Query         gi|254780834|ref|YP_003065247.1| DNA primase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 648
No_of_seqs    198 out of 1905
Neff          7.9 
Searched_HMMs 39220
Date          Mon May 30 01:38:42 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780834.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK05667 dnaG DNA primase; Val 100.0       0       0 1218.7  59.9  592    1-632     2-598 (600)
  2 COG0358 DnaG DNA primase (bact 100.0       0       0  939.4  45.6  413    2-442     1-415 (568)
  3 TIGR01391 dnaG DNA primase; In 100.0       0       0  702.8  35.5  413    2-431     1-423 (424)
  4 pfam08275 Toprim_N DNA primase 100.0 1.5E-31 3.8E-36  309.8   8.5  128  127-255     1-128 (128)
  5 PRK08624 hypothetical protein; 100.0 3.7E-29 9.4E-34  287.8  18.0  273    9-324     5-300 (373)
  6 pfam01807 zf-CHC2 CHC2 zinc fi 100.0 2.5E-28 6.4E-33  280.1  11.9   96    3-103     1-96  (98)
  7 smart00400 ZnF_CHCC zinc finge  99.8 1.3E-18 3.3E-23  190.8   6.3   55   39-93      1-55  (55)
  8 cd03364 TOPRIM_DnaG_primases T  99.7   5E-17 1.3E-21  176.2   7.6   78  273-353     2-79  (79)
  9 PHA02415 DNA primase domain-co  99.7 8.7E-14 2.2E-18  146.4  22.4  314    6-381     2-354 (930)
 10 cd01029 TOPRIM_primases TOPRIM  99.3 6.8E-12 1.7E-16  129.0   7.4   77  273-352     2-78  (79)
 11 PHA02031 putative DnaG-like pr  99.1 4.5E-10 1.2E-14  112.2   9.4  165  166-377    93-266 (274)
 12 TIGR02760 TraI_TIGR conjugativ  98.9 2.3E-07 5.8E-12   87.4  14.9  303   45-385  1759-2113(2193)
 13 pfam01751 Toprim Toprim domain  98.8   1E-08 2.5E-13   99.9   6.8   79  273-354     2-89  (89)
 14 smart00493 TOPRIM topoisomeras  98.8 2.1E-08 5.3E-13   96.9   6.2   68  273-340     2-73  (76)
 15 PRK04031 DNA primase; Provisio  98.4 1.8E-06 4.6E-11   79.1   8.8  102  270-385   167-269 (420)
 16 TIGR00646 MG010 DNA primase ho  98.4   1E-06 2.6E-11   81.4   7.5  197  124-375    11-212 (218)
 17 COG4643 Uncharacterized protei  98.3   4E-05   1E-09   66.7  13.5  266   42-375    34-310 (366)
 18 cd00188 TOPRIM Topoisomerase-p  97.9 3.4E-05 8.8E-10   67.4   6.8   67  273-339     2-72  (83)
 19 cd01027 TOPRIM_RNase_M5_like T  97.8 4.3E-05 1.1E-09   66.5   5.9   66  272-337     2-68  (81)
 20 pfam10410 DnaB_bind DnaB-helic  97.8 3.9E-05 9.9E-10   66.9   5.5   56  381-436     1-56  (59)
 21 PRK06904 replicative DNA helic  97.5   0.022 5.5E-07   41.6  15.3   48  214-288   220-267 (472)
 22 LOAD_Toprim consensus           97.4 0.00077   2E-08   55.0   7.4   66  273-338     2-70  (98)
 23 PRK08760 replicative DNA helic  97.3   0.036 9.1E-07   39.6  15.2   48  214-288   228-275 (476)
 24 TIGR03600 phage_DnaB phage rep  97.3   0.032 8.1E-07   40.1  14.3   47  214-287   193-239 (421)
 25 PRK08006 replicative DNA helic  97.1    0.05 1.3E-06   38.3  15.2   48  214-288   223-270 (471)
 26 PRK07004 replicative DNA helic  97.1   0.051 1.3E-06   38.2  13.9   48  214-288   212-259 (460)
 27 PRK05748 replicative DNA helic  97.0   0.067 1.7E-06   37.1  14.1   48  214-288   202-249 (448)
 28 PRK08082 consensus              96.9   0.052 1.3E-06   38.1  12.6   48  214-288   202-249 (453)
 29 PRK08694 consensus              96.9   0.074 1.9E-06   36.7  14.5   49  213-288   216-264 (468)
 30 smart00766 DnaG_DnaB_bind DNA   96.9   0.033 8.5E-07   39.9  11.4  109  484-603     1-109 (125)
 31 COG1658 Small primase-like pro  96.9  0.0019 4.8E-08   51.4   4.8   63  271-333     9-74  (127)
 32 PRK08840 replicative DNA helic  96.8   0.085 2.2E-06   36.2  14.1   47  214-287   216-262 (464)
 33 PRK04017 hypothetical protein;  96.8  0.0099 2.5E-07   44.7   8.2   82  270-366    21-103 (132)
 34 PRK07263 consensus              96.7   0.099 2.5E-06   35.5  13.9   70  214-311   202-277 (453)
 35 PRK07773 replicative DNA helic  96.7     0.1 2.5E-06   35.5  13.5   23  231-253   421-444 (868)
 36 PRK06321 replicative DNA helic  96.7     0.1 2.6E-06   35.4  14.1   71  214-312   225-301 (472)
 37 PRK05636 replicative DNA helic  96.6    0.11 2.9E-06   35.1  14.9   10  156-165     8-17  (507)
 38 PRK08506 replicative DNA helic  96.6    0.12 3.1E-06   34.7  12.8   69  214-311   192-266 (473)
 39 PRK05595 replicative DNA helic  96.5    0.13 3.3E-06   34.4  13.9   69  214-310   200-274 (444)
 40 pfam08278 DnaG_DnaB_bind DNA p  96.4    0.16   4E-06   33.7  14.0  109  484-603     2-110 (126)
 41 PRK09165 replicative DNA helic  96.2    0.18 4.6E-06   33.1  14.7   48   52-99     41-95  (484)
 42 COG3593 Predicted ATP-dependen  96.1   0.086 2.2E-06   36.1   9.5   85  243-337   378-471 (581)
 43 COG0305 DnaB Replicative DNA h  96.0    0.23 5.8E-06   32.2  15.2   49   52-100    35-90  (435)
 44 pfam00772 DnaB DnaB-like helic  95.9   0.069 1.8E-06   37.0   8.3   65  482-546     7-71  (103)
 45 PRK06749 replicative DNA helic  95.4    0.36 9.2E-06   30.4  12.8   47  214-288   185-231 (428)
 46 TIGR00334 primaseG_like primas  90.8    0.52 1.3E-05   28.9   4.8   65  272-336     3-69  (176)
 47 PRK05301 pyrroloquinoline quin  90.6     1.6 4.2E-05   24.3   7.3   85  270-357    70-169 (375)
 48 pfam08273 Prim_Zn_Ribbon Zinc-  89.8    0.27 6.9E-06   31.5   2.7   33   40-73      3-38  (39)
 49 cd01026 TOPRIM_OLD TOPRIM_OLD:  89.1    0.79   2E-05   27.3   4.6   55  272-328     4-69  (97)
 50 PRK13758 anaerobic sulfatase-m  89.0     1.2 3.2E-05   25.5   5.5   72  290-364    92-179 (370)
 51 KOG2373 consensus               86.2     2.9 7.3E-05   22.1   7.4  133  230-383    94-229 (514)
 52 COG0641 AslB Arylsulfatase reg  85.7       3 7.7E-05   21.9   6.7  131  289-433    89-241 (378)
 53 PRK09897 hypothetical protein;  85.3     2.1 5.5E-05   23.3   5.1  191  142-398    79-297 (535)
 54 PRK13745 anaerobic sulfatase-m  81.1     3.7 9.5E-05   21.1   4.9   70  291-363   102-187 (412)
 55 TIGR03470 HpnH hopanoid biosyn  80.3     4.6 0.00012   20.3   7.9   89  271-363    80-181 (318)
 56 pfam03291 Pox_MCEL mRNA cappin  80.3    0.71 1.8E-05   27.7   1.0   75   12-100     5-94  (327)
 57 PRK12383 putative mutase; Prov  79.3     4.9 0.00012   20.0   6.5  140  213-360   178-344 (406)
 58 TIGR00678 holB DNA polymerase   76.1     5.2 0.00013   19.7   4.4   67  294-363    68-165 (216)
 59 smart00778 Prim_Zn_Ribbon Zinc  74.4     2.4   6E-05   22.9   2.3   30   40-70      3-34  (37)
 60 KOG2593 consensus               73.8     2.7 6.8E-05   22.4   2.4   48   43-95    131-182 (436)
 61 PRK00133 metG methionyl-tRNA s  73.2     3.4 8.6E-05   21.5   2.8   60  355-414   334-397 (666)
 62 TIGR00396 leuS_bact leucyl-tRN  72.1     5.3 0.00013   19.7   3.6   56  354-416   669-725 (916)
 63 PRK00076 recR recombination pr  71.1     7.4 0.00019   18.3   7.1   81  271-356    78-172 (197)
 64 TIGR03655 anti_R_Lar restricti  71.0       4  0.0001   20.8   2.8   42   42-91      3-48  (53)
 65 PRK00390 leuS leucyl-tRNA synt  70.7     7.5 0.00019   18.3   4.8   18  206-223   231-248 (822)
 66 TIGR01418 PEP_synth phosphoeno  70.0     7.7  0.0002   18.1   6.5  281   87-435   294-648 (877)
 67 TIGR00014 arsC arsenate reduct  70.0     3.8 9.6E-05   21.0   2.5   48  136-186    11-59  (114)
 68 TIGR02478 6PF1K_euk 6-phosphof  68.3       6 0.00015   19.2   3.2   15  321-335   582-596 (777)
 69 pfam01921 tRNA-synt_1f tRNA sy  68.0     8.2 0.00021   17.9   3.9   25  356-380   286-310 (355)
 70 TIGR01059 gyrB DNA gyrase, B s  67.5     8.5 0.00022   17.8   5.8   99  286-396   477-582 (818)
 71 COG2604 Uncharacterized protei  66.4     8.2 0.00021   17.9   3.6   55  295-366   229-284 (594)
 72 TIGR01430 aden_deam adenosine   66.3     8.1 0.00021   17.9   3.6   68   78-146     8-80  (346)
 73 TIGR01696 deoB phosphopentomut  66.1     5.6 0.00014   19.5   2.7   85  277-361   246-352 (404)
 74 TIGR02482 PFKA_ATP 6-phosphofr  65.4       7 0.00018   18.5   3.1   29  271-300    92-124 (302)
 75 COG2137 OraA Uncharacterized p  64.9     9.4 0.00024   17.4   4.3   45  498-545    54-98  (174)
 76 TIGR00600 rad2 DNA excision re  64.6     3.8 9.6E-05   21.0   1.6   22    3-24    265-286 (1127)
 77 cd01025 TOPRIM_recR TOPRIM_rec  64.2     9.7 0.00025   17.2   6.6   79  273-356     2-94  (112)
 78 COG5440 Uncharacterized conser  64.1       7 0.00018   18.5   2.9   57  294-365    56-113 (161)
 79 PRK13738 conjugal transfer pil  63.8     9.8 0.00025   17.2   4.0   82  187-280    75-156 (210)
 80 PRK13844 recombination protein  63.5     9.9 0.00025   17.1   7.2   80  271-356    82-175 (200)
 81 TIGR00020 prfB peptide chain r  62.2      10 0.00026   17.0  11.2   95  535-633    19-121 (373)
 82 pfam04273 DUF442 Putative phos  60.9      11 0.00028   16.8   7.1   84  292-384     6-92  (110)
 83 PRK02853 hypothetical protein;  60.9     9.1 0.00023   17.5   3.0   81  203-322    63-145 (161)
 84 TIGR01980 sufB FeS assembly pr  60.1     5.3 0.00013   19.7   1.7   34  299-339    18-51  (469)
 85 pfam06840 DUF1241 Protein of u  58.3      10 0.00027   16.9   3.0   28  514-541    31-58  (154)
 86 KOG3578 consensus               57.2     3.3 8.5E-05   21.5   0.3   35   68-102    79-125 (1058)
 87 pfam00133 tRNA-synt_1 tRNA syn  56.9     7.9  0.0002   18.0   2.1   19  205-223   189-208 (606)
 88 TIGR00658 orni_carb_tr ornithi  56.8      12  0.0003   16.5   3.0   70  305-380   147-222 (341)
 89 pfam01113 DapB_N Dihydrodipico  56.7     7.4 0.00019   18.3   2.0   42  278-321    76-118 (122)
 90 pfam01458 UPF0051 Uncharacteri  56.6     6.9 0.00018   18.6   1.8   12  357-368   204-217 (230)
 91 TIGR01981 sufD FeS assembly pr  56.0     6.3 0.00016   19.0   1.5   69  345-422   324-395 (397)
 92 PRK00578 prfB peptide chain re  55.6      13 0.00033   16.1  11.5   16  198-215   120-135 (367)
 93 pfam09133 SANTA SANTA (SANT As  55.6     5.1 0.00013   19.8   1.0   26  270-295    48-73  (93)
 94 TIGR01286 nifK nitrogenase mol  54.6     3.4 8.6E-05   21.5  -0.1  226  115-411   128-389 (526)
 95 pfam03428 RP-C Replication pro  54.3      11 0.00028   16.7   2.5   33  181-221    93-126 (177)
 96 PRK12366 replication factor A;  54.1      14 0.00035   15.9   3.1   14   88-101    41-54  (649)
 97 pfam04407 DUF531 Protein of un  54.0      14 0.00035   15.9   5.1   59  318-379     7-76  (174)
 98 TIGR02082 metH methionine synt  53.9     8.1 0.00021   18.0   1.8  262   64-378    33-372 (1265)
 99 PRK12268 methionyl-tRNA synthe  53.5      14 0.00035   15.8   6.1   27  354-380   340-366 (558)
100 PHA02130 hypothetical protein   53.4       4  0.0001   20.7   0.2   11   38-48     43-53  (81)
101 KOG2767 consensus               53.2     5.9 0.00015   19.2   1.0   39  257-295    92-130 (400)
102 pfam08209 Sgf11 Sgf11 (transcr  53.2     4.8 0.00012   20.1   0.5   72    5-81     13-90  (99)
103 TIGR02684 dnstrm_HI1420 probab  52.9      14 0.00036   15.8   3.4   52  122-179    15-72  (91)
104 PRK12300 leuS leucyl-tRNA synt  52.8      14 0.00036   15.7   5.7   33  355-387   578-611 (888)
105 COG0289 DapB Dihydrodipicolina  52.4      14 0.00036   15.7   4.2   38  278-317    80-118 (266)
106 pfam01780 Ribosomal_L37ae Ribo  52.3     8.2 0.00021   17.9   1.6   26   41-69     36-61  (90)
107 PRK13824 replication initiatio  52.2      12  0.0003   16.4   2.4   33  181-221   105-138 (404)
108 pfam11672 DUF3268 Protein of u  52.0      14 0.00037   15.6   4.7   28   43-70      5-40  (102)
109 cd03770 SR_TndX_transposase Se  50.8      15 0.00038   15.5   3.9   64  296-361    46-113 (140)
110 TIGR01215 minE cell division t  50.6     8.7 0.00022   17.7   1.5   20    5-26     38-57  (89)
111 TIGR00464 gltX_bact glutamyl-t  50.5      13 0.00034   16.0   2.4   33  301-335   232-271 (513)
112 pfam03776 MinE Septum formatio  50.4      11 0.00028   16.7   2.0   23    5-29     23-45  (69)
113 pfam01641 SelR SelR domain. Me  50.4     8.3 0.00021   17.9   1.4   34   24-70     13-46  (124)
114 TIGR03297 Ppyr-DeCO2ase phosph  50.3     8.1 0.00021   18.0   1.3   40  314-356   238-277 (361)
115 pfam06793 UPF0262 Uncharacteri  50.2      11 0.00028   16.8   2.0   50  272-322    92-143 (159)
116 pfam01194 RNA_pol_N RNA polyme  50.1      13 0.00033   16.2   2.3   16   63-78      6-22  (60)
117 PRK01544 bifunctional N5-gluta  50.0      12 0.00031   16.3   2.2  109  249-363   163-274 (503)
118 pfam02631 RecX RecX family. Re  49.7      16  0.0004   15.4   4.4   50  496-547     9-58  (121)
119 KOG0183 consensus               49.7      15 0.00038   15.5   2.6   69  245-334    14-83  (249)
120 COG1644 RPB10 DNA-directed RNA  49.4      14 0.00037   15.7   2.5   30   63-92      6-38  (63)
121 pfam07057 TraI DNA helicase Tr  49.1      14 0.00036   15.8   2.4   22  205-226    93-114 (126)
122 pfam05129 Elf1 Transcription e  49.0      11 0.00027   16.8   1.8   30   41-70     18-50  (74)
123 KOG1422 consensus               48.6     6.7 0.00017   18.7   0.7   53  271-325    18-70  (221)
124 TIGR03364 HpnW_proposed FAD de  48.6      16 0.00041   15.2   4.1   14   87-100    65-78  (365)
125 KOG0435 consensus               48.5      16 0.00041   15.2   3.0  107  278-414   562-677 (876)
126 PRK00750 lysK lysyl-tRNA synth  48.1      16 0.00042   15.2   4.1   32  356-387   293-325 (513)
127 COG0353 RecR Recombinational D  47.5      17 0.00042   15.1   7.6   81  270-356    78-173 (198)
128 PRK05508 methionine sulfoxide   47.1      11 0.00029   16.7   1.6   22   57-80     29-50  (119)
129 PRK12446 N-acetylglucosaminyl   46.9      17 0.00043   15.0   4.4   66  246-324    75-147 (352)
130 KOG0856 consensus               46.8      12  0.0003   16.5   1.7   11   58-68     51-61  (146)
131 COG1422 Predicted membrane pro  46.8      17 0.00043   15.0   8.2   37  587-623    73-109 (201)
132 PRK04016 DNA-directed RNA poly  46.7      16  0.0004   15.3   2.3   15   63-77      6-21  (63)
133 pfam05991 DUF901 Protein of un  46.4      17 0.00044   15.0   3.4   43  315-366    44-86  (166)
134 PTZ00255 60S ribosomal protein  46.1      11 0.00029   16.6   1.5   26   41-69     37-62  (90)
135 PRK06667 motB flagellar motor   46.1      15 0.00039   15.4   2.2   23  271-293   160-183 (254)
136 PRK06163 hypothetical protein;  46.0      11 0.00028   16.8   1.4   60  294-357    55-114 (202)
137 cd01575 PBP1_GntR Ligand-bindi  45.8      17 0.00045   14.9   4.5   50  318-378    95-145 (268)
138 PRK03976 rpl37ae 50S ribosomal  45.2      14 0.00035   15.9   1.8   25   41-69     37-62  (90)
139 cd07048 BMC_PduB_repeat2 1,2-p  45.0      18 0.00046   14.8   2.4   28  297-335    35-62  (70)
140 cd01320 ADA Adenosine deaminas  44.9      18 0.00046   14.8   3.8   28   79-106    10-37  (325)
141 COG1198 PriA Primosomal protei  44.8      18 0.00046   14.8   3.3   97  290-403   268-382 (730)
142 cd00764 Eukaryotic_PFK Phospho  44.7      18 0.00046   14.8   3.2   60  289-351   353-425 (762)
143 pfam00782 DSPc Dual specificit  44.5      18 0.00046   14.7   4.0   40   61-100    75-116 (131)
144 pfam08856 DUF1826 Protein of u  44.4      12 0.00031   16.3   1.5   27  213-239   157-184 (196)
145 TIGR00665 DnaB replicative DNA  44.2      18 0.00047   14.7  13.1   27  395-421   354-380 (465)
146 PRK00296 minE cell division to  44.1      18 0.00047   14.7   2.4   19  516-534    40-58  (85)
147 COG1205 Distinct helicase fami  43.9      17 0.00043   15.1   2.1   17  356-373   421-437 (851)
148 COG0646 MetH Methionine syntha  43.9      17 0.00044   14.9   2.2   53   79-131    45-105 (311)
149 KOG4717 consensus               43.5      19 0.00048   14.6   4.4   26   56-81     87-112 (864)
150 KOG3497 consensus               42.9      11 0.00029   16.7   1.1   25   62-86      5-30  (69)
151 smart00195 DSPc Dual specifici  42.6      19 0.00049   14.5   4.1   37   61-97     82-120 (138)
152 TIGR01058 parE_Gpos DNA topois  42.5      19 0.00049   14.5   3.4   13  343-355   322-335 (655)
153 cd03371 TPP_PpyrDC Thiamine py  42.5      14 0.00036   15.7   1.6   58  294-356    46-104 (188)
154 COG0229 Conserved domain frequ  42.3      16 0.00042   15.1   1.9   12   58-69     39-50  (140)
155 pfam06587 DUF1137 Protein of u  42.1      11 0.00029   16.6   1.0   20   46-65     41-71  (159)
156 cd01971 Nitrogenase_VnfN_like   41.9      20  0.0005   14.4   4.1   10  250-259   134-143 (427)
157 PRK01008 queuine tRNA-ribosylt  41.7      20  0.0005   14.4   6.1   67  302-370   140-219 (372)
158 pfam04405 ScdA_N Domain of Unk  41.6      17 0.00042   15.1   1.8   35  151-185    16-50  (56)
159 PRK05729 valS valyl-tRNA synth  41.3      20 0.00051   14.4   2.2   34  354-387   528-562 (877)
160 cd01987 USP_OKCHK USP domain i  41.0      20 0.00051   14.3   4.8   35  316-353     1-35  (124)
161 pfam04723 GRDA Glycine reducta  40.8      14 0.00037   15.7   1.4   71  278-363    46-126 (150)
162 cd03362 TOPRIM_TopoIA_TopoIII   40.5      20 0.00052   14.3   3.5   36  303-338    85-123 (151)
163 pfam09334 tRNA-synt_1g tRNA sy  40.2      21 0.00053   14.2   5.0   25  355-379   331-356 (388)
164 PRK10026 arsenate reductase; P  40.0      19 0.00047   14.6   1.8   48  136-186    14-61  (141)
165 PRK00726 murG N-acetylglucosam  39.8      21 0.00053   14.2   4.0   65  246-323    75-146 (359)
166 KOG2026 consensus               39.8      17 0.00044   14.9   1.7   26   43-69     24-49  (442)
167 PHA00202 DNA replication initi  39.7     6.9 0.00018   18.6  -0.4   21   67-87     31-51  (379)
168 COG0426 FpaA Uncharacterized f  39.7      21 0.00054   14.2   7.4   63  299-364   223-293 (388)
169 COG2139 RPL21A Ribosomal prote  39.6      19 0.00048   14.6   1.8   36  194-238    49-89  (98)
170 COG2719 SpoVR Uncharacterized   39.4      21 0.00053   14.2   2.0   17   85-101    18-34  (495)
171 cd01525 RHOD_Kc Member of the   39.2      21 0.00054   14.1   4.3   61  291-358    33-101 (105)
172 TIGR00807 s1 malonate transpor  39.2      14 0.00036   15.7   1.2   26  140-170    46-71  (127)
173 COG0535 Predicted Fe-S oxidore  39.2      21 0.00054   14.1   7.3   95  271-368    73-187 (347)
174 PRK13265 glycine/sarcosine/bet  39.1      16 0.00041   15.3   1.4   71  278-363    47-127 (157)
175 cd01724 Sm_D1 The eukaryotic S  39.1      13 0.00033   16.1   0.9   22  344-365    60-81  (90)
176 PRK12655 fructose-6-phosphate   39.0      21 0.00055   14.1   2.7   74   77-150    31-105 (220)
177 PRK05563 DNA polymerase III su  38.8      22 0.00055   14.0  10.9  119  277-417   210-343 (541)
178 PRK05431 seryl-tRNA synthetase  38.5      22 0.00056   14.0   9.4   14  240-253   195-208 (422)
179 KOG1903 consensus               38.5      12 0.00031   16.3   0.7   33  341-373    38-71  (217)
180 TIGR00337 PyrG CTP synthase; I  38.4      20 0.00051   14.3   1.8   90   70-163   151-279 (571)
181 KOG2924 consensus               38.3     1.5 3.8E-05   24.7  -4.0  161   63-239    34-219 (366)
182 pfam01983 CofC Guanylyl transf  38.3      22 0.00056   14.0   2.6   27  302-329   101-129 (217)
183 COG2971 Predicted N-acetylgluc  38.3      22 0.00056   14.0   4.8   28  209-241    20-48  (301)
184 TIGR02279 PaaC-3OHAcCoADH 3-hy  38.1      14 0.00037   15.7   1.0   24   39-62    175-198 (508)
185 TIGR00422 valS valyl-tRNA synt  38.0      20  0.0005   14.4   1.7  121   38-172   285-424 (970)
186 COG1997 RPL43A Ribosomal prote  37.8      22 0.00057   13.9   2.2   26   41-70     36-62  (89)
187 TIGR03652 FeS_repair_RIC iron-  37.8      21 0.00053   14.2   1.8   12  355-366    37-48  (216)
188 PRK10992 cell morphogenesis/ce  37.7      21 0.00054   14.1   1.8   11  355-365    44-54  (220)
189 PRK09358 adenosine deaminase;   37.5      22 0.00057   13.9   5.4   27   79-105    17-43  (333)
190 PRK13782 phosphocarrier protei  37.2      23 0.00058   13.9   5.4   62  306-377    22-83  (85)
191 KOG2802 consensus               37.2      13 0.00033   16.1   0.7   18   47-68     61-78  (503)
192 COG0018 ArgS Arginyl-tRNA synt  37.2      23 0.00058   13.9  15.8   49  482-531   491-539 (577)
193 KOG2164 consensus               37.2      13 0.00033   16.1   0.7   17  298-314   204-220 (513)
194 cd02001 TPP_ComE_PpyrDC Thiami  36.8      16 0.00042   15.2   1.1   40  315-357    59-98  (157)
195 PRK05627 bifunctional riboflav  36.6      23 0.00058   13.8   1.9   39  291-333   230-269 (303)
196 COG0066 LeuD 3-isopropylmalate  36.5      21 0.00053   14.2   1.7   84  207-299     1-98  (191)
197 pfam08271 TF_Zn_Ribbon TFIIB z  36.4      23 0.00059   13.8   2.5   26   42-69      2-27  (40)
198 TIGR00615 recR recombination p  36.3      23 0.00059   13.7   6.6   83  269-356    79-182 (205)
199 COG1794 RacX Aspartate racemas  36.2      23  0.0006   13.7   2.8   50  286-336   112-161 (230)
200 pfam03405 FA_desaturase_2 Fatt  36.1      23  0.0006   13.7   4.0   14  300-313   108-121 (330)
201 PTZ00317 malic enzyme; Provisi  36.0      24  0.0006   13.7   2.6   66  289-356   235-303 (570)
202 PRK13182 racA polar chromosome  35.9      24  0.0006   13.7   6.9   49  590-641    99-147 (178)
203 PRK00222 methionine sulfoxide   35.8      19 0.00049   14.5   1.4   52   23-89     18-73  (141)
204 PRK11020 hypothetical protein;  35.7      24 0.00061   13.7   7.5   39  594-632    13-51  (118)
205 PRK10076 pyruvate formate lyas  35.7      24 0.00061   13.7   7.3   80  285-365    62-149 (213)
206 TIGR01969 minD_arch cell divis  35.4      15 0.00038   15.5   0.8  122  290-433    13-160 (258)
207 pfam08348 PAS_6 YheO-like PAS   35.2      24 0.00061   13.6   4.5   55  158-221    46-100 (118)
208 pfam00500 Late_protein_L1 L1 (  35.2      24 0.00061   13.6   2.2   24  198-221    90-116 (503)
209 TIGR00963 secA preprotein tran  35.1      24 0.00062   13.6   2.0   91  187-313   348-454 (904)
210 PRK01143 rpl11p 50S ribosomal   35.0      24 0.00062   13.6   3.7   63  301-377    96-159 (163)
211 TIGR00354 polC DNA polymerase   35.0      18 0.00047   14.7   1.2   59   34-98    685-749 (1173)
212 pfam06246 Isy1 Isy1-like splic  34.7      24 0.00062   13.5   4.6   53  394-446    42-95  (253)
213 TIGR00010 TIGR00010 hydrolase,  34.6      17 0.00042   15.1   0.9   21  282-303    22-43  (269)
214 PRK13520 L-tyrosine decarboxyl  34.5      25 0.00063   13.5   2.1   50  278-327   140-196 (375)
215 PRK00283 xerD site-specific ty  34.5      22 0.00055   14.0   1.5   40  139-183     8-48  (296)
216 COG5328 Uncharacterized protei  34.3      23 0.00059   13.8   1.6  106  178-322    33-144 (160)
217 TIGR01426 MGT glycosyltransfer  34.2      25 0.00063   13.5   2.3  103  293-429   262-368 (429)
218 PRK09490 metH B12-dependent me  33.8      24 0.00061   13.6   1.6   63   64-131    48-118 (1229)
219 pfam03393 Pneumo_matrix Pneumo  33.7      16  0.0004   15.3   0.6   16  176-191    10-25  (252)
220 TIGR03287 methan_mark_16 putat  33.6      16 0.00041   15.3   0.7   12  302-313   253-264 (391)
221 PTZ00124 adenosine deaminase;   33.5      25 0.00065   13.4   4.2  125   55-188    10-148 (362)
222 pfam04392 ABC_sub_bind ABC tra  33.4      26 0.00065   13.4   6.1   81  274-357    82-171 (292)
223 KOG3214 consensus               33.4      23 0.00059   13.7   1.5   54   39-94     22-83  (109)
224 cd03372 TPP_ComE Thiamine pyro  32.8      26 0.00066   13.3   4.2   59  294-357    40-98  (179)
225 pfam05566 Pox_vIL-18BP Orthopo  32.8      24 0.00062   13.6   1.5   35   41-75     13-50  (126)
226 TIGR00357 TIGR00357 methionine  32.8      21 0.00054   14.1   1.2   15   55-69     34-48  (135)
227 COG1859 KptA RNA:NAD 2'-phosph  32.6      26 0.00067   13.3   4.4   65  159-234    57-123 (211)
228 COG3454 Metal-dependent hydrol  32.4      26 0.00067   13.3   1.6   11  397-407   189-199 (377)
229 KOG0257 consensus               32.4      26 0.00067   13.3   3.5  104  295-412   182-295 (420)
230 LOAD_USPA consensus             32.4      26 0.00067   13.2   4.7   38  315-355     1-38  (135)
231 PRK08645 bifunctional homocyst  32.0      27 0.00068   13.2   3.9   78  285-364   259-344 (608)
232 pfam00949 Peptidase_S7 Peptida  32.0      27 0.00068   13.2   1.7   18  209-226   118-135 (150)
233 pfam10911 DUF2717 Protein of u  31.8      27 0.00068   13.2   1.7   12  170-181    41-52  (77)
234 cd00817 ValRS_core This is the  31.7      27 0.00069   13.2   2.9   27  355-381   331-357 (363)
235 PRK13804 ileS isoleucyl-tRNA s  31.7      27 0.00069   13.2   4.5   27  354-380   642-668 (966)
236 KOG2361 consensus               31.6      24 0.00061   13.6   1.3   16  330-345   161-176 (264)
237 pfam03976 PPK2 Polyphosphate k  31.6      27 0.00069   13.2   3.5   42  294-336    10-52  (229)
238 COG1206 Gid NAD(FAD)-utilizing  31.6      19 0.00049   14.5   0.8  146  202-366   159-311 (439)
239 cd03785 GT1_MurG MurG is an N-  31.4      27 0.00069   13.1   3.7   66  246-324    73-145 (350)
240 PRK04023 DNA polymerase II lar  31.4      26 0.00066   13.3   1.4   19   83-102   453-471 (1128)
241 TIGR01943 rnfA electron transp  31.2      13 0.00034   16.0  -0.1   13  397-409    37-49  (193)
242 PRK05550 bifunctional methioni  30.9      27 0.00068   13.2   1.4   42   24-80     12-53  (284)
243 TIGR02918 TIGR02918 conserved   30.9      17 0.00043   15.0   0.4  253  158-426    54-402 (511)
244 TIGR03329 Phn_aa_oxid putative  30.8      28 0.00071   13.0   3.9   19   38-56     33-53  (460)
245 TIGR00300 TIGR00300 conserved   30.4      19  0.0005   14.5   0.7   34  278-313   238-288 (418)
246 KOG2518 consensus               30.4      28 0.00072   13.0   2.8   27  284-313   219-245 (556)
247 cd00250 CAS_like Clavaminic ac  30.3      28 0.00072   13.0   2.9   62  207-288    77-140 (262)
248 TIGR01389 recQ ATP-dependent D  30.1      23 0.00059   13.8   1.0   21  169-190   242-262 (607)
249 TIGR02431 pcaR_pcaU beta-ketoa  29.9      22 0.00056   14.0   0.9   19  415-433    78-96  (252)
250 cd00762 NAD_bind_malic_enz NAD  29.9      29 0.00073   12.9   2.7   39   60-98     26-70  (254)
251 cd00763 Bacterial_PFK Phosphof  29.9      29 0.00073   12.9   3.9   16  348-363   185-201 (317)
252 PRK06850 hypothetical protein;  29.8      16  0.0004   15.3   0.1   15  212-226   143-158 (488)
253 TIGR02483 PFK_mixed phosphofru  29.6      25 0.00065   13.4   1.2   13  323-335     9-21  (339)
254 CHL00010 infA translation init  29.6      29 0.00074   12.9   1.5   19  197-215    58-76  (78)
255 COG2957 Peptidylarginine deimi  29.3      29 0.00074   12.8   4.6   27  349-377   199-225 (346)
256 COG1180 PflA Pyruvate-formate   29.3      29 0.00074   12.8   6.6  120  271-394    92-223 (260)
257 KOG2168 consensus               29.3      24  0.0006   13.7   1.0   27  618-644   795-821 (835)
258 cd03361 TOPRIM_TopoIA_RevGyr T  29.3      29 0.00074   12.8   3.9   36  304-339   106-144 (170)
259 TIGR02201 heptsyl_trn_III lipo  29.0      29 0.00075   12.8   1.4   78  270-377   133-211 (347)
260 pfam02969 TAF TATA box binding  28.9      30 0.00075   12.8   5.2   48   85-133     5-53  (66)
261 PRK06645 DNA polymerase III su  28.6      30 0.00076   12.7   5.6   73  276-366   218-297 (507)
262 cd03363 TOPRIM_TopoIA_TopoI TO  28.5      30 0.00076   12.7   3.8   33  305-337    64-96  (123)
263 PRK05362 phosphopentomutase; P  28.3      30 0.00077   12.7   7.4   88  271-360   236-338 (393)
264 pfam12324 HTH_15 Helix-turn-he  28.2      24 0.00062   13.6   0.9   22  518-539    25-46  (77)
265 PRK00048 dihydrodipicolinate r  28.2      30 0.00077   12.7   4.3   42  278-321    80-122 (265)
266 PRK13208 valS valyl-tRNA synth  28.0      30 0.00078   12.7   5.8   31  354-384   544-574 (809)
267 TIGR00539 hemN_rel putative ox  28.0      20 0.00051   14.3   0.4   39  275-315    95-140 (371)
268 cd00293 USP_Like Usp: Universa  27.6      31 0.00079   12.6   4.9   35  316-353     1-35  (130)
269 TIGR00538 hemN oxygen-independ  27.5      31 0.00079   12.6   1.9   12  301-312   117-128 (462)
270 PRK01287 xerC site-specific ty  27.4      28 0.00072   13.0   1.1   34  140-178    30-63  (361)
271 PRK01611 argS arginyl-tRNA syn  27.1      31  0.0008   12.5  15.1   47  481-528   483-529 (570)
272 KOG4657 consensus               26.8      32 0.00081   12.5   3.4   63  199-261   151-220 (246)
273 TIGR02727 MTHFS_bact 5,10-meth  26.8      17 0.00043   15.1  -0.2   18  205-222   118-137 (183)
274 pfam06447 consensus             26.8      32 0.00081   12.5   8.6   13  271-283   253-265 (407)
275 pfam07282 Transposase_35 Putat  26.7      32 0.00081   12.5   2.3   28   42-72     30-57  (69)
276 pfam09445 Methyltransf_15 RNA   26.7      22 0.00056   14.0   0.4   15   65-79      7-21  (165)
277 COG4888 Uncharacterized Zn rib  26.7      32 0.00081   12.5   1.9   28   43-70     25-55  (104)
278 cd05312 NAD_bind_1_malic_enz N  26.6      32 0.00081   12.5   2.8   38  280-317    97-134 (279)
279 pfam06945 DUF1289 Protein of u  26.6      32 0.00082   12.5   1.7   13   63-75     16-28  (56)
280 TIGR02329 propionate_PrpR prop  26.6      32 0.00082   12.5   1.7   12  212-223   214-225 (658)
281 pfam09332 Mcm10 Mcm10 replicat  26.4      32 0.00082   12.4   1.7   12  626-637   229-240 (346)
282 KOG0340 consensus               26.4      32 0.00082   12.4   5.2   24  357-380   333-356 (442)
283 PRK10850 phosphohistidinoprote  26.4      32 0.00082   12.4   6.0   62  306-377    22-83  (85)
284 pfam07014 Hs1pro-1_C Hs1pro-1   26.4      29 0.00075   12.8   1.0   46  334-388    91-136 (261)
285 KOG0177 consensus               26.2      32 0.00083   12.4   1.8   48   46-101    28-76  (200)
286 KOG0456 consensus               26.2      31  0.0008   12.6   1.1   32  141-172   208-239 (559)
287 PRK00380 panC pantoate--beta-a  26.0      33 0.00083   12.4   2.7   59  294-355    25-93  (283)
288 cd01816 Raf_RBD The Raf serine  25.9      21 0.00054   14.1   0.2   33  143-175    29-66  (74)
289 cd00807 Gln_GluRS_non_core Glu  25.9      33 0.00084   12.4   1.8   25  289-313   120-145 (238)
290 COG4230 Delta 1-pyrroline-5-ca  25.8      27  0.0007   13.1   0.8   16  293-308   353-368 (769)
291 pfam00944 Peptidase_S3 Alphavi  25.7      33 0.00084   12.4   1.5   23  186-220   100-122 (157)
292 PRK09040 hypothetical protein;  25.6      28  0.0007   13.1   0.8   23  270-292   121-145 (215)
293 cd01532 4RHOD_Repeat_1 Member   25.6      33 0.00085   12.3   2.1   56  289-351    25-83  (92)
294 COG1915 Uncharacterized conser  25.5      15 0.00038   15.6  -0.6   25  278-304   226-254 (415)
295 cd06325 PBP1_ABC_uncharacteriz  25.5      33 0.00085   12.3   5.7   83  274-362    83-174 (281)
296 KOG0164 consensus               25.4      33 0.00085   12.3   2.6   61  269-331   223-293 (1001)
297 smart00828 PKS_MT Methyltransf  25.4      33 0.00084   12.4   1.1   17   64-80      5-21  (224)
298 cd01196 INT_VanD VanD integras  25.4      33 0.00083   12.4   1.1   18  141-158     2-19  (263)
299 pfam05480 Staph_haemo Staphylo  25.4      30 0.00076   12.8   0.9   25  278-302     2-27  (43)
300 COG3673 Uncharacterized conser  25.4      33 0.00085   12.3   1.3   23   43-66     16-38  (423)
301 KOG2730 consensus               25.2      34 0.00086   12.3   1.3   16  275-290   147-162 (263)
302 KOG4672 consensus               25.1      34 0.00086   12.3   1.6   14  167-180   102-115 (487)
303 pfam03811 Ins_element1 Inserti  25.1      34 0.00086   12.3   2.7   28   42-70      7-38  (88)
304 pfam06819 Arc_PepC Archaeal Pe  25.0      27  0.0007   13.1   0.7   24  292-315    78-101 (111)
305 cd00687 Terpene_cyclase_nonpla  25.0      34 0.00087   12.2   3.9   31  284-314    36-66  (303)
306 PRK00443 nagB glucosamine-6-ph  24.9      34 0.00087   12.2   4.0   16  313-328   231-246 (264)
307 PRK08174 DNA topoisomerase III  24.9      34 0.00087   12.2   3.5   13  481-493   487-499 (670)
308 PRK06674 DNA polymerase III su  24.9      34 0.00087   12.2  12.5   77  277-375   210-293 (563)
309 pfam09393 DUF2001 Protein of u  24.9      30 0.00077   12.7   0.8   35  328-362    66-100 (141)
310 COG0172 SerS Seryl-tRNA synthe  24.8      34 0.00087   12.2   9.8   10  288-297   190-199 (429)
311 PRK05580 primosome assembly pr  24.7      34 0.00087   12.2   2.5   20  293-312   240-259 (699)
312 COG4963 CpaE Flp pilus assembl  24.7      34 0.00088   12.2   8.5   31  354-385   191-221 (366)
313 TIGR01326 OAH_OAS_sulfhy O-ace  24.7      18 0.00046   14.8  -0.3   40  343-385   119-163 (434)
314 PRK09401 reverse gyrase; Revie  24.7      34 0.00088   12.2   6.7   37  305-341   707-746 (1176)
315 cd00127 DSPc Dual specificity   24.6      34 0.00088   12.2   3.5   11  285-295    22-32  (139)
316 COG0125 Tmk Thymidylate kinase  24.5      34 0.00088   12.2   5.0   37  318-356     5-42  (208)
317 COG4847 Uncharacterized protei  24.3      14 0.00035   15.9  -1.0   18   61-78      6-26  (103)
318 pfam10191 COG7 Golgi complex c  24.2      35 0.00089   12.1  12.0   10  354-363   418-427 (768)
319 TIGR00176 mobB molybdopterin-g  24.2      33 0.00083   12.4   0.9   25  250-283    84-108 (165)
320 KOG2185 consensus               24.2      35 0.00089   12.1   8.1   48  590-639   424-471 (486)
321 PRK12267 methionyl-tRNA synthe  24.2      35 0.00089   12.1   5.8   60  355-414   306-368 (644)
322 pfam09740 DUF2043 Uncharacteri  24.2      27 0.00068   13.2   0.5   15  201-217    92-106 (111)
323 TIGR01858 tag_bisphos_ald clas  24.2      30 0.00077   12.7   0.7   89  289-379   165-273 (282)
324 PRK10116 universal stress prot  24.2      35 0.00089   12.1   4.7   43  315-362     4-46  (142)
325 pfam07212 Hyaluronidase_1 Hyal  24.2      35 0.00089   12.1   1.5   14  211-224   105-118 (273)
326 PRK13559 hypothetical protein;  24.1      35 0.00089   12.1   3.4   36  188-227   123-159 (363)
327 KOG0385 consensus               24.0      35  0.0009   12.1   3.8   42  315-361   559-603 (971)
328 COG4026 Uncharacterized protei  24.0      35  0.0009   12.1  13.4   96  270-371     6-116 (290)
329 TIGR02087 LEUD_arch 3-isopropy  24.0      31 0.00079   12.6   0.8   73  215-299     1-84  (159)
330 PRK13209 L-xylulose 5-phosphat  24.0      35  0.0009   12.1   1.9   34  322-356    88-121 (283)
331 KOG2874 consensus               23.8      35  0.0009   12.1   3.4   23  329-351   168-192 (356)
332 TIGR00791 gntP transporter, gl  23.7      26 0.00067   13.3   0.4   15  512-526   273-287 (458)
333 PRK09111 DNA polymerase III su  23.7      36 0.00091   12.1  10.2   48  277-328   222-276 (600)
334 KOG0260 consensus               23.7      27  0.0007   13.1   0.4   21  234-254   789-809 (1605)
335 pfam00396 Granulin Granulin.    23.7      33 0.00084   12.4   0.9   10   39-48      9-18  (43)
336 pfam00282 Pyridoxal_deC Pyrido  23.5      15 0.00038   15.5  -0.9   35  293-327   196-234 (370)
337 pfam11464 Rbsn FYVE-finger-con  23.2      36 0.00092   12.0   4.6   38  593-630     3-40  (42)
338 pfam00365 PFK Phosphofructokin  23.2      36 0.00092   12.0   4.0   14  350-363   188-202 (279)
339 COG2380 Uncharacterized protei  23.0      17 0.00044   14.9  -0.7   23  157-179     1-23  (327)
340 TIGR00036 dapB dihydrodipicoli  22.9      37 0.00093   11.9   2.0   94  277-415    85-186 (281)
341 smart00433 TOP2c Topoisomerase  22.8      37 0.00094   11.9   4.0   11  232-242   194-204 (594)
342 KOG1818 consensus               22.8      34 0.00086   12.3   0.8   39  200-239   167-205 (634)
343 PRK09846 recT recombination an  22.7      37 0.00094   11.9   1.8   79  137-224    85-169 (270)
344 pfam03194 LUC7 LUC7 N_terminus  22.6      37 0.00095   11.9  10.0   42  591-632   128-169 (252)
345 TIGR03183 DNA_S_dndC putative   22.6      26 0.00067   13.3   0.2   15  212-226   135-150 (447)
346 pfam00098 zf-CCHC Zinc knuckle  22.5      31  0.0008   12.6   0.5   11   63-73      2-12  (26)
347 PRK10787 DNA-binding ATP-depen  22.5      37 0.00095   11.9   7.9   13  247-259   323-335 (784)
348 TIGR02410 carnitine_TMLD trime  22.5      37 0.00095   11.9   3.6   25   56-80    216-247 (397)
349 PRK13780 phosphocarrier protei  22.5      37 0.00095   11.9   5.6   62  306-377    22-83  (88)
350 pfam04055 Radical_SAM Radical   22.4      37 0.00095   11.9   5.7   21  343-363   137-159 (165)
351 TIGR02029 AcsF magnesium-proto  22.3      23  0.0006   13.7  -0.1   30  492-524   183-216 (344)
352 PRK12442 translation initiatio  22.3      37 0.00096   11.8   1.6   19  197-215    58-76  (87)
353 pfam05028 PARG_cat Poly (ADP-r  22.3      35 0.00089   12.1   0.7   23  356-378   200-222 (339)
354 COG3313 Predicted Fe-S protein  22.3      38 0.00096   11.8   1.9   25   49-75      7-33  (74)
355 cd06481 ACD_HspB9_like Alpha c  22.2      37 0.00094   11.9   0.9   22  348-369    57-78  (87)
356 KOG4506 consensus               22.2      38 0.00096   11.8   5.2  103  281-392   249-371 (598)
357 PRK10903 peptidyl-prolyl cis-t  22.2      38 0.00096   11.8   3.9   14  275-289   151-164 (190)
358 TIGR00456 argS arginyl-tRNA sy  22.2      38 0.00096   11.8   7.9   54  481-535   513-566 (600)
359 KOG1177 consensus               22.1      13 0.00033   16.1  -1.5   71   51-133    30-100 (596)
360 pfam02330 MAM33 Mitochondrial   22.1      38 0.00096   11.8   1.5   34  351-388   147-183 (203)
361 TIGR00457 asnS asparaginyl-tRN  22.1      35 0.00088   12.2   0.7   32  345-378   101-133 (495)
362 pfam02614 UxaC Glucuronate iso  22.1      38 0.00097   11.8   3.2   15  169-183    57-71  (465)
363 COG5014 Predicted Fe-S oxidore  22.0      16  0.0004   15.4  -1.1   61  301-367   103-165 (228)
364 cd01833 XynB_like SGNH_hydrola  21.9      38 0.00097   11.8   1.9   20  295-330     3-22  (157)
365 cd00223 TOPRIM_TopoIIB_SPO TOP  21.9      38 0.00097   11.8   3.9   88  273-364     2-102 (160)
366 pfam03949 Malic_M Malic enzyme  21.9      38 0.00097   11.8   2.2   38  281-318    99-136 (255)
367 TIGR02009 PGMB-YQAB-SF beta-ph  21.8      38 0.00098   11.8   7.9   82   73-165    44-133 (211)
368 COG0703 AroK Shikimate kinase   21.7      38 0.00098   11.7   3.6   19  356-374    42-60  (172)
369 PRK11460 esterase YpfH; Provis  21.7      38 0.00098   11.7   1.5   42  342-391   175-219 (230)
370 KOG1432 consensus               21.7      38 0.00098   11.7   1.7   37  314-359   318-354 (379)
371 PRK13547 hmuV hemin importer A  21.6      39 0.00098   11.7   3.7   56  302-359   211-268 (273)
372 PRK04025 S-adenosylmethionine   21.4      39 0.00099   11.7   1.9   39   47-97     61-101 (139)
373 KOG2578 consensus               21.4      31 0.00078   12.6   0.3   46   98-157    42-87  (388)
374 KOG1409 consensus               21.3      39 0.00099   11.7   2.1   20  345-364   268-287 (404)
375 KOG2150 consensus               21.3      39   0.001   11.7  11.9   15  318-332   294-308 (575)
376 TIGR02776 NHEJ_ligase_prk DNA   21.3      39   0.001   11.7   1.2   46  284-329   224-275 (645)
377 pfam06189 5-nucleotidase 5'-nu  21.2      39   0.001   11.7   3.5   67  274-374    85-151 (263)
378 TIGR02434 CobF precorrin-6A sy  21.2      39   0.001   11.7   0.9   27  346-374    27-53  (259)
379 PRK13529 malate dehydrogenase;  21.2      39   0.001   11.7   2.7   67  288-357   235-305 (563)
380 KOG0440 consensus               21.1      39   0.001   11.7   2.1   29  345-373    68-96  (243)
381 pfam04710 Pellino Pellino. Pel  21.1      39   0.001   11.6   1.9   11  309-319   131-141 (416)
382 COG0585 Uncharacterized conser  21.1      24 0.00062   13.6  -0.3   45   52-100    31-75  (406)
383 pfam05131 Pep3_Vps18 Pep3/Vps1  21.1      39   0.001   11.6   4.1   17  295-311    34-50  (147)
384 KOG4090 consensus               21.1      24 0.00061   13.6  -0.3   20  271-290   133-152 (157)
385 KOG0402 consensus               21.1      31  0.0008   12.5   0.3   50   41-95     37-89  (92)
386 smart00803 TAF TATA box bindin  21.1      39   0.001   11.6   5.4   50   84-133     3-52  (65)
387 PRK10575 iron-hydroxamate tran  21.0      39   0.001   11.6   2.4   59  303-363   204-264 (265)
388 pfam09059 TyeA TyeA. Members o  21.0      40   0.001   11.6   6.5   44  386-429    26-74  (81)
389 KOG1253 consensus               20.9      40   0.001   11.6   0.9   10  251-260   199-208 (525)
390 pfam04630 Phage_tail Phage maj  20.9      40   0.001   11.6   1.0   20  310-329   163-182 (199)
391 cd06394 PBP1_iGluR_Kainate_KA1  20.9      40   0.001   11.6   3.5   48  315-366   135-182 (333)
392 TIGR02013 rpoB DNA-directed RN  20.9      40   0.001   11.6   1.1   37  293-329   275-311 (1449)
393 TIGR00393 kpsF sugar isomerase  20.9      31  0.0008   12.5   0.3   72  138-219   124-202 (272)
394 pfam04989 CmcI Cephalosporin h  20.8      40   0.001   11.6   3.0   85  303-391    95-186 (202)
395 cd07968 OBF_DNA_ligase_IV The   20.7      36 0.00091   12.0   0.6   18  295-312    46-63  (140)
396 cd01028 TOPRIM_TopoIA TOPRIM_T  20.7      40   0.001   11.6   3.7   55  304-362    78-135 (142)
397 cd04777 HTH_MerR-like_sg1 Heli  20.6      40   0.001   11.6   2.1   10  594-603    89-98  (107)
398 PRK13239 alkylmercury lyase; P  20.5      40   0.001   11.6   1.5   38  210-258    64-101 (206)
399 KOG1207 consensus               20.5      40   0.001   11.5   3.8   60  272-335     7-72  (245)
400 PRK13551 agmatine deiminase; P  20.3      41   0.001   11.5   3.6   54  302-355   207-265 (360)
401 pfam08448 PAS_4 PAS fold. The   20.2      41   0.001   11.5   2.5   23  204-226    82-104 (110)
402 COG3484 Predicted proteasome-t  20.2      34 0.00086   12.3   0.3   16  235-250   139-154 (255)
403 KOG0415 consensus               20.2      14 0.00036   15.7  -1.6   46   39-89     36-81  (479)
404 cd06544 GH18_narbonin Narbonin  20.1      41   0.001   11.5   7.0   84  301-411    55-141 (253)
405 PRK00423 tfb transcription ini  20.1      41   0.001   11.5   2.5   36   42-79     13-50  (310)
406 TIGR02418 acolac_catab acetola  20.1      26 0.00067   13.2  -0.2   43  396-439   212-261 (553)
407 pfam02403 Seryl_tRNA_N Seryl-t  20.1      41   0.001   11.5  10.2   53  584-638    41-93  (108)
408 KOG1597 consensus               20.1      41   0.001   11.5   2.6   68  287-363    17-86  (308)

No 1  
>PRK05667 dnaG DNA primase; Validated
Probab=100.00  E-value=0  Score=1218.74  Aligned_cols=592  Identities=36%  Similarity=0.583  Sum_probs=500.8

Q ss_pred             CCCCHHHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHH
Q ss_conf             98788899999874888887541222101588777775575345888858787981789746713688887898998988
Q gi|254780834|r    1 MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSAL   80 (648)
Q Consensus         1 m~i~~~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~   80 (648)
                      ||||+++||+|++++|||||||+||+|+|+|+|     ||||||||+||||||+|||+||+|||||||+|||||+|||++
T Consensus         2 grIp~e~Ie~i~~~~dIvdvi~~yv~Lkk~G~~-----~~glCPFH~EktPSF~V~~~k~~~~CFgCg~~Gdv~~Flm~~   76 (600)
T PRK05667          2 GRIPPEFIDELRARVDIVDVIGEYVKLKKAGRN-----YKGLCPFHDEKTPSFTVSPDKQFYHCFGCGAGGDAIKFLMEY   76 (600)
T ss_pred             CCCCHHHHHHHHHHCCHHHHHCCCEEEEECCCC-----CEEECCCCCCCCCCCEEECCCCEEEECCCCCCCCHHHHHHHH
T ss_conf             999989999999849999875162289988998-----378796999999994797899979869999695578978976


Q ss_pred             CCCCHHHHHHHHHHHHCCCCCCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCC
Q ss_conf             59997999999999818858776820-36777889999999999999999973267775789999850688535101244
Q gi|254780834|r   81 LGCSFIESVQRLAAIAGVPLPVVDPK-IEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKL  159 (648)
Q Consensus        81 ~~~~f~ea~~~la~~~gi~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~l  159 (648)
                      ||++|+|||+.||+++||++|..++. .......+..++++|+.|+.|||++|.++.|..|++||++|||++++|++|+|
T Consensus        77 e~lsF~eAv~~LA~~~gi~l~~~~~~~~~~~~~~~~~l~~~~~~a~~~f~~~L~~~~~~~a~~YL~~Rgl~~~~i~~F~l  156 (600)
T PRK05667         77 EGLSFVEAVEELADRAGIELPYEDGGSAQEEKSRRQELYEIMELAAKFYQQQLRTPEGAEARQYLYERGLSEETIERFGI  156 (600)
T ss_pred             HCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHCC
T ss_conf             29987999999999959975766775134425689999999999999999984896208999999975999999998383


Q ss_pred             CCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCC
Q ss_conf             22567741034554205997345232012100346541000016716888970778588850100146553001038767
Q gi|254780834|r  160 GYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPET  239 (648)
Q Consensus       160 G~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT  239 (648)
                      ||||++|+.|+++|.++||+.++|.++||+..+++| .+||||||||||||+|.+|+|||||||+|+++..|||||||||
T Consensus       157 Gyap~~~~~l~~~l~~~g~~~~~l~~~GL~~~~~~g-~~yDrFr~RimFPI~d~~G~vIgFgGR~l~~~~~pKYlNSpET  235 (600)
T PRK05667        157 GYAPDGWDALLKHLGKKGIEPKLLEEAGLLIKNEDG-RPYDRFRNRIMFPIRDLRGRVIGFGGRVLGKDDEPKYLNSPET  235 (600)
T ss_pred             CCCCCCHHHHHHHHHHCCCHHHHHHHHCCEEECCCC-CCCHHHCCCEEEEEECCCCCEEEEECEECCCCCCCCCCCCCCC
T ss_conf             547771789999987369729999982682599999-8751320805676556899876441203488899870179887


Q ss_pred             CCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEE
Q ss_conf             65352101108178888643310000235678708997143889998743554211343213662678988512681899
Q gi|254780834|r  240 ILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVL  319 (648)
Q Consensus       240 ~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl  319 (648)
                      +||+||++|||||.|+++|++.          +.+||||||||||+|||+||+|||||||||||++|+++|+|+|++|||
T Consensus       236 ~lF~K~~~Lygl~~A~~~i~~~----------~~~ilvEGymDvIal~q~Gi~naVA~lGTAlT~~h~~~L~r~~~~vil  305 (600)
T PRK05667        236 PLFHKGRELYGLDEARKAIAKK----------DRVIVVEGYMDVIALHQAGITNAVASLGTALTEEHLQLLRRYTDEVIL  305 (600)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCC----------CCEEEEECCHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHCCCEEEE
T ss_conf             3401016886358999986235----------857998063999999984986775334341639999999736893899


Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCHH
Q ss_conf             61788662257778888887775369730675257888888997203668899886414992799999998530233145
Q gi|254780834|r  320 CFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPD  399 (648)
Q Consensus       320 ~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~~~l~~~~dl~spe  399 (648)
                      |||||+||++||+||++++++++.+|+.|+|+.||+|+|||||++++|+++|.+++++|.|+++|+|+++..+.++++|+
T Consensus       306 ~fDgD~AG~~Aa~ra~~~~~~~~~~g~~v~v~~lp~g~DPD~~i~~~G~~~f~~~l~~a~~~~~f~~~~~~~~~~l~~~e  385 (600)
T PRK05667        306 CFDGDRAGRKAALRALELALPLLKDGRQLRFLFLPDGKDPDDLVRKEGKEAFRALLEQAIPLSEFLIRRLIPGKDLDTPE  385 (600)
T ss_pred             EECCCHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHH
T ss_conf             96885888999999999878886389779996189998938999875999999999738998999999997148999999


Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             79999999998854179989999999999999887657767764332001235555554556643333222233445553
Q gi|254780834|r  400 ERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVKGKLSKK  479 (648)
Q Consensus       400 ~ka~~~~~l~~~I~~I~d~~~R~~yl~~la~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  479 (648)
                      +|+.+++.+.++|+.|+|+++|++|++.++++++........................           ...........
T Consensus       386 ~k~~~~~~~~~~i~~i~d~i~r~~y~~~la~~l~i~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~  454 (600)
T PRK05667        386 GRAALLERAAPLIAKIPDPTLRDSYRQKLAELLGIFDDAQVEQLVPKLRRQRSRLAPP-----------PSPKKLSPRSP  454 (600)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCC-----------CCCCCCCCCCH
T ss_conf             9999999999999968999999999999999859898999999864310246667888-----------77667888987


Q ss_pred             HHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH---HHHHHHHHHHHHHH
Q ss_conf             037999999999847788999984430023799889999999999975388999899998851---11289999999998
Q gi|254780834|r  480 PSLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLC---ERGFGELLKQLDRQ  556 (648)
Q Consensus       480 ~~~~E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~~l~~~L~---~~~l~elL~~L~~~  556 (648)
                      ....|+.||++|+++|+++..+........|.++.++.|+..+.... +.+..+...+...+.   +.....++..+.  
T Consensus       455 ~~~aE~~lL~~ll~~p~l~~~~~~~~~~~~~~~~~~~~l~~~i~~~~-~~~~~~~~~l~~~l~~~~~~~~~~~l~~l~--  531 (600)
T PRK05667        455 KERAERELLALLLQHPELAEEVRELDALEDFKLPGLRLLYELIDAAG-EQPGLTGAQLLELLRDLRDEELAELLERLA--  531 (600)
T ss_pred             HHHHHHHHHHHHHHCHHHHHHHHHCCCHHHCCCHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHHCCCHHHHHHHHHHH--
T ss_conf             78999999999982989999875013423138878999999999987-478998799999998436859999999997--


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6543332025689988999999999999985899999999999999872-412798999999999999999999988
Q gi|254780834|r  557 VRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQV-TAKGEAEKTAILISILHEVHIQIHQIE  632 (648)
Q Consensus       557 ~~~~~~~~~~~e~~~~d~~e~~~~~l~l~~r~~~L~r~l~ele~~l~e~-~~~~d~e~~~~l~~el~elk~~L~~l~  632 (648)
                           .+.    ...+.....+.+++..+.+. .+.+++.++..++... .+..+.+...+++.++++++++++.++
T Consensus       532 -----~~~----~~~e~~~~~i~d~i~~L~~~-~l~~~~~~L~~k~~~~~~~~~e~~el~~ll~el~~l~~~~~~l~  598 (600)
T PRK05667        532 -----VED----LPAELAEQELEDALAKLRKA-LLELRLEELLKKERRLGLAEEEKEELLALLQELKALEQELRALE  598 (600)
T ss_pred             -----CCC----CCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             -----276----78740899999999999983-79999999999984538985539999999999999999999863


No 2  
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=100.00  E-value=0  Score=939.43  Aligned_cols=413  Identities=43%  Similarity=0.689  Sum_probs=391.1

Q ss_pred             CCCHHHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHC
Q ss_conf             87888999998748888875412221015887777755753458888587879817897467136888878989989885
Q gi|254780834|r    2 NYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALL   81 (648)
Q Consensus         2 ~i~~~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~   81 (648)
                      +||+++|++|++++|||||||+||+|+|+|+|     ||||||||+||||||+|+|+||+|||||||+|||+|.|||+++
T Consensus         1 ~i~~~~i~~l~~~~dIvdvI~~~v~Lkk~G~~-----y~~lCPFH~EktPSf~V~~~k~~yhCFGCg~~Gd~i~Fl~~~~   75 (568)
T COG0358           1 RIPREFIDELRERIDIVDVIGEYVKLKKQGAN-----YTGLCPFHAEKTPSFTVSPEKGFYHCFGCGAGGDAIKFLMELL   75 (568)
T ss_pred             CCCHHHHHHHHHHCCHHHHHHHCEEEEECCCC-----CEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHH
T ss_conf             99879999998618989876130145775888-----5103888777778748966887698416899851777899970


Q ss_pred             CCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCC
Q ss_conf             99979999999998188587768203677788999999999999999997326777578999985068853510124422
Q gi|254780834|r   82 GCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGY  161 (648)
Q Consensus        82 ~~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~  161 (648)
                      |++|.||++.||.++||++|...+   +....+..++++++.++.||+..|. +.+++|++||.+||++.+++..|+|||
T Consensus        76 ~~sf~eav~~La~~~gi~~~~~~~---~~~~~~~~l~~~~~~~~~fy~~~L~-~~~~~a~~yL~~Rgls~~~i~~f~iG~  151 (568)
T COG0358          76 GLSFDEAVLQLAGRAGIELPYEKG---KRIEKRQKLYDGKEEAAIFYQSSLD-PEGAAALKYLETRGLAAELIAHFRLGY  151 (568)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCCCC---CCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHCCCCHHHHHHHHHCC
T ss_conf             997899999998872887775432---2117888888789999999998731-300788999987268888998865088


Q ss_pred             CCCCCCHHHHHHHCCC-CCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCC
Q ss_conf             5677410345542059-973452320121003465410000167168889707785888501001465530010387676
Q gi|254780834|r  162 APDSRYSLREHLRQKG-FSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETI  240 (648)
Q Consensus       162 ap~~~~~l~~~l~~~~-~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~  240 (648)
                      ||++ +.+. ++..++ |+.+.+.++||+..++ | .+|||||+||||||+|.+|+|||||||+++ +++|||+|||||+
T Consensus       152 ap~~-~~~~-~~~~k~~~~~~~l~~~Gl~~~~~-~-~~ydrFr~RImfPI~d~~g~vigFggR~l~-~~~~KYlNspet~  226 (568)
T COG0358         152 APPN-DSLL-PFLAKKEYREEKLEDLGLLKRKE-G-KIYDRFRNRIMFPIRDLRGDVIGFGGRVLG-DDKPKYLNSPETE  226 (568)
T ss_pred             CCCC-CHHH-HHHHCCCCCHHHHHHCCCHHHCC-C-CHHHHHHCHHEEEEECCCCCCCCCCCEECC-CCCCCCCCCCCCC
T ss_conf             9874-3044-54421342477898655134157-7-337888442327510799984240212436-7775334788873


Q ss_pred             CCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEE
Q ss_conf             53521011081788886433100002356787089971438899987435542113432136626789885126818996
Q gi|254780834|r  241 LFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLC  320 (648)
Q Consensus       241 if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~  320 (648)
                      +|+||++|||++.|++.|++          .+++||||||||||+||++||+||||+||||+|++|+.+|+|++++||+|
T Consensus       227 if~Kg~~Lyg~~~a~~~~~~----------~~~iivVEGymDViaL~~aGi~naVA~lGTalt~ehi~~L~r~~~~vil~  296 (568)
T COG0358         227 LFKKGEELYGLDPARKKIAK----------ADQIIVVEGYMDVIALHKAGIKNAVASLGTALTEEHIKLLSRGKKKVILC  296 (568)
T ss_pred             CCCCCHHCCCCCHHHHHCCC----------CCEEEEEECHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHHCCCEEEEE
T ss_conf             65677430585455563056----------88399994189999999719752786587679999999998469819999


Q ss_pred             ECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH-CCCHHHHHHHHHHHHCCCCCHH
Q ss_conf             178866225777888888777536973067525788888899720366889988641-4992799999998530233145
Q gi|254780834|r  321 FDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE-SLPLVDMLWKRETENRSFNTPD  399 (648)
Q Consensus       321 fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~-A~~l~dFl~~~l~~~~dl~spe  399 (648)
                      ||||.||++||+|+++.++++...|  |+|+.+|+|+|||||++++|.++|...+.+ +.++++|+++.+... ++++ +
T Consensus       297 fDgD~AG~~Aa~ral~~~~~~~~~~--v~v~~~P~GkDpDel~~k~g~~al~~~l~~~~~~~~~~~~~~~~~~-~~~~-~  372 (568)
T COG0358         297 FDGDRAGRKAAKRALQLVLPLDFVG--VFVILLPDGKDPDELIRKEGAEALRKKLPNERLPLIEFLIEYLIPS-NLDT-E  372 (568)
T ss_pred             ECCCHHHHHHHHHHHHHHHHCCCCC--EEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCH-H
T ss_conf             6896789999999998543315664--4887478999868999873179999875652456899999861453-3212-7


Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             7999999999885417998999999999999988765776776
Q gi|254780834|r  400 ERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITE  442 (648)
Q Consensus       400 ~ka~~~~~l~~~I~~I~d~~~R~~yl~~la~~L~~~~~~~~~~  442 (648)
                      +++.+...+.+.++.++++..|.+|.+.+++.++.........
T Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  415 (568)
T COG0358         373 GKARLVEEAVPLIKVIPDEVLRDYYLQKLAELLGISDDALLQL  415 (568)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             7899999976787602765779999999998737546778888


No 3  
>TIGR01391 dnaG DNA primase; InterPro: IPR006295   DNA primase synthesizes the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. The C-terminal region of these proteins is poorly conserved between species.   In Escherichia coli, primase (DnaG) interacts with the replicative DnaB helicase, single-stranded DNA binding protein (SSB), and DNA polymerase III holoenzyme , , , . Although DnaG is capable of synthesizing 60-nucleotide-long primers in vitro  this primer length is restrained to 11 (±1) nucleotides in the context of the replisome .   Members of this entry are homologs of DnaG and have been identified in all prokaryotes, as well as in several bacteriophage. On the basis of sequence analysis, these proteins appear structurally distinct from primases known to act in archaeal, eukaryotic replication  or to either of the two subunits, p50 and p60, of the heterodimeric eukaryotic DNA primase (IPR002755 from INTERPRO).   DnaG has been shown by proteolysis to comprise three structural domains: a 12-kD NH2-terminal Zn2+-binding domain (ZBD), a 36-kD core domain containing the polymerase region, and a 15-kD COOH-terminal DnaB-interaction domain (DnaB-ID) , .; GO: 0003896 DNA primase activity, 0006269 DNA replication synthesis of RNA primer.
Probab=100.00  E-value=0  Score=702.79  Aligned_cols=413  Identities=44%  Similarity=0.749  Sum_probs=391.3

Q ss_pred             CCCHHHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHC
Q ss_conf             87888999998748888875412221015887777755753458888587879817897467136888878989989885
Q gi|254780834|r    2 NYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALL   81 (648)
Q Consensus         2 ~i~~~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~   81 (648)
                      ++|+++++++++++||++||++||.|+|+|+|     |+||||||+||||||+|+|+|++|||||||++||+|.|+|+++
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~-----~~~~cPfh~~~~ps~~~~~~~~~~~cfgc~~~G~~~~f~~~~~   75 (424)
T TIGR01391         1 RIPEEVIDELKERVDIVDLVSEYVKLKKKGKN-----YVGLCPFHHEKTPSFSVSPEKGFYHCFGCGAGGDAIKFLMEIE   75 (424)
T ss_pred             CCCHHHHHHHHHHCCHHHHHHHHHHHHCCCCC-----CEEECCCCCCCCCCEEEECCCCEEEEEECCCCCCHHHHHHHHH
T ss_conf             97467899998620057776544311004774-----0453365455676224301335355530466660577777761


Q ss_pred             CCCHHHHHHHHHHHHCCCCCCCCCCHHH------HHHHHHHHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHCCCCHHHH
Q ss_conf             9997999999999818858776820367------778899999999999999999732677-757899998506885351
Q gi|254780834|r   82 GCSFIESVQRLAAIAGVPLPVVDPKIEK------KEKIQTDLIRLIEVATDFFHHSLKNAR-DKRLHYYLDERGIDSHAI  154 (648)
Q Consensus        82 ~~~f~ea~~~la~~~gi~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~a~~yl~~Rg~~~~~~  154 (648)
                      +++|.||++.||.++|++++... ....      ....+..++.+++.+..||+..|.... +..+++||.+||++++++
T Consensus        76 ~~~~~~~~~~l~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~yl~~rg~~~~~~  154 (424)
T TIGR01391        76 GLSFVEAVKELAKRAGLDLPLEK-ESEKSPDKAEEKSERKELLELLELAAEFFKNELKNTPEGNRALDYLLSRGLSDETI  154 (424)
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHH
T ss_conf             57678999999987377321000-22210233343335678999999999999987520101468899998628888789


Q ss_pred             CCCCCCCCCCCCCHHHHHHHCC-CCCHHHHHHHCCCEECCCC-CCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCE
Q ss_conf             0124422567741034554205-9973452320121003465-4100001671688897077858885010014655300
Q gi|254780834|r  155 EMFKLGYAPDSRYSLREHLRQK-GFSEEKIIEAGLLIDGDNS-ATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVK  232 (648)
Q Consensus       155 ~~f~lG~ap~~~~~l~~~l~~~-~~~~~~~~~~gl~~~~~~~-~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~K  232 (648)
                      .+|++||+|..|..+..++..+ +++.+.+.++|++...++| ..+||+|++||||||+|..|++||||||.++ +..||
T Consensus       155 ~~f~~G~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~f~~r~~~p~~~~~g~~~~fggr~~~-~~~~k  233 (424)
T TIGR01391       155 SRFGLGYAPDNWDFLLDFLENKKGFDLELLLEAGLLVKKENGDQKYYDRFRNRIIFPIHDPKGKVVGFGGRALG-DEKPK  233 (424)
T ss_pred             HHHHCCCCCCCHHHHHHHHHHHCCCCHHHHHHCCCCEECCCCCCHHHHHHHCEEEEEEECCCCCEEEECCCCCC-CCCCC
T ss_conf             87403677552467888763201555567865033000145541023222220254433367865540430015-66663


Q ss_pred             ECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHH
Q ss_conf             10387676535210110817888864331000023567870899714388999874355421134321366267898851
Q gi|254780834|r  233 YLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWK  312 (648)
Q Consensus       233 YlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r  312 (648)
                      |+|||||++|+|+++|||++.|++.+.+          .+.+++||||||||++|++|+.++||++||++|++|+.++++
T Consensus       234 y~n~p~~~~~~k~~~l~~~~~~~~~~~~----------~~~~~~~eG~~d~~~~~~~g~~~~~~~~g~~~~~~~~~~~~~  303 (424)
T TIGR01391       234 YLNSPETPLFKKGELLYGLDKARKEIRK----------EKELLLVEGYMDVIALHQAGIKNAVASLGTALTEEHLKLLKR  303 (424)
T ss_pred             CCCCCCCCHHCCHHHHHHHHHHHHHHHC----------CCEEEEECCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             1156533000010356546677776512----------660688602567788765055402444312201789999863


Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH-CCCHHHHHHHHHHH
Q ss_conf             26818996178866225777888888777536973067525788888899720366889988641-49927999999985
Q gi|254780834|r  313 LSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE-SLPLVDMLWKRETE  391 (648)
Q Consensus       313 ~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~-A~~l~dFl~~~l~~  391 (648)
                      +++++++|||||.||.+|++|+++.+++....+..++++.+|+|+|||++++++|.+.|..++.+ +.++.+|++.....
T Consensus       304 ~~~~~~~~~dgd~aG~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~dpd~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~  383 (424)
T TIGR01391       304 YADEIILCFDGDSAGLKAALRALELLLPLGKDGISVKVVLLPGGKDPDELLRKEGAEALKKLLENGSLPLIEFLLEYLLS  383 (424)
T ss_pred             CCCCEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHCCHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             25727898557412378899999987641256622789865777887999862047889999741664079999998730


Q ss_pred             HCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             3023314579999999998854179989999999999999
Q gi|254780834|r  392 NRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDR  431 (648)
Q Consensus       392 ~~dl~spe~ka~~~~~l~~~I~~I~d~~~R~~yl~~la~~  431 (648)
                      ..++++++++..+...+.+.+..++++..+..|.+.+++.
T Consensus       384 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  423 (424)
T TIGR01391       384 GYNLDSPEEKAKLLEELLPLLKKLPDPLLRDSYLQKLAEL  423 (424)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
T ss_conf             1355435689999999988875202157899999998750


No 4  
>pfam08275 Toprim_N DNA primase catalytic core, N-terminal domain.
Probab=99.97  E-value=1.5e-31  Score=309.83  Aligned_cols=128  Identities=49%  Similarity=0.854  Sum_probs=123.1

Q ss_pred             HHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEE
Q ss_conf             99997326777578999985068853510124422567741034554205997345232012100346541000016716
Q gi|254780834|r  127 FFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRL  206 (648)
Q Consensus       127 ~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri  206 (648)
                      |||.+|.++.+..|++||.+||+++++|++|+|||||++|+.|.++|.++||+.+++.++||+..+++|. +||+|+|||
T Consensus         1 fy~~~L~~~~~~~a~~YL~~Rgi~~~~i~~F~iGyap~~~~~L~~~l~~~~~~~~~l~~~Gl~~~~~~~~-~~D~F~~Ri   79 (128)
T pfam08275         1 FYHELLKTKEGAAARDYLKSRGLSPETIKRFGLGYAPDGWDNLLNHLEKKGFDLELLLEAGLLVKREDGG-YYDRFRNRI   79 (128)
T ss_pred             CHHHHHCCCCCHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHHHHHHCCCEEECCCCC-EEEEECCEE
T ss_conf             9378857975589999999859999999984878787606899998753289899998689869879998-855441248


Q ss_pred             EEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHH
Q ss_conf             8889707785888501001465530010387676535210110817888
Q gi|254780834|r  207 IFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGAL  255 (648)
Q Consensus       207 ~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~  255 (648)
                      ||||+|.+|+|||||||+|+++.+|||||||||+||+||++||||++|+
T Consensus        80 ~fPI~d~~g~vigFgGR~l~~~~~~KYlNS~et~iF~K~~~Lygl~~Ak  128 (128)
T pfam08275        80 MFPIRDESGRVVGFGGRALDDEEPPKYLNSPETPLFKKGKVLYGLDEAK  128 (128)
T ss_pred             EEEEECCCCCEEEEEEEECCCCCCCCEECCCCCCCEECCCCEECCCCCC
T ss_conf             9988779998999871577999998704799984685640103831049


No 5  
>PRK08624 hypothetical protein; Provisional
Probab=99.97  E-value=3.7e-29  Score=287.80  Aligned_cols=273  Identities=18%  Similarity=0.250  Sum_probs=198.7

Q ss_pred             HHHHHHCCHHHH------HHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEEC-CCCCCCCHHHHH----
Q ss_conf             999874888887------541222101588777775575345888858787981789746713-688887898998----
Q gi|254780834|r    9 KDLLIHIPISNL------IGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCF-SCHVKGDHLSFL----   77 (648)
Q Consensus         9 ~~i~~~~~i~~v------v~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf-~c~~~gd~~~f~----   77 (648)
                      +++++....-|+      +|.--.+.+.|.-    =+.-.|-=|+--+--+.-+++.+.|||| |||++||||+|+    
T Consensus         5 ~e~k~sLT~edI~kil~~lg~~~~~~k~g~~----i~~t~ch~~~g~s~kL~yY~e~~~FHCytgCG~~~DV~~li~k~~   80 (373)
T PRK08624          5 DELKESLTPEDIIKILEEVGCENVRGKDGNT----IAETACHNDGGGSTKLYYYIENDNFHCYTRCGDIFDVFELLCKRL   80 (373)
T ss_pred             HHHHHHCCHHHHHHHHHHHCCCCCCCCCCCE----EEEEEEECCCCCCEEEEEEECCCEEEEECCCCCCCHHHHHHHHHH
T ss_conf             7887636898999999995777876889978----766543058999458999616853665426787511999999887


Q ss_pred             -HHHCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CCHHHHHHHHHCCCCHHHH
Q ss_conf             -9885999799999999981885877682036777889999999999999999973267--7757899998506885351
Q gi|254780834|r   78 -SALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNA--RDKRLHYYLDERGIDSHAI  154 (648)
Q Consensus        78 -~~~~~~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~a~~yl~~Rg~~~~~~  154 (648)
                       |+.+++||.|||+.||.++||.+-..+.    ....+..        ..++++..|..  +.++...+.- |.++..++
T Consensus        81 kmeg~~lSF~eAi~~la~i~Gis~~~~~k----~~~ik~~--------~~ki~d~~w~~k~e~~k~i~~~L-k~~~e~Il  147 (373)
T PRK08624         81 KMEGKALSFSKAIRKITKILGLSYFYEPK----QQGIKPS--------FLKILDWVWTGKKEKKEKIQPQL-KSFNENIL  147 (373)
T ss_pred             HHCCCCCCHHHHHHHHHHHHCCCCCCCCH----HHHHHHH--------HHHHHHHHHHCCHHHHHHHHHHH-HCCCHHHH
T ss_conf             61043565999999999985853456810----3102477--------99988787650111467788776-05668889


Q ss_pred             CCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCC--CCE
Q ss_conf             012442256774103455420599734523201210034654100001671688897077858885010014655--300
Q gi|254780834|r  155 EMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGE--SVK  232 (648)
Q Consensus       155 ~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~--~~K  232 (648)
                      ..| ++|+|+.|       .+.|++.+.+.+.++       +.|||.|+|||||||+|..|++|||+||.|+++.  .+|
T Consensus       148 ~~F-~~yp~~~W-------i~EGIS~et~kk~~i-------~yY~d~f~NrIiIPh~D~~G~lVGirgR~L~ke~~~~~K  212 (373)
T PRK08624        148 NQF-VKIPNRKW-------LDEGISEKTQKYWEI-------KFYLDVISQRIIIPHRDESGELIGIRGRLLDKELVDKNK  212 (373)
T ss_pred             HHH-HCCCHHHH-------HHCCCCHHHHHHHCC-------CCCCCHHCCEEEEEEECCCCCEEEEEECCCCHHHHHCCC
T ss_conf             875-35671778-------875889999987464-------542120036468666457887888960115586752476


Q ss_pred             ECCCC-CCCC--CCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHH---HHHHCCCCCCHHHHHCCCCHHH
Q ss_conf             10387-6765--3521011081788886433100002356787089971438899---9874355421134321366267
Q gi|254780834|r  233 YLNSP-ETIL--FHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVL---SLCQAGVQNVVSSLGTALTEYQ  306 (648)
Q Consensus       233 YlNSp-eT~i--f~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi---~l~~~G~~n~va~~Gtalt~~~  306 (648)
                      |+-.- ....  +.+|..||||++-+++|..          .+.+|||||.--|+   .++.-+ ..+||.||..+|+.|
T Consensus       213 Y~Pl~~~~~~ynhp~g~nLYGL~~N~~~I~~----------~~kviifEsEKSVl~~~t~y~~~-n~~VAicGs~~s~~Q  281 (373)
T PRK08624        213 YFPIYVNDTGYNHPKGKILYGLWQNKKYIKE----------KKKVIIVESEKSVLFSDKFYGEG-NFVVAICGSNISEVQ  281 (373)
T ss_pred             EEEEEECCCCCCCCCHHHHHHHHHCHHHHHH----------CCCEEEEECCCCEEEHHHHCCCC-CEEEEECCCCCCHHH
T ss_conf             2579976713578330245412326899985----------48289997140301315442578-736996367679999


