Query         gi|254781172|ref|YP_003065585.1| NAD-dependent DNA ligase LigA [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 731
No_of_seqs    179 out of 2993
Neff          6.4 
Searched_HMMs 39220
Date          Mon May 30 08:29:17 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781172.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00575 dnlj DNA ligase, NAD 100.0       0       0 1781.7  46.4  663   24-714     1-706 (706)
  2 PRK07956 ligA NAD-dependent DN 100.0       0       0 1659.2  62.7  666   13-721     1-668 (668)
  3 COG0272 Lig NAD-dependent DNA  100.0       0       0 1632.5  56.2  663   12-719     2-667 (667)
  4 PRK08097 ligB NAD-dependent DN 100.0       0       0 1232.1  42.9  535    9-635    23-560 (563)
  5 smart00532 LIGANc Ligase N fam 100.0       0       0 1127.9  40.3  439   17-480     1-441 (441)
  6 pfam01653 DNA_ligase_aden NAD- 100.0       0       0  747.0  28.2  312   15-333     1-315 (315)
  7 cd00114 LIGANc NAD+ dependent  100.0       0       0  725.0  26.1  306   19-332     1-307 (307)
  8 pfam03120 DNA_ligase_OB NAD-de  99.9 1.3E-24 3.3E-29  209.5   8.4   82  335-427     1-82  (82)
  9 PRK06195 DNA polymerase III su  99.8 1.3E-18 3.3E-23  163.1   8.7   77  644-720   218-308 (309)
 10 COG5275 BRCT domain type II [G  99.5 1.8E-14 4.7E-19  131.0   6.6  114  598-725   122-236 (276)
 11 PRK06063 DNA polymerase III su  99.4 2.7E-12 6.8E-17  114.3   8.2   75  646-721   232-308 (313)
 12 PHA00454 ATP-dependent DNA lig  98.8 5.1E-06 1.3E-10   65.7  19.7  240  125-404    26-291 (312)
 13 PRK05601 DNA polymerase III su  98.7 6.4E-08 1.6E-12   80.4   7.6   78  645-723   293-372 (377)
 14 LOAD_ligase consensus           98.7 3.4E-07 8.7E-12   74.8  10.9  155  127-311     1-166 (184)
 15 pfam00533 BRCT BRCA1 C Terminu  98.7 1.7E-07 4.3E-12   77.2   8.9   74  644-718     3-77  (77)
 16 PRK09125 DNA ligase; Provision  98.6 3.1E-05 7.9E-10   59.7  17.8  213  124-405    36-256 (277)
 17 cd07898 Adenylation_DNA_ligase  98.5 4.3E-06 1.1E-10   66.3  13.2  161  124-311    19-186 (201)
 18 smart00292 BRCT breast cancer   98.5 1.4E-06 3.6E-11   70.0   8.9   76  645-720     1-79  (80)
 19 cd07901 Adenylation_DNA_ligase  98.5 1.9E-05 4.8E-10   61.3  14.7  177   92-311     5-192 (207)
 20 COG1793 CDC9 ATP-dependent DNA  98.4 0.00015 3.8E-09   54.4  17.6  216  125-382   132-367 (444)
 21 cd07906 Adenylation_DNA_ligase  98.4 2.1E-05 5.5E-10   60.9  13.0  151  124-311    14-171 (186)
 22 cd07903 Adenylation_DNA_ligase  98.3 6.2E-05 1.6E-09   57.3  14.1  172  125-324    32-218 (227)
 23 pfam01068 DNA_ligase_A_M ATP d  98.2   3E-05 7.6E-10   59.8  11.5  155  124-312    16-178 (190)
 24 cd07900 Adenylation_DNA_ligase  98.2 8.5E-05 2.2E-09   56.3  13.8  173   92-306    10-196 (219)
 25 PRK03180 ligB ATP-dependent DN  98.2 0.00023 5.9E-09   52.9  15.8  239   91-380   182-434 (509)
 26 cd07907 Adenylation_DNA_ligase  98.2 0.00013 3.3E-09   54.8  14.5  153  124-311    31-197 (213)
 27 PRK07636 ligB ATP-dependent DN  98.2 7.8E-05   2E-09   56.5  13.1  160  123-326    15-181 (269)
 28 cd07896 Adenylation_kDNA_ligas  98.2 1.8E-05 4.7E-10   61.4   9.6  142  124-313    14-163 (174)
 29 PRK01109 ATP-dependent DNA lig  98.2 0.00089 2.3E-08   48.4  18.1  237   93-382   228-491 (589)
 30 cd00027 BRCT Breast Cancer Sup  98.2 1.1E-05 2.9E-10   63.0   8.2   70  649-718     1-71  (72)
 31 cd06846 Adenylation_DNA_ligase  98.1 9.1E-05 2.3E-09   56.0  11.3  158  124-324    19-182 (187)
 32 cd07897 Adenylation_DNA_ligase  98.1 0.00015 3.8E-09   54.4  12.1  154  125-312    23-192 (208)
 33 PRK09633 ligD ATP-dependent DN  98.0 0.00055 1.4E-08   50.0  13.8  195  123-353    10-224 (604)
 34 cd07905 Adenylation_DNA_ligase  97.9 0.00041 1.1E-08   50.9  11.8  160  124-312    14-181 (194)
 35 PRK09247 ATP-dependent DNA lig  97.9 0.00087 2.2E-08   48.5  13.2  218  126-382   225-463 (537)
 36 KOG1968 consensus               97.8 1.7E-05 4.3E-10   61.7   3.9   20  349-368   495-514 (871)
 37 cd07902 Adenylation_DNA_ligase  97.8 0.00074 1.9E-08   49.0  12.1  176   92-311    14-199 (213)
 38 PRK13766 Hef nuclease; Provisi  97.8 4.2E-05 1.1E-09   58.6   5.1   52  558-619   710-761 (764)
 39 PRK00558 uvrC excinuclease ABC  97.7 8.5E-05 2.2E-09   56.3   5.6   52  557-618   557-608 (609)
 40 PRK08224 ligC ATP-dependent DN  97.7  0.0015 3.8E-08   46.7  11.7  217  124-382    22-251 (345)
 41 KOG2841 consensus               97.6 0.00012   3E-09   55.2   5.4   78  530-620   173-251 (254)
 42 cd07894 Adenylation_RNA_ligase  97.6  0.0015 3.8E-08   46.6  10.7  169   81-308    24-194 (340)
 43 TIGR02776 NHEJ_ligase_prk DNA   97.6  0.0011 2.9E-08   47.6  10.0  165  125-325     4-194 (645)
 44 PRK08609 hypothetical protein;  97.6 0.00026 6.7E-09   52.5   6.6   22  217-240   177-198 (570)
 45 PRK09632 ATP-dependent DNA lig  97.4  0.0046 1.2E-07   42.8  11.5   26  128-154   470-495 (753)
 46 PHA02142 putative RNA ligase    97.4  0.0027 6.8E-08   44.7   9.7  148  124-308   167-344 (366)
 47 TIGR02779 NHEJ_ligase_lig DNA   97.4   0.015 3.9E-07   38.8  13.5  171  123-326    12-205 (328)
 48 PRK05972 ligD ATP-dependent DN  97.3   0.011 2.9E-07   39.8  12.5  161  123-325   216-384 (832)
 49 cd08039 Adenylation_DNA_ligase  97.3   0.024 6.1E-07   37.3  14.6  163  125-311    21-214 (235)
 50 cd00141 NT_POLXc Nucleotidyltr  97.3 0.00085 2.2E-08   48.5   6.1   81  529-614    21-103 (307)
 51 COG1423 ATP-dependent DNA liga  97.2   0.012 3.1E-07   39.6  11.8  174   90-320    69-246 (382)
 52 pfam09414 RNA_ligase RNA ligas  97.2    0.01 2.6E-07   40.2  11.4  150  127-308     2-168 (183)
 53 smart00483 POLXc DNA polymeras  97.2  0.0024   6E-08   45.1   7.8   83  522-614    48-140 (334)
 54 TIGR00574 dnl1 DNA ligase I, A  96.8   0.038 9.8E-07   35.7  11.3  221   92-343   196-451 (705)
 55 PRK00116 ruvA Holliday junctio  96.7   0.037 9.4E-07   35.9  10.6   73  523-616    56-128 (198)
 56 COG1948 MUS81 ERCC4-type nucle  96.7  0.0036 9.1E-08   43.7   5.1   54  556-619   184-237 (254)
 57 COG0322 UvrC Nuclease subunit   96.7  0.0054 1.4E-07   42.3   6.0   49  557-616   533-581 (581)
 58 pfam03119 DNA_ligase_ZBD NAD-d  96.6 0.00092 2.3E-08   48.3   1.7   27  433-466     1-27  (27)
 59 TIGR00084 ruvA Holliday juncti  96.6   0.016 4.1E-07   38.7   8.1  138  467-678    49-187 (217)
 60 TIGR00575 dnlj DNA ligase, NAD  96.5 0.00035 8.9E-09   51.5  -1.3  161  525-724   455-627 (706)
 61 PRK01172 ski2-like helicase; P  96.5   0.018 4.5E-07   38.4   7.4   51  554-614   612-663 (674)
 62 PRK07997 consensus              96.4   0.027 6.9E-07   36.9   8.2   83   31-115    18-125 (928)
 63 COG0632 RuvA Holliday junction  96.2   0.025 6.5E-07   37.1   7.1   53  558-617    77-129 (201)
 64 PRK08609 hypothetical protein;  96.1  0.0025 6.5E-08   44.9   1.8   10  698-707   511-520 (570)
 65 PRK13901 ruvA Holliday junctio  96.1   0.024   6E-07   37.4   6.5   74  522-616    54-127 (196)
 66 PRK07898 consensus              96.0   0.019 4.9E-07   38.1   5.5   48   31-78     26-81  (902)
 67 smart00483 POLXc DNA polymeras  95.9   0.018 4.5E-07   38.3   5.3   56  556-614    50-107 (334)
 68 PRK13482 DNA integrity scannin  95.6   0.036 9.2E-07   35.9   5.8   58  559-626   292-349 (352)
 69 TIGR01448 recD_rel helicase, R  95.6   0.057 1.5E-06   34.4   6.8  129  467-616    84-215 (769)
 70 PRK08928 consensus              95.6   0.057 1.4E-06   34.4   6.8   47   31-78     16-69  (861)
 71 COG1796 POL4 DNA polymerase IV  95.6  0.0091 2.3E-07   40.6   2.6   58  479-545    94-151 (326)
 72 pfam09513 consensus             95.5    0.24 6.2E-06   29.6  11.2  156  124-311   164-341 (356)
 73 KOG1929 consensus               95.5   0.036 9.1E-07   36.0   5.4   79  643-722   490-568 (811)
 74 PRK00254 ski2-like helicase; P  95.4   0.024   6E-07   37.4   4.1   50  557-616   647-697 (717)
 75 PRK05797 consensus              95.2    0.12   3E-06   32.0   7.4   46   32-78     15-67  (869)
 76 TIGR02236 recomb_radA DNA repa  95.0   0.025 6.5E-07   37.1   3.5  153  482-674     4-167 (333)
 77 PRK08076 consensus              94.9     0.1 2.6E-06   32.5   6.3   45   32-78     15-67  (877)
 78 TIGR01259 comE comEA protein;   94.9   0.034 8.6E-07   36.2   3.8   57  542-616    66-122 (124)
 79 pfam01367 5_3_exonuc 5'-3' exo  94.8   0.052 1.3E-06   34.7   4.7   44  557-617    21-64  (100)
 80 PRK09482 xni exonuclease IX; P  94.8   0.042 1.1E-06   35.4   4.1   41  557-614   185-225 (256)
 81 PRK05929 consensus              94.8   0.042 1.1E-06   35.4   4.1   46   31-78     13-67  (870)
 82 PRK07456 consensus              94.7     0.1 2.6E-06   32.4   5.9   83   31-114    19-131 (975)
 83 PRK07300 consensus              94.7    0.06 1.5E-06   34.2   4.6   84   31-115    16-127 (880)
 84 PRK05755 DNA polymerase I; Pro  94.6   0.065 1.7E-06   34.0   4.7   47   31-78     16-69  (889)
 85 PRK00254 ski2-like helicase; P  94.6    0.02 5.2E-07   37.8   2.0   66  590-680   638-704 (717)
 86 PRK07956 ligA NAD-dependent DN  94.6   0.035   9E-07   36.0   3.2   86  479-579   480-568 (668)
 87 PRK06887 consensus              94.5    0.17 4.3E-06   30.8   6.6   47   31-78     18-71  (954)
 88 PRK07556 consensus              94.4   0.078   2E-06   33.3   4.6   47   31-78     19-77  (977)
 89 PRK07625 consensus              94.2   0.076 1.9E-06   33.5   4.3   46   31-78     17-70  (922)
 90 COG1796 POL4 DNA polymerase IV  94.2    0.51 1.3E-05   27.1  13.5   53  554-615    93-147 (326)
 91 PRK08835 consensus              94.2    0.11 2.7E-06   32.3   5.0   83   31-114    18-124 (931)
 92 PRK08786 consensus              94.1   0.066 1.7E-06   33.9   3.9   46   31-78     13-65  (927)
 93 TIGR01448 recD_rel helicase, R  94.1    0.16   4E-06   31.0   5.7   67  254-324   152-224 (769)
 94 PRK08434 consensus              93.9    0.07 1.8E-06   33.7   3.7   83   31-115    13-120 (887)
 95 smart00475 53EXOc 5'-3' exonuc  93.5    0.11 2.9E-06   32.1   4.1   42  557-615   189-230 (259)
 96 COG2231 Uncharacterized protei  93.5    0.17 4.4E-06   30.7   5.1   40  568-616    96-135 (215)
 97 TIGR02236 recomb_radA DNA repa  93.5   0.039 9.9E-07   35.7   1.8   46  559-614     5-51  (333)
 98 PRK02362 ski2-like helicase; P  93.4    0.29 7.4E-06   29.0   6.1   67   35-110    16-87  (736)
 99 cd00008 53EXOc 5'-3' exonuclea  93.4     0.2   5E-06   30.3   5.2   29  557-585   186-214 (240)
100 PRK01172 ski2-like helicase; P  93.4   0.056 1.4E-06   34.5   2.4   30  590-619   606-636 (674)
101 KOG2534 consensus               93.1    0.77   2E-05   25.7   8.4   62  521-582    55-126 (353)
102 TIGR00593 pola DNA polymerase   92.9   0.076 1.9E-06   33.4   2.5   46   33-78     12-68  (1005)
103 PRK08097 ligB NAD-dependent DN  92.6    0.13 3.3E-06   31.7   3.3  109  555-681   427-537 (563)
104 KOG3226 consensus               92.5    0.35 8.9E-06   28.3   5.4   67  646-713   317-383 (508)
105 PRK13913 3-methyladenine DNA g  92.4    0.33 8.3E-06   28.6   5.1   23  593-615   118-140 (218)
106 pfam00763 THF_DHG_CYH Tetrahyd  92.3     0.5 1.3E-05   27.1   6.0   61  664-727    14-88  (117)
107 KOG0966 consensus               92.2    0.98 2.5E-05   24.9   8.8  198  124-353   248-466 (881)
108 KOG0967 consensus               92.2    0.99 2.5E-05   24.8  13.7  178   92-308   344-532 (714)
109 PRK07220 DNA topoisomerase I;   92.1    0.24 6.2E-06   29.5   4.2   21  479-499   476-501 (740)
110 PRK00558 uvrC excinuclease ABC  92.1   0.088 2.2E-06   33.0   1.9   24   42-65     70-93  (609)
111 COG0190 FolD 5,10-methylene-te  91.3     0.6 1.5E-05   26.5   5.5   13  485-497   259-271 (283)
112 COG1623 Predicted nucleic-acid  91.1    0.38 9.7E-06   28.0   4.3   50  558-617   297-346 (349)
113 PRK00116 ruvA Holliday junctio  91.1    0.62 1.6E-05   26.4   5.4   55  480-543    75-129 (198)
114 smart00478 ENDO3c endonuclease  91.1    0.96 2.5E-05   24.9   6.4   23  593-615    69-91  (149)
115 COG0177 Nth Predicted EndoIII-  91.0    0.55 1.4E-05   26.8   5.1   45  487-540    47-91  (211)
116 COG0272 Lig NAD-dependent DNA   90.8    0.25 6.3E-06   29.5   3.1   82  478-577   479-566 (667)
117 PRK10702 endonuclease III; Pro  90.6    0.79   2E-05   25.6   5.5   22  594-615   107-128 (211)
118 cd00056 ENDO3c endonuclease II  90.5    0.86 2.2E-05   25.3   5.7   24  593-616    80-103 (158)
119 TIGR01083 nth endonuclease III  90.5     0.6 1.5E-05   26.5   4.9   74  489-614    47-125 (192)
120 cd00141 NT_POLXc Nucleotidyltr  90.3    0.55 1.4E-05   26.8   4.6   60  523-582    46-114 (307)
121 PRK00024 radC DNA repair prote  90.2     1.5 3.8E-05   23.5  11.8  144  547-710    26-206 (224)
122 TIGR01239 galT_2 galactose-1-p  90.0    0.29 7.5E-06   28.9   3.0   46  306-351   232-278 (502)
123 COG0632 RuvA Holliday junction  89.7     0.1 2.6E-06   32.4   0.4   53  520-573    71-127 (201)
124 cd00128 XPG Xeroderma pigmento  89.5    0.94 2.4E-05   25.0   5.2   29  557-585   226-254 (316)
125 TIGR00084 ruvA Holliday juncti  89.5    0.28 7.1E-06   29.1   2.5   68  467-543    65-140 (217)
126 cd07895 Adenylation_mRNA_cappi  89.3     1.7 4.4E-05   23.0  12.4  154  126-332    40-214 (216)
127 cd00080 HhH2_motif Helix-hairp  89.3    0.44 1.1E-05   27.6   3.4   29  557-585    25-53  (75)
128 PRK10792 bifunctional 5,10-met  89.2    0.96 2.4E-05   24.9   5.1   14  484-497   261-274 (288)
129 COG1555 ComEA DNA uptake prote  88.9    0.87 2.2E-05   25.3   4.7   46  559-616   102-147 (149)
130 PRK04301 radA DNA repair and r  88.8    0.21 5.3E-06   30.0   1.5   18    1-18      4-21  (318)
131 COG2003 RadC DNA repair protei  88.3       2 5.1E-05   22.5  10.7  116  547-674    26-166 (224)
132 TIGR00354 polC DNA polymerase   88.0    0.16 4.2E-06   30.9   0.5   51  133-203   389-439 (1173)
133 pfam00633 HHH Helix-hairpin-he  88.0    0.31 7.9E-06   28.7   1.9   25  591-615     6-30  (30)
134 KOG1921 consensus               87.1     1.3 3.2E-05   24.0   4.6   36  564-613   140-176 (286)
135 TIGR01259 comE comEA protein;   86.4    0.44 1.1E-05   27.6   1.9   98  524-630     8-106 (124)
136 pfam00730 HhH-GPD HhH-GPD supe  86.1     2.4 6.2E-05   21.8   5.7   22  594-615    79-100 (144)
137 PRK00420 hypothetical protein;  85.8    0.36 9.1E-06   28.3   1.3   25  429-460    17-41  (107)
138 PRK02362 ski2-like helicase; P  85.7    0.42 1.1E-05   27.7   1.5   48  557-616   655-703 (736)
139 TIGR02317 prpB methylisocitrat  85.2     1.3 3.3E-05   24.0   3.9  131  519-691     9-151 (287)
140 PRK00421 murC UDP-N-acetylmura  84.3     3.1 7.9E-05   21.0   6.4   13  302-314   215-227 (459)
141 pfam03118 RNA_pol_A_CTD Bacter  84.1     0.6 1.5E-05   26.5   1.8   50  483-543    12-61  (62)
142 KOG2043 consensus               84.1     2.2 5.7E-05   22.1   4.7   68  651-721   661-728 (896)
143 PRK13766 Hef nuclease; Provisi  83.8    0.53 1.4E-05   26.9   1.4   28  597-624   707-734 (764)
144 PRK11088 rrmA 23S rRNA methylt  82.9    0.39 9.9E-06   28.0   0.4   35  433-476     4-38  (272)
145 pfam06044 DRP Dam-replacing fa  81.3    0.82 2.1E-05   25.5   1.6   49  411-471    17-66  (254)
146 TIGR00600 rad2 DNA excision re  81.0     4.1  0.0001   20.1   5.5   25   39-63    188-212 (1127)
147 COG0258 Exo 5'-3' exonuclease   80.9     1.7 4.3E-05   23.0   3.1   15  214-228    38-52  (310)
148 TIGR01497 kdpB K+-transporting  80.7    0.85 2.2E-05   25.4   1.5  157  547-709   262-466 (675)
149 PRK07726 DNA topoisomerase III  80.6    0.84 2.1E-05   25.4   1.4   18  482-499   511-533 (716)
150 TIGR01265 tyr_nico_aTase tyros  80.4    0.81 2.1E-05   25.5   1.3  107  534-656   282-404 (424)
151 COG1110 Reverse gyrase [DNA re  79.9     1.4 3.4E-05   23.8   2.3   40  402-442   680-719 (1187)
152 PTZ00111 DNA replication licen  79.8     1.3 3.4E-05   23.8   2.3   41   11-52     82-122 (916)
153 TIGR01954 nusA_Cterm_rpt trans  79.6     3.7 9.4E-05   20.4   4.5   42  563-614     2-46  (52)
154 TIGR00608 radc DNA repair prot  79.4     4.5 0.00011   19.7   7.1  126  565-710    37-205 (223)
155 TIGR03674 fen_arch flap struct  79.4     2.6 6.8E-05   21.5   3.7   27  557-583   239-265 (338)
156 PRK07219 DNA topoisomerase I;   79.3    0.89 2.3E-05   25.2   1.2   15   21-35     91-105 (769)
157 COG1645 Uncharacterized Zn-fin  79.1    0.82 2.1E-05   25.5   1.0   23  430-460    27-49  (131)
158 TIGR00426 TIGR00426 competence  78.6    0.85 2.2E-05   25.3   0.9   40  560-614    24-66  (70)
159 TIGR01057 topA_arch DNA topois  77.9     1.1 2.8E-05   24.4   1.4   63   88-162   186-249 (637)
160 PRK08620 DNA topoisomerase III  77.7     1.1 2.9E-05   24.4   1.4   51  674-724   655-709 (726)
161 PRK06398 aldose dehydrogenase;  77.6     3.6 9.3E-05   20.5   3.9   16  644-659   231-246 (256)
162 TIGR01209 TIGR01209 conserved   76.4     5.4 0.00014   19.1   8.4  153  124-308    78-237 (388)
163 PRK12766 50S ribosomal protein  76.2     3.5 8.9E-05   20.6   3.5   48  481-539    13-60  (238)
164 PRK01438 murD UDP-N-acetylmura  75.8     5.6 0.00014   19.0   8.5   14  300-313   226-239 (481)
165 TIGR01862 N2-ase-Ialpha nitrog  75.8     5.6 0.00014   19.0   5.8  120  535-680   237-361 (510)
166 smart00278 HhH1 Helix-hairpin-  75.8     1.4 3.7E-05   23.6   1.5   20  597-616     2-21  (26)
167 CHL00013 rpoA RNA polymerase a  75.0     2.1 5.3E-05   22.3   2.1   50  485-545   278-327 (333)
168 KOG0442 consensus               74.6     4.3 0.00011   19.9   3.6   52  556-618   823-874 (892)
169 PRK09137 DNA topoisomerase I;   74.6     1.6   4E-05   23.3   1.4   22   16-37     58-79  (761)
170 pfam02571 CbiJ Precorrin-6x re  74.4     6.1 0.00015   18.7   5.8   53  645-710   164-220 (246)
171 COG4469 CoiA Competence protei  74.3    0.84 2.1E-05   25.4  -0.0   17  431-447    25-41  (342)
172 PTZ00217 flap endonuclease-1;   73.8     3.3 8.3E-05   20.8   2.9   26  558-583   239-264 (394)
173 TIGR00615 recR recombination p  73.1     3.4 8.7E-05   20.7   2.8   35  645-679   101-140 (205)
174 TIGR00336 pyrE orotate phospho  72.3     6.7 0.00017   18.4   5.1   66  642-711   109-181 (187)
175 pfam06677 Auto_anti-p27 Sjogre  72.2     1.9 4.8E-05   22.7   1.3   24  430-460    16-39  (41)
176 TIGR03190 benz_CoA_bzdN benzoy  72.1     6.8 0.00017   18.4   7.9   98  619-725   206-316 (377)
177 COG1096 Predicted RNA-binding   71.7     6.9 0.00018   18.3   4.7   62  393-473   117-180 (188)
178 pfam09511 RNA_lig_T4_1 RNA lig  71.1     5.6 0.00014   19.0   3.5   56   92-156    15-70  (212)
179 PRK03980 flap endonuclease-1;   70.9     7.2 0.00018   18.2   6.2   28  557-584   192-219 (295)
180 PRK08173 DNA topoisomerase III  70.7     2.5 6.3E-05   21.7   1.7   21  479-499   513-538 (857)
181 COG5241 RAD10 Nucleotide excis  70.7     2.9 7.3E-05   21.3   2.0   52  558-619   171-222 (224)
182 PRK09521 exosome complex RNA-b  70.6     5.4 0.00014   19.1   3.4   61  393-472   118-180 (187)
183 PRK13844 recombination protein  70.5     3.7 9.4E-05   20.4   2.5   16  644-659   100-115 (200)
184 pfam01331 mRNA_cap_enzyme mRNA  70.3     7.4 0.00019   18.1  11.7  143  126-311    16-178 (190)
185 pfam08304 consensus             70.0     7.5 0.00019   18.0   5.2  218   73-332    55-283 (378)
186 PRK00076 recR recombination pr  69.9     3.8 9.7E-05   20.3   2.5   16  644-659    96-111 (197)
187 PRK05182 DNA-directed RNA poly  69.8     3.7 9.5E-05   20.4   2.4   50  484-544   250-299 (306)
188 COG1656 Uncharacterized conser  69.5     3.9  0.0001   20.2   2.5   60  398-460    65-135 (165)
189 COG0122 AlkA 3-methyladenine D  69.3     7.8  0.0002   17.9   4.2   23  593-615   195-217 (285)
190 pfam03811 Ins_element1 Inserti  69.2     3.5   9E-05   20.6   2.2   65  432-510     6-72  (88)
191 pfam04551 GcpE GcpE protein. I  68.4     5.2 0.00013   19.3   2.9   42  395-440   219-265 (345)
192 TIGR01405 polC_Gram_pos DNA po  68.4       2 5.2E-05   22.4   0.9   29   23-52    419-447 (1264)
193 TIGR03491 RecB family nuclease  68.4     5.5 0.00014   19.1   3.0   12  257-268   219-230 (457)
194 PRK08057 cobalt-precorrin-6x r  68.2     8.1 0.00021   17.8   5.8   50  648-710   165-218 (241)
195 PRK09401 reverse gyrase; Revie  68.0     2.3 5.8E-05   22.0   1.0   45  398-443   659-703 (1176)
196 KOG3123 consensus               68.0     4.6 0.00012   19.7   2.6   11  257-267   233-243 (272)
197 PTZ00035 Rad51; Provisional     67.7     4.7 0.00012   19.6   2.6   16  524-539    70-85  (350)
198 PRK03369 murD UDP-N-acetylmura  67.6     8.3 0.00021   17.7   9.2   15  300-314   217-231 (487)
199 COG0052 RpsB Ribosomal protein  67.5     8.4 0.00021   17.7   4.2   32  662-693   165-203 (252)
200 PRK08938 DNA topoisomerase I;   67.5     2.9 7.4E-05   21.2   1.5   20  479-498   468-492 (692)
201 TIGR02770 nickel_nikD nickel i  66.5     8.7 0.00022   17.5   5.0   75  134-220     2-81  (239)
202 pfam02371 Transposase_20 Trans  66.2     7.6 0.00019   18.0   3.4   39  597-635     3-41  (87)
203 COG1241 MCM2 Predicted ATPase   66.1     2.8 7.1E-05   21.3   1.2   19  708-726   652-670 (682)
204 pfam09151 DUF1936 Domain of un  65.8     3.4 8.6E-05   20.7   1.5   31  433-466     3-34  (36)
205 COG0821 gcpE 1-hydroxy-2-methy  65.2     6.2 0.00016   18.6   2.8   77  395-494   224-312 (361)
206 pfam01927 DUF82 Protein of unk  64.9     5.8 0.00015   18.9   2.6   40  404-444    64-103 (146)
207 COG4468 GalT Galactose-1-phosp  64.9       7 0.00018   18.2   3.0   12  262-273   207-218 (503)
208 PRK02472 murD UDP-N-acetylmura  64.7     9.4 0.00024   17.3   8.3   10  666-675   440-449 (450)
209 PRK00366 ispG 4-hydroxy-3-meth  64.7     6.5 0.00017   18.5   2.8   42  395-440   230-276 (367)
210 KOG3084 consensus               64.7     3.2 8.1E-05   20.9   1.2   29  431-466   150-178 (345)
211 PRK08115 ribonucleotide-diphos  63.5     3.4 8.7E-05   20.7   1.2   22  549-571   553-574 (857)
212 PRK09536 btuD corrinoid ABC tr  62.7       9 0.00023   17.4   3.2   30  365-410   188-217 (409)
213 PRK06196 oxidoreductase; Provi  62.4     8.3 0.00021   17.7   3.0   14  152-165    31-44  (316)
214 PRK12481 2-deoxy-D-gluconate 3  62.3      10 0.00026   17.0   6.4   14  644-657   234-247 (251)
215 COG1439 Predicted nucleic acid  62.2     2.9 7.3E-05   21.2   0.6   14  431-444   153-166 (177)
216 COG0353 RecR Recombinational D  61.2     7.8  0.0002   17.9   2.7   17  645-661    98-114 (198)
217 TIGR02707 butyr_kinase butyrat  61.0       4  0.0001   20.1   1.2   76  257-364    52-132 (353)
218 PRK03806 murD UDP-N-acetylmura  61.0      11 0.00028   16.8   8.2   26  649-674   405-438 (438)
219 COG1198 PriA Primosomal protei  61.0       3 7.7E-05   21.1   0.6   54  432-497   445-502 (730)
220 pfam03786 UxuA D-mannonate deh  60.6     5.7 0.00014   19.0   1.9   81   91-200    34-114 (350)
221 COG3877 Uncharacterized protei  60.4     3.7 9.5E-05   20.4   1.0   24  428-461     3-26  (122)
222 PRK08305 spoVFB dipicolinate s  60.1      11 0.00028   16.7   4.9   27  213-247   135-161 (195)
223 KOG4362 consensus               60.0      11 0.00029   16.7   4.2   62  644-705   585-658 (684)
224 pfam09862 DUF2089 Protein of u  59.7     4.3 0.00011   19.9   1.2   26  434-472     1-26  (113)
225 TIGR02644 Y_phosphoryl pyrimid  59.6      11 0.00029   16.6   3.6   44  102-165    49-92  (425)
226 KOG2703 consensus               59.6     4.8 0.00012   19.5   1.4   58  555-617   333-391 (460)
227 KOG2875 consensus               59.2      12 0.00029   16.6   3.9   43  566-614   191-236 (323)
228 PRK08174 DNA topoisomerase III  59.1     5.5 0.00014   19.1   1.6   21   16-36     78-98  (670)
229 pfam10391 DNA_pol_lambd_f Fing  58.9     3.5 8.8E-05   20.6   0.6   25  481-510     5-29  (52)
230 PRK07141 DNA topoisomerase I;   58.9     4.1  0.0001   20.1   0.9   21  479-499   456-481 (622)
231 PRK06139 short chain dehydroge  58.9     7.9  0.0002   17.9   2.4   13  533-545   216-228 (324)
232 TIGR01588 citE citrate lyase,   58.5     7.9  0.0002   17.8   2.4   15  485-499    72-86  (288)
233 KOG2379 consensus               58.4      12  0.0003   16.5   7.4   29  557-585   433-461 (501)
234 TIGR01203 HGPRTase hypoxanthin  58.4      11 0.00029   16.6   3.2   20   12-31      3-22  (183)
235 KOG0323 consensus               58.3     7.3 0.00019   18.1   2.2   81  644-725   439-524 (635)
236 COG2176 PolC DNA polymerase II  58.1       4  0.0001   20.1   0.8   35  233-268   334-368 (1444)
237 TIGR02605 CxxC_CxxC_SSSS putat  58.0     4.1  0.0001   20.1   0.8   15  430-444    26-41  (43)
238 PRK10246 exonuclease subunit S  57.8     3.6 9.3E-05   20.5   0.5   13  429-441   501-513 (1047)
239 PRK02048 4-hydroxy-3-methylbut  57.4     8.6 0.00022   17.6   2.4   63  644-723   542-609 (613)
240 KOG0477 consensus               56.3     6.9 0.00018   18.3   1.8   65  646-710   543-621 (854)
241 PRK06200 2,3-dihydroxy-2,3-dih  56.1      12 0.00031   16.4   3.0   13  646-658   245-257 (263)
242 PRK07239 bifunctional uroporph  56.1      13 0.00033   16.2   4.7  163   93-305    39-208 (381)
243 PRK06556 vitamin B12-dependent  55.7     5.7 0.00015   18.9   1.3   87   16-117    95-182 (957)
244 PRK12496 hypothetical protein;  55.7     3.6 9.3E-05   20.5   0.2   21  294-315    87-107 (166)
245 COG1571 Predicted DNA-binding   55.6     8.1 0.00021   17.8   2.0   68  394-474   315-383 (421)
246 TIGR01054 rgy reverse gyrase;   55.5      13 0.00034   16.1   3.2  232   19-308   599-877 (1843)
247 PRK06319 DNA topoisomerase I/S  54.8     6.2 0.00016   18.6   1.3   21   16-36     59-79  (864)
248 COG3743 Uncharacterized conser  54.7     5.7 0.00015   18.9   1.1   43  482-529    71-113 (133)
249 TIGR00679 hpr-ser HPr(Ser) kin  54.7     8.7 0.00022   17.5   2.0   61  441-510   168-229 (309)
250 cd01075 NAD_bind_Leu_Phe_Val_D  54.6      14 0.00035   16.0   5.5   27  235-268    28-54  (200)
251 PRK06599 DNA topoisomerase I;   54.5     9.1 0.00023   17.4   2.1   36   15-51     56-96  (776)
252 PRK01390 murD UDP-N-acetylmura  54.4      14 0.00035   16.0   8.2   10  300-309   216-225 (457)
253 PRK03564 formate dehydrogenase  54.4     6.5 0.00017   18.5   1.4   10  431-440   187-196 (307)
254 KOG2906 consensus               53.9     4.9 0.00013   19.4   0.7   16  432-447     2-17  (105)
255 PRK05823 consensus              53.9      10 0.00025   17.1   2.3   20   17-36     72-91  (691)
256 smart00350 MCM minichromosome   53.6     5.4 0.00014   19.1   0.9   15  560-574   436-450 (509)
257 COG1458 Predicted DNA-binding   53.5      14 0.00036   15.9   5.9   55  656-723   157-211 (221)
258 pfam00122 E1-E2_ATPase E1-E2 A  53.1     5.3 0.00013   19.2   0.7   24  393-418    50-73  (222)
259 TIGR01647 ATPase-IIIA_H plasma  53.1     7.7  0.0002   17.9   1.6   16  395-411   117-132 (835)
260 PRK06197 short chain dehydroge  53.0      13 0.00033   16.2   2.7   14  152-165    21-34  (306)
261 cd00729 rubredoxin_SM Rubredox  52.9     4.7 0.00012   19.6   0.4   12  430-441    17-28  (34)
262 PRK10355 xylF D-xylose transpo  52.5      12 0.00032   16.3   2.6   45  257-308    47-91  (330)
263 PRK06500 short chain dehydroge  52.5      15 0.00037   15.8   3.2   15  644-658   232-246 (249)
264 PRK09001 DNA topoisomerase I;   52.4     6.8 0.00017   18.3   1.2   17   19-35     96-112 (869)
265 PRK12825 fabG 3-ketoacyl-(acyl  52.3      15 0.00037   15.8   2.9   16  644-659   233-248 (250)
266 COG4277 Predicted DNA-binding   52.2      12 0.00031   16.4   2.4   87  519-634   278-366 (404)
267 smart00279 HhH2 Helix-hairpin-  52.0     8.3 0.00021   17.7   1.6   19  596-614    16-34  (36)
268 TIGR02027 rpoA DNA-directed RN  51.8      13 0.00034   16.1   2.6   56  481-547   261-318 (324)
269 pfam09538 FYDLN_acid Protein o  51.7     5.8 0.00015   18.9   0.8   11  431-441    26-36  (104)
270 TIGR02354 thiF_fam2 thiamine b  51.4     6.8 0.00017   18.4   1.1  121  532-672     9-129 (200)
271 TIGR00143 hypF [NiFe] hydrogen  51.1     4.4 0.00011   19.8   0.1   28  650-677   748-777 (799)
272 PRK09202 nusA transcription el  50.8     9.1 0.00023   17.4   1.6   48  557-614   377-425 (428)
273 PRK00141 murD UDP-N-acetylmura  50.8      15 0.00039   15.6   8.5   12  300-311   225-236 (476)
274 PRK08628 short chain dehydroge  50.6      15 0.00039   15.6   2.8   16  644-659   236-251 (258)
275 COG2099 CobK Precorrin-6x redu  50.3      16  0.0004   15.6   5.5   48  649-709   174-226 (257)
276 pfam11672 DUF3268 Protein of u  50.3       6 0.00015   18.8   0.7   15  430-444     1-15  (102)
277 TIGR01900 dapE-gram_pos succin  50.2     9.7 0.00025   17.2   1.7  105  405-562   243-355 (373)
278 PRK03906 mannonate dehydratase  50.0     8.9 0.00023   17.4   1.5   83   89-200    30-112 (389)
279 TIGR01186 proV glycine betaine  49.9     7.5 0.00019   18.0   1.1   30  365-410   181-210 (372)
280 pfam06054 CoiA Competence prot  49.7       7 0.00018   18.3   0.9   18  251-268    66-83  (348)
281 pfam10941 DUF2620 Protein of u  49.6      16 0.00041   15.5   3.4   72  650-724     1-97  (117)
282 TIGR00789 flhB_rel FlhB domain  49.5      13 0.00033   16.2   2.3   24  699-722    34-57  (84)
283 TIGR02634 xylF D-xylose ABC tr  49.5      16 0.00041   15.5   3.3   13  530-542   165-177 (307)
284 TIGR00340 zpr1_rel zinc finger  49.3     5.9 0.00015   18.9   0.5   37  596-632    92-134 (168)
285 KOG0478 consensus               49.0      12  0.0003   16.5   2.0   44  657-700   534-585 (804)
286 COG1326 Uncharacterized archae  48.5     5.9 0.00015   18.8   0.4   15  358-372    90-105 (201)
287 PRK00080 ruvB Holliday junctio  48.3      13 0.00033   16.2   2.1   21  353-373   143-163 (328)
288 COG0474 MgtA Cation transport   48.3     8.2 0.00021   17.7   1.1   48  524-575   538-585 (917)
289 PRK05876 short chain dehydroge  48.2      17 0.00043   15.3   2.8   16  481-496   224-239 (275)
290 COG3845 ABC-type uncharacteriz  48.1     9.8 0.00025   17.1   1.5   43  354-412   167-221 (501)
291 pfam05876 Terminase_GpA Phage   48.1      15 0.00039   15.7   2.4   19   49-67     77-95  (552)
292 PRK00349 uvrA excinuclease ABC  47.7      17 0.00043   15.3   4.7   26  367-404   616-641 (944)
293 PRK05866 short chain dehydroge  47.6      17 0.00043   15.3   2.6   13  532-544   245-257 (290)
294 PRK05582 DNA topoisomerase I;   47.6      10 0.00026   17.0   1.5   22   15-36     57-78  (692)
295 PRK12823 benD 1,6-dihydroxycyc  47.3      17 0.00044   15.2   3.1   12  645-656   245-256 (260)
296 PRK09783 copper/silver efflux   47.3     7.3 0.00019   18.1   0.7   95  294-406   209-318 (407)
297 PRK13812 orotate phosphoribosy  47.2      17 0.00044   15.2   5.1   62  648-720   106-173 (174)
298 COG1997 RPL43A Ribosomal prote  47.1     9.6 0.00024   17.2   1.3   28  431-467    35-62  (89)
299 PRK09138 DNA topoisomerase I;   47.1     8.7 0.00022   17.5   1.1   35  430-467   601-635 (887)
300 pfam08745 UPF0278 UPF0278 fami  47.0      17 0.00044   15.2   3.5   52  656-722   150-203 (206)
301 TIGR01701 Fdhalpha-like oxidor  47.0      17 0.00045   15.2   3.2   81  648-729   502-596 (824)
302 TIGR01525 ATPase-IB_hvy heavy   47.0      11 0.00028   16.8   1.5   39  663-708   452-493 (639)
303 pfam11382 DUF3186 Protein of u  46.8      18 0.00045   15.2   5.7   14  130-143    77-90  (307)
304 PRK12278 50S ribosomal protein  46.6     8.4 0.00022   17.6   0.9   21  594-614   151-171 (216)
305 COG0773 MurC UDP-N-acetylmuram  46.6      18 0.00045   15.1   5.5   67  302-376   214-282 (459)
306 COG1885 Uncharacterized protei  46.6     7.6 0.00019   18.0   0.7   11  432-442    50-60  (115)
307 PRK00448 polC DNA polymerase I  46.4     8.4 0.00021   17.7   0.9   45  672-717  1345-1406(1436)
308 PRK08413 consensus              46.4      11 0.00029   16.6   1.6   21   16-36     59-79  (733)
309 PRK01710 murD UDP-N-acetylmura  46.3      18 0.00045   15.1   8.7   15  705-719   403-417 (458)
310 PRK13130 H/ACA RNA-protein com  46.3     8.6 0.00022   17.6   0.9   21  424-444    10-30  (54)
311 TIGR00588 ogg 8-oxoguanine DNA  46.0      11 0.00028   16.7   1.5   91  520-614   191-292 (379)
312 PRK08324 short chain dehydroge  45.8      18 0.00046   15.1   5.1   56   41-108    90-149 (676)
313 TIGR01523 ATPase-IID_K-Na pota  45.8      12  0.0003   16.5   1.6   40  313-354   329-368 (1001)
314 TIGR02194 GlrX_NrdH Glutaredox  45.8      13 0.00034   16.1   1.8   30  239-273    24-53  (72)
315 pfam04606 Ogr_Delta Ogr/Delta-  45.6     7.8  0.0002   17.9   0.6   37  433-470     1-39  (47)
316 PRK01216 DNA polymerase IV; Va  45.5      11 0.00029   16.6   1.5   49  479-540   179-227 (351)
317 TIGR00596 rad1 DNA repair prot  45.4      18 0.00047   15.0   3.8   50  557-618   884-935 (939)
318 cd00513 Ribosomal_L32_L32e Rib  45.3     3.7 9.3E-05   20.4  -1.1   36  479-514    36-72  (107)
319 COG0419 SbcC ATPase involved i  45.2     8.3 0.00021   17.7   0.7   14  431-444   457-470 (908)
320 COG1312 UxuA D-mannonate dehyd  45.1      14 0.00036   15.9   1.9   82   90-200    31-112 (362)
321 TIGR01562 FdhE formate dehydro  45.0     7.8  0.0002   17.9   0.6   80  167-271    15-94  (312)
322 smart00661 RPOL9 RNA polymeras  44.9      11 0.00029   16.6   1.4   29  432-467     1-29  (52)
323 pfam05559 DUF763 Protein of un  44.7      19 0.00048   14.9   4.3   32  581-612   254-285 (319)
324 PRK13809 orotate phosphoribosy  44.6      19 0.00048   14.9   5.8   68  648-726   117-190 (206)
325 PRK12859 3-ketoacyl-(acyl-carr  44.6      19 0.00048   14.9   4.9   14  644-657   241-254 (257)
326 TIGR00375 TIGR00375 conserved   44.4      19 0.00048   14.9   3.7  118  430-615   246-366 (384)
327 TIGR02339 thermosome_arch ther  44.4      19 0.00048   14.9   3.2   22  535-556   375-396 (522)
328 pfam01396 zf-C4_Topoisom Topoi  44.3      13 0.00033   16.2   1.6   30  433-466     3-32  (39)
329 PRK07062 short chain dehydroge  44.3      19 0.00049   14.9   2.9   15  644-658   247-261 (265)
330 PRK05867 short chain dehydroge  44.2      19 0.00049   14.9   2.9   14  644-657   236-249 (253)
331 PRK13945 formamidopyrimidine-D  44.0     8.7 0.00022   17.5   0.7   24  433-460   257-280 (283)
332 PRK06988 putative formyltransf  44.0      19 0.00049   14.9   5.9   15  704-718   293-307 (313)
333 PRK07677 short chain dehydroge  44.0      19 0.00049   14.9   3.0   14  644-657   233-246 (254)
334 PRK06701 short chain dehydroge  43.9      19 0.00049   14.8   3.9   15  152-166    50-64  (289)
335 TIGR03655 anti_R_Lar restricti  43.8      13 0.00032   16.3   1.5   10  433-442     3-12  (53)
336 PRK04358 hypothetical protein;  43.6      19  0.0005   14.8   3.4   55  656-725   163-219 (223)
337 PRK03922 hypothetical protein;  43.3     8.8 0.00023   17.5   0.6   11  432-442    50-60  (113)
338 pfam08442 ATP-grasp_2 ATP-gras  43.3      20  0.0005   14.8   3.4   43  254-306     4-46  (202)
339 COG5222 Uncharacterized conser  43.2      13 0.00033   16.2   1.5  112  362-490   199-330 (427)
340 TIGR01652 ATPase-Plipid phosph  43.2     9.9 0.00025   17.1   0.9   39  308-369   468-507 (1249)
341 PRK06128 oxidoreductase; Provi  43.2      20  0.0005   14.8   3.1   15  152-166    60-74  (300)
342 cd00528 MoaC MoaC family. Memb  43.1      20  0.0005   14.8   2.5   53  338-408    84-136 (136)
343 pfam04475 DUF555 Protein of un  43.1     8.9 0.00023   17.5   0.6   11  432-442    48-58  (102)
344 TIGR00715 precor6x_red precorr  43.1      20 0.00051   14.8   3.1   43  159-203    78-123 (260)
345 PRK07063 short chain dehydroge  43.0      20 0.00051   14.8   3.0   15  644-658   239-253 (259)
346 TIGR01367 pyrE_Therm orotate p  42.9      20 0.00051   14.7   3.5   27  649-679   111-143 (205)
347 PRK06194 hypothetical protein;  42.9      20 0.00051   14.7   2.6   20  473-494   160-179 (301)
348 TIGR02397 dnaX_nterm DNA polym  42.8      16  0.0004   15.5   1.9   20  465-484   177-196 (363)
349 COG3024 Uncharacterized protei  42.7     9.7 0.00025   17.1   0.8   34  431-488     7-40  (65)
350 PRK08277 D-mannonate oxidoredu  42.7      20 0.00051   14.7   3.1   15  645-659   259-273 (278)
351 PRK06079 enoyl-(acyl carrier p  42.5      20 0.00051   14.7   3.4   12  645-656   236-247 (252)
352 PRK07168 bifunctional uroporph  42.4      20 0.00052   14.7   6.4  130  335-498   207-348 (474)
353 PRK12495 hypothetical protein;  42.3      11 0.00027   16.8   0.9   13  432-444    43-55  (221)
354 PRK06550 fabG 3-ketoacyl-(acyl  42.3      20 0.00052   14.7   2.8   15  644-658   220-234 (237)
355 KOG4236 consensus               42.3     6.5 0.00017   18.5  -0.2   86  338-438   395-482 (888)
356 PRK08226 short chain dehydroge  42.3      20 0.00052   14.7   3.1   15  644-658   239-253 (263)
357 COG1579 Zn-ribbon protein, pos  42.3     7.6 0.00019   18.0   0.2   14  431-444   221-234 (239)
358 COG1327 Predicted transcriptio  42.1      11 0.00027   16.9   0.9   36  595-630   113-149 (156)
359 smart00834 CxxC_CXXC_SSSS Puta  42.0      11 0.00028   16.8   0.9   14  430-443    25-38  (41)
360 TIGR01512 ATPase-IB2_Cd cadmiu  41.8      14 0.00035   16.0   1.4   54  316-375   268-324 (494)
361 PRK10517 magnesium-transportin  41.8      12  0.0003   16.5   1.0   15  365-379   564-578 (900)
362 COG4213 XylF ABC-type xylose t  41.8      13 0.00033   16.2   1.3   20  465-484   200-219 (341)
363 PRK07758 hypothetical protein;  41.7      19 0.00048   15.0   2.1   24  522-545    67-90  (95)
364 COG3791 Uncharacterized conser  41.6      10 0.00026   17.0   0.7   42  433-477    71-112 (133)
365 PRK13810 orotate phosphoribosy  41.4      21 0.00053   14.6   5.5   60  648-718   121-186 (187)
366 PRK08217 fabG 3-ketoacyl-(acyl  41.3      21 0.00053   14.6   3.1   11  646-656   239-249 (253)
367 PRK06227 consensus              41.3      21 0.00054   14.6   2.9   15  644-658   234-248 (256)
368 PRK05855 short chain dehydroge  41.3      21 0.00054   14.6   3.2   26  474-499   312-340 (582)
369 COG2100 Predicted Fe-S oxidore  41.2      21 0.00054   14.6   4.9   15  601-615   265-279 (414)
370 PRK01103 formamidopyrimidine-D  41.2      11 0.00028   16.7   0.8   24  433-460   246-269 (273)
371 PRK06171 sorbitol-6-phosphate   41.2      21 0.00054   14.6   2.9   15  644-658   249-263 (266)
372 TIGR01082 murC UDP-N-acetylmur  41.1      21 0.00054   14.5   4.4   66  276-346   198-265 (491)
373 COG2216 KdpB High-affinity K+   40.9      19 0.00048   15.0   2.0   16  217-232   201-216 (681)
374 cd00350 rubredoxin_like Rubred  40.7      10 0.00027   16.9   0.7   12  430-441    16-27  (33)
375 PRK04690 murD UDP-N-acetylmura  40.6      21 0.00055   14.5   8.1   14  592-605   453-466 (468)
376 COG2260 Predicted Zn-ribbon RN  40.6      13 0.00034   16.1   1.2   20  425-444    11-30  (59)
377 PRK07231 fabG 3-ketoacyl-(acyl  40.6      21 0.00055   14.5   2.8   14  644-657   234-247 (250)
378 PRK00464 nrdR transcriptional   40.6      14 0.00035   16.0   1.2   34  595-628   113-147 (149)
379 PRK07985 oxidoreductase; Provi  40.4      22 0.00055   14.5   3.1   14  153-166    55-68  (294)
380 TIGR02109 PQQ_syn_pqqE coenzym  40.4      10 0.00026   17.0   0.6   74  485-585    92-167 (363)
381 PRK06057 short chain dehydroge  40.3      22 0.00055   14.5   5.8   15  644-658   233-247 (255)
382 PRK08220 2,3-dihydroxybenzoate  40.3      22 0.00055   14.5   3.1   14  644-657   235-248 (253)
383 PRK08063 enoyl-(acyl carrier p  40.1      22 0.00056   14.4   2.6   14  644-657   232-245 (250)
384 PRK08993 2-deoxy-D-gluconate 3  40.0      22 0.00056   14.4   6.5   13  645-657   237-249 (253)
385 PRK05854 short chain dehydroge  39.9      22 0.00056   14.4   3.5   14  152-165    19-32  (314)
386 PTZ00159 60S ribosomal protein  39.8     8.1 0.00021   17.8  -0.0   55  454-513    32-87  (134)
387 PRK10445 endonuclease VIII; Pr  39.7      12  0.0003   16.5   0.8   24  433-460   237-260 (263)
388 pfam11290 DUF3090 Protein of u  39.4      19 0.00049   14.9   1.9   24  411-444   144-167 (171)
389 TIGR02187 GlrX_arch Glutaredox  39.4      14 0.00035   16.0   1.1   14  398-411   121-134 (237)
390 PRK08351 DNA-directed RNA poly  39.4      12  0.0003   16.5   0.8   18  429-446    13-31  (61)
391 PRK07889 enoyl-(acyl carrier p  39.3      22 0.00057   14.3   3.1   13  645-657   238-250 (256)
392 PRK06172 short chain dehydroge  39.2      22 0.00057   14.3   2.8   15  644-658   236-250 (253)
393 COG2093 DNA-directed RNA polym  39.1      10 0.00027   16.9   0.4   18  428-445    13-33  (64)
394 PRK06463 fabG 3-ketoacyl-(acyl  39.0      23 0.00058   14.3   7.2   14  644-657   232-245 (254)
395 PRK07791 short chain dehydroge  38.7      23 0.00058   14.3   3.2   14  644-657   242-255 (285)
396 PRK07109 short chain dehydroge  38.7      23 0.00058   14.3   2.9   12  153-164    14-25  (338)
397 cd01701 Pol_zeta Pol_zeta, a m  38.7      18 0.00046   15.1   1.6   16  482-497   228-243 (405)
398 PRK02406 DNA polymerase IV; Va  38.6      18 0.00045   15.1   1.6   27  482-513   184-210 (355)
399 PRK05270 galactose-1-phosphate  38.4      23 0.00059   14.3   3.4   12  262-273   205-216 (496)
400 PRK08936 glucose-1-dehydrogena  38.3      23 0.00059   14.2   3.1   15  645-659   237-251 (261)
401 cd02173 ECT CTP:phosphoethanol  38.2      23 0.00059   14.2   5.6   29  524-552   119-147 (152)
402 PRK06603 enoyl-(acyl carrier p  38.2      23 0.00059   14.2   4.5   15  644-658   238-252 (260)
403 PRK07825 short chain dehydroge  38.1      23  0.0006   14.2   2.8   15  532-546   203-217 (273)
404 TIGR02869 spore_SleB spore cor  37.9      17 0.00044   15.2   1.4   31  467-497    40-71  (232)
405 PRK08562 rpl32e 50S ribosomal   37.9     5.5 0.00014   19.0  -1.1   26  488-513    67-92  (127)
406 pfam08394 Arc_trans_TRASH Arch  37.7      16  0.0004   15.6   1.1   37  434-472     1-37  (37)
407 TIGR00577 fpg formamidopyrimid  36.9      16  0.0004   15.5   1.1   27  432-460   260-290 (292)
408 COG3058 FdhE Uncharacterized p  36.8      12 0.00032   16.3   0.6   12  431-442   185-196 (308)
409 COG0266 Nei Formamidopyrimidin  36.7      13 0.00034   16.1   0.7   24  433-460   247-270 (273)
410 PRK11827 hypothetical protein;  36.6      17 0.00042   15.4   1.2   15  433-447    10-24  (60)
411 pfam01655 Ribosomal_L32e Ribos  36.6     5.3 0.00013   19.2  -1.4   27  487-513    47-73  (110)
412 PRK03754 DNA-directed RNA poly  36.5      13 0.00034   16.1   0.7   13  433-445    26-38  (49)
413 PRK07060 short chain dehydroge  36.4      25 0.00063   14.0   3.1   15  644-658   228-242 (245)
414 PRK07792 fabG 3-ketoacyl-(acyl  36.4      25 0.00063   14.0   2.9   14  644-657   237-250 (303)
415 TIGR02098 MJ0042_CXXC MJ0042 f  36.3      19 0.00048   14.9   1.4   30  431-460     2-32  (40)
416 pfam08645 PNK3P Polynucleotide  36.2      25 0.00063   14.0   2.7   46  666-714   102-157 (158)
417 PRK03352 DNA polymerase IV; Va  36.2      21 0.00052   14.6   1.6   27  482-513   181-207 (345)
418 cd01703 Pol_iota Pol iota is m  36.1      21 0.00053   14.6   1.6   49  482-542   214-262 (394)
419 PRK02794 DNA polymerase IV; Pr  35.8      22 0.00055   14.5   1.6   31  481-516   212-242 (417)
420 COG4888 Uncharacterized Zn rib  35.8      14 0.00037   15.8   0.7   11  433-443    24-34  (104)
421 pfam06750 DiS_P_DiS Bacterial   35.8      13 0.00034   16.1   0.6   19  428-446    24-42  (86)
422 KOG1247 consensus               35.7     9.5 0.00024   17.2  -0.2   49  189-237   198-250 (567)
423 PRK00241 nudC NADH pyrophospha  35.6      17 0.00043   15.3   1.1   13  432-444   101-113 (257)
424 PRK13638 cbiO cobalt transport  35.6      23 0.00059   14.3   1.7   31  365-411   186-216 (271)
425 LOAD_Hrd consensus              35.4      26 0.00065   13.9   4.1   26  591-616    42-67  (77)
426 TIGR02311 HpaI 2,4-dihydroxyhe  35.3      24  0.0006   14.2   1.8   68  557-629   111-194 (249)
427 PRK12367 short chain dehydroge  35.3      26 0.00065   13.9   4.4   23  145-168    16-38  (250)
428 TIGR02390 RNA_pol_rpoA1 DNA-di  35.3      14 0.00036   15.9   0.6   63   39-115   124-195 (901)
429 KOG4169 consensus               35.2      26 0.00066   13.9   2.6   17  151-167     9-25  (261)
430 PRK03918 chromosome segregatio  35.1      14 0.00036   15.9   0.6   12  432-443   439-450 (882)
431 cd01403 Cyt_c_Oxidase_VIIb Cyt  35.1      22 0.00055   14.5   1.5   21  335-355    27-47  (51)
432 PTZ00180 60S ribosomal protein  35.1      26 0.00066   13.9   4.7   87  328-443    34-120 (260)
433 PRK12829 short chain dehydroge  35.1      26 0.00066   13.9   2.9   16  644-659   247-262 (264)
434 pfam04423 Rad50_zn_hook Rad50   35.0      14 0.00035   16.0   0.5   10  433-442    22-31  (54)
435 COG1570 XseA Exonuclease VII,   35.0      26 0.00066   13.9   3.1   16   99-114     3-18  (440)
436 PRK08416 7-alpha-hydroxysteroi  35.0      26 0.00066   13.9   3.1   13  645-657   244-256 (260)
437 PRK09242 tropinone reductase;   34.5      26 0.00067   13.8   3.1   15  644-658   239-253 (258)
438 PRK01122 potassium-transportin  34.5      17 0.00043   15.3   0.9   56  648-708   511-570 (684)
439 PRK13811 orotate phosphoribosy  34.5      26 0.00067   13.8   6.6   63  645-718   100-168 (170)
440 PRK12826 3-ketoacyl-(acyl-carr  34.5      26 0.00067   13.8   2.9   13  645-657   236-248 (253)
441 pfam11376 DUF3179 Protein of u  34.5      14 0.00035   16.0   0.5   11  133-143    54-64  (261)
442 TIGR02487 NrdD anaerobic ribon  34.5      15 0.00038   15.7   0.6   86  479-607   414-508 (655)
443 COG1569 Predicted nucleic acid  34.4      25 0.00063   14.0   1.7   38  681-720   101-139 (142)
444 PRK06997 enoyl-(acyl carrier p  34.4      26 0.00067   13.8   3.2   15  644-658   237-251 (260)
445 PRK08245 hypothetical protein;  34.4      26 0.00067   13.8   4.0   21  349-369   149-169 (239)
446 PRK12429 3-hydroxybutyrate deh  34.4      26 0.00067   13.8   3.0   14  645-658   242-255 (258)
447 PRK11281 potassium efflux prot  34.2      18 0.00047   15.0   1.1   45  659-705   964-1014(1107)
448 COG1137 YhbG ABC-type (unclass  34.1      17 0.00043   15.3   0.8   10  603-612   169-178 (243)
449 PRK07562 ribonucleotide-diphos  34.1      21 0.00053   14.6   1.4   94   14-118   103-225 (1177)
450 pfam00406 ADK Adenylate kinase  33.9      26 0.00065   13.9   1.8   34  428-477   139-172 (186)
451 pfam01967 MoaC MoaC family. Me  33.7      27 0.00069   13.7   2.9   52  339-408    85-136 (136)
452 KOG2661 consensus               33.7      23 0.00059   14.2   1.5   16  424-439   256-271 (424)
453 PRK00724 formate dehydrogenase  33.7      27 0.00069   13.7   4.6   52  646-710   196-247 (262)
454 COG1717 RPL32 Ribosomal protei  33.6      21 0.00055   14.5   1.3   28  488-515    68-95  (133)
455 TIGR01011 rpsB_bact ribosomal   33.5      22 0.00057   14.4   1.4   24  533-556    74-99  (227)
456 pfam05129 Elf1 Transcription e  33.4      10 0.00027   16.9  -0.3   30  430-459    14-45  (74)
457 PRK11033 zntA zinc/cadmium/mer  33.2      19 0.00048   14.9   1.0   25  393-419   256-280 (739)
458 TIGR01051 topA_bact DNA topois  33.2      16 0.00041   15.5   0.6   18  560-577   562-579 (688)
459 PRK08589 short chain dehydroge  33.1      28  0.0007   13.7   3.0   18  644-661   238-255 (272)
460 pfam01215 COX5B Cytochrome c o  33.1      16  0.0004   15.5   0.6   10  431-440    81-90  (99)
461 PRK07523 gluconate 5-dehydroge  33.1      28  0.0007   13.6   2.7   15  644-658   233-247 (251)
462 PRK13646 cbiO cobalt transport  32.9      28 0.00071   13.6   1.8   31  365-411   196-226 (286)
463 PRK00694 4-hydroxy-3-methylbut  32.9      13 0.00033   16.2   0.1   66  644-726   534-604 (606)
464 PRK10671 copA copper exporting  32.8      20 0.00051   14.7   1.1   24  394-419   340-363 (834)
465 PRK08690 enoyl-(acyl carrier p  32.5      28 0.00072   13.6   3.2   13  645-657   239-251 (261)
466 pfam09889 DUF2116 Uncharacteri  32.4      20  0.0005   14.8   1.0   30  430-471     2-31  (59)
467 TIGR01161 purK phosphoribosyla  32.4      28 0.00072   13.6   3.8   54  251-320   100-154 (386)
468 COG4068 Uncharacterized protei  32.4      14 0.00035   16.0   0.2   16  429-444     6-21  (64)
469 KOG4450 consensus               32.3      23 0.00058   14.3   1.3   21  172-194    54-75  (168)
470 PRK07041 short chain dehydroge  32.1      29 0.00073   13.5   3.1   15  152-166    12-26  (240)
471 PRK06523 short chain dehydroge  32.1      29 0.00073   13.5   3.6   15  643-657   241-255 (260)
472 TIGR00705 SppA_67K signal pept  32.0      29 0.00073   13.5   4.0   36  139-174   322-358 (614)
473 PRK08270 anaerobic ribonucleos  32.0      17 0.00044   15.2   0.7   10  359-368   283-292 (681)
474 PRK09072 short chain dehydroge  31.9      29 0.00073   13.5   2.8   16  532-547   208-223 (262)
475 pfam08996 zf-DNA_Pol DNA Polym  31.9      29 0.00073   13.5   1.8   25  420-446     9-33  (186)
476 PRK06138 short chain dehydroge  31.9      29 0.00074   13.5   2.9   31  647-678     3-33  (252)
477 TIGR00463 gltX_arch glutamyl-t  31.8      29 0.00073   13.5   1.7   20  184-203   454-473 (600)
478 TIGR02870 spore_II_D stage II   31.7      15 0.00037   15.8   0.2   73  320-410   227-314 (358)
479 TIGR01966 RNasePH ribonuclease  31.6      29 0.00074   13.5   2.6   22  649-670   186-218 (237)
480 PRK12828 short chain dehydroge  31.6      29 0.00074   13.5   3.3   34  644-678     2-35  (239)
481 COG2816 NPY1 NTP pyrophosphohy  31.5      26 0.00066   13.8   1.5   22  433-460   113-134 (279)
482 pfam03129 HGTP_anticodon Antic  31.4      29 0.00075   13.4   3.6   43  664-714    18-63  (93)
483 PRK06720 hypothetical protein;  31.3      29 0.00075   13.4   3.1   31  647-678    14-44  (169)
484 PRK07890 short chain dehydroge  31.3      29 0.00075   13.4   3.1   31  647-678     3-33  (258)
485 KOG2463 consensus               31.3      16 0.00041   15.4   0.4   10  432-441   258-267 (376)
486 pfam06676 DUF1178 Protein of u  31.3      18 0.00045   15.1   0.6    9  434-442    35-43  (145)
487 PRK12428 3-alpha-hydroxysteroi  31.2      29 0.00075   13.4   2.9   31  647-678     3-33  (261)
488 TIGR00515 accD acetyl-CoA carb  31.1      20 0.00051   14.7   0.8   41  432-476    34-74  (292)
489 PHA00439 exonuclease            31.1      23 0.00058   14.3   1.1   15  558-572   191-205 (288)
490 PHA00732 hypothetical protein   31.0      27 0.00068   13.8   1.5   49  433-486     3-53  (79)
491 COG1888 Uncharacterized protei  31.0      30 0.00076   13.4   4.1   29  649-679    50-78  (97)
492 PRK07577 short chain dehydroge  31.0      30 0.00076   13.4   2.7   31  647-678     1-31  (234)
493 PRK06935 2-deoxy-D-gluconate 3  30.9      30 0.00076   13.4   2.8   31  647-678    13-43  (258)
494 PRK10348 ribosome-associated h  30.8      30 0.00076   13.4   2.6   28  361-409    36-63  (133)
495 PRK07776 consensus              30.7      30 0.00076   13.4   2.9   31  647-678     6-36  (252)
496 pfam09297 zf-NADH-PPase NADH p  30.7      26 0.00067   13.8   1.4   22  433-460     5-26  (32)
497 PRK12742 oxidoreductase; Provi  30.7      30 0.00077   13.4   3.1   33  645-678     2-34  (237)
498 pfam08605 Rad9_Rad53_bind Fung  30.7      13 0.00032   16.3  -0.2   42  375-429    51-92  (131)
499 pfam02680 DUF211 Uncharacteriz  30.7      30 0.00077   13.4   5.2   61  617-679    15-76  (91)
500 TIGR02389 RNA_pol_rpoA2 DNA-di  30.6      24 0.00061   14.1   1.2   78  604-687    48-140 (397)

No 1  
>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=100.00  E-value=0  Score=1781.73  Aligned_cols=663  Identities=42%  Similarity=0.733  Sum_probs=619.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCC-CCEEECCCCCCCHHHCC
Q ss_conf             99999999984331779820878999999999999897720311589999620036432357-75045166425702159
Q gi|254781172|r   24 LEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLS-LFKVTHSIPTLSLEKIW  102 (731)
Q Consensus        24 L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~-~~kv~H~~pMlSL~k~~  102 (731)
                      |++.|++|+|.||++++|.|||++||+|+++|++||++||+|+   +|||||||||+.+.+. |.||+|..|||||||+|
T Consensus         1 L~~~i~~h~y~YYVld~P~i~D~~YD~L~~~L~~LE~~~PeL~---~pDSPTqrVG~~~~~~~F~~v~H~~PMLSLdNAF   77 (706)
T TIGR00575         1 LRKLIRKHDYRYYVLDEPSISDAEYDRLMRELQELEEKHPELI---TPDSPTQRVGAAPLSADFPKVRHSTPMLSLDNAF   77 (706)
T ss_pred             CHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHCC
T ss_conf             9467776755134657798882888899999999865488853---6898642137600215787267776520132214


Q ss_pred             CHHHHHHHHHHHHHHHCCCCC--CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCC-
Q ss_conf             999999999999986124677--76119999415818999998599899888659865566699977531024322335-
Q gi|254781172|r  103 NIEDLRKFITRIYRFWQKKDD--NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSL-  179 (731)
Q Consensus       103 ~~~el~~w~~~~~~~~~~~~~--~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~-  179 (731)
                      +.+||.+|.+|+.+.+.....  ....|+|||||||+||+|+||||.|++|+|||||.+|||||.|+|||++||++|.. 
T Consensus        78 ~~~el~~f~~R~~~~~~~~~~~~~~~~~~~EpKiDG~s~~L~Ye~G~L~~A~TRGDG~~GEDvT~NvrTI~~IP~~~~~~  157 (706)
T TIGR00575        78 DEDELRAFIKRIRRALGSKEKQEEKVEYVVEPKIDGLSISLTYENGVLVRAATRGDGTTGEDVTANVRTIRSIPLRLAGD  157 (706)
T ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCEEEEEEEECCEEEEEEECCCCCCCCCHHCCCHHHCCCCCCCCCC
T ss_conf             88899999999998603335755460689702427157889983765898667488833751211302100244413588


Q ss_pred             ---CCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEEC--CCCCCC---
Q ss_conf             ---44550489999998520212345564314854334234567777523455553-011105664102--454332---
Q gi|254781172|r  180 ---NIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLG--KTSEIF---  250 (731)
Q Consensus       180 ---~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~--~~~~~~---  250 (731)
                         +.|..+||||||||++++|++||+++.+.|+++|||||||||||||||||+++ .|+|+|++|+++  ......   
T Consensus       158 ~~~n~p~~~EvRGEVf~~k~~F~~lN~~~~~~ge~~FANPRNaAAGsLRqlDp~ita~R~L~~~~Y~~G~~~~~~~~~~L  237 (706)
T TIGR00575       158 GVGNPPERLEVRGEVFMPKEDFEALNEERLEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGNAEGLELKGSL  237 (706)
T ss_pred             CCCCCCCEEEEEEEEEECHHHHHHHHHHHHHCCCCCCCCCCHHHCCCEECCCCCCEECCCCEEEEEECCCCCCCCCCCCC
T ss_conf             87664325898436885658999999999970889666841333130000473111116636898762554577777657


Q ss_pred             -CCCCHHHHHHHHHCCCC-CCCCEEEEE--CCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEE
Q ss_conf             -10000368999975996-654148874--03211345566553100112343763777311000111587656866312
Q gi|254781172|r  251 -AKGQYEMLQKMRCLGFP-VNNGVRQAN--TFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMI  326 (731)
Q Consensus       251 -~~~~~e~l~~L~~~GF~-v~~~~~~~~--~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prwai  326 (731)
                       +.||++.|++|++|||+ |+++...|.  +.++|++++++|.+.|+.|||+|||+|||||++++|+.||+|||+|||||
T Consensus       238 ~~~t~~~~L~~L~~~GF~TV~~~~~~~~ln~~~eV~~~~~~~~~~R~~L~y~IDGvV~Kvd~l~~Q~~LG~t~k~PRWAi  317 (706)
T TIGR00575       238 PFRTQYEALAWLKKLGFPTVNPHIRLCKLNSIEEVLEYYEEIEKKRDSLPYEIDGVVVKVDDLALQEELGFTSKAPRWAI  317 (706)
T ss_pred             CCCCHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHHHCHHCCCCCHHH
T ss_conf             86778999999986388420125776303898899999999998752078730437898378799987111027860010


Q ss_pred             EECCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf             31145621589987889940356225899997433302640001014898999750234543222468440768999835
Q gi|254781172|r  327 SHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRA  406 (731)
Q Consensus       327 A~Kf~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~Ra  406 (731)
                      ||||||+++.|+|+||+|||||||+|||||.||||.|+|||||||||||.|||++           +||||||+|+|.||
T Consensus       318 AYKFpa~e~~T~L~dv~~qVGRTG~iTPvA~LePV~vaG~~Vs~ATLHN~D~I~~-----------kdiriGD~Vvv~kA  386 (706)
T TIGR00575       318 AYKFPAEEAQTKLLDVVVQVGRTGAITPVAKLEPVFVAGTTVSRATLHNEDEIEE-----------KDIRIGDTVVVRKA  386 (706)
T ss_pred             CCCCCCCCCCEEEEEEEEEECCEEEECCEEEECCEEECCEEEEEEEECCHHHHHC-----------CCCCCCCEEEEEEC
T ss_conf             2366743010089878998465677600367565587207862344016002420-----------27665888999844


Q ss_pred             CCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             87025665410123578730477704326577501033786544521010035434411446655332130123103541
Q gi|254781172|r  407 GEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGL  486 (731)
Q Consensus       407 GdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GL  486 (731)
                      |||||+|++|+.++|++++++|.||++||+|||+|++..++      +++||+|+.+||+|..++|.|||||+||||+||
T Consensus       387 GdVIP~vv~v~~~~R~~~~~~~~~P~~CP~C~s~lv~~~~e------~~~rC~Ng~~Cpa~~~e~i~hFaSr~AmdI~GL  460 (706)
T TIGR00575       387 GDVIPKVVEVLLEKRTGEERPIKFPTHCPSCGSPLVRIEEE------VDIRCTNGLNCPAQLVERIKHFASRNAMDIDGL  460 (706)
T ss_pred             CCCCHHHHHCCCCCCCCCCCEEECCCCCCCCCCEEECCCCC------EEEECCCCCCCHHHHHHHEEEEEEECCCCCCCC
T ss_conf             86253554102357888887034287188888331115787------216538876653676511023454110332222


Q ss_pred             HHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             0355556530576540454101101067775310001000134-210014568999987522346667763010111168
Q gi|254781172|r  487 GKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILG-FGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAE  565 (731)
Q Consensus       487 G~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~G-fgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~  565 (731)
                      |+++|++|+|++    +|++++|||+|+.+    .++|+++|| ||+|||+||++||++||+.||+|||+||||||||+.
T Consensus       461 G~~~I~~LfE~~----Lv~~~~DLY~L~~k----~~~Ll~le~~~g~~sa~nLl~aIe~sK~~pl~RlL~aLGIr~VG~~  532 (706)
T TIGR00575       461 GEKVIEQLFEEK----LVRSVADLYALKEK----LEDLLELEGKFGEKSAQNLLSAIEKSKKKPLARLLFALGIRHVGEV  532 (706)
T ss_pred             CHHHHHHHHHCC----CCCCHHHHHHHHHH----HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf             389999998726----66785666577889----9998706403556889999999998521048999986286035799


Q ss_pred             HHHHHHHHCCCHHHHHHHHHH-HHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHH--------HHHHHHHHHCCCCC
Q ss_conf             999999882998999997897-761251177876138886789999999996697999--------99999997338776
Q gi|254781172|r  566 IARSLAKYYLSYQNFAQEINN-IIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNI--------CAVEALLKEVSPSI  636 (731)
Q Consensus       566 ~Ak~La~~f~si~~l~~~~~~-~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~--------~~i~~L~~~~~~~~  636 (731)
                      +|+.|+++|.|++++.++..+ +-.....+..+|++|+|||+++|++|++||+++.|.        +++++|...++...
T Consensus       533 ~A~~La~~f~tl~~L~~A~~e~~~~~~~f~~s~L~~~~g~G~~vA~~~~~~F~~~~~~~~qPYRta~~~~~L~~~gv~~~  612 (706)
T TIGR00575       533 TAKLLAKHFGTLDKLKAASLETLESIYQFDRSELLSVEGVGPKVAESIVNFFHDPNNLSLQPYRTAELIEKLEELGVNME  612 (706)
T ss_pred             HHHHHHHHCCCHHHHHHCCHHHHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCH
T ss_conf             99999985588689985082167788751605564101402789999999871200013560468999999988316310


Q ss_pred             C----------CCC-----CCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCC-HHHH
Q ss_conf             5----------432-----24688216866999725889987899999998298499811163217997788886-3798
Q gi|254781172|r  637 G----------RHE-----KNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGS-KLEK  700 (731)
Q Consensus       637 ~----------~~~-----~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gS-Kl~K  700 (731)
                      .          ...     ...+++|+||+|||||+|++|||++++++|+++||||+||||+||||||+|++||| |++|
T Consensus       613 ~~D~~~~LL~~~~~~~~~~~~~~~~~~GK~fVlTG~L~~~sR~~a~~~~~~lGgkv~sSVS~kTD~viaG~~aGs~Kl~k  692 (706)
T TIGR00575       613 SEDEFCRLLDQALKEKVEAELAGSPLAGKTFVLTGTLSQMSRDEAKELLEALGGKVASSVSKKTDYVIAGEKAGSRKLAK  692 (706)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCEEECCCEEEEEEEEEECCCCHHHHHH
T ss_conf             11357877764201100100057520277689951568888899999999809978004000440789855855468999


Q ss_pred             HHHCCCEEECHHHH
Q ss_conf             99749917379999
Q gi|254781172|r  701 AQQLGVKIMNEEQF  714 (731)
Q Consensus       701 A~~LgI~Ii~e~ef  714 (731)
                      |++|||+||||++|
T Consensus       693 A~~Lgi~il~Ee~l  706 (706)
T TIGR00575       693 AQELGIPILNEEEL  706 (706)
T ss_pred             HHHCCCCCCCCCCC
T ss_conf             99718942343149


No 2  
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=100.00  E-value=0  Score=1659.17  Aligned_cols=666  Identities=42%  Similarity=0.732  Sum_probs=637.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEECC
Q ss_conf             99999999999999999999843317798208789999999999998977203115899996200364323577504516
Q gi|254781172|r   13 SIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHS   92 (731)
Q Consensus        13 s~~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H~   92 (731)
                      +|+++++||.+|+++|++||++||++++|+|||+|||+|+++|+.||++||++.   +||||||+||+.+..+|.||+|+
T Consensus         1 ~m~~~~~~i~~L~~~i~~~n~~YY~~~~p~isD~eYD~L~~eL~~lE~~~P~~~---~~~SPt~~VG~~~~~~f~kv~H~   77 (668)
T PRK07956          1 TMEEAKKRIEELREELNHHAYAYYVLDNPEISDAEYDRLYRELLALEAEHPELI---TPDSPTQRVGGAPLDGFEKVRHL   77 (668)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             977999999999999999999864389987888999999999999998690555---89998443366612478733689


Q ss_pred             CCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCC
Q ss_conf             64257021599999999999999861246777611999941581899999859989988865986556669997753102
Q gi|254781172|r   93 IPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPT  172 (731)
Q Consensus        93 ~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~  172 (731)
                      .|||||+|+|+.+||.+|++|+.+.+.   .....|+||||+||+|++|+|++|+|++|+|||||.+|||||+|+++|++
T Consensus        78 ~pMlSL~k~~~~~el~~~~~r~~k~l~---~~~~~~~~epKiDGlsisL~Ye~G~L~~a~TRGdG~~GeDVT~nv~~I~~  154 (668)
T PRK07956         78 VPMLSLDNAFSEEELRAFDKRVRKRLS---GPSLTYVCELKIDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRS  154 (668)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHCC---CCCCCEEEEEECCCEEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf             877460133999999999999998618---88865798860461689999989999887615899731338788876526


Q ss_pred             CCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCC-CCC
Q ss_conf             432233544550489999998520212345564314854334234567777523455553-011105664102454-332
Q gi|254781172|r  173 IPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTS-EIF  250 (731)
Q Consensus       173 iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~-~~~  250 (731)
                      ||++|..++|+.+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||..+ .|+|+||+|+++... ...
T Consensus       155 iP~~l~~~~p~~leiRGEv~~~~~~F~~lN~~~~~~g~~~faNpRNaaAGslrqld~~~~~~R~L~~~~y~~~~~~~~~~  234 (668)
T PRK07956        155 IPLRLQDNVPEVLEVRGEVFMPKADFEALNEERREAGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGVLEGGEL  234 (668)
T ss_pred             CCCCCCCCCCCEEEEEEEEEEEHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCHHCCCCCEEEEEECCCCCCCCC
T ss_conf             64312246886599988999986689999899997178766784889877977589311203776699997013478888


Q ss_pred             CCCCHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECC
Q ss_conf             10000368999975996654148874032113455665531001123437637773110001115876568663123114
Q gi|254781172|r  251 AKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKF  330 (731)
Q Consensus       251 ~~~~~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf  330 (731)
                      +.+|++.|++|+.|||+|+++...|.+++++.+++++|.+.|+.+||+|||+||||||+.+|+.||+|+|+|||||||||
T Consensus       235 ~~t~~e~l~~l~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~LG~tsk~PrwAiA~Kf  314 (668)
T PRK07956        235 PDSQSEALEFLKAWGFPVNPYTKLCSSIEEVLAFYEYIEEERHDLPYDIDGVVIKVDDLALQEELGFTSKAPRWAIAYKF  314 (668)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCEEEECCHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCHHHHHHCCCCCCCCCEEEEECC
T ss_conf             66799999999977998886759958899999999999987751776667469995538878753976689780478747


Q ss_pred             CCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCH
Q ss_conf             56215899878899403562258999974333026400010148989997502345432224684407689998358702
Q gi|254781172|r  331 AEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVI  410 (731)
Q Consensus       331 ~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVI  410 (731)
                      |+++++|+|.+|+|||||||+|||||+|+||.|+|++|+||||||+++|++           +||+|||+|.|+||||||
T Consensus       315 ~~e~~~T~l~~I~~qVGRTG~iTPvA~l~PV~l~G~~VsrATLHN~~~I~~-----------~~i~iGd~V~v~raGdVI  383 (668)
T PRK07956        315 PAEEATTKLLDIEVQVGRTGAVTPVARLEPVEVAGVTVSRATLHNADEIER-----------KDIRIGDTVVVRRAGDVI  383 (668)
T ss_pred             CCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCEEEEECCCCCHHHHHH-----------CCCCCCCEEEEEECCCCC
T ss_conf             736799997777997347635626999987871560675236478899997-----------078999989999888887


Q ss_pred             HHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             56654101235787304777043265775010337865445210100354344114466553321301231035410355
Q gi|254781172|r  411 PKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQ  490 (731)
Q Consensus       411 P~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GLG~k~  490 (731)
                      |+|++|+.++|++++++|.||++||+||+++++..+.      +++||+|+.+||+|++++|.|||||+||||+|||+++
T Consensus       384 P~I~~v~~~~r~~~~~~~~~P~~CP~C~s~l~~~~~~------~~~~C~N~~~Cpaq~~~~i~hF~Sr~amdI~GlG~~~  457 (668)
T PRK07956        384 PEVVGVVLEKRPGDEREIVMPTHCPVCGSELVREEGE------AVLRCTNGLSCPAQLKERLIHFVSRNAMDIDGLGEKI  457 (668)
T ss_pred             CCEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEECCC------EEEECCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHH
T ss_conf             2004641301899887543677876779857993696------3787789989989999988865244531646659999


Q ss_pred             HHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             55653057654045410110106777531000100013421001456899998752234666776301011116899999
Q gi|254781172|r  491 LDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSL  570 (731)
Q Consensus       491 Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~L  570 (731)
                      |++|+++    |+|++++|||.|+.+      +|++++|||+|||+||+++|++||+++|+|||+||||||||+++|++|
T Consensus       458 i~~L~~~----g~i~~~~Diy~L~~~------~L~~l~gfgeKsa~nLl~aIe~SK~~~l~r~L~ALGI~~VG~~~Ak~L  527 (668)
T PRK07956        458 IEQLFEK----GLIHTPADLFKLTEE------DLLQLEGFGEKSAQNLLDAIEKSKETPLARFLYALGIRHVGEKAAKAL  527 (668)
T ss_pred             HHHHHHC----CCCCCHHHHHCCCHH------HHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHH
T ss_conf             9999876----876658999728854------540212355669999999999854775888998627864129999999


Q ss_pred             HHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             98829989999978977612511778761388867899999999966979999999999733877654322468821686
Q gi|254781172|r  571 AKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENK  650 (731)
Q Consensus       571 a~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk  650 (731)
                      +++|++++++..+          +.++|.+|+|||+++|+||++||+++.|++++++|.+.+...........+++|+||
T Consensus       528 a~~f~sl~~l~~a----------s~e~L~~I~giG~~~A~si~~ff~~~~n~~~i~~L~~~g~~~~~~~~~~~~~~l~Gk  597 (668)
T PRK07956        528 ARHFGSLEALEAA----------SEEELAAVEGIGEEVAQSIVEFFAVEHNRELIDELLEEGLGPEDEKEEAADSPLAGK  597 (668)
T ss_pred             HHHHCCHHHHHHC----------CHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
T ss_conf             9996689999708----------999985768844999999999970976899999999837986655444668865898


Q ss_pred             EEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHH
Q ss_conf             69997258899878999999982984998111632179977888863798997499173799999999882
Q gi|254781172|r  651 KLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQY  721 (731)
Q Consensus       651 ~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~  721 (731)
                      +|||||+|++|+|++++++||++||+|+|||||||||||+|+++|||++||++|||+||+|+||++||++.
T Consensus       598 t~ViTGtl~~~sR~e~k~~ie~~Ggkv~sSVSkkTd~LV~Ge~~GSKl~KA~~LGI~Ii~E~ef~~ll~~g  668 (668)
T PRK07956        598 TVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDYVVAGEAAGSKLAKAQELGVKVLDEEEFLRLLGEG  668 (668)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCEECCCCCCCCEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHCC
T ss_conf             89998069998989999999987999946401675299988998858999998699083499999998478


No 3  
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=100.00  E-value=0  Score=1632.49  Aligned_cols=663  Identities=42%  Similarity=0.750  Sum_probs=630.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEEC
Q ss_conf             89999999999999999999984331779820878999999999999897720311589999620036432357750451
Q gi|254781172|r   12 LSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTH   91 (731)
Q Consensus        12 ~s~~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H   91 (731)
                      +++.+++++|.+|+++|++|+|.||++++|+|||+|||+|+++|.+||++||++++   ||||||+||+.++.+|.||+|
T Consensus         2 ~~~~~~~~~i~~L~~~L~~~~~~Yyv~d~P~VsD~eYD~L~reL~~lE~~~Pel~~---~dSPtqrVG~~~~~~F~kv~H   78 (667)
T COG0272           2 WSMAEAQEEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQELEEKHPELIT---PDSPTQRVGAAPLNAFKKVRH   78 (667)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCC---CCCCCCCCCCCCHHCCCCCCC
T ss_conf             53678999999999999997788722699979858999999999999986877678---999965557430100453347


Q ss_pred             CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHC
Q ss_conf             66425702159999999999999986124677761199994158189999985998998886598655666999775310
Q gi|254781172|r   92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIP  171 (731)
Q Consensus        92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~  171 (731)
                      ..|||||+|+||.+||.+|++|+.+.+..    ...|+|||||||+|+||+|+||+|++|+|||||.+|||||+|+|||+
T Consensus        79 ~~pMlSL~naf~~~el~~f~~ri~~~~~~----~~~y~~EpKiDGlsisL~YenG~Lv~aaTRGdG~~GEDiT~NvrtI~  154 (667)
T COG0272          79 PVPMLSLDNAFDEEELRAFDRRIRKFLGD----SVEYVVEPKIDGLAISLVYENGKLVRAATRGDGTTGEDITANVRTIR  154 (667)
T ss_pred             CCCCCCHHHCCCHHHHHHHHHHHHHHCCC----CCCEEEEEECCEEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHH
T ss_conf             87554344227989999999999875178----86568886236189999997899988624679962642222140265


Q ss_pred             CCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCCC-C
Q ss_conf             2432233544550489999998520212345564314854334234567777523455553-0111056641024543-3
Q gi|254781172|r  172 TIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSE-I  249 (731)
Q Consensus       172 ~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~~-~  249 (731)
                      +||++|.. .|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||+.+ .|+|.||+|+|+.... .
T Consensus       155 ~IP~~l~~-~p~~lEVRGEvfm~k~~F~~lN~~~~~~g~~~faNpRNaAAGsLRqlD~~ita~R~L~~f~y~~~~~~~~~  233 (667)
T COG0272         155 SIPLKLPG-APAVLEVRGEVFMPKEDFEALNEEREEEGEKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEGL  233 (667)
T ss_pred             HHHHHCCC-CCCEEEEEEEEEEEHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCHHHHHCCCCEEEEEECCCCCCCC
T ss_conf             54333257-88538997689977899999999999847988678044555466536968774177359998677667677


Q ss_pred             CCCCCHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEEC
Q ss_conf             21000036899997599665414887403211345566553100112343763777311000111587656866312311
Q gi|254781172|r  250 FAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHK  329 (731)
Q Consensus       250 ~~~~~~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~K  329 (731)
                      .+.||++.|++|+.|||+|+++...|.+.+++.++|++|...|++|||+|||+|||+||+++|+.||+|+|+||||||||
T Consensus       234 ~~~t~~e~l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~L~y~IDGvViKvn~l~~q~~lG~tsk~PrWAiAyK  313 (667)
T COG0272         234 LADTQSERLAFLKAWGFPVNPYTRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVNDLALQRELGFTSKAPRWAIAYK  313 (667)
T ss_pred             CCCCHHHHHHHHHHCCCCCCCHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCHHHHHHHCCCCCCCCEEEEEC
T ss_conf             74579999999997599988076660899999999999986322289766438999676888987097068986323553


Q ss_pred             CCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCC
Q ss_conf             45621589987889940356225899997433302640001014898999750234543222468440768999835870
Q gi|254781172|r  330 FAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEV  409 (731)
Q Consensus       330 f~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdV  409 (731)
                      |||+++.|+|.||+|||||||+|||||.++||.|+|++|+||||||.|+|++           +||+|||+|.|.|||||
T Consensus       314 Fpa~e~~T~l~dI~~qVGRTG~iTPvA~L~PV~laG~~VsrATLHN~d~I~r-----------kdIrIGDtV~V~kAGdV  382 (667)
T COG0272         314 FPAEEAVTKLLDIEVQVGRTGAITPVARLEPVELAGVTVSRATLHNVDEIKR-----------KDIRIGDTVVVRKAGDV  382 (667)
T ss_pred             CCCHHEEEEEEEEEEECCCCEEEEEEEEEEEEEECCEEEEEEECCCHHHHHH-----------CCCCCCCEEEEEECCCC
T ss_conf             7732214689999995268536413379776998798999762388888986-----------38787999999736887


Q ss_pred             HHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             25665410123578730477704326577501033786544521010035434411446655332130123103541035
Q gi|254781172|r  410 IPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQ  489 (731)
Q Consensus       410 IP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GLG~k  489 (731)
                      ||+|++|+.++|++++++|.||++||+|||++++..++      +++||+|+.+||+|.+++|.||+||+||||+|||++
T Consensus       383 IP~V~~Vv~e~R~~~~~~~~~P~~CP~C~s~l~r~~~e------~~~rC~n~~~C~aq~~e~l~hfvSr~AmdI~GLG~k  456 (667)
T COG0272         383 IPQVVGVVLEKRPGNEKPIPFPTHCPVCGSELVREEGE------VVIRCTNGLNCPAQLKERLIHFVSRNALDIDGLGEK  456 (667)
T ss_pred             CCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEECCCC------EEEECCCCCCCHHHHHHHEEEEECCCCCCCCCCCHH
T ss_conf             77323554344779998888999798899976742675------568668987885888623346744786577776799


Q ss_pred             HHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             55565305765404541011010677753100010001342100145689999875223466677630101111689999
Q gi|254781172|r  490 QLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARS  569 (731)
Q Consensus       490 ~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~  569 (731)
                      +|++|++++    +|++++|||+|+.++      ++.++||++||++||+++|++||+++|+|||+||||||||+++|+.
T Consensus       457 ~i~~L~e~~----lI~~~~Dly~Lt~~~------l~~l~~~~~ks~~nLl~aIe~sK~~~l~r~l~aLGIr~VG~~~Ak~  526 (667)
T COG0272         457 IIEQLFEKG----LIKDIADLYTLTEED------LLSLEGFGEKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTAKS  526 (667)
T ss_pred             HHHHHHHCC----CCCCHHHHHHCCHHH------HHHCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf             999999737----537879877378988------8416224465799999999986049899999987971140899999


Q ss_pred             HHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCC-CCCCC
Q ss_conf             99882998999997897761251177876138886789999999996697999999999973387765432246-88216
Q gi|254781172|r  570 LAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNV-SSEIE  648 (731)
Q Consensus       570 La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~-~~~l~  648 (731)
                      |+++|++++++..+          +.++|..|+|||+++|.||++||+++.|++++++|...+........... .++|+
T Consensus       527 La~~f~sl~~l~~a----------~~e~l~~i~giG~~vA~si~~ff~~~~~~~li~~L~~~g~~~~~~~~~~~~~~~l~  596 (667)
T COG0272         527 LARHFGTLEALLAA----------SEEELASIPGIGEVVARSIIEFFANEENRELIDELLAAGVKWEEEEKISIETSPLA  596 (667)
T ss_pred             HHHHHHHHHHHHHC----------CHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
T ss_conf             99876029999842----------99999506661289999999997277789999999971787221002333444457


Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHH
Q ss_conf             86699972588998789999999829849981116321799778888637989974991737999999998
Q gi|254781172|r  649 NKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQ  719 (731)
Q Consensus       649 gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~  719 (731)
                      ||||||||+|++|+|++++++|+++||||++||||||||||+|++||||++||++|||+||||++|++||+
T Consensus       597 gkt~V~TGtL~~~sR~eak~~le~lGakv~~SVSkktD~vvaG~~aGSKl~kA~eLgv~i~~E~~~~~ll~  667 (667)
T COG0272         597 GKTFVLTGTLEGMSRDEAKALLEALGAKVSGSVSKKTDYVVAGENAGSKLAKAQELGVKIIDEEEFLALLG  667 (667)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHCCCEEECEECCCCEEEEECCCCCHHHHHHHHCCCEEECHHHHHHHHC
T ss_conf             97799966678789999999999869999210415410899758977078889974986745999998649


No 4  
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=100.00  E-value=0  Score=1232.11  Aligned_cols=535  Identities=23%  Similarity=0.389  Sum_probs=482.9

Q ss_pred             HHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             46889999999999999999999984331779820878999999999999897720311589999620036432357750
Q gi|254781172|r    9 IEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFK   88 (731)
Q Consensus         9 ~~~~s~~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~k   88 (731)
                      -.+||.++||++|++|+++|++||++||++++|+|||+|||+|+++|..||++||++.   +|+|||++||+       |
T Consensus        23 ~~~~~p~~ak~~I~~Lr~~i~~hn~~YY~~d~P~IsD~eYD~L~~eL~~LE~~~p~~~---~~~SPt~~vgg-------k   92 (563)
T PRK08097         23 CPDWSPARAQEEISALQQQLAQWDDAYWRQGKSPVDDEVYDQLRARLTQWQRCFGLPV---PRDPPLPPANG-------P   92 (563)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCC-------C
T ss_conf             9698989999999999999999999875289997888999999999999998686767---99999789998-------5


Q ss_pred             EECCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHH
Q ss_conf             45166425702159999999999999986124677761199994158189999985998998886598655666999775
Q gi|254781172|r   89 VTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIR  168 (731)
Q Consensus        89 v~H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~  168 (731)
                      |+|++|||||+|+|+.+|+.+|.++.           ..|+||||+||+|++|+|+||+|++|+|||||.+|||||+|++
T Consensus        93 v~H~~pMlSL~n~~~~~el~~~~~~~-----------~~~~vEpKiDGlaisL~YenG~Lv~A~TRGDG~~GEDVT~Nv~  161 (563)
T PRK08097         93 VMHPVAHTGVRKLADKQALARWMRGR-----------SDLWVQPKVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKAR  161 (563)
T ss_pred             CCCCCCCCCHHHCCCHHHHHHHHHCC-----------CCCEEEEECCCEEEEEEEECCEEEEEECCCCCCCCEEHHHHHH
T ss_conf             25898764711118989999998413-----------0617622056468999998998988871379976504888777


Q ss_pred             HHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCC
Q ss_conf             31024322335445504899999985202123455643148543342345677775234555530111056641024543
Q gi|254781172|r  169 AIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSE  248 (731)
Q Consensus       169 ~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~  248 (731)
                      +|++||++|+.. |..+|||||+||++++|.+.        ...|+||||+|||+||++++..+.|+|.||+|++..   
T Consensus       162 tI~~IP~~L~~~-p~~levRGEv~~~~~~~~~~--------~~~~aNPRNaAAGsLr~~~~~~~~~~l~~f~y~~~~---  229 (563)
T PRK08097        162 LIPAIPQTLPGA-PANLVLQGELFLRREGHIQA--------QMGGINARSKVAGLMMRKDLSPALNSIGLFVWAWPD---  229 (563)
T ss_pred             HHCCCCHHHCCC-CCEEEEEEEEEEECCHHHHH--------HCCCCCCCHHHHHHHHHCCCHHHHHCCCEEEEECCC---
T ss_conf             770603221799-96479977999861458887--------437889734552045523848777416779994588---


Q ss_pred             CCCCCCHHHHHHHHHCCCCCCC-CEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEE
Q ss_conf             3210000368999975996654-148874032113455665531001123437637773110001115876568663123
Q gi|254781172|r  249 IFAKGQYEMLQKMRCLGFPVNN-GVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMIS  327 (731)
Q Consensus       249 ~~~~~~~e~l~~L~~~GF~v~~-~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA  327 (731)
                       .+.+|++.|++|+.|||++++ +...+.+++++.+++++|  .|+.|||+|||+|||+|+..+|+.  +|+|+||||||
T Consensus       230 -g~~~~~e~l~~L~~~GF~v~~~~~~~~~~~~ev~~~~~~~--~R~~L~y~iDGiViK~~~~~~~~~--~tsk~PRWAIA  304 (563)
T PRK08097        230 -GPATMPERLAQLATAGFPLTQKYSHAVKNADEVARWRQHW--YRSPLPFVTDGVVVRQAKEPPGRR--WQPGQGEWLVA  304 (563)
T ss_pred             -CCCCHHHHHHHHHHCCCCCCHHHCEECCCHHHHHHHHHHH--HHCCCCCCCCEEEEEECCHHHHHH--HCCCCCCCEEE
T ss_conf             -9779999999999779998856612048899999999997--533588777538998356888875--25689873146


