Query         gi|254780751|ref|YP_003065164.1| ribonuclease E [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 723
No_of_seqs    290 out of 2083
Neff          6.5 
Searched_HMMs 39220
Date          Sun May 29 19:35:52 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780751.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK10811 rne ribonuclease E; R 100.0       0       0 1291.3  46.8  498    2-579     1-500 (1063)
  2 PRK11712 ribonuclease G; Provi 100.0       0       0 1157.6  47.5  487    1-566     1-487 (489)
  3 TIGR00757 RNaseEG ribonuclease 100.0       0       0 1139.0  31.8  453   14-505     1-464 (464)
  4 COG1530 CafA Ribonucleases G a 100.0       0       0  945.0  35.8  485    2-571     1-486 (487)
  5 pfam10150 RNase_E_G Ribonuclea 100.0       0       0  652.6  27.6  271  201-473     1-271 (271)
  6 cd04453 S1_RNase_E S1_RNase_E:  99.9 3.4E-28 8.6E-33  215.0   6.7   87   34-205     2-88  (88)
  7 PRK07252 hypothetical protein;  98.3 8.1E-07 2.1E-11   66.5   5.2   40   38-79      2-41  (120)
  8 cd05692 S1_RPS1_repeat_hs4 S1_  98.2 3.2E-06 8.3E-11   62.3   5.6   38   40-79      1-38  (69)
  9 PRK08582 hypothetical protein;  98.2 2.7E-06 6.9E-11   62.8   5.1   40   38-79      4-43  (139)
 10 PRK05807 hypothetical protein;  98.1 3.4E-06 8.8E-11   62.1   4.9   39   38-79      4-42  (136)
 11 PRK03987 translation initiatio  98.1 1.2E-05   3E-10   58.4   7.3  125   37-277     6-135 (262)
 12 cd04452 S1_IF2_alpha S1_IF2_al  98.1 5.8E-06 1.5E-10   60.5   5.3   39   38-78      2-42  (76)
 13 cd05686 S1_pNO40 S1_pNO40: pNO  98.0 7.9E-06   2E-10   59.6   5.0   38   38-77      2-40  (73)
 14 TIGR03591 polynuc_phos polyrib  98.0 1.1E-05 2.9E-10   58.5   5.1   39  517-555   551-589 (684)
 15 PRK08059 general stress protei  98.0 1.1E-05 2.9E-10   58.5   4.9   41   36-78      3-43  (119)
 16 cd04472 S1_PNPase S1_PNPase: P  98.0 1.6E-05 4.2E-10   57.4   5.7   37   40-78      1-37  (68)
 17 pfam00575 S1 S1 RNA binding do  97.9 1.8E-05 4.7E-10   57.1   5.6   40   37-78      2-41  (74)
 18 PRK11824 polynucleotide phosph  97.9 1.8E-05 4.6E-10   57.1   5.0   39  517-555   554-592 (694)
 19 cd04473 S1_RecJ_like S1_RecJ_l  97.9 3.2E-05 8.1E-10   55.4   5.6   40   35-76     12-51  (77)
 20 COG1098 VacB Predicted RNA bin  97.8 1.6E-05 4.2E-10   57.4   3.8   79   38-213     4-82  (129)
 21 PRK13806 rpsA 30S ribosomal pr  97.8 2.9E-05 7.3E-10   55.7   5.0   38   36-75     30-67  (489)
 22 COG0539 RpsA Ribosomal protein  97.8 3.4E-05 8.7E-10   55.2   5.3   40   34-75     16-55  (541)
 23 smart00316 S1 Ribosomal protei  97.8 4.1E-05   1E-09   54.6   5.4   70   39-198     2-71  (72)
 24 cd05708 S1_Rrp5_repeat_sc12 S1  97.7  0.0001 2.6E-09   51.9   5.4   39   38-78      1-40  (77)
