Query         gi|254780625|ref|YP_003065038.1| formamidopyrimidine-DNA glycosylase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 289
No_of_seqs    122 out of 2796
Neff          7.7 
Searched_HMMs 39220
Date          Sun May 29 21:20:15 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780625.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00577 fpg formamidopyrimid 100.0       0       0  610.7  21.0  273    1-288     1-292 (292)
  2 PRK01103 formamidopyrimidine-D 100.0       0       0  586.9  24.8  272    1-289     1-272 (273)
  3 COG0266 Nei Formamidopyrimidin 100.0       0       0  578.0  25.0  273    1-289     1-273 (273)
  4 PRK13945 formamidopyrimidine-D 100.0       0       0  568.3  25.9  273    1-289     1-283 (283)
  5 PRK10445 endonuclease VIII; Pr 100.0       0       0  511.3  24.1  260    1-289     1-263 (263)
  6 pfam06831 H2TH Formamidopyrimi 100.0 8.4E-31 2.1E-35  217.9   6.6   93  142-240     1-93  (93)
  7 pfam01149 Fapy_DNA_glyco Forma 100.0 1.6E-27   4E-32  196.9  14.0  116    2-126     1-117 (117)
  8 pfam05833 FbpA Fibronectin-bin  98.0 9.9E-05 2.5E-09   50.5  10.2   79  141-228   162-240 (447)
  9 pfam06827 zf-FPG_IleRS Zinc fi  97.7 2.7E-05 6.9E-10   54.1   2.8   29  260-289     1-29  (30)
 10 COG1293 Predicted RNA-binding   97.5  0.0024 6.2E-08   41.5  10.3   71  145-226   168-238 (564)
 11 PRK04184 DNA topoisomerase VI   97.0   0.003 7.6E-08   41.0   6.7   75  140-224   230-305 (533)
 12 PTZ00134 40S ribosomal protein  96.7  0.0036 9.2E-08   40.4   5.2   50  164-222    25-74  (154)
 13 pfam00416 Ribosomal_S13 Riboso  96.1    0.01 2.6E-07   37.5   4.6   51  164-223    10-60  (106)
 14 PRK04053 rps13p 30S ribosomal   95.9   0.013 3.3E-07   36.8   4.3   53  163-224    19-71  (149)
 15 COG0099 RpsM Ribosomal protein  95.5   0.012 3.1E-07   37.1   3.1   48  166-222    14-61  (121)
 16 PRK05179 rpsM 30S ribosomal pr  95.5   0.014 3.7E-07   36.6   3.4   49  165-222    13-61  (122)
 17 TIGR03629 arch_S13P archaeal r  95.3   0.023 5.8E-07   35.3   4.0   51  164-223    16-66  (144)
 18 TIGR03631 bact_S13 30S ribosom  95.1   0.025 6.3E-07   35.1   3.6   48  165-221    11-58  (113)
 19 CHL00137 rps13 ribosomal prote  94.8   0.039   1E-06   33.8   3.9   48  165-221    13-60  (122)
 20 PRK12495 hypothetical protein;  93.1   0.026 6.5E-07   35.0   0.3   26  259-289    41-66  (221)
 21 pfam06677 Auto_anti-p27 Sjogre  91.4    0.11 2.8E-06   30.9   1.8   26  259-288    16-41  (41)
 22 COG1645 Uncharacterized Zn-fin  90.4    0.15 3.8E-06   30.0   1.8   24  261-289    29-52  (131)
 23 COG1389 DNA topoisomerase VI,   89.5    0.74 1.9E-05   25.6   4.7  105  112-224   206-311 (538)
 24 PRK00420 hypothetical protein;  88.9    0.22 5.5E-06   29.0   1.6   25  261-289    20-44  (107)
 25 PRK07220 DNA topoisomerase I;   88.0    0.51 1.3E-05   26.6   3.0   29  259-288   634-664 (740)
 26 COG1096 Predicted RNA-binding   87.8    0.39 9.8E-06   27.4   2.3   27  254-289   147-173 (188)
 27 PRK08413 consensus              85.4    0.89 2.3E-05   25.1   3.1   28  201-228   528-555 (733)
 28 PRK08938 DNA topoisomerase I;   84.5    0.84 2.1E-05   25.2   2.7   27  202-228   536-562 (692)
 29 PRK05823 consensus              83.2    0.67 1.7E-05   25.8   1.7   78  151-228   485-586 (691)
 30 cd04476 RPA1_DBD_C RPA1_DBD_C:  82.2     0.6 1.5E-05   26.1   1.2   20   98-118    69-88  (166)
 31 PRK08173 DNA topoisomerase III  79.3     5.1 0.00013   20.2   5.2   24  260-288   624-647 (857)
 32 pfam00398 RrnaAD Ribosomal RNA  78.6     2.1 5.4E-05   22.6   3.0   53  158-222   205-257 (258)
 33 KOG3311 consensus               78.6     1.7 4.4E-05   23.2   2.5   50  164-222    23-72  (152)
 34 pfam08273 Prim_Zn_Ribbon Zinc-  78.3       1 2.6E-05   24.7   1.3   27  261-288     4-33  (39)
 35 PRK09137 DNA topoisomerase I;   78.2     2.1 5.5E-05   22.6   2.9   79  150-228   472-574 (761)
 36 pfam03486 HI0933_like HI0933-l  77.8     1.7 4.4E-05   23.2   2.3   65  149-224   267-336 (405)
 37 PRK07219 DNA topoisomerase I;   76.2       3 7.6E-05   21.7   3.2   25  260-285   716-740 (769)
 38 smart00778 Prim_Zn_Ribbon Zinc  72.9     2.6 6.7E-05   22.0   2.2   27  261-288     4-32  (37)
 39 smart00661 RPOL9 RNA polymeras  72.6     3.5   9E-05   21.2   2.8   26  262-288     2-27  (52)
 40 PRK08665 ribonucleotide-diphos  71.4     5.4 0.00014   20.1   3.5   53  215-287   675-727 (733)
 41 PRK00274 ksgA dimethyladenosin  71.4     4.3 0.00011   20.7   3.0   56  158-224   210-265 (267)
 42 PRK08620 DNA topoisomerase III  70.3     4.3 0.00011   20.7   2.8   24  260-284   648-671 (726)
 43 COG0675 Transposase and inacti  69.7       3 7.5E-05   21.7   1.9   22  260-289   309-330 (364)
 44 TIGR00755 ksgA dimethyladenosi  69.1     5.2 0.00013   20.1   3.0   59  156-220   215-276 (277)
 45 pfam07282 Transposase_35 Putat  68.7     2.4 6.1E-05   22.3   1.2   27  259-288    27-53  (69)
 46 PRK05582 DNA topoisomerase I;   66.9     3.8 9.8E-05   21.0   2.0   79  151-229   457-559 (692)
 47 COG2888 Predicted Zn-ribbon RN  63.8     2.7 6.9E-05   22.0   0.7   25  262-287    29-56  (61)
 48 PRK07141 DNA topoisomerase I;   63.7      12  0.0003   17.9   5.0   29  259-288   564-597 (622)
 49 PRK12366 replication factor A;  63.2     4.1 0.00011   20.8   1.6   23  261-288   534-556 (649)
 50 PRK07726 DNA topoisomerase III  63.1      12  0.0003   17.8   5.2   22  262-288   632-658 (716)
 51 PRK09521 exosome complex RNA-b  62.6     6.6 0.00017   19.5   2.5   23  262-289   152-174 (187)
 52 TIGR00617 rpa1 replication fac  62.3     4.7 0.00012   20.4   1.8   53  230-289   504-562 (671)
 53 smart00532 LIGANc Ligase N fam  62.2     6.8 0.00017   19.4   2.5   23  261-286   400-422 (441)
 54 TIGR01544 HAD-SF-IE HAD-superf  61.1     5.8 0.00015   19.8   2.0   43  153-202   133-177 (287)
 55 COG3024 Uncharacterized protei  60.7     2.3 5.8E-05   22.5  -0.1   27  261-288     8-34  (65)
 56 COG2081 Predicted flavoprotein  60.1     8.2 0.00021   18.9   2.7   64  149-224   268-333 (408)
 57 COG2956 Predicted N-acetylgluc  59.4     4.4 0.00011   20.6   1.2   20  262-289   356-376 (389)
 58 COG1571 Predicted DNA-binding   59.2     4.2 0.00011   20.8   1.0   29  256-288   346-374 (421)
 59 COG0272 Lig NAD-dependent DNA   56.3     9.1 0.00023   18.6   2.4   22  262-286   406-427 (667)
 60 PRK00432 30S ribosomal protein  55.9     8.2 0.00021   18.9   2.1   28  258-288    21-48  (54)
 61 TIGR00575 dnlj DNA ligase, NAD  54.4     7.8  0.0002   19.0   1.8   22  262-286   413-434 (706)
 62 COG1656 Uncharacterized conser  54.0     5.5 0.00014   20.0   0.9   28  261-289    98-138 (165)
 63 CHL00174 accD acetyl-CoA carbo  53.8     1.8 4.6E-05   23.1  -1.6   28  165-192   143-171 (305)
 64 COG0030 KsgA Dimethyladenosine  52.9      12  0.0003   17.9   2.5   52  157-223   204-256 (259)
 65 PRK00635 excinuclease ABC subu  51.7      18 0.00047   16.6   3.4   17  191-207   321-337 (1809)
 66 PRK03681 hypA hydrogenase nick  50.7       8  0.0002   18.9   1.3   23  262-288    72-94  (114)
 67 PRK00564 hypA hydrogenase nick  48.5     7.8  0.0002   19.0   1.0   22  262-288    73-95  (117)
 68 pfam10263 SprT-like SprT-like   48.4      19 0.00048   16.5   2.9   26  262-288   121-146 (153)
 69 TIGR02159 PA_CoA_Oxy4 phenylac  47.5       9 0.00023   18.6   1.2   32  256-288   107-143 (152)
 70 TIGR02483 PFK_mixed phosphofru  47.1     9.2 0.00024   18.5   1.2   22  174-195   259-280 (339)
 71 COG1439 Predicted nucleic acid  46.5      17 0.00045   16.8   2.5   26  254-280   147-172 (177)
 72 PRK08271 anaerobic ribonucleos  45.9     8.6 0.00022   18.7   0.9   48  176-231   415-462 (625)
 73 TIGR00387 glcD glycolate oxida  45.1      23 0.00059   16.0   3.0   80  138-235   296-390 (437)
 74 PRK07956 ligA NAD-dependent DN  44.4      21 0.00054   16.2   2.7   23  261-286   405-427 (668)
 75 pfam03119 DNA_ligase_ZBD NAD-d  44.3      16  0.0004   17.0   2.0   21  263-286     2-22  (27)
 76 pfam08394 Arc_trans_TRASH Arch  44.2     4.9 0.00013   20.3  -0.6   23  267-289     4-31  (37)
 77 PRK00349 uvrA excinuclease ABC  44.2      24 0.00061   15.9   4.2   29  179-207   315-346 (944)
 78 pfam02591 DUF164 Putative zinc  43.9     4.5 0.00011   20.6  -0.8   30  259-289    21-54  (56)
 79 COG3677 Transposase and inacti  43.8      16 0.00042   16.9   2.0   27  261-289    31-61  (129)
 80 PRK08174 DNA topoisomerase III  43.6      24 0.00062   15.8   5.3   29  258-288   613-645 (670)
 81 COG1997 RPL43A Ribosomal prote  42.8      17 0.00043   16.8   2.0   25  261-288    36-60  (89)
 82 TIGR02890 spore_yteA sporulati  42.6     9.1 0.00023   18.6   0.6  107  154-289     4-117 (167)
 83 PRK06556 vitamin B12-dependent  42.0      16  0.0004   17.1   1.7   24  259-287   927-950 (957)
 84 TIGR00630 uvra excinuclease AB  41.8     9.9 0.00025   18.3   0.7   17  191-207   351-367 (956)
 85 COG3350 Uncharacterized conser  41.7      17 0.00043   16.8   1.9   22  265-286     6-33  (53)
 86 COG0375 HybF Zn finger protein  40.3      11 0.00028   18.0   0.7   23  261-288    71-93  (115)
 87 TIGR03670 rpoB_arch DNA-direct  39.6      23  0.0006   15.9   2.3   73  123-197   366-445 (599)
 88 pfam07191 DUF1407 Protein of u  38.6     3.6 9.3E-05   21.1  -2.0   26  261-287    31-56  (70)
 89 PRK12860 transcriptional activ  38.4      29 0.00075   15.3   3.9   84  166-288    78-161 (189)
 90 TIGR01341 aconitase_1 aconitat  38.0      11 0.00029   18.0   0.5   56  154-239   514-569 (896)
 91 PRK07225 DNA-directed RNA poly  37.7      27 0.00069   15.5   2.4   75  123-198   372-452 (605)
 92 TIGR01405 polC_Gram_pos DNA po  37.4      11 0.00028   18.1   0.3   13   69-81    544-556 (1264)
 93 TIGR02661 MauD methylamine deh  37.3     9.7 0.00025   18.4   0.1   11  212-222   169-179 (189)
 94 PRK12380 hydrogenase nickel in  37.0      15 0.00037   17.2   0.9   22  262-288    72-93  (113)
 95 pfam08271 TF_Zn_Ribbon TFIIB z  36.8      26 0.00067   15.6   2.2   10  278-287    16-25  (40)
 96 pfam01155 HypA Hydrogenase exp  36.2      16 0.00041   17.0   1.0   22  262-288    71-92  (112)
 97 PRK12722 transcriptional activ  35.4      33 0.00083   15.0   5.4   84  166-288    78-161 (185)
 98 KOG2169 consensus               35.1      17 0.00044   16.8   1.0   12  278-289   342-353 (636)
 99 pfam01927 DUF82 Protein of unk  34.8      15 0.00038   17.2   0.7   27  262-289    92-131 (146)
100 PRK06319 DNA topoisomerase I/S  34.8      33 0.00085   15.0   5.1   80  150-230   478-582 (864)
101 PRK11788 hypothetical protein;  34.7      24 0.00061   15.9   1.7   21  261-289   355-376 (389)
102 pfam03811 Ins_element1 Inserti  34.6      22 0.00055   16.1   1.5   12  278-289    26-37  (88)
103 TIGR01206 lysW lysine biosynth  34.6      26 0.00067   15.6   1.9   23  265-287     6-28  (54)
104 TIGR02642 phage_xxxx uncharact  34.5      13 0.00033   17.6   0.3   80  176-288   126-206 (270)
105 cd02967 mauD Methylamine utili  34.4     8.4 0.00021   18.8  -0.7   23   44-66      7-30  (114)
106 TIGR00395 leuS_arch leucyl-tRN  33.3      21 0.00053   16.3   1.2   40   44-83    303-344 (1109)
107 TIGR00469 pheS_mito phenylalan  33.2      23 0.00059   15.9   1.5   43  177-224   292-335 (460)
108 cd01675 RNR_III Class III ribo  32.2      37 0.00094   14.7   2.6   49  176-231   361-409 (555)
109 pfam04919 DUF655 Protein of un  32.1      37 0.00094   14.7   2.7   53  153-206    98-150 (181)
110 KOG3053 consensus               32.0      13 0.00034   17.5   0.1   20  165-184   218-237 (293)
111 COG5216 Uncharacterized conser  31.9      33 0.00083   15.0   2.0   25  262-288    24-51  (67)
112 PRK09194 prolyl-tRNA synthetas  31.4      33 0.00083   15.0   2.0   18  256-274   388-405 (570)
113 pfam08274 PhnA_Zn_Ribbon PhnA   30.8      36 0.00091   14.8   2.1   23  262-288     4-26  (30)
114 pfam09788 Tmemb_55A Transmembr  30.3      32 0.00083   15.0   1.8   27  262-289   161-187 (258)
115 TIGR03655 anti_R_Lar restricti  30.3      25 0.00064   15.7   1.2   27  261-288     2-33  (53)
116 COG1592 Rubrerythrin [Energy p  30.0      16  0.0004   17.1   0.1   21  262-288   136-156 (166)
117 TIGR00354 polC DNA polymerase   29.9      27 0.00068   15.6   1.3  104  166-287  1006-1112(1173)
118 PRK08402 replication factor A;  29.1      18 0.00046   16.7   0.3   24  261-287   215-238 (357)
119 COG1998 RPS31 Ribosomal protei  27.9      24  0.0006   15.9   0.7   27  258-287    17-43  (51)
120 KOG2324 consensus               27.5      21 0.00053   16.3   0.4   26  262-288   229-254 (457)
121 TIGR00019 prfA peptide chain r  26.5      19 0.00049   16.5   0.1   33  165-197   263-295 (373)
122 pfam05280 FlhC Flagellar trans  26.1      47  0.0012   14.0   4.2   84  166-288    78-161 (176)
123 KOG2923 consensus               25.9      30 0.00076   15.3   1.0   25  262-288    24-51  (67)
124 PRK13804 ileS isoleucyl-tRNA s  25.5      27 0.00068   15.6   0.7   10  266-275   554-563 (966)
125 PRK12300 leuS leucyl-tRNA synt  25.2      38 0.00096   14.6   1.4   22   45-66    181-202 (888)
126 pfam09297 zf-NADH-PPase NADH p  25.0      34 0.00087   14.9   1.1   26  261-289     4-29  (32)
127 PRK07418 acetolactate synthase  24.8      31  0.0008   15.1   0.9   21  261-288   592-612 (615)
128 PRK07562 ribonucleotide-diphos  24.8      39 0.00099   14.5   1.4   27  256-287  1143-1170(1177)
129 COG2046 MET3 ATP sulfurylase (  24.3      29 0.00074   15.3   0.7   11  279-289   318-328 (397)
130 PRK00390 leuS leucyl-tRNA synt  24.1      42  0.0011   14.3   1.5   12  262-274   471-482 (822)
131 PRK06039 ileS isoleucyl-tRNA s  24.1      41  0.0011   14.4   1.4   12  262-274   503-514 (1042)
132 pfam00085 Thioredoxin Thioredo  24.0      21 0.00053   16.3  -0.1   11   57-67     18-28  (104)
133 TIGR00515 accD acetyl-CoA carb  23.7      16 0.00041   17.0  -0.8   10  176-185   117-126 (292)
134 pfam04945 YHS YHS domain. This  23.2      53  0.0013   13.7   2.1   21  265-285     1-26  (44)
135 TIGR02311 HpaI 2,4-dihydroxyhe  23.1      37 0.00094   14.7   1.0   21  165-185   114-134 (249)
136 cd02993 PDI_a_APS_reductase PD  22.9      16 0.00042   16.9  -0.8   24   38-67      8-31  (109)
137 pfam01258 zf-dskA_traR Prokary  22.8      11 0.00029   18.0  -1.7   26  263-289     6-32  (32)
138 PRK05743 ileS isoleucyl-tRNA s  22.4      52  0.0013   13.7   1.7   16  254-270   872-887 (910)
139 TIGR03147 cyt_nit_nrfF cytochr  22.2      31  0.0008   15.1   0.5   32  196-234    44-75  (126)
140 TIGR00959 ffh signal recogniti  22.1      32 0.00081   15.1   0.5   37  148-187   332-370 (439)
141 TIGR02738 TrbB type-F conjugat  22.1      30 0.00076   15.3   0.4   10   60-69     58-67  (176)
142 KOG2846 consensus               22.1      36 0.00093   14.7   0.8   29  258-288   218-249 (328)
143 PRK08565 DNA-directed RNA poly  21.8      56  0.0014   13.5   2.2   59  140-198   884-948 (1101)
144 pfam04423 Rad50_zn_hook Rad50   21.5      35 0.00088   14.9   0.6   10  262-272    22-31  (54)
145 pfam10571 UPF0547 Uncharacteri  21.4      43  0.0011   14.2   1.1   20  262-288     2-21  (26)
146 PRK10144 formate-dependent nit  21.3      34 0.00086   14.9   0.5   32  196-234    44-75  (126)
147 pfam09723 CxxC_CxxC_SSSS Zinc   21.2      58  0.0015   13.4   2.7   25  263-288     8-33  (42)
148 pfam06044 DRP Dam-replacing fa  20.9      44  0.0011   14.2   1.0   13  161-173   179-191 (254)
149 PRK05580 primosome assembly pr  20.8      59  0.0015   13.4   1.7   26  262-288   415-451 (699)
150 PRK13208 valS valyl-tRNA synth  20.7      45  0.0012   14.1   1.1   24  164-189   348-371 (809)
151 COG0419 SbcC ATPase involved i  20.7      38 0.00096   14.6   0.7   13   95-107    70-82  (908)
152 TIGR00385 dsbE periplasmic pro  20.7      33 0.00084   15.0   0.3   49   37-85     41-100 (175)
153 KOG2851 consensus               20.5      45  0.0012   14.1   1.0   15  252-266   329-343 (412)
154 pfam00133 tRNA-synt_1 tRNA syn  20.5      41  0.0011   14.3   0.8   12  262-274   476-487 (606)
155 COG0178 UvrA Excinuclease ATPa  20.4      60  0.0015   13.3   5.1   15  193-207   324-338 (935)
156 KOG2907 consensus               20.4      47  0.0012   14.0   1.1   27  261-288    75-109 (116)

No 1  
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase; InterPro: IPR000191   Formamidopyrimidine-DNA glycosylase (3.2.2.23 from EC)  (Fapy-DNA glycosylase) (gene fpg) is a bacterial enzyme involved in DNA repair and which excise oxidized purine bases to release 2,6-diamino-4-hydroxy-5N-methylformamido- pyrimidine (Fapy) and 7,8-dihydro-8-oxoguanine (8-OxoG) residues. In addition to its glycosylase activity, FPG can also nick DNA at apurinic/apyrimidinic sites (AP sites). FPG is a monomeric protein of about 32 Kd which binds and require zinc for its activity.   The C-terminal region is the zinc binding site in the enzyme where four conserved and essential cysteines are located ..
Probab=100.00  E-value=0  Score=610.67  Aligned_cols=273  Identities=38%  Similarity=0.673  Sum_probs=259.6

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCC--CCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCC------CCCC
Q ss_conf             96764367889889998679778899964833--265787789997289889999605308999503553------1001
Q gi|254780625|r    1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKN--LRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNL------SIIV   72 (289)
Q Consensus         1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~--~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~------~L~~   72 (289)
                      |||||||||++|.|++.++|++|.+|.+..++  .++..+++|...|.|++|.++.|||||||++|+++.      +|++
T Consensus         1 MPELPEVETvrR~L~~~~~gktI~~V~V~~~~~~~~~~~~~~l~~~L~g~~i~~~~RRGKYLl~~L~~~~~~~~ag~lv~   80 (292)
T TIGR00577         1 MPELPEVETVRRGLEPLVLGKTIKSVEVVLRRVVKRPAGVEDLQKELLGQTILSIQRRGKYLLFELDDGVFQFMAGALVS   80 (292)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCHHHHHHHHCCCEEEEECCCEEEEEEEECCCEEECCCEEEEE
T ss_conf             99861289987633434068510148995262100478858999874797688603330456764057700015404788


Q ss_pred             CCCCCCEEEEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCC--CEECCCCCCHHHCCCCCCCCCCCC-CC
Q ss_conf             525532799814785422458766338999706887604899981587664--100145530100532356555332-21
Q gi|254780625|r   73 HLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFG--FMDLVETSLKYQYPPLRTLGPEPA-DN  149 (289)
Q Consensus        73 HlgM~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG--~~~~~~~~~~~~~~~l~~lGpD~l-~~  149 (289)
                      ||||+|++++...+...   .++|.|+.+.|+||.     .|.|.|+|+||  +|.+++....+....+++|||||| |+
T Consensus        81 HLrM~G~y~~~~~~~~~---~~kH~hv~~~f~dG~-----~L~y~D~R~FG~~~~~l~~~~~~~~~~~l~~LGpEPly~~  152 (292)
T TIGR00577        81 HLRMEGKYRLEEVPDAP---PDKHVHVDFLFDDGT-----ELRYHDPRKFGKVTWLLLDRGEVEASLLLAKLGPEPLYSE  152 (292)
T ss_pred             EEEEEEEEEECCCCCCC---CCCCCEEEEEECCCC-----EEEEECCCEEEEEEEEECCCCCHHHHHHHHHHCCCCCCCH
T ss_conf             43312221101178788---888656999986996-----7887557635568987167753012013667288888652