Q ss_pred             ECCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf             11456215899878899403562258999974333026400010148989997502345432224684407689998358
Q gi|254781172|r  328 HKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAG  407 (731)
Q Consensus       328 ~Kf~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaG  407 (731)
                      ||||+++++|+|++|+|||||||+|||||+|+||.|+|+|||||||||+++|++           +||+|||+|.|+|||
T Consensus       305 yKF~ae~~~T~l~~I~~qVGRTG~iTPVA~lePV~l~G~tVsrATLHN~d~I~r-----------~diriGD~V~V~rAG  373 (563)
T PRK08097        305 WKYPPVQQVAEVRAIQFAVGRTGKITVVLSLAPVMLDDKRVQRVNIGSVRRWQQ-----------WDIAPGDQILVSLAG  373 (563)
T ss_pred             ECCCCCCCEEEEEEEEEEECCCCEEEEEEEEEEEEECCEEEEECCCCCHHHHHH-----------CCCCCCCEEEEEECC
T ss_conf             657510307999888998667511325899887887789998403578889987-----------499989999999678


Q ss_pred             CCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECC--CCCCCCHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             702566541012357873047770432657750103378654452101003--543441144665533213012310354
Q gi|254781172|r  408 EVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRC--TGGLACSAQQLERLKHFVSRDAFNIEG  485 (731)
Q Consensus       408 dVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC--~n~~~Cpaq~~~~i~hF~SK~aldI~G  485 (731)
                      ||||+|++|+.  |.+...++.+|..|+.                 ..++|  +|. +||+|.+++|.||+||+||||+|
T Consensus       374 dVIP~V~~Vv~--r~~~~~~~~~P~~~~~-----------------~~~~C~~~~~-~C~aq~~~rl~hF~Sr~amdI~G  433 (563)
T PRK08097        374 QGIPRLDEVVW--RGAERAKPTPPDADRF-----------------HSLSCFQASP-GCQEQFIARLVWLGGKQGLGLDG  433 (563)
T ss_pred             CCCCCCCEECC--CCCCCCCCCCCCCCCC-----------------CCCEECCCCC-CCHHHHHHHHHHHHCCCCCCCCC
T ss_conf             86787044126--6778899889987788-----------------8852178999-99799999978600234158567


Q ss_pred             HHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             10355556530576540454101101067775310001000134210014568999987522346667763010111168
Q gi|254781172|r  486 LGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAE  565 (731)
Q Consensus       486 LG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~  565 (731)
                      ||+++|++|+++    |+|++++|||+|+.+      +|.+++|||+|||+||+++|++||+++|+|||+|||||+||+.
T Consensus       434 LGek~i~~L~~~----gli~~~~Dly~L~~~------~L~~l~g~geKsa~nLl~aIe~SK~~~l~r~l~aLGI~~vG~~  503 (563)
T PRK08097        434 IGEGTWRALHQT----GRFEHLFSWLALTPE------QLANTPGIGKARAAQLWHQFNLARQQPFTRWLKALGIPLTQAA  503 (563)
T ss_pred             CCHHHHHHHHHC----CCCCCHHHHHHCCHH------HHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHH
T ss_conf             699999999975----888997997508999------9855898578999999999999728999999998699508999


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCC
Q ss_conf             9999998829989999978977612511778761388867899999999966979999999999733877
Q gi|254781172|r  566 IARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPS  635 (731)
Q Consensus       566 ~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~~  635 (731)
                      +|+.|+.+|   +.++          ..+.++|.+|+|||+++|+||++||+++.|++++++|.+.|...
T Consensus       504 ~a~~l~~~~---~~L~----------~as~e~l~~i~gIG~~~A~si~~fF~~~~n~~li~~L~~~Gvn~  560 (563)
T PRK08097        504 LNASLDRSW---QQLL----------SRTEQQWQQLPGIGEGRARQLIAFFDHPQVQALAEWLAAQGITG  560 (563)
T ss_pred             HHHHHHCCH---HHHH----------CCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHCCCCC
T ss_conf             999986199---9997----------39998995579848999999999985988999999999769998


No 5  
>smart00532 LIGANc Ligase N family.
Probab=100.00  E-value=0  Score=1127.94  Aligned_cols=439  Identities=45%  Similarity=0.784  Sum_probs=421.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCC
Q ss_conf             99999999999999998433177982087899999999999989772031158999962003643235775045166425
Q gi|254781172|r   17 ARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTL   96 (731)
Q Consensus        17 ~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H~~pMl   96 (731)
                      |++||.+|+++|++||++||+.++|+|||++||+|+++|..||++||++.   +|+||||+||+++...|.||+|+.|||
T Consensus         1 ak~~i~~L~~~I~~~n~~YY~~~~p~ISD~eYD~L~~eL~~Le~~~P~l~---~~~SPt~~VG~~~~~~f~kv~H~~pMl   77 (441)
T smart00532        1 AQKEISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELK---TPDSPTQRVGGKPLEGFNKVRHPVPML   77 (441)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             97899999999999999876189987998999999999999998691446---899985455766166886217898675


Q ss_pred             CHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCC
Q ss_conf             70215999999999999998612467776119999415818999998599899888659865566699977531024322
Q gi|254781172|r   97 SLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRV  176 (731)
Q Consensus        97 SL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~  176 (731)
                      ||+|+|+.+||.+|++|+.+.+.    ....|+|||||||+|++|+|++|+|++|+|||||.+|||||+|+++|++||++
T Consensus        78 SL~k~~~~~el~~w~~r~~k~l~----~~~~~~~epKiDGlsisL~Y~~G~L~~a~TRGDG~~GeDVT~nv~~I~~iP~~  153 (441)
T smart00532       78 SLDNAFDEDELRAFDERIEKALG----SPFAYVVEPKIDGLSVSLLYENGKLVQAATRGDGTVGEDVTQNVKTIRSIPLR  153 (441)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHC----CCCCEEEEECCCCEEEEEEEECCEEEEEEECCCCCHHHHHHHHHHHCCCCCHH
T ss_conf             70334899999999999998624----66435787614752689999799998887247982555455555311578532


Q ss_pred             CCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCCCC-CCCCC
Q ss_conf             33544550489999998520212345564314854334234567777523455553-01110566410245433-21000
Q gi|254781172|r  177 LSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSEI-FAKGQ  254 (731)
Q Consensus       177 l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~~~-~~~~~  254 (731)
                      |..+.|+.+|||||+||++++|++||+++.+.|+++|+||||+|||+|||+||..+ .|+|+||+|+|+..+.. .+.+|
T Consensus       154 l~~~~p~~leiRGEv~~~~~~F~~lN~~~~~~~~~~faNpRNaaAGslrqld~~~~~~r~L~f~~y~~~~~~~~~~~~t~  233 (441)
T smart00532      154 LSGDVPERLEVRGEVFMPKEDFLALNEELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEELFLPKTQ  233 (441)
T ss_pred             HCCCCCCEEEEEEEEEEEHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCHHHHCCCEEEEEEECCCCCCCCCCCH
T ss_conf             14788863899889998721344788999864887667837898899876793015425516999980246777785689


Q ss_pred             HHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCCCE
Q ss_conf             03689999759966541488740321134556655310011234376377731100011158765686631231145621
Q gi|254781172|r  255 YEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQ  334 (731)
Q Consensus       255 ~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~e~  334 (731)
                      ++.|++|+.|||+|+++...+.+.+++..++++|.+.|+.+||+|||+|||+||+.+|+.||+|+|+|||||||||++++
T Consensus       234 ~e~l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwAiA~Kf~~e~  313 (441)
T smart00532      234 SEALKWLKELGFPVSPHTRLCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPAEE  313 (441)
T ss_pred             HHHHHHHHHCCCCCCCCEEEECCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHHCCCCCCCCCEEEEECCCCCE
T ss_conf             99999999779924876199689999999999999665629988772699985889875428546898834897688665


Q ss_pred             EEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHHH
Q ss_conf             58998788994035622589999743330264000101489899975023454322246844076899983587025665
Q gi|254781172|r  335 ASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVV  414 (731)
Q Consensus       335 ~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP~I~  414 (731)
                      ++|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++           ||+|||+|.|+|||||||+|+
T Consensus       314 ~~T~l~~I~~qVGRtG~itPva~lePV~l~G~~Vs~aTLhN~~~i~~~-----------~i~iGd~V~i~raGdVIPkI~  382 (441)
T smart00532      314 AETKLLDIIVQVGRTGKITPVAELEPVFLAGSTVSRATLHNEDEIEEK-----------DIRIGDTVVVRKAGDVIPKVV  382 (441)
T ss_pred             EEEEEEEEEEECCCCEEEEEEEEEEEEEECCEEEEEECCCCHHHHHHC-----------CCCCCCEEEEEECCCCCCCEE
T ss_conf             789999999973786287689999768867869997056898999975-----------999999999997788887431


Q ss_pred             HHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             410123578730477704326577501033786544521010035434411446655332130123
Q gi|254781172|r  415 DIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDA  480 (731)
Q Consensus       415 ~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~a  480 (731)
                      +|++++|++++++|.+|+.||+||+++++..++      +++||+|. +||+|+.++|.|||||+|
T Consensus       383 ~vv~~~r~~~~~~~~~P~~CP~C~s~l~~~~~~------~~~~C~n~-~C~aq~~~~i~hf~Sr~A  441 (441)
T smart00532      383 GVVKEKRPGDEREIEMPTHCPSCGSELVREEGE------VDIRCPNP-LCPAQLIERIIHFASRKA  441 (441)
T ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCCEEEECCCC------EEEECCCC-CCHHHHHHHEEEEECCCC
T ss_conf             411023899885655899898997983843898------78988999-898999701148756799


No 6  
>pfam01653 DNA_ligase_aden NAD-dependent DNA ligase adenylation 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 domain is the catalytic adenylation domain. The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism.
Probab=100.00  E-value=0  Score=747.00  Aligned_cols=312  Identities=41%  Similarity=0.725  Sum_probs=296.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf             99999999999999999984331779820878999999999999897720311589999620036432357750451664
Q gi|254781172|r   15 EQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIP   94 (731)
Q Consensus        15 ~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H~~p   94 (731)
                      ++||+||++|+++|++||++||+.++|+|||++||+|+++|+.||++||++.   +|+|||++||+++.++|.||+|+.|
T Consensus         1 e~~k~~i~~L~~~I~~~n~~YY~~~~p~ISD~eYD~L~~eL~~le~~~P~l~---~~~spt~~VG~~~~~~f~kv~H~~p   77 (315)
T pfam01653         1 EEAQQEIARLRELIRQYDYHYYVLDNPEVPDAEYDRLYRRLQALEEKFPELI---TPDSPTQRVGAPLLGDFKKVRHPAP   77 (315)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCHHCC---CCCCCCCCCCCCCCCCCCCEECCCC
T ss_conf             9589999999999999999986489997999999999999999998691004---8999522358765577750036875


Q ss_pred             CCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCC
Q ss_conf             25702159999999999999986124677761199994158189999985998998886598655666999775310243
Q gi|254781172|r   95 TLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIP  174 (731)
Q Consensus        95 MlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP  174 (731)
                      ||||+|+|+.+||.+|++|+.+.+..   ....|+|||||||+|++|+|++|+|++|+|||||.+|||||+|+++|++||
T Consensus        78 MlSL~k~~~~~el~~w~~r~~~~~~~---~~~~~~~e~KiDGlsisL~Y~~G~L~~a~TRGDG~~GeDIT~nv~~I~~iP  154 (315)
T pfam01653        78 MLSLDNAFDEDELAAWIRRIRRRLGN---SEKAYVVEPKIDGVAVSLTYEDGVLVRAATRGDGTTGEDVTQNVKTIRAIP  154 (315)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCCC---CCCCEEEEECCCCCEEEEEEECCEEEEEEECCCCCCCCCHHHHHHHHCCCH
T ss_conf             65521115667799999999875188---875358876247710478980890568875589864217176564333660


Q ss_pred             CCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCCC--CCC
Q ss_conf             2233544550489999998520212345564314854334234567777523455553-0111056641024543--321
Q gi|254781172|r  175 RVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSE--IFA  251 (731)
Q Consensus       175 ~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~~--~~~  251 (731)
                      ++|+.+ |+.+|||||+||++++|+++|+++.+.|+++|+||||+|||+||++||..+ .|+|+||||+|+....  ..+
T Consensus       155 ~~l~~~-~~~ievRGEv~i~~~~F~~lN~~~~~~~~~~faNpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~  233 (315)
T pfam01653       155 LTLPGD-PARLEVRGEVFMPKEDFEALNEEREEEGEKPFANPRNAAAGSLRQLDPEITAKRKLRFFVYGLGLPEGLELGP  233 (315)
T ss_pred             HHCCCC-CCEEEEEEEEEEEHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCHHHCCCCEEEEEECCCCCCCCCCC
T ss_conf             211799-8728999999964789889889999727886778289999998625951221687779998676666677785


Q ss_pred             CCCHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCC
Q ss_conf             00003689999759966541488740321134556655310011234376377731100011158765686631231145
Q gi|254781172|r  252 KGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFA  331 (731)
Q Consensus       252 ~~~~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~  331 (731)
                      .+|++.|++|+.|||+|+++...+.+++++.+++++|.+.|+.++|+|||||||+||+.+|+.||+|+|+||||||||||
T Consensus       234 ~t~~e~l~~L~~~GF~~~~~~~~~~~~~~v~~~~~~~~~~R~~l~y~iDGiVikvn~~~~q~~LG~ts~~PrwAiA~Kf~  313 (315)
T pfam01653       234 QTQSEALKQLKSLGFPVSPHTRLCKNIDEVLDYYAEWEKKRDELPFEIDGVVVKVNELPLQRELGFTSKAPRWAIAYKFP  313 (315)
T ss_pred             CCHHHHHHHHHHCCCCCCCCCEEECCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHHHCCCCCCCCCEEEECCC
T ss_conf             68999999999779976871178799999999999999777629988874799980989999828767998843786768


Q ss_pred             CC
Q ss_conf             62
Q gi|254781172|r  332 EK  333 (731)
Q Consensus       332 ~e  333 (731)
                      ||
T Consensus       314 ~E  315 (315)
T pfam01653       314 AE  315 (315)
T ss_pred             CC
T ss_conf             99


No 7  
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=100.00  E-value=0  Score=724.98  Aligned_cols=306  Identities=42%  Similarity=0.750  Sum_probs=293.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCH
Q ss_conf             99999999999999843317798208789999999999998977203115899996200364323577504516642570
Q gi|254781172|r   19 KELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSL   98 (731)
Q Consensus        19 ~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H~~pMlSL   98 (731)
                      +||.+|+++|++||++||+.++|+|||++||+|+++|+.||++||++.   .++|||++||+++..+|.||+|+.|||||
T Consensus         1 ~ri~~L~~~I~~~n~~Yy~~~~p~ISD~eYD~L~~eL~~le~~~p~l~---~~~spt~~VG~~~~~~~~kv~H~~pMlSL   77 (307)
T cd00114           1 ERIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELK---TPDSPTQRVGGTPLSGFKKVRHPVPMLSL   77 (307)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             979999999999999986489997988999999999999998682336---89998655587525667642178655453


Q ss_pred             HHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             21599999999999999861246777611999941581899999859989988865986556669997753102432233
Q gi|254781172|r   99 EKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLS  178 (731)
Q Consensus        99 ~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~  178 (731)
                      +|+|+++||.+|++|+.+.+.    ....|+|||||||+|++|+|++|+|++|+|||||.+|||||+|+++|++||++|+
T Consensus        78 ~k~~~~~el~~w~~r~~~~~~----~~~~~~vepKlDGlaisl~Y~~G~L~~a~TRGDG~~GeDIT~nv~~i~~iP~~l~  153 (307)
T cd00114          78 DNAFDEEELRAFDERIKRFLG----EEPAYVVEPKIDGLSISLRYENGVLVQAATRGDGTTGEDVTENVRTIRSIPLTLA  153 (307)
T ss_pred             CCCCCHHHHHHHHHHHHHHHC----CCCCEEEEECCCCEEEEEEEECCEEEEEEECCCCCCCCCCCCCHHHHCCCHHHCC
T ss_conf             443889999999999998515----6744588761376368999809966676625898655483023212227313237


Q ss_pred             CCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCCCCCCCCCHHH
Q ss_conf             544550489999998520212345564314854334234567777523455553-0111056641024543321000036
Q gi|254781172|r  179 LNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSEIFAKGQYEM  257 (731)
Q Consensus       179 ~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~~~~~~~~~e~  257 (731)
                      . .|+.+|||||+||++++|+++|+++.+.|+++|+||||+|||+||++||..+ .|+|+||+|+|+.+....+.+|++.
T Consensus       154 ~-~~~~levRGEi~~~~~~F~~~n~~~~~~~~~~f~NpRN~aAG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~t~~e~  232 (307)
T cd00114         154 G-APETLEVRGEVFMPKADFEALNKEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLGPKTQSEA  232 (307)
T ss_pred             C-CCCEEEEEEEEEECHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHHHHCCCCEEEEEEECCCCCCCCCHHHH
T ss_conf             9-986299999997528879999999998178866573378761656248532440766178998552578886778999


Q ss_pred             HHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCC
Q ss_conf             899997599665414887403211345566553100112343763777311000111587656866312311456
Q gi|254781172|r  258 LQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAE  332 (731)
Q Consensus       258 l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~  332 (731)
                      |++|+.|||+|+++...+.+.+++..++++|...|..++|+|||||||+||+.+|+.||+|+|+|||||||||||
T Consensus       233 l~~L~~~GF~~~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVvkvn~~~~~~~lG~ts~~PrwAiA~KfpA  307 (307)
T cd00114         233 LAFLKEWGFPVSPETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPA  307 (307)
T ss_pred             HHHHHHCCCCCCCCCEEECCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECHHHHHHHCCCCCCCCCEEEECCCC
T ss_conf             999997799668861897999999999999997642399887737999829899998487678987606856369


No 8  
>pfam03120 DNA_ligase_OB NAD-dependent DNA ligase OB-fold 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 domain found after the adenylation domain pfam01653 in NAD dependent ligases. OB-fold domains generally are involved in nucleic acid binding.
Probab=99.91  E-value=1.3e-24  Score=209.54  Aligned_cols=82  Identities=55%  Similarity=0.973  Sum_probs=78.7

Q ss_pred             EEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHHH
Q ss_conf             58998788994035622589999743330264000101489899975023454322246844076899983587025665
Q gi|254781172|r  335 ASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVV  414 (731)
Q Consensus       335 ~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP~I~  414 (731)
                      |+|+|++|+|||||||++||||+|+||.|+|++|+||||||++||+++           ||++||.|.|.|||||||+|+
T Consensus         1 A~T~v~~I~~~vgRtG~itPva~~ePV~l~G~~V~~atlhN~~~i~~~-----------~i~~Gd~V~I~raGdVIP~I~   69 (82)
T pfam03120         1 AVTKLLDIEVQVGRTGVITPVAILEPVELAGTTVSRATLHNEDEIEEK-----------DIRIGDTVVVRKAGDVIPKIV   69 (82)
T ss_pred             CEEEEEEEEEECCCCEEEEEEEEEEEEEECCEEEEEEECCCHHHHHHC-----------CCCCCCEEEEEECCCCCCCEE
T ss_conf             958999999955887088699999989989999999975798998645-----------999899999999788766673


Q ss_pred             HHCCCCCCCCCCE
Q ss_conf             4101235787304
Q gi|254781172|r  415 DIIVNERHPDAQP  427 (731)
Q Consensus       415 ~Vi~~~r~~~~~~  427 (731)
                      +|++++|+++++|
T Consensus        70 ~Vi~~~R~~~~~p   82 (82)
T pfam03120        70 GVVLEKRPGDTRP   82 (82)
T ss_pred             EEEHHHCCCCCCC
T ss_conf             8786238998999


No 9  
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.77  E-value=1.3e-18  Score=163.09  Aligned_cols=77  Identities=31%  Similarity=0.531  Sum_probs=73.2

Q ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECC---------CCCCHHHHHHHC-----CCEEE
Q ss_conf             8821686699972588998789999999829849981116321799778---------888637989974-----99173
Q gi|254781172|r  644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGD---------NPGSKLEKAQQL-----GVKIM  709 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge---------~~gSKl~KA~~L-----gI~Ii  709 (731)
                      ..+|+||+|||||+|+.|+|+|++++++++||+|.+||||+|||||+|+         .+|||++||++|     +|+||
T Consensus       218 ~~~~~g~~vvfTG~l~~~~R~ea~~~~~~~Gg~v~~sVskkT~~lV~G~~d~~~~~~~~~~sK~~kA~~L~~~G~~I~ii  297 (309)
T PRK06195        218 FTAFKEEVVVFTGGLASMTRDEAIGLVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKEGQNIKFL  297 (309)
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEECCCCCCCCCEEEECCCCHHHCCCCCCCHHHHHHHHHHHCCCCCEEE
T ss_conf             89878998999457997799999999998599966871677778998886311003677766999999998479996796


Q ss_pred             CHHHHHHHHHH
Q ss_conf             79999999988
Q gi|254781172|r  710 NEEQFLFLLQQ  720 (731)
Q Consensus       710 ~e~ef~~ll~~  720 (731)
                      +|++|++||++
T Consensus       298 ~E~~fl~~i~~  308 (309)
T PRK06195        298 NEEEFLQKIKE  308 (309)
T ss_pred             CHHHHHHHHHC
T ss_conf             59999998741


No 10 
>COG5275 BRCT domain type II [General function prediction only]
Probab=99.53  E-value=1.8e-14  Score=130.98  Aligned_cols=114  Identities=31%  Similarity=0.447  Sum_probs=89.6

Q ss_pred             HHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEE
Q ss_conf             61388867899999999966979999999999733877654322468821686699972588998789999999829849
Q gi|254781172|r  598 LIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVV  677 (731)
Q Consensus       598 L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv  677 (731)
                      |.+++-||-..+.++.+    +.  ...    ...+    .-..-....|.|++|||||-|...+|++++.+++.+||+|
T Consensus       122 ~~d~~~~~~~a~~t~~e----~~--~~~----~~~G----S~peg~~~cL~G~~fVfTG~l~TlsR~~a~~lvk~yGgrv  187 (276)
T COG5275         122 LIDVDSMGVMAPGTFYE----RA--ATT----QTPG----SVPEGERECLKGKVFVFTGDLKTLSRDDAKTLVKVYGGRV  187 (276)
T ss_pred             CEECCCCCCCCCCCCCC----HH--HHH----CCCC----CCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHCCEE
T ss_conf             12102235226876567----25--441----4777----7788986432561799942430003203888999868734


Q ss_pred             EEEEECCEEEEEECCCCC-CHHHHHHHCCCEEECHHHHHHHHHHHCCCC
Q ss_conf             981116321799778888-637989974991737999999998828656
Q gi|254781172|r  678 SAILSRKTDIIIVGDNPG-SKLEKAQQLGVKIMNEEQFLFLLQQYNTTL  725 (731)
Q Consensus       678 ~sSVSkkT~~LI~ge~~g-SKl~KA~~LgI~Ii~e~ef~~ll~~~~~~~  725 (731)
                      +.+.|.+|+|||.||++| +|++|+++|+|+.|+|++|..||+..-.++
T Consensus       188 T~~pSskTtflvlGdnaGP~K~ekiKqlkIkaidEegf~~LI~~~pa~g  236 (276)
T COG5275         188 TAVPSSKTTFLVLGDNAGPSKMEKIKQLKIKAIDEEGFDSLIKDTPAAG  236 (276)
T ss_pred             ECCCCCCEEEEEECCCCCHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCC
T ss_conf             4056654158996588881787889872875016778899973585347


No 11 
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.37  E-value=2.7e-12  Score=114.29  Aligned_cols=75  Identities=23%  Similarity=0.362  Sum_probs=68.9

Q ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCC--CCHHHHHHHCCCEEECHHHHHHHHHHH
Q ss_conf             2168669997258899878999999982984998111632179977888--863798997499173799999999882
Q gi|254781172|r  646 EIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNP--GSKLEKAQQLGVKIMNEEQFLFLLQQY  721 (731)
Q Consensus       646 ~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~--gSKl~KA~~LgI~Ii~e~ef~~ll~~~  721 (731)
                      .++|++|||||.++ +.|+++++.+...|..+++|||++|++||+|+..  +.|..||+++|||||+|.+|++||+.-
T Consensus       232 L~~Gm~VVfTGel~-~~r~e~~~~a~~aGl~~~~sVTr~TsllV~nd~~~~~gKa~~A~~~giPv~~e~~Fl~~l~~v  308 (313)
T PRK06063        232 LVQGMRVALSAEVS-RTHEELVERILHAGLAYSDSVDRETSLVVCNDPAPEQGKGYHARQLGVPVLPEAAFLELLRAV  308 (313)
T ss_pred             CCCCCEEEEECCCC-CCHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHC
T ss_conf             50688899958976-798999999997298304763476369995799986427787887199725899999999751


No 12 
>PHA00454 ATP-dependent DNA ligase
Probab=98.80  E-value=5.1e-06  Score=65.70  Aligned_cols=240  Identities=16%  Similarity=0.117  Sum_probs=118.0

Q ss_pred             CCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCC---CCCCCEEEEEEEEEEECHHHHHH
Q ss_conf             611999941581899999859989988865986556669997753102432233---54455048999999852021234
Q gi|254781172|r  125 SIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLS---LNIPEIIEVRGEVYISKNDFLAL  201 (731)
Q Consensus       125 ~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~---~~~~~~ieiRGEv~m~~~~F~~l  201 (731)
                      ...+.||||+||+=+-++..+..-+..++| .|..=..+.|.... ..++..+.   .-+|..+.+=||+++.--+|+  
T Consensus        26 ~G~~ivE~KyDGvRvqi~~~g~~~~~~~SR-~gk~~p~L~hi~~~-~~~~~l~~~~~~~~~~g~VLDGEv~~~~~dFq--  101 (312)
T PHA00454         26 AGYLIADVKYDGVRGNIVVDGTADSVWLSR-VSKRIPALEHLNGD-RRWRKLLNDDRCIFPDGFMLDGELMVKGVDFN--  101 (312)
T ss_pred             CCCEEEEECCCEEEEEEEEECCEEEEEEEC-CCCCCCCCHHHHHH-HHHHHHHCHHHHHCCCCEEEEEEEECCCCCHH--
T ss_conf             894899966350799999948914999944-88765441556666-66787614255516898799848965889988--


Q ss_pred             HHHHHHCCCCCCCCHHHHHHHHHHCCCHHH-H-HCCCEEEEEEECCCCC------C-----CCCCCHHHHHHHHHCCCCC
Q ss_conf             556431485433423456777752345555-3-0111056641024543------3-----2100003689999759966
Q gi|254781172|r  202 NDEMIAVGRKPYANPRNAASGILRRLNPTD-I-TRYLNFFVHGLGKTSE------I-----FAKGQYEMLQKMRCLGFPV  268 (731)
Q Consensus       202 N~~~~~~g~~~f~NpRN~aaG~lr~~d~~~-~-~r~L~f~ay~~~~~~~------~-----~~~~~~e~l~~L~~~GF~v  268 (731)
                                       ..+|.+|++.+.. . ..++.|++|++.....      .     ....+...+..+-.-.|+.
T Consensus       102 -----------------~i~~rvRrK~~~~~~~~~~l~~~~FDil~l~~~~~g~~~~~~~~~~~err~~l~~~l~~~~~~  164 (312)
T PHA00454        102 -----------------TGSGLLRTKKVLFKLHLKKLHVVVYDVTPLDVIESGEDYDVMHLVMREHVEAMRPLLEEYFPE  164 (312)
T ss_pred             -----------------HHHHHHEECCCCCCCCCCCEEEEEEEEEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             -----------------998876017786211000638999778831110356543200121399999999988760886


Q ss_pred             CCCE----EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCCC-EEEEEEEEEE
Q ss_conf             5414----8874032113455665531001123437637773110001115876568663123114562-1589987889
Q gi|254781172|r  269 NNGV----RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEK-QASTRLLDID  343 (731)
Q Consensus       269 ~~~~----~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~e-~~~T~v~~I~  343 (731)
                      ....    ..+.+.+++..++++.      +.=.-+|+++|--+..++  -|   |...   -||+.+. ++.-+|.+++
T Consensus       165 i~~~~~e~~~v~~~~~l~~l~~~a------l~~g~EG~m~k~~~~~y~--~g---r~~~---~~K~Kp~~~~d~~v~~~~  230 (312)
T PHA00454        165 IDWVLAESYEVYDMESLQELYEKK------RAEGHEGLVVKDPLLIYK--RG---KKSG---WWKMKPECEADGIIVGVV  230 (312)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHH------HHCCCCEEEEECCCCCCC--CC---CCCC---EEEECCCCEEEEEEEEEE
T ss_conf             526985203368999999999999------857984688867998755--88---7265---088655604579999887


Q ss_pred             EEECCC---CEEE-EEEEEEEEEECCCEEEEECCCCHHHHHHHCCC-CCCCCCCCCCCCCCEEEEE
Q ss_conf             940356---2258-99997433302640001014898999750234-5432224684407689998
Q gi|254781172|r  344 IQIGRT---GILT-PVARLEPVNIGGALITNATLHNEDYIKGLDAS-GKVMRGGRDIRVGDRVLVK  404 (731)
Q Consensus       344 wqvgRt---G~it-Pva~~ePV~l~G~~V~ratlhN~~~I~~l~~~-~~~~~~~~~I~iGd~V~I~  404 (731)
                      |-.|+.   |++- -.+.++    +|.. -.++......+..+.-. ....|...+.-+|-.|.|.
T Consensus       231 ~G~~~~~~~Gk~~~f~v~~e----dg~~-~~~~g~~~~~~~~~t~~~~~~~~~~~~~~~G~~~ei~  291 (312)
T PHA00454        231 WGTPGLANEGKVIGFRVLLE----DGRV-VNATGISRALMDEFTANVKEHHIDEPMPYNGWACQVS  291 (312)
T ss_pred             ECCCCCCCCCCEEEEEEEEC----CCCE-EECCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEE
T ss_conf             04677666564688999956----8977-8636776667656308788650124566465599999


No 13 
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=98.71  E-value=6.4e-08  Score=80.41  Aligned_cols=78  Identities=15%  Similarity=0.283  Sum_probs=70.1

Q ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCC--CHHHHHHHCCCEEECHHHHHHHHHHHC
Q ss_conf             821686699972588998789999999829849981116321799778888--637989974991737999999998828
Q gi|254781172|r  645 SEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG--SKLEKAQQLGVKIMNEEQFLFLLQQYN  722 (731)
Q Consensus       645 ~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~g--SKl~KA~~LgI~Ii~e~ef~~ll~~~~  722 (731)
                      ...+||.|||||..+ ..|+++.+.+...|=.++.|||..|+.||+++..+  +|...|..+|||+|++.+|+++|+.-.
T Consensus       293 ~LvqGMrVvvage~~-~~rd~Li~rav~AGL~ysesvsR~TSLVVcN~~~~~~GKa~hA~r~GIPlv~d~~Fl~ll~~V~  371 (377)
T PRK05601        293 GLVAGMEVVVAPEIE-MDPDIIIQAGVDAGLSYSEKLTRQTSVVVCNQTRDIDGKAMHAQRKGIPLLSDVAFLAAVERVK  371 (377)
T ss_pred             CCCCCCEEEEECCCC-CCHHHHHHHHHHHCCHHHHCCCCCEEEEEECCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHCC
T ss_conf             565788899817877-8989999999870620200204542279957998763066777761998468899999998577


Q ss_pred             C
Q ss_conf             6
Q gi|254781172|r  723 T  723 (731)
Q Consensus       723 ~  723 (731)
                      .
T Consensus       372 p  372 (377)
T PRK05601        372 E  372 (377)
T ss_pred             C
T ss_conf             5


No 14 
>LOAD_ligase consensus
Probab=98.69  E-value=3.4e-07  Score=74.80  Aligned_cols=155  Identities=21%  Similarity=0.278  Sum_probs=88.7

Q ss_pred             EEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHH---HHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf             1999941581899999859989988865986556669997---7531024322335445504899999985202123455
Q gi|254781172|r  127 FFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSAC---IRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALND  203 (731)
Q Consensus       127 ~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n---~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~  203 (731)
                      +|++|+|+||+-+.+++.+|. +.+.||    .|.++|+.   +......+.  ....+..+.+-||++.....+     
T Consensus         1 e~~~e~K~DG~R~~~~~~~~~-v~~~SR----~g~~~t~~f~~~~~~~~~~~--~~~~~~~~iLDGEl~~~~~~~-----   68 (184)
T LOAD_ligase       1 EYYVEEKYDGERVQIHKDGDG-VYFFSR----NGEDITDYFPDVKTALKIPL--KLSGLKNLILDGELVVDDVDF-----   68 (184)
T ss_pred             CCEEEEEECEEEEEEEEECCE-EEEECC----CCCCCCCCCCHHHHHHHHHH--HCCCCCCEEEEEEEEEECCCC-----
T ss_conf             936898886089999998999-999979----99876100417899987665--025788779987999736999-----


Q ss_pred             HHHHCCCCCCCCHHHHHHHHHHCCCHH-HHHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHCCCCCCCC-----EEEE
Q ss_conf             643148543342345677775234555-530111056641024543321--00003689999759966541-----4887
Q gi|254781172|r  204 EMIAVGRKPYANPRNAASGILRRLNPT-DITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCLGFPVNNG-----VRQA  275 (731)
Q Consensus       204 ~~~~~g~~~f~NpRN~aaG~lr~~d~~-~~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~GF~v~~~-----~~~~  275 (731)
                              +|...++.+    +...+. ....++.|++|++...++...  ....+..+.|..+--.+...     ....
T Consensus        69 --------~f~~~~~~~----~~~~~~~~~~~~~~~~vFDil~~~g~~~~~~~~~~R~~~L~~~~~~~~~~~~~~~~~~~  136 (184)
T LOAD_ligase      69 --------PFQLLRNRK----RKSVRVKDMKEPLEYFVFDILYLNGEDLTDLPLEERRKILEKLIKEIKDVRAIKNITVI  136 (184)
T ss_pred             --------CHHHHHHHH----CCCCCCHHHCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEEC
T ss_conf             --------989998775----33665122215618999996364898154588999999999974125883598789954


Q ss_pred             ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf             403211345566553100112343763777311000
Q gi|254781172|r  276 NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL  311 (731)
Q Consensus       276 ~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~  311 (731)
                      .+.+++.++++...      ....+|+|+|-.+..+
T Consensus       137 ~~~~~~~~~~~~~~------~~g~EGimiK~~~s~Y  166 (184)
T LOAD_ligase     137 DDVEELNKFLEKAL------GEGIEGLVIKDPDSPY  166 (184)
T ss_pred             CCHHHHHHHHHHHH------HCCCCEEEEECCCCCC
T ss_conf             99999999999998------6899679987899978


No 15 
>pfam00533 BRCT BRCA1 C Terminus (BRCT) domain. The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerisation mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.
Probab=98.67  E-value=1.7e-07  Score=77.19  Aligned_cols=74  Identities=39%  Similarity=0.589  Sum_probs=67.2

Q ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCC-CHHHHHHHCCCEEECHHHHHHHH
Q ss_conf             8821686699972588998789999999829849981116321799778888-63798997499173799999999
Q gi|254781172|r  644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG-SKLEKAQQLGVKIMNEEQFLFLL  718 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~g-SKl~KA~~LgI~Ii~e~ef~~ll  718 (731)
                      ...|.|.+|++|| +..+.|++++++|+.+||++..++++.|++||+++..+ .|..+|...|++|++++.+.+.+
T Consensus         3 ~~~f~~~~~~i~~-~~~~~r~~l~~~i~~~Gg~~~~~~~~~~thli~~~~~~~~k~~~a~~~~i~iV~~~Wi~~ci   77 (77)
T pfam00533         3 EKLFKGKTFVITG-LDSLEREELEELIEKLGGKVTDSLSKKTTHVIVGENAGTLKLLKAIALGIPIVTEEWLLDCI   77 (77)
T ss_pred             CCCCCCCEEEEEC-CCCCCHHHHHHHHHHHCCEEECCCCCCEEEEEECCCCCCHHHHHHHHCCCEEECHHHHHHHC
T ss_conf             8537996899979-49849999999999959947164346678999828988479998886896795399999869


No 16 
>PRK09125 DNA ligase; Provisional
Probab=98.56  E-value=3.1e-05  Score=59.66  Aligned_cols=213  Identities=19%  Similarity=0.268  Sum_probs=125.3

Q ss_pred             CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf             76119999415818999998599899888659865566699977531024322335445504899999985202123455
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALND  203 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~  203 (731)
                      ....|.++.|+||+=+   |=+|+  +..||.    |..+..        |.......|. +.+=||+++.+.+|++   
T Consensus        36 ~~~~w~~SeKlDGvRa---~wdG~--~l~SR~----G~~~~a--------P~wf~~~lP~-~~LDGELw~gR~~Fe~---   94 (277)
T PRK09125         36 DISGYLVSEKLDGVRA---YWDGK--QLLTRQ----GNPIAA--------PAWFTAGFPP-FALDGELWAGRGQFEQ---   94 (277)
T ss_pred             CCCCEEEEEEEEEEEE---EEECC--EEECCC----CCCCCC--------CHHHHHCCCC-CCEEEEEEECCCCHHH---
T ss_conf             8423589874137999---99789--888069----977789--------7788830999-6542468707788999---


Q ss_pred             HHHHCCCCCCCCHHHHHHHHHHCCCHHHHH-CCCEEEEEEECCCCCCCCCCCHHHHHHHHHC----CCCCCCC--EEEEE
Q ss_conf             643148543342345677775234555530-1110566410245433210000368999975----9966541--48874
Q gi|254781172|r  204 EMIAVGRKPYANPRNAASGILRRLNPTDIT-RYLNFFVHGLGKTSEIFAKGQYEMLQKMRCL----GFPVNNG--VRQAN  276 (731)
Q Consensus       204 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~-r~L~f~ay~~~~~~~~~~~~~~e~l~~L~~~----GF~v~~~--~~~~~  276 (731)
                                      .++++|++.|.... +.+.|++|++....+ +   ..+.++.|+.+    .-+....  ...+.
T Consensus        95 ----------------l~s~Vr~~~p~d~~W~~I~y~VFDlP~~~g-p---f~eR~~~L~~ll~~~~~~~l~~v~q~~v~  154 (277)
T PRK09125         95 ----------------ISSTVRDQTPDDAEWRKVRFMVFDLPDAGG-D---FEERLAVLRKLLAKLPSPYLKIIEQIPVD  154 (277)
T ss_pred             ----------------HHHHHHCCCCCHHHHHEEEEEEEECCCCCC-C---HHHHHHHHHHHHHHCCCCCEEEEEEEEEC
T ss_conf             ----------------987883589980443204899986788899-9---99999999999965899718998458979


Q ss_pred             CCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEEECC-CCEEEEE
Q ss_conf             032113455665531001123437637773110001115876568663123114562158998788994035-6225899
Q gi|254781172|r  277 TFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGR-TGILTPV  355 (731)
Q Consensus       277 ~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~wqvgR-tG~itPv  355 (731)
                      +.+++..+++++.+      -.--|+++|-.+..++.  |.   + +.-+=+| +-..++.+|.+..--.|| .|.+-- 
T Consensus       155 ~~~~l~~~l~~~~~------~G~EGlmlr~~~~~Y~~--gR---s-~~llK~K-~~~d~E~~Vvg~~~G~Gk~~g~lGa-  220 (277)
T PRK09125        155 SEEALLQFLDQIVA------AGGEGLMLHRPDAPYEA--GR---S-DDLLKLK-PYQDAEATVIGHLPGKGKFAGMLGA-  220 (277)
T ss_pred             CHHHHHHHHHHHHH------CCCCEEEEECCCCCCCC--CC---C-CCCEEEE-CCCCEEEEEEEEECCCCCCCCCEEE-
T ss_conf             99999999999996------79838778879996578--89---8-5427873-2364799999677599864684579-


Q ss_pred             EEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEE
Q ss_conf             99743330264000101489899975023454322246844076899983
Q gi|254781172|r  356 ARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKR  405 (731)
Q Consensus       356 a~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~R  405 (731)
                        +.=..-+|.+.+--|+.+-..=            ++.--||..|++.-
T Consensus       221 --l~~~~~~G~~f~vGsGfsd~~R------------~~pp~iG~~it~ky  256 (277)
T PRK09125        221 --LLVETPDGREFKIGSGFSDEER------------ENPPKIGSIITYKY  256 (277)
T ss_pred             --EEEEECCCCEEEECCCCCHHHH------------CCCCCCCCEEEEEE
T ss_conf             --9999689978985899998997------------59976898999998


No 17 
>cd07898 Adenylation_DNA_ligase The Adenylation domain of ATP-dependent DNA Ligases is a component of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to a specific function. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-sit
Probab=98.55  E-value=4.3e-06  Score=66.32  Aligned_cols=161  Identities=15%  Similarity=0.134  Sum_probs=89.7

Q ss_pred             CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf             76119999415818999998599899888659865566699977531024322335445504899999985202123455
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALND  203 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~  203 (731)
                      .+..|++|||+||+=+-+++.+|. ++..||    .|.++|++...|......+  ..+..+.+=||++.-.....    
T Consensus        19 ~~~~~~~E~K~DG~R~~~~~~~~~-v~l~SR----~gk~~t~~fpei~~~~~~~--~~~~~~IlDGElv~~d~~~~----   87 (201)
T cd07898          19 GPREMSFEIKYDGERCQVHKDGDR-VKLFSR----SGKDVTDDFPELAAAAKDC--ALPHSCILDGEIVAWDDNGG----   87 (201)
T ss_pred             CCCCEEEEEEECCEEEEEEEECCE-EEEEEC----CCCCCHHHHHHHHHHHHHC--CCCCCEEEEEEEEEECCCCC----
T ss_conf             898489998887189999998999-999958----9870012358899999854--68744599506999728999----


Q ss_pred             HHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHCCCCCCCCE-----EEEE
Q ss_conf             643148543342345677775234555530111056641024543321--000036899997599665414-----8874
Q gi|254781172|r  204 EMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCLGFPVNNGV-----RQAN  276 (731)
Q Consensus       204 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~GF~v~~~~-----~~~~  276 (731)
                               +.-+-.......+.+. ....-++.|++|++....+...  ....+..+.|+.+-=+..+..     ..+.
T Consensus        88 ---------~~~~f~~~~~~~~~~~-~~~~~~~~~~vFDil~l~g~~l~~~pl~eR~~~L~~~~~~~~~~i~~~~~~~~~  157 (201)
T cd07898          88 ---------KPLPFKALGRRFRGKR-LDEDVPVCLYAFDLLYLNGESLLDRPLSERRALLEDLVKEIPGRIRVAEQLIVD  157 (201)
T ss_pred             ---------CCCCHHHHHHHCCCCC-CCCCCCCEEEEEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEEECC
T ss_conf             ---------7769999852355432-110378289999765188850112879999999998751289838999999759


Q ss_pred             CCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf             03211345566553100112343763777311000
Q gi|254781172|r  277 TFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL  311 (731)
Q Consensus       277 ~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~  311 (731)
                      +.+++.++++.+.+      -.-.|+|+|--|-.+
T Consensus       158 ~~~~i~~~~~~~~~------~G~EGimiK~~ds~Y  186 (201)
T cd07898         158 SIEELATAFSEARK------EGWEGLMLKRPDSTY  186 (201)
T ss_pred             CHHHHHHHHHHHHH------CCCCEEEEECCCCCC
T ss_conf             89999999999997------899779973799962


No 18 
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=98.46  E-value=1.4e-06  Score=70.00  Aligned_cols=76  Identities=34%  Similarity=0.479  Sum_probs=67.4

Q ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEEC-CEEEEEECCCCCCH--HHHHHHCCCEEECHHHHHHHHHH
Q ss_conf             821686699972588998789999999829849981116-32179977888863--79899749917379999999988
Q gi|254781172|r  645 SEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSR-KTDIIIVGDNPGSK--LEKAQQLGVKIMNEEQFLFLLQQ  720 (731)
Q Consensus       645 ~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSk-kT~~LI~ge~~gSK--l~KA~~LgI~Ii~e~ef~~ll~~  720 (731)
                      ..|.|++|++||.+....|++++++|+.+||++..++++ .++++|+++..+.+  +..|...|++|++++.+.+.+..
T Consensus         1 ~~f~~~~~~i~g~~~~~~~~~l~~~i~~~Gg~v~~~~~~~~~th~I~~~~~~~~~~~~~~~~~~~~iV~~~Wi~~c~~~   79 (80)
T smart00292        1 KLFKGKVFVITGKFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIALGIPIVTEDWLLDCLKA   79 (80)
T ss_pred             CCCCCCEEEEEEECCCCCHHHHHHHHHHHCCEECCCCCCCCEEEEEEECCCCCCHHHHHHHHCCCCEECHHHHHHHHHC
T ss_conf             9579989999861698899999999998399250432577507999837988607789999809928759999999977


No 19 
>cd07901 Adenylation_DNA_ligase_Arch_LigB The Adenylation domain of archaeal and bacterial LigB-like DNA ligases is a component of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculo
Probab=98.46  E-value=1.9e-05  Score=61.34  Aligned_cols=177  Identities=16%  Similarity=0.136  Sum_probs=96.2

Q ss_pred             CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHC
Q ss_conf             66425702159999999999999986124677761199994158189999985998998886598655666999775310
Q gi|254781172|r   92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIP  171 (731)
Q Consensus        92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~  171 (731)
                      -.|||.-- +.+.+++...             ....|.+|+|+||.=+-+.+.+|. ++..||    -|+|+|+..-.|.
T Consensus         5 i~PMLA~~-~~~~~~~~~~-------------~~~~~~~E~K~DG~R~~i~~~~~~-v~l~SR----~g~~~t~~fPei~   65 (207)
T cd07901           5 VRPMLAQR-ASSVEEALEK-------------EGGPAAVEYKYDGARVQIHKDGDK-VRIFSR----RLEDVTNALPDVV   65 (207)
T ss_pred             CCCCCCCC-CCCHHHHHHH-------------CCCCEEEEEEECEEEEEEEEECCE-EEEEEC----CCCCCCCCCHHHH
T ss_conf             74415898-7997899863-------------089669998588188999998999-999973----6860223466899


Q ss_pred             C-CCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHH-H--HHCCCEEEEEEECCCC
Q ss_conf             2-4322335445504899999985202123455643148543342345677775234555-5--3011105664102454
Q gi|254781172|r  172 T-IPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPT-D--ITRYLNFFVHGLGKTS  247 (731)
Q Consensus       172 ~-iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~-~--~~r~L~f~ay~~~~~~  247 (731)
                      . +..   ......+.+=||++.-..+           |..   .|-....+-++++++. .  ...++.|++|++...+
T Consensus        66 ~~~~~---~~~~~~~ILDGElv~~d~~-----------g~~---~~F~~l~~r~~~~~~~~~~~~~~p~~~~vFDiL~l~  128 (207)
T cd07901          66 EAVRE---AVKADEAILDGEAVAYDPD-----------GRP---LPFQETLRRFRRKYDVAEAAEEIPLTLFLFDILYLD  128 (207)
T ss_pred             HHHHH---CCCCCCEEEEEEEEEECCC-----------CCC---CCHHHHHHHHCCCCCHHHHHHCCCEEEEEEEEEEEC
T ss_conf             99985---4898877985599998899-----------998---789999977533653556542087489998776688


Q ss_pred             CCCC--CCCHHHHHHHHHCCCCCCCCEE-----EEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf             3321--0000368999975996654148-----87403211345566553100112343763777311000
Q gi|254781172|r  248 EIFA--KGQYEMLQKMRCLGFPVNNGVR-----QANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL  311 (731)
Q Consensus       248 ~~~~--~~~~e~l~~L~~~GF~v~~~~~-----~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~  311 (731)
                      +...  ....+..+.|+.+ |+..+...     .+++.+++.++++...+      -..-|||+|--+-.+
T Consensus       129 g~~l~~~pl~eRr~~L~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~g~EGiv~K~~~s~Y  192 (207)
T cd07901         129 GEDLLDLPLEERRKILEEI-VPESEEISLAPRLVTDDPEEAEEFFEEALE------AGHEGVMVKSLDSPY  192 (207)
T ss_pred             CCCHHCCCHHHHHHHHHHH-CCCCCCEEEEEEEECCCHHHHHHHHHHHHH------CCCCEEEEECCCCCC
T ss_conf             7214208799999999975-265797388304865999999999999997------899769985799976


No 20 
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=98.38  E-value=0.00015  Score=54.37  Aligned_cols=216  Identities=19%  Similarity=0.198  Sum_probs=125.0

Q ss_pred             CCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHH-HHCCCCCCCCCCCCCEEEEEEEEEEE----CHHHH
Q ss_conf             61199994158189999985998998886598655666999775-31024322335445504899999985----20212
Q gi|254781172|r  125 SIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIR-AIPTIPRVLSLNIPEIIEVRGEVYIS----KNDFL  199 (731)
Q Consensus       125 ~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~-~i~~iP~~l~~~~~~~ieiRGEv~m~----~~~F~  199 (731)
                      ...|.+|.|+||.=+-++..+|. ++.+||    -|+|||+... .+..+-..++   +..+.+-||+++-    ..+|+
T Consensus       132 ~~~w~~E~K~DG~R~q~h~~~~~-vrl~SR----~g~d~T~~fP~~~~~~~~~l~---~~~~iiDGE~V~~~~~~~~~F~  203 (444)
T COG1793         132 GGDWAYEEKFDGYRVQIHIDGGK-VRLYSR----NGEDWTGRFPDILEAAAEALP---ADDFILDGEIVVLDEEGRLDFQ  203 (444)
T ss_pred             CCCEEEEEEECEEEEEEEECCCE-EEEEEC----CCCCCHHHCCHHHHHHHHCCC---CCCEEEECEEEEECCCCCCCHH
T ss_conf             67779998635699999976987-999957----984124458288999863278---7776896769987888889989


Q ss_pred             HHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHH---HHCCCEEEEEEECCCCCCCCC--CCHHHHHHHHHC-----CCCCC
Q ss_conf             34556431485433423456777752345555---301110566410245433210--000368999975-----99665
Q gi|254781172|r  200 ALNDEMIAVGRKPYANPRNAASGILRRLNPTD---ITRYLNFFVHGLGKTSEIFAK--GQYEMLQKMRCL-----GFPVN  269 (731)
Q Consensus       200 ~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~---~~r~L~f~ay~~~~~~~~~~~--~~~e~l~~L~~~-----GF~v~  269 (731)
                      .|-.                   .+|++.+..   ..-++.|++|++.+.++....  .-.+.-+.|..+     -|...
T Consensus       204 ~Lq~-------------------r~~~~~~v~~~~~~~~~~~~aFDlL~~dG~dL~~~pl~eRr~~Le~lv~~~~~~~~~  264 (444)
T COG1793         204 ALQQ-------------------RLRRKYDVAKLRRETPLVLFAFDLLYLDGEDLRGLPLEERRALLEELVKSSDKIEIA  264 (444)
T ss_pred             HHHH-------------------HHHHCCCHHHHCCCCCEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9998-------------------751044334414677617999977401675402287899999999985523543424


Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEEECCC
Q ss_conf             41488740321134556655310011234376377731100011158765686631231145621589987889940356
Q gi|254781172|r  270 NGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRT  349 (731)
Q Consensus       270 ~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~wqvgRt  349 (731)
                      +.... .+.++...+++...+      ..+.|||+|--|-.++..    .+.-.| +=+| +.++..-+|.+..|+-|+-
T Consensus       265 ~~i~~-~~~~~~~~~~~~a~~------~g~EGvv~K~~ds~Y~~g----~R~~~W-~K~K-~~~~~d~vv~G~~~g~Gkr  331 (444)
T COG1793         265 ERIPF-SDAEEGEAFLEAAIE------LGLEGVVAKRPDSPYRAG----GRSNKW-LKVK-RDETLDLVVVGAEYGKGKR  331 (444)
T ss_pred             CCEEE-CCHHHHHHHHHHHHH------CCCEEEEEECCCCCCCCC----CCCCCC-EEEC-CCCCEEEEEEEEEECCCCC
T ss_conf             51451-776789999998886------396689970799986789----988774-5651-4775008999788468854


Q ss_pred             CEEEEEEEEEEEEECCC-----EEEEECCCCHHHHHHH
Q ss_conf             22589999743330264-----0001014898999750
Q gi|254781172|r  350 GILTPVARLEPVNIGGA-----LITNATLHNEDYIKGL  382 (731)
Q Consensus       350 G~itPva~~ePV~l~G~-----~V~ratlhN~~~I~~l  382 (731)
                      +  .--+.+-.+.-++.     .++=.|++..++.+.|
T Consensus       332 ~--~~~slll~~~~~~~~~~~~v~kVgtGf~~~~l~~l  367 (444)
T COG1793         332 S--LYGSLLLGVYDGDGGGLLYVGKVGTGFSDAELEEL  367 (444)
T ss_pred             C--CCCCEEEEEEECCCCEEEEEEEECCCCCHHHHHHH
T ss_conf             5--52206999980898638999874477798999999


No 21 
>cd07906 Adenylation_DNA_ligase_LigD The Adenylation domain of Mycobacterium tuberculosis LigD-like ATP-dependent DNA ligases is a component of the catalytic core unit. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold dom
Probab=98.37  E-value=2.1e-05  Score=60.89  Aligned_cols=151  Identities=19%  Similarity=0.158  Sum_probs=86.8

Q ss_pred             CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECH----HHH
Q ss_conf             7611999941581899999859989988865986556669997753102432233544550489999998520----212
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN----DFL  199 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~----~F~  199 (731)
                      .+..|++|+|+||+=+-+++.+|. ++..||    .|+|+|+....|......+   .+..+.+=||++.-..    +|+
T Consensus        14 ~~~~~~~E~K~DG~R~~~~~~~~~-v~l~SR----~g~~~t~~fp~i~~~~~~~---~~~~~ILDGElv~~~~~~~~~F~   85 (186)
T cd07906          14 DGEDWLYEIKWDGYRALARVDGGR-VRLYSR----NGLDWTARFPELADALAAL---PVRSAVLDGEIVVLDEGGRPDFQ   85 (186)
T ss_pred             CCCCEEEEEEECCEEEEEEEECCE-EEEEEC----CCCCCCHHCHHHHHHHHHC---CCCCEEEEEEEEEECCCCCCCHH
T ss_conf             999768998478199999998999-999969----9984410167899999847---98758994369986799888989


Q ss_pred             HHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHCCCCCCCCEEEEEC
Q ss_conf             3455643148543342345677775234555530111056641024543321--00003689999759966541488740
Q gi|254781172|r  200 ALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCLGFPVNNGVRQANT  277 (731)
Q Consensus       200 ~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~GF~v~~~~~~~~~  277 (731)
                      .+...                   .+.    ....++.|++|++...++...  ....+..+.|+.+--+..+....+..
T Consensus        86 ~l~~r-------------------~~~----~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~l~~~~~~~i~~~~~  142 (186)
T cd07906          86 ALQNR-------------------LRL----ARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAASPRLRFSEH  142 (186)
T ss_pred             HHHHH-------------------HHC----CCCCCEEEEEEEEEEECCCCHHHCCHHHHHHHHHHHHCCCCCCEEECCC
T ss_conf             99867-------------------512----6777749999960028871500088999999999874247995897872


Q ss_pred             C-CCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf             3-211345566553100112343763777311000
Q gi|254781172|r  278 F-HGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL  311 (731)
Q Consensus       278 ~-~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~  311 (731)
                      . ++...+++...+      -...|||+|--+-.+
T Consensus       143 ~~~~~~~~~~~~~~------~g~EGimiK~~~s~Y  171 (186)
T cd07906         143 FEGDGAALLEAACE------LGLEGIVAKRADSPY  171 (186)
T ss_pred             CCCCHHHHHHHHHH------CCCCEEEEECCCCCC
T ss_conf             55649999999997------799569986799941


No 22 
>cd07903 Adenylation_DNA_ligase_IV The Adenylation domain of DNA Ligase IV is a component of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consist
Probab=98.30  E-value=6.2e-05  Score=57.33  Aligned_cols=172  Identities=18%  Similarity=0.166  Sum_probs=92.9

Q ss_pred             CCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHH----HHCCCCCCCC--CCCCCEEEEEEEEEEECHHH
Q ss_conf             61199994158189999985998998886598655666999775----3102432233--54455048999999852021
Q gi|254781172|r  125 SIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIR----AIPTIPRVLS--LNIPEIIEVRGEVYISKNDF  198 (731)
Q Consensus       125 ~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~----~i~~iP~~l~--~~~~~~ieiRGEv~m~~~~F  198 (731)
                      ...|.+|+|+||+=+-+++.+|. ++..||    -|+|+|+.-.    .+...|....  ...+..+.+=||++.-...-
T Consensus        32 ~~~~~~E~K~DG~R~~~h~~~~~-v~l~SR----ng~d~t~~fpe~~~~~~~~~~~~~~~~~~~~~~ILDGElv~~d~~~  106 (227)
T cd07903          32 GDPFYIETKFDGERIQLHKDGEE-FKYFSR----NGNDYTYLYGESLDEGSLTPYIHLAFAKSVKSCILDGEMMVWDKET  106 (227)
T ss_pred             CCCEEEEEEECEEEEEEEEECCE-EEEEEC----CCCCCHHHCCCHHHHHHHCHHHHHHHHCCCCCEEEEEEEEEEECCC
T ss_conf             98469998775189999995999-999977----8870023253056553202556777513688689960598873677


Q ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHHCCCH--HHHHCCCEEEEEEECCCCCCC--CCCCHHHHHHHHHCCCCCCCCE--
Q ss_conf             2345564314854334234567777523455--553011105664102454332--1000036899997599665414--
Q gi|254781172|r  199 LALNDEMIAVGRKPYANPRNAASGILRRLNP--TDITRYLNFFVHGLGKTSEIF--AKGQYEMLQKMRCLGFPVNNGV--  272 (731)
Q Consensus       199 ~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~r~L~f~ay~~~~~~~~~--~~~~~e~l~~L~~~GF~v~~~~--  272 (731)
                      .+         --+|.--+.    ..+....  ......+.|++|++...++..  -....+..+.|+.+--+.....  
T Consensus       107 ~~---------~~~f~~l~~----~~~~~~~~~~~~~~~~~~~~FDiL~l~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~  173 (227)
T cd07903         107 KR---------FLPFGTLKD----VAALRESRLEDSNLQPCFVVFDILYLNGKSLTNLPLHERKELLRKIITPVPGRIEI  173 (227)
T ss_pred             CC---------CCCCCHHHH----HHHHCCCCCCCCCCCEEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCEEE
T ss_conf             75---------255303667----98742344333455427999877515883165437899999999862568982798


Q ss_pred             ---EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCC
Q ss_conf             ---8874032113455665531001123437637773110001115876568663
Q gi|254781172|r  273 ---RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRW  324 (731)
Q Consensus       273 ---~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prw  324 (731)
                         ..+.+.+++..+++...+.      .-.|||+|--+-.++-  |  .|+..|
T Consensus       174 ~~~~~~~~~~~i~~~~~~~~~~------g~EGimiK~~~s~Y~~--g--kRs~~W  218 (227)
T cd07903         174 VKRKEASTKEDIEEALNEAIDN------REEGIVVKDLDSKYRP--G--KRGDGW  218 (227)
T ss_pred             EEEEECCCHHHHHHHHHHHHHC------CCCEEEEECCCCCCCC--C--CCCCCC
T ss_conf             7778739999999999999987------9978998179996479--9--989982


No 23 
>pfam01068 DNA_ligase_A_M ATP dependent DNA ligase domain. This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653.
Probab=98.25  E-value=3e-05  Score=59.80  Aligned_cols=155  Identities=17%  Similarity=0.146  Sum_probs=89.0

Q ss_pred             CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCC-CCCCCCCCCCCEEEEEEEEEEECHHHHHHH
Q ss_conf             7611999941581899999859989988865986556669997753102-432233544550489999998520212345
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPT-IPRVLSLNIPEIIEVRGEVYISKNDFLALN  202 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~-iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN  202 (731)
                      ....|++|||+||+=+-+++.+|. +++.||    .|.++|+....|.. +...+... ...+.+=||++.......   
T Consensus        16 ~~~~~~~E~K~DG~R~~i~~~~~~-v~~~SR----~gk~~t~~~p~l~~~~~~~~~~~-~~~~iLDGElv~~~~~~~---   86 (190)
T pfam01068        16 GGGAFIVEEKYDGERVQIHKDGGE-VKLLSR----NGKPITATYPELLEFLLEAFFPD-VKSFILDGEIVAIPETGR---   86 (190)
T ss_pred             CCCCEEEEEEECEEEEEEEEECCE-EEEECC----CCCCCCCCCHHHHHHHHHHHCCC-CCCEEEEEEEEEECCCCC---
T ss_conf             799689999886099999998999-999929----99886101689999998763467-875799868998768998---


Q ss_pred             HHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCC--CCCCCHHHHHHHHHCCCCCCCCE-----EEE
Q ss_conf             56431485433423456777752345555301110566410245433--21000036899997599665414-----887
Q gi|254781172|r  203 DEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEI--FAKGQYEMLQKMRCLGFPVNNGV-----RQA  275 (731)
Q Consensus       203 ~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~--~~~~~~e~l~~L~~~GF~v~~~~-----~~~  275 (731)
                                 .++....+   ++.    ...++.|++|++...++.  .-....+..+.|..+--+ .+..     ..+
T Consensus        87 -----------~~~~~~~~---~~~----~~~~~~~~vFDil~~~~~~l~~~p~~~R~~~L~~~~~~-~~~i~~~~~~~~  147 (190)
T pfam01068        87 -----------ILPFQTLA---VRK----KKEPLCFFVFDVLYLDGESLTDKPLKERRELLEEYFKI-PVRIEIAETIET  147 (190)
T ss_pred             -----------CCCHHHHH---HHC----CCCCEEEEEEEEEEECCCCHHCCCHHHHHHHHHHHHCC-CCCEEEEEEEEC
T ss_conf             -----------36167765---222----35772899998767887532108899999999986076-883599899862


Q ss_pred             ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCC
Q ss_conf             4032113455665531001123437637773110001
Q gi|254781172|r  276 NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQ  312 (731)
Q Consensus       276 ~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q  312 (731)
                      .+.+++.++++++.+.      .--|+|+|--+-.+.
T Consensus       148 ~~~~~~~~~~~~~~~~------G~EGim~K~~~s~Y~  178 (190)
T pfam01068       148 NDIEELAEFLEEAIKE------GLEGVVVKDPDSRYE  178 (190)
T ss_pred             CCHHHHHHHHHHHHHC------CCCEEEEECCCCCCC
T ss_conf             9999999999999878------997899968999646


No 24 
>cd07900 Adenylation_DNA_ligase_I_Euk The Adenylation domain of eukaryotic DNA Ligase I is a component of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to a specific function. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The ad
Probab=98.24  E-value=8.5e-05  Score=56.26  Aligned_cols=173  Identities=20%  Similarity=0.146  Sum_probs=90.8

Q ss_pred             CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEE-CCEEEEEEECCCCHHHHHHHHHHHHH
Q ss_conf             66425702159999999999999986124677761199994158189999985-99899888659865566699977531
Q gi|254781172|r   92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYE-KGKFVYAALRGDGHSGEDVSACIRAI  170 (731)
Q Consensus        92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~-~G~L~~a~TRGdG~~GeDVT~n~~~i  170 (731)
                      -.|||.- -+.+.+|+.+   +         .....|++|+|+||.=+-+.+. +|. ++..||    -|+|+|+.--.|
T Consensus        10 i~PMLA~-~~~~~~~~~~---~---------~~~~~~~~E~K~DG~R~qih~~~~~~-v~l~SR----ng~d~T~~fPel   71 (219)
T cd07900          10 LKPMLAK-PTKGISEVLK---R---------FEDKAFTCEYKYDGERAQIHLLEDGK-VKIFSR----NLENMTEKYPDV   71 (219)
T ss_pred             CCCEECC-CCCCHHHHHH---H---------CCCCCEEEEEEECCEEEEEEEECCCE-EEEEEC----CCCCCCCCCHHH
T ss_conf             7871279-8898689997---3---------58981689960980579999908997-999957----997341104579


Q ss_pred             CCCCCCCCCCCCCEEEEEEEEEEECH------HHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEEC
Q ss_conf             02432233544550489999998520------212345564314854334234567777523455553011105664102
Q gi|254781172|r  171 PTIPRVLSLNIPEIIEVRGEVYISKN------DFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLG  244 (731)
Q Consensus       171 ~~iP~~l~~~~~~~ieiRGEv~m~~~------~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~  244 (731)
                      .+.-..+.......+.+=||++.-..      .|+.+-.+.           |    ..   .+.....-++.|++|++.
T Consensus        72 ~~~~~~~~~~~~~~~ILDGEiv~~d~~~~~~~~Fq~l~~r~-----------r----~~---~~~~~~~~~~~~~~FDiL  133 (219)
T cd07900          72 IEIIKESLKPNVKSFILDCEVVAYDRETGKILPFQVLSTRK-----------R----KD---VDANDIKVQVCVFAFDLL  133 (219)
T ss_pred             HHHHHHHHCCCCCEEEEEEEEEEEECCCCCCCCHHHHHHHH-----------H----CC---CCHHHCCCCEEEEEEEEE
T ss_conf             99999862477630799637987607999605788985553-----------3----23---341321476689998540


Q ss_pred             CCCCCC--CCCCHHHHHHHHHCCCCCCCCE-----EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf             454332--1000036899997599665414-----8874032113455665531001123437637773
Q gi|254781172|r  245 KTSEIF--AKGQYEMLQKMRCLGFPVNNGV-----RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKV  306 (731)
Q Consensus       245 ~~~~~~--~~~~~e~l~~L~~~GF~v~~~~-----~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikv  306 (731)
                      +.++..  -....+..+.|+.+-=++....     ..+.+.+++.++++...+      -...|||+|-
T Consensus       134 ~l~g~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~a~~------~g~EGiv~K~  196 (219)
T cd07900         134 YLNGESLLDKPLRERRELLHSSFKEVPGEFQFATSKDSEDIEEIQEFLEEAVK------NNCEGLMVKT  196 (219)
T ss_pred             CCCCCCHHHCCHHHHHHHHHHHHCCCCCEEEEEEEEECCCHHHHHHHHHHHHH------CCCCEEEEEC
T ss_conf             03883443281999999999864338981898876754999999999999998------6993699966


No 25 
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=98.23  E-value=0.00023  Score=52.90  Aligned_cols=239  Identities=18%  Similarity=0.220  Sum_probs=126.1

Q ss_pred             CCC-CCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHH
Q ss_conf             166-4257021599999999999999861246777611999941581899999859989988865986556669997753
Q gi|254781172|r   91 HSI-PTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRA  169 (731)
Q Consensus        91 H~~-pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~  169 (731)
                      +|+ |||.-. +.+.+|+..-+             ...+.+|.|.||.=+-+++++|. ++..||    -|+|||+..--
T Consensus       182 ~Pv~pmLA~~-~~~~~~~~~~~-------------~~~~~~E~K~DG~R~Qih~~g~~-v~l~SR----~~ediT~~fPe  242 (509)
T PRK03180        182 RPVGPMLAQT-ATSVAEALERL-------------GGTAAVEAKLDGARVQIHRDGDD-VRVYTR----SLDDVTARLPE  242 (509)
T ss_pred             CCCCCEECCC-CCCHHHHHHHC-------------CCCEEEEEEECEEEEEEEEECCE-EEEECC----CCCCCHHHHHH
T ss_conf             9867630897-99989999864-------------98747997305189999997999-999858----98602345579


Q ss_pred             HCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCC-CHHH--HHCCCEEEEEEECCC
Q ss_conf             1024322335445504899999985202123455643148543342345677775234-5555--301110566410245
Q gi|254781172|r  170 IPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRL-NPTD--ITRYLNFFVHGLGKT  246 (731)
Q Consensus       170 i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~-d~~~--~~r~L~f~ay~~~~~  246 (731)
                      |-..-..++   ...+.+=||++.-..+           |..   .|=+.-..-++++ +...  ..-++.+++|++.+.
T Consensus       243 iv~~~~~~~---~~~~ILDGEiva~~~~-----------G~~---~~Fq~l~~R~~rk~~~~~~~~~~pv~~~~FDlL~~  305 (509)
T PRK03180        243 VVEAVLALP---VRSLVLDGEAIALRPD-----------GRP---RPFQVTASRFGRSVDVAAAAATQPLSVFFFDILHL  305 (509)
T ss_pred             HHHHHHHCC---CCCEEECCEEEEECCC-----------CCC---CCHHHHHHHHCCCCCHHHHHHCCCEEEEEEEEEEE
T ss_conf             999998479---8534675479998899-----------988---73799987641255067775308859998745203


Q ss_pred             CCCC--CCCCHHHHHHHHHCC---CCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCC
Q ss_conf             4332--100003689999759---96654148874032113455665531001123437637773110001115876568
Q gi|254781172|r  247 SEIF--AKGQYEMLQKMRCLG---FPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARS  321 (731)
Q Consensus       247 ~~~~--~~~~~e~l~~L~~~G---F~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~  321 (731)
                      ++..  -....+..+.|.++=   ..+ + .....+.+++..+++.      ...-...|+|+|--|-.++-    ..+.
T Consensus       306 ~G~dl~~~Pl~eRR~~Le~~~~~~~~~-~-~~~~~~~~~~~~~~~~------a~~~g~EGlm~K~~dS~Y~p----GrR~  373 (509)
T PRK03180        306 DGRDLLDAPTTERLAALDALVPARHRV-P-RLVTADPAAAAAFLDA------TLAAGHEGVMAKSLAAPYEA----GRRG  373 (509)
T ss_pred             CCCCHHHCCHHHHHHHHHHHCCCCCCC-C-CEECCCHHHHHHHHHH------HHHCCCEEEEEECCCCCCCC----CCCC
T ss_conf             884033187999999999844631356-7-1224899999999999------98669806898269998789----9878


Q ss_pred             CCCEEEECCCC-CEEEEEEEEEEEEECC-CCEEEE--EEEEEEEEECCCEEEEE-CCCCHHHHH
Q ss_conf             66312311456-2158998788994035-622589--99974333026400010-148989997
Q gi|254781172|r  322 PRWMISHKFAE-KQASTRLLDIDIQIGR-TGILTP--VARLEPVNIGGALITNA-TLHNEDYIK  380 (731)
Q Consensus       322 PrwaiA~Kf~~-e~~~T~v~~I~wqvgR-tG~itP--va~~ePV~l~G~~V~ra-tlhN~~~I~  380 (731)
                      ..|   +|+.. .+...+|..-.|--|| +|.+..  .|..+|-.-.=++|.++ |++.-.+++
T Consensus       374 ~~W---~K~K~~~tlD~ViiGa~~G~GkR~g~~s~~llg~~d~~~~~~~~vgKvgsGftD~~l~  434 (509)
T PRK03180        374 AGW---LKVKPVHTLDLVVLAVEWGSGRRRGKLSNLHLGARDPATGGFVMLGKTFKGMTDAMLA  434 (509)
T ss_pred             CCC---EEECCCCCCEEEEEEEECCCCCCCCCCCCEEEEEECCCCCCEEEEEEECCCCCHHHHH
T ss_conf             772---6644776540899963518888788744259998838999589997636789989999


No 26 
>cd07907 Adenylation_DNA_ligase_Bac2 The Adenylation domain of putative bacterial ATP-dependent DNA ligases is inferred by similarity to be a component of the catalytic core unit. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. The adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenyl
Probab=98.23  E-value=0.00013  Score=54.82  Aligned_cols=153  Identities=20%  Similarity=0.154  Sum_probs=87.0

Q ss_pred             CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECH----HHH
Q ss_conf             7611999941581899999859989988865986556669997753102432233544550489999998520----212
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN----DFL  199 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~----~F~  199 (731)
                      ++..|.+|+|+||.=+-+++.+|. ++..||    -|+|+|+.---|...=.    ..++.+.+=||++.-..    .|.
T Consensus        31 ~~~~~~~E~K~DG~R~qih~~~~~-v~l~SR----ng~d~T~~fPel~~~~~----~l~~~~ILDGEiv~~~~~~~~~F~  101 (213)
T cd07907          31 APPAAWLEDKYDGIRAQLHKSEGR-VELYSR----DLEDITEQFPELADAAR----ALPHEFILDGEILAWRYGRALPFS  101 (213)
T ss_pred             CCCCCEEEECCCCEEEEEEEECCE-EEEEEC----CCCCCHHHHHHHHHHHH----HCCCCEEEEEEEEEECCCCCCCHH
T ss_conf             999887996438078999998999-999918----98704335578999998----279985998078997389879889


Q ss_pred             HHHHHHHHCCCCCCCCHHHHHHHHHHCCCHH-H--HHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHCCCCCCCCE--
Q ss_conf             3455643148543342345677775234555-5--30111056641024543321--000036899997599665414--
Q gi|254781172|r  200 ALNDEMIAVGRKPYANPRNAASGILRRLNPT-D--ITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCLGFPVNNGV--  272 (731)
Q Consensus       200 ~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~-~--~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~GF~v~~~~--  272 (731)
                      .+..                   -++++.+. .  ...++.|++|++...++...  ....+..+.|..+--+. +..  
T Consensus       102 ~lq~-------------------r~~~k~~~~~~~~~~pv~~~~FDiL~lng~~L~~~pl~eRr~~L~~l~~~~-~~~~l  161 (213)
T cd07907         102 ELQK-------------------RLGRKAEDDFMQEEIPVVYVAFDLLWLNGELLLDRPLEERRQKLESLLSPP-PKLRL  161 (213)
T ss_pred             HHHH-------------------HHHCCCCCHHHHHHCCEEEEEEEEEEECCCCHHHCCHHHHHHHHHHHCCCC-CCEEE
T ss_conf             9998-------------------752046416667317838999764116871732189999999999733788-87596


Q ss_pred             ---EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf             ---887403211345566553100112343763777311000
Q gi|254781172|r  273 ---RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL  311 (731)
Q Consensus       273 ---~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~  311 (731)
                         ..+.+.+++.+.++..      ..-...|||+|--+-.+
T Consensus       162 ~~~~~~~~~~~~~~~~~~a------~~~g~EGIv~K~~dS~Y  197 (213)
T cd07907         162 APATQASSAEQIEAAFAAA------RERGNEGLMIKDPASPY  197 (213)
T ss_pred             CCEEECCCHHHHHHHHHHH------HHCCCCEEEECCCCCCC
T ss_conf             3448579999999999999------97699559972799987


No 27 
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=98.21  E-value=7.8e-05  Score=56.55  Aligned_cols=160  Identities=21%  Similarity=0.282  Sum_probs=96.3

Q ss_pred             CCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECH----HH
Q ss_conf             77611999941581899999859989988865986556669997753102432233544550489999998520----21
Q gi|254781172|r  123 DNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN----DF  198 (731)
Q Consensus       123 ~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~----~F  198 (731)
                      ...-.|+.|.|+||.=+-+.+.+|. ++..||    -|.|+|+..-.+-      ....|....+=||++....    +|
T Consensus        15 ~~~~~W~~E~K~DG~R~~~~~~~g~-v~l~SR----ng~d~t~~fPel~------~~~~~~~~iLDGEiVv~~~~g~~~F   83 (269)
T PRK07636         15 FNSDNYITELKFDGIRLIASKNDGL-IRLYTR----HNNEVTAKFPELL------TLDIPDGTILDGELIVPGSTGAPDF   83 (269)
T ss_pred             CCCCCEEEEEEECEEEEEEEEECCE-EEEEEC----CCCCCHHHCHHHH------HHCCCCCEEEECEEEEECCCCCCCH
T ss_conf             8999747885277099999998999-999908----9988333476889------7348854088245899888988898


Q ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCC--CCCCHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf             2345564314854334234567777523455553011105664102454332--10000368999975996654148874
Q gi|254781172|r  199 LALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIF--AKGQYEMLQKMRCLGFPVNNGVRQAN  276 (731)
Q Consensus       199 ~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~--~~~~~e~l~~L~~~GF~v~~~~~~~~  276 (731)
                      +.+...                   ++..   ....++.|++|++...++..  -....+..+.|+.+--+. ++...+.
T Consensus        84 ~~lq~r-------------------~~~~---~~~~pv~y~vFDlL~l~G~~L~~~Pl~eRr~~L~~l~~~~-~~~~~~~  140 (269)
T PRK07636         84 EAVMER-------------------FQSR---KSFYPIVFCVFDVIRIEGVSVTAKPLSERKELLAGLKLDH-PNVKIIE  140 (269)
T ss_pred             HHHHHH-------------------HHCC---CCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCC-CCEEECC
T ss_conf             999754-------------------5405---8766359999957345864300378999999998643579-9658756


Q ss_pred             CCC-CHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEE
Q ss_conf             032-11345566553100112343763777311000111587656866312
Q gi|254781172|r  277 TFH-GIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMI  326 (731)
Q Consensus       277 ~~~-~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prwai  326 (731)
                      ..+ +..++++...+      -...|||.|--|..++.    ..|++.|--
T Consensus       141 ~~~~~~~~~~~~a~~------~glEGIvaKr~dS~Y~~----G~Rs~~WlK  181 (269)
T PRK07636        141 GVRGHATAYFELVKE------NKLEGIVIKQANSPYAI----NKRSDRWLK  181 (269)
T ss_pred             CCCCHHHHHHHHHHH------CCCCEEEECCCCCCCCC----CCCCCCEEE
T ss_conf             554519999999997------69924785179998679----998735089


No 28 
>cd07896 Adenylation_kDNA_ligase_like The Adenylation domain of kDNA ligase and similar proteins, which is involved in kDNA replication or repair, is a component of the catalytic core unit. The mitochondrial DNA of parasitic protozoan is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligouncleotide/olig
Probab=98.20  E-value=1.8e-05  Score=61.42  Aligned_cols=142  Identities=23%  Similarity=0.365  Sum_probs=85.0

Q ss_pred             CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf             76119999415818999998599899888659865566699977531024322335445504899999985202123455
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALND  203 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~  203 (731)
                      ....|.+|||+||+=+-  . +|.  +..||    .|.+++..       + .+....| .+++=||+|....+|+.+  
T Consensus        14 ~~~~w~~e~K~DG~R~~--~-~~~--~l~SR----~G~~~~~~-------~-~~~~~~~-~~vlDGEl~~~~~~F~~l--   73 (174)
T cd07896          14 DISGYLVSEKLDGVRAY--W-DGK--QLLSR----SGKPIAAP-------D-WFTAGLP-PFPLDGELWIGRGQFEQL--   73 (174)
T ss_pred             CCCCEEEEEEECEEEEE--E-ECC--EEEEC----CCCCCCCH-------H-HHHHHCC-CCCEEEEEEECCCCHHHH--
T ss_conf             94043876511479999--9-889--99966----99867894-------9-9995498-851745886078987999--


Q ss_pred             HHHHCCCCCCCCHHHHHHHHHHCCCHHH-HHCCCEEEEEEECCCCCCCCCCCHHHHHHHHHC----CCC---CCCCEEEE
Q ss_conf             6431485433423456777752345555-301110566410245433210000368999975----996---65414887
Q gi|254781172|r  204 EMIAVGRKPYANPRNAASGILRRLNPTD-ITRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCL----GFP---VNNGVRQA  275 (731)
Q Consensus       204 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~-~~r~L~f~ay~~~~~~~~~~~~~~e~l~~L~~~----GF~---v~~~~~~~  275 (731)
                                       .|.+|++.+.. ....+.|++|++...++ +   ..+..+.|..+    ..+   +++ ...+
T Consensus        74 -----------------~~~~~~~~~~~~~~~~l~y~vFDll~~~~-p---~~~R~~~L~~~~~~~~~~~v~~v~-~~~v  131 (174)
T cd07896          74 -----------------SSIVRRKGPDDEAWRKVKYMVFDLPSADG-P---FEERLERLKNLLEKAPNPHIKIVP-QIRV  131 (174)
T ss_pred             -----------------HHHHHCCCCCHHHCCCCEEEEEECCCCCC-C---HHHHHHHHHHHHHHCCCCEEEEEC-EEEE
T ss_conf             -----------------99986169883330341599987245689-9---999999999998657998099736-1880


Q ss_pred             ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCC
Q ss_conf             40321134556655310011234376377731100011
Q gi|254781172|r  276 NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQK  313 (731)
Q Consensus       276 ~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~  313 (731)
                      .+.+++..++++..+.      .-.|+|+|-.+..++.
T Consensus       132 ~~~~el~~~~~~~~~~------G~EGimlK~~~s~Y~~  163 (174)
T cd07896         132 KSNAHLDSYLDEVVAQ------GGEGLMLRRPDAPYEA  163 (174)
T ss_pred             CCHHHHHHHHHHHHHC------CCCEEEEECCCCCCCC
T ss_conf             9999999999999877------9876478889995789


No 29 
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=98.19  E-value=0.00089  Score=48.37  Aligned_cols=237  Identities=17%  Similarity=0.181  Sum_probs=127.1

Q ss_pred             CCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCC
Q ss_conf             64257021599999999999999861246777611999941581899999859989988865986556669997753102
Q gi|254781172|r   93 IPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPT  172 (731)
Q Consensus        93 ~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~  172 (731)
                      .|||.- .+.+.+|+   .+++          ...+.+|.|+||.=+-+++.+|. ++..||    -|||+|+..--|-.
T Consensus       228 ~PMLA~-~~~~~~e~---~~~~----------~~~~~~E~K~DG~R~QiH~~~~~-v~~fSR----~~ed~T~~fPel~~  288 (589)
T PRK01109        228 RPMLAE-RLSSPKEI---LAKM----------GGKAIFEYKYDGERAQIHKKGDK-VKIFSR----RLENITHQYPDVVE  288 (589)
T ss_pred             CCCCCC-CCCCHHHH---HHHC----------CCCEEEEEEECCEEEEEEEECCE-EEEEEC----CCHHHHHHHHHHHH
T ss_conf             642489-88998999---9755----------98679999873568999981998-999836----84231344448999


Q ss_pred             -CCCCCCCCCCCEEEEEEEEEEECH------HHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH--HCCCEEEEEEE
Q ss_conf             -432233544550489999998520------212345564314854334234567777523455553--01110566410
Q gi|254781172|r  173 -IPRVLSLNIPEIIEVRGEVYISKN------DFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI--TRYLNFFVHGL  243 (731)
Q Consensus       173 -iP~~l~~~~~~~ieiRGEv~m~~~------~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~--~r~L~f~ay~~  243 (731)
                       +...+   .+..+.+=||++.-..      .|+.+-.+                   .|..+....  .-++.|++|++
T Consensus       289 ~~~~~~---~~~~~ILDGEiv~~d~~~g~~~pFq~l~~R-------------------~rk~~~~~~~~~~pv~~~~FDi  346 (589)
T PRK01109        289 AAKEAI---KAEEAIVEGEIVAVDPETGEMRPFQELMHR-------------------KRKHDIAEAIEEYPVNVFLFDV  346 (589)
T ss_pred             HHHHHC---CCCCEEEEEEEEEECCCCCCCCCHHHHHHH-------------------CCCCCHHHHHHHCCEEEEEEEE
T ss_conf             999627---877669844799872888964576899863-------------------3143356676408748999988


Q ss_pred             CCCCCCC--CCCCHHHHHHHHHCCCCCCCCE-----EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEE-C-CHHCCCC
Q ss_conf             2454332--1000036899997599665414-----8874032113455665531001123437637773-1-1000111
Q gi|254781172|r  244 GKTSEIF--AKGQYEMLQKMRCLGFPVNNGV-----RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKV-D-EFSLQKQ  314 (731)
Q Consensus       244 ~~~~~~~--~~~~~e~l~~L~~~GF~v~~~~-----~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikv-n-~~~~q~~  314 (731)
                      .+.++..  .....+..+.|..+ |...+..     ..+.+.+++.+++++-      ..-...|+|+|- | +..++  
T Consensus       347 L~~ng~~l~~~pl~eRr~~L~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~a------~~~~~EGlmiK~l~~~s~Y~--  417 (589)
T PRK01109        347 LYVDGEDLTDKPLPERRKKLEEI-VKENDKVKLAERIITDDVEELEKFFHQA------IEEGCEGLMAKSLGPDSIYQ--  417 (589)
T ss_pred             EEECCCCHHCCCHHHHHHHHHHH-CCCCCCEEEEEEEECCCHHHHHHHHHHH------HHCCCCCEEEECCCCCCCCC--
T ss_conf             40377371107899999999985-1878856984147559999999999999------86476523630378877656--


Q ss_pred             CCCCCCCCCCEEEEC--C--C-CCEEEEEEEEEEEEECCCCE-EE--EEEEEEEEEECCCEEEEE-CCCCHHHHHHH
Q ss_conf             587656866312311--4--5-62158998788994035622-58--999974333026400010-14898999750
Q gi|254781172|r  315 LGERARSPRWMISHK--F--A-EKQASTRLLDIDIQIGRTGI-LT--PVARLEPVNIGGALITNA-TLHNEDYIKGL  382 (731)
Q Consensus       315 lG~ts~~PrwaiA~K--f--~-~e~~~T~v~~I~wqvgRtG~-it--Pva~~ePV~l~G~~V~ra-tlhN~~~I~~l  382 (731)
                      -|  .|.-.| +=+|  |  + .++..-+|.+=.|-.||-+- ++  -+|..+|-.=.=.+|.+| |+++-.+++.|
T Consensus       418 pg--~R~~~W-~K~K~dy~~~~~dtlDlVviga~~G~GrR~~~~s~fl~a~~d~~~~~~~~v~KvgsGftd~~l~~l  491 (589)
T PRK01109        418 AG--ARGWLW-IKYKRDYKSEMMDTVDLVVVGAFYGRGRRAGLYGALLLAAYDPETDTFETVCKVGSGFTDEDLDEL  491 (589)
T ss_pred             CC--CCCCCE-EEEEECCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEECCCCCEEEEEEEECCCCCHHHHHHH
T ss_conf             88--747870-687421045655520179998674798766753423788872899879999996889999999999


No 30 
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=98.18  E-value=1.1e-05  Score=63.02  Aligned_cols=70  Identities=37%  Similarity=0.551  Sum_probs=63.0

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCC-HHHHHHHCCCEEECHHHHHHHH
Q ss_conf             866999725889987899999998298499811163217997788886-3798997499173799999999
Q gi|254781172|r  649 NKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGS-KLEKAQQLGVKIMNEEQFLFLL  718 (731)
Q Consensus       649 gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gS-Kl~KA~~LgI~Ii~e~ef~~ll  718 (731)
                      |+.|++||.+....|++++++|+.+||++..+++.+++++|++...+. ++..|...|++|++++.+.+.+
T Consensus         1 ~~~~~i~~~~~~~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~   71 (72)
T cd00027           1 GLTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIPIVTPEWLLDCL   71 (72)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCCCEEECCCCCCCCEEEECCCCCCHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf             98999950489889999999999849989581558855999868778289999997599573799999985


No 31 
>cd06846 Adenylation_DNA_ligase_family The Adenylation domain of proteins from the ATP-dependent polynucleotide ligase family is the minimal catalytic unit that is common to all family members. ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the A
Probab=98.09  E-value=9.1e-05  Score=56.05  Aligned_cols=158  Identities=13%  Similarity=0.092  Sum_probs=88.9

Q ss_pred             CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf             76119999415818999998599899888659865566699977531024322335445504899999985202123455
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALND  203 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~  203 (731)
                      .+-.|++|+|+||.=+-+.+.+|. ++..||    -|+|+|+.--.   ++.... ..+..+.+=||+++....+.    
T Consensus        19 ~~~~w~~E~K~DG~R~~~~~~~~~-v~l~SR----~g~~~t~~~p~---~~~~~~-~~~~~~iLDGElv~~~~~~~----   85 (187)
T cd06846          19 EDDGYYAQEKADGERALLSVLNGG-VFGISR----TGLEVPLPTII---ILAAKL-KLLPGFILDGEAVGERRGVK----   85 (187)
T ss_pred             CCCCEEEEEEECCEEEEEEEECCE-EEEEEC----CCCCCCCCCHH---HHHHHH-HCCCCCEEEEEEEEECCCCC----
T ss_conf             899789998073279999998999-999969----89985553877---999986-44898158989998758765----


Q ss_pred             HHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCC--CCCCCHHHHHHHHHCCCCCC----CCEEEEEC
Q ss_conf             6431485433423456777752345555301110566410245433--21000036899997599665----41488740
Q gi|254781172|r  204 EMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEI--FAKGQYEMLQKMRCLGFPVN----NGVRQANT  277 (731)
Q Consensus       204 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~--~~~~~~e~l~~L~~~GF~v~----~~~~~~~~  277 (731)
                                 .++-           .....++.|++|++...++.  ......+..+.|.++.=...    +.......
T Consensus        86 -----------~~~~-----------~~~~~~~~~~~FDiL~l~g~~l~~~pl~~R~~~L~~~~~~~~~~~~~~~~~~~~  143 (187)
T cd06846          86 -----------LIRP-----------FEANPKLQYYAFDVLELEGKDLRLLPYSRRLAYLKELGEEFAVKIVPLISAGKV  143 (187)
T ss_pred             -----------CCCH-----------HHHCCCCEEEEECCCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCEEEEEECCCC
T ss_conf             -----------6330-----------342268479998334689835245619999999999762168752675550457


Q ss_pred             CCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCC
Q ss_conf             32113455665531001123437637773110001115876568663
Q gi|254781172|r  278 FHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRW  324 (731)
Q Consensus       278 ~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prw  324 (731)
                      ..++.++++...+      -...|||+|--|-.++  .|.+++.+.|
T Consensus       144 ~~~~~~~~~~~~~------~G~EGiv~K~~ds~Y~--~Gr~~~~~~W  182 (187)
T cd06846         144 DSPLDQLLARLDK------KGKEGIVFKHPDAPYK--AGRPGSGGTQ  182 (187)
T ss_pred             HHHHHHHHHHHHH------CCCCEEEEECCCCCCC--CCCCCCCCCE
T ss_conf             0589999999987------6996278748999658--9987999987


No 32 
>cd07897 Adenylation_DNA_ligase_Bac1 The Adenylation domain of putative bacterial ATP-dependent DNA ligases is inferred by similarity to be a component of the catalytic core unit. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. The adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenyl
Probab=98.07  E-value=0.00015  Score=54.36  Aligned_cols=154  Identities=16%  Similarity=0.122  Sum_probs=87.2

Q ss_pred             CCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECH-----HHH
Q ss_conf             611999941581899999859989988865986556669997753102432233544550489999998520-----212
Q gi|254781172|r  125 SIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN-----DFL  199 (731)
Q Consensus       125 ~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~-----~F~  199 (731)
                      ...|++|+|+||.=+-++..+|. ++..||    -|+|+|+.--.|..+...+    |....+=||++.-..     .|.
T Consensus        23 ~~dw~~E~K~DG~R~~~~~~~~~-v~l~SR----ng~~~t~~fPei~~~~~~~----~~~~ILDGEiv~~~~~g~~~~F~   93 (208)
T cd07897          23 PSDWQAEWKWDGIRGQLVRRGGE-VFLWSR----GEELISGSFPELLAAAEAL----PDGTVLDGELLVWRDGGEPLPFN   93 (208)
T ss_pred             CCCEEEEEEECCEEEEEEEECCE-EEEEEC----CCCCCCHHCHHHHHHHHHC----CCCEEEEEEEEEECCCCCCCCHH
T ss_conf             67679995376188999997999-999948----9870210164789999848----87859985899973899845889


Q ss_pred             HHHHHHHHCCCCCCCCHHHHHHHHHHCCCHH--H-HHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHCCCCCC-CCE-
Q ss_conf             3455643148543342345677775234555--5-30111056641024543321--000036899997599665-414-
Q gi|254781172|r  200 ALNDEMIAVGRKPYANPRNAASGILRRLNPT--D-ITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCLGFPVN-NGV-  272 (731)
Q Consensus       200 ~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~--~-~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~GF~v~-~~~-  272 (731)
                      .+-.+                   ++++.+.  . ...++.|++|++.+..+...  ....+..+.|..+==++. +.. 
T Consensus        94 ~l~~r-------------------~~rk~~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRk~~L~~l~~~~~~~~i~  154 (208)
T cd07897          94 DLQQR-------------------LGRKTVGKKLLADAPAAFRAYDLLELNGEDLRALPLRERRARLEALLAELPPPRLD  154 (208)
T ss_pred             HHHHH-------------------HCCCCCCHHHHHCCCEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCEEE
T ss_conf             99977-------------------53357426677318759999875303797201187999999999987315898299


Q ss_pred             ----EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCC
Q ss_conf             ----8874032113455665531001123437637773110001
Q gi|254781172|r  273 ----RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQ  312 (731)
Q Consensus       273 ----~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q  312 (731)
                          ..+.+.+++.++++..      ......|||+|--|-.++
T Consensus       155 ~s~~~~~~~~~~~~~l~~~a------~~~G~EGIm~K~~dS~Y~  192 (208)
T cd07897         155 LSPLVPFSSWEELAALRAES------RERGVEGLMLKRRDSPYL  192 (208)
T ss_pred             EECEEECCCHHHHHHHHHHH------HHCCCCEEEECCCCCCCC
T ss_conf             81407369999999999999------876995299728999668


No 33 
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.99  E-value=0.00055  Score=49.97  Aligned_cols=195  Identities=15%  Similarity=0.200  Sum_probs=103.1

Q ss_pred             CCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCC----CCCCCCEEEEEEEEEEE----
Q ss_conf             7761199994158189999985998998886598655666999775310243223----35445504899999985----
Q gi|254781172|r  123 DNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVL----SLNIPEIIEVRGEVYIS----  194 (731)
Q Consensus       123 ~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l----~~~~~~~ieiRGEv~m~----  194 (731)
                      ...-.|+-|.|+||.=+.+...+|. ++..||    -|+|+|+..-.|...-..+    ....|  +++=||++.-    
T Consensus        10 P~G~dWiyEiK~DG~R~la~~~~~~-VrL~SR----ng~d~T~~fPEl~~a~~~l~~~~~~~lp--~VLDGEiVald~~g   82 (604)
T PRK09633         10 PTGDEWRYEVKYDGFRCLLIIDETG-ITLISR----NGRNLNNQFPEIIEFCEQIREHLKAELP--LTFDGELVCLLNPY   82 (604)
T ss_pred             CCCCCEEEEEEECEEEEEEEEECCE-EEEEEC----CCCCCHHHHHHHHHHHHHHHHHHCCCCC--CEEEEEEEEECCCC
T ss_conf             6999666874266068999998999-999928----9987376759999999975542102467--34764799888999


Q ss_pred             CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCC-----CCCCHHHHHHH-HHCCCCC
Q ss_conf             20212345564314854334234567777523455553011105664102454332-----10000368999-9759966
Q gi|254781172|r  195 KNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIF-----AKGQYEMLQKM-RCLGFPV  268 (731)
Q Consensus       195 ~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~-----~~~~~e~l~~L-~~~GF~v  268 (731)
                      +.+|..|.....      ..++.+.+.        ....+++.|++|++...++..     .....+.|+.| +..+.+.
T Consensus        83 ~p~F~~LQ~R~~------~~~~~~i~~--------~~~~~Pv~y~vFDLL~LdG~dL~~lPL~eRK~~L~~ll~~~~~p~  148 (604)
T PRK09633         83 RSDFAHVQTRGR------LKNTEVIAK--------SANKRPCQLLAFDLLVLKGESLTSLPYTERKKQLFQLMKAAKLPA  148 (604)
T ss_pred             CCCHHHHHHHHH------CCCCHHHHH--------HHHCCCCEEEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             999899997642------367146666--------532277479999702078714000879999999999986434666


Q ss_pred             CC------CEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEE
Q ss_conf             54------148874032113455665531001123437637773110001115876568663123114562158998788
Q gi|254781172|r  269 NN------GVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDI  342 (731)
Q Consensus       269 ~~------~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I  342 (731)
                      .+      .........+..++++...+      -...|||.|--|..++.    ..|++.| +=.|.. ..++.+|-  
T Consensus       149 ~~~~~~~~~~~~~~~~~dg~~l~~~A~~------~glEGIVaKR~DS~Y~~----GrRs~~W-lKiK~~-~~qe~VIg--  214 (604)
T PRK09633        149 SPDPMGKARIQYIPSTTDFQALWKAVKR------YDGEGIVAKKKTSKWAE----NKRSKDW-LKLKNW-RLVHVIVT--  214 (604)
T ss_pred             CCCCCCCCEEEECCCCCCHHHHHHHHHH------CCCCEEEEECCCCCCCC----CCCCCCE-EEEEEC-CCCEEEEE--
T ss_conf             6665677606733672429999999998------49970686269998789----9998660-786204-63029999--


