6.1.1.7 from EC) is an alpha4 tetramer that belongs to class IIc. ; GO: 0004813 alanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006419 alanyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=94.11  E-value=0.057  Score=34.28  Aligned_cols=100  Identities=16%  Similarity=0.229  Sum_probs=77.3

Q ss_pred             CCCHHHEEECCCCC-----CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEE----EEHHHHHHHCCCCCC
Q ss_conf             99989975357866-----654579999987704678853855689888777889826896----001123443047887
Q gi|254780191|r  145 GLSADKIIRITTND-----NFWSMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEI----WNLVFMQFEQQNKQE  215 (898)
Q Consensus       145 gi~~~~i~~~~~~d-----NfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEi----wNlVFmq~~~~~~g~  215 (898)
                      ++|.+++.-.-.++     ++|..+  |..+||.+|.-       +           ..|.    -..+|+++...+.|.
T Consensus       126 ~~p~~~~~~~~~~~d~~~~~~w~~~--~~~~p~~~~~~-------~-----------g~~~gp~~~~~~w~~~~~~p~gp  185 (914)
T TIGR00344       126 GLPKERLYVTVYEEDDEAYELWEKG--GGAGPCERIIR-------G-----------GDELGPYAADNFWDLGDTGPCGP  185 (914)
T ss_pred             CCCCCEEEEEEECCCHHHHHHHHCC--CCCCCHHHHHH-------C-----------CCCCCCCCCHHHHHHCCCCCCCC
T ss_conf             4432016888753732567765314--55453134431-------3-----------54236420001232035677764


Q ss_pred             ----CCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCC-CCC
Q ss_conf             ----565766531017579999999887985300576999999999730678-543
Q gi|254780191|r  216 ----RFILPKMSIDTGMGLERMATVLQEKTNNYDIDLFKHLIQASEQVTGMK-YEG  266 (898)
Q Consensus       216 ----~~~Lp~~~IDTGmGLERl~~vlqg~~s~ydtD~f~pii~~i~~~~g~~-y~~  266 (898)
                          +...+.+..+||+|+|++.|.. +.++.|.. +|..++.......+.. +..
T Consensus       186 ~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  239 (914)
T TIGR00344       186 CTEIYYDRGEKIGDTGYGPEKLFWES-GEPDRYLE-IWNLVFSQFNRDGDGNDLTP  239 (914)
T ss_pred             CHHHHHHCCCCCCCCCCCCCCCCCCC-CCCCHHHH-HHHHHHHHHHCCCCCCCCCH
T ss_conf             10132211431145446743123466-77621356-77778886520357640001


No 31 
>cd00669 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=93.98  E-value=0.27  Score=28.93  Aligned_cols=215  Identities=16%  Similarity=0.201  Sum_probs=100.4

Q ss_pred             CHHHHHHHHHHHHHHCCCEECCCCCCCC--CCCCCHHEEECCCCCCCCCCCCCCC---------CCCCCCCCCCCCEECC
Q ss_conf             8789999999999978988911667566--7787100230143475540058879---------9999851115432248
Q gi|254780191|r    3 NVSSIRTTFLEFFQKNGHELLPSSSLIP--CNDPTLMFTNSGMVPFKNIFTGQEK---------PVYQAVTTVQKCVRAG   71 (898)
Q Consensus         3 s~~eiR~~fl~fF~~~~H~~~~s~slvp--~~d~~llft~Agm~~fk~~f~G~~~---------p~~~r~~~~QkCiR~g   71 (898)
                      --++|-+.+-+||.++|-.-|..--++.  -....-+|...--..=++.||-+.+         -...|+-..-||.|+ 
T Consensus         3 ~Rs~i~~~iR~ff~~~~f~EV~TP~l~~~~~~~~~~~f~~~~~~~~~~~~L~~Spel~~k~ll~~g~~~if~i~~~FR~-   81 (269)
T cd00669           3 VRSKIIKAIRDFMDDRGFLEVETPMLQKITGGAGARPFLVKYNALGLDYYLRISPQLFKKRLMVGGLDRVFEINRNFRN-   81 (269)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEECCEEECCCCCCCCCEEEEECCCCCCEEEECCCHHHHHHHHHHCCCCCEEEEECCCCC-
T ss_conf             6999999999999988989987985305789876742573137899407734388999999986588867998462107-


Q ss_pred             CCCCCHHHCCCCCCCHHHHHHHHH-HHHCCC-----CHHHHHHHHHHHHHHH-----------CCCCHHHEEEEECCCHH
Q ss_conf             987863434648850017888542-231475-----3788999899861334-----------18981237999718828
Q gi|254780191|r   72 GKHNDLDNVGRTNRHHTFFEMLGN-FSFGGY-----FKERAIQLAWDLLTKE-----------FDLDQRRLYITVYDEDE  134 (898)
Q Consensus        72 gkhnDld~VG~t~rH~TfFEMlGn-~SfgdY-----fK~eai~~awe~lt~~-----------~~l~~~~l~vtv~~~D~  134 (898)
                          +    +.+.||++=|-||-= .+|.||     +-++-|.+.++-+...           ++.|-.+  +|+    +
T Consensus        82 ----e----~~~~rH~~EFtmlE~y~~~~d~~~~m~~~e~li~~~~~~~~~~~~~~~~~~~~~~~~~~~~--i~~----~  147 (269)
T cd00669          82 ----E----DLRARHQPEFTMMDLEMAFADYEDVIELTERLVRHLAREVLGVTAVTYGFELEDFGLPFPR--LTY----R  147 (269)
T ss_pred             ----C----CCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCCCE--EEH----H
T ss_conf             ----8----9865543487757875148999999999999999999999655524535544445899878--579----9


Q ss_pred             HHHHHHHHHCCCCHHHEEECCC-CCCCCCCC-CCC-CCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHHH--HHH
Q ss_conf             9999756634999899753578-66654579-999-987704678853855689888777889826896001123--443
Q gi|254780191|r  135 EAFKLWKKISGLSADKIIRITT-NDNFWSMA-ETG-PCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNLVFM--QFE  209 (898)
Q Consensus       135 e~~~iW~~~~gi~~~~i~~~~~-~dNfW~~g-~~G-pcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNlVFm--q~~  209 (898)
                      |+.+.-    | ++-=|+.+.. .-.|..+- +.+ ..--+.|+|+ .|-+..+|          |.|+++-.=.  .|+
T Consensus       148 ea~e~~----~-~p~fi~dyP~~~~~~~~~~~~~~~~~a~rfdl~~-~G~El~nG----------~~r~~d~~~~~~r~~  211 (269)
T cd00669         148 EALERY----G-QPLFLTDYPAEMHSPLASPHDVNPEIADAFDLFI-NGVEVGNG----------SSRLHDPDIQAEVFQ  211 (269)
T ss_pred             HHHHHH----C-CCEEEECCCHHCCCCCCCCCCCCCCHHHHCCCCC-CCEEECCC----------CCCCCCHHHHHHHHH
T ss_conf             999984----9-9789989850107802090799966766502467-86067032----------520488899999999


Q ss_pred             CCC---------CCCCC-----CCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHH
Q ss_conf             047---------88756-----57665310175799999998879853005769
Q gi|254780191|r  210 QQN---------KQERF-----ILPKMSIDTGMGLERMATVLQEKTNNYDIDLF  249 (898)
Q Consensus       210 ~~~---------~g~~~-----~Lp~~~IDTGmGLERl~~vlqg~~s~ydtD~f  249 (898)
                      ...         +..|.     -+| +|=-.|+|+|||++.+-|.++.=|+=.|
T Consensus       212 ~~~~~~~~~~~~~~~yl~a~~~G~p-p~~G~glG~dRL~m~~~g~~~Irdv~~F  264 (269)
T cd00669         212 EQGINKEAGMEYFEFYLKALEYGLP-PHGGLGIGIDRLIMLMTNSPTIREVIAF  264 (269)
T ss_pred             HHCCCHHHHHHHHHHHHHHHHCCCC-CCEEEEEHHHHHHHHHHCCCCHHHCCCC
T ss_conf             8560744556658999999877999-9716634799999998089968862478


No 32 
>cd00496 PheRS_alpha_core Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA,  PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs.  PheRS is an alpha-2/ beta-2 tetramer.
Probab=93.63  E-value=0.62  Score=26.13  Aligned_cols=182  Identities=13%  Similarity=0.094  Sum_probs=83.8

Q ss_pred             HHHHHHHHHHHHHHCCCEECCCCCCCCCCCC-CH---------------HEEECCC-CCCCCCCCC-------CCCCCCC
Q ss_conf             7899999999999789889116675667787-10---------------0230143-475540058-------8799999
Q gi|254780191|r    4 VSSIRTTFLEFFQKNGHELLPSSSLIPCNDP-TL---------------MFTNSGM-VPFKNIFTG-------QEKPVYQ   59 (898)
Q Consensus         4 ~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~-~l---------------lft~Agm-~~fk~~f~G-------~~~p~~~   59 (898)
                      +.++++...++|.+.|-+++.+..+.+-+.. +.               +|.+..- .-+-.-.+.       ..+|| -
T Consensus         3 l~~~~~~i~~~f~~~GF~~~~gp~ie~~~~NFD~Ln~P~dHPaR~~~DTfy~~~~~~~lLRtHTS~~q~r~l~~~~~p-~   81 (218)
T cd00496           3 LNKVIEEIEDIFVSMGFTEVEGPEVETDFYNFDALNIPQDHPARDMQDTFYINDPARLLLRTHTSAVQARALAKLKPP-I   81 (218)
T ss_pred             HHHHHHHHHHHHHHCCCEEECCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCCEECCCCCHHHHHHHHHCCCC-C
T ss_conf             789999999999877986822895123103045338598875537243278637766021578756679999745898-1


Q ss_pred             CCCCCCCCEECCCCCCCHHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHH
Q ss_conf             85111543224898786343464885001788854223147537889998998613341898123799971882899997
Q gi|254780191|r   60 AVTTVQKCVRAGGKHNDLDNVGRTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKL  139 (898)
Q Consensus        60 r~~~~QkCiR~ggkhnDld~VG~t~rH~TfFEMlGn~SfgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~i  139 (898)
                      |+.+.-+|.|     +|=    .++.|.-.|-++--+-.+.=..-.-..+.-+-+.+.+.-+.                 
T Consensus        82 ~~~~~G~VyR-----~D~----iDatH~~~FhQ~Eg~~v~~~~~~~~Lk~~l~~~~~~lfg~~-----------------  135 (218)
T cd00496          82 RIFSIGRVYR-----NDE----IDATHLPEFHQIEGLVVDKGLTFADLKGTLEEFAKELFGPI-----------------  135 (218)
T ss_pred             EEEECCCEEE-----CCC----CCCCCCCEEEEEEEEEEECCCCHHHHHHHHHHHHHHHCCCC-----------------
T ss_conf             7994250465-----388----98431531257637999565119999999999999973876-----------------


Q ss_pred             HHHHCCCCHHHEEECCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEH-HHHHHHCCCCCCCCC
Q ss_conf             5663499989975357866654579999987704678853855689888777889826896001-123443047887565
Q gi|254780191|r  140 WKKISGLSADKIIRITTNDNFWSMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNL-VFMQFEQQNKQERFI  218 (898)
Q Consensus       140 W~~~~gi~~~~i~~~~~~dNfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNl-VFmq~~~~~~g~~~~  218 (898)
                                ..++       |...-.-=-=|+.||...+.            .|..+|||... ++-+ +-..+..+. 
T Consensus       136 ----------~~~r-------~rp~yFPFTePS~Evdv~~~------------~~~~WlEv~G~G~v~p-~vL~~~G~d-  184 (218)
T cd00496         136 ----------TKVR-------FRPSYFPFTEPSFEVDVYCP------------GCLGWLEILGCGMVRP-EVLENAGID-  184 (218)
T ss_pred             ----------CEEE-------ECCCCCCCCCCCEEEEEEEC------------CCCCCEEEECCCCCCH-HHHHHCCCC-
T ss_conf             ----------6453-------67788999998269999965------------8787148850465488-999866979-


Q ss_pred             CCCCCCCCCCCHHHHHHHHCCCCCC
Q ss_conf             7665310175799999998879853
Q gi|254780191|r  219 LPKMSIDTGMGLERMATVLQEKTNN  243 (898)
Q Consensus       219 Lp~~~IDTGmGLERl~~vlqg~~s~  243 (898)
                      =+-...--||||||||+++-|.+..
T Consensus       185 ~~~~g~AfG~GlERlaMl~~gI~DI  209 (218)
T cd00496         185 EEYSGFAFGIGLERLAMLKYGIPDI  209 (218)
T ss_pred             CCCEEEEEEECHHHHHHHHCCCCHH
T ss_conf             9988999852588999998399768


No 33 
>PRK06462 asparagine synthetase A; Reviewed
Probab=93.26  E-value=0.71  Score=25.70  Aligned_cols=99  Identities=20%  Similarity=0.174  Sum_probs=53.7

Q ss_pred             HHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCC------CCCCCCCC---------CCCCCCCCCCCEE
Q ss_conf             89999999999978988911667566778710023014347554------00588799---------9998511154322
Q gi|254780191|r    5 SSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKN------IFTGQEKP---------VYQAVTTVQKCVR   69 (898)
Q Consensus         5 ~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~------~f~G~~~p---------~~~r~~~~QkCiR   69 (898)
                      +.|=+.+-+||.++|-.-|..--|.+...+.    +|+..+|+.      .+|-+.+-         -..|+=..-||.|
T Consensus        33 s~i~~~iR~f~~~~gF~EV~TPiL~~~~~~~----~~~~~~~~~~~~~~~~~L~~Spql~lk~li~~g~~rVfeIg~~FR  108 (332)
T PRK06462         33 SSILRYTREFLDGRGFVEVLPPIISPSTDPL----MGDAKPASIDFYGVEYYLADSMIFHKQLMLRLLKGKVFYLSPNFR  108 (332)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCCCCCC----CCCCCCCEEECCCCCEEECCCHHHHHHHHHHCCCCCEEEECCHHH
T ss_conf             9999999999988899998797236778876----677601058448986331458699999998638997799745231


Q ss_pred             CCCCCCCHHHCCCCCCCHHHHHHHHH-HHHCCC-----CHHHHHHHHHHH
Q ss_conf             48987863434648850017888542-231475-----378899989986
Q gi|254780191|r   70 AGGKHNDLDNVGRTNRHHTFFEMLGN-FSFGGY-----FKERAIQLAWDL  113 (898)
Q Consensus        70 ~ggkhnDld~VG~t~rH~TfFEMlGn-~SfgdY-----fK~eai~~awe~  113 (898)
                      +.    ++|.  .|.||+.=|-||== ++|.||     +-++.|.+...-
T Consensus       109 ~E----~~d~--~t~rHlpEFt~lE~y~a~~d~~d~m~~~E~li~~i~~~  152 (332)
T PRK06462        109 LE----PVDK--DTGRHLYEFTQLDIEIEGADLEEVMSLAEDLIKYLVKE  152 (332)
T ss_pred             CC----CCCC--CCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
T ss_conf             68----7776--77765457776558787389999999999999999999


No 34 
>TIGR00644 recJ single-stranded-DNA-specific exonuclease RecJ; InterPro: IPR004610 All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair. RecJ is a single-stranded DNA-specific endonuclease which is required for many types of recombination events, although the stringency of the requirement for RecJ appears to vary with the type of recombinational event monitored, and the other recombination gene products which are available.; GO: 0008409 5'-3' exonuclease activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=92.71  E-value=0.83  Score=25.14  Aligned_cols=139  Identities=16%  Similarity=0.166  Sum_probs=85.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEEECC
Q ss_conf             88999999999999999999999999998763653555369527999957999789999999999754997899999538
Q gi|254780191|r  753 QGNVVGRVEEIWEEYRKLQLIHAKRKLQLNVEDLSCHKIADVNFMSHIISEVDSKELKSVMDALQKKIQSGIIMLVGISK  832 (898)
Q Consensus       753 ~~~i~~ki~~L~~e~K~l~k~~~k~k~~~~~~~~~~~~i~~~~~i~~~~~~~d~~~Lr~l~d~l~~k~~~~vvvL~~~~~  832 (898)
                      ..++.++++++.++.|..+....+................+-++++..=++....-+==+|.+|+++...+++++. .. 
T Consensus       428 a~~la~~l~~~N~~Rk~i~~~~~~ea~~~~~~~~~~~~l~~~~~~V~~~~~WH~GV~GIvAsrL~~~~~KP~~v~~-~~-  505 (705)
T TIGR00644       428 ARELAEELDELNEERKKIEQEVLKEAEKIAEAELEKSDLTNDSVIVVAKENWHPGVLGIVASRLAETFNKPVIVLA-ID-  505 (705)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEE-CC-
T ss_conf             9999999999889999999999999999998414423445781289961786863187788889886389789998-38-


Q ss_pred             CCEEEEEEEECHHHHCCCCHHHHHHHHHH----HHCCCCCCCCCHHCCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             98179999867789726798999999998----834999999810114589998788999999999861
Q gi|254780191|r  833 EKKASVLIVVTEDLLDRFNAVDLARLSAK----VLGGGGGGGRPHMAQSGGPNGNKADQAIAGVASFLK  897 (898)
Q Consensus       833 ~~k~~ivv~vs~~~~~~~~A~~lik~ia~----~l~GGgGGGkpd~AQgGG~~~~~l~eal~~vk~~Lk  897 (898)
                      +++..+.-|.-.. ..+++-.++++....    .+- + +|| -.||=|=.=..++|++..+...+.++
T Consensus       506 ~~~g~~~KGS~RS-i~~~~l~~~l~~~~~~~a~l~~-~-~GG-H~~AAGl~~~~~~l~~f~~~l~~~~~  570 (705)
T TIGR00644       506 EEKGVIAKGSARS-ISGIDLLDLLSELREKGAGLLL-K-FGG-HAMAAGLTLKRENLEEFREKLEEKFK  570 (705)
T ss_pred             CCCCEEEEEEECC-CCCCCHHHHHHHHHHCCCHHHH-C-CCC-CHHHCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             9985799877202-1331069899765201301331-2-788-04650555666211899999999998


No 35 
>COG0016 PheS Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]
Probab=92.67  E-value=0.21  Score=29.84  Aligned_cols=14  Identities=21%  Similarity=0.453  Sum_probs=9.7

Q ss_pred             CCCCCCCCHHHHHH
Q ss_conf             56222588646011
Q gi|254780191|r  694 CGGTHVSSTGEIML  707 (898)
Q Consensus       694 CGGTHV~nTgeIG~  707 (898)
                      ||=-|.+=+.-+|.
T Consensus       282 ~Gmv~P~VL~~~G~  295 (335)
T COG0016         282 CGMVHPNVLEAVGI  295 (335)
T ss_pred             CCCCCHHHHHHCCC
T ss_conf             65457888974599


No 36 
>cd00777 AspRS_core Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. AspRS in this family differ from those found in the AsxRS family by a GAD insert in the core domain.
Probab=92.16  E-value=0.96  Score=24.64  Aligned_cols=102  Identities=18%  Similarity=0.236  Sum_probs=55.8

Q ss_pred             CCHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCC---HHEEECCCCCCCCCCCCCCC---------CCCCCCCCCCCCEE
Q ss_conf             7878999999999997898891166756677871---00230143475540058879---------99998511154322
Q gi|254780191|r    2 SNVSSIRTTFLEFFQKNGHELLPSSSLIPCNDPT---LMFTNSGMVPFKNIFTGQEK---------PVYQAVTTVQKCVR   69 (898)
Q Consensus         2 ~s~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~---llft~Agm~~fk~~f~G~~~---------p~~~r~~~~QkCiR   69 (898)
                      +--++|-+.+-+||.++|-.-|..--|. ..++.   -.++.+.-.+-+.++|-+.+         -...|+-...||.|
T Consensus         2 r~Rs~i~~~iR~ff~~~gflEV~TPiL~-~~~~ega~~f~~~~~~~~~~~~~L~~Spel~~k~l~~~g~~rvf~i~~~FR   80 (280)
T cd00777           2 RLRSRVIKAIRNFLDEQGFVEIETPILT-KSTPEGARDFLVPSRLHPGKFYALPQSPQLFKQLLMVSGFDRYFQIARCFR   80 (280)
T ss_pred             CHHHHHHHHHHHHHHHCCCEEEECCCCC-CCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEECEEC
T ss_conf             6699999999999998898998798106-878776766442441688760368879899999998568777579845174


Q ss_pred             CCCCCCCHHHCCCCCCCHHHHHHHH-HHHHCCCCHHHHHHHHHHHHH
Q ss_conf             4898786343464885001788854-223147537889998998613
Q gi|254780191|r   70 AGGKHNDLDNVGRTNRHHTFFEMLG-NFSFGGYFKERAIQLAWDLLT  115 (898)
Q Consensus        70 ~ggkhnDld~VG~t~rH~TfFEMlG-n~SfgdYfK~eai~~awe~lt  115 (898)
                      +.       +.  +++||+=|-||- -.+|.||  ++.+...=+++.
T Consensus        81 ~E-------~~--~~~h~~EFtmLE~e~~~~~~--~d~m~~~E~li~  116 (280)
T cd00777          81 DE-------DL--RADRQPEFTQIDIEMSFVDQ--EDIMSLIEGLLK  116 (280)
T ss_pred             CC-------CC--CCCCCHHHHHHHHHCCCCCH--HHHHHHHHHHHH
T ss_conf             78-------88--87663477623442268889--999999999999


No 37 
>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated
Probab=91.94  E-value=0.36  Score=27.97  Aligned_cols=13  Identities=23%  Similarity=0.434  Sum_probs=6.0

Q ss_pred             CCCCCCCCHHHHH
Q ss_conf             5622258864601
Q gi|254780191|r  694 CGGTHVSSTGEIM  706 (898)
Q Consensus       694 CGGTHV~nTgeIG  706 (898)
                      ||=-|.+=....|
T Consensus       284 ~Gmv~p~Vl~~~g  296 (338)
T PRK00488        284 CGMVHPNVLRNVG  296 (338)
T ss_pred             CCCCCHHHHHHCC
T ss_conf             6667889998669


No 38 
>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase; InterPro: IPR005246   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   All known phenylalanyl-tRNA synthetases, excepting a monomeric mitochondrial form, have an alpha 2 beta 2 heterotetrameric structure. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains but is longer and of unknown function; more generally, it resembles class 2 aminoacyl tRNA ligases. .
Probab=91.94  E-value=0.29  Score=28.73  Aligned_cols=29  Identities=21%  Similarity=0.297  Sum_probs=20.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHCCCCCCCHH
Q ss_conf             5657665310175799999998879853005
Q gi|254780191|r  216 RFILPKMSIDTGMGLERMATVLQEKTNNYDI  246 (898)
Q Consensus       216 ~~~Lp~~~IDTGmGLERl~~vlqg~~s~ydt  246 (898)
                      |--||+|+|  |.|=||+-.|=+=+-..-|-
T Consensus       107 LagLPrPdv--Glg~eki~~Ie~~gid~~de  135 (558)
T TIGR00470       107 LAGLPRPDV--GLGAEKIRIIEDLGIDVSDE  135 (558)
T ss_pred             HCCCCCCCC--CCCCHHHHHHHHCCCCCCCC
T ss_conf             257878863--55602778888707742101


No 39 
>KOG1501 consensus
Probab=91.16  E-value=0.17  Score=30.55  Aligned_cols=73  Identities=22%  Similarity=0.280  Sum_probs=52.2

Q ss_pred             CCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCC---CCC----CCCHHHHHH----HHHHHHHH---HHHHH
Q ss_conf             31017579999999887985300576999999999730678---543----350248999----99898999---98740
Q gi|254780191|r  223 SIDTGMGLERMATVLQEKTNNYDIDLFKHLIQASEQVTGMK---YEG----NNIVNHRVI----VDHLRSSS---FLIAD  288 (898)
Q Consensus       223 ~IDTGmGLERl~~vlqg~~s~ydtD~f~pii~~i~~~~g~~---y~~----~~~~~~rvI----aDH~Ra~~---f~I~D  288 (898)
                      .|+||-||=-+.++-.|..++|...+|.|..+...++..+.   ...    +-.+...|+    ||-+-+-.   =+|+.
T Consensus        72 digtGTGLLSmMAvragaD~vtA~EvfkPM~d~arkI~~kng~SdkI~vInkrStev~vg~~~RadI~v~e~fdtElige  151 (636)
T KOG1501          72 DIGTGTGLLSMMAVRAGADSVTACEVFKPMVDLARKIMHKNGMSDKINVINKRSTEVKVGGSSRADIAVREDFDTELIGE  151 (636)
T ss_pred             ECCCCCCHHHHHHHHHCCCEEEEEHHHCHHHHHHHHHHHCCCCCCCEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHCC
T ss_conf             72688108999988735770775212221899999988418876522662036631555576244434576654555223


Q ss_pred             CCCCCCC
Q ss_conf             3333444
Q gi|254780191|r  289 GILPANE  295 (898)
Q Consensus       289 Gv~PsN~  295 (898)
                      |++||=+
T Consensus       152 Galps~q  158 (636)
T KOG1501         152 GALPSLQ  158 (636)
T ss_pred             CCCHHHH
T ss_conf             4304389


No 40 
>cd00776 AsxRS_core Asx tRNA synthetase (AspRS/AsnRS) class II core domain.  Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS.  AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the appropriate tRNA.  While archaea lack asnRS, they possess a non-discriminating aspRS, which can mischarge Asp-tRNA with Asn. Subsequently, a tRNA-dependent aspartate amidotransferase converts the bound aspartate to asparagine. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.
Probab=90.69  E-value=1.3  Score=23.66  Aligned_cols=94  Identities=26%  Similarity=0.405  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCC------CCCCCCCC--------CCCCCCCCCCCEEC
Q ss_conf             89999999999978988911667566778710023014347554------00588799--------99985111543224
Q gi|254780191|r    5 SSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKN------IFTGQEKP--------VYQAVTTVQKCVRA   70 (898)
Q Consensus         5 ~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~------~f~G~~~p--------~~~r~~~~QkCiR~   70 (898)
                      ++|-+.+-+||.++|-.-|..--|++. .+     -+|-.+|+.      .+|-+.+-        ...|+=..-||.|.
T Consensus        28 s~i~~~iR~fl~~~gF~EVeTP~L~~~-~~-----eg~a~~f~~~~~~~~~yL~~Spel~Kqlli~G~~rVfei~~~FR~  101 (322)
T cd00776          28 SEVLRAFREFLRENGFTEVHTPKITST-DT-----EGGAELFKVSYFGKPAYLAQSPQLYKEMLIAALERVYEIGPVFRA  101 (322)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCC-CC-----CCCCCCCCCCCCCCCEEECCCHHHHHHHHHCCCCCEEEECCEEEC
T ss_conf             999999999999889999979840078-89-----865466762105876001548588999975342443887261407


Q ss_pred             CCCCCCHHHCCCCCCCHHHHHHHH-HHHHC-CC-----CHHHHHHHHHH
Q ss_conf             898786343464885001788854-22314-75-----37889998998
Q gi|254780191|r   71 GGKHNDLDNVGRTNRHHTFFEMLG-NFSFG-GY-----FKERAIQLAWD  112 (898)
Q Consensus        71 ggkhnDld~VG~t~rH~TfFEMlG-n~Sfg-dY-----fK~eai~~awe  112 (898)
                      .    +    +.|.||..=|-||= -+||. ||     .-++-|...+.
T Consensus       102 E----~----~~t~rH~pEFTmlE~e~af~~d~~d~m~~~E~li~~i~~  142 (322)
T cd00776         102 E----K----SNTRRHLSEFWMLEAEMAFIEDYNEVMDLIEELIKYIFK  142 (322)
T ss_pred             C----C----CCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             9----9----987534788876525552332899999999999999999


No 41 
>COG2024 Phenylalanyl-tRNA synthetase alpha subunit (archaeal type) [Translation, ribosomal structure and biogenesis]
Probab=88.92  E-value=0.9  Score=24.86  Aligned_cols=55  Identities=29%  Similarity=0.372  Sum_probs=25.8

Q ss_pred             HHCCCCCEEEEEECCCCCCCCCEECCCCC-------------CCCCHHHHHHHHEECCCCCCCCCEEEEEEECH
Q ss_conf             31555624899844767785531015622-------------25886460110011012126882899997168
Q gi|254780191|r  669 GTKYNDRVRVVSVEYEDGGVHSSALCGGT-------------HVSSTGEIMLLYIVSESSIRAGIRRIEAITGQ  729 (898)
Q Consensus       669 gekygd~VRVV~I~~~d~~~~S~ElCGGT-------------HV~nTgeIG~fkIise~si~sGvRRIeavtG~  729 (898)
                      ||--|..|+|--++...+    .-|||-.             -+.+|.+-+..-..  .++.+|||=|++++-.
T Consensus       406 gef~gr~v~V~~~E~Een----tkL~GPa~~NeVyvydGniygiPpt~~~~~e~~~--~gv~tgIryieg~aa~  473 (536)
T COG2024         406 GEFGGRRVKVSAVEEEEN----TKLLGPAVFNEVYVYDGNIYGIPPTKEWGSEFEE--EGVYTGIRYIEGLAAR  473 (536)
T ss_pred             CCCCCEEEEEEEECCCCC----CCCCCHHHHCEEEEECCCEEECCCCCHHHHHHHH--CCCCCCCCHHHHHHHH
T ss_conf             112771789999425789----8656805635699953847616986404467763--5765571268889999


No 42 
>PTZ00326 phenylalanyl-tRNA synthetase; Provisional
Probab=87.99  E-value=1.1  Score=24.29  Aligned_cols=14  Identities=7%  Similarity=-0.095  Sum_probs=7.6

Q ss_pred             CCCCCCCCHHHHHH
Q ss_conf             56222588646011
Q gi|254780191|r  694 CGGTHVSSTGEIML  707 (898)
Q Consensus       694 CGGTHV~nTgeIG~  707 (898)
                      ||=.|..=+.-.|.
T Consensus       456 ~Gm~~p~vl~~~g~  469 (505)
T PTZ00326        456 SGLFRPEMLRPMGF  469 (505)
T ss_pred             CCCCCHHHHHHCCC
T ss_conf             65758788732595


No 43 
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=87.41  E-value=1.4  Score=23.47  Aligned_cols=19  Identities=21%  Similarity=0.400  Sum_probs=8.4

Q ss_pred             CCCCCCCCCCEECCCEEEEE
Q ss_conf             25444445530024300000
Q gi|254780191|r  601 LGSHVSQNGSCITPDGLRFD  620 (898)
Q Consensus       601 LG~hv~Q~GS~v~~~~lrfD  620 (898)
                      +|.... .|++|..+..-||
T Consensus       261 mGF~e~-~g~~ve~~fwNfd  279 (501)
T PRK04172        261 MGFEEV-KGPIVETEFWNFD  279 (501)
T ss_pred             CCCEEE-ECCCEECCCCCHH
T ss_conf             897685-3661010000334


No 44 
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=87.07  E-value=2.2  Score=21.77  Aligned_cols=30  Identities=23%  Similarity=0.045  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             999999999999999998399988999999
Q gi|254780191|r  731 ARSHLMGQDEKLKSLASFLKVSQGNVVGRV  760 (898)
Q Consensus       731 A~~~~~~~~~~l~~la~~L~~~~~~i~~ki  760 (898)
                      +..-+-+...++-.++=.-++|.++++++.
T Consensus      1017 ~~~slmnafAiaISigLQyGVPLee~V~~f 1046 (1177)
T PRK07562       1017 AFRSLMNNFAIAVSLGLQYGVPLEEYVDAF 1046 (1177)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             679999999999999743189989999985


No 45 
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type; InterPro: IPR004635   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. This group of sequences represent both long and short forms of the bacterial SppA and homologs found in the archaea and plants.   Signal peptides of secretory proteins seem to serve at least two important biological functions. First, they are required for protein targeting to and translocation across membranes, such as the eubacterial plasma membrane and the endoplasmic reticular membrane of eukaryotes. Second, in addition to their role as determinants for protein targeting and translocation, certain signal peptides have a signaling function.  During or shortly after pre-protein translocation, the signal peptide is removed by signal peptidases. The integral membrane protein, SppA (protease IV), of Escherichia coli was shown experimentally to degrade signal peptides. The member of this family from Bacillus subtilis has only been shown to be required for efficient processing of pre-proteins under conditions of hyper-secretion . ; GO: 0008233 peptidase activity, 0006508 proteolysis.
Probab=86.60  E-value=1.2  Score=23.80  Aligned_cols=91  Identities=19%  Similarity=0.271  Sum_probs=64.1

Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHCCCCCCCCCCEE
Q ss_conf             9998487433104568999998645555557-64678899998748989999998999--99999861154642457437
Q gi|254780191|r  311 YARLLGYTEPLMMHLLPALCTEMGSAYPELI-QAKLLIEETLRSEDERFGKTLDRGLV--LLDGVLSHLGKDEILNGDVA  387 (898)
Q Consensus       311 ~~~~lg~~~~fl~~lv~~v~~~m~~~ypeL~-~~~~~I~~ii~~EE~~F~~TL~~G~~--~l~~~i~~~~~~~~lsg~~a  387 (898)
                      +..++|++..-+..  .. -..|+..|-+|. +.++.+++.|+++-+.|-++..+++.  +=.+.++++..+++++|.+|
T Consensus       124 L~~k~GI~~~~iK~--G~-yKd~~~~~R~lt~eE~~~lQ~~v~~~Y~~F~~~V~~~R~nkl~~~~vK~~AdGRvf~GrqA  200 (224)
T TIGR00706       124 LLEKLGIEFEAIKS--GE-YKDIGSPTRELTPEERKILQSLVNESYEQFVQVVAKGRNNKLSVEDVKKFADGRVFTGRQA  200 (224)
T ss_pred             HHHHCCCEEEEEEC--CC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCEECHHHH
T ss_conf             99864915656651--66-5678987577629999999998888875789999984167789788765206860104334


Q ss_pred             EEE--ECCCCCCHHHHHHH
Q ss_conf             998--52458888999987
Q gi|254780191|r  388 FKL--YDTHGLPLDIMQDI  404 (898)
Q Consensus       388 f~L--yDTyGfP~dlt~ei  404 (898)
                      -+|  -|+-|.--+=.+.+
T Consensus       201 ~~l~LVD~lG~~d~A~~~l  219 (224)
T TIGR00706       201 LKLRLVDKLGTLDDALKWL  219 (224)
T ss_pred             HHCCCEECCCCHHHHHHHH
T ss_conf             3114600128989999999


No 46 
>KOG1637 consensus
Probab=86.51  E-value=0.23  Score=29.52  Aligned_cols=25  Identities=20%  Similarity=0.224  Sum_probs=13.6

Q ss_pred             EEEECCC-CEEECCCCCCCCCCEEEE
Q ss_conf             9997375-200036876566514540
Q gi|254780191|r  512 EVVFDQT-PFYAEAGGQLGDTGCAIG  536 (898)
Q Consensus       512 ~ivLd~T-~FY~E~GGQ~~D~G~i~~  536 (898)
                      .+++... -=|-|-+=-.+|.|.|..
T Consensus       259 cLmf~~r~rS~reLPlR~aDFg~LHR  284 (560)
T KOG1637         259 CLMFAHRDRSYRELPLRFADFGVLHR  284 (560)
T ss_pred             CCCCCCCCCCHHHCCCCCCCCCEEEE
T ss_conf             01336677427447842267522530


No 47 
>TIGR00457 asnS asparaginyl-tRNA synthetase; InterPro: IPR004522   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   AsparaginyltRNA synthetase (6.1.1.22 from EC) is an alpha2 dimer that belongs to class IIb. There is a striking similarity between asparaginyl-tRNA synthetases and archaeal/eukaryotic type aspartyl-tRNA synthetases (IPR004523 from INTERPRO) and a striking divergence of bacterial type aspartyl-tRNA synthetases (IPR004524 from INTERPRO). This family, AsnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.; GO: 0000166 nucleotide binding, 0004816 asparagine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006421 asparaginyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=86.02  E-value=2  Score=22.17  Aligned_cols=31  Identities=26%  Similarity=0.324  Sum_probs=12.1

Q ss_pred             EEEEEECCCCEEEEEEEECHHHHCCCCHHHHH
Q ss_conf             99999538981799998677897267989999
Q gi|254780191|r  825 IMLVGISKEKKASVLIVVTEDLLDRFNAVDLA  856 (898)
Q Consensus       825 vvL~~~~~~~k~~ivv~vs~~~~~~~~A~~li  856 (898)
                      |++.-=..+=|+.++=..|+| .+-+.|.||+
T Consensus       380 vfV~~YPk~~KaFYMk~NS~D-~~tV~a~DlL  410 (495)
T TIGR00457       380 VFVTDYPKDIKAFYMKLNSDD-GKTVAAVDLL  410 (495)
T ss_pred             EEEECCCCCCCCHHCCCCCCC-CCEEEEEEEE
T ss_conf             899738855580105366788-8747899983


No 48 
>COG0104 PurA Adenylosuccinate synthase [Nucleotide transport and metabolism]
Probab=81.35  E-value=3.8  Score=19.99  Aligned_cols=168  Identities=19%  Similarity=0.157  Sum_probs=79.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCC---------CCCCCCHHHHHHHHHHH
Q ss_conf             047887565766531017579999999887985300576999999999730678---------54335024899999898
Q gi|254780191|r  210 QQNKQERFILPKMSIDTGMGLERMATVLQEKTNNYDIDLFKHLIQASEQVTGMK---------YEGNNIVNHRVIVDHLR  280 (898)
Q Consensus       210 ~~~~g~~~~Lp~~~IDTGmGLERl~~vlqg~~s~ydtD~f~pii~~i~~~~g~~---------y~~~~~~~~rvIaDH~R  280 (898)
                      -.+.|-+.|=-.-.|-.||              +-+-+.|..=++.+++. |+.         +...-.+.|-+-.|.+|
T Consensus        54 LiPSGil~~~~~~vIGnGv--------------VvdP~~L~~Ei~~L~~~-g~~~~~~rL~Is~~ahlIlpyH~~lD~~~  118 (430)
T COG0104          54 LIPSGILRPGATLVIGNGV--------------VVDPEVLLKEIEELEER-GVDVVRDRLRISDRAHLILPYHIELDRAR  118 (430)
T ss_pred             ECCCCCCCCCCEEEECCCE--------------EECHHHHHHHHHHHHHC-CCCCCCCEEEECCCCCCCCHHHHHHHHHH
T ss_conf             6664456799658863867--------------88799999999999864-88666010787367662437789875531


Q ss_pred             HHHHHHHHCCCCCCCCCCH---HHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999874033334446412---57788999999999848743--310456899999864555555764678899998748
Q gi|254780191|r  281 SSSFLIADGILPANEGRGY---VLRRIMRRAMCYARLLGYTE--PLMMHLLPALCTEMGSAYPELIQAKLLIEETLRSED  355 (898)
Q Consensus       281 a~~f~I~DGv~PsN~GrGY---vlRrilRRa~r~~~~lg~~~--~fl~~lv~~v~~~m~~~ypeL~~~~~~I~~ii~~EE  355 (898)
                      -..-.  + --=+-+|||-   -.-|+.||++|.+.++..+.  ..|..+.+..-..+...|-.-.-..+.|.+.+..--
T Consensus       119 E~~~~--~-~kIGTTgrGIGPaY~DKv~R~giRv~DL~d~~~l~~kle~~~~~~n~~l~~~y~~~~~~~~~~~~~~~~~~  195 (430)
T COG0104         119 EKALG--K-KKIGTTGRGIGPAYEDKVARRGIRVGDLLDPETLREKLERLLEYKNFQLVKYYGAEAVDFEDILDEYYEYA  195 (430)
T ss_pred             HHHCC--C-CCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf             65437--8-74557888637002456765311256523878899999999987778888750766333899999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCC
Q ss_conf             98999999899999999861154642457437998524588
Q gi|254780191|r  356 ERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGL  396 (898)
Q Consensus       356 ~~F~~TL~~G~~~l~~~i~~~~~~~~lsg~~af~LyDTyGf  396 (898)
                      +++..-+..-..++++.++. .++=.+-|.+.+.|-=-||.
T Consensus       196 ~~l~~~v~D~~~~l~~a~~~-g~~VLfEGAQG~lLDidhGT  235 (430)
T COG0104         196 ERLKPYVTDVSVLLNDALDA-GKRVLFEGAQGTLLDIDHGT  235 (430)
T ss_pred             HHHCCHHHHHHHHHHHHHHC-CCEEEEECCCCCEECCCCCC
T ss_conf             86324233169999999975-98599973753033456785


No 49 
>KOG1759 consensus
Probab=80.79  E-value=1.8  Score=22.53  Aligned_cols=28  Identities=36%  Similarity=0.563  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHCCCCHHHEEEEECCCH
Q ss_conf             9998998613341898123799971882
Q gi|254780191|r  106 AIQLAWDLLTKEFDLDQRRLYITVYDED  133 (898)
Q Consensus       106 ai~~awe~lt~~~~l~~~~l~vtv~~~D  133 (898)
                      -..--.|||.+.|+|||+|+|+++|.-+
T Consensus        76 ~sa~l~~il~~~L~l~~~rv~I~f~dl~  103 (115)
T KOG1759          76 YSAALTEILEKELSLDPDRVYIKFYDLN  103 (115)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEEEECCC
T ss_conf             9999999999870889786999995288


No 50 
>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed
Probab=78.12  E-value=1.3  Score=23.51  Aligned_cols=26  Identities=31%  Similarity=0.566  Sum_probs=16.8