Q ss_pred             CCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             11067888742014542100111265435641368999999871787783122220010158999999998788767654
Q gi|254780625|r  150 SFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAI  229 (289)
Q Consensus       150 ~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~  229 (289)
                      +|+.+++.+.+++++++||++||||++|||||||||||+||+|||||.+.+++|+.+|      ++.|+++|.+||.+||
T Consensus       153 ~F~~~~l~~~l~~~~r~~K~~LLDQ~~V~G~GNIYADE~LF~A~ihP~~~A~~L~~~~------~~~L~~~i~~vL~~Ai  226 (292)
T TIGR00577       153 DFTAEYLFEKLAKSKRKIKTALLDQRLVAGLGNIYADEVLFRAGIHPERLANQLSKEE------CELLHKAIKEVLRKAI  226 (292)
T ss_pred             HCCHHHHHHHHHHCCCHHHHHHHCCCEEEEEHHHHHHHHHHHHCCCCCHHHHCCCHHH------HHHHHHHHHHHHHHHH
T ss_conf             1173899999874040345686548757651010666899873688101000158889------9999999999999998


Q ss_pred             HCCCCCCCC--CCCCCCCCCCCHHHEEEECCCCCCCCC-CCCCEEEEEEEC-----CCCEEECCCCC
Q ss_conf             218875531--116778778741331665738771078-778878999987-----81206387767
Q gi|254780625|r  230 DAGGSSLRD--YVHIDGSIGYFQNAFSVYGKTGEPCLS-NCGQMIRRIVQA-----GRSTFYCTYCQ  288 (289)
Q Consensus       230 ~~gG~~~~~--~~~~~g~~g~~~~~~~vy~r~g~~C~~-~CG~~I~~~~~~-----gR~ty~Cp~CQ  288 (289)
                      +.||||++|  |++++|++|+|+..+.||||+|+|| + +||++|++++++     ||+|||||+||
T Consensus       227 e~GGtt~~~q~f~~~~G~~G~fq~~l~VYGrkg~pC-~a~CGt~I~k~~~~LYGkDgRgthfCp~CQ  292 (292)
T TIGR00577       227 EAGGTTIRDQLFVQSDGENGYFQQELQVYGRKGEPC-RARCGTTIEKEKVGLYGKDGRGTHFCPQCQ  292 (292)
T ss_pred             HCCCCCCCCEEEEECCCCCCCCCCEEEEECCCCCCC-CCCCCCEEEEEEEECCCCCCCCEECCCCCC
T ss_conf             648970002002304787875344210025638834-367884478876530151675101268889


No 2  
>PRK01103 formamidopyrimidine-DNA glycosylase; Validated
Probab=100.00  E-value=0  Score=586.88  Aligned_cols=272  Identities=45%  Similarity=0.797  Sum_probs=259.1

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEE
Q ss_conf             96764367889889998679778899964833265787789997289889999605308999503553100152553279
Q gi|254780625|r    1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSF   80 (289)
Q Consensus         1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~   80 (289)
                      ||||||||+++++|++.+.|++|++|++.+++.++..+++|.+.|.|++|.+|+|+||+|+|+||++ +|++||||+|+|
T Consensus         1 MPElPEVe~~~~~l~~~~~g~~I~~v~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~-~l~~HlgMtG~~   79 (273)
T PRK01103          1 MPELPEVETVRRGLEPHVVGKTIERVEVRNPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDG-TLISHLGMSGSL   79 (273)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHCCCCEEEEEECCCEEEEEECCCC-EEEEEEECCEEE
T ss_conf             9865899999999999848999989998985322788588997748999987871303999981698-289987323379


Q ss_pred             EEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             98147854224587663389997068876048999815876641001455301005323565553322111067888742
Q gi|254780625|r   81 IIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQF  160 (289)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l  160 (289)
                      .+...+.    ..++|.|+.|.|+++.     .++|.|+|+||++.+++..+...++.+++||||||+++|+.++|.+.+
T Consensus        80 ~~~~~~~----~~~k~~~l~l~~~~g~-----~l~f~D~R~fG~i~~~~~~~~~~~~~l~~lGpD~L~~~~~~~~~~~~l  150 (273)
T PRK01103         80 RVLPGET----PPEKHDHVDFVLDDGT-----VLRYNDPRRFGAMLLAEEGDLHAHPLLAKLGPEPLSDAFDGEYLAAKL  150 (273)
T ss_pred             EEECCCC----CCCCEEEEEEEECCCC-----EEEEECCCCCEEEEEEECCCCCCCHHHHHCCCCCCCCCCCHHHHHHHH
T ss_conf             9955899----9886328999958995-----899973775317999967750004078766998465557999999876


Q ss_pred             HCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             01454210011126543564136899999987178778312222001015899999999878876765421887553111
Q gi|254780625|r  161 HKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYV  240 (289)
Q Consensus       161 ~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~  240 (289)
                      ++++++||++||||++||||||||+|||||+|||||++++++||++|      +.+|+++++.||..|++.||+|++||+
T Consensus       151 ~~~~~~Ik~~LlDQ~~iaGiGNiyadEiLf~a~IhP~~~~~~Ls~~e------~~~L~~~~~~vl~~ai~~~G~t~~d~~  224 (273)
T PRK01103        151 RKKKTAIKPALLDQTIVVGVGNIYADEALFRAGIHPERPAGSLSKAR------AERLVEAIKAVLAEAIEQGGTTLRDYV  224 (273)
T ss_pred             HCCCCHHHHHHCCCCEEECCCHHHHHHHHHHCCCCCCCHHCCCCHHH------HHHHHHHHHHHHHHHHHCCCCCCHHCC
T ss_conf             43654266762258846035398999999876487135001179999------999999999999999981897402200


Q ss_pred             CCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             6778778741331665738771078778878999987812063877679
Q gi|254780625|r  241 HIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       241 ~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      +++|++|+|+++++||+|+|+|| |+||++|++++++||+|||||.|||
T Consensus       225 ~~~g~~G~~~~~~~Vy~r~g~~C-~~Cg~~I~~~~~~gR~t~~CP~CQk  272 (273)
T PRK01103        225 NADGEPGYFQQSLQVYGREGEPC-RRCGTPIEKIKQGGRSTFFCPKCQK  272 (273)
T ss_pred             CCCCCCCCCCEEEEECCCCCCCC-CCCCCEEEEEEECCCCCEECCCCCC
T ss_conf             66888675330578808898948-9999967899988971199957618


No 3  
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00  E-value=0  Score=578.00  Aligned_cols=273  Identities=47%  Similarity=0.804  Sum_probs=261.2

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEE
Q ss_conf             96764367889889998679778899964833265787789997289889999605308999503553100152553279
Q gi|254780625|r    1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSF   80 (289)
Q Consensus         1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~   80 (289)
                      ||||||||++++.|++.+.|++|++|++..+++++..+++|...|.|++|.++.||||||+++|+++.+|++||||+|+|
T Consensus         1 MPELPEVetv~rgL~~~~~G~~I~~v~v~~p~l~~~~~~~~~~~L~G~~I~~v~rRgKyLl~~l~g~~~Li~HLgM~G~~   80 (273)
T COG0266           1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPRLRWPDSEEFAERLTGQRITSVERRGKYLLIELSGDLTLISHLGMSGSL   80 (273)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCEECCCCHHHHHHCCCCEEEEEECCCCEEEEECCCCCEEEEECCCCEEE
T ss_conf             99874779898766887579878899953875113677778965589698367512125999917994899966764689


Q ss_pred             EEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             98147854224587663389997068876048999815876641001455301005323565553322111067888742
Q gi|254780625|r   81 IIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQF  160 (289)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l  160 (289)
                      ++...+.+    ..+|+|+.|.|+|+.    ..+.|.|+|+||++.+.+..+ ..++.+++||||||+++||.+++.+.+
T Consensus        81 ~~~~~~~~----~~kH~hv~~~~~~g~----~~l~y~D~R~FG~~~~~~~~~-~~~~~l~~LGpePl~~~f~~~~l~~~l  151 (273)
T COG0266          81 RLEARGEP----DEKHDHVDFVLSDGK----DVLRYNDPRRFGTMLLIEDLE-EVHPVLAKLGPEPLSDDFDPEYLAEKL  151 (273)
T ss_pred             EEECCCCC----CCCCEEEEEEECCCC----EEEEEECCCCCCEEEEECCCC-CCCHHHHHCCCCCCCCCCCHHHHHHHH
T ss_conf             98517888----886308999975993----599986387674899945665-432779865999885436999999987


Q ss_pred             HCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             01454210011126543564136899999987178778312222001015899999999878876765421887553111
Q gi|254780625|r  161 HKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYV  240 (289)
Q Consensus       161 ~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~  240 (289)
                      ++++++||++||||++||||||||+|||||+|||||.+++++|+++|      +..|+++|+.||.+|++.||+|++||.
T Consensus       152 ~~~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~------~~~l~~~i~~vl~~ai~~gGtt~r~~~  225 (273)
T COG0266         152 AKKKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQ------LALLHEAIKDVLADAIERGGTTLRDFV  225 (273)
T ss_pred             HCCCCCHHHHHHCCCCEECCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHHHHHHHHHHHCCCCCCCEE
T ss_conf             32764167776407703034178888899873798546703027899------999999999999999981898024324


Q ss_pred             CCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             6778778741331665738771078778878999987812063877679
Q gi|254780625|r  241 HIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       241 ~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      +.+|+.|+|+..++||+|+|+|| ++||++|++++++||+|||||+|||
T Consensus       226 ~~~g~~G~fq~~l~VYgR~GepC-~~CGt~I~k~~~~gR~t~~CP~CQ~  273 (273)
T COG0266         226 NADGKPGYFQQELKVYGRAGEPC-RRCGTPIEKIKLGGRSTFYCPVCQK  273 (273)
T ss_pred             CCCCCCCCCCEEEEEECCCCCCC-CCCCCEEEEEEECCCCCEECCCCCC
T ss_conf             56898774312689855789988-7458876799986876776878789


No 4  
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=100.00  E-value=0  Score=568.33  Aligned_cols=273  Identities=37%  Similarity=0.598  Sum_probs=249.4

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCC-CC-CCCHHHHHHHCCCEEEEEEECCEEEEEEECCCC------CCCC
Q ss_conf             967643678898899986797788999648332-65-787789997289889999605308999503553------1001
Q gi|254780625|r    1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNL-RF-DFPHHFSAATRGKKIIDVSRRAKYLLIELEGNL------SIIV   72 (289)
Q Consensus         1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~-~~-~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~------~L~~   72 (289)
                      ||||||||++++.|++.+.|++|++|++..++. .. ..+++|.+.|.|++|.+|.|+||||+|+|+++.      +|++
T Consensus         1 MPELPEVe~~~~~L~~~~~g~~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~l~~~l~~~~~~~~~~~l~~   80 (283)
T PRK13945          1 MPELPEVETVRRGLEQLLLNFIIKGVEVLRERTIASPGGVEEFIKGLQGSLIGKWHRRGKYLLASLKKEGSENSAGWLGV   80 (283)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCHHHHHHHCCCCEEEEEEEEEEEEEEEECCCCCCCCCCEEEE
T ss_conf             98468899999999998689989899990773312889979999764898997887678999998047655566757999


Q ss_pred             CCCCCCEEEEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCC--HHHCCCCCCCCCCCCCCC
Q ss_conf             525532799814785422458766338999706887604899981587664100145530--100532356555332211
Q gi|254780625|r   73 HLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSL--KYQYPPLRTLGPEPADNS  150 (289)
Q Consensus        73 HlgM~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~--~~~~~~l~~lGpD~l~~~  150 (289)
                      ||||||+|.+.+.+    ..+++|.|+.|.|+++.     .++|.|+|+||++.++....  ....+.+++||||||+++
T Consensus        81 HLgMtG~~~~~~~~----~~~~kh~~~~l~~~~~~-----~l~f~D~R~FG~v~~~~~~~~~~~~~~~l~~LGpDpl~~~  151 (283)
T PRK13945         81 HLRMTGQFLWVEQD----TPPCKHTRVRLFNKKNQ-----ELRFVDIRSFGQMWWVPPGLSPESIITGLKKLGPEPFSPE  151 (283)
T ss_pred             EEEEEEEEEEECCC----CCCCCCEEEEEEECCCC-----EEEEEEECCCCEEEEECCCCCHHHHHHHHHHCCCCCCCCC
T ss_conf             86312478873687----78998259999979998-----8999970225458995587455666677763398711232


Q ss_pred             CHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10678887420145421001112654356413689999998717877831222200101589999999987887676542
Q gi|254780625|r  151 FNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAID  230 (289)
Q Consensus       151 ~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~  230 (289)
                      |+.++|.+.+++++++||++||||++||||||||+|||||+|||||.+++++||++|      +++|++++++||..|++
T Consensus       152 ~~~~~~~~~l~~~~~~IK~~LlDQ~~iaGIGNiyadEiLf~a~I~P~~~~~~Ls~~e------~~~L~~~i~~vL~~ai~  225 (283)
T PRK13945        152 FNVEYLKKKLKGRTRSIKTALLDQSIVAGIGNIYADESLFKAGIRPTTEAGTLKKNQ------LERLREAIVEVLKTSIG  225 (283)
T ss_pred             CCHHHHHHHHHHCCCCCCEEEECCCEECCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHHHHHHHHHH
T ss_conf             689999988752675435177518852345499999999985999778603089999------99999999999999998


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             18875531116778778741331665738771078778878999987812063877679
Q gi|254780625|r  231 AGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       231 ~gG~~~~~~~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      .||+|++||++++|..|+|+..++||+|+|+|| ++||++|++++++||+|||||.|||
T Consensus       226 ~ggtt~~d~~~~~g~~g~~~~~~~Vy~r~g~~C-~~Cg~~I~~~~~~gR~t~~CP~CQk  283 (283)
T PRK13945        226 AGGTTFSDFRDLEGVNGNYGGQAWVYRRTGQPC-RKCGTPIERIKLAGRSTHWCPNCQK  283 (283)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCC-CCCCCEEEEEEECCCCCEECCCCCC
T ss_conf             489845013477787688775388967898948-9999888899999975788921149


No 5  
>PRK10445 endonuclease VIII; Provisional
Probab=100.00  E-value=0  Score=511.25  Aligned_cols=260  Identities=22%  Similarity=0.418  Sum_probs=223.7

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEE
Q ss_conf             96764367889889998679778899964833265787789997289889999605308999503553100152553279
Q gi|254780625|r    1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSF   80 (289)
Q Consensus         1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~   80 (289)
                      ||||||||++++.|++.+.|++|++|.+..+..     ..|.+.|.|++|.+|+|+||||+|+|+++.+|++||||||+|
T Consensus         1 MPELPEVe~v~~~L~~~l~g~~I~~v~~~~~~~-----~~~~~~l~g~~i~~v~RrGK~L~~~~~~~~~L~~HLgMtG~~   75 (263)
T PRK10445          1 MPEGPEIRRAADNLEAAIKGKPLTDVWFAFPQL-----KPYESQLIGQHVTHIETRGKALLTHFSNGLTLYSHNQLYGVW   75 (263)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCC-----CCHHHHCCCCEEEEEEEEEEEEEEEECCCCEEEEECCEEEEE
T ss_conf             997389999999999985898887999558775-----226876599999699987289999978996899806420699


Q ss_pred             EEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             98147854224587663389997068876048999815876641001455301005323565553322111067888742
Q gi|254780625|r   81 IIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQF  160 (289)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l  160 (289)
                      .+.+.+..    ++++.++++.|.++..   ..+.|.+.    .+++++......++.+++||||||+++|+.++|.+.+
T Consensus        76 ~~~~~~~~----~~~~~~~~~~~~~~~~---~~~~~~~~----~~~~~~~~~~~~~~~l~~LGPdpL~~~~~~~~~~~~l  144 (263)
T PRK10445         76 RVVDTGEE----PQTTRVLRVRLQTADK---TILLYSAS----DIEMLTAEQLTTHPFLQRVGPDVLDPNLTPEVVKERL  144 (263)
T ss_pred             EEECCCCC----CCCCCEEEEEEECCCC---EEEEECCC----EEEEECHHHHHHCHHHHHCCCCCCCCCCCHHHHHHHH
T ss_conf             97469889----9978569999985991---79998498----5899731331106078765986577779999999998


Q ss_pred             HC---CCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             01---454210011126543564136899999987178778312222001015899999999878876765421887553
Q gi|254780625|r  161 HK---KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLR  237 (289)
Q Consensus       161 ~~---~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~  237 (289)
                      ..   ++++||++||||++||||||||+|||||+|||||.+++++||++|      +++|++++++||..|++.||++..
T Consensus       145 ~~~~~~~~~IK~~LLDQ~vvaGIGNIYa~EiLf~a~I~P~~~~~~Ls~~~------~~~L~~~i~~vl~~ai~~gG~~~~  218 (263)
T PRK10445        145 LSPRFRNRQFSGLLLDQAFLAGLGNYLRVEILWQVGLTGQHKAKDLNAAQ------LDALAHALLDIPRLSYATRGQVDE  218 (263)
T ss_pred             HHCCCCCCHHHHHHHCCCEEEECCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             63302575076651168867511388998999982899788702099999------999999999999999982993267


Q ss_pred             CCCCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             1116778778741331665738771078778878999987812063877679
Q gi|254780625|r  238 DYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       238 ~~~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      +  ...|   .+ ..|+||+|+|+|| ++||++|++++++||+|||||.||-
T Consensus       219 ~--~~~g---~~-~~~~Vy~R~g~~C-~~Cg~~I~~~~~~gRst~~Cp~CQ~  263 (263)
T PRK10445        219 N--KHHG---AL-FRFKVFHRDGEAC-ERCGGIIEKTTLSSRPFYWCPGCQH  263 (263)
T ss_pred             C--CCCC---CE-EEEEEECCCCCCC-CCCCCEEEEEEECCCCCEECCCCCC
T ss_conf             7--7788---66-4689967797938-9999762799988987887956489


No 6  
>pfam06831 H2TH Formamidopyrimidine-DNA glycosylase H2TH domain. Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.
Probab=99.97  E-value=8.4e-31  Score=217.90  Aligned_cols=93  Identities=41%  Similarity=0.666  Sum_probs=90.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             55533221110678887420145421001112654356413689999998717877831222200101589999999987
Q gi|254780625|r  142 LGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEI  221 (289)
Q Consensus       142 lGpD~l~~~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i  221 (289)
                      ||||||+++|+.++|.+++++++++||.+||||++||||||||+|||||+|||||++++++|+++|      +.+||+++
T Consensus         1 LGpDpL~~~~~~~~f~~~l~~~~~~Ik~~LlDQ~~iaGiGNiy~dEiLf~a~I~P~~~~~~Ls~~~------~~~L~~~i   74 (93)
T pfam06831         1 LGPDPLSEPFTADEFAERLAKKKRPIKTALLDQRVVAGIGNIYADEVLFRAGIHPERPASSLSKKE------CEALHTVI   74 (93)
T ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHH
T ss_conf             998989986899999999865875199998667742565399999999991899678706199999------99999999


Q ss_pred             HHHHHHHHHCCCCCCCCCC
Q ss_conf             8876765421887553111
Q gi|254780625|r  222 QKVLIDAIDAGGSSLRDYV  240 (289)
Q Consensus       222 ~~vl~~a~~~gG~~~~~~~  240 (289)
                      +.||.+|++.||+|++||.
T Consensus        75 ~~vl~~ai~~gGtti~dys   93 (93)
T pfam06831        75 KDVLQKAIEMGGGGIRTFS   93 (93)
T ss_pred             HHHHHHHHHCCCCCCCCCC
T ss_conf             9999999994999730184


No 7  
>pfam01149 Fapy_DNA_glyco Formamidopyrimidine-DNA glycosylase N-terminal domain. Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges.
Probab=99.95  E-value=1.6e-27  Score=196.88  Aligned_cols=116  Identities=41%  Similarity=0.721  Sum_probs=105.3

Q ss_pred             CCCCHHHHHHHHHHHHHCCCEEEEEEECCCC-CCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEE
Q ss_conf             6764367889889998679778899964833-265787789997289889999605308999503553100152553279
Q gi|254780625|r    2 PELPEVEIIRRNLMMVMKNMTVTDICLHRKN-LRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSF   80 (289)
Q Consensus         2 PElPEVe~~~~~l~~~l~g~~I~~V~~~~~~-~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~   80 (289)
                      |||||||++++.|++.+.|++|++|++.+++ ++...++.|.+.|.|++|++|+|+||||+++|+++.+|++||||||+|
T Consensus         1 PELPEVe~~~~~l~~~~~g~~I~~v~~~~~~~~~~~~~~~~~~~l~G~~i~~v~RrGK~i~~~l~~~~~l~~HLgMtG~~   80 (117)
T pfam01149         1 PELPEVETVRRGLEPLLVGRRITKVEVRRPKILRGPEPEEFIEALEGRTITDVRRRGKYLLLELDGGLVLVIHLGMTGRL   80 (117)
T ss_pred             CCCCCHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCCEEEEEEEEEEEEEEEECCCCEEEEECCCCEEE
T ss_conf             98701999999999985899888999756871467784999977499998469850269999999998899816775689


Q ss_pred             EEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEE
Q ss_conf             9814785422458766338999706887604899981587664100
Q gi|254780625|r   81 IIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMD  126 (289)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~  126 (289)
                      .+....    ...++|+|+.|.|+++.     .++|.|+|+||+++
T Consensus        81 ~~~~~~----~~~~kh~~v~~~f~~g~-----~l~f~D~R~FG~i~  117 (117)
T pfam01149        81 RVVEPE----DPPPKHTHVVLHLDDGR-----ELRFVDPRRFGRVR  117 (117)
T ss_pred             EECCCC----CCCCCCEEEEEEECCCC-----EEEEECCCCCCCCC
T ss_conf             963787----89998589999979999-----99998588883139


No 8  
>pfam05833 FbpA Fibronectin-binding protein A N-terminus (FbpA). This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host.
Probab=98.01  E-value=9.9e-05  Score=50.45  Aligned_cols=79  Identities=16%  Similarity=0.200  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             65553322111067888742014542100111265435641368999999871787783122220010158999999998
Q gi|254780625|r  141 TLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQE  220 (289)
Q Consensus       141 ~lGpD~l~~~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~  220 (289)
                      ..+.||++.+ +.+.|.+.+.....++..+|  ++.+.|+|..++.|++++|++++..++..|++.+      +.+|+++
T Consensus       162 ~~k~~p~~~~-~~~~~~~~~~~~~~~l~~~l--~~~~~G~sp~la~El~~rag~~~~~~~~~l~~~~------~~~L~~~  232 (447)
T pfam05833       162 QDKLNPLEIE-EFEEFKERLSLVPGDLVKAL--VQAFQGLSPLLAEELCYRAGLDKNTPVEELSDED------WERLYEA  232 (447)
T ss_pred             CCCCCCCCCC-HHHHHHHHHHCCCCHHHHHH--HHHHCCCCHHHHHHHHHHHCCCCCCCHHHCCHHH------HHHHHHH
T ss_conf             0258955476-47889986411864099999--9982699889999999982898677711249899------9999999


Q ss_pred             HHHHHHHH
Q ss_conf             78876765
Q gi|254780625|r  221 IQKVLIDA  228 (289)
Q Consensus       221 i~~vl~~a  228 (289)
                      +..++.+-
T Consensus       233 ~~~~~~~~  240 (447)
T pfam05833       233 FKELLNDL  240 (447)
T ss_pred             HHHHHHHH
T ss_conf             99999986


No 9  
>pfam06827 zf-FPG_IleRS Zinc finger found in FPG and IleRS. This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23.
Probab=97.68  E-value=2.7e-05  Score=54.06  Aligned_cols=29  Identities=52%  Similarity=1.027  Sum_probs=27.4

Q ss_pred             CCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             771078778878999987812063877679
Q gi|254780625|r  260 GEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       260 g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      |++| ++|+..|.++..++|.++|||+||+
T Consensus         1 g~kC-~RCw~~~~~~~~~~r~~~~C~rCq~   29 (30)
T pfam06827         1 GEKC-PRCWTYIEKVGQGGRSTFLCPRCQK   29 (30)
T ss_pred             CCCC-CCCCCEEEEEEECCCCCCCCCCCCC
T ss_conf             9827-7479971576855888811805324