 25 cd05684 S1_DHX8_helicase S1_DH  97.6   1E-04 2.5E-09   51.9   5.2   36   40-77      1-39  (79)
 26 cd04461 S1_Rrp5_repeat_hs8_sc7  97.6 0.00015 3.7E-09   50.8   5.3   40   37-78     12-51  (83)
 27 PRK07400 30S ribosomal protein  97.5 0.00015 3.9E-09   50.7   5.1   40   34-75     26-65  (314)
 28 cd05685 S1_Tex S1_Tex: The C-t  97.5 0.00022 5.6E-09   49.6   5.3   38   40-79      1-38  (68)
 29 PRK00087 4-hydroxy-3-methylbut  97.5 0.00018 4.6E-09   50.1   4.8   10  416-425   362-371 (670)
 30 PRK07899 rpsA 30S ribosomal pr  97.5 0.00021 5.2E-09   49.8   4.8   62   12-75      6-69  (484)
 31 cd05688 S1_RPS1_repeat_ec3 S1_  97.4 0.00026 6.6E-09   49.1   4.8   36   39-77      1-36  (68)
 32 PRK06299 rpsA 30S ribosomal pr  97.4 0.00029 7.3E-09   48.8   4.8   38   36-75     17-54  (556)
 33 PRK06299 rpsA 30S ribosomal pr  97.4 0.00024 6.2E-09   49.2   4.4   37   38-77    190-226 (556)
 34 cd05698 S1_Rrp5_repeat_hs6_sc5  97.4 0.00037 9.5E-09   48.0   5.2   37   40-78      1-37  (70)
 35 cd05687 S1_RPS1_repeat_ec1_hs1  97.4 0.00043 1.1E-08   47.5   5.4   35   40-76      1-35  (70)
 36 COG1185 Pnp Polyribonucleotide  97.4  0.0002 5.1E-09   49.9   3.7   62  248-309   187-255 (692)
 37 cd05689 S1_RPS1_repeat_ec4 S1_  97.3 0.00048 1.2E-08   47.2   5.5   38   38-77      2-39  (72)
 38 COG0539 RpsA Ribosomal protein  97.3 0.00049 1.2E-08   47.1   5.2   83   37-210   190-272 (541)
 39 PRK06676 rpsA 30S ribosomal pr  97.3 0.00073 1.9E-08   45.9   5.9   39   36-76     14-53  (390)
 40 cd05691 S1_RPS1_repeat_ec6 S1_  97.3 0.00066 1.7E-08   46.3   5.4   37   40-78      1-37  (73)
 41 cd05706 S1_Rrp5_repeat_sc10 S1  97.2 0.00095 2.4E-08   45.2   5.9   40   38-79      2-41  (73)
 42 cd05690 S1_RPS1_repeat_ec5 S1_  97.2 0.00097 2.5E-08   45.1   5.5   36   40-77      1-36  (69)
 43 PRK07899 rpsA 30S ribosomal pr  97.0   0.001 2.7E-08   44.8   4.8   37   38-77    207-243 (484)
 44 PRK07400 30S ribosomal protein  96.9  0.0023 5.8E-08   42.5   5.7   35   38-75    117-151 (314)
 45 cd05707 S1_Rrp5_repeat_sc11 S1  96.9  0.0016 4.2E-08   43.5   5.0   38   40-79      1-38  (68)
 46 cd00164 S1_like S1_like: Ribos  96.9  0.0016 4.1E-08   43.5   4.7   34   43-78      1-34  (65)
 47 PRK13806 rpsA 30S ribosomal pr  96.8  0.0012 3.1E-08   44.4   3.4   39   38-78    200-238 (489)
 48 PRK12269 bifunctional cytidyla  96.8  0.0017 4.4E-08   43.3   4.1   13   50-62     54-66  (863)
 49 cd04471 S1_RNase_R S1_RNase_R:  96.7  0.0032 8.2E-08   41.5   5.0   40   39-80      1-41  (83)
 50 cd05697 S1_Rrp5_repeat_hs5 S1_  96.7  0.0038 9.7E-08   41.0   5.4   34   40-75      1-34  (69)
 51 PRK00087 4-hydroxy-3-methylbut  96.6   0.004   1E-07   40.8   4.9   36   37-74    302-337 (670)
 52 PRK12269 bifunctional cytidyla  96.5   0.006 1.5E-07   39.6   5.3   14  450-463   495-508 (863)