Q ss_pred             HHHHHHCCC-EEEEEECCC
Q ss_conf             898851268-189961788
Q gi|254780834|r  307 LRLLWKLSP-RIVLCFDGD  324 (648)
Q Consensus       307 ~~~l~r~~~-~vvl~fDgD  324 (648)
                      .++|.++.- +|+|+||-+
T Consensus       282 ~~~ll~LgVeeviiA~Dke  300 (373)
T PRK08624        282 AEKLLRLGVEEVTIALDKE  300 (373)
T ss_pred             HHHHHHCCCEEEEEEECCH
T ss_conf             9999847964898774205


No 6  
>pfam01807 zf-CHC2 CHC2 zinc finger. This domain is principally involved in DNA binding in DNA primases.
Probab=99.96  E-value=2.5e-28  Score=280.14  Aligned_cols=96  Identities=46%  Similarity=0.823  Sum_probs=94.0

Q ss_pred             CCHHHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHCC
Q ss_conf             78889999987488888754122210158877777557534588885878798178974671368888789899898859
Q gi|254780834|r    3 YPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLG   82 (648)
Q Consensus         3 i~~~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~   82 (648)
                      ||+++|++||+++||++|||+||+|+|+|+|     |||+||||+||||||+|+|+||+|||||||+|||+|+|||++||
T Consensus         1 I~~~~I~~ik~~~~i~~vv~~~v~L~~~G~~-----~~~~CPFH~ek~PS~~V~~~k~~f~CF~Cg~~Gd~i~fv~~~e~   75 (98)
T pfam01807         1 IPEESIDDLKNRIDIVDIIGQYVKLKKKGRD-----YKGLCPFHDEKTPSFSVSPDKQFYHCFGCGAGGDAISFLMKIDK   75 (98)
T ss_pred             CCHHHHHHHHHHCCHHHHHHHCCEEEECCCC-----EEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHHC
T ss_conf             9889999999859999998622516888986-----58879988999982799769996997789999767878998859


Q ss_pred             CCHHHHHHHHHHHHCCCCCCC
Q ss_conf             997999999999818858776
Q gi|254780834|r   83 CSFIESVQRLAAIAGVPLPVV  103 (648)
Q Consensus        83 ~~f~ea~~~la~~~gi~~~~~  103 (648)
                      ++|+|||++||+++||++|..
T Consensus        76 ~~f~eAv~~LA~~~gi~l~~~   96 (98)
T pfam01807        76 LSFVEAVKKLADRAGIDLPYE   96 (98)
T ss_pred             CCHHHHHHHHHHHHCCCCCCC
T ss_conf             799999999999969988876


No 7  
>smart00400 ZnF_CHCC zinc finger.
Probab=99.75  E-value=1.3e-18  Score=190.84  Aligned_cols=55  Identities=47%  Similarity=0.894  Sum_probs=54.3

Q ss_pred             EEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             5753458888587879817897467136888878989989885999799999999
Q gi|254780834|r   39 YWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLA   93 (648)
Q Consensus        39 ~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la   93 (648)
                      |||+||||+||||||+|||+||+|||||||+|||+|+|||+++|++|+|||++||
T Consensus         1 ~~~~CPFH~d~~pS~~V~~~k~~~~CF~Cg~~Gd~i~fv~~~~~~~f~eAv~~LA   55 (55)
T smart00400        1 YKGLCPFHGEKTPSFSVSPDKQFFHCFGCGAGGNVISFLMKYDKLSFVEAVKKLA   55 (55)
T ss_pred             CEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHHCCCHHHHHHHHC
T ss_conf             9466949899999879977999799678999986554689884989999999869


No 8  
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.  E. coli DnaG is a single subunit enzyme.
Probab=99.70  E-value=5e-17  Score=176.18  Aligned_cols=78  Identities=54%  Similarity=0.823  Sum_probs=73.9

Q ss_pred             EEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             08997143889998743554211343213662678988512681899617886622577788888877753697306752
Q gi|254780834|r  273 FIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVL  352 (648)
Q Consensus       273 ~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~  352 (648)
                      .+||||||||||++||+|++|+||++||++|++|+++|++++.+|++|||+|+||++|+.|+++.++   +.|++++|+.
T Consensus         2 ~viivEG~~D~i~~~~~G~~n~VA~~Gt~~t~~q~~~L~~~~~~vil~~D~D~AG~~Aa~r~~~~l~---~~g~~v~i~~   78 (79)
T cd03364           2 KVILVEGYMDVIALHQAGIKNVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAALRALELLL---KLGLNVRVLT   78 (79)
T ss_pred             EEEEEECHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHHHH---HCCCEEEEEE
T ss_conf             8999967799999998599625625665471999997723158679997898899999999999999---7799699997


Q ss_pred             C
Q ss_conf             5
Q gi|254780834|r  353 L  353 (648)
Q Consensus       353 L  353 (648)
                      |
T Consensus        79 l   79 (79)
T cd03364          79 L   79 (79)
T ss_pred             C
T ss_conf             9


No 9  
>PHA02415 DNA primase domain-containing protein
Probab=99.68  E-value=8.7e-14  Score=146.42  Aligned_cols=314  Identities=20%  Similarity=0.305  Sum_probs=206.4

Q ss_pred             HHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEEC---CCC-EEEECCCCCCCCHHHHHHHHC
Q ss_conf             8999998748888875412221015887777755753458888587879817---897-467136888878989989885
Q gi|254780834|r    6 DFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCND---SKG-FYYCFSCHVKGDHLSFLSALL   81 (648)
Q Consensus         6 ~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~---~~~-~~~cf~c~~~gd~~~f~~~~~   81 (648)
                      ..||++|.++|+-|+..+ +.|+| |.+.-++.|  .+|-|.||+||+++..   .++ -|+.++.++||..||.||.-.
T Consensus         2 as~dqLK~~IDLhdLA~R-Lgl~R-~~~G~~~~Y--hsP~h~Dk~pSlSIf~nh~~~g~~WkDhs~~~gGSciDLV~~~r   77 (930)
T PHA02415          2 ATIDELKQRIDLHDLADR-LGLKR-GRGGDKALY--HSPQHEDKSPSLSIYVNHPKHGTGWRDHSADAGGSCIDLVIHAR   77 (930)
T ss_pred             CCHHHHHHCCCHHHHHHH-HCCCC-CCCCCCCCC--CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHCC
T ss_conf             657888610669889998-47603-689985555--69988888985578734743576423356788974678888606


Q ss_pred             CCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHC----CC
Q ss_conf             99979999999998188587768203677788999999999999999997326777578999985068853510----12
Q gi|254780834|r   82 GCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIE----MF  157 (648)
Q Consensus        82 ~~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~----~f  157 (648)
                      +-+-.||+++|.+.|||+.+...+..   ..++.++-    ..+   ..++..+  ..|+.||.+|||++..|+    .=
T Consensus        78 ~~~~~dA~k~L~d~ygiP~~~pA~~~---~~~kSt~e----yIA---erc~a~~--~~a~aYLagRGI~~av~~~ai~~~  145 (930)
T PHA02415         78 GGTVADAVRYLHDAYGIPLDRPAPAE---RREKSTVE----YIA---DRCLAER--ERVREYLGGRGISAAAIDAAFAAR  145 (930)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCCCCCC---CCCCCHHH----HHH---HHHHCCC--HHHHHHHHCCCCCHHHHHHHHHHC
T ss_conf             99889999998897579988876200---24313799----999---8873261--256777621796389999999846


Q ss_pred             CCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEEC-CCCEEEEECCCCCCCCC--CEEC
Q ss_conf             44225677410345542059973452320121003465410000167168889707-78588850100146553--0010
Q gi|254780834|r  158 KLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSS-RGQVIAFGGRTLSKGES--VKYL  234 (648)
Q Consensus       158 ~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~-~g~~i~f~gR~l~~~~~--~KYl  234 (648)
                      -+||.  .|++-...             +|=+.  -.|  +      -..|+++.. .|+|||.-=|-.|+.-+  .|--
T Consensus       146 ~lG~n--~WtS~kv~-------------aGe~G--hgG--P------AaaFivr~~~~~~VvaVDlRy~DPAlNG~vKTq  200 (930)
T PHA02415        146 SLGFN--TWTSSKVA-------------AGEVG--HAG--P------AAAFIVREPADGRVVAVDMRYVDPALNGGVKTQ  200 (930)
T ss_pred             CCCCC--CCCCCCCC-------------CCCCC--CCC--C------CEEEEEECCCCCCEEEEEEEECCCCCCCCCCCC
T ss_conf             57635--45676778-------------98878--787--5------135577227887379987112270016885210


Q ss_pred             CCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCC--HHHHHCCCCHHHHHHHHH
Q ss_conf             387676535210110817888864331000023567870899714388999874355421--134321366267898851
Q gi|254780834|r  235 NSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNV--VSSLGTALTEYQLRLLWK  312 (648)
Q Consensus       235 NSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~--va~~Gtalt~~~~~~l~r  312 (648)
                      ---     .|.-.-|--+.++-  +          ....|+|||....++|..-+-.+++  +|.-|+|-.++ |-.-+-
T Consensus       201 ~qG-----eK~G~gwt~D~~rL--~----------rA~~VyiVESpINAlSi~~c~~pg~aa~alRG~aNvd~-IDwsfl  262 (930)
T PHA02415        201 TQG-----DKAGYGWTADARRL--D----------KAKRVFIVESAINALSIDTCAMPGAAALALRGLANVDA-IDFSSL  262 (930)
T ss_pred             CCC-----CCCCCCCCCCHHHH--H----------HCCEEEEEECCCHHHHHHHHCCCCCEEEEEECCCCCCC-CCHHHH
T ss_conf             145-----44577876798888--3----------27489998245014436663389830133104455553-110111


Q ss_pred             CCCEEEEEECCCC------------CCHHHHHHHHHHHHHHHHCCCCEEEEEC-------CCC-------CCHHHHHHCC
Q ss_conf             2681899617886------------6225777888888777536973067525-------788-------8888997203
Q gi|254780834|r  313 LSPRIVLCFDGDD------------PGLRAAYKAIDLVLCHLIPGNRVNFVLL-------SRG-------EDPDSFIRCY  366 (648)
Q Consensus       313 ~~~~vvl~fDgD~------------AG~kAa~Ra~e~~l~~l~~g~~v~vv~L-------P~G-------~DPDe~ir~~  366 (648)
                      -.++|++|+|.|+            +|..||++.-|.+..+   ++....|-.       .+|       .|-.||++.+
T Consensus       263 rGKrvvi~lD~~dp~~e~~pr~g~RPG~eAAW~l~E~lta~---~I~~~LVD~~~W~~gl~~~e~~~~~i~DiND~Lq~~  339 (930)
T PHA02415        263 RGKQVVICLDNDEPFEDGHPRAGHRPGPEAAWALYERLASL---NISAVLVDQAGWLADLADGETKQQPINDVNDYLQLR  339 (930)
T ss_pred             CCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHC---CCCCEEEEHHHHHCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             58769999368875445785447898778899999988763---853124516544324554422235510278999971


Q ss_pred             CHHHHHHHHHHCCCH
Q ss_conf             668899886414992
Q gi|254780834|r  367 GKTAFEKLIVESLPL  381 (648)
Q Consensus       367 G~eaf~~ll~~A~~l  381 (648)
                      |++.+...+++=.|+
T Consensus       340 Ga~el~~~l~~lepW  354 (930)
T PHA02415        340 GPEELARALEQLEPW  354 (930)
T ss_pred             CHHHHHHHHHHCCCC
T ss_conf             789999999724411


No 10 
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Probab=99.31  E-value=6.8e-12  Score=129.01  Aligned_cols=77  Identities=52%  Similarity=0.796  Sum_probs=70.3

Q ss_pred             EEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             08997143889998743554211343213662678988512681899617886622577788888877753697306752
Q gi|254780834|r  273 FIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVL  352 (648)
Q Consensus       273 ~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~  352 (648)
                      .++|||||+||++++|+|+.++||++||+.+..|+..+++..++|+||||+|.||++|+.|+.+.++..   +..++++.
T Consensus         2 ~v~i~EG~~Dals~~~~g~~~~va~~G~~~~~~~~~~l~~~~~~vii~~D~D~aG~~~~~~~~~~~~~~---~~~~~i~~   78 (79)
T cd01029           2 EVIIVEGYMDVLALHQAGIKNVVAALGTANTEEQLRLLKRFARTVILAFDNDEAGKKAAARALELLLAL---GGRVRVPP   78 (79)
T ss_pred             EEEEEECHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHHHHHC---CCEEEEEE
T ss_conf             399996479999999718654425887677499999985557765999688899999999999999977---99699851


No 11 
>PHA02031 putative DnaG-like primase
Probab=99.13  E-value=4.5e-10  Score=112.23  Aligned_cols=165  Identities=21%  Similarity=0.287  Sum_probs=116.2

Q ss_pred             CCHHHHHHHCCCCCHHHHHH-HCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEEC---CCCCCCC
Q ss_conf             41034554205997345232-0121003465410000167168889707785888501001465530010---3876765
Q gi|254780834|r  166 RYSLREHLRQKGFSEEKIIE-AGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYL---NSPETIL  241 (648)
Q Consensus       166 ~~~l~~~l~~~~~~~~~~~~-~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYl---NSpeT~i  241 (648)
                      +.+++.++..||++.-.+.. .||         ||-.=.+||+||+.+.      .-||..+ +.+|||+   |-+-   
T Consensus        93 ~~~iy~~ll~Kgi~~~~~~~~l~l---------y~S~r~~Rlilp~~~g------W~gRs~~-~~~PKW~gYg~p~~---  153 (274)
T PHA02031         93 YQSLYGLLLSKGIDYNVMTPGLPL---------LYSERQHRLIFPTDAG------WIGRATA-DQNPKWVGYGYPAP---  153 (274)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCC---------HHHHHCCEEEEECCCC------HHHHCCC-CCCCCCCCCCCCCC---
T ss_conf             777655421046555546775332---------0021068389753430------3121115-67873003799973---


Q ss_pred             CCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCC----CCHHHHHCCCCHHHHHHHHH-CCCE
Q ss_conf             352101108178888643310000235678708997143889998743554----21134321366267898851-2681
Q gi|254780834|r  242 FHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQ----NVVSSLGTALTEYQLRLLWK-LSPR  316 (648)
Q Consensus       242 f~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~----n~va~~Gtalt~~~~~~l~r-~~~~  316 (648)
                           -+.++..+.             ...+.+||+|   |+||.+.-|.-    .++|.|||.|+.-|...|-. .+++
T Consensus       154 -----~~~~~~~~~-------------~~g~~~VLTE---D~lSA~KV~~a~~~~~A~alLGT~L~~~~AA~Llq~~~k~  212 (274)
T PHA02031        154 -----DYHGWPQEL-------------SMGRPWVLTE---DYLSALKVRWACPEVFAVGLNGTRLRDRLAAIMLQQTCKR  212 (274)
T ss_pred             -----CCCCCCCCC-------------CCCCCEEEEH---HHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHCCCC
T ss_conf             -----313434223-------------7887279754---5554554431036412321105653368999999844995


Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf             8996178866225777888888777536973067525788888899720366889988641
Q gi|254780834|r  317 IVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE  377 (648)
Q Consensus       317 vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~  377 (648)
                      |+++||||.||..++-.+...+-++   |++++++.-|+|.||-++=    ....+++|..
T Consensus       213 V~~wLD~D~AG~~Ga~~i~k~LR~~---gl~~~~~~~~~~~DPKd~~----~~qI~~ii~g  266 (274)
T PHA02031        213 AFIFLDGDPAGVRGSAGVMRRLRSL---LIEGQVIHTPDGFDPKDLT----REQIRSLVIG  266 (274)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHHH---HCCCEEEECCCCCCCCCCC----HHHHHHHHCC
T ss_conf             7999569831213589999998874---0512256247789922089----9999999746


No 12 
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI; InterPro: IPR014129   This entry represents TraI, which is a component of the relaxosome complex. In the process of conjugative plasmid transfer the relaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein ..
Probab=98.88  E-value=2.3e-07  Score=87.43  Aligned_cols=303  Identities=19%  Similarity=0.293  Sum_probs=197.8

Q ss_pred             CCCCCCCCEEEE---CCCCEEEECCCCCCCCHHHHHHHHCCCC-HHHHHHHHHHHHCCCCC---CCCCCHHH-HHHHHHH
Q ss_conf             888858787981---7897467136888878989989885999-79999999998188587---76820367-7788999
Q gi|254780834|r   45 FHDEKTPSFHCN---DSKGFYYCFSCHVKGDHLSFLSALLGCS-FIESVQRLAAIAGVPLP---VVDPKIEK-KEKIQTD  116 (648)
Q Consensus        45 fh~ektpsf~v~---~~~~~~~cf~c~~~gd~~~f~~~~~~~~-f~ea~~~la~~~gi~~~---~~~~~~~~-~~~~~~~  116 (648)
                      |-.-|. ++.|+   ..||+||-|+.|.+|..|+.+|..++|| |.||+..=+...|++=-   .-...+++ .......
T Consensus      1759 fg~~KG-~Lkv~L~g~yrG~w~~f~tG~~G~li~li~~~~~LSG~KEal~~A~~l~~~p~~~~~~i~~~a~~~~~~~~~k 1837 (2193)
T TIGR02760      1759 FGTAKG-SLKVSLTGKYRGLWKDFETGEKGTLIDLIEAKKGLSGFKEALNKAASLLGEPEHYQLSINKKAPQLLNTEPEK 1837 (2193)
T ss_pred             ECCCCC-CEEEEECCCCCCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             006752-2588750453422242467888768888751058877799999999862787412544142341234344566


Q ss_pred             HHHHHH-----HHHHHHHHHHCCCCCHHHHHHH-HHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCE
Q ss_conf             999999-----9999999973267775789999-8506885351012442256774103455420599734523201210
Q gi|254780834|r  117 LIRLIE-----VATDFFHHSLKNARDKRLHYYL-DERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLI  190 (648)
Q Consensus       117 ~~~~~~-----~~~~~~~~~l~~~~~~~a~~yl-~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~  190 (648)
                      +-++-.     .|..+|..-. .-+|..|-.|| ..||+.  .++.-.|-|+|....+  +-|.+.          |++.
T Consensus      1838 ~~~~e~r~kvi~A~~~f~~s~-~~~gTlAe~YL~~~~G~~--~~D~~~~Rf~P~vy~W--knCneq----------G~~~ 1902 (2193)
T TIGR02760      1838 LAQLEKRNKVILAKKLFQESQ-ELKGTLAEKYLKQHRGLA--SIDNDDIRFHPSVYSW--KNCNEQ----------GKLS 1902 (2193)
T ss_pred             HHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHCCCCC--CCCCCCCCCCCCCCCC--CCCCCC----------CCCC
T ss_conf             765544456788899863480-167889999998617863--3456451132576751--010112----------5555


Q ss_pred             ECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCC--CCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCC
Q ss_conf             034654100001671688897077858885010014655--300103876765352101108178888643310000235
Q gi|254780834|r  191 DGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGE--SVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRR  268 (648)
Q Consensus       191 ~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~--~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~  268 (648)
                      . +....|+      ++.+++|..|++-|..=--|+++.  .-|-+.++--.+=.|+...-.|+...+.           
T Consensus      1903 ~-~~~~~PA------li~~~~~~~g~~~gi~~~yL~~~~a~k~~~~~~~krv~G~~s~~~~~ln~g~~g----------- 1964 (2193)
T TIGR02760      1903 D-KKKKHPA------LIAAAKDEKGEIKGIQITYLDKDDANKDKDMDSNKRVLGSKSGQFVVLNKGRQG----------- 1964 (2193)
T ss_pred             C-CCCCCCE------EEEECCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEECCCEEECCCCCCH-----------
T ss_conf             6-4345530------010111889854116851368655567663656874112013624430477640-----------


Q ss_pred             CCCCEEEEECCHHHHHHHHHCCCCC--CHHHHHC-------CCCHHH---------HHHHH--HCCCEEEEEECCCCCCH
Q ss_conf             6787089971438899987435542--1134321-------366267---------89885--12681899617886622
Q gi|254780834|r  269 NSSSFIILVEGYMDVLSLCQAGVQN--VVSSLGT-------ALTEYQ---------LRLLW--KLSPRIVLCFDGDDPGL  328 (648)
Q Consensus       269 ~~~~~~i~vEGy~Dvi~l~~~G~~n--~va~~Gt-------alt~~~---------~~~l~--r~~~~vvl~fDgD~AG~  328 (648)
                         +..||.||.=+.++-.++--.+  +|+..|-       |+|-..         ++-+.  ..-.+||||.|.|.-=.
T Consensus      1965 ---~~~~~a~G~E~g~~I~~~n~~~~~~~~v~~~~~PWnPvaitGGrvWGdiPd~n~~~i~~~~~~~~v~I~l~n~~~~~ 2041 (2193)
T TIGR02760      1965 ---DISYLAEGIETGLSIAEANPKATVVIAVVGKNRPWNPVAITGGRVWGDIPDNNVSPIAPKDIPKNVVIVLDNDGEEA 2041 (2193)
T ss_pred             ---HHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCEEEECCEEECCCCCCCCCCCCCCCCCEEEEEEECCCCHHH
T ss_conf             ---07888886899999975489960699980488764664640660233577334788888887306999724773689


Q ss_pred             -----HHHHHHH-HHHHHHHHCCCCEEEEECCC------CCCHHHHHHCCCHHHHHHHHHH----CCCHHHHH
Q ss_conf             -----5777888-88877753697306752578------8888899720366889988641----49927999
Q gi|254780834|r  329 -----RAAYKAI-DLVLCHLIPGNRVNFVLLSR------GEDPDSFIRCYGKTAFEKLIVE----SLPLVDML  385 (648)
Q Consensus       329 -----kAa~Ra~-e~~l~~l~~g~~v~vv~LP~------G~DPDe~ir~~G~eaf~~ll~~----A~~l~dFl  385 (648)
                           +-.-|.+ ++...+-.+|..+.+|+ |+      .-|=.+..-+.|.+.+.+-|..    +...+++.
T Consensus      2042 yky~~~e~~~~i~ki~~kl~~d~~~~~i~~-P~GlqGK~~TD~Nd~~l~~~~~~~~k~~~~kDiG~i~~~~~k 2113 (2193)
T TIGR02760      2042 YKYVKRESQRAIEKIIKKLKEDNISASIVI-PDGLQGKEKTDLNDVLLKKGEEELKKQLKRKDIGAISSIEDK 2113 (2193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCEEEEEE-CCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             999853534329999999616898089981-378676111660001003863799999745422012010036


No 13 
>pfam01751 Toprim Toprim domain. This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.
Probab=98.83  E-value=1e-08  Score=99.90  Aligned_cols=79  Identities=39%  Similarity=0.578  Sum_probs=72.1

Q ss_pred             EEEEECCHHHHHHHHHCCC--CCCHHHHHCC-----CCHHHHHHHHHCCCE--EEEEECCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             0899714388999874355--4211343213-----662678988512681--899617886622577788888877753
Q gi|254780834|r  273 FIILVEGYMDVLSLCQAGV--QNVVSSLGTA-----LTEYQLRLLWKLSPR--IVLCFDGDDPGLRAAYKAIDLVLCHLI  343 (648)
Q Consensus       273 ~~i~vEGy~Dvi~l~~~G~--~n~va~~Gta-----lt~~~~~~l~r~~~~--vvl~fDgD~AG~kAa~Ra~e~~l~~l~  343 (648)
                      .++||||++||+++.+.|+  .++++++|+.     ++++|++.|++..++  ||+|+|+|.+|+.++++..+.+.+.  
T Consensus         2 ~l~IVE~~~d~~~i~~~~~~~~~~~~~~G~~~~l~~~~~~~~~~l~~~~~~~eViiatD~D~eGe~~a~~l~~~l~~~--   79 (89)
T pfam01751         2 VLIIVEGPSDAIALAKAGGYKGNVVALLGHLSDVIPLTKEQLKLLKKLAKKDEVILATDPDREGEAIAWKLLELLKPL--   79 (89)
T ss_pred             EEEEECCHHHHHHHHHHCCCCEEEEEEECEECCCCCCCHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHHHHC--
T ss_conf             899989889999999624888799984157057655424679999986237749998798948999999999983122--


Q ss_pred             CCCCEEEEECC
Q ss_conf             69730675257
Q gi|254780834|r  344 PGNRVNFVLLS  354 (648)
Q Consensus       344 ~g~~v~vv~LP  354 (648)
                       +..++.+.+|
T Consensus        80 -~~~v~ri~~~   89 (89)
T pfam01751        80 -GKKVRRIFLP   89 (89)
T ss_pred             -CCCEEEEECC
T ss_conf             -9816999669


No 14 
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=98.75  E-value=2.1e-08  Score=96.93  Aligned_cols=68  Identities=34%  Similarity=0.468  Sum_probs=63.0

Q ss_pred             EEEEECCHHHHHHHHHCCC--CCCHHHHHCCCCHHHHHHHHHCCCE--EEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             0899714388999874355--4211343213662678988512681--899617886622577788888877
Q gi|254780834|r  273 FIILVEGYMDVLSLCQAGV--QNVVSSLGTALTEYQLRLLWKLSPR--IVLCFDGDDPGLRAAYKAIDLVLC  340 (648)
Q Consensus       273 ~~i~vEGy~Dvi~l~~~G~--~n~va~~Gtalt~~~~~~l~r~~~~--vvl~fDgD~AG~kAa~Ra~e~~l~  340 (648)
                      .++||||++||+++++.|.  .++++++|+..+.+|+..|++..++  ||||+|+|.+|+++++++.+.+.+
T Consensus         2 ~liIVEg~~d~~~i~~~~~~~~~~~~~~G~~~~~~~i~~l~~~~~~~eViiatD~D~eGe~~a~~i~~~l~~   73 (76)
T smart00493        2 VLIIVEGPADAIALEKAGGFGGNVVALGGHLLKKEIIKLLKRLAKKKEVILATDPDREGEAIAWKLAELLKP   73 (76)
T ss_pred             EEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             799987888999999856999799982152350448999998633897999769894469999999998776


No 15 
>PRK04031 DNA primase; Provisional
Probab=98.43  E-value=1.8e-06  Score=79.13  Aligned_cols=102  Identities=27%  Similarity=0.420  Sum_probs=78.4

Q ss_pred             CCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHC-CCCE
Q ss_conf             787089971438899987435542113432136626789885126818996178866225777888888777536-9730
Q gi|254780834|r  270 SSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIP-GNRV  348 (648)
Q Consensus       270 ~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~-g~~v  348 (648)
                      ..+.+|||||--||+-|-.+||+|+||..||.+-+.-+.+-++  +.|+.+.|||.        +.++.|..|.+ +.--
T Consensus       167 ~sd~iIvVEGRaDV~nLLk~GikN~ia~~G~~ip~~i~~L~~~--k~vtaF~DGDr--------GG~liLKELlqVadID  236 (420)
T PRK04031        167 DSDAIIVVEGRADVLNLLRYGIKNVIAVEGTSVPETIIELSKK--KTVTAFLDGDR--------GGELILKELLQVADID  236 (420)
T ss_pred             CCCEEEEEECHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHCC--CEEEEEECCCC--------CHHHHHHHHHHHCCEE
T ss_conf             8880899956588999987363327862688888899998638--65899953885--------4378999998546735


Q ss_pred             EEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHH
Q ss_conf             6752578888889972036688998864149927999
Q gi|254780834|r  349 NFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDML  385 (648)
Q Consensus       349 ~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl  385 (648)
                      +|++-|+|+---++-++    .....|.+..|...|+
T Consensus       237 YVArAP~GKEVEeLT~K----EI~KALR~KVP~eq~~  269 (420)
T PRK04031        237 YVARAPPGKEVEELTKK----EIAKALRNKVPVEQYL  269 (420)
T ss_pred             EEEECCCCCCHHHCCHH----HHHHHHHCCCCHHHHH
T ss_conf             99979899635326887----9999987248889998


No 16 
>TIGR00646 MG010 DNA primase homolog; InterPro: IPR004611   The DNA primase DnaG of Escherichia coli and its apparent orthologs in other bacterial species are approximately 600 residues in length. Within this set, a conspicuous outlier in percent identity, as seen in a UPGMA difference tree, is the branch containing the Mycoplasmas. This lineage is also unique in containing the small, DNA primase-related protein found in this family, which is homologous to the central third of DNA primase. Several small regions of sequence similarity specifically to Mycoplasma sequences rather than to all DnaG homologs suggests that the divergence of this protein from DnaG post-dated the separation of bacterial lineages. The function of this DNA primase-related protein is unknown..
Probab=98.43  E-value=1e-06  Score=81.42  Aligned_cols=197  Identities=22%  Similarity=0.299  Sum_probs=141.4

Q ss_pred             HHHHHHHHHCCC---CCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCC
Q ss_conf             999999973267---77578999985068853510124422567741034554205997345232012100346541000
Q gi|254780834|r  124 ATDFFHHSLKNA---RDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYD  200 (648)
Q Consensus       124 ~~~~~~~~l~~~---~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d  200 (648)
                      ..-.||..|++.   +-..+..|+.+||++-+..-..+=|.+         |+                           
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~d~~~~ggg~~---------~~---------------------------   54 (218)
T TIGR00646        11 LFFVYHKNLKNQSKSKYRCPVNYLKKRGFNLQDLLKVGGGLG---------YL---------------------------   54 (218)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHCCCCHH---------HC---------------------------
T ss_conf             666554210100012455567777632775356654044200---------00---------------------------


Q ss_pred             CCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCH
Q ss_conf             01671688897077858885010014655300103876765352101108178888643310000235678708997143
Q gi|254780834|r  201 RFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGY  280 (648)
Q Consensus       201 ~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy  280 (648)
                      .-+.-+-.|+.+..|.++||-.|.+.-  ..+++-+|-..-=.|+....|+....-             ....+++|||-
T Consensus        55 ~~~~w~~~~~~~~~~~~~g~~~~~~~~--~~~~~~~p~~~pp~~~~~~~g~~~~~~-------------~~~~~~~~~gd  119 (218)
T TIGR00646        55 GEKEWLNLPLYNFDGNLVGFLNRKVGF--EKEFLYLPFNKPPSKSEAFLGLKELPT-------------EDNTIYLVEGD  119 (218)
T ss_pred             CCCCCCCCEEECCCCCCHHHHHHHCCC--CCCEEECCCCCCCCCCHHHHHHHHHCC-------------CCCEEEEEECC
T ss_conf             342100000001366101122211011--100022146788541012310122000-------------25505886166


Q ss_pred             HHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHC-CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCC-CC
Q ss_conf             889998743554211343213662678988512-6818996178866225777888888777536973067525788-88
Q gi|254780834|r  281 MDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKL-SPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRG-ED  358 (648)
Q Consensus       281 ~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~-~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G-~D  358 (648)
                      +|-++....|+-|.+..||..++..+++.+.+- ..++++|+|.|-||..++...-+.   +...|..++++.+... +|
T Consensus       120 ~dw~~~~~~g~~~~~p~cg~~~~~~~~~~~~~~~~~~~~~c~d~d~~g~~~~~~~~~~---~~~~g~~~~~~~~~~~~~d  196 (218)
T TIGR00646       120 FDWLAFRKGGILNCLPLCGLTLSDKQVKWLKQKKIEKVFLCLDNDLAGKNGAKNLEEY---LKNAGFITKVVELKGKAKD  196 (218)
T ss_pred             CHHHHHHHCCCHHHHHHCCCCCCHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHH---HHHCCCEEEHHHHHHHHCC
T ss_conf             2011221033100000103100203566655411004566523530000235568888---7404731210002100012


Q ss_pred             HHHHHHCCCHHHHHHHH
Q ss_conf             88997203668899886
Q gi|254780834|r  359 PDSFIRCYGKTAFEKLI  375 (648)
Q Consensus       359 PDe~ir~~G~eaf~~ll  375 (648)
                      =.+++.-+ +..+...+
T Consensus       197 w~~~~~~~-~~~w~~~~  212 (218)
T TIGR00646       197 WNDLLLLY-PKNWAKAL  212 (218)
T ss_pred             CCCEEEEC-CCCHHHHH
T ss_conf             00012421-64045666


No 17 
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.32  E-value=4e-05  Score=66.75  Aligned_cols=266  Identities=23%  Similarity=0.285  Sum_probs=147.1

Q ss_pred             ECCCCCCCCCCEEEECCC--CEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCH-HHHHHHHHHHH
Q ss_conf             345888858787981789--746713688887898998988599979999999998188587768203-67778899999
Q gi|254780834|r   42 CCPFHDEKTPSFHCNDSK--GFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKI-EKKEKIQTDLI  118 (648)
Q Consensus        42 ~cPfh~ektpsf~v~~~~--~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~gi~~~~~~~~~-~~~~~~~~~~~  118 (648)
                      .||-..-|. -|-+.++|  |.|.||-|+ +||=.+.|....+.++.|+........|...|...... .....+.+..-
T Consensus        34 ~cpvcg~k~-RFr~dD~kGrGtw~c~y~~-~GDGl~lvs~v~~~~~~eaa~~i~~~i~~~~~~~~a~~~s~a~~~~~~~~  111 (366)
T COG4643          34 PCPVCGGKD-RFRFDDRKGRGTWFCNYCG-HGDGLPLVSLVRQRTGIEAAWEIKGDIGNDAPESKAMRASIAPAKADRAA  111 (366)
T ss_pred             CCCCCCCCC-CCCCCCCCCCCCEEEEEEC-CCCCCCCEEECCCCCHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             898557766-3015675677646886404-67885315530577258999987311047613212334221335577788


Q ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCC
Q ss_conf             99999999999973267775789999850688535101244225677410345542059973452320121003465410
Q gi|254780834|r  119 RLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATS  198 (648)
Q Consensus       119 ~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~  198 (648)
                      +--..+...+...    .+.-.-.|+.++|.                     -||..++++..             ++.+
T Consensus       112 ~~~~la~~~a~~~----~gts~~a~~~~~g~---------------------p~Lp~~~it~~-------------~~i~  153 (366)
T COG4643         112 ERAKLAALLAAKS----RGTSGYAYLVSLGH---------------------PYLPAKGITPA-------------AGIG  153 (366)
T ss_pred             HHHHHHHHHHHHH----HHHHHHHHHCCCCC---------------------CCCCCCCCCCC-------------CCCC
T ss_conf             9999999999863----30235688735896---------------------15424546512-------------3356


Q ss_pred             CCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEEC
Q ss_conf             00016716888970778588850100146553001038767653521011081788886433100002356787089971
Q gi|254780834|r  199 YDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVE  278 (648)
Q Consensus       199 ~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vE  278 (648)
                      -+-|+.--++|..|..|...+.-  .+.++         -|.=|.||.--=|.+........         ....+|++|
T Consensus       154 ~~~~~~~slip~~d~~Gel~~lq--~I~~d---------G~Krf~~Ggr~kg~f~p~~g~~~---------~aa~lvi~E  213 (366)
T COG4643         154 GVQLRDGSLIPLRDADGELTGLQ--LIQPD---------GTKRFLKGGRVKGCFIPLGGLAG---------PAARLVIAE  213 (366)
T ss_pred             CCCCCCCCEEEEECCCCCEEEEE--EECCC---------CCCEECCCCCCCCCEEECCCCCC---------CCCCEEEEE
T ss_conf             54446663687772788775368--87678---------65000358742340432588754---------343057740


Q ss_pred             CHHHHHHHHHCC-CCCCHHHHHCCCCHHHHHHHHHC-CCEEEEEECCCC-----CCHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             438899987435-54211343213662678988512-681899617886-----62257778888887775369730675
Q gi|254780834|r  279 GYMDVLSLCQAG-VQNVVSSLGTALTEYQLRLLWKL-SPRIVLCFDGDD-----PGLRAAYKAIDLVLCHLIPGNRVNFV  351 (648)
Q Consensus       279 Gy~Dvi~l~~~G-~~n~va~~Gtalt~~~~~~l~r~-~~~vvl~fDgD~-----AG~kAa~Ra~e~~l~~l~~g~~v~vv  351 (648)
                      ||--+.+++|+= ..-++|-.-+.|+.--..+-++| +..||||=|.|.     +|+.++..+..-+      +..+  .
T Consensus       214 GyATal~i~~~~ga~v~aAi~agNll~VA~al~~~~Pda~iIIaAD~D~~~~nnpG~t~A~eaA~Av------ng~~--~  285 (366)
T COG4643         214 GYATALSISQATGAPVAAAIDAGNLLAVASALRKKFPDAQIIIAADDDINTANNPGLTKAEEAAQAV------NGTV--A  285 (366)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCHHHHHHHHHHH------CCEE--E
T ss_conf             2367879998741066544402358999999997689763699745654467880167899998752------7666--3


Q ss_pred             ECCCC-CCHHHHHHCCCHHHHHHHH
Q ss_conf             25788-8888997203668899886
Q gi|254780834|r  352 LLSRG-EDPDSFIRCYGKTAFEKLI  375 (648)
Q Consensus       352 ~LP~G-~DPDe~ir~~G~eaf~~ll  375 (648)
                      .+|-+ -|=+|+...+|..+-+.-+
T Consensus       286 lP~~~~adwpD~~tq~n~la~r~~~  310 (366)
T COG4643         286 LPPFGPADWPDGFTQFNDLATRCAF  310 (366)
T ss_pred             CCCCCCCCCCHHHHHCCHHHHHHHH
T ss_conf             6887887784054332205555332


No 18 
>cd00188 TOPRIM Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=97.94  E-value=3.4e-05  Score=67.36  Aligned_cols=67  Identities=34%  Similarity=0.430  Sum_probs=59.2

Q ss_pred             EEEEECCHHHHHHHHHCCC--CCCHHHHHCCC--CHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             0899714388999874355--42113432136--6267898851268189961788662257778888887
Q gi|254780834|r  273 FIILVEGYMDVLSLCQAGV--QNVVSSLGTAL--TEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVL  339 (648)
Q Consensus       273 ~~i~vEGy~Dvi~l~~~G~--~n~va~~Gtal--t~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l  339 (648)
                      .++||||..|++++.+.+.  ..++++.|+..  +..++..+.+...+|++++|+|.+|..++.+......
T Consensus         2 ~viivEG~~d~~~l~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~vii~~D~D~~g~~~~~~~~~~~~   72 (83)
T cd00188           2 KLIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLK   72 (83)
T ss_pred             EEEEECCHHHHHHHHHHCCCCEEEEEEEEEECCCHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHH
T ss_conf             79998888999999985699979999755738438999999876899999974989379999999999732


No 19 
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea.  RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=97.84  E-value=4.3e-05  Score=66.47  Aligned_cols=66  Identities=23%  Similarity=0.357  Sum_probs=59.8

Q ss_pred             CEEEEECCHHHHHHHHHCCCC-CCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             708997143889998743554-211343213662678988512681899617886622577788888
Q gi|254780834|r  272 SFIILVEGYMDVLSLCQAGVQ-NVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDL  337 (648)
Q Consensus       272 ~~~i~vEGy~Dvi~l~~~G~~-n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~  337 (648)
                      +.+|||||-.|..++.++|++ ..+.+.|++++..-+.++++....|+++.|.|.+|.+-+.+-.+.
T Consensus         2 ~evIvVEGk~D~~~l~~~~~~~~ii~t~g~~~~~~~~~~i~~~~~~VIIlTD~D~~Gekirk~i~~~   68 (81)
T cd01027           2 GEVIIVEGKNDTESLKKLGIEAEIIETNGSIINKETIELIKKAYRGVIILTDPDRKGEKIRKKLSEY   68 (81)
T ss_pred             CEEEEEECCCHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHH
T ss_conf             7699995561899999863781399989903459999999985598599968996707999999998


No 20 
>pfam10410 DnaB_bind DnaB-helicase binding domain of primase. This domain is the C-terminal region three-helical domain of primase. Primases synthesize short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases, and this domain is the region of the primase which binds DnaB-helicase. It is associated with the Toprim domain (pfam01751) which is the central catalytic core.
Probab=97.83  E-value=3.9e-05  Score=66.88  Aligned_cols=56  Identities=30%  Similarity=0.361  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             27999999985302331457999999999885417998999999999999988765
Q gi|254780834|r  381 LVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLF  436 (648)
Q Consensus       381 l~dFl~~~l~~~~dl~spe~ka~~~~~l~~~I~~I~d~~~R~~yl~~la~~L~~~~  436 (648)
                      +++|+|+++.++.|+++|++|+++.+.+.|+|++|+|++.|+.|+++++++++...
T Consensus         1 l~~f~~~~l~~~~dl~~~egk~~~~~~~~pli~~i~~~~~r~~y~~~la~~~gi~~   56 (59)
T pfam10410         1 LSEFLFRRLLEGYDLDTPEGRAALLREALPLIAKIPDPVLRELYLQELAELLGISE   56 (59)
T ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             92889999873589999889999999970787559838899999999999878284


No 21 
>PRK06904 replicative DNA helicase; Validated
Probab=97.47  E-value=0.022  Score=41.60  Aligned_cols=48  Identities=15%  Similarity=0.117  Sum_probs=32.3

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ  288 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~  288 (648)
                      .|..|=.+||-   +               =|+..+.++.|..+..+.         ..+|.+.--.|..-.+..
T Consensus       220 ~g~LiViAaRP---s---------------mGKTa~alnia~n~A~~~---------~~~V~~fSLEM~~~~l~~  267 (472)
T PRK06904        220 PSDLIIVAARP---S---------------MGKTTFAMNLCENAAMAS---------EKPVLVFSLEMPAEQIMM  267 (472)
T ss_pred             CCCEEEEEECC---C---------------CCHHHHHHHHHHHHHHHC---------CCCEEEECCCCCHHHHHH
T ss_conf             57579997379---8---------------756899999999999955---------995799778799999999


No 22 
>LOAD_Toprim consensus
Probab=97.43  E-value=0.00077  Score=54.96  Aligned_cols=66  Identities=30%  Similarity=0.374  Sum_probs=54.3

Q ss_pred             EEEEECCHHHHHHHHHCC-CCCCHHHHHCCC--CHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             089971438899987435-542113432136--626789885126818996178866225777888888
Q gi|254780834|r  273 FIILVEGYMDVLSLCQAG-VQNVVSSLGTAL--TEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLV  338 (648)
Q Consensus       273 ~~i~vEGy~Dvi~l~~~G-~~n~va~~Gtal--t~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~  338 (648)
                      .+|||||..|+-.+.+.+ -.+++|++|...  +...++...+-+++|+|+.|.|..|..-++...+++
T Consensus         2 ~liIVEsp~k~k~I~~~l~~~~vias~GHi~~~~~~~~~~~~~~~~~VilATDpDrEGEaIa~hl~~~l   70 (98)
T LOAD_Toprim       2 KIIVVEGPADAKAIERFGGDKNVIASKGHARKKSVLELIKLALKAKEVIIATDPDREGEKIAKKLLELL   70 (98)
T ss_pred             EEEEEECHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             499992848899999985998799795883251699999998469929994696965289999999983


No 23 
>PRK08760 replicative DNA helicase; Provisional
Probab=97.31  E-value=0.036  Score=39.62  Aligned_cols=48  Identities=19%  Similarity=0.108  Sum_probs=31.2

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ  288 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~  288 (648)
                      .|..|-.+||-=                  -|+.-+.++.|.....+.         ...|.+.--.|..-.+.+
T Consensus       228 ~G~LiViaaRPs------------------mGKTalalnia~~~A~~~---------~~~V~~fSLEMs~~ql~~  275 (476)
T PRK08760        228 PTDLIILAARPA------------------MGKTTFALNIAEYAAIKS---------KKGVAVFSMEMSASQLAM  275 (476)
T ss_pred             CCCEEEEEECCC------------------CCHHHHHHHHHHHHHHHC---------CCCEEEEECCCCHHHHHH
T ss_conf             777799987788------------------747899999999999837---------997899703699999999


No 24 
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=97.28  E-value=0.032  Score=40.10  Aligned_cols=47  Identities=21%  Similarity=0.254  Sum_probs=28.7

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             78588850100146553001038767653521011081788886433100002356787089971438899987
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLC  287 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~  287 (648)
                      .|..|-.+||.   +               =|+..+.++.|.....+         ...+|.+.=-.|..-.+.
T Consensus       193 ~g~LiIiaARP---s---------------mGKTafalnia~n~A~~---------~g~~Vl~fSLEMs~eql~  239 (421)
T TIGR03600       193 KGDLIVIGARP---S---------------MGKTTLALNIAENVALR---------EGKPVLFFSLEMSAEQLG  239 (421)
T ss_pred             CCCEEEEEEEC---C---------------CCHHHHHHHHHHHHHHH---------CCCEEEEEECCCCHHHHH
T ss_conf             88689998546---7---------------87459999999999986---------698389992579999999


No 25 
>PRK08006 replicative DNA helicase; Provisional
Probab=97.15  E-value=0.05  Score=38.31  Aligned_cols=48  Identities=13%  Similarity=0.059  Sum_probs=31.1

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ  288 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~  288 (648)
                      .|..|-.+||-=                  -|+.-+.++.|.....+         ...+|.+.--.|..-.+..
T Consensus       223 ~G~LiviaaRPs------------------mGKTalalnia~~~a~~---------~~~~V~~fSlEMs~~ql~~  270 (471)
T PRK08006        223 PSDLIIVAARPS------------------MGKTTFAMNLCENAAML---------QDKPVLIFSLEMPGEQIMM  270 (471)
T ss_pred             CCCEEEEEECCC------------------CCHHHHHHHHHHHHHHH---------CCCCEEEEECCCCHHHHHH
T ss_conf             173899994699------------------87699999999999986---------6995799816799999999


No 26 
>PRK07004 replicative DNA helicase; Provisional
Probab=97.11  E-value=0.051  Score=38.20  Aligned_cols=48  Identities=17%  Similarity=0.138  Sum_probs=31.0

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ  288 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~  288 (648)
                      .|..|-.+||-   +               -|++-+.++.|+....+         ....|.++=-.|..-.+.+
T Consensus       212 ~gdLiIIAARP---s---------------mGKTafAlniA~n~A~~---------~g~~V~~FSLEMs~eql~~  259 (460)
T PRK07004        212 GGELIIVAGRP---S---------------MGKTAFSMNIGEYVAVE---------YGLPVAVFSMEMPGTQLAM  259 (460)
T ss_pred             CCCEEEEEECC---C---------------CCHHHHHHHHHHHHHHH---------CCCCEEEECCCCCHHHHHH
T ss_conf             77579997368---7---------------64269999999999872---------5886699847799999999


No 27 
>PRK05748 replicative DNA helicase; Provisional
Probab=96.98  E-value=0.067  Score=37.09  Aligned_cols=48  Identities=21%  Similarity=0.184  Sum_probs=30.4

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ  288 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~  288 (648)
                      .|..|-.+||-=-                  |+.-+.++.|.....+.         ...|.+.--.|..-.+.+
T Consensus       202 ~g~LiviaaRP~m------------------GKTa~alnia~~~a~~~---------~~~v~~fSlEM~~~~l~~  249 (448)
T PRK05748        202 PNDLIIVAARPSV------------------GKTAFALNIAQNVATKT---------DKNVAIFSLEMGAESLVM  249 (448)
T ss_pred             CCCEEEEEECCCC------------------CHHHHHHHHHHHHHHHC---------CCEEEEEECCCCHHHHHH
T ss_conf             6737999847998------------------76899999999999856---------980899817788889999


No 28 
>PRK08082 consensus
Probab=96.93  E-value=0.052  Score=38.13  Aligned_cols=48  Identities=21%  Similarity=0.214  Sum_probs=31.5

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ  288 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~  288 (648)
                      .|..|-.+||-   +               -|+.-+.++.|....-+         ....|.+.-..|..-.+..
T Consensus       202 ~g~LiviaaRP---s---------------mGKTa~alnia~~~a~~---------~~~~V~~fSlEM~~~~l~~  249 (453)
T PRK08082        202 RNDLIIVAARP---S---------------VGKTAFALNIAQNVATK---------TDENVAIFSLEMGADQLVM  249 (453)
T ss_pred             CCCEEEEEECC---C---------------CCHHHHHHHHHHHHHHH---------CCCCEEEEECCCCHHHHHH
T ss_conf             58579998678---8---------------75789999999999985---------5994899731389899999


No 29 
>PRK08694 consensus
Probab=96.92  E-value=0.074  Score=36.72  Aligned_cols=49  Identities=18%  Similarity=0.175  Sum_probs=31.9

Q ss_pred             CCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             7785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r  213 SRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ  288 (648)
Q Consensus       213 ~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~  288 (648)
                      ..|..|-.+||-   +               -|+.-+.++.|.....+.         ...+.++--.|..-.+.+
T Consensus       216 ~~G~LiVIaaRP---s---------------mGKTalalnia~~~a~~~---------~~~V~~fSLEMs~~~l~~  264 (468)
T PRK08694        216 QPGDLIIVAGRP---S---------------MGKTAFSINIAEHVAVEG---------KLPVAVFSMEMGGAQLVM  264 (468)
T ss_pred             CCCCEEEEEECC---C---------------CCHHHHHHHHHHHHHHHC---------CCCEEEECCCCCHHHHHH
T ss_conf             878479996178---6---------------537899999999999847---------984799778899999999


No 30 
>smart00766 DnaG_DnaB_bind DNA primase DnaG DnaB-binding. DnaG_DnaB_bind defines a domain of primase required for functional interaction with DnaB that attracts primase to the replication fork. DnaG_DnaB_bind is responsible for the interaction between DnaG and DnaB.
Probab=96.90  E-value=0.033  Score=39.91  Aligned_cols=109  Identities=17%  Similarity=0.207  Sum_probs=77.8

Q ss_pred             HHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999847788999984430023799889999999999975388999899998851112899999999986543332
Q gi|254780834|r  484 EAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLW  563 (648)
Q Consensus       484 E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~~l~~~L~~~~l~elL~~L~~~~~~~~~~  563 (648)
                      +|.+|+++++||++...+.+......|.+|.+. +...+++.+..++......+.++..+.....++..+...-.     
T Consensus         1 ~R~~I~llLq~P~la~~v~~~~~~~~~~~~~~~-ll~~L~~~~~~~p~~~t~~Lle~~rd~~~~~~L~~La~~~~-----   74 (125)
T smart00766        1 MRELIRLLLQNPELASLVPDLLTLEDFTHPGLA-LLAELLATCRGNPGLTTGQLLEHWRDTPYEELLSELAVWDH-----   74 (125)
T ss_pred             CHHHHHHHHHCHHHHHHCCCCHHHHHCCCCHHH-HHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCC-----
T ss_conf             989999998692988658881345545681079-99999999854999879999989549808999999985574-----


Q ss_pred             HCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0256899889999999999999858999999999999998
Q gi|254780834|r  564 SATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIA  603 (648)
Q Consensus       564 ~~~~e~~~~d~~e~~~~~l~l~~r~~~L~r~l~ele~~l~  603 (648)
                          ....++....+.+++....+. .+.+++..+..+.+
T Consensus        75 ----~~~~~~~~~ef~d~l~~L~~~-~~~~ri~~L~~k~~  109 (125)
T smart00766       75 ----LIDEENLEEEFLDTLARLRKQ-LLERRIEELIAKLR  109 (125)
T ss_pred             ----CCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
T ss_conf             ----578067999999999999999-99999999999873


No 31 
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=96.87  E-value=0.0019  Score=51.40  Aligned_cols=63  Identities=29%  Similarity=0.312  Sum_probs=57.1

Q ss_pred             CCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCC-HHHHHHHHH--CCCEEEEEECCCCCCHHHHHH
Q ss_conf             870899714388999874355421134321366-267898851--268189961788662257778
Q gi|254780834|r  271 SSFIILVEGYMDVLSLCQAGVQNVVSSLGTALT-EYQLRLLWK--LSPRIVLCFDGDDPGLRAAYK  333 (648)
Q Consensus       271 ~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt-~~~~~~l~r--~~~~vvl~fDgD~AG~kAa~R  333 (648)
                      .+.+|||||--|..++-+.|+..++-++|-|+. .+-+.+|++  ....||+..|.|.+|.+=..+
T Consensus         9 ~~~vIVVEGK~D~~~l~~~~~~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D~~Ge~Irk~   74 (127)
T COG1658           9 LKEVIVVEGKDDTASLKRLGDAGVIITNGSAINSLETIELIKKAQKYKGVIILTDPDRKGERIRKK   74 (127)
T ss_pred             CCCEEEEECCCHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHH
T ss_conf             496699967767999998546863897586542788999999864258779986898562899999


No 32 
>PRK08840 replicative DNA helicase; Provisional
Probab=96.84  E-value=0.085  Score=36.17  Aligned_cols=47  Identities=15%  Similarity=0.131  Sum_probs=31.0

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             78588850100146553001038767653521011081788886433100002356787089971438899987
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLC  287 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~  287 (648)
                      .|..|-.+||-   +.               |+.-+.++.|..++.+.         ...|.+.-..|..-.+.
T Consensus       216 ~G~LiviaaRP---sm---------------GKTalalnia~n~a~~~---------~~~v~~fSlEMs~~ql~  262 (464)
T PRK08840        216 GSDLIIVAARP---SM---------------GKTTFAMNLCENAAMDQ---------DKPVLIFSLEMPAEQLM  262 (464)
T ss_pred             CCCEEEEEECC---CC---------------CHHHHHHHHHHHHHHHC---------CCCEEEECCCCCHHHHH
T ss_conf             57679998379---87---------------36899999999999965---------99679976779989999


No 33 
>PRK04017 hypothetical protein; Provisional
Probab=96.82  E-value=0.0099  Score=44.74  Aligned_cols=82  Identities=27%  Similarity=0.221  Sum_probs=60.6

Q ss_pred             CCCEEEEECCHHHHHHHHHCCCCCC-HHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             7870899714388999874355421-134321366267898851268189961788662257778888887775369730
Q gi|254780834|r  270 SSSFIILVEGYMDVLSLCQAGVQNV-VSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRV  348 (648)
Q Consensus       270 ~~~~~i~vEGy~Dvi~l~~~G~~n~-va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v  348 (648)
                      ..+.+|||||-=|+.||-..||+.- +-.....+.+ -...+.++..+||+++|-|..|.+=+.+..+.+..        
T Consensus        21 ~~g~~IlVEGkRD~~ALr~LG~~G~Ii~l~r~~l~~-ia~~~~~~~~~vIlL~DwDr~G~~L~~kl~~~L~~--------   91 (132)
T PRK04017         21 ENGAVIIVEGKRDELSLRKLGVRGEIIKLSRLPLFE-IALRASRLKKEVIILTDFDRKGEELAKKLSEYLQG--------   91 (132)
T ss_pred             CCCCEEEEECCCHHHHHHHCCCCCEEEEECCCCHHH-HHHHHHHCCCEEEEEEECCCCHHHHHHHHHHHHHH--------
T ss_conf             599879996363699999849983189874840999-99999855983999971363217999999999986--------


Q ss_pred             EEEECCCCCCHHHHHHCC
Q ss_conf             675257888888997203
Q gi|254780834|r  349 NFVLLSRGEDPDSFIRCY  366 (648)
Q Consensus       349 ~vv~LP~G~DPDe~ir~~  366 (648)
                            -|..||..+|+.
T Consensus        92 ------~g~kvD~~~R~~  103 (132)
T PRK04017         92 ------YGIKVDLEIRRK  103 (132)
T ss_pred             ------CCCCCCHHHHHH
T ss_conf             ------899757899999


No 34 
>PRK07263 consensus
Probab=96.73  E-value=0.099  Score=35.54  Aligned_cols=70  Identities=21%  Similarity=0.161  Sum_probs=37.8

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHH------
Q ss_conf             78588850100146553001038767653521011081788886433100002356787089971438899987------
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLC------  287 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~------  287 (648)
                      .|..|-.+||-   +.               |+.-+.++.|....-+         ....|.+.---|..-.+.      
T Consensus       202 ~GdLiviaaRP---sm---------------GKTa~alnia~~iA~~---------~~~~V~~fSlEMs~~ql~~R~la~  254 (453)
T PRK07263        202 PDQLIILAARP---AV---------------GKTAFVLNIAQNVGTK---------QKKTVAIFSLEMGAESLVDRMLAA  254 (453)
T ss_pred             CCCEEEEEECC---CC---------------CHHHHHHHHHHHHHHH---------CCCEEEEEECCCCHHHHHHHHHHH
T ss_conf             78689997278---88---------------4789999999999985---------598289992469989999999998


Q ss_pred             HCCCCCCHHHHHCCCCHHHHHHHH
Q ss_conf             435542113432136626789885
Q gi|254780834|r  288 QAGVQNVVSSLGTALTEYQLRLLW  311 (648)
Q Consensus       288 ~~G~~n~va~~Gtalt~~~~~~l~  311 (648)
                      ..||...---.| .+|+++...+.
T Consensus       255 ~~~i~~~~i~~g-~l~~~e~~~~~  277 (453)
T PRK07263        255 EGMVDSHSLRTG-QLTDQDWNNVT  277 (453)
T ss_pred             HCCCCHHCCCCC-CCCHHHHHHHH
T ss_conf             617331033136-52479999999


No 35 
>PRK07773 replicative DNA helicase; Validated
Probab=96.73  E-value=0.1  Score=35.52  Aligned_cols=23  Identities=13%  Similarity=0.374  Sum_probs=9.8

Q ss_pred             CEECCCCCCCCCCC-CHHCCCHHH
Q ss_conf             00103876765352-101108178
Q gi|254780834|r  231 VKYLNSPETILFHK-GKNLYNFFG  253 (648)
Q Consensus       231 ~KYlNSpeT~if~K-~~~Ly~l~~  253 (648)
                      -|+...+-|.+|.- .+.+|.+..
T Consensus       421 ~~~~~~~~~~v~~~G~k~v~~l~t  444 (868)
T PRK07773        421 LRMVARPMSNVFPTGRKEVFRLRT  444 (868)
T ss_pred             CEEEECCCCCEECCCCCEEEEEEE
T ss_conf             518750333200056534899985


No 36 
>PRK06321 replicative DNA helicase; Provisional
Probab=96.70  E-value=0.1  Score=35.39  Aligned_cols=71  Identities=17%  Similarity=0.168  Sum_probs=37.6

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHH------H
Q ss_conf             7858885010014655300103876765352101108178888643310000235678708997143889998------7
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSL------C  287 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l------~  287 (648)
                      .|..|=.+||-   +               -|++-+.++.|.....+.         ...|.+.--.|..-.+      .
T Consensus       225 ~GdliviaaRP---s---------------mGKTalalnia~~~a~~~---------~~~v~~fSLEMs~~ql~~R~ls~  277 (472)
T PRK06321        225 PSNLMILAARP---A---------------MGKTALALNIAENFCFQN---------RLPVGIFSLEMTVDQLIHRIICS  277 (472)
T ss_pred             CCCEEEEECCC---C---------------CCHHHHHHHHHHHHHHHC---------CCCEEEECCCCCHHHHHHHHHHH
T ss_conf             67579985389---9---------------977999999999999856---------99469975779999999999874


Q ss_pred             HCCCCCCHHHHHCCCCHHHHHHHHH
Q ss_conf             4355421134321366267898851
Q gi|254780834|r  288 QAGVQNVVSSLGTALTEYQLRLLWK  312 (648)
Q Consensus       288 ~~G~~n~va~~Gtalt~~~~~~l~r  312 (648)
                      .+||...--..| .+|.++...+..
T Consensus       278 ~s~i~~~~i~~g-~l~~~e~~~~~~  301 (472)
T PRK06321        278 RSEVESKKISVG-DLSGRDFQRIVS  301 (472)
T ss_pred             HCCCCCCCCCCC-CCCHHHHHHHHH
T ss_conf             037675521047-999999999999


No 37 
>PRK05636 replicative DNA helicase; Provisional
Probab=96.64  E-value=0.11  Score=35.06  Aligned_cols=10  Identities=40%  Similarity=0.640  Sum_probs=4.9

Q ss_pred             CCCCCCCCCC
Q ss_conf             1244225677
Q gi|254780834|r  156 MFKLGYAPDS  165 (648)
Q Consensus       156 ~f~lG~ap~~  165 (648)
                      .|.=||.|++
T Consensus         8 ~~~~~~~~~~   17 (507)
T PRK05636          8 SFDDDYVPPS   17 (507)
T ss_pred             CCCCCCCCCC
T ss_conf             6777778999


No 38 
>PRK08506 replicative DNA helicase; Provisional
Probab=96.58  E-value=0.12  Score=34.73  Aligned_cols=69  Identities=17%  Similarity=0.168  Sum_probs=37.9

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHH------H
Q ss_conf             7858885010014655300103876765352101108178888643310000235678708997143889998------7
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSL------C  287 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l------~  287 (648)
                      .|..|=.+||-   +.               |++-+.++.|..+++.          ...|.+.=-.|..-.+      .
T Consensus       192 ~gdLiIIAARP---sm---------------GKTAfAlniA~~~a~~----------~~~V~~FSLEMs~~ql~~Rlls~  243 (473)
T PRK08506        192 KGDLIIIAARP---SM---------------GKTTLVLNMVLKALNQ----------GKGVAFFSLEMPAEQLMLRMLSA  243 (473)
T ss_pred             CCCEEEEECCC---CC---------------CHHHHHHHHHHHHHHC----------CCCEEEEECCCCHHHHHHHHHHH
T ss_conf             56279995079---98---------------6789999999999965----------99658982247999999999997


Q ss_pred             HCCCCCCHHHHHCCCCHHHHHHHH
Q ss_conf             435542113432136626789885
Q gi|254780834|r  288 QAGVQNVVSSLGTALTEYQLRLLW  311 (648)
Q Consensus       288 ~~G~~n~va~~Gtalt~~~~~~l~  311 (648)
                      .+||+..---.| .+|++....+.
T Consensus       244 ~s~V~~~~lr~g-~l~~~e~~~~~  266 (473)
T PRK08506        244 KTSIPLQNLRTG-DLDDDEWENLS  266 (473)
T ss_pred             HCCCCCCCCCCC-CCCHHHHHHHH
T ss_conf             288783100068-99999999999


No 39 
>PRK05595 replicative DNA helicase; Provisional
Probab=96.52  E-value=0.13  Score=34.43  Aligned_cols=69  Identities=17%  Similarity=0.213  Sum_probs=35.5

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHH------
Q ss_conf             78588850100146553001038767653521011081788886433100002356787089971438899987------
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLC------  287 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~------  287 (648)
                      .|..|=.+||-   +               -|+.-+.++.|.....+         ....|.+.---|..-.+.      
T Consensus       200 ~GdLiiiaaRP---~---------------mGKTa~alnia~~~a~~---------~g~~V~~fSlEMs~~ql~~R~ls~  252 (444)
T PRK05595        200 KGDMILIAARP---S---------------MGKTTFALNIAEYAALR---------EGKSVVIFSLEMSKEQLAYKLLCS  252 (444)
T ss_pred             CCCEEEEEECC---C---------------CCCHHHHHHHHHHHHHH---------CCCCEEEEECCCCHHHHHHHHHHH
T ss_conf             57779998579---8---------------98079999999999986---------699379995889999999999996


Q ss_pred             HCCCCCCHHHHHCCCCHHHHHHH
Q ss_conf             43554211343213662678988
Q gi|254780834|r  288 QAGVQNVVSSLGTALTEYQLRLL  310 (648)
Q Consensus       288 ~~G~~n~va~~Gtalt~~~~~~l  310 (648)
                      ..|++..---.| .+++++...+
T Consensus       253 ~s~i~~~~i~~g-~l~~~~~~~~  274 (444)
T PRK05595        253 EANVDMLRLRTG-NLEDKDWENI  274 (444)
T ss_pred             HCCCCCCCCCCC-CCCHHHHHHH
T ss_conf             469884423268-9799999999


No 40 
>pfam08278 DnaG_DnaB_bind DNA primase DnaG DnaB-binding. Eubacterial DnaG primases interact with several factors to from the replisome. One of these factors in DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB.
Probab=96.36  E-value=0.16  Score=33.69  Aligned_cols=109  Identities=19%  Similarity=0.165  Sum_probs=75.5

Q ss_pred             HHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999847788999984430023799889999999999975388999899998851112899999999986543332
Q gi|254780834|r  484 EAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLW  563 (648)
Q Consensus       484 E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~~l~~~L~~~~l~elL~~L~~~~~~~~~~  563 (648)
                      .+.+|.++++||.+...+.+......+.+|... ++..+++.+..++..+...+.++..+......+..+....      
T Consensus         2 ~r~ai~LLLq~P~LA~~v~~~~~l~~~~~~~~~-lL~~L~~~~~~~P~~~t~~Lle~~r~t~~~~~L~~La~~~------   74 (126)
T pfam08278         2 MRRAIALLLQNPALAALVPDLLALEDLKDPGLA-LLLELVELCRGNPNINTGQLLEHWRGTPYGELLAKLATWE------   74 (126)
T ss_pred             HHHHHHHHHHCHHHHHHCCCHHHHHHCCCHHHH-HHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHCC------
T ss_conf             899999998694987568774544115670289-9999999998589985999999970991799999998642------


Q ss_pred             HCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0256899889999999999999858999999999999998
Q gi|254780834|r  564 SATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIA  603 (648)
Q Consensus       564 ~~~~e~~~~d~~e~~~~~l~l~~r~~~L~r~l~ele~~l~  603 (648)
                         ...+.++....+.+++...... .+.+++.++..+..
T Consensus        75 ---~~~~~~~~~~ef~d~l~~L~~~-~~~~r~~~L~~k~~  110 (126)
T pfam08278        75 ---HLIDEDNIEQEFDDTLARLQEQ-LLERRIEELIAKSR  110 (126)
T ss_pred             ---CCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
T ss_conf             ---2466067999999999999999-99999999998774


No 41 
>PRK09165 replicative DNA helicase; Provisional
Probab=96.23  E-value=0.18  Score=33.14  Aligned_cols=48  Identities=17%  Similarity=0.095  Sum_probs=25.7

Q ss_pred             CEEEECCCCEEEECC----CCCCCCHHHHHHHHCC---CCHHHHHHHHHHHHCCC
Q ss_conf             879817897467136----8888789899898859---99799999999981885
Q gi|254780834|r   52 SFHCNDSKGFYYCFS----CHVKGDHLSFLSALLG---CSFIESVQRLAAIAGVP   99 (648)
Q Consensus        52 sf~v~~~~~~~~cf~----c~~~gd~~~f~~~~~~---~~f~ea~~~la~~~gi~   99 (648)
                      .|+....+.+|.|..    -|..-|+++....+..   +.-..-+.+|++.+.-.
T Consensus        41 dFy~~~H~~If~ai~~L~~~g~~iD~itv~~~L~~~~~l~~vGG~~yL~~L~~~~   95 (484)
T PRK09165         41 HFFEPLHQRIYEAIAKIIRKGKLATPVTLKTFLENDEALGELGGVQYLAKLATEA   95 (484)
T ss_pred             HCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHCCCHHHHHHHHHCC
T ss_conf             7798999999999999997699987989999986458723227799999999708


No 42 
>COG3593 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]
Probab=96.12  E-value=0.086  Score=36.10  Aligned_cols=85  Identities=21%  Similarity=0.213  Sum_probs=57.9

Q ss_pred             CCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHH----HCCCCC---CHHHHH--CCCCHHHHHHHHHC
Q ss_conf             521011081788886433100002356787089971438899987----435542---113432--13662678988512
Q gi|254780834|r  243 HKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLC----QAGVQN---VVSSLG--TALTEYQLRLLWKL  313 (648)
Q Consensus       243 ~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~----~~G~~n---~va~~G--talt~~~~~~l~r~  313 (648)
                      .|+++.|+++-+|...-          =.+.+|+|||..++|-+.    ++|+.-   .|+..+  -+=...=++.-.++
T Consensus       378 ~~r~i~r~l~~trs~~l----------FAr~vIlVEG~aE~ill~~la~~~~~~L~~~gi~VI~~~gs~~k~f~kf~~~~  447 (581)
T COG3593         378 DKRRIKRHLDATRSSLL----------FARGVILVEGEAEVILLPELARQCGIDLEKEGIIVIEFAGSGLKPFIKFAEAM  447 (581)
T ss_pred             CHHHHHHHCCCCCCHHH----------HHCEEEEEECCCHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHCC
T ss_conf             30456641464520123----------33336997133021017999998445644374799960555737888776504


Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             681899617886622577788888
Q gi|254780834|r  314 SPRIVLCFDGDDPGLRAAYKAIDL  337 (648)
Q Consensus       314 ~~~vvl~fDgD~AG~kAa~Ra~e~  337 (648)
                      ..++.+..|||+||.++..+.-.+
T Consensus       448 gI~~~vitD~D~~g~~~~~~~~~l  471 (581)
T COG3593         448 GIRVHVITDGDEAGKKYEATVRDL  471 (581)
T ss_pred             CCEEEEEECCCCCCCHHHHHHHHC
T ss_conf             945999935885413456655301


No 43 
>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]
Probab=95.99  E-value=0.23  Score=32.24  Aligned_cols=49  Identities=12%  Similarity=0.084  Sum_probs=25.7

Q ss_pred             CEEEECCCCEE----EECCCCCCCCHHHHHHHHCCCCHHHH---HHHHHHHHCCCC
Q ss_conf             87981789746----71368888789899898859997999---999999818858
Q gi|254780834|r   52 SFHCNDSKGFY----YCFSCHVKGDHLSFLSALLGCSFIES---VQRLAAIAGVPL  100 (648)
Q Consensus        52 sf~v~~~~~~~----~cf~c~~~gd~~~f~~~~~~~~f~ea---~~~la~~~gi~~  100 (648)
                      .|...+.+-+|    .+|.-|..=|++++-.+....+-.+.   ..+|++.+.-..
T Consensus        35 dFy~~~H~~IF~a~~~l~~~~~~id~vtv~~~l~~~~~~~~igg~~yl~~L~~~~p   90 (435)
T COG0305          35 DFYRPAHRLIYQAILDLYGQGEPIDLVTVSEELSDRGLLTRIGGANYLATLIDRTP   90 (435)
T ss_pred             HCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCHHHHCCCHHHHHHHHHCCC
T ss_conf             20767899999999999866898767289999864144766075899999986288


No 44 
>pfam00772 DnaB DnaB-like helicase N terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity.
Probab=95.95  E-value=0.069  Score=36.97  Aligned_cols=65  Identities=17%  Similarity=0.209  Sum_probs=59.2

Q ss_pred             HHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             79999999998477889999844300237998899999999999753889998999988511128
Q gi|254780834|r  482 LREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGF  546 (648)
Q Consensus       482 ~~E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~~l~~~L~~~~l  546 (648)
                      -.|+.+|..++.+|+.+.++.+.+...+|.++.++.+|..+.+.+.++...+...+...+...+.
T Consensus         7 eaE~~lLg~lL~~~~~~~~i~~~l~~edF~~~~h~~If~~i~~l~~~~~~iD~~tl~~~l~~~~~   71 (103)
T pfam00772         7 EAEQAVLGALLLDPEAIDEVADILKPEDFYDPAHRLIFEAILELYDKGKPIDPVTVAEELERKGK   71 (103)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCC
T ss_conf             99999999999697489999972799984959999999999999845699689999999976798


No 45 
>PRK06749 replicative DNA helicase; Provisional
Probab=95.37  E-value=0.36  Score=30.39  Aligned_cols=47  Identities=19%  Similarity=0.274  Sum_probs=31.3

Q ss_pred             CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r  214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ  288 (648)
Q Consensus       214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~  288 (648)
                      .|..|-.+||-   +               -|+.-+.++.|....+.          ...+.+.---|..-.+..
T Consensus       185 ~g~LiviaaRP---s---------------mGKTa~alnia~~~a~~----------g~~v~~fSlEMs~~~l~~  231 (428)
T PRK06749        185 EGDFVVLGARP---S---------------MGKTAFALNVGLHAAKS----------GAAVGLFSLEMSSKQLLK  231 (428)
T ss_pred             CCCEEEEECCC---C---------------CCHHHHHHHHHHHHHHC----------CCCEEEEECCCCHHHHHH
T ss_conf             88689996279---8---------------97689999999999964----------992799837899999999


No 46 
>TIGR00334 primaseG_like primase homolog; InterPro: IPR004466 This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases..
Probab=90.81  E-value=0.52  Score=28.92  Aligned_cols=65  Identities=28%  Similarity=0.338  Sum_probs=56.5

Q ss_pred             CEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCC--EEEEEECCCCCCHHHHHHHHH
Q ss_conf             70899714388999874355421134321366267898851268--189961788662257778888
Q gi|254780834|r  272 SFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSP--RIVLCFDGDDPGLRAAYKAID  336 (648)
Q Consensus       272 ~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~--~vvl~fDgD~AG~kAa~Ra~e  336 (648)
                      +.+++|||-.|.-.+.+.---.++.+.|.|+..+-+.+++....  .+++..|.|.+|.+-..+..+
T Consensus         3 ~~~~~~~g~~d~~~~~~~~d~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~dpd~~g~~~~~~~~~   69 (176)
T TIGR00334         3 KGVIVCEGKDDLARLKELFDVDVIETNGSALKDETINLLKKALKKKGVILLLDPDKPGEKIRKKLEE   69 (176)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHHH
T ss_conf             7426640761467777764001100354023578899999877536736875687322689999998


No 47 
>PRK05301 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional
Probab=90.56  E-value=1.6  Score=24.34  Aligned_cols=85  Identities=20%  Similarity=0.234  Sum_probs=58.2

Q ss_pred             CCCEEEEECCHHHHHH-HHHCCCCCCHHHHHCCCCHHHHHHHHHC-CCEEEEEECCCCC-------C----HHHHHHHHH
Q ss_conf             7870899714388999-8743554211343213662678988512-6818996178866-------2----257778888
Q gi|254780834|r  270 SSSFIILVEGYMDVLS-LCQAGVQNVVSSLGTALTEYQLRLLWKL-SPRIVLCFDGDDP-------G----LRAAYKAID  336 (648)
Q Consensus       270 ~~~~~i~vEGy~Dvi~-l~~~G~~n~va~~Gtalt~~~~~~l~r~-~~~vvl~fDgD~A-------G----~kAa~Ra~e  336 (648)
                      .+++-.+-...++.+. +...|+...+.|.||-+|++-++.|+.. ...|.+.+||-.+       |    ...++++++
T Consensus        70 tGGEPllr~D~~ei~~~a~~~G~~~~l~TNG~lit~~~a~~L~~~gl~~v~vSlDg~~~e~hD~~rG~~G~f~~~~~~i~  149 (375)
T PRK05301         70 SGGEPLLRKDLEELVAHARRLGLYTNLITSGVGLTEARLAALKAAGLDHIQLSFQDSDPELADRIAGTRGAFAQKLEVAR  149 (375)
T ss_pred             CCCCCCCCCCHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHCCCEEEEECCCCCHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             18652456689999999997697589960674557999999985099889995677987787776378862999999999


Q ss_pred             HHHHHHHCCCCEEEEE--CCCCC
Q ss_conf             8877753697306752--57888
Q gi|254780834|r  337 LVLCHLIPGNRVNFVL--LSRGE  357 (648)
Q Consensus       337 ~~l~~l~~g~~v~vv~--LP~G~  357 (648)
                      .   +.+.|+.+.+-+  -..+.
T Consensus       150 ~---l~~~Gi~v~i~~ti~r~N~  169 (375)
T PRK05301        150 L---VKAHGYPLTLNAVIHRHNI  169 (375)
T ss_pred             H---HHHCCCCEEEEEEECCCCH
T ss_conf             9---9974981699987230568


No 48 
>pfam08273 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase.
Probab=89.81  E-value=0.27  Score=31.52  Aligned_cols=33  Identities=36%  Similarity=0.759  Sum_probs=26.8

Q ss_pred             EEECCCCCCCCCCEEEECCC---CEEEECCCCCCCCH
Q ss_conf             75345888858787981789---74671368888789
Q gi|254780834|r   40 WACCPFHDEKTPSFHCNDSK---GFYYCFSCHVKGDH   73 (648)
Q Consensus        40 ~~~cPfh~ektpsf~v~~~~---~~~~cf~c~~~gd~   73 (648)
                      -+.||-+.-+. -|.+.+++   +.|+|+.||..||-
T Consensus         3 h~pCP~CGg~D-rfr~fdd~~g~G~~~C~~Cg~~GDG   38 (39)
T pfam08273         3 HGPCPNCGGSD-RFRIFDDKDGRGTWFCFSCGYAGDG   38 (39)
T ss_pred             CCCCCCCCCCC-CCEECCCCCCCCCEECCCCCCCCCC
T ss_conf             66777777857-5256557899757783888777888


No 49 
>cd01026 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family.  The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=89.07  E-value=0.79  Score=27.25  Aligned_cols=55  Identities=25%  Similarity=0.370  Sum_probs=40.7

Q ss_pred             CEEEEECCHHHHHHHH-----------HCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCH
Q ss_conf             7089971438899987-----------43554211343213662678988512681899617886622
Q gi|254780834|r  272 SFIILVEGYMDVLSLC-----------QAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGL  328 (648)
Q Consensus       272 ~~~i~vEGy~Dvi~l~-----------~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~  328 (648)
                      +.+|+|||..|.+.+.           ++|| .+|..-|.++-.. ++++..+.-.+++..|.|....
T Consensus         4 ~~viLVEG~tE~~~l~~~~~~~~~~l~~~~i-~ii~v~G~~~~~~-~~l~~~l~i~~~vi~D~D~~~~   69 (97)
T cd01026           4 DKVILVEGDSEEILLPALAKKLGLDLDEAGI-SIIPVGGKNFKPF-IKLLNALGIPVAVLTDLDAKRN   69 (97)
T ss_pred             CEEEEEECHHHHHHHHHHHHHHCCCHHHCCC-EEEEECCCCHHHH-HHHHHHCCCCEEEEECCCCCCC
T ss_conf             7799994413999999999996979778797-8998589274999-9999976993899971898746


No 50 
>PRK13758 anaerobic sulfatase-maturase; Provisional
Probab=88.99  E-value=1.2  Score=25.47  Aligned_cols=72  Identities=18%  Similarity=0.192  Sum_probs=48.9

Q ss_pred             CCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCC----------C---HHHHHHHHHHHHHHHHCCCC--EEEEECC
Q ss_conf             5542113432136626789885126818996178866----------2---25777888888777536973--0675257
Q gi|254780834|r  290 GVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDP----------G---LRAAYKAIDLVLCHLIPGNR--VNFVLLS  354 (648)
Q Consensus       290 G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~A----------G---~kAa~Ra~e~~l~~l~~g~~--v~vv~LP  354 (648)
                      .+.+++.|.||-||++.+..|+++.-.|-+.+||.++          |   -..+.++++++   .+.+..  +..+.-.
T Consensus        92 ~i~~~i~TNGtLL~~e~~~~l~~~~~~I~ISlDG~~~~HD~~R~~~~G~Gsf~~v~~~i~~l---~~~~~~~~i~~~i~~  168 (370)
T PRK13758         92 KIYNSLQTNGTLIDESWAKFLSENKFLVGLSMDGPKEIHNLNRKDCCGLDTFSKVERAAELF---KKYKVEFNILCVVTS  168 (370)
T ss_pred             EEEEEEEECCEECCHHHHHHHHHCCEEEEEECCCCHHHHHHHCCCCCCCCHHHHHHHHHHHH---HHCCCCEEEEEEEEC
T ss_conf             69999851887668999999997694899964688888740068889970599999999999---973997008999918


Q ss_pred             CC-CCHHHHHH
Q ss_conf             88-88889972
Q gi|254780834|r  355 RG-EDPDSFIR  364 (648)
Q Consensus       355 ~G-~DPDe~ir  364 (648)
                      ++ .+++++++
T Consensus       169 ~~~~~~~~i~~  179 (370)
T PRK13758        169 NTARHVNKIYK  179 (370)
T ss_pred             CCCCCHHHHHH
T ss_conf             73118999999


No 51 
>KOG2373 consensus
Probab=86.18  E-value=2.9  Score=22.09  Aligned_cols=133  Identities=15%  Similarity=0.164  Sum_probs=90.5