Q ss_pred             HHCCCCCEEEEEECCCCCCCCCEECCCCCC
Q ss_conf             315556248998447677855310156222
Q gi|254780191|r  669 GTKYNDRVRVVSVEYEDGGVHSSALCGGTH  698 (898)
Q Consensus       669 gekygd~VRVV~I~~~d~~~~S~ElCGGTH  698 (898)
                      |+-+|-+|+|.-++...+    .-|||..-
T Consensus       397 g~~~gr~i~V~v~E~Een----~kL~GPa~  422 (527)
T PRK06253        397 GEIFGRNVKVSVEEPEEN----TKLCGPAA  422 (527)
T ss_pred             CCCCCCEEEEEEECCCCC----CCCCCHHH
T ss_conf             310480689999646788----86657367


No 51 
>pfam01187 MIF Macrophage migration inhibitory factor (MIF).
Probab=75.66  E-value=2  Score=22.07  Aligned_cols=28  Identities=36%  Similarity=0.654  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHCCCCHHHEEEEECCCH
Q ss_conf             9998998613341898123799971882
Q gi|254780191|r  106 AIQLAWDLLTKEFDLDQRRLYITVYDED  133 (898)
Q Consensus       106 ai~~awe~lt~~~~l~~~~l~vtv~~~D  133 (898)
                      -..--.+|+.+.||+|++|+|+.++.-+
T Consensus        75 ~s~~l~~~l~~~LgI~~~RiyI~F~d~~  102 (114)
T pfam01187        75 HSALLFKFLTKELGLPKDRIYIRFFDLE  102 (114)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEEEEECC
T ss_conf             9999999999862979464999999699


No 52 
>KOG2783 consensus
Probab=75.10  E-value=3  Score=20.83  Aligned_cols=14  Identities=14%  Similarity=0.385  Sum_probs=5.8

Q ss_pred             CCCHHHHHHHHHHH
Q ss_conf             99978999999999
Q gi|254780191|r  803 EVDSKELKSVMDAL  816 (898)
Q Consensus       803 ~~d~~~Lr~l~d~l  816 (898)
                      +.+.++.-+++..+
T Consensus       361 ~f~endf~~viR~V  374 (436)
T KOG2783         361 GFDENDFYDVIRTV  374 (436)
T ss_pred             CCCHHHHHHHHHHH
T ss_conf             88825899999987


No 53 
>TIGR00469 pheS_mito phenylalanyl-tRNA synthetase; InterPro: IPR004530   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases .   This family describes the mitochondrial phenylalanyl-tRNA synthetases. Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases.; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=70.41  E-value=2.5  Score=21.37  Aligned_cols=40  Identities=15%  Similarity=0.227  Sum_probs=17.3

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCEEE--EEEECCCCEEEEEEEE
Q ss_conf             999789999999999754997899--9995389817999986
Q gi|254780191|r  803 EVDSKELKSVMDALQKKIQSGIIM--LVGISKEKKASVLIVV  842 (898)
Q Consensus       803 ~~d~~~Lr~l~d~l~~k~~~~vvv--L~~~~~~~k~~ivv~v  842 (898)
                      +..+++|.+++-.+...+=+.|-+  -+.-.+.||-+++.-+
T Consensus       386 ~~~~NDl~~~~R~~AGDlVE~~~LVD~F~HPKTG~~S~CyRI  427 (460)
T TIGR00469       386 QVSENDLYDLVRSVAGDLVESVKLVDKFKHPKTGKKSVCYRI  427 (460)
T ss_pred             CCCCCHHHHHHHHHHCCEEEEEEEEECCCCCCCCCCCEEEEE
T ss_conf             688334899998751340335677641358888873135886


No 54 
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=69.87  E-value=4.2  Score=19.65  Aligned_cols=39  Identities=8%  Similarity=0.078  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCEEEEEEEECH
Q ss_conf             7999789999999999754997899999538981799998677
Q gi|254780191|r  802 SEVDSKELKSVMDALQKKIQSGIIMLVGISKEKKASVLIVVTE  844 (898)
Q Consensus       802 ~~~d~~~Lr~l~d~l~~k~~~~vvvL~~~~~~~k~~ivv~vs~  844 (898)
                      ++++....|.++    ++...+.+++..-..+-|+.+.--.++
T Consensus       303 dDl~~e~Er~l~----e~~~~~~vfv~~yP~~~kpFYm~~~~d  341 (435)
T COG0017         303 DDLGTEHERYLG----EEYFKPPVFVTNYPKEIKPFYMRPDPD  341 (435)
T ss_pred             CCCCCHHHHHHH----HHHCCCCEEEEECCCCCCCCCCCCCCC
T ss_conf             756889999999----875799499981764446650333799


No 55 
>smart00788 Adenylsucc_synt Adenylosuccinate synthetase. Adenylosuccinate synthetase plays an important role in purine biosynthesis, by catalyzing the GTP-dependent conversion of IMP and aspartic acid to AMP. Adenylosuccinate synthetase has been characterized from various sources ranging from Escherichia coli (gene purA) to vertebrate tissues. In vertebrates, two isozymes are present - one involved in purine biosynthesis and the other in the purine nucleotide cycle. The crystal structure of adenylosuccinate synthetase from E. coli reveals that the dominant structural element of each monomer of the homodimer is a central beta-sheet of 10 strands. The first nine strands of the sheet are mutually parallel with right-handed crossover connections between the strands. The 10th strand is antiparallel with respect to the first nine strands. In addition, the enzyme has two antiparallel beta-sheets, comprised of two strands and three strands each, 11 alpha-helices and two short 3/10-helices. Furt
Probab=69.81  E-value=5.6  Score=18.63  Aligned_cols=173  Identities=20%  Similarity=0.165  Sum_probs=80.4

Q ss_pred             HCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHC--CCCCCCC--------CCHHHHHHHHH
Q ss_conf             3047887565766531017579999999887985300576999999999730--6785433--------50248999998
Q gi|254780191|r  209 EQQNKQERFILPKMSIDTGMGLERMATVLQEKTNNYDIDLFKHLIQASEQVT--GMKYEGN--------NIVNHRVIVDH  278 (898)
Q Consensus       209 ~~~~~g~~~~Lp~~~IDTGmGLERl~~vlqg~~s~ydtD~f~pii~~i~~~~--g~~y~~~--------~~~~~rvIaDH  278 (898)
                      ...+.|.+.|=-.-.|-.||              +-|-.   -++++++.+.  |+...+.        -.+.|-+..|-
T Consensus        51 hllPSGi~~~~~~~vIG~Gv--------------Vidp~---~L~~Ei~~L~~~gi~~~~rL~IS~rahli~P~H~~lD~  113 (421)
T smart00788       51 HLLPSGILNPNKKCVIGNGV--------------VIDPE---ALFKEIDQLEAKGVDVRDRLFISDRAHLILPYHIALDK  113 (421)
T ss_pred             EECCCEECCCCCEEEECCCE--------------EECHH---HHHHHHHHHHHCCCCCCCCEEECCCCCCCCCHHHHHHH
T ss_conf             71783513799607877968--------------98599---99999999996289985488986874448831488889


Q ss_pred             HHHHHHHHHHCCCCCCCCCCH---HHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             989999874033334446412---57788999999999848743--3104568999998645555557646788999987
Q gi|254780191|r  279 LRSSSFLIADGILPANEGRGY---VLRRIMRRAMCYARLLGYTE--PLMMHLLPALCTEMGSAYPELIQAKLLIEETLRS  353 (898)
Q Consensus       279 ~Ra~~f~I~DGv~PsN~GrGY---vlRrilRRa~r~~~~lg~~~--~fl~~lv~~v~~~m~~~ypeL~~~~~~I~~ii~~  353 (898)
                      +|-..-  ++..+ +-.|||-   ...++.||++|.+.++..+.  .-|..+++..-..+...|..-.-+.+.+.+.+..
T Consensus       114 ~~E~~~--g~~~I-GTTgrGIGPaY~DK~~R~giR~~DL~~~~~l~~kl~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  190 (421)
T smart00788      114 LREKAR--GKKKI-GTTGRGIGPAYEDKVARRGIRVGDLFDEDVFREKLEELLDYKNFLLKKLYGAEPVDVEEILEELLE  190 (421)
T ss_pred             HHHHHH--CCCCC-CCCCCCCCHHHHHHCCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf             999973--88755-666777326664011334552132429888999999999999999986348888999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHH
Q ss_conf             4898999999899999999861154642457437998524588889999
Q gi|254780191|r  354 EDERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLDIMQ  402 (898)
Q Consensus       354 EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsg~~af~LyDTyGfP~dlt~  402 (898)
                      --+++..-+..-...+++.+++ +++=.+-|.+.+.|---||+-|=.|.
T Consensus       191 ~~~~l~~~i~dt~~~l~~a~~~-gk~ILfEGAQG~lLDid~GtYP~VTS  238 (421)
T smart00788      191 YAERLKPYVVDVSELLNDALKA-GKKVLFEGAQGTLLDIDHGTYPYVTS  238 (421)
T ss_pred             HHHHHHHHEECHHHHHHHHHHC-CCEEEEECCCEEEECCCCCCCCCCCC
T ss_conf             9999751362599999999977-99599952630455046687777465


No 56 
>TIGR01677 pln_FAD_oxido plant-specific FAD-dependent oxidoreductase; InterPro: IPR010030   This entry identifies a family of uncharacterised plant-specific FAD-dependent oxidoreductases. At least seven distinct members are found in Arabidopsis thaliana. The family shows considerable sequence similarity to three different enzymes of ascorbic acid biosynthesis: L-galactono-1,4-lactone dehydrogenase (1.3.2.3 from EC) from higher plants, D-arabinono-1,4-lactone oxidase (1.1.3.37 from EC) from Saccharomyces cerevisiae, and L-gulonolactone oxidase (1.1.3.8 from EC) from mouse, as well as to a bacterial sorbitol oxidase. The class of compound acted on by members of this family is unknown..
Probab=69.08  E-value=4.3  Score=19.56  Aligned_cols=34  Identities=24%  Similarity=0.248  Sum_probs=27.6

Q ss_pred             CCCEECCCEEEEECCCCCC-------CCHHHHHHHHHHHHH
Q ss_conf             5530024300000247678-------999999999999989
Q gi|254780191|r  608 NGSCITPDGLRFDVTHSKP-------ITSAELKSIEDNVND  641 (898)
Q Consensus       608 ~GS~v~~~~lrfDfsh~~~-------lt~eel~~IE~~vN~  641 (898)
                      +|-=...|.+=||||+|++       |.+|-++|||+++==
T Consensus       436 aGGGq~~d~v~~D~~YYRA~D~~~pRL~~Dv~EEiEQ~A~~  476 (577)
T TIGR01677       436 AGGGQEEDAVVFDFTYYRAKDPLTPRLYEDVLEEIEQMAFV  476 (577)
T ss_pred             CCCCCCCCEEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             88788656488511244158777866135589988865620


No 57 
>COG1244 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=69.06  E-value=7.5  Score=17.68  Aligned_cols=104  Identities=22%  Similarity=0.395  Sum_probs=71.7

Q ss_pred             CCCCCCCCCCCCHH----HHHHHHCCCCCCCHHHHHHHHHHHHHHHC--CCC---CC---CCCCHHHHHHHHHHHHHHHH
Q ss_conf             57665310175799----99999887985300576999999999730--678---54---33502489999989899998
Q gi|254780191|r  218 ILPKMSIDTGMGLE----RMATVLQEKTNNYDIDLFKHLIQASEQVT--GMK---YE---GNNIVNHRVIVDHLRSSSFL  285 (898)
Q Consensus       218 ~Lp~~~IDTGmGLE----Rl~~vlqg~~s~ydtD~f~pii~~i~~~~--g~~---y~---~~~~~~~rvIaDH~Ra~~f~  285 (898)
                      -|+-+.++.|.|||    ++.-..-++-++|.     ..+++++.+.  |.+   |-   -....--..|.|-++++. +
T Consensus       159 il~gk~~EvaIGLETanD~ire~sINKGftF~-----df~~A~~~ir~~g~~vktYlllKP~FlSE~eAI~D~i~Si~-~  232 (358)
T COG1244         159 ILEGKIVEVAIGLETANDKIREDSINKGFTFE-----DFVRAAEIIRNYGAKVKTYLLLKPPFLSEKEAIEDVISSIV-A  232 (358)
T ss_pred             HHCCCEEEEEEECCCCCHHHHHHHHHCCCCHH-----HHHHHHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHHHHHH-H
T ss_conf             60895389997124474889987651388689-----99999999997497515788831653476889999999999-7


Q ss_pred             HHHCC-----CCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             74033-----33444641257788999999999848743310456899999864
Q gi|254780191|r  286 IADGI-----LPANEGRGYVLRRIMRRAMCYARLLGYTEPLMMHLLPALCTEMG  334 (898)
Q Consensus       286 I~DGv-----~PsN~GrGYvlRrilRRa~r~~~~lg~~~~fl~~lv~~v~~~m~  334 (898)
                      ..+|.     -|.|+-+|-++-.+-||..       ...|.|-.++.++.+.++
T Consensus       233 ~~~~~d~iSinptnVqKgTlvE~lw~~g~-------YRPPwLWSivEVL~~~~~  279 (358)
T COG1244         233 AKPGTDTISINPTNVQKGTLVEKLWRRGL-------YRPPWLWSIVEVLREAKK  279 (358)
T ss_pred             HCCCCCEEEECCCCCCHHHHHHHHHHCCC-------CCCCHHHHHHHHHHHHHH
T ss_conf             43678758844542213109999997378-------789557799999999985


No 58 
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=68.83  E-value=1  Score=24.49  Aligned_cols=20  Identities=20%  Similarity=0.331  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHHHCCCEECC
Q ss_conf             89999999999978988911
Q gi|254780191|r    5 SSIRTTFLEFFQKNGHELLP   24 (898)
Q Consensus         5 ~eiR~~fl~fF~~~~H~~~~   24 (898)
                      -++|.+=|+=..+.|-..+|
T Consensus         7 ~~~r~~kl~~l~~~g~~pyp   26 (491)
T PRK00484          7 IAVRREKLAELREEGINPYP   26 (491)
T ss_pred             HHHHHHHHHHHHHCCCCCCC
T ss_conf             99999999999974999999


No 59 
>TIGR00016 ackA acetate kinase; InterPro: IPR004372 Acetate kinase is involved in the activation of acetate to acetyl CoA and in the secretion of acetate. It catalyzes the reaction ATP + acetate = ADP + acetyl phosphate.; GO: 0016301 kinase activity, 0016774 phosphotransferase activity carboxyl group as acceptor, 0006082 organic acid metabolic process.
Probab=68.31  E-value=4.3  Score=19.52  Aligned_cols=34  Identities=18%  Similarity=0.157  Sum_probs=18.3

Q ss_pred             CCCCCCCCCEEEEEEEC---HHHHHHHHHHH-HHHHHHHHHHC
Q ss_conf             01212688289999716---89999999999-99999999839
Q gi|254780191|r  712 SESSIRAGIRRIEAITG---QRARSHLMGQD-EKLKSLASFLK  750 (898)
Q Consensus       712 se~si~sGvRRIeavtG---~~A~~~~~~~~-~~l~~la~~L~  750 (898)
                      =-|+..=|+|     +|   ++.+.|+.++. ...+++.+.|+
T Consensus       246 PLEGL~MGTR-----SGdIDPAii~y~~~~~~~s~~~i~~~LN  283 (416)
T TIGR00016       246 PLEGLVMGTR-----SGDIDPAIISYLAETLGMSADDIENTLN  283 (416)
T ss_pred             HHHHHCCCCC-----CCCCCHHHHHHHHHHHCCCHHHHHHHHC
T ss_conf             1465013424-----4740179999999872898889998750


No 60 
>PRK09982 universal stress protein UspD; Provisional
Probab=68.02  E-value=7  Score=17.90  Aligned_cols=56  Identities=18%  Similarity=0.111  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Q ss_conf             78899999999984874331045689999986455555576-46788999987489899999
Q gi|254780191|r  302 RRIMRRAMCYARLLGYTEPLMMHLLPALCTEMGSAYPELIQ-AKLLIEETLRSEDERFGKTL  362 (898)
Q Consensus       302 RrilRRa~r~~~~lg~~~~fl~~lv~~v~~~m~~~ypeL~~-~~~~I~~ii~~EE~~F~~TL  362 (898)
                      .++++||+..++.++.+-.|++=-+     .+.+.||++.. +.+.+...+..|-..|.+.|
T Consensus        17 ~~Li~KAv~lAk~~~AklSlIhvd~-----~~~elY~gl~~~~~~~~~~~~~e~~~~~L~~L   73 (142)
T PRK09982         17 ALLVNKALELARHNDAHLTLIHIDD-----GLSELYPGIYFPATEDILQLLKNKSDNKLYKL   73 (142)
T ss_pred             HHHHHHHHHHHHHCCCEEEEEEEEC-----CCHHHCCHHCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999876098399999908-----84665110205312568899999999999999


No 61 
>PRK11649 hypothetical protein; Provisional
Probab=66.38  E-value=8.4  Score=17.29  Aligned_cols=108  Identities=12%  Similarity=0.164  Sum_probs=66.1

Q ss_pred             CCCCEEECCCCCCCCCCEEEECCEEEEEECCCCCCCEEEEEEECCCCCCCCCCCEEE-----EEEHHHHHHHHHHCCCHH
Q ss_conf             375200036876566514540424898522456553389985104678755673388-----842125567775201368
Q gi|254780191|r  516 DQTPFYAEAGGQLGDTGCAIGDGIRLQITDVQKKAEGIFVHHAIVERGILRTEMSLV-----LTIDYQNRRQLSINHSAT  590 (898)
Q Consensus       516 d~T~FY~E~GGQ~~D~G~i~~~~~~~~V~dv~k~~~g~i~H~~~~~~g~l~~g~~V~-----~~VD~~rR~~~~~~HTat  590 (898)
                      --||-||-+-|.+--.|+-.+.+..+.+.    .++++...++.+.+-.++.|+.|.     +.|-.      .=.-|+-
T Consensus       301 ~GTPV~A~~dG~V~~ag~~~~yG~~V~I~----H~~~~~T~Y~HLs~~~V~~Gq~V~~Gq~Ig~vGs------TG~sTGP  370 (418)
T PRK11649        301 QGTPVLSVGDGEVVVAKRSGAAGNYVAIR----HGRQYTTRYMHLRKLLVKPGQKVKRGDRIALSGN------TGRSTGP  370 (418)
T ss_pred             CCCEEEEECCEEEEEEEECCCCCCEEEEE----CCCCEEEEEECCCCCCCCCCCEECCCCEEEEECC------CCCCCCC
T ss_conf             89989852487999978818999779998----1993099961768477799499998998980268------8378897


Q ss_pred             HHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             899999752125444445530024300000247678999999999999989887
Q gi|254780191|r  591 HLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIA  644 (898)
Q Consensus       591 HlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~  644 (898)
                      | ||.        .++..|-.|+|=.  .++.-.++|+..++.+-...+.+++.
T Consensus       371 H-LHy--------Ev~~ng~~vnPl~--vklP~~~~l~~~e~~~F~~~~~~~~~  413 (418)
T PRK11649        371 H-LHY--------EVWINQQAVNPLT--AKLPRTEGLTGSDRREYLAQVKEVVP  413 (418)
T ss_pred             E-EEE--------EEEECCEECCCCC--CCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             3-389--------9999997959953--46889997898999999999999999


No 62 
>pfam00587 tRNA-synt_2b tRNA synthetase class II core domain (G, H, P, S and T). Other tRNA synthetase sub-families are too dissimilar to be included. This domain is the core catalytic domain of tRNA synthetases and includes glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases.
Probab=64.94  E-value=6.6  Score=18.12  Aligned_cols=104  Identities=21%  Similarity=0.346  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECC--------CCCCCC-----CCC-CCCC---------------
Q ss_conf             89999999999978988911667566778710023014--------347554-----005-8879---------------
Q gi|254780191|r    5 SSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSG--------MVPFKN-----IFT-GQEK---------------   55 (898)
Q Consensus         5 ~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Ag--------m~~fk~-----~f~-G~~~---------------   55 (898)
                      +.|-+.+++.|++.|+..|..-.+.+.   +++.. +|        |..|++     +.| ....               
T Consensus         3 ~~l~~~~~~~~~~~G~~~i~tP~l~~~---~~~~~-sg~~~~~~~~my~~~d~~~~~l~Lrp~~~~~~~~~~~~~~~~~~   78 (170)
T pfam00587         3 NALENFIRDLFKRYGYQEVDTPILEPK---ELWEG-SGHWDDYFDEMYRFKDRGGEELYLRPTAEVGITRLFKNEILSYR   78 (170)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCEEEEH---HHHHH-CCCCCCCHHHEEEEECCCCCEEEEECCCCHHHHHHHHHHCCCCC
T ss_conf             999999999999859989999917567---89834-47765575312567358997688732574588899886200323


Q ss_pred             -CCCCCCCCCCCCEECCCCCCCH-HHCCCCCCCHHHHHHHHHHHHCCC-----CHHHHHHHHHHHHHHHCCCC
Q ss_conf             -9999851115432248987863-434648850017888542231475-----37889998998613341898
Q gi|254780191|r   56 -PVYQAVTTVQKCVRAGGKHNDL-DNVGRTNRHHTFFEMLGNFSFGGY-----FKERAIQLAWDLLTKEFDLD  121 (898)
Q Consensus        56 -p~~~r~~~~QkCiR~ggkhnDl-d~VG~t~rH~TfFEMlGn~SfgdY-----fK~eai~~awe~lt~~~~l~  121 (898)
                       .| .|++..++|.|.     .. +.=|. .|-|- |.|.+-++||.-     .=.|.|..+.+++ +.||||
T Consensus        79 ~lP-~r~~~~~~~fR~-----E~~~~~Gl-~R~re-F~q~d~~~~~~~e~s~~~~~e~~~~~~~~~-~~lgl~  142 (170)
T pfam00587        79 DLP-LKLYQIGPCFRY-----EARPRRGL-GRVRE-FTQVDAEIFGTPEQSEEEDEELLKLAEEIL-QDLGLP  142 (170)
T ss_pred             CCC-CEEECCCCCCCC-----CCCCCCCC-CEEEE-EEEECEEEEECCCHHHHHHHHHHHHHHHHH-HHCCCC
T ss_conf             586-013306530067-----77766677-43678-898047999670042999999999999999-987996


No 63 
>PRK09275 aspartate aminotransferase; Provisional
Probab=64.21  E-value=9.1  Score=17.00  Aligned_cols=98  Identities=22%  Similarity=0.402  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCHHH------------HHHHHHHHHHHH-HHCCCC-CCHHHHHHHHHHHHHHHHHHH
Q ss_conf             999898999987403333444641257------------788999999999-848743-310456899999864555555
Q gi|254780191|r  275 IVDHLRSSSFLIADGILPANEGRGYVL------------RRIMRRAMCYAR-LLGYTE-PLMMHLLPALCTEMGSAYPEL  340 (898)
Q Consensus       275 IaDH~Ra~~f~I~DGv~PsN~GrGYvl------------RrilRRa~r~~~-~lg~~~-~fl~~lv~~v~~~m~~~ypeL  340 (898)
                      +.+--|+....-.=|-+|.-+|-..=.            =..|++++.|++ .+|++. .|++++++.+   +|+.||-=
T Consensus        61 ~~Es~r~~~~~~~lgG~p~~~Gi~~Rf~~fl~~~~~~pG~~fL~~~~~y~~~~~g~d~d~~v~El~dgi---iGdnYPvP  137 (531)
T PRK09275         61 VEESRRSFSYPGGLGGMPQKEGIAERFETFLEEHKDVPGIDFLRAAISYVRDELGFDPDEFVYEMVDGI---IGDNYPVP  137 (531)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH---HCCCCCCC
T ss_conf             999998746568867875702299999999985899836899999999999886999889999999886---33889996


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCCCEEEEEECCCC
Q ss_conf             7646788999987489899999989999999986-115464245743799852458
Q gi|254780191|r  341 IQAKLLIEETLRSEDERFGKTLDRGLVLLDGVLS-HLGKDEILNGDVAFKLYDTHG  395 (898)
Q Consensus       341 ~~~~~~I~~ii~~EE~~F~~TL~~G~~~l~~~i~-~~~~~~~lsg~~af~LyDTyG  395 (898)
                      -.....+++|+                  ...+. ++-++...+|  -|.|+-|=|
T Consensus       138 ~RmL~~~E~Iv------------------~~YL~~em~~~~~~~~--~fdlFatEG  173 (531)
T PRK09275        138 DRMLVHTEKIV------------------KDYLRQEMCGNRPPPG--EFDLFAVEG  173 (531)
T ss_pred             HHHHHHHHHHH------------------HHHHHHHHCCCCCCCC--CCCEEECCC
T ss_conf             78889899999------------------9999999628999988--731674167


No 64 
>pfam05882 consensus
Probab=62.23  E-value=1.9  Score=22.37  Aligned_cols=45  Identities=20%  Similarity=0.248  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHHHHH--HHHHHHHHH---HHHH-HHHHHHHHHHHHHHHH
Q ss_conf             0456899999864555--555764678---8999-9874898999999899
Q gi|254780191|r  322 MMHLLPALCTEMGSAY--PELIQAKLL---IEET-LRSEDERFGKTLDRGL  366 (898)
Q Consensus       322 l~~lv~~v~~~m~~~y--peL~~~~~~---I~~i-i~~EE~~F~~TL~~G~  366 (898)
                      ++.-.|.....|||.|  .|++.+++.   ..-+ ...|=+.|..+|+.|.
T Consensus         8 lHr~LP~~~R~LGD~YVK~EFrrHk~~~~p~~~~~Fl~eW~~Y~~~L~~~~   58 (90)
T pfam05882         8 LHRGLPPDLRELGDQYVKDEFRRHKDADNPLHIIGFLSSWQDYLDQLEGQI   58 (90)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             882598899998889999999987368985999999999999999985012


No 65 
>pfam01343 Peptidase_S49 Peptidase family S49.
Probab=61.97  E-value=7.1  Score=17.85  Aligned_cols=47  Identities=11%  Similarity=0.188  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEE
Q ss_conf             76467889999874898999999899999999861154642457437
Q gi|254780191|r  341 IQAKLLIEETLRSEDERFGKTLDRGLVLLDGVLSHLGKDEILNGDVA  387 (898)
Q Consensus       341 ~~~~~~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsg~~a  387 (898)
                      .+.++.+...+..-...|.....+++.+-...+..+....+++|++|
T Consensus        82 ~e~r~~~~~~l~~~~~~F~~~Va~~R~~~~~~~~~~~~g~v~~g~~A  128 (154)
T pfam01343        82 PEEREALQRMLDETYQMFVQKVAKNRNLTVDQVDKIAEGRVWTGQQA  128 (154)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHH
T ss_conf             99999999999999999999999866999899999867998779999


No 66 
>TIGR01343 hacA_fam homoaconitate hydratase family protein; InterPro: IPR006251   3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus .    This entry represents the large subunit of 3-isopropylmalate dehydratase (LeuC), as well as homoaconitase, certain aconitases and uncharacterised proteins, and is a subgroup of those represented in IPR012095. Homoaconitase, aconitase and 3-isopropylmalate dehydratase have similar overall structures and domain organisation . All are dehydratases that bind a [4Fe-4S]-cluster. The majority of the members of this family have been designated as 3-isopropylmalate dehydratase large subunit (LeuC) in microbial genome annotation, but the only characterised member is T. thermophilus homoaconitase, an enzyme of a non-aspartate pathway of lysine biosynthesis.    Information about related proteins can be found at Protein of the Month: Aconitase .; GO: 0016836 hydro-lyase activity, 0051539 4 iron 4 sulfur cluster binding, 0008652 amino acid biosynthetic process.
Probab=61.68  E-value=10  Score=16.67  Aligned_cols=56  Identities=27%  Similarity=0.382  Sum_probs=33.8

Q ss_pred             CEEEEEEECCCCCCCCCCCEEEEEEHHHHHHHHHHCCCHHHHHHHHHHHC-----------CCCCCCCCCCEECCCEEEE
Q ss_conf             33899851046787556733888421255677752013688999997521-----------2544444553002430000
Q gi|254780191|r  551 EGIFVHHAIVERGILRTEMSLVLTIDYQNRRQLSINHSATHLLHHALSTI-----------LGSHVSQNGSCITPDGLRF  619 (898)
Q Consensus       551 ~g~i~H~~~~~~g~l~~g~~V~~~VD~~rR~~~~~~HTatHlL~~alr~v-----------LG~hv~Q~GS~v~~~~lrf  619 (898)
                      .| |.|.+..+.|-..+|+.|.+ =|         .||.||==-+|+=.=           .|+ +|    +.=||..||
T Consensus        97 eG-I~HqvL~E~glv~PG~~vvG-aD---------SHTCTyGA~GAFaTG~GsTD~A~a~A~Gk-~W----~rVPEs~~v  160 (432)
T TIGR01343        97 EG-ICHQVLPEEGLVKPGDLVVG-AD---------SHTCTYGALGAFATGVGSTDIAYAIATGK-VW----FRVPESIKV  160 (432)
T ss_pred             CC-CEEEEECCCCEECCCCEEEE-CC---------CCHHHHHHHHHHHCCCCHHHHHHHHHHCC-CE----EECCCEEEE
T ss_conf             54-16898326870067877993-47---------31223455765413744589999998286-10----215718999


Q ss_pred             ECC
Q ss_conf             024
Q gi|254780191|r  620 DVT  622 (898)
Q Consensus       620 Dfs  622 (898)
                      +|+
T Consensus       161 ~~~  163 (432)
T TIGR01343       161 QLT  163 (432)
T ss_pred             EEE
T ss_conf             988


No 67 
>KOG0121 consensus
Probab=57.80  E-value=11  Score=16.34  Aligned_cols=19  Identities=47%  Similarity=0.954  Sum_probs=12.2

Q ss_pred             HHHHHHCCCCHHHHHHHHHHHHHH
Q ss_conf             542231475378899989986133
Q gi|254780191|r   93 LGNFSFGGYFKERAIQLAWDLLTK  116 (898)
Q Consensus        93 lGn~SfgdYfK~eai~~awe~lt~  116 (898)
                      .||-||  |-+||.|   |||+.+
T Consensus        41 VgNlSf--yttEEqi---yELFs~   59 (153)
T KOG0121          41 VGNLSF--YTTEEQI---YELFSK   59 (153)
T ss_pred             EEEEEE--EECHHHH---HHHHHH
T ss_conf             952035--5309999---999983


No 68 
>TIGR00392 ileS isoleucyl-tRNA synthetase; InterPro: IPR002301   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .    Isoleucyl-tRNA synthetase (6.1.1.5 from EC) is an alpha monomer that belongs to class Ia. The enzyme, isoleucyl-transfer RNA synthetase, activates not only the cognate substrate L-isoleucine but also the minimally distinct L-valine in the first, aminoacylation step. Then, in a second, "editing" step, the synthetase itself rapidly hydrolyzes only the valylated products ,  as shown from the crystal structures. ; GO: 0000166 nucleotide binding, 0004822 isoleucine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006428 isoleucyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=57.14  E-value=5.5  Score=18.74  Aligned_cols=19  Identities=16%  Similarity=-0.073  Sum_probs=7.7

Q ss_pred             EHHHHHHHHHHCCCHHHHH
Q ss_conf             2125567775201368899
Q gi|254780191|r  575 IDYQNRRQLSINHSATHLL  593 (898)
Q Consensus       575 VD~~rR~~~~~~HTatHlL  593 (898)
                      .|-.|=+-.+++=+||++.
T Consensus       628 ~DQ~RGWFySsl~~~~~~~  646 (938)
T TIGR00392       628 SDQTRGWFYSSLLIGVALF  646 (938)
T ss_pred             CCCCCHHHHHHHHHHHHHH
T ss_conf             3555327799999999987


No 69 
>COG3981 Predicted acetyltransferase [General function prediction only]
Probab=56.21  E-value=9.5  Score=16.85  Aligned_cols=25  Identities=28%  Similarity=0.283  Sum_probs=15.2

Q ss_pred             EHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             2125567775201368899999752
Q gi|254780191|r  575 IDYQNRRQLSINHSATHLLHHALST  599 (898)
Q Consensus       575 VD~~rR~~~~~~HTatHlL~~alr~  599 (898)
                      |-..-|-.-.+.+-||++|--+|.+
T Consensus       101 IGY~VrPseR~KGYA~emLkl~L~~  125 (174)
T COG3981         101 IGYSVRPSERRKGYAKEMLKLALEK  125 (174)
T ss_pred             CCCEECHHHHCCCHHHHHHHHHHHH
T ss_conf             6411476352467899999999999


No 70 
>pfam04536 DUF477 Domain of unknown function (DUF477). The function of this presumed domain is unknown. It is found in both eukarya and eubacteria.
Probab=55.22  E-value=13  Score=15.89  Aligned_cols=94  Identities=14%  Similarity=0.259  Sum_probs=57.2

Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHHHHC-------CCCEEEEEEECCCCEEEEEEEECHHHHCCCCHHHHHHHHHHHHC
Q ss_conf             69527999957999789999999999754-------99789999953898179999867789726798999999998834
Q gi|254780191|r  792 ADVNFMSHIISEVDSKELKSVMDALQKKI-------QSGIIMLVGISKEKKASVLIVVTEDLLDRFNAVDLARLSAKVLG  864 (898)
Q Consensus       792 ~~~~~i~~~~~~~d~~~Lr~l~d~l~~k~-------~~~vvvL~~~~~~~k~~ivv~vs~~~~~~~~A~~lik~ia~~l~  864 (898)
                      .+..+.+..++..+...++..+..+.++.       .+++++|++ ..+.++.+..  ...+...+....|-+.+...+.
T Consensus        22 t~~ei~Vv~v~~~~~~~~~~~A~~~f~~~gig~~~~~nGvLilv~-~~~r~~~I~~--g~gle~~l~d~~~~~i~~~~~~   98 (124)
T pfam04536        22 TGGEIVVVTVPSLDGEDIEDYALRLFRAWGLGDTEKDNGVLLLVA-LNDRKVRIEV--GYGLEGKLPDARWDRIIDDTIV   98 (124)
T ss_pred             HCCEEEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEEE-ECCCEEEEEE--CHHHHCCCCHHHHHHHHHHHHH
T ss_conf             097599999706786538999999999808986577897799998-1687799997--7467523589999999999842


Q ss_pred             CCCCCCCCHHCCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             999999810114589998788999999999861
Q gi|254780191|r  865 GGGGGGRPHMAQSGGPNGNKADQAIAGVASFLK  897 (898)
Q Consensus       865 GGgGGGkpd~AQgGG~~~~~l~eal~~vk~~Lk  897 (898)
                             |.|.+|  .-...+..+++.+...|.
T Consensus        99 -------p~fk~g--~y~~g~~~~i~~i~~~l~  122 (124)
T pfam04536        99 -------PAFRQG--DYAEGLVAAIDAIGAVLA  122 (124)
T ss_pred             -------HHHHCC--CHHHHHHHHHHHHHHHHC
T ss_conf             -------887679--999999999999999873


No 71 
>TIGR02088 LEU3_arch isopropylmalate/isohomocitrate dehydrogenases; InterPro: IPR011828    This entry represents a group of archaeal decarboxylating dehydrogenases which include the leucine biosynthesis enzyme 3-isopropylmalate dehydrogenase (LeuB, LEU3) and the methanogenic cofactor CoB biosynthesis enzyme isohomocitrate dehydrogenase (AksF). Both of these have been characterised in Methanococcus janaschii . Sequences from the non-methanogenic archaea are also represented in this entry, presumably LeuB, although phylogenetic trees cannot establish which gene is which in the methanogens.; GO: 0003862 3-isopropylmalate dehydrogenase activity, 0051287 NAD binding, 0009098 leucine biosynthetic process.
Probab=54.96  E-value=13  Score=15.86  Aligned_cols=14  Identities=14%  Similarity=0.349  Sum_probs=9.7

Q ss_pred             CCCCCHHHHHHHHH
Q ss_conf             67899999999999
Q gi|254780191|r  624 SKPITSAELKSIED  637 (898)
Q Consensus       624 ~~~lt~eel~~IE~  637 (898)
                      -++|++|+|.+|++
T Consensus        48 G~Alpe~tl~~i~k   61 (350)
T TIGR02088        48 GSALPEDTLEEIKK   61 (350)
T ss_pred             CCCCCHHHHHHHHH
T ss_conf             89989768999962


No 72 
>cd03578 NTR_netrin-4_like NTR domain, Netrin-4-like subfamily; composed of the C-terminal NTR domains of netrin-4 (beta netrin) and similar proteins. Netrins are secreted proteins that function as tropic cues in the direction of axon growth and cell migration during neural development. Netrin-4 is a basement membrane component that is important in neural, kidney and vascular development. It may also be involved in regulating the outgrowth and shape of epithelial cells during lung branching morphogenesis.
Probab=54.25  E-value=11  Score=16.50  Aligned_cols=12  Identities=17%  Similarity=0.387  Sum_probs=6.2

Q ss_pred             EEECCCCEEECC
Q ss_conf             997375200036
Q gi|254780191|r  513 VVFDQTPFYAEA  524 (898)
Q Consensus       513 ivLd~T~FY~E~  524 (898)
                      |-=..+..||+|
T Consensus        44 i~RG~~~Lyp~S   55 (111)
T cd03578          44 LSRGKRTLYPES   55 (111)
T ss_pred             EECCCEEEEEEE
T ss_conf             404870476434


No 73 
>pfam04199 Cyclase Putative cyclase. Proteins in this family are thought to be cyclase enzymes. They are found in proteins involved in antibiotic synthesis. However they are also found in organisms that do not make antibiotics pointing to a wider role for these proteins. The proteins contain a conserved motif HXGTHXDXPXH that is likely to form part of the active site.
Probab=54.09  E-value=8.3  Score=17.33  Aligned_cols=61  Identities=21%  Similarity=0.248  Sum_probs=31.5

Q ss_pred             HHHCCCHHHH---HHHHHHHCCCCCCCCCCC--EECCCEEEEECCCC----CCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             7520136889---999975212544444553--00243000002476----7899999999999998988730
Q gi|254780191|r  583 LSINHSATHL---LHHALSTILGSHVSQNGS--CITPDGLRFDVTHS----KPITSAELKSIEDNVNDIIAQN  646 (898)
Q Consensus       583 ~~~~HTatHl---L~~alr~vLG~hv~Q~GS--~v~~~~lrfDfsh~----~~lt~eel~~IE~~vN~~I~~n  646 (898)
                      .|..||+||+   .|. ....-|..+.|-.-  ++++-. -+|+++.    ..+|.++|++.+. .+.-|.++
T Consensus        41 ~~~~H~GTHiDaP~Hf-~~~~~g~~id~~pl~~~ig~av-viDv~~~~~~~~~It~~dl~~~~~-~~~~i~~g  110 (162)
T pfam04199        41 TTSTHTGTHVDAPGHF-TFGPDGRSIDELPLEWFVGPGV-LLDVAHKLPPGYEITAEDLEAALK-QGGTIKPG  110 (162)
T ss_pred             EECCCCCCCCCCHHHH-CCCCCCCCCCCCCHHHHCCEEE-EEEEECCCCCCCCCCHHHHHHHHH-HCCCCCCC
T ss_conf             8347677464756451-3489987525479899728259-999525568997728999999998-65998888


No 74 
>TIGR00388 glyQ glycyl-tRNA synthetase, alpha subunit; InterPro: IPR002310   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   In eubacteria, glycyl-tRNA synthetase (6.1.1.14 from EC) is an alpha2/beta2 tetramer composed of 2 different subunits , , . In some eubacteria, in archaea and eukaryota, glycyl-tRNA synthetase is an alpha2 dimer (see IPR002315 from INTERPRO). It belongs to class IIc and is one of the most complex synthetases. What is most interesting is the lack of similarity between the two types: divergence at the sequence level is so great that it is impossible to infer descent from common genes. The alpha and beta subunits (see IPR002311 from INTERPRO) also lack significant sequence similarity. However, they are translated from a single mRNA , and a single chain glycyl-tRNA synthetase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain .; GO: 0000166 nucleotide binding, 0004820 glycine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006426 glycyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=53.62  E-value=13  Score=15.70  Aligned_cols=173  Identities=22%  Similarity=0.293  Sum_probs=91.4

Q ss_pred             CHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCEECCCCCCCHHHCC
Q ss_conf             87899999999999789889116675667787100230143475540-05887999998511154322489878634346
Q gi|254780191|r    3 NVSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNI-FTGQEKPVYQAVTTVQKCVRAGGKHNDLDNVG   81 (898)
Q Consensus         3 s~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~-f~G~~~p~~~r~~~~QkCiR~ggkhnDld~VG   81 (898)
                      +...+--+.-+|+.+.|+.++.++.+-           +|.-.+.|+ ++-...|.--.++-.++|-|-    .|= ..|
T Consensus         2 ~~~~~~~~~~~~w~~~gc~~~~p~d~~-----------~g~g~~~p~~~~~~~gp~p~~~~~~~p~~~p----~dg-~~g   65 (295)
T TIGR00388         2 TFQGLLLKLQEYWANQGCLLVQPYDVE-----------KGAGTLHPATFLRSLGPEPWSVAYVEPSRRP----TDG-RYG   65 (295)
T ss_pred             CHHHHHHHHHHHHHCCCCEEEECCCCC-----------CCCCCCCHHHHHHHCCCCCCEEEEECCCCCC----CCC-CCC
T ss_conf             358899998886410671464112332-----------2455220467876507652101000344576----666-567


Q ss_pred             CC---CCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHCCCCHHHEEECCCCC
Q ss_conf             48---850017888542231475378899989986133418981237999718828999975663499989975357866
Q gi|254780191|r   82 RT---NRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKLWKKISGLSADKIIRITTND  158 (898)
Q Consensus        82 ~t---~rH~TfFEMlGn~SfgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~iW~~~~gi~~~~i~~~~~~d  158 (898)
                      ..   -.|+--|+++-.-|=      +-|+-.+--..+.+|++|                         .++-+++  .+
T Consensus        66 ~~p~~~~~~~~~~~~~~p~p------~~~~~~~~~~~~~~g~~~-------------------------~~~d~~~--~~  112 (295)
T TIGR00388        66 ENPNRLGHYYQFQVVIKPSP------DNIQELYLDSLRALGIDP-------------------------TEHDIRF--VE  112 (295)
T ss_pred             CCHHHHHHEEEEEEEECCCC------CHHHHHHHHHHHHHCCCC-------------------------CCCCCEE--EC
T ss_conf             77013211002567861684------125787765566633773-------------------------2011000--00


