Query         gi|254780788|ref|YP_003065201.1| transcription elongation factor NusA [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 526
No_of_seqs    242 out of 1121
Neff          5.2 
Searched_HMMs 39220
Date          Sun May 29 18:46:27 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780788.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK09202 nusA transcription el 100.0       0       0 1079.2  48.4  427    5-506     2-428 (428)
  2 PRK12329 nusA transcription el 100.0       0       0  997.0  43.1  406    6-411     6-448 (457)
  3 PRK12327 nusA transcription el 100.0       0       0  977.3  42.7  351    5-355     1-352 (353)
  4 PRK12328 nusA transcription el 100.0       0       0  975.5  43.0  349    7-355     2-357 (375)
  5 TIGR01953 NusA transcription t 100.0       0       0  983.3  37.2  339    8-346     1-366 (366)
  6 COG0195 NusA Transcription elo 100.0       0       0  425.9  17.6  182  160-347     1-183 (190)
  7 pfam08529 NusA_N NusA N-termin 100.0   8E-31   2E-35  245.8  14.5  122    8-129     1-122 (122)
  8 PRK08406 transcription elongat  99.9   8E-26   2E-30  209.0   6.0   94  250-344    44-139 (142)
  9 cd04455 S1_NusA S1_NusA: N-uti  99.8   7E-19 1.8E-23  158.0   8.6   67  136-202     1-67  (67)
 10 cd02134 NusA_KH NusA_K homolog  99.7 9.6E-17 2.4E-21  142.3   4.8   60  283-342     1-61  (61)
 11 TIGR01954 nusA_Cterm_rpt trans  99.1 5.1E-11 1.3E-15  100.2   4.5   50  368-417     1-52  (52)
 12 PRK00087 4-hydroxy-3-methylbut  98.8 7.7E-07   2E-11   69.5  14.4   72  137-210   303-381 (670)
 13 PRK07899 rpsA 30S ribosomal pr  98.6   1E-06 2.6E-11   68.6  11.5  270   23-342    18-347 (484)
 14 TIGR01954 nusA_Cterm_rpt trans  98.6 6.1E-08 1.6E-12   77.6   4.8   50  443-511     1-52  (52)
 15 PRK07400 30S ribosomal protein  98.6 2.3E-06 5.9E-11   66.0  12.8   64  137-203   117-183 (314)
 16 cd05687 S1_RPS1_repeat_ec1_hs1  98.5 5.7E-07 1.4E-11   70.5   8.2   63  139-203     1-70  (70)
 17 PRK06299 rpsA 30S ribosomal pr  98.5 8.6E-06 2.2E-10   61.8  13.0   64  138-203   104-171 (556)
 18 PRK13806 rpsA 30S ribosomal pr  98.4 1.2E-06   3E-11   68.1   7.7  124   73-201   140-273 (489)
 19 pfam00575 S1 S1 RNA binding do  98.4 1.9E-06 4.8E-11   66.7   7.9   65  136-202     2-73  (74)
 20 PRK06299 rpsA 30S ribosomal pr  98.4   2E-06   5E-11   66.5   7.8  109   88-202   143-259 (556)
 21 PRK07899 rpsA 30S ribosomal pr  98.4 2.5E-06 6.4E-11   65.7   8.1  123   73-202   147-276 (484)
 22 PRK06676 rpsA 30S ribosomal pr  98.3   6E-06 1.5E-10   63.0   9.4  188   89-312    61-260 (390)
 23 PRK13806 rpsA 30S ribosomal pr  98.3 2.9E-05 7.4E-10   58.0  12.0  115   75-204    57-182 (489)
 24 PRK00087 4-hydroxy-3-methylbut  98.2 1.9E-05 4.9E-10   59.2   9.9  160   73-259   326-502 (670)
 25 PRK07400 30S ribosomal protein  98.2 1.3E-05 3.4E-10   60.4   8.5   78  130-209    21-107 (314)
 26 PRK12269 bifunctional cytidyla  98.1   2E-05 5.2E-10   59.1   8.1   68  135-208   318-386 (863)
 27 TIGR00717 rpsA ribosomal prote  98.1 3.3E-05 8.4E-10   57.5   9.1  174   69-269    39-234 (534)
 28 smart00316 S1 Ribosomal protei  98.1 2.8E-05 7.2E-10   58.0   8.6   64  137-202     1-71  (72)
 29 cd05691 S1_RPS1_repeat_ec6 S1_  98.1 2.9E-05 7.5E-10   57.9   8.5   62  139-202     1-69  (73)
 30 cd04461 S1_Rrp5_repeat_hs8_sc7  98.0 2.8E-05 7.3E-10   58.0   8.1   67  131-201     9-82  (83)
 31 COG0539 RpsA Ribosomal protein  98.0 5.1E-05 1.3E-09   56.1   9.1  112   79-201   134-259 (541)
 32 PRK06676 rpsA 30S ribosomal pr  98.0   7E-05 1.8E-09   55.1   9.5   73  126-202   182-260 (390)
 33 PRK08059 general stress protei  97.9 5.7E-05 1.5E-09   55.8   7.6   65  137-203     5-76  (119)
 34 cd05697 S1_Rrp5_repeat_hs5 S1_  97.9 7.9E-05   2E-09   54.7   8.1   61  139-201     1-68  (69)
 35 TIGR00717 rpsA ribosomal prote  97.9 0.00016   4E-09   52.5   9.6  152   41-201   101-269 (534)
 36 COG0539 RpsA Ribosomal protein  97.9 0.00056 1.4E-08   48.5  12.4  122   75-205    45-174 (541)
 37 cd02409 KH-II KH-II  (K homolo  97.9 2.2E-05 5.6E-10   58.8   5.1   58  284-341     1-67  (68)
 38 cd05698 S1_Rrp5_repeat_hs6_sc5  97.9 7.7E-05   2E-09   54.8   7.9   62  139-202     1-69  (70)
 39 TIGR02236 recomb_radA DNA repa  97.9 3.1E-05   8E-10   57.7   5.7   56  363-418     3-58  (333)
 40 cd05688 S1_RPS1_repeat_ec3 S1_  97.8 7.5E-05 1.9E-09   54.9   6.8   58  138-195     1-64  (68)
 41 cd05685 S1_Tex S1_Tex: The C-t  97.8 0.00012   3E-09   53.4   7.6   61  139-201     1-68  (68)
 42 cd04465 S1_RPS1_repeat_ec2_hs2  97.8 0.00019 4.9E-09   51.9   8.2   62  139-203     1-67  (67)
 43 cd04452 S1_IF2_alpha S1_IF2_al  97.8 0.00016 4.2E-09   52.4   7.8   65  136-202     1-74  (76)
 44 PRK07252 hypothetical protein;  97.7 0.00019 4.9E-09   51.9   7.5   66  137-204     2-74  (120)
 45 cd04472 S1_PNPase S1_PNPase: P  97.7 0.00017 4.3E-09   52.3   7.0   61  139-202     1-68  (68)
 46 TIGR02236 recomb_radA DNA repa  97.7 4.3E-05 1.1E-09   56.7   3.9   58  436-510     1-58  (333)
 47 cd05708 S1_Rrp5_repeat_sc12 S1  97.7 0.00019 4.8E-09   52.0   7.2   66  137-204     1-74  (77)
 48 PRK12269 bifunctional cytidyla  97.6 0.00043 1.1E-08   49.3   8.0  124   69-204   339-474 (863)
 49 PRK07956 ligA NAD-dependent DN  97.5 0.00061 1.6E-08   48.2   8.1   99  363-474   448-549 (668)
 50 cd05692 S1_RPS1_repeat_hs4 S1_  97.4 0.00082 2.1E-08   47.3   7.7   61  139-202     1-68  (69)
 51 PRK04301 radA DNA repair and r  97.4 0.00033 8.3E-09   50.2   5.3   56  362-417     9-64  (318)
 52 PRK03987 translation initiatio  97.4   0.002 5.2E-08   44.4   9.3   75  136-210     6-89  (262)
 53 cd00164 S1_like S1_like: Ribos  97.4 0.00087 2.2E-08   47.1   7.3   58  142-201     1-65  (65)
 54 cd05706 S1_Rrp5_repeat_sc10 S1  97.3  0.0021 5.3E-08   44.3   8.7   63  137-201     2-71  (73)
 55 cd05690 S1_RPS1_repeat_ec5 S1_  97.3  0.0013 3.2E-08   45.9   7.3   56  139-194     1-64  (69)
 56 PRK08406 transcription elongat  97.3 0.00064 1.6E-08   48.1   5.4   70  278-347     4-75  (142)
 57 cd05689 S1_RPS1_repeat_ec4 S1_  97.2  0.0017 4.4E-08   44.9   7.5   59  137-195     2-68  (72)
 58 cd05707 S1_Rrp5_repeat_sc11 S1  97.2  0.0021 5.3E-08   44.3   7.3   61  139-201     1-68  (68)
 59 PRK05807 hypothetical protein;  97.2  0.0019   5E-08   44.5   7.2   64  137-203     4-73  (136)
 60 PRK01172 ski2-like helicase; P  97.2   0.018 4.6E-07   37.4  12.1  107  387-510   548-670 (674)
 61 PRK01172 ski2-like helicase; P  97.1  0.0015 3.8E-08   45.4   5.8   57  362-418   614-670 (674)
 62 cd05694 S1_Rrp5_repeat_hs2_sc2  97.0  0.0041   1E-07   42.1   7.6   64  137-200     3-68  (74)
 63 PRK08582 hypothetical protein;  97.0  0.0039   1E-07   42.3   7.2   63  137-202     4-73  (139)
 64 PRK04301 radA DNA repair and r  96.9  0.0027 6.9E-08   43.4   5.8   22   14-35     40-61  (318)
 65 cd04471 S1_RNase_R S1_RNase_R:  96.9  0.0071 1.8E-07   40.4   7.9   58  138-195     1-77  (83)
 66 cd05684 S1_DHX8_helicase S1_DH  96.7  0.0091 2.3E-07   39.6   7.5   61  139-203     1-72  (79)
 67 PRK09202 nusA transcription el  96.7  0.0016 4.2E-08   45.1   3.5  170  178-414   255-428 (428)
 68 PTZ00035 Rad51; Provisional     96.7  0.0031 7.8E-08   43.1   4.9   56  362-417    34-92  (350)
 69 cd04473 S1_RecJ_like S1_RecJ_l  96.7  0.0083 2.1E-07   39.9   7.1   56  137-194    15-71  (77)
 70 cd04460 S1_RpoE S1_RpoE: RpoE,  96.7  0.0083 2.1E-07   39.9   7.0   68  140-207     1-88  (99)
 71 PTZ00162 RNA polymerase II sub  96.7   0.011 2.7E-07   39.1   7.5   72  134-205    77-164 (170)
 72 PRK08563 DNA-directed RNA poly  96.6  0.0085 2.2E-07   39.8   6.7   74  134-207    77-170 (182)
 73 PRK00254 ski2-like helicase; P  96.5  0.0039   1E-07   42.3   4.3  105  387-508   578-700 (717)
 74 COG1095 RPB7 DNA-directed RNA   96.4  0.0086 2.2E-07   39.8   5.7   73  134-207    77-170 (183)
 75 COG1093 SUI2 Translation initi  96.4   0.026 6.6E-07   36.3   8.1   71  136-206     9-88  (269)
 76 PRK05054 exoribonuclease II; P  96.4   0.047 1.2E-06   34.4   9.1   65  142-206    86-158 (644)
 77 PRK08097 ligB NAD-dependent DN  96.3   0.024 6.1E-07   36.5   7.6  116  363-518   429-547 (563)
 78 TIGR00575 dnlj DNA ligase, NAD  96.2    0.06 1.5E-06   33.6   9.2  285  128-504   315-663 (706)
 79 cd05789 S1_Rrp4 S1_Rrp4: Rrp4   96.2   0.022 5.6E-07   36.8   6.8   59  134-192     2-71  (86)
 80 cd05703 S1_Rrp5_repeat_hs12_sc  96.2   0.042 1.1E-06   34.7   8.1   63  139-203     1-72  (73)
 81 PRK04163 exosome complex RNA-b  96.1   0.025 6.2E-07   36.4   6.8   63  132-194    56-129 (232)
 82 cd04454 S1_Rrp4_like S1_Rrp4_l  96.1   0.016 4.1E-07   37.8   5.8   70  134-206     2-78  (82)
 83 cd04453 S1_RNase_E S1_RNase_E:  96.1    0.03 7.5E-07   35.8   6.8   66  135-200     4-81  (88)
 84 PRK11642 exoribonuclease R; Pr  95.9    0.17 4.2E-06   30.3  10.6   25   14-38     38-62  (813)
 85 cd02134 NusA_KH NusA_K homolog  95.9  0.0067 1.7E-07   40.6   2.9   58  205-277     2-61  (61)
 86 TIGR02063 RNase_R ribonuclease  95.9   0.087 2.2E-06   32.4   8.6   93  105-197   637-750 (755)
 87 COG2996 Predicted RNA-bindinin  95.9   0.017 4.5E-07   37.5   5.0  106   78-193   101-209 (287)
 88 PTZ00248 eukaryotic translatio  95.8   0.043 1.1E-06   34.6   6.9   82  129-210     8-98  (324)
 89 TIGR00575 dnlj DNA ligase, NAD  95.8   0.076 1.9E-06   32.8   8.0  118  363-517   455-589 (706)
 90 PRK11824 polynucleotide phosph  95.8    0.11 2.7E-06   31.8   8.7   61  282-342   514-590 (694)
 91 PRK13766 Hef nuclease; Provisi  95.8   0.019 4.7E-07   37.3   4.8   46  365-411   711-756 (764)
 92 PRK11712 ribonuclease G; Provi  95.7   0.057 1.5E-06   33.7   7.0  181  136-323    36-282 (489)
 93 PRK00254 ski2-like helicase; P  95.6    0.21 5.4E-06   29.5  11.9   53  362-414   646-698 (717)
 94 PRK06418 transcription elongat  95.5    0.23 5.8E-06   29.3  12.3  135  199-342    28-165 (167)
 95 pfam10246 MRP-S35 Mitochondria  95.5   0.029 7.5E-07   35.8   5.1   66  128-194    13-79  (105)
 96 COG0272 Lig NAD-dependent DNA   95.5   0.099 2.5E-06   32.0   7.6   49  362-411   510-561 (667)
 97 cd05791 S1_CSL4 S1_CSL4: CSL4,  95.4     0.1 2.6E-06   31.8   7.6   70  135-207     3-89  (92)
 98 cd05693 S1_Rrp5_repeat_hs1_sc1  95.4     0.1 2.6E-06   31.8   7.6   66  137-202     2-94  (100)
 99 smart00322 KH K homology RNA-b  95.4   0.017 4.2E-07   37.7   3.4   41  305-345     2-42  (69)
100 TIGR03491 RecB family nuclease  95.3   0.042 1.1E-06   34.7   5.1   58  362-419   209-266 (457)
101 cd05686 S1_pNO40 S1_pNO40: pNO  95.2   0.072 1.8E-06   33.0   6.2   64  137-203     2-73  (73)
102 PRK02362 ski2-like helicase; P  95.0    0.34 8.6E-06   28.1  11.0  100  388-507   589-705 (736)
103 PRK07956 ligA NAD-dependent DN  94.9    0.14 3.5E-06   30.9   7.1   51  360-411   508-561 (668)
104 COG1097 RRP4 RNA-binding prote  94.9    0.12 3.1E-06   31.4   6.6   63  132-194    58-131 (239)
105 TIGR03591 polynuc_phos polyrib  94.8    0.18 4.6E-06   30.1   7.4   62  281-342   510-587 (684)
106 KOG1070 consensus               94.8    0.15 3.9E-06   30.6   6.9   91  136-226  1160-1261(1710)
107 PRK02362 ski2-like helicase; P  94.5   0.072 1.8E-06   33.0   4.8   49  362-412   654-702 (736)
108 cd05705 S1_Rrp5_repeat_hs14 S1  94.4    0.35   9E-06   27.9   8.0   59  137-195     2-70  (74)
109 PRK08609 hypothetical protein;  94.4    0.32 8.3E-06   28.2   7.8   33  311-343   243-281 (570)
110 COG2183 Tex Transcriptional ac  94.2    0.17 4.3E-06   30.3   6.1  162  229-411   333-527 (780)
111 cd05702 S1_Rrp5_repeat_hs11_sc  94.1    0.29 7.3E-06   28.6   7.1   55  139-193     1-64  (70)
112 cd02410 archeal_CPSF_KH The ar  94.0    0.19 4.9E-06   29.8   6.0  100  238-346    10-116 (145)
113 smart00483 POLXc DNA polymeras  93.9    0.15 3.7E-06   30.7   5.3   12    7-18      4-15  (334)
114 cd05704 S1_Rrp5_repeat_hs13 S1  93.9    0.31   8E-06   28.3   6.9   61  137-201     2-70  (72)
115 PRK09521 exosome complex RNA-b  93.8    0.15 3.9E-06   30.6   5.2   68  135-207    61-146 (187)
116 pfam10447 EXOSC1 Exosome compo  93.8    0.35 9.1E-06   27.9   7.1   53  136-188     2-71  (72)
117 cd00141 NT_POLXc Nucleotidyltr  93.8    0.28 7.2E-06   28.6   6.5   34  311-344   237-276 (307)
118 COG1855 ATPase (PilT family) [  93.7    0.35   9E-06   27.9   6.8  299   19-349   178-529 (604)
119 cd05695 S1_Rrp5_repeat_hs3 S1_  93.6    0.63 1.6E-05   26.1   8.3   61  139-201     1-66  (66)
120 PRK12704 phosphodiesterase; Pr  93.5    0.64 1.6E-05   26.0   8.9  150  284-470   126-289 (455)
121 PRK10811 rne ribonuclease E; R  93.4    0.24 6.1E-06   29.1   5.7  162  136-303    36-260 (1063)
122 PRK12766 50S ribosomal protein  93.2     0.1 2.6E-06   31.9   3.5   53  359-411     9-61  (238)
123 PTZ00035 Rad51; Provisional     93.0    0.26 6.7E-06   28.9   5.3   51  441-508    41-91  (350)
124 PRK12705 hypothetical protein;  93.0    0.63 1.6E-05   26.1   7.3  168  260-470   137-318 (485)
125 COG0272 Lig NAD-dependent DNA   93.0    0.77   2E-05   25.4   8.2   99  363-474   448-549 (667)
126 PRK13764 ATPase; Provisional    92.8    0.21 5.4E-06   29.5   4.7  150  186-348   344-526 (605)
127 pfam03118 RNA_pol_A_CTD Bacter  92.6    0.19 4.9E-06   29.9   4.2   55  358-412     5-59  (62)
128 KOG3409 consensus               92.6    0.46 1.2E-05   27.1   6.1   75  128-205    58-149 (193)
129 COG2251 Predicted nuclease (Re  92.6    0.15 3.8E-06   30.7   3.6   71  367-441   232-302 (474)
130 KOG2193 consensus               92.5    0.18 4.7E-06   30.0   4.0   40  303-342   408-447 (584)
131 TIGR03319 YmdA_YtgF conserved   92.4    0.92 2.3E-05   24.9   8.5  129  308-470   206-348 (514)
132 KOG3298 consensus               92.3    0.39   1E-05   27.6   5.5   63  133-195    76-155 (170)
133 COG2996 Predicted RNA-bindinin  92.2     0.7 1.8E-05   25.7   6.7  113   78-212    31-147 (287)
134 COG1185 Pnp Polyribonucleotide  92.2    0.95 2.4E-05   24.7   8.2   67  396-463   507-578 (692)
135 COG1530 CafA Ribonucleases G a  92.0    0.33 8.5E-06   28.1   4.8   64  136-199    35-111 (487)
136 cd02396 PCBP_like_KH K homolog  92.0    0.18 4.6E-06   30.1   3.4   39  307-345     1-39  (65)
137 TIGR02239 recomb_RAD51 DNA rep  91.8     1.1 2.7E-05   24.4   7.6   90  365-458     6-95  (317)
138 TIGR03491 RecB family nuclease  91.7    0.31   8E-06   28.3   4.4   31  436-466   208-238 (457)
139 TIGR03675 arCOG00543 arCOG0178  91.5    0.72 1.8E-05   25.6   6.1  161   37-215    73-274 (630)
140 KOG2190 consensus               91.4     1.2   3E-05   24.1   7.5  100  248-347   264-379 (485)
141 COG1096 Predicted RNA-binding   91.2    0.54 1.4E-05   26.6   5.2   57  134-190    60-133 (188)
142 cd03586 Pol_IV_kappa Pol_IV_ka  91.1     1.2 3.1E-05   23.9   7.5   36  437-472   174-209 (337)
143 PRK00558 uvrC excinuclease ABC  89.9    0.93 2.4E-05   24.8   5.4   50  362-412   556-605 (609)
144 pfam02889 Sec63 Sec63 Brl doma  89.4     1.1 2.7E-05   24.4   5.5   42  433-474   146-187 (309)
145 TIGR01009 rpsC_bact ribosomal   89.3     1.2 2.9E-05   24.1   5.6   59  283-341    40-107 (217)
146 PRK05182 DNA-directed RNA poly  89.2    0.66 1.7E-05   25.9   4.3   54  358-411   242-295 (306)
147 smart00322 KH K homology RNA-b  88.5    0.62 1.6E-05   26.1   3.8   40  236-281     4-43  (69)
148 cd05790 S1_Rrp40 S1_Rrp40: Rrp  88.0     1.7 4.4E-05   22.8   5.8   68  134-204     2-75  (86)
149 KOG4078 consensus               87.6    0.93 2.4E-05   24.8   4.2   75  116-194    64-138 (173)
150 pfam00013 KH_1 KH domain. KH m  87.3    0.67 1.7E-05   25.9   3.3   34  308-341     2-35  (57)
151 CHL00013 rpoA RNA polymerase a  87.3     1.2   3E-05   24.0   4.6   32   88-120    24-55  (333)
152 pfam00730 HhH-GPD HhH-GPD supe  87.2     2.3 5.8E-05   21.9   6.5   78  372-452    17-98  (144)
153 PRK07220 DNA topoisomerase I;   86.9     1.6 4.1E-05   23.1   5.0   39  435-473   686-724 (740)
154 COG0092 RpsC Ribosomal protein  86.7     1.2 2.9E-05   24.1   4.2   57  282-338    27-87  (233)
155 pfam00313 CSD 'Cold-shock' DNA  86.5     1.7 4.3E-05   22.9   5.0   54  142-198     1-60  (66)
156 PRK00468 hypothetical protein;  86.3     1.2 3.1E-05   24.0   4.2   49  282-330     3-54  (75)
157 cd00105 KH-I K homology RNA-bi  86.1    0.78   2E-05   25.4   3.1   39  308-346     2-40  (64)
158 smart00611 SEC63 Domain of unk  86.1     1.8 4.7E-05   22.6   5.0   41  434-474   150-190 (312)
159 cd02411 archeal_30S_S3_KH K ho  85.8     1.1 2.7E-05   24.4   3.7   46  284-329    16-61  (85)
160 TIGR01952 nusA_arch NusA famil  85.7    0.73 1.9E-05   25.6   2.8   96  247-343    40-139 (143)
161 COG1782 Predicted metal-depend  84.7       3 7.6E-05   21.1  10.6   37   30-67     73-110 (637)
162 PRK00106 hypothetical protein;  84.5       3 7.7E-05   21.0   8.8  151  283-470   205-369 (535)
163 pfam08292 RNA_pol_Rbc25 RNA po  84.0     2.8 7.1E-05   21.3   5.2   55  137-191     2-76  (120)
164 PRK02821 hypothetical protein;  84.0     2.1 5.3E-05   22.2   4.5   49  282-330     4-55  (77)
165 LOAD_cold consensus             83.9     3.2 8.2E-05   20.9   5.7   54  141-197     1-60  (67)
166 COG0122 AlkA 3-methyladenine D  83.8     2.8 7.1E-05   21.3   5.1   87  378-465   141-233 (285)
167 PRK07758 hypothetical protein;  83.8     1.9 4.9E-05   22.5   4.2   40  372-411    46-85  (95)
168 PRK13482 DNA integrity scannin  83.5     2.6 6.5E-05   21.6   4.8   55  358-413   285-339 (352)
169 TIGR00448 rpoE DNA-directed RN  83.3     2.8 7.1E-05   21.3   4.9   74  133-206    76-174 (184)
170 COG1948 MUS81 ERCC4-type nucle  83.3     2.4 6.2E-05   21.7   4.6   55  362-417   184-238 (254)
171 PRK10354 major cold shock prot  83.1     3.4 8.8E-05   20.6   5.6   56  140-198     3-64  (70)
172 TIGR00596 rad1 DNA repair prot  82.9     1.3 3.3E-05   23.7   3.1   44  431-474   875-920 (939)
173 KOG0950 consensus               82.9     2.9 7.3E-05   21.2   4.8   38  436-473   895-932 (1008)
174 PRK01064 hypothetical protein;  82.8     2.2 5.6E-05   22.1   4.2   48  282-329     3-53  (78)
175 PRK02794 DNA polymerase IV; Pr  82.5     3.2 8.1E-05   20.9   4.9   12   79-90     89-100 (417)
176 TIGR02062 RNase_B exoribonucle  81.9     1.6   4E-05   23.1   3.2  128  201-342   207-362 (664)
177 TIGR02027 rpoA DNA-directed RN  80.9       2 5.2E-05   22.3   3.5   31  443-473   268-298 (324)
178 pfam04994 TfoX_C TfoX C-termin  80.9     2.1 5.5E-05   22.1   3.6   35  437-471     1-35  (77)
179 PRK01216 DNA polymerase IV; Va  80.7     3.4 8.5E-05   20.7   4.6   48  364-413   182-229 (351)
180 PRK03103 DNA polymerase IV; Re  80.6     3.9   1E-04   20.2   4.9   34  367-400   189-222 (410)
181 PRK02406 DNA polymerase IV; Va  80.6     3.6 9.1E-05   20.5   4.7   49  364-415   184-232 (355)
182 KOG1676 consensus               80.6       2 5.2E-05   22.3   3.4  105  231-344   224-356 (600)
183 PRK03352 DNA polymerase IV; Va  80.3     4.3 0.00011   20.0   5.6   34  367-400   184-217 (345)
184 PTZ00084 40S ribosomal protein  79.9     3.6 9.1E-05   20.5   4.5   50  283-332    21-70  (220)
185 COG1107 Archaea-specific RecJ-  79.7     3.9  0.0001   20.2   4.6   58  137-194   121-179 (715)
186 cd04462 S1_RNAPII_Rpb7 S1_RNAP  79.4     4.3 0.00011   19.9   4.7   44  138-181     1-44  (88)
187 cd02414 jag_KH jag_K homology   79.2     2.8 7.1E-05   21.3   3.7   44  297-340    15-58  (77)
188 cd02393 PNPase_KH Polynucleoti  79.0     2.4 6.2E-05   21.7   3.4   35  308-342     4-38  (61)
189 PRK12278 50S ribosomal protein  78.4     2.2 5.6E-05   22.1   3.0   44  431-474   149-192 (216)
190 cd00424 Pol_Y Y-family of DNA   78.3     3.8 9.8E-05   20.3   4.2   38  436-473   174-211 (341)
191 COG1796 POL4 DNA polymerase IV  78.2     4.9 0.00013   19.5   5.6   70  394-467    54-126 (326)
192 cd02394 vigilin_like_KH K homo  78.0       2   5E-05   22.4   2.7   37  308-344     2-38  (62)
193 smart00478 ENDO3c endonuclease  77.6     5.1 0.00013   19.4   5.2   78  372-456    13-93  (149)
194 COG1098 VacB Predicted RNA bin  75.7     5.7 0.00015   19.0   5.6   57  136-192     3-66  (129)
195 PRK04191 rps3p 30S ribosomal p  75.3     5.8 0.00015   19.0   4.6   46  284-329    18-63  (225)
196 TIGR02238 recomb_DMC1 meiotic   75.1     5.9 0.00015   18.9   4.9  133  365-507     6-170 (314)
197 PRK09507 cspE cold shock prote  74.7       6 0.00015   18.8   5.5   55  141-198     3-63  (69)
198 KOG2916 consensus               74.5     6.1 0.00016   18.8   4.5  164  130-296     8-209 (304)
199 pfam11731 Cdd1 Pathogenicity l  74.5     3.4 8.6E-05   20.7   3.1   42  435-476    12-53  (92)
200 KOG1856 consensus               74.2     6.2 0.00016   18.8   4.8  149  109-290   542-718 (1299)
201 cd01700 Pol_V Pol V was discov  74.1     4.7 0.00012   19.6   3.7   37  365-401   180-216 (344)
202 COG3743 Uncharacterized conser  74.0     3.7 9.4E-05   20.4   3.2   41  433-473    65-105 (133)
203 PRK00024 radC DNA repair prote  73.9     5.6 0.00014   19.1   4.1   41  370-411    44-84  (224)
204 PRK10702 endonuclease III; Pro  73.8     6.3 0.00016   18.7   4.8   76  371-453    49-127 (211)
205 TIGR01259 comE comEA protein;   73.5       3 7.8E-05   21.0   2.7   58  385-454    64-121 (124)
206 KOG3013 consensus               73.5     1.7 4.2E-05   23.0   1.3   62  129-190    76-154 (301)
207 PRK01810 DNA polymerase IV; Va  72.8     4.6 0.00012   19.7   3.4   34  367-400   186-219 (410)
208 PRK03348 DNA polymerase IV; Pr  72.8     2.8 7.1E-05   21.3   2.3   45  367-413   186-230 (456)
209 PRK03858 DNA polymerase IV; Va  72.7     4.9 0.00013   19.5   3.6   32  367-398   180-211 (398)
210 pfam07650 KH_2 KH domain.       72.0     3.1   8E-05   20.9   2.4   31  308-338     2-32  (55)
211 pfam10391 DNA_pol_lambd_f Fing  71.7       4  0.0001   20.2   2.9   27  361-387     3-29  (52)
212 cd00056 ENDO3c endonuclease II  70.9     7.3 0.00019   18.2   5.9   82  372-457    21-105 (158)
213 TIGR00757 RNaseEG ribonuclease  70.3     2.5 6.5E-05   21.6   1.7   44  134-177    23-70  (464)
214 cd02412 30S_S3_KH K homology R  69.3     7.1 0.00018   18.3   3.8   46  284-329    39-84  (109)
215 PRK04203 rpl1P 50S ribosomal p  68.6       7 0.00018   18.4   3.6   41   22-62      3-46  (216)
216 cd03468 Pol_Y_like Pol_Y_like:  68.1     8.3 0.00021   17.8   4.6   52  360-414   167-218 (330)
217 COG1837 Predicted RNA-binding   67.0       7 0.00018   18.4   3.3   49  282-330     3-54  (76)
218 COG0557 VacB Exoribonuclease R  66.8     8.8 0.00022   17.6  11.0   85   88-192   102-190 (706)
219 KOG2534 consensus               66.0     9.1 0.00023   17.5   4.7   40    4-44     10-49  (353)
220 TIGR03665 arCOG04150 arCOG0415  64.9     4.8 0.00012   19.6   2.2   23  319-341   102-124 (172)
221 COG0322 UvrC Nuclease subunit   64.3     9.7 0.00025   17.3   5.0   99  182-286   291-428 (581)
222 COG0202 RpoA DNA-directed RNA   63.9     2.7 6.9E-05   21.4   0.8  107  312-418   185-302 (317)
223 PRK12311 rpsB 30S ribosomal pr  63.4     7.9  0.0002   18.0   3.1   46  429-474   263-308 (332)
224 COG0177 Nth Predicted EndoIII-  62.4      11 0.00027   17.1   5.4   68  378-451    55-125 (211)
225 PRK03609 umuC DNA polymerase V  62.1     7.9  0.0002   18.0   2.9   38  364-401   183-220 (422)
226 COG0295 Cdd Cytidine deaminase  61.6     7.1 0.00018   18.4   2.5   46  229-282    65-111 (134)
227 KOG2191 consensus               61.4      11 0.00028   17.0   7.2   36  306-341   244-279 (402)
228 cd01701 Pol_zeta Pol_zeta, a m  60.7      11 0.00029   16.9   4.4  159  229-414    94-277 (405)
229 smart00357 CSP Cold shock prot  58.0      12 0.00032   16.6   5.5   54  143-197     1-57  (64)
230 PRK10917 ATP-dependent DNA hel  57.8      11 0.00028   16.9   3.0   65   94-158   306-387 (677)
231 KOG3127 consensus               57.2     1.4 3.7E-05   23.4  -1.6   48  229-283    73-122 (230)
232 KOG1918 consensus               57.1     6.3 0.00016   18.7   1.7   84  379-463   108-198 (254)
233 pfam00633 HHH Helix-hairpin-he  57.1     6.1 0.00016   18.8   1.6   28  384-411     2-29  (30)
234 PRK00310 rpsC 30S ribosomal pr  56.8      13 0.00033   16.4   4.2   46  284-329    40-85  (233)
235 TIGR02851 spore_V_T stage V sp  56.6     9.3 0.00024   17.5   2.5   48  143-205     3-50  (184)
236 PRK01250 inorganic pyrophospha  56.6     6.2 0.00016   18.8   1.5   75  216-299    12-93  (176)
237 KOG2841 consensus               56.3      12 0.00031   16.6   3.0   45  366-411   201-245 (254)
238 COG1623 Predicted nucleic-acid  56.1      13 0.00034   16.3   3.3  138  248-411   205-343 (349)
239 COG1555 ComEA DNA uptake prote  55.1      14 0.00035   16.2   4.8   60  383-454    87-146 (149)
240 KOG1433 consensus               52.7     7.2 0.00018   18.3   1.4   58  360-417    24-81  (326)
241 cd05696 S1_Rrp5_repeat_hs4 S1_  51.4      16  0.0004   15.8   6.7   56  139-194     1-65  (71)
242 TIGR01008 rpsC_E_A ribosomal p  50.8      16 0.00041   15.8   5.3   56  207-271    14-69  (204)
243 PRK09890 cold shock protein Cs  50.5      16 0.00041   15.7   6.5   55  140-197     3-63  (70)
244 COG1847 Jag Predicted RNA-bind  49.3     9.2 0.00023   17.5   1.5   73  286-360    73-154 (208)
245 COG2106 Uncharacterized conser  49.0      17 0.00043   15.6   4.4   48  135-189   102-150 (272)
246 PRK10880 adenine DNA glycosyla  48.2      17 0.00044   15.5   6.7   68  379-452    57-126 (350)
247 TIGR01083 nth endonuclease III  46.6      18 0.00047   15.3   4.7   67  379-451    54-123 (192)
248 cd01703 Pol_iota Pol iota is m  45.7      19 0.00048   15.2   4.0   93  318-417   172-266 (394)
249 COG0335 RplS Ribosomal protein  45.5      19 0.00048   15.2   3.8   15  176-190    21-35  (115)
250 KOG1004 consensus               45.3      19 0.00049   15.2   5.6   84  130-213    57-163 (230)
251 KOG0187 consensus               44.7      16 0.00041   15.7   2.1   55  337-391    67-121 (134)
252 PRK00296 minE cell division to  44.0      20 0.00051   15.0   5.1   55   16-70     26-82  (85)
253 cd00501 Peptidase_C15 Pyroglut  42.4     8.8 0.00022   17.6   0.5   56  262-318   117-175 (194)
254 pfam00719 Pyrophosphatase Inor  41.7      16 0.00041   15.7   1.8   64  233-300     8-77  (156)
255 pfam02738 Ald_Xan_dh_C2 Molybd  41.7      22 0.00055   14.8   3.7   15   49-64     52-66  (543)
256 KOG4384 consensus               41.7      22 0.00055   14.8   5.5   95  321-417   173-275 (361)
257 pfam05557 MAD Mitotic checkpoi  41.6      13 0.00034   16.3   1.3   17  331-347   640-656 (722)
258 TIGR02544 III_secr_YscJ type I  41.5      14 0.00036   16.2   1.4   20  130-149   119-138 (203)
259 CHL00162 thiG thiamin biosynth  41.3      20 0.00052   15.0   2.2   11  139-149    41-51  (267)
260 TIGR00426 TIGR00426 competence  40.9      22 0.00056   14.7   3.6   54  386-451    10-64  (70)
261 cd02395 SF1_like-KH Splicing f  40.7      22 0.00057   14.7   3.5   33  317-349    17-49  (120)
262 TIGR00118 acolac_lg acetolacta  40.4      14 0.00035   16.2   1.2   63   54-140   293-373 (593)
263 KOG2279 consensus               39.2      15 0.00039   15.9   1.3   36  308-343   298-333 (608)
264 KOG3297 consensus               39.0      24  0.0006   14.5   5.9  123   20-190    11-134 (202)
265 KOG3853 consensus               38.9      24  0.0006   14.5   2.4   71  194-275   228-304 (350)
266 KOG2767 consensus               37.7      25 0.00063   14.4   3.6   71  442-523   327-397 (400)
267 pfam01470 Peptidase_C15 Pyrogl  37.1      20  0.0005   15.1   1.6   67  249-316    97-173 (203)
268 PRK13913 3-methyladenine DNA g  35.9      26 0.00067   14.2   7.6   68  382-451    67-137 (218)
269 PTZ00225 60S ribosomal protein  35.8      26 0.00067   14.2   2.9   33   21-53      3-35  (214)
270 pfam00833 Ribosomal_S17e Ribos  35.7      20  0.0005   15.1   1.4   46  339-384    69-114 (122)
271 TIGR00643 recG ATP-dependent D  35.2      23 0.00059   14.6   1.7   33  117-149   569-602 (721)
272 PRK13910 DNA glycosylase MutY;  34.2      28 0.00071   14.0   6.8   16  197-212   199-214 (290)
273 PRK00378 nucleoid-associated p  33.5      28 0.00073   13.9   3.3  156  259-423    60-236 (334)
274 TIGR01077 L13_A_E ribosomal pr  33.1      26 0.00067   14.2   1.7   15  105-119     9-23  (144)
275 cd01702 Pol_eta Pol eta is mem  33.0      29 0.00074   13.8   3.6   48  367-414   189-237 (358)
276 KOG0438 consensus               32.9      29 0.00074   13.8   3.7   34  226-259   105-139 (312)
277 pfam11694 DUF3290 Protein of u  32.8      22 0.00057   14.6   1.3   64    7-72     79-142 (149)
278 PRK13453 F0F1 ATP synthase sub  32.8      29 0.00075   13.8   4.1   16  406-421   112-127 (173)
279 COG0389 DinP Nucleotidyltransf  32.5      29 0.00075   13.8   3.0   39  436-474   177-215 (354)
280 TIGR02660 nifV_homocitr homoci  31.4      30 0.00076   13.8   1.8   63  371-459    27-89  (369)
281 PRK13763 putative RNA-processi  31.2      31 0.00079   13.6   3.1   38  308-345     6-43  (185)
282 PRK00642 inorganic pyrophospha  30.9      29 0.00074   13.8   1.6   22  397-418   184-206 (212)
283 KOG2093 consensus               30.8      31  0.0008   13.6   8.5  137  319-473   421-587 (1016)
284 PRK05578 cytidine deaminase; V  30.4      32 0.00081   13.5   4.0   30  245-282    80-109 (132)
285 COG4776 Rnb Exoribonuclease II  30.3      32 0.00081   13.5   4.0   90  199-305   201-293 (645)
286 PRK10929 hypothetical protein;  30.3      32 0.00082   13.5   6.7   36    4-39     23-58  (1109)
287 cd05701 S1_Rrp5_repeat_hs10 S1  30.0      32 0.00082   13.5   4.2   56  143-198     5-68  (69)
288 PRK13193 pyrrolidone-carboxyla  29.8      21 0.00053   14.9   0.7  116  179-313    33-166 (201)
289 PRK13194 pyrrolidone-carboxyla  29.6      20 0.00051   15.0   0.6   52  261-313   116-168 (204)
290 COG2003 RadC DNA repair protei  29.0      33 0.00085   13.4   4.5   40  379-418    52-94  (224)
291 PRK11281 potassium efflux prot  28.8      34 0.00086   13.3   6.7   33    5-37     35-69  (1107)
292 cd00412 pyrophosphatase Inorga  28.5      34 0.00087   13.3   2.2   67  233-303    11-85  (155)
293 TIGR02701 shell_carb_anhy carb  28.3      34 0.00086   13.3   1.6  112   49-192   263-389 (463)
294 PRK09970 xanthine dehydrogenas  28.2      34 0.00088   13.3   3.8   27  231-260   338-365 (762)
295 PRK10737 FKBP-type peptidyl-pr  27.8      35 0.00089   13.2   2.2   70   89-160    50-123 (196)
296 cd01296 Imidazolone-5PH Imidaz  27.5      35  0.0009   13.2   3.0   13  206-218   159-171 (371)
297 COG1529 CoxL Aerobic-type carb  27.4      36 0.00091   13.2   3.7   17  196-212   197-213 (731)
298 TIGR03194 4hydrxCoA_A 4-hydrox  27.2      36 0.00091   13.2   3.7   28  232-262   323-351 (746)
299 cd02413 40S_S3_KH K homology R  27.2      36 0.00092   13.2   5.5   54  208-270     7-60  (81)
300 pfam09953 DUF2187 Uncharacteri  27.1      36 0.00092   13.1   2.2   18  142-159    16-33  (57)
301 TIGR02704 carboxysome_B carbox  26.8      36 0.00093   13.1   2.0   32  226-257    10-47  (80)
302 KOG0196 consensus               25.8      38 0.00097   13.0   1.9   25  449-473   940-964 (996)
303 KOG1921 consensus               25.8      38 0.00097   13.0   6.5   75  371-453    98-177 (286)
304 KOG3873 consensus               24.5      35 0.00089   13.2   1.1   32  252-283   225-258 (422)
305 PRK13680 hypothetical protein;  24.3      28 0.00073   13.9   0.6   45  239-286    23-69  (121)
306 pfam03459 TOBE TOBE domain. Th  24.3      40   0.001   12.8   5.4   48  139-189     4-57  (61)
307 PRK09618 flgD flagellar basal   24.2      40   0.001   12.8   3.2   31  136-166   102-135 (146)
308 TIGR02592 cas_Cas5h CRISPR-ass  24.2      24 0.00062   14.4   0.3   64  327-390   114-181 (268)
309 pfam08414 NADPH_Ox Respiratory  24.1      19  0.0005   15.1  -0.2   16  450-465    34-49  (96)
310 TIGR01522 ATPase-IIA2_Ca calci  23.9      37 0.00095   13.0   1.2   34  155-189   121-156 (856)
311 TIGR00350 lytR_cpsA_psr cell e  23.6      41  0.0011   12.7   2.5   21  103-125   160-180 (182)
312 PRK13197 pyrrolidone-carboxyla  23.6      27 0.00068   14.1   0.4  103  204-314    49-170 (215)
313 PRK10676 DNA-binding transcrip  23.5      42  0.0011   12.7   5.1   97  141-245   130-236 (262)
314 TIGR03196 pucD xanthine dehydr  23.3      42  0.0011   12.7   3.7   22  161-182   258-279 (768)
315 pfam03293 Pox_RNA_pol Poxvirus  23.1      42  0.0011   12.6   6.0   64  137-200    80-155 (160)
316 pfam07431 DUF1512 Protein of u  23.0      42  0.0011   12.6   1.3   63  239-326   220-282 (356)
317 PRK07352 F0F1 ATP synthase sub  23.0      43  0.0011   12.6   4.0   12  407-418   114-125 (174)
318 COG1094 Predicted RNA-binding   22.8      43  0.0011   12.6   4.2   40  307-346     9-48  (194)
319 TIGR02885 spore_sigF RNA polym  22.7      43  0.0011   12.6   1.8   23   19-41     33-55  (231)
320 CHL00127 rpl11 ribosomal prote  21.5      42  0.0011   12.6   1.1   35  238-272    10-45  (140)
321 pfam01330 RuvA_N RuvA N termin  21.3      46  0.0012   12.4   6.3   50  141-193     4-55  (61)
322 cd04458 CSP_CDS Cold-Shock Pro  21.1      46  0.0012   12.4   6.2   53  142-197     1-59  (65)
323 pfam09883 DUF2110 Uncharacteri  21.1      46  0.0012   12.4   5.2   36  138-173    75-110 (226)
324 pfam00029 Connexin Connexin.    21.1      25 0.00063   14.4  -0.2   17  278-294    42-58  (107)
325 COG3264 Small-conductance mech  20.9      47  0.0012   12.3   7.1   85  136-235   661-753 (835)
326 COG1255 Uncharacterized protei  20.9      47  0.0012   12.3   1.3   66   10-80      2-68  (129)
327 PRK13460 F0F1 ATP synthase sub  20.9      47  0.0012   12.3   3.8   15  406-420   110-124 (173)
328 TIGR02888 spore_YlmC_YmxH spor  20.7      47  0.0012   12.3   1.9   46   41-90     17-70  (76)
329 TIGR01578 MiaB-like-B MiaB-lik  20.5      47  0.0012   12.3   2.9  161   70-246   309-479 (487)
330 TIGR01204 bioW 6-carboxyhexano  20.5      33 0.00085   13.4   0.3   38   19-57     11-49  (238)
331 PRK00591 prfA peptide chain re  20.3      45  0.0011   12.5   1.0   25  299-330   217-241 (360)
332 COG1460 Uncharacterized protei  20.2      48  0.0012   12.2   5.7   87  393-502    19-105 (114)
333 PRK00140 rplK 50S ribosomal pr  20.1      47  0.0012   12.3   1.0   63  238-316    10-75  (142)

No 1  
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=100.00  E-value=0  Score=1079.23  Aligned_cols=427  Identities=55%  Similarity=0.923  Sum_probs=418.2

Q ss_pred             CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHH
Q ss_conf             88999999999986239999999999999999999613687453599974998839999998851767787532348999
Q gi|254780788|r    5 NRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVA   84 (526)
Q Consensus         5 ~~~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A   84 (526)
                      ++.+++.+++++|+||||+++.+++|+++||.+||||+||++.+++|.||++||++++|+.|.||+++++|..||+|++|
T Consensus         2 m~~e~l~~i~~la~EK~I~~e~v~~aie~Al~~A~kK~~~~~~~i~V~Id~~tG~i~v~~~~~VVe~v~d~~~eI~L~~A   81 (428)
T PRK09202          2 MSKELLLAIEAVAREKGIDREVIIEALEEALATAYKKKYGPEANVRVEIDRKTGDIEVFRRWEVVEEVEDPAKEISLEDA   81 (428)
T ss_pred             CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEEEECCCCCCCCCEEEHHHH
T ss_conf             74999999999998759699999999999999998442499676799998889819999999853787787647459999


Q ss_pred             HHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEE
Q ss_conf             86288986473799850845620799999999999999999988779999852083899999840576389995793587
Q gi|254780788|r   85 RDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGV  164 (526)
Q Consensus        85 ~~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~  164 (526)
                      ++++|++++||++.++++|.+|||+|||+|||+|.||+|++||+.+|++|++|+|+||+|+|+|+++++++||||++||+
T Consensus        82 ~~~~p~~~iGd~i~~~i~~~~fgRiaaq~AkQvi~QkireaEr~~i~~ef~~r~Geiv~G~V~r~~~~~i~Vdlg~~ea~  161 (428)
T PRK09202         82 RKIDPDAEVGDYIEEEIEPIDFGRIAAQAAKQVIVQKIREAERERVYEEYKDRVGEIITGTVKRVERGNIIVDLGRAEAI  161 (428)
T ss_pred             HHHCCCCCCCCEEEEECCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCEEEEECCEEEE
T ss_conf             86589875186688865834258899999999999999999999999999873298899999997278389997882575


Q ss_pred             EEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEEC
Q ss_conf             44787488751152766999997611358702898715988999999997667775580878566316775034999940
Q gi|254780788|r  165 IRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSS  244 (526)
Q Consensus       165 Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~  244 (526)
                      ||+++|||||+|++|||+||||.+|+.++|||||+||||||+||++||++|||||++|+|+||+|||+||+||||||+|+
T Consensus       162 Lp~~e~ip~E~~~~Gdrik~~i~~V~~~~kg~qi~lSRt~p~~v~~Lfe~EVPEI~dG~IeIk~iaRepG~RtKiAV~s~  241 (428)
T PRK09202        162 LPRDEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIAEGLIEIKAIARDPGSRAKIAVKSN  241 (428)
T ss_pred             CCHHHCCCCCCCCCCCEEEEEEEEHHCCCCCCEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCCEEEEEECC
T ss_conf             64787699866799987999872021258985799954878999999986456853882999986136787237999725


Q ss_pred             CCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCC
Q ss_conf             89988127655488621788998627782679955987899999762866542489875678799998534221102544
Q gi|254780788|r  245 DSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRR  324 (526)
Q Consensus       245 d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~  324 (526)
                      |++||||||||||||||||+|++||+|||||||+||+||++||+|||+||+|.+|++|++++++.|+||++||||||||+
T Consensus       242 d~~iDpVGAcVG~rGsRI~~I~~EL~gEkIDIi~~s~d~~~fi~nAlsPA~v~~V~ide~~~~~~VvV~d~qlSlAIGk~  321 (428)
T PRK09202        242 DKRIDPVGACVGMRGSRIQAISNELNGEKIDIILWSDDPAQFIINALSPAEVSSIVVDEDKHSMDVVVPDDQLSLAIGKN  321 (428)
T ss_pred             CCCCCCCEEEECCCCCCHHHHHHHHCCCEEEEEECCCCHHHHHHHHCCCCCCEEEEECCCCCEEEEEECCCCHHHHHCCC
T ss_conf             99978513777788642999998746776899967888899999817942121899727788899998865224775778


Q ss_pred             HHHHHHHHHHHCCEEEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHH
Q ss_conf             27899999861674578552200110100122100011122588846788887732111477750588887765305889
Q gi|254780788|r  325 GQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEE  404 (526)
Q Consensus       325 GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee  404 (526)
                      ||||||||+||||+|||+|++++.++++.++....+.|++.+++++.+++.                             
T Consensus       322 GqNvrLAs~Ltgw~IdI~s~~~~~e~~~~e~~~~~~~f~~~~~~~e~~~~~-----------------------------  372 (428)
T PRK09202        322 GQNVRLASKLTGWKIDIMTEEEASEKQQAEFARLIDLFMEALDVDEDIAQL-----------------------------  372 (428)
T ss_pred             CEEHHHHHHHHCCEEEEEEHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH-----------------------------
T ss_conf             685999999779869995589999987778888999877752622888887-----------------------------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCC
Q ss_conf             99999999999999999998987754284356640779998999999987984788965326775212312344432112
Q gi|254780788|r  405 TAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKF  484 (526)
Q Consensus       405 ~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~  484 (526)
                                                   .++|.+++|++++++..|.++|+.|++|||+++.|||.++.          
T Consensus       373 -----------------------------~~~l~~~~~~~~~~~~~l~~~g~~~~edl~~~~~del~~~~----------  413 (428)
T PRK09202        373 -----------------------------ADDLLNLEGLDPELAFKLAEKGVKTLEDLAELAVDELIDIE----------  413 (428)
T ss_pred             -----------------------------HHHHHHCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHCC----------
T ss_conf             -----------------------------77786456999999999998699879999657988896377----------


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHC
Q ss_conf             4533435889999999999841
Q gi|254780788|r  485 DGFLSSLGTPKDQVESMIIHAR  506 (526)
Q Consensus       485 ~gil~~~~l~~~~A~~lIM~AR  506 (526)
                             ++++++|+.|||.||
T Consensus       414 -------~~~~e~a~~li~~ar  428 (428)
T PRK09202        414 -------GLDEEEAGELIMAAR  428 (428)
T ss_pred             -------CCCHHHHHHHHHHCC
T ss_conf             -------989999999998419


No 2  
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=100.00  E-value=0  Score=997.00  Aligned_cols=406  Identities=34%  Similarity=0.530  Sum_probs=382.1

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHC-----------CCCC--CCEEEEECCCCCEEEEEEEEEEECCC
Q ss_conf             8999999999986239999999999999999999613-----------6874--53599974998839999998851767
Q gi|254780788|r    6 RLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSL-----------YGTM--SDIRVEINPETGDISLFRLLEVVEEV   72 (526)
Q Consensus         6 ~~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~-----------~~~~--~~i~V~iD~~tG~i~i~~~~~VVedv   72 (526)
                      --.|..++++||+||||+++.+++|||+||++||||.           |+.+  .+++|.||++||+|.+|+.|.||+++
T Consensus         6 ~~~L~~vIe~vs~EKgI~ke~I~eAlE~AL~sAykK~~~~~~~~~~~~~~e~~~~n~~V~ID~~tG~~~v~~~k~VVeev   85 (457)
T PRK12329          6 LPGLNNLIEDISEEKNLPKQAVEAALREALLKGYERYRRTLYLGSEDPFDEDYFSNFDVELDLEEEGFRVLATKIIVEEV   85 (457)
T ss_pred             CHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEEEECCC
T ss_conf             36599999999860298989999999999999986410443333223345455450799998889968999999985267


Q ss_pred             CCCCCEECHHHHHHHCCCCCCCCEEEEECCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC
Q ss_conf             7875323489998628898647379985084--56207999999999999999999887799998520838999998405
Q gi|254780788|r   73 ENYTCQISLKVARDRDPSIDIGGVVSDPLPP--MDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVE  150 (526)
Q Consensus        73 ed~~~eI~l~~A~~~~~~~~iGD~i~~~i~~--~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e  150 (526)
                      +|+..||+|++|++++|++++||.+..+++|  .+|||||||+|||+|.||||++||+++|++|++|+|+||+|+|+|++
T Consensus        86 ed~~~EIsL~eA~ei~p~~eiGD~i~~ev~pe~~dFGRIAAqtAKQvI~QKIREaER~~I~eef~~k~GeIVtG~V~Rve  165 (457)
T PRK12329         86 ENEDHQIALAEVQQVADDAQLGDTVVLDVTPEKEDFGRMAAIQTKQVLAQKLRDQQRKMIQEEFADLEDPVLTARVLRFE  165 (457)
T ss_pred             CCCCCCCCHHHHHHHCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEE
T ss_conf             68765414999986588885698799953865246367999999999999999999999999998555967999999981


Q ss_pred             CCEEEEEECC------CEEEEEHHHCCCCCCCCCCCEEEEEEEEECCC-CCEEEEEEECCCHHHHHHHHHHHHHHHHCCE
Q ss_conf             7638999579------35874478748875115276699999761135-8702898715988999999997667775580
Q gi|254780788|r  151 YGNVIVDLGN------SDGVIRRDETISRENLRPGDRVKSYIYDVRRE-QRGPQVLLSRTHPQFMVKLFHMEVPEIYNGI  223 (526)
Q Consensus       151 ~~~iiVdlg~------~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~-~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~  223 (526)
                      +++++|++|+      +||+||+++|||+|+|++|||+||||++|+.+ .|||||+||||||+||++||++|||||++|+
T Consensus       166 ~~~viv~l~~~lG~~~~EAiLP~~EqIP~E~yr~Gdrira~i~~V~~~~~kGpqIiLSRt~p~fv~kLFe~EVPEI~dG~  245 (457)
T PRK12329        166 RQSVIMAVSSGFGRPEVEAELPKREQLPNDNYRANATFKVFLKEVSEGPRRGPQLFVSRANAGLVVYLFENEVPEIEEGV  245 (457)
T ss_pred             CCCEEEEECCCCCCCCEEEEECHHHCCCCCCCCCCCEEEEEEEEEECCCCCCCEEEEECCCHHHHHHHHHHHCHHHHCCC
T ss_conf             69779996477776423697278886999878999989999999764678885699954877999999986455863894


Q ss_pred             EEEEEEECCC-------CCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCC
Q ss_conf             8785663167-------750349999408998812765548862178899862778267995598789999976286654
Q gi|254780788|r  224 VQVKAVSRDP-------GSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIV  296 (526)
Q Consensus       224 ieIk~iaR~p-------G~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v  296 (526)
                      |+||+|||+|       |+||||||+|+|++||||||||||||+|||+|++||+|||||||+||+||++||+|||+||+|
T Consensus       246 VeIk~iARep~~~~r~~G~RtKIAV~S~d~~iDPVGaCVG~rG~RIq~I~~EL~gEkIDii~ws~d~~~~i~nALsPA~v  325 (457)
T PRK12329        246 VRIVAVAREANPPSRAVGPRTKIAVDTLERDVDPVGACIGARGSRIQQVVNELRGEKIDVIRWSPDPATYIANSLSPARV  325 (457)
T ss_pred             EEEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEEECCCCHHHHHHHHCCCCCC
T ss_conf             89999984488777788650389998069997731478889974299999885796389997578789999984396535


Q ss_pred             CEE-EECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHHHHH-------CCCCCCCCCCCCCCCC
Q ss_conf             248-98756787999985342211025442789999986167457855220011010-------0122100011122588
Q gi|254780788|r  297 TKV-VLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQ-------KDFNERTQFFMQAINV  368 (526)
Q Consensus       297 ~~v-~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~~~~~-------~e~~~~~~~f~e~LdV  368 (526)
                      .+| ++|++++++.|+||++||||||||+||||||||+||||+|||+|++++.+...       .+..+..+.|.+.++.
T Consensus       326 ~~v~~~d~~~~~~~V~V~~dqLslAIGk~GqNvrLAa~Ltgw~IdIks~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~  405 (457)
T PRK12329        326 DEVRLVDPEGQHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDSAEYDQEAEDAQVAELISQREEEEALQREAEL  405 (457)
T ss_pred             CEEEEECCCCCEEEEEECCCCCHHHHCCCCCHHHHHHHHHCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             17999858888799998854103762798757999999779878856689988877888765667888778888776533


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             8467888877321114777505888877653058899999999
Q gi|254780788|r  369 DEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG  411 (526)
Q Consensus       369 DE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~  411 (526)
                      ++..++.|+.+||+++++++|++.+++..++|||++...-...
T Consensus       406 ~~~~~~~~~~e~~~~~~e~~~~~~~e~~~~~~~de~~~~~~~~  448 (457)
T PRK12329        406 RLEAEQAERAEEDARLRELYPLPEDEEEEEEEEDEDELEDEDD  448 (457)
T ss_pred             HHHHHHHHHHCCCCCCHHCCCCCHHHHHHHCCCCCCCCCCCCC
T ss_conf             1568988875453320011157837766301444310013320


No 3  
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=100.00  E-value=0  Score=977.30  Aligned_cols=351  Identities=43%  Similarity=0.735  Sum_probs=344.6

Q ss_pred             CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHH
Q ss_conf             88999999999986239999999999999999999613687453599974998839999998851767787532348999
Q gi|254780788|r    5 NRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVA   84 (526)
Q Consensus         5 ~~~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A   84 (526)
                      ++.|||.+++++|+||||+++.+++|+|+||.+||+|+||++.+++|.||++||++++|+.|.||++++|+..||+|++|
T Consensus         1 M~kell~al~~la~EK~I~~e~v~~aie~Al~~A~kK~~~~~~~i~V~iD~~tG~i~v~~~~~Vveev~d~~~eI~L~eA   80 (353)
T PRK12327          1 MSKEFLEALRALEEEKGISKDVLIEAIEAALLSAYKKNYGQAQNVRVEFDEKTGEVKVYAQKEVVDEVFDSRLEISLEDA   80 (353)
T ss_pred             CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEEEECCCCCCCCCEEEHHHH
T ss_conf             97899999999998749799999999999999998542399776799997899869999999836887687547777665


Q ss_pred             HHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEE
Q ss_conf             86288986473799850845620799999999999999999988779999852083899999840576389995793587
Q gi|254780788|r   85 RDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGV  164 (526)
Q Consensus        85 ~~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~  164 (526)
                      ++++|++++||++.++++|.+|||+|||+|||+|.||||++||+++|++|++|+|+||+|+|+|+++++++||||++||+
T Consensus        81 k~~~~~~~vGD~i~~~i~~~~fgRiAaq~AKQvi~QkireaEr~~i~~ey~~r~GeiV~G~V~r~~~~~~~Vdlg~~ea~  160 (353)
T PRK12327         81 LAINPAYELGDVIEIEVTPKDFGRIAAQTAKQVIMQRLREAEREVIYNEFKEREGDIVTGTVQRDDNRFVYVNLGKIEAV  160 (353)
T ss_pred             HHCCCCCCCCCEEEEECCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCEEEEECCEEEE
T ss_conf             52477651386589964835459899999999999999999999999999874396699999997588589997882464


Q ss_pred             EEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEEC
Q ss_conf             44787488751152766999997611358702898715988999999997667775580878566316775034999940
Q gi|254780788|r  165 IRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSS  244 (526)
Q Consensus       165 Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~  244 (526)
                      ||+++|||||+|++|||+||||.+|+.++|||||+||||||+||++||++|||||++|+|+||+|||+||+||||||+|+
T Consensus       161 LP~~eqip~E~~~~Gdrika~i~~V~~~~kgp~I~lSRt~p~~v~~Lfe~EVPEI~dG~VeIk~iaRepG~RtKvAV~s~  240 (353)
T PRK12327        161 LPPAEQIPGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTHPGLVKRLFELEVPEIYDGTVEIVSIAREAGDRTKIAVRSN  240 (353)
T ss_pred             CCHHHCCCCCCCCCCCEEEEEEEEEEECCCCCEEEEECCCHHHHHHHHHHHCHHHHCCEEEEEEEECCCCCCEEEEEEEC
T ss_conf             68798699877799997999999999759974799964988999999986366863882999996016787148999925


Q ss_pred             CCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEE-CCCCCEEEEEECCCCCCCCCCC
Q ss_conf             899881276554886217889986277826799559878999997628665424898-7567879999853422110254
Q gi|254780788|r  245 DSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVL-DEDVGRIEVIVPKEQLSLAIGR  323 (526)
Q Consensus       245 d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~-de~~~~~~v~v~~~qls~AIGk  323 (526)
                      |++||||||||||||+|||+|++||+|||||||+||+||++||+|||+||+|.+|.+ |++++++.|+||++||||||||
T Consensus       241 d~~iDpvGAcVG~~G~RI~~I~~EL~gEkIDii~~s~d~~~fi~nALsPA~v~~V~i~de~~k~~~ViV~~~qlslAIGk  320 (353)
T PRK12327        241 NPNVDAIGACVGPKGQRVQNIVNELKGEKIDIIDWSEDPAEFIANALSPAKVVSVEVDDEEEKAARVVVPDYQLSLAIGK  320 (353)
T ss_pred             CCCCCCCEEEECCCCCHHHHHHHHHCCCEEEEEECCCCHHHHHHHHCCCCCEEEEEEECCCCCEEEEEECCHHHHHHHCC
T ss_conf             99988405888799725999998747777889967898899999737976103899975878669999881041576279


Q ss_pred             CHHHHHHHHHHHCCEEEEEECCCHHHHHHCCC
Q ss_conf             42789999986167457855220011010012
Q gi|254780788|r  324 RGQNVRLASQLTGWTIDIITEEEDSINRQKDF  355 (526)
Q Consensus       324 ~GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~  355 (526)
                      +||||||||+||||+|||+|++++.++..++.
T Consensus       321 ~GqNvrLAs~Ltgw~IdI~s~~~~~e~~~e~~  352 (353)
T PRK12327        321 EGQNARLAAKLTGWKIDIKSESEAEELGIEEE  352 (353)
T ss_pred             CCCHHHHHHHHHCCEEEEEEHHHHHHHCCHHC
T ss_conf             97749999997799799856889767364101


No 4  
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=100.00  E-value=0  Score=975.52  Aligned_cols=349  Identities=33%  Similarity=0.548  Sum_probs=341.1

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECC-----CCCCCCEECH
Q ss_conf             99999999998623999999999999999999961368745359997499883999999885176-----7787532348
Q gi|254780788|r    7 LELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEE-----VENYTCQISL   81 (526)
Q Consensus         7 ~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVed-----ved~~~eI~l   81 (526)
                      .|||.+++++|+||||+++.+++|+++||.+||||+||++.+++|.||++||++.+|+.|.||++     ++++..+|+|
T Consensus         2 ~Ell~~i~~la~EKgI~~e~i~~aie~Al~~A~kK~~g~~~~i~V~id~~tG~i~i~~~~~VVed~de~~~~d~~~eIsL   81 (375)
T PRK12328          2 EKISDIIESIAYEKGLPKEMVSEAVKEALINTAKRELGPLYEYEVVIDPKNKTLKLYQKIEVVADDDERLINDPEKFISL   81 (375)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEEEEECCCCCCCCCCCCCEECH
T ss_conf             58999999999775969999999999999999734049835679999889985999999999768864454685443029


Q ss_pred             HHHHHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCC-CEEEEEECC
Q ss_conf             9998628898647379985084562079999999999999999998877999985208389999984057-638999579
Q gi|254780788|r   82 KVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEY-GNVIVDLGN  160 (526)
Q Consensus        82 ~~A~~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~-~~iiVdlg~  160 (526)
                      ++|++++|++++||++.++++|.+|||+|||+|||+|.||+|++||+++|++|++|+|+||+|+|+|+++ ++++||||+
T Consensus        82 ~eA~~~~~~~~iGd~i~~~i~~~~FgRiAaq~AKQvi~QkireaEr~~i~~efk~r~GeiV~G~V~r~~~~~~~~vdlg~  161 (375)
T PRK12328         82 SKAKEMDPDVEIGDELSYELSLENMGRTAANTLFKELEYHIQRLLEDSIFEKYKEKVGSVVFGTVVRVDNEENTFIEIDE  161 (375)
T ss_pred             HHHHHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCCEEEECCC
T ss_conf             99987489984178899842844541899999999999999999999999999864294899999999658848997398


Q ss_pred             CEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCC-EEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEE
Q ss_conf             3587447874887511527669999976113587-028987159889999999976677755808785663167750349
Q gi|254780788|r  161 SDGVIRRDETISRENLRPGDRVKSYIYDVRREQR-GPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKL  239 (526)
Q Consensus       161 ~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~r-gpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKI  239 (526)
                      +||+||+++|||+|+|++||||||||.+|+.+++ ||||+||||||+||++||++|||||+||+|+||+|||+||+||||
T Consensus       162 ~ea~Lp~~eqip~E~y~~Gdrik~~i~~V~~~~~~gpqI~lSRt~p~fv~~LFe~EVPEI~dG~VeIk~IaRepG~RtKI  241 (375)
T PRK12328        162 IRAILPMKNRIKGEKFKVGDVVKAVLRRVKIDKKNGIKLELSRTSPKFLEALLELEVPEIKDGEVIIIHCARIPGERAKV  241 (375)
T ss_pred             CEEEECHHHCCCCCCCCCCCEEEEEEEEEECCCCCCCEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCEEE
T ss_conf             17980277638865589998699999998727899958999679889999999988899848968999985378874069


Q ss_pred             EEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCC
Q ss_conf             99940899881276554886217889986277826799559878999997628665424898756787999985342211
Q gi|254780788|r  240 AVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSL  319 (526)
Q Consensus       240 AV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~  319 (526)
                      ||+|+|++||||||||||||+|||+|++||+|||||||+||+||++||+|||+||+|.+|.+|++.+++.|+||++||||
T Consensus       242 AV~S~d~~iDpVGAcVG~kG~RI~~I~~EL~gEkIDii~~s~d~~~fi~nALsPA~V~~V~i~e~~~~a~viV~~~qlSl  321 (375)
T PRK12328        242 ALFSNSANIDPVGATVGVKGVRINAVSKELNGENIDCIEYSNIPEIFIARALAPAIILSVKIEKIPKKAIVTLPSEQKSK  321 (375)
T ss_pred             EEEECCCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEEECCCCHHHHHHHCCCCCCCEEEEEECCCCEEEEEECCHHHHH
T ss_conf             99925998674047888886309999998579627899778888999986378553018999568887999988014337


Q ss_pred             CCCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHCCC
Q ss_conf             025442789999986167457855220011010012
Q gi|254780788|r  320 AIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDF  355 (526)
Q Consensus       320 AIGk~GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~  355 (526)
                      ||||+||||||||+||||+|||+|++++.++++.+.
T Consensus       322 AIGk~GqNvrLAskLtgw~IDI~s~~~~~e~~~~~~  357 (375)
T PRK12328        322 AIGKNGINIRLASMLTGYEIELNEIGSVKENASNES  357 (375)
T ss_pred             HHCCCCCHHHHHHHHHCCEEEEEEHHHHHHHHHHHH
T ss_conf             626998719999997798799867788778876343


No 5  
>TIGR01953 NusA transcription termination factor NusA; InterPro: IPR010213   This entry describes NusA, or N utilisation substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents a region of NusA shared by all bacterial forms, and includes the S1 (IPR003029 from INTERPRO) and KH RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this entry, with two repeats of 50-residue domain rich in acidic amino acids.; GO: 0003723 RNA binding, 0030528 transcription regulator activity.
Probab=100.00  E-value=0  Score=983.31  Aligned_cols=339  Identities=53%  Similarity=0.875  Sum_probs=333.5