Q ss_pred             CCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCC-CCCCHHHHHCCCCH-HHH
Q ss_conf             3001038767653521011081788886433100002356787089971438899987435-54211343213662-678
Q gi|254780834|r  230 SVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAG-VQNVVSSLGTALTE-YQL  307 (648)
Q Consensus       230 ~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G-~~n~va~~Gtalt~-~~~  307 (648)
                      +.-|=-.-||++=++-+.+|||+.|-..             ...++++--..|.|+++++- +..+.-|-|+-+-+ .-+
T Consensus        94 g~~ye~~~~~~~r~a~~~~fGL~l~~rr-------------d~~vVltsne~D~lal~~~t~~~t~~LP~g~~~lP~~~L  160 (514)
T KOG2373          94 GENYELPDETSVRQAFNGVFGLHLATRR-------------DRSVVLTSNERDALALYEATKALTFALPHGEILLPQLVL  160 (514)
T ss_pred             CCCCCCCCCCCHHHHHCCEECEEECCCC-------------CCEEEEEECCHHHHHHHHHCCCEEEECCCCCCCCCHHHH
T ss_conf             6667997665334454212030312434-------------544897505145777764148637872665434827777


Q ss_pred             HHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC-CCCCCHHHHHHCCCHHHHHHHHHHCCCHHH
Q ss_conf             9885126818996178866225777888888777536973067525-788888899720366889988641499279
Q gi|254780834|r  308 RLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLL-SRGEDPDSFIRCYGKTAFEKLIVESLPLVD  383 (648)
Q Consensus       308 ~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~L-P~G~DPDe~ir~~G~eaf~~ll~~A~~l~d  383 (648)
                      --|-+| ++||++|--|.....||. ..-..  + .   ..|++.. |+..-|.-...-.+.=.+..+++.|.|.-+
T Consensus       161 PyLE~F-~~i~fWl~~d~~sw~aAk-~fa~k--L-n---~~rClLvrp~e~~p~p~~al~~rlnl~~il~~a~p~~h  229 (514)
T KOG2373         161 PYLEEF-DKIYFWLPVDHVSWSAAK-DFASK--L-N---TLRCLLVRPEERPPEPVRALDHRLNLNSILNSAVPMRH  229 (514)
T ss_pred             HHHHHH-HEEEEEECCCCCCHHHHH-HHHHH--C-C---CCEEEEECCCCCCCCHHHHHCCCCCHHHHHHHHCHHHH
T ss_conf             889865-259998025442368999-99862--2-8---41379977888896556653455028888755122465


No 52 
>COG0641 AslB Arylsulfatase regulator (Fe-S oxidoreductase) [General function prediction only]
Probab=85.68  E-value=3  Score=21.90  Aligned_cols=131  Identities=15%  Similarity=0.176  Sum_probs=68.0

Q ss_pred             CCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCC-------------CCCHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             355421134321366267898851268189961788-------------6622577788888877753697306752578
Q gi|254780834|r  289 AGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGD-------------DPGLRAAYKAIDLVLCHLIPGNRVNFVLLSR  355 (648)
Q Consensus       289 ~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD-------------~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~  355 (648)
                      .-|.|++-|.||.||++-+..+++.--.|-+..||-             ..--.+++|+++.+..   -+..+.+..-  
T Consensus        89 ~~i~~siqTNg~LL~~e~~e~l~~~~~~IgISiDGp~eihD~~R~~~~GkgTfd~i~~~i~~L~~---~~v~~~~~~v--  163 (378)
T COG0641          89 KTISNALQTNGTLLNDEWAEFLAEHDFLIGISIDGPEEIHDKYRVTKSGKGTFDRVMKGLELLQA---HGVDFNTLTV--  163 (378)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHCCCEEEEECCCCHHHHCCCCCCCCCCCCHHHHHHHHHHHHH---CCCCEEEEEE--
T ss_conf             82578998760325799999998529669996668177611103578998569999999999997---5884699999--


Q ss_pred             CCCHHHHHHCCCHHHHHHHH-HHCCCHHHHHHHHHHHHCC--------CCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             88888997203668899886-4149927999999985302--------33145799999999988541799899999999
Q gi|254780834|r  356 GEDPDSFIRCYGKTAFEKLI-VESLPLVDMLWKRETENRS--------FNTPDERAELEIHLKNCINHIKDQKLRYYYSQ  426 (648)
Q Consensus       356 G~DPDe~ir~~G~eaf~~ll-~~A~~l~dFl~~~l~~~~d--------l~spe~ka~~~~~l~~~I~~I~d~~~R~~yl~  426 (648)
                       .+++.+  .+ ..++-+++ +.....+.|+ . +.+..+        ..++++-..+...+.....+..   ....+++
T Consensus       164 -v~~~n~--~~-~~ei~~~l~~~g~~~i~fi-p-~~~~~~~~~~~~~~~~~~~~~~~fl~~~~~~~~~~~---~~~i~i~  234 (378)
T COG0641         164 -VNRQNV--LH-PEEIYHFLKSEGSKFIQFI-P-LVESDNRGDSLLEFSVTAEEYGQFLIAIFDEWVRHD---VGRIFIQ  234 (378)
T ss_pred             -ECHHHH--HC-HHHHHHHHHHCCCCEEEEE-E-CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC---CCCCCHH
T ss_conf             -764453--07-9999999997376638988-5-116888775322123466679999999999999714---7741014


Q ss_pred             HHHHHHH
Q ss_conf             9999988
Q gi|254780834|r  427 AIRDRLQ  433 (648)
Q Consensus       427 ~la~~L~  433 (648)
                      .+...+.
T Consensus       235 ~f~~~~~  241 (378)
T COG0641         235 NFDQLLK  241 (378)
T ss_pred             HHHHHHH
T ss_conf             7999999


No 53 
>PRK09897 hypothetical protein; Provisional
Probab=85.33  E-value=2.1  Score=23.27  Aligned_cols=191  Identities=17%  Similarity=0.198  Sum_probs=107.0

Q ss_pred             HHHHHCCCCHHHHCCCC------CC-CCCCCCCHHHHHHHCCCCCHHHHHHHCCCEE--CCCCCCCCCCCCCEEEEEEEE
Q ss_conf             99985068853510124------42-2567741034554205997345232012100--346541000016716888970
Q gi|254780834|r  142 YYLDERGIDSHAIEMFK------LG-YAPDSRYSLREHLRQKGFSEEKIIEAGLLID--GDNSATSYDRFRNRLIFPIRS  212 (648)
Q Consensus       142 ~yl~~Rg~~~~~~~~f~------lG-~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~--~~~~~~~~d~Fr~Ri~fPi~~  212 (648)
                      +||...|++.+.+...+      +| |--+....|++...++|++......+-+.-.  +.+|..         +.....
T Consensus        79 ~~L~~~~id~~~l~~rqflPRiLlGeYl~~QF~~Lve~a~~~G~~i~Vh~~~~VtDi~~~~~gv~---------l~~~~~  149 (535)
T PRK09897         79 SHLQRYGVKKETLHDRQFLPRILLGEYFRDQFLRLVDQARQQKFAVAVYESCQVTDLQITNAGVM---------LATNQD  149 (535)
T ss_pred             HHHHHCCCCHHHCCCCCEEHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCEEEEEEECCCCEE---------EEECCC
T ss_conf             78987199832264101004888889999999999999986596699975766676443699559---------983378


Q ss_pred             CC----CCEEEEECCCCCC--CCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHH
Q ss_conf             77----8588850100146--55300103876765352101108178888643310000235678708997143889998
Q gi|254780834|r  213 SR----GQVIAFGGRTLSK--GESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSL  286 (648)
Q Consensus       213 ~~----g~~i~f~gR~l~~--~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l  286 (648)
                      ..    -.+|==+|-...+  +.+++|.-||=+          |+-.|                                
T Consensus       150 ~~~~~FD~vVIaTGH~WP~~~e~~~~YF~SPw~----------~l~~a--------------------------------  187 (535)
T PRK09897        150 LPSETFDLAVIATGHVWPDEEEATRTYFPSPWS----------GLMEA--------------------------------  187 (535)
T ss_pred             CCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCC----------CHHHC--------------------------------
T ss_conf             876432079980798799877677666789997----------36542--------------------------------


Q ss_pred             HHCCCC-CCHHHHHCCCCH-HHHHHHHHC----C---C-EEEEEECCCCCCHHHHHHHHHHHHHHHHCCC--CEEEEECC
Q ss_conf             743554-211343213662-678988512----6---8-1899617886622577788888877753697--30675257
Q gi|254780834|r  287 CQAGVQ-NVVSSLGTALTE-YQLRLLWKL----S---P-RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN--RVNFVLLS  354 (648)
Q Consensus       287 ~~~G~~-n~va~~Gtalt~-~~~~~l~r~----~---~-~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~--~v~vv~LP  354 (648)
                         -++ ..||.+||+||- +-+..|.+-    +   + .+.+..|.|.-+.+=++-+        ..|+  +++|- .|
T Consensus       188 ---~ip~~~VgI~GSSLSAIDAa~ala~~hG~F~~~~d~~l~F~~~~~se~~~I~mmS--------r~GiLPeadFy-~p  255 (535)
T PRK09897        188 ---KVDACNVGIMGTSLSGLDAAMAVAIQHGSFIEDDKQHVVFHRDNASEKLNITLMS--------RTGILPEADFY-CP  255 (535)
T ss_pred             ---CCCCCEEEEECCCHHHHHHHHHHHHHCCEEEECCCCEEEEEECCCCCCEEEEEEE--------CCCCCCCCCCC-CC
T ss_conf             ---5787527762376578999999998768058768850788878998652699972--------37877653203-78


Q ss_pred             CCCCHHHHHHCCCHHHHHHHHHH-CCCHHHHHHHHHHHHCCCCCH
Q ss_conf             88888899720366889988641-499279999999853023314
Q gi|254780834|r  355 RGEDPDSFIRCYGKTAFEKLIVE-SLPLVDMLWKRETENRSFNTP  398 (648)
Q Consensus       355 ~G~DPDe~ir~~G~eaf~~ll~~-A~~l~dFl~~~l~~~~dl~sp  398 (648)
                      .-..|=+++   ..++....+++ +..++||+|+...+.....+|
T Consensus       256 ~pye~L~il---T~~ai~~~ia~g~~gLLDrVF~l~~~el~~~DP  297 (535)
T PRK09897        256 IPYEPLHIV---TDQALNAEIQKGEEGLLDRVFRLIVEEIKFADP  297 (535)
T ss_pred             CCCCCHHHC---CHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCH
T ss_conf             998713217---899999999748883189999999999986684


No 54 
>PRK13745 anaerobic sulfatase-maturase; Provisional
Probab=81.10  E-value=3.7  Score=21.05  Aligned_cols=70  Identities=21%  Similarity=0.254  Sum_probs=48.2

Q ss_pred             CCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCC----------CH---HHHHHHHHHHHHHHHCCCCEEEE--EC-C
Q ss_conf             542113432136626789885126818996178866----------22---57778888887775369730675--25-7
Q gi|254780834|r  291 VQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDP----------GL---RAAYKAIDLVLCHLIPGNRVNFV--LL-S  354 (648)
Q Consensus       291 ~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~A----------G~---kAa~Ra~e~~l~~l~~g~~v~vv--~L-P  354 (648)
                      |.|++-|.||.||++.+..++++-=.|-+..||..+          |+   .+.+|+++++.   +.|.+..++  .- .
T Consensus       102 i~~siQTNGtLL~dew~~ff~~~~f~VgiSiDGp~~~HD~~R~~~~G~gs~~~v~~~i~lL~---~~~v~fn~L~vv~~~  178 (412)
T PRK13745        102 IDNCIQTNGTLLTDEWCEFFRENNWLVGVSIDGPQEFHDEYRKNKMGKPSFVKVMKGINLLK---KHGVEWNAMAVVNDF  178 (412)
T ss_pred             EEEEEEECCEECCHHHHHHHHHCCCEEEEECCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHH---HCCCCEEEEEEEECH
T ss_conf             68999877875499999999985967999625887887402798899877999999999999---849964699998111


Q ss_pred             CCCCHHHHH
Q ss_conf             888888997
Q gi|254780834|r  355 RGEDPDSFI  363 (648)
Q Consensus       355 ~G~DPDe~i  363 (648)
                      ....|.++.
T Consensus       179 n~~~p~~iY  187 (412)
T PRK13745        179 NADYPLDFY  187 (412)
T ss_pred             HHHCHHHHH
T ss_conf             545889999


No 55 
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH
Probab=80.34  E-value=4.6  Score=20.26  Aligned_cols=89  Identities=18%  Similarity=0.101  Sum_probs=57.6

Q ss_pred             CCEEEEECCHHHHHH-HHHCCCCCCHHHHHCCCCHHHHHHHHHCCC-EEEEEECCCCC----------CHHHHHHHHHHH
Q ss_conf             870899714388999-874355421134321366267898851268-18996178866----------225777888888
Q gi|254780834|r  271 SSFIILVEGYMDVLS-LCQAGVQNVVSSLGTALTEYQLRLLWKLSP-RIVLCFDGDDP----------GLRAAYKAIDLV  338 (648)
Q Consensus       271 ~~~~i~vEGy~Dvi~-l~~~G~~n~va~~Gtalt~~~~~~l~r~~~-~vvl~fDgD~A----------G~kAa~Ra~e~~  338 (648)
                      +++-++-....+.+. +.+.|+.-++.|.|| |.++.+..++.... .+-+.+||.+.          .-..|++++..+
T Consensus        80 GGEPLLr~dl~eIv~~a~~~g~~v~l~TNG~-Ll~k~i~~~~~~~~~~~~VsLDG~~e~HD~~r~~~G~Fd~av~aIr~a  158 (318)
T TIGR03470        80 GGEPLLHPEIDEIVRGLVARKKFVYLCTNAL-LLEKKLDKFEPSPYLTFSVHLDGLREHHDASVCREGVFDRAVEAIREA  158 (318)
T ss_pred             CCCCCCCCCHHHHHHHHHHCCCEEEEECCHH-HHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             8874556479999999997599799977552-009999998518883699980178788668871797799999999999


Q ss_pred             HHHHHCCCCEEEEE-CCCCCCHHHHH
Q ss_conf             77753697306752-57888888997
Q gi|254780834|r  339 LCHLIPGNRVNFVL-LSRGEDPDSFI  363 (648)
Q Consensus       339 l~~l~~g~~v~vv~-LP~G~DPDe~i  363 (648)
                      .   +.|+.|.+-+ +=++.||++..
T Consensus       159 k---~~G~~V~iN~Tvf~~~n~~~i~  181 (318)
T TIGR03470       159 K---ARGFRVTTNTTLFNDTDPEEVA  181 (318)
T ss_pred             H---HCCCCEEEEEEEECCCCHHHHH
T ss_conf             9---8699467998970689999999


No 56 
>pfam03291 Pox_MCEL mRNA capping enzyme. This family of enzymes are related to pfam03919.
Probab=80.29  E-value=0.71  Score=27.71  Aligned_cols=75  Identities=16%  Similarity=0.215  Sum_probs=45.2

Q ss_pred             HHHCCHHHHH-HHHCCCEECCCC---CCCCCEEEECCCCC-----------CCCCCEEEECCCCEEEECCCCCCCCHHHH
Q ss_conf             8748888875-412221015887---77775575345888-----------85878798178974671368888789899
Q gi|254780834|r   12 LIHIPISNLI-GQYVDWDRRKTN---AVKGDYWACCPFHD-----------EKTPSFHCNDSKGFYYCFSCHVKGDHLSF   76 (648)
Q Consensus        12 ~~~~~i~~vv-~~~v~l~~~g~n---~~~~~~~~~cPfh~-----------ektpsf~v~~~~~~~~cf~c~~~gd~~~f   76 (648)
                      ...-||++|| .+|=+++.+|..   +....-.+|.=|||           .+++   ....+..-=..+||+|||..+|
T Consensus         5 ~~~~~~~~~V~~HYN~~~~~~~~~~~R~~S~I~~LR~FNNwVKs~LI~~~~~~~~---~~~~~~~VLDl~CGkGGDL~Kw   81 (327)
T pfam03291         5 ETESNIVDIVAAHYNELPESGIDLKKRQDSTIDQLRNFNNWIKSLLISLYASKTF---QDKPKRKVLDLDCGKGGDLEKY   81 (327)
T ss_pred             CCCCCHHHHHHHHHCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH---CCCCCCEEEEECCCCCCCHHHH
T ss_conf             2048853699987331101261223341385177887318999999999988751---4688987998368664457889


Q ss_pred             HHHHCCCCHHHHHHHHHHHHCCCC
Q ss_conf             898859997999999999818858
Q gi|254780834|r   77 LSALLGCSFIESVQRLAAIAGVPL  100 (648)
Q Consensus        77 ~~~~~~~~f~ea~~~la~~~gi~~  100 (648)
                      ...  +++|         ..||++
T Consensus        82 ~~~--~i~~---------~vgiDi   94 (327)
T pfam03291        82 FKG--GISG---------LIGTDI   94 (327)
T ss_pred             HHC--CCCE---------EEEECC
T ss_conf             747--9868---------999668


No 57 
>PRK12383 putative mutase; Provisional
Probab=79.32  E-value=4.9  Score=20.00  Aligned_cols=140  Identities=18%  Similarity=0.217  Sum_probs=60.1

Q ss_pred             CCCCEEEEECCCCCCCC--------CCEE--CCCCCCCCCCCCHHC----CCHHHHHHHHHHHHCCCCCCCCCCEEEEEC
Q ss_conf             77858885010014655--------3001--038767653521011----081788886433100002356787089971
Q gi|254780834|r  213 SRGQVIAFGGRTLSKGE--------SVKY--LNSPETILFHKGKNL----YNFFGALNYLQKSIRKDVRRNSSSFIILVE  278 (648)
Q Consensus       213 ~~g~~i~f~gR~l~~~~--------~~KY--lNSpeT~if~K~~~L----y~l~~a~~~~~~~~~~~~~~~~~~~~i~vE  278 (648)
                      .-||||+|+++-...+.        .+.+  +|+|.+-.|.+....    |++...........      .....|+.|=
T Consensus       178 ~v~RvIa~~~~g~~~~~~~~~~~~~~~~~~g~~~P~~~~~~~~~~~rh~~y~~~P~~~v~~~L~------~aG~~V~~VG  251 (406)
T PRK12383        178 QVGRVIAFGGLLTDSQRILDAAESKEGGFIGINAPKSGVYDNGFQVVHLGYGVDPKVQVPQLLY------EAGVPVVLVG  251 (406)
T ss_pred             CCCEEEEECCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH------HCCCEEEEEE
T ss_conf             7213897556677513321000124766543458877755665321235557898510569999------7799389995


Q ss_pred             CHHHHHHHHHCCCCCCHHHHHCCCCHHHHHH-HHHCCCEEEEE----EC-----CCCCCHHHHHHHHHHHHHHHHCCC--
Q ss_conf             4388999874355421134321366267898-85126818996----17-----886622577788888877753697--
Q gi|254780834|r  279 GYMDVLSLCQAGVQNVVSSLGTALTEYQLRL-LWKLSPRIVLC----FD-----GDDPGLRAAYKAIDLVLCHLIPGN--  346 (648)
Q Consensus       279 Gy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~-l~r~~~~vvl~----fD-----gD~AG~kAa~Ra~e~~l~~l~~g~--  346 (648)
                      =--|..+  .-||...+-+.+++-.-+++.. +++-.+-.+++    ||     -|.+|...++..++.-|+.+.+.+  
T Consensus       252 KI~DIfa--~~Gi~~~~~~~~n~~~~~~t~~~~~~~~~gliF~NlVdfDl~GHRrD~~GYa~aLe~fD~~L~ell~~l~~  329 (406)
T PRK12383        252 KVADIVN--NPYGASWQPLVDTQRVLDITLDEFNTHPTAFICANIQETDLAGHAEDVARYAERLEVVDRNLARLLEAMQP  329 (406)
T ss_pred             CHHHCCC--CCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             3598317--88864345579889999999999960699569972223125445558889999999999989999983898


Q ss_pred             -CEEEEECCCCCCHH
Q ss_conf             -30675257888888
Q gi|254780834|r  347 -RVNFVLLSRGEDPD  360 (648)
Q Consensus       347 -~v~vv~LP~G~DPD  360 (648)
                       ++-|++-..|-||-
T Consensus       330 dDLLiITADHGnDPT  344 (406)
T PRK12383        330 DDCLVVMADHGNDPT  344 (406)
T ss_pred             CCEEEEECCCCCCCC
T ss_conf             878999387788988


No 58 
>TIGR00678 holB DNA polymerase III, delta' subunit; InterPro: IPR004622   DNA-directed DNA polymerase (2.7.7.7 from EC) catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. DNA polymerase III is a complex, multi-chain enzyme responsible for most of the replicative synthesis in bacteria. The enzyme also has 3' to 5' exonuclease activity. It has a core composed of alpha, epsilon and theta chains, that associate with a tau subunit which allows the core dimerisation to form the PolIII' complex. PolIII' associates with the gamma complex (gamma, delta, delta', psi and chi chains) and with the beta chain. This domain is the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tightly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classified as delta'. The noise cut-off is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits.; GO: 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication.
Probab=76.08  E-value=5.2  Score=19.74  Aligned_cols=67  Identities=21%  Similarity=0.312  Sum_probs=54.7

Q ss_pred             CHHHHHCC-----------------------CCHHHHHHHHHC--------CCEEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             11343213-----------------------662678988512--------68189961788662257778888887775
Q gi|254780834|r  294 VVSSLGTA-----------------------LTEYQLRLLWKL--------SPRIVLCFDGDDPGLRAAYKAIDLVLCHL  342 (648)
Q Consensus       294 ~va~~Gta-----------------------lt~~~~~~l~r~--------~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l  342 (648)
                      .|.|-|.+                       +..+|||.|.++        ..+|||..|.|.=..+||---+..   +-
T Consensus        68 ~~~P~~~~~~~~~de~~~~~~g~a~~~~~~~Ik~dq~R~l~~~~~~~~~~~~~rVviI~~Ae~mn~~AANALLKt---LE  144 (216)
T TIGR00678        68 RLEPEGQSKSLTADEAAEGEEGSAKRRALPQIKVDQVRELVEFLSLTPQESGRRVVIIEDAERMNEAAANALLKT---LE  144 (216)
T ss_pred             EEEEECCCCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHHCCHHHHHHHHHH---EE
T ss_conf             874234777777645897625642113678787278999999986064214751799767323258989865101---01


Q ss_pred             HCCCCEEEEECCCCCCHHHHH
Q ss_conf             369730675257888888997
Q gi|254780834|r  343 IPGNRVNFVLLSRGEDPDSFI  363 (648)
Q Consensus       343 ~~g~~v~vv~LP~G~DPDe~i  363 (648)
                      ++.-++.|+++-..-||+.++
T Consensus       145 EPp~~t~fiL~~~~~DP~~lL  165 (216)
T TIGR00678       145 EPPPNTLFILITHSPDPERLL  165 (216)
T ss_pred             CCCCCEEEEEECCCCCHHHHC
T ss_conf             279870798850888843322


No 59 
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=74.39  E-value=2.4  Score=22.87  Aligned_cols=30  Identities=23%  Similarity=0.641  Sum_probs=22.2

Q ss_pred             EEECCCCCCCCCCEEEE--CCCCEEEECCCCCC
Q ss_conf             75345888858787981--78974671368888
Q gi|254780834|r   40 WACCPFHDEKTPSFHCN--DSKGFYYCFSCHVK   70 (648)
Q Consensus        40 ~~~cPfh~ektpsf~v~--~~~~~~~cf~c~~~   70 (648)
                      -+.||.+.-|. -|...  ...+.|+|+.||+|
T Consensus         3 h~pCP~CGG~D-rfrf~dk~g~G~~~C~~Cg~G   34 (37)
T smart00778        3 HGPCPNCGGSD-RFRFDDKDGRGTWFCSVCGAG   34 (37)
T ss_pred             CCCCCCCCCCC-CEEEECCCCCEEEECCCCCCC
T ss_conf             66788677865-536746999740782788789


No 60 
>KOG2593 consensus
Probab=73.81  E-value=2.7  Score=22.42  Aligned_cols=48  Identities=21%  Similarity=0.349  Sum_probs=24.6

Q ss_pred             CCCCCCCCCCEEE----ECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             4588885878798----1789746713688887898998988599979999999998
Q gi|254780834|r   43 CPFHDEKTPSFHC----NDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAI   95 (648)
Q Consensus        43 cPfh~ektpsf~v----~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~   95 (648)
                      ||+++-|=-|+-+    +.+.+.|||.-||--     .|+.-..+.-.+++..|+.+
T Consensus       131 Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~ge-----lveDe~~~~~~e~~~~l~~~  182 (436)
T KOG2593         131 CPNCQKKYTSLEALQLLDNETGEFHCENCGGE-----LVEDENKLPSKESRTALNRL  182 (436)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCCEEEEECCCCC-----HHCCCCCCCHHHHHHHHHHH
T ss_conf             87412411266787752146766987247970-----21022447448888888998


No 61 
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=73.17  E-value=3.4  Score=21.46  Aligned_cols=60  Identities=10%  Similarity=0.140  Sum_probs=43.1

Q ss_pred             CCCCHHHHHHCCCHHHHHHHHHHCCC----HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             88888899720366889988641499----2799999998530233145799999999988541
Q gi|254780834|r  355 RGEDPDSFIRCYGKTAFEKLIVESLP----LVDMLWKRETENRSFNTPDERAELEIHLKNCINH  414 (648)
Q Consensus       355 ~G~DPDe~ir~~G~eaf~~ll~~A~~----l~dFl~~~l~~~~dl~spe~ka~~~~~l~~~I~~  414 (648)
                      ...||++++.++|+|+++-++-...|    -.+|=|+.+....+-+-...--.+++++..++.+
T Consensus       334 nvv~p~~~l~~yg~D~lRY~l~~~~p~~~~D~dfs~~~~~~r~NsdLan~lGNl~~R~~~~~~k  397 (666)
T PRK00133        334 TFIWARTYLDHLDPDYLRYYLAAKLPSRIDDIDFNWEDFQQRVNSDLVGKLVNFASRAAGFINK  397 (666)
T ss_pred             EEEEHHHHHHHCCCCCEEHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             1761799998669645302033107898767786999999998688887666899999999998


No 62 
>TIGR00396 leuS_bact leucyl-tRNA synthetase; InterPro: IPR002302   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .    Leucyl tRNA synthetase (6.1.1.4 from EC) is an alpha monomer that belongs to class Ia. There are two different families of leucyl-tRNA synthetases. This family includes the eubacterial and mitochondrial synthetases. The crystal structure of leucyl-tRNA synthetase from the hyperthermophile Thermus thermophilus has an overall architecture that is similar to that of isoleucyl-tRNA synthetase, except that the putative editing domain is inserted at a different position in the primary structure. This feature is unique to prokaryote-like leucyl-tRNA synthetases, as is the presence of a novel additional flexibly inserted domain . ; GO: 0000166 nucleotide binding, 0004823 leucine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006429 leucyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=72.11  E-value=5.3  Score=19.66  Aligned_cols=56  Identities=21%  Similarity=0.370  Sum_probs=42.1

Q ss_pred             CCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHH-HHHHHHHCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             78888889972036688998864149927999-9999853023314579999999998854179
Q gi|254780834|r  354 SRGEDPDSFIRCYGKTAFEKLIVESLPLVDML-WKRETENRSFNTPDERAELEIHLKNCINHIK  416 (648)
Q Consensus       354 P~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl-~~~l~~~~dl~spe~ka~~~~~l~~~I~~I~  416 (648)
                      -+|-||+++|.+||+|+.+-++==+-|+.+-+ |+       -+..+|..++++++-.+...+.
T Consensus       669 ~N~i~P~e~~~~yGADa~Rlf~mF~~P~~~~L~W~-------~~g~~G~~RFL~RVw~l~~~~~  725 (916)
T TIGR00396       669 GNGIDPQEIVKKYGADALRLFIMFMGPIAASLEWN-------ESGLEGARRFLDRVWNLVKEIL  725 (916)
T ss_pred             CCCCCCHHHHHHCCHHHHHHHHHHCCCHHHCCCCC-------CCCHHHHHHHHHHHHHHHHHHC
T ss_conf             79887038974048027999997048831414777-------1110135688899999998732


No 63 
>PRK00076 recR recombination protein RecR; Reviewed
Probab=71.05  E-value=7.4  Score=18.33  Aligned_cols=81  Identities=27%  Similarity=0.299  Sum_probs=54.9

Q ss_pred             CCEEEEECCHHHHHHHHHCCCCCCH-HHHHCCCC------HHHH---HHHHHC----CCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             8708997143889998743554211-34321366------2678---988512----68189961788662257778888
Q gi|254780834|r  271 SSFIILVEGYMDVLSLCQAGVQNVV-SSLGTALT------EYQL---RLLWKL----SPRIVLCFDGDDPGLRAAYKAID  336 (648)
Q Consensus       271 ~~~~i~vEGy~Dvi~l~~~G~~n~v-a~~Gtalt------~~~~---~~l~r~----~~~vvl~fDgD~AG~kAa~Ra~e  336 (648)
                      ...+.|||-..|++++-+.|.-+.. -.||-.++      ++++   .++.|.    .++|||++..+--|+.-|.=..+
T Consensus        78 ~~~icVVE~~~Dl~~iE~s~~y~G~YhVLgG~lSpl~gi~pe~l~i~~L~~Ri~~~~v~EVIlA~~~t~EGe~Ta~yi~~  157 (197)
T PRK00076         78 RSLLCVVESPADVLAIERTGEYRGLYHVLGGLLSPLDGIGPEDLNIDELLERLADGEVKEVILATNPTVEGEATAHYIAR  157 (197)
T ss_pred             CCEEEEECCHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHH
T ss_conf             76799986899999997579454783585662482128983226889999986579951799864898650899999999


Q ss_pred             HHHHHHHCCCCEEEEECCCC
Q ss_conf             88777536973067525788
Q gi|254780834|r  337 LVLCHLIPGNRVNFVLLSRG  356 (648)
Q Consensus       337 ~~l~~l~~g~~v~vv~LP~G  356 (648)
                      .    ++ +..++|-.|-.|
T Consensus       158 ~----lk-~~~ikitrlA~G  172 (197)
T PRK00076        158 L----LK-PLGVKVTRLAHG  172 (197)
T ss_pred             H----HH-HCCCEEEEEEEC
T ss_conf             8----65-549707776544


No 64 
>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=71.01  E-value=4  Score=20.82  Aligned_cols=42  Identities=21%  Similarity=0.434  Sum_probs=26.6

Q ss_pred             ECCCCCCCCC----CEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHH
Q ss_conf             3458888587----8798178974671368888789899898859997999999
Q gi|254780834|r   42 CCPFHDEKTP----SFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQR   91 (648)
Q Consensus        42 ~cPfh~ektp----sf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~   91 (648)
                      .|||.....=    ++.......++.|=+||+.|.+        .-+-.+|++.
T Consensus         3 pCPFCG~~~~~~~~~~~~~~~~~~~~C~~CgA~~~~--------~~~~~~ai~~   48 (53)
T TIGR03655         3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV--------EEDEAEAIEA   48 (53)
T ss_pred             CCCCCCCCHHHEECCCCCCCCEEEEECCCCCCCCCC--------CCCHHHHHHH
T ss_conf             888789753100025787665268877777787663--------1279999999


No 65 
>PRK00390 leuS leucyl-tRNA synthetase; Validated
Probab=70.71  E-value=7.5  Score=18.27  Aligned_cols=18  Identities=22%  Similarity=0.466  Sum_probs=9.3

Q ss_pred             EEEEEEECCCCEEEEECC
Q ss_conf             688897077858885010
Q gi|254780834|r  206 LIFPIRSSRGQVIAFGGR  223 (648)
Q Consensus       206 i~fPi~~~~g~~i~f~gR  223 (648)
                      |-||+.+..+.+..|+-|
T Consensus       231 v~F~~~~~~~~l~v~TTr  248 (822)
T PRK00390        231 VTFKVKGSDEKLEVFTTR  248 (822)
T ss_pred             EEEECCCCCCEEEEEECC
T ss_conf             863316998559999688


No 66 
>TIGR01418 PEP_synth phosphoenolpyruvate synthase; InterPro: IPR006319   This family represents phosphoenolpyruvate synthase; also called pyruvate,water dikinase and PEP synthase. The member from Methanococcus jannaschii contains a large intein. This enzyme generates phosphoenolpyruvate (PEP) from pyruvate, hydrolyzing ATP to AMP and releasing inorganic phosphate in the process. The enzyme shows extensive homology to other enzymes that use PEP as substrate or product. This enzyme may provide PEP for gluconeogenesis, for PTS-type carbohydrate transport systems, or for other processes. ; GO: 0008986 pyruvate water dikinase activity, 0006094 gluconeogenesis.
Probab=69.97  E-value=7.7  Score=18.15  Aligned_cols=281  Identities=14%  Similarity=0.224  Sum_probs=121.8

Q ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCCCCCC
Q ss_conf             99999999818858776820367778899999999999999999732677757899998506885351012442256774
Q gi|254780834|r   87 ESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSR  166 (648)
Q Consensus        87 ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~  166 (648)
                      -||..+.++|||....+.-+..    +=..|-.+-...-++|...-        -.|   |=++-|=++.|.||..  + 
T Consensus       294 PavaevvekyGirPd~fsL~De----Ei~~LA~~a~~IE~HY~k~~--------g~y---rPMDIEWAkD~~LG~~--g-  355 (877)
T TIGR01418       294 PAVAEVVEKYGIRPDKFSLSDE----EILELAKLAVKIEKHYSKKA--------GRY---RPMDIEWAKDFDLGED--G-  355 (877)
T ss_pred             CHHHHHHHHHCCCCCCCCCCHH----HHHHHHHHHHHHHHHHCCCC--------CCC---CCCCEEEEEECCCCCC--C-
T ss_conf             4265777761788886517878----99999888633532107898--------830---6862252001037989--7-


Q ss_pred             CHHHHHHHCCCCCHHHHHHHCCCEECCCCCC-CCCCCCCEEEEEEEE----CCCCEEEEECCCCCCC--C-CCEECCCCC
Q ss_conf             1034554205997345232012100346541-000016716888970----7785888501001465--5-300103876
Q gi|254780834|r  167 YSLREHLRQKGFSEEKIIEAGLLIDGDNSAT-SYDRFRNRLIFPIRS----SRGQVIAFGGRTLSKG--E-SVKYLNSPE  238 (648)
Q Consensus       167 ~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~-~~d~Fr~Ri~fPi~~----~~g~~i~f~gR~l~~~--~-~~KYlNSpe  238 (648)
                      +.+  -++..   +++.....   ..++.+. ...+      |++.+    .+|+||.= ||...+.  . ++|=+    
T Consensus       356 ~if--ivQAR---PETv~S~k---~~E~~n~P~~e~------~~~~~P~Eerkg~vlv~-G~a~g~~Ia~GkvkVi----  416 (877)
T TIGR01418       356 EIF--IVQAR---PETVQSRK---KKEAENKPVEER------YELKGPEEERKGKVLVK-GRAAGPGIASGKVKVI----  416 (877)
T ss_pred             CEE--EEECC---CCCEEECC---CCCCCCCCCEEE------ECCCCCCCCCCCEEEEE-EECCCCCCCCCCCEEE----
T ss_conf             578--99758---73110124---530023870565------02887860136718999-6322664035652687----


Q ss_pred             CCCCCCCHHCCCHHHH-HHHHHHHHCCCCCCCCCCEEEEE--------------------CCHHH---HHHHHHCCCCCC
Q ss_conf             7653521011081788-88643310000235678708997--------------------14388---999874355421
Q gi|254780834|r  239 TILFHKGKNLYNFFGA-LNYLQKSIRKDVRRNSSSFIILV--------------------EGYMD---VLSLCQAGVQNV  294 (648)
Q Consensus       239 T~if~K~~~Ly~l~~a-~~~~~~~~~~~~~~~~~~~~i~v--------------------EGy~D---vi~l~~~G~~n~  294 (648)
                                ..+.++ -..+           ..|.++|+                    ||=|=   +|-.=..|||-|
T Consensus       417 ----------~~~~e~k~~~~-----------~~GdiLVT~mTDPDWeP~MK~AsAIVTn~GG~TcHAAIVaRELGiPAV  475 (877)
T TIGR01418       417 ----------LDLKEMKVDKF-----------EEGDILVTDMTDPDWEPVMKRASAIVTNEGGRTCHAAIVARELGIPAV  475 (877)
T ss_pred             ----------CCHHHHCCCCC-----------CCCCEEEECCCCCCCHHHCCCCCEEEECCCCCHHHHHHHHHHCCCCCE
T ss_conf             ----------57434320443-----------886468757874281212213030470788750089999875588826


Q ss_pred             HHHHHCCCCHHHHHHHHHCCCEEEEE-ECCCC----CCHHH-HHHHHHH-HHHHHH--CCCCEEEEECCCCCCHHH--HH
Q ss_conf             13432136626789885126818996-17886----62257-7788888-877753--697306752578888889--97
Q gi|254780834|r  295 VSSLGTALTEYQLRLLWKLSPRIVLC-FDGDD----PGLRA-AYKAIDL-VLCHLI--PGNRVNFVLLSRGEDPDS--FI  363 (648)
Q Consensus       295 va~~Gtalt~~~~~~l~r~~~~vvl~-fDgD~----AG~kA-a~Ra~e~-~l~~l~--~g~~v~vv~LP~G~DPDe--~i  363 (648)
                      |.+-. |-+.     |+- ...|++| ==||+    ||+-- |--+.+. +-+.+.  ...   =+.|+.--.+..  ++
T Consensus       476 VG~~~-AT~~-----lkd-G~~VTVdc~eGdtG~VY~Gr~~~T~E~~~~~~~~ev~iq~~~---~v~l~~~P~t~Tki~m  545 (877)
T TIGR01418       476 VGTGD-ATKK-----LKD-GEEVTVDCAEGDTGYVYAGRVEKTEEAVEEKLEYEVEIQEDA---EVELSNMPETATKIYM  545 (877)
T ss_pred             ECCCH-HHHH-----HCC-CCEEEEECCCCCCCCEECCCEEECHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCEEEE
T ss_conf             64703-4565-----108-786898544488131345702300232544315674112665---3316767876647898


Q ss_pred             HCCCH---HHHH-HHHHHCCC--HHHHHHHHHHHHCCC---CCHHHHHHHHHHHHHHH--------------------HH
Q ss_conf             20366---8899-88641499--279999999853023---31457999999999885--------------------41
Q gi|254780834|r  364 RCYGK---TAFE-KLIVESLP--LVDMLWKRETENRSF---NTPDERAELEIHLKNCI--------------------NH  414 (648)
Q Consensus       364 r~~G~---eaf~-~ll~~A~~--l~dFl~~~l~~~~dl---~spe~ka~~~~~l~~~I--------------------~~  414 (648)
                      +=-.|   +.|. .+=.+...  =+||++-..+..+++   +.++.+...-.++.+++                    ++
T Consensus       546 Nvg~Pe~Af~~ar~lP~dGVGLaR~EfII~~~i~~HP~aLi~~~d~~~~~K~EI~el~dekGfvqfkliyhyanGrlanK  625 (877)
T TIGR01418       546 NVGNPERAFRFARALPNDGVGLARIEFIILNWIKIHPLALIDDDDLKEVEKAEIEELMDEKGFVQFKLIYHYANGRLANK  625 (877)
T ss_pred             ECCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCEEEEEEEEEECCCHHHHH
T ss_conf             53885457899752578862278899999857765468745776877588899986320576056677654204326677


Q ss_pred             CCCH--HHHHHHHHHHHHHHHHH
Q ss_conf             7998--99999999999998876
Q gi|254780834|r  415 IKDQ--KLRYYYSQAIRDRLQQL  435 (648)
Q Consensus       415 I~d~--~~R~~yl~~la~~L~~~  435 (648)
                      +.--  .-+++|+++|++-+...
T Consensus       626 L~aGY~~~~~~fv~kLaeGia~v  648 (877)
T TIGR01418       626 LAAGYANPRDFFVDKLAEGIAKV  648 (877)
T ss_pred             HHCCCCCCHHHHHHHHHHHHHHH
T ss_conf             65045881257889999999999


No 67 
>TIGR00014 arsC arsenate reductase; InterPro: IPR006659   This entry describes a distinct clade, including ArsC itself, of the broader family of ArsC and related proteins. This clade is almost completely restricted to the proteobacteria. An anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773 . When expressed in Escherichia coli this ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. The pump is composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate. ; GO: 0008794 arsenate reductase (glutaredoxin) activity, 0006118 electron transport.
Probab=69.95  E-value=3.8  Score=21.01  Aligned_cols=48  Identities=21%  Similarity=0.492  Sum_probs=33.2

Q ss_pred             CCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCH-HHHHHH
Q ss_conf             775789999850688535101244225677410345542059973-452320
Q gi|254780834|r  136 RDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSE-EKIIEA  186 (648)
Q Consensus       136 ~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~-~~~~~~  186 (648)
                      ++..+++||+.+|+.+++++...=   |.+...|.+.+.+.|++. .+++..
T Consensus        11 kSR~tLalL~dkgi~P~vV~YL~~---pp~~seL~~~~~~LG~~~ar~~~R~   59 (114)
T TIGR00014        11 KSRQTLALLEDKGIEPEVVKYLKN---PPTKSELKALLAKLGISSAREMIRT   59 (114)
T ss_pred             HHHHHHHHHHHCCCCCEEEECCCC---CCCHHHHHHHHHHCCCCHHHHHCCC
T ss_conf             468999999856999547414589---7486889999987089703630117


No 68 
>TIGR02478 6PF1K_euk 6-phosphofructokinase; InterPro: IPR009161    Members of this family are eukaryotic (with one exception) ATP-dependent 6-phosphofructokinases (2.7.1.11 from EC) in which two tandem copies of the phosphofructokinase are found . Members are found, often including several isozymes, in animals and fungi and in the bacterium Propionibacterium acnes KPA171202 (a human skin commensal).   Phosphofructokinase (PFK) catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate, which then enters the Embden-Meyerhof pathway. PFK is a key regulatory enzyme in glycolysis.   For additional information please see , , .; GO: 0003872 6-phosphofructokinase activity, 0006096 glycolysis, 0005737 cytoplasm.
Probab=68.26  E-value=6  Score=19.16  Aligned_cols=15  Identities=20%  Similarity=0.206  Sum_probs=7.4

Q ss_pred             ECCCCCCHHHHHHHH
Q ss_conf             178866225777888
Q gi|254780834|r  321 FDGDDPGLRAAYKAI  335 (648)
Q Consensus       321 fDgD~AG~kAa~Ra~  335 (648)
                      ==|=..|.=|++=++
T Consensus       582 tmGG~sGYLAt~~GL  596 (777)
T TIGR02478       582 TMGGYSGYLATMAGL  596 (777)
T ss_pred             EECCCHHHHHHHHHH
T ss_conf             708971689999988


No 69 
>pfam01921 tRNA-synt_1f tRNA synthetases class I (K). This family includes only lysyl tRNA synthetases from prokaryotes.
Probab=67.95  E-value=8.2  Score=17.92  Aligned_cols=25  Identities=12%  Similarity=0.238  Sum_probs=12.9

Q ss_pred             CCCHHHHHHCCCHHHHHHHHHHCCC
Q ss_conf             8888899720366889988641499
Q gi|254780834|r  356 GEDPDSFIRCYGKTAFEKLIVESLP  380 (648)
Q Consensus       356 G~DPDe~ir~~G~eaf~~ll~~A~~  380 (648)
                      |.=|+++++-.-++.++-++-+..|
T Consensus       286 ~is~~e~L~~~~pE~Lr~l~~~~~P  310 (355)
T pfam01921       286 GITIEEWLEYAPPESLRFLMFRVKP  310 (355)
T ss_pred             CCCHHHHHHHCCHHHHHHHHCCCCC
T ss_conf             7699999986699999999804288


No 70 
>TIGR01059 gyrB DNA gyrase, B subunit; InterPro: IPR011557   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .    Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.   This entry represents the B subunit (gyrB) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrB has two functional domains: an N-terminal ATPase and a C-terminal responsible for subunit interactions, the latter differing between subunit B and single polypeptide topoisomerase II .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=67.51  E-value=8.5  Score=17.75  Aligned_cols=99  Identities=17%  Similarity=0.241  Sum_probs=65.0

Q ss_pred             HHHCCCCCCHHHHHCCCCHHHHHHHH-HCCCEEEEEECCCCCCHHHHHHHHHHHH------HHHHCCCCEEEEECCCCCC
Q ss_conf             87435542113432136626789885-1268189961788662257778888887------7753697306752578888
Q gi|254780834|r  286 LCQAGVQNVVSSLGTALTEYQLRLLW-KLSPRIVLCFDGDDPGLRAAYKAIDLVL------CHLIPGNRVNFVLLSRGED  358 (648)
Q Consensus       286 l~~~G~~n~va~~Gtalt~~~~~~l~-r~~~~vvl~fDgD~AG~kAa~Ra~e~~l------~~l~~g~~v~vv~LP~G~D  358 (648)
                      |.-.-|.+-|+.|||.+-++-.-+=+ || .+||||=|+|==|..  .|++-|..      ++++.|. |+++..|    
T Consensus       477 l~N~Ei~~~ItALG~GI~~d~Fdl~KLRY-HKIIIMTDADVDGSH--IRTLLLTFFYR~M~~LIE~Gy-vYIAqPP----  548 (818)
T TIGR01059       477 LSNDEIQAIITALGCGIGKDEFDLEKLRY-HKIIIMTDADVDGSH--IRTLLLTFFYRYMRPLIENGY-VYIAQPP----  548 (818)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCC-CCEEEEECCCCCHHH--HHHHHHHHHHHHHHHHHHCCC-EEEECCC----
T ss_conf             21253388899736886766787232464-436884067878368--999999988740158874587-2650786----


Q ss_pred             HHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHCCCC
Q ss_conf             88997203668899886414992799999998530233
Q gi|254780834|r  359 PDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFN  396 (648)
Q Consensus       359 PDe~ir~~G~eaf~~ll~~A~~l~dFl~~~l~~~~dl~  396 (648)
                        =|=-+.|++.  .+|.+..-+-.|++...++...+-
T Consensus       549 --LYKvk~gk~~--~Yikdd~e~d~yll~~~~~~~~l~  582 (818)
T TIGR01059       549 --LYKVKKGKKE--RYIKDDKELDHYLLNLGINEAELV  582 (818)
T ss_pred             --CHHHHCCCCC--CCCCCHHHHHHHHHHHHCCCEEEE
T ss_conf             --0212046551--122277899889887532420265


No 71 
>COG2604 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.38  E-value=8.2  Score=17.91  Aligned_cols=55  Identities=29%  Similarity=0.469  Sum_probs=31.2

Q ss_pred             HHHHHCCCCHHHHHHHHHCCCEE-EEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCC
Q ss_conf             13432136626789885126818-9961788662257778888887775369730675257888888997203
Q gi|254780834|r  295 VSSLGTALTEYQLRLLWKLSPRI-VLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCY  366 (648)
Q Consensus       295 va~~Gtalt~~~~~~l~r~~~~v-vl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~  366 (648)
                      |-+-|-+|+ -|+.+|+.|.++. |+|=|          ||+.+   +++.|+.+.+|.   -.||||++-+.
T Consensus       229 IVSaGPSL~-Kql~lLK~y~~k~~IFcad----------sal~~---L~k~GIkPDyVc---~ld~~di~~e~  284 (594)
T COG2604         229 IVSAGPSLE-KQLPLLKKYQDKATIFCAD----------SALPI---LAKHGIKPDYVC---SLDPDDIAYEF  284 (594)
T ss_pred             EECCCCCHH-HCCHHHHHHCCCEEEEECC----------CCCHH---HHHCCCCCCEEE---EECCHHHHHHH
T ss_conf             980786744-4368888605553999889----------75457---986799977699---85641889999


No 72 
>TIGR01430 aden_deam adenosine deaminase; InterPro: IPR006330    This family includes the experimentally verified adenosine deaminases of mammals and Escherichia coli. Other members of this family are predicted also to be adenosine deaminase, an enzyme of nucleotide degradation. This family is distantly related to AMP deaminase. ; GO: 0004000 adenosine deaminase activity, 0009168 purine ribonucleoside monophosphate biosynthetic process.
Probab=66.33  E-value=8.1  Score=17.94  Aligned_cols=68  Identities=21%  Similarity=0.267  Sum_probs=39.8

Q ss_pred             HHHCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH--HHHC-CCCC--HHHHHHHHH
Q ss_conf             9885999799999999981885877682036777889999999999999999--9732-6777--578999985
Q gi|254780834|r   78 SALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFH--HSLK-NARD--KRLHYYLDE  146 (648)
Q Consensus        78 ~~~~~~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~-~~~~--~~a~~yl~~  146 (648)
                      +++||-==||-+-.||.|+||.+| ..++..+-...-..-.++...-..||.  .+|. +...  .-|.+|+.+
T Consensus         8 ~HleG~~~P~l~l~la~k~gi~LP-~~~~~~e~~~~~~~~~~L~~FL~~yd~~~~~L~G~~~d~~rlAy~~~~~   80 (346)
T TIGR01430         8 LHLEGSLRPELLLELAQKNGIPLP-DLQSLEELKEAYEKFRDLQDFLAKYDFGVEVLRGTEDDFKRLAYEYVEK   80 (346)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCCCC-CCCCCCHHHHHHCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             574325567889988864389888-6312100232111267878999999999887428998999999999999


No 73 
>TIGR01696 deoB phosphopentomutase; InterPro: IPR010045   This entry describes bacterial phosphopentomutase. This protein is involved in the purine and pyrimidine salvage pathway of nucleotide synthesis. It catalyses a phosphotransfer on ribose and deoxyribose, converting D-ribose 1-phosphate to D-ribose 5-phosphate, and 2-deoxy-D-ribose 1-phosphate to 2-deoxy-D-ribose 5-phosphate . ; GO: 0000287 magnesium ion binding, 0008973 phosphopentomutase activity, 0009117 nucleotide metabolic process, 0043094 metabolic compound salvage, 0005737 cytoplasm.
Probab=66.11  E-value=5.6  Score=19.46  Aligned_cols=85  Identities=26%  Similarity=0.344  Sum_probs=54.7

Q ss_pred             ECCHHHHHHH-------HHCCCCCCHHHHHC-CCCHHHHHHHHHCCCE-EEEE----ECC------CCCCHHHHHHHHHH
Q ss_conf             7143889998-------74355421134321-3662678988512681-8996----178------86622577788888
Q gi|254780834|r  277 VEGYMDVLSL-------CQAGVQNVVSSLGT-ALTEYQLRLLWKLSPR-IVLC----FDG------DDPGLRAAYKAIDL  337 (648)
Q Consensus       277 vEGy~Dvi~l-------~~~G~~n~va~~Gt-alt~~~~~~l~r~~~~-vvl~----fDg------D~AG~kAa~Ra~e~  337 (648)
                      =+||-||||.       ...||+..|-+.|. ++-..-++.++.-..+ |+|.    ||+      |.+|..++++-.+.
T Consensus       246 D~~~G~VisiGKI~DIY~~~GiT~~~~~~s~~~~~D~~i~~~k~~f~~ti~F~NlVDFDa~~GHRRD~~GYa~al~~FD~  325 (404)
T TIGR01696       246 DEGYGDVISIGKIADIYDGEGITKKVRTTSNMDGMDKVIKELKEDFTGTISFTNLVDFDALYGHRRDKAGYAAALEEFDR  325 (404)
T ss_pred             CCCCCCEEEECCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEHHHCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             17776568853200110578844223310036788999999853137717885200100246756582578999998742


Q ss_pred             HHHHHHCCC---CEEEEECCCCCCHHH
Q ss_conf             877753697---306752578888889
Q gi|254780834|r  338 VLCHLIPGN---RVNFVLLSRGEDPDS  361 (648)
Q Consensus       338 ~l~~l~~g~---~v~vv~LP~G~DPDe  361 (648)
                      =||.+-..+   ++-|++--.|-||=-
T Consensus       326 RLPEl~s~lr~DDllI~TADHG~DP~~  352 (404)
T TIGR01696       326 RLPELFSKLREDDLLIITADHGNDPTA  352 (404)
T ss_pred             HHHHHHHHCCCCCEEEEECCCCCCCCC
T ss_conf             226887403768579983067887788


No 74 
>TIGR02482 PFKA_ATP 6-phosphofructokinase; InterPro: IPR012828    6-phosphofructokinase (2.7.1.11 from EC) catalyses the addition of phosphate from ATP to fructose 6-phosphate to give fructose 1,6-bisphosphate. This represents a key control step in glycolysis. This entry contains bacterial ATP-dependent 6-phosphofructokinases, which lack a beta-hairpin loop present in IPR012829 from INTERPRO family members. IPR012829 from INTERPRO contains members that are ATP-dependent as well as members that are pyrophosphate-dependent. IPR011183 from INTERPRO represents the pyrophosphate-dependent phosphofructokinase, diphosphate--fructose-6-phosphate 1-phosphotransferase (2.7.1.90 from EC).; GO: 0003872 6-phosphofructokinase activity, 0005524 ATP binding, 0006002 fructose 6-phosphate metabolic process, 0006096 glycolysis.
Probab=65.36  E-value=7  Score=18.55  Aligned_cols=29  Identities=24%  Similarity=0.517  Sum_probs=15.1

Q ss_pred             CCEEEEECC---HHHHHHHHHCC-CCCCHHHHHC
Q ss_conf             870899714---38899987435-5421134321
Q gi|254780834|r  271 SSFIILVEG---YMDVLSLCQAG-VQNVVSSLGT  300 (648)
Q Consensus       271 ~~~~i~vEG---y~Dvi~l~~~G-~~n~va~~Gt  300 (648)
                      -+.+||+=|   ||=+-.||+-| |+ +|+.=||
T Consensus        92 I~~LVViGGDGSy~GA~~L~~~gg~~-~iGlPGT  124 (302)
T TIGR02482        92 IEALVVIGGDGSYTGAQKLYEEGGIP-VIGLPGT  124 (302)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHCCCC-EEEECCC
T ss_conf             86689986844068899999717984-7874585


No 75 
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=64.92  E-value=9.4  Score=17.36  Aligned_cols=45  Identities=18%  Similarity=0.273  Sum_probs=16.6

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf             999984430023799889999999999975388999899998851112
Q gi|254780834|r  498 LQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERG  545 (648)
Q Consensus       498 ~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~~l~~~L~~~~  545 (648)
                      +..+++.+....+.|.  .......+..-...+ ..+..+.+.|...+
T Consensus        54 Ie~Vi~~l~~~~~ldD--~~fAe~~i~~r~~~g-~G~~rl~qeL~qkG   98 (174)
T COG2137          54 IEEVIDRLAEEGYLDD--TRFAEAYIRSRSRKG-KGPARLKQELKQKG   98 (174)
T ss_pred             HHHHHHHHHHCCCCCH--HHHHHHHHHHHHHCC-CCHHHHHHHHHHCC
T ss_conf             9999999999286567--999999999987646-67299999999849


No 76 
>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=64.63  E-value=3.8  Score=21.03  Aligned_cols=22  Identities=18%  Similarity=0.271  Sum_probs=11.4

Q ss_pred             CCHHHHHHHHHHCCHHHHHHHH
Q ss_conf             7888999998748888875412
Q gi|254780834|r    3 YPRDFIKDLLIHIPISNLIGQY   24 (648)
Q Consensus         3 i~~~~i~~i~~~~~i~~vv~~~   24 (648)
                      |++==|+.|+.+.++-.-|..+
T Consensus       265 FS~yQl~~l~~kN~L~q~l~~~  286 (1127)
T TIGR00600       265 FSRYQLKGLLKKNDLNQKLENV  286 (1127)
T ss_pred             HHHHHHHHHHHHCHHHHHHHHH
T ss_conf             1089999876522034568865


No 77 
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR.  RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Probab=64.16  E-value=9.7  Score=17.25  Aligned_cols=79  Identities=24%  Similarity=0.292  Sum_probs=51.7

Q ss_pred             EEEEECCHHHHHHHHHCCCCCCH-HHHHCCCCH------HHH---HHHHHC----CCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             08997143889998743554211-343213662------678---988512----6818996178866225777888888
Q gi|254780834|r  273 FIILVEGYMDVLSLCQAGVQNVV-SSLGTALTE------YQL---RLLWKL----SPRIVLCFDGDDPGLRAAYKAIDLV  338 (648)
Q Consensus       273 ~~i~vEGy~Dvi~l~~~G~~n~v-a~~Gtalt~------~~~---~~l~r~----~~~vvl~fDgD~AG~kAa~Ra~e~~  338 (648)
                      .+.|||-..|++++-+.|.-+.. -.||-.+++      +++   .++.|.    .++|||++...--|..-|.=-.+. 
T Consensus         2 ~lcVVe~~~Dl~~iE~s~~y~G~YhVL~G~lspl~g~~p~~l~i~~L~~ri~~~~i~EvIlA~~~t~EGe~Ta~yi~~~-   80 (112)
T cd01025           2 KLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL-   80 (112)
T ss_pred             EEEEECCHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHH-
T ss_conf             7999898999999972175656999852634755699833031999999983589418999748996608999999998-


Q ss_pred             HHHHHCCCCEEEEECCCC
Q ss_conf             777536973067525788
Q gi|254780834|r  339 LCHLIPGNRVNFVLLSRG  356 (648)
Q Consensus       339 l~~l~~g~~v~vv~LP~G  356 (648)
                         ++ ...++|-.|-.|
T Consensus        81 ---l~-~~~ikitrLA~G   94 (112)
T cd01025          81 ---LK-DFGVKVTRLAQG   94 (112)
T ss_pred             ---HH-HCCCCEEEEEEC
T ss_conf             ---54-359727988744


No 78 
>COG5440 Uncharacterized conserved protein [Function unknown]
Probab=64.09  E-value=7  Score=18.53  Aligned_cols=57  Identities=32%  Similarity=0.387  Sum_probs=37.3

Q ss_pred             CHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHH-HHHHHHHHHHCCCCEEEEECCCCCCHHHHHHC
Q ss_conf             1134321366267898851268189961788662257778-88888777536973067525788888899720
Q gi|254780834|r  294 VVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYK-AIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRC  365 (648)
Q Consensus       294 ~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~R-a~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~  365 (648)
                      ++-.+|++++.+|.+-|+.+..+           .+  .+ +..+-..++.-|  |.|..+|.-.||-++.-.
T Consensus        56 viVA~gi~ls~eH~~al~aL~~e-----------~R--~efi~~l~~dLlr~~--v~F~~~Pn~~~pqsiqvs  113 (161)
T COG5440          56 VIVAIGIALSQEHRRALMALNPE-----------KR--EEFIWKLRRDLLRLG--VDFQALPNPRDPQSIQVS  113 (161)
T ss_pred             EEEEEEECCCHHHHHHHHHCCHH-----------HH--HHHHHHHHHHHHHCC--CCEEECCCCCCCCEEEEE
T ss_conf             99997633299999998840967-----------78--999999999999638--735954996677436744


No 79 
>PRK13738 conjugal transfer pilus assembly protein TraW; Provisional
Probab=63.82  E-value=9.8  Score=17.20  Aligned_cols=82  Identities=24%  Similarity=0.299  Sum_probs=47.1

Q ss_pred             CCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCC
Q ss_conf             12100346541000016716888970778588850100146553001038767653521011081788886433100002
Q gi|254780834|r  187 GLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDV  266 (648)
Q Consensus       187 gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~  266 (648)
                      ||....+....+||-. =.+-..|.|..|+|++=.|-.+++   -.|+.-+++.+|=-++--=-+..|+.....      
T Consensus        75 gl~~a~~~rt~~~DPS-~tl~~DI~d~~G~via~aGt~vNP---Ld~v~~~~~LvF~DgdD~~Qv~Wa~~~~~~------  144 (210)
T PRK13738         75 GIGRAEKYGSRLFDPS-VRLAADIRDNEGRVFARQGEVMNP---LQYVPFNQTLYFINGDDPAQVAWMKRQTPP------  144 (210)
T ss_pred             CCCCCCCCCEEEECCC-EEECCCCCCCCCCEEECCCCEECC---CCCCCCCCEEEEEECCCHHHHHHHHHHCCC------
T ss_conf             8755434625995786-884575238999899758877786---412468872899959899999999974005------


Q ss_pred             CCCCCCEEEEECCH
Q ss_conf             35678708997143
Q gi|254780834|r  267 RRNSSSFIILVEGY  280 (648)
Q Consensus       267 ~~~~~~~~i~vEGy  280 (648)
                        .....+|+|.|-
T Consensus       145 --~~~~K~ILv~Gs  156 (210)
T PRK13738        145 --TLESKIILVQGS  156 (210)
T ss_pred             --CCCCEEEEECCC
T ss_conf             --777139996898


No 80 
>PRK13844 recombination protein RecR; Provisional
Probab=63.47  E-value=9.9  Score=17.15  Aligned_cols=80  Identities=15%  Similarity=0.247  Sum_probs=51.0

Q ss_pred             CCEEEEECCHHHHHHHHHCCCCCCH-HHHHCCC------CHHHHH--HH-HHC----CCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             8708997143889998743554211-3432136------626789--88-512----68189961788662257778888
Q gi|254780834|r  271 SSFIILVEGYMDVLSLCQAGVQNVV-SSLGTAL------TEYQLR--LL-WKL----SPRIVLCFDGDDPGLRAAYKAID  336 (648)
Q Consensus       271 ~~~~i~vEGy~Dvi~l~~~G~~n~v-a~~Gtal------t~~~~~--~l-~r~----~~~vvl~fDgD~AG~kAa~Ra~e  336 (648)
                      ...+-|||-..|++++-+.|.-+.+ -.||-.+      ++++++  .| .|.    .++|||+++.+--|..-|.= +.
T Consensus        82 ~~~iCVVE~~~Dl~aiE~s~~y~G~YhVL~G~iSpl~gigp~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~y-i~  160 (200)
T PRK13844         82 DTKLCIIESMLDMIAIEEAGIYRGKYFVLNGRISPLDGIGPSELKLDILQQIIADRKIDEVILAISPTVEGETTAHF-IS  160 (200)
T ss_pred             CCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCHHHHCHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHH-HH
T ss_conf             98899983689999999744106688874874473238882230679999886379974799967999650999999-99


Q ss_pred             HHHHHHHCCCCEEEEECCCC
Q ss_conf             88777536973067525788
Q gi|254780834|r  337 LVLCHLIPGNRVNFVLLSRG  356 (648)
Q Consensus       337 ~~l~~l~~g~~v~vv~LP~G  356 (648)
                      .   +++.  .|+|-.|-.|
T Consensus       161 ~---~l~~--~ikitrLA~G  175 (200)
T PRK13844        161 Q---MIAK--DIKISRIGFG  175 (200)
T ss_pred             H---HHCC--CCCEEEEEEC
T ss_conf             9---8449--9727766544


No 81 
>TIGR00020 prfB peptide chain release factor 2; InterPro: IPR004374 In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a superfamily IPR000352 from INTERPRO of RF-1, RF-2, mitochondrial, RF-H, etc proteins.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=62.23  E-value=10  Score=16.97  Aligned_cols=95  Identities=15%  Similarity=0.326  Sum_probs=49.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH-
Q ss_conf             9999885111289999999998654333202568998-89999999999999858999999999999998724127989-
Q gi|254780834|r  535 EEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANI-VDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQVTAKGEAE-  612 (648)
Q Consensus       535 ~~l~~~L~~~~l~elL~~L~~~~~~~~~~~~~~e~~~-~d~~e~~~~~l~l~~r~~~L~r~l~ele~~l~e~~~~~d~e-  612 (648)
                      ..+...|..+.+..-|+++.........|.-...+.. ......++..+.   +...|.+.+.++..- .++....+.+ 
T Consensus        19 ~~~~~~Ld~e~~~~rle~le~e~~dP~fW~D~~rAq~v~~e~~~l~~~l~---~~~~l~~~~~dl~~L-~Ela~ee~d~a   94 (373)
T TIGR00020        19 DDVRGILDPEKLKARLEELEKEMEDPNFWNDQERAQKVIKERSSLEEELD---TLEELKNSLDDLSEL-LELAKEEDDEA   94 (373)
T ss_pred             HHHHHHCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH-HHHHCCCCHHH
T ss_conf             98775138668999999998775078666125899999999999998632---799987553257889-98743760357


Q ss_pred             ------HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ------999999999999999999884
Q gi|254780834|r  613 ------KTAILISILHEVHIQIHQIES  633 (648)
Q Consensus       613 ------~~~~l~~el~elk~~L~~l~~  633 (648)
                            ...++-.|+..|.+++++++-
T Consensus        95 aasGm~~~~el~~El~~Le~~~~~lE~  121 (373)
T TIGR00020        95 AASGMETFAELEEELKALEKELEELEL  121 (373)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             778999999999999999999999999


No 82 
>pfam04273 DUF442 Putative phosphatase (DUF442). Although this domain is uncharacterized it seems likely that it performs a phosphatase function.
Probab=60.90  E-value=11  Score=16.79  Aligned_cols=84  Identities=14%  Similarity=0.184  Sum_probs=49.4

Q ss_pred             CCCHHHHHCCCCHHHHHHHHHCCCEEEEEEC--CCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHH
Q ss_conf             4211343213662678988512681899617--88662257778888887775369730675257888888997203668
Q gi|254780834|r  292 QNVVSSLGTALTEYQLRLLWKLSPRIVLCFD--GDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKT  369 (648)
Q Consensus       292 ~n~va~~Gtalt~~~~~~l~r~~~~vvl~fD--gD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~e  369 (648)
                      ..-++..| .++++++..|....=+.|||.=  +.+.|+-....--+.+.   ..|++..-+.+..|.-.++-     .+
T Consensus         6 ~~~~~vs~-Qi~~~di~~la~~GfktIInnRPd~E~~~qp~~~~~~~~a~---~~Gl~y~~iPv~~~~~t~~~-----v~   76 (110)
T pfam04273         6 NEDLSVSP-QIQPDDIAAAARAGFRSVINNRPDGEEPGQPSNAAEQAAAR---AAGLAYRFIPVISGQITEAD-----VE   76 (110)
T ss_pred             CCCEEECC-CCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCHHHHHHHHH---HCCCEEEEEECCCCCCCHHH-----HH
T ss_conf             78875759-98999999999859838853388877789988899999999---83997999644778989999-----99


Q ss_pred             HHHHHHHHC-CCHHHH
Q ss_conf             899886414-992799
Q gi|254780834|r  370 AFEKLIVES-LPLVDM  384 (648)
Q Consensus       370 af~~ll~~A-~~l~dF  384 (648)
                      .|.++++++ .|.+-|
T Consensus        77 ~f~~~l~~~~~Pvl~~   92 (110)
T pfam04273        77 AFQRALAAAEGPVLAH   92 (110)
T ss_pred             HHHHHHHHCCCCEEEE
T ss_conf             9999998589989998


No 83 
>PRK02853 hypothetical protein; Provisional
Probab=60.85  E-value=9.1  Score=17.50  Aligned_cols=81  Identities=22%  Similarity=0.428  Sum_probs=43.0

Q ss_pred             CCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHH
Q ss_conf             67168889707785888501001465530010387676535210110817888864331000023567870899714388
Q gi|254780834|r  203 RNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMD  282 (648)
Q Consensus       203 r~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~D  282 (648)
                      -+|++|-|++..|..+.=                          ....|..-|..++            ++..+||.|+|
T Consensus        63 d~rLvfdI~~~~~~~~~~--------------------------~~lsl~pfRriik------------DYf~iCeSYy~  104 (161)
T PRK02853         63 ENRLVFDIRREDGEPVAT--------------------------HILSLTPFRRIVK------------DYFMICESYYQ  104 (161)
T ss_pred             CCEEEEEEECCCCCEEEE--------------------------EEECCHHHHHHHH------------HHHHHHHHHHH
T ss_conf             798999973688982058--------------------------9962444899999------------99999999999


Q ss_pred             HHHHHHCCCCCCHHHHH-CCCCHHHHHHHH-HCCCEEEEEEC
Q ss_conf             99987435542113432-136626789885-12681899617
Q gi|254780834|r  283 VLSLCQAGVQNVVSSLG-TALTEYQLRLLW-KLSPRIVLCFD  322 (648)
Q Consensus       283 vi~l~~~G~~n~va~~G-talt~~~~~~l~-r~~~~vvl~fD  322 (648)
                      +|.-....-=.+| -|| -++-.+-..+|. |+..+|.+=||
T Consensus       105 AIk~~~p~qIEaI-DMgRRglHnEga~lL~eRL~gki~~D~~  145 (161)
T PRK02853        105 AIRTATPSQIEAI-DMGRRGLHNEGSELLQERLEGKIDVDFD  145 (161)
T ss_pred             HHHHCCHHHHHHH-HHHHHCCCHHHHHHHHHHHHCCEEECHH
T ss_conf             9960998786787-6542022247899999998287354202


No 84 
>TIGR01980 sufB FeS assembly protein SufB; InterPro: IPR010231   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents SufB, which is part of the SUF system and forms a complex with SufBCD.; GO: 0005515 protein binding, 0016226 iron-sulfur cluster assembly.
Probab=60.13  E-value=5.3  Score=19.69  Aligned_cols=34  Identities=24%  Similarity=0.192  Sum_probs=18.9

Q ss_pred             HCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             21366267898851268189961788662257778888887
Q gi|254780834|r  299 GTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVL  339 (648)
Q Consensus       299 Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l  339 (648)
                      +--||++=|+.|.+.-.++=-|+|=       =|||+|...
T Consensus        18 ~kGLt~~VV~~IS~~K~EP~WMLd~-------RLrale~f~   51 (469)
T TIGR01980        18 EKGLTEEVVREISEKKGEPDWMLDF-------RLRALELFL   51 (469)
T ss_pred             CCCCCHHHHHHHHHHCCCCHHHHHH-------HHHHHHHHH
T ss_conf             7898889999997305888689999-------999999884


No 85 
>pfam06840 DUF1241 Protein of unknown function (DUF1241). This family consists of several programmed cell death 10 protein (PDCD10 or TFAR15) sequences. The function of this family is unknown.
Probab=58.29  E-value=10  Score=16.93  Aligned_cols=28  Identities=21%  Similarity=0.078  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q ss_conf             8999999999997538899989999885
Q gi|254780834|r  514 ELQKLWSFLFSDFVEQKYFLPEEIHQRL  541 (648)
Q Consensus       514 ~~~~L~~~i~~~~~~~~~~~~~~l~~~L  541 (648)
                      ..+.|+.++...-.+.+.+..+-+..-+
T Consensus        31 a~q~Lr~Af~kaE~~~PGf~~d~v~~il   58 (154)
T pfam06840        31 AAQKLRAAFTKAEKENPGFTYDLVKGIL   58 (154)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             9999999999987218966999999999


No 86 
>KOG3578 consensus
Probab=57.15  E-value=3.3  Score=21.49  Aligned_cols=35  Identities=11%  Similarity=0.057  Sum_probs=21.6

Q ss_pred             CCCCCHHHHHHHHCC------------CCHHHHHHHHHHHHCCCCCC
Q ss_conf             888789899898859------------99799999999981885877
Q gi|254780834|r   68 HVKGDHLSFLSALLG------------CSFIESVQRLAAIAGVPLPV  102 (648)
Q Consensus        68 ~~~gd~~~f~~~~~~------------~~f~ea~~~la~~~gi~~~~  102 (648)
                      +--|.++.|++++.-            +-|.-|.+.+++.+|..+..
T Consensus        79 ~~mg~~~~~~qe~~~fv~~~y~~irn~v~~l~a~~~~~~~~~~~i~~  125 (1058)
T KOG3578          79 AYMGTVGKVYQESRKFVFAHYKNIRNMVLFLTAEESLMDTDGHRINN  125 (1058)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECC
T ss_conf             77568999998877999999999999999999999974005812001


No 87 
>pfam00133 tRNA-synt_1 tRNA synthetases class I (I, L, M and V). Other tRNA synthetase sub-families are too dissimilar to be included.
Probab=56.90  E-value=7.9  Score=18.04  Aligned_cols=19  Identities=16%  Similarity=0.599  Sum_probs=10.3

Q ss_pred             EEEEEEEECCC-CEEEEECC
Q ss_conf             16888970778-58885010
Q gi|254780834|r  205 RLIFPIRSSRG-QVIAFGGR  223 (648)
Q Consensus       205 Ri~fPi~~~~g-~~i~f~gR  223 (648)
                      .+-||+.+..+ .++.|+-|
T Consensus       189 ~v~f~l~~~~~~~l~i~TTr  208 (606)
T pfam00133       189 HVAFPLADGKGASLVIWTTT  208 (606)
T ss_pred             EEECCCCCCCCCEEEEEECC
T ss_conf             65044578987669999435


No 88 
>TIGR00658 orni_carb_tr ornithine carbamoyltransferase; InterPro: IPR002292 The ornithine carbamoyltransferases are a family of enzymes that catalyse the production of citrulline from carbamoyl-phosphate and ornithine . This reaction is part of the arginine biosynthetic pathway, and in some organisms the reaction is also part of the arginine deaminase pathway . In most prokaryotes, and some lower eukaryotes, the enzyme is found in the cytoplasm, but in higher eukaryotes, such as mammals, the enzyme is found in the mitochondrial matrix and functions as part of the urea cycle. In most organisms analysed to date, the enzyme has been shown to consist of a trimer of identical or nonidentical subunits . Extensive similarity has been found within the ornithine carbamoyltransferase family, some of the conserved areas being important in catalysis .   The C-terminal region of these enzymes shows a degree of similarity to the aspartate carbamoyltransferases, which are also known to bind carbamoyl- phosphate . This region contains a highly conserved Cys residue (in a His-Cys-Lys-Pro motif) implicated in ornithine binding . ; GO: 0004585 ornithine carbamoyltransferase activity, 0006520 amino acid metabolic process, 0009348 ornithine carbamoyltransferase complex.
Probab=56.76  E-value=12  Score=16.49  Aligned_cols=70  Identities=19%  Similarity=0.182  Sum_probs=45.4

Q ss_pred             HHHH--HHHHC----CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHC
Q ss_conf             6789--88512----68189961788662257778888887775369730675257888888997203668899886414
Q gi|254780834|r  305 YQLR--LLWKL----SPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVES  378 (648)
Q Consensus       305 ~~~~--~l~r~----~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A  378 (648)
                      ||.-  .|+..    .+++-+.|=||.  +|=.--+  |++.-.+-|++++|+. |+|.+||+.|.+. ..++.+--..+
T Consensus       147 E~~g~~~l~g~nkGinsklk~vy~GDg--RNNVcnS--L~la~a~~Gm~~~v~t-P~gyeP~~~~v~~-A~~~a~e~Gg~  220 (341)
T TIGR00658       147 EHFGEKKLKGVNKGINSKLKVVYVGDG--RNNVCNS--LLLAAAKLGMDVVVAT-PEGYEPDAEIVKK-AKKIAKENGGS  220 (341)
T ss_pred             HHCCCCCCCHHCCCCCCCCEEEEECCC--CHHHHHH--HHHHHHHHCCEEEEEC-CCCCCCCHHHHHH-HHHHHHHCCCE
T ss_conf             746795600000352442168997378--5126889--9999997285478878-8888878789999-99999717985


Q ss_pred             CC
Q ss_conf             99
Q gi|254780834|r  379 LP  380 (648)
Q Consensus       379 ~~  380 (648)
                      ..
T Consensus       221 ~~  222 (341)
T TIGR00658       221 VE  222 (341)
T ss_pred             EE
T ss_conf             99


No 89 
>pfam01113 DapB_N Dihydrodipicolinate reductase, N-terminus. Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH.
Probab=56.73  E-value=7.4  Score=18.31  Aligned_cols=42  Identities=26%  Similarity=0.313  Sum_probs=30.9

Q ss_pred             CCHHHHHH-HHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEE
Q ss_conf             14388999-874355421134321366267898851268189961
Q gi|254780834|r  278 EGYMDVLS-LCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCF  321 (648)
Q Consensus       278 EGy~Dvi~-l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~f  321 (648)
                      ++-++.+. +..+|++-||+|  |-||++|...|+++++++-+++
T Consensus        76 ~~~~~~~~~~~~~~~~~ViGT--TG~s~~~~~~i~~~a~~ipi~~  118 (122)
T pfam01113        76 EATLENLELALKHGKPLVIGT--TGFTEEQLAELKEAAKKIPIVI  118 (122)
T ss_pred             HHHHHHHHHHHHCCCCEEEEC--CCCCHHHHHHHHHHHCCCCEEE
T ss_conf             899999999996799889989--9999999999999844598898


No 90 
>pfam01458 UPF0051 Uncharacterized protein family (UPF0051).
Probab=56.57  E-value=6.9  Score=18.62  Aligned_cols=12  Identities=17%  Similarity=0.371  Sum_probs=5.1

Q ss_pred             CCHHH--HHHCCCH
Q ss_conf             88889--9720366
Q gi|254780834|r  357 EDPDS--FIRCYGK  368 (648)
Q Consensus       357 ~DPDe--~ir~~G~  368 (648)
                      .|||.  |++..|.
T Consensus       204 id~e~lfYL~sRGi  217 (230)
T pfam01458       204 LDEEQLFYLMSRGL  217 (230)
T ss_pred             CCHHHHHHHHHCCC
T ss_conf             79899999987698


No 91 
>TIGR01981 sufD FeS assembly protein SufD; InterPro: IPR011542   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents SufD proteins that form part of the SufBCD complex in the SUF system. No specific functions have been assigned to these proteins.; GO: 0005515 protein binding, 0016226 iron-sulfur cluster assembly.
Probab=55.95  E-value=6.3  Score=19.00  Aligned_cols=69  Identities=19%  Similarity=0.205  Sum_probs=34.4

Q ss_pred             CCCEEEEECCCC-CCHHHHHHC-CCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCHHHHHHH-HHHHHHHHHHCCCHHHH
Q ss_conf             973067525788-888899720-366889988641499279999999853023314579999-99999885417998999
Q gi|254780834|r  345 GNRVNFVLLSRG-EDPDSFIRC-YGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAEL-EIHLKNCINHIKDQKLR  421 (648)
Q Consensus       345 g~~v~vv~LP~G-~DPDe~ir~-~G~eaf~~ll~~A~~l~dFl~~~l~~~~dl~spe~ka~~-~~~l~~~I~~I~d~~~R  421 (648)
                      +...++..-|.= -|=||..-. ||+. .-.+=+      +-+|-  +....++..+-|.-+ ..++.++|..|+++.+|
T Consensus       324 s~~A~~d~~P~LeI~~ddV~~~gHgAt-Vg~iD~------e~LFY--LrSRGi~~~~A~~L~i~gF~~e~i~~i~~~~l~  394 (397)
T TIGR01981       324 SDKARADTKPQLEIDADDVKCSGHGAT-VGQIDD------EQLFY--LRSRGIDEEEARRLLIRGFLGEIIEEIPDESLK  394 (397)
T ss_pred             CCCCEEEECEEEEEECCCEEECCEECC-CCCCCH------HHHHH--HHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf             787628712167997582432110110-033574------46576--763788989999999998864333213881565


Q ss_pred             H
Q ss_conf             9
Q gi|254780834|r  422 Y  422 (648)
Q Consensus       422 ~  422 (648)
                      +
T Consensus       395 ~  395 (397)
T TIGR01981       395 E  395 (397)
T ss_pred             H
T ss_conf             2


No 92 
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=55.62  E-value=13  Score=16.10  Aligned_cols=16  Identities=31%  Similarity=0.696  Sum_probs=7.0

Q ss_pred             CCCCCCCEEEEEEEECCC
Q ss_conf             000016716888970778
Q gi|254780834|r  198 SYDRFRNRLIFPIRSSRG  215 (648)
Q Consensus       198 ~~d~Fr~Ri~fPi~~~~g  215 (648)
                      +||. +|-|| -|+-..|
T Consensus       120 ~~D~-~nail-eI~aGaG  135 (367)
T PRK00578        120 EYDA-NNAIL-TIHAGAG  135 (367)
T ss_pred             CCCC-CCEEE-EEECCCC
T ss_conf             8867-88479-9984899


No 93 
>pfam09133 SANTA SANTA (SANT Associated). The SANTA domain (SANT Associated domain) is approximately 90 amino acids in length and is conserved in Eukaryota. It is sometimes found in association with the SANT domain (pfam00249, also known as Myb-like DNA-binding domain) implying a putative function in regulating chromatin remodelling. Sequence analysis has showed that the SANTA domain is likely to form four central beta-sheets with three flanking alpha- helixes. Many conserved hydrophobic residues are present which implying a possible role in protein-protein interactions.
Probab=55.57  E-value=5.1  Score=19.80  Aligned_cols=26  Identities=15%  Similarity=0.351  Sum_probs=17.0