Q ss_pred             CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHC
Q ss_conf             65457999998770467885385568988877788982689600112344304788756576653101757999999988
Q gi|254780191|r  159 NFWSMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLERMATVLQ  238 (898)
Q Consensus       159 NfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNlVFmq~~~~~~g~~~~Lp~~~IDTGmGLERl~~vlq  238 (898)
                      +-|+.-..|..|---|+..|-                  +|+-...+.|  +.  |.+.--| -.++.-+||||++..+|
T Consensus       113 d~w~~p~~g~wg~gw~~w~~g------------------~~~~~~~~~~--~~--gg~~c~p-~~~~~~~g~~~~~~~~~  169 (295)
T TIGR00388       113 DNWENPTLGAWGLGWEVWLDG------------------LEVTQFTYFQ--QV--GGLECKP-VSVEITYGLERLALYLQ  169 (295)
T ss_pred             CCCCCCCCCCCCCCHHHHCCC------------------CHHHHHHHHH--HH--CCCCCCC-CCEEHHHHHHHHHHHHH
T ss_conf             256775443122433222054------------------1123333344--30--6632243-21100221788888762


Q ss_pred             CCCCCCHHH
Q ss_conf             798530057
Q gi|254780191|r  239 EKTNNYDID  247 (898)
Q Consensus       239 g~~s~ydtD  247 (898)
                      ++.+.|+..
T Consensus       170 ~~~~~~~~~  178 (295)
T TIGR00388       170 GVENVLDLE  178 (295)
T ss_pred             HHHHHHHHH
T ss_conf             011233311


No 75 
>pfam06557 DUF1122 Protein of unknown function (DUF1122). This family consists of several hypothetical archaeal and bacterial proteins of unknown function.
Probab=52.66  E-value=14  Score=15.59  Aligned_cols=44  Identities=18%  Similarity=0.310  Sum_probs=21.2

Q ss_pred             CHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHCCCCHH
Q ss_conf             378899989986133418981237999718828999975663499989
Q gi|254780191|r  102 FKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKLWKKISGLSAD  149 (898)
Q Consensus       102 fK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~iW~~~~gi~~~  149 (898)
                      |..+.=..-+.|+-+.+ -|.++|||+|+.+-+..+++-   .|+|+.
T Consensus        60 ~~~~~E~~l~~l~~~~l-~pgg~lfVeY~~D~eT~~~L~---~G~pp~  103 (170)
T pfam06557        60 FGSGVEAELFDFLSDYL-PPGGRLFVEYVWDKETMYELQ---RGFPPA  103 (170)
T ss_pred             CCCHHHHHHHHHHHHHC-CCCCEEEEEEECCHHHHHHHH---CCCCCC
T ss_conf             37748899999999964-989749999962888999997---589942


No 76 
>cd07215 Pat17_PNPLA8_PNPLA9_like2 Patatin-like phospholipase of bacteria. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Members of this family have been found also in vertebrates. This family includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9 (iPLA2-beta) like phospholipases from human as well as the Pat17 isozyme from Solanum cardiophyllum.
Probab=52.23  E-value=14  Score=15.55  Aligned_cols=70  Identities=9%  Similarity=0.066  Sum_probs=50.2

Q ss_pred             EEEHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCC------CCCHHHHHHHHHHHHHHHHHC
Q ss_conf             84212556777520136889999975212544444553002430000024767------899999999999998988730
Q gi|254780191|r  573 LTIDYQNRRQLSINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSK------PITSAELKSIEDNVNDIIAQN  646 (898)
Q Consensus       573 ~~VD~~rR~~~~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~------~lt~eel~~IE~~vN~~I~~n  646 (898)
                      +.+.|.+..--+-...+++..+..++..++.+-      -...|+|||..-.+      ..+++.|++++..+.++|.+|
T Consensus       245 G~~~W~~~l~~i~~~~~~~~~d~~~~~l~~~~~------~~~~Y~Ri~p~l~~~~~~lDd~s~~ni~~L~~~a~~~i~~~  318 (329)
T cd07215         245 GLLGWAKPLIDIMMDGASQTVDYQLKQIFDAEG------DQQQYLRIQPELEDADPEMDDASPENLEKLREVGQALAEDH  318 (329)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC------CCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             678888999999997008999999999862458------87818997588876754413699999999999999999981


Q ss_pred             CC
Q ss_conf             45
Q gi|254780191|r  647 LP  648 (898)
Q Consensus       647 ~~  648 (898)
                      ..
T Consensus       319 ~~  320 (329)
T cd07215         319 KD  320 (329)
T ss_pred             HH
T ss_conf             99


No 77 
>PRK06153 hypothetical protein; Provisional
Probab=52.22  E-value=2.6  Score=21.24  Aligned_cols=35  Identities=14%  Similarity=0.247  Sum_probs=21.7

Q ss_pred             HHHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCE
Q ss_conf             35553695279999579997899999999997549978
Q gi|254780191|r  787 SCHKIADVNFMSHIISEVDSKELKSVMDALQKKIQSGI  824 (898)
Q Consensus       787 ~~~~i~~~~~i~~~~~~~d~~~Lr~l~d~l~~k~~~~v  824 (898)
                      ......++.++...++.-+.+-  .+++.|.+. +-..
T Consensus       260 nv~~L~g~~FvFvcvD~G~~r~--~I~~~L~~~-gIpF  294 (393)
T PRK06153        260 NVDELDGVTFVFVCVDKGSSRK--VIFDYLEAL-GIPF  294 (393)
T ss_pred             HHHHHCCCCEEEEEECCCCHHH--HHHHHHHHC-CCCE
T ss_conf             2556439718999944880478--999999983-9986


No 78 
>TIGR02156 PA_CoA_Oxy1 phenylacetate-CoA oxygenase, PaaG subunit; InterPro: IPR011881 Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation , . Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA .    .
Probab=51.63  E-value=9.8  Score=16.74  Aligned_cols=10  Identities=30%  Similarity=0.428  Sum_probs=5.3

Q ss_pred             CCCCHHHHHH
Q ss_conf             7899999999
Q gi|254780191|r  625 KPITSAELKS  634 (898)
Q Consensus       625 ~~lt~eel~~  634 (898)
                      +..|.|||++
T Consensus       216 k~~sNdelRQ  225 (297)
T TIGR02156       216 KRKSNDELRQ  225 (297)
T ss_pred             CCCCCHHHHH
T ss_conf             2146667889


No 79 
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family; InterPro: IPR014298   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    This group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=51.31  E-value=14  Score=15.64  Aligned_cols=39  Identities=21%  Similarity=0.305  Sum_probs=19.9

Q ss_pred             HHHHHHHHH-HHHHCCCCCCCC-C------CHHHHHHHHHHHHHHHH
Q ss_conf             769999999-997306785433-5------02489999989899998
Q gi|254780191|r  247 DLFKHLIQA-SEQVTGMKYEGN-N------IVNHRVIVDHLRSSSFL  285 (898)
Q Consensus       247 D~f~pii~~-i~~~~g~~y~~~-~------~~~~rvIaDH~Ra~~f~  285 (898)
                      ||.+.++.. +.++...++.++ +      .+|..+|+||.|...+-
T Consensus        40 DL~s~vF~~~L~~i~~f~~~~~t~f~~WLf~iA~N~v~Dyfr~~~r~   86 (171)
T TIGR02952        40 DLTSEVFLRVLRKIDSFKEQKNTDFEAWLFTIARNVVADYFRKSKRR   86 (171)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             64789999997312210125787722478999999999885113455


No 80 
>COG2509 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]
Probab=51.29  E-value=4.2  Score=19.63  Aligned_cols=86  Identities=17%  Similarity=0.210  Sum_probs=46.9

Q ss_pred             HHHHCCCCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCC--CCCCCCEEEEEEECHHHHHHHH---HHHHH
Q ss_conf             443155562489984476778553101562225886460110011012--1268828999971689999999---99999
Q gi|254780191|r  667 LLGTKYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSES--SIRAGIRRIEAITGQRARSHLM---GQDEK  741 (898)
Q Consensus       667 lfgekygd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~--si~sGvRRIeavtG~~A~~~~~---~~~~~  741 (898)
                      .+--||++.||.-.+     |+      ||+=|..+.|=|.+..-+.|  +..+-..-.-++++..-.+++.   +....
T Consensus       277 ~~t~k~~~~VrtFCm-----cP------~G~VV~e~~e~g~~~vNG~S~~~r~s~NtNfAllV~i~~tep~~~~~ey~r~  345 (486)
T COG2509         277 YYTKKYGDGVRTFCM-----CP------GGEVVAENYEDGFVVVNGHSYYARKSENTNFALLVTIEFTEPFEDGIEYGRS  345 (486)
T ss_pred             EEECCCCCEEEEEEE-----CC------CCEEEEEECCCCEEEECCCCHHCCCCCCCCEEEEEECCCCCCCCCHHHHHHH
T ss_conf             883157986789898-----89------9769856414866877561020123567633799844535787765799999


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             99999983999889999999999
Q gi|254780191|r  742 LKSLASFLKVSQGNVVGRVEEIW  764 (898)
Q Consensus       742 l~~la~~L~~~~~~i~~ki~~L~  764 (898)
                      +..++..|+-.. -+.+++-.++
T Consensus       346 ia~lA~~lgGg~-~i~Q~~gDf~  367 (486)
T COG2509         346 IARLATTLGGGK-AIIQRVGDFL  367 (486)
T ss_pred             HHHHHHHHCCCC-CHHHHHHHHH
T ss_conf             999988752896-1577766887


No 81 
>KOG4215 consensus
Probab=51.04  E-value=11  Score=16.51  Aligned_cols=82  Identities=18%  Similarity=0.193  Sum_probs=43.9

Q ss_pred             EHHHHHHHHHHCCCHHHHHHHHHHH--CCCCCCCCCCCEECCCEE-EEECCCCCCCCHHHHHHHHHHHHHHHHHCC-CCE
Q ss_conf             2125567775201368899999752--125444445530024300-000247678999999999999989887304-530
Q gi|254780191|r  575 IDYQNRRQLSINHSATHLLHHALST--ILGSHVSQNGSCITPDGL-RFDVTHSKPITSAELKSIEDNVNDIIAQNL-PVV  650 (898)
Q Consensus       575 VD~~rR~~~~~~HTatHlL~~alr~--vLG~hv~Q~GS~v~~~~l-rfDfsh~~~lt~eel~~IE~~vN~~I~~n~-~V~  650 (898)
                      ++-+-.-.+-++|+|+|||-.++.+  .|-++++     .+.+++ +-+-+        ++-++-+.+..+|-+=. |..
T Consensus       183 l~l~DqvaLLk~~a~~hllLg~a~RSm~l~~v~l-----l~N~~v~~~~~~--------~~~eis~v~~RIiDElv~Pmr  249 (432)
T KOG4215         183 LPLDDQVALLKAHAGQHLLLGAAFRSMHLKDVCL-----LNNTYVLHRHAP--------DLPEISRVAPRIIDELVNPMR  249 (432)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCEEE-----ECCCEEECCCCC--------CHHHHHHHHHHHHHHHHHHHH
T ss_conf             7711489998725514523455540323035488-----568566125789--------727777888999999861898


Q ss_pred             EEEECCCCCCCCHHHHHHH
Q ss_conf             4661232221000355443
Q gi|254780191|r  651 TRIMNREDAIASGAAALLG  669 (898)
Q Consensus       651 ~~~~~~~eA~~~ga~alfg  669 (898)
                      -..|+..|-....|++||.
T Consensus       250 ~L~md~~Ey~cLKAi~Ffd  268 (432)
T KOG4215         250 RLQMDEIEYVCLKAIAFFD  268 (432)
T ss_pred             HHCCCHHHHHHHHHHHHCC
T ss_conf             8454358899999998518


No 82 
>PRK09537 pylS pyrolysyl-tRNA synthetase; Reviewed
Probab=50.96  E-value=8.9  Score=17.09  Aligned_cols=10  Identities=10%  Similarity=0.481  Sum_probs=4.4

Q ss_pred             CCCEEEEEEC
Q ss_conf             5624899844
Q gi|254780191|r  673 NDRVRVVSVE  682 (898)
Q Consensus       673 gd~VRVV~I~  682 (898)
                      +|+|||-+||
T Consensus       283 pdPIrIFEIG  292 (420)
T PRK09537        283 PDPIKIFEIG  292 (420)
T ss_pred             CCCEEEEEEC
T ss_conf             8871588620


No 83 
>KOG1159 consensus
Probab=50.20  E-value=6.9  Score=17.93  Aligned_cols=38  Identities=24%  Similarity=0.438  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             999898999987403333444641257788999999999848743
Q gi|254780191|r  275 IVDHLRSSSFLIADGILPANEGRGYVLRRIMRRAMCYARLLGYTE  319 (898)
Q Consensus       275 IaDH~Ra~~f~I~DGv~PsN~GrGYvlRrilRRa~r~~~~lg~~~  319 (898)
                      +.-|++..+|-++|--.|   +=.|+.++|-||-+    .||.+.
T Consensus        83 ~L~~~~~AvlGLGDSSY~---KfNy~aKKL~~RL~----qLGA~~  120 (574)
T KOG1159          83 ILQHMQFAVLGLGDSSYP---KFNYAAKKLHRRLR----QLGANS  120 (574)
T ss_pred             HHHHHHHEEEECCCCCCH---HHHHHHHHHHHHHH----HHCCCC
T ss_conf             875212013505766532---22188999999999----837641


No 84 
>cd00773 HisRS-like_core Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain.
Probab=50.17  E-value=15  Score=15.31  Aligned_cols=24  Identities=25%  Similarity=0.397  Sum_probs=12.1

Q ss_pred             HHHHHHHHHHHHHCCCEECCCCCC
Q ss_conf             899999999999789889116675
Q gi|254780191|r    5 SSIRTTFLEFFQKNGHELLPSSSL   28 (898)
Q Consensus         5 ~eiR~~fl~fF~~~~H~~~~s~sl   28 (898)
                      ..|++++.+.|+++|...|....+
T Consensus         6 ~~i~~~l~~~f~~~Gy~~I~~P~l   29 (261)
T cd00773           6 RYIEDTLREVFERYGYEEIDTPVF   29 (261)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCC
T ss_conf             999999999999869978667764


No 85 
>COG3494 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.11  E-value=14  Score=15.55  Aligned_cols=35  Identities=17%  Similarity=0.159  Sum_probs=16.1

Q ss_pred             EECCCCCCC-CCHHHHHH-HHEECCCCCCCCCEEEEEEECH
Q ss_conf             101562225-88646011-0011012126882899997168
Q gi|254780191|r  691 SALCGGTHV-SSTGEIML-LYIVSESSIRAGIRRIEAITGQ  729 (898)
Q Consensus       691 ~ElCGGTHV-~nTgeIG~-fkIise~si~sGvRRIeavtG~  729 (898)
                      .|+|.=-|- -+-|++|. +|.+.++.    +.||.+.-+-
T Consensus        42 ~~~~~~e~~~~~iG~vg~lik~l~~~~----v~~vVl~G~v   78 (279)
T COG3494          42 PELKEFEYKEVSIGEVGKLIKLLKTEG----VDRVVLAGGV   78 (279)
T ss_pred             HHHHCCCCEEEEHHHHHHHHHHHHHCC----CCEEEEECCC
T ss_conf             555258870775787999999999848----8689996452


No 86 
>cd01017 AdcA Metal binding protein AcdA.  These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion.  The AcdA proteins 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 they bind their ligand in the cleft between these domains.  In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).
Probab=49.98  E-value=15  Score=15.29  Aligned_cols=200  Identities=12%  Similarity=0.076  Sum_probs=85.4

Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             36889999975212544444553002430000024767899999999999998988730453046612322210003554
Q gi|254780191|r  588 SATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIASGAAAL  667 (898)
Q Consensus       588 TatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~~ga~al  667 (898)
                      |.+..+....+++.|++|. --+++.+.   .| .|.-.+++.+++.+++- .-+|+....       ++.    +.-.+
T Consensus         8 ~S~~p~~~lv~~I~Gd~v~-V~~lv~~g---~d-PH~yep~p~d~~~l~~A-dli~~nG~~-------lE~----~l~~~   70 (282)
T cd01017           8 TTFYPLYEFTKAIGGDKAD-VKLIIPAG---TE-PHDFEPSPKDIARIADA-DVFVYNGLG-------MET----WAEKV   70 (282)
T ss_pred             EECHHHHHHHHHHCCCCEE-EEEECCCC---CC-CCCCCCCHHHHHHHHCC-CEEEEECCC-------CHH----HHHHH
T ss_conf             9888999999998199448-99815989---79-63675899999999669-999991878-------368----99999


Q ss_pred             HHHCCCCCEEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHEECCCCCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHH
Q ss_conf             43155562489984476778553101562225886460110011012126882899997168999999999999999999
Q gi|254780191|r  668 LGTKYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSESSIRAGIRRIEAITGQRARSHLMGQDEKLKSLAS  747 (898)
Q Consensus       668 fgekygd~VRVV~I~~~d~~~~S~ElCGGTHV~nTgeIG~fkIise~si~sGvRRIeavtG~~A~~~~~~~~~~l~~la~  747 (898)
                      ...--.+.+.+|.....   .--...++.-|-...+         +.....+.=-=.-+.=..+..   -...+.+.+++
T Consensus        71 ~~~~~~~~~~vi~~~~~---~~~~~~~~~~~~~~~~---------~~~~~~~~DPH~Wldp~~~~~---~a~~I~~~L~~  135 (282)
T cd01017          71 LKSLQNKKLKVVEASKG---IKLLKAGGAEHDHDHS---------HSHHHGDYDPHVWLSPVLAIQ---QVENIKDALIK  135 (282)
T ss_pred             HHHCCCCCCEEEECCCC---CCCCCCCCCCCCCCCC---------CCCCCCCCCCCCCCCHHHHHH---HHHHHHHHHHH
T ss_conf             98536899779987789---5235567765555555---------445579999825578155999---99999999998


Q ss_pred             HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHCCCCEEEEE--EC--CCCHHHHHHHHHH
Q ss_conf             839998899999999999999999999999999876365--------35553695279999--57--9997899999999
Q gi|254780191|r  748 FLKVSQGNVVGRVEEIWEEYRKLQLIHAKRKLQLNVEDL--------SCHKIADVNFMSHI--IS--EVDSKELKSVMDA  815 (898)
Q Consensus       748 ~L~~~~~~i~~ki~~L~~e~K~l~k~~~k~k~~~~~~~~--------~~~~i~~~~~i~~~--~~--~~d~~~Lr~l~d~  815 (898)
                      +.........+..+++.+++..+..+..+.........+        ...+--|.+.+...  ..  ..+++.|..+.+.
T Consensus       136 ~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~~~~~~~v~~H~af~Yf~~~ygl~~~~~~~~~~~~eps~~~l~~l~~~  215 (282)
T cd01017         136 LDPDNKEYYEKNAAAYAKKLEALDQEYRAKLAKAKGKTFVTQHAAFGYLARRYGLKQIAIVGVSPEVEPSPKQLAELVEF  215 (282)
T ss_pred             HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCHHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHHHH
T ss_conf             68441799999999999999999999999874436785687353378999866984865433488889999999999999


Q ss_pred             HHHH
Q ss_conf             9975
Q gi|254780191|r  816 LQKK  819 (898)
Q Consensus       816 l~~k  819 (898)
                      ++++
T Consensus       216 ik~~  219 (282)
T cd01017         216 VKKS  219 (282)
T ss_pred             HHHC
T ss_conf             9985


No 87 
>pfam00709 Adenylsucc_synt Adenylosuccinate synthetase.
Probab=49.44  E-value=15  Score=15.23  Aligned_cols=170  Identities=19%  Similarity=0.185  Sum_probs=76.1

Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHC--CCCCCCC--------CCHHHHHHHH
Q ss_conf             43047887565766531017579999999887985300576999999999730--6785433--------5024899999
Q gi|254780191|r  208 FEQQNKQERFILPKMSIDTGMGLERMATVLQEKTNNYDIDLFKHLIQASEQVT--GMKYEGN--------NIVNHRVIVD  277 (898)
Q Consensus       208 ~~~~~~g~~~~Lp~~~IDTGmGLERl~~vlqg~~s~ydtD~f~pii~~i~~~~--g~~y~~~--------~~~~~rvIaD  277 (898)
                      |...+.|.+.|=-.-.|--||=              -|-.   -++++++.+.  |+...+.        -.+.|-+..|
T Consensus        50 lhliPSGil~~~~~~vIG~GvV--------------idp~---~L~~Ei~~L~~~Gi~~~~rL~IS~rahli~P~H~~~D  112 (420)
T pfam00709        50 LHLLPSGILNPGVINVIGNGVV--------------VDPE---ALLEEIEELEKKGVDVRDRLFISDRAHLILPYHRALD  112 (420)
T ss_pred             EECCCCEECCCCCEEEECCCEE--------------ECHH---HHHHHHHHHHHCCCCCCCCEEECCCCCCCCCHHHHHH
T ss_conf             9517836327997189899789--------------8599---9999999999759897457898588555880469988


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCH---HHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8989999874033334446412---57788999999999848743--310456899999864555555764678899998
Q gi|254780191|r  278 HLRSSSFLIADGILPANEGRGY---VLRRIMRRAMCYARLLGYTE--PLMMHLLPALCTEMGSAYPELIQAKLLIEETLR  352 (898)
Q Consensus       278 H~Ra~~f~I~DGv~PsN~GrGY---vlRrilRRa~r~~~~lg~~~--~fl~~lv~~v~~~m~~~ypeL~~~~~~I~~ii~  352 (898)
                      -+|-..  -+++-+ +-.|||-   .-.++.||++|.+.++..+.  .-|..+++..-..+...|....-+.+.    +.
T Consensus       113 ~~~E~~--~g~~~i-GTTgrGIGPaY~DK~~R~giR~~DL~~~~~l~~kl~~~~~~~~~~l~~~~~~~~~~~~~----~~  185 (420)
T pfam00709       113 RLREEA--RGKGKI-GTTGRGIGPAYADKVARRGIRVGDLLDEEVLREKLEQLLEEKNAILEKLYGAEPLDVEE----IL  185 (420)
T ss_pred             HHHHHH--CCCCCC-CCCCCEEEHHHHHHHCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH----HH
T ss_conf             988886--067656-77786441876524225552188763958899999999999999987634778899999----99


Q ss_pred             HHHHHHHHHHH----HHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHH
Q ss_conf             74898999999----899999999861154642457437998524588889999
Q gi|254780191|r  353 SEDERFGKTLD----RGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLDIMQ  402 (898)
Q Consensus       353 ~EE~~F~~TL~----~G~~~l~~~i~~~~~~~~lsg~~af~LyDTyGfP~dlt~  402 (898)
                      .+-..|.+.|.    .-..++++.+++ +++=.+-|.+.+.|---||+=|=.|.
T Consensus       186 ~~~~~~~~~l~~~i~d~~~~l~~a~~~-gk~iLfEGAQG~lLDid~GtYP~VTS  238 (420)
T pfam00709       186 EEYLEYAERLRPYITDTSELLNRALKE-GKKVLFEGAQGTLLDIDHGTYPYVTS  238 (420)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHC-CCEEEEECCCCEEECCCCCCCCCCCC
T ss_conf             999999999861363599999999974-99489950550023135586887575


No 88 
>pfam10440 WIYLD WIYLD domain. This presumed domain has been predicted to contain three alpha helices. The domain was named the WIYLD domain based on the pattern of most conserved residues. The domain appears to be specific to plant SET-domain proteins.
Probab=49.14  E-value=15  Score=15.20  Aligned_cols=40  Identities=18%  Similarity=0.236  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8899999999984874331045689999986455555576
Q gi|254780191|r  303 RIMRRAMCYARLLGYTEPLMMHLLPALCTEMGSAYPELIQ  342 (898)
Q Consensus       303 rilRRa~r~~~~lg~~~~fl~~lv~~v~~~m~~~ypeL~~  342 (898)
                      +=+..|+.+++.+|+.++-....+..+.+.++..++-+.+
T Consensus         9 ~RidaA~dam~~~G~~~~~v~~vlk~LL~~yg~nW~~IEe   48 (65)
T pfam10440         9 RRIDAAIDRMREFGIPDAVIRPVLKELLELYGGNWFLIEE   48 (65)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHHC
T ss_conf             8899999999982998799999999999996788277760


No 89 
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=48.66  E-value=16  Score=15.15  Aligned_cols=24  Identities=25%  Similarity=0.261  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             999999999839998899999999
Q gi|254780191|r  739 DEKLKSLASFLKVSQGNVVGRVEE  762 (898)
Q Consensus       739 ~~~l~~la~~L~~~~~~i~~ki~~  762 (898)
                      .-.+.+++...+=+..++.++++.
T Consensus       134 ~c~lG~ls~evGWky~~vv~~LE~  157 (201)
T PTZ00068        134 YCVLGDLCAHVGWNYSDVVKKLEE  157 (201)
T ss_pred             EECHHHHHHHHCCCHHHHHHHHHH
T ss_conf             030888888719638999999999


No 90 
>TIGR01283 nifE nitrogenase MoFe cofactor biosynthesis protein NifE; InterPro: IPR005973    The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene. Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes. It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I. ; GO: 0005515 protein binding, 0006461 protein complex assembly, 0009399 nitrogen fixation.
Probab=46.95  E-value=17  Score=14.96  Aligned_cols=162  Identities=20%  Similarity=0.278  Sum_probs=90.7

Q ss_pred             CCCCCCCCHHHHHHHHEECC--------CCCCCCCEEEEEEECHHHHHHHH-----------------------------
Q ss_conf             56222588646011001101--------21268828999971689999999-----------------------------
Q gi|254780191|r  694 CGGTHVSSTGEIMLLYIVSE--------SSIRAGIRRIEAITGQRARSHLM-----------------------------  736 (898)
Q Consensus       694 CGGTHV~nTgeIG~fkIise--------~si~sGvRRIeavtG~~A~~~~~-----------------------------  736 (898)
                      --+|.+.+-.=||-|-|=+|        +.  =|||=+-.+||+.-++..+                             
T Consensus       203 ~~~~~~~diNliGEFN~AGE~W~v~pLlek--lGi~V~~~~tGD~r~~ev~~aHrA~lN~v~CSks~~nlA~~m~~~YGI  280 (470)
T TIGR01283       203 RAGTTVHDINLIGEFNVAGEFWLVKPLLEK--LGIRVLATITGDSRYAEVQTAHRAKLNMVQCSKSMINLARKMEEKYGI  280 (470)
T ss_pred             CCCCCCCCCCEEECHHCCCCCCCCCCHHHH--CCCEEEEECCCCCCHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHCCC
T ss_conf             676656741115230000111100101433--891799973788878998404115543357523678899999964689


Q ss_pred             -----------HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCC
Q ss_conf             -----------9999999999983999889999999999999-9999999999999876365355536952799995799
Q gi|254780191|r  737 -----------GQDEKLKSLASFLKVSQGNVVGRVEEIWEEY-RKLQLIHAKRKLQLNVEDLSCHKIADVNFMSHIISEV  804 (898)
Q Consensus       737 -----------~~~~~l~~la~~L~~~~~~i~~ki~~L~~e~-K~l~k~~~k~k~~~~~~~~~~~~i~~~~~i~~~~~~~  804 (898)
                                 ...+.|.++|+.|+-  +++.+|.++|..+- +++..++...+          +...|.+++..  .+-
T Consensus       281 Pyf~~SFyGi~Dt~~aLr~~A~~fgd--~~l~~RtE~li~~E~~~~~~~l~~yR----------~~L~GKkaaiY--~GG  346 (470)
T TIGR01283       281 PYFEVSFYGIEDTSKALRDIAELFGD--EELLKRTEELIAEEEAKIRPELEPYR----------ERLKGKKAAIY--TGG  346 (470)
T ss_pred             CEEEECCCHHHHHHHHHHHHHHHCCC--HHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHCCCEEEEE--CCC
T ss_conf             75872141088899999999976398--87999999999999999999999989----------97349889986--586


Q ss_pred             CHHHHHHHHHHHHHHCCCCEEEEEEECCC---CEEEEEEEECHHH--HCCCCHHHHHHHHHHHHCCCCCCCCCHHCCCCC
Q ss_conf             97899999999997549978999995389---8179999867789--726798999999998834999999810114589
Q gi|254780191|r  805 DSKELKSVMDALQKKIQSGIIMLVGISKE---KKASVLIVVTEDL--LDRFNAVDLARLSAKVLGGGGGGGRPHMAQSGG  879 (898)
Q Consensus       805 d~~~Lr~l~d~l~~k~~~~vvvL~~~~~~---~k~~ivv~vs~~~--~~~~~A~~lik~ia~~l~GGgGGGkpd~AQgGG  879 (898)
                      ..|.. .++..+.+ ++-.||+ .++.+.   +|..|--.+.++.  .++-++.+|++.+.+.        +||+-=|||
T Consensus       347 a~Ksw-Slv~Al~d-LGMeVV~-~GTqkg~~EDy~~I~e~~~~~~~m~Dd~~p~~L~~~~~~~--------~ADlliaGg  415 (470)
T TIGR01283       347 AVKSW-SLVSALQD-LGMEVVA-TGTQKGTEEDYERIRELMGEGTVMLDDANPRELLKLLLEY--------KADLLIAGG  415 (470)
T ss_pred             HHHHH-HHHHHHHH-CCCEEEE-EEECCCCHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHH--------CCCEEEECC
T ss_conf             47899-99988845-7917999-8300798889999999707996786258878999999872--------898898573


Q ss_pred             CCH
Q ss_conf             998
Q gi|254780191|r  880 PNG  882 (898)
Q Consensus       880 ~~~  882 (898)
                      ++.
T Consensus       416 k~~  418 (470)
T TIGR01283       416 KER  418 (470)
T ss_pred             HHH
T ss_conf             123


No 91 
>cd01140 FatB Siderophore binding protein FatB.  These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species.  They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=46.35  E-value=11  Score=16.42  Aligned_cols=16  Identities=25%  Similarity=0.559  Sum_probs=11.8

Q ss_pred             EEEECCCCEEECCCCC
Q ss_conf             9997375200036876
Q gi|254780191|r  512 EVVFDQTPFYAEAGGQ  527 (898)
Q Consensus       512 ~ivLd~T~FY~E~GGQ  527 (898)
                      ...+|...||-.+||=
T Consensus       243 V~~vd~~~w~~~~g~~  258 (270)
T cd01140         243 VIYLDPDLWYLSGGGL  258 (270)
T ss_pred             EEEECHHHEECCCCHH
T ss_conf             8997768836577069


No 92 
>TIGR00170 leuC 3-isopropylmalate dehydratase, large subunit; InterPro: IPR004430   3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus .    Members of this entry are 3-isopropylmalate dehydratase, large subunit, or the large subunit domain of single-chain forms. Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures. All are dehydratases (4.2.1 from EC) and bind a [4Fe-4S]-cluster. 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. The archaeal leuC-like proteins are not included in group.; GO: 0003861 3-isopropylmalate dehydratase activity, 0051539 4 iron 4 sulfur cluster binding, 0009098 leucine biosynthetic process, 0009316 3-isopropylmalate dehydratase complex.
Probab=46.23  E-value=17  Score=14.88  Aligned_cols=46  Identities=28%  Similarity=0.403  Sum_probs=31.7

Q ss_pred             EEEECCCCCCCEEEEEEECCCCCCCCCCCEEEEEEHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             985224565533899851046787556733888421255677752013688999997
Q gi|254780191|r  541 LQITDVQKKAEGIFVHHAIVERGILRTEMSLVLTIDYQNRRQLSINHSATHLLHHAL  597 (898)
Q Consensus       541 ~~V~dv~k~~~g~i~H~~~~~~g~l~~g~~V~~~VD~~rR~~~~~~HTatHlL~~al  597 (898)
                      ++..|.....-| |||..=.+.|.--+|.+|.|          =-.|||||==.+||
T Consensus       101 v~l~dl~~~~QG-IVHv~GPE~GlTLPG~TiVC----------GDSHTsTHGAFGaL  146 (472)
T TIGR00170       101 VKLFDLSSAEQG-IVHVVGPEQGLTLPGMTIVC----------GDSHTSTHGAFGAL  146 (472)
T ss_pred             CEEECCCCCCCC-EEEEECCCCCCCCCCCEEEE----------CCCCCHHHHHHHHH
T ss_conf             321057788874-69986788885388875885----------88763023455666


No 93 
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination.  Sup35NM  
Probab=46.20  E-value=17  Score=14.87  Aligned_cols=14  Identities=29%  Similarity=0.385  Sum_probs=4.9

Q ss_pred             ECCCCCCCCCCCEE
Q ss_conf             10467875567338
Q gi|254780191|r  558 AIVERGILRTEMSL  571 (898)
Q Consensus       558 ~~~~~g~l~~g~~V  571 (898)
                      |++++|.++.||+|
T Consensus        20 G~v~sG~i~~Gd~v   33 (83)
T cd03698          20 GKVESGSIQKGDTL   33 (83)
T ss_pred             EEEEECEECCCCEE
T ss_conf             99902587289999


No 94 
>TIGR00468 pheS phenylalanyl-tRNA synthetase, alpha subunit; InterPro: IPR004529   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases .   This family describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this family. ; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=46.04  E-value=17  Score=14.86  Aligned_cols=32  Identities=13%  Similarity=0.240  Sum_probs=18.0

Q ss_pred             CCHHHH-HHHHHHHHHHHHHCCCCEEE--EECCCC
Q ss_conf             999999-99999998988730453046--612322
Q gi|254780191|r  627 ITSAEL-KSIEDNVNDIIAQNLPVVTR--IMNRED  658 (898)
Q Consensus       627 lt~eel-~~IE~~vN~~I~~n~~V~~~--~~~~~e  658 (898)
                      ++-..+ --++...+..-.++..+..+  +.|..+
T Consensus       240 ~~~~~l~g~~~~~~~~~~~~~~~~~~~p~~fp~t~  274 (362)
T TIGR00468       240 VSFTNLKGLLEEFLKKLFGEDTEVRFRPSYFPFTE  274 (362)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCC
T ss_conf             64678899999999974132212023103366555


No 95 
>pfam04931 DNA_pol_phi DNA polymerase phi. This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.
Probab=45.90  E-value=8.3  Score=17.31  Aligned_cols=11  Identities=9%  Similarity=0.311  Sum_probs=5.7

Q ss_pred             HHHHHHHHHHH
Q ss_conf             28999975663
Q gi|254780191|r  133 DEEAFKLWKKI  143 (898)
Q Consensus       133 D~e~~~iW~~~  143 (898)
                      -+|.-.||...
T Consensus       151 ~~e~l~i~l~~  161 (784)
T pfam04931       151 SEKVLSVFLSY  161 (784)
T ss_pred             CHHHHHHHHHC
T ss_conf             86699999857


No 96 
>pfam04336 DUF479 Protein of unknown function, DUF479. This family includes several bacterial proteins of uncharacterized function.
Probab=45.76  E-value=17  Score=14.83  Aligned_cols=31  Identities=29%  Similarity=0.269  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHCCCCC---CCCCCHHHHHHHHHHH
Q ss_conf             989999874033334---4464125778899999
Q gi|254780191|r  279 LRSSSFLIADGILPA---NEGRGYVLRRIMRRAM  309 (898)
Q Consensus       279 ~Ra~~f~I~DGv~Ps---N~GrGYvlRrilRRa~  309 (898)
                      .|.+..|+...-+.+   =+|-+.+|++|-||.-
T Consensus        40 ~~~~~~M~~~dWL~~Y~~~~gI~~aL~~m~~R~~   73 (106)
T pfam04336        40 QRLLPRMIEQDWLGSYADLEGIERALDRMARRLS   73 (106)
T ss_pred             HHHHHHHHHCCHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf             9999999881899775888899999999987448


No 97 
>cd07213 Pat17_PNPLA8_PNPLA9_like1 Patatin-like phospholipase. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Members of this family have been found also in vertebrates. This family includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9 (iPLA2-beta) like phospholipases from human as well as the Pat17 isozyme from Solanum cardiophyllum.
Probab=45.28  E-value=18  Score=14.77  Aligned_cols=57  Identities=16%  Similarity=0.121  Sum_probs=37.0

Q ss_pred             EEEHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHH
Q ss_conf             84212556777520136889999975212544444553002430000024767899999999999998
Q gi|254780191|r  573 LTIDYQNRRQLSINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVN  640 (898)
Q Consensus       573 ~~VD~~rR~~~~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN  640 (898)
                      +.+.|-+..--+-.+.+.+..+..++..+|           ..|+|||..-++.+.-++..+||.++-
T Consensus       223 G~~~W~~~l~~~~~~a~~~~~~~~~~~l~~-----------~~Y~Ri~p~l~~~i~ldd~~~ie~l~~  279 (288)
T cd07213         223 GLLQWLPDLLDLFMDAGVDAADFQCRQLLG-----------ERYFRLDPVLPANIDLDDNKQIEELVE  279 (288)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-----------CCEEEECCCCCCCCCCCCHHHHHHHHH
T ss_conf             487728899999998689999999998668-----------987996899998778788899999999


No 98 
>PRK01346 hypothetical protein; Provisional
Probab=45.17  E-value=18  Score=14.76  Aligned_cols=47  Identities=21%  Similarity=0.272  Sum_probs=18.5

Q ss_pred             CCEEEEEEECCCCEEEEEEEECHHHH-CCCCHHHHHHHHHHHHCCCCCCCCC-HHCCCCC
Q ss_conf             97899999538981799998677897-2679899999999883499999981-0114589
Q gi|254780191|r  822 SGIIMLVGISKEKKASVLIVVTEDLL-DRFNAVDLARLSAKVLGGGGGGGRP-HMAQSGG  879 (898)
Q Consensus       822 ~~vvvL~~~~~~~k~~ivv~vs~~~~-~~~~A~~lik~ia~~l~GGgGGGkp-d~AQgGG  879 (898)
                      ++...|- +. +++..+.  .+++.. -.++...    +++.+.|+.   ++ .+|++|=
T Consensus       335 ~G~~~L~-~~-~g~~~v~--~t~~~~dl~Ldi~~----L~~lylG~~---s~~~L~~aG~  383 (411)
T PRK01346        335 GGRFRLD-VG-DGGARCT--PTDAPADLALDVAD----LGSLYLGGH---RASTLAAAGR  383 (411)
T ss_pred             CCEEEEE-EE-CCEEEEE--ECCCCCCEEEEHHH----HHHHHHCCC---CHHHHHHCCC
T ss_conf             9879999-81-8914898--87898637980999----999981898---8999997698


No 99 
>COG1480 Predicted membrane-associated HD superfamily hydrolase [General function prediction only]
Probab=44.19  E-value=18  Score=14.70  Aligned_cols=71  Identities=17%  Similarity=0.293  Sum_probs=37.7

Q ss_pred             HHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCCHH--------------------HHHHHHHHHH
Q ss_conf             77752013688999997521254444455300243000002476789999--------------------9999999998
Q gi|254780191|r  581 RQLSINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSA--------------------ELKSIEDNVN  640 (898)
Q Consensus       581 ~~~~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~e--------------------el~~IE~~vN  640 (898)
                      .+++.+|-||-|+...-.+     ..|..-.|.++-+|.  +-++|=|.|                    ...+||+++|
T Consensus       577 idii~eHhGTsLikYFY~k-----Ake~~~~v~Ee~FRY--~GPkPqSKEtaIImlADSvEAAvRSl~~p~~~ki~~~v~  649 (700)
T COG1480         577 IDIIPEHHGTSLIKYFYYK-----AKEENPNVKEEEFRY--PGPKPQSKETAIIMLADSVEAAVRSLKEPNPEKIEEMVD  649 (700)
T ss_pred             HHHHHHHCCCCHHHHHHHH-----HHHHCCCCCHHHCCC--CCCCCCCCHHHEEHHHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             9999984683489999999-----987378887765407--999987431210113768999986405999899999999


Q ss_pred             HHHHHCC---CCEEEEECCCC
Q ss_conf             9887304---53046612322
Q gi|254780191|r  641 DIIAQNL---PVVTRIMNRED  658 (898)
Q Consensus       641 ~~I~~n~---~V~~~~~~~~e  658 (898)
                      ++|..-+   ......++++|
T Consensus       650 ~II~~rl~DgQl~~s~lT~~E  670 (700)
T COG1480         650 KIIQARLQDGQLSESGLTLKE  670 (700)
T ss_pred             HHHHHHHHCCCCCCCCCCHHH
T ss_conf             999988861886546774899


No 100
>TIGR02364 dha_pts dihydroxyacetone kinase, phosphotransfer subunit; InterPro: IPR012844   In Escherichia coli and many other bacteria, unlike the yeasts and a few bacteria such as Citrobacter freundii, the dihydroxyacetone kinase (also called glycerone kinase) transfers a phosphate from a phosphoprotein rather than from ATP and contains multiple subunits..
Probab=43.99  E-value=18  Score=14.63  Aligned_cols=14  Identities=29%  Similarity=0.484  Sum_probs=6.8

Q ss_pred             CCCHHHHHHHHHHH
Q ss_conf             99987889999999
Q gi|254780191|r  879 GPNGNKADQAIAGV  892 (898)
Q Consensus       879 G~~~~~l~eal~~v  892 (898)
                      |+++.++.+|++.+
T Consensus        45 GTs~~~I~eaI~~~   58 (128)
T TIGR02364        45 GTSADKIKEAIEKA   58 (128)
T ss_pred             CCCHHHHHHHHHHH
T ss_conf             78989999998653