Q ss_pred             EEEECCCCEEE
Q ss_conf             99403562258
Q gi|254781172|r  343 DIQIGRTGILT  353 (731)
Q Consensus       343 ~wqvgRtG~it  353 (731)
                      =|..+ .|.+.
T Consensus       215 Gy~~~-~G~l~  224 (604)
T PRK09633        215 GYNPS-NGYFT  224 (604)
T ss_pred             EEECC-CCCEE
T ss_conf             87279-98178


No 34 
>cd07905 Adenylation_DNA_ligase_LigC The Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases is a component of the catalytic core unit. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold dom
Probab=97.90  E-value=0.00041  Score=50.95  Aligned_cols=160  Identities=18%  Similarity=0.155  Sum_probs=85.1

Q ss_pred             CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEEC---HHHHH
Q ss_conf             761199994158189999985998998886598655666999775310243223354455048999999852---02123
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISK---NDFLA  200 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~---~~F~~  200 (731)
                      ..-.|++|+|+||.=+-++..+|. ++..||    -|+|+|+..--|...   +....+..+.+=||++.-.   .+|..
T Consensus        14 ~~~~w~~E~K~DG~R~~~h~~~~~-v~l~SR----~g~~~t~~fpei~~~---~~~~~~~~~ILDGElv~~~~~~~~F~~   85 (194)
T cd07905          14 LGGGWLYEPKWDGFRCLVFRDGDE-VELQSR----SGKPLTRYFPELVAA---ARALLPERCVLDGELVVWRGGRLDFDA   85 (194)
T ss_pred             CCCCEEEEEEECCEEEEEEEECCE-EEEEEC----CCCHHHHHCHHHHHH---HHHHCCCCEEEEEEEEEECCCCCCHHH
T ss_conf             999669998177299999998999-999949----998234557699999---987388656997479984599889899


Q ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCC--CCCCHHHHHHHHHCCCCCCCCEEEE---
Q ss_conf             45564314854334234567777523455553011105664102454332--1000036899997599665414887---
Q gi|254781172|r  201 LNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIF--AKGQYEMLQKMRCLGFPVNNGVRQA---  275 (731)
Q Consensus       201 lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~--~~~~~e~l~~L~~~GF~v~~~~~~~---  275 (731)
                      +..+..         +|  .+    .........++.|++|++...++..  -....+..+.|+.+-=++......+   
T Consensus        86 l~~r~~---------~~--~~----~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~~~  150 (194)
T cd07905          86 LQQRIH---------PA--AS----RVRKLAEETPASFVAFDLLALGGVDLRGRPLRERRARLEELLAGWGPPLQLSPAT  150 (194)
T ss_pred             HHHHHH---------HC--CC----CHHHHHHCCCEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEE
T ss_conf             998865---------13--43----0556542288079998888889715223889999999999862589958997443


Q ss_pred             ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCC
Q ss_conf             4032113455665531001123437637773110001
Q gi|254781172|r  276 NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQ  312 (731)
Q Consensus       276 ~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q  312 (731)
                      .+.+++..++++..+      -..-|||+|--|-.++
T Consensus       151 ~~~~~~~~~~~~a~~------~g~EGiv~K~~dS~Y~  181 (194)
T cd07905         151 TDPAEAEEWLEAFEG------AGLDGVVAKRLDGRYR  181 (194)
T ss_pred             CCHHHHHHHHHHHHH------CCCCEEEECCCCCCCC
T ss_conf             898999999999987------7995699718999718


No 35 
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=97.89  E-value=0.00087  Score=48.46  Aligned_cols=218  Identities=14%  Similarity=0.095  Sum_probs=116.7

Q ss_pred             CEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECH----HHHHH
Q ss_conf             11999941581899999859989988865986556669997753102432233544550489999998520----21234
Q gi|254781172|r  126 IFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN----DFLAL  201 (731)
Q Consensus       126 ~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~----~F~~l  201 (731)
                      ..|.+|.|+||.=+-++..+|. ++..||    -|||||+..--|-..   + ...|....+-||++.-..    .|+.|
T Consensus       225 ~~~~~E~K~DG~R~Qih~~~~~-v~l~SR----~~e~it~~fPei~~~---~-~~~~~~~ilDGEiv~~~~~~~~~F~~l  295 (537)
T PRK09247        225 ADWQAEWKWDGIRVQLVRRGGE-VRLWSR----GEELITERFPELVEA---A-EALPDGTVLDGELLVWRPGRVQPFAAL  295 (537)
T ss_pred             HCCEEEECCCCEEEEEEEECCE-EEEEEC----CCCCCHHHHHHHHHH---H-HHCCCCEEEEEEEEEECCCCCCCHHHH
T ss_conf             0065461148268999995999-999937----986031242889999---9-838988478768997359986888999


Q ss_pred             HHHHHHCCCCCCCCHHHHHHHHHHCCCHH--HH-HCCCEEEEEEECCCCCCC--CCCCHHHHHHHHHCCCCCC-CCE---
Q ss_conf             55643148543342345677775234555--53-011105664102454332--1000036899997599665-414---
Q gi|254781172|r  202 NDEMIAVGRKPYANPRNAASGILRRLNPT--DI-TRYLNFFVHGLGKTSEIF--AKGQYEMLQKMRCLGFPVN-NGV---  272 (731)
Q Consensus       202 N~~~~~~g~~~f~NpRN~aaG~lr~~d~~--~~-~r~L~f~ay~~~~~~~~~--~~~~~e~l~~L~~~GF~v~-~~~---  272 (731)
                                         .--++++.+.  .. .-++.|++|++.+.++..  -....+..+.|..+=-.+. +..   
T Consensus       296 -------------------q~Rl~rk~~~~~~~~~~Pv~~~~FDlL~~~G~dl~~~pl~eRR~~L~~~~~~~~~~~~~~s  356 (537)
T PRK09247        296 -------------------QQRIGRKTVGKKLLAEYPAFLRAYDLLEDGGEDLRELPLAERRARLEALIARLPDPRLDLS  356 (537)
T ss_pred             -------------------HHHHCCCCCCHHHHHCCCEEEEEEEHHHHCCCCHHHCCHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             -------------------8774236753767514886999862044278614438899999999998733689849960


Q ss_pred             --EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEEEC-CC
Q ss_conf             --887403211345566553100112343763777311000111587656866312311456215899878899403-56
Q gi|254781172|r  273 --RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIG-RT  349 (731)
Q Consensus       273 --~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~wqvg-Rt  349 (731)
                        ...++.+++..++++      ...-...|||+|--|-.++-  |  .+.-.| +=+|-.+.+...+|..-.|--| |+
T Consensus       357 ~~~~~~~~~e~~~~~~~------a~~~g~EGlm~K~~ds~Y~p--G--rR~~~W-~K~K~d~~tlDlVviga~~G~GrR~  425 (537)
T PRK09247        357 PLVPFSDWDELAALRAA------ARERGVEGLMLKRRDSPYLV--G--RKKGDW-WKWKRDPLTIDAVLIYAQRGHGRRA  425 (537)
T ss_pred             CCCCCCCHHHHHHHHHH------HHHCCCEEEEEECCCCCCCC--C--CCCCCE-EEECCCCCCCEEEEEECCCCCCCCC
T ss_conf             51406999999999998------87538704798458998679--9--878974-7880575310048972245876645


Q ss_pred             CEEEE--EEEEEEEEECCC--EEEE-ECCCCHHHHHHH
Q ss_conf             22589--999743330264--0001-014898999750
Q gi|254781172|r  350 GILTP--VARLEPVNIGGA--LITN-ATLHNEDYIKGL  382 (731)
Q Consensus       350 G~itP--va~~ePV~l~G~--~V~r-atlhN~~~I~~l  382 (731)
                      |.++.  .|..++-.-...  +|.+ .|++.-.++++|
T Consensus       426 ~~~~~~~la~~~~~~~~~~l~~v~K~~sG~td~el~~l  463 (537)
T PRK09247        426 SLYTDYTFGVWDGGEGGRQLVPFAKAYSGLTDEEILQL  463 (537)
T ss_pred             CCCCCEEEEEEECCCCCCEEEEEEEECCCCCHHHHHHH
T ss_conf             54244579998079986168887886478999999999


No 36 
>KOG1968 consensus
Probab=97.85  E-value=1.7e-05  Score=61.70  Aligned_cols=20  Identities=10%  Similarity=0.323  Sum_probs=11.2

Q ss_pred             CCEEEEEEEEEEEEECCCEE
Q ss_conf             62258999974333026400
Q gi|254781172|r  349 TGILTPVARLEPVNIGGALI  368 (731)
Q Consensus       349 tG~itPva~~ePV~l~G~~V  368 (731)
                      +++|++++.-|-+.|++.-+
T Consensus       495 ~~ri~si~~se~~ki~~~~l  514 (871)
T KOG1968         495 RSRIMSICKSEGIKISDDVL  514 (871)
T ss_pred             HHHHHHHHCCCCEECCCHHH
T ss_conf             76665330246424172788


No 37 
>cd07902 Adenylation_DNA_ligase_III The Adenylation domain of DNA Ligase III is a component of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing
Probab=97.83  E-value=0.00074  Score=48.98  Aligned_cols=176  Identities=15%  Similarity=0.131  Sum_probs=90.4

Q ss_pred             CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHH-HHHH
Q ss_conf             664257021599999999999999861246777611999941581899999859989988865986556669997-7531
Q gi|254781172|r   92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSAC-IRAI  170 (731)
Q Consensus        92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n-~~~i  170 (731)
                      -.|||-- -+.+.++...   +          .+..|.+|+|+||.=+-+++.+|. ++..||    -|+|+|.. ...+
T Consensus        14 i~PMLA~-~~~~~~~~~~---~----------~~~~~~~E~K~DG~R~qih~~~~~-v~l~SR----n~~d~~~~~~~~~   74 (213)
T cd07902          14 VKPMLAE-ACKSVEYAMK---K----------CPNGMYAEIKYDGERVQLHKQGDN-FSFFSR----SLKPVLPHKVSHF   74 (213)
T ss_pred             CCCEECC-CCCCHHHHHH---H----------CCCCEEEEEEECEEEEEEEECCCE-EEEEEC----CCCCCCCCHHHHH
T ss_conf             8243589-8799799997---5----------799759997158189999982999-999927----8830364217789


Q ss_pred             C-CCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCC-CCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCC
Q ss_conf             0-2432233544550489999998520212345564314854-3342345677775234555530111056641024543
Q gi|254781172|r  171 P-TIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRK-PYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSE  248 (731)
Q Consensus       171 ~-~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~-~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~  248 (731)
                      . -||..++  ....+.+=||++.-...          .|.. +|..-     + ++++.. ....++.+++|++.+.++
T Consensus        75 ~~~i~~~~~--~~~~~ILDGEiv~~d~~----------~g~~~~f~~l-----~-~~~~~~-~~~~~~~~~vFDlL~l~g  135 (213)
T cd07902          75 KDYIPKAFP--HGHSMILDSEVLLVDTK----------TGKPLPFGTL-----G-IHKKSA-FKDANVCLFVFDCLYFNG  135 (213)
T ss_pred             HHHHHHHCC--CCCCEEEEEEEEEEECC----------CCCCCCCHHH-----H-HHHHHH-CCCCCEEEEEEEEEEECC
T ss_conf             999998647--78747997047998668----------9975503004-----4-554541-245781699997700598


Q ss_pred             C--CCCCCHHHHHHHHHCCCCCCCCEEE-----EECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf             3--2100003689999759966541488-----7403211345566553100112343763777311000
Q gi|254781172|r  249 I--FAKGQYEMLQKMRCLGFPVNNGVRQ-----ANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL  311 (731)
Q Consensus       249 ~--~~~~~~e~l~~L~~~GF~v~~~~~~-----~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~  311 (731)
                      .  .-....+..+.|..+--++......     ..+.+++.+++++..+      -...|||+|--+-.+
T Consensus       136 ~~l~~~pl~eRr~~L~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~a~~------~g~EGiv~K~~~S~Y  199 (213)
T cd07902         136 ESLMDKPLRERRKILEDNMVEIPNRIMFSEMKFVKKADDLAALITRVIR------EGLEGLVLKDIKSVY  199 (213)
T ss_pred             EEHHHCCHHHHHHHHHHHHCCCCCCEEEEEEEECCCHHHHHHHHHHHHH------CCCEEEEEECCCCCC
T ss_conf             1833088999999999740568984798744755999999999999997------698389975898976


No 38 
>PRK13766 Hef nuclease; Provisional
Probab=97.78  E-value=4.2e-05  Score=58.62  Aligned_cols=52  Identities=25%  Similarity=0.264  Sum_probs=46.8

Q ss_pred             CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCH
Q ss_conf             10111168999999882998999997897761251177876138886789999999996697
Q gi|254781172|r  558 GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNP  619 (731)
Q Consensus       558 GI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~  619 (731)
                      +|||||.++|+.|..+|+|+..+..          ++.++|.+|+|||+++|+.|.+++..+
T Consensus       710 ~~pgvg~~~a~~ll~~fgsi~~i~~----------a~~~eL~~v~giG~~~A~~i~~~~~~~  761 (764)
T PRK13766        710 SLPDVGPVLARNLLDHFGSVENVMT----------ASEEELKAVEGIGEKTAKKIREVVTSE  761 (764)
T ss_pred             HCCCCCHHHHHHHHHHCCCHHHHHC----------CCHHHHHHCCCCCHHHHHHHHHHHCCC
T ss_conf             3899999999999997199999965----------999999547496999999999985251


No 39 
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=97.70  E-value=8.5e-05  Score=56.26  Aligned_cols=52  Identities=21%  Similarity=0.273  Sum_probs=47.9

Q ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCC
Q ss_conf             01011116899999988299899999789776125117787613888678999999999669
Q gi|254781172|r  557 LGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQN  618 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~  618 (731)
                      ..|||||+++.+.|.++|+|++++..+          +.++|..++|||.++|+.|.++|+.
T Consensus       557 d~I~GIG~kr~~~Ll~~Fgs~~~i~~A----------s~eeL~~v~Gi~~~~A~~I~~~l~~  608 (609)
T PRK00558        557 DDIPGIGPKRRKALLKHFGSLKAIKEA----------SVEELAKVPGISKKLAEKIYEALHK  608 (609)
T ss_pred             CCCCCCCHHHHHHHHHHCCCHHHHHHC----------CHHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf             478997999999999970799999738----------9999964899899999999999705


No 40 
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=97.68  E-value=0.0015  Score=46.69  Aligned_cols=217  Identities=17%  Similarity=0.194  Sum_probs=104.7

Q ss_pred             CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECH---HHHH
Q ss_conf             7611999941581899999859989988865986556669997753102432233544550489999998520---2123
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN---DFLA  200 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~---~F~~  200 (731)
                      ....|..|.|+||.=+-+...+|. ++..||    -|+|+|+.---|...-..+   .+....+=||+++...   +|..
T Consensus        22 ~~~~w~~E~K~DG~R~~~~~~~~~-v~L~SR----~g~d~T~~fPel~~~~~~~---~~~~~VLDGEiV~~~~~~~~F~~   93 (345)
T PRK08224         22 PGGGWSYEPKWDGFRCLVFRDGDE-VELGSR----NGKPLTRYFPELVAALRAE---LPERCVLDGEIVIATDGGLDFEA   93 (345)
T ss_pred             CCCCEEEEEEECCEEEEEEEECCE-EEEECC----CCCCCHHHCHHHHHHHHHC---CCCCEEEEEEEEECCCCCCCHHH
T ss_conf             999758996277099999998999-999938----9752034578999999752---78657985069960699789899


Q ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHCCCCCCCCEEEE---
Q ss_conf             455643148543342345677775234555530111056641024543321--000036899997599665414887---
Q gi|254781172|r  201 LNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCLGFPVNNGVRQA---  275 (731)
Q Consensus       201 lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~GF~v~~~~~~~---  275 (731)
                      |..+.         +|   +++..+.+   ....++.|++|++.+.++...  ....+.-+.|..+-=...+....+   
T Consensus        94 Lq~R~---------~~---~~~r~~~l---~~~~Pv~~~~FDlL~l~G~dL~~~Pl~eRr~~L~~ll~~~~~~~~~~~~~  158 (345)
T PRK08224         94 LQQRI---------HP---AASRVRKL---AEETPASFVAFDLLALGDEDLTGRPFAERRAALEAALAGAGPPVHLTPAT  158 (345)
T ss_pred             HHHHC---------CC---CCCHHHHH---HHHCCCEEEEEEEEEECCEEHHHCCHHHHHHHHHHHHCCCCCCEEECCCC
T ss_conf             96452---------22---33137776---43078479999775599637454879999999998752479857974520


Q ss_pred             ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCC-CEEEEEEEEEEEEECCCCEE--
Q ss_conf             403211345566553100112343763777311000111587656866312311456-21589987889940356225--
Q gi|254781172|r  276 NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAE-KQASTRLLDIDIQIGRTGIL--  352 (731)
Q Consensus       276 ~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~-e~~~T~v~~I~wqvgRtG~i--  352 (731)
                      .+.++...+++...+      -...|||.|--|..++-  |.  +  .|   .|... .+++.+|.+-  ..|+.+..  
T Consensus       159 ~~~~~~~~~~~~a~~------~G~EGIvaKr~dS~Y~~--Gr--R--~w---lKiK~~~~~d~VI~G~--~~~~~~~~~g  221 (345)
T PRK08224        159 TDLATARRWFEEFEG------AGLDGVIAKPLDGPYQP--GK--R--VM---FKVKHERTADCVVAGF--RYHKSGDAVG  221 (345)
T ss_pred             CCHHHHHHHHHHHHH------CCCCEEEEECCCCCCCC--CC--C--CC---EEECCCCEEEEEEEEE--ECCCCCCCCC
T ss_conf             788899999999997------69932798669997678--98--6--66---7963446031999956--7489877544


Q ss_pred             -EEEEEEEEE-EECCCEEEEECCCCHHHHHHH
Q ss_conf             -899997433-302640001014898999750
Q gi|254781172|r  353 -TPVARLEPV-NIGGALITNATLHNEDYIKGL  382 (731)
Q Consensus       353 -tPva~~ePV-~l~G~~V~ratlhN~~~I~~l  382 (731)
                       -=++..++- .|  ..|..+|.++....++|
T Consensus       222 slllG~y~~~g~l--~~vGv~tgf~~~~~~~L  251 (345)
T PRK08224        222 SLLLGLYDDDGLL--HHVGVTSAFPMAERRAL  251 (345)
T ss_pred             CEEEEEECCCCCE--EEEEEECCCCHHHHHHH
T ss_conf             0789998599758--99753068798999999


No 41 
>KOG2841 consensus
Probab=97.62  E-value=0.00012  Score=55.16  Aligned_cols=78  Identities=18%  Similarity=0.209  Sum_probs=58.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHC-CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHH
Q ss_conf             2100145689999875223466677630-101111689999998829989999978977612511778761388867899
Q gi|254781172|r  530 FGDVSVTNLYDSINKRRNISLERFIFSL-GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDII  608 (731)
Q Consensus       530 fgeKsa~nL~~sIe~sK~~~L~r~L~AL-GI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~  608 (731)
                      +..|+++++...++..   .+.+++..| .||+|+++-|-.|..+|++++.+..+          +.++|..++|+|+..
T Consensus       173 ~ek~p~dli~~~~~~d---~ls~~~~~Lt~i~~VnKtda~~LL~~FgsLq~~~~A----------S~~ele~~~G~G~~k  239 (254)
T KOG2841         173 YEKKPIDLIMERKDRD---LLSSLLGFLTTIPGVNKTDAQLLLQKFGSLQQISNA----------SEGELEQCPGLGPAK  239 (254)
T ss_pred             HHCCCCHHHHHCCCCC---HHHHHHHHHHHCCCCCCCCHHHHHHHCCCHHHHHHC----------CHHHHHHCCCCCHHH
T ss_conf             6038804555333530---889999998817897700189998855359998741----------776798675737899


Q ss_pred             HHHHHHHHCCHH
Q ss_conf             999999966979
Q gi|254781172|r  609 AQAIVEFYQNPR  620 (731)
Q Consensus       609 A~si~~ff~~~~  620 (731)
                      |+.|.+||+.+.
T Consensus       240 ak~l~~~l~~pf  251 (254)
T KOG2841         240 AKRLHKFLHQPF  251 (254)
T ss_pred             HHHHHHHHHCCC
T ss_conf             999999984511


No 42 
>cd07894 Adenylation_RNA_ligase The Adenylation domain of RNA circularization protein, which catalyzes the circularization of RNA molecules in an ATP-dependent reaction, comprises the enzyme's catalytic unit. RNA circularization protein is capable of circularizing RNA molecules in an ATP-dependent reaction. RNA circularization may protect RNA from exonuclease activity. This model comprises the adenylation domain, the minimal catalytic unit that is common to all members of the ATP-dependent DNA ligase family, and the carboxy-terminal extension of RNA circularization protein that serves as a dimerization module. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. The adenylation domain binds ATP and contains many active site residues.
Probab=97.59  E-value=0.0015  Score=46.63  Aligned_cols=169  Identities=20%  Similarity=0.164  Sum_probs=105.6

Q ss_pred             CCCCCCCEEECCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHH
Q ss_conf             32357750451664257021599999999999999861246777611999941581899999859989988865986556
Q gi|254781172|r   81 EMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSG  160 (731)
Q Consensus        81 ~~~~~~~kv~H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~G  160 (731)
                      .+..+|.|   -..++.|+..     |..++             ...++||-|+||--+-+..-+|+ +.|+||| |.+=
T Consensus        24 ~vV~GyP~---I~R~~~L~~g-----i~~~F-------------~~~v~vEEK~dGYNVRI~~~~g~-vlA~TRG-G~IC   80 (340)
T cd07894          24 RVVPGYPK---IRRALLLEPG-----LKRHF-------------IDPVAVEEKMNGYNVRIVRVGGE-VLAFTRG-GFIC   80 (340)
T ss_pred             CEECCCCC---CCEEECCCCC-----HHHHC-------------CCCEEEEEECCCCEEEEEEECCE-EEEEECC-CEEC
T ss_conf             68837997---1245403420-----69776-------------89858998216706999999999-9999058-7207


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEE
Q ss_conf             66999775310243223354455048999999852021234556431485433423456777752345555301110566
Q gi|254781172|r  161 EDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFV  240 (731)
Q Consensus       161 eDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~a  240 (731)
                      -=-|+.++.  -++..+-.++|+ +.+=||++=+.                   ||=  +.+     ++- ...++.||+
T Consensus        81 PfTT~r~~~--~~~~~fF~d~P~-lvLCgE~~Gpe-------------------NPY--v~~-----~~p-~~edi~ffv  130 (340)
T cd07894          81 PFTTDRLRE--LDLPEFFDDYPD-LMLCGEVVGPE-------------------NPY--VPY-----DYP-VAEDVGFFV  130 (340)
T ss_pred             CCCHHHHHH--HHHHHHHHHCCC-CEEEEEEECCC-------------------CCC--CCC-----CCC-CCCCCEEEE
T ss_conf             873478776--400777865898-68999860689-------------------999--789-----998-757731899


Q ss_pred             EEECCCCCCCCCCCHHHHHHHHHCCCCCCCCEEEEECC--CCHHHHHHHHHHHHCCCCCCCCCEEEEECC
Q ss_conf             41024543321000036899997599665414887403--211345566553100112343763777311
Q gi|254781172|r  241 HGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTF--HGIVSYYNEMKSIRSTLPYDIDGLVYKVDE  308 (731)
Q Consensus       241 y~~~~~~~~~~~~~~e~l~~L~~~GF~v~~~~~~~~~~--~~~~~~~~~~~~~r~~l~y~iDGiVikvn~  308 (731)
                      |++-......+-.+.+.++.+.+.|++.++..-.+..-  +++.+.+.++.+      =.--|+|+|-.+
T Consensus       131 FDi~~k~t~~~Lpv~er~~L~e~Yglp~V~~fg~~~~~~~~~l~eiI~~L~~------egrEGVVlKdp~  194 (340)
T cd07894         131 FDIRKKNTGKPLPVEERRELLEEYGLPHVRLFGTFTVDEVEELKEIIRELDK------EGREGVVLKDPD  194 (340)
T ss_pred             EEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCEECHHHHHHHHHHHHHHHH------CCCCEEEECCCC
T ss_conf             9866879898579999999999739997644127839999999999998735------488318974866


No 43 
>TIGR02776 NHEJ_ligase_prk DNA ligase D; InterPro: IPR014143   Members of this entry are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NheJ). The system of the bacterial Ku protein (IPR009187 from INTERPRO) plus this DNA ligase is seen in about 200f bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This entry describes a central and C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs. An additional N-terminal 3 -phosphoesterase (PE) domain (IPR014144 from INTERPRO) is present in some members of this ligase. Most examples of genes for this ligase are adjacent to the gene for Ku..
Probab=97.59  E-value=0.0011  Score=47.58  Aligned_cols=165  Identities=20%  Similarity=0.212  Sum_probs=98.1

Q ss_pred             CCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCC-----CCCCCEEEEEEEEEEEC----
Q ss_conf             611999941581899999859989988865986556669997753102432233-----54455048999999852----
Q gi|254781172|r  125 SIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLS-----LNIPEIIEVRGEVYISK----  195 (731)
Q Consensus       125 ~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~-----~~~~~~ieiRGEv~m~~----  195 (731)
                      ..+|+-|.|+||-=+-++-++|. |+.+||    -|.|+|+..-.   |+.-+.     ...-..+.|=||||+-.    
T Consensus         4 G~~W~yEvKyDGYR~~~~i~~g~-vrL~tR----nG~dwt~~fp~---i~~~~~~~~~~~l~~~~~~lDGEiVvL~~~g~   75 (645)
T TIGR02776         4 GDGWLYEVKYDGYRCLLRIEDGD-VRLITR----NGHDWTERFPE---IVKALAEIIEKLLKLLPAWLDGEIVVLDERGR   75 (645)
T ss_pred             CCCCEEEECCCCCEEEEEEECCE-EEEEEC----CCCCHHHHHHH---HHHHHHHHHHHHHHCCCEEECCEEEEECCCCC
T ss_conf             88843763124223566785481-799852----88785552068---99999999986520563121335797278898


Q ss_pred             HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHH---HHHCCCEEEEEEECCCCCC-----CCCCCHHHH-HHHHHCCC
Q ss_conf             02123455643148543342345677775234555---5301110566410245433-----210000368-99997599
Q gi|254781172|r  196 NDFLALNDEMIAVGRKPYANPRNAASGILRRLNPT---DITRYLNFFVHGLGKTSEI-----FAKGQYEML-QKMRCLGF  266 (731)
Q Consensus       196 ~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~---~~~r~L~f~ay~~~~~~~~-----~~~~~~e~l-~~L~~~GF  266 (731)
                      ++|+.|..+                 |-|++-|-.   ...+++.|+||++..-++.     +....-..| +.|+....
T Consensus        76 ~~F~~LQ~R-----------------gr~~~~~~a~~~~~~~~~~~~aFDLl~l~G~dL~~lPL~~RK~~L~~LL~~~~~  138 (645)
T TIGR02776        76 ADFAALQNR-----------------GRLKKTDRALSEGASEPLLYYAFDLLFLSGEDLRALPLEERKKRLKELLKAQDG  138 (645)
T ss_pred             CCHHHHHCC-----------------HHCCCHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             781886202-----------------001334589997218980899971566880677862489999999999984468


Q ss_pred             C-----CCCCEEE--EECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCC-CCCCCE
Q ss_conf             6-----6541488--740321134556655310011234376377731100011158765-686631
Q gi|254781172|r  267 P-----VNNGVRQ--ANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERA-RSPRWM  325 (731)
Q Consensus       267 ~-----v~~~~~~--~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts-~~Prwa  325 (731)
                      +     ...++..  +.+..++.+.++.-..      |.--|||-|=-+-.++.     . |++.|-
T Consensus       139 ~~~~~~~~~~~~~r~~~~~~~~~~ll~~a~~------~~lEGvv~Kr~~s~Y~s-----gkRs~~W~  194 (645)
T TIGR02776       139 PAEPDPAIRYSDHRVFEEDGDGQALLESACR------LGLEGVVSKRLDSPYRS-----GKRSKDWL  194 (645)
T ss_pred             CCCCCCCCCCEECCCCCCCCHHHHHHHHHHH------HCCCEEEEECCCCCCCC-----CCCCCCHH
T ss_conf             7567741200001100685158999999998------57973898547773016-----77686024


No 44 
>PRK08609 hypothetical protein; Provisional
Probab=97.57  E-value=0.00026  Score=52.47  Aligned_cols=22  Identities=32%  Similarity=0.604  Sum_probs=9.2

Q ss_pred             HHHHHHHHHCCCHHHHHCCCEEEE
Q ss_conf             456777752345555301110566
Q gi|254781172|r  217 RNAASGILRRLNPTDITRYLNFFV  240 (731)
Q Consensus       217 RN~aaG~lr~~d~~~~~r~L~f~a  240 (731)
                      |-.+|||+|+.-  +...++++++
T Consensus       177 ~veiaGS~RR~k--etvGDIDiLv  198 (570)
T PRK08609        177 RFSRAGSLRRAR--ETVKDLDFII  198 (570)
T ss_pred             EEEEECHHHHCC--CCCCCEEEEE
T ss_conf             798602023146--6546734899


No 45 
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=97.44  E-value=0.0046  Score=42.85  Aligned_cols=26  Identities=23%  Similarity=0.391  Sum_probs=9.4

Q ss_pred             EEEEEECCEEEEEEEEECCEEEEEEEC
Q ss_conf             999941581899999859989988865
Q gi|254781172|r  128 FTLEPKIDGTMITIRYEKGKFVYAALR  154 (731)
Q Consensus       128 ~~vepKiDG~sisl~Y~~G~L~~a~TR  154 (731)
                      |+.|+|.||.=+-+..++|. ++..||
T Consensus       470 W~yEiKwDGyR~la~~~~g~-VrL~SR  495 (753)
T PRK09632        470 WAFEGKWDGYRLLVEADHGA-LRLRSR  495 (753)
T ss_pred             EEEECCCCEEEEEEEEECCE-EEEECC
T ss_conf             56770075399999998999-999818


No 46 
>PHA02142 putative RNA ligase
Probab=97.37  E-value=0.0027  Score=44.70  Aligned_cols=148  Identities=18%  Similarity=0.119  Sum_probs=80.5

Q ss_pred             CCCEEEEEEECCEEEEEEEEE---------------------CCEEEEEEECCCCHHHHH---HHHHHHHHCCCCCCCCC
Q ss_conf             761199994158189999985---------------------998998886598655666---99977531024322335
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRYE---------------------KGKFVYAALRGDGHSGED---VSACIRAIPTIPRVLSL  179 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y~---------------------~G~L~~a~TRGdG~~GeD---VT~n~~~i~~iP~~l~~  179 (731)
                      ....|.++-|+||.|+++.|-                     +|++  ++.+.|-..=+|   .-..+-.--+||.+|. 
T Consensus       167 ~~~~~~vTeKLDGsS~tvy~v~~~~~~~~~g~~~~~~~~~~~~~~f--gvcsrn~~L~~~~~n~yW~~a~~~~i~~~l~-  243 (366)
T PHA02142        167 ADVKFAKSLKLDGSSITMAWVTDPDLFLDLGTEDEPYAHDYDDAQF--IVASRNQVLRYNADSKWWKGVENYQIVDRLK-  243 (366)
T ss_pred             CCCEEEEEEEECCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCE--EEECCCEEEEECCCCHHHHHHHHCCCHHHHH-
T ss_conf             7926999997525358999814774000134235665444456640--6861642563178872999988758288997-


Q ss_pred             CCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCCCCCHHHHH
Q ss_conf             44550489999998520212345564314854334234567777523455553011105664102454332100003689
Q gi|254781172|r  180 NIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQ  259 (731)
Q Consensus       180 ~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~~~~~e~l~  259 (731)
                      .....+-|+||++=+.=                =.|+-++              ..-.|++|++-..+....-++.++..
T Consensus       244 klg~nIAIQGEliGpgI----------------QgN~y~l--------------~~~~f~vF~v~dId~~ryl~~~e~~~  293 (366)
T PHA02142        244 ELGMSVAIQGELMGPGI----------------QKNRENF--------------DKYRIFAFRAWFIDEQRFATDEEFQD  293 (366)
T ss_pred             HCCCCEEEEEEEECCCC----------------CCCCCCC--------------CCCEEEEEEEEECCCCEECCHHHHHH
T ss_conf             54872799888876543----------------5764457--------------88669999999828867778899999


Q ss_pred             HHHHCCCCCCCCEEE------EECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECC
Q ss_conf             999759966541488------7403211345566553100112343763777311
Q gi|254781172|r  260 KMRCLGFPVNNGVRQ------ANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDE  308 (731)
Q Consensus       260 ~L~~~GF~v~~~~~~------~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~  308 (731)
                      +++.+|.+.+|..-.      ..+.++++++-+    ......-.=-|+|+|-.+
T Consensus       294 ~~~~lgl~~VPvlgy~~~~~~~~sv~ell~~Ae----~~~~~~~~REGiV~rs~~  344 (366)
T PHA02142        294 LCRTLGMEIVPQLGYSYPFQEFTNVKEMLAAAD----IPSINHKIAEGVVYKSVE  344 (366)
T ss_pred             HHHHCCCCEEEECCCCCCCCCCCCHHHHHHHCC----CCCCCCCCCCEEEEEECC
T ss_conf             998769962404265454343212999975422----788788611329996326


No 47 
>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain; InterPro: IPR014146   DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see IPR009187 from INTERPRO), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This region represents the central ligase domain..
Probab=97.36  E-value=0.015  Score=38.82  Aligned_cols=171  Identities=19%  Similarity=0.265  Sum_probs=101.5

Q ss_pred             CCCCEEEEEEECCEEEEEEEEE-CCEEEEEEECCCCHHHHHHHHHH-HHHCCC----CCCCCCCCCCEEEEEEEEEEEC-
Q ss_conf             7761199994158189999985-99899888659865566699977-531024----3223354455048999999852-
Q gi|254781172|r  123 DNSIFFTLEPKIDGTMITIRYE-KGKFVYAALRGDGHSGEDVSACI-RAIPTI----PRVLSLNIPEIIEVRGEVYISK-  195 (731)
Q Consensus       123 ~~~~~~~vepKiDG~sisl~Y~-~G~L~~a~TRGdG~~GeDVT~n~-~~i~~i----P~~l~~~~~~~ieiRGEv~m~~-  195 (731)
                      +..-.|+-|.|+||-=+-+.-+ .|+ |+..||    -|.|+|+.- -.|.-.    -..++.   ....+=||||+-. 
T Consensus        12 P~G~~W~yEvK~DGYR~l~~i~~~g~-vrL~sR----ng~dwT~~fP~~~~~~~~~~~~~l~~---~~~~lDGE~VvL~~   83 (328)
T TIGR02779        12 PTGDDWLYEVKFDGYRLLARIEEGGK-VRLISR----NGHDWTEKFPPELAAAEEIILAALPI---LPAILDGEIVVLDE   83 (328)
T ss_pred             CCCCCCEEEEEECCEEEEEEEECCCC-EEEEEC----CCCCHHHHCCHHHHHHHHHHHHHCCC---CEEEEEEEEEEECC
T ss_conf             88678127851124047888840883-899735----88551442686689999999875478---80677037999468


Q ss_pred             ---HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCC-----CCCCHHHHHH-HHHCCC
Q ss_conf             ---0212345564314854334234567777523455553011105664102454332-----1000036899-997599
Q gi|254781172|r  196 ---NDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIF-----AKGQYEMLQK-MRCLGF  266 (731)
Q Consensus       196 ---~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~-----~~~~~e~l~~-L~~~GF  266 (731)
                         ++|..|......       -.+...+.       .-..+++.|+||++.+.++..     ....-..|+. |+.++-
T Consensus        84 ~G~~~F~~LQ~~~~~-------~~~~~I~~-------~~~~~~~~y~aFDLL~~~G~dL~~~pL~eRk~~L~~Ll~~~~~  149 (328)
T TIGR02779        84 SGRSDFQALQNRLDA-------GKAEKIEK-------AAAKRPLTYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAQKG  149 (328)
T ss_pred             CCCCCHHHHHHHHHC-------CCHHHHHH-------HHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             898787999776414-------76257899-------9722993799970456782476620289999999998611578


Q ss_pred             CCCC-----CEEEEECC-CCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCC-CCCCEE
Q ss_conf             6654-----14887403-211345566553100112343763777311000111587656-866312
Q gi|254781172|r  267 PVNN-----GVRQANTF-HGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERAR-SPRWMI  326 (731)
Q Consensus       267 ~v~~-----~~~~~~~~-~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~-~Prwai  326 (731)
                      +.++     .+..+..+ .+..+.++.-.      .+.-=|||=|--|-.++.     .| ++.|-=
T Consensus       150 ~~~p~~~~~~~~~s~~~~~~g~~l~~~a~------~~glEGvvaKr~dS~Y~~-----GrR~~~W~K  205 (328)
T TIGR02779       150 PLAPDPQAKAIRYSEHFEGDGQALLEAAC------RLGLEGVVAKRRDSPYRS-----GRRSADWLK  205 (328)
T ss_pred             CCCCCCCCCEEEEEEECCCCHHHHHHHHH------HHCCCEEEEECCCCCCCC-----CCCCCCCCE
T ss_conf             87878775404788753675789999999------828962799527787678-----861565401


No 48 
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.33  E-value=0.011  Score=39.84  Aligned_cols=161  Identities=23%  Similarity=0.251  Sum_probs=91.9

Q ss_pred             CCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEE----CHHH
Q ss_conf             776119999415818999998599899888659865566699977531024322335445504899999985----2021
Q gi|254781172|r  123 DNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYIS----KNDF  198 (731)
Q Consensus       123 ~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~----~~~F  198 (731)
                      ...-.|+-|.|+||.=+-+..++|. ++..||    -|.|+|+.--.|...-..|+.   ....+=|||+.-    +.+|
T Consensus       216 P~g~~W~~EiK~DGyR~la~i~~g~-v~L~SR----nG~D~T~~fPel~~a~~~l~~---~~avLDGEIVald~~Grp~F  287 (832)
T PRK05972        216 PSGDGWIYEIKFDGYRILARIEGGE-VRLFTR----NGLDWTAKLPALAKAAAALGL---PDAWLDGEIVVLDENGVPDF  287 (832)
T ss_pred             CCCCCEEEEEEECEEEEEEEEECCE-EEEEEC----CCCCCHHHHHHHHHHHHHCCC---CCEEEEEEEEEECCCCCCCH
T ss_conf             9999725886554288999980998-899816----998534455999999984688---76356206998679998798


Q ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCCC--CCHHHHHHHHHCCCCC-CCCEEEE
Q ss_conf             234556431485433423456777752345555301110566410245433210--0003689999759966-5414887
Q gi|254781172|r  199 LALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAK--GQYEMLQKMRCLGFPV-NNGVRQA  275 (731)
Q Consensus       199 ~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~~--~~~e~l~~L~~~GF~v-~~~~~~~  275 (731)
                      ..|....               +        ......+.|++|++...++....  ...+.-+.|+.+-=.. .+....+
T Consensus       288 ~~LQ~~~---------------~--------~~~~~~l~y~~FDLL~ldG~dL~~~Pl~eRk~~L~~Ll~~~~~~~ir~s  344 (832)
T PRK05972        288 QALQNAF---------------D--------EGRTEDLVYFAFDLPFLEGEDLRALPLEERRARLRALLEAARSDRLRFS  344 (832)
T ss_pred             HHHHHHH---------------H--------CCCCCCEEEEEEEECCCCCCCCHHCCHHHHHHHHHHHHCCCCCCCEECC
T ss_conf             9999887---------------4--------4787753899962103388510007899999999987502689837637


Q ss_pred             ECCC-CHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCE
Q ss_conf             4032-1134556655310011234376377731100011158765686631
Q gi|254781172|r  276 NTFH-GIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWM  325 (731)
Q Consensus       276 ~~~~-~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prwa  325 (731)
                      ..++ +-.+.++.-.+      ...-|||-|--|-.++  -   .|++.|-
T Consensus       345 ~~~~~~g~~~~~~a~~------~glEGIVaKr~dS~Y~--~---gRS~~Wl  384 (832)
T PRK05972        345 EHFDAGGDAVLASACR------LGLEGVIGKRADSPYV--S---GRSEDWI  384 (832)
T ss_pred             CCCCCCHHHHHHHHHH------CCCCCEEEECCCCCCC--C---CCCHHHH
T ss_conf             5405799999999987------1885326513788656--8---8864334


No 49 
>cd08039 Adenylation_DNA_ligase_Fungal The Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins is inferred by similarity to be a component of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain
Probab=97.28  E-value=0.024  Score=37.32  Aligned_cols=163  Identities=18%  Similarity=0.185  Sum_probs=84.9

Q ss_pred             CCEEEEEEECCEEEEEEEE---ECCEEEEEEECCCCHHHHHHHHHHH----HHCCCCCC--CCCCCCCEEEEEEEEEEEC
Q ss_conf             6119999415818999998---5998998886598655666999775----31024322--3354455048999999852
Q gi|254781172|r  125 SIFFTLEPKIDGTMITIRY---EKGKFVYAALRGDGHSGEDVSACIR----AIPTIPRV--LSLNIPEIIEVRGEVYISK  195 (731)
Q Consensus       125 ~~~~~vepKiDG~sisl~Y---~~G~L~~a~TRGdG~~GeDVT~n~~----~i~~iP~~--l~~~~~~~ieiRGEv~m~~  195 (731)
                      .-.|++|.|+||-=+-++|   +.|.=++..||    -|+|+|...-    .+..-...  ........+.+=||++.=.
T Consensus        21 ~~~f~~E~KyDGeR~QiH~~~~k~~~~irifSR----n~ed~T~~~p~~~~~i~~~l~~~~~~~~~~~~~ILDGE~va~d   96 (235)
T cd08039          21 RRRMSAERKYDGEYCQIHVDLSKGPNPIRIFSK----SGKDSTADRHGIHDVIRKSLRIGKPDCKFKKNCILEGEMLVWN   96 (235)
T ss_pred             CCEEEEEEEECEEEEEEEECCCCCCCEEEEECC----CCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCEEEEEEEEEEE
T ss_conf             984999980380359999721478999999889----8641545432267999986411566544652079971589986


Q ss_pred             H------HHHHHHHHHHHCCCCCCCCHHHHHHHHHH-CC-C-HHHHHCCCEEEEEEECCCCCC--CCCCCHHHHHHHHHC
Q ss_conf             0------21234556431485433423456777752-34-5-555301110566410245433--210000368999975
Q gi|254781172|r  196 N------DFLALNDEMIAVGRKPYANPRNAASGILR-RL-N-PTDITRYLNFFVHGLGKTSEI--FAKGQYEMLQKMRCL  264 (731)
Q Consensus       196 ~------~F~~lN~~~~~~g~~~f~NpRN~aaG~lr-~~-d-~~~~~r~L~f~ay~~~~~~~~--~~~~~~e~l~~L~~~  264 (731)
                      .      .|+.+......             ++..+ .+ + +....+++.+++|++.+.++.  .-....+..+.|..+
T Consensus        97 ~~~~~~lpFq~l~~~~~r-------------~~~~~~~~~~~~~~~~~~~~~~~FDiLylnG~~L~~~Pl~eRR~~Le~l  163 (235)
T cd08039          97 DRKSDILPFHKLRKHISR-------------SGSFIGTDNDSPPHPYEHLMIVFFDVLLLDDDSLLSKPYRERRDLLESL  163 (235)
T ss_pred             CCCCCCCCHHHHHHHHHC-------------CCCHHHHHHCCCCCCCCEEEEEEEEEEEECCHHHHCCCHHHHHHHHHHH
T ss_conf             788960777888767520-------------3210222212644464127999988998988534308799999999986


Q ss_pred             CCCCCCC-EEEE----------ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf             9966541-4887----------403211345566553100112343763777311000
Q gi|254781172|r  265 GFPVNNG-VRQA----------NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL  311 (731)
Q Consensus       265 GF~v~~~-~~~~----------~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~  311 (731)
                       |...+. ...+          .+.+++..+.++-      +.=..-|||+|--+-.+
T Consensus       164 -~~~~~g~~~~~~~~~i~~~~~~~~~~i~~~~~~a------i~~~~EGlmiK~~~S~Y  214 (235)
T cd08039         164 -VSPIPGRAILAEQFPIDFSHPDAYSRLRTIFARA------IAEHQEGLVLKASEEPY  214 (235)
T ss_pred             -HCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHH------HHCCCCEEEECCCCCCC
T ss_conf             -2657881788888742367778899999999999------98699879972699977


No 50 
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=97.26  E-value=0.00085  Score=48.53  Aligned_cols=81  Identities=17%  Similarity=0.205  Sum_probs=44.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCH
Q ss_conf             4210014568999987522346667763010111168999999882--99899999789776125117787613888678
Q gi|254781172|r  529 GFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYY--LSYQNFAQEINNIIAHNNDDWLSLIRVPLVGD  606 (731)
Q Consensus       529 GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f--~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~  606 (731)
                      -|+-++-.+-..+|++- ..++..+--...|||||.+.+..|....  +++..+.    .+.........+|++|+|+||
T Consensus        21 ~fr~rAY~~Aa~~l~~~-~~~i~~~~~~~~lpGIG~~ia~kI~Eil~tG~~~~le----~l~~~~p~~l~~l~~I~GiGp   95 (307)
T cd00141          21 PFRVRAYRKAARALESL-PEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLE----ELREDVPPGLLLLLRVPGVGP   95 (307)
T ss_pred             CHHHHHHHHHHHHHHHC-CCCCCCHHHHCCCCCCCHHHHHHHHHHHHHCCHHHHH----HHHCCCCHHHHHHHCCCCCCH
T ss_conf             26699999999999869-9564789987179996489999999999979808999----986656378999964788788


Q ss_pred             HHHHHHHH
Q ss_conf             99999999
Q gi|254781172|r  607 IIAQAIVE  614 (731)
Q Consensus       607 ~~A~si~~  614 (731)
                      ++|..+.+
T Consensus        96 k~a~~l~~  103 (307)
T cd00141          96 KTARKLYE  103 (307)
T ss_pred             HHHHHHHH
T ss_conf             99999998


No 51 
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=97.24  E-value=0.012  Score=39.63  Aligned_cols=174  Identities=18%  Similarity=0.184  Sum_probs=105.7

Q ss_pred             ECCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHH
Q ss_conf             51664257021599999999999999861246777611999941581899999859989988865986556669997753
Q gi|254781172|r   90 THSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRA  169 (731)
Q Consensus        90 ~H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~  169 (731)
                      .|-..|+-|+.+     |..|.            +...++||-|+||--+-+.--+|. +.|+||| |.+--=-|+.++.
T Consensus        69 PkI~R~llL~p~-----ik~~F------------~~~~v~VEEKmnGYNVRV~k~~g~-vyAiTRg-G~ICPfTT~r~~~  129 (382)
T COG1423          69 PKIRRALLLEPT-----IKKHF------------GRGKVVVEEKMNGYNVRVVKLGGE-VYAITRG-GLICPFTTERLRD  129 (382)
T ss_pred             CHHHEEECCCHH-----HHHHC------------CCCCEEEEEECCCCEEEEEEECCE-EEEEECC-CEECCCHHHHHHH
T ss_conf             404213226633-----68654------------898479997226715899998899-9998148-5246760677776


Q ss_pred             HCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCC
Q ss_conf             10243223354455048999999852021234556431485433423456777752345555301110566410245433
Q gi|254781172|r  170 IPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEI  249 (731)
Q Consensus       170 i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~  249 (731)
                      .  +|+.+-.++|+ +.+=||.+=+.                   ||=  +.     .++ -..+++.||.|++-+-...
T Consensus       130 l--~~~eff~d~p~-lvlcgEmvG~e-------------------nPY--v~-----~~~-y~~e~v~fFvFDire~~tg  179 (382)
T COG1423         130 L--IDLEFFDDYPD-LVLCGEMVGPE-------------------NPY--VP-----GPY-YEKEDVGFFVFDIREKNTG  179 (382)
T ss_pred             H--CCHHHHHHCCC-CEEEEEECCCC-------------------CCC--CC-----CCC-CCCCCCEEEEEEEEECCCC
T ss_conf             4--35456763898-58999750678-------------------998--77-----898-7657740899998755889


Q ss_pred             CCCCCHHHHHHHHHCCCCCCCCEEEEECCCCH----HHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCC
Q ss_conf             21000036899997599665414887403211----345566553100112343763777311000111587656
Q gi|254781172|r  250 FAKGQYEMLQKMRCLGFPVNNGVRQANTFHGI----VSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERAR  320 (731)
Q Consensus       250 ~~~~~~e~l~~L~~~GF~v~~~~~~~~~~~~~----~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~  320 (731)
                      .+-.+.+.++.+.+.||+.+...-.. ..+++    ..-+.++.+      =.=.|+|+|-.|... ..|-+|++
T Consensus       180 r~Lp~eer~~l~ekYgl~~V~~fg~~-~~~e~~eei~eIve~L~k------eGREGVV~Kdpdm~~-~plKYtTs  246 (382)
T COG1423         180 RPLPVEERLELAEKYGLPHVEIFGEF-PADEAGEEIYEIVERLNK------EGREGVVMKDPDMRV-PPLKYTTS  246 (382)
T ss_pred             CCCCHHHHHHHHHHCCCCCEEEEEEE-CHHHHHHHHHHHHHHHHH------CCCCCEEECCCCCCC-CCCEEECC
T ss_conf             97899999978987098706774266-366768999999999735------577535863813356-86331125


No 52 
>pfam09414 RNA_ligase RNA ligase. This is a family of RNA ligases. The enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes.
Probab=97.24  E-value=0.01  Score=40.18  Aligned_cols=150  Identities=19%  Similarity=0.168  Sum_probs=81.3

Q ss_pred             EEEEEEECCEEEEEEEEECCE-EEEEEECCCCHHHH----------HHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEEC
Q ss_conf             199994158189999985998-99888659865566----------6999775310243223354455048999999852
Q gi|254781172|r  127 FFTLEPKIDGTMITIRYEKGK-FVYAALRGDGHSGE----------DVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISK  195 (731)
Q Consensus       127 ~~~vepKiDG~sisl~Y~~G~-L~~a~TRGdG~~Ge----------DVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~  195 (731)
                      +|+++-||||.++++.+.++. .+...+|+=|...+          .-+..++.. .++.++....+..+.|.||+|=+.
T Consensus         2 e~vvTEKLhGtn~~~~~~~~~~~~~~r~~~~g~~~~~~~~~~~~~n~~~~~~~~~-~~~~~~~~~~~~~v~i~GEl~Gp~   80 (183)
T pfam09414         2 EWVATEKLHGTNFSVYIVRDESQFAKRKRLVGVPAEDFFGYEILDNIYWAAIEAL-QILLRLAYLIPESVAVYGELFGPG   80 (183)
T ss_pred             CEEEEEEECCEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHH-HHHHHHHCCCCCEEEEEEEEECCC
T ss_conf             2899983747658999989821588732001345556310323115899999971-278775303875189998883475


Q ss_pred             HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCC--CCCCCCHHHHHHHHHCCCCCCCCEE
Q ss_conf             02123455643148543342345677775234555530111056641024543--3210000368999975996654148
Q gi|254781172|r  196 NDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSE--IFAKGQYEMLQKMRCLGFPVNNGVR  273 (731)
Q Consensus       196 ~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~--~~~~~~~e~l~~L~~~GF~v~~~~~  273 (731)
                                                   -|.+.- ....+.|++|++-....  ...-++.+...+++.+|++++|-..
T Consensus        81 -----------------------------IQ~~~y-~~~~~~fy~Fdi~~~~~~~~~~l~~d~~~~~~~~lgl~~vP~L~  130 (183)
T pfam09414        81 -----------------------------IQKNTY-YQGDLHFYVFDIWYIDAQETRFLDDDEVEAFCKTLGLKTVPVLG  130 (183)
T ss_pred             -----------------------------CCCCCC-CCCCCEEEEEEEEECCCCCEEECCHHHHHHHHHHCCCCCCCEEE
T ss_conf             -----------------------------357632-58876599999998169916978889999999876998178895


Q ss_pred             EEECCCCHHHHHHHHHHH----HCCCCCCCCCEEEEECC
Q ss_conf             874032113455665531----00112343763777311
Q gi|254781172|r  274 QANTFHGIVSYYNEMKSI----RSTLPYDIDGLVYKVDE  308 (731)
Q Consensus       274 ~~~~~~~~~~~~~~~~~~----r~~l~y~iDGiVikvn~  308 (731)
                       -..++++..+-......    -..-+----|+|||-..
T Consensus       131 -rG~~~e~~~~~~~~~~~~~~~~~~~~~i~EGvVikp~~  168 (183)
T pfam09414       131 -RGPFDELKAFDVELEMLAGALLGLEGNLAEGVVLKPVR  168 (183)
T ss_pred             -EECHHHHHCCCHHCCCCCCCCCCCCCCEEEEEEEEECC
T ss_conf             -98079952040112544577788888566369971144


No 53 
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=97.19  E-value=0.0024  Score=45.11  Aligned_cols=83  Identities=13%  Similarity=0.200  Sum_probs=48.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH--------HHH-CCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCC
Q ss_conf             01000134210014568999987522346667--------763-01011116899999988-299899999789776125
Q gi|254781172|r  522 TKIENILGFGDVSVTNLYDSINKRRNISLERF--------IFS-LGIRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHN  591 (731)
Q Consensus       522 ~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~--------L~A-LGI~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~  591 (731)
                      +++.+++|+|++.+++|.+=++.-+-..+..+        |.- ++|+|||.++|+.+-+. +.|++.+..+-+      
T Consensus        48 ~~l~~ipGIG~~ia~kI~Eil~TG~~~~~e~~~~~~~~~~l~el~~I~GvGpk~a~~l~~~Gi~tl~dL~~a~~------  121 (334)
T smart00483       48 KDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKE------  121 (334)
T ss_pred             HHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHHHH------
T ss_conf             99727999878999999999984994899998728651689998538887789999999849887999998788------


Q ss_pred             CCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             11778761388867899999999
Q gi|254781172|r  592 NDDWLSLIRVPLVGDIIAQAIVE  614 (731)
Q Consensus       592 ~~~~e~L~~I~GiG~~~A~si~~  614 (731)
                          ..|....++|-+.-+.+..
T Consensus       122 ----~~l~~~q~~Glk~~ed~~~  140 (334)
T smart00483      122 ----LKLTKQQKAGLKYYEDILK  140 (334)
T ss_pred             ----HHHHHHHHHHHHHHHHHHC
T ss_conf             ----7678898876999999972


No 54 
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1); InterPro: IPR000977   DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing 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), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination ,.   Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold , . ; GO: 0003910 DNA ligase (ATP) activity, 0005524 ATP binding, 0006260 DNA replication, 0006281 DNA repair, 0006310 DNA recombination.
Probab=96.83  E-value=0.038  Score=35.75  Aligned_cols=221  Identities=18%  Similarity=0.145  Sum_probs=123.1

Q ss_pred             CCCCCCHHHCCCHHHHHHHHHHHH-------HHHCCCCCCCCEEEEEEECCEEEEEEEE-ECCEEEEEEECCCCHHHHHH
Q ss_conf             664257021599999999999999-------8612467776119999415818999998-59989988865986556669
Q gi|254781172|r   92 SIPTLSLEKIWNIEDLRKFITRIY-------RFWQKKDDNSIFFTLEPKIDGTMITIRY-EKGKFVYAALRGDGHSGEDV  163 (731)
Q Consensus        92 ~~pMlSL~k~~~~~el~~w~~~~~-------~~~~~~~~~~~~~~vepKiDG~sisl~Y-~~G~L~~a~TRGdG~~GeDV  163 (731)
                      ..|||+-.=.-..+.|..+.+|-.       +-.+..+. .-.|.+|-|+||-=+-+++ .++. +.-.+|    -||||
T Consensus       196 ~kPMLA~~~~~~~e~l~~~~~RkhemDPPYekkfqeLGL-e~~~~~E~KYDGeR~Q~Hkl~Gd~-~~~FSR----rlen~  269 (705)
T TIGR00574       196 LKPMLAERAKSIEEALKKLGNRKHEMDPPYEKKFQELGL-EDKFLVEYKYDGERVQIHKLDGDE-VKIFSR----RLENI  269 (705)
T ss_pred             CCCHHHHHCCCHHHHHHHCCCCCCCCCCCHHHHHHHCCC-CCCEEEEEECCCHHEEEEEEECCE-EEEEEE----CCCCH
T ss_conf             662047445774799984588724688853234655177-451587640451010012331884-899873----78640


Q ss_pred             HHHHHHHC----C--CCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCC-C-----HHH
Q ss_conf             99775310----2--4322335445504899999985202123455643148543342345677775234-5-----555
Q gi|254781172|r  164 SACIRAIP----T--IPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRL-N-----PTD  231 (731)
Q Consensus       164 T~n~~~i~----~--iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~-d-----~~~  231 (731)
                      |+..-.+.    .  |+..++.+ ...+.|=||++.-...=          |+..   |=-.....+|++ |     -..
T Consensus       270 T~~~p~~~~~s~~~~~~~a~~~~-~~~~IldGE~va~D~~~----------g~~l---PFq~l~~r~~~k~dRqftt~~~  335 (705)
T TIGR00574       270 TYQYPEILSESLTEFIKKAFPGD-IKSCILDGEMVAIDPET----------GKIL---PFQTLLTRAKRKYDRQFTTIDS  335 (705)
T ss_pred             HHHCCCHHHHHHHHHHHHHCCCC-CCEEEEEEEEEEECCCC----------CCCC---CCCHHHHHHHHHHHHHHHHHHH
T ss_conf             22304214564488899745888-66179714678731145----------8216---6413301311112001355676


Q ss_pred             --HHCCCEEE-EEEECCCCCCC--CCCCHHHHHHHHHCCCCCCC-CE-----EEE-ECCCCHHHHHHHHHHHHCCCCCCC
Q ss_conf             --30111056-64102454332--10000368999975996654-14-----887-403211345566553100112343
Q gi|254781172|r  232 --ITRYLNFF-VHGLGKTSEIF--AKGQYEMLQKMRCLGFPVNN-GV-----RQA-NTFHGIVSYYNEMKSIRSTLPYDI  299 (731)
Q Consensus       232 --~~r~L~f~-ay~~~~~~~~~--~~~~~e~l~~L~~~GF~v~~-~~-----~~~-~~~~~~~~~~~~~~~~r~~l~y~i  299 (731)
                        ..-.+.+| +|++.+.++..  ...-.++-+.|...==++.. ..     ..+ ++.+++.+++++-      +.-.+
T Consensus       336 ~~~~~~~~~fl~FD~LY~ng~~L~~~pL~~RR~~L~~i~~~~~nWr~~~~~~~~~~~~~ee~~~~l~~a------i~~g~  409 (705)
T TIGR00574       336 MEKKVPVCLFLVFDILYLNGESLIDEPLIERREILESIVKPIPNWRIEIAEMIDVSDNVEELEKFLNEA------ISEGC  409 (705)
T ss_pred             HHHHCCCEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCHHHHHHHHHHH------HHCCC
T ss_conf             752014024444656232780355677388999988753528881799974463127989999999999------96389


Q ss_pred             CCEEEEECC---HHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEE
Q ss_conf             763777311---00011158765686631231145621589987889
Q gi|254781172|r  300 DGLVYKVDE---FSLQKQLGERARSPRWMISHKFAEKQASTRLLDID  343 (731)
Q Consensus       300 DGiVikvn~---~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~  343 (731)
                      =|+|+|--.   -.++-    .+|.+.| +=+|..-.+...-=.|++
T Consensus       410 EGlm~K~~~p~~~~Y~p----g~R~~~w-~K~K~~Y~~~~~d~LDLv  451 (705)
T TIGR00574       410 EGLMVKDLEPDEAIYEP----GKRGWLW-LKFKPDYLEGMGDTLDLV  451 (705)
T ss_pred             CEEEECCCCCCCCCCCC----CCCCCCC-EEEECCCCCCCCCEEEEE
T ss_conf             73897046879863147----7778875-033002366567510168


No 55 
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=96.74  E-value=0.037  Score=35.89  Aligned_cols=73  Identities=27%  Similarity=0.358  Sum_probs=51.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCC
Q ss_conf             10001342100145689999875223466677630101111689999998829989999978977612511778761388
Q gi|254781172|r  523 KIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVP  602 (731)
Q Consensus       523 ~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~  602 (731)
                      +-..|-||....-..++..+              +++.|||.++|-.+...+ +.+.+..++.      +.+...|..++
T Consensus        56 d~~~LyGF~~~~Er~~F~~L--------------i~V~GIGpK~AL~ILs~~-~~~~l~~aI~------~~D~~~L~~vp  114 (198)
T PRK00116         56 DAQLLYGFLTKEERELFRLL--------------ISVSGVGPKLALAILSGL-SPEELAQAIA------NGDIKALTKVP  114 (198)
T ss_pred             CCCEEEEECCHHHHHHHHHH--------------HCCCCCCHHHHHHHHCCC-CHHHHHHHHH------HCCHHHHCCCC
T ss_conf             88757840888999999998--------------566885789999887029-9999999998------58999970688


Q ss_pred             CCCHHHHHHHHHHH
Q ss_conf             86789999999996
Q gi|254781172|r  603 LVGDIIAQAIVEFY  616 (731)
Q Consensus       603 GiG~~~A~si~~ff  616 (731)
                      |||+++|+.|+--+
T Consensus       115 GIG~KtA~rIi~EL  128 (198)
T PRK00116        115 GVGKKTAERIVLEL  128 (198)
T ss_pred             CCCHHHHHHHHHHH
T ss_conf             97889999999999


No 56 
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=96.69  E-value=0.0036  Score=43.71  Aligned_cols=54  Identities=22%  Similarity=0.294  Sum_probs=48.0

Q ss_pred             HCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCH
Q ss_conf             3010111168999999882998999997897761251177876138886789999999996697
Q gi|254781172|r  556 SLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNP  619 (731)
Q Consensus       556 ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~  619 (731)
                      =.+||+||...|..|..+|+++.++..+          +..+|+.++|||++.|.-|..||..+
T Consensus       184 l~s~pgig~~~a~~ll~~fgS~~~~~ta----------s~~eL~~v~gig~k~A~~I~~~~~t~  237 (254)
T COG1948         184 LESIPGIGPKLAERLLKKFGSVEDVLTA----------SEEELMKVKGIGEKKAREIYRFLRTE  237 (254)
T ss_pred             HHCCCCCCHHHHHHHHHHHCCHHHHHHC----------CHHHHHHHCCCCHHHHHHHHHHHHCH
T ss_conf             9708996489999999985688877655----------99999774484688999999998344


No 57 
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=96.68  E-value=0.0054  Score=42.31  Aligned_cols=49  Identities=20%  Similarity=0.219  Sum_probs=44.3

Q ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             010111168999999882998999997897761251177876138886789999999996
Q gi|254781172|r  557 LGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFY  616 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff  616 (731)
                      .+|||||++..+.|.+||+++..+..+          +.++|..+ ||+...|+.|.++|
T Consensus       533 d~I~GiG~~r~~~LL~~Fgs~~~i~~A----------s~eel~~v-gi~~~~a~~i~~~~  581 (581)
T COG0322         533 DDIPGIGPKRRKALLKHFGSLKGIKSA----------SVEELAKV-GISKKLAEKIYEAL  581 (581)
T ss_pred             CCCCCCCHHHHHHHHHHHHCHHHHHHC----------CHHHHHHC-CCCHHHHHHHHHHC
T ss_conf             048886889999999983178888855----------99999874-99999999998529


No 58 
>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=96.62  E-value=0.00092  Score=48.27  Aligned_cols=27  Identities=44%  Similarity=1.015  Sum_probs=23.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHH
Q ss_conf             3265775010337865445210100354344114
Q gi|254781172|r  433 FCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSA  466 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpa  466 (731)
                      +||+||+++++..++      +++||+|. .|||
T Consensus         1 ~CP~C~s~l~r~~~e------v~~rC~n~-~CpA   27 (27)
T pfam03119         1 HCPVCGSPLVREEGE------VDIRCTNG-SCPA   27 (27)
T ss_pred             CCCCCCCEEECCCCC------EEEECCCC-CCCC
T ss_conf             988898974856897------86888898-8879


No 59 
>TIGR00084 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR000085   In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure . In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB.; GO: 0003678 DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=96.62  E-value=0.016  Score=38.66  Aligned_cols=138  Identities=17%  Similarity=0.233  Sum_probs=71.6

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             46655332130123103541035555653057654045410110106777531000100013421001456899998752
Q gi|254781172|r  467 QQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRR  546 (731)
Q Consensus       467 q~~~~i~hF~SK~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK  546 (731)
                      |-.+-++|++-|  .|    -..++..||-      +         ++.....-+.+|+++.|.|.|.|=+|++++.   
T Consensus        49 ~~~~~Ft~~~~R--ed----aNQi~~~LfG------F---------~~~~Er~lF~~Li~~nGvGpk~ALaiL~~~~---  104 (217)
T TIGR00084        49 QKAQLFTHLVVR--ED----ANQILHLLFG------F---------NTLEERELFKELIKVNGVGPKLALAILSNMS---  104 (217)
T ss_pred             CCCEEEEEEEEE--CC----HHHHHHHHHC------C---------CCHHHHHHHHHHHHCCCCHHHHHHHHHCCCC---
T ss_conf             863467877776--04----6789999734------7---------9877899999985148802899999866788---


Q ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             23466677630101111689999998829989999978977612511778761388867899999999966979999999
Q gi|254781172|r  547 NISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVE  626 (731)
Q Consensus       547 ~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~  626 (731)
                                                    .+.+..+++      ..+...|.+++|||.|+|+.+..       .++..
T Consensus       105 ------------------------------~~~~~~ai~------~~~~~~L~k~pGvGKK~A~~l~~-------leL~g  141 (217)
T TIGR00084       105 ------------------------------PEEFVQAIE------TEEVKALVKIPGVGKKTAERLLA-------LELKG  141 (217)
T ss_pred             ------------------------------HHHHHHHHH------HHHHHHHHCCCCCCHHHHHHHHH-------HHHHH
T ss_conf             ------------------------------758988886------41044420458857378999987-------77545


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCH-HHHHHHHHHCCCEEE
Q ss_conf             9997338776543224688216866999725889987-899999998298499
Q gi|254781172|r  627 ALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQR-HKAQEYVTQLGAVVS  678 (731)
Q Consensus       627 ~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R-~e~~~~ie~~Ggkv~  678 (731)
                      ++...........  ..+ ++.-..=-.|-    -.| +|+.+.|.++|++-.
T Consensus       142 k~~~~~~~~~~~~--~~~-~~~~~~~~~~~----~~~y~E~~~aL~sLGY~~~  187 (217)
T TIGR00084       142 KLKGVKNLEMFTN--LAN-HLETDEKLTAE----AARYDELFEALVSLGYKPQ  187 (217)
T ss_pred             HHCCCCCCCCCCC--CCC-CCCCCCHHHHH----HHHHHHHHHHHHHCCCCHH
T ss_conf             4405521124554--335-33554101210----2118899999997298888


No 60 
>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=96.46  E-value=0.00035  Score=51.51  Aligned_cols=161  Identities=19%  Similarity=0.262  Sum_probs=76.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHH--HH--CCHHH-HHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHH-
Q ss_conf             001342100145689999875223466677--63--01011-1168999999882998999997897761251177876-
Q gi|254781172|r  525 ENILGFGDVSVTNLYDSINKRRNISLERFI--FS--LGIRH-VGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSL-  598 (731)
Q Consensus       525 ~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L--~A--LGI~~-vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L-  598 (731)
                      +.++|+|+|.++.|++.=--..-.+|.+|=  ..  |++++ +|++.|+.|.+.          |+   ..+...+.+| 
T Consensus       455 mdI~GLG~~~I~~LfE~~Lv~~~~DLY~L~~k~~~Ll~le~~~g~~sa~nLl~a----------Ie---~sK~~pl~RlL  521 (706)
T TIGR00575       455 MDIDGLGEKVIEQLFEEKLVRSVADLYALKEKLEDLLELEGKFGEKSAQNLLSA----------IE---KSKKKPLARLL  521 (706)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH----------HH---HHHHHHHHHHH
T ss_conf             332222389999998726667856665778899998706403556889999999----------99---85210489999


Q ss_pred             --HCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCE
Q ss_conf             --138886789999999996697999999999973387765432246882168669997258899878999999982984
Q gi|254781172|r  599 --IRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAV  676 (731)
Q Consensus       599 --~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggk  676 (731)
                        +.|++||+.+|+.+...|..      +++|.++..-      . ..+        +|    .|.|.++. .++..|.+
T Consensus       522 ~aLGIr~VG~~~A~~La~~f~t------l~~L~~A~~e------~-~~~--------~~----~f~~s~L~-~~~g~G~~  575 (706)
T TIGR00575       522 FALGIRHVGEVTAKLLAKHFGT------LDKLKAASLE------T-LES--------IY----QFDRSELL-SVEGVGPK  575 (706)
T ss_pred             HHCCCHHHHHHHHHHHHHHCCC------HHHHHHCCHH------H-HHH--------HH----HHCCHHHH-HCCCCHHH
T ss_conf             8628603579999999985588------6899850821------6-778--------87----51605564-10140278


Q ss_pred             EEEEEECCEEEEEEC----CCCCCHHHHHHHCCCEEECHHHHHHHHHHHCCC
Q ss_conf             998111632179977----888863798997499173799999999882865
Q gi|254781172|r  677 VSAILSRKTDIIIVG----DNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNTT  724 (731)
Q Consensus       677 v~sSVSkkT~~LI~g----e~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~~~~  724 (731)
                      |..||..-=..-...    =.+..++++=+++|+.+.++++|.+||.+-..+
T Consensus       576 vA~~~~~~F~~~~~~~~qPYRta~~~~~L~~~gv~~~~~D~~~~LL~~~~~~  627 (706)
T TIGR00575       576 VAESIVNFFHDPNNLSLQPYRTAELIEKLEELGVNMESEDEFCRLLDQALKE  627 (706)
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             9999999871200013560468999999988316310113578777642011


No 61 
>PRK01172 ski2-like helicase; Provisional
Probab=96.45  E-value=0.018  Score=38.37  Aligned_cols=51  Identities=25%  Similarity=0.232  Sum_probs=39.2

Q ss_pred             HHHCCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             76301011116899999988-29989999978977612511778761388867899999999
Q gi|254781172|r  554 IFSLGIRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE  614 (731)
Q Consensus       554 L~ALGI~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~  614 (731)
                      +-=.-||+||...|+.|.++ |.|+..+..          ++.++|..|.|+|++.|++|++
T Consensus       612 l~L~~I~gigr~RAR~Ly~aG~~s~~dia~----------a~~~~L~~i~g~~~~~A~~Ii~  663 (674)
T PRK01172        612 IDLVLIPKVGRVRARRLYDAGFKTVDDIAR----------SSPERIKKIYGFSDTLANAIVN  663 (674)
T ss_pred             HHHCCCCCCCHHHHHHHHHCCCCCHHHHHH----------CCHHHHHHCCCCCHHHHHHHHH
T ss_conf             977188999989999999869999999970----------9998987641989999999999


No 62 
>PRK07997 consensus
Probab=96.41  E-value=0.027  Score=36.90  Aligned_cols=83  Identities=16%  Similarity=0.117  Sum_probs=40.1

Q ss_pred             HHHHHHHCCCCC------CCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCCCCCC---------CCC----CCEE-
Q ss_conf             998433177982------0878999999999999897720311-589999620036432---------357----7504-
Q gi|254781172|r   31 HDDCYYQYSKPI------ILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKIGGEM---------NLS----LFKV-   89 (731)
Q Consensus        31 ~~~~Yy~~~~p~------isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~Vg~~~---------~~~----~~kv-   89 (731)
                      .-++||.. .|.      =+.+.|-.+---++.++...|+++. ..|...||.|----+         ..+    +.-+ 
T Consensus        18 ifRAfyAl-~~l~~s~G~pTnAi~GF~~mL~kli~~~~P~~iavaFD~~~~TFR~e~y~~YKA~R~~~PedL~~Qip~i~   96 (928)
T PRK07997         18 LYRAYHAF-PPLTNSAGEPTGAMYGVLNMLRSLIMQYKPTHAAVVFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLH   96 (928)
T ss_pred             HHHHHCCC-CCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf             99998078-86779989662079999999999998649987999980889960343305652899999878999999999


Q ss_pred             ----ECCCCCCCHHHCCCHHHHHHHHHHHH
Q ss_conf             ----51664257021599999999999999
Q gi|254781172|r   90 ----THSIPTLSLEKIWNIEDLRKFITRIY  115 (731)
Q Consensus        90 ----~H~~pMlSL~k~~~~~el~~w~~~~~  115 (731)
                          ..-+|.++++. |--||+..=+.+..
T Consensus        97 e~l~a~gIp~~~~~G-yEADDiIgTla~~~  125 (928)
T PRK07997         97 AMVKAMGLPLLAVSG-VEADDVIGTLAREA  125 (928)
T ss_pred             HHHHHCCCCEECCCC-CCHHHHHHHHHHHH
T ss_conf             999987998855589-24999999999999


No 63 
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=96.21  E-value=0.025  Score=37.13  Aligned_cols=53  Identities=25%  Similarity=0.384  Sum_probs=35.1

Q ss_pred             CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHC
Q ss_conf             101111689999998829989999978977612511778761388867899999999966
Q gi|254781172|r  558 GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ  617 (731)
Q Consensus       558 GI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~  617 (731)
                      ++.|||.++|-.|.+.+ +.+.+..++.      ..++..|.++||||.|+|+.++--+.
T Consensus        77 sVnGIGpK~ALaiLs~~-~~~~l~~aI~------~~d~~~L~k~PGIGkKtAerivleLk  129 (201)
T COG0632          77 SVNGIGPKLALAILSNL-DPEELAQAIA------NEDVKALSKIPGIGKKTAERIVLELK  129 (201)
T ss_pred             CCCCCCHHHHHHHHCCC-CHHHHHHHHH------HCCHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf             11880589999998489-9999999998------32867644189877889999999976


No 64 
>PRK08609 hypothetical protein; Provisional
Probab=96.15  E-value=0.0025  Score=44.85  Aligned_cols=10  Identities=70%  Similarity=0.843  Sum_probs=3.8

Q ss_pred             HHHHHHCCCE
Q ss_conf             7989974991
Q gi|254781172|r  698 LEKAQQLGVK  707 (731)
Q Consensus       698 l~KA~~LgI~  707 (731)
                      +..|++.|++
T Consensus       511 ~~~A~~~gv~  520 (570)
T PRK08609        511 LKKAQAAGVK  520 (570)
T ss_pred             HHHHHHCCCE
T ss_conf             9999986996


No 65 
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional
Probab=96.08  E-value=0.024  Score=37.36  Aligned_cols=74  Identities=19%  Similarity=0.354  Sum_probs=52.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCC
Q ss_conf             01000134210014568999987522346667763010111168999999882998999997897761251177876138
Q gi|254781172|r  522 TKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRV  601 (731)
Q Consensus       522 ~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I  601 (731)
                      ++-..|-||..+.-..++..+              +.+.|||.++|-.+...+ +.+.+..++.      ..+...|..+
T Consensus        54 Ed~~~LyGF~~~~Er~~F~~L--------------isVsGIGpk~Al~iLs~~-~~~~l~~aI~------~~D~~~L~~v  112 (196)
T PRK13901         54 EDELKLFGFLNSSEREVFEEL--------------IGVDGIGPRAALRVLSGI-KYNEFRDAID------REDIELISKV  112 (196)
T ss_pred             ECCCEEECCCCHHHHHHHHHH--------------HCCCCCCHHHHHHHHCCC-CHHHHHHHHH------HCCHHHHHHC
T ss_conf             167713365988999999998--------------765882689999997579-9999999999------2899998319


Q ss_pred             CCCCHHHHHHHHHHH
Q ss_conf             886789999999996
Q gi|254781172|r  602 PLVGDIIAQAIVEFY  616 (731)
Q Consensus       602 ~GiG~~~A~si~~ff  616 (731)
                      +|||+++|+.|+--+
T Consensus       113 pGIG~KtA~rIi~EL  127 (196)
T PRK13901        113 KGIGNKMAGKIFLKL  127 (196)
T ss_pred             CCCCHHHHHHHHHHH
T ss_conf             995899999999999


No 66 
>PRK07898 consensus
Probab=95.96  E-value=0.019  Score=38.07  Aligned_cols=48  Identities=8%  Similarity=0.081  Sum_probs=26.4

Q ss_pred             HHHHHHHCC-CCC------CCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf             998433177-982------0878999999999999897720311-58999962003
Q gi|254781172|r   31 HDDCYYQYS-KPI------ILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI   78 (731)
Q Consensus        31 ~~~~Yy~~~-~p~------isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V   78 (731)
                      .-++||..- .|.      =+.+.|-.+---++.++...|+++. ..|.-.||.|-
T Consensus        26 ~fRAy~Al~~~~l~~~~G~pTnAi~GF~~ml~kli~~~~P~~iavaFD~~~~TFRh   81 (902)
T PRK07898         26 AFRAFYALPAENFSTSGGQTTNAVYGFTAMLINLLRDEQPTHVAVAFDVSRQTFRT   81 (902)
T ss_pred             HHHHHCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCH
T ss_conf             99997169976683999987025999999999999873998899999795996031


No 67 
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=95.94  E-value=0.018  Score=38.34  Aligned_cols=56  Identities=13%  Similarity=0.075  Sum_probs=29.4

Q ss_pred             HCCHHHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             30101111689999998829--989999978977612511778761388867899999999
Q gi|254781172|r  556 SLGIRHVGAEIARSLAKYYL--SYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE  614 (731)
Q Consensus       556 ALGI~~vG~~~Ak~La~~f~--si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~  614 (731)
                      ..+|||||++.|+.|...+.  .+..+...   +.......+.+|++|+|+||++|..+.+
T Consensus        50 l~~ipGIG~~ia~kI~Eil~TG~~~~~e~~---~~~~~~~~l~el~~I~GvGpk~a~~l~~  107 (334)
T smart00483       50 LKGLPGIGDKIKKKIEEIIETGKSSKVLEI---LNDEVYKSLKLFTNVFGVGPKTAAKWYR  107 (334)
T ss_pred             HCCCCCCCHHHHHHHHHHHHCCCCHHHHHH---HCCCCCHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             727999878999999999984994899998---7286516899985388877899999998


No 68 
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=95.63  E-value=0.036  Score=35.93  Aligned_cols=58  Identities=19%  Similarity=0.202  Sum_probs=47.4

Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             01111689999998829989999978977612511778761388867899999999966979999999
Q gi|254781172|r  559 IRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVE  626 (731)
Q Consensus       559 I~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~  626 (731)
                      ||.+-......|.++|+++++++.+          +.++|.+|+|||+.-|.+|.+.++--.+...++
T Consensus       292 iprlp~~vie~lV~~Fg~L~~ll~A----------s~eeL~~VeGIGe~RAr~IregL~Rl~e~~~~~  349 (352)
T PRK13482        292 IPRLPSAVIENLVKHFGTLQGLLEA----------SIEDLDDVEGIGEVRARAIREGLSRLAEQLILD  349 (352)
T ss_pred             CCCCCHHHHHHHHHHHCCHHHHHHC----------CHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999985279999868----------998886567967999999999999999988776


No 69 
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345   These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. .
Probab=95.61  E-value=0.057  Score=34.39  Aligned_cols=129  Identities=18%  Similarity=0.216  Sum_probs=81.2

Q ss_pred             HHHHH-HHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             46655-33213012310354103555565305765404541011010677753100010001342100145689999875
Q gi|254781172|r  467 QQLER-LKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKR  545 (731)
Q Consensus       467 q~~~~-i~hF~SK~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~s  545 (731)
                      +..+. +.||-|   =.|+|+|+++..++++.-   | =..+.+|       ...-+.|.+++|.+++.-..+..++.+.
T Consensus        84 ~~~~gi~~Yl~S---~~~KGvGk~~Aq~Iv~Tf---G-e~~~~~l-------~~~P~kL~~V~G~s~~~~~~~~~~~~~~  149 (769)
T TIGR01448        84 TSKEGIVAYLSS---SSIKGVGKKLAQRIVETF---G-EAAIDVL-------DDDPEKLLEVSGISKANLEKIVSQLSKQ  149 (769)
T ss_pred             CHHHHHHHHHHC---CCCCCCCHHHHHHHHHHH---H-HHHHHHH-------HCCCHHEEEECCCCHHHHHHHHHHHHHH
T ss_conf             506787655522---541672057789999987---6-9999887-------4086010330775667789999999975


Q ss_pred             HH-HHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHC-CCCCCHHHHHHHHHHH
Q ss_conf             22-34666776301011116899999988299899999789776125117787613-8886789999999996
Q gi|254781172|r  546 RN-ISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIR-VPLVGDIIAQAIVEFY  616 (731)
Q Consensus       546 K~-~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~-I~GiG~~~A~si~~ff  616 (731)
                      +. ..+=-+|+.||   +|..-|..+.++|..-+-..+.++.    -..+.-.|.+ |.|||=.+|+++-.-+
T Consensus       150 ~~~~~~l~~L~~lG---~~~~l~~~~~k~y~eadP~~dtLd~----v~~~Py~L~~d~~GiGF~~AD~lA~~l  215 (769)
T TIGR01448       150 KDERKLLLKLQQLG---IGIKLALRIYKFYREADPQADTLDV----VEKDPYLLAEDVKGIGFKTADQLAEEL  215 (769)
T ss_pred             HHHHHHHHHHHHCC---CCHHHHHHHHHHHCCCCCCCCHHHH----HHCCHHHHHHHHCCCCHHHHHHHHHHC
T ss_conf             58999999998538---7678999999984035872116888----621720136751374056899999971


No 70 
>PRK08928 consensus
Probab=95.61  E-value=0.057  Score=34.43  Aligned_cols=47  Identities=17%  Similarity=0.228  Sum_probs=24.0

Q ss_pred             HHHHHHHCCCCC------CCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf             998433177982------0878999999999999897720311-58999962003
Q gi|254781172|r   31 HDDCYYQYSKPI------ILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI   78 (731)
Q Consensus        31 ~~~~Yy~~~~p~------isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V   78 (731)
                      .-++||... |.      -+.+.|-.+---++.+....|+++. ..|...||.|-
T Consensus        16 ~fRAf~Al~-~l~t~~G~pTnAi~GF~~mL~~~~~~~~P~~~~v~fD~~~~TFR~   69 (861)
T PRK08928         16 LFRAYYALQ-PLTTSKGEPIGGVYGFINMLLKLLSDFKPDYLAVVFDSGGKNFRH   69 (861)
T ss_pred             HHHHHCCCC-CCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCH
T ss_conf             999980799-887999988244999999999999863998899999795996224


No 71 
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=95.56  E-value=0.0091  Score=40.56  Aligned_cols=58  Identities=21%  Similarity=0.388  Sum_probs=43.1

Q ss_pred             CCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             2310354103555565305765404541011010677753100010001342100145689999875
Q gi|254781172|r  479 DAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKR  545 (731)
Q Consensus       479 ~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~s  545 (731)
                      .-|.+.|+|++.|..||..-    .|++..+|-.   .-.  .-.+..+.|||+||+.+|+.+|...
T Consensus        94 ~Ll~v~GlGpkKi~~Ly~el----gi~~~e~l~~---a~~--~~~~~~l~GfG~kse~~il~~i~~~  151 (326)
T COG1796          94 PLLKVPGLGPKKIVSLYKEL----GIKDLEELQE---ALE--NGKIRGLRGFGKKSEAKILENIEFA  151 (326)
T ss_pred             HHHHCCCCCCHHHHHHHHHH----CCCCHHHHHH---HHH--HCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             78607798928899999997----8664999999---998--4770326785602199999999997


No 72 
>pfam09513 consensus
Probab=95.54  E-value=0.24  Score=29.56  Aligned_cols=156  Identities=17%  Similarity=0.045  Sum_probs=73.2

Q ss_pred             CCCEEEEEEECCEEEEEEEE-------ECCEEEEEEECCCCHHH---HHHHHHHHHHCCCC-------CCCCCCCCCEEE
Q ss_conf             76119999415818999998-------59989988865986556---66999775310243-------223354455048
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRY-------EKGKFVYAALRGDGHSG---EDVSACIRAIPTIP-------RVLSLNIPEIIE  186 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y-------~~G~L~~a~TRGdG~~G---eDVT~n~~~i~~iP-------~~l~~~~~~~ie  186 (731)
                      ....|.++-|+||.|++.-|       ..|+.-- -+|. =..-   .++=..+....++|       .++.. ....+.
T Consensus       164 ~~~~~~vTeKLdGtS~tvy~v~~~~~~~~g~~Gv-csrn-l~l~~~~~n~~W~~a~~~~i~~~~~~l~~~l~~-~~~nia  240 (356)
T pfam09513       164 IGEEVVVTEKLHGTSITVFNTPERRKVLVWSKGV-CSRN-LVLPEDADNVYWKAAENKNLKAQANHLQRRLKL-IDGGVA  240 (356)
T ss_pred             CCCEEEEEEEECCEEEEEEEECCCCCCCCCEEEE-EECC-EECCCCCCCHHHHHHHHCCHHHHHHHHHHHHHH-CCCCEE
T ss_conf             9947999997547158999945755542433676-0166-771468875799998860617788777777640-388569


Q ss_pred             EEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCCCCCHHHHH-HHHHCC
Q ss_conf             9999998520212345564314854334234567777523455553011105664102454332100003689-999759
Q gi|254781172|r  187 VRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQ-KMRCLG  265 (731)
Q Consensus       187 iRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~~~~~e~l~-~L~~~G  265 (731)
                      |.||+|=+.=                =.|+=++.           ..+...|++|.+-..+....-++.+.+. +.+.+|
T Consensus       241 iQGElvGpgI----------------QgN~~~~~-----------~~~~~~f~~F~v~dI~~~~~~~~~~~~~~~~~~lg  293 (356)
T pfam09513       241 IQGELVGPGI----------------QGNYLNYG-----------KNGDAHFLVFRVFDIDSQRRATDLEWGDALCRQLG  293 (356)
T ss_pred             EEEEEECCCC----------------CCCCCCCC-----------CCCCCEEEEEEEEECCCCCCCCHHHHHHHHHHHCC
T ss_conf             9988867776----------------67753466-----------67884179999998247653584899999998679


Q ss_pred             CCCCCCEEEEECCCCHHHHHHHHHHHHCCC----CCCCCCEEEEECCHHC
Q ss_conf             966541488740321134556655310011----2343763777311000
Q gi|254781172|r  266 FPVNNGVRQANTFHGIVSYYNEMKSIRSTL----PYDIDGLVYKVDEFSL  311 (731)
Q Consensus       266 F~v~~~~~~~~~~~~~~~~~~~~~~~r~~l----~y~iDGiVikvn~~~~  311 (731)
                      .+++|..- .....++...+..+.. +.+.    .+.=-|||+|-.+-..
T Consensus       294 l~~VPvlg-y~~~~~~~~~~~~~~~-~~~~~~~~~~~REGiVirs~~~~~  341 (356)
T pfam09513       294 LKTVPVLG-YSGPFDIARVREDMGG-GATVSGSGKHIREGVVIKSVDTRF  341 (356)
T ss_pred             CCEEEECC-CCCCCHHHHHHHHHHC-CCCCCCCCCCEEEEEEEEECCCCC
T ss_conf             86024646-2246228789987534-454358887332149983255554


No 73 
>KOG1929 consensus
Probab=95.50  E-value=0.036  Score=35.99  Aligned_cols=79  Identities=22%  Similarity=0.309  Sum_probs=63.2

Q ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHHC
Q ss_conf             68821686699972588998789999999829849981116321799778888637989974991737999999998828
Q gi|254781172|r  643 VSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYN  722 (731)
Q Consensus       643 ~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~~  722 (731)
                      ...+|.|.+|++.+.=. ..|+-+-..+...|+.+......+...|+.....|||+.-|.+-+||+.+.+.+.......+
T Consensus       490 l~~~~e~~~~~~s~~~~-~~~e~ln~~~~~~gas~~~~f~r~~~~l~~~~~k~s~~~~~~kw~ip~vT~~wL~e~~rq~~  568 (811)
T KOG1929         490 LSQPFENLTISNSQSAE-AEREKLNNLANDLGASNVKTFTRKSTTLLTTSAKGSKYEIAGKWSIPIVTPDWLYECVRQNK  568 (811)
T ss_pred             CCCCCCCCEEEEEECHH-HHHHHHHHHHHHCCCCCCCEEEECCCEEECCCCCCCHHHHCCCCCCCCCCHHHHHHHCCCCC
T ss_conf             66666672688651518-88888767666506652330121441786344455543313666787557558875033567


No 74 
>PRK00254 ski2-like helicase; Provisional
Probab=95.36  E-value=0.024  Score=37.37  Aligned_cols=50  Identities=20%  Similarity=0.317  Sum_probs=38.8

Q ss_pred             CCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             01011116899999988-2998999997897761251177876138886789999999996
Q gi|254781172|r  557 LGIRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFY  616 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff  616 (731)
                      ..||+||...|+.|-++ |.|+..+.          +++..+|..|+|||+++|++|.+..
T Consensus       647 ~~I~gvgr~RAR~Ly~aGi~s~~~ia----------~A~p~~l~~i~g~g~~~a~~i~~~~  697 (717)
T PRK00254        647 MELPMIGRKRARALYNAGFRDLEDIM----------NAKPSELLAVEGIGAKIVEGIFKHL  697 (717)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCHHHHH----------CCCHHHEECCCCCCHHHHHHHHHHH
T ss_conf             64899898999999986999999996----------5999990302372789999999983


No 75 
>PRK05797 consensus
Probab=95.23  E-value=0.12  Score=31.95  Aligned_cols=46  Identities=15%  Similarity=0.237  Sum_probs=24.2

Q ss_pred             HHHHHHCCCCC------CCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf             98433177982------0878999999999999897720311-58999962003
Q gi|254781172|r   32 DDCYYQYSKPI------ILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI   78 (731)
Q Consensus        32 ~~~Yy~~~~p~------isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V   78 (731)
                      -++||... |.      -+-+.|-.+---++.++...|+++. ..|...||.|-
T Consensus        15 ~Ra~~a~~-~l~~~~G~pt~ai~Gf~~~l~~~~~~~~p~~~~v~fD~~~~tfR~   67 (869)
T PRK05797         15 NRAFYALP-PLTNSEGIHTNAIYGFTNMLLKMKEEIKPDYIVVAFDKKAPTFRH   67 (869)
T ss_pred             HHHHCCCC-CCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCH
T ss_conf             99980799-888998987054999999999999873998899998593996042


No 76 
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938   This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=95.04  E-value=0.025  Score=37.14  Aligned_cols=153  Identities=16%  Similarity=0.219  Sum_probs=85.9

Q ss_pred             CHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH-HHHHHHHHHCCHH
Q ss_conf             035410355556530576540454101101067775310001000134210014568999987522-3466677630101
Q gi|254781172|r  482 NIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRN-ISLERFIFSLGIR  560 (731)
Q Consensus       482 dI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK~-~~L~r~L~ALGI~  560 (731)
                      |+.|+||.|-+||-|+||.           ++...=-.+..+|....|.+|..|.+++++   +|. ..+..|..|.-.-
T Consensus         4 dLPGVGp~TA~KL~EaGy~-----------t~~~iA~A~~~EL~~~~gI~E~~A~kiI~A---AR~a~~~~~F~~a~~vl   69 (333)
T TIGR02236         4 DLPGVGPATAEKLREAGYD-----------TLEAIAVASPKELSEIAGIGEGTAAKIIQA---ARKAADLGGFETADDVL   69 (333)
T ss_pred             CCCCCCHHHHHHHHHHHHH-----------HHHHHHCCCHHHHHHHCCCCHHHHHHHHHH---HHHHHCCCCCHHHHHHH
T ss_conf             5789757688998861078-----------899984458579532037877789999999---99984676721489999


Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHC---CHHHHHHHHHHHHHCCCC--
Q ss_conf             111689999998829989999978977612511778761388867899999999966---979999999999733877--
Q gi|254781172|r  561 HVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ---NPRNICAVEALLKEVSPS--  635 (731)
Q Consensus       561 ~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~---~~~n~~~i~~L~~~~~~~--  635 (731)
                       -=++.-+.|+.-..++|.++                     | |-+=.++|-++|-   .=+ .++..+|  ++.++  
T Consensus        70 -~rR~~v~kitTgs~~LDeLL---------------------G-GGiETqaiTE~~GEFGSGK-TQ~~HqL--AVnVQlP  123 (333)
T TIGR02236        70 -ERRKSVGKITTGSKELDELL---------------------G-GGIETQAITEVFGEFGSGK-TQICHQL--AVNVQLP  123 (333)
T ss_pred             -HHHHCCCEEECCCHHHHHHC---------------------C-CCCCCEEEEEEEEEECCCH-HHHHHHH--HHHHCCC
T ss_conf             -98720750444863676560---------------------7-9600005888771007865-7876676--5532287


Q ss_pred             ---CCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHH--HCC
Q ss_conf             ---654322468821686699972588998789999999--829
Q gi|254781172|r  636 ---IGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVT--QLG  674 (731)
Q Consensus       636 ---~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie--~~G  674 (731)
                         +..++....+-|.|-++||==|=..||=.-++++.+  ..|
T Consensus       124 ~flfydeeave~GGL~gp~av~IDTEnTFRPERI~qmA~GL~~g  167 (333)
T TIGR02236       124 EFLFYDEEAVEKGGLEGPKAVYIDTENTFRPERIEQMAKGLARG  167 (333)
T ss_pred             CHHHCCCHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             11210110001477678768998559798625799999863111


No 77 
>PRK08076 consensus
Probab=94.93  E-value=0.1  Score=32.50  Aligned_cols=45  Identities=9%  Similarity=0.142  Sum_probs=23.7

Q ss_pred             HHHHHHCCCCCC-------CHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf             984331779820-------878999999999999897720311-58999962003
Q gi|254781172|r   32 DDCYYQYSKPII-------LDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI   78 (731)
Q Consensus        32 ~~~Yy~~~~p~i-------sD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V   78 (731)
                      -++||..  |.+       +.+.|-.+---++.+....|+.+. ..|...||.|-
T Consensus        15 ~Ra~~a~--p~l~~~~G~~t~ai~Gf~~~l~k~~~~~~p~~~~v~fD~~~~tfR~   67 (877)
T PRK08076         15 YRAFFAL--PLLNNDKGIHTNAVYGFTMMLMKILEEEKPTHMLVAFDAGKTTFRH   67 (877)
T ss_pred             HHHHCCC--CCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCH
T ss_conf             9998189--8787999987134999999999999864998899998694896322


No 78 
>TIGR01259 comE comEA protein; InterPro: IPR004787   The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable .   ComEA has been shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Human herpesvirus 4 (Epstein-Barr virus) ..
Probab=94.89  E-value=0.034  Score=36.19  Aligned_cols=57  Identities=16%  Similarity=0.256  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             987522346667763010111168999999882998999997897761251177876138886789999999996
Q gi|254781172|r  542 INKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFY  616 (731)
Q Consensus       542 Ie~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff  616 (731)
                      |+++....|..+      ||||...|+.|..|       ++     ..-.-.+.++|+++.|||+++-+.|.++.
T Consensus        66 lN~As~~EL~~l------~GiGP~kA~aIi~Y-------Re-----~nG~F~SvddL~kVsGIG~k~~eKLk~~~  122 (124)
T TIGR01259        66 LNKASLEELQAL------PGIGPAKAKAIIEY-------RE-----ENGAFKSVDDLTKVSGIGEKSLEKLKDYV  122 (124)
T ss_pred             HHHHHHHHHHHC------CCCCCHHHHHHHHH-------HH-----HCCCCCCHHHHHCCCCCCHHHHHHHHHCC
T ss_conf             406789998636------99981337999999-------98-----56997775550035788546687420003


No 79 
>pfam01367 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold.
Probab=94.84  E-value=0.052  Score=34.70  Aligned_cols=44  Identities=18%  Similarity=0.290  Sum_probs=32.6