No 10 
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=97.46  E-value=0.0024  Score=41.55  Aligned_cols=71  Identities=15%  Similarity=0.219  Sum_probs=47.1

Q ss_pred             CCCCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             33221110678887420145421001112654356413689999998717877831222200101589999999987887
Q gi|254780625|r  145 EPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKV  224 (289)
Q Consensus       145 D~l~~~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~v  224 (289)
                      +|++  ++.+.|.........-+..   -+..+.|+|-.|++|+|++|++.+..++.++...+      +..+..++...
T Consensus       168 ~p~~--~~~~~~~~~~~~~~~~~~~---~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~------~~~v~~~~~~~  236 (564)
T COG1293         168 NPYE--QSEEDFKELQLNSGADIVR---LLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEE------IKKVREALEEL  236 (564)
T ss_pred             CHHH--CCHHHHHHHHHCCCHHHHH---HHHHHCCCCHHHHHHHHHHCCCCCCCCHHHHHHHH------HHHHHHHHHHH
T ss_conf             9222--6766899986225247778---87875386577899999861787577513440889------99998766665


Q ss_pred             HH
Q ss_conf             67
Q gi|254780625|r  225 LI  226 (289)
Q Consensus       225 l~  226 (289)
                      +.
T Consensus       237 ~~  238 (564)
T COG1293         237 LN  238 (564)
T ss_pred             HH
T ss_conf             30


No 11 
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=96.99  E-value=0.003  Score=40.95  Aligned_cols=75  Identities=21%  Similarity=0.298  Sum_probs=62.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHC-CCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             56555332211106788874201-45421001112654356413689999998717877831222200101589999999
Q gi|254780625|r  140 RTLGPEPADNSFNAIYLTHQFHK-KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLI  218 (289)
Q Consensus       140 ~~lGpD~l~~~~~~~~~~~~l~~-~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~  218 (289)
                      ..+-|-|-  ..+...+...++. +++++..+|  ++-|++||.-.++||+=.|+|.|..+..+|+++|      +.+|+
T Consensus       230 ~eikPHP~--Gvelg~L~~ml~~t~~~tl~~FL--~~eFsrVg~~~A~ei~~~agl~~~~~p~~l~~~e------~~~L~  299 (533)
T PRK04184        230 KEIKPHPH--GVDLGTLKRMAARTDRSTLSEFL--VSEFSRVGEKTAKEILEYAGLDPNKKPKELTWEE------AERLV  299 (533)
T ss_pred             CCCCCCCC--CCCHHHHHHHHHHCCCCCHHHHH--HHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHH
T ss_conf             76789986--26588999999875997789999--8543556989999999972899999900189999------99999


Q ss_pred             HHHHHH
Q ss_conf             987887
Q gi|254780625|r  219 QEIQKV  224 (289)
Q Consensus       219 ~~i~~v  224 (289)
                      ++++++
T Consensus       300 ~a~~~~  305 (533)
T PRK04184        300 EAMKKM  305 (533)
T ss_pred             HHHHHC
T ss_conf             999847


No 12 
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=96.69  E-value=0.0036  Score=40.41  Aligned_cols=50  Identities=20%  Similarity=0.331  Sum_probs=41.5

Q ss_pred             CCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             54210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r  164 NSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ  222 (289)
Q Consensus       164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~  222 (289)
                      +.+|.-+|   +.|-|||.-+|.+||..++|+|.+++++||++|      +.+|...|.
T Consensus        25 ~K~v~~aL---t~I~GIG~~~A~~Ic~~~gid~~~r~g~Lteee------i~~i~~~I~   74 (154)
T PTZ00134         25 REKVTIAL---TAIKGIGRRFATVVCKQAGVDVTKRAGELTQEE------INKIVAIIS   74 (154)
T ss_pred             CCEEEEEE---EEECCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHC
T ss_conf             95889985---322064899999999980989454216499999------999999972


No 13 
>pfam00416 Ribosomal_S13 Ribosomal protein S13/S18. This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.
Probab=96.08  E-value=0.01  Score=37.52  Aligned_cols=51  Identities=20%  Similarity=0.298  Sum_probs=41.6

Q ss_pred             CCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             542100111265435641368999999871787783122220010158999999998788
Q gi|254780625|r  164 NSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQK  223 (289)
Q Consensus       164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~  223 (289)
                      +.+|.-+|.   .|-|||.-.|..||..++|+|..++++||++|      +..|-+.+.+
T Consensus        10 ~K~v~~ALt---~I~GIG~~~A~~Ic~~lgi~~~~k~~~Lt~~q------i~~l~~~i~~   60 (106)
T pfam00416        10 NKKIEIALT---YIKGIGRRKANQILKKAGVDKDKRVGELTEEE------IDRIRDIISN   60 (106)
T ss_pred             CCEEEEEEC---CCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHHH
T ss_conf             968644411---21052899999999991959775715499999------9999999975


No 14 
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=95.85  E-value=0.013  Score=36.84  Aligned_cols=53  Identities=19%  Similarity=0.219  Sum_probs=42.8

Q ss_pred             CCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             45421001112654356413689999998717877831222200101589999999987887
Q gi|254780625|r  163 KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKV  224 (289)
Q Consensus       163 ~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~v  224 (289)
                      .+.+|.-+|   +.|-|||.-.|..||-.++|+|..++.+||++|      +..|-+.+.+-
T Consensus        19 ~~K~i~~AL---t~IyGIG~~~A~~Ic~~lgId~~~k~~~Lte~q------i~~l~~~i~~~   71 (149)
T PRK04053         19 GTKPVEYAL---TGIKGIGRRTARAIARKLGLDPHAKLGYLSDEE------IEKIEEALENP   71 (149)
T ss_pred             CCCEEEEEC---CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHH------HHHHHHHHHHH
T ss_conf             996864441---111484899999999991899877307499999------99999999746


No 15 
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=95.52  E-value=0.012  Score=37.05  Aligned_cols=48  Identities=25%  Similarity=0.330  Sum_probs=39.5

Q ss_pred             CCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r  166 NLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ  222 (289)
Q Consensus       166 ~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~  222 (289)
                      .+.-+|   +.|-|||--.+.|||-.++|+|..++.+||++|      +.+|-+++.
T Consensus        14 ~v~iAL---t~IyGIG~~~a~~I~~~~gi~~~~r~~~Lteee------i~~ir~~i~   61 (121)
T COG0099          14 RVVIAL---TYIYGIGRRRAKEICKKAGIDPDKRVGELTEEE------IERLRDAIQ   61 (121)
T ss_pred             EEEEHH---HHHCCCCHHHHHHHHHHCCCCHHHHHCCCCHHH------HHHHHHHHH
T ss_conf             576504---630353699999999991988667645299999------999999998


No 16 
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=95.50  E-value=0.014  Score=36.56  Aligned_cols=49  Identities=31%  Similarity=0.381  Sum_probs=39.3

Q ss_pred             CCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             4210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r  165 SNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ  222 (289)
Q Consensus       165 ~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~  222 (289)
                      .+|.-+|   +.|-|||.-.|..||-.++|||..++.+||++|      +..|-+.|.
T Consensus        13 K~v~~AL---t~I~GIG~~~A~~Ic~~lgId~~~k~g~Ls~~q------i~~I~~~I~   61 (122)
T PRK05179         13 KRVVIAL---TYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEE------LDKLREEID   61 (122)
T ss_pred             CCHHHHH---HHHCCCCHHHHHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHHH
T ss_conf             7868477---300275899999999982999766887656999------999999998


No 17 
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=95.35  E-value=0.023  Score=35.30  Aligned_cols=51  Identities=22%  Similarity=0.292  Sum_probs=40.9

Q ss_pred             CCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             542100111265435641368999999871787783122220010158999999998788
Q gi|254780625|r  164 NSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQK  223 (289)
Q Consensus       164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~  223 (289)
                      +.+|.-+|   +.|-|||.-+|..||-.++|+|..++.+||++|      +..|-+.+..
T Consensus        16 ~K~v~~aL---t~I~GIG~~~A~~Ic~~~gid~~~k~~~Lt~~e------i~~i~~~i~~   66 (144)
T TIGR03629        16 NKPVEYAL---TGIKGIGRRFARAIARKLGVDPNAKLGYLDDEE------IEKLEEAVEN   66 (144)
T ss_pred             CCEEEEEE---EEECCCCHHHHHHHHHHHCCCCCCCCCCCCHHH------HHHHHHHHHH
T ss_conf             96898872---212372899999999990999353604199999------9999999985


No 18 
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=95.10  E-value=0.025  Score=35.07  Aligned_cols=48  Identities=25%  Similarity=0.410  Sum_probs=38.8

Q ss_pred             CCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             421001112654356413689999998717877831222200101589999999987
Q gi|254780625|r  165 SNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEI  221 (289)
Q Consensus       165 ~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i  221 (289)
                      .+|.-+|   +-|-|||--.|..||-.++|+|..++.+||++|      +..|-+.+
T Consensus        11 K~v~~AL---t~I~GIG~~~A~~Ic~~lgId~~~k~g~Ls~~q------i~~I~~~I   58 (113)
T TIGR03631        11 KRVEIAL---TYIYGIGRTRARKILEKAGIDPDKRVKDLTEEE------LNAIREEI   58 (113)
T ss_pred             CCHHHHH---HCEECCCHHHHHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHH
T ss_conf             6746065---200275899999999992999877864499999------99999999


No 19 
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=94.79  E-value=0.039  Score=33.76  Aligned_cols=48  Identities=25%  Similarity=0.344  Sum_probs=38.7

Q ss_pred             CCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             421001112654356413689999998717877831222200101589999999987
Q gi|254780625|r  165 SNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEI  221 (289)
Q Consensus       165 ~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i  221 (289)
                      .+|.-+|.   .|-|||--.|..||..++|+|..++++||++|      +..|-+.+
T Consensus        13 K~v~~aLt---~I~GIG~~~A~~Ic~~lgi~~~~k~~~Ls~~q------i~~i~~~i   60 (122)
T CHL00137         13 KRIEIALT---YIYGIGLTSAKKILEKANIDPDTRTKDLTDEQ------IVSIRQII   60 (122)
T ss_pred             CEEEEHHH---HHCCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHH
T ss_conf             77313111---00061899999999984989885526299999------99999999


No 20 
>PRK12495 hypothetical protein; Provisional
Probab=93.11  E-value=0.026  Score=34.96  Aligned_cols=26  Identities=35%  Similarity=0.732  Sum_probs=18.8

Q ss_pred             CCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             8771078778878999987812063877679
Q gi|254780625|r  259 TGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       259 ~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      ++..| ..||.+|=+..    ..-|||.||.
T Consensus        41 TN~HC-~~CGdPIFR~d----GqeFCPTCQ~   66 (221)
T PRK12495         41 TNAHC-DECGSPIFRHD----GQEFCPTCQH   66 (221)
T ss_pred             CCCCC-CCCCCHHHHCC----CCCCCCCCCC
T ss_conf             21200-22367234047----6614864235


No 21 
>pfam06677 Auto_anti-p27 Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis.
Probab=91.40  E-value=0.11  Score=30.92  Aligned_cols=26  Identities=27%  Similarity=0.814  Sum_probs=20.6

Q ss_pred             CCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             877107877887899998781206387767
Q gi|254780625|r  259 TGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       259 ~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      -++.| |.||+++-+.+.|.   .|||.||
T Consensus        16 L~~~C-~~Cg~pLf~~k~g~---~~Cp~C~   41 (41)
T pfam06677        16 LDEHC-PKCGTPLFRLKDGK---VFCPSCE   41 (41)
T ss_pred             HHCCC-CCCCCEEEECCCCC---EECCCCC
T ss_conf             54325-45698305848999---9578779


No 22 
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=90.44  E-value=0.15  Score=30.04  Aligned_cols=24  Identities=25%  Similarity=0.783  Sum_probs=17.3

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             71078778878999987812063877679
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      ..| |.||.++-+ +.   .+-|||.|++
T Consensus        29 ~hC-p~Cg~PLF~-Kd---G~v~CPvC~~   52 (131)
T COG1645          29 KHC-PKCGTPLFR-KD---GEVFCPVCGY   52 (131)
T ss_pred             HHC-CCCCCCCEE-EC---CEEECCCCCC
T ss_conf             448-655883163-08---9587777776


No 23 
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=89.46  E-value=0.74  Score=25.58  Aligned_cols=105  Identities=23%  Similarity=0.352  Sum_probs=70.3

Q ss_pred             EEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHHC-CCCCCCEEEECCCCCCCCCHHHHHHHHH
Q ss_conf             899981587664100145530100532356555332211106788874201-4542100111265435641368999999
Q gi|254780625|r  112 YRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHK-KNSNLKNALLNQKIVAGIGNIYVCEALW  190 (289)
Q Consensus       112 ~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l~~-~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf  190 (289)
                      ..+.|.||-  |.+.+++.....-=++-..+-|-|-  ..+.+.+...++. ++.++..+|+  +-|+-||---++|+|=
T Consensus       206 A~I~l~dPd--G~~~vf~r~t~~lP~pP~E~kPHP~--gvd~~~L~~M~~~T~~~tv~~fL~--sef~rig~~ta~e~~e  279 (538)
T COG1389         206 ARIVLKDPD--GNLVVFPRSTDKLPKPPKEIKPHPH--GVDLDTLKKMAHRTRRSTVREFLV--SEFSRIGEKTADELLE  279 (538)
T ss_pred             EEEEEECCC--CCEEEECCCHHHCCCCCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHH
T ss_conf             179998899--8678713314117999300489976--457889999998753435999999--9987762667999999


Q ss_pred             HHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8717877831222200101589999999987887
Q gi|254780625|r  191 RAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKV  224 (289)
Q Consensus       191 ~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~v  224 (289)
                      .++.+|..+...|+.+.  ..+.+++|.++.+++
T Consensus       280 ~~g~~~~~~p~~L~~~~--~~eea~~lv~a~~~~  311 (538)
T COG1389         280 YAGFDPDKKPRELTKKK--TREEAEKLVEAFKKM  311 (538)
T ss_pred             HHCCCCCCCHHHHHCCC--CHHHHHHHHHHHHHC
T ss_conf             84679654878860345--789999999999858


No 24 
>PRK00420 hypothetical protein; Validated
Probab=88.89  E-value=0.22  Score=29.00  Aligned_cols=25  Identities=20%  Similarity=0.486  Sum_probs=17.7

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             71078778878999987812063877679
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      .+| |.||.++-+.+-|   ..|||.|-|
T Consensus        20 ~~C-~~Cg~plf~~k~G---~~~Cp~cgk   44 (107)
T PRK00420         20 KHC-PVCGLPLFELKDG---EVVCPNHGK   44 (107)
T ss_pred             HHC-CCCCCCEEECCCC---CEECCCCCC
T ss_conf             137-6579840574898---776898987


No 25 
>PRK07220 DNA topoisomerase I; Validated
Probab=87.97  E-value=0.51  Score=26.61  Aligned_cols=29  Identities=24%  Similarity=0.657  Sum_probs=23.8

Q ss_pred             CCCCCCCCCCCEEEEEEECCCCEE-E-CCCCC
Q ss_conf             877107877887899998781206-3-87767
Q gi|254780625|r  259 TGEPCLSNCGQMIRRIVQAGRSTF-Y-CTYCQ  288 (289)
Q Consensus       259 ~g~~C~~~CG~~I~~~~~~gR~ty-~-Cp~CQ  288 (289)
                      .+..| +.||-++.++.-+|+..| . ||.|.
T Consensus       634 ~~~~C-~~~~~~~~~~~~~~~~~~~~~cp~c~  664 (740)
T PRK07220        634 TDKVC-EAHGLHHIKIINGGKRPWDLGCPQCN  664 (740)
T ss_pred             CCCCC-CCCCCEEEEEEECCCCCCCCCCCCCC
T ss_conf             78868-77998379998089875767899877


No 26 
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=87.83  E-value=0.39  Score=27.39  Aligned_cols=27  Identities=22%  Similarity=0.717  Sum_probs=21.2

Q ss_pred             EEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             665738771078778878999987812063877679
Q gi|254780625|r  254 SVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       254 ~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      -||.+    | ++|++.+.+    ...+-+||+||.
T Consensus       147 VI~A~----C-srC~~~L~~----~~~~l~Cp~Cg~  173 (188)
T COG1096         147 VIYAR----C-SRCRAPLVK----KGNMLKCPNCGN  173 (188)
T ss_pred             EEEEE----C-CCCCCCEEE----CCCEEECCCCCC
T ss_conf             99998----3-677762088----475998887798


No 27 
>PRK08413 consensus
Probab=85.36  E-value=0.89  Score=25.06  Aligned_cols=28  Identities=4%  Similarity=0.131  Sum_probs=11.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2222001015899999999878876765
Q gi|254780625|r  201 RSLIQNNGTPKDILYKLIQEIQKVLIDA  228 (289)
Q Consensus       201 ~~Ls~~e~~~~~~~~~L~~~i~~vl~~a  228 (289)
                      +.+.+.+...++.+...|....+.+.++
T Consensus       528 d~Ia~G~~~~~~~l~~f~~~f~~~i~~~  555 (733)
T PRK08413        528 DEIAEDKADWQKVLKDFYYPFMDKIEEG  555 (733)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             9998598659999999999999999999


No 28 
>PRK08938 DNA topoisomerase I; Validated
Probab=84.51  E-value=0.84  Score=25.22  Aligned_cols=27  Identities=11%  Similarity=0.126  Sum_probs=13.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             222001015899999999878876765
Q gi|254780625|r  202 SLIQNNGTPKDILYKLIQEIQKVLIDA  228 (289)
Q Consensus       202 ~Ls~~e~~~~~~~~~L~~~i~~vl~~a  228 (289)
                      .+.+.+..-.+.+...|....+.+..+
T Consensus       536 ~Ia~G~~~~~~~l~~f~~~f~~~l~~a  562 (692)
T PRK08938        536 EVEEGKEQWVKVIDEFYKPFEKELEKA  562 (692)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             997697429999999999999999999


No 29 
>PRK05823 consensus
Probab=83.20  E-value=0.67  Score=25.84  Aligned_cols=78  Identities=12%  Similarity=0.113  Sum_probs=35.6

Q ss_pred             CHHHHHHHHHHCC-------CCCCCEEEECCCCCCCCCHHHH--------HHHH---HHHHCCCC------CCCCCCCHH
Q ss_conf             1067888742014-------5421001112654356413689--------9999---98717877------831222200
Q gi|254780625|r  151 FNAIYLTHQFHKK-------NSNLKNALLNQKIVAGIGNIYV--------CEAL---WRAKLSPI------RKTRSLIQN  206 (289)
Q Consensus       151 ~~~~~~~~~l~~~-------~~~Ik~~LlDQ~~iaGIGN~y~--------~EiL---f~a~I~P~------~~~~~Ls~~  206 (289)
                      ||...+.+.+.+.       ...|=..|.|-.+|-.-|+-+.        .+.|   |-.=++|.      ...+.+.+.
T Consensus       485 yTEasLi~~ME~~GIGtpATrA~II~~L~~R~Yv~~~~k~l~pT~~G~~l~~~L~~~~~~l~~~~~Ta~~E~~Ld~I~~G  564 (691)
T PRK05823        485 YTQASLIEALEKAGIGRPSTYSTMASINLERGYANLDKRAYIPTDLGEKVNQELSKHFPKIINKEFTKNMEESLDEIAEG  564 (691)
T ss_pred             CCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEECCCEEEEHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC
T ss_conf             89999999999679997576899999887368289519767451899999999987525634977999999988999769


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1015899999999878876765
Q gi|254780625|r  207 NGTPKDILYKLIQEIQKVLIDA  228 (289)
Q Consensus       207 e~~~~~~~~~L~~~i~~vl~~a  228 (289)
                      +....+.+...+....+.+..+
T Consensus       565 ~~~~~~~l~~f~~~~~~~~~~~  586 (691)
T PRK05823        565 KVNWKSFLKTFWPNFKEEVKLA  586 (691)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHH
T ss_conf             9889999999999999999999


No 30 
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=82.15  E-value=0.6  Score=26.14  Aligned_cols=20  Identities=5%  Similarity=0.337  Sum_probs=9.4

Q ss_pred             EEEEEEECCCCCEEEEEEEEC
Q ss_conf             389997068876048999815
Q gi|254780625|r   98 HVTISLTNNTNTKKYRVIYND  118 (289)
Q Consensus        98 ~~~~~~~~~~~~~~~~l~~~D  118 (289)
                      .+.+.+.|++.... ...|.+
T Consensus        69 ~l~~~i~D~Tg~~~-~~~F~~   88 (166)
T cd04476          69 ILSLNVADHTGEAW-LTLFDE   88 (166)
T ss_pred             EEEEEEECCCCCEE-EEEEHH
T ss_conf             99999986889999-998667


No 31 
>PRK08173 DNA topoisomerase III; Validated
Probab=79.29  E-value=5.1  Score=20.19  Aligned_cols=24  Identities=38%  Similarity=1.027  Sum_probs=13.3

Q ss_pred             CCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             77107877887899998781206387767
Q gi|254780625|r  260 GEPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       260 g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      +.|| |.||..|.    .+...|-|..|.
T Consensus       624 ~~~C-P~Cg~~i~----~~~k~y~C~~C~  647 (857)
T PRK08173        624 QTPC-PNCGGVVK----ENYRRFACTKCD  647 (857)
T ss_pred             CCCC-CCCCCEEE----ECCCEEECCCCC
T ss_conf             5788-88895167----556189779997


No 32 
>pfam00398 RrnaAD Ribosomal RNA adenine dimethylase.
Probab=78.63  E-value=2.1  Score=22.62  Aligned_cols=53  Identities=15%  Similarity=0.141  Sum_probs=38.3

Q ss_pred             HHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             74201454210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r  158 HQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ  222 (289)
Q Consensus       158 ~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~  222 (289)
                      ..+..++.+|++.|-      +++..-..++|..++|+|...+.+||.+|      +.+|++.+.
T Consensus       205 ~~F~~RRK~L~n~L~------~~~~~~~~~~l~~~gi~~~~R~e~Ls~e~------~~~L~~~l~  257 (258)
T pfam00398       205 KLFNGKGRSLFTSLR------RLFPGGQVQALSKTRINDNALVGKLSPEQ------WLTIFKELA  257 (258)
T ss_pred             HHHHCCCHHHHHHHH------HHCCHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHC
T ss_conf             998116378999998------73880799999987769888861599999------999999970


No 33 
>KOG3311 consensus
Probab=78.58  E-value=1.7  Score=23.22  Aligned_cols=50  Identities=20%  Similarity=0.368  Sum_probs=41.0

Q ss_pred             CCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             54210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r  164 NSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ  222 (289)
Q Consensus       164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~  222 (289)
                      +..|.-+|+-   |.|||--||.+++=.+++++...+.+|++.|      +..+...+.
T Consensus        23 ~~~V~fAl~~---i~Gig~~~A~~ic~K~~~~~~~r~gelt~~q------i~~i~~i~~   72 (152)
T KOG3311          23 KRKVTFALTS---IKGIGRRYAEIVCKKADLDLTKRAGELTEEQ------ILRILQILN   72 (152)
T ss_pred             CCEEEEEEEE---EEEECHHHHHHHHHHCCCCHHHHHCCCCHHH------HHHHHHHHC
T ss_conf             8006898888---8651122444444203740555413124999------999999861


No 34 
>pfam08273 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase.
Probab=78.28  E-value=1  Score=24.66  Aligned_cols=27  Identities=41%  Similarity=0.896  Sum_probs=20.9

Q ss_pred             CCCCCCCCCEEEEE---EECCCCEEECCCCC
Q ss_conf             71078778878999---98781206387767
Q gi|254780625|r  261 EPCLSNCGQMIRRI---VQAGRSTFYCTYCQ  288 (289)
Q Consensus       261 ~~C~~~CG~~I~~~---~~~gR~ty~Cp~CQ  288 (289)
                      .|| |.||.+=..-   ...+|.+|||-+|-
T Consensus         4 ~pC-P~CGg~Drfr~fdd~~g~G~~~C~~Cg   33 (39)
T pfam08273         4 GPC-PNCGGSDRFRIFDDKDGRGTWFCFSCG   33 (39)
T ss_pred             CCC-CCCCCCCCCEECCCCCCCCCEECCCCC
T ss_conf             677-777785752565578997577838887