No 101
>PRK12421 ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=43.91  E-value=18  Score=14.62  Aligned_cols=36  Identities=19%  Similarity=0.421  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECC
Q ss_conf             789999999999978988911667566778710023014
Q gi|254780191|r    4 VSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSG   42 (898)
Q Consensus         4 ~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Ag   42 (898)
                      ...+|+++++.|+++|...|..-.+= .-  ++|.+.+|
T Consensus        24 ~~~l~~~l~~~f~~~Gy~~V~tP~lE-~~--e~l~~~~g   59 (391)
T PRK12421         24 IERLRRRLLDLFASRGYQLVMPPFIE-YL--ESLLTGAG   59 (391)
T ss_pred             HHHHHHHHHHHHHHCCCEEEECCCCC-CH--HHHCCCCC
T ss_conf             99999999999998699762167607-28--78565668


No 102
>PRK01117 adenylosuccinate synthetase; Provisional
Probab=43.56  E-value=19  Score=14.58  Aligned_cols=173  Identities=17%  Similarity=0.138  Sum_probs=78.1

Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHC--CCCC-CCC--------CCHHHHHHH
Q ss_conf             43047887565766531017579999999887985300576999999999730--6785-433--------502489999
Q gi|254780191|r  208 FEQQNKQERFILPKMSIDTGMGLERMATVLQEKTNNYDIDLFKHLIQASEQVT--GMKY-EGN--------NIVNHRVIV  276 (898)
Q Consensus       208 ~~~~~~g~~~~Lp~~~IDTGmGLERl~~vlqg~~s~ydtD~f~pii~~i~~~~--g~~y-~~~--------~~~~~rvIa  276 (898)
                      +...+.|.+.|-....|-.||              +-|-.   -++++++.+.  |+.. .+.        -.+.|-+..
T Consensus        52 lhllPSGil~~~~~~vIG~Gv--------------Vidp~---~L~~Ei~~L~~~Gi~~~~~rL~IS~rahli~P~H~~l  114 (431)
T PRK01117         52 LHLIPSGILRPGKTCVIGNGV--------------VLDPE---ALLKEIDELEARGVDTVRERLRISERAHLILPYHRAL  114 (431)
T ss_pred             EEECCCEECCCCCCEEECCCE--------------EECHH---HHHHHHHHHHHCCCCCCCCCEEECCCCCCCCHHHHHH
T ss_conf             960782751699717857978--------------98699---9999999999769998766689909984745516888


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCH---HHHHHHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98989999874033334446412---5778899999999984874331---04568999998645555557646788999
Q gi|254780191|r  277 DHLRSSSFLIADGILPANEGRGY---VLRRIMRRAMCYARLLGYTEPL---MMHLLPALCTEMGSAYPELIQAKLLIEET  350 (898)
Q Consensus       277 DH~Ra~~f~I~DGv~PsN~GrGY---vlRrilRRa~r~~~~lg~~~~f---l~~lv~~v~~~m~~~ypeL~~~~~~I~~i  350 (898)
                      |.+|-..-  ++.. =+-+|||-   ---++.||++|.+.++.-+ -|   |..+++..-..+...|.+..-+.+.+.+.
T Consensus       115 D~~~E~~~--g~~~-IGTT~rGIGPaY~DK~~R~gIR~~DL~~~~-~l~~kl~~~~~~~n~~l~~~~~~~~~d~e~~~~~  190 (431)
T PRK01117        115 DQAREKAR--GDKK-IGTTGRGIGPAYEDKVARRGIRVGDLLDPE-TFAEKLEENLEYHNFLLTKYYGAEAVDFEEILDE  190 (431)
T ss_pred             HHHHHHHC--CCCC-CCCCCCCCCHHHHHHHCCCCCHHHHHCCHH-HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             89889863--8866-667889782755402103342213633878-8999999999999999997369988899999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHH
Q ss_conf             9874898999999899999999861154642457437998524588889999
Q gi|254780191|r  351 LRSEDERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLDIMQ  402 (898)
Q Consensus       351 i~~EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsg~~af~LyDTyGfP~dlt~  402 (898)
                      +..=-++...-+..-..++++.+++ +++=.+-|.+.+.|---||+-|=.|.
T Consensus       191 ~~~~~~~l~~~i~dt~~~l~~a~~~-gk~ILfEGAQG~lLDid~GtYPyVTS  241 (431)
T PRK01117        191 YLEYAERLKPYVTDVSLLLNDALKA-GKRVLFEGAQGTLLDIDHGTYPFVTS  241 (431)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHC-CCCEEEECCCEEEECCCCCCCCCCCC
T ss_conf             9999999750312699999999975-99489850432576156787886465


No 103
>KOG1035 consensus
Probab=42.48  E-value=19  Score=14.47  Aligned_cols=11  Identities=45%  Similarity=0.567  Sum_probs=4.8

Q ss_pred             CCHHHHHHHHH
Q ss_conf             13688999997
Q gi|254780191|r  587 HSATHLLHHAL  597 (898)
Q Consensus       587 HTatHlL~~al  597 (898)
                      -||+-||+..|
T Consensus       863 PtA~eLL~s~l  873 (1351)
T KOG1035         863 PTATELLNSEL  873 (1351)
T ss_pred             CCHHHHHHCCC
T ss_conf             78899962457


No 104
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=42.18  E-value=19  Score=14.43  Aligned_cols=53  Identities=21%  Similarity=0.285  Sum_probs=31.3

Q ss_pred             ECCCCCCCCHHHHHHHHHHHHHHHHHCC-CCEE--EEECCCCCCCCHHHHHHHH-CCCC
Q ss_conf             0247678999999999999989887304-5304--6612322210003554431-5556
Q gi|254780191|r  620 DVTHSKPITSAELKSIEDNVNDIIAQNL-PVVT--RIMNREDAIASGAAALLGT-KYND  674 (898)
Q Consensus       620 Dfsh~~~lt~eel~~IE~~vN~~I~~n~-~V~~--~~~~~~eA~~~ga~alfge-kygd  674 (898)
                      |.+  ..|+..|...+|+..-..=.+.- .|-+  .-..-.+.++.+|..+|.+ |+|+
T Consensus        38 D~t--~~Ls~~e~~~Leq~l~~L~~kt~~QiaVv~vpSt~g~~IE~ya~rlfd~W~lG~   94 (271)
T COG1512          38 DLT--GTLSAAERGALEQQLADLEQKTGAQIAVVTVPSTGGETIEQYATRLFDKWKLGD   94 (271)
T ss_pred             CCC--CCCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHHHHHCCCCC
T ss_conf             053--458755777899999999735586189999458999798999999988517874


No 105
>COG0060 IleS Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=41.94  E-value=20  Score=14.41  Aligned_cols=97  Identities=16%  Similarity=0.202  Sum_probs=44.4

Q ss_pred             CCHHHHHHHHHHHHHHH------CC--CCHHHEEEEECCCHHHHHHHHHHHCCCCHHHEEECCCCCCCCCCCCCCCCCCC
Q ss_conf             53788999899861334------18--98123799971882899997566349998997535786665457999998770
Q gi|254780191|r  101 YFKERAIQLAWDLLTKE------FD--LDQRRLYITVYDEDEEAFKLWKKISGLSADKIIRITTNDNFWSMAETGPCGPC  172 (898)
Q Consensus       101 YfK~eai~~awe~lt~~------~~--l~~~~l~vtv~~~D~e~~~iW~~~~gi~~~~i~~~~~~dNfW~~g~~GpcGPc  172 (898)
                      =|-++|=+||++.+-.+      ||  .|=+.=|.|.- .+=|+..+|.-. -+-..-.+.=|.|==+|+.-. +-.=--
T Consensus       124 efr~~Cr~~a~~~v~~q~~~f~RLGv~~Dw~npY~Tmd-~~ye~~~~~~f~-~~~~kGllyrg~Kpv~wsp~c-~TaLAe  200 (933)
T COG0060         124 EFREKCREFALEQVDEQKEQFKRLGVWGDWENPYKTMD-PSYEESVWWAFK-ELYEKGLLYRGYKPVPWSPRC-ETALAE  200 (933)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCCEECCC-HHHHHHHHHHHH-HHHHCCCEECCCEEEEECCCC-CCCHHH
T ss_conf             99999999999999999999876367632689803278-899999999999-999779752277001226877-760036


Q ss_pred             EEEEEE-CC-C----CCCCCCCCCCCCCCCEEEEEE
Q ss_conf             467885-38-5----568988877788982689600
Q gi|254780191|r  173 SEIFFD-QG-E----CIPGGLPGSSEEGERYIEIWN  202 (898)
Q Consensus       173 sEi~~d-~g-~----~~~~~~~~~~~~~~r~lEiwN  202 (898)
                      .||=|. +- |    .|+-...  +.+.+-++=||+
T Consensus       201 aEvey~d~~dpSIyV~F~v~~~--~~~~~~~lviWT  234 (933)
T COG0060         201 AEVEYGDVKDPSIYVKFPVKDE--GLDENAYLVIWT  234 (933)
T ss_pred             HHHCCCCCCCCEEEEEEEECCC--CCCCCCEEEEEE
T ss_conf             6640256689628999773357--887770799994


No 106
>KOG0554 consensus
Probab=41.08  E-value=11  Score=16.25  Aligned_cols=30  Identities=30%  Similarity=0.360  Sum_probs=14.3

Q ss_pred             CEEEEEECCCCEEECCCCCCCCCCEEEECCEEEEEE
Q ss_conf             769999737520003687656651454042489852
Q gi|254780191|r  509 QKVEVVFDQTPFYAEAGGQLGDTGCAIGDGIRLQIT  544 (898)
Q Consensus       509 ~~~~ivLd~T~FY~E~GGQ~~D~G~i~~~~~~~~V~  544 (898)
                      +...||.+.      -=+|..-+|+-..-.+...|.
T Consensus        50 ~~lQvVv~~------~~~q~la~Gt~i~~~g~l~~~   79 (446)
T KOG0554          50 SPLQVVVDS------EQSQLLATGTCISAEGVLKVS   79 (446)
T ss_pred             CCEEEEECH------HHHHHCCCCCEEEEEEEEEEC
T ss_conf             664999562------784020565269997568734


No 107
>PRK10528 multifunctional acyl-CoA thioesterase I and protease I and lysophospholipase L1; Provisional
Probab=40.72  E-value=20  Score=14.27  Aligned_cols=14  Identities=29%  Similarity=0.615  Sum_probs=8.0

Q ss_pred             CCCCCHHHHHHHHC
Q ss_conf             01757999999988
Q gi|254780191|r  225 DTGMGLERMATVLQ  238 (898)
Q Consensus       225 DTGmGLERl~~vlq  238 (898)
                      -|.-||+|+.|++.
T Consensus        55 TT~~gL~Rl~~~L~   68 (191)
T PRK10528         55 TSQQGLARLPALLK   68 (191)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             25469999898874


No 108
>KOG2384 consensus
Probab=40.67  E-value=20  Score=14.27  Aligned_cols=20  Identities=30%  Similarity=0.695  Sum_probs=12.1

Q ss_pred             HCCCCCCCCCCHHHHHHHHH
Q ss_conf             03333444641257788999
Q gi|254780191|r  288 DGILPANEGRGYVLRRIMRR  307 (898)
Q Consensus       288 DGv~PsN~GrGYvlRrilRR  307 (898)
                      -|.=|+|+||-|-+|-+|+|
T Consensus       144 ~GLGp~~~Grr~PvrTvlkk  163 (223)
T KOG2384         144 AGLGPENQGRRAPVRTVLKK  163 (223)
T ss_pred             CCCCCCCCCCCCCHHHHHHH
T ss_conf             58796666760643678762


No 109
>PRK11118 hypothetical protein; Provisional
Probab=40.42  E-value=21  Score=14.24  Aligned_cols=54  Identities=15%  Similarity=0.155  Sum_probs=39.7

Q ss_pred             EEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHH
Q ss_conf             000024767899999999999998988730453046612322210003554431
Q gi|254780191|r  617 LRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIASGAAALLGT  670 (898)
Q Consensus       617 lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~~ga~alfge  670 (898)
                      |-+||.+..+..+|-....+.++-.+-.+---+...|+.-++...-|++-||.+
T Consensus         5 LQidF~~~Gp~g~e~~~a~~~LA~sI~~epGliwKIWtene~~~eaGGiYlFe~   58 (100)
T PRK11118          5 LQVDFPFNGPFGEEMAKALKPLAESINEEPGFIWKIWTENEKTQEAGGIYLFED   58 (100)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCEEEEECC
T ss_conf             998347899878999999999888874288836778420678771453899657


No 110
>COG3957 Phosphoketolase [Carbohydrate transport and metabolism]
Probab=38.91  E-value=17  Score=14.96  Aligned_cols=30  Identities=17%  Similarity=0.227  Sum_probs=24.3

Q ss_pred             CCHHHEEECCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             9989975357866654579999987704678
Q gi|254780191|r  146 LSADKIIRITTNDNFWSMAETGPCGPCSEIF  176 (898)
Q Consensus       146 i~~~~i~~~~~~dNfW~~g~~GpcGPcsEi~  176 (898)
                      .-..||+...+.+-.|-||+ |-|||..+..
T Consensus        74 ~H~nr~i~~~d~~~~yv~Gp-GHg~~~~~~~  103 (793)
T COG3957          74 AHLNRLISKYDANMAYVMGP-GHGGPAIVAN  103 (793)
T ss_pred             HHHHHHHHHHCCCEEEEECC-CCCCCEEEEC
T ss_conf             33347887627325899637-8886515532


No 111
>KOG0556 consensus
Probab=38.64  E-value=19  Score=14.51  Aligned_cols=28  Identities=11%  Similarity=0.201  Sum_probs=20.1

Q ss_pred             EECCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             9579997899999999997549978999
Q gi|254780191|r  800 IISEVDSKELKSVMDALQKKIQSGIIML  827 (898)
Q Consensus       800 ~~~~~d~~~Lr~l~d~l~~k~~~~vvvL  827 (898)
                      ..++++...=|.+..-+++++.....+|
T Consensus       396 ~~dDlsTe~Ek~LG~lV~eky~tdfyil  423 (533)
T KOG0556         396 DEDDLSTESEKKLGQLVREKYDTDFYIL  423 (533)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCEEEE
T ss_conf             7223588658899999998717847997


No 112
>TIGR02155 PA_CoA_ligase phenylacetate-CoA ligase; InterPro: IPR011880    Phenylacetate-CoA ligase (PA-CoA ligase) catalyzes the first step in aromatic catabolism of phenylacetic acid (PA) into phenylacetyl-CoA (PA-CoA) . Often located in a conserved gene cluster with enzymes involved in phenylacetic acid activation (paaG/H/I/J), phenylacetate-CoA ligase has been found among the proteobacteria as well as in Gram-positive prokaryotes . In the B-subclass proteobacterium Azoarcus evansii, phenylacetate-CoA ligase has been shown to be induced under aerobic and anaerobic growth conditions. It remains unclear however, whether this induction is due to the same enzyme or to another isoenzyme restricted to specific anaerobic growth conditions ..
Probab=38.50  E-value=22  Score=14.03  Aligned_cols=19  Identities=11%  Similarity=0.279  Sum_probs=9.1

Q ss_pred             CHHHHHHHHHHHHHHCCCC
Q ss_conf             9789999999999754997
Q gi|254780191|r  805 DSKELKSVMDALQKKIQSG  823 (898)
Q Consensus       805 d~~~Lr~l~d~l~~k~~~~  823 (898)
                      +-..-..++.++..++++.
T Consensus       383 ~h~~~~~l~~~i~~~iK~~  401 (431)
T TIGR02155       383 NHEQKSLLAKEIQHQIKAE  401 (431)
T ss_pred             CHHHHHHHHHHHHHHHHHH
T ss_conf             4268999999999986555


No 113
>PRK09819 alpha-mannosidase; Provisional
Probab=38.21  E-value=22  Score=13.99  Aligned_cols=53  Identities=15%  Similarity=0.161  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHH
Q ss_conf             89999874898999999899999999861154642457437998524588889
Q gi|254780191|r  347 IEETLRSEDERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLD  399 (898)
Q Consensus       347 I~~ii~~EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsg~~af~LyDTyGfP~d  399 (898)
                      |..+-..=+.+|.+..+.+..+++..+..+...-.-+..+.+.++-|.++|-.
T Consensus       345 id~Vy~d~~~~~~~~~~~~~~l~~~~~~~i~~~~~~~~~~~~vvfN~l~~~R~  397 (874)
T PRK09819        345 SDKVHREIVARYKLAEDMADNLLDFYMRKIADNMPQSDADKLTLFNLMPYPRE  397 (874)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCC
T ss_conf             47899999999999999999999999999985234578984999959997562


No 114
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=37.88  E-value=22  Score=13.96  Aligned_cols=48  Identities=19%  Similarity=0.404  Sum_probs=20.4

Q ss_pred             HHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             5201368899999752125444445530024300000247678999999999999989887
Q gi|254780191|r  584 SINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIA  644 (898)
Q Consensus       584 ~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~  644 (898)
                      +-|-...|++..-+++ ||..    |+. +.++++|    ....++.+   ||...+..|.
T Consensus        49 ~L~Rdpehv~kfl~~E-LgT~----G~i-dg~rlil----~Gkf~~~~---i~~~l~~Yi~   96 (201)
T PRK12336         49 ALNRDPDHLMKFLTRE-LGTA----GKI-EGNRAIF----NGKFTDEQ---ISAAIDEYVD   96 (201)
T ss_pred             HHCCCHHHHHHHHHHH-HCCC----CEE-ECCEEEE----EEEECHHH---HHHHHHHHHH
T ss_conf             8789989999999897-5787----365-1888999----84419999---9999999998


No 115
>PRK07757 acetyltransferase; Provisional
Probab=37.84  E-value=22  Score=13.95  Aligned_cols=23  Identities=17%  Similarity=0.293  Sum_probs=12.3

Q ss_pred             CHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             99999999999989887304530
Q gi|254780191|r  628 TSAELKSIEDNVNDIIAQNLPVV  650 (898)
Q Consensus       628 t~eel~~IE~~vN~~I~~n~~V~  650 (898)
                      +.+++..|.++++....++.-+.
T Consensus         8 ~~~Dv~~I~~Li~~~~~~g~Ll~   30 (152)
T PRK07757          8 RLSDVKAIHALINEYAKEGLMLP   30 (152)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             78889999999988876894526


No 116
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator; InterPro: IPR014264   Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC (see Q06065 from SWISSPROT). These proteins have a Fis family DNA binding sequence, a response regulator receiver domain, and sigma-54 interaction domain. They are found strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system  common in Gram-positive bacteria, where members of IPR014265 from INTERPRO and IPR014266 from INTERPRO also occur..
Probab=37.79  E-value=22  Score=13.95  Aligned_cols=38  Identities=29%  Similarity=0.486  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHCCCCCC--CCCCE-------EEEE--ECCCCCCHHH
Q ss_conf             9899999999861154642--45743-------7998--5245888899
Q gi|254780191|r  363 DRGLVLLDGVLSHLGKDEI--LNGDV-------AFKL--YDTHGLPLDI  400 (898)
Q Consensus       363 ~~G~~~l~~~i~~~~~~~~--lsg~~-------af~L--yDTyGfP~dl  400 (898)
                      +-|+..|+++++=....|+  |+|.+       |..|  ||=|-=|+|.
T Consensus        59 ~EGl~~L~qIL~~~P~TKVIViTGN~~r~NAlkAi~lGAYDFyqKP~d~  107 (451)
T TIGR02915        59 SEGLAALQQILAIAPDTKVIVITGNDDRENALKAIGLGAYDFYQKPIDP  107 (451)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHCCCCCCCCCCCCH
T ss_conf             5899999999963898048998668983889999643751013578757


No 117
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=37.62  E-value=7.7  Score=17.58  Aligned_cols=10  Identities=20%  Similarity=0.152  Sum_probs=5.4

Q ss_pred             HHHHHHHCCC
Q ss_conf             9999752125
Q gi|254780191|r  593 LHHALSTILG  602 (898)
Q Consensus       593 L~~alr~vLG  602 (898)
                      +-.++|+.|-
T Consensus       782 Vi~aiR~~L~  791 (1099)
T PRK02983        782 VLRAVRETLV  791 (1099)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999998


No 118
>COG5405 HslV ATP-dependent protease HslVU (ClpYQ), peptidase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=37.53  E-value=23  Score=13.92  Aligned_cols=42  Identities=17%  Similarity=0.305  Sum_probs=19.4

Q ss_pred             EEEEECHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf             99971689999999999999999998399988999999999999999
Q gi|254780191|r  723 IEAITGQRARSHLMGQDEKLKSLASFLKVSQGNVVGRVEEIWEEYRK  769 (898)
Q Consensus       723 IeavtG~~A~~~~~~~~~~l~~la~~L~~~~~~i~~ki~~L~~e~K~  769 (898)
                      |-..+|-.|-.     ..++..+...|...+.++....-.|..+|..
T Consensus        47 laGFAGstADa-----ftLfe~fe~kle~~~g~L~raavelaKdwr~   88 (178)
T COG5405          47 LAGFAGSTADA-----FTLFERFEAKLEQYQGDLFRAAVELAKDWRT   88 (178)
T ss_pred             EEEECCCCHHH-----HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             88743540169-----9999999999987568089999999875610


No 119
>PRK13137 consensus
Probab=37.26  E-value=23  Score=13.89  Aligned_cols=42  Identities=24%  Similarity=0.328  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCH-HHHHHHHH
Q ss_conf             99989999999986115464245743799852458888-99998766
Q gi|254780191|r  361 TLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPL-DIMQDILC  406 (898)
Q Consensus       361 TL~~G~~~l~~~i~~~~~~~~lsg~~af~LyDTyGfP~-dlt~eia~  406 (898)
                      |-++|+.++++..+++++    .++.||--|=|-|+|= |-+.+++.
T Consensus         4 ~~~~~m~Ri~~~F~~~k~----~~~~ali~yitaG~P~~~~s~~~~~   46 (266)
T PRK13137          4 TTNRGVQRLHAAFARARA----EGRAAFIPFLTAGYPSAAGFLQVAE   46 (266)
T ss_pred             CCHHHHHHHHHHHHHHHH----CCCCEEEEEECCCCCCHHHHHHHHH
T ss_conf             302048899999999997----6995388786681888789999999


No 120
>PRK01233 glyS glycyl-tRNA synthetase subunit beta; Validated
Probab=37.21  E-value=23  Score=13.88  Aligned_cols=15  Identities=7%  Similarity=0.195  Sum_probs=8.4

Q ss_pred             HHHHHHHHHHHHHCC
Q ss_conf             899999999999789
Q gi|254780191|r    5 SSIRTTFLEFFQKNG   19 (898)
Q Consensus         5 ~eiR~~fl~fF~~~~   19 (898)
                      .++.+.+.+.|++++
T Consensus        23 ~~l~~~~~~~l~~~~   37 (687)
T PRK01233         23 EQLAEKVTAELEEAG   37 (687)
T ss_pred             HHHHHHHHHHHHHCC
T ss_conf             999999999999879


No 121
>pfam08803 ydhR Putative mono-oxygenase ydhR. ydhR is a homodimeric protein that comprises of a central four-stranded beta sheet and four surrounding alpha helices. It shows structural homology to the ActVA-Orf6 and YgiN proteins which indicates it could be a mono-oxygenase.
Probab=36.95  E-value=23  Score=13.85  Aligned_cols=54  Identities=15%  Similarity=0.191  Sum_probs=38.8

Q ss_pred             EEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHH
Q ss_conf             000024767899999999999998988730453046612322210003554431
Q gi|254780191|r  617 LRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIASGAAALLGT  670 (898)
Q Consensus       617 lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~~ga~alfge  670 (898)
                      |-+||.+..+..+|-......++-.+-.+---+...|+.-++...-|++-+|.+
T Consensus         2 LQvdF~~~Gp~g~e~~~a~~~LA~sI~~epGliwKIWtene~~~~aGGiYlFe~   55 (97)
T pfam08803         2 LQVDFPFNGPFGEEMATALKDLAESINQEPGLIWKIWTENEETQEAGGIYLFED   55 (97)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCEEEEECC
T ss_conf             178427899878999999999988874488836888521688761465899667


No 122
>COG3673 Uncharacterized conserved protein [Function unknown]
Probab=36.84  E-value=21  Score=14.11  Aligned_cols=121  Identities=13%  Similarity=0.076  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             24899999898999987403333444641257788999999999848743310456899999864555555764678899
Q gi|254780191|r  270 VNHRVIVDHLRSSSFLIADGILPANEGRGYVLRRIMRRAMCYARLLGYTEPLMMHLLPALCTEMGSAYPELIQAKLLIEE  349 (898)
Q Consensus       270 ~~~rvIaDH~Ra~~f~I~DGv~PsN~GrGYvlRrilRRa~r~~~~lg~~~~fl~~lv~~v~~~m~~~ypeL~~~~~~I~~  349 (898)
                      -|||-++-|-+     -+|-+.-=---||--.-|+|--.+|+.-+|--+   +..+++..-.++..--|.+..+..... 
T Consensus       109 ~AYrFL~~~ye-----pGD~Iy~FGFSRGAf~aRVlagmir~vGlls~~---~~~~~d~Aw~~y~~r~~~~dp~~~~~t-  179 (423)
T COG3673         109 EAYRFLIFNYE-----PGDEIYAFGFSRGAFSARVLAGMIRHVGLLSRK---HAARIDEAWAHYRQRLSGLDPEGQKVT-  179 (423)
T ss_pred             HHHHHHHHHCC-----CCCEEEEEECCCHHHHHHHHHHHHHHHHHHCCC---CHHHHHHHHHHHHHHCCCCCHHHHHHH-
T ss_conf             99999998468-----777689862152169999999999874011166---589999999999854489982043556-


Q ss_pred             HHHHHHHHHHHHHHHHHH---HHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHH
Q ss_conf             998748989999998999---99999861154642457437998524588889999
Q gi|254780191|r  350 TLRSEDERFGKTLDRGLV---LLDGVLSHLGKDEILNGDVAFKLYDTHGLPLDIMQ  402 (898)
Q Consensus       350 ii~~EE~~F~~TL~~G~~---~l~~~i~~~~~~~~lsg~~af~LyDTyGfP~dlt~  402 (898)
                        ..--+-|.++-..+.+   .|+.+....+.-+.+ -+-.|-+|-.|-=-+|.+.
T Consensus       180 --r~rae~f~~~~~~dyeVk~HF~glfdtvnsvG~v-~d~l~~~~~~~n~vvd~Vr  232 (423)
T COG3673         180 --RFRAEYFRNICVDDYEVKAHFEGLFDTVNSVGYV-QDSLPLLQIKYNGVVDTVR  232 (423)
T ss_pred             --HHHHHHHHHHCCCCHHHHHHHHHHHHHHHEEEEE-CCCCCCCEECCCHHHHHHH
T ss_conf             --7654888754123443334566566542000487-4676665322440999998


No 123
>cd01138 FeuA Periplasmic binding protein FeuA.  These proteins have predicted to function as initial receptors in ABC transport of metal ions in some eubacterial species.  They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=36.56  E-value=16  Score=15.01  Aligned_cols=14  Identities=29%  Similarity=0.434  Sum_probs=9.6

Q ss_pred             EEEECCCCEEECCC
Q ss_conf             99973752000368
Q gi|254780191|r  512 EVVFDQTPFYAEAG  525 (898)
Q Consensus       512 ~ivLd~T~FY~E~G  525 (898)
                      .+.+|.-.||--+|
T Consensus       235 Vy~vd~~~f~~~~g  248 (248)
T cd01138         235 VYIVDAWVFYFADG  248 (248)
T ss_pred             EEEECCCCEEECCC
T ss_conf             89987121772789


No 124
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=36.25  E-value=24  Score=13.77  Aligned_cols=55  Identities=24%  Similarity=0.281  Sum_probs=38.0

Q ss_pred             CCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             126882899997168999999999999999999839998899999999999999999
Q gi|254780191|r  715 SIRAGIRRIEAITGQRARSHLMGQDEKLKSLASFLKVSQGNVVGRVEEIWEEYRKLQ  771 (898)
Q Consensus       715 si~sGvRRIeavtG~~A~~~~~~~~~~l~~la~~L~~~~~~i~~ki~~L~~e~K~l~  771 (898)
                      +|++|+.  -..+=..|++++++.-+.+......+.....++..++..+..+...+.
T Consensus        81 ~iGsg~~--ae~~~~eAie~l~k~~~~l~~~~~~l~~~l~~l~~~~~~l~~~~q~~~  135 (145)
T COG1730          81 SIGSGYY--AEKSADEAIEFLKKRIEELEKAIEKLQQALAELAQRIEQLEQEAQQLQ  135 (145)
T ss_pred             ECCCCEE--EEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7588556--653198899999999999999999999999999999999999999999


No 125
>TIGR01068 thioredoxin thioredoxin; InterPro: IPR005746 Thioredoxins , , ,  are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of 2 cysteine thiol groups to a disulphide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulphide and a dithiol. TR-S_2 + NADPH + H^+ -> TR-(SH)_2 + NADP^+ (1) trx-S_2 + TR-(SH)_2 -> trx-(SH)_2 + TR-S_2 (2) Protein-S_2 + trx-(SH)_2 -> Protein-(SH)_2 + trx-S_2 (3) In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide (steps 1 and 2). Reduced thioredoxin then directly reduces the disulphide in the substrate protein (step 3) . Protein disulphide isomerase (PDI), a resident foldase of the endoplasmic recticulum, is a multi-functional protein that catalyses the formation and isomerisation of disulphide bonds during protein folding , . PDI contains 2 redox active domains, near the N- and C-termini, that are similar to thioredoxin: both contribute to disulphide isomerase activity, but are functionally non-equivalent . Interestingly, a mutant PDI, with all 4 of the active cysteines replaced by serine, displays a low but detectable level of disulphide isomerase activity . Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity . A number of endoplasmic reticulum proteins that differ from the PDI major isozyme contain 2 (ERp60, ERp5) or 3 (ERp72 ) thioredoxin domains; all of them seem to be PDIs. 3D-structures have been determined for a number of thioredoxins . The molecule has a doubly-wound alternating alpha/beta fold, consisting of a 5-stranded parallel beta-sheet core, enclosed by 4 alpha-helices. The active site disulphide is located at the N-terminus of helix 2 in a short segment that is separated from the rest of the helix by a kink caused by a conserved proline. The 4-membered disulphide ring is located on the surface of the protein. A flat hydrophobic surface lies adjacent to the disulphide, which presumably facilitates interaction with other proteins.   One invariant feature of all thioredoxins is a cis-proline located in a loop preceding beta-strand 4. This residue is positioned in van der Waals contact with the active site cysteines and is important both for stability and function . Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase . Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0006662 glycerol ether metabolic process, 0045454 cell redox homeostasis.
Probab=35.84  E-value=12  Score=16.06  Aligned_cols=17  Identities=18%  Similarity=0.212  Sum_probs=7.7

Q ss_pred             HHHHHHCCCCEEEEEEC
Q ss_conf             53555369527999957
Q gi|254780191|r  786 LSCHKIADVNFMSHIIS  802 (898)
Q Consensus       786 ~~~~~i~~~~~i~~~~~  802 (898)
                      ++.+..+++.++..-++
T Consensus        39 ~a~e~~~~v~~~KlnvD   55 (101)
T TIGR01068        39 LAKEYEGKVKFVKLNVD   55 (101)
T ss_pred             HHHHCCCCCEEEEEECC
T ss_conf             87541697468885347


No 126
>pfam08318 COG4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi an intra Golgi transport.
Probab=35.82  E-value=24  Score=13.72  Aligned_cols=22  Identities=9%  Similarity=-0.197  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             9999989899998740333344
Q gi|254780191|r  273 RVIVDHLRSSSFLIADGILPAN  294 (898)
Q Consensus       273 rvIaDH~Ra~~f~I~DGv~PsN  294 (898)
                      .+||+.+|...=....+.-++.
T Consensus        54 ~~ia~~ar~~l~~~~~~~~~~~   75 (330)
T pfam08318        54 DIIAVKSRKLLENSMGIAKETR   75 (330)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCC
T ss_conf             9999999999874315665665


No 127
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=35.60  E-value=24  Score=13.70  Aligned_cols=60  Identities=20%  Similarity=0.267  Sum_probs=42.1

Q ss_pred             HHHHHHHCCCCCCCCCCEEEEEECCCCCCH------HHHHHHHHHCCCCCCC-HHHHHHHHHHHHHHH
Q ss_conf             999986115464245743799852458888------9999876650774435-888999999999764
Q gi|254780191|r  369 LDGVLSHLGKDEILNGDVAFKLYDTHGLPL------DIMQDILCARGLAGID-IISFNQALEEQRSRA  429 (898)
Q Consensus       369 l~~~i~~~~~~~~lsg~~af~LyDTyGfP~------dlt~eia~e~gi~~vD-~~~f~~~m~~qk~~s  429 (898)
                      +++.|-++.+++.-+..+-..|=|.||+|.      .-+..|++++|+. -+ ++..+.+|.++-.--
T Consensus        30 ve~~I~klakkG~t~SqIG~~LRD~~gip~Vk~vtG~ki~~ILk~~gl~-p~iPEDL~~LikKAv~ir   96 (148)
T PTZ00072         30 VVDQICKLAKKGLTPSQIGVYLRDSMGIPQVKNVTGRKILRILKHRGLA-PEIPEDLYFLIKKAVQMR   96 (148)
T ss_pred             HHHHHHHHHHCCCCHHHCCCEECCCCCCCCEEECCCCHHHHHHHHCCCC-CCCCHHHHHHHHHHHHHH
T ss_conf             9999999997799987712013345775532111356399999987998-999589999999999999


No 128
>PRK13787 adenylosuccinate synthetase; Provisional
Probab=34.97  E-value=25  Score=13.63  Aligned_cols=171  Identities=17%  Similarity=0.168  Sum_probs=82.6

Q ss_pred             HCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCC--CCCCCC--------CCHHHHHHHHH
Q ss_conf             30478875657665310175799999998879853005769999999997306--785433--------50248999998
Q gi|254780191|r  209 EQQNKQERFILPKMSIDTGMGLERMATVLQEKTNNYDIDLFKHLIQASEQVTG--MKYEGN--------NIVNHRVIVDH  278 (898)
Q Consensus       209 ~~~~~g~~~~Lp~~~IDTGmGLERl~~vlqg~~s~ydtD~f~pii~~i~~~~g--~~y~~~--------~~~~~rvIaDH  278 (898)
                      ...+.|.+.|=+...|--||=              -|-   .-++++++.+..  +...+.        -.+.|-+..|-
T Consensus        53 hllPSGil~~~~~~vIG~GvV--------------vdp---~~L~~Ei~~L~~~g~~~~~rL~Is~rahli~P~H~~lD~  115 (423)
T PRK13787         53 HLVPSGVIYDQTICVIGNGVV--------------LDP---LFFIEECDRLQKEGFPVKDKLLLSDACHLLFPYHSQIDS  115 (423)
T ss_pred             ECCCCEECCCCCEEEECCCEE--------------ECH---HHHHHHHHHHHHCCCCCCCCEEEECCCCCCCHHHHHHHH
T ss_conf             527717607996489899899--------------969---999999999863650567886996872368817999989


Q ss_pred             HHHHHHHHHHCCCCCCCCCC----HHHHHHHHHHHHHHHHHCCCCCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98999987403333444641----257788999999999848743310---45689999986455555576467889999
Q gi|254780191|r  279 LRSSSFLIADGILPANEGRG----YVLRRIMRRAMCYARLLGYTEPLM---MHLLPALCTEMGSAYPELIQAKLLIEETL  351 (898)
Q Consensus       279 ~Ra~~f~I~DGv~PsN~GrG----YvlRrilRRa~r~~~~lg~~~~fl---~~lv~~v~~~m~~~ypeL~~~~~~I~~ii  351 (898)
                      +|-..-.- + --=+-.|||    | -.++.|+++|.+.++.  ..|.   ..+++.....+...|..-.-..+.+.+.+
T Consensus       116 ~~E~~~~~-~-~~IGTTgrGIGPaY-~DK~~R~GIRv~DL~d--~~l~~kl~~~~~~kn~~l~~~~~~~~~~~~~~~e~l  190 (423)
T PRK13787        116 ARETTSSQ-E-HKIGTTKKGIGICY-ADKMMRTGLRVGDLLD--KSYKRRLKHLVDEKNRELDKLYGMPPVSYNDINDGL  190 (423)
T ss_pred             HHHHHCCC-C-CCCCCCCCCCHHHH-HHHCCCCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf             99986389-8-76788899601866-6534354651376640--019999999999999999985599868999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHH
Q ss_conf             874898999999899999999861154642457437998524588889999
Q gi|254780191|r  352 RSEDERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLDIMQ  402 (898)
Q Consensus       352 ~~EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsg~~af~LyDTyGfP~dlt~  402 (898)
                      ..=-++...-+-.-..+++..+++ +++=.+-|.+...|---||+=|=.|.
T Consensus       191 ~~~~~~l~~~i~dt~~~l~~al~~-gk~ILfEGAQG~lLDiD~GtYPfVTS  240 (423)
T PRK13787        191 KFFLSKVGKNIINTAYYLDTELKK-GKRVLLEGAQGTGLDVDFGTYPYVTS  240 (423)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHC-CCEEEEECCCCEEECCCCCCCCCCCC
T ss_conf             999999876535789999999965-99799962651165366786775467


No 129
>KOG0434 consensus
Probab=34.91  E-value=14  Score=15.46  Aligned_cols=51  Identities=14%  Similarity=0.245  Sum_probs=34.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Q ss_conf             74331045689999986455555576467889999-8748989999998999
Q gi|254780191|r  317 YTEPLMMHLLPALCTEMGSAYPELIQAKLLIEETL-RSEDERFGKTLDRGLV  367 (898)
Q Consensus       317 ~~~~fl~~lv~~v~~~m~~~ypeL~~~~~~I~~ii-~~EE~~F~~TL~~G~~  367 (898)
                      -+.|+|++.||+.--..++.-|+|.++-+.+.=+= ..-|+||..=|+..+.
T Consensus       404 SDTPLiYraVPsWFVrVk~~v~~ll~nn~~t~WVP~~ikeKRF~NWL~nARD  455 (1070)
T KOG0434         404 SDTPLIYRAVPSWFVRVKNIVDQLLRNNMKTHWVPQNIKEKRFANWLKNARD  455 (1070)
T ss_pred             CCCHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             8970787634276511997799998515544347705567788888753031


No 130
>pfam11079 YqhG Bacterial protein YqhG of unknown function. This family of putative proteins is conserved in the Bacillaceae family of the Firmicutes. The function is not known.
Probab=34.50  E-value=25  Score=13.57  Aligned_cols=11  Identities=27%  Similarity=0.389  Sum_probs=4.4

Q ss_pred             HHHHHCCCCEE
Q ss_conf             99975499789
Q gi|254780191|r  815 ALQKKIQSGII  825 (898)
Q Consensus       815 ~l~~k~~~~vv  825 (898)
                      .|+.+....+.
T Consensus       238 aL~~qYePrI~  248 (260)
T pfam11079       238 ALKEQYEPKIK  248 (260)
T ss_pred             HHHHHHCCCEE
T ss_conf             99998678339


No 131
>PRK11805 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=34.43  E-value=25  Score=13.56  Aligned_cols=27  Identities=19%  Similarity=0.335  Sum_probs=22.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             678999999999999989887304530
Q gi|254780191|r  624 SKPITSAELKSIEDNVNDIIAQNLPVV  650 (898)
Q Consensus       624 ~~~lt~eel~~IE~~vN~~I~~n~~V~  650 (898)
                      ..+++++|+.+++.++.+-+.+..|+.
T Consensus        65 d~~l~~~e~~~~~~lv~rR~~~r~Pla   91 (307)
T PRK11805         65 DARLTPSEKERILELIERRINERIPAA   91 (307)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             589999999999999999983798589


No 132
>TIGR01428 HAD_type_II haloacid dehalogenase, type II; InterPro: IPR006328   These proteins catalyze the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids . They belong to the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases, class (subfamily) I. Note that the Type I HAD enzymes have not yet been fully characterised, but clearly utilise a substantially different catalytic mechanism and are thus unlikely to be related.; GO: 0019120 hydrolase activity acting on acid halide bonds in C-halide compounds, 0008152 metabolic process.
Probab=33.62  E-value=26  Score=13.47  Aligned_cols=13  Identities=8%  Similarity=0.312  Sum_probs=7.1

Q ss_pred             CHHHHHHHHHHCC
Q ss_conf             8899998766507
Q gi|254780191|r  397 PLDIMQDILCARG  409 (898)
Q Consensus       397 P~dlt~eia~e~g  409 (898)
                      ++++++.+++..|
T Consensus       125 ~~~~~~~~~~~aG  137 (207)
T TIGR01428       125 SPAMLKSLVKHAG  137 (207)
T ss_pred             CHHHHHHHHHHCC
T ss_conf             8678999999628