Q ss_pred             HHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHCCCCC---CCEEEEECCCCCEEEEEEEEEEE--CCCCCCCC----
Q ss_conf             9999999998623999-99999999999999996136874---53599974998839999998851--76778753----
Q gi|254780788|r    8 ELLQIADAVAYEKSID-RDVVLSVMADSIQKAARSLYGTM---SDIRVEINPETGDISLFRLLEVV--EEVENYTC----   77 (526)
Q Consensus         8 ell~vie~va~EK~I~-~e~i~~aie~Al~~a~kK~~~~~---~~i~V~iD~~tG~i~i~~~~~VV--edved~~~----   77 (526)
                      +++++++++|+||||+ .+.|+.+||+||.+||||+|+.+   .|++|.||++||++++|+.|.||  |+++|+.+    
T Consensus         1 ~~~~~~~~~a~~K~i~i~e~v~~~~e~Al~~Aykk~~~~~~~~~n~~v~id~~~G~~~v~~~~~vV~de~v~d~~~~~~~   80 (366)
T TIGR01953         1 ELLAAIEALAEEKGISIIETVIEAIEEALEQAYKKTFGSDTNAENVEVNIDRKTGEIEVYRRKEVVEDEEVEDPSLDYSL   80 (366)
T ss_pred             CHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEEECCCCCCCCCCCCCCCC
T ss_conf             95798999998708722699999999999999997368777642179998288655999985540345231064335351


Q ss_pred             ----EECHHHHHHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEE--CCC
Q ss_conf             ----23489998628898647379985084562079999999999999999998877999985208389999984--057
Q gi|254780788|r   78 ----QISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKR--VEY  151 (526)
Q Consensus        78 ----eI~l~~A~~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r--~e~  151 (526)
                          ||+|++|++++|++++||++..|+++.+|||+|||+|||+|.||+||+||+.+|++|++++|+||+|+|+|  +++
T Consensus        81 dd~leI~L~~A~~~~p~~~iGd~~~~~~~~~~FgR~a~~~a~Q~~~Qk~re~e~~~~~~ef~~~~g~~i~g~V~r~d~~~  160 (366)
T TIGR01953        81 DDMLEISLEDAREIDPDVQIGDEVKKEINPENFGRIAAQAAKQVITQKIREAERERVYDEFKSKVGEIISGTVKRVDVNK  160 (366)
T ss_pred             HHHEECCHHHHHHCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEEEEEECC
T ss_conf             14135220785210779621537887427666447899999999988889999876776643331808999999975257


Q ss_pred             CE----EEEEE-CCCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCE--EEEEEECCCHHHHHHHHHHHHHHHHCCEE
Q ss_conf             63----89995-7935874478748875115276699999761135870--28987159889999999976677755808
Q gi|254780788|r  152 GN----VIVDL-GNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRG--PQVLLSRTHPQFMVKLFHMEVPEIYNGIV  224 (526)
Q Consensus       152 ~~----iiVdl-g~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rg--pqi~lSRt~p~~l~~Lf~~EVPEI~~G~i  224 (526)
                      ++    ++|+| |+++|+||+++|||+|+|++|||||+||++|+++++|  |||+||||||+||++||++|||||+||+|
T Consensus       161 ~~~~~g~~v~l~g~~e~~lp~~e~iP~E~~~~Gd~i~~~~~eV~~~~~g~~~~i~lSRt~p~fl~~Ll~~EvPEI~dG~v  240 (366)
T TIGR01953       161 EGNETGLIVELAGKTEAILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGGLPQIILSRTHPEFLKELLKLEVPEIADGIV  240 (366)
T ss_pred             CCCCCEEEEEECCCEEEECCHHHCCCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHCCCCEEECCEE
T ss_conf             87521079998575025213533788875235888999999999868896689999708979999998616965417819


Q ss_pred             EEEEEECCCCCEEEEEEEE-CCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEE-EEC
Q ss_conf             7856631677503499994-08998812765548862178899862778267995598789999976286654248-987
Q gi|254780788|r  225 QVKAVSRDPGSRAKLAVFS-SDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKV-VLD  302 (526)
Q Consensus       225 eIk~iaR~pG~RsKIAV~s-~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v-~~d  302 (526)
                      +||+|||+||+||||||+| ||++||||||||||||+|||+|++||+|||||||.||+||++||.|||+||+|.+| ++|
T Consensus       241 eIk~iAR~pG~R~KiAV~SH~d~~iDPvGAcvG~~G~Ri~~i~~EL~gEkIDii~y~~d~~~Fi~nAL~PA~V~~v~i~d  320 (366)
T TIGR01953       241 EIKKIAREPGSRTKIAVESHNDENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAEVISVEILD  320 (366)
T ss_pred             EEEEEECCCCCCCEEEEEEECCCCCCEEEEEECCCCCCHHHHHHHHCCCEEEEEECCCCHHHHHHHHCCCCEECEEEEEE
T ss_conf             99999817887613578850789987046588898865433388747871789836888799999741863121148985


Q ss_pred             CCC--CEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCC
Q ss_conf             567--87999985342211025442789999986167457855220
Q gi|254780788|r  303 EDV--GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE  346 (526)
Q Consensus       303 e~~--~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~  346 (526)
                      +|+  |++.|+||++|||+||||+||||||||+||||+|||+|.++
T Consensus       321 ~d~~~~~a~v~V~~~QlslAIGK~GqNvRLAs~Ltgw~Idv~~~~~  366 (366)
T TIGR01953       321 EDKRDKSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWKIDVKTESQ  366 (366)
T ss_pred             CCCCCCEEEEEECCCCCCHHCCCCCCCHHHHHHHCCCEEEEEECCC
T ss_conf             3778837999857557750113356338877512263122212379


No 6  
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=100.00  E-value=0  Score=425.88  Aligned_cols=182  Identities=55%  Similarity=0.878  Sum_probs=177.2

Q ss_pred             CCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEE
Q ss_conf             93587447874887511527669999976113587028987159889999999976677755808785663167750349
Q gi|254780788|r  160 NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKL  239 (526)
Q Consensus       160 ~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKI  239 (526)
                      +++|+||+++|+|+|+|++|||+++|+++|+++.+| |+++|||||.|+.+||++|||||++|+++|++++|+|  |+  
T Consensus         1 ~~~~~l~~~~~~~~e~~~~g~ri~~~~~~v~~~~~g-~~~~srt~~~~~~~L~~~evpEi~~g~i~ik~i~rd~--r~--   75 (190)
T COG0195           1 KVEAILPKREQIPGENFKVGDRIRALLYEVQKEAKG-QIELSRTIPELLEKLFEIEVPEIGDGVIEIKCVARDP--RA--   75 (190)
T ss_pred             CCEEECCHHHCCCCCCCCCCCEEEEEEEEEEECCCC-CEEEEECCHHHHHHHHHHHCCCCCCCCEEEEEEEECC--CC--
T ss_conf             941671554538886443476799998255405766-5999824678999999851430047857999998267--55--


Q ss_pred             EEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECC-CCCEEEEEECCCCCC
Q ss_conf             9994089988127655488621788998627782679955987899999762866542489875-678799998534221
Q gi|254780788|r  240 AVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDE-DVGRIEVIVPKEQLS  318 (526)
Q Consensus       240 AV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de-~~~~~~v~v~~~qls  318 (526)
                      ||.|++.++||+|||||++|+|||+|++||| ||||||.||+||++||.|||+||+|.+|.+++ +++.+.|+||++|+|
T Consensus        76 av~~~~~~~d~vG~~iG~~G~rvk~i~~eLg-ekIdVVe~s~d~~~fI~nal~Pa~v~~V~~~~~d~~~~~v~V~~~~~~  154 (190)
T COG0195          76 AVVSNVVKIDPVGACIGKRGSRVKAVSEELG-EKIDVVEWSEDPAEFIKNALAPAEVLSVNIKEDDGHVAIVVVPPDQLS  154 (190)
T ss_pred             CEEEEECCCCCHHHHCCCCCHHHHHHHHHHC-CCEEEEEECCCHHHHHHHHCCCCEEEEEEEEECCCCEEEEEECHHHHH
T ss_conf             0399615768445421777628999999868-954899906999999998608354778999957981899998989974


Q ss_pred             CCCCCCHHHHHHHHHHHCCEEEEEECCCH
Q ss_conf             10254427899999861674578552200
Q gi|254780788|r  319 LAIGRRGQNVRLASQLTGWTIDIITEEED  347 (526)
Q Consensus       319 ~AIGk~GqNvrLas~Ltg~~idi~~~~~~  347 (526)
                      +||||+|||+|||++||||++||++..+.
T Consensus       155 ~aIGk~G~Nvrla~~Ltg~~i~I~~~~~~  183 (190)
T COG0195         155 LAIGKGGQNVRLASQLTGWEIDIETISEA  183 (190)
T ss_pred             HCCCCCCHHHHHHHHHHCCEEEEEEHHHH
T ss_conf             44686658899999986887777762111


No 7  
>pfam08529 NusA_N NusA N-terminal domain. This domain represents the RNA polymerase binding domain of NusA.
Probab=99.97  E-value=8e-31  Score=245.79  Aligned_cols=122  Identities=48%  Similarity=0.782  Sum_probs=119.4

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHHHHH
Q ss_conf             99999999986239999999999999999999613687453599974998839999998851767787532348999862
Q gi|254780788|r    8 ELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDR   87 (526)
Q Consensus         8 ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A~~~   87 (526)
                      +|+.+++++|+||||+++.+++++++||.+||+|+||.+.+++|.||++||++.+|+.|.||++++|+..+|+|++|+++
T Consensus         1 eil~~i~~la~EK~i~~e~v~~aie~al~~a~kk~~~~~~~~~V~id~~tG~i~v~~~~~VVe~~~d~~~eI~L~~A~~~   80 (122)
T pfam08529         1 ELLEAIDAIAREKGIDKEVLIEAIEEALLSAYKKKYGEDENVRVEIDRETGEIEVYRRKEVVEEVEDPDTEISLEEAKEI   80 (122)
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCEEEEEEEEEECCCCCCCCCEEEHHHHHHH
T ss_conf             97999999998709899999999999999999873399676799996789839999999815666798667657878741


Q ss_pred             CCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             889864737998508456207999999999999999999887
Q gi|254780788|r   88 DPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDR  129 (526)
Q Consensus        88 ~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~  129 (526)
                      +|++++||++..+++|.+|||+|||+|||+|+||+|++||++
T Consensus        81 ~~~~~iGd~i~~~i~~~~fgRiaaq~akQ~i~qklre~Er~~  122 (122)
T pfam08529        81 DPDAEIGDEIEEEVTPKDFGRIAAQTAKQVIIQKIREAERER  122 (122)
T ss_pred             CCCCEECCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             788703562668417677488999999999999999998159


No 8  
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=99.92  E-value=8e-26  Score=209.02  Aligned_cols=94  Identities=31%  Similarity=0.467  Sum_probs=86.6

Q ss_pred             CEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECC--CCCEEEEEECCCCCCCCCCCCHHH
Q ss_conf             127655488621788998627782679955987899999762866542489875--678799998534221102544278
Q gi|254780788|r  250 PVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDE--DVGRIEVIVPKEQLSLAIGRRGQN  327 (526)
Q Consensus       250 pVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de--~~~~~~v~v~~~qls~AIGk~GqN  327 (526)
                      -+|+|||.+|+||+.+.+.| |+|||||+||+||.+||.|||+||+|.+|.+.+  +.+.+.|.||++|+|+||||+|||
T Consensus        44 ~mG~AIGk~G~~Ik~l~~~l-gkkIdiVe~seDp~~FI~N~l~Pa~V~~V~i~~~~~~~~a~V~V~~~~~~lAIGK~G~N  122 (142)
T PRK08406         44 DMGLAIGKGGENVKRLKEKL-GKDIELVEYSEDPEEFIKNLLAPAKVKSVKISEKNGKKVAYVTVAPEDKGIAIGKNGKN  122 (142)
T ss_pred             HHHHHHCCCCCHHHHHHHHH-CCCEEEEECCCCHHHHHHHCCCCCEEEEEEEECCCCCEEEEEEECHHHHHHHHCCCCCC
T ss_conf             68897587960799999985-89458996478999999870693256799998279968999996856520433757644


Q ss_pred             HHHHHHHHCCEEEEEEC
Q ss_conf             99999861674578552
Q gi|254780788|r  328 VRLASQLTGWTIDIITE  344 (526)
Q Consensus       328 vrLas~Ltg~~idi~~~  344 (526)
                      +|||++|++|++||.+.
T Consensus       123 i~lA~~L~~r~~dI~~i  139 (142)
T PRK08406        123 IKRAKDLAKRHFDIDDI  139 (142)
T ss_pred             HHHHHHHHHHHCCCEEE
T ss_conf             99999987534697079


No 9  
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=99.78  E-value=7e-19  Score=158.01  Aligned_cols=67  Identities=52%  Similarity=1.003  Sum_probs=65.9

Q ss_pred             HHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf             5208389999984057638999579358744787488751152766999997611358702898715
Q gi|254780788|r  136 DKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSR  202 (526)
Q Consensus       136 ~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSR  202 (526)
                      +|+|+||+|+|+|+++++++||||++||+||++||||+|+|++||||||||.+|+.++|||||+|||
T Consensus         1 ~k~geiv~G~V~r~~~~~v~vdlg~~eailp~~eqip~E~~~~Gdrik~~i~~V~~~~kgp~i~lSR   67 (67)
T cd04455           1 DREGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKGPQIILSR   67 (67)
T ss_pred             CCCCCEEEEEEEEEECCCEEEEECCCEEECCHHHCCCCCCCCCCCEEEEEEEEEEECCCCCEEEEEC
T ss_conf             9878889999999808979999899489737899578866399998999999987469988899839


No 10 
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2.   The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=99.65  E-value=9.6e-17  Score=142.31  Aligned_cols=60  Identities=55%  Similarity=0.783  Sum_probs=56.0

Q ss_pred             HHHHHHHHCCCCCCCEEEECC-CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf             899999762866542489875-678799998534221102544278999998616745785
Q gi|254780788|r  283 SATFVINALRPAIVTKVVLDE-DVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII  342 (526)
Q Consensus       283 ~~~fi~nAl~PA~v~~v~~de-~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~  342 (526)
                      |++||.|||+||+|.+|.+++ ..+.+.|+|+++|+|+||||+||||||||+||||+|||+
T Consensus         1 p~~fi~nal~Pa~v~~V~i~~~~~~~~~V~V~~~~~~~AIGk~G~Nvrla~~l~g~~IdI~   61 (61)
T cd02134           1 PAEFIRNALSPAKVTSVTVLDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDIV   61 (61)
T ss_pred             CHHHHHHHCCCCEEEEEEECCCCCCEEEEEECHHHHHHHHCCCCEEHHHHHHHHCCEEEEC
T ss_conf             9789986369875579884478773799998857843876678670999999779877649


No 11 
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication; InterPro: IPR010214    NusA, or N utilisation substance protein A, is a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents an acidic 50-residue region found in two copies toward the C terminus of most proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic  ; GO: 0030528 transcription regulator activity.
Probab=99.13  E-value=5.1e-11  Score=100.20  Aligned_cols=50  Identities=60%  Similarity=0.837  Sum_probs=48.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCHHHHHH--HHCCCHHHHHHHHHHHHHHH
Q ss_conf             884678888773211147775058888776--53058899999999999999
Q gi|254780788|r  368 VDEIIAHLLVAEGFADVEELACVKISEIAS--IEGFDEETAVEIQGRAREYL  417 (526)
Q Consensus       368 VDE~iA~~LV~eGf~SiEeIa~a~~eeL~~--IeGfdee~a~eL~~rA~~~L  417 (526)
                      ||+.+|+.||.+||+|+|+|||+|+++|++  |+|||+|+|.+|+.||++++
T Consensus         1 ~~e~~a~~Lv~eGf~t~EdlAy~~~~EL~~fGIeG~~Ee~A~~L~~~Ar~~~   52 (52)
T TIGR01954         1 IDEEIAQLLVEEGFTTVEDLAYVPVDELLSFGIEGLDEETAKELINRARNAL   52 (52)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHC
T ss_conf             9578899999736731788750455668863589988788999999987529


No 12 
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.76  E-value=7.7e-07  Score=69.54  Aligned_cols=72  Identities=31%  Similarity=0.509  Sum_probs=37.4

Q ss_pred             HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHH
Q ss_conf             20838999998405763899957-935874478748------87511527669999976113587028987159889999
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMV  209 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~  209 (526)
                      +.|+||.|+|.+++.+.++||+| +.||++|++|..      +.+.|++||.+++||..++....  +++|||.-....+
T Consensus       303 ~~G~iV~G~Vv~v~~~~v~VDiG~KseG~Ip~~E~~~~~~~~~~~~~kvGDei~v~V~k~ed~~G--~i~LS~kka~~~~  380 (670)
T PRK00087        303 RRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLEELTKDEDSSLKESVKVGDEIEVKVLKLENEDG--YVVLSKKEADREK  380 (670)
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCCCCEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCC--CEEEEHHHHHHHH
T ss_conf             78987999999993898999836784368889993667677733457999989999999868998--2998889999888


Q ss_pred             H
Q ss_conf             9
Q gi|254780788|r  210 K  210 (526)
Q Consensus       210 ~  210 (526)
                      .
T Consensus       381 ~  381 (670)
T PRK00087        381 A  381 (670)
T ss_pred             H
T ss_conf             7


No 13 
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.61  E-value=1e-06  Score=68.59  Aligned_cols=270  Identities=19%  Similarity=0.252  Sum_probs=142.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCE---EEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHHH---HHCC--CCCCC
Q ss_conf             999999999999999996136874535---999749988399999988517677875323489998---6288--98647
Q gi|254780788|r   23 DRDVVLSVMADSIQKAARSLYGTMSDI---RVEINPETGDISLFRLLEVVEEVENYTCQISLKVAR---DRDP--SIDIG   94 (526)
Q Consensus        23 ~~e~i~~aie~Al~~a~kK~~~~~~~i---~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A~---~~~~--~~~iG   94 (526)
                      +.+.+..+++.++     |+|....-+   .+.|+.+.         .+|+=-.....-|++.+..   ..++  .+++|
T Consensus        18 S~edf~~~le~s~-----k~~~eGdIV~GtVv~I~~d~---------VlVDIG~KsEGiIP~~E~s~~~d~d~~e~vkvG   83 (484)
T PRK07899         18 SAEDFLAAIDKTI-----KYFNDGDIVEGTVVKVDRDE---------VLLDIGYKTEGVIPSRELSIKHDVDPNEVVSVG   83 (484)
T ss_pred             CHHHHHHHHHHHH-----HCCCCCCEEEEEEEEEECCE---------EEEEECCCEEEEEEHHHHCCCCCCCCCCCCCCC
T ss_conf             9999999888787-----35889988999999997898---------999826870478799994667577845457899


Q ss_pred             CEEEEECCH-H-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCC-
Q ss_conf             379985084-5-6207999999999999999999887799998520838999998405763899957935874478748-
Q gi|254780788|r   95 GVVSDPLPP-M-DFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETI-  171 (526)
Q Consensus        95 D~i~~~i~~-~-~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~i-  171 (526)
                      |.++.-+.. . .-|++....-|-   ++.+  -.+.+-..|.  .|++|+|+|...-+|.++||+ ++.|+||.++.- 
T Consensus        84 DeIeV~Vi~~ed~eG~vvLSkkkA---~~~k--~W~~Leea~e--~~~vVeGkV~~~vKGGliVdi-GvraFlP~Sqid~  155 (484)
T PRK07899         84 DEVEALVLTKEDKEGRLILSKKRA---QYER--AWGTIEKLKE--KDGVVTGTVIEVVKGGLILDI-GLRGFLPASLVEM  155 (484)
T ss_pred             CEEEEEEEEEECCCCCEEEEHHHH---HHHH--HHHHHHHHHH--CCCEEEEEEEEEECCCEEEEC-CCEEEEECCCCCC
T ss_conf             999999998737887499888997---6567--8999999975--798699999999667099982-6579986422565


Q ss_pred             -CCCCCC--CCCEEEEEEEEECCCCCEEEEEEECCCH------HHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEE
Q ss_conf             -875115--2766999997611358702898715988------9999999976677755808785663167750349999
Q gi|254780788|r  172 -SRENLR--PGDRVKSYIYDVRREQRGPQVLLSRTHP------QFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVF  242 (526)
Q Consensus       172 -p~E~~~--~Gdrika~i~~V~~~~rgpqi~lSRt~p------~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~  242 (526)
                       |-+++.  .|..+++.|.++++..+  .|+|||..-      .--.++|+    .+..|.|-==            -| 
T Consensus       156 r~v~dl~~~vGk~l~~kIieid~~r~--nIVlSRRa~LEee~~~~r~e~l~----~L~~G~vveG------------~V-  216 (484)
T PRK07899        156 RRVRDLQPYIGQEIEAKIIELDKNRN--NVVLSRRAWLEQTQSEVRSEFLN----QLQKGQVRKG------------VV-  216 (484)
T ss_pred             CCCCCHHHHCCCEEEEEEEEECCCCC--CEEEEHHHHHHHHHHHHHHHHHH----HCCCCCEEEE------------EE-
T ss_conf             10478388779879999999757668--06501999999999889999997----4778987999------------99-


Q ss_pred             ECCCCCCCEEEEECCCC------------HHHHHHHHHH-CCCCEEEEE----------------CCCCHHHHHHHHCCC
Q ss_conf             40899881276554886------------2178899862-778267995----------------598789999976286
Q gi|254780788|r  243 SSDSSIDPVGACVGMRG------------SRVQAVVTEL-RDEKIDIVV----------------WSPDSATFVINALRP  293 (526)
Q Consensus       243 s~d~~iDpVGAcVG~rG------------sRiq~I~~EL-~gEkIDii~----------------ws~d~~~fi~nAl~P  293 (526)
                         .+|-+-||.|-..|            .||+..+.-| -|.++.+..                -.+||=.-+..-+.+
T Consensus       217 ---k~It~fGAFVDLGGVDGLvHiSEiSW~Rv~~Psev~~vGd~V~VkVl~iD~Ek~RISLslKql~~dPW~~~~~k~~v  293 (484)
T PRK07899        217 ---SSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGDEVTVEVLDVDLDRERVSLSLKATQEDPWQVFARTHAI  293 (484)
T ss_pred             ---EEECCCEEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHCCC
T ss_conf             ---98216468999557237898134035677998995779987999998774767889886254778838989864899


Q ss_pred             CCC-----CEEEE----CCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHH--CCEEEEE
Q ss_conf             654-----24898----7567879999853422110254427899999861--6745785
Q gi|254780788|r  294 AIV-----TKVVL----DEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLT--GWTIDII  342 (526)
Q Consensus       294 A~v-----~~v~~----de~~~~~~v~v~~~qls~AIGk~GqNvrLas~Lt--g~~idi~  342 (526)
                      ..+     .++.-    -+=..-++=.|.=.+||   .+   +++-.+...  |=.+.++
T Consensus       294 G~vv~GkV~~l~~fGAFVel~~GIEGLVHISElS---~~---~v~~P~dvv~~GdeV~vk  347 (484)
T PRK07899        294 GQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELA---ER---HVEVPEQVVSVGDEVMVK  347 (484)
T ss_pred             CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCC---CC---CCCCHHHHCCCCCEEEEE
T ss_conf             8989999998726605999369967667877645---64---447988847799889999


No 14 
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication; InterPro: IPR010214    NusA, or N utilisation substance protein A, is a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents an acidic 50-residue region found in two copies toward the C terminus of most proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic  ; GO: 0030528 transcription regulator activity.
Probab=98.60  E-value=6.1e-08  Score=77.62  Aligned_cols=50  Identities=38%  Similarity=0.507  Sum_probs=47.8

Q ss_pred             CCHHHHHHHHHCCCCCHHHHHHCCHHHHCC--CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCC
Q ss_conf             998999999987984788965326775212--312344432112453343588999999999984122578
Q gi|254780788|r  443 IDSKIKVALGENGIKTMEDLAGCSVDDLLG--WSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGW  511 (526)
Q Consensus       443 l~~~~~~~L~e~gIktleDlAels~dEL~~--~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~~gW  511 (526)
                      |+..|+..|++.|+.|+||||++++|||++  |.                 |++++.|.+|||.||.+  |
T Consensus         1 ~~e~~a~~Lv~eGf~t~EdlAy~~~~EL~~fGIe-----------------G~~Ee~A~~L~~~Ar~~--~   52 (52)
T TIGR01954         1 IDEEIAQLLVEEGFTTVEDLAYVPVDELLSFGIE-----------------GLDEETAKELINRARNA--L   52 (52)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHCCCHHHHHHHCCC-----------------CCCHHHHHHHHHHHHHH--C
T ss_conf             9578899999736731788750455668863589-----------------98878899999998752--9


No 15 
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.59  E-value=2.3e-06  Score=66.00  Aligned_cols=64  Identities=20%  Similarity=0.339  Sum_probs=37.9

Q ss_pred             HCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCC---CCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf             208389999984057638999579358744787488---7511527669999976113587028987159
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETIS---RENLRPGDRVKSYIYDVRREQRGPQVLLSRT  203 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip---~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt  203 (526)
                      ..|++|+|+|....+|.++|++++.+|+||.++.-.   .+.| +|+.+++-+.+++...+  .|+|||.
T Consensus       117 ~~~~~V~gkV~~~~kgG~~V~i~gl~gFiP~Sqls~~~~~~~~-vG~~~~~kIieid~~~~--rivlS~r  183 (314)
T PRK07400        117 KEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKEEL-VGEELPLKFLEVDEERN--RLVLSHR  183 (314)
T ss_pred             HCCCEEEEEEEEEECCCEEEEECCEEEEEEHHHCCCCCCCHHH-CCCEEEEEEEEEECCCC--CEEEEEE
T ss_conf             2598799999999638489997686568552451635563210-69768899999715668--2489983


No 16 
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.53  E-value=5.7e-07  Score=70.49  Aligned_cols=63  Identities=37%  Similarity=0.671  Sum_probs=57.2

Q ss_pred             CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf             838999998405763899957-935874478748------87511527669999976113587028987159
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSRT  203 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt  203 (526)
                      |++|+|+|.+++...++||+| +.+|++|.+|..      |.+.|++||.+.|+|..++.+.+  ++.|||-
T Consensus         1 G~iV~G~V~~i~~~gv~Vdig~k~eG~ip~~E~s~~~~~~~~~~~~vGd~i~~~V~~~d~~~g--~i~LS~k   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEG--NVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEECCEEEEEECCCCCEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCC--EEEEECC
T ss_conf             998999999997886999968985026899994533238974712699999999999999999--7998509


No 17 
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.46  E-value=8.6e-06  Score=61.83  Aligned_cols=64  Identities=19%  Similarity=0.357  Sum_probs=35.8

Q ss_pred             CCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCC--C--CCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf             083899999840576389995793587447874887--5--11527669999976113587028987159
Q gi|254780788|r  138 VGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISR--E--NLRPGDRVKSYIYDVRREQRGPQVLLSRT  203 (526)
Q Consensus       138 ~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~--E--~~~~Gdrika~i~~V~~~~rgpqi~lSRt  203 (526)
                      .|+.|+|+|....+|.++|+++++.|+||.++.-.+  +  ..-.|..+++.|.++++..+  .|++||.
T Consensus       104 ~~~~v~g~i~~~vKGG~~V~i~gv~aFlP~Sq~d~~~v~d~~~~vG~~l~~kIi~~d~~~~--~iVvSrr  171 (556)
T PRK06299        104 NGEIVEGVINGKVKGGFTVDLNGVRAFLPGSQVDVRPVRDTDPLEGKELEFKVIKLDKKRN--NIVVSRR  171 (556)
T ss_pred             CCCEEEEEEEEEECCEEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCEEEEEEEEEECCCC--EEEEEHH
T ss_conf             8987999999997780999988989997858825755566176579669999999752358--0897328


No 18 
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.42  E-value=1.2e-06  Score=68.12  Aligned_cols=124  Identities=22%  Similarity=0.333  Sum_probs=68.7

Q ss_pred             CCCCCEECHHHHHHHCCCCCCCCEEEEECCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCC
Q ss_conf             787532348999862889864737998508456-2079999999999999999998877999985208389999984057
Q gi|254780788|r   73 ENYTCQISLKVARDRDPSIDIGGVVSDPLPPMD-FGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEY  151 (526)
Q Consensus        73 ed~~~eI~l~~A~~~~~~~~iGD~i~~~i~~~~-fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~  151 (526)
                      +-|..|+.+..  -.+++--+|..+...+--.+ -+|...-+ +-.+.+.-++..|+..++.+  ++|+++.|+|+++..
T Consensus       140 FlP~Sqid~r~--v~d~~~~vGk~~~~~Iikid~~~~nIVvS-RR~lLe~e~~~~~~~~~~~l--~~G~vv~G~V~~i~~  214 (489)
T PRK13806        140 FCPVSQIDLHQ--VEDPESFVGQTFQFLITRVEQNGRNIVVS-RRALLEREQAESLATFLEGV--KEGDVLEGTVTRLAP  214 (489)
T ss_pred             EEEHHHCCCCC--CCCHHHHCCCEEEEEEEEECCCCCEEEEE-HHHHHHHHHHHHHHHHHHHH--CCCCEECEEEEEECC
T ss_conf             42316604666--67858967965899999970568707866-89988888777899999861--148800429999757


Q ss_pred             CEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCC--EEEEEEE
Q ss_conf             63899957-935874478748------87511527669999976113587--0289871
Q gi|254780788|r  152 GNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQR--GPQVLLS  201 (526)
Q Consensus       152 ~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~r--gpqi~lS  201 (526)
                      -.++|||| +++|++|.+|+.      |.+.|++||.|++.|.++.++++  ++.|-||
T Consensus       215 ~GaFVdl~~GvdGllHiSeiSw~rv~~p~~~~~vGd~v~vkVl~id~e~~~~~~risLs  273 (489)
T PRK13806        215 FGAFVEIAPGVEGMVHISELSWSRVQQADEAVSVGDRVRVKVLGIGEAPKGKGLRISLS  273 (489)
T ss_pred             CEEEEEECCCCEEEEEHHHCCCCCCCCHHHEECCCCEEEEEEEEEECCCCCCCEEEEEE
T ss_conf             53899937980799983555865668888945169889999999864456665069860


No 19 
>pfam00575 S1 S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Probab=98.38  E-value=1.9e-06  Score=66.66  Aligned_cols=65  Identities=35%  Similarity=0.590  Sum_probs=60.0

Q ss_pred             HHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf             520838999998405763899957-935874478748------8751152766999997611358702898715
Q gi|254780788|r  136 DKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSR  202 (526)
Q Consensus       136 ~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSR  202 (526)
                      .++|+++.|+|.++++..++|+|+ +.+|++|.+++.      |.+.|++||+++|.|.+++.+.+  ++.||+
T Consensus         2 ~~~G~iv~G~V~~i~~~G~fV~l~~~~~g~v~~s~ls~~~~~~~~~~~~~G~~v~~~V~~vd~~~~--~i~lS~   73 (74)
T pfam00575         2 PEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLKVDKERG--RIILSI   73 (74)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHHHCCCCEEEEEEEEEECCCC--EEEEEE
T ss_conf             889999999999998775999978997999984461365556776830599999999999999999--999983


No 20 
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.37  E-value=2e-06  Score=66.54  Aligned_cols=109  Identities=24%  Similarity=0.389  Sum_probs=81.2

Q ss_pred             CCCCCCCCEEEEECCHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEEE
Q ss_conf             889864737998508456--207999999999999999999887799998520838999998405763899957935874
Q gi|254780788|r   88 DPSIDIGGVVSDPLPPMD--FGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVI  165 (526)
Q Consensus        88 ~~~~~iGD~i~~~i~~~~--fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~L  165 (526)
                      +++.=+|..+...+--.+  -+++ .-+ +..+.+.-++.+++..++.++  +|+++.|+|+++..-.++||||+++|++
T Consensus       143 d~~~~vG~~l~~kIi~~d~~~~~i-VvS-rr~~lee~~~~~~~~~~~~l~--~G~vv~G~V~~i~~~GaFVdlggvdGll  218 (556)
T PRK06299        143 DTDPLEGKELEFKVIKLDKKRNNI-VVS-RRAVLEEERAEEREELLENLE--EGQVVEGVVKNITDYGAFVDLGGVDGLL  218 (556)
T ss_pred             CHHHHCCCEEEEEEEEEECCCCEE-EEE-HHHHHHHHHHHHHHHHHHHCC--CCCEEEEEEEEEECCCEEEEECCEEEEE
T ss_conf             617657966999999975235808-973-289888888888999998524--7972789999970575899958958999


Q ss_pred             EHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf             478748------8751152766999997611358702898715
Q gi|254780788|r  166 RRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSR  202 (526)
Q Consensus       166 p~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSR  202 (526)
                      |.+++.      |.+.|++||.+++.|.+++.+.+  +|-||-
T Consensus       219 hiseiSw~rv~~p~~~~~~G~~v~vkVl~id~e~~--risLsl  259 (556)
T PRK06299        219 HITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKK--RVSLGL  259 (556)
T ss_pred             EHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCC--EEEEEE
T ss_conf             85671556669989926689889999998826563--899997


No 21 
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.36  E-value=2.5e-06  Score=65.74  Aligned_cols=123  Identities=22%  Similarity=0.296  Sum_probs=87.8

Q ss_pred             CCCCCEECHHHHHHHCCCCCCCCEEEEECCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCC
Q ss_conf             78753234899986288986473799850845620-79999999999999999998877999985208389999984057
Q gi|254780788|r   73 ENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFG-RVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEY  151 (526)
Q Consensus        73 ed~~~eI~l~~A~~~~~~~~iGD~i~~~i~~~~fg-RiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~  151 (526)
                      +-|..++.+.-.+  |.+.-+|..+...+--.+-. |...-+ +..+.+.-++..|+..++.+  .+|+++.|+|+++..
T Consensus       147 FlP~Sqid~r~v~--dl~~~vGk~l~~kIieid~~r~nIVlS-RRa~LEee~~~~r~e~l~~L--~~G~vveG~Vk~It~  221 (484)
T PRK07899        147 FLPASLVEMRRVR--DLQPYIGQEIEAKIIELDKNRNNVVLS-RRAWLEQTQSEVRSEFLNQL--QKGQVRKGVVSSIVN  221 (484)
T ss_pred             EEECCCCCCCCCC--CHHHHCCCEEEEEEEEECCCCCCEEEE-HHHHHHHHHHHHHHHHHHHC--CCCCEEEEEEEEECC
T ss_conf             9864225651047--838877987999999975766806501-99999999988999999747--789879999998216


Q ss_pred             CEEEEEECCCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf             6389995793587447874------88751152766999997611358702898715
Q gi|254780788|r  152 GNVIVDLGNSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSR  202 (526)
Q Consensus       152 ~~iiVdlg~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSR  202 (526)
                      -..+||||+++|+++-+++      -|.|.|++||.|+++|.++.++..  .|-||.
T Consensus       222 fGAFVDLGGVDGLvHiSEiSW~Rv~~Psev~~vGd~V~VkVl~iD~Ek~--RISLsl  276 (484)
T PRK07899        222 FGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGDEVTVEVLDVDLDRE--RVSLSL  276 (484)
T ss_pred             CEEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCC--EEEEEE
T ss_conf             4689995572378981340356779989957799879999987747678--898862


No 22 
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.33  E-value=6e-06  Score=62.97  Aligned_cols=188  Identities=21%  Similarity=0.314  Sum_probs=101.1

Q ss_pred             CCCCCCCEEEEECCHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEEEE
Q ss_conf             8986473799850845--62079999999999999999998877999985208389999984057638999579358744
Q gi|254780788|r   89 PSIDIGGVVSDPLPPM--DFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIR  166 (526)
Q Consensus        89 ~~~~iGD~i~~~i~~~--~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp  166 (526)
                      .-.++||.++..+-..  +-+++.. +.|+.    -.....+.+.+.|  ..|+++.|+|.++.++.++|++++..|+||
T Consensus        61 ~~~kvGd~V~~~Vl~~~~~~~~l~L-S~kk~----~~~~~w~~~~~~~--~~g~~v~g~V~~~~kgG~~V~~~gv~gFlP  133 (390)
T PRK06676         61 DVVKVGDTLEVYVLKVEDGEGNYLL-SKRRL----EARKAWDKLEEKF--EEGEVVEVKVTEVVKGGLVVDVGGVRGFIP  133 (390)
T ss_pred             HCCCCCCEEEEEEEEEECCCCEEEE-EHHHH----HHCHHHHHHHHHH--HCCCEEEEEEEEEECCCEEEEECCCEEEEE
T ss_conf             2469989999999999889973999-96792----2010088888765--379779999999955859999768168775


Q ss_pred             HHHCCCC-----CCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEE
Q ss_conf             7874887-----51152766999997611358702898715988999999997667775580878566316775034999
Q gi|254780788|r  167 RDETISR-----ENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAV  241 (526)
Q Consensus       167 ~~e~ip~-----E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV  241 (526)
                      .++.-..     ..| .|+.++|.|.++....+  .|+|||-.  ++..--.....++.+        .-.||.--+-.|
T Consensus       134 ~S~ls~~~~~~~~~~-vGq~v~~kVi~vd~~~~--~ivlS~K~--~l~~~~~~~~~~~~~--------~l~~Gdvv~G~V  200 (390)
T PRK06676        134 ASLISTRFVEDLSDF-KGKTLDVKIIELDPEKN--RVILSRRA--VVEEERAEKKKELLS--------SLKEGDVVEGKV  200 (390)
T ss_pred             HHHCCCCCCCCCHHH-CCEEEEEEEEEEECCCC--CEEECCHH--HHHHHHHHHHHHHHH--------HCCCCCEEEEEE
T ss_conf             487256445770554-37169999999853788--28970324--546667665766776--------346898478999


Q ss_pred             EECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECC--CCHHHHHHHHCCCCCCCEEE---ECCCCCEEEEEE
Q ss_conf             940899881276554886217889986277826799559--87899999762866542489---875678799998
Q gi|254780788|r  242 FSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWS--PDSATFVINALRPAIVTKVV---LDEDVGRIEVIV  312 (526)
Q Consensus       242 ~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws--~d~~~fi~nAl~PA~v~~v~---~de~~~~~~v~v  312 (526)
                      .    +|.+-|+-|-..|  |.+.+      .+.=+-|+  .+|..    -+.+.+-.++.   +|.+++++.+-.
T Consensus       201 ~----~i~~~G~FV~lgg--v~glv------h~sels~~~~~~~~~----~~k~G~~v~~~Vl~id~~~~ri~Lsl  260 (390)
T PRK06676        201 A----RLTDFGAFVDIGG--VDGLV------HISELSHERVNKPSE----VVSVGQEVEVKVLSIDEETERISLSL  260 (390)
T ss_pred             E----EEECCCEEEECCC--EEEEE------EECCCCHHHHCCHHH----HHCCCCEEEEEEEEEECCCCEEEEEE
T ss_conf             9----9945636998077--67999------961057333359888----30479757999999946788999998


No 23 
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.28  E-value=2.9e-05  Score=57.95  Aligned_cols=115  Identities=14%  Similarity=0.098  Sum_probs=77.7

Q ss_pred             CCCEECHHHHHHHCC--CCCCCCEEEEECCHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEE
Q ss_conf             753234899986288--9864737998508456-----207999999999999999999887799998520838999998
Q gi|254780788|r   75 YTCQISLKVARDRDP--SIDIGGVVSDPLPPMD-----FGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVK  147 (526)
Q Consensus        75 ~~~eI~l~~A~~~~~--~~~iGD~i~~~i~~~~-----fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~  147 (526)
                      ...-|++.+-...+.  .+++||.++.-+...+     ++|-.++   +.        ..+.+.+.|.  .|+.|.|.|.
T Consensus        57 sEG~Ip~~E~~d~~~~~~~kvGD~Iev~V~~~~dgei~LSr~~~~---~~--------~~~~l~ea~e--~~~~V~g~I~  123 (489)
T PRK13806         57 VDGVIDRRELEDAEGNLPYAVGDRLDLYVVAVNGGEIRLSKAMGG---QG--------GAAVLEEARD--NGVPVEGKVT  123 (489)
T ss_pred             EEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEECCCCEEEEHHHHH---HH--------HHHHHHHHHH--CCCEEEEEEE
T ss_conf             289958999257557756589989999999964981899889988---87--------8999999975--8986999999


Q ss_pred             ECCCCEEEEEECCCEEEEEHHHCCCC--CC--CCCCCEEEEEEEEECCCCCEEEEEEECCC
Q ss_conf             40576389995793587447874887--51--15276699999761135870289871598
Q gi|254780788|r  148 RVEYGNVIVDLGNSDGVIRRDETISR--EN--LRPGDRVKSYIYDVRREQRGPQVLLSRTH  204 (526)
Q Consensus       148 r~e~~~iiVdlg~~ea~Lp~~e~ip~--E~--~~~Gdrika~i~~V~~~~rgpqi~lSRt~  204 (526)
                      ..-+|.++|+++++.|+||.++.-.+  +.  .-.|..+++.|.++++..+  .|++||-.
T Consensus       124 ~~vKGG~~V~i~Gv~aFlP~Sqid~r~v~d~~~~vGk~~~~~Iikid~~~~--nIVvSRR~  182 (489)
T PRK13806        124 GTCKGGFNVEVLRRRAFCPVSQIDLHQVEDPESFVGQTFQFLITRVEQNGR--NIVVSRRA  182 (489)
T ss_pred             EEECCCEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCEEEEEEEEECCCCC--EEEEEHHH
T ss_conf             998675999989977642316604666678589679658999999705687--07866899


No 24 
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.21  E-value=1.9e-05  Score=59.24  Aligned_cols=160  Identities=21%  Similarity=0.310  Sum_probs=101.4

Q ss_pred             CCCCCEECHHHHH-----HHCCCCCCCCEEEEECCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEE
Q ss_conf             7875323489998-----628898647379985084--562079999999999999999998877999985208389999
Q gi|254780788|r   73 ENYTCQISLKVAR-----DRDPSIDIGGVVSDPLPP--MDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGT  145 (526)
Q Consensus        73 ed~~~eI~l~~A~-----~~~~~~~iGD~i~~~i~~--~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~  145 (526)
                      .-...-|++++-.     ...+.+++||.++.-+..  ...|++....-|-     .+....+.+.+.|..  |++|+|+
T Consensus       326 ~KseG~Ip~~E~~~~~~~~~~~~~kvGDei~v~V~k~ed~~G~i~LS~kka-----~~~~~w~~l~~a~e~--~e~V~g~  398 (670)
T PRK00087        326 YKSEGVIPLEELTKDEDSSLKESVKVGDEIEVKVLKLENEDGYVVLSKKEA-----DREKAWKELEEAFEN--GETVKGK  398 (670)
T ss_pred             CCCCEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCEEEEHHHH-----HHHHHHHHHHHHHHC--CCEEEEE
T ss_conf             784368889993667677733457999989999999868998299888999-----988879999999868--9869999


Q ss_pred             EEECCCCEEEEEECCCEEEEEHHHCCCC--CC--CCCCCEEEEEEEEECCCCCEEEEEEECCCH------HHHHHHHHHH
Q ss_conf             9840576389995793587447874887--51--152766999997611358702898715988------9999999976
Q gi|254780788|r  146 VKRVEYGNVIVDLGNSDGVIRRDETISR--EN--LRPGDRVKSYIYDVRREQRGPQVLLSRTHP------QFMVKLFHME  215 (526)
Q Consensus       146 V~r~e~~~iiVdlg~~ea~Lp~~e~ip~--E~--~~~Gdrika~i~~V~~~~rgpqi~lSRt~p------~~l~~Lf~~E  215 (526)
                      |....+|.++|+++++.|+||.++.-.+  +.  --.|..+++.|.+++...|.+.+++||..-      .--.++|+  
T Consensus       399 V~~~vKGG~~V~i~gi~~FiP~Sq~~~~~~~d~~~~vG~~~~~kIie~d~~k~r~niV~Srr~vlee~~~~~k~~~~~--  476 (670)
T PRK00087        399 VKEVVKGGLLVDYGGVRAFLPASHVELGYVEDLSAYKGQELEVKIIEFDKKRKKTKVVLSRKALLKEEKEKQKEETWN--  476 (670)
T ss_pred             EEEEECCCEEEEECCEEEEECHHHCCCCCCCCHHHHCCCEEEEEEEEECCCCCCCCEEEECHHHHHHHHHHHHHHHHH--
T ss_conf             999985859999899899802276156656772787697489999998444576748978099999889999999997--


Q ss_pred             HHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCC
Q ss_conf             67775580878566316775034999940899881276554886
Q gi|254780788|r  216 VPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRG  259 (526)
Q Consensus       216 VPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rG  259 (526)
                        .+..|.+ +.+           -|    .+|.|-||.|...|
T Consensus       477 --~l~~G~~-v~G-----------~V----~~i~~~GaFvdlgG  502 (670)
T PRK00087        477 --SLEEGDV-VEG-----------EV----KRLTDFGAFVDIGG  502 (670)
T ss_pred             --HCCCCCE-EEE-----------EE----EEEECCCEEEEECC
T ss_conf             --4889988-999-----------99----99973407999779


No 25 
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.18  E-value=1.3e-05  Score=60.44  Aligned_cols=78  Identities=26%  Similarity=0.401  Sum_probs=64.1

Q ss_pred             HHHHH--HHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf             79999--8520838999998405763899957-93587447874------887511527669999976113587028987
Q gi|254780788|r  130 QYLEF--KDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLL  200 (526)
Q Consensus       130 i~~ef--~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~l  200 (526)
                      ++++|  .-+.|++|.|+|..++.+.++||+| +++|++|.+|.      -|.+.+..||.+.++|..++.+..  ++.|
T Consensus        21 lLe~~~~~~k~GdiVeG~V~~I~~~~v~VdiG~k~eG~i~~~E~s~~~~~~~~e~~~vGd~iev~V~~~~~~~g--~i~L   98 (314)
T PRK07400         21 LLDKYDYHFKPGDIVNGTVFSLEPKGALIDIGAKTAAFMPLQEMSINRVEGPSEVLQPGETREFFILSEENEDG--QLTL   98 (314)
T ss_pred             HHHHHHCCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCC--CEEE
T ss_conf             99875236999998999999997998999977980799999993666568943013589769999999856889--6899


Q ss_pred             ECCCHHHHH
Q ss_conf             159889999
Q gi|254780788|r  201 SRTHPQFMV  209 (526)
Q Consensus       201 SRt~p~~l~  209 (526)
                      |+.-.....
T Consensus        99 S~k~~~~~~  107 (314)
T PRK07400         99 SIRRIEYMR  107 (314)
T ss_pred             EECHHHHHH
T ss_conf             860432120


No 26 
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.10  E-value=2e-05  Score=59.07  Aligned_cols=68  Identities=34%  Similarity=0.565  Sum_probs=34.2

Q ss_pred             HHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHH
Q ss_conf             8520838999998405763899957-9358744787488751152766999997611358702898715988999
Q gi|254780788|r  135 KDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFM  208 (526)
Q Consensus       135 ~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l  208 (526)
                      ..+.|+||+|+|-+++.++++||.| +.||.+|.+|-  ...-++||.+.+||..++.  .|++  |||.-..-+
T Consensus       318 ~~~~G~vi~g~Vv~i~~d~V~vdvG~KsEg~ip~~eF--~~~~~vGD~v~V~ie~~e~--~~~~--LSr~kA~r~  386 (863)
T PRK12269        318 APEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEF--EAPPKAGDGVRVYVERVTP--YGPE--LSKTKADRL  386 (863)
T ss_pred             CCCCCCEEEEEEEEEECCEEEEECCCCCCCCCCHHHC--CCCCCCCCEEEEEEEEECC--CCCE--ECHHHHHHH
T ss_conf             7998625899999995897999647744553269992--7788999999999999708--8975--618999878


No 27 
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   Ribosomal protein S1  contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities .    Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=98.09  E-value=3.3e-05  Score=57.53  Aligned_cols=174  Identities=22%  Similarity=0.265  Sum_probs=112.2

Q ss_pred             ECCCCCCCCEECHHHHHHHC--CCCCCCCEEEEECCHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEE
Q ss_conf             17677875323489998628--8986473799850845--6207999999999999999999887799998520838999
Q gi|254780788|r   69 VEEVENYTCQISLKVARDRD--PSIDIGGVVSDPLPPM--DFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISG  144 (526)
Q Consensus        69 Vedved~~~eI~l~~A~~~~--~~~~iGD~i~~~i~~~--~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G  144 (526)
                      |+=---...-|++++-....  -.++.||.|...|+-.  .+|+-.-..-|+   ||.+    ..++-+-..+.|++|.|
T Consensus        39 VDvG~KsEg~ip~~Ef~~~~G~l~~~~Gd~v~V~l~~~~~~~g~~~LS~~ka---~r~~----~~~~l~~~~~~~~~V~G  111 (534)
T TIGR00717        39 VDVGLKSEGRIPVEEFLDAQGELEIQVGDEVEVYLDRVEDRIGETVLSREKA---QRKE----AWIKLEKAYEEGSIVEG  111 (534)
T ss_pred             EEEECCCCCCCCHHHCCCCCCCCEEECCCEEEEEEEEECCCCCCCEEECCHH---HHHH----HHHHHHHHHHCCCEEEE
T ss_conf             9831563123417682688884000058879999984428999702304525---7888----99999998616984567


Q ss_pred             EEEECC--CCEEEEEEC-CCEEEEEHHHCCCC----CCCCCCCEEEEEEEEECCCC--CE-EEEEEECCC------HHHH
Q ss_conf             998405--763899957-93587447874887----51152766999997611358--70-289871598------8999
Q gi|254780788|r  145 TVKRVE--YGNVIVDLG-NSDGVIRRDETISR----ENLRPGDRVKSYIYDVRREQ--RG-PQVLLSRTH------PQFM  208 (526)
Q Consensus       145 ~V~r~e--~~~iiVdlg-~~ea~Lp~~e~ip~----E~~~~Gdrika~i~~V~~~~--rg-pqi~lSRt~------p~~l  208 (526)
                      .+.|-.  +|.++|||+ +++|+||.++-=-+    ..--.|-+.+++|..++...  || ++|++||-.      ..-.
T Consensus       112 ~I~~kvekKGGf~Vdl~aGv~AFLP~Sq~d~k~~~~~~~~~g~~~~f~i~k~d~~rqhrGn~nivvSRr~~lE~~~~~~r  191 (534)
T TIGR00717       112 KIVGKVEKKGGFIVDLEAGVEAFLPGSQVDVKKIKDLDSLIGKTLKFKIIKLDKKRQHRGNNNIVVSRRAYLEEERSQAR  191 (534)
T ss_pred             EEEEEEECCCCEEEECCCCEEEECCCCCCCCCCCCCCCCCCCCEEEEEEEEECCHHCCCCCCCEEEEEEEEECHHHHHHH
T ss_conf             98776605657799923681786164604662666403034307789999863100125799769941001042568889


Q ss_pred             HHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEE--EEECCCCHHHHHHHHHH
Q ss_conf             99999766777558087856631677503499994089988127--65548862178899862
Q gi|254780788|r  209 VKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVG--ACVGMRGSRVQAVVTEL  269 (526)
Q Consensus       209 ~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVG--AcVG~rGsRiq~I~~EL  269 (526)
                      ..||+.    |            .+|.+-+=-|+    +|+|-|  |-|=..|.+==-=.+++
T Consensus       192 ~e~le~----l------------~~g~~v~GvVk----~iT~fGGv~Fvdlgg~dGLLH~~d~  234 (534)
T TIGR00717       192 EELLEK----L------------KEGEVVKGVVK----NITDFGGVAFVDLGGVDGLLHITDM  234 (534)
T ss_pred             HHHHHH----C------------CCCCEEEEEEE----EECCCCCEEEEECCCEEECCCHHHC
T ss_conf             888761----5------------55857610888----8889874999981643320350121


No 28 
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.09  E-value=2.8e-05  Score=58.03  Aligned_cols=64  Identities=34%  Similarity=0.562  Sum_probs=58.4

Q ss_pred             HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCCC------CCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf             20838999998405763899957-93587447874887------51152766999997611358702898715
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISR------ENLRPGDRVKSYIYDVRREQRGPQVLLSR  202 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip~------E~~~~Gdrika~i~~V~~~~rgpqi~lSR  202 (526)
                      +.|+++.|+|.++..+.++|+++ +.+|++|..++.+.      +.|++||.++|.|.++....+  ++.||+
T Consensus         1 ~~G~iv~g~V~~v~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~--~i~ls~   71 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKG--RIILSL   71 (72)
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHEECCCCEEEEEEEEEECCCC--EEEEEE
T ss_conf             99989999999997873999976998999980750555547846836389899999999999999--999985


No 29 
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.07  E-value=2.9e-05  Score=57.89  Aligned_cols=62  Identities=34%  Similarity=0.576  Sum_probs=56.3

Q ss_pred             CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf             838999998405763899957-935874478748------8751152766999997611358702898715
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSR  202 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSR  202 (526)
                      |++|+|+|.++....++|+|+ +.+|++|.+|..      |.+.|+.||.|+|.|.+++...|  +|.||.
T Consensus         1 G~iV~G~V~~i~~~G~fV~l~~~v~G~ih~sels~~~~~~~~~~~~vGd~v~akIi~iD~~~~--ri~LSi   69 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNR--KISLSI   69 (73)
T ss_pred             CCEEEEEEEEEECCCEEEEECCCCEEEEEHHHCCCCHHHCHHHCCCCCCEEEEEEEEEECCCC--EEEEEE
T ss_conf             999999999997786899928996999998997821132925438999999999999978899--998674


No 30 
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits.  Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.05  E-value=2.8e-05  Score=58.00  Aligned_cols=67  Identities=21%  Similarity=0.352  Sum_probs=58.3

Q ss_pred             HHHHHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf             99998520838999998405763899957-93587447874------8875115276699999761135870289871
Q gi|254780788|r  131 YLEFKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLS  201 (526)
Q Consensus       131 ~~ef~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lS  201 (526)
                      |+++  ++|.+++|+|+++....++|+++ +.+|++|.++.      -|.+.|++|+.++|.|.+|+.+.+  +|.||
T Consensus         9 ~~~l--k~G~iv~G~V~~i~~~G~FV~l~~~v~Glv~~s~ls~~~~~~~~~~~~vGq~V~~~V~~iD~e~~--ri~LS   82 (83)
T cd04461           9 FSDL--KPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQ--RFLLS   82 (83)
T ss_pred             HHHC--CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEECCCC--EEEEE
T ss_conf             7787--99999999999992781999956994899899996864226989945599999999999958988--78875


No 31 
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.03  E-value=5.1e-05  Score=56.14  Aligned_cols=112  Identities=28%  Similarity=0.352  Sum_probs=67.7

Q ss_pred             ECHHHHHHHC-CCCCCCCEEEEEC---CH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC
Q ss_conf             3489998628-8986473799850---84----56207999999999999999999887799998520838999998405
Q gi|254780788|r   79 ISLKVARDRD-PSIDIGGVVSDPL---PP----MDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVE  150 (526)
Q Consensus        79 I~l~~A~~~~-~~~~iGD~i~~~i---~~----~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e  150 (526)
                      .|+.+.+.++ .+.-+|-++...+   +.    ...+|.++..+       =+..+|+..++..  .+|+++.|+|+++.
T Consensus       134 ~S~v~~r~v~d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~-------~~~~~r~e~~~~l--~~G~vV~G~V~~It  204 (541)
T COG0539         134 GSLVDVRPVRDLDPLIGKELEFKILELDKKRNNVVLSRRAVLEE-------ERSEQREELLNKL--EVGEVVEGVVKNIT  204 (541)
T ss_pred             HHHHCCCCCCCCCCCCCCEEEEEEEEECCCCCCEEEEHHHHHHH-------HHHHHHHHHHHCC--CCCCEEEEEEEEEE
T ss_conf             78715452346523478658999999853348478771777667-------7888799997247--88766999999861


Q ss_pred             CCEEEEEECCCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf             76389995793587447874------8875115276699999761135870289871
Q gi|254780788|r  151 YGNVIVDLGNSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLS  201 (526)
Q Consensus       151 ~~~iiVdlg~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lS  201 (526)
                      .-+++||||+++|+||.+++      -|.+.|++||.|++.|.+++.+.+  .|-||
T Consensus       205 ~~GafVdigGvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~--RVsLS  259 (541)
T COG0539         205 DYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERG--RVSLS  259 (541)
T ss_pred             CCCEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCC--EEEEE
T ss_conf             57479992571668864760655558989953569889999999726788--69999


No 32 
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.01  E-value=7e-05  Score=55.11  Aligned_cols=73  Identities=23%  Similarity=0.412  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf             988779999852083899999840576389995793587447874------88751152766999997611358702898
Q gi|254780788|r  126 ERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVL  199 (526)
Q Consensus       126 Er~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~  199 (526)
                      .++..++.|  ++|+++.|+|.++....++|+||+++|+++.++.      -|.+.|++||.+++.|.+++.+.+  +|.
T Consensus       182 ~~~~~~~~l--~~Gdvv~G~V~~i~~~G~FV~lggv~glvh~sels~~~~~~~~~~~k~G~~v~~~Vl~id~~~~--ri~  257 (390)
T PRK06676        182 KKKELLSSL--KEGDVVEGKVARLTDFGAFVDIGGVDGLVHISELSHERVNKPSEVVSVGQEVEVKVLSIDEETE--RIS  257 (390)
T ss_pred             HHHHHHHHC--CCCCEEEEEEEEEECCCEEEECCCEEEEEEECCCCHHHHCCHHHHHCCCCEEEEEEEEEECCCC--EEE
T ss_conf             576677634--6898478999999456369980776799996105733335988830479757999999946788--999


Q ss_pred             EEC
Q ss_conf             715
Q gi|254780788|r  200 LSR  202 (526)
Q Consensus       200 lSR  202 (526)
                      ||.
T Consensus       258 Lsl  260 (390)
T PRK06676        258 LSL  260 (390)
T ss_pred             EEE
T ss_conf             998


No 33 
>PRK08059 general stress protein 13; Validated
Probab=97.91  E-value=5.7e-05  Score=55.77  Aligned_cols=65  Identities=26%  Similarity=0.433  Sum_probs=58.0

Q ss_pred             HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf             20838999998405763899957-935874478748------87511527669999976113587028987159
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSRT  203 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt  203 (526)
                      ++|+++.|+|.++..-+++|+++ +.+|++|.+|.-      |.+.|++||.|+|-|.+++.+.+  .|-||.-
T Consensus         5 kvGdiv~G~V~~I~~fG~FV~l~~gv~GLihiSEls~~~v~~~~~~~~vGd~V~vkVi~iD~e~~--ri~LSlK   76 (119)
T PRK08059          5 EVGVVVTGKVTGIQDYGAFVALDEETQGLVHISEITHGFVKDIHDFLKVGDEVKVKVLSVDEEHG--KISLSIR   76 (119)
T ss_pred             CCCCEEEEEEEEEECEEEEEEEECCCEEEEEHHHHCCCCCCCHHHHHCCCCEEEEEEEEEECCCC--EEEEECC
T ss_conf             99999999999997404899994395378887882456667999970589989999999989999--9987503


No 34 
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.90  E-value=7.9e-05  Score=54.74  Aligned_cols=61  Identities=21%  Similarity=0.537  Sum_probs=54.9

Q ss_pred             CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf             838999998405763899957-93587447874------8875115276699999761135870289871
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLS  201 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lS  201 (526)
                      |+++.|+|+++..-.++|+|+ +++|++|.+++      -|.+.|++||.++|.|.+|+.+.+  +|.||
T Consensus         1 G~iv~G~V~~i~~fG~fV~l~~~i~Glv~~s~lsd~~v~~p~~~fk~G~~Vk~rVl~vD~~~~--ri~LS   68 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERK--RLVLT   68 (69)
T ss_pred             CCEEEEEEEEECCCEEEEEECCCEEEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCC--EEEEE
T ss_conf             999999999973842799957990699878990865206988908999999999999948879--98865


No 35 
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   Ribosomal protein S1  contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities .    Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=97.89  E-value=0.00016  Score=52.51  Aligned_cols=152  Identities=20%  Similarity=0.253  Sum_probs=96.2

Q ss_pred             HCCCCCCCEEEEECCCC---CEEEEEEEEEEECCCCCCCCEECHHHHHHHCC-CCCCCCEEEEECCHHHHHH-----HHH
Q ss_conf             13687453599974998---83999999885176778753234899986288-9864737998508456207-----999
Q gi|254780788|r   41 SLYGTMSDIRVEINPET---GDISLFRLLEVVEEVENYTCQISLKVARDRDP-SIDIGGVVSDPLPPMDFGR-----VAV  111 (526)
Q Consensus        41 K~~~~~~~i~V~iD~~t---G~i~i~~~~~VVedved~~~eI~l~~A~~~~~-~~~iGD~i~~~i~~~~fgR-----iaA  111 (526)
                      +.|-..+.+.-.|.+++   |-|.+=.     .---...+-+|..+.|+++. .--+|=..++.+-..|-.|     -..
T Consensus       101 ~~~~~~~~V~G~I~~kvekKGGf~Vdl-----~aGv~AFLP~Sq~d~k~~~~~~~~~g~~~~f~i~k~d~~rqhrGn~ni  175 (534)
T TIGR00717       101 KAYEEGSIVEGKIVGKVEKKGGFIVDL-----EAGVEAFLPGSQVDVKKIKDLDSLIGKTLKFKIIKLDKKRQHRGNNNI  175 (534)
T ss_pred             HHHHCCCEEEEEEEEEEECCCCEEEEC-----CCCEEEECCCCCCCCCCCCCCCCCCCCEEEEEEEEECCHHCCCCCCCE
T ss_conf             986169845679877660565779992-----368178616460466266640303430778999986310012579976


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCE--EEEEECCCEEEEEHHHC------CCCCCCCCCCEEE
Q ss_conf             999999999999999887799998520838999998405763--89995793587447874------8875115276699
Q gi|254780788|r  112 QSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGN--VIVDLGNSDGVIRRDET------ISRENLRPGDRVK  183 (526)
Q Consensus       112 q~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~--iiVdlg~~ea~Lp~~e~------ip~E~~~~Gdrik  183 (526)
                      -.-|..++.--|..+|+..++.-  ..|+-+.|+|+.++.-.  ++||||+++|+||..++      -|.|.+..||.|+
T Consensus       176 vvSRr~~lE~~~~~~r~e~le~l--~~g~~v~GvVk~iT~fGGv~Fvdlgg~dGLLH~~d~sWkr~~~P~e~~~~G~~~~  253 (534)
T TIGR00717       176 VVSRRAYLEEERSQAREELLEKL--KEGEVVKGVVKNITDFGGVAFVDLGGVDGLLHITDMSWKRVKHPSEYVKVGQEVK  253 (534)
T ss_pred             EEEEEEEECHHHHHHHHHHHHHC--CCCCEEEEEEEEECCCCCEEEEECCCEEECCCHHHCCCCCCCCCHHHCCCCCEEE
T ss_conf             99410010425688898887615--5585761088888898749999816433203501214788788346400798899


Q ss_pred             EEEEEECCCCCEEEEEEE
Q ss_conf             999761135870289871
Q gi|254780788|r  184 SYIYDVRREQRGPQVLLS  201 (526)
Q Consensus       184 a~i~~V~~~~rgpqi~lS  201 (526)
                      +-+..++.+.+  .|.||
T Consensus       254 Vkv~~~D~~~~--Ri~Ls  269 (534)
T TIGR00717       254 VKVIKFDKEKK--RISLS  269 (534)
T ss_pred             EEEEEECCCCC--EEEEE
T ss_conf             99996526576--07787


No 36 
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.89  E-value=0.00056  Score=48.46  Aligned_cols=122  Identities=19%  Similarity=0.298  Sum_probs=83.0

Q ss_pred             CCCEECHHHHHHHCCC--CCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HCCCEEEEEEEECC
Q ss_conf             7532348999862889--8647379985084562079999999999999999998877999985--20838999998405
Q gi|254780788|r   75 YTCQISLKVARDRDPS--IDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKD--KVGEIISGTVKRVE  150 (526)
Q Consensus        75 ~~~eI~l~~A~~~~~~--~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~--r~Geiv~G~V~r~e  150 (526)
                      ...-|++++-......  +++||.+..-+...+.+.-      + +.-..|.+++.+.+..-.+  ..|++|.|.|...-
T Consensus        45 seg~ip~~E~~~~~~~~~~~~gd~v~v~v~~~e~~~g------~-~~lS~~k~~~~~~w~~l~~~~e~~~~V~~~v~~~v  117 (541)
T COG0539          45 SEGVIPISEFSNEPVEDVVQVGDEVEVLVLRVEDGEG------E-LVLSRRKAERERAWEKLEEAFENGEIVEGKITGKV  117 (541)
T ss_pred             CCCEEEHHHCCCCCCCCEECCCCEEEEEEEEEECCCC------E-EEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEE
T ss_conf             1557688980566655131589889999999836886------0-88617788877778999988745983899999884


Q ss_pred             CCEEEEEECCCEEEEEHHHCCCC----CCCCCCCEEEEEEEEECCCCCEEEEEEECCCH
Q ss_conf             76389995793587447874887----51152766999997611358702898715988
Q gi|254780788|r  151 YGNVIVDLGNSDGVIRRDETISR----ENLRPGDRVKSYIYDVRREQRGPQVLLSRTHP  205 (526)
Q Consensus       151 ~~~iiVdlg~~ea~Lp~~e~ip~----E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p  205 (526)
                      +|.++||+++..|+||.+..--+    -.-..|..+.+.+.++++..+  .+++||-.-
T Consensus       118 KGG~~Vdi~gvr~FlP~S~v~~r~v~d~~~~~Gk~~~~kiie~d~~~n--~vv~SrR~~  174 (541)
T COG0539         118 KGGLTVDIEGVRAFLPGSLVDVRPVRDLDPLIGKELEFKILELDKKRN--NVVLSRRAV  174 (541)
T ss_pred             CCCEEEEECCEEEECCHHHHCCCCCCCCCCCCCCEEEEEEEEECCCCC--CEEEEHHHH
T ss_conf             484899987878865578715452346523478658999999853348--478771777


No 37 
>cd02409 KH-II KH-II  (K homology RNA-binding domain, type II).  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins  (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=97.89  E-value=2.2e-05  Score=58.84  Aligned_cols=58  Identities=31%  Similarity=0.487  Sum_probs=50.5

Q ss_pred             HHHHHHHCCCCCCCEEEECCC--CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHC-------CEEEE
Q ss_conf             999997628665424898756--78799998534221102544278999998616-------74578
Q gi|254780788|r  284 ATFVINALRPAIVTKVVLDED--VGRIEVIVPKEQLSLAIGRRGQNVRLASQLTG-------WTIDI  341 (526)
Q Consensus       284 ~~fi~nAl~PA~v~~v~~de~--~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg-------~~idi  341 (526)
                      .+|+.+.|.||.+.+|.+...  .....+++...|.+++|||+|+|+++...|++       |.||+
T Consensus         1 ~~~l~~~l~~~~~~~V~i~~~~~~~~~~i~~~~~~~g~~IGk~G~~l~~l~~ll~~~~~~~~~~i~v   67 (68)
T cd02409           1 REFLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRKKRVKIDV   67 (68)
T ss_pred             CHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCCCEEECCCCHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             9578745565685569999779967999998777996489888363999999999982899843853


No 38 
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.89  E-value=7.7e-05  Score=54.82  Aligned_cols=62  Identities=31%  Similarity=0.449  Sum_probs=56.0

Q ss_pred             CCEEEEEEEECCCCEEEEEE-CCCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf             83899999840576389995-7935874478748------8751152766999997611358702898715
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDL-GNSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSR  202 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdl-g~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSR  202 (526)
                      |.++.|+|.++.....+|++ ++.+|++|.+|.-      |.+.|++|+.++|.|.+|+.+.+  ++.||.
T Consensus         1 G~vv~G~V~~i~~~G~fV~~~~~i~Glvp~seis~~~v~~p~~~f~~Gq~V~v~Vl~vd~~~~--ri~LS~   69 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQ--RLLLSC   69 (70)
T ss_pred             CCEEEEEEEEEECCCEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCC--EEEEEC
T ss_conf             999999999998171899948996999898992832028989937799999999999808999--999971


No 39 
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938   This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=97.87  E-value=3.1e-05  Score=57.70  Aligned_cols=56  Identities=27%  Similarity=0.335  Sum_probs=51.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             12258884678888773211147775058888776530588999999999999999
Q gi|254780788|r  363 MQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLE  418 (526)
Q Consensus       363 ~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~  418 (526)
                      -+-.+|...+|+.|.++||.|++.||.|++.||+.+.|+.+..|.++++.|++++.
T Consensus         3 edLPGVGp~TA~KL~EaGy~t~~~iA~A~~~EL~~~~gI~E~~A~kiI~AAR~a~~   58 (333)
T TIGR02236         3 EDLPGVGPATAEKLREAGYDTLEAIAVASPKELSEIAGIGEGTAAKIIQAARKAAD   58 (333)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHHHHC
T ss_conf             65789757688998861078899984458579532037877789999999999846