No 35 
>PRK09137 DNA topoisomerase I; Validated
Probab=78.20  E-value=2.1  Score=22.61  Aligned_cols=79  Identities=8%  Similarity=0.045  Sum_probs=34.4

Q ss_pred             CCHHHHHHHHHHCC-------CCCCCEEEECCCCCCCCCHH--------HHHHHHHH---HHCCCC------CCCCCCCH
Q ss_conf             11067888742014-------54210011126543564136--------89999998---717877------83122220
Q gi|254780625|r  150 SFNAIYLTHQFHKK-------NSNLKNALLNQKIVAGIGNI--------YVCEALWR---AKLSPI------RKTRSLIQ  205 (289)
Q Consensus       150 ~~~~~~~~~~l~~~-------~~~Ik~~LlDQ~~iaGIGN~--------y~~EiLf~---a~I~P~------~~~~~Ls~  205 (289)
                      .+|...+.+.+.+.       ..+|=..|+|..+|---|+-        .-.+.|-.   .=++|.      ...+.+.+
T Consensus       472 ryTEasLIk~ME~~GIGtpsT~A~II~~L~~R~Yv~~~~k~l~pT~lG~~v~~~L~~~f~~iv~~~~Ta~mE~~Ld~Ia~  551 (761)
T PRK09137        472 RYTEASLVKALEEYGIGRPSTYASIISTLQQREYVRLDKKRFIPTDVGRIVNKFLTEHFTKYVDYNFTAGLEDELDEIAR  551 (761)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHHHHC
T ss_conf             88999999999737999623689999989738969965998856467999999998855231596689999998899976


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             01015899999999878876765
Q gi|254780625|r  206 NNGTPKDILYKLIQEIQKVLIDA  228 (289)
Q Consensus       206 ~e~~~~~~~~~L~~~i~~vl~~a  228 (289)
                      .+..-.+.+...|......+..+
T Consensus       552 G~~~~~~vl~~f~~~f~~~~~~~  574 (761)
T PRK09137        552 GEKDWIPVLEEFWHPFIELIKEK  574 (761)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             99608999999999999999999


No 36 
>pfam03486 HI0933_like HI0933-like protein.
Probab=77.83  E-value=1.7  Score=23.24  Aligned_cols=65  Identities=23%  Similarity=0.221  Sum_probs=45.8

Q ss_pred             CCCHHHHHHHHHHC-----CCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             11106788874201-----4542100111265435641368999999871787783122220010158999999998788
Q gi|254780625|r  149 NSFNAIYLTHQFHK-----KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQK  223 (289)
Q Consensus       149 ~~~~~~~~~~~l~~-----~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~  223 (289)
                      |+++.+.+.+.+..     .++.++.+|-     .-+=.=+...+|-.++|+|.+++++|+.++      +.+|.+.+++
T Consensus       267 P~~~~~~l~~~l~~~~~~~~~~~~~~~l~-----~~lp~rl~~~ll~~~~i~~~~~~~~l~~~~------~~~l~~~lk~  335 (405)
T pfam03486       267 PDLDAEELAARLEKPRGAHPKKSLKNALA-----GLLPKRLALFLLEQAGIDPDKKLAQLSKKD------LAALADLLKA  335 (405)
T ss_pred             CCCCHHHHHHHHHHHHHHCCHHHHHHHHH-----HHHHHHHHHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHHHC
T ss_conf             99999999999999988682323999888-----775899999999971998688636579999------9999999866


Q ss_pred             H
Q ss_conf             7
Q gi|254780625|r  224 V  224 (289)
Q Consensus       224 v  224 (289)
                      .
T Consensus       336 ~  336 (405)
T pfam03486       336 W  336 (405)
T ss_pred             C
T ss_conf             9


No 37 
>PRK07219 DNA topoisomerase I; Validated
Probab=76.18  E-value=3  Score=21.69  Aligned_cols=25  Identities=32%  Similarity=0.745  Sum_probs=10.3

Q ss_pred             CCCCCCCCCCEEEEEEECCCCEEECC
Q ss_conf             77107877887899998781206387
Q gi|254780625|r  260 GEPCLSNCGQMIRRIVQAGRSTFYCT  285 (289)
Q Consensus       260 g~~C~~~CG~~I~~~~~~gR~ty~Cp  285 (289)
                      +++| |.||.++...+-+.+.-.+||
T Consensus       716 ~e~C-p~Cg~~~~~~~~~~~~~~~C~  740 (769)
T PRK07219        716 GEKC-PYCGAPILVLINGRRHWKFCP  740 (769)
T ss_pred             CCCC-CCCCCEEEEEECCCCCEEECC
T ss_conf             8847-778983799972784300689


No 38 
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=72.87  E-value=2.6  Score=22.04  Aligned_cols=27  Identities=41%  Similarity=0.951  Sum_probs=19.8

Q ss_pred             CCCCCCCCCEEEEE--EECCCCEEECCCCC
Q ss_conf             71078778878999--98781206387767
Q gi|254780625|r  261 EPCLSNCGQMIRRI--VQAGRSTFYCTYCQ  288 (289)
Q Consensus       261 ~~C~~~CG~~I~~~--~~~gR~ty~Cp~CQ  288 (289)
                      .|| |.||..=..-  .-.||.+|+|-+|-
T Consensus         4 ~pC-P~CGG~Drfrf~dk~g~G~~~C~~Cg   32 (37)
T smart00778        4 GPC-PNCGGSDRFRFDDKDGRGTWFCSVCG   32 (37)
T ss_pred             CCC-CCCCCCCCEEEECCCCCEEEECCCCC
T ss_conf             678-86778655367469997407827887


No 39 
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=72.60  E-value=3.5  Score=21.22  Aligned_cols=26  Identities=27%  Similarity=0.682  Sum_probs=19.1

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      -| |.||..+.-..-.+...|.|++|.
T Consensus         2 FC-p~C~n~l~p~~~~~~~~~~C~~C~   27 (52)
T smart00661        2 FC-PKCGNMLIPKEGKEKRRFVCRKCG   27 (52)
T ss_pred             CC-CCCCCEEEEEECCCCEEEECCCCC
T ss_conf             78-652888768536995389748999


No 40 
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=71.38  E-value=5.4  Score=20.06  Aligned_cols=53  Identities=23%  Similarity=0.430  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf             9999987887676542188755311167787787413316657387710787788789999878120638776
Q gi|254780625|r  215 YKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYC  287 (289)
Q Consensus       215 ~~L~~~i~~vl~~a~~~gG~~~~~~~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~C  287 (289)
                      ..+..+|-++|..-+..++....     ....          .-.+.+| |.||.++.+.  +|  =+.|+.|
T Consensus       675 ~S~~daI~~~L~~~~~~~~~~~~-----~~~~----------~~~~~~C-P~CG~~l~~~--eG--C~~C~~C  727 (733)
T PRK08665        675 LSCPDAIAKVLEKHLLANGYDPV-----EEEA----------DPERGAC-PECGSILEHE--EG--CAVCHSC  727 (733)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCC-----CCCC----------CCCCCCC-CCCCCEEEEC--CC--CCCCCCC
T ss_conf             54999999999999973577766-----5546----------6678979-9998747876--89--8727778


No 41 
>PRK00274 ksgA dimethyladenosine transferase; Reviewed
Probab=71.36  E-value=4.3  Score=20.66  Aligned_cols=56  Identities=20%  Similarity=0.380  Sum_probs=40.8

Q ss_pred             HHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             7420145421001112654356413689999998717877831222200101589999999987887
Q gi|254780625|r  158 HQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKV  224 (289)
Q Consensus       158 ~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~v  224 (289)
                      ..+..+++.|++.|-  ..+   .+--.+++|-.++|+|...+.+||.+|      +.+|++.+...
T Consensus       210 ~~F~~RRK~l~n~Lk--~~~---~~~~~~~~l~~~~i~~~~RpeeLs~~~------~~~L~~~l~~~  265 (267)
T PRK00274        210 AAFNQRRKTLRNNLK--NLA---GKELLEELLEALGIDPNRRAETLSVEE------FVRLANALADL  265 (267)
T ss_pred             HHHHCCHHHHHHHHH--HHC---CHHHHHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHHHHH
T ss_conf             998146489999998--752---888899999986979677824399999------99999999997


No 42 
>PRK08620 DNA topoisomerase III; Provisional
Probab=70.27  E-value=4.3  Score=20.67  Aligned_cols=24  Identities=21%  Similarity=0.534  Sum_probs=9.2

Q ss_pred             CCCCCCCCCCEEEEEEECCCCEEEC
Q ss_conf             7710787788789999878120638
Q gi|254780625|r  260 GEPCLSNCGQMIRRIVQAGRSTFYC  284 (289)
Q Consensus       260 g~~C~~~CG~~I~~~~~~gR~ty~C  284 (289)
                      |..| |.||..+..-.-+....|.|
T Consensus       648 ~~~C-p~C~~~~~~~~~~~g~~~~c  671 (726)
T PRK08620        648 NARC-PNCKKKLELRGEGEGQIFVC  671 (726)
T ss_pred             CCCC-CCCCCEEEEEECCCCCEEEE
T ss_conf             8949-99998568985677878997


No 43 
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=69.72  E-value=3  Score=21.71  Aligned_cols=22  Identities=27%  Similarity=0.753  Sum_probs=16.7

Q ss_pred             CCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             771078778878999987812063877679
Q gi|254780625|r  260 GEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       260 g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      -+.| ++||.       -....|.||.|..
T Consensus       309 S~~C-~~cg~-------~~~r~~~C~~cg~  330 (364)
T COG0675         309 SKTC-PCCGH-------LSGRLFKCPRCGF  330 (364)
T ss_pred             CCCC-CCCCC-------CCCCEEECCCCCC
T ss_conf             7778-87787-------4785488899897


No 44 
>TIGR00755 ksgA dimethyladenosine transferase; InterPro: IPR011530   This family of proteins represent the rRNA adenine dimethylases (e.g. KsgA).    The bacterial enzyme KsgA catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In yeast, and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding.   The crystal structure of KsgA from Escherichia coli has been solved to a resolution of 2.1A. It bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to the yeast mitochondrial transcription factor, sc-mtTFB .; GO: 0016433 rRNA (adenine) methyltransferase activity, 0006364 rRNA processing.
Probab=69.09  E-value=5.2  Score=20.13  Aligned_cols=59  Identities=20%  Similarity=0.260  Sum_probs=47.0

Q ss_pred             HHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCC---CCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             887420145421001112654356413689999998717877---83122220010158999999998
Q gi|254780625|r  156 LTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPI---RKTRSLIQNNGTPKDILYKLIQE  220 (289)
Q Consensus       156 ~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~---~~~~~Ls~~e~~~~~~~~~L~~~  220 (289)
                      ....+..|++++.+.|-+-..-..+.+.+..+.|...+|++.   +++-+|+-+|      +.+|++.
T Consensus       215 ~~~~F~~RRK~l~n~L~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~R~e~L~~~d------f~~L~~~  276 (277)
T TIGR00755       215 LKAAFSQRRKTLRNNLKNSLKDNLLAKEKLEEVLEQLGLDPTKLNARAEQLSPED------FLRLANL  276 (277)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHCCHHCCCHHH------HHHHHHH
T ss_conf             9998617871015556542221011124566678870888650006611148899------9999960


No 45 
>pfam07282 Transposase_35 Putative transposase DNA-binding domain. This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesize this domain is DNA-binding.
Probab=68.66  E-value=2.4  Score=22.31  Aligned_cols=27  Identities=41%  Similarity=0.886  Sum_probs=19.2

Q ss_pred             CCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             877107877887899998781206387767
Q gi|254780625|r  259 TGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       259 ~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      +-+.| +.||....+ ...+| .|.||.|-
T Consensus        27 TS~~C-~~Cg~~~~~-~~~~r-~~~C~~Cg   53 (69)
T pfam07282        27 TSKTC-SVCGHKNKE-SLSGR-TFKCPNCG   53 (69)
T ss_pred             CCCCC-CCCCCCCCC-CCCCC-EEECCCCC
T ss_conf             86427-999899867-48887-89899899


No 46 
>PRK05582 DNA topoisomerase I; Validated
Probab=66.90  E-value=3.8  Score=20.98  Aligned_cols=79  Identities=14%  Similarity=0.153  Sum_probs=35.8

Q ss_pred             CHHHHHHHHHHCC-------CCCCCEEEECCCCCCCCCHHH--------HHHHHHH---HHCCCC------CCCCCCCHH
Q ss_conf             1067888742014-------542100111265435641368--------9999998---717877------831222200
Q gi|254780625|r  151 FNAIYLTHQFHKK-------NSNLKNALLNQKIVAGIGNIY--------VCEALWR---AKLSPI------RKTRSLIQN  206 (289)
Q Consensus       151 ~~~~~~~~~l~~~-------~~~Ik~~LlDQ~~iaGIGN~y--------~~EiLf~---a~I~P~------~~~~~Ls~~  206 (289)
                      ||...+.+.+...       ..+|=..|++..+|.--|+-+        -.|.|-.   .=++|.      ...+.+.++
T Consensus       457 yTEasLik~ME~~GIGtpATrA~II~~L~~R~Yv~~~~k~l~pT~~G~~v~~~L~~~f~~i~~~~~Ta~~E~~Ld~I~~G  536 (692)
T PRK05582        457 YSEASLIKKLESLGIGRPSTYAPTISTLLSRKYVEREKKQLIPTELGFKVIEILEKHFPQIVDSEFTANMEEKLDEIAEG  536 (692)
T ss_pred             CCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHHHHCC
T ss_conf             79999999998479986045899998887467099409888475799999999988553322854899999999999859


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10158999999998788767654
Q gi|254780625|r  207 NGTPKDILYKLIQEIQKVLIDAI  229 (289)
Q Consensus       207 e~~~~~~~~~L~~~i~~vl~~a~  229 (289)
                      +..-++.+...|....+.+..+.
T Consensus       537 ~~~~~~~l~~f~~~f~~~i~~~~  559 (692)
T PRK05582        537 KADWQEVLKDFYYPFMEKIEEAK  559 (692)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             87799999999999999999998


No 47 
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=63.76  E-value=2.7  Score=21.96  Aligned_cols=25  Identities=36%  Similarity=0.875  Sum_probs=16.7

Q ss_pred             CCCCCCC-CEEEEEEEC--CCCEEECCCC
Q ss_conf             1078778-878999987--8120638776
Q gi|254780625|r  262 PCLSNCG-QMIRRIVQA--GRSTFYCTYC  287 (289)
Q Consensus       262 ~C~~~CG-~~I~~~~~~--gR~ty~Cp~C  287 (289)
                      +| |+|| ..|-|-.--  -..+|-||+|
T Consensus        29 ~C-PnCGe~~I~Rc~~CRk~g~~Y~Cp~C   56 (61)
T COG2888          29 PC-PNCGEVEIYRCAKCRKLGNPYRCPKC   56 (61)
T ss_pred             EC-CCCCCEEEEHHHHHHHCCCCEECCCC
T ss_conf             48-99982424105668774994478876


No 48 
>PRK07141 DNA topoisomerase I; Validated
Probab=63.69  E-value=12  Score=17.90  Aligned_cols=29  Identities=21%  Similarity=0.580  Sum_probs=16.9

Q ss_pred             CCCCCCCCCCCEEE--EEEECCCCEEECCC---CC
Q ss_conf             87710787788789--99987812063877---67
Q gi|254780625|r  259 TGEPCLSNCGQMIR--RIVQAGRSTFYCTY---CQ  288 (289)
Q Consensus       259 ~g~~C~~~CG~~I~--~~~~~gR~ty~Cp~---CQ  288 (289)
                      .|.+| |.||..+.  +.+.|+..-|-|..   |.
T Consensus       564 ~~~~C-P~Cg~~l~~r~~~~g~~~F~gCs~yp~Ck  597 (622)
T PRK07141        564 LGESC-PDCNGDLVYRNNRKGDQRFIGCSNFPNCR  597 (622)
T ss_pred             CCCCC-CCCCCCEEEEECCCCCCEEEECCCCCCCC
T ss_conf             79988-78998225787368898698789998888


No 49 
>PRK12366 replication factor A; Reviewed
Probab=63.18  E-value=4.1  Score=20.77  Aligned_cols=23  Identities=22%  Similarity=0.713  Sum_probs=17.4

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             7107877887899998781206387767
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      ..| |.|+..+....    ..|-||.|-
T Consensus       534 ~~C-P~C~krv~~~e----~~y~C~~cG  556 (649)
T PRK12366        534 TLC-PNCRKRVNLVD----NKYVCEECG  556 (649)
T ss_pred             EEC-CCCCCEEEECC----CCEECCCCC
T ss_conf             728-66676056458----825277678


No 50 
>PRK07726 DNA topoisomerase III; Provisional
Probab=63.14  E-value=12  Score=17.84  Aligned_cols=22  Identities=23%  Similarity=0.664  Sum_probs=15.3

Q ss_pred             CCCCCCCCEEEEEEECCCCEEEC-----CCCC
Q ss_conf             10787788789999878120638-----7767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYC-----TYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~C-----p~CQ  288 (289)
                      +| |.||..|..    +...|.|     |.|.
T Consensus       632 ~C-P~Cg~~v~~----~~k~~~Cs~y~~~~C~  658 (716)
T PRK07726        632 SC-KKCDGDVID----KGTFYGCSNYNTTQCD  658 (716)
T ss_pred             CC-CCCCCEEEE----CCEEEECCCCCCCCCC
T ss_conf             59-999998377----6758973799899999


No 51 
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=62.64  E-value=6.6  Score=19.49  Aligned_cols=23  Identities=26%  Similarity=0.667  Sum_probs=18.1

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             1078778878999987812063877679
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      .| +.||.++..    ......||.|.+
T Consensus       152 ~C-~~cg~~m~~----~~~~~~Cp~cg~  174 (187)
T PRK09521        152 LC-SRCRTPLVK----KGNTLKCPNCGN  174 (187)
T ss_pred             EC-CCCCCCEEE----ECCEEECCCCCC
T ss_conf             57-767885867----399999999999


No 52 
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1); InterPro: IPR004591 All proteins in this family for which functions are known are part of a multiprotein complex made up of homologs of RPA1, RPA2 and RPA3 that bind single-stranded DNA and function in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian virus 40 origin of replication. This family is Replication factor-a protein 1 (RPA1); GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus.
Probab=62.28  E-value=4.7  Score=20.40  Aligned_cols=53  Identities=28%  Similarity=0.718  Sum_probs=29.7

Q ss_pred             HCCC-CCCCCCCCCCCCCCCCHHH-EEEECCCCCCCCCC----CCCEEEEEEECCCCEEECCCCCC
Q ss_conf             2188-7553111677877874133-16657387710787----78878999987812063877679
Q gi|254780625|r  230 DAGG-SSLRDYVHIDGSIGYFQNA-FSVYGKTGEPCLSN----CGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       230 ~~gG-~~~~~~~~~~g~~g~~~~~-~~vy~r~g~~C~~~----CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      ..|. +.-.||.-..+..-+.+.. =..| |   .|+..    |..+|   .-.+-.+|||.+|||
T Consensus       504 ~lG~DsdKPDyfs~kA~I~~~k~~qN~~Y-~---ACp~~~DrPCnKKV---~d~~~g~yRCEKC~k  562 (671)
T TIGR00617       504 NLGKDSDKPDYFSVKATIVYLKKDQNALY-R---ACPKEGDRPCNKKV---VDQGDGTYRCEKCDK  562 (671)
T ss_pred             HCCCCCCCCCEEEEEEEEEEECCCCEEEE-C---CCCCCCCCCCCCEE---EECCCCCEEEECCCC
T ss_conf             36898875616999899999716740542-4---67445788866456---745979358612688


No 53 
>smart00532 LIGANc Ligase N family.
Probab=62.16  E-value=6.8  Score=19.39  Aligned_cols=23  Identities=26%  Similarity=0.668  Sum_probs=16.1

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCC
Q ss_conf             71078778878999987812063877
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTY  286 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~  286 (289)
                      ..| |.||+.+.+.  ++...++||.
T Consensus       400 ~~C-P~C~s~l~~~--~~~~~~~C~n  422 (441)
T smart00532      400 THC-PSCGSELVRE--EGEVDIRCPN  422 (441)
T ss_pred             CCC-CCCCCEEEEC--CCCEEEECCC
T ss_conf             989-8997983843--8987898899


No 54 
>TIGR01544 HAD-SF-IE HAD-superfamily (subfamily IE) hydrolase, TIGR01544; InterPro: IPR006434   This family is a small group of metazoan sequences with one sequence from Arabidopsis thaliana. The sequences from mouse are annotated as pyrimidine 5-nucleotidases, apparently in reference to HSPC233, the human homolog. However, no such annotation can currently be found for this gene. This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily (IPR005834 from INTERPRO). All of the conserved catalytic motifs  are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches of that subfamily (IA-ID) as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB..
Probab=61.12  E-value=5.8  Score=19.84  Aligned_cols=43  Identities=30%  Similarity=0.343  Sum_probs=30.4

Q ss_pred             HHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHH--CCCCCCCCC
Q ss_conf             67888742014542100111265435641368999999871--787783122
Q gi|254780625|r  153 AIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAK--LSPIRKTRS  202 (289)
Q Consensus       153 ~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~--I~P~~~~~~  202 (289)
                      .+.|.+.|.+..-|  .+.    +=|||||++- ++|=||.  +||..++=|
T Consensus       133 ~e~Ff~~Lq~h~IP--~~i----FSAGiGn~~e-~vlrQa~Gv~hpNvkvvS  177 (287)
T TIGR01544       133 AEDFFEKLQRHSIP--VLI----FSAGIGNVVE-EVLRQALGVLHPNVKVVS  177 (287)
T ss_pred             HHHHHHHHHHCCCC--EEE----EECCCHHHHH-HHHHHHCCCCCCCCEEEE
T ss_conf             16799998745898--999----9357217999-999863588899743886


No 55 
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.69  E-value=2.3  Score=22.45  Aligned_cols=27  Identities=22%  Similarity=0.546  Sum_probs=20.5

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             7107877887899998781206387767
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      -+| |.||.++.....+--.-|-|.+||
T Consensus         8 v~C-P~Cgkpv~w~~~s~frPFCSkRCk   34 (65)
T COG3024           8 VPC-PTCGKPVVWGEESPFRPFCSKRCK   34 (65)
T ss_pred             CCC-CCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf             538-877883334666776763367662


No 56 
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=60.12  E-value=8.2  Score=18.87  Aligned_cols=64  Identities=23%  Similarity=0.208  Sum_probs=47.5

Q ss_pred             CCCHHHHHHHHHHC--CCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             11106788874201--45421001112654356413689999998717877831222200101589999999987887
Q gi|254780625|r  149 NSFNAIYLTHQFHK--KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKV  224 (289)
Q Consensus       149 ~~~~~~~~~~~l~~--~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~v  224 (289)
                      |+.+.+.+.+.+++  +++++|++|-.     .++-=+..=+|=+++| |..+..+||.++      ++.|...++.-
T Consensus       268 P~~~~~~l~~~l~~~~~~kslkn~L~~-----~lp~rlv~~~l~~~~i-~~~~~~~ls~~~------~~~l~~~ik~~  333 (408)
T COG2081         268 PDVDAEELLRELRRANPKKSLKNALAK-----LLPKRLVEFLLERAGI-PDEPLAQLSPKE------LAQLAAALKAW  333 (408)
T ss_pred             CCCCHHHHHHHHHHHCHHHHHHHHHHH-----HHHHHHHHHHHHHCCC-CCCCHHHCCHHH------HHHHHHHHHCC
T ss_conf             999999999999765855689999987-----7326799999985357-874256559888------99999997547


No 57 
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=59.37  E-value=4.4  Score=20.58  Aligned_cols=20  Identities=30%  Similarity=1.016  Sum_probs=13.4