Q ss_pred             CCCEEEEECCHHHHHHHHHCCCCCCH
Q ss_conf             78708997143889998743554211
Q gi|254780834|r  270 SSSFIILVEGYMDVLSLCQAGVQNVV  295 (648)
Q Consensus       270 ~~~~~i~vEGy~Dvi~l~~~G~~n~v  295 (648)
                      ..+..|+..|.||...++++|++.-|
T Consensus        48 ~dG~~~~L~G~in~~~~~~nGfs~~v   73 (93)
T pfam09133        48 VDGITYVLVGFIDRSRMLKNGFPSEV   73 (93)
T ss_pred             CCCEEEEEECCCCHHHHHHCCCCHHH
T ss_conf             58709999465688889885999899


No 94 
>TIGR01286 nifK nitrogenase molybdenum-iron protein beta chain; InterPro: IPR005976    The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene , . Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes . It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .; GO: 0016163 nitrogenase activity, 0009399 nitrogen fixation, 0016612 molybdenum-iron nitrogenase complex.
Probab=54.64  E-value=3.4  Score=21.46  Aligned_cols=226  Identities=16%  Similarity=0.182  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHHHHHH-------HHHCCC-CCHHHHHHHHHCCCCHHHHCCCCCCCCC---------CCCCHH----HHHH
Q ss_conf             999999999999999-------973267-7757899998506885351012442256---------774103----4554
Q gi|254780834|r  115 TDLIRLIEVATDFFH-------HSLKNA-RDKRLHYYLDERGIDSHAIEMFKLGYAP---------DSRYSL----REHL  173 (648)
Q Consensus       115 ~~~~~~~~~~~~~~~-------~~l~~~-~~~~a~~yl~~Rg~~~~~~~~f~lG~ap---------~~~~~l----~~~l  173 (648)
                      +.|.+.++=....|.       ..++.. .|..-.+|+.+=.=.+-+-+.|-+-||.         .+||..    .++|
T Consensus       128 ~NmvdGL~N~~alYkPkmIAVSTTCMAEVIGdDL~AFi~nAk~~g~ip~dfPVpFAHTPsFVGSHitGYD~M~kGil~~l  207 (526)
T TIGR01286       128 KNMVDGLQNIYALYKPKMIAVSTTCMAEVIGDDLRAFIGNAKEEGVIPDDFPVPFAHTPSFVGSHITGYDSMLKGILETL  207 (526)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEECCCCHHHHHHHHHH
T ss_conf             77999997404325896466304544011013589999875306888888767865477732650025322689999985


Q ss_pred             HCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECC--CCE---------EEEECCCCCCCCCCEECCCCCCCCC
Q ss_conf             20599734523201210034654100001671688897077--858---------8850100146553001038767653
Q gi|254780834|r  174 RQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSR--GQV---------IAFGGRTLSKGESVKYLNSPETILF  242 (648)
Q Consensus       174 ~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~--g~~---------i~f~gR~l~~~~~~KYlNSpeT~if  242 (648)
                      .++.  .++   |.=.....+++.        =++|=+|..  |.+         .|.++-+|. | ...||-||.-==|
T Consensus       208 ~~~~--~~d---as~~~~~~~~~i--------N~ipGFdTYCiGN~R~~Kr~L~~mGv~~~~L~-D-~~~~LDsP~dGey  272 (526)
T TIGR01286       208 TKGS--EDD---ASDKKKSANGKI--------NIIPGFDTYCIGNVREIKRILSLMGVEYTLLS-D-AEESLDSPADGEY  272 (526)
T ss_pred             HCCC--HHH---HHHHHHCCCCEE--------EEEECCCCCEECCHHHHHHHHHHHCCCCEEEC-C-CHHHCCCCCCCCC
T ss_conf             0585--113---345442038627--------78407675111656889789987289830304-6-5543679888871


Q ss_pred             CCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCE----EE
Q ss_conf             52101108178888643310000235678708997143889998743554211343213662678988512681----89
Q gi|254780834|r  243 HKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPR----IV  318 (648)
Q Consensus       243 ~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~----vv  318 (648)
                          -||                           -+|-.   ---.++=.|+-||+  .|=+.+++.=+.|+.+    =+
T Consensus       273 ----~mY---------------------------~gGT~---lee~~~A~nA~atl--~LQ~y~l~kT~eYie~~W~~et  316 (526)
T TIGR01286       273 ----RMY---------------------------DGGTK---LEELKDALNAEATL--VLQEYTLRKTKEYIEKKWKQET  316 (526)
T ss_pred             ----CCC---------------------------CCCCC---HHHHHCCCCHHHEE--ECCCCCCHHHHHHHCCCCCCEE
T ss_conf             ----226---------------------------77886---57642360101122--2124342356886527775124


Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCH
Q ss_conf             96178866225777888888777536973067525788888899720366889988641499279999999853023314
Q gi|254780834|r  319 LCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTP  398 (648)
Q Consensus       319 l~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~~~l~~~~dl~sp  398 (648)
                      ..|. =.=|.++|.--+ |.++.           +-+..=|.++-.+.|.  +-+.+.++..+     =+-.+-.--.+|
T Consensus       317 ~~l~-~PlGv~~TDeFL-m~vs~-----------isg~eiP~~l~~eRGR--lVDamtDs~aw-----lHGKr~Ai~GDP  376 (526)
T TIGR01286       317 VKLE-IPLGVKGTDEFL-MKVSE-----------ISGQEIPAELTIERGR--LVDAMTDSQAW-----LHGKRVAIYGDP  376 (526)
T ss_pred             EEEC-CCCCCCHHHHHH-HHHHH-----------HCCCCCHHHHHHHCCC--HHHHHHHHHHH-----HHHCCEEEECCC
T ss_conf             4524-788740778999-99998-----------5078762788851033--02555543343-----400304540581


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             5799999999988
Q gi|254780834|r  399 DERAELEIHLKNC  411 (648)
Q Consensus       399 e~ka~~~~~l~~~  411 (648)
                      +=-..+.++++++
T Consensus       377 DlV~al~~F~LEl  389 (526)
T TIGR01286       377 DLVMALVRFVLEL  389 (526)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             5899999999981


No 95 
>pfam03428 RP-C Replication protein C N-terminal domain. Replication protein C is involved in the early stages of viral DNA replication.
Probab=54.32  E-value=11  Score=16.70  Aligned_cols=33  Identities=33%  Similarity=0.701  Sum_probs=21.1

Q ss_pred             HHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEE-EEE
Q ss_conf             45232012100346541000016716888970778588-850
Q gi|254780834|r  181 EKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVI-AFG  221 (648)
Q Consensus       181 ~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i-~f~  221 (648)
                      ..|+++||+..+|..++  -||      +.+|..|.|+ +||
T Consensus        93 a~LveaGLi~rrDS~Ng--KRy------~rR~~~G~i~~A~G  126 (177)
T pfam03428        93 AALVDAGLIIRRDSPNG--KRY------ARRGGDGEIEEAFG  126 (177)
T ss_pred             HHHHHCCCEEECCCCCC--CCC------CEECCCCCEEEEEC
T ss_conf             99998897452369998--501------62379987763446


No 96 
>PRK12366 replication factor A; Reviewed
Probab=54.08  E-value=14  Score=15.90  Aligned_cols=14  Identities=21%  Similarity=0.332  Sum_probs=6.2

Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             99999998188587
Q gi|254780834|r   88 SVQRLAAIAGVPLP  101 (648)
Q Consensus        88 a~~~la~~~gi~~~  101 (648)
                      |+..+|...|++++
T Consensus        41 AamlVA~elG~~~~   54 (649)
T PRK12366         41 AVMLVAQEIGIEIT   54 (649)
T ss_pred             HHHHHHHHHCCCCC
T ss_conf             99999998544555


No 97 
>pfam04407 DUF531 Protein of unknown function (DUF531). Family of hypothetical archaeal proteins.
Probab=54.02  E-value=14  Score=15.90  Aligned_cols=59  Identities=12%  Similarity=0.128  Sum_probs=42.1

Q ss_pred             EEEECCC---CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHC--------CCHHHHHHHHHHCC
Q ss_conf             9961788---66225777888888777536973067525788888899720--------36688998864149
Q gi|254780834|r  318 VLCFDGD---DPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRC--------YGKTAFEKLIVESL  379 (648)
Q Consensus       318 vl~fDgD---~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~--------~G~eaf~~ll~~A~  379 (648)
                      |=.||++   +|-.+|..||+.+|..+   |+.+-.+-.|-...|.+++..        .|.+.+.+++++.+
T Consensus         7 yNtYd~~k~~e~H~RaIARAapic~Af---~~~LAL~~FP~~~~~~el~~~v~~~TtIG~~G~yl~~L~~~nr   76 (174)
T pfam04407         7 YNTYDKKKVHEAHYRAIARAAPICYAF---GFHLALFGFPFDMTPKELAEYVADKTTIGESGKYLLELAESNK   76 (174)
T ss_pred             EECCCCCCCCCHHHHHHHHHHHHHHHC---CCCEEEECCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHCCC
T ss_conf             844687756608999998460476641---7877987798877879999997642732776799999987496


No 98 
>TIGR02082 metH methionine synthase; InterPro: IPR011822   Vitamin B12 dependent methionine synthase 2.1.1.13 from EC (5-methyltetrahydrofolate--homocysteine S-methyltransferase) catalyses the conversion of 5-methyltetrahydrofolate and L-homocysteine to tetrahydrofolate and L-methionine as the final step in de novo methionine biosynthesis. The enzyme requires methylcobalamin as a cofactor. In humans, defects in this enzyme are the cause of autosomal recessive inherited methylcobalamin deficiency (CBLG), which causes mental retardation, macrocytic anemia and homocystinuria. Mild deficiencies in activity may result in mild hyperhomocysteinemia, and mutations in the enzyme may be involved in tumorigenesis. Vitamin B12 dependent methionine synthase is found in prokaryotes and eukaryotes, but in prokaryotes the cofactor is cobalamin.   This enzyme is a large protein composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and tetrahydrofolate , the third module binds the B12 cofactor , and the C-terminal module (activation domain) binds S-adenosylmethionine. The activation domain is essential for the reductive activation of the enzyme. During the catalytic cycle, the highly reactive cob(I)alamin intermediate can be oxidised to produce an inactive cob(II)alamin enzyme; the enzyme is then reactivated via reductive methylation by the activation domain . The activation domain adopts an unusual alpha/beta fold.Recent studies suggest that this enzyme exists as an ensemble of conformations with equilibria dependent on the oxidation and methylation state of the cobalamin and on the concentrations of substrates or products .; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0050897 cobalt ion binding, 0009086 methionine biosynthetic process.
Probab=53.87  E-value=8.1  Score=17.96  Aligned_cols=262  Identities=18%  Similarity=0.181  Sum_probs=132.7

Q ss_pred             ECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH---CCCCCCCCCC-----HHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             136888878989989885999799999999981---8858776820-----36777889999999999999999973267
Q gi|254780834|r   64 CFSCHVKGDHLSFLSALLGCSFIESVQRLAAIA---GVPLPVVDPK-----IEKKEKIQTDLIRLIEVATDFFHHSLKNA  135 (648)
Q Consensus        64 cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~---gi~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  135 (648)
                      .+-|.-.||-     ++-++|-||+|+..=..|   |=++=+.++.     ...........|+++..+++.=+.+    
T Consensus        33 d~~~~l~GnN-----d~L~~TkPdvi~~iHr~YfEAGADiiETNTF~sT~i~~aDY~~~~~~y~~N~~gA~lAr~v----  103 (1265)
T TIGR02082        33 DHARELKGNN-----DILNLTKPDVIATIHRAYFEAGADIIETNTFNSTTIALADYDLEDLIYDLNFKGAKLARRV----  103 (1265)
T ss_pred             CCCCCCCCCC-----HHHHCCCHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH----
T ss_conf             8887766760-----0320684379999988773318867873577765032532127999999879999999999----


Q ss_pred             CCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHH-------CCCCCHHHHHHH------CCCEECCCC-------
Q ss_conf             775789999850688535101244225677410345542-------059973452320------121003465-------
Q gi|254780834|r  136 RDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLR-------QKGFSEEKIIEA------GLLIDGDNS-------  195 (648)
Q Consensus       136 ~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~-------~~~~~~~~~~~~------gl~~~~~~~-------  195 (648)
                           -+|+..|  +++ .+||=.|--=+++..  --|.       =++++.+.|.+|      ||+   |.|       
T Consensus       104 -----A~E~~~~--~p~-kpRfVAGs~GPtnkt--~tlsPdVe~P~FRnvtyD~L~~AY~e~~~gL~---dGGvDllLiE  170 (1265)
T TIGR02082       104 -----ADEFTAL--TPE-KPRFVAGSLGPTNKT--ATLSPDVERPEFRNVTYDELVDAYKEQIKGLL---DGGVDLLLIE  170 (1265)
T ss_pred             -----HHHHHHC--CCC-CCEEEEECCCCCCCC--CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH---HCCCHHHHHH
T ss_conf             -----8776410--889-865887315775557--74588888778875787989999999999877---3260354774


Q ss_pred             ------------CCCCCCCC-CEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHH------HH
Q ss_conf             ------------41000016-716888970778588850100146553001038767653521011081788------88
Q gi|254780834|r  196 ------------ATSYDRFR-NRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGA------LN  256 (648)
Q Consensus       196 ------------~~~~d~Fr-~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a------~~  256 (648)
                                  ...-+-|. --.-.||. .+|=++-=+||+|-..+..=.++|    +=+-+=...|||.|      ++
T Consensus       171 T~fDtLnaKAAlfA~~~~F~~~g~~lPi~-iSGti~d~sGr~LsGqt~~Af~~s----l~~~~~~~iGLNCAlGpdel~~  245 (1265)
T TIGR02082       171 TVFDTLNAKAALFAAETVFEEKGRELPIM-ISGTIVDTSGRTLSGQTLEAFLAS----LEHAEILIIGLNCALGPDELRP  245 (1265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCEE-EEEEEECCCCCCCCCCCHHHHHHH----HCCCCCCEECCCCCCCHHHHHH
T ss_conf             79999999999999999999728978768-860262276872026208999998----5468730241231147778999


Q ss_pred             HHHHHHCCCCCCCCCCEEEEE---------CC---H---------HHHHHHHHCCCCCCH-HHHHCCCCHHHHHHHHHCC
Q ss_conf             643310000235678708997---------14---3---------889998743554211-3432136626789885126
Q gi|254780834|r  257 YLQKSIRKDVRRNSSSFIILV---------EG---Y---------MDVLSLCQAGVQNVV-SSLGTALTEYQLRLLWKLS  314 (648)
Q Consensus       257 ~~~~~~~~~~~~~~~~~~i~v---------EG---y---------~Dvi~l~~~G~~n~v-a~~Gtalt~~~~~~l~r~~  314 (648)
                      .++...+..      ...|.|         =|   .         +-+--+.+.|.-|+| ..|||  |++||+-|.+-+
T Consensus       246 h~~~Ls~~~------~~~Vs~~PNAGLPn~~G~~AeY~l~P~~~A~~l~~fa~eg~lniVGGCCGT--TP~HIraiA~aV  317 (1265)
T TIGR02082       246 HVKELSEHA------EAYVSVHPNAGLPNAFGKQAEYDLTPDELAKALKDFAEEGGLNIVGGCCGT--TPDHIRAIAEAV  317 (1265)
T ss_pred             HHHHHHHHC------CEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEECCCCC--CHHHHHHHHHHH
T ss_conf             999987008------813888337888100477768755578999999999986390377426899--678999999998


Q ss_pred             CE----EEEE--ECCCCCCHHHHHHHHHHHHHHHHC---CCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHC
Q ss_conf             81----8996--178866225777888888777536---9730675257888888997203668899886414
Q gi|254780834|r  315 PR----IVLC--FDGDDPGLRAAYKAIDLVLCHLIP---GNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVES  378 (648)
Q Consensus       315 ~~----vvl~--fDgD~AG~kAa~Ra~e~~l~~l~~---g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A  378 (648)
                      ++    ..--  +-.-            +.++.+++   +.+-.||.+-      |=.+-.|...|+++|..-
T Consensus       318 k~i~Pr~~~~ta~~~~------------~~~Sgle~~~~~~~~~FvniG------ERtNv~GS~KF~~li~ae  372 (1265)
T TIGR02082       318 KDIKPRKRPETALYEP------------SRLSGLEAITIAQESNFVNIG------ERTNVAGSKKFRKLIIAE  372 (1265)
T ss_pred             HCCCCCCCCCCCCCHH------------HHHHCCCCCCCCCCCCEEEEE------EEECCCCCHHHHHHHHCC
T ss_conf             1687688876556324------------676303134636635668874------300787686799985123


No 99 
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=53.45  E-value=14  Score=15.82  Aligned_cols=27  Identities=11%  Similarity=0.073  Sum_probs=21.8

Q ss_pred             CCCCCHHHHHHCCCHHHHHHHHHHCCC
Q ss_conf             788888899720366889988641499
Q gi|254780834|r  354 SRGEDPDSFIRCYGKTAFEKLIVESLP  380 (648)
Q Consensus       354 P~G~DPDe~ir~~G~eaf~~ll~~A~~  380 (648)
                      -...||++++.++|.|+++-++-...|
T Consensus       340 Gnvi~p~~~i~~yg~D~lRy~L~~~~~  366 (558)
T PRK12268        340 GWGIWVDDALERLPPDYLRYYLAANAP  366 (558)
T ss_pred             CCCCCHHHHHHHCCCHHHHHHHHHCCC
T ss_conf             887798999987490777899885488


No 100
>PHA02130 hypothetical protein
Probab=53.40  E-value=4  Score=20.73  Aligned_cols=11  Identities=36%  Similarity=1.340  Sum_probs=7.4

Q ss_pred             CEEEECCCCCC
Q ss_conf             55753458888
Q gi|254780834|r   38 DYWACCPFHDE   48 (648)
Q Consensus        38 ~~~~~cPfh~e   48 (648)
                      -|||||||.++
T Consensus        43 v~w~lcp~~qd   53 (81)
T PHA02130         43 VYWDLCPYAQD   53 (81)
T ss_pred             EEECCCCCHHH
T ss_conf             54135732465


No 101
>KOG2767 consensus
Probab=53.21  E-value=5.9  Score=19.20  Aligned_cols=39  Identities=13%  Similarity=0.146  Sum_probs=20.3

Q ss_pred             HHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCH
Q ss_conf             643310000235678708997143889998743554211
Q gi|254780834|r  257 YLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVV  295 (648)
Q Consensus       257 ~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~v  295 (648)
                      .|+|..-+-.+.++...++|.--.|=...+-.+|+...+
T Consensus        92 FIkKFVlC~~C~NPETel~itk~q~i~~~CkACG~r~~~  130 (400)
T KOG2767          92 FIKKFVLCPSCENPETELIITKKQTISLKCKACGFRSDM  130 (400)
T ss_pred             HHHHHEECCCCCCCCEEEEECCCCHHHHHHHHCCCCCCC
T ss_conf             998824676889975047753662265678872885543


No 102
>pfam08209 Sgf11 Sgf11 (transcriptional regulation protein). The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae. The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation.
Probab=53.17  E-value=4.8  Score=20.06  Aligned_cols=72  Identities=15%  Similarity=0.282  Sum_probs=43.2

Q ss_pred             HHHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECC------CCEEEECCCCCCCCHHHHHH
Q ss_conf             889999987488888754122210158877777557534588885878798178------97467136888878989989
Q gi|254780834|r    5 RDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDS------KGFYYCFSCHVKGDHLSFLS   78 (648)
Q Consensus         5 ~~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~------~~~~~cf~c~~~gd~~~f~~   78 (648)
                      +++.+.|... =|-|+|++++...+-    ...+|=++=|+|-+..|+..|+-.      -+.|+|--||..=-+=.|-.
T Consensus        13 ~sIy~NLL~~-~i~divsr~~~~~s~----~~~~~p~~k~y~~d~~~~lDi~g~~~~~~~s~yf~C~nC~R~v~~~rfa~   87 (99)
T pfam08209        13 DSIYNNLLTS-MIQDIVSRETSRQKL----LKSRYPDLKSYHIDPNGSLDIYGNPKQQESSQYFHCENCGRDVSGNRFAA   87 (99)
T ss_pred             HHHHHHHHHH-HHHHHHHHHHHHHHH----HHCCCCCCCCEEECCCCCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHHH
T ss_conf             9999999999-999999999888888----86149987666766898736679956776253667777675445552399


Q ss_pred             HHC
Q ss_conf             885
Q gi|254780834|r   79 ALL   81 (648)
Q Consensus        79 ~~~   81 (648)
                      ++|
T Consensus        88 Hl~   90 (99)
T pfam08209        88 HLQ   90 (99)
T ss_pred             HHH
T ss_conf             999


No 103
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057   Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within the helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module..
Probab=52.86  E-value=14  Score=15.75  Aligned_cols=52  Identities=19%  Similarity=0.259  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHCCC--CC---HHHHHHH-HHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCC
Q ss_conf             99999999973267--77---5789999-85068853510124422567741034554205997
Q gi|254780834|r  122 EVATDFFHHSLKNA--RD---KRLHYYL-DERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFS  179 (648)
Q Consensus       122 ~~~~~~~~~~l~~~--~~---~~a~~yl-~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~  179 (648)
                      +..+.|-.++|-+.  ..   ..|+-|+ +.||+| ++.++=|||     +.+||+.|..+|=+
T Consensus        15 E~~a~YL~~a~e~gGdDp~~~~~ALG~iArArGMt-qlA~~tGls-----REsLYkALs~~GnP   72 (91)
T TIGR02684        15 EEVAEYLAQALEDGGDDPALIAAALGVIARARGMT-QLAKKTGLS-----RESLYKALSGGGNP   72 (91)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHH-HHHHHHCCC-----HHHHHHHHCCCCCC
T ss_conf             89999999997436999889999988998651657-899982876-----78878873568895


No 104
>PRK12300 leuS leucyl-tRNA synthetase; Reviewed
Probab=52.77  E-value=14  Score=15.74  Aligned_cols=33  Identities=12%  Similarity=0.045  Sum_probs=25.0

Q ss_pred             CCCCHHHHHHCCCHHHHHHHHH-HCCCHHHHHHH
Q ss_conf             8888889972036688998864-14992799999
Q gi|254780834|r  355 RGEDPDSFIRCYGKTAFEKLIV-ESLPLVDMLWK  387 (648)
Q Consensus       355 ~G~DPDe~ir~~G~eaf~~ll~-~A~~l~dFl~~  387 (648)
                      +..||++.+.++|+|+++-++- .|.+.-|.-|.
T Consensus       578 NvV~P~eiI~~YGADalRl~l~~~a~~~~d~~~~  611 (888)
T PRK12300        578 NVLPLREAIEEYGADVVRLYLASTAELSQDADFR  611 (888)
T ss_pred             CCCCHHHHHHHCCCCHHHHHHHHCCCCCCCCCCC
T ss_conf             9899899997619629999999718855686457


No 105
>COG0289 DapB Dihydrodipicolinate reductase [Amino acid transport and metabolism]
Probab=52.44  E-value=14  Score=15.70  Aligned_cols=38  Identities=26%  Similarity=0.354  Sum_probs=25.2

Q ss_pred             CCHHHHHH-HHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEE
Q ss_conf             14388999-87435542113432136626789885126818
Q gi|254780834|r  278 EGYMDVLS-LCQAGVQNVVSSLGTALTEYQLRLLWKLSPRI  317 (648)
Q Consensus       278 EGy~Dvi~-l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~v  317 (648)
                      |+-+..+. +.++|+.-||.|  |-||++|+..|..++.++
T Consensus        80 ~~~~~~l~~~~~~~~~lVIGT--TGf~~e~~~~l~~~a~~v  118 (266)
T COG0289          80 EATLENLEFALEHGKPLVIGT--TGFTEEQLEKLREAAEKV  118 (266)
T ss_pred             HHHHHHHHHHHHCCCCEEEEC--CCCCHHHHHHHHHHHHHC
T ss_conf             546999999997699869979--999989999999998538


No 106
>pfam01780 Ribosomal_L37ae Ribosomal L37ae protein family. This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc.
Probab=52.28  E-value=8.2  Score=17.89  Aligned_cols=26  Identities=23%  Similarity=0.594  Sum_probs=18.8

Q ss_pred             EECCCCCCCCCCEEEECCCCEEEECCCCC
Q ss_conf             53458888587879817897467136888
Q gi|254780834|r   41 ACCPFHDEKTPSFHCNDSKGFYYCFSCHV   69 (648)
Q Consensus        41 ~~cPfh~ektpsf~v~~~~~~~~cf~c~~   69 (648)
                      -.|||.+-..   .--..-|+|+|=.||.
T Consensus        36 y~Cp~Cgk~~---vkR~a~GIW~C~~C~~   61 (90)
T pfam01780        36 YTCPFCGKDA---VKRKAVGIWKCRKCGK   61 (90)
T ss_pred             CCCCCCCCCE---EEEEEEEEEECCCCCC
T ss_conf             3089999887---7888888887279899


No 107
>PRK13824 replication initiation protein RepC; Provisional
Probab=52.23  E-value=12  Score=16.42  Aligned_cols=33  Identities=33%  Similarity=0.648  Sum_probs=24.1

Q ss_pred             HHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEE-EEE
Q ss_conf             45232012100346541000016716888970778588-850
Q gi|254780834|r  181 EKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVI-AFG  221 (648)
Q Consensus       181 ~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i-~f~  221 (648)
                      ..|+++||+..+|..+  +-||      ..+|..|+|+ |||
T Consensus       105 a~LveaGLI~rrDSpN--GKRY------arR~~~G~I~~AyG  138 (404)
T PRK13824        105 AALVEAGLIIRRDSPN--GKRY------ARKGRGGEIEEAFG  138 (404)
T ss_pred             HHHHHCCCEEECCCCC--CCCC------CEECCCCCEEEEEC
T ss_conf             9999769556123889--8871------13479997875646


No 108
>pfam11672 DUF3268 Protein of unknown function (DUF3268). This family of proteins has no known function.
Probab=52.02  E-value=14  Score=15.65  Aligned_cols=28  Identities=25%  Similarity=0.577  Sum_probs=15.9

Q ss_pred             CCCCCCCC---CCEEEEC-----CCCEEEECCCCCC
Q ss_conf             45888858---7879817-----8974671368888
Q gi|254780834|r   43 CPFHDEKT---PSFHCND-----SKGFYYCFSCHVK   70 (648)
Q Consensus        43 cPfh~ekt---psf~v~~-----~~~~~~cf~c~~~   70 (648)
                      ||+...++   ++=.|++     .+-+|.|=+|++-
T Consensus         5 CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~Ay   40 (102)
T pfam11672         5 CPYCGGKVELRPAEVVYGRGYGDWPYLYLCTGCDAY   40 (102)
T ss_pred             CCCCCCEEEEEECCEECCCCCCCCCEEEECCCCCCE
T ss_conf             799999558821664057667888347888999854


No 109
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=50.82  E-value=15  Score=15.50  Aligned_cols=64  Identities=19%  Similarity=0.148  Sum_probs=32.9

Q ss_pred             HHHHCCCCHHHHHHHHHCCC----EEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHH
Q ss_conf             34321366267898851268----1899617886622577788888877753697306752578888889
Q gi|254780834|r  296 SSLGTALTEYQLRLLWKLSP----RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDS  361 (648)
Q Consensus       296 a~~Gtalt~~~~~~l~r~~~----~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe  361 (648)
                      +..||.+...++..|...+.    .+|+|++=|.=|++...= +. .+..+.+...|+|+.+-++.|..+
T Consensus        46 g~SG~~~~Rp~~~~ml~~~~~g~~d~vlv~~ldRl~R~~~~~-~~-~~~~l~~~~gv~~is~~e~iDt~~  113 (140)
T cd03770          46 GFSGTTFDRPGFNRMIEDIEAGKIDIVIVKDMSRLGRNYLKV-GL-YMEILFPKKGVRFIAINDGVDSAD  113 (140)
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCCCCEEEEEECCHHCCCHHHH-HH-HHHHHHHHCCCEEEEECCCCCCCC
T ss_conf             867763358889999999986997589998583433677999-99-999998767938999357877998


No 110
>TIGR01215 minE cell division topological specificity factor MinE; InterPro: IPR005527    Cytokinesis needs to be regulated spatially in order to ensure that it occurs between the daughter genomes. In prokaryotes such as Escherichia coli, cytokinesis is initiated by FtsZ, a tubulin-like protein that assembles into a ring structure at the cell centre called the Z ring. A fundamental problem in prokaryotic cell biology is to understand how the midcell division site is identified. Two major negative regulatory systems are known to be involved in preventing Z-ring assembly at all sites except the midcell. One of these systems, called nucleoid occlusion, blocks Z-ring assembly in the area occupied by an unsegregated nucleoid until a critical stage in chromosome replication or segregation is reached. The other system consists of three proteins, MinC, MinD and MinE, which prevent assembly of Z rings in regions of the cell not covered by the nucleoid, such as the cell poles. MinC is an inhibitor of FtsZ polymerization, resulting in the inhibition of Z ring assembly in the cell; MinD greatly enhances the inhibitory effects of MinC in vivo; and MinE antagonizes the effects of MinC and MinD .     MinE is a small bifunctional protein. The amino terminus of MinE is required to interact with MinD, while the carboxyl terminus is required for 'topological specificity' - that is, the ability of MinE to antagonize MinCD inhibition of Z rings at the midcell position but not at the poles..
Probab=50.60  E-value=8.7  Score=17.69  Aligned_cols=20  Identities=30%  Similarity=0.571  Sum_probs=7.7

Q ss_pred             HHHHHHHHHHCCHHHHHHHHCC
Q ss_conf             8899999874888887541222
Q gi|254780834|r    5 RDFIKDLLIHIPISNLIGQYVD   26 (648)
Q Consensus         5 ~~~i~~i~~~~~i~~vv~~~v~   26 (648)
                      |+.++++|.  ||++||..||+
T Consensus        38 P~yle~lR~--dileVi~KYv~   57 (89)
T TIGR01215        38 PDYLEELRK--DILEVIQKYVP   57 (89)
T ss_pred             CHHHHHHHH--HHHHHHHHHCC
T ss_conf             712388899--99988773113


No 111
>TIGR00464 gltX_bact glutamyl-tRNA synthetase; InterPro: IPR004527   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=50.48  E-value=13  Score=16.02  Aligned_cols=33  Identities=15%  Similarity=0.157  Sum_probs=21.4

Q ss_pred             CCCHHHHHHHHHCCCE-------EEEEECCCCCCHHHHHHHH
Q ss_conf             3662678988512681-------8996178866225777888
Q gi|254780834|r  301 ALTEYQLRLLWKLSPR-------IVLCFDGDDPGLRAAYKAI  335 (648)
Q Consensus       301 alt~~~~~~l~r~~~~-------vvl~fDgD~AG~kAa~Ra~  335 (648)
                      +=|+-||.+.+-+.-.       +-|..  |+-|+|=+.|=.
T Consensus       232 sNTPkQI~iy~Alg~~~iP~f~H~p~I~--~~~gKKLSKRdg  271 (513)
T TIGR00464       232 SNTPKQILIYKALGWKRIPTFAHLPLIL--NEDGKKLSKRDG  271 (513)
T ss_pred             CCCHHHHHHHHHCCCCCCCCEEEEEEEE--CCCCCEEECCCC
T ss_conf             6718999999970889888155353585--698840012064


No 112
>pfam03776 MinE Septum formation topological specificity factor MinE. The E. coli minicell locus was shown to code for three gene products (MinC, MinD, and MinE) whose coordinate action is required for proper placement of the division septum. The minE gene codes for a topological specificity factor that, in wild-type cells, prevents the division inhibitor from acting at internal division sites while permitting it to block septation at polar sites.
Probab=50.38  E-value=11  Score=16.73  Aligned_cols=23  Identities=30%  Similarity=0.573  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHCCHHHHHHHHCCCEE
Q ss_conf             8899999874888887541222101
Q gi|254780834|r    5 RDFIKDLLIHIPISNLIGQYVDWDR   29 (648)
Q Consensus         5 ~~~i~~i~~~~~i~~vv~~~v~l~~   29 (648)
                      +++++.++.  ||.+||+.||....
T Consensus        23 ~d~l~~lk~--dil~VI~KYv~id~   45 (69)
T pfam03776        23 QDYLPQLKE--EILEVISKYVEIDP   45 (69)
T ss_pred             HHHHHHHHH--HHHHHHHHHEECCH
T ss_conf             999999999--99999998763063


No 113
>pfam01641 SelR SelR domain. Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfo
Probab=50.37  E-value=8.3  Score=17.86  Aligned_cols=34  Identities=21%  Similarity=0.377  Sum_probs=19.9

Q ss_pred             HCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCC
Q ss_conf             22210158877777557534588885878798178974671368888
Q gi|254780834|r   24 YVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVK   70 (648)
Q Consensus        24 ~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~   70 (648)
                      |--|+..|.-     --...|+.+++        ++|+|+|-+||.-
T Consensus        13 y~Vlr~~gTE-----~pfsg~y~~~~--------~~G~Y~C~~C~~~   46 (124)
T pfam01641        13 YRVLRNKGTE-----KPFTGEYDDHF--------EEGIYVCIGCGEP   46 (124)
T ss_pred             HHHHHHCCCC-----CCCCCCCCCCC--------CCEEEEECCCCCC
T ss_conf             9999856888-----99877776888--------9889981689983


No 114
>TIGR03297 Ppyr-DeCO2ase phosphonopyruvate decarboxylase. This family consists of examples of phosphonopyruvate an decarboxylase enzyme that produces phosphonoacetaldehyde (Pald), the second step in the biosynthesis phosphonate-containing compounds. Since the preceding enzymate step, PEP phosphomutase (AepX, TIGR02320) favors the substrate PEP energetically, the decarboxylase is required to drive the reaction in the direction of phosphonate production. Pald is a precursor of natural products including antibiotics like bialaphos and phosphonothricin in Streptomyces species, phosphonate-modified molecules such as the polysaccharide B of Bacteroides fragilis, the phosphonolipids of Tetrahymena pyroformis, the glycosylinositolphospholipids of Trypanosoma cruzi. This gene generally occurs in prokaryotic organisms adjacent to the gene for AepX. Most often an aminotansferase (aepZ) is also present which leads to the production of the most common phosphonate compound, 2-aminoethylphosphonate (A
Probab=50.25  E-value=8.1  Score=17.97  Aligned_cols=40  Identities=25%  Similarity=0.353  Sum_probs=22.0

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             6818996178866225777888888777536973067525788
Q gi|254780834|r  314 SPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRG  356 (648)
Q Consensus       314 ~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G  356 (648)
                      .++-|+|+|||.|=.-   .-..++.--.....++..+.|.+|
T Consensus       238 ~~~~Vi~lDGDGs~LM---h~Gslati~~~~~~Nl~hivlnN~  277 (361)
T TIGR03297       238 PDQRVVCLDGDGAALM---HMGGLATIGTQGPANLIHVLFNNG  277 (361)
T ss_pred             CCCEEEEEECCHHHHH---CCCHHHHHHHCCCCCEEEEEEECC
T ss_conf             8970899908689985---440687887438874799998288


No 115
>pfam06793 UPF0262 Uncharacterized protein family (UPF0262).
Probab=50.24  E-value=11  Score=16.77  Aligned_cols=50  Identities=20%  Similarity=0.439  Sum_probs=26.6

Q ss_pred             CEEEEECCHHHHHHHHHCCCCCCHHHHH-CCCCHHHHHHHH-HCCCEEEEEEC
Q ss_conf             7089971438899987435542113432-136626789885-12681899617
Q gi|254780834|r  272 SFIILVEGYMDVLSLCQAGVQNVVSSLG-TALTEYQLRLLW-KLSPRIVLCFD  322 (648)
Q Consensus       272 ~~~i~vEGy~Dvi~l~~~G~~n~va~~G-talt~~~~~~l~-r~~~~vvl~fD  322 (648)
                      ++..+||.|+|+|.-...+-=.+| -|| -++-.+-..+|. |+..+|.+=+|
T Consensus        92 DYf~iCeSYy~AIk~~~p~qIEaI-DMgRRglHNEGa~lL~eRL~gki~~D~d  143 (159)
T pfam06793        92 DYFMICESYYEAIRTATPSQIEAI-DMGRRGLHNEGSELLRERLEGKIEVDFD  143 (159)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHH-HHHHHCCCHHHHHHHHHHHHCCEEECCH
T ss_conf             999999999999960999887787-7642032248899999998397341230


No 116
>pfam01194 RNA_pol_N RNA polymerases N / 8 kDa subunit.
Probab=50.08  E-value=13  Score=16.15  Aligned_cols=16  Identities=31%  Similarity=0.623  Sum_probs=9.4

Q ss_pred             EECCCCC-CCCHHHHHH
Q ss_conf             7136888-878989989
Q gi|254780834|r   63 YCFSCHV-KGDHLSFLS   78 (648)
Q Consensus        63 ~cf~c~~-~gd~~~f~~   78 (648)
                      .||+||+ =||.+..+.
T Consensus         6 RCftCGkvi~~k~~~y~   22 (60)
T pfam01194         6 RCFTCGKVIGDKWEEYL   22 (60)
T ss_pred             CCCCCCCCHHHHHHHHH
T ss_conf             65789888699899999


No 117
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=50.03  E-value=12  Score=16.31  Aligned_cols=109  Identities=10%  Similarity=0.099  Sum_probs=55.9

Q ss_pred             CCHHHHHHHHHHHHCCCCCCCCCCEEEEECCH-HHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHC--CCEEEEEECCCC
Q ss_conf             08178888643310000235678708997143-889998743554211343213662678988512--681899617886
Q gi|254780834|r  249 YNFFGALNYLQKSIRKDVRRNSSSFIILVEGY-MDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKL--SPRIVLCFDGDD  325 (648)
Q Consensus       249 y~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy-~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~--~~~vvl~fDgD~  325 (648)
                      .+.|...++..-..++....+-.+.+-+++|- |+.+.-  .-+.-.|+.= -=+....+..|..-  .-++-+++||.+
T Consensus       163 ~avDIS~~AL~vAk~Na~~~~v~~ri~fi~sdwfe~l~~--~kFDlIVSNP-PYI~~~e~~~L~~eV~~yEP~lAL~gge  239 (503)
T PRK01544        163 IATDISLDAIEVAKSNAIKYEVTDRIQIIHSNWFENIGK--QKFDFIVSNP-PYISHSEKSEMAIETINYEPSIALFAEE  239 (503)
T ss_pred             EEEECCHHHHHHHHHHHHHCCCCCCEEEEECCCHHCCCC--CCCCEEEECC-CCCCHHHHHHCCHHHHCCCCHHHHCCCC
T ss_conf             999898999999999999808820179996553101588--8724798389-9887566665276653169378864887


Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHH
Q ss_conf             62257778888887775369730675257888888997
Q gi|254780834|r  326 PGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFI  363 (648)
Q Consensus       326 AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~i  363 (648)
                      -|..+-.+.++.+..+|+++=   .+.+--|.|=.+-|
T Consensus       240 DGL~~Yr~Ia~~a~~~Lkp~G---~l~lEIGy~Q~e~V  274 (503)
T PRK01544        240 DGLQAYFIIAENAKQFLKPNG---KIILEIGFKQAEAV  274 (503)
T ss_pred             CCHHHHHHHHHHHHHHCCCCC---EEEEEECCCHHHHH
T ss_conf             628999999998898528898---89999787868999


No 118
>pfam02631 RecX RecX family. RecX is a putative bacterial regulatory protein. The gene encoding RecX is found downstream of recA, and is thought to interact with the RecA protein.
Probab=49.68  E-value=16  Score=15.36  Aligned_cols=50  Identities=18%  Similarity=0.325  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             8899998443002379988999999999997538899989999885111289
Q gi|254780834|r  496 AILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFG  547 (648)
Q Consensus       496 ~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~~l~~~L~~~~l~  547 (648)
                      +.+..+++.+....+.+..  ......+..........+..+...|...++.
T Consensus         9 ~~I~~vi~~L~~~gyldD~--rya~~~i~~~~~~~~~G~~~I~~~L~~kGI~   58 (121)
T pfam02631         9 EVIEAVLERLKELGYLDDE--RFAESFVRSRLRTKGKGPRRIRQELRQKGVD   58 (121)
T ss_pred             HHHHHHHHHHHHCCCCCHH--HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCC
T ss_conf             9999999999996997999--9999999999882681199999999995999


No 119
>KOG0183 consensus
Probab=49.68  E-value=15  Score=15.51  Aligned_cols=69  Identities=26%  Similarity=0.357  Sum_probs=32.3

Q ss_pred             CHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCC-CHHHHHCCCCHHHHHHHHHCCCEEEEEECC
Q ss_conf             1011081788886433100002356787089971438899987435542-113432136626789885126818996178
Q gi|254780834|r  245 GKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQN-VVSSLGTALTEYQLRLLWKLSPRIVLCFDG  323 (648)
Q Consensus       245 ~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n-~va~~Gtalt~~~~~~l~r~~~~vvl~fDg  323 (648)
                      --+|+..-.|..+.+|.          ..++-|-|- |+|.   .|++- .|+-|-   -+.-++.|.-+-++|++.|  
T Consensus        14 DGhL~QVEYAqEAvrkG----------staVgvrg~-~~vv---lgvEkkSv~~Lq---~~r~~rkI~~ld~hV~maf--   74 (249)
T KOG0183          14 DGHLFQVEYAQEAVRKG----------STAVGVRGN-NCVV---LGVEKKSVPKLQ---DERTVRKISMLDDHVVMAF--   74 (249)
T ss_pred             CCCEEEEHHHHHHHHCC----------CEEEEECCC-CEEE---EEEEECCHHHHH---HHHHHHHHEEECCEEEEEE--
T ss_conf             98777327589998627----------637986068-5599---998405526652---1110322101045146773--


Q ss_pred             CCCCHHHHHHH
Q ss_conf             86622577788
Q gi|254780834|r  324 DDPGLRAAYKA  334 (648)
Q Consensus       324 D~AG~kAa~Ra  334 (648)
                        ||.+|-.|.
T Consensus        75 --aGl~aDAri   83 (249)
T KOG0183          75 --AGLTADARI   83 (249)
T ss_pred             --CCCCCCCEE
T ss_conf             --378864001


No 120
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=49.36  E-value=14  Score=15.66  Aligned_cols=30  Identities=27%  Similarity=0.309  Sum_probs=14.5

Q ss_pred             EECCCCC-CCCHHHHHHHH--CCCCHHHHHHHH
Q ss_conf             7136888-87898998988--599979999999
Q gi|254780834|r   63 YCFSCHV-KGDHLSFLSAL--LGCSFIESVQRL   92 (648)
Q Consensus        63 ~cf~c~~-~gd~~~f~~~~--~~~~f~ea~~~l   92 (648)
                      .||+||+ =|+.+.=+.+.  ++-+-.+|+-.|
T Consensus         6 RCFsCGkvi~~~w~~y~~rv~~ge~p~~vLDdL   38 (63)
T COG1644           6 RCFSCGKVIGHKWEEYKRRVEEGEDPGEVLDDL   38 (63)
T ss_pred             EEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             752388787888999999998489888888870


No 121
>pfam07057 TraI DNA helicase TraI. This family represents a conserved region approximately 130 residues long within the bacterial DNA helicase TraI (EC:3.6.1.-). TraI is a bifunctional protein that catalyses the unwinding of duplex DNA as well as acts as a sequence-specific DNA trans-esterase, providing the site- and strand-specific nick required to initiate DNA transfer.
Probab=49.08  E-value=14  Score=15.76  Aligned_cols=22  Identities=14%  Similarity=0.190  Sum_probs=16.9

Q ss_pred             EEEEEEEECCCCEEEEECCCCC
Q ss_conf             1688897077858885010014
Q gi|254780834|r  205 RLIFPIRSSRGQVIAFGGRTLS  226 (648)
Q Consensus       205 Ri~fPi~~~~g~~i~f~gR~l~  226 (648)
                      .++||++|..|+.-|.-=.-|.
T Consensus        93 ~vAlPv~D~NGK~AG~~L~~l~  114 (126)
T pfam07057        93 HVALPVWDRNGKSAGALLVELT  114 (126)
T ss_pred             CEECEEECCCCCEEEEEEEEEE
T ss_conf             3402105478843005776545


No 122
>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=49.05  E-value=11  Score=16.83  Aligned_cols=30  Identities=23%  Similarity=0.472  Sum_probs=21.3

Q ss_pred             EECCCCC-CCCCCEEEECC--CCEEEECCCCCC
Q ss_conf             5345888-85878798178--974671368888
Q gi|254780834|r   41 ACCPFHD-EKTPSFHCNDS--KGFYYCFSCHVK   70 (648)
Q Consensus        41 ~~cPfh~-ektpsf~v~~~--~~~~~cf~c~~~   70 (648)
                      =-|||.+ |++=+..+.-.  .+.-+|-.||..
T Consensus        18 F~CpfC~h~~sv~vkidk~~~~g~l~C~vCg~~   50 (74)
T pfam05129        18 FDCPFCNHKKSVSVKIDKKTGIAKLHCRVCGLS   50 (74)
T ss_pred             EECCCCCCCCEEEEEEECCCCEEEEEEECCCCE
T ss_conf             747867998759999981479899996217885


No 123
>KOG1422 consensus
Probab=48.64  E-value=6.7  Score=18.73  Aligned_cols=53  Identities=15%  Similarity=0.004  Sum_probs=37.7

Q ss_pred             CCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCC
Q ss_conf             8708997143889998743554211343213662678988512681899617886
Q gi|254780834|r  271 SSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDD  325 (648)
Q Consensus       271 ~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~  325 (648)
                      -|.+..+.-+|  +.|+..|.+.-|-+.-+.-+++-++.+.--+.=+++.||++.
T Consensus        18 ~Gdcpf~qr~~--m~L~~k~~~f~vttVd~~~kp~~f~~~sp~~~~P~l~~d~~~   70 (221)
T KOG1422          18 LGDCPFCQRLF--MTLELKGVPFKVTTVDLSRKPEWFLDISPGGKPPVLKFDEKW   70 (221)
T ss_pred             CCCCHHHHHHH--HHHHHCCCCCEEEEEECCCCCHHHHHHCCCCCCCEEEECCCE
T ss_conf             78974478999--999981887348986168896999952888899869758724


No 124
>TIGR03364 HpnW_proposed FAD dependent oxidoreductase TIGR03364. This clade of FAD dependent oxidoreductases (members of the pfam01266 family) is syntenically associated with a family of proposed phosphonatase-like enzymes (TIGR03351) and is also found (less frequently) in association with phosphonate transporter components. A likely role for this enzyme involves the oxidative deamination of an aminophosphonate differring slightly from 2-aminoethylphosphonate, possibly 1-hydroxy-2-aminoethylphosphonate (see the comments for TIGR03351). Many members of the larger FAD dependent oxidoreductase family act as amino acid oxidative deaminases.
Probab=48.63  E-value=16  Score=15.23  Aligned_cols=14  Identities=43%  Similarity=0.325  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHCCCC
Q ss_conf             99999999818858
Q gi|254780834|r   87 ESVQRLAAIAGVPL  100 (648)
Q Consensus        87 ea~~~la~~~gi~~  100 (648)
                      +..+.|++..|+.+
T Consensus        65 ~~~~~l~~~~~~~~   78 (365)
T TIGR03364        65 EIWLELAAKAGIWV   78 (365)
T ss_pred             HHHHHHHHHCCCCE
T ss_conf             99999887349897


No 125
>KOG0435 consensus
Probab=48.49  E-value=16  Score=15.22  Aligned_cols=107  Identities=16%  Similarity=0.187  Sum_probs=56.5

Q ss_pred             CCHHHHHHH-HHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC---
Q ss_conf             143889998-7435542113432136626789885126818996178866225777888888777536973067525---
Q gi|254780834|r  278 EGYMDVLSL-CQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLL---  353 (648)
Q Consensus       278 EGy~Dvi~l-~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~L---  353 (648)
                      |-+.++|.- .-.|-...++..|-=|.++-+..+.---+.+|+-=|                       .++.++.-   
T Consensus       562 EPF~~Li~QGmV~G~tf~~~~sG~yl~~~ev~~~nd~~~~~vlk~~-----------------------~e~~v~t~eKM  618 (876)
T KOG0435         562 EPFTKLITQGMVRGKTFRTKESGKYLGPEEVQQVNDHQNKFVLKND-----------------------KEVVVVTYEKM  618 (876)
T ss_pred             CCHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHCCCCCEEEECCC-----------------------CCCEEEEHHHH
T ss_conf             7488887510003417862777762787776663477663575379-----------------------95035448873


Q ss_pred             ----CCCCCHHHHHHCCCHHHHHHHHH-HCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             ----78888889972036688998864-14992799999998530233145799999999988541
Q gi|254780834|r  354 ----SRGEDPDSFIRCYGKTAFEKLIV-ESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINH  414 (648)
Q Consensus       354 ----P~G~DPDe~ir~~G~eaf~~ll~-~A~~l~dFl~~~l~~~~dl~spe~ka~~~~~l~~~I~~  414 (648)
                          -+|.||++.+.++|.|..+.++= .|.+--.-.|+       -+...|.-+...++-.++..
T Consensus       619 SKSK~NGVdP~~~v~~yG~D~tRl~ilf~ap~~~~~nW~-------es~i~Gi~rwl~riw~l~~~  677 (876)
T KOG0435         619 SKSKHNGVDPADVVLEYGVDTTRLYILFAAPPRDPINWN-------ESAIPGIKRWLQRIWALVSQ  677 (876)
T ss_pred             HHCCCCCCCHHHHHHHHCCHHHHHHHHHHCCCCCCCCCC-------CCCCHHHHHHHHHHHHHHHH
T ss_conf             202357989899998848317789998617865666666-------33245499999999999887


No 126
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=48.13  E-value=16  Score=15.17  Aligned_cols=32  Identities=6%  Similarity=0.285  Sum_probs=15.6

Q ss_pred             CCCHHHHHHCCCHHHHHHHH-HHCCCHHHHHHH
Q ss_conf             88888997203668899886-414992799999
Q gi|254780834|r  356 GEDPDSFIRCYGKTAFEKLI-VESLPLVDMLWK  387 (648)
Q Consensus       356 G~DPDe~ir~~G~eaf~~ll-~~A~~l~dFl~~  387 (648)
                      |.=|+|+++=.-+|++..++ .+.+|.=.+-|+
T Consensus       293 git~~ewL~~~~PEsl~rfm~~~pkpaK~l~fd  325 (513)
T PRK00750        293 GISIEDWLEYAPPESLARFMYARPKPAKRLYFD  325 (513)
T ss_pred             CCCHHHHHHHCCHHHHHHHHHHCCCCCCCCCHH
T ss_conf             238999997559999999997188988401565


No 127
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=47.49  E-value=17  Score=15.10  Aligned_cols=81  Identities=26%  Similarity=0.267  Sum_probs=53.2

Q ss_pred             CCCEEEEECCHHHHHHHHHCCCCCC--------HHHHHCCCCHHHH--H-HHHHC---CC-EEEEEECCCCCCHHHHHHH
Q ss_conf             7870899714388999874355421--------1343213662678--9-88512---68-1899617886622577788
Q gi|254780834|r  270 SSSFIILVEGYMDVLSLCQAGVQNV--------VSSLGTALTEYQL--R-LLWKL---SP-RIVLCFDGDDPGLRAAYKA  334 (648)
Q Consensus       270 ~~~~~i~vEGy~Dvi~l~~~G~~n~--------va~~Gtalt~~~~--~-~l~r~---~~-~vvl~fDgD~AG~kAa~Ra  334 (648)
                      ....+.|||-.-||+++-+.|.-+.        ++|+ .-..++++  . ++.|.   .. +|||+.+.--.|+.-|.=.
T Consensus        78 d~~~icVVe~p~Dv~a~E~~~~f~G~YhVL~G~lspl-~gigpe~l~i~~L~~Rl~~~~~~EvIlAtnpTvEGeaTA~YI  156 (198)
T COG0353          78 DKSQLCVVEEPKDVLALEKTGEFRGLYHVLGGLLSPL-DGIGPEDLNIDELLQRLAEGSIKEVILATNPTVEGEATALYI  156 (198)
T ss_pred             CCCEEEEECCHHHHHHHHHHCCCCEEEEEECCCCCCC-CCCCCCCCCHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHH
T ss_conf             8866899866499999997452572788845733734-589910126799999984699755999658986436899999


Q ss_pred             HHHHHHHHHCCCCEEEEECCCC
Q ss_conf             8888777536973067525788
Q gi|254780834|r  335 IDLVLCHLIPGNRVNFVLLSRG  356 (648)
Q Consensus       335 ~e~~l~~l~~g~~v~vv~LP~G  356 (648)
                      .+++.     +..++|-.|-.|
T Consensus       157 ~~~l~-----~~~ikvtRlA~G  173 (198)
T COG0353         157 ARLLK-----PLGLKVTRLAQG  173 (198)
T ss_pred             HHHHH-----HCCCEEEEEEEC
T ss_conf             99975-----359717877605


No 128
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=47.05  E-value=11  Score=16.67  Aligned_cols=22  Identities=23%  Similarity=0.378  Sum_probs=13.7

Q ss_pred             CCCCEEEECCCCCCCCHHHHHHHH
Q ss_conf             789746713688887898998988
Q gi|254780834|r   57 DSKGFYYCFSCHVKGDHLSFLSAL   80 (648)
Q Consensus        57 ~~~~~~~cf~c~~~gd~~~f~~~~   80 (648)
                      .+.|+|+|-+||.-  .|+--.++
T Consensus        29 ~~~G~Y~C~~C~~~--LF~S~~Kf   50 (119)
T PRK05508         29 YEKGTYICRQCGAP--LYKSEDKF   50 (119)
T ss_pred             CCCEEEEECCCCCC--CCCCCCCC
T ss_conf             88859993799960--02743223


No 129
>PRK12446 N-acetylglucosaminyl transferase; Reviewed
Probab=46.90  E-value=17  Score=15.02  Aligned_cols=66  Identities=15%  Similarity=0.235  Sum_probs=50.7

Q ss_pred             HHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHH---HHHHHCCCCCCH----HHHHCCCCHHHHHHHHHCCCEEE
Q ss_conf             01108178888643310000235678708997143889---998743554211----34321366267898851268189
Q gi|254780834|r  246 KNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDV---LSLCQAGVQNVV----SSLGTALTEYQLRLLWKLSPRIV  318 (648)
Q Consensus       246 ~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dv---i~l~~~G~~n~v----a~~Gtalt~~~~~~l~r~~~~vv  318 (648)
                      ++++++.++...+++.++        +-||-+=||.-+   ++.+-.+++-++    |..|.|     -+++.++++.|.
T Consensus        75 ~l~~~~~~s~~il~~~kP--------d~Vig~GGY~S~P~~lAA~ll~iP~~ihEqNav~G~a-----Nr~l~~~a~~i~  141 (352)
T PRK12446         75 LVMKGVMDAYVRIRKLKP--------DVIFSKGGFVSVPVVIGGWLNRVPVLLHESDMTPGLA-----NKIALRFASKIF  141 (352)
T ss_pred             HHHHHHHHHHHHHHHCCC--------CEEEECCCHHHHHHHHHHHHCCCCEEEECCCHHHHHH-----HHHHHHHHCCEE
T ss_conf             999999999999996399--------9999749877799999999859996998874677789-----999998707128


Q ss_pred             EEECCC
Q ss_conf             961788
Q gi|254780834|r  319 LCFDGD  324 (648)
Q Consensus       319 l~fDgD  324 (648)
                      ++|+..
T Consensus       142 ~~f~~~  147 (352)
T PRK12446        142 VTFEEA  147 (352)
T ss_pred             ECCHHH
T ss_conf             996245


No 130
>KOG0856 consensus
Probab=46.82  E-value=12  Score=16.46  Aligned_cols=11  Identities=36%  Similarity=1.044  Sum_probs=4.5

Q ss_pred             CCCEEEECCCC
Q ss_conf             89746713688
Q gi|254780834|r   58 SKGFYYCFSCH   68 (648)
Q Consensus        58 ~~~~~~cf~c~   68 (648)
                      +.|+|+|-+||
T Consensus        51 e~GvY~C~~C~   61 (146)
T KOG0856          51 EEGVYVCAGCG   61 (146)
T ss_pred             CCCEEEEEECC
T ss_conf             88448875059


No 131
>COG1422 Predicted membrane protein [Function unknown]
Probab=46.78  E-value=17  Score=15.01  Aligned_cols=37  Identities=19%  Similarity=0.303  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             5899999999999999872412798999999999999
Q gi|254780834|r  587 RFRLLSRQKEEIEKQIAQVTAKGEAEKTAILISILHE  623 (648)
Q Consensus       587 r~~~L~r~l~ele~~l~e~~~~~d~e~~~~l~~el~e  623 (648)
                      +...++++.++.+++..++..++|..+.+.+.++.+|
T Consensus        73 km~~~qk~m~efq~e~~eA~~~~d~~~lkkLq~~qme  109 (201)
T COG1422          73 KMKELQKMMKEFQKEFREAQESGDMKKLKKLQEKQME  109 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf             9999999999999999999980889999999999999


No 132
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=46.70  E-value=16  Score=15.34  Aligned_cols=15  Identities=27%  Similarity=0.656  Sum_probs=9.5

Q ss_pred             EECCCCC-CCCHHHHH
Q ss_conf             7136888-87898998
Q gi|254780834|r   63 YCFSCHV-KGDHLSFL   77 (648)
Q Consensus        63 ~cf~c~~-~gd~~~f~   77 (648)
                      .||+||+ =||.+..+
T Consensus         6 RCFTCGkvi~~k~~~y   21 (63)
T PRK04016          6 RCFTCGKVIGELWEEF   21 (63)
T ss_pred             CCCCCCCCHHHHHHHH
T ss_conf             5478978789889999


No 133
>pfam05991 DUF901 Protein of unknown function (DUF901). This family consists of several hypothetical bacterial proteins as well as some uncharacterized sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=46.36  E-value=17  Score=14.96  Aligned_cols=43  Identities=21%  Similarity=0.246  Sum_probs=29.4

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCC
Q ss_conf             8189961788662257778888887775369730675257888888997203
Q gi|254780834|r  315 PRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCY  366 (648)
Q Consensus       315 ~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~  366 (648)
                      -+|++.|||....-.....         ..--.+.|++=++|+.-|+||...
T Consensus        44 ~~v~vVFDa~~~~~~~~~~---------~~~~~i~vvfT~~~etAD~~IEr~   86 (166)
T pfam05991        44 YRVIVVFDAHYVPGSEEEY---------EKYGGIEVVFTKEGETADSYIEKL   86 (166)
T ss_pred             CEEEEEEECCCCCCCCCCE---------EECCCEEEEECCCCCCHHHHHHHH
T ss_conf             6799998566489998743---------450988999888999878999999


No 134
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=46.14  E-value=11  Score=16.64  Aligned_cols=26  Identities=19%  Similarity=0.525  Sum_probs=18.1

Q ss_pred             EECCCCCCCCCCEEEECCCCEEEECCCCC
Q ss_conf             53458888587879817897467136888
Q gi|254780834|r   41 ACCPFHDEKTPSFHCNDSKGFYYCFSCHV   69 (648)
Q Consensus        41 ~~cPfh~ektpsf~v~~~~~~~~cf~c~~   69 (648)
                      -.|||.+-.  ++ --..-|+|+|=.||.
T Consensus        37 y~Cp~Cgk~--~v-kR~a~GIW~C~~C~~   62 (90)
T PTZ00255         37 YFCSFCGKH--AT-KRKAVGIWRCKGCSK   62 (90)
T ss_pred             CCCCCCCCC--EE-EEEEEEEEECCCCCC
T ss_conf             628999997--66-888888887689999


No 135
>PRK06667 motB flagellar motor protein MotB; Validated
Probab=46.06  E-value=15  Score=15.42  Aligned_cols=23  Identities=17%  Similarity=0.351  Sum_probs=15.0

Q ss_pred             CCEEEEECCHHHHHHHHHCC-CCC
Q ss_conf             87089971438899987435-542
Q gi|254780834|r  271 SSFIILVEGYMDVLSLCQAG-VQN  293 (648)
Q Consensus       271 ~~~~i~vEGy~Dvi~l~~~G-~~n  293 (648)
                      ...-|.||||+|-....-.+ +++
T Consensus       160 ~~~~I~VeGHTD~~pi~~~~~~~s  183 (254)
T PRK06667        160 AGYNFRIEGHTDNVDVNPEGAWKS  183 (254)
T ss_pred             CCCEEEEEECCCCCCCCCCCCCCC
T ss_conf             574289994378776687888886


No 136
>PRK06163 hypothetical protein; Provisional
Probab=45.95  E-value=11  Score=16.79  Aligned_cols=60  Identities=18%  Similarity=0.227  Sum_probs=29.9

Q ss_pred             CHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             1134321366267898851268189961788662257778888887775369730675257888
Q gi|254780834|r  294 VVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGE  357 (648)
Q Consensus       294 ~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~  357 (648)
                      .|.+||-|..-.---.|.+ .++-|+|+|||.+=.-   .-.+++.--.....++.++.|.+|.
T Consensus        55 ~vGsMG~as~iaLG~Ala~-p~k~Vi~iDGDGs~LM---~mGsLaTi~~~~p~Nl~hIvlnN~~  114 (202)
T PRK06163         55 MLGSMGLAFPIALGVALAQ-PKRRVIALEGDGSLLM---QLGALGTIAALAPKNLTIIVMDNGV  114 (202)
T ss_pred             EECCCCCHHHHHHHHHHHC-CCCEEEEEECCHHHHH---CHHHHHHHHHHCCCCEEEEEECCCC
T ss_conf             7522101889999999878-9982899947668873---5688999997178856999986964


No 137
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding, 
Probab=45.76  E-value=17  Score=14.89  Aligned_cols=50  Identities=16%  Similarity=0.187  Sum_probs=26.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHCCC-CEEEEECCCCCCHHHHHHCCCHHHHHHHHHHC
Q ss_conf             99617886622577788888877753697-30675257888888997203668899886414
Q gi|254780834|r  318 VLCFDGDDPGLRAAYKAIDLVLCHLIPGN-RVNFVLLSRGEDPDSFIRCYGKTAFEKLIVES  378 (648)
Q Consensus       318 vl~fDgD~AG~kAa~Ra~e~~l~~l~~g~-~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A  378 (648)
                      .+++|..+||..|+...+       +.|. .+-++.-    ++++..-..-.++|.+.++++
T Consensus        95 ~V~~Dn~~~~~~a~~~L~-------~~G~~~i~~i~~----~~~~~~~~~R~~G~~~al~~~  145 (268)
T cd01575          95 AVGFSHAEAGRAMARHLL-------ARGYRRIGFLGA----RMDDTRAQQRLEGFRAALRAA  145 (268)
T ss_pred             EEECCHHHHHHHHHHHHH-------HCCCCEEEEECC----CCCCHHHHHHHHHHHHHHHHC
T ss_conf             897388999999999999-------749976999848----988736999999999999976


No 138
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=45.22  E-value=14  Score=15.91  Aligned_cols=25  Identities=20%  Similarity=0.592  Sum_probs=18.0

Q ss_pred             EECCCCCCCCCCEEEE-CCCCEEEECCCCC
Q ss_conf             5345888858787981-7897467136888
Q gi|254780834|r   41 ACCPFHDEKTPSFHCN-DSKGFYYCFSCHV   69 (648)
Q Consensus        41 ~~cPfh~ektpsf~v~-~~~~~~~cf~c~~   69 (648)
                      -.|||.+-.    .|. ..-|+|+|=.||.
T Consensus        37 y~Cp~Cg~~----~vkR~a~GIW~C~kC~~   62 (90)
T PRK03976         37 HVCPVCGRP----KVKRIATGIWQCRKCGA   62 (90)
T ss_pred             CCCCCCCCC----EEEEEEEEEEECCCCCC
T ss_conf             649989997----45888888888899998


No 139
>cd07048 BMC_PduB_repeat2 1,2-propanediol utilization protein B (PduB), Bacterial Micro-Compartment (BMC) domain repeat 2. PduB proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduB might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the pdu organelles at present no experimental evidence directly supports this view. PduB proteins contain two tandem BMC domains repeats. This CD contains repeat 2 (the second BMC domain of PduB).
Probab=44.97  E-value=18  Score=14.79  Aligned_cols=28  Identities=32%  Similarity=0.490  Sum_probs=20.8

Q ss_pred             HHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHH
Q ss_conf             432136626789885126818996178866225777888
Q gi|254780834|r  297 SLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAI  335 (648)
Q Consensus       297 ~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~  335 (648)
                      .-||++|           ++|++++-||..-.+.++.+.
T Consensus        35 ~~gts~s-----------NEvi~~isGDsgAVrqAv~aa   62 (70)
T cd07048          35 SGGTSFS-----------NEVILTISGDSGAVRQALIAA   62 (70)
T ss_pred             CCCCCCC-----------CEEEEEEECCHHHHHHHHHHH
T ss_conf             9986204-----------359999935779999999999


No 140
>cd01320 ADA Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in the purine pathway. Low, as well as high levels of ADA activity have been linked to several diseases.
Probab=44.86  E-value=18  Score=14.78  Aligned_cols=28  Identities=32%  Similarity=0.396  Sum_probs=22.4

Q ss_pred             HHCCCCHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             8859997999999999818858776820
Q gi|254780834|r   79 ALLGCSFIESVQRLAAIAGVPLPVVDPK  106 (648)
Q Consensus        79 ~~~~~~f~ea~~~la~~~gi~~~~~~~~  106 (648)
                      +.+|-=-++.+..||.+.|+++|..+..
T Consensus        10 HL~Gsi~~~tl~~la~~~~~~lp~~~~~   37 (325)
T cd01320          10 HLDGSLRPETILELAKKNGITLPASDVE   37 (325)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCCCCCCHH
T ss_conf             7778889999999999719999988877


No 141
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=44.83  E-value=18  Score=14.78  Aligned_cols=97  Identities=16%  Similarity=0.252  Sum_probs=44.6

Q ss_pred             CCCCCHHHHHCCCCHHHHHHHHHCCC----EEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHC
Q ss_conf             55421134321366267898851268----18996178866225777888888777536973067525788888899720
Q gi|254780834|r  290 GVQNVVSSLGTALTEYQLRLLWKLSP----RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRC  365 (648)
Q Consensus       290 G~~n~va~~Gtalt~~~~~~l~r~~~----~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~  365 (648)
                      =|..-||.+--.|++.+-...|+-+.    +||+       |-    |++ +.+|+-.    +..+.+-+-.|+ +|-+.
T Consensus       268 rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVI-------Gt----RSA-lF~Pf~~----LGLIIvDEEHD~-sYKq~  330 (730)
T COG1198         268 RFGAKVAVLHSGLSPGERYRVWRRARRGEARVVI-------GT----RSA-LFLPFKN----LGLIIVDEEHDS-SYKQE  330 (730)
T ss_pred             HHCCCHHHHCCCCCHHHHHHHHHHHHCCCCEEEE-------EE----CHH-HCCCHHH----CCEEEEECCCCC-CCCCC
T ss_conf             8678745314657927899999998559715999-------71----223-3072312----576997024564-32477


Q ss_pred             CCH--------------HHHHHHHHHCCCHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf             366--------------88998864149927999999985302331457999
Q gi|254780834|r  366 YGK--------------TAFEKLIVESLPLVDMLWKRETENRSFNTPDERAE  403 (648)
Q Consensus       366 ~G~--------------eaf~~ll~~A~~l~dFl~~~l~~~~dl~spe~ka~  403 (648)
                      .++              +...-.|.+|+|.+|-+.......+.+.....|+.
T Consensus       331 ~~prYhARdvA~~Ra~~~~~pvvLgSATPSLES~~~~~~g~y~~~~L~~R~~  382 (730)
T COG1198         331 DGPRYHARDVAVLRAKKENAPVVLGSATPSLESYANAESGKYKLLRLTNRAG  382 (730)
T ss_pred             CCCCCCHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHCCCEEEEECCCCCC
T ss_conf             7777678999999988609988982688778999866538558997035455


No 142
>cd00764 Eukaryotic_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include eukaryotic ATP-dependent phosphofructokinases. These have evolved from the bacterial PFKs by gene duplication and fusion events and exhibit complex allosteric behavior.
Probab=44.74  E-value=18  Score=14.77  Aligned_cols=60  Identities=17%  Similarity=0.191  Sum_probs=35.6

Q ss_pred             CCCCCCHHHHHCCCCHHHHHHHHHC------------CCEE-EEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             3554211343213662678988512------------6818-9961788662257778888887775369730675
Q gi|254780834|r  289 AGVQNVVSSLGTALTEYQLRLLWKL------------SPRI-VLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFV  351 (648)
Q Consensus       289 ~G~~n~va~~Gtalt~~~~~~l~r~------------~~~v-vl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv  351 (648)
                      .-|..++..=|.+|.+.. ...+..            .-+| ||.--||++|.|||.||+=..  -+..|.+|.-+
T Consensus       353 k~f~~a~~lr~~~F~~~~-~~~~~~~~~~~~~~~~~~~~rIaIlt~GgdapGMNAAiRA~Vr~--~~~~G~~v~gI  425 (762)
T cd00764         353 KRFDEAAALRGKSFDKNW-NLYKLLAIELPQPLPEKTNLNIAIVNVGAPAAGMNAAVRSAVRY--GLAHGHRPYAI  425 (762)
T ss_pred             CCHHHHHHHCCHHHHHHH-HHHHHHCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHH--HHHCCCEEEEE
T ss_conf             278999974377789999-99998603477778866770699985688961477999999999--99889999999


No 143
>pfam00782 DSPc Dual specificity phosphatase, catalytic domain. Ser/Thr and Tyr protein phosphatases. The enzyme's tertiary fold is highly similar to that of tyrosine-specific phosphatases, except for a "recognition" region.
Probab=44.55  E-value=18  Score=14.74  Aligned_cols=40  Identities=10%  Similarity=0.068  Sum_probs=26.6

Q ss_pred             EEEECC-CCCCCCH-HHHHHHHCCCCHHHHHHHHHHHHCCCC
Q ss_conf             467136-8888789-899898859997999999999818858
Q gi|254780834|r   61 FYYCFS-CHVKGDH-LSFLSALLGCSFIESVQRLAAIAGVPL  100 (648)
Q Consensus        61 ~~~cf~-c~~~gd~-~~f~~~~~~~~f~ea~~~la~~~gi~~  100 (648)
                      +-||.. -+.++-+ +-++|.++++++.+|+..+-.+-.+-.
T Consensus        75 LVHC~~G~sRS~~i~~aYLm~~~~~~~~~A~~~v~~~R~~~~  116 (131)
T pfam00782        75 LVHCQAGISRSATLIIAYLMKTRNLSLNEAYSFVKERRPIIS  116 (131)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCC
T ss_conf             999999874019999999999829999999999999899889


No 144
>pfam08856 DUF1826 Protein of unknown function (DUF1826). These proteins are functionally uncharacterized.
Probab=44.38  E-value=12  Score=16.32  Aligned_cols=27  Identities=22%  Similarity=0.364  Sum_probs=14.4

Q ss_pred             CCCCEEEEECCCCCCCCCCEECC-CCCC
Q ss_conf             77858885010014655300103-8767
Q gi|254780834|r  213 SRGQVIAFGGRTLSKGESVKYLN-SPET  239 (648)
Q Consensus       213 ~~g~~i~f~gR~l~~~~~~KYlN-SpeT  239 (648)
                      ..|.|+=|-|-....++..--+- ||..
T Consensus       157 ~~G~vallKG~~W~~~~~~glvHRSP~~  184 (196)
T pfam08856       157 PTGDVALLKGELWPGNEGAGLVHRSPPI  184 (196)
T ss_pred             CCCCEEEEECCCCCCCCCCCEEECCCCC
T ss_conf             8998899867857888999817579898


No 145
>TIGR00665 DnaB replicative DNA helicase; InterPro: IPR007692   This family includes the replicative DNA helicases, helicase DnaB, which exhibit DNA-dependent ATPase activity. Helicase DnaB is a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of more than 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. Replication protein, GP12 from  Bacteriophage P22 also belongs to this family .; GO: 0003677 DNA binding, 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication.
Probab=44.18  E-value=18  Score=14.70  Aligned_cols=27  Identities=22%  Similarity=0.165  Sum_probs=15.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             331457999999999885417998999
Q gi|254780834|r  395 FNTPDERAELEIHLKNCINHIKDQKLR  421 (648)
Q Consensus       395 l~spe~ka~~~~~l~~~I~~I~d~~~R  421 (648)
                      .+-.++.+...+.+..+...+.-|++.
T Consensus       354 ~~r~~~~~~i~~~lk~~a~e~~~P~~a  380 (465)
T TIGR00665       354 DNRHQEVAEISRSLKALARELNVPVIA  380 (465)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCHHHH
T ss_conf             404688999989999888774141665


No 146
>PRK00296 minE cell division topological specificity factor MinE; Reviewed
Probab=44.10  E-value=18  Score=14.69  Aligned_cols=19  Identities=11%  Similarity=0.067  Sum_probs=6.3

Q ss_pred             HHHHHHHHHHHHCCCCCCH
Q ss_conf             9999999999753889998
Q gi|254780834|r  516 QKLWSFLFSDFVEQKYFLP  534 (648)
Q Consensus       516 ~~L~~~i~~~~~~~~~~~~  534 (648)
                      ..+...|++.+......+.
T Consensus        40 ~~lk~eil~VI~KYv~Id~   58 (85)
T PRK00296         40 PQLRKEILEVICKYVQIDP   58 (85)
T ss_pred             HHHHHHHHHHHHHHEEECH
T ss_conf             9999999999987603662


No 147
>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]
Probab=43.90  E-value=17  Score=15.05  Aligned_cols=17  Identities=12%  Similarity=0.090  Sum_probs=7.9

Q ss_pred             CCCHHHHHHCCCHHHHHH
Q ss_conf             888889972036688998
Q gi|254780834|r  356 GEDPDSFIRCYGKTAFEK  373 (648)
Q Consensus       356 G~DPDe~ir~~G~eaf~~  373 (648)
                      ...=|+|...+ ++.|.+
T Consensus       421 ~~~~d~yy~~~-p~~~~~  437 (851)
T COG1205         421 SDPLDSYYLRH-PEELLE  437 (851)
T ss_pred             CCCCCHHHHHC-CHHHHH
T ss_conf             88400445508-375654


No 148
>COG0646 MetH Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]
Probab=43.89  E-value=17  Score=14.90  Aligned_cols=53  Identities=8%  Similarity=0.061  Sum_probs=28.1

Q ss_pred             HHCCCCHHHHHHHHHHHH---CCCCCCCCCCH-----HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             885999799999999981---88587768203-----677788999999999999999997
Q gi|254780834|r   79 ALLGCSFIESVQRLAAIA---GVPLPVVDPKI-----EKKEKIQTDLIRLIEVATDFFHHS  131 (648)
Q Consensus        79 ~~~~~~f~ea~~~la~~~---gi~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~  131 (648)
                      +.-+++-||.|+.+-..|   |-++-+.++..     ..........++++..+++.-+..
T Consensus        45 E~LnlT~Pd~I~~IH~aY~eAGADiIeTNTFgat~i~lady~led~v~~in~~aa~iAR~a  105 (311)
T COG0646          45 ELLNLTKPDVIEAIHRAYIEAGADIIETNTFGATTIKLADYGLEDKVYEINQKAARIARRA  105 (311)
T ss_pred             HHHHCCCCHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHH
T ss_conf             7875479499999999999646767873477865365755073889999999999999999


No 149
>KOG4717 consensus
Probab=43.54  E-value=19  Score=14.62  Aligned_cols=26  Identities=12%  Similarity=0.241  Sum_probs=22.0

Q ss_pred             ECCCCEEEECCCCCCCCHHHHHHHHC
Q ss_conf             17897467136888878989989885
Q gi|254780834|r   56 NDSKGFYYCFSCHVKGDHLSFLSALL   81 (648)
Q Consensus        56 ~~~~~~~~cf~c~~~gd~~~f~~~~~   81 (648)
                      ..+..+|--.--|.+||.|+|+|++|
T Consensus        87 DTQTKlyLiLELGD~GDl~DyImKHe  112 (864)
T KOG4717          87 DTQTKLYLILELGDGGDLFDYIMKHE  112 (864)
T ss_pred             CCCCEEEEEEEECCCCCHHHHHHHHC
T ss_conf             25533899998167730899998610


No 150
>KOG3497 consensus
Probab=42.89  E-value=11  Score=16.66  Aligned_cols=25  Identities=28%  Similarity=0.579  Sum_probs=15.1

Q ss_pred             EEECCCCC-CCCHHHHHHHHCCCCHH
Q ss_conf             67136888-87898998988599979
Q gi|254780834|r   62 YYCFSCHV-KGDHLSFLSALLGCSFI   86 (648)
Q Consensus        62 ~~cf~c~~-~gd~~~f~~~~~~~~f~   86 (648)
                      -.||.||+ -||-+.-+.+.-+.++.
T Consensus         5 iRCFtCGKvig~KWe~Yl~lLq~d~~   30 (69)
T KOG3497           5 IRCFTCGKVIGDKWETYLELLQADYT   30 (69)
T ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHH
T ss_conf             57521356230108999999987520


No 151
>smart00195 DSPc Dual specificity phosphatase, catalytic domain.
Probab=42.62  E-value=19  Score=14.51  Aligned_cols=37  Identities=8%  Similarity=0.060  Sum_probs=20.5

Q ss_pred             EEEEC-CCCCCC-CHHHHHHHHCCCCHHHHHHHHHHHHC
Q ss_conf             46713-688887-89899898859997999999999818
Q gi|254780834|r   61 FYYCF-SCHVKG-DHLSFLSALLGCSFIESVQRLAAIAG   97 (648)
Q Consensus        61 ~~~cf-~c~~~g-d~~~f~~~~~~~~f~ea~~~la~~~g   97 (648)
                      +-||. |.+.++ =|+.|+|.+.++++.+|++.+..+-.
T Consensus        82 LVHC~~G~sRS~~vv~aYLm~~~~~~~~~A~~~v~~~Rp  120 (138)
T smart00195       82 LVHCQAGVSRSATLIIAYLMKYRNLSLNDAYDFVKDRRP  120 (138)
T ss_pred             EEECCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCC
T ss_conf             999998775549999999999839999999999999799


No 152
>TIGR01058 parE_Gpos DNA topoisomerase IV, B subunit; InterPro: IPR005740   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit B (parE) of topoisomerase IV from Gram positive bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=42.54  E-value=19  Score=14.50  Aligned_cols=13  Identities=23%  Similarity=0.082  Sum_probs=5.4

Q ss_pred             HCCCC-EEEEECCC
Q ss_conf             36973-06752578
Q gi|254780834|r  343 IPGNR-VNFVLLSR  355 (648)
Q Consensus       343 ~~g~~-v~vv~LP~  355 (648)
                      .+|++ |=-|.+|+
T Consensus       322 ReGL~avi~v~~PE  335 (655)
T TIGR01058       322 REGLSAVISVRIPE  335 (655)
T ss_pred             HHHHHHEEEEECCH
T ss_conf             53202115532575


No 153
>cd03371 TPP_PpyrDC Thiamine pyrophosphate (TPP) family, PpyrDC subfamily, TPP-binding module; composed of proteins similar to phosphonopyruvate decarboxylase (PpyrDC) proteins. PpyrDC is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. These proteins require TPP and divalent metal cation cofactors.
Probab=42.47  E-value=14  Score=15.70  Aligned_cols=58  Identities=26%  Similarity=0.224  Sum_probs=30.5

Q ss_pred             CHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCC-CEEEEECCCC
Q ss_conf             11343213662678988512681899617886622577788888877753697-3067525788
Q gi|254780834|r  294 VVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN-RVNFVLLSRG  356 (648)
Q Consensus       294 ~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~-~v~vv~LP~G  356 (648)
                      .+.+||-++.-.--..+. .-++-|+|+|||.+=.-   ...+++. ..+.+. .+.++.+.++
T Consensus        46 ~~GsMG~a~p~AiG~ala-~p~r~Vv~l~GDGs~lM---~~geL~T-~~~~~~~n~~~vv~nN~  104 (188)
T cd03371          46 TVGSMGHASQIALGIALA-RPDRKVVCIDGDGAALM---HMGGLAT-IGGLAPANLIHIVLNNG  104 (188)
T ss_pred             EECHHHHHHHHHHHHHHH-CCCCEEEEEECCHHHHH---HHHHHHH-HHHHCCCCEEEEEECCC
T ss_conf             543123178999999983-99981899957338888---8579999-99727887799998796