No 40 
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.81  E-value=7.5e-05  Score=54.89  Aligned_cols=58  Identities=28%  Similarity=0.517  Sum_probs=53.1

Q ss_pred             CCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCE
Q ss_conf             0838999998405763899957935874478748------875115276699999761135870
Q gi|254780788|r  138 VGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRG  195 (526)
Q Consensus       138 ~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rg  195 (526)
                      +|+++.|+|+++..-.++|++++.+|++|.+|..      |++.|++||.++|.|.+++.+.+-
T Consensus         1 eG~iv~g~V~~i~~fG~FV~l~gi~Glihisels~~~~~~~~~~~k~Gd~v~~kVi~iD~~k~r   64 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKR   64 (68)
T ss_pred             CCCEEEEEEEEEECCEEEEEECCEEEEEECHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCE
T ss_conf             9999999999995638899979989999843646666689889147999999999999999798


No 41 
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=97.80  E-value=0.00012  Score=53.42  Aligned_cols=61  Identities=26%  Similarity=0.440  Sum_probs=54.8

Q ss_pred             CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf             838999998405763899957-93587447874------8875115276699999761135870289871
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLS  201 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lS  201 (526)
                      |+++.|+|+++..-.++|+|+ +.+|++|.++.      -|.+.|++||.++|.|.+|+.+.+  +|-||
T Consensus         1 G~iv~G~V~~i~~fG~FV~l~~~~~GLvhisels~~~~~~~~~~~~vGd~v~~kVi~id~e~~--ri~LS   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERG--RISLS   68 (68)
T ss_pred             CCEEEEEEEEEECEEEEEEECCCCEEEEECHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCC--EEECC
T ss_conf             999999999996528999914997899981897678767986857999999999999989999--88779


No 42 
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.76  E-value=0.00019  Score=51.88  Aligned_cols=62  Identities=29%  Similarity=0.495  Sum_probs=53.8

Q ss_pred             CCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCC-----CCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf             83899999840576389995793587447874887-----511527669999976113587028987159
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISR-----ENLRPGDRVKSYIYDVRREQRGPQVLLSRT  203 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~-----E~~~~Gdrika~i~~V~~~~rgpqi~lSRt  203 (526)
                      |++|+|+|....+|.++|++++.+|+||.++.-..     +.| .|..+++.|.++++..+  .+++||-
T Consensus         1 g~~v~g~I~~~~kGG~~v~~~gv~~FiP~Sq~~~~~~~~~~~~-vG~~i~~~Ii~~d~~~~--~ivvSrk   67 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEY-VGKELKFKIIEIDRERN--NIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCCEEEEECCEEEEEECHHCCCCCCCCHHHH-CCCEEEEEEEEEECCCC--EEEEECC
T ss_conf             9999999999985719999999999988025255456896897-89989999999927889--9999879


No 43 
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=97.76  E-value=0.00016  Score=52.42  Aligned_cols=65  Identities=26%  Similarity=0.295  Sum_probs=56.9

Q ss_pred             HHCCCEEEEEEEECCCCEEEEEEC---CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf             520838999998405763899957---935874478748------8751152766999997611358702898715
Q gi|254780788|r  136 DKVGEIISGTVKRVEYGNVIVDLG---NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSR  202 (526)
Q Consensus       136 ~r~Geiv~G~V~r~e~~~iiVdlg---~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSR  202 (526)
                      +.+|+++.|+|.++..-.++|+|+   +.+|++|-+|.-      |.+.|++||+++|.+.+|+.+.+  +|-||+
T Consensus         1 Pe~G~iv~G~V~~i~~~GafV~l~e~~g~eGlihiSEis~~~v~~~~d~~~~G~~v~~kVi~vD~~k~--~i~LS~   74 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKG--YIDLSK   74 (76)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCCCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEECCCC--EEEEEE
T ss_conf             98899999999999734699997336991999997996845115999955899999999999978999--998223


No 44 
>PRK07252 hypothetical protein; Provisional
Probab=97.70  E-value=0.00019  Score=51.89  Aligned_cols=66  Identities=23%  Similarity=0.358  Sum_probs=57.2

Q ss_pred             HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEECCC
Q ss_conf             20838999998405763899957-935874478748------875115276699999761135870289871598
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSRTH  204 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~  204 (526)
                      ++|+++.|+|.++..-.++|+|+ +++|+++-+|.-      |.+.|++||.|+|.|.+|+.+.+  +|-||.-.
T Consensus         2 kvGdiv~G~V~~I~~fGaFV~l~~gv~GLiHISEis~~~v~~~~~~~kvGd~V~vkVi~ID~e~~--rIsLSiK~   74 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGNEVLVQVIDIDEYTK--KASLSMRT   74 (120)
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCC--EEECCHHH
T ss_conf             88889999999997545799957995788886660102004999947899999999999868999--88613633


No 45 
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase  is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=97.69  E-value=0.00017  Score=52.32  Aligned_cols=61  Identities=28%  Similarity=0.444  Sum_probs=52.9

Q ss_pred             CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf             838999998405763899957-93587447874------88751152766999997611358702898715
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSR  202 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSR  202 (526)
                      |+++.|+|.++..-.++|+|+ +.+|+++-+|.      -|.+.|++||.++|.+.+++...   .|-|||
T Consensus         1 G~iv~G~V~~i~~fG~FV~l~~g~~GLiHiSeis~~~v~~~~~~~~~Gd~v~vkVi~iD~~~---ri~LSr   68 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRG---RISLSR   68 (68)
T ss_pred             CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCC---CCCCCC
T ss_conf             99999999999732999995799624888689345654698890789999999999999999---720529


No 46 
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938   This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=97.69  E-value=4.3e-05  Score=56.71  Aligned_cols=58  Identities=26%  Similarity=0.361  Sum_probs=53.6

Q ss_pred             HHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             664077999899999998798478896532677521231234443211245334358899999999998412257
Q gi|254780788|r  436 ELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMG  510 (526)
Q Consensus       436 ~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~~g  510 (526)
                      +|.+|||+.+.++.+|-++|..|++.+|--|..||..+.                 ++++..|.++|+.||+-++
T Consensus         1 ~ledLPGVGp~TA~KL~EaGy~t~~~iA~A~~~EL~~~~-----------------gI~E~~A~kiI~AAR~a~~   58 (333)
T TIGR02236         1 DLEDLPGVGPATAEKLREAGYDTLEAIAVASPKELSEIA-----------------GIGEGTAAKIIQAARKAAD   58 (333)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHC-----------------CCCHHHHHHHHHHHHHHHC
T ss_conf             966578975768899886107889998445857953203-----------------7877789999999999846


No 47 
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions.  Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.69  E-value=0.00019  Score=51.99  Aligned_cols=66  Identities=33%  Similarity=0.575  Sum_probs=57.1

Q ss_pred             HCCCEEEEEEEECCCCEEEEEE-C-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCC
Q ss_conf             2083899999840576389995-7-93587447874------8875115276699999761135870289871598
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDL-G-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTH  204 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdl-g-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~  204 (526)
                      ++|+++.|+|.++..-.++|++ | +.+|+++.+|.      -|.+.|++||.++|.|.+++.+.+  +|-||.-.
T Consensus         1 kVG~~v~G~V~~i~~fG~FV~l~g~~i~GLvHiSels~~~~~~~~~~~~~Gd~V~vkVl~iD~e~~--rI~LSiKa   74 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKK--RISLGLKA   74 (77)
T ss_pred             CCCCEEEEEEEEEECEEEEEEECCCCEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCC--EEEEEEEC
T ss_conf             998999999999964178999678980799887881756568988916899999999999989999--99989841


No 48 
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.60  E-value=0.00043  Score=49.35  Aligned_cols=124  Identities=15%  Similarity=0.211  Sum_probs=78.4

Q ss_pred             ECCCCCCCCEECHHHHHHHCCCCCCCCEEEEECCHH-HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEE
Q ss_conf             176778753234899986288986473799850845-62-0799999999999999999988779999852083899999
Q gi|254780788|r   69 VEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPM-DF-GRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTV  146 (526)
Q Consensus        69 Vedved~~~eI~l~~A~~~~~~~~iGD~i~~~i~~~-~f-gRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V  146 (526)
                      |+-......-|++++-   ....++||.+..-++.. ++ |+.+-.-||+.-       -...+-..  -..|++|+|+|
T Consensus       339 vdvG~KsEg~ip~~eF---~~~~~vGD~v~V~ie~~e~~~~~LSr~kA~r~~-------~w~~le~a--~~~~~~v~G~i  406 (863)
T PRK12269        339 VDIGGKSEGRVPVEEF---EAPPKAGDGVRVYVERVTPYGPELSKTKADRLG-------LKVKLRDA--ERDGTPVEGRI  406 (863)
T ss_pred             EECCCCCCCCCCHHHC---CCCCCCCCEEEEEEEEECCCCCEECHHHHHHHH-------HHHHHHHH--HHCCCEEEEEE
T ss_conf             9647744553269992---778899999999999970889756189998789-------99999999--75699079999


Q ss_pred             EECC--CCEEEEEEC-CCEEEEEHHHC----CCCCCCCCCCEEEEEEEEECCC--CCE-EEEEEECCC
Q ss_conf             8405--763899957-93587447874----8875115276699999761135--870-289871598
Q gi|254780788|r  147 KRVE--YGNVIVDLG-NSDGVIRRDET----ISRENLRPGDRVKSYIYDVRRE--QRG-PQVLLSRTH  204 (526)
Q Consensus       147 ~r~e--~~~iiVdlg-~~ea~Lp~~e~----ip~E~~~~Gdrika~i~~V~~~--~rg-pqi~lSRt~  204 (526)
                      .|+.  +|.+.|||| ++.|+||-++-    ++.-.+-.|....+.+..+...  .|| ..|++||..
T Consensus       407 ~~~~~vkgG~~Vdl~~gv~AFLPgSqvd~rpv~d~~~~~g~~~~f~iik~~~~~~~r~~~NiVvSRra  474 (863)
T PRK12269        407 VRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPESLIGLTSKFYIERISQSKQHRGNDNIVINRRR  474 (863)
T ss_pred             EECCCCCCCEEEECCCCCEEECCHHHCCCEECCCCHHHCCCCCCEEEEEEEHHHHCCCCCCEEEECHH
T ss_conf             74461045379985889678676656471136886321588741599995313312677888997679


No 49 
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=97.53  E-value=0.00061  Score=48.21  Aligned_cols=99  Identities=21%  Similarity=0.314  Sum_probs=69.6

Q ss_pred             CCCCCCCHHHHHHHHHHHH-HHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH--C
Q ss_conf             1225888467888877321-114777505888877653058899999999999999999999898775428435664--0
Q gi|254780788|r  363 MQAINVDEIIAHLLVAEGF-ADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELC--S  439 (526)
Q Consensus       363 ~e~LdVDE~iA~~LV~eGf-~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~--~  439 (526)
                      |+.-++.+.+.+.|++.|| .++.+|.....++|..++||.+..|..|.+.-..         .   +......=|.  .
T Consensus       448 mdI~GlG~~~i~~L~~~g~i~~~~Diy~L~~~~L~~l~gfgeKsa~nLl~aIe~---------S---K~~~l~r~L~ALG  515 (668)
T PRK07956        448 MDIDGLGEKIIEQLFEKGLIHTPADLFKLTEEDLLQLEGFGEKSAQNLLDAIEK---------S---KETPLARFLYALG  515 (668)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCCHHHHHCCCHHHHHCCCCHHHHHHHHHHHHHHH---------H---CCCCHHHHHHHCC
T ss_conf             164665999999998768766589997288545402123556699999999998---------5---4775888998627


Q ss_pred             CCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf             77999899999998798478896532677521231
Q gi|254780788|r  440 IPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS  474 (526)
Q Consensus       440 l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~  474 (526)
                      ++++....+-.|+.+ .+|++.|...+.++|..+.
T Consensus       516 I~~VG~~~Ak~La~~-f~sl~~l~~as~e~L~~I~  549 (668)
T PRK07956        516 IRHVGEKAAKALARH-FGSLEALEAASEEELAAVE  549 (668)
T ss_pred             CCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHCCC
T ss_conf             864129999999999-6689999708999985768


No 50 
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.44  E-value=0.00082  Score=47.26  Aligned_cols=61  Identities=30%  Similarity=0.543  Sum_probs=53.1

Q ss_pred             CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf             838999998405763899957-93587447874------88751152766999997611358702898715
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSR  202 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSR  202 (526)
                      |+++.|+|.++..-.++|+++ +.+|+++-+|.      -|.+.|++||.+++.+.+++.  +| .|-||+
T Consensus         1 G~vv~G~V~~I~~fGaFV~l~~g~~GL~HiSeis~~~v~~~~~~~~~Gd~v~vkVi~id~--~~-ri~LS~   68 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA--RG-RISLSI   68 (69)
T ss_pred             CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECC--CC-CEEECC
T ss_conf             999999999998538999968998899996983456557988917899999999999999--99-668015


No 51 
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=97.40  E-value=0.00033  Score=50.22  Aligned_cols=56  Identities=32%  Similarity=0.395  Sum_probs=51.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             11225888467888877321114777505888877653058899999999999999
Q gi|254780788|r  362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYL  417 (526)
Q Consensus       362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L  417 (526)
                      +.+-.+|....++.|-++||.|+++++++++.+|.++.|+++..|.+++..|++.+
T Consensus         9 l~~lpGv~~~~~~kL~~aG~~tv~~l~~~~~~~L~~~~gis~~~a~ki~~~a~~~~   64 (318)
T PRK04301          9 LEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEIAGISESTAAKIIEAAREAL   64 (318)
T ss_pred             CCCCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf             45589989999999998699549998748999999850999999999999999853


No 52 
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=97.39  E-value=0.002  Score=44.39  Aligned_cols=75  Identities=25%  Similarity=0.354  Sum_probs=62.5

Q ss_pred             HHCCCEEEEEEEECCCCEEEEEE---CCCEEEEEHHHCCC------CCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHH
Q ss_conf             52083899999840576389995---79358744787488------7511527669999976113587028987159889
Q gi|254780788|r  136 DKVGEIISGTVKRVEYGNVIVDL---GNSDGVIRRDETIS------RENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQ  206 (526)
Q Consensus       136 ~r~Geiv~G~V~r~e~~~iiVdl---g~~ea~Lp~~e~ip------~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~  206 (526)
                      +.+|++|.|+|.++..-..+|+|   |+.+|++|-+|..+      ++.+++|+++.|.|..|+.+.+.--+-+-|.+|+
T Consensus         6 Pe~g~~v~~~V~~i~~~Ga~v~l~ey~~~eG~i~isEis~~~v~~i~d~~k~G~~v~~kVi~vd~~kg~IdLS~k~Vs~~   85 (262)
T PRK03987          6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVCKVIRVDPKKGHIDLSLKRVNEH   85 (262)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCCCCCCEEEEHHHCCHHHHHCHHHHCCCCCEEEEEEEEECCCCCEEEEECCCCCHH
T ss_conf             99998899999999566799993565993167887983467751999851589889999998838788787110449989


Q ss_pred             HHHH
Q ss_conf             9999
Q gi|254780788|r  207 FMVK  210 (526)
Q Consensus       207 ~l~~  210 (526)
                      =.++
T Consensus        86 e~~~   89 (262)
T PRK03987         86 QRRE   89 (262)
T ss_pred             HHHH
T ss_conf             9999


No 53 
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=97.38  E-value=0.00087  Score=47.07  Aligned_cols=58  Identities=26%  Similarity=0.426  Sum_probs=50.1

Q ss_pred             EEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf             999998405763899957-935874478748------875115276699999761135870289871
Q gi|254780788|r  142 ISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLS  201 (526)
Q Consensus       142 v~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lS  201 (526)
                      +.|+|.++....++|+++ +.+|++|.++..      |.+.|++||.++|.+.+++...+  .+.||
T Consensus         1 v~G~V~~i~~~G~fV~~~~~~~gli~~s~~s~~~~~~~~~~~~~G~~V~~~Vi~vd~~~~--~i~LS   65 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKG--RISLS   65 (65)
T ss_pred             CEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCHHHEECCCCEEEEEEEEEECCCC--EEECC
T ss_conf             989999997845999989871788988891676535951098599999999999989999--89769


No 54 
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.33  E-value=0.0021  Score=44.29  Aligned_cols=63  Identities=27%  Similarity=0.432  Sum_probs=56.7

Q ss_pred             HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf             20838999998405763899957-93587447874------8875115276699999761135870289871
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLS  201 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lS  201 (526)
                      ++|.++.|.|.++....++|+|| +.+|.....|.      -|.+.|+.||.++|-+.+|..+.|  +|-||
T Consensus         2 kvG~~l~G~Vt~V~~~g~fV~L~~~~~Glvhisel~dd~~~~~~~~~~~g~~V~v~Vl~VD~~~k--rI~LS   71 (73)
T cd05706           2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNK--KIALS   71 (73)
T ss_pred             CCCCEEEEEEEEECCCEEEEEECCCCEEEEEHHHHCCCCCCCCHHHCCCCCEEEEEEEEEECCCC--EEEEE
T ss_conf             88989999999988887999908994799998993046013817516899999999999988899--89886


No 55 
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.30  E-value=0.0013  Score=45.89  Aligned_cols=56  Identities=21%  Similarity=0.452  Sum_probs=50.8

Q ss_pred             CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC-------CCCCCCCCCEEEEEEEEECCCCC
Q ss_conf             838999998405763899957-935874478748-------87511527669999976113587
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI-------SRENLRPGDRVKSYIYDVRREQR  194 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i-------p~E~~~~Gdrika~i~~V~~~~r  194 (526)
                      |+++.|+|.++..-.++|+|. +.+|+++.+|+.       |.+.|+.||.++|.|.+++.+.+
T Consensus         1 G~~v~G~V~~i~~fG~FV~l~~gieGLvHiselsw~~~~~~~~~~~~~Gd~V~vkVl~iD~e~~   64 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERE   64 (69)
T ss_pred             CCEEEEEEEEECCCEEEEEECCCCEEEEEHHHHCCCCCCCCHHHCCCCCCEEEEEEEEEECCCC
T ss_conf             9999999999913189999769965999948824566667976825899999999999979868


No 56 
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.26  E-value=0.00064  Score=48.06  Aligned_cols=70  Identities=26%  Similarity=0.490  Sum_probs=56.7

Q ss_pred             ECCCCHHHHHH--HHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCH
Q ss_conf             55987899999--76286654248987567879999853422110254427899999861674578552200
Q gi|254780788|r  278 VWSPDSATFVI--NALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEED  347 (526)
Q Consensus       278 ~ws~d~~~fi~--nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~~  347 (526)
                      ..+.+.-.|+.  ..+.-|.+...++|++..+..-+|++.++.+||||+|.|++-.+.+.|-+|||.-.++.
T Consensus         4 ~l~~e~~ryi~lFe~~T~~~~~DCi~d~~~~riiFvV~~g~mG~AIGk~G~~Ik~l~~~lgkkIdiVe~seD   75 (142)
T PRK08406          4 KLTTEEIRYIALFESITGATVRDCIIDEEYDRIIFVVKEGDMGLAIGKGGENVKRLKEKLGKDIELVEYSED   75 (142)
T ss_pred             EECHHHHHHHHHHHHHHCCCEEEEEECCCCCEEEEEECCCHHHHHHCCCCCHHHHHHHHHCCCEEEEECCCC
T ss_conf             988899999999999879972356870899889999876768897587960799999985894589964789


No 57 
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.24  E-value=0.0017  Score=44.92  Aligned_cols=59  Identities=22%  Similarity=0.357  Sum_probs=52.5

Q ss_pred             HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC-------CCCCCCCCCEEEEEEEEECCCCCE
Q ss_conf             20838999998405763899957-935874478748-------875115276699999761135870
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI-------SRENLRPGDRVKSYIYDVRREQRG  195 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i-------p~E~~~~Gdrika~i~~V~~~~rg  195 (526)
                      .+|.+++|+|.++..-.++|+|+ +.+|+++-+|+-       |.+.|++||.+++.|.+++.+.|-
T Consensus         2 ~~G~~v~G~V~~It~fG~FV~i~~g~eGLvHiSelsw~~~~~~p~~~~~~Gd~v~vkIl~iD~e~~r   68 (72)
T cd05689           2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRR   68 (72)
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCE
T ss_conf             8899999999899476239996699389999766316546679636038999999999999599799


No 58 
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.17  E-value=0.0021  Score=44.28  Aligned_cols=61  Identities=25%  Similarity=0.464  Sum_probs=53.5

Q ss_pred             CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf             838999998405763899957-935874478748------875115276699999761135870289871
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLS  201 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lS  201 (526)
                      |+++.|+|+++..-.++|+|| +.+|++|-++..      |.+.|++|+.+++-|.+++.+.+  +|-||
T Consensus         1 G~~v~G~V~~i~~~G~FV~l~~~~~glVhiselsd~fVkd~~~~f~vGq~V~~kV~~iD~~~~--ri~LS   68 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNG--RIEMT   68 (68)
T ss_pred             CCEEEEEEEEECCCCEEEEECCCCEEEEEHHHHCHHHHCCHHHHCCCCCEEEEEEEEEECCCC--EEECC
T ss_conf             999899999803640799917996799995991723564998917999999999999828758--67359


No 59 
>PRK05807 hypothetical protein; Provisional
Probab=97.17  E-value=0.0019  Score=44.52  Aligned_cols=64  Identities=27%  Similarity=0.455  Sum_probs=54.9

Q ss_pred             HCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf             20838999998405763899957935874478748------87511527669999976113587028987159
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSRT  203 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt  203 (526)
                      .+|+++.|+|.++..-..+|+|++.+|+++-+|.-      +.+.|+.||.|+|.|..|..  +| .|-||.-
T Consensus         4 evG~iv~G~V~~I~~fGaFV~l~g~~GLvHISEis~~~Vk~i~d~lk~Gd~V~vkVl~iD~--~g-kI~LSiK   73 (136)
T PRK05807          4 EAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD--NG-KISLSIK   73 (136)
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECC--CC-CCEEEHH
T ss_conf             5788999999999724479997892768985670776436999967899999999999899--99-8143322


No 60 
>PRK01172 ski2-like helicase; Provisional
Probab=97.17  E-value=0.018  Score=37.38  Aligned_cols=107  Identities=16%  Similarity=0.161  Sum_probs=73.8

Q ss_pred             HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHCCHHHH---HHCCCCCCHHHHHH
Q ss_conf             75058888776530588999999999999999-------------999998987754284356---64077999899999
Q gi|254780788|r  387 LACVKISEIASIEGFDEETAVEIQGRAREYLE-------------GIDITLQKKIRELGVSEE---LCSIPGIDSKIKVA  450 (526)
Q Consensus       387 Ia~a~~eeL~~IeGfdee~a~eL~~rA~~~L~-------------~~~~~~~e~~~e~~~~e~---L~~l~gl~~~~~~~  450 (526)
                      +..++...+.+--|++.-....+.+.|.-+.-             ......-..+-..|+.++   |+.++|+...-+-+
T Consensus       548 i~E~~~~~I~~~y~v~~G~lq~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~l~~Rl~~Gv~~eLl~L~~I~gigr~RAR~  627 (674)
T PRK01172        548 ISEASMQKITDTYGIAPGDVQARASSADWISYSLARLSSIYKPEMRRKLEILNIRIKEGIREDLIDLVLIPKVGRVRARR  627 (674)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHH
T ss_conf             73899999999869894899999999999999999999861199999999999999819868889771889999899999


Q ss_pred             HHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             998798478896532677521231234443211245334358899999999998412257
Q gi|254780788|r  451 LGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMG  510 (526)
Q Consensus       451 L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~~g  510 (526)
                      |-++||+|++|+|..+.++|..+.                 +++..-|.++|=.||.=++
T Consensus       628 Ly~aG~~s~~dia~a~~~~L~~i~-----------------g~~~~~A~~Ii~~A~~l~~  670 (674)
T PRK01172        628 LYDAGFKTVDDIARSSPERIKKIY-----------------GFSDTLANAIVNRAMKISS  670 (674)
T ss_pred             HHHCCCCCHHHHHHCCHHHHHHCC-----------------CCCHHHHHHHHHHHHHHHH
T ss_conf             998699999999709998987641-----------------9899999999999997775


No 61 
>PRK01172 ski2-like helicase; Provisional
Probab=97.07  E-value=0.0015  Score=45.36  Aligned_cols=57  Identities=26%  Similarity=0.335  Sum_probs=50.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             112258884678888773211147775058888776530588999999999999999
Q gi|254780788|r  362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLE  418 (526)
Q Consensus       362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~  418 (526)
                      |+...+|....|..|+.+||+|+++||.+++++|.+|.|+....|..+++.|+..+.
T Consensus       614 L~~I~gigr~RAR~Ly~aG~~s~~dia~a~~~~L~~i~g~~~~~A~~Ii~~A~~l~~  670 (674)
T PRK01172        614 LVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRAMKISS  670 (674)
T ss_pred             HCCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHH
T ss_conf             718899998999999986999999997099989876419899999999999997775


No 62 
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.02  E-value=0.0041  Score=42.13  Aligned_cols=64  Identities=22%  Similarity=0.352  Sum_probs=55.3

Q ss_pred             HCCCEEEEEEEECCCCEEEEEEC--CCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf             20838999998405763899957--93587447874887511527669999976113587028987
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLG--NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLL  200 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg--~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~l  200 (526)
                      ..|-+++|.|+.+|-..+++|+|  +..|+||+++.-+...+++|.-+-|.|..|+...|-.++-.
T Consensus         3 ~~g~~l~a~V~SvEDHGyild~Gi~~~~gFl~~k~~~~~~~l~~G~v~~c~V~~v~~~g~vv~ls~   68 (74)
T cd05694           3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNFSKLKVGQLLLCVVEKVKDDGRVVSLSA   68 (74)
T ss_pred             CCCCEEEEEEEEEECCEEEEECCCCCCEEEEEHHHCCCCCCCCCCCEEEEEEEEEECCCEEEEEEC
T ss_conf             678299999856714418998477772667301334755633488789999999928960999966


No 63 
>PRK08582 hypothetical protein; Provisional
Probab=96.98  E-value=0.0039  Score=42.27  Aligned_cols=63  Identities=24%  Similarity=0.390  Sum_probs=54.0

Q ss_pred             HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf             20838999998405763899957-935874478748------8751152766999997611358702898715
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSR  202 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSR  202 (526)
                      .+|+++.|+|.++..-.++|+|+ +.+|+++-+|.-      +.+.|++||.|+|-|.+|..+.   .|-||-
T Consensus         4 evG~iv~G~V~~I~~fGaFV~l~~g~~GLvHISeis~~~V~~i~d~lkvGd~V~vKVi~id~~g---KI~LSi   73 (139)
T PRK08582          4 EVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLSVGDEVEVKVLNVEDDG---KIGLSI   73 (139)
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCC---CEEEEH
T ss_conf             4787999999899641789995699667887366256656899995789999999999888999---705165


No 64 
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=96.89  E-value=0.0027  Score=43.44  Aligned_cols=22  Identities=5%  Similarity=0.099  Sum_probs=13.3

Q ss_pred             HHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             9998623999999999999999
Q gi|254780788|r   14 DAVAYEKSIDRDVVLSVMADSI   35 (526)
Q Consensus        14 e~va~EK~I~~e~i~~aie~Al   35 (526)
                      ..+++.+||+...+..+++.|-
T Consensus        40 ~~L~~~~gis~~~a~ki~~~a~   61 (318)
T PRK04301         40 KELSEIAGISESTAAKIIEAAR   61 (318)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHH
T ss_conf             9999850999999999999999


No 65 
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=96.88  E-value=0.0071  Score=40.37  Aligned_cols=58  Identities=26%  Similarity=0.402  Sum_probs=50.2

Q ss_pred             CCCEEEEEEEECCCCEEEEEEC--CCEEEEEHHHCC-----------------CCCCCCCCCEEEEEEEEECCCCCE
Q ss_conf             0838999998405763899957--935874478748-----------------875115276699999761135870
Q gi|254780788|r  138 VGEIISGTVKRVEYGNVIVDLG--NSDGVIRRDETI-----------------SRENLRPGDRVKSYIYDVRREQRG  195 (526)
Q Consensus       138 ~Geiv~G~V~r~e~~~iiVdlg--~~ea~Lp~~e~i-----------------p~E~~~~Gdrika~i~~V~~~~rg  195 (526)
                      +|+...|+|..+..-.++|.|.  .+||++|.++.-                 ++..|+.||++++-|.+|....+.
T Consensus         1 IG~~f~g~I~~v~~~GiFV~l~~~~ieGli~~~~l~~d~y~~d~~~~~l~g~~~~~~~~lGd~v~V~i~~vd~~~~~   77 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRK   77 (83)
T ss_pred             CCCEEEEEEEEEEEEEEEEEEECCCEEEEEECCCCCCCCEEECCCCEEEECCCCCCEEECCCEEEEEEEEEECCCCE
T ss_conf             99999999998983069999828873999982214567224474021898134775997899999999999430398


No 66 
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The  N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide.  The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=96.73  E-value=0.0091  Score=39.59  Aligned_cols=61  Identities=20%  Similarity=0.369  Sum_probs=50.4

Q ss_pred             CCEEEEEEEECCCCEEEEEEC----CCEEEEEHHHCC-------CCCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf             838999998405763899957----935874478748-------87511527669999976113587028987159
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDLG----NSDGVIRRDETI-------SRENLRPGDRVKSYIYDVRREQRGPQVLLSRT  203 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdlg----~~ea~Lp~~e~i-------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt  203 (526)
                      |+++.|+|+++..-..+|+|.    +.+|++.-+|.-       |.+.|++||++++-|.++++.    .|-||+.
T Consensus         1 G~i~~G~V~~i~~fGaFV~l~~~~~~~~GLvHiSeis~~~~~~~~~~~~~~G~~V~vkVi~id~~----ki~LS~K   72 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNG----KISLSMK   72 (79)
T ss_pred             CCEEEEEEEEEEEEEEEEEEECCCCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEECC----EEEEEEE
T ss_conf             99999999899753399999678898067899568157555589889367999999999998699----8887226


No 67 
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.71  E-value=0.0016  Score=45.07  Aligned_cols=170  Identities=26%  Similarity=0.405  Sum_probs=96.9

Q ss_pred             CCCEEEEEEEEECCCCCEEEE---EEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCC-EEEEEEEECCCCCCCEEE
Q ss_conf             276699999761135870289---8715988999999997667775580878566316775-034999940899881276
Q gi|254780788|r  178 PGDRVKSYIYDVRREQRGPQV---LLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGS-RAKLAVFSSDSSIDPVGA  253 (526)
Q Consensus       178 ~Gdrika~i~~V~~~~rgpqi---~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~-RsKIAV~s~d~~iDpVGA  253 (526)
                      .|.||++++.+    -+|=.|   .-|--...|+..-+.   |      -++.+|-=++-. ++.|.|  .|.   -.--
T Consensus       255 rGsRI~~I~~E----L~gEkIDIi~~s~d~~~fi~nAls---P------A~v~~V~ide~~~~~~VvV--~d~---qlSl  316 (428)
T PRK09202        255 RGSRIQAISNE----LNGEKIDIILWSDDPAQFIINALS---P------AEVSSIVVDEDKHSMDVVV--PDD---QLSL  316 (428)
T ss_pred             CCCCHHHHHHH----HCCCEEEEEECCCCHHHHHHHHCC---C------CCCEEEEECCCCCEEEEEE--CCC---CHHH
T ss_conf             86429999987----467768999678888999998179---4------2121899727788899998--865---2247


Q ss_pred             EECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHH
Q ss_conf             55488621788998627782679955987899999762866542489875678799998534221102544278999998
Q gi|254780788|r  254 CVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQ  333 (526)
Q Consensus       254 cVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas~  333 (526)
                      .+|-+|.-|+-- ..|-|=+|||...++--..-..                                     ...+.. .
T Consensus       317 AIGk~GqNvrLA-s~Ltgw~IdI~s~~~~~e~~~~-------------------------------------e~~~~~-~  357 (428)
T PRK09202        317 AIGKNGQNVRLA-SKLTGWKIDIMTEEEASEKQQA-------------------------------------EFARLI-D  357 (428)
T ss_pred             HHCCCCEEHHHH-HHHHCCEEEEEEHHHHHHHHHH-------------------------------------HHHHHH-H
T ss_conf             757786859999-9977986999558999998777-------------------------------------888899-9


Q ss_pred             HHCCEEEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             61674578552200110100122100011122588846788887732111477750588887765305889999999999
Q gi|254780788|r  334 LTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRA  413 (526)
Q Consensus       334 Ltg~~idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA  413 (526)
                      +..-.+++   .+       .+....+.+....++++..+..|+.+||.|+++++.++.++|..++|++++.+.+|...|
T Consensus       358 ~f~~~~~~---~e-------~~~~~~~~l~~~~~~~~~~~~~l~~~g~~~~edl~~~~~del~~~~~~~~e~a~~li~~a  427 (428)
T PRK09202        358 LFMEALDV---DE-------DIAQLADDLLNLEGLDPELAFKLAEKGVKTLEDLAELAVDELIDIEGLDEEEAGELIMAA  427 (428)
T ss_pred             HHHHHCCC---HH-------HHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHC
T ss_conf             87775262---28-------888877778645699999999999869987999965798889637798999999999841


Q ss_pred             H
Q ss_conf             9
Q gi|254780788|r  414 R  414 (526)
Q Consensus       414 ~  414 (526)
                      +
T Consensus       428 r  428 (428)
T PRK09202        428 R  428 (428)
T ss_pred             C
T ss_conf             9


No 68 
>PTZ00035 Rad51; Provisional
Probab=96.70  E-value=0.0031  Score=43.05  Aligned_cols=56  Identities=20%  Similarity=0.307  Sum_probs=50.9

Q ss_pred             CCCCC---CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             11225---888467888877321114777505888877653058899999999999999
Q gi|254780788|r  362 FMQAI---NVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYL  417 (526)
Q Consensus       362 f~e~L---dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L  417 (526)
                      .++.|   +|...-.+.|-++||.|++.|++++..+|..|.||.+-.|++|++.|+..+
T Consensus        34 ~i~~l~~~Gi~~~di~kl~~aG~~tv~~v~~~~~k~L~~ikgise~k~~Ki~~~a~k~~   92 (350)
T PTZ00035         34 KIEQLLAKGFVKRDLELLKEGGLQTVECVAYAPMRTLCAIKGISEQKAEKLKKACKELC   92 (350)
T ss_pred             CHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHC
T ss_conf             29999877999899999998491248999850999897737946999999999999755


No 69 
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=96.70  E-value=0.0083  Score=39.89  Aligned_cols=56  Identities=29%  Similarity=0.472  Sum_probs=49.1

Q ss_pred             HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCC
Q ss_conf             20838999998405763899957-93587447874887511527669999976113587
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQR  194 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~r  194 (526)
                      .+|++..|+|.++..=.++|+|+ +.+|.+..++..+  .|++||.+.+-+.+++...|
T Consensus        15 evG~~y~G~V~~v~~fGaFV~l~~~~~GLiHiS~l~~--~~~vGD~V~VkV~~I~~~Gk   71 (77)
T cd04473          15 EVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLR--DYEVGDEVIVQVTDIPENGN   71 (77)
T ss_pred             CCCCEEEEEEEEEEECCEEEECCCCCEEEEEEHHCCC--CCCCCCEEEEEEEEECCCCC
T ss_conf             2399999999889662889992699879689316668--78999999999999999997


No 70 
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=96.69  E-value=0.0083  Score=39.87  Aligned_cols=68  Identities=25%  Similarity=0.411  Sum_probs=56.9

Q ss_pred             CEEEEEEEECCCCEEEEEECCCEEEEEHHHC-----------------CCCCCCCCCCEEEEEEEEECCCC---CEEEEE
Q ss_conf             3899999840576389995793587447874-----------------88751152766999997611358---702898
Q gi|254780788|r  140 EIISGTVKRVEYGNVIVDLGNSDGVIRRDET-----------------ISRENLRPGDRVKSYIYDVRREQ---RGPQVL  199 (526)
Q Consensus       140 eiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~-----------------ip~E~~~~Gdrika~i~~V~~~~---rgpqi~  199 (526)
                      |++.|+|..+..-.++|.||.+||+++-+++                 =.+..|+.||++++-|..|..+.   ..+.|-
T Consensus         1 Ev~eG~Vs~Vt~fG~FV~L~~ieGLvHiS~l~dD~~~fd~~~~~liG~r~~~~~~~GD~V~vrV~~V~~~~r~i~~~~Ig   80 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIG   80 (99)
T ss_pred             CEEEEEEEEEEECCEEEEECCCEEEEEHHHCCCCEEEECHHHCEEEECCCCCEECCCCEEEEEEEEEECCCCCCCCCEEE
T ss_conf             97999999588256699932810689936757843998124468985127869847999999999980620676764665


Q ss_pred             EECCCHHH
Q ss_conf             71598899
Q gi|254780788|r  200 LSRTHPQF  207 (526)
Q Consensus       200 lSRt~p~~  207 (526)
                      ||.-.|.+
T Consensus        81 Ltmrqp~l   88 (99)
T cd04460          81 LTMRQPGL   88 (99)
T ss_pred             ECCCCCCC
T ss_conf             02247889


No 71 
>PTZ00162 RNA polymerase II subunit 7; Provisional
Probab=96.67  E-value=0.011  Score=39.07  Aligned_cols=72  Identities=14%  Similarity=0.193  Sum_probs=56.0

Q ss_pred             HHHHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCC----------------CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf             9852083899999840576389995793587447874887----------------511527669999976113587028
Q gi|254780788|r  134 FKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISR----------------ENLRPGDRVKSYIYDVRREQRGPQ  197 (526)
Q Consensus       134 f~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~----------------E~~~~Gdrika~i~~V~~~~rgpq  197 (526)
                      |+.-.||++.|.|..+..-.+++++|..+++++++..-+.                ...+.||++|+-|..++.+.+..+
T Consensus        77 fkP~~~EVvdg~V~~v~~~G~fv~~GPl~~fv~~s~i~~d~~yd~~~~~~~~~~~~~~i~kgd~VR~rIvg~~~~~~~~~  156 (170)
T PTZ00162         77 FKPFKDEVLDAIVTDVNKLGFFAQAGPLKIFVSRTAIPPNFVYDSDSAYPCFSDGTISIKPQSEVRLRLQGIRYDNSNLF  156 (170)
T ss_pred             EECCCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHCCCCCEECCCCCCCEECCCCCEECCCCEEEEEEEEEEECCCCCE
T ss_conf             93367989999999996407999912808998989999864897899860482788388889999999999873556746


Q ss_pred             EEEECCCH
Q ss_conf             98715988
Q gi|254780788|r  198 VLLSRTHP  205 (526)
Q Consensus       198 i~lSRt~p  205 (526)
                      .+.|-..|
T Consensus       157 aigtm~~d  164 (170)
T PTZ00162        157 AIATINSD  164 (170)
T ss_pred             EEEEECCC
T ss_conf             99996687


No 72 
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=96.62  E-value=0.0085  Score=39.80  Aligned_cols=74  Identities=28%  Similarity=0.485  Sum_probs=61.3

Q ss_pred             HHHHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCC-----------------CCCCCCCEEEEEEEEEC---CCC
Q ss_conf             9852083899999840576389995793587447874887-----------------51152766999997611---358
Q gi|254780788|r  134 FKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISR-----------------ENLRPGDRVKSYIYDVR---REQ  193 (526)
Q Consensus       134 f~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~-----------------E~~~~Gdrika~i~~V~---~~~  193 (526)
                      |+.-.||++.|.|..+..-.++|.+|-.++++.+++..+-                 -.|+.||.||+=|..+.   .++
T Consensus        77 frPf~~EVv~g~V~~~~~~G~fv~~Gp~d~~vh~sqi~dd~~~fD~~~~~~ig~~s~~~i~~Gd~VR~RIv~vs~~~~~~  156 (182)
T PRK08563         77 FKPELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDEKNGALIGKESKRTLKVGDVVRARIVAVSLNEREP  156 (182)
T ss_pred             EECCCCCEEEEEEEEEECCEEEEEEECCCEEEEHHHCCCCCCEECCCCCEEEEECCCEEECCCCEEEEEEEEEECCCCCC
T ss_conf             94136848999999996676999984661176099947776238365651999068649828998999999977188887


Q ss_pred             CEEEEEEECCCHHH
Q ss_conf             70289871598899
Q gi|254780788|r  194 RGPQVLLSRTHPQF  207 (526)
Q Consensus       194 rgpqi~lSRt~p~~  207 (526)
                      +++.|-|+...|.|
T Consensus       157 ~~~kIglTmrq~gL  170 (182)
T PRK08563        157 RDSKIGLTMRQPGL  170 (182)
T ss_pred             CCCEEEEEECCCCC
T ss_conf             76626689538887


No 73 
>PRK00254 ski2-like helicase; Provisional
Probab=96.50  E-value=0.0039  Score=42.25  Aligned_cols=105  Identities=22%  Similarity=0.246  Sum_probs=73.9

Q ss_pred             HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH-------H--------HHHHHHHHHHCCHHHH---HHCCCCCCHHHH
Q ss_conf             750588887765305889999999999999999-------9--------9998987754284356---640779998999
Q gi|254780788|r  387 LACVKISEIASIEGFDEETAVEIQGRAREYLEG-------I--------DITLQKKIRELGVSEE---LCSIPGIDSKIK  448 (526)
Q Consensus       387 Ia~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~-------~--------~~~~~e~~~e~~~~e~---L~~l~gl~~~~~  448 (526)
                      +...+..++.+--|++.-.+..+++.|.-+.-.       .        ....-...-..|+.++   |+.++|+...-+
T Consensus       578 i~E~~~~~I~~ky~v~~G~lq~l~~~a~~~a~~~~~~~~~l~~~~~~~~~l~~l~~Rl~~Gv~~ELl~L~~I~gvgr~RA  657 (717)
T PRK00254        578 INEVPEGEIVEKYNVEPGDIYRIVETAEWLVYSLKEIAKVLEASQDVVDYLETLRLRVKHGIREELIPLMELPMIGRKRA  657 (717)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHCCCCCCCHHHH
T ss_conf             55999999999879697899999999999999999999983851889999999999998099765683564899898999


Q ss_pred             HHHHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             999987984788965326775212312344432112453343588999999999984122
Q gi|254780788|r  449 VALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYK  508 (526)
Q Consensus       449 ~~L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~  508 (526)
                      -+|-++||+|++|+|.....+|..+.                 ++...-|++++-.++..
T Consensus       658 R~Ly~aGi~s~~~ia~A~p~~l~~i~-----------------g~g~~~a~~i~~~~~~~  700 (717)
T PRK00254        658 RALYNAGFRDLEDIMNAKPSELLAVE-----------------GIGAKIVEGIFKHLGKE  700 (717)
T ss_pred             HHHHHCCCCCHHHHHCCCHHHEECCC-----------------CCCHHHHHHHHHHHCCE
T ss_conf             99998699999999659999903023-----------------72789999999983864


No 74 
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=96.43  E-value=0.0086  Score=39.77  Aligned_cols=73  Identities=29%  Similarity=0.464  Sum_probs=59.3

Q ss_pred             HHHHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCCC------------------CCCCCCEEEEEEEEECCCCC-
Q ss_conf             98520838999998405763899957935874478748875------------------11527669999976113587-
Q gi|254780788|r  134 FKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRE------------------NLRPGDRVKSYIYDVRREQR-  194 (526)
Q Consensus       134 f~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~E------------------~~~~Gdrika~i~~V~~~~r-  194 (526)
                      |+...||+|.|.|.++..-.++|.+|-.++++|.++ |+.+                  .++.||+|||=|..+....+ 
T Consensus        77 fkP~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sq-i~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~  155 (183)
T COG1095          77 FKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQ-IMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR  155 (183)
T ss_pred             EEECCCCEEEEEEEEEEECCEEEEECCCCCCCCHHH-CCCCCCCCCCCCCEEEECCCCEEEECCCEEEEEEEEEECCCCC
T ss_conf             970356389999999961446999636222113866-6575325275554124036515884198899999996146776


Q ss_pred             --EEEEEEECCCHHH
Q ss_conf             --0289871598899
Q gi|254780788|r  195 --GPQVLLSRTHPQF  207 (526)
Q Consensus       195 --gpqi~lSRt~p~~  207 (526)
                        ...|.++...|.+
T Consensus       156 ~~~~~I~lTmrq~~L  170 (183)
T COG1095         156 PRESKIGLTMRQPGL  170 (183)
T ss_pred             CCCCEEEEEECCCCC
T ss_conf             542169999536667


No 75 
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=96.42  E-value=0.026  Score=36.27  Aligned_cols=71  Identities=27%  Similarity=0.388  Sum_probs=58.5

Q ss_pred             HHCCCEEEEEEEECCCCEEEEEE---CCCEEEEEHHHCCCC------CCCCCCCEEEEEEEEECCCCCEEEEEEECCCHH
Q ss_conf             52083899999840576389995---793587447874887------511527669999976113587028987159889
Q gi|254780788|r  136 DKVGEIISGTVKRVEYGNVIVDL---GNSDGVIRRDETISR------ENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQ  206 (526)
Q Consensus       136 ~r~Geiv~G~V~r~e~~~iiVdl---g~~ea~Lp~~e~ip~------E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~  206 (526)
                      +.+||||.|+|+++..-+.+|.|   ++.||++|-+|...|      ...|.|.++-|-+..|++..+---+-|+|..++
T Consensus         9 PeeGEiVv~tV~~V~~~GA~v~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~~   88 (269)
T COG1093           9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTEH   88 (269)
T ss_pred             CCCCCEEEEEEEEEECCCCEEEEECCCCEEEEEEHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEHHHCCHH
T ss_conf             98886899999986046427984205996226778998778998899986169869999988868777476254338787


No 76 
>PRK05054 exoribonuclease II; Provisional
Probab=96.36  E-value=0.047  Score=34.35  Aligned_cols=65  Identities=15%  Similarity=0.121  Sum_probs=30.4

Q ss_pred             EEEEEEECCCCE-EEEEECCCEEEEEH-HHCCCCCCCCCCCEEEEEEEEECC-CCCEE-----EEEEECCCHH
Q ss_conf             999998405763-89995793587447-874887511527669999976113-58702-----8987159889
Q gi|254780788|r  142 ISGTVKRVEYGN-VIVDLGNSDGVIRR-DETISRENLRPGDRVKSYIYDVRR-EQRGP-----QVLLSRTHPQ  206 (526)
Q Consensus       142 v~G~V~r~e~~~-iiVdlg~~ea~Lp~-~e~ip~E~~~~Gdrika~i~~V~~-~~rgp-----qi~lSRt~p~  206 (526)
                      +.|++++..... ++-|..+..-.+|. ...-.....+.||.+.|-|..--. ..++|     +++-+...|.
T Consensus        86 ~vG~~~~~~~~~~v~Pd~~~~~~~i~~~~~~~~~~~~~~gd~V~v~i~~~P~~~~~~~~g~i~~vlG~~~d~~  158 (644)
T PRK05054         86 FVGRVQKKDDRLSIVPDHPLLKDAIPCRAAKGLNHEFKEGDWVVAELRRHPLKGDRGFYAEITQFITDADDHF  158 (644)
T ss_pred             EEEEEEEECCEEEEEECCCCCCCCEECCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEEEECCCCCCC
T ss_conf             9999999898799997897776765514765555567899899999987888888886379999978789871


No 77 
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=96.34  E-value=0.024  Score=36.50  Aligned_cols=116  Identities=13%  Similarity=0.206  Sum_probs=81.1

Q ss_pred             CCCCCCCHHHHHHHHHHHH-HHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCC-
Q ss_conf             1225888467888877321-11477750588887765305889999999999999999999989877542843566407-
Q gi|254780788|r  363 MQAINVDEIIAHLLVAEGF-ADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSI-  440 (526)
Q Consensus       363 ~e~LdVDE~iA~~LV~eGf-~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l-  440 (526)
                      |+.-++.+.+.+.|++.|+ .++-++...+.++|.+++||.+..+..|.+         +++..   +......=|..| 
T Consensus       429 mdI~GLGek~i~~L~~~gli~~~~Dly~L~~~~L~~l~g~geKsa~nLl~---------aIe~S---K~~~l~r~l~aLG  496 (563)
T PRK08097        429 LGLDGIGEGTWRALHQTGRFEHLFSWLALTPEQLANTPGIGKARAAQLWH---------QFNLA---RQQPFTRWLKALG  496 (563)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCCHHHHHHCCHHHHHCCCCHHHHHHHHHHH---------HHHHH---CCCCHHHHHHHCC
T ss_conf             58567699999999975888997997508999985589857899999999---------99997---2899999999869


Q ss_pred             -CCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             -799989999999879847889653267752123123444321124533435889999999999841225788800024
Q gi|254780788|r  441 -PGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKVA  518 (526)
Q Consensus       441 -~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~~gWf~~e~~~  518 (526)
                       ++.....+..|+    .+.++|+..+.+||..+.                 ++...-|.+|.     .  ||.++.+.
T Consensus       497 I~~vG~~~a~~l~----~~~~~L~~as~e~l~~i~-----------------gIG~~~A~si~-----~--fF~~~~n~  547 (563)
T PRK08097        497 IPLTQAALNASLD----RSWQQLLSRTEQQWQQLP-----------------GIGEGRARQLI-----A--FFDHPQVQ  547 (563)
T ss_pred             CCCHHHHHHHHHH----CCHHHHHCCCHHHHHCCC-----------------CCCHHHHHHHH-----H--HHCCHHHH
T ss_conf             9508999999986----199999739998995579-----------------84899999999-----9--98598899


No 78 
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679   DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC).   This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=96.24  E-value=0.06  Score=33.59  Aligned_cols=285  Identities=19%  Similarity=0.271  Sum_probs=136.3

Q ss_pred             HHHHHHHHHHCC-CEEEEEEEECCC-CEE-----E--EEECCC---EEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCE
Q ss_conf             877999985208-389999984057-638-----9--995793---5874478748875115276699999761135870
Q gi|254780788|r  128 DRQYLEFKDKVG-EIISGTVKRVEY-GNV-----I--VDLGNS---DGVIRRDETISRENLRPGDRVKSYIYDVRREQRG  195 (526)
Q Consensus       128 ~~i~~ef~~r~G-eiv~G~V~r~e~-~~i-----i--Vdlg~~---ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rg  195 (526)
                      =.|-=+|..+.. ..+.+++-+|-| |-|     .  |.++|+   .|-|-..+.|..=..|+||+|-+.       ..|
T Consensus       315 WAiAYKFpa~e~~T~L~dv~~qVGRTG~iTPvA~LePV~vaG~~Vs~ATLHN~D~I~~kdiriGD~Vvv~-------kAG  387 (706)
T TIGR00575       315 WAIAYKFPAEEAQTKLLDVVVQVGRTGAITPVAKLEPVFVAGTTVSRATLHNEDEIEEKDIRIGDTVVVR-------KAG  387 (706)
T ss_pred             HHHCCCCCCCCCCEEEEEEEEEECCEEEECCEEEECCEEECCEEEEEEEECCHHHHHCCCCCCCCEEEEE-------ECC
T ss_conf             0102366743010089878998465677600367565587207862344016002420276658889998-------448


Q ss_pred             EEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEE
Q ss_conf             28987159889999999976677755808785663167750349999408998812765548862178899862778267
Q gi|254780788|r  196 PQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKID  275 (526)
Q Consensus       196 pqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkID  275 (526)
                      = |                 ||+|    |.+..=.| ||+...+-.=++=|      +|    |              =.
T Consensus       388 d-V-----------------IP~v----v~v~~~~R-~~~~~~~~~P~~CP------~C----~--------------s~  420 (706)
T TIGR00575       388 D-V-----------------IPKV----VEVLLEKR-TGEERPIKFPTHCP------SC----G--------------SP  420 (706)
T ss_pred             C-C-----------------CHHH----HHCCCCCC-CCCCCEEECCCCCC------CC----C--------------CE
T ss_conf             6-2-----------------5355----41023578-88887034287188------88----8--------------33


Q ss_pred             EEECCCCHHHHHHH-HCCCCCCCEEEE-CCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEE-----EEEECC--C
Q ss_conf             99559878999997-628665424898-75678799998534221102544278999998616745-----785522--0
Q gi|254780788|r  276 IVVWSPDSATFVIN-ALRPAIVTKVVL-DEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTI-----DIITEE--E  346 (526)
Q Consensus       276 ii~ws~d~~~fi~n-Al~PA~v~~v~~-de~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~i-----di~~~~--~  346 (526)
                      ++..-+....|-.| -.-||....-+. --..+.|+|             .|-.-++..+|---++     |+++-.  .
T Consensus       421 lv~~~~e~~~rC~Ng~~Cpa~~~e~i~hFaSr~AmdI-------------~GLG~~~I~~LfE~~Lv~~~~DLY~L~~k~  487 (706)
T TIGR00575       421 LVRIEEEVDIRCTNGLNCPAQLVERIKHFASRNAMDI-------------DGLGEKVIEQLFEEKLVRSVADLYALKEKL  487 (706)
T ss_pred             EECCCCCEEEECCCCCCCHHHHHHHEEEEEEECCCCC-------------CCCCHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             1115787216538876653676511023454110332-------------222389999998726667856665778899


Q ss_pred             HHHHHHCC-CC----------------CCCCCCCCCCC---CCHHHHHHHHHHHHHHHHHHHHCCHH-----------HH
Q ss_conf             01101001-22----------------10001112258---88467888877321114777505888-----------87
Q gi|254780788|r  347 DSINRQKD-FN----------------ERTQFFMQAIN---VDEIIAHLLVAEGFADVEELACVKIS-----------EI  395 (526)
Q Consensus       347 ~~~~~~~e-~~----------------~~~~~f~e~Ld---VDE~iA~~LV~eGf~SiEeIa~a~~e-----------eL  395 (526)
                      ..=.+-+- |.                .-...|.-+|+   |.+..|..|+..+. |++.+..|+.|           +|
T Consensus       488 ~~Ll~le~~~g~~sa~nLl~aIe~sK~~pl~RlL~aLGIr~VG~~~A~~La~~f~-tl~~L~~A~~e~~~~~~~f~~s~L  566 (706)
T TIGR00575       488 EDLLELEGKFGEKSAQNLLSAIEKSKKKPLARLLFALGIRHVGEVTAKLLAKHFG-TLDKLKAASLETLESIYQFDRSEL  566 (706)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC-CHHHHHHCCHHHHHHHHHHCCHHH
T ss_conf             9987064035568899999999985210489999862860357999999998558-868998508216778875160556


Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH-HCCCCCCHHHHHHHHHCCCCCHH----------HHHH
Q ss_conf             765305889999999999999999999989877542843566-40779998999999987984788----------9653
Q gi|254780788|r  396 ASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEEL-CSIPGIDSKIKVALGENGIKTME----------DLAG  464 (526)
Q Consensus       396 ~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L-~~l~gl~~~~~~~L~e~gIktle----------DlAe  464 (526)
                      ++++|+.+.+|..|.+-               +..   ...+ + -+.-|.+.+..|-+.|+.+.+          ...+
T Consensus       567 ~~~~g~G~~vA~~~~~~---------------F~~---~~~~~~-qPYRta~~~~~L~~~gv~~~~~D~~~~LL~~~~~~  627 (706)
T TIGR00575       567 LSVEGVGPKVAESIVNF---------------FHD---PNNLSL-QPYRTAELIEKLEELGVNMESEDEFCRLLDQALKE  627 (706)
T ss_pred             HHCCCCHHHHHHHHHHH---------------HHC---CCCCCC-CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             41014027899999998---------------712---000135-60468999999988316310113578777642011


Q ss_pred             CCHHHHCC-CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             26775212-31234443211245334358899999999998
Q gi|254780788|r  465 CSVDDLLG-WSENKGGNIEKFDGFLSSLGTPKDQVESMIIH  504 (526)
Q Consensus       465 ls~dEL~~-~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~  504 (526)
                      ..-.++.+ +   ..||..=+-|-|+.  ||+++|.++|-.
T Consensus       628 ~~~~~~~~~~---~~GK~fVlTG~L~~--~sR~~a~~~~~~  663 (706)
T TIGR00575       628 KVEAELAGSP---LAGKTFVLTGTLSQ--MSRDEAKELLEA  663 (706)
T ss_pred             HCCCCCCCCC---CCCCEEEEECCCCC--CCHHHHHHHHHH
T ss_conf             0010005752---02776899515688--888999999998


No 79 
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=96.21  E-value=0.022  Score=36.78  Aligned_cols=59  Identities=25%  Similarity=0.423  Sum_probs=51.5

Q ss_pred             HHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC-C---------CCCCCCCCEEEEEEEEECCC
Q ss_conf             98520838999998405763899957-935874478748-8---------75115276699999761135
Q gi|254780788|r  134 FKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI-S---------RENLRPGDRVKSYIYDVRRE  192 (526)
Q Consensus       134 f~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i-p---------~E~~~~Gdrika~i~~V~~~  192 (526)
                      |..+.|++|.|.|..+....+.||+| ...|+||-++.. |         ++.|..||-|-|=|.+|...
T Consensus         2 Y~P~~GD~ViG~V~~i~~~~w~vdi~s~~~a~L~ls~v~~~~~~~d~~~mr~~l~iGDli~a~V~~v~~~   71 (86)
T cd05789           2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD   71 (86)
T ss_pred             CCCCCCCEEEEEEEEEECCCEEEECCCCEEEEEEHHHCCCCCCCHHHHHHHHHCCCCCEEEEEEEEECCC
T ss_conf             8798899999999998088189974996077987454467776314677886566898999999998899


No 80 
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions.  Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.18  E-value=0.042  Score=34.68  Aligned_cols=63  Identities=21%  Similarity=0.302  Sum_probs=54.7

Q ss_pred             CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC--------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf             838999998405763899957-93587447874--------887511527669999976113587028987159
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET--------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSRT  203 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~--------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt  203 (526)
                      |+.++|.|.++.++.+.|.+. .+.|.+|.-+.        -|-.+|.+|..++|.+..|+.+.+  .+.||.+
T Consensus         1 G~~v~gfV~n~~~~~~wv~iSp~V~gri~~l~lSdd~s~l~~~e~~FpvG~avk~~V~~vD~e~~--~l~LS~r   72 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHK--LLRLSAR   72 (73)
T ss_pred             CCEEEEEEEECCCCEEEEEECCCEEEEEEHHHHCCCHHHHCCHHHHCCCCCEEEEEEEEECCCCC--EEEEEEC
T ss_conf             98799999972598499998888189997054268856853888729998459999999828778--8999803


No 81 
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.14  E-value=0.025  Score=36.43  Aligned_cols=63  Identities=22%  Similarity=0.384  Sum_probs=52.1

Q ss_pred             HHHHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCC----------CCCCCCCCEEEEEEEEECCCCC
Q ss_conf             9998520838999998405763899957-9358744787488----------7511527669999976113587
Q gi|254780788|r  132 LEFKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETIS----------RENLRPGDRVKSYIYDVRREQR  194 (526)
Q Consensus       132 ~ef~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip----------~E~~~~Gdrika~i~~V~~~~r  194 (526)
                      ..|..+.|++|-|.|..+....+.||+| ...|+||-.+...          +..|.+||-|-|=|..|..+..
T Consensus        56 grY~P~~GD~VIG~V~~v~~~~W~VDI~s~~~a~L~~s~~~~r~~~~~~~~mr~~l~~GDlI~ArV~~v~~~~~  129 (232)
T PRK04163         56 GKYIPKKGDLVIGKVTDVGFSGWEVDINSPYKAILPVSEVLGRPVDVESTDLRKYLDIGDYIIAKVKDVDETKD  129 (232)
T ss_pred             CCCCCCCCCEEEEEEEEECCCEEEEECCCCCEEEECHHHCCCCCCCCCHHHHHHHCCCCCEEEEEEEEECCCCC
T ss_conf             51058769989999998318717998699605585244456655556435677517889889999999668997


No 82 
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=96.13  E-value=0.016  Score=37.78  Aligned_cols=70  Identities=23%  Similarity=0.378  Sum_probs=54.7

Q ss_pred             HHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHH------HCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHH
Q ss_conf             98520838999998405763899957-935874478------74887511527669999976113587028987159889
Q gi|254780788|r  134 FKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRD------ETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQ  206 (526)
Q Consensus       134 f~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~------e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~  206 (526)
                      |..++|++|.|.|.++....+.||++ ...|.||-.      +.--++.|++||-|.|-+..+.....   +.||..+++
T Consensus         2 Y~P~vGDvVigrV~~v~~~~w~vdI~~~~~a~l~~~~~~~~D~~~m~~~f~~GDlI~A~V~~~~~~~~---~~L~T~~~~   78 (82)
T cd04454           2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMN---VLLTTADNE   78 (82)
T ss_pred             CCCCCCCEEEEEEEEECCCEEEEEECCCEEEEEEEHHCCCCCHHHHHHHCCCCCEEEEEEEEECCCCC---EEEEECCCC
T ss_conf             87989999999999970781899968632889730216773066798745877689999999769997---899956655


No 83 
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme)  to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=96.05  E-value=0.03  Score=35.83  Aligned_cols=66  Identities=23%  Similarity=0.443  Sum_probs=52.0

Q ss_pred             HHHCCCEEEEEEEECCCC--EEEEEEC-CCEEEEEHHHCC---------CCCCCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf             852083899999840576--3899957-935874478748---------87511527669999976113587028987
Q gi|254780788|r  135 KDKVGEIISGTVKRVEYG--NVIVDLG-NSDGVIRRDETI---------SRENLRPGDRVKSYIYDVRREQRGPQVLL  200 (526)
Q Consensus       135 ~~r~Geiv~G~V~r~e~~--~iiVdlg-~~ea~Lp~~e~i---------p~E~~~~Gdrika~i~~V~~~~rgpqi~l  200 (526)
                      +..+|+|..|.|.++..+  ..+||+| +-.|+||.++..         ..+.++.||.|-+=|..=-...|||.+.-
T Consensus         4 ~~~vGnIY~GkV~~v~p~i~AAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~l~~G~~ilVQV~Ke~~~~Kgp~lT~   81 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTT   81 (88)
T ss_pred             CCCCCCEEEEEEEEECCCCCEEEEECCCCCCEEEECHHCCHHHHCCCCCHHHHCCCCCEEEEEEEECCCCCCCCEEEE
T ss_conf             561124899999886668748999658986899990345723513578877837799999999976687997860884


No 84 
>PRK11642 exoribonuclease R; Provisional
Probab=95.92  E-value=0.17  Score=30.33  Aligned_cols=25  Identities=16%  Similarity=0.300  Sum_probs=13.2

Q ss_pred             HHHHHHCCCCHHHHHHHHHHHHHHH
Q ss_conf             9998623999999999999999999
Q gi|254780788|r   14 DAVAYEKSIDRDVVLSVMADSIQKA   38 (526)
Q Consensus        14 e~va~EK~I~~e~i~~aie~Al~~a   38 (526)
                      ..+++.=+|..+.-++++...|...
T Consensus        38 ~el~~~~~l~~~~~~~~L~~~L~~l   62 (813)
T PRK11642         38 EELAVELNIEGEEQLEALRRRLRAM   62 (813)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             9999981999889999999999999


No 85 
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2.   The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=95.90  E-value=0.0067  Score=40.57  Aligned_cols=58  Identities=31%  Similarity=0.446  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHHHHHCCEEEEEEEECCCC--CEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEE
Q ss_conf             899999999766777558087856631677--5034999940899881276554886217889986277826799
Q gi|254780788|r  205 PQFMVKLFHMEVPEIYNGIVQVKAVSRDPG--SRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIV  277 (526)
Q Consensus       205 p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG--~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii  277 (526)
                      .+|+..+|.-+         ++.++...+.  .+++|.|..     |+.|.|+|.+|.+|+..++.++ .+|||+
T Consensus         2 ~~fi~nal~Pa---------~v~~V~i~~~~~~~~~V~V~~-----~~~~~AIGk~G~Nvrla~~l~g-~~IdI~   61 (61)
T cd02134           2 AEFIRNALSPA---------KVTSVTVLDDEEKRARVVVPD-----DQLGLAIGKGGQNVRLASKLLG-EKIDIV   61 (61)
T ss_pred             HHHHHHHCCCC---------EEEEEEECCCCCCEEEEEECH-----HHHHHHHCCCCEEHHHHHHHHC-CEEEEC
T ss_conf             78998636987---------557988447877379999885-----7843876678670999999779-877649


No 86 
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805    This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity.
Probab=95.89  E-value=0.087  Score=32.37  Aligned_cols=93  Identities=20%  Similarity=0.273  Sum_probs=67.7

Q ss_pred             HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEC--CCEEEEEHH------------
Q ss_conf             62079999999999--99999999887799998520838999998405763899957--935874478------------
Q gi|254780788|r  105 DFGRVAVQSAKQVI--IQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLG--NSDGVIRRD------------  168 (526)
Q Consensus       105 ~fgRiaAq~AKQvI--~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg--~~ea~Lp~~------------  168 (526)
                      .+.-++.++-++-.  ..-=||+..-...+-..+|+|+.-.|+|.-|++=+++|.|.  .+||..|-+            
T Consensus       637 ~l~~~~~h~S~~ERrA~~AERd~~d~kkaeyM~~~iG~~f~G~Is~VT~FG~FVeL~~~~ieGLVhI~~L~dDYY~Fd~~  716 (755)
T TIGR02063       637 KLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEK  716 (755)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEEEEEEEECCCEEEEEEECCCCCCCCCEECCC
T ss_conf             89999986112112155312779999999999850796887799756620138973674111026327898856307522


Q ss_pred             -HCCCCC----CCCCCCEEEEEEEEECCCCCEEE
Q ss_conf             -748875----11527669999976113587028
Q gi|254780788|r  169 -ETISRE----NLRPGDRVKSYIYDVRREQRGPQ  197 (526)
Q Consensus       169 -e~ip~E----~~~~Gdrika~i~~V~~~~rgpq  197 (526)
                       ..+-|+    .||.||+|++-|.+|+...|.--
T Consensus       717 ~~~L~G~R~gk~frLGD~v~V~V~~ad~~~~~id  750 (755)
T TIGR02063       717 GLALVGERTGKVFRLGDRVKVRVVKADLDTGKID  750 (755)
T ss_pred             CCEEEEECCCCEEECCCEEEEEEEEECCCCCEEE
T ss_conf             0788643268737248748999999610336698


No 87 
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=95.86  E-value=0.017  Score=37.50  Aligned_cols=106  Identities=19%  Similarity=0.223  Sum_probs=72.7

Q ss_pred             EECHHHHHHHCCC--CCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC-CCEE
Q ss_conf             2348999862889--864737998508456207999999999999999999887799998520838999998405-7638
Q gi|254780788|r   78 QISLKVARDRDPS--IDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVE-YGNV  154 (526)
Q Consensus        78 eI~l~~A~~~~~~--~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e-~~~i  154 (526)
                      -+++++-... ++  .++||.+...+.-..=|||.+..|.+-+.+++-.       ..+.+..++.+.|+|.|.. -|..
T Consensus       101 ~vp~~elp~~-~~~wpq~Gd~l~v~l~~Dkk~Ri~g~~a~~~~l~~l~~-------~~~~~l~nq~v~~tVYr~~~~G~f  172 (287)
T COG2996         101 LVPLDELPTL-KSLWPQKGDKLLVYLYVDKKGRIWGTLAIEKILENLAT-------PAYNNLKNQEVDATVYRLLESGTF  172 (287)
T ss_pred             EEEHHHCCCC-CCCCCCCCCEEEEEEEECCCCCEEEEECCHHHHHHCCC-------CCCHHHHCCEEEEEEEEEECCCEE
T ss_conf             6162536443-12377879899999998567847777331557876177-------211145437610599998214239


Q ss_pred             EEEECCCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCC
Q ss_conf             999579358744787488751152766999997611358
Q gi|254780788|r  155 IVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQ  193 (526)
Q Consensus       155 iVdlg~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~  193 (526)
                      .+-=++--|+++++|.-  ..+|.|+|+.++|..|+.+.
T Consensus       173 v~~e~~~~GfIh~sEr~--~~prlG~~l~~rVi~~reDg  209 (287)
T COG2996         173 VITENGYLGFIHKSERF--AEPRLGERLTARVIGVREDG  209 (287)
T ss_pred             EEECCCEEEEECCHHHC--CCCCCCCEEEEEEEEECCCC
T ss_conf             99718768998606600--66667755788999982487


No 88 
>PTZ00248 eukaryotic translation initiation factor 2 alpha subunit; Provisional
Probab=95.82  E-value=0.043  Score=34.60  Aligned_cols=82  Identities=21%  Similarity=0.276  Sum_probs=64.9