Q ss_pred             CCCCCCCCEEEEEEECCCCEEE-CCCCCC
Q ss_conf             1078778878999987812063-877679
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFY-CTYCQK  289 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~-Cp~CQk  289 (289)
                      .| ++||-+.       ++.|| ||.|-+
T Consensus       356 RC-~~CGF~a-------~~l~W~CPsC~~  376 (389)
T COG2956         356 RC-QNCGFTA-------HTLYWHCPSCRA  376 (389)
T ss_pred             EE-CCCCCCH-------HEEEEECCCCCC
T ss_conf             10-0168631-------013541887565


No 58 
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=59.18  E-value=4.2  Score=20.75  Aligned_cols=29  Identities=34%  Similarity=0.863  Sum_probs=22.0

Q ss_pred             ECCCCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             573877107877887899998781206387767
Q gi|254780625|r  256 YGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       256 y~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      |-+.+-.| |+||..+   +..||+-|-||+|-
T Consensus       346 ~~~~~p~C-p~Cg~~m---~S~G~~g~rC~kCg  374 (421)
T COG1571         346 YERVNPVC-PRCGGRM---KSAGRNGFRCKKCG  374 (421)
T ss_pred             EEECCCCC-CCCCCCH---HHCCCCCCCCCCCC
T ss_conf             67717889-7667713---11678985266426


No 59 
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=56.30  E-value=9.1  Score=18.57  Aligned_cols=22  Identities=32%  Similarity=0.756  Sum_probs=14.1

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCC
Q ss_conf             1078778878999987812063877
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTY  286 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~  286 (289)
                      .| |.||+.+.+  .-+-...+|+.
T Consensus       406 ~C-P~C~s~l~r--~~~e~~~rC~n  427 (667)
T COG0272         406 HC-PVCGSELVR--EEGEVVIRCTN  427 (667)
T ss_pred             CC-CCCCCEEEE--CCCCEEEECCC
T ss_conf             79-889997674--26755686689


No 60 
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=55.89  E-value=8.2  Score=18.86  Aligned_cols=28  Identities=21%  Similarity=0.578  Sum_probs=20.3

Q ss_pred             CCCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             3877107877887899998781206387767
Q gi|254780625|r  258 KTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       258 r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      |..+.| |+||.-|-.....+|  ++|-.|-
T Consensus        21 r~~k~C-PrCG~GvfmA~H~dR--~~CGKCg   48 (54)
T PRK00432         21 RKNKFC-PRCGPGVFMAEHKDR--WACGKCG   48 (54)
T ss_pred             ECCCCC-CCCCCCEEEEECCCC--CCCCCCC
T ss_conf             867859-799994640125887--6635866


No 61 
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679   DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC).   This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=54.40  E-value=7.8  Score=19.00  Aligned_cols=22  Identities=32%  Similarity=0.691  Sum_probs=11.8

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCC
Q ss_conf             1078778878999987812063877
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTY  286 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~  286 (289)
                      .| |.||+++.++.  +-..+|||+
T Consensus       413 ~C-P~C~s~lv~~~--~e~~~rC~N  434 (706)
T TIGR00575       413 HC-PSCGSPLVRIE--EEVDIRCTN  434 (706)
T ss_pred             CC-CCCCCEEECCC--CCEEEECCC
T ss_conf             18-88883311157--872165388


No 62 
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=54.04  E-value=5.5  Score=19.98  Aligned_cols=28  Identities=18%  Similarity=0.612  Sum_probs=18.9

Q ss_pred             CCCCCCCCCEEEEEEEC-------------CCCEEECCCCCC
Q ss_conf             71078778878999987-------------812063877679
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQA-------------GRSTFYCTYCQK  289 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~-------------gR~ty~Cp~CQk  289 (289)
                      .-| |.|++.+.+..-.             ....|.||+|-|
T Consensus        98 ~RC-p~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgk  138 (165)
T COG1656          98 SRC-PECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGK  138 (165)
T ss_pred             CCC-CCCCCEECCCCHHHHHHCCCHHHHHCCCCEEECCCCCC
T ss_conf             327-43497801076777752065244202001467799762


No 63 
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=53.76  E-value=1.8  Score=23.11  Aligned_cols=28  Identities=7%  Similarity=0.143  Sum_probs=16.9

Q ss_pred             CCCCEEEECCCCCCC-CCHHHHHHHHHHH
Q ss_conf             421001112654356-4136899999987
Q gi|254780625|r  165 SNLKNALLNQKIVAG-IGNIYVCEALWRA  192 (289)
Q Consensus       165 ~~Ik~~LlDQ~~iaG-IGN~y~~EiLf~a  192 (289)
                      .++-...||-.++-| +|-....-|...+
T Consensus       143 ~~vvv~vmDF~FmGGSMGsvvGEki~ra~  171 (305)
T CHL00174        143 IPVALGVMDFQFMGGSMGSVVGEKITRLI  171 (305)
T ss_pred             EEEEEEEEECCCCCCCCHHHHHHHHHHHH
T ss_conf             77999997240115652078899999999


No 64 
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=52.94  E-value=12  Score=17.85  Aligned_cols=52  Identities=23%  Similarity=0.432  Sum_probs=38.7

Q ss_pred             HHHHHCCCCCCCEEEECCCCCCCCCHHH-HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             8742014542100111265435641368-999999871787783122220010158999999998788
Q gi|254780625|r  157 THQFHKKNSNLKNALLNQKIVAGIGNIY-VCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQK  223 (289)
Q Consensus       157 ~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y-~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~  223 (289)
                      ...+..+++++.+.|-         |++ ..|+|=+++|+|.+.+.+||-+|      +.+|++....
T Consensus       204 ~~~F~~RRKtl~n~l~---------~~~~~~~~l~~~~i~~~~R~e~ls~~~------f~~L~~~l~~  256 (259)
T COG0030         204 KAAFSQRRKTLRNNLK---------NLFGLEEVLEAAGIDPNARAENLSPED------FLKLANALKG  256 (259)
T ss_pred             HHHHHHHHHHHHHHHH---------HHHHHHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHHHH
T ss_conf             9998600688999877---------541199999866998113956599999------9999998764


No 65 
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=51.68  E-value=18  Score=16.62  Aligned_cols=17  Identities=12%  Similarity=-0.027  Sum_probs=12.2

Q ss_pred             HHHCCCCCCCCCCCHHH
Q ss_conf             87178778312222001
Q gi|254780625|r  191 RAKLSPIRKTRSLIQNN  207 (289)
Q Consensus       191 ~a~I~P~~~~~~Ls~~e  207 (289)
                      .-++++.+|..+|++++
T Consensus       321 ~~~~~~d~P~~~L~~~~  337 (1809)
T PRK00635        321 TLNFSLSTPWKDLSPEI  337 (1809)
T ss_pred             HCCCCCCCCHHHCCHHH
T ss_conf             76989899928799999


No 66 
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=50.70  E-value=8  Score=18.94  Aligned_cols=23  Identities=22%  Similarity=0.544  Sum_probs=13.3

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      .| +.||....-   -....+.||.|+
T Consensus        72 ~C-~~C~~~~~~---~~~~~~~CP~Cg   94 (114)
T PRK03681         72 WC-ETCQQYVTL---LTQRVRRCPQCH   94 (114)
T ss_pred             EC-CCCCCEEEE---CCCCCCCCCCCC
T ss_conf             96-559985540---677677390883


No 67 
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.53  E-value=7.8  Score=18.99  Aligned_cols=22  Identities=18%  Similarity=0.777  Sum_probs=12.2

Q ss_pred             CCCCCCCCEEEEEEECCCCEE-ECCCCC
Q ss_conf             107877887899998781206-387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTF-YCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty-~Cp~CQ  288 (289)
                      .| +.||....-.    ...| -||.|+
T Consensus        73 ~C-~~Cg~~f~~~----~~~~~~CP~Cg   95 (117)
T PRK00564         73 EC-KDCSHVFKPN----ALDYGVCEKCH   95 (117)
T ss_pred             EC-CCCCCEEECC----CCCCCCCCCCC
T ss_conf             91-0089988227----74068590988


No 68 
>pfam10263 SprT-like SprT-like family. This family represents a domain found in eukaryotes and prokaryotes. The domain contains a characteristic motif of the zinc metallopeptidases. This family includes the bacterial SprT protein.
Probab=48.37  E-value=19  Score=16.54  Aligned_cols=26  Identities=31%  Similarity=0.795  Sum_probs=20.7

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      .| ..||..+.+...-++..|.|+.|+
T Consensus       121 ~C-~~C~~~~~r~~~~~~~~y~C~~C~  146 (153)
T pfam10263       121 RC-TSCGQLYPRKRRIRRHRYRCGRCG  146 (153)
T ss_pred             EC-CCCCCEEEEEEECCCCCEECCCCC
T ss_conf             99-999887357874157557755689


No 69 
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit; InterPro: IPR011883 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=47.50  E-value=9  Score=18.61  Aligned_cols=32  Identities=19%  Similarity=0.510  Sum_probs=21.7

Q ss_pred             ECCCCCCCCCCCCCEEEEE--EECC---CCEEECCCCC
Q ss_conf             5738771078778878999--9878---1206387767
Q gi|254780625|r  256 YGKTGEPCLSNCGQMIRRI--VQAG---RSTFYCTYCQ  288 (289)
Q Consensus       256 y~r~g~~C~~~CG~~I~~~--~~~g---R~ty~Cp~CQ  288 (289)
                      +-+.--.| ||||..=-+.  .+|.   |..|+|-.|.
T Consensus       107 ~~~~~v~C-PRCgS~~T~~~s~FG~TaCKaLy~C~aC~  143 (152)
T TIGR02159       107 LEPPSVQC-PRCGSADTTITSEFGPTACKALYRCRACK  143 (152)
T ss_pred             CCCCCCCC-CCCCCCCEEEECCCCCHHHHHHHHCCCCC
T ss_conf             46877788-88775211333034331446754110247


No 70 
>TIGR02483 PFK_mixed phosphofructokinase; InterPro: IPR012829    Members of this family that are characterised, save one, are phosphofructokinases dependent on pyrophosphate (2.7.1.90 from EC) rather than ATP (2.7.1.11 from EC). The exception is one of three phosphofructokinases from Streptomyces coelicolor. Family members are both bacterial and archaeal.; GO: 0005524 ATP binding, 0008443 phosphofructokinase activity, 0006002 fructose 6-phosphate metabolic process, 0006096 glycolysis.
Probab=47.06  E-value=9.2  Score=18.53  Aligned_cols=22  Identities=27%  Similarity=0.324  Sum_probs=17.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             6543564136899999987178
Q gi|254780625|r  174 QKIVAGIGNIYVCEALWRAKLS  195 (289)
Q Consensus       174 Q~~iaGIGN~y~~EiLf~a~I~  195 (289)
                      ...+.||||++|+||=-+.++.
T Consensus       259 ~~RLGGiG~~lA~~i~~rtg~E  280 (339)
T TIGR02483       259 HVRLGGIGNWLAEEIERRTGIE  280 (339)
T ss_pred             CEECCCHHHHHHHHHHHHCCCC
T ss_conf             5001321889999999871982


No 71 
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=46.52  E-value=17  Score=16.75  Aligned_cols=26  Identities=23%  Similarity=0.539  Sum_probs=18.1

Q ss_pred             EEECCCCCCCCCCCCCEEEEEEECCCC
Q ss_conf             665738771078778878999987812
Q gi|254780625|r  254 SVYGKTGEPCLSNCGQMIRRIVQAGRS  280 (289)
Q Consensus       254 ~vy~r~g~~C~~~CG~~I~~~~~~gR~  280 (289)
                      .+|--++.-| |.||+++.+...-.++
T Consensus       147 ~~f~~~~~~C-p~CG~~~~~~~~~~~~  172 (177)
T COG1439         147 RIFPEPKDFC-PICGSPLKRKRVKSRS  172 (177)
T ss_pred             EECCCCCCCC-CCCCCCEEEEEECHHH
T ss_conf             2508988807-7899911785500000


No 72 
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=45.91  E-value=8.6  Score=18.75  Aligned_cols=48  Identities=15%  Similarity=0.016  Sum_probs=23.9

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             43564136899999987178778312222001015899999999878876765421
Q gi|254780625|r  176 IVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDA  231 (289)
Q Consensus       176 ~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~  231 (289)
                      .|+=||=+=..|++-..+++..      ..++  ..+-..++.+.|++.+.+.-+.
T Consensus       415 hFsTIGi~GmnEa~~~~g~~~~------~~~e--g~~fa~~vL~~mr~~~~~~qee  462 (625)
T PRK08271        415 QFLTIGINGMWEAAEFQGLTVG------YNEE--GEAFVQEVLKVIYEANEEASKE  462 (625)
T ss_pred             CCCCCCHHHHHHHHHHCCCCCC------CCHH--HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             2766304059999997599878------9989--9999999999999999999999


No 73 
>TIGR00387 glcD glycolate oxidase, subunit GlcD; InterPro: IPR004490 The glc locus of Escherichia coli encodes the subunits of glycolate oxidase and the glc regulator protein. The subunit GlcD is similar to that of several D-lactate dehydrogenases, including that of E. coli. Glycolate oxidase has been found to have some D-lactate dehydrogenase activity.; GO: 0008891 glycolate oxidase activity, 0009339 glycolate oxidase complex.
Probab=45.06  E-value=23  Score=15.97  Aligned_cols=80  Identities=21%  Similarity=0.148  Sum_probs=48.0

Q ss_pred             CCCCCC----CCCCCCCCHH-----HHHHH---HHHCCC--CCCCEEEECCCCC-CCCCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             235655----5332211106-----78887---420145--4210011126543-5641368999999871787783122
Q gi|254780625|r  138 PLRTLG----PEPADNSFNA-----IYLTH---QFHKKN--SNLKNALLNQKIV-AGIGNIYVCEALWRAKLSPIRKTRS  202 (289)
Q Consensus       138 ~l~~lG----pD~l~~~~~~-----~~~~~---~l~~~~--~~Ik~~LlDQ~~i-aGIGN~y~~EiLf~a~I~P~~~~~~  202 (289)
                      .+++++    |+.+-.|.+-     ..+.+   .|..+.  ..|.++-.- .++ +|=||           +||.-..+.
T Consensus       296 a~~~~~Gtkk~~~~~eD~tVPR~~Lp~~l~~I~~ia~Ky~~~~~ANF~i~-~~gHaGDGN-----------lHP~i~~d~  363 (437)
T TIGR00387       296 AASKLSGTKKPKYLIEDGTVPRSKLPEVLKGIADIASKYDDLAVANFKIF-IVGHAGDGN-----------LHPLILTDE  363 (437)
T ss_pred             HHHHHHCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEE-EEEECCCCC-----------CCCEEECCC
T ss_conf             99874055575525623300456778999999999975186345402677-887417787-----------543222378


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             220010158999999998788767654218875
Q gi|254780625|r  203 LIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSS  235 (289)
Q Consensus       203 Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~  235 (289)
                      =.      ++.++|-.+..-+||+.|++.|||-
T Consensus       364 ~~------~~~~er~e~~~~EI~e~a~~LGGti  390 (437)
T TIGR00387       364 ED------KGEMERVEELGGEILELAIELGGTI  390 (437)
T ss_pred             CC------HHHHHHHHHHHHHHHHHHHHCCCCE
T ss_conf             86------6689999999999999872227705


No 74 
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=44.40  E-value=21  Score=16.24  Aligned_cols=23  Identities=30%  Similarity=0.703  Sum_probs=16.3

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCC
Q ss_conf             71078778878999987812063877
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTY  286 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~  286 (289)
                      ..| |.||+++.+.  .+...++|++
T Consensus       405 ~~C-P~C~s~l~~~--~~~~~~~C~N  427 (668)
T PRK07956        405 THC-PVCGSELVRE--EGEAVLRCTN  427 (668)
T ss_pred             CCC-CCCCCEEEEE--CCCEEEECCC
T ss_conf             787-6779857993--6963787789


No 75 
>pfam03119 DNA_ligase_ZBD NAD-dependent DNA ligase C4 zinc finger domain. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor. This family is a small zinc binding motif that is presumably DNA binding. IT is found only in NAD dependent DNA ligases.
Probab=44.34  E-value=16  Score=17.02  Aligned_cols=21  Identities=33%  Similarity=0.733  Sum_probs=16.6

Q ss_pred             CCCCCCCEEEEEEECCCCEEECCC
Q ss_conf             078778878999987812063877
Q gi|254780625|r  263 CLSNCGQMIRRIVQAGRSTFYCTY  286 (289)
Q Consensus       263 C~~~CG~~I~~~~~~gR~ty~Cp~  286 (289)
                      | |.||+.+.+.  .+...++|+.
T Consensus         2 C-P~C~s~l~r~--~~ev~~rC~n   22 (27)
T pfam03119         2 C-PVCGSPLVRE--EGEVDIRCTN   22 (27)
T ss_pred             C-CCCCCEEECC--CCCEEEECCC
T ss_conf             8-8898974856--8978688889


No 76 
>pfam08394 Arc_trans_TRASH Archaeal TRASH domain. This region is found in the C-terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module.
Probab=44.19  E-value=4.9  Score=20.29  Aligned_cols=23  Identities=26%  Similarity=0.663  Sum_probs=11.3

Q ss_pred             CCCEEE----EEEECCCCEEE-CCCCCC
Q ss_conf             788789----99987812063-877679
Q gi|254780625|r  267 CGQMIR----RIVQAGRSTFY-CTYCQK  289 (289)
Q Consensus       267 CG~~I~----~~~~~gR~ty~-Cp~CQk  289 (289)
                      ||..|.    ..++++|.-|. ||+||+
T Consensus         4 CG~eI~g~Pi~~k~~nrvYy~CC~tC~~   31 (37)
T pfam08394         4 CGKEIKGEPITYKVKNRVYYVCCPTCLS   31 (37)
T ss_pred             CCCCCCCCCEEEEECCEEEEEECHHHHH
T ss_conf             6775059957999757799998768889


No 77 
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=44.19  E-value=24  Score=15.88  Aligned_cols=29  Identities=7%  Similarity=-0.156  Sum_probs=21.6

Q ss_pred             CCCHHHHHHHHHH---HHCCCCCCCCCCCHHH
Q ss_conf             6413689999998---7178778312222001
Q gi|254780625|r  179 GIGNIYVCEALWR---AKLSPIRKTRSLIQNN  207 (289)
Q Consensus       179 GIGN~y~~EiLf~---a~I~P~~~~~~Ls~~e  207 (289)
                      .-.+||.....-.   .++++.+|.++|++++
T Consensus       315 ~~~~~~~~~L~~~a~~~gf~~d~P~~dLs~e~  346 (944)
T PRK00349        315 KSSSYYFQMLKSLAEHYGFDLDTPWKDLPEEV  346 (944)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCCCHHHCCHHH
T ss_conf             87648999999999975998678146699999


No 78 
>pfam02591 DUF164 Putative zinc ribbon domain.
Probab=43.90  E-value=4.5  Score=20.57  Aligned_cols=30  Identities=20%  Similarity=0.559  Sum_probs=20.1

Q ss_pred             CCCCCCCCCCCEEEEEEE----CCCCEEECCCCCC
Q ss_conf             877107877887899998----7812063877679
Q gi|254780625|r  259 TGEPCLSNCGQMIRRIVQ----AGRSTFYCTYCQK  289 (289)
Q Consensus       259 ~g~~C~~~CG~~I~~~~~----~gR~ty~Cp~CQk  289 (289)
                      .+..| .-|+..|.-..+    .+....+||.|+|
T Consensus        21 ~~~~C-~gC~~~i~~q~~~~l~~~~~i~~Cp~CgR   54 (56)
T pfam02591        21 EGGAC-GGCRMKLPPQTLNELRKGDEIVRCPHCGR   54 (56)
T ss_pred             CCCCC-CCCCEECCHHHHHHHHCCCCEEECCCCCC
T ss_conf             59956-76874739999999986998579979886


No 79 
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.83  E-value=16  Score=16.95  Aligned_cols=27  Identities=19%  Similarity=0.548  Sum_probs=16.8

Q ss_pred             CCCCCCCCCEEEEEEECC----CCEEECCCCCC
Q ss_conf             710787788789999878----12063877679
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAG----RSTFYCTYCQK  289 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~g----R~ty~Cp~CQk  289 (289)
                      ..| |.|+..- ..+.|+    ..-|-|+.|++
T Consensus        31 ~~c-P~C~s~~-~~k~g~~~~~~qRyrC~~C~~   61 (129)
T COG3677          31 VNC-PRCKSSN-VVKIGGIRRGHQRYKCKSCGS   61 (129)
T ss_pred             CCC-CCCCCCC-EEEECCCCCCCCCCCCCCCCC
T ss_conf             768-9888511-023777426652535687586


No 80 
>PRK08174 DNA topoisomerase III; Validated
Probab=43.62  E-value=24  Score=15.82  Aligned_cols=29  Identities=21%  Similarity=0.572  Sum_probs=17.0

Q ss_pred             CCCCCCCCCCCCEEEEEEECC-CCEEEC---CCCC
Q ss_conf             387710787788789999878-120638---7767
Q gi|254780625|r  258 KTGEPCLSNCGQMIRRIVQAG-RSTFYC---TYCQ  288 (289)
Q Consensus       258 r~g~~C~~~CG~~I~~~~~~g-R~ty~C---p~CQ  288 (289)
                      ..+.+| |.||..+..- .+. ..-|=|   |.|-
T Consensus       613 ~~~~~C-P~Cg~~l~~r-~~k~G~F~gCs~yP~Ck  645 (670)
T PRK08174        613 PPSPAC-PQCGAPTRQR-NGKSGPFWGCSRYPDCK  645 (670)
T ss_pred             CCCCCC-CCCCCEEEEE-ECCCCCEEECCCCCCCC
T ss_conf             989978-7899750367-06887378699998888


No 81 
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=42.76  E-value=17  Score=16.85  Aligned_cols=25  Identities=20%  Similarity=0.656  Sum_probs=17.2

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             7107877887899998781206387767
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      -.| |.||.+.  .+=.+..+|.|..|-
T Consensus        36 ~~C-p~C~~~~--VkR~a~GIW~C~kCg   60 (89)
T COG1997          36 HVC-PFCGRTT--VKRIATGIWKCRKCG   60 (89)
T ss_pred             CCC-CCCCCCC--EEEECCCEEECCCCC
T ss_conf             769-9789740--455236758717888


No 82 
>TIGR02890 spore_yteA sporulation protein, yteA family; InterPro: IPR014240   This entry contains predicted regulatory proteins that are found in nearly every species of the endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria), with the exception of Clostridium perfringens. Some (but not all) of these proteins contain an unusual DksA/TraR C4-type zinc finger, where only one of the four key Cys residues is conserved. All members of this entry share an additional C-terminal domain. The function of proteins in this family is unknown. YteA is found in mature spores of Bacillus subtilis and its expression appeasr to be regulated by sigma-K ..
Probab=42.57  E-value=9.1  Score=18.57  Aligned_cols=107  Identities=21%  Similarity=0.295  Sum_probs=55.7

Q ss_pred             HHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHC---CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH---
Q ss_conf             78887420145421001112654356413689999998717---877831222200101589999999987887676---
Q gi|254780625|r  154 IYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKL---SPIRKTRSLIQNNGTPKDILYKLIQEIQKVLID---  227 (289)
Q Consensus       154 ~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I---~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~---  227 (289)
                      ..|++.|...|..+=..|..=..=-|||.....|..=.=-.   ||.=.+++|=+.|..     ..|...+...|.+   
T Consensus         4 ~~lK~~L~~~K~~l~~~~~~~~~~~~~~~~~~~e~~gELS~YDNHPaD~ATElyEReKD-----~AL~~~~~~~L~~Ie~   78 (167)
T TIGR02890         4 AELKNALLQEKEELEQRLKQMNKEDGLGEASQRESVGELSSYDNHPADLATELYEREKD-----IALKEHEKRELREIEH   78 (167)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH-----HHHHHHHHHHHHHHHH
T ss_conf             88999999999999999998752122100023332111001368853344304577532-----6889999999988999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEE-CCCCEEECCCCCC
Q ss_conf             5421887553111677877874133166573877107877887899998-7812063877679
Q gi|254780625|r  228 AIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQ-AGRSTFYCTYCQK  289 (289)
Q Consensus       228 a~~~gG~~~~~~~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~-~gR~ty~Cp~CQk  289 (289)
                      |+..-            ..|       -||    -| .+||.+|-.+.. +-=+|-.|-.||+
T Consensus        79 AL~~i------------e~G-------tYG----IC-e~cG~~Ip~ERLEA~P~A~~c~~~~~  117 (167)
T TIGR02890        79 ALQKI------------ENG-------TYG----IC-EVCGKPIPYERLEALPTATTCVECQN  117 (167)
T ss_pred             HHHHH------------HCC-------CCE----EE-CCCCCCCCHHHHHCCHHHHHHHHHHC
T ss_conf             99998------------578-------970----00-44878798444200417889998722