No 154
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=42.31  E-value=16  Score=15.13  Aligned_cols=12  Identities=42%  Similarity=1.038  Sum_probs=5.9

Q ss_pred             CCCEEEECCCCC
Q ss_conf             897467136888
Q gi|254780834|r   58 SKGFYYCFSCHV   69 (648)
Q Consensus        58 ~~~~~~cf~c~~   69 (648)
                      ++|+|+|-+||.
T Consensus        39 ~~GiY~c~~cg~   50 (140)
T COG0229          39 EKGIYVCIVCGE   50 (140)
T ss_pred             CCCEEEEECCCC
T ss_conf             885698614797


No 155
>pfam06587 DUF1137 Protein of unknown function (DUF1137). This family consists of several hypothetical proteins specific to Chlamydia species. The function of this family is unknown.
Probab=42.09  E-value=11  Score=16.57  Aligned_cols=20  Identities=35%  Similarity=0.748  Sum_probs=13.8

Q ss_pred             CCCCCCCE-----------EEECCCCEEEEC
Q ss_conf             88858787-----------981789746713
Q gi|254780834|r   46 HDEKTPSF-----------HCNDSKGFYYCF   65 (648)
Q Consensus        46 h~ektpsf-----------~v~~~~~~~~cf   65 (648)
                      |-++.|-|           .++|+||||||-
T Consensus        41 ~~~~aPPFLKIKKlgV~KqI~SPekqfF~C~   71 (159)
T pfam06587        41 HFTPAPPFLKIKKLGVRKQIISPEKQFFYCT   71 (159)
T ss_pred             CCCCCCCCEEEEECCCEEEECCCHHHEEEEE
T ss_conf             6778998147666152003258268648867


No 156
>cd01971 Nitrogenase_VnfN_like Nitrogenase_vnfN_like: VnfN subunit of the VnfEN complex-like.  This group in addition to VnfN contains a subset of the beta subunit of the nitrogenase MoFe protein and NifN-like proteins. The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia.  NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of MoFe protein of the molybdenum(Mo)-nitrogenase.  NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to NifEN where it is further processed to FeMoco. VnfEN  may similarly be a scaffolding protien for the iron-vanadium cofactor (FeVco) of  the vanadium-dependent (V)-nitrogenase.  NifE and NifN are essential for the Mo-nitrogenase, VnfE and VnfN are not essential for the V-nitrogenase. NifE and NifN can substitute when the vnfEN genes are inactivated.
Probab=41.91  E-value=20  Score=14.43  Aligned_cols=10  Identities=10%  Similarity=-0.147  Sum_probs=4.3

Q ss_pred             CHHHHHHHHH
Q ss_conf             8178888643
Q gi|254780834|r  250 NFFGALNYLQ  259 (648)
Q Consensus       250 ~l~~a~~~~~  259 (648)
                      |++.|..++-
T Consensus       134 G~~~a~~aiv  143 (427)
T cd01971         134 GHEIVLKAII  143 (427)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 157
>PRK01008 queuine tRNA-ribosyltransferase; Provisional
Probab=41.73  E-value=20  Score=14.40  Aligned_cols=67  Identities=16%  Similarity=0.158  Sum_probs=41.9

Q ss_pred             CCHHH-HHHHHHCCCEEEEEEC---CCCCCHHHHHHHHHHHHHHHH---------CCCCEEEEECCCCCCHHHHHHCCCH
Q ss_conf             66267-8988512681899617---886622577788888877753---------6973067525788888899720366
Q gi|254780834|r  302 LTEYQ-LRLLWKLSPRIVLCFD---GDDPGLRAAYKAIDLVLCHLI---------PGNRVNFVLLSRGEDPDSFIRCYGK  368 (648)
Q Consensus       302 lt~~~-~~~l~r~~~~vvl~fD---gD~AG~kAa~Ra~e~~l~~l~---------~g~~v~vv~LP~G~DPDe~ir~~G~  368 (648)
                      ||++. +..-..+..-|+++||   +-.+..+-+.+++++...+++         ++.+.-|...-.|.|||  +|+...
T Consensus       140 ltPE~~i~~Q~~iGsDI~m~lD~~~~~~~~~~~~~~s~~rT~rW~~r~~~~~~~~~~~q~lfgIVQGG~~~d--LR~~sa  217 (372)
T PRK01008        140 LSPEVSVQAQKDLGADIIIPLDELLPFHTDPTYFLQSCSRTYVWEKRSLDYHLKNPRHQSMYGVIHGGIDPD--QRKIGC  217 (372)
T ss_pred             ECHHHHHHHHHHHCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCHH--HHHHHH
T ss_conf             289999999997489889987878899977999999999999999999999852975526874246788799--999999


Q ss_pred             HH
Q ss_conf             88
Q gi|254780834|r  369 TA  370 (648)
Q Consensus       369 ea  370 (648)
                      +.
T Consensus       218 ~~  219 (372)
T PRK01008        218 AF  219 (372)
T ss_pred             HH
T ss_conf             99


No 158
>pfam04405 ScdA_N Domain of Unknown function (DUF542). This domain is always found in conjunction with the HHE domain (pfam03794) at the N-terminus.
Probab=41.63  E-value=17  Score=15.09  Aligned_cols=35  Identities=17%  Similarity=0.450  Sum_probs=27.2

Q ss_pred             HHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHH
Q ss_conf             53510124422567741034554205997345232
Q gi|254780834|r  151 SHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIE  185 (648)
Q Consensus       151 ~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~  185 (648)
                      ..+-++|+|-|+=.+...|.+.+.++|.+.+.+++
T Consensus        16 a~vF~~~gIDFCCgG~~~L~eA~~~~~ld~~~vl~   50 (56)
T pfam04405        16 ARVFRKYGIDFCCGGKVSLAEACKEKGLDPEEVLA   50 (56)
T ss_pred             HHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf             99999949665689980699999882989999999


No 159
>PRK05729 valS valyl-tRNA synthetase; Reviewed
Probab=41.29  E-value=20  Score=14.35  Aligned_cols=34  Identities=24%  Similarity=0.296  Sum_probs=24.8

Q ss_pred             CCCCCHHHHHHCCCHHHHHHHH-HHCCCHHHHHHH
Q ss_conf             7888888997203668899886-414992799999
Q gi|254780834|r  354 SRGEDPDSFIRCYGKTAFEKLI-VESLPLVDMLWK  387 (648)
Q Consensus       354 P~G~DPDe~ir~~G~eaf~~ll-~~A~~l~dFl~~  387 (648)
                      -+..||.+.+.++|+|+++-.+ ..+.+..|..|+
T Consensus       528 GNvidP~~vi~~yGaDalR~~l~~~~~~g~di~~~  562 (877)
T PRK05729        528 GNVIDPLDLIDKYGADALRFTLAALASPGRDIRFD  562 (877)
T ss_pred             CCCCCHHHHHHHCCHHHHHHHHHHCCCCCCCCCCC
T ss_conf             89899899998719199999999707767660006


No 160
>cd01987 USP_OKCHK USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity.
Probab=41.03  E-value=20  Score=14.32  Aligned_cols=35  Identities=23%  Similarity=0.268  Sum_probs=27.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             18996178866225777888888777536973067525
Q gi|254780834|r  316 RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLL  353 (648)
Q Consensus       316 ~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~L  353 (648)
                      +|..|.|+...+.++..||..++..+   +-++.++..
T Consensus         1 rILV~vd~s~~s~~lir~a~rlA~~~---~a~l~vl~V   35 (124)
T cd01987           1 RILVCISGGPNAERLIRRAARLADRL---KAPWYVVYV   35 (124)
T ss_pred             CEEEEECCCHHHHHHHHHHHHHHHHC---CCCEEEEEE
T ss_conf             99999589850799999999999964---998999999


No 161
>pfam04723 GRDA Glycine reductase complex selenoprotein A. Found in clostridia, this protein contains one active site selenocysteine and catalyses the reductive deamination of glycine, which is coupled to the esterification of orthophosphate resulting in the formation of ATP. A member of this family may also exist in Treponema denticola.
Probab=40.76  E-value=14  Score=15.67  Aligned_cols=71  Identities=28%  Similarity=0.276  Sum_probs=36.9

Q ss_pred             CCHHHHH-------HHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             1438899-------987435542113432136626789885126818996178866225777888888777536973067
Q gi|254780834|r  278 EGYMDVL-------SLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNF  350 (648)
Q Consensus       278 EGy~Dvi-------~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~v  350 (648)
                      -|-||.=       ..-+.|-+|+|-.+|.|=.+.     ..++-+-|-.=|.--||--|-   +++       |+.|+-
T Consensus        46 agaMDLEnQ~rVK~~aEk~G~ENvvVvlGaaeaE~-----aglaaETVt~GDPTfAGPLAG---V~L-------gL~vYH  110 (150)
T pfam04723        46 AGAMDLENQQKVKDATESIGAENLVVLLGAAEAES-----AGLAAETVTAGDPTFAGPLAG---VEL-------GLRVYH  110 (150)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCHHH-----CCCEEEEEECCCCCCCCCCCC---CCC-------CCEEEE
T ss_conf             44122687899999998709752899964667001-----144334540689865555556---652-------856566


Q ss_pred             EECCC---CCCHHHHH
Q ss_conf             52578---88888997
Q gi|254780834|r  351 VLLSR---GEDPDSFI  363 (648)
Q Consensus       351 v~LP~---G~DPDe~i  363 (648)
                      +.=|+   --||+-|=
T Consensus       111 i~EpEiK~~~d~~vye  126 (150)
T pfam04723       111 AVEPEFKAEVDEAIYD  126 (150)
T ss_pred             ECCHHHHHHCCHHHHH
T ss_conf             4689898456888999


No 162
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=40.54  E-value=20  Score=14.26  Aligned_cols=36  Identities=25%  Similarity=0.372  Sum_probs=27.0

Q ss_pred             CHHHHHHHHHC---CCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             62678988512---6818996178866225777888888
Q gi|254780834|r  303 TEYQLRLLWKL---SPRIVLCFDGDDPGLRAAYKAIDLV  338 (648)
Q Consensus       303 t~~~~~~l~r~---~~~vvl~fDgD~AG~kAa~Ra~e~~  338 (648)
                      +..|++.|+++   ++.||++-|.|.=|..=++..++.+
T Consensus        85 ~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I~~ei~~~~  123 (151)
T cd03362          85 KKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYA  123 (151)
T ss_pred             HHHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             899999999998539989987788720459999999984


No 163
>pfam09334 tRNA-synt_1g tRNA synthetases class I (M). This family includes methionyl tRNA synthetases.
Probab=40.21  E-value=21  Score=14.22  Aligned_cols=25  Identities=28%  Similarity=0.444  Sum_probs=18.3

Q ss_pred             CCCCHHHHHHCCCHHHHHHHH-HHCC
Q ss_conf             888888997203668899886-4149
Q gi|254780834|r  355 RGEDPDSFIRCYGKTAFEKLI-VESL  379 (648)
Q Consensus       355 ~G~DPDe~ir~~G~eaf~~ll-~~A~  379 (648)
                      +..||++++.++|+|+++-+| .++.
T Consensus       331 N~i~~~d~i~~ygaDalR~~L~~~~~  356 (388)
T pfam09334       331 NVVDPDELLDRYGVDALRYYLAREAP  356 (388)
T ss_pred             CCCCHHHHHHHCCCHHHHHHHHHCCC
T ss_conf             87888999988782899999995399


No 164
>PRK10026 arsenate reductase; Provisional
Probab=39.96  E-value=19  Score=14.65  Aligned_cols=48  Identities=13%  Similarity=0.182  Sum_probs=31.9

Q ss_pred             CCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHH
Q ss_conf             775789999850688535101244225677410345542059973452320
Q gi|254780834|r  136 RDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEA  186 (648)
Q Consensus       136 ~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~  186 (648)
                      ++..|+++|++.|+..+++..+.-...   .+.|...+...|.+..+++..
T Consensus        14 KSR~aL~lL~e~g~e~~vv~YLk~p~s---~~eL~~l~~~Lg~~~~~liRk   61 (141)
T PRK10026         14 TSRNTLEMIRNSGTEPTIIYYLETPPT---RDELVKLIADMGISVRALLRK   61 (141)
T ss_pred             HHHHHHHHHHHCCCCCEEEHHHCCCCC---HHHHHHHHHHCCCCHHHHHHC
T ss_conf             899999999986999587156217999---999999999859999999873


No 165
>PRK00726 murG N-acetylglucosaminyl transferase; Provisional
Probab=39.80  E-value=21  Score=14.17  Aligned_cols=65  Identities=22%  Similarity=0.319  Sum_probs=45.3

Q ss_pred             HHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHH---HHHHHCCCCCCH----HHHHCCCCHHHHHHHHHCCCEEE
Q ss_conf             01108178888643310000235678708997143889---998743554211----34321366267898851268189
Q gi|254780834|r  246 KNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDV---LSLCQAGVQNVV----SSLGTALTEYQLRLLWKLSPRIV  318 (648)
Q Consensus       246 ~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dv---i~l~~~G~~n~v----a~~Gtalt~~~~~~l~r~~~~vv  318 (648)
                      +.+.++.+++..+++.++        +-+|-+=||.-+   ++.+..|++-++    +.+|.|-     +++.++++.|.
T Consensus        75 ~l~~~~~~~~~il~~~kP--------d~Vig~GGY~s~P~~laA~l~~iP~iiHEqN~v~G~aN-----r~l~~~a~~i~  141 (359)
T PRK00726         75 KLLKGVLQARKILKRFKP--------DVVVGFGGYVSGPAGLAARLLGIPLVIHEQNAVPGLAN-----KLLARFAKKVA  141 (359)
T ss_pred             HHHHHHHHHHHHHHHCCC--------CEEEECCCHHHHHHHHHHHHCCCCEEEECCCCCCCCCH-----HHHHHHCCEEE
T ss_conf             999999999999997499--------99997897412899999998299869974542356233-----78888509789


Q ss_pred             EEECC
Q ss_conf             96178
Q gi|254780834|r  319 LCFDG  323 (648)
Q Consensus       319 l~fDg  323 (648)
                      ++|+.
T Consensus       142 ~~f~~  146 (359)
T PRK00726        142 TAFEE  146 (359)
T ss_pred             ECCHH
T ss_conf             97755


No 166
>KOG2026 consensus
Probab=39.79  E-value=17  Score=14.91  Aligned_cols=26  Identities=27%  Similarity=0.425  Sum_probs=22.9

Q ss_pred             CCCCCCCCCCEEEECCCCEEEECCCCC
Q ss_conf             458888587879817897467136888
Q gi|254780834|r   43 CPFHDEKTPSFHCNDSKGFYYCFSCHV   69 (648)
Q Consensus        43 cPfh~ektpsf~v~~~~~~~~cf~c~~   69 (648)
                      --||.||-||.+.|+ -..|-|--||.
T Consensus        24 ldfd~ek~c~vslsn-LnvyAclvcg~   49 (442)
T KOG2026          24 LDFDFEKPCSVSLSN-LNVYACLVCGK   49 (442)
T ss_pred             CCCCCCCCCCCCCCC-CCEEEEEEECC
T ss_conf             246578999623466-65145542070


No 167
>PHA00202 DNA replication initiation protein
Probab=39.71  E-value=6.9  Score=18.62  Aligned_cols=21  Identities=19%  Similarity=0.143  Sum_probs=12.0

Q ss_pred             CCCCCCHHHHHHHHCCCCHHH
Q ss_conf             888878989989885999799
Q gi|254780834|r   67 CHVKGDHLSFLSALLGCSFIE   87 (648)
Q Consensus        67 c~~~gd~~~f~~~~~~~~f~e   87 (648)
                      |...+....+-..+-++.|+.
T Consensus        31 ~~~a~~~~~~~~~~~~~~~~~   51 (379)
T PHA00202         31 CHDAVRRLHKHEEYKGFAKSG   51 (379)
T ss_pred             HHHHCCCCCCCCCCCCCCCCC
T ss_conf             554023345621024567755


No 168
>COG0426 FpaA Uncharacterized flavoproteins [Energy production and conversion]
Probab=39.71  E-value=21  Score=14.16  Aligned_cols=63  Identities=14%  Similarity=0.187  Sum_probs=34.4

Q ss_pred             HCCCCHHHHHHHHHC--------CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHH
Q ss_conf             213662678988512--------681899617886622577788888877753697306752578888889972
Q gi|254780834|r  299 GTALTEYQLRLLWKL--------SPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIR  364 (648)
Q Consensus       299 Gtalt~~~~~~l~r~--------~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir  364 (648)
                      |--++..-.+++.+|        +.+|.+.||.+--=-.-..++  ++..+.+.|..|.++.+-.. ||-+.++
T Consensus       223 G~i~~~~~~~i~~~Y~~W~~~~~~~~V~l~Y~smyg~T~~ma~a--iaegl~~~gv~v~~~~~~~~-~~~eI~~  293 (388)
T COG0426         223 GPIWRGNPKEIVEAYRDWAEGQPKGKVDLIYDSMYGNTEKMAQA--IAEGLMKEGVDVEVINLEDA-DPSEIVE  293 (388)
T ss_pred             CCEEECCHHHHHHHHHHHHCCCCCCEEEEEEECCCCCHHHHHHH--HHHHHHHCCCCEEEEECCCC-CHHHHHH
T ss_conf             85255798999999999970687661799984223787999999--98776115996299991558-8999999


No 169
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=39.57  E-value=19  Score=14.63  Aligned_cols=36  Identities=31%  Similarity=0.542  Sum_probs=24.5

Q ss_pred             CCCCCCCCCCCEEEEEEEECCCCEEEEECCCCC----CCCCCEECC-CCC
Q ss_conf             654100001671688897077858885010014----655300103-876
Q gi|254780834|r  194 NSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLS----KGESVKYLN-SPE  238 (648)
Q Consensus       194 ~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~----~~~~~KYlN-Spe  238 (648)
                      +|. ++-||-|+        .|.|+|-.||...    .+..-|+|+ +||
T Consensus        49 kGm-Ph~rf~G~--------TG~Vvg~~g~ay~V~v~~G~k~K~liv~pe   89 (98)
T COG2139          49 KGM-PHPRFQGK--------TGTVVGVRGRAYKVEVYDGNKEKTLIVRPE   89 (98)
T ss_pred             CCC-CCCCCCCC--------CEEEEECCCCEEEEEEECCCCEEEEEECHH
T ss_conf             698-77530476--------307984148779999961894589986778


No 170
>COG2719 SpoVR Uncharacterized conserved protein [Function unknown]
Probab=39.43  E-value=21  Score=14.19  Aligned_cols=17  Identities=24%  Similarity=0.479  Sum_probs=11.5

Q ss_pred             HHHHHHHHHHHHCCCCC
Q ss_conf             79999999998188587
Q gi|254780834|r   85 FIESVQRLAAIAGVPLP  101 (648)
Q Consensus        85 f~ea~~~la~~~gi~~~  101 (648)
                      ..+.+..+|..+|.+..
T Consensus        18 ~~~eI~~ia~~~gLD~Y   34 (495)
T COG2719          18 YLEEIERIAKEYGLDTY   34 (495)
T ss_pred             HHHHHHHHHHHHCCCCC
T ss_conf             99999999997087877


No 171
>cd01525 RHOD_Kc Member of the Rhodanese Homology Domain superfamily. Included in this CD are the rhodanese-like domains found C-terminal of the serine/threonine protein kinases catalytic (S_TKc) domain and the Tre-2, BUB2p, Cdc16p (TBC) domain. The putative active site Cys residue is not present in this CD.
Probab=39.23  E-value=21  Score=14.10  Aligned_cols=61  Identities=13%  Similarity=0.139  Sum_probs=41.9

Q ss_pred             CCCCHH-HHHCCCCH-------HHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCC
Q ss_conf             542113-43213662-------678988512681899617886622577788888877753697306752578888
Q gi|254780834|r  291 VQNVVS-SLGTALTE-------YQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGED  358 (648)
Q Consensus       291 ~~n~va-~~Gtalt~-------~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~D  358 (648)
                      |+++|- |..|++++       .++..|.++-.++|++.+.  +|+.|+.=|-.    +.+.|. .+|+.|-.|.+
T Consensus        33 i~~siniPf~~~~~~~~~L~~~~~~~~Lek~Kgk~VViV~~--~g~~a~~fa~~----Lvk~Gf-~rVcvL~GGi~  101 (105)
T cd01525          33 IEGSINIPFSSVFLKEGELEQLPTVPRLENYKGKIIVIVSH--SHKHAALFAAF----LVKCGV-PRVCILDGGIN  101 (105)
T ss_pred             ECCCCCCCCHHHCCCCCCCCCCCCHHHHHHCCCCEEEEECC--CCCCHHHHHHH----HHHCCC-CEEEEECCHHH
T ss_conf             12755057302015544221364258999758982999889--98679999999----998499-86999338275


No 172
>TIGR00807 s1 malonate transporter, MadL subunit; InterPro: IPR004690 The MSS family includes the monobasic malonate:Na+ symporter of Malonomonas rubra. It consists of two integral membrane proteins, MadL and MadM. The transporter is believed to catalyze the electroneutral reversible uptake of H+-malonate with one Na+, and both subunits have been shown to be essential for activity..
Probab=39.20  E-value=14  Score=15.69  Aligned_cols=26  Identities=15%  Similarity=0.328  Sum_probs=19.3

Q ss_pred             HHHHHHHCCCCHHHHCCCCCCCCCCCCCHHH
Q ss_conf             8999985068853510124422567741034
Q gi|254780834|r  140 LHYYLDERGIDSHAIEMFKLGYAPDSRYSLR  170 (648)
Q Consensus       140 a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~  170 (648)
                      +++||.+||-= ....+|++||    |+..|
T Consensus        46 ~~~~l~k~G~l-~q~~qfGvgf----W~aMY   71 (127)
T TIGR00807        46 AKELLAKKGKL-KQVSQFGVGF----WSAMY   71 (127)
T ss_pred             HHHHHHHCCCC-CCCCCCCCEE----ECCEE
T ss_conf             99998743999-7220156010----04501


No 173
>COG0535 Predicted Fe-S oxidoreductases [General function prediction only]
Probab=39.17  E-value=21  Score=14.09  Aligned_cols=95  Identities=20%  Similarity=0.247  Sum_probs=57.6

Q ss_pred             CCEEEEECCHHHHHHHHH--CCCCCCHHHHHCCCCHHHHHHHHHC-CCEEEEEECC-CCCC------H----HHHHHHHH
Q ss_conf             870899714388999874--3554211343213662678988512-6818996178-8662------2----57778888
Q gi|254780834|r  271 SSFIILVEGYMDVLSLCQ--AGVQNVVSSLGTALTEYQLRLLWKL-SPRIVLCFDG-DDPG------L----RAAYKAID  336 (648)
Q Consensus       271 ~~~~i~vEGy~Dvi~l~~--~G~~n~va~~Gtalt~~~~~~l~r~-~~~vvl~fDg-D~AG------~----kAa~Ra~e  336 (648)
                      .++..+-.-.++.+....  .|+.-++.|.||.++++=++.+... .+.|.+.+|| |...      .    +++.+++.
T Consensus        73 gGEPll~~~~~ei~~~~~~~~~~~~~~~TnG~~~~~~~~~~l~~~g~~~v~iSld~~~~e~hd~~rg~~g~~~~~~~~i~  152 (347)
T COG0535          73 GGEPLLRPDLLEIVEYARKKGGIRVSLSTNGTLLTEEVLEKLKEAGLDYVSISLDGLDPETHDPIRGVKGVFKRAVEAIK  152 (347)
T ss_pred             CCCCEECCCHHHHHHHHHHCCCEEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             98733345799999998513872898826875453889998876688769999745885321400277626999999999


Q ss_pred             HHHHHHHCCC--CEEEEECCCC----CCHHHHHHCCCH
Q ss_conf             8877753697--3067525788----888899720366
Q gi|254780834|r  337 LVLCHLIPGN--RVNFVLLSRG----EDPDSFIRCYGK  368 (648)
Q Consensus       337 ~~l~~l~~g~--~v~vv~LP~G----~DPDe~ir~~G~  368 (648)
                      .+   .+.|+  .+.+......    .+..+++...|.
T Consensus       153 ~~---~~~g~~~~~~~~v~~~n~~~l~~~~~~~~~~g~  187 (347)
T COG0535         153 NL---KEAGILVVINTTVTKINYDELPEIADLAAELGV  187 (347)
T ss_pred             HH---HHHCCEEEEEEEEECCCHHHHHHHHHHHHHCCC
T ss_conf             99---873970489999956634658999999986597


No 174
>PRK13265 glycine/sarcosine/betaine reductase complex protein A; Reviewed
Probab=39.11  E-value=16  Score=15.25  Aligned_cols=71  Identities=28%  Similarity=0.277  Sum_probs=36.9

Q ss_pred             CCHHHHH-------HHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             1438899-------987435542113432136626789885126818996178866225777888888777536973067
Q gi|254780834|r  278 EGYMDVL-------SLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNF  350 (648)
Q Consensus       278 EGy~Dvi-------~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~v  350 (648)
                      -|-||.=       ..-+.|-+|+|-.+|.|=.+.     ..++-+-|-.=|.--||--|-   +++       |+.|+-
T Consensus        47 agaMDLEnQ~rVK~~aek~G~ENvvVvlGaaeaE~-----aglaaETVT~GDPTfAGPLAG---V~L-------gL~vYH  111 (157)
T PRK13265         47 AGAMDLENQKRVKDLTEKHGAENIVVILGAAEAEA-----AGLAAETVTNGDPTFAGPLAG---VQL-------GLRVYH  111 (157)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCHHH-----CCCEEEEECCCCCCCCCCCCC---CCC-------CCEEEE
T ss_conf             44122687899999998709752899964667001-----144323440689865555556---642-------866566


Q ss_pred             EECCC---CCCHHHHH
Q ss_conf             52578---88888997
Q gi|254780834|r  351 VLLSR---GEDPDSFI  363 (648)
Q Consensus       351 v~LP~---G~DPDe~i  363 (648)
                      +.=|+   --||+-|=
T Consensus       112 i~EpEiK~~~d~~vye  127 (157)
T PRK13265        112 AVEPEIKEEVDEEVYE  127 (157)
T ss_pred             ECCHHHHHHCCHHHHH
T ss_conf             4689898456888999


No 175
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation.  Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=39.07  E-value=13  Score=16.09  Aligned_cols=22  Identities=18%  Similarity=0.434  Sum_probs=19.2

Q ss_pred             CCCCEEEEECCCCCCHHHHHHC
Q ss_conf             6973067525788888899720
Q gi|254780834|r  344 PGNRVNFVLLSRGEDPDSFIRC  365 (648)
Q Consensus       344 ~g~~v~vv~LP~G~DPDe~ir~  365 (648)
                      -|-+||++.||+..|.|+++..
T Consensus        60 RGs~IRyi~lPD~l~~d~lL~d   81 (90)
T cd01724          60 RGNNIRYFILPDSLNLDTLLVD   81 (90)
T ss_pred             CCCCEEEEECCCCCCCCCCEEE
T ss_conf             5773899988787766451210


No 176
>PRK12655 fructose-6-phosphate aldolase; Reviewed
Probab=39.01  E-value=21  Score=14.08  Aligned_cols=74  Identities=16%  Similarity=0.069  Sum_probs=33.4

Q ss_pred             HHHHCCCCHHHHHHHHHHHHCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCC
Q ss_conf             898859997999999999818858776-82036777889999999999999999973267775789999850688
Q gi|254780834|r   77 LSALLGCSFIESVQRLAAIAGVPLPVV-DPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGID  150 (648)
Q Consensus        77 ~~~~~~~~f~ea~~~la~~~gi~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~  150 (648)
                      +|..+|.+|.+.++.+++..+-+.|-. +......++.-..-..+.++....+-+.-.+..|-.|...|.+.|+.
T Consensus        31 ll~k~g~~~~~~~~~i~~~~~~~~~l~~ev~~~d~~~m~~~a~~l~~~~~~ivVKIP~t~~Gl~ai~~L~~~gi~  105 (220)
T PRK12655         31 IIAASKESIWEVLPRLQKAIGGEGILFAQTMSRDAQGMVEEAKRLRNAIPGIVVKIPVTAEGLAAIKKLKKEGIP  105 (220)
T ss_pred             HHHHCCCCHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHCCCEEEECCCCHHHHHHHHHHHHCCCC
T ss_conf             998659987999999999828999789999559999999999999974787399868877899999999986997


No 177
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=38.75  E-value=22  Score=14.04  Aligned_cols=119  Identities=18%  Similarity=0.105  Sum_probs=62.8

Q ss_pred             ECCHH-HHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCE------EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             71438-89998743554211343213662678988512681------899617886622577788888877753697306
Q gi|254780834|r  277 VEGYM-DVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPR------IVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVN  349 (648)
Q Consensus       277 vEGy~-Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~------vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~  349 (648)
                      -+|=| |++++-.    .+++..+..+|.+.+..+-.+++.      +-.++++|.+   +++..++-   +.       
T Consensus       210 s~GsmRDAlslLd----Q~is~~~~~it~~~v~~~lG~~~~~~l~~l~~~i~~~d~~---~~l~~~~~---i~-------  272 (541)
T PRK05563        210 SDGAMRDALSILD----QAISMGDGKVDYDDVVSMLGLVTNENLFDITDSIIEKDIE---KSMEIIDD---IV-------  272 (541)
T ss_pred             CCCCHHHHHHHHH----HHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHH---HHHHHHHH---HH-------
T ss_conf             5997788999999----9998359986699999996899989999999999858999---99999999---99-------


Q ss_pred             EEECCCCCCHHHHHHCCCHHHHHHHHH-H-CCCHH------HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             752578888889972036688998864-1-49927------99999998530233145799999999988541799
Q gi|254780834|r  350 FVLLSRGEDPDSFIRCYGKTAFEKLIV-E-SLPLV------DMLWKRETENRSFNTPDERAELEIHLKNCINHIKD  417 (648)
Q Consensus       350 vv~LP~G~DPDe~ir~~G~eaf~~ll~-~-A~~l~------dFl~~~l~~~~dl~spe~ka~~~~~l~~~I~~I~d  417 (648)
                          -.|.||-.|++.- ..-|++++- + +....      +-.++.+......-+.+.-..+++.+......++-
T Consensus       273 ----~~G~d~~~fl~dL-i~~~R~lll~k~~~~~~~~l~~~~e~~~~l~~~a~~~~~~~l~~~~~~L~~~~~~lk~  343 (541)
T PRK05563        273 ----LSGKDIYNFIKDL-ITHFRNLLMVKVSSNPEEILDMSEENIELLKEQSKKIRIEEIMRCIRILQEAEEQSKW  343 (541)
T ss_pred             ----HCCCCHHHHHHHH-HHHHHHHHHHHCCCCHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             ----8699999999999-9999999997606973765217999999999999708999999999999999999614


No 178
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=38.49  E-value=22  Score=14.01  Aligned_cols=14  Identities=7%  Similarity=0.052  Sum_probs=7.4

Q ss_pred             CCCCCCHHCCCHHH
Q ss_conf             65352101108178
Q gi|254780834|r  240 ILFHKGKNLYNFFG  253 (648)
Q Consensus       240 ~if~K~~~Ly~l~~  253 (648)
                      |.+-++..++|--+
T Consensus       195 P~lv~~~~~~gtGq  208 (422)
T PRK05431        195 PYLVNEESMYGTGQ  208 (422)
T ss_pred             HHHHHHHHHHHHCC
T ss_conf             37636788744537


No 179
>KOG1903 consensus
Probab=38.48  E-value=12  Score=16.33  Aligned_cols=33  Identities=21%  Similarity=0.293  Sum_probs=24.6

Q ss_pred             HHHCCCCEE-EEECCCCCCHHHHHHCCCHHHHHH
Q ss_conf             753697306-752578888889972036688998
Q gi|254780834|r  341 HLIPGNRVN-FVLLSRGEDPDSFIRCYGKTAFEK  373 (648)
Q Consensus       341 ~l~~g~~v~-vv~LP~G~DPDe~ir~~G~eaf~~  373 (648)
                      -+..|+++| +|.||.|+|-|||+--|-.|-|..
T Consensus        38 sL~sG~dLr~aV~LPpgEn~nDW~AVHvVDFFNR   71 (217)
T KOG1903          38 SLNSGLDLRSAVRLPPGENLNDWLAVHVVDFFNR   71 (217)
T ss_pred             HHHCCCCHHHHCCCCCCCCCCCEEEEEHHHHHHH
T ss_conf             7743725687510899887443023211335556


No 180
>TIGR00337 PyrG CTP synthase; InterPro: IPR004468 CTP synthase is involved in pyrimidine ribonucleotide/ribonucleoside metabolism. The enzyme catalyzes the reaction L-glutamine + H2O + UTP + ATP = CTP + phosphate + ADP + L-glutamate. The enzyme exists as a dimer of identical chains that aggregates as a tetramer. This gene has been found circa 500 bp 5 upstream of enolase in both beta (Nitrosomonas europaea) and gamma (Escherichia coli) subdivisions of Proteobacterium .; GO: 0003883 CTP synthase activity, 0006221 pyrimidine nucleotide biosynthetic process.
Probab=38.42  E-value=20  Score=14.33  Aligned_cols=90  Identities=19%  Similarity=0.325  Sum_probs=45.7

Q ss_pred             CCCHHHHHHHHCCCCHHHHHHHHHHHHCCC---------CCCCC-------CCHHHH-HHHHH--------------HH-
Q ss_conf             878989989885999799999999981885---------87768-------203677-78899--------------99-
Q gi|254780834|r   70 KGDHLSFLSALLGCSFIESVQRLAAIAGVP---------LPVVD-------PKIEKK-EKIQT--------------DL-  117 (648)
Q Consensus        70 ~gd~~~f~~~~~~~~f~ea~~~la~~~gi~---------~~~~~-------~~~~~~-~~~~~--------------~~-  117 (648)
                      ||.|=    .+|++.|.||++.+....|=+         +|.-.       ..++.+ .+.|.              .| 
T Consensus       151 GGTVG----DIEs~PFLEAiRQ~~~e~G~Env~~iHvTLVP~i~aagE~KTKPTQhSVKeLRs~Gi~PD~i~cRs~~~l~  226 (571)
T TIGR00337       151 GGTVG----DIESLPFLEAIRQLKKEVGRENVLFIHVTLVPYIAAAGELKTKPTQHSVKELRSLGIQPDIIICRSSEPLD  226 (571)
T ss_pred             CCCCC----CCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEEECCCCCCC
T ss_conf             77000----00362589999999987389867999840026314487478775127899998609888689981887689


Q ss_pred             HHHHHHHHHHHH---HHHCCCCCHH----HHHHHHHCCCCHHHHCCCCCCCCC
Q ss_conf             999999999999---9732677757----899998506885351012442256
Q gi|254780834|r  118 IRLIEVATDFFH---HSLKNARDKR----LHYYLDERGIDSHAIEMFKLGYAP  163 (648)
Q Consensus       118 ~~~~~~~~~~~~---~~l~~~~~~~----a~~yl~~Rg~~~~~~~~f~lG~ap  163 (648)
                      -.+-++.|-|++   .+.-+..++.    .---|.+-|+.+-+.++|+|.-.|
T Consensus       227 ~~~k~KiAlFCdV~~~aVI~~~Da~sIY~vPl~L~~egl~~~~~~rl~L~~~~  279 (571)
T TIGR00337       227 KSLKKKIALFCDVEEEAVINAEDASSIYEVPLLLKKEGLDDYLCRRLNLNEKP  279 (571)
T ss_pred             HHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCEECCCCHHHHHHHHHCCCCCC
T ss_conf             77764521005889732578655524011352100043357999984378777


No 181
>KOG2924 consensus
Probab=38.35  E-value=1.5  Score=24.72  Aligned_cols=161  Identities=22%  Similarity=0.267  Sum_probs=81.9

Q ss_pred             EECCCCCCCCHHHHHHHHCCCCH-----HHHHHHHHHHHCCCCCCC---CCCHHHHHHHHHHHHHHHHHHHHH--HHHHH
Q ss_conf             71368888789899898859997-----999999999818858776---820367778899999999999999--99973
Q gi|254780834|r   63 YCFSCHVKGDHLSFLSALLGCSF-----IESVQRLAAIAGVPLPVV---DPKIEKKEKIQTDLIRLIEVATDF--FHHSL  132 (648)
Q Consensus        63 ~cf~c~~~gd~~~f~~~~~~~~f-----~ea~~~la~~~gi~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~--~~~~l  132 (648)
                      +.|.-+.  |.-..+.-+....|     -+||+.+-..........   +.+.....-.+...    ....-|  |-.+|
T Consensus        34 ~Dfnk~~--~~~~l~~s~~t~GFQatnl~~Av~~in~M~~~rd~~~~~d~d~~~~~~~~~r~~----~~ctIFlGyTSNl  107 (366)
T KOG2924          34 YDFNKGV--DYSALLESFGTTGFQATNLGRAVQQINRMLNWRDEPLSADDDSHEDLTFSRRPL----TSCTIFLGYTSNL  107 (366)
T ss_pred             CCCCCCC--CHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC----CCEEEEEECCHHH
T ss_conf             6656520--599999998602641000889999999998434576644455444467121455----3148997423033


Q ss_pred             CCCCCHHHHHHHHHC-----------CCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCC
Q ss_conf             267775789999850-----------688535101244225677410345542059973452320121003465410000
Q gi|254780834|r  133 KNARDKRLHYYLDER-----------GIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDR  201 (648)
Q Consensus       133 ~~~~~~~a~~yl~~R-----------g~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~  201 (648)
                      -+.--.+...||-+|           |+.++.|+-+.--|.-+ +..--..|+.+|.+.-    -+|+++|++    |-.
T Consensus       108 iSSGlRetirylvqh~mVdviVttaGGvEEDlIKclaPTy~g~-F~L~G~~LR~~GlNRi----GNllvPndN----Yck  178 (366)
T KOG2924         108 ISSGLRETIRYLVQHNMVDVIVTTAGGVEEDLIKCLAPTYLGD-FSLDGKELRENGLNRI----GNLLVPNDN----YCK  178 (366)
T ss_pred             HHHHHHHHHHHHHHHCCEEEEEECCCCCHHHHHHHHCCCCEEE-EECCHHHHHHHHHHHH----CCEECCCCC----HHH
T ss_conf             3350899999999746135999548862788998707530202-5347287776013332----467247865----155


Q ss_pred             CCCEEEEEEEECCCCEEEEECCCCCCCCC----CEECCCCCC
Q ss_conf             16716888970778588850100146553----001038767
Q gi|254780834|r  202 FRNRLIFPIRSSRGQVIAFGGRTLSKGES----VKYLNSPET  239 (648)
Q Consensus       202 Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~----~KYlNSpeT  239 (648)
                      |.+-|| ||.|..=.--.=-|+++.++..    .|-+|-+.|
T Consensus       179 fEdWl~-pIld~mleeq~~~~~iwTPSk~I~rlGk~IndesS  219 (366)
T KOG2924         179 FEDWLM-PILDEMLEEQKTEGVIWTPSKMIARLGKEINDESS  219 (366)
T ss_pred             HHHHHH-HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCC
T ss_conf             899988-99999998765248624879999998655089221


No 182
>pfam01983 CofC Guanylyl transferase CofC like. Coenzyme F420 is a hydride carrier cofactor that functions during methanogenesis. This family of proteins represents CofC, a nucleotidyl transferase that is involved in coenzyme F420 biosynthesis. CofC has been shown to catalyse the formation of lactyl-2-diphospho-5'-guanosine from 2-phospho-L-lactate and GTP.
Probab=38.31  E-value=22  Score=13.99  Aligned_cols=27  Identities=11%  Similarity=0.202  Sum_probs=11.7

Q ss_pred             CCHHHHHHHHHCCC--EEEEEECCCCCCHH
Q ss_conf             66267898851268--18996178866225
Q gi|254780834|r  302 LTEYQLRLLWKLSP--RIVLCFDGDDPGLR  329 (648)
Q Consensus       302 lt~~~~~~l~r~~~--~vvl~fDgD~AG~k  329 (648)
                      +|.+.+..+-....  .|+||=|-|. |-|
T Consensus       101 i~~~~l~~ll~~~~~~~vvI~P~r~g-GTN  129 (217)
T pfam01983       101 ISKEVLKRFLETEGRADVVIAPGRGG-GTN  129 (217)
T ss_pred             CCHHHHHHHHHHCCCCCEEECCCCCC-CEE
T ss_conf             99899999998377888897456789-633


No 183
>COG2971 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]
Probab=38.26  E-value=22  Score=13.98  Aligned_cols=28  Identities=18%  Similarity=0.227  Sum_probs=18.7

Q ss_pred             EEEECCCCEEEEECCCCCCCCCCEECCCC-CCCC
Q ss_conf             89707785888501001465530010387-6765
Q gi|254780834|r  209 PIRSSRGQVIAFGGRTLSKGESVKYLNSP-ETIL  241 (648)
Q Consensus       209 Pi~~~~g~~i~f~gR~l~~~~~~KYlNSp-eT~i  241 (648)
                      -+.|.+|+|+|.|     ..-++-|.|+| |+.+
T Consensus        20 ~l~~~~g~vlg~g-----~sGpAN~~~~~~e~A~   48 (301)
T COG2971          20 VLADEDGNVLGRG-----KSGPANIQLVGKEEAV   48 (301)
T ss_pred             EEECCCCCEEEEE-----CCCCCEECCCCHHHHH
T ss_conf             9975897589775-----1688521356367899


No 184
>TIGR02279 PaaC-3OHAcCoADH 3-hydroxyacyl-CoA dehydrogenase PaaC; InterPro: IPR011967    This 3-hydroxyacyl-CoA dehydrogenase is involved in the degradation of phenylacetic acid, presumably in steps following the opening of the phenyl ring . The sequences included in this entry are all found in possible operons with other related genes such as paaA, paaB, paaD, paaE, paaF and paaN . Some genomes contain these other genes without an apparent paaC in the same operon - possibly in these cases a different dehydrogenase involved in fatty acid degradation may fill in the needed activity. .
Probab=38.06  E-value=14  Score=15.66  Aligned_cols=24  Identities=33%  Similarity=0.578  Sum_probs=19.5

Q ss_pred             EEEECCCCCCCCCCEEEECCCCEE
Q ss_conf             575345888858787981789746
Q gi|254780834|r   39 YWACCPFHDEKTPSFHCNDSKGFY   62 (648)
Q Consensus        39 ~~~~cPfh~ektpsf~v~~~~~~~   62 (648)
                      =||.-|-|-..||-|.||-==.=|
T Consensus       175 aWGK~PVh~~STPGFIVNRVARPy  198 (508)
T TIGR02279       175 AWGKQPVHARSTPGFIVNRVARPY  198 (508)
T ss_pred             HCCCCCCCCCCCCCCEECCCCCCH
T ss_conf             328856323469882342656731


No 185
>TIGR00422 valS valyl-tRNA synthetase; InterPro: IPR002303   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 .   Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=38.04  E-value=20  Score=14.43  Aligned_cols=121  Identities=12%  Similarity=0.190  Sum_probs=69.6

Q ss_pred             CEEEECCCCC---------CCC-CCEEEECCCCE--EEE--CCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH---CCCC
Q ss_conf             5575345888---------858-78798178974--671--36888878989989885999799999999981---8858
Q gi|254780834|r   38 DYWACCPFHD---------EKT-PSFHCNDSKGF--YYC--FSCHVKGDHLSFLSALLGCSFIESVQRLAAIA---GVPL  100 (648)
Q Consensus        38 ~~~~~cPfh~---------ekt-psf~v~~~~~~--~~c--f~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~---gi~~  100 (648)
                      -=+=+|||||         .+= |--+|-.++|.  =+|  |+.|.. +++..=-++.||+-.||=+.+-+..   |.-+
T Consensus       285 G~VKvTPAHD~ND~~~g~RH~LLe~i~~l~~dG~Lne~a~~~~tG~~-~~Y~iP~~y~GL~~~eAR~kiv~~L~~~glL~  363 (970)
T TIGR00422       285 GAVKVTPAHDFNDYEVGKRHNLLEFINILDEDGLLNENAEVIDTGKE-DVYAIPGEYQGLERFEARKKIVEDLKEEGLLV  363 (970)
T ss_pred             CEEEEECCCCCCCHHHCCEECCCCHHHHCCCCCCCCCEECEEECCCC-CCCCCCHHCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             12776087497760013412114143331799750110011007772-33106522058888999999999998668800


Q ss_pred             CCCCCCHHH--HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHH
Q ss_conf             776820367--778899999999999999999732677757899998506885351012442256774103455
Q gi|254780834|r  101 PVVDPKIEK--KEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREH  172 (648)
Q Consensus       101 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~  172 (648)
                      .. .+....  ...+-....+.+ ....||...=.  -...|++-+++-|         .+-|.|..|...+.+
T Consensus       364 k~-~p~~~~VG~c~Rsg~vvEP~-ls~QWFV~~~~--La~~a~~~~~~~g---------~~~fvP~~~~~~y~~  424 (970)
T TIGR00422       364 KI-EPHTHNVGHCERSGTVVEPL-LSKQWFVKVEK--LADKALEAAEEDG---------EIKFVPKRFEKRYLN  424 (970)
T ss_pred             CC-CEECCCCCEECCCCCEEECC-CCCCCEECHHH--HHHHHHHHHHHCC---------CCEEECHHHHHHHHH
T ss_conf             11-10003456214789343042-69986217177--7899999985458---------833602167889999


No 186
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=37.79  E-value=22  Score=13.93  Aligned_cols=26  Identities=31%  Similarity=0.727  Sum_probs=19.8

Q ss_pred             EECCCCCCCCCCEEEE-CCCCEEEECCCCCC
Q ss_conf             5345888858787981-78974671368888
Q gi|254780834|r   41 ACCPFHDEKTPSFHCN-DSKGFYYCFSCHVK   70 (648)
Q Consensus        41 ~~cPfh~ektpsf~v~-~~~~~~~cf~c~~~   70 (648)
                      -.|||..-++    |. -..++|.|=.||..
T Consensus        36 ~~Cp~C~~~~----VkR~a~GIW~C~kCg~~   62 (89)
T COG1997          36 HVCPFCGRTT----VKRIATGIWKCRKCGAK   62 (89)
T ss_pred             CCCCCCCCCC----EEEECCCEEECCCCCCE
T ss_conf             7699789740----45523675871788873


No 187
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=37.78  E-value=21  Score=14.21  Aligned_cols=12  Identities=33%  Similarity=0.664  Sum_probs=7.1

Q ss_pred             CCCCHHHHHHCC
Q ss_conf             888888997203
Q gi|254780834|r  355 RGEDPDSFIRCY  366 (648)
Q Consensus       355 ~G~DPDe~ir~~  366 (648)
                      .|.||+.++..-
T Consensus        37 ~~ld~~~ll~~L   48 (216)
T TIGR03652        37 KGLDPDEILAEL   48 (216)
T ss_pred             CCCCHHHHHHHH
T ss_conf             498999999999


No 188
>PRK10992 cell morphogenesis/cell wall metabolism regulator; Provisional
Probab=37.71  E-value=21  Score=14.12  Aligned_cols=11  Identities=18%  Similarity=0.015  Sum_probs=6.2

Q ss_pred             CCCCHHHHHHC
Q ss_conf             88888899720
Q gi|254780834|r  355 RGEDPDSFIRC  365 (648)
Q Consensus       355 ~G~DPDe~ir~  365 (648)
                      .|.||+.++.+
T Consensus        44 ~~ld~~~l~~e   54 (220)
T PRK10992         44 KELDIDVIEAR   54 (220)
T ss_pred             CCCCHHHHHHH
T ss_conf             49899999999


No 189
>PRK09358 adenosine deaminase; Provisional
Probab=37.46  E-value=22  Score=13.89  Aligned_cols=27  Identities=33%  Similarity=0.383  Sum_probs=22.2

Q ss_pred             HHCCCCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             885999799999999981885877682
Q gi|254780834|r   79 ALLGCSFIESVQRLAAIAGVPLPVVDP  105 (648)
Q Consensus        79 ~~~~~~f~ea~~~la~~~gi~~~~~~~  105 (648)
                      +.+|.--+|.+..||.+.|+++|..+.
T Consensus        17 HL~Gsi~~etl~~la~~~~~~lp~~~~   43 (333)
T PRK09358         17 HLDGSLRPETILELARRNGIDLPATDI   43 (333)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCCCCCCH
T ss_conf             776888999999999982999997899


No 190
>PRK13782 phosphocarrier protein Chr; Provisional
Probab=37.24  E-value=23  Score=13.86  Aligned_cols=62  Identities=15%  Similarity=0.281  Sum_probs=40.5

Q ss_pred             HHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf             789885126818996178866225777888888777536973067525788888899720366889988641
Q gi|254780834|r  306 QLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE  377 (648)
Q Consensus       306 ~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~  377 (648)
                      =++...+|...|.+.+||..+--|..+..+-+   -...|-.|.|.  -+|.|-++-+     +++.+++++
T Consensus        22 lv~~a~~f~s~I~l~~~~~~~naKSil~lm~L---g~~~G~~i~i~--a~G~De~~Al-----~~l~~lie~   83 (85)
T PRK13782         22 FVQEANRFHADIFIEKDGKKVNAKSIMGLMSL---AIGTGSMITII--TEGSDEEEAL-----EALAAYVQE   83 (85)
T ss_pred             HHHHHHCCCCEEEEEECCEEECHHHHHHHHHC---CCCCCCEEEEE--EECCCHHHHH-----HHHHHHHHC
T ss_conf             99999728986999989999835829999851---77898999999--9788999999-----999999845


No 191
>KOG2802 consensus
Probab=37.22  E-value=13  Score=16.09  Aligned_cols=18  Identities=22%  Similarity=0.381  Sum_probs=8.0

Q ss_pred             CCCCCCEEEECCCCEEEECCCC
Q ss_conf             8858787981789746713688
Q gi|254780834|r   47 DEKTPSFHCNDSKGFYYCFSCH   68 (648)
Q Consensus        47 ~ektpsf~v~~~~~~~~cf~c~   68 (648)
                      .+|.|-|-|+.-.    ||+..
T Consensus        61 ~~k~~~l~vs~vp----s~sta   78 (503)
T KOG2802          61 KEKSQTLRVSKVP----SFSTA   78 (503)
T ss_pred             HCCCCEEEEECCC----CCCCC
T ss_conf             0578357851255----54336


No 192
>COG0018 ArgS Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=37.17  E-value=23  Score=13.85  Aligned_cols=49  Identities=27%  Similarity=0.233  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             79999999998477889999844300237998899999999999753889
Q gi|254780834|r  482 LREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKY  531 (648)
Q Consensus       482 ~~E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~  531 (648)
                      ..|+.|+..|..+|+++....+.+..- .....+..|....-.+|...+.
T Consensus       491 ~~E~~L~~~L~~fp~vl~~aa~~~~Ph-~la~YL~~LA~~Fn~fY~~~~V  539 (577)
T COG0018         491 LEERELVKKLLEFPEVLEEAAEELEPH-RLANYLYDLAGSFNSFYNACPV  539 (577)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHHHHHHHHCCC
T ss_conf             279999999998499999999856955-9999999999999999850877


No 193
>KOG2164 consensus
Probab=37.15  E-value=13  Score=16.06  Aligned_cols=17  Identities=18%  Similarity=0.303  Sum_probs=7.8

Q ss_pred             HHCCCCHHHHHHHHHCC
Q ss_conf             32136626789885126
Q gi|254780834|r  298 LGTALTEYQLRLLWKLS  314 (648)
Q Consensus       298 ~Gtalt~~~~~~l~r~~  314 (648)
                      ||-.|--.=+-..|++.
T Consensus       204 CGHiFC~~CiLqy~~~s  220 (513)
T KOG2164         204 CGHIFCGPCILQYWNYS  220 (513)
T ss_pred             CCCEEEHHHHHHHHHHH
T ss_conf             67331068999998553


No 194
>cd02001 TPP_ComE_PpyrDC Thiamine pyrophosphate (TPP) family, ComE and PpyrDC subfamily, TPP-binding module; composed of proteins similar to sulfopyruvate decarboxylase beta subunit (ComE) and phosphonopyruvate decarboxylase (Ppyr decarboxylase). Methanococcus jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits which, catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway.  Ppyr decarboxylase is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. Ppyr decarboxylase and ComDE require TPP and divalent metal cation cofactors.
Probab=36.81  E-value=16  Score=15.17  Aligned_cols=40  Identities=23%  Similarity=0.210  Sum_probs=21.1

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             8189961788662257778888887775369730675257888
Q gi|254780834|r  315 PRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGE  357 (648)
Q Consensus       315 ~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~  357 (648)
                      ++-|+|+|||.+=.-   ...+++..--.....+.++.|.++-
T Consensus        59 p~kVi~idGDGs~lM---~lg~LaTi~~~~~~nl~~ivlnN~~   98 (157)
T cd02001          59 SRKVIVVDGDGSLLM---NPGVLLTAGEFTPLNLILVVLDNRA   98 (157)
T ss_pred             CCCEEEEECCHHHHH---CCCHHHHHHHCCCCCEEEEEEECCC
T ss_conf             996899957558875---2461999986389887999997975


No 195
>PRK05627 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed
Probab=36.65  E-value=23  Score=13.85  Aligned_cols=39  Identities=26%  Similarity=0.170  Sum_probs=19.8

Q ss_pred             CCCCHHHHHCCCCHHHHHHHHHCCCEE-EEEECCCCCCHHHHHH
Q ss_conf             542113432136626789885126818-9961788662257778
Q gi|254780834|r  291 VQNVVSSLGTALTEYQLRLLWKLSPRI-VLCFDGDDPGLRAAYK  333 (648)
Q Consensus       291 ~~n~va~~Gtalt~~~~~~l~r~~~~v-vl~fDgD~AG~kAa~R  333 (648)
                      .-.+|+..|+.-|-+.-    +.+-++ +|=||+|-=|+.-...
T Consensus       230 ~y~gv~niG~rPTf~~~----~~~iE~hildf~~dlYg~~i~v~  269 (303)
T PRK05627        230 PYPGVANIGTRPTVDGG----RQLLEVHLLDFSGDLYGEHIAVE  269 (303)
T ss_pred             EEEEEEEECCCCCCCCC----CEEEEEEECCCCCCCCCCEEEEE
T ss_conf             78744440468844898----55899996478977089879999


No 196
>COG0066 LeuD 3-isopropylmalate dehydratase small subunit [Amino acid transport and metabolism]
Probab=36.51  E-value=21  Score=14.17  Aligned_cols=84  Identities=12%  Similarity=0.154  Sum_probs=46.1

Q ss_pred             EEEEEECCCCEEEEECCCCCCCC--CCEECCCCCCCCCCCCHHCCCHHHHH---H-HHHHHHCCCCCCCCCCEEEEECCH
Q ss_conf             88897077858885010014655--30010387676535210110817888---8-643310000235678708997143
Q gi|254780834|r  207 IFPIRSSRGQVIAFGGRTLSKGE--SVKYLNSPETILFHKGKNLYNFFGAL---N-YLQKSIRKDVRRNSSSFIILVEGY  280 (648)
Q Consensus       207 ~fPi~~~~g~~i~f~gR~l~~~~--~~KYlNSpeT~if~K~~~Ly~l~~a~---~-~~~~~~~~~~~~~~~~~~i~vEGy  280 (648)
                      |-++.-..|+++-|+.--+|.|.  +.+||.+-+-.-|-|  .+|  +..|   + ...+..+     -..+.++|+---
T Consensus         1 m~~f~~~~G~~~pl~~dnIDTD~IIP~~fLk~i~~~gl~k--~~f--~~~r~~~PdF~~n~~~-----yq~g~IlVag~N   71 (191)
T COG0066           1 MEKFTKITGRVWPLGRDNVDTDQIIPKRFLKTITRTGLGK--HLF--EDWRYLDPDFVLNVPP-----YQGGDILVAGEN   71 (191)
T ss_pred             CCCEEEEEEEEEECCCCCCCCCCCCCHHHHCCCCHHHHHH--CCC--CCCCCCCCCHHHCCCC-----CCCCCEEEECCC
T ss_conf             9853888525970688877604386288745368746642--153--1010249643215886-----678648996688


Q ss_pred             --------HHHHHHHHCCCCCCHHHHH
Q ss_conf             --------8899987435542113432
Q gi|254780834|r  281 --------MDVLSLCQAGVQNVVSSLG  299 (648)
Q Consensus       281 --------~Dvi~l~~~G~~n~va~~G  299 (648)
                              --+++|..+||..|||++-
T Consensus        72 FGcGSSREHApwALk~~Gi~~VIA~SF   98 (191)
T COG0066          72 FGCGSSREHAPWALKDYGIRAVIAPSF   98 (191)
T ss_pred             CCCCCCHHHHHHHHHHCCEEEEEECCH
T ss_conf             778852778999999759249993629


No 197
>pfam08271 TF_Zn_Ribbon TFIIB zinc-binding. The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.
Probab=36.43  E-value=23  Score=13.76  Aligned_cols=26  Identities=23%  Similarity=0.562  Sum_probs=21.1

Q ss_pred             ECCCCCCCCCCEEEECCCCEEEECCCCC
Q ss_conf             3458888587879817897467136888
Q gi|254780834|r   42 CCPFHDEKTPSFHCNDSKGFYYCFSCHV   69 (648)
Q Consensus        42 ~cPfh~ektpsf~v~~~~~~~~cf~c~~   69 (648)
                      .||....  +++..++++|-+-|-.||.
T Consensus         2 ~Cp~Cg~--~~~~~D~~~Ge~vC~~CG~   27 (40)
T pfam08271         2 KCPNCGS--TEIVFDYERGEYVCTECGL   27 (40)
T ss_pred             CCCCCCC--CCEEEECCCCCEECCCCCE
T ss_conf             3887999--7067727789787057971


No 198
>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=36.26  E-value=23  Score=13.74  Aligned_cols=83  Identities=25%  Similarity=0.318  Sum_probs=58.4

Q ss_pred             CC-CCEEEEECCHHHHHHHHHCC--------CCCCHHHHHCCCCHHHHH---HHH----HC----CCEEEEEECCCCCCH
Q ss_conf             67-87089971438899987435--------542113432136626789---885----12----681899617886622
Q gi|254780834|r  269 NS-SSFIILVEGYMDVLSLCQAG--------VQNVVSSLGTALTEYQLR---LLW----KL----SPRIVLCFDGDDPGL  328 (648)
Q Consensus       269 ~~-~~~~i~vEGy~Dvi~l~~~G--------~~n~va~~Gtalt~~~~~---~l~----r~----~~~vvl~fDgD~AG~  328 (648)
                      ++ ++.+-|||-.=||.++-+.+        ..+++||| +...++|++   +++    |+    .++|||++|.=-.|-
T Consensus        79 Rde~s~iCvV~~p~Dv~a~E~~~~f~G~YhVL~G~isPl-~Gigp~~~~i~~L~~riGeRl~~~~~~EVIlA~nPt~EGe  157 (205)
T TIGR00615        79 RDENSVICVVEDPKDVFALEKTKEFRGRYHVLGGLISPL-DGIGPEDLKIAALLKRIGERLQEESVKEVILATNPTVEGE  157 (205)
T ss_pred             CCCCCEEEEECCHHHHHHHHHHHHHCCCEEEECCEECCC-CCCCCCCCCHHHHHHHHHCCCCCCCCCEEEEECCCCCHHH
T ss_conf             344753687447267999876542166014315641764-5768322146889988600000057977886078984134


Q ss_pred             HHHHHHHHHHHHHHHCCC-CEEEEECCCC
Q ss_conf             577788888877753697-3067525788
Q gi|254780834|r  329 RAAYKAIDLVLCHLIPGN-RVNFVLLSRG  356 (648)
Q Consensus       329 kAa~Ra~e~~l~~l~~g~-~v~vv~LP~G  356 (648)
                      .-|+=..++    +++-. .|+|-.+-.|
T Consensus       158 aTa~Yi~~~----l~~~fP~~~~tRiA~G  182 (205)
T TIGR00615       158 ATALYIARL----LRPLFPGVKVTRIASG  182 (205)
T ss_pred             HHHHHHHHH----HHHCCCCCEEEEEEEC
T ss_conf             799999999----8623898378655422


No 199
>COG1794 RacX Aspartate racemase [Cell envelope biogenesis, outer membrane]
Probab=36.19  E-value=23  Score=13.73  Aligned_cols=50  Identities=24%  Similarity=0.136  Sum_probs=29.4

Q ss_pred             HHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             874355421134321366267898851268189961788662257778888
Q gi|254780834|r  286 LCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAID  336 (648)
Q Consensus       286 l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e  336 (648)
                      .-.+|++ .|+.|||.+|-+|----+|+..+=+=..=.|+++|.+..|.+-
T Consensus       112 ik~~g~k-kvgLLgT~~Tm~~~fY~~~l~~~gievvvPdd~~q~~v~~iIy  161 (230)
T COG1794         112 IKAAGAK-KVGLLGTRFTMEQGFYRKRLEEKGIEVVVPDDDEQAEVNRIIY  161 (230)
T ss_pred             HHHCCCC-EEEEEECCCHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHH
T ss_conf             8765886-1588613005776899999997796475677788999999999


No 200
>pfam03405 FA_desaturase_2 Fatty acid desaturase.
Probab=36.13  E-value=23  Score=13.72  Aligned_cols=14  Identities=36%  Similarity=0.126  Sum_probs=8.0

Q ss_pred             CCCCHHHHHHHHHC
Q ss_conf             13662678988512
Q gi|254780834|r  300 TALTEYQLRLLWKL  313 (648)
Q Consensus       300 talt~~~~~~l~r~  313 (648)
                      ||=-.-|--+|.+|
T Consensus       108 TAEEnRHg~~Lr~Y  121 (330)
T pfam03405       108 TAEENRHGDLLNKY  121 (330)
T ss_pred             CCCCCHHHHHHHHH
T ss_conf             64434147899765


No 201
>PTZ00317 malic enzyme; Provisional
Probab=35.98  E-value=24  Score=13.70  Aligned_cols=66  Identities=17%  Similarity=0.079  Sum_probs=31.9

Q ss_pred             CCCCCCHHHHHCCC-CHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHH-HHHHHHHCC-CCEEEEECCCC
Q ss_conf             35542113432136-6267898851268189961788662257778888-887775369-73067525788
Q gi|254780834|r  289 AGVQNVVSSLGTAL-TEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAID-LVLCHLIPG-NRVNFVLLSRG  356 (648)
Q Consensus       289 ~G~~n~va~~Gtal-t~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e-~~l~~l~~g-~~v~vv~LP~G  356 (648)
                      .-+++++ ..---| +.+-.++|.||-++ +.||.-|-=|-.|..=|.- .++...... .+.+||+.-.|
T Consensus       235 ~~~P~~l-iqfEDF~~~nA~~lL~~Yr~~-~~~FNDDiQGTaaV~LAgll~Alritg~~l~d~riv~~GAG  303 (570)
T PTZ00317        235 ATWPSAV-VQFEDFSNNHCFDMLERYQKK-YRCFNDDIQGTGAVIAAGFLNAVKLSGVPPLEQRIVFFGAG  303 (570)
T ss_pred             HHCCCEE-EEECCCCCHHHHHHHHHHHHC-CCEECCCCHHHHHHHHHHHHHHHHHHCCCHHHCEEEEECCC
T ss_conf             8789828-972448954489999999853-76421442138899999999999984998646179997788


No 202
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=35.93  E-value=24  Score=13.70  Aligned_cols=49  Identities=22%  Similarity=0.356  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999872412798999999999999999999988413267621
Q gi|254780834|r  590 LLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIEGF  641 (648)
Q Consensus       590 ~L~r~l~ele~~l~e~~~~~d~e~~~~l~~el~elk~~L~~l~~~Eal~e~~  641 (648)
                      .+..++.++++++.+   +.|+--+-+|+++.+|+..-+.+++.-|+.+.-.
T Consensus        99 ~~~~Rl~~LE~qL~q---KADDVVSyQLLqHRrEiEEm~~~lq~Le~ri~kl  147 (178)
T PRK13182         99 TITRRLDELEEQLQQ---KADDVVSYQLLQHRREMEEMLERIQKLEARLKKL  147 (178)
T ss_pred             HHHHHHHHHHHHHHH---HCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999986---4232001899987999999999999999999986


No 203
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=35.83  E-value=19  Score=14.48  Aligned_cols=52  Identities=27%  Similarity=0.369  Sum_probs=25.1

Q ss_pred             HHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHC---CC-CHHHHH
Q ss_conf             12221015887777755753458888587879817897467136888878989989885---99-979999
Q gi|254780834|r   23 QYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALL---GC-SFIESV   89 (648)
Q Consensus        23 ~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~---~~-~f~ea~   89 (648)
                      +|--|+..|..+     -...++-+++        +.|+|+|-+||.-  .|+--.+++   |. +|.+++
T Consensus        18 ~y~V~r~~gTE~-----pfsg~y~~~~--------~~G~Y~C~~Cg~~--LF~S~~KfdSg~GWPSF~~~i   73 (141)
T PRK00222         18 QYRVTQEHGTER-----PFTGEYLDNK--------RKGIYVCIVCGEP--LFSSDTKFDSGCGWPSFTKPI   73 (141)
T ss_pred             HHHHHHHCCCCC-----CCCCCCCCCC--------CCEEEEECCCCCE--EEECCCCCCCCCCCCHHHHHC
T ss_conf             999998659889-----9887775888--------9989984699898--441155147999872031224


No 204
>PRK11020 hypothetical protein; Provisional
Probab=35.68  E-value=24  Score=13.67  Aligned_cols=39  Identities=18%  Similarity=0.330  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999872412798999999999999999999988
Q gi|254780834|r  594 QKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIE  632 (648)
Q Consensus       594 ~l~ele~~l~e~~~~~d~e~~~~l~~el~elk~~L~~l~  632 (648)
                      ++.....++..+...+|.+.+.+...++..+.+++.+++
T Consensus        13 rLD~~r~Klaaa~~rgd~~~i~qf~~E~~~l~k~I~~lk   51 (118)
T PRK11020         13 RLDAIRHKLAAASLRGDADKIAQFEKEKATLEKEIARLK   51 (118)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999988999974788999999999999999999998


No 205
>PRK10076 pyruvate formate lyase II activase; Provisional
Probab=35.65  E-value=24  Score=13.66  Aligned_cols=80  Identities=15%  Similarity=0.077  Sum_probs=52.0

Q ss_pred             HHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHH------HHHHHHHHHHHHCCC--CEEEEECCCC
Q ss_conf             98743554211343213662678988512681899617886622577------788888877753697--3067525788
Q gi|254780834|r  285 SLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAA------YKAIDLVLCHLIPGN--RVNFVLLSRG  356 (648)
Q Consensus       285 ~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa------~Ra~e~~l~~l~~g~--~v~vv~LP~G  356 (648)
                      .+++.||..+|=|+|.+ ..+.+..+..+++-+.+.+-.=+.-..-.      .+.++.+.-+.+.|.  -+|++.+|.=
T Consensus        62 ~~k~~gihtaieTsG~~-~~~~~~~~~~~~Dl~L~DiK~~d~~~h~~~TG~~n~~il~Nl~~l~~~~~~v~iR~pvIPg~  140 (213)
T PRK10076         62 RLRLWGVSCAIETAGDA-PASKLLPLAKLCDEVLFDLKIMDATQARDVVKMNLPRVLENLRLLVSEGVNVIPRLPLIPGF  140 (213)
T ss_pred             HHHHCCCCEEEECCCCC-CHHHHHHHHHHCCEEEEEECCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEEEEEEECCC
T ss_conf             99866998899768888-89999999984598998617798489999979993999999999996799689988677997


Q ss_pred             CCHHHHHHC
Q ss_conf             888899720
Q gi|254780834|r  357 EDPDSFIRC  365 (648)
Q Consensus       357 ~DPDe~ir~  365 (648)
                      -|=++-++.
T Consensus       141 nd~~e~i~~  149 (213)
T PRK10076        141 TLSRENMQQ  149 (213)
T ss_pred             CCCHHHHHH
T ss_conf             899999999


No 206
>TIGR01969 minD_arch cell division ATPase MinD; InterPro: IPR010224   Proper placement of the bacterial cell division site requires the site-specific inactivation of other potential division sites. In Escherichia coli, selection of the correct mid-cell site is mediated by the MinC, MinD and MinE proteins. Several members of this family are found in archaeal genomes but their function is uncharacterised. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins.    This entry represents the archaeal MinD family. The exact roles of the various archaeal MinD homologs are unknown. .
Probab=35.40  E-value=15  Score=15.50  Aligned_cols=122  Identities=18%  Similarity=0.234  Sum_probs=68.0

Q ss_pred             CCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHH---------------------HCCCC-
Q ss_conf             55421134321366267898851268189961788662257778888887775---------------------36973-
Q gi|254780834|r  290 GVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHL---------------------IPGNR-  347 (648)
Q Consensus       290 G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l---------------------~~g~~-  347 (648)
                      |=+.+.|+||+||.+-         -+=|+..|||=|     +-=+++.|-+-                     +--.. 
T Consensus        13 GKTT~tANLgVALA~~---------Gk~V~~~DADI~-----MANL~LiLgmE~~~VTLhDVLAGeA~i~DAIY~gp~Gn   78 (258)
T TIGR01969        13 GKTTITANLGVALAKL---------GKKVLVLDADIT-----MANLELILGMEDKPVTLHDVLAGEADIKDAIYEGPEGN   78 (258)
T ss_pred             CHHHEEEHHHHHHHHC---------CCEEEEEECCHH-----HHHHHHHHCCCCCCCCCCCCCCCCCCHHHHCCCCCCCC
T ss_conf             6140000077889860---------976899946766-----77689884468889675221344561001100288984


Q ss_pred             EEEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHH-HHHHHHCCCCCHHHHHHHHHH---HHHHHHHCCCHHHHHH
Q ss_conf             067525788888899720366889988641499279999-999853023314579999999---9988541799899999
Q gi|254780834|r  348 VNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLW-KRETENRSFNTPDERAELEIH---LKNCINHIKDQKLRYY  423 (648)
Q Consensus       348 v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~-~~l~~~~dl~spe~ka~~~~~---l~~~I~~I~d~~~R~~  423 (648)
                      |+|  +|.|.+=--|-|.+ +|-+++.+++=....||++ |. =-+-..+...-.+...+-   +.|-|+.|.|...-. 
T Consensus        79 V~V--~PagvSLEg~rKA~-~~~L~dV~~~i~~~~D~lLIDA-PAGL~~~a~~Al~~a~elLLVvNPEi~SItDaLK~k-  153 (258)
T TIGR01969        79 VKV--IPAGVSLEGLRKAD-PDKLEDVLKEIIDDTDFLLIDA-PAGLERDAVTALAAADELLLVVNPEISSITDALKVK-  153 (258)
T ss_pred             EEE--ECCCCCHHHCCCCC-HHHHHHHHHHHHCCCCEEEEEC-CCCCCHHHHHHHHHCCCCEEEECCCHHHHHHHHHHH-
T ss_conf             478--50612210001268-3332899998720437788747-898337899999861866486676544677788999-


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999988
Q gi|254780834|r  424 YSQAIRDRLQ  433 (648)
Q Consensus       424 yl~~la~~L~  433 (648)
                         .++++++
T Consensus       154 ---~va~~lG  160 (258)
T TIGR01969       154 ---IVAEKLG  160 (258)
T ss_pred             ---HHHHHCC
T ss_conf             ---9987608


No 207
>pfam08348 PAS_6 YheO-like PAS domain. This family contains various hypothetical bacterial proteins that are similar to the E. coli protein YheO. Their function is unknown, but are likely to be involved in signalling based on the presence of this PAS domain.
Probab=35.24  E-value=24  Score=13.61  Aligned_cols=55  Identities=20%  Similarity=0.205  Sum_probs=29.1

Q ss_pred             CCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEE
Q ss_conf             4422567741034554205997345232012100346541000016716888970778588850
Q gi|254780834|r  158 KLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFG  221 (648)
Q Consensus       158 ~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~  221 (648)
                      ++| +|.. +...+.+.+..+..+.+  .+....+.+|+..     .-..|+|+|..|++||.=
T Consensus        46 ~vG-~p~t-~~~l~~l~~~~~~~~~~--~~Y~~~~~dGr~l-----kSsT~~ird~~g~~iG~L  100 (118)
T pfam08348        46 KVG-DPIT-DLALELLKEDESEEDVL--GNYETRTADGRLL-----KSSTIVIRDSDGKPIGML  100 (118)
T ss_pred             CCC-CCCC-HHHHHHHHCCCCCCCCC--CCCEEECCCCCEE-----EEEEEEEECCCCCEEEEE
T ss_conf             679-8616-89999986445467725--2640277999899-----999999999999999999


No 208
>pfam00500 Late_protein_L1 L1 (late) protein.
Probab=35.19  E-value=24  Score=13.61  Aligned_cols=24  Identities=33%  Similarity=0.673  Sum_probs=10.1

Q ss_pred             CCCCCCCEEEEEEEE---CCCCEEEEE
Q ss_conf             000016716888970---778588850
Q gi|254780834|r  198 SYDRFRNRLIFPIRS---SRGQVIAFG  221 (648)
Q Consensus       198 ~~d~Fr~Ri~fPi~~---~~g~~i~f~  221 (648)
                      .||.=+.|+++-++-   .+|+..|.|
T Consensus        90 ~ynPe~eRLVW~l~Giei~RG~PLGvg  116 (503)
T pfam00500        90 LYNPDKERLVWACRGVEVGRGQPLGVG  116 (503)
T ss_pred             CCCCCCCEEEEEEEEEEECCCCCCCCC
T ss_conf             779875467778888982378888127


No 209
>TIGR00963 secA preprotein translocase, SecA subunit; InterPro: IPR000185   Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component. . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.     The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB  is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion .   SecA is a cytoplasmic protein of 800 to 960 amino acid residues. Homologs of secA are also encoded in the chloroplast genome of some algae  as well as in the nuclear genome of plants . It could be involved in the intraorganellar protein transport into thylakoids.; GO: 0005524 ATP binding, 0006605 protein targeting, 0006886 intracellular protein transport.
Probab=35.13  E-value=24  Score=13.60  Aligned_cols=91  Identities=20%  Similarity=0.270  Sum_probs=44.3

Q ss_pred             CCCEECCCC----CCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCC-CCEECCCCCCCCCCCCHHCCCHH-----HHHH
Q ss_conf             121003465----4100001671688897077858885010014655-30010387676535210110817-----8888
Q gi|254780834|r  187 GLLIDGDNS----ATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGE-SVKYLNSPETILFHKGKNLYNFF-----GALN  256 (648)
Q Consensus       187 gl~~~~~~~----~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~-~~KYlNSpeT~if~K~~~Ly~l~-----~a~~  256 (648)
                      |+-+.+++-    =.|.-+|   .|||      +.-|.+|-+.++.. --|               .|+|.     ..|+
T Consensus       348 ~V~I~~En~T~AtITyQNfF---rlY~------KLsGMTGTA~TE~~EF~~---------------IYnL~Vv~vPTNrp  403 (904)
T TIGR00963       348 GVEIQNENQTLATITYQNFF---RLYE------KLSGMTGTAKTEEEEFEK---------------IYNLEVVVVPTNRP  403 (904)
T ss_pred             CCEEECCCCEEEEHHHHHHH---HHHH------HHCCCCCCHHHHHHHHHC---------------CCCCEEEECCCCCC
T ss_conf             86010355224404457676---5426------544687756899998404---------------57751355166772


Q ss_pred             HHHHHHCCCCCCCCCCEEEEECCH------HHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHC
Q ss_conf             643310000235678708997143------889998743554211343213662678988512
Q gi|254780834|r  257 YLQKSIRKDVRRNSSSFIILVEGY------MDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKL  313 (648)
Q Consensus       257 ~~~~~~~~~~~~~~~~~~i~vEGy------~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~  313 (648)
                      .+|+.        ..|.|+..|=-      -||..+|+.|=|-=|.|-    +-+.-.+|.++
T Consensus       404 ~~R~D--------~~DlvY~te~~Kw~Av~~e~~~~h~~GqPvLvGT~----svE~SE~LS~l  454 (904)
T TIGR00963       404 VIRKD--------LPDLVYKTEEEKWKAVVDEIKEIHAKGQPVLVGTT----SVEKSELLSKL  454 (904)
T ss_pred             CCCCC--------CCCCEECCHHHHHHHHHHHHHHHHHCCCCEEEEEC----CHHHHHHHHHH
T ss_conf             34467--------77734647688999999999998746898777522----17778999999


No 210
>PRK01143 rpl11p 50S ribosomal protein L11P; Validated
Probab=35.04  E-value=24  Score=13.59  Aligned_cols=63  Identities=21%  Similarity=0.262  Sum_probs=42.0

Q ss_pred             CCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHH-HHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf             36626789885126818996178866225777888-888777536973067525788888899720366889988641
Q gi|254780834|r  301 ALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAI-DLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE  377 (648)
Q Consensus       301 alt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~-e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~  377 (648)
                      .+|-+|+..|.+.-..     |--..-.+++.|.+ -.|.++   |+.|      +|+||-|.++.-...+|.+++..
T Consensus        96 ~is~~qv~eIAk~K~~-----dl~~~~l~~a~k~V~GTarSm---Gi~V------eG~~Pkev~~~i~~G~~d~~~~~  159 (163)
T PRK01143         96 NLSIEQVIKIAIMKKP-----DLLAYDLKAAVKEVLGTCVSM---GVTV------EGKDPKEVQKEVDEGKYDDLLAK  159 (163)
T ss_pred             CCCHHHHHHHHHHHCC-----CCCCCCHHHHHHHHHHHHHCC---EEEE------ECCCHHHHHHHCCCCCHHHHHHH
T ss_conf             2379999999998573-----547899999999999876135---4898------57798999987176327799986


No 211
>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=34.96  E-value=18  Score=14.66  Aligned_cols=59  Identities=24%  Similarity=0.312  Sum_probs=30.4

Q ss_pred             CCCCCEEEECCCCCCCC------CCEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCC
Q ss_conf             77775575345888858------787981789746713688887898998988599979999999998188
Q gi|254780834|r   34 AVKGDYWACCPFHDEKT------PSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGV   98 (648)
Q Consensus        34 ~~~~~~~~~cPfh~ekt------psf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~gi   98 (648)
                      +...++|-.|||+.++|      ||+....  ..--|=+||..-.-   +|+. +++..+=.+.=+++.||
T Consensus       685 Cgk~s~~~~Cp~CG~~te~~~~gPsCrmkn--tssvCesCGreCeG---ymkr-k~~L~~l~~~A~~nlg~  749 (1173)
T TIGR00354       685 CGKESLYRVCPVCGEKTELDEYGPSCRMKN--TSSVCESCGRECEG---YMKR-KVDLKELYKEALKNLGV  749 (1173)
T ss_pred             CCCCCEEEECCCCCCEEEECCCCCCCCCCC--CCCHHHCCCCCCCC---CEEE-CCCHHHHHHHHHHHCCC
T ss_conf             664000014577885454457788530035--42022105754453---1121-14389999999985752


No 212
>pfam06246 Isy1 Isy1-like splicing family. Isy1 protein is important in the optimisation of splicing.
Probab=34.72  E-value=24  Score=13.55  Aligned_cols=53  Identities=17%  Similarity=0.313  Sum_probs=41.3

Q ss_pred             CCCCHHH-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2331457-9999999998854179989999999999999887657767764332
Q gi|254780834|r  394 SFNTPDE-RAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHSGY  446 (648)
Q Consensus       394 dl~spe~-ka~~~~~l~~~I~~I~d~~~R~~yl~~la~~L~~~~~~~~~~~~~~  446 (648)
                      ++...+. |..++++|-..|+.|.|+.+=++-++++.+.++.+++.-..-....
T Consensus        42 ~L~~AekWR~~vikEIs~kvt~Iqn~~L~e~~iRdLNDeiNkL~rEK~~WE~~I   95 (253)
T pfam06246        42 SLPEAEKWRSQVIKEISRKVTEIQDPSLGEYQIRDLNDEINKLFREKRHWEDRI   95 (253)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999999999999999888831899777899999999999999999999999