Q ss_pred             HHHHHHHHHCCCEEEEEEEECCCCEEEEEE---CCCEEEEEHHHCCCC------CCCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf             779999852083899999840576389995---793587447874887------51152766999997611358702898
Q gi|254780788|r  129 RQYLEFKDKVGEIISGTVKRVEYGNVIVDL---GNSDGVIRRDETISR------ENLRPGDRVKSYIYDVRREQRGPQVL  199 (526)
Q Consensus       129 ~i~~ef~~r~Geiv~G~V~r~e~~~iiVdl---g~~ea~Lp~~e~ip~------E~~~~Gdrika~i~~V~~~~rgpqi~  199 (526)
                      +.|+.=-+.+|++|.++|+++..-..||.|   ++.||++|.+|..++      ...|+|...-|.|..|..+..---+-
T Consensus         8 RfYe~~~Pe~~e~V~~~V~~i~~~gayV~LlEY~~~egmI~~sEls~rrir~I~k~ikvG~~~v~~VlRVD~~KGyIDLS   87 (324)
T PTZ00248          8 RFYENKYPEENDLVMVKVNRIEEMGVYVSLLEYDDIEGMILLSELSKRRIRSINKLVKVGRHEVVLVLRVDKDKGYIDLS   87 (324)
T ss_pred             CCCCCCCCCCCCEEEEEEEEEECCEEEEEEEEECCCCCEEEHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCEECH
T ss_conf             02355699988889999999802568999840088222146888637888637887106877899999985877824441


Q ss_pred             EECCCHHHHHH
Q ss_conf             71598899999
Q gi|254780788|r  200 LSRTHPQFMVK  210 (526)
Q Consensus       200 lSRt~p~~l~~  210 (526)
                      +.|.+|+=..+
T Consensus        88 ~rrVs~ed~~k   98 (324)
T PTZ00248         88 KRRVTPEDIIK   98 (324)
T ss_pred             HHCCCHHHHHH
T ss_conf             50299889999


No 89 
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679   DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC).   This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=95.79  E-value=0.076  Score=32.80  Aligned_cols=118  Identities=21%  Similarity=0.326  Sum_probs=89.4

Q ss_pred             CCCCCCCHHHHHHHHHHHH-HHHHHHHHCC--HHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             1225888467888877321-1147775058--888776530-58899999999999999999999898775428435664
Q gi|254780788|r  363 MQAINVDEIIAHLLVAEGF-ADVEELACVK--ISEIASIEG-FDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELC  438 (526)
Q Consensus       363 ~e~LdVDE~iA~~LV~eGf-~SiEeIa~a~--~eeL~~IeG-fdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~  438 (526)
                      |+.=++.+.+++.|+++|+ .|+-|+....  .++|+.++| |.+..|..|.+         +++   +-+....+-=|.
T Consensus       455 mdI~GLG~~~I~~LfE~~Lv~~~~DLY~L~~k~~~Ll~le~~~g~~sa~nLl~---------aIe---~sK~~pl~RlL~  522 (706)
T TIGR00575       455 MDIDGLGEKVIEQLFEEKLVRSVADLYALKEKLEDLLELEGKFGEKSAQNLLS---------AIE---KSKKKPLARLLF  522 (706)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH---------HHH---HHHHHHHHHHHH
T ss_conf             33222238999999872666785666577889999870640355688999999---------999---852104899998


Q ss_pred             --CCCCCCHHHHHHHHHCCCCCHHHHHHCCHH-----------HHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             --077999899999998798478896532677-----------5212312344432112453343588999999999984
Q gi|254780788|r  439 --SIPGIDSKIKVALGENGIKTMEDLAGCSVD-----------DLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHA  505 (526)
Q Consensus       439 --~l~gl~~~~~~~L~e~gIktleDlAels~d-----------EL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~A  505 (526)
                        .++++...++-.|+.+.= |+|.|...|.|           +|+.+.                 ++...-|.+++-  
T Consensus       523 aLGIr~VG~~~A~~La~~f~-tl~~L~~A~~e~~~~~~~f~~s~L~~~~-----------------g~G~~vA~~~~~--  582 (706)
T TIGR00575       523 ALGIRHVGEVTAKLLAKHFG-TLDKLKAASLETLESIYQFDRSELLSVE-----------------GVGPKVAESIVN--  582 (706)
T ss_pred             HCCCHHHHHHHHHHHHHHCC-CHHHHHHCCHHHHHHHHHHCCHHHHHCC-----------------CCHHHHHHHHHH--
T ss_conf             62860357999999998558-8689985082167788751605564101-----------------402789999999--


Q ss_pred             CCCCCCCCCCCC
Q ss_conf             122578880002
Q gi|254780788|r  506 RYKMGWIEKEKV  517 (526)
Q Consensus       506 R~~~gWf~~e~~  517 (526)
                           ||..+.+
T Consensus       583 -----~F~~~~~  589 (706)
T TIGR00575       583 -----FFHDPNN  589 (706)
T ss_pred             -----HHHCCCC
T ss_conf             -----8712000


No 90 
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.79  E-value=0.11  Score=31.77  Aligned_cols=61  Identities=20%  Similarity=0.239  Sum_probs=43.7

Q ss_pred             CHHHHHHHHCCCCCCCEE--------EE-------CCCC-CEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf             789999976286654248--------98-------7567-8799998534221102544278999998616745785
Q gi|254780788|r  282 DSATFVINALRPAIVTKV--------VL-------DEDV-GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII  342 (526)
Q Consensus       282 d~~~fi~nAl~PA~v~~v--------~~-------de~~-~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~  342 (526)
                      =+.+.+..||.-|+.-+.        .+       .+.. +...+-+|.+.....||.+|.|+|--..-||-+|||-
T Consensus       514 i~~~il~~Al~qA~~gR~~IL~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~gGk~Ik~i~e~tg~~Idi~  590 (694)
T PRK11824        514 ITREIMEEALEQAKEGRLHILGKMNEAISEPRTELSPYAPRIETIKIDPDKIRDVIGPGGKTIREITEETGAKIDIE  590 (694)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECHHHHHHEECCCHHHHHHHHHHHCCEEEEE
T ss_conf             69899999999999999999999987366654333568987999997879866506863388999999889889996


No 91 
>PRK13766 Hef nuclease; Provisional
Probab=95.78  E-value=0.019  Score=37.31  Aligned_cols=46  Identities=28%  Similarity=0.456  Sum_probs=32.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             25888467888877321114777505888877653058899999999
Q gi|254780788|r  365 AINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG  411 (526)
Q Consensus       365 ~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~  411 (526)
                      -.+|....|..|... |.|++.|+.|+.++|.+++|+.+.+|.+|+.
T Consensus       711 ~pgvg~~~a~~ll~~-fgsi~~i~~a~~~eL~~v~giG~~~A~~i~~  756 (764)
T PRK13766        711 LPDVGPVLARNLLDH-FGSVENVMTASEEELKAVEGIGEKTAKKIRE  756 (764)
T ss_pred             CCCCCHHHHHHHHHH-CCCHHHHHCCCHHHHHHCCCCCHHHHHHHHH
T ss_conf             899999999999997-1999999659999995474969999999999


No 92 
>PRK11712 ribonuclease G; Provisional
Probab=95.67  E-value=0.057  Score=33.72  Aligned_cols=181  Identities=16%  Similarity=0.227  Sum_probs=111.1

Q ss_pred             HHCCCEEEEEEEECCCC--EEEEEEC-CCEEEEEHHHCCCC------------------CCCCCCCEEEEEEEEECCCCC
Q ss_conf             52083899999840576--3899957-93587447874887------------------511527669999976113587
Q gi|254780788|r  136 DKVGEIISGTVKRVEYG--NVIVDLG-NSDGVIRRDETISR------------------ENLRPGDRVKSYIYDVRREQR  194 (526)
Q Consensus       136 ~r~Geiv~G~V~r~e~~--~iiVdlg-~~ea~Lp~~e~ip~------------------E~~~~Gdrika~i~~V~~~~r  194 (526)
                      ..+|.|..|.|.++.+|  ..+||+| +-.|+||.++..|.                  +-+++|+.|-+=|..=...+|
T Consensus        36 ~~vGnIY~G~V~~V~pgl~AAFVdiG~~k~gFL~~~di~~~~~~~~~~~~~~~~~~~I~~~l~~Gq~ilVQV~Ke~~~~K  115 (489)
T PRK11712         36 GIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTK  115 (489)
T ss_pred             CCCCCEEEEEEEEECCCCCEEEEEECCCCCEEEEHHHCCCCHHCCCCCCCCCCCCCCHHHHCCCCCEEEEEEEECCCCCC
T ss_conf             76676699999430688776999847987428785543852111333223566646767746799989999962687898


Q ss_pred             EEEEE--------------------EECCC-----HHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECC----
Q ss_conf             02898--------------------71598-----89999999976677755808785663167750349999408----
Q gi|254780788|r  195 GPQVL--------------------LSRTH-----PQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSD----  245 (526)
Q Consensus       195 gpqi~--------------------lSRt~-----p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d----  245 (526)
                      ||.+.                    +||.-     -.-++.++..-.|+-+ | +-|+..|-....    .....|    
T Consensus       116 Ga~lT~~isl~GRylVl~P~~~~igiSrkI~~~~eR~rLk~i~~~~~~~~~-G-~IiRT~a~~~~~----e~l~~d~~~L  189 (489)
T PRK11712        116 GARLTTDITLPSRYLVFMPGASHVGVSQRIESEEERERLKKIVAPYCDEQG-G-FIIRTAAEGVGE----EELAQDAAFL  189 (489)
T ss_pred             CCCEEEEEEECCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC-C-EEEECHHHCCCH----HHHHHHHHHH
T ss_conf             876751255453269995389987643167987899999998885388888-6-698413202999----9999999999


Q ss_pred             ----------CCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHH-----HHHHCCCCCCCEEEECCCC-CEEE
Q ss_conf             ----------99881276554886217889986277826799559878999-----9976286654248987567-8799
Q gi|254780788|r  246 ----------SSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATF-----VINALRPAIVTKVVLDEDV-GRIE  309 (526)
Q Consensus       246 ----------~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~f-----i~nAl~PA~v~~v~~de~~-~~~~  309 (526)
                                ..--+--+|+-.-.+-+..+++.+-++.++-|.-+ |+..|     ......|.-..+|....+. .-++
T Consensus       190 ~~~W~~I~~~~~~~~~p~ll~~e~~~~~r~lRD~~~~~~~~I~vD-~~~~~~~~~~~~~~~~p~~~~~v~~y~~~~plF~  268 (489)
T PRK11712        190 KRVWTKVMERKKRPQTRYQLYGELALAQRVLRDFVGAELDRIRVD-SRLTYEELKEFTSEYIPELTDKLEHYSGRQPIFD  268 (489)
T ss_pred             HHHHHHHHHHHHCCCCCCEEECCCHHHHHHHHHHCCCCCCEEEEC-CHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHH
T ss_conf             999999999985499961464272389999998447765278857-8899999999998759410011343268621776


Q ss_pred             EEECCCCCCCCCCC
Q ss_conf             99853422110254
Q gi|254780788|r  310 VIVPKEQLSLAIGR  323 (526)
Q Consensus       310 v~v~~~qls~AIGk  323 (526)
                      .+=-+.|+..|..|
T Consensus       269 ~y~ie~~I~~~l~~  282 (489)
T PRK11712        269 LYDVENEIQRALER  282 (489)
T ss_pred             HCCHHHHHHHHHCC
T ss_conf             42899999997168


No 93 
>PRK00254 ski2-like helicase; Provisional
Probab=95.63  E-value=0.21  Score=29.53  Aligned_cols=53  Identities=25%  Similarity=0.328  Sum_probs=47.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             11225888467888877321114777505888877653058899999999999
Q gi|254780788|r  362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAR  414 (526)
Q Consensus       362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~  414 (526)
                      ++...+|.-..|..|+.+||+|+++||.+++++|..|.||.+.+|..|.+-+.
T Consensus       646 L~~I~gvgr~RAR~Ly~aGi~s~~~ia~A~p~~l~~i~g~g~~~a~~i~~~~~  698 (717)
T PRK00254        646 LMELPMIGRKRARALYNAGFRDLEDIMNAKPSELLAVEGIGAKIVEGIFKHLG  698 (717)
T ss_pred             HCCCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHEECCCCCCHHHHHHHHHHHC
T ss_conf             56489989899999998699999999659999903023727899999999838


No 94 
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=95.54  E-value=0.23  Score=29.32  Aligned_cols=135  Identities=19%  Similarity=0.148  Sum_probs=98.8

Q ss_pred             EEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEE
Q ss_conf             87159889999999976677755808785663167750349999408998812765548862178899862778267995
Q gi|254780788|r  199 LLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVV  278 (526)
Q Consensus       199 ~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~  278 (526)
                      .++-.+-+.++.|+++|= .....-++-++ |.+.|.--=+.|.+.|  .    .-+|..|.=.++.+++| |.|+-||.
T Consensus        28 ~v~~~dV~v~~~L~kL~e-~~~l~~~~y~k-a~ev~~lvIi~~~~~~--~----~~i~k~~ki~k~Ls~~l-g~kVrVvE   98 (167)
T PRK06418         28 EVTELDVEVSKALLKLTQ-FIGLSDVEYKK-AYEVDDLVILLVGSGD--R----IPIGKGGKIEKALSRAL-GKRVRVVE   98 (167)
T ss_pred             CEEEEHHHHHHHHHHHHH-HCCCCCEEEEE-EEEECCEEEEEECCCC--C----CCHHHHHHHHHHHHHHH-CCCEEEEE
T ss_conf             545306799999998875-05755338999-9998999999984788--5----43578899999999986-89279997


Q ss_pred             CCCCHHHHHHHHCCCCCCCEEEE--CCCC-CEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf             59878999997628665424898--7567-8799998534221102544278999998616745785
Q gi|254780788|r  279 WSPDSATFVINALRPAIVTKVVL--DEDV-GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII  342 (526)
Q Consensus       279 ws~d~~~fi~nAl~PA~v~~v~~--de~~-~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~  342 (526)
                      +.+|..+|+.--++||.+..|..  -++. ....|.|+-.....-=++.-+=.++-|++||-++-|.
T Consensus        99 ~~~dik~li~qLl~PArvlgVNtvwlPdG~~~~~v~V~~rd~rrlp~~~e~le~ils~i~g~~vkI~  165 (167)
T PRK06418         99 KTSDIKKLAVQLLSPARVLGVNTVWLPDGTTEYVVRIPSRDRRRLPAKPEVLESILSQITGTEVKVR  165 (167)
T ss_pred             CCCCHHHHHHHHHCCHHHCEEEEEECCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHCCCEEEE
T ss_conf             3675889999972525131278899189958999996377402279998999999999649955899


No 95 
>pfam10246 MRP-S35 Mitochondrial ribosomal protein MRP-S35. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. that are highly conserved from worms to humans. The structure has previously been referred to as MRP-S18 but the current numbering fits the preferred nomenclature from these authors.
Probab=95.52  E-value=0.029  Score=35.85  Aligned_cols=66  Identities=20%  Similarity=0.460  Sum_probs=53.7

Q ss_pred             HHHHHHHHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCC
Q ss_conf             87799998520838999998405763899957-93587447874887511527669999976113587
Q gi|254780788|r  128 DRQYLEFKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQR  194 (526)
Q Consensus       128 ~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~r  194 (526)
                      ..-+-..-+-.|.++.|+|..+-.+.+|||.| +--++.++- ..++|.|+.|.|++.-+++-+-+.|
T Consensus        13 ~S~fi~lG~~~gk~v~G~I~hvv~dDLYIDfG~KFhcVc~rP-~~~~~~y~~G~rV~lrLkdlELt~~   79 (105)
T pfam10246        13 NSKFVQLGDAEGKLVIGKIFHIVEDDLYIDFGGKFHCVCKRP-AVNGEKYQRGSRVRLRLKDLELTSR   79 (105)
T ss_pred             CCCHHHCCCCCCCEEEEEEEEEECCCEEEEECCEEEEEECCC-CCCHHHCCCCCEEEEEECCHHHHHH
T ss_conf             591210578557788999999706725998377167887376-6471005778889999668756445


No 96 
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=95.49  E-value=0.099  Score=31.98  Aligned_cols=49  Identities=35%  Similarity=0.425  Sum_probs=28.8

Q ss_pred             CCCCCC---CCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             112258---88467888877321114777505888877653058899999999
Q gi|254780788|r  362 FMQAIN---VDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG  411 (526)
Q Consensus       362 f~e~Ld---VDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~  411 (526)
                      |.-+|+   |.+..|..|.. .|.|++.+..++.++|..++|+.+..|..+.+
T Consensus       510 ~l~aLGIr~VG~~~Ak~La~-~f~sl~~l~~a~~e~l~~i~giG~~vA~si~~  561 (667)
T COG0272         510 FLYALGIRHVGETTAKSLAR-HFGTLEALLAASEEELASIPGIGEVVARSIIE  561 (667)
T ss_pred             HHHHCCCCHHHHHHHHHHHH-HHHHHHHHHHCCHHHHHHCCCHHHHHHHHHHH
T ss_conf             99987971140899999998-76029999842999995066612899999999


No 97 
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=95.43  E-value=0.1  Score=31.82  Aligned_cols=70  Identities=29%  Similarity=0.478  Sum_probs=52.8

Q ss_pred             HHHCCCEEEEEEEECCCCEEEEEE---C------CCEEEEEHHHCCCC--------CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf             852083899999840576389995---7------93587447874887--------511527669999976113587028
Q gi|254780788|r  135 KDKVGEIISGTVKRVEYGNVIVDL---G------NSDGVIRRDETISR--------ENLRPGDRVKSYIYDVRREQRGPQ  197 (526)
Q Consensus       135 ~~r~Geiv~G~V~r~e~~~iiVdl---g------~~ea~Lp~~e~ip~--------E~~~~Gdrika~i~~V~~~~rgpq  197 (526)
                      -.++|.+|+|.|.|+......+++   +      ...|++.+.+.-+.        +.|||||-|||-+...-.   +.+
T Consensus         3 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~l~~~f~g~Ir~~dVr~te~d~v~m~~~FrpGDIVrA~Vislgd---~~~   79 (92)
T cd05791           3 LPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD---ASS   79 (92)
T ss_pred             CCCCCCEEEEEEEEECCCEEEEEEEEECCEECCCEEEEEEEHHHCCCCCCCCEEHHHCCCCCCEEEEEEEECCC---CCE
T ss_conf             68899999999999711378999999999983762578879244343555304341354999899999997478---724


Q ss_pred             EEEECCCHHH
Q ss_conf             9871598899
Q gi|254780788|r  198 VLLSRTHPQF  207 (526)
Q Consensus       198 i~lSRt~p~~  207 (526)
                      ..||-+.++|
T Consensus        80 y~LSTa~neL   89 (92)
T cd05791          80 YYLSTAENEL   89 (92)
T ss_pred             EEEEECCCCC
T ss_conf             9998537876


No 98 
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=95.43  E-value=0.1  Score=31.82  Aligned_cols=66  Identities=17%  Similarity=0.314  Sum_probs=53.0

Q ss_pred             HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCC-------------------------CCCCCCCCEEEEEEEEEC
Q ss_conf             20838999998405763899957-9358744787488-------------------------751152766999997611
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETIS-------------------------RENLRPGDRVKSYIYDVR  190 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip-------------------------~E~~~~Gdrika~i~~V~  190 (526)
                      ..|-++.|.|+.+..-.+.|-|. +.-|+.|..+...                         .+-|++|+.+||+|..+.
T Consensus         2 ~~G~lvLG~V~~I~~~~l~isLP~~L~G~V~it~ISd~~t~~le~~~~~~~~~~~~~e~~~L~~lF~vGq~vr~~V~s~~   81 (100)
T cd05693           2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLD   81 (100)
T ss_pred             CCCCEEEEEEEEECCCCEEEECCCCCEEEEEHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHCCCCCEEEEEEEECC
T ss_conf             88989999998984663899858985899887885299999999987300236763234587884768989999999845


Q ss_pred             CCCCE-EEEEEEC
Q ss_conf             35870-2898715
Q gi|254780788|r  191 REQRG-PQVLLSR  202 (526)
Q Consensus       191 ~~~rg-pqi~lSR  202 (526)
                      ...+| ..|.||-
T Consensus        82 ~~~~~~krI~LSl   94 (100)
T cd05693          82 KSKSGKKRIELSL   94 (100)
T ss_pred             CCCCCCEEEEEEC
T ss_conf             8877854899982


No 99 
>smart00322 KH K homology RNA-binding domain.
Probab=95.39  E-value=0.017  Score=37.68  Aligned_cols=41  Identities=32%  Similarity=0.558  Sum_probs=36.6

Q ss_pred             CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECC
Q ss_conf             78799998534221102544278999998616745785522
Q gi|254780788|r  305 VGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEE  345 (526)
Q Consensus       305 ~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~  345 (526)
                      .....+.||.+.....||++|.|++...+.|||+|++....
T Consensus         2 ~~~~~i~vp~~~~g~iIG~~G~~i~~i~~~~~~~I~i~~~~   42 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG   42 (69)
T ss_pred             CEEEEEEECHHHCCEEECCCCCCHHHHHHHHCCEEEECCCC
T ss_conf             87999998978768549999845799999728889977999


No 100
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=95.25  E-value=0.042  Score=34.69  Aligned_cols=58  Identities=21%  Similarity=0.238  Sum_probs=51.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf             1122588846788887732111477750588887765305889999999999999999
Q gi|254780788|r  362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEG  419 (526)
Q Consensus       362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~  419 (526)
                      +....+|...-.+.|.+.|++|++++|.++++.|....++..+.+..|+..|+..+..
T Consensus       209 LslVagi~~~q~~~L~~~GI~Ti~~LA~~~~~~l~~~~~~~~~~~~~l~~qA~a~~~~  266 (457)
T TIGR03491       209 LSLVPGIGPSRYRLLQELGIHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQARAQLEG  266 (457)
T ss_pred             HHHHCCCCHHHHHHHHHCCCCCHHHHHCCCHHHCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             7660599999999999859987999862994330356663669999999999984379


No 101
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal.  pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=95.23  E-value=0.072  Score=33.00  Aligned_cols=64  Identities=17%  Similarity=0.248  Sum_probs=50.6

Q ss_pred             HCCCEEEEEEEECCCCEEEEEEC--CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf             20838999998405763899957--93587447874------887511527669999976113587028987159
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLG--NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSRT  203 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg--~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt  203 (526)
                      .+|+++.|+|.++..-..+|++.  +.+|++--+|+      -|.+.++.||.+++-+.+++...   .+-||-|
T Consensus         2 evg~i~~G~V~~i~~fGAFV~i~g~~~~GLvHiSeis~~rv~~~~dvv~vGd~V~Vkvi~id~~~---ki~LSls   73 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD---KMKLSLS   73 (73)
T ss_pred             CCCCEEEEEEEEEEECCEEEEECCCCCCEEEEEECCCCCCCCCHHHHCCCCCEEEEEEEEECCCC---CEEEECC
T ss_conf             78869999998997532399908988435599560541202899995579999999999886899---8898419


No 102
>PRK02362 ski2-like helicase; Provisional
Probab=94.96  E-value=0.34  Score=28.07  Aligned_cols=100  Identities=19%  Similarity=0.133  Sum_probs=65.7

Q ss_pred             HHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHCCHHHH---HHCCCCCCHHHHHH
Q ss_conf             50588887765305889999999999999999--------------99998987754284356---64077999899999
Q gi|254780788|r  388 ACVKISEIASIEGFDEETAVEIQGRAREYLEG--------------IDITLQKKIRELGVSEE---LCSIPGIDSKIKVA  450 (526)
Q Consensus       388 a~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~--------------~~~~~~e~~~e~~~~e~---L~~l~gl~~~~~~~  450 (526)
                      ...+..++..--|++.-....+++.|.-++-.              ...... .+=..|+.++   |+.++|+...-+-+
T Consensus       589 ~E~~~~~I~~ky~v~~G~l~~l~~~a~~~~~~~~~~~~~l~~~~~~~l~~l~-~Rl~~Gv~~ELl~L~~I~gvgr~RAR~  667 (736)
T PRK02362        589 DEVSEDRICERYGVGPGDIRGKVETAEWLMHAAERLAGELDLKCTREARELE-KRVHYGVREELLDLVGLRGIGRVRARR  667 (736)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHCCCCHHHHHHCCCCCCCHHHHHH
T ss_conf             0798999999879892899999999999999999999986668999999999-999859877689770889999899999


Q ss_pred             HHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC
Q ss_conf             998798478896532677521231234443211245334358899999999998412
Q gi|254780788|r  451 LGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARY  507 (526)
Q Consensus       451 L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~  507 (526)
                      |-++||+|++|||.....+|..+                   +.+.-|.+++..+..
T Consensus       668 Ly~aGi~s~~dla~A~p~~l~~i-------------------lg~~~a~~i~~~~~~  705 (736)
T PRK02362        668 LYNAGITSRADLRAADKEVVAAI-------------------LGPKIAERVLEQLGR  705 (736)
T ss_pred             HHHCCCCCHHHHHHCCHHHHHHH-------------------HHHHHHHHHHHHHCC
T ss_conf             99879999999970999999999-------------------777899999998388


No 103
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=94.95  E-value=0.14  Score=30.88  Aligned_cols=51  Identities=31%  Similarity=0.457  Sum_probs=44.0

Q ss_pred             CCCCCCCCC---CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             011122588---8467888877321114777505888877653058899999999
Q gi|254780788|r  360 QFFMQAINV---DEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG  411 (526)
Q Consensus       360 ~~f~e~LdV---DE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~  411 (526)
                      ..|.-+|+|   .+..|..|... |.|++.+..++.++|.+|+||.+.+|..|.+
T Consensus       508 ~r~L~ALGI~~VG~~~Ak~La~~-f~sl~~l~~as~e~L~~I~giG~~~A~si~~  561 (668)
T PRK07956        508 ARFLYALGIRHVGEKAAKALARH-FGSLEALEAASEEELAAVEGIGEEVAQSIVE  561 (668)
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHCCCCCCHHHHHHHHH
T ss_conf             88998627864129999999999-6689999708999985768844999999999


No 104
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=94.89  E-value=0.12  Score=31.36  Aligned_cols=63  Identities=24%  Similarity=0.337  Sum_probs=53.4

Q ss_pred             HHHHHHCCCEEEEEEEECCCCEEEEEECC-CEEEEEHHHC----------CCCCCCCCCCEEEEEEEEECCCCC
Q ss_conf             99985208389999984057638999579-3587447874----------887511527669999976113587
Q gi|254780788|r  132 LEFKDKVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDET----------ISRENLRPGDRVKSYIYDVRREQR  194 (526)
Q Consensus       132 ~ef~~r~Geiv~G~V~r~e~~~iiVdlg~-~ea~Lp~~e~----------ip~E~~~~Gdrika~i~~V~~~~r  194 (526)
                      ..|...+|++|-|.|.-+...++.||+|. .-|+||-++.          =.+..|++||-+-|-|.+|.++..
T Consensus        58 g~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~  131 (239)
T COG1097          58 GRYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGE  131 (239)
T ss_pred             CCCCCCCCCEEEEEEEEECCCCEEEECCCCCCEEEEHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCC
T ss_conf             75248889999999999715633897289532374266620022554223452226768789999997267775


No 105
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=94.84  E-value=0.18  Score=30.06  Aligned_cols=62  Identities=23%  Similarity=0.251  Sum_probs=45.4

Q ss_pred             CCHHHHHHHHCCCCCCCEE--------EECCC--------CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf             8789999976286654248--------98756--------78799998534221102544278999998616745785
Q gi|254780788|r  281 PDSATFVINALRPAIVTKV--------VLDED--------VGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII  342 (526)
Q Consensus       281 ~d~~~fi~nAl~PA~v~~v--------~~de~--------~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~  342 (526)
                      -=+.+.+..||.-|+.-+.        .+.+-        -+...+-+|.+.....||.+|.|+|--..-||-+|||-
T Consensus       510 Gi~~~il~~Al~qA~~~R~~IL~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~gGk~Ik~i~~~tg~~I~i~  587 (684)
T TIGR03591       510 GITREIMEQALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE  587 (684)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECHHHHHHEECCCCHHHHHHHHHHCCEEEEE
T ss_conf             978999999999999999999999997352543344578875799997878866507875288989999889889985


No 106
>KOG1070 consensus
Probab=94.80  E-value=0.15  Score=30.60  Aligned_cols=91  Identities=20%  Similarity=0.295  Sum_probs=69.1

Q ss_pred             HHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEH------HHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEC----CC
Q ss_conf             520838999998405763899957-93587447------87488751152766999997611358702898715----98
Q gi|254780788|r  136 DKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRR------DETISRENLRPGDRVKSYIYDVRREQRGPQVLLSR----TH  204 (526)
Q Consensus       136 ~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~------~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSR----t~  204 (526)
                      -++|++++|.|.-+....+++-|+ +++|+.|-      -+-.+.-.|.+|+.+.+-++.|+..++--.+.|--    -.
T Consensus      1160 lk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~ 1239 (1710)
T KOG1070        1160 LKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDT 1239 (1710)
T ss_pred             CCCCCEEEEEEEEECCCCEEEEECCCEEEEEECCCCCCCHHHHHHCCCCCCCEEEEEEEEEECCCCEEEEEEECCCCCCC
T ss_conf             25576468899970377489997156289998345664023222113885444315899852368628999852666884


Q ss_pred             HHHHHHHHHHHHHHHHCCEEEE
Q ss_conf             8999999997667775580878
Q gi|254780788|r  205 PQFMVKLFHMEVPEIYNGIVQV  226 (526)
Q Consensus       205 p~~l~~Lf~~EVPEI~~G~ieI  226 (526)
                      +..++-+=.+-+-+-++|+|+-
T Consensus      1240 ~~~~~~~~~l~~gd~~~g~v~~ 1261 (1710)
T KOG1070        1240 VKLLKDSKDLKKGDREDGTVEV 1261 (1710)
T ss_pred             HHHHHHHHHHHCCCCCCCEEEE
T ss_conf             4443455664226300434999


No 107
>PRK02362 ski2-like helicase; Provisional
Probab=94.55  E-value=0.072  Score=32.98  Aligned_cols=49  Identities=14%  Similarity=0.227  Sum_probs=40.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             112258884678888773211147775058888776530588999999999
Q gi|254780788|r  362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGR  412 (526)
Q Consensus       362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~r  412 (526)
                      ++...+|...-|..|+.+||+|+++||.|+++.|..|  +.+.+|+.+.+-
T Consensus       654 L~~I~gvgr~RAR~Ly~aGi~s~~dla~A~p~~l~~i--lg~~~a~~i~~~  702 (736)
T PRK02362        654 LVGLRGIGRVRARRLYNAGITSRADLRAADKEVVAAI--LGPKIAERVLEQ  702 (736)
T ss_pred             HCCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH--HHHHHHHHHHHH
T ss_conf             7088999989999999879999999970999999999--777899999998


No 108
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=94.38  E-value=0.35  Score=27.92  Aligned_cols=59  Identities=20%  Similarity=0.276  Sum_probs=48.9

Q ss_pred             HCCCEEEEEEEECCCCEEEEEECC-CEEEEEHHHC---CCC------CCCCCCCEEEEEEEEECCCCCE
Q ss_conf             208389999984057638999579-3587447874---887------5115276699999761135870
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDET---ISR------ENLRPGDRVKSYIYDVRREQRG  195 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg~-~ea~Lp~~e~---ip~------E~~~~Gdrika~i~~V~~~~rg  195 (526)
                      +.|+++.|.|+.+....++|.|++ +.|.....+.   .+.      ..|..|.-+++-+..|+.+.+-
T Consensus         2 keGq~vRGyVk~v~~~GvFv~Ls~~v~grv~~~nls~~~v~dp~~~~~~fp~GkLv~~kVlsvd~~~~~   70 (74)
T cd05705           2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNL   70 (74)
T ss_pred             CCCCEEEEEEEECCCCCEEEEECCCEEEEEEEECCCHHHHCCHHHHHCCCCCCCEEEEEEEEECCCCCE
T ss_conf             988798999998268739999568748999970036212068268861489998999999998677684


No 109
>PRK08609 hypothetical protein; Provisional
Probab=94.36  E-value=0.32  Score=28.18  Aligned_cols=33  Identities=24%  Similarity=0.414  Sum_probs=16.4

Q ss_pred             EECCCCCCCCC----CCCHHHHHHHH--HHHCCEEEEEE
Q ss_conf             98534221102----54427899999--86167457855
Q gi|254780788|r  311 IVPKEQLSLAI----GRRGQNVRLAS--QLTGWTIDIIT  343 (526)
Q Consensus       311 ~v~~~qls~AI----Gk~GqNvrLas--~Ltg~~idi~~  343 (526)
                      +||+++...|+    |.+-.|++|-.  .=-||+++=+.
T Consensus       243 vv~~~~fg~aLlyFTGSk~hNi~lR~~A~~kG~~LnEyG  281 (570)
T PRK08609        243 LVEPEAFATTLHHFTGSKDHNVRMRQLAKARGEKISEYG  281 (570)
T ss_pred             EECHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             808899899999976669999999999997488503024


No 110
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=94.24  E-value=0.17  Score=30.30  Aligned_cols=162  Identities=21%  Similarity=0.278  Sum_probs=76.6

Q ss_pred             EECCCCCEE--EEEEEECCCCCCCEEEEECCC--C--HHHHHH-HHHHCCCCEEEEE-----CCCCHHHHHHH---HCCC
Q ss_conf             631677503--499994089988127655488--6--217889-9862778267995-----59878999997---6286
Q gi|254780788|r  229 VSRDPGSRA--KLAVFSSDSSIDPVGACVGMR--G--SRVQAV-VTELRDEKIDIVV-----WSPDSATFVIN---ALRP  293 (526)
Q Consensus       229 iaR~pG~Rs--KIAV~s~d~~iDpVGAcVG~r--G--sRiq~I-~~EL~gEkIDii~-----ws~d~~~fi~n---Al~P  293 (526)
                      ..=+||.|+  |+||.-.-...=-...|+-..  +  .--++- .+=+...++..|-     -|....+|+..   .+.+
T Consensus       333 lglDPg~rtG~k~Avvd~tGk~l~~~~Iyp~~p~~~~~~~~~~l~~l~~~~~Ve~iaIGngTaSrete~fv~~vl~~~~~  412 (780)
T COG2183         333 LGLDPGFRTGCKVAVVDDTGKLLDTATIYPHPPVNQSDKAEATLKDLIRKYKVELIAIGNGTASRETEKFVADVLKELPK  412 (780)
T ss_pred             EECCCCCCCCCEEEEECCCCCEECEEEEECCCCCCCHHHHHHHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHHCCC
T ss_conf             20487630130799983788555316997279754157899999999998371079873687655479999999984667


Q ss_pred             CCCCEEEECCCCCEEE-------EEECCCCCC----CCCCCCHHHHHHHHHHHCCEEEEEE--CCCHHH-----HHHCCC
Q ss_conf             6542489875678799-------998534221----1025442789999986167457855--220011-----010012
Q gi|254780788|r  294 AIVTKVVLDEDVGRIE-------VIVPKEQLS----LAIGRRGQNVRLASQLTGWTIDIIT--EEEDSI-----NRQKDF  355 (526)
Q Consensus       294 A~v~~v~~de~~~~~~-------v~v~~~qls----~AIGk~GqNvrLas~Ltg~~idi~~--~~~~~~-----~~~~e~  355 (526)
                      -.+..|++.|+.-+..       --.|+-+.+    .+|+|+=|+-.  ++|.  +||-+|  ..++.-     +-....
T Consensus       413 ~~~~~viVsEagAsvYsaSe~A~~EFPdL~v~~r~aVSIaRrlqdPL--aElv--kIdpKSiGVgqyQHdv~q~~L~~~L  488 (780)
T COG2183         413 EKVLKVIVSEAGASVYSASERAAEEFPDLDVSLRGAVSIARRLQDPL--AELV--KIDPKSIGVGQYQHDVSQKKLAESL  488 (780)
T ss_pred             CCCCEEEECCCCCCHHCCCHHHHHHCCCCCHHHHHHHHHHHHHCCHH--HHHH--HCCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf             89867997265310213448899877999666776877988620647--6876--1475314555321468878999999


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             21000111225888467888877321114777505888877653058899999999
Q gi|254780788|r  356 NERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG  411 (526)
Q Consensus       356 ~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~  411 (526)
                      .......++..+||...                 |+..-|..+-|+..-.|..+..
T Consensus       489 d~vved~VN~VGVdvNt-----------------Asa~lL~~VsGL~kt~A~nIv~  527 (780)
T COG2183         489 DAVVEDCVNAVGVDVNT-----------------ASASLLSYVSGLNKTLAKNIVA  527 (780)
T ss_pred             HHHHHHHHCCCCCCCCC-----------------CCHHHHHHHHHHCHHHHHHHHH
T ss_conf             99999873102611342-----------------7899998774025667899999


No 111
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=94.14  E-value=0.29  Score=28.59  Aligned_cols=55  Identities=22%  Similarity=0.371  Sum_probs=48.0

Q ss_pred             CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC--------CCCCCCCCCCEEEEEEEEECCCC
Q ss_conf             838999998405763899957-93587447874--------88751152766999997611358
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET--------ISRENLRPGDRVKSYIYDVRREQ  193 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~--------ip~E~~~~Gdrika~i~~V~~~~  193 (526)
                      |+++.|+|+.+..-.+.|.|+ +..|.+.-+|.        -|...|+.||.|+|-|.-++...
T Consensus         1 G~vv~g~V~sik~~~l~V~L~d~~~GrVhiSei~D~~~~~k~P~~~~k~Gq~V~~rViG~~d~k   64 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK   64 (70)
T ss_pred             CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCCCHHHHCCCCCEEEEEEEEEECCC
T ss_conf             9779999999946708999689957789845521355555694685689999999999765462


No 112
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH).  The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold.  The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.  In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=94.02  E-value=0.19  Score=29.85  Aligned_cols=100  Identities=30%  Similarity=0.570  Sum_probs=72.5

Q ss_pred             EEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEE-----EECCCCHHHHHHHHCCC--CCCCEEEECCCCCEEEE
Q ss_conf             499994089988127655488621788998627782679-----95598789999976286--65424898756787999
Q gi|254780788|r  238 KLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDI-----VVWSPDSATFVINALRP--AIVTKVVLDEDVGRIEV  310 (526)
Q Consensus       238 KIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDi-----i~ws~d~~~fi~nAl~P--A~v~~v~~de~~~~~~v  310 (526)
                      -|++|+.||+.      +.-.|.=|+.+.+.|.- ||=|     ++-+++-+.=+++.+-|  |.+..+..|+...  +|
T Consensus        10 ~ivIYt~~p~~------f~~~~~li~~iAk~ikK-RIviRpdpsil~~~e~a~~~I~~ivPeeA~i~~i~FD~~~g--EV   80 (145)
T cd02410          10 ELVVYTKNPEL------FAEDGDLVKDLAKDLRK-RIVIRPDPSVLKPPEEAIKIILEIVPEEAGITDIYFDDDTG--EV   80 (145)
T ss_pred             EEEEEECCHHH------HCCCCHHHHHHHHHHHC-EEEECCCHHHCCCHHHHHHHHHHHCCCCCCCEEEEECCCCC--EE
T ss_conf             28999799799------72674099999998720-27973880341899999999998589646844689748885--79


Q ss_pred             EECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCC
Q ss_conf             985342211025442789999986167457855220
Q gi|254780788|r  311 IVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE  346 (526)
Q Consensus       311 ~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~  346 (526)
                      +..-+.=.++|||+|.|.+--..=|||...|....-
T Consensus        81 ~Iea~kPg~viGk~g~~l~eI~~~tGW~p~v~RtPp  116 (145)
T cd02410          81 IIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP  116 (145)
T ss_pred             EEEECCCEEEECCCCHHHHHHHHHHCCEEEEEECCC
T ss_conf             999779777972761679999997398157886599


No 113
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=93.91  E-value=0.15  Score=30.72  Aligned_cols=12  Identities=8%  Similarity=0.138  Sum_probs=4.8

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999986
Q gi|254780788|r    7 LELLQIADAVAY   18 (526)
Q Consensus         7 ~ell~vie~va~   18 (526)
                      .++..+++.+|.
T Consensus         4 ~~i~~~L~~la~   15 (334)
T smart00483        4 RGIIDALEILAE   15 (334)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 114
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits.  Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions.  Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=93.87  E-value=0.31  Score=28.30  Aligned_cols=61  Identities=23%  Similarity=0.361  Sum_probs=45.9

Q ss_pred             HCCCEEEEEEEECCCC-EEEEEEC-CCEEEEE------HHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf             2083899999840576-3899957-9358744------78748875115276699999761135870289871
Q gi|254780788|r  137 KVGEIISGTVKRVEYG-NVIVDLG-NSDGVIR------RDETISRENLRPGDRVKSYIYDVRREQRGPQVLLS  201 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~-~iiVdlg-~~ea~Lp------~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lS  201 (526)
                      ..|.++.|.|.++..+ .++|.|+ +.-|..-      ...-.|-|.|++|+-+||+|..    .++..+.||
T Consensus         2 ~~G~i~~G~V~kV~p~~Gl~Vqlp~g~~G~V~itdl~D~y~~~Pl~~f~~~qiVrc~VLs----~~~g~~~LS   70 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILS----KKDGKYQLS   70 (72)
T ss_pred             CCCCEEEEEEEEECCCCCEEEECCCCCEEEEEEEEECCCCCCCCHHHCCCCCEEEEEEEE----CCCCEEEEE
T ss_conf             887474039999728985699848996668999971474544967765789789999995----369989987


No 115
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=93.83  E-value=0.15  Score=30.62  Aligned_cols=68  Identities=21%  Similarity=0.278  Sum_probs=44.7

Q ss_pred             HHHCCCEEEEEEEECCCCEEEEEECC------------CEEEEEHHHCCC------CCCCCCCCEEEEEEEEECCCCCEE
Q ss_conf             85208389999984057638999579------------358744787488------751152766999997611358702
Q gi|254780788|r  135 KDKVGEIISGTVKRVEYGNVIVDLGN------------SDGVIRRDETIS------RENLRPGDRVKSYIYDVRREQRGP  196 (526)
Q Consensus       135 ~~r~Geiv~G~V~r~e~~~iiVdlg~------------~ea~Lp~~e~ip------~E~~~~Gdrika~i~~V~~~~rgp  196 (526)
                      ..++|++|+|.|.++......|.+-.            ..|.+..++.-.      .+.||+||-|||-|....     +
T Consensus        61 ~p~vGdiVig~V~~v~~~~a~v~I~~v~g~~~~~l~~~~~g~i~i~~v~~~~~~~~~d~fr~gDIVrAkVis~~-----~  135 (187)
T PRK09521         61 LLKKGDIVYGRVVDVKEQRALVRIVSIEGRGNRELATSKLGGIHISQVSDGYVEDLTDAFKIGDIVRAKVISTT-----D  135 (187)
T ss_pred             CCCCCCEEEEEEEEECCCEEEEEEEEECCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHCCCCCEEEEEEEECC-----C
T ss_conf             88989999999999547679999999868688625654488888543786674526752487868999997359-----8


Q ss_pred             EEEEECCCHHH
Q ss_conf             89871598899
Q gi|254780788|r  197 QVLLSRTHPQF  207 (526)
Q Consensus       197 qi~lSRt~p~~  207 (526)
                      ++.||-..|+|
T Consensus       136 ~~~Lst~~~eL  146 (187)
T PRK09521        136 PIQLSTKGKDL  146 (187)
T ss_pred             CEEEEECCCCC
T ss_conf             46999538884


No 116
>pfam10447 EXOSC1 Exosome component EXOSC1/CSL4. This family of proteins are components of the exosome 3'-5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions.
Probab=93.83  E-value=0.35  Score=27.89  Aligned_cols=53  Identities=32%  Similarity=0.595  Sum_probs=41.7

Q ss_pred             HHCCCEEEEEEEECCCCEEEEEE---C------CCEEEEEHHHCCCCC--------CCCCCCEEEEEEEE
Q ss_conf             52083899999840576389995---7------935874478748875--------11527669999976
Q gi|254780788|r  136 DKVGEIISGTVKRVEYGNVIVDL---G------NSDGVIRRDETISRE--------NLRPGDRVKSYIYD  188 (526)
Q Consensus       136 ~r~Geiv~G~V~r~e~~~iiVdl---g------~~ea~Lp~~e~ip~E--------~~~~Gdrika~i~~  188 (526)
                      .++|.+|++.|.|+......+++   |      .-.|++.+.+.=+.|        .|||||-|+|-+..
T Consensus         2 P~vGdiV~arVtrv~~~~a~~~Il~v~~~~l~~~f~G~IR~~DVRate~Dkv~~~~~FrPGDiVrA~ViS   71 (72)
T pfam10447         2 PKVGDIVLARVTRVTPRQAYCEILAVGGTALKETFKGIIRKQDVRATEKDRVKIYECFRPGDIVRAKVIS   71 (72)
T ss_pred             CCCCCEEEEEEEEECHHEEEEEEEEECCEECCCCEEEEEEHHHCCCCCCCEEEHHHCCCCCCEEEEEEEE
T ss_conf             9899999999999750157999999999987885558989476665641018384683999899999962


No 117
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=93.77  E-value=0.28  Score=28.60  Aligned_cols=34  Identities=24%  Similarity=0.377  Sum_probs=17.3

Q ss_pred             EECCCCCCCCC----CCCHHHHHH--HHHHHCCEEEEEEC
Q ss_conf             98534221102----544278999--99861674578552
Q gi|254780788|r  311 IVPKEQLSLAI----GRRGQNVRL--ASQLTGWTIDIITE  344 (526)
Q Consensus       311 ~v~~~qls~AI----Gk~GqNvrL--as~Ltg~~idi~~~  344 (526)
                      +||.++...|.    |.+--|+.|  -++=-||+++=++-
T Consensus       237 ~~~~~~~~~aLl~fTGS~~fn~~lR~~A~~kG~~Lne~GL  276 (307)
T cd00141         237 VVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGL  276 (307)
T ss_pred             ECCHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             8389999999998447699999999999985996542017


No 118
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=93.66  E-value=0.35  Score=27.92  Aligned_cols=299  Identities=22%  Similarity=0.292  Sum_probs=147.7

Q ss_pred             HCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEE--CCCCCCCCEECHHHH--HHHCCCCCCC
Q ss_conf             239999999999999999999613687453599974998839999998851--767787532348999--8628898647
Q gi|254780788|r   19 EKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVV--EEVENYTCQISLKVA--RDRDPSIDIG   94 (526)
Q Consensus        19 EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VV--edved~~~eI~l~~A--~~~~~~~~iG   94 (526)
                      +|-++++.+-....+-+..|.+-     .+-.++|++.--.+--++...+|  .-......||+...-  +.--.++.+.
T Consensus       178 d~pl~~~ele~ia~eIi~~a~~~-----~~sfIEi~r~GatVvQlrn~RIvIarPPfSd~~EITavRPvvk~~ledY~L~  252 (604)
T COG1855         178 DKPLTREELEEIAREIIERAKRD-----PDSFIEIDRPGATVVQLRNYRIVIARPPFSDRWEITAVRPVVKLSLEDYGLS  252 (604)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHC-----CCCEEEEECCCCEEEEECCEEEEEECCCCCCCEEEEEEEEEEEEEHHHCCCC
T ss_conf             76688999999999999987528-----6764898069966998435799994599877628999713699605542879


Q ss_pred             CEEEEECCHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCC-CE------------EEEEE
Q ss_conf             37998508456207---9999999999999999998877999985208389999984057-63------------89995
Q gi|254780788|r   95 GVVSDPLPPMDFGR---VAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEY-GN------------VIVDL  158 (526)
Q Consensus        95 D~i~~~i~~~~fgR---iaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~-~~------------iiVdl  158 (526)
                      |.+.+-+....=|=   -+-.+-|..|.|-         ..+|-...|.||    |-++. ++            ..-++
T Consensus       253 dkl~eRL~eraeGILIAG~PGaGKsTFaqA---------lAefy~~~GkiV----KTmEsPRDl~v~~eITQYs~l~g~m  319 (604)
T COG1855         253 DKLKERLEERAEGILIAGAPGAGKSTFAQA---------LAEFYASQGKIV----KTMESPRDLQVSPEITQYSPLEGDM  319 (604)
T ss_pred             HHHHHHHHHHHCCEEEECCCCCCHHHHHHH---------HHHHHHHCCCEE----EECCCCCCCCCCHHHHHCCCCCCCH
T ss_conf             899999886416469956999974689999---------999998669688----6324751356886663206445645


Q ss_pred             CCCEEE--E-EHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCH-----HHHHHHHHHHHHHHHCCEEEEEEEE
Q ss_conf             793587--4-4787488751152766999997611358702898715988-----9999999976677755808785663
Q gi|254780788|r  159 GNSDGV--I-RRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHP-----QFMVKLFHMEVPEIYNGIVQVKAVS  230 (526)
Q Consensus       159 g~~ea~--L-p~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p-----~~l~~Lf~~EVPEI~~G~ieIk~ia  230 (526)
                      +.+--+  | .++..|-.|- |.-+-++.| .+.+.-.-|--=++--|.|     .|+.+.=--=+|-|-|-+|=|+   
T Consensus       320 e~t~DiLLLvRPDYTIyDEm-R~t~DF~vy-aDmRLAGVGMVGVVHATrpIDAiQR~igRVELG~IPqIvDTVIfI~---  394 (604)
T COG1855         320 EKTADILLLVRPDYTIYDEM-RKTEDFQVY-ADLRLAGVGMVGVVHATRPIDAIQRFIGRVELGMIPQIVDTVIFIK---  394 (604)
T ss_pred             HHHCCEEEEECCCCEEHHHH-HCCCCEEEE-EEEECCCCCEEEEEECCCHHHHHHHHHCCEEECCCCCCEEEEEEEE---
T ss_conf             55233799965884510334-156661676-6500115754768961780589998644063146641226899981---


Q ss_pred             CCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHH--------HHHHH------CCCCEEEEECCCCH--------HHHH-
Q ss_conf             1677503499994089988127655488621788--------99862------77826799559878--------9999-
Q gi|254780788|r  231 RDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQA--------VVTEL------RDEKIDIVVWSPDS--------ATFV-  287 (526)
Q Consensus       231 R~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~--------I~~EL------~gEkIDii~ws~d~--------~~fi-  287 (526)
                        .|.-+||-..|.--.+     --||+-.-.-.        ++.+|      -||.+=+++-....        ..-| 
T Consensus       395 --~G~V~kVy~ls~tVKV-----P~Gm~EeDLARPVIeVrDfeTg~~eYEIYtfGEqvvVvPv~~~~~~~~~~~a~~~i~  467 (604)
T COG1855         395 --DGEVAKVYELSYTVKV-----PTGMTEEDLARPVIEVRDFETGELEYEIYTFGEQVVVVPVKEEEESPALKLAEEEIE  467 (604)
T ss_pred             --CCEEEEEEEEEEEEEC-----CCCCCHHHHCCCEEEEEECCCCCEEEEEEECCCEEEEEECCCCCCCCHHHHHHHHHH
T ss_conf             --8818899999999976-----788786771585389765036854689997164799997568777726677999999


Q ss_pred             --HHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHH
Q ss_conf             --97628665424898756787999985342211025442789999986167457855220011
Q gi|254780788|r  288 --INALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSI  349 (526)
Q Consensus       288 --~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~~  349 (526)
                        ++.+.|. -..|.+ ...+++.|.||+..++..|||+|+|+.=-.+-.|.+|+++..++..+
T Consensus       468 ~~i~r~~p~-~~eVe~-~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~~~~  529 (604)
T COG1855         468 REIKRYLPG-DVEVEV-VGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEE  529 (604)
T ss_pred             HHHHHHCCC-CCEEEE-ECCCEEEEEECHHHHHHHHHCCCCHHHHHHHHHCCEEEEEECCCCCC
T ss_conf             999974799-825999-61871799948788567761055318999987498068888665666


No 119
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=93.60  E-value=0.63  Score=26.08  Aligned_cols=61  Identities=23%  Similarity=0.342  Sum_probs=46.5

Q ss_pred             CCEEEEEEEECCCCEEEEEE-CCCEEEEEHHHCCC----CCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf             83899999840576389995-79358744787488----75115276699999761135870289871
Q gi|254780788|r  139 GEIISGTVKRVEYGNVIVDL-GNSDGVIRRDETIS----RENLRPGDRVKSYIYDVRREQRGPQVLLS  201 (526)
Q Consensus       139 Geiv~G~V~r~e~~~iiVdl-g~~ea~Lp~~e~ip----~E~~~~Gdrika~i~~V~~~~rgpqi~lS  201 (526)
                      |-+|.+.|+++-.+.+++.+ +--.|..-.-+.-|    ...|++|+++||-|.-|...+|  +|-||
T Consensus         1 GmlV~a~V~kV~~~Gl~~~fl~~F~G~Vd~~HL~~~~~~~~~Y~~~~~v~ArIL~Vdp~tK--~V~Ls   66 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTK--VVGLS   66 (66)
T ss_pred             CCEEEEEEEEECCCCEEEEEECCEEEEEEHHHCCCCCCCCCCCCCCCEEEEEEEEECCCCC--EEECC
T ss_conf             9559999999817948999651289998876768776870004679889999999988747--88539


No 120
>PRK12704 phosphodiesterase; Provisional
Probab=93.52  E-value=0.64  Score=25.99  Aligned_cols=150  Identities=20%  Similarity=0.284  Sum_probs=94.2

Q ss_pred             HHHHHHHCCCCCCCEEEECCCCCEEEEEECCCC-CCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHCCCCCCCCCC
Q ss_conf             999997628665424898756787999985342-2110254427899999861674578552200110100122100011
Q gi|254780788|r  284 ATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQ-LSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFF  362 (526)
Q Consensus       284 ~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~q-ls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~~~~~~~f  362 (526)
                      ...+..|++---..-+   -+...-.|-.|.+. .-.-|||.|.|+|---.+||-.|-|-...+.               
T Consensus       126 r~Ii~~AIQR~A~e~~---~E~tvsvV~LPsdemKGRIIGREGRNIRa~E~~TGVDlIIDDtPe~---------------  187 (455)
T PRK12704        126 KEILAQAIQRCAAEHA---AENTVSVVNLPNDEMKGRIIGREGRNIRTLETLTGVDIIIDDTPEA---------------  187 (455)
T ss_pred             HHHHHHHHHHHCCCCC---CHHEEEEEECCCHHHHCCCCCCCCCHHHHHHHHHCCEEEECCCCCE---------------
T ss_conf             9999999986364300---1310466854856764640077752399999986964897599983---------------


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHH-HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCC
Q ss_conf             1225888467888877321114-777505888877653058899999999999999999999898775428435664077
Q gi|254780788|r  363 MQAINVDEIIAHLLVAEGFADV-EELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIP  441 (526)
Q Consensus       363 ~e~LdVDE~iA~~LV~eGf~Si-EeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~  441 (526)
                                   .+-.||+.+ -+||....+.|..=.-+.+..++++.++|+.-+...-.+..+..-     .+ +.+.
T Consensus       188 -------------V~lS~FDpvRREiAr~aLe~Li~DGRIhPaRIEe~v~k~~~ei~~~i~~~Ge~a~-----~e-lgi~  248 (455)
T PRK12704        188 -------------VILSGFDPIRREIARLALEKLVEDGRIHPARIEEMVEKVRKEVDEEIREEGEQAV-----FE-LGIH  248 (455)
T ss_pred             -------------EEEECCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HH-CCCC
T ss_conf             -------------7885687788999999999998848958899999999999999999999999999-----98-0999


Q ss_pred             CCCHHHHHHHHHCCCCC------------HHHHHHCCHHHH
Q ss_conf             99989999999879847------------889653267752
Q gi|254780788|r  442 GIDSKIKVALGENGIKT------------MEDLAGCSVDDL  470 (526)
Q Consensus       442 gl~~~~~~~L~e~gIkt------------leDlAels~dEL  470 (526)
                      ||.++++-.|+.=...|            +-.||++-..||
T Consensus       249 ~l~peli~~lGrLkyRtSygQNvL~Hs~Eva~lag~~A~el  289 (455)
T PRK12704        249 GLHPELIKLIGRLKYRTSYGQNVLQHSREVAHLAGLMAAEL  289 (455)
T ss_pred             CCCHHHHHHHHHEECCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99979999986310202040479999999999999999982


No 121
>PRK10811 rne ribonuclease E; Reviewed
Probab=93.44  E-value=0.24  Score=29.14  Aligned_cols=162  Identities=22%  Similarity=0.326  Sum_probs=97.8

Q ss_pred             HHCCCEEEEEEEECCCC--EEEEEEC-CCEEEEEHHHCCCC---------------CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf             52083899999840576--3899957-93587447874887---------------511527669999976113587028
Q gi|254780788|r  136 DKVGEIISGTVKRVEYG--NVIVDLG-NSDGVIRRDETISR---------------ENLRPGDRVKSYIYDVRREQRGPQ  197 (526)
Q Consensus       136 ~r~Geiv~G~V~r~e~~--~iiVdlg-~~ea~Lp~~e~ip~---------------E~~~~Gdrika~i~~V~~~~rgpq  197 (526)
                      .+.|.|--|.|.|+..+  -.+||+| .-.||||-++..+.               +.++.|+.|-+=|..=...+|||.
T Consensus        36 q~kgNIYKGkV~rVePgLqAAFVDiG~eR~GFLp~kEI~~ey~~~~~~~~grp~I~dvLkeGQeILVQV~KEp~GtKGAr  115 (1063)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAA  115 (1063)
T ss_pred             CCCCCCEEEEEEEECCCCEEEEEECCCCCCCCCCHHHCCHHHCCCCCCCCCCCCHHHHCCCCCEEEEEEEECCCCCCCCC
T ss_conf             34054268999785688605777238975542168882865426553435687878836799989999966787897836


Q ss_pred             EE---------------------EECCCH-----HHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECC------
Q ss_conf             98---------------------715988-----9999999976677755808785663167750349999408------
Q gi|254780788|r  198 VL---------------------LSRTHP-----QFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSD------  245 (526)
Q Consensus       198 i~---------------------lSRt~p-----~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d------  245 (526)
                      +.                     +||--.     .|-.-|-.+++|+ .-|+     |.|-+|.-....-...|      
T Consensus       116 LTT~ISLaGRYLVLMPn~~~~gGISRKIe~eER~rLkeiL~~L~~Pe-g~Gl-----IVRTAa~g~s~eeL~~Dl~~Ll~  189 (1063)
T PRK10811        116 LTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPE-GMGL-----IVRTAGVGKSAEALQWDLSFRLK  189 (1063)
T ss_pred             EEEEEEECCEEEEECCCCCCCCCEECCCCCHHHHHHHHHHHHCCCCC-CCEE-----EEECCCCCCCHHHHHHHHHHHHH
T ss_conf             64215434201898248987761514789078999999997135788-8269-----99757689999999999999999


Q ss_pred             --------CCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCC-HHHHHH---HHC-CCCCCCEEEECC
Q ss_conf             --------9988127655488621788998627782679955987-899999---762-866542489875
Q gi|254780788|r  246 --------SSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPD-SATFVI---NAL-RPAIVTKVVLDE  303 (526)
Q Consensus       246 --------~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d-~~~fi~---nAl-~PA~v~~v~~de  303 (526)
                              ..--|--.|+-.-+.-+..+++.+-++.|+-|.-++. ..+++.   ..+ .|-...+|....
T Consensus       190 ~W~~I~k~~~~~~AP~LIyqE~~li~R~iRD~l~~di~eIiVDd~e~ye~ak~~i~~l~~P~~~~kVklY~  260 (1063)
T PRK10811        190 HWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYT  260 (1063)
T ss_pred             HHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCCCCEEEEC
T ss_conf             99999999735899868753754899999986217778899969999999999999744733337458857


No 122
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=93.25  E-value=0.1  Score=31.90  Aligned_cols=53  Identities=25%  Similarity=0.350  Sum_probs=45.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             00111225888467888877321114777505888877653058899999999
Q gi|254780788|r  359 TQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG  411 (526)
Q Consensus       359 ~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~  411 (526)
                      .+.|.+.-+|.+.-|+.|-.+||.|++++..++.++|+.+.|+..-+|..|+.
T Consensus         9 ~~~l~disgvg~~~a~~l~~ag~e~~~d~~~a~q~~l~~~~gignalaarika   61 (238)
T PRK12766          9 YEELTDISGVGPSKAESLREAGFESVEDVRAADQSELADVDGIGNALAARIKA   61 (238)
T ss_pred             HHHHHCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             67764123668003678887040128989764277664201313899998741


No 123
>PTZ00035 Rad51; Provisional
Probab=93.00  E-value=0.26  Score=28.86  Aligned_cols=51  Identities=20%  Similarity=0.223  Sum_probs=38.9

Q ss_pred             CCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             79998999999987984788965326775212312344432112453343588999999999984122
Q gi|254780788|r  441 PGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYK  508 (526)
Q Consensus       441 ~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~  508 (526)
                      .|++...+.+|.++|+.|++-+|-.+.-+|+.+-                 ++|+..|++|+..||+-
T Consensus        41 ~Gi~~~di~kl~~aG~~tv~~v~~~~~k~L~~ik-----------------gise~k~~Ki~~~a~k~   91 (350)
T PTZ00035         41 KGFVKRDLELLKEGGLQTVECVAYAPMRTLCAIK-----------------GISEQKAEKLKKACKEL   91 (350)
T ss_pred             CCCCHHHHHHHHHCCCCHHHHHHHCCHHHHHHCC-----------------CCCHHHHHHHHHHHHHH
T ss_conf             7999899999998491248999850999897737-----------------94699999999999975


No 124
>PRK12705 hypothetical protein; Provisional
Probab=92.99  E-value=0.63  Score=26.08  Aligned_cols=168  Identities=20%  Similarity=0.240  Sum_probs=98.5

Q ss_pred             HHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCC-CCCCCCCCHHHHHHHHHHHCCE
Q ss_conf             217889986277826799559878999997628665424898756787999985342-2110254427899999861674
Q gi|254780788|r  260 SRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQ-LSLAIGRRGQNVRLASQLTGWT  338 (526)
Q Consensus       260 sRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~q-ls~AIGk~GqNvrLas~Ltg~~  338 (526)
                      .+|+.+-.+..-+      .+......+..|++-.-...+  .|.+ ...|-.|.+. --.-|||.|.|+|.--.|||-.
T Consensus       137 ~~ik~~e~eak~~------a~~~Ar~Ii~~AiqR~a~d~~--~E~t-vsvV~LPsdemKGRIIGREGRNIRa~E~~TGVD  207 (485)
T PRK12705        137 QRIAKIEEEANLE------AERTAQYILVFTMQRIAEDTI--ANIS-VSNVLLPSESMKGKIIGREGRNKRAFEELTGVD  207 (485)
T ss_pred             HHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHH--HHHC-CCCEECCCHHHHCCCCCCCCCCHHHHHHHHCCE
T ss_conf             9999999999988------999999999999988434677--7751-320245877873730487765299999987955


Q ss_pred             EEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH-HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             5785522001101001221000111225888467888877321114-777505888877653058899999999999999
Q gi|254780788|r  339 IDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADV-EELACVKISEIASIEGFDEETAVEIQGRAREYL  417 (526)
Q Consensus       339 idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~Si-EeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L  417 (526)
                      +=|  ++....                          .+-.||+.+ .++|....+.|..=.-+....++++..+|+..+
T Consensus       208 lII--DDtPe~--------------------------VvlS~FdPiRREiAr~aLe~Li~DGRIhPaRIEe~v~ka~~e~  259 (485)
T PRK12705        208 LII--DDTPEA--------------------------VVISSFNPIRREIARITLEKLLLDGRIDPARIEEYVQKANEEF  259 (485)
T ss_pred             EEE--CCCCCE--------------------------EEEECCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf             897--499985--------------------------8885797789999999999999848918899999999999999


Q ss_pred             HHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHCCCCC------------HHHHHHCCHHHH
Q ss_conf             99999989877542843566407799989999999879847------------889653267752
Q gi|254780788|r  418 EGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKT------------MEDLAGCSVDDL  470 (526)
Q Consensus       418 ~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L~e~gIkt------------leDlAels~dEL  470 (526)
                      ...-.+..+..     -.+ +.+.||.++++-.|+.=...|            +-.||++-..||
T Consensus       260 ~~~i~e~Ge~a-----~~e-lgi~~l~pelikllGrLkyRtSyGQNvL~HSiEvA~lag~mA~El  318 (485)
T PRK12705        260 EQKCYEIGKEV-----LEE-LGIFDLSPGLVRLLGRLYFRTSYGQNVLSHSLEVAFLAAILAALI  318 (485)
T ss_pred             HHHHHHHHHHH-----HHH-CCCCCCCHHHHHHHHCEECCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999-----998-099999978999986010002340579999999999999999983


No 125
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=92.96  E-value=0.77  Score=25.40  Aligned_cols=99  Identities=21%  Similarity=0.323  Sum_probs=72.2

Q ss_pred             CCCCCCCHHHHHHHHHHH-HHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH--C
Q ss_conf             122588846788887732-1114777505888877653058899999999999999999999898775428435664--0
Q gi|254780788|r  363 MQAINVDEIIAHLLVAEG-FADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELC--S  439 (526)
Q Consensus       363 ~e~LdVDE~iA~~LV~eG-f~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~--~  439 (526)
                      |+.-++.+.+.+.|++.| +.++-++.+...++|+.+++|.+..+..|.+.            .+..++-...-=|.  .
T Consensus       448 mdI~GLG~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l~~~~~ks~~nLl~a------------Ie~sK~~~l~r~l~aLG  515 (667)
T COG0272         448 LDIDGLGEKIIEQLFEKGLIKDIADLYTLTEEDLLSLEGFGEKSAENLLNA------------IEKSKKQPLARFLYALG  515 (667)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCCHHHHHHCCHHHHHHCCCHHHHHHHHHHHH------------HHHHCCCCHHHHHHHCC
T ss_conf             577776799999999737537879877378988841622446579999999------------99860498999999879


Q ss_pred             CCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf             77999899999998798478896532677521231
Q gi|254780788|r  440 IPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS  474 (526)
Q Consensus       440 l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~  474 (526)
                      ++++.+.++..|+. ...|++.|-..+.++|..+.
T Consensus       516 Ir~VG~~~Ak~La~-~f~sl~~l~~a~~e~l~~i~  549 (667)
T COG0272         516 IRHVGETTAKSLAR-HFGTLEALLAASEEELASIP  549 (667)
T ss_pred             CCHHHHHHHHHHHH-HHHHHHHHHHCCHHHHHHCC
T ss_conf             71140899999998-76029999842999995066


No 126
>PRK13764 ATPase; Provisional
Probab=92.83  E-value=0.21  Score=29.54  Aligned_cols=150  Identities=21%  Similarity=0.273  Sum_probs=85.6

Q ss_pred             EEEECCCCCEEEEEEECCCH-----HHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCH
Q ss_conf             97611358702898715988-----9999999976677755808785663167750349999408998812765548862
Q gi|254780788|r  186 IYDVRREQRGPQVLLSRTHP-----QFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGS  260 (526)
Q Consensus       186 i~~V~~~~rgpqi~lSRt~p-----~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGs  260 (526)
                      ..+.+...-|--=++--|+|     .|+-+.=--=+|-|-|-+|=|++     |.=+||--.+--     |..--||+-.
T Consensus       344 faD~RlaGvGmvGvvHA~~~iDAiQRfigRVELG~IPqivDTVIfI~~-----G~v~kVy~l~~t-----VKvP~Gm~e~  413 (605)
T PRK13764        344 FADMRLAGVGMVGVVHATSPIDAIQRFIGRVELGMIPQIVDTVIFIKD-----GEVAKVYDLEFT-----VKVPTGMKEE  413 (605)
T ss_pred             EEHHHHCCCCEEEEEECCCHHHHHHHHHCCCHHCCCCHHEEEEEEEEC-----CEEEEEEEEEEE-----EECCCCCCHH
T ss_conf             010100057447688528878999987330110564214048999807-----848899998888-----8578998845