No 83 
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=41.97  E-value=16  Score=17.08  Aligned_cols=24  Identities=29%  Similarity=0.822  Sum_probs=17.0

Q ss_pred             CCCCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf             87710787788789999878120638776
Q gi|254780625|r  259 TGEPCLSNCGQMIRRIVQAGRSTFYCTYC  287 (289)
Q Consensus       259 ~g~~C~~~CG~~I~~~~~~gR~ty~Cp~C  287 (289)
                      ++.+| |.||.++.+   . -+=|.|..|
T Consensus       927 dap~C-peCGs~mvR---n-GgC~kC~~C  950 (957)
T PRK06556        927 DAPLC-PTCGTIMVR---N-GSCYVCEGC  950 (957)
T ss_pred             CCCCC-CCCCCCEEE---C-CCCCCCCCC
T ss_conf             89878-755765378---6-874323568


No 84 
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).  During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=41.80  E-value=9.9  Score=18.35  Aligned_cols=17  Identities=6%  Similarity=-0.107  Sum_probs=10.6

Q ss_pred             HHHCCCCCCCCCCCHHH
Q ss_conf             87178778312222001
Q gi|254780625|r  191 RAKLSPIRKTRSLIQNN  207 (289)
Q Consensus       191 ~a~I~P~~~~~~Ls~~e  207 (289)
                      +-+++..+|+.+|++++
T Consensus       351 ~~~Fdl~~P~~~L~~~~  367 (956)
T TIGR00630       351 HYGFDLDTPWKDLPEEV  367 (956)
T ss_pred             HHCCCHHHHHHCCCHHH
T ss_conf             72888646754158667


No 85 
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=41.68  E-value=17  Score=16.83  Aligned_cols=22  Identities=18%  Similarity=0.679  Sum_probs=16.6

Q ss_pred             CCCCCEEE------EEEECCCCEEECCC
Q ss_conf             87788789------99987812063877
Q gi|254780625|r  265 SNCGQMIR------RIVQAGRSTFYCTY  286 (289)
Q Consensus       265 ~~CG~~I~------~~~~~gR~ty~Cp~  286 (289)
                      |+||.+|.      +..++|.+=|||..
T Consensus         6 PVcgm~v~~~~a~~k~~Y~GktYYFcse   33 (53)
T COG3350           6 PVCGMKVDNENAEYKSSYGGKTYYFCSE   33 (53)
T ss_pred             CCCCCCCCCCCCCEEEEECCEEEEEECH
T ss_conf             7767652665551058758878997089


No 86 
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=40.28  E-value=11  Score=18.03  Aligned_cols=23  Identities=26%  Similarity=0.592  Sum_probs=13.8

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             7107877887899998781206387767
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      ..| ..|+..+.....    .|+||+|.
T Consensus        71 ~~C-~~C~~~~~~e~~----~~~CP~C~   93 (115)
T COG0375          71 CWC-LDCGQEVELEEL----DYRCPKCG   93 (115)
T ss_pred             EEE-CCCCCEECCHHH----EEECCCCC
T ss_conf             894-239976021553----10888999


No 87 
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=39.56  E-value=23  Score=15.93  Aligned_cols=73  Identities=12%  Similarity=0.142  Sum_probs=51.0

Q ss_pred             CCEECCCCCCHHHCCCC-CCCCCCCC-CC-----CCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             41001455301005323-56555332-21-----1106788874201454210011126543564136899999987178
Q gi|254780625|r  123 GFMDLVETSLKYQYPPL-RTLGPEPA-DN-----SFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLS  195 (289)
Q Consensus       123 G~~~~~~~~~~~~~~~l-~~lGpD~l-~~-----~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~  195 (289)
                      |.+.++-..++  .|+. ..+-||+. +|     ++|...+.+.+.++-..+.....|-+-|.+.-.=.-.|.|-.+|.+
T Consensus       366 Gvig~i~~qeD--MPFt~dGi~PDIIiNPHa~PSRMTIGqllE~l~gK~~~~~G~~~d~tpF~~~~~~~~~~~L~~~g~~  443 (599)
T TIGR03670       366 GVIGMIVPQED--MPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFK  443 (599)
T ss_pred             CEEEEECCHHH--CCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEECCCCCCCHHHHHHHHHHHCCC
T ss_conf             33320126753--9978899987089899878765508999999989999966984224789999999999999981999


Q ss_pred             CC
Q ss_conf             77
Q gi|254780625|r  196 PI  197 (289)
Q Consensus       196 P~  197 (289)
                      +.
T Consensus       444 ~~  445 (599)
T TIGR03670       444 PD  445 (599)
T ss_pred             CC
T ss_conf             88


No 88 
>pfam07191 DUF1407 Protein of unknown function (DUF1407). This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family have 8 highly conserved cysteine residues, which form two zinc ribbon domains.
Probab=38.65  E-value=3.6  Score=21.14  Aligned_cols=26  Identities=23%  Similarity=0.791  Sum_probs=20.8

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf             710787788789999878120638776
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYC  287 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~C  287 (289)
                      .-| |.|+.++++.+-=|-..|||.+|
T Consensus        31 a~C-P~C~~~Lq~LkACGAvdYfC~~c   56 (70)
T pfam07191        31 ALC-PDCHQELEVLKACGAVDYFCNHC   56 (70)
T ss_pred             EEC-CCCCCHHHHHHHCCCCCCCCCCC
T ss_conf             989-76243789987727602020679


No 89 
>PRK12860 transcriptional activator FlhC; Provisional
Probab=38.43  E-value=29  Score=15.31  Aligned_cols=84  Identities=23%  Similarity=0.357  Sum_probs=54.8

Q ss_pred             CCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             21001112654356413689999998717877831222200101589999999987887676542188755311167787
Q gi|254780625|r  166 NLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGS  245 (289)
Q Consensus       166 ~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~~~~g~  245 (289)
                      .|-..|+.+.-..||--++++==||.--+....-       +  |.-.+-|-|.     |..-++.|             
T Consensus        78 niY~~l~~~~~~~~i~A~ikaYrLYlEq~~~~~~-------e--pvLslTRAWt-----LvRF~dsg-------------  130 (189)
T PRK12860         78 NAYRFLVNEARCSGLDALTKGYRLYLEHCCATGT-------E--PVLSLTRAWT-----LVRFFDAG-------------  130 (189)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCC-------C--CHHHHHHHHH-----HHHHHHCC-------------
T ss_conf             9999999706985299999999999996535589-------7--1236888999-----99997458-------------


Q ss_pred             CCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             7874133166573877107877887899998781206387767
Q gi|254780625|r  246 IGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       246 ~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                        -    +     .=.+| ++||+.-......-...|-|.-||
T Consensus       131 --m----L-----~~~~C-~~CgG~FV~ha~d~~~~fvC~lC~  161 (189)
T PRK12860        131 --M----L-----QLARC-RRCGGKFVTHAHDLRHNFVCGLCQ  161 (189)
T ss_pred             --C----E-----EECCC-CCCCCCEECCCCCCCCCCCCCCCC
T ss_conf             --7----0-----00677-777881552235678887778988


No 90 
>TIGR01341 aconitase_1 aconitate hydratase 1; InterPro: IPR006249   Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop , . Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) . Below is a description of some of the multi-functional activities associated with different aconitases.   Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway . The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA.    Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) , . As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated .   IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis . Although IRP2 is homologous to IRP1, IPR2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes . In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system.   Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica , . In S.enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress.   This entry represents bacterial aconitase A (AcnA), eukaryotic cytosolic aconitase (cAcn/IRP1), iron regulatory protein 2 (IRP2), and a few mitochondrial aconitases (certain mAcn proteins, but not the majority of these enzymes).   More information about these proteins can be found at Protein of the Month: Aconitase .; GO: 0051539 4 iron 4 sulfur cluster binding, 0008152 metabolic process.
Probab=37.97  E-value=11  Score=17.97  Aligned_cols=56  Identities=18%  Similarity=0.265  Sum_probs=35.2

Q ss_pred             HHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             78887420145421001112654356413689999998717877831222200101589999999987887676542188
Q gi|254780625|r  154 IYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGG  233 (289)
Q Consensus       154 ~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG  233 (289)
                      +.+.+++++-.      |.=-+|+||==|       |.+||||..|++=|-..                 .|.-||+.-|
T Consensus       514 ~~~e~AI~~Nd------L~~~aVLSGNRN-------FEGRIHPLvK~NyLASP-----------------PLVVAYALAG  563 (896)
T TIGR01341       514 EEVEEAIVKND------LVVVAVLSGNRN-------FEGRIHPLVKANYLASP-----------------PLVVAYALAG  563 (896)
T ss_pred             HHHHHHHHHCC------EEEEEEEECCCC-------CCCEECCCCCCCCCCCC-----------------HHHHHHHHCC
T ss_conf             88998966288------289998315546-------33201600123534572-----------------5798985148


Q ss_pred             CCCCCC
Q ss_conf             755311
Q gi|254780625|r  234 SSLRDY  239 (289)
Q Consensus       234 ~~~~~~  239 (289)
                      +..-|+
T Consensus       564 ~~~Inl  569 (896)
T TIGR01341       564 NVDINL  569 (896)
T ss_pred             CEEECC
T ss_conf             135545


No 91 
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=37.66  E-value=27  Score=15.54  Aligned_cols=75  Identities=11%  Similarity=0.109  Sum_probs=52.0

Q ss_pred             CCEECCCCCCHHHCCCCCCCCCCCC-CC-----CCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCC
Q ss_conf             4100145530100532356555332-21-----11067888742014542100111265435641368999999871787
Q gi|254780625|r  123 GFMDLVETSLKYQYPPLRTLGPEPA-DN-----SFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSP  196 (289)
Q Consensus       123 G~~~~~~~~~~~~~~~l~~lGpD~l-~~-----~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P  196 (289)
                      |.+.++-+.++.... -..+-||+. +|     ++|...+.+.+.++-..+.....|-+-|.+.-.-.-.|.|-.+|.++
T Consensus       372 Gvig~i~~~eDMPFt-~dGi~PDiIiNPH~~PSRMTIGqllE~l~gK~~~~~G~~~d~tpF~~~~~~~~~~~L~~~g~~~  450 (605)
T PRK07225        372 GVIGLIVPQEDMPFT-ESGVVPDLIINPHAIPSRMTIGHVLEMIGGKVGSLEGRRVDGTAFSGEPEEDLRESLKKLGFEH  450 (605)
T ss_pred             CEEECCCCCCCCCCC-CCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHCCCC
T ss_conf             312110254039938-8999871888988687656089999998778887449635307889988899999999838998


Q ss_pred             CC
Q ss_conf             78
Q gi|254780625|r  197 IR  198 (289)
Q Consensus       197 ~~  198 (289)
                      .-
T Consensus       451 ~G  452 (605)
T PRK07225        451 TG  452 (605)
T ss_pred             CC
T ss_conf             99


No 92 
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308   These are the polypeptide chains of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm.
Probab=37.40  E-value=11  Score=18.06  Aligned_cols=13  Identities=8%  Similarity=0.302  Sum_probs=6.4

Q ss_pred             CCCCCCCCCCEEE
Q ss_conf             1001525532799
Q gi|254780625|r   69 SIIVHLGMSGSFI   81 (289)
Q Consensus        69 ~L~~HlgM~G~~~   81 (289)
                      +|+.-.|..|.|.
T Consensus       544 il~~s~G~~~~~n  556 (1264)
T TIGR01405       544 ILVASQGLENKLN  556 (1264)
T ss_pred             HHCCCCCCCCCCC
T ss_conf             1002778886547


No 93 
>TIGR02661 MauD methylamine dehydrogenase accessory protein MauD; InterPro: IPR013478    MauD appears critical to proper formation of the small subunit of methylamine dehydrogenase, which has both an unusual tryptophan tryptophylquinone cofactor and multiple disulphide bonds. MauD shares sequence similarity, including a CPxC motif, with a number of thiol:disulphide interchange proteins. In MauD mutants, the small subunit apparently does not form properly and is rapidly degraded .; GO: 0030416 methylamine metabolic process.
Probab=37.31  E-value=9.7  Score=18.39  Aligned_cols=11  Identities=18%  Similarity=0.247  Sum_probs=5.0

Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999878
Q gi|254780625|r  212 DILYKLIQEIQ  222 (289)
Q Consensus       212 ~~~~~L~~~i~  222 (289)
                      +.++.|+++++
T Consensus       169 EHlESLlEa~r  179 (189)
T TIGR02661       169 EHLESLLEADR  179 (189)
T ss_pred             HHHHHHHHHCC
T ss_conf             88999886200


No 94 
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=36.98  E-value=15  Score=17.24  Aligned_cols=22  Identities=23%  Similarity=0.605  Sum_probs=12.4

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      -| +.||....-.    ...+.||.|+
T Consensus        72 ~C-~~C~~~~~~~----~~~~~CP~Cg   93 (113)
T PRK12380         72 WC-WDCSQVVEIH----QHDAQCPHCH   93 (113)
T ss_pred             EC-CCCCCEEECC----CCCCCCCCCC
T ss_conf             96-5599987247----8888390697


No 95 
>pfam08271 TF_Zn_Ribbon TFIIB zinc-binding. The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.
Probab=36.77  E-value=26  Score=15.63  Aligned_cols=10  Identities=40%  Similarity=1.032  Sum_probs=4.6

Q ss_pred             CCCEEECCCC
Q ss_conf             8120638776
Q gi|254780625|r  278 GRSTFYCTYC  287 (289)
Q Consensus       278 gR~ty~Cp~C  287 (289)
                      .|.-+.|+.|
T Consensus        16 ~~Ge~vC~~C   25 (40)
T pfam08271        16 ERGEYVCTEC   25 (40)
T ss_pred             CCCCEECCCC
T ss_conf             7897870579


No 96 
>pfam01155 HypA Hydrogenase expression/synthesis hypA family. Four conserved cysteines lie either side of the least conserved region.
Probab=36.17  E-value=16  Score=16.96  Aligned_cols=22  Identities=32%  Similarity=0.774  Sum_probs=12.7

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      .| +.||..-.-.    ...+.||.|+
T Consensus        71 ~C-~~Cg~~~~~~----~~~~~CP~Cg   92 (112)
T pfam01155        71 RC-RDCGQEFELE----ERFFRCPKCG   92 (112)
T ss_pred             EC-CCCCCEECCC----CCCCCCCCCC
T ss_conf             99-8999714257----7767990897


No 97 
>PRK12722 transcriptional activator FlhC; Provisional
Probab=35.40  E-value=33  Score=15.01  Aligned_cols=84  Identities=20%  Similarity=0.381  Sum_probs=57.0

Q ss_pred             CCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             21001112654356413689999998717877831222200101589999999987887676542188755311167787
Q gi|254780625|r  166 NLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGS  245 (289)
Q Consensus       166 ~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~~~~g~  245 (289)
                      .|-..|..+.-+.||--++++==||.--+.+...-.-||         +-|-|.-++-     ++.|             
T Consensus        78 n~y~~l~~~~~~~~i~alvkaYrLYlE~~~~~~~ep~Ls---------~TRAWtLvrF-----~dsg-------------  130 (185)
T PRK12722         78 NIYRFLLKTGLCSGIDAVIKAYRLYLEQCPLAEEEPLLS---------LTRAWTLVRF-----VDSG-------------  130 (185)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEE---------HHHHHHHHHH-----HCCC-------------
T ss_conf             999999981699849999999999999744478985321---------5789999999-----6168-------------


Q ss_pred             CCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             7874133166573877107877887899998781206387767
Q gi|254780625|r  246 IGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       246 ~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                        -    +.     =..| ++||+.-......-...|-|+-||
T Consensus       131 --m----L~-----lt~C-~~CgG~Fv~ha~~~~~~fvC~lC~  161 (185)
T PRK12722        131 --M----LQ-----LSSC-NCCGGHFVTHAHDPHGSFVCGLCQ  161 (185)
T ss_pred             --C----EE-----ECCC-CCCCCCEEECCCCCCCCCCCCCCC
T ss_conf             --6----65-----3356-646880253014678886068888


No 98 
>KOG2169 consensus
Probab=35.08  E-value=17  Score=16.81  Aligned_cols=12  Identities=42%  Similarity=0.952  Sum_probs=10.7

Q ss_pred             CCCEEECCCCCC
Q ss_conf             812063877679
Q gi|254780625|r  278 GRSTFYCTYCQK  289 (289)
Q Consensus       278 gR~ty~Cp~CQk  289 (289)
                      .+.||.||.|||
T Consensus       342 ~~pTW~CPVC~~  353 (636)
T KOG2169         342 QKPTWRCPVCQK  353 (636)
T ss_pred             CCCEEECCCCCC
T ss_conf             687134555766


No 99 
>pfam01927 DUF82 Protein of unknown function DUF82. This prokaryotic protein family has no known function. The protein contains four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=34.85  E-value=15  Score=17.20  Aligned_cols=27  Identities=15%  Similarity=0.518  Sum_probs=17.2

Q ss_pred             CCCCCCCCEEEEEEEC-------------CCCEEECCCCCC
Q ss_conf             1078778878999987-------------812063877679
Q gi|254780625|r  262 PCLSNCGQMIRRIVQA-------------GRSTFYCTYCQK  289 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~-------------gR~ty~Cp~CQk  289 (289)
                      -| +.|++++..+.-.             ...-|.||.|.|
T Consensus        92 RC-~~CN~~L~~v~k~~v~~~vp~~v~~~~~~F~~C~~Cgk  131 (146)
T pfam01927        92 RC-LKCNGPLEPVSKEEVAGRVPPYVYERYDEFWRCPKCGR  131 (146)
T ss_pred             CC-CCCCCCCEECCHHHHHHHCCCHHHHCCCCEEECCCCCC
T ss_conf             56-56798995818789854567202225881477899999


No 100
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=34.85  E-value=33  Score=14.95  Aligned_cols=80  Identities=14%  Similarity=0.225  Sum_probs=34.4

Q ss_pred             CCHHHHHHHHHHCC-------CCCCCEEEECCCCC---------CCCCHHHHHHHH---HHHHCCCC------CCCCCCC
Q ss_conf             11067888742014-------54210011126543---------564136899999---98717877------8312222
Q gi|254780625|r  150 SFNAIYLTHQFHKK-------NSNLKNALLNQKIV---------AGIGNIYVCEAL---WRAKLSPI------RKTRSLI  204 (289)
Q Consensus       150 ~~~~~~~~~~l~~~-------~~~Ik~~LlDQ~~i---------aGIGN~y~~EiL---f~a~I~P~------~~~~~Ls  204 (289)
                      .||...+.+.|...       ..+|=..|+|-.++         .=+|- ...+.|   |-.=+++.      ...+.+.
T Consensus       478 RYTEAsLIk~ME~~GIGRPSTyA~II~tL~~R~YV~~e~k~l~PT~lG~-~V~~~L~~~f~~ivd~~fTA~mE~~LD~Ia  556 (864)
T PRK06319        478 RFTEASLVKELEKSGIGRPSTYATIMNKIQSREYTLKENQRLRPTELGK-IISQFLETNFPRIMDIGFTALMEDELELIA  556 (864)
T ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCEEEECCEECCHHHHH-HHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             9888999999971799950106999998986798810198868007899-999999986464348531789998899997


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00101589999999987887676542
Q gi|254780625|r  205 QNNGTPKDILYKLIQEIQKVLIDAID  230 (289)
Q Consensus       205 ~~e~~~~~~~~~L~~~i~~vl~~a~~  230 (289)
                      +.+..-+..+...|..-...+..+.+
T Consensus       557 ~G~~~w~~vL~~F~~~f~~~l~~a~~  582 (864)
T PRK06319        557 DNKKPWKLLLQEFWEQFLPVVVTAEK  582 (864)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             38741999999999999999999986


No 101
>PRK11788 hypothetical protein; Provisional
Probab=34.70  E-value=24  Score=15.90  Aligned_cols=21  Identities=33%  Similarity=0.871  Sum_probs=14.2

Q ss_pred             CCCCCCCCCEEEEEEECCCC-EEECCCCCC
Q ss_conf             71078778878999987812-063877679
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRS-TFYCTYCQK  289 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~-ty~Cp~CQk  289 (289)
                      =.| ..||-.       +++ -|-||.|+.
T Consensus       355 Y~C-~~CGF~-------~~~~~WqCPsC~~  376 (389)
T PRK11788        355 YRC-RNCGFT-------ARTLYWHCPSCKA  376 (389)
T ss_pred             EEC-CCCCCC-------CCCEEEECCCCCC
T ss_conf             769-999998-------8831457909998


No 102
>pfam03811 Ins_element1 Insertion element protein.
Probab=34.63  E-value=22  Score=16.15  Aligned_cols=12  Identities=25%  Similarity=0.980  Sum_probs=6.0

Q ss_pred             CCCEEECCCCCC
Q ss_conf             812063877679
Q gi|254780625|r  278 GRSTFYCTYCQK  289 (289)
Q Consensus       278 gR~ty~Cp~CQk  289 (289)
                      |.--|+|..|.|
T Consensus        26 G~QRYrC~~C~r   37 (88)
T pfam03811        26 GHQRYRCRHCRR   37 (88)
T ss_pred             CCCCEEECCCCC
T ss_conf             985777277895


No 103
>TIGR01206 lysW lysine biosynthesis protein LysW; InterPro: IPR005906    This very small, poorly characterised protein in Thermus thermophilus has been shown to be essential for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate.; GO: 0019878 lysine biosynthetic process via aminoadipic acid.
Probab=34.62  E-value=26  Score=15.61  Aligned_cols=23  Identities=22%  Similarity=0.394  Sum_probs=8.8

Q ss_pred             CCCCCEEEEEEECCCCEEECCCC
Q ss_conf             87788789999878120638776
Q gi|254780625|r  265 SNCGQMIRRIVQAGRSTFYCTYC  287 (289)
Q Consensus       265 ~~CG~~I~~~~~~gR~ty~Cp~C  287 (289)
                      |.||+.|+-...-=...-.|+.|
T Consensus         6 P~~GA~i~L~N~ELg~lV~c~~~   28 (54)
T TIGR01206         6 PECGAEIELENPELGELVVCDEC   28 (54)
T ss_pred             CCCCCEEEECCCCCCCEEECCCC
T ss_conf             87675567408876616752899


No 104
>TIGR02642 phage_xxxx uncharacterized phage protein; InterPro: IPR013464    This uncharacterised protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus (strain YJ016), Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to the phage lambda antitermination protein Q..
Probab=34.54  E-value=13  Score=17.58  Aligned_cols=80  Identities=26%  Similarity=0.361  Sum_probs=39.6

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHEEE
Q ss_conf             43564136899999987178778312222001015899999999878876765421887553111677877874133166
Q gi|254780625|r  176 IVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSV  255 (289)
Q Consensus       176 ~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~~~~g~~g~~~~~~~v  255 (289)
                      .++|.-|-|+.  |-.++..      .|++++      +..|...| +.++.-|++...+++||.....  +        
T Consensus       126 ~~dgl~~~ik~--Le~~~~~------~l~~g~------I~~L~~~I-~~~~~~I~TE~~~Lrd~a~~~a--~--------  180 (270)
T TIGR02642       126 VVDGLKKEIKR--LEKEKAE------KLDDGE------IKLLEDEI-KALKAKIDTERRALRDYAVAKA--A--------  180 (270)
T ss_pred             HHHHHHHHHHH--HHHHHHH------HCCCCH------HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH--H--------
T ss_conf             77423789999--9999986------358233------78999999-9998776777888999999987--4--------