Q ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHC
Q ss_conf             0101111689999998829989999978977612511778761388867899999999966
Q gi|254781172|r  557 LGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ  617 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~  617 (731)
                      =|+||||+++|..|.+.|++++++....+                 .+-.+..+.|.++..
T Consensus        21 PGv~GiG~KtA~~Ll~~~gsle~i~~n~d-----------------~i~~k~~~~l~~~~~   64 (100)
T pfam01367        21 PGVPGIGEKTAAKLLKEYGSLENIYENLD-----------------KLKGKLREKLLNGKE   64 (100)
T ss_pred             CCCCCCCCHHHHHHHHHCCCHHHHHHHHH-----------------HCCHHHHHHHHHHHH
T ss_conf             99999881689999998198999998198-----------------717999999997899


No 80 
>PRK09482 xni exonuclease IX; Provisional
Probab=94.82  E-value=0.042  Score=35.44  Aligned_cols=41  Identities=15%  Similarity=0.281  Sum_probs=29.9

Q ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             0101111689999998829989999978977612511778761388867899999999
Q gi|254781172|r  557 LGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE  614 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~  614 (731)
                      =||||||+++|..|.+.|++++++.+.++                 .++++..+.+.+
T Consensus       185 PGV~GIG~KtA~~LL~~fgsle~i~~n~d-----------------~i~~k~~~~l~~  225 (256)
T PRK09482        185 PGVAGIGPKSAAELLNQFRSLEGIYESLD-----------------ALPEKWRKKLEE  225 (256)
T ss_pred             CCCCCCCHHHHHHHHHHHCCHHHHHHHHH-----------------HCCHHHHHHHHH
T ss_conf             99998588899999998550999998377-----------------556899999996


No 81 
>PRK05929 consensus
Probab=94.80  E-value=0.042  Score=35.42  Aligned_cols=46  Identities=15%  Similarity=0.246  Sum_probs=24.6

Q ss_pred             HHHHHHHCCCCCC-------CHHHHHHHHHHHHHHHHHCCHHHC-CCC-CCCCCCCC
Q ss_conf             9984331779820-------878999999999999897720311-589-99962003
Q gi|254781172|r   31 HDDCYYQYSKPII-------LDSEYDALKRRCDAIAHAFPDLAR-SED-PNGPLNKI   78 (731)
Q Consensus        31 ~~~~Yy~~~~p~i-------sD~eYD~L~~~L~~le~~~p~~~~-~~~-p~spt~~V   78 (731)
                      .-++||..  |.+       +-+.|-.+---++.++...|..+. ..| |..||.|-
T Consensus        13 ~fRAy~Al--p~l~~s~G~pTnAv~GF~~mL~kll~~~~p~~~avaFD~~~~~tfRh   67 (870)
T PRK05929         13 VFRAYFAL--PEMKNPNGESTQAVFGFIRSLNKLIKEFSPEYMVAVFDGPNNKQSRQ   67 (870)
T ss_pred             HHHHHCCC--CCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHH
T ss_conf             99998079--98879999870509999999999998659988999987979997164


No 82 
>PRK07456 consensus
Probab=94.71  E-value=0.1  Score=32.43  Aligned_cols=83  Identities=16%  Similarity=0.185  Sum_probs=39.6

Q ss_pred             HHHHHHHCCC----CC------CCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCCCCCC---------CCC----C
Q ss_conf             9984331779----82------0878999999999999897720311-589999620036432---------357----7
Q gi|254781172|r   31 HDDCYYQYSK----PI------ILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKIGGEM---------NLS----L   86 (731)
Q Consensus        31 ~~~~Yy~~~~----p~------isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~Vg~~~---------~~~----~   86 (731)
                      .-++||....    |.      -+.+.|-.+---++.++...|+++. ..|.-.||.|----+         ..+    +
T Consensus        19 ~fRay~A~~~~~~~pl~~~~G~~tnAv~GF~~~l~kli~~~~P~~iavaFD~~~~TFR~e~y~~YKA~R~~~PedL~~Qi   98 (975)
T PRK07456         19 AFRSFYAFSKGGEGGLRTKTGIPTSVTYGFLKSLLDNCKTQKPQGVAIAFDTAEPTFRHEADPNYKANRDVAPDDFFQDL   98 (975)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             99998077867888864899987214999999999999863998899998288995254231364079999988899999


Q ss_pred             ---CE-EE--CCCCCCCHHHCCCHHHHHHHHHHH
Q ss_conf             ---50-45--166425702159999999999999
Q gi|254781172|r   87 ---FK-VT--HSIPTLSLEKIWNIEDLRKFITRI  114 (731)
Q Consensus        87 ---~k-v~--H~~pMlSL~k~~~~~el~~w~~~~  114 (731)
                         .+ ++  .-+|.++++. |--|++..=+.+.
T Consensus        99 p~i~e~l~~algIp~~e~~G-yEADDiIaTla~~  131 (975)
T PRK07456         99 EQLQEILEEALNLPICTAPG-YEADDVLGTLANR  131 (975)
T ss_pred             HHHHHHHHHHCCCCEEEECC-CCHHHHHHHHHHH
T ss_conf             99999999836998741788-0199999999999


No 83 
>PRK07300 consensus
Probab=94.65  E-value=0.06  Score=34.23  Aligned_cols=84  Identities=8%  Similarity=0.057  Sum_probs=40.8

Q ss_pred             HHHHHHHCCC--CCC-------CHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCCCCCCC-------------CCCC
Q ss_conf             9984331779--820-------878999999999999897720311-5899996200364323-------------5775
Q gi|254781172|r   31 HDDCYYQYSK--PII-------LDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKIGGEMN-------------LSLF   87 (731)
Q Consensus        31 ~~~~Yy~~~~--p~i-------sD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~Vg~~~~-------------~~~~   87 (731)
                      .-++||..-.  |.+       +-+.|-.+---++.++...|+.+. ..|...||.|----+.             ..+.
T Consensus        16 ifRAfyAl~~~~~~l~ts~G~pTnAi~GF~~mL~kli~~~~P~~iavaFD~~~~TFR~~~~~~YKa~R~~~P~~l~~Q~~   95 (880)
T PRK07300         16 AFRAFFALYNQIDRFKNHSGLHTNAIYGFHLMLDHMMKRVQPTHVLVAFDAGKTTFRTEMYADYKAGRAKTPDEFREQFP   95 (880)
T ss_pred             HHHHHCCCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHCCCCCCCCHHHHHHHH
T ss_conf             99987178877788729999882359999999999998649988999996959960142315752799999889999999


Q ss_pred             EE-----ECCCCCCCHHHCCCHHHHHHHHHHHH
Q ss_conf             04-----51664257021599999999999999
Q gi|254781172|r   88 KV-----THSIPTLSLEKIWNIEDLRKFITRIY  115 (731)
Q Consensus        88 kv-----~H~~pMlSL~k~~~~~el~~w~~~~~  115 (731)
                      -+     .+-+|+++.+. |--|++..=+.+..
T Consensus        96 ~i~~~~~~~~i~~~~~~g-~EADDvi~tlak~a  127 (880)
T PRK07300         96 YIREMLTALGIAYYELEH-YEADDIIGTLDKMA  127 (880)
T ss_pred             HHHHHHHHCCCCEECCCC-CCHHHHHHHHHHHH
T ss_conf             999999987998825289-14999999999999


No 84 
>PRK05755 DNA polymerase I; Provisional
Probab=94.63  E-value=0.065  Score=33.98  Aligned_cols=47  Identities=15%  Similarity=0.176  Sum_probs=25.7

Q ss_pred             HHHHHHHCCCC------CCCHHHHHHHHHHHHHHHHHCCHHH-CCCCCCCCCCCC
Q ss_conf             99843317798------2087899999999999989772031-158999962003
Q gi|254781172|r   31 HDDCYYQYSKP------IILDSEYDALKRRCDAIAHAFPDLA-RSEDPNGPLNKI   78 (731)
Q Consensus        31 ~~~~Yy~~~~p------~isD~eYD~L~~~L~~le~~~p~~~-~~~~p~spt~~V   78 (731)
                      .-++||.. .|      .-+.+.|-.+---++.++...|+.+ -..|...||.|-
T Consensus        16 ~~Ra~~a~-~~l~~~~G~~tnai~Gf~~~l~~~~~~~~p~~~~v~fD~~~~tfR~   69 (889)
T PRK05755         16 AFRAFYAL-PPLTNSDGLPTGAVYGFLNMLLKLLKDEKPTHIAVAFDAKGKTFRH   69 (889)
T ss_pred             HHHHHCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCC
T ss_conf             99998078-9887999987252999999999999862998899996398996352


No 85 
>PRK00254 ski2-like helicase; Provisional
Probab=94.57  E-value=0.02  Score=37.85  Aligned_cols=66  Identities=18%  Similarity=0.350  Sum_probs=37.4

Q ss_pred             CCCCCHHHHHCCCCCCHHHHHHHHHH-HCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHH
Q ss_conf             25117787613888678999999999-66979999999999733877654322468821686699972588998789999
Q gi|254781172|r  590 HNNDDWLSLIRVPLVGDIIAQAIVEF-YQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQE  668 (731)
Q Consensus       590 ~~~~~~e~L~~I~GiG~~~A~si~~f-f~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~  668 (731)
                      .-..+..+|++|+|||...|..+.+. |..+.      .+..+           ...    .-.-+.|    +..+-+++
T Consensus       638 Gv~~ELl~L~~I~gvgr~RAR~Ly~aGi~s~~------~ia~A-----------~p~----~l~~i~g----~g~~~a~~  692 (717)
T PRK00254        638 GIREELIPLMELPMIGRKRARALYNAGFRDLE------DIMNA-----------KPS----ELLAVEG----IGAKIVEG  692 (717)
T ss_pred             CCCHHHHHHCCCCCCCHHHHHHHHHCCCCCHH------HHHCC-----------CHH----HEECCCC----CCHHHHHH
T ss_conf             99765683564899898999999986999999------99659-----------999----9030237----27899999


Q ss_pred             HHHHCCCEEEEE
Q ss_conf             999829849981
Q gi|254781172|r  669 YVTQLGAVVSAI  680 (731)
Q Consensus       669 ~ie~~Ggkv~sS  680 (731)
                      ++++.|-+|.=+
T Consensus       693 i~~~~~~~~~~~  704 (717)
T PRK00254        693 IFKHLGKEVKIN  704 (717)
T ss_pred             HHHHHCCEEEHH
T ss_conf             999838644300


No 86 
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=94.56  E-value=0.035  Score=36.01  Aligned_cols=86  Identities=20%  Similarity=0.351  Sum_probs=52.1

Q ss_pred             CCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHH---HHHHHHHHHHHHHH
Q ss_conf             231035410355556530576540454101101067775310001000134210014568999---98752234666776
Q gi|254781172|r  479 DAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDS---INKRRNISLERFIF  555 (731)
Q Consensus       479 ~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~s---Ie~sK~~~L~r~L~  555 (731)
                      +-+.++|+|++.++.|+++      |..--.. .|....     -=+.+++.|++.|..|.+.   |++-.+.+...+  
T Consensus       480 ~L~~l~gfgeKsa~nLl~a------Ie~SK~~-~l~r~L-----~ALGI~~VG~~~Ak~La~~f~sl~~l~~as~e~L--  545 (668)
T PRK07956        480 DLLQLEGFGEKSAQNLLDA------IEKSKET-PLARFL-----YALGIRHVGEKAAKALARHFGSLEALEAASEEEL--  545 (668)
T ss_pred             HHHCCCCHHHHHHHHHHHH------HHHHCCC-CHHHHH-----HHCCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHH--
T ss_conf             5402123556699999999------9985477-588899-----8627864129999999999668999970899998--


Q ss_pred             HCCHHHHHHHHHHHHHHHCCCHHH
Q ss_conf             301011116899999988299899
Q gi|254781172|r  556 SLGIRHVGAEIARSLAKYYLSYQN  579 (731)
Q Consensus       556 ALGI~~vG~~~Ak~La~~f~si~~  579 (731)
                       +.|++||+.+|..|...|.+-.+
T Consensus       546 -~~I~giG~~~A~si~~ff~~~~n  568 (668)
T PRK07956        546 -AAVEGIGEEVAQSIVEFFAVEHN  568 (668)
T ss_pred             -HCCCCCCHHHHHHHHHHHCCHHH
T ss_conf             -57688449999999999709768


No 87 
>PRK06887 consensus
Probab=94.52  E-value=0.17  Score=30.76  Aligned_cols=47  Identities=15%  Similarity=0.171  Sum_probs=24.1

Q ss_pred             HHHHHHHCCCCC------CCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf             998433177982------0878999999999999897720311-58999962003
Q gi|254781172|r   31 HDDCYYQYSKPI------ILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI   78 (731)
Q Consensus        31 ~~~~Yy~~~~p~------isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V   78 (731)
                      .-++||.. .|.      =+.+.|-.+---++.++..-|+.+. ..|...||.|-
T Consensus        18 ~fRAfyAl-~~l~ts~G~pTnAi~GF~~ml~kli~~~kP~~iavaFD~~~~TFR~   71 (954)
T PRK06887         18 LYRAFHAF-PPLTNSAGEPTGAMYGVLNMLKSLISQVQPSHIAVVFDAKGKTFRD   71 (954)
T ss_pred             HHHHHCCC-CCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCH
T ss_conf             99998078-8675998987335999999999999871998899998088996033


No 88 
>PRK07556 consensus
Probab=94.37  E-value=0.078  Score=33.35  Aligned_cols=47  Identities=11%  Similarity=-0.032  Sum_probs=22.0

Q ss_pred             HHHHHHHCCCCCC-------CHHHHHHHHHHHHHHHHHC----CHHH-CCCCCCCCCCCC
Q ss_conf             9984331779820-------8789999999999998977----2031-158999962003
Q gi|254781172|r   31 HDDCYYQYSKPII-------LDSEYDALKRRCDAIAHAF----PDLA-RSEDPNGPLNKI   78 (731)
Q Consensus        31 ~~~~Yy~~~~p~i-------sD~eYD~L~~~L~~le~~~----p~~~-~~~~p~spt~~V   78 (731)
                      .-++||.. .|+.       +-+.|-.+---++.++...    |.++ -..|...||.|-
T Consensus        19 ~fRAyyAl-p~l~~~s~G~pTnAvyGF~~mL~kll~~~~~~~~p~~iavaFD~~~~TFRh   77 (977)
T PRK07556         19 IFRAYHAL-PPLTRKSDGLPVGAVSGFCNMLWKLLRDARNTDVPTHLAVIFDYSSKTFRN   77 (977)
T ss_pred             HHHHHCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCH
T ss_conf             99998179-976779999471369999999999998623567998899998088996012


No 89 
>PRK07625 consensus
Probab=94.24  E-value=0.076  Score=33.46  Aligned_cols=46  Identities=11%  Similarity=0.052  Sum_probs=25.7

Q ss_pred             HHHHHHHCCCCCC-------CHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf             9984331779820-------878999999999999897720311-58999962003
Q gi|254781172|r   31 HDDCYYQYSKPII-------LDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI   78 (731)
Q Consensus        31 ~~~~Yy~~~~p~i-------sD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V   78 (731)
                      .-++||..  |.+       +.+.|-.+---++.++..-|+++. ..|...||.|-
T Consensus        17 ifRAfyAl--p~l~ts~G~pTnAi~GF~~mL~kli~e~~P~~iavaFD~~~~TFR~   70 (922)
T PRK07625         17 LYRAYHAM--PDLRGPGGEPTGALYGIVNMLRRMRKDVSAEYSACVFDAKGKTFRD   70 (922)
T ss_pred             HHHHHHCC--CCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCH
T ss_conf             99998278--8887998987117999999999999865998899997198996340


No 90 
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=94.23  E-value=0.51  Score=27.07  Aligned_cols=53  Identities=17%  Similarity=0.110  Sum_probs=30.4

Q ss_pred             HHHCCHHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             763010111168999999882--99899999789776125117787613888678999999999
Q gi|254781172|r  554 IFSLGIRHVGAEIARSLAKYY--LSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEF  615 (731)
Q Consensus       554 L~ALGI~~vG~~~Ak~La~~f--~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~f  615 (731)
                      +.=|.+|++|.+.-+.|-+.+  .+++.+.++..+         -.+..+.|||.+.+..|..+
T Consensus        93 ~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~---------~~~~~l~GfG~kse~~il~~  147 (326)
T COG1796          93 EPLLKVPGLGPKKIVSLYKELGIKDLEELQEALEN---------GKIRGLRGFGKKSEAKILEN  147 (326)
T ss_pred             HHHHHCCCCCCHHHHHHHHHHCCCCHHHHHHHHHH---------CCCCCCCCCCCHHHHHHHHH
T ss_conf             87860779892889999999786649999999984---------77032678560219999999


No 91 
>PRK08835 consensus
Probab=94.18  E-value=0.11  Score=32.27  Aligned_cols=83  Identities=11%  Similarity=0.089  Sum_probs=37.5

Q ss_pred             HHHHHHHCCCC-----CCCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCCCCCCC-------------CCCCEE--
Q ss_conf             99843317798-----20878999999999999897720311-5899996200364323-------------577504--
Q gi|254781172|r   31 HDDCYYQYSKP-----IILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKIGGEMN-------------LSLFKV--   89 (731)
Q Consensus        31 ~~~~Yy~~~~p-----~isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~Vg~~~~-------------~~~~kv--   89 (731)
                      .-++||....-     .-+.+.|-.+---++.++...|+++. ..|...||.|----+.             ..|.-+  
T Consensus        18 ifRAfyA~p~l~ts~G~pTnAv~GF~~mL~kli~~~~P~~iavaFD~~~~TfR~~~y~~YKa~R~~~pedL~~Q~p~i~e   97 (931)
T PRK08835         18 LYRAFHAYPGTMSNGEIPTNAVYGVVNMLRSMMRQFASDRIAVIFDAKGKTFRDDMYPEYKANRPPMPDDLRCQIEPLHQ   97 (931)
T ss_pred             HHHHHHCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             99998279987899998830699999999999986499879999749899623434057517999998789999999999


Q ss_pred             ---ECCCCCCCHHHCCCHHHHHHHHHHH
Q ss_conf             ---5166425702159999999999999
Q gi|254781172|r   90 ---THSIPTLSLEKIWNIEDLRKFITRI  114 (731)
Q Consensus        90 ---~H~~pMlSL~k~~~~~el~~w~~~~  114 (731)
                         .+-+|.++++. |--|++..=+.+.
T Consensus        98 ~l~a~gIp~~~~~G-yEADDiIgTla~~  124 (931)
T PRK08835         98 VIKAMGLPLIAIEG-VEADDVIGTLAYQ  124 (931)
T ss_pred             HHHHCCCCEEEECC-CCHHHHHHHHHHH
T ss_conf             99987998844589-1499999999999


No 92 
>PRK08786 consensus
Probab=94.15  E-value=0.066  Score=33.93  Aligned_cols=46  Identities=11%  Similarity=0.114  Sum_probs=21.8

Q ss_pred             HHHHHHHCCCCCC------CHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf             9984331779820------878999999999999897720311-58999962003
Q gi|254781172|r   31 HDDCYYQYSKPII------LDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI   78 (731)
Q Consensus        31 ~~~~Yy~~~~p~i------sD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V   78 (731)
                      .-++||.. .|..      +-+.|-.+- -|..+-...|.++. ..|...||.|-
T Consensus        13 ifRAy~A~-~~l~~~~G~pTnAv~GF~~-mL~kl~~e~p~~~~v~fD~~~~tfR~   65 (927)
T PRK08786         13 LYRAFHAL-PPLTNAQGEPTGALFGVVN-MLRATLKERPAYVAFVVDAPGKTFRD   65 (927)
T ss_pred             HHHHHCCC-CCCCCCCCCEECHHHHHHH-HHHHHHHHCCCEEEEEEECCCCCCCC
T ss_conf             99998079-9887999988207999999-99999987889899999695997451


No 93 
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345   These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. .
Probab=94.10  E-value=0.16  Score=30.98  Aligned_cols=67  Identities=22%  Similarity=0.357  Sum_probs=38.5

Q ss_pred             CHHHHHHHHHCCCCCC------CCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCC
Q ss_conf             0036899997599665------4148874032113455665531001123437637773110001115876568663
Q gi|254781172|r  254 QYEMLQKMRCLGFPVN------NGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRW  324 (731)
Q Consensus       254 ~~e~l~~L~~~GF~v~------~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prw  324 (731)
                      ....|..|..+||+..      .++...+-..+-++..+   +-=-.|-+||-||=++--| .+...||--...||-
T Consensus       152 ~~~~l~~L~~lG~~~~l~~~~~k~y~eadP~~dtLd~v~---~~Py~L~~d~~GiGF~~AD-~lA~~lG~~~~dP~R  224 (769)
T TIGR01448       152 ERKLLLKLQQLGIGIKLALRIYKFYREADPQADTLDVVE---KDPYLLAEDVKGIGFKTAD-QLAEELGIALNDPRR  224 (769)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCHHHHHH---CCHHHHHHHHCCCCHHHHH-HHHHHCCCCCCCCHH
T ss_conf             999999998538767899999998403587211688862---1720136751374056899-999971862358447


No 94 
>PRK08434 consensus
Probab=93.93  E-value=0.07  Score=33.72  Aligned_cols=83  Identities=14%  Similarity=0.050  Sum_probs=42.9

Q ss_pred             HHHHHHHCCCCC------CCHHHHHHHHHHHHHHHHHCCHHHCC-CCCCCCCCCCCCCCC---------CC----CCEE-
Q ss_conf             998433177982------08789999999999998977203115-899996200364323---------57----7504-
Q gi|254781172|r   31 HDDCYYQYSKPI------ILDSEYDALKRRCDAIAHAFPDLARS-EDPNGPLNKIGGEMN---------LS----LFKV-   89 (731)
Q Consensus        31 ~~~~Yy~~~~p~------isD~eYD~L~~~L~~le~~~p~~~~~-~~p~spt~~Vg~~~~---------~~----~~kv-   89 (731)
                      .-++||.. .|.      -+.+.|-.+---++.++...|+++.. .|...||.|----+.         .+    +.-+ 
T Consensus        13 ~fRAy~A~-~~l~t~~G~pTnAv~GF~~mL~kli~~~~P~~iavaFD~~~~TFRhe~y~~YKAnR~~~PedL~~Qip~i~   91 (887)
T PRK08434         13 FFRSYYAL-PPLKNSQGFPTGLLSGFANFIYSLKNEFKSDYIVFALDSKGKTFRSEIDPNYKANRPPPPEELLEQLPIAI   91 (887)
T ss_pred             HHHHHCCC-CCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf             99997079-99879999880359999999999998659988999984959962210205752899999989999999999


Q ss_pred             ----ECCCCCCCHHHCCCHHHHHHHHHHHH
Q ss_conf             ----51664257021599999999999999
Q gi|254781172|r   90 ----THSIPTLSLEKIWNIEDLRKFITRIY  115 (731)
Q Consensus        90 ----~H~~pMlSL~k~~~~~el~~w~~~~~  115 (731)
                          ..-+|.++++. |--|++..=+.+..
T Consensus        92 e~l~algIp~~e~~G-yEADDiIgTla~~a  120 (887)
T PRK08434         92 EWIEKMGFKSLSQEG-YEADDIIASFVKFA  120 (887)
T ss_pred             HHHHHCCCCEECCCC-CCHHHHHHHHHHHH
T ss_conf             999987998845589-24999999999999


No 95 
>smart00475 53EXOc 5'-3' exonuclease.
Probab=93.54  E-value=0.11  Score=32.12  Aligned_cols=42  Identities=17%  Similarity=0.353  Sum_probs=30.7

Q ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             01011116899999988299899999789776125117787613888678999999999
Q gi|254781172|r  557 LGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEF  615 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~f  615 (731)
                      =||||||+++|..|.+.|++++++++.++.                 +.++..+.+.+.
T Consensus       189 pGV~GIG~KtA~kLL~~ygsle~i~~~~d~-----------------i~~k~~~~l~~~  230 (259)
T smart00475      189 PGVPGIGEKTAAKLLKEFGSLENILENLDK-----------------LKKKLREKLLAH  230 (259)
T ss_pred             CCCCCCCHHHHHHHHHHCCCHHHHHHHHHH-----------------CCHHHHHHHHHH
T ss_conf             999984789999999983999999983985-----------------488999999977


No 96 
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=93.54  E-value=0.17  Score=30.70  Aligned_cols=40  Identities=23%  Similarity=0.475  Sum_probs=27.6

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             9999882998999997897761251177876138886789999999996
Q gi|254781172|r  568 RSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFY  616 (731)
Q Consensus       568 k~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff  616 (731)
                      +.|+.+|.+++.+.+..         ..++|..|+|||+.+|++|.-|-
T Consensus        96 k~l~~~~~~~~~~~~~~---------~R~~LL~iKGIG~ETaDsILlYa  135 (215)
T COG2231          96 KNLAKFFINLESFKSEV---------LREELLSIKGIGKETADSILLYA  135 (215)
T ss_pred             HHHHHHHHHHHCCCHHH---------HHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             99999864231115188---------99998726886622399999998


No 97 
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938   This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=93.52  E-value=0.039  Score=35.70  Aligned_cols=46  Identities=22%  Similarity=0.264  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             011116899999988-29989999978977612511778761388867899999999
Q gi|254781172|r  559 IRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE  614 (731)
Q Consensus       559 I~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~  614 (731)
                      +||||..||.+|-.+ |.+++.+.          .++..+|.++.|||+.+|..|++
T Consensus         5 LPGVGp~TA~KL~EaGy~t~~~iA----------~A~~~EL~~~~gI~E~~A~kiI~   51 (333)
T TIGR02236         5 LPGVGPATAEKLREAGYDTLEAIA----------VASPKELSEIAGIGEGTAAKIIQ   51 (333)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHH----------CCCHHHHHHHCCCCHHHHHHHHH
T ss_conf             789757688998861078899984----------45857953203787778999999


No 98 
>PRK02362 ski2-like helicase; Provisional
Probab=93.44  E-value=0.29  Score=28.97  Aligned_cols=67  Identities=16%  Similarity=0.123  Sum_probs=30.3

Q ss_pred             HHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCC-----CCCCCEEECCCCCCCHHHCCCHHHHHH
Q ss_conf             331779820878999999999999897720311589999620036432-----357750451664257021599999999
Q gi|254781172|r   35 YYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEM-----NLSLFKVTHSIPTLSLEKIWNIEDLRK  109 (731)
Q Consensus        35 Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~-----~~~~~kv~H~~pMlSL~k~~~~~el~~  109 (731)
                      |-..|-..+-+.+.+++..-+  ++-++- ++.  .|+|-=..+-++.     .....|+--..|+-||.+    |-+..
T Consensus        16 ~~~~gI~~Lyp~Q~eal~~gl--~~g~Nl-vvs--aPTgsGKTlvAElail~~l~~g~k~vYi~P~kALa~----EK~~~   86 (736)
T PRK02362         16 YEGSGIEELYPPQAEAVEAGL--LEGKNL-LAA--IPTASGKTLLAELAMLKAIAEGGKALYIVPLRALAS----EKFEE   86 (736)
T ss_pred             HHHCCCCCCCHHHHHHHHHHH--CCCCCE-EEE--CCCCCCHHHHHHHHHHHHHHHCCEEEEECCHHHHHH----HHHHH
T ss_conf             997699757899999998643--569818-997--999985899999999999983997999858799999----99999


Q ss_pred             H
Q ss_conf             9
Q gi|254781172|r  110 F  110 (731)
Q Consensus       110 w  110 (731)
                      |
T Consensus        87 ~   87 (736)
T PRK02362         87 F   87 (736)
T ss_pred             H
T ss_conf             9


No 99 
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=93.41  E-value=0.2  Score=30.28  Aligned_cols=29  Identities=24%  Similarity=0.412  Sum_probs=24.3

Q ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             01011116899999988299899999789
Q gi|254781172|r  557 LGIRHVGAEIARSLAKYYLSYQNFAQEIN  585 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~  585 (731)
                      =||||||.++|..|.+.|++++++.+..+
T Consensus       186 pGV~GiG~KtA~kLl~~~gsle~i~~~~~  214 (240)
T cd00008         186 PGVPGIGEKTAAKLLKEYGSLEGILENLD  214 (240)
T ss_pred             CCCCCCCHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             99998578999999998099999998298


No 100
>PRK01172 ski2-like helicase; Provisional
Probab=93.39  E-value=0.056  Score=34.49  Aligned_cols=30  Identities=20%  Similarity=0.453  Sum_probs=19.4

Q ss_pred             CCCCCHHHHHCCCCCCHHHHHHHHHH-HCCH
Q ss_conf             25117787613888678999999999-6697
Q gi|254781172|r  590 HNNDDWLSLIRVPLVGDIIAQAIVEF-YQNP  619 (731)
Q Consensus       590 ~~~~~~e~L~~I~GiG~~~A~si~~f-f~~~  619 (731)
                      .-..+..+|++|+|||.+.|..+.+. |..+
T Consensus       606 Gv~~eLl~L~~I~gigr~RAR~Ly~aG~~s~  636 (674)
T PRK01172        606 GIREDLIDLVLIPKVGRVRARRLYDAGFKTV  636 (674)
T ss_pred             CCHHHHHHHCCCCCCCHHHHHHHHHCCCCCH
T ss_conf             9868889771889999899999998699999


No 101
>KOG2534 consensus
Probab=93.10  E-value=0.77  Score=25.68  Aligned_cols=62  Identities=15%  Similarity=0.187  Sum_probs=35.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH---------HHHHCCHHHHHHHHHHHHHH-HCCCHHHHHH
Q ss_conf             00100013421001456899998752234666---------77630101111689999998-8299899999
Q gi|254781172|r  521 TTKIENILGFGDVSVTNLYDSINKRRNISLER---------FIFSLGIRHVGAEIARSLAK-YYLSYQNFAQ  582 (731)
Q Consensus       521 ~~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r---------~L~ALGI~~vG~~~Ak~La~-~f~si~~l~~  582 (731)
                      .+++.+|+|+|+|.|.++..=++.-.-..+.+         +.+=-.|-|||.++|+.--+ .|.+++.+++
T Consensus        55 ~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~~GfrTled~Rk  126 (353)
T KOG2534          55 GEEAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYREGFRTLEDVRK  126 (353)
T ss_pred             HHHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             788557999777799999999970873667877545067899999987255778999999951467999875


No 102
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298   DNA carries the biological information that instructs cells how to exist in an ordered fashion. Accurate replication is thus one of the most important events in the cell life cycle. This function is mediated by DNA-directed DNA polymerases, which add nucleotide triphosphate (dNTP) residues to the 5'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. DNA-dependent DNA polymerases have been grouped into families, denoted A, B and X, on the basis of sequence similarities , . Members of family A, which includes bacterial and bacteriophage polymerases, share significant similarity to Escherichia coli polymerase I; hence family A is also known as the pol I family. The bacterial polymerases also contain an exonuclease activity, which is coded for in the N-terminal portion. Three motifs, A, B and C , are seen to be conserved across all DNA polymerases, with motifs A and C also seen in RNA polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (E. coli) structure. Motif A contains a strictly-conserved aspartate at the junction of a beta-strand and an alpha-helix; motif B contains an alpha-helix with positive charges; and motif C has a doublet of negative charges, located in a beta-turn-beta secondary structure .; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication.
Probab=92.92  E-value=0.076  Score=33.43  Aligned_cols=46  Identities=13%  Similarity=0.188  Sum_probs=23.9

Q ss_pred             HHHHHCCC---CC------CCHHHHHHHHHHHHHHHHHCC-HHH-CCCCCCCCCCCC
Q ss_conf             84331779---82------087899999999999989772-031-158999962003
Q gi|254781172|r   33 DCYYQYSK---PI------ILDSEYDALKRRCDAIAHAFP-DLA-RSEDPNGPLNKI   78 (731)
Q Consensus        33 ~~Yy~~~~---p~------isD~eYD~L~~~L~~le~~~p-~~~-~~~~p~spt~~V   78 (731)
                      ++||....   |+      -+++.|=...-=+..|++.-| .++ -..|...||.|-
T Consensus        12 RayfAl~~~~~~L~~~~G~~t~A~yGF~~~L~~~l~~~~Pm~~~~~aFD~~~~TFR~   68 (1005)
T TIGR00593        12 RAYFALPNNKKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPMTYVAVAFDSGTKTFRH   68 (1005)
T ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCHHH
T ss_conf             998862211466666788711677888999999997418951699887688885166


No 103
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=92.63  E-value=0.13  Score=31.68  Aligned_cols=109  Identities=15%  Similarity=0.164  Sum_probs=61.3

Q ss_pred             HHCCHHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHC
Q ss_conf             63010111168999999882--9989999978977612511778761388867899999999966979999999999733
Q gi|254781172|r  555 FSLGIRHVGAEIARSLAKYY--LSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEV  632 (731)
Q Consensus       555 ~ALGI~~vG~~~Ak~La~~f--~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~  632 (731)
                      -||.|.|+|+++...|....  .++..++.          .+.++|.+++|||++.|+++++-+...++ ..+.+++..+
T Consensus       427 ~amdI~GLGek~i~~L~~~gli~~~~Dly~----------L~~~~L~~l~g~geKsa~nLl~aIe~SK~-~~l~r~l~aL  495 (563)
T PRK08097        427 QGLGLDGIGEGTWRALHQTGRFEHLFSWLA----------LTPEQLANTPGIGKARAAQLWHQFNLARQ-QPFTRWLKAL  495 (563)
T ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCHHHHHH----------CCHHHHHCCCCHHHHHHHHHHHHHHHHCC-CCHHHHHHHC
T ss_conf             415856769999999997588899799750----------89999855898578999999999999728-9999999986


Q ss_pred             CCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEE
Q ss_conf             8776543224688216866999725889987899999998298499811
Q gi|254781172|r  633 SPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAIL  681 (731)
Q Consensus       633 ~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSV  681 (731)
                      ++...-..  ....+.+ .|   .+|...+.+++.+ |+..|-+++.||
T Consensus       496 GI~~vG~~--~a~~l~~-~~---~~L~~as~e~l~~-i~gIG~~~A~si  537 (563)
T PRK08097        496 GIPLTQAA--LNASLDR-SW---QQLLSRTEQQWQQ-LPGIGEGRARQL  537 (563)
T ss_pred             CCCCHHHH--HHHHHHC-CH---HHHHCCCHHHHHC-CCCCCHHHHHHH
T ss_conf             99508999--9999861-99---9997399989955-798489999999


No 104
>KOG3226 consensus
Probab=92.48  E-value=0.35  Score=28.32  Aligned_cols=67  Identities=19%  Similarity=0.213  Sum_probs=32.6

Q ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHH
Q ss_conf             21686699972588998789999999829849981116321799778888637989974991737999
Q gi|254781172|r  646 EIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQ  713 (731)
Q Consensus       646 ~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~e  713 (731)
                      .|.|-.||++| |++-.|.++-.+.-.+|+|-.-..+...++||+.-.-.-|+..-+-+|=.|++.+.
T Consensus       317 lL~GVV~VlSG-fqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTPKy~QV~g~Gg~IV~keW  383 (508)
T KOG3226         317 LLEGVVFVLSG-FQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTPKYRQVEGNGGTIVSKEW  383 (508)
T ss_pred             HHHCEEEEEEC-CCCCHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCHHHCCCCCCEEEEHHH
T ss_conf             65114899725-66810777888887616602677678963689723899515320157854864899


No 105
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=92.38  E-value=0.33  Score=28.56  Aligned_cols=23  Identities=22%  Similarity=0.128  Sum_probs=18.9

Q ss_pred             CCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             17787613888678999999999
Q gi|254781172|r  593 DDWLSLIRVPLVGDIIAQAIVEF  615 (731)
Q Consensus       593 ~~~e~L~~I~GiG~~~A~si~~f  615 (731)
                      ...++|..++|||++||++|.-|
T Consensus       118 ~~Re~LL~lkGIG~ETADsILlY  140 (218)
T PRK13913        118 VTREWLLDQKGIGKESADAILCY  140 (218)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             58999974898663339999999


No 106
>pfam00763 THF_DHG_CYH Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain.
Probab=92.28  E-value=0.5  Score=27.13  Aligned_cols=61  Identities=31%  Similarity=0.533  Sum_probs=33.0

Q ss_pred             HHHHHHHHHCCCEEEEEEECCEEEEEECCCCCC------HHHHHHHCCCEE--------ECHHHHHHHHHHHCCCCCC
Q ss_conf             899999998298499811163217997788886------379899749917--------3799999999882865687
Q gi|254781172|r  664 HKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGS------KLEKAQQLGVKI--------MNEEQFLFLLQQYNTTLRI  727 (731)
Q Consensus       664 ~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gS------Kl~KA~~LgI~I--------i~e~ef~~ll~~~~~~~~~  727 (731)
                      .++++.++.+..+   .+.-+...+.+|++++|      |.+.|+++||..        ++++++++.|.+.|.+...
T Consensus        14 ~~l~~~i~~l~~~---g~~P~Laii~vg~~~~s~~Yv~~k~k~~~~~Gi~~~~~~l~~~~s~~~l~~~I~~lN~D~~V   88 (117)
T pfam00763        14 EELKEEVAKLKEK---GVTPKLAVILVGDDPASQVYVRSKRKAAEELGIESELIRLPEDITEEELLALIEKLNADPSV   88 (117)
T ss_pred             HHHHHHHHHHHHC---CCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCC
T ss_conf             9999999999857---99971899984897567999999999999728716998777633499999999999678878


No 107
>KOG0966 consensus
Probab=92.23  E-value=0.98  Score=24.87  Aligned_cols=198  Identities=19%  Similarity=0.228  Sum_probs=105.0

Q ss_pred             CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHH---HHCCCCCCCCCCCC---CEEEEEEEEEEECHH
Q ss_conf             761199994158189999985998998886598655666999775---31024322335445---504899999985202
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIR---AIPTIPRVLSLNIP---EIIEVRGEVYISKND  197 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~---~i~~iP~~l~~~~~---~~ieiRGEv~m~~~~  197 (731)
                      ....|.+|-|+||=-+-|+|..|.. +=.||    -|-|-|.+.-   ....+-.+|-...+   +....-||.+.=...
T Consensus       248 ~~~~f~lEtK~DGERiQlHk~g~~~-~yfSR----Ng~dyT~~yg~s~~~g~lt~~i~~~f~~~v~~cILDGEMm~wD~~  322 (881)
T KOG0966         248 GGQDFYLETKFDGERIQLHKDGGEY-KYFSR----NGNDYTYEYGASYAHGTLTQRIHGAFNKEVESCILDGEMMTWDTK  322 (881)
T ss_pred             CCCCEEEEEECCCCEEEEEECCCEE-EEEEC----CCCCHHHHCCCCCCCCCCCHHHHHHHHHCCHHEEECCEEEEEECC
T ss_conf             5993699862167057998438778-99832----775315440765111420188876413102401734647886053


Q ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCC--CCCCCHHHHHHHHHCCCCCCCCE---
Q ss_conf             1234556431485433423456777752345555301110566410245433--21000036899997599665414---
Q gi|254781172|r  198 FLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEI--FAKGQYEMLQKMRCLGFPVNNGV---  272 (731)
Q Consensus       198 F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~--~~~~~~e~l~~L~~~GF~v~~~~---  272 (731)
                      -+++    ...|.     .+.+     ....+.+..-+..++.|++.+..+.  ...+-.+..+.|+..--+...-.   
T Consensus       323 ~~~f----~~~G~-----~~di-----k~~~~~~~~~qp~yvvfDLLylNgksL~~~~l~qR~e~L~~v~~p~~~~iei~  388 (881)
T KOG0966         323 TKRF----CPFGS-----NSDI-----KELSSRDGSQQPCYVVFDLLYLNGKSLFGAPLHQRLEILKKVIVPKSGRIEIV  388 (881)
T ss_pred             HHHH----CCCCC-----HHHH-----HHHHCCCCCCCCEEEEEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCEEEEE
T ss_conf             1121----14786-----2568-----87520256777317886550015853677528999999874246778705886


Q ss_pred             --EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCC-------CEEEEEEEEEE
Q ss_conf             --887403211345566553100112343763777311000111587656866312311456-------21589987889
Q gi|254781172|r  273 --RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAE-------KQASTRLLDID  343 (731)
Q Consensus       273 --~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~-------e~~~T~v~~I~  343 (731)
                        ..+...+++.++.++--+      -.-.|||+|--+-.++-    ..|.-.|   +|..|       +.-.--|.+.-
T Consensus       389 ~~~~~~~~edi~~~f~~ai~------~~~EGIVlK~~~S~Y~p----g~R~~gW---~K~KPeYlkg~g~dLD~lIiGgy  455 (881)
T KOG0966         389 RSEVGSTKEDIEQFFEEAID------NGEEGIVLKKPDSSYVP----GQRSNGW---IKLKPEYLKGFGEDLDLLIIGGY  455 (881)
T ss_pred             EHHHCCCHHHHHHHHHHHHH------CCCCCEEEECCCCCCCC----CCCCCCC---EEECHHHHHHCCCCCCEEEEECC
T ss_conf             24301529999999999985------68872598456764475----5457983---76468998423766537999324


Q ss_pred             EEEC-CCCEEE
Q ss_conf             9403-562258
Q gi|254781172|r  344 IQIG-RTGILT  353 (731)
Q Consensus       344 wqvg-RtG~it  353 (731)
                      |.-| |.|.+.
T Consensus       456 ~G~g~rgg~~~  466 (881)
T KOG0966         456 YGRGDRGGKVL  466 (881)
T ss_pred             CCCCCCCCEEE
T ss_conf             58777787121


No 108
>KOG0967 consensus
Probab=92.17  E-value=0.99  Score=24.81  Aligned_cols=178  Identities=19%  Similarity=0.172  Sum_probs=92.9

Q ss_pred             CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEE-ECCEEEEEEECCCCHHHHHHHHHHHH-
Q ss_conf             6642570215999999999999998612467776119999415818999998-59989988865986556669997753-
Q gi|254781172|r   92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRY-EKGKFVYAALRGDGHSGEDVSACIRA-  169 (731)
Q Consensus        92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y-~~G~L~~a~TRGdG~~GeDVT~n~~~-  169 (731)
                      ..|||.-- ++.   +...++|.         .+..|+||.|+||=-.-+++ ++|. +...+|    -+|+.|...-- 
T Consensus       344 lKPMLAkp-TK~---i~evl~rf---------~~~~FTCEyKYDGeRAQIH~~edG~-v~IfSR----N~E~~T~kYPDi  405 (714)
T KOG0967         344 LKPMLAKP-TKG---IQEVLERF---------QDKAFTCEYKYDGERAQIHKLEDGT-VEIFSR----NSENNTGKYPDI  405 (714)
T ss_pred             CCCHHCCC-CHH---HHHHHHHH---------HCCEEEEEEECCCEEEEEEECCCCC-EEEEEC----CCCCCCCCCCCH
T ss_conf             74000375-210---99999985---------3751688863076022568726885-899833----653356658539


Q ss_pred             HCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCH--HHHHCCCEEEEEEECCCC
Q ss_conf             102432233544550489999998520212345564314854334234567777523455--553011105664102454
Q gi|254781172|r  170 IPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNP--TDITRYLNFFVHGLGKTS  247 (731)
Q Consensus       170 i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~r~L~f~ay~~~~~~  247 (731)
                      |..++...... -..+.+-||++--..    -|.+     --||.     +.-+=++++.  ..+.-.+..|+|++.+..
T Consensus       406 ~~~~~~~~kp~-v~sFIlD~EvVA~Dr----~~~~-----IlpFQ-----vLSTRkRk~v~v~dikV~Vcvf~FDily~n  470 (714)
T KOG0967         406 IEVISKLKKPS-VKSFILDCEVVAWDR----EKGK-----ILPFQ-----VLSTRKRKNVDVNDIKVKVCVFVFDILYLN  470 (714)
T ss_pred             HHHHHHHHCCC-CCEEEEEEEEEEEEC----CCCC-----CCCHH-----HHHHHHCCCCCHHHCEEEEEEEEEEEEEEC
T ss_conf             99988752775-211577415899714----4780-----47435-----442453045306354588999998546667


Q ss_pred             CCCC--CCCHHHHHHHHHCCCCCCCCEEEE-----ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECC
Q ss_conf             3321--000036899997599665414887-----403211345566553100112343763777311
Q gi|254781172|r  248 EIFA--KGQYEMLQKMRCLGFPVNNGVRQA-----NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDE  308 (731)
Q Consensus       248 ~~~~--~~~~e~l~~L~~~GF~v~~~~~~~-----~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~  308 (731)
                      +...  ..-.+.-++|.+-.=.+..+....     ++++++..+.++      +.+--+-|+-||+=|
T Consensus       471 g~~Li~~pL~eRR~~l~e~f~e~~g~f~fat~~~tn~~~eiq~Fl~~------sv~~~cEGlMvKtLd  532 (714)
T KOG0967         471 GESLIQEPLRERRELLHESFKEIPGEFQFATSLDTNDIDEIQEFLEE------SVQNSCEGLMVKTLD  532 (714)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCHHHHHHHHHH------HHCCCCCEEEEEEEC
T ss_conf             74565421999999877514567880667653034789999999998------632576436887506


No 109
>PRK07220 DNA topoisomerase I; Validated
Probab=92.07  E-value=0.24  Score=29.52  Aligned_cols=21  Identities=14%  Similarity=0.272  Sum_probs=12.9

Q ss_pred             CCCCHHHHH-----HHHHHHHHCCCC
Q ss_conf             231035410-----355556530576
Q gi|254781172|r  479 DAFNIEGLG-----KQQLDFFFKSED  499 (731)
Q Consensus       479 ~aldI~GLG-----~k~Ie~L~e~~~  499 (731)
                      ++|+=.|||     ..+|+.|++.+|
T Consensus       476 k~ME~~GIGtpATrA~iIe~L~~R~Y  501 (740)
T PRK07220        476 KLMEDLGLGTKATRHEIISKLYSRAY  501 (740)
T ss_pred             HHHHHCCCCCCCCHHHHHHHHHHCCC
T ss_conf             99973899850049999999986188


No 110
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=92.06  E-value=0.088  Score=32.95  Aligned_cols=24  Identities=29%  Similarity=0.277  Sum_probs=13.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             208789999999999998977203
Q gi|254781172|r   42 IILDSEYDALKRRCDAIAHAFPDL   65 (731)
Q Consensus        42 ~isD~eYD~L~~~L~~le~~~p~~   65 (731)
                      ++++.|.|+|.-|-..+-+--|.+
T Consensus        70 ivt~sE~EALlLE~~LIK~~kP~Y   93 (609)
T PRK00558         70 IVTRSETEALLLENNLIKKYKPRY   93 (609)
T ss_pred             EEECCHHHHHHHHHHHHHHHCCCC
T ss_conf             996998999999999986758985


No 111
>COG0190 FolD 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]
Probab=91.35  E-value=0.6  Score=26.53  Aligned_cols=13  Identities=15%  Similarity=0.580  Sum_probs=6.6

Q ss_pred             HHHHHHHHHHHCC
Q ss_conf             4103555565305
Q gi|254781172|r  485 GLGKQQLDFFFKS  497 (731)
Q Consensus       485 GLG~k~Ie~L~e~  497 (731)
                      |+||-|+.-|+++
T Consensus       259 GVGPmTvamLl~N  271 (283)
T COG0190         259 GVGPMTVAMLLEN  271 (283)
T ss_pred             CCCHHHHHHHHHH
T ss_conf             6479999999999


No 112
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=91.09  E-value=0.38  Score=28.05  Aligned_cols=50  Identities=20%  Similarity=0.166  Sum_probs=40.8

Q ss_pred             CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHC
Q ss_conf             101111689999998829989999978977612511778761388867899999999966
Q gi|254781172|r  558 GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ  617 (731)
Q Consensus       558 GI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~  617 (731)
                      .||-+-......|.+.|++++.+.++          +.++|.+++|||+.-|..|.+.++
T Consensus       297 kIpRlp~~iv~nlV~~F~~l~~il~A----------s~edL~~VeGIGe~rAr~i~~Gl~  346 (349)
T COG1623         297 KIPRLPFAIVENLVRAFGTLDGILEA----------SAEDLDAVEGIGEARARAIKEGLS  346 (349)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHH----------CHHHHHHHCCHHHHHHHHHHHHHH
T ss_conf             17676378999999997528999871----------476776621366999999997675


No 113
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=91.08  E-value=0.62  Score=26.41  Aligned_cols=55  Identities=9%  Similarity=0.222  Sum_probs=23.8

Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             3103541035555653057654045410110106777531000100013421001456899998
Q gi|254781172|r  480 AFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSIN  543 (731)
Q Consensus       480 aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe  543 (731)
                      -+.|.|+||++.-.+...       -++.+|...=.  .-+...|.+++|.|.|+|++|+-+++
T Consensus        75 Li~V~GIGpK~AL~ILs~-------~~~~~l~~aI~--~~D~~~L~~vpGIG~KtA~rIi~ELk  129 (198)
T PRK00116         75 LISVSGVGPKLALAILSG-------LSPEELAQAIA--NGDIKALTKVPGVGKKTAERIVLELK  129 (198)
T ss_pred             HHCCCCCCHHHHHHHHCC-------CCHHHHHHHHH--HCCHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf             856688578999988702-------99999999998--58999970688978899999999999


No 114
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=91.06  E-value=0.96  Score=24.92  Aligned_cols=23  Identities=39%  Similarity=0.642  Sum_probs=19.8

Q ss_pred             CCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             17787613888678999999999
Q gi|254781172|r  593 DDWLSLIRVPLVGDIIAQAIVEF  615 (731)
Q Consensus       593 ~~~e~L~~I~GiG~~~A~si~~f  615 (731)
                      .+.++|.+++|||+++|..+..|
T Consensus        69 ~~~~~L~~lpGVG~~tA~~vl~~   91 (149)
T smart00478       69 DDREELLKLPGVGRKTANAVLSF   91 (149)
T ss_pred             CHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             55999875898659999999999


No 115
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=91.01  E-value=0.55  Score=26.78  Aligned_cols=45  Identities=13%  Similarity=0.264  Sum_probs=22.0

Q ss_pred             HHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHH
Q ss_conf             035555653057654045410110106777531000100013421001456899
Q gi|254781172|r  487 GKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYD  540 (731)
Q Consensus       487 G~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~  540 (731)
                      -.+.-..|++.      ..+|.|+..+..+.   ++++++-=||-..+|.||+.
T Consensus        47 vn~at~~Lf~~------~~t~e~l~~a~~~~---l~~~I~~iGlyr~KAk~I~~   91 (211)
T COG0177          47 VNKATPALFKR------YPTPEDLLNADEEE---LEELIKSIGLYRNKAKNIKE   91 (211)
T ss_pred             HHHHHHHHHHH------CCCHHHHHCCCHHH---HHHHHHHCCCCHHHHHHHHH
T ss_conf             99999999997------59999997499999---99999863871899999999


No 116
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=90.75  E-value=0.25  Score=29.47  Aligned_cols=82  Identities=17%  Similarity=0.373  Sum_probs=42.1

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCC---CCCCCCCCCCHHHHHHHHH---HHHHHHHHH
Q ss_conf             1231035410355556530576540454101101067775310001---0001342100145689999---875223466
Q gi|254781172|r  478 RDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTK---IENILGFGDVSVTNLYDSI---NKRRNISLE  551 (731)
Q Consensus       478 K~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~---l~~l~GfgeKsa~nL~~sI---e~sK~~~L~  551 (731)
                      .+-+.++++|++.+++|+++               +...+......   =+.++..|++.|.+|....   ++-...+++
T Consensus       479 ~~l~~l~~~~~ks~~nLl~a---------------Ie~sK~~~l~r~l~aLGIr~VG~~~Ak~La~~f~sl~~l~~a~~e  543 (667)
T COG0272         479 EDLLSLEGFGEKSAENLLNA---------------IEKSKKQPLARFLYALGIRHVGETTAKSLARHFGTLEALLAASEE  543 (667)
T ss_pred             HHHHHCCCHHHHHHHHHHHH---------------HHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCHH
T ss_conf             88841622446579999999---------------998604989999998797114089999999876029999842999


Q ss_pred             HHHHHCCHHHHHHHHHHHHHHHCCCH
Q ss_conf             67763010111168999999882998
Q gi|254781172|r  552 RFIFSLGIRHVGAEIARSLAKYYLSY  577 (731)
Q Consensus       552 r~L~ALGI~~vG~~~Ak~La~~f~si  577 (731)
                      .+   ..|++||...|+.|...|..-
T Consensus       544 ~l---~~i~giG~~vA~si~~ff~~~  566 (667)
T COG0272         544 EL---ASIPGIGEVVARSIIEFFANE  566 (667)
T ss_pred             HH---HHCCCHHHHHHHHHHHHHCCH
T ss_conf             99---506661289999999997277


No 117
>PRK10702 endonuclease III; Provisional
Probab=90.55  E-value=0.79  Score=25.58  Aligned_cols=22  Identities=27%  Similarity=0.342  Sum_probs=18.5

Q ss_pred             CHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             7787613888678999999999
Q gi|254781172|r  594 DWLSLIRVPLVGDIIAQAIVEF  615 (731)
Q Consensus       594 ~~e~L~~I~GiG~~~A~si~~f  615 (731)
                      +.++|+.++|||+++|..|..|
T Consensus       107 ~~~~L~~LpGIG~kTA~aIl~~  128 (211)
T PRK10702        107 DRAALEALPGVGRKTANVVLNT  128 (211)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHH
T ss_conf             6999998766358899999999


No 118
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=90.51  E-value=0.86  Score=25.28  Aligned_cols=24  Identities=29%  Similarity=0.397  Sum_probs=20.3

Q ss_pred             CCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             177876138886789999999996
Q gi|254781172|r  593 DDWLSLIRVPLVGDIIAQAIVEFY  616 (731)
Q Consensus       593 ~~~e~L~~I~GiG~~~A~si~~ff  616 (731)
                      ...++|+.++|||+++|+.+.-|-
T Consensus        80 ~~~~~L~~l~GIG~~TA~~vl~~~  103 (158)
T cd00056          80 DAREELLALPGVGRKTANVVLLFA  103 (158)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             899998758982899999999998


No 119
>TIGR01083 nth endonuclease III; InterPro: IPR005759    The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases. Among these modified bases, 7,8-dihydro-8-oxoguanine (8-oxoG) is an important mutagenic lesion. Base excision repair is a critical mechanism for preventing mutations by removing the oxidative lesion from the DNA. Escherichia coli Nth protein (endonuclease III) has an 8-oxoG DNA glycosylase/AP lyase activity which removes 8-oxoG preferentially from 8-oxoG/G mispairs. Human hNTH1 protein, a homolog of E. coli Nth protein, has similar DNA glycosylase/AP lyase activity that removes 8-oxoG from 8-oxoG/G mispairs . ; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0006284 base-excision repair, 0005622 intracellular.
Probab=90.50  E-value=0.6  Score=26.52  Aligned_cols=74  Identities=23%  Similarity=0.355  Sum_probs=42.4

Q ss_pred             HHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH----HHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             555565305765404541011010677753100010001342100145689999----8752234666776301011116
Q gi|254781172|r  489 QQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSI----NKRRNISLERFIFSLGIRHVGA  564 (731)
Q Consensus       489 k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sI----e~sK~~~L~r~L~ALGI~~vG~  564 (731)
                      +.=.+||+.      =.+|.|+-.+..+.+                 +.++.+|    .|||++               .
T Consensus        47 kaT~~LF~~------Y~tp~~~a~a~~eel-----------------~~~Ik~iGlYr~KAk~I---------------~   88 (192)
T TIGR01083        47 KATKKLFEV------YPTPQALAAAGLEEL-----------------EEYIKSIGLYRNKAKNI---------------I   88 (192)
T ss_pred             HCCHHHHHC------CCCHHHHHCCCHHHH-----------------HHHHHCCCCCHHHHHHH---------------H
T ss_conf             316786512------778689960893134-----------------77642258645689999---------------9


Q ss_pred             HHHHHHHHHCC-CHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             89999998829-989999978977612511778761388867899999999
Q gi|254781172|r  565 EIARSLAKYYL-SYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE  614 (731)
Q Consensus       565 ~~Ak~La~~f~-si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~  614 (731)
                      ..|+.|...|+ .+              -.+.++|++.||+|-|||+-+..
T Consensus        89 ~~~~~LvE~y~GeV--------------P~~~~eL~~LPGVGRKTANVVL~  125 (192)
T TIGR01083        89 ALCRKLVERYGGEV--------------PEDREELVKLPGVGRKTANVVLN  125 (192)
T ss_pred             HHHHHHHHHHCCCC--------------CCCHHHHHCCCCCCCHHHHHHHH
T ss_conf             99999999818987--------------75537661789987114562433


No 120
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=90.26  E-value=0.55  Score=26.77  Aligned_cols=60  Identities=17%  Similarity=0.330  Sum_probs=30.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHH--------HHHHCCHHHHHHHHHHHHHHH-CCCHHHHHH
Q ss_conf             100013421001456899998752234666--------776301011116899999988-299899999
Q gi|254781172|r  523 KIENILGFGDVSVTNLYDSINKRRNISLER--------FIFSLGIRHVGAEIARSLAKY-YLSYQNFAQ  582 (731)
Q Consensus       523 ~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r--------~L~ALGI~~vG~~~Ak~La~~-f~si~~l~~  582 (731)
                      ++.+++|+|++.+++|.+=++.=+-..+..        ++.=+.|+|||.++|+.|-+. +.|++.+..
T Consensus        46 ~~~~lpGIG~~ia~kI~Eil~tG~~~~le~l~~~~p~~l~~l~~I~GiGpk~a~~l~~~Gi~sl~dL~~  114 (307)
T cd00141          46 EAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLYELGIRTLEDLRK  114 (307)
T ss_pred             HHCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHH
T ss_conf             871799964899999999999798089999866563789999647887889999999829997999997


No 121
>PRK00024 radC DNA repair protein RadC; Reviewed
Probab=90.23  E-value=1.5  Score=23.46  Aligned_cols=144  Identities=18%  Similarity=0.299  Sum_probs=76.9

Q ss_pred             HHHHHHHHHHCCHHHHH-HHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHH-----
Q ss_conf             23466677630101111-689999998829989999978977612511778761388867899999999966979-----
Q gi|254781172|r  547 NISLERFIFSLGIRHVG-AEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPR-----  620 (731)
Q Consensus       547 ~~~L~r~L~ALGI~~vG-~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~-----  620 (731)
                      +.+|=-+|-..|.|+-- ...|+.|.+.|+++..+..+          +.++|.+|+|||+..|..|.--+.--+     
T Consensus        26 D~ELLallL~~g~~~~d~~~lA~~ll~~~g~l~~l~~a----------~~~eL~~i~GiG~~kA~~l~a~~El~rR~~~~   95 (224)
T PRK00024         26 DAELLAILLRTGTKGKSVLDLARELLERFGSLRGLLDA----------SLEELQEIKGIGPAKAAQLKAALELARRILAE   95 (224)
T ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHC----------CHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             79999999846999999899999999985999999870----------88988447898899999999999999999752


Q ss_pred             ---------HHHHHHHHHH-HCCCCCCCC----CCCCCCCCCCCEEEEECCCCCC---CHHHHHHHHHHCCCEEEEEEEC
Q ss_conf             ---------9999999997-338776543----2246882168669997258899---8789999999829849981116
Q gi|254781172|r  621 ---------NICAVEALLK-EVSPSIGRH----EKNVSSEIENKKLVFTGTLQKI---QRHKAQEYVTQLGAVVSAILSR  683 (731)
Q Consensus       621 ---------n~~~i~~L~~-~~~~~~~~~----~~~~~~~l~gk~vV~TGtl~~~---~R~e~~~~ie~~Ggkv~sSVSk  683 (731)
                               +.+.+.+++. .......+.    --+..+.+-....++.|++..-   .|+-++..|....         
T Consensus        96 ~~~~~~~l~s~~~v~~~~~~~l~~~~~E~f~vl~Ld~~n~li~~~~i~~Gt~~~~~v~pReI~~~Al~~~A---------  166 (224)
T PRK00024         96 RLREREVLTSPEDVADYLQAELRDEEQEVFVVLFLDTKNRLIADEELFIGTLNSSIVHPREIVKEALKLNA---------  166 (224)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEECCCCCEEEEEEEECCCCCEEEECHHHHHHHHHHHCC---------
T ss_conf             10469874899999999999865667867999998787775568997047886467628999999998278---------


Q ss_pred             CEEEEEE-----CC-CCCC-------HHHH-HHHCCCEEEC
Q ss_conf             3217997-----78-8886-------3798-9974991737
Q gi|254781172|r  684 KTDIIIV-----GD-NPGS-------KLEK-AQQLGVKIMN  710 (731)
Q Consensus       684 kT~~LI~-----ge-~~gS-------Kl~K-A~~LgI~Ii~  710 (731)
                       +.++++     |+ .||.       ++.+ ++.+||+++|
T Consensus       167 -~~iIl~HNHPSG~~~PS~~Di~~T~~l~~a~~~lgI~llD  206 (224)
T PRK00024        167 -AALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLD  206 (224)
T ss_pred             -CEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             -8799995469999998988999999999999768986861


No 122
>TIGR01239 galT_2 galactose-1-phosphate uridylyltransferase; InterPro: IPR000766   Galactose-1-phosphate uridyl transferase 2.7.7.12 from EC (galT) catalyzes the transfer of an uridyldiphosphate group on galactose (or glucose) 1-phosphate. During the reaction, the uridyl moiety links to a histidine residue. In the Escherichia coli enzyme, it has been shown  that two histidine residues separated by a single proline residue are essential for enzyme activity.   On the basis of sequence similarities, two apparently unrelated families seem to exist. Class-I enzymes are found in eukaryotes as well as some bacteria such as E. coli or Streptomyces lividans, while class-II enzymes have been found so far only in bacteria such as Bacillus subtilis or Lactobacillus helveticus .; GO: 0008108 UDP-glucose:hexose-1-phosphate uridylyltransferase activity, 0006012 galactose metabolic process, 0005737 cytoplasm.
Probab=90.01  E-value=0.29  Score=28.91  Aligned_cols=46  Identities=15%  Similarity=0.195  Sum_probs=26.6

Q ss_pred             ECCHHCCCCCCCCCCCCCCEEEECCC-CCEEEEEEEEEEEEECCCCE
Q ss_conf             31100011158765686631231145-62158998788994035622
Q gi|254781172|r  306 VDEFSLQKQLGERARSPRWMISHKFA-EKQASTRLLDIDIQIGRTGI  351 (731)
Q Consensus       306 vn~~~~q~~lG~ts~~PrwaiA~Kf~-~e~~~T~v~~I~wqvgRtG~  351 (731)
                      ++.....+.|+...++|.|-+====- |.-.=|.|..=.+|.||.--
T Consensus       232 I~k~tF~~LL~fl~~FP~Yf~GSNADLPIVGGsILsHdHYQ~GrH~F  278 (502)
T TIGR01239       232 ISKKTFERLLSFLEKFPHYFIGSNADLPIVGGSILSHDHYQGGRHDF  278 (502)
T ss_pred             CCHHHHHHHHHHHHHCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             28476888998975258750214566665577215634446888887


No 123
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=89.67  E-value=0.1  Score=32.40  Aligned_cols=53  Identities=13%  Similarity=0.173  Sum_probs=32.5

Q ss_pred             HCCCCCCCCCCCCCHHHHHHHHHHHH--HH-HHHHHHHHH-CCHHHHHHHHHHHHHHH
Q ss_conf             00010001342100145689999875--22-346667763-01011116899999988
Q gi|254781172|r  520 STTKIENILGFGDVSVTNLYDSINKR--RN-ISLERFIFS-LGIRHVGAEIARSLAKY  573 (731)
Q Consensus       520 ~~~~l~~l~GfgeKsa~nL~~sIe~s--K~-~~L~r~L~A-LGI~~vG~~~Ak~La~~  573 (731)
                      .+..|+++.|.|.|+|-++++++.-.  .+ +.... +.+ -.+||||+++|+.|.-.
T Consensus        71 lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d-~~~L~k~PGIGkKtAerivle  127 (201)
T COG0632          71 LFRLLISVNGIGPKLALAILSNLDPEELAQAIANED-VKALSKIPGIGKKTAERIVLE  127 (201)
T ss_pred             HHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCC-HHHHHCCCCCCHHHHHHHHHH
T ss_conf             999987118805899999984899999999998328-676441898778899999999


No 124
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1;  divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=89.46  E-value=0.94  Score=25.01  Aligned_cols=29  Identities=24%  Similarity=0.274  Sum_probs=21.3

Q ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             01011116899999988299899999789
Q gi|254781172|r  557 LGIRHVGAEIARSLAKYYLSYQNFAQEIN  585 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~  585 (731)
                      =|||+||.++|-.|.+.|++++++...+.
T Consensus       226 ~gi~giG~k~A~kli~~~~~~e~~~~~l~  254 (316)
T cd00128         226 EGIPGIGPVTALKLIKKYGDIEKDIERLK  254 (316)
T ss_pred             CCCCCCCHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             99997359999999999199999999998


No 125
>TIGR00084 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR000085   In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure . In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB.; GO: 0003678 DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=89.45  E-value=0.28  Score=29.10  Aligned_cols=68  Identities=16%  Similarity=0.287  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHH-------CCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHH
Q ss_conf             46655332130-------12310354103555565305765404541011010677753100010001342100145689
Q gi|254781172|r  467 QQLERLKHFVS-------RDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLY  539 (731)
Q Consensus       467 q~~~~i~hF~S-------K~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~  539 (731)
                      |++..+-=|..       ++=|++.|+|+++.=.+.++...    .  .=-|.+...   .+..|.+++|.|.|.|++|+
T Consensus        65 Qi~~~LfGF~~~~Er~lF~~Li~~nGvGpk~ALaiL~~~~~----~--~~~~ai~~~---~~~~L~k~pGvGKK~A~~l~  135 (217)
T TIGR00084        65 QILHLLFGFNTLEERELFKELIKVNGVGPKLALAILSNMSP----E--EFVQAIETE---EVKALVKIPGVGKKTAERLL  135 (217)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCH----H--HHHHHHHHH---HHHHHHCCCCCCHHHHHHHH
T ss_conf             89999734798778999999851488028999998667887----5--898888641---04442045885737899998


Q ss_pred             -HHHH
Q ss_conf             -9998
Q gi|254781172|r  540 -DSIN  543 (731)
Q Consensus       540 -~sIe  543 (731)
                       =.+.
T Consensus       136 ~leL~  140 (217)
T TIGR00084       136 ALELK  140 (217)
T ss_pred             HHHHH
T ss_conf             77754


No 126
>cd07895 Adenylation_mRNA_capping The Adenylation domain of GTP-dependent mRNA capping enzyme is a component of the catalytic core unit. RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues.
Probab=89.35  E-value=1.7  Score=22.97  Aligned_cols=154  Identities=18%  Similarity=0.225  Sum_probs=71.6

Q ss_pred             CEEEEEEECCEEEEEEEEE-CCEEEEEEECCCCHHHHHHHHHHHHHCC--CCC--CCCCCCCCEEEEEEEEEEECHHHHH
Q ss_conf             1199994158189999985-9989988865986556669997753102--432--2335445504899999985202123
Q gi|254781172|r  126 IFFTLEPKIDGTMITIRYE-KGKFVYAALRGDGHSGEDVSACIRAIPT--IPR--VLSLNIPEIIEVRGEVYISKNDFLA  200 (731)
Q Consensus       126 ~~~~vepKiDG~sisl~Y~-~G~L~~a~TRGdG~~GeDVT~n~~~i~~--iP~--~l~~~~~~~ieiRGEv~m~~~~F~~  200 (731)
                      -.|+|..|-||+=.-|.-- +|. +-.++|-+-.         ..+..  .|.  .......+.+ +=||++.....   
T Consensus        40 ~~Y~VteKaDG~R~lL~i~~~~~-~yLidR~~~~---------~~~~~~~~~~~~~~~~~~~~Tl-lDGElV~~~~~---  105 (216)
T cd07895          40 KDYYVCEKSDGVRYLLLIDGRGE-VYLIDRNNEF---------FKVPGLFFPRPKNLKEHHQNTL-LDGELVIDKDP---  105 (216)
T ss_pred             CCEEEEECCCCEEEEEEEECCCE-EEEEECCCEE---------EECCCCCCCCCCCCCCCCCCEE-EEEEEEEECCC---
T ss_conf             98699985576599999957985-9999689817---------9844424565566765447888-96479987479---


Q ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCC--CCCCHHHHHHHHHC-----------CCC
Q ss_conf             45564314854334234567777523455553011105664102454332--10000368999975-----------996
Q gi|254781172|r  201 LNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIF--AKGQYEMLQKMRCL-----------GFP  267 (731)
Q Consensus       201 lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~--~~~~~e~l~~L~~~-----------GF~  267 (731)
                              +     +                  ....|++|++....+..  .....+++..++.+           +..
T Consensus       106 --------~-----~------------------~~~~ylifDi~~~~g~~v~~~~~~~Rl~~l~~~v~~~~~~~~~~~~~  154 (216)
T cd07895         106 --------G-----K------------------KVPRYLIFDILAFNGEPVTNRPLSERLGCLQKEVIKPRKNLKKKGPI  154 (216)
T ss_pred             --------C-----C------------------EEEEEEEEEEEEECCEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             --------9-----7------------------87888999999999918455987999999999877778887752533


Q ss_pred             ---CCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCC
Q ss_conf             ---65414887403211345566553100112343763777311000111587656866312311456
Q gi|254781172|r  268 ---VNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAE  332 (731)
Q Consensus       268 ---v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~  332 (731)
                         ..+......++-.+.....-+......++|++||+|+.-++..+.  .|      +|.-.|||.+
T Consensus       155 ~~~~~~f~i~~K~f~~~~~~~~i~~~~~~~l~h~~DGLIFtP~~~py~--~G------t~~~~~KWKP  214 (216)
T cd07895         155 DKPKEPFSVRLKDFFPLYGIEKLLEKIPRSLPHENDGLIFTPNDEPYV--PG------TDKGLLKWKP  214 (216)
T ss_pred             CCCCCCEEEEECCCEEHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCC--CC------CCCCCEEECC
T ss_conf             366777499975728777689999866440888898599868999897--78------6776675588


No 127
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=89.32  E-value=0.44  Score=27.57  Aligned_cols=29  Identities=28%  Similarity=0.447  Sum_probs=24.0

Q ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             01011116899999988299899999789
Q gi|254781172|r  557 LGIRHVGAEIARSLAKYYLSYQNFAQEIN  585 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~  585 (731)
                      =|||+||.++|..|.+.|++++.+....+
T Consensus        25 pGV~GIG~ktA~~ll~~~~~l~~i~~~~~   53 (75)
T cd00080          25 PGVPGIGPKTALKLLKEYGSLENLLENLD   53 (75)
T ss_pred             CCCCCCCHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             77586379999999999099999998387


No 128
>PRK10792 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=89.16  E-value=0.96  Score=24.93  Aligned_cols=14  Identities=14%  Similarity=0.406  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHCC
Q ss_conf             54103555565305
Q gi|254781172|r  484 EGLGKQQLDFFFKS  497 (731)
Q Consensus       484 ~GLG~k~Ie~L~e~  497 (731)
                      -|+||-|+..|+++
T Consensus       261 GGVGP~Tva~L~~N  274 (288)
T PRK10792        261 GGVGPMTVATLIEN  274 (288)
T ss_pred             CCCCHHHHHHHHHH
T ss_conf             96169999999999


No 129
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=88.88  E-value=0.87  Score=25.26  Aligned_cols=46  Identities=15%  Similarity=0.266  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             0111168999999882998999997897761251177876138886789999999996
Q gi|254781172|r  559 IRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFY  616 (731)
Q Consensus       559 I~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff  616 (731)
                      +||||.+.|+.|..+=       +.     ...-.++++|..++|||+++-+.+.+++
T Consensus       102 lpgIG~~kA~aIi~yR-------e~-----~G~f~sv~dL~~v~GiG~~~~ekl~~~i  147 (149)
T COG1555         102 LPGIGPKKAQAIIDYR-------EE-----NGPFKSVDDLAKVKGIGPKTLEKLKDYI  147 (149)
T ss_pred             CCCCCHHHHHHHHHHH-------HH-----CCCCCCHHHHCCCCCCCHHHHHHHHHHC
T ss_conf             6798999999999999-------97-----3997657887107777899999877561


No 130
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=88.75  E-value=0.21  Score=30.05  Aligned_cols=18  Identities=22%  Similarity=0.337  Sum_probs=10.2

Q ss_pred             CCCCCCCCHHHCCHHHHH
Q ss_conf             997779994688999999
Q gi|254781172|r    1 MKKRQLIPIEALSIEQAR   18 (731)
Q Consensus         1 ~~~~~~~~~~~~s~~~~~   18 (731)
                      |+.+++..++-++...++
T Consensus         4 ~~~~~l~~lpGv~~~~~~   21 (318)
T PRK04301          4 MKEKDLEDLPGVGPATAE   21 (318)
T ss_pred             CCCCCCCCCCCCCHHHHH
T ss_conf             554774558998999999


No 131
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=88.31  E-value=2  Score=22.47  Aligned_cols=116  Identities=18%  Similarity=0.185  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHCCHHHHH-HHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHC--------
Q ss_conf             23466677630101111-689999998829989999978977612511778761388867899999999966--------
Q gi|254781172|r  547 NISLERFIFSLGIRHVG-AEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ--------  617 (731)
Q Consensus       547 ~~~L~r~L~ALGI~~vG-~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~--------  617 (731)
                      +..|--++-.-|+|+-- ...|+.|.++|+++..+..+          +.++|+.++|+|...|-++..-..        
T Consensus        26 d~ELLailLrtG~~~~~~~~la~~lL~~fg~L~~l~~a----------~~~el~~v~GiG~aka~~l~a~~El~~R~~~~   95 (224)
T COG2003          26 DAELLAILLRTGTKGESVLDLAKELLQEFGSLAELLKA----------SVEELSSVKGIGLAKAIQIKAAIELGKRILAE   95 (224)
T ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHC----------CHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             68999999962899987899999999973258888737----------99999517883388999999999999999998


Q ss_pred             ---------CHHHHHHHHHHHHHCCCCCCCCC----CCCCCCCCCCEEEEECCCCC---CCHHHHHHHHHHCC
Q ss_conf             ---------97999999999973387765432----24688216866999725889---98789999999829
Q gi|254781172|r  618 ---------NPRNICAVEALLKEVSPSIGRHE----KNVSSEIENKKLVFTGTLQK---IQRHKAQEYVTQLG  674 (731)
Q Consensus       618 ---------~~~n~~~i~~L~~~~~~~~~~~~----~~~~~~l~gk~vV~TGtl~~---~~R~e~~~~ie~~G  674 (731)
                               ++..  ..+-+.........+.-    -+..+.+-....+|+||+..   +.|.-++..+..+-
T Consensus        96 ~~~~~~~i~sp~~--~~~~l~~~l~~~~~E~f~vL~Ld~qnrlI~~e~lf~GTi~~s~V~PREI~k~Al~~nA  166 (224)
T COG2003          96 RLREGVVITSPEA--VAEYLRAELGGEEREHFVVLYLDSQNRLIATETLFIGTLNVSEVHPREIFKEALKYNA  166 (224)
T ss_pred             HHCCCCCCCCHHH--HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCCCEECHHHHHHHHHHHCC
T ss_conf             7505775489999--9999999861348899999995476843310037752014504337999999998221


No 132
>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=88.03  E-value=0.16  Score=30.87  Aligned_cols=51  Identities=24%  Similarity=0.507  Sum_probs=30.3

Q ss_pred             ECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf             15818999998599899888659865566699977531024322335445504899999985202123455
Q gi|254781172|r  133 KIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALND  203 (731)
Q Consensus       133 KiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~  203 (731)
                      -|||=.+-|  +||--++.-|=   +.-.+|-..+-.|      |      .|   ||+.+.+.+|-+=|+
T Consensus       389 tIegP~VkL--kNGDViri~t~---e~A~~vr~eVeeI------L------fL---Gd~LvnyGdFLeNNH  439 (1173)
T TIGR00354       389 TIEGPVVKL--KNGDVIRIDTL---EKAKAVRSEVEEI------L------FL---GDVLVNYGDFLENNH  439 (1173)
T ss_pred             CCCCCEEEE--ECCCEEEECCH---HHHHHHHHHHHHH------H------HH---HHHHHHHHHHHHCCC
T ss_conf             588786584--17887882576---8888887789988------8------76---578876300432475


No 133
>pfam00633 HHH Helix-hairpin-helix motif. The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
Probab=87.96  E-value=0.31  Score=28.72  Aligned_cols=25  Identities=28%  Similarity=0.371  Sum_probs=21.1

Q ss_pred             CCCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             5117787613888678999999999
Q gi|254781172|r  591 NNDDWLSLIRVPLVGDIIAQAIVEF  615 (731)
Q Consensus       591 ~~~~~e~L~~I~GiG~~~A~si~~f  615 (731)
                      ...+.++|..++|||+++|+.|.+|
T Consensus         6 ~~as~eeL~~lpGVG~~tA~~I~~~   30 (30)
T pfam00633         6 IPASREELLALPGVGPKTAEAILSY   30 (30)
T ss_pred             CCCCHHHHHHCCCCCHHHHHHHHCC
T ss_conf             5235999972889776889988539


No 134
>KOG1921 consensus
Probab=87.07  E-value=1.3  Score=24.00  Aligned_cols=36  Identities=22%  Similarity=0.280  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHCCC-HHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHH
Q ss_conf             6899999988299-8999997897761251177876138886789999999
Q gi|254781172|r  564 AEIARSLAKYYLS-YQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIV  613 (731)
Q Consensus       564 ~~~Ak~La~~f~s-i~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~  613 (731)
                      .++|+.|..+|.+ +              -.+.++|..++|+||++|--..
T Consensus       140 kkta~IL~d~f~gDI--------------P~~v~dLlsLPGVGPKMa~L~m  176 (286)
T KOG1921         140 KKTAKILQDKFDGDI--------------PDTVEDLLSLPGVGPKMAHLTM  176 (286)
T ss_pred             HHHHHHHHHHHCCCC--------------CHHHHHHHCCCCCCHHHHHHHH
T ss_conf             999999998707997--------------5559988558997659999999


No 135
>TIGR01259 comE comEA protein; InterPro: IPR004787   The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable .   ComEA has been shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Human herpesvirus 4 (Epstein-Barr virus) ..
Probab=86.36  E-value=0.44  Score=27.57  Aligned_cols=98  Identities=20%  Similarity=0.289  Sum_probs=50.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCC
Q ss_conf             0001342100145689999875-223466677630101111689999998829989999978977612511778761388
Q gi|254781172|r  524 IENILGFGDVSVTNLYDSINKR-RNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVP  602 (731)
Q Consensus       524 l~~l~GfgeKsa~nL~~sIe~s-K~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~  602 (731)
                      +.+.-||-++.+...++.+... .+-.   |+|   ||.-|+.++-.-  ....... .........+|.++.++|..|+
T Consensus         8 ~~kagg~~e~a~~~~~ntLa~k~~d~~---~vy---~P~~Ge~~~s~q--~G~~~~s-~~~~~~~VnlN~As~~EL~~l~   78 (124)
T TIGR01259         8 IEKAGGLTEQADEKSVNTLAEKLSDEM---FVY---VPKKGEEEASQQ--TGLEVQS-EAGKEAAVNLNKASLEELQALP   78 (124)
T ss_pred             HHHHCCHHHHHHHHHHHHHHHHHCCCC---EEE---CCCCCCCCCCCC--CCCCCCC-CCCCCCHHHHHHHHHHHHHHCC
T ss_conf             986133389998999999988750781---575---027652000026--7731010-0115001344067899986369


Q ss_pred             CCCHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             8678999999999669799999999997
Q gi|254781172|r  603 LVGDIIAQAIVEFYQNPRNICAVEALLK  630 (731)
Q Consensus       603 GiG~~~A~si~~ff~~~~n~~~i~~L~~  630 (731)
                      ||||..|+.|++|=..-=-...+++|.+
T Consensus        79 GiGP~kA~aIi~YRe~nG~F~SvddL~k  106 (124)
T TIGR01259        79 GIGPAKAKAIIEYREENGAFKSVDDLTK  106 (124)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCCHHHHHC
T ss_conf             9981337999999985699777555003


No 136
>pfam00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein. This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.
Probab=86.14  E-value=2.4  Score=21.81  Aligned_cols=22  Identities=32%  Similarity=0.522  Sum_probs=18.2

Q ss_pred             CHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             7787613888678999999999
Q gi|254781172|r  594 DWLSLIRVPLVGDIIAQAIVEF  615 (731)
Q Consensus       594 ~~e~L~~I~GiG~~~A~si~~f  615 (731)
                      ..++|+.++|||+.+|+.+.-|
T Consensus        79 ~~~~L~~l~GIG~~ta~~~l~~  100 (144)
T pfam00730        79 ELEALLALPGVGRWTAEAVLLF  100 (144)
T ss_pred             HHHHHHCCCCCCHHHHHHHHHH
T ss_conf             6999860889769999999999


No 137
>PRK00420 hypothetical protein; Validated
Probab=85.82  E-value=0.36  Score=28.27  Aligned_cols=25  Identities=16%  Similarity=0.460  Sum_probs=17.9

Q ss_pred             EECCCCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf             77043265775010337865445210100354
Q gi|254781172|r  429 SFPSFCPICQSRVVRDLNPKTGKLVAAHRCTG  460 (731)
Q Consensus       429 ~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n  460 (731)
                      -.+.+||.||+|+.+..+.       ..+|++
T Consensus        17 ml~~~C~~Cg~plf~~k~G-------~~~Cp~   41 (107)
T PRK00420         17 MLDKHCPVCGLPLFELKDG-------EVVCPN   41 (107)
T ss_pred             HHHHHCCCCCCCEEECCCC-------CEECCC
T ss_conf             6351376579840574898-------776898


No 138
>PRK02362 ski2-like helicase; Provisional
Probab=85.66  E-value=0.42  Score=27.72  Aligned_cols=48  Identities=25%  Similarity=0.333  Sum_probs=26.2

Q ss_pred             CCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             01011116899999988-2998999997897761251177876138886789999999996
Q gi|254781172|r  557 LGIRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFY  616 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff  616 (731)
                      +.||+||...|+.|-++ |.|+..+..          ++.++|..|  +|+++|++|.+.+
T Consensus       655 ~~I~gvgr~RAR~Ly~aGi~s~~dla~----------A~p~~l~~i--lg~~~a~~i~~~~  703 (736)
T PRK02362        655 VGLRGIGRVRARRLYNAGITSRADLRA----------ADKEVVAAI--LGPKIAERVLEQL  703 (736)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCHHHHHH----------CCHHHHHHH--HHHHHHHHHHHHH
T ss_conf             088999989999999879999999970----------999999999--7778999999983


No 139
>TIGR02317 prpB methylisocitrate lyase; InterPro: IPR012695   Propionate is the second most abundant low molecular mass carbon source found in soil, being generated by the degradation of several amino acids, fementation of crabohydrates and the oxidation of odd-chain fatty acids. Many different organisms are capable of metabolising propionate and several distinct pathways for utilising this compound exist, all of which begin with its activation to propionyl-CoA . Many bacteria metabolise propionate to pyruvate by the 2-methylcitric acid cycle. In the first step, catalysed by methycitrate synthase, oxaloacetate and propionyl-CoA are condensed to form 2-methylcitrate and CoA. The 2-methylcitrate is subsequently converted to 2-methylisocitrate by the combined actions of a dehydratase and an aconitase. In the final step, 2-methylisocitrate lyase cleaves a C-C bond within this compound to form succinate and pyruvate. The succinate is further oxidised to oxaloacetate which re-enters the cycle, while the pyruvate can be used further for either energy generation or biomass synthesis.   Proteins in this entry are mostly 2-methylisocitrate lyases. Some of them have been annotated (incorrectly it seems) as the related protein carboxyphosphoenolpyruvate phosphomutase, which is involved in synthesizing the antibiotic bialaphos in Streptomyces hygroscopicus. Structural studies indicate that these enzymes belong to the isocitrate lyase family, binding a Mg(2+) cofactor and forming a TIM barrel fold , . As with other enzymes in this family, substrate-binding induces a conformational change that prevents solvent access to the active site and which is important for catalysis.  .
Probab=85.21  E-value=1.3  Score=23.96  Aligned_cols=131  Identities=19%  Similarity=0.237  Sum_probs=73.7

Q ss_pred             HHCCCCCCCCCCCCCHHHHHHHHH--HHH--HHHHHH--HHHH-HCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf             100010001342100145689999--875--223466--6776-301011116899999988299899999789776125
Q gi|254781172|r  519 TSTTKIENILGFGDVSVTNLYDSI--NKR--RNISLE--RFIF-SLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHN  591 (731)
Q Consensus       519 ~~~~~l~~l~GfgeKsa~nL~~sI--e~s--K~~~L~--r~L~-ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~  591 (731)
                      +...++++++|     +=|=+-|+  |++  +-+-|+  =+=. +||+|.+|-++..-++..-..|-..          .
T Consensus         9 ~~~~~ilq~pG-----a~n~~~AL~Ae~aGF~A~YLSGaa~aa~sLGlPDLG~~tL~Eva~~~r~Itr~----------~   73 (287)
T TIGR02317         9 IAKEDILQIPG-----AINGLVALLAERAGFEAIYLSGAAVAAGSLGLPDLGITTLTEVAERARRITRV----------T   73 (287)
T ss_pred             HHCCCCEEECC-----HHHHHHHHHHHHCCCCEEEEHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH----------C
T ss_conf             85689748714-----06189999998637556610168774132067767667878999998877753----------0


Q ss_pred             CCCHHHHHCCC-CCCHHH--HHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHH
Q ss_conf             11778761388-867899--999999966979999999999733877654322468821686699972588998789999
Q gi|254781172|r  592 NDDWLSLIRVP-LVGDII--AQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQE  668 (731)
Q Consensus       592 ~~~~e~L~~I~-GiG~~~--A~si~~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~  668 (731)
                        +.--|..+| |||+-.  +..+.+         +.+--...+.++....++. =++|.||.+|        +++|+.+
T Consensus        74 --~LPlLVD~DTGFGea~nvaRTVre---------me~AGaAa~HiEDQv~pKr-CGHL~gK~lv--------~~~eMv~  133 (287)
T TIGR02317        74 --DLPLLVDADTGFGEALNVARTVRE---------MEDAGAAAVHIEDQVLPKR-CGHLNGKELV--------SRDEMVR  133 (287)
T ss_pred             --CCCEEEEEECCCCCHHHHHHHHHH---------HHHHHHHHCCHHHHCCCCC-CCCCCCCCCC--------CHHHHHH
T ss_conf             --487278633289835449999999---------9984454004677425442-6789887404--------8877999


Q ss_pred             HHHHCCCEEEEEEECCE--EEEEEC
Q ss_conf             99982984998111632--179977
Q gi|254781172|r  669 YVTQLGAVVSAILSRKT--DIIIVG  691 (731)
Q Consensus       669 ~ie~~Ggkv~sSVSkkT--~~LI~g  691 (731)
                      +|.+.       |+.+.  |++|+-
T Consensus       134 kI~AA-------v~Ar~De~f~iiA  151 (287)
T TIGR02317       134 KIKAA-------VDARRDEDFVIIA  151 (287)
T ss_pred             HHHHH-------HCCCCCCCCEEEE
T ss_conf             99997-------1478999727753


No 140
>PRK00421 murC UDP-N-acetylmuramate--L-alanine ligase; Provisional
Probab=84.28  E-value=3.1  Score=20.98  Aligned_cols=13  Identities=31%  Similarity=0.207  Sum_probs=5.6

Q ss_pred             EEEEECCHHCCCC
Q ss_conf             3777311000111
Q gi|254781172|r  302 LVYKVDEFSLQKQ  314 (731)
Q Consensus       302 iVikvn~~~~q~~  314 (731)
                      +|+-.||...+..
T Consensus       215 ~ViN~DD~~~~~l  227 (459)
T PRK00421        215 LVACGDDPELREL  227 (459)
T ss_pred             EECCCCCHHHHHH
T ss_conf             1146879899998


No 141
>pfam03118 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C terminal domain. The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal.
Probab=84.07  E-value=0.6  Score=26.49  Aligned_cols=50  Identities=14%  Similarity=0.278  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             3541035555653057654045410110106777531000100013421001456899998
Q gi|254781172|r  483 IEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSIN  543 (731)
Q Consensus       483 I~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe  543 (731)
                      --+|+..+...|-.++     |.++.||..++..      +|.++++||.||.+-+.+.++
T Consensus        12 ~L~LS~R~~N~Lk~~~-----I~tv~dL~~~s~~------dLl~i~N~G~kSl~EI~~~L~   61 (62)
T pfam03118        12 ELELSVRSYNCLKRAG-----INTVGDLLSKSEE------DLLKIKNFGKKSLEEIKEKLE   61 (62)
T ss_pred             HHCCCHHHHHHHHHCC-----CCCHHHHHHCCHH------HHHHCCCCCHHHHHHHHHHHC
T ss_conf             8168689999998949-----9679999858999------997488986857999999982


No 142
>KOG2043 consensus
Probab=84.07  E-value=2.2  Score=22.08  Aligned_cols=68  Identities=16%  Similarity=0.101  Sum_probs=51.7

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHH
Q ss_conf             69997258899878999999982984998111632179977888863798997499173799999999882
Q gi|254781172|r  651 KLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQY  721 (731)
Q Consensus       651 ~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~  721 (731)
                      .++|+|.+   .+.-++.+++.+||.+.+|.+.-|++++-.---..|+--|-.+|++|++++.+.+.+...
T Consensus       661 ~~lfs~~~---~~~~~k~~~k~lg~s~~ss~~e~Th~i~~rirRT~k~Leai~~G~~ivT~~wL~s~~k~g  728 (896)
T KOG2043         661 EVLFSDKN---DGKNYKLAKKFLGGSVASSDSEATHFIADRIRRTLKFLEAISSGKPLVTPQWLVSSLKSG  728 (896)
T ss_pred             EEEEEECC---CCHHHHHHHHHCCCEEECCCCCCEEEEEHHHHCCHHHHHHHCCCCCCCCHHHHHHHHHCC
T ss_conf             36665135---754555677650650103530100243020221178775022487412548988776416


No 143
>PRK13766 Hef nuclease; Provisional
Probab=83.83  E-value=0.53  Score=26.91  Aligned_cols=28  Identities=18%  Similarity=0.472  Sum_probs=22.5

Q ss_pred             HHHCCCCCCHHHHHHHHHHHCCHHHHHH
Q ss_conf             7613888678999999999669799999
Q gi|254781172|r  597 SLIRVPLVGDIIAQAIVEFYQNPRNICA  624 (731)
Q Consensus       597 ~L~~I~GiG~~~A~si~~ff~~~~n~~~  624 (731)
                      -|..+|||||+.|..+.+-|...+++..
T Consensus       707 ~l~~~pgvg~~~a~~ll~~fgsi~~i~~  734 (764)
T PRK13766        707 IVSSLPDVGPVLARNLLDHFGSVENVMT  734 (764)
T ss_pred             HHHHCCCCCHHHHHHHHHHCCCHHHHHC
T ss_conf             9983899999999999997199999965


No 144
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=82.85  E-value=0.39  Score=27.96  Aligned_cols=35  Identities=14%  Similarity=0.328  Sum_probs=28.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHH
Q ss_conf             32657750103378654452101003543441144665533213
Q gi|254781172|r  433 FCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFV  476 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~  476 (731)
                      .||.|+.++....        ..++|.|+ .|.....+-..++-
T Consensus         4 ~CPvC~~~L~~~~--------~sl~C~~~-H~FD~AkqGYvnLL   38 (272)
T PRK11088          4 QCPLCHQPLTLEE--------NSWICPQN-HQFDCAKEGYVNLL   38 (272)
T ss_pred             ECCCCCCCCEECC--------CEEECCCC-CCCCCCCCCEEEEC
T ss_conf             0899991201079--------68885899-88745678467703


No 145
>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=81.33  E-value=0.82  Score=25.46  Aligned_cols=49  Identities=20%  Similarity=0.490  Sum_probs=28.6

Q ss_pred             HHHHHHCCCCCCCCCCEEEECCCCCCCCCC-CCCCCCCCCCCCCEEECCCCCCCCHHHHHHH
Q ss_conf             566541012357873047770432657750-1033786544521010035434411446655
Q gi|254781172|r  411 PKVVDIIVNERHPDAQPFSFPSFCPICQSR-VVRDLNPKTGKLVAAHRCTGGLACSAQQLER  471 (731)
Q Consensus       411 P~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~-l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~  471 (731)
                      +++++|+.+.=-      .--..||.||+. +..-.+...   .+|.+|+   +|.++..=+
T Consensus        17 sQi~RVLsE~Wv------~~n~yCP~Cg~~~l~~~~NN~P---VaDFyC~---~C~e~yELK   66 (254)
T pfam06044        17 SQIIRVLSEDWV------AKQGYCPNCGSNPLSRFANNQP---VADFYCP---NCHEDYELK   66 (254)
T ss_pred             CCEEEECCHHHH------HHCCCCCCCCCCHHHHCCCCCC---CCEEECC---CCCHHHHHH
T ss_conf             044564037789------8668799889722122337992---3303547---740666003


No 146
>TIGR00600 rad2 DNA excision repair protein (rad2); InterPro: IPR001044   Xeroderma pigmentosum (XP)  is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair , . XP-G can be corrected by a 133 Kd nuclear protein, XPGC . XPGC is an acidic protein that confers normal UV resistance in expressing cells . It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms , . XPGC cleaves one strand of the duplex at the border with the single-stranded region .   XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases , ; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C-terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved.   This entry represents XPGC, an acidic protein that confers normal UV resistance in expressing cells, can correct XP-G. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms. XPGC cleaves one strand of the duplex at the border with the single-stranded region , .; GO: 0003697 single-stranded DNA binding, 0004519 endonuclease activity, 0006289 nucleotide-excision repair, 0005634 nucleus.
Probab=80.98  E-value=4.1  Score=20.09  Aligned_cols=25  Identities=8%  Similarity=0.108  Sum_probs=17.2

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             7982087899999999999989772
Q gi|254781172|r   39 SKPIILDSEYDALKRRCDAIAHAFP   63 (731)
Q Consensus        39 ~~p~isD~eYD~L~~~L~~le~~~p   63 (731)
                      +.-+.|..+|..++.+...|+..+-
T Consensus       188 ~s~~~~~~~~~~~mn~~q~~~~~~~  212 (1127)
T TIGR00600       188 DSEEESEKEWEERMNQKQKLQEEFF  212 (1127)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCC
T ss_conf             7331224899999888852043103


No 147
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=80.89  E-value=1.7  Score=23.01  Aligned_cols=15  Identities=40%  Similarity=0.594  Sum_probs=7.7

Q ss_pred             CCHHHHHHHHHHCCC
Q ss_conf             423456777752345
Q gi|254781172|r  214 ANPRNAASGILRRLN  228 (731)
Q Consensus       214 ~NpRN~aaG~lr~~d  228 (731)
                      -.|.|++.|.++.+.
T Consensus        38 g~~~~~~~~~~~~l~   52 (310)
T COG0258          38 GDPTGAVSGFLGMLY   52 (310)
T ss_pred             CCCCCHHHHHHHHHH
T ss_conf             784449999999999


No 148
>TIGR01497 kdpB K+-transporting ATPase, B subunit; InterPro: IPR006391   These sequences describe the P-type ATPase subunit of the complex responsible for translocating potassium ions across biological membranes in microbes. In Escherichia coli and other species, this complex consists of the proteins KdpA, KdpB, KdpC and KdpF. KdpB is the ATPase subunit, while KdpA is the potassium-ion translocating subunit . The function of KdpC is unclear, although it has been suggested to couple the ATPase subunit to the ion-translocating subunit , while KdpF serves to stabilize the complex . The potassium P-type ATPases have been characterised as Type IA based on a phylogenetic analysis which places this clade closest to the heavy-metal translocating ATPases (Type IB) . Others place this clade closer to the Na+/K+ antiporter type (Type IIC) based on physical characteristics . ; GO: 0008556 potassium-transporting ATPase activity, 0006813 potassium ion transport, 0016021 integral to membrane.
Probab=80.67  E-value=0.85  Score=25.35  Aligned_cols=157  Identities=15%  Similarity=0.261  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHCCHHHHHHHHH-HHHHH------HCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHH---HHH
Q ss_conf             234666776301011116899-99998------82998999997897761251177876138886789999999---996
Q gi|254781172|r  547 NISLERFIFSLGIRHVGAEIA-RSLAK------YYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIV---EFY  616 (731)
Q Consensus       547 ~~~L~r~L~ALGI~~vG~~~A-k~La~------~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~---~ff  616 (731)
                      ..+.-=+|.|.||-|.-+-+- ..||.      +.++.+.+.=+-...+-..|...+++.-+.|...+.--+.-   .-+
T Consensus       262 PTTIGGLLSAIGiAGMdRv~~fNVIAtSGrAVEAcGDVdtl~LDKTGTITlGNRlA~eFIp~~G~d~~~lad~a~~aSl~  341 (675)
T TIGR01497       262 PTTIGGLLSAIGIAGMDRVLRFNVIATSGRAVEACGDVDTLVLDKTGTITLGNRLAEEFIPVQGVDKKKLADVAVLASLA  341 (675)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCEEEECCCEEEECCCCCEEEECCCCCCCCCCHHHHHCCCCCCCCHHHHHHHHHHHCCC
T ss_conf             00033688886542355673055245246402412872347764657403321105334455883488898588760113