Q ss_pred             H-HHH-------HHHHH------CCCCEEEEECCC-----CH---------HHHHHHHCCCCCCCEEEECCCCCEEEEEE
Q ss_conf             1-788-------99862------778267995598-----78---------99999762866542489875678799998
Q gi|254780788|r  261 R-VQA-------VVTEL------RDEKIDIVVWSP-----DS---------ATFVINALRPAIVTKVVLDEDVGRIEVIV  312 (526)
Q Consensus       261 R-iq~-------I~~EL------~gEkIDii~ws~-----d~---------~~fi~nAl~PA~v~~v~~de~~~~~~v~v  312 (526)
                      - .+.       .++++      -||.+=+++-..     .|         ...+.+-+. . -..|.+. ..+++.|.|
T Consensus       414 DLARPVI~V~Df~t~~~eyEIYtfGeq~vVvPv~~~~~~~~~~~~~a~~~i~~~i~r~~~-~-~~eV~~~-~d~~avv~v  490 (605)
T PRK13764        414 DLARPVIEVKDFETGEPEYEIYTFGEQTVVVPVKREEEEKSPVWKLAEEEIEREIKRYLK-G-PVEVEVI-SDNKAVVYV  490 (605)
T ss_pred             HCCCCEEEEEECCCCCEEEEEEEECCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHCC-C-CCEEEEE-CCCEEEEEE
T ss_conf             514864998762789888999983877999987888766575889999999999987468-9-8349996-498689997


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCHH
Q ss_conf             534221102544278999998616745785522001
Q gi|254780788|r  313 PKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDS  348 (526)
Q Consensus       313 ~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~  348 (526)
                      |+...+.+|||+|.|+.=--+-.|.+|||...++..
T Consensus       491 ~~~~i~~~igK~g~~i~~ie~~lgi~IdV~~~~e~~  526 (605)
T PRK13764        491 PEKDIPAVIGKGGKNISKIEKKLGIDIDVRPLSEEE  526 (605)
T ss_pred             CCCCCHHHHCCCCCCHHHHHHHHCCCEEEEECCCCC
T ss_conf             645313665559747999998648835765766566


No 127
>pfam03118 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C terminal domain. The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal.
Probab=92.60  E-value=0.19  Score=29.86  Aligned_cols=55  Identities=15%  Similarity=0.229  Sum_probs=43.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             0001112258884678888773211147775058888776530588999999999
Q gi|254780788|r  358 RTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGR  412 (526)
Q Consensus       358 ~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~r  412 (526)
                      .....++.|+++--....|-.+|+.|+.++...+.++|.++++|......|+++.
T Consensus         5 ~l~~~I~~L~LS~R~~N~Lk~~~I~tv~dL~~~s~~dLl~i~N~G~kSl~EI~~~   59 (62)
T pfam03118         5 LLSIPIEELELSVRSYNCLKRAGINTVGDLLSKSEEDLLKIKNFGKKSLEEIKEK   59 (62)
T ss_pred             HHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
T ss_conf             8639899816868999999894996799998589999974889868579999999


No 128
>KOG3409 consensus
Probab=92.58  E-value=0.46  Score=27.07  Aligned_cols=75  Identities=28%  Similarity=0.497  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHCCCEEEEEEEECCCCEEEEEE---C------CCEEEEEHHHCCCCC--------CCCCCCEEEEEEEEEC
Q ss_conf             8779999852083899999840576389995---7------935874478748875--------1152766999997611
Q gi|254780788|r  128 DRQYLEFKDKVGEIISGTVKRVEYGNVIVDL---G------NSDGVIRRDETISRE--------NLRPGDRVKSYIYDVR  190 (526)
Q Consensus       128 ~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdl---g------~~ea~Lp~~e~ip~E--------~~~~Gdrika~i~~V~  190 (526)
                      +..+++-....|.||++.|.|+.-.+.-+++   |      .-.|+|++.+.=+.|        .|||||-|+|-+.+-.
T Consensus        58 ~~~~~~~LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~  137 (193)
T KOG3409          58 KQLFNELLPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLG  137 (193)
T ss_pred             CCCHHHCCCCCCCEEEEEEEEECCCEEEEEEEEECCEEHHHHHCCEEEHHHCCCCCCCHHHHHHCCCCCCEEEEEEEECC
T ss_conf             65143307765767999987624413567899986797001121143354356444011216343698868888885147


Q ss_pred             CCCCEEEEEEECCCH
Q ss_conf             358702898715988
Q gi|254780788|r  191 REQRGPQVLLSRTHP  205 (526)
Q Consensus       191 ~~~rgpqi~lSRt~p  205 (526)
                         -|..-+|+-+..
T Consensus       138 ---~~~~y~LTtAen  149 (193)
T KOG3409         138 ---DGSNYLLTTAEN  149 (193)
T ss_pred             ---CCCCEEEEEECC
T ss_conf             ---787279987516


No 129
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=92.56  E-value=0.15  Score=30.68  Aligned_cols=71  Identities=18%  Similarity=0.162  Sum_probs=56.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCC
Q ss_conf             888467888877321114777505888877653058899999999999999999999898775428435664077
Q gi|254780788|r  367 NVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIP  441 (526)
Q Consensus       367 dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~  441 (526)
                      ||...-...|-..|++|++++|.++...+....|+..+.+..++-.|+...+.......    -+.+.+...+++
T Consensus       232 Gi~~~r~~~l~~~GI~Ti~~LA~~~~~~~~~~~ga~~~~~~~l~~qa~~~~e~~~~~~~----P~~P~e~~fD~E  302 (474)
T COG2251         232 GITPSRYDVLEEVGITTIEDLADASLPILELVAGALTALAAQLVLQARARVEGRPLMEI----PLFPVELYFDFE  302 (474)
T ss_pred             CCCHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEECC----CCCCCCCEEECC
T ss_conf             99878899999738223999975255402566546777789999999852468850126----899754534102


No 130
>KOG2193 consensus
Probab=92.54  E-value=0.18  Score=29.99  Aligned_cols=40  Identities=23%  Similarity=0.563  Sum_probs=30.8

Q ss_pred             CCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf             5678799998534221102544278999998616745785
Q gi|254780788|r  303 EDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII  342 (526)
Q Consensus       303 e~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~  342 (526)
                      .+.....+.+|+.-.---||++|||++-.++.+|-.|-|-
T Consensus       408 pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIa  447 (584)
T KOG2193         408 PEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIA  447 (584)
T ss_pred             CCHHHEEEECCHHHHHHHHCCCCHHHHHHHHHCCCEEEEC
T ss_conf             0212201444088888887124221899987427603435


No 131
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=92.38  E-value=0.92  Score=24.86  Aligned_cols=129  Identities=22%  Similarity=0.302  Sum_probs=84.1

Q ss_pred             EEEEECCCC-CCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH-H
Q ss_conf             999985342-21102544278999998616745785522001101001221000111225888467888877321114-7
Q gi|254780788|r  308 IEVIVPKEQ-LSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADV-E  385 (526)
Q Consensus       308 ~~v~v~~~q-ls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~Si-E  385 (526)
                      -.|-.|.+. --.-|||.|.|+|---.+||-.+-|-...+.                            .+-.||+.+ -
T Consensus       206 svV~LPsdemKGRIIGrEGRNIRa~E~~TGVDlIIDDtPe~----------------------------V~lS~FdpvRR  257 (514)
T TIGR03319       206 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEA----------------------------VILSGFDPVRR  257 (514)
T ss_pred             EEEECCCHHHHCCCCCCCCCHHHHHHHHHCCEEEECCCCCE----------------------------EEEECCCHHHH
T ss_conf             66863977875501086752399999986974898599985----------------------------88867886889


Q ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHCCCCC-------
Q ss_conf             7750588887765305889999999999999999999989877542843566407799989999999879847-------
Q gi|254780788|r  386 ELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKT-------  458 (526)
Q Consensus       386 eIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L~e~gIkt-------  458 (526)
                      +||....+.|..=.-+.+..++++..+|+.-+...-.+..+..-      .=+.+.||.++++-.|+.=...|       
T Consensus       258 EiAr~aLe~Li~DGRIhP~rIEe~v~k~~~e~~~~i~~~Ge~a~------~elgi~~~~peli~~lGrlkyRtSygQNvL  331 (514)
T TIGR03319       258 EIARMALEKLIQDGRIHPARIEEMVEKATKEVDNAIREEGEQAA------FDLGVHGLHPELIKLLGRLKFRTSYGQNVL  331 (514)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHCCCCCCHHHHHHHHHEEHHHHCCHHHH
T ss_conf             99999999998749948899999999999999999999999999------981999999789999875000102405899


Q ss_pred             -----HHHHHHCCHHHH
Q ss_conf             -----889653267752
Q gi|254780788|r  459 -----MEDLAGCSVDDL  470 (526)
Q Consensus       459 -----leDlAels~dEL  470 (526)
                           +-.||++-..||
T Consensus       332 ~Hs~Eva~lag~~A~El  348 (514)
T TIGR03319       332 QHSIEVAHLAGIMAAEL  348 (514)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             99999999999999983


No 132
>KOG3298 consensus
Probab=92.28  E-value=0.39  Score=27.56  Aligned_cols=63  Identities=25%  Similarity=0.305  Sum_probs=47.1

Q ss_pred             HHHHHCCCEEEEEEEECCCCEEEEEECCCEEEE------EHHHCCCCCC-----------CCCCCEEEEEEEEECCCCCE
Q ss_conf             998520838999998405763899957935874------4787488751-----------15276699999761135870
Q gi|254780788|r  133 EFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVI------RRDETISREN-----------LRPGDRVKSYIYDVRREQRG  195 (526)
Q Consensus       133 ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~L------p~~e~ip~E~-----------~~~Gdrika~i~~V~~~~rg  195 (526)
                      -|+.-.||||.|+|.++.+-.++++.|-.+-+.      |--+-+|+|+           .+.|++||.-|..++-..+-
T Consensus        76 ~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~~  155 (170)
T KOG3298          76 TFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDETE  155 (170)
T ss_pred             EEEECCCCEEEEEEEEEEEEEEEEECCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEEEEEEEEE
T ss_conf             97404776888999998424489960566753232527987421789999852266432455076899999999970156


No 133
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=92.24  E-value=0.7  Score=25.71  Aligned_cols=113  Identities=19%  Similarity=0.227  Sum_probs=78.9

Q ss_pred             EECHHHHHHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC-CCEEEE
Q ss_conf             2348999862889864737998508456207999999999999999999887799998520838999998405-763899
Q gi|254780788|r   78 QISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVE-YGNVIV  156 (526)
Q Consensus        78 eI~l~~A~~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e-~~~iiV  156 (526)
                      .+.|...-....+.++||++..-+=...=+|.+|++-..                  +-.+|+--.+.|-.+. +-.+++
T Consensus        31 ~ilL~k~~~~~~e~evGdev~vFiY~D~~~rl~aTt~~p------------------~~tvg~~g~~~Vv~v~~~lGaFl   92 (287)
T COG2996          31 TILLPKSEPEEDELEVGDEVTVFIYVDSEDRLIATTREP------------------KATVGEYGWLKVVEVNKDLGAFL   92 (287)
T ss_pred             EEECCCCCCCCCCCCCCCEEEEEEEECCCCCEEHEEECC------------------EEEECCEEEEEEEEECCCCCEEE
T ss_conf             786256677678511376899999988877630101041------------------37405323799998737751589


Q ss_pred             EEC-CCEEEEEHHHCCCCCC--CCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHH
Q ss_conf             957-9358744787488751--1527669999976113587028987159889999999
Q gi|254780788|r  157 DLG-NSDGVIRRDETISREN--LRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLF  212 (526)
Q Consensus       157 dlg-~~ea~Lp~~e~ip~E~--~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf  212 (526)
                      |.| .-+.++|-+++-+-..  .++||++-+|++-=++. |   |.-.-...+.+..|+
T Consensus        93 D~Gl~KDl~vp~~elp~~~~~wpq~Gd~l~v~l~~Dkk~-R---i~g~~a~~~~l~~l~  147 (287)
T COG2996          93 DWGLPKDLLVPLDELPTLKSLWPQKGDKLLVYLYVDKKG-R---IWGTLAIEKILENLA  147 (287)
T ss_pred             ECCCCCCEEEEHHHCCCCCCCCCCCCCEEEEEEEECCCC-C---EEEEECCHHHHHHCC
T ss_conf             659870036162536443123778798999999985678-4---777733155787617


No 134
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=92.23  E-value=0.95  Score=24.74  Aligned_cols=67  Identities=22%  Similarity=0.215  Sum_probs=36.2

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCHH-HHHHCCCCCCHHHHHHHHHCCCCCHHHHH
Q ss_conf             76530588999999999999999999998987754----2843-56640779998999999987984788965
Q gi|254780788|r  396 ASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRE----LGVS-EELCSIPGIDSKIKVALGENGIKTMEDLA  463 (526)
Q Consensus       396 ~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e----~~~~-e~L~~l~gl~~~~~~~L~e~gIktleDlA  463 (526)
                      .+|.|++.++...-..-|+.+-......+++...+    ++.- ..+..+ -++++-+....-+|=++...+-
T Consensus       507 iKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~-~i~~dKI~dvIG~gGk~I~~I~  578 (692)
T COG1185         507 IKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETI-KIDPDKIRDVIGPGGKTIKAIT  578 (692)
T ss_pred             EEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEE-CCCHHHHHHCCCCCCCCHHHHH
T ss_conf             66458889999999987999999999999998751143442458724996-1388887632188632034655


No 135
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=92.04  E-value=0.33  Score=28.11  Aligned_cols=64  Identities=27%  Similarity=0.435  Sum_probs=53.0

Q ss_pred             HHCCCEEEEEEEECCCC--EEEEEECC-CEEEEEHHHCCC----------CCCCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf             52083899999840576--38999579-358744787488----------751152766999997611358702898
Q gi|254780788|r  136 DKVGEIISGTVKRVEYG--NVIVDLGN-SDGVIRRDETIS----------RENLRPGDRVKSYIYDVRREQRGPQVL  199 (526)
Q Consensus       136 ~r~Geiv~G~V~r~e~~--~iiVdlg~-~ea~Lp~~e~ip----------~E~~~~Gdrika~i~~V~~~~rgpqi~  199 (526)
                      ...|.|..|.|.|++++  ..+||+|. -.|+|+-++..|          .+.++.|+.+-+-+.......+|+++.
T Consensus        35 ~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT  111 (487)
T COG1530          35 QIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARLT  111 (487)
T ss_pred             EEECCCEEEEECCCCCCCHHHEEECCCCCCCEEEECCCCHHHHHCCCCCCEEEECCCCEEEEEEEEECCCCCCCCCE
T ss_conf             63067168886231766322205516876606884105534420002350055417862899998625766034212


No 136
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and  poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in  AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=91.99  E-value=0.18  Score=30.07  Aligned_cols=39  Identities=23%  Similarity=0.406  Sum_probs=34.9

Q ss_pred             EEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECC
Q ss_conf             799998534221102544278999998616745785522
Q gi|254780788|r  307 RIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEE  345 (526)
Q Consensus       307 ~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~  345 (526)
                      ++.+.||..+...-|||+|.|+|--.+-||-+|.|....
T Consensus         1 t~rilvP~~~vG~vIGk~G~~I~~i~~~sga~I~i~~~~   39 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSV   39 (65)
T ss_pred             CEEEEEEHHHEEEEECCCCHHHHHHHHHHCCEEEECCCC
T ss_conf             989998746722899799878999999849889999889


No 137
>TIGR02239 recomb_RAD51 DNA repair protein RAD51; InterPro: IPR011941   Homologous recombination is an evolutionarily conserved mechanism for the repair of double-strand breaks in DNA and the generation of genetic diversity. The primary function of homologous recombination in mitotic cells is to repair double-strand breaks or single-strand gaps that form as a result of replication fork collapse, from processing of spontaneous damage, and from exposure to DNA-damaging agents. During meiosis, homologous recombination is essential to establish a physical connection between homologous chromosomes to ensure their correct disjunction at the first meiotic division. In addition, the high frequency of meiotic recombination contributes to diversity by creating new linkage arrangements between genes, or parts of genes .   The central step of homologous recombination is synapsis, the process of bringing together the two homologous strands. Rad51, a eukaryotic homologue of the prokaryotic recombinase RecA, mediates this process in eukaryotes . Firstly a single-stranded DNA tail is coated by ATP-bound Rad51 to yield a nucleoprotein filament. This filament then searches for a homologous sequence within double-stranded DNA, and catalyses the exchange of strands between the single-stranded and double-stranded DNA substrates. The original broken end of the resulting branched DNA is now aligned with an appropriate matching sequence in an intact duplex, and is further processed by other enzymes .   Rad51 contains an N-terminal alpha-helical DNA binding domain not found in RecA, and a RecA-like C-terminal ATPase domain , . The active form of this protein is a long helical filament where the catalytically active unit is a homodimer . ; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair.
Probab=91.80  E-value=1.1  Score=24.40  Aligned_cols=90  Identities=22%  Similarity=0.171  Sum_probs=66.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCC
Q ss_conf             25888467888877321114777505888877653058899999999999999999999898775428435664077999
Q gi|254780788|r  365 AINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGID  444 (526)
Q Consensus       365 ~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~  444 (526)
                      .-+|...-...|.+.||.+++.++|.+...|..|.|+.+..++.+...|...+-..-....+   -.....++..+. -.
T Consensus         6 ~~g~~~~d~~~l~~~g~~~~~~~a~~~~k~l~~~~G~~~~k~~~~~~~~~~lv~~gf~~a~~---~~~~r~~~~~~~-~G   81 (317)
T TIGR02239         6 EKGIAAADIKKLKEAGLHTVESVAYAPKKQLLEIKGISEAKADKILAEAAKLVPLGFTTATE---LHKKRKEVIQLT-TG   81 (317)
T ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHEECC-CC
T ss_conf             30542788999986136789998876555565424730778999999988776543677999---998776541210-35


Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             89999999879847
Q gi|254780788|r  445 SKIKVALGENGIKT  458 (526)
Q Consensus       445 ~~~~~~L~e~gIkt  458 (526)
                      ...+..|-..||-|
T Consensus        82 s~~ld~~l~GG~e~   95 (317)
T TIGR02239        82 SKELDKLLEGGIET   95 (317)
T ss_pred             HHHHHHHHCCCCCC
T ss_conf             06899986087554


No 138
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=91.69  E-value=0.31  Score=28.29  Aligned_cols=31  Identities=42%  Similarity=0.569  Sum_probs=11.6

Q ss_pred             HHHCCCCCCHHHHHHHHHCCCCCHHHHHHCC
Q ss_conf             6640779998999999987984788965326
Q gi|254780788|r  436 ELCSIPGIDSKIKVALGENGIKTMEDLAGCS  466 (526)
Q Consensus       436 ~L~~l~gl~~~~~~~L~e~gIktleDlAels  466 (526)
                      +|..+.||+.....+|.+.||.|+++||.+.
T Consensus       208 ~LslVagi~~~q~~~L~~~GI~Ti~~LA~~~  238 (457)
T TIGR03491       208 HLSLVPGIGPSRYRLLQELGIHTLEDLAAAD  238 (457)
T ss_pred             CHHHHCCCCHHHHHHHHHCCCCCHHHHHCCC
T ss_conf             9766059999999999985998799986299


No 139
>TIGR03675 arCOG00543 arCOG01782 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=91.47  E-value=0.72  Score=25.62  Aligned_cols=161  Identities=12%  Similarity=0.164  Sum_probs=75.9

Q ss_pred             HHHHHCCCCCCCE-EEEECCCCCEEEEEEEE--EEECCCCCCCCEECHHHHHHHCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             9996136874535-99974998839999998--85176778753234899986288986473799850845620799999
Q gi|254780788|r   37 KAARSLYGTMSDI-RVEINPETGDISLFRLL--EVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQS  113 (526)
Q Consensus        37 ~a~kK~~~~~~~i-~V~iD~~tG~i~i~~~~--~VVedved~~~eI~l~~A~~~~~~~~iGD~i~~~i~~~~fgRiaAq~  113 (526)
                      ...++-.+.++.+ .+.||+.+|++.+...+  .|+-.--.     .+   +++.  .+.|=.....=.|.-.++. .+.
T Consensus        73 ~~i~~~vp~~a~i~~~~fd~~~~ev~i~~~kpg~~~g~~g~-----~~---~~i~--~~~gw~~~v~r~p~~~s~~-~~~  141 (630)
T TIGR03675        73 EKIKEIVPEEAGITDIYFDDVTGEVIIEAEKPGLVIGKGGS-----TL---REIT--AETGWTPKVVRTPPIESKT-IKN  141 (630)
T ss_pred             HHHHHHCCCCCCCEEEEECCCCCEEEEEECCCEEEECCCCH-----HH---HHHH--HHHCCEEEEEECCCCCHHH-HHH
T ss_conf             99997589535841589748972799997796367647516-----79---9999--9749746888659997078-999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCC-EEE-------------------EEEEECCCCEEEEEECC-----CEEEEEHH
Q ss_conf             999999999999988779999852083-899-------------------99984057638999579-----35874478
Q gi|254780788|r  114 AKQVIIQKVREAERDRQYLEFKDKVGE-IIS-------------------GTVKRVEYGNVIVDLGN-----SDGVIRRD  168 (526)
Q Consensus       114 AKQvI~QkireaEr~~i~~ef~~r~Ge-iv~-------------------G~V~r~e~~~iiVdlg~-----~ea~Lp~~  168 (526)
                      .++.+.+-  ..||..+...+-.++.. .+.                   +...+.....+.+|-|=     ...-+|.-
T Consensus       142 ir~~~~~~--~~~r~~~l~~~g~~i~r~~~~~~~~vrit~LG~~~eVGRSc~l~~~~~~~illDcG~~~~~~~~~~~P~~  219 (630)
T TIGR03675       142 IREYLRSE--SEERKEFLRKLGRRIHRDPIFKDRWVRVTALGGFREVGRSALLLSTPESRILLDCGVNVGANGDNAYPYL  219 (630)
T ss_pred             HHHHHHHH--HHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCCC
T ss_conf             99999970--7999999999888746897688974999834676702645899963981799988888777775458865


Q ss_pred             HCCCCCCCCCCCEEEEEEEE-------------ECCCCCEEEEEEECCCHHHHHHHHHHH
Q ss_conf             74887511527669999976-------------113587028987159889999999976
Q gi|254780788|r  169 ETISRENLRPGDRVKSYIYD-------------VRREQRGPQVLLSRTHPQFMVKLFHME  215 (526)
Q Consensus       169 e~ip~E~~~~Gdrika~i~~-------------V~~~~rgpqi~lSRt~p~~l~~Lf~~E  215 (526)
                      + +|.  |. =+.|.|++..             ++..-+|| |+.+...-+++.-|+.--
T Consensus       220 d-~~e--~~-~~~IDAVvlTHAHLDH~G~LP~L~k~Gf~Gp-Iy~T~pT~dL~~llL~D~  274 (630)
T TIGR03675       220 D-VPE--FQ-LDELDAVVITHAHLDHSGLVPLLFKYGYDGP-VYCTPPTRDLMTLLQLDY  274 (630)
T ss_pred             C-CCC--CC-CCCCCEEEEECCCCCCCCCCCHHHHCCCCCC-EEECHHHHHHHHHHHHHH
T ss_conf             6-777--98-0118589983353212563218876488898-886545999999999989


No 140
>KOG2190 consensus
Probab=91.40  E-value=1.2  Score=24.11  Aligned_cols=100  Identities=23%  Similarity=0.340  Sum_probs=63.5

Q ss_pred             CCCEEEEECCCCHHHHHHHHHHCCCC------EE---EEECCCCHH---HHHHHHC--CCCCCCEEEECC--CCCEEEEE
Q ss_conf             88127655488621788998627782------67---995598789---9999762--866542489875--67879999
Q gi|254780788|r  248 IDPVGACVGMRGSRVQAVVTELRDEK------ID---IVVWSPDSA---TFVINAL--RPAIVTKVVLDE--DVGRIEVI  311 (526)
Q Consensus       248 iDpVGAcVG~rGsRiq~I~~EL~gEk------ID---ii~ws~d~~---~fi~nAl--~PA~v~~v~~de--~~~~~~v~  311 (526)
                      .|-+|+|+|..|+++.++-++.+-=.      -|   .+.-.+.|.   -.-.+|+  .+........+.  -.-+....
T Consensus       264 ~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~  343 (485)
T KOG2190         264 SDKVGSVIGKGGLVIRALRNETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLL  343 (485)
T ss_pred             HHHCEEEECCCCCCHHHHHHCCCCCEEECCCCCCCEEEECCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCEEEEEEC
T ss_conf             22202551588851065664037745732666763465035458643221003556421221245556665522212321


Q ss_pred             ECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCH
Q ss_conf             853422110254427899999861674578552200
Q gi|254780788|r  312 VPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEED  347 (526)
Q Consensus       312 v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~~  347 (526)
                      ||.+..---|||+|-++-=--++||-.|-|...++.
T Consensus       344 vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~  379 (485)
T KOG2190         344 VPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV  379 (485)
T ss_pred             CCCCCCCEEECCCCCCHHHHHHHCCCCEEECCCCCC
T ss_conf             570000013256653057898732883697256666


No 141
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=91.22  E-value=0.54  Score=26.57  Aligned_cols=57  Identities=21%  Similarity=0.254  Sum_probs=38.2

Q ss_pred             HHHHCCCEEEEEEEECCCCEEEEEECCC-----------EEEEEHHHC------CCCCCCCCCCEEEEEEEEEC
Q ss_conf             9852083899999840576389995793-----------587447874------88751152766999997611
Q gi|254780788|r  134 FKDKVGEIISGTVKRVEYGNVIVDLGNS-----------DGVIRRDET------ISRENLRPGDRVKSYIYDVR  190 (526)
Q Consensus       134 f~~r~Geiv~G~V~r~e~~~iiVdlg~~-----------ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~  190 (526)
                      ...+.|.+|.|.|.++...-+.|.+-.+           .|.++-++.      --.+.|++||-|||++...-
T Consensus        60 ~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~  133 (188)
T COG1096          60 PLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG  133 (188)
T ss_pred             CCCCCCCEEEEEEEECCCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEECC
T ss_conf             76898879999995326608999999994333367887402589782023111020134464617999998617


No 142
>cd03586 Pol_IV_kappa Pol_IV_kappa, a member of the Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases. Originally called the DinB family, they belong to the recently described Y-family of DNA polymerases. Pol IV is mostly found in bacteria and archaea. Although the structure of Pol IV is similar to that of Pol eta, it shows markedly differenct efficiencies and fidelities in bypassing various DNA lesions. All Pol IV-like polymerases studied to date are able to b
Probab=91.11  E-value=1.2  Score=23.92  Aligned_cols=36  Identities=31%  Similarity=0.350  Sum_probs=18.0

Q ss_pred             HHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCC
Q ss_conf             640779998999999987984788965326775212
Q gi|254780788|r  437 LCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLG  472 (526)
Q Consensus       437 L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~  472 (526)
                      +.+++|+...+...|...||+|..||+.++.+.|..
T Consensus       174 v~~l~GIG~~~~~~L~~~gI~t~~dl~~~~~~~l~~  209 (337)
T cd03586         174 VRKIWGIGKVTAEKLNRLGIRTIGDLAAADLELLKK  209 (337)
T ss_pred             CHHCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHH
T ss_conf             302078468999999980896899986499999987


No 143
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=89.87  E-value=0.93  Score=24.83  Aligned_cols=50  Identities=14%  Similarity=0.248  Sum_probs=34.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             112258884678888773211147775058888776530588999999999
Q gi|254780788|r  362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGR  412 (526)
Q Consensus       362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~r  412 (526)
                      |-+.-||.+.....|... |.|++.|..|+.++|.+++|+...+|..+.+.
T Consensus       556 Ld~I~GIG~kr~~~Ll~~-Fgs~~~i~~As~eeL~~v~Gi~~~~A~~I~~~  605 (609)
T PRK00558        556 LDDIPGIGPKRRKALLKH-FGSLKAIKEASVEELAKVPGISKKLAEKIYEA  605 (609)
T ss_pred             CCCCCCCCHHHHHHHHHH-CCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
T ss_conf             647899799999999997-07999997389999964899899999999999


No 144
>pfam02889 Sec63 Sec63 Brl domain. This domain (also known as the Brl domain) is required for assembly of functional endoplasmic reticulum translocons.
Probab=89.40  E-value=1.1  Score=24.35  Aligned_cols=42  Identities=24%  Similarity=0.355  Sum_probs=37.7

Q ss_pred             HHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf             435664077999899999998798478896532677521231
Q gi|254780788|r  433 VSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS  474 (526)
Q Consensus       433 ~~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~  474 (526)
                      .+..|+.|++++++.+.+|.++|+.|+++|.+++.+|+.++.
T Consensus       146 ~~~pL~Qlp~~~~~~i~~l~~~~i~sl~~l~~~~~~el~~ll  187 (309)
T pfam02889       146 SDSPLRQLPHIPPEVIKKLEKKGISSLEDLMDLDPEELGELL  187 (309)
T ss_pred             CCCHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHH
T ss_conf             998545179999999999997799989999609999999997


No 145
>TIGR01009 rpsC_bact ribosomal protein S3; InterPro: IPR005704   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    Ribosomal protein S3 is one of the proteins from the small ribosomal subunit. This family describes the bacterial type of ribosomal protein S3 and also and many chloroplast forms. Chloroplast and mitochondrial forms have large, variable inserts between conserved N-terminal and C-terminal domains. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=89.30  E-value=1.2  Score=24.12  Aligned_cols=59  Identities=19%  Similarity=0.430  Sum_probs=50.3

Q ss_pred             HHHHHHHHCC--CCCCCEEEECCCCCE-EEEEECCCCCCCCCCCCHHHHH----HHHHHHC--CEEEE
Q ss_conf             8999997628--665424898756787-9999853422110254427899----9998616--74578
Q gi|254780788|r  283 SATFVINALR--PAIVTKVVLDEDVGR-IEVIVPKEQLSLAIGRRGQNVR----LASQLTG--WTIDI  341 (526)
Q Consensus       283 ~~~fi~nAl~--PA~v~~v~~de~~~~-~~v~v~~~qls~AIGk~GqNvr----Las~Ltg--~~idi  341 (526)
                      ...|+.+-|+  -|.|+.|.+--...+ +.|.+.--+=-+.|||+|+||-    .-.+|||  -+++|
T Consensus        40 IR~~i~k~l~~~~a~iS~veIeR~~~~~v~V~IhtArPg~vIGkkG~~iE~l~~~l~k~~~~~k~v~i  107 (217)
T TIGR01009        40 IRNLIKKELKKKNAGISDVEIERTADKKVRVTIHTARPGIVIGKKGSEIEKLKKALQKLTGSVKEVQI  107 (217)
T ss_pred             HHHHHHHHCCCCCCCCCEEEEEECCCCEEEEEEEECCCCEEECCCCCHHHHHHHHHHHHHCCEEEEEE
T ss_conf             99987321133543313279981699788999982788658857884589999999988478358999


No 146
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=89.19  E-value=0.66  Score=25.93  Aligned_cols=54  Identities=11%  Similarity=0.103  Sum_probs=27.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             000111225888467888877321114777505888877653058899999999
Q gi|254780788|r  358 RTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG  411 (526)
Q Consensus       358 ~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~  411 (526)
                      ....-++.|++.--...-|-.+|+.|+.++..-+.++|+++..|...-++|+.+
T Consensus       242 ~l~~~IeeLeLSvRs~NcLk~a~I~tI~dLv~~se~dLl~ikNfGkKSl~EI~~  295 (306)
T PRK05182        242 ILLRPIEELELSVRSYNCLKRAGINTIGDLVQRTEEELLKTPNLGKKSLEEIKE  295 (306)
T ss_pred             HHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCCCCHHHHHH
T ss_conf             644969881386888755878599369998747999996189976203999999


No 147
>smart00322 KH K homology RNA-binding domain.
Probab=88.52  E-value=0.62  Score=26.09  Aligned_cols=40  Identities=28%  Similarity=0.356  Sum_probs=32.3

Q ss_pred             EEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             0349999408998812765548862178899862778267995598
Q gi|254780788|r  236 RAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSP  281 (526)
Q Consensus       236 RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~  281 (526)
                      +.+|.|.+     +.+|..+|.+|++|+.+.++. |-+|++....+
T Consensus         4 ~~~i~vp~-----~~~g~iIG~~G~~i~~i~~~~-~~~I~i~~~~~   43 (69)
T smart00322        4 TIEVLIPA-----DKVGLIIGKGGSTIKKIEEET-GVKIDIPEDGS   43 (69)
T ss_pred             EEEEEECH-----HHCCEEECCCCCCHHHHHHHH-CCEEEECCCCC
T ss_conf             99999897-----876854999984579999972-88899779999


No 148
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=88.03  E-value=1.7  Score=22.83  Aligned_cols=68  Identities=22%  Similarity=0.234  Sum_probs=49.3

Q ss_pred             HHHHCCCEEEEEEEECCCCEEEEEECC-CEEEEEHHH-----CCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCC
Q ss_conf             985208389999984057638999579-358744787-----48875115276699999761135870289871598
Q gi|254780788|r  134 FKDKVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDE-----TISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTH  204 (526)
Q Consensus       134 f~~r~Geiv~G~V~r~e~~~iiVdlg~-~ea~Lp~~e-----~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~  204 (526)
                      |....|++|.|+|.+...+++.||+|. ..|.||.--     .=.+-++++||-|-|-|....++   -...||..+
T Consensus         2 YiP~~gD~VIGiV~~~~~d~y~vdi~~~~~a~L~~laFegATKknrP~L~~GdlVYaRV~~a~~~---~e~EL~Cvd   75 (86)
T cd05790           2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRD---MEPELSCVD   75 (86)
T ss_pred             CCCCCCCEEEEEEEEECCCEEEEECCCCCCEEECCCEECCCCCCCCCCCCCCCEEEEEEEECCCC---CCEEEEEEC
T ss_conf             62889998999994432766899767986648500101787655688788788999999874899---970489888


No 149
>KOG4078 consensus
Probab=87.63  E-value=0.93  Score=24.83  Aligned_cols=75  Identities=17%  Similarity=0.383  Sum_probs=56.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCC
Q ss_conf             9999999999988779999852083899999840576389995793587447874887511527669999976113587
Q gi|254780788|r  116 QVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQR  194 (526)
Q Consensus       116 QvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~r  194 (526)
                      |.+..-+|    ..-+-..-+-.|.+|.|.+-.+-.+++|+|.|.---..-++--..+|.|+.|.|++--+.+.+...|
T Consensus        64 qsFASlLR----nSkl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n~e~Y~~GaRVrlRl~DlELs~r  138 (173)
T KOG4078          64 QSFASLLR----NSKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALNGEAYQKGARVRLRLIDLELSER  138 (173)
T ss_pred             HHHHHHHH----CCCCCCCCCCCCCEEEEEEEEEECCCEEEECCCEEEEEECCCCCCHHHHHCCCEEEEEECCHHHHHH
T ss_conf             56999970----5840115576785887652011044238961874888873767587775057669999727667666


No 150
>pfam00013 KH_1 KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Q4R966.1/333-392;
Probab=87.29  E-value=0.67  Score=25.87  Aligned_cols=34  Identities=29%  Similarity=0.516  Sum_probs=31.9

Q ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEE
Q ss_conf             9999853422110254427899999861674578
Q gi|254780788|r  308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDI  341 (526)
Q Consensus       308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi  341 (526)
                      ..+.||.+....-||++|.|++--.+.||-+|++
T Consensus         2 ~~v~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i   35 (57)
T pfam00013         2 EEILIPSSLVGRIIGKGGSNIKEIREETGAKIRI   35 (57)
T ss_pred             EEEEECHHHCCEEECCCCCHHHHHHHHCCCEEEE
T ss_conf             8999875542068998964769999973999996


No 151
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=87.27  E-value=1.2  Score=24.02  Aligned_cols=32  Identities=9%  Similarity=0.161  Sum_probs=20.3

Q ss_pred             CCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             889864737998508456207999999999999
Q gi|254780788|r   88 DPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQ  120 (526)
Q Consensus        88 ~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~Q  120 (526)
                      ++....|-++-.|+++ .||---..+-|.++.-
T Consensus        24 ~~~~~YgrF~~~Ple~-G~g~TlGNaLRRvLLs   55 (333)
T CHL00013         24 SKRLYYGRFILSPLMK-GQADTIGIALRRALLG   55 (333)
T ss_pred             CCCCEEEEEEECCCCC-CCHHHHHHHHHHHHHH
T ss_conf             6876278999705888-7421467889888774


No 152
>pfam00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein. This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.
Probab=87.15  E-value=2.3  Score=21.94  Aligned_cols=78  Identities=28%  Similarity=0.273  Sum_probs=53.3

Q ss_pred             HHHHHHH-HHHHHHHHHHHCCHHHHHHH---HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHH
Q ss_conf             7888877-32111477750588887765---3058899999999999999999999898775428435664077999899
Q gi|254780788|r  372 IAHLLVA-EGFADVEELACVKISEIASI---EGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKI  447 (526)
Q Consensus       372 iA~~LV~-eGf~SiEeIa~a~~eeL~~I---eGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~  447 (526)
                      +.+.|.. -||-|.++++.++.++|.++   -||..-.+.-|++-|+.+......   .........+.|+.++|+.+..
T Consensus        17 i~~rl~~~~~~pt~~~l~~~~~~~l~~~i~~~G~~~~Ka~~I~~~a~~~~~~~~~---~~~~~~~~~~~L~~l~GIG~~t   93 (144)
T pfam00730        17 ITKRLFERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKELARILVEGYLG---LVPLDLEELEALLALPGVGRWT   93 (144)
T ss_pred             HHHHHHHHHCCCCHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC---CCCCCHHHHHHHHCCCCCCHHH
T ss_conf             9999999828989999985999999999870897699999999999888986289---7886115699986088976999


Q ss_pred             HHHHH
Q ss_conf             99999
Q gi|254780788|r  448 KVALG  452 (526)
Q Consensus       448 ~~~L~  452 (526)
                      +....
T Consensus        94 a~~~l   98 (144)
T pfam00730        94 AEAVL   98 (144)
T ss_pred             HHHHH
T ss_conf             99999


No 153
>PRK07220 DNA topoisomerase I; Validated
Probab=86.85  E-value=1.6  Score=23.07  Aligned_cols=39  Identities=28%  Similarity=0.314  Sum_probs=29.5

Q ss_pred             HHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf             566407799989999999879847889653267752123
Q gi|254780788|r  435 EELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGW  473 (526)
Q Consensus       435 e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~  473 (526)
                      +.|.+++||+...+.+|...||.|+++|++.--++|..-
T Consensus       686 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  724 (740)
T PRK07220        686 KSIKDIEGVGKATAGKLEEAGITTVEALAEADPIELAKA  724 (740)
T ss_pred             CHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH
T ss_conf             201215565889999999768875999851898999987


No 154
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=86.68  E-value=1.2  Score=24.12  Aligned_cols=57  Identities=21%  Similarity=0.317  Sum_probs=46.5

Q ss_pred             CHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHH----HHHHHCCE
Q ss_conf             7899999762866542489875678799998534221102544278999----99861674
Q gi|254780788|r  282 DSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRL----ASQLTGWT  338 (526)
Q Consensus       282 d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrL----as~Ltg~~  338 (526)
                      -..+|+..-|+-|.+..|.+--....+.|++--..-.+.|||+|.|++.    ..+++|-+
T Consensus        27 kIre~l~k~l~~Ag~s~veIeR~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~   87 (233)
T COG0092          27 KIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKE   87 (233)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCCEECCCCCCHHHHHHHHHHHHCCC
T ss_conf             9999999998757845489996698439999957983157579710999999999984999


No 155
>pfam00313 CSD 'Cold-shock' DNA-binding domain.
Probab=86.48  E-value=1.7  Score=22.90  Aligned_cols=54  Identities=26%  Similarity=0.414  Sum_probs=37.0

Q ss_pred             EEEEEEECC--CCE--EEEEECCCEEEEEHHHCCCC--CCCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf             999998405--763--89995793587447874887--5115276699999761135870289
Q gi|254780788|r  142 ISGTVKRVE--YGN--VIVDLGNSDGVIRRDETISR--ENLRPGDRVKSYIYDVRREQRGPQV  198 (526)
Q Consensus       142 v~G~V~r~e--~~~--iiVdlg~~ea~Lp~~e~ip~--E~~~~Gdrika~i~~V~~~~rgpqi  198 (526)
                      ++|+|+.++  +|+  |.-+-|.-+-++-.+..-..  ..+++|++|.+-   +...+||||-
T Consensus         1 ~tG~VK~f~~~kGfGFI~~~~~~~DiFvH~s~l~~~~~~~L~~G~~V~f~---v~~~~kG~~A   60 (66)
T pfam00313         1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQRVEFD---IVEGTKGPQA   60 (66)
T ss_pred             CCEEEEEEECCCCEEEEEECCCCCEEEEEHHHHCCCCCCCCCCCCEEEEE---EEECCCCCEE
T ss_conf             94899999599996999978998469999268121478617999999999---9979998663


No 156
>PRK00468 hypothetical protein; Provisional
Probab=86.34  E-value=1.2  Score=23.96  Aligned_cols=49  Identities=22%  Similarity=0.311  Sum_probs=35.1

Q ss_pred             CHHHHHHHHCC--CCCCCEE-EECCCCCEEEEEECCCCCCCCCCCCHHHHHH
Q ss_conf             78999997628--6654248-9875678799998534221102544278999
Q gi|254780788|r  282 DSATFVINALR--PAIVTKV-VLDEDVGRIEVIVPKEQLSLAIGRRGQNVRL  330 (526)
Q Consensus       282 d~~~fi~nAl~--PA~v~~v-~~de~~~~~~v~v~~~qls~AIGk~GqNvrL  330 (526)
                      +..+||+.+|-  |-+|.=- .-++..-.+++.|.++++-..|||+|..++=
T Consensus         3 ~Lve~iv~~LVd~Pd~V~V~~~~~~~~~~~~l~V~~~D~GkVIGk~GrtakA   54 (75)
T PRK00468          3 ELVETIAKALVDNPDAVQVNEIEGEQSIILELKVAPEDMGKVIGKQGRIAKA   54 (75)
T ss_pred             HHHHHHHHHHCCCCCEEEEEEEECCCEEEEEEEECHHHCCCEECCCCHHHHH
T ss_conf             8999999984899883899999679879999999935586466778714999


No 157
>cd00105 KH-I K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=86.15  E-value=0.78  Score=25.36  Aligned_cols=39  Identities=26%  Similarity=0.381  Sum_probs=34.2

Q ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCC
Q ss_conf             999985342211025442789999986167457855220
Q gi|254780788|r  308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE  346 (526)
Q Consensus       308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~  346 (526)
                      ..+.||.......||++|.|++--.+-||-+|.|.....
T Consensus         2 ~~i~ip~~~~g~vIG~~G~~I~~I~~~~~~~I~i~~~~~   40 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS   40 (64)
T ss_pred             EEEEECHHHCCEEECCCCCHHHHHHHHCCCEEEECCCCC
T ss_conf             899973665426799898134799997598999888899


No 158
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=86.06  E-value=1.8  Score=22.63  Aligned_cols=41  Identities=17%  Similarity=0.211  Sum_probs=37.3

Q ss_pred             HHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf             35664077999899999998798478896532677521231
Q gi|254780788|r  434 SEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS  474 (526)
Q Consensus       434 ~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~  474 (526)
                      +..|+.|++++++.+..|.+.++.++++|.+++.+|+.++.
T Consensus       150 ~~pL~Qlp~~~~~~~~~l~~~~i~~l~~l~~~~~~e~~~ll  190 (312)
T smart00611      150 DSPLLQLPHLPEEILKRLEKKKVLSLEDLLELEDEERGELL  190 (312)
T ss_pred             CCCHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHH
T ss_conf             99012489999999999996699989999738999999997


No 159
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3  is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel.   The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.  In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=85.82  E-value=1.1  Score=24.43  Aligned_cols=46  Identities=20%  Similarity=0.275  Sum_probs=25.6

Q ss_pred             HHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHH
Q ss_conf             9999976286654248987567879999853422110254427899
Q gi|254780788|r  284 ATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR  329 (526)
Q Consensus       284 ~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvr  329 (526)
                      .+|+..-|+-|-+++|.+.-......|++--..--+.|||+|++++
T Consensus        16 reyl~k~l~~Ag~s~ieIeRtp~~~~I~I~t~rPG~VIGr~G~~I~   61 (85)
T cd02411          16 DEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIR   61 (85)
T ss_pred             HHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCEEECCCCHHHH
T ss_conf             9999998886786559999889966999997899847778866599


No 160
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal; InterPro: IPR010212   This entry represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains and is most closely related to the central region bacterial NusA, a transcription termination factor named for its interaction with phage lambda protein N in Escherichia coli. The proteins required for antitermination by N include NusA, NusB, NusE (ribosomal protein S10), and NusG. This system, on the whole, appears not to be present in the archaea..
Probab=85.71  E-value=0.73  Score=25.60  Aligned_cols=96  Identities=32%  Similarity=0.473  Sum_probs=78.7

Q ss_pred             CCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHH--HCCCCCCCEEEECC--CCCEEEEEECCCCCCCCCC
Q ss_conf             9881276554886217889986277826799559878999997--62866542489875--6787999985342211025
Q gi|254780788|r  247 SIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVIN--ALRPAIVTKVVLDE--DVGRIEVIVPKEQLSLAIG  322 (526)
Q Consensus       247 ~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~n--Al~PA~v~~v~~de--~~~~~~v~v~~~qls~AIG  322 (526)
                      .....|...|..|..+... ..+.+-.+.++.++.++..|+.|  .++|+.+..+.+.+  ......+.+.......+||
T Consensus        40 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  118 (143)
T TIGR01952        40 KAGEMGAAIGKGGLNVKRL-EELIGKSIELIEYSEDLEEFVANILALAPAAVKNVTVSESNGSKVAYVEVSPRDKGIAIG  118 (143)
T ss_pred             CCCCCCCCCCCCCCCHHHH-HHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEECCCCCCEEEECCCCCCCCCCCC
T ss_conf             2222111113332100001-110122000011211001222100000000000000001234300110012111110012


Q ss_pred             CCHHHHHHHHHHHCCEEEEEE
Q ss_conf             442789999986167457855
Q gi|254780788|r  323 RRGQNVRLASQLTGWTIDIIT  343 (526)
Q Consensus       323 k~GqNvrLas~Ltg~~idi~~  343 (526)
                      +.|.|...+..+.....++..
T Consensus       119 ~~~~~~~~~~~~~~~~~~~~~  139 (143)
T TIGR01952       119 KGGKNIERAKELAKRHLDIDD  139 (143)
T ss_pred             CCCCCCHHHHHHHHHCCCCCC
T ss_conf             343210012222210012222


No 161
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=84.71  E-value=3  Score=21.10  Aligned_cols=37  Identities=8%  Similarity=0.083  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHHHCCCCCCCE-EEEECCCCCEEEEEEEEE
Q ss_conf             99999999996136874535-999749988399999988
Q gi|254780788|r   30 VMADSIQKAARSLYGTMSDI-RVEINPETGDISLFRLLE   67 (526)
Q Consensus        30 aie~Al~~a~kK~~~~~~~i-~V~iD~~tG~i~i~~~~~   67 (526)
                      .-+.|... .++-...++.+ .+.+|.+||++-++..+-
T Consensus        73 ~~e~A~~~-I~eivP~ea~i~~i~Fd~~tGEViIea~KP  110 (637)
T COG1782          73 PPEEARKI-ILEIVPEEAGITDIYFDDDTGEVIIEAKKP  110 (637)
T ss_pred             CHHHHHHH-HHHHCCCCCCCEEEEECCCCCEEEEEECCC
T ss_conf             98999999-997486213703678618874499995589


No 162
>PRK00106 hypothetical protein; Provisional
Probab=84.52  E-value=3  Score=21.05  Aligned_cols=151  Identities=21%  Similarity=0.282  Sum_probs=90.4

Q ss_pred             HHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCC-CCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHCCCCCCCCC
Q ss_conf             8999997628665424898756787999985342-211025442789999986167457855220011010012210001
Q gi|254780788|r  283 SATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQ-LSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQF  361 (526)
Q Consensus       283 ~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~q-ls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~~~~~~~  361 (526)
                      ....+..|++-.-..-+  .| ...-.|-.|++. --.-|||.|.|+|---.+||-.|=|-...+.              
T Consensus       205 Ar~Ii~~AiqR~a~d~~--~E-~tvsvV~Lp~demKGRIIGREGRNIRa~E~~TGVDlIIDDTPe~--------------  267 (535)
T PRK00106        205 AKDLLAQAMQRLAGEYV--TE-QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPEV--------------  267 (535)
T ss_pred             HHHHHHHHHHHCCCCCC--CH-HCEEEEECCCHHHHCCCCCCCCCCHHHHHHHHCCEEEECCCCCE--------------
T ss_conf             99999999975163210--12-10356855977875520087754199999975964898599985--------------


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHH-HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCC
Q ss_conf             11225888467888877321114-77750588887765305889999999999999999999989877542843566407
Q gi|254780788|r  362 FMQAINVDEIIAHLLVAEGFADV-EELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSI  440 (526)
Q Consensus       362 f~e~LdVDE~iA~~LV~eGf~Si-EeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l  440 (526)
                                    .+-.||+.+ .+||....+.|..=.-+.+..++++..+++.-+...-.+..+..     -.+ +.+
T Consensus       268 --------------V~lS~FDpvRREiAr~aLe~Li~DGRIhPaRIEe~v~k~~~e~~~~i~e~Ge~a-----~~e-lgi  327 (535)
T PRK00106        268 --------------VVLSGFDPIRREIARMTLESLIKDGRIHPARIEELVEKNRLEMDNRIREYGEAA-----AYE-IGA  327 (535)
T ss_pred             --------------EEEECCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHH-CCC
T ss_conf             --------------788679878999999999999981892888899999999999999999999999-----998-099


Q ss_pred             CCCCHHHHHHHHHCCCCC------------HHHHHHCCHHHH
Q ss_conf             799989999999879847------------889653267752
Q gi|254780788|r  441 PGIDSKIKVALGENGIKT------------MEDLAGCSVDDL  470 (526)
Q Consensus       441 ~gl~~~~~~~L~e~gIkt------------leDlAels~dEL  470 (526)
                      .||.++++-.|+.=...|            +-.||++-..||
T Consensus       328 ~~lhpelik~lGrLkyRtSygQNvL~HS~Eva~lag~mA~El  369 (535)
T PRK00106        328 PNLHPDLIKIMGRLQFRTSYGQNVLRHSVEVGKLAGILAGEL  369 (535)
T ss_pred             CCCCHHHHHHHHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999978999987600010240589999999999999999983


No 163
>pfam08292 RNA_pol_Rbc25 RNA polymerase III subunit Rpc25. Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III.
Probab=84.03  E-value=2.8  Score=21.32  Aligned_cols=55  Identities=25%  Similarity=0.286  Sum_probs=41.8

Q ss_pred             HCCCEEEEEEEECCCCEEEEEECC-CEEEEEHHHCCCCCC-------------------CCCCCEEEEEEEEECC
Q ss_conf             208389999984057638999579-358744787488751-------------------1527669999976113
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDETISREN-------------------LRPGDRVKSYIYDVRR  191 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg~-~ea~Lp~~e~ip~E~-------------------~~~Gdrika~i~~V~~  191 (526)
                      -+|||++|+|+.-++..+.|.||= -+-++|...+-..-.                   |..|+.||+-|.++.-
T Consensus         2 F~gEIl~G~I~s~~~eGi~vslgFFdDI~IP~~~L~~ps~fd~~eq~WvW~~d~~~~l~~d~~e~IRFRV~~~~f   76 (120)
T pfam08292         2 FVGEIITGKIKSSTAEGIKVSLGFFDDIFIPPDLLPEPSEFDEEEQAWVWEYDEETELYFDVGEEIRFRVESEIF   76 (120)
T ss_pred             CCCCEEEEEEEECCCCCEEEEEECCCEEEECHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCCCEEEEEEEEEEE
T ss_conf             876589999940587847997102420689989978866307334679924898640103689969999988798


No 164
>PRK02821 hypothetical protein; Provisional
Probab=83.98  E-value=2.1  Score=22.24  Aligned_cols=49  Identities=24%  Similarity=0.361  Sum_probs=35.0

Q ss_pred             CHHHHHHHHCC--CCCCCE-EEECCCCCEEEEEECCCCCCCCCCCCHHHHHH
Q ss_conf             78999997628--665424-89875678799998534221102544278999
Q gi|254780788|r  282 DSATFVINALR--PAIVTK-VVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRL  330 (526)
Q Consensus       282 d~~~fi~nAl~--PA~v~~-v~~de~~~~~~v~v~~~qls~AIGk~GqNvrL  330 (526)
                      +..+|++.+|-  |-.|.= ..-++.....++-|.++++-..|||+|..++-
T Consensus         4 elve~ivk~LVd~Pd~V~V~~~e~~~~~~~el~V~~eD~GkVIGk~Grta~A   55 (77)
T PRK02821          4 DAVEHLVRGIVDNPDDVRVDSVTNRRGRTLEVRVHPDDLGKVIGRGGRTATA   55 (77)
T ss_pred             HHHHHHHHHCCCCCCEEEEEEEECCCEEEEEEEECHHHCCCEECCCCHHHHH
T ss_conf             9999999874799882799999789827999999934474454778677999


No 165
>LOAD_cold consensus
Probab=83.88  E-value=3.2  Score=20.86  Aligned_cols=54  Identities=26%  Similarity=0.429  Sum_probs=38.1

Q ss_pred             EEEEEEEECC--CC--EEEEEECCCEEEEEHHHCCCC--CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf             8999998405--76--389995793587447874887--511527669999976113587028
Q gi|254780788|r  141 IISGTVKRVE--YG--NVIVDLGNSDGVIRRDETISR--ENLRPGDRVKSYIYDVRREQRGPQ  197 (526)
Q Consensus       141 iv~G~V~r~e--~~--~iiVdlg~~ea~Lp~~e~ip~--E~~~~Gdrika~i~~V~~~~rgpq  197 (526)
                      +++|+|+..+  +|  +|..|-|+-+-++-.+..-..  ..++.|++|.+-+.+   ..||||
T Consensus         1 M~~G~VK~f~~~kGfGFI~~~~g~~DvFvH~s~l~~~~~~~l~~G~~V~f~~~~---~~kG~~   60 (67)
T LOAD_cold         1 MVKGTVKWFNVKKGFGFITPEDGGEDVFVHQSAIQGDGFRSLTEGQEVEFDIVE---GPKGPQ   60 (67)
T ss_pred             CCCEEEEEEECCCCCEEEEECCCCCEEEEEHHHHCCCCCCCCCCCCEEEEEEEE---CCCCCE
T ss_conf             998699999899994788757998218999478140478647999999999998---999967


No 166
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=83.82  E-value=2.8  Score=21.31  Aligned_cols=87  Identities=25%  Similarity=0.295  Sum_probs=62.6

Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCCHHHHHHCCCCCCHHHH-----HHH
Q ss_conf             7321114777505888877653058899999999999999999-9998987754284356640779998999-----999
Q gi|254780788|r  378 AEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGI-DITLQKKIRELGVSEELCSIPGIDSKIK-----VAL  451 (526)
Q Consensus       378 ~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~-~~~~~e~~~e~~~~e~L~~l~gl~~~~~-----~~L  451 (526)
                      -..|-|.|.++.++.+.|... |+..-.++-|+.-|+.+...+ .............-+.|+.+.|+.+-.+     ..|
T Consensus       141 ~~~fptpe~l~~~~~~~l~~~-g~s~~Ka~yi~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~l  219 (285)
T COG0122         141 YHSFPTPEQLAAADEEALRRC-GLSGRKAEYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGL  219 (285)
T ss_pred             CCCCCCHHHHHHCCHHHHHHH-CCCHHHHHHHHHHHHHHHCCCCCHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHC
T ss_conf             667989999984799999883-7857789999999999985996567662588999999987378867999999999816


Q ss_pred             HHCCCCCHHHHHHC
Q ss_conf             98798478896532
Q gi|254780788|r  452 GENGIKTMEDLAGC  465 (526)
Q Consensus       452 ~e~gIktleDlAel  465 (526)
                      +..++-..+|++=.
T Consensus       220 gr~dvfP~~D~~lr  233 (285)
T COG0122         220 GRPDVFPADDLGLR  233 (285)
T ss_pred             CCCCCCCCHHHHHH
T ss_conf             88986771559999


No 167
>PRK07758 hypothetical protein; Provisional
Probab=83.75  E-value=1.9  Score=22.49  Aligned_cols=40  Identities=23%  Similarity=0.303  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             7888877321114777505888877653058899999999
Q gi|254780788|r  372 IAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG  411 (526)
Q Consensus       372 iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~  411 (526)
                      --..|+++|++|+++++..+..+|+++-||.......|++
T Consensus        46 ARRAL~~~GI~TLedLskytEkELL~LHGmGP~ai~~L~~   85 (95)
T PRK07758         46 ARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRK   85 (95)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             8999998281149999885199999984868888999999


No 168
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=83.48  E-value=2.6  Score=21.60  Aligned_cols=55  Identities=18%  Similarity=0.279  Sum_probs=45.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             00011122588846788887732111477750588887765305889999999999
Q gi|254780788|r  358 RTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRA  413 (526)
Q Consensus       358 ~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA  413 (526)
                      .+-.+....-+...+++.||.. |.++..+..|+.++|.+++|+.+-.|..+++.-
T Consensus       285 GYR~L~kiprlp~~vie~lV~~-Fg~L~~ll~As~eeL~~VeGIGe~RAr~IregL  339 (352)
T PRK13482        285 GYRILAKIPRLPSAVIENLVKH-FGTLQGLLEASIEDLDDVEGIGEVRARAIREGL  339 (352)
T ss_pred             HHHHHCCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             5888605999999999999998-527999986899888656796799999999999


No 169
>TIGR00448 rpoE DNA-directed RNA polymerase; InterPro: IPR004519   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.   This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to Escherichia coli RpoE.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription, 0005634 nucleus.
Probab=83.26  E-value=2.8  Score=21.34  Aligned_cols=74  Identities=31%  Similarity=0.519  Sum_probs=54.5

Q ss_pred             HHHHHCCCEEEEEEEECCCCEEEEE-ECCCEEEEEHH-------------HC-CC---CC---CCCCCCEEEEEEEEEC-
Q ss_conf             9985208389999984057638999-57935874478-------------74-88---75---1152766999997611-
Q gi|254780788|r  133 EFKDKVGEIISGTVKRVEYGNVIVD-LGNSDGVIRRD-------------ET-IS---RE---NLRPGDRVKSYIYDVR-  190 (526)
Q Consensus       133 ef~~r~Geiv~G~V~r~e~~~iiVd-lg~~ea~Lp~~-------------e~-ip---~E---~~~~Gdrika~i~~V~-  190 (526)
                      -|+...+|||+|-|..+.--..+|- ||-.++++-.+             .. |-   +|   .|..||.|||=|.... 
T Consensus        76 ~FkP~l~EiVeGev~~~~efG~fV~LlGp~D~l~h~sq~~ddy~~YdPk~~~liGPmD~Etk~~ld~gd~vRaRIv~~sl  155 (184)
T TIGR00448        76 VFKPELGEIVEGEVIEIVEFGAFVSLLGPFDGLLHVSQVLDDYVVYDPKESALIGPMDKETKKVLDVGDKVRARIVALSL  155 (184)
T ss_pred             EECCCCEEEEEEEEEEEEECCCEEEEECCCCCEEEEEEEEECCEEECCCCCCEECCCCHHCCCEEECCCEEEEEEEEEEE
T ss_conf             96035216786589989852742675223132344100113563662656604567401217351016756678888764


Q ss_pred             --CCC-CEEEEEEECCCHH
Q ss_conf             --358-7028987159889
Q gi|254780788|r  191 --REQ-RGPQVLLSRTHPQ  206 (526)
Q Consensus       191 --~~~-rgpqi~lSRt~p~  206 (526)
                        +.+ +|..+-|..-.|-
T Consensus       156 k~~~pk~~~k~~LtmRqp~  174 (184)
T TIGR00448       156 KDRRPKEGSKIGLTMRQPL  174 (184)
T ss_pred             CCCCCCCCCEEEEECCCCC
T ss_conf             0413788851100115731


No 170
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=83.26  E-value=2.4  Score=21.75  Aligned_cols=55  Identities=22%  Similarity=0.283  Sum_probs=44.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             11225888467888877321114777505888877653058899999999999999
Q gi|254780788|r  362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYL  417 (526)
Q Consensus       362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L  417 (526)
                      +..-.+|....|.-|.. -|.|++.+..++.++|..++|++++.|.+|+.--....
T Consensus       184 l~s~pgig~~~a~~ll~-~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~~  238 (254)
T COG1948         184 LESIPGIGPKLAERLLK-KFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLRTEY  238 (254)
T ss_pred             HHCCCCCCHHHHHHHHH-HHCCHHHHHHCCHHHHHHHCCCCHHHHHHHHHHHHCHH
T ss_conf             97089964899999999-85688877655999997744846889999999983444


No 171
>PRK10354 major cold shock protein; Provisional
Probab=83.08  E-value=3.4  Score=20.63  Aligned_cols=56  Identities=21%  Similarity=0.343  Sum_probs=38.4

Q ss_pred             CEEEEEEEECC--CC--EEEEEECCCEEEEEHHHCC--CCCCCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf             38999998405--76--3899957935874478748--875115276699999761135870289
Q gi|254780788|r  140 EIISGTVKRVE--YG--NVIVDLGNSDGVIRRDETI--SRENLRPGDRVKSYIYDVRREQRGPQV  198 (526)
Q Consensus       140 eiv~G~V~r~e--~~--~iiVdlg~~ea~Lp~~e~i--p~E~~~~Gdrika~i~~V~~~~rgpqi  198 (526)
                      +-++|+|+-++  +|  +|.-|-|.-+-++-.+..-  .-..+..|+||.+   ++....||||-
T Consensus         3 ~~~tG~VKwFn~~KGyGFI~~d~g~~DvFvH~s~l~~~g~~~L~~Gq~V~f---~~~~g~kG~~A   64 (70)
T PRK10354          3 GKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSF---TIESGAKGPAA   64 (70)
T ss_pred             CCEEEEEEEEECCCCEEEEECCCCCCEEEEEHHHHCCCCCCCCCCCCEEEE---EEEECCCCCEE
T ss_conf             750799998709998599842799842999858917048972599999999---99979998620


No 172
>TIGR00596 rad1 DNA repair protein (rad1); InterPro: IPR006167    All proteins in this family, for which functions are known, are components in a multiprotein endonuclease complex, usually made up of Rad1 and Rad10 homologues. This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologues of these genes, but the function of the Archaeal proteins is not known, so are not included in this family.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity, 0006281 DNA repair.
Probab=82.94  E-value=1.3  Score=23.73  Aligned_cols=44  Identities=27%  Similarity=0.379  Sum_probs=39.5

Q ss_pred             CCHHHH--HHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf             284356--64077999899999998798478896532677521231
Q gi|254780788|r  431 LGVSEE--LCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS  474 (526)
Q Consensus       431 ~~~~e~--L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~  474 (526)
                      .++.+=  |+.+||++.....-|-.+|++++..|+.+|.+||-++.
T Consensus       875 ~~~~dfkrLl~~PGV~~kN~rnl~~~G~k~~~el~~~S~~El~eL~  920 (939)
T TIGR00596       875 SGPQDFKRLLKLPGVTKKNIRNLLKKGVKSIRELAKLSQEELEELI  920 (939)
T ss_pred             CCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             5158999855789856023455554315559999998799999750


No 173
>KOG0950 consensus
Probab=82.93  E-value=2.9  Score=21.24  Aligned_cols=38  Identities=16%  Similarity=0.297  Sum_probs=27.7

Q ss_pred             HHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf             66407799989999999879847889653267752123
Q gi|254780788|r  436 ELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGW  473 (526)
Q Consensus       436 ~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~  473 (526)
                      +|+.++++..+-+.+|-..|.+|+-++|.-...+|.-.
T Consensus       895 ~Lmrv~~~~~~RAr~lf~Agf~tv~~iA~a~p~klvke  932 (1008)
T KOG0950         895 PLMRVPDVKAERARQLFKAGFTSVGSIANATPEKLVKE  932 (1008)
T ss_pred             HHHCCCHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHH
T ss_conf             45257436789999999844533588855882778987


No 174
>PRK01064 hypothetical protein; Provisional
Probab=82.83  E-value=2.2  Score=22.06  Aligned_cols=48  Identities=21%  Similarity=0.364  Sum_probs=34.6

Q ss_pred             CHHHHHHHHCC--CCCCCE-EEECCCCCEEEEEECCCCCCCCCCCCHHHHH
Q ss_conf             78999997628--665424-8987567879999853422110254427899
Q gi|254780788|r  282 DSATFVINALR--PAIVTK-VVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR  329 (526)
Q Consensus       282 d~~~fi~nAl~--PA~v~~-v~~de~~~~~~v~v~~~qls~AIGk~GqNvr  329 (526)
                      +.-+||+.+|-  |-+|.= ..-.+..-...+-|.++++-..|||+|.+++
T Consensus         3 eLve~ivk~LVd~Pd~V~V~~~~~~~~~~~~l~V~~~D~GkVIGk~Grtak   53 (78)
T PRK01064          3 EFLAYIVKNLVDRPEEVHIKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIK   53 (78)
T ss_pred             HHHHHHHHHHCCCCCEEEEEEEECCCEEEEEEEECCCCCCCEECCCCHHHH
T ss_conf             899999998579987389999947987999999990018558788874699


No 175
>PRK02794 DNA polymerase IV; Provisional
Probab=82.49  E-value=3.2  Score=20.92  Aligned_cols=12  Identities=17%  Similarity=0.116  Sum_probs=5.9

Q ss_pred             ECHHHHHHHCCC
Q ss_conf             348999862889
Q gi|254780788|r   79 ISLKVARDRDPS   90 (526)
Q Consensus        79 I~l~~A~~~~~~   90 (526)
                      +++.+|+++-|+
T Consensus        89 mp~~~A~~lcP~  100 (417)
T PRK02794         89 MPMFKALKLCPD  100 (417)
T ss_pred             CCHHHHHHHCCC
T ss_conf             929999987899


No 176
>TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804    This family consists of exoribonuclease II (RNase II), the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process.
Probab=81.94  E-value=1.6  Score=23.13  Aligned_cols=128  Identities=19%  Similarity=0.287  Sum_probs=80.3

Q ss_pred             ECCCHHHHHHHHHHHHHH--HHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEE
Q ss_conf             159889999999976677--755808785663167750349999408998812765548862178899862778267995
Q gi|254780788|r  201 SRTHPQFMVKLFHMEVPE--IYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVV  278 (526)
Q Consensus       201 SRt~p~~l~~Lf~~EVPE--I~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~  278 (526)
                      |-+..+|=-.||-.++|.  -.++.==|.||| ||-     |--+.++.+|        +-.|.++=++=|=|=+|=..|
T Consensus       207 ~~sT~DmDDALy~~~l~~nstq~~l~L~vAIA-DPT-----AYI~~~s~ld--------~~A~~R~FTnYLPGfNiPMLP  272 (664)
T TIGR02062       207 SESTKDMDDALYIEELPNNSTQGDLKLIVAIA-DPT-----AYIAEGSKLD--------KEAKKRGFTNYLPGFNIPMLP  272 (664)
T ss_pred             CCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEE-CCC-----CCCCCCCHHH--------HHHHHHCCCCCCCCCCCCCCC
T ss_conf             88864423589998600555578837999971-884-----3268865789--------999870872468778898887


Q ss_pred             C--CCCHHHHHHHHCCCCCCCEEEECCCCC-----EEEE-------EECCCCCCCCCCCC------------HHHHHHHH
Q ss_conf             5--987899999762866542489875678-----7999-------98534221102544------------27899999
Q gi|254780788|r  279 W--SPDSATFVINALRPAIVTKVVLDEDVG-----RIEV-------IVPKEQLSLAIGRR------------GQNVRLAS  332 (526)
Q Consensus       279 w--s~d~~~fi~nAl~PA~v~~v~~de~~~-----~~~v-------~v~~~qls~AIGk~------------GqNvrLas  332 (526)
                      =  |||.--+..|-.=||=+..|.++-+..     .+..       -..=|+.|==+=++            -|-|||-.
T Consensus       273 R~LSdeLCSL~~ne~RP~L~C~it~~~dG~I~~~i~Ff~A~i~SkAkL~Yd~VSDwLE~~~~e~WqPE~~~ia~qv~~L~  352 (664)
T TIGR02062       273 RELSDELCSLIANEVRPVLACSITISKDGNITDKIEFFAAYIKSKAKLVYDKVSDWLEKASSEAWQPESEEIAQQVRLLH  352 (664)
T ss_pred             HHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCCCCEEEEEEEEEEEECCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             42368872464356785789999970684122586179988862345401211123205878667887678999999999


Q ss_pred             HHHCCEEEEE
Q ss_conf             8616745785
Q gi|254780788|r  333 QLTGWTIDII  342 (526)
Q Consensus       333 ~Ltg~~idi~  342 (526)
                      ++|.-+|+=.
T Consensus       353 ~~~~~R~~WR  362 (664)
T TIGR02062       353 QFCQARIEWR  362 (664)
T ss_pred             HHHHHHHHHH
T ss_conf             9988764132