No 213
>TIGR00010 TIGR00010 hydrolase, TatD family; InterPro: IPR015991   Escherichia coli TatD (synonym MttC) has been shown experimentally to be a DNase . On the basis of operon structure, it was originally thought to be involved in the Sec-independent export of protein precursors bearing twin arginine signal peptides by the Tat system . This alternative membrane targeting and translocation system (Mtt), also called twin arginine translocase (Tat) (MttA1A2BC or TatABCD), has been shown to transport fully folded proteins to, or across, the membrane , . However, it was later determined that TatD is not required for this translocation process , . Furthermore, it was noted that no exact correlation exists between the ability of an organism to synthesise a TatD-like protein and whether that organism has a Tat protein transport pathway . Also, with the exception of Escherichia coli , the genetic linkage between TatD and other Tat genes (operon structure) is not maintained.  Members of this group may be distantly related to a large 3D fold-based domain superfamily of metalloenzymes . The description of this fold superfamily was based on an analysis of conservation patterns in three dimensions, and the discovery that the same active-site architecture occurs in a large set of enzymes involved primarily in nucleotide metabolism. The group is thought to include urease, dihydroorotase, allantoinase, hydantoinase, AMP-, adenine- and cytosine- deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolase, formylmethanofuran dehydrogenase, and other enzymes ..
Probab=34.56  E-value=17  Score=15.11  Aligned_cols=21  Identities=38%  Similarity=0.534  Sum_probs=10.2

Q ss_pred             HHHH-HHHCCCCCCHHHHHCCCC
Q ss_conf             8999-874355421134321366
Q gi|254780834|r  282 DVLS-LCQAGVQNVVSSLGTALT  303 (648)
Q Consensus       282 Dvi~-l~~~G~~n~va~~Gtalt  303 (648)
                      +||. +.+.|++.+|++ ||.+.
T Consensus        22 ~v~~ra~~~~v~~~v~v-g~~l~   43 (269)
T TIGR00010        22 EVIERAKAEGVTAVVDV-GTDLE   43 (269)
T ss_pred             HHHHHHHHCCCEEEEEE-CCCCC
T ss_conf             99999997499299973-46700


No 214
>PRK13520 L-tyrosine decarboxylase; Provisional
Probab=34.53  E-value=25  Score=13.52  Aligned_cols=50  Identities=26%  Similarity=0.172  Sum_probs=22.8

Q ss_pred             CCHHHHHHHHHCCCCC---CHHHHHCCCCH--HHHHHHHHCCCE--EEEEECCCCCC
Q ss_conf             1438899987435542---11343213662--678988512681--89961788662
Q gi|254780834|r  278 EGYMDVLSLCQAGVQN---VVSSLGTALTE--YQLRLLWKLSPR--IVLCFDGDDPG  327 (648)
Q Consensus       278 EGy~Dvi~l~~~G~~n---~va~~Gtalt~--~~~~~l~r~~~~--vvl~fDgD~AG  327 (648)
                      +|-||+-.+..+==+|   +||+.||-.|-  +-+..|..++.+  +.|=-||=-.|
T Consensus       140 ~~~~d~~~l~~~i~~~ti~vvatagtt~~G~iDpi~~i~~i~~~~~i~lHVDaa~GG  196 (375)
T PRK13520        140 DYRVDVKSVEDLIDDNTIGIVGIAGTTELGQVDPIPELSKIALENDIFLHVDAAFGG  196 (375)
T ss_pred             CCCCCHHHHHHHHHHCCEEEEEECCCCCCEEECCHHHHHHHHHHCCCEEEEECCCCE
T ss_conf             886989999998864957999925887882235999999999975974998625520


No 215
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=34.51  E-value=22  Score=14.02  Aligned_cols=40  Identities=20%  Similarity=0.300  Sum_probs=24.7

Q ss_pred             HHHHHHH-HCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHH
Q ss_conf             7899998-50688535101244225677410345542059973452
Q gi|254780834|r  139 RLHYYLD-ERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKI  183 (648)
Q Consensus       139 ~a~~yl~-~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~  183 (648)
                      +-++||. .||+++.|++.|.-..     ..+..|+..++.+.+.+
T Consensus         8 ~fl~~L~~erg~S~~Ti~~Y~~~l-----~~f~~~l~~~~~~~~~i   48 (296)
T PRK00283          8 QFLDALWVERGLAENTLSSYRRDL-----ELFAEWLAARGLSLAEA   48 (296)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHH-----HHHHHHHHHCCCCHHHC
T ss_conf             999999998790799999999999-----99999998759994779


No 216
>COG5328 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.35  E-value=23  Score=13.78  Aligned_cols=106  Identities=18%  Similarity=0.312  Sum_probs=54.1

Q ss_pred             CCHHHHHHHCCCEECCCCCCCCCC----CCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHH
Q ss_conf             973452320121003465410000----1671688897077858885010014655300103876765352101108178
Q gi|254780834|r  178 FSEEKIIEAGLLIDGDNSATSYDR----FRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFG  253 (648)
Q Consensus       178 ~~~~~~~~~gl~~~~~~~~~~~d~----Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~  253 (648)
                      +..-++++-+.|-+-..+.++|+-    --.|++|.|..+.|.-++-                          ++.-|..
T Consensus        33 VAIFDLiEeN~FeP~~~~~GPYrl~lSL~e~rLvF~i~~e~g~~v~t--------------------------HiLSLtP   86 (160)
T COG5328          33 VAIFDLIEENSFEPVGHGGGPYRLKLSLVEARLVFAIAREGGTAVAT--------------------------HILSLTP   86 (160)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCHHHHH--------------------------HHHCCCC
T ss_conf             68988762036554778999767774402004356751168606777--------------------------6331470


Q ss_pred             HHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCHHHHHC-CCCHHHHH-HHHHCCCEEEEEEC
Q ss_conf             88864331000023567870899714388999874355421134321-36626789-88512681899617
Q gi|254780834|r  254 ALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGT-ALTEYQLR-LLWKLSPRIVLCFD  322 (648)
Q Consensus       254 a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gt-alt~~~~~-~l~r~~~~vvl~fD  322 (648)
                      -+..+            ++++++||.|.++|.-..-.--.++ -||- .+-.+--+ +..|+..+|-+-||
T Consensus        87 fRriv------------kDYfmICeSYY~AIRsstPsqIEAi-DMGRRGlHNeGSqtL~dRL~GKi~~DfD  144 (160)
T COG5328          87 FRRIV------------KDYFMICESYYQAIRSSTPSQIEAI-DMGRRGLHNEGSQTLMDRLSGKIKVDFD  144 (160)
T ss_pred             HHHHH------------HHHHHHHHHHHHHHHHCCHHHHHHH-HHCCCCCCCCCHHHHHHHHCCCEEECHH
T ss_conf             88888------------7898879999999970887664576-5112224451078999986496441428


No 217
>TIGR01426 MGT glycosyltransferase, MGT family; InterPro: IPR006326   These sequences belong to the MGT (macroside glycosyltransferase) subfamily of the UDP-glucuronosyltransferase family. Members include a number of glucosyl transferases for macrolide antibiotic inactivation, but also include transferases of glucose-related sugars for macrolide antibiotic production. ; GO: 0016758 transferase activity transferring hexosyl groups, 0016999 antibiotic metabolic process.
Probab=34.19  E-value=25  Score=13.48  Aligned_cols=103  Identities=14%  Similarity=0.097  Sum_probs=52.5

Q ss_pred             CCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCC--EEEEECCCCCCHHHHHHCCCHHH
Q ss_conf             2113432136626789885126818996178866225777888888777536973--06752578888889972036688
Q gi|254780834|r  293 NVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNR--VNFVLLSRGEDPDSFIRCYGKTA  370 (648)
Q Consensus       293 n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~--v~vv~LP~G~DPDe~ir~~G~ea  370 (648)
                      -+..+|||+||..-.++.+-|                  .+|+.        +..  .=|+.+-.+.||++|=  .=++.
T Consensus       262 V~liSLGTvFn~~p~~fyr~f------------------~~AF~--------~~~GW~vV~~~g~~vDp~~L~--~~P~N  313 (429)
T TIGR01426       262 VVLISLGTVFNAQPSKFYRTF------------------VEAFR--------DLPGWHVVLSVGKGVDPADLG--ELPKN  313 (429)
T ss_pred             EEEEECCHHHCCCHHHHHHHH------------------HHHCC--------CCCCCEEEEEECCCCCHHHHC--CCCCC
T ss_conf             699975614412447999999------------------98608--------998707999726702646616--79887


Q ss_pred             HHHHHHHCCCHHHHHH--HHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             9988641499279999--9998530233145799999999988541799899999999999
Q gi|254780834|r  371 FEKLIVESLPLVDMLW--KRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIR  429 (648)
Q Consensus       371 f~~ll~~A~~l~dFl~--~~l~~~~dl~spe~ka~~~~~l~~~I~~I~d~~~R~~yl~~la  429 (648)
                      |  .+.+..|-.|.|=  +.......++|.   .+++..-.|++. ||-...+.+..+.++
T Consensus       314 v--~VR~~VPq~evL~~A~lfvTHgGmnSt---~EaL~~gVP~va-~P~~adQ~~~A~R~~  368 (429)
T TIGR01426       314 V--EVRRWVPQLEVLEKADLFVTHGGMNST---MEALAAGVPLVA-VPQGADQPMTARRIA  368 (429)
T ss_pred             E--EEECCCCHHHHHHHHHHHHHCCCCHHH---HHHHHCCCCEEE-ECCCCCCHHHHHHHH
T ss_conf             7--885465627789888888631660158---999964996898-517888013765751


No 218
>PRK09490 metH B12-dependent methionine synthase; Provisional
Probab=33.81  E-value=24  Score=13.63  Aligned_cols=63  Identities=13%  Similarity=0.176  Sum_probs=33.8

Q ss_pred             ECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH---CCCCCCCCCCHHHH-----HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             136888878989989885999799999999981---88587768203677-----788999999999999999997
Q gi|254780834|r   64 CFSCHVKGDHLSFLSALLGCSFIESVQRLAAIA---GVPLPVVDPKIEKK-----EKIQTDLIRLIEVATDFFHHS  131 (648)
Q Consensus        64 cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~---gi~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~  131 (648)
                      .+.|.-.|+     -++-|++-||.|+.+-..|   |-++=+.++....+     .......++++..+++.-+..
T Consensus        48 ~~~~~l~g~-----~e~Lnlt~Pd~I~~IH~~YleAGaDiIeTNTFgan~~~l~~ygle~~v~ein~~aa~lAr~a  118 (1229)
T PRK09490         48 DWPCDLKGN-----NDLLVLTQPDVIEAIHRAYLEAGADIIETNTFNATTIAQADYGMESLVYELNVEAARLAREA  118 (1229)
T ss_pred             CCCCCCCCC-----CCHHHCCCHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf             475435698-----20523588899999999999836999983699888424544593778999999999999999


No 219
>pfam03393 Pneumo_matrix Pneumovirus matrix protein.
Probab=33.70  E-value=16  Score=15.34  Aligned_cols=16  Identities=13%  Similarity=0.169  Sum_probs=7.3

Q ss_pred             CCCCHHHHHHHCCCEE
Q ss_conf             5997345232012100
Q gi|254780834|r  176 KGFSEEKIIEAGLLID  191 (648)
Q Consensus       176 ~~~~~~~~~~~gl~~~  191 (648)
                      .|.+....++..|+-+
T Consensus        10 ~GvpYTAAVQ~~lvEK   25 (252)
T pfam03393        10 EGSPYTAAVQYNVLEK   25 (252)
T ss_pred             CCCCCEEEEEEEEEEC
T ss_conf             5875013788513413


No 220
>TIGR03287 methan_mark_16 putative methanogenesis marker 16 metalloprotein. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This protein is a predicted to bind FeS clusters, based on the presence of two copies of the Fer4 domain (pfam00037), with each copy having four Cys residues invariant across all members.
Probab=33.62  E-value=16  Score=15.26  Aligned_cols=12  Identities=42%  Similarity=0.255  Sum_probs=4.8

Q ss_pred             CCHHHHHHHHHC
Q ss_conf             662678988512
Q gi|254780834|r  302 LTEYQLRLLWKL  313 (648)
Q Consensus       302 lt~~~~~~l~r~  313 (648)
                      |+++.+.-+...
T Consensus       253 Lneev~~~~~v~  264 (391)
T TIGR03287       253 LSEEVLENLKVL  264 (391)
T ss_pred             CCHHHHHHHCCC
T ss_conf             699999860575


No 221
>PTZ00124 adenosine deaminase; Provisional
Probab=33.54  E-value=25  Score=13.40  Aligned_cols=125  Identities=10%  Similarity=0.028  Sum_probs=64.8

Q ss_pred             EECCCCEEEECCCCCCCCHHHHHHHH---------CCCCHHHHHHHHHHHHCCCCCCCCCCHHHHH---HHHHHHHHHHH
Q ss_conf             81789746713688887898998988---------5999799999999981885877682036777---88999999999
Q gi|254780834|r   55 CNDSKGFYYCFSCHVKGDHLSFLSAL---------LGCSFIESVQRLAAIAGVPLPVVDPKIEKKE---KIQTDLIRLIE  122 (648)
Q Consensus        55 v~~~~~~~~cf~c~~~gd~~~f~~~~---------~~~~f~ea~~~la~~~gi~~~~~~~~~~~~~---~~~~~~~~~~~  122 (648)
                      |-|.-.+---|+|=..-+++.|+.++         +|-=-++.+..||.+.|++++.........-   ..-..+.+.++
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~k~LPKvELH~HLdGslrp~tl~eLA~~~~i~~~~~~~e~~~~~~~~~~~~sL~~fL~   89 (362)
T PTZ00124         10 VLPKDELNIDLSKMGKKERYKIWKRMPKCELHCHLDICFSVDFFIDIIRKYNEQPNLSDEEILDYYLFNKKGKSLVEFVE   89 (362)
T ss_pred             HCCCCCCCCCHHHCCHHHHHHHHHHCHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCHHHHHH
T ss_conf             33201157326556627899999859247877076288899999999998198999996999999871467687999999


Q ss_pred             HHHHHHHHHHCCCCC--HHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCC
Q ss_conf             999999997326777--578999985068853510124422567741034554205997345232012
Q gi|254780834|r  123 VATDFFHHSLKNARD--KRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGL  188 (648)
Q Consensus       123 ~~~~~~~~~l~~~~~--~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl  188 (648)
                      . ..+-...|.+.+.  ..|.+|+..  ...+=+....+-|+|.-      +..+.|++.++.+++-+
T Consensus        90 ~-f~~~~~vl~~~e~l~r~a~e~~~d--~~~dgV~Y~EiRf~P~~------~~~~~g~s~~~v~~av~  148 (362)
T PTZ00124         90 K-ARMICDIFADYSVLEDLAKHAVFN--KYKEGVVLMEFRYSPAF------LAFKCNLDYDLIHNAIV  148 (362)
T ss_pred             H-HHHHHHHHCCHHHHHHHHHHHHHH--HHHCCCEEEEEEECCCC------CCCCCCCCHHHHHHHHH
T ss_conf             9-999999974999999999999999--99739828999757320------26678998899999999


No 222
>pfam04392 ABC_sub_bind ABC transporter substrate binding protein. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.
Probab=33.41  E-value=26  Score=13.38  Aligned_cols=81  Identities=17%  Similarity=0.134  Sum_probs=52.8

Q ss_pred             EEEECCHHHHHH------HHHCCCCCCHHHHHCCCCHHHHHHHHHCC---CEEEEEECCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf             899714388999------87435542113432136626789885126---818996178866225777888888777536
Q gi|254780834|r  274 IILVEGYMDVLS------LCQAGVQNVVSSLGTALTEYQLRLLWKLS---PRIVLCFDGDDPGLRAAYKAIDLVLCHLIP  344 (648)
Q Consensus       274 ~i~vEGy~Dvi~------l~~~G~~n~va~~Gtalt~~~~~~l~r~~---~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~  344 (648)
                      -||.-+..|-+.      +.+-| .|+-...-......|+.+++++.   ++|.+.||.++++-.+..+.+....+  +.
T Consensus        82 PIVf~~v~dPv~aglv~s~~~pg-~NvTGvs~~~~~~~~l~ll~~l~P~~k~igviyn~~e~~s~~~~~~~~~~a~--~~  158 (292)
T pfam04392        82 PIVFAAVTDPVGAKLVPSKEQPG-ENVTGVSDLVDVEQTIELIKKLLPNVKSIGVYYSPSEANSVSLVEEIKKYAK--KS  158 (292)
T ss_pred             CEEEEEECCHHHHCCCCCCCCCC-CEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHH--HC
T ss_conf             98999726856606644566899-8267852774799999999986889858999957998657999999999999--76


Q ss_pred             CCCEEEEECCCCC
Q ss_conf             9730675257888
Q gi|254780834|r  345 GNRVNFVLLSRGE  357 (648)
Q Consensus       345 g~~v~vv~LP~G~  357 (648)
                      |+++..+..+...
T Consensus       159 gi~l~~~~v~~~~  171 (292)
T pfam04392       159 GIKVVEASVPSSN  171 (292)
T ss_pred             CCEEEEEECCCHH
T ss_conf             9989999668866


No 223
>KOG3214 consensus
Probab=33.39  E-value=23  Score=13.75  Aligned_cols=54  Identities=20%  Similarity=0.268  Sum_probs=28.8

Q ss_pred             EEEECCCCC-CCCCCEEEE--CCCCEEEECCCCCCC-CHHHHHHHHCCC----CHHHHHHHHHH
Q ss_conf             575345888-858787981--789746713688887-898998988599----97999999999
Q gi|254780834|r   39 YWACCPFHD-EKTPSFHCN--DSKGFYYCFSCHVKG-DHLSFLSALLGC----SFIESVQRLAA   94 (648)
Q Consensus        39 ~~~~cPfh~-ektpsf~v~--~~~~~~~cf~c~~~g-d~~~f~~~~~~~----~f~ea~~~la~   94 (648)
                      -+=-|||.+ ||.-|.++.  ...|+-+|=-|+++- --|+.+.  +.+    ++.+|++....
T Consensus        22 t~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFqt~it~Ls--epIDVYSdWiDaCe~vn~   83 (109)
T KOG3214          22 TQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQTTITALS--EPIDVYSDWIDACEAVNN   83 (109)
T ss_pred             EEECCCCCCCCCCEEEEEHHHCCCCEEEEEEHHHHHCCCHHHHC--CCHHHHHHHHHHHHHHHC
T ss_conf             16516743551110244113217562644405445255267645--544788999999998613


No 224
>cd03372 TPP_ComE Thiamine pyrophosphate (TPP) family, ComE subfamily, TPP-binding module; composed of proteins similar to Methanococcus jannaschii sulfopyruvate decarboxylase beta subunit (ComE). M. jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits, which catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. ComDE requires TPP and divalent metal cation cofactors.
Probab=32.80  E-value=26  Score=13.30  Aligned_cols=59  Identities=25%  Similarity=0.232  Sum_probs=30.9

Q ss_pred             CHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             1134321366267898851268189961788662257778888887775369730675257888
Q gi|254780834|r  294 VVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGE  357 (648)
Q Consensus       294 ~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~  357 (648)
                      .+.+||-++.-.--..+.+  ++-|+|+|||.+=+-   ...+++..-.....++.++.|.++.
T Consensus        40 ~lGtMG~~~p~aiGaa~a~--p~kVi~i~GDGs~lM---~~geL~Ti~~~~~~n~~~ivlnN~~   98 (179)
T cd03372          40 MLGSMGLASSIGLGLALAQ--PRKVIVIDGDGSLLM---NLGALATIAAEKPKNLIIVVLDNGA   98 (179)
T ss_pred             EECHHHHHHHHHHHHHHCC--CCCEEEEECCHHHHH---HHHHHHHHHHHCCCCEEEEEEECCC
T ss_conf             3134450889999998657--996899967804654---3669999997268978999983887


No 225
>pfam05566 Pox_vIL-18BP Orthopoxvirus interleukin 18 binding protein. Interleukin-18 (IL-18) is a proinflammatory cytokine that plays a key role in the activation of natural killer and T helper 1 cell responses principally by inducing interferon-gamma (IFN-gamma). Several poxvirus genes encode proteins with sequence similarity to IL-18BPs. It has been shown that vaccinia, ectromelia and cowpox viruses secrete from infected cells a soluble IL-18BP (vIL-18BP) that may modulate the host antiviral response. The expression of vIL-18BPs by distinct poxvirus genera that cause local or general viral dissemination, or persistent or acute infections in the host, emphasises the importance of IL-18 in response to viral infections.
Probab=32.78  E-value=24  Score=13.60  Aligned_cols=35  Identities=23%  Similarity=0.401  Sum_probs=24.2

Q ss_pred             EECCCCC---CCCCCEEEECCCCEEEECCCCCCCCHHH
Q ss_conf             5345888---8587879817897467136888878989
Q gi|254780834|r   41 ACCPFHD---EKTPSFHCNDSKGFYYCFSCHVKGDHLS   75 (648)
Q Consensus        41 ~~cPfh~---ektpsf~v~~~~~~~~cf~c~~~gd~~~   75 (648)
                      +.-|+-+   -|-|.+.+....|-|||-||-+.---|+
T Consensus        13 cvh~yvna~e~kcpnl~ivtssgef~csgcv~~mp~fs   50 (126)
T pfam05566        13 CVHPYVNADEIKCPNLDIVTSSGEFRCSGCVEFMPKFS   50 (126)
T ss_pred             CCCCCCCCCCCCCCCCCEEECCCCEEEEEHHHHCCCCH
T ss_conf             67531261002489832680468288611454385611


No 226
>TIGR00357 TIGR00357 methionine-R-sulfoxide reductase; InterPro: IPR002579   Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine . It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set , .   The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A . The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin.   In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N-terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity.
Probab=32.76  E-value=21  Score=14.09  Aligned_cols=15  Identities=27%  Similarity=0.525  Sum_probs=11.7

Q ss_pred             EECCCCEEEECCCCC
Q ss_conf             817897467136888
Q gi|254780834|r   55 CNDSKGFYYCFSCHV   69 (648)
Q Consensus        55 v~~~~~~~~cf~c~~   69 (648)
                      -+-+.|+|+|-.||+
T Consensus        34 ~~~~~GiY~di~~g~   48 (135)
T TIGR00357        34 DNKEDGIYVDITCGE   48 (135)
T ss_pred             CCCCCCCEEEECCCC
T ss_conf             124787427621688


No 227
>COG1859 KptA RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]
Probab=32.60  E-value=26  Score=13.28  Aligned_cols=65  Identities=25%  Similarity=0.297  Sum_probs=37.3

Q ss_pred             CCCCCCCCCHHHHHHHCC--CCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEEC
Q ss_conf             422567741034554205--9973452320121003465410000167168889707785888501001465530010
Q gi|254780834|r  159 LGYAPDSRYSLREHLRQK--GFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYL  234 (648)
Q Consensus       159 lG~ap~~~~~l~~~l~~~--~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYl  234 (648)
                      =|||+  -+.|...+.+.  ..+.+.+  -+++..++++.  |-.+ +   .-|+-.+|.-|-..=+ +.+++.|++|
T Consensus        57 ~Gwa~--i~~l~~~~~k~~~~~~~~~l--~~iV~~d~K~R--f~l~-~---~~IRA~yGHSi~V~l~-~~~~~~p~~L  123 (211)
T COG1859          57 EGWAD--IDELLEGLRKAGRWLTRELL--LAVVATDDKGR--FELK-E---GKIRARYGHSIPVDLR-LPEAEPPAVL  123 (211)
T ss_pred             CCCHH--HHHHHHHHHHHCCCCCHHHH--HHHHHCCCCCE--EEEC-C---CCEEECCCCCEEEECC-CCCCCCCCEE
T ss_conf             66561--99999888762467799999--99984288750--6841-6---6266404753577514-7777898677


No 228
>COG3454 Metal-dependent hydrolase involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=32.45  E-value=26  Score=13.26  Aligned_cols=11  Identities=27%  Similarity=0.211  Sum_probs=4.0

Q ss_pred             CHHHHHHHHHH
Q ss_conf             14579999999
Q gi|254780834|r  397 TPDERAELEIH  407 (648)
Q Consensus       397 spe~ka~~~~~  407 (648)
                      |.++.+.++.+
T Consensus       189 s~~e~~~~i~~  199 (377)
T COG3454         189 SDEEFAEFIEE  199 (377)
T ss_pred             CHHHHHHHHHH
T ss_conf             99999999999


No 229
>KOG0257 consensus
Probab=32.41  E-value=26  Score=13.25  Aligned_cols=104  Identities=15%  Similarity=0.154  Sum_probs=56.1

Q ss_pred             HHHHHCCCCHHHHHHHHHCCC--EEEEEECCCCCCHHHHHHHHHHHHHHHHCCC-CEEEEECCCCCC----HHHHHHCCC
Q ss_conf             134321366267898851268--1899617886622577788888877753697-306752578888----889972036
Q gi|254780834|r  295 VSSLGTALTEYQLRLLWKLSP--RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN-RVNFVLLSRGED----PDSFIRCYG  367 (648)
Q Consensus       295 va~~Gtalt~~~~~~l~r~~~--~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~-~v~vv~LP~G~D----PDe~ir~~G  367 (648)
                      =-|.|+.+|++++..|-++|.  .+++.+|.          +-+.   ++-+|. -+|++.||+=.+    --|+-+..|
T Consensus       182 hNPtGkvfsReeLe~ia~l~~k~~~lvisDe----------vYe~---~v~d~~~h~r~aslPgm~ertitvgS~gKtf~  248 (420)
T KOG0257         182 HNPTGKVFSREELERIAELCKKHGLLVISDE----------VYEW---LVYDGNKHIRIASLPGMYERTITVGSFGKTFG  248 (420)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCEEEEEHH----------HHHH---HHHCCCCCEEEECCCCHHHEEEEECCCCCEEE
T ss_conf             9986730579999999999987897999825----------7478---82178765146227762244788514521000


Q ss_pred             HHHHHHH-HHHCCCHHHHHHHHHHH--HCCCCCHHHHHHHHHHHHHHH
Q ss_conf             6889988-64149927999999985--302331457999999999885
Q gi|254780834|r  368 KTAFEKL-IVESLPLVDMLWKRETE--NRSFNTPDERAELEIHLKNCI  412 (648)
Q Consensus       368 ~eaf~~l-l~~A~~l~dFl~~~l~~--~~dl~spe~ka~~~~~l~~~I  412 (648)
                      .-+|+-= +--...+.... .....  .+...||-+.|.+...-.++.
T Consensus       249 ~TGWrlGW~igp~~L~~~~-~~vh~~~~~~~~Tp~q~A~a~a~~~~~~  295 (420)
T KOG0257         249 VTGWRLGWAIGPKHLYSAL-FPVHQNFVFTCPTPIQEASAAAFALELA  295 (420)
T ss_pred             EEEEEEEEEECHHHHHHHH-HHHHHCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             0345653464548764647-8786455202680778999998740020


No 230
>LOAD_USPA consensus
Probab=32.37  E-value=26  Score=13.25  Aligned_cols=38  Identities=21%  Similarity=0.311  Sum_probs=29.6

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             81899617886622577788888877753697306752578
Q gi|254780834|r  315 PRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSR  355 (648)
Q Consensus       315 ~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~  355 (648)
                      ++|+++.|+.+...+|...|++++...   +-.+.++..=+
T Consensus         1 k~Ilv~vd~s~~s~~a~~~A~~la~~~---~a~l~~lhV~~   38 (135)
T LOAD_USPA         1 KKILVAIDGSPESEKALRWAVDLAKRR---GAELILLHVIP   38 (135)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHHHHHC---CCEEEEEEEEC
T ss_conf             989999869989999999999999874---99899999962


No 231
>PRK08645 bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein; Reviewed
Probab=32.05  E-value=27  Score=13.21  Aligned_cols=78  Identities=17%  Similarity=0.123  Sum_probs=39.0

Q ss_pred             HHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCE--E----EEEECCCCCCHHHHH-HHHHHHHHHHHCCCCEEE-EECCCC
Q ss_conf             98743554211343213662678988512681--8----996178866225777-888888777536973067-525788
Q gi|254780834|r  285 SLCQAGVQNVVSSLGTALTEYQLRLLWKLSPR--I----VLCFDGDDPGLRAAY-KAIDLVLCHLIPGNRVNF-VLLSRG  356 (648)
Q Consensus       285 ~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~--v----vl~fDgD~AG~kAa~-Ra~e~~l~~l~~g~~v~v-v~LP~G  356 (648)
                      .+...|..-+=..|||  |++||+.|.+-.+.  +    ..-=..-........ +.-..+...+..++.|-| +..|.|
T Consensus       259 ~~~~~Ga~iIGGCCGT--TPeHIraia~al~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~vEldpP~~  336 (608)
T PRK08645        259 EFVEEGVRLIGGCCGT--TPEHIRAMKEALRGLKPVVEKEVIPIPKKEPFHPKPSKVKSSLLEKVKKKFTVIVELDPPKG  336 (608)
T ss_pred             HHHHCCCCEEEECCCC--CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCEEEEEECCCCC
T ss_conf             9998599799757799--99999999998447899775555666666667887766777589996379679999549999


Q ss_pred             CCHHHHHH
Q ss_conf             88889972
Q gi|254780834|r  357 EDPDSFIR  364 (648)
Q Consensus       357 ~DPDe~ir  364 (648)
                      .|++-++.
T Consensus       337 ~d~~~~~~  344 (608)
T PRK08645        337 LDTDKFLE  344 (608)
T ss_pred             CCHHHHHH
T ss_conf             98789999


No 232
>pfam00949 Peptidase_S7 Peptidase S7, Flavivirus NS3 serine protease. The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor.
Probab=31.95  E-value=27  Score=13.19  Aligned_cols=18  Identities=33%  Similarity=0.604  Sum_probs=12.5

Q ss_pred             EEEECCCCEEEEECCCCC
Q ss_conf             897077858885010014
Q gi|254780834|r  209 PIRSSRGQVIAFGGRTLS  226 (648)
Q Consensus       209 Pi~~~~g~~i~f~gR~l~  226 (648)
                      ||.|..|+|+|+.|-.+.
T Consensus       118 pI~N~~g~ivGlYgngl~  135 (150)
T pfam00949       118 PIFNQNGQIVGLYGNGLV  135 (150)
T ss_pred             CEECCCCCEEEEECCEEE
T ss_conf             658689979999536499


No 233
>pfam10911 DUF2717 Protein of unknown function (DUF2717). Members in this family of proteins are annotated as gene 6.5 protein however currently there is no known function.
Probab=31.82  E-value=27  Score=13.18  Aligned_cols=12  Identities=42%  Similarity=0.736  Sum_probs=4.1

Q ss_pred             HHHHHCCCCCHH
Q ss_conf             455420599734
Q gi|254780834|r  170 REHLRQKGFSEE  181 (648)
Q Consensus       170 ~~~l~~~~~~~~  181 (648)
                      ++.|+..||++.
T Consensus        41 i~~Lr~aGySE~   52 (77)
T pfam10911        41 IDDLRAAGYSES   52 (77)
T ss_pred             HHHHHHCCCCHH
T ss_conf             999988466299


No 234
>cd00817 ValRS_core This is the catalytic core domain of valine amino-acyl tRNA synthetases (ValRS) . This enzyme is a monomer, which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.  ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=31.70  E-value=27  Score=13.16  Aligned_cols=27  Identities=22%  Similarity=0.260  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHCCCHHHHHHHHHHCCCH
Q ss_conf             888888997203668899886414992
Q gi|254780834|r  355 RGEDPDSFIRCYGKTAFEKLIVESLPL  381 (648)
Q Consensus       355 ~G~DPDe~ir~~G~eaf~~ll~~A~~l  381 (648)
                      +..||++++.++|.|+++-++-.+.|+
T Consensus       331 Nvv~p~~~l~~yg~D~lRy~l~~~~~~  357 (363)
T cd00817         331 NVIDPLDVIDGYGADALRFTLASAASQ  357 (363)
T ss_pred             CCCCHHHHHHHCCCHHHHHHHHHHCCC
T ss_conf             866989999877927999999952998


No 235
>PRK13804 ileS isoleucyl-tRNA synthetase; Provisional
Probab=31.67  E-value=27  Score=13.16  Aligned_cols=27  Identities=15%  Similarity=0.150  Sum_probs=21.9

Q ss_pred             CCCCCHHHHHHCCCHHHHHHHHHHCCC
Q ss_conf             788888899720366889988641499
Q gi|254780834|r  354 SRGEDPDSFIRCYGKTAFEKLIVESLP  380 (648)
Q Consensus       354 P~G~DPDe~ir~~G~eaf~~ll~~A~~  380 (648)
                      -+..||++.+.++|+|+++-.+..+-.
T Consensus       642 GNvvdP~~ii~~yGADalRl~~as~~~  668 (966)
T PRK13804        642 GNVVDPQDVIKQSGADILRLWVASVDY  668 (966)
T ss_pred             CCCCCHHHHHHHCCCHHHHHHHHHCCC
T ss_conf             898998999987292188899984775


No 236
>KOG2361 consensus
Probab=31.62  E-value=24  Score=13.63  Aligned_cols=16  Identities=25%  Similarity=0.256  Sum_probs=6.3

Q ss_pred             HHHHHHHHHHHHHHCC
Q ss_conf             7778888887775369
Q gi|254780834|r  330 AAYKAIDLVLCHLIPG  345 (648)
Q Consensus       330 Aa~Ra~e~~l~~l~~g  345 (648)
                      +..++++.+..++++|
T Consensus       161 k~~~a~~nl~~llKPG  176 (264)
T KOG2361         161 KMQSVIKNLRTLLKPG  176 (264)
T ss_pred             HHHHHHHHHHHHHCCC
T ss_conf             7899999999974888


No 237
>pfam03976 PPK2 Polyphosphate kinase 2 (PPK2). Inorganic polyphosphate (polyP) plays a role in metabolism and regulation and has been proposed to serve as a energy source in a pre-ATP world. In prokaryotes, the synthesis and utilisation of polyP are catalysed by PPK1, PPK2 and polyphosphatases. Proteins with a single PPK2 domain catalyse polyP-dependent phosphorylation of ADP to ATP, whereas proteins containing 2 fused PPK2 domains phosphorylate AMP to ADP. The structure of PPK2 from Pseudomonas aeruginosa has revealed a a 3-layer alpha/beta/alpha sandwich fold with an alpha-helical lid similar to the structures of microbial thymidylate kinases.
Probab=31.62  E-value=27  Score=13.15  Aligned_cols=42  Identities=26%  Similarity=0.359  Sum_probs=28.4

Q ss_pred             CHHHHHCCCCHHHHHHHHHCCCEEEEEECC-CCCCHHHHHHHHH
Q ss_conf             113432136626789885126818996178-8662257778888
Q gi|254780834|r  294 VVSSLGTALTEYQLRLLWKLSPRIVLCFDG-DDPGLRAAYKAID  336 (648)
Q Consensus       294 ~va~~Gtalt~~~~~~l~r~~~~vvl~fDg-D~AG~kAa~Ra~e  336 (648)
                      .+..|...|..-|-.+-. ....|++.|.| |.||+-.+.+.+-
T Consensus        10 ~~~~L~~~L~~lQ~~l~~-~~~~viIv~eG~daaGKg~~I~~l~   52 (229)
T pfam03976        10 ELAKLQIELVKLQEWVYA-EGKKLVVIFEGRDAAGKGGAIKRIT   52 (229)
T ss_pred             HHHHHHHHHHHHHHHHHH-CCCCEEEEEECCCCCCCHHHHHHHH
T ss_conf             999999999999999997-5994899996657787369999998


No 238
>COG1206 Gid NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]
Probab=31.58  E-value=19  Score=14.54  Aligned_cols=146  Identities=21%  Similarity=0.250  Sum_probs=82.4

Q ss_pred             CCCEEEEEEEECC---CCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEEC
Q ss_conf             1671688897077---8588850100146553001038767653521011081788886433100002356787089971
Q gi|254780834|r  202 FRNRLIFPIRSSR---GQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVE  278 (648)
Q Consensus       202 Fr~Ri~fPi~~~~---g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vE  278 (648)
                      |.|-+- ||.+.-   -.++-|..|- |+++ .-|||-|=|     ....+.++.|.-...+....    ...+. ...|
T Consensus       159 FyDAaA-PIi~~dSIdmd~~~~~sRY-dKg~-a~YiNCPmt-----kEey~~F~eaL~~ae~~~~k----~fEk~-~~Fe  225 (439)
T COG1206         159 FYDAAA-PIIEFDSIDMDKAYLKSRY-DKGE-ADYINCPMT-----KEEYLAFYEALIEAEKAPLK----DFEKE-KYFE  225 (439)
T ss_pred             EECCCC-CEEECCCCCHHHHHHHHCC-CCCC-CHHHCCCCC-----HHHHHHHHHHHHHCCCCCHH----HHCCC-CCCC
T ss_conf             621247-4332055434777765003-5564-112069888-----99999999999743457834----41256-1214


Q ss_pred             CHHHHHHHHHCCCCCC----HHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             4388999874355421----134321366267898851268189961788662257778888887775369730675257
Q gi|254780834|r  279 GYMDVLSLCQAGVQNV----VSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLS  354 (648)
Q Consensus       279 Gy~Dvi~l~~~G~~n~----va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP  354 (648)
                      |-|-.=-+.+-|.+.-    .-|.|  |+.-+--.-++ .--||=.---|++|.--.+=+.+.   .|+-|-+-+|..+=
T Consensus       226 gCmPIE~mA~rG~~Tl~~GPmKPvG--L~~p~~~tgk~-pYAVVQLRqdna~GtLynmVGFQT---~LkwgeQkrVf~mI  299 (439)
T COG1206         226 GCMPIEVMAERGRKTLRFGPMKPVG--LEDPRDPTGKR-PYAVVQLRQDNAAGTLYNMVGFQT---HLKWGEQKRVFRMI  299 (439)
T ss_pred             CCCCHHHHHHHCCCHHCCCCCCCCC--CCCCCCCCCCC-CEEEEEEECCCCCCCEEEEEEEEE---CCCHHHHHHHHHHC
T ss_conf             5676999986270001248888757--77887777888-617998520465664465430130---35210255465536


Q ss_pred             CCCCHHHHHHCC
Q ss_conf             888888997203
Q gi|254780834|r  355 RGEDPDSFIRCY  366 (648)
Q Consensus       355 ~G~DPDe~ir~~  366 (648)
                      .|..-.+|+|-.
T Consensus       300 PgLeNAefvRyG  311 (439)
T COG1206         300 PGLENAEFVRYG  311 (439)
T ss_pred             CCCCHHHHHHCC
T ss_conf             783111444203


No 239
>cd03785 GT1_MurG MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide (NAM). The resulting disaccharide is then transported across the cell membrane, where it is polymerized into NAG-NAM cell-wall repeat structure. MurG belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains, each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology.  The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.
Probab=31.43  E-value=27  Score=13.13  Aligned_cols=66  Identities=27%  Similarity=0.341  Sum_probs=41.0

Q ss_pred             HHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHH---HHHHHCCCCCCH----HHHHCCCCHHHHHHHHHCCCEEE
Q ss_conf             01108178888643310000235678708997143889---998743554211----34321366267898851268189
Q gi|254780834|r  246 KNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDV---LSLCQAGVQNVV----SSLGTALTEYQLRLLWKLSPRIV  318 (648)
Q Consensus       246 ~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dv---i~l~~~G~~n~v----a~~Gtalt~~~~~~l~r~~~~vv  318 (648)
                      +.+.++.++...+++.++        +-+|-+=||.-+   ++.+..|++-++    +.+|.+     -+++.++++.|.
T Consensus        73 ~~~~~~~~~~~~l~~~kP--------d~vi~~GGY~s~P~~laA~~~~iP~~ihEqN~v~G~a-----nr~l~~~a~~i~  139 (350)
T cd03785          73 KLLKGVLQARKILKKFKP--------DVVVGFGGYVSGPVGLAAKLLGIPLVIHEQNAVPGLA-----NRLLARFADRVA  139 (350)
T ss_pred             HHHHHHHHHHHHHHHCCC--------CEEEECCCCHHHHHHHHHHHCCCCCEEECCCCCCCHH-----HHHHCCCCCEEE
T ss_conf             999999999999996499--------9999889810389999999729985565677225713-----233210039899


Q ss_pred             EEECCC
Q ss_conf             961788
Q gi|254780834|r  319 LCFDGD  324 (648)
Q Consensus       319 l~fDgD  324 (648)
                      +.|+..
T Consensus       140 ~~f~~~  145 (350)
T cd03785         140 LSFPET  145 (350)
T ss_pred             ECCHHH
T ss_conf             857565


No 240
>PRK04023 DNA polymerase II large subunit; Validated
Probab=31.42  E-value=26  Score=13.34  Aligned_cols=19  Identities=37%  Similarity=0.364  Sum_probs=12.9

Q ss_pred             CCHHHHHHHHHHHHCCCCCC
Q ss_conf             99799999999981885877
Q gi|254780834|r   83 CSFIESVQRLAAIAGVPLPV  102 (648)
Q Consensus        83 ~~f~ea~~~la~~~gi~~~~  102 (648)
                      .++-||++ ++..+|+++..
T Consensus       453 ps~eEA~~-iS~~~~vPLHP  471 (1128)
T PRK04023        453 PSQEEALK-LSEEYGVPLHP  471 (1128)
T ss_pred             CCHHHHHH-HHHHHCCCCCC
T ss_conf             89999999-99983999899


No 241
>TIGR01943 rnfA electron transport complex, RnfABCDGE type, A subunit; InterPro: IPR011293   The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation . A closely related complex in Escherichia coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized . This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This entry describes the A subunit.; GO: 0006118 electron transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=31.22  E-value=13  Score=16.03  Aligned_cols=13  Identities=8%  Similarity=-0.210  Sum_probs=4.2

Q ss_pred             CHHHHHHHHHHHH
Q ss_conf             1457999999999
Q gi|254780834|r  397 TPDERAELEIHLK  409 (648)
Q Consensus       397 spe~ka~~~~~l~  409 (648)
                      ++-|...+.-.+.
T Consensus        37 ~A~GMg~AvtFVm   49 (193)
T TIGR01943        37 TAVGMGLAVTFVM   49 (193)
T ss_pred             HHCCCCHHHHHHH
T ss_conf             3216618999999


No 242
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=30.87  E-value=27  Score=13.20  Aligned_cols=42  Identities=19%  Similarity=0.301  Sum_probs=23.0

Q ss_pred             HCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHH
Q ss_conf             222101588777775575345888858787981789746713688887898998988
Q gi|254780834|r   24 YVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSAL   80 (648)
Q Consensus        24 ~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~   80 (648)
                      |--|+..|.-     .-...++.+++        +.|+|+|-+||.-  .|+--+++
T Consensus        12 y~v~r~~gTE-----~pfsg~y~~~~--------~~G~y~C~~C~~~--LF~s~~Kf   53 (284)
T PRK05550         12 YRVIEDKGTE-----RPFSGEYYDHD--------EKGVYLCKKCGAP--LFRSEDKF   53 (284)
T ss_pred             HHHHHHCCCC-----CCCCCCCCCCC--------CCEEEEECCCCCC--CCCCCCCC
T ss_conf             9999736889-----99877554898--------9879994589970--45566514


No 243
>TIGR02918 TIGR02918 conserved hypothetical protein TIGR02918; InterPro: IPR014267   Members of this entry are found only in Gram-positive bacteria of the Firmicutes lineage, including several species of Staphylococcus, Streptococcus, and Lactobacillus..
Probab=30.86  E-value=17  Score=15.03  Aligned_cols=253  Identities=18%  Similarity=0.262  Sum_probs=113.9

Q ss_pred             CCCCCCCCCCHHHHHHHC-----CCCCHHHHHHH-CCC--EECC-CCCCCCCCCC-CE---EEEEEEECCCCEEE-----
Q ss_conf             442256774103455420-----59973452320-121--0034-6541000016-71---68889707785888-----
Q gi|254780834|r  158 KLGYAPDSRYSLREHLRQ-----KGFSEEKIIEA-GLL--IDGD-NSATSYDRFR-NR---LIFPIRSSRGQVIA-----  219 (648)
Q Consensus       158 ~lG~ap~~~~~l~~~l~~-----~~~~~~~~~~~-gl~--~~~~-~~~~~~d~Fr-~R---i~fPi~~~~g~~i~-----  219 (648)
                      .|||--+.==+|++|...     ..|+.++|.+. |.-  .... +|+..-=.|. +-   |+.=..|+.-++|-     
T Consensus        54 NiGF~D~eiIWLY~yFTDiKIAPTtYTvd~l~~~l~~~~~~~E~vnGK~~~~ff~l~~~~fv~cyL~~E~~~~VdRvEyV  133 (511)
T TIGR02918        54 NIGFKDDEIIWLYQYFTDIKIAPTTYTVDDLEKELGLEITRREKVNGKVVKLFFNLNDSIFVTCYLKNESKDIVDRVEYV  133 (511)
T ss_pred             HCCCCCCCEEEEEECCCCCEECCCCCCHHHHHHHHCCCCEEEEEECCCEEEEEEEECCCEEEEEEEECCCCCCEEEEEEE
T ss_conf             44898775788430246530524544078989751885403510066089999984697399998634888804676777


Q ss_pred             EECCCCC-------------------------------CCCC--CEECCCCCCCCCC-CC-HHCCCHHHHHHHHHHHHCC
Q ss_conf             5010014-------------------------------6553--0010387676535-21-0110817888864331000
Q gi|254780834|r  220 FGGRTLS-------------------------------KGES--VKYLNSPETILFH-KG-KNLYNFFGALNYLQKSIRK  264 (648)
Q Consensus       220 f~gR~l~-------------------------------~~~~--~KYlNSpeT~if~-K~-~~Ly~l~~a~~~~~~~~~~  264 (648)
                      +.|..+.                               ++.-  --|||.-+..+|+ +- .+||+    |++.-...--
T Consensus       134 ~~G~LiRKDfYSYTr~fsEYYAP~Dn~A~LY~R~FYNEDGSIAY~e~~dqG~~s~F~F~dG~iLYs----K~eliayFl~  209 (511)
T TIGR02918       134 SNGKLIRKDFYSYTRVFSEYYAPADNKAKLYQRTFYNEDGSIAYEEYVDQGDESVFVFKDGKILYS----KQELIAYFLK  209 (511)
T ss_pred             ECCEEEEEECCCCEEEEEEECCCCCCCCEEEECEEECCCCCHHHHHCCCCCCCEEEECCCCCEECC----HHHHHHHHHH
T ss_conf             378224231134132356411776798547101124258834344203798843678379745418----6999999999


Q ss_pred             CCCCCCCCEEEEECCHHH--HHHHHHCCCCC-CHHHHHC----------CCCHHHHHHHHHC--------CCEEEEEECC
Q ss_conf             023567870899714388--99987435542-1134321----------3662678988512--------6818996178
Q gi|254780834|r  265 DVRRNSSSFIILVEGYMD--VLSLCQAGVQN-VVSSLGT----------ALTEYQLRLLWKL--------SPRIVLCFDG  323 (648)
Q Consensus       265 ~~~~~~~~~~i~vEGy~D--vi~l~~~G~~n-~va~~Gt----------alt~~~~~~l~r~--------~~~vvl~fDg  323 (648)
                      +......|-+| +-=-.|  -+.-=|+=++| .-|=+|.          +.|+.||  ||+-        ++.|=+.   
T Consensus       210 ~L~LT~~Di~I-lDR~~~dknliiGQ~Vl~Nkg~AklgVVvHAEHf~~~~t~e~~I--LWNNyYEYqF~nA~~iDFF---  283 (511)
T TIGR02918       210 QLNLTKKDIII-LDRSTGDKNLIIGQAVLENKGPAKLGVVVHAEHFSESATNETYI--LWNNYYEYQFSNADYIDFF---  283 (511)
T ss_pred             HCCCCCCCEEE-EECCCCCCEEEEEEEEEEECCCEEEEEEEEEEECCCCCCCCCCC--CCCCCHHHHCCCCCEEEEE---
T ss_conf             60698566899-97368993058713888750870289999746368886168602--2146525531568665113---


Q ss_pred             CCCCHHHHHHHHHHHHHHHHC--CCCEEEEECCCCCCHHHHHHC--CCHHHHHHHHHH--C-CCHHHHHHHHHHHHCCCC
Q ss_conf             866225777888888777536--973067525788888899720--366889988641--4-992799999998530233
Q gi|254780834|r  324 DDPGLRAAYKAIDLVLCHLIP--GNRVNFVLLSRGEDPDSFIRC--YGKTAFEKLIVE--S-LPLVDMLWKRETENRSFN  396 (648)
Q Consensus       324 D~AG~kAa~Ra~e~~l~~l~~--g~~v~vv~LP~G~DPDe~ir~--~G~eaf~~ll~~--A-~~l~dFl~~~l~~~~dl~  396 (648)
                          .-||..==+++...-+.  +.++||.++|=| ==|++-..  ++...|.-+-.+  | .--+|++++...+.+. +
T Consensus       284 ----ItATd~Q~~~l~~QF~kY~~~~P~i~TIPVG-Sl~~L~~p~W~~Rkp~SiiTASRLA~EKHiDWLV~AVv~Ak~-~  357 (511)
T TIGR02918       284 ----ITATDIQNQILLEQFKKYKNIEPKIYTIPVG-SLDELQYPEWQERKPFSIITASRLAKEKHIDWLVKAVVKAKK-S  357 (511)
T ss_pred             ----EECHHHHHHHHHHHHHHHCCCCCEEEEEECC-CHHHCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCC-C
T ss_conf             ----4005788999999888747998778885057-543357886346452156777341376712688899999513-3


Q ss_pred             CH----------HHHHHH-----HHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             14----------579999-----9999988541799899999999
Q gi|254780834|r  397 TP----------DERAEL-----EIHLKNCINHIKDQKLRYYYSQ  426 (648)
Q Consensus       397 sp----------e~ka~~-----~~~l~~~I~~I~d~~~R~~yl~  426 (648)
                      -|          .++.++     .+++-..|.......+.+.|.+
T Consensus       358 ~P~l~FDIYG~GgE~~~L~~iI~~n~A~DYI~LkGH~~L~~vY~~  402 (511)
T TIGR02918       358 VPELTFDIYGEGGEKSKLKKIINENQAEDYIRLKGHKNLSEVYKD  402 (511)
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHCC
T ss_conf             885110003563788999998763120012431154335666232


No 244
>TIGR03329 Phn_aa_oxid putative aminophosphonate oxidoreductase. This clade of sequences are members of the pfam01266 family of FAD-dependent oxidoreductases. Characterized proteins within this family include glycerol-3-phosphate dehydrogenase (1.1.99.5), sarcosine oxidase beta subunit (1.5.3.1) and a number of deaminating amino acid oxidases (1.4.-.-). These genes have been consistently observed in a genomic context including genes for the import and catabolism of 2-aminoethylphosphonate (AEP). If the substrate of this oxidoreductase is AEP itself, then it is probably acting in the manner of a deaminating oxidase, resulting in the same product (phosphonoacetaldehyde) as the transaminase PhnW (TIGR02326), but releasing ammonia instead of coupling to pyruvate:alanine. Alternatively, it is reasonable to suppose that the various ABC cassette transporters which are also associated with these loci allow the import of phosphonates closely related to AEP which may not be substrates for PhnW.
Probab=30.83  E-value=28  Score=13.05  Aligned_cols=19  Identities=5%  Similarity=0.209  Sum_probs=8.8

Q ss_pred             CEEEE-CCCC-CCCCCCEEEE
Q ss_conf             55753-4588-8858787981
Q gi|254780834|r   38 DYWAC-CPFH-DEKTPSFHCN   56 (648)
Q Consensus        38 ~~~~~-cPfh-~ektpsf~v~   56 (648)
                      -|.|| |=.| .+..|+..|-
T Consensus        33 G~tGLstA~~L~~~~pg~~Vv   53 (460)
T TIGR03329        33 GFTGLWTAIMIKQQRPALDVL   53 (460)
T ss_pred             CHHHHHHHHHHHHHCCCCCEE
T ss_conf             399999999999748999889


No 245
>TIGR00300 TIGR00300 conserved hypothetical protein TIGR00300; InterPro: IPR005239    This family of conserved hypothetical proteins has no known function..
Probab=30.42  E-value=19  Score=14.46  Aligned_cols=34  Identities=32%  Similarity=0.544  Sum_probs=23.7

Q ss_pred             CCHHHHHH----HHHCCCCCCHHHHHCCCCH-------------HHHHHHHHC
Q ss_conf             14388999----8743554211343213662-------------678988512
Q gi|254780834|r  278 EGYMDVLS----LCQAGVQNVVSSLGTALTE-------------YQLRLLWKL  313 (648)
Q Consensus       278 EGy~Dvi~----l~~~G~~n~va~~Gtalt~-------------~~~~~l~r~  313 (648)
                      +||.|++-    |.-|.|+  .|++||+|.-             .|++.+...
T Consensus       238 ~GYv~~Ll~GNAlA~HDIE--~~~~GTSLGvD~~~G~~V~gGhrHHl~~In~v  288 (418)
T TIGR00300       238 EGYVDALLAGNALAVHDIE--IALYGTSLGVDIKRGKPVPGGHRHHLKAINKV  288 (418)
T ss_pred             HHHHHHHHCCCCHHHHHHH--HHHCCCCCCEECCCCCCCCCCCHHHHHHHHHH
T ss_conf             4478887516701012266--76404423205246855898843688888888


No 246
>KOG2518 consensus
Probab=30.40  E-value=28  Score=12.99  Aligned_cols=27  Identities=19%  Similarity=0.203  Sum_probs=14.1

Q ss_pred             HHHHHCCCCCCHHHHHCCCCHHHHHHHHHC
Q ss_conf             998743554211343213662678988512
Q gi|254780834|r  284 LSLCQAGVQNVVSSLGTALTEYQLRLLWKL  313 (648)
Q Consensus       284 i~l~~~G~~n~va~~Gtalt~~~~~~l~r~  313 (648)
                      --|.-+.+...|.-+|-  .. -.++|.+|
T Consensus       219 ciLSGCDYl~slpGvGl--~t-A~k~l~k~  245 (556)
T KOG2518         219 CILSGCDYLSSLPGVGL--AT-AHKLLSKY  245 (556)
T ss_pred             HHHCCCCCCCCCCCCCH--HH-HHHHHHHC
T ss_conf             98427731124765229--99-99999853


No 247
>cd00250 CAS_like Clavaminic acid synthetase (CAS) -like;  CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases catalyze a hydroxylation reaction, which leads to the incorporation of an oxygen atom from dioxygen into a hydroxyl group and conversion of 2OG to succinate and CO2
Probab=30.27  E-value=28  Score=12.97  Aligned_cols=62  Identities=18%  Similarity=0.234  Sum_probs=29.8

Q ss_pred             EEEEEECC-CCEEEEECCCCCCC-CCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHH
Q ss_conf             88897077-85888501001465-53001038767653521011081788886433100002356787089971438899
Q gi|254780834|r  207 IFPIRSSR-GQVIAFGGRTLSKG-ESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVL  284 (648)
Q Consensus       207 ~fPi~~~~-g~~i~f~gR~l~~~-~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi  284 (648)
                      +|++.... -.-++++...|..- +.|-|-..|.   +   ..|..+..+              ..++.-++|-|+--+-
T Consensus        77 ~~~v~~~~~~~n~AyT~~~L~~HtD~~y~~~~Pg---~---q~LhCl~~~--------------~~GGeS~~vDg~~va~  136 (262)
T cd00250          77 VVPVPGKENAQNGAYTNTLLPLHTDLAYHEYRPG---L---QILHCLRNT--------------ATGGATLLVDGFRVAL  136 (262)
T ss_pred             EEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCC---E---EEEEEECCC--------------CCCCCEEEEEHHHHHH
T ss_conf             0797516997664546565454557887779981---6---778703137--------------8899349872999999


Q ss_pred             HHHH
Q ss_conf             9874
Q gi|254780834|r  285 SLCQ  288 (648)
Q Consensus       285 ~l~~  288 (648)
                      .|-+
T Consensus       137 ~L~~  140 (262)
T cd00250         137 KLLR  140 (262)
T ss_pred             HHHH
T ss_conf             9988


No 248
>TIGR01389 recQ ATP-dependent DNA helicase RecQ; InterPro: IPR006293   The ATP-dependent DNA helicase RecQ (3.6.1 from EC) is involved in genome maintenance . All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novo synthesis DNA, such as the replication fork, and protein levels peak during S-phase.    A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that is necessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and the RecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response. ; GO: 0004003 ATP-dependent DNA helicase activity, 0006310 DNA recombination, 0009432 SOS response.
Probab=30.15  E-value=23  Score=13.79  Aligned_cols=21  Identities=38%  Similarity=0.452  Sum_probs=10.0

Q ss_pred             HHHHHHCCCCCHHHHHHHCCCE
Q ss_conf             3455420599734523201210
Q gi|254780834|r  169 LREHLRQKGFSEEKIIEAGLLI  190 (648)
Q Consensus       169 l~~~l~~~~~~~~~~~~~gl~~  190 (648)
                      +..+|.++|++ ....-|||-.
T Consensus       242 ~~~~L~s~G~~-A~~YHAGL~~  262 (607)
T TIGR01389       242 LAERLESQGIS-ALAYHAGLSN  262 (607)
T ss_pred             HHHHHHHCCCC-EEECCCCCCH
T ss_conf             99999747962-0403679877


No 249
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794    Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=29.93  E-value=22  Score=14.01  Aligned_cols=19  Identities=5%  Similarity=-0.055  Sum_probs=7.8

Q ss_pred             CCCHHHHHHHHHHHHHHHH
Q ss_conf             7998999999999999988
Q gi|254780834|r  415 IKDQKLRYYYSQAIRDRLQ  433 (648)
Q Consensus       415 I~d~~~R~~yl~~la~~L~  433 (648)
                      .+=+.+-+=+++.+++.+.
T Consensus        78 ~~Lp~~aqP~l~~ls~~~~   96 (252)
T TIGR02431        78 APLPKVAQPLLERLSAQTH   96 (252)
T ss_pred             HHHHHHHHHHHHHHHHHHC
T ss_conf             1589999999999998537


No 250
>cd00762 NAD_bind_malic_enz NAD(P) binding domain of malic enzyme. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically  Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+.  ME has been found in all organisms and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2.  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 glut
Probab=29.92  E-value=29  Score=12.93  Aligned_cols=39  Identities=15%  Similarity=0.082  Sum_probs=17.0

Q ss_pred             CEEEECCCCCCC----CHHHHHHHHCCCCHHHHHHH--HHHHHCC
Q ss_conf             746713688887----89899898859997999999--9998188
Q gi|254780834|r   60 GFYYCFSCHVKG----DHLSFLSALLGCSFIESVQR--LAAIAGV   98 (648)
Q Consensus        60 ~~~~cf~c~~~g----d~~~f~~~~~~~~f~ea~~~--la~~~gi   98 (648)
                      +.+=|||.|..|    +.+--.|..+|++-.||.+.  +.++.|+
T Consensus        26 ~riv~~GAGsAg~gia~~l~~~~~~~Gl~~~ea~~~i~lvD~~GL   70 (254)
T cd00762          26 HKVLFNGAGAAALGIANLIVXLXVKEGISKEEACKRIWXVDRKGL   70 (254)
T ss_pred             CEEEEECCCHHHHHHHHHHHHHHHHCCCCHHHHHCCEEEECCCCC
T ss_conf             589998832999999999999864326532433210788537773


No 251
>cd00763 Bacterial_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include bacterial ATP-dependent phosphofructokinases. These are allosrterically regulated homotetramers; the subunits are of about 320 amino acids.
Probab=29.88  E-value=29  Score=12.92  Aligned_cols=16  Identities=13%  Similarity=0.399  Sum_probs=7.5

Q ss_pred             EEEEECCCC-CCHHHHH
Q ss_conf             067525788-8888997
Q gi|254780834|r  348 VNFVLLSRG-EDPDSFI  363 (648)
Q Consensus       348 v~vv~LP~G-~DPDe~i  363 (648)
                      ..++.+|+- .|+|+++
T Consensus       185 ad~iliPE~~~~~~~~~  201 (317)
T cd00763         185 AEFIVIPEAEFDREEVA  201 (317)
T ss_pred             CCEEEECCCCCCHHHHH
T ss_conf             98999689999999999


No 252
>PRK06850 hypothetical protein; Provisional
Probab=29.77  E-value=16  Score=15.28  Aligned_cols=15  Identities=40%  Similarity=0.605  Sum_probs=6.9

Q ss_pred             ECCCCEEE-EECCCCC
Q ss_conf             07785888-5010014
Q gi|254780834|r  212 SSRGQVIA-FGGRTLS  226 (648)
Q Consensus       212 ~~~g~~i~-f~gR~l~  226 (648)
                      +..|.+|= .|-|.-.
T Consensus       143 ~~~ge~IlvLGtR~~E  158 (488)
T PRK06850        143 SAFGEVIVVLGTRKAE  158 (488)
T ss_pred             HHCCCEEEEEECCHHH
T ss_conf             7539789998545277


No 253
>TIGR02483 PFK_mixed phosphofructokinase; InterPro: IPR012829    Members of this family that are characterised, save one, are phosphofructokinases dependent on pyrophosphate (2.7.1.90 from EC) rather than ATP (2.7.1.11 from EC). The exception is one of three phosphofructokinases from Streptomyces coelicolor. Family members are both bacterial and archaeal.; GO: 0005524 ATP binding, 0008443 phosphofructokinase activity, 0006002 fructose 6-phosphate metabolic process, 0006096 glycolysis.
Probab=29.58  E-value=25  Score=13.40  Aligned_cols=13  Identities=46%  Similarity=0.889  Sum_probs=5.7

Q ss_pred             CCCCCHHHHHHHH
Q ss_conf             8866225777888
Q gi|254780834|r  323 GDDPGLRAAYKAI  335 (648)
Q Consensus       323 gD~AG~kAa~Ra~  335 (648)
                      ||-+|.||..|++
T Consensus         9 GDCPGLNAVIR~v   21 (339)
T TIGR02483         9 GDCPGLNAVIRGV   21 (339)
T ss_pred             CCCCHHHHHHHHH
T ss_conf             7741123898787


No 254
>CHL00010 infA translation initiation factor 1
Probab=29.57  E-value=29  Score=12.88  Aligned_cols=19  Identities=26%  Similarity=0.656  Sum_probs=12.8

Q ss_pred             CCCCCCCCEEEEEEEECCC
Q ss_conf             1000016716888970778
Q gi|254780834|r  197 TSYDRFRNRLIFPIRSSRG  215 (648)
Q Consensus       197 ~~~d~Fr~Ri~fPi~~~~g  215 (648)
                      ++||--+|||+|-.+|..+
T Consensus        58 SpYDltkGRI~~R~k~~~~   76 (78)
T CHL00010         58 SPYDLTKGRIIYRLRNKDS   76 (78)
T ss_pred             CCCCCCCEEEEEEECCCCC
T ss_conf             7567885789999045656


No 255
>COG2957 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]
Probab=29.32  E-value=29  Score=12.85  Aligned_cols=27  Identities=11%  Similarity=0.127  Sum_probs=11.6

Q ss_pred             EEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf             67525788888899720366889988641
Q gi|254780834|r  349 NFVLLSRGEDPDSFIRCYGKTAFEKLIVE  377 (648)
Q Consensus       349 ~vv~LP~G~DPDe~ir~~G~eaf~~ll~~  377 (648)
                      +|+-|+.|..+|+=  ....|.+..++..
T Consensus       199 kvlWL~~Gl~~D~T--DgHiDtlarFv~p  225 (346)
T COG2957         199 KVLWLEYGLKNDDT--DGHIDTLARFVAP  225 (346)
T ss_pred             EEEECCCCCCCCCC--CCHHHHHHHHCCC
T ss_conf             78982678767766--5104546654278


No 256
>COG1180 PflA Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=29.32  E-value=29  Score=12.85  Aligned_cols=120  Identities=14%  Similarity=0.137  Sum_probs=69.9

Q ss_pred             CCEEEEECCHHHHHHH-HHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEE---ECCC------CCCHHHHHHHHHHHHH
Q ss_conf             8708997143889998-7435542113432136626789885126818996---1788------6622577788888877
Q gi|254780834|r  271 SSFIILVEGYMDVLSL-CQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLC---FDGD------DPGLRAAYKAIDLVLC  340 (648)
Q Consensus       271 ~~~~i~vEGy~Dvi~l-~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~---fDgD------~AG~kAa~Ra~e~~l~  340 (648)
                      ..+.+-.|...|+..+ ...|+.+++-|.|. ++++-+..|..+++-+.+=   ++.|      .|.-+-.++.++.+..
T Consensus        92 GEP~~q~e~~~~~~~~ake~Gl~~~l~TnG~-~~~~~~~~l~~~~D~v~~DlK~~~~~~yr~~tg~~~~~vl~~~~~l~~  170 (260)
T COG1180          92 GEPTLQAEFALDLLRAAKERGLHVALDTNGF-LPPEALEELLPLLDAVLLDLKAFDDELYRKLTGADNEPVLENLELLAD  170 (260)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCEEEEECCCC-CCHHHHHHHHHHCCCEEEECCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             6044439999999999998799089976899-882689999974231488406688788898756871688999999861


Q ss_pred             HHHCCCCEEEEECCCC-CCHHHHHHCCCHHHHHHHH-HHCCCHHHHHHHHHHHHCC
Q ss_conf             7536973067525788-8888997203668899886-4149927999999985302
Q gi|254780834|r  341 HLIPGNRVNFVLLSRG-EDPDSFIRCYGKTAFEKLI-VESLPLVDMLWKRETENRS  394 (648)
Q Consensus       341 ~l~~g~~v~vv~LP~G-~DPDe~ir~~G~eaf~~ll-~~A~~l~dFl~~~l~~~~d  394 (648)
                      . ..-..++.+..|.- .|+++. +.- .+.+.++. ..+..+.-|...+..+...
T Consensus       171 ~-g~~ve~r~lviPg~~d~~e~i-~~i-~~~i~~~~~~~p~~~l~fhp~~~~~~~p  223 (260)
T COG1180         171 L-GVHVEIRTLVIPGYNDDEEEI-REL-AEFIADLGPEIPIHLLRFHPDYKLKDLP  223 (260)
T ss_pred             C-CCEEEEEEEECCCCCCCHHHH-HHH-HHHHHHCCCCCCEEEECCCCCHHCCCCC
T ss_conf             7-983999887338988999999-999-9999730866655875668740113579


No 257
>KOG2168 consensus
Probab=29.31  E-value=24  Score=13.69  Aligned_cols=27  Identities=22%  Similarity=-0.002  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999988413267621230
Q gi|254780834|r  618 ISILHEVHIQIHQIESQEAMIEGFGKM  644 (648)
Q Consensus       618 ~~el~elk~~L~~l~~~Eal~e~~~~~  644 (648)
                      ...++.++.+-+.+-..-+.|+.++++
T Consensus       795 ~~~l~~lr~~a~~i~~~a~~I~yRmps  821 (835)
T KOG2168         795 ETKLDRLRDQARAIVMMAAMIPYRMPS  821 (835)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCH
T ss_conf             789999999999999999754521873


No 258
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=29.29  E-value=29  Score=12.84  Aligned_cols=36  Identities=19%  Similarity=0.222  Sum_probs=28.5

Q ss_pred             HHHHHHHHHC---CCEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             2678988512---68189961788662257778888887
Q gi|254780834|r  304 EYQLRLLWKL---SPRIVLCFDGDDPGLRAAYKAIDLVL  339 (648)
Q Consensus       304 ~~~~~~l~r~---~~~vvl~fDgD~AG~kAa~Ra~e~~l  339 (648)
                      ...++.|+++   +++|+|+-|.|.-|-.=|+.+.+++.
T Consensus       106 ~k~v~~lk~lak~ad~v~lATD~DREGEaIa~hi~~~l~  144 (170)
T cd03361         106 LETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALR  144 (170)
T ss_pred             HHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHC
T ss_conf             999999999986089799857998222299999999955


No 259
>TIGR02201 heptsyl_trn_III lipopolysaccharide heptosyltransferase III, putative; InterPro: IPR011916    This family consists of examples of the putative ADP-heptose:LPS heptosyltransferase III, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria. This enzyme may be less widely distributed than heptosyltransferases I and II..
Probab=29.04  E-value=29  Score=12.81  Aligned_cols=78  Identities=23%  Similarity=0.349  Sum_probs=36.3

Q ss_pred             CCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCC-CE
Q ss_conf             78708997143889998743554211343213662678988512681899617886622577788888877753697-30
Q gi|254780834|r  270 SSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN-RV  348 (648)
Q Consensus       270 ~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~-~v  348 (648)
                      ..+++=+||-..           -+.+|||-..+..+.        +-|+.|      +.|.+.+.-..  +-++|. +-
T Consensus       133 ~~n~LHtV~~NL-----------s~L~PLGl~~~~~~~--------rCvm~y------~~adw~a~ral--L~eaGv~~~  185 (347)
T TIGR02201       133 QSNTLHTVEQNL-----------SVLAPLGLDSLAKEA--------RCVMSY------SEADWKAVRAL--LDEAGVSEN  185 (347)
T ss_pred             CCCEEEEEEHHH-----------HHHCCCCCCCCCCCC--------EEECCC------CHHHHHHHHHH--HHHCCCCCC
T ss_conf             887234210124-----------664246888565766--------021378------86459999985--232579998


Q ss_pred             EEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf             67525788888899720366889988641
Q gi|254780834|r  349 NFVLLSRGEDPDSFIRCYGKTAFEKLIVE  377 (648)
Q Consensus       349 ~vv~LP~G~DPDe~ir~~G~eaf~~ll~~  377 (648)
                      +||.=|.--   -|.|---.+-|..+++-
T Consensus       186 YiVIqPtsR---wfFKCW~~drfsali~A  211 (347)
T TIGR02201       186 YIVIQPTSR---WFFKCWEDDRFSALIDA  211 (347)
T ss_pred             CEEECCCCC---CCCCCCHHHHHHHHHHH
T ss_conf             178736736---31016621358999998


No 260
>pfam02969 TAF TATA box binding protein associated factor (TAF). TAF proteins adopt a histone-like fold.
Probab=28.90  E-value=30  Score=12.79  Aligned_cols=48  Identities=23%  Similarity=0.324  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHCCC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             799999999981885-8776820367778899999999999999999732
Q gi|254780834|r   85 FIESVQRLAAIAGVP-LPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLK  133 (648)
Q Consensus        85 f~ea~~~la~~~gi~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  133 (648)
                      -+|+|+..|+..||. ++. +....-...-.-++-++.+.|.+|-++--+
T Consensus         5 ~~esik~iAeS~Gi~~l~d-e~a~~La~dveyRl~eiiqeA~KFMrhskR   53 (66)
T pfam02969         5 PQESMKVIAESLGITNLSD-EAAALLAEDVEYRLKEIVQDAAKFMRHSKR   53 (66)
T ss_pred             CHHHHHHHHHHCCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             5888999999949888999-999998999999999999999999998675


No 261
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=28.58  E-value=30  Score=12.75  Aligned_cols=73  Identities=10%  Similarity=0.078  Sum_probs=44.1

Q ss_pred             EECCHH-HHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCE------EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             971438-89998743554211343213662678988512681------89961788662257778888887775369730
Q gi|254780834|r  276 LVEGYM-DVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPR------IVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRV  348 (648)
Q Consensus       276 ~vEGy~-Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~------vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v  348 (648)
                      ..||=| |++++-.-.+... +..|..++.++++.+-.++++      +-.+|+||..+--..+|.      +..     
T Consensus       218 ~a~Gs~RDalslldqai~~~-~~~~~~I~~~~V~~MLGl~Drs~lidL~e~Il~Gd~~kaL~~l~~------iy~-----  285 (507)
T PRK06645        218 KSEGSARDAVSILDQAASMS-AKSDNIISPQVINQMLGLVDLSVIIEFVEYIIERETEKAINLINK------LYG-----  285 (507)
T ss_pred             HCCCCHHHHHHHHHHHHHHH-CCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHH------HHH-----
T ss_conf             55998678999999999975-489870269999998389985679999999982999999999999------998-----


Q ss_pred             EEEECCCCCCHHHHHHCC
Q ss_conf             675257888888997203
Q gi|254780834|r  349 NFVLLSRGEDPDSFIRCY  366 (648)
Q Consensus       349 ~vv~LP~G~DPDe~ir~~  366 (648)
                            .|-||+.+++.-
T Consensus       286 ------~G~Dp~~iL~DL  297 (507)
T PRK06645        286 ------SSVNLEIFIESV  297 (507)
T ss_pred             ------CCCCHHHHHHHH
T ss_conf             ------499999999999


No 262
>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=28.48  E-value=30  Score=12.73  Aligned_cols=33  Identities=27%  Similarity=0.312  Sum_probs=25.4

Q ss_pred             HHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             678988512681899617886622577788888
Q gi|254780834|r  305 YQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDL  337 (648)
Q Consensus       305 ~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~  337 (648)
                      .+++.+.+-+++||++-|.|.-|..=++...+.
T Consensus        64 ~~ik~l~~~ad~viiAtD~DrEGE~I~~~i~~~   96 (123)
T cd03363          64 KELKKLAKKADEIYLATDPDREGEAIAWHLAEV   96 (123)
T ss_pred             HHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHH
T ss_conf             999999850998998489982479999999999


No 263
>PRK05362 phosphopentomutase; Provisional
Probab=28.27  E-value=30  Score=12.71  Aligned_cols=88  Identities=19%  Similarity=0.255  Sum_probs=44.6

Q ss_pred             CCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHH-HHHHHHCC-CEEEEE----ECC------CCCCHHHHHHHHHHH
Q ss_conf             870899714388999874355421134321366267-89885126-818996----178------866225777888888
Q gi|254780834|r  271 SSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQ-LRLLWKLS-PRIVLC----FDG------DDPGLRAAYKAIDLV  338 (648)
Q Consensus       271 ~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~-~~~l~r~~-~~vvl~----fDg------D~AG~kAa~Ra~e~~  338 (648)
                      ...|+.|==--|..+  -.||...+-+.+++=.-++ +..+++-. +-.+++    ||.      |.+|...++..++.-
T Consensus       236 g~~V~~IGKi~DIf~--~~Gi~~~~~~~~n~~~~~~~l~~~~~~~~~glif~NlvdfD~lyGHrrD~~gYa~aLe~fD~~  313 (393)
T PRK05362        236 GGEVIAVGKIADIFA--GQGITEKVKAKSNMDGMDATIEEMKEAGDNGLVFTNLVDFDSLYGHRRDVAGYAKALEEFDRR  313 (393)
T ss_pred             CCEEEEECCHHHHHC--CCCCCCEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             984999815798644--788660116888199999999999746469779985201154405655878999999999998


Q ss_pred             HHHHHCCC---CEEEEECCCCCCHH
Q ss_conf             77753697---30675257888888
Q gi|254780834|r  339 LCHLIPGN---RVNFVLLSRGEDPD  360 (648)
Q Consensus       339 l~~l~~g~---~v~vv~LP~G~DPD  360 (648)
                      |+.+.+.+   ++-|++-..|-||-
T Consensus       314 L~~il~~l~~dDLLIITADHGnDPT  338 (393)
T PRK05362        314 LPELLALLKEDDLLIITADHGNDPT  338 (393)
T ss_pred             HHHHHHHCCCCCEEEEECCCCCCCC
T ss_conf             9999984797878999487788999


No 264
>pfam12324 HTH_15 Helix-turn-helix domain of alkylmercury lyase. Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This is the N terminal helix-turn-helix domain associated with pfam03243.
Probab=28.24  E-value=24  Score=13.55  Aligned_cols=22  Identities=14%  Similarity=0.229  Sum_probs=8.3

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             9999999975388999899998
Q gi|254780834|r  518 LWSFLFSDFVEQKYFLPEEIHQ  539 (648)
Q Consensus       518 L~~~i~~~~~~~~~~~~~~l~~  539 (648)
                      |+.-++.....+..++.+.+..
T Consensus        25 l~~~LLr~La~G~PVt~~~LA~   46 (77)
T pfam12324        25 LFRPLLRMLADGRPVTREDLAG   46 (77)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHH
T ss_conf             9999999994799868999998


No 265
>PRK00048 dihydrodipicolinate reductase; Provisional
Probab=28.16  E-value=30  Score=12.69  Aligned_cols=42  Identities=24%  Similarity=0.304  Sum_probs=30.0

Q ss_pred             CCHHHHHH-HHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEE
Q ss_conf             14388999-874355421134321366267898851268189961
Q gi|254780834|r  278 EGYMDVLS-LCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCF  321 (648)
Q Consensus       278 EGy~Dvi~-l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~f  321 (648)
                      ++-++.+. +.++|++-|++|-  -|+++|+..|+++++++-+++
T Consensus        80 ~~~~~~~~~~~~~~~~~ViGTT--G~~~~~~~~i~~~s~~ipil~  122 (265)
T PRK00048         80 EATLENLEFALEHGKPLVIGTT--GFTEEQLAALREAAKKIPVVI  122 (265)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEC--CCCHHHHHHHHHHCCCCCEEE
T ss_conf             9999999999974997799608--999899999997465887899


No 266
>PRK13208 valS valyl-tRNA synthetase; Reviewed
Probab=28.04  E-value=30  Score=12.67  Aligned_cols=31  Identities=23%  Similarity=0.258  Sum_probs=23.7

Q ss_pred             CCCCCHHHHHHCCCHHHHHHHHHHCCCHHHH
Q ss_conf             7888888997203668899886414992799
Q gi|254780834|r  354 SRGEDPDSFIRCYGKTAFEKLIVESLPLVDM  384 (648)
Q Consensus       354 P~G~DPDe~ir~~G~eaf~~ll~~A~~l~dF  384 (648)
                      -+..||++++.++|+|+++=.+..+.+..|.
T Consensus       544 GNvi~p~eii~~yGADalR~~la~~~~~~d~  574 (809)
T PRK13208        544 GNVVDPEELLEKYGADAVRYWAANSRLGSDT  574 (809)
T ss_pred             CCCCCHHHHHHHCCCHHHHHHHHCCCCCCCC
T ss_conf             8968978986533809999999618944465


No 267
>TIGR00539 hemN_rel putative oxygen-independent coproporphyrinogen III oxidase; InterPro: IPR004559   Experimentally determined examples of oxygen-independent coproporphyrinogen III oxidase, an enzyme that replaces HemF function under anaerobic conditions, belong to a family of proteins called HemN (IPR004558 from INTERPRO). This family contains a closely related protein, shorter at the amino end and lacking the region containing the motif PYRT[SC]YP found in members of the hemN family. Several species, including Escherichia coli, Helicobacter pylori, Aquifex aeolicus, and Chlamydia trachomatis, have members of both this family and the Escherichia coli hemN family. The member of this family from Bacillus subtilis was shown to complement a hemF/hemN double mutant of Salmonella typhimurium and to prevent accumulation of coproporphyrinogen III under anaerobic conditions, but the exact role of this protein is still uncertain. It is found in a number of species that do not synthesize haem de novo. ; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin biosynthetic process, 0005737 cytoplasm.
Probab=27.99  E-value=20  Score=14.33  Aligned_cols=39  Identities=28%  Similarity=0.401  Sum_probs=19.4

Q ss_pred             EEECCHHHHHHH------HHCCCCCCHHHHHC-CCCHHHHHHHHHCCC
Q ss_conf             997143889998------74355421134321-366267898851268
Q gi|254780834|r  275 ILVEGYMDVLSL------CQAGVQNVVSSLGT-ALTEYQLRLLWKLSP  315 (648)
Q Consensus       275 i~vEGy~Dvi~l------~~~G~~n~va~~Gt-alt~~~~~~l~r~~~  315 (648)
                      |-||--=|.|+.      -.+||..  =+||. +|.++.+..|-|..+
T Consensus        95 it~eANP~~~~ae~~kglk~aGinR--lS~GvQsF~dDkL~~lgR~H~  140 (371)
T TIGR00539        95 ITVEANPDLVEAEKLKGLKEAGINR--LSLGVQSFEDDKLEKLGRVHK  140 (371)
T ss_pred             EEECCCCCHHHHHHHHHHHHCCEEE--EECCCCCCHHHHHHHHHHHCC
T ss_conf             1110782125698863676557023--321334541557888642113


No 268
>cd00293 USP_Like Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, athough Usp lacks ATP-binding activity.
Probab=27.62  E-value=31  Score=12.62  Aligned_cols=35  Identities=26%  Similarity=0.323  Sum_probs=27.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             18996178866225777888888777536973067525
Q gi|254780834|r  316 RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLL  353 (648)
Q Consensus       316 ~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~L  353 (648)
                      +|.++.|++...++|...|++++..   .|-.+.++..
T Consensus         1 ~Ilv~vd~s~~s~~al~~a~~la~~---~~~~l~~v~v   35 (130)
T cd00293           1 RILVAVDGSEESERALRWAARLARR---LGAELVLLHV   35 (130)
T ss_pred             CEEEEECCCHHHHHHHHHHHHHHHH---CCCEEEEEEE
T ss_conf             9999989898999999999999987---2997999999