 53 PRK06676 rpsA 30S ribosomal pr  96.2   0.011 2.9E-07   37.7   5.4   39   37-78    103-141 (390)
 54 COG1093 SUI2 Translation initi  95.9   0.029 7.5E-07   34.8   6.4   38   37-76      9-48  (269)
 55 cd05704 S1_Rrp5_repeat_hs13 S1  95.6   0.036 9.3E-07   34.1   5.7   41   39-80      3-43  (72)
 56 cd05789 S1_Rrp4 S1_Rrp4: Rrp4   95.5   0.051 1.3E-06   33.1   6.2   38   37-76      4-41  (86)
 57 cd04460 S1_RpoE S1_RpoE: RpoE,  95.2   0.037 9.4E-07   34.1   4.8   38   41-81      1-38  (99)
 58 COG2183 Tex Transcriptional ac  95.2   0.044 1.1E-06   33.6   5.0   15  400-414   441-455 (780)
 59 cd04455 S1_NusA S1_NusA: N-uti  95.0   0.086 2.2E-06   31.5   6.1   34   38-74      2-35  (67)
 60 TIGR00717 rpsA ribosomal prote  94.8   0.066 1.7E-06   32.3   5.0   35   40-74     20-54  (534)
 61 TIGR00717 rpsA ribosomal prote  94.6   0.095 2.4E-06   31.3   5.4   37   38-76    286-322 (534)
 62 PTZ00248 eukaryotic translatio  94.2   0.079   2E-06   31.8   4.3   89   36-237    14-104 (324)
 63 PRK12327 nusA transcription el  93.9    0.18 4.7E-06   29.3   5.8   34   38-74    133-166 (353)
 64 PRK08563 DNA-directed RNA poly  93.8    0.54 1.4E-05   26.0   9.1   65   13-80     55-119 (182)
 65 PRK11642 exoribonuclease R; Pr  92.7    0.26 6.5E-06   28.3   4.9   90  313-412   378-476 (813)
 66 PRK09202 nusA transcription el  92.4    0.46 1.2E-05   26.5   5.9   52  282-338   246-298 (428)
 67 cd05702 S1_Rrp5_repeat_hs11_sc  92.2     0.4   1E-05   26.9   5.5   34   40-75      1-34  (70)
 68 PRK00499 rnpA ribonuclease P;   91.9    0.73 1.9E-05   25.1   6.5   62  216-277    42-111 (116)
 69 KOG1070 consensus               91.8    0.53 1.3E-05   26.1   5.7   66   12-79    570-637 (1710)
 70 COG2996 Predicted RNA-bindinin  91.8       1 2.5E-05   24.2   7.3   54   21-75     45-108 (287)
 71 PTZ00162 RNA polymerase II sub  90.8     1.3 3.2E-05   23.5   8.7   63   13-78     55-117 (170)
 72 TIGR03147 cyt_nit_nrfF cytochr  90.1     0.8   2E-05   24.8   5.2   58  481-556    40-97  (126)
 73 PRK12328 nusA transcription el  89.6     1.1 2.8E-05   23.9   5.6   52  282-338   251-303 (375)
 74 pfam03918 CcmH Cytochrome C bi  89.4    0.88 2.2E-05   24.5   5.0   58  481-556    37-94  (145)
 75 PRK10144 formate-dependent nit  89.2     1.1 2.7E-05   24.0   5.3   58  481-556    40-97  (126)
 76 cd05791 S1_CSL4 S1_CSL4: CSL4,  88.9     1.5 3.8E-05   22.9   5.9   23   37-61      4-26  (92)
 77 PRK01732 rnpA ribonuclease P;   87.8       2 5.2E-05   22.0   6.5   61  216-279    48-116 (119)
 78 PRK01313 rnpA ribonuclease P;   87.7     1.8 4.6E-05   22.4   5.7   58  215-272    53-119 (133)
 79 PRK04163 exosome complex RNA-b  86.7     2.3 5.9E-05   21.6   8.9   38   35-74     58-95  (232)
 80 cd05694 S1_Rrp5_repeat_hs2_sc2  86.7       2 5.1E-05   22.0   5.4   35   38-74      3-38  (74)