Q ss_pred             CC-HHHHHHHHHHHHHCCCCCCCCCCC-C-------CC-----CCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEE
Q ss_conf             69-799999999997338776543224-6-------88-----2168669997258899878999999982984998111
Q gi|254781172|r  617 QN-PRNICAVEALLKEVSPSIGRHEKN-V-------SS-----EIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILS  682 (731)
Q Consensus       617 ~~-~~n~~~i~~L~~~~~~~~~~~~~~-~-------~~-----~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVS  682 (731)
                      .+ |+-+..+ +|-+++++.....+.. .       .+     .|.|=+-+==|     +=+-++..+++++|.+...+-
T Consensus       342 DdTPEGkSIV-~Lakqlgir~d~~~~~~a~fveFtAqtRMSGinl~nGr~~rKG-----avdAIk~~V~~~~G~ip~dlD  415 (675)
T TIGR01497       342 DDTPEGKSIV-ELAKQLGIRIDDKKSESAEFVEFTAQTRMSGINLDNGREVRKG-----AVDAIKKFVEERKGRIPKDLD  415 (675)
T ss_pred             CCCCCCHHHH-HHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCEEECC-----CHHHHHHHHHHCCCCCCHHHH
T ss_conf             5898836888-8887808610147453232101323333454438988436227-----617887898763797783767


Q ss_pred             CC---------EEEEEE-----------CC--CCC--CHHHHHHHCCCEEE
Q ss_conf             63---------217997-----------78--888--63798997499173
Q gi|254781172|r  683 RK---------TDIIIV-----------GD--NPG--SKLEKAQQLGVKIM  709 (731)
Q Consensus       683 kk---------T~~LI~-----------ge--~~g--SKl~KA~~LgI~Ii  709 (731)
                      .+         |=++|+           +|  |+|  -..++=++.||+-|
T Consensus       416 ~av~qVa~~GgTPLvVc~dn~iyGVIyLKDiVK~Gi~ERF~qLR~~GikTi  466 (675)
T TIGR01497       416 EAVDQVAKQGGTPLVVCVDNKIYGVIYLKDIVKSGIKERFEQLRKMGIKTI  466 (675)
T ss_pred             HHHHHHHHCCCCCEEEEECCEEEEEEEEECCCCCCHHHHHHHHHHCCCEEE
T ss_conf             889998732898479997577898898730137860457888722586689


No 149
>PRK07726 DNA topoisomerase III; Provisional
Probab=80.56  E-value=0.84  Score=25.40  Aligned_cols=18  Identities=22%  Similarity=0.362  Sum_probs=12.3

Q ss_pred             CHHHHH-----HHHHHHHHCCCC
Q ss_conf             035410-----355556530576
Q gi|254781172|r  482 NIEGLG-----KQQLDFFFKSED  499 (731)
Q Consensus       482 dI~GLG-----~k~Ie~L~e~~~  499 (731)
                      +.+|||     ..+|+.|++.+|
T Consensus       511 ~~~GIGTpATRA~IIe~L~~r~Y  533 (716)
T PRK07726        511 KTEGLGTEATRAGIITMLKDRKY  533 (716)
T ss_pred             HCCCCCCCCCHHHHHHHHHHCCC
T ss_conf             45688884108999999874571


No 150
>TIGR01265 tyr_nico_aTase tyrosine/nicotianamine aminotransferases; InterPro: IPR005958   This entry describes tyrosine aminotransferase (2.6.1.5 from EC) as found in animals and Trypanosoma cruzi (Euglenozoa). It is the first enzyme of a pathway of tyrosine degradation via homogentisate.  L-tyrosine + 2-oxoglutarate = 4-hydroxyphenylpyruvate + L-glutamate. Several plant enzyme designated as probable tyrosine aminotransferases are very closely related to an experimentally demonstrated nicotianamine aminotransferase, an enzyme in a siderophore (iron uptake chelator) biosynthesis pathway are included in this family. ; GO: 0008483 transaminase activity, 0030170 pyridoxal phosphate binding, 0006519 amino acid and derivative metabolic process.
Probab=80.43  E-value=0.81  Score=25.50  Aligned_cols=107  Identities=12%  Similarity=0.097  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHHHHH--HHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH-HCCCCCHHHHHCCCCCCHHH-H
Q ss_conf             14568999987522--34666776301011116899999988299899999789776-12511778761388867899-9
Q gi|254781172|r  534 SVTNLYDSINKRRN--ISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNII-AHNNDDWLSLIRVPLVGDII-A  609 (731)
Q Consensus       534 sa~nL~~sIe~sK~--~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~-~~~~~~~e~L~~I~GiG~~~-A  609 (731)
                      .-++++++|.+--+  ..-..|+-|        -.-+.|.+   |-++|.+.+-+.+ ...+.-+++|.+|+|+-+.. =
T Consensus       282 ~~~k~~~gl~~~~~~~~gP~Ti~Qg--------ALP~IL~~---Tp~efF~~~~~~lk~na~l~y~~L~~ipg~~c~~KP  350 (424)
T TIGR01265       282 RDTKVLQGLKNVLQLILGPATIVQG--------ALPDILEN---TPQEFFDKKISVLKENAELCYEELKDIPGLTCPKKP  350 (424)
T ss_pred             CCCCHHHHHHHHHCCCCCCHHHHHH--------HHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             4440338989984234781578999--------99999851---687688999999885188999997348876476488


Q ss_pred             -----------HHHHHHHCCHHHHHHHHHHHHHCCCCCCCC-CCCCCCCCCCCEEEEEC
Q ss_conf             -----------999999669799999999997338776543-22468821686699972
Q gi|254781172|r  610 -----------QAIVEFYQNPRNICAVEALLKEVSPSIGRH-EKNVSSEIENKKLVFTG  656 (731)
Q Consensus       610 -----------~si~~ff~~~~n~~~i~~L~~~~~~~~~~~-~~~~~~~l~gk~vV~TG  656 (731)
                                 -+..+-|++  ..++.++|.++=....-+- .-...+-   ..||||=
T Consensus       351 ~G~MY~mvkl~~~~~~~ikd--D~dFc~kL~~EESv~~LPG~~f~~pnw---~Rit~t~  404 (424)
T TIGR01265       351 EGSMYLMVKLELELLEEIKD--DVDFCEKLVKEESVICLPGSAFGLPNW---VRITITV  404 (424)
T ss_pred             CCCEEEHHHCCHHHCCCCCC--CHHHHHHHHHHCCCEECCCEEECCCCC---EEEEECC
T ss_conf             87500020101653446464--189999998737633546002559984---7998527


No 151
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=79.85  E-value=1.4  Score=23.78  Aligned_cols=40  Identities=33%  Similarity=0.488  Sum_probs=27.4

Q ss_pred             EEEECCCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCC
Q ss_conf             99835870256654101235787304777043265775010
Q gi|254781172|r  402 LVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVV  442 (731)
Q Consensus       402 ~I~RaGdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~  442 (731)
                      ++...|.-+| |..+++..|..+.+-...-..||-||+.-+
T Consensus       680 vl~~~~~~vP-vY~tIKrC~dcg~q~~~~~~~cP~Cgs~~v  719 (1187)
T COG1110         680 VLVKDGKYVP-VYDTIKRCRDCGEQFVDSEDKCPRCGSRNV  719 (1187)
T ss_pred             EECCCCCEEE-HHHHHHHHHHCCCEECCCCCCCCCCCCCCC
T ss_conf             5605870686-278888885158440443235988788320


No 152
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=79.85  E-value=1.3  Score=23.85  Aligned_cols=41  Identities=7%  Similarity=0.041  Sum_probs=17.3

Q ss_pred             HCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf             889999999999999999999984331779820878999999
Q gi|254781172|r   11 ALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALK   52 (731)
Q Consensus        11 ~~s~~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~   52 (731)
                      +-.+++.+++......+...++.-| ..-+.-++-.+|+.|+
T Consensus        82 d~~~e~~~e~f~~f~~~ft~~~~~~-~~~d~~~~~~~~~~ly  122 (916)
T PTZ00111         82 DNRLEELSERFTNFLKNFTEFDANS-EDKDEQQNKPANTELY  122 (916)
T ss_pred             HCCHHHHHHHHHHHHHHCCCCCCHH-HHHHHHHCCHHHHHHH
T ss_conf             4309999999999998426643012-2346542212678899


No 153
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication; InterPro: IPR010214    NusA, or N utilisation substance protein A, is a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents an acidic 50-residue region found in two copies toward the C terminus of most proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic  ; GO: 0030528 transcription regulator activity.
Probab=79.56  E-value=3.7  Score=20.40  Aligned_cols=42  Identities=17%  Similarity=0.237  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHC--CCCCCHHHHHHHHH
Q ss_conf             16899999988-299899999789776125117787613--88867899999999
Q gi|254781172|r  563 GAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIR--VPLVGDIIAQAIVE  614 (731)
Q Consensus       563 G~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~--I~GiG~~~A~si~~  614 (731)
                      .+..|+.|+.+ |.|++.+..          ..+.+|..  |+|+-+.+|+.+..
T Consensus         2 ~e~~a~~Lv~eGf~t~EdlAy----------~~~~EL~~fGIeG~~Ee~A~~L~~   46 (52)
T TIGR01954         2 DEEIAQLLVEEGFTTVEDLAY----------VPVDELLSFGIEGLDEETAKELIN   46 (52)
T ss_pred             CHHHHHHHHHHCCCHHHHHHC----------CCHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             578899999736731788750----------455668863589988788999999


No 154
>TIGR00608 radc DNA repair protein RadC; InterPro: IPR001405 RadC is a DNA repair protein found in many bacteria. They share a region of similarity at the C-terminus that contains two perfectly conserved histidine residues.; GO: 0006281 DNA repair.
Probab=79.45  E-value=4.5  Score=19.74  Aligned_cols=126  Identities=21%  Similarity=0.363  Sum_probs=65.3

Q ss_pred             HHHHHHHHHCC--CHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH-------HH----------CCHHHHHHH
Q ss_conf             89999998829--989999978977612511778761388867899999999-------96----------697999999
Q gi|254781172|r  565 EIARSLAKYYL--SYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE-------FY----------QNPRNICAV  625 (731)
Q Consensus       565 ~~Ak~La~~f~--si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~-------ff----------~~~~n~~~i  625 (731)
                      .-||.|.++|+  .++.+.       .....+.++|.+|+|||...|.++.-       ++          .+|+   ..
T Consensus        37 ~Lsk~lL~~fG~~~~d~l~-------~L~~~~~~~L~~v~GiG~ak~~qlka~~El~~R~~~~~~~~~~~i~sPe---~~  106 (223)
T TIGR00608        37 SLSKELLKQFGQEELDSLD-------LLLSAEPEELSSVPGIGLAKAIQLKAIVELAKRYAKSRMLERPVIRSPE---AA  106 (223)
T ss_pred             HHHHHHHHHHCHHCCCCHH-------HHHCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHH---HH
T ss_conf             7899999870700013001-------4321585785046885088999999999998677524421466648989---99


Q ss_pred             HHHH-HHCCCCCCCCC----CCCCCCCCCCEEEEECCCCC---CCHHHHHHHHHHCCCEEEEEEECCEEEEEE-----C-
Q ss_conf             9999-73387765432----24688216866999725889---987899999998298499811163217997-----7-
Q gi|254781172|r  626 EALL-KEVSPSIGRHE----KNVSSEIENKKLVFTGTLQK---IQRHKAQEYVTQLGAVVSAILSRKTDIIIV-----G-  691 (731)
Q Consensus       626 ~~L~-~~~~~~~~~~~----~~~~~~l~gk~vV~TGtl~~---~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~-----g-  691 (731)
                      ..++ +.......+.-    =+..+.|=-+..||.||+..   +.|+=+++.|+..          -+.+.+|     | 
T Consensus       107 ~~~l~~~l~~~~~E~F~vlfLD~~nrli~~~~~~~Gt~~~v~v~PREi~keA~k~~----------A~alI~aHNHPSGG  176 (223)
T TIGR00608       107 AEFLSTDLAHEEREHFMVLFLDLKNRLIAKEVVFIGTVNHVLVHPREIIKEALKLS----------ASALILAHNHPSGG  176 (223)
T ss_pred             HHHHHHHHCCCCCEEEEEEEECCCCCEECCEEEEEEEEEEEEECCCHHHHHHHHHC----------CCCEEEEEECCCCC
T ss_conf             99999863347642678887168541010024565412422366507877887617----------43025565375529


Q ss_pred             -C-CCC-------CHHHH-HHHCCCEEEC
Q ss_conf             -8-888-------63798-9974991737
Q gi|254781172|r  692 -D-NPG-------SKLEK-AQQLGVKIMN  710 (731)
Q Consensus       692 -e-~~g-------SKl~K-A~~LgI~Ii~  710 (731)
                       + +||       -++.+ |+=+||+++|
T Consensus       177 l~p~PS~~D~~~T~~l~~aae~l~i~lLD  205 (223)
T TIGR00608       177 LEPSPSKEDILITERLLKAAELLGIELLD  205 (223)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             89986877799999999888662862411


No 155
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=79.37  E-value=2.6  Score=21.52  Aligned_cols=27  Identities=19%  Similarity=0.244  Sum_probs=23.3

Q ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf             010111168999999882998999997
Q gi|254781172|r  557 LGIRHVGAEIARSLAKYYLSYQNFAQE  583 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~f~si~~l~~~  583 (731)
                      =||||||.++|-.|.+.|++++++.+.
T Consensus       239 ~gI~GIG~k~A~klIkk~~~ie~i~~~  265 (338)
T TIGR03674       239 EGVKGIGPKTALKLIKEHGDLEKVLKA  265 (338)
T ss_pred             CCCCCCCHHHHHHHHHHHCCHHHHHHH
T ss_conf             899985689999999985999999986


No 156
>PRK07219 DNA topoisomerase I; Validated
Probab=79.34  E-value=0.89  Score=25.20  Aligned_cols=15  Identities=13%  Similarity=0.107  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999843
Q gi|254781172|r   21 LSSLEQEISYHDDCY   35 (731)
Q Consensus        21 i~~L~~~i~~~~~~Y   35 (731)
                      +..|.+....++..|
T Consensus        91 ~~~Lk~lak~ad~Ii  105 (769)
T PRK07219         91 YQTLKNFKGKADEII  105 (769)
T ss_pred             HHHHHHHHHCCCEEE
T ss_conf             999999981699999


No 157
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=79.06  E-value=0.82  Score=25.48  Aligned_cols=23  Identities=22%  Similarity=0.628  Sum_probs=16.8

Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf             7043265775010337865445210100354
Q gi|254781172|r  430 FPSFCPICQSRVVRDLNPKTGKLVAAHRCTG  460 (731)
Q Consensus       430 ~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n  460 (731)
                      .-++||.||++|.+. +       ..++|++
T Consensus        27 L~~hCp~Cg~PLF~K-d-------G~v~CPv   49 (131)
T COG1645          27 LAKHCPKCGTPLFRK-D-------GEVFCPV   49 (131)
T ss_pred             HHHHCCCCCCCCEEE-C-------CEEECCC
T ss_conf             874486558831630-8-------9587777


No 158
>TIGR00426 TIGR00426 competence protein ComEA helix-hairpin-helix repeat region; InterPro: IPR004509   This domain is found in competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This domain represents a region of two tandem copies of a helix-hairpin-helix domain, each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to this domain..
Probab=78.60  E-value=0.85  Score=25.34  Aligned_cols=40  Identities=23%  Similarity=0.341  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHHH---CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             11116899999988---29989999978977612511778761388867899999999
Q gi|254781172|r  560 RHVGAEIARSLAKY---YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE  614 (731)
Q Consensus       560 ~~vG~~~Ak~La~~---f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~  614 (731)
                      .|||.+.|..|.++   ++.+               ...|+|.+++|||..+-+...+
T Consensus        24 ~GvG~kKAeAIv~YREe~G~F---------------~t~Edl~~V~GiG~~~~Ek~~~   66 (70)
T TIGR00426        24 SGVGAKKAEAIVAYREEYGRF---------------KTVEDLKKVSGIGEKLLEKNKA   66 (70)
T ss_pred             CCCCHHHHHHHHHHHHCCCCC---------------CCHHHHHHCCCCCHHHHHHHHH
T ss_conf             288723789998875327795---------------7622232147876245555644


No 159
>TIGR01057 topA_arch DNA topoisomerase I; InterPro: IPR005739   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.     This entry describes topoisomerase I from archaea, which is more closely related to bacterial than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils.    More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=77.93  E-value=1.1  Score=24.44  Aligned_cols=63  Identities=11%  Similarity=0.056  Sum_probs=28.8

Q ss_pred             EEECCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEE-ECCEEEEEEECCCCHHHHH
Q ss_conf             04516642570215999999999999998612467776119999415818999998-5998998886598655666
Q gi|254781172|r   88 KVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRY-EKGKFVYAALRGDGHSGED  162 (731)
Q Consensus        88 kv~H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y-~~G~L~~a~TRGdG~~GeD  162 (731)
                      ++.-..-.||-.-|.+.. |.--++|-++.-.-.  |...|++.         ++. +||.-..|...++=.+-+.
T Consensus       186 ~a~gr~v~LS~GRVQ~Pt-L~~l~eRe~EI~~F~--P~pywvi~---------~~~~~gG~~~~A~~~~~K~~~~e  249 (637)
T TIGR01057       186 AAAGRWVILSAGRVQGPT-LAFLVEREREIKKFV--PKPYWVIK---------ALLEKGGGVFKAESEKEKIWKEE  249 (637)
T ss_pred             HHHCCEEEEECCCCCCHH-HHHHHHHHHHHHCCC--CCCEEEEE---------EEEECCCCEEEEECCCCCCCHHH
T ss_conf             972998999517652079-999998899985289--98302677---------85406885587522578741246


No 160
>PRK08620 DNA topoisomerase III; Provisional
Probab=77.72  E-value=1.1  Score=24.39  Aligned_cols=51  Identities=8%  Similarity=0.031  Sum_probs=20.8

Q ss_pred             CCEEEEEEECCEEEEEECCCCCCHH---HHH-HHCCCEEECHHHHHHHHHHHCCC
Q ss_conf             9849981116321799778888637---989-97499173799999999882865
Q gi|254781172|r  674 GAVVSAILSRKTDIIIVGDNPGSKL---EKA-QQLGVKIMNEEQFLFLLQQYNTT  724 (731)
Q Consensus       674 Ggkv~sSVSkkT~~LI~ge~~gSKl---~KA-~~LgI~Ii~e~ef~~ll~~~~~~  724 (731)
                      |++..---+++--+.++.-+---|+   +|- ++-+=.=++..|-.+.+++.+..
T Consensus       655 ~~~~~~~~~~~g~~~~c~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  709 (726)
T PRK08620        655 KKKLELRGEGEGQIFVCVCGHREKLSQFQKRRKKESSGKVSKREVKKYMKKQKKE  709 (726)
T ss_pred             CCEEEEEECCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCC
T ss_conf             9856898567787899738988788889998764026888889999999873302


No 161
>PRK06398 aldose dehydrogenase; Validated
Probab=77.56  E-value=3.6  Score=20.45  Aligned_cols=16  Identities=38%  Similarity=0.310  Sum_probs=11.2

Q ss_pred             CCCCCCCEEEEECCCC
Q ss_conf             8821686699972588
Q gi|254781172|r  644 SSEIENKKLVFTGTLQ  659 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~  659 (731)
                      ++..+|.++++-|-++
T Consensus       231 as~iTG~~i~VDGG~t  246 (256)
T PRK06398        231 SSFITGTCLYVDGGLS  246 (256)
T ss_pred             HCCCCCCEEEECCCHH
T ss_conf             3383386177893932


No 162
>TIGR01209 TIGR01209 conserved hypothetical protein TIGR01209; InterPro: IPR001072 The uncharacterised protein MJ0414 from Methanococcus jannaschii belongs to a conserved family that includes proteins from other archaea and from the thermophilic bacterium Aquifex aeolicus . Nothing is known about the function of this conserved family..
Probab=76.42  E-value=5.4  Score=19.11  Aligned_cols=153  Identities=20%  Similarity=0.211  Sum_probs=90.5

Q ss_pred             CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCC--CCCCCCCCC--CCEEEEEEEEEEECHHHH
Q ss_conf             7611999941581899999859989988865986556669997753102--432233544--550489999998520212
Q gi|254781172|r  124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPT--IPRVLSLNI--PEIIEVRGEVYISKNDFL  199 (731)
Q Consensus       124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~--iP~~l~~~~--~~~ieiRGEv~m~~~~F~  199 (731)
                      ....++++.|+||..+.+.--.|.+ .++||| |.+---.|..++.+-+  +. .+-.+.  |. +.+-||+.-+.+-+-
T Consensus        78 ~~~~~~~~~~~~g~~~~~~~~~~~~-~~~~~~-g~~cp~~~~~~~~~~~g~~~-~~~~~~g~~~-~~~~~~~~g~~~p~~  153 (388)
T TIGR01209        78 KDPEVLVEEKLNGYNVRIVKLGGEL-YALTRG-GLICPFTTERLPDLLDGALS-EFLDDYGAPD-LVLCGEVVGPENPYL  153 (388)
T ss_pred             CCCCEEEEECCCCCEEEEEEECCEE-EEEECC-CEECCCCHHHHHHHHCHHHH-HHHHHHCCCC-EEEEEHHCCCCCCCC
T ss_conf             7760577421476225789863706-653137-50133204556665143577-8887508864-054200105667743


Q ss_pred             HHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHH---CCCEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf             3455643148543342345677775234555530---1110566410245433210000368999975996654148874
Q gi|254781172|r  200 ALNDEMIAVGRKPYANPRNAASGILRRLNPTDIT---RYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQAN  276 (731)
Q Consensus       200 ~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~---r~L~f~ay~~~~~~~~~~~~~~e~l~~L~~~GF~v~~~~~~~~  276 (731)
                      .                          .++..+.   ..+.|+.|++........-...+.+......|++.........
T Consensus       154 ~--------------------------~~~~~~~~g~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  207 (388)
T TIGR01209       154 P--------------------------EDPPEVKRGFEDLGFFLFDLREGNTGRPLPVEEKLELAEKYGLPHVELLGKFP  207 (388)
T ss_pred             C--------------------------CCCCHHCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHHCCCC
T ss_conf             3--------------------------45310014533220345542113567656677888776650774101110025


Q ss_pred             CCCCHHHHHHHHHHHHCCCCCCCCCEEEEECC
Q ss_conf             03211345566553100112343763777311
Q gi|254781172|r  277 TFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDE  308 (731)
Q Consensus       277 ~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~  308 (731)
                      ..++....+.++-+.  .-.-.-+|+|++-.+
T Consensus       208 ~~~~~~~~~~~~~~~--~~~~g~~g~~~~~~~  237 (388)
T TIGR01209       208 ADEEGVEELYEIVER--LNKEGREGVVLKDPE  237 (388)
T ss_pred             CCHHHHHHHHHHHHH--HHCCCCCCEEEECCH
T ss_conf             304578999999998--520344530330741


No 163
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=76.16  E-value=3.5  Score=20.61  Aligned_cols=48  Identities=13%  Similarity=0.272  Sum_probs=33.3

Q ss_pred             CCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHH
Q ss_conf             10354103555565305765404541011010677753100010001342100145689
Q gi|254781172|r  481 FNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLY  539 (731)
Q Consensus       481 ldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~  539 (731)
                      -||.|+|+...+.|-++||     .++.|+-.-      .-++|...+|.|-..|..|-
T Consensus        13 ~disgvg~~~a~~l~~ag~-----e~~~d~~~a------~q~~l~~~~gignalaarik   60 (238)
T PRK12766         13 TDISGVGPSKAESLREAGF-----ESVEDVRAA------DQSELADVDGIGNALAARIK   60 (238)
T ss_pred             HCCCCCCHHHHHHHHHCCC-----CHHHHHHHH------HHHHHHHCCCHHHHHHHHHH
T ss_conf             4123668003678887040-----128989764------27766420131389999874


No 164
>PRK01438 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=75.82  E-value=5.6  Score=19.00  Aligned_cols=14  Identities=21%  Similarity=0.290  Sum_probs=5.6

Q ss_pred             CCEEEEECCHHCCC
Q ss_conf             76377731100011
Q gi|254781172|r  300 DGLVYKVDEFSLQK  313 (731)
Q Consensus       300 DGiVikvn~~~~q~  313 (731)
                      +.+|+-.+|...++
T Consensus       226 ~~~v~n~dD~~~~~  239 (481)
T PRK01438        226 VACVYNVADPATED  239 (481)
T ss_pred             EEEEEECCCHHHHH
T ss_conf             14997057788999


No 165
>TIGR01862 N2-ase-Ialpha nitrogenase component I, alpha chain; InterPro: IPR010143   This entry represents all three varieties (Fe-Fe, Mo-Fe and V-Fe) of the component I alpha chain of nitrogenase.   Nitrogenase (1.18.6.1 from EC)  is the enzyme system responsible for biological nitrogen fixation. Nitrogenase is an oligomeric complex which consists of two components: component 2 is an homodimer of an iron-sulphur protein, while component 1 which contains the active site for the reduction of nitrogen to ammonia exists in three different forms: the molybdenum-iron containing protein (MoFe) is a hetero-tetramer consisting of two pairs of alpha (nifD) and beta (nifK) subunits; the vanadium-iron containing protein (VFe) is a hexamer of two pairs each of alpha (vnfD), beta (vnfK), and delta (vnfG) subunits; the third form seems to only contain iron and is a hexamer composed of alpha (anfD), beta (anfK), and delta (anfG) subunits. The alpha and beta chains of the three types of component 1 are evolutionary related and they are also related to proteins nifE and nifN, which are most probably involved in the iron-molybdenum cofactor biosynthesis .; GO: 0016163 nitrogenase activity, 0051536 iron-sulfur cluster binding, 0009399 nitrogen fixation.
Probab=75.80  E-value=5.6  Score=19.00  Aligned_cols=120  Identities=18%  Similarity=0.233  Sum_probs=71.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHH-HHHHHH
Q ss_conf             4568999987522346667763010111168999999882998999997897761251177876138886789-999999
Q gi|254781172|r  535 VTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDI-IAQAIV  613 (731)
Q Consensus       535 a~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~-~A~si~  613 (731)
                      -+-.++.|+..-.+.|.-+=++=++-    -.|+.|-.+|+        +            --+++++||.. ++++|.
T Consensus       237 Gdg~yd~~~~mh~A~LNlV~C~RS~n----YIa~~le~rYG--------I------------P~~~~dffG~~~~~e~LR  292 (510)
T TIGR01862       237 GDGTYDEIRLMHKAKLNLVECARSAN----YIANELEERYG--------I------------PWLKIDFFGFEYIAESLR  292 (510)
T ss_pred             CCCCHHHHHCCCCCCCCCEEECCHHH----HHHHHHHHCCC--------C------------CEEEECCCCCHHHHHHHH
T ss_conf             44222663126621101111014057----99998553078--------7------------537754657037899899


Q ss_pred             ---HHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEE-ECCCCCCCHHHHHHHHHHCCCEEEEE
Q ss_conf             ---99669799999999997338776543224688216866999-72588998789999999829849981
Q gi|254781172|r  614 ---EFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVF-TGTLQKIQRHKAQEYVTQLGAVVSAI  680 (731)
Q Consensus       614 ---~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~-TGtl~~~~R~e~~~~ie~~Ggkv~sS  680 (731)
                         .||.+++-.+--+++...-.....+.-.-=...|.||++|+ +|-..  .|--+..+.+++|=.|++.
T Consensus       293 ~I~~~Fg~~eI~~r~EevIae~~a~w~p~ld~yKerL~GK~v~ly~GG~r--~wH~~~~~~~~lG~~VV~~  361 (510)
T TIGR01862       293 AIAAFFGDSEIEKRAEEVIAEEIAKWKPELDYYKERLQGKRVCLYVGGSR--LWHWIKSLEEDLGVEVVAV  361 (510)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCEEEEECCCCC--HHHHHHHHHHHCCCEEEEE
T ss_conf             99964588542268888778744210412454113114988999758880--0111125777639459997


No 166
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=75.78  E-value=1.4  Score=23.55  Aligned_cols=20  Identities=35%  Similarity=0.557  Sum_probs=13.1

Q ss_pred             HHHCCCCCCHHHHHHHHHHH
Q ss_conf             76138886789999999996
Q gi|254781172|r  597 SLIRVPLVGDIIAQAIVEFY  616 (731)
Q Consensus       597 ~L~~I~GiG~~~A~si~~ff  616 (731)
                      +|++|+|||+++|+++.++.
T Consensus         2 ~L~~v~GIG~k~A~~ll~~~   21 (26)
T smart00278        2 ELLKVPGIGPKTAEKILEAX   21 (26)
T ss_pred             CCCCCCCCCCHHHHHHHHHH
T ss_conf             21017998811599999976


No 167
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=74.98  E-value=2.1  Score=22.32  Aligned_cols=50  Identities=22%  Similarity=0.418  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             4103555565305765404541011010677753100010001342100145689999875
Q gi|254781172|r  485 GLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKR  545 (731)
Q Consensus       485 GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~s  545 (731)
                      .|+-....-|=.++     |.++.||...+..      +|+++..||.||.+-+.+.+++.
T Consensus       278 eLSvRs~NCLKra~-----I~tvgdLv~~se~------dLl~ikNfGkKSl~EI~ekL~e~  327 (333)
T CHL00013        278 ELSVRAYNCLKRAN-----IHTLLDLLNYSQE------DLLKIKNFGQKSVKQVLDALEKR  327 (333)
T ss_pred             CCCHHHHHHHHHCC-----CCCHHHHHHCCHH------HHHCCCCCCHHHHHHHHHHHHHH
T ss_conf             18788774363738-----9379998638999------99418998630299999999886


No 168
>KOG0442 consensus
Probab=74.62  E-value=4.3  Score=19.91  Aligned_cols=52  Identities=19%  Similarity=0.152  Sum_probs=41.4

Q ss_pred             HCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCC
Q ss_conf             301011116899999988299899999789776125117787613888678999999999669
Q gi|254781172|r  556 SLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQN  618 (731)
Q Consensus       556 ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~  618 (731)
                      =|++|||-..++..+..+|+++..+...          ++++|..+=|. ...|+.|.+||+.
T Consensus       823 ll~lPgVs~~n~~~l~~k~ks~~~La~s----------S~~el~el~~~-~~~a~~LYdFi~~  874 (892)
T KOG0442         823 LLSLPGVSYINYRNLRHKFKSLKELANS----------SQEELSELLGV-HENAKLLYDFIHT  874 (892)
T ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHHHC----------CHHHHHHHHCC-HHHHHHHHHHHHH
T ss_conf             7518980088899999986679999867----------39999999665-6779999999988


No 169
>PRK09137 DNA topoisomerase I; Validated
Probab=74.61  E-value=1.6  Score=23.25  Aligned_cols=22  Identities=14%  Similarity=0.418  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999984331
Q gi|254781172|r   16 QARKELSSLEQEISYHDDCYYQ   37 (731)
Q Consensus        16 ~~~~~i~~L~~~i~~~~~~Yy~   37 (731)
                      ..++.+..|.+.++.++..|-.
T Consensus        58 ~~kk~i~~lk~l~k~ad~IilA   79 (761)
T PRK09137         58 RSKKHIDAIKKAAKDADNLYLA   79 (761)
T ss_pred             CHHHHHHHHHHHHHCCCEEEEC
T ss_conf             4789999999998389989989


No 170
>pfam02571 CbiJ Precorrin-6x reductase CbiJ/CobK. This family consists of Precorrin-6x reductase EC:1.3.1.54. This enzyme catalyses the reaction: precorrin-6Y + NADP(+) <= precorrin-6X + NADPH. CbiJ and CobK both catalyse the reduction of macocycle in the colbalmin biosynthesis pathway.
Probab=74.36  E-value=6.1  Score=18.73  Aligned_cols=53  Identities=17%  Similarity=0.353  Sum_probs=37.8

Q ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCC--C--CHHHHHHHCCCEEEC
Q ss_conf             82168669997258899878999999982984998111632179977888--8--637989974991737
Q gi|254781172|r  645 SEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNP--G--SKLEKAQQLGVKIMN  710 (731)
Q Consensus       645 ~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~--g--SKl~KA~~LgI~Ii~  710 (731)
                      +.-....+.+.|-   ||...-.+++++.+.          ++||.+++.  |  .|+.-|+++||+||-
T Consensus       164 g~~~~~iIa~~gP---fs~e~n~al~~~~~i----------~~lVtK~SG~~g~~~Ki~AA~~lgi~viv  220 (246)
T pfam02571       164 GFPNAEIIAARGP---FSLELERALLRRHGI----------DVLVTKNSGGAGTYAKLAAARELGLPVIM  220 (246)
T ss_pred             CCCHHCEEEECCC---CCHHHHHHHHHHCCC----------CEEEEECCCCHHHHHHHHHHHHCCCEEEE
T ss_conf             9980018990499---998999999997099----------99999288865069999999984992999


No 171
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease    domain [General function prediction only]
Probab=74.35  E-value=0.84  Score=25.39  Aligned_cols=17  Identities=29%  Similarity=0.696  Sum_probs=12.9

Q ss_pred             CCCCCCCCCCCCCCCCC
Q ss_conf             04326577501033786
Q gi|254781172|r  431 PSFCPICQSRVVRDLNP  447 (731)
Q Consensus       431 P~~CP~Cgs~l~~~~~~  447 (731)
                      +=+||+||++|....+.
T Consensus        25 ~ffCPaC~~~l~lK~G~   41 (342)
T COG4469          25 RFFCPACGSQLILKQGL   41 (342)
T ss_pred             CCCCCCCCCEEEEECCC
T ss_conf             40267789841453375


No 172
>PTZ00217 flap endonuclease-1; Provisional
Probab=73.76  E-value=3.3  Score=20.82  Aligned_cols=26  Identities=27%  Similarity=0.347  Sum_probs=14.1

Q ss_pred             CHHHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf             10111168999999882998999997
Q gi|254781172|r  558 GIRHVGAEIARSLAKYYLSYQNFAQE  583 (731)
Q Consensus       558 GI~~vG~~~Ak~La~~f~si~~l~~~  583 (731)
                      ||||||.++|-.|.+.|++++++.+.
T Consensus       239 ~I~GIGpk~A~klIk~~~sie~il~~  264 (394)
T PTZ00217        239 TIEGIGPKTAYELIKKYGSIEEILEH  264 (394)
T ss_pred             CCCCCCHHHHHHHHHHHCCHHHHHHH
T ss_conf             99874889999999995999999987


No 173
>TIGR00615 recR recombination protein RecR; InterPro: IPR000093 The bacterial protein recR seems to play a role in a recombinational process of DNA repair . It may act with recF and recO. RecR is a protein of about 200 amino acid residues. This protein contains a putative C4-type zinc finger in the N-terminal section.; GO: 0006281 DNA repair, 0006310 DNA recombination.
Probab=73.13  E-value=3.4  Score=20.69  Aligned_cols=35  Identities=14%  Similarity=0.329  Sum_probs=17.5

Q ss_pred             CCCCCCEEEEECCCCCCC---HH--HHHHHHHHCCCEEEE
Q ss_conf             821686699972588998---78--999999982984998
Q gi|254781172|r  645 SEIENKKLVFTGTLQKIQ---RH--KAQEYVTQLGAVVSA  679 (731)
Q Consensus       645 ~~l~gk~vV~TGtl~~~~---R~--e~~~~ie~~Ggkv~s  679 (731)
                      ..|.|+-+|.-|.++=+.   =+  .+..+++..|-++..
T Consensus       101 ~~f~G~YhVL~G~isPl~Gigp~~~~i~~L~~riGeRl~~  140 (205)
T TIGR00615       101 KEFRGRYHVLGGLISPLDGIGPEDLKIAALLKRIGERLQE  140 (205)
T ss_pred             HHHCCCEEEECCEECCCCCCCCCCCCHHHHHHHHHCCCCC
T ss_conf             4216601431564176457683221468899886000000


No 174
>TIGR00336 pyrE orotate phosphoribosyltransferase; InterPro: IPR004467 Orotate phosphoribosyl transferase (OPRTase) is involved in the biosynthesis of pyrimidine nucleotides. Alpha-D-ribosyldiphosphate 5-phosphate (PRPP) and orotate are utilised to form pyrophosphate and orotidine 5 -monophosphate (OMP) in the presence of divalent cations, preferably Mg2+. In a number of eukaryotes, this protein is fused to a domain that catalyses the reaction (4.1.1.23 from EC). The combined activity of 2.4.2.10 from EC and 4.1.1.23 from EC is termed uridine 5 -monophosphate synthase. The conserved Lys (K) residue at position 101 of the seed alignment has been proposed as the active site for the enzyme.; GO: 0004588 orotate phosphoribosyltransferase activity, 0006221 pyrimidine nucleotide biosynthetic process.
Probab=72.28  E-value=6.7  Score=18.38  Aligned_cols=66  Identities=17%  Similarity=0.161  Sum_probs=46.0

Q ss_pred             CCC-CCCCCCEEEE------ECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECH
Q ss_conf             468-8216866999------725889987899999998298499811163217997788886379899749917379
Q gi|254781172|r  642 NVS-SEIENKKLVF------TGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNE  711 (731)
Q Consensus       642 ~~~-~~l~gk~vV~------TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e  711 (731)
                      -.. ..+.|+++|+      ||+    +=-++.+.|.++||.|.+.++-=+--.......|+.-+=.++.|+++++.
T Consensus       109 i~GP~~~eG~kvvvveDV~TtG~----s~~~A~~~i~~ag~~V~~v~~~vDR~e~~~~E~~A~~~f~~~y~~~~~sl  181 (187)
T TIGR00336       109 IEGPELLEGDKVVVVEDVITTGG----SILEAVEAIQEAGGEVAGVIVIVDRQERGKGELSAGQEFEKEYGLPLISL  181 (187)
T ss_pred             EECCCCCCCCEEEEEECCCCHHH----HHHHHHHHHHHCCCEEEEEEEEEECCCCCCCCCCHHHHHHHHHCCEEEEE
T ss_conf             45676578963899951434247----99999999986188899999998267243310133455465528644323


No 175
>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=72.16  E-value=1.9  Score=22.69  Aligned_cols=24  Identities=21%  Similarity=0.515  Sum_probs=17.3

Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf             7043265775010337865445210100354
Q gi|254781172|r  430 FPSFCPICQSRVVRDLNPKTGKLVAAHRCTG  460 (731)
Q Consensus       430 ~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n  460 (731)
                      ..++||.||+++.++.+.       ..+|++
T Consensus        16 L~~~C~~Cg~pLf~~k~g-------~~~Cp~   39 (41)
T pfam06677        16 LDEHCPKCGTPLFRLKDG-------KVFCPS   39 (41)
T ss_pred             HHCCCCCCCCEEEECCCC-------CEECCC
T ss_conf             543254569830584899-------995787


No 176
>TIGR03190 benz_CoA_bzdN benzoyl-CoA reductase, bzd-type, N subunit. Members of this family are the N subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=72.14  E-value=6.8  Score=18.36  Aligned_cols=98  Identities=11%  Similarity=0.101  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEE--EEECCEEEEEECCCCCC
Q ss_conf             7999999999973387765432246882168669997258899878999999982984998--11163217997788886
Q gi|254781172|r  619 PRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSA--ILSRKTDIIIVGDNPGS  696 (731)
Q Consensus       619 ~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~s--SVSkkT~~LI~ge~~gS  696 (731)
                      .+....+.+++..+....       ...-.|+.|++||+..  ..-.+.++||.+||.|+.  +-|.-=.+.-.-+..+.
T Consensus       206 ~e~~~~l~~ll~~l~~~~-------~~~~~~~RIlvtG~~~--~~~kl~~iIEe~G~~VV~de~C~G~R~~~~~~~~~~d  276 (377)
T TIGR03190       206 REHNEMLKKVLAALPSRK-------VERKTGARFMTIGSEN--DDIAFMAMVESVGATIVIDDQCSGTRYFWNASKPEDD  276 (377)
T ss_pred             HHHHHHHHHHHHHHHCCC-------CCCCCCCEEEEECCCC--CCCHHHHHHHHCCCEEEEECCCCCCCCCCCCCCCCCC
T ss_conf             999999999999986065-------5467997799978999--9735999999869989997777751200578887777


Q ss_pred             HH-HHHHHC----CCEEEC------HHHHHHHHHHHCCCC
Q ss_conf             37-989974----991737------999999998828656
Q gi|254781172|r  697 KL-EKAQQL----GVKIMN------EEQFLFLLQQYNTTL  725 (731)
Q Consensus       697 Kl-~KA~~L----gI~Ii~------e~ef~~ll~~~~~~~  725 (731)
                      -+ .=|+.+    +-++++      -+.+.+|+++|+.+.
T Consensus       277 pl~alA~rYl~~~~C~~~~~pn~~R~~~i~~lvke~~aDG  316 (377)
T TIGR03190       277 VIKAIAERYCDRPACPTKDYPVHTRYDHVLGLAKEYNVQG  316 (377)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCE
T ss_conf             9999999982789987888880458999999999968899


No 177
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=71.68  E-value=6.9  Score=18.29  Aligned_cols=62  Identities=23%  Similarity=0.466  Sum_probs=35.3

Q ss_pred             CCCCCCCEEE--EEECCCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHH
Q ss_conf             6844076899--98358702566541012357873047770432657750103378654452101003543441144665
Q gi|254781172|r  393 RDIRVGDRVL--VKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLE  470 (731)
Q Consensus       393 ~~I~iGd~V~--I~RaGdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~  470 (731)
                      ..++|||.|.  |.+-|  =|.-++.   .++ +-.  ++-..|+-|++++++...        .++|+|   |-..-.+
T Consensus       117 d~f~~GDivrA~Vis~~--~~~~Lst---~~~-dlG--VI~A~CsrC~~~L~~~~~--------~l~Cp~---Cg~tEkR  177 (188)
T COG1096         117 DAFRIGDIVRARVISTG--DPIQLST---KGN-DLG--VIYARCSRCRAPLVKKGN--------MLKCPN---CGNTEKR  177 (188)
T ss_pred             CCCCCCCEEEEEEEECC--CCEEEEE---CCC-CCE--EEEEECCCCCCCEEECCC--------EEECCC---CCCEEEE
T ss_conf             34464617999998617--8718985---278-616--999983677762088475--------998887---7987766


Q ss_pred             HHH
Q ss_conf             533
Q gi|254781172|r  471 RLK  473 (731)
Q Consensus       471 ~i~  473 (731)
                      +|.
T Consensus       178 Kia  180 (188)
T COG1096         178 KIA  180 (188)
T ss_pred             EEC
T ss_conf             422


No 178
>pfam09511 RNA_lig_T4_1 RNA ligase. Members of this family include T4 phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. This family also includes fungal tRNA ligases that have adenylyltransferase activity. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns.
Probab=71.08  E-value=5.6  Score=19.03  Aligned_cols=56  Identities=21%  Similarity=0.406  Sum_probs=37.2

Q ss_pred             CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCC
Q ss_conf             66425702159999999999999986124677761199994158189999985998998886598
Q gi|254781172|r   92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGD  156 (731)
Q Consensus        92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGd  156 (731)
                      .+...|.+|-|+.+|... .+     +.  ......|.+.-|+||.=+.+.+.+|++ ...|||.
T Consensus        15 ~Iv~R~f~KFFN~~E~~~-t~-----~~--~l~~~p~~v~~K~dGsLi~~~~~~g~~-~~~SK~s   70 (212)
T pfam09511        15 RIVSRSYDKFFNVNEVPE-TK-----WD--DLERGPYEVYEKEDGSLIISYLDDGKL-VVCSKHS   70 (212)
T ss_pred             EEEECCCCCCEECCCCCC-CC-----CC--CCCCCCEEEEEECCCEEEEEEEECCEE-EEEECCC
T ss_conf             399877887367797645-66-----44--245788899995198899999879999-9997787


No 179
>PRK03980 flap endonuclease-1; Provisional
Probab=70.89  E-value=7.2  Score=18.16  Aligned_cols=28  Identities=18%  Similarity=0.287  Sum_probs=22.8

Q ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             0101111689999998829989999978
Q gi|254781172|r  557 LGIRHVGAEIARSLAKYYLSYQNFAQEI  584 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~f~si~~l~~~~  584 (731)
                      =|||+||.++|-.|.+.|++++++.+.+
T Consensus       192 ~gI~gIGpk~Alklikk~~~ie~il~~~  219 (295)
T PRK03980        192 PGVKGIGPKTALKLIKKHGDLEKVLEAV  219 (295)
T ss_pred             CCCCCCCHHHHHHHHHHHCCHHHHHHHC
T ss_conf             9999842999999999969999999863


No 180
>PRK08173 DNA topoisomerase III; Validated
Probab=70.71  E-value=2.5  Score=21.74  Aligned_cols=21  Identities=19%  Similarity=0.371  Sum_probs=13.2

Q ss_pred             CCCCHHHHH-----HHHHHHHHCCCC
Q ss_conf             231035410-----355556530576
Q gi|254781172|r  479 DAFNIEGLG-----KQQLDFFFKSED  499 (731)
Q Consensus       479 ~aldI~GLG-----~k~Ie~L~e~~~  499 (731)
                      ++|.=.|||     ..+|+.|++.+|
T Consensus       513 ~~lk~~GiGTpATRA~IIe~L~~r~Y  538 (857)
T PRK08173        513 EAMAAKGLGTPATRAAIIEGLLGEKY  538 (857)
T ss_pred             HHHHHCCCCCCCHHHHHHHHHHHCCC
T ss_conf             99864789985108899999975786


No 181
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=70.66  E-value=2.9  Score=21.26  Aligned_cols=52  Identities=13%  Similarity=-0.044  Sum_probs=42.4

Q ss_pred             CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCH
Q ss_conf             10111168999999882998999997897761251177876138886789999999996697
Q gi|254781172|r  558 GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNP  619 (731)
Q Consensus       558 GI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~  619 (731)
                      -||.|-...|..+...|+++..+..          ++..++..+.|+|+..|+.++++++.+
T Consensus       171 ~i~~Vnksds~~~L~d~g~L~rf~g----------aSrdE~e~l~g~g~~ka~~~ieyln~p  222 (224)
T COG5241         171 LIFIVNKSDSEDTLNDIGKLCRFNG----------ASRDEFELLLGFGFEKAAKYIEYLNLP  222 (224)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHHC----------CCHHHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf             8984446418989988878999856----------461588999700888999999985466


No 182
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=70.60  E-value=5.4  Score=19.14  Aligned_cols=61  Identities=20%  Similarity=0.452  Sum_probs=34.5

Q ss_pred             CCCCCCCEEE--EEECCCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHH
Q ss_conf             6844076899--98358702566541012357873047770432657750103378654452101003543441144665
Q gi|254781172|r  393 RDIRVGDRVL--VKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLE  470 (731)
Q Consensus       393 ~~I~iGd~V~--I~RaGdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~  470 (731)
                      .-.|+||.|.  |...||.  .-   +.-. .++--  +.-..||.||.++...++        .+.|++   |-..-.+
T Consensus       118 d~fr~gDIVrAkVis~~~~--~~---Lst~-~~eLG--Vv~A~C~~cg~~m~~~~~--------~~~Cp~---cg~~e~R  178 (187)
T PRK09521        118 DAFKIGDIVRAKVISTTDP--IQ---LSTK-GKDLG--VIKALCSRCRTPLVKKGN--------TLKCPN---CGNVETR  178 (187)
T ss_pred             HHCCCCCEEEEEEEECCCC--EE---EEEC-CCCCE--EEEEECCCCCCCEEEECC--------EEECCC---CCCEEEE
T ss_conf             5248786899999735984--69---9953-88844--999957767885867399--------999999---9998967


Q ss_pred             HH
Q ss_conf             53
Q gi|254781172|r  471 RL  472 (731)
Q Consensus       471 ~i  472 (731)
                      ++
T Consensus       179 Kv  180 (187)
T PRK09521        179 KL  180 (187)
T ss_pred             EE
T ss_conf             01


No 183
>PRK13844 recombination protein RecR; Provisional
Probab=70.49  E-value=3.7  Score=20.41  Aligned_cols=16  Identities=19%  Similarity=0.362  Sum_probs=8.8

Q ss_pred             CCCCCCCEEEEECCCC
Q ss_conf             8821686699972588
Q gi|254781172|r  644 SSEIENKKLVFTGTLQ  659 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~  659 (731)
                      ++.+.|.-+|+-|.++
T Consensus       100 s~~y~G~YhVL~G~iS  115 (200)
T PRK13844        100 AGIYRGKYFVLNGRIS  115 (200)
T ss_pred             HCCCCEEEEECCCCCC
T ss_conf             4410668887487447


No 184
>pfam01331 mRNA_cap_enzyme mRNA capping enzyme, catalytic domain. This family represents the ATP binding catalytic domain of the mRNA capping enzyme.
Probab=70.26  E-value=7.4  Score=18.06  Aligned_cols=143  Identities=16%  Similarity=0.166  Sum_probs=64.5

Q ss_pred             CEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCC--CCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf             11999941581899999859989988865986556669997753102432233--5445504899999985202123455
Q gi|254781172|r  126 IFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLS--LNIPEIIEVRGEVYISKNDFLALND  203 (731)
Q Consensus       126 ~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~--~~~~~~ieiRGEv~m~~~~F~~lN~  203 (731)
                      -.|+|..|-||+=.-|.--++. +-.+.|.+=..  .|+ ++    ..|....  ....+++ +=||+++....      
T Consensus        16 ~~Y~V~eKaDG~R~lL~i~~~~-~ylidr~~~~~--~~~-~~----~~p~~~~~~~~~~~Tl-lDGElv~d~~~------   80 (190)
T pfam01331        16 NDYYVCEKADGIRYMMLITDDG-VYLIDRDNEYF--LVE-NL----RFPLKLNKSKVHHGTL-LDGELVIDTVP------   80 (190)
T ss_pred             CCEEEEECCCCEEEEEEEECCE-EEEEECCCCEE--ECC-CC----CCCCCCCCCCCCCCEE-EEEEEEEEECC------
T ss_conf             9869988757779999995884-99997898369--813-40----0455465543014268-73589974047------


Q ss_pred             HHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHC----------CCCC---
Q ss_conf             643148543342345677775234555530111056641024543321--0000368999975----------9966---
Q gi|254781172|r  204 EMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCL----------GFPV---  268 (731)
Q Consensus       204 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~----------GF~v---  268 (731)
                           +                      -...+.|++|++....+...  ....++|..+...          ..+.   
T Consensus        81 -----~----------------------~~~~~~yl~fD~l~~~g~~v~~~~l~~Rl~~l~~~i~~~~~~~~~~~~~~~~  133 (190)
T pfam01331        81 -----G----------------------TQAKLRYLIYDIVAINGVSVSQRPFSKRLEILKKEIIKPRNANKKRSHIRYD  133 (190)
T ss_pred             -----C----------------------CCCEEEEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             -----8----------------------8741789999899999978446998999999998764245565431554346


Q ss_pred             -CCCEEEEECCCCHHHHHHHH--HHHHCCCCCCCCCEEEEECCHHC
Q ss_conf             -54148874032113455665--53100112343763777311000
Q gi|254781172|r  269 -NNGVRQANTFHGIVSYYNEM--KSIRSTLPYDIDGLVYKVDEFSL  311 (731)
Q Consensus       269 -~~~~~~~~~~~~~~~~~~~~--~~~r~~l~y~iDGiVikvn~~~~  311 (731)
                       .|.......+-.+.. .+.+  ......++|++||+++.-.+.++
T Consensus       134 ~~pf~i~~K~f~~~~~-~~~~~~~~~~~~l~h~~DGLIFTP~~~py  178 (190)
T pfam01331       134 LFPFIVRFKSFWLLSA-SEKLLSKKKIKTLSHEIDGLIFQPWDTPY  178 (190)
T ss_pred             CCCEEEEEECCHHHHH-HHHHHHHHHCCCCCCCCCEEEECCCCCCC
T ss_conf             6765999402065677-89887676348778879869989999889


No 185
>pfam08304 consensus
Probab=69.95  E-value=7.5  Score=18.02  Aligned_cols=218  Identities=17%  Similarity=0.204  Sum_probs=109.8

Q ss_pred             CCCCCCCCCCCCCCCEEECCCCCCCHHHCCCHHHHH--HHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEE-ECCEEE
Q ss_conf             962003643235775045166425702159999999--99999998612467776119999415818999998-599899
Q gi|254781172|r   73 GPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLR--KFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRY-EKGKFV  149 (731)
Q Consensus        73 spt~~Vg~~~~~~~~kv~H~~pMlSL~k~~~~~el~--~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y-~~G~L~  149 (731)
                      -||.-=|--....  +-.|.+-.-.-||-|+.+|+.  +|.. +      ......+|-++.|=-||-|=+.= ++|.|+
T Consensus        55 LPt~ARGLFt~~~--~~~~~IvvRGYDKFFNv~EV~~Tkw~~-i------~~~T~GPYeltlKENGCIIFISgL~dgtLl  125 (378)
T pfam08304        55 LPCNARGLFITND--KDNPEIVARGYDKFFNVDEVPFTKWDN-L------ENNTEGPYEVTLKENGCIIFISGLADGTLV  125 (378)
T ss_pred             CCCCCCCCEEECC--CCCCEEEEECCCCCCCCCCCCCCCHHH-H------HHCCCCCEEEEECCCCEEEEEECCCCCCEE
T ss_conf             8650342334358--999559984156654478766776788-9------735878818886057609998307999789


Q ss_pred             EEEECCCCHHH-HHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCC
Q ss_conf             88865986556-66999775310243223354455048999999852021234556431485433423456777752345
Q gi|254781172|r  150 YAALRGDGHSG-EDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLN  228 (731)
Q Consensus       150 ~a~TRGdG~~G-eDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d  228 (731)
                      --+----|..+ .+.+|....=.-+-.+|...        |   .+..++.+          .++  .+|+.|=+=-..|
T Consensus       126 VcSKHStG~r~d~~~sHA~aGe~~l~~~l~~~--------g---kt~~dLA~----------~L~--~~N~TAVaElCDD  182 (378)
T pfam08304       126 VCSKHSTGPRDDVDRNHAEAGEQFLEQQLAEI--------G---KSKKDLAR----------ELY--ENNVTAVAEYCDD  182 (378)
T ss_pred             EECCCCCCCCCCCCCHHHHHHHHHHHHHHHHC--------C---CCHHHHHH----------HHH--HCCHHHHHHHCCC
T ss_conf             96377688888754038999999999999980--------9---98999999----------999--7371466776075


Q ss_pred             H-HH----HH-CCCEEEEEEECCC-CCCCCCCCHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             5-55----30-1110566410245-4332100003689999759966541488740321134556655310011234376
Q gi|254781172|r  229 P-TD----IT-RYLNFFVHGLGKT-SEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDG  301 (731)
Q Consensus       229 ~-~~----~~-r~L~f~ay~~~~~-~~~~~~~~~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDG  301 (731)
                      . .+    .. ..-..+.+|+-.. .....-...+.-++-.+|||.-..+ ...++++++.++.++..+.-.--.=+|.|
T Consensus       183 ~FEEHVL~Y~~~~aGLyLHGlN~N~p~F~T~p~~~V~~FA~ewGFk~~~~-~~~d~i~~vk~Fle~caeTGt~~GreiEG  261 (378)
T pfam08304       183 SFEEHILPYPKDKAGLYLHGLNYNTIEFKTYPMPKVSQFAEEWGFKKVDY-FTKNDIEELKKFLEECSETGTYNGQEVEG  261 (378)
T ss_pred             CHHHHHCCCCHHHCCEEEECCCCCCCCEEECCHHHHHHHHHHHCCEEEEE-EEECCHHHHHHHHHHHHHCCCCCCEECCE
T ss_conf             17765347890104234301356877625278899999999838805558-87278999999998665328657863121


Q ss_pred             EEEEECCHHCCCCCCCCCCCCCCEEEECCCC
Q ss_conf             3777311000111587656866312311456
Q gi|254781172|r  302 LVYKVDEFSLQKQLGERARSPRWMISHKFAE  332 (731)
Q Consensus       302 iVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~  332 (731)
                      .||+....       ..  .--|=+-|||..
T Consensus       262 FVIRc~~~-------~~--g~d~FFKyKFeE  283 (378)
T pfam08304       262 FVIRCKMK-------SD--GDDFFFKYKFEE  283 (378)
T ss_pred             EEEEEECC-------CC--CCCCEEEECCCC
T ss_conf             69987438-------88--876436762577


No 186
>PRK00076 recR recombination protein RecR; Reviewed
Probab=69.88  E-value=3.8  Score=20.30  Aligned_cols=16  Identities=25%  Similarity=0.279  Sum_probs=9.3

Q ss_pred             CCCCCCCEEEEECCCC
Q ss_conf             8821686699972588
Q gi|254781172|r  644 SSEIENKKLVFTGTLQ  659 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~  659 (731)
                      ++.+.|.-+|+-|.++
T Consensus        96 s~~y~G~YhVLgG~lS  111 (197)
T PRK00076         96 TGEYRGLYHVLGGLLS  111 (197)
T ss_pred             CCCEEEEEEECCCCCC
T ss_conf             7945478358566248


No 187
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=69.77  E-value=3.7  Score=20.38  Aligned_cols=50  Identities=10%  Similarity=0.206  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             5410355556530576540454101101067775310001000134210014568999987
Q gi|254781172|r  484 EGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINK  544 (731)
Q Consensus       484 ~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~  544 (731)
                      -.|+-+...-|=.++     |.++.||...+..      +|+++..||.||.+-+.+.++.
T Consensus       250 LeLSvRs~NcLk~a~-----I~tI~dLv~~se~------dLl~ikNfGkKSl~EI~~kL~~  299 (306)
T PRK05182        250 LELSVRSYNCLKRAG-----INTIGDLVQRTEE------ELLKTPNLGKKSLEEIKEKLAE  299 (306)
T ss_pred             HCCCHHHHHHHHHCC-----CCCHHHHHHCCHH------HHHHCCCCCCCCHHHHHHHHHH
T ss_conf             138688875587859-----9369998747999------9961899762039999999997


No 188
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=69.52  E-value=3.9  Score=20.20  Aligned_cols=60  Identities=18%  Similarity=0.394  Sum_probs=34.7

Q ss_pred             CCEEEEEECCCCHHHHHHHCCCCCCCCCCEEEEC--CCCCCCCCCCCCCCCCC---------CCCCCEEECCCC
Q ss_conf             7689998358702566541012357873047770--43265775010337865---------445210100354
Q gi|254781172|r  398 GDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFP--SFCPICQSRVVRDLNPK---------TGKLVAAHRCTG  460 (731)
Q Consensus       398 Gd~V~I~RaGdVIP~I~~Vi~~~r~~~~~~~~~P--~~CP~Cgs~l~~~~~~~---------~~~~~~~~rC~n  460 (731)
                      |-....+++.++.=++..++.....   .+...|  +.||.||++|+...-+.         .......++|++
T Consensus        65 g~~~i~i~~~s~~~Ql~e~~~~~~l---~~~~~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~  135 (165)
T COG1656          65 GIKAILIRSDSIEEQLAEFLARLGL---KPRLFPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPK  135 (165)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHCC---CHHCCCCCCCCCCCCCEECCCCHHHHHHCCCHHHHHCCCCEEECCC
T ss_conf             6732897179879999999998352---2001601032743497801076777752065244202001467799


No 189
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=69.26  E-value=7.8  Score=17.91  Aligned_cols=23  Identities=17%  Similarity=0.213  Sum_probs=19.3

Q ss_pred             CCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             17787613888678999999999
Q gi|254781172|r  593 DDWLSLIRVPLVGDIIAQAIVEF  615 (731)
Q Consensus       593 ~~~e~L~~I~GiG~~~A~si~~f  615 (731)
                      .-++.|+.|+|||+.+|+.+.=|
T Consensus       195 ~a~e~L~~i~GIG~WTAe~~llf  217 (285)
T COG0122         195 EAIEELTALKGIGPWTAEMFLLF  217 (285)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             99999873788679999999998


No 190
>pfam03811 Ins_element1 Insertion element protein.
Probab=69.23  E-value=3.5  Score=20.58  Aligned_cols=65  Identities=23%  Similarity=0.310  Sum_probs=36.4

Q ss_pred             CCCCCCCC-C-CCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHH
Q ss_conf             43265775-0-103378654452101003543441144665533213012310354103555565305765404541011
Q gi|254781172|r  432 SFCPICQS-R-VVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPAD  509 (731)
Q Consensus       432 ~~CP~Cgs-~-l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~D  509 (731)
                      -+||.|++ + +.+..-...  ...-.+|.   +|.-+++....|=+.+     .|+-+++++--++.   + -|++++-
T Consensus         6 v~Cp~C~s~~~V~KnG~~~~--G~QRYrC~---~C~r~Fql~ytY~a~~-----p~vkeqiv~m~~nG---~-GiRdtaR   71 (88)
T pfam03811         6 IHCPRCSSTEGVYRHGQSTA--GHQRYRCR---HCRRTFQLTYTYEARQ-----PGTKEQIVDMAMNG---A-GCRYTAR   71 (88)
T ss_pred             EECCCCCCCCCEEECCCCCC--CCCCEEEC---CCCCEEEEEECCCCCC-----CCHHHHHHHHHHCC---C-CHHHHHH
T ss_conf             47978889876771896899--98577727---7895566630114658-----14789999997679---8-5404478


Q ss_pred             H
Q ss_conf             0
Q gi|254781172|r  510 I  510 (731)
Q Consensus       510 L  510 (731)
                      +
T Consensus        72 v   72 (88)
T pfam03811        72 T   72 (88)
T ss_pred             H
T ss_conf             7


No 191
>pfam04551 GcpE GcpE protein. In a variety of organisms, including plants and several eubacteria, isoprenoids are synthesized by the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Although different enzymes of this pathway have been described, the terminal biosynthetic steps of the MEP pathway have not been fully elucidated. GcpE gene of Escherichia coli is involved in this pathway.
Probab=68.43  E-value=5.2  Score=19.28  Aligned_cols=42  Identities=21%  Similarity=0.404  Sum_probs=25.1

Q ss_pred             CCCCCEEEEEECCCCHHHHH---HHCC--CCCCCCCCEEEECCCCCCCCCC
Q ss_conf             44076899983587025665---4101--2357873047770432657750
Q gi|254781172|r  395 IRVGDRVLVKRAGEVIPKVV---DIIV--NERHPDAQPFSFPSFCPICQSR  440 (731)
Q Consensus       395 I~iGd~V~I~RaGdVIP~I~---~Vi~--~~r~~~~~~~~~P~~CP~Cgs~  440 (731)
                      =||||++.|+-++|-.-+|.   ..+.  ..|...   .. --.||.||-.
T Consensus       219 ~GIGDTIRVSLt~dP~~EV~v~~~IL~sl~lR~~g---~~-iISCPtCGR~  265 (345)
T pfam04551       219 EGIGDTIRVSLTEDPVEEVKVAFEILQSLGLRKRG---VE-IISCPTCGRT  265 (345)
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCC---CE-EEECCCCCCC
T ss_conf             18865399967899547899999999972877578---64-8758874661


No 192
>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=68.42  E-value=2  Score=22.39  Aligned_cols=29  Identities=24%  Similarity=0.335  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf             999999999984331779820878999999
Q gi|254781172|r   23 SLEQEISYHDDCYYQYSKPIILDSEYDALK   52 (731)
Q Consensus        23 ~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~   52 (731)
                      .|=+.+....--||- ..|.|.=..++.-.
T Consensus       419 nLykLvS~s~~~Yfy-~~Pri~~s~L~~~~  447 (1264)
T TIGR01405       419 NLYKLVSISLTKYFY-TRPRILRSLLKKYR  447 (1264)
T ss_pred             HHHHHHHHHHHHHHC-CCCCCCHHHHHHHC
T ss_conf             899998799865314-68975178898643


No 193
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=68.39  E-value=5.5  Score=19.10  Aligned_cols=12  Identities=17%  Similarity=0.266  Sum_probs=5.0

Q ss_pred             HHHHHHHCCCCC
Q ss_conf             689999759966
Q gi|254781172|r  257 MLQKMRCLGFPV  268 (731)
Q Consensus       257 ~l~~L~~~GF~v  268 (731)
                      ....|++.|..|
T Consensus       219 q~~~L~~~GI~T  230 (457)
T TIGR03491       219 RYRLLQELGIHT  230 (457)
T ss_pred             HHHHHHHCCCCC
T ss_conf             999999859987


No 194
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=68.22  E-value=8.1  Score=17.76  Aligned_cols=50  Identities=18%  Similarity=0.391  Sum_probs=36.7

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCC--C--CHHHHHHHCCCEEEC
Q ss_conf             68669997258899878999999982984998111632179977888--8--637989974991737
Q gi|254781172|r  648 ENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNP--G--SKLEKAQQLGVKIMN  710 (731)
Q Consensus       648 ~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~--g--SKl~KA~~LgI~Ii~  710 (731)
                      ....+.+.|-   ||.+.-.++++..|.          ++||.+++.  |  .|+.-|+++|||||-
T Consensus       165 ~~~iia~~gP---fs~e~e~al~~~~~i----------~~lVtK~SG~~g~~~Ki~AA~~lgi~vi~  218 (241)
T PRK08057        165 RAEIIAARGP---FSLELERALLRQHRI----------DVVVTKNSGGAGTEAKLDAARELGIPVVM  218 (241)
T ss_pred             HHCEEEECCC---CCHHHHHHHHHHHCC----------CEEEEECCCCHHHHHHHHHHHHCCCEEEE
T ss_conf             3208995599---999999999997099----------99999388865069999999984991999


No 195
>PRK09401 reverse gyrase; Reviewed
Probab=68.01  E-value=2.3  Score=22.05  Aligned_cols=45  Identities=24%  Similarity=0.315  Sum_probs=27.9

Q ss_pred             CCEEEEEECCCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf             7689998358702566541012357873047770432657750103
Q gi|254781172|r  398 GDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVR  443 (731)
Q Consensus       398 Gd~V~I~RaGdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~  443 (731)
                      |-+=+...-|.+|| |...++..|.-..+=......||-||+..+.
T Consensus       659 g~~GV~~~~~~fiP-vY~~IkrC~~cg~qft~~~~~cP~Cgs~~i~  703 (1176)
T PRK09401        659 GYYGVLVGNGKFVP-VYNSIKRCRDCGHQFTDESDRCPRCGSTNID  703 (1176)
T ss_pred             CCEEEEEECCEEEE-EEHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
T ss_conf             62269963780898-4166767753586012466668877888756


No 196
>KOG3123 consensus
Probab=67.97  E-value=4.6  Score=19.68  Aligned_cols=11  Identities=9%  Similarity=0.326  Sum_probs=4.7

Q ss_pred             HHHHHHHCCCC
Q ss_conf             68999975996
Q gi|254781172|r  257 MLQKMRCLGFP  267 (731)
Q Consensus       257 ~l~~L~~~GF~  267 (731)
                      .+..|....|.
T Consensus       233 t~~~l~~~d~G  243 (272)
T KOG3123         233 TIKDLAEVDFG  243 (272)
T ss_pred             EHHHHHHCCCC
T ss_conf             18767635247


No 197
>PTZ00035 Rad51; Provisional
Probab=67.70  E-value=4.7  Score=19.62  Aligned_cols=16  Identities=19%  Similarity=0.281  Sum_probs=5.7

Q ss_pred             CCCCCCCCCCHHHHHH
Q ss_conf             0001342100145689
Q gi|254781172|r  524 IENILGFGDVSVTNLY  539 (731)
Q Consensus       524 l~~l~GfgeKsa~nL~  539 (731)
                      |..+.|++|..|+||+
T Consensus        70 L~~ikgise~k~~Ki~   85 (350)
T PTZ00035         70 LCAIKGISEQKAEKLK   85 (350)
T ss_pred             HHHCCCCCHHHHHHHH
T ss_conf             9773794699999999


No 198
>PRK03369 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=67.57  E-value=8.3  Score=17.67  Aligned_cols=15  Identities=13%  Similarity=-0.039  Sum_probs=7.3

Q ss_pred             CCEEEEECCHHCCCC
Q ss_conf             763777311000111
Q gi|254781172|r  300 DGLVYKVDEFSLQKQ  314 (731)
Q Consensus       300 DGiVikvn~~~~q~~  314 (731)
                      +-.|+-.||...+..
T Consensus       217 ~~~v~n~DD~~~~~l  231 (487)
T PRK03369        217 RVAVAGLDDSRAAAL  231 (487)
T ss_pred             CEEEEECCCHHHHHH
T ss_conf             879996876889999


No 199
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=67.51  E-value=8.4  Score=17.66  Aligned_cols=32  Identities=25%  Similarity=0.427  Sum_probs=17.9

Q ss_pred             CHHHHHHHHH--HCCCEEEEEEECCE-----EEEEECCC
Q ss_conf             8789999999--82984998111632-----17997788
Q gi|254781172|r  662 QRHKAQEYVT--QLGAVVSAILSRKT-----DIIIVGDN  693 (731)
Q Consensus       662 ~R~e~~~~ie--~~Ggkv~sSVSkkT-----~~LI~ge~  693 (731)
                      .|.|-....|  +.|--|..=|-.++     ||.|=|.+
T Consensus       165 p~~e~iAv~EA~klgIPVvAlvDTn~dpd~VD~~IP~Nd  203 (252)
T COG0052         165 PRKEKIAVKEANKLGIPVVALVDTNCDPDGVDYVIPGND  203 (252)
T ss_pred             CCHHHHHHHHHHHCCCCEEEEECCCCCCCCCCEEECCCC
T ss_conf             817689999999759998998418999765765522887


No 200
>PRK08938 DNA topoisomerase I; Validated
Probab=67.47  E-value=2.9  Score=21.20  Aligned_cols=20  Identities=25%  Similarity=0.381  Sum_probs=11.4

Q ss_pred             CCCCHHHHH-----HHHHHHHHCCC
Q ss_conf             231035410-----35555653057
Q gi|254781172|r  479 DAFNIEGLG-----KQQLDFFFKSE  498 (731)
Q Consensus       479 ~aldI~GLG-----~k~Ie~L~e~~  498 (731)
                      ++|.=.|+|     ..+|+.|++.+
T Consensus       468 k~ME~~GIGrpsT~A~II~~L~~R~  492 (692)
T PRK08938        468 KTLEENGIGRPSTYAPTLDTIQKRY  492 (692)
T ss_pred             HHHHHCCCCCCCCHHHHHHHHHHCC
T ss_conf             9998579997165899999998568


No 201
>TIGR02770 nickel_nikD nickel import ATP-binding protein NikD; InterPro: IPR014138   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are related families..
Probab=66.53  E-value=8.7  Score=17.52  Aligned_cols=75  Identities=25%  Similarity=0.445  Sum_probs=41.1

Q ss_pred             CCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHH--HHHHHHCCC-
Q ss_conf             58189999985998998886598655666999775310243223354455048999999852021234--556431485-
Q gi|254781172|r  134 IDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLAL--NDEMIAVGR-  210 (731)
Q Consensus       134 iDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~l--N~~~~~~g~-  210 (731)
                      ++|++++|  +.|+- -|+==..| -|.=+|..+-        |+.-.|+..++||||++.=.+...+  .+.+.-.|. 
T Consensus         2 V~~~~L~l--k~G~~-~aLvG~SG-SGKS~tc~A~--------Lg~L~~~~~~~~G~i~l~G~~~~~~p~kemr~~Rg~~   69 (239)
T TIGR02770         2 VQDVNLSL--KRGEV-LALVGESG-SGKSLTCLAI--------LGLLPPGLTQTSGEILLDGRPLLALPKKEMRSIRGRH   69 (239)
T ss_pred             CCCCCCEE--ECCEE-EEEECCCC-CCHHHHHHHH--------HCCCCCCCEEEEEEEEECCCCCCCCCHHHHHHHHHHH
T ss_conf             41675203--32437-88874878-7589999998--------5035865223102667717231458736899886666


Q ss_pred             --CCCCCHHHHH
Q ss_conf             --4334234567
Q gi|254781172|r  211 --KPYANPRNAA  220 (731)
Q Consensus       211 --~~f~NpRN~a  220 (731)
                        -.+-|||++=
T Consensus        70 ~~~imQnPr~AF   81 (239)
T TIGR02770        70 IATIMQNPRTAF   81 (239)
T ss_pred             HHHHCCCCCCCC
T ss_conf             301102850000


No 202
>pfam02371 Transposase_20 Transposase IS116/IS110/IS902 family. Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. This region is often found with pfam01548. The exact function of this region is uncertain. This family contains a HHH motif suggesting a DNA-binding function.
Probab=66.19  E-value=7.6  Score=18.00  Aligned_cols=39  Identities=18%  Similarity=0.216  Sum_probs=27.8

Q ss_pred             HHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCC
Q ss_conf             761388867899999999966979999999999733877
Q gi|254781172|r  597 SLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPS  635 (731)
Q Consensus       597 ~L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~~  635 (731)
                      -|+.|+|||+.+|..|+..+.+........++....+..
T Consensus         3 ~L~sipGiG~~~a~~l~aeigd~~rF~~~~~~~s~~Gl~   41 (87)
T pfam02371         3 LLLSIPGIGPITAAALLAEIGDISRFKSARQLAAYAGLA   41 (87)
T ss_pred             HHHCCCCCCHHHHHHHHHHHCCHHHCCCHHHHHHHCCCC
T ss_conf             342699952999999999929853278999999983999


No 203
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=66.10  E-value=2.8  Score=21.35  Aligned_cols=19  Identities=11%  Similarity=0.022  Sum_probs=9.0

Q ss_pred             EECHHHHHHHHHHHCCCCC
Q ss_conf             7379999999988286568
Q gi|254781172|r  708 IMNEEQFLFLLQQYNTTLR  726 (731)
Q Consensus       708 Ii~e~ef~~ll~~~~~~~~  726 (731)
                      -+++.+....|........
T Consensus       652 g~~~~~~e~~l~~l~~~g~  670 (682)
T COG1241         652 GISEKEVEEALEKLKKKGD  670 (682)
T ss_pred             CCCHHHHHHHHHHHHHCCC
T ss_conf             7888999999999975694


No 204
>pfam09151 DUF1936 Domain of unknown function (DUF1936). This domain is found in a set of hypothetical Archaeal proteins. Its exact function has not, as yet, been defined. It possesses a zinc ribbon fold.
Probab=65.82  E-value=3.4  Score=20.70  Aligned_cols=31  Identities=32%  Similarity=0.785  Sum_probs=18.9

Q ss_pred             CCCCCCCCCC-CCCCCCCCCCCEEECCCCCCCCHH
Q ss_conf             3265775010-337865445210100354344114
Q gi|254781172|r  433 FCPICQSRVV-RDLNPKTGKLVAAHRCTGGLACSA  466 (731)
Q Consensus       433 ~CP~Cgs~l~-~~~~~~~~~~~~~~rC~n~~~Cpa  466 (731)
                      .||-||-.+. ...+++ ++ ..+.||+|+ .|..
T Consensus         3 lcpkcgvgvlepvydek-ge-ikvfrcsnp-acdy   34 (36)
T pfam09151         3 LCPKCGVGVLEPVYDEK-GE-IKVFRCSNP-ACDY   34 (36)
T ss_pred             CCCCCCCCCEEEECCCC-CC-EEEEECCCC-CCCC
T ss_conf             47745611003200577-73-889972797-6665


No 205
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=65.23  E-value=6.2  Score=18.64  Aligned_cols=77  Identities=18%  Similarity=0.295  Sum_probs=40.4

Q ss_pred             CCCCCEEEEEECCCCHHHHH---HHCC--CCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHH
Q ss_conf             44076899983587025665---4101--235787304777043265775010337865445210100354344114466
Q gi|254781172|r  395 IRVGDRVLVKRAGEVIPKVV---DIIV--NERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQL  469 (731)
Q Consensus       395 I~iGd~V~I~RaGdVIP~I~---~Vi~--~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~  469 (731)
                      =||||++.|+-++|=.-+|.   +.+.  ..|+..    ..--.||.||-...            +++     .--.|..
T Consensus       224 eGIGDTIRVSLt~~P~~EV~V~~eILqslglR~~~----v~~iaCP~CGR~~~------------dv~-----~~~~~~~  282 (361)
T COG0821         224 EGIGDTIRVSLTADPVEEVKVAQEILQSLGLRSRG----VEVIACPTCGRTEF------------DVI-----QTLNEVE  282 (361)
T ss_pred             HCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCC----CEEEECCCCCCEEE------------HHH-----HHHHHHH
T ss_conf             25776599965888325579999999980866358----66998998776225------------699-----9999999


Q ss_pred             HHHHHHHHCCCCCH-------HHHHHHHHHHH
Q ss_conf             55332130123103-------54103555565
Q gi|254781172|r  470 ERLKHFVSRDAFNI-------EGLGKQQLDFF  494 (731)
Q Consensus       470 ~~i~hF~SK~aldI-------~GLG~k~Ie~L  494 (731)
                      +++.|--  .-|+|       .|.||.....+
T Consensus       283 ~~~~~~~--~pl~VAVMGCVVNGPGEak~Adi  312 (361)
T COG0821         283 QRLEHLK--TPLKVAVMGCVVNGPGEAKHADI  312 (361)
T ss_pred             HHHHCCC--CCCEEEEEEEEECCCCCCCCCCE
T ss_conf             9864468--77349999757407850001652


No 206
>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=64.95  E-value=5.8  Score=18.88  Aligned_cols=40  Identities=13%  Similarity=-0.025  Sum_probs=23.9

Q ss_pred             EECCCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCC
Q ss_conf             83587025665410123578730477704326577501033
Q gi|254781172|r  404 KRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRD  444 (731)
Q Consensus       404 ~RaGdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~  444 (731)
                      .++.|+-=++.+|+..-.-.- ..-.+.+.||.||++++..
T Consensus        64 l~~~~~~~Ql~ev~~~~~l~~-~~~~~~sRC~~CN~~L~~v  103 (146)
T pfam01927        64 VRSLDPEEQLREVIERFGLKL-SLKPEFSRCLKCNGPLEPV  103 (146)
T ss_pred             ECCCCHHHHHHHHHHHCCCCC-CCCCCCCCCCCCCCCCEEC
T ss_conf             789999999999999669974-3377778565679899581


No 207
>COG4468 GalT Galactose-1-phosphate uridyltransferase [Carbohydrate transport and metabolism]
Probab=64.89  E-value=7  Score=18.24  Aligned_cols=12  Identities=25%  Similarity=0.202  Sum_probs=8.3

Q ss_pred             HHCCCCCCCCEE
Q ss_conf             975996654148
Q gi|254781172|r  262 RCLGFPVNNGVR  273 (731)
Q Consensus       262 ~~~GF~v~~~~~  273 (731)
                      ..|||.-.||..
T Consensus       207 e~W~fQySPY~Y  218 (503)
T COG4468         207 EQWGFQYSPYVY  218 (503)
T ss_pred             CEEEEEECCCEE
T ss_conf             355676166215


No 208
>PRK02472 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=64.71  E-value=9.4  Score=17.28  Aligned_cols=10  Identities=20%  Similarity=0.152  Sum_probs=4.0

Q ss_pred             HHHHHHHCCC
Q ss_conf             9999998298
Q gi|254781172|r  666 AQEYVTQLGA  675 (731)
Q Consensus       666 ~~~~ie~~Gg  675 (731)
                      .++++.++.|
T Consensus       440 F~~~V~~L~g  449 (450)
T PRK02472        440 FIDAVHELKG  449 (450)
T ss_pred             HHHHHHHCCC
T ss_conf             9999997479


No 209
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=64.69  E-value=6.5  Score=18.50  Aligned_cols=42  Identities=21%  Similarity=0.389  Sum_probs=24.2

Q ss_pred             CCCCCEEEEEECCCCHHHHH---HHCC--CCCCCCCCEEEECCCCCCCCCC
Q ss_conf             44076899983587025665---4101--2357873047770432657750
Q gi|254781172|r  395 IRVGDRVLVKRAGEVIPKVV---DIIV--NERHPDAQPFSFPSFCPICQSR  440 (731)
Q Consensus       395 I~iGd~V~I~RaGdVIP~I~---~Vi~--~~r~~~~~~~~~P~~CP~Cgs~  440 (731)
                      =||||++.|+-++|-.-+|.   +.+.  ..|...   .. --.||.||-.
T Consensus       230 ~GIGDTIRVSLT~dPv~EV~va~~IL~slglR~~g---~~-iISCPtCGRt  276 (367)
T PRK00366        230 EGIGDTIRVSLTADPVEEVKVGQEILQSLGLRSRG---PN-VISCPTCGRT  276 (367)
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCC---CE-EEECCCCCCC
T ss_conf             59964289856888177999999999972866368---51-7658875553


No 210
>KOG3084 consensus
Probab=64.65  E-value=3.2  Score=20.92  Aligned_cols=29  Identities=24%  Similarity=0.592  Sum_probs=19.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHH
Q ss_conf             043265775010337865445210100354344114
Q gi|254781172|r  431 PSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSA  466 (731)
Q Consensus       431 P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpa  466 (731)
                      -.+||.||+++..++....      .-|.+. .||.
T Consensus       150 ykFCp~CG~~tkp~e~g~k------~~Cs~~-~C~~  178 (345)
T KOG3084         150 YKFCPGCGSPTKPEEAGTK------LQCSDE-TCPS  178 (345)
T ss_pred             HCCCCCCCCCCCCCCCCCC------CEEECC-CCCC
T ss_conf             3107566898643568853------230014-4884


No 211
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=63.51  E-value=3.4  Score=20.67  Aligned_cols=22  Identities=18%  Similarity=0.276  Sum_probs=12.0

Q ss_pred             HHHHHHHHCCHHHHHHHHHHHHH
Q ss_conf             46667763010111168999999
Q gi|254781172|r  549 SLERFIFSLGIRHVGAEIARSLA  571 (731)
Q Consensus       549 ~L~r~L~ALGI~~vG~~~Ak~La  571 (731)
                      .|...|..||||+ |...|..++
T Consensus       553 GLAD~Li~LGi~Y-gSeEA~~la  574 (857)
T PRK08115        553 GLHDLLIYCEKKY-GSEEGNKLV  574 (857)
T ss_pred             HHHHHHHHCCCCC-CCHHHHHHH
T ss_conf             0999999839986-999999999


No 212
>PRK09536 btuD corrinoid ABC transporter ATPase; Reviewed
Probab=62.74  E-value=9  Score=17.43  Aligned_cols=30  Identities=20%  Similarity=0.367  Sum_probs=23.9

Q ss_pred             CCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCH
Q ss_conf             6400010148989997502345432224684407689998358702
Q gi|254781172|r  365 GALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVI  410 (731)
Q Consensus       365 G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVI  410 (731)
                      |.||= .++|+.+...++               -|+|.+.+.|.|+
T Consensus       188 G~TVI-~vtHDL~lA~~~---------------cDrVivl~~GrIv  217 (409)
T PRK09536        188 GKTVV-AAIHDLNLAARY---------------CDELVLLADGRVH  217 (409)
T ss_pred             CCEEE-EEECCHHHHHHH---------------CCEEEEEECCEEE
T ss_conf             99999-995689999986---------------9999999899899


No 213
>PRK06196 oxidoreductase; Provisional
Probab=62.38  E-value=8.3  Score=17.67  Aligned_cols=14  Identities=14%  Similarity=0.143  Sum_probs=6.3

Q ss_pred             EECCCCHHHHHHHH
Q ss_conf             86598655666999
Q gi|254781172|r  152 ALRGDGHSGEDVSA  165 (731)
Q Consensus       152 ~TRGdG~~GeDVT~  165 (731)
                      +|=|+.-+|--...
T Consensus        31 ITGa~sGIG~~tA~   44 (316)
T PRK06196         31 VTGGYSGLGLETTR   44 (316)
T ss_pred             ECCCCCHHHHHHHH
T ss_conf             91799679999999


No 214
>PRK12481 2-deoxy-D-gluconate 3-dehydrogenase; Provisional
Probab=62.33  E-value=10  Score=16.97  Aligned_cols=14  Identities=21%  Similarity=0.266  Sum_probs=9.4

Q ss_pred             CCCCCCCEEEEECC
Q ss_conf             88216866999725
Q gi|254781172|r  644 SSEIENKKLVFTGT  657 (731)
Q Consensus       644 ~~~l~gk~vV~TGt  657 (731)
                      ++..+|.++++.|-
T Consensus       234 a~~iTG~~i~VDGG  247 (251)
T PRK12481        234 SDYVTGYTLAVDGG  247 (251)
T ss_pred             HCCCCCCEEEECCC
T ss_conf             35904855897846


No 215
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=62.24  E-value=2.9  Score=21.25  Aligned_cols=14  Identities=50%  Similarity=1.120  Sum_probs=10.6

Q ss_pred             CCCCCCCCCCCCCC
Q ss_conf             04326577501033
Q gi|254781172|r  431 PSFCPICQSRVVRD  444 (731)
Q Consensus       431 P~~CP~Cgs~l~~~  444 (731)
                      -+.||+||+++.+.
T Consensus       153 ~~~Cp~CG~~~~~~  166 (177)
T COG1439         153 KDFCPICGSPLKRK  166 (177)
T ss_pred             CCCCCCCCCCEEEE
T ss_conf             88077899911785


No 216
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=61.15  E-value=7.8  Score=17.90  Aligned_cols=17  Identities=24%  Similarity=0.309  Sum_probs=8.5

Q ss_pred             CCCCCCEEEEECCCCCC
Q ss_conf             82168669997258899
Q gi|254781172|r  645 SEIENKKLVFTGTLQKI  661 (731)
Q Consensus       645 ~~l~gk~vV~TGtl~~~  661 (731)
                      +.+.|.-+|.-|.++-+
T Consensus        98 ~~f~G~YhVL~G~lspl  114 (198)
T COG0353          98 GEFRGLYHVLGGLLSPL  114 (198)
T ss_pred             CCCCEEEEEECCCCCCC
T ss_conf             52572788845733734


No 217
>TIGR02707 butyr_kinase butyrate kinase; InterPro: IPR011245   This group represents bacterial butyrate kinase, an enzyme that facilitates the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl phosphate . The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-CoA:acetate CoA-transferase, the latter providing the dominant route for butyrate formation in human colonic bacteria .; GO: 0005524 ATP binding, 0047761 butyrate kinase activity, 0016310 phosphorylation, 0005737 cytoplasm.
Probab=61.03  E-value=4  Score=20.11  Aligned_cols=76  Identities=24%  Similarity=0.309  Sum_probs=47.0

Q ss_pred             HHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCC----CCCCCCCCCEEEECCCC
Q ss_conf             68999975996654148874032113455665531001123437637773110001115----87656866312311456
Q gi|254781172|r  257 MLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQL----GERARSPRWMISHKFAE  332 (731)
Q Consensus       257 ~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~l----G~ts~~PrwaiA~Kf~~  332 (731)
                      .+++|++.||++....-.+               -|--|==||.|=++-|||.=+++..    |.++.+==--||.+|++
T Consensus        52 i~~~L~e~Gi~~~~l~AvV---------------gRGGLLkPi~GGTY~Vn~~MleDLk~~~~GeHASNLGaIIA~~lA~  116 (353)
T TIGR02707        52 ILEVLEEKGINISKLDAVV---------------GRGGLLKPIEGGTYLVNEKMLEDLKEGKRGEHASNLGAIIARELAD  116 (353)
T ss_pred             HHHHHHHCCCCHHHEEEEE---------------ECCCCCCCCCCCEEEECHHHHHHHHHCCCCCCCCCHHHHHHHHHHH
T ss_conf             9999874088712431579---------------7277023338960477655688885105887843368999999876


Q ss_pred             CEEEEEEEEEEEEECCCCEE-EEEEEEEEEEEC
Q ss_conf             21589987889940356225-899997433302
Q gi|254781172|r  333 KQASTRLLDIDIQIGRTGIL-TPVARLEPVNIG  364 (731)
Q Consensus       333 e~~~T~v~~I~wqvgRtG~i-tPva~~ePV~l~  364 (731)
                      +                 .= -|.=.+|||-++
T Consensus       117 ~-----------------~~diPafIVDPVVVD  132 (353)
T TIGR02707       117 E-----------------LNDIPAFIVDPVVVD  132 (353)
T ss_pred             H-----------------CCCCCEEEECCCEEC
T ss_conf             5-----------------189435882683350


No 218
>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=61.02  E-value=11  Score=16.80  Aligned_cols=26  Identities=15%  Similarity=0.378  Sum_probs=11.9

Q ss_pred             CCEEEEECC---CCCCC----HH-HHHHHHHHCC
Q ss_conf             866999725---88998----78-9999999829
Q gi|254781172|r  649 NKKLVFTGT---LQKIQ----RH-KAQEYVTQLG  674 (731)
Q Consensus       649 gk~vV~TGt---l~~~~----R~-e~~~~ie~~G  674 (731)
                      |-+|+|+=.   |..|+    |- ..+++++++|
T Consensus       405 gd~VLlSPacaSfD~f~nye~RG~~F~~lv~~Lg  438 (438)
T PRK03806        405 GDMVLLSPACASLDQFKNFEQRGDEFARLAKELG  438 (438)
T ss_pred             CCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             9989989745030142499999999999999629


No 219
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=60.98  E-value=3  Score=21.07  Aligned_cols=54  Identities=22%  Similarity=0.396  Sum_probs=24.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEECCCC----CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC
Q ss_conf             43265775010337865445210100354----3441144665533213012310354103555565305
Q gi|254781172|r  432 SFCPICQSRVVRDLNPKTGKLVAAHRCTG----GLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKS  497 (731)
Q Consensus       432 ~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n----~~~Cpaq~~~~i~hF~SK~aldI~GLG~k~Ie~L~e~  497 (731)
                      -.||.|...+......   ....+++|--    +..||.=-...|.         .-|.|-..|+.-+..
T Consensus       445 ~~Cp~Cd~~lt~H~~~---~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~---------~~G~GterieeeL~~  502 (730)
T COG1198         445 AECPNCDSPLTLHKAT---GQLRCHYCGYQEPIPQSCPECGSEHLR---------AVGPGTERIEEELKR  502 (730)
T ss_pred             CCCCCCCCCEEEECCC---CEEEECCCCCCCCCCCCCCCCCCCEEE---------EECCCHHHHHHHHHH
T ss_conf             2489999512786479---806707799989988779899997369---------964619999999998


No 220
>pfam03786 UxuA D-mannonate dehydratase (UxuA). UxuA (this family) and UxuB are required for hexuronate degradation.
Probab=60.55  E-value=5.7  Score=18.97  Aligned_cols=81  Identities=17%  Similarity=0.247  Sum_probs=40.6

Q ss_pred             CCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHH
Q ss_conf             16642570215999999999999998612467776119999415818999998599899888659865566699977531
Q gi|254781172|r   91 HSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAI  170 (731)
Q Consensus        91 H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i  170 (731)
                      |..|-   ..+++.++|.+--+.+...                  |+..+.+ |+--....+-+|.+..-+-|-.-..+|
T Consensus        34 h~~p~---GevW~~~~I~~~k~~ie~~------------------GL~~~vV-ESvPvhe~Ik~g~~~rd~~Ieny~~ti   91 (350)
T pfam03786        34 HDIPV---GEVWPKEEIMALKEIIEDA------------------GLTLSVI-ESVPVHEDIKLGTPTRDRYIENYKQTI   91 (350)
T ss_pred             CCCCC---CCCCCHHHHHHHHHHHHHC------------------CCEEEEE-ECCCCHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             68999---8948999999999999974------------------9969999-477866888749987899999999999


Q ss_pred             CCCCCCCCCCCCCEEEEEEEEEEECHHHHH
Q ss_conf             024322335445504899999985202123
Q gi|254781172|r  171 PTIPRVLSLNIPEIIEVRGEVYISKNDFLA  200 (731)
Q Consensus       171 ~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~  200 (731)
                      +++-. .+      +.+=+==||+--+|-+
T Consensus        92 rNLa~-~G------I~vicYNFMPv~dW~R  114 (350)
T pfam03786        92 RNLAR-AG------IKVICYNFMPVFDWTR  114 (350)
T ss_pred             HHHHH-CC------CCEEEEECCCCCCCCC
T ss_conf             99997-79------9889872455455114


No 221
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.43  E-value=3.7  Score=20.36  Aligned_cols=24  Identities=17%  Similarity=0.713  Sum_probs=17.5

Q ss_pred             EEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCC
Q ss_conf             7770432657750103378654452101003543
Q gi|254781172|r  428 FSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGG  461 (731)
Q Consensus       428 ~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~  461 (731)
                      +.+|-.||.||-++..          ..++|+|.
T Consensus         3 ~~~~~~cPvcg~~~iV----------TeL~c~~~   26 (122)
T COG3877           3 YKVINRCPVCGRKLIV----------TELKCSNC   26 (122)
T ss_pred             CCCCCCCCCCCCCCEE----------EEEECCCC
T ss_conf             7778899855632036----------78742888


No 222
>PRK08305 spoVFB dipicolinate synthase subunit B; Reviewed
Probab=60.09  E-value=11  Score=16.69  Aligned_cols=27  Identities=22%  Similarity=0.288  Sum_probs=14.9

Q ss_pred             CCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCC
Q ss_conf             34234567777523455553011105664102454
Q gi|254781172|r  213 YANPRNAASGILRRLNPTDITRYLNFFVHGLGKTS  247 (731)
Q Consensus       213 f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~  247 (731)
                      +.|++|... .++       .+++-|+.|+-..+.
T Consensus       135 ~~n~~Ni~~-Ll~-------~kniyfvPfgqd~~~  161 (195)
T PRK08305        135 GLNAVNLGR-LLN-------TKNIYFVPFGQDDPE  161 (195)
T ss_pred             HHCHHHHHH-HHH-------CCCEEEEECCCCCCC
T ss_conf             768999999-982-------697899956886734


No 223
>KOG4362 consensus
Probab=60.00  E-value=11  Score=16.68  Aligned_cols=62  Identities=24%  Similarity=0.395  Sum_probs=49.1

Q ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE------EEEECCEEEEEECCCCC--C----HHHHHHHCC
Q ss_conf             88216866999725889987899999998298499------81116321799778888--6----379899749
Q gi|254781172|r  644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS------AILSRKTDIIIVGDNPG--S----KLEKAQQLG  705 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~------sSVSkkT~~LI~ge~~g--S----Kl~KA~~Lg  705 (731)
                      ...|.|+.|+|-|.|++...+++.+++...||.+.      +|-+|+++..+..+.+.  +    |..+|..++
T Consensus       585 ~kLf~gl~~~~~g~fs~~p~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k~~~~ea~~  658 (684)
T KOG4362         585 PKLFEGLKFYFVGDFSNPPKEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQKVNDAEALA  658 (684)
T ss_pred             CCHHCCCCCEEECCCCCCCHHHHHHHHHHCCCCEEECCCCCCCCCCCCCEEEEECCCCCCCHHHHHHCCHHHHH
T ss_conf             50114884136455344728998888764574265056765666533211575104688841555421288998


No 224
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=59.66  E-value=4.3  Score=19.86  Aligned_cols=26  Identities=23%  Similarity=0.733  Sum_probs=16.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHH
Q ss_conf             265775010337865445210100354344114466553
Q gi|254781172|r  434 CPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERL  472 (731)
Q Consensus       434 CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i  472 (731)
                      ||+||+++..          .-++|++   |.--+.+.+
T Consensus         1 CPvCg~~l~V----------t~L~C~~---C~t~ieG~F   26 (113)
T pfam09862         1 CPVCGEELTV----------TRLECSK---CGTTIEGRF   26 (113)
T ss_pred             CCCCCCCEEE----------EEEECCC---CCCEEEEEE
T ss_conf             9989981389----------9988489---986797365