Q ss_pred             ECCCCCCCCCCCCCEEEEEEECCCCE-EECCCCC
Q ss_conf             57387710787788789999878120-6387767
Q gi|254780625|r  256 YGKTGEPCLSNCGQMIRRIVQAGRST-FYCTYCQ  288 (289)
Q Consensus       256 y~r~g~~C~~~CG~~I~~~~~~gR~t-y~Cp~CQ  288 (289)
                         .-..| |+|-++    ...-|+- --|++|.
T Consensus       181 ---~~~~C-P~C~Gt----g~~~~~~P~~C~~C~  206 (270)
T TIGR02642       181 ---ESRKC-PRCRGT----GLRLRRQPEECDKCA  206 (270)
T ss_pred             ---HCCCC-CCCCCC----CCCCCCCCCCCCCCC
T ss_conf             ---14887-986566----788897788777778


No 105
>cd02967 mauD Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for the biosynthesis of methylamine dehydrogenase (MADH), the enzyme that catalyzes the oxidation of methylamine and other primary amines. MADH possesses an alpha2beta2 subunit structure; the alpha subunit is also referred to as the large subunit. Each beta (small) subunit contains a tryptophan tryptophylquinone (TTQ) prosthetic group. Accessory proteins are essential for the proper transport of MADH to the periplasm, TTQ synthesis and the formation of several structural disulfide bonds. Bacterial mutants containing an insertion on the mauD gene were unable to grow on methylamine as a sole carbon source, were found to lack the MADH small subunit and had decreased amounts of the MADH large subunit.
Probab=34.37  E-value=8.4  Score=18.81  Aligned_cols=23  Identities=9%  Similarity=-0.036  Sum_probs=11.1

Q ss_pred             HHCCCEEEEEEE-CCEEEEEEECC
Q ss_conf             728988999960-53089995035
Q gi|254780625|r   44 ATRGKKIIDVSR-RAKYLLIELEG   66 (289)
Q Consensus        44 ~L~G~~I~~v~r-~GK~l~l~l~~   66 (289)
                      .|.|+++.=-.- -||..++.|-.
T Consensus         7 ~ldG~~v~L~~~~~gk~vll~Fwa   30 (114)
T cd02967           7 TIDGAPVRIGGISPGRPTLLFFLS   30 (114)
T ss_pred             CCCCCEEEECCCCCCCEEEEEEEC
T ss_conf             389986980553699849999978


No 106
>TIGR00395 leuS_arch leucyl-tRNA synthetase; InterPro: IPR004493   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 .    Leucyl tRNA synthetase (6.1.1.4 from EC) is an alpha monomer that belongs to class Ia. There are two different families of leucyl-tRNA synthetases. This family includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases.; GO: 0000166 nucleotide binding, 0004823 leucine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006429 leucyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=33.26  E-value=21  Score=16.30  Aligned_cols=40  Identities=20%  Similarity=0.280  Sum_probs=22.9

Q ss_pred             HHCCCEEEEEEECCEEEEEEECCCC--CCCCCCCCCCEEEEE
Q ss_conf             7289889999605308999503553--100152553279981
Q gi|254780625|r   44 ATRGKKIIDVSRRAKYLLIELEGNL--SIIVHLGMSGSFIIE   83 (289)
Q Consensus        44 ~L~G~~I~~v~r~GK~l~l~l~~~~--~L~~HlgM~G~~~~~   83 (289)
                      .+-|.|-+-|..---|..++.++..  -=.+.|--+|-|.+.
T Consensus       303 T~yG~Tn~wv~P~~~Yv~~~~~~e~etenGielienGiwi~~  344 (1109)
T TIGR00395       303 TVYGVTNVWVNPDITYVIAEVGGEKETENGIELIENGIWIVS  344 (1109)
T ss_pred             HHHCCEEEEECCCCCEEEEEECCCCCHHHHHHHHHCCHHHHH
T ss_conf             100755355557751689973374001200445542257778


No 107
>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=33.18  E-value=23  Score=15.95  Aligned_cols=43  Identities=21%  Similarity=0.217  Sum_probs=27.1

Q ss_pred             CCCCCHHHHHHHHHHHHCCCC-CCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             356413689999998717877-831222200101589999999987887
Q gi|254780625|r  177 VAGIGNIYVCEALWRAKLSPI-RKTRSLIQNNGTPKDILYKLIQEIQKV  224 (289)
Q Consensus       177 iaGIGN~y~~EiLf~a~I~P~-~~~~~Ls~~e~~~~~~~~~L~~~i~~v  224 (289)
                      +-|.| +++.|||-+||.||- +-+=...    ...+.+.-|.-.|.++
T Consensus       292 ~~GCG-~~R~~~L~R~G~~~SetIGyAFG----~GL~R~AM~LF~IPDI  335 (460)
T TIGR00469       292 LLGCG-LIRQDVLLRAGVKQSETIGYAFG----LGLDRLAMLLFDIPDI  335 (460)
T ss_pred             EECCC-HHHHHHHHHCCCCCCCCCCEEEC----CCHHHHHHHHHCCCCE
T ss_conf             51551-46778988458973332200001----0088999887348861


No 108
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=32.24  E-value=37  Score=14.68  Aligned_cols=49  Identities=14%  Similarity=0.077  Sum_probs=21.8

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             43564136899999987178778312222001015899999999878876765421
Q gi|254780625|r  176 IVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDA  231 (289)
Q Consensus       176 ~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~  231 (289)
                      .+.-||=+=-.|.+-.-....+.     .+++  ..+...++.+.+++.+.+.-+.
T Consensus       361 ~~~tIG~iGL~Ea~~~l~G~~~~-----e~~e--~~~f~~~il~~m~~~~~~~~~e  409 (555)
T cd01675         361 HTLTIGFIGLNEAAEALTGKGIG-----ESEE--AREFGIRILEHIRERADEFKEE  409 (555)
T ss_pred             EEEECHHHHHHHHHHHHCCCCCC-----CCHH--HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             36831485799999997099978-----9988--9999999999999999999898


No 109
>pfam04919 DUF655 Protein of unknown function, DUF655. This family includes several uncharacterized archaeal proteins.
Probab=32.11  E-value=37  Score=14.67  Aligned_cols=53  Identities=15%  Similarity=0.248  Sum_probs=38.7

Q ss_pred             HHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHH
Q ss_conf             678887420145421001112654356413689999998717877831222200
Q gi|254780625|r  153 AIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQN  206 (289)
Q Consensus       153 ~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~  206 (289)
                      .+.|.+-+ ++..||..-|--=..++||||-.+.+||=.-+-.|+..-.+|.+.
T Consensus        98 E~~FV~Ff-N~A~pit~rlH~leLLPGIGkK~~~~ileeR~~~~FeSFedi~~R  150 (181)
T pfam04919        98 EDRFVKFF-NEAEPITTRLHQLELLPGIGKKMMWAILEERKKKPFESFEDIKER  150 (181)
T ss_pred             HHHHHHHH-HCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             46766765-136874487888875334038999999999655998899999988


No 110
>KOG3053 consensus
Probab=32.00  E-value=13  Score=17.50  Aligned_cols=20  Identities=30%  Similarity=0.313  Sum_probs=9.4

Q ss_pred             CCCCEEEECCCCCCCCCHHH
Q ss_conf             42100111265435641368
Q gi|254780625|r  165 SNLKNALLNQKIVAGIGNIY  184 (289)
Q Consensus       165 ~~Ik~~LlDQ~~iaGIGN~y  184 (289)
                      +.++-+|+=.++-.=+||++
T Consensus       218 rv~CgAl~lPTis~~vG~~l  237 (293)
T KOG3053         218 RVLCGALLLPTISTIVGRVL  237 (293)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             33103343006999999999


No 111
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=31.94  E-value=33  Score=15.01  Aligned_cols=25  Identities=28%  Similarity=0.804  Sum_probs=16.0

Q ss_pred             CCCCCCCCEEEEEE---ECCCCEEECCCCC
Q ss_conf             10787788789999---8781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIV---QAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~---~~gR~ty~Cp~CQ  288 (289)
                      || | ||...+-.-   ..|-..--||.|-
T Consensus        24 PC-P-CGDRFeIsLeDl~~GE~VArCPSCS   51 (67)
T COG5216          24 PC-P-CGDRFEISLEDLRNGEVVARCPSCS   51 (67)
T ss_pred             CC-C-CCCEEEEEHHHHHCCCEEEECCCCE
T ss_conf             47-8-8877578877853986688769851


No 112
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=31.37  E-value=33  Score=15.01  Aligned_cols=18  Identities=17%  Similarity=0.342  Sum_probs=13.2

Q ss_pred             ECCCCCCCCCCCCCEEEEE
Q ss_conf             5738771078778878999
Q gi|254780625|r  256 YGKTGEPCLSNCGQMIRRI  274 (289)
Q Consensus       256 y~r~g~~C~~~CG~~I~~~  274 (289)
                      .-++|.+| |.||.++...
T Consensus       388 ~v~~GD~C-p~c~~~L~~~  405 (570)
T PRK09194        388 NVVEGDPS-PDGGGTLKIA  405 (570)
T ss_pred             HCCCCCCC-CCCCCEEEEE
T ss_conf             52568889-8899712774


No 113
>pfam08274 PhnA_Zn_Ribbon PhnA Zinc-Ribbon.
Probab=30.81  E-value=36  Score=14.75  Aligned_cols=23  Identities=17%  Similarity=0.522  Sum_probs=16.2

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      +| |.|+..   .++.....+.||.|-
T Consensus         4 ~C-p~C~se---ytY~d~~~~vCpeC~   26 (30)
T pfam08274         4 KC-PLCNSE---YTYEDGALLVCPECA   26 (30)
T ss_pred             CC-CCCCCC---CEECCCCEEECCCCC
T ss_conf             78-878981---247479997997545


No 114
>pfam09788 Tmemb_55A Transmembrane protein 55A. Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=30.31  E-value=32  Score=15.02  Aligned_cols=27  Identities=19%  Similarity=0.447  Sum_probs=17.9

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             1078778878999987812063877679
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      .| ..|..+....+..+++.--||+|.|
T Consensus       161 ~C-gHC~~~Flf~~~~~ntlArCPhCrK  187 (258)
T pfam09788       161 IC-GHCNNTFLWNELTDNTLARCPHCRK  187 (258)
T ss_pred             EC-CCCCCCEEECCCCCCCCCCCCCCCC
T ss_conf             83-5789827841567772013887642


No 115
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=30.29  E-value=25  Score=15.73  Aligned_cols=27  Identities=26%  Similarity=0.730  Sum_probs=14.9

Q ss_pred             CCCCCCCCCEEEEEEE----CCCCEEE-CCCCC
Q ss_conf             7107877887899998----7812063-87767
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQ----AGRSTFY-CTYCQ  288 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~----~gR~ty~-Cp~CQ  288 (289)
                      +|| |=||.....+..    .+.+.|+ |-.|+
T Consensus         2 kpC-PFCG~~~~~~~~~~~~~~~~~~~~C~~Cg   33 (53)
T TIGR03655         2 KPC-PFCGGADVYLRRGFDPLDLSHYFECSTCG   33 (53)
T ss_pred             CCC-CCCCCCHHHEECCCCCCCCEEEEECCCCC
T ss_conf             888-87897531000257876652688777777


No 116
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=30.01  E-value=16  Score=17.06  Aligned_cols=21  Identities=24%  Similarity=0.618  Sum_probs=13.5

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      .| ++||.+...     -.---||.|-
T Consensus       136 vC-~vCGy~~~g-----e~P~~CPiCg  156 (166)
T COG1592         136 VC-PVCGYTHEG-----EAPEVCPICG  156 (166)
T ss_pred             EC-CCCCCCCCC-----CCCCCCCCCC
T ss_conf             76-878881268-----9987699999


No 117
>TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, of a two subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process.
Probab=29.87  E-value=27  Score=15.57  Aligned_cols=104  Identities=18%  Similarity=0.351  Sum_probs=45.1

Q ss_pred             CCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             210011126543564136899999987178778312---22200101589999999987887676542188755311167
Q gi|254780625|r  166 NLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTR---SLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHI  242 (289)
Q Consensus       166 ~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~---~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~~~  242 (289)
                      .+++-|=|.+.+.||+  |.-|.   ++|+-.-|++   +|...+--...++ .|++.|+.|=+..+.-+=  +..+ ..
T Consensus      1006 ~VedRLgkpeqy~Gl~--ftH~T---srId~GpKvcaYK~L~tM~eKv~sQ~-~lA~kIrAvDerdVaE~V--i~sH-Fl 1076 (1173)
T TIGR00354      1006 KVEDRLGKPEQYEGLF--FTHDT---SRIDAGPKVCAYKSLKTMKEKVESQL-ELAKKIRAVDERDVAEKV--IQSH-FL 1076 (1173)
T ss_pred             HHHHHCCCCCCEECCC--EECCC---CHHCCCCCEEECCCCHHHHHHHHHHH-HHHHHHHHCCCCCCCCCH--HHCC-CC
T ss_conf             8886548812244020--20362---00105873321014402578999999-987562001451000201--1103-43


Q ss_pred             CCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf             787787413316657387710787788789999878120638776
Q gi|254780625|r  243 DGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYC  287 (289)
Q Consensus       243 ~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~C  287 (289)
                      +.-.|+.    ..|.|.---| ++||++=+|+.+.|.    ||+|
T Consensus      1077 PD~iGNl----RAFSRQ~vRC-TkCn~KYRRIPL~Gk----C~kC 1112 (1173)
T TIGR00354      1077 PDLIGNL----RAFSRQEVRC-TKCNAKYRRIPLKGK----CLKC 1112 (1173)
T ss_pred             HHHHHHH----HHHHCCCCCC-CCCCCCCCCCCCCCC----CCCC
T ss_conf             0255453----1431265101-358684133478664----4466


No 118
>PRK08402 replication factor A; Reviewed
Probab=29.09  E-value=18  Score=16.67  Aligned_cols=24  Identities=17%  Similarity=0.573  Sum_probs=16.8

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf             710787788789999878120638776
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYC  287 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~C  287 (289)
                      ..| |.|+..+..-  -|-.+|.||.|
T Consensus       215 dAC-PeC~rkvd~d--~~~~~wiCpEh  238 (357)
T PRK08402        215 DAC-PECKKKVDYD--PGTDVWICPEH  238 (357)
T ss_pred             HHC-HHHHHCCCCC--CCCCCEECCCC
T ss_conf             748-2431102447--88762667666


No 119
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=27.89  E-value=24  Score=15.92  Aligned_cols=27  Identities=19%  Similarity=0.529  Sum_probs=16.7

Q ss_pred             CCCCCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf             387710787788789999878120638776
Q gi|254780625|r  258 KTGEPCLSNCGQMIRRIVQAGRSTFYCTYC  287 (289)
Q Consensus       258 r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~C  287 (289)
                      |.+.-| |+||.-+-......  -|+|-.|
T Consensus        17 rk~~~C-PrCG~gvfmA~H~d--R~~CGkC   43 (51)
T COG1998          17 RKNRFC-PRCGPGVFMADHKD--RWACGKC   43 (51)
T ss_pred             ECCCCC-CCCCCCCHHHHCCC--EEEECCC
T ss_conf             814528-88888434341576--0674354


No 120
>KOG2324 consensus
Probab=27.48  E-value=21  Score=16.29  Aligned_cols=26  Identities=19%  Similarity=0.400  Sum_probs=15.7

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      .| +.||-.--.+++..-.+--||.||
T Consensus       229 ~C-~~C~~s~n~e~~~~sk~~~Cp~C~  254 (457)
T KOG2324         229 SC-PSCGYSKNSEDLDLSKIASCPKCN  254 (457)
T ss_pred             EC-CCCCCCCCHHHHCCCCCCCCCCCC
T ss_conf             46-767755760121377656687656


No 121
>TIGR00019 prfA peptide chain release factor 1; InterPro: IPR004373 This family describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognise and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cut-off for this model. RF-1 does not have a translational frameshift.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=26.49  E-value=19  Score=16.47  Aligned_cols=33  Identities=15%  Similarity=-0.080  Sum_probs=16.4

Q ss_pred             CCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCC
Q ss_conf             421001112654356413689999998717877
Q gi|254780625|r  165 SNLKNALLNQKIVAGIGNIYVCEALWRAKLSPI  197 (289)
Q Consensus       165 ~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~  197 (289)
                      -|-+=+.--|.==|=.=|==++=-.-+|||.=.
T Consensus       263 LPTGIVV~CQdErSQ~kNK~kAmk~L~ArL~~~  295 (373)
T TIGR00019       263 LPTGIVVSCQDERSQHKNKDKAMKILRARLYEK  295 (373)
T ss_pred             CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             688417885478520567999999999999999


No 122
>pfam05280 FlhC Flagellar transcriptional activator (FlhC). This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in E. coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator.
Probab=26.14  E-value=47  Score=14.01  Aligned_cols=84  Identities=20%  Similarity=0.347  Sum_probs=56.6

Q ss_pred             CCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             21001112654356413689999998717877831222200101589999999987887676542188755311167787
Q gi|254780625|r  166 NLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGS  245 (289)
Q Consensus       166 ~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~~~~g~  245 (289)
                      .|-..|..+.-..||--++++=-||.--+.+...-.-|+         +-|-|.     |..-++.|             
T Consensus        78 niy~fl~~~~~~~~i~a~ikaYrLYlEq~~~~~~epvLs---------lTRAWt-----LvRF~dsg-------------  130 (176)
T pfam05280        78 NIYRFLIKHGGCSGIEAVIKAYRLYLEQIPADELEPVLS---------LTRAWT-----LVRFFDSG-------------  130 (176)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHH---------HHHHHH-----HHHHHHCC-------------
T ss_conf             999999972898519999999999998678768863014---------888999-----99997358-------------


Q ss_pred             CCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             7874133166573877107877887899998781206387767
Q gi|254780625|r  246 IGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       246 ~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                        -    +     .=.+| .+||+.-......-...|.|.-||
T Consensus       131 --m----L-----~~~~C-~~CgG~FV~ha~~~~~~fvC~lC~  161 (176)
T pfam05280       131 --M----L-----QLTRC-KCCGGHFVTHAHDLQHNFVCGLCQ  161 (176)
T ss_pred             --C----E-----ECCCC-CCCCCCEECCCCCCCCCCCCCCCC
T ss_conf             --7----1-----00566-777881550013578885567988


No 123
>KOG2923 consensus
Probab=25.92  E-value=30  Score=15.28  Aligned_cols=25  Identities=28%  Similarity=0.857  Sum_probs=17.6

Q ss_pred             CCCCCCCCEEEEEEE---CCCCEEECCCCC
Q ss_conf             107877887899998---781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQ---AGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~---~gR~ty~Cp~CQ  288 (289)
                      || | ||..-+-.+-   .|+..--||.|-
T Consensus        24 PC-p-CGDrf~It~edL~~ge~Va~CpsCS   51 (67)
T KOG2923          24 PC-P-CGDRFQITLEDLENGEDVARCPSCS   51 (67)
T ss_pred             CC-C-CCCEEEECHHHHHCCCEEECCCCCE
T ss_conf             77-7-8873365399986788063189966


No 124
>PRK13804 ileS isoleucyl-tRNA synthetase; Provisional
Probab=25.50  E-value=27  Score=15.57  Aligned_cols=10  Identities=10%  Similarity=0.275  Sum_probs=4.3

Q ss_pred             CCCCEEEEEE
Q ss_conf             7788789999
Q gi|254780625|r  266 NCGQMIRRIV  275 (289)
Q Consensus       266 ~CG~~I~~~~  275 (289)
                      .||...++++
T Consensus       554 ~~~~~~~r~~  563 (966)
T PRK13804        554 HPGEEWTKVT  563 (966)
T ss_pred             CCHHHHEECC
T ss_conf             8745507413


No 125
>PRK12300 leuS leucyl-tRNA synthetase; Reviewed
Probab=25.18  E-value=38  Score=14.62  Aligned_cols=22  Identities=27%  Similarity=0.434  Sum_probs=8.7

Q ss_pred             HCCCEEEEEEECCEEEEEEECC
Q ss_conf             2898899996053089995035
Q gi|254780625|r   45 TRGKKIIDVSRRAKYLLIELEG   66 (289)
Q Consensus        45 L~G~~I~~v~r~GK~l~l~l~~   66 (289)
                      |-|.+...|..-..|+.+..++
T Consensus       181 l~g~ta~~v~Pd~~Yv~~~~~~  202 (888)
T PRK12300        181 VFGVTNLWVNPDAEYVVAEVDG  202 (888)
T ss_pred             HHHHHEEEECCCCCEEEEECCC
T ss_conf             4300003777763234564277


No 126
>pfam09297 zf-NADH-PPase NADH pyrophosphatase zinc ribbon domain. This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.
Probab=25.02  E-value=34  Score=14.90  Aligned_cols=26  Identities=23%  Similarity=0.512  Sum_probs=18.0

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             71078778878999987812063877679
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      .-| .+||++.+...  +-..-.||.|+.
T Consensus         4 rfC-~~CG~~t~~~~--~g~~r~C~~Cg~   29 (32)
T pfam09297         4 RFC-GRCGAPTEPAE--GGWARVCPSCGH   29 (32)
T ss_pred             CCC-CCCCCCCCCCC--CCCEEECCCCCC
T ss_conf             442-44688475077--851766887676


No 127
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=24.83  E-value=31  Score=15.12  Aligned_cols=21  Identities=33%  Similarity=0.773  Sum_probs=13.6

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             7107877887899998781206387767
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      -.| +.||++      .--+--|||.|-
T Consensus       592 ~~~-~~~~~~------~~~~~~~~~~~~  612 (615)
T PRK07418        592 IYC-SNCGTK------NPSTHKFCPECG  612 (615)
T ss_pred             EEC-CCCCCC------CCCCCCCCCCCC
T ss_conf             105-888888------863355364226


No 128
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=24.79  E-value=39  Score=14.52  Aligned_cols=27  Identities=41%  Similarity=0.893  Sum_probs=17.6

Q ss_pred             ECCCCCCCCCCCCC-EEEEEEECCCCEEECCCC
Q ss_conf             57387710787788-789999878120638776
Q gi|254780625|r  256 YGKTGEPCLSNCGQ-MIRRIVQAGRSTFYCTYC  287 (289)
Q Consensus       256 y~r~g~~C~~~CG~-~I~~~~~~gR~ty~Cp~C  287 (289)
                      -+-+|.+| |.||. ++.+.    .+-|-|..|
T Consensus      1143 ~g~~g~~C-peCGs~tmvrn----G~C~~C~~C 1170 (1177)
T PRK07562       1143 QGYTGESC-SECGNFTLVRN----GTCLKCDTC 1170 (1177)
T ss_pred             CCCCCCCC-CCCCCCCEEEC----CCCCCCCCC
T ss_conf             48889978-88899640735----860310138


No 129
>COG2046 MET3 ATP sulfurylase (sulfate adenylyltransferase) [Inorganic ion transport and metabolism]
Probab=24.35  E-value=29  Score=15.33  Aligned_cols=11  Identities=36%  Similarity=1.050  Sum_probs=8.8

Q ss_pred             CCEEECCCCCC
Q ss_conf             12063877679
Q gi|254780625|r  279 RSTFYCTYCQK  289 (289)
Q Consensus       279 R~ty~Cp~CQk  289 (289)
                      +-.||||.|+.
T Consensus       318 ~e~~YC~~c~~  328 (397)
T COG2046         318 EEFFYCPKCGQ  328 (397)
T ss_pred             CCEEECCCCCC
T ss_conf             23164132057


No 130
>PRK00390 leuS leucyl-tRNA synthetase; Validated
Probab=24.10  E-value=42  Score=14.30  Aligned_cols=12  Identities=42%  Similarity=0.996  Sum_probs=6.7

Q ss_pred             CCCCCCCCEEEEE
Q ss_conf             1078778878999
Q gi|254780625|r  262 PCLSNCGQMIRRI  274 (289)
Q Consensus       262 ~C~~~CG~~I~~~  274 (289)
                      .| +.||..-.|+
T Consensus       471 ~c-~~~g~~~~Re  482 (822)
T PRK00390        471 TC-PKCGKPARRE  482 (822)
T ss_pred             EC-CCCCCCCEEC
T ss_conf             14-7778721453