 81 PRK03031 rnpA ribonuclease P;   86.1     1.3 3.4E-05   23.3   4.3   58  216-273    50-116 (122)
 82 TIGR02696 pppGpp_PNP guanosine  85.3     0.3 7.7E-06   27.7   0.7  162  405-567   326-528 (725)
 83 PRK00396 rnpA ribonuclease P;   84.4       3 7.6E-05   20.9   6.9   62  216-280    49-118 (134)
 84 pfam01630 Glyco_hydro_56 Hyalu  84.3     1.6   4E-05   22.8   3.9   33  396-428    79-112 (339)
 85 COG1095 RPB7 DNA-directed RNA   84.2       3 7.7E-05   20.8   8.4   65   12-79     54-118 (183)
 86 PRK12329 nusA transcription el  84.1     3.1 7.8E-05   20.8   5.8   32  283-314   279-310 (457)
 87 PRK00349 uvrA excinuclease ABC  83.7     3.2 8.1E-05   20.7   5.4   42  291-332   526-567 (944)
 88 TIGR02063 RNase_R ribonuclease  83.3     3.3 8.4E-05   20.6   5.5  157  313-480   393-565 (755)
 89 cd04454 S1_Rrp4_like S1_Rrp4_l  83.2     2.4 6.2E-05   21.5   4.6   36   37-74      4-39  (82)
 90 TIGR02349 DnaJ_bact chaperone   82.1    0.58 1.5E-05   25.8   1.1   25  477-501   224-248 (386)
 91 COG1096 Predicted RNA-binding   81.3     3.9 9.9E-05   20.1   7.2   55   23-79     47-112 (188)
 92 pfam10447 EXOSC1 Exosome compo  81.3     3.9 9.9E-05   20.1   5.4   23   37-61      2-24  (72)
 93 TIGR02349 DnaJ_bact chaperone   81.2    0.24 6.1E-06   28.5  -1.2   44  480-529   213-256 (386)
 94 pfam07092 DUF1356 Protein of u  79.3    0.62 1.6E-05   25.6   0.4   34  454-496    13-46  (231)
 95 cd05696 S1_Rrp5_repeat_hs4 S1_  76.0     2.5 6.4E-05   21.4   2.7   34   40-74      1-35  (71)
 96 cd04465 S1_RPS1_repeat_ec2_hs2  76.0     3.3 8.4E-05   20.6   3.3   33   40-75      1-33  (67)
 97 COG1107 Archaea-specific RecJ-  75.2     2.8   7E-05   21.1   2.8   49   25-75    108-156 (715)
 98 PRK04820 rnpA ribonuclease P;   75.1     5.8 0.00015   18.8   6.6   60  216-278    51-118 (145)
 99 TIGR02642 phage_xxxx uncharact  74.3     1.2   3E-05   23.7   0.7   48  440-498   168-216 (270)
100 COG0484 DnaJ DnaJ-class molecu  73.3     1.8 4.7E-05   22.3   1.5   19  476-494   178-196 (371)
101 TIGR01213 TIGR01213 conserved   72.4     1.1 2.9E-05   23.8   0.3   39  349-387   149-188 (450)
102 COG1568 Predicted methyltransf  72.1     3.1   8E-05   20.7   2.4   12  409-420   193-204 (354)
103 COG2425 Uncharacterized protei  71.0     7.2 0.00018   18.2   4.5   99  362-470   312-418 (437)
104 COG0178 UvrA Excinuclease ATPa  70.9     7.2 0.00018   18.2   6.0   13  480-492   397-409 (935)
105 pfam00825 Ribonuclease_P Ribon  70.8     7.3 0.00018   18.2   5.8   57  215-271    40-105 (107)
106 PRK00635 excinuclease ABC subu  70.7     7.3 0.00019   18.1   6.1   42  291-332   513-554 (1809)
107 pfam03589 Antiterm Antitermina  69.3     2.8 7.2E-05   21.0   1.7   31  477-507    28-58  (95)