No 177
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit; InterPro: IPR011773   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.    This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins , .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription DNA-dependent.
Probab=80.95  E-value=2  Score=22.34  Aligned_cols=31  Identities=26%  Similarity=0.359  Sum_probs=20.7

Q ss_pred             CCHHHHHHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf             9989999999879847889653267752123
Q gi|254780788|r  443 IDSKIKVALGENGIKTMEDLAGCSVDDLLGW  473 (526)
Q Consensus       443 l~~~~~~~L~e~gIktleDlAels~dEL~~~  473 (526)
                      ||-.-..+|...||.|+-||..+|-.||+.+
T Consensus       268 LSVRs~NCLk~~gI~t~geL~~~~e~eLl~i  298 (324)
T TIGR02027       268 LSVRSYNCLKRAGIHTLGELVSKSEEELLKI  298 (324)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC
T ss_conf             5489886464603541788886038988417


No 178
>pfam04994 TfoX_C TfoX C-terminal domain. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found associated with pfam00383 in a cytidine and deoxycytidylate deaminase family protein from Neisseria meningitidis serogroup B. It is also found as an isolated domain in some proteins suggesting this is an autonomous domain.
Probab=80.88  E-value=2.1  Score=22.14  Aligned_cols=35  Identities=29%  Similarity=0.433  Sum_probs=31.0

Q ss_pred             HHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHC
Q ss_conf             64077999899999998798478896532677521
Q gi|254780788|r  437 LCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLL  471 (526)
Q Consensus       437 L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~  471 (526)
                      |.+|+.|++.+...|.+-||.|.+||-.+...+-.
T Consensus         1 l~dLpNlg~~~er~L~~vGI~t~~~L~~~Ga~~ay   35 (77)
T pfam04994         1 LKDLPNLGLKLERMLKKAGIHTVEDLRELGAVEAY   35 (77)
T ss_pred             CCCCCCCCHHHHHHHHHCCCCCHHHHHHHCHHHHH
T ss_conf             98788989999999999499989999981899999


No 179
>PRK01216 DNA polymerase IV; Validated
Probab=80.74  E-value=3.4  Score=20.73  Aligned_cols=48  Identities=17%  Similarity=0.270  Sum_probs=32.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             22588846788887732111477750588887765305889999999999
Q gi|254780788|r  364 QAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRA  413 (526)
Q Consensus       364 e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA  413 (526)
                      +-.+|....++.|-..|+.|+.+++..+.+.|..+.|  .-....|...|
T Consensus       182 ~i~GIG~~t~~~L~~~GI~ti~dL~~~~~~~L~~~fG--~~~~~~l~~~a  229 (351)
T PRK01216        182 DVPGIGKVLSERLNELGINKLRDILSKSFNKLKSIIG--EAKANYLYSLA  229 (351)
T ss_pred             EECCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHC--HHHHHHHHHHH
T ss_conf             8548579999999985996899975299999999977--79999999983


No 180
>PRK03103 DNA polymerase IV; Reviewed
Probab=80.61  E-value=3.9  Score=20.23  Aligned_cols=34  Identities=21%  Similarity=0.294  Sum_probs=14.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHC
Q ss_conf             8884678888773211147775058888776530
Q gi|254780788|r  367 NVDEIIAHLLVAEGFADVEELACVKISEIASIEG  400 (526)
Q Consensus       367 dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeG  400 (526)
                      +|...++..|-..|+.|+.+++.++.+.|....|
T Consensus       189 GIG~~~~~kL~~~GI~t~~dL~~~~~~~l~~~fG  222 (410)
T PRK03103        189 GVGRRMEHHLRRMGISTIGQLAQTPLERLKKRWG  222 (410)
T ss_pred             CCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHHC
T ss_conf             8788999999985897499986599999999839


No 181
>PRK02406 DNA polymerase IV; Validated
Probab=80.61  E-value=3.6  Score=20.51  Aligned_cols=49  Identities=20%  Similarity=0.215  Sum_probs=37.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             2258884678888773211147775058888776530588999999999999
Q gi|254780788|r  364 QAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRARE  415 (526)
Q Consensus       364 e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~  415 (526)
                      +--+|....++.|-..|+.|+.+++..+...|....|   .....|...|+-
T Consensus       184 ~l~GIG~~~~~~L~~~GI~ti~DL~~~~~~~L~~~fG---~~g~~l~~~a~G  232 (355)
T PRK02406        184 KIPGVGKVTAEKLHALGIRTCADLQKWDLATLLRRFG---KFGRRLYERARG  232 (355)
T ss_pred             CCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHC---HHHHHHHHHHCC
T ss_conf             0588588999999982981799976099999999979---899999999659


No 182
>KOG1676 consensus
Probab=80.55  E-value=2  Score=22.33  Aligned_cols=105  Identities=22%  Similarity=0.324  Sum_probs=70.9

Q ss_pred             CCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEE-----------
Q ss_conf             167750349999408998812765548862178899862778267995598789999976286654248-----------
Q gi|254780788|r  231 RDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKV-----------  299 (526)
Q Consensus       231 R~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v-----------  299 (526)
                      +.+|--+.+-|.--.   --||+.+|--|.-|+.+.+|- |-||-+.+=++ |    ..++-||.|...           
T Consensus       224 ~~~g~~~~~~V~VPr---~~VG~IIGkgGE~IKklq~et-G~KIQfkpDd~-p----~speR~~~IiG~~d~ie~Aa~lI  294 (600)
T KOG1676         224 VRGGGSATREVKVPR---SKVGIIIGKGGEMIKKLQNET-GAKIQFKPDDD-P----SSPERPAQIIGTVDQIEHAAELI  294 (600)
T ss_pred             CCCCCCCEEEEECCC---CCEEEEEECCCHHHHHHHHCC-CCEEEEECCCC-C----CCCCCEEEEECCHHHHHHHHHHH
T ss_conf             676654136885456---523468704716788876335-74268623888-8----87544256526799999999999


Q ss_pred             --EEC--CCCC-------------EEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEEC
Q ss_conf             --987--5678-------------79999853422110254427899999861674578552
Q gi|254780788|r  300 --VLD--EDVG-------------RIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITE  344 (526)
Q Consensus       300 --~~d--e~~~-------------~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~  344 (526)
                        +|.  +...             .|...||.+..-|.|||+|.|+|=-.+=+|-++..--.
T Consensus       295 ~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~  356 (600)
T KOG1676         295 NEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ  356 (600)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCC
T ss_conf             99999986047777677875410158896451000445478863001110367751365678


No 183
>PRK03352 DNA polymerase IV; Validated
Probab=80.33  E-value=4.3  Score=19.96  Aligned_cols=34  Identities=26%  Similarity=0.298  Sum_probs=18.5

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHC
Q ss_conf             8884678888773211147775058888776530
Q gi|254780788|r  367 NVDEIIAHLLVAEGFADVEELACVKISEIASIEG  400 (526)
Q Consensus       367 dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeG  400 (526)
                      +|....++.|-..|+.|+.+++.++...|....|
T Consensus       184 GIG~~~~~kL~~~GI~Ti~DL~~~~~~~L~~~fG  217 (345)
T PRK03352        184 GVGPKTAKKLAALGITTVADLAATDPAVLTATFG  217 (345)
T ss_pred             CCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHHC
T ss_conf             8289999999975997199986699999999978


No 184
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=79.89  E-value=3.6  Score=20.52  Aligned_cols=50  Identities=20%  Similarity=0.264  Sum_probs=33.8

Q ss_pred             HHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHH
Q ss_conf             89999976286654248987567879999853422110254427899999
Q gi|254780788|r  283 SATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLAS  332 (526)
Q Consensus       283 ~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas  332 (526)
                      ..+|+...|+-|-+++|.+.-......|++--..--+.|||+|++++--.
T Consensus        21 ire~l~k~L~~AG~s~ieIert~~~~~I~I~tarPG~VIGrkG~~I~~L~   70 (220)
T PTZ00084         21 LNEFLSRELADDGYAGVELRVTPVRTEIIIRATKTREVLGEKGRRIRELT   70 (220)
T ss_pred             HHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCEEECCCCHHHHHHH
T ss_conf             99999988886787759999889847999996898558868854699999


No 185
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=79.65  E-value=3.9  Score=20.21  Aligned_cols=58  Identities=31%  Similarity=0.455  Sum_probs=44.6

Q ss_pred             HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCC
Q ss_conf             20838999998405763899957-93587447874887511527669999976113587
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQR  194 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~r  194 (526)
                      +.|++-.|+|.|++.-.++|+|+ .+-|.|-++++..-..|.+||.+-+-+..|+...+
T Consensus       121 e~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~~~~~vgdeiiV~v~~vr~~~g  179 (715)
T COG1107         121 EAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGDPDYAVGDEIIVQVSDVRPEKG  179 (715)
T ss_pred             CCCEEEECCCCCHHHHCCEEECCHHHHCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCC
T ss_conf             46405403102143406524337354334440124788777878748998421577777


No 186
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=79.39  E-value=4.3  Score=19.95  Aligned_cols=44  Identities=20%  Similarity=0.291  Sum_probs=34.3

Q ss_pred             CCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCCCCCCCCCE
Q ss_conf             08389999984057638999579358744787488751152766
Q gi|254780788|r  138 VGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDR  181 (526)
Q Consensus       138 ~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~E~~~~Gdr  181 (526)
                      .||++-|+|.++.+-.++.+.|....+..+..+-|.=.|.++..
T Consensus         1 KGEVvDavVt~Vnk~G~Fa~~GPl~~fvS~~~ip~d~~f~~~~~   44 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNAS   44 (88)
T ss_pred             CCCEEEEEEEEECCEEEEEEECCEEEEEECCCCCCCEEECCCCC
T ss_conf             99579999999834789998047589999111899709989999


No 187
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation.  The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=79.17  E-value=2.8  Score=21.31  Aligned_cols=44  Identities=23%  Similarity=0.469  Sum_probs=31.9

Q ss_pred             CEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEE
Q ss_conf             24898756787999985342211025442789999986167457
Q gi|254780788|r  297 TKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTID  340 (526)
Q Consensus       297 ~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~id  340 (526)
                      .+|.+.++...+.+-+.-+++++.|||+|+...=--.|+.--++
T Consensus        15 ~~v~~~~~~~~~~~~i~g~~~~~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          15 ADVDVEEEGDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             EEEEEEEECCEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             79999997998999994498774166898647999999999997


No 188
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=79.05  E-value=2.4  Score=21.75  Aligned_cols=35  Identities=26%  Similarity=0.416  Sum_probs=31.0

Q ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf             99998534221102544278999998616745785
Q gi|254780788|r  308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII  342 (526)
Q Consensus       308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~  342 (526)
                      ..+-+|.+.....||++|.|+|=-..-||-+|||-
T Consensus         4 ~~~~I~~dkIg~vIGpGGk~Ik~I~e~tg~~I~I~   38 (61)
T cd02393           4 ETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIE   38 (61)
T ss_pred             EEEEECHHHHHHHCCCCCHHHHHHHHHHCCEEEEC
T ss_conf             99996989987644886089999999889889983


No 189
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=78.37  E-value=2.2  Score=22.09  Aligned_cols=44  Identities=25%  Similarity=0.472  Sum_probs=33.5

Q ss_pred             CCHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf             28435664077999899999998798478896532677521231
Q gi|254780788|r  431 LGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS  474 (526)
Q Consensus       431 ~~~~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~  474 (526)
                      .+-.+||..+.|+.+.+..+|.+.||.|.+.+|.++-+++..+.
T Consensus       149 ~g~aDDLk~I~GIGP~~e~~Ln~~GI~~F~QIA~~t~~dia~id  192 (216)
T PRK12278        149 AGEADDLTKITGVGPALAKKLNEAGITTFAQIAALTDEDIAAID  192 (216)
T ss_pred             CCCCCCCCEECCCCHHHHHHHHHHCCCHHHHHHCCCHHHHHHHH
T ss_conf             78996543602658899999998187239998559999999987


No 190
>cd00424 Pol_Y Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases.
Probab=78.27  E-value=3.8  Score=20.30  Aligned_cols=38  Identities=37%  Similarity=0.388  Sum_probs=28.9

Q ss_pred             HHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf             66407799989999999879847889653267752123
Q gi|254780788|r  436 ELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGW  473 (526)
Q Consensus       436 ~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~  473 (526)
                      .+.+++|+...+...|.+.||.|.-||+.+..++|...
T Consensus       174 pv~~l~GIG~~~~~~L~~~gi~ti~dl~~~~~~~l~~~  211 (341)
T cd00424         174 PLSDIPGIGSVTASRLEALGIIRKCDLLALQPDQLLAS  211 (341)
T ss_pred             CHHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH
T ss_conf             87887487889999999849935999871899999999


No 191
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=78.16  E-value=4.9  Score=19.49  Aligned_cols=70  Identities=24%  Similarity=0.343  Sum_probs=30.9

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHCCCCCCHHHHHHHH-HCCCCCHHHHHHCCH
Q ss_conf             87765305889999999999999999999989877542--843566407799989999999-879847889653267
Q gi|254780788|r  394 EIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIREL--GVSEELCSIPGIDSKIKVALG-ENGIKTMEDLAGCSV  467 (526)
Q Consensus       394 eL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~--~~~e~L~~l~gl~~~~~~~L~-e~gIktleDlAels~  467 (526)
                      -+..++|+..-+|..|..-    +.+-....-+.++..  ..-.+|+.++|+.+.-+..|- +-||+++++|-+-+-
T Consensus        54 ~~t~l~gIGk~ia~~I~e~----l~tG~~~~le~lk~~~P~gl~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~  126 (326)
T COG1796          54 RLTELPGIGKGIAEKISEY----LDTGEVKKLEALKKEVPEGLEPLLKVPGLGPKKIVSLYKELGIKDLEELQEALE  126 (326)
T ss_pred             CCCCCCCCCHHHHHHHHHH----HHCCCCHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             1477887568899999999----972860789999885795558786077989288999999978664999999998


No 192
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like.  The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=78.04  E-value=2  Score=22.45  Aligned_cols=37  Identities=32%  Similarity=0.464  Sum_probs=32.0

Q ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEEC
Q ss_conf             9999853422110254427899999861674578552
Q gi|254780788|r  308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITE  344 (526)
Q Consensus       308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~  344 (526)
                      ..+-||....+.-||++|.|++---.-||-+|++-..
T Consensus         2 ~~i~vp~~~h~~iIG~~G~~i~~i~~~~~~~I~~P~~   38 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP   38 (62)
T ss_pred             CEEEECHHHCCCEECCCCCCHHHHHHHHCCEEEECCC
T ss_conf             4899897881975889997399999985979995899


No 193
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=77.64  E-value=5.1  Score=19.39  Aligned_cols=78  Identities=26%  Similarity=0.284  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHH---HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHH
Q ss_conf             788887732111477750588887765---30588999999999999999999998987754284356640779998999
Q gi|254780788|r  372 IAHLLVAEGFADVEELACVKISEIASI---EGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIK  448 (526)
Q Consensus       372 iA~~LV~eGf~SiEeIa~a~~eeL~~I---eGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~  448 (526)
                      ....|. ..|-|+++++.++.++|.+.   -||-.-.+..|++-|+.......    .  .-....++|+.|+|+.+.++
T Consensus        13 ~~~~l~-~~~pt~~~l~~a~~~~l~~~i~~~g~~~~ka~~i~~~a~~i~~~~~----~--~~p~~~~~L~~lpGVG~~tA   85 (149)
T smart00478       13 ATERLF-EKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYG----G--EVPDDREELLKLPGVGRKTA   85 (149)
T ss_pred             HHHHHH-HHCCCHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC----C--CCCCHHHHHHCCCCCCHHHH
T ss_conf             999999-9885999998689999999999868899999999999999998665----5--58855999875898659999


Q ss_pred             HHHHHCCC
Q ss_conf             99998798
Q gi|254780788|r  449 VALGENGI  456 (526)
Q Consensus       449 ~~L~e~gI  456 (526)
                      ......+-
T Consensus        86 ~~vl~~~~   93 (149)
T smart00478       86 NAVLSFAL   93 (149)
T ss_pred             HHHHHHHC
T ss_conf             99999987


No 194
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=75.73  E-value=5.7  Score=19.03  Aligned_cols=57  Identities=23%  Similarity=0.418  Sum_probs=46.9

Q ss_pred             HHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCCC------CCCCCCCEEEEEEEEECCC
Q ss_conf             520838999998405763899957-93587447874887------5115276699999761135
Q gi|254780788|r  136 DKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISR------ENLRPGDRVKSYIYDVRRE  192 (526)
Q Consensus       136 ~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip~------E~~~~Gdrika~i~~V~~~  192 (526)
                      -++|+++.|.|-.+..-..+|+|. +..|++--+|.-.+      +.+++||.|.+=|.++...
T Consensus         3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~   66 (129)
T COG1098           3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDEN   66 (129)
T ss_pred             CCCCCEEEEEEEEEEECCEEEEECCCCCCEEEEHHHHHHHHHHHHHHHCCCCEEEEEEEEECCC
T ss_conf             5346467888975674334898239973148835754436773998842788799999721468


No 195
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=75.28  E-value=5.8  Score=18.95  Aligned_cols=46  Identities=17%  Similarity=0.294  Sum_probs=24.8

Q ss_pred             HHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHH
Q ss_conf             9999976286654248987567879999853422110254427899
Q gi|254780788|r  284 ATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR  329 (526)
Q Consensus       284 ~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvr  329 (526)
                      .+|+..-|.-|-+.+|.+.-......|++--..--+.|||+|++++
T Consensus        18 reyl~k~l~~Agis~IeIeRt~~~~~I~I~tarPG~vIGr~G~~i~   63 (225)
T PRK04191         18 DEYLAKELERAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKTIR   63 (225)
T ss_pred             HHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCEEECCCHHHHH
T ss_conf             9999987776785459999868946999994898515557837799


No 196
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1; InterPro: IPR011940    This entry describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (IPR011938 from INTERPRO) and RadB (IPR011939 from INTERPRO) and bacterial RecA. It has been characterised for human as a recombinase active only in meiosis .; GO: 0003677 DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0007131 meiotic recombination, 0005634 nucleus.
Probab=75.13  E-value=5.9  Score=18.92  Aligned_cols=133  Identities=19%  Similarity=0.236  Sum_probs=83.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCC
Q ss_conf             25888467888877321114777505888877653058899999999999999999999898775428435664077999
Q gi|254780788|r  365 AINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGID  444 (526)
Q Consensus       365 ~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~  444 (526)
                      ..+|.-.-...|-..|+.|+..|.......|..|.|+.|-.+++|.+.|.......=....+..+   .......+. -.
T Consensus         6 ~~GIn~~Di~KLk~~g~~T~~~~~~~T~r~L~~iKGlSEaKVdKi~EaA~K~~~~~f~ta~~~~~---~R~~V~~i~-TG   81 (314)
T TIGR02238         6 AHGINAADIKKLKSAGICTVNGVIMTTKRELLKIKGLSEAKVDKIKEAASKIINVGFITAVEILD---KRKKVLKIS-TG   81 (314)
T ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHH---HCCEEEEEE-CC
T ss_conf             43887889999886368999999998888874037851677999999998764146640578874---062467762-31


Q ss_pred             HHHHHHHHHCCCCCHHHHHHCCHHHHCC-------------------------------CC-CCCCCCCCCCCCCCCCCC
Q ss_conf             8999999987984788965326775212-------------------------------31-234443211245334358
Q gi|254780788|r  445 SKIKVALGENGIKTMEDLAGCSVDDLLG-------------------------------WS-ENKGGNIEKFDGFLSSLG  492 (526)
Q Consensus       445 ~~~~~~L~e~gIktleDlAels~dEL~~-------------------------------~~-~~~~~~~~~~~gil~~~~  492 (526)
                      ...+..+-=.||.|.      |+-|+.|                               |. .+--.-+.+...|-+.|+
T Consensus        82 s~~~d~~LGGGi~s~------~ITE~fGEfR~GKTQl~HTL~VtaQLP~~~~g~~GKv~yIDTEgTFRPdri~~IAerf~  155 (314)
T TIGR02238        82 SKALDKILGGGIESM------SITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGEGKVAYIDTEGTFRPDRIKAIAERFG  155 (314)
T ss_pred             HHHHHHHCCCCEEEE------EHEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHCC
T ss_conf             588743407870000------00000045567714655566553206312579984289981788858178998875407


Q ss_pred             CCHHHHHHHHHHHCC
Q ss_conf             899999999998412
Q gi|254780788|r  493 TPKDQVESMIIHARY  507 (526)
Q Consensus       493 l~~~~A~~lIM~AR~  507 (526)
                      ++.+.+=.=|+-||+
T Consensus       156 ~D~~~~L~Ni~yaRA  170 (314)
T TIGR02238       156 VDGEAVLDNILYARA  170 (314)
T ss_pred             CCHHHHHHHHHHHHH
T ss_conf             898899988898875


No 197
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=74.67  E-value=6  Score=18.84  Aligned_cols=55  Identities=24%  Similarity=0.401  Sum_probs=38.0

Q ss_pred             EEEEEEEECC--CC--EEEEEECCCEEEEEHHHCCCC--CCCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf             8999998405--76--389995793587447874887--5115276699999761135870289
Q gi|254780788|r  141 IISGTVKRVE--YG--NVIVDLGNSDGVIRRDETISR--ENLRPGDRVKSYIYDVRREQRGPQV  198 (526)
Q Consensus       141 iv~G~V~r~e--~~--~iiVdlg~~ea~Lp~~e~ip~--E~~~~Gdrika~i~~V~~~~rgpqi  198 (526)
                      -++|+|+-++  +|  +|.-+-|+-+-++..+.....  ..++.|++|.+   ++....||||-
T Consensus         3 ~i~G~VKwF~~~kGyGFI~~~dG~~DvFvH~s~i~~~g~~~L~~Gq~V~f---~v~~~~kG~~A   63 (69)
T PRK09507          3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEF---EITNGAKGPSA   63 (69)
T ss_pred             CEEEEEEEEECCCCEEEEECCCCCCCEEEEHHHCCCCCCCCCCCCCEEEE---EEEECCCCCEE
T ss_conf             47889999839998799970799832999907705257861699999999---99969999851


No 198
>KOG2916 consensus
Probab=74.54  E-value=6.1  Score=18.82  Aligned_cols=164  Identities=20%  Similarity=0.261  Sum_probs=94.6

Q ss_pred             HHHHHHHHCCCEEEEEEEECCCCEEEEEE---CCCEEEEEHHHCCCCC------CCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf             79999852083899999840576389995---7935874478748875------11527669999976113587028987
Q gi|254780788|r  130 QYLEFKDKVGEIISGTVKRVEYGNVIVDL---GNSDGVIRRDETISRE------NLRPGDRVKSYIYDVRREQRGPQVLL  200 (526)
Q Consensus       130 i~~ef~~r~Geiv~G~V~r~e~~~iiVdl---g~~ea~Lp~~e~ip~E------~~~~Gdrika~i~~V~~~~rgpqi~l  200 (526)
                      .|+.--+.++++|.+.|+.+---+.+|.|   |+.||++.-+|...+-      ..|+|-.=-+.+..|.++..---+--
T Consensus         8 ~ye~kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSk   87 (304)
T KOG2916           8 FYENKYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSK   87 (304)
T ss_pred             HHHCCCCCCCCEEEEEEEEEHHCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCEECHH
T ss_conf             01015997532799875370206216762102781111003577788889899998407753489999717787066213


Q ss_pred             ECCCHHHH--------------------HHHHHHHHHHHHCCEEEEEEEECCCCC---EEEEEEEECCCCCCCEEEEECC
Q ss_conf             15988999--------------------999997667775580878566316775---0349999408998812765548
Q gi|254780788|r  201 SRTHPQFM--------------------VKLFHMEVPEIYNGIVQVKAVSRDPGS---RAKLAVFSSDSSIDPVGACVGM  257 (526)
Q Consensus       201 SRt~p~~l--------------------~~Lf~~EVPEI~~G~ieIk~iaR~pG~---RsKIAV~s~d~~iDpVGAcVG~  257 (526)
                      +|.+|+=+                    .+-|..++-|.|.-+==  .--|.-|+   --|++| +++.-.|+.---=+.
T Consensus        88 rrVs~ed~~kC~Er~~ksK~v~sIlrhvAe~~g~~LeeLY~~igW--~~~rk~g~aYdaFK~~v-td~tV~d~l~~~~~v  164 (304)
T KOG2916          88 RRVSPEDKEKCEERFAKSKLVYSILRHVAEKLGYELEELYQRIGW--PLERKYGHAYDAFKIAV-TDPTVLDELDLSEEV  164 (304)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCC--CHHHHHCHHHHHHHHHC-CCCCCCCCCCCCHHH
T ss_conf             138877889999988776789999999999949839999998377--43666360999998862-684302666777789


Q ss_pred             CCHHHHHHHHHHCC------CCEEEEECCCCHHHHHHHHCCCCCC
Q ss_conf             86217889986277------8267995598789999976286654
Q gi|254780788|r  258 RGSRVQAVVTELRD------EKIDIVVWSPDSATFVINALRPAIV  296 (526)
Q Consensus       258 rGsRiq~I~~EL~g------EkIDii~ws~d~~~fi~nAl~PA~v  296 (526)
                      +-.=.+.|.+.|.-      --|++..|+-+-.--|..||.-|.-
T Consensus       165 k~~Llk~Irrrltpq~vKIRADIEv~Cf~yeGI~aIK~alk~a~~  209 (304)
T KOG2916         165 KEVLLKNIRRRLTPQTVKIRADIEVSCFGYEGIDAIKAALKAALN  209 (304)
T ss_pred             HHHHHHHHHHHCCCCCEEEEEEEEEEECCCCCHHHHHHHHHHHHH
T ss_conf             999999998754886557873258986065679999999998872


No 199
>pfam11731 Cdd1 Pathogenicity locus. Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=74.50  E-value=3.4  Score=20.72  Aligned_cols=42  Identities=26%  Similarity=0.276  Sum_probs=31.3

Q ss_pred             HHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCC
Q ss_conf             566407799989999999879847889653267752123123
Q gi|254780788|r  435 EELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSEN  476 (526)
Q Consensus       435 e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~~~  476 (526)
                      .+|.+|+++.+.++.-|..=||.+.++|++..-+||..-...
T Consensus        12 ~~L~~lPnIG~a~a~DL~~LGi~~~~~L~g~dp~elY~~lc~   53 (92)
T pfam11731        12 KELTDLPNIGKATAKDLRLLGINSPAQLAGRDPLELYERLCE   53 (92)
T ss_pred             HHHHCCCCCCHHHHHHHHHHCCCCHHHHHCCCHHHHHHHHHH
T ss_conf             987418974699999999918998999917999999999999


No 200
>KOG1856 consensus
Probab=74.21  E-value=6.2  Score=18.76  Aligned_cols=149  Identities=15%  Similarity=0.160  Sum_probs=69.4

Q ss_pred             HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHCCCEEEEEE-EECCCCEEEE-EECCCEEEEEHHHCCCCCCCCCC--CEEE
Q ss_conf             999999999999-99999988779999852083899999-8405763899-95793587447874887511527--6699
Q gi|254780788|r  109 VAVQSAKQVIIQ-KVREAERDRQYLEFKDKVGEIISGTV-KRVEYGNVIV-DLGNSDGVIRRDETISRENLRPG--DRVK  183 (526)
Q Consensus       109 iaAq~AKQvI~Q-kireaEr~~i~~ef~~r~Geiv~G~V-~r~e~~~iiV-dlg~~ea~Lp~~e~ip~E~~~~G--drik  183 (526)
                      -+.+.|-|.+++ -+...-|..+-.+++.+++....+.. .+...+-+.= |-+.-+.-.|+  .+-+=.|.++  +-+.
T Consensus       542 ~~v~~A~~k~~~~~m~~elr~~L~~rak~~v~k~c~~kl~~~ls~apy~p~~~~~~d~~~p~--rvl~~~~~~~~~~a~f  619 (1299)
T KOG1856         542 EIVNSAVQKFFKPDMVKELRSTLTSRAKKRVAKVCRVKLYSKLSQAPYRPDDDTFEDEKIPK--RVLAVCGGTERSDAIF  619 (1299)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC--EEEEECCCCCCCCEEE
T ss_conf             99999999997888899999999999999999999999997612377678888743445551--4787415888875179


Q ss_pred             EEEEEECCCC----CEEEEEEECCC------HHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEE
Q ss_conf             9997611358----70289871598------8999999997667775580878566316775034999940899881276
Q gi|254780788|r  184 SYIYDVRREQ----RGPQVLLSRTH------PQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGA  253 (526)
Q Consensus       184 a~i~~V~~~~----rgpqi~lSRt~------p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGA  253 (526)
                      |.+.+..-+.    |-+-+..-++.      ++....+|..=                         |....|      -
T Consensus       620 ~v~vn~~Gd~vD~lrl~~~~kr~~~~n~~~r~~k~~d~f~kF-------------------------I~~~kP------~  668 (1299)
T KOG1856         620 CVLVNFEGDLVDYLRLVDITKRKTLVNDEERKKKFQDLFKKF-------------------------IEKKKP------H  668 (1299)
T ss_pred             EEEECCCCCEEEEEECCCHHHHHHCCCHHHHHHHHHHHHHHH-------------------------HHHCCC------C
T ss_conf             999767776244565153033320232034366689999999-------------------------984399------8


Q ss_pred             EECCCCH---------HHHHHHHHH----CCCCEEEEECCCCHHHHHHHH
Q ss_conf             5548862---------178899862----778267995598789999976
Q gi|254780788|r  254 CVGMRGS---------RVQAVVTEL----RDEKIDIVVWSPDSATFVINA  290 (526)
Q Consensus       254 cVG~rGs---------Riq~I~~EL----~gEkIDii~ws~d~~~fi~nA  290 (526)
                      |||.-|.         +|+-++.+|    ++.-|++|.-++..|..-.|+
T Consensus       669 vi~v~g~~r~~q~~~~~I~~~v~el~~~~~~~~ipv~~vd~ela~lY~nS  718 (1299)
T KOG1856         669 VIGVSGENRLKQKIYEAIRQLVHELLISDQGHPIPVIYVDNELARLYQNS  718 (1299)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHH
T ss_conf             89962777126779999999998435312479865240361888999860


No 201
>cd01700 Pol_V Pol V was discovered in Escherichia coli as Umuc and UmuD proteins induced by UV. This branch of DNA polymerases is mostly found in bacteria. Pol V enables DNA replication to bypass covalently linked cys-sin T-T photo-dimers and 6-4 T-T or T-C photoproducts, which would otherwise stall the DNA replication fork.
Probab=74.08  E-value=4.7  Score=19.64  Aligned_cols=37  Identities=16%  Similarity=0.084  Sum_probs=30.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCC
Q ss_conf             2588846788887732111477750588887765305
Q gi|254780788|r  365 AINVDEIIAHLLVAEGFADVEELACVKISEIASIEGF  401 (526)
Q Consensus       365 ~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGf  401 (526)
                      --+|....++.|-..|+.|+.+++..+.+.|....|.
T Consensus       180 i~GIG~~t~~kL~~~GI~Ti~dLa~~~~~~l~~~fg~  216 (344)
T cd01700         180 VWGIGRRLSKRLAAMGIHTALDLAQADPKWIRKRFSV  216 (344)
T ss_pred             CCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHHHH
T ss_conf             2783699999999869978999870999999999768


No 202
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=73.98  E-value=3.7  Score=20.41  Aligned_cols=41  Identities=29%  Similarity=0.406  Sum_probs=36.8

Q ss_pred             HHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf             43566407799989999999879847889653267752123
Q gi|254780788|r  433 VSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGW  473 (526)
Q Consensus       433 ~~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~  473 (526)
                      +.+||..+.|+.+.+.-.|.+.||.|-.++|-++.+|+.-+
T Consensus        65 ~~DDLt~I~GIGPk~e~~Ln~~GI~tfaQIAAwt~~di~~i  105 (133)
T COG3743          65 PKDDLTRISGIGPKLEKVLNELGIFTFAQIAAWTRADIAWI  105 (133)
T ss_pred             CCCCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH
T ss_conf             86542110043788998998747763999974489999999


No 203
>PRK00024 radC DNA repair protein RadC; Reviewed
Probab=73.85  E-value=5.6  Score=19.10  Aligned_cols=41  Identities=20%  Similarity=0.337  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             467888877321114777505888877653058899999999
Q gi|254780788|r  370 EIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG  411 (526)
Q Consensus       370 E~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~  411 (526)
                      ..+|+.|.+ -|.++..+..+++++|.+++|+....|..|+.
T Consensus        44 ~~lA~~ll~-~~g~l~~l~~a~~~eL~~i~GiG~~kA~~l~a   84 (224)
T PRK00024         44 LDLARELLE-RFGSLRGLLDASLEELQEIKGIGPAKAAQLKA   84 (224)
T ss_pred             HHHHHHHHH-HCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHH
T ss_conf             999999999-85999999870889884478988999999999


No 204
>PRK10702 endonuclease III; Provisional
Probab=73.78  E-value=6.3  Score=18.69  Aligned_cols=76  Identities=13%  Similarity=0.147  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHH-H--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHH
Q ss_conf             6788887732111477750588887765-3--058899999999999999999999898775428435664077999899
Q gi|254780788|r  371 IIAHLLVAEGFADVEELACVKISEIASI-E--GFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKI  447 (526)
Q Consensus       371 ~iA~~LV~eGf~SiEeIa~a~~eeL~~I-e--Gfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~  447 (526)
                      .....|... |.|++++|.++.++|.++ .  ||-.-.|..|+..|+..++.-.    -.+  ...-++|+.|+|+.+.+
T Consensus        49 ~~~~~L~~~-~~t~e~la~a~~~el~~~i~~~G~y~~KA~~L~~~a~~i~~~~~----G~v--P~~~~~L~~LpGIG~kT  121 (211)
T PRK10702         49 KATAKLYPV-ANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEKHN----GEV--PEDRAALEALPGVGRKT  121 (211)
T ss_pred             HHHHHHHHH-CCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----CCC--HHHHHHHHHHHCCCHHH
T ss_conf             999999997-79999987099999999999863599999999999999999909----987--66699999876635889


Q ss_pred             HHHHHH
Q ss_conf             999998
Q gi|254780788|r  448 KVALGE  453 (526)
Q Consensus       448 ~~~L~e  453 (526)
                      +.....
T Consensus       122 A~aIl~  127 (211)
T PRK10702        122 ANVVLN  127 (211)
T ss_pred             HHHHHH
T ss_conf             999999


No 205
>TIGR01259 comE comEA protein; InterPro: IPR004787   The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable .   ComEA has been shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Human herpesvirus 4 (Epstein-Barr virus) ..
Probab=73.52  E-value=3  Score=21.03  Aligned_cols=58  Identities=17%  Similarity=0.207  Sum_probs=42.7

Q ss_pred             HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf             7775058888776530588999999999999999999998987754284356640779998999999987
Q gi|254780788|r  385 EELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGEN  454 (526)
Q Consensus       385 EeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L~e~  454 (526)
                      =-|-.|+.+||..++|+....|..|++         --+.+=.+   .-=|||+.+.|+.+..+.+|...
T Consensus        64 VnlN~As~~EL~~l~GiGP~kA~aIi~---------YRe~nG~F---~SvddL~kVsGIG~k~~eKLk~~  121 (124)
T TIGR01259        64 VNLNKASLEELQALPGIGPAKAKAIIE---------YREENGAF---KSVDDLTKVSGIGEKSLEKLKDY  121 (124)
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHH---------HHHHCCCC---CCHHHHHCCCCCCHHHHHHHHHC
T ss_conf             344067899986369998133799999---------99856997---77555003578854668742000


No 206
>KOG3013 consensus
Probab=73.47  E-value=1.7  Score=22.96  Aligned_cols=62  Identities=27%  Similarity=0.368  Sum_probs=49.6

Q ss_pred             HHHHHHHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEH----------------HHCCCCCCCCCCCEEEEEEEEEC
Q ss_conf             7799998520838999998405763899957-93587447----------------87488751152766999997611
Q gi|254780788|r  129 RQYLEFKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRR----------------DETISRENLRPGDRVKSYIYDVR  190 (526)
Q Consensus       129 ~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~----------------~e~ip~E~~~~Gdrika~i~~V~  190 (526)
                      -+...|..-+|++|.|.|.-+-+.-+-||++ +..++|+-                +|+--+..|+.||-|-|-+..|-
T Consensus        76 plk~rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~  154 (301)
T KOG3013          76 PLKSRYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVF  154 (301)
T ss_pred             EHHHHCCCCCCCEEEEEEEEEECCEEEEECCCCCCEEEEEECCCCCCHHHHCCCHHHHHHHHHHHHCCCEEHHHHHHHC
T ss_conf             4332037755777888764440233577516654337875302488614330223568999977550675317788761


No 207
>PRK01810 DNA polymerase IV; Validated
Probab=72.82  E-value=4.6  Score=19.75  Aligned_cols=34  Identities=18%  Similarity=0.119  Sum_probs=14.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHC
Q ss_conf             8884678888773211147775058888776530
Q gi|254780788|r  367 NVDEIIAHLLVAEGFADVEELACVKISEIASIEG  400 (526)
Q Consensus       367 dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeG  400 (526)
                      +|....++.|-..|+.|+.+++.++.+.|....|
T Consensus       186 GIG~~~~~~L~~~GI~Ti~dl~~~~~~~l~~~fG  219 (410)
T PRK01810        186 GIGEKTAEKLKDIHIHTIGDLAKADEHILRAKLG  219 (410)
T ss_pred             CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHH
T ss_conf             8677899999986996899987499999998765


No 208
>PRK03348 DNA polymerase IV; Provisional
Probab=72.77  E-value=2.8  Score=21.32  Aligned_cols=45  Identities=18%  Similarity=0.297  Sum_probs=23.5

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             88846788887732111477750588887765305889999999999
Q gi|254780788|r  367 NVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRA  413 (526)
Q Consensus       367 dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA  413 (526)
                      +|....++.|-..|+.|+.+++.++...|....|  ......|.+.|
T Consensus       186 GIG~~t~~kL~~~GI~TigDLa~~~~~~L~~~~G--~~~G~~L~~~a  230 (456)
T PRK03348        186 GIGPVAEEKLHRLGIETIGDLAALSEAEVANLLG--ATIGPALHRLA  230 (456)
T ss_pred             CCCHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHH
T ss_conf             7759999999986981468776099999999981--99999999997


No 209
>PRK03858 DNA polymerase IV; Validated
Probab=72.67  E-value=4.9  Score=19.48  Aligned_cols=32  Identities=28%  Similarity=0.371  Sum_probs=14.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             88846788887732111477750588887765
Q gi|254780788|r  367 NVDEIIAHLLVAEGFADVEELACVKISEIASI  398 (526)
Q Consensus       367 dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~I  398 (526)
                      +|...++..|-..|+.|+.+++.++...|...
T Consensus       180 GIG~~~~~~L~~~GI~T~~dLa~~~~~~l~~~  211 (398)
T PRK03858        180 GVGAVTAAKLRAHGIETVADVAELSESTLSSM  211 (398)
T ss_pred             CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH
T ss_conf             86879999999849968999760999999999


No 210
>pfam07650 KH_2 KH domain.
Probab=71.95  E-value=3.1  Score=20.94  Aligned_cols=31  Identities=19%  Similarity=0.341  Sum_probs=20.4

Q ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHCCE
Q ss_conf             9999853422110254427899999861674
Q gi|254780788|r  308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWT  338 (526)
Q Consensus       308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~  338 (526)
                      ..+++...+-.++|||+|+|++-..+..+-.
T Consensus         2 v~v~i~~srpGiiIGk~G~~I~~l~~~l~k~   32 (55)
T pfam07650         2 VIVVIRTSQPGIVIGKGGSNIKKLGKELRKR   32 (55)
T ss_pred             EEEEEEECCCCEEECCCCCCHHHHHHHHHHH
T ss_conf             8999991899679998960399999999998


No 211
>pfam10391 DNA_pol_lambd_f Fingers domain of DNA polymerase lambda. DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone.
Probab=71.67  E-value=4  Score=20.17  Aligned_cols=27  Identities=22%  Similarity=0.329  Sum_probs=14.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             111225888467888877321114777
Q gi|254780788|r  361 FFMQAINVDEIIAHLLVAEGFADVEEL  387 (526)
Q Consensus       361 ~f~e~LdVDE~iA~~LV~eGf~SiEeI  387 (526)
                      .|+..-+|....|..+++.||+|++++
T Consensus         3 ~f~~I~GvGp~~A~~~~~~G~~ti~dL   29 (52)
T pfam10391         3 LFTNIWGVGPKTARKWYRQGIRTLEDL   29 (52)
T ss_pred             HHHHCCCCCHHHHHHHHHHCCCCHHHH
T ss_conf             366354406999999999478889999


No 212
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=70.88  E-value=7.3  Score=18.23  Aligned_cols=82  Identities=20%  Similarity=0.157  Sum_probs=50.5

Q ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHH
Q ss_conf             7888877321114777505888877653058---8999999999999999999998987754284356640779998999
Q gi|254780788|r  372 IAHLLVAEGFADVEELACVKISEIASIEGFD---EETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIK  448 (526)
Q Consensus       372 iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfd---ee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~  448 (526)
                      +...|.....-|++.++.++.++|.++ |+.   .-.|..|+.-|+........   .........+.|+.|+|+.+.++
T Consensus        21 ~~~~l~~~~~pt~~~l~~~~~~~l~~~-~~~~gy~~Ka~~i~~~a~~i~~~~~~---~~~~~~~~~~~L~~l~GIG~~TA   96 (158)
T cd00056          21 AYERLFERYGPTPEALAAADEEELREL-IRSLGYRRKAKYLKELARAIVEGFGG---LVLDDPDAREELLALPGVGRKTA   96 (158)
T ss_pred             HHHHHHHHCCCCHHHHHCCCHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHCCC---CCCCCHHHHHHHHCCCCCCHHHH
T ss_conf             999999854998999980999999999-73356899999999988888986089---57898889999875898289999


Q ss_pred             HHHHHCCCC
Q ss_conf             999987984
Q gi|254780788|r  449 VALGENGIK  457 (526)
Q Consensus       449 ~~L~e~gIk  457 (526)
                      ....-.+-.
T Consensus        97 ~~vl~~~~~  105 (158)
T cd00056          97 NVVLLFALG  105 (158)
T ss_pred             HHHHHHHCC
T ss_conf             999999879


No 213
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR004659   The eubacterial degradosome is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria .    The components of the RNA degradosome in E. coli (EBI-1169250 from INTACT) are:  Ribonuclease E (Rne), P21513 from SWISSPROT, IPR004659 from INTERPRO ATP-dependent RNA helicase (RhlB), P0A8J8 from SWISSPROT, IPR000629 from INTERPRO Polynucleotide phosphorylase (Pnp), , IPR012162 from INTERPRO Enolase (Eno), P0A6P9 from SWISSPROT, IPR000941 from INTERPRO       Associated components:   The chaperone protein DnaK (,IPR012725 from INTERPRO) associates to abnormal complexes in which the canonical components RhlB and PNPase are not present or present in limiting amount and could be involved in repairing such incorrectly assembled degradosomes. Polyphosphate kinase (Ppk), P0A7B1 from SWISSPROT, IPR003414 from INTERPRO appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP.   Subunit composition of the E. coli degradosome(see: http://biocyc.org/ECOLI/NEW-IMAGE?type=POLYPEPTIDE&object=CPLX0-2381): [(Ppk)4][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2]      In vitro a "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur . RNase E provides the organizational structure for the degradosome . It is tethered to the cytoplasmic membrane via its amino-terminus and its carboxy-terminal half, which is largly unstructured and poorly conserved, cooridnates the binding of PNPase, RhlB and enolase. The loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I , , .    Ribonuclease E 3.1.4 from EC is responsible for maturing 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of ColE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in Escherichia coli, and initiates decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly A tails by an endonucleolytic process. Ribonuclease G is smaller than RNase E lacking the C-terminal region. It is involved in processing of the 5' end of 16S rRNA, and may be involved in chromosome segregation and cell division too.   RNase E is a major subunit the eubacterial degradosome. It is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . It consists of the RNA degradation enzymes RNase E (Rne) and PNPase (Pnp), as well as the ATP-dependent RNA helicase (RhlB) and the metabolic enzyme enolase (Eno) , , .; GO: 0004540 ribonuclease activity, 0006396 RNA processing, 0005737 cytoplasm.
Probab=70.34  E-value=2.5  Score=21.60  Aligned_cols=44  Identities=30%  Similarity=0.456  Sum_probs=36.3

Q ss_pred             HHHHCCCEEEEEEEECCCC--EEEEEECC-CEEEEEHHHCCCC-CCCC
Q ss_conf             9852083899999840576--38999579-3587447874887-5115
Q gi|254780788|r  134 FKDKVGEIISGTVKRVEYG--NVIVDLGN-SDGVIRRDETISR-ENLR  177 (526)
Q Consensus       134 f~~r~Geiv~G~V~r~e~~--~iiVdlg~-~ea~Lp~~e~ip~-E~~~  177 (526)
                      -+.++|.|--|.|.|+.++  ..+||+|. -.|+||-++..++ +.|.
T Consensus        23 ~~~~~GnIY~G~V~~vlPsl~AAFvdiG~~~~GFLh~sdi~~~~~~~~   70 (464)
T TIGR00757        23 SRQLVGNIYKGRVTRVLPSLQAAFVDIGLEKNGFLHASDIGENSEKLE   70 (464)
T ss_pred             HHCCHHHHHHCEEEEECCCCCEEEEECCCCCCCCCCHHHCCCCHHHHH
T ss_conf             101100232020202203764477420688355630332033245688


No 214
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3  is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel.  The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.  In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=69.35  E-value=7.1  Score=18.32  Aligned_cols=46  Identities=20%  Similarity=0.517  Sum_probs=33.1

Q ss_pred             HHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHH
Q ss_conf             9999976286654248987567879999853422110254427899
Q gi|254780788|r  284 ATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR  329 (526)
Q Consensus       284 ~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvr  329 (526)
                      ..|+.+-+.-|-|++|.+.-..+.+.|.+--.---+-|||+|+++.
T Consensus        39 R~~i~~~~~~agIs~I~IeR~~~~i~V~I~tarPG~vIGk~G~~Ie   84 (109)
T cd02412          39 RKFIKKKLKKAGISRIEIERKADRVEVTIHTARPGIIIGKKGAGIE   84 (109)
T ss_pred             HHHHHHHHHHCCCCEEEEEECCCEEEEEEEECCCCEEECCCCCCHH
T ss_conf             9999999976894369999857738999994699559867852489


No 215
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=68.65  E-value=7  Score=18.39  Aligned_cols=41  Identities=7%  Similarity=0.284  Sum_probs=32.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEE---CCCCCEEEE
Q ss_conf             99999999999999999961368745359997---499883999
Q gi|254780788|r   22 IDRDVVLSVMADSIQKAARSLYGTMSDIRVEI---NPETGDISL   62 (526)
Q Consensus        22 I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~i---D~~tG~i~i   62 (526)
                      +|++.+-+|+++++..+.+++|.+..++.+.+   |++.++-.+
T Consensus         3 ~d~~~l~eAv~~~~~~~k~rkF~esvel~i~Lk~iDpkk~dq~v   46 (216)
T PRK04203          3 MDREKIEEAVKEALEESKPRNFTQSVELIVNLKDLDLKKPENRI   46 (216)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCCCEE
T ss_conf             56899999999999868766887418999961688998766545


No 216
>cd03468 Pol_Y_like Pol_Y_like: a group of putative Y-family DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases.
Probab=68.09  E-value=8.3  Score=17.83  Aligned_cols=52  Identities=17%  Similarity=0.136  Sum_probs=38.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             0111225888467888877321114777505888877653058899999999999
Q gi|254780788|r  360 QFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAR  414 (526)
Q Consensus       360 ~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~  414 (526)
                      .+-+..|++....++.|-.-|+.|+.+++..+...|..-.|  .+.. .+..+|+
T Consensus       167 ~lPv~~l~i~~~~~~~L~~lGi~tigdL~~lp~~~L~~RfG--~~~~-~~l~~a~  218 (330)
T cd03468         167 PLPVAALRLPPETVERLRRLGLRTLGDLAALPRAGLARRFG--PELL-RRLDQAL  218 (330)
T ss_pred             CCCHHHHCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHHC--HHHH-HHHHHHC
T ss_conf             59866738898999999985996799986599999999879--7999-9999962


No 217
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=67.00  E-value=7  Score=18.39  Aligned_cols=49  Identities=24%  Similarity=0.409  Sum_probs=33.1

Q ss_pred             CHHHHHHHHC--CCCCCCEE-EECCCCCEEEEEECCCCCCCCCCCCHHHHHH
Q ss_conf             7899999762--86654248-9875678799998534221102544278999
Q gi|254780788|r  282 DSATFVINAL--RPAIVTKV-VLDEDVGRIEVIVPKEQLSLAIGRRGQNVRL  330 (526)
Q Consensus       282 d~~~fi~nAl--~PA~v~~v-~~de~~~~~~v~v~~~qls~AIGk~GqNvrL  330 (526)
                      +...|+...|  .|.+|.=- ...+......+.|.+++.-..|||+|.+++-
T Consensus         3 ~lv~~ivk~lVd~Pd~v~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GRti~A   54 (76)
T COG1837           3 ELVEFIVKPLVDNPDDVRVDEEEGEKTVTIELRVAPEDMGKVIGKQGRTIQA   54 (76)
T ss_pred             HHHHHHHHHHCCCCCCEEEEEEECCCEEEEEEEECCCCCCCEECCCCHHHHH
T ss_conf             6999999986689650689998169749999998720046356678705999


No 218
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=66.77  E-value=8.8  Score=17.64  Aligned_cols=85  Identities=14%  Similarity=0.073  Sum_probs=36.1

Q ss_pred             CCCCCCCCEEEEECCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEC-CC--EE
Q ss_conf             88986473799850845-6207999999999999999999887799998520838999998405763899957-93--58
Q gi|254780788|r   88 DPSIDIGGVVSDPLPPM-DFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLG-NS--DG  163 (526)
Q Consensus        88 ~~~~~iGD~i~~~i~~~-~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg-~~--ea  163 (526)
                      -..+.-||.+...+.+. .-+|  .+  ++.+.+.+.             |.-..+-|+........+++-.. +.  .-
T Consensus       102 ~~~a~~gD~V~v~~~~~~~~~~--~~--~~~v~~il~-------------r~~~~~vG~~~~~~~~~~~~p~d~r~~~~i  164 (706)
T COG0557         102 LNRALHGDRVLVELLPSDKRGR--FK--EAAVVRILE-------------RANSALVGELRPSQGIGRVLPDDKRLPFLI  164 (706)
T ss_pred             HHHCCCCCEEEEEECCCCCCCC--CC--EEEEEHHHH-------------HHHHHHEEEEEECCCEEEEEECCCCCCCCE
T ss_conf             5320169989999676556666--62--268662555-------------532102488871477069975565565424


Q ss_pred             EEEHHHCCCCCCCCCCCEEEEEEEEECCC
Q ss_conf             74478748875115276699999761135
Q gi|254780788|r  164 VIRRDETISRENLRPGDRVKSYIYDVRRE  192 (526)
Q Consensus       164 ~Lp~~e~ip~E~~~~Gdrika~i~~V~~~  192 (526)
                      .+| .++.+  ....|+++.+-+..--..
T Consensus       165 ~i~-~~~~~--~~~~~~~v~~~i~~~~~~  190 (706)
T COG0557         165 AIP-PEQAP--GAEEGHLVVVEITRWPDT  190 (706)
T ss_pred             EEC-CCCCC--CCCCCCEEEEEEEECCCC
T ss_conf             536-10035--100486699998324665


No 219
>KOG2534 consensus
Probab=65.99  E-value=9.1  Score=17.54  Aligned_cols=40  Identities=8%  Similarity=-0.046  Sum_probs=20.4

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             88899999999998623999999999999999999961368
Q gi|254780788|r    4 ANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYG   44 (526)
Q Consensus         4 ~~~~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~   44 (526)
                      .||.=+..+++-++..+++.-+.. .+.-=..+++.-|.|+
T Consensus        10 ~~N~~~~~aleiLa~~~ev~g~~~-r~~~y~~Aasvlk~~p   49 (353)
T KOG2534          10 NNNQIFTEALEILAEAYEVEGEED-RARAYRRAASVLKSLP   49 (353)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCCHH-HHHHHHHHHHHHHHCC
T ss_conf             353878899999998632342178-9999999999998499


No 220
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=64.89  E-value=4.8  Score=19.56  Aligned_cols=23  Identities=35%  Similarity=0.606  Sum_probs=13.0

Q ss_pred             CCCCCCHHHHHHHHHHHCCEEEE
Q ss_conf             10254427899999861674578
Q gi|254780788|r  319 LAIGRRGQNVRLASQLTGWTIDI  341 (526)
Q Consensus       319 ~AIGk~GqNvrLas~Ltg~~idi  341 (526)
                      .-||++|...+.-..|||-+|-|
T Consensus       102 RIIGk~Gktr~~IE~~T~~~I~v  124 (172)
T TIGR03665       102 RIIGEGGKTRRIIEELTGVSISV  124 (172)
T ss_pred             HHCCCCCHHHHHHHHHHCCEEEE
T ss_conf             31589961999999976874997


No 221
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=64.31  E-value=9.7  Score=17.32  Aligned_cols=99  Identities=17%  Similarity=0.269  Sum_probs=46.6

Q ss_pred             EEEEEEEECCCCC-EEEEEEECCCHHH-HHHHH-HH-----HHHHHHC------------------------------CE
Q ss_conf             9999976113587-0289871598899-99999-97-----6677755------------------------------80
Q gi|254780788|r  182 VKSYIYDVRREQR-GPQVLLSRTHPQF-MVKLF-HM-----EVPEIYN------------------------------GI  223 (526)
Q Consensus       182 ika~i~~V~~~~r-gpqi~lSRt~p~~-l~~Lf-~~-----EVPEI~~------------------------------G~  223 (526)
                      +..|+...-..+. ..+|+++...++. |...+ +.     .+|-..+                              .+
T Consensus       291 ~~~fi~Q~Y~~~~~P~~Ill~~~~~~~~l~~~l~~~~~~~i~~p~~G~kk~l~~~A~~NA~~~l~~l~~~~~~~~~l~~l  370 (581)
T COG0322         291 LEAFILQFYKSNEIPKEILLPQELPEEELEEALSEAAGLEIRVPKRGEKKSLLELATKNAKEALEQLKERSDEKQALEAL  370 (581)
T ss_pred             HHHHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             99999997227889645780788775899999986147731268865588999999999999999988513356899999


Q ss_pred             EEEEEEECCCCCEEEEEEEECCCCCCCEEEEECC-CCHHHHHHHHHHCCCCEEEEECCCCHHHH
Q ss_conf             8785663167750349999408998812765548-86217889986277826799559878999
Q gi|254780788|r  224 VQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGM-RGSRVQAVVTELRDEKIDIVVWSPDSATF  286 (526)
Q Consensus       224 ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~-rGsRiq~I~~EL~gEkIDii~ws~d~~~f  286 (526)
                      =++-++.  ++.|--+-=.||-..-+|||+||=- .|.-.+.   +...=+|. +.-.||-+.+
T Consensus       371 ~~~l~l~--~p~rIE~~D~Sh~~g~~~V~smvvf~~g~~~k~---~YRry~i~-~~~~dDya~m  428 (581)
T COG0322         371 AALLGLP--APYRIECFDISHIQGEDTVGSMVVFEDGGPSKK---DYRRYNIK-ITGGDDYASM  428 (581)
T ss_pred             HHHHCCC--CCEEEEEEECCCCCCCCCEEEEEEECCCCCCHH---HCCCCCCC-CCCCCHHHHH
T ss_conf             9985889--861689851675356664457999768987754---36522446-7897559999


No 222
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=63.89  E-value=2.7  Score=21.39  Aligned_cols=107  Identities=14%  Similarity=0.147  Sum_probs=73.1

Q ss_pred             ECCCCCCCCCCCCHH-----HHHHHHHHHCCEEEEEECCCHH----HHHHC--CCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             853422110254427-----8999998616745785522001----10100--122100011122588846788887732
Q gi|254780788|r  312 VPKEQLSLAIGRRGQ-----NVRLASQLTGWTIDIITEEEDS----INRQK--DFNERTQFFMQAINVDEIIAHLLVAEG  380 (526)
Q Consensus       312 v~~~qls~AIGk~Gq-----NvrLas~Ltg~~idi~~~~~~~----~~~~~--e~~~~~~~f~e~LdVDE~iA~~LV~eG  380 (526)
                      ..-+.+.+-+--+|+     -+..|++...|+.+....-...    .....  .........++.|+.+-....-|-.+|
T Consensus       185 ~~~Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~I~~l~lsvrs~ncLk~~~  264 (317)
T COG0202         185 TDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPKAVEIEEEKPEFPILLVLEAPIDELDLSVRSYNCLKREG  264 (317)
T ss_pred             CCCEEEEEEEEECCEEEHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCCCCCCCCCCCCEEEEHHHCCCC
T ss_conf             77406999976463750279999999988999999875365544010156544233233465341231333501231158


Q ss_pred             HHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             11147775058888776530588999999999999999
Q gi|254780788|r  381 FADVEELACVKISEIASIEGFDEETAVEIQGRAREYLE  418 (526)
Q Consensus       381 f~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~  418 (526)
                      +.++.++...+..+|.+++.|.....++++.++.++-+
T Consensus       265 i~~i~~L~~~se~~l~~v~n~G~ksleEi~~kl~~~~l  302 (317)
T COG0202         265 IETIGELVQRTEEELLKVENLGKKSLEEIKEKLAELGL  302 (317)
T ss_pred             CHHHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             11468777457988850436566999999999998513


No 223
>PRK12311 rpsB 30S ribosomal protein S2; Provisional
Probab=63.41  E-value=7.9  Score=18.00  Aligned_cols=46  Identities=22%  Similarity=0.260  Sum_probs=40.7

Q ss_pred             HHCCHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf             5428435664077999899999998798478896532677521231
Q gi|254780788|r  429 RELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS  474 (526)
Q Consensus       429 ~e~~~~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~  474 (526)
                      .-.|..+||..+.|+++.+..+|-+.||...-++|.++-|+..-+.
T Consensus       263 ~p~g~~ddl~ki~gvgp~~~~~ln~~g~~h~~qia~~t~~~~~~~d  308 (332)
T PRK12311        263 GPRGAPDDLKKLTGVSGAIEKKLNDLGIFHYWQLAELDPDTAHKIG  308 (332)
T ss_pred             CCCCCCCHHHHHCCCCHHHHHHHHHCCCEEHHHHHCCCHHHHHHHH
T ss_conf             7889842577715767889998501241218988627999999888


No 224
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=62.37  E-value=11  Score=17.08  Aligned_cols=68  Identities=25%  Similarity=0.284  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHHHCCHHHHHH---HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHH
Q ss_conf             73211147775058888776---530588999999999999999999998987754284356640779998999999
Q gi|254780788|r  378 AEGFADVEELACVKISEIAS---IEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVAL  451 (526)
Q Consensus       378 ~eGf~SiEeIa~a~~eeL~~---IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L  451 (526)
                      -.-|.|.++++.++.++|.+   --||-...|..|+.-|+-.++.-.-      +-....++|+.|+|....++..-
T Consensus        55 f~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g------~vP~~~~eL~~LPGVGrKTAnvV  125 (211)
T COG0177          55 FKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG------EVPDTREELLSLPGVGRKTANVV  125 (211)
T ss_pred             HHHCCCHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCC------CCCCHHHHHHHCCCCCHHHHHHH
T ss_conf             997599999974999999999986387189999999999999997499------99815999974899665778989


No 225
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=62.09  E-value=7.9  Score=18.00  Aligned_cols=38  Identities=24%  Similarity=0.146  Sum_probs=32.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCC
Q ss_conf             22588846788887732111477750588887765305
Q gi|254780788|r  364 QAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGF  401 (526)
Q Consensus       364 e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGf  401 (526)
                      +-.+|...++..|-..|+.|+.+++.+++..|.+..|.
T Consensus       183 ~lwGIG~~~~~kL~~~GI~Ti~dLa~~~~~~l~k~fgv  220 (422)
T PRK03609        183 EVWGVGRRISKKLNAMGIKTALDLADTDIRFIRKHFNV  220 (422)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHH
T ss_conf             98611399999999878810899872998999988889


No 226
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=61.56  E-value=7.1  Score=18.35  Aligned_cols=46  Identities=22%  Similarity=0.455  Sum_probs=28.6

Q ss_pred             EECCCCCEEEEEEEE-CCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             631677503499994-089988127655488621788998627782679955987
Q gi|254780788|r  229 VSRDPGSRAKLAVFS-SDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPD  282 (526)
Q Consensus       229 iaR~pG~RsKIAV~s-~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d  282 (526)
                      ++...+.=.+|+|.+ +++.+-|-|+|        +-+.+|++++...|+..+.+
T Consensus        65 is~G~~~~~~v~v~~~~~~~~sPCG~C--------RQ~i~Ef~~~d~~ii~~~~~  111 (134)
T COG0295          65 ISEGKRKFDAVVVVADTGKPVSPCGAC--------RQVLAEFCGDDTLIILLPKD  111 (134)
T ss_pred             HHCCCCCEEEEEEECCCCCCCCCCHHH--------HHHHHHHCCCCCEEEEECCC
T ss_conf             973997179999974899975985889--------99999866877459996699


No 227
>KOG2191 consensus
Probab=61.36  E-value=11  Score=16.95  Aligned_cols=36  Identities=25%  Similarity=0.133  Sum_probs=22.7

Q ss_pred             CEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEE
Q ss_conf             879999853422110254427899999861674578
Q gi|254780788|r  306 GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDI  341 (526)
Q Consensus       306 ~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi  341 (526)
                      .....-|++..+-.|-|++|-|.---+..||-.+-|
T Consensus       244 tas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~i  279 (402)
T KOG2191         244 TASTISVAAGLIGGANGAGGAFGAALSGFTGALIAI  279 (402)
T ss_pred             CHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCEEE
T ss_conf             012101221135654554555443430345653552


No 228
>cd01701 Pol_zeta Pol_zeta, a member of the Y-family of DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. Pol zeta has also been named Rev1; this subfamily is mainly present in eukaryotes.
Probab=60.71  E-value=11  Score=16.87  Aligned_cols=159  Identities=14%  Similarity=0.147  Sum_probs=76.8

Q ss_pred             EECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEE
Q ss_conf             63167750349999408998812765548862178899862778267995598789999976286654248987567879
Q gi|254780788|r  229 VSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRI  308 (526)
Q Consensus       229 iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~  308 (526)
                      .||.-|.|+=+.++- -.+.-|=.-+|.++-..-+.+++++..               |....+| .|..+-+||.  .+
T Consensus        94 eAR~~GV~s~m~~~~-A~~lCP~li~v~~~~~~Y~~~S~~i~~---------------il~~~~~-~vE~~SIDEa--yl  154 (405)
T cd01701          94 EARKYGVKNGMFVGQ-AKKLCPELQTLPYDFDAYEEVSLAFYE---------------ILASYTD-NIEAVSCDEA--LV  154 (405)
T ss_pred             HHHHHCCCCCCCHHH-HHHHCCCCEEECCCHHHHHHHHHHHHH---------------HHHHHCC-CCEECCCCCE--EE
T ss_conf             999749987895999-998788969989988999999999999---------------9998597-5145123324--67


Q ss_pred             EEEE---------------------CCCC--CCCCCCCCHHHHHHHHHHHCC-EEEEEECCCHHHHHHCCCCCCCCCCCC
Q ss_conf             9998---------------------5342--211025442789999986167-457855220011010012210001112
Q gi|254780788|r  309 EVIV---------------------PKEQ--LSLAIGRRGQNVRLASQLTGW-TIDIITEEEDSINRQKDFNERTQFFMQ  364 (526)
Q Consensus       309 ~v~v---------------------~~~q--ls~AIGk~GqNvrLas~Ltg~-~idi~~~~~~~~~~~~e~~~~~~~f~e  364 (526)
                      ++.=                     ..-.  .|.-||-+-.=+||||.+-.= -+-+...++.     .+|-.-. ..-+
T Consensus       155 Dvt~~~~~~~~~~~~~a~~Ir~~I~~~tglt~SiGIa~nK~lAKiAs~~~KP~G~~~i~~~~~-----~~~L~~l-pv~~  228 (405)
T cd01701         155 DITSLLEETYELPEELAETIRNEIKETTGCSASVGIGPNILLARLATRKAKPNGQYYLSPEKV-----EEFLDTL-PVKD  228 (405)
T ss_pred             ECCCCHHHCCCCHHHHHHHHHHHHHHHHCCCEEECCCCCHHHHHHHHHHCCCCCCCCCCHHHH-----HHHHHHC-CCCC
T ss_conf             335411112677999999999999998799756443764999999887369987323687899-----9999855-2111


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             2588846788887732111477750588-8877653058899999999999
Q gi|254780788|r  365 AINVDEIIAHLLVAEGFADVEELACVKI-SEIASIEGFDEETAVEIQGRAR  414 (526)
Q Consensus       365 ~LdVDE~iA~~LV~eGf~SiEeIa~a~~-eeL~~IeGfdee~a~eL~~rA~  414 (526)
                      -.+|...+++.|-..|+.|+.+++..+. +.|....|  ......|...|+
T Consensus       229 i~GIG~~t~~kL~~~gi~t~~dl~~~~~~~~L~~~fG--~k~G~~l~~~a~  277 (405)
T cd01701         229 LPGVGSSTKEKLKSLGIDTCGDLQLISTKEKLQKVFG--KKTGEKLYNYCR  277 (405)
T ss_pred             CCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHHHH--HHHHHHHHHHHC
T ss_conf             5871789999999849916899862787999999977--899999999967


No 229
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=58.01  E-value=12  Score=16.56  Aligned_cols=54  Identities=26%  Similarity=0.360  Sum_probs=37.8

Q ss_pred             EEEEEECCCC--EEEEEECCCEEEEEHHHCCCC-CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf             9999840576--389995793587447874887-511527669999976113587028
Q gi|254780788|r  143 SGTVKRVEYG--NVIVDLGNSDGVIRRDETISR-ENLRPGDRVKSYIYDVRREQRGPQ  197 (526)
Q Consensus       143 ~G~V~r~e~~--~iiVdlg~~ea~Lp~~e~ip~-E~~~~Gdrika~i~~V~~~~rgpq  197 (526)
                      +|+|+-.++|  ++.-+-|+-+-+++.++.-.+ ..++.||+|.+.+.+- +..++|+
T Consensus         1 tG~Vk~f~kGfGFI~~~~g~~DvFvH~s~i~~~~~~l~~Gd~V~f~v~~~-~~~~~~~   57 (64)
T smart00357        1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSP-RGGGKPE   57 (64)
T ss_pred             CCEEEEEECCEEEEEECCCCCCEEEEHHHHCCCCCCCCCCCEEEEEEEEC-CCCCCCE
T ss_conf             94796982844888618999409998699546777447587899999988-9999844


No 230
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=57.81  E-value=11  Score=16.90  Aligned_cols=65  Identities=22%  Similarity=0.241  Sum_probs=34.5

Q ss_pred             CCEEEEECCHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHCCCEEEEEEEE----CCC---CEEEE
Q ss_conf             737998508456207999999999999----------9999998877999985208389999984----057---63899
Q gi|254780788|r   94 GGVVSDPLPPMDFGRVAVQSAKQVIIQ----------KVREAERDRQYLEFKDKVGEIISGTVKR----VEY---GNVIV  156 (526)
Q Consensus        94 GD~i~~~i~~~~fgRiaAq~AKQvI~Q----------kireaEr~~i~~ef~~r~Geiv~G~V~r----~e~---~~iiV  156 (526)
                      |-..-.-.|..-+.+--.++++..+..          ..+..+|..+++..++-.-.|+.||---    +..   |-++|
T Consensus       306 g~q~a~maPTeiLa~Qh~~~~~~~~~~~~i~v~lltg~~~~~~~~~~~~~~~~g~~~i~iGTHal~~~~v~f~~Lglvvi  385 (677)
T PRK10917        306 GYQAALMAPTEILAEQHYRNLKKWLEPLGIRVALLTGSLKGKERREILEALASGEADIVIGTHALIQDDVEFHNLGLVII  385 (677)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHCCCCCEEEEHHHHHHCCCCCCCCCEEEE
T ss_conf             99489987679999999999998776349889984077417789999999857997789730787735564466656995


Q ss_pred             EE
Q ss_conf             95
Q gi|254780788|r  157 DL  158 (526)
Q Consensus       157 dl  158 (526)
                      |=
T Consensus       386 DE  387 (677)
T PRK10917        386 DE  387 (677)
T ss_pred             CH
T ss_conf             30


No 231
>KOG3127 consensus
Probab=57.18  E-value=1.4  Score=23.41  Aligned_cols=48  Identities=25%  Similarity=0.384  Sum_probs=31.6