No 269
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase; InterPro: IPR004558   This family represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. HemN catalyses the anaerobic transformation of coproporhyrinogen-III into protoporphyrinogen-IX during porphyrin biosynthesis. Several species, including Escherichia coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity, IPR004559 from INTERPRO. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterised protein.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin biosynthetic process, 0005737 cytoplasm.
Probab=27.54  E-value=31  Score=12.61  Aligned_cols=12  Identities=33%  Similarity=0.263  Sum_probs=7.1

Q ss_pred             CCCHHHHHHHHH
Q ss_conf             366267898851
Q gi|254780834|r  301 ALTEYQLRLLWK  312 (648)
Q Consensus       301 alt~~~~~~l~r  312 (648)
                      =||.+|+..|.+
T Consensus       117 YL~~~Q~~~l~~  128 (462)
T TIGR00538       117 YLSPEQIEELMK  128 (462)
T ss_pred             CCCHHHHHHHHH
T ss_conf             378899999999


No 270
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=27.45  E-value=28  Score=12.97  Aligned_cols=34  Identities=15%  Similarity=0.298  Sum_probs=24.2

Q ss_pred             HHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCC
Q ss_conf             899998506885351012442256774103455420599
Q gi|254780834|r  140 LHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGF  178 (648)
Q Consensus       140 a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~  178 (648)
                      -++||..||+|+.||+-|.--     ...+..|+.+.|.
T Consensus        30 Fl~yL~er~~S~~Ti~aY~~d-----L~~F~~fl~~~g~   63 (361)
T PRK01287         30 FVEWLQERNWSERTLKVQTHH-----TYHFILWCEERGL   63 (361)
T ss_pred             HHHHHHHCCCCHHHHHHHHHH-----HHHHHHHHHHCCC
T ss_conf             999999839989999999999-----9999999998489


No 271
>PRK01611 argS arginyl-tRNA synthetase; Reviewed
Probab=27.11  E-value=31  Score=12.55  Aligned_cols=47  Identities=23%  Similarity=0.262  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             379999999998477889999844300237998899999999999753
Q gi|254780834|r  481 SLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVE  528 (648)
Q Consensus       481 ~~~E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~  528 (648)
                      ...|+.|+..|..+|+.+....+.+..... ...+..|....-..|..
T Consensus       483 ~~~E~~Li~~l~~fp~vv~~a~~~~~Ph~l-~~YL~~La~~Fn~fY~~  529 (570)
T PRK01611        483 EEEELELIKKLAEFPEVVESAAEELEPHRI-ANYLYELAGAFHSFYNA  529 (570)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCHHHH-HHHHHHHHHHHHHHHHC
T ss_conf             989999999998879999999996881899-99999999999999851


No 272
>KOG4657 consensus
Probab=26.84  E-value=32  Score=12.51  Aligned_cols=63  Identities=14%  Similarity=0.210  Sum_probs=45.4

Q ss_pred             CCCCCCEEEEEEEECCCCEEEEECCCCCCCCC-------CEECCCCCCCCCCCCHHCCCHHHHHHHHHHH
Q ss_conf             00016716888970778588850100146553-------0010387676535210110817888864331
Q gi|254780834|r  199 YDRFRNRLIFPIRSSRGQVIAFGGRTLSKGES-------VKYLNSPETILFHKGKNLYNFFGALNYLQKS  261 (648)
Q Consensus       199 ~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~-------~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~  261 (648)
                      -++|++++=|-|.-..|.||-|.=--||+.++       .-|=++.++++-+-+-.|||+..|....++.
T Consensus       151 a~wy~dyLGleie~~hgevikfiFTnIdpkdp~~~FsF~vhL~e~~Dy~Vvd~~P~L~gl~~a~s~vr~t  220 (246)
T KOG4657         151 ASWYNDYLGLEIEAGHGEVIKFIFTNIDPKDPTREFSFTVHLGEDIDYQVVDHSPQLQGLTSAISAVRPT  220 (246)
T ss_pred             HHHHHHHCCCEEEECCCCEEEEEEECCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCC
T ss_conf             8899985073455135746889872258888764503687534545765667688763478899875112


No 273
>TIGR02727 MTHFS_bact 5,10-methenyltetrahydrofolate synthetase; InterPro: IPR002698 5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase 6.3.3.2 from EC catalyses the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg^2+ . 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin .; GO: 0005524 ATP binding, 0030272 5-formyltetrahydrofolate cyclo-ligase activity, 0009396 folic acid and derivative biosynthetic process.
Probab=26.83  E-value=17  Score=15.08  Aligned_cols=18  Identities=33%  Similarity=0.700  Sum_probs=9.2

Q ss_pred             EEEEE--EEECCCCEEEEEC
Q ss_conf             16888--9707785888501
Q gi|254780834|r  205 RLIFP--IRSSRGQVIAFGG  222 (648)
Q Consensus       205 Ri~fP--i~~~~g~~i~f~g  222 (648)
                      =|+.|  .+|.+|.=+||||
T Consensus       118 l~~VP~vAfD~~G~RlGyGg  137 (183)
T TIGR02727       118 LIIVPGVAFDRRGYRLGYGG  137 (183)
T ss_pred             EEEECCEEECCCCCEEECCC
T ss_conf             68826376889886740568


No 274
>pfam06447 consensus
Probab=26.79  E-value=32  Score=12.50  Aligned_cols=13  Identities=8%  Similarity=0.174  Sum_probs=6.0

Q ss_pred             CCEEEEECCHHHH
Q ss_conf             8708997143889
Q gi|254780834|r  271 SSFIILVEGYMDV  283 (648)
Q Consensus       271 ~~~~i~vEGy~Dv  283 (648)
                      +++.|+.++|=|.
T Consensus       253 ~~C~v~~s~~Gdl  265 (407)
T pfam06447       253 RGCFVTGSAWGDL  265 (407)
T ss_pred             CCCEEEEEEEEEC
T ss_conf             7748998888632


No 275
>pfam07282 Transposase_35 Putative transposase DNA-binding domain. This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesize this domain is DNA-binding.
Probab=26.74  E-value=32  Score=12.49  Aligned_cols=28  Identities=21%  Similarity=0.407  Sum_probs=17.8

Q ss_pred             ECCCCCCCCCCEEEECCCCEEEECCCCCCCC
Q ss_conf             3458888587879817897467136888878
Q gi|254780834|r   42 CCPFHDEKTPSFHCNDSKGFYYCFSCHVKGD   72 (648)
Q Consensus        42 ~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd   72 (648)
                      .||=.....+.   +.....|+|-.||..+|
T Consensus        30 ~C~~Cg~~~~~---~~~~r~~~C~~Cg~~~~   57 (69)
T pfam07282        30 TCSVCGHKNKE---SLSGRTFKCPNCGFVAD   57 (69)
T ss_pred             CCCCCCCCCCC---CCCCCEEECCCCCCEEC
T ss_conf             27999899867---48887898998996899


No 276
>pfam09445 Methyltransf_15 RNA cap guanine-N2 methyltransferase. RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe Tgs1 and Giardia lamblia Tgs2 catalyse methylation of the exocyclic N2 amine of 7-methylguanosine.
Probab=26.70  E-value=22  Score=13.96  Aligned_cols=15  Identities=20%  Similarity=0.549  Sum_probs=11.9

Q ss_pred             CCCCCCCCHHHHHHH
Q ss_conf             368888789899898
Q gi|254780834|r   65 FSCHVKGDHLSFLSA   79 (648)
Q Consensus        65 f~c~~~gd~~~f~~~   79 (648)
                      -.||.||+.|.|-..
T Consensus         7 ~fcG~Ggn~I~fA~~   21 (165)
T pfam09445         7 VFCGAGGNTIQFANV   21 (165)
T ss_pred             CCCCCCHHHHHHHHH
T ss_conf             377807999999975


No 277
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=26.69  E-value=32  Score=12.49  Aligned_cols=28  Identities=29%  Similarity=0.477  Sum_probs=20.6

Q ss_pred             CCCCC-CCCCCEEEE--CCCCEEEECCCCCC
Q ss_conf             45888-858787981--78974671368888
Q gi|254780834|r   43 CPFHD-EKTPSFHCN--DSKGFYYCFSCHVK   70 (648)
Q Consensus        43 cPfh~-ektpsf~v~--~~~~~~~cf~c~~~   70 (648)
                      |||.+ |+.-|.+|.  ...++-+|=.||..
T Consensus        25 Cp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls   55 (104)
T COG4888          25 CPRCGHEKVSSCTVKKTVNIGTAVCGNCGLS   55 (104)
T ss_pred             CCCCCCEEEEEEEEEECCCEEEEECCCCCCE
T ss_conf             6855872355788974274568971457553


No 278
>cd05312 NAD_bind_1_malic_enz NAD(P) binding domain of malic enzyme (ME), subgroup 1. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically  Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+.  ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2.  This subfamily consists of eukaryotic and bacterial ME.  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
Probab=26.64  E-value=32  Score=12.48  Aligned_cols=38  Identities=26%  Similarity=0.283  Sum_probs=17.3

Q ss_pred             HHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEE
Q ss_conf             38899987435542113432136626789885126818
Q gi|254780834|r  280 YMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRI  317 (648)
Q Consensus       280 y~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~v  317 (648)
                      -.|||.....-+--.+++.|-+||++.++.+.+.++++
T Consensus        97 L~e~v~~~kp~vlIG~S~~~g~ft~e~v~~Ma~~~e~P  134 (279)
T cd05312          97 LLEVVKAVKPTVLIGLSGVGGAFTEEVVRAMAKSNERP  134 (279)
T ss_pred             HHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHCCCCC
T ss_conf             99999724897799806898977999999998459997


No 279
>pfam06945 DUF1289 Protein of unknown function (DUF1289). This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N-terminus. The function of this family is unknown.
Probab=26.62  E-value=32  Score=12.48  Aligned_cols=13  Identities=23%  Similarity=0.618  Sum_probs=9.6

Q ss_pred             EECCCCCCCCHHH
Q ss_conf             7136888878989
Q gi|254780834|r   63 YCFSCHVKGDHLS   75 (648)
Q Consensus        63 ~cf~c~~~gd~~~   75 (648)
                      +|.||+...+=|.
T Consensus        16 ~C~GC~Rt~~EI~   28 (56)
T pfam06945        16 ICVGCGRTLDEIA   28 (56)
T ss_pred             EEECCCCCHHHHH
T ss_conf             7419999989998


No 280
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR; InterPro: IPR012704   At least five distinct pathways exist for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR which is, in most cases, divergently transcribed from the operon that encodes the genes involved in the methylcitric acid cycle of propionate catabolism. This protein is required for the expression of the proteins involved in this pathway . 2-methylcitric acid, an intermediate in this pathway, has been proposed to be a co-activator of PrpR .; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0019629 propionate catabolic process 2-methylcitrate cycle, 0005737 cytoplasm.
Probab=26.57  E-value=32  Score=12.47  Aligned_cols=12  Identities=33%  Similarity=0.540  Sum_probs=4.5

Q ss_pred             ECCCCEEEEECC
Q ss_conf             077858885010
Q gi|254780834|r  212 SSRGQVIAFGGR  223 (648)
Q Consensus       212 ~~~g~~i~f~gR  223 (648)
                      |.+|+|-+..-|
T Consensus       214 daqGrveainqr  225 (658)
T TIGR02329       214 DAQGRVEAINQR  225 (658)
T ss_pred             CCCCHHHHHHHH
T ss_conf             144327899888


No 281
>pfam09332 Mcm10 Mcm10 replication factor. Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha.
Probab=26.40  E-value=32  Score=12.45  Aligned_cols=12  Identities=25%  Similarity=0.371  Sum_probs=4.6

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999998841326
Q gi|254780834|r  626 IQIHQIESQEAM  637 (648)
Q Consensus       626 ~~L~~l~~~Eal  637 (648)
                      +....|+.-|.+
T Consensus       229 ~yF~~LekKE~m  240 (346)
T pfam09332       229 EYFNPLEKKEQM  240 (346)
T ss_pred             HHHHHHHHHHHH
T ss_conf             998888889999


No 282
>KOG0340 consensus
Probab=26.39  E-value=32  Score=12.44  Aligned_cols=24  Identities=25%  Similarity=0.344  Sum_probs=11.8

Q ss_pred             CCHHHHHHCCCHHHHHHHHHHCCC
Q ss_conf             888899720366889988641499
Q gi|254780834|r  357 EDPDSFIRCYGKTAFEKLIVESLP  380 (648)
Q Consensus       357 ~DPDe~ir~~G~eaf~~ll~~A~~  380 (648)
                      .|||+||..-|..+=.-....|.+
T Consensus       333 r~P~~yiHRvGRtARAGR~G~aiS  356 (442)
T KOG0340         333 RDPKDYIHRVGRTARAGRKGMAIS  356 (442)
T ss_pred             CCHHHHHHHHCCHHCCCCCCCEEE
T ss_conf             987888876030120567764289


No 283
>PRK10850 phosphohistidinoprotein-hexose phosphotransferase component of PTS system (Hpr); Provisional
Probab=26.37  E-value=32  Score=12.44  Aligned_cols=62  Identities=21%  Similarity=0.336  Sum_probs=39.8

Q ss_pred             HHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf             789885126818996178866225777888888777536973067525788888899720366889988641
Q gi|254780834|r  306 QLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE  377 (648)
Q Consensus       306 ~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~  377 (648)
                      =++..++|..+|.+.++|..|--|..+..+-+   -...|-.|.|.  -+|.|-++-+     +++.+++.+
T Consensus        22 ~v~~a~~f~s~I~l~~~~~~anakSi~~im~L---g~~~G~~i~i~--a~G~De~~Al-----~~l~~ll~e   83 (85)
T PRK10850         22 FVKEAKGFTSEITVTSNGKSASAKSLFKLQTL---GLTQGTVVTIS--AEGEDEQKAV-----EHLVKLMAE   83 (85)
T ss_pred             HHHHHHHCCCEEEEEECCEEECHHHHHHHHHC---CCCCCCEEEEE--EECCCHHHHH-----HHHHHHHHH
T ss_conf             99999628986999989999845849999974---98998999999--9788999999-----999999984


No 284
>pfam07014 Hs1pro-1_C Hs1pro-1 protein C-terminus. This family represents the C-terminus (approximately 270 residues) of a number of plant Hs1pro-1 proteins, which are believed to confer nematode resistance.
Probab=26.35  E-value=29  Score=12.84  Aligned_cols=46  Identities=17%  Similarity=0.156  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             8888877753697306752578888889972036688998864149927999999
Q gi|254780834|r  334 AIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKR  388 (648)
Q Consensus       334 a~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~~~  388 (648)
                      .+|....++.+-.     -|--=+|||||+|-+..-+.    +.+.+-..|.+++
T Consensus        91 ~vERiWKLL~~ie-----DlhllMDPdDFlrLK~qL~i----ks~~~~~afCfRS  136 (261)
T pfam07014        91 LLERIWKLLADIE-----DLHLLMDPDDFLRLKKQLSI----KSSPESAAFCFRS  136 (261)
T ss_pred             HHHHHHHHHHHHH-----HHHHHCCHHHHHHHHHHHCC----CCCCCCCCCCHHH
T ss_conf             9999999999888-----99861598899989987431----2478886411007


No 285
>KOG0177 consensus
Probab=26.23  E-value=32  Score=12.42  Aligned_cols=48  Identities=17%  Similarity=0.238  Sum_probs=26.2

Q ss_pred             CCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHH-HHHHHHHHCCCCC
Q ss_conf             8885878798178974671368888789899898859997999-9999998188587
Q gi|254780834|r   46 HDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIES-VQRLAAIAGVPLP  101 (648)
Q Consensus        46 h~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea-~~~la~~~gi~~~  101 (648)
                      +.+..--+++-.++..--|  ||++||+++|--      |..+ +..---|-|++++
T Consensus        28 ~k~~~dK~~~ls~~~lm~~--~Ge~GDt~qF~e------yi~~Ni~LY~irnGyeLS   76 (200)
T KOG0177          28 LKDDHDKIHRLSDHILMAT--VGEAGDTVQFTE------YIQKNIQLYKIRNGYELS   76 (200)
T ss_pred             ECCCCCCEEEECCCEEEEE--ECCCCCEEHHHH------HHHHHHHHHHHHCCCCCC
T ss_conf             7366440267243104553--058865107999------998530576542687678


No 286
>KOG0456 consensus
Probab=26.23  E-value=31  Score=12.57  Aligned_cols=32  Identities=16%  Similarity=0.470  Sum_probs=22.5

Q ss_pred             HHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHH
Q ss_conf             99998506885351012442256774103455
Q gi|254780834|r  141 HYYLDERGIDSHAIEMFKLGYAPDSRYSLREH  172 (648)
Q Consensus       141 ~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~  172 (648)
                      -+||..+|.....++-|.||+..-+|.++-+-
T Consensus       208 aA~lnd~G~kar~~D~~~I~~~~~d~~t~~d~  239 (559)
T KOG0456         208 AAYLNDIGHKARQYDAFEIGFITTDDFTNDDI  239 (559)
T ss_pred             HHHHHHCCCCCEEECHHHEECCCCCCCCCHHH
T ss_conf             99987328532351143420332433343247


No 287
>PRK00380 panC pantoate--beta-alanine ligase; Reviewed
Probab=25.96  E-value=33  Score=12.38  Aligned_cols=59  Identities=22%  Similarity=0.365  Sum_probs=32.6

Q ss_pred             CHHHHHCCCCHHHHHHHHHC---CCEEEEE-------ECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             11343213662678988512---6818996-------17886622577788888877753697306752578
Q gi|254780834|r  294 VVSSLGTALTEYQLRLLWKL---SPRIVLC-------FDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSR  355 (648)
Q Consensus       294 ~va~~Gtalt~~~~~~l~r~---~~~vvl~-------fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~  355 (648)
                      -|.||| ||-+.|+.++++-   ++.+|..       |...+ -.+.==|.++.-+.+++ ...|.+++.|.
T Consensus        25 ~VPTMG-aLH~GHlsLI~~A~~~~d~vvVSIFVNP~QF~~~e-D~~~YPr~~e~D~~~l~-~~gvD~vF~P~   93 (283)
T PRK00380         25 FVPTMG-NLHEGHLSLVREARAEADVVVVSIFVNPLQFGPNE-DLDRYPRTLEADLAKLE-AAGVDLVFAPS   93 (283)
T ss_pred             EECCCC-HHHHHHHHHHHHHHHHCCEEEEEEEECCCCCCCCC-CCCCCCCCHHHHHHHHH-HCCCCEEECCC
T ss_conf             985872-27589999999999749929999850601059875-40128987899999999-86998997887


No 288
>cd01816 Raf_RBD The Raf serine/threonine kinases are composed of three conserved regions, CR1, CR2 and CR3.  CR1 has two Ras binding domains (RBD and CRD), CR2 is a serine/threonine rich domain and CR3 is the catalytic kinase domain.  The RBD of Raf is structurally similar to ubiquitin with little of no sequence similarity.The Raf signalling pathway plays an important role in the proliferation and survival of tumor cells.
Probab=25.92  E-value=21  Score=14.14  Aligned_cols=33  Identities=21%  Similarity=0.210  Sum_probs=24.8

Q ss_pred             HHHHCCCCHHHHCCCCCCC-----CCCCCCHHHHHHHC
Q ss_conf             9985068853510124422-----56774103455420
Q gi|254780834|r  143 YLDERGIDSHAIEMFKLGY-----APDSRYSLREHLRQ  175 (648)
Q Consensus       143 yl~~Rg~~~~~~~~f~lG~-----ap~~~~~l~~~l~~  175 (648)
                      -|+.|||++|...-|.+|-     .|-+|+.....|..
T Consensus        29 alk~R~L~pe~C~V~~~~~~~~t~~~i~WdTd~~~L~g   66 (74)
T cd01816          29 ALKVRGLQPECCAVFRLGDGSSKKLRIDWDTDISSLIG   66 (74)
T ss_pred             HHHHCCCCHHHEEEEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf             99874998658599975688777853575465531015


No 289
>cd00807 Gln_GluRS_non_core Glutaminyl-tRNA synthetase (GlnRS) and non-descriminating Glutamyl-tRNA synthetase (GluRS) cataytic core domain. These enzymes attach Gln or Glu, respectively, to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. These enzymes function as monomers. Archaea and most bacteria lack GlnRS. In these organisms, the "non-descriminating" form of GluRS aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu, which is converted to Gln when appropriate by a transamidation enzyme.
Probab=25.86  E-value=33  Score=12.37  Aligned_cols=25  Identities=16%  Similarity=-0.013  Sum_probs=10.4

Q ss_pred             CCCCCCHHHH-HCCCCHHHHHHHHHC
Q ss_conf             3554211343-213662678988512
Q gi|254780834|r  289 AGVQNVVSSL-GTALTEYQLRLLWKL  313 (648)
Q Consensus       289 ~G~~n~va~~-Gtalt~~~~~~l~r~  313 (648)
                      -||+.||=.. -..-|+-|+.+...+
T Consensus       120 ~gITHViRG~D~l~nt~~q~~l~~aL  145 (238)
T cd00807         120 EGITHSLRTKEFQDRREKYDWLYEYL  145 (238)
T ss_pred             CCCCEEEECCCCCCCCHHHHHHHHHC
T ss_conf             78876887621013879999999984


No 290
>COG4230 Delta 1-pyrroline-5-carboxylate dehydrogenase [Energy production and conversion]
Probab=25.83  E-value=27  Score=13.10  Aligned_cols=16  Identities=25%  Similarity=0.194  Sum_probs=7.4

Q ss_pred             CCHHHHHCCCCHHHHH
Q ss_conf             2113432136626789
Q gi|254780834|r  293 NVVSSLGTALTEYQLR  308 (648)
Q Consensus       293 n~va~~Gtalt~~~~~  308 (648)
                      |+.-.=-|||++.-+.
T Consensus       353 NAMIVDSsAL~EQVv~  368 (769)
T COG4230         353 NAMIVDSSALAEQVVA  368 (769)
T ss_pred             CEEEEECHHHHHHHHH
T ss_conf             3388622010899999


No 291
>pfam00944 Peptidase_S3 Alphavirus core protein. Also known as coat protein C and capsid protein C. This makes the literature very confusing. Alphaviruses consist of a nucleoprotein core, a lipid membrane which envelopes the core, and glycoprotein spikes protruding from the lipid membrane.
Probab=25.74  E-value=33  Score=12.35  Aligned_cols=23  Identities=35%  Similarity=0.583  Sum_probs=15.3

Q ss_pred             HCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEE
Q ss_conf             01210034654100001671688897077858885
Q gi|254780834|r  186 AGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAF  220 (648)
Q Consensus       186 ~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f  220 (648)
                      +|.-.+.+.|+            ||.|-+|+|||.
T Consensus       100 ~g~g~~GDSGR------------pi~DN~GrVVaI  122 (157)
T pfam00944       100 KGVGGKGDSGR------------PILDNTGRVVAI  122 (157)
T ss_pred             CCCCCCCCCCC------------CCCCCCCCEEEE
T ss_conf             46778888898------------116588878999


No 292
>PRK09040 hypothetical protein; Provisional
Probab=25.65  E-value=28  Score=13.07  Aligned_cols=23  Identities=17%  Similarity=0.309  Sum_probs=16.2

Q ss_pred             CCCEEEEECCHHHHHHHHHC--CCC
Q ss_conf             78708997143889998743--554
Q gi|254780834|r  270 SSSFIILVEGYMDVLSLCQA--GVQ  292 (648)
Q Consensus       270 ~~~~~i~vEGy~Dvi~l~~~--G~~  292 (648)
                      ..+.+|.||||+|-...+..  .|+
T Consensus       121 ~~~~~i~V~GhTD~~pi~~~~~~f~  145 (215)
T PRK09040        121 ARDEILMVSGFTDDQPVRAGNRRFA  145 (215)
T ss_pred             CCCCEEEEEECCCCCCCCCCCCCCC
T ss_conf             7986599873489976767788889


No 293
>cd01532 4RHOD_Repeat_1 Member of the Rhodanese Homology Domain superfamily, repeat 1. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative catalytic Cys residue.
Probab=25.59  E-value=33  Score=12.33  Aligned_cols=56  Identities=14%  Similarity=0.097  Sum_probs=24.7

Q ss_pred             CCCCCCHH-HHHCCCCHHHH-HHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCC-CEEEE
Q ss_conf             35542113-43213662678-988512681899617886622577788888877753697-30675
Q gi|254780834|r  289 AGVQNVVS-SLGTALTEYQL-RLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN-RVNFV  351 (648)
Q Consensus       289 ~G~~n~va-~~Gtalt~~~~-~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~-~v~vv  351 (648)
                      .-|++++- |+++ | +.++ ..+-+ .+.+|++||.. .++..+.+|++.+   .+.|. +|+++
T Consensus        25 gHI~gA~niP~~~-l-e~~~~~~~p~-kd~~Ivvyc~~-g~~~~s~~Aa~~L---~~~Gy~~V~~L   83 (92)
T cd01532          25 SHPLWAANLPLSR-L-ELDAWVRIPR-RDTPIVVYGEG-GGEDLAPRAARRL---SELGYTDVALL   83 (92)
T ss_pred             CCCCCCCCCCHHH-H-HHHHHHHCCC-CCCEEEEEECC-CCCHHHHHHHHHH---HHCCCCCEEEC
T ss_conf             8885677298889-8-7767763879-99829999699-9962999999999---98699686885


No 294
>COG1915 Uncharacterized conserved protein [Function unknown]
Probab=25.51  E-value=15  Score=15.56  Aligned_cols=25  Identities=32%  Similarity=0.530  Sum_probs=13.0

Q ss_pred             CCHHHHHHH----HHCCCCCCHHHHHCCCCH
Q ss_conf             143889998----743554211343213662
Q gi|254780834|r  278 EGYMDVLSL----CQAGVQNVVSSLGTALTE  304 (648)
Q Consensus       278 EGy~Dvi~l----~~~G~~n~va~~Gtalt~  304 (648)
                      |||.|++-.    .-+.|+  .|.+||+|.-
T Consensus       226 ~GyV~~L~~GNAlA~HDIE--~~l~GTSLGv  254 (415)
T COG1915         226 EGYVDALLAGNALAVHDIE--QALMGTSLGV  254 (415)
T ss_pred             HHHHHHHHCCCCEEECHHH--HHHHCCCCCE
T ss_conf             3058876557701320467--8761353021


No 295
>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
Probab=25.49  E-value=33  Score=12.32  Aligned_cols=83  Identities=19%  Similarity=0.159  Sum_probs=52.8

Q ss_pred             EEEECCHHHHHHH------HHCCCCCCHHHHHCCCCHHHHHHHHHCC---CEEEEEECCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf             8997143889998------7435542113432136626789885126---818996178866225777888888777536
Q gi|254780834|r  274 IILVEGYMDVLSL------CQAGVQNVVSSLGTALTEYQLRLLWKLS---PRIVLCFDGDDPGLRAAYKAIDLVLCHLIP  344 (648)
Q Consensus       274 ~i~vEGy~Dvi~l------~~~G~~n~va~~Gtalt~~~~~~l~r~~---~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~  344 (648)
                      -||.-+..|-+..      .+-| .|+....-..-...|+++++++.   ++|-+.||..+++-.+..+.++.+.  -+.
T Consensus        83 PIVF~~V~dPv~aglv~s~~~pg-~NvTGvs~~~~~~~~l~l~~~l~P~~k~igvlyn~~e~ns~~~~~~~~~~a--~~~  159 (281)
T cd06325          83 PIVFTAVTDPVGAGLVKSLEKPG-GNVTGVSDLVPVETQLELLKKLLPDAKTVGVLYNPSEANSVVQVKELKKAA--AKL  159 (281)
T ss_pred             CEEEEECCCHHHCCCCCCCCCCC-CCEEEEECCCCHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHH--HHC
T ss_conf             98999516866627543567899-957998787478999999998588985899995799865699999999999--976


Q ss_pred             CCCEEEEECCCCCCHHHH
Q ss_conf             973067525788888899
Q gi|254780834|r  345 GNRVNFVLLSRGEDPDSF  362 (648)
Q Consensus       345 g~~v~vv~LP~G~DPDe~  362 (648)
                      |+++..+..+   ++.|+
T Consensus       160 Gi~v~~~~v~---~~~ei  174 (281)
T cd06325         160 GIEVVEATVS---SSNDV  174 (281)
T ss_pred             CCEEEEEECC---CHHHH
T ss_conf             9889999459---88899


No 296
>KOG0164 consensus
Probab=25.44  E-value=33  Score=12.31  Aligned_cols=61  Identities=20%  Similarity=0.326  Sum_probs=29.1

Q ss_pred             CCCCEEEEECCHHHHHHHHH----CCCCCCHHHHHCCCCHHHHHHHHHCC------CEEEEEECCCCCCHHHH
Q ss_conf             67870899714388999874----35542113432136626789885126------81899617886622577
Q gi|254780834|r  269 NSSSFIILVEGYMDVLSLCQ----AGVQNVVSSLGTALTEYQLRLLWKLS------PRIVLCFDGDDPGLRAA  331 (648)
Q Consensus       269 ~~~~~~i~vEGy~Dvi~l~~----~G~~n~va~~Gtalt~~~~~~l~r~~------~~vvl~fDgD~AG~kAa  331 (648)
                      +...+.++.-|-++|.+.+.    .++.++..+.|  |+++-+..+|+..      .+|-+.=+.|..|+.+.
T Consensus       223 ~~~~Y~ylnqg~~~v~sinD~~dfk~V~~Am~vIg--Fs~eEVe~v~~iiAavLhLGNv~f~~~ed~~~~~~~  293 (1001)
T KOG0164         223 NPQSYNYLNQGSAKVSSINDASDFKAVQKAMRVIG--FSEEEVESVLSIIAAVLHLGNVEFADNEDSSGIVNG  293 (1001)
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHH
T ss_conf             75300222000233046551777999998888738--888999999999999985066688514765454005


No 297
>smart00828 PKS_MT Methyltransferase  in polyketide synthase (PKS) enzymes.
Probab=25.40  E-value=33  Score=12.35  Aligned_cols=17  Identities=18%  Similarity=0.337  Sum_probs=11.5

Q ss_pred             ECCCCCCCCHHHHHHHH
Q ss_conf             13688887898998988
Q gi|254780834|r   64 CFSCHVKGDHLSFLSAL   80 (648)
Q Consensus        64 cf~c~~~gd~~~f~~~~   80 (648)
                      .+|||.|+..+....++
T Consensus         5 DiGCG~G~~~~~LA~~~   21 (224)
T smart00828        5 DFGCGYGSDLIDLAERH   21 (224)
T ss_pred             EEECCCCHHHHHHHHHC
T ss_conf             98366888899999977


No 298
>cd01196 INT_VanD VanD integrase, IntD, and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases including those similar to IntD, a putative integrase-like protein, a component of the vanD glycopeptide resistance cluster in Enterococcus faecium BM4339. Members of this CD are predominantly bacterial in origin.
Probab=25.38  E-value=33  Score=12.40  Aligned_cols=18  Identities=11%  Similarity=0.348  Sum_probs=13.5

Q ss_pred             HHHHHHCCCCHHHHCCCC
Q ss_conf             999985068853510124
Q gi|254780834|r  141 HYYLDERGIDSHAIEMFK  158 (648)
Q Consensus       141 ~~yl~~Rg~~~~~~~~f~  158 (648)
                      .+||.+||+|+.||+.|.
T Consensus         2 ~~yL~e~g~S~~Ti~sY~   19 (263)
T cd01196           2 EEYLYKNNLSKNTVSSYL   19 (263)
T ss_pred             HHHHHHCCCCHHHHHHHH
T ss_conf             587967697899999999


No 299
>pfam05480 Staph_haemo Staphylococcus haemolytic protein. This family consists of several different short Staphylococcal proteins, it contains SLUSH A, B and C proteins as well as haemolysin and gonococcal growth inhibitor. Some strains of the coagulase-negative Staphylococcus lugdunensis produce a synergistic hemolytic activity (SLUSH), phenotypically similar to the delta-hemolysin of S. aureus. Gonococcal growth inhibitor from Staphylococcus act on the cytoplasmic membrane of the gonococcal cell causing cytoplasmic leakage and, eventually, death.
Probab=25.38  E-value=30  Score=12.77  Aligned_cols=25  Identities=28%  Similarity=0.546  Sum_probs=16.4

Q ss_pred             CCHHHHHH-HHHCCCCCCHHHHHCCC
Q ss_conf             14388999-87435542113432136
Q gi|254780834|r  278 EGYMDVLS-LCQAGVQNVVSSLGTAL  302 (648)
Q Consensus       278 EGy~Dvi~-l~~~G~~n~va~~Gtal  302 (648)
                      ||.+++|+ ..++|+.+-=|.|||++
T Consensus         2 ~~l~eAI~n~V~Ag~~~DwaklGtSI   27 (43)
T pfam05480         2 SGLFEAIKNAVQAGIAQDWAKLGTSI   27 (43)
T ss_pred             CHHHHHHHHHHHHHHCCCHHHHCCHH
T ss_conf             17999999999986026389842069


No 300
>COG3673 Uncharacterized conserved protein [Function unknown]
Probab=25.37  E-value=33  Score=12.30  Aligned_cols=23  Identities=22%  Similarity=0.600  Sum_probs=14.7

Q ss_pred             CCCCCCCCCCEEEECCCCEEEECC
Q ss_conf             458888587879817897467136
Q gi|254780834|r   43 CPFHDEKTPSFHCNDSKGFYYCFS   66 (648)
Q Consensus        43 cPfh~ektpsf~v~~~~~~~~cf~   66 (648)
                      |-|...- |+..-+.-|++-.||-
T Consensus        16 ~g~~s~~-~~~~~ds~k~lV~CfD   38 (423)
T COG3673          16 CGFTSDL-NLLAEDSMKRLVFCFD   38 (423)
T ss_pred             CCCCCCC-CCCCCCCCCEEEEEEC
T ss_conf             6788887-5332357642899963


No 301
>KOG2730 consensus
Probab=25.21  E-value=34  Score=12.28  Aligned_cols=16  Identities=19%  Similarity=0.395  Sum_probs=9.3

Q ss_pred             EEECCHHHHHHHHHCC
Q ss_conf             9971438899987435
Q gi|254780834|r  275 ILVEGYMDVLSLCQAG  290 (648)
Q Consensus       275 i~vEGy~Dvi~l~~~G  290 (648)
                      .++--+.|+.+-.|+.
T Consensus       147 FI~GD~ld~~~~lq~~  162 (263)
T KOG2730         147 FICGDFLDLASKLKAD  162 (263)
T ss_pred             EEECHHHHHHHHHHHH
T ss_conf             8833099999988641


No 302
>KOG4672 consensus
Probab=25.10  E-value=34  Score=12.26  Aligned_cols=14  Identities=14%  Similarity=0.197  Sum_probs=5.8

Q ss_pred             CHHHHHHHCCCCCH
Q ss_conf             10345542059973
Q gi|254780834|r  167 YSLREHLRQKGFSE  180 (648)
Q Consensus       167 ~~l~~~l~~~~~~~  180 (648)
                      -..+.+|+++-+..
T Consensus       102 p~~~~~L~r~evey  115 (487)
T KOG4672         102 PVMFSHLQRREVEY  115 (487)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             07889999876666


No 303
>pfam03811 Ins_element1 Insertion element protein.
Probab=25.08  E-value=34  Score=12.26  Aligned_cols=28  Identities=18%  Similarity=0.443  Sum_probs=17.9

Q ss_pred             ECCCCCCCCCCE----EEECCCCEEEECCCCCC
Q ss_conf             345888858787----98178974671368888
Q gi|254780834|r   42 CCPFHDEKTPSF----HCNDSKGFYYCFSCHVK   70 (648)
Q Consensus        42 ~cPfh~ektpsf----~v~~~~~~~~cf~c~~~   70 (648)
                      .|||.+... +-    .-...+|.|.|..|+..
T Consensus         7 ~Cp~C~s~~-~V~KnG~~~~G~QRYrC~~C~r~   38 (88)
T pfam03811         7 HCPRCSSTE-GVYRHGQSTAGHQRYRCRHCRRT   38 (88)
T ss_pred             ECCCCCCCC-CEEECCCCCCCCCCEEECCCCCE
T ss_conf             797888987-67718968999857772778955


No 304
>pfam06819 Arc_PepC Archaeal Peptidase A24 C-terminal Domain. This region is of unknown function but is found in some archaeal pfam01478. It is predicted to be of mixed alpha/beta secondary structure by JPred.
Probab=25.05  E-value=27  Score=13.08  Aligned_cols=24  Identities=38%  Similarity=0.435  Sum_probs=17.8

Q ss_pred             CCCHHHHHCCCCHHHHHHHHHCCC
Q ss_conf             421134321366267898851268
Q gi|254780834|r  292 QNVVSSLGTALTEYQLRLLWKLSP  315 (648)
Q Consensus       292 ~n~va~~Gtalt~~~~~~l~r~~~  315 (648)
                      +.++.|.|--||++|+..|+++..
T Consensus        78 ~~i~~~~~EGLs~E~IE~LkkLv~  101 (111)
T pfam06819        78 EEVAGTSGEGLTEEQIEKLKKLVS  101 (111)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             757515645677989999999997


No 305
>cd00687 Terpene_cyclase_nonplant_C1 NonPlant Terpene Cyclases, Class 1 (C1). This CD includes terpenoid cyclases such as pentalenene synthase and aristolochene synthase which, using an all-trans pathway, catalyze the ionization of farnesyl diphosphate, followed by the formation of a macrocyclic intermediate by bond formation between C1 with either C10 (aristolochene synthase) or C11 (pentalenene synthase), resulting in production of tricyclic hydrocarbon pentalenene or bicyclic hydrocarbon aristolochene. As with other enzymes with the 'terpenoid synthase fold', they have two conserved metal binding motifs, proposed to coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP to the enzymes. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function in the monomeric form and are foun
Probab=24.97  E-value=34  Score=12.24  Aligned_cols=31  Identities=13%  Similarity=0.065  Sum_probs=18.2

Q ss_pred             HHHHHCCCCCCHHHHHCCCCHHHHHHHHHCC
Q ss_conf             9987435542113432136626789885126
Q gi|254780834|r  284 LSLCQAGVQNVVSSLGTALTEYQLRLLWKLS  314 (648)
Q Consensus       284 i~l~~~G~~n~va~~Gtalt~~~~~~l~r~~  314 (648)
                      -.+...++...+|-+----+.+++.++..+.
T Consensus        36 ~~~~~~~~~~~~a~~~P~a~~e~L~l~~~~~   66 (303)
T cd00687          36 KRFLSADFGDLAALFYPDADDERLMLAADLM   66 (303)
T ss_pred             HHHHCCCHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             9987499998898868999989999999999


No 306
>PRK00443 nagB glucosamine-6-phosphate deaminase; Provisional
Probab=24.93  E-value=34  Score=12.23  Aligned_cols=16  Identities=19%  Similarity=0.395  Sum_probs=8.7

Q ss_pred             CCCEEEEEECCCCCCH
Q ss_conf             2681899617886622
Q gi|254780834|r  313 LSPRIVLCFDGDDPGL  328 (648)
Q Consensus       313 ~~~~vvl~fDgD~AG~  328 (648)
                      ..+++++..|-++|..
T Consensus       231 ~H~~~~~~lD~~AAs~  246 (264)
T PRK00443        231 LHPNATVVLDEEAASE  246 (264)
T ss_pred             CCCCEEEEECHHHHHC
T ss_conf             4998899988899806


No 307
>PRK08174 DNA topoisomerase III; Validated
Probab=24.91  E-value=34  Score=12.23  Aligned_cols=13  Identities=23%  Similarity=0.378  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             3799999999984
Q gi|254780834|r  481 SLREAALLLTLIN  493 (648)
Q Consensus       481 ~~~E~~LL~llI~  493 (648)
                      ...|..|+..|-+
T Consensus       487 ryTEasLi~~M~~  499 (670)
T PRK08174        487 PYTEGTLIKAMKN  499 (670)
T ss_pred             CCCHHHHHHHHHH
T ss_conf             9898999999986


No 308
>PRK06674 DNA polymerase III subunits gamma and tau; Validated
Probab=24.86  E-value=34  Score=12.22  Aligned_cols=77  Identities=19%  Similarity=0.284  Sum_probs=44.8

Q ss_pred             ECCHH-HHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCE------EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             71438-89998743554211343213662678988512681------899617886622577788888877753697306
Q gi|254780834|r  277 VEGYM-DVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPR------IVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVN  349 (648)
Q Consensus       277 vEGy~-Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~------vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~  349 (648)
                      -||=| |++++-.    .+++-.|..+|.+++..+...++.      +--++++|.+   +++..++.   ++       
T Consensus       210 a~GsmRDAlsiLd----Q~~s~~~~~i~~~~v~~~lG~~~~~~~~~l~~~i~~~d~~---~~l~~~~~---~~-------  272 (563)
T PRK06674        210 ADGGMRDALSLLD----QAISFSDERVTTEDVLAVTGAVSQQYLGNLVECIRENDVS---RALRIIDE---MM-------  272 (563)
T ss_pred             CCCCHHHHHHHHH----HHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHH---HHHHHHHH---HH-------
T ss_conf             6997889999999----9997159976899999986899889999999999848999---99999999---99-------


Q ss_pred             EEECCCCCCHHHHHHCCCHHHHHHHH
Q ss_conf             75257888888997203668899886
Q gi|254780834|r  350 FVLLSRGEDPDSFIRCYGKTAFEKLI  375 (648)
Q Consensus       350 vv~LP~G~DPDe~ir~~G~eaf~~ll  375 (648)
                          -.|+||.-|+..- ..-|++++
T Consensus       273 ----~~G~d~~~~~~dl-~~~~r~~l  293 (563)
T PRK06674        273 ----GQGKDPVRLMEDF-IYYYRDML  293 (563)
T ss_pred             ----HCCCCHHHHHHHH-HHHHHHHH
T ss_conf             ----8799999999999-99999988


No 309
>pfam09393 DUF2001 Protein of unknown function (DUF2001). This family includes phage-like element PBSX protein whose structure adopts a beta barrel flanked with alpha helical regions.
Probab=24.85  E-value=30  Score=12.72  Aligned_cols=35  Identities=26%  Similarity=0.447  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHH
Q ss_conf             25777888888777536973067525788888899
Q gi|254780834|r  328 LRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSF  362 (648)
Q Consensus       328 ~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~  362 (648)
                      .+-+-|..++....++.|..++|-..-...||+++
T Consensus        66 ~kvtS~~~~~~~~~ik~G~~~~f~Ii~~l~DP~s~  100 (141)
T pfam09393        66 YKVTSRFRKLMIDYIKTGKDPYFEIISKLEDPDSY  100 (141)
T ss_pred             EEECHHHHHHHHHHHHCCCCCEEEEEEEECCCCCC
T ss_conf             98568999999999964998228999990799766


No 310
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=24.82  E-value=34  Score=12.22  Aligned_cols=10  Identities=20%  Similarity=0.478  Sum_probs=5.2

Q ss_pred             HCCCCCCHHH
Q ss_conf             4355421134
Q gi|254780834|r  288 QAGVQNVVSS  297 (648)
Q Consensus       288 ~~G~~n~va~  297 (648)
                      ++|+.-+..|
T Consensus       190 ~~Gf~e~~~P  199 (429)
T COG0172         190 KHGFTEVLPP  199 (429)
T ss_pred             HCCCEEEECC
T ss_conf             7696586576


No 311
>PRK05580 primosome assembly protein PriA; Validated
Probab=24.68  E-value=34  Score=12.20  Aligned_cols=20  Identities=20%  Similarity=0.275  Sum_probs=9.8

Q ss_pred             CCHHHHHCCCCHHHHHHHHH
Q ss_conf             21134321366267898851
Q gi|254780834|r  293 NVVSSLGTALTEYQLRLLWK  312 (648)
Q Consensus       293 n~va~~Gtalt~~~~~~l~r  312 (648)
                      .-|+.+.-.+|+.+-...|+
T Consensus       240 ~~v~v~HS~ls~~eR~~~w~  259 (699)
T PRK05580        240 ARVAVLHSGLSDGERYRAWL  259 (699)
T ss_pred             CCEEEECCCCCHHHHHHHHH
T ss_conf             95799648898579999999


No 312
>COG4963 CpaE Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]
Probab=24.66  E-value=34  Score=12.19  Aligned_cols=31  Identities=13%  Similarity=0.003  Sum_probs=17.9

Q ss_pred             CCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHH
Q ss_conf             78888889972036688998864149927999
Q gi|254780834|r  354 SRGEDPDSFIRCYGKTAFEKLIVESLPLVDML  385 (648)
Q Consensus       354 P~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl  385 (648)
                      |.--+|+.+. ..+.+++..+++...+.++|+
T Consensus       191 ~a~~~~~~~~-d~~~~~~~~Ll~~~~~~~~~v  221 (366)
T COG4963         191 AAPTELAKNY-DLKTGAVERLLDLLRGSFDFV  221 (366)
T ss_pred             CCCCCHHHHC-CCCCCHHHHHHHHHHCCCCEE
T ss_conf             3774456521-533126999999764028838


No 313
>TIGR01326 OAH_OAS_sulfhy O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase; InterPro: IPR006235   This family of sequences is a distinct clade of the Cys/Met metabolism pyridoxal phosphate-dependent enzyme superfamily. Members include examples of OAH/OAS sulfhydrylase, an enzyme with activity both as O-acetylhomoserine sulfhydrylase (OAH, 2.5.1.49 from EC) and O-acetylserine sulfhydrylase (OAS, 2.5.1.47 from EC). An alternate name for OAH sulfhydrylase is homocysteine synthase.; GO: 0016765 transferase activity transferring alkyl or aryl (other than methyl) groups, 0006520 amino acid metabolic process.
Probab=24.66  E-value=18  Score=14.77  Aligned_cols=40  Identities=30%  Similarity=0.444  Sum_probs=25.7

Q ss_pred             HCCCCEEEEECCCCCC-HHHH---HHCCCHHHHHHHHHHCC-CHHHHH
Q ss_conf             3697306752578888-8899---72036688998864149-927999
Q gi|254780834|r  343 IPGNRVNFVLLSRGED-PDSF---IRCYGKTAFEKLIVESL-PLVDML  385 (648)
Q Consensus       343 ~~g~~v~vv~LP~G~D-PDe~---ir~~G~eaf~~ll~~A~-~l~dFl  385 (648)
                      +-|++||||   ++.| |++|   |+.+-+--|.+-|.|.. ...||-
T Consensus       119 rlGIevrFv---d~dd~pe~~~k~id~nTKAvf~EtIgNP~~~v~Die  163 (434)
T TIGR01326       119 RLGIEVRFV---DGDDDPEELEKAIDENTKAVFAETIGNPALNVPDIE  163 (434)
T ss_pred             HCCEEEEEE---CCCCCHHHHHHHCCCCCEEEEEECCCCCCCCCCCHH
T ss_conf             448148872---788887899976066751898401238776767858


No 314
>PRK09401 reverse gyrase; Reviewed
Probab=24.66  E-value=34  Score=12.19  Aligned_cols=37  Identities=19%  Similarity=0.214  Sum_probs=28.3

Q ss_pred             HHHHHHHHC---CCEEEEEECCCCCCHHHHHHHHHHHHHH
Q ss_conf             678988512---6818996178866225777888888777
Q gi|254780834|r  305 YQLRLLWKL---SPRIVLCFDGDDPGLRAAYKAIDLVLCH  341 (648)
Q Consensus       305 ~~~~~l~r~---~~~vvl~fDgD~AG~kAa~Ra~e~~l~~  341 (648)
                      +-++.|+++   +++|+|+-|.|.=|-+=||...+.+.+.
T Consensus       707 ~vv~aLR~lA~EvDeVyIATDPDREGEaIAwhl~~~Lk~~  746 (1176)
T PRK09401        707 EIIEALRELALEVDEVLIATDPDTEGEKIAWDVYLLLSPY  746 (1176)
T ss_pred             HHHHHHHHHHHHCCEEEECCCCCCCCHHHHHHHHHHHCCC
T ss_conf             9999999998755989987899856389999999983554


No 315
>cd00127 DSPc Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
Probab=24.57  E-value=34  Score=12.18  Aligned_cols=11  Identities=27%  Similarity=0.471  Sum_probs=4.1

Q ss_pred             HHHHCCCCCCH
Q ss_conf             98743554211
Q gi|254780834|r  285 SLCQAGVQNVV  295 (648)
Q Consensus       285 ~l~~~G~~n~v  295 (648)
                      .|.+.||+.+|
T Consensus        22 ~L~~~gI~~Ii   32 (139)
T cd00127          22 LLKKLGITHVL   32 (139)
T ss_pred             HHHHCCCEEEE
T ss_conf             99878980999


No 316
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=24.54  E-value=34  Score=12.18  Aligned_cols=37  Identities=16%  Similarity=0.197  Sum_probs=16.8

Q ss_pred             EEEECC-CCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             996178-866225777888888777536973067525788
Q gi|254780834|r  318 VLCFDG-DDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRG  356 (648)
Q Consensus       318 vl~fDg-D~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G  356 (648)
                      .++|.| |.||+-...+.+.-.  +...|..|.+..-|.|
T Consensus         5 fI~iEGiDGaGKTT~~~~L~~~--l~~~g~~v~~trEP~~   42 (208)
T COG0125           5 FIVIEGIDGAGKTTQAELLKER--LEERGIKVVLTREPGG   42 (208)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH--HHHCCCEEEEEECCCC
T ss_conf             9999788889889999999999--9982980799868999


No 317
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.34  E-value=14  Score=15.91  Aligned_cols=18  Identities=22%  Similarity=0.724  Sum_probs=9.9

Q ss_pred             EEEECCCCC---CCCHHHHHH
Q ss_conf             467136888---878989989
Q gi|254780834|r   61 FYYCFSCHV---KGDHLSFLS   78 (648)
Q Consensus        61 ~~~cf~c~~---~gd~~~f~~   78 (648)
                      -|+|..||.   .|-.|+|..
T Consensus         6 ewkC~VCg~~iieGqkFTF~~   26 (103)
T COG4847           6 EWKCYVCGGTIIEGQKFTFTK   26 (103)
T ss_pred             EEEEEEECCEEEECCEEEEEE
T ss_conf             056764088744155788831


No 318
>pfam10191 COG7 Golgi complex component 7 (COG7). COG7 is a component of the conserved oligomeric Golgi complex which is required for normal Golgi morphology and localisation. Mutation in COG7 causes a congenital disorder of glycosylation.
Probab=24.24  E-value=35  Score=12.13  Aligned_cols=10  Identities=20%  Similarity=0.248  Sum_probs=3.4

Q ss_pred             CCCCCHHHHH
Q ss_conf             7888888997
Q gi|254780834|r  354 SRGEDPDSFI  363 (648)
Q Consensus       354 P~G~DPDe~i  363 (648)
                      .+|..-+.++
T Consensus       418 T~g~~~~~Ll  427 (768)
T pfam10191       418 TQGLALCGLI  427 (768)
T ss_pred             HCCCCHHHHH
T ss_conf             2763428899


No 319
>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein B; InterPro: IPR004435   The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cisdithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism , .    In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which coverts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner . MoCF is the active co-factor in eukaryotic and some prokaryotic molybdoenzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdoenzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF . Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 () of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) .   The MobB domain is similar to that of the urease accessory protein UreG and the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocentres of their respective target enzymes. It is involved in the final step of molybdenum-cofactor biosynthesis. While its precise function has not been identified it is thought to be involved in the transfer of a guanine dinucleotide moiety to molybdopterin, as it shows GTP-binding and weak GTPase activity . The MobB protein (P32125 from SWISSPROT) from Escherichia coli, which is comprised of this domain, is a homodimer . Each molecule is composed of two distinct regions - an outer region comprised of 6 beta-strands and three alpha helices, and an inner region comprised of a two-strand beta hairpin followed by an alpha helix. These regions require interaction with the second monomer to allow proper folding to occur. The two monomers are intertwined and form an extensive 16-stranded beta-sheet. While the active site could not be positively identified, the presence of highly conserved residues suggests the substrate binding site occurs in the central solvent channel.; GO: 0005525 GTP binding, 0006777 Mo-molybdopterin cofactor biosynthetic process.
Probab=24.23  E-value=33  Score=12.41  Aligned_cols=25  Identities=36%  Similarity=0.445  Sum_probs=14.5

Q ss_pred             CHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHH
Q ss_conf             8178888643310000235678708997143889
Q gi|254780834|r  250 NFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDV  283 (648)
Q Consensus       250 ~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dv  283 (648)
                      .|..+.+...-         .+--++|||||=|-
T Consensus        84 ~L~~~l~~~~~---------~~~D~~LvEGfK~~  108 (165)
T TIGR00176        84 DLEALLKRLAD---------RELDIILVEGFKDS  108 (165)
T ss_pred             CHHHHHHHCCC---------CCCCEEEEECCCCC
T ss_conf             87999864285---------52687898524557


No 320
>KOG2185 consensus
Probab=24.22  E-value=35  Score=12.13  Aligned_cols=48  Identities=23%  Similarity=0.315  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999998724127989999999999999999999884132676
Q gi|254780834|r  590 LLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIE  639 (648)
Q Consensus       590 ~L~r~l~ele~~l~e~~~~~d~e~~~~l~~el~elk~~L~~l~~~Eal~e  639 (648)
                      .+++.+..++..++.  ..+|......+...+++.+++|..+.++|+-+.
T Consensus       424 rlkrdm~klkq~l~R--N~gd~v~s~~lqe~L~ev~~~Lasl~aqea~ls  471 (486)
T KOG2185         424 RLKRDMLKLKQMLNR--NKGDLVVSEALQERLKEVRKALASLLAQEAALS  471 (486)
T ss_pred             HHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999862--453178999999999999999999999998876


No 321
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=24.20  E-value=35  Score=12.13  Aligned_cols=60  Identities=18%  Similarity=0.220  Sum_probs=36.8

Q ss_pred             CCCCHHHHHHCCCHHHHHHHHHHCCC---HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             88888899720366889988641499---2799999998530233145799999999988541
Q gi|254780834|r  355 RGEDPDSFIRCYGKTAFEKLIVESLP---LVDMLWKRETENRSFNTPDERAELEIHLKNCINH  414 (648)
Q Consensus       355 ~G~DPDe~ir~~G~eaf~~ll~~A~~---l~dFl~~~l~~~~dl~spe~ka~~~~~l~~~I~~  414 (648)
                      ...||.+++.++|+|+++-++-...|   -.+|=|+......+.+-...--.+++++...+.+
T Consensus       306 n~i~~~~~~~~~g~D~lRyyl~~~~~~~~D~dfs~~~f~~r~NsdL~n~lGNl~~R~~~~~~k  368 (644)
T PRK12267        306 NVVDPEELVDRYGLDALRYYLLREVPFGSDGDFSPEAFVERINSDLANDLGNLLNRTVAMINK  368 (644)
T ss_pred             CEECHHHHHHHCCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             422379998755940436464444887877778999999998899887777899999999887


No 322
>pfam09740 DUF2043 Uncharacterized conserved protein (DUF2043). This is a 100 residue conserved region of a family of proteins found from fungi to humans. This region contains three conserved Cysteines and a motif of {CP}{y/l}{HG}.
Probab=24.19  E-value=27  Score=13.19  Aligned_cols=15  Identities=27%  Similarity=0.793  Sum_probs=5.6

Q ss_pred             CCCCEEEEEEEECCCCE
Q ss_conf             01671688897077858
Q gi|254780834|r  201 RFRNRLIFPIRSSRGQV  217 (648)
Q Consensus       201 ~Fr~Ri~fPi~~~~g~~  217 (648)
                      -|.|+|| | +|..|++
T Consensus        92 PFHGkII-p-RDd~G~P  106 (111)
T pfam09740        92 PFHGKIV-P-RDDEGRP  106 (111)
T ss_pred             CCCCCCC-C-CCCCCCC
T ss_conf             8778644-8-4436897


No 323
>TIGR01858 tag_bisphos_ald class II aldolase, tagatose bisphosphate family; InterPro: IPR011288   This entry describes tagatose-1,6-bisphosphate aldolases, and perhaps other closely related class II aldolases. This tetrameric, Zn2+-dependent enzyme is related to the class II fructose bisphosphate aldolase; fructose 1,6-bisphosphate and tagatose 1,6 bisphosphate differ only in chirality at C4 , .; GO: 0008270 zinc ion binding, 0016832 aldehyde-lyase activity, 0019512 lactose catabolic process via tagatose-6-phosphate.
Probab=24.17  E-value=30  Score=12.68  Aligned_cols=89  Identities=21%  Similarity=0.340  Sum_probs=50.5

Q ss_pred             CCCCC-CHHHHHCC---------CCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCC----------CE
Q ss_conf             35542-11343213---------662678988512681899617886622577788888877753697----------30
Q gi|254780834|r  289 AGVQN-VVSSLGTA---------LTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN----------RV  348 (648)
Q Consensus       289 ~G~~n-~va~~Gta---------lt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~----------~v  348 (648)
                      -||.- +||. |||         |-=+-+..|++.++=+..+==+=.=--+-..|++||-..-+--+-          .-
T Consensus       165 TGvDSLAvAI-GTAHGlY~~aP~LDF~RL~~IR~~v~vPLVLHGASdvpde~v~~~IeLGi~KvNVATeLKiAFS~AlK~  243 (282)
T TIGR01858       165 TGVDSLAVAI-GTAHGLYKEAPKLDFDRLAKIREKVDVPLVLHGASDVPDEDVRRTIELGICKVNVATELKIAFSGALKA  243 (282)
T ss_pred             CCCHHHHHHH-HHHHHHHHCCCCCCHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHHHCCCEEECCHHCCHHHHHHHHH
T ss_conf             2754788988-665323212675337899875220377724217778876789999870741341111100368999999


Q ss_pred             EEEECCCCCCHHHHHHCCCHHHHHHHHHHCC
Q ss_conf             6752578888889972036688998864149
Q gi|254780834|r  349 NFVLLSRGEDPDSFIRCYGKTAFEKLIVESL  379 (648)
Q Consensus       349 ~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~  379 (648)
                      +|+.-|++-||=.|++. |++++++.+++-.
T Consensus       244 Yf~enp~AnDPR~Ym~~-ak~AMk~vv~~kI  273 (282)
T TIGR01858       244 YFLENPEANDPRKYMRP-AKEAMKKVVEKKI  273 (282)
T ss_pred             HHHHCCCCCCCHHHHHH-HHHHHHHHHHHHH
T ss_conf             99748899983252366-7999999988664


No 324
>PRK10116 universal stress protein UspC; Provisional
Probab=24.16  E-value=35  Score=12.12  Aligned_cols=43  Identities=14%  Similarity=0.306  Sum_probs=34.4

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHH
Q ss_conf             818996178866225777888888777536973067525788888899
Q gi|254780834|r  315 PRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSF  362 (648)
Q Consensus       315 ~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~  362 (648)
                      ++|.+.-|+-....++..||++++..+   |-++.++..  ..||+-|
T Consensus         4 khILVAvDlS~~S~~~i~kA~~lA~~~---~AklslihV--~~~~~~y   46 (142)
T PRK10116          4 SNILVAVAVTPESQQLLAKAVSIARPV---NGKISLITL--ASDPEMY   46 (142)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHHHHHC---CCEEEEEEE--ECCHHHH
T ss_conf             689999418850699999999999981---998999999--3576665


No 325
>pfam07212 Hyaluronidase_1 Hyaluronidase protein (HylP). This family consists of several phage associated hyaluronidase proteins (EC:3.2.1.35) which seem to be specific to Streptococcus pyogenes and Streptococcus pyogenes bacteriophages. The substrate of hyaluronidase is hyaluronic acid, a sugar polymer composed of alternating N-acetylglucosamine and glucuronic acid residues. Hyaluronic acid is found in the ground substance of human connective tissue and the vitreous of the eye and also is the sole component of the capsule of group A streptococci. The capsule has been shown to be an important virulence factor of this organism by virtue of its ability to resist phagocytosis. Production by S. pyogenes of both a hyaluronic acid capsule and hyaluronidase enzymatic activity capable of destroying the capsule is an interesting, yet-unexplained, phenomenon.
Probab=24.15  E-value=35  Score=12.12  Aligned_cols=14  Identities=14%  Similarity=0.297  Sum_probs=6.3

Q ss_pred             EECCCCEEEEECCC
Q ss_conf             70778588850100
Q gi|254780834|r  211 RSSRGQVIAFGGRT  224 (648)
Q Consensus       211 ~~~~g~~i~f~gR~  224 (648)
                      +|..-+.|-++|..
T Consensus       105 f~qsa~fvdy~gkt  118 (273)
T pfam07212       105 FNQSALFVDYKGTT  118 (273)
T ss_pred             CCCCEEEEEECCCC
T ss_conf             24412678603764


No 326
>PRK13559 hypothetical protein; Provisional
Probab=24.08  E-value=35  Score=12.11  Aligned_cols=36  Identities=25%  Similarity=0.335  Sum_probs=25.4

Q ss_pred             CCEECCCCCCCCCCCCCE-EEEEEEECCCCEEEEECCCCCC
Q ss_conf             210034654100001671-6888970778588850100146
Q gi|254780834|r  188 LLIDGDNSATSYDRFRNR-LIFPIRSSRGQVIAFGGRTLSK  227 (648)
Q Consensus       188 l~~~~~~~~~~~d~Fr~R-i~fPi~~~~g~~i~f~gR~l~~  227 (648)
                      +...+++|.    .|.+. -|=||+|..|+|+.|-|=..|=
T Consensus       123 l~nyrKDGs----~fwn~l~isPV~D~~G~v~~fig~q~Dv  159 (363)
T PRK13559        123 LLNYRKDGS----PFWNALHLGPIYDEDGKLLYFFGSQWDV  159 (363)
T ss_pred             EEEECCCCC----EEEEEEEEEEEECCCCCEEEEEEEEEEE
T ss_conf             999826998----2477689888798999799999999851


No 327
>KOG0385 consensus
Probab=24.05  E-value=35  Score=12.10  Aligned_cols=42  Identities=19%  Similarity=0.187  Sum_probs=22.4

Q ss_pred             CEEEEEECCC---CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHH
Q ss_conf             8189961788---6622577788888877753697306752578888889
Q gi|254780834|r  315 PRIVLCFDGD---DPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDS  361 (648)
Q Consensus       315 ~~vvl~fDgD---~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe  361 (648)
                      --+||.||+|   +.-..|..||--+     -+...|+|..|=...--++
T Consensus       559 ADtVIlyDSDWNPQ~DLQAmDRaHRI-----GQ~K~V~V~RLitentVEe  603 (971)
T KOG0385         559 ADTVILYDSDWNPQVDLQAMDRAHRI-----GQKKPVVVYRLITENTVEE  603 (971)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHC-----CCCCCEEEEEEECCCHHHH
T ss_conf             64799966899821437889988860-----7877159999753551899


No 328
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=24.05  E-value=35  Score=12.10  Aligned_cols=96  Identities=23%  Similarity=0.299  Sum_probs=56.1

Q ss_pred             CCCEEEEECCHHHHHHHHHC------CCCC--CHHHHHCCCCHHHHHHHHHC---CCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             78708997143889998743------5542--11343213662678988512---6818996178866225777888888
Q gi|254780834|r  270 SSSFIILVEGYMDVLSLCQA------GVQN--VVSSLGTALTEYQLRLLWKL---SPRIVLCFDGDDPGLRAAYKAIDLV  338 (648)
Q Consensus       270 ~~~~~i~vEGy~Dvi~l~~~------G~~n--~va~~Gtalt~~~~~~l~r~---~~~vvl~fDgD~AG~kAa~Ra~e~~  338 (648)
                      .-+--|+|||--||=+...+      |-+.  +|.+. ..-|  |+..-+|-   ++-|+|+-|.|..|++-|.|..+-+
T Consensus         6 pVDVRIiVEGAsDvE~iSkalQr~aLG~eYnITisSI-iPTT--~~eIA~raaeGADlvlIATDaD~~GReLA~kf~eeL   82 (290)
T COG4026           6 PVDVRIIVEGASDVEVISKALQRLALGSEYNITISSI-IPTT--NVEIAKRAAEGADLVLIATDADRVGRELAEKFFEEL   82 (290)
T ss_pred             CCEEEEEEECCCHHHHHHHHHHHHHHCCCCEEEEEEE-CCCC--HHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHH
T ss_conf             6317998606533899999998864056110588862-2675--199998763568779996057604599999999999


Q ss_pred             HHHHHCCCCEEEEECCCCCCHH----HHHHCCCHHHH
Q ss_conf             7775369730675257888888----99720366889
Q gi|254780834|r  339 LCHLIPGNRVNFVLLSRGEDPD----SFIRCYGKTAF  371 (648)
Q Consensus       339 l~~l~~g~~v~vv~LP~G~DPD----e~ir~~G~eaf  371 (648)
                      -.+  -| .+-=+.+|-|+|-.    +++++.=..++
T Consensus        83 rg~--VG-hiERmK~PiGHDvEhiD~elvrkEl~nAl  116 (290)
T COG4026          83 RGM--VG-HIERMKIPIGHDVEHIDVELVRKELKNAL  116 (290)
T ss_pred             HHH--HH-HHHEECCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             875--30-45112267787722058999999999999


No 329
>TIGR02087 LEUD_arch 3-isopropylmalate dehydratase, small subunit; InterPro: IPR011827   3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus .     This entry is most closely related to the 3-isopropylmalate dehydratase IPR004431 from INTERPRO. It also includes members, which cluster with other genes of leucine biosynthesis.    The structure of the Pyrococcus horikoshii small subunit (O59393 from SWISSPROT) has recently been determined . As expected the structure of this polypeptide is similar to that of aconitase domain 4, though one alpha helix is replaced by a short loop with relatively high temperature factor values. This loop region is thought to be important for substrate recognition. Unlike other aconitase family proteins, this subunit formed a tetramer through disulphide linkages, though it is not expected to interfere with its interaction with the large subunit. These disulphide linkages would be expected to confer thermostability on the enzyme, reflecting the thermophilic lifestyle of the organism.; GO: 0003861 3-isopropylmalate dehydratase activity, 0009098 leucine biosynthetic process, 0009316 3-isopropylmalate dehydratase complex.
Probab=24.02  E-value=31  Score=12.58  Aligned_cols=73  Identities=21%  Similarity=0.204  Sum_probs=42.7

Q ss_pred             CCEEEEECCCCCCCC--CCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHH---------HH
Q ss_conf             858885010014655--3001038767653521011081788886433100002356787089971438---------89
Q gi|254780834|r  215 GQVIAFGGRTLSKGE--SVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYM---------DV  283 (648)
Q Consensus       215 g~~i~f~gR~l~~~~--~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~---------Dv  283 (648)
                      |||.=||=-+ |.|.  +.+||-+-+-+          -..|+.++--..|....+-..+- |||=|--         =|
T Consensus         1 GrvwkFGDdv-DTD~IIPGrYLR~~~D~----------~eLA~haM~g~~PeF~~kvr~GD-viVAGkNFGcGSSREQA~   68 (159)
T TIGR02087         1 GRVWKFGDDV-DTDVIIPGRYLRTTDDP----------DELASHAMEGIDPEFAKKVREGD-VIVAGKNFGCGSSREQAA   68 (159)
T ss_pred             CCEEECCCCC-CCCEECCCCCCCCCCCH----------HHHHHHCCCCCCCCHHHHCCCCC-EEEECCCCCCCCCHHHHH
T ss_conf             9377606864-67704585225754777----------88998705589963134078997-887141647788778899


Q ss_pred             HHHHHCCCCCCHHHHH
Q ss_conf             9987435542113432
Q gi|254780834|r  284 LSLCQAGVQNVVSSLG  299 (648)
Q Consensus       284 i~l~~~G~~n~va~~G  299 (648)
                      |||-++||..|||=+-
T Consensus        69 ~ALK~aGv~aviA~SF   84 (159)
T TIGR02087        69 LALKAAGVAAVIAESF   84 (159)
T ss_pred             HHHHHCCEEEEEEEEC
T ss_conf             9997479048985201


No 330
>PRK13209 L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=23.95  E-value=35  Score=12.09  Aligned_cols=34  Identities=9%  Similarity=0.031  Sum_probs=15.2

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             78866225777888888777536973067525788
Q gi|254780834|r  322 DGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRG  356 (648)
Q Consensus       322 DgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G  356 (648)
                      +.|.+=++.++..+..++.+ ...+.++++.++.+
T Consensus        88 S~D~~~R~~~~e~~~kaI~l-A~~LGi~~I~lag~  121 (283)
T PRK13209         88 SEDDAVRAQGLEIMRKAIQL-AQDLGIRVIQLAGY  121 (283)
T ss_pred             CCCHHHHHHHHHHHHHHHHH-HHHCCCCEEEECCC
T ss_conf             97999999999999999999-99809998996887


No 331
>KOG2874 consensus
Probab=23.78  E-value=35  Score=12.06  Aligned_cols=23  Identities=30%  Similarity=0.501  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHH--HHHCCCCEEEE
Q ss_conf             577788888877--75369730675
Q gi|254780834|r  329 RAAYKAIDLVLC--HLIPGNRVNFV  351 (648)
Q Consensus       329 kAa~Ra~e~~l~--~l~~g~~v~vv  351 (648)
                      -++++|++++-.  .+-+|.+|.++
T Consensus       168 g~TLKAlelLT~CYilVqG~TVsai  192 (356)
T KOG2874         168 GSTLKALELLTNCYILVQGNTVSAI  192 (356)
T ss_pred             CHHHHHHHHHHHCEEEEECCEEEEE
T ss_conf             2057999997521798607677763


No 332
>TIGR00791 gntP transporter, gluconate:H+ symporter (GntP) family; InterPro: IPR003474 This is a family of integral membrane permeases that are involved in gluconate uptake. Escherichia coli contains several members of this family including GntU, a low affinity transporter  and GntT, a high affinity transporter .; GO: 0015128 gluconate transmembrane transporter activity, 0015725 gluconate transport, 0016020 membrane.
Probab=23.71  E-value=26  Score=13.26  Aligned_cols=15  Identities=20%  Similarity=0.162  Sum_probs=5.3

Q ss_pred             CHHHHHHHHHHHHHH
Q ss_conf             988999999999997
Q gi|254780834|r  512 NNELQKLWSFLFSDF  526 (648)
Q Consensus       512 ~~~~~~L~~~i~~~~  526 (648)
                      ||...-+-..++..|
T Consensus       273 np~~Am~IA~lvA~y  287 (458)
T TIGR00791       273 NPITAMLIAVLVAIY  287 (458)
T ss_pred             CHHHHHHHHHHHHHH
T ss_conf             858999999999999


No 333
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=23.69  E-value=36  Score=12.05  Aligned_cols=48  Identities=27%  Similarity=0.290  Sum_probs=34.5

Q ss_pred             ECCHH-HHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEE------EEEECCCCCCH
Q ss_conf             71438-899987435542113432136626789885126818------99617886622
Q gi|254780834|r  277 VEGYM-DVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRI------VLCFDGDDPGL  328 (648)
Q Consensus       277 vEGy~-Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~v------vl~fDgD~AG~  328 (648)
                      -||=| |++||-.    .++|..|..+|.++++.+..++++-      -.+++||....
T Consensus       222 a~GS~RDaLSlLD----Qai~~~~~~i~~~~v~~mLGl~d~~~i~~Ll~~i~~Gd~~~a  276 (600)
T PRK09111        222 AEGSVRDGLSLLD----QAIAHGAGEVTAEQVRDMLGLADRARVIDLFEALMRGDVAAA  276 (600)
T ss_pred             CCCCCCHHHHHHH----HHHHCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHH
T ss_conf             4898421899999----999727987569999998688767789999999985586889


No 334
>KOG0260 consensus
Probab=23.67  E-value=27  Score=13.11  Aligned_cols=21  Identities=24%  Similarity=0.137  Sum_probs=9.9

Q ss_pred             CCCCCCCCCCCCHHCCCHHHH
Q ss_conf             038767653521011081788
Q gi|254780834|r  234 LNSPETILFHKGKNLYNFFGA  254 (648)
Q Consensus       234 lNSpeT~if~K~~~Ly~l~~a  254 (648)
                      =||||+.=|-+...|-||+.-
T Consensus       789 dysPesrGfVENSyL~GLtP~  809 (1605)
T KOG0260         789 DYSPESRGFVENSYLTGLTPQ  809 (1605)
T ss_pred             CCCCCCCCEEECCCCCCCCHH
T ss_conf             998210442321202579889


No 335
>pfam00396 Granulin Granulin.
Probab=23.66  E-value=33  Score=12.35  Aligned_cols=10  Identities=40%  Similarity=1.434  Sum_probs=7.7

Q ss_pred             EEEECCCCCC
Q ss_conf             5753458888
Q gi|254780834|r   39 YWACCPFHDE   48 (648)
Q Consensus        39 ~~~~cPfh~e   48 (648)
                      =||+|||.+-
T Consensus         9 ~wgCCP~~~A   18 (43)
T pfam00396         9 GWGCCPLPQA   18 (43)
T ss_pred             CEECCCCCCC
T ss_conf             8930779988


No 336
>pfam00282 Pyridoxal_deC Pyridoxal-dependent decarboxylase conserved domain.
Probab=23.46  E-value=15  Score=15.49  Aligned_cols=35  Identities=26%  Similarity=0.285  Sum_probs=21.2

Q ss_pred             CCHHHHHCCCCH--HHHHHHHHCCCE--EEEEECCCCCC
Q ss_conf             211343213662--678988512681--89961788662
Q gi|254780834|r  293 NVVSSLGTALTE--YQLRLLWKLSPR--IVLCFDGDDPG  327 (648)
Q Consensus       293 n~va~~Gtalt~--~~~~~l~r~~~~--vvl~fDgD~AG  327 (648)
                      -+||+.||.-|-  +-+..|..++.+  +.+=-||--+|
T Consensus       196 ~VvataGTT~tGaiD~l~~i~~i~~~~~lWlHVDaA~GG  234 (370)
T pfam00282       196 FVCATLGTTGSGAFDPLQELGDICNKYDLWLHVDAAYAG  234 (370)
T ss_pred             EEEEECCCCCCCCCCCHHHHHHHHHHCCCEEEEEHHHHH
T ss_conf             999863771771347899999999983980884233334


No 337
>pfam11464 Rbsn FYVE-finger-containing Rab5 effector protein rabenosyn-5. Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family.Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively. Rab proteins are GTPases involved in the regulation of all stages of membrane trafficking.
Probab=23.20  E-value=36  Score=11.98  Aligned_cols=38  Identities=21%  Similarity=0.263  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998724127989999999999999999999
Q gi|254780834|r  593 RQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQ  630 (648)
Q Consensus       593 r~l~ele~~l~e~~~~~d~e~~~~l~~el~elk~~L~~  630 (648)
                      .++..++.-|.++...+.-|....|..-|++++.+.-+
T Consensus         3 qQi~nIk~yI~qAr~a~R~DEV~~Le~NLreLq~e~~~   40 (42)
T pfam11464         3 QQINNIKGYIRQARQAGRFDEVETLEENLRELQDELYE   40 (42)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             79999999999999854516999999999999999874


No 338
>pfam00365 PFK Phosphofructokinase.
Probab=23.19  E-value=36  Score=11.97  Aligned_cols=14  Identities=0%  Similarity=0.154  Sum_probs=5.5

Q ss_pred             EEECCC-CCCHHHHH
Q ss_conf             752578-88888997
Q gi|254780834|r  350 FVLLSR-GEDPDSFI  363 (648)
Q Consensus       350 vv~LP~-G~DPDe~i  363 (648)
                      ++.+|+ ..|+++++
T Consensus       188 ~iliPE~~~~~~~~~  202 (279)
T pfam00365       188 YIFIPEAPFWEEELC  202 (279)
T ss_pred             EEEECCCCCCHHHHH
T ss_conf             999679887589999


No 339
>COG2380 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.98  E-value=17  Score=14.91  Aligned_cols=23  Identities=22%  Similarity=0.316  Sum_probs=11.7

Q ss_pred             CCCCCCCCCCCHHHHHHHCCCCC
Q ss_conf             24422567741034554205997
Q gi|254780834|r  157 FKLGYAPDSRYSLREHLRQKGFS  179 (648)
Q Consensus       157 f~lG~ap~~~~~l~~~l~~~~~~  179 (648)
                      |+|-++|.--+.|-.|+..+-|.
T Consensus         1 ~RI~~d~w~~~~le~hv~~~~f~   23 (327)
T COG2380           1 MRIELDEWIEDELEEHVGDKPFA   23 (327)
T ss_pred             CCEECCCCHHHHHHHHHCCCCCC
T ss_conf             91003522466777552356422


No 340
>TIGR00036 dapB dihydrodipicolinate reductase; InterPro: IPR011770   Dihydrodipicolinate reductase is an enzyme found in bacteria and higher plants which is involved in the biosynthesis of diaminopimelic acid, a component of bacterial cell walls, and the essential amino acid L-lysine. It catalyses the the reduced pyridine nucleotide-dependent reduction of the alpha,beta-unsaturated cyclic imine, dihydrodipicolinate, to generate tetrahydrodipicolinate as shown below : 2,3-dihydrodipicolinate + NAD(P)H = 2,3,4,5-tetrahydrodipicolinate + NAD(P)(+) As this enzyme is not found in mammals it is a potential target for the development of novel antibacterial and herbicidal compounds.   The structures of the Escherichia coli (P04036 from SWISSPROT) and Mycobacterium tuberculosis (P72024 from SWISSPROT) enzymes have been determined , . The enzyme is a homotetramer where each monomer is composed of two domains, an N-terminal NAD(P)H-binding domain which forms a Rossman fold, and a C-terminal substrate-binding domain that forms an open, mixed alpha-beta sandwich.Tetramerisation occurs exclusively through interactions between C-terminal domain residues. Both enzymes show relatively little preference for either NADH or NADPH as cofactor. Conformational changes upon substrate binding bring the cofactor and substrate into close proximity and allow catalysis to occur. ; GO: 0008839 dihydrodipicolinate reductase activity, 0009089 lysine biosynthetic process via diaminopimelate, 0005737 cytoplasm.
Probab=22.93  E-value=37  Score=11.93  Aligned_cols=94  Identities=22%  Similarity=0.299  Sum_probs=57.8

Q ss_pred             ECCHHHHHH-HHHCCCCCCHHHHHCCCCHHHHHHHHHCCCE--EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             714388999-8743554211343213662678988512681--8996178866225777888888777536973067525
Q gi|254780834|r  277 VEGYMDVLS-LCQAGVQNVVSSLGTALTEYQLRLLWKLSPR--IVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLL  353 (648)
Q Consensus       277 vEGy~Dvi~-l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~--vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~L  353 (648)
                      =||-++-+. +.++|..=||.|  |-||+++.+.|..++.+  |=+.                     ..+++.|     
T Consensus        85 p~g~~~~~~~a~~~Gv~~V~GT--TGf~e~~~~~~~~~a~~~~~~~v---------------------~A~NFa~-----  136 (281)
T TIGR00036        85 PEGVVENVKIALENGVRLVVGT--TGFSEEDLQELRDLAEKKGVAAV---------------------IAPNFAI-----  136 (281)
T ss_pred             CHHHHHHHHHHHHCCCEEEECC--CCCCHHHHHHHHHHHHHCCCCEE---------------------EECCCHH-----
T ss_conf             0567899999996688557716--68998999999999986499789---------------------8465068-----


Q ss_pred             CCCCCHHHHHHCCCHHHHHHHHHHC-CCHHHH----HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             7888888997203668899886414-992799----9999985302331457999999999885417
Q gi|254780834|r  354 SRGEDPDSFIRCYGKTAFEKLIVES-LPLVDM----LWKRETENRSFNTPDERAELEIHLKNCINHI  415 (648)
Q Consensus       354 P~G~DPDe~ir~~G~eaf~~ll~~A-~~l~dF----l~~~l~~~~dl~spe~ka~~~~~l~~~I~~I  415 (648)
                                   |..=|.++++.| +-+-|+    +++. =.++-.|.|.|-|--   +.+.|+..
T Consensus       137 -------------GV~~~~K~~~~aA~~l~D~~DiEIIE~-HHr~K~DAPSGTAL~---~~E~i~~~  186 (281)
T TIGR00036       137 -------------GVNLMFKLLEKAAKYLGDYTDIEIIEL-HHRHKKDAPSGTALK---LAEIIAEA  186 (281)
T ss_pred             -------------HHHHHHHHHHHHHHHHCCCCCEEEEEC-HHCCCCCCCCHHHHH---HHHHHHHH
T ss_conf             -------------999999999999876245655454412-002589997078999---99999987