108 PRK00588 rnpA ribonuclease P;   69.0     7.9  0.0002   17.9   6.1   58  215-272    45-110 (116)
109 PRK02083 imidazole glycerol ph  69.0     6.6 0.00017   18.4   3.6   16  410-425   158-173 (253)
110 PRK05973 replicative DNA helic  68.8     7.2 0.00018   18.2   3.7   85  405-492   133-232 (237)
111 KOG1067 consensus               68.5     6.7 0.00017   18.4   3.5   34  281-314   270-303 (760)
112 PRK13597 imidazole glycerol ph  68.2     7.1 0.00018   18.2   3.6   16  299-314    90-105 (252)
113 COG3088 CcmH Uncharacterized p  67.9     8.3 0.00021   17.8   4.8   57  481-555    44-100 (153)
114 pfam00684 DnaJ_CXXCXGXG DnaJ c  67.8     3.9 9.8E-05   20.1   2.2   21  475-495    48-68  (79)
115 PRK09521 exosome complex RNA-b  67.5     8.5 0.00022   17.7   7.2   24   36-61     61-84  (187)
116 COG0594 RnpA RNase P protein c  66.8     8.7 0.00022   17.6   5.7   57  216-272    44-108 (117)
117 PRK03220 consensus              66.3     7.9  0.0002   17.9   3.5   19  408-426   162-180 (257)
118 COG1198 PriA Primosomal protei  65.4     5.6 0.00014   18.9   2.6  154  412-566   373-573 (730)
119 KOG1015 consensus               65.1     7.1 0.00018   18.2   3.1  135  305-462   726-860 (1567)
120 PRK01659 consensus              64.7     9.5 0.00024   17.3   3.7   15  410-424   158-172 (252)
121 TIGR02034 CysN sulfate adenyly  64.2    0.82 2.1E-05   24.8  -1.9   69  360-428   328-401 (411)
122 PRK04281 consensus              62.9      10 0.00026   17.1   3.6   18  409-426   158-175 (254)
123 PRK06937 type III secretion sy  61.6      11 0.00027   17.0   5.4   50  515-566   129-178 (204)
124 PRK04390 rnpA ribonuclease P;   61.4      11 0.00028   16.9   5.6   56  216-271    48-111 (121)
125 KOG3409 consensus               61.2      11 0.00028   16.9   8.2   57    6-74     33-94  (193)
126 cd05792 S1_eIF1AD_like S1_eIF1  60.6     4.4 0.00011   19.6   1.4   22  356-377    30-51  (78)
127 PRK02621 consensus              59.8      12 0.00029   16.8   3.8   16  411-426   160-175 (254)
128 PRK05054 exoribonuclease II; P  59.5      12  0.0003   16.7   4.8   92  312-413   308-408 (644)
129 cd01889 SelB_euk SelB subfamil  59.5      12  0.0003   16.7   7.5   70  378-462    95-169 (192)
130 cd05693 S1_Rrp5_repeat_hs1_sc1  59.0      12  0.0003   16.7   6.1   41   38-80      2-42  (100)
131 KOG2228 consensus               59.0      12  0.0003   16.7   7.7   83  400-487    89-173 (408)
132 pfam02108 FliH Flagellar assem  58.2      12 0.00031   16.6   5.3   59  503-567    52-112 (128)
133 COG1317 FliH Flagellar biosynt  57.4      13 0.00032   16.5   4.5   48  516-567   157-204 (234)
134 cd00881 GTP_translation_factor  56.9      13 0.00033   16.4   8.5   59  377-450    88-146 (189)
135 PRK11032 hypothetical protein;  56.9     6.4 0.00016   18.5   1.7   53  443-496   104-157 (160)