Q ss_pred             EECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHH--CCCCEEEEECCCCH
Q ss_conf             63167750349999408998812765548862178899862--77826799559878
Q gi|254780788|r  229 VSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTEL--RDEKIDIVVWSPDS  283 (526)
Q Consensus       229 iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL--~gEkIDii~ws~d~  283 (526)
                      +|+-.-.|||      ||+ --|||||+.++.||=++---.  +|+--|+.+|.++.
T Consensus        73 iA~LsA~RSk------Dpn-tqVGaCiv~~~n~iVg~GYNgfP~gc~~~vfp~~~~~  122 (230)
T KOG3127          73 IAFLSAKRSK------DPN-TQVGACIVDRENRIVGTGYNGFPRGCSDDVFPWCKAA  122 (230)
T ss_pred             HHHHHHHHCC------CCC-CCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf             9999998535------965-6602699737987999603787677777777544344


No 232
>KOG1918 consensus
Probab=57.13  E-value=6.3  Score=18.69  Aligned_cols=84  Identities=23%  Similarity=0.320  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH--HHHHHHHHHHCCHHHHHHCCCCCC-----HHHHHHH
Q ss_conf             321114777505888877653058899999999999999999--999898775428435664077999-----8999999
Q gi|254780788|r  379 EGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGI--DITLQKKIRELGVSEELCSIPGID-----SKIKVAL  451 (526)
Q Consensus       379 eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~--~~~~~e~~~e~~~~e~L~~l~gl~-----~~~~~~L  451 (526)
                      +.|-+.|.+-.++.++|.++ ||..-.+..|..-|..|....  ...-.++..+....+.|.++.|+.     .-|+..|
T Consensus       108 ~~~~~pe~i~~~~~~~lrkc-G~S~rK~~yLh~lA~~~~ng~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL  186 (254)
T KOG1918         108 EKFPTPEFIDPLDCEELRKC-GFSKRKASYLHSLAEAYTNGYIPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSL  186 (254)
T ss_pred             CCCCCCHHCCCCCHHHHHHH-CCCHHHHHHHHHHHHHHHCCCCCCHHHHHHCCHHHHHHHHHHCCCCCCEEEEEEEEECC
T ss_conf             67788321276789999985-73324679999999998647777667776157999999998604755112443211014


Q ss_pred             HHCCCCCHHHHH
Q ss_conf             987984788965
Q gi|254780788|r  452 GENGIKTMEDLA  463 (526)
Q Consensus       452 ~e~gIktleDlA  463 (526)
                      ..-+|.-.+||.
T Consensus       187 ~R~DVmp~dDlg  198 (254)
T KOG1918         187 HRPDVMPADDLG  198 (254)
T ss_pred             CCCCCCCCHHHH
T ss_conf             777666850366


No 233
>pfam00633 HHH Helix-hairpin-helix motif. The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
Probab=57.06  E-value=6.1  Score=18.79  Aligned_cols=28  Identities=25%  Similarity=0.294  Sum_probs=21.8

Q ss_pred             HHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             4777505888877653058899999999
Q gi|254780788|r  384 VEELACVKISEIASIEGFDEETAVEIQG  411 (526)
Q Consensus       384 iEeIa~a~~eeL~~IeGfdee~a~eL~~  411 (526)
                      ++.+..++.++|.+++|+.+.+|..+..
T Consensus         2 ~~~~~~as~eeL~~lpGVG~~tA~~I~~   29 (30)
T pfam00633         2 LEGLIPASREELLALPGVGPKTAEAILS   29 (30)
T ss_pred             CCCCCCCCHHHHHHCCCCCHHHHHHHHC
T ss_conf             6443523599997288977688998853


No 234
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=56.85  E-value=13  Score=16.42  Aligned_cols=46  Identities=20%  Similarity=0.526  Sum_probs=31.7

Q ss_pred             HHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHH
Q ss_conf             9999976286654248987567879999853422110254427899
Q gi|254780788|r  284 ATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR  329 (526)
Q Consensus       284 ~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvr  329 (526)
                      ..|+.+-+.-|.|++|.+.-..+.+.|.+--..--+.|||+|+++.
T Consensus        40 R~yi~k~~~~agIs~I~IeR~~~~i~V~I~tarPgiiIGkkG~~Ie   85 (233)
T PRK00310         40 RKFLKKKLKKAGVSRIVIERPAKKVRVTIHTARPGIVIGKKGEDIE   85 (233)
T ss_pred             HHHHHHHCHHCCEEEEEEEECCCEEEEEEEECCCCCHHCCCCCHHH
T ss_conf             9999750101572489999738879999996788631215663689


No 235
>TIGR02851 spore_V_T stage V sporulation protein T; InterPro: IPR014213   Members of this protein entry include the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB..
Probab=56.61  E-value=9.3  Score=17.47  Aligned_cols=48  Identities=33%  Similarity=0.625  Sum_probs=23.9

Q ss_pred             EEEEEECCCCEEEEEECCCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCH
Q ss_conf             999984057638999579358744787488751152766999997611358702898715988
Q gi|254780788|r  143 SGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHP  205 (526)
Q Consensus       143 ~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p  205 (526)
                      ||+|+|+|      ||||+  ++| +|.=.+=+.|-||.+-.|+-      |.-.|+|-.-||
T Consensus         3 TGIVRRID------DLGRV--ViP-KEIRRTLRIrEGDPLEIF~D------r~GevILKKYSP   50 (184)
T TIGR02851         3 TGIVRRID------DLGRV--VIP-KEIRRTLRIREGDPLEIFVD------REGEVILKKYSP   50 (184)
T ss_pred             CEEEEEEE------CCCCE--EEC-CCCCCCCCCCCCCCCEEEEE------CCCCEEEEECCC
T ss_conf             24677550------46867--626-43411010125997148880------789789871078


No 236
>PRK01250 inorganic pyrophosphatase; Provisional
Probab=56.57  E-value=6.2  Score=18.79  Aligned_cols=75  Identities=20%  Similarity=0.216  Sum_probs=31.5

Q ss_pred             HHHHHCCEEEEEEEECCCCCEE-EEEEEECCC--CCCCE---E-EEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHH
Q ss_conf             6777558087856631677503-499994089--98812---7-655488621788998627782679955987899999
Q gi|254780788|r  216 VPEIYNGIVQVKAVSRDPGSRA-KLAVFSSDS--SIDPV---G-ACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVI  288 (526)
Q Consensus       216 VPEI~~G~ieIk~iaR~pG~Rs-KIAV~s~d~--~iDpV---G-AcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~  288 (526)
                      .|+..+-+|||-     .|+|. |-.+--...  .+|-+   + ..=+.-|-==|..  .--|--+|++..++.|.  ..
T Consensus        12 ~P~~vnvvIEIP-----~gs~~~KyE~d~~~g~~~ldR~l~~~~~YP~nYGfiP~Tl--~~DgDPLDvlvl~~~p~--~p   82 (176)
T PRK01250         12 LPEDINVIIEIP-----ANSDPIKYEVDKESGALFVDRFLYTAMFYPCNYGFIPHTL--SLDGDPVDVLVVTPYPL--VP   82 (176)
T ss_pred             CCCEEEEEEEEC-----CCCCCEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCCHH--CCCCCCCEEEEECCCCC--CC
T ss_conf             988899999947-----9999712898068996999986687885986543341011--16999515898527543--89


Q ss_pred             HHCCCCCCCEE
Q ss_conf             76286654248
Q gi|254780788|r  289 NALRPAIVTKV  299 (526)
Q Consensus       289 nAl~PA~v~~v  299 (526)
                      .++-.|.+..+
T Consensus        83 G~vv~~r~IG~   93 (176)
T PRK01250         83 GSVIRCRPVGV   93 (176)
T ss_pred             CCEEEEEEEEE
T ss_conf             62899999789


No 237
>KOG2841 consensus
Probab=56.30  E-value=12  Score=16.63  Aligned_cols=45  Identities=18%  Similarity=0.319  Sum_probs=32.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             5888467888877321114777505888877653058899999999
Q gi|254780788|r  366 INVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG  411 (526)
Q Consensus       366 LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~  411 (526)
                      -+|...-|+.|.. -|-|++.+..||.++|..++|+..-.|.+|..
T Consensus       201 ~~VnKtda~~LL~-~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~  245 (254)
T KOG2841         201 PGVNKTDAQLLLQ-KFGSLQQISNASEGELEQCPGLGPAKAKRLHK  245 (254)
T ss_pred             CCCCCCCHHHHHH-HCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHH
T ss_conf             8977001899988-55359998741776798675737899999999


No 238
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=56.10  E-value=13  Score=16.34  Aligned_cols=138  Identities=14%  Similarity=0.176  Sum_probs=71.1

Q ss_pred             CCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHH
Q ss_conf             88127655488621788998627782679955987899999762866542489875678799998534221102544278
Q gi|254780788|r  248 IDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQN  327 (526)
Q Consensus       248 iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqN  327 (526)
                      ||+-=--.|-.|--|+-=.+||-+-.      ++.-.-||..-.+--++     |.       -..-++|.--.-+.=-|
T Consensus       205 I~~yv~ELG~eGrli~mQl~EL~~d~------d~e~~l~i~DY~~~~e~-----d~-------~~~l~~l~~ls~~~lL~  266 (349)
T COG1623         205 IDRYVVELGTEGRLIRMQLSELIGDN------DEERELIIRDYHKEDEV-----DI-------EAVLEELQSLSDEELLD  266 (349)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHCCC------HHHHHHHHHHHHCCCCC-----CH-------HHHHHHHHHCCCHHHCC
T ss_conf             78999971644211363299885632------78899999987507556-----88-------99999998455040178


Q ss_pred             HHHHHHHHCCEEEEEECCCHHHHHHCCC-CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHH
Q ss_conf             9999986167457855220011010012-210001112258884678888773211147775058888776530588999
Q gi|254780788|r  328 VRLASQLTGWTIDIITEEEDSINRQKDF-NERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETA  406 (526)
Q Consensus       328 vrLas~Ltg~~idi~~~~~~~~~~~~e~-~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a  406 (526)
                      .--.+++.||.=       ..+-...-. ...+-.+....-+.-.+.+.||. -|.++.++..|+.++|.+++|+.+-.|
T Consensus       267 ~~~i~kvlGY~~-------~~~~~d~~vspRGYR~l~kIpRlp~~iv~nlV~-~F~~l~~il~As~edL~~VeGIGe~rA  338 (349)
T COG1623         267 PENIAKVLGYPK-------TTEADDSLVSPRGYRLLNKIPRLPFAIVENLVR-AFGTLDGILEASAEDLDAVEGIGEARA  338 (349)
T ss_pred             HHHHHHHHCCCC-------CCHHCCCCCCCHHHHHHHCCCCCCHHHHHHHHH-HHHHHHHHHHHCHHHHHHHCCHHHHHH
T ss_conf             899999967997-------210013425722668871176763789999999-975289998714767766213669999


Q ss_pred             HHHHH
Q ss_conf             99999
Q gi|254780788|r  407 VEIQG  411 (526)
Q Consensus       407 ~eL~~  411 (526)
                      ..+++
T Consensus       339 r~i~~  343 (349)
T COG1623         339 RAIKE  343 (349)
T ss_pred             HHHHH
T ss_conf             99997


No 239
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=55.15  E-value=14  Score=16.23  Aligned_cols=60  Identities=15%  Similarity=0.242  Sum_probs=42.1

Q ss_pred             HHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf             147775058888776530588999999999999999999998987754284356640779998999999987
Q gi|254780788|r  383 DVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGEN  454 (526)
Q Consensus       383 SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L~e~  454 (526)
                      ..=.|-.++.++|..++|+....|..|+.-            .++-.....-+||....|+.+.++.+|...
T Consensus        87 ~~vNiNtAs~eeL~~lpgIG~~kA~aIi~y------------Re~~G~f~sv~dL~~v~GiG~~~~ekl~~~  146 (149)
T COG1555          87 KKVNINTASAEELQALPGIGPKKAQAIIDY------------REENGPFKSVDDLAKVKGIGPKTLEKLKDY  146 (149)
T ss_pred             CCCCCCCCCHHHHHHCCCCCHHHHHHHHHH------------HHHCCCCCCHHHHCCCCCCCHHHHHHHHHH
T ss_conf             413666108999988679899999999999------------997399765788710777789999987756


No 240
>KOG1433 consensus
Probab=52.74  E-value=7.2  Score=18.26  Aligned_cols=58  Identities=21%  Similarity=0.148  Sum_probs=40.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             0111225888467888877321114777505888877653058899999999999999
Q gi|254780788|r  360 QFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYL  417 (526)
Q Consensus       360 ~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L  417 (526)
                      -.|.....++......|-..+|.+++.+++++..++..|.|+.......+...+...-
T Consensus        24 ~~~~~~~~ita~~v~~l~~~~l~~v~~l~~~~~~el~~i~~~s~~~~~k~~~~l~~~~   81 (326)
T KOG1433          24 VRFLLAGGITAEDVLLLSEGELSTVEGLAYAGKEELLLIIGLSEAKSGKTVLGLHKLV   81 (326)
T ss_pred             HHHHHCCCCCHHHHHHHCCCCEEEEECCCCCCCHHHHHEEEECHHHCCCHHHHHHHHH
T ss_conf             3456215666777654143524788501457604443200001220010899999851


No 241
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=51.42  E-value=16  Score=15.82  Aligned_cols=56  Identities=16%  Similarity=0.236  Sum_probs=40.5

Q ss_pred             CCEEE-EEEEECCCC-EEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCC
Q ss_conf             83899-999840576-3899957-93587447874------887511527669999976113587
Q gi|254780788|r  139 GEIIS-GTVKRVEYG-NVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQR  194 (526)
Q Consensus       139 Geiv~-G~V~r~e~~-~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~r  194 (526)
                      |.|+- .+|.|++.+ +++++|+ +..|+.-.+..      -+...|++|...+|=|..-..--.
T Consensus         1 G~i~~~~~V~~v~~~~G~~~~l~~g~~gfvhiS~lsD~kv~~~~~~fk~Gs~H~~RVig~s~~D~   65 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDG   65 (71)
T ss_pred             CCCCCEEEEEEECCCCCEEEEECCCCEEEEEEHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCCC
T ss_conf             96233405999858853799969996899996012666423665786479988899983474341


No 242
>TIGR01008 rpsC_E_A ribosomal protein S3; InterPro: IPR005703   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    Ribosomal protein S3 is one of the proteins from the small ribosomal subunit. This family describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=50.80  E-value=16  Score=15.76  Aligned_cols=56  Identities=18%  Similarity=0.361  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCC
Q ss_conf             99999997667775580878566316775034999940899881276554886217889986277
Q gi|254780788|r  207 FMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRD  271 (526)
Q Consensus       207 ~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~g  271 (526)
                      ++.+-|+.|+-+=.=|=++|+.-    -.-|+|-+|+..|     |-.+|-+|.||+++..-|+.
T Consensus        14 ~idE~l~~El~~AGYsgvdv~~T----PlGT~vii~AerP-----g~VIGr~G~rIr~LT~~l~~   69 (204)
T TIGR01008        14 LIDEFLKKELREAGYSGVDVRKT----PLGTKVIIYAERP-----GLVIGRGGRRIRELTEKLQK   69 (204)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEC----CCCCEEEEEEECC-----CCEECCCCCHHHHHHHHHHH
T ss_conf             78889999886517775516877----7896799998368-----63772797218899999987


No 243
>PRK09890 cold shock protein CspG; Provisional
Probab=50.50  E-value=16  Score=15.72  Aligned_cols=55  Identities=25%  Similarity=0.369  Sum_probs=37.2

Q ss_pred             CEEEEEEEECC--CC--EEEEEECCCEEEEEHHHCCCC--CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf             38999998405--76--389995793587447874887--511527669999976113587028
Q gi|254780788|r  140 EIISGTVKRVE--YG--NVIVDLGNSDGVIRRDETISR--ENLRPGDRVKSYIYDVRREQRGPQ  197 (526)
Q Consensus       140 eiv~G~V~r~e--~~--~iiVdlg~~ea~Lp~~e~ip~--E~~~~Gdrika~i~~V~~~~rgpq  197 (526)
                      +-++|+|+.++  +|  +|.-|-|+-+-++..+..-..  ..++.|++|.+-   |....||||
T Consensus         3 ~~~tG~VKwFn~~KGyGFI~~ddg~~DvFvH~s~i~~~~~~~L~~Gq~V~f~---v~~g~kG~~   63 (70)
T PRK09890          3 NKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFS---IEQGQRGPA   63 (70)
T ss_pred             CCEEEEEEEECCCCCEEEECCCCCCCCEEEEHHHHCCCCCCCCCCCCEEEEE---EEECCCCCC
T ss_conf             7506999988399986997038999429998689272688332999999999---997999861


No 244
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=49.34  E-value=9.2  Score=17.52  Aligned_cols=73  Identities=12%  Similarity=0.190  Sum_probs=43.8

Q ss_pred             HHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHH--------HHCCEEEEE-ECCCHHHHHHCCCC
Q ss_conf             999762866542489875678799998534221102544278999998--------616745785-52200110100122
Q gi|254780788|r  286 FVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQ--------LTGWTIDII-TEEEDSINRQKDFN  356 (526)
Q Consensus       286 fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas~--------Ltg~~idi~-~~~~~~~~~~~e~~  356 (526)
                      .+.-.|.|.  ..|.++++.+.+.+-..-++..+-||+.|++..=---        .+|-...|. ....|.++|++++.
T Consensus        73 ell~~m~~~--~~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~~yRerR~e~L~  150 (208)
T COG1847          73 ELLELMDFE--VTITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVGDYRERRKETLI  150 (208)
T ss_pred             HHHHHHCCC--EEEEEEECCCEEEEEECCCCHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEHHHHHHHHHHHHH
T ss_conf             999983986--599996247579999448861023036774017999999998535059615899982068999999999


Q ss_pred             CCCC
Q ss_conf             1000
Q gi|254780788|r  357 ERTQ  360 (526)
Q Consensus       357 ~~~~  360 (526)
                      ..++
T Consensus       151 ~LA~  154 (208)
T COG1847         151 KLAE  154 (208)
T ss_pred             HHHH
T ss_conf             9999


No 245
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=48.97  E-value=17  Score=15.56  Aligned_cols=48  Identities=29%  Similarity=0.376  Sum_probs=37.9

Q ss_pred             HHHCCCEEEEEEEECCCCEEEEEECCCE-EEEEHHHCCCCCCCCCCCEEEEEEEEE
Q ss_conf             8520838999998405763899957935-874478748875115276699999761
Q gi|254780788|r  135 KDKVGEIISGTVKRVEYGNVIVDLGNSD-GVIRRDETISRENLRPGDRVKSYIYDV  189 (526)
Q Consensus       135 ~~r~Geiv~G~V~r~e~~~iiVdlg~~e-a~Lp~~e~ip~E~~~~Gdrika~i~~V  189 (526)
                      +.++|++--|.|.++.....+||+|... +.|+.  +     +.+|.|+-+-+...
T Consensus       102 ~~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~~--~-----~~~~~RvTvri~~~  150 (272)
T COG2106         102 SPKEGEYREGLVIRRGKKGNLVDIGKDKLAKLSS--P-----APPGARVTVRIISR  150 (272)
T ss_pred             CCCCEEECCEEEEEECCCCEEEECCCCCCEECCC--C-----CCCCCEEEEEEEEC
T ss_conf             8662561050798736882389805875133058--7-----89985699999731


No 246
>PRK10880 adenine DNA glycosylase; Provisional
Probab=48.16  E-value=17  Score=15.47  Aligned_cols=68  Identities=21%  Similarity=0.277  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHCCHHHHHHH-HCCCHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCHHHHHHCCCCCCHHHHHHHH
Q ss_conf             32111477750588887765-30588999999999999999999998987-7542843566407799989999999
Q gi|254780788|r  379 EGFADVEELACVKISEIASI-EGFDEETAVEIQGRAREYLEGIDITLQKK-IRELGVSEELCSIPGIDSKIKVALG  452 (526)
Q Consensus       379 eGf~SiEeIa~a~~eeL~~I-eGfdee~a~eL~~rA~~~L~~~~~~~~e~-~~e~~~~e~L~~l~gl~~~~~~~L~  452 (526)
                      +-|-|++++|.++.++++.. +|+.=      ..||++.......-..+- -.-...-++|+.|+|+.+-++.+..
T Consensus        57 ~~fP~~~~LA~A~~~~vl~~W~GLGY------Y~RArnLh~aA~~i~~~~~G~~P~~~~~L~~LPGIG~yTA~AI~  126 (350)
T PRK10880         57 ARFPTVTDLANAPLDEVLHLWTGLGY------YARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAIL  126 (350)
T ss_pred             HHCCCHHHHHCCCHHHHHHHHHHCCC------HHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCHHHHHHHH
T ss_conf             98839999977999999998640693------89999999999999997589898259998626688727999999


No 247
>TIGR01083 nth endonuclease III; InterPro: IPR005759    The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases. Among these modified bases, 7,8-dihydro-8-oxoguanine (8-oxoG) is an important mutagenic lesion. Base excision repair is a critical mechanism for preventing mutations by removing the oxidative lesion from the DNA. Escherichia coli Nth protein (endonuclease III) has an 8-oxoG DNA glycosylase/AP lyase activity which removes 8-oxoG preferentially from 8-oxoG/G mispairs. Human hNTH1 protein, a homolog of E. coli Nth protein, has similar DNA glycosylase/AP lyase activity that removes 8-oxoG from 8-oxoG/G mispairs . ; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0006284 base-excision repair, 0005622 intracellular.
Probab=46.65  E-value=18  Score=15.31  Aligned_cols=67  Identities=22%  Similarity=0.308  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHCCHHHHHHH---HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHH
Q ss_conf             32111477750588887765---30588999999999999999999998987754284356640779998999999
Q gi|254780788|r  379 EGFADVEELACVKISEIASI---EGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVAL  451 (526)
Q Consensus       379 eGf~SiEeIa~a~~eeL~~I---eGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L  451 (526)
                      +-|.|.+++|+++.|+|.+.   -||=-..|..|+.-++.-++.-.   .   +=....++|+.|+|....+|..-
T Consensus        54 ~~Y~tp~~~a~a~~eel~~~Ik~iGlYr~KAk~I~~~~~~LvE~y~---G---eVP~~~~eL~~LPGVGRKTANVV  123 (192)
T TIGR01083        54 EVYPTPQALAAAGLEELEEYIKSIGLYRNKAKNIIALCRKLVERYG---G---EVPEDREELVKLPGVGRKTANVV  123 (192)
T ss_pred             HCCCCHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHC---C---CCCCCHHHHHCCCCCCCHHHHHH
T ss_conf             1277868996089313477642258645689999999999999818---9---87755376617899871145624


No 248
>cd01703 Pol_iota Pol iota is member of the DNA polymerase Y-family, and has also been called Rad30 homolog B. Unlike classic DNA polymerases,Y-family polymerases are induced by DNA damage. They can transverse normal replication-blocking DNA lesions. Unlike Pol eta, Pol iota is unable to replicate through a cis-syn T-T dimer. In human Pol iota, the base-pairing mode in the active site at the replicative end mat bee Hoogsteen instead of Watson-Click. Human Pol iota can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine. Pol iota prefers to insert Guanosine instead of Adenosine opposite Thymidine.
Probab=45.66  E-value=19  Score=15.21  Aligned_cols=93  Identities=14%  Similarity=0.070  Sum_probs=53.4

Q ss_pred             CCCCCCCHHHHHHHHHHHCC-EEEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC-HHHH
Q ss_conf             11025442789999986167-457855220011010012210001112258884678888773211147775058-8887
Q gi|254780788|r  318 SLAIGRRGQNVRLASQLTGW-TIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVK-ISEI  395 (526)
Q Consensus       318 s~AIGk~GqNvrLas~Ltg~-~idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~-~eeL  395 (526)
                      |.-||.+-.=++|||.+-.= ..-++.-...     .++-...-.+-+.-+|...+++.|-..|..++.+++..+ .+.|
T Consensus       172 S~GIa~NKlLAKlas~~~KPngqt~l~p~~~-----~~~l~~~~~i~ki~GIG~kt~~~L~~~gi~ti~dl~~~~~~~~l  246 (394)
T cd01703         172 CAGIASNKLLAKLVGSVHKPNQQTTLLPESA-----DHLIMDLGSLRKIPGIGYKTAKKLEDHGISSVRDLQECSELLLL  246 (394)
T ss_pred             EEEECCCHHHHHHHHHCCCCCCEEEECCCCH-----HHHHCCCCCHHHHCCCCHHHHHHHHHCCCEEHHHHHCCCHHHHH
T ss_conf             7766340328987753258898059777118-----77843668805527817999999998389267987658879999


Q ss_pred             HHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             7653058899999999999999
Q gi|254780788|r  396 ASIEGFDEETAVEIQGRAREYL  417 (526)
Q Consensus       396 ~~IeGfdee~a~eL~~rA~~~L  417 (526)
                      ...  |....+..|.+.|+-..
T Consensus       247 ~~~--fG~~~g~~l~~~a~GiD  266 (394)
T cd01703         247 EKG--FGKGIAQRIWGLAHGRD  266 (394)
T ss_pred             HHH--HHHHHHHHHHHHHCCCC
T ss_conf             998--78899999999956978


No 249
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=45.51  E-value=19  Score=15.19  Aligned_cols=15  Identities=40%  Similarity=0.651  Sum_probs=8.0

Q ss_pred             CCCCCEEEEEEEEEC
Q ss_conf             152766999997611
Q gi|254780788|r  176 LRPGDRVKSYIYDVR  190 (526)
Q Consensus       176 ~~~Gdrika~i~~V~  190 (526)
                      |++||++++.+.=++
T Consensus        21 f~~GDtvrv~vki~E   35 (115)
T COG0335          21 FRPGDTVRVHVKIVE   35 (115)
T ss_pred             CCCCCEEEEEEEEEE
T ss_conf             999988999999986


No 250
>KOG1004 consensus
Probab=45.32  E-value=19  Score=15.17  Aligned_cols=84  Identities=21%  Similarity=0.266  Sum_probs=56.4

Q ss_pred             HHHHHHHHCCCEEEEEEEECCCCEEEEEECCC-EEEEEHH-----HCCCCCCCCCCCEEEEEEEEECCC-----------
Q ss_conf             79999852083899999840576389995793-5874478-----748875115276699999761135-----------
Q gi|254780788|r  130 QYLEFKDKVGEIISGTVKRVEYGNVIVDLGNS-DGVIRRD-----ETISRENLRPGDRVKSYIYDVRRE-----------  192 (526)
Q Consensus       130 i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~-ea~Lp~~-----e~ip~E~~~~Gdrika~i~~V~~~-----------  192 (526)
                      .-..|...+|+.|.|+|.--..+++-||+|+. -|.||.-     -.=.+-++++||-|-|-+.+-.++           
T Consensus        57 ~~kRYiP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrPnl~vGdliyakv~~a~~~~Epel~Cids~  136 (230)
T KOG1004          57 QQKRYIPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRPNLQVGDLIYAKVVDANKDMEPELTCIDST  136 (230)
T ss_pred             CCCEECCCCCCEEEEEEEECCCCEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEECCC
T ss_conf             45043378899899999850465179963898665331002368543578864316578999870677766406887355


Q ss_pred             CC--E--E--EEEEECCCHHHHHHHHH
Q ss_conf             87--0--2--89871598899999999
Q gi|254780788|r  193 QR--G--P--QVLLSRTHPQFMVKLFH  213 (526)
Q Consensus       193 ~r--g--p--qi~lSRt~p~~l~~Lf~  213 (526)
                      .|  |  +  -=++--+++.+.++|+-
T Consensus       137 graaGfG~LkdG~if~vs~~~~R~Ll~  163 (230)
T KOG1004         137 GRAAGFGVLKDGMIFKVSLGLCRKLLL  163 (230)
T ss_pred             CCCCCCCCCCCCEEEEECHHHHHHHHC
T ss_conf             754575342686698605888678875


No 251
>KOG0187 consensus
Probab=44.66  E-value=16  Score=15.69  Aligned_cols=55  Identities=22%  Similarity=0.253  Sum_probs=42.0

Q ss_pred             CEEEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             7457855220011010012210001112258884678888773211147775058
Q gi|254780788|r  337 WTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVK  391 (526)
Q Consensus       337 ~~idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~  391 (526)
                      -.|-|+..+|+.|++..-.-+.+.+-.+...||.++-++|-..||.++-.+..++
T Consensus        67 RGISiKLQEEERErrdnyVPevSaLd~d~ieVD~dT~eMlk~lg~~~~~~~~~~~  121 (134)
T KOG0187          67 RGISIKLQEEERERRDNYVPEVSALDQDIIEVDPDTKEMLKLLGFGSLSGVQVTE  121 (134)
T ss_pred             CCEEEEECHHHHHHHCCCCCCHHHCCHHHEEECHHHHHHHHHCCCCCCCCEEEEC
T ss_conf             6446860277887552557622220334404276599999984877767536646


No 252
>PRK00296 minE cell division topological specificity factor MinE; Reviewed
Probab=44.02  E-value=20  Score=15.03  Aligned_cols=55  Identities=20%  Similarity=0.198  Sum_probs=40.8

Q ss_pred             HHHHCC-CCHHHHHHHHHHHHHHHHHHCCCC-CCCEEEEECCCCCEEEEEEEEEEEC
Q ss_conf             986239-999999999999999999613687-4535999749988399999988517
Q gi|254780788|r   16 VAYEKS-IDRDVVLSVMADSIQKAARSLYGT-MSDIRVEINPETGDISLFRLLEVVE   70 (526)
Q Consensus        16 va~EK~-I~~e~i~~aie~Al~~a~kK~~~~-~~~i~V~iD~~tG~i~i~~~~~VVe   70 (526)
                      ++.|++ ...-..+..++.-|.....|+..- ..++.|.++...|++.+........
T Consensus        26 laheR~~~~~pd~l~~lk~eil~VI~KYv~Id~d~i~v~le~~~~~~~vLE~nI~lP   82 (85)
T PRK00296         26 VAHERRSDGEPDYLPQLRKEILEVICKYVQIDPDMVHVQLEQKDGDISTLELNITLP   82 (85)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHHHHEEECHHHEEEEEEECCCCEEEEEEEEECC
T ss_conf             342005799868999999999999987603662674999986489778999986778


No 253
>cd00501 Peptidase_C15 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I:  Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from proteolysis by other proteases until the pGlu is removed by a PGP.  PGPs are cysteine proteases with a Cys-His-Glu/Asp catalytic triad. Type I PGPs are found in a wide variety of prokaryotes and eukaryotes. It is not clear whether the functional form is a monomer, a homodimer, or a homotetramer.
Probab=42.43  E-value=8.8  Score=17.64  Aligned_cols=56  Identities=25%  Similarity=0.274  Sum_probs=35.6

Q ss_pred             HHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEE-ECCCCCEEEEEEC--CCCCC
Q ss_conf             788998627782679955987899999762866542489-8756787999985--34221
Q gi|254780788|r  262 VQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVV-LDEDVGRIEVIVP--KEQLS  318 (526)
Q Consensus       262 iq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~-~de~~~~~~v~v~--~~qls  318 (526)
                      +.++++.|+...|+ +.||.|+-.|+||.+.=--..... -....+...|-||  ++|.+
T Consensus       117 ~~~~~~~l~~~g~~-~~~S~dAG~YlCN~~~Y~sL~~~~~~~~~~~~~FvHvP~~~e~~~  175 (194)
T cd00501         117 VKAIVKALREAGIP-ARVSNDAGTYLCNHVYYGSLHESATRGPFIRAGFIHVPYSPEQVA  175 (194)
T ss_pred             HHHHHHHHHHCCCC-CEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHC
T ss_conf             99999999974999-468078753434699999999999729998166987289978816


No 254
>pfam00719 Pyrophosphatase Inorganic pyrophosphatase.
Probab=41.73  E-value=16  Score=15.71  Aligned_cols=64  Identities=20%  Similarity=0.212  Sum_probs=32.2

Q ss_pred             CCCEEEEEEEECCC--CCCCE----EEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEE
Q ss_conf             77503499994089--98812----7655488621788998627782679955987899999762866542489
Q gi|254780788|r  233 PGSRAKLAVFSSDS--SIDPV----GACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVV  300 (526)
Q Consensus       233 pG~RsKIAV~s~d~--~iDpV----GAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~  300 (526)
                      .|+|.|..+-...+  .+|.+    -.|-+.-|.==|..  +--|.=+|++..++.|.  ...++-+|++..+.
T Consensus         8 ~gs~~KyE~d~~~~~~~ldr~l~~~~~yP~nYGfiP~T~--~~DgDPLDvlvl~~~~~--~~G~vv~~r~iG~l   77 (156)
T pfam00719         8 KGSRVKYEIDKESGLLPVDRVLYTSMGYPFNYGFIPQTL--EGDGDPLDVLVLGPEPL--FPGSVVRVRPIGVL   77 (156)
T ss_pred             CCCCEEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCC--CCCCCCEEEEEECCCCC--CCCCEEEEEEEEEE
T ss_conf             999867998368897038766467888983540346611--36999468998448743--89418999888999


No 255
>pfam02738 Ald_Xan_dh_C2 Molybdopterin-binding domain of aldehyde dehydrogenase.
Probab=41.68  E-value=22  Score=14.78  Aligned_cols=15  Identities=7%  Similarity=0.295  Sum_probs=8.3

Q ss_pred             EEEEECCCCCEEEEEE
Q ss_conf             5999749988399999
Q gi|254780788|r   49 IRVEINPETGDISLFR   64 (526)
Q Consensus        49 i~V~iD~~tG~i~i~~   64 (526)
                      +.+..| .+|.+.+|.
T Consensus        52 ~vA~~d-~~g~l~i~~   66 (543)
T pfam02738        52 ALAVPD-EDDELTIYS   66 (543)
T ss_pred             EEEEEC-CCCCEEEEE
T ss_conf             999987-899399998


No 256
>KOG4384 consensus
Probab=41.66  E-value=22  Score=14.78  Aligned_cols=95  Identities=15%  Similarity=0.186  Sum_probs=53.6

Q ss_pred             CCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHCCC--------CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf             25442789999986167457855220011010012--------2100011122588846788887732111477750588
Q gi|254780788|r  321 IGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDF--------NERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKI  392 (526)
Q Consensus       321 IGk~GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~--------~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~  392 (526)
                      ++-++-|-+-++ .+=-.+++.++++...++-.-.        ......+...+++.+ -.+.|..+||.++|.+..+..
T Consensus       173 ~~~g~~~~kv~~-f~~~~v~~~s~e~~~~~~p~~~~~~~~~~~~~~~~ewL~~i~le~-y~~~~L~nGYd~le~~k~i~e  250 (361)
T KOG4384         173 TWLGLLNNKVGS-FKFIYVDVISEEEPAPKRPLRRLRRSPHPHPKSLEEWLRRIGLEE-YIETLLENGYDTLEDLKDITE  250 (361)
T ss_pred             CCCCCCCCCCCC-CCCCEECCCCCCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHH-HHHHHHHCCHHHHHHHHHCCH
T ss_conf             233544676533-356400232322346301456532378987048999999863888-878998706488899875268


Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             8877653058899999999999999
Q gi|254780788|r  393 SEIASIEGFDEETAVEIQGRAREYL  417 (526)
Q Consensus       393 eeL~~IeGfdee~a~eL~~rA~~~L  417 (526)
                      ++|.++-=-+.+.-..|...++-..
T Consensus       251 ~dL~~lgI~nP~Hr~kLL~av~~~~  275 (361)
T KOG4384         251 EDLEELGIDNPDHRKKLLSAVELLK  275 (361)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             7799847898789999999999987


No 257
>pfam05557 MAD Mitotic checkpoint protein. This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.
Probab=41.65  E-value=13  Score=16.29  Aligned_cols=17  Identities=29%  Similarity=0.440  Sum_probs=14.1

Q ss_pred             HHHHHCCEEEEEECCCH
Q ss_conf             99861674578552200
Q gi|254780788|r  331 ASQLTGWTIDIITEEED  347 (526)
Q Consensus       331 as~Ltg~~idi~~~~~~  347 (526)
                      +-.|+||+||+.++..|
T Consensus       640 cY~L~GYkID~~~~~~y  656 (722)
T pfam05557       640 CYMLFGYKIDITPNSQY  656 (722)
T ss_pred             HHHHHCEEEEECCCCEE
T ss_conf             99985703674478727


No 258
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family; InterPro: IPR003282 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia.   The type III secretion system is of great interest as it is used to transport virulence factors from the pathogen directly into the host cell  and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis . However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself, type III subunits in the outer membrane translocate secreted proteins through a channel-like structure.    One of the outer membrane protein subunit families, termed "K" here for nomenclature purposes, aids in the structural assembly of the invasion complex . It is also described as a lipoprotein. Members of this family include the Salmonella PrgK and SsaJ genes, MxiJ from Shigella, YscJ from Yersinia, and from the plant enteropathogens NolT (Rhizobium) and HrcJ Erwinia). The flagellar M-ring protein FliF also shares a low level of similarity, presumably due to evolution of the type III secretion system from the flagellar biosynthetic pathway.; GO: 0009306 protein secretion.
Probab=41.51  E-value=14  Score=16.15  Aligned_cols=20  Identities=20%  Similarity=0.263  Sum_probs=9.8

Q ss_pred             HHHHHHHHCCCEEEEEEEEC
Q ss_conf             79999852083899999840
Q gi|254780788|r  130 QYLEFKDKVGEIISGTVKRV  149 (526)
Q Consensus       130 i~~ef~~r~Geiv~G~V~r~  149 (526)
                      ..+.=-..+.-++++.|+=+
T Consensus       119 ~Le~tLs~IdGV~~ArVhVv  138 (203)
T TIGR02544       119 ELEQTLSQIDGVISARVHVV  138 (203)
T ss_pred             HHHHHHHHCCCEEEEEEEEE
T ss_conf             99998601792686679997


No 259
>CHL00162 thiG thiamin biosynthesis protein G; Validated
Probab=41.30  E-value=20  Score=14.97  Aligned_cols=11  Identities=27%  Similarity=0.549  Sum_probs=5.6

Q ss_pred             CCEEEEEEEEC
Q ss_conf             83899999840
Q gi|254780788|r  139 GEIISGTVKRV  149 (526)
Q Consensus       139 Geiv~G~V~r~  149 (526)
                      -||||--++|+
T Consensus        41 aeiVTVAlRR~   51 (267)
T CHL00162         41 CEIVTVAIRRA   51 (267)
T ss_pred             CCEEEEEEECC
T ss_conf             98799997325


No 260
>TIGR00426 TIGR00426 competence protein ComEA helix-hairpin-helix repeat region; InterPro: IPR004509   This domain is found in competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This domain represents a region of two tandem copies of a helix-hairpin-helix domain, each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to this domain..
Probab=40.91  E-value=22  Score=14.70  Aligned_cols=54  Identities=17%  Similarity=0.289  Sum_probs=39.5

Q ss_pred             HHHHCCHHHHHH-HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHH
Q ss_conf             775058888776-530588999999999999999999998987754284356640779998999999
Q gi|254780788|r  386 ELACVKISEIAS-IEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVAL  451 (526)
Q Consensus       386 eIa~a~~eeL~~-IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L  451 (526)
                      .|-.|+.+||.. |.|+....|+.|..            ..|+.-...--|||+.++||....+.+-
T Consensus        10 nINtAtaeElq~~~~GvG~kKAeAIv~------------YREe~G~F~t~Edl~~V~GiG~~~~Ek~   64 (70)
T TIGR00426        10 NINTATAEELQKALSGVGAKKAEAIVA------------YREEYGRFKTVEDLKKVSGIGEKLLEKN   64 (70)
T ss_pred             ECCHHCHHHHHHHHCCCCHHHHHHHHH------------HHHCCCCCCCHHHHHHCCCCCHHHHHHH
T ss_conf             101104788887642887237899988------------7532779576222321478762455556


No 261
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=40.74  E-value=22  Score=14.68  Aligned_cols=33  Identities=24%  Similarity=0.320  Sum_probs=26.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHH
Q ss_conf             211025442789999986167457855220011
Q gi|254780788|r  317 LSLAIGRRGQNVRLASQLTGWTIDIITEEEDSI  349 (526)
Q Consensus       317 ls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~~  349 (526)
                      ..+-||-+|.+.|---+-||.+|-|....-...
T Consensus        17 vg~ilGprG~t~k~l~~~t~~~i~irG~GS~Kd   49 (120)
T cd02395          17 VGLILGPRGNTLKQLEKETGAKISIRGKGSMKD   49 (120)
T ss_pred             EEEEECCCCCHHHHHHHHHCCEEEEEECCCCCC
T ss_conf             678877985069999998798799971787667


No 262
>TIGR00118 acolac_lg acetolactate synthase, large subunit, biosynthetic type; InterPro: IPR012846   Two groups of proteins form acetolactate from two molecules of pyruvate. The type of acetolactate synthase described in this entry also catalyzes the formation of acetohydroxybutyrate from pyruvate and 2-oxobutyrate, an early step in the branched chain amino acid biosynthesis; it is therefore also termed acetohydroxyacid synthase. In bacteria, this catalytic chain is associated with a smaller regulatory chain in an alpha2/beta2 heterotetramer. Acetolactate synthase is a thiamine pyrophosphate enzyme. In this type, FAD and Mg++ are also found. Several isozymes of this enzyme are found in E. coli K12, one of which contains a frameshift in the large subunit gene and is not expressed.; GO: 0000287 magnesium ion binding, 0003984 acetolactate synthase activity, 0030976 thiamin pyrophosphate binding, 0050660 FAD binding, 0009082 branched chain family amino acid biosynthetic process.
Probab=40.36  E-value=14  Score=16.24  Aligned_cols=63  Identities=17%  Similarity=0.460  Sum_probs=41.3

Q ss_pred             CCCCCEEEEEEEEEEECCCCCCCCEECHHHHHHHCCCCC------CCCEEEEECCHHHHHHHHH------HHHHHHHHHH
Q ss_conf             499883999999885176778753234899986288986------4737998508456207999------9999999999
Q gi|254780788|r   54 NPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSID------IGGVVSDPLPPMDFGRVAV------QSAKQVIIQK  121 (526)
Q Consensus        54 D~~tG~i~i~~~~~VVedved~~~eI~l~~A~~~~~~~~------iGD~i~~~i~~~~fgRiaA------q~AKQvI~Qk  121 (526)
                      ||-||++.-|.                        |+++      -|..|-.+|+|.+.|.+-.      --||+|+.|-
T Consensus       293 DRvTGnl~~FA------------------------p~AkraaaeGrGGiiHiDIDPaeIgK~v~~diPiVGDAr~VL~~l  348 (593)
T TIGR00118       293 DRVTGNLAKFA------------------------PNAKRAAAEGRGGIIHIDIDPAEIGKNVRVDIPIVGDARNVLEEL  348 (593)
T ss_pred             CCCCCCHHHHC------------------------HHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf             66348776723------------------------165675414787369998537655771146401036758999999


Q ss_pred             HHHHHHH----HHHH--HHHHHCCC
Q ss_conf             9999988----7799--99852083
Q gi|254780788|r  122 VREAERD----RQYL--EFKDKVGE  140 (526)
Q Consensus       122 ireaEr~----~i~~--ef~~r~Ge  140 (526)
                      +......    ..-+  .|.+++.+
T Consensus       349 l~~~~~~~~~~~~~~~~~W~~~i~~  373 (593)
T TIGR00118       349 LKKLEKEKALKERSEEQAWLEQINK  373 (593)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             9998763035672248899999999


No 263
>KOG2279 consensus
Probab=39.24  E-value=15  Score=15.86  Aligned_cols=36  Identities=22%  Similarity=0.210  Sum_probs=18.2

Q ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEE
Q ss_conf             999985342211025442789999986167457855
Q gi|254780788|r  308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIIT  343 (526)
Q Consensus       308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~  343 (526)
                      .++-+|.-+..+-||..|--+.--|.-+|-++-|.+
T Consensus       298 ~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t  333 (608)
T KOG2279         298 PEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWT  333 (608)
T ss_pred             CEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEE
T ss_conf             024447665410221013444465641575424775


No 264
>KOG3297 consensus
Probab=39.04  E-value=24  Score=14.50  Aligned_cols=123  Identities=22%  Similarity=0.271  Sum_probs=70.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHHHHHCCCCCCCCEEEE
Q ss_conf             39999999999999999999613687453599974998839999998851767787532348999862889864737998
Q gi|254780788|r   20 KSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSD   99 (526)
Q Consensus        20 K~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A~~~~~~~~iGD~i~~   99 (526)
                      =.|+...+-.-++.|+..-.+++|-...-..+.+     .+.+|....|-+-.                  +..||--..
T Consensus        11 VrI~P~qf~~~~~~ai~~eL~~k~anKvl~nvGL-----CI~vyDi~~v~e~~------------------v~pGDGas~   67 (202)
T KOG3297          11 VRIPPSQFEKPLEDAIKEELNRKLANKVLPNVGL-----CICVYDILEVEEGI------------------VLPGDGASY   67 (202)
T ss_pred             EECCHHHHCCHHHHHHHHHHHHHHHHHHCCCCCE-----EEEEEEEEEECCEE------------------EECCCCCEE
T ss_conf             6449689074578999999999987543246647-----99986750313407------------------803888657


Q ss_pred             ECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECC-CEEEEEHHHCCCCCCCCC
Q ss_conf             5084562079999999999999999998877999985208389999984057638999579-358744787488751152
Q gi|254780788|r  100 PLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDETISRENLRP  178 (526)
Q Consensus       100 ~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~-~ea~Lp~~e~ip~E~~~~  178 (526)
                      -  ..-|--                       --|+.-+||+|+|.++.-.+..+-|.||= -+-++|+.-+-+.-.|.+
T Consensus        68 ~--~V~FR~-----------------------vVFrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~  122 (202)
T KOG3297          68 A--RVWFRV-----------------------VVFRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEP  122 (202)
T ss_pred             E--EEEEEE-----------------------EEEECCCCEEEEEEEECCCCCCEEEEEEEEECEEECHHHCCCCCCCCC
T ss_conf             9--999999-----------------------998514650899883037725418998831011306645899731560


Q ss_pred             CCEEEEEEEEEC
Q ss_conf             766999997611
Q gi|254780788|r  179 GDRVKSYIYDVR  190 (526)
Q Consensus       179 Gdrika~i~~V~  190 (526)
                      -.++=+..++-+
T Consensus       123 ~e~vWVWey~~E  134 (202)
T KOG3297         123 DEQVWVWEYEQE  134 (202)
T ss_pred             CCEEEEEEECCC
T ss_conf             347999985166


No 265
>KOG3853 consensus
Probab=38.89  E-value=24  Score=14.49  Aligned_cols=71  Identities=15%  Similarity=0.367  Sum_probs=41.4

Q ss_pred             CEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEE------EECCCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             702898715988999999997667775580878566316775034999------94089988127655488621788998
Q gi|254780788|r  194 RGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAV------FSSDSSIDPVGACVGMRGSRVQAVVT  267 (526)
Q Consensus       194 rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV------~s~d~~iDpVGAcVG~rGsRiq~I~~  267 (526)
                      +.|-|++||+|...++.+-+.    ++-.-+.|-- |--+|++.---|      +-+-..|----.|-|      .||.+
T Consensus       228 q~PiivVSRSH~g~vK~ia~~----vfG~~~~i~p-AgGaGYKvL~lv~~~A~lYlHtt~IKKWDiCAG------dAIL~  296 (350)
T KOG3853         228 QNPIIVVSRSHAGKVKEIAEK----VFGDKMNIEP-AGGAGYKVLRLVNGTAELYLHTTAIKKWDICAG------DAILR  296 (350)
T ss_pred             CCCEEEEECCCCCHHHHHHHH----HHCCCCEEEE-CCCCCEEEEEEECCCCEEEEEEHHHHHCCCCCH------HHHHH
T ss_conf             798799963444038999998----7367624665-587761566763375348987013201110330------89999


Q ss_pred             HHCCCCEE
Q ss_conf             62778267
Q gi|254780788|r  268 ELRDEKID  275 (526)
Q Consensus       268 EL~gEkID  275 (526)
                      -|+|---+
T Consensus       297 alGG~Mtt  304 (350)
T KOG3853         297 ALGGAMTT  304 (350)
T ss_pred             HCCCCEEC
T ss_conf             70463012


No 266
>KOG2767 consensus
Probab=37.66  E-value=25  Score=14.35  Aligned_cols=71  Identities=14%  Similarity=0.208  Sum_probs=48.9

Q ss_pred             CCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99989999999879847889653267752123123444321124533435889999999999841225788800024564
Q gi|254780788|r  442 GIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKVADEE  521 (526)
Q Consensus       442 gl~~~~~~~L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~~gWf~~e~~~~~~  521 (526)
                      ++....+......=++.+-|.-=|+-++++.|.++...+           -.+++.+..+.-.|..-+-|+.+.+.++++
T Consensus       327 ~~~~~el~~kva~ilk~lYd~DI~~e~vi~~w~~K~skk-----------~vsk~~sk~i~e~a~Pfi~WL~~AESe~ee  395 (400)
T KOG2767         327 EKHEAELISKVAGILKELYDEDILEEEVIIKWGEKPSKK-----------YVSKEKSKKIRENAKPFIEWLKNAESEDEE  395 (400)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-----------CCCHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             860787888889999998761022089999987514444-----------442544234676332799998741355532


Q ss_pred             HH
Q ss_conf             11
Q gi|254780788|r  522 VQ  523 (526)
Q Consensus       522 ~~  523 (526)
                      ++
T Consensus       396 Ee  397 (400)
T KOG2767         396 EE  397 (400)
T ss_pred             CC
T ss_conf             23


No 267
>pfam01470 Peptidase_C15 Pyroglutamyl peptidase.
Probab=37.06  E-value=20  Score=15.10  Aligned_cols=67  Identities=25%  Similarity=0.293  Sum_probs=41.2

Q ss_pred             CCEEEEECCCCH-------HHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEE-ECCCCCEEEEEEC--CCC
Q ss_conf             812765548862-------1788998627782679955987899999762866542489-8756787999985--342
Q gi|254780788|r  249 DPVGACVGMRGS-------RVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVV-LDEDVGRIEVIVP--KEQ  316 (526)
Q Consensus       249 DpVGAcVG~rGs-------Riq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~-~de~~~~~~v~v~--~~q  316 (526)
                      -|.+.|+-..|.       -++++++.|+..-|+. .||.|.-.|+||.+.=--....- -....+...|-||  .+|
T Consensus        97 ~p~~~~i~~~gp~ay~stLp~~~i~~~l~~~gip~-~iS~dAG~ylCN~v~Y~sL~~~~~~~~~~~agFiHvP~~~~q  173 (203)
T pfam01470        97 QPIDEPIVPDGPAAYFATLPVKAMVKAMREAGIPA-AVSNTAGTFVCNHVMYLLLHHSAKKGPPVRAGFIHVPYLPEQ  173 (203)
T ss_pred             CCCCCCEECCCCCHHHCCCCHHHHHHHHHHCCCCC-EECCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHH
T ss_conf             65897451599733205899999999999639984-773775523028999999999996299973899986899688


No 268
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=35.86  E-value=26  Score=14.16  Aligned_cols=68  Identities=18%  Similarity=0.278  Sum_probs=45.5

Q ss_pred             HHHHHHHHCCHHHHHHH---HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHH
Q ss_conf             11477750588887765---30588999999999999999999998987754284356640779998999999
Q gi|254780788|r  382 ADVEELACVKISEIASI---EGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVAL  451 (526)
Q Consensus       382 ~SiEeIa~a~~eeL~~I---eGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L  451 (526)
                      .+++.|+..+.++|.++   -||=--.|..|++-++.++..-.  .-+........+.|+++.|+.++++...
T Consensus        67 ~~l~~i~~l~~e~La~lIrPaGFy~~KA~rLk~l~~~~~~d~~--~~~~~~~~~~Re~LL~lkGIG~ETADsI  137 (218)
T PRK13913         67 INLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSKNILKDFQ--SFENFKQEVTREWLLDQKGIGKESADAI  137 (218)
T ss_pred             CCHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--HHHHCCCHHHHHHHHCCCCCCHHHHHHH
T ss_conf             5999997189999999950401589999999999999998752--5751453658999974898663339999


No 269
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=35.84  E-value=26  Score=14.16  Aligned_cols=33  Identities=9%  Similarity=0.216  Sum_probs=28.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             999999999999999999961368745359997
Q gi|254780788|r   21 SIDRDVVLSVMADSIQKAARSLYGTMSDIRVEI   53 (526)
Q Consensus        21 ~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~i   53 (526)
                      -++++.+.+|+++++..+-+++|.+..++.+.+
T Consensus         3 ~v~~~~l~eai~~~l~~~k~rkF~ESvdl~i~L   35 (214)
T PTZ00225          3 KIPPQTLSEAIQAVLKVDKERKFKESIDLQVNL   35 (214)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEEC
T ss_conf             788899999999999747677887308999973


No 270
>pfam00833 Ribosomal_S17e Ribosomal S17.
Probab=35.74  E-value=20  Score=15.10  Aligned_cols=46  Identities=24%  Similarity=0.357  Sum_probs=19.4

Q ss_pred             EEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             5785522001101001221000111225888467888877321114
Q gi|254780788|r  339 IDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADV  384 (526)
Q Consensus       339 idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~Si  384 (526)
                      |-++.-++..+++..-.-+.+.+-.+...||.+..++|...||.++
T Consensus        69 is~klqEeErerr~~yvPe~S~ld~~~ievd~~T~~ml~~~~~~~~  114 (122)
T pfam00833        69 ISLKLQEEERERRDNYVPEVSELDVPLIEVDPDTKEMLKSLGFGNI  114 (122)
T ss_pred             CCEEHHHHHHHHHCCCCCCCCCCCCCCEEECHHHHHHHHHCCCCCC
T ss_conf             0103447888755034776320246415788789999997598888


No 271
>TIGR00643 recG ATP-dependent DNA helicase RecG; InterPro: IPR004609 The ATP-dependent DNA helicase RecG 3.6.1 from EC plays a critical role in recombination and DNA repair. It helps to process Holliday junction intermediates to mature products by catalysing branch migration. RecG has DNA unwinding activity characteristic of a DNA helicase with 3' to 5' polarity.; GO: 0004003 ATP-dependent DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=35.15  E-value=23  Score=14.56  Aligned_cols=33  Identities=21%  Similarity=0.389  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCEEEE-EEEEC
Q ss_conf             9999999999887799998520838999-99840
Q gi|254780788|r  117 VIIQKVREAERDRQYLEFKDKVGEIISG-TVKRV  149 (526)
Q Consensus       117 vI~QkireaEr~~i~~ef~~r~Geiv~G-~V~r~  149 (526)
                      .+--|+.+.||+.++.+|+.+.++|+.. +|.-|
T Consensus       569 LlHGrm~~~eK~~vm~~F~~~~~~ILVsTTVIEV  602 (721)
T TIGR00643       569 LLHGRMKSDEKEAVMEEFREGEVDILVSTTVIEV  602 (721)
T ss_pred             EECCCCCHHHHHHHHHHHHHCCCEEEEEEEEEEE
T ss_conf             3306898478999999852158369999768999


No 272
>PRK13910 DNA glycosylase MutY; Provisional
Probab=34.24  E-value=28  Score=13.98  Aligned_cols=16  Identities=13%  Similarity=0.372  Sum_probs=6.9

Q ss_pred             EEEEECCCHHHHHHHH
Q ss_conf             8987159889999999
Q gi|254780788|r  197 QVLLSRTHPQFMVKLF  212 (526)
Q Consensus       197 qi~lSRt~p~~l~~Lf  212 (526)
                      ++.|-|....++..|+
T Consensus       199 ~ilL~k~~~~~~~Glw  214 (290)
T PRK13910        199 QIALEKIEQKLYLGMH  214 (290)
T ss_pred             EEEEEECCCCCCCCCC
T ss_conf             9999817886667766


No 273
>PRK00378 nucleoid-associated protein NdpA; Validated
Probab=33.53  E-value=28  Score=13.90  Aligned_cols=156  Identities=14%  Similarity=0.218  Sum_probs=88.7

Q ss_pred             CHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCE---EEE----CCCCCEEEEEECCCCCCCCCCC--------
Q ss_conf             6217889986277826799559878999997628665424---898----7567879999853422110254--------
Q gi|254780788|r  259 GSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTK---VVL----DEDVGRIEVIVPKEQLSLAIGR--------  323 (526)
Q Consensus       259 GsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~---v~~----de~~~~~~v~v~~~qls~AIGk--------  323 (526)
                      .+......++...+..|.+.+|......+...|....-..   ++.    ........|.+-...-+.+|.-        
T Consensus        60 ~~~f~~~L~~y~~~~~dF~~fS~~a~~~L~~~l~~~~~a~gG~llf~~Y~~~~~dyL~IalL~~~~g~~v~~~L~l~~~~  139 (334)
T PRK00378         60 ESEFAQALREYREGELDFLAFSRQAAKRLQDELAKYPFAEGGFLLFCHYQYLATDYLFIALLSSKESMRVNEELDISPTH  139 (334)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCEEEEEEECCCCCEEECCCCCCCCCE
T ss_conf             86439999999707987799999999999999724886556189999997288538999998376725788875724140


Q ss_pred             --CHHHHHHHHH--HHCCEEEEEECC--CHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             --4278999998--616745785522--0011010012210001112258884678888773211147775058888776
Q gi|254780788|r  324 --RGQNVRLASQ--LTGWTIDIITEE--EDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIAS  397 (526)
Q Consensus       324 --~GqNvrLas~--Ltg~~idi~~~~--~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~  397 (526)
                        .=.+..||++  ||.|..+--+..  -+...|.  -...++-|++-|+..+-+.-.--+..+-.       .+++..+
T Consensus       140 ~LDl~kl~~AaRInLt~w~~~~~s~rYlsFikgr~--grkvsdyF~~flGc~e~~~~~~~t~~Ll~-------av~df~~  210 (334)
T PRK00378        140 YLDINQLDLAARIDLTEWETNPESNRYLSFIKGRV--GRKVADFFLDFLGAEEGLNTKAQNRTLLQ-------AVSDFVA  210 (334)
T ss_pred             EEEHHHCCEEEEEEHHHHHCCCCCCCEEEEECCCC--CCHHHHHHHHHHCCCCCCCHHHHHHHHHH-------HHHHHHH
T ss_conf             86066621667998278526887771799985778--76199999997287445764999999999-------9999997


Q ss_pred             HHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             53058899999999999999999999
Q gi|254780788|r  398 IEGFDEETAVEIQGRAREYLEGIDIT  423 (526)
Q Consensus       398 IeGfdee~a~eL~~rA~~~L~~~~~~  423 (526)
                      -.+++.+.+.+.+.++-+|+..+...
T Consensus       211 ~~~l~~~~~~~~r~~v~~Yc~eq~~~  236 (334)
T PRK00378        211 SADLDKEERQEVRKQVYDYCNEQLKA  236 (334)
T ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             55899899999999999999999866


No 274
>TIGR01077 L13_A_E ribosomal protein L13; InterPro: IPR005755   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    Ribosomal protein L13 is one of the proteins from the large ribosomal subunit . In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=33.14  E-value=26  Score=14.16  Aligned_cols=15  Identities=33%  Similarity=0.426  Sum_probs=10.8

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             620799999999999
Q gi|254780788|r  105 DFGRVAVQSAKQVII  119 (526)
Q Consensus       105 ~fgRiaAq~AKQvI~  119 (526)
                      -+||.|+..|||++.
T Consensus         9 ilGRLAS~VAK~lL~   23 (144)
T TIGR01077         9 ILGRLASVVAKRLLN   23 (144)
T ss_pred             HHHHHHHHHHHHHHC
T ss_conf             137689999998757


No 275
>cd01702 Pol_eta Pol eta is member of the DNA polimerase Y-family. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced cis-syn cyclobutane thymine-thumine (T-T) lesions. It synthesizes AA opposite a TT dimer. Pol eta is able to replicate through a variety of other distorting DNA lesion as well.
Probab=33.01  E-value=29  Score=13.84  Aligned_cols=48  Identities=15%  Similarity=0.189  Sum_probs=24.3

Q ss_pred             CCCHHHHHHHHHH-HHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             8884678888773-21114777505888877653058899999999999
Q gi|254780788|r  367 NVDEIIAHLLVAE-GFADVEELACVKISEIASIEGFDEETAVEIQGRAR  414 (526)
Q Consensus       367 dVDE~iA~~LV~e-Gf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~  414 (526)
                      +|...+++.|... |..++.+++.....+..-+..+.......|.+.|+
T Consensus       189 GvG~k~~~~L~~~lgi~ti~dl~~~~~~~~~l~~~~~~~~g~~l~~~a~  237 (358)
T cd01702         189 GLGGKLGESIIEVLGVPTEGDLLWFRSSEAQLQEKLGDKTGTWLYNLVR  237 (358)
T ss_pred             CCCHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             8678999999998399658989875148599999982799999999975


No 276
>KOG0438 consensus
Probab=32.93  E-value=29  Score=13.83  Aligned_cols=34  Identities=26%  Similarity=0.460  Sum_probs=27.8

Q ss_pred             EEEEECCCCCEEEEEEEEC-CCCCCCEEEEECCCC
Q ss_conf             8566316775034999940-899881276554886
Q gi|254780788|r  226 VKAVSRDPGSRAKLAVFSS-DSSIDPVGACVGMRG  259 (526)
Q Consensus       226 Ik~iaR~pG~RsKIAV~s~-d~~iDpVGAcVG~rG  259 (526)
                      |-.|-+|||--+|||+... ++..--+=||.||+-
T Consensus       105 v~~i~yDP~Rs~~iaLv~~~~~~~~~Ila~egm~a  139 (312)
T KOG0438         105 VIEIEYDPGRSAKIALVAGGTGELRYILATEGLKA  139 (312)
T ss_pred             EEEEEECCCCCCCEEEEECCCCCEEEEEEECCCCC
T ss_conf             79999789864317888326777059998468878


No 277
>pfam11694 DUF3290 Protein of unknown function (DUF3290). This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=32.83  E-value=22  Score=14.65  Aligned_cols=64  Identities=14%  Similarity=0.221  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCC
Q ss_conf             999999999986239999999999999999999613687453599974998839999998851767
Q gi|254780788|r    7 LELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEV   72 (526)
Q Consensus         7 ~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedv   72 (526)
                      ..++..+++||++++++++.|.-.-...---+. =+.+ +...+|.+|.+...+.+-+...+..++
T Consensus        79 sq~~~Fi~~va~d~~V~~~~v~VNst~l~dG~i-Vki~-~~~Yrv~~n~d~~sY~Lek~~li~~~i  142 (149)
T pfam11694        79 QQIVHFIESVAKDLGVDKSEVYVNTSALTDGMI-VKIG-KNYYRVNLNTDNNSYTLEKATLIQPKI  142 (149)
T ss_pred             HHHHHHHHHHHHHCCCCHHHEEEECCCCCCCEE-EEEC-CEEEEEEECCCCCEEEEEEEEEECCCC
T ss_conf             999999999988729987888994355657769-9987-827999987998706899999807874


No 278
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=32.77  E-value=29  Score=13.81  Aligned_cols=16  Identities=13%  Similarity=0.067  Sum_probs=6.8

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999
Q gi|254780788|r  406 AVEIQGRAREYLEGID  421 (526)
Q Consensus       406 a~eL~~rA~~~L~~~~  421 (526)
                      ++.+++.|+..+....
T Consensus       112 a~~i~~~A~~~Ie~ek  127 (173)
T PRK13453        112 ANGMIETAQSEINSQK  127 (173)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999999999999


No 279
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=32.54  E-value=29  Score=13.79  Aligned_cols=39  Identities=26%  Similarity=0.250  Sum_probs=18.6

Q ss_pred             HHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf             664077999899999998798478896532677521231
Q gi|254780788|r  436 ELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS  474 (526)
Q Consensus       436 ~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~  474 (526)
                      .+.++.|+...++.+|...||.|.-||+.+..|.|....
T Consensus       177 pv~~~~GvG~~~~~~l~~~Gi~ti~dl~~~~~~~L~~~~  215 (354)
T COG0389         177 PVLEFWGVGKVTAEKLRRLGISTIGDLAETDLDALKKRF  215 (354)
T ss_pred             CHHHHCCCCHHHHHHHHHCCCHHHHHHHHCCHHHHHHHH
T ss_conf             567726845899999997284889998735899999999


No 280
>TIGR02660 nifV_homocitr homocitrate synthase; InterPro: IPR013477    Most NifV-type homocitrate synthases are encoded within operons for nitrogen fixation. They are homologous to enzymes that include 2-isopropylmalate synthase, (R)-citramalate synthase, and homocitrate synthases associated with other processes. The homocitrate made by these enzymes becomes a part of the iron-molybdenum cofactor of nitrogenase.; GO: 0004410 homocitrate synthase activity, 0051188 cofactor biosynthetic process.
Probab=31.43  E-value=30  Score=13.76  Aligned_cols=63  Identities=24%  Similarity=0.290  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHH
Q ss_conf             67888877321114777505888877653058899999999999999999999898775428435664077999899999
Q gi|254780788|r  371 IIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVA  450 (526)
Q Consensus       371 ~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~  450 (526)
                      .||+.|...|...+|          ..||.|.++-...|+.                +-.+++.-.|+.=.=|....+..
T Consensus        27 aIA~aLd~aGV~ElE----------vGiPAMG~~E~~~ira----------------I~~~~l~a~l~~WcR~~~~Di~a   80 (369)
T TIGR02660        27 AIARALDEAGVDELE----------VGIPAMGEEERAVIRA----------------IVALGLKARLMAWCRARDADIEA   80 (369)
T ss_pred             HHHHHHHHHCCCEEE----------ECCCCCCHHHHHHHHH----------------HHHCCCCCEEEHHHHCCHHHHHH
T ss_conf             999999980962476----------1577687889999999----------------99628993031100104799999


Q ss_pred             HHHCCCCCH
Q ss_conf             998798478
Q gi|254780788|r  451 LGENGIKTM  459 (526)
Q Consensus       451 L~e~gIktl  459 (526)
                      -.+.|+..+
T Consensus        81 a~~~G~~~V   89 (369)
T TIGR02660        81 AARCGVDAV   89 (369)
T ss_pred             HHHHHHHEE
T ss_conf             987205203


No 281
>PRK13763 putative RNA-processing protein; Provisional
Probab=31.18  E-value=31  Score=13.63  Aligned_cols=38  Identities=26%  Similarity=0.502  Sum_probs=24.5

Q ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECC
Q ss_conf             99998534221102544278999998616745785522
Q gi|254780788|r  308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEE  345 (526)
Q Consensus       308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~  345 (526)
                      ..+-||.+-+...||+.|...+-.-+.+|-+|+|-+++
T Consensus         6 ~~v~IP~~Ri~~Lig~~g~~~~~Iee~~~~~i~idsk~   43 (185)
T PRK13763          6 EYVKIPKDRIGVLIGKKGETKKEIEEKTGVKLEIDSET   43 (185)
T ss_pred             EEEECCCHHEEEEECCCCCCHHHHHHHHCCEEEEECCC
T ss_conf             56417805456455788563789999979779995899


No 282
>PRK00642 inorganic pyrophosphatase; Provisional
Probab=30.88  E-value=29  Score=13.84  Aligned_cols=22  Identities=23%  Similarity=0.205  Sum_probs=13.3

Q ss_pred             HHHCC-CHHHHHHHHHHHHHHHH
Q ss_conf             65305-88999999999999999
Q gi|254780788|r  397 SIEGF-DEETAVEIQGRAREYLE  418 (526)
Q Consensus       397 ~IeGf-dee~a~eL~~rA~~~L~  418 (526)
                      .+.|+ +.+.|.+++.+|.+...
T Consensus       184 ~v~g~~~~e~A~~iI~~s~e~Y~  206 (212)
T PRK00642        184 EIVGIYGKKEAQKVIQLAHEDYL  206 (212)
T ss_pred             EECCCCCHHHHHHHHHHHHHHHH
T ss_conf             98868699999999999999999


No 283
>KOG2093 consensus
Probab=30.81  E-value=31  Score=13.59  Aligned_cols=137  Identities=21%  Similarity=0.207  Sum_probs=77.1