No 133
>PRK10045 acyl carrier protein phosphodiesterase; Provisional
Probab=33.62  E-value=26  Score=13.47  Aligned_cols=59  Identities=15%  Similarity=0.250  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHH------HHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             99999898999987403333444641257788999------999999848743310456899999864555
Q gi|254780191|r  273 RVIVDHLRSSSFLIADGILPANEGRGYVLRRIMRR------AMCYARLLGYTEPLMMHLLPALCTEMGSAY  337 (898)
Q Consensus       273 rvIaDH~Ra~~f~I~DGv~PsN~GrGYvlRrilRR------a~r~~~~lg~~~~fl~~lv~~v~~~m~~~y  337 (898)
                      ..++|.+|.-.    .+-+|...-+|-.|-|-|=+      .++.++.+ +..+ +-...+++++.+-|.|
T Consensus        20 N~lgDfvKG~~----~~~~p~~i~~GI~LHR~ID~fTD~Hp~~~~~~~~-~~~~-~rryagI~vDi~~DHf   84 (193)
T PRK10045         20 NLLADFVRGNP----EESYPPDVVAGIYMHRRIDVLTDNLPEVREAREW-FRSE-TRRVAPITLDVMWDHF   84 (193)
T ss_pred             HHHHHHCCCCC----HHHCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHH-CCCC-CCCHHHHHHHHHHHHH
T ss_conf             78888207877----4549999999999999998886369999999985-6730-1305899999999999


No 134
>pfam00853 Runt Runt domain.
Probab=33.53  E-value=11  Score=16.44  Aligned_cols=17  Identities=47%  Similarity=0.681  Sum_probs=8.9

Q ss_pred             CCCCCHHHCCCCCCCHH
Q ss_conf             98786343464885001
Q gi|254780191|r   72 GKHNDLDNVGRTNRHHT   88 (898)
Q Consensus        72 gkhnDld~VG~t~rH~T   88 (898)
                      +|||||--||+++|--+
T Consensus        81 AkFndLRFvgRSgrgKs   97 (134)
T pfam00853        81 AKFNDLRFVGRSGRGKS   97 (134)
T ss_pred             CCCCCEEEEEECCCCCE
T ss_conf             54056079874478723


No 135
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=33.24  E-value=26  Score=13.48  Aligned_cols=51  Identities=31%  Similarity=0.371  Sum_probs=35.2

Q ss_pred             HHHHHCCC--------CCCCCCCCEECCCEE-E------EECCCCCCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99752125--------444445530024300-0------002476789999999999999898873045
Q gi|254780191|r  595 HALSTILG--------SHVSQNGSCITPDGL-R------FDVTHSKPITSAELKSIEDNVNDIIAQNLP  648 (898)
Q Consensus       595 ~alr~vLG--------~hv~Q~GS~v~~~~l-r------fDfsh~~~lt~eel~~IE~~vN~~I~~n~~  648 (898)
                      ..|-+.||        -+-||+||.=+.+.| |      +||   ..+|+++|..|+...|..=++.+-
T Consensus       237 ~~l~~~l~~~vyfcdp~apWQRGtnENtNgliRrf~PKgTdl---a~vt~~el~~i~~~lN~rPRK~Lg  302 (318)
T COG2826         237 SELEKRLGADVYFADPYASWQRGTNENTNGLIRRFLPKGTDL---AAVTQEELAAIADLLNHRPRKCLG  302 (318)
T ss_pred             HHHHHHCCCCEEECCCCCCHHCCCCCCCCCHHHHHCCCCCCH---HHCCHHHHHHHHHHHHCCCHHHHC
T ss_conf             888862388158638998120366534420789867798753---018999999999998267446528


No 136
>TIGR02707 butyr_kinase butyrate kinase; InterPro: IPR011245   This group represents bacterial butyrate kinase, an enzyme that facilitates the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl phosphate . The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-CoA:acetate CoA-transferase, the latter providing the dominant route for butyrate formation in human colonic bacteria .; GO: 0005524 ATP binding, 0047761 butyrate kinase activity, 0016310 phosphorylation, 0005737 cytoplasm.
Probab=33.01  E-value=24  Score=13.77  Aligned_cols=19  Identities=32%  Similarity=0.429  Sum_probs=7.7

Q ss_pred             HHHHHHHHHCCCCCCCHHH
Q ss_conf             9999876650774435888
Q gi|254780191|r  399 DIMQDILCARGLAGIDIIS  417 (898)
Q Consensus       399 dlt~eia~e~gi~~vD~~~  417 (898)
                      |=.+++|+-.|+..+....
T Consensus       132 DEledvARISG~P~i~RkS  150 (353)
T TIGR02707       132 DELEDVARISGLPEIERKS  150 (353)
T ss_pred             CCCCCHHHHCCCCCCCCEE
T ss_conf             0551013213889864110


No 137
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=32.62  E-value=27  Score=13.35  Aligned_cols=58  Identities=12%  Similarity=0.090  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCC-----------CCCCCCCEEEEEECCCCCCHHHHHH
Q ss_conf             889999874898999999899999999861----154-----------6424574379985245888899998
Q gi|254780191|r  346 LIEETLRSEDERFGKTLDRGLVLLDGVLSH----LGK-----------DEILNGDVAFKLYDTHGLPLDIMQD  403 (898)
Q Consensus       346 ~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~----~~~-----------~~~lsg~~af~LyDTyGfP~dlt~e  403 (898)
                      .|.+++..|..+-..-+.+-+..+.+.+..    +.+           ++.|.--||-++.-|||.|++.++-
T Consensus        21 e~l~~~~~ed~~v~~Av~~~l~~I~~av~~~~~~l~~gGRL~YvGAGTSGRlgvlDa~E~~PTfg~~~~~v~~   93 (296)
T PRK12570         21 DIVTLINQEDKKVPLAVEKVLPQIAQAVDKIVAAFKQGGRLIYMGAGTSGRLGVLDASECPPTFSVSPEMVIG   93 (296)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHCCCCCCCCHHHEEE
T ss_conf             9999999988999999999999999999999999965983999778705899999998727865899899676


No 138
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=32.61  E-value=27  Score=13.35  Aligned_cols=60  Identities=18%  Similarity=0.244  Sum_probs=40.5

Q ss_pred             HHHHHHHCCCCCCCCCCEEEEEECCCCCCHH------HHHHHHHHCCCCCCC-HHHHHHHHHHHHHHH
Q ss_conf             9999861154642457437998524588889------999876650774435-888999999999764
Q gi|254780191|r  369 LDGVLSHLGKDEILNGDVAFKLYDTHGLPLD------IMQDILCARGLAGID-IISFNQALEEQRSRA  429 (898)
Q Consensus       369 l~~~i~~~~~~~~lsg~~af~LyDTyGfP~d------lt~eia~e~gi~~vD-~~~f~~~m~~qk~~s  429 (898)
                      ++..|-++.+++.-|..+-..|=|.||+|.=      =+..|++++|+. .+ ++..+.+|.++-.--
T Consensus        33 ve~~I~klaKkG~spS~IG~~LRD~~gip~Vk~vtGkki~~iLk~~gl~-p~iPEDL~~LikkAv~lr   99 (151)
T PRK08561         33 IEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENGLA-PEIPEDLMNLIKKAVNLR   99 (151)
T ss_pred             HHHHHHHHHHCCCCHHHHHCEECCCCCCCCCHHHCCCCHHHHHHHCCCC-CCCCHHHHHHHHHHHHHH
T ss_conf             9999999996799887861012232566520122278399999976998-889679999999999999


No 139
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=32.45  E-value=21  Score=14.15  Aligned_cols=47  Identities=23%  Similarity=0.290  Sum_probs=23.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHCCCCCEEEEEE
Q ss_conf             89999999999999898873045304661232221000355443155562489984
Q gi|254780191|r  626 PITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIASGAAALLGTKYNDRVRVVSV  681 (898)
Q Consensus       626 ~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~~ga~alfgekygd~VRVV~I  681 (898)
                      -|++||..+        |.+.+.+....+|.=.+..-=|. ..|.|.||.|+||.=
T Consensus        20 vls~eE~~~--------vLk~l~i~~~qLPkI~~~DPva~-~lgak~GdvVkIvRk   66 (80)
T COG2012          20 VLSEEEAKE--------VLKELGIEPEQLPKIKASDPVAK-ALGAKPGDVVKIVRK   66 (80)
T ss_pred             ECCHHHHHH--------HHHHHCCCHHHCCCCCCCCHHHH-HHCCCCCCEEEEEEC
T ss_conf             739999999--------99994989788885024676677-706787867999863


No 140
>TIGR03443 alpha_am_amid L-aminoadipate-semialdehyde dehydrogenase. Members of this protein family are L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31), product of the LYS2 gene. It is also called alpha-aminoadipate reductase. In fungi, lysine is synthesized via aminoadipate. Currently, all members of this family are fungal.
Probab=32.03  E-value=23  Score=13.83  Aligned_cols=11  Identities=0%  Similarity=-0.003  Sum_probs=5.7

Q ss_pred             CCCCHHHHHHH
Q ss_conf             26798999999
Q gi|254780191|r  848 DRFNAVDLARL  858 (898)
Q Consensus       848 ~~~~A~~lik~  858 (898)
                      .++...+|+.+
T Consensus      1148 ~GY~qSKWvaE 1158 (1389)
T TIGR03443      1148 TGYGQSKWVAE 1158 (1389)
T ss_pred             CCHHHHHHHHH
T ss_conf             74388899999


No 141
>cd06008 NF-X1-zinc-finger Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.
Probab=31.89  E-value=17  Score=14.96  Aligned_cols=11  Identities=55%  Similarity=1.410  Sum_probs=9.1

Q ss_pred             CCCCCCCEEEE
Q ss_conf             99987704678
Q gi|254780191|r  166 TGPCGPCSEIF  176 (898)
Q Consensus       166 ~GpcGPcsEi~  176 (898)
                      .|||+||.++-
T Consensus        22 ~G~C~pC~~~~   32 (49)
T cd06008          22 EGPCPPCPETV   32 (49)
T ss_pred             CCCCCCCCCCC
T ss_conf             98592917717


No 142
>COG0282 ackA Acetate kinase [Energy production and conversion]
Probab=31.88  E-value=8.6  Score=17.20  Aligned_cols=54  Identities=15%  Similarity=0.274  Sum_probs=23.1

Q ss_pred             HHCCCCEEEEEEC-CCCHHHHHHHHHH-H----------HHHCCCCEEEEEEECCCCEEEEEEEECHH
Q ss_conf             5369527999957-9997899999999-9----------97549978999995389817999986778
Q gi|254780191|r  790 KIADVNFMSHIIS-EVDSKELKSVMDA-L----------QKKIQSGIIMLVGISKEKKASVLIVVTED  845 (898)
Q Consensus       790 ~i~~~~~i~~~~~-~~d~~~Lr~l~d~-l----------~~k~~~~vvvL~~~~~~~k~~ivv~vs~~  845 (898)
                      ..+++..++..-. +.+....|+.+-. +          ++. ..+...+++ ..+.++.+++..|+.
T Consensus       316 ~L~glDaiVFTaGIGENs~~iR~~v~~~L~~lGi~lD~e~N~-~~g~~~~Is-~~~S~v~v~VIpTnE  381 (396)
T COG0282         316 ALGGLDALVFTAGIGENSALVRELVCEGLAFLGIELDPEKNL-RSGGEGIIS-TADSKVKVLVIPTNE  381 (396)
T ss_pred             HHCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCEEECHHHHC-CCCCCEEEC-CCCCCCEEEEECCCH
T ss_conf             857998899917646685899999985532247577777854-667652534-899861599956868


No 143
>COG0430 RCL1 RNA 3'-terminal phosphate cyclase [RNA processing and modification]
Probab=31.77  E-value=27  Score=13.25  Aligned_cols=18  Identities=28%  Similarity=0.516  Sum_probs=8.5

Q ss_pred             CEEEEEECCCCEEECCCC
Q ss_conf             769999737520003687
Q gi|254780191|r  509 QKVEVVFDQTPFYAEAGG  526 (898)
Q Consensus       509 ~~~~ivLd~T~FY~E~GG  526 (898)
                      .+..+.+.+-=|||+|||
T Consensus       146 ~~~~l~vlkRG~yP~GGG  163 (341)
T COG0430         146 IECELEVLKRGFYPRGGG  163 (341)
T ss_pred             CCEEEEEEECCCCCCCCC
T ss_conf             205999983245879982


No 144
>TIGR03533 L3_gln_methyl protein-(glutamine-N5) methyltransferase, ribosomal protein L3-specific. Members of this protein family methylate ribosomal protein L3 on a glutamine side chain. This family is related to HemK, a protein-glutamine methyltranferase for peptide chain release factors.
Probab=31.61  E-value=28  Score=13.24  Aligned_cols=27  Identities=22%  Similarity=0.379  Sum_probs=22.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             678999999999999989887304530
Q gi|254780191|r  624 SKPITSAELKSIEDNVNDIIAQNLPVV  650 (898)
Q Consensus       624 ~~~lt~eel~~IE~~vN~~I~~n~~V~  650 (898)
                      ..+++++|..+++.++.+-+....|+.
T Consensus        53 ~~~l~~~e~~~~~~lv~RR~~~r~Pl~   79 (284)
T TIGR03533        53 DARLTPSEKERILELIERRIEERIPVA   79 (284)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             488999999999999999982798589


No 145
>COG0751 GlyS Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]
Probab=31.43  E-value=28  Score=13.21  Aligned_cols=44  Identities=16%  Similarity=0.313  Sum_probs=24.1

Q ss_pred             HHHHHHHH-HHHHHHCCCC---CCCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             57699999-9999730678---543350248999998989999874033334
Q gi|254780191|r  246 IDLFKHLI-QASEQVTGMK---YEGNNIVNHRVIVDHLRSSSFLIADGILPA  293 (898)
Q Consensus       246 tD~f~pii-~~i~~~~g~~---y~~~~~~~~rvIaDH~Ra~~f~I~DGv~Ps  293 (898)
                      .++...++ +.|.++.--+   .++.+ ..|   +--+|.++.+..|-|+|-
T Consensus       130 ~~iL~~i~~~~i~~l~~pK~MrWg~~~-~~f---iRPi~~iv~L~g~evip~  177 (691)
T COG0751         130 EELLPEIVPEAIASLPFPKSMRWGSKD-VRF---IRPIHWIVALLGDEVIPF  177 (691)
T ss_pred             HHHHHHHHHHHHHCCCCCCCEEECCCC-EEE---ECCHHHHHHHHCCEEEEE
T ss_conf             999999999999759898750457987-188---530556666608845200


No 146
>PRK11619 lytic murein transglycosylase; Provisional
Probab=31.42  E-value=28  Score=13.21  Aligned_cols=42  Identities=7%  Similarity=0.000  Sum_probs=24.9

Q ss_pred             HHHEECCCCCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             1001101212688289999716899999999999999999983999
Q gi|254780191|r  707 LLYIVSESSIRAGIRRIEAITGQRARSHLMGQDEKLKSLASFLKVS  752 (898)
Q Consensus       707 ~fkIise~si~sGvRRIeavtG~~A~~~~~~~~~~l~~la~~L~~~  752 (898)
                      .+-|+..||-    ....|.++-.|.-.++-.-.+-+.+++.++.+
T Consensus       498 ~~ai~RqES~----f~~~a~S~~gA~GlmQ~mP~Ta~~~a~~~~~~  539 (645)
T PRK11619        498 AMAIARQESA----WNPKVKSPVGASGLMQIMPGTATHTVKMFSIP  539 (645)
T ss_pred             HHHHHHHHHC----CCCCCCCCCCCCCCHHHCHHHHHHHHHHCCCC
T ss_conf             9999987733----89878767787313631779999999983997


No 147
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.18  E-value=28  Score=13.18  Aligned_cols=38  Identities=29%  Similarity=0.483  Sum_probs=30.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf             379985245888899998766507744358889999999
Q gi|254780191|r  386 VAFKLYDTHGLPLDIMQDILCARGLAGIDIISFNQALEE  424 (898)
Q Consensus       386 ~af~LyDTyGfP~dlt~eia~e~gi~~vD~~~f~~~m~~  424 (898)
                      .+..+|-+||+.+=.++||..|+||. ||.+.-.....+
T Consensus        16 ~~V~~yl~~~Ls~r~v~eml~eRgi~-v~h~Ti~rwv~k   53 (215)
T COG3316          16 VAVWLYLRYGLSLRDVEEMLAERGIE-VDHETIHRWVQK   53 (215)
T ss_pred             HHHHHHHHCCHHHCCHHHHHHHCCCC-HHHHHHHHHHHH
T ss_conf             88998870632333499999983972-509999999999


No 148
>cd06815 PLPDE_III_AR_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1. This subfamily is composed of uncharacterized bacterial proteins with similarity to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Probab=31.16  E-value=28  Score=13.18  Aligned_cols=21  Identities=10%  Similarity=0.115  Sum_probs=14.1

Q ss_pred             CCCCCCEEEEEEHHHHHHHHH
Q ss_conf             755673388842125567775
Q gi|254780191|r  564 ILRTEMSLVLTIDYQNRRQLS  584 (898)
Q Consensus       564 ~l~~g~~V~~~VD~~rR~~~~  584 (898)
                      .+++||.|.-.+++.-=...|
T Consensus       323 ~~kvGD~i~F~l~Y~a~l~~m  343 (353)
T cd06815         323 DYKVGDEIRFNLDYGALLRAM  343 (353)
T ss_pred             CCCCCCEEEEECCHHHHHHHH
T ss_conf             888898899965999999984


No 149
>pfam02031 Peptidase_M7 Streptomyces extracellular neutral proteinase (M7) family.
Probab=31.05  E-value=20  Score=14.30  Aligned_cols=19  Identities=21%  Similarity=0.359  Sum_probs=8.6

Q ss_pred             HHCCCHHHHHHHHHHHCCC
Q ss_conf             5201368899999752125
Q gi|254780191|r  584 SINHSATHLLHHALSTILG  602 (898)
Q Consensus       584 ~~~HTatHlL~~alr~vLG  602 (898)
                      .++|..|-|...-+-.+||
T Consensus        72 ~qgy~~~RI~aHE~GH~LG   90 (132)
T pfam02031        72 NQQYDSTRVTAHETGHVLG   90 (132)
T ss_pred             HCCCCCHHHHHHHHCCCCC
T ss_conf             6588723110013222247


No 150
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit ClpA; InterPro: IPR013461    Proteins in this entry are related to ClpA () from Escherichia coli. ClpA is an ATP-dependent chaperone and part of the ClpAP protease that participates in regulatory protein degradation and the dissolution and degradation of protein aggregates . ClpA recognises sequences in specific proteins, which it then unfolds in an ATP-dependent manner and transports into the degradation chamber of the associated ClpP protein , . A small adaptor-like protein, ClpS, modulates the activity of ClpA and is an important regulatory factor for this protein . It protects ClpA from autodegradation and appears to redirect its activity away from soluble proteins and toward aggregated proteins..
Probab=31.04  E-value=28  Score=13.17  Aligned_cols=114  Identities=23%  Similarity=0.300  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCC----CCHHHH--HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH------------
Q ss_conf             57788999999999848743----310456--899999864555-55576467889999874898999------------
Q gi|254780191|r  300 VLRRIMRRAMCYARLLGYTE----PLMMHL--LPALCTEMGSAY-PELIQAKLLIEETLRSEDERFGK------------  360 (898)
Q Consensus       300 vlRrilRRa~r~~~~lg~~~----~fl~~l--v~~v~~~m~~~y-peL~~~~~~I~~ii~~EE~~F~~------------  360 (898)
                      -|+|+|++|+..++.=.-+-    =+|+-|  -+.-+++|...+ -.+..-++.+.+=+..+.+.+.+            
T Consensus         4 ~l~~~L~~A~~~AK~~~HEf~T~EH~Llal~~~~~~~~il~~cgd~d~~~L~~~L~~yl~~~~~~~~~~qlGyGg~~~~e   83 (774)
T TIGR02639         4 ELERILSEALEEAKERRHEFVTLEHLLLALLDDNEAIEILEECGDGDVELLRKKLEDYLEENLEVLEEEQLGYGGSEEEE   83 (774)
T ss_pred             HHHHHHHHHHHHHHHHCCCEECHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
T ss_conf             89999999999998618942438999999703767899998533311899999999987513887760224468886556


Q ss_pred             ---HHHHHHHHHHHHHHHC---CCCCCCCCCEEEEEE---CCCCCCHHHHHHHHHHCCCCCCCHHHHHH
Q ss_conf             ---9998999999998611---546424574379985---24588889999876650774435888999
Q gi|254780191|r  361 ---TLDRGLVLLDGVLSHL---GKDEILNGDVAFKLY---DTHGLPLDIMQDILCARGLAGIDIISFNQ  420 (898)
Q Consensus       361 ---TL~~G~~~l~~~i~~~---~~~~~lsg~~af~Ly---DTyGfP~dlt~eia~e~gi~~vD~~~f~~  420 (898)
                         |+-- -+.|++++-+.   +++.+=-|+.+-.||   +||.      .=.+..+|+...|.-.|=+
T Consensus        84 p~~T~g~-~~Viq~A~~h~~s~~~~~~~~gD~Lvalf~E~~S~a------~Y~Lk~qgi~Rl~~~~~is  145 (774)
T TIGR02639        84 PEQTVGV-QRVIQRALLHVKSAGKKEIDIGDLLVALFDEEDSHA------SYFLKSQGITRLDILNYIS  145 (774)
T ss_pred             CHHHHHH-HHHHHHHHHHHHHCCCCCCCCCHHHHEECCCCCCHH------HHHHHHCCCCHHHHHHHHC
T ss_conf             3001447-899999999853148860231110011102786131------0203321786999999741


No 151
>TIGR00871 zwf glucose-6-phosphate 1-dehydrogenase; InterPro: IPR001282   Glucose-6-phosphate dehydrogenase (1.1.1.49 from EC) (G6PDH) is a ubiquitous protein, present in bacteria and all eukaryotic cell types . The enzyme catalyses the the first step in the pentose pathway, i.e. the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the presence of NADP, producing NADPH. The ubiquitous expression of the enzyme gives it a major role in the production of NADPH for the many NADPH-mediated reductive processes in all cells . Deficiency of G6PDH is a common genetic abnormality affecting millions of people worldwide. Many sequence variants, most caused by single point mutations, are known, exhibiting a wide variety of phenotypes .; GO: 0004345 glucose-6-phosphate dehydrogenase activity, 0006006 glucose metabolic process.
Probab=30.99  E-value=28  Score=13.16  Aligned_cols=326  Identities=16%  Similarity=0.207  Sum_probs=152.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHCCCCCCCHH-HHHHHHHHHHHHHCCCCCCCCCC---------HHHHHHHHHHHHHHHH
Q ss_conf             5657665310175799999998879853005-76999999999730678543350---------2489999989899998
Q gi|254780191|r  216 RFILPKMSIDTGMGLERMATVLQEKTNNYDI-DLFKHLIQASEQVTGMKYEGNNI---------VNHRVIVDHLRSSSFL  285 (898)
Q Consensus       216 ~~~Lp~~~IDTGmGLERl~~vlqg~~s~ydt-D~f~pii~~i~~~~g~~y~~~~~---------~~~rvIaDH~Ra~~f~  285 (898)
                      +..=+..-+|... ||+++.-+-=.+.+||. +-|..|-+.+.++... |....+         .-|-.|+.++.+....
T Consensus        59 ~~~~~~~~~~~~~-~d~F~~~~~Y~~g~~dd~~~y~~L~~~L~~l~~~-~~~~gNr~fYLa~PP~~F~~i~~~L~~~~l~  136 (498)
T TIGR00871        59 LIKFETEEIDEQL-LDEFAQRLSYVSGDVDDDESYKKLAELLEKLDKT-YQTEGNRLFYLATPPSLFGTIIKQLKKHGLN  136 (498)
T ss_pred             HHCCCCCCCCHHH-HHHHHCCCEEEECCCCCHHHHHHHHHHHHHHHHH-CCCCCCEEEECCCCCCCCHHHHHHHHHHHCC
T ss_conf             3105786644225-9998607357744678768899999999899985-1888974565047844102678877653100


Q ss_pred             HHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH--HHHHHHHHHHHHH-------HHHHHHHHHHHHHH
Q ss_conf             74033334446412577889999999998487433104568999--9986455555576-------46788999987489
Q gi|254780191|r  286 IADGILPANEGRGYVLRRIMRRAMCYARLLGYTEPLMMHLLPAL--CTEMGSAYPELIQ-------AKLLIEETLRSEDE  356 (898)
Q Consensus       286 I~DGv~PsN~GrGYvlRrilRRa~r~~~~lg~~~~fl~~lv~~v--~~~m~~~ypeL~~-------~~~~I~~ii~~EE~  356 (898)
                      =      -|...|--+.           ++=++.||=++|-.+.  =..+...|.|=.=       -++.   |-+.+--
T Consensus       137 ~------~nq~~~~~w~-----------Rvv~EKPFG~DL~SA~~Ln~~~~~~F~E~qiYRIDHYLGKEt---VqNllvl  196 (498)
T TIGR00871       137 E------RNQEQGKTWS-----------RVVIEKPFGHDLASAQELNKQLRAVFKEDQIYRIDHYLGKET---VQNLLVL  196 (498)
T ss_pred             C------CCCCCCCCEE-----------EEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCCHH---HHHHHHH
T ss_conf             0------1355788447-----------999878899987899999999886548464467410126457---8899999


Q ss_pred             HHHHHHHHHHHHHHHH-----HHHC--CCCCCCCCCEEEEEECCCCCCHHHHH--------HHHHHCCCCCCCHHHHHHH
Q ss_conf             8999999899999999-----8611--54642457437998524588889999--------8766507744358889999
Q gi|254780191|r  357 RFGKTLDRGLVLLDGV-----LSHL--GKDEILNGDVAFKLYDTHGLPLDIMQ--------DILCARGLAGIDIISFNQA  421 (898)
Q Consensus       357 ~F~~TL~~G~~~l~~~-----i~~~--~~~~~lsg~~af~LyDTyGfP~dlt~--------eia~e~gi~~vD~~~f~~~  421 (898)
                      ||...+      |+.+     |++.  .-.+.|--|.=..-||..|.==||+|        .+|=|.=++ +|-+.-...
T Consensus       197 RFAN~~------Fep~WNr~~Id~VqIT~aE~~GvEgRggYyD~~GalRDmvQNHLLQlL~L~AME~P~~-~~a~~iRdE  269 (498)
T TIGR00871       197 RFANQI------FEPLWNRRYIDHVQITVAESFGVEGRGGYYDKSGALRDMVQNHLLQLLALVAMEPPVS-FDADSIRDE  269 (498)
T ss_pred             HHHHHH------HHHHCCCCCCCEEEEEEEEECCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCC-CCHHHHHHH
T ss_conf             647887------5321157764448997665046586301545404266788989999999982588875-686775203


Q ss_pred             HHH-HHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEE-----
Q ss_conf             999-99764443311001201356788873048862643444443211122211134445445556553489999-----
Q gi|254780191|r  422 LEE-QRSRARAHSLGLGSGTTEKIWFSLKEKYGATQFIGYDLLRGSKFMKEDRKVLCQKPPIDLTNGVSSIVKAI-----  495 (898)
Q Consensus       422 m~~-qk~~sr~~~~~~~~~~~~~~~~~~~~~~~~t~F~GYe~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~i-----  495 (898)
                      -.+ -|..+..+.....+...-.+|..= ...+ -.-.||-..++                 ...++++-+..|+     
T Consensus       270 KVKVL~a~r~~~~~dv~~~~VrGQY~ag-~~~G-~~v~GY~eE~g-----------------V~~dS~TeTF~A~~~~Id  330 (498)
T TIGR00871       270 KVKVLKALRPIDPDDVENNVVRGQYGAG-EIGG-VSVPGYLEEEG-----------------VDKDSNTETFAALKLEID  330 (498)
T ss_pred             HHHHHHHHCCCCHHHHHCCCEEEEECCC-CCCC-EECCCCCCCCC-----------------CCCCCCCCEEEEEEEEEC
T ss_conf             6668864151483213104020032255-5588-72256337788-----------------874548211367786761


Q ss_pred             ----------EECCCEEEECCCCCEEEEEECCCC---EEECCCCCCCCCCEEEECCEEEEEECCCCCCCEEEEEEECCCC
Q ss_conf             ----------747813200047976999973752---0003687656651454042489852245655338998510467
Q gi|254780191|r  496 ----------VQQGEIVEEAVSGQKVEVVFDQTP---FYAEAGGQLGDTGCAIGDGIRLQITDVQKKAEGIFVHHAIVER  562 (898)
Q Consensus       496 ----------~~~~~~v~~~~~g~~~~ivLd~T~---FY~E~GGQ~~D~G~i~~~~~~~~V~dv~k~~~g~i~H~~~~~~  562 (898)
                                ++-||...+  .-.++.|.|-+.|   |++..==-       ..+ ...-|+.+| +-+|+-+-...-.+
T Consensus       331 N~RW~GVPFYlRtGKrL~~--k~tEi~~~Fk~~p~~~F~~~~~~~-------~pE-~N~LvIRiQ-PDEGv~lkf~~K~P  399 (498)
T TIGR00871       331 NWRWAGVPFYLRTGKRLPE--KVTEIRIQFKTVPLNLFKANERDA-------NPE-RNALVIRIQ-PDEGVYLKFNAKKP  399 (498)
T ss_pred             CCCCCCCCHHHHCCCCCCC--CCCEEEEEEECCCCHHHHCCCCCC-------CCC-CCCEEEEEC-CCHHHHHHHHCCCC
T ss_conf             4326878234102631157--630489983066511100012346-------766-760689866-96468785414688


Q ss_pred             CCCCCCCEEEEEEHHHHHHHHHHCCCHHH---HHHHHHHHCCCCCC
Q ss_conf             87556733888421255677752013688---99999752125444
Q gi|254780191|r  563 GILRTEMSLVLTIDYQNRRQLSINHSATH---LLHHALSTILGSHV  605 (898)
Q Consensus       563 g~l~~g~~V~~~VD~~rR~~~~~~HTatH---lL~~alr~vLG~hv  605 (898)
                      |.-  -.......|.........+|+..=   ||.-||   +|+|.
T Consensus       400 G~~--~~~~~~~lDf~Y~~~~~~~~~peAYERLllD~l---~GD~t  440 (498)
T TIGR00871       400 GLA--FETRPVKLDFSYASRFGETKLPEAYERLLLDAL---LGDQT  440 (498)
T ss_pred             CCC--CEEEEEEEEECCCHHHCCCCCCCHHHHHHHHHH---CCCCC
T ss_conf             754--423786542020011022577344579999985---35777


No 152
>PRK11411 fecB iron-dicitrate transporter substrate-binding subunit; Provisional
Probab=30.95  E-value=28  Score=13.16  Aligned_cols=23  Identities=26%  Similarity=0.421  Sum_probs=11.4

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCC
Q ss_conf             437998524588889999876650774
Q gi|254780191|r  385 DVAFKLYDTHGLPLDIMQDILCARGLA  411 (898)
Q Consensus       385 ~~af~LyDTyGfP~dlt~eia~e~gi~  411 (898)
                      +.-|.+|....|    +..+....|+.
T Consensus       186 ~~~~~v~~~~s~----~g~il~~lG~~  208 (297)
T PRK11411        186 EQQFNLHSPESY----AGSVLAALGLQ  208 (297)
T ss_pred             CCCEEEECCCCH----HHHHHHHCCCC
T ss_conf             894699679841----79999983998


No 153
>PRK11070 ssDNA exonuclease RecJ; Provisional
Probab=30.92  E-value=28  Score=13.15  Aligned_cols=91  Identities=10%  Similarity=0.076  Sum_probs=50.0

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCEEEEEEEECHHHHCCCCHHHHHHHHHH----HHCCCCCCCCC
Q ss_conf             99995799978999999999975499789999953898179999867789726798999999998----83499999981
Q gi|254780191|r  797 MSHIISEVDSKELKSVMDALQKKIQSGIIMLVGISKEKKASVLIVVTEDLLDRFNAVDLARLSAK----VLGGGGGGGRP  872 (898)
Q Consensus       797 i~~~~~~~d~~~Lr~l~d~l~~k~~~~vvvL~~~~~~~k~~ivv~vs~~~~~~~~A~~lik~ia~----~l~GGgGGGkp  872 (898)
                      ++..-++....-+--+|.+|.++....++++. ...++.   +-+... ...+++..+.++.+..    .+  -++||- 
T Consensus       355 ivl~~~~WH~GViGIVAsRL~e~y~rP~ivl~-~~~dG~---~kGS~R-Si~g~~l~~aL~~~~~~~~~lL--~~fGGH-  426 (574)
T PRK11070        355 LAMYHPEWHQGVVGILASRIKERFHRPVIAFA-PAGDGT---LKGSGR-SIQGLHMRDALERLDTLYPGLI--LKFGGH-  426 (574)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHCCCEEEEE-ECCCCE---EEEEEC-CCCCCCHHHHHHHHHHHCHHHH--HHCCCC-
T ss_conf             99964886750699999999999799889999-878972---786421-7899768999999986474456--426675-


Q ss_pred             HHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             01145899987889999999998
Q gi|254780191|r  873 HMAQSGGPNGNKADQAIAGVASF  895 (898)
Q Consensus       873 d~AQgGG~~~~~l~eal~~vk~~  895 (898)
                      .+|=|=.-+.+++++..+...++
T Consensus       427 ~~AAG~tl~~~~l~~f~~~l~~~  449 (574)
T PRK11070        427 AMAAGLSLEEDKFELFQQRFGEL  449 (574)
T ss_pred             CCCCEEEECHHHHHHHHHHHHHH
T ss_conf             52230157699999999999999


No 154
>CHL00130 rbcS ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
Probab=30.89  E-value=28  Score=13.15  Aligned_cols=91  Identities=9%  Similarity=0.052  Sum_probs=60.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC----CHHHHHHHHC---------------CCC-CEEEEE
Q ss_conf             24767899999999999998988730453046612322210----0035544315---------------556-248998
Q gi|254780191|r  621 VTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIA----SGAAALLGTK---------------YND-RVRVVS  680 (898)
Q Consensus       621 fsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~----~ga~alfgek---------------ygd-~VRVV~  680 (898)
                      ||+--+||++||.   +.++-+|.++-.+.+++.+...+..    ++.+-+||.+               |++ -|||+-
T Consensus         8 fSyLP~LTdeqI~---kQI~Y~i~~GW~p~iEft~~~~~~n~YW~MWkLPMFg~tD~~~Vl~Ei~~Crka~P~~yIRvig   84 (138)
T CHL00130          8 FSFLPDLTDQQIY---KQIQYAISKGWSPNVEWTDDPHPRNSYWELWGLPLFDVKDPAAVMFEINACRKAKPNGYIKLVA   84 (138)
T ss_pred             ECCCCCCCHHHHH---HHHHHHHHCCCCCEEEECCCCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             0358999999999---9999999789921067668998564531000776679979999999999999879985799998


Q ss_pred             ECCCCCCCCCEEC-CCCCCCCCHHHHHHHHEECCCCCCC
Q ss_conf             4476778553101-5622258864601100110121268
Q gi|254780191|r  681 VEYEDGGVHSSAL-CGGTHVSSTGEIMLLYIVSESSIRA  718 (898)
Q Consensus       681 I~~~d~~~~S~El-CGGTHV~nTgeIG~fkIise~si~s  718 (898)
                      ++..-    -+|- |=.-=|.+-.+=-.|.+...+..+.
T Consensus        85 FDn~r----q~Qs~~~SFIv~rP~~epgf~l~r~e~~gr  119 (138)
T CHL00130         85 FDATR----GVESCVLSFIVNRPANEPGFYLERTESEGR  119 (138)
T ss_pred             EECCC----CEEEEEEEEEEECCCCCCCCEEEEEECCCC
T ss_conf             71776----368867999961799898727997644883


No 155
>cd01553 EPT_RTPC-like This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while  RTPC has 3 similar repeats with a 4th slightly different domain inserted between the 2nd and 3rd repeat. They evidently share the same active site location, although the catalytic residues differ.
Probab=30.77  E-value=27  Score=13.29  Aligned_cols=21  Identities=29%  Similarity=0.539  Sum_probs=15.9

Q ss_pred             CCEEEEEECCCCEEECCCCCC
Q ss_conf             976999973752000368765
Q gi|254780191|r  508 GQKVEVVFDQTPFYAEAGGQL  528 (898)
Q Consensus       508 g~~~~ivLd~T~FY~E~GGQ~  528 (898)
                      |-.+.+-+.+-=|||.|||++
T Consensus       141 G~~~~~~~~rrG~yP~GGG~v  161 (211)
T cd01553         141 GAHQEETLLRHGFYPAGGGVV  161 (211)
T ss_pred             CCCEEEEEEECCCCCCCCEEE
T ss_conf             996799998656043898289


No 156
>smart00022 PLAc Cytoplasmic phospholipase A2, catalytic subunit. Cytosolic phospholipases A2 hydrolyse arachidonyl phospholipids. Family includes phospholipases B isoforms.
Probab=30.63  E-value=29  Score=13.12  Aligned_cols=11  Identities=18%  Similarity=0.344  Sum_probs=5.4

Q ss_pred             CHHHHHHHHHH
Q ss_conf             36889999975
Q gi|254780191|r  588 SATHLLHHALS  598 (898)
Q Consensus       588 TatHlL~~alr  598 (898)
                      |...|.|..+.
T Consensus       301 TSSslFN~~~l  311 (549)
T smart00022      301 TSSSLFNRFLL  311 (549)
T ss_pred             ECHHHHHHHHH
T ss_conf             04989999999


No 157
>CHL00176 ftsH cell division protein; Validated
Probab=30.57  E-value=29  Score=13.11  Aligned_cols=15  Identities=20%  Similarity=0.348  Sum_probs=11.5

Q ss_pred             EHHHHHHHHHHCCCH
Q ss_conf             212556777520136
Q gi|254780191|r  575 IDYQNRRQLSINHSA  589 (898)
Q Consensus       575 VD~~rR~~~~~~HTa  589 (898)
                      =|.+-|..|-+.|..
T Consensus       347 PD~~gR~~IL~vh~k  361 (631)
T CHL00176        347 PDFEGRLDILKVHAR  361 (631)
T ss_pred             CCHHHHHHHHHHHHH
T ss_conf             898999999999970


No 158
>KOG0037 consensus
Probab=30.25  E-value=7.6  Score=17.63  Aligned_cols=30  Identities=20%  Similarity=0.067  Sum_probs=15.9

Q ss_pred             CCCCHHHHHHHHHH---C-CCCCCCHHHHHHHHHH
Q ss_conf             58888999987665---0-7744358889999999
Q gi|254780191|r  394 HGLPLDIMQDILCA---R-GLAGIDIISFNQALEE  424 (898)
Q Consensus       394 yGfP~dlt~eia~e---~-gi~~vD~~~f~~~m~~  424 (898)
                      |=+|+++.+.+.+.   . +- .++.+.|-++...
T Consensus       155 y~Lspq~~~~lv~kyd~~~~g-~i~FD~FI~ccv~  188 (221)
T KOG0037         155 YRLSPQFYNLLVRKYDRFGGG-RIDFDDFIQCCVV  188 (221)
T ss_pred             CCCCHHHHHHHHHHHCCCCCC-CCCHHHHHHHHHH
T ss_conf             477899999999986604688-4009999999999


No 159
>TIGR00458 aspS_arch aspartyl-tRNA synthetase; InterPro: IPR004523   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Aspartyl tRNA synthetase 6.1.1.12 from EC is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module .     This family represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). ; GO: 0000166 nucleotide binding, 0004815 aspartate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006422 aspartyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=30.19  E-value=23  Score=13.79  Aligned_cols=206  Identities=10%  Similarity=0.114  Sum_probs=97.2

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHCCC----CEEEEECCCCCCCCHHHHHHHHCCCCCEEEEEECCCCCCCCCEECCCCCCCC
Q ss_conf             789999999999999898873045----3046612322210003554431555624899844767785531015622258
Q gi|254780191|r  625 KPITSAELKSIEDNVNDIIAQNLP----VVTRIMNREDAIASGAAALLGTKYNDRVRVVSVEYEDGGVHSSALCGGTHVS  700 (898)
Q Consensus       625 ~~lt~eel~~IE~~vN~~I~~n~~----V~~~~~~~~eA~~~ga~alfgekygd~VRVV~I~~~d~~~~S~ElCGGTHV~  700 (898)
                      ..++..-|-+|...+-+.+++-+.    +++..+.+=-+-..|+..+|.--|=+.==-..=    ...+-+..-=-|-..
T Consensus       147 R~~~~~AIF~I~~~~~~~vR~~L~~~~F~Ev~TPKlv~~~tEGGt~lF~i~YF~~~AfL~Q----SPQlyKQ~l~~~g~~  222 (466)
T TIGR00458       147 RRPKVQAIFRIRSEVLESVREFLAEEGFIEVHTPKLVASATEGGTELFPITYFEREAFLGQ----SPQLYKQVLMAAGLE  222 (466)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEECCCCCCCCCCEEEEECCCCCCCC----CCHHHHHHHHHCCCC
T ss_conf             5654021255689999999998730882563076214216688853320122123000135----703566877652652


Q ss_pred             CHHHHHHHHEECCCCCCCCCEEEEEEECHHHHHHHHHH-HHHHHHHHHHHCCCHHHHHHHHHHHHHHH-HHHHHHHHHH-
Q ss_conf             86460110011012126882899997168999999999-99999999983999889999999999999-9999999999-
Q gi|254780191|r  701 STGEIMLLYIVSESSIRAGIRRIEAITGQRARSHLMGQ-DEKLKSLASFLKVSQGNVVGRVEEIWEEY-RKLQLIHAKR-  777 (898)
Q Consensus       701 nTgeIG~fkIise~si~sGvRRIeavtG~~A~~~~~~~-~~~l~~la~~L~~~~~~i~~ki~~L~~e~-K~l~k~~~k~-  777 (898)
                      +.=|||++-=--++   .-.|-+.=++|-...-.+.+. ++.++-+.+++..--.++.++.++-.+-. |.++....++ 
T Consensus       223 rVyEI~PiFRAE~~---nT~RHl~E~~siDiE~~F~dhy~~v~d~L~~lv~~~~~dv~~~~~~e~el~r~~~~~~~~~le  299 (466)
T TIGR00458       223 RVYEIGPIFRAEEH---NTRRHLNEAISIDIEMAFEDHYEDVMDILEELVVRVFEDVAEKCAKEIELVRKELETLEVKLE  299 (466)
T ss_pred             CEEEECCEEECCCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEC
T ss_conf             03550552205666---521455444442244442753789999999999999999998878889999875210231324