136 TIGR02716 C20_methyl_CrtF C-20  56.4     9.2 0.00023   17.5   2.4   33  342-374   217-253 (306)
137 smart00333 TUDOR Tudor domain.  56.0      11 0.00028   16.9   2.7   34   39-74     15-50  (57)
138 PRK08903 hypothetical protein;  55.8      13 0.00034   16.3   6.3  109  420-545    91-199 (227)
139 PRK02747 consensus              55.7      13 0.00034   16.3   3.7   19  408-426   159-177 (257)
140 cd05705 S1_Rrp5_repeat_hs14 S1  55.3      13 0.00034   16.3   3.1   38   39-79      3-40  (74)
141 TIGR00393 kpsF sugar isomerase  53.4      14 0.00036   16.1   3.0   41  437-477   151-193 (272)
142 cd04508 TUDOR Tudor domains ar  53.3      13 0.00033   16.4   2.7   34   39-74     11-46  (48)
143 PRK03459 rnpA ribonuclease P;   52.7      15 0.00038   16.0   5.8   60  215-274    57-124 (129)
144 TIGR02390 RNA_pol_rpoA1 DNA-di  51.7      16  0.0004   15.9   3.5  231  166-449   425-699 (901)
145 KOG0546 consensus               51.3     7.9  0.0002   17.9   1.4   37  478-514   126-162 (372)
146 TIGR01953 NusA transcription t  50.3      16 0.00042   15.7   5.9  161   36-338   142-318 (366)
147 TIGR00137 gid gid protein; Int  49.9      11 0.00029   16.8   2.0   37   44-80    298-336 (444)
148 PRK00694 4-hydroxy-3-methylbut  49.6     7.2 0.00018   18.2   1.0   61  403-490   459-519 (606)
149 PRK06328 type III secretion sy  48.7      17 0.00044   15.6   4.8   50  515-566   130-179 (223)
150 cd02394 vigilin_like_KH K homo  46.5      17 0.00044   15.5   2.5   35  519-553     2-36  (62)
151 cd04731 HisF The cyclase subun  46.4      19 0.00047   15.3   3.6   22  230-251    61-82  (243)
152 cd05703 S1_Rrp5_repeat_hs12_sc  46.2      19 0.00048   15.3   5.1   35   40-76      1-35  (73)
153 COG1278 CspC Cold shock protei  46.1      19 0.00048   15.3   4.5   34   44-77      3-37  (67)
154 PTZ00037 DnaJ_C chaperone prot  45.3      10 0.00027   17.1   1.2   49  210-273     7-55  (422)
155 cd01890 LepA LepA subfamily.    45.2      19 0.00049   15.2   6.0   66  378-461    94-159 (179)
156 KOG2002 consensus               43.8      20 0.00052   15.1   3.6   15  401-415   659-673 (1018)
157 PHA02114 hypothetical protein   43.7      20 0.00052   15.0   3.0   23  245-267     1-23  (127)
158 KOG0712 consensus               43.4     9.3 0.00024   17.4   0.7   33  465-497   154-186 (337)
159 TIGR01544 HAD-SF-IE HAD-superf  42.9      20 0.00051   15.1   2.4   45  437-490    12-56  (287)
160 PRK06669 fliH flagellar assemb  42.9      21 0.00053   15.0   6.3   49  516-566   197-245 (268)
161 TIGR00459 aspS_bact aspartyl-t  42.4     6.7 0.00017   18.4  -0.1   56  212-277   222-278 (653)
162 pfam07013 DUF1314 Protein of u  42.2      21 0.00053   15.0   2.4   37  354-394     4-40  (177)