Q ss_pred             CCCC-CCHHHHHHHHHHHCCEEEEEE--CCCHHHHHHC--CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             1025-442789999986167457855--2200110100--1221000111225888467888877321114777505888
Q gi|254780788|r  319 LAIG-RRGQNVRLASQLTGWTIDIIT--EEEDSINRQK--DFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKIS  393 (526)
Q Consensus       319 ~AIG-k~GqNvrLas~Ltg~~idi~~--~~~~~~~~~~--e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~e  393 (526)
                      .+-| |+|.=||-|-+|+- ++-++-  -+.+.+.-+.  |....+.+++++...||..-                 ...
T Consensus       421 R~~GIKNGMfV~~A~klCP-qL~~lPY~FE~Ykevs~tlYetlasytl~I~aVSCDEa~v-----------------d~s  482 (1016)
T KOG2093         421 RAYGIKNGMFVRHAKKLCP-QLVILPYDFEAYKEVSETLYETLASYTLNIEAVSCDEAFV-----------------DVS  482 (1016)
T ss_pred             HHHCCCCCEEHHHHHHHCC-CCEEECCCHHHHHHHHHHHHHHHHHHCCCEEEECCHHHHH-----------------HHH
T ss_conf             8738413401788987493-2076166389999999999999986400102312016552-----------------110


Q ss_pred             HHHHHHCCCH-HHHHHHHHHHH-------------HHHHH-HHHH----------HHHHHHHCCHHHHHHCCCCCCHHHH
Q ss_conf             8776530588-99999999999-------------99999-9999----------8987754284356640779998999
Q gi|254780788|r  394 EIASIEGFDE-ETAVEIQGRAR-------------EYLEG-IDIT----------LQKKIRELGVSEELCSIPGIDSKIK  448 (526)
Q Consensus       394 eL~~IeGfde-e~a~eL~~rA~-------------~~L~~-~~~~----------~~e~~~e~~~~e~L~~l~gl~~~~~  448 (526)
                      +|..+...+. ..|..||.--.             .-|++ .+..          .-++.++.-....|-+|+|....|.
T Consensus       483 ~~~~~~~~tp~~la~~IRqEI~e~TgC~aS~Gig~t~LLARlATr~AKP~Gq~~l~a~~veeFis~~~v~~LPGVG~sm~  562 (1016)
T KOG2093         483 DLSDEENETPAVLAEHIRQEILEKTGCPASAGIGGTMLLARLATRVAKPNGQFYLSAEKVEEFISQLKVDDLPGVGSSMK  562 (1016)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCCCCCCCCHHHH
T ss_conf             13544316899999999999986249862313144799999987305888616635889999861055566877428999


Q ss_pred             HHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf             9999879847889653267752123
Q gi|254780788|r  449 VALGENGIKTMEDLAGCSVDDLLGW  473 (526)
Q Consensus       449 ~~L~e~gIktleDlAels~dEL~~~  473 (526)
                      .+|...+|+|.-||--.+-+.|.--
T Consensus       563 ~kL~s~~i~tCgdLq~~T~~kl~k~  587 (1016)
T KOG2093         563 SKLVSQFIQTCGDLQLITLIKLRKV  587 (1016)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             9999852424688999999987765


No 284
>PRK05578 cytidine deaminase; Validated
Probab=30.36  E-value=32  Score=13.54  Aligned_cols=30  Identities=17%  Similarity=0.479  Sum_probs=19.4

Q ss_pred             CCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             89988127655488621788998627782679955987
Q gi|254780788|r  245 DSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPD  282 (526)
Q Consensus       245 d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d  282 (526)
                      +.-+-|-|+|        +-+..|+.+..+.|+..+.+
T Consensus        80 ~~~~~PCG~C--------RQvl~Ef~~~~~~i~l~~~~  109 (132)
T PRK05578         80 GEPLSPCGRC--------RQVLAEFGGPDLLVTLVAKK  109 (132)
T ss_pred             CCCCCCCHHH--------HHHHHHHCCCCCEEEEECCC
T ss_conf             9826975248--------99999856899489998799


No 285
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=30.35  E-value=32  Score=13.54  Aligned_cols=90  Identities=24%  Similarity=0.409  Sum_probs=63.0

Q ss_pred             EEECCCHHHHHHHHHHHHHHHHCCEEE-EEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEE
Q ss_conf             871598899999999766777558087-8566316775034999940899881276554886217889986277826799
Q gi|254780788|r  199 LLSRTHPQFMVKLFHMEVPEIYNGIVQ-VKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIV  277 (526)
Q Consensus       199 ~lSRt~p~~l~~Lf~~EVPEI~~G~ie-Ik~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii  277 (526)
                      +=|-+..+|=-.||-+..|   +|-.. |.+|| +|-     |-...++.+|        +-.|.++-.|=|-|=+|-..
T Consensus       201 ID~~sT~DmDDALy~~~~~---~~~~~L~vAIA-DPT-----AyI~~~s~ld--------~~A~~R~FTnYLPGfNIPML  263 (645)
T COG4776         201 IDSESTEDMDDALYAEPLP---DGDWQLIVAIA-DPT-----AYIAEGSKLD--------KEAKIRAFTNYLPGFNIPML  263 (645)
T ss_pred             ECCCCCCCCCHHHHCCCCC---CCCEEEEEEEC-CCC-----CCCCCCCHHH--------HHHHHHHHHHCCCCCCCCCC
T ss_conf             5586545522234221278---99769999961-874-----2027842676--------99998777504887887778


Q ss_pred             EC--CCCHHHHHHHHCCCCCCCEEEECCCC
Q ss_conf             55--98789999976286654248987567
Q gi|254780788|r  278 VW--SPDSATFVINALRPAIVTKVVLDEDV  305 (526)
Q Consensus       278 ~w--s~d~~~fi~nAl~PA~v~~v~~de~~  305 (526)
                      +-  |||.-.+..|-.-||-+..|.++.+.
T Consensus       264 PreLsd~lCSL~~ne~RPaL~C~it~~~~G  293 (645)
T COG4776         264 PRELSDDLCSLRANEVRPALACRITIDKDG  293 (645)
T ss_pred             CHHHHHHHHHCCCCCCCCEEEEEEEECCCC
T ss_conf             823405664235466673389999981477


No 286
>PRK10929 hypothetical protein; Provisional
Probab=30.26  E-value=32  Score=13.53  Aligned_cols=36  Identities=8%  Similarity=0.142  Sum_probs=27.8

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf             888999999999986239999999999999999999
Q gi|254780788|r    4 ANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAA   39 (526)
Q Consensus         4 ~~~~ell~vie~va~EK~I~~e~i~~aie~Al~~a~   39 (526)
                      .+..++-+=++.+...|+-+...+++.++.|+..-.
T Consensus        23 P~~~~iq~~L~~~~~~k~p~q~~~i~~lq~aL~~L~   58 (1109)
T PRK10929         23 PDEKQITQELEQAKAAKTPAQPEVVEALQSALNALE   58 (1109)
T ss_pred             CCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             898999999999764799437999999999999999


No 287
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=29.95  E-value=32  Score=13.49  Aligned_cols=56  Identities=18%  Similarity=0.234  Sum_probs=40.6

Q ss_pred             EEEEEECCCCEEEEEECC--CEEEEEHH-H-----CCCCCCCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf             999984057638999579--35874478-7-----48875115276699999761135870289
Q gi|254780788|r  143 SGTVKRVEYGNVIVDLGN--SDGVIRRD-E-----TISRENLRPGDRVKSYIYDVRREQRGPQV  198 (526)
Q Consensus       143 ~G~V~r~e~~~iiVdlg~--~ea~Lp~~-e-----~ip~E~~~~Gdrika~i~~V~~~~rgpqi  198 (526)
                      +++|+..+..+.++.|-.  --+..|-. .     +--.|++++|..+.+-++.++....||-+
T Consensus         5 ~a~VQH~~k~FAi~SL~~Tg~L~afp~~sHlNdtFrfdSeKL~vGq~~~v~lk~~~~~~~g~ll   68 (69)
T cd05701           5 TAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLL   68 (69)
T ss_pred             HHHHHHHHHCEEEEEEECCCCEEEEECHHHCCCCCCCCCCEEECCCEEEEEEECCCCCCCCEEC
T ss_conf             2533212110689996044647999714643664345731153365499998137767654111


No 288
>PRK13193 pyrrolidone-carboxylate peptidase; Provisional
Probab=29.78  E-value=21  Score=14.90  Aligned_cols=116  Identities=18%  Similarity=0.109  Sum_probs=62.2

Q ss_pred             CCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEE-----EECCCC------
Q ss_conf             766999997611358702898715988999999997667775580878566316775034999-----940899------
Q gi|254780788|r  179 GDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAV-----FSSDSS------  247 (526)
Q Consensus       179 Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV-----~s~d~~------  247 (526)
                      |.++...+.-|...          .+.+.+..+.+..=|    ..|-   .-=.+|.|++|.+     --.|.+      
T Consensus        33 ~~~v~~~~LPv~~~----------~~~~~l~~~i~~~~P----d~vi---~lG~a~gr~~i~lErvAiN~~d~~ipDn~G   95 (201)
T PRK13193         33 KEEVKGVILPVEYD----------KIEDMIVTKIREYKP----ILTL---GIGLAPGRAKITPEKIAINYKYSREGDNAG   95 (201)
T ss_pred             CCEEEEEEECCCHH----------HHHHHHHHHHHHCCC----CEEE---ECCCCCCCCCCCHHHHHHHHCCCCCCCCCC
T ss_conf             84589999687088----------899999999985199----6899---805678977110768510010067897788


Q ss_pred             CCCEEEEECCCC-------HHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEEC
Q ss_conf             881276554886-------217889986277826799559878999997628665424898756787999985
Q gi|254780788|r  248 IDPVGACVGMRG-------SRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVP  313 (526)
Q Consensus       248 iDpVGAcVG~rG-------sRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~  313 (526)
                      --|.+.||=..|       --++++++.|+..-|+. .+|.+.-.|+||.+.=--... .-....+...|-||
T Consensus        96 ~~p~~~~i~~~Gp~ay~stLPi~~i~~~l~~~Gipa-~vS~~AGtyvCN~~~Y~~L~~-~~~~~~~~gFIHvP  166 (201)
T PRK13193         96 KKYKGEKIDPLGQDGIFTNIPVEDLVDLLNENGIPA-ELSLSAGSYLCNNAMYIIIRE-ARKYNSLGGFIHVP  166 (201)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEECCCCCCHHHHHHHHHHHH-HCCCCCEEEEEECC
T ss_conf             987998637899751445789999999998679987-995886531416999999997-35699815899848


No 289
>PRK13194 pyrrolidone-carboxylate peptidase; Provisional
Probab=29.56  E-value=20  Score=15.00  Aligned_cols=52  Identities=17%  Similarity=0.149  Sum_probs=33.6

Q ss_pred             HHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEE-ECCCCCEEEEEEC
Q ss_conf             1788998627782679955987899999762866542489-8756787999985
Q gi|254780788|r  261 RVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVV-LDEDVGRIEVIVP  313 (526)
Q Consensus       261 Riq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~-~de~~~~~~v~v~  313 (526)
                      -++++++.|+...|+. .||.|.-.|+||.+.=--..... -....+...|-||
T Consensus       116 P~~~i~~~l~~~gipa-~vS~~AGtyvCN~~~Y~~L~~~~~~~~~~~~gFiHvP  168 (204)
T PRK13194        116 PTREIVEEMKENGIPA-VLSYTAGTYLCNFVMYLTLHHSATKGYPKMAGFIHVP  168 (204)
T ss_pred             CHHHHHHHHHHCCCCE-EEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECC
T ss_conf             9999999999769981-7847875216379999999999974999747899889


No 290
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=29.02  E-value=33  Score=13.38  Aligned_cols=40  Identities=23%  Similarity=0.446  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHH---HHHHHHHH
Q ss_conf             32111477750588887765305889999999---99999999
Q gi|254780788|r  379 EGFADVEELACVKISEIASIEGFDEETAVEIQ---GRAREYLE  418 (526)
Q Consensus       379 eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~---~rA~~~L~  418 (526)
                      .-|.|+..+..++.++|..+.|+....+..++   +.++.++.
T Consensus        52 ~~fg~L~~l~~a~~~el~~v~GiG~aka~~l~a~~El~~R~~~   94 (224)
T COG2003          52 QEFGSLAELLKASVEELSSVKGIGLAKAIQIKAAIELGKRILA   94 (224)
T ss_pred             HHCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             9732588887379999951788338899999999999999999


No 291
>PRK11281 potassium efflux protein KefA; Provisional
Probab=28.77  E-value=34  Score=13.35  Aligned_cols=33  Identities=9%  Similarity=0.212  Sum_probs=18.4

Q ss_pred             CHHHHHHHHHHHHHHCCCCHH--HHHHHHHHHHHH
Q ss_conf             889999999999862399999--999999999999
Q gi|254780788|r    5 NRLELLQIADAVAYEKSIDRD--VVLSVMADSIQK   37 (526)
Q Consensus         5 ~~~ell~vie~va~EK~I~~e--~i~~aie~Al~~   37 (526)
                      +..++-+=++.+.+.|..+.+  .++..++++|..
T Consensus        35 t~~~iq~~L~~l~~~~~~~~~~k~~~q~Lq~aL~~   69 (1107)
T PRK11281         35 TEADVQAQLDKLNKQKDLEAQDKLVQQDLEQTLAL   69 (1107)
T ss_pred             CHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             99999999998626779997789999999999999


No 292
>cd00412 pyrophosphatase Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers.
Probab=28.46  E-value=34  Score=13.31  Aligned_cols=67  Identities=19%  Similarity=0.172  Sum_probs=32.9

Q ss_pred             CCCEEEEEEEECCC--CCCCE----EEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEE--ECC
Q ss_conf             77503499994089--98812----7655488621788998627782679955987899999762866542489--875
Q gi|254780788|r  233 PGSRAKLAVFSSDS--SIDPV----GACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVV--LDE  303 (526)
Q Consensus       233 pG~RsKIAV~s~d~--~iDpV----GAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~--~de  303 (526)
                      .|+|.|.-+-....  .+|-+    ...=+.-|-==|..  +--|--+|++..++.|..  ..++-.|++..+.  +|+
T Consensus        11 ~gs~~KyE~d~~~g~~~~DR~l~~~~~yP~nYGfIP~T~--~~DgDPLDvlvl~~~p~~--~G~vv~~r~iG~l~m~D~   85 (155)
T cd00412          11 KGSNAKYEIDKETGPIKVDRFLYSSMGYPWNYGFIPQTL--EDDGDPLDVLVIGEEPLF--PGSVIRVRPLGVLKMIDE   85 (155)
T ss_pred             CCCCEEEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHH--CCCCCCEEEEEECCCCCC--CCCEEEEEEEEEEEECCC
T ss_conf             999857999168898889565167898986623012344--269997579985487538--930899999899996228


No 293
>TIGR02701 shell_carb_anhy carboxysome shell carbonic anhydrase; InterPro: IPR014074   This entry describes a carboxysome shell protein that proves to be a novel class, designated epsilon, of carbonic anhydrase. It tends to be encoded near genes for RuBisCo and other carboxysome shell proteins..
Probab=28.29  E-value=34  Score=13.35  Aligned_cols=112  Identities=16%  Similarity=0.301  Sum_probs=58.0

Q ss_pred             EEEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHHHHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             59997499883999999885176778753234899986288986473799850845620799999999999999999988
Q gi|254780788|r   49 IRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERD  128 (526)
Q Consensus        49 i~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A~~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~  128 (526)
                      |||+|=-..|++..||..   +.             .++               ..+-=-.+|+.|||.|.|.|-++.+.
T Consensus       263 irvH~PdadG~~~lyR~V---~~-------------~~L---------------Y~eT~~L~a~~Ar~~I~~~i~~a~~~  311 (463)
T TIGR02701       263 IRVHVPDADGKVNLYRYV---DT-------------EEL---------------YKETVGLTADEARQHIAERIDAANAK  311 (463)
T ss_pred             CEEECCCCCCCCCCCCCC---CH-------------HHH---------------HHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_conf             166122267855700035---76-------------899---------------98510688889999999999997626


Q ss_pred             H--------HHHHHHHHCCCEEEEEEEECCC-----CEEEE--EECCCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCC
Q ss_conf             7--------7999985208389999984057-----63899--957935874478748875115276699999761135
Q gi|254780788|r  129 R--------QYLEFKDKVGEIISGTVKRVEY-----GNVIV--DLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRRE  192 (526)
Q Consensus       129 ~--------i~~ef~~r~Geiv~G~V~r~e~-----~~iiV--dlg~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~  192 (526)
                      .        --+=-...++.++..-..++++     ++=|=  |+|..|=++---+-- .|.--.+-.+-||+--|+..
T Consensus       312 dgwa~G~Gvp~eGmr~lI~~L~~NNlSQI~YV~~~h~GrYpPnDiGHaERFI~VG~GF-~EVQ~RNL~YfahLDTVEEG  389 (463)
T TIGR02701       312 DGWAKGNGVPQEGMRRLIAKLLANNLSQIEYVVRSHGGRYPPNDIGHAERFISVGDGF-DEVQLRNLAYFAHLDTVEEG  389 (463)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEECCCCC-CEEEEEECEEEEEEEEEEEC
T ss_conf             8851256667645899999999863005888536787988823367464412016761-23464311024554457537


No 294
>PRK09970 xanthine dehydrogenase subunit XdhA; Provisional
Probab=28.24  E-value=34  Score=13.29  Aligned_cols=27  Identities=11%  Similarity=0.128  Sum_probs=11.3

Q ss_pred             CCCCCEEEE-EEEECCCCCCCEEEEECCCCH
Q ss_conf             167750349-999408998812765548862
Q gi|254780788|r  231 RDPGSRAKL-AVFSSDSSIDPVGACVGMRGS  260 (526)
Q Consensus       231 R~pG~RsKI-AV~s~d~~iDpVGAcVG~rGs  260 (526)
                      +.|..|... +|+||.+   |.||+=|..+.
T Consensus       338 ~i~~~~~~~~~v~TN~~---~~ga~RG~G~p  365 (762)
T PRK09970        338 PRCAYKYSSKTCYTNLP---SAGAMRGYGAP  365 (762)
T ss_pred             CCCEEEEEEEEEECCCC---CCCCCCCCCHH
T ss_conf             67607999899978999---87762169658


No 295
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=27.81  E-value=35  Score=13.23  Aligned_cols=70  Identities=17%  Similarity=0.277  Sum_probs=35.5

Q ss_pred             CCCCCCCEEEEECCHHH-HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECC
Q ss_conf             89864737998508456-207999999999---9999999998877999985208389999984057638999579
Q gi|254780788|r   89 PSIDIGGVVSDPLPPMD-FGRVAVQSAKQV---IIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGN  160 (526)
Q Consensus        89 ~~~~iGD~i~~~i~~~~-fgRiaAq~AKQv---I~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~  160 (526)
                      ...++||...+.|+|.+ ||-.--....++   .++...+.+--+++ ....--|. +.++|..++.+.|.||.+.
T Consensus        50 ~G~~~Gd~~~vtl~peeAYG~~de~lv~~vp~~~f~~~~~le~Gm~~-~~~~~~G~-~~~~V~eV~~~~VtvD~NH  123 (196)
T PRK10737         50 EGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGVDELQVGMRF-LAETDQGP-VPVEITAVEDDHVVVDGNH  123 (196)
T ss_pred             CCCCCCCEEEEEECHHHHCCCCCHHHEEEECHHHCCCCCCCCCCCEE-EECCCCCE-EEEEEEEECCCEEEEECCC
T ss_conf             79999977899978799168889799488258896876434567099-88079984-8899999779989995898


No 296
>cd01296 Imidazolone-5PH Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria, the enzyme is part of histidine utilization (hut) operon.
Probab=27.50  E-value=35  Score=13.20  Aligned_cols=13  Identities=8%  Similarity=0.335  Sum_probs=4.3

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999976677
Q gi|254780788|r  206 QFMVKLFHMEVPE  218 (526)
Q Consensus       206 ~~l~~Lf~~EVPE  218 (526)
                      .++..++..-.|.
T Consensus       159 ~~~~~~~~~~~~~  171 (371)
T cd01296         159 EYIDLVIEEVLPA  171 (371)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9999999999999


No 297
>COG1529 CoxL Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]
Probab=27.41  E-value=36  Score=13.18  Aligned_cols=17  Identities=18%  Similarity=0.180  Sum_probs=6.5

Q ss_pred             EEEEEECCCHHHHHHHH
Q ss_conf             28987159889999999
Q gi|254780788|r  196 PQVLLSRTHPQFMVKLF  212 (526)
Q Consensus       196 pqi~lSRt~p~~l~~Lf  212 (526)
                      .-+..|-.+|-.++..+
T Consensus       197 lt~~~~tQ~~~~~~~~l  213 (731)
T COG1529         197 LTVWASTQIPHRLRGML  213 (731)
T ss_pred             EEEEECCCCCHHHHHHH
T ss_conf             89997655523558899


No 298
>TIGR03194 4hydrxCoA_A 4-hydroxybenzoyl-CoA reductase, alpha subunit. This model represents the largest chain, alpha, of the enzyme 4-hydroxybenzoyl-CoA reductase. In species capable of degrading various aromatic compounds by way of benzoyl-CoA, this enzyme can convert 4-hydroxybenzoyl-CoA to benzoyl-CoA.
Probab=27.20  E-value=36  Score=13.16  Aligned_cols=28  Identities=21%  Similarity=0.366  Sum_probs=13.2

Q ss_pred             CCCCEEE-EEEEECCCCCCCEEEEECCCCHHH
Q ss_conf             6775034-999940899881276554886217
Q gi|254780788|r  232 DPGSRAK-LAVFSSDSSIDPVGACVGMRGSRV  262 (526)
Q Consensus       232 ~pG~RsK-IAV~s~d~~iDpVGAcVG~rGsRi  262 (526)
                      .|-.|.. .+|+||.+   |.||+=|.-+.-.
T Consensus       323 ipn~~~~~~~V~TN~~---p~ga~RG~G~pq~  351 (746)
T TIGR03194       323 IPAVKYDGYRVYTNTP---PCGAMRGHGTVDT  351 (746)
T ss_pred             CCEEEEEEEEEECCCC---CCCCEECCCCCCH
T ss_conf             6607999999956899---9751567886202


No 299
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3  is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel.  The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.  In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=27.16  E-value=36  Score=13.15  Aligned_cols=54  Identities=15%  Similarity=0.295  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHC
Q ss_conf             999999766777558087856631677503499994089988127655488621788998627
Q gi|254780788|r  208 MVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELR  270 (526)
Q Consensus       208 l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~  270 (526)
                      |.++|..|..+=.-+-+||+    ---.||+|.+++..|     |.++|-+|.||+....-|+
T Consensus         7 LnEfl~reL~~~GYsGvevr----~Tp~~teIiI~atrp-----~~ViG~kg~rIreLt~~lq   60 (81)
T cd02413           7 LNEFLTRELAEDGYSGVEVR----VTPTRTEIIIRATRT-----QNVLGEKGRRIRELTSLVQ   60 (81)
T ss_pred             HHHHHHHHHHHCCCCCEEEE----ECCCCEEEEEEECCC-----CEEECCCCEEHHHHHHHHH
T ss_conf             89999999986787735999----658861999995365-----1556358804999999999


No 300
>pfam09953 DUF2187 Uncharacterized protein conserved in bacteria (DUF2187). This domain, found in various hypothetical bacterial proteins, has no known function.
Probab=27.08  E-value=36  Score=13.14  Aligned_cols=18  Identities=44%  Similarity=0.696  Sum_probs=15.8

Q ss_pred             EEEEEEECCCCEEEEEEC
Q ss_conf             999998405763899957
Q gi|254780788|r  142 ISGTVKRVEYGNVIVDLG  159 (526)
Q Consensus       142 v~G~V~r~e~~~iiVdlg  159 (526)
                      +.|+|.++..+.+||||-
T Consensus        16 l~GiVeKvNeNSVIVdlT   33 (57)
T pfam09953        16 LQGIVEKVNENSVIVDLT   33 (57)
T ss_pred             CEEEEEEECCCCEEEEEE
T ss_conf             201001304783899988


No 301
>TIGR02704 carboxysome_B carboxysome peptide B; InterPro: IPR014077    This entry describes the carboxysome operon protein orfB (protein B of Thiobacillus denitrificans). It distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins are components of other types of shell such as the shell of the ethanolamine degradation organelle..
Probab=26.80  E-value=36  Score=13.11  Aligned_cols=32  Identities=34%  Similarity=0.559  Sum_probs=20.3

Q ss_pred             EEEEECCCCCEE-EEEEEECCCC-----CCCEEEEECC
Q ss_conf             856631677503-4999940899-----8812765548
Q gi|254780788|r  226 VKAVSRDPGSRA-KLAVFSSDSS-----IDPVGACVGM  257 (526)
Q Consensus       226 Ik~iaR~pG~Rs-KIAV~s~d~~-----iDpVGAcVG~  257 (526)
                      ..+--|.||... ..=|..+...     .|||||-.|.
T Consensus        10 Lv~TrR~pGL~~~sLRvL~~~~G~~~VA~DPvG~p~G~   47 (80)
T TIGR02704        10 LVCTRRIPGLKNASLRVLEDAKGKISVAVDPVGAPEGK   47 (80)
T ss_pred             EEEEECCCCCCCCEEEEECCCCCCEEEEECCCCCCCCC
T ss_conf             13420255655502565229996467854576789897


No 302
>KOG0196 consensus
Probab=25.81  E-value=38  Score=12.98  Aligned_cols=25  Identities=32%  Similarity=0.470  Sum_probs=15.9

Q ss_pred             HHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf             9999879847889653267752123
Q gi|254780788|r  449 VALGENGIKTMEDLAGCSVDDLLGW  473 (526)
Q Consensus       449 ~~L~e~gIktleDlAels~dEL~~~  473 (526)
                      ..+.++|+.|++++|.++.++|.-+
T Consensus       940 ~~F~~ag~~s~~~V~q~s~eDl~~~  964 (996)
T KOG0196         940 EHFAAAGYTSFEDVAQMSAEDLLRL  964 (996)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf             7777638541999976248889863


No 303
>KOG1921 consensus
Probab=25.78  E-value=38  Score=12.98  Aligned_cols=75  Identities=23%  Similarity=0.247  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHH---HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHCCCCCCH
Q ss_conf             678888773211147775058888776---5305889999999999999999999989877542--84356640779998
Q gi|254780788|r  371 IIAHLLVAEGFADVEELACVKISEIAS---IEGFDEETAVEIQGRAREYLEGIDITLQKKIREL--GVSEELCSIPGIDS  445 (526)
Q Consensus       371 ~iA~~LV~eGf~SiEeIa~a~~eeL~~---IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~--~~~e~L~~l~gl~~  445 (526)
                      .-...|-..|--|+|.|..++...|.+   --||-.-.|        .||..-+.-...+...-  ..-++|+.|+|+.+
T Consensus        98 ~Am~rL~~~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA--------~ylkkta~IL~d~f~gDIP~~v~dLlsLPGVGP  169 (286)
T KOG1921          98 AAMLRLKEYGGLTLEAVLKIDEPTLNELIYPVGFYTRKA--------KYLKKTAKILQDKFDGDIPDTVEDLLSLPGVGP  169 (286)
T ss_pred             HHHHHHHHHCCCCHHHHHCCCHHHHHHHHHHCCCHHHHH--------HHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCH
T ss_conf             999999985597899986167576876500012157888--------999999999998707997555998855899765


Q ss_pred             HHHHHHHH
Q ss_conf             99999998
Q gi|254780788|r  446 KIKVALGE  453 (526)
Q Consensus       446 ~~~~~L~e  453 (526)
                      .|+...-.
T Consensus       170 KMa~L~m~  177 (286)
T KOG1921         170 KMAHLTMQ  177 (286)
T ss_pred             HHHHHHHH
T ss_conf             99999999


No 304
>KOG3873 consensus
Probab=24.54  E-value=35  Score=13.23  Aligned_cols=32  Identities=22%  Similarity=0.267  Sum_probs=17.3

Q ss_pred             EEEECCCCHHHHHHHHHHC--CCCEEEEECCCCH
Q ss_conf             7655488621788998627--7826799559878
Q gi|254780788|r  252 GACVGMRGSRVQAVVTELR--DEKIDIVVWSPDS  283 (526)
Q Consensus       252 GAcVG~rGsRiq~I~~EL~--gEkIDii~ws~d~  283 (526)
                      ++|--+..+-..+--++=.  |-|||-+.++.+-
T Consensus       225 ~tcd~~~N~y~~aqk~~ddp~~~RiDYvl~k~~~  258 (422)
T KOG3873         225 NTCDSPLNCYTSAQKREDDPLGKRIDYVLVKPGD  258 (422)
T ss_pred             CCCCCCCHHHHHHHHCCCCCCCEEEEEEEECCCC
T ss_conf             7656751036678747887543156689973761


No 305
>PRK13680 hypothetical protein; Provisional
Probab=24.35  E-value=28  Score=13.90  Aligned_cols=45  Identities=20%  Similarity=0.395  Sum_probs=35.0

Q ss_pred             EEEEECCCCCCCEEEEECCCCHHHHHHHHH--HCCCCEEEEECCCCHHHH
Q ss_conf             999940899881276554886217889986--277826799559878999
Q gi|254780788|r  239 LAVFSSDSSIDPVGACVGMRGSRVQAVVTE--LRDEKIDIVVWSPDSATF  286 (526)
Q Consensus       239 IAV~s~d~~iDpVGAcVG~rGsRiq~I~~E--L~gEkIDii~ws~d~~~f  286 (526)
                      +++.+.+++..++.+|.|+.-+-|-+=++.  |+|   -|..|.+|...+
T Consensus        23 ~~a~~ee~r~akf~~C~gL~~~qIAaqVKrDflQN---Ri~rW~~DkK~l   69 (121)
T PRK13680         23 FSANAEESKSVKFPKCEGLDAAGIAASVKRDYQQN---RIVRWADDQKQV   69 (121)
T ss_pred             HHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC---CCCCHHHHHHHH
T ss_conf             76650576533445457989899999999999871---142205558760


No 306
>pfam03459 TOBE TOBE domain. The TOBE domain (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum and sulfate. Found in ABC transporters immediately after the ATPase domain.
Probab=24.28  E-value=40  Score=12.79  Aligned_cols=48  Identities=38%  Similarity=0.389  Sum_probs=34.7

Q ss_pred             CCEEEEEEEECCCCE----EEEEECC--CEEEEEHHHCCCCCCCCCCCEEEEEEEEE
Q ss_conf             838999998405763----8999579--35874478748875115276699999761
Q gi|254780788|r  139 GEIISGTVKRVEYGN----VIVDLGN--SDGVIRRDETISRENLRPGDRVKSYIYDV  189 (526)
Q Consensus       139 Geiv~G~V~r~e~~~----iiVdlg~--~ea~Lp~~e~ip~E~~~~Gdrika~i~~V  189 (526)
                      -..+.|+|..++.+.    +.+++|+  ..+.++++....   +++|+.+.+.++-.
T Consensus         4 rN~l~g~V~~ie~~g~~~~V~v~~~~~~l~a~it~~s~~~---L~~G~~V~~~ik~~   57 (61)
T pfam03459         4 RNQLPGTVDVVEPLGSETEVRVDLGGGELTARITRRSAEE---LAPGDEVYAGIKAE   57 (61)
T ss_pred             CCEEEEEEEEEEECCCEEEEEEEECCCEEEEEECHHHHHH---CCCCCEEEEEEEHH
T ss_conf             4388799999998997699999979938999984889965---59998899999822


No 307
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=24.24  E-value=40  Score=12.78  Aligned_cols=31  Identities=35%  Similarity=0.574  Sum_probs=21.2

Q ss_pred             HHCCCEEEEEEEECC---CCEEEEEECCCEEEEE
Q ss_conf             520838999998405---7638999579358744
Q gi|254780788|r  136 DKVGEIISGTVKRVE---YGNVIVDLGNSDGVIR  166 (526)
Q Consensus       136 ~r~Geiv~G~V~r~e---~~~iiVdlg~~ea~Lp  166 (526)
                      +-.|+.++|+|.++.   .|.+.+.|+....|.|
T Consensus       102 ~~dg~~~sG~V~sv~~~~~g~v~~~ldnG~~i~~  135 (146)
T PRK09618        102 HGDGEIVKGTVTSVKTGINGQVMVELDDGKWYVA  135 (146)
T ss_pred             CCCCCEEEEEEEEEEECCCCEEEEEECCCCEECH
T ss_conf             3899888778999998659849999769949857


No 308
>TIGR02592 cas_Cas5h CRISPR-associated protein Cas5, Hmari subtype; InterPro: IPR013421    This entry represents a CRISPR-associated protein unique to the hmari subtype of cas genes and CRISPR repeats, which is the only subtype present in Haloarcula marismortui ATCC 43049. The hmari type, though uncommon, is also found in the Aquificae, Thermotogae, Firmicutes, and Dictyoglomi..
Probab=24.20  E-value=24  Score=14.40  Aligned_cols=64  Identities=19%  Similarity=0.233  Sum_probs=45.4

Q ss_pred             HHHHHHHHH---CCEEEEEECC-CHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             899999861---6745785522-001101001221000111225888467888877321114777505
Q gi|254780788|r  327 NVRLASQLT---GWTIDIITEE-EDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACV  390 (526)
Q Consensus       327 NvrLas~Lt---g~~idi~~~~-~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a  390 (526)
                      |.+.-.++.   .|+|+|.-++ +.-+.-..-+......|+-.||+.|-+|.+=...-|+..+.++..
T Consensus       114 r~~~~~~~L~dP~Yrifv~~~~s~~~~~L~~~L~~~~~~y~PyLG~~~~~A~l~y~~~~~~~~~~~~~  181 (268)
T TIGR02592       114 RLRVNLELLKDPAYRIFVSWEDSEKYKELKDRLENSKSIYTPYLGVSEHIANLDYVGKLEAEEKLDDT  181 (268)
T ss_pred             CCEEEHHHHCCCCEEEEEEECCCCCHHHHHHHHHCCCEEEECCCCHHHHHHCCCCCCEEEEEECCCCC
T ss_conf             61220454249653798853668887899999871871242146634553225500024342045677


No 309
>pfam08414 NADPH_Ox Respiratory burst NADPH oxidase. This domain is found in plant proteins such as respiratory burst NADPH oxidase proteins which produce reactive oxygen species as a defence mechanism. It tends to occur to the N-terminus of an EF-hand (pfam00036), which suggests a direct regulatory effect of Ca2+ on the activity of the NADPH oxidase in plants.
Probab=24.12  E-value=19  Score=15.11  Aligned_cols=16  Identities=19%  Similarity=0.428  Sum_probs=7.5

Q ss_pred             HHHHCCCCCHHHHHHC
Q ss_conf             9998798478896532
Q gi|254780788|r  450 ALGENGIKTMEDLAGC  465 (526)
Q Consensus       450 ~L~e~gIktleDlAel  465 (526)
                      .|+.+|....++|++|
T Consensus        34 ~la~dG~L~rs~Fg~C   49 (96)
T pfam08414        34 KLAVDGYLPRSKFGEC   49 (96)
T ss_pred             HHHHCCCCCHHHHHHH
T ss_conf             9874376128888674


No 310
>TIGR01522 ATPase-IIA2_Ca calcium-transporting P-type ATPase, PMR1-type; InterPro: IPR006413   This family describes the P-type ATPase responsible for translocating calcium ions across the golgi membrane of fungi and animals , , and is of particular importance in the sarcoplasmic reticulum of skeletal and cardiac muscle in vertebrates . The calcium P-type ATPases have been characterised as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump  represented by IPR006408 from INTERPRO. ; GO: 0005388 calcium-transporting ATPase activity, 0006816 calcium ion transport, 0016021 integral to membrane.
Probab=23.90  E-value=37  Score=13.03  Aligned_cols=34  Identities=24%  Similarity=0.392  Sum_probs=24.7

Q ss_pred             EEEECCCEEEEEHHHCCCCCC--CCCCCEEEEEEEEE
Q ss_conf             999579358744787488751--15276699999761
Q gi|254780788|r  155 IVDLGNSDGVIRRDETISREN--LRPGDRVKSYIYDV  189 (526)
Q Consensus       155 iVdlg~~ea~Lp~~e~ip~E~--~~~Gdrika~i~~V  189 (526)
                      .|--|+.+.+|- +..+||+-  |++||||=|=+.=|
T Consensus       121 ~~R~G~~~hvlA-s~LVPGDlV~l~vGDRvPADlRiv  156 (856)
T TIGR01522       121 LIRAGKEEHVLA-STLVPGDLVILSVGDRVPADLRIV  156 (856)
T ss_pred             EEECCCCCEEEE-ECCCCCCEEEEEECCCCCCCCEEE
T ss_conf             473588430575-107898679986278563140256


No 311
>TIGR00350 lytR_cpsA_psr cell envelope-related function transcriptional attenuator common domain; InterPro: IPR004474 This entry describes a domain of unknown function that is found in the predicted extracellular domain of a number of putative membrane-bound proteins. One of these is protein psr, described as a penicillin binding protein 5 (PDP-5) synthesis repressor. Another is Bacillus subtilis LytR, described as a transcriptional attenuator of itself and the LytABC operon, where LytC is N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a putative regulatory protein involved in exocellular polysaccharide biosynthesis. These proteins share the property of having a short putative N-terminal cytoplasmic domain and transmembrane domain forming a signal-anchor..
Probab=23.58  E-value=41  Score=12.70  Aligned_cols=21  Identities=29%  Similarity=0.452  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             45620799999999999999999
Q gi|254780788|r  103 PMDFGRVAVQSAKQVIIQKVREA  125 (526)
Q Consensus       103 ~~~fgRiaAq~AKQvI~Qkirea  125 (526)
                      ..|||||--|  ||++.+-++.+
T Consensus       160 ~gD~GRi~rQ--~~~l~aL~~~~  180 (182)
T TIGR00350       160 RGDYGRIDRQ--QQVLSALLERM  180 (182)
T ss_pred             CCCHHHHHHH--HHHHHHHHHHH
T ss_conf             8833267899--99999999986


No 312
>PRK13197 pyrrolidone-carboxylate peptidase; Provisional
Probab=23.57  E-value=27  Score=14.11  Aligned_cols=103  Identities=17%  Similarity=0.221  Sum_probs=58.5

Q ss_pred             CHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEE-----ECCCC------CCCEEEEECCCCH-------HHHHH
Q ss_conf             889999999976677755808785663167750349999-----40899------8812765548862-------17889
Q gi|254780788|r  204 HPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVF-----SSDSS------IDPVGACVGMRGS-------RVQAV  265 (526)
Q Consensus       204 ~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~-----s~d~~------iDpVGAcVG~rGs-------Riq~I  265 (526)
                      +...+.++++..-|.+    |--.+   .+|.|++|.+-     -.|.+      --|++.||=..|.       =++++
T Consensus        49 ~~~~l~~~l~~~~Pd~----Vl~lG---~a~gr~~i~lErvAiN~~d~~ipDn~G~~p~~~~i~~~Gp~ay~stLPv~~i  121 (215)
T PRK13197         49 SLDVLKEAIEEVQPDA----VIAIG---QAGGRADITPERVAINIDDARIPDNEGNQPIDEPIVEDGPAAYFSTLPIKAM  121 (215)
T ss_pred             HHHHHHHHHHHHCCCE----EEEEC---CCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCHHHH
T ss_conf             8999999999879988----99924---5689871002667872454756787899869974138997312068999999


Q ss_pred             HHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEE-CCCCCEEEEEECC
Q ss_conf             986277826799559878999997628665424898-7567879999853
Q gi|254780788|r  266 VTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVL-DEDVGRIEVIVPK  314 (526)
Q Consensus       266 ~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~-de~~~~~~v~v~~  314 (526)
                      ++.|+.+-|+. .||.|--.|+||.+.=--...+.- ....+...|-||-
T Consensus       122 ~~~l~~~gipa-~iS~~AGtYvCN~v~Y~~l~~~~~~~~~~~agFIHvP~  170 (215)
T PRK13197        122 VKAIREAGIPA-SVSNTAGTFVCNHVMYGLLHLLDKHYPNIRGGFIHIPY  170 (215)
T ss_pred             HHHHHHCCCCC-EEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf             99999779982-68578752121699999999999639997068997899


No 313
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=23.52  E-value=42  Score=12.69  Aligned_cols=97  Identities=18%  Similarity=0.144  Sum_probs=35.8

Q ss_pred             EEEEEEEECCCCE----EEEEECC----CEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHH--HHHH
Q ss_conf             8999998405763----8999579----3587447874887511527669999976113587028987159889--9999
Q gi|254780788|r  141 IISGTVKRVEYGN----VIVDLGN----SDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQ--FMVK  210 (526)
Q Consensus       141 iv~G~V~r~e~~~----iiVdlg~----~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~--~l~~  210 (526)
                      -..|+|..+..+.    +.+.+..    .-+.+. .+-..+=.+.+|..+-|+|+       -|-|+|+...+.  =-+-
T Consensus       130 qf~G~V~~I~~g~Vn~eV~l~l~~G~~~I~A~IT-~~S~~~LgL~~G~~v~AlIK-------As~V~L~~~~~~~~SArN  201 (262)
T PRK10676        130 QWFGTITARDHDQVQQHVDVLLADGKTRLKVAIT-AQSGERLGLDEGKEVLILLK-------APWVGITQDPAVAQAADN  201 (262)
T ss_pred             CCCCEEEEEEECCCCEEEEEEECCCCCEEEEEEE-HHHHHHCCCCCCCEEEEEEE-------CCEEEEECCCCCCCCCCC
T ss_conf             0164479988758612999998799848999973-79998649889999999997-------476799738766655543


Q ss_pred             HHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECC
Q ss_conf             99976677755808785663167750349999408
Q gi|254780788|r  211 LFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSD  245 (526)
Q Consensus       211 Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d  245 (526)
                      .|.=.|-.|.+|-+.--=....||..+=.|+.+++
T Consensus       202 ~l~GtV~~I~~G~vnaEV~l~l~~G~tl~A~it~~  236 (262)
T PRK10676        202 QLPGTISHIERGAEQCEVLMALPDGQTLCATVPNN  236 (262)
T ss_pred             EEEEEEEEEEECCCCEEEEEEECCCCEEEEEECCH
T ss_conf             67689999987784159999958999999997677


No 314
>TIGR03196 pucD xanthine dehydrogenase D subunit. This gene has been characterized in B. subtilis as the molybdopterin binding-subunit of xanthine dehydrogenase (pucD), acting in conjunction with pucC, the FAD-binding subunit and pucE, the FeS-binding subunit. The more common XDH complex (GenProp0640) includes the xdhB gene which is related to pucD. It appears that most of the relatives of pucD outside of this narrow clade are involved in other processes as they are found in unrelated genomic contexts, contain the more common XDH complex and/or do not appear to process purines to allantoin.
Probab=23.32  E-value=42  Score=12.66  Aligned_cols=22  Identities=14%  Similarity=0.049  Sum_probs=8.7

Q ss_pred             CEEEEEHHHCCCCCCCCCCCEE
Q ss_conf             3587447874887511527669
Q gi|254780788|r  161 SDGVIRRDETISRENLRPGDRV  182 (526)
Q Consensus       161 ~ea~Lp~~e~ip~E~~~~Gdri  182 (526)
                      +.-++.|.|..-.-.+|+.-++
T Consensus       258 Vk~~~~R~e~~~~~~~r~~~~~  279 (768)
T TIGR03196       258 VKIAQDRKESFLGGIHRHPAKI  279 (768)
T ss_pred             EEEEEEHHHCCCCCCCCCCEEE
T ss_conf             7999511110044578675599


No 315
>pfam03293 Pox_RNA_pol Poxvirus DNA-directed RNA polymerase, 18 kD subunit.
Probab=23.07  E-value=42  Score=12.63  Aligned_cols=64  Identities=23%  Similarity=0.342  Sum_probs=33.0

Q ss_pred             HCCCEEEEEEEECCCCEEEEEECCCEEEEEHHH------------CCCCCCCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf             208389999984057638999579358744787------------4887511527669999976113587028987
Q gi|254780788|r  137 KVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDE------------TISRENLRPGDRVKSYIYDVRREQRGPQVLL  200 (526)
Q Consensus       137 r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e------------~ip~E~~~~Gdrika~i~~V~~~~rgpqi~l  200 (526)
                      |+|++|+|+..-.+-.++.|.-|..-.-|.|+.            .-.|-.|..|+++.+.+++-+......-+||
T Consensus        80 k~GDvV~GTLnIedESnitV~cgDLiCkl~rdsGtVSf~dsKYCfirng~vY~ngs~Vsv~LkEaq~g~~S~FvFl  155 (160)
T pfam03293        80 KVGDVVSGTLNIEDESNITVQCGDLICKLSRDSGTVSFNDSKYCFIRNGKVYDNGSTVSVVLKEAQSGMESNFVFL  155 (160)
T ss_pred             EECCEEEEEEEECCCCCEEEECCCEEEEEECCCCEEEECCCEEEEEECCEEECCCCEEEEEEHHHHCCCCCEEEEE
T ss_conf             6087889899841567528972768999724686178658607999788996289889999547347864148999


No 316
>pfam07431 DUF1512 Protein of unknown function (DUF1512). This family consists of several archaeal proteins of around 370 residues in length. The function of this family is unknown.
Probab=23.03  E-value=42  Score=12.62  Aligned_cols=63  Identities=27%  Similarity=0.338  Sum_probs=37.0

Q ss_pred             EEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCC
Q ss_conf             99994089988127655488621788998627782679955987899999762866542489875678799998534221
Q gi|254780788|r  239 LAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLS  318 (526)
Q Consensus       239 IAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls  318 (526)
                      +-|++.-|     |+.||.-|.-++.|+++|+| |.|.|.--|--       |         --|-+++..|.   +-.-
T Consensus       220 ~v~KAeGP-----gstvGrpg~ave~iv~~~~~-k~~~IItiDAA-------l---------KLEGE~tg~iA---eG~G  274 (356)
T pfam07431       220 YIVKAEGP-----GSTVGRPGEAVENVVERLDG-KVSRIITVDAA-------L---------KLEGEKTGAVA---EGVG  274 (356)
T ss_pred             EEEECCCC-----CCCCCCHHHHHHHHHHHHCC-CCCEEEEEEHH-------H---------HCCCCCCCCHH---CCCC
T ss_conf             99964589-----88789857999999997068-97689996055-------5---------51787562132---0556


Q ss_pred             CCCCCCHH
Q ss_conf             10254427
Q gi|254780788|r  319 LAIGRRGQ  326 (526)
Q Consensus       319 ~AIGk~Gq  326 (526)
                      .|||--|.
T Consensus       275 ~AiG~~G~  282 (356)
T pfam07431       275 VAMGDPGP  282 (356)
T ss_pred             CCCCCCCC
T ss_conf             01378871


No 317
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=22.99  E-value=43  Score=12.62  Aligned_cols=12  Identities=17%  Similarity=0.191  Sum_probs=4.3

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780788|r  407 VEIQGRAREYLE  418 (526)
Q Consensus       407 ~eL~~rA~~~L~  418 (526)
                      +.+...|+.-+.
T Consensus       114 e~i~~~A~~~Ie  125 (174)
T PRK07352        114 ARLKQTAAADLS  125 (174)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 318
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=22.82  E-value=43  Score=12.59  Aligned_cols=40  Identities=23%  Similarity=0.401  Sum_probs=23.8

Q ss_pred             EEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCC
Q ss_conf             7999985342211025442789999986167457855220
Q gi|254780788|r  307 RIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE  346 (526)
Q Consensus       307 ~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~  346 (526)
                      +..|.+|++-++.-||+.|.-.|+--+.||-++.+-+.+-
T Consensus         9 ~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~   48 (194)
T COG1094           9 SEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTG   48 (194)
T ss_pred             EEEEECCCHHHEEEECCCCCCHHHHHHHCCEEEEEECCCC
T ss_conf             0455457045101225663105898861575899977877


No 319
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=22.68  E-value=43  Score=12.57  Aligned_cols=23  Identities=9%  Similarity=0.156  Sum_probs=13.6

Q ss_pred             HCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             23999999999999999999961
Q gi|254780788|r   19 EKSIDRDVVLSVMADSIQKAARS   41 (526)
Q Consensus        19 EK~I~~e~i~~aie~Al~~a~kK   41 (526)
                      .+|-+.|++|++=.-.|.+|.-|
T Consensus        33 nRGYe~eDlFQIGciGLvKAidk   55 (231)
T TIGR02885        33 NRGYEYEDLFQIGCIGLVKAIDK   55 (231)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             06887000022211556665542


No 320
>CHL00127 rpl11 ribosomal protein L11; Validated
Probab=21.52  E-value=42  Score=12.63  Aligned_cols=35  Identities=26%  Similarity=0.458  Sum_probs=25.6

Q ss_pred             EEEEEECCCCC-CCEEEEECCCCHHHHHHHHHHCCC
Q ss_conf             49999408998-812765548862178899862778
Q gi|254780788|r  238 KLAVFSSDSSI-DPVGACVGMRGSRVQAVVTELRDE  272 (526)
Q Consensus       238 KIAV~s~d~~i-DpVGAcVG~rGsRiq~I~~EL~gE  272 (526)
                      |+-|.+-..+- -|+|.-.|++|.-+...+++.|..
T Consensus        10 kl~v~aG~A~p~PPvGpaLG~~GvNi~~Fck~fN~~   45 (140)
T CHL00127         10 KLALPAGKATPAPPVGPALGQHGVNINLFCKEYNAR   45 (140)
T ss_pred             EEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             998516777899998631134697999999999998


No 321
>pfam01330 RuvA_N RuvA N terminal domain. The N terminal domain of RuvA has an OB-fold structure. This domain forms the RuvA tetramer contacts.
Probab=21.28  E-value=46  Score=12.38  Aligned_cols=50  Identities=20%  Similarity=0.301  Sum_probs=36.4

Q ss_pred             EEEEEEEECCCCEEEEEECCC--EEEEEHHHCCCCCCCCCCCEEEEEEEEECCCC
Q ss_conf             899999840576389995793--58744787488751152766999997611358
Q gi|254780788|r  141 IISGTVKRVEYGNVIVDLGNS--DGVIRRDETISRENLRPGDRVKSYIYDVRREQ  193 (526)
Q Consensus       141 iv~G~V~r~e~~~iiVdlg~~--ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~  193 (526)
                      -+.|+|...+.+.+++|.|++  +-.+|.+..   ..+..|..++.|..-+-++.
T Consensus         4 ~l~G~i~~~~~~~ivi~~~GvGY~v~is~~~~---~~l~~~~~v~l~t~~~vRED   55 (61)
T pfam01330         4 YLRGKVTEVGPDYIVVEVNGVGYEINVSARTL---AELPEGGEVKLFTHLIVRED   55 (61)
T ss_pred             EEEEEEEEECCCEEEEEECCEEEEEEECHHHH---HHCCCCCEEEEEEEEEEEEC
T ss_conf             99999999729999999678799999888999---76799988999999999016


No 322
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea.  CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA.  CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and  the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=21.15  E-value=46  Score=12.36  Aligned_cols=53  Identities=30%  Similarity=0.449  Sum_probs=36.5

Q ss_pred             EEEEEEECC--CCE--EEEEECCCEEEEEHHHCCCC--CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf             999998405--763--89995793587447874887--511527669999976113587028
Q gi|254780788|r  142 ISGTVKRVE--YGN--VIVDLGNSDGVIRRDETISR--ENLRPGDRVKSYIYDVRREQRGPQ  197 (526)
Q Consensus       142 v~G~V~r~e--~~~--iiVdlg~~ea~Lp~~e~ip~--E~~~~Gdrika~i~~V~~~~rgpq  197 (526)
                      ++|+|+..+  +|+  |..+-++-+-++..+.....  ..+++|++|..-+..-   .+||+
T Consensus         1 ~~G~Vk~f~~~kGfGFI~~~~~~~diF~H~s~~~~~~~~~l~~G~~V~f~~~~~---~~g~~   59 (65)
T cd04458           1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG---DKGPQ   59 (65)
T ss_pred             CEEEEEEEECCCCEEEEEECCCCCCEEEEHHHHCCCCCCCCCCCCEEEEEEEEC---CCCCE
T ss_conf             938999997999969999579982299995892434697479898999999989---89976


No 323
>pfam09883 DUF2110 Uncharacterized protein conserved in archaea (DUF2110). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=21.13  E-value=46  Score=12.36  Aligned_cols=36  Identities=22%  Similarity=0.222  Sum_probs=28.5

Q ss_pred             CCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCC
Q ss_conf             083899999840576389995793587447874887
Q gi|254780788|r  138 VGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISR  173 (526)
Q Consensus       138 ~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~  173 (526)
                      .|++..|+....+...+.++.++.-.-.|.++.+|-
T Consensus        75 ~Ge~y~G~l~~~~e~G~~~~v~G~~~~ip~deL~~L  110 (226)
T pfam09883        75 EGEVYVGTLISWDEDGYGLDVDGVTVPIPADELLPL  110 (226)
T ss_pred             CCCEEEEEEEECCCCCEEEEECCEECCCCHHHHCCC
T ss_conf             887789998760664169986573646717885345


No 324
>pfam00029 Connexin Connexin.
Probab=21.11  E-value=25  Score=14.37  Aligned_cols=17  Identities=41%  Similarity=0.952  Sum_probs=14.1

Q ss_pred             ECCCCHHHHHHHHCCCC
Q ss_conf             55987899999762866
Q gi|254780788|r  278 VWSPDSATFVINALRPA  294 (526)
Q Consensus       278 ~ws~d~~~fi~nAl~PA  294 (526)
                      .|+|+...|++|.++|.
T Consensus        42 V~~DEQs~F~CNT~QPG   58 (107)
T pfam00029        42 VWGDEQSDFVCNTLQPG   58 (107)
T ss_pred             CCCCHHHHCCCCCCCCC
T ss_conf             32421442644799998


No 325
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=20.93  E-value=47  Score=12.33  Aligned_cols=85  Identities=20%  Similarity=0.325  Sum_probs=53.0

Q ss_pred             HHCCCEE-----EEEEEECCCC-EEEEEECCCEEEEEHHHCCCCC--CCCCCCEEEEEEEEECCCCCEEEEEEECCCHHH
Q ss_conf             5208389-----9999840576-3899957935874478748875--115276699999761135870289871598899
Q gi|254780788|r  136 DKVGEII-----SGTVKRVEYG-NVIVDLGNSDGVIRRDETISRE--NLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQF  207 (526)
Q Consensus       136 ~r~Geiv-----~G~V~r~e~~-~iiVdlg~~ea~Lp~~e~ip~E--~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~  207 (526)
                      =|+|+-|     +|+|+|+.-+ ..|-+-.+.+-++|.+..|.+-  |+..++.+.-+...|--.-        -|+|+.
T Consensus       661 vkvGD~It~g~~~G~V~~I~vRAT~I~~fd~~~vIVPNs~fI~~qV~NWs~~~~~~R~~i~v~vay--------~sD~~~  732 (835)
T COG3264         661 VKVGDTVTIGTVSGTVRKISVRATTIRTFDRKEVIVPNSAFITEQVINWSLRDTTTRLVIPVGVAY--------GSDPEL  732 (835)
T ss_pred             CCCCCEEEECCCEEEEEEEEEEEEEEEECCCCEEEECCHHHHHHHEEEEECCCCEEEEEEEECCCC--------CCCHHH
T ss_conf             356777998782489999875579998278875970557887644023102572389999830567--------898899


Q ss_pred             HHHHHHHHHHHHHCCEEEEEEEECCCCC
Q ss_conf             9999997667775580878566316775
Q gi|254780788|r  208 MVKLFHMEVPEIYNGIVQVKAVSRDPGS  235 (526)
Q Consensus       208 l~~Lf~~EVPEI~~G~ieIk~iaR~pG~  235 (526)
                      |++++-+    ++.+.   ..|-++|--
T Consensus       733 V~~~Ll~----~A~~~---p~Vl~~P~P  753 (835)
T COG3264         733 VRELLLE----AAREH---PRVLKDPAP  753 (835)
T ss_pred             HHHHHHH----HHHHC---CCCCCCCCC
T ss_conf             9999999----99739---876599997


No 326
>COG1255 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.93  E-value=47  Score=12.33  Aligned_cols=66  Identities=20%  Similarity=0.216  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCCCCCCCEEC
Q ss_conf             999999986239999999999-99999999961368745359997499883999999885176778753234
Q gi|254780788|r   10 LQIADAVAYEKSIDRDVVLSV-MADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQIS   80 (526)
Q Consensus        10 l~vie~va~EK~I~~e~i~~a-ie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedved~~~eI~   80 (526)
                      +++++.+++|.+=.|=+=+.+ .--.+ +.+-+++|-+- +-+.|+++++.   .-.+-||+|+.+|...|.
T Consensus         2 ~e~a~~iAre~~~gkVvEVGiG~~~~V-A~~L~e~g~dv-~atDI~~~~a~---~g~~~v~DDitnP~~~iY   68 (129)
T COG1255           2 IEVAEYIARENARGKVVEVGIGFFLDV-AKRLAERGFDV-LATDINEKTAP---EGLRFVVDDITNPNISIY   68 (129)
T ss_pred             CCHHHHHHHHHCCCCEEEECCCHHHHH-HHHHHHCCCCE-EEEECCCCCCC---CCCEEEECCCCCCCHHHH
T ss_conf             418999998705883799814117999-99999748868-99852301376---553388724779647776


No 327
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=20.91  E-value=47  Score=12.33  Aligned_cols=15  Identities=13%  Similarity=-0.004  Sum_probs=6.1

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999999
Q gi|254780788|r  406 AVEIQGRAREYLEGI  420 (526)
Q Consensus       406 a~eL~~rA~~~L~~~  420 (526)
                      +..+.++|+.-+...
T Consensus       110 a~~i~~~A~~~Ie~e  124 (173)
T PRK13460        110 VKAQKDQAVKEIELA  124 (173)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999999999999999


No 328
>TIGR02888 spore_YlmC_YmxH sporulation protein, YlmC/YmxH family; InterPro: IPR014238   Proteins in this entry belong to the broader family of PRC-barrel domain proteins, but are found only in endospore-forming bacteria within the Firmicutes (low-GC, Gram-positive bacteria). Most species encode two of these proteins, though their function is unknown. In Bacillus subtilis, which encodes YlmC and YmxH, YmxH is strongly induced by the mother cell-specific sigma-E factor ..
Probab=20.65  E-value=47  Score=12.29  Aligned_cols=46  Identities=20%  Similarity=0.358  Sum_probs=29.4

Q ss_pred             HCCCCCCCEEEEECCCCCEEEEEEEEEEECC--------CCCCCCEECHHHHHHHCCC
Q ss_conf             1368745359997499883999999885176--------7787532348999862889
Q gi|254780788|r   41 SLYGTMSDIRVEINPETGDISLFRLLEVVEE--------VENYTCQISLKVARDRDPS   90 (526)
Q Consensus        41 K~~~~~~~i~V~iD~~tG~i~i~~~~~VVed--------ved~~~eI~l~~A~~~~~~   90 (526)
                      ++||.=.+..++||.++|.+..+    |++.        -..+..+|+=+.-+++-++
T Consensus        17 ~rLG~~~~~D~~ID~~~G~I~~l----Iip~~g~~~glf~~~~~~~IpW~~IkKIG~d   70 (76)
T TIGR02888        17 KRLGLIGNIDLEIDEEDGKIESL----IIPGKGKKFGLFSKGEEIEIPWKAIKKIGSD   70 (76)
T ss_pred             EEEEEECCCCEEEECCCCEEEEE----EECCCCEEEECEECCCCEEECCHHCEEECCE
T ss_conf             38873348457980899959898----8718970522100687548663002780790


No 329
>TIGR01578 MiaB-like-B MiaB-like tRNA modifying enzyme, archaeal-type; InterPro: IPR006466   This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see IPR006463 from INTERPRO). Sequence alignments suggest that this family of sequences perform the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade represents a subfamily that spans the archaea and eukaryotes. The only archaeal miaB-like genes are in this group of sequences , , ..
Probab=20.52  E-value=47  Score=12.27  Aligned_cols=161  Identities=17%  Similarity=0.222  Sum_probs=101.8

Q ss_pred             CCCCCCCCEECHHHHHHHCCCC-CCCCEEEEECC-HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHCCCEEEEEE
Q ss_conf             7677875323489998628898-64737998508-456207999999999999999999-88779999852083899999
Q gi|254780788|r   70 EEVENYTCQISLKVARDRDPSI-DIGGVVSDPLP-PMDFGRVAVQSAKQVIIQKVREAE-RDRQYLEFKDKVGEIISGTV  146 (526)
Q Consensus        70 edved~~~eI~l~~A~~~~~~~-~iGD~i~~~i~-~~~fgRiaAq~AKQvI~QkireaE-r~~i~~ef~~r~Geiv~G~V  146 (526)
                      ....|...|=+++--+++.|+. -+--|-.=|.+ ..+|-++-++.-|+-    =+... -=.-|+-|.+|+|+|-+-.|
T Consensus       309 p~EtdddFE~T~~l~~k~RPe~In~~~fS~RpgT~Aa~~~~~~~~i~K~R----s~~l~dlfysyePyadrvGeiytvlv  384 (487)
T TIGR01578       309 PTETDDDFEETMELLRKYRPEKINVTKFSPRPGTEAAKMKRLDTNIKKKR----SKALTDLFYSYEPYADRVGEIYTVLV  384 (487)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHCCCCCCEEHHH----HHHHHHHHHHCCCCCCCCCCEEEEEE
T ss_conf             89883558999999998289834530246888871133058996201166----67777654202630012241577877


Q ss_pred             EECCCCEE-EEEECCCEEEEEHHHCCCCCC--CCCCCEEEEEEEE-ECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCC
Q ss_conf             84057638-999579358744787488751--1527669999976-1135870289871598899999999766777558
Q gi|254780788|r  147 KRVEYGNV-IVDLGNSDGVIRRDETISREN--LRPGDRVKSYIYD-VRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNG  222 (526)
Q Consensus       147 ~r~e~~~i-iVdlg~~ea~Lp~~e~ip~E~--~~~Gdrika~i~~-V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G  222 (526)
                      ..+..+-+ ||-.++.      .+||..+.  =-.|.|.+++|.+ -+.+..|--+.-.+..-.   ---.+|.|.   -
T Consensus       385 tevshdklhyvGhnk~------~~~~~~~~~~~~iG~~~~Vlv~~asKy~g~G~~~~~~d~~~r---CaknqelPn---~  452 (487)
T TIGR01578       385 TEVSHDKLHYVGHNKL------KEEVLLEKKENLIGKREKVLVTEASKYEGKGDSLKDEDDAYR---CAKNQELPN---R  452 (487)
T ss_pred             EEEECCCEEECCHHHH------HHHHHCCHHHCCCCCCEEEEEEECCCCCCCCCEECCCHHHHH---HHHCCCCCC---C
T ss_conf             5310131011140567------887510001105640104899731210242431446414565---331056898---5


Q ss_pred             EEEEEEEE---CCCCCEEEEEEEECCC
Q ss_conf             08785663---1677503499994089
Q gi|254780788|r  223 IVQVKAVS---RDPGSRAKLAVFSSDS  246 (526)
Q Consensus       223 ~ieIk~ia---R~pG~RsKIAV~s~d~  246 (526)
                      -|.|.+--   |.||.=++|++.+..+
T Consensus       453 ~Vv~~~~~dhGl~~gef~~V~iT~~~~  479 (487)
T TIGR01578       453 QVVISEKTDHGLEPGEFAKVEITGAKT  479 (487)
T ss_pred             CEEEECCCCCCCCCCCEEEEEEECCCE
T ss_conf             458724866566443301278962310


No 330
>TIGR01204 bioW 6-carboxyhexanoate--CoA ligase; InterPro: IPR005499 This family contains the enzyme 6-carboxyhexanoate--CoA ligase 6.2.1.14 from EC. This enzyme is involved in the first step of biotin synthesis, where it converts pimelate into pimeloyl-CoA . The enzyme requires magnesium as a cofactor and forms a homodimer .; GO: 0009102 biotin biosynthetic process.
Probab=20.46  E-value=33  Score=13.40  Aligned_cols=38  Identities=13%  Similarity=0.384  Sum_probs=18.9

Q ss_pred             HCCCCHHHHHHHHHHHHHHHHHHCCCCCCC-EEEEECCCC
Q ss_conf             239999999999999999999613687453-599974998
Q gi|254780788|r   19 EKSIDRDVVLSVMADSIQKAARSLYGTMSD-IRVEINPET   57 (526)
Q Consensus        19 EK~I~~e~i~~aie~Al~~a~kK~~~~~~~-i~V~iD~~t   57 (526)
                      |+=+++..+-.++++-|.++-...-|. .| +.|.+-.-+
T Consensus        11 ERi~~~~e~e~~Vk~LLnk~~~HSRG~-~DF~qi~vEkv~   49 (238)
T TIGR01204        11 ERIVKKEELETIVKELLNKAKSHSRGE-ADFMQIKVEKVK   49 (238)
T ss_pred             EECCCHHHHHHHHHHHHHCCCCCCCCC-CCEEEEEEEEEE
T ss_conf             003655568899999873223467898-653567899870


No 331
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=20.27  E-value=45  Score=12.47  Aligned_cols=25  Identities=28%  Similarity=0.356  Sum_probs=14.8

Q ss_pred             EEECCCCCEEEEEECCCCCCCCCCCCHHHHHH
Q ss_conf             89875678799998534221102544278999
Q gi|254780788|r  299 VVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRL  330 (526)
Q Consensus       299 v~~de~~~~~~v~v~~~qls~AIGk~GqNvrL  330 (526)
                      |.+++..-++++.       .|=|.+||||.=
T Consensus       217 i~i~~~dl~idt~-------RssGaGGQhVNk  241 (360)
T PRK00591        217 VEINPKDLRIDTF-------RSSGAGGQHVNT  241 (360)
T ss_pred             CCCCCCCEEEEEE-------ECCCCCCCCCCC
T ss_conf             2568540258875-------357999887676


No 332
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.15  E-value=48  Score=12.22  Aligned_cols=87  Identities=26%  Similarity=0.260  Sum_probs=50.8

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCC
Q ss_conf             88776530588999999999999999999998987754284356640779998999999987984788965326775212
Q gi|254780788|r  393 SEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLG  472 (526)
Q Consensus       393 eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~  472 (526)
                      .+++.=-+-+.++. -.+.+|-+|+..-..-.-++.++  .-++|+++.+|++..+++++.=-=.|.        +||.-
T Consensus        19 k~il~~~~~~~eL~-y~~~~al~y~~kFakldpe~a~e--~veEL~~i~~~~e~~avkIadI~P~t~--------~ElRs   87 (114)
T COG1460          19 KKILSKVEREEELT-YEQREALEYAEKFAKLDPEKARE--LVEELLSIVKMSEKIAVKIADIMPRTP--------DELRS   87 (114)
T ss_pred             HHHHHHHCCCCCCH-HHHHHHHHHHHHHHCCCHHHHHH--HHHHHHHHCCCCHHHHHHHHHHCCCCH--------HHHHH
T ss_conf             99999861242103-89999999999871589999999--999998632456999999998089988--------99999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             312344432112453343588999999999
Q gi|254780788|r  473 WSENKGGNIEKFDGFLSSLGTPKDQVESMI  502 (526)
Q Consensus       473 ~~~~~~~~~~~~~gil~~~~l~~~~A~~lI  502 (526)
                      |+.+            ...-++.+++++|.
T Consensus        88 Ila~------------e~~~~s~E~l~~Il  105 (114)
T COG1460          88 ILAK------------ERVMLSDEELDKIL  105 (114)
T ss_pred             HHHH------------CCCCCCHHHHHHHH
T ss_conf             9998------------06889899999999


No 333
>PRK00140 rplK 50S ribosomal protein L11; Validated
Probab=20.09  E-value=47  Score=12.32  Aligned_cols=63  Identities=17%  Similarity=0.310  Sum_probs=37.1

Q ss_pred             EEEEEECCCCC-CCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCC--CEEEECCCCCEEEEEECC
Q ss_conf             49999408998-812765548862178899862778267995598789999976286654--248987567879999853
Q gi|254780788|r  238 KLAVFSSDSSI-DPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIV--TKVVLDEDVGRIEVIVPK  314 (526)
Q Consensus       238 KIAV~s~d~~i-DpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v--~~v~~de~~~~~~v~v~~  314 (526)
                      |+-|..-..+- -|||--.|++|.-+..++++.|..-=|               +.+-.+  +.|.+++| +++++.+..
T Consensus        10 kl~i~aG~A~p~PPvGpaLG~~GiNi~~F~k~fN~~T~~---------------~~~g~~vpV~Itv~~D-ksf~f~ikt   73 (142)
T PRK00140         10 KLQIPAGKANPSPPVGPALGQRGVNIMEFCKAFNARTQD---------------QEKGLPIPVVITVYAD-RSFTFITKT   73 (142)
T ss_pred             EEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH---------------CCCCCEEEEEEEECCC-CEEEEEECC
T ss_conf             999745777899998731134698999999999998861---------------5799807589999389-719999818


Q ss_pred             CC
Q ss_conf             42
Q gi|254780788|r  315 EQ  316 (526)
Q Consensus       315 ~q  316 (526)
                      --
T Consensus        74 Pp   75 (142)
T PRK00140         74 PP   75 (142)
T ss_pred             CC
T ss_conf             86


Done!