Q ss_pred             ----HHHHHHHH--HHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEE-ECCCCEEEEEE
Q ss_conf             ----99987636--53555369527999957999789999999999754997899999-53898179999
Q gi|254780191|r  778 ----KLQLNVED--LSCHKIADVNFMSHIISEVDSKELKSVMDALQKKIQSGIIMLVG-ISKEKKASVLI  840 (898)
Q Consensus       778 ----k~~~~~~~--~~~~~i~~~~~i~~~~~~~d~~~Lr~l~d~l~~k~~~~vvvL~~-~~~~~k~~ivv  840 (898)
                          +......+  +......|..  +...++++....+.+...++++... ..++.. ...+-|+.++.
T Consensus       300 ~P~~~~~Rl~Y~Ea~e~~~~~G~e--i~~gEDLs~~a~K~~G~l~re~~~g-~yfI~d~wP~ei~PFY~M  366 (466)
T TIGR00458       300 VPEEKFERLTYDEAIEIANAKGKE--IKWGEDLSTEAEKALGKLVREEMDG-LYFITDKWPTEIRPFYTM  366 (466)
T ss_pred             CCCCCCCCCCCHHHHHHHHHCCCC--CCCCCCCCHHHHHHHHHHHHHHHCC-CEEEEECCCCCCCCCCCC
T ss_conf             888755532207789999865971--5554665435788764788774276-168740587646762138


No 160
>TIGR01181 dTDP_gluc_dehyt dTDP-glucose 4,6-dehydratase; InterPro: IPR005888    The conversion of dTDP-glucose into dTDP-4-keto-6-deoxyglucose by Escherichia coli dTDP-glucose 4,6-dehydratase) takes place in the active site in three steps: dehydrogenation to dTDP-4-ketoglucose, dehydration to dTDP-4-ketoglucose-5,6-ene, and rereduction of C6 to the methyl group. The 4,6-dehydratase makes use of tightly bound NAD^+ as the coenzyme for transiently oxidizing the substrate, activating it for the dehydration step . This and other 4,6-dehydratases catalyze the first committed step in all 6-deoxysugar biosynthetic pathways described to date. Numerous 6-deoxysugars are used in bacterial lipopolysaccharide production as well as in the biosynthesis of a diverse array of secondary metabolites.; GO: 0008460 dTDP-glucose 46-dehydratase activity, 0009225 nucleotide-sugar metabolic process.
Probab=29.92  E-value=29  Score=13.03  Aligned_cols=17  Identities=24%  Similarity=0.184  Sum_probs=9.1

Q ss_pred             HHHCCCHHHHHHHHHHH
Q ss_conf             75201368899999752
Q gi|254780191|r  583 LSINHSATHLLHHALST  599 (898)
Q Consensus       583 ~~~~HTatHlL~~alr~  599 (898)
                      +.-|=-||+.|--|.|+
T Consensus        97 ~~TNv~GT~tLLEA~R~  113 (340)
T TIGR01181        97 IETNVVGTYTLLEAVRK  113 (340)
T ss_pred             HHCCHHHHHHHHHHHHH
T ss_conf             44033788999999974


No 161
>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=29.69  E-value=29  Score=13.00  Aligned_cols=162  Identities=17%  Similarity=0.161  Sum_probs=78.6

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHH----HHHHHHHHHHHHCCCCCCCCCCHHHHH---HHHHHHHHHHHH
Q ss_conf             8756576653101757999999988798530057----699999999973067854335024899---999898999987
Q gi|254780191|r  214 QERFILPKMSIDTGMGLERMATVLQEKTNNYDID----LFKHLIQASEQVTGMKYEGNNIVNHRV---IVDHLRSSSFLI  286 (898)
Q Consensus       214 g~~~~Lp~~~IDTGmGLERl~~vlqg~~s~ydtD----~f~pii~~i~~~~g~~y~~~~~~~~rv---IaDH~Ra~~f~I  286 (898)
                      +-++..+-..--+|-.++|+..+...+.-....|    -|......+.+.-..--..+...++|-   .-..+|+...=+
T Consensus        29 ~~~hgfD~~~~~~~~~~~rl~~l~~a~n~il~~e~~kkrF~~~v~~L~kA~aLc~~~~~a~~~r~evaff~AVra~l~K~  108 (333)
T pfam11867        29 GMFHGFDYSDFFTGDPAERLKLLLGAANHILGLDDGKKRFLDAVLALSKAFALCSPHDEAQAIRDEVAFFQAVRAALVKF  108 (333)
T ss_pred             HHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             88168991664389999999999999999857844888999999999999998669888999889899999999999871


Q ss_pred             HHCC-CCCCCCCCHHHHHHHHHHHHHHH------HHCCCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4033-33444641257788999999999------84874331045689999986455-5555764678899998748989
Q gi|254780191|r  287 ADGI-LPANEGRGYVLRRIMRRAMCYAR------LLGYTEPLMMHLLPALCTEMGSA-YPELIQAKLLIEETLRSEDERF  358 (898)
Q Consensus       287 ~DGv-~PsN~GrGYvlRrilRRa~r~~~------~lg~~~~fl~~lv~~v~~~m~~~-ypeL~~~~~~I~~ii~~EE~~F  358 (898)
                      .-|- -||++..-+.+|.||..|+...-      ..|++.|=++-|-+...+.+... +|.|  ..+..++.|..|-+.+
T Consensus       109 ~~~~~~~~~~e~~~~i~qll~~ai~s~~Vidif~~~g~~kpdisilsdeFL~ev~~~~~knl--aiE~L~kLL~~~Ik~~  186 (333)
T pfam11867       109 TTGSTGRSDEERNLAIRQLVDQAVVSDGVVDIFAAAGLDKPDISILSDEFLAEVKNMKHKNL--ALELLKKLLNDEIKSR  186 (333)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCHHHCCHHHHHHHHCCCCCCH--HHHHHHHHHHHHHHHH
T ss_conf             57889999999999999999998524340109976499987856517999998753877137--9999999999999999


Q ss_pred             HHH-HHHH---HHHHHHHHHHCC
Q ss_conf             999-9989---999999986115
Q gi|254780191|r  359 GKT-LDRG---LVLLDGVLSHLG  377 (898)
Q Consensus       359 ~~T-L~~G---~~~l~~~i~~~~  377 (898)
                      .+| +-++   .++|++.+.+.+
T Consensus       187 ~~~N~v~~~~FsE~Le~~i~~Y~  209 (333)
T pfam11867       187 SKTNLVQSKKFSERLEEAINKYH  209 (333)
T ss_pred             HHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             70068989999999999999998


No 162
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=29.68  E-value=29  Score=13.00  Aligned_cols=59  Identities=20%  Similarity=0.195  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCCC-----------CCCCCCEEEEEECCCCCCHHHHHHH
Q ss_conf             889999874898999999899999999861----1546-----------4245743799852458888999987
Q gi|254780191|r  346 LIEETLRSEDERFGKTLDRGLVLLDGVLSH----LGKD-----------EILNGDVAFKLYDTHGLPLDIMQDI  404 (898)
Q Consensus       346 ~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~----~~~~-----------~~lsg~~af~LyDTyGfP~dlt~ei  404 (898)
                      .|.+++..|..+-.+.+.+-+..++..++.    ++++           +.|.--||-++.-|||.|++.++-+
T Consensus        12 e~l~~~~~ed~~v~~av~~~lp~I~~~i~~~~~~l~~gGRl~Y~GAGTSGrlgvlDa~E~~PTFg~~~~~v~gl   85 (257)
T cd05007          12 EILRLLNEEDKKVAAAVEAALPQIARAVDAAAERLRAGGRLIYVGAGTSGRLGVLDASELPPTFGTPPERVVGL   85 (257)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHCCCCCCCCHHHHEEE
T ss_conf             99999999889999999998999999999999999659828998786058899988997398779998991102


No 163
>pfam09637 Med18 Med18 protein. Med18 is one subunit of Mediator, a head-module multiprotein complex, that stimulates basal RNA polymerase II (Pol II) transcription. Med18 consists of an eight-stranded beta-barrel with a central pore and three flanking helices. It complexes with Med8 and Med20 proteins by forming a heterodimer of two-fold symmetry with Med20 and binding the C-terminal alpha-helix region of Med8 across the top of its barrel. This complex creates a multipartite TBP-binding site that can be modulated by transcriptional activators.
Probab=29.58  E-value=19  Score=14.59  Aligned_cols=13  Identities=8%  Similarity=0.232  Sum_probs=4.9

Q ss_pred             EEECCCCEEECCC
Q ss_conf             9973752000368
Q gi|254780191|r  513 VVFDQTPFYAEAG  525 (898)
Q Consensus       513 ivLd~T~FY~E~G  525 (898)
                      |.|-+.-.+|+++
T Consensus       163 I~l~rv~~~p~~~  175 (239)
T pfam09637       163 ITLSKVFRIPDEG  175 (239)
T ss_pred             EEEEEEEECCCCC
T ss_conf             9999999727766


No 164
>TIGR03076 near_not_gcvH Chlamydial GcvH homolog upstream region protein. The H protein (GcvH) of the glycine cleavage system shuttles the methylamine group of glycine from the P protein to the T protein. Most Chlamydia but lack the P and T proteins, and have a single homolog of GcvH that appears deeply split from canonical GcvH in molecular phylogenetic trees. The protein family modeled here is observed so far only in the Chlamydiae, always as part of a two-gene operon, upstream of the homolog of GcvH. Its function is unknown.
Probab=29.45  E-value=18  Score=14.66  Aligned_cols=36  Identities=14%  Similarity=0.032  Sum_probs=26.4

Q ss_pred             CCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             243000002476789999999999999898873045304
Q gi|254780191|r  613 TPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVT  651 (898)
Q Consensus       613 ~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~  651 (898)
                      ..-..++||-+   |.+.-+.+|-..+...|....|-.+
T Consensus       432 ETc~S~~d~~~---Lkp~l~eKi~s~~RkeiLra~P~ri  467 (686)
T TIGR03076       432 ETCSSLKDFQN---LKPALVEKIHSFTRKEILRADPGRI  467 (686)
T ss_pred             CCCCHHHHHHH---CCHHHHHHHHHHHHHHHHHHCHHHH
T ss_conf             00234778985---3899999999998999987599999


No 165
>KOG1576 consensus
Probab=29.17  E-value=30  Score=12.94  Aligned_cols=12  Identities=25%  Similarity=0.769  Sum_probs=8.0

Q ss_pred             EEECCCCEEECC
Q ss_conf             997375200036
Q gi|254780191|r  513 VVFDQTPFYAEA  524 (898)
Q Consensus       513 ivLd~T~FY~E~  524 (898)
                      =-.|..|||.-|
T Consensus        69 NyiDTsp~Ygqs   80 (342)
T KOG1576          69 NYIDTSPYYGQS   80 (342)
T ss_pred             CCEECCCCCCCC
T ss_conf             620057655753


No 166
>TIGR02873 spore_ylxY probable sporulation protein, polysaccharide deacetylase family; InterPro: IPR014228   Members of this entry include YlxY, and are related to IPR014132 from INTERPRO, which represents a subset of the polysaccharide deacetylase family found in a species if, and only if, the species forms endospores e.g. Bacillus subtilis or Clostridium tetani. Proteins in this entry are likewise restricted to spore-formers, but are not universally found among endospore-forming species..
Probab=29.11  E-value=30  Score=12.93  Aligned_cols=43  Identities=21%  Similarity=0.399  Sum_probs=35.0

Q ss_pred             HCCCCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             21254444455300243000002476789999999999999898873045304661
Q gi|254780191|r  599 TILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIM  654 (898)
Q Consensus       599 ~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~  654 (898)
                      ...|.|     ||-.||.        +.||.|++.+==+..|++|.+-+.++.+|-
T Consensus       139 heiGNH-----aY~HPdM--------~~Ls~~~~~dql~~TN~~i~a~i~~~pkWF  181 (269)
T TIGR02873       139 HEIGNH-----AYNHPDM--------KTLSKERISDQLDKTNEVIEATIGVKPKWF  181 (269)
T ss_pred             CEECCC-----CCCCCCH--------HHCCHHHHHHHHHHHHHHHHHHHCCCCCEE
T ss_conf             646353-----4588562--------230347789999888999999857987040


No 167
>pfam01113 DapB_N Dihydrodipicolinate reductase, N-terminus. Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH.
Probab=29.08  E-value=26  Score=13.38  Aligned_cols=17  Identities=12%  Similarity=0.306  Sum_probs=13.8

Q ss_pred             CCCCHHHHHHHHHHHHH
Q ss_conf             78999999999999989
Q gi|254780191|r  625 KPITSAELKSIEDNVND  641 (898)
Q Consensus       625 ~~lt~eel~~IE~~vN~  641 (898)
                      ..++++|+.+|++.+++
T Consensus        97 TG~s~~~~~~i~~~a~~  113 (122)
T pfam01113        97 TGFTEEQLAELKEAAKK  113 (122)
T ss_pred             CCCCHHHHHHHHHHHCC
T ss_conf             99999999999998445


No 168
>TIGR01099 galU UTP-glucose-1-phosphate uridylyltransferase; InterPro: IPR005771   Uridine 5'-triphosphate:glucose-1-phosphate uridylyltransferase (uridine diphosphoglucose pyrophosphorylase, 2.7.7.9 from EC) is responsible for the synthesis of UDP-glucose, a key compound in the biosynthesis of polysaccharides. Glucose is fermented through the glycolysis step to pyruvate, which in turn is converted to lactate. The glycolytic intermediate glucose 6-phosphate is converted to glucose 1-phosphate by phosphoglucomutase activity, and this metabolite is subsequently converted to UDP-glucose by UDP-glucose pyrophosphorylase (GalU) activity. ; GO: 0003983 UTP:glucose-1-phosphate uridylyltransferase activity, 0006011 UDP-glucose metabolic process.
Probab=28.87  E-value=30  Score=12.90  Aligned_cols=121  Identities=23%  Similarity=0.288  Sum_probs=63.9

Q ss_pred             CCCCCCCCCEEEEEEECH--HHH-HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH--H
Q ss_conf             012126882899997168--999-9999999999999998399988999999999999-999999999999998763--6
Q gi|254780191|r  712 SESSIRAGIRRIEAITGQ--RAR-SHLMGQDEKLKSLASFLKVSQGNVVGRVEEIWEE-YRKLQLIHAKRKLQLNVE--D  785 (898)
Q Consensus       712 se~si~sGvRRIeavtG~--~A~-~~~~~~~~~l~~la~~L~~~~~~i~~ki~~L~~e-~K~l~k~~~k~k~~~~~~--~  785 (898)
                      =||.|.+|+.-|-+|||.  +|+ +||-..+++...|.+.   +..++.+.|+++.+. ..-.-   -+.+.++-..  -
T Consensus        39 VEEav~aGie~i~~VTGr~K~aIEDHFD~s~ELE~~L~~~---~K~~lL~~v~~I~~~~~~i~y---vRQke~kGLGhAv  112 (270)
T TIGR01099        39 VEEAVEAGIEDILIVTGRGKRAIEDHFDTSYELEHQLEKK---NKEELLKEVRKISNLNANIFY---VRQKEQKGLGHAV  112 (270)
T ss_pred             HHHHHHCCCCEEEEEECCCCCCCCCCCCCCHHHHHHHHHH---HHHHHHHHHHHHCCCCCCEEE---EECCCCCCCCHHH
T ss_conf             7989864893479996588501014258788899998751---048899999986269972899---8138888551275


Q ss_pred             HHH-HHHCCCCEEEEEECC-----CC--HHHHHHHHHHHHHHCCCCEEEEEEECCC--CEEEEE
Q ss_conf             535-553695279999579-----99--7899999999997549978999995389--817999
Q gi|254780191|r  786 LSC-HKIADVNFMSHIISE-----VD--SKELKSVMDALQKKIQSGIIMLVGISKE--KKASVL  839 (898)
Q Consensus       786 ~~~-~~i~~~~~i~~~~~~-----~d--~~~Lr~l~d~l~~k~~~~vvvL~~~~~~--~k~~iv  839 (898)
                      +.+ .-+++-.|.+..-|+     ..  .+.||++++...+ .+..+|.+-.+..+  .|..++
T Consensus       113 L~a~~~vGdEpFaV~LgDdi~~~~~~D~~~~Lkqm~~~Y~~-~g~s~iaV~~Vp~e~V~~YGii  175 (270)
T TIGR01099       113 LCARPLVGDEPFAVLLGDDIVVSEEPDLQEALKQMIDLYEK-YGCSIIAVEEVPKEEVSKYGII  175 (270)
T ss_pred             HHCCCCCCCCCEEEEECCEEEECCCCCHHHHHHHHHHHHHH-HCCEEEEEEECCHHHCCCCEEE
T ss_conf             43521258886067635265635887546899999999986-3881788863445517755157


No 169
>COG1482 ManA Phosphomannose isomerase [Carbohydrate transport and metabolism]
Probab=28.85  E-value=30  Score=12.90  Aligned_cols=25  Identities=40%  Similarity=0.349  Sum_probs=10.7

Q ss_pred             HHHHHCCCCHHHEEEEECCCHHHHHH
Q ss_conf             61334189812379997188289999
Q gi|254780191|r  113 LLTKEFDLDQRRLYITVYDEDEEAFK  138 (898)
Q Consensus       113 ~lt~~~~l~~~~l~vtv~~~D~e~~~  138 (898)
                      |||++|.... -|=|-||++|+.|.+
T Consensus        79 lL~KiLdA~~-~LSiQVHP~d~~A~~  103 (312)
T COG1482          79 LLFKILDAND-PLSIQVHPSDEYAEE  103 (312)
T ss_pred             CEEEEECCCC-CCEEEECCCHHHHHH
T ss_conf             2223520698-646787889799863


No 170
>KOG0673 consensus
Probab=28.61  E-value=31  Score=12.87  Aligned_cols=15  Identities=13%  Similarity=0.456  Sum_probs=6.0

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             645555557646788
Q gi|254780191|r  333 MGSAYPELIQAKLLI  347 (898)
Q Consensus       333 m~~~ypeL~~~~~~I  347 (898)
                      |.+.||=|..++-+-
T Consensus        47 Lr~tfPLLTTkrVfw   61 (293)
T KOG0673          47 LRDTFPLLTTKRVFW   61 (293)
T ss_pred             HHCCCCCHHHHHHHH
T ss_conf             111565201235778


No 171
>KOG0414 consensus
Probab=28.31  E-value=24  Score=13.67  Aligned_cols=20  Identities=25%  Similarity=0.466  Sum_probs=9.2

Q ss_pred             EECCCCCCHHHHHHHHHHCC
Q ss_conf             85245888899998766507
Q gi|254780191|r  390 LYDTHGLPLDIMQDILCARG  409 (898)
Q Consensus       390 LyDTyGfP~dlt~eia~e~g  409 (898)
                      |.+-+-.|+-..++++++-.
T Consensus       386 l~~~~s~p~~~~~eV~~la~  405 (1251)
T KOG0414         386 LFQQHSIPLGSRTEVLELAI  405 (1251)
T ss_pred             HHHCCCCCCCHHHHHHHHHH
T ss_conf             98703777307999999971


No 172
>pfam01297 SBP_bac_9 Periplasmic solute binding protein family. This family includes periplasmic solute binding proteins such as TroA that interacts with an ATP-binding cassette transport system in Treponema pallidum.
Probab=28.26  E-value=31  Score=12.83  Aligned_cols=81  Identities=6%  Similarity=0.085  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHCCCCEEEEE--EC--CCCH
Q ss_conf             999999999839998899999999999999999999999999876365--------35553695279999--57--9997
Q gi|254780191|r  739 DEKLKSLASFLKVSQGNVVGRVEEIWEEYRKLQLIHAKRKLQLNVEDL--------SCHKIADVNFMSHI--IS--EVDS  806 (898)
Q Consensus       739 ~~~l~~la~~L~~~~~~i~~ki~~L~~e~K~l~k~~~k~k~~~~~~~~--------~~~~i~~~~~i~~~--~~--~~d~  806 (898)
                      ..+.+.++++.....+...+..+++.++++.+.+...+.........+        ...+--|.+.+...  ..  ..++
T Consensus       121 ~~I~~~L~~~dP~~~~~y~~N~~~~~~~l~~l~~~~~~~l~~~~~~~~v~~H~af~Y~~~~~gl~~~~~~~~~~~~eps~  200 (272)
T pfam01297       121 EAIADALSELDPENAATYEKNAAAFLKKLDELDAEIKAKLAPIPGKRVITFHDAFGYFAKAYGLEQIAILGESPESEPSP  200 (272)
T ss_pred             HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHCCCEEEEEECCCCCCCCCH
T ss_conf             99999999868540899999999999999999999998751347643898555069999977992754030035678899


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             8999999999975
Q gi|254780191|r  807 KELKSVMDALQKK  819 (898)
Q Consensus       807 ~~Lr~l~d~l~~k  819 (898)
                      +.|.++.+.+++.
T Consensus       201 ~~l~~l~~~ik~~  213 (272)
T pfam01297       201 ADLAELIKLIKEH  213 (272)
T ss_pred             HHHHHHHHHHHHC
T ss_conf             9999999999984


No 173
>TIGR02367 PylS pyrrolysyl-tRNA synthetase; InterPro: IPR012739    PylS is the archaeal enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, e.g. trimethylamine methyltransferase. .
Probab=28.18  E-value=31  Score=12.82  Aligned_cols=59  Identities=12%  Similarity=0.240  Sum_probs=29.0

Q ss_pred             CCCCCEEEEEEHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             55673388842125567775201368899999752125444445530024300000247678999999999999989887
Q gi|254780191|r  565 LRTEMSLVLTIDYQNRRQLSINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIA  644 (898)
Q Consensus       565 l~~g~~V~~~VD~~rR~~~~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~vN~~I~  644 (898)
                      +..||.  +.|+..|-     ..||--+-|.-.|++.             .+        -.+++|+|.+.=..+|+   
T Consensus        39 maCGdh--lvvnnsrs-----~rtara~rhhkyrktC-------------kr--------Crvsded~n~flt~~~e---   87 (453)
T TIGR02367        39 MACGDH--LVVNNSRS-----SRTARALRHHKYRKTC-------------KR--------CRVSDEDLNKFLTKATE---   87 (453)
T ss_pred             EECCCE--EEEECCCH-----HHHHHHHHHHHHHHHH-------------CC--------CCCCHHHHHHHHHHCCC---
T ss_conf             524756--78736620-----3578877654443221-------------00--------44457889888641013---


Q ss_pred             HCCCCEEEEE
Q ss_conf             3045304661
Q gi|254780191|r  645 QNLPVVTRIM  654 (898)
Q Consensus       645 ~n~~V~~~~~  654 (898)
                      ..-.|+++.+
T Consensus        88 ~~~svkv~vv   97 (453)
T TIGR02367        88 DKTSVKVKVV   97 (453)
T ss_pred             CCCEEEEEEE
T ss_conf             4550579997


No 174
>PRK10628 hypothetical protein; Provisional
Probab=27.89  E-value=24  Score=13.77  Aligned_cols=15  Identities=20%  Similarity=0.352  Sum_probs=12.2

Q ss_pred             EEEECCCCCCHHHHH
Q ss_conf             998524588889999
Q gi|254780191|r  388 FKLYDTHGLPLDIMQ  402 (898)
Q Consensus       388 f~LyDTyGfP~dlt~  402 (898)
                      -.+||=||||.+|=+
T Consensus        47 ~tihDF~GFP~~lY~   61 (246)
T PRK10628         47 PTIHDFGGFPQALYD   61 (246)
T ss_pred             CCCCCCCCCCHHHEE
T ss_conf             876699999899824


No 175
>pfam03473 MOSC MOSC domain. The MOSC (MOCO sulfurase C-terminal) domain is a superfamily of beta-strand-rich domains identified in the molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. These MOSC domains contain an absolutely conserved cysteine and occur either as stand-alone forms, or fused to other domains such as NifS-like catalytic domain in Molybdenum cofactor sulfurase. The MOSC domain is predicted to be a sulfur-carrier domain that receives sulfur abstracted by the pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulfur-metal clusters.
Probab=27.39  E-value=32  Score=12.72  Aligned_cols=13  Identities=15%  Similarity=0.286  Sum_probs=8.7

Q ss_pred             CCCCCCCCCCEEE
Q ss_conf             4678755673388
Q gi|254780191|r  560 VERGILRTEMSLV  572 (898)
Q Consensus       560 ~~~g~l~~g~~V~  572 (898)
                      +.+|.+.+||+|.
T Consensus       111 ~~~G~I~~GD~v~  123 (124)
T pfam03473       111 LRPGTIRVGDEVE  123 (124)
T ss_pred             ECCCEECCCCEEE
T ss_conf             6284885999877


No 176
>COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=27.37  E-value=29  Score=13.10  Aligned_cols=14  Identities=7%  Similarity=0.133  Sum_probs=6.5

Q ss_pred             HCCCCHHHHHHHHH
Q ss_conf             14753788999899
Q gi|254780191|r   98 FGGYFKERAIQLAW  111 (898)
Q Consensus        98 fgdYfK~eai~~aw  111 (898)
                      |.||+-+|++.|.|
T Consensus        10 ~~D~lp~d~~~~~~   23 (429)
T COG0124          10 TRDFLPEDMALREY   23 (429)
T ss_pred             CCCCCHHHHHHHHH
T ss_conf             66558677899999


No 177
>pfam00413 Peptidase_M10 Matrixin. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis.
Probab=26.74  E-value=33  Score=12.63  Aligned_cols=49  Identities=20%  Similarity=0.256  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHH---CCC-CCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHH
Q ss_conf             68899999752---125-444445530024300000247678999999999999
Q gi|254780191|r  589 ATHLLHHALST---ILG-SHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDN  638 (898)
Q Consensus       589 atHlL~~alr~---vLG-~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~  638 (898)
                      +..|++-|+++   .|| .|....+|.+.|-+...+ +....|+.+++..|+.+
T Consensus       104 g~~l~~va~HEIGHaLGL~Hs~~~~siM~p~y~~~~-~~~~~L~~dDi~gIq~L  156 (158)
T pfam00413       104 GTNLFLVAAHEIGHALGLGHSSDPDAIMYPYYSPYK-DPVFRLDQDDIKGIQSL  156 (158)
T ss_pred             CCHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCC-CCCCCCCHHHHHHHHHH
T ss_conf             511556654540200266889998667776023787-88787998999999986


No 178
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=26.65  E-value=33  Score=12.62  Aligned_cols=59  Identities=15%  Similarity=0.219  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCC-----------CCCCCCCEEEEEECCCCCCHHHHHHH
Q ss_conf             889999874898999999899999999861----154-----------64245743799852458888999987
Q gi|254780191|r  346 LIEETLRSEDERFGKTLDRGLVLLDGVLSH----LGK-----------DEILNGDVAFKLYDTHGLPLDIMQDI  404 (898)
Q Consensus       346 ~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~----~~~-----------~~~lsg~~af~LyDTyGfP~dlt~ei  404 (898)
                      .|.+++..|...-..-+.+-+..++..++.    +.+           ++.|.--||-+|.-|||.|++.++-+
T Consensus        21 eil~~i~~ed~~v~~Av~~~lp~I~~~v~~~~~~l~~gGRL~YvGAGTSGRlgvlDa~E~~PTFg~~~~~v~~l   94 (273)
T PRK05441         21 ELLRLINEEDKKVALAVEKALPQIAAAVDAIAAALRSGGRLIYIGAGTSGRLGVLDASECPPTFGVPPELVVGL   94 (273)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHCCCCCCCCHHHHEEE
T ss_conf             99999999889999999998789999999999999759829997476158899988986487668998991446


No 179
>pfam00634 BRCA2 BRCA2 repeat. The alignment covers only the most conserved region of the repeat.
Probab=26.60  E-value=23  Score=13.84  Aligned_cols=26  Identities=8%  Similarity=0.281  Sum_probs=18.7

Q ss_pred             HHCCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             01145899987889999999998619
Q gi|254780191|r  873 HMAQSGGPNGNKADQAIAGVASFLKK  898 (898)
Q Consensus       873 d~AQgGG~~~~~l~eal~~vk~~Lke  898 (898)
                      .|-+|.|++..=-+++|.++++++++
T Consensus         7 ~F~TAsgK~v~VSe~sL~Kak~~l~e   32 (35)
T pfam00634         7 GFQTASGKKVSVSEESLKKAKKLLRE   32 (35)
T ss_pred             EEEECCCCEEEECHHHHHHHHHHHHH
T ss_conf             88725782786448999999999998


No 180
>cd00375 Urease_alpha Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of external and internally generated urea as a nitrogen source. The enzyme consists of 3 subunits, alpha, beta and gamma, which can be fused and present on a single protein chain and which in turn forms multimers, mainly trimers. The large alpha subunit is the catalytic domain containing an active site with a bi-nickel center complexed by a carbamylated lysine. The beta and gamma subunits play a role in subunit association to form the higher order trimers.
Probab=26.50  E-value=31  Score=12.83  Aligned_cols=128  Identities=19%  Similarity=0.206  Sum_probs=67.1

Q ss_pred             HHHHCCCCHHHEEEEECCCHHHHHHHHHHHCCCCHHHEEECCCCCCCCCCCCCC---CCCCCEEEEEECCCCCCCCCCCC
Q ss_conf             133418981237999718828999975663499989975357866654579999---98770467885385568988877
Q gi|254780191|r  114 LTKEFDLDQRRLYITVYDEDEEAFKLWKKISGLSADKIIRITTNDNFWSMAETG---PCGPCSEIFFDQGECIPGGLPGS  190 (898)
Q Consensus       114 lt~~~~l~~~~l~vtv~~~D~e~~~iW~~~~gi~~~~i~~~~~~dNfW~~g~~G---pcGPcsEi~~d~g~~~~~~~~~~  190 (898)
                      +|+.+=+|.    .-+|+.|          |||..-||..+|+.-|.=-|-..-   ..||++||.--.      +.-.-
T Consensus        69 ITNalIiD~----~GI~KAD----------IGIkdGrI~~IGKAGNPd~mdgV~p~~viG~~TevIagE------g~I~T  128 (567)
T cd00375          69 ITNALIIDY----TGIYKAD----------IGIKDGRIVAIGKAGNPDIMDGVTPNMIVGPSTEVIAGE------GKIVT  128 (567)
T ss_pred             EECEEEECC----CCEEECE----------ECCCCCEEEEEECCCCCCCCCCCCCCEEECCCCCEECCC------CEEEE
T ss_conf             966399647----7617630----------033377797742478976567899880777785257378------40673


Q ss_pred             CCCCCCEEEEEEHHHH---HHHC-CCCCC-------CCCCCCCCCCC----CCCHHHHHHHHCCCCCCCH------HHHH
Q ss_conf             7889826896001123---4430-47887-------56576653101----7579999999887985300------5769
Q gi|254780191|r  191 SEEGERYIEIWNLVFM---QFEQ-QNKQE-------RFILPKMSIDT----GMGLERMATVLQEKTNNYD------IDLF  249 (898)
Q Consensus       191 ~~~~~r~lEiwNlVFm---q~~~-~~~g~-------~~~Lp~~~IDT----GmGLERl~~vlqg~~s~yd------tD~f  249 (898)
                      ...-|-  -|   -|+   |.+. ...|.       .-|-.-.+--|    -+-++|+.....+.|-|+-      +..-
T Consensus       129 AGgiDt--Hv---Hfi~Pqq~~~AL~sGiTT~iGGGtGPa~Gt~atT~TpG~~~i~~ml~a~d~~P~N~g~lgKGn~s~~  203 (567)
T cd00375         129 AGGIDT--HV---HFICPQQIEEALASGITTMIGGGTGPAAGTKATTCTPGPWNIKRMLQAADGLPVNIGFLGKGNGSSP  203 (567)
T ss_pred             CCCEEE--EE---EECCHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCH
T ss_conf             262167--88---8438888999986587676358667877777644689779999999865527721356313666885


Q ss_pred             HHHHHHHHH-HCCCCCCC
Q ss_conf             999999997-30678543
Q gi|254780191|r  250 KHLIQASEQ-VTGMKYEG  266 (898)
Q Consensus       250 ~pii~~i~~-~~g~~y~~  266 (898)
                      .||.+.++- .+|+|...
T Consensus       204 ~~l~eqi~AGa~GlKiHE  221 (567)
T cd00375         204 DALAEQIEAGACGLKLHE  221 (567)
T ss_pred             HHHHHHHHHHHCCCCCCC
T ss_conf             789999986534011122


No 181
>KOG4445 consensus
Probab=26.40  E-value=33  Score=12.59  Aligned_cols=32  Identities=19%  Similarity=0.393  Sum_probs=22.2

Q ss_pred             EEEECCCCCCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             00002476789999999999999898873045
Q gi|254780191|r  617 LRFDVTHSKPITSAELKSIEDNVNDIIAQNLP  648 (898)
Q Consensus       617 lrfDfsh~~~lt~eel~~IE~~vN~~I~~n~~  648 (898)
                      -+|-++.+..|++.++.+|...+|++|.+|+-
T Consensus        62 Ptvtl~nPRGl~d~~~~~i~~~~~~iikq~~g   93 (368)
T KOG4445          62 PTVTLSNPRGLGDPEFREIQRQIQEIIKQNSG   93 (368)
T ss_pred             CCEEECCCCCCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             71472288888818899999999999985689


No 182
>TIGR01840 esterase_phb esterase, PHB depolymerase family; InterPro: IPR010126   This entry describes a group of lipases of the ab-hydrolase family. They include bacterial depolymerases for poly(3-hydroxybutyrate) (PHB) and related polyhydroxyalkanoates (PHA), as well as acetyl xylan esterases, and feruloyl esterases from fungi.; GO: 0005576 extracellular region.
Probab=26.39  E-value=29  Score=13.05  Aligned_cols=11  Identities=36%  Similarity=1.002  Sum_probs=6.6

Q ss_pred             CCCCHHHEEEE
Q ss_conf             18981237999
Q gi|254780191|r  118 FDLDQRRLYIT  128 (898)
Q Consensus       118 ~~l~~~~l~vt  128 (898)
                      |.|||.|+|||
T Consensus       106 ~~IDP~rvyvT  116 (231)
T TIGR01840       106 YSIDPNRVYVT  116 (231)
T ss_pred             CCCCCCEEEEE
T ss_conf             86388545884


No 183
>KOG2021 consensus
Probab=26.31  E-value=33  Score=12.58  Aligned_cols=51  Identities=16%  Similarity=0.232  Sum_probs=35.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             10456899999864555555764678899998748989999998999999998611
Q gi|254780191|r  321 LMMHLLPALCTEMGSAYPELIQAKLLIEETLRSEDERFGKTLDRGLVLLDGVLSHL  376 (898)
Q Consensus       321 fl~~lv~~v~~~m~~~ypeL~~~~~~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~~  376 (898)
                      +++++..++...|  .|.|.+.+-+.   +-..|||.|..+.++-++.|.+.+...
T Consensus       379 ~l~~illai~kqi--cydemy~nddn---~tg~EeEa~f~e~RkkLk~fqdti~~i  429 (980)
T KOG2021         379 PLHKILLAIFKQI--CYDEMYFNDDN---VTGDEEEAFFEEVRKKLKNFQDTIVVI  429 (980)
T ss_pred             CHHHHHHHHHHHH--HCCHHHHCCCC---CCCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             3999999999998--13677516667---888357899999999999999999854


No 184
>LOAD_rna_Cyc consensus
Probab=26.27  E-value=33  Score=12.57  Aligned_cols=18  Identities=28%  Similarity=0.567  Sum_probs=12.1

Q ss_pred             EEEEECCCCEEECCCCCC
Q ss_conf             999973752000368765
Q gi|254780191|r  511 VEVVFDQTPFYAEAGGQL  528 (898)
Q Consensus       511 ~~ivLd~T~FY~E~GGQ~  528 (898)
                      +.+-+.+-=|||.|||++
T Consensus       144 ~~l~i~rRGfyP~GgG~V  161 (329)
T LOAD_rna_Cyc    144 GELKILKRGFYPKGGGEV  161 (329)
T ss_pred             EEEEEEECCCCCCCCCEE
T ss_conf             699998536689999579


No 185
>KOG2805 consensus
Probab=26.09  E-value=17  Score=14.89  Aligned_cols=22  Identities=36%  Similarity=0.552  Sum_probs=14.6

Q ss_pred             EEEEEHHHHHHHCC-CCCCCCCCC
Q ss_conf             89600112344304-788756576
Q gi|254780191|r  198 IEIWNLVFMQFEQQ-NKQERFILP  220 (898)
Q Consensus       198 lEiwNlVFmq~~~~-~~g~~~~Lp  220 (898)
                      =|.||.||.+|-+. ..| ++|-|
T Consensus        77 kEYW~~Vfs~~L~~Y~~G-~TPNP   99 (377)
T KOG2805          77 KEYWNDVFSPFLEEYENG-RTPNP   99 (377)
T ss_pred             HHHHHHHHHHHHHHHHCC-CCCCC
T ss_conf             999999999998887658-99999


No 186
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR; InterPro: IPR014310   Members of this protein are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter found in most Proteobacteria, and related proteins from Gram-positive organisms are excluded. The phoR gene usually is adjacent to the response regulator phoB gene (IPR011879 from INTERPRO)..
Probab=26.00  E-value=33  Score=12.66  Aligned_cols=12  Identities=33%  Similarity=0.592  Sum_probs=5.9

Q ss_pred             CHHHHHHHHHHH
Q ss_conf             978999999999
Q gi|254780191|r  805 DSKELKSVMDAL  816 (898)
Q Consensus       805 d~~~Lr~l~d~l  816 (898)
                      +..+|+.+...|
T Consensus       232 ~e~~L~SAf~NL  243 (339)
T TIGR02966       232 NEDELRSAFSNL  243 (339)
T ss_pred             CHHHHHHHHHHH
T ss_conf             477799999999


No 187
>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=25.85  E-value=34  Score=12.52  Aligned_cols=37  Identities=16%  Similarity=0.183  Sum_probs=27.2

Q ss_pred             HHHHHHHHEE--CCCCCCCCCEEEEEEECH-HHHHHHHHHH
Q ss_conf             6460110011--012126882899997168-9999999999
Q gi|254780191|r  702 TGEIMLLYIV--SESSIRAGIRRIEAITGQ-RARSHLMGQD  739 (898)
Q Consensus       702 TgeIG~fkIi--se~si~sGvRRIeavtG~-~A~~~~~~~~  739 (898)
                      -.+||..+|+  ++++--.|- ||.||.+. ....|....+
T Consensus       192 gkeiGYvRITplKe~G~e~Gg-RvfFvs~~~el~~yIh~Le  231 (238)
T TIGR01204       192 GKEIGYVRITPLKEKGTEEGG-RVFFVSDKVELEEYIHDLE  231 (238)
T ss_pred             CCEECCEECCCCCCCCCCCCC-EEEEECCCCCHHHHHHHHC
T ss_conf             745244640321116899996-6899608511778988643


No 188
>PHA02103 hypothetical protein
Probab=25.82  E-value=25  Score=13.55  Aligned_cols=15  Identities=27%  Similarity=0.793  Sum_probs=10.1

Q ss_pred             ECCCHHHHHHHHHHH
Q ss_conf             718828999975663
Q gi|254780191|r  129 VYDEDEEAFKLWKKI  143 (898)
Q Consensus       129 v~~~D~e~~~iW~~~  143 (898)
                      ||-+..|+.+||.+.
T Consensus        84 yf~ee~e~ie~we~y   98 (135)
T PHA02103         84 YFGEEAEGVELWEEY   98 (135)
T ss_pred             HHCCCCHHHHHHHHH
T ss_conf             750320133289872


No 189
>COG5127 Vacuolar H+-ATPase V1 sector, subunit C [Energy production and conversion]
Probab=25.81  E-value=34  Score=12.51  Aligned_cols=26  Identities=12%  Similarity=-0.013  Sum_probs=10.7

Q ss_pred             EHHHHHHHHHHCCCHHHHHHHHHHHC
Q ss_conf             21255677752013688999997521
Q gi|254780191|r  575 IDYQNRRQLSINHSATHLLHHALSTI  600 (898)
Q Consensus       575 VD~~rR~~~~~~HTatHlL~~alr~v  600 (898)
                      ++.+.|.....-..|-.-+.++-|+.
T Consensus       131 ~~~d~r~~~~~f~~Ak~~~~~~qrk~  156 (383)
T COG5127         131 ISKDYREKAEEFDGAKRECEKLQRKT  156 (383)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             77889999987658889999987552


No 190
>pfam11554 DUF3232 Protein of unknown function (DUF3232). This bacterial family of proteins has no known function.
Probab=25.66  E-value=25  Score=13.62  Aligned_cols=11  Identities=27%  Similarity=0.616  Sum_probs=3.7

Q ss_pred             HHHHHHHHHHH
Q ss_conf             78999999999
Q gi|254780191|r  806 SKELKSVMDAL  816 (898)
Q Consensus       806 ~~~Lr~l~d~l  816 (898)
                      .+++|.+...|
T Consensus        70 gee~Re~~e~L   80 (149)
T pfam11554        70 GEELRDLTEEL   80 (149)
T ss_pred             CHHHHHHHHHH
T ss_conf             38899999998


No 191
>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]
Probab=25.23  E-value=35  Score=12.44  Aligned_cols=12  Identities=8%  Similarity=0.135  Sum_probs=5.7

Q ss_pred             ECCCCCCCCHHH
Q ss_conf             024767899999
Q gi|254780191|r  620 DVTHSKPITSAE  631 (898)
Q Consensus       620 Dfsh~~~lt~ee  631 (898)
                      ||-|+.++..+-
T Consensus        61 n~d~p~A~D~dL   72 (218)
T COG0572          61 NYDHPEAFDLDL   72 (218)
T ss_pred             CCCCHHHHCHHH
T ss_conf             744823436899