No 225
>TIGR02644 Y_phosphoryl pyrimidine-nucleoside phosphorylase; InterPro: IPR000053   Two highly similar activities are represented in this group: thymidine phosphorylase (TP, gene deoA, 2.4.2.4 from EC) and pyrimidine-nucleoside phosphorylase (PyNP, gene pdp, 2.4.2.2 from EC). Both are dimeric enzymes that function in the salvage pathway to catalyse the reversible phosphorolysis of pyrimidine nucleosides to the free base and sugar moieties. In the case of thymidine phosphorylase, thymidine (and to a lesser extent, 2'-deoxyuridine) is lysed to produce thymine (or uracil) and 2'-deoxyribose-1-phosphate. Pyrimidine-nucleoside phosphorylase performs the analogous reaction on thymidine (to produce the same products) and uridine (to produce uracil and ribose-1-phosphate). PyNP is typically the only pyrimidine nucleoside phosphorylase encoded by Gram positive bacteria, while eukaryotes and proteobacteria encode two: TP, and the unrelated uridine phosphorylase. In humans, TP was originally characterised as platelet-derived endothelial cell growth factor and gliostatin . Structurally, the enzymes are homodimers, each composed of a rigid all alpha-helix lobe and a mixed alpha-helix/beta-sheet lobe, which are connected by a flexible hinge , . Prior to substrate binding, the lobes are separated by a large cleft. A functional active site and subsequent catalysis occurs upon closing of the cleft. The active site, composed of a phosphate binding site and a (deoxy)ribonucleotide binding site within the cleft region, is highly conserved between the two enzymes of this group. Active site residues (Escherichia coli DeoA numbering) include the phosphate binding Lys84 and Ser86 (close to a glycine-rich loop), Ser113, and Thr123, and the pyrimidine nucleoside-binding Arg171, Ser186, and Lys190. Sequence comparison between the active site residues for both enzymes reveals only one difference , which has been proposed to partially mediate substrate specificity. In TP, position 111 is a methionine, while the analogous position in PyNP is lysine. It should be noted that the uncharacterised archaeal members of this family differ in a number of respects from either of the characterised activities. The residue at position 108 is lysine, indicating the activity might be PyNP-like (though the determinants of substrate specificity have not been fully elucidated). Position 171 is glutamate (negative charge side chain) rather than arginine (positive charge side chain). In addition, a large loop that may "lock in" the substrates within the active site is much smaller than in the characterised members. It is not clear what effect these and other differences have on activity and specificity.; GO: 0006206 pyrimidine base metabolic process.
Probab=59.63  E-value=11  Score=16.63  Aligned_cols=44  Identities=14%  Similarity=0.175  Sum_probs=23.7

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHH
Q ss_conf             9999999999999986124677761199994158189999985998998886598655666999
Q gi|254781172|r  102 WNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSA  165 (731)
Q Consensus       102 ~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~  165 (731)
                      -+.+|...|...+...     +...+|   ..+-|..+         -+=+|=|   +|+-||-
T Consensus        49 M~~~Et~~LT~AM~~S-----G~~~Dl---s~~~g~~v---------DKHSTGG---VGDK~SL   92 (425)
T TIGR02644        49 MTDEETAYLTKAMIDS-----GEVLDL---SSLKGPKV---------DKHSTGG---VGDKVSL   92 (425)
T ss_pred             CCHHHHHHHHHHHHHH-----CCEEEC---CCCCCCEE---------CCCCCCC---CCHHHHH
T ss_conf             9988999999999973-----867400---23788514---------0355788---3402467


No 226
>KOG2703 consensus
Probab=59.56  E-value=4.8  Score=19.50  Aligned_cols=58  Identities=14%  Similarity=0.178  Sum_probs=31.2

Q ss_pred             HHCCHHHHHHHHH-HHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHC
Q ss_conf             6301011116899-99998829989999978977612511778761388867899999999966
Q gi|254781172|r  555 FSLGIRHVGAEIA-RSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ  617 (731)
Q Consensus       555 ~ALGI~~vG~~~A-k~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~  617 (731)
                      ++|.||.++-... -.|.-.|.+++.++..+...........     -+...+-..+...+|+.
T Consensus       333 cs~~IPEl~lel~~~~LgGrfTTiEGLl~~~~e~l~~~~f~~-----~DS~~~~~~~~~~~F~~  391 (460)
T KOG2703         333 CSLSIPELDLELGGGTLGGRFTTIEGLLTQIREQLDGRSFTF-----GDSMDEGQKARWQEFLA  391 (460)
T ss_pred             CCEECCCCCEECCCCCCCCEEEEHHHHHHHHHHHHHCCCEEC-----CCCCCHHHHHHHHHHHH
T ss_conf             303444432000476245324537999999999972574002-----45678889999999999


No 227
>KOG2875 consensus
Probab=59.18  E-value=12  Score=16.58  Aligned_cols=43  Identities=23%  Similarity=0.257  Sum_probs=26.4

Q ss_pred             HHHHHHHHCCC---HHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             99999988299---89999978977612511778761388867899999999
Q gi|254781172|r  566 IARSLAKYYLS---YQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE  614 (731)
Q Consensus       566 ~Ak~La~~f~s---i~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~  614 (731)
                      +|+.|.+..+-   +..+.+.      .-++..+.|+.++|+|+|+|+.|-=
T Consensus       191 ta~~l~~~~g~~~wLqslr~~------~yeear~~L~~lpGVG~KVADCI~L  236 (323)
T KOG2875         191 TARALQEKQGGLAWLQSLRKS------SYEEAREALCSLPGVGPKVADCICL  236 (323)
T ss_pred             HHHHHHHHCCCCHHHHHHHCC------CHHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf             999999723500599988545------2899999985288876147562231


No 228
>PRK08174 DNA topoisomerase III; Validated
Probab=59.11  E-value=5.5  Score=19.08  Aligned_cols=21  Identities=0%  Similarity=0.096  Sum_probs=13.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999998433
Q gi|254781172|r   16 QARKELSSLEQEISYHDDCYY   36 (731)
Q Consensus        16 ~~~~~i~~L~~~i~~~~~~Yy   36 (731)
                      +.++++..|.+.+.+++..|.
T Consensus        78 ~~~~q~~~ik~l~k~ad~ii~   98 (670)
T PRK08174         78 KTASQFKVVKRLLKQATELVI   98 (670)
T ss_pred             CHHHHHHHHHHHHHCCCEEEE
T ss_conf             078999999999965999998


No 229
>pfam10391 DNA_pol_lambd_f Fingers domain of DNA polymerase lambda. DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone.
Probab=58.94  E-value=3.5  Score=20.62  Aligned_cols=25  Identities=28%  Similarity=0.488  Sum_probs=16.2

Q ss_pred             CCHHHHHHHHHHHHHCCCCCCEEEEEHHHH
Q ss_conf             103541035555653057654045410110
Q gi|254781172|r  481 FNIEGLGKQQLDFFFKSEDPAFSIRIPADI  510 (731)
Q Consensus       481 ldI~GLG~k~Ie~L~e~~~~~g~I~~~~DL  510 (731)
                      ++|=|+||++.+++++.|     ++++.||
T Consensus         5 ~~I~GvGp~~A~~~~~~G-----~~ti~dL   29 (52)
T pfam10391         5 TNIWGVGPKTARKWYRQG-----IRTLEDL   29 (52)
T ss_pred             HHCCCCCHHHHHHHHHHC-----CCCHHHH
T ss_conf             635440699999999947-----8889999


No 230
>PRK07141 DNA topoisomerase I; Validated
Probab=58.91  E-value=4.1  Score=20.07  Aligned_cols=21  Identities=5%  Similarity=0.063  Sum_probs=14.2

Q ss_pred             CCCCHHHHH-----HHHHHHHHCCCC
Q ss_conf             231035410-----355556530576
Q gi|254781172|r  479 DAFNIEGLG-----KQQLDFFFKSED  499 (731)
Q Consensus       479 ~aldI~GLG-----~k~Ie~L~e~~~  499 (731)
                      ++|+=.|||     ..+|+.|++.+|
T Consensus       456 ~~Me~~gIGtpATrA~iIe~L~~R~Y  481 (622)
T PRK07141        456 EKLDDIKVGRPSTFASTVKILKDRLY  481 (622)
T ss_pred             HHHHHCCCCCCCCHHHHHHHHHHCCC
T ss_conf             99874799852029999999975773


No 231
>PRK06139 short chain dehydrogenase; Provisional
Probab=58.87  E-value=7.9  Score=17.87  Aligned_cols=13  Identities=0%  Similarity=-0.013  Sum_probs=5.7

Q ss_pred             CHHHHHHHHHHHH
Q ss_conf             0145689999875
Q gi|254781172|r  533 VSVTNLYDSINKR  545 (731)
Q Consensus       533 Ksa~nL~~sIe~s  545 (731)
                      +-|+.|+.+.++-
T Consensus       216 ~vA~ai~~~~~~~  228 (324)
T PRK06139        216 RVAKAMVRLADRP  228 (324)
T ss_pred             HHHHHHHHHHHCC
T ss_conf             9999999998389


No 232
>TIGR01588 citE citrate lyase, beta subunit; InterPro: IPR006475   This group of sequences represent the beta subunit of the holoenzyme citrate lyase (4.1.3.6 from EC) composed of alpha (2.8.3.10 from EC), beta, and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The beta subunit catalyzes the reaction (3S)-citryl-CoA = acetyl-CoA + oxaloacetate. The group contains an experimentally characterised member from Leuconostoc mesenteroides . The group contains sequences from a wide range of Gram-positive bacteria. For Gram-negative bacteria, it appears that only the sequences from gamma proteobacteria are present.; GO: 0008816 citryl-CoA lyase activity, 0006084 acetyl-CoA metabolic process, 0005737 cytoplasm, 0009346 citrate lyase complex.
Probab=58.47  E-value=7.9  Score=17.84  Aligned_cols=15  Identities=20%  Similarity=0.235  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHCCCC
Q ss_conf             410355556530576
Q gi|254781172|r  485 GLGKQQLDFFFKSED  499 (731)
Q Consensus       485 GLG~k~Ie~L~e~~~  499 (731)
                      -||..=|+..+.+|.
T Consensus        72 pFG~~Dl~AvVkAgv   86 (288)
T TIGR01588        72 PFGLEDLKAVVKAGV   86 (288)
T ss_pred             HHHHHHHHHHHHCCC
T ss_conf             545888998875388


No 233
>KOG2379 consensus
Probab=58.45  E-value=12  Score=16.49  Aligned_cols=29  Identities=14%  Similarity=0.275  Sum_probs=14.6

Q ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             01011116899999988299899999789
Q gi|254781172|r  557 LGIRHVGAEIARSLAKYYLSYQNFAQEIN  585 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~  585 (731)
                      |-|++++...|-.|+.+|+++-.+..+.+
T Consensus       433 Mqvkg~S~erAiAI~d~YpTl~sLl~AY~  461 (501)
T KOG2379         433 MQVKGMSLERAIAIADRYPTLRSLLSAYE  461 (501)
T ss_pred             HHCCCCCHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             84347548889999996568999999986


No 234
>TIGR01203 HGPRTase hypoxanthine phosphoribosyltransferase; InterPro: IPR005904    Phosphoribosyltransferases (PRT) are enzymes that catalyze the synthesis of beta-n-5'-monophosphates from phosphoribosylpyrophosphate (PRPP) and an enzyme specific amine. A number of PRT's are involved in the biosynthesis of purine, pyrimidine, and pyridine nucleotides, or in the salvage of purines and pyrimidines. Purine nucleotides are synthesized both via the de novo pathway and via the salvage pathway and are vital for cell functions and cell proliferation through DNA and RNA syntheses and ATP energy supply.    This entry presents hypoxanthine phosphoribosyltransferase (2.4.2.8 from EC), which belongs to phosphoribosyltransferase family and is involved in purine salvage.; GO: 0004422 hypoxanthine phosphoribosyltransferase activity, 0006166 purine ribonucleoside salvage, 0005737 cytoplasm.
Probab=58.39  E-value=11  Score=16.61  Aligned_cols=20  Identities=25%  Similarity=0.418  Sum_probs=17.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999999999999
Q gi|254781172|r   12 LSIEQARKELSSLEQEISYH   31 (731)
Q Consensus        12 ~s~~~~~~~i~~L~~~i~~~   31 (731)
                      ++.+++++|+++|+++|+.+
T Consensus         3 i~~~~i~~r~~eLa~~I~~~   22 (183)
T TIGR01203         3 ISEEQIKARIAELAKQITED   22 (183)
T ss_pred             CCHHHHHHHHHHHHHHHHHH
T ss_conf             67899999999999999987


No 235
>KOG0323 consensus
Probab=58.33  E-value=7.3  Score=18.10  Aligned_cols=81  Identities=26%  Similarity=0.325  Sum_probs=59.7

Q ss_pred             CCCCCCCEEEEECCCCCCC---HHHHHHHHHHCCCEEEEEEECCEEEEEECCCCC-CHHHHHHHCC-CEEECHHHHHHHH
Q ss_conf             8821686699972588998---789999999829849981116321799778888-6379899749-9173799999999
Q gi|254781172|r  644 SSEIENKKLVFTGTLQKIQ---RHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG-SKLEKAQQLG-VKIMNEEQFLFLL  718 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~~~~---R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~g-SKl~KA~~Lg-I~Ii~e~ef~~ll  718 (731)
                      ...+.|..+||+|....+.   +.++--.....|+.++-.++.+|..||+ .++| -|..+|...+ +.|....+++.-+
T Consensus       439 ~~v~~~~~~vfSg~~P~~~~~~~s~~~~~~~~~g~vs~~~~~~~~th~i~-~~~gt~k~~~a~~~~~~~Vv~~~wl~~~~  517 (635)
T KOG0323         439 TKVLKGSQIVFSGLHPTGSTDESADILGVAQQLGAVSAPDVSDKTTHLIA-ANAGTKKVYKAVVSGSAKVVNAAWLWRSL  517 (635)
T ss_pred             HHHHHCCCEEECCCCCCCCCCCHHHHHHHHHCCCCEECCCCCCHHHHHHH-HCCCCCEEECCCCCCCEEEECHHHHHHHH
T ss_conf             67763231010256667677001256664420353102566611355776-53585123312234540675134888878


Q ss_pred             HHHCCCC
Q ss_conf             8828656
Q gi|254781172|r  719 QQYNTTL  725 (731)
Q Consensus       719 ~~~~~~~  725 (731)
                      ++.+.-.
T Consensus       518 e~w~~v~  524 (635)
T KOG0323         518 EKWGKVE  524 (635)
T ss_pred             HHHCCHH
T ss_conf             8752211


No 236
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=58.10  E-value=4  Score=20.11  Aligned_cols=35  Identities=9%  Similarity=0.094  Sum_probs=21.2

Q ss_pred             HCCCEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCC
Q ss_conf             011105664102454332100003689999759966
Q gi|254781172|r  233 TRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPV  268 (731)
Q Consensus       233 ~r~L~f~ay~~~~~~~~~~~~~~e~l~~L~~~GF~v  268 (731)
                      .+++.+-++.-. +......+-.+..++-++||++.
T Consensus       334 eKRVELh~HTkM-S~mDai~sv~~~vk~A~kwghka  368 (1444)
T COG2176         334 EKRVELHFHTKM-SQMDAITSVEELVKQAKKWGHKA  368 (1444)
T ss_pred             CCEEEEEECCCH-HHHCCCCCHHHHHHHHHHCCCCE
T ss_conf             304899851532-44216678999999999759964


No 237
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family; InterPro: IPR013429    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=57.99  E-value=4.1  Score=20.08  Aligned_cols=15  Identities=20%  Similarity=0.554  Sum_probs=11.2

Q ss_pred             ECCCCCCCCCC-CCCC
Q ss_conf             70432657750-1033
Q gi|254781172|r  430 FPSFCPICQSR-VVRD  444 (731)
Q Consensus       430 ~P~~CP~Cgs~-l~~~  444 (731)
                      ..+.||+||++ +.+.
T Consensus        26 pl~~CP~C~~~~~~k~   41 (43)
T TIGR02605        26 PLTTCPACGGPALRKQ   41 (43)
T ss_pred             CCCCCCCCCCCCEEEE
T ss_conf             3447876787641241


No 238
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=57.83  E-value=3.6  Score=20.46  Aligned_cols=13  Identities=31%  Similarity=0.669  Sum_probs=9.0

Q ss_pred             EECCCCCCCCCCC
Q ss_conf             7704326577501
Q gi|254781172|r  429 SFPSFCPICQSRV  441 (731)
Q Consensus       429 ~~P~~CP~Cgs~l  441 (731)
                      ..-+-||+|||.-
T Consensus       501 ~~G~pCPVCGS~~  513 (1047)
T PRK10246        501 QAGQPCPLCGSTS  513 (1047)
T ss_pred             CCCCCCCCCCCCC
T ss_conf             7999899999978


No 239
>PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional
Probab=57.39  E-value=8.6  Score=17.55  Aligned_cols=63  Identities=19%  Similarity=0.257  Sum_probs=29.4

Q ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCC--C--HHHHHHHCCCEEEC-HHHHHHHH
Q ss_conf             8821686699972588998789999999829849981116321799778888--6--37989974991737-99999999
Q gi|254781172|r  644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG--S--KLEKAQQLGVKIMN-EEQFLFLL  718 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~g--S--Kl~KA~~LgI~Ii~-e~ef~~ll  718 (731)
                      .+.|.|.++-+-|-.-+-.    -++.             +-||=-||..+|  +  +-++.-+-|||-=. .+++++||
T Consensus       542 t~HLkGvkI~iMGCIVNGp----GEMA-------------DADfGYVG~~~gkI~LY~gk~~V~~nip~~~Avd~Li~LI  604 (613)
T PRK02048        542 TSHLKGLKIGIMGCIVNGP----GEMA-------------DADYGYVGAGRGKISLYKQKECVEKNIPEEEAVEKLIELI  604 (613)
T ss_pred             HCCCCCCEEEEEEEEECCC----CCCC-------------CCCCCCCCCCCCEEEEECCCEEEECCCCHHHHHHHHHHHH
T ss_conf             3788787599983040287----4011-------------2666753788886888607564534898789999999999


Q ss_pred             HHHCC
Q ss_conf             88286
Q gi|254781172|r  719 QQYNT  723 (731)
Q Consensus       719 ~~~~~  723 (731)
                      ++...
T Consensus       605 k~~gr  609 (613)
T PRK02048        605 KENGD  609 (613)
T ss_pred             HHCCC
T ss_conf             96490


No 240
>KOG0477 consensus
Probab=56.32  E-value=6.9  Score=18.30  Aligned_cols=65  Identities=22%  Similarity=0.322  Sum_probs=31.9

Q ss_pred             CCCCCEEEEECCCCCCC---HHHHHHHHHHCCCEEE-----EEEECCEEEEEECCCC-C---CHHHHHH--HCCCEEEC
Q ss_conf             21686699972588998---7899999998298499-----8111632179977888-8---6379899--74991737
Q gi|254781172|r  646 EIENKKLVFTGTLQKIQ---RHKAQEYVTQLGAVVS-----AILSRKTDIIIVGDNP-G---SKLEKAQ--QLGVKIMN  710 (731)
Q Consensus       646 ~l~gk~vV~TGtl~~~~---R~e~~~~ie~~Ggkv~-----sSVSkkT~~LI~ge~~-g---SKl~KA~--~LgI~Ii~  710 (731)
                      .|+.+-+|.---|.+|.   |..+.+..|+.-..++     .|...-++++-+..-- |   +-+.-|+  +|-=||++
T Consensus       543 VLADkGvClIDEFDKMndqDRtSIHEAMEQQSISISKAGIVtsLqArctvIAAanPigGRY~~s~tFaqNV~ltePIlS  621 (854)
T KOG0477         543 VLADKGVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGIVTSLQARCTVIAAANPIGGRYNPSLTFAQNVDLTEPILS  621 (854)
T ss_pred             EECCCCEEEEEHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCCHHHCCCCCCCHHH
T ss_conf             9726853774121120401101599998751201446668998875544300027777756875114330554444121


No 241
>PRK06200 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase; Provisional
Probab=56.09  E-value=12  Score=16.37  Aligned_cols=13  Identities=15%  Similarity=0.194  Sum_probs=7.1

Q ss_pred             CCCCCEEEEECCC
Q ss_conf             2168669997258
Q gi|254781172|r  646 EIENKKLVFTGTL  658 (731)
Q Consensus       646 ~l~gk~vV~TGtl  658 (731)
                      ..+|.++++.|-+
T Consensus       245 ~iTG~~i~vDGG~  257 (263)
T PRK06200        245 ALTGVVINADGGL  257 (263)
T ss_pred             CEECCEEEECCCH
T ss_conf             8458678889362


No 242
>PRK07239 bifunctional uroporphyrinogen-III synthetase/response regulator domain protein; Validated
Probab=56.06  E-value=13  Score=16.21  Aligned_cols=163  Identities=15%  Similarity=0.167  Sum_probs=71.1

Q ss_pred             CCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCC
Q ss_conf             64257021599999999999999861246777611999941581899999859989988865986556669997753102
Q gi|254781172|r   93 IPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPT  172 (731)
Q Consensus        93 ~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~  172 (731)
                      .|++..--..+..||..|.+++..               -..|=+             ..|-|-|..|=  -+.+... +
T Consensus        39 aPalriVPl~DD~eL~~~t~~lia---------------~ppD~v-------------V~TTGiGfr~w--leaAe~~-G   87 (381)
T PRK07239         39 APALRIVPLADDDELRAATEALIA---------------APPDIV-------------VATTGIGFRGW--VEAADGW-G   87 (381)
T ss_pred             CCCCCEECCCCCHHHHHHHHHHHC---------------CCCCEE-------------EEECHHHHHHH--HHHHHHC-C
T ss_conf             465330338885999999999854---------------899989-------------99236889999--9999971-7


Q ss_pred             CCCCCCCC-CCCEEEEEEEEEEECHHHHHHHHHHHHCCCCC-CCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCCCC
Q ss_conf             43223354-45504899999985202123455643148543-34234567777523455553-01110566410245433
Q gi|254781172|r  173 IPRVLSLN-IPEIIEVRGEVYISKNDFLALNDEMIAVGRKP-YANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSEI  249 (731)
Q Consensus       173 iP~~l~~~-~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~-f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~~~  249 (731)
                      +-..|-.. -...+..||-=    .    .+. ..+.|... ++-+=+.-++.+..+....+ .+++..--||.....+.
T Consensus        88 l~d~Ll~aL~~ari~aRGPK----a----~gA-lRaaGL~e~wsp~ses~~Evl~~Ll~~gv~G~rIAVQlHGa~~~~eP  158 (381)
T PRK07239         88 LADELLEALSSARLVARGPK----A----TGA-LRAAGLREEWSPASESSAEVLEYLLEEGVAGKRIAVQLHGAADEWDP  158 (381)
T ss_pred             CHHHHHHHHHCCEEEEECCC----H----HHH-HHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEEECCCCCCCCC
T ss_conf             77899999732807877764----6----878-98649986427999877999999971798888899981476666687


Q ss_pred             CCCCCHHHHHHHHHCCCCC---CCCEEEE-ECCCCHHHHHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             2100003689999759966---5414887-403211345566553100112343763777
Q gi|254781172|r  250 FAKGQYEMLQKMRCLGFPV---NNGVRQA-NTFHGIVSYYNEMKSIRSTLPYDIDGLVYK  305 (731)
Q Consensus       250 ~~~~~~e~l~~L~~~GF~v---~~~~~~~-~~~~~~~~~~~~~~~~r~~l~y~iDGiVik  305 (731)
                          .-++.+.|+.-|-.|   .+|.+.. .+...+...++.+-.      =++|-+.+.
T Consensus       159 ----~p~~~~~Lr~aGAeV~~V~vYRW~~p~d~~~l~~Lv~~i~~------g~vDAVtFT  208 (381)
T PRK07239        159 ----LPEFLEALRAAGAEVVPVPVYRWVPPPDGGPFDRLVDLIAT------RQLDAVTFT  208 (381)
T ss_pred             ----CHHHHHHHHHCCCEEEEECCEECCCCCCCCHHHHHHHHHHH------CCCCEEEEC
T ss_conf             ----88999999977986889565432699985479999999970------888889965


No 243
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=55.74  E-value=5.7  Score=18.94  Aligned_cols=87  Identities=9%  Similarity=0.097  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCC-CCCCCCCCCCCCEEECCCC
Q ss_conf             999999999999999998433177982087899999999999989772031158999962-0036432357750451664
Q gi|254781172|r   16 QARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPL-NKIGGEMNLSLFKVTHSIP   94 (731)
Q Consensus        16 ~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt-~~Vg~~~~~~~~kv~H~~p   94 (731)
                      ..|+-+..|+..+.+|-..+    -=--|+.+-...++||.-+-     +.....||||. ..+|-.    -.+.-|...
T Consensus        95 s~~q~~~r~~~~~~~~g~~~----gyf~~~~d~~~f~~e~~~~l-----~~q~~a~nsp~wfn~g~~----~~~Q~sACF  161 (957)
T PRK06556         95 SLRQLIDRVVKTYTAAGRED----GYFATEADAEIFEHELTWLL-----LHQKFSFNSPVWFNVGTS----SRQQVSACF  161 (957)
T ss_pred             CHHHHHHHHHHHHHHHHHHC----CCCCCHHHHHHHHHHHHHHH-----HHHHCCCCCCEEEECCCC----CCCCCCEEE
T ss_conf             19999999999999987527----85278778999999999999-----975527999802667888----888741577


Q ss_pred             CCCHHHCCCHHHHHHHHHHHHHH
Q ss_conf             25702159999999999999986
Q gi|254781172|r   95 TLSLEKIWNIEDLRKFITRIYRF  117 (731)
Q Consensus        95 MlSL~k~~~~~el~~w~~~~~~~  117 (731)
                      .+|.+.  +.+.|.+|+++-...
T Consensus       162 v~~v~D--~~~~I~d~~~~~a~i  182 (957)
T PRK06556        162 ILSVDD--SMESILDWYKEEGML  182 (957)
T ss_pred             EECCCC--CHHHHHHHHHHHHHH
T ss_conf             723655--699999999997762


No 244
>PRK12496 hypothetical protein; Provisional
Probab=55.66  E-value=3.6  Score=20.47  Aligned_cols=21  Identities=29%  Similarity=0.797  Sum_probs=16.5

Q ss_pred             CCCCCCCCEEEEECCHHCCCCC
Q ss_conf             1123437637773110001115
Q gi|254781172|r  294 TLPYDIDGLVYKVDEFSLQKQL  315 (731)
Q Consensus       294 ~l~y~iDGiVikvn~~~~q~~l  315 (731)
                      .|.|+.+|+++. ||+..|+.+
T Consensus        87 ALA~el~~~l~T-DDy~~QNva  107 (166)
T PRK12496         87 ALAYELKGTLYT-DDYGIQNVA  107 (166)
T ss_pred             HHHHHHCCEEEE-CCHHHHHHH
T ss_conf             999985998984-648889999


No 245
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=55.64  E-value=8.1  Score=17.75  Aligned_cols=68  Identities=24%  Similarity=0.475  Sum_probs=36.0

Q ss_pred             CCCCCCEEEEEECCCCHHHHHHHCCCCCCCCCCEEEECC-CCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHH
Q ss_conf             844076899983587025665410123578730477704-3265775010337865445210100354344114466553
Q gi|254781172|r  394 DIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPS-FCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERL  472 (731)
Q Consensus       394 ~I~iGd~V~I~RaGdVIP~I~~Vi~~~r~~~~~~~~~P~-~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i  472 (731)
                      .+..||.|++  .|.|=|+.+.+-+-.-. .-.++..-+ .||.||.-+.--     +..  .+||.   .|--+.-...
T Consensus       315 ~L~pGD~i~~--~G~~~~~~~n~ek~~v~-~l~~~~~~~p~Cp~Cg~~m~S~-----G~~--g~rC~---kCg~~~~~~~  381 (421)
T COG1571         315 KLIPGDEITV--YGSVKPGTLNLEKFQVL-KLARYERVNPVCPRCGGRMKSA-----GRN--GFRCK---KCGTRARETL  381 (421)
T ss_pred             HCCCCCEEEE--ECCCCCCCEEEEEEEEE-EEEEEEECCCCCCCCCCCHHHC-----CCC--CCCCC---CCCCCCCCCC
T ss_conf             5689998998--05745662368999999-8666677178897667713116-----789--85266---4266177553


Q ss_pred             HH
Q ss_conf             32
Q gi|254781172|r  473 KH  474 (731)
Q Consensus       473 ~h  474 (731)
                      ..
T Consensus       382 ~~  383 (421)
T COG1571         382 IK  383 (421)
T ss_pred             CC
T ss_conf             23


No 246
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.    Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=55.45  E-value=13  Score=16.14  Aligned_cols=232  Identities=21%  Similarity=0.283  Sum_probs=102.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCC---CCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCC--CCEEECCC
Q ss_conf             99999999999999843317798---20878999999999999897720311589999620036432357--75045166
Q gi|254781172|r   19 KELSSLEQEISYHDDCYYQYSKP---IILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLS--LFKVTHSI   93 (731)
Q Consensus        19 ~~i~~L~~~i~~~~~~Yy~~~~p---~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~--~~kv~H~~   93 (731)
                      +-+..|.+++.    +||-..+.   -||+-....|.+++.+=-.+                ++--....  -+-+.|-.
T Consensus       599 ~~~~aL~kr~~----lyy~~~ei~fk~i~EVDL~~l~rEIDEdR~k----------------~r~~~~g~~~A~~~dLvK  658 (1843)
T TIGR01054       599 EAFEALKKRLK----LYYFTQEIEFKRIDEVDLEKLLREIDEDREK----------------VRRIVEGKVKAKVKDLVK  658 (1843)
T ss_pred             HHHHHHHHHHH----HHHHHHCCCCCCCCCCCHHHHHHHHHHCCCC----------------CCEEEECCEEEEEECCCC
T ss_conf             89999998886----6665201355445600178887764101012----------------401220762664202424


Q ss_pred             CCC----CHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEC-CEEEEEEEEE--CCE------------EEEEEEC
Q ss_conf             425----70215999999999999998612467776119999415-8189999985--998------------9988865
Q gi|254781172|r   94 PTL----SLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKI-DGTMITIRYE--KGK------------FVYAALR  154 (731)
Q Consensus        94 pMl----SL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKi-DG~sisl~Y~--~G~------------L~~a~TR  154 (731)
                      |-|    |=+||-+          |.+++++   |+.     -|| +|   +-+||  =|.            +.-.+|=
T Consensus       659 t~L~vVESPnKART----------IA~FFGk---P~~-----R~iP~~---~~vYEv~~gDkilmim~~~G~V~~L~iTa  717 (1843)
T TIGR01054       659 TALLVVESPNKART----------IARFFGK---PSV-----RKIPGG---SVVYEVPVGDKILMIMAETGDVLVLVITA  717 (1843)
T ss_pred             CEEEEEECCCCHHH----------HHHHCCC---CCC-----EECCCC---CEEEEEEECCEEEEEECCCCCEEEEEEEE
T ss_conf             13799827860445----------5343069---963-----551598---53899861682899851898378999984


Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCCCCC---C-CCE--E-EEE--EEEEEECHHHHH-HHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             98655666999775310243223354---4-550--4-899--999985202123-455643148543342345677775
Q gi|254781172|r  155 GDGHSGEDVSACIRAIPTIPRVLSLN---I-PEI--I-EVR--GEVYISKNDFLA-LNDEMIAVGRKPYANPRNAASGIL  224 (731)
Q Consensus       155 GdG~~GeDVT~n~~~i~~iP~~l~~~---~-~~~--i-eiR--GEv~m~~~~F~~-lN~~~~~~g~~~f~NpRN~aaG~l  224 (731)
                      -=|+.=+=||.....+-|+-..-...   + |-.  | -+|  ||=|...++.+. +.+...+.|...-.|.+|.+=| |
T Consensus       718 s~GHv~DL~t~~~~~f~GV~~~~~~g~~~Y~PvY~sIKrC~dcG~QfTd~~~leeli~e~cpkcgs~~~~d~~~~ve~-l  796 (1843)
T TIGR01054       718 SLGHVFDLVTDKVGGFYGVLVENGEGAEAYVPVYTSIKRCRDCGEQFTDEEDLEELIKELCPKCGSENIEDSKSIVEI-L  796 (1843)
T ss_pred             ECCCHHHHCCCCCCCEEEEEEECCCCCCCCEEEECCCCEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHH-H
T ss_conf             110021103674463421153058896542004411011335887436715589999986025787555652678899-9


Q ss_pred             HCCCHHHHHCCCEEEEEEECCCCCCCCCCCHHHH-----HHHHHCCCCCCCCEEEEECCCCHH--HHHHHHHHHH--CCC
Q ss_conf             2345555301110566410245433210000368-----999975996654148874032113--4556655310--011
Q gi|254781172|r  225 RRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEML-----QKMRCLGFPVNNGVRQANTFHGIV--SYYNEMKSIR--STL  295 (731)
Q Consensus       225 r~~d~~~~~r~L~f~ay~~~~~~~~~~~~~~e~l-----~~L~~~GF~v~~~~~~~~~~~~~~--~~~~~~~~~r--~~l  295 (731)
                      |.+-     ...+++.=+      ..|.|.-|.+     ..++    |-+|..++. .+++|-  +..+.+++-|  +.|
T Consensus       797 R~lA-----~EvD~v~ia------TDPDtEGEKIgwDl~~~~~----Py~pnv~R~-eFHEVT~rAi~eAl~s~rkGeel  860 (1843)
T TIGR01054       797 RELA-----SEVDEVFIA------TDPDTEGEKIGWDLALLLR----PYNPNVKRA-EFHEVTKRAILEALESPRKGEEL  860 (1843)
T ss_pred             HHHH-----HHHCEEEEC------CCCCCCCCCHHHHHHHHHC----CCCCCEEEE-CCCCCCHHHHHHHHCCCCCCCCC
T ss_conf             8754-----442988872------5889875408999999808----877752462-14562379999986087657501


Q ss_pred             CCC---CCCEEEE-ECC
Q ss_conf             234---3763777-311
Q gi|254781172|r  296 PYD---IDGLVYK-VDE  308 (731)
Q Consensus       296 ~y~---iDGiVik-vn~  308 (731)
                      ++|   +++=||+ +-|
T Consensus       861 ~vd~NLVkAQvVRRI~D  877 (1843)
T TIGR01054       861 SVDENLVKAQVVRRIED  877 (1843)
T ss_pred             CCCCCCCCEEEEEEEEE
T ss_conf             00023101158889875


No 247
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=54.75  E-value=6.2  Score=18.65  Aligned_cols=21  Identities=10%  Similarity=0.129  Sum_probs=15.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999998433
Q gi|254781172|r   16 QARKELSSLEQEISYHDDCYY   36 (731)
Q Consensus        16 ~~~~~i~~L~~~i~~~~~~Yy   36 (731)
                      ..++.+.+|.+..++.+..|-
T Consensus        59 ~k~k~i~~Lkklak~ad~V~l   79 (864)
T PRK06319         59 DKQEVIRKICKLAKKCDVVYL   79 (864)
T ss_pred             CHHHHHHHHHHHHHCCCEEEE
T ss_conf             768999999999846997998


No 248
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=54.72  E-value=5.7  Score=18.95  Aligned_cols=43  Identities=21%  Similarity=0.159  Sum_probs=30.3

Q ss_pred             CHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf             035410355556530576540454101101067775310001000134
Q gi|254781172|r  482 NIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILG  529 (731)
Q Consensus       482 dI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~G  529 (731)
                      .|.|+|++.-..|-+.|     |.++++|=.++..+...+++++.++|
T Consensus        71 ~I~GIGPk~e~~Ln~~G-----I~tfaQIAAwt~~di~~id~~l~f~G  113 (133)
T COG3743          71 RISGIGPKLEKVLNELG-----IFTFAQIAAWTRADIAWIDDYLNFDG  113 (133)
T ss_pred             HHCCCCHHHHHHHHHCC-----CCCHHHHHHCCHHHHHHHHHHCCCCC
T ss_conf             10043788998998747-----76399997448999999985448862


No 249
>TIGR00679 hpr-ser HPr(Ser) kinase/phosphatase; InterPro: IPR003755 HPr(Ser) kinase is the sensor in a multicomponent phosphorelay system that controls catabolite repression, sugar transport and carbon metabolism in Gram-positive bacteria. These are all phosphorylation-dependent carbon control mechanisms. This kinase in unusual in that it recognises the tertiary structure of its target protein, HPr, a phosphocarrier protein of the bacterial phosphotransferase system and a transcriptional cofactor controlling the phenomenon of catabolite repression .; GO: 0000155 two-component sensor activity, 0004672 protein kinase activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006109 regulation of carbohydrate metabolic process.
Probab=54.67  E-value=8.7  Score=17.53  Aligned_cols=61  Identities=18%  Similarity=0.215  Sum_probs=39.5

Q ss_pred             CCCCCCCCCCCCCEEECCCCCCCCHHH-HHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHH
Q ss_conf             103378654452101003543441144-6655332130123103541035555653057654045410110
Q gi|254781172|r  441 VVRDLNPKTGKLVAAHRCTGGLACSAQ-QLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADI  510 (731)
Q Consensus       441 l~~~~~~~~~~~~~~~rC~n~~~Cpaq-~~~~i~hF~SK~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DL  510 (731)
                      |+...+..-+++.+.++|.|+..=-.+ ..+.+.||     |.|.|||-=.|++||-.    |-+++--.|
T Consensus       168 Li~rgH~LvaDD~vEI~~~~gn~L~GrGa~~~~~~~-----mEIRGLGIINv~~lyG~----~~~r~~~eI  229 (309)
T TIGR00679       168 LINRGHRLVADDAVEIYRLDGNRLVGRGAQELIKHF-----MEIRGLGIINVERLYGL----GIVRERKEI  229 (309)
T ss_pred             HHHCCCCEEECCEEEEEEECCCEEECCHHHHHHHHC-----CEECCCHHHHHHHHHCC----CEEECCCEE
T ss_conf             975688077515368875258751140089888520-----21135407677566235----312014102


No 250
>cd01075 NAD_bind_Leu_Phe_Val_DH NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. For example, leucine DH catalyzes the reversible oxidative deamination of L-leucine and several other straight or branched chain amino acids to the corresponding 2-oxoacid derivative. Amino acid DH -like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily inc
Probab=54.55  E-value=14  Score=16.03  Aligned_cols=27  Identities=26%  Similarity=0.381  Sum_probs=14.8

Q ss_pred             CCEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCC
Q ss_conf             1105664102454332100003689999759966
Q gi|254781172|r  235 YLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPV  268 (731)
Q Consensus       235 ~L~f~ay~~~~~~~~~~~~~~e~l~~L~~~GF~v  268 (731)
                      ...+..-|++...       +..-.+|.+.|-.+
T Consensus        28 gk~VaIqG~GnVG-------~~~A~~l~~~Gakv   54 (200)
T cd01075          28 GKTVAVQGLGKVG-------YKLAEHLLEEGAKL   54 (200)
T ss_pred             CCEEEEECCCHHH-------HHHHHHHHHCCCEE
T ss_conf             9999998987999-------99999999679979


No 251
>PRK06599 DNA topoisomerase I; Validated
Probab=54.46  E-value=9.1  Score=17.37  Aligned_cols=36  Identities=14%  Similarity=0.213  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCC-----CCHHHHHHH
Q ss_conf             9999999999999999998433177982-----087899999
Q gi|254781172|r   15 EQARKELSSLEQEISYHDDCYYQYSKPI-----ILDSEYDAL   51 (731)
Q Consensus        15 ~~~~~~i~~L~~~i~~~~~~Yy~~~~p~-----isD~eYD~L   51 (731)
                      ...++.+..|.+.++.++..|- ..+|-     |+.+.|+.|
T Consensus        56 ~~~~k~i~~lk~l~k~ad~V~l-ATDpDREGEaIawhi~e~l   96 (776)
T PRK06599         56 DKAGKYVDAIVKDAKKAEAVYL-ATDPDREGESISWHVAEVI   96 (776)
T ss_pred             CCHHHHHHHHHHHHHCCCEEEE-CCCCCCCHHHHHHHHHHHH
T ss_conf             7678899999999847998998-9899704369999999985


No 252
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=54.37  E-value=14  Score=16.01  Aligned_cols=10  Identities=30%  Similarity=0.265  Sum_probs=4.4

Q ss_pred             CCEEEEECCH
Q ss_conf             7637773110
Q gi|254781172|r  300 DGLVYKVDEF  309 (731)
Q Consensus       300 DGiVikvn~~  309 (731)
                      |-.|+-+||-
T Consensus       216 ~~~Vin~DD~  225 (457)
T PRK01390        216 GTAVIGVDDA  225 (457)
T ss_pred             CEEEEECCCH
T ss_conf             8699968888


No 253
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=54.37  E-value=6.5  Score=18.49  Aligned_cols=10  Identities=40%  Similarity=1.251  Sum_probs=7.8

Q ss_pred             CCCCCCCCCC
Q ss_conf             0432657750
Q gi|254781172|r  431 PSFCPICQSR  440 (731)
Q Consensus       431 P~~CP~Cgs~  440 (731)
                      +..||+||+.
T Consensus       187 ~~~CPvCGs~  196 (307)
T PRK03564        187 RQYCPVCGSM  196 (307)
T ss_pred             CCCCCCCCCC
T ss_conf             8859988987


No 254
>KOG2906 consensus
Probab=53.94  E-value=4.9  Score=19.45  Aligned_cols=16  Identities=25%  Similarity=0.760  Sum_probs=12.8

Q ss_pred             CCCCCCCCCCCCCCCC
Q ss_conf             4326577501033786
Q gi|254781172|r  432 SFCPICQSRVVRDLNP  447 (731)
Q Consensus       432 ~~CP~Cgs~l~~~~~~  447 (731)
                      .+||.||+-|+.+.+.
T Consensus         2 ~FCP~Cgn~Live~g~   17 (105)
T KOG2906           2 LFCPTCGNMLIVESGE   17 (105)
T ss_pred             CCCCCCCCEEEEECCC
T ss_conf             4468878889994287


No 255
>PRK05823 consensus
Probab=53.93  E-value=10  Score=17.06  Aligned_cols=20  Identities=15%  Similarity=0.361  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998433
Q gi|254781172|r   17 ARKELSSLEQEISYHDDCYY   36 (731)
Q Consensus        17 ~~~~i~~L~~~i~~~~~~Yy   36 (731)
                      .++.+..|.+.+..++..|-
T Consensus        72 k~~~ik~l~~~~k~ad~vii   91 (691)
T PRK05823         72 KKEIIKSIKDKASKANNIYL   91 (691)
T ss_pred             HHHHHHHHHHHHHCCCEEEE
T ss_conf             99999999999847998998


No 256
>smart00350 MCM minichromosome  maintenance proteins.
Probab=53.65  E-value=5.4  Score=19.10  Aligned_cols=15  Identities=33%  Similarity=0.457  Sum_probs=6.1

Q ss_pred             HHHHHHHHHHHHHHC
Q ss_conf             111168999999882
Q gi|254781172|r  560 RHVGAEIARSLAKYY  574 (731)
Q Consensus       560 ~~vG~~~Ak~La~~f  574 (731)
                      |-+-+...+.|.++|
T Consensus       436 P~ls~eA~~~i~~~Y  450 (509)
T smart00350      436 PKLSEEAAEKLVKAY  450 (509)
T ss_pred             CCCCHHHHHHHHHHH
T ss_conf             978999999999999


No 257
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=53.47  E-value=14  Score=15.91  Aligned_cols=55  Identities=22%  Similarity=0.326  Sum_probs=36.8

Q ss_pred             CCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHHCC
Q ss_conf             25889987899999998298499811163217997788886379899749917379999999988286
Q gi|254781172|r  656 GTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNT  723 (731)
Q Consensus       656 Gtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~~~  723 (731)
                      |.|..-.+=+.--+.+.+||-|++|            ..| =.+=|++||++.++...|..||++|-.
T Consensus       157 GiLDSapDlDvLLLAkELdaavVss------------D~G-ir~WAe~LGlrfv~a~~Fp~ml~eylk  211 (221)
T COG1458         157 GILDSAPDLDVLLLAKELDAAVVSS------------DEG-IRTWAEKLGLRFVDAFKFPEMLEEYLK  211 (221)
T ss_pred             CCCCCCCHHHHHHHHHHHCCEEEEC------------CHH-HHHHHHHHCCEEECHHHHHHHHHHHHH
T ss_conf             4446654068999999838637735------------366-999999819765677665999999999


No 258
>pfam00122 E1-E2_ATPase E1-E2 ATPase.
Probab=53.09  E-value=5.3  Score=19.20  Aligned_cols=24  Identities=33%  Similarity=0.663  Sum_probs=18.7

Q ss_pred             CCCCCCCEEEEEECCCCHHHHHHHCC
Q ss_conf             68440768999835870256654101
Q gi|254781172|r  393 RDIRVGDRVLVKRAGEVIPKVVDIIV  418 (731)
Q Consensus       393 ~~I~iGd~V~I~RaGdVIP~I~~Vi~  418 (731)
                      .++.+||.|.| ++||.|| ...++.
T Consensus        50 ~~l~~GDiv~v-~~G~~IP-aDg~vi   73 (222)
T pfam00122        50 DELVVGDIVLL-KPGDRVP-ADGRII   73 (222)
T ss_pred             HHCCCCCEEEE-CCCCEEE-CCCEEE
T ss_conf             99788999998-9999962-174575


No 259
>TIGR01647 ATPase-IIIA_H plasma-membrane proton-efflux P-type ATPase; InterPro: IPR006534   These sequences represent the plasma membrane proton efflux P-type ATPase found in plants, fungi, protozoa, slime molds and archaea. The best studied representative is from yeast . ; GO: 0016887 ATPase activity, 0015992 proton transport, 0016021 integral to membrane.
Probab=53.05  E-value=7.7  Score=17.94  Aligned_cols=16  Identities=31%  Similarity=0.748  Sum_probs=5.4

Q ss_pred             CCCCCEEEEEECCCCHH
Q ss_conf             44076899983587025
Q gi|254781172|r  395 IRVGDRVLVKRAGEVIP  411 (731)
Q Consensus       395 I~iGd~V~I~RaGdVIP  411 (731)
                      +=+||.|.+ |.|||||
T Consensus       117 LVPGDvv~l-~~GdivP  132 (835)
T TIGR01647       117 LVPGDVVRL-KLGDIVP  132 (835)
T ss_pred             CCCCCEEEE-ECCCEEE
T ss_conf             797638987-2076401


No 260
>PRK06197 short chain dehydrogenase; Provisional
Probab=52.96  E-value=13  Score=16.17  Aligned_cols=14  Identities=14%  Similarity=0.145  Sum_probs=6.0

Q ss_pred             EECCCCHHHHHHHH
Q ss_conf             86598655666999
Q gi|254781172|r  152 ALRGDGHSGEDVSA  165 (731)
Q Consensus       152 ~TRGdG~~GeDVT~  165 (731)
                      +|=|+.-+|-....
T Consensus        21 ITGa~sGIG~~~A~   34 (306)
T PRK06197         21 VTGANTGLGYETAA   34 (306)
T ss_pred             ECCCCCHHHHHHHH
T ss_conf             91689599999999


No 261
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and  believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=52.88  E-value=4.7  Score=19.61  Aligned_cols=12  Identities=42%  Similarity=0.952  Sum_probs=9.5

Q ss_pred             ECCCCCCCCCCC
Q ss_conf             704326577501
Q gi|254781172|r  430 FPSFCPICQSRV  441 (731)
Q Consensus       430 ~P~~CP~Cgs~l  441 (731)
                      .|+.||.||.+-
T Consensus        17 aP~~CPvC~~~~   28 (34)
T cd00729          17 APEKCPICGAPK   28 (34)
T ss_pred             CCCCCCCCCCCH
T ss_conf             987586999967


No 262
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=52.52  E-value=12  Score=16.33  Aligned_cols=45  Identities=16%  Similarity=0.135  Sum_probs=21.9

Q ss_pred             HHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECC
Q ss_conf             6899997599665414887403211345566553100112343763777311
Q gi|254781172|r  257 MLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDE  308 (731)
Q Consensus       257 ~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~  308 (731)
                      .-+..+++|..+.    ..+.-.+.....+++   .+.+.-.+|+|||--.|
T Consensus        47 ~~~~Ake~G~~v~----v~dA~~D~~~Qi~qI---e~~I~qgvdaIiv~p~D   91 (330)
T PRK10355         47 FVKKAESLGAKVF----VQSANGNEETQMSQI---ENMINRGVDVLVIIPYN   91 (330)
T ss_pred             HHHHHHHCCCEEE----EECCCCCHHHHHHHH---HHHHHCCCCEEEEECCC
T ss_conf             9999997599899----971899989999999---99998599999996998


No 263
>PRK06500 short chain dehydrogenase; Provisional
Probab=52.47  E-value=15  Score=15.80  Aligned_cols=15  Identities=20%  Similarity=0.390  Sum_probs=9.0

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++++.|-+
T Consensus       232 as~iTG~~i~vDGG~  246 (249)
T PRK06500        232 SAFIVGSEIIVDGGM  246 (249)
T ss_pred             HCCCCCCEEEECCCC
T ss_conf             228148638889581


No 264
>PRK09001 DNA topoisomerase I; Validated
Probab=52.44  E-value=6.8  Score=18.34  Aligned_cols=17  Identities=29%  Similarity=0.348  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999843
Q gi|254781172|r   19 KELSSLEQEISYHDDCY   35 (731)
Q Consensus        19 ~~i~~L~~~i~~~~~~Y   35 (731)
                      +.+.+|.+..+.++.-|
T Consensus        96 kvv~~Lkklak~ad~V~  112 (869)
T PRK09001         96 KVVSELKKLAEKADHIY  112 (869)
T ss_pred             HHHHHHHHHHHCCCEEE
T ss_conf             99999999985699899


No 265
>PRK12825 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=52.26  E-value=15  Score=15.77  Aligned_cols=16  Identities=13%  Similarity=0.277  Sum_probs=9.7

Q ss_pred             CCCCCCCEEEEECCCC
Q ss_conf             8821686699972588
Q gi|254781172|r  644 SSEIENKKLVFTGTLQ  659 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~  659 (731)
                      ++..+|.++++.|-+.
T Consensus       233 s~~itG~~i~vDGGl~  248 (250)
T PRK12825        233 AGYITGQVIAVDGGMG  248 (250)
T ss_pred             HCCCCCCEEEECCCCC
T ss_conf             2282488689896813


No 266
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=52.19  E-value=12  Score=16.44  Aligned_cols=87  Identities=21%  Similarity=0.231  Sum_probs=47.4

Q ss_pred             HHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH--HHCCCHHHHHHHHHHHHHCCCCCHH
Q ss_conf             10001000134210014568999987522346667763010111168999999--8829989999978977612511778
Q gi|254781172|r  519 TSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLA--KYYLSYQNFAQEINNIIAHNNDDWL  596 (731)
Q Consensus       519 ~~~~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La--~~f~si~~l~~~~~~~~~~~~~~~e  596 (731)
                      -+.+-|+..-||.   +.-|+    .++.-.|+        +.+-.+++-.|-  ..|+            ...+.++++
T Consensus       278 YQADwLlrfYgF~---~~Ei~----~~g~~~ld--------~~lDPK~~wAl~~~d~FP------------Vdvn~A~~~  330 (404)
T COG4277         278 YQADWLLRFYGFS---ADEIL----ASGGDFLD--------PDLDPKTAWALKHMDRFP------------VDVNKAPYK  330 (404)
T ss_pred             HHHHHHHHHHCCC---HHHHH----HCCCCCCC--------CCCCHHHHHHHHCCCCCC------------CCCCCCCHH
T ss_conf             7777899970888---78887----44897557--------887834577773355365------------133456777


Q ss_pred             HHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCC
Q ss_conf             76138886789999999996697999999999973387
Q gi|254781172|r  597 SLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSP  634 (731)
Q Consensus       597 ~L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~  634 (731)
                      +|..++|||.++|..|+.-=.  ...-.++.|.+.++.
T Consensus       331 ~llRVPGiG~ksa~rIv~~Rr--~~rl~~e~Lkk~Gvv  366 (404)
T COG4277         331 ELLRVPGIGVKSARRIVMTRR--RTRLTLEDLKKLGVV  366 (404)
T ss_pred             HHCCCCCCCHHHHHHHHHHHH--HCCCCHHHHHHHCEE
T ss_conf             821168877378899988742--302679898653303


No 267
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=52.00  E-value=8.3  Score=17.70  Aligned_cols=19  Identities=16%  Similarity=0.111  Sum_probs=10.8

Q ss_pred             HHHHCCCCCCHHHHHHHHH
Q ss_conf             8761388867899999999
Q gi|254781172|r  596 LSLIRVPLVGDIIAQAIVE  614 (731)
Q Consensus       596 e~L~~I~GiG~~~A~si~~  614 (731)
                      +.+-.|+|||+++|..++.
T Consensus        16 DnipGV~GIG~ktA~~ll~   34 (36)
T smart00279       16 DNIPGVKGIGPKTALKLLR   34 (36)
T ss_pred             CCCCCCCCCCHHHHHHHHH
T ss_conf             6889999747899999998


No 268
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit; InterPro: IPR011773   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.    This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins , .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription DNA-dependent.
Probab=51.82  E-value=13  Score=16.10  Aligned_cols=56  Identities=14%  Similarity=0.323  Sum_probs=40.6

Q ss_pred             CCHHH--HHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             10354--10355556530576540454101101067775310001000134210014568999987522
Q gi|254781172|r  481 FNIEG--LGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRN  547 (731)
Q Consensus       481 ldI~G--LG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK~  547 (731)
                      |.|+.  |+-....=|=.+|     |.+++||-.++..      +|+++.-||.||.+=|.+.+++...
T Consensus       261 ~~IeeLdLSVRs~NCLk~~g-----I~t~geL~~~~e~------eLl~i~NfGkKSl~EI~ekL~~~lg  318 (324)
T TIGR02027       261 IKIEELDLSVRSYNCLKRAG-----IHTLGELVSKSEE------ELLKIKNFGKKSLDEIKEKLAEKLG  318 (324)
T ss_pred             CCCHHHHHHHHHHHHHHHHC-----CHHHHHHHHHHHH------HHHCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             78003245489886464603-----5417888860389------8841788573338999999887618


No 269
>pfam09538 FYDLN_acid Protein of unknown function (FYDLN_acid). Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=51.73  E-value=5.8  Score=18.88  Aligned_cols=11  Identities=45%  Similarity=1.132  Sum_probs=5.1

Q ss_pred             CCCCCCCCCCC
Q ss_conf             04326577501
Q gi|254781172|r  431 PSFCPICQSRV  441 (731)
Q Consensus       431 P~~CP~Cgs~l  441 (731)
                      |-.||+||...
T Consensus        26 p~~cp~cg~~~   36 (104)
T pfam09538        26 PIVCPKCGEEV   36 (104)
T ss_pred             CCCCCCCCCEE
T ss_conf             87189988874


No 270
>TIGR02354 thiF_fam2 thiamine biosynthesis protein ThiF; InterPro: IPR012729    Members of the HesA/MoeB/ThiF family of proteins (IPR000594 from INTERPRO) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees. The Escherichia coli ThiF and MoeB proteins are seemingly more closely related than the E. coli ThiF and Campylobacter (for example) ThiF. This entry represents the divergent clade of putative ThiF proteins as found in Campylobacter..
Probab=51.43  E-value=6.8  Score=18.36  Aligned_cols=121  Identities=16%  Similarity=0.227  Sum_probs=56.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHH
Q ss_conf             00145689999875223466677630101111689999998829989999978977612511778761388867899999
Q gi|254781172|r  532 DVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQA  611 (731)
Q Consensus       532 eKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~s  611 (731)
                      .|...++++.+++++-     -++|||  |+|...|=.||+..-....+-+ . +..+-++..++. -.|..+|...+++
T Consensus         9 ar~tpk~~~kL~~a~V-----AicGlG--GLGS~~AinLAR~GigkLiLvD-f-DvvepsNLnRQq-Y~~s~~G~~KteA   78 (200)
T TIGR02354         9 ARHTPKVYEKLKKASV-----AICGLG--GLGSNVAINLARAGIGKLILVD-F-DVVEPSNLNRQQ-YKVSDVGKKKTEA   78 (200)
T ss_pred             HCCCHHHHHHHCCCCE-----EEEECC--CCHHHHHHHHHHHCCCCEEEEE-E-CEECCCCCCHHH-HHHHHCCCHHHHH
T ss_conf             4178268898505827-----897016--1168999999873022025664-0-432366561325-7876248621799


Q ss_pred             HHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHH
Q ss_conf             9999669799999999997338776543224688216866999725889987899999998
Q gi|254781172|r  612 IVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQ  672 (731)
Q Consensus       612 i~~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~  672 (731)
                      |.|-++.-.   -.-++ +  .....-.+.+.++.|.+-=||+--    |...+++.++.+
T Consensus        79 lke~i~ein---Py~~i-e--~~d~ki~E~N~~~~fkdaDiv~EA----FDna~aKam~~n  129 (200)
T TIGR02354        79 LKENISEIN---PYVEI-E--IIDEKIDEENLDKLFKDADIVCEA----FDNAEAKAMLVN  129 (200)
T ss_pred             HHHHHHHHC---CCCEE-E--EEECCCCHHHHHHHHHCCCEEEEC----CCCHHHHHHHHH
T ss_conf             998786508---84212-3--110212766798784067478871----699889999999


No 271
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF; InterPro: IPR004421   The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins , , . Members of the HypF family are accessory proteins involved in hydrogenase maturation. They contain the following domains: acylphosphatase, zinc fingers (2 repeats), a YrdC-like domain, and a C-terminal domain with a putative O-carbamoyltransferase motif.   The presence of CO and CN- ligands of the active site iron atoms is essential for [NiFe]-hydrogenase enzyme activity . Both ligands have been suggested to originate from carbamoylphosphate , which is required for maturation of [NiFe]-hydrogenases . Escherichia coli HypF interacts with carbamoylphosphate as a substrate and releases inorganic phosphate . In addition, HypF also cleaves ATP into AMP and pyrophosphate in the presence of carbamoylphosphate. This, and the fact that HypF catalyzes a carbamoylphosphate-dependent pyrophosphate ATP exchange reaction, suggest that the protein catalyzes the activation of carbamoylphosphate .   The mechanism of action of HypF, as well as of its individual domains, is not yet clear. Mutations in any of the three major signature motifs, the acylphosphatase, the zinc fingers, and the O-carbamoyltransferase motif, can block carbamoylphosphate phosphatase activity. This indicates an integrated cooperativity between these domains in the cleavage reaction .   The N-terminal acylphosphatase (ACP) domain is thought to support the conversion of carbamoylphosphate into CO and CN- , . Biochemical results demonstrating its ACP activity are not available , . ACPs are small enzymes that specifically catalyze the hydrolysis of carboxylphosphate bonds in acylphosphates, including carbamoylphosphate . Zinc fingers have been implicated in bivalent cation binding or as part of a chaperone domain interacting with the large subunit precursor, but experimental studies on such a function are lacking thus far. The YrdC-like domain is present in protein families with regulatory functions (IPR012200 from INTERPRO, IPR010923 from INTERPRO) and has been implicated in RNA binding . It is not clear what function it may have in members of the HypF family. A C-terminal domain is distantly related to peptidase M22, but contains a conserved O-carbamoyltransferase motif required for the carbamoylphosphate phosphatase activity . The function of this domain is not clear.   Nomenclature note: the following names are used as synonyms of HypF: HupY in Azotobacter chroococcum, HupN in Rhizobium leguminosarum, HydA in Escherichia coli. In other organisms, these names are used to designate various "hydrogenase cluster" proteins unrelated to the members of this family. ; GO: 0030528 transcription regulator activity.
Probab=51.07  E-value=4.4  Score=19.79  Aligned_cols=28  Identities=18%  Similarity=0.375  Sum_probs=16.2

Q ss_pred             CEEEEECCCCC--CCHHHHHHHHHHCCCEE
Q ss_conf             66999725889--98789999999829849
Q gi|254781172|r  650 KKLVFTGTLQK--IQRHKAQEYVTQLGAVV  677 (731)
Q Consensus       650 k~vV~TGtl~~--~~R~e~~~~ie~~Ggkv  677 (731)
                      ++|++||-.-.  +=+.++...+...|...
T Consensus       748 ~~i~~sGGV~~N~~l~~~~~~~~~~~gf~~  777 (799)
T TIGR00143       748 EKIVISGGVFYNRLLLERVAKYLKKAGFEF  777 (799)
T ss_pred             EEEEECCCHHHHHHHHHHHHHHHHHCCCCE
T ss_conf             699933843888999999999998579714


No 272
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=50.84  E-value=9.1  Score=17.39  Aligned_cols=48  Identities=19%  Similarity=0.188  Sum_probs=35.9

Q ss_pred             CCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             01011116899999988-29989999978977612511778761388867899999999
Q gi|254781172|r  557 LGIRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE  614 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~  614 (731)
                      +.++++....+..|... |.+++.+.          ..+.++|..++|+++..|..+..
T Consensus       377 ~~~~~~~~~~~~~l~~~g~~~~edl~----------~~~~del~~~~~~~~e~a~~li~  425 (428)
T PRK09202        377 LNLEGLDPELAFKLAEKGVKTLEDLA----------ELAVDELIDIEGLDEEEAGELIM  425 (428)
T ss_pred             HHCCCCCHHHHHHHHHCCCCCHHHHH----------CCCHHHHHHCCCCCHHHHHHHHH
T ss_conf             64569999999999986998799996----------57988896377989999999998


No 273
>PRK00141 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=50.80  E-value=15  Score=15.61  Aligned_cols=12  Identities=17%  Similarity=0.003  Sum_probs=5.2

Q ss_pred             CCEEEEECCHHC
Q ss_conf             763777311000
Q gi|254781172|r  300 DGLVYKVDEFSL  311 (731)
Q Consensus       300 DGiVikvn~~~~  311 (731)
                      +..|+-.||-..
T Consensus       225 ~~~vi~~Dd~~~  236 (476)
T PRK00141        225 PVAVIGADDPYV  236 (476)
T ss_pred             CCEEEECCCHHH
T ss_conf             824997787899


No 274
>PRK08628 short chain dehydrogenase; Provisional
Probab=50.63  E-value=15  Score=15.59  Aligned_cols=16  Identities=19%  Similarity=0.202  Sum_probs=8.6

Q ss_pred             CCCCCCCEEEEECCCC
Q ss_conf             8821686699972588
Q gi|254781172|r  644 SSEIENKKLVFTGTLQ  659 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~  659 (731)
                      ++..+|..+.+-|-+-
T Consensus       236 s~~iTG~~i~VDGG~v  251 (258)
T PRK08628        236 ASHTTGQWLFVDGGYV  251 (258)
T ss_pred             HCCCCCCEEEECCCEE
T ss_conf             3493388799739888


No 275
>COG2099 CobK Precorrin-6x reductase [Coenzyme metabolism]
Probab=50.30  E-value=16  Score=15.56  Aligned_cols=48  Identities=19%  Similarity=0.512  Sum_probs=25.3

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCC---CC--HHHHHHHCCCEEE
Q ss_conf             8669997258899878999999982984998111632179977888---86--3798997499173
Q gi|254781172|r  649 NKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNP---GS--KLEKAQQLGVKIM  709 (731)
Q Consensus       649 gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~---gS--Kl~KA~~LgI~Ii  709 (731)
                      ...|.+-|-   |+-+.=+.++++.+.          ++||.+++.   |+  |+.-|.+||||||
T Consensus       174 ~~Iia~~GP---fs~~~n~all~q~~i----------d~vItK~SG~~Gg~~~Ki~aA~eLgi~VI  226 (257)
T COG2099         174 ARIIAMRGP---FSEEDNKALLEQYRI----------DVVVTKNSGGAGGTYEKIEAARELGIPVI  226 (257)
T ss_pred             HHEEEECCC---CCHHHHHHHHHHHCC----------CEEEECCCCCCCCCHHHHHHHHHCCCCEE
T ss_conf             668982388---675889999998488----------89998267766673898999998699389


No 276
>pfam11672 DUF3268 Protein of unknown function (DUF3268). This family of proteins has no known function.
Probab=50.28  E-value=6  Score=18.75  Aligned_cols=15  Identities=33%  Similarity=0.691  Sum_probs=11.9

Q ss_pred             ECCCCCCCCCCCCCC
Q ss_conf             704326577501033
Q gi|254781172|r  430 FPSFCPICQSRVVRD  444 (731)
Q Consensus       430 ~P~~CP~Cgs~l~~~  444 (731)
                      .|..||.||...+..
T Consensus         1 ~p~~CpYCg~~~~l~   15 (102)
T pfam11672         1 KPVRCPYCGGKVELR   15 (102)
T ss_pred             CCCCCCCCCCEEEEE
T ss_conf             994079999955882


No 277
>TIGR01900 dapE-gram_pos succinyl-diaminopimelate desuccinylase; InterPro: IPR010174   This entry represents a clade of succinyl-diaminopimelate desuccinylases from actinobacteria (high-GC Gram-positives) and is based on the characterisation of the enzyme from Corynebacterium glutamicum . This enzyme is involved in the biosynthesis of lysine, and is related to the enzyme acetylornithine deacetylase and other amidases and peptidases. They are classified as non-peptidases homologs belonging to MEROPS peptidase family M20A.
Probab=50.23  E-value=9.7  Score=17.17  Aligned_cols=105  Identities=22%  Similarity=0.385  Sum_probs=62.8

Q ss_pred             ECCCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHH
Q ss_conf             35870256654101235787304777043265775010337865445210100354344114466553321301231035
Q gi|254781172|r  405 RAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIE  484 (731)
Q Consensus       405 RaGdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~  484 (731)
                      ++.-|||....|-.+-|-+       |..          +.++.     ..+..-.  +. ..-.+.++|-+  .++..+
T Consensus       243 ~~~NVIPD~~~~~~NyRFA-------P~~----------~L~EA-----kalmmGa--da-GaelGn~EHV~--~~~~l~  295 (373)
T TIGR01900       243 KATNVIPDLARVNLNYRFA-------PDK----------DLAEA-----KALMMGA--DA-GAELGNIEHVV--ETLVLD  295 (373)
T ss_pred             CCCCCCCCCEEEEEEEECC-------CCC----------CHHHH-----HHHHHCC--CC-CCCCCCCCEEE--EEEEEC
T ss_conf             4244156512674212018-------872----------57889-----8886302--23-42115721467--401641


Q ss_pred             HHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHH-HHHHH-------HHH
Q ss_conf             4103555565305765404541011010677753100010001342100145689999875223-46667-------763
Q gi|254781172|r  485 GLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNI-SLERF-------IFS  556 (731)
Q Consensus       485 GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK~~-~L~r~-------L~A  556 (731)
                      |-+-  |+.=++.                        +.-..+||.+...++-|++.+.+.+.. ||.+|       -.+
T Consensus       296 G~~G--ie~~~~D------------------------~~~~A~PGL~~~~~~~L~~~V~~~~~RdPlAKlGWTDV~RFS~  349 (373)
T TIGR01900       296 GYDG--IEIEVKD------------------------EAGSALPGLNAQLASDLVDLVKRRKIRDPLAKLGWTDVARFSA  349 (373)
T ss_pred             CCCC--EEEEEEC------------------------CCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHH
T ss_conf             7774--4799862------------------------8888788776356789999863114666222325303566653


Q ss_pred             CCHHHH
Q ss_conf             010111
Q gi|254781172|r  557 LGIRHV  562 (731)
Q Consensus       557 LGI~~v  562 (731)
                      ||||-+
T Consensus       350 lGIPA~  355 (373)
T TIGR01900       350 LGIPAL  355 (373)
T ss_pred             CCCCEE
T ss_conf             276602


No 278
>PRK03906 mannonate dehydratase; Provisional
Probab=50.04  E-value=8.9  Score=17.45  Aligned_cols=83  Identities=16%  Similarity=0.219  Sum_probs=42.2

Q ss_pred             EECCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHH
Q ss_conf             45166425702159999999999999986124677761199994158189999985998998886598655666999775
Q gi|254781172|r   89 VTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIR  168 (731)
Q Consensus        89 v~H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~  168 (731)
                      -=|.+|   -..+++.+||.+--+.|...                  |+..+.+ |.--....+-+|.|..-+-|-.-..
T Consensus        30 aLh~ip---~GevW~~eeI~~~k~~Ie~~------------------GL~w~VV-ESvPVhe~IK~g~~~~d~~Ienyk~   87 (389)
T PRK03906         30 ALHHIP---NGEVWPVEEILKRKAEIEAA------------------GLEWSVV-ESVPVHEDIKTGTPNRDQYIENYKQ   87 (389)
T ss_pred             ECCCCC---CCCCCCHHHHHHHHHHHHHC------------------CCCEEEE-ECCCCHHHHHCCCCCHHHHHHHHHH
T ss_conf             023689---98867999999999999974------------------9818998-4678568887499878999999999


Q ss_pred             HHCCCCCCCCCCCCCEEEEEEEEEEECHHHHH
Q ss_conf             31024322335445504899999985202123
Q gi|254781172|r  169 AIPTIPRVLSLNIPEIIEVRGEVYISKNDFLA  200 (731)
Q Consensus       169 ~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~  200 (731)
                      +|+++-.   ..    +.+=+==|||--||-+
T Consensus        88 sirNLa~---~G----I~viCYNFMPv~DWtR  112 (389)
T PRK03906         88 TLRNLAA---AG----IKVVCYNFMPVFDWTR  112 (389)
T ss_pred             HHHHHHH---CC----CCEEEEECCCCCCCCC
T ss_conf             9999997---69----9789650366465003


No 279
>TIGR01186 proV glycine betaine/L-proline transport ATP binding subunit; InterPro: IPR005892   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation.   Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits this transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L. lactis functionally complements an Escherichia coli proU mutant. The complementing locus is similar to a opuA locus in Bacillus subtlis. This clarifies the differences in nomenclature.; GO: 0005524 ATP binding, 0015171 amino acid transmembrane transporter activity, 0006865 amino acid transport, 0016020 membrane.
Probab=49.85  E-value=7.5  Score=18.02  Aligned_cols=30  Identities=37%  Similarity=0.673  Sum_probs=24.2

Q ss_pred             CCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCH
Q ss_conf             6400010148989997502345432224684407689998358702
Q gi|254781172|r  365 GALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVI  410 (731)
Q Consensus       365 G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVI  410 (731)
                      +-||=.+| |-.|+=               |+|||+|.|-++|+|.
T Consensus       181 ~kTIvFit-HDlDEA---------------~rigDRIvilk~GeiV  210 (372)
T TIGR01186       181 QKTIVFIT-HDLDEA---------------LRIGDRIVILKAGEIV  210 (372)
T ss_pred             CCEEEEEE-CCHHHH---------------HHHHHHHHHEECCCEE
T ss_conf             98089994-176788---------------7675132011068678


No 280
>pfam06054 CoiA Competence protein CoiA-like family. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterized protein.
Probab=49.68  E-value=7  Score=18.25  Aligned_cols=18  Identities=17%  Similarity=0.193  Sum_probs=12.4

Q ss_pred             CCCCHHHHHHHHHCCCCC
Q ss_conf             100003689999759966
Q gi|254781172|r  251 AKGQYEMLQKMRCLGFPV  268 (731)
Q Consensus       251 ~~~~~e~l~~L~~~GF~v  268 (731)
                      .........+++..|++|
T Consensus        66 l~gK~~L~~~l~~~~~~v   83 (348)
T pfam06054        66 LAAKLLLYQWLKRQEFKV   83 (348)
T ss_pred             HHHHHHHHHHHHHCCCCE
T ss_conf             999999999998579976


No 281
>pfam10941 DUF2620 Protein of unknown function DUF2620. This is a bacterial family of proteins with unknown function.
Probab=49.64  E-value=16  Score=15.48  Aligned_cols=72  Identities=22%  Similarity=0.340  Sum_probs=37.4

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHHCCC-EEEEEEECC-----------EEEEEECCCCC--CHHHHHHHC-C------C--
Q ss_conf             66999725889987899999998298-499811163-----------21799778888--637989974-9------9--
Q gi|254781172|r  650 KKLVFTGTLQKIQRHKAQEYVTQLGA-VVSAILSRK-----------TDIIIVGDNPG--SKLEKAQQL-G------V--  706 (731)
Q Consensus       650 k~vV~TGtl~~~~R~e~~~~ie~~Gg-kv~sSVSkk-----------T~~LI~ge~~g--SKl~KA~~L-g------I--  706 (731)
                      |+||+.|-   ..|+++++.|++.|+ ++.-.|..+           .||-+=-=++|  .-|.=|--| |      |  
T Consensus         1 ~kivIgGq---l~K~~i~~~i~~~~~~~~ev~i~sDmdAAM~vK~G~aDYYiGACnTGgGgALamAIallG~~~C~Tvs~   77 (117)
T pfam10941         1 KRIVIGGQ---LQKEEIAELIEETAGGAVEVTIKSDLDAAMAVKNGKADYYIGACNTGAGGALAMAIAILGKDKCATIAM   77 (117)
T ss_pred             CEEEECCC---CCHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHCCCCEEEEEC
T ss_conf             91888472---259999999998689836999705099998876699676666447896199999999948463578556


Q ss_pred             --EEECHHHHHHHHHHHCCC
Q ss_conf             --173799999999882865
Q gi|254781172|r  707 --KIMNEEQFLFLLQQYNTT  724 (731)
Q Consensus       707 --~Ii~e~ef~~ll~~~~~~  724 (731)
                        .+.+|++..+++++.+..
T Consensus        78 pg~~~~eeeI~~~v~~GKkA   97 (117)
T pfam10941        78 PGKPPKEEEIEKAVDEGKKA   97 (117)
T ss_pred             CCCCCCHHHHHHHHHCCCCE
T ss_conf             99999999999999748804


No 282
>TIGR00789 flhB_rel FlhB domain protein; InterPro: IPR004683 This group describes a short protein (80-93 residues) homologous to the C-terminus of the flagellar biosynthetic protein FlhB. It is found so far only in species that also have FlhB. In a phylogenetic tree based on alignment of both this family and the homologous region of FlhB and its homologs, the members of this family form a monophyletic set..
Probab=49.51  E-value=13  Score=16.19  Aligned_cols=24  Identities=25%  Similarity=0.445  Sum_probs=9.5

Q ss_pred             HHHHHCCCEEECHHHHHHHHHHHC
Q ss_conf             989974991737999999998828
Q gi|254781172|r  699 EKAQQLGVKIMNEEQFLFLLQQYN  722 (731)
Q Consensus       699 ~KA~~LgI~Ii~e~ef~~ll~~~~  722 (731)
                      +.|++.||||-..+.+.+.|.+-+
T Consensus        34 ~~AK~~gipi~ed~~L~~~L~~l~   57 (84)
T TIGR00789        34 ELAKKHGIPIKEDEDLVDVLLKLD   57 (84)
T ss_pred             HHHHHCCCCCCCCHHHHHHHHHCC
T ss_conf             999763899765828999874405


No 283
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein; InterPro: IPR013456   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This entry represents the D-xylose ABC transporter substrate-binding protein which is a periplasmic (when in Gram-negative bacteria) binding protein for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter..
Probab=49.46  E-value=16  Score=15.46  Aligned_cols=13  Identities=0%  Similarity=0.066  Sum_probs=4.4

Q ss_pred             CCCCHHHHHHHHH
Q ss_conf             2100145689999
Q gi|254781172|r  530 FGDVSVTNLYDSI  542 (731)
Q Consensus       530 fgeKsa~nL~~sI  542 (731)
                      |-...|.++++++
T Consensus       165 Wlp~~A~~~~E~~  177 (307)
T TIGR02634       165 WLPENALKIMENA  177 (307)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             2568899999988


No 284
>TIGR00340 zpr1_rel zinc finger protein ZPR1 homolog; InterPro: IPR004470   Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, however they are now recognised to bind DNA, RNA, protein and/or lipid substrates , , , , . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.    (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries).   This entry represents ZPR1-type zinc finger domains. ZPR1 was shown experimentally to bind approximately two moles of zinc, and has two copies of a domain homologous to this protein, each containing a putative zinc finger of the form CXXCX(25)CXXC. ZPR1 binds the tyrosine kinase domain of epidermal growth factor receptor but is displaced by receptor activation and autophosphorylation after which it redistributes in part to the nucleus. The proteins described by this family by analogy may be suggested to play a role in signal transduction as proven for other Z-finger binding proteins.   Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) . ZPR1 interacts with complexes formed by SMN , and may act as a modifier that effects the severity of SMA.   More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0008270 zinc ion binding.
Probab=49.35  E-value=5.9  Score=18.85  Aligned_cols=37  Identities=14%  Similarity=0.225  Sum_probs=20.2

Q ss_pred             HHHHCCCCCCHHHHHHHH---HHHCCH---HHHHHHHHHHHHC
Q ss_conf             876138886789999999---996697---9999999999733
Q gi|254781172|r  596 LSLIRVPLVGDIIAQAIV---EFYQNP---RNICAVEALLKEV  632 (731)
Q Consensus       596 e~L~~I~GiG~~~A~si~---~ff~~~---~n~~~i~~L~~~~  632 (731)
                      -.+++|+||=+...+.+.   +|+.++   +....++.+++..
T Consensus        92 G~IsniEGvleR~~~~l~~~~~~~e~d~dEE~v~~~~~il~~I  134 (168)
T TIGR00340        92 GYISNIEGVLERVEEVLKTALDLEEEDRDEEKVKKVEEILKKI  134 (168)
T ss_pred             CEEEHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf             0352146777889999988630013221047789999999875


No 285
>KOG0478 consensus
Probab=49.00  E-value=12  Score=16.47  Aligned_cols=44  Identities=20%  Similarity=0.249  Sum_probs=22.3

Q ss_pred             CCCCCC---HHHHHHHHHHC-----CCEEEEEEECCEEEEEECCCCCCHHHH
Q ss_conf             588998---78999999982-----984998111632179977888863798
Q gi|254781172|r  657 TLQKIQ---RHKAQEYVTQL-----GAVVSAILSRKTDIIIVGDNPGSKLEK  700 (731)
Q Consensus       657 tl~~~~---R~e~~~~ie~~-----Ggkv~sSVSkkT~~LI~ge~~gSKl~K  700 (731)
                      -|.+|+   |+-+.+..|+.     -|=+-.|.+.-|+.|-+..-.+||+..
T Consensus       534 EFDKM~dStrSvLhEvMEQQTvSIAKAGII~sLNAR~SVLAaANP~~skynp  585 (804)
T KOG0478         534 EFDKMSDSTRSVLHEVMEQQTLSIAKAGIIASLNARCSVLAAANPIRSKYNP  585 (804)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEECCCCCEEEEEECCCCCCCCC
T ss_conf             2333327788999999987631174302234216653034453543245799


No 286
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=48.49  E-value=5.9  Score=18.82  Aligned_cols=15  Identities=20%  Similarity=0.603  Sum_probs=5.5

Q ss_pred             EEEEEEC-CCEEEEEC
Q ss_conf             7433302-64000101
Q gi|254781172|r  358 LEPVNIG-GALITNAT  372 (731)
Q Consensus       358 ~ePV~l~-G~~V~rat  372 (731)
                      +.-++++ |-.|.+|.
T Consensus        90 ITSIE~~~gkRV~~A~  105 (201)
T COG1326          90 ITSIELGGGKRVKSAK  105 (201)
T ss_pred             EEEEEECCCCCCCCCC
T ss_conf             9998508875223021


No 287
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=48.29  E-value=13  Score=16.24  Aligned_cols=21  Identities=24%  Similarity=0.243  Sum_probs=11.2

Q ss_pred             EEEEEEEEEEECCCEEEEECC
Q ss_conf             899997433302640001014
Q gi|254781172|r  353 TPVARLEPVNIGGALITNATL  373 (731)
Q Consensus       353 tPva~~ePV~l~G~~V~ratl  373 (731)
                      +-...+.|-+|=|+|-.-..|
T Consensus       143 ~~~i~L~pFTLIGATTr~g~L  163 (328)
T PRK00080        143 SIRLDLPPFTLIGATTRAGLL  163 (328)
T ss_pred             EEECCCCCEEEEECCCCCCCC
T ss_conf             455589983474013676657


No 288
>COG0474 MgtA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=48.29  E-value=8.2  Score=17.73  Aligned_cols=48  Identities=19%  Similarity=0.239  Sum_probs=25.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC
Q ss_conf             0001342100145689999875223466677630101111689999998829
Q gi|254781172|r  524 IENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYL  575 (731)
Q Consensus       524 l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~  575 (731)
                      ++.+-||-++-=+..-++|+..++....-.+    |-|=...||+.+++..+
T Consensus       538 ~lGl~g~~Dppr~~v~~aI~~l~~AGI~v~M----iTGD~~~TA~aIa~~~G  585 (917)
T COG0474         538 FLGLTGIEDPPREDVKEAIEELREAGIKVWM----ITGDHVETAIAIAKECG  585 (917)
T ss_pred             EEEEEEECCCCCCCHHHHHHHHHHCCCCEEE----ECCCCHHHHHHHHHHHC
T ss_conf             0200121289971189999999988994799----87999899999999819


No 289
>PRK05876 short chain dehydrogenase; Provisional
Probab=48.20  E-value=17  Score=15.32  Aligned_cols=16  Identities=6%  Similarity=0.320  Sum_probs=6.8

Q ss_pred             CCHHHHHHHHHHHHHC
Q ss_conf             1035410355556530
Q gi|254781172|r  481 FNIEGLGKQQLDFFFK  496 (731)
Q Consensus       481 ldI~GLG~k~Ie~L~e  496 (731)
                      |..+-+++.+++.+-+
T Consensus       224 ~~~d~vA~~v~~~i~~  239 (275)
T PRK05876        224 LGVDDIAQLTADAILA  239 (275)
T ss_pred             CCHHHHHHHHHHHHHC
T ss_conf             9999999999999960


No 290
>COG3845 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]
Probab=48.12  E-value=9.8  Score=17.13  Aligned_cols=43  Identities=35%  Similarity=0.482  Sum_probs=30.1

Q ss_pred             EEEEEEEEEEC------------CCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHH
Q ss_conf             99997433302------------640001014898999750234543222468440768999835870256
Q gi|254781172|r  354 PVARLEPVNIG------------GALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPK  412 (731)
Q Consensus       354 Pva~~ePV~l~------------G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP~  412 (731)
                      |+|++.|-+++            |.+|=..| |-.++|.++               -|+|+|.|.|.|+-.
T Consensus       167 PTaVLTP~E~~~lf~~l~~l~~~G~tIi~IT-HKL~Ev~~i---------------aDrvTVLR~Gkvvgt  221 (501)
T COG3845         167 PTAVLTPQEADELFEILRRLAAEGKTIIFIT-HKLKEVMAI---------------ADRVTVLRRGKVVGT  221 (501)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCEEEEEE-CCHHHHHHH---------------HCEEEEEECCEEEEE
T ss_conf             7535898999999999999997799799993-508999976---------------373699857748866


No 291
>pfam05876 Terminase_GpA Phage terminase large subunit (GpA). This family consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities.
Probab=48.06  E-value=15  Score=15.66  Aligned_cols=19  Identities=32%  Similarity=0.342  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHHHHCCHHHC
Q ss_conf             9999999999897720311
Q gi|254781172|r   49 DALKRRCDAIAHAFPDLAR   67 (731)
Q Consensus        49 D~L~~~L~~le~~~p~~~~   67 (731)
                      |....+|.-+=...|.+..
T Consensus        77 ~~s~~rl~Pmi~~sP~L~~   95 (552)
T pfam05876        77 RFSKDRLDPMIRASPALRE   95 (552)
T ss_pred             HHHHHHHHHHHHCCHHHHH
T ss_conf             9999989999861989997


No 292
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=47.71  E-value=17  Score=15.27  Aligned_cols=26  Identities=19%  Similarity=0.220  Sum_probs=15.0

Q ss_pred             EEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf             00010148989997502345432224684407689998
Q gi|254781172|r  367 LITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVK  404 (731)
Q Consensus       367 ~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~  404 (731)
                      +|+.|+.||.+.|.            -+|-+|..+.|.
T Consensus       616 ~l~~a~~~NLk~v~------------v~iPlg~lt~Vt  641 (944)
T PRK00349        616 KLKGARENNLKNVD------------VEIPLGKFTCVT  641 (944)
T ss_pred             EECCCCCCCCCCCC------------EEECCCCEEEEE
T ss_conf             62583020588764------------354389668996


No 293
>PRK05866 short chain dehydrogenase; Provisional
Probab=47.64  E-value=17  Score=15.29  Aligned_cols=13  Identities=8%  Similarity=0.072  Sum_probs=7.7

Q ss_pred             CCHHHHHHHHHHH
Q ss_conf             0014568999987
Q gi|254781172|r  532 DVSVTNLYDSINK  544 (731)
Q Consensus       532 eKsa~nL~~sIe~  544 (731)
                      |.-|+.+++++++
T Consensus       245 e~~A~~iv~a~~~  257 (290)
T PRK05866        245 DEAAEWMVTAART  257 (290)
T ss_pred             HHHHHHHHHHHHC
T ss_conf             9999999999844


No 294
>PRK05582 DNA topoisomerase I; Validated
Probab=47.57  E-value=10  Score=16.96  Aligned_cols=22  Identities=9%  Similarity=0.241  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999998433
Q gi|254781172|r   15 EQARKELSSLEQEISYHDDCYY   36 (731)
Q Consensus        15 ~~~~~~i~~L~~~i~~~~~~Yy   36 (731)
                      ...++.+..|.+.+.+++..|-
T Consensus        57 ~~~~k~i~~lk~l~k~ad~iii   78 (692)
T PRK05582         57 KDKKELVKKIKKLAKKADKIYL   78 (692)
T ss_pred             CCHHHHHHHHHHHHHCCCEEEE
T ss_conf             6679999999999865998998


No 295
>PRK12823 benD 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase; Provisional
Probab=47.32  E-value=17  Score=15.23  Aligned_cols=12  Identities=33%  Similarity=0.279  Sum_probs=6.9

Q ss_pred             CCCCCCEEEEEC
Q ss_conf             821686699972
Q gi|254781172|r  645 SEIENKKLVFTG  656 (731)
Q Consensus       645 ~~l~gk~vV~TG  656 (731)
                      +..+|.++.+.|
T Consensus       245 ~~iTG~~i~VDG  256 (260)
T PRK12823        245 SYITGSVLPVGG  256 (260)
T ss_pred             CCCCCCEEEECC
T ss_conf             480478688685


No 296
>PRK09783 copper/silver efflux system membrane fusion protein CusB; Provisional
Probab=47.30  E-value=7.3  Score=18.12  Aligned_cols=95  Identities=16%  Similarity=0.103  Sum_probs=47.4

Q ss_pred             CCCCCCCCEEEEECCHHCCCCC-CC-----CCCCCCCEEEECCCCCEE-EEEEEEEE----EEECCC--CEEEEEEEEEE
Q ss_conf             1123437637773110001115-87-----656866312311456215-89987889----940356--22589999743
Q gi|254781172|r  294 TLPYDIDGLVYKVDEFSLQKQL-GE-----RARSPRWMISHKFAEKQA-STRLLDID----IQIGRT--GILTPVARLEP  360 (731)
Q Consensus       294 ~l~y~iDGiVikvn~~~~q~~l-G~-----ts~~PrwaiA~Kf~~e~~-~T~v~~I~----wqvgRt--G~itPva~~eP  360 (731)
                      .+-=++||+|...+-..-+-.- |.     ..-+.-|..|-=|+.+.. ...-..+.    -..|++  |++.   .+.|
T Consensus       209 ti~AP~sGvV~~~~v~~G~~V~~G~~Lf~IaDLs~vWv~a~V~E~d~~~vk~Gq~v~v~~~a~Pg~~f~G~V~---~I~P  285 (407)
T PRK09783        209 TLKAPIDGVITAFDLRAGMNIAKDNVVAKIQGMDPVWVTAAIPESIAWLVKDASQFTLTVPARPDKTLTIRKW---TLLP  285 (407)
T ss_pred             EEECCCCCEEEEEECCCCCEECCCCEEEEEECCCEEEEEEEECHHHHHHCCCCCEEEEEECCCCCCCEEEEEE---EEEC
T ss_conf             9976888079997447895667998069996477289999962786864568988999832689961258999---9804


Q ss_pred             EE--ECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf             33--02640001014898999750234543222468440768999835
Q gi|254781172|r  361 VN--IGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRA  406 (731)
Q Consensus       361 V~--l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~Ra  406 (731)
                      .-  -..+.--|+++-|.+.               .+++|-.+.|.-.
T Consensus       286 ~vD~~TRT~~VRv~l~N~d~---------------~LkPGMfa~v~i~  318 (407)
T PRK09783        286 GVDAATRTLQLRLEVDNADE---------------ALKPGMNAWLQLN  318 (407)
T ss_pred             CCCCCCCEEEEEEEECCCCC---------------CCCCCCEEEEEEC
T ss_conf             55777754999999549987---------------3089988999982


No 297
>PRK13812 orotate phosphoribosyltransferase; Provisional
Probab=47.19  E-value=17  Score=15.21  Aligned_cols=62  Identities=24%  Similarity=0.316  Sum_probs=42.7

Q ss_pred             CCCEEEE------ECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHH
Q ss_conf             6866999------725889987899999998298499811163217997788886379899749917379999999988
Q gi|254781172|r  648 ENKKLVF------TGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQ  720 (731)
Q Consensus       648 ~gk~vV~------TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~  720 (731)
                      .|+++++      ||    -|=.+..+.+++.|++|..-+.      |+.-..|.+ +..++.||++.+--.+.++|++
T Consensus       106 ~g~rVlivEDViTTG----~S~~eai~~l~~~G~~V~~v~v------ivDR~eg~~-e~l~~~gv~~~sl~t~~dlla~  173 (174)
T PRK13812        106 DGEEVVVLEDIATTG----QSAVDAVEALRDAGATVNRVLV------VVDREEGAR-ENLAEHDVEMEALVTASDLLAD  173 (174)
T ss_pred             CCCEEEEEEEEECCC----CCHHHHHHHHHHCCCEEEEEEE------EEECCCCHH-HHHHHCCCEEEEEECHHHHHCC
T ss_conf             786699998644578----0199999999987997999999------997785658-9999779809997029997148


No 298
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=47.14  E-value=9.6  Score=17.20  Aligned_cols=28  Identities=25%  Similarity=0.788  Sum_probs=18.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHH
Q ss_conf             0432657750103378654452101003543441144
Q gi|254781172|r  431 PSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQ  467 (731)
Q Consensus       431 P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq  467 (731)
                      +-.||+|+.+.++....      ..|.|.   .|-..
T Consensus        35 ~~~Cp~C~~~~VkR~a~------GIW~C~---kCg~~   62 (89)
T COG1997          35 KHVCPFCGRTTVKRIAT------GIWKCR---KCGAK   62 (89)
T ss_pred             CCCCCCCCCCCEEEECC------CEEECC---CCCCE
T ss_conf             77699789740455236------758717---88873


No 299
>PRK09138 DNA topoisomerase I; Validated
Probab=47.13  E-value=8.7  Score=17.52  Aligned_cols=35  Identities=29%  Similarity=0.519  Sum_probs=21.1

Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHH
Q ss_conf             70432657750103378654452101003543441144
Q gi|254781172|r  430 FPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQ  467 (731)
Q Consensus       430 ~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq  467 (731)
                      -|..||.|++.-..   ...+.++..+-|.|--.|...
T Consensus       601 d~r~cp~c~~g~l~---l~~gk~G~figcsnypec~~t  635 (887)
T PRK09138        601 DPRICPTCGTGRLS---LKLGKFGAFVGCSNYPECRYT  635 (887)
T ss_pred             CCCCCCCCCCCCEE---EECCCCCCCCCCCCCCCCCCC
T ss_conf             76336678887368---870576566656788644355


No 300
>pfam08745 UPF0278 UPF0278 family. Members of this family are uncharacterized proteins about 200 amino acids in length.
Probab=47.04  E-value=17  Score=15.20  Aligned_cols=52  Identities=25%  Similarity=0.410  Sum_probs=34.7

Q ss_pred             CCCCCCCHHHHH--HHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHHC
Q ss_conf             258899878999--9999829849981116321799778888637989974991737999999998828
Q gi|254781172|r  656 GTLQKIQRHKAQ--EYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYN  722 (731)
Q Consensus       656 Gtl~~~~R~e~~--~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~~  722 (731)
                      |.|.  |+.++.  =+...++|.++++            ..| =.+=|+++||+.++...|..+|++|=
T Consensus       150 GiLD--S~eD~DvlLLA~ELda~vVt~------------D~G-i~kWA~~lGlr~i~~~~F~~~Lee~l  203 (206)
T pfam08745       150 GILD--SAEDLDVLLLAKELDAAVVAS------------DEG-IRKWAEKLGLRFVDASNFPEMLEEYL  203 (206)
T ss_pred             CCCC--CHHHHHHHHHHHHHCCEEECC------------CHH-HHHHHHHCCCEEECHHHHHHHHHHHH
T ss_conf             6656--532378999999848757706------------264-99999980978878888689999999


No 301
>TIGR01701 Fdhalpha-like oxidoreductase alpha (molybdopterin) subunit; InterPro: IPR010046   This entry represents a well-defined clade of molybdopterin-dependent formate dehydrogenases, bacterial type , , , . It represents the alpha subunit, which contains a molybdopterin cofactor and generally associate with two other subunits which contain iron-sulphur clusters and cytochromes.; GO: 0008863 formate dehydrogenase activity, 0030151 molybdenum ion binding, 0051539 4 iron 4 sulfur cluster binding.
Probab=46.97  E-value=17  Score=15.19  Aligned_cols=81  Identities=17%  Similarity=0.298  Sum_probs=40.2

Q ss_pred             CCCEEEE---ECCC-CCCC-HHHHHHHHHHCCCEEEEEEE--CCEEEEEECCCC------CCHHHH-HHHCCCEEECHHH
Q ss_conf             6866999---7258-8998-78999999982984998111--632179977888------863798-9974991737999
Q gi|254781172|r  648 ENKKLVF---TGTL-QKIQ-RHKAQEYVTQLGAVVSAILS--RKTDIIIVGDNP------GSKLEK-AQQLGVKIMNEEQ  713 (731)
Q Consensus       648 ~gk~vV~---TGtl-~~~~-R~e~~~~ie~~Ggkv~sSVS--kkT~~LI~ge~~------gSKl~K-A~~LgI~Ii~e~e  713 (731)
                      .||.=+|   =|.| +-+. +..+++-+++.-=.|.=+.-  -+-++|++|+.+      | -.+. -+.-+-+..|-++
T Consensus       502 eG~~~~f~~~GGNF~~A~PD~a~~~~~L~~~~L~V~vatk~nLnrsH~l~~~~~~iLP~lg-R~E~d~~~~~~QavS~e~  580 (824)
T TIGR01701       502 EGKVRAFICLGGNFLEAMPDTAAIEEALRQLDLRVHVATKFNLNRSHVLAKEEALILPVLG-RIEQDGQKTGKQAVSVED  580 (824)
T ss_pred             CCEEEEEECCCHHHHHCCCCHHHHHHHHHHCCEEEEEEEECCCCCHHHHHCCEEEEECCCC-CCCCCCCCCCCCEEEECC
T ss_conf             6627544304326652088989999886424367898862256402433203135512566-301788888541476010


Q ss_pred             HHHHHHHHCCCCCCCC
Q ss_conf             9999988286568756
Q gi|254781172|r  714 FLFLLQQYNTTLRIHD  729 (731)
Q Consensus       714 f~~ll~~~~~~~~~~~  729 (731)
                      +.+|+-.....+.+..
T Consensus       581 s~~m~h~Srg~~~P~~  596 (824)
T TIGR01701       581 SMRMVHESRGILKPRG  596 (824)
T ss_pred             CEEHHHCCCCCCCCCC
T ss_conf             1000213765577711


No 302
>TIGR01525 ATPase-IB_hvy heavy metal translocating P-type ATPase; InterPro: IPR006416    This group encompasses the copper and cadmium-type heavy metal transporting P-type ATPases as well as those which cannot be assigned to one or other of the groups. ; GO: 0015662 ATPase activity coupled to transmembrane movement of ions phosphorylative mechanism, 0030001 metal ion transport, 0016021 integral to membrane.
Probab=46.95  E-value=11  Score=16.80  Aligned_cols=39  Identities=31%  Similarity=0.555  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHC---CCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEE
Q ss_conf             78999999982---98499811163217997788886379899749917
Q gi|254781172|r  663 RHKAQEYVTQL---GAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKI  708 (731)
Q Consensus       663 R~e~~~~ie~~---Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~I  708 (731)
                      |.|+++.|..+   ||.       ..-+++.||+...=-.=|++|||++
T Consensus       452 R~~a~~~i~~Lk~~~g~-------~~~~mLTGD~~~~A~~~A~~lGI~~  493 (639)
T TIGR01525       452 RPEAKEAIAALKRKGGI-------IEVVMLTGDNRAAAEAVAAELGIEI  493 (639)
T ss_pred             CHHHHHHHHHHHHHCCC-------CEEEEECCCCHHHHHHHHHHHCCCC
T ss_conf             85479999999974387-------3477621888899999999829850


No 303
>pfam11382 DUF3186 Protein of unknown function (DUF3186). This bacterial family of proteins has no known function.
Probab=46.75  E-value=18  Score=15.16  Aligned_cols=14  Identities=7%  Similarity=0.328  Sum_probs=7.8