No 341
>smart00433 TOP2c TopoisomeraseII. Eukaryotic DNA topoisomerase II, GyrB, ParE
Probab=22.85  E-value=37  Score=11.92  Aligned_cols=11  Identities=27%  Similarity=0.404  Sum_probs=4.3

Q ss_pred             EECCCCCCCCC
Q ss_conf             01038767653
Q gi|254780834|r  232 KYLNSPETILF  242 (648)
Q Consensus       232 KYlNSpeT~if  242 (648)
                      +|+|...++++
T Consensus       194 ~~~~~~~~~~~  204 (594)
T smart00433      194 ELLNKNKELLS  204 (594)
T ss_pred             HHHCCCCCCCC
T ss_conf             98538987678


No 342
>KOG1818 consensus
Probab=22.83  E-value=34  Score=12.25  Aligned_cols=39  Identities=21%  Similarity=0.301  Sum_probs=26.0

Q ss_pred             CCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCC
Q ss_conf             0016716888970778588850100146553001038767
Q gi|254780834|r  200 DRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPET  239 (648)
Q Consensus       200 d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT  239 (648)
                      +..|=|..|-..+..+....-| |+.-..-..|++-=|-.
T Consensus       167 ~C~rCr~~F~~~~rkHHCr~CG-~vFC~qcss~s~~lP~~  205 (634)
T KOG1818         167 ECLRCRVKFGLTNRKHHCRNCG-QVFCGQCSSKSLTLPKL  205 (634)
T ss_pred             CCCEEEEEEEECCCCCCCCCCC-HHHCCCCCCCCCCCCCC
T ss_conf             0111234410015653430021-02225744133676533


No 343
>PRK09846 recT recombination and repair protein RecT; Reviewed
Probab=22.67  E-value=37  Score=11.89  Aligned_cols=79  Identities=16%  Similarity=0.230  Sum_probs=34.8

Q ss_pred             CHHHHHHHH----HCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCC-CCCE-EEEEE
Q ss_conf             757899998----50688535101244225677410345542059973452320121003465410000-1671-68889
Q gi|254780834|r  137 DKRLHYYLD----ERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDR-FRNR-LIFPI  210 (648)
Q Consensus       137 ~~~a~~yl~----~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~-Fr~R-i~fPi  210 (648)
                      +..+..||-    ++.-+...-.+|+|||     .++++-+...|-=  .-+.|..+..+|.-  -|+. ...+ .--|-
T Consensus        85 ~~LG~AYlVPy~nk~~~~g~~eaQfqiGY-----kG~IqLA~RSGqi--~~I~A~~Vye~D~F--~y~~Gl~~~l~h~p~  155 (270)
T PRK09846         85 SALGHAYLLPFGNKNEKSGKKEAQLIIGY-----RGMIDLARRSGQI--ASISARVVYENDEF--EFEYGLEEKLVHRPG  155 (270)
T ss_pred             CCCCEEEEEECCCCCCCCCCEEEEEEEEH-----HHHHHHHHHCCCE--EEEEEEEEECCCEE--EEECCCCCEEEECCC
T ss_conf             75543899743665566775259999607-----8999999857773--58999999659735--562588743664677


Q ss_pred             EECCCCEEEEECCC
Q ss_conf             70778588850100
Q gi|254780834|r  211 RSSRGQVIAFGGRT  224 (648)
Q Consensus       211 ~~~~g~~i~f~gR~  224 (648)
                      .+..|.+||+.+=.
T Consensus       156 ~~~~geiigyYA~~  169 (270)
T PRK09846        156 ENGDGPVTHVYAVA  169 (270)
T ss_pred             CCCCCCEEEEEEEE
T ss_conf             68888778999999


No 344
>pfam03194 LUC7 LUC7 N_terminus. This family contains the N terminal region of several LUC7 protein homologues and only contains eukaryotic proteins. LUC7 has been shown to be a U1 snRNA associated protein with a role in splice site recognition. The family also contains human and mouse LUC7 like (LUC7L) proteins and human cisplatin resistance-associated overexpressed protein (CROP).
Probab=22.58  E-value=37  Score=11.88  Aligned_cols=42  Identities=12%  Similarity=0.288  Sum_probs=20.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999872412798999999999999999999988
Q gi|254780834|r  591 LSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIE  632 (648)
Q Consensus       591 L~r~l~ele~~l~e~~~~~d~e~~~~l~~el~elk~~L~~l~  632 (648)
                      |..++..+-.++.++...|+.+.+..++.++.+++.+..++.
T Consensus       128 l~~~I~~ll~e~E~LGe~G~VdeA~~~~~~~e~Lk~er~~l~  169 (252)
T pfam03194       128 LDEEIGKLLAEAEALGEEGKVDEAMKLMKEVEELKAKKKELE  169 (252)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999867999999999999999999999998


No 345
>TIGR03183 DNA_S_dndC putative sulfurtransferase DndC. Members of this protein family are the DndC protein from the dnd (degradation during electrophoresis) operon. The dnd phenotype reflects a sulfur-containing modification to DNA. This operon is sparsely and sporadically distributed among bactera; among the first eight examples are members from the Actinobacteria, Firmicutes, Gammaproteobacteria, Cyanobacteria. DndC is suggested to be a sulfurtransferase.
Probab=22.58  E-value=26  Score=13.26  Aligned_cols=15  Identities=33%  Similarity=0.618  Sum_probs=7.2

Q ss_pred             ECCCCEE-EEECCCCC
Q ss_conf             0778588-85010014
Q gi|254780834|r  212 SSRGQVI-AFGGRTLS  226 (648)
Q Consensus       212 ~~~g~~i-~f~gR~l~  226 (648)
                      +..|.+| -.|-|.-.
T Consensus       135 ~~~ge~ilvLGtR~~E  150 (447)
T TIGR03183       135 AANGEVILVLGTRKNE  150 (447)
T ss_pred             HCCCCEEEEEECCHHH
T ss_conf             2149689999565277


No 346
>pfam00098 zf-CCHC Zinc knuckle. The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.
Probab=22.54  E-value=31  Score=12.58  Aligned_cols=11  Identities=27%  Similarity=0.911  Sum_probs=7.2

Q ss_pred             EECCCCCCCCH
Q ss_conf             71368888789
Q gi|254780834|r   63 YCFSCHVKGDH   73 (648)
Q Consensus        63 ~cf~c~~~gd~   73 (648)
                      .||-||..|-+
T Consensus         2 ~C~nCG~~GH~   12 (26)
T pfam00098         2 KCYNCGKEGHL   12 (26)
T ss_pred             CCCCCCCCCCC
T ss_conf             32136865411


No 347
>PRK10787 DNA-binding ATP-dependent protease La; Provisional
Probab=22.53  E-value=37  Score=11.87  Aligned_cols=13  Identities=8%  Similarity=0.135  Sum_probs=8.9

Q ss_pred             HCCCHHHHHHHHH
Q ss_conf             1108178888643
Q gi|254780834|r  247 NLYNFFGALNYLQ  259 (648)
Q Consensus       247 ~Ly~l~~a~~~~~  259 (648)
                      -=|||...|+.|-
T Consensus       323 dHyGL~~vKeRil  335 (784)
T PRK10787        323 DHYGLERVKDRIL  335 (784)
T ss_pred             HHCCHHHHHHHHH
T ss_conf             4306577999999


No 348
>TIGR02410 carnitine_TMLD trimethyllysine dioxygenase; InterPro: IPR012776    Members of this family with known function act as trimethyllysine dioxygenase, an enzyme in the pathway for carnitine biosynthesis from lysine. This enzyme is homologous to gamma-butyrobetaine,2-oxoglutarate dioxygenase, which catalyzes the last step in carnitine biosynthesis. Members of this family appear to be eukaryotic only.; GO: 0005506 iron ion binding, 0031418 L-ascorbic acid binding, 0050353 trimethyllysine dioxygenase activity, 0045329 carnitine biosynthetic process.
Probab=22.52  E-value=37  Score=11.87  Aligned_cols=25  Identities=12%  Similarity=0.101  Sum_probs=11.3

Q ss_pred             ECCCCEEEECC-CC-CCC-----CHHHHHHHH
Q ss_conf             17897467136-88-887-----898998988
Q gi|254780834|r   56 NDSKGFYYCFS-CH-VKG-----DHLSFLSAL   80 (648)
Q Consensus        56 ~~~~~~~~cf~-c~-~~g-----d~~~f~~~~   80 (648)
                      .|.-|.|||.- -| .||     |+|.-+.+.
T Consensus       216 tPGlQlFHlL~H~GG~GG~T~LVD~f~~a~~l  247 (397)
T TIGR02410       216 TPGLQLFHLLKHDGGTGGETLLVDGFYAAEQL  247 (397)
T ss_pred             CCCCCCCCCCCCCCCCCCCEEEHHHHHHHHHH
T ss_conf             77452000205688989850100489999999


No 349
>PRK13780 phosphocarrier protein HPr; Provisional
Probab=22.50  E-value=37  Score=11.87  Aligned_cols=62  Identities=19%  Similarity=0.335  Sum_probs=36.9

Q ss_pred             HHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf             789885126818996178866225777888888777536973067525788888899720366889988641
Q gi|254780834|r  306 QLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE  377 (648)
Q Consensus       306 ~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~  377 (648)
                      =++...+|...|.+.+||-.|--|..+..+-+   -...|-.|.|.  -+|.|-++.+     +++.+++++
T Consensus        22 lv~~a~~f~s~I~i~~~~k~~naKSi~~lm~L---g~~~G~~i~i~--a~G~De~~A~-----~~l~~~l~~   83 (88)
T PRK13780         22 LVQTASKFDSDITLEYNGKSVNLKSIMGVMSL---GVGQGADITIS--AEGADEADAI-----AAIEETMKK   83 (88)
T ss_pred             HHHHHHHCCCEEEEEECCEEECCHHHHHHHHH---CCCCCCEEEEE--EECCCHHHHH-----HHHHHHHHH
T ss_conf             99999738977999989999821749999961---78898999999--9788999999-----999999987


No 350
>pfam04055 Radical_SAM Radical SAM superfamily. Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.
Probab=22.43  E-value=37  Score=11.86  Aligned_cols=21  Identities=19%  Similarity=0.235  Sum_probs=10.4

Q ss_pred             HCCCC--EEEEECCCCCCHHHHH
Q ss_conf             36973--0675257888888997
Q gi|254780834|r  343 IPGNR--VNFVLLSRGEDPDSFI  363 (648)
Q Consensus       343 ~~g~~--v~vv~LP~G~DPDe~i  363 (648)
                      +.|..  +.++....|+.++++.
T Consensus       137 ~~gi~~~~~~i~~~~~e~~~~~~  159 (165)
T pfam04055       137 EAGIPVVVDNIVGLPGENDEDLE  159 (165)
T ss_pred             HCCCCEEEEEEEECCCCCHHHHH
T ss_conf             87997889999979999999999


No 351
>TIGR02029 AcsF magnesium-protoporphyrin IX monomethyl ester aerobic oxidative cyclase; InterPro: IPR008434   This family represents the oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under aerobic conditions . This enzyme is believed to utilise a binuclear iron centre and molecular oxygen. There are two isoforms of this enzyme in some plants and cyanobacteria, which are differentially regulated based on the levels of copper and oxygen , . This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under aerobic conditions (a separate enzyme, BchE, acts under anaerobic conditions). This enzyme is found in plants, cyanobacteria and other photosynthetic bacteria.   CRD1 (AcsF) is required for the maintenance of photosystem I and its associated light-harvesting complexes in copper-deficient (-Cu) and oxygen-deficient (-O(2)) Chlamydomonas reinhardtii cells and is localised to the thylakoid membrane. The family also contains the Rhodocyclus gelatinosus (Rhodopseudomonas gelatinosa) AcsF protein .; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process.
Probab=22.35  E-value=23  Score=13.71  Aligned_cols=30  Identities=10%  Similarity=0.244  Sum_probs=16.0

Q ss_pred             HHCHHH----HHHHHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf             847788----999984430023799889999999999
Q gi|254780834|r  492 INHPAI----LQEQYQELADIRYDNNELQKLWSFLFS  524 (648)
Q Consensus       492 I~~P~l----~~~~~e~l~~~~f~~~~~~~L~~~i~~  524 (648)
                      =.||++    +-.+.+.-++.++.|   +.++..|..
T Consensus       183 ~~nPe~qfyPIF~yFe~WC~DE~~H---Gd~F~~Lmk  216 (344)
T TIGR02029       183 EENPENQFYPIFKYFEEWCQDENRH---GDAFALLMK  216 (344)
T ss_pred             CCCCCCCCCCCCHHHHHHCCHHHHH---HHHHHHHHC
T ss_conf             0188875446514465320221015---899999840


No 352
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=22.35  E-value=37  Score=11.84  Aligned_cols=19  Identities=26%  Similarity=0.531  Sum_probs=13.4

Q ss_pred             CCCCCCCCEEEEEEEECCC
Q ss_conf             1000016716888970778
Q gi|254780834|r  197 TSYDRFRNRLIFPIRSSRG  215 (648)
Q Consensus       197 ~~~d~Fr~Ri~fPi~~~~g  215 (648)
                      ++||--+|||+|=.+|..+
T Consensus        58 SpYDltkGRIvyR~k~~~~   76 (87)
T PRK12442         58 SPYDLTKGRINFRHKDERS   76 (87)
T ss_pred             CCCCCCCEEEEEEECCCCC
T ss_conf             8777887489988478889


No 353
>pfam05028 PARG_cat Poly (ADP-ribose) glycohydrolase (PARG). Poly(ADP-ribose) glycohydrolase (PARG), is a ubiquitously expressed exo- and endoglycohydrolase which mediates oxidative and excitotoxic neuronal death.
Probab=22.28  E-value=35  Score=12.14  Aligned_cols=23  Identities=13%  Similarity=0.042  Sum_probs=12.0

Q ss_pred             CCCHHHHHHCCCHHHHHHHHHHC
Q ss_conf             88888997203668899886414
Q gi|254780834|r  356 GEDPDSFIRCYGKTAFEKLIVES  378 (648)
Q Consensus       356 G~DPDe~ir~~G~eaf~~ll~~A  378 (648)
                      -++++|-+.-.|.+.|..+-.-+
T Consensus       200 ~l~dnE~i~i~G~~r~s~y~GY~  222 (339)
T pfam05028       200 VLEDNEAIIIVGAERFSSYTGYA  222 (339)
T ss_pred             CCCCCCEEEEECCEEEEEECCCC
T ss_conf             56888379997502356401242


No 354
>COG3313 Predicted Fe-S protein [General function prediction only]
Probab=22.27  E-value=38  Score=11.83  Aligned_cols=25  Identities=28%  Similarity=0.582  Sum_probs=14.3

Q ss_pred             CCCCEEEE--CCCCEEEECCCCCCCCHHH
Q ss_conf             58787981--7897467136888878989
Q gi|254780834|r   49 KTPSFHCN--DSKGFYYCFSCHVKGDHLS   75 (648)
Q Consensus        49 ktpsf~v~--~~~~~~~cf~c~~~gd~~~   75 (648)
                      ++|--.|=  ++++  +|+||+..-|=|.
T Consensus         7 ~SPCv~vCs~D~~~--~C~GC~Rt~~Ei~   33 (74)
T COG3313           7 KSPCVGVCSTDEKD--FCRGCGRTRDEIF   33 (74)
T ss_pred             CCCEEEEEEECCCC--HHHCCCCCHHHHH
T ss_conf             99801234455765--2014454489998


No 355
>cd06481 ACD_HspB9_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB9 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB9 is expressed exclusively in the normal testis and in various tumor samples and is a cancer/testis antigen. hHspB9  interacts with TCTEL1 (T-complex testis expressed protein -1), a subunit of dynein. hHspB9 and TCTEL1 are co-expressed in similar cells within the testis and in tumor cells. Included in this group is Xenopus Hsp30, a developmentally-regulated heat-inducible molecular chaperone.
Probab=22.23  E-value=37  Score=11.90  Aligned_cols=22  Identities=18%  Similarity=0.223  Sum_probs=12.4

Q ss_pred             EEEEECCCCCCHHHHHHCCCHH
Q ss_conf             0675257888888997203668
Q gi|254780834|r  348 VNFVLLSRGEDPDSFIRCYGKT  369 (648)
Q Consensus       348 v~vv~LP~G~DPDe~ir~~G~e  369 (648)
                      .|-..||+|.||+++.-.-+.+
T Consensus        57 ~R~~~LP~~vd~~~v~s~Ls~d   78 (87)
T cd06481          57 VREAQLPEHVDPEAVTCSLSPS   78 (87)
T ss_pred             EEEEECCCCCCHHHCEEEECCC
T ss_conf             9986788996976809963799


No 356
>KOG4506 consensus
Probab=22.20  E-value=38  Score=11.82  Aligned_cols=103  Identities=20%  Similarity=0.217  Sum_probs=62.2

Q ss_pred             HHHHHHHHCCCCCCHHHHHC----------CCCHHHHHHHHHCCCEEEEE----------ECCCCCCHHHHHHHHHHHHH
Q ss_conf             88999874355421134321----------36626789885126818996----------17886622577788888877
Q gi|254780834|r  281 MDVLSLCQAGVQNVVSSLGT----------ALTEYQLRLLWKLSPRIVLC----------FDGDDPGLRAAYKAIDLVLC  340 (648)
Q Consensus       281 ~Dvi~l~~~G~~n~va~~Gt----------alt~~~~~~l~r~~~~vvl~----------fDgD~AG~kAa~Ra~e~~l~  340 (648)
                      .|-|.+..+.|+..||+.|.          +||..--..|+...+--.+-          ..||..|.+-.  -+++++.
T Consensus       249 lddiildeha~pepVaa~gr~g~~adgleESFTI~iGaQLKsMHNlcLlraDrl~DfCk~~egd~sgvk~~--RLemA~k  326 (598)
T KOG4506         249 LDDIILDEHAFPEPVAAIGRIGEEADGLEESFTIHIGAQLKSMHNLCLLRADRLLDFCKHKEGDRSGVKLH--RLEMALK  326 (598)
T ss_pred             HHHHHCCHHCCCCHHHHHHHHHHHHHCCCCCEEEEHHHHHHHHHCCCEEEHHHHHHHHHHHCCCCCCCHHH--HHHHHHH
T ss_conf             55541482106635888752344431443027873175677554202022778889876421773310079--9999999


Q ss_pred             HHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             7536973067525788888899720366889988641499279999999853
Q gi|254780834|r  341 HLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETEN  392 (648)
Q Consensus       341 ~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~~~l~~~  392 (648)
                      +...++.=-++..|  .||..++..  +-.|...-++..   ||-|+++.++
T Consensus       327 LYSrnL~G~tLLV~--~d~mmhi~~--krDF~kiCee~T---DfHFdriaEQ  371 (598)
T KOG4506         327 LYSRNLCGLTLLVD--NDIMMHIGI--KRDFAKICEECT---DFHFDRIAEQ  371 (598)
T ss_pred             HHHHCCCCEEEEEC--CCCHHHCCC--HHHHHHHHHHHC---CCCCHHHHHH
T ss_conf             98514445279845--860543051--148999988730---4473679999


No 357
>PRK10903 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional
Probab=22.16  E-value=38  Score=11.82  Aligned_cols=14  Identities=36%  Similarity=0.463  Sum_probs=9.4

Q ss_pred             EEECCHHHHHHHHHC
Q ss_conf             997143889998743
Q gi|254780834|r  275 ILVEGYMDVLSLCQA  289 (648)
Q Consensus       275 i~vEGy~Dvi~l~~~  289 (648)
                      -|+|| |||+--...
T Consensus       151 ~VveG-mdVvdkI~~  164 (190)
T PRK10903        151 KVVKG-MDVADKISQ  164 (190)
T ss_pred             EEECC-HHHHHHHHC
T ss_conf             99127-799999973


No 358
>TIGR00456 argS arginyl-tRNA synthetase; InterPro: IPR001278   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 .   Arginyl-tRNA synthetase (6.1.1.19 from EC) has been crystallized and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes is available . ; GO: 0000166 nucleotide binding, 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006420 arginyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=22.16  E-value=38  Score=11.81  Aligned_cols=54  Identities=22%  Similarity=0.202  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHH
Q ss_conf             3799999999984778899998443002379988999999999997538899989
Q gi|254780834|r  481 SLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPE  535 (648)
Q Consensus       481 ~~~E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~  535 (648)
                      ...|+.|+..+..+|+++....+....- .....+..|...+-.+|...+..+..
T Consensus       513 ~~~E~~L~~~L~~fp~~~~~~~~~~~p~-~l~~Yly~LA~~F~sfY~~~~v~~~~  566 (600)
T TIGR00456       513 EEKEKELLKLLLQFPEVIEEAAEEREPH-VLTNYLYELAKLFSSFYKACPVLDAE  566 (600)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             8889999999856489999999854718-88999999977642366417788986


No 359
>KOG1177 consensus
Probab=22.15  E-value=13  Score=16.10  Aligned_cols=71  Identities=8%  Similarity=0.019  Sum_probs=29.5

Q ss_pred             CCEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             78798178974671368888789899898859997999999999818858776820367778899999999999999999
Q gi|254780834|r   51 PSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHH  130 (648)
Q Consensus        51 psf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  130 (648)
                      +++.+| .+   |--||..-    .|    .+-+-++-++..+++++...-..-.....+..-.+-..++...|+-|++-
T Consensus        30 ~~~~~~-~~---~~~g~~~i----pl----~~~Tigq~l~~~t~~v~dkea~Vf~~eg~R~Tf~~~~~ev~slAaGll~l   97 (596)
T KOG1177          30 WVLLSS-HR---YVHGCSQI----PL----DSETIGQLLETTTERVPDKEAAVFDHEGIRLTFSEFVSEVESLAAGLLSL   97 (596)
T ss_pred             CEECCC-CC---CCCCCCCC----CC----CCCCHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             412023-43---01798777----74----31527889877765067514789961341234999999999997568863


Q ss_pred             HHC
Q ss_conf             732
Q gi|254780834|r  131 SLK  133 (648)
Q Consensus       131 ~l~  133 (648)
                      -|+
T Consensus        98 GL~  100 (596)
T KOG1177          98 GLK  100 (596)
T ss_pred             CCC
T ss_conf             477


No 360
>pfam02330 MAM33 Mitochondrial glycoprotein. This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q. It is thought to be involved in mitochondrial oxidative phosphorylation and in nucleus-mitochondrion interactions.
Probab=22.09  E-value=38  Score=11.80  Aligned_cols=34  Identities=12%  Similarity=0.151  Sum_probs=17.7

Q ss_pred             EECCCCCCHHHHHHCCCHHHHHHHHHH-CC--CHHHHHHHH
Q ss_conf             525788888899720366889988641-49--927999999
Q gi|254780834|r  351 VLLSRGEDPDSFIRCYGKTAFEKLIVE-SL--PLVDMLWKR  388 (648)
Q Consensus       351 v~LP~G~DPDe~ir~~G~eaf~~ll~~-A~--~l~dFl~~~  388 (648)
                      ..=|...+=|+-++    ++|..+|+. ..  .+.+|+-++
T Consensus       147 y~gp~f~~Ld~~lq----~~~~~yLe~rGi~~~~~~fl~~~  183 (203)
T pfam02330       147 YYGPSFKNLDPELQ----DLFHRYLEERGVDATFAKFLVAY  183 (203)
T ss_pred             CCCCCCCCCCHHHH----HHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             46988141499999----99999999949998999999999


No 361
>TIGR00457 asnS asparaginyl-tRNA synthetase; InterPro: IPR004522   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   AsparaginyltRNA synthetase (6.1.1.22 from EC) is an alpha2 dimer that belongs to class IIb. There is a striking similarity between asparaginyl-tRNA synthetases and archaeal/eukaryotic type aspartyl-tRNA synthetases (IPR004523 from INTERPRO) and a striking divergence of bacterial type aspartyl-tRNA synthetases (IPR004524 from INTERPRO). This family, AsnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.; GO: 0000166 nucleotide binding, 0004816 asparagine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006421 asparaginyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=22.09  E-value=35  Score=12.16  Aligned_cols=32  Identities=22%  Similarity=0.225  Sum_probs=16.2

Q ss_pred             CCCEEEEECCCCCCHHHHHHCCCH-HHHHHHHHHC
Q ss_conf             973067525788888899720366-8899886414
Q gi|254780834|r  345 GNRVNFVLLSRGEDPDSFIRCYGK-TAFEKLIVES  378 (648)
Q Consensus       345 g~~v~vv~LP~G~DPDe~ir~~G~-eaf~~ll~~A  378 (648)
                      -+++.|+-  .-.|||+|=.+.-. ..++=|.+.+
T Consensus       101 vk~~ev~g--~a~~p~~YPl~~K~Ghs~efLr~~~  133 (495)
T TIGR00457       101 VKKIEVVG--EAEDPDDYPLQKKEGHSLEFLRDIA  133 (495)
T ss_pred             CEEEEEEE--ECCCCCCCCCCCCCCCCHHHHHCCC
T ss_conf             31468877--4178877776422368767763276


No 362
>pfam02614 UxaC Glucuronate isomerase. This is a family of Glucuronate isomerases also known as D-glucuronate isomerase, uronic isomerase, uronate isomerase, or uronic acid isomerase, EC:5.3.1.12. This enzyme catalyses the reactions: D-glucuronate <= D-fructuronate and D-galacturonate <= D-tagaturonate. It is not however clear where the experimental evidence for this functional assignment came from and thus this family has no literature reference.
Probab=22.06  E-value=38  Score=11.80  Aligned_cols=15  Identities=27%  Similarity=0.430  Sum_probs=7.1

Q ss_pred             HHHHHHCCCCCHHHH
Q ss_conf             345542059973452
Q gi|254780834|r  169 LREHLRQKGFSEEKI  183 (648)
Q Consensus       169 l~~~l~~~~~~~~~~  183 (648)
                      .++.+...|++++.+
T Consensus        57 kwR~Mra~GV~e~~i   71 (465)
T pfam02614        57 KWRAMRANGVPEDLI   71 (465)
T ss_pred             HHHHHHHCCCCHHHC
T ss_conf             999999859988880


No 363
>COG5014 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=21.98  E-value=16  Score=15.36  Aligned_cols=61  Identities=23%  Similarity=0.190  Sum_probs=28.6

Q ss_pred             CCCHHHHHHHHHCCCE--EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCC
Q ss_conf             3662678988512681--899617886622577788888877753697306752578888889972036
Q gi|254780834|r  301 ALTEYQLRLLWKLSPR--IVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYG  367 (648)
Q Consensus       301 alt~~~~~~l~r~~~~--vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G  367 (648)
                      -+..+|+..+--+..+  .|+--.|---|..   |++-..+ --..+.-|||..  .|.||.||.+--|
T Consensus       103 ~l~~EHvlevIeLl~~~tFvlETNG~~~g~d---rslv~el-~nr~nv~vRVsv--KG~dpesF~kIT~  165 (228)
T COG5014         103 ILGREHVLEVIELLVNNTFVLETNGLMFGFD---RSLVDEL-VNRLNVLVRVSV--KGWDPESFEKITG  165 (228)
T ss_pred             CCCHHHHHHHHHHCCCCEEEEEECCEEEECC---HHHHHHH-HCCCCEEEEEEE--CCCCHHHHHHHHC
T ss_conf             4468999999986347649997577688358---8899997-137863999983--5798899898756


No 364
>cd01833 XynB_like SGNH_hydrolase subfamily, similar to Ruminococcus flavefaciens XynB. Most likely a secreted hydrolase with xylanase activity. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=21.94  E-value=38  Score=11.78  Aligned_cols=20  Identities=30%  Similarity=0.401  Sum_probs=11.5

Q ss_pred             HHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHH
Q ss_conf             134321366267898851268189961788662257
Q gi|254780834|r  295 VSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRA  330 (648)
Q Consensus       295 va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kA  330 (648)
                      |.++|-++|.-                |+|.+|.-.
T Consensus         3 ~~~~gdsit~g----------------d~~n~G~~G   22 (157)
T cd01833           3 IMPLGDSITWG----------------DKDHEGHSG   22 (157)
T ss_pred             EEEECCCCCCC----------------CCCCCCCCC
T ss_conf             89822755457----------------899999784


No 365
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11.  This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11.   Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions.  TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis.  S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=21.93  E-value=38  Score=11.78  Aligned_cols=88  Identities=24%  Similarity=0.305  Sum_probs=46.8

Q ss_pred             EEEEECCHHHHHHHHHCCCCC---CHHHHHC----CCCHHHHHHHHHCC-CEEEEEECCCCCCHHH--HHHHHHHHHHHH
Q ss_conf             089971438899987435542---1134321----36626789885126-8189961788662257--778888887775
Q gi|254780834|r  273 FIILVEGYMDVLSLCQAGVQN---VVSSLGT----ALTEYQLRLLWKLS-PRIVLCFDGDDPGLRA--AYKAIDLVLCHL  342 (648)
Q Consensus       273 ~~i~vEGy~Dvi~l~~~G~~n---~va~~Gt----alt~~~~~~l~r~~-~~vvl~fDgD~AG~kA--a~Ra~e~~l~~l  342 (648)
                      .++|||-..=--.|.+.++.+   .|-.-|.    -.|..=++.|.... -.|+.++|+|.-|..=  +.|.....+++.
T Consensus         2 ~vlVVEK~avf~~L~~~~~~~~~~~iliTgKG~Pd~~TR~fl~~L~~~~~lpv~~l~D~DP~Gi~I~~~Yk~Gs~~~~~~   81 (160)
T cd00223           2 FVLVVEKEAVFQRLIEEGFHERNNCILITGKGYPDRATRRFLRRLHEELDLPVYILVDGDPYGISILLTYKYGSIKLAYE   81 (160)
T ss_pred             EEEEEECHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCEEEEEEEEECCCCCCCC
T ss_conf             79999649999999974856448889994688887899999999999878988999758866106778886266223124


Q ss_pred             HCCC---CEEEEECCCCCCHHHHHH
Q ss_conf             3697---306752578888889972
Q gi|254780834|r  343 IPGN---RVNFVLLSRGEDPDSFIR  364 (648)
Q Consensus       343 ~~g~---~v~vv~LP~G~DPDe~ir  364 (648)
                      ....   .++.    -|.-|.++.+
T Consensus        82 ~~~~~~p~i~w----lGl~~sd~~~  102 (160)
T cd00223          82 SESLATPDLRW----LGLRPSDIIR  102 (160)
T ss_pred             CCCCCCCCCEE----EECCHHHHHC
T ss_conf             44455887289----5076999860


No 366
>pfam03949 Malic_M Malic enzyme, NAD binding domain.
Probab=21.92  E-value=38  Score=11.78  Aligned_cols=38  Identities=18%  Similarity=0.146  Sum_probs=17.3

Q ss_pred             HHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEE
Q ss_conf             88999874355421134321366267898851268189
Q gi|254780834|r  281 MDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIV  318 (648)
Q Consensus       281 ~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vv  318 (648)
                      -|||...+-.+--.++..|-+||++.++.+.+.++++|
T Consensus        99 ~e~v~~~kP~vlIG~S~~~g~ft~evv~~Ma~~~~~PI  136 (255)
T pfam03949        99 AEAVKGAKPDVLIGVSGVPGVFTEEIVRAMAEHTERPI  136 (255)
T ss_pred             HHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCCE
T ss_conf             99986268877998168889889999999981699984


No 367
>TIGR02009 PGMB-YQAB-SF beta-phosphoglucomutase family hydrolase; InterPro: IPR010976   Phosphoglucomutases interconvert D-glucose 1-phosphate and D-glucose 6-phosphate, a reaction which is important for energy metabolism in many organisms and for cell wall biosynthesis in bacteria , . Beta-phosphoglucomutases are monomeric enzymes which interconvert the beta anomers of these compounds using Mg2+ as a cofactor.   This entry groups together three clades: the characterised beta-phosphoglucomutases (bPGMs) (including those from Escherichia coli, Bacillus subtilus and Lactococcus lactis, a clade of putative bPGMs from mycobacteria and a clade including the uncharacterised Escherichia coli and Haemophilus influenzae yqaB genes which may prove to be beta-mutases of a related 1-phosphosugar. All of these are members of the larger Haloacid dehalogenase (HAD) subfamily IA and include the 'variant 3' Glu-Asp version of the third conserved HAD domain.   The Lactococcus enzyme has been crystallised and studied in detail . It is composed of two distinct regions, an alpha/beta core domain similar to that found in other HAD family members, and a helical cap domain. The core domain contains a central six-stranded parallel beta sheet surrounded by six alpha helices, while the cap domain consists of an antiparallel four alpha-helix bundle. Overall, the monomer forms a "kidney-bean" shape similar to that observed in other HAD family members such as phosphoserine phosphatase. The active site of the enzyme is located at the interface of the two domains..
Probab=21.76  E-value=38  Score=11.75  Aligned_cols=82  Identities=16%  Similarity=0.224  Sum_probs=53.8

Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC--CC-CC-----HHHHHHH
Q ss_conf             9899898859997999999999818858776820367778899999999999999999732--67-77-----5789999
Q gi|254780834|r   73 HLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLK--NA-RD-----KRLHYYL  144 (648)
Q Consensus        73 ~~~f~~~~~~~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~--~~-~~-----~~a~~yl  144 (648)
                      ..++.....|++-.+.++..-+.+||++|+......-...+   ..++-+.=..+|+..|.  .. ..     ..-+++|
T Consensus        44 ~~~~~~~l~G~~r~~~~~~il~~~~~~IP~~~~ed~~~~~~---~~~l~~~K~~~y~~ll~qE~~~~~~lp~~~~~l~~l  120 (211)
T TIGR02009        44 EEQYNESLKGLSREDILRAILKLRAVDIPDGSKEDGLSLEK---IEQLAERKNELYRELLRQELTGAEVLPGIENLLKEL  120 (211)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCHHH---HHHHHHHHHHHHHHHHHHCCCCCHHCCCHHHHHHHH
T ss_conf             99999983899768999999874277699988896889889---999999999999999862267210036558999999


Q ss_pred             HHCCCCHHHHCCCCCCCCCCC
Q ss_conf             850688535101244225677
Q gi|254780834|r  145 DERGIDSHAIEMFKLGYAPDS  165 (648)
Q Consensus       145 ~~Rg~~~~~~~~f~lG~ap~~  165 (648)
                      ++++|.        +|-++.+
T Consensus       121 ~~~~i~--------~a~gS~S  133 (211)
T TIGR02009       121 KKKGIA--------VALGSSS  133 (211)
T ss_pred             HHCCCC--------EEEEECC
T ss_conf             866985--------7884054


No 368
>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]
Probab=21.74  E-value=38  Score=11.75  Aligned_cols=19  Identities=21%  Similarity=0.377  Sum_probs=7.8

Q ss_pred             CCCHHHHHHCCCHHHHHHH
Q ss_conf             8888899720366889988
Q gi|254780834|r  356 GEDPDSFIRCYGKTAFEKL  374 (648)
Q Consensus       356 G~DPDe~ir~~G~eaf~~l  374 (648)
                      |+..-+++.++|-++|+.+
T Consensus        42 g~sI~eIF~~~GE~~FR~~   60 (172)
T COG0703          42 GMSIAEIFEEEGEEGFRRL   60 (172)
T ss_pred             CCCHHHHHHHHHHHHHHHH
T ss_conf             9699999999828999999


No 369
>PRK11460 esterase YpfH; Provisional
Probab=21.74  E-value=38  Score=11.75  Aligned_cols=42  Identities=14%  Similarity=0.249  Sum_probs=23.3

Q ss_pred             HHCCCCEEEEECC---CCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             5369730675257---8888889972036688998864149927999999985
Q gi|254780834|r  342 LIPGNRVNFVLLS---RGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETE  391 (648)
Q Consensus       342 l~~g~~v~vv~LP---~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~~~l~~  391 (648)
                      .+.|.+|..-..|   .+-||+.+      +.-.++|++..|.  -.|+.++.
T Consensus       175 ~~~G~~v~~~~~~glGH~I~~egl------~~a~~FLk~~lp~--~~~~~~~~  219 (230)
T PRK11460        175 IALGGDVTLDIAEDLGHAIDPRLM------QFALDRLRYTVPK--RYWDEALS  219 (230)
T ss_pred             HHCCCCEEEEECCCCCCCCCHHHH------HHHHHHHHHHCCH--HHHHHHHC
T ss_conf             987992799862899998899999------9999999873728--67999864


No 370
>KOG1432 consensus
Probab=21.67  E-value=38  Score=11.74  Aligned_cols=37  Identities=19%  Similarity=0.267  Sum_probs=21.8

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCH
Q ss_conf             6818996178866225777888888777536973067525788888
Q gi|254780834|r  314 SPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDP  359 (648)
Q Consensus       314 ~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DP  359 (648)
                      -+++.|||-|- ||.-+=-++.     .   -..+||+.+-.++|-
T Consensus       318 k~~~wlCygGg-aGyggYg~~g-----w---~Rr~Rv~e~d~~~~~  354 (379)
T KOG1432         318 KGELWLCYGGG-AGYGGYGIGG-----W---ERRARVFELDLNKDR  354 (379)
T ss_pred             CCEEEEEECCC-CCCCCCCCCC-----C---CCCEEEEECCCCCCC
T ss_conf             88079994587-7547767588-----5---440489981456040


No 371
>PRK13547 hmuV hemin importer ATP-binding subunit; Provisional
Probab=21.59  E-value=39  Score=11.73  Aligned_cols=56  Identities=21%  Similarity=0.145  Sum_probs=30.6

Q ss_pred             CCHHHHHHHHHCCCEEEEEECCCCC--CHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCH
Q ss_conf             6626789885126818996178866--225777888888777536973067525788888
Q gi|254780834|r  302 LTEYQLRLLWKLSPRIVLCFDGDDP--GLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDP  359 (648)
Q Consensus       302 lt~~~~~~l~r~~~~vvl~fDgD~A--G~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DP  359 (648)
                      +....+....+++++|+++.||---  |--+-.-.-+...  -.-|..++|+.-|+|+=|
T Consensus       211 ~vtHdl~~~~~~aDri~vL~~G~iv~~G~p~evl~~e~l~--~~yg~~~~v~~~~~g~~~  268 (273)
T PRK13547        211 AIVHDPNLAARHADRIAMLADGAIVAHGAPADVMTPEHIA--RCYGFAVKLVDAGDGVPP  268 (273)
T ss_pred             EEECCHHHHHHHCCEEEEEECCEEEEECCHHHHCCHHHHH--HHHCCCEEEEECCCCCCC
T ss_conf             9988999999979999999898799984879972989999--982995699998999851


No 372
>PRK04025 S-adenosylmethionine decarboxylase proenzyme; Validated
Probab=21.45  E-value=39  Score=11.70  Aligned_cols=39  Identities=18%  Similarity=0.231  Sum_probs=31.5

Q ss_pred             CCCCCCEEEECCCCE--EEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHC
Q ss_conf             885878798178974--671368888789899898859997999999999818
Q gi|254780834|r   47 DEKTPSFHCNDSKGF--YYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAG   97 (648)
Q Consensus        47 ~ektpsf~v~~~~~~--~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~g   97 (648)
                      .|..=|++-+|++++  .-+|.||..-            +...|+++|.++.+
T Consensus        61 aESHiSIHTWPE~g~aavDiFTCGd~~------------~P~~A~~~l~~~l~  101 (139)
T PRK04025         61 AESHISVHTWPEKGYAALDVYTCGETA------------DPEKAVDYILEQFK  101 (139)
T ss_pred             EEEEEEEEECCCCCEEEEEEECCCCCC------------CHHHHHHHHHHHHC
T ss_conf             511689996564786999998689989------------99999999999849


No 373
>KOG2578 consensus
Probab=21.36  E-value=31  Score=12.64  Aligned_cols=46  Identities=17%  Similarity=0.143  Sum_probs=23.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCC
Q ss_conf             858776820367778899999999999999999732677757899998506885351012
Q gi|254780834|r   98 VPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMF  157 (648)
Q Consensus        98 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f  157 (648)
                      +.+-..+..+.+-.-+|.++|+|.+..              ++..-+.+||-+.-+++-|
T Consensus        42 vdlvgLddaA~KlgVErRRIYDiVNvl--------------Esig~var~~KnqYsWkGf   87 (388)
T KOG2578          42 VDLVGLDDAARKLGVERRRIYDIVNVL--------------ESIGAVARRGKNQYSWKGF   87 (388)
T ss_pred             CCEECHHHHHHHCCCHHHHHHHHHHHH--------------HHHHHHHHCCCCCCCCCCH
T ss_conf             443140667876070477788899999--------------9878998605672011341


No 374
>KOG1409 consensus
Probab=21.35  E-value=39  Score=11.69  Aligned_cols=20  Identities=25%  Similarity=0.082  Sum_probs=11.7

Q ss_pred             CCCEEEEECCCCCCHHHHHH
Q ss_conf             97306752578888889972
Q gi|254780834|r  345 GNRVNFVLLSRGEDPDSFIR  364 (648)
Q Consensus       345 g~~v~vv~LP~G~DPDe~ir  364 (648)
                      +++++.+.-|+=+|-|..=+
T Consensus       268 ~mn~~r~etpewl~s~~cQ~  287 (404)
T KOG1409         268 NMNVKRVETPEWLDSDSCQK  287 (404)
T ss_pred             ECCCEEECCCCCCCCCHHHH
T ss_conf             52540561866030640656


No 375
>KOG2150 consensus
Probab=21.30  E-value=39  Score=11.68  Aligned_cols=15  Identities=7%  Similarity=0.100  Sum_probs=5.7

Q ss_pred             EEEECCCCCCHHHHH
Q ss_conf             996178866225777
Q gi|254780834|r  318 VLCFDGDDPGLRAAY  332 (648)
Q Consensus       318 vl~fDgD~AG~kAa~  332 (648)
                      .+.+|.=.+|--|+.
T Consensus       294 ~~~~~~~s~~A~aaA  308 (575)
T KOG2150         294 PIGIDASSSAAPSGA  308 (575)
T ss_pred             CCCCCCCCCCCCHHH
T ss_conf             545577765431122


No 376
>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=21.27  E-value=39  Score=11.67  Aligned_cols=46  Identities=17%  Similarity=0.295  Sum_probs=31.5

Q ss_pred             HHHHH---CCCCCCHHHHHCCCCHHHHHHHHHCCCEE---EEEECCCCCCHH
Q ss_conf             99874---35542113432136626789885126818---996178866225
Q gi|254780834|r  284 LSLCQ---AGVQNVVSSLGTALTEYQLRLLWKLSPRI---VLCFDGDDPGLR  329 (648)
Q Consensus       284 i~l~~---~G~~n~va~~Gtalt~~~~~~l~r~~~~v---vl~fDgD~AG~k  329 (648)
                      +++|+   .|--+=|+..||-|+.+-++.|...-+.-   -=-|+|-.||.+
T Consensus       224 ~gv~~~~d~G~L~y~G~VgtGF~~~~~~~l~~~L~~~~~~~sPf~~~~~~~~  275 (645)
T TIGR02776       224 VGVYEQEDGGQLRYAGKVGTGFGADTLKTLLARLKALGAKASPFAGKPAGAK  275 (645)
T ss_pred             HHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             7651468889427888602788889999999999987430778778888776


No 377
>pfam06189 5-nucleotidase 5'-nucleotidase. This family consists of both eukaryotic and prokaryotic 5'-nucleotidase sequences (EC:3.1.3.5).
Probab=21.23  E-value=39  Score=11.67  Aligned_cols=67  Identities=21%  Similarity=0.324  Sum_probs=38.7

Q ss_pred             EEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             89971438899987435542113432136626789885126818996178866225777888888777536973067525
Q gi|254780834|r  274 IILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLL  353 (648)
Q Consensus       274 ~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~L  353 (648)
                      +.|---..||-..-++|+.-+.-.-.+.-...       -.+++=|+||||.                        |++ 
T Consensus        85 LFLS~~~~DV~~Ai~~G~aAa~v~~~~~~~~~-------~~~qlRIAFDgDa------------------------VLF-  132 (263)
T pfam06189        85 LFLSANAEDVREALDAGVAAATVLPSTPDDSE-------SDDQLRIAFDGDA------------------------VLF-  132 (263)
T ss_pred             EEEECCHHHHHHHHHCCCCEEEEECCCCCCCC-------CCCCEEEEECCCE------------------------EEE-
T ss_conf             68668889999999759971996278867778-------8874589736874------------------------786-


Q ss_pred             CCCCCHHHHHHCCCHHHHHHH
Q ss_conf             788888899720366889988
Q gi|254780834|r  354 SRGEDPDSFIRCYGKTAFEKL  374 (648)
Q Consensus       354 P~G~DPDe~ir~~G~eaf~~l  374 (648)
                        ...-....+++|-++|.+-
T Consensus       133 --sDesE~vyq~~GL~aF~~~  151 (263)
T pfam06189       133 --SDESERVYKAQGLEAFQEH  151 (263)
T ss_pred             --CCCHHHHHHHHCHHHHHHH
T ss_conf             --5707888986088989986


No 378
>TIGR02434 CobF precorrin-6A synthase (deacetylating); InterPro: IPR012797   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 CobF precorrin-6A synthase (2.1.1.152 from EC), a pathway-specific enzyme in the aerobic pathway. After precorrin-4 is methylated at C-11 by CobM to produce precorrin-5, the extruded acyl group is then removed in the subsequent step, which also sees a methyl group added at C-1 in a reaction catalysed by CobF. The product of this reaction is precorrin-6A, which is subsequently reduced by an NADH-dependent reductase to precorrin-6B . This entry identifies CobF in high GC Gram-positive, alphaproteobacteria and pseudomonas-related species..
Probab=21.17  E-value=39  Score=11.66  Aligned_cols=27  Identities=26%  Similarity=0.501  Sum_probs=14.5

Q ss_pred             CCEEEEECCCCCCHHHHHHCCCHHHHHHH
Q ss_conf             73067525788888899720366889988
Q gi|254780834|r  346 NRVNFVLLSRGEDPDSFIRCYGKTAFEKL  374 (648)
Q Consensus       346 ~~v~vv~LP~G~DPDe~ir~~G~eaf~~l  374 (648)
                      -+|-| .+-.|++=+|++.-. .+=...+
T Consensus        27 adV~f-~~dKG~~KsdL~~lR-r~I~~r~   53 (259)
T TIGR02434        27 ADVFF-VLDKGEDKSDLVELR-REICERY   53 (259)
T ss_pred             CCEEE-EECCCCCHHHHHHHH-HHHHHHH
T ss_conf             83899-975873237999999-9999871


No 379
>PRK13529 malate dehydrogenase; Provisional
Probab=21.16  E-value=39  Score=11.66  Aligned_cols=67  Identities=22%  Similarity=0.233  Sum_probs=35.9

Q ss_pred             HCCCCCCHHHHHCCC-CHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCC---CEEEEECCCCC
Q ss_conf             435542113432136-62678988512681899617886622577788888877753697---30675257888
Q gi|254780834|r  288 QAGVQNVVSSLGTAL-TEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN---RVNFVLLSRGE  357 (648)
Q Consensus       288 ~~G~~n~va~~Gtal-t~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~---~v~vv~LP~G~  357 (648)
                      +.-+++++-- ---| +.+-.++|.||-++ +.||.-|-=|-.|..=|.-+.- +-..|.   +.+||++-.|-
T Consensus       235 ~~~fP~~liq-fEDF~~~nA~~lL~rYr~~-~~~FNDDiQGTaaV~LAgll~A-lri~g~~l~d~riv~~GAGs  305 (563)
T PRK13529        235 KRRFPNALLQ-FEDFAQKNAMRLLERYRDE-ICTFNDDIQGTAAVTLAGLLAA-LKIAGEPLSDQRVVFLGAGS  305 (563)
T ss_pred             HHHCCCCEEE-HHCCCCHHHHHHHHHHHHC-CCEECCCCCHHHHHHHHHHHHH-HHHHCCCHHHCEEEEECCCH
T ss_conf             9978982785-0107961389999998650-6422453103779999999999-99829987784799965774


No 380
>KOG0440 consensus
Probab=21.15  E-value=39  Score=11.65  Aligned_cols=29  Identities=28%  Similarity=0.394  Sum_probs=20.4

Q ss_pred             CCCEEEEECCCCCCHHHHHHCCCHHHHHH
Q ss_conf             97306752578888889972036688998
Q gi|254780834|r  345 GNRVNFVLLSRGEDPDSFIRCYGKTAFEK  373 (648)
Q Consensus       345 g~~v~vv~LP~G~DPDe~ir~~G~eaf~~  373 (648)
                      |---.+|.||+|+|-+||+-.+--+-|..
T Consensus        68 g~l~~aV~LP~G~D~nEWlA~nt~~fF~q   96 (243)
T KOG0440          68 GNLREAVKLPEGEDLNEWLAVNTLDFFNQ   96 (243)
T ss_pred             CCHHHHHCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             45999843998776117899847999999


No 381
>pfam04710 Pellino Pellino. Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase.
Probab=21.12  E-value=39  Score=11.65  Aligned_cols=11  Identities=27%  Similarity=0.349  Sum_probs=4.9

Q ss_pred             HHHHCCCEEEE
Q ss_conf             88512681899
Q gi|254780834|r  309 LLWKLSPRIVL  319 (648)
Q Consensus       309 ~l~r~~~~vvl  319 (648)
                      .|.||+=+|++
T Consensus       131 TISRfACRI~~  141 (416)
T pfam04710       131 TISRFACRIVC  141 (416)
T ss_pred             HHHHEEEEEEE
T ss_conf             31010577885


No 382
>COG0585 Uncharacterized conserved protein [Function unknown]
Probab=21.11  E-value=24  Score=13.59  Aligned_cols=45  Identities=24%  Similarity=0.372  Sum_probs=37.5

Q ss_pred             CEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCC
Q ss_conf             8798178974671368888789899898859997999999999818858
Q gi|254780834|r   52 SFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPL  100 (648)
Q Consensus        52 sf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~gi~~  100 (648)
                      -|.|.....+.    =+.+|+..-|..+..+++=.+|++.||.+.||+.
T Consensus        31 dF~V~Ei~~~~----~~~~G~~~~~~l~K~~~dT~~a~~~iak~lgv~~   75 (406)
T COG0585          31 DFIVEEILGYE----PSGDGEYLLFLLRKRGWDTLDAAREIAKRLGVPR   75 (406)
T ss_pred             CCEEEEECCCC----CCCCCCEEEEEEEECCCCHHHHHHHHHHHHCCCH
T ss_conf             52798624768----7898788999999768876999999999969973


No 383
>pfam05131 Pep3_Vps18 Pep3/Vps18/deep orange family. This region is found in a number of protein identified as involved in golgi function and vacuolar sorting. The molecular function of this region is unknown. The members of this family contain a C-terminal ring finger domain.
Probab=21.11  E-value=39  Score=11.65  Aligned_cols=17  Identities=29%  Similarity=0.532  Sum_probs=11.5

Q ss_pred             HHHHHCCCCHHHHHHHH
Q ss_conf             13432136626789885
Q gi|254780834|r  295 VSSLGTALTEYQLRLLW  311 (648)
Q Consensus       295 va~~Gtalt~~~~~~l~  311 (648)
                      ..|.+-+||+.|+-+|.
T Consensus        34 ~~p~si~LTefH~llL~   50 (147)
T pfam05131        34 SPPKSIALTQFHILLLY   50 (147)
T ss_pred             CCCCEEECCHHEEEEEE
T ss_conf             99716870110024575


No 384
>KOG4090 consensus
Probab=21.07  E-value=24  Score=13.62  Aligned_cols=20  Identities=40%  Similarity=0.665  Sum_probs=14.1

Q ss_pred             CCEEEEECCHHHHHHHHHCC
Q ss_conf             87089971438899987435
Q gi|254780834|r  271 SSFIILVEGYMDVLSLCQAG  290 (648)
Q Consensus       271 ~~~~i~vEGy~Dvi~l~~~G  290 (648)
                      .+.+-+||||+|++.-.+.-
T Consensus       133 ~~d~slC~~f~e~Lk~Ck~~  152 (157)
T KOG4090         133 GSDISLCEGYNEMLKQCKKN  152 (157)
T ss_pred             CCCHHHHHHHHHHHHHHHHH
T ss_conf             76158889999999999987


No 385
>KOG0402 consensus
Probab=21.05  E-value=31  Score=12.54  Aligned_cols=50  Identities=22%  Similarity=0.498  Sum_probs=28.5

Q ss_pred             EECCCCCCCCCCEEEECCCCEEEECCCCC---CCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             53458888587879817897467136888---87898998988599979999999998
Q gi|254780834|r   41 ACCPFHDEKTPSFHCNDSKGFYYCFSCHV---KGDHLSFLSALLGCSFIESVQRLAAI   95 (648)
Q Consensus        41 ~~cPfh~ektpsf~v~~~~~~~~cf~c~~---~gd~~~f~~~~~~~~f~ea~~~la~~   95 (648)
                      --|+|..-+|--   -..-|+|+|=+|+.   ||- +. +----..++.-+++.|-+.
T Consensus        37 y~CsfCGK~~vK---R~AvGiW~C~~C~kv~agga-~~-~~t~aa~t~rs~irrlre~   89 (92)
T KOG0402          37 YTCSFCGKKTVK---RKAVGIWKCGSCKKVVAGGA-YT-VTTAAAATVRSTIRRLREL   89 (92)
T ss_pred             HHHHHCCHHHHH---HHCEEEEECCCCCEEECCCE-EE-ECCCHHHHHHHHHHHHHHH
T ss_conf             133122605653---23034784167540540524-78-7063368999999999987


No 386
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=21.05  E-value=39  Score=11.64  Aligned_cols=50  Identities=16%  Similarity=0.201  Sum_probs=31.3

Q ss_pred             CHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             97999999999818858776820367778899999999999999999732
Q gi|254780834|r   84 SFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLK  133 (648)
Q Consensus        84 ~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  133 (648)
                      .-.|.++..|+..||.--..+....-...-.-++-++.+.|..|.++.-+
T Consensus         3 ~p~esik~iAes~Gi~~l~de~a~~La~dveyRlkei~q~A~Kfm~hskR   52 (65)
T smart00803        3 LPKETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKR   52 (65)
T ss_pred             CCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             81788999999859888899999999999999999999999999997576


No 387
>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional
Probab=21.02  E-value=39  Score=11.63  Aligned_cols=59  Identities=17%  Similarity=0.184  Sum_probs=32.9

Q ss_pred             CHHHHHHHHHCCCEEEEEECCC--CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHH
Q ss_conf             6267898851268189961788--662257778888887775369730675257888888997
Q gi|254780834|r  303 TEYQLRLLWKLSPRIVLCFDGD--DPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFI  363 (648)
Q Consensus       303 t~~~~~~l~r~~~~vvl~fDgD--~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~i  363 (648)
                      +...+..+.++|++|+++.+|-  +.|--+.+-.-+.+..  --|..++++.=|.+--|=+|+
T Consensus       204 vtHdl~~~~~~aDrv~vl~~G~iv~~G~~~evl~~~~l~~--~yg~~~~v~~~p~~~~~~~~~  264 (265)
T PRK10575        204 VLHDINMAARYCDYLVALRGGEMIAQGTPAELMRGETLEQ--IYGIPMGILPHPAGAAPVSFV  264 (265)
T ss_pred             EECCHHHHHHHCCEEEEEECCEEEEECCHHHHCCHHHHHH--HHCCCCEEEECCCCCCCEEEE
T ss_conf             9388899999699999998996999848899789879999--869965898387879856983


No 388
>pfam09059 TyeA TyeA. Members of this family are composed of two pairs of parallel alpha-helices, and interact with the bacterial protein YopN via hydrophobic residues located on the helices. Association of TyeA with the C terminus of YopN is accompanied by conformational changes in both polypeptides that create order out of disorder: the resulting structure then serves as an impediment to type III secretion of YopN.
Probab=20.98  E-value=40  Score=11.63  Aligned_cols=44  Identities=14%  Similarity=0.140  Sum_probs=30.5

Q ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHCC-----CHHHHHHHHHHHH
Q ss_conf             9999853023314579999999998854179-----9899999999999
Q gi|254780834|r  386 WKRETENRSFNTPDERAELEIHLKNCINHIK-----DQKLRYYYSQAIR  429 (648)
Q Consensus       386 ~~~l~~~~dl~spe~ka~~~~~l~~~I~~I~-----d~~~R~~yl~~la  429 (648)
                      ++.+.....+.+++.+..|..+++.++..||     |+-.|.-.++.+-
T Consensus        26 i~~la~~~~l~d~e~~I~F~~el~~l~R~iP~~vF~d~e~R~~lL~a~Q   74 (81)
T pfam09059        26 IEKLVNALELQDVEKQVLFYQELKRLVRLFPIEVFSDEEQRQNLLQACQ   74 (81)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHH
T ss_conf             9999997079857899899999999999789875589889999999999


No 389
>KOG1253 consensus
Probab=20.89  E-value=40  Score=11.61  Aligned_cols=10  Identities=10%  Similarity=0.149  Sum_probs=5.1

Q ss_pred             HHHHHHHHHH
Q ss_conf             1788886433
Q gi|254780834|r  251 FFGALNYLQK  260 (648)
Q Consensus       251 l~~a~~~~~~  260 (648)
                      ||-|.++++.
T Consensus       199 LDsAvqav~~  208 (525)
T KOG1253         199 LDSAVQAVRD  208 (525)
T ss_pred             HHHHHHHHHC
T ss_conf             9999998640


No 390
>pfam04630 Phage_tail Phage major tail protein.
Probab=20.89  E-value=40  Score=11.61  Aligned_cols=20  Identities=15%  Similarity=-0.001  Sum_probs=11.2

Q ss_pred             HHHCCCEEEEEECCCCCCHH
Q ss_conf             85126818996178866225
Q gi|254780834|r  310 LWKLSPRIVLCFDGDDPGLR  329 (648)
Q Consensus       310 l~r~~~~vvl~fDgD~AG~k  329 (648)
                      ..++..+++-.|.++++|..
T Consensus       163 ~~~~~~~~yk~~~s~d~~Fd  182 (199)
T pfam04630       163 DNAGGNQPYKIFYSGDSGFD  182 (199)
T ss_pred             CCCCCCCEEEEEECCCCCCC
T ss_conf             56668951699846998989


No 391
>cd06394 PBP1_iGluR_Kainate_KA1_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels act
Probab=20.89  E-value=40  Score=11.61  Aligned_cols=48  Identities=19%  Similarity=0.286  Sum_probs=29.1

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCC
Q ss_conf             8189961788662257778888887775369730675257888888997203
Q gi|254780834|r  315 PRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCY  366 (648)
Q Consensus       315 ~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~  366 (648)
                      +++.++||.|++-.    |.-++.......+..+.+-.++.+.||-..+|+-
T Consensus       135 ~~ftiiYe~~~~L~----rLq~ll~~~~~~~~~i~vr~l~~~~d~r~vLkeI  182 (333)
T cd06394         135 PTASLICAKAECLL----RLEELLRQFLISKETLSVRMLDDSRDPTPLLKEI  182 (333)
T ss_pred             CEEEEEEECCHHHH----HHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHH
T ss_conf             66999970735689----9999987216789807999878899867999999


No 392
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit; InterPro: IPR010243   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 entry describes orthologues of the beta subunit of bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=20.88  E-value=40  Score=11.61  Aligned_cols=37  Identities=14%  Similarity=-0.021  Sum_probs=16.7

Q ss_pred             CCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHH
Q ss_conf             2113432136626789885126818996178866225
Q gi|254780834|r  293 NVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLR  329 (648)
Q Consensus       293 n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~k  329 (648)
                      .+++.-|+-.|..|.+++-.-..+.....+.+-++.-
T Consensus       275 ~~~~~~g~~itar~~~~~e~~~~~~~~~~~~~~~~~~  311 (1449)
T TIGR02013       275 KILLAKGKKITARIKKKLENKSLKRELLLEELLAEDL  311 (1449)
T ss_pred             EEEECCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             7984278500489999873131344666688886665


No 393
>TIGR00393 kpsF sugar isomerase, KpsF/GutQ family; InterPro: IPR004800 This is a family of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. The group includes GutQ, a protein of the glucitol operon and KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of Escherichia coli.; GO: 0016853 isomerase activity, 0005975 carbohydrate metabolic process.
Probab=20.85  E-value=31  Score=12.54  Aligned_cols=72  Identities=19%  Similarity=0.238  Sum_probs=39.1

Q ss_pred             HHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHC--CCEECCCCCCCCCCC----CCEE-EEEE
Q ss_conf             57899998506885351012442256774103455420599734523201--210034654100001----6716-8889
Q gi|254780834|r  138 KRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAG--LLIDGDNSATSYDRF----RNRL-IFPI  210 (648)
Q Consensus       138 ~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~g--l~~~~~~~~~~~d~F----r~Ri-~fPi  210 (648)
                      +-|..-++.|||++|.=.+|.-|=+      |=+.|.-|   ..++.+.+  |-.-... .+..|..    |.|+ |-=|
T Consensus       124 aLa~al~~ArnF~~eDFA~~HPGG~------LG~kLL~k---V~dlm~t~d~lP~v~~t-as~~DAL~e~~~~~LG~~~v  193 (272)
T TIGR00393       124 ALAVALMKARNFSEEDFAKFHPGGA------LGRKLLVK---VKDLMQTDDELPLVAPT-ASFKDALLEMSRKRLGLAVV  193 (272)
T ss_pred             HHHHHHHHHCCCCHHHHHCCCCCHH------HHHHHHHH---HHHHHCCCCCCCCEECC-CCCEEEEEEEECCCCCEEEE
T ss_conf             9999998525888424411487046------66788887---67764066567822236-77202102331378617999


Q ss_pred             EECCCCEEE
Q ss_conf             707785888
Q gi|254780834|r  211 RSSRGQVIA  219 (648)
Q Consensus       211 ~~~~g~~i~  219 (648)
                      .|.+-++.|
T Consensus       194 ~~~~~~~~G  202 (272)
T TIGR00393       194 CDENEQLKG  202 (272)
T ss_pred             EECCCCEEE
T ss_conf             715552467


No 394
>pfam04989 CmcI Cephalosporin hydroxylase. Members of this family are about 220 amino acids long. The CmcI protein is presumed to represent the cephalosporin-7--hydroxylase. However this has not been experimentally verified.
Probab=20.78  E-value=40  Score=11.59  Aligned_cols=85  Identities=15%  Similarity=0.119  Sum_probs=50.7

Q ss_pred             CHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCE-----EEEECCCCCCHHH-HHHCCCH-HHHHHHH
Q ss_conf             6267898851268189961788662257778888887775369730-----6752578888889-9720366-8899886
Q gi|254780834|r  303 TEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRV-----NFVLLSRGEDPDS-FIRCYGK-TAFEKLI  375 (648)
Q Consensus       303 t~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v-----~vv~LP~G~DPDe-~ir~~G~-eaf~~ll  375 (648)
                      +-++++.+.+..+++.++.|+|-. ....++.++..-++++.|-=+     -+=.+|+...|+. +-+.+|+ .|+.++|
T Consensus        95 ~~~~v~~~~~~~~~vlVilDs~Ht-~~hVl~eL~~y~~lv~~GsY~IVeDTii~~~p~~~~~~r~w~~gnnP~~Av~eFL  173 (202)
T pfam04989        95 IIEQVRSLAEPPHPVLVILDSDHT-HEHVLAELRAYAPLVSEGSYLVVEDTIIEDLPESPFPDRPWGKGNNPKTAVTEFL  173 (202)
T ss_pred             HHHHHHHHHCCCCCEEEEECCCCC-HHHHHHHHHHHHHHCCCCCEEEEECCCHHHCCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             998899985379858999648865-6889999998752157688999957624317556678886878989799999999


Q ss_pred             HHCCCHHHHHHHHHHH
Q ss_conf             4149927999999985
Q gi|254780834|r  376 VESLPLVDMLWKRETE  391 (648)
Q Consensus       376 ~~A~~l~dFl~~~l~~  391 (648)
                      ++...   |.++....
T Consensus       174 ~~~~~---F~iD~~~~  186 (202)
T pfam04989       174 AEHPE---FEIDTAIE  186 (202)
T ss_pred             HHCCC---CEECCCCC
T ss_conf             87899---38653202


No 395
>cd07968 OBF_DNA_ligase_IV The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part 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 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 pro
Probab=20.73  E-value=36  Score=12.02  Aligned_cols=18  Identities=11%  Similarity=0.385  Sum_probs=7.4

Q ss_pred             HHHHHCCCCHHHHHHHHH
Q ss_conf             134321366267898851
Q gi|254780834|r  295 VSSLGTALTEYQLRLLWK  312 (648)
Q Consensus       295 va~~Gtalt~~~~~~l~r  312 (648)
                      |+-.||.||.++++.|.+
T Consensus        46 ~~kvgtGfsd~~l~~l~~   63 (140)
T cd07968          46 FCKVGSGFSDEELDEIRR   63 (140)
T ss_pred             EEEECCCCCHHHHHHHHH
T ss_conf             999856899999999999


No 396
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA).  This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  For topoisomerases the conserved glutamate is believed to act as a general b
Probab=20.68  E-value=40  Score=11.58  Aligned_cols=55  Identities=27%  Similarity=0.393  Sum_probs=32.9

Q ss_pred             HHHHHHHHH---CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHH
Q ss_conf             267898851---26818996178866225777888888777536973067525788888899
Q gi|254780834|r  304 EYQLRLLWK---LSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSF  362 (648)
Q Consensus       304 ~~~~~~l~r---~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~  362 (648)
                      ..|++.|++   -+++||++-|.|.=|..=++..++.+-.   ....++=+.+.+ ..|.+.
T Consensus        78 ~~~~~~i~~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~---~~~~v~R~~fss-lT~~~I  135 (142)
T cd01028          78 KKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKC---DNKPVKRAWFSE-ITPKAI  135 (142)
T ss_pred             HHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHCC---CCCCCEEEEEEC-CCHHHH
T ss_conf             9999999999861999998889982279999999999578---899927899835-799999


No 397
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.61  E-value=40  Score=11.57  Aligned_cols=10  Identities=50%  Similarity=0.876  Sum_probs=3.6

Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999998
Q gi|254780834|r  594 QKEEIEKQIA  603 (648)
Q Consensus       594 ~l~ele~~l~  603 (648)
                      ++.+++++|.
T Consensus        89 k~~eie~ki~   98 (107)
T cd04777          89 KKDELEKEIE   98 (107)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 398
>PRK13239 alkylmercury lyase; Provisional
Probab=20.51  E-value=40  Score=11.55  Aligned_cols=38  Identities=29%  Similarity=0.515  Sum_probs=21.9

Q ss_pred             EEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHH
Q ss_conf             9707785888501001465530010387676535210110817888864
Q gi|254780834|r  210 IRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYL  258 (648)
Q Consensus       210 i~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~  258 (648)
                      -+|..|+|||| |=++.+.. -.+.        --|+.|| -..|.+++
T Consensus        64 eyD~~G~Iig~-GLTlrpT~-Hrf~--------v~G~~Ly-TWCAlDaL  101 (206)
T PRK13239         64 EYDEDGRIIGY-GLTLRPTP-HRFE--------VDGRQLY-TWCALDTL  101 (206)
T ss_pred             EECCCCCEEEE-ECCCCCCC-CEEE--------ECCEEEE-HHHHHHHH
T ss_conf             58589858865-04116668-6789--------8992555-78888876


No 399
>KOG1207 consensus
Probab=20.46  E-value=40  Score=11.54  Aligned_cols=60  Identities=37%  Similarity=0.464  Sum_probs=44.9

Q ss_pred             CEEEEECCH------HHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHH
Q ss_conf             708997143------8899987435542113432136626789885126818996178866225777888
Q gi|254780834|r  272 SFIILVEGY------MDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAI  335 (648)
Q Consensus       272 ~~~i~vEGy------~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~  335 (648)
                      +.+++|-|-      -=|.+|+.+|-. |||.   |=+++++..|-++++-.|+-.-+|-.|..|..|++
T Consensus         7 G~~vlvTgagaGIG~~~v~~La~aGA~-ViAv---aR~~a~L~sLV~e~p~~I~Pi~~Dls~wea~~~~l   72 (245)
T KOG1207           7 GVIVLVTGAGAGIGKEIVLSLAKAGAQ-VIAV---ARNEANLLSLVKETPSLIIPIVGDLSAWEALFKLL   72 (245)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHCCCE-EEEE---ECCHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHH
T ss_conf             619996056664149999999866887-9999---56988999998529764245575133899999761


No 400
>PRK13551 agmatine deiminase; Provisional
Probab=20.26  E-value=41  Score=11.51  Aligned_cols=54  Identities=11%  Similarity=0.142  Sum_probs=30.4

Q ss_pred             CCHHHHHHHHHCCC--EEEEEECCCCCCHHH--HHHHHHHHHHH-HHCCCCEEEEECCC
Q ss_conf             66267898851268--189961788662257--77888888777-53697306752578
Q gi|254780834|r  302 LTEYQLRLLWKLSP--RIVLCFDGDDPGLRA--AYKAIDLVLCH-LIPGNRVNFVLLSR  355 (648)
Q Consensus       302 lt~~~~~~l~r~~~--~vvl~fDgD~AG~kA--a~Ra~e~~l~~-l~~g~~v~vv~LP~  355 (648)
                      -|..|+-.|.||+.  .|+++.-.|..--+.  .....+.+... -..|...+++.||-
T Consensus       207 dTdGHID~lARFv~p~~Vl~~~~~d~~d~~~~~~~~~~~~L~~~~da~G~~~~iv~lP~  265 (360)
T PRK13551        207 ETDGHVDNMCCFVRPGEVALAWTDDENDPQYARSKAALEVLENTTDAKGRKLKVHKLPI  265 (360)
T ss_pred             CCCCCEECEEEECCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECC
T ss_conf             99987304377438980999944899884679999999999965643698327999369


No 401
>pfam08448 PAS_4 PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Probab=20.24  E-value=41  Score=11.50  Aligned_cols=23  Identities=22%  Similarity=0.274  Sum_probs=16.6

Q ss_pred             CEEEEEEEECCCCEEEEECCCCC
Q ss_conf             71688897077858885010014
Q gi|254780834|r  204 NRLIFPIRSSRGQVIAFGGRTLS  226 (648)
Q Consensus       204 ~Ri~fPi~~~~g~~i~f~gR~l~  226 (648)
                      .=.+.||+|..|+++|+-+=..|
T Consensus        82 ~~~~~pi~d~~G~~~g~v~~~~D  104 (110)
T pfam08448        82 ELRLTPLRDPDGEVIGVLVISRD  104 (110)
T ss_pred             EEEEEEEECCCCCEEEEEEEEEE
T ss_conf             43576689899999999999998


No 402
>COG3484 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]
Probab=20.23  E-value=34  Score=12.26  Aligned_cols=16  Identities=31%  Similarity=0.621  Sum_probs=14.3

Q ss_pred             CCCCCCCCCCCHHCCC
Q ss_conf             3876765352101108
Q gi|254780834|r  235 NSPETILFHKGKNLYN  250 (648)
Q Consensus       235 NSpeT~if~K~~~Ly~  250 (648)
                      -+||||+|+-|..-||
T Consensus       139 aT~etpf~QiGEtKYG  154 (255)
T COG3484         139 ATPETPFLQIGETKYG  154 (255)
T ss_pred             CCCCCCEEECCCCCCC
T ss_conf             5899851671431258


No 403
>KOG0415 consensus
Probab=20.16  E-value=14  Score=15.74  Aligned_cols=46  Identities=17%  Similarity=0.179  Sum_probs=27.2

Q ss_pred             EEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHH
Q ss_conf             575345888858787981789746713688887898998988599979999
Q gi|254780834|r   39 YWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESV   89 (648)
Q Consensus        39 ~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~   89 (648)
                      |.-.|+||+=.. -|+.    |.----|.|.||+-|==+|.-++-.|-||-
T Consensus        36 YYN~clfh~vq~-~f~a----QTGDPtGtG~GG~si~~~lyG~q~rffeaE   81 (479)
T KOG0415          36 YYNFCLFHTVQR-DFTA----QTGDPTGTGDGGESIYGVLYGEQARFFEAE   81 (479)
T ss_pred             HCCCCEEEECCC-CCEE----ECCCCCCCCCCCCEEEEECCCCCCHHHHHH
T ss_conf             406450224011-6353----138988778885432000036321011322


No 404
>cd06544 GH18_narbonin Narbonin is a plant 2S protein from the globulin fraction of narbon bean (Vicia narbonensis L.) cotyledons with unknown function.  Narbonin has a glycosyl hydrolase family 18 (GH18) domain without the conserved catalytic residues and with no known enzymatic activity.  Narbonin amounts to up to 3% of the total seed globulins of mature seeds and was thought to be a storage protein but was found to degrade too slowly during germination.  This family also includes the VfNOD32 nodulin from Vicia faba.
Probab=20.15  E-value=41  Score=11.49  Aligned_cols=84  Identities=17%  Similarity=0.191  Sum_probs=53.4

Q ss_pred             CCCHHHHHHHHHCCC--EEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH-
Q ss_conf             366267898851268--18996178866225777888888777536973067525788888899720366889988641-
Q gi|254780834|r  301 ALTEYQLRLLWKLSP--RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE-  377 (648)
Q Consensus       301 alt~~~~~~l~r~~~--~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~-  377 (648)
                      -||+++++.||+..+  +|++..-||..|-.                   .+.+-|.  ..|+|+.+- ...+..+|++ 
T Consensus        55 ~ltP~~V~~~K~~~pnvKV~iSiGG~~v~~~-------------------~~~f~p~--s~~~WV~NA-v~SL~~iI~~Y  112 (253)
T cd06544          55 NLTPEAVKSIKAQHPNVKVVISIGGRGVQNN-------------------PTPFDPS--NVDSWVSNA-VSSLTSIIQTY  112 (253)
T ss_pred             CCCHHHHHHHHHHCCCCEEEEEECCCCCCCC-------------------CEECCCC--HHHHHHHHH-HHHHHHHHHHH
T ss_conf             7499999998852998059999568756687-------------------2111762--077899999-99999999970


Q ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             4992799999998530233145799999999988
Q gi|254780834|r  378 SLPLVDMLWKRETENRSFNTPDERAELEIHLKNC  411 (648)
Q Consensus       378 A~~l~dFl~~~l~~~~dl~spe~ka~~~~~l~~~  411 (648)
                      ..+.+|.=|++..     .+++.-++.+.+|...
T Consensus       113 ~lDGIDIDyE~f~-----~d~~tF~~cIG~LIt~  141 (253)
T cd06544         113 NLDGIDIDYEHFP-----ADPDTFVECIGQLITE  141 (253)
T ss_pred             CCCCEECCHHHCC-----CCHHHHHHHHHHHHHH
T ss_conf             8886112565446-----8778999999999998


No 405
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.14  E-value=41  Score=11.49  Aligned_cols=36  Identities=14%  Similarity=0.291  Sum_probs=24.7

Q ss_pred             ECCCCCCCCCCEEEECCCCEEEECCCCC--CCCHHHHHHH
Q ss_conf             3458888587879817897467136888--8789899898
Q gi|254780834|r   42 CCPFHDEKTPSFHCNDSKGFYYCFSCHV--KGDHLSFLSA   79 (648)
Q Consensus        42 ~cPfh~ektpsf~v~~~~~~~~cf~c~~--~gd~~~f~~~   79 (648)
                      -||-+.  .+.+..++..|.+-|=.||.  .-++||-=.+
T Consensus        13 kCp~Cg--~~~ii~D~~~G~~vC~~CG~Vi~e~~ID~~~E   50 (310)
T PRK00423         13 RCPECG--SDKLIYDYERGEIVCADCGYVIEENLIDQGPE   50 (310)
T ss_pred             ECCCCC--CCCEEEECCCCCEECCCCCCEEECCCCCCCCC
T ss_conf             898986--98535678998775302887611320236753


No 406
>TIGR02418 acolac_catab acetolactate synthase, catabolic; InterPro: IPR012782    Acetolactate synthase is a thiamin pyrophosphate-dependent enzyme that combines two molecules of pyruvate to yield 2-acetolactate with the release of CO2. It exists in two distinct forms that have different properties, though they are clearly related , . The biosynthetic form, found in plants, fungi and bacteria, is involved in the biosynthesis of branched-chain amino acids and contains non-catalytic FAD. The catabolic form is found only in some bacteria, participates in butanediol fermentation, and does not contain FAD.   This entry represents the catabolic form of acetolactate synthase, generally found in species that posses acetolactate decarboxylase, which is often encoded in the same operon. The enzyme is thought to be a homotetramer, though this has not conclusively been shown. Each monomer consists of three distinct domains, designated, starting from the N-terminus, as alpha, beta and gamma . The core of the alpha and gamma domains is a six-stranded parallel beta sheet surrounded by alpha helices, while the the beta domain forms a double Rossman fold. The thiamin pyrophosphate cofactor has an unusual conformation that has not been seen in other enzymes using this cofactor, including the biosynthetic form of acetolactate synthase. The active site is located in a funnel at the dimer interface, bordered by residues from all three domains.; GO: 0000287 magnesium ion binding, 0003984 acetolactate synthase activity, 0030976 thiamin pyrophosphate binding, 0050660 FAD binding.
Probab=20.12  E-value=26  Score=13.24  Aligned_cols=43  Identities=16%  Similarity=0.082  Sum_probs=20.4

Q ss_pred             CCHHHHHHHHHHHHHHHHH-------CCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3145799999999988541-------7998999999999999988765776
Q gi|254780834|r  396 NTPDERAELEIHLKNCINH-------IKDQKLRYYYSQAIRDRLQQLFQKY  439 (648)
Q Consensus       396 ~spe~ka~~~~~l~~~I~~-------I~d~~~R~~yl~~la~~L~~~~~~~  439 (648)
                      .|.++.++++++++.....       =.-.+-|++|-+.|+.|++ +|+++
T Consensus       212 aS~~~~~~Av~rll~k~~LPvVeTfQgAG~vsrele~~TFfGRvG-LFrNQ  261 (553)
T TIGR02418       212 ASSQETTEAVRRLLKKTQLPVVETFQGAGVVSRELEDETFFGRVG-LFRNQ  261 (553)
T ss_pred             CCCHHHHHHHHHHHCCCCCCCEEEEECCEEECHHCCCCCCEECCC-CCCCC
T ss_conf             888899999999864606882140200513110024565210011-44587


No 407
>pfam02403 Seryl_tRNA_N Seryl-tRNA synthetase N-terminal domain. This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.
Probab=20.10  E-value=41  Score=11.48  Aligned_cols=53  Identities=21%  Similarity=0.349  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9985899999999999999872412798999999999999999999988413267
Q gi|254780834|r  584 LYKRFRLLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMI  638 (648)
Q Consensus       584 l~~r~~~L~r~l~ele~~l~e~~~~~d~e~~~~l~~el~elk~~L~~l~~~Eal~  638 (648)
                      +......+..+...+.+++......+.  ....+..+..+++.++..++.+..-+
T Consensus        41 ~~~~~e~L~~~~N~~sk~ig~~~~~~~--~~~~l~~~~~~lk~~i~~le~~~~~~   93 (108)
T pfam02403        41 LQVELEELQAERNELSKEIGKAKKKKE--DAEALIAEVKELKDELKALEAELREL   93 (108)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999998598999999875774--16889999999999999999999999


No 408
>KOG1597 consensus
Probab=20.07  E-value=41  Score=11.48  Aligned_cols=68  Identities=21%  Similarity=0.233  Sum_probs=35.7

Q ss_pred             HHCCCCCCHHHHHCCCCHHHHH--HHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHH
Q ss_conf             7435542113432136626789--8851268189961788662257778888887775369730675257888888997
Q gi|254780834|r  287 CQAGVQNVVSSLGTALTEYQLR--LLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFI  363 (648)
Q Consensus       287 ~~~G~~n~va~~Gtalt~~~~~--~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~i  363 (648)
                      |.+|.. +.+.||--+...++.  ..||.       |-+|.+|..-+ |..+-.-|+|..|.-.-++..|.|.+++..-
T Consensus        17 ~~~gdt-vC~~CGlVl~~r~Id~~sEwrt-------fsnd~~~~DPs-rvG~~sNPlL~~g~L~T~I~~g~g~~s~~~s   86 (308)
T KOG1597          17 HSAGDT-VCSECGLVLEDRIIDEGSEWRT-------FSNDDSDADPS-RVGASSNPLLDGGDLSTFISKGTGTSSSFAS   86 (308)
T ss_pred             CCCCCE-ECCCCCEEECCCCCCCCCCCCC-------CCCCCCCCCCC-CCCCCCCCCCCCCCCCEEEECCCCCCHHHHH
T ss_conf             268856-6023772621424256522100-------14677788965-4688889878899854054058887778899


Done!