No 192
>cd00775 LysRS_core Lys_tRNA synthetase (LysRS) class II core domain.  Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three characteristic sequence motifs in the core domain. It is found in eukaryotes as well as some prokaryotes and archaea.  However, LysRS belongs to class I aaRS's  in some prokaryotes and archaea. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.
Probab=24.96  E-value=35  Score=12.40  Aligned_cols=87  Identities=16%  Similarity=0.263  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHHHHCCCEECCCCCC--CCCCCCCHHEEECCCCCC-CCCCCCCCCC---------CCCCCCCCCCCEECCC
Q ss_conf             899999999999789889116675--667787100230143475-5400588799---------9998511154322489
Q gi|254780191|r    5 SSIRTTFLEFFQKNGHELLPSSSL--IPCNDPTLMFTNSGMVPF-KNIFTGQEKP---------VYQAVTTVQKCVRAGG   72 (898)
Q Consensus         5 ~eiR~~fl~fF~~~~H~~~~s~sl--vp~~d~~llft~Agm~~f-k~~f~G~~~p---------~~~r~~~~QkCiR~gg   72 (898)
                      ++|-+.+-+||.++|-.-|..--|  .|-....=.|..- .+.| ++.||-+.+-         ...|+-..-||.|+  
T Consensus        12 s~i~~~iR~ff~~~gF~Ev~TPiL~~~~~g~~~~~f~~~-~~~~~~~~yL~qSpQl~~q~l~~~g~~rvfqI~p~FR~--   88 (329)
T cd00775          12 SKIISYIRKFLDDRGFLEVETPMLQPIAGGAAARPFITH-HNALDMDLYLRIAPELYLKRLIVGGFERVYEIGRNFRN--   88 (329)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCEEEC-CCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEEEECCCC--
T ss_conf             999999999999889889979865566887567531322-44678672306898999999985677767998102247--


Q ss_pred             CCCCHHHCCCCCCCHHHHHHHHH-HHHCCC
Q ss_conf             87863434648850017888542-231475
Q gi|254780191|r   73 KHNDLDNVGRTNRHHTFFEMLGN-FSFGGY  101 (898)
Q Consensus        73 khnDld~VG~t~rH~TfFEMlGn-~SfgdY  101 (898)
                           |  +.++||++=|-||-= .||-||
T Consensus        89 -----E--~~~~rHl~EFtmle~E~~f~d~  111 (329)
T cd00775          89 -----E--GIDLTHNPEFTMIEFYEAYADY  111 (329)
T ss_pred             -----C--CCCCCCCCHHHHHHHHHHCCCH
T ss_conf             -----9--9997747345634577744799


No 193
>TIGR00459 aspS_bact aspartyl-tRNA synthetase; InterPro: IPR004524   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Aspartyl tRNA synthetase 6.1.1.12 from EC is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module .     This family represents aspartyl-tRNA synthetases from the bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). ; GO: 0000166 nucleotide binding, 0004815 aspartate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006422 aspartyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=24.76  E-value=23  Score=13.83  Aligned_cols=25  Identities=8%  Similarity=0.197  Sum_probs=10.4

Q ss_pred             HHHHH-HHCCCHHHHHHHHHHHHHHH
Q ss_conf             99999-83999889999999999999
Q gi|254780191|r  743 KSLAS-FLKVSQGNVVGRVEEIWEEY  767 (898)
Q Consensus       743 ~~la~-~L~~~~~~i~~ki~~L~~e~  767 (898)
                      +.+-+ .|+..+++-.++.-=|++-+
T Consensus       559 ~~~F~d~Lgid~eea~EkFGFLLeA~  584 (653)
T TIGR00459       559 EKVFEDILGIDPEEAREKFGFLLEAF  584 (653)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             99998762889899877635687587


No 194
>pfam10503 Esterase_phd Esterase PHB depolymerase. This family of proteins include acetyl xylan esterases (AXE), feruloyl esterases (FAE), and poly(3-hydroxybutyrate) (PHB) depolymerases.
Probab=24.61  E-value=36  Score=12.35  Aligned_cols=77  Identities=16%  Similarity=0.199  Sum_probs=37.5

Q ss_pred             CCCCHHEEECCCCCCCCC--CCCCCCCCCCCCCCCCCCEECCCCCCCHHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             787100230143475540--058879999985111543224898786343464885001788854223147537889998
Q gi|254780191|r   32 NDPTLMFTNSGMVPFKNI--FTGQEKPVYQAVTTVQKCVRAGGKHNDLDNVGRTNRHHTFFEMLGNFSFGGYFKERAIQL  109 (898)
Q Consensus        32 ~d~~llft~Agm~~fk~~--f~G~~~p~~~r~~~~QkCiR~ggkhnDld~VG~t~rH~TfFEMlGn~SfgdYfK~eai~~  109 (898)
                      .+++-+...+||+.+=+-  |.= .-|...+-.+.|.|---.    +-... ..++             ||   -..|.-
T Consensus        32 q~a~~~~~~t~~~~lAd~~GFiV-vyPeq~~~~n~~~cWnw~----~~~~~-~~g~-------------gd---~~~I~~   89 (226)
T pfam10503        32 QHADDFAAGTRMNALADEHGFAV-LYPEQSLRAHAHGCWHWF----EPDHD-QAGR-------------GE---AATIAA   89 (226)
T ss_pred             CCHHHHHHHCCHHHHHHHCCCEE-EECCCCCCCCCCCCCCCC----CCCCC-CCCC-------------CC---HHHHHH
T ss_conf             99999985557289998779289-936774667899888878----86455-6899-------------76---999999


Q ss_pred             HHHHHHHHCCCCHHHEEEEEC
Q ss_conf             998613341898123799971
Q gi|254780191|r  110 AWDLLTKEFDLDQRRLYITVY  130 (898)
Q Consensus       110 awe~lt~~~~l~~~~l~vtv~  130 (898)
                      --+.+...+++|++|+|||=+
T Consensus        90 mi~~v~~~y~iD~~RVyvtGl  110 (226)
T pfam10503        90 LADAIADAHGFDAARVYVAGL  110 (226)
T ss_pred             HHHHHHHHCCCCCCCEEEEEE
T ss_conf             999999972998031789875


No 195
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=24.56  E-value=36  Score=12.35  Aligned_cols=53  Identities=23%  Similarity=0.234  Sum_probs=27.5

Q ss_pred             CCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             2688289999716899999999999999999983999889999999999999999
Q gi|254780191|r  716 IRAGIRRIEAITGQRARSHLMGQDEKLKSLASFLKVSQGNVVGRVEEIWEEYRKL  770 (898)
Q Consensus       716 i~sGvRRIeavtG~~A~~~~~~~~~~l~~la~~L~~~~~~i~~ki~~L~~e~K~l  770 (898)
                      ||+|+. +|. +-..|.+++.++-..+......+......+.+.+..+..+..++
T Consensus        83 iG~g~~-vE~-~~~eA~~~l~~r~~~l~~~~~~l~~~l~~~~~~~~~i~~~l~~l  135 (141)
T PRK03947         83 LGAGYS-AEK-DLDEAIEILDKRIEELEKALEKLEEALAKLAERIAQIAQELERL  135 (141)
T ss_pred             CCCCEE-EEE-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             389869-997-59999999999999999999999999999999999999999999


No 196
>cd00477 FTHFS Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2 fixation (acetogenesis) and the glycine synthase/reductase pathways of purinolysis. The key physiological role of this enzyme in acetogens is to catalyze the formylation of tetrahydrofolate, an initial step in the reduction of carbon dioxide and other one-carbon precursors to acetate. In purinolytic organisms, the enzymatic reaction is reversed, liberating formate from 10-formyltetrahydrofolate with concurrent production of ATP.
Probab=24.48  E-value=21  Score=14.17  Aligned_cols=34  Identities=9%  Similarity=0.039  Sum_probs=15.3

Q ss_pred             HHHHHHHEECCCCCCCCCE--EEEEEECHHHHHHHH
Q ss_conf             4601100110121268828--999971689999999
Q gi|254780191|r  703 GEIMLLYIVSESSIRAGIR--RIEAITGQRARSHLM  736 (898)
Q Consensus       703 geIG~fkIise~si~sGvR--RIeavtG~~A~~~~~  736 (898)
                      +++|.=|...-..-.+|.+  =+..|+--||++|.-
T Consensus       287 aDLGaEKF~dIkcr~~gl~P~a~VlVaTvRALK~hG  322 (524)
T cd00477         287 ADLGAEKFFNIKCRYSGLKPDAVVLVATVRALKMHG  322 (524)
T ss_pred             CCCCCHHHHCCCCCCCCCCCCEEEEEEEEHHHHHCC
T ss_conf             465605541130014799987899998735777548


No 197
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively.   Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=24.43  E-value=36  Score=12.33  Aligned_cols=34  Identities=29%  Similarity=0.417  Sum_probs=28.3

Q ss_pred             CCCCCCEEEEEEEECCCEEEECCCCCEEEEEECC
Q ss_conf             5565534899997478132000479769999737
Q gi|254780191|r  484 LTNGVSSIVKAIVQQGEIVEEAVSGQKVEVVFDQ  517 (898)
Q Consensus       484 ~~~~~~s~v~~i~~~~~~v~~~~~g~~~~ivLd~  517 (898)
                      ......++|..|...++.++++..|+.+.+.|+.
T Consensus        36 ~Psg~~a~Vk~I~~~~~~~~~A~aG~~v~l~L~~   69 (81)
T cd03695          36 LPSGKTSRVKSIETFDGELDEAGAGESVTLTLED   69 (81)
T ss_pred             CCCCCCEEEEEEEECCCCCCEECCCCEEEEEECC
T ss_conf             8999818998999589982488799828999787


No 198
>pfam05634 DUF794 Arabidopsis thaliana protein of unknown function (DUF794). This family consists of several proteins of unknown function from Arabidopsis thaliana.
Probab=24.37  E-value=29  Score=13.07  Aligned_cols=10  Identities=30%  Similarity=0.833  Sum_probs=4.4

Q ss_pred             EEEEEECCCC
Q ss_conf             3799852458
Q gi|254780191|r  386 VAFKLYDTHG  395 (898)
Q Consensus       386 ~af~LyDTyG  395 (898)
                      .+|.|||.+|
T Consensus       149 esyHL~d~~g  158 (378)
T pfam05634       149 ESYHLFDRFG  158 (378)
T ss_pred             HHHCCCCCCC
T ss_conf             1400013324


No 199
>pfam06925 MGDG_synth Monogalactosyldiacylglycerol (MGDG) synthase. This family represents a conserved region of approximately 180 residues within plant and bacterial monogalactosyldiacylglycerol (MGDG) synthase (EC:2.4.1.46). In Arabidopsis, there are two types of MGDG synthase which differ in their N-terminal portion: type A and type B.
Probab=24.36  E-value=36  Score=12.32  Aligned_cols=35  Identities=31%  Similarity=0.487  Sum_probs=18.6

Q ss_pred             HHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHCCC
Q ss_conf             99999986115464245743799852458888999987665077
Q gi|254780191|r  367 VLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLDIMQDILCARGL  410 (898)
Q Consensus       367 ~~l~~~i~~~~~~~~lsg~~af~LyDTyGfP~dlt~eia~e~gi  410 (898)
                      +.|.+.|++.+-.-+++         ||=||..+....++++|.
T Consensus        79 ~~l~~~i~~~~PD~IV~---------Thp~~~~~~l~~lk~~~~  113 (169)
T pfam06925        79 RELAALLKEFQPDIIIS---------THPLPAAVPLSVLKSKGL  113 (169)
T ss_pred             HHHHHHHHHHCCCEEEE---------CCHHHHHHHHHHHHHCCC
T ss_conf             99999999849399999---------976266789999998387


No 200
>KOG2484 consensus
Probab=24.26  E-value=36  Score=12.31  Aligned_cols=12  Identities=17%  Similarity=0.429  Sum_probs=5.3

Q ss_pred             CEEEEEECCCCE
Q ss_conf             769999737520
Q gi|254780191|r  509 QKVEVVFDQTPF  520 (898)
Q Consensus       509 ~~~~ivLd~T~F  520 (898)
                      ....+||+++-.
T Consensus       178 KkLILVLNK~DL  189 (435)
T KOG2484         178 KKLILVLNKIDL  189 (435)
T ss_pred             CEEEEEEEHHCC
T ss_conf             249999502104


No 201
>PRK05963 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed
Probab=24.03  E-value=37  Score=12.27  Aligned_cols=13  Identities=8%  Similarity=0.151  Sum_probs=8.7

Q ss_pred             CCCCCEEEEEECC
Q ss_conf             5556248998447
Q gi|254780191|r  671 KYNDRVRVVSVEY  683 (898)
Q Consensus       671 kygd~VRVV~I~~  683 (898)
                      +.||.|=++.+|.
T Consensus       304 ~~Gd~vll~g~G~  316 (327)
T PRK05963        304 REGERLLFAAAGA  316 (327)
T ss_pred             CCCCEEEEEEEEH
T ss_conf             9979999999866


No 202
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=23.95  E-value=37  Score=12.26  Aligned_cols=15  Identities=7%  Similarity=0.401  Sum_probs=6.7

Q ss_pred             CCHHHHHHHHHHHHH
Q ss_conf             999999999999989
Q gi|254780191|r  627 ITSAELKSIEDNVND  641 (898)
Q Consensus       627 lt~eel~~IE~~vN~  641 (898)
                      +..+++.++++.+++
T Consensus       281 vP~~~~~~l~~~l~~  295 (640)
T PRK05771        281 VPEDSVKELKELIDK  295 (640)
T ss_pred             CCHHHHHHHHHHHHH
T ss_conf             228889999999998


No 203
>pfam09292 Neil1-DNA_bind Endonuclease VIII-like 1, DNA bind. Members of this family are predominantly found in Endonuclease VIII-like 1 and adopt a glucocorticoid receptor-like fold. They allow for DNA binding.
Probab=23.94  E-value=37  Score=12.26  Aligned_cols=37  Identities=24%  Similarity=0.598  Sum_probs=25.1

Q ss_pred             HHHHHHHHHCCCCHHHEEECCCCCCCCCCCCCCCCCC
Q ss_conf             9999756634999899753578666545799999877
Q gi|254780191|r  135 EAFKLWKKISGLSADKIIRITTNDNFWSMAETGPCGP  171 (898)
Q Consensus       135 e~~~iW~~~~gi~~~~i~~~~~~dNfW~~g~~GpcGP  171 (898)
                      -+++-|+..-.+|.-.-++=..-.-.|--|++||--|
T Consensus         3 s~f~~Wl~CY~vpgm~sl~D~~gRTiWF~GdpGPlaP   39 (39)
T pfam09292         3 SAFQAWLRCYGVPGMSSLRDHNGRTIWFQGDPGPLAP   39 (39)
T ss_pred             HHHHHHHHHHCCCCHHHHHCCCCCEEEECCCCCCCCC
T ss_conf             8999999998578614432279977985289888897


No 204
>cd04162 Arl9_Arfrp2_like Arl9/Arfrp2-like subfamily.  Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project.  It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2).  This is a novel subfamily identified in human cancers that is uncharacterized to date.
Probab=23.90  E-value=37  Score=12.26  Aligned_cols=95  Identities=15%  Similarity=0.196  Sum_probs=50.0

Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCEEEEEEEECHHHHCCCCHHHHHHHHHHHHCCCCCCCC
Q ss_conf             69527999957999789999999999754997899999538981799998677897267989999999988349999998
Q gi|254780191|r  792 ADVNFMSHIISEVDSKELKSVMDALQKKIQSGIIMLVGISKEKKASVLIVVTEDLLDRFNAVDLARLSAKVLGGGGGGGR  871 (898)
Q Consensus       792 ~~~~~i~~~~~~~d~~~Lr~l~d~l~~k~~~~vvvL~~~~~~~k~~ivv~vs~~~~~~~~A~~lik~ia~~l~GGgGGGk  871 (898)
                      .+...++.+++..|...+.+..+.+..-+..         ..+.+.++++-..|+..-+++.++...+-  + ..=..+|
T Consensus        66 ~~~~gIIfVVDssD~~rl~eak~~L~~ll~~---------~~~~PlLIlaNKqDl~~a~s~~ei~~~L~--L-~~i~~~r  133 (164)
T cd04162          66 SGSQGLIFVVDSADSERLPLARQELHQLLQH---------PPDLPLVVLANKQDLPAARSVQEIHKELE--L-EPIARGR  133 (164)
T ss_pred             HCCCEEEEEEECCCHHHHHHHHHHHHHHHHC---------CCCCEEEEEEECCCCCCCCCHHHHHHHCC--C-CCCCCCC
T ss_conf             1775899999568888999999999999708---------79986999986324336999999998669--9-4637999


Q ss_pred             CHHCCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             101145899987889999999998619
Q gi|254780191|r  872 PHMAQSGGPNGNKADQAIAGVASFLKK  898 (898)
Q Consensus       872 pd~AQgGG~~~~~l~eal~~vk~~Lke  898 (898)
                      +-.-|+..-....++++++.+.+++.|
T Consensus       134 ~w~iq~~s~~g~gl~~~~~~l~~~~~~  160 (164)
T cd04162         134 RWILQGTSLDDDGSPSRMEAVKDLLSQ  160 (164)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHH
T ss_conf             889971104799858999999999999


No 205
>COG1210 GalU UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]
Probab=23.85  E-value=37  Score=12.25  Aligned_cols=112  Identities=20%  Similarity=0.234  Sum_probs=46.2

Q ss_pred             ECCCCCCCCCEEEEEEECHH--H-HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH
Q ss_conf             10121268828999971689--9-99999999999999998399988999999999999999---999999999998763
Q gi|254780191|r  711 VSESSIRAGIRRIEAITGQR--A-RSHLMGQDEKLKSLASFLKVSQGNVVGRVEEIWEEYRK---LQLIHAKRKLQLNVE  784 (898)
Q Consensus       711 ise~si~sGvRRIeavtG~~--A-~~~~~~~~~~l~~la~~L~~~~~~i~~ki~~L~~e~K~---l~k~~~k~k~~~~~~  784 (898)
                      +-++.+++|+.+|-+|||..  | .+|+....++...+.+.   +..++.+.++++-+...-   .|++    .+-+--+
T Consensus        41 iVeEa~~aGIe~i~iVTgr~K~~IeDhFD~s~ELE~~L~~~---~K~~~L~~v~~i~~~~~i~~vRQ~e----~~GLGhA  113 (291)
T COG1210          41 IVEEAVAAGIEEILIVTGRGKRAIEDHFDTSYELENTLEKR---GKRELLEEVRSIPPLVTISFVRQKE----PLGLGHA  113 (291)
T ss_pred             HHHHHHHCCCCEEEEEECCCCCHHHHHCCCCHHHHHHHHHH---CHHHHHHHHHHCCCCCEEEEEECCC----CCCHHHH
T ss_conf             99999986997799996698356888676869999999872---7799999997235775399986587----6760178


Q ss_pred             HHHHH-HHCCCCEEEEEECCC---CHHHHHHHHHHHHHHCCCCEEEEEEE
Q ss_conf             65355-536952799995799---97899999999997549978999995
Q gi|254780191|r  785 DLSCH-KIADVNFMSHIISEV---DSKELKSVMDALQKKIQSGIIMLVGI  830 (898)
Q Consensus       785 ~~~~~-~i~~~~~i~~~~~~~---d~~~Lr~l~d~l~~k~~~~vvvL~~~  830 (898)
                      -+.++ -+++-.+.+..-+++   +...|+.+++... +.+.+++.+-.+
T Consensus       114 Vl~A~~~vg~EpFaVlL~Ddl~~~~~~~l~qmi~~y~-~~g~svi~v~ev  162 (291)
T COG1210         114 VLCAKPFVGDEPFAVLLPDDLVDSEKPCLKQMIELYE-ETGGSVIGVEEV  162 (291)
T ss_pred             HHHHHHHCCCCCEEEEECCEEECCCCHHHHHHHHHHH-HHCCCEEEEEEC
T ss_conf             8853543289856998177263278069999999999-859927999988


No 206
>PRK10707 hypothetical protein; Provisional
Probab=23.85  E-value=37  Score=12.25  Aligned_cols=10  Identities=30%  Similarity=0.345  Sum_probs=5.8

Q ss_pred             HHHHHHHHHC
Q ss_conf             8999997521
Q gi|254780191|r  591 HLLHHALSTI  600 (898)
Q Consensus       591 HlL~~alr~v  600 (898)
                      .++++|||+.
T Consensus        75 ~~~~TALREt   84 (190)
T PRK10707         75 SLIAAALREA   84 (190)
T ss_pred             CHHHHHHHHH
T ss_conf             8899999988


No 207
>smart00762 Cog4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport.
Probab=23.72  E-value=37  Score=12.23  Aligned_cols=13  Identities=31%  Similarity=0.391  Sum_probs=7.7

Q ss_pred             CCHHHHHHHHHHH
Q ss_conf             3588899999999
Q gi|254780191|r  413 IDIISFNQALEEQ  425 (898)
Q Consensus       413 vD~~~f~~~m~~q  425 (898)
                      +|+...+.+++|-
T Consensus       173 id~reid~lL~Ei  185 (324)
T smart00762      173 LDPRELDAILEEI  185 (324)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             9989999999999


No 208
>PRK13308 ureC urease subunit alpha; Reviewed
Probab=23.40  E-value=37  Score=12.19  Aligned_cols=131  Identities=15%  Similarity=0.140  Sum_probs=67.5

Q ss_pred             HHHHCCCCHHHEEEEECCCHHHHHHHHHHHCCCCHHHEEECCCCCCCCCCCCCC---CCCCCEEEEEECCCCC-CCCCCC
Q ss_conf             133418981237999718828999975663499989975357866654579999---9877046788538556-898887
Q gi|254780191|r  114 LTKEFDLDQRRLYITVYDEDEEAFKLWKKISGLSADKIIRITTNDNFWSMAETG---PCGPCSEIFFDQGECI-PGGLPG  189 (898)
Q Consensus       114 lt~~~~l~~~~l~vtv~~~D~e~~~iW~~~~gi~~~~i~~~~~~dNfW~~g~~G---pcGPcsEi~~d~g~~~-~~~~~~  189 (898)
                      +|+.+=+|+   |--||+.|          |||..-||..+|+.-|.=-|-..-   .-||++||.--.|.=. .|+-..
T Consensus        72 ITNa~IiD~---~~GI~KAD----------IGIkdGrI~~IGKAGNPd~mdgV~p~~viG~~TevIagEg~I~TAGgiDt  138 (569)
T PRK13308         72 LCNATVIDP---VLGIVKGD----------IGIRDGRIVGIGKAGNPDIMDGVDPRLVVGAGTTVRDAEGLIATPGAIDV  138 (569)
T ss_pred             EECCEEEEC---CCCEEEEE----------ECCCCCEEEEEECCCCCCCCCCCCCCEEECCCCCEECCCCCEEECCCEEE
T ss_conf             847199806---77779712----------12227779774247896656799988177778525737851660363045


Q ss_pred             -CCCCCCCEEEEEEHHHHHHHCCCCC-------CCCCCCCCCCCCCCCHHHHHHHHCCCCCCCH------HHHHHHHHHH
Q ss_conf             -7788982689600112344304788-------7565766531017579999999887985300------5769999999
Q gi|254780191|r  190 -SSEEGERYIEIWNLVFMQFEQQNKQ-------ERFILPKMSIDTGMGLERMATVLQEKTNNYD------IDLFKHLIQA  255 (898)
Q Consensus       190 -~~~~~~r~lEiwNlVFmq~~~~~~g-------~~~~Lp~~~IDTGmGLERl~~vlqg~~s~yd------tD~f~pii~~  255 (898)
                       ..--||+-+|         .....|       -.-|-...|--..+-++|+.-...+.|-|+-      +..-.||.+.
T Consensus       139 HvHfi~Pqq~~---------~AL~sGiTT~iGGGtGp~att~Tpg~~~i~~ml~a~d~~P~N~g~lgKGn~s~~~~L~eq  209 (569)
T PRK13308        139 HVHFDSAGLVD---------HALASGITTMIGGGLGPTVGIDSGGPFNTGRFLQAAEAWPVNFGFLGRGNSSDPAALIEQ  209 (569)
T ss_pred             EEEECCHHHHH---------HHHHCCCEEEECCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHH
T ss_conf             66633877899---------998618623257875787656689889999999764417731455103666880789999


Q ss_pred             HHH-HCCCCCCC
Q ss_conf             997-30678543
Q gi|254780191|r  256 SEQ-VTGMKYEG  266 (898)
Q Consensus       256 i~~-~~g~~y~~  266 (898)
                      ++- .+|+|...
T Consensus       210 i~AGa~GlKiHE  221 (569)
T PRK13308        210 VEAGVMGLKIHE  221 (569)
T ss_pred             HHHHHCCCCCCC
T ss_conf             985433133346


No 209
>PRK10957 iron-enterobactin transporter periplasmic binding protein; Provisional
Probab=23.37  E-value=28  Score=13.18  Aligned_cols=27  Identities=11%  Similarity=0.076  Sum_probs=14.9

Q ss_pred             CCCCC--CCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             47887--5657665310175799999998
Q gi|254780191|r  211 QNKQE--RFILPKMSIDTGMGLERMATVL  237 (898)
Q Consensus       211 ~~~g~--~~~Lp~~~IDTGmGLERl~~vl  237 (898)
                      +..|+  +..=|+++|-+.++.-=.+..|
T Consensus        35 h~~G~t~i~~~PqRVV~l~~~~~d~llaL   63 (319)
T PRK10957         35 DSRGTHTLEPKPARIVSTSVTLTGTLLAI   63 (319)
T ss_pred             CCCCCEECCCCCCEEEEECCCCHHHHHHC
T ss_conf             19842766899967999548627889867


No 210
>PTZ00179 60S ribosomal protein L9; Provisional
Probab=23.14  E-value=23  Score=13.91  Aligned_cols=44  Identities=14%  Similarity=0.086  Sum_probs=21.0

Q ss_pred             EEEEEHHHHHHHHHHCCC-HHHHHHHHHHHCCCCCCCCCCCEECC-CEEEEECCCCC
Q ss_conf             888421255677752013-68899999752125444445530024-30000024767
Q gi|254780191|r  571 LVLTIDYQNRRQLSINHS-ATHLLHHALSTILGSHVSQNGSCITP-DGLRFDVTHSK  625 (898)
Q Consensus       571 V~~~VD~~rR~~~~~~HT-atHlL~~alr~vLG~hv~Q~GS~v~~-~~lrfDfsh~~  625 (898)
                      +.....+.+|...+..-| +.||=+-. +          |-..+. =++|+-++|+-
T Consensus        53 i~v~~~~~~rk~~A~igT~~shI~NMi-k----------GVT~Gf~Ykmk~vyaHFP   98 (189)
T PTZ00179         53 FTAVRWFGSKIPNSTINTALSHVRNMI-T----------GVTKGFRFKVRFAYAHFP   98 (189)
T ss_pred             EEEEECCCCHHHEEEHHHHHHHHHHHH-H----------HCCCCEEEEEEEEEEECC
T ss_conf             999873787414000461999999877-5----------301874999999987565


No 211
>cd02948 TRX_NDPK TRX domain, TRX and NDP-kinase (NDPK) fusion protein family; most members of this group are fusion proteins which contain one redox active TRX domain containing a CXXC motif and three NDPK domains, and are characterized as intermediate chains (ICs) of axonemal outer arm dynein. Dyneins are molecular motors that generate force against microtubules to produce cellular movement, and are divided into two classes: axonemal and cytoplasmic. They are supramolecular complexes consisting of three protein groups classified according to size: dynein heavy, intermediate and light chains. Axonemal dyneins form two structures, the inner and outer arms, which are attached to doublet microtubules throughout the cilia and flagella. The human homolog is the sperm-specific Sptrx-2, presumed to be a  component of the human sperm axoneme architecture. Included in this group is another human protein, TRX-like protein 2, a smaller fusion protein containing one TRX and one NDPK domain, which 
Probab=23.06  E-value=26  Score=13.45  Aligned_cols=14  Identities=14%  Similarity=0.432  Sum_probs=5.5

Q ss_pred             HHHHHHHHHHHHHC
Q ss_conf             89999999999754
Q gi|254780191|r  807 KELKSVMDALQKKI  820 (898)
Q Consensus       807 ~~Lr~l~d~l~~k~  820 (898)
                      +.+.-..+.+..+.
T Consensus        33 k~i~P~~~~l~~e~   46 (102)
T cd02948          33 KAVVSLFKKIKNEL   46 (102)
T ss_pred             HHHHHHHHHHHHHC
T ss_conf             88789999999874


No 212
>PRK09258 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed
Probab=23.05  E-value=38  Score=12.14  Aligned_cols=90  Identities=16%  Similarity=0.172  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEC----CCCCCHHHHHHH
Q ss_conf             645555557646788999987489899----999989999999986115464245743799852----458888999987
Q gi|254780191|r  333 MGSAYPELIQAKLLIEETLRSEDERFG----KTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYD----THGLPLDIMQDI  404 (898)
Q Consensus       333 m~~~ypeL~~~~~~I~~ii~~EE~~F~----~TL~~G~~~l~~~i~~~~~~~~lsg~~af~LyD----TyGfP~dlt~ei  404 (898)
                      +...++++...+..|++..-.+|.+|.    .+.+-+.+--++.+++.+-   -+.++=.-+|-    -|=+| -.-..+
T Consensus        24 ~~~~~~~~~~~~~~i~~~tGI~~Rr~a~~~e~~sdma~~Aa~~AL~~agi---~p~dIDllI~at~tpd~~~P-~tA~~v   99 (339)
T PRK09258         24 LAPLYQRLRIPMGQLEALTGIRERRWWPKGHQLSDGATEAARKALAEAGI---DASDIGLLINTSVCRDQLEP-ATACRV   99 (339)
T ss_pred             HCCCHHHHCCCCCHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCC---CHHHCCEEEEECCCCCCCCC-CHHHHH
T ss_conf             53304542587113233467303536799998899999999999997599---98999999990511485378-189999


Q ss_pred             HHHCCCC----CCCH----HHHHHHHHHHH
Q ss_conf             6650774----4358----88999999999
Q gi|254780191|r  405 LCARGLA----GIDI----ISFNQALEEQR  426 (898)
Q Consensus       405 a~e~gi~----~vD~----~~f~~~m~~qk  426 (898)
                      +.+.|+.    .+|+    .||-..|.-..
T Consensus       100 ~~~LGl~~~~~afDi~~aCsGf~~aL~~A~  129 (339)
T PRK09258        100 HAELGLSKDCAIFDISNACLGFLNGMLDAA  129 (339)
T ss_pred             HHHHCCCCCEEEEEECCCCHHHHHHHHHHH
T ss_conf             998479987478651043167999999999


No 213
>TIGR02924 ICDH_alpha isocitrate dehydrogenase; InterPro: IPR014273   This entry represents a group of isocitrate dehydrogenases found mainly in the alphaproteobacteria. Many of the species containing these proteins appear to have a TCA cycle lacking only a determined isocitrate dehydrogenase. The precise identity of the cofactor (NADH -- 1.1.1.41 from EC vs. NADPH -- 1.1.1.42 from EC) is unclear..
Probab=23.05  E-value=38  Score=12.14  Aligned_cols=23  Identities=26%  Similarity=0.316  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHHHCCCCEEEEEEE
Q ss_conf             99999999997549978999995
Q gi|254780191|r  808 ELKSVMDALQKKIQSGIIMLVGI  830 (898)
Q Consensus       808 ~Lr~l~d~l~~k~~~~vvvL~~~  830 (898)
                      ++.++++.|.+-....++-|...
T Consensus       389 d~~~l~~~L~~~~~~~v~~L~~I  411 (481)
T TIGR02924       389 DLNQLVKLLEKIKLDDVIKLKLI  411 (481)
T ss_pred             CHHHHHHHHHHCCCCCEEEEEEE
T ss_conf             48999999985389973689875


No 214
>PRK13985 UreB urease subunit beta; Provisional
Probab=23.05  E-value=24  Score=13.66  Aligned_cols=50  Identities=26%  Similarity=0.374  Sum_probs=37.8

Q ss_pred             HHHHCCCCHHHEEEEECCCHHHHHHHHHHHCCCCHHHEEECCCCCCCCCCCCC---CCCCCCEEEEE
Q ss_conf             13341898123799971882899997566349998997535786665457999---99877046788
Q gi|254780191|r  114 LTKEFDLDQRRLYITVYDEDEEAFKLWKKISGLSADKIIRITTNDNFWSMAET---GPCGPCSEIFF  177 (898)
Q Consensus       114 lt~~~~l~~~~l~vtv~~~D~e~~~iW~~~~gi~~~~i~~~~~~dNfW~~g~~---GpcGPcsEi~~  177 (898)
                      +|+.+=+|    |.-+|+.|          |||..-||..+|+.-|.=-|-..   =--|||+||.-
T Consensus        69 ITNalIiD----~~GI~KAD----------IGIkdG~I~gIGKAGNPd~mdgV~p~lviG~~Tevia  121 (568)
T PRK13985         69 ITNALIVD----YTGIYKAD----------IGIKDGKIAGIGKGGNKDMQDGVKNNLSVGPATEALA  121 (568)
T ss_pred             EEEEEEEE----CCCEEECC----------CCCCCCEEEEEECCCCCCCCCCCCCCEEECCCCCEEC
T ss_conf             85049973----37658740----------0232776977434789765678888807777853573


No 215
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=23.01  E-value=38  Score=12.13  Aligned_cols=48  Identities=13%  Similarity=0.192  Sum_probs=33.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC----CHHHHHHHHC
Q ss_conf             24767899999999999998988730453046612322210----0035544315
Q gi|254780191|r  621 VTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIA----SGAAALLGTK  671 (898)
Q Consensus       621 fsh~~~lt~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~----~ga~alfgek  671 (898)
                      ||+--+||++||.   +.++-+|.++-.+-+++.+...+..    ++.+.+||++
T Consensus         6 fSyLP~ltd~qi~---~QI~y~l~qGw~p~iE~~d~~~~~~~yW~mWkLPmF~~~   57 (99)
T cd03527           6 FSYLPPLTDEQIA---KQIDYIISNGWAPCLEFTEPEHYDNRYWTMWKLPMFGCT   57 (99)
T ss_pred             CCCCCCCCHHHHH---HHHHHHHHCCCEEEEEEECCCCCCCCEEEECCCCCCCCC
T ss_conf             4569999999999---999999968998789984157666773334467467898


No 216
>TIGR00113 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase; InterPro: IPR003699   Queuosine is a hypermodified nucleoside that usually occurs in the first position of the anticodon of tRNAs specifying the amino acids asparagine, aspartate, histidine, and tyrosine. The hypermodified nucleoside is found in bacteria and eukaryotes . Queuosine is synthesized de novo exclusively in bacteria; for eukaryotes the compound is a nutrient factor. Queuosine biosynthesis protein, or S-adenosylmethionine:tRNA -ribosyltransferase-isomerase, is required for the synthesis of the queuosine precursor (oQ). ; GO: 0003824 catalytic activity, 0008616 queuosine biosynthetic process.
Probab=22.88  E-value=38  Score=12.11  Aligned_cols=60  Identities=12%  Similarity=0.061  Sum_probs=27.1

Q ss_pred             EEEECCC-CEEECCCCCCCCCCEEEECCEEEEEECCCCCCCEEEEEEECCCCCCCCCCCEEEEEEH
Q ss_conf             9997375-2000368765665145404248985224565533899851046787556733888421
Q gi|254780191|r  512 EVVFDQT-PFYAEAGGQLGDTGCAIGDGIRLQITDVQKKAEGIFVHHAIVERGILRTEMSLVLTID  576 (898)
Q Consensus       512 ~ivLd~T-~FY~E~GGQ~~D~G~i~~~~~~~~V~dv~k~~~g~i~H~~~~~~g~l~~g~~V~~~VD  576 (898)
                      .+||+.| ..=|--=||-.++  +-+...++-|.+-. ..+-+.-|. + .+..++.|+.|..-=|
T Consensus        56 LlvlNnTkV~pARlfG~K~~~--lPg~~vE~L~~~~~-~~~~~~a~~-k-~sK~~K~G~~~~f~~~  116 (364)
T TIGR00113        56 LLVLNNTKVIPARLFGRKESF--LPGGKVEVLLLRRL-DENRFLALI-K-PSKKLKVGAKVKFGED  116 (364)
T ss_pred             EEEECCCCCCCCCCCCCCCCC--CCCCEEEEEEEECC-CCCEEEEEE-C-CCCCCCCCCEEECCCC
T ss_conf             688437651110001251101--88740799852003-685578776-1-4676036624666876


No 217
>TIGR03257 met_CoM_red_bet methyl-coenzyme M reductase, beta subunit. Members of this protein family are the beta subunit of methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes.
Probab=22.86  E-value=30  Score=12.99  Aligned_cols=79  Identities=20%  Similarity=0.276  Sum_probs=35.6

Q ss_pred             CCCCCCCCCCCCCCH-----HHHHHHHCCCCCCCHHHHHH-HHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             565766531017579-----99999988798530057699-999999973067854335024899999898999987403
Q gi|254780191|r  216 RFILPKMSIDTGMGL-----ERMATVLQEKTNNYDIDLFK-HLIQASEQVTGMKYEGNNIVNHRVIVDHLRSSSFLIADG  289 (898)
Q Consensus       216 ~~~Lp~~~IDTGmGL-----ERl~~vlqg~~s~ydtD~f~-pii~~i~~~~g~~y~~~~~~~~rvIaDH~Ra~~f~I~DG  289 (898)
                      +...|..-|+.+.-.     ---+++.|-.-..|++|.|- |.++..- .-  .|...-+..=       -.+..++   
T Consensus       109 lvqvPs~Ri~~aa~y~~~~~~~~~A~~~aIid~f~v~mfda~~VkaAv-~G--~YPqt~d~~g-------gnv~~ll---  175 (433)
T TIGR03257       109 LIQVPSSRLIAAAEYSVATLVTAAAVTQTIIDMFGIDPYDAPIVKSAV-WG--SYPQTMDYMG-------GNIAGIL---  175 (433)
T ss_pred             EEECCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH-HC--CCCCCCCCCC-------CCCHHHH---
T ss_conf             996777876533001388888899999999998188754207788998-73--6988778777-------6204541---


Q ss_pred             CCCC-CCCCCHHHHHHHHH
Q ss_conf             3334-44641257788999
Q gi|254780191|r  290 ILPA-NEGRGYVLRRIMRR  307 (898)
Q Consensus       290 v~Ps-N~GrGYvlRrilRR  307 (898)
                      -+|. |||-||-||.|.--
T Consensus       176 ~iP~~~EGlGyaLRNI~~N  194 (433)
T TIGR03257       176 SIPQKLEGLGYALRNIMVN  194 (433)
T ss_pred             CCCCCCCCCCHHHHCCHHH
T ss_conf             7763256764212203066


No 218
>COG4402 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.84  E-value=32  Score=12.77  Aligned_cols=14  Identities=29%  Similarity=0.370  Sum_probs=8.8

Q ss_pred             CHHHHHHHHHHHHC
Q ss_conf             00178885422314
Q gi|254780191|r   86 HHTFFEMLGNFSFG   99 (898)
Q Consensus        86 H~TfFEMlGn~Sfg   99 (898)
                      ....||-|-+||--
T Consensus        95 e~kiierLD~fSAP  108 (457)
T COG4402          95 EQKIIERLDTFSAP  108 (457)
T ss_pred             CHHHHHHHHCCCCH
T ss_conf             36678766424650


No 219
>TIGR01803 CM-like chorismate mutase related enzymes; InterPro: IPR008241   Isochorismate pyruvate-lyase (IPL; PchB) catalyses the second reaction in the pyochelin biosynthetic pathway of Pseudomonas aeruginosa, conversion of isochorismate to salicylate plus pyruvate (following the initial PchA-dependent conversion of chorismate to isochorismate) . This enzyme can also carry out the chorismate mutase (CM) reaction, but with a low catalytic efficiency. It is unlikely that PchB plays a significant role in aromatic amino acid biosynthesis. This enzyme is a stand-alone version of a chorismate mutase domain of the AroQ class.   The three types of CM are AroQ class, Prokaryotic type (e.g., IPR008239 from INTERPRO and others); AroQ class, Eukaryotic type (IPR008238 from INTERPRO); and AroH class (IPR008243 from INTERPRO). They fall into two structural folds (AroQ class and AroH class) which are completely unrelated . The two types of the AroQ structural class (the Escherichia coli CM dimer and the yeast CM monomer) can be structurally superimposed, and the topology of the four-helix bundle forming the active site is conserved .   The PchB-type of chorismate mutase domain, while sharing conserved residues and the predicted secondary structure with the other subgroups of the AroQ class (Prokaryotic type), has isochorismate pyruvate-lyase (IPL) as a primary catalytic activity. PchB can still use the same active site either for the IPL or for the CM reaction. It has been suggested that PchB was derived from an AroQ-class CM by a gene duplication event followed by selection for efficient IPL function in the course of the evolution of the pyochelin siderophore pathway, with only residual CM activity remaining. It can be further speculated that contemporary CMs may already possess (weak) IPL activity .   For additional information please see , , ..
Probab=22.56  E-value=39  Score=12.07  Aligned_cols=25  Identities=24%  Similarity=0.312  Sum_probs=13.8

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             9999998487433104568999998
Q gi|254780191|r  308 AMCYARLLGYTEPLMMHLLPALCTE  332 (898)
Q Consensus       308 a~r~~~~lg~~~~fl~~lv~~v~~~  332 (898)
                      +-|++...|++.+|+-.|.+.+++.
T Consensus        53 aaR~A~e~GlDp~F~e~l~~~ii~~   77 (82)
T TIGR01803        53 AARYAAELGLDPDFLETLYDQIIER   77 (82)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             7766786389988999999999999