Q ss_pred             EEEECCEEEEEEEE
Q ss_conf             99415818999998
Q gi|254781172|r  130 LEPKIDGTMITIRY  143 (731)
Q Consensus       130 vepKiDG~sisl~Y  143 (731)
                      +.-++-|..+.++.
T Consensus        77 v~g~L~g~~Valv~   90 (307)
T pfam11382        77 VAGRLTGKSVALVR   90 (307)
T ss_pred             HHCCCCCCEEEEEE
T ss_conf             73754897599997


No 304
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=46.59  E-value=8.4  Score=17.63  Aligned_cols=21  Identities=24%  Similarity=0.311  Sum_probs=15.4

Q ss_pred             CHHHHHCCCCCCHHHHHHHHH
Q ss_conf             778761388867899999999
Q gi|254781172|r  594 DWLSLIRVPLVGDIIAQAIVE  614 (731)
Q Consensus       594 ~~e~L~~I~GiG~~~A~si~~  614 (731)
                      ..++|..|.||||+.++.+.+
T Consensus       151 ~aDDLk~I~GIGP~~e~~Ln~  171 (216)
T PRK12278        151 EADDLTKITGVGPALAKKLNE  171 (216)
T ss_pred             CCCCCCEECCCCHHHHHHHHH
T ss_conf             996543602658899999998


No 305
>COG0773 MurC UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]
Probab=46.57  E-value=18  Score=15.15  Aligned_cols=67  Identities=21%  Similarity=0.192  Sum_probs=38.0

Q ss_pred             EEEEECCHHCCCCCCCCCCCCCCE--EEECCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCH
Q ss_conf             377731100011158765686631--231145621589987889940356225899997433302640001014898
Q gi|254781172|r  302 LVYKVDEFSLQKQLGERARSPRWM--ISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNE  376 (731)
Q Consensus       302 iVikvn~~~~q~~lG~ts~~Prwa--iA~Kf~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~  376 (731)
                      +|+-.||-.+++.+...    .|.  +-|=|.++ +.....++.-+-+++   +--+.+.--.++..++.-.--||.
T Consensus       214 ~v~~~dd~~l~~l~~~~----~~~~v~tyG~~~~-ad~~a~ni~~~~~~~---~F~V~~~g~~~~~~~l~~pG~HNv  282 (459)
T COG0773         214 AVVCGDDPNLRELLSRG----CWSPVVTYGFDDE-ADWRAENIRQDGSGT---TFDVLFRGEELGEVKLPLPGRHNV  282 (459)
T ss_pred             EEEECCCHHHHHHHHCC----CCCCEEEECCCCC-CCEEEEEEEEECCCC---EEEEEECCCEEEEEEECCCCHHHH
T ss_conf             99978888899987222----5873794247876-728999768706642---799998685567999726762268


No 306
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=46.57  E-value=7.6  Score=17.99  Aligned_cols=11  Identities=27%  Similarity=0.718  Sum_probs=8.6

Q ss_pred             CCCCCCCCCCC
Q ss_conf             43265775010
Q gi|254781172|r  432 SFCPICQSRVV  442 (731)
Q Consensus       432 ~~CP~Cgs~l~  442 (731)
                      +.||.||+++.
T Consensus        50 t~CP~Cg~~~e   60 (115)
T COG1885          50 TSCPKCGEPFE   60 (115)
T ss_pred             CCCCCCCCCCC
T ss_conf             55887799663


No 307
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=46.41  E-value=8.4  Score=17.67  Aligned_cols=45  Identities=24%  Similarity=0.369  Sum_probs=27.1

Q ss_pred             HCCCEEE-EEEECC--EEEEEECCC----------CC----CHHHHHHHCCCEEECHHHHHHH
Q ss_conf             8298499-811163--217997788----------88----6379899749917379999999
Q gi|254781172|r  672 QLGAVVS-AILSRK--TDIIIVGDN----------PG----SKLEKAQQLGVKIMNEEQFLFL  717 (731)
Q Consensus       672 ~~Ggkv~-sSVSkk--T~~LI~ge~----------~g----SKl~KA~~LgI~Ii~e~ef~~l  717 (731)
                      ..|.++. -.|.+.  +.|+|.|+.          -|    -.+-+|++-| |-.|.++|.+-
T Consensus      1345 ~rGi~~lppDinkS~a~~F~i~~~~Ir~pl~AIkgvG~~aa~~IveaR~eg-~F~S~eDf~~R 1406 (1436)
T PRK00448       1345 ERGFKFQKVDLYKSDATEFIIEGDTLIPPFNAIPGLGENVAKSIVEAREEG-EFLSKEDLRKR 1406 (1436)
T ss_pred             HCCCEECCCCCCCCCCCCEEECCCEEEECHHHHCCCHHHHHHHHHHHHHCC-CCCCHHHHHHH
T ss_conf             779845388402457854077299077674664461199999999998079-98998999987


No 308
>PRK08413 consensus
Probab=46.36  E-value=11  Score=16.60  Aligned_cols=21  Identities=10%  Similarity=0.143  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999998433
Q gi|254781172|r   16 QARKELSSLEQEISYHDDCYY   36 (731)
Q Consensus        16 ~~~~~i~~L~~~i~~~~~~Yy   36 (731)
                      ..++.+..|.+.+++++..|-
T Consensus        59 ~~~k~~k~lk~l~k~ad~vil   79 (733)
T PRK08413         59 DHSAIVKEIKELAKKADTIYI   79 (733)
T ss_pred             CHHHHHHHHHHHHHCCCEEEE
T ss_conf             689999999999856998998


No 309
>PRK01710 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=46.31  E-value=18  Score=15.12  Aligned_cols=15  Identities=7%  Similarity=0.020  Sum_probs=5.7

Q ss_pred             CCEEECHHHHHHHHH
Q ss_conf             991737999999998
Q gi|254781172|r  705 GVKIMNEEQFLFLLQ  719 (731)
Q Consensus       705 gI~Ii~e~ef~~ll~  719 (731)
                      .+++...+.+.+.+.
T Consensus       403 ~~~~~~~~~l~~Av~  417 (458)
T PRK01710        403 KIPIVIVNSLEEAVK  417 (458)
T ss_pred             CCCEEHHHHHHHHHH
T ss_conf             865233735999999


No 310
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=46.30  E-value=8.6  Score=17.58  Aligned_cols=21  Identities=14%  Similarity=0.524  Sum_probs=15.6

Q ss_pred             CCCEEEECCCCCCCCCCCCCC
Q ss_conf             730477704326577501033
Q gi|254781172|r  424 DAQPFSFPSFCPICQSRVVRD  444 (731)
Q Consensus       424 ~~~~~~~P~~CP~Cgs~l~~~  444 (731)
                      +-..+.+-+.||.||++++..
T Consensus        10 ~Cg~YTL~~~CP~CG~~t~~~   30 (54)
T PRK13130         10 KCGRYTLKETCPECGGKTKNP   30 (54)
T ss_pred             CCCCEECCCCCCCCCCCCCCC
T ss_conf             356430325286688726767


No 311
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg); InterPro: IPR004577 All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. The enzyme incises DNA at 8-oxoG residues, and excises 7,8-dihydro-8-oxoguanine from damaged DNA. It has beta-lyase activity that nicks DNA 3' to the lesion.; GO: 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006281 DNA repair, 0005634 nucleus.
Probab=45.96  E-value=11  Score=16.71  Aligned_cols=91  Identities=22%  Similarity=0.300  Sum_probs=46.7

Q ss_pred             HCCCCCCCCCCCCCHHHHHHHHHHHHH--HHHHHHHHHHCCH----HHHHHHHHHHHHHHCCCH-----HHHHHHHHHHH
Q ss_conf             000100013421001456899998752--2346667763010----111168999999882998-----99999789776
Q gi|254781172|r  520 STTKIENILGFGDVSVTNLYDSINKRR--NISLERFIFSLGI----RHVGAEIARSLAKYYLSY-----QNFAQEINNII  588 (731)
Q Consensus       520 ~~~~l~~l~GfgeKsa~nL~~sIe~sK--~~~L~r~L~ALGI----~~vG~~~Ak~La~~f~si-----~~l~~~~~~~~  588 (731)
                      ++..+..|-|..|-|-+.| .+.|..-  +-++.. |-.||+    |+|-+ +||.|++.-...     ...++.+.. .
T Consensus       191 ~FP~~~~LtgvaeGsledl-~~~E~nlPsdfsfn~-LR~lG~GYRA~Yi~~-tar~l~ee~~~~nitsdta~LQ~ic~-~  266 (379)
T TIGR00588       191 GFPSLHALTGVAEGSLEDL-PEAEANLPSDFSFNH-LRKLGLGYRARYIRE-TARALLEEQGGRNITSDTAWLQQICK-D  266 (379)
T ss_pred             CCCCHHHHHHHHHHHHHHH-HHHHHHCCCCCCHHH-HHHCCCCCCCHHHHH-HHHHHHHHCCCCCCHHHHHHHHHHCC-C
T ss_conf             7987566521210016679-998751564346265-752488754068999-99998841266420023579998606-6


Q ss_pred             HCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             12511778761388867899999999
Q gi|254781172|r  589 AHNNDDWLSLIRVPLVGDIIAQAIVE  614 (731)
Q Consensus       589 ~~~~~~~e~L~~I~GiG~~~A~si~~  614 (731)
                      +.-++..+.|+..+|+|+|+|+.|.=
T Consensus       267 ~~Yedar~~L~~l~GVG~KVADCicL  292 (379)
T TIGR00588       267 ADYEDAREALLELPGVGPKVADCICL  292 (379)
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf             88678999972169997048888886


No 312
>PRK08324 short chain dehydrogenase; Validated
Probab=45.83  E-value=18  Score=15.06  Aligned_cols=56  Identities=20%  Similarity=0.224  Sum_probs=35.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCC----CCCCCCCCEEECCCCCCCHHHCCCHHHHH
Q ss_conf             820878999999999999897720311589999620036----43235775045166425702159999999
Q gi|254781172|r   41 PIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIG----GEMNLSLFKVTHSIPTLSLEKIWNIEDLR  108 (731)
Q Consensus        41 p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg----~~~~~~~~kv~H~~pMlSL~k~~~~~el~  108 (731)
                      +.+||   |.|+..|+..         ..+|++|.-.|-    +-....|--..|+-+.++|.|.-+-+++.
T Consensus        90 ~~~sd---~~Mv~~~~~~---------l~~~~~p~pSvEtlLHA~lP~k~VDHtHadailal~n~~~g~~~~  149 (676)
T PRK08324         90 GVLSD---DEMVNYLRHC---------LFDPNAPAPSIETLLHAFLPFKHVDHTHPDAIIAIANQPDGEELT  149 (676)
T ss_pred             CCCCH---HHHHHHHHHH---------HCCCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCHHHHH
T ss_conf             87888---9999999985---------079999998577887860671002446852999976599759999


No 313
>TIGR01523 ATPase-IID_K-Na potassium/sodium efflux P-type ATPase, fungal-type; InterPro: IPR006414   Initially described as a calcium efflux ATPase , more recent work has shown that the Schizosaccharomyces pombe CTA3 gene is in fact a potassium ion efflux pump . These sequences form the clade which represents the fungal P-type ATPases which are responsible for potassium and sodium efflux. The degree to which these pumps show preference for sodium or potassium varies. This group of ATPases has been classified by phylogentic analysis as type IID . ; GO: 0015662 ATPase activity coupled to transmembrane movement of ions phosphorylative mechanism, 0006812 cation transport, 0016021 integral to membrane.
Probab=45.77  E-value=12  Score=16.48  Aligned_cols=40  Identities=28%  Similarity=0.337  Sum_probs=30.0

Q ss_pred             CCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEEECCCCEEEE
Q ss_conf             115876568663123114562158998788994035622589
Q gi|254781172|r  313 KQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTP  354 (731)
Q Consensus       313 ~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~wqvgRtG~itP  354 (731)
                      =.+|...=.-|-.|-=|..+-||.--|.||==.  |||.||-
T Consensus       329 M~~G~~~M~~R~VIVRKL~~LEALG~V~DICSD--KTGT~TQ  368 (1001)
T TIGR01523       329 MAVGAKVMVKRRVIVRKLDALEALGAVTDICSD--KTGTLTQ  368 (1001)
T ss_pred             HHHCHHHHCCCCEEEEEHHHHHHHCCCCCCCCC--CCCCCCC
T ss_conf             872224322562157502555530475431358--7665333


No 314
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH; InterPro: IPR011909   Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system .    Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond.   Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed  that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro.    NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterised by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase .; GO: 0006118 electron transport, 0045454 cell redox homeostasis.
Probab=45.76  E-value=13  Score=16.09  Aligned_cols=30  Identities=17%  Similarity=0.118  Sum_probs=21.1

Q ss_pred             EEEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCEE
Q ss_conf             66410245433210000368999975996654148
Q gi|254781172|r  239 FVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVR  273 (731)
Q Consensus       239 ~ay~~~~~~~~~~~~~~e~l~~L~~~GF~v~~~~~  273 (731)
                      ++|+.++     +..|.|.+++|+++||.-.|-..
T Consensus        24 i~Fe~in-----id~~pea~d~vk~lGF~~~PVi~   53 (72)
T TIGR02194        24 IAFEEIN-----IDEQPEAVDYVKALGFRQVPVIV   53 (72)
T ss_pred             CCEEEEE-----CCCCHHHHHHHHHCCCEECCEEE
T ss_conf             9615763-----58884378999874863076267


No 315
>pfam04606 Ogr_Delta Ogr/Delta-like zinc finger. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F. This family also includes zinc fingers in recombinase proteins.
Probab=45.56  E-value=7.8  Score=17.91  Aligned_cols=37  Identities=22%  Similarity=0.450  Sum_probs=18.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC--EEECCCCCCCCHHHHHH
Q ss_conf             326577501033786544521--01003543441144665
Q gi|254781172|r  433 FCPICQSRVVRDLNPKTGKLV--AAHRCTGGLACSAQQLE  470 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~~~~~~~--~~~rC~n~~~Cpaq~~~  470 (731)
                      .||.||+.....-...-....  ...-|.|. .|-...+.
T Consensus         1 ~CP~Cg~~a~irts~~~s~~~~e~Y~qC~N~-~Cg~tfv~   39 (47)
T pfam04606         1 RCPHCGAKARIRTSRRLSALVRELYYQCTNP-ECGHTFVT   39 (47)
T ss_pred             CCCCCCCCEEEEEHHHCCHHHHEEEEECCCC-CCCCEEEE
T ss_conf             9598898389968356297553138880896-45968999


No 316
>PRK01216 DNA polymerase IV; Validated
Probab=45.53  E-value=11  Score=16.62  Aligned_cols=49  Identities=20%  Similarity=0.311  Sum_probs=31.7

Q ss_pred             CCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHH
Q ss_conf             23103541035555653057654045410110106777531000100013421001456899
Q gi|254781172|r  479 DAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYD  540 (731)
Q Consensus       479 ~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~  540 (731)
                      ..=+|-|+|+++-++|-+.|     |.++.||+......      |..  -||++.+.-+++
T Consensus       179 pv~~i~GIG~~t~~~L~~~G-----I~ti~dL~~~~~~~------L~~--~fG~~~~~~l~~  227 (351)
T PRK01216        179 DIDDVPGIGKVLSERLNELG-----INKLRDILSKSFNK------LKS--IIGEAKANYLYS  227 (351)
T ss_pred             CCCEECCCCHHHHHHHHHCC-----CCCHHHHHHCCHHH------HHH--HHCHHHHHHHHH
T ss_conf             94385485799999999859-----96899975299999------999--977799999999


No 317
>TIGR00596 rad1 DNA repair protein (rad1); InterPro: IPR006167    All proteins in this family, for which functions are known, are components in a multiprotein endonuclease complex, usually made up of Rad1 and Rad10 homologues. This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologues of these genes, but the function of the Archaeal proteins is not known, so are not included in this family.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity, 0006281 DNA repair.
Probab=45.35  E-value=18  Score=15.01  Aligned_cols=50  Identities=22%  Similarity=0.274  Sum_probs=31.3

Q ss_pred             CCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCC-HHHHHHHHHHHCC
Q ss_conf             01011116899999988-29989999978977612511778761388867-8999999999669
Q gi|254781172|r  557 LGIRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVG-DIIAQAIVEFYQN  618 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG-~~~A~si~~ff~~  618 (731)
                      |++|||-.+..+-|..+ .+++.++...          +..+|.++  || +..|..|++||+.
T Consensus       884 l~~PGV~~kN~rnl~~~G~k~~~el~~~----------S~~El~eL--~g~~e~a~~lY~Fl~~  935 (939)
T TIGR00596       884 LKLPGVTKKNIRNLLKKGVKSIRELAKL----------SQEELEEL--IGDEEAAKRLYDFLRK  935 (939)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHH----------HHHHHHHH--CCCHHHHHHHHHHHHH
T ss_conf             5789856023455554315559999998----------79999975--0797576689999876


No 318
>cd00513 Ribosomal_L32_L32e Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. L32 does not appear to play a role in forming the A (aminacyl), P (peptidyl) or E (exit) sites of the ribosome, but does interact with 23S rRNA, which has a "kink-turn" secondary structure motif. L32 is overexpressed in human prostate cancer and has been identified as a stably expressed housekeeping gene in macrophages of human chronic obstructive pulmonary disease (COPD) patients. In Schizosaccharomyces pombe, L32 has also been suggested to play a role as a transcriptional regulator in the nucleus. Found in archaea and eukaryotes, this protein is known as L32 in eukaryotes and L32e in archaea.
Probab=45.25  E-value=3.7  Score=20.43  Aligned_cols=36  Identities=14%  Similarity=0.065  Sum_probs=18.4

Q ss_pred             CCCCHHHHH-HHHHHHHHCCCCCCEEEEEHHHHCCHH
Q ss_conf             231035410-355556530576540454101101067
Q gi|254781172|r  479 DAFNIEGLG-KQQLDFFFKSEDPAFSIRIPADIFTLQ  514 (731)
Q Consensus       479 ~aldI~GLG-~k~Ie~L~e~~~~~g~I~~~~DLy~L~  514 (731)
                      ..|---|.| ++.+.-|.-.|+...+|.++.||-.|.
T Consensus        36 ~~~p~iGYgs~k~~Rgl~PsG~~~vlV~n~~dLe~l~   72 (107)
T cd00513          36 PAMPKIGYGSPKKTRGLHPSGFKKVLVHNVKELEVLD   72 (107)
T ss_pred             CCCCCCCCCCCHHHCCCCCCCCEEEEECCHHHHHHHC
T ss_conf             6787667787776657797888888866988988860


No 319
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=45.17  E-value=8.3  Score=17.67  Aligned_cols=14  Identities=21%  Similarity=0.755  Sum_probs=9.7

Q ss_pred             CCCCCCCCCCCCCC
Q ss_conf             04326577501033
Q gi|254781172|r  431 PSFCPICQSRVVRD  444 (731)
Q Consensus       431 P~~CP~Cgs~l~~~  444 (731)
                      -..||+||.++-..
T Consensus       457 ~~~CPvCg~~l~~~  470 (908)
T COG0419         457 GEKCPVCGQELPEE  470 (908)
T ss_pred             CCCCCCCCCCCCCH
T ss_conf             99999888978607


No 320
>COG1312 UxuA D-mannonate dehydratase [Carbohydrate transport and metabolism]
Probab=45.08  E-value=14  Score=15.86  Aligned_cols=82  Identities=17%  Similarity=0.242  Sum_probs=44.2

Q ss_pred             ECCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHH
Q ss_conf             51664257021599999999999999861246777611999941581899999859989988865986556669997753
Q gi|254781172|r   90 THSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRA  169 (731)
Q Consensus        90 ~H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~  169 (731)
                      -|..|-   +.++..+++.+--+.+...                  |+..+.+ |.--..+.+-+|.+...+.|-.-..+
T Consensus        31 Lh~iP~---g~~W~~~~I~~~k~~ie~~------------------Gl~~~vv-ESvPvhedIK~g~~~rd~~Ieny~~t   88 (362)
T COG1312          31 LHHIPA---GEVWPVEEILKRKEEIESA------------------GLTWSVV-ESVPVHEDIKLGTPTRDRYIENYKQT   88 (362)
T ss_pred             CCCCCC---CCCCCHHHHHHHHHHHHHC------------------CCEEEEE-CCCCHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             777889---8857689999999999973------------------9669863-57788889871698478999999999


Q ss_pred             HCCCCCCCCCCCCCEEEEEEEEEEECHHHHH
Q ss_conf             1024322335445504899999985202123
Q gi|254781172|r  170 IPTIPRVLSLNIPEIIEVRGEVYISKNDFLA  200 (731)
Q Consensus       170 i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~  200 (731)
                      |+++-. .++      .+=.==||+--+|-+
T Consensus        89 irnLa~-~GI------~vvCYNfMpv~dWtR  112 (362)
T COG1312          89 IRNLAR-AGI------KVVCYNFMPVFDWTR  112 (362)
T ss_pred             HHHHHH-CCC------CEEEECCCCCCCCCC
T ss_conf             999996-698------779851552137312


No 321
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE; InterPro: IPR006452   This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex . The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. .
Probab=45.04  E-value=7.8  Score=17.90  Aligned_cols=80  Identities=23%  Similarity=0.275  Sum_probs=36.3

Q ss_pred             HHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCC
Q ss_conf             75310243223354455048999999852021234556431485433423456777752345555301110566410245
Q gi|254781172|r  167 IRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKT  246 (731)
Q Consensus       167 ~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~  246 (731)
                      .+|-..||-.|..+....+-=|||      .|+.|     +.| .+...==|++||.-|....-.         |.....
T Consensus        15 ~~tad~iPp~L~p~l~~LfnrRae------Rl~~L-----Aeg-~plgdYLrf~Agi~r~Q~~ll---------~~~P~~   73 (312)
T TIGR01562        15 KRTADKIPPLLKPRLKDLFNRRAE------RLEEL-----AEG-SPLGDYLRFVAGIARIQEELL---------SDLPAE   73 (312)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH------HHHHH-----HCC-CCCHHHHHHHHHHHHHHHHHH---------HCCCCC
T ss_conf             763125886467126778878999------99998-----568-981058999999999999996---------347898


Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCC
Q ss_conf             4332100003689999759966541
Q gi|254781172|r  247 SEIFAKGQYEMLQKMRCLGFPVNNG  271 (731)
Q Consensus       247 ~~~~~~~~~e~l~~L~~~GF~v~~~  271 (731)
                      .    .-.-+.++.-+..|-|=..+
T Consensus        74 ~----pl~~~R~~~ara~g~PPld~   94 (312)
T TIGR01562        74 E----PLDADRVKKARANGMPPLDI   94 (312)
T ss_pred             C----CCCHHHHHHHHHCCCCCHHH
T ss_conf             8----88979999998618885237


No 322
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=44.90  E-value=11  Score=16.65  Aligned_cols=29  Identities=21%  Similarity=0.639  Sum_probs=17.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHH
Q ss_conf             432657750103378654452101003543441144
Q gi|254781172|r  432 SFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQ  467 (731)
Q Consensus       432 ~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq  467 (731)
                      .+||.||+-+....+...    ..+.|.   +|+..
T Consensus         1 kFCp~C~n~l~p~~~~~~----~~~~C~---~C~y~   29 (52)
T smart00661        1 KFCPKCGNMLIPKEGKEK----RRFVCR---KCGYE   29 (52)
T ss_pred             CCCCCCCCEEEEEECCCC----EEEECC---CCCCC
T ss_conf             978652888768536995----389748---99984


No 323
>pfam05559 DUF763 Protein of unknown function (DUF763). This family consists of several uncharacterized bacterial and archaeal proteins of unknown function.
Probab=44.67  E-value=19  Score=14.94  Aligned_cols=32  Identities=19%  Similarity=0.241  Sum_probs=22.7

Q ss_pred             HHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHH
Q ss_conf             99789776125117787613888678999999
Q gi|254781172|r  581 AQEINNIIAHNNDDWLSLIRVPLVGDIIAQAI  612 (731)
Q Consensus       581 ~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si  612 (731)
                      ........+..-.++++|..++|+|+.+..++
T Consensus       254 ~~~L~~a~e~~p~dfeeLLl~~GvGp~TlRAL  285 (319)
T pfam05559       254 WKVLRAAYERNPEDFEELLLLKGVGPSTLRAL  285 (319)
T ss_pred             HHHHHHHHHCCCCCHHHHHHCCCCCHHHHHHH
T ss_conf             99999876268016999971479888999999


No 324
>PRK13809 orotate phosphoribosyltransferase; Provisional
Probab=44.61  E-value=19  Score=14.93  Aligned_cols=68  Identities=12%  Similarity=0.096  Sum_probs=41.8

Q ss_pred             CCCEEEE------ECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHH
Q ss_conf             6866999------7258899878999999982984998111632179977888863798997499173799999999882
Q gi|254781172|r  648 ENKKLVF------TGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQY  721 (731)
Q Consensus       648 ~gk~vV~------TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~  721 (731)
                      .|+++|+      ||    -|=-++.+.+++.|+.|...+.     ++--+..|  .+.-++.||++.+--.+.+||+-.
T Consensus       117 ~G~kVvvIEDViTTG----gSil~ai~~lr~~G~~V~~v~v-----ivDReegg--~e~l~~~Gi~l~sl~t~~~ll~~l  185 (206)
T PRK13809        117 PGQTCLVINDMVSSG----KSIIETAVALEENGLVVREALV-----FLDRRKEA--CQPLGPQGIKVSSVFTVPTLIKAL  185 (206)
T ss_pred             CCCEEEEEEEEECCC----HHHHHHHHHHHHCCCEEEEEEE-----EEECCCCH--HHHHHHCCCCEEEECCHHHHHHHH
T ss_conf             998899997334468----0099999999987996999999-----99265167--999997799189967799999999


Q ss_pred             CCCCC
Q ss_conf             86568
Q gi|254781172|r  722 NTTLR  726 (731)
Q Consensus       722 ~~~~~  726 (731)
                      -.+..
T Consensus       186 ~~~g~  190 (206)
T PRK13809        186 IAYGK  190 (206)
T ss_pred             HHCCC
T ss_conf             98499


No 325
>PRK12859 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=44.58  E-value=19  Score=14.93  Aligned_cols=14  Identities=14%  Similarity=0.110  Sum_probs=10.2

Q ss_pred             CCCCCCCEEEEECC
Q ss_conf             88216866999725
Q gi|254781172|r  644 SSEIENKKLVFTGT  657 (731)
Q Consensus       644 ~~~l~gk~vV~TGt  657 (731)
                      ++..+|.++.+.|-
T Consensus       241 a~~iTGq~i~VDGG  254 (257)
T PRK12859        241 AEWITGQVIHSEGG  254 (257)
T ss_pred             HCCEECCEEEECCC
T ss_conf             25861875896879


No 326
>TIGR00375 TIGR00375 conserved hypothetical protein TIGR00375; InterPro: IPR005287    This family of conserved hypothetical proteins has no known function. .
Probab=44.41  E-value=19  Score=14.91  Aligned_cols=118  Identities=21%  Similarity=0.328  Sum_probs=60.4

Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHH-HHHHHHCCCCCCEEEEEHH
Q ss_conf             704326577501033786544521010035434411446655332130123103541035-5556530576540454101
Q gi|254781172|r  430 FPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQ-QLDFFFKSEDPAFSIRIPA  508 (731)
Q Consensus       430 ~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GLG~k-~Ie~L~e~~~~~g~I~~~~  508 (731)
                      .-|.|-.|+....-+...+     .+++|+   .|.+++.+-+.+=       |.-|+.. -++.=         .-.|.
T Consensus       246 h~TAC~~C~~~~~~E~a~~-----~~~~Cp---kCgg~ikKGV~~R-------~~ELSd~d~~e~p---------~~RPp  301 (384)
T TIGR00375       246 HLTACEKCYERYKSEDAKK-----ADAKCP---KCGGKIKKGVSDR-------VRELSDQDKLEHP---------KFRPP  301 (384)
T ss_pred             HHHHHHHCCCCCCCCCHHH-----HHCCCC---CCCCEEECCHHHH-------HHHCCCCCCCCCC---------CCCCC
T ss_conf             7778875476466400255-----524697---9786055373567-------7633677867887---------56348


Q ss_pred             HHCCHHHHHHHHCCCCCCCCCCCCCH--HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             10106777531000100013421001--4568999987522346667763010111168999999882998999997897
Q gi|254781172|r  509 DIFTLQRRQQTSTTKIENILGFGDVS--VTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINN  586 (731)
Q Consensus       509 DLy~L~~~~~~~~~~l~~l~GfgeKs--a~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~  586 (731)
                       -|+|     +   =|+.+.|++-++  .+|.+++|       +++|+-++|     ...+= |                
T Consensus       302 -Yvhl-----i---PLae~ig~~~~kG~~TK~VQ~~-------wekl~k~fG-----tEi~V-L----------------  343 (384)
T TIGR00375       302 -YVHL-----I---PLAEVIGLKIDKGVFTKAVQSL-------WEKLVKKFG-----TEIEV-L----------------  343 (384)
T ss_pred             -CEEE-----C---CCEEECCCCCCCCEEEHHHHHH-------HHHHHHHHC-----CHHHH-H----------------
T ss_conf             -5020-----5---6300035345873130346778-------999864104-----15667-6----------------


Q ss_pred             HHHCCCCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             76125117787613888678999999999
Q gi|254781172|r  587 IIAHNNDDWLSLIRVPLVGDIIAQAIVEF  615 (731)
Q Consensus       587 ~~~~~~~~~e~L~~I~GiG~~~A~si~~f  615 (731)
                          -++..|+|..|.-  |++|..|..|
T Consensus       344 ----~~A~~edla~~~p--PkvA~~i~~f  366 (384)
T TIGR00375       344 ----LEAALEDLAKVDP--PKVAALIEKF  366 (384)
T ss_pred             ----HCCCHHHHHCCCC--CHHHHHHHHH
T ss_conf             ----4278458733588--3588999986


No 327
>TIGR02339 thermosome_arch thermosome, various subunits, archaeal; InterPro: IPR012714    Thermosome is the name given to the archaeal rather than eukaryotic form of the group II chaperonin (counterpart to the group I chaperonin, GroEL/GroES, in bacteria), a toroidal, ATP-dependent molecular chaperone that assists in the folding or refolding of nascent or denatured proteins. Various homologous subunits, one to five per archaeal genome, may be designated alpha, beta, etc., but phylogenetic analysis does not show distinct alpha subunit and beta subunit lineages traceable to ancient paralogs.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=44.37  E-value=19  Score=14.90  Aligned_cols=22  Identities=9%  Similarity=0.134  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4568999987522346667763
Q gi|254781172|r  535 VTNLYDSINKRRNISLERFIFS  556 (731)
Q Consensus       535 a~nL~~sIe~sK~~~L~r~L~A  556 (731)
                      .+.++++.|+|-+=.|+-+-.+
T Consensus       375 tehVVDE~ERsl~DAL~VV~~~  396 (522)
T TIGR02339       375 TEHVVDELERSLQDALHVVASA  396 (522)
T ss_pred             CCEEHHHHHHHHHHHHHHHHHH
T ss_conf             7501021346688899999998


No 328
>pfam01396 zf-C4_Topoisom Topoisomerase DNA binding C4 zinc finger.
Probab=44.33  E-value=13  Score=16.16  Aligned_cols=30  Identities=20%  Similarity=0.388  Sum_probs=20.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHH
Q ss_conf             3265775010337865445210100354344114
Q gi|254781172|r  433 FCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSA  466 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpa  466 (731)
                      .||.||++++.....    .+..+=|+|=-+|..
T Consensus         3 kCP~Cg~~l~~r~~r----~G~F~gCs~yP~C~~   32 (39)
T pfam01396         3 KCPKCGGDLVLKRGK----FGKFVGCSNYPECKF   32 (39)
T ss_pred             CCCCCCCEEEEEECC----CCEEEECCCCCCCCC
T ss_conf             377899981688368----770872899989888


No 329
>PRK07062 short chain dehydrogenase; Provisional
Probab=44.27  E-value=19  Score=14.89  Aligned_cols=15  Identities=20%  Similarity=0.248  Sum_probs=10.8

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++++.|-+
T Consensus       247 s~~iTG~~i~VDGG~  261 (265)
T PRK07062        247 SSYTTGSHIDVSGGF  261 (265)
T ss_pred             HCCCCCCEEEECCCC
T ss_conf             257358427989780


No 330
>PRK05867 short chain dehydrogenase; Provisional
Probab=44.22  E-value=19  Score=14.89  Aligned_cols=14  Identities=29%  Similarity=0.425  Sum_probs=7.9

Q ss_pred             CCCCCCCEEEEECC
Q ss_conf             88216866999725
Q gi|254781172|r  644 SSEIENKKLVFTGT  657 (731)
Q Consensus       644 ~~~l~gk~vV~TGt  657 (731)
                      ++..+|.++++.|-
T Consensus       236 s~~iTG~~i~VDGG  249 (253)
T PRK05867        236 SSYMTGSDIVIDGG  249 (253)
T ss_pred             HCCCCCCEEEECCC
T ss_conf             14854871885889


No 331
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=43.99  E-value=8.7  Score=17.52  Aligned_cols=24  Identities=21%  Similarity=0.392  Sum_probs=13.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf             3265775010337865445210100354
Q gi|254781172|r  433 FCPICQSRVVRDLNPKTGKLVAAHRCTG  460 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n  460 (731)
                      .||.||+++++..-..    -..++|++
T Consensus       257 ~C~~Cg~~I~~~~~~g----R~t~~CP~  280 (283)
T PRK13945        257 PCRKCGTPIERIKLAG----RSTHWCPN  280 (283)
T ss_pred             CCCCCCCEEEEEEECC----CCCEECCC
T ss_conf             4899998888999999----75788921


No 332
>PRK06988 putative formyltransferase; Provisional
Probab=43.97  E-value=19  Score=14.86  Aligned_cols=15  Identities=20%  Similarity=0.352  Sum_probs=7.0

Q ss_pred             CCCEEECHHHHHHHH
Q ss_conf             499173799999999
Q gi|254781172|r  704 LGVKIMNEEQFLFLL  718 (731)
Q Consensus       704 LgI~Ii~e~ef~~ll  718 (731)
                      =|=+.|+-.+|.+=|
T Consensus       293 ~GKk~m~a~dFa~G~  307 (313)
T PRK06988        293 GGETVVTPAQFAQFI  307 (313)
T ss_pred             CCCCEECHHHHHHHC
T ss_conf             989751899996122


No 333
>PRK07677 short chain dehydrogenase; Provisional
Probab=43.96  E-value=19  Score=14.86  Aligned_cols=14  Identities=14%  Similarity=0.287  Sum_probs=9.2

Q ss_pred             CCCCCCCEEEEECC
Q ss_conf             88216866999725
Q gi|254781172|r  644 SSEIENKKLVFTGT  657 (731)
Q Consensus       644 ~~~l~gk~vV~TGt  657 (731)
                      .+..+|.++++.|-
T Consensus       233 asyiTG~~i~VDGG  246 (254)
T PRK07677        233 AAYINGTCITMDGG  246 (254)
T ss_pred             HCCCCCCEEEECCC
T ss_conf             24824872886899


No 334
>PRK06701 short chain dehydrogenase; Provisional
Probab=43.86  E-value=19  Score=14.85  Aligned_cols=15  Identities=27%  Similarity=0.384  Sum_probs=8.6

Q ss_pred             EECCCCHHHHHHHHH
Q ss_conf             865986556669997
Q gi|254781172|r  152 ALRGDGHSGEDVSAC  166 (731)
Q Consensus       152 ~TRGdG~~GeDVT~n  166 (731)
                      +|=|.+-+|.-+...
T Consensus        50 VTGgs~GIG~aiA~~   64 (289)
T PRK06701         50 ITGGDSGIGRAVAVA   64 (289)
T ss_pred             EECCCCHHHHHHHHH
T ss_conf             968257999999999


No 335
>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=43.79  E-value=13  Score=16.26  Aligned_cols=10  Identities=40%  Similarity=0.903  Sum_probs=8.3

Q ss_pred             CCCCCCCCCC
Q ss_conf             3265775010
Q gi|254781172|r  433 FCPICQSRVV  442 (731)
Q Consensus       433 ~CP~Cgs~l~  442 (731)
                      -||.||+.-+
T Consensus         3 pCPFCG~~~~   12 (53)
T TIGR03655         3 PCPFCGGADV   12 (53)
T ss_pred             CCCCCCCCHH
T ss_conf             8887897531


No 336
>PRK04358 hypothetical protein; Provisional
Probab=43.58  E-value=19  Score=14.82  Aligned_cols=55  Identities=22%  Similarity=0.376  Sum_probs=36.3

Q ss_pred             CCCCCCCHHHHH--HHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHHCCCC
Q ss_conf             258899878999--9999829849981116321799778888637989974991737999999998828656
Q gi|254781172|r  656 GTLQKIQRHKAQ--EYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNTTL  725 (731)
Q Consensus       656 Gtl~~~~R~e~~--~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~~~~~  725 (731)
                      |.|.  |+.++.  =+...++|.|+++            ..| =.+=|+++||+.++...|..+|.+|-...
T Consensus       163 GiLD--S~eD~DvlLLA~ELda~vVt~------------D~G-I~kWAe~lGlr~i~a~~F~~~Lee~l~~~  219 (223)
T PRK04358        163 GILD--SAEDLDVLLLAKELDAAVVSA------------DEG-IRKWAEKLGLRFVDARKFPEMLEEYLRHS  219 (223)
T ss_pred             CCCC--CHHHHHHHHHHHHHCCEEECC------------CHH-HHHHHHHHCCEEECHHHHHHHHHHHHHHC
T ss_conf             6656--521378999999838757706------------264-99999980978778888689999999846


No 337
>PRK03922 hypothetical protein; Provisional
Probab=43.31  E-value=8.8  Score=17.48  Aligned_cols=11  Identities=27%  Similarity=0.688  Sum_probs=8.7

Q ss_pred             CCCCCCCCCCC
Q ss_conf             43265775010
Q gi|254781172|r  432 SFCPICQSRVV  442 (731)
Q Consensus       432 ~~CP~Cgs~l~  442 (731)
                      +.||+||.++.
T Consensus        50 ~~cP~Cge~~~   60 (113)
T PRK03922         50 TSCPKCGEPFD   60 (113)
T ss_pred             CCCCCCCCCCC
T ss_conf             21887778667


No 338
>pfam08442 ATP-grasp_2 ATP-grasp domain.
Probab=43.27  E-value=20  Score=14.78  Aligned_cols=43  Identities=16%  Similarity=0.115  Sum_probs=30.1

Q ss_pred             CHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf             00368999975996654148874032113455665531001123437637773
Q gi|254781172|r  254 QYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKV  306 (731)
Q Consensus       254 ~~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikv  306 (731)
                      .|+..+.|++.|.+|++ ...+.+.+++.+..+++         ..+-+|+|.
T Consensus         4 EyqaK~ll~~~gIpvp~-g~~~~~~~ea~~~~~~l---------~~~~~VvKa   46 (202)
T pfam08442         4 EYQAKEILAKYGVPVPR-GEVAFSPEEAEEIAKKL---------GGKVYVVKA   46 (202)
T ss_pred             HHHHHHHHHHCCCCCCC-EEEECCHHHHHHHHHHH---------CCCEEEEEE
T ss_conf             88999999985998999-15969999999999980---------998699987


No 339
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=43.25  E-value=13  Score=16.18  Aligned_cols=112  Identities=24%  Similarity=0.398  Sum_probs=54.3

Q ss_pred             EECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCC---CCEEEEEECCCCHHHHHHHC-----CCCC--CCC----CCE
Q ss_conf             302640001014898999750234543222468440---76899983587025665410-----1235--787----304
Q gi|254781172|r  362 NIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRV---GDRVLVKRAGEVIPKVVDII-----VNER--HPD----AQP  427 (731)
Q Consensus       362 ~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~i---Gd~V~I~RaGdVIP~I~~Vi-----~~~r--~~~----~~~  427 (731)
                      ..+|..|.|.|+---+|.+...+-.. . ....|.|   |++|++.      |.+.+--     .+.+  .++    .++
T Consensus       199 nfdgkRirrttGIPk~FLk~ve~p~e-~-~~a~imit~EG~yVv~q------pdvqsWe~Yq~r~~a~~~~~Dqv~k~~~  270 (427)
T COG5222         199 NFDGKRIRRTTGIPKDFLKPVEGPNE-P-SNAAIMITPEGGYVVAQ------PDVQSWEKYQQRTKAVAEIPDQVYKMQP  270 (427)
T ss_pred             CCCCEEEECCCCCCHHHCCCCCCCCC-C-CCCCEEECCCCCEEEEC------CCHHHHHHHHHHHHHHHHCCHHHHCCCC
T ss_conf             76630530368897776354557786-5-41235873788837855------3267799999887766408303310488


Q ss_pred             EEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHH--H----HHCCCCCHHHHHHHH
Q ss_conf             77704326577501033786544521010035434411446655332--1----301231035410355
Q gi|254781172|r  428 FSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKH--F----VSRDAFNIEGLGKQQ  490 (731)
Q Consensus       428 ~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~h--F----~SK~aldI~GLG~k~  490 (731)
                      -.+|-.||.|+.-+..- ..        --||+..-|.+-+...|..  |    |+|+-+=++||-+-+
T Consensus       271 ~~i~LkCplc~~Llrnp-~k--------T~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~l~pD~  330 (427)
T COG5222         271 PNISLKCPLCHCLLRNP-MK--------TPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLTPDI  330 (427)
T ss_pred             CCCCCCCCCHHHHHHCC-CC--------CCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCCCCH
T ss_conf             88631375210365385-45--------76566257999875555412654777654120020258217


No 340
>TIGR01652 ATPase-Plipid phospholipid-translocating P-type ATPase, flippase; InterPro: IPR006539    These sequences represent the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other . These ATPases are found only in eukaryotes. ; GO: 0000287 magnesium ion binding, 0004012 phospholipid-translocating ATPase activity, 0005524 ATP binding, 0015914 phospholipid transport, 0016021 integral to membrane.
Probab=43.16  E-value=9.9  Score=17.09  Aligned_cols=39  Identities=26%  Similarity=0.457  Sum_probs=29.3

Q ss_pred             CHHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEEECCCCEEEEEE-EEEEEEECCCEEE
Q ss_conf             1000111587656866312311456215899878899403562258999-9743330264000
Q gi|254781172|r  308 EFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVA-RLEPVNIGGALIT  369 (731)
Q Consensus       308 ~~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~wqvgRtG~itPva-~~ePV~l~G~~V~  369 (731)
                      ...+-+.||.        |=|=|.+               |||-||=-. +|.-..|+|++..
T Consensus       468 tsnl~EeLGQ--------veYifSD---------------KTGTLT~N~MeFkkcsI~Gv~Yg  507 (1249)
T TIGR01652       468 TSNLNEELGQ--------VEYIFSD---------------KTGTLTQNIMEFKKCSIAGVSYG  507 (1249)
T ss_pred             ECCCCCCCCC--------EEEEEEC---------------CCCCCCCCCCEEEEEEECCEEEC
T ss_conf             3788520361--------4068754---------------73465545301488876556411


No 341
>PRK06128 oxidoreductase; Provisional
Probab=43.15  E-value=20  Score=14.77  Aligned_cols=15  Identities=13%  Similarity=0.153  Sum_probs=8.4

Q ss_pred             EECCCCHHHHHHHHH
Q ss_conf             865986556669997
Q gi|254781172|r  152 ALRGDGHSGEDVSAC  166 (731)
Q Consensus       152 ~TRGdG~~GeDVT~n  166 (731)
                      +|=|+.-+|.-|...
T Consensus        60 VTGgssGIG~AiA~~   74 (300)
T PRK06128         60 ITGADSGIGRATAIA   74 (300)
T ss_pred             EECCCCHHHHHHHHH
T ss_conf             917366999999999


No 342
>cd00528 MoaC MoaC family. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
Probab=43.13  E-value=20  Score=14.77  Aligned_cols=53  Identities=21%  Similarity=0.364  Sum_probs=34.9

Q ss_pred             EEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCC
Q ss_conf             98788994035622589999743330264000101489899975023454322246844076899983587
Q gi|254781172|r  338 RLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGE  408 (731)
Q Consensus       338 ~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGd  408 (731)
                      .+.--.=..||||.       |-=-|-|++|.--|.  +|.++-+         ++++.|++.-+++++|.
T Consensus        84 ~i~~~v~~~~kTGV-------EMEALtavsva~LTi--yDM~Kav---------dk~~~I~~i~L~~K~GG  136 (136)
T cd00528          84 RIRATVRTTGKTGV-------EMEALTAVSVAALTI--YDMCKAV---------DKDMVIENIRLLEKSGG  136 (136)
T ss_pred             EEEEEEEECCCCCH-------HHHHHHHHHHHHHHH--HHHHHHC---------CCCCEEEEEEEEEECCC
T ss_conf             99999996689416-------886999999999999--9987631---------79978955799983188


No 343
>pfam04475 DUF555 Protein of unknown function (DUF555). Family of uncharacterized, hypothetical archaeal proteins.
Probab=43.07  E-value=8.9  Score=17.47  Aligned_cols=11  Identities=27%  Similarity=0.824  Sum_probs=8.7

Q ss_pred             CCCCCCCCCCC
Q ss_conf             43265775010
Q gi|254781172|r  432 SFCPICQSRVV  442 (731)
Q Consensus       432 ~~CP~Cgs~l~  442 (731)
                      +.||+||.++.
T Consensus        48 ~~cP~Cge~~~   58 (102)
T pfam04475        48 TACPKCGEELE   58 (102)
T ss_pred             CCCCCCCCCCC
T ss_conf             10887678667


No 344
>TIGR00715 precor6x_red precorrin-6x reductase; InterPro: IPR003723   Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase .    There are at least two distinct cobalamin biosynthetic pathways in bacteria :  Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii.     Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.   This entry represents CobK and CbiJ precorrin-6x reductase (1.3.1.54 from EC). In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y , .; GO: 0016994 precorrin-6A reductase activity, 0009236 cobalamin biosynthetic process.
Probab=43.05  E-value=20  Score=14.76  Aligned_cols=43  Identities=19%  Similarity=0.245  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHHC---CCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf             5666999775310---24322335445504899999985202123455
Q gi|254781172|r  159 SGEDVSACIRAIP---TIPRVLSLNIPEIIEVRGEVYISKNDFLALND  203 (731)
Q Consensus       159 ~GeDVT~n~~~i~---~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~  203 (731)
                      +-=.+|.|+..+-   +|| .+...-|+.. +-|.-++.-+||+.+..
T Consensus        78 FA~~~t~~a~~vc~E~~~~-YvrfeRp~e~-~~~~~ii~V~d~~~a~~  123 (260)
T TIGR00715        78 FAAQITKNALEVCKELGIP-YVRFERPEEL-VLGKNIIEVSDIEEAAR  123 (260)
T ss_pred             HHHHHHHHHHHHHHHCCCE-EEEECCCCCC-CCCCCEEEECCHHHHHH
T ss_conf             5899999999999761981-7996088353-69986688567788877


No 345
>PRK07063 short chain dehydrogenase; Provisional
Probab=43.01  E-value=20  Score=14.76  Aligned_cols=15  Identities=13%  Similarity=0.149  Sum_probs=10.9

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++++.|-+
T Consensus       239 as~iTG~~i~VDGG~  253 (259)
T PRK07063        239 APFINATCITIDGGR  253 (259)
T ss_pred             HCCCCCCEEEECCCH
T ss_conf             258248718988196


No 346
>TIGR01367 pyrE_Therm orotate phosphoribosyltransferase; InterPro: IPR006273   This group of sequences are a distinct clade of orotate phosphoribosyltransferases. Members include the experimentally determined example from Thermus aquaticus and additional examples from Caulobacter crescentus, Helicobacter pylori (Campylobacter pylori), Mesorhizobium loti, and related species. ; GO: 0004588 orotate phosphoribosyltransferase activity, 0019856 pyrimidine base biosynthetic process.
Probab=42.90  E-value=20  Score=14.74  Aligned_cols=27  Identities=30%  Similarity=0.356  Sum_probs=22.6

Q ss_pred             CCEEEE------ECCCCCCCHHHHHHHHHHCCCEEEE
Q ss_conf             866999------7258899878999999982984998
Q gi|254781172|r  649 NKKLVF------TGTLQKIQRHKAQEYVTQLGAVVSA  679 (731)
Q Consensus       649 gk~vV~------TGtl~~~~R~e~~~~ie~~Ggkv~s  679 (731)
                      |.+||+      ||    -|-.|..++||..||.|..
T Consensus       111 Gek~v~vEDvvTTG----GS~~e~~~~i~~~GG~vvg  143 (205)
T TIGR01367       111 GEKVVVVEDVVTTG----GSLLEAIKAIEELGGQVVG  143 (205)
T ss_pred             CCEEEEEEEEECCC----HHHHHHHHHHHHCCCCEEE
T ss_conf             97799996211047----4489999999857982798


No 347
>PRK06194 hypothetical protein; Provisional
Probab=42.89  E-value=20  Score=14.74  Aligned_cols=20  Identities=20%  Similarity=0.112  Sum_probs=7.7

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             3213012310354103555565
Q gi|254781172|r  473 KHFVSRDAFNIEGLGKQQLDFF  494 (731)
Q Consensus       473 ~hF~SK~aldI~GLG~k~Ie~L  494 (731)
                      .|-+||.+  +.||.+..-..|
T Consensus       160 ~Y~ASK~A--V~glT~sLa~EL  179 (301)
T PRK06194        160 VYNVSKHA--VVSLTETLYQDL  179 (301)
T ss_pred             HHHHHHHH--HHHHHHHHHHHH
T ss_conf             78999999--999999999999


No 348
>TIGR02397 dnaX_nterm DNA polymerase III, subunits gamma and tau; InterPro: IPR012763    This entry represents the well-conserved first N-terminal domain of DnaX, approx. 365 aa. The full-length product of the dnaX gene in Escherichia coli encodes the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the extreme thermophile Thermus thermophilis.; GO: 0003887 DNA-directed DNA polymerase activity, 0005524 ATP binding, 0006260 DNA replication, 0009360 DNA polymerase III complex.
Probab=42.83  E-value=16  Score=15.52  Aligned_cols=20  Identities=30%  Similarity=0.557  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHHHCCCCCHH
Q ss_conf             14466553321301231035
Q gi|254781172|r  465 SAQQLERLKHFVSRDAFNIE  484 (731)
Q Consensus       465 paq~~~~i~hF~SK~aldI~  484 (731)
                      ..+++++|.+=+.+..+++|
T Consensus       177 ~~~i~~~L~~I~~~E~I~~e  196 (363)
T TIGR02397       177 LEDIVERLKKILDKEGIKIE  196 (363)
T ss_pred             HHHHHHHHHHHHHHHCCCCC
T ss_conf             89999999999987088317


No 349
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.74  E-value=9.7  Score=17.15  Aligned_cols=34  Identities=29%  Similarity=0.508  Sum_probs=20.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf             0432657750103378654452101003543441144665533213012310354103
Q gi|254781172|r  431 PSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGK  488 (731)
Q Consensus       431 P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GLG~  488 (731)
                      --.||-||.+++|-...                       .+--||||.|-+| .||+
T Consensus         7 ~v~CP~Cgkpv~w~~~s-----------------------~frPFCSkRCklI-DLg~   40 (65)
T COG3024           7 TVPCPTCGKPVVWGEES-----------------------PFRPFCSKRCKLI-DLGE   40 (65)
T ss_pred             CCCCCCCCCCCCCCCCC-----------------------CCCCCHHHHHHHC-CHHH
T ss_conf             15388778833346667-----------------------7676336766212-1536


No 350
>PRK08277 D-mannonate oxidoreductase; Provisional
Probab=42.66  E-value=20  Score=14.72  Aligned_cols=15  Identities=20%  Similarity=0.186  Sum_probs=8.8

Q ss_pred             CCCCCCEEEEECCCC
Q ss_conf             821686699972588
Q gi|254781172|r  645 SEIENKKLVFTGTLQ  659 (731)
Q Consensus       645 ~~l~gk~vV~TGtl~  659 (731)
                      +..+|.++++.|-+.
T Consensus       259 ~yiTG~~i~VDGG~t  273 (278)
T PRK08277        259 SFVTGVVLPVDGGFS  273 (278)
T ss_pred             CCCCCCEEEECCCHH
T ss_conf             773387288692545


No 351
>PRK06079 enoyl-(acyl carrier protein) reductase; Provisional
Probab=42.49  E-value=20  Score=14.70  Aligned_cols=12  Identities=0%  Similarity=0.091  Sum_probs=5.0

Q ss_pred             CCCCCCEEEEEC
Q ss_conf             821686699972
Q gi|254781172|r  645 SEIENKKLVFTG  656 (731)
Q Consensus       645 ~~l~gk~vV~TG  656 (731)
                      +..+|.++.+.|
T Consensus       236 ~~iTGq~i~VDG  247 (252)
T PRK06079        236 TGVTGDIIYVDK  247 (252)
T ss_pred             CCCCCCEEEECC
T ss_conf             682597289794


No 352
>PRK07168 bifunctional uroporphyrinogen-III methyltransferase/uroporphyrinogen-III synthase; Reviewed
Probab=42.39  E-value=20  Score=14.69  Aligned_cols=130  Identities=13%  Similarity=0.169  Sum_probs=68.8

Q ss_pred             EEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEE-EECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHH
Q ss_conf             58998788994035622589999743330264000-10148989997502345432224684407689998358702566
Q gi|254781172|r  335 ASTRLLDIDIQIGRTGILTPVARLEPVNIGGALIT-NATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKV  413 (731)
Q Consensus       335 ~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~-ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP~I  413 (731)
                      .+++|.+|.=.+-+.|.-.|...     +=|-.|+ |.+|               .|.++.=--|-+|+|.|+-+---..
T Consensus       207 v~gTL~~Ia~~v~~~~i~~PAvI-----VVGeVV~lR~~L---------------~WfE~kPLfG~rVLVtRtreQA~~l  266 (474)
T PRK07168        207 VTGTLSTIVSIVKNENISNPSMT-----IVGDVVSLRNQI---------------AWKERKPLHGKKVLFTSATNKTSVM  266 (474)
T ss_pred             EEEEHHHHHHHHHHCCCCCCEEE-----EECCCCCCCCCC---------------CCCCCCCCCCCEEEECCCHHHHHHH
T ss_conf             99999999999997378998299-----988400555536---------------7535688788679977866776999


Q ss_pred             HHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECC-CCCCCCHHHHHHHHHHHHH---CCCCCHHH----
Q ss_conf             541012357873047770432657750103378654452101003-5434411446655332130---12310354----
Q gi|254781172|r  414 VDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRC-TGGLACSAQQLERLKHFVS---RDAFNIEG----  485 (731)
Q Consensus       414 ~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC-~n~~~Cpaq~~~~i~hF~S---K~aldI~G----  485 (731)
                      ..-+.   .-.+.++++|+.-|.-.+++....... ..++-..++ .|+          ..+|+.   +..+||..    
T Consensus       267 s~~L~---~~GA~v~E~PtI~~~~~~~~~~~i~~l-~~ydwlvFTS~Ng----------V~~Ff~~L~~~g~D~R~L~~k  332 (474)
T PRK07168        267 KQKLQ---EAGAEIYQIPTFKKEEYTLTLEQINEI-FNVDRLVFCSAES----------VEILMQSCSKYKKDIRSLQAE  332 (474)
T ss_pred             HHHHH---HCCCCEEEECCCCCCCCCHHHHHHHHH-CCCCEEEEECHHH----------HHHHHHHHHHCCCCHHHCCCE
T ss_conf             99999---769938994453168856379998753-3389899938789----------999999999739845760761


Q ss_pred             ---HHHHHHHHHHCCC
Q ss_conf             ---1035555653057
Q gi|254781172|r  486 ---LGKQQLDFFFKSE  498 (731)
Q Consensus       486 ---LG~k~Ie~L~e~~  498 (731)
                         +|++|-+.|-+.|
T Consensus       333 iaaiG~aT~~~L~~~G  348 (474)
T PRK07168        333 LQHMNVATQEKLMQYG  348 (474)
T ss_pred             EEEECHHHHHHHHHCC
T ss_conf             7887589999999769


No 353
>PRK12495 hypothetical protein; Provisional
Probab=42.35  E-value=11  Score=16.82  Aligned_cols=13  Identities=31%  Similarity=0.749  Sum_probs=6.4

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             4326577501033
Q gi|254781172|r  432 SFCPICQSRVVRD  444 (731)
Q Consensus       432 ~~CP~Cgs~l~~~  444 (731)
                      .+|+-||+++.+.
T Consensus        43 ~HC~~CGdPIFR~   55 (221)
T PRK12495         43 AHCDECGSPIFRH   55 (221)
T ss_pred             CCCCCCCCHHHHC
T ss_conf             2002236723404


No 354
>PRK06550 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=42.35  E-value=20  Score=14.68  Aligned_cols=15  Identities=7%  Similarity=0.164  Sum_probs=10.6

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++.+.|-+
T Consensus       220 as~iTG~~i~VDGG~  234 (237)
T PRK06550        220 ADYMQGTIVPIDGGW  234 (237)
T ss_pred             HCCCCCCEEEECCCC
T ss_conf             338148628968273


No 355
>KOG4236 consensus
Probab=42.34  E-value=6.5  Score=18.51  Aligned_cols=86  Identities=13%  Similarity=0.085  Sum_probs=35.3

Q ss_pred             EEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHH--HHHH
Q ss_conf             98788994035622589999743330264000101489899975023454322246844076899983587025--6654
Q gi|254781172|r  338 RLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIP--KVVD  415 (731)
Q Consensus       338 ~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP--~I~~  415 (731)
                      -|.-|.-+|+-|-+-+     ......|=.|-+.+-.|..      ..++|+..-|.|-.=---.-.|-=-.||  +|.+
T Consensus       395 PLmRvv~svkhtkRks-----st~~kEGWmvHyt~~d~lR------krHYWrldsk~itlfqn~s~~ryYkeIPLsEIl~  463 (888)
T KOG4236         395 PLMRVVQSVKHTKRKS-----STKLKEGWMVHYTSKDNLR------KRHYWRLDSKCITLFQNESTNRYYKEIPLSEILS  463 (888)
T ss_pred             CEEEECHHHCCCCCCC-----HHHHHCCEEEEEECHHHHH------HHHHHEECCCEEEEEECCCCCEEEEEECHHHHHE
T ss_conf             4165200212220001-----2422104389875336664------5454200366567653277743677502788312


Q ss_pred             HCCCCCCCCCCEEEECCCCCCCC
Q ss_conf             10123578730477704326577
Q gi|254781172|r  416 IIVNERHPDAQPFSFPSFCPICQ  438 (731)
Q Consensus       416 Vi~~~r~~~~~~~~~P~~CP~Cg  438 (731)
                      |....    .....++.+-|.|-
T Consensus       464 v~~~~----~~~~vp~~~~phcF  482 (888)
T KOG4236         464 VSSNN----GFSLVPAGTNPHCF  482 (888)
T ss_pred             EECCC----CCCCCCCCCCCCEE
T ss_conf             00368----85347899998338


No 356
>PRK08226 short chain dehydrogenase; Provisional
Probab=42.30  E-value=20  Score=14.68  Aligned_cols=15  Identities=27%  Similarity=0.251  Sum_probs=10.8

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++.+.|-+
T Consensus       239 a~yiTG~~i~VDGG~  253 (263)
T PRK08226        239 SSYLTGTQNVIDGGS  253 (263)
T ss_pred             HCCCCCCEEEECCCC
T ss_conf             348048828858883


No 357
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=42.27  E-value=7.6  Score=17.97  Aligned_cols=14  Identities=36%  Similarity=0.792  Sum_probs=8.5

Q ss_pred             CCCCCCCCCCCCCC
Q ss_conf             04326577501033
Q gi|254781172|r  431 PSFCPICQSRVVRD  444 (731)
Q Consensus       431 P~~CP~Cgs~l~~~  444 (731)
                      +-+||+||.-|.++
T Consensus       221 iv~CP~CgRILy~~  234 (239)
T COG1579         221 IVFCPYCGRILYYD  234 (239)
T ss_pred             CCCCCCCCHHHHHH
T ss_conf             75287611367775


No 358
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=42.10  E-value=11  Score=16.87  Aligned_cols=36  Identities=14%  Similarity=0.093  Sum_probs=23.9

Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHCCHH-HHHHHHHHHH
Q ss_conf             78761388867899999999966979-9999999997
Q gi|254781172|r  595 WLSLIRVPLVGDIIAQAIVEFYQNPR-NICAVEALLK  630 (731)
Q Consensus       595 ~e~L~~I~GiG~~~A~si~~ff~~~~-n~~~i~~L~~  630 (731)
                      .+.|..+|.++-+-=.|+.--|.+.. ..+.+.+|..
T Consensus       113 M~~Lk~lD~VAYvRFASVYr~F~dv~~F~e~i~~l~~  149 (156)
T COG1327         113 MEELKKLDEVAYVRFASVYRSFKDVDDFEEEIEELTK  149 (156)
T ss_pred             HHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             9999710502323466687032789999999999974


No 359
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS 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=42.04  E-value=11  Score=16.81  Aligned_cols=14  Identities=36%  Similarity=0.617  Sum_probs=8.1

Q ss_pred             ECCCCCCCCCCCCC
Q ss_conf             70432657750103
Q gi|254781172|r  430 FPSFCPICQSRVVR  443 (731)
Q Consensus       430 ~P~~CP~Cgs~l~~  443 (731)
                      .|..||.||+.+.+
T Consensus        25 ~~~~CP~Cg~~~~r   38 (41)
T smart00834       25 PLATCPECGGDVRR   38 (41)
T ss_pred             CCCCCCCCCCCCEE
T ss_conf             78858689992277


No 360
>TIGR01512 ATPase-IB2_Cd cadmium-translocating P-type ATPase; InterPro: IPR006404   These sequences describe the P-type ATPase primarily responsible for translocating cadmium ions (and other closely-related divalent heavy metals such as cobalt, mercury, lead and zinc) across biological membranes. These transporters are found in prokaryotes and plants. Experimentally characterised members include P37617 from SWISSPROT from Escherichia coli, Q10866 from SWISSPROT from Mycobacterium tuberculosis and Q59998 from SWISSPROT from Synechocystis PCC6803. The cadmium P-type ATPases have been characterised as Type IB based on a phylogenetic analysis which combines the copper-translocating ATPases with the cadmium-translocating species . This family and that describing the copper-ATPases (IPR006403 from INTERPRO) are well separated, and thus the copper-ATPases can be typed as IB1 and the cadmium-ATPases as IB2. ; GO: 0005524 ATP binding, 0016818 hydrolase activity acting on acid anhydrides in phosphorus-containing anhydrides, 0046872 metal ion binding, 0046873 metal ion transmembrane transporter activity, 0030001 metal ion transport, 0016020 membrane.
Probab=41.82  E-value=14  Score=16.01  Aligned_cols=54  Identities=19%  Similarity=0.324  Sum_probs=29.6

Q ss_pred             CCCCCCC--CCEEEEC-CCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCC
Q ss_conf             8765686--6312311-4562158998788994035622589999743330264000101489
Q gi|254781172|r  316 GERARSP--RWMISHK-FAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHN  375 (731)
Q Consensus       316 G~ts~~P--rwaiA~K-f~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN  375 (731)
                      ...|.||  +==++|. +|.+=...++.+-.|-+|+..-+-      .|.+++..+..-.++-
T Consensus       268 E~~S~HPlA~AIv~~~e~pG~G~~a~~~g~~v~~G~~~t~~------~v~~~~~~~G~i~l~D  324 (494)
T TIGR01512       268 EQQSSHPLARAIVAAEEVPGEGVKAVVDGEEVRIGNKRTLV------LVAVDGKLIGVILLSD  324 (494)
T ss_pred             HHCCCCHHHHHHHHHHHCCCCCEEEEECCEEEEEECCCCEE------EEEECCEEEEEEEEEC
T ss_conf             31066868999997420477744899957799997376589------9998584999999733


No 361
>PRK10517 magnesium-transporting ATPase MgtA; Provisional
Probab=41.80  E-value=12  Score=16.53  Aligned_cols=15  Identities=20%  Similarity=0.020  Sum_probs=8.2

Q ss_pred             CCEEEEECCCCHHHH
Q ss_conf             640001014898999
Q gi|254781172|r  365 GALITNATLHNEDYI  379 (731)
Q Consensus       365 G~~V~ratlhN~~~I  379 (731)
                      |..|.=.|+-|..--
T Consensus       564 GI~V~MITGD~~~TA  578 (900)
T PRK10517        564 GITVKILTGDSELVA  578 (900)
T ss_pred             CCEEEEECCCCHHHH
T ss_conf             993899899998999


No 362
>COG4213 XylF ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=41.79  E-value=13  Score=16.22  Aligned_cols=20  Identities=5%  Similarity=0.258  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHHCCCCCHH
Q ss_conf             14466553321301231035
Q gi|254781172|r  465 SAQQLERLKHFVSRDAFNIE  484 (731)
Q Consensus       465 paq~~~~i~hF~SK~aldI~  484 (731)
                      |++..+++..|.++..-+|+
T Consensus       200 ps~Aq~~men~lta~~~~vd  219 (341)
T COG4213         200 PSNAQQIMENLLTANYNDID  219 (341)
T ss_pred             HHHHHHHHHHHHHCCCCCEE
T ss_conf             88999999988742367600


No 363
>PRK07758 hypothetical protein; Provisional
Probab=41.70  E-value=19  Score=14.96  Aligned_cols=24  Identities=21%  Similarity=0.443  Sum_probs=18.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             010001342100145689999875
Q gi|254781172|r  522 TKIENILGFGDVSVTNLYDSINKR  545 (731)
Q Consensus       522 ~~l~~l~GfgeKsa~nL~~sIe~s  545 (731)
                      .+|+++-|||.++...|-+++++.
T Consensus        67 kELL~LHGmGP~ai~~L~~aLke~   90 (95)
T PRK07758         67 KEILKLHGMGPASLPKLRKALEES   90 (95)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             999998486888899999999983


No 364
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=41.56  E-value=10  Score=17.04  Aligned_cols=42  Identities=17%  Similarity=0.242  Sum_probs=23.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHH
Q ss_conf             326577501033786544521010035434411446655332130
Q gi|254781172|r  433 FCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVS  477 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~S  477 (731)
                      +||.||++|-+.....+....+...|.++   |+...-.+..|++
T Consensus        71 FC~~CGs~l~~~~~~~~~~~~v~~~~ld~---p~~~~p~~~~~~~  112 (133)
T COG3791          71 FCPTCGSPLFWRGPDEDPFVGVNAGALDD---PEFLPPQVQIFVG  112 (133)
T ss_pred             ECCCCCCCCEEECCCCCCEEEEEEEEECC---CCCCCCCEEEEEE
T ss_conf             26668985163179987518898884258---5437973488860


No 365
>PRK13810 orotate phosphoribosyltransferase; Provisional
Probab=41.42  E-value=21  Score=14.58  Aligned_cols=60  Identities=23%  Similarity=0.342  Sum_probs=40.5

Q ss_pred             CCCEEEE------ECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHH
Q ss_conf             6866999------7258899878999999982984998111632179977888863798997499173799999999
Q gi|254781172|r  648 ENKKLVF------TGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLL  718 (731)
Q Consensus       648 ~gk~vV~------TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll  718 (731)
                      .|.++++      ||    -|=-++.+.+++.|+.|..-+.      |+.-..| ..+..++.||++++--.+.++|
T Consensus       121 ~g~rVlvVEDViTTG----gS~~eai~~l~~~G~~V~~v~~------ivDR~~g-~~e~l~~~gv~~~sl~t~~dll  186 (187)
T PRK13810        121 PEDRIVMLEDVTTSG----GSVRDAIEVVREAGAIVKYVIT------VVDREEG-ATENLKEADVELVPLVSASDLL  186 (187)
T ss_pred             CCCEEEEEEEEECCC----CCHHHHHHHHHHCCCEEEEEEE------EEECCCC-HHHHHHHCCCCEEEECCHHHHH
T ss_conf             998899998543568----2399999999988997999999------9977847-6999997799099946198961


No 366
>PRK08217 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=41.33  E-value=21  Score=14.57  Aligned_cols=11  Identities=18%  Similarity=0.347  Sum_probs=4.6

Q ss_pred             CCCCCEEEEEC
Q ss_conf             21686699972
Q gi|254781172|r  646 EIENKKLVFTG  656 (731)
Q Consensus       646 ~l~gk~vV~TG  656 (731)
                      .++|.++++.|
T Consensus       239 ~iTG~~i~VDG  249 (253)
T PRK08217        239 YVTGRVLEIDG  249 (253)
T ss_pred             CCCCCEEEECC
T ss_conf             98899678696


No 367
>PRK06227 consensus
Probab=41.27  E-value=21  Score=14.57  Aligned_cols=15  Identities=20%  Similarity=0.364  Sum_probs=9.7

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++++.|-+
T Consensus       234 as~iTG~~i~VDGG~  248 (256)
T PRK06227        234 ASFITGVNFIVDGGM  248 (256)
T ss_pred             HCCCCCCEEEECCCE
T ss_conf             249258638967891


No 368
>PRK05855 short chain dehydrogenase; Validated
Probab=41.27  E-value=21  Score=14.57  Aligned_cols=26  Identities=15%  Similarity=0.213  Sum_probs=13.5

Q ss_pred             HHHHCCCC---CHHHHHHHHHHHHHCCCC
Q ss_conf             21301231---035410355556530576
Q gi|254781172|r  474 HFVSRDAF---NIEGLGKQQLDFFFKSED  499 (731)
Q Consensus       474 hF~SK~al---dI~GLG~k~Ie~L~e~~~  499 (731)
                      .|..|-++   --.|+|..+...|-+.|.
T Consensus       312 rFsGKvAvVTGA~sGIGrA~A~~fA~~GA  340 (582)
T PRK05855        312 RFGGKLVVVTGAGSGIGRATALAFAREGA  340 (582)
T ss_pred             CCCCCEEEEECCCCHHHHHHHHHHHHCCC
T ss_conf             74995899958757899999999997799


No 369
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=41.17  E-value=21  Score=14.56  Aligned_cols=15  Identities=33%  Similarity=0.446  Sum_probs=6.0

Q ss_pred             CCCCCHHHHHHHHHH
Q ss_conf             888678999999999
Q gi|254781172|r  601 VPLVGDIIAQAIVEF  615 (731)
Q Consensus       601 I~GiG~~~A~si~~f  615 (731)
                      ++|+.+.-+..|++|
T Consensus       265 lPG~ND~E~~~iIe~  279 (414)
T COG2100         265 LPGVNDDEMPKIIEW  279 (414)
T ss_pred             CCCCCHHHHHHHHHH
T ss_conf             278681778999999


No 370
>PRK01103 formamidopyrimidine-DNA glycosylase; Validated
Probab=41.16  E-value=11  Score=16.72  Aligned_cols=24  Identities=13%  Similarity=0.257  Sum_probs=13.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf             3265775010337865445210100354
Q gi|254781172|r  433 FCPICQSRVVRDLNPKTGKLVAAHRCTG  460 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n  460 (731)
                      .||.||+++.+..-..    -..++|++
T Consensus       246 ~C~~Cg~~I~~~~~~g----R~t~~CP~  269 (273)
T PRK01103        246 PCRRCGTPIEKIKQGG----RSTFFCPK  269 (273)
T ss_pred             CCCCCCCEEEEEEECC----CCCEECCC
T ss_conf             4899999678999889----71199957


No 371
>PRK06171 sorbitol-6-phosphate 2-dehydrogenase; Provisional
Probab=41.16  E-value=21  Score=14.55  Aligned_cols=15  Identities=20%  Similarity=0.109  Sum_probs=10.5

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++.+.|-+
T Consensus       249 as~iTG~~i~VDGG~  263 (266)
T PRK06171        249 ASYITGVTTNIAGGK  263 (266)
T ss_pred             HCCCCCCEEEECCCC
T ss_conf             258058628987882


No 372
>TIGR01082 murC UDP-N-acetylmuramate--alanine ligase; InterPro: IPR005758   The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:    (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.    Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC)  and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .    This entry represents UDP-N-acetylmuramate-alanine ligase (MurC). MurC is an essential, cytoplasmic peptidoglycan biosynthetic enzyme, catalyzes the ATP-dependent ligation of L-alanine (Ala) and UDP-N-acetylmuramic acid (UNAM) to form UDP-N-acetylmuramyl-L-alanine (UNAM-Ala). The enzyme is a nonribosomal peptide ligase which utilises ATP to form an amide bond between L-alanine and UNAM.1 Mechanistic studies on the Escherichia coli MurC enzyme using oxygen isotope analyses demonstrated that the enzyme-catalyzed reaction proceeds through an acyl phosphate UNAM intermediate prior to L-alanine addition.; GO: 0005524 ATP binding, 0008763 UDP-N-acetylmuramate-L-alanine ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=41.11  E-value=21  Score=14.55  Aligned_cols=66  Identities=17%  Similarity=0.197  Sum_probs=36.3

Q ss_pred             ECCCCHHHHHHHHHHHHCCCCCCCCC-EEEEECCHHCCCCCCCCCC-CCCCEEEECCCCCEEEEEEEEEEEEE
Q ss_conf             40321134556655310011234376-3777311000111587656-86631231145621589987889940
Q gi|254781172|r  276 NTFHGIVSYYNEMKSIRSTLPYDIDG-LVYKVDEFSLQKQLGERAR-SPRWMISHKFAEKQASTRLLDIDIQI  346 (731)
Q Consensus       276 ~~~~~~~~~~~~~~~~r~~l~y~iDG-iVikvn~~~~q~~lG~ts~-~PrwaiA~Kf~~e~~~T~v~~I~wqv  346 (731)
                      ++++.+...+.++.   ..+|  --| +|+-.||--+++..-.... -|+-.+-|-++.+.+.-++.++.-+-
T Consensus       198 ~~~E~~~~aF~~F~---~~l~--~~G~~v~c~DD~~~~~l~~~~~~~r~d~~~~y~~~~~~~~~~~~~~~~~~  265 (491)
T TIGR01082       198 SSLERLKAAFEKFI---HNLP--FYGLAVICADDPVLRKLVPKATESRKDVVITYGGSGEDADIRAENIQQSG  265 (491)
T ss_pred             CCHHHHHHHHHHHH---HHCC--CCCEEEEECCCHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEECC
T ss_conf             57899999999999---8278--88799998386547877635553387047866877764147788743226


No 373
>COG2216 KdpB High-affinity K+ transport system, ATPase chain B [Inorganic ion transport and metabolism]
Probab=40.88  E-value=19  Score=14.95  Aligned_cols=16  Identities=25%  Similarity=0.393  Sum_probs=12.3

Q ss_pred             HHHHHHHHHCCCHHHH
Q ss_conf             4567777523455553
Q gi|254781172|r  217 RNAASGILRRLNPTDI  232 (731)
Q Consensus       217 RN~aaG~lr~~d~~~~  232 (731)
                      =+++-|+-|||-|.+.
T Consensus       201 I~LVEgA~R~KTPNEI  216 (681)
T COG2216         201 IALVEGAERQKTPNEI  216 (681)
T ss_pred             HHHHHCHHCCCCHHHH
T ss_conf             9986352015891489


No 374
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer.  Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain.  Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=40.72  E-value=10  Score=16.91  Aligned_cols=12  Identities=33%  Similarity=0.924  Sum_probs=8.6

Q ss_pred             ECCCCCCCCCCC
Q ss_conf             704326577501
Q gi|254781172|r  430 FPSFCPICQSRV  441 (731)
Q Consensus       430 ~P~~CP~Cgs~l  441 (731)
                      .|..||.||.+-
T Consensus        16 ~p~~CP~Cg~~k   27 (33)
T cd00350          16 APWVCPVCGAPK   27 (33)
T ss_pred             CCCCCCCCCCCH
T ss_conf             987287889978


No 375
>PRK04690 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=40.63  E-value=21  Score=14.50  Aligned_cols=14  Identities=21%  Similarity=0.254  Sum_probs=6.6

Q ss_pred             CCCHHHHHCCCCCC
Q ss_conf             11778761388867
Q gi|254781172|r  592 NDDWLSLIRVPLVG  605 (731)
Q Consensus       592 ~~~~e~L~~I~GiG  605 (731)
                      ..+...+..|||+|
T Consensus       453 ~~~~~~~~~~~~~~  466 (468)
T PRK04690        453 GFDPAAISAIPGLG  466 (468)
T ss_pred             CCCHHHHHHCCCCC
T ss_conf             80877785267757


No 376
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=40.62  E-value=13  Score=16.06  Aligned_cols=20  Identities=15%  Similarity=0.532  Sum_probs=14.9

Q ss_pred             CCEEEECCCCCCCCCCCCCC
Q ss_conf             30477704326577501033
Q gi|254781172|r  425 AQPFSFPSFCPICQSRVVRD  444 (731)
Q Consensus       425 ~~~~~~P~~CP~Cgs~l~~~  444 (731)
                      -..+.+-+.||.||+.+..-
T Consensus        11 cg~YTLke~Cp~CG~~t~~~   30 (59)
T COG2260          11 CGRYTLKEKCPVCGGDTKVP   30 (59)
T ss_pred             CCCEEECCCCCCCCCCCCCC
T ss_conf             88146113377888745467


No 377
>PRK07231 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=40.62  E-value=21  Score=14.49  Aligned_cols=14  Identities=29%  Similarity=0.223  Sum_probs=9.0

Q ss_pred             CCCCCCCEEEEECC
Q ss_conf             88216866999725
Q gi|254781172|r  644 SSEIENKKLVFTGT  657 (731)
Q Consensus       644 ~~~l~gk~vV~TGt  657 (731)
                      ++.++|.++++.|-
T Consensus       234 s~~itG~~i~VDGG  247 (250)
T PRK07231        234 ASFITGVALEVDGG  247 (250)
T ss_pred             HCCCCCCEEEECCC
T ss_conf             32946871884888


No 378
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=40.58  E-value=14  Score=16.01  Aligned_cols=34  Identities=12%  Similarity=0.080  Sum_probs=20.7

Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHCCHH-HHHHHHHH
Q ss_conf             78761388867899999999966979-99999999
Q gi|254781172|r  595 WLSLIRVPLVGDIIAQAIVEFYQNPR-NICAVEAL  628 (731)
Q Consensus       595 ~e~L~~I~GiG~~~A~si~~ff~~~~-n~~~i~~L  628 (731)
                      .+.|..+|.++-+-=.|+..-|.+.. ..+.+++|
T Consensus       113 m~~Lk~lD~VAYvRFASVYr~F~d~~~F~~ei~~L  147 (149)
T PRK00464        113 MEELKKLDEVAYVRFASVYRSFKDVDDFEEEIEEL  147 (149)
T ss_pred             HHHHHHCCCEEEHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             99886209310000245606779999999999997


No 379
>PRK07985 oxidoreductase; Provisional
Probab=40.42  E-value=22  Score=14.47  Aligned_cols=14  Identities=21%  Similarity=0.330  Sum_probs=6.1

Q ss_pred             ECCCCHHHHHHHHH
Q ss_conf             65986556669997
Q gi|254781172|r  153 LRGDGHSGEDVSAC  166 (731)
Q Consensus       153 TRGdG~~GeDVT~n  166 (731)
                      |=|.+-+|.-|...
T Consensus        55 TGas~GIG~aiA~~   68 (294)
T PRK07985         55 TGGDSGIGRAAAIA   68 (294)
T ss_pred             ECCCCHHHHHHHHH
T ss_conf             17266999999999


No 380
>TIGR02109 PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E; InterPro: IPR011843    This entry describes coenzyme PQQ biosynthesis protein E, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases.; GO: 0051539 4 iron 4 sulfur cluster binding, 0018189 pyrroloquinoline quinone biosynthetic process.
Probab=40.38  E-value=10  Score=16.97  Aligned_cols=74  Identities=12%  Similarity=0.159  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH--HHHHHHHHHHHCCHHHH
Q ss_conf             4103555565305765404541011010677753100010001342100145689999875--22346667763010111
Q gi|254781172|r  485 GLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKR--RNISLERFIFSLGIRHV  562 (731)
Q Consensus       485 GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~s--K~~~L~r~L~ALGI~~v  562 (731)
                      ||-+.-++.|.++|.+     ++          ++      .+-|--+-.+++| ...+++  ++....|.+.++|||++
T Consensus        92 GLt~~rl~~L~~aGLD-----Hv----------Ql------SfQ~vd~~~a~~i-aG~k~A~~~Kl~~A~~v~~~g~Plt  149 (363)
T TIGR02109        92 GLTEARLDALADAGLD-----HV----------QL------SFQGVDEALADRI-AGLKNAFEQKLAVARAVKAAGLPLT  149 (363)
T ss_pred             HHHHHHHHHHHHCCCC-----EE----------EE------EEECCCHHHHHHH-CCHHHHHHHHHHHHHHHHHCCCCEE
T ss_conf             5679999999757985-----78----------87------6414787888641-2502589999999999996189817


Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             16899999988299899999789
Q gi|254781172|r  563 GAEIARSLAKYYLSYQNFAQEIN  585 (731)
Q Consensus       563 G~~~Ak~La~~f~si~~l~~~~~  585 (731)
                      =-    . .-|=.||+++-.-|+
T Consensus       150 LN----~-V~HR~Ni~~i~~~i~  167 (363)
T TIGR02109       150 LN----F-VLHRHNIDQIPEIIE  167 (363)
T ss_pred             EE----H-CCCCCHHHHHHHHHH
T ss_conf             60----2-002420213678999


No 381
>PRK06057 short chain dehydrogenase; Provisional
Probab=40.26  E-value=22  Score=14.46  Aligned_cols=15  Identities=20%  Similarity=0.344  Sum_probs=10.2

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++.+.|-+
T Consensus       233 ss~iTG~~i~VDGG~  247 (255)
T PRK06057        233 ASFITASTFLVDGGI  247 (255)
T ss_pred             HCCCCCCEEEECCCH
T ss_conf             248268738869383


No 382
>PRK08220 2,3-dihydroxybenzoate-2,3-dehydrogenase; Validated
Probab=40.26  E-value=22  Score=14.45  Aligned_cols=14  Identities=29%  Similarity=0.458  Sum_probs=8.9

Q ss_pred             CCCCCCCEEEEECC
Q ss_conf             88216866999725
Q gi|254781172|r  644 SSEIENKKLVFTGT  657 (731)
Q Consensus       644 ~~~l~gk~vV~TGt  657 (731)
                      ++..+|.++++.|-
T Consensus       235 s~~itGq~i~vDGG  248 (253)
T PRK08220        235 ASHITMQDIVVDGG  248 (253)
T ss_pred             HCCCCCCEEEECCC
T ss_conf             33924832889937


No 383
>PRK08063 enoyl-(acyl carrier protein) reductase; Provisional
Probab=40.06  E-value=22  Score=14.43  Aligned_cols=14  Identities=14%  Similarity=0.418  Sum_probs=8.7

Q ss_pred             CCCCCCCEEEEECC
Q ss_conf             88216866999725
Q gi|254781172|r  644 SSEIENKKLVFTGT  657 (731)
Q Consensus       644 ~~~l~gk~vV~TGt  657 (731)
                      ++..+|.++.+.|-
T Consensus       232 s~~iTG~~i~VDGG  245 (250)
T PRK08063        232 ADMIRGQTIIVDGG  245 (250)
T ss_pred             HCCCCCCEEEECCC
T ss_conf             34822870885948


No 384
>PRK08993 2-deoxy-D-gluconate 3-dehydrogenase; Validated
Probab=40.01  E-value=22  Score=14.43  Aligned_cols=13  Identities=15%  Similarity=0.248  Sum_probs=7.6

Q ss_pred             CCCCCCEEEEECC
Q ss_conf             8216866999725
Q gi|254781172|r  645 SEIENKKLVFTGT  657 (731)
Q Consensus       645 ~~l~gk~vV~TGt  657 (731)
                      +..+|.++.+.|-
T Consensus       237 ~~iTG~~i~VDGG  249 (253)
T PRK08993        237 DYINGYTIAVDGG  249 (253)
T ss_pred             CCCCCCEEEECCC
T ss_conf             2825853898957


No 385
>PRK05854 short chain dehydrogenase; Provisional
Probab=39.91  E-value=22  Score=14.42  Aligned_cols=14  Identities=7%  Similarity=0.022  Sum_probs=5.9

Q ss_pred             EECCCCHHHHHHHH
Q ss_conf             86598655666999
Q gi|254781172|r  152 ALRGDGHSGEDVSA  165 (731)
Q Consensus       152 ~TRGdG~~GeDVT~  165 (731)
                      +|=|+.-+|.-...
T Consensus        19 ITGa~sGIG~~~a~   32 (314)
T PRK05854         19 VTGASSGLGFGLAR   32 (314)
T ss_pred             ECCCCCHHHHHHHH
T ss_conf             90688299999999


No 386
>PTZ00159 60S ribosomal protein L32; Provisional
Probab=39.84  E-value=8.1  Score=17.76  Aligned_cols=55  Identities=20%  Similarity=0.315  Sum_probs=35.2

Q ss_pred             EEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHHH-HHHHHHHHCCCCCCEEEEEHHHHCCH
Q ss_conf             0100354344114466553321301231035410-35555653057654045410110106
Q gi|254781172|r  454 AAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLG-KQQLDFFFKSEDPAFSIRIPADIFTL  513 (731)
Q Consensus       454 ~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GLG-~k~Ie~L~e~~~~~g~I~~~~DLy~L  513 (731)
                      ..||.+-+.++.-+     .+|-++..|---|.| ++-+.-|.-.|+...+|.++.||-.|
T Consensus        32 ~~WRkPrGidnkvR-----r~~kG~~~mp~iGYgs~k~tR~l~PsG~~~~lV~N~~eLe~L   87 (134)
T PTZ00159         32 PSWRKPRGIDNRVR-----RRFKGQRAMPKIGYGSDKKTRYLLPSGFKKFPISNVQDLEML   87 (134)
T ss_pred             CCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEECCHHHHHHH
T ss_conf             56559888656511-----224775688766768667760558676878886788998998


No 387
>PRK10445 endonuclease VIII; Provisional
Probab=39.71  E-value=12  Score=16.54  Aligned_cols=24  Identities=17%  Similarity=0.353  Sum_probs=13.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf             3265775010337865445210100354
Q gi|254781172|r  433 FCPICQSRVVRDLNPKTGKLVAAHRCTG  460 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n  460 (731)
                      .||.||+++.+..-..    -...+|++
T Consensus       237 ~C~~Cg~~I~~~~~~g----Rst~~Cp~  260 (263)
T PRK10445        237 ACERCGGIIEKTTLSS----RPFYWCPG  260 (263)
T ss_pred             CCCCCCCEEEEEEECC----CCCEECCC
T ss_conf             3899997627999889----87887956


No 388
>pfam11290 DUF3090 Protein of unknown function (DUF3090). This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=39.45  E-value=19  Score=14.86  Aligned_cols=24  Identities=25%  Similarity=0.704  Sum_probs=17.1

Q ss_pred             HHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCC
Q ss_conf             5665410123578730477704326577501033
Q gi|254781172|r  411 PKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRD  444 (731)
Q Consensus       411 P~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~  444 (731)
                      =+-..||...|+.          ||.||.++..+
T Consensus       144 ~ra~~VV~AGRp~----------Cp~Cg~Pidp~  167 (171)
T pfam11290       144 KRARRVVAAGRPP----------CPLCGQPLDPD  167 (171)
T ss_pred             HHHHHHHHCCCCC----------CCCCCCCCCCC
T ss_conf             9999999669999----------99889976999


No 389
>TIGR02187 GlrX_arch Glutaredoxin-like domain protein; InterPro: IPR011903   Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system .    Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond.   Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed  that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro.    This entry of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different..
Probab=39.38  E-value=14  Score=16.02  Aligned_cols=14  Identities=21%  Similarity=0.155  Sum_probs=6.2

Q ss_pred             CCEEEEEECCCCHH
Q ss_conf             76899983587025
Q gi|254781172|r  398 GDRVLVKRAGEVIP  411 (731)
Q Consensus       398 Gd~V~I~RaGdVIP  411 (731)
                      -|.+.|++.+-=.+
T Consensus       121 edI~~vS~g~~~L~  134 (237)
T TIGR02187       121 EDIVRVSEGESGLS  134 (237)
T ss_pred             HHHHHHCCCCCCCC
T ss_conf             99985268999850


No 390
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=39.36  E-value=12  Score=16.49  Aligned_cols=18  Identities=22%  Similarity=0.571  Sum_probs=11.4

Q ss_pred             EECCCCCCCCC-CCCCCCC
Q ss_conf             77043265775-0103378
Q gi|254781172|r  429 SFPSFCPICQS-RVVRDLN  446 (731)
Q Consensus       429 ~~P~~CP~Cgs-~l~~~~~  446 (731)
                      ...+.||.||+ ++..++.
T Consensus        13 ~~~~~CP~Cgs~~~s~dW~   31 (61)
T PRK08351         13 TTEDRCPVCGSRDLSEEWF   31 (61)
T ss_pred             CCCCCCCCCCCCCCCCCCC
T ss_conf             6899589997986887734


No 391
>PRK07889 enoyl-(acyl carrier protein) reductase; Provisional
Probab=39.28  E-value=22  Score=14.35  Aligned_cols=13  Identities=8%  Similarity=0.146  Sum_probs=7.4

Q ss_pred             CCCCCCEEEEECC
Q ss_conf             8216866999725
Q gi|254781172|r  645 SEIENKKLVFTGT  657 (731)
Q Consensus       645 ~~l~gk~vV~TGt  657 (731)
                      +..+|.++.+.|-
T Consensus       238 ~~iTG~~l~VDGG  250 (256)
T PRK07889        238 PATTGEIIHVDGG  250 (256)
T ss_pred             CCCCCCEEEECCC
T ss_conf             3716885887959


No 392
>PRK06172 short chain dehydrogenase; Provisional
Probab=39.20  E-value=22  Score=14.34  Aligned_cols=15  Identities=20%  Similarity=0.220  Sum_probs=10.0

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++.+.|-+
T Consensus       236 a~~iTG~~i~VDGG~  250 (253)
T PRK06172        236 ASFTTGHSLMVDGGA  250 (253)
T ss_pred             HCCCCCCEEEECCCH
T ss_conf             268259828739241


No 393
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=39.12  E-value=10  Score=16.92  Aligned_cols=18  Identities=22%  Similarity=0.674  Sum_probs=11.1

Q ss_pred             EEECCC--CCCCCCC-CCCCC
Q ss_conf             777043--2657750-10337
Q gi|254781172|r  428 FSFPSF--CPICQSR-VVRDL  445 (731)
Q Consensus       428 ~~~P~~--CP~Cgs~-l~~~~  445 (731)
                      +..++.  ||.||++ +..++
T Consensus        13 l~~~d~e~CP~Cgs~~~te~W   33 (64)
T COG2093          13 LTPEDTEICPVCGSTDLTEEW   33 (64)
T ss_pred             CCCCCCCCCCCCCCCCCCHHH
T ss_conf             378877408788994000101


No 394
>PRK06463 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=38.99  E-value=23  Score=14.32  Aligned_cols=14  Identities=21%  Similarity=0.280  Sum_probs=8.2

Q ss_pred             CCCCCCCEEEEECC
Q ss_conf             88216866999725
Q gi|254781172|r  644 SSEIENKKLVFTGT  657 (731)
Q Consensus       644 ~~~l~gk~vV~TGt  657 (731)
                      .+..+|.++++-|-
T Consensus       232 a~~iTG~~i~VDGG  245 (254)
T PRK06463        232 ARYITGQVIVADGG  245 (254)
T ss_pred             HCCCCCCEEEECCC
T ss_conf             24915865996399


No 395
>PRK07791 short chain dehydrogenase; Provisional
Probab=38.74  E-value=23  Score=14.29  Aligned_cols=14  Identities=21%  Similarity=0.363  Sum_probs=9.0

Q ss_pred             CCCCCCCEEEEECC
Q ss_conf             88216866999725
Q gi|254781172|r  644 SSEIENKKLVFTGT  657 (731)
Q Consensus       644 ~~~l~gk~vV~TGt  657 (731)
                      ++..+|.++.+.|-
T Consensus       242 asyITGq~l~VDGG  255 (285)
T PRK07791        242 SRDVTGKVFEVEGG  255 (285)
T ss_pred             CCCCCCCEEEECCC
T ss_conf             07877875997799


No 396
>PRK07109 short chain dehydrogenase; Provisional
Probab=38.68  E-value=23  Score=14.28  Aligned_cols=12  Identities=8%  Similarity=0.130  Sum_probs=4.5

Q ss_pred             ECCCCHHHHHHH
Q ss_conf             659865566699
Q gi|254781172|r  153 LRGDGHSGEDVS  164 (731)
Q Consensus       153 TRGdG~~GeDVT  164 (731)
                      |=+.+-+|..+.
T Consensus        14 TGASsGIGra~A   25 (338)
T PRK07109         14 TGASAGVGRATA   25 (338)
T ss_pred             ECCCCHHHHHHH
T ss_conf             484349999999


No 397
>cd01701 Pol_zeta Pol_zeta, a member of the Y-family of DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. Pol zeta has also been named Rev1; this subfamily is mainly present in eukaryotes.
Probab=38.66  E-value=18  Score=15.06  Aligned_cols=16  Identities=13%  Similarity=0.289  Sum_probs=7.2

Q ss_pred             CHHHHHHHHHHHHHCC
Q ss_conf             0354103555565305
Q gi|254781172|r  482 NIEGLGKQQLDFFFKS  497 (731)
Q Consensus       482 dI~GLG~k~Ie~L~e~  497 (731)
                      +|-|+|+++.++|-+.
T Consensus       228 ~i~GIG~~t~~kL~~~  243 (405)
T cd01701         228 DLPGVGSSTKEKLKSL  243 (405)
T ss_pred             CCCCCCHHHHHHHHHC
T ss_conf             1587178999999984


No 398
>PRK02406 DNA polymerase IV; Validated
Probab=38.60  E-value=18  Score=15.15  Aligned_cols=27  Identities=30%  Similarity=0.365  Sum_probs=12.2

Q ss_pred             CHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCH
Q ss_conf             03541035555653057654045410110106
Q gi|254781172|r  482 NIEGLGKQQLDFFFKSEDPAFSIRIPADIFTL  513 (731)
Q Consensus       482 dI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L  513 (731)
                      ++-|+|+++.++|-+.|     |.++.||..+
T Consensus       184 ~l~GIG~~~~~~L~~~G-----I~ti~DL~~~  210 (355)
T PRK02406        184 KIPGVGKVTAEKLHALG-----IRTCADLQKW  210 (355)
T ss_pred             CCCCCCHHHHHHHHHCC-----CCCHHHHHHC
T ss_conf             05885889999999829-----8179997609


No 399
>PRK05270 galactose-1-phosphate uridylyltransferase; Provisional
Probab=38.41  E-value=23  Score=14.25  Aligned_cols=12  Identities=17%  Similarity=0.180  Sum_probs=7.7

Q ss_pred             HHCCCCCCCCEE
Q ss_conf             975996654148
Q gi|254781172|r  262 RCLGFPVNNGVR  273 (731)
Q Consensus       262 ~~~GF~v~~~~~  273 (731)
                      ..|||.-.||..
T Consensus       205 e~W~fQYSPYaY  216 (496)
T PRK05270        205 ESWGFQYSPYAY  216 (496)
T ss_pred             CEEEEEECCCCE
T ss_conf             701467454105


No 400
>PRK08936 glucose-1-dehydrogenase; Provisional
Probab=38.29  E-value=23  Score=14.24  Aligned_cols=15  Identities=20%  Similarity=0.246  Sum_probs=8.3

Q ss_pred             CCCCCCEEEEECCCC
Q ss_conf             821686699972588
Q gi|254781172|r  645 SEIENKKLVFTGTLQ  659 (731)
Q Consensus       645 ~~l~gk~vV~TGtl~  659 (731)
                      +..+|.++.+.|-+.
T Consensus       237 syiTG~~i~VDGG~t  251 (261)
T PRK08936        237 SYVTGITLFADGGMT  251 (261)
T ss_pred             CCCCCCEEEECCCCC
T ss_conf             683387388795810


No 401
>cd02173 ECT CTP:phosphoethanolamine cytidylyltransferase (ECT) catalyzes the conversion of phosphoethanolamine to CDP-ethanolamine as part of the CDP#ethanolamine biosynthesis pathway.  ECT expression in hepatocytes is localized predominantly to areas of the cytoplasm that are rich in rough endoplasmic reticulum. Several ECT's, including yeast and human ECT, have large repetitive sequences located within their N- and C-termini.
Probab=38.24  E-value=23  Score=14.23  Aligned_cols=29  Identities=21%  Similarity=0.194  Sum_probs=18.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             00013421001456899998752234666
Q gi|254781172|r  524 IENILGFGDVSVTNLYDSINKRRNISLER  552 (731)
Q Consensus       524 l~~l~GfgeKsa~nL~~sIe~sK~~~L~r  552 (731)
                      +..++...--|.+.|++-|-+++..-..|
T Consensus       119 ~~~~~~~~giSTt~II~RIl~~r~~y~~R  147 (152)
T cd02173         119 FKEIDSGSDLTTRDIVQRIIKNRLAYEAR  147 (152)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             99958999967999999999829999998