No 131
>PRK06039 ileS isoleucyl-tRNA synthetase; Reviewed
Probab=24.06  E-value=41  Score=14.36  Aligned_cols=12  Identities=50%  Similarity=1.423  Sum_probs=6.0

Q ss_pred             CCCCCCCCEEEEE
Q ss_conf             1078778878999
Q gi|254780625|r  262 PCLSNCGQMIRRI  274 (289)
Q Consensus       262 ~C~~~CG~~I~~~  274 (289)
                      +| +.||....++
T Consensus       503 ~~-~~~~~~~~r~  514 (1042)
T PRK06039        503 PC-PDCGTGMRRV  514 (1042)
T ss_pred             CC-CCCCCCCCCC
T ss_conf             58-9986210305


No 132
>pfam00085 Thioredoxin Thioredoxin. Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise.
Probab=24.03  E-value=21  Score=16.29  Aligned_cols=11  Identities=18%  Similarity=0.313  Sum_probs=4.6

Q ss_pred             CEEEEEEECCC
Q ss_conf             30899950355
Q gi|254780625|r   57 AKYLLIELEGN   67 (289)
Q Consensus        57 GK~l~l~l~~~   67 (289)
                      +|-+++.|-.+
T Consensus        18 ~k~vlv~F~a~   28 (104)
T pfam00085        18 DKPVLVDFYAP   28 (104)
T ss_pred             CCCEEEEEECC
T ss_conf             99499999899


No 133
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit; InterPro: IPR000438 Fatty acid synthesis involves a set of reactions, commencing with carboxylation of acetyl-CoA to malonyl-CoA. This is an irreversible reaction, catalysed by the acetyl-CoA carboxylase complex (6.4.1.2 from EC); a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association . The reaction involves two steps:   Biotin carrier protein + ATP + HCO_3^- = Carboxybiotin carrier protein + ADP + P_i  Carboxybiotin carrier protein + Acetyl-CoA = Malonyl-CoA + Biotin carrier protein   In the first step, biotin carboxylase catalyses the carboxylation of the carrier protein to form an intermediate. Next, the transcarboxylase complex transfers the carboxyl group from the intermediate to acetyl-CoA forming malonyl-CoA.; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex.
Probab=23.74  E-value=16  Score=17.01  Aligned_cols=10  Identities=40%  Similarity=0.866  Sum_probs=4.4

Q ss_pred             CCCCCCHHHH
Q ss_conf             4356413689
Q gi|254780625|r  176 IVAGIGNIYV  185 (289)
Q Consensus       176 ~iaGIGN~y~  185 (289)
                      ++.|=|.+|.
T Consensus       117 v~tg~G~l~~  126 (292)
T TIGR00515       117 VVTGKGTLYG  126 (292)
T ss_pred             EEEEEEEECC
T ss_conf             6860037548


No 134
>pfam04945 YHS YHS domain. This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterized membrane proteins. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.
Probab=23.22  E-value=53  Score=13.66  Aligned_cols=21  Identities=24%  Similarity=0.793  Sum_probs=13.2

Q ss_pred             CCCCCEEE-----EEEECCCCEEECC
Q ss_conf             87788789-----9998781206387
Q gi|254780625|r  265 SNCGQMIR-----RIVQAGRSTFYCT  285 (289)
Q Consensus       265 ~~CG~~I~-----~~~~~gR~ty~Cp  285 (289)
                      |+||-.|.     +...+|++-|||.
T Consensus         1 PVCGM~V~~~~~~~~~y~G~~Y~FCS   26 (44)
T pfam04945         1 PVCGMYVKPRAAYKLEYEGRRYHFCS   26 (44)
T ss_pred             CCCCCEECCCCCCCEEECCEEEEEEC
T ss_conf             98887868888871689994899858


No 135
>TIGR02311 HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; InterPro: IPR012689    This entry represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde. The gene for enzyme is generally found adjacent to other genes for this pathway.; GO: 0018802 24-dihydroxyhept-2-ene-17-dioate aldolase activity, 0010124 phenylacetate catabolic process.
Probab=23.14  E-value=37  Score=14.66  Aligned_cols=21  Identities=14%  Similarity=0.055  Sum_probs=12.6

Q ss_pred             CCCCEEEECCCCCCCCCHHHH
Q ss_conf             421001112654356413689
Q gi|254780625|r  165 SNLKNALLNQKIVAGIGNIYV  185 (289)
Q Consensus       165 ~~Ik~~LlDQ~~iaGIGN~y~  185 (289)
                      |-|.++|-==+.+.=|=||+-
T Consensus       114 RGVGSALARASrwNrIp~Ylq  134 (249)
T TIGR02311       114 RGVGSALARASRWNRIPDYLQ  134 (249)
T ss_pred             CCCHHHHHHHHHCCCHHHHHC
T ss_conf             340078776322176125760


No 136
>cd02993 PDI_a_APS_reductase PDIa family, 5'-Adenylylsulfate (APS) reductase subfamily; composed of plant-type APS reductases containing a C-terminal redox active TRX domain and an N-terminal reductase domain which is part of a superfamily that includes N type ATP PPases. APS reductase catalyzes the reduction of activated sulfate to sulfite, a key step in the biosynthesis of sulfur-containing metabolites. Sulfate is first activated by ATP sulfurylase, forming APS, which can be phosphorylated to 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Depending on the organism, either APS or PAPS can be used for sulfate reduction. Prokaryotes and fungi use PAPS, whereas plants use both APS and PAPS. Since plant-type APS reductase uses glutathione (GSH) as its electron donor, the C-terminal domain may function like glutaredoxin, a GSH-dependent member of the TRX superfamily. The flow of reducing equivalents goes from GSH - C-terminal TRX domain - N-terminal reductase domain - APS. Plant-type APS red
Probab=22.95  E-value=16  Score=16.94  Aligned_cols=24  Identities=25%  Similarity=0.358  Sum_probs=11.2

Q ss_pred             CHHHHHHHCCCEEEEEEECCEEEEEEECCC
Q ss_conf             778999728988999960530899950355
Q gi|254780625|r   38 PHHFSAATRGKKIIDVSRRAKYLLIELEGN   67 (289)
Q Consensus        38 ~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~   67 (289)
                      +++|.+.+.|+      ...|..++.|=.+
T Consensus         8 ~~~f~~~v~~~------~~~k~~lV~FYAP   31 (109)
T cd02993           8 RAEIEALAKGE------RRNQSTLVVLYAP   31 (109)
T ss_pred             HHHHHHHHHCC------CCCCCEEEEEECC
T ss_conf             77399997043------5699889999999


No 137
>pfam01258 zf-dskA_traR Prokaryotic dksA/traR C4-type zinc finger.
Probab=22.78  E-value=11  Score=17.98  Aligned_cols=26  Identities=27%  Similarity=0.658  Sum_probs=18.8

Q ss_pred             CCCCCCCEEEEEEECCC-CEEECCCCCC
Q ss_conf             07877887899998781-2063877679
Q gi|254780625|r  263 CLSNCGQMIRRIVQAGR-STFYCTYCQK  289 (289)
Q Consensus       263 C~~~CG~~I~~~~~~gR-~ty~Cp~CQk  289 (289)
                      | ..||..|.......+ ...+|..||.
T Consensus         6 C-~~CGE~i~~~R~~~~~~~~~C~~C~~   32 (32)
T pfam01258         6 C-EDCGEPIPEARLEAVPGATLCIECQE   32 (32)
T ss_pred             C-CCCCCCCCHHHHHCCCCCCCCHHCCC
T ss_conf             0-51789258999717988787031349


No 138
>PRK05743 ileS isoleucyl-tRNA synthetase; Reviewed
Probab=22.40  E-value=52  Score=13.70  Aligned_cols=16  Identities=31%  Similarity=0.588  Sum_probs=7.7

Q ss_pred             EEECCCCCCCCCCCCCE
Q ss_conf             66573877107877887
Q gi|254780625|r  254 SVYGKTGEPCLSNCGQM  270 (289)
Q Consensus       254 ~vy~r~g~~C~~~CG~~  270 (289)
                      .|..-.|..| +||=.-
T Consensus       872 ~v~~a~g~KC-~RCW~~  887 (910)
T PRK05743        872 VVEKAEGEKC-ERCWHY  887 (910)
T ss_pred             EEEECCCCCC-CCCCCC
T ss_conf             9997999977-130989


No 139
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=22.20  E-value=31  Score=15.14  Aligned_cols=32  Identities=16%  Similarity=0.405  Sum_probs=17.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             778312222001015899999999878876765421887
Q gi|254780625|r  196 PIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGS  234 (289)
Q Consensus       196 P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~  234 (289)
                      |.-...++.+.+       ..+.+.++...++.+..|-+
T Consensus        44 pvCq~qsi~~S~-------a~~A~dmR~~I~~~i~~G~s   75 (126)
T TIGR03147        44 PQCQNQNLVESN-------SPIAYDLRHEVYSMVNEGKS   75 (126)
T ss_pred             CCCCCCCHHHCC-------HHHHHHHHHHHHHHHHCCCC
T ss_conf             777997740076-------19999999999999985999


No 140
>TIGR00959 ffh signal recognition particle protein; InterPro: IPR004780    The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane.    This entry represents various SRP subunits.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=22.11  E-value=32  Score=15.08  Aligned_cols=37  Identities=22%  Similarity=0.397  Sum_probs=28.7

Q ss_pred             CCCCHHHHHHHHHHC-CC-CCCCEEEECCCCCCCCCHHHHHH
Q ss_conf             211106788874201-45-42100111265435641368999
Q gi|254780625|r  148 DNSFNAIYLTHQFHK-KN-SNLKNALLNQKIVAGIGNIYVCE  187 (289)
Q Consensus       148 ~~~~~~~~~~~~l~~-~~-~~Ik~~LlDQ~~iaGIGN~y~~E  187 (289)
                      ...||++.|.+.++. +| .++..+|   +.+||+|++-.++
T Consensus       332 ~~~FdleDfl~Ql~~~~KMG~l~~L~---~MiPG~g~~~~~~  370 (439)
T TIGR00959       332 KGQFDLEDFLEQLRQIKKMGPLSSLL---KMIPGMGGMKPSL  370 (439)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCHHHHH---HHHCCCCCCCHHH
T ss_conf             05889899999999997227903588---8602202443357


No 141
>TIGR02738 TrbB type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB; InterPro: IPR014109   This entry includes thiol-disulphide isomerase (TrbB), a protein that is involved in conjugative transfer of plasmid DNA, specifically in the F-type system. TrbB has been predicted to contain a thioredoxin fold, it also contains a conserved pair of cysteines and has been shown to function as a thiol disulphide isomerase by complementation of Escherichia coli DsbA mutants . TtbB is believed to be involved in pilin assembly . TrbB is closely related to TraF (IPR014110 from INTERPRO) though somewhat longer lacking the cysteine motif and is apparently not functional as a disulphide bond isomerase..
Probab=22.10  E-value=30  Score=15.27  Aligned_cols=10  Identities=10%  Similarity=0.126  Sum_probs=5.6

Q ss_pred             EEEEECCCCC
Q ss_conf             9995035531
Q gi|254780625|r   60 LLIELEGNLS   69 (289)
Q Consensus        60 l~l~l~~~~~   69 (289)
                      .|+.|++++.
T Consensus        58 ~Wy~Ls~~r~   67 (176)
T TIGR02738        58 VWYRLSNGRK   67 (176)
T ss_pred             EEEEECHHHH
T ss_conf             0011033678


No 142
>KOG2846 consensus
Probab=22.08  E-value=36  Score=14.71  Aligned_cols=29  Identities=28%  Similarity=0.555  Sum_probs=16.7

Q ss_pred             CCCCCCCCCCC---CEEEEEEECCCCEEECCCCC
Q ss_conf             38771078778---87899998781206387767
Q gi|254780625|r  258 KTGEPCLSNCG---QMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       258 r~g~~C~~~CG---~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      |.+.-| +.|-   +...++.+. =.+||||.|-
T Consensus       218 ryALIC-~~C~~HNGla~~ee~~-yi~F~C~~Cn  249 (328)
T KOG2846         218 RYALIC-SQCHHHNGLARKEEYE-YITFRCPHCN  249 (328)
T ss_pred             HHHHCC-HHHCCCCCCCCHHHCC-CEEEECCCCC
T ss_conf             054521-2102015867765567-6289875554


No 143
>PRK08565 DNA-directed RNA polymerase subunit beta; Provisional
Probab=21.79  E-value=56  Score=13.48  Aligned_cols=59  Identities=12%  Similarity=0.134  Sum_probs=40.6

Q ss_pred             CCCCCCCC-CC-----CCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCC
Q ss_conf             56555332-21-----1106788874201454210011126543564136899999987178778
Q gi|254780625|r  140 RTLGPEPA-DN-----SFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIR  198 (289)
Q Consensus       140 ~~lGpD~l-~~-----~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~  198 (289)
                      ..+-||+. +|     ++|...+.+.+.++-..+.....|-+.|.+...-...|.|..+|.++.-
T Consensus       884 dG~~pDiI~NPhg~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G  948 (1101)
T PRK08565        884 EGIVPDLILNPHAIPSRMTVGQLLEAIAGKVAALTGRFVDATPFEGEPEEELRKELLKLGFKPSG  948 (1101)
T ss_pred             CCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCC
T ss_conf             99885188789878776709999999876888725973114898998899999999975989999


No 144
>pfam04423 Rad50_zn_hook Rad50 zinc hook motif. The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.
Probab=21.48  E-value=35  Score=14.86  Aligned_cols=10  Identities=30%  Similarity=0.876  Sum_probs=6.5

Q ss_pred             CCCCCCCCEEE
Q ss_conf             10787788789
Q gi|254780625|r  262 PCLSNCGQMIR  272 (289)
Q Consensus       262 ~C~~~CG~~I~  272 (289)
                      .| |+||..+.
T Consensus        22 ~C-PvC~r~l~   31 (54)
T pfam04423        22 CC-PVCGRPLD   31 (54)
T ss_pred             CC-CCCCCCCC
T ss_conf             77-76699766


No 145
>pfam10571 UPF0547 Uncharacterized protein family UPF0547. This domain contains a zinc-ribbon motif.
Probab=21.40  E-value=43  Score=14.24  Aligned_cols=20  Identities=25%  Similarity=0.773  Sum_probs=11.4

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      .| |.|+..|-.      +.-.||.|.
T Consensus         2 ~C-P~C~~~vp~------~~~~Cp~CG   21 (26)
T pfam10571         2 TC-PECGAEVPL------AAKICPHCG   21 (26)
T ss_pred             CC-CCCCCCCCH------HCCCCCCCC
T ss_conf             68-755483640------034477888


No 146
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=21.28  E-value=34  Score=14.93  Aligned_cols=32  Identities=16%  Similarity=0.340  Sum_probs=18.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             778312222001015899999999878876765421887
Q gi|254780625|r  196 PIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGS  234 (289)
Q Consensus       196 P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~  234 (289)
                      |.-...++.+.+       ..+.+.++...++.++.|-+
T Consensus        44 pvCq~qsi~~S~-------s~iA~dmR~~Ir~~i~~G~s   75 (126)
T PRK10144         44 PQCQNQNLLESN-------APVAVSMRHQVYSMVAEGKS   75 (126)
T ss_pred             CCCCCCCHHHCC-------HHHHHHHHHHHHHHHHCCCC
T ss_conf             778998841157-------79999999999999986999


No 147
>pfam09723 CxxC_CxxC_SSSS Zinc ribbon domain. This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.17  E-value=58  Score=13.40  Aligned_cols=25  Identities=20%  Similarity=0.663  Sum_probs=12.6

Q ss_pred             CCCCCCCEEEEEEE-CCCCEEECCCCC
Q ss_conf             07877887899998-781206387767
Q gi|254780625|r  263 CLSNCGQMIRRIVQ-AGRSTFYCTYCQ  288 (289)
Q Consensus       263 C~~~CG~~I~~~~~-~gR~ty~Cp~CQ  288 (289)
                      | ..||...+...- +.+..--||.|+
T Consensus         8 C-~~Cg~~fe~~~~~~~~~~~~CP~C~   33 (42)
T pfam09723         8 C-EDCGHTFEVLQKISDAPLATCPECG   33 (42)
T ss_pred             E-CCCCCEEEEEEECCCCCCCCCCCCC
T ss_conf             4-8899989999865799887697999


No 148
>pfam06044 DRP Dam-replacing family. Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis.
Probab=20.91  E-value=44  Score=14.17  Aligned_cols=13  Identities=8%  Similarity=0.135  Sum_probs=6.0

Q ss_pred             HCCCCCCCEEEEC
Q ss_conf             0145421001112
Q gi|254780625|r  161 HKKNSNLKNALLN  173 (289)
Q Consensus       161 ~~~~~~Ik~~LlD  173 (289)
                      +.++..-+..+||
T Consensus       179 r~~~~e~rGW~ld  191 (254)
T pfam06044       179 RNQSIESRGWTLD  191 (254)
T ss_pred             HHCCCHHCCHHHH
T ss_conf             8511310101899


No 149
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.76  E-value=59  Score=13.35  Aligned_cols=26  Identities=15%  Similarity=0.351  Sum_probs=12.5

Q ss_pred             CCCCCCCCEEEEEEECC-----------CCEEECCCCC
Q ss_conf             10787788789999878-----------1206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAG-----------RSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~g-----------R~ty~Cp~CQ  288 (289)
                      .| ++|+..+...+-.+           ...+-||.|.
T Consensus       415 ~C-~~C~~~L~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg  451 (699)
T PRK05580        415 RC-PHCDGPLTLHRAGRRLRCHHCGYQEPIPRACPECG  451 (699)
T ss_pred             EC-CCCCCEEEECCCCCCEECCCCCCCCCCCCCCCCCC
T ss_conf             65-67898634206898332264688365755465679


No 150
>PRK13208 valS valyl-tRNA synthetase; Reviewed
Probab=20.71  E-value=45  Score=14.09  Aligned_cols=24  Identities=13%  Similarity=-0.062  Sum_probs=11.6

Q ss_pred             CCCCCEEEECCCCCCCCCHHHHHHHH
Q ss_conf             54210011126543564136899999
Q gi|254780625|r  164 NSNLKNALLNQKIVAGIGNIYVCEAL  189 (289)
Q Consensus       164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiL  189 (289)
                      +.+|--.+.||=++.- . -++++++
T Consensus       348 ~~pi~~~~~~QWfi~~-~-~~k~~~~  371 (809)
T PRK13208        348 KTPIEILVTRQWFIKV-L-DLKEELL  371 (809)
T ss_pred             CCCCEEEECHHHHHHH-H-HHHHHHH
T ss_conf             9721687524566532-7-7788888


No 151
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=20.70  E-value=38  Score=14.60  Aligned_cols=13  Identities=15%  Similarity=0.245  Sum_probs=7.1

Q ss_pred             CCCEEEEEEECCC
Q ss_conf             6633899970688
Q gi|254780625|r   95 QHNHVTISLTNNT  107 (289)
Q Consensus        95 ~~~~~~~~~~~~~  107 (289)
                      +...+.|.|+.++
T Consensus        70 ~~~~V~l~F~~~g   82 (908)
T COG0419          70 KSASVELEFEVNG   82 (908)
T ss_pred             CCEEEEEEEEECC
T ss_conf             6079999999899


No 152
>TIGR00385 dsbE periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; InterPro: IPR004799 Periplasmic protein thiol:disulphide oxidoreductase is involved in the biogenesis of c-type cytochromes as well as in disulphide bond formation in some periplasmic proteins. This group defines the DsbE subfamily.; GO: 0015036 disulfide oxidoreductase activity, 0017004 cytochrome complex assembly, 0030288 outer membrane-bounded periplasmic space.
Probab=20.68  E-value=33  Score=14.99  Aligned_cols=49  Identities=22%  Similarity=0.263  Sum_probs=26.5

Q ss_pred             CCHHHHHHHCC--CEEE-EEEECCEEEEEEE--------CCCCCCCCCCCCCCEEEEECC
Q ss_conf             87789997289--8899-9960530899950--------355310015255327998147
Q gi|254780625|r   37 FPHHFSAATRG--KKII-DVSRRAKYLLIEL--------EGNLSIIVHLGMSGSFIIEHT   85 (289)
Q Consensus        37 ~~~~~~~~L~G--~~I~-~v~r~GK~l~l~l--------~~~~~L~~HlgM~G~~~~~~~   85 (289)
                      .|+...+.|.+  +.++ ++.+.||-.++-+        -.++=++..|--+|++.+..-
T Consensus        41 vP~~~~a~L~~~~q~~~~~~~~qG~~~LlNVWAsWCp~CraEHp~L~eLak~Grl~ivG~  100 (175)
T TIGR00385        41 VPAFGLAALREPLQLYTADIFRQGKPVLLNVWASWCPPCRAEHPYLNELAKEGRLPIVGV  100 (175)
T ss_pred             CCCCHHHHCCCCCCCCCHHHHHCCCEEEEEEEECCCCCCHHCCHHHHHHHHCCCCEEEEE
T ss_conf             885112202467861364453089606998840368883100057899975397307886


No 153
>KOG2851 consensus
Probab=20.52  E-value=45  Score=14.09  Aligned_cols=15  Identities=40%  Similarity=0.640  Sum_probs=10.7

Q ss_pred             HEEEECCCCCCCCCC
Q ss_conf             316657387710787
Q gi|254780625|r  252 AFSVYGKTGEPCLSN  266 (289)
Q Consensus       252 ~~~vy~r~g~~C~~~  266 (289)
                      -|-||-++|..|-|.
T Consensus       329 PFcVHP~Tg~VcVPi  343 (412)
T KOG2851         329 PFCVHPKTGRVCVPI  343 (412)
T ss_pred             CCCCCCCCCCEEEEC
T ss_conf             742258888667642


No 154
>pfam00133 tRNA-synt_1 tRNA synthetases class I (I, L, M and V). Other tRNA synthetase sub-families are too dissimilar to be included.
Probab=20.46  E-value=41  Score=14.34  Aligned_cols=12  Identities=0%  Similarity=-0.130  Sum_probs=6.5

Q ss_pred             CCCCCCCCEEEEE
Q ss_conf             1078778878999
Q gi|254780625|r  262 PCLSNCGQMIRRI  274 (289)
Q Consensus       262 ~C~~~CG~~I~~~  274 (289)
                      .| +.|+....++
T Consensus       476 ~~-~~~~~~~~re  487 (606)
T pfam00133       476 LL-GKGAGTLEQD  487 (606)
T ss_pred             HC-CCCCCCEEEC
T ss_conf             53-5788751567


No 155
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=20.43  E-value=60  Score=13.30  Aligned_cols=15  Identities=7%  Similarity=-0.022  Sum_probs=11.2

Q ss_pred             HCCCCCCCCCCCHHH
Q ss_conf             178778312222001
Q gi|254780625|r  193 KLSPIRKTRSLIQNN  207 (289)
Q Consensus       193 ~I~P~~~~~~Ls~~e  207 (289)
                      +++...|..+|++++
T Consensus       324 ~~d~~~P~~~L~~e~  338 (935)
T COG0178         324 GFDLDTPWKDLPEEQ  338 (935)
T ss_pred             CCCCCCCHHHCCHHH
T ss_conf             998468536699999


No 156
>KOG2907 consensus
Probab=20.38  E-value=47  Score=14.01  Aligned_cols=27  Identities=22%  Similarity=0.635  Sum_probs=14.6

Q ss_pred             CCCCCCCCCEE--------EEEEECCCCEEECCCCC
Q ss_conf             71078778878--------99998781206387767
Q gi|254780625|r  261 EPCLSNCGQMI--------RRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       261 ~~C~~~CG~~I--------~~~~~~gR~ty~Cp~CQ  288 (289)
                      ..| |.||..=        +...-|.-.-|-||+|-
T Consensus        75 ~kC-pkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~  109 (116)
T KOG2907          75 HKC-PKCGHEEMSYHTLQLRSADEGQTVFYTCPKCK  109 (116)
T ss_pred             CCC-CCCCCCHHHHHHHHCCCCCCCCEEEEECCCCC
T ss_conf             017-55698312155664023468953899757654


Done!