No 220
>COG1944 Uncharacterized conserved protein [Function unknown]
Probab=22.53  E-value=34  Score=12.56  Aligned_cols=22  Identities=14%  Similarity=0.223  Sum_probs=10.8

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             7899999999997549978999
Q gi|254780191|r  806 SKELKSVMDALQKKIQSGIIML  827 (898)
Q Consensus       806 ~~~Lr~l~d~l~~k~~~~vvvL  827 (898)
                      ...+..+.+.+++..-..+.++
T Consensus       336 ~~~~~~~~~~~~e~g~~~~~~v  357 (398)
T COG1944         336 ATLMAILLDRLKEAGIEDYIVV  357 (398)
T ss_pred             CHHHHHHHHHHHHHCCCEEEEE
T ss_conf             2048999999886063516996


No 221
>PRK02948 cysteine desulfurase; Provisional
Probab=22.47  E-value=39  Score=12.06  Aligned_cols=22  Identities=9%  Similarity=0.184  Sum_probs=14.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             5899987889999999998619
Q gi|254780191|r  877 SGGPNGNKADQAIAGVASFLKK  898 (898)
Q Consensus       877 gGG~~~~~l~eal~~vk~~Lke  898 (898)
                      |-.+..+.+|.+++.+++++++
T Consensus       353 g~ynT~eeId~~i~al~~i~~~  374 (381)
T PRK02948        353 GQQTTKDQIDTTIHALETIGNQ  374 (381)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHH
T ss_conf             7999999999999999999999


No 222
>pfam10075 PCI_Csn8 COP9 signalosome, subunit CSN8. This PCI_Csn8 domain is conserved from plants to humans. It is a signature protein motif found in components of CSN (COP9 signalosome). It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development.
Probab=22.46  E-value=39  Score=12.06  Aligned_cols=24  Identities=21%  Similarity=0.256  Sum_probs=15.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             331045689999986455555576
Q gi|254780191|r  319 EPLMMHLLPALCTEMGSAYPELIQ  342 (898)
Q Consensus       319 ~~fl~~lv~~v~~~m~~~ypeL~~  342 (898)
                      .|.+..++...-..|...|+++.+
T Consensus        38 ~p~i~~~~~L~~~L~~~~y~~~~~   61 (144)
T pfam10075        38 DPEIQQLLTLGQLLWENDYAKFYQ   61 (144)
T ss_pred             CHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf             977999999999998188999999


No 223
>KOG1227 consensus
Probab=22.46  E-value=32  Score=12.71  Aligned_cols=42  Identities=19%  Similarity=0.192  Sum_probs=18.6

Q ss_pred             CCC-CCCCCHHHHHHHHEECCCCCCCCCEEEEEEE-CHHHHHHHHH
Q ss_conf             562-2258864601100110121268828999971-6899999999
Q gi|254780191|r  694 CGG-THVSSTGEIMLLYIVSESSIRAGIRRIEAIT-GQRARSHLMG  737 (898)
Q Consensus       694 CGG-THV~nTgeIG~fkIise~si~sGvRRIeavt-G~~A~~~~~~  737 (898)
                      |-| +=|.=-.-||.|...+.  +.+|-+-+.|.- .+.+++.++.
T Consensus       193 c~~eviVDLYAGIGYFTlpfl--V~agAk~V~A~EwNp~svEaLrR  236 (351)
T KOG1227         193 CDGEVIVDLYAGIGYFTLPFL--VTAGAKTVFACEWNPWSVEALRR  236 (351)
T ss_pred             CCCCHHHHHHCCCCEEEEEHH--HCCCCCEEEEEECCHHHHHHHHH
T ss_conf             565301223426544874023--00574579999458799999998


No 224
>TIGR00434 cysH phosophoadenylyl-sulfate reductase; InterPro: IPR004511 Phosphoadenosine phosphosulphate reductase (1.8.4.8 from EC), involved in the assimilation of inorganic sulphate, is designated cysH in bacteria and MET16 in Saccharomyces cerevisiae. Synonyms include phosphoadenosine phosphosulphate reductase and PAPS reductase. In a reaction requiring reduced thioredoxin and NADPH, it converts 3'-phosphoadenylylsulphate (PAPS) to sulphite and adenosine 3',5' diphosphate (PAP). A related family of plant enzymes, scoring below the trusted cut-off, differs in having a thioredoxin-like C-terminal domain, not requiring thioredoxin, and in having a preference for 5'-adenylylsulphate (APS) over PAPS.; GO: 0004604 phosphoadenylyl-sulfate reductase (thioredoxin) activity, 0019379 sulfate assimilation phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin).
Probab=22.37  E-value=39  Score=12.04  Aligned_cols=23  Identities=17%  Similarity=0.332  Sum_probs=10.8

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             4379985245888899998766507
Q gi|254780191|r  385 DVAFKLYDTHGLPLDIMQDILCARG  409 (898)
Q Consensus       385 ~~af~LyDTyGfP~dlt~eia~e~g  409 (898)
                      ..+.++|..-|-  +=.++++++.|
T Consensus        73 glni~vy~p~GC--lS~a~~~~~YG   95 (226)
T TIGR00434        73 GLNIKVYKPDGC--LSLAEQAAKYG   95 (226)
T ss_pred             CCEEEEECCCCC--CCHHHHHHHHC
T ss_conf             750677678888--79789997716


No 225
>pfam01268 FTHFS Formate--tetrahydrofolate ligase.
Probab=22.34  E-value=23  Score=13.84  Aligned_cols=34  Identities=9%  Similarity=0.079  Sum_probs=17.9

Q ss_pred             HHHHHHHEECCCCCCCCCE--EEEEEECHHHHHHHH
Q ss_conf             4601100110121268828--999971689999999
Q gi|254780191|r  703 GEIMLLYIVSESSIRAGIR--RIEAITGQRARSHLM  736 (898)
Q Consensus       703 geIG~fkIise~si~sGvR--RIeavtG~~A~~~~~  736 (898)
                      +++|.=|...-..-.+|.+  =+.-|+--||++|.-
T Consensus       303 aDLGaEKF~dIKcr~~gl~P~~~VlVaTvRALK~HG  338 (555)
T pfam01268       303 ADLGAEKFFDIKCRKSGLKPDAVVLVATVRALKMHG  338 (555)
T ss_pred             CCCCCHHHCCEEHHCCCCCCCEEEEEEEHHHHHHCC
T ss_conf             665623430100220599987799970289998728


No 226
>cd07211 Pat_PNPLA8 Patatin-like phospholipase domain containing protein 8. PNPLA8 is a Ca-independent myocardial phospholipase which maintains mitochondrial integrity. PNPLA8 is also known as iPLA2-gamma. In humans, it is predominantly expressed in heart tissue. iPLA2-gamma can catalyze both phospholipase A1 and A2 reactions (PLA1 and PLA2 respectively). This family includes PNPLA8 (iPLA2-gamma) from Homo sapiens and iPLA2-2 from Mus musculus.
Probab=22.13  E-value=39  Score=12.01  Aligned_cols=56  Identities=23%  Similarity=0.293  Sum_probs=36.0

Q ss_pred             HHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEECCCEEEEECCCCCC-----CCHHHHHHHHHHHHHHHHHC
Q ss_conf             7775201368899999752125444445530024300000247678-----99999999999998988730
Q gi|254780191|r  581 RQLSINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKP-----ITSAELKSIEDNVNDIIAQN  646 (898)
Q Consensus       581 ~~~~~~HTatHlL~~alr~vLG~hv~Q~GS~v~~~~lrfDfsh~~~-----lt~eel~~IE~~vN~~I~~n  646 (898)
                      .+++..-|.++..|..++..+.          ...|+||+....+.     .+++.|.+++..+.+.|++|
T Consensus       248 ~~i~~~~~~~~~~~~~~~~~~~----------~~~Y~R~np~l~~~~~lD~~~~~~l~~l~~~t~~yl~~n  308 (308)
T cd07211         248 LNLIDSATDTERVHTALDDLLP----------PDVYFRFNPVMSECVELDETRPEKLDQLQDDTLEYIKRN  308 (308)
T ss_pred             HHHHHHCCCHHHHHHHHHHHCC----------CCCEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             9999962289999999997448----------980799678987666678899899999999999999609


No 227
>pfam03455 dDENN dDENN domain. This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family.
Probab=21.95  E-value=40  Score=11.98  Aligned_cols=13  Identities=38%  Similarity=0.879  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             8999999999997
Q gi|254780191|r    5 SSIRTTFLEFFQK   17 (898)
Q Consensus         5 ~eiR~~fl~fF~~   17 (898)
                      ++||+.||.||.+
T Consensus         3 ~~vr~aFlrff~~   15 (68)
T pfam03455         3 DQVREAFLRFFAS   15 (68)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             7899999999999


No 228
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family; InterPro: IPR014304   This entry is a group of RNA polymerase sigma factors where one of the members is designated as SigZ in Bacillus subtilis . This group has a very sporadic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member Dechloromonas aromatica (strain RCB), that appears to have two of these sigma factors. A member of which appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri (strain ATCC 700601 / ES114), where a second one is chromosomally encoded..
Probab=21.94  E-value=40  Score=11.98  Aligned_cols=60  Identities=25%  Similarity=0.371  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf             4898999999899999999861154642457437998524588889999876650774435888999999999
Q gi|254780191|r  354 EDERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLDIMQDILCARGLAGIDIISFNQALEEQR  426 (898)
Q Consensus       354 EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsg~~af~LyDTyGfP~dlt~eia~e~gi~~vD~~~f~~~m~~qk  426 (898)
                      +|+.|.+-|..=   +..+|++++..    -..|..|+|=.|+|.   +++|.+.|++   ..|-.+-.+..|
T Consensus        82 ~ee~~~~e~~~C---l~~~i~~LP~~----~r~a~~L~el~G~sQ---~e~A~kLGlS---lSGaKSRVQRGR  141 (170)
T TIGR02959        82 EEETFVKELSQC---LRPMIKELPDE----YREAIRLTELEGLSQ---KEIAEKLGLS---LSGAKSRVQRGR  141 (170)
T ss_pred             CCCCHHHHHHHH---HHHHHHHCCHH----HHHHHHHHHCCCCCH---HHHHHHCCCC---CCCHHHHHHHHH
T ss_conf             666404568888---89988756986----788988875079982---7998761753---351567889999


No 229
>PRK10252 entF enterobactin synthase subunit F; Provisional
Probab=21.92  E-value=40  Score=11.98  Aligned_cols=25  Identities=8%  Similarity=0.074  Sum_probs=13.8

Q ss_pred             EEEEECCCCCCCCHHHHHHHHHHHH
Q ss_conf             0000024767899999999999998
Q gi|254780191|r  616 GLRFDVTHSKPITSAELKSIEDNVN  640 (898)
Q Consensus       616 ~lrfDfsh~~~lt~eel~~IE~~vN  640 (898)
                      .+|.=+.-.++++.+.+.......+
T Consensus       715 ~lr~v~~gGE~l~~~l~~~~~~~~~  739 (1293)
T PRK10252        715 SLRQVFCSGEALPADLCREWQQLTG  739 (1293)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHCCC
T ss_conf             6018999806899999999997129


No 230
>TIGR01508 rib_reduct_arch diaminohydroxyphosphoribosylaminopyrimidine reductase; InterPro: IPR006401   These sequences represent a specific reductase of riboflavin biosynthesis in the archaea, diaminohydroxyphosphoribosylaminopyrimidine reductase. It should not be confused with bacterial 5-amino-6-(5-phosphoribosylamino)uracil reductase. The intermediate 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine in riboflavin biosynthesis is reduced first and then deaminated in both archaea and fungi, opposite to the order in bacteria. The subsequent deaminase is not presently known and is not closely homologous to the deaminase domain fused to the reductase domain, which is similar to this protein but found in most bacteria. .
Probab=21.80  E-value=28  Score=13.13  Aligned_cols=66  Identities=20%  Similarity=0.357  Sum_probs=41.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCEEEEEEEECHHHHCCCCHHHHHHHHHHHHCCCCCCCCCHHCCCCC
Q ss_conf             799978999999999975499789999953898179999867789726798999999998834999999810114589
Q gi|254780191|r  802 SEVDSKELKSVMDALQKKIQSGIIMLVGISKEKKASVLIVVTEDLLDRFNAVDLARLSAKVLGGGGGGGRPHMAQSGG  879 (898)
Q Consensus       802 ~~~d~~~Lr~l~d~l~~k~~~~vvvL~~~~~~~k~~ivv~vs~~~~~~~~A~~lik~ia~~l~GGgGGGkpd~AQgGG  879 (898)
                      -+-...+|..+.|.|..+.   |==|. .+ +|...+-..+.+++.+.+.-     -+++.+.||+-+  |.++||=|
T Consensus       131 ~G~~~v~L~~lld~L~~kg---v~rLm-vE-GGG~Li~~l~~~~LvDEi~v-----y~aP~~~GGr~a--pt~~dGeG  196 (224)
T TIGR01508       131 FGEERVDLEKLLDILEDKG---VRRLM-VE-GGGTLIWSLIKENLVDEIRV-----YIAPKIIGGRDA--PTLVDGEG  196 (224)
T ss_pred             ECCCCCCHHHHHHHHHHCC---CEEEE-EE-CCCEEEHHHHHCCCEEEEEE-----EECCEEECCCCC--CEEEECCC
T ss_conf             2478534689999987479---70999-82-48510102230284358999-----881467627778--80773772


No 231
>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]
Probab=21.71  E-value=40  Score=11.95  Aligned_cols=35  Identities=29%  Similarity=0.521  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             99999898999987403333444641257788999999999848
Q gi|254780191|r  273 RVIVDHLRSSSFLIADGILPANEGRGYVLRRIMRRAMCYARLLG  316 (898)
Q Consensus       273 rvIaDH~Ra~~f~I~DGv~PsN~GrGYvlRrilRRa~r~~~~lg  316 (898)
                      |+|.|.+-.+.+.+.+.        +.. |+++++..+..++++
T Consensus       127 ~~ViDsi~~~~~~~~~~--------~~~-r~~~~~l~~~~~~~~  161 (260)
T COG0467         127 RVVIDSITELTLYLNDP--------ALV-RRILLLLKRFLKKLG  161 (260)
T ss_pred             EEEEECCHHHHHHCCCH--------HHH-HHHHHHHHHHHHHCC
T ss_conf             89996630776652782--------578-999999998765068


No 232
>TIGR02706 P_butyryltrans phosphate butyryltransferase; InterPro: IPR014079   Members of this family are phosphate butyryltransferase enzymes, also called phosphotransbutyrylase. In general, this enzyme is found in butyrate-producing anaerobic bacteria, encoded next to the gene for butyrate kinase. Together, these two enzymes represent what may be the less common of two pathways for butyrate production from butyryl-CoA. The alternative is transfer of the CoA group to acetate by butyryl-CoA:acetate CoA transferase. This entry does not include the homologue from Thermotoga maritima, whose activity on butyryl-CoA is only 30 0f its activity with acetyl-CoA..
Probab=21.60  E-value=40  Score=11.93  Aligned_cols=16  Identities=31%  Similarity=0.590  Sum_probs=6.2

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             5555576467889999
Q gi|254780191|r  336 AYPELIQAKLLIEETL  351 (898)
Q Consensus       336 ~ypeL~~~~~~I~~ii  351 (898)
                      .||||+++.+.|.+.+
T Consensus       142 ~yP~Lk~K~~ii~NaV  157 (295)
T TIGR02706       142 IYPELKDKVQIINNAV  157 (295)
T ss_pred             CCCCHHHHHHHHHHHH
T ss_conf             2878789999976475


No 233
>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=21.55  E-value=38  Score=12.10  Aligned_cols=15  Identities=27%  Similarity=0.622  Sum_probs=12.1

Q ss_pred             EEEECCCCCCHHHHH
Q ss_conf             998524588889999
Q gi|254780191|r  388 FKLYDTHGLPLDIMQ  402 (898)
Q Consensus       388 f~LyDTyGfP~dlt~  402 (898)
                      =.+||=||||.++-+
T Consensus        57 ~~iyDf~GFP~~lY~   71 (253)
T cd07363          57 ETIYDFYGFPPELYE   71 (253)
T ss_pred             CCCCCCCCCCHHHEE
T ss_conf             866699999778827


No 234
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=21.47  E-value=41  Score=11.91  Aligned_cols=256  Identities=23%  Similarity=0.323  Sum_probs=108.4

Q ss_pred             HHHHHHHH-CCCEECCCCCC-CCCCCCCHHEEECCCCCCCCCCCCCCCCCCCCCCCCCC----CEECCCCCC-CHHHCCC
Q ss_conf             99999997-89889116675-66778710023014347554005887999998511154----322489878-6343464
Q gi|254780191|r   10 TFLEFFQK-NGHELLPSSSL-IPCNDPTLMFTNSGMVPFKNIFTGQEKPVYQAVTTVQK----CVRAGGKHN-DLDNVGR   82 (898)
Q Consensus        10 ~fl~fF~~-~~H~~~~s~sl-vp~~d~~llft~Agm~~fk~~f~G~~~p~~~r~~~~Qk----CiR~ggkhn-Dld~VG~   82 (898)
                      ..-+||.- .|.-..|..|- |-..+|-=++...=++|..+-.-...+ .+.-++..||    ||-  ||.. =.+|-|-
T Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~  316 (1748)
T PRK08332        240 EIEEYFRLMTGQIFMPNTPALINSGRPLGMLSACFVVPIEDDMESIMK-AAHDVAMIQKAGGGCID--GKAKIIFENDGE  316 (1748)
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHCCCCCCCCEEEEEEEECCCHHHHHHH-HHHHHHHHHHCCCCCCC--CCEEEEECCCCH
T ss_conf             999999986085215898677428985320103679862113999998-76678998760687415--731488716758


Q ss_pred             CCCCHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHH--------HHHHHCC--CCHHHE
Q ss_conf             885001788854223-14753788999899861334189812379997188289999--------7566349--998997
Q gi|254780191|r   83 TNRHHTFFEMLGNFS-FGGYFKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFK--------LWKKISG--LSADKI  151 (898)
Q Consensus        83 t~rH~TfFEMlGn~S-fgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~--------iW~~~~g--i~~~~i  151 (898)
                       ..-.|+-||.-.+- .|.++-+|--+         ||+|-+..-+-|-.=|.|+.+        ||+-..|  +|.-.|
T Consensus       317 -~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  386 (1748)
T PRK08332        317 -EHIMTMAEMYERYKDLGEFYDEEYNR---------WGIDVEEVPIYVKSFDPESKEITKGKVKVIWKYELGEDVPKYEI  386 (1748)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHHHH---------CCCCHHHCEEEEECCCCCCCHHCCCCEEEEEEEECCCCCCCEEE
T ss_conf             -99999999999987677665666441---------27762224046731586532002660589998503678764267


Q ss_pred             EECCCCCCCCCCCCCCCCCCCEEEEEEC------CCCCCCCCCCC--CCCCCCE---EEEEEHHHHHHHCCCCCCCCCCC
Q ss_conf             5357866654579999987704678853------85568988877--7889826---89600112344304788756576
Q gi|254780191|r  152 IRITTNDNFWSMAETGPCGPCSEIFFDQ------GECIPGGLPGS--SEEGERY---IEIWNLVFMQFEQQNKQERFILP  220 (898)
Q Consensus       152 ~~~~~~dNfW~~g~~GpcGPcsEi~~d~------g~~~~~~~~~~--~~~~~r~---lEiwNlVFmq~~~~~~g~~~~Lp  220 (898)
                      +.-  |-   .-=-|.|--|-.-|--|+      .++...|.-..  -.|+|.|   ...|-.-|+    ..||.+-..-
T Consensus       387 ~~~--~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~  457 (1748)
T PRK08332        387 ITN--KG---TKILTSPWHPFFVITPDFKIVEKRADELKEGDILIGGMPDDDDYEFIFDYWLAGFI----AGDGCFDKYH  457 (1748)
T ss_pred             EEC--CC---CEEECCCCCCCEEECCCCCHHHHHHHHHCCCCEEECCCCCCCCHHHHHHHHHHHHH----CCCCHHHHHH
T ss_conf             705--88---54623788651785686311564444540377665378887540123887877743----3674056555


Q ss_pred             CCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCC-------HHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             6531017579999999887985300576999999999730678543350-------248999998989999874033334
Q gi|254780191|r  221 KMSIDTGMGLERMATVLQEKTNNYDIDLFKHLIQASEQVTGMKYEGNNI-------VNHRVIVDHLRSSSFLIADGILPA  293 (898)
Q Consensus       221 ~~~IDTGmGLERl~~vlqg~~s~ydtD~f~pii~~i~~~~g~~y~~~~~-------~~~rvIaDH~Ra~~f~I~DGv~Ps  293 (898)
                      ...    -|-|-+.--|.  --.|-+..|.-|-+.+++.-|++|....+       +..+-|.-|---+.--|-.|+-|-
T Consensus       458 ~~~----~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  531 (1748)
T PRK08332        458 SHV----KGHEYIYDRLR--IYDYRIETFEIINDHLEKTFGKKYSIQKDRNIHYIDIKAKGITSHYIELLEGIDNGIPPP  531 (1748)
T ss_pred             HHC----CCHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCCCEEEECCCCEEEEEEECCCCHHHHHHHHHCCCCCCCCH
T ss_conf             304----51177775641--221111243677788887535220220257414887421641588999985002689970


No 235
>pfam06623 MHC_I_C MHC_I C-terminus. This family represents the C-terminal region of the MHC class I antigen. The family is found in conjunction with pfam00129 and pfam00047.
Probab=21.31  E-value=38  Score=12.17  Aligned_cols=17  Identities=41%  Similarity=0.777  Sum_probs=10.0

Q ss_pred             CCCCCCCCHHCCCCCCCHHH
Q ss_conf             99999981011458999878
Q gi|254780191|r  865 GGGGGGRPHMAQSGGPNGNK  884 (898)
Q Consensus       865 GGgGGGkpd~AQgGG~~~~~  884 (898)
                      ||+||   +.||+-++|..+
T Consensus         3 Ggkgg---~y~~a~~~DSaQ   19 (29)
T pfam06623         3 GGKGG---DYAQAPGRDSAQ   19 (29)
T ss_pred             CCCCC---CCCCCCCCCCCC
T ss_conf             77576---114477876433


No 236
>PRK03147 thiol-disulfide oxidoreductase; Provisional
Probab=21.21  E-value=27  Score=13.33  Aligned_cols=14  Identities=29%  Similarity=0.524  Sum_probs=7.1

Q ss_pred             EEEECCCCCCHHHH
Q ss_conf             99852458888999
Q gi|254780191|r  388 FKLYDTHGLPLDIM  401 (898)
Q Consensus       388 f~LyDTyGfP~dlt  401 (898)
                      |.|-|..|=|+.+.
T Consensus        45 f~l~~l~G~~v~ls   58 (176)
T PRK03147         45 FVLTDLEGKKIELK   58 (176)
T ss_pred             CEEECCCCCEEEHH
T ss_conf             16278998987189


No 237
>pfam05631 DUF791 Protein of unknown function (DUF791). This family consists of several eukaryotic proteins of unknown function.
Probab=21.13  E-value=20  Score=14.36  Aligned_cols=27  Identities=26%  Similarity=0.190  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             489999989899998740333344464
Q gi|254780191|r  271 NHRVIVDHLRSSSFLIADGILPANEGR  297 (898)
Q Consensus       271 ~~rvIaDH~Ra~~f~I~DGv~PsN~Gr  297 (898)
                      +.=-|+-..-+..|.--=|.+...-||
T Consensus        72 a~Lfv~GF~Ss~~fgt~vG~laD~~GR   98 (354)
T pfam05631        72 GILFIAGFGSSMLFGTIVGSLADKQGR   98 (354)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999999988899999888888875174


No 238
>PRK12292 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=21.04  E-value=41  Score=11.85  Aligned_cols=34  Identities=18%  Similarity=0.121  Sum_probs=16.8

Q ss_pred             CHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC
Q ss_conf             9999999999998988730453046612322210
Q gi|254780191|r  628 TSAELKSIEDNVNDIIAQNLPVVTRIMNREDAIA  661 (898)
Q Consensus       628 t~eel~~IE~~vN~~I~~n~~V~~~~~~~~eA~~  661 (898)
                      ..+...+.-+.+++.=.++..|.+.....+.+..
T Consensus       334 ~~~~~~~a~~~a~~LR~~G~~v~~~l~~~~~~~~  367 (388)
T PRK12292        334 PWERLEAALAAAQALRKKGEIVVLALPGHDDAEA  367 (388)
T ss_pred             CHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHH
T ss_conf             8676999999999999779889998999986889


No 239
>COG3235 Predicted membrane protein [Function unknown]
Probab=21.02  E-value=38  Score=12.11  Aligned_cols=14  Identities=21%  Similarity=0.026  Sum_probs=5.2

Q ss_pred             HHHHHHHHCCCCCC
Q ss_conf             99998740333344
Q gi|254780191|r  281 SSSFLIADGILPAN  294 (898)
Q Consensus       281 a~~f~I~DGv~PsN  294 (898)
                      |+.+.++=|++|-|
T Consensus        94 cLlg~~s~~A~p~n  107 (223)
T COG3235          94 CLLGAQSWGAYPPN  107 (223)
T ss_pred             HHHHHHHHHHCCCC
T ss_conf             99604446306853


No 240
>TIGR03400 18S_RNA_Rcl1p 18S rRNA biogenesis protein RCL1. Members of this strictly eukaryotic protein family are not RNA 3'-phosphate cyclase (6.5.1.4), but rather a homolog with a distinct function, found in the nucleolus and required for ribosomal RNA processing. Homo sapiens has both a member of this RCL (RNA terminal phosphate cyclase like) family and EC 6.5.1.4, while Saccharomyces has a member of this family only.
Probab=20.93  E-value=42  Score=11.83  Aligned_cols=18  Identities=17%  Similarity=0.231  Sum_probs=13.7

Q ss_pred             EEEEECCCCEEECCCCCC
Q ss_conf             999973752000368765
Q gi|254780191|r  511 VEVVFDQTPFYAEAGGQL  528 (898)
Q Consensus       511 ~~ivLd~T~FY~E~GGQ~  528 (898)
                      +.+-+.+-=|||.|||++
T Consensus       143 ~~l~v~kRG~yP~GGGeV  160 (360)
T TIGR03400       143 LELKILKRGAAPLGGGEV  160 (360)
T ss_pred             CEEEEEECCCCCCCCCEE
T ss_conf             079999645689998179


No 241
>pfam04526 DUF568 Protein of unknown function (DUF568). Family of uncharacterized plant proteins.
Probab=20.90  E-value=31  Score=12.86  Aligned_cols=13  Identities=31%  Similarity=0.355  Sum_probs=9.9

Q ss_pred             CCCCCCCCEECCC
Q ss_conf             4444455300243
Q gi|254780191|r  603 SHVSQNGSCITPD  615 (898)
Q Consensus       603 ~hv~Q~GS~v~~~  615 (898)
                      .||||.|+.|.-.
T Consensus        69 n~VWQ~G~~v~g~   81 (101)
T pfam04526        69 NQVWQVGPVVTGG   81 (101)
T ss_pred             EEEECCCCCCCCC
T ss_conf             9897758724699


No 242
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=20.88  E-value=19  Score=14.59  Aligned_cols=18  Identities=17%  Similarity=0.350  Sum_probs=8.5

Q ss_pred             EEEECCCCHHHHHHHHHH
Q ss_conf             999579997899999999
Q gi|254780191|r  798 SHIISEVDSKELKSVMDA  815 (898)
Q Consensus       798 ~~~~~~~d~~~Lr~l~d~  815 (898)
                      +..+...+.+++++++..
T Consensus       602 TGtl~~~sR~e~k~~ie~  619 (668)
T PRK07956        602 TGTLEQLSRDEAKEKLEA  619 (668)
T ss_pred             EECCCCCCHHHHHHHHHH
T ss_conf             806999898999999998


No 243
>PRK06052 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional
Probab=20.71  E-value=42  Score=11.80  Aligned_cols=39  Identities=21%  Similarity=0.302  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             889999999998487433104568999998645555557646788999987489
Q gi|254780191|r  303 RIMRRAMCYARLLGYTEPLMMHLLPALCTEMGSAYPELIQAKLLIEETLRSEDE  356 (898)
Q Consensus       303 rilRRa~r~~~~lg~~~~fl~~lv~~v~~~m~~~ypeL~~~~~~I~~ii~~EE~  356 (898)
                      -|+|+|+..--..|.+-|               .||++++.-+.-.++|+.|..
T Consensus        38 siv~~af~~Ki~aGV~VP---------------tYPQfrDMi~qFl~iIkd~k~   76 (343)
T PRK06052         38 SIVRDAFQQKIDAGVQVP---------------TYPQFRDMIEQFLDIIKDEKN   76 (343)
T ss_pred             HHHHHHHHHHHHCCCCCC---------------CCHHHHHHHHHHHHHHCCCCC
T ss_conf             999999998861386688---------------965688999999998547666


No 244
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=20.71  E-value=36  Score=12.29  Aligned_cols=30  Identities=10%  Similarity=-0.067  Sum_probs=18.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             999999999999989887304530466123
Q gi|254780191|r  627 ITSAELKSIEDNVNDIIAQNLPVVTRIMNR  656 (898)
Q Consensus       627 lt~eel~~IE~~vN~~I~~n~~V~~~~~~~  656 (898)
                      ++++.....-..++..=..++.+++...+.
T Consensus       333 ~~~~~~~~~~~ia~~LR~~gi~~e~~~~~~  362 (424)
T CHL00201        333 KGNVAIKIAFSIQRFLHNQGLKSELDLSSS  362 (424)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCEEEEEECCC
T ss_conf             784999999999999998899399970899


No 245
>KOG0128 consensus
Probab=20.38  E-value=23  Score=13.86  Aligned_cols=18  Identities=11%  Similarity=-0.005  Sum_probs=10.7

Q ss_pred             CCCCCCCCCCCHHHHHHHH
Q ss_conf             7665310175799999998
Q gi|254780191|r  219 LPKMSIDTGMGLERMATVL  237 (898)
Q Consensus       219 Lp~~~IDTGmGLERl~~vl  237 (898)
                      |-++ +|.-.+-+-++|+.
T Consensus       258 l~~~-~D~~~~~~~~~~~s  275 (881)
T KOG0128         258 LKQP-LDEDTRGWDLSEQS  275 (881)
T ss_pred             HHCC-CHHHHHHHHHHHHH
T ss_conf             7166-30134477888887


No 246
>pfam09404 DUF2003 Eukaryotic protein of unknown function (DUF2003). This is a family of proteins of unknown function which adopt an alpha helical and beta sheet structure.
Probab=20.34  E-value=43  Score=11.74  Aligned_cols=14  Identities=50%  Similarity=0.895  Sum_probs=12.4

Q ss_pred             CHHHHHHHHHHHHC
Q ss_conf             00178885422314
Q gi|254780191|r   86 HHTFFEMLGNFSFG   99 (898)
Q Consensus        86 H~TfFEMlGn~Sfg   99 (898)
                      =+|||+-||+|||-
T Consensus        18 L~tfF~~L~~~~~D   31 (447)
T pfam09404        18 LESFFTQLGMFSFD   31 (447)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999987543067


No 247
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular    trafficking, secretion, and vesicular transport]
Probab=20.30  E-value=31  Score=12.85  Aligned_cols=60  Identities=20%  Similarity=0.372  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCC-------------EEEEEECCCCCCHHHHHHHHHHCCCCCCCH--HHHHHHH
Q ss_conf             9999998999999998611546424574-------------379985245888899998766507744358--8899999
Q gi|254780191|r  358 FGKTLDRGLVLLDGVLSHLGKDEILNGD-------------VAFKLYDTHGLPLDIMQDILCARGLAGIDI--ISFNQAL  422 (898)
Q Consensus       358 F~~TL~~G~~~l~~~i~~~~~~~~lsg~-------------~af~LyDTyGfP~dlt~eia~e~gi~~vD~--~~f~~~m  422 (898)
                      |.+.+..|.+.++--+...+..++-+|+             ...+-||||       .+|++|.+|..|+.  ..|+..+
T Consensus        11 ylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~~~l~v~V~~vr~Y~tF-------~~mlreepiE~v~p~~~S~ee~l   83 (111)
T COG4043          11 YLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNGDKLKVEVIDVRVYDTF-------EEMLREEPIENVLPDVPSFEEGL   83 (111)
T ss_pred             HHHHHHCCCCEEEEEECCHHHCCCCCCCEEEECCCEEEEEEEEEEEHHHH-------HHHHHHCCHHHHCCCCCCHHHHH
T ss_conf             99998704436899955776627898998998388467999987605689-------99998548665189986399999


Q ss_pred             HH
Q ss_conf             99
Q gi|254780191|r  423 EE  424 (898)
Q Consensus       423 ~~  424 (898)
                      .-
T Consensus        84 ~~   85 (111)
T COG4043          84 RR   85 (111)
T ss_pred             HH
T ss_conf             99


No 248
>pfam02906 Fe_hyd_lg_C Iron only hydrogenase large subunit, C-terminal domain.
Probab=20.21  E-value=42  Score=11.81  Aligned_cols=60  Identities=17%  Similarity=0.149  Sum_probs=33.7

Q ss_pred             HHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4033334446412577889999999998487433104568999998645555557646788
Q gi|254780191|r  287 ADGILPANEGRGYVLRRIMRRAMCYARLLGYTEPLMMHLLPALCTEMGSAYPELIQAKLLI  347 (898)
Q Consensus       287 ~DGv~PsN~GrGYvlRrilRRa~r~~~~lg~~~~fl~~lv~~v~~~m~~~ypeL~~~~~~I  347 (898)
                      .|.|.-.+.|+..++..--+--.++ ..-+-+.|++..--|.++......||+|..+...+
T Consensus        50 f~~V~d~a~gad~~~~~~~~E~~~~-~~~~~~~P~isS~CP~~V~~iEk~~PeLi~~ls~v  109 (286)
T pfam02906        50 FDYVFDTAFGADLTIMEEASEFLER-LKKGEKLPMFTSCCPAWVKYVEKYYPELLPNLSTC  109 (286)
T ss_pred             CCEEEECHHHHHHHHHHHHHHHHHH-HHCCCCCCEEECCCHHHHHHHHHHCHHHCCCCCCC
T ss_conf             9899984788999999999999999-85599975485379899999998675434887888


No 249
>PRK13309 ureC urease subunit alpha; Reviewed
Probab=20.20  E-value=43  Score=11.72  Aligned_cols=51  Identities=22%  Similarity=0.208  Sum_probs=37.0

Q ss_pred             HHHHCCCCHHHEEEEECCCHHHHHHHHHHHCCCCHHHEEECCCCCCCCCCCCCC---CCCCCEEEEE
Q ss_conf             133418981237999718828999975663499989975357866654579999---9877046788
Q gi|254780191|r  114 LTKEFDLDQRRLYITVYDEDEEAFKLWKKISGLSADKIIRITTNDNFWSMAETG---PCGPCSEIFF  177 (898)
Q Consensus       114 lt~~~~l~~~~l~vtv~~~D~e~~~iW~~~~gi~~~~i~~~~~~dNfW~~g~~G---pcGPcsEi~~  177 (898)
                      +|+.+=+|+   |--+|+.|          |||..-||..+|+.-|.=-|-..-   ..||++||.-
T Consensus        72 ITNalIiD~---~~GI~KAD----------IGIkdG~I~gIGKAGNPd~mdgV~p~~viG~~Tevia  125 (572)
T PRK13309         72 ITNVTIVDA---RLGVIKAD----------VGIRDGKIAGIGKSGNPGVMDGVTQGMVVGVSTDAIS  125 (572)
T ss_pred             EECEEEEEC---CCCEEECC----------CCCCCCEEEEEECCCCCCCCCCCCCCEEECCCCCEEC
T ss_conf             967099846---77769742----------1443777976324789765679988807767852573


No 250
>KOG2250 consensus
Probab=20.15  E-value=43  Score=11.73  Aligned_cols=20  Identities=15%  Similarity=0.391  Sum_probs=13.6

Q ss_pred             EECCCCCCHHHHHHHHHHCC
Q ss_conf             85245888899998766507
Q gi|254780191|r  390 LYDTHGLPLDIMQDILCARG  409 (898)
Q Consensus       390 LyDTyGfP~dlt~eia~e~g  409 (898)
                      |||--|+-++-..+++.+++
T Consensus       287 l~np~Gid~~eL~~~~~~k~  306 (514)
T KOG2250         287 LINPDGIDIEELLDLADEKK  306 (514)
T ss_pred             EECCCCCCHHHHHHHHHHHC
T ss_conf             98999989899999998642


No 251
>PRK06720 hypothetical protein; Provisional
Probab=20.14  E-value=40  Score=11.97  Aligned_cols=26  Identities=4%  Similarity=-0.036  Sum_probs=13.2

Q ss_pred             EEEEEECCCCHHHHHHHHHHHHHHCC
Q ss_conf             79999579997899999999997549
Q gi|254780191|r  796 FMSHIISEVDSKELKSVMDALQKKIQ  821 (898)
Q Consensus       796 ~i~~~~~~~d~~~Lr~l~d~l~~k~~  821 (898)
                      ......+-.+.++.+.+++.+.++.+
T Consensus        67 a~~~~~Dvs~~~~v~~~i~~~~~~~g   92 (169)
T PRK06720         67 ALFVSYDMEKQGDWQRVISITLNAFS   92 (169)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHCC
T ss_conf             37897588999999999999999759


No 252
>KOG1372 consensus
Probab=20.12  E-value=36  Score=12.34  Aligned_cols=47  Identities=26%  Similarity=0.466  Sum_probs=23.6

Q ss_pred             CCCHHHHHHHHHHHHHH--HH--HCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             64125778899999999--98--4874331045689999986455555576467889
Q gi|254780191|r  296 GRGYVLRRIMRRAMCYA--RL--LGYTEPLMMHLLPALCTEMGSAYPELIQAKLLIE  348 (898)
Q Consensus       296 GrGYvlRrilRRa~r~~--~~--lg~~~~fl~~lv~~v~~~m~~~ypeL~~~~~~I~  348 (898)
                      +.||-+--||||+..+-  +.  |-.+ |     ....-..|+-.|..+.++...|+
T Consensus        50 ~KgYeVHGiiRRsSsFNT~RIeHlY~n-P-----~~h~~~~mkLHYgDmTDss~L~k  100 (376)
T KOG1372          50 SKGYEVHGIIRRSSSFNTARIEHLYSN-P-----HTHNGASMKLHYGDMTDSSCLIK  100 (376)
T ss_pred             CCCCEEEEEEEECCCCCHHHHHHHHCC-C-----CCCCCCEEEEEECCCCCHHHHHH
T ss_conf             088567678860466534557776458-4-----00256404785345554388999


No 253
>pfam07897 DUF1675 Protein of unknown function (DUF1675). The members of this family are sequences derived from hypothetical plant proteins of unknown function. One member of this family is annotated as a putative RNA-binding protein, but no evidence was found to support this.
Probab=20.06  E-value=43  Score=11.70  Aligned_cols=46  Identities=26%  Similarity=0.511  Sum_probs=23.5

Q ss_pred             HHHHHHHCCCCEEEEECCCCCCC-CHHHHHHHHCC--CCCEEEEEECCCCCCCCCEECCCCCCCC
Q ss_conf             98988730453046612322210-00355443155--5624899844767785531015622258
Q gi|254780191|r  639 VNDIIAQNLPVVTRIMNREDAIA-SGAAALLGTKY--NDRVRVVSVEYEDGGVHSSALCGGTHVS  700 (898)
Q Consensus       639 vN~~I~~n~~V~~~~~~~~eA~~-~ga~alfgeky--gd~VRVV~I~~~d~~~~S~ElCGGTHV~  700 (898)
                      +-..++++.|-...--.-...++ .|-+  |  ||  +++||||.+            |-|.+..
T Consensus       214 ~~~~~~~~mp~v~~~~~gp~g~~~~g~l--y--~y~~~~~~~i~c~------------chg~~~~  262 (283)
T pfam07897       214 ASLNILEDMPCVSTTGDGPNGKRVDGFL--Y--RYGKGEEVRIVCV------------CHGSFLS  262 (283)
T ss_pred             HHHHHHHHCCEEEECCCCCCCCEEEEEE--E--EECCCCEEEEEEE------------ECCCCCC
T ss_conf             6565675388156425689985630478--8--7248882789998------------2488578


No 254
>cd04278 ZnMc_MMP Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases).
Probab=20.02  E-value=43  Score=11.69  Aligned_cols=46  Identities=24%  Similarity=0.267  Sum_probs=29.8

Q ss_pred             CCHHHHHHHHHHHCCC-CCCCCCCCEECCCEEEEECCCCCCCCHHHHHHHHHH
Q ss_conf             1368899999752125-444445530024300000247678999999999999
Q gi|254780191|r  587 HSATHLLHHALSTILG-SHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDN  638 (898)
Q Consensus       587 HTatHlL~~alr~vLG-~hv~Q~GS~v~~~~lrfDfsh~~~lt~eel~~IE~~  638 (898)
                      ++|+|=+-.|    || .|....+|.+.|-+....  ....|+.+++..|..+
T Consensus       109 ~va~HEIGHa----LGL~Hs~~~~siM~p~y~~~~--~~~~L~~dDi~giq~L  155 (157)
T cd04278         109 SVAAHEIGHA----LGLGHSSDPDSIMYPYYQGPV--PKFKLSQDDIRGIQAL  155 (157)
T ss_pred             HHHHHHHHHH----CCCCCCCCCCCEECCCCCCCC--CCCCCCHHHHHHHHHH
T ss_conf             9999875654----068888999753335035888--7899898999999987


Done!