No 402
>PRK06603 enoyl-(acyl carrier protein) reductase; Provisional
Probab=38.24  E-value=23  Score=14.23  Aligned_cols=15  Identities=7%  Similarity=-0.042  Sum_probs=7.6

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++++-|-+
T Consensus       238 s~~iTG~~i~vDGG~  252 (260)
T PRK06603        238 SKGVTGEIHYVDCGY  252 (260)
T ss_pred             HCCCCCCEEEECCCC
T ss_conf             237258717889798


No 403
>PRK07825 short chain dehydrogenase; Provisional
Probab=38.06  E-value=23  Score=14.21  Aligned_cols=15  Identities=13%  Similarity=0.186  Sum_probs=9.1

Q ss_pred             CCHHHHHHHHHHHHH
Q ss_conf             001456899998752
Q gi|254781172|r  532 DVSVTNLYDSINKRR  546 (731)
Q Consensus       532 eKsa~nL~~sIe~sK  546 (731)
                      |.-|+.++++|++.+
T Consensus       203 e~vA~~iv~~i~~~~  217 (273)
T PRK07825        203 EDVAAAIVALVAKPR  217 (273)
T ss_pred             HHHHHHHHHHHHCCC
T ss_conf             999999999996899


No 404
>TIGR02869 spore_SleB spore cortex-lytic enzyme; InterPro: IPR014224   The entry represents the spore cortex-lytic enzyme SleB from Bacillus subtilis and other Gram-positive, endospore-forming bacterial species. SleB is stored in an inactive form in the spore and activated during germination..
Probab=37.95  E-value=17  Score=15.24  Aligned_cols=31  Identities=16%  Similarity=0.508  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHCCCCCHHHH-HHHHHHHHHCC
Q ss_conf             46655332130123103541-03555565305
Q gi|254781172|r  467 QQLERLKHFVSRDAFNIEGL-GKQQLDFFFKS  497 (731)
Q Consensus       467 q~~~~i~hF~SK~aldI~GL-G~k~Ie~L~e~  497 (731)
                      +....+..|=+|.+|.+||| |++|..+|+++
T Consensus        40 ~Ty~AVr~FQ~knGL~VDGivG~~T~~aLv~A   71 (232)
T TIGR02869        40 KTYKAVRKFQSKNGLTVDGIVGPKTKAALVKA   71 (232)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHH
T ss_conf             69999999888708855642075789999876


No 405
>PRK08562 rpl32e 50S ribosomal protein L32e; Validated
Probab=37.88  E-value=5.5  Score=19.04  Aligned_cols=26  Identities=8%  Similarity=-0.007  Sum_probs=13.3

Q ss_pred             HHHHHHHHCCCCCCEEEEEHHHHCCH
Q ss_conf             35555653057654045410110106
Q gi|254781172|r  488 KQQLDFFFKSEDPAFSIRIPADIFTL  513 (731)
Q Consensus       488 ~k~Ie~L~e~~~~~g~I~~~~DLy~L  513 (731)
                      ++.+.-|.-.|+...+|.++.||-.|
T Consensus        67 ~k~~Rgl~PsG~~~vlV~n~~dLe~L   92 (127)
T PRK08562         67 PKAVRGLHPSGYEEVLVHNVKELEAL   92 (127)
T ss_pred             CHHHCCCCCCCCEEEEECCHHHHHHH
T ss_conf             58766869776878886788998854


No 406
>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=37.65  E-value=16  Score=15.58  Aligned_cols=37  Identities=16%  Similarity=0.284  Sum_probs=19.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHH
Q ss_conf             265775010337865445210100354344114466553
Q gi|254781172|r  434 CPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERL  472 (731)
Q Consensus       434 CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i  472 (731)
                      |-.||.++.-+.-......-+-..|++  +|..++.+++
T Consensus         1 CDYCG~eI~g~Pi~~k~~nrvYy~CC~--tC~~~lkk~l   37 (37)
T pfam08394         1 CDYCGKEIKGEPITYKVKNRVYYVCCP--TCLSDLKKKL   37 (37)
T ss_pred             CCCCCCCCCCCCEEEEECCEEEEEECH--HHHHHHHHHC
T ss_conf             985677505995799975779999876--8889988519


No 407
>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=36.90  E-value=16  Score=15.52  Aligned_cols=27  Identities=22%  Similarity=0.545  Sum_probs=16.0

Q ss_pred             CCCC-CCCCCCCCCCCC---CCCCCCEEECCCC
Q ss_conf             4326-577501033786---5445210100354
Q gi|254781172|r  432 SFCP-ICQSRVVRDLNP---KTGKLVAAHRCTG  460 (731)
Q Consensus       432 ~~CP-~Cgs~l~~~~~~---~~~~~~~~~rC~n  460 (731)
                      +.|| .||+++++..-.   ++++  ..+||++
T Consensus       260 ~pC~a~CGt~I~k~~~~LYGkDgR--gthfCp~  290 (292)
T TIGR00577       260 EPCRARCGTTIEKEKVGLYGKDGR--GTHFCPQ  290 (292)
T ss_pred             CCCCCCCCCEEEEEEEECCCCCCC--CEECCCC
T ss_conf             834367884478876530151675--1012688


No 408
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=36.82  E-value=12  Score=16.31  Aligned_cols=12  Identities=42%  Similarity=1.088  Sum_probs=8.8

Q ss_pred             CCCCCCCCCCCC
Q ss_conf             043265775010
Q gi|254781172|r  431 PSFCPICQSRVV  442 (731)
Q Consensus       431 P~~CP~Cgs~l~  442 (731)
                      -.+||+|||.-+
T Consensus       185 ~~~CPvCGS~Pv  196 (308)
T COG3058         185 RQYCPVCGSMPV  196 (308)
T ss_pred             CCCCCCCCCCCC
T ss_conf             410777688774


No 409
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=36.75  E-value=13  Score=16.06  Aligned_cols=24  Identities=13%  Similarity=0.195  Sum_probs=13.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf             3265775010337865445210100354
Q gi|254781172|r  433 FCPICQSRVVRDLNPKTGKLVAAHRCTG  460 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n  460 (731)
                      -||.||+.+++..-..    -...+|++
T Consensus       247 pC~~CGt~I~k~~~~g----R~t~~CP~  270 (273)
T COG0266         247 PCRRCGTPIEKIKLGG----RSTFYCPV  270 (273)
T ss_pred             CCCCCCCEEEEEEECC----CCCEECCC
T ss_conf             8874588767999868----76776878


No 410
>PRK11827 hypothetical protein; Provisional
Probab=36.64  E-value=17  Score=15.35  Aligned_cols=15  Identities=20%  Similarity=0.744  Sum_probs=12.0

Q ss_pred             CCCCCCCCCCCCCCC
Q ss_conf             326577501033786
Q gi|254781172|r  433 FCPICQSRVVRDLNP  447 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~  447 (731)
                      .||.|.++|.++...
T Consensus        10 vCP~ckg~L~yd~~~   24 (60)
T PRK11827         10 ACPVCNGKLWYNQEK   24 (60)
T ss_pred             ECCCCCCCCEECCCC
T ss_conf             577889903398768


No 411
>pfam01655 Ribosomal_L32e Ribosomal protein L32. This family includes ribosomal protein L32 from eukaryotes and archaebacteria.
Probab=36.62  E-value=5.3  Score=19.20  Aligned_cols=27  Identities=11%  Similarity=-0.001  Sum_probs=16.0

Q ss_pred             HHHHHHHHHCCCCCCEEEEEHHHHCCH
Q ss_conf             035555653057654045410110106
Q gi|254781172|r  487 GKQQLDFFFKSEDPAFSIRIPADIFTL  513 (731)
Q Consensus       487 G~k~Ie~L~e~~~~~g~I~~~~DLy~L  513 (731)
                      +++.+.-|.-.|+...+|.++.||-.|
T Consensus        47 s~k~~Rgl~PsG~~~vlV~n~~dLe~l   73 (110)
T pfam01655        47 SPKKVRGLHPSGFKEVLVHNVKDLELL   73 (110)
T ss_pred             CCHHHCCCCCCCCEEEEECCHHHHHHH
T ss_conf             766664779888878886798998998


No 412
>PRK03754 DNA-directed RNA polymerase subunit P; Provisional
Probab=36.50  E-value=13  Score=16.09  Aligned_cols=13  Identities=31%  Similarity=0.817  Sum_probs=8.9

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             3265775010337
Q gi|254781172|r  433 FCPICQSRVVRDL  445 (731)
Q Consensus       433 ~CP~Cgs~l~~~~  445 (731)
                      .||.||+++....
T Consensus        26 rcpycgskilykp   38 (49)
T PRK03754         26 RCPYCGSKILYKP   38 (49)
T ss_pred             CCCCCCCEEEECC
T ss_conf             3777677545458


No 413
>PRK07060 short chain dehydrogenase; Provisional
Probab=36.45  E-value=25  Score=14.03  Aligned_cols=15  Identities=20%  Similarity=0.251  Sum_probs=11.2

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++++-|-+
T Consensus       228 ss~iTG~~i~VDGG~  242 (245)
T PRK07060        228 ASMVSGVSLPVDGGY  242 (245)
T ss_pred             HCCCCCCEEEECCCH
T ss_conf             258148428869563


No 414
>PRK07792 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=36.36  E-value=25  Score=14.02  Aligned_cols=14  Identities=7%  Similarity=0.363  Sum_probs=7.3

Q ss_pred             CCCCCCCEEEEECC
Q ss_conf             88216866999725
Q gi|254781172|r  644 SSEIENKKLVFTGT  657 (731)
Q Consensus       644 ~~~l~gk~vV~TGt  657 (731)
                      .+..+|++|++-|-
T Consensus       237 as~ITGq~l~VdGG  250 (303)
T PRK07792        237 AAGVNGQLFIVYGP  250 (303)
T ss_pred             CCCCCCCEEEECCC
T ss_conf             06987987998699


No 415
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain; InterPro: IPR011723   Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, however they are now recognised to bind DNA, RNA, protein and/or lipid substrates , , , , . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.    (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries).   This entry represents a region, which contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterised gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility .   More information about these proteins can be found at Protein of the Month: Zinc Fingers ..
Probab=36.30  E-value=19  Score=14.92  Aligned_cols=30  Identities=20%  Similarity=0.279  Sum_probs=19.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC-EEECCCC
Q ss_conf             04326577501033786544521-0100354
Q gi|254781172|r  431 PSFCPICQSRVVRDLNPKTGKLV-AAHRCTG  460 (731)
Q Consensus       431 P~~CP~Cgs~l~~~~~~~~~~~~-~~~rC~n  460 (731)
                      -..||.|.+......+....... +..||.+
T Consensus         2 ~~~CP~C~t~y~V~~~~~G~~g~kv~VrC~~   32 (40)
T TIGR02098         2 RIQCPNCKTSYRVDDSQLGANGRKVKVRCGK   32 (40)
T ss_pred             EEECCCCCCEEEEECCCCCCCCCEEEEEECC
T ss_conf             6568998506888433478789878888189


No 416
>pfam08645 PNK3P Polynucleotide kinase 3 phosphatase. Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin.
Probab=36.23  E-value=25  Score=14.01  Aligned_cols=46  Identities=24%  Similarity=0.390  Sum_probs=29.5

Q ss_pred             HHHHHHHCCCEEEEEEECCEEEEEECCCCC----------CHHHHHHHCCCEEECHHHH
Q ss_conf             999999829849981116321799778888----------6379899749917379999
Q gi|254781172|r  666 AQEYVTQLGAVVSAILSRKTDIIIVGDNPG----------SKLEKAQQLGVKIMNEEQF  714 (731)
Q Consensus       666 ~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~g----------SKl~KA~~LgI~Ii~e~ef  714 (731)
                      +..+++..-+  ..+|..+-+| .+||.||          |=++=|.-+||+..++|||
T Consensus       102 ~~~~~~~~~~--~~~iD~~~Sf-~vGDaagr~~~~~D~s~sD~~FA~N~gikF~tpee~  157 (158)
T pfam08645       102 WDELLEDYND--GITIDLEKSF-YVGDAAGRPARKKDFSDSDRKFALNVGIKFKTPEEF  157 (158)
T ss_pred             HHHHHHHCCC--CCCCCCCCEE-EEECCCCCCCCCCCCCHHHHHHHHHCCCEECCCHHC
T ss_conf             9999997256--7544653018-984366887777775403799999859816580202


No 417
>PRK03352 DNA polymerase IV; Validated
Probab=36.16  E-value=21  Score=14.64  Aligned_cols=27  Identities=19%  Similarity=0.185  Sum_probs=13.3

Q ss_pred             CHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCH
Q ss_conf             03541035555653057654045410110106
Q gi|254781172|r  482 NIEGLGKQQLDFFFKSEDPAFSIRIPADIFTL  513 (731)
Q Consensus       482 dI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L  513 (731)
                      +|-|+|+++-++|-..|     |.++.||...
T Consensus       181 ~i~GIG~~~~~kL~~~G-----I~Ti~DL~~~  207 (345)
T PRK03352        181 ALWGVGPKTAKKLAALG-----ITTVADLAAT  207 (345)
T ss_pred             HCCCCCHHHHHHHHHCC-----CCCHHHHHCC
T ss_conf             12782899999999759-----9719998669


No 418
>cd01703 Pol_iota Pol iota is member of the DNA polymerase Y-family, and has also been called Rad30 homolog B. Unlike classic DNA polymerases,Y-family polymerases are induced by DNA damage. They can transverse normal replication-blocking DNA lesions. Unlike Pol eta, Pol iota is unable to replicate through a cis-syn T-T dimer. In human Pol iota, the base-pairing mode in the active site at the replicative end mat bee Hoogsteen instead of Watson-Click. Human Pol iota can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine. Pol iota prefers to insert Guanosine instead of Adenosine opposite Thymidine.
Probab=36.14  E-value=21  Score=14.60  Aligned_cols=49  Identities=18%  Similarity=0.242  Sum_probs=32.4

Q ss_pred             CHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             0354103555565305765404541011010677753100010001342100145689999
Q gi|254781172|r  482 NIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSI  542 (731)
Q Consensus       482 dI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sI  542 (731)
                      +|-|+|.++.++|-+.|     |.++.||.......     .|.  ..||+..+..|++-.
T Consensus       214 ki~GIG~kt~~~L~~~g-----i~ti~dl~~~~~~~-----~l~--~~fG~~~g~~l~~~a  262 (394)
T cd01703         214 KIPGIGYKTAKKLEDHG-----ISSVRDLQECSELL-----LLE--KGFGKGIAQRIWGLA  262 (394)
T ss_pred             HHCCCCHHHHHHHHHCC-----CEEHHHHHCCCHHH-----HHH--HHHHHHHHHHHHHHH
T ss_conf             52781799999999838-----92679876588799-----999--987889999999995


No 419
>PRK02794 DNA polymerase IV; Provisional
Probab=35.84  E-value=22  Score=14.47  Aligned_cols=31  Identities=19%  Similarity=0.111  Sum_probs=20.1

Q ss_pred             CCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHH
Q ss_conf             103541035555653057654045410110106777
Q gi|254781172|r  481 FNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRR  516 (731)
Q Consensus       481 ldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~  516 (731)
                      =+|-|+|+++-++|-..|     |.++.||..++..
T Consensus       212 ~diwGIG~rt~~kL~~~G-----I~Ti~DL~~~~~~  242 (417)
T PRK02794        212 GFIWGVGPATAARLAADG-----IRTIGDLQRADEA  242 (417)
T ss_pred             HHHCCCCHHHHHHHHHCC-----CCCHHHHHCCCHH
T ss_conf             551684689999999849-----9099998659998


No 420
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=35.77  E-value=14  Score=15.83  Aligned_cols=11  Identities=36%  Similarity=0.809  Sum_probs=9.1

Q ss_pred             CCCCCCCCCCC
Q ss_conf             32657750103
Q gi|254781172|r  433 FCPICQSRVVR  443 (731)
Q Consensus       433 ~CP~Cgs~l~~  443 (731)
                      +||.||.+.+.
T Consensus        24 tCp~Cghe~vs   34 (104)
T COG4888          24 TCPRCGHEKVS   34 (104)
T ss_pred             ECCCCCCEEEE
T ss_conf             16855872355


No 421
>pfam06750 DiS_P_DiS Bacterial Peptidase A24 N-terminal domain. This family is found at the N-terminus of the pre-pilin peptidases (pfam01478). It's function has not been specifically determined; however some of the family have been characterized as bifunctional. and this domain may contain the N-methylation activity (EC:2.1.1.-). It consists of an intracellular region between a pair of transmembrane. This region contains an invariant proline and two almost fully conserved disulphide bridges - hence the name DiS-P-DiS. The cysteines have been shown to be essential to the overall function of the enzyme in, but their role was incorrectly ascribed.
Probab=35.75  E-value=13  Score=16.08  Aligned_cols=19  Identities=26%  Similarity=0.349  Sum_probs=13.9

Q ss_pred             EEECCCCCCCCCCCCCCCC
Q ss_conf             7770432657750103378
Q gi|254781172|r  428 FSFPSFCPICQSRVVRDLN  446 (731)
Q Consensus       428 ~~~P~~CP~Cgs~l~~~~~  446 (731)
                      +..+++||.|+..+.+...
T Consensus        24 ~~prS~C~~C~~~L~~~~l   42 (86)
T pfam06750        24 VFPRSHCPHCGHKLRWYDN   42 (86)
T ss_pred             CCCCCCCCCCCCCCHHHHH
T ss_conf             8999809356996754783


No 422
>KOG1247 consensus
Probab=35.74  E-value=9.5  Score=17.22  Aligned_cols=49  Identities=22%  Similarity=0.265  Sum_probs=27.5

Q ss_pred             EEEEEECHHHHH-HHHHHHHCC--CCCCCCHHHHHHHHHHC-CCHHHHHCCCE
Q ss_conf             999985202123-455643148--54334234567777523-45555301110
Q gi|254781172|r  189 GEVYISKNDFLA-LNDEMIAVG--RKPYANPRNAASGILRR-LNPTDITRYLN  237 (731)
Q Consensus       189 GEv~m~~~~F~~-lN~~~~~~g--~~~f~NpRN~aaG~lr~-~d~~~~~r~L~  237 (731)
                      --+|++...|+. +-+-....+  ..==.|++|..--.||. +.|.-..|+|.
T Consensus       198 ~h~Fl~L~kl~~~lee~~~~~~~~~~WS~Na~~it~sWlk~gl~pRCiTRDLk  250 (567)
T KOG1247         198 QHLFLSLDKLEPRLEEWLRRTLVEGDWSQNAQNITRSWLKDGLKPRCITRDLK  250 (567)
T ss_pred             EEEEEEHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             27998757767899999973054577761167899999974666520002255


No 423
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=35.62  E-value=17  Score=15.29  Aligned_cols=13  Identities=23%  Similarity=0.590  Sum_probs=7.3

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             4326577501033
Q gi|254781172|r  432 SFCPICQSRVVRD  444 (731)
Q Consensus       432 ~~CP~Cgs~l~~~  444 (731)
                      .+||.||+++...
T Consensus       101 rfC~~CG~~t~~~  113 (257)
T PRK00241        101 RFCGYCGHPTHPS  113 (257)
T ss_pred             CCCCCCCCCCCCC
T ss_conf             8456567366338


No 424
>PRK13638 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=35.58  E-value=23  Score=14.27  Aligned_cols=31  Identities=29%  Similarity=0.491  Sum_probs=22.4

Q ss_pred             CCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHH
Q ss_conf             64000101489899975023454322246844076899983587025
Q gi|254781172|r  365 GALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIP  411 (731)
Q Consensus       365 G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP  411 (731)
                      |.||=- +-|+.+++.++               -|+|.|.+.|.||=
T Consensus       186 G~tiii-vsHdl~~v~~~---------------aDrv~vl~~G~iva  216 (271)
T PRK13638        186 GNHVII-SSHDIDLIYEI---------------SDAVYVLRQGQILT  216 (271)
T ss_pred             CCEEEE-ECCCHHHHHHH---------------CCEEEEEECCEEEE
T ss_conf             999999-84888999996---------------99999998998999


No 425
>LOAD_Hrd consensus
Probab=35.37  E-value=26  Score=13.91  Aligned_cols=26  Identities=12%  Similarity=0.026  Sum_probs=19.8

Q ss_pred             CCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             51177876138886789999999996
Q gi|254781172|r  591 NNDDWLSLIRVPLVGDIIAQAIVEFY  616 (731)
Q Consensus       591 ~~~~~e~L~~I~GiG~~~A~si~~ff  616 (731)
                      .-.+.++|..|+|||+...+.+-+.|
T Consensus        42 ~P~t~~eL~~I~Gig~~k~~~yG~~i   67 (77)
T LOAD_Hrd         42 LPTTVSELLAIDGVGEAKVEKYGDRI   67 (77)
T ss_pred             CCCCHHHHCCCCCCCHHHHHHHHHHH
T ss_conf             89999998289996999999999999


No 426
>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=35.33  E-value=24  Score=14.17  Aligned_cols=68  Identities=24%  Similarity=0.324  Sum_probs=37.0

Q ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHHHH----------HHHCCCCCHHHHHCCCCCCHH------HHHHHHHHHCCHH
Q ss_conf             010111168999999882998999997897----------761251177876138886789------9999999966979
Q gi|254781172|r  557 LGIRHVGAEIARSLAKYYLSYQNFAQEINN----------IIAHNNDDWLSLIRVPLVGDI------IAQAIVEFYQNPR  620 (731)
Q Consensus       557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~~----------~~~~~~~~~e~L~~I~GiG~~------~A~si~~ff~~~~  620 (731)
                      -||||||.--||  +..|..+.+..+.-++          ..++  ...+++.++||+.-+      .|.|+ -|.-+|.
T Consensus       111 ~GiRGVGSALAR--ASrwNrIp~Ylq~AdeeiClLlQVEtr~al--~NL~~Ia~VeGVDGVFiGPADLaasm-GH~GnPs  185 (249)
T TIGR02311       111 KGIRGVGSALAR--ASRWNRIPDYLQQADEEICLLLQVETREAL--ENLEEIAAVEGVDGVFIGPADLAASM-GHLGNPS  185 (249)
T ss_pred             CCCCCCHHHHHH--HHHCCCHHHHHCCHHHHEEHHHHHHHHHHH--HHHHHHHCCCCCCCEEECCHHHHHHC-CCCCCCC
T ss_conf             951340078776--322176125760521320232326579988--62157750178662475712443401-5688869


Q ss_pred             HHHHHHHHH
Q ss_conf             999999999
Q gi|254781172|r  621 NICAVEALL  629 (731)
Q Consensus       621 n~~~i~~L~  629 (731)
                      +-+..+...
T Consensus       186 HPEV~~AI~  194 (249)
T TIGR02311       186 HPEVQDAID  194 (249)
T ss_pred             CHHHHHHHH
T ss_conf             615899999


No 427
>PRK12367 short chain dehydrogenase; Provisional
Probab=35.30  E-value=26  Score=13.90  Aligned_cols=23  Identities=22%  Similarity=0.341  Sum_probs=14.8

Q ss_pred             CCEEEEEEECCCCHHHHHHHHHHH
Q ss_conf             998998886598655666999775
Q gi|254781172|r  145 KGKFVYAALRGDGHSGEDVSACIR  168 (731)
Q Consensus       145 ~G~L~~a~TRGdG~~GeDVT~n~~  168 (731)
                      +|+= -|+|-..|..|.-.|...+
T Consensus        16 kgKt-IgITGAsGaLG~AL~k~f~   38 (250)
T PRK12367         16 NGKR-IGITGASGALGKALTKLFR   38 (250)
T ss_pred             CCCE-EEEECCCCHHHHHHHHHHH
T ss_conf             8987-9996787389999999999


No 428
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'; InterPro: IPR012758   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.    This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0008270 zinc ion binding, 0006350 transcription.
Probab=35.25  E-value=14  Score=15.89  Aligned_cols=63  Identities=14%  Similarity=0.071  Sum_probs=32.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCHHHC---------CCHHHHHH
Q ss_conf             798208789999999999998977203115899996200364323577504516642570215---------99999999
Q gi|254781172|r   39 SKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKI---------WNIEDLRK  109 (731)
Q Consensus        39 ~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H~~pMlSL~k~---------~~~~el~~  109 (731)
                      ..|..+...-+.|..++.....+.-.        .|      -....-.||+...|.-=.++.         -+.+|+.+
T Consensus       124 ~~~a~~nfiq~~l~~~i~k~A~k~~~--------CP------hCg~~q~~ik~eKP~~f~e~~~~G~eeW~KLTP~eiRE  189 (901)
T TIGR02390       124 GSLALSNFIQETLIEKIVKEAAKRMK--------CP------HCGEEQKKIKFEKPTYFYEEDKEGKEEWVKLTPSEIRE  189 (901)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCC--------CC------CCCCCCCCEEEECCEEEEECCCCCCCCCEECCCHHHHH
T ss_conf             87467888888889999999861787--------98------88741243245277157755755551214428179999


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254781172|r  110 FITRIY  115 (731)
Q Consensus       110 w~~~~~  115 (731)
                      |.+||-
T Consensus       190 rLEkiP  195 (901)
T TIGR02390       190 RLEKIP  195 (901)
T ss_pred             HHHCCC
T ss_conf             751687


No 429
>KOG4169 consensus
Probab=35.20  E-value=26  Score=13.89  Aligned_cols=17  Identities=24%  Similarity=0.294  Sum_probs=11.5

Q ss_pred             EEECCCCHHHHHHHHHH
Q ss_conf             88659865566699977
Q gi|254781172|r  151 AALRGDGHSGEDVSACI  167 (731)
Q Consensus       151 a~TRGdG~~GeDVT~n~  167 (731)
                      .+|-|-|-+|-+.+..+
T Consensus         9 ~vtggagGIGl~~sk~L   25 (261)
T KOG4169           9 LVTGGAGGIGLATSKAL   25 (261)
T ss_pred             EEECCCCHHHHHHHHHH
T ss_conf             99637863669999999


No 430
>PRK03918 chromosome segregation protein; Provisional
Probab=35.14  E-value=14  Score=15.93  Aligned_cols=12  Identities=25%  Similarity=0.894  Sum_probs=9.0

Q ss_pred             CCCCCCCCCCCC
Q ss_conf             432657750103
Q gi|254781172|r  432 SFCPICQSRVVR  443 (731)
Q Consensus       432 ~~CP~Cgs~l~~  443 (731)
                      ..||+||+++..
T Consensus       439 ~~CPvcg~~~~~  450 (882)
T PRK03918        439 GKCPVCGRELTE  450 (882)
T ss_pred             CCCCCCCCCCCC
T ss_conf             999989995761


No 431
>cd01403 Cyt_c_Oxidase_VIIb Cytochrome C oxidase chain VIIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane.  The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. The VIIb subunit is found only in eukaryotes and its specific function remains unclear. A rare polymorphism of the CcO VIIb gene may be associated with the high risk of nasopharyngeal carcinoma in a Cantonese family.
Probab=35.09  E-value=22  Score=14.48  Aligned_cols=21  Identities=19%  Similarity=0.248  Sum_probs=17.0

Q ss_pred             EEEEEEEEEEEECCCCEEEEE
Q ss_conf             589987889940356225899
Q gi|254781172|r  335 ASTRLLDIDIQIGRTGILTPV  355 (731)
Q Consensus       335 ~~T~v~~I~wqvgRtG~itPv  355 (731)
                      ...+-.+|+|+.|--|++||-
T Consensus        27 yv~TQ~gI~WnlSPVGrVtPk   47 (51)
T cd01403          27 YVMTQTGIEWNLSPVGRVTPK   47 (51)
T ss_pred             HEEEEEEEEECCCCCCCCCCC
T ss_conf             203531123636654433640


No 432
>PTZ00180 60S ribosomal protein L2; Provisional
Probab=35.07  E-value=26  Score=13.88  Aligned_cols=87  Identities=17%  Similarity=0.188  Sum_probs=46.9

Q ss_pred             ECCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf             11456215899878899403562258999974333026400010148989997502345432224684407689998358
Q gi|254781172|r  328 HKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAG  407 (731)
Q Consensus       328 ~Kf~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaG  407 (731)
                      ||-...-...+|.+|+...+||..|   |.++          +....++++++..-+.      -.+|.+||.|..   |
T Consensus        34 f~r~~~~i~g~V~~IeyDPnRsA~I---Alv~----------y~dG~~~~~~k~yIlA------peGl~vGd~I~s---G   91 (260)
T PTZ00180         34 YAERHGYMRGVVKSIEHEAGRGAAL---ARVE----------FRHPYKFRRVKELMVA------PEGMFTGQSVFC---G   91 (260)
T ss_pred             CCCCCCCCCEEEEEEEECCCCCCEE---EEEE----------ECCCCCCCCCEEEEEE------ECCCCCCCEEEE---C
T ss_conf             4333699778999989898998608---8999----------4377755662689980------389889998986---9


Q ss_pred             CCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf             702566541012357873047770432657750103
Q gi|254781172|r  408 EVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVR  443 (731)
Q Consensus       408 dVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~  443 (731)
                      +-.|--.+.....       -.+|.=+..||=|+..
T Consensus        92 ~~a~i~~GN~lpL-------~~IP~Gt~IhNIE~~P  120 (260)
T PTZ00180         92 QKAPLAIGNVLPL-------GQITEGCIVCNVEAKP  120 (260)
T ss_pred             CCCCCCCCCCCCH-------HHCCCCCEEEEEEECC
T ss_conf             8667777563546-------3389987788673038


No 433
>PRK12829 short chain dehydrogenase; Provisional
Probab=35.07  E-value=26  Score=13.88  Aligned_cols=16  Identities=13%  Similarity=0.337  Sum_probs=11.6

Q ss_pred             CCCCCCCEEEEECCCC
Q ss_conf             8821686699972588
Q gi|254781172|r  644 SSEIENKKLVFTGTLQ  659 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~  659 (731)
                      ++..+|.++.+.|-++
T Consensus       247 ss~iTG~~i~VDGGl~  262 (264)
T PRK12829        247 ARYITGQAISVDGNVE  262 (264)
T ss_pred             HCCCCCCEEEECCCCC
T ss_conf             4580587779787802


No 434
>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=34.98  E-value=14  Score=15.97  Aligned_cols=10  Identities=30%  Similarity=0.989  Sum_probs=7.6

Q ss_pred             CCCCCCCCCC
Q ss_conf             3265775010
Q gi|254781172|r  433 FCPICQSRVV  442 (731)
Q Consensus       433 ~CP~Cgs~l~  442 (731)
                      .||+||.++.
T Consensus        22 ~CPvC~r~l~   31 (54)
T pfam04423        22 CCPVCGRPLD   31 (54)
T ss_pred             CCCCCCCCCC
T ss_conf             7776699766


No 435
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=34.98  E-value=26  Score=13.87  Aligned_cols=16  Identities=38%  Similarity=0.802  Sum_probs=9.3

Q ss_pred             HHCCCHHHHHHHHHHH
Q ss_conf             2159999999999999
Q gi|254781172|r   99 EKIWNIEDLRKFITRI  114 (731)
Q Consensus        99 ~k~~~~~el~~w~~~~  114 (731)
                      ++.|+..||....++.
T Consensus         3 ~~~~sVSeln~~ik~l   18 (440)
T COG1570           3 EKILSVSELNDYIKRL   18 (440)
T ss_pred             CCEECHHHHHHHHHHH
T ss_conf             8705199999999999


No 436
>PRK08416 7-alpha-hydroxysteroid dehydrogenase; Provisional
Probab=34.97  E-value=26  Score=13.86  Aligned_cols=13  Identities=15%  Similarity=0.363  Sum_probs=7.0

Q ss_pred             CCCCCCEEEEECC
Q ss_conf             8216866999725
Q gi|254781172|r  645 SEIENKKLVFTGT  657 (731)
Q Consensus       645 ~~l~gk~vV~TGt  657 (731)
                      +..+|.++++-|-
T Consensus       244 s~iTG~~i~VDGG  256 (260)
T PRK08416        244 SWLTGQTIIVDGG  256 (260)
T ss_pred             CCCCCCEEEECCC
T ss_conf             6865983898977


No 437
>PRK09242 tropinone reductase; Provisional
Probab=34.53  E-value=26  Score=13.81  Aligned_cols=15  Identities=20%  Similarity=0.308  Sum_probs=8.4

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++.+-|-+
T Consensus       239 s~~iTGq~i~VDGG~  253 (258)
T PRK09242        239 ASYITGECIAVDGGF  253 (258)
T ss_pred             HCCCCCCEEEECCCH
T ss_conf             247548538989073


No 438
>PRK01122 potassium-transporting ATPase subunit B; Provisional
Probab=34.53  E-value=17  Score=15.33  Aligned_cols=56  Identities=18%  Similarity=0.327  Sum_probs=30.1

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCCEE---EEEEECCE-EEEEECCCCCCHHHHHHHCCCEE
Q ss_conf             686699972588998789999999829849---98111632-17997788886379899749917
Q gi|254781172|r  648 ENKKLVFTGTLQKIQRHKAQEYVTQLGAVV---SAILSRKT-DIIIVGDNPGSKLEKAQQLGVKI  708 (731)
Q Consensus       648 ~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv---~sSVSkkT-~~LI~ge~~gSKl~KA~~LgI~I  708 (731)
                      .|+.+.|||-    -=+|+-.+-.+.=|..   .+.|.|.. |.++..|+++ |+-.|-+-|=.|
T Consensus       511 ~G~vVAMtGD----GvNDAPALa~ADVGIAMgsGTdvAkEAADmVLLDdnf~-~iv~aV~~Gr~i  570 (684)
T PRK01122        511 EGRLVAMTGD----GTNDAPALAQADVGVAMNSGTQAAKEAGNMVDLDSNPT-KLIEVVEIGKQL  570 (684)
T ss_pred             CCCEEEEECC----CCCHHHHHHHCCEEEEECCCCHHHHHHHCEEEECCCHH-HHHHHHHHHHHH
T ss_conf             8597999628----82158888409977873775689998608999459848-899999999999


No 439
>PRK13811 orotate phosphoribosyltransferase; Provisional
Probab=34.51  E-value=26  Score=13.81  Aligned_cols=63  Identities=21%  Similarity=0.320  Sum_probs=40.3

Q ss_pred             CCCCCCEEEE------ECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHH
Q ss_conf             8216866999------7258899878999999982984998111632179977888863798997499173799999999
Q gi|254781172|r  645 SEIENKKLVF------TGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLL  718 (731)
Q Consensus       645 ~~l~gk~vV~------TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll  718 (731)
                      +.+.|++|++      ||    -|=.++.+.+++.|++|..-++      |+.-+.| .-+...+.||++.+--.+.++|
T Consensus       100 G~~~G~~VlvVEDViTTG----~S~~e~i~~l~~~G~~V~~v~~------ivDR~eg-~~e~l~~~Gv~~~sl~t~~dll  168 (170)
T PRK13811        100 GDVAGKRVLLVEDVTTSG----GSALYGIEQLRSAGAVVDDVVT------VVDREEG-AEELLAELDITLTPLVRVSELL  168 (170)
T ss_pred             CCCCCCEEEEEEEEECCC----CCHHHHHHHHHHCCCEEEEEEE------EEECCCC-HHHHHHHCCCEEEEEEEHHHHH
T ss_conf             234899899999644578----1189999999988997999999------9977747-7999996699099953289942


No 440
>PRK12826 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed
Probab=34.49  E-value=26  Score=13.81  Aligned_cols=13  Identities=23%  Similarity=0.279  Sum_probs=7.0

Q ss_pred             CCCCCCEEEEECC
Q ss_conf             8216866999725
Q gi|254781172|r  645 SEIENKKLVFTGT  657 (731)
Q Consensus       645 ~~l~gk~vV~TGt  657 (731)
                      +..+|..+.+.|-
T Consensus       236 ~~itG~~i~vDGG  248 (253)
T PRK12826        236 RYITGQTLPVDGG  248 (253)
T ss_pred             CCCCCCEEEECCC
T ss_conf             2956873887899


No 441
>pfam11376 DUF3179 Protein of unknown function (DUF3179). This family of proteins has no known function.
Probab=34.49  E-value=14  Score=15.96  Aligned_cols=11  Identities=18%  Similarity=0.649  Sum_probs=5.2

Q ss_pred             ECCEEEEEEEE
Q ss_conf             15818999998
Q gi|254781172|r  133 KIDGTMITIRY  143 (731)
Q Consensus       133 KiDG~sisl~Y  143 (731)
                      -++|..+.++|
T Consensus        54 ~igg~pv~vTy   64 (261)
T pfam11376        54 TLGGRPVAVTY   64 (261)
T ss_pred             EECCEEEEEEE
T ss_conf             57898789986


No 442
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase; InterPro: IPR012833    This entry is found in the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centred radical , a C-terminal zinc binding site , and a set of conserved active site cysteines and asparagines . This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (IPR012837 from INTERPRO). Together the two form an alpha-2/beta-2 heterodimer.; GO: 0008998 ribonucleoside-triphosphate reductase activity, 0016491 oxidoreductase activity.
Probab=34.46  E-value=15  Score=15.70  Aligned_cols=86  Identities=13%  Similarity=0.106  Sum_probs=41.1

Q ss_pred             CCCCHHHHHHHHHHHHHCC-CCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH-HHH-HHHHHHH
Q ss_conf             2310354103555565305-765404541011010677753100010001342100145689999875-223-4666776
Q gi|254781172|r  479 DAFNIEGLGKQQLDFFFKS-EDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKR-RNI-SLERFIF  555 (731)
Q Consensus       479 ~aldI~GLG~k~Ie~L~e~-~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~s-K~~-~L~r~L~  555 (731)
                      .++++-||-|.. ..|+.. +    +..++.      .      -++.+    +-+.+-+++.-|... .+- .=..+.+
T Consensus       414 ~siGfiGl~E~~-~~l~G~e~----~~e~~~------r------rDWi~----a~~l~~~~~~~~~~~~~~~~~e~~~~~  472 (655)
T TIGR02487       414 LSIGFIGLNEAL-VALTGKEH----LHEEEN------R------RDWIE----ARELAIKILEFIRDKVDELKKETGLNY  472 (655)
T ss_pred             EEEEHHHHHHHH-HHHCCCCC----EEECCC------C------HHHHH----HHHHHHHHHHHHHHHHHHHHHHHCCCE
T ss_conf             874036789999-99719983----224775------2------46999----999999999999999999998619716


Q ss_pred             HC-CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCC-HHHHHC---CC-CCCHH
Q ss_conf             30-1011116899999988299899999789776125117-787613---88-86789
Q gi|254781172|r  556 SL-GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDD-WLSLIR---VP-LVGDI  607 (731)
Q Consensus       556 AL-GI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~-~e~L~~---I~-GiG~~  607 (731)
                      ++ .-|  +|++|-.+|+.                    + .++.-.   |+ |++++
T Consensus       473 sv~~TP--AEsl~~Rfa~~--------------------Dl~~~fg~a~~i~kG~~d~  508 (655)
T TIGR02487       473 SVYATP--AESLCGRFAKK--------------------DLREEFGEAAKIPKGVTDK  508 (655)
T ss_pred             EEEECC--CHHHHHHHHHH--------------------HHHHHCCCCEEEECCCCCC
T ss_conf             899668--42078999998--------------------7676466410541033666


No 443
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=34.44  E-value=25  Score=14.04  Aligned_cols=38  Identities=24%  Similarity=0.347  Sum_probs=24.5

Q ss_pred             EECCEEEEEECCCCCCHHHHHHHC-CCEEECHHHHHHHHHH
Q ss_conf             116321799778888637989974-9917379999999988
Q gi|254781172|r  681 LSRKTDIIIVGDNPGSKLEKAQQL-GVKIMNEEQFLFLLQQ  720 (731)
Q Consensus       681 VSkkT~~LI~ge~~gSKl~KA~~L-gI~Ii~e~ef~~ll~~  720 (731)
                      +++|-+|||.||...  +.---+. -+.|++.+||+.....
T Consensus       101 ~~~kA~~lvTgD~dL--L~lr~~n~~~~Iltp~eF~~~~~~  139 (142)
T COG1569         101 YESKADYLVTGDQDL--LVLRDENKRVEILTPQEFLEEVLK  139 (142)
T ss_pred             HHCCCCEEEECCHHH--HEECCCCCCEEECCHHHHHHHHHH
T ss_conf             964688899726155--010366785797379999999997


No 444
>PRK06997 enoyl-(acyl carrier protein) reductase; Provisional
Probab=34.39  E-value=26  Score=13.80  Aligned_cols=15  Identities=7%  Similarity=0.071  Sum_probs=9.3

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      .+..+|.++.+.|-+
T Consensus       237 as~iTGq~i~VDGG~  251 (260)
T PRK06997        237 ASGVTGEITHVDSGF  251 (260)
T ss_pred             HCCCCCCEEEECCCH
T ss_conf             337058726879785


No 445
>PRK08245 hypothetical protein; Validated
Probab=34.38  E-value=26  Score=13.80  Aligned_cols=21  Identities=24%  Similarity=0.205  Sum_probs=16.4

Q ss_pred             CCEEEEEEEEEEEEECCCEEE
Q ss_conf             622589999743330264000
Q gi|254781172|r  349 TGILTPVARLEPVNIGGALIT  369 (731)
Q Consensus       349 tG~itPva~~ePV~l~G~~V~  369 (731)
                      .++..|++.=.||.++|++|.
T Consensus       149 ~~~~~~~~~n~pi~iggv~V~  169 (239)
T PRK08245        149 LTGHTAVDINVPIGCGGVAVF  169 (239)
T ss_pred             CCCCEEEEECCCEEECCEEEE
T ss_conf             876414662677897888982


No 446
>PRK12429 3-hydroxybutyrate dehydrogenase; Provisional
Probab=34.36  E-value=26  Score=13.80  Aligned_cols=14  Identities=14%  Similarity=0.273  Sum_probs=8.8

Q ss_pred             CCCCCCEEEEECCC
Q ss_conf             82168669997258
Q gi|254781172|r  645 SEIENKKLVFTGTL  658 (731)
Q Consensus       645 ~~l~gk~vV~TGtl  658 (731)
                      +.++|.++++.|-+
T Consensus       242 ~~itGq~i~VDGG~  255 (258)
T PRK12429        242 KGVTGQAWVVDGGW  255 (258)
T ss_pred             CCCCCCEEEECCCH
T ss_conf             49017638969463


No 447
>PRK11281 potassium efflux protein KefA; Provisional
Probab=34.19  E-value=18  Score=15.01  Aligned_cols=45  Identities=29%  Similarity=0.426  Sum_probs=22.1

Q ss_pred             CCCCHHHH----HHHHHHCCCEEEEEEECCEEEEE--ECCCCCCHHHHHHHCC
Q ss_conf             89987899----99999829849981116321799--7788886379899749
Q gi|254781172|r  659 QKIQRHKA----QEYVTQLGAVVSAILSRKTDIII--VGDNPGSKLEKAQQLG  705 (731)
Q Consensus       659 ~~~~R~e~----~~~ie~~Ggkv~sSVSkkT~~LI--~ge~~gSKl~KA~~Lg  705 (731)
                      ..|.|+|+    ++.|...  -+-=|.|-..+-+|  +|-.-||-+++++++=
T Consensus       964 ~d~DrkEiivPNK~FiT~~--~iNWsLsd~itRv~i~vgvaygsD~~~v~~ll 1014 (1107)
T PRK11281        964 TDFDRKEVIVPNKAFVTER--LINWSLSDTVTRLVIKVGVAYGSDLEKVRKLL 1014 (1107)
T ss_pred             ECCCCCEEECCCHHHHHHH--HHCEECCCCCEEEEEEECCCCCCCHHHHHHHH
T ss_conf             4477754734756567413--31001368605899981566688889999999


No 448
>COG1137 YhbG ABC-type (unclassified) transport system, ATPase component [General function prediction only]
Probab=34.14  E-value=17  Score=15.34  Aligned_cols=10  Identities=30%  Similarity=0.119  Sum_probs=4.8

Q ss_pred             CCCHHHHHHH
Q ss_conf             8678999999
Q gi|254781172|r  603 LVGDIIAQAI  612 (731)
Q Consensus       603 GiG~~~A~si  612 (731)
                      |+.|+....|
T Consensus       169 GVDPiaV~dI  178 (243)
T COG1137         169 GVDPIAVIDI  178 (243)
T ss_pred             CCCCHHHHHH
T ss_conf             8994029999


No 449
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=34.14  E-value=21  Score=14.58  Aligned_cols=94  Identities=16%  Similarity=0.115  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH--HHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCC-CCCCCCC--------C
Q ss_conf             999999999999999999984--3317798208789999999999998977203115899996-2003643--------2
Q gi|254781172|r   14 IEQARKELSSLEQEISYHDDC--YYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGP-LNKIGGE--------M   82 (731)
Q Consensus        14 ~~~~~~~i~~L~~~i~~~~~~--Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~sp-t~~Vg~~--------~   82 (731)
                      ...+|+-+..|+..+.+|-..  |+      -|+.+-.+.++||.-+-.     .....|||| ...+|-.        .
T Consensus       103 e~s~~q~~~r~~~~~~~wg~~~gyf------~~~~da~~f~~e~~~~l~-----~q~~a~nsp~wfn~gl~~~ygi~g~~  171 (1177)
T PRK07562        103 ETSAKQVFDRLAGCWTYWGWKGGYF------DSEEDARAFYDELRYMLA-----TQMVAPNSPQWFNTGLHWAYGIDGPG  171 (1177)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCC------CCHHHHHHHHHHHHHHHH-----HHHCCCCCCCEEECCCCHHCCCCCCC
T ss_conf             4409999999999999887637830------788899999999999999-----74527899832786740101666777


Q ss_pred             ------CCCCC-------EEECCC----CCCCHHHCC-CHHHHHHHHHHHHHHH
Q ss_conf             ------35775-------045166----425702159-9999999999999861
Q gi|254781172|r   83 ------NLSLF-------KVTHSI----PTLSLEKIW-NIEDLRKFITRIYRFW  118 (731)
Q Consensus        83 ------~~~~~-------kv~H~~----pMlSL~k~~-~~~el~~w~~~~~~~~  118 (731)
                            .....       --.|++    ..+|.+..- ++..+.+|+.+=.++.
T Consensus       172 ~g~~~~d~~~~~~~~~~~~y~~pq~~acfi~sv~d~l~~~~~i~~~~~~ea~~f  225 (1177)
T PRK07562        172 QGHFYVDPKTGKLTKSKSAYEHPQPHACFIQSVEDDLVNEGGIMDLWVREARLF  225 (1177)
T ss_pred             CCCEEECCCCCCEECCCCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHE
T ss_conf             773322565572111576233777654678852333447540999999866543


No 450
>pfam00406 ADK Adenylate kinase.
Probab=33.90  E-value=26  Score=13.90  Aligned_cols=34  Identities=9%  Similarity=0.088  Sum_probs=22.0

Q ss_pred             EEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHH
Q ss_conf             77704326577501033786544521010035434411446655332130
Q gi|254781172|r  428 FSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVS  477 (731)
Q Consensus       428 ~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~S  477 (731)
                      ...|..|++||+.++...+                +.++.+.+|+..|-.
T Consensus       139 p~~~~~~~~~~~~l~~R~D----------------D~~e~i~~Rl~~y~~  172 (186)
T pfam00406       139 PKVPGKDDVTGEPLSQRSD----------------DNEETVKKRLETYHK  172 (186)
T ss_pred             CCCCCCCCCCCCCCCCCCC----------------CCHHHHHHHHHHHHH
T ss_conf             5213645444223537899----------------999999999999999


No 451
>pfam01967 MoaC MoaC family. Members of this family are involved in molybdenum cofactor biosynthesis. However their molecular function is not known.
Probab=33.75  E-value=27  Score=13.72  Aligned_cols=52  Identities=19%  Similarity=0.331  Sum_probs=34.2

Q ss_pred             EEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCC
Q ss_conf             8788994035622589999743330264000101489899975023454322246844076899983587
Q gi|254781172|r  339 LLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGE  408 (731)
Q Consensus       339 v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGd  408 (731)
                      +.--.=..||||.       |-=-|-|++|.--|.  +|.++-+         ++++.|++.-++.++|.
T Consensus        85 i~~~v~~~~kTGV-------EMEALtavsva~LTi--YDM~Kav---------dk~~~I~~i~L~~K~GG  136 (136)
T pfam01967        85 IQATVRTTGKTGV-------EMEALTAVSVAALTI--YDMCKAV---------DKDMVIEGIRLLEKSGG  136 (136)
T ss_pred             EEEEEEECCCCCH-------HHHHHHHHHHHHHHH--HHHHHHC---------CCCCEEEEEEEEEECCC
T ss_conf             9999997079404-------250898999999999--9988611---------89979942699983088


No 452
>KOG2661 consensus
Probab=33.73  E-value=23  Score=14.23  Aligned_cols=16  Identities=19%  Similarity=0.503  Sum_probs=8.9

Q ss_pred             CCCEEEECCCCCCCCC
Q ss_conf             7304777043265775
Q gi|254781172|r  424 DAQPFSFPSFCPICQS  439 (731)
Q Consensus       424 ~~~~~~~P~~CP~Cgs  439 (731)
                      ..+.|+|-..-|+|.+
T Consensus       256 gGKvfVFtgiLn~ck~  271 (424)
T KOG2661         256 GGKVFVFTGILNSCKD  271 (424)
T ss_pred             CCEEEEEECHHHCCCC
T ss_conf             9739999511010368


No 453
>PRK00724 formate dehydrogenase accessory protein; Reviewed
Probab=33.66  E-value=27  Score=13.71  Aligned_cols=52  Identities=17%  Similarity=0.335  Sum_probs=41.3

Q ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEEC
Q ss_conf             21686699972588998789999999829849981116321799778888637989974991737
Q gi|254781172|r  646 EIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMN  710 (731)
Q Consensus       646 ~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~  710 (731)
                      .++++.+++||-++    .|+..+.-..|.-+.-|+|.-|+.         =++-|+++||.++.
T Consensus       196 ~~~~~~l~~SGR~s----~emV~Ka~~aGipvlvS~sapTsl---------AvelA~~~giTLig  247 (262)
T PRK00724        196 PLRDGALLVSGRAS----SEMVQKAAMAGIPILVAVSAPTSL---------AVELAEELGLTLVG  247 (262)
T ss_pred             CCCCEEEEEECCCH----HHHHHHHHHCCCCEEEECCCCHHH---------HHHHHHHCCCEEEE
T ss_conf             86780999907663----999999998499899998632199---------99999981998999


No 454
>COG1717 RPL32 Ribosomal protein L32E [Translation, ribosomal structure and biogenesis]
Probab=33.59  E-value=21  Score=14.49  Aligned_cols=28  Identities=11%  Similarity=0.012  Sum_probs=15.2

Q ss_pred             HHHHHHHHCCCCCCEEEEEHHHHCCHHH
Q ss_conf             3555565305765404541011010677
Q gi|254781172|r  488 KQQLDFFFKSEDPAFSIRIPADIFTLQR  515 (731)
Q Consensus       488 ~k~Ie~L~e~~~~~g~I~~~~DLy~L~~  515 (731)
                      |+-|.-|.-.|+..-+|.++.||=.|+.
T Consensus        68 Pk~vRglhPSG~~~VlV~Nv~dLe~ldp   95 (133)
T COG1717          68 PKAVRGLHPSGYEEVLVHNVKDLEKLDP   95 (133)
T ss_pred             CHHHCCCCCCCCCEEEEECHHHHHHCCC
T ss_conf             2765256877660235516888742380


No 455
>TIGR01011 rpsB_bact ribosomal protein S2; InterPro: IPR005706   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    This family describes the bacterial, mitochondrial and chloroplast forms of ribosomal protein S2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=33.46  E-value=22  Score=14.35  Aligned_cols=24  Identities=8%  Similarity=0.158  Sum_probs=15.0

Q ss_pred             CHHHHHHHHHHHHHHHHH--HHHHHH
Q ss_conf             014568999987522346--667763
Q gi|254781172|r  533 VSVTNLYDSINKRRNISL--ERFIFS  556 (731)
Q Consensus       533 Ksa~nL~~sIe~sK~~~L--~r~L~A  556 (731)
                      |-|+.++.+...+-..++  .|+|-|
T Consensus        74 kQA~~~i~~~A~r~g~~YVn~RWLGG   99 (227)
T TIGR01011        74 KQAKEIIKEEAERCGMFYVNQRWLGG   99 (227)
T ss_pred             HHHHHHHHHHHHHCCCCEECCCCCCC
T ss_conf             89999999999874896211333464


No 456
>pfam05129 Elf1 Transcription elongation factor Elf1 like. This family of short proteins contains a putative zinc binding domain with four conserved cysteines. Elf1 has been identified as a transcription elongation factor in Saccharomyces cerevisiae.
Probab=33.44  E-value=10  Score=16.92  Aligned_cols=30  Identities=20%  Similarity=0.528  Sum_probs=14.2

Q ss_pred             ECC--CCCCCCCCCCCCCCCCCCCCCEEECCC
Q ss_conf             704--326577501033786544521010035
Q gi|254781172|r  430 FPS--FCPICQSRVVRDLNPKTGKLVAAHRCT  459 (731)
Q Consensus       430 ~P~--~CP~Cgs~l~~~~~~~~~~~~~~~rC~  459 (731)
                      +|+  .||.||.+...............+.|.
T Consensus        14 L~~~F~CpfC~h~~sv~vkidk~~~~g~l~C~   45 (74)
T pfam05129        14 LPTVFDCPFCNHKKSVSVKIDKKTGIAKLHCR   45 (74)
T ss_pred             CCCEEECCCCCCCCEEEEEEECCCCEEEEEEE
T ss_conf             98567478679987599999814798999962


No 457
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=33.24  E-value=19  Score=14.93  Aligned_cols=25  Identities=24%  Similarity=0.456  Sum_probs=18.7

Q ss_pred             CCCCCCCEEEEEECCCCHHHHHHHCCC
Q ss_conf             684407689998358702566541012
Q gi|254781172|r  393 RDIRVGDRVLVKRAGEVIPKVVDIIVN  419 (731)
Q Consensus       393 ~~I~iGd~V~I~RaGdVIP~I~~Vi~~  419 (731)
                      .++.+||.|.| |+||.|| +.+++.+
T Consensus       256 ~~l~~GDiV~V-~~Ge~IP-aDG~vv~  280 (739)
T PRK11033        256 NSLRPGDVIEV-APGGRLP-ADGKLLS  280 (739)
T ss_pred             HHCCCCCEEEE-CCCCEEE-CCEEEEC
T ss_conf             99799999998-8999842-2279970


No 458
>TIGR01051 topA_bact DNA topoisomerase I; InterPro: IPR005733   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.     This entry describes topoisomerase I from bacteria, which is more closely related to archaeal than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. Prokaryotic topoisomerase I folds in an unusual way to give 4 distinct domains, enclosing a hole large enough to accommodate a double-stranded DNA segment. A tyrosine at the active site, which lies at the interface of 2 domains, is involved in transient breakage of a DNA strand, and the formation of a covalent protein-DNA intermediate through a 5-phosphotyrosine linkage. The structure reveals a plausible mechanism by which this and related enzymes could catalyse the passage of one DNA strand through a transient break in another strand . Topoisomerase I require Mg2+ as a cofactor for catalysis to take place.    More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=33.17  E-value=16  Score=15.47  Aligned_cols=18  Identities=17%  Similarity=0.252  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHHHCCCH
Q ss_conf             111168999999882998
Q gi|254781172|r  560 RHVGAEIARSLAKYYLSY  577 (731)
Q Consensus       560 ~~vG~~~Ak~La~~f~si  577 (731)
                      --+|.....+|..||+.+
T Consensus       562 ~~~g~~V~~~Le~hF~~~  579 (688)
T TIGR01051       562 TELGFAVTDLLEKHFGEL  579 (688)
T ss_pred             HHHHHHHHHHHHHHCCCC
T ss_conf             277899999988642643


No 459
>PRK08589 short chain dehydrogenase; Validated
Probab=33.13  E-value=28  Score=13.65  Aligned_cols=18  Identities=22%  Similarity=0.244  Sum_probs=11.6

Q ss_pred             CCCCCCCEEEEECCCCCC
Q ss_conf             882168669997258899
Q gi|254781172|r  644 SSEIENKKLVFTGTLQKI  661 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~~~  661 (731)
                      ++..+|.++++-|-+.-|
T Consensus       238 asyiTG~~i~VDGG~~A~  255 (272)
T PRK08589        238 SSFITGETIRIDGGVMAY  255 (272)
T ss_pred             HCCCCCCEEEECCCHHHC
T ss_conf             178368548989085427


No 460
>pfam01215 COX5B Cytochrome c oxidase subunit Vb.
Probab=33.10  E-value=16  Score=15.52  Aligned_cols=10  Identities=50%  Similarity=1.099  Sum_probs=5.5

Q ss_pred             CCCCCCCCCC
Q ss_conf             0432657750
Q gi|254781172|r  431 PSFCPICQSR  440 (731)
Q Consensus       431 P~~CP~Cgs~  440 (731)
                      |..||.||+-
T Consensus        81 p~RC~eCG~~   90 (99)
T pfam01215        81 PTRCPECGSV   90 (99)
T ss_pred             CCCCCCCCCE
T ss_conf             7307878878


No 461
>PRK07523 gluconate 5-dehydrogenase; Provisional
Probab=33.09  E-value=28  Score=13.65  Aligned_cols=15  Identities=27%  Similarity=0.337  Sum_probs=10.2

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             882168669997258
Q gi|254781172|r  644 SSEIENKKLVFTGTL  658 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl  658 (731)
                      ++..+|.++++.|-+
T Consensus       233 s~~iTG~~i~VDGG~  247 (251)
T PRK07523        233 SSFVNGHVLYVDGGI  247 (251)
T ss_pred             HCCCCCCEEEECCCC
T ss_conf             248268748809381


No 462
>PRK13646 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=32.86  E-value=28  Score=13.64  Aligned_cols=31  Identities=19%  Similarity=0.401  Sum_probs=24.3

Q ss_pred             CCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHH
Q ss_conf             64000101489899975023454322246844076899983587025
Q gi|254781172|r  365 GALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIP  411 (731)
Q Consensus       365 G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP  411 (731)
                      |.||=-+| |+.+++.++               -|+|.|-..|.||=
T Consensus       196 g~TiI~iT-Hdm~~v~~~---------------adrv~vm~~G~Iv~  226 (286)
T PRK13646        196 NKAIILIS-HDMNEVARY---------------ADEVIVMKEGSIVS  226 (286)
T ss_pred             CCEEEEEC-CCHHHHHHH---------------CCEEEEEECCEEEE
T ss_conf             98999991-389999996---------------99999998989999


No 463
>PRK00694 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated
Probab=32.86  E-value=13  Score=16.21  Aligned_cols=66  Identities=17%  Similarity=0.249  Sum_probs=31.5

Q ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCC--C--HHHHHHHCCCEEEC-HHHHHHHH
Q ss_conf             8821686699972588998789999999829849981116321799778888--6--37989974991737-99999999
Q gi|254781172|r  644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG--S--KLEKAQQLGVKIMN-EEQFLFLL  718 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~g--S--Kl~KA~~LgI~Ii~-e~ef~~ll  718 (731)
                      .+.|.|.++-+-|-.-+-.    -++.             +-||==||..+|  |  +=+.--+-|||-=. -+++++||
T Consensus       534 T~HLKGvKIgIMGCIVNGP----GEMA-------------DADfGYVGsGpGKIsLY~GKe~VkrNIPeeeAVD~LIeLI  596 (606)
T PRK00694        534 TQHLPGLKIAVMGCIVNGP----GEMA-------------DADFGFVGSKTGMIDLYVKHTCVKAHIPMEDAEEELVRLL  596 (606)
T ss_pred             HCCCCCCEEEEEEEEECCC----CCCC-------------CCCCCCCCCCCCEEEEEECCEEEECCCCHHHHHHHHHHHH
T ss_conf             4788787489983040287----4011-------------3666754788886888607563424898789999999999


Q ss_pred             HHHCCCCC
Q ss_conf             88286568
Q gi|254781172|r  719 QQYNTTLR  726 (731)
Q Consensus       719 ~~~~~~~~  726 (731)
                      ++...=.+
T Consensus       597 Ke~G~WvD  604 (606)
T PRK00694        597 KEHGVWKD  604 (606)
T ss_pred             HHCCCCCC
T ss_conf             86587279


No 464
>PRK10671 copA copper exporting ATPase; Provisional
Probab=32.85  E-value=20  Score=14.74  Aligned_cols=24  Identities=25%  Similarity=0.436  Sum_probs=18.2

Q ss_pred             CCCCCCEEEEEECCCCHHHHHHHCCC
Q ss_conf             84407689998358702566541012
Q gi|254781172|r  394 DIRVGDRVLVKRAGEVIPKVVDIIVN  419 (731)
Q Consensus       394 ~I~iGd~V~I~RaGdVIP~I~~Vi~~  419 (731)
                      +|.+||.|.| |+||.|| +.+++.+
T Consensus       340 ~l~~GDiv~V-~~Ge~IP-aDG~vv~  363 (834)
T PRK10671        340 DVQPGMLLRL-TTGDRVP-VDGEITQ  363 (834)
T ss_pred             HCCCCCEEEE-CCCCEEC-CCEEEEE
T ss_conf             9688999998-9999832-3369997


No 465
>PRK08690 enoyl-(acyl carrier protein) reductase; Provisional
Probab=32.48  E-value=28  Score=13.58  Aligned_cols=13  Identities=23%  Similarity=0.207  Sum_probs=6.9

Q ss_pred             CCCCCCEEEEECC
Q ss_conf             8216866999725
Q gi|254781172|r  645 SEIENKKLVFTGT  657 (731)
Q Consensus       645 ~~l~gk~vV~TGt  657 (731)
                      +..+|.++++-|-
T Consensus       239 s~iTG~~i~VDGG  251 (261)
T PRK08690        239 SGITGEITYVDGG  251 (261)
T ss_pred             CCCCCCEEEECCC
T ss_conf             4705863997969


No 466
>pfam09889 DUF2116 Uncharacterized protein containing a Zn-ribbon (DUF2116). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=32.42  E-value=20  Score=14.79  Aligned_cols=30  Identities=17%  Similarity=0.474  Sum_probs=19.0

Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHH
Q ss_conf             704326577501033786544521010035434411446655
Q gi|254781172|r  430 FPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLER  471 (731)
Q Consensus       430 ~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~  471 (731)
                      +-.+||.||...--++          .+|+.  .|.....++
T Consensus         2 pHkHC~vCG~~Ipp~e----------~fCS~--kC~~~~~~~   31 (59)
T pfam09889         2 PHKHCIVCGTAIPPDE----------SFCSE--KCQEEYRKK   31 (59)
T ss_pred             CCCCCCCCCCCCCCCC----------CCCCH--HHHHHHHHH
T ss_conf             9853565799789432----------23148--899999999


No 467
>TIGR01161 purK phosphoribosylaminoimidazole carboxylase, ATPase subunit; InterPro: IPR005875    Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This family represents PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, which catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP.    PurK belongs to the ATP grasp superfamily of C-N ligase enzymes. Each subunit of PurK is composed of three domains (A, B, and C). The B domain contains a flexible, glycine-rich loop (B loop, T123-G130) that is disordered in the sulphate-PurK structure and becomes ordered in the MgADP-PurK structure. MgADP is wedged between the B and C domains, as with all members of the ATP grasp superfamily. Other enzymes in this superfamily contain a conserved Omega loop proposed to interact with the B loop, define the specificity of their nonnucleotide substrate, and protect the acyl phosphate intermediate formed from this substrate. PurK contains a minimal Omega loop without conserved residues. In the reaction catalyzed by PurK, carboxyphosphate is the putative acyl phosphate intermediate. The sulphate of the sulphate ion-liganded PurK interacts electrostatically with Arg 242 and the backbone amide group of Asn 245, components of the J loop of the C domain. This sulphate may reveal the location of the carboxyphosphate binding site. Conserved residues within the C-terminus of the C domain define a pocket that is proposed to bind AIR in collaboration with an N-terminal strand loop helix motif in the A domain (P loop, G8-L1). The P loop is proposed to bind the phosphate of AIR on the basis of similar binding sites observed in PurN and PurE and proposed in PurD and PurT, four other enzymes in the purine pathway .; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process, 0009320 phosphoribosylaminoimidazole carboxylase complex.
Probab=32.39  E-value=28  Score=13.57  Aligned_cols=54  Identities=22%  Similarity=0.220  Sum_probs=33.5

Q ss_pred             CCCCHHHHHHHHHCCCCCCCCEEEE-ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCC
Q ss_conf             1000036899997599665414887-403211345566553100112343763777311000111587656
Q gi|254781172|r  251 AKGQYEMLQKMRCLGFPVNNGVRQA-NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERAR  320 (731)
Q Consensus       251 ~~~~~e~l~~L~~~GF~v~~~~~~~-~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~  320 (731)
                      ..+.+..=++|+++|++|+++.... .+.+++...       ...++|+.   |+|      ++++||.+|
T Consensus       100 ~~dk~~qK~~L~~~g~~vp~f~~~~~~~~~~~~~~-------~~~~g~p~---VlK------~~~gGYDGr  154 (386)
T TIGR01161       100 IQDKLTQKQFLQKLGLPVPPFVVIEIKDEEELDSA-------LQELGFPV---VLK------ARRGGYDGR  154 (386)
T ss_pred             HHCHHHHHHHHHHCCCCCCCCCEEECCCHHHHHHH-------HHHCCCCE---EEE------EEECCCCCC
T ss_conf             83658999999966899884120223684257899-------98739847---998------420652773


No 468
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=32.37  E-value=14  Score=15.98  Aligned_cols=16  Identities=19%  Similarity=0.453  Sum_probs=11.9

Q ss_pred             EECCCCCCCCCCCCCC
Q ss_conf             7704326577501033
Q gi|254781172|r  429 SFPSFCPICQSRVVRD  444 (731)
Q Consensus       429 ~~P~~CP~Cgs~l~~~  444 (731)
                      .+-.+||+||.....+
T Consensus         6 ~PH~HC~VCg~aIp~d   21 (64)
T COG4068           6 VPHRHCVVCGKAIPPD   21 (64)
T ss_pred             CCCCCCCCCCCCCCCC
T ss_conf             8876566058868974


No 469
>KOG4450 consensus
Probab=32.28  E-value=23  Score=14.31  Aligned_cols=21  Identities=38%  Similarity=0.605  Sum_probs=11.9

Q ss_pred             CCCCCCCCCCCCE-EEEEEEEEEE
Q ss_conf             2432233544550-4899999985
Q gi|254781172|r  172 TIPRVLSLNIPEI-IEVRGEVYIS  194 (731)
Q Consensus       172 ~iP~~l~~~~~~~-ieiRGEv~m~  194 (731)
                      +||--|..  |+. -.|+||+|--
T Consensus        54 nIPfLLnk--pGsG~~V~GElY~V   75 (168)
T KOG4450          54 NIPFLLNK--PGSGYHVEGELYEV   75 (168)
T ss_pred             CCCEEECC--CCCCCEEEEEEEEE
T ss_conf             77258727--88763651479886


No 470
>PRK07041 short chain dehydrogenase; Provisional
Probab=32.09  E-value=29  Score=13.53  Aligned_cols=15  Identities=13%  Similarity=0.220  Sum_probs=6.4

Q ss_pred             EECCCCHHHHHHHHH
Q ss_conf             865986556669997
Q gi|254781172|r  152 ALRGDGHSGEDVSAC  166 (731)
Q Consensus       152 ~TRGdG~~GeDVT~n  166 (731)
                      +|=|.+-+|.-+...
T Consensus        12 ITGgs~GIG~aia~~   26 (240)
T PRK07041         12 VVGGSSGIGLAAARA   26 (240)
T ss_pred             EECCCCHHHHHHHHH
T ss_conf             957788899999999


No 471
>PRK06523 short chain dehydrogenase; Provisional
Probab=32.06  E-value=29  Score=13.53  Aligned_cols=15  Identities=20%  Similarity=0.355  Sum_probs=11.1

Q ss_pred             CCCCCCCCEEEEECC
Q ss_conf             688216866999725
Q gi|254781172|r  643 VSSEIENKKLVFTGT  657 (731)
Q Consensus       643 ~~~~l~gk~vV~TGt  657 (731)
                      .++..+|.++.+.|-
T Consensus       241 ~s~~iTG~~i~VDGG  255 (260)
T PRK06523        241 RAASITGTEYVIDGG  255 (260)
T ss_pred             HHCCEECCEEEECCC
T ss_conf             426860855788788


No 472
>TIGR00705 SppA_67K signal peptide peptidase SppA, 67K type; InterPro: IPR004634   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain.   Signal peptides of secretory proteins seem to serve at least two important biological functions. First, they are required for protein targeting to and translocation across membranes, such as the eubacterial plasma membrane and the endoplasmic reticular membrane of eukaryotes. Second, in addition to their role as determinants for protein targeting and translocation, certain signal peptides have a signalling function.  During or shortly after pre-protein translocation, the signal peptide is removed by signal peptidases. The integral membrane protein, SppA (protease IV), of Escherichia coli was shown experimentally to degrade signal peptides. The member of this family from Bacillus subtilis has only been shown to be required for efficient processing of pre-proteins under conditions of hyper-secretion . These enzymes have a molecular mass around 67 kDa and a duplication such that the N-terminal half shares extensive homology with the C-terminal half and was shown in E. coli to form homotetramers. E. coli SohB, which is most closely homologous to the C-terminal duplication of SppA, is predicted to perform a similar function of small peptide degradation, but in the periplasm. Many prokaryotes have a single SppA/SohB homolog that may perform the function of either or both. ; GO: 0009003 signal peptidase activity, 0006465 signal peptide processing, 0016021 integral to membrane.
Probab=31.99  E-value=29  Score=13.52  Aligned_cols=36  Identities=31%  Similarity=0.484  Sum_probs=17.2

Q ss_pred             EEEEEECCEEEEE-EECCCCHHHHHHHHHHHHHCCCC
Q ss_conf             9999859989988-86598655666999775310243
Q gi|254781172|r  139 ITIRYEKGKFVYA-ALRGDGHSGEDVSACIRAIPTIP  174 (731)
Q Consensus       139 isl~Y~~G~L~~a-~TRGdG~~GeDVT~n~~~i~~iP  174 (731)
                      |.++|-+|-.+.. -|.+||..|+.+.+.+|.++.=|
T Consensus       322 iaiv~~~G~I~~G~~t~~nG~ggD~~a~lLr~a~~D~  358 (614)
T TIGR00705       322 IAIVYLEGSIVDGRDTEENGVGGDTVAALLRKARSDP  358 (614)
T ss_pred             EEEEEEECCEECCCCCCCCCCHHHHHHHHHHHHCCCC
T ss_conf             6999700642357756678600367999999870799


No 473
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=31.97  E-value=17  Score=15.19  Aligned_cols=10  Identities=50%  Similarity=0.893  Sum_probs=3.8

Q ss_pred             EEEEECCCEE
Q ss_conf             4333026400
Q gi|254781172|r  359 EPVNIGGALI  368 (731)
Q Consensus       359 ePV~l~G~~V  368 (731)
                      +|+-++|...
T Consensus       283 ~~~iigg~~~  292 (681)
T PRK08270        283 QPVIIGGEEM  292 (681)
T ss_pred             CCCEECCCCC
T ss_conf             3221177312


No 474
>PRK09072 short chain dehydrogenase; Provisional
Probab=31.88  E-value=29  Score=13.51  Aligned_cols=16  Identities=13%  Similarity=0.297  Sum_probs=9.3

Q ss_pred             CCHHHHHHHHHHHHHH
Q ss_conf             0014568999987522
Q gi|254781172|r  532 DVSVTNLYDSINKRRN  547 (731)
Q Consensus       532 eKsa~nL~~sIe~sK~  547 (731)
                      +.-|+.++.+|++.|.
T Consensus       208 e~vA~~i~~~i~~~k~  223 (262)
T PRK09072        208 EDVAAAVLQAIEQERA  223 (262)
T ss_pred             HHHHHHHHHHHHCCCC
T ss_conf             9999999999946998


No 475
>pfam08996 zf-DNA_Pol DNA Polymerase alpha zinc finger. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain.
Probab=31.88  E-value=29  Score=13.51  Aligned_cols=25  Identities=24%  Similarity=0.389  Sum_probs=15.1

Q ss_pred             CCCCCCCEEEECCCCCCCCCCCCCCCC
Q ss_conf             357873047770432657750103378
Q gi|254781172|r  420 ERHPDAQPFSFPSFCPICQSRVVRDLN  446 (731)
Q Consensus       420 ~r~~~~~~~~~P~~CP~Cgs~l~~~~~  446 (731)
                      .|-.+-.+|.+  .||.||++......
T Consensus         9 eRfr~c~~l~l--~Cp~C~~~~~f~gv   33 (186)
T pfam08996         9 ERFRDCARLKL--KCPSCGTEFPFPGI   33 (186)
T ss_pred             HHHCCCCEEEE--ECCCCCCCEECCCE
T ss_conf             98667870597--89999984577886


No 476
>PRK06138 short chain dehydrogenase; Provisional
Probab=31.85  E-value=29  Score=13.50  Aligned_cols=31  Identities=26%  Similarity=0.345  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf             16866999725889987899999998298499
Q gi|254781172|r  647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS  678 (731)
Q Consensus       647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~  678 (731)
                      |.||++++||.=.+.-|.-++.+. +.|++|.
T Consensus         3 L~gKvalVTGas~GIG~aia~~la-~~Ga~V~   33 (252)
T PRK06138          3 LAGRVAIVTGAGSGIGRATAKLFA-REGARVV   33 (252)
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHH-HCCCEEE
T ss_conf             899889994746799999999999-8799899


No 477
>TIGR00463 gltX_arch glutamyl-tRNA synthetase; InterPro: IPR004526   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 .    Glutamyl-tRNA synthetase (6.1.1.17 from EC) is a class Ic synthetase and shows several similarities with glutaminyl-tRNA synthetase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamyl-tRNA synthetase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I synthetases and resembles the corresponding part of E. coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure . ; GO: 0000166 nucleotide binding, 0004818 glutamate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006424 glutamyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=31.83  E-value=29  Score=13.53  Aligned_cols=20  Identities=35%  Similarity=0.698  Sum_probs=0.0

Q ss_pred             EEEEEEEEEEECHHHHHHHH
Q ss_conf             04899999985202123455
Q gi|254781172|r  184 IIEVRGEVYISKNDFLALND  203 (731)
Q Consensus       184 ~ieiRGEv~m~~~~F~~lN~  203 (731)
                      .|..+||||++++||+.+|.
T Consensus       454 ~l~~~~~iyv~kDd~~~~n~  473 (600)
T TIGR00463       454 KLIYEGEIYVDKDDLEVLNE  473 (600)
T ss_pred             EEEEEEEEEEECCCCCCCCC
T ss_conf             79860018870775100168


No 478
>TIGR02870 spore_II_D stage II sporulation protein D; InterPro: IPR014225   This entry contains the stage II sporulation protein D (SpoIID), which is a protein involved in the endospore formation program. SpoIID is one of the three genes (spoIID, spoIIM and spoIIP, , , ), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan - mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the engulfment stage. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers .
Probab=31.68  E-value=15  Score=15.80  Aligned_cols=73  Identities=18%  Similarity=0.254  Sum_probs=0.0

Q ss_pred             CCCCCEEEECCCCCEEEEEE-------EEEEEEECCCC----EE---EEEEEEEEEEECCCEEEEECCCCHHHHHHHCCC
Q ss_conf             68663123114562158998-------78899403562----25---899997433302640001014898999750234
Q gi|254781172|r  320 RSPRWMISHKFAEKQASTRL-------LDIDIQIGRTG----IL---TPVARLEPVNIGGALITNATLHNEDYIKGLDAS  385 (731)
Q Consensus       320 ~~PrwaiA~Kf~~e~~~T~v-------~~I~wqvgRtG----~i---tPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~  385 (731)
                      |+||+.---+|+.++..-+|       ....-.=++.|    .|   |+--+++-|.|+|.|++      .+.||..   
T Consensus       227 hspky~~e~~~s~~~F~~klGl~~~~p~~~l~~~~~~G~~Pv~I~~RT~gGrV~~~~ig~~tl~------G~~~Re~---  297 (358)
T TIGR02870       227 HSPKYKTETVMSIEEFVDKLGLKSSVPNLKLQNAASVGEKPVKILARTAGGRVKTIKIGGKTLK------GREIRER---  297 (358)
T ss_pred             CCCCCCCCEEECHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEECCEEEE------EEEHHHH---
T ss_conf             1666554137438999987505522575100012222789825886278971658898787886------0410256---


Q ss_pred             CCCCCCCCCCCCCCE-EEEEECCCCH
Q ss_conf             543222468440768-9998358702
Q gi|254781172|r  386 GKVMRGGRDIRVGDR-VLVKRAGEVI  410 (731)
Q Consensus       386 ~~~~~~~~~I~iGd~-V~I~RaGdVI  410 (731)
                               ||..++ -.+.+.+|=|
T Consensus       298 ---------lGLnStdF~~~~~~d~I  314 (358)
T TIGR02870       298 ---------LGLNSTDFTWKVQGDKI  314 (358)
T ss_pred             ---------HCCCCCCEEEEEECCEE
T ss_conf             ---------47874121899867879


No 479
>TIGR01966 RNasePH ribonuclease PH; InterPro: IPR002381   Prokaryotic ribonuclease PH (2.7.7.56 from EC) (RNase PH) is a phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates . There is a similar protein in Caenorhabditis elegans that belongs to this group.   More information about these proteins can be found at Protein of the Month: RNA Exosomes .; GO: 0000049 tRNA binding, 0004549 tRNA-specific ribonuclease activity, 0008033 tRNA processing.
Probab=31.57  E-value=29  Score=13.47  Aligned_cols=22  Identities=23%  Similarity=0.427  Sum_probs=0.0

Q ss_pred             CCEEEEECCC-----------CCCCHHHHHHHH
Q ss_conf             8669997258-----------899878999999
Q gi|254781172|r  649 NKKLVFTGTL-----------QKIQRHKAQEYV  670 (731)
Q Consensus       649 gk~vV~TGtl-----------~~~~R~e~~~~i  670 (731)
                      .++||+||+.           .-|||+|+-+++
T Consensus       186 D~NvVmT~~G~fvEvQGTaE~~pFsr~EL~~LL  218 (237)
T TIGR01966       186 DMNVVMTGSGGFVEVQGTAEEEPFSRDELNELL  218 (237)
T ss_pred             CCEEEECCCCCEEEEEECCCCCCHHHHHHHHHH
T ss_conf             520588578765888705788970189999999


No 480
>PRK12828 short chain dehydrogenase; Provisional
Probab=31.57  E-value=29  Score=13.47  Aligned_cols=34  Identities=24%  Similarity=0.403  Sum_probs=0.0

Q ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf             88216866999725889987899999998298499
Q gi|254781172|r  644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS  678 (731)
Q Consensus       644 ~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~  678 (731)
                      +..|+||++++||.-.++-|.-++ .+-+.|++|.
T Consensus         2 ~~~L~gKvalITGas~GIG~aia~-~la~~Ga~V~   35 (239)
T PRK12828          2 EHSLQGKVVAITGGFGGLGRATAA-WLAARGARVA   35 (239)
T ss_pred             CCCCCCCEEEEECCCCHHHHHHHH-HHHHCCCEEE
T ss_conf             999698989994725489999999-9998799899


No 481
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=31.53  E-value=26  Score=13.84  Aligned_cols=22  Identities=23%  Similarity=0.468  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf             3265775010337865445210100354
Q gi|254781172|r  433 FCPICQSRVVRDLNPKTGKLVAAHRCTG  460 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n  460 (731)
                      +||-||+++.....+      ....|++
T Consensus       113 FCg~CG~~~~~~~~g------~~~~C~~  134 (279)
T COG2816         113 FCGRCGTKTYPREGG------WARVCPK  134 (279)
T ss_pred             CCCCCCCCCCCCCCC------EEEECCC
T ss_conf             777789807435673------2455798


No 482
>pfam03129 HGTP_anticodon Anticodon binding domain. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases it is probably the anticodon binding domain.
Probab=31.36  E-value=29  Score=13.45  Aligned_cols=43  Identities=21%  Similarity=0.417  Sum_probs=0.0

Q ss_pred             HHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCE---EECHHHH
Q ss_conf             89999999829849981116321799778888637989974991---7379999
Q gi|254781172|r  664 HKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVK---IMNEEQF  714 (731)
Q Consensus       664 ~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~---Ii~e~ef  714 (731)
                      .++.+.+.+.|      ++-..|+  -+.+.|.|+..|..+|+|   |+.++|+
T Consensus        18 ~~i~~~Lr~~g------i~v~~d~--~~~~~~~k~~~a~~~g~p~~iiiG~~E~   63 (93)
T pfam03129        18 QKLAEELREAG------IRVELDD--RNESLGKKFRDADLIGIPFRLVVGEKEL   63 (93)
T ss_pred             HHHHHHHHHCC------CEEEEEC--CCCCHHHHHHHHHHHCCCEEEEECHHHH
T ss_conf             99999998789------9799988--9999789999898709990788977888


No 483
>PRK06720 hypothetical protein; Provisional
Probab=31.35  E-value=29  Score=13.44  Aligned_cols=31  Identities=29%  Similarity=0.306  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf             16866999725889987899999998298499
Q gi|254781172|r  647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS  678 (731)
Q Consensus       647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~  678 (731)
                      |+||++++||.=.+.-|.-+. .+-+.|++|.
T Consensus        14 L~gKvalITGa~~GIG~a~A~-~la~~Ga~Vv   44 (169)
T PRK06720         14 LAGKVAIVTGGGIGIGRNTAL-LLAKQGAKVI   44 (169)
T ss_pred             CCCCEEEEECCCCHHHHHHHH-HHHHCCCEEE
T ss_conf             299999998975489999999-9998699899


No 484
>PRK07890 short chain dehydrogenase; Provisional
Probab=31.33  E-value=29  Score=13.44  Aligned_cols=31  Identities=23%  Similarity=0.234  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf             16866999725889987899999998298499
Q gi|254781172|r  647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS  678 (731)
Q Consensus       647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~  678 (731)
                      |+||++++||.=.+.-|.-++ .+-+.|++|.
T Consensus         3 L~gK~alVTG~s~GIG~aia~-~la~~Ga~V~   33 (258)
T PRK07890          3 LKDKVVVVSGVGPGLGTTLAV-RAAREGADVV   33 (258)
T ss_pred             CCCCEEEEECCCCHHHHHHHH-HHHHCCCEEE
T ss_conf             899889996856589999999-9998799899


No 485
>KOG2463 consensus
Probab=31.31  E-value=16  Score=15.42  Aligned_cols=10  Identities=40%  Similarity=1.258  Sum_probs=0.0

Q ss_pred             CCCCCCCCCC
Q ss_conf             4326577501
Q gi|254781172|r  432 SFCPICQSRV  441 (731)
Q Consensus       432 ~~CP~Cgs~l  441 (731)
                      .+||+||..+
T Consensus       258 ~FCp~CG~~T  267 (376)
T KOG2463         258 DFCPSCGHKT  267 (376)
T ss_pred             HCCCCCCCCE
T ss_conf             0010049973


No 486
>pfam06676 DUF1178 Protein of unknown function (DUF1178). This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=31.28  E-value=18  Score=15.15  Aligned_cols=9  Identities=56%  Similarity=1.339  Sum_probs=0.0

Q ss_pred             CCCCCCCCC
Q ss_conf             265775010
Q gi|254781172|r  434 CPICQSRVV  442 (731)
Q Consensus       434 CP~Cgs~l~  442 (731)
                      ||.||+.-+
T Consensus        35 CP~Cgs~~V   43 (145)
T pfam06676        35 CPVCGSTEV   43 (145)
T ss_pred             CCCCCCCEE
T ss_conf             999999836


No 487
>PRK12428 3-alpha-hydroxysteroid dehydrogenase; Provisional
Probab=31.22  E-value=29  Score=13.43  Aligned_cols=31  Identities=32%  Similarity=0.422  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf             16866999725889987899999998298499
Q gi|254781172|r  647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS  678 (731)
Q Consensus       647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~  678 (731)
                      |+||++++||.=.++-|.-++ .+-+.|++|.
T Consensus         3 L~gK~alVTG~s~GIG~aia~-~la~~GA~V~   33 (261)
T PRK12428          3 LDGKTIVVTGVASGIGAEVAR-LLRFLGARVI   33 (261)
T ss_pred             CCCCEEEEECCCCHHHHHHHH-HHHHCCCEEE
T ss_conf             999889997857799999999-9998699999


No 488
>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=31.15  E-value=20  Score=14.72  Aligned_cols=41  Identities=17%  Similarity=0.391  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHH
Q ss_conf             432657750103378654452101003543441144665533213
Q gi|254781172|r  432 SFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFV  476 (731)
Q Consensus       432 ~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~  476 (731)
                      +.||.|+.-+  ...+....+.|...|.-..  +-...+||...+
T Consensus        34 tKCp~C~~~~--Y~keL~~n~~VC~~C~hH~--R~~A~eRi~~L~   74 (292)
T TIGR00515        34 TKCPKCGQLL--YTKELQRNLSVCLKCDHHF--RMDARERIESLL   74 (292)
T ss_pred             ECCCHHHHHH--HHHHHHCCCEECCCCCCCC--CCCHHHHHHHHC
T ss_conf             0144243443--4665303555742379877--468799998741


No 489
>PHA00439 exonuclease
Probab=31.07  E-value=23  Score=14.30  Aligned_cols=15  Identities=27%  Similarity=0.450  Sum_probs=0.0

Q ss_pred             CHHHHHHHHHHHHHH
Q ss_conf             101111689999998
Q gi|254781172|r  558 GIRHVGAEIARSLAK  572 (731)
Q Consensus       558 GI~~vG~~~Ak~La~  572 (731)
                      |||+||.++|..|..
T Consensus       191 GvpGiG~ktA~klL~  205 (288)
T PHA00439        191 GIPGWGPDTAEAFLN  205 (288)
T ss_pred             CCCCCCHHHHHHHHC
T ss_conf             998848899999863


No 490
>PHA00732 hypothetical protein
Probab=31.03  E-value=27  Score=13.76  Aligned_cols=49  Identities=35%  Similarity=0.579  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCCCCCC--CCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             3265775010337865--44521010035434411446655332130123103541
Q gi|254781172|r  433 FCPICQSRVVRDLNPK--TGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGL  486 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~~--~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GL  486 (731)
                      .||.||-..++--..+  .-..-+-..|+   -|.-.-..--.||.|+  -||+.|
T Consensus         3 kCPiCgF~tv~lFalKqH~R~~H~l~kCP---VC~~~y~~l~QHfy~~--~D~~HL   53 (79)
T PHA00732          3 RCPICGFTTVRLFALKQHTRKNHVLTKCP---VCNNSYRRLNQHFYSQ--YDIEHL   53 (79)
T ss_pred             CCCCCCCEEEEEEHHHHHHHHHCCCCCCC---CCCHHHHHHHHHHHHH--CCCHHH
T ss_conf             68726857886412677776504652277---5047899999877643--420562


No 491
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.01  E-value=30  Score=13.40  Aligned_cols=29  Identities=24%  Similarity=0.522  Sum_probs=0.0

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHHCCCEEEE
Q ss_conf             8669997258899878999999982984998
Q gi|254781172|r  649 NKKLVFTGTLQKIQRHKAQEYVTQLGAVVSA  679 (731)
Q Consensus       649 gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~s  679 (731)
                      |.++.+-|+  +..=+++++.||+.||.+.|
T Consensus        50 ~~~itIeG~--~ldydei~~~iE~~Gg~IHS   78 (97)
T COG1888          50 NLKITIEGT--NLDYDEIEEVIEELGGAIHS   78 (97)
T ss_pred             CEEEEEECC--CCCHHHHHHHHHHCCCEEEE
T ss_conf             358999737--78989999999972974565


No 492
>PRK07577 short chain dehydrogenase; Provisional
Probab=30.95  E-value=30  Score=13.40  Aligned_cols=31  Identities=16%  Similarity=0.234  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf             16866999725889987899999998298499
Q gi|254781172|r  647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS  678 (731)
Q Consensus       647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~  678 (731)
                      |+||++++||.=.+.-|.=++.+.+. |++|.
T Consensus         1 L~~K~alITGas~GIG~aia~~la~~-G~~Vv   31 (234)
T PRK07577          1 MSSRTVLVTGATKGIGLALSLRLANL-GHQVI   31 (234)
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHC-CCEEE
T ss_conf             94198999377888999999999987-99999


No 493
>PRK06935 2-deoxy-D-gluconate 3-dehydrogenase; Provisional
Probab=30.92  E-value=30  Score=13.39  Aligned_cols=31  Identities=19%  Similarity=0.216  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf             16866999725889987899999998298499
Q gi|254781172|r  647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS  678 (731)
Q Consensus       647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~  678 (731)
                      |+||++++||.=.+.-|.-++.+.+. |++|.
T Consensus        13 L~gKvalVTGas~GIG~aiA~~la~~-Ga~Vv   43 (258)
T PRK06935         13 LKGKVAIVTGGNTGLGQGYAVALAKA-GADII   43 (258)
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHC-CCEEE
T ss_conf             99998999485758999999999987-99999


No 494
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=30.82  E-value=30  Score=13.38  Aligned_cols=28  Identities=7%  Similarity=0.201  Sum_probs=0.0

Q ss_pred             EEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCC
Q ss_conf             3302640001014898999750234543222468440768999835870
Q gi|254781172|r  361 VNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEV  409 (731)
Q Consensus       361 V~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdV  409 (731)
                      |.++|..++-+.                     .+++||.|.|.+.+.+
T Consensus        36 V~vnG~~~Kps~---------------------~V~~GD~l~i~~~~~~   63 (133)
T PRK10348         36 VHYNGQRSKPSK---------------------IVELNATLTLRQGNDE   63 (133)
T ss_pred             EEECCEECCCCC---------------------CCCCCCEEEEEECCEE
T ss_conf             898998868888---------------------7689999999869959


No 495
>PRK07776 consensus
Probab=30.74  E-value=30  Score=13.37  Aligned_cols=31  Identities=26%  Similarity=0.314  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf             16866999725889987899999998298499
Q gi|254781172|r  647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS  678 (731)
Q Consensus       647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~  678 (731)
                      |+||++++||.-.+.-|.-++. +-+.|++|.
T Consensus         6 L~gKv~lITG~~~GIG~aiA~~-la~~Ga~V~   36 (252)
T PRK07776          6 LTGRTAIVTGASRGIGLAIAQA-LAAAGANVV   36 (252)
T ss_pred             CCCCEEEEECCCCHHHHHHHHH-HHHCCCEEE
T ss_conf             9999899947787999999999-998799899


No 496
>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=30.73  E-value=26  Score=13.83  Aligned_cols=22  Identities=23%  Similarity=0.418  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf             3265775010337865445210100354
Q gi|254781172|r  433 FCPICQSRVVRDLNPKTGKLVAAHRCTG  460 (731)
Q Consensus       433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n  460 (731)
                      +|+.||+++.....+      -..+|++
T Consensus         5 fC~~CG~~t~~~~~g------~~r~C~~   26 (32)
T pfam09297         5 FCGRCGAPTEPAEGG------WARVCPS   26 (32)
T ss_pred             CCCCCCCCCCCCCCC------CEEECCC
T ss_conf             424468847507785------1766887


No 497
>PRK12742 oxidoreductase; Provisional
Probab=30.72  E-value=30  Score=13.37  Aligned_cols=33  Identities=18%  Similarity=0.162  Sum_probs=0.0

Q ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf             8216866999725889987899999998298499
Q gi|254781172|r  645 SEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS  678 (731)
Q Consensus       645 ~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~  678 (731)
                      +.|+||++++||.=.+.-+.-++ .+-+.|++|.
T Consensus         2 ~~l~gK~alITGas~GIG~aia~-~la~~Ga~V~   34 (237)
T PRK12742          2 GAFTGKSVLVLGGSRGIGAAIVR-RFVTDGANVV   34 (237)
T ss_pred             CCCCCCEEEEECCCCHHHHHHHH-HHHHCCCEEE
T ss_conf             99899989992788799999999-9998799999


No 498
>pfam08605 Rad9_Rad53_bind Fungal Rad9-like Rad53-binding. In Saccharomyces cerevisiae the Rad9 a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via Rad53 pfam00498 domains. This region is structurally composed of a pair of TUDOR domains.
Probab=30.70  E-value=13  Score=16.25  Aligned_cols=42  Identities=19%  Similarity=0.181  Sum_probs=0.0

Q ss_pred             CHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHHHHHCCCCCCCCCCEEE
Q ss_conf             9899975023454322246844076899983587025665410123578730477
Q gi|254781172|r  375 NEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFS  429 (731)
Q Consensus       375 N~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP~I~~Vi~~~r~~~~~~~~  429 (731)
                      +.+.++.|           ||||||.|.+.  +--+|+|+.=+..+.+.+..++.
T Consensus        51 ~~~dv~~L-----------dLRIGD~Vkvd--~~k~~~iV~Gl~~~~s~~~~~i~   92 (131)
T pfam08605        51 KNGDLYYL-----------DLRIGDAVKCD--MNKYTYIVTGLECLISADDKDIR   92 (131)
T ss_pred             CCCCEEEE-----------EEECCCEEEEC--CCCCCEEEEEEEECCCCCCCCEE
T ss_conf             52513478-----------65118999879--99867899986762788898438


No 499
>pfam02680 DUF211 Uncharacterized ArCR, COG1888.
Probab=30.67  E-value=30  Score=13.36  Aligned_cols=61  Identities=21%  Similarity=0.345  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHHHH-HCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEE
Q ss_conf             69799999999997-3387765432246882168669997258899878999999982984998
Q gi|254781172|r  617 QNPRNICAVEALLK-EVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSA  679 (731)
Q Consensus       617 ~~~~n~~~i~~L~~-~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~s  679 (731)
                      +.|...++...|.+ .+.....-.-......-.|.++++-|.  +..=+++++.||.+||.+.|
T Consensus        15 ~~p~i~d~A~~l~~~~gv~gVni~v~EvD~~t~~~kitIEG~--~id~d~i~~~IE~~Gg~IHS   76 (91)
T pfam02680        15 HEPSIVDLARELAELEGVDGVNITVTEIDVETENIKVTIEGS--DIDFDEIKEAIEELGGVIHS   76 (91)
T ss_pred             CCCCHHHHHHHHHHCCCCCEEEEEEEEEECCCEEEEEEEEEC--CCCHHHHHHHHHHCCCEEEE
T ss_conf             999799999999727796549999999613650689999947--87979999999975983774


No 500
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''; InterPro: IPR012757   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.    This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=30.61  E-value=24  Score=14.14  Aligned_cols=78  Identities=22%  Similarity=0.243  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHHHCCHHHHHHHHHHHHHCC------------CCCCCCCCCCCCCCCCCEEEEECCCCC---CCHHHHHH
Q ss_conf             678999999999669799999999997338------------776543224688216866999725889---98789999
Q gi|254781172|r  604 VGDIIAQAIVEFYQNPRNICAVEALLKEVS------------PSIGRHEKNVSSEIENKKLVFTGTLQK---IQRHKAQE  668 (731)
Q Consensus       604 iG~~~A~si~~ff~~~~n~~~i~~L~~~~~------------~~~~~~~~~~~~~l~gk~vV~TGtl~~---~~R~e~~~  668 (731)
                      +|-++||||-+    |--+-.+..|--+|.            +.+-...+..+.|+  |++=++.-+.+   |.|+-+++
T Consensus        48 vGiVAAQSiGE----PGTQMTmRTFHYAGv~ElnVTlGLPRLIEIVDArk~PSTP~--MtIYL~~ey~~dyaydrE~a~~  121 (397)
T TIGR02389        48 VGIVAAQSIGE----PGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPSTPL--MTIYLEDEYEKDYAYDREKAEE  121 (397)
T ss_pred             CEEEEEEEECC----CHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCE--EEEEECCCCCCCCCCCHHHHHH
T ss_conf             10388442188----45478777665776678876447840145450666789863--7996278863224566789999


Q ss_pred             HHHHCCCEEEEEEECCEEE
Q ss_conf             9998298499811163217
Q gi|254781172|r  669 YVTQLGAVVSAILSRKTDI  687 (731)
Q Consensus       669 ~ie~~Ggkv~sSVSkkT~~  687 (731)
                      ...+...+--++|.++++.
T Consensus       122 va~kie~t~l~~v~~~i~~  140 (397)
T TIGR02389       122 VAKKIEATKLEDVAKDISI  140 (397)
T ss_pred             HHHHHHHCCHHHHHCEEEE
T ss_conf             9987520333252241248


Done!