163 pfam02691 VacA Vacuolating cyo  41.9      21 0.00055   14.9   2.4   32  354-385   578-617 (1002)
164 cd00765 Pyrophosphate_PFK Phos  40.9      22 0.00057   14.8   5.3   44  218-264   143-187 (550)
165 cd02396 PCBP_like_KH K homolog  40.9      22 0.00057   14.8   2.6   44  519-562     2-45  (65)
166 PRK02145 consensus              40.8      23 0.00057   14.7   3.5   14  411-424   163-176 (257)
167 pfam06635 NolV Nodulation prot  40.7      23 0.00058   14.7   3.5   49  514-566   128-177 (207)
168 COG2895 CysN GTPases - Sulfate  39.7     4.9 0.00012   19.4  -1.2   31  360-390   330-361 (431)
169 pfam04025 DUF370 Domain of unk  39.5      24  0.0006   14.6   3.2   27    4-30     37-64  (73)
170 pfam04606 Ogr_Delta Ogr/Delta-  39.4      15 0.00039   15.9   1.3   19  483-501     1-19  (47)
171 TIGR02836 spore_IV_A stage IV   39.3      13 0.00033   16.4   1.0   37   27-74      3-40  (492)
172 TIGR02533 type_II_gspE general  39.1       8  0.0002   17.9  -0.1   80  400-493   346-433 (495)
173 TIGR00630 uvra excinuclease AB  38.8      13 0.00033   16.4   0.9   78  419-498   229-312 (956)
174 TIGR00340 zpr1_rel zinc finger  38.3      11 0.00028   16.9   0.4   14  484-497     1-14  (168)
175 PRK06032 fliH flagellar assemb  38.0      25 0.00063   14.5   6.1   63  503-567   112-175 (208)
176 pfam00013 KH_1 KH domain. KH m  38.0      16 0.00041   15.7   1.3   34  519-552     2-35  (57)
177 pfam07295 DUF1451 Protein of u  37.9      15 0.00037   16.1   1.0   44  453-496   103-147 (148)
178 PRK00964 tetrahydromethanopter  37.6      24 0.00062   14.5   2.1   56  385-451   101-156 (243)
179 TIGR02405 trehalos_R_Ecol treh  36.7     8.2 0.00021   17.8  -0.4   90  407-501   104-198 (311)
180 pfam05262 Borrelia_P83 Borreli  36.7      11 0.00029   16.8   0.3   11   53-63      8-18  (489)
181 PRK12366 replication factor A;  35.8      12  0.0003   16.7   0.3   54  512-565   570-629 (649)
182 cd01129 PulE-GspE PulE/GspE Th  35.7     9.2 0.00023   17.5  -0.3   62  195-261    33-96  (264)
183 TIGR01037 pyrD_sub1_fam dihydr  35.4      27 0.00069   14.2   2.5   46  482-531   129-176 (308)
184 cd04702 ASRGL1_like ASRGL1_lik  35.3      27 0.00069   14.2   2.7   17  397-415   186-202 (261)
185 pfam00567 TUDOR Tudor domain.   34.8      28 0.00071   14.1   3.2   24   40-63     63-88  (118)
186 cd01883 EF1_alpha Eukaryotic e  34.1      28 0.00073   14.0   8.8   94  377-489   103-205 (219)
187 COG2052 Uncharacterized protei  34.0      29 0.00073   14.0   2.6   19    4-22     41-59  (89)
188 PRK01172 ski2-like helicase; P  33.8      29 0.00073   14.0   3.6   13  215-227   171-183 (674)
189 pfam00009 GTP_EFTU Elongation   33.3      29 0.00074   14.0   7.1   70  378-462    94-167 (185)
190 pfam01153 Glypican Glypican.    33.2      21 0.00054   14.9   1.2   26  481-506   247-272 (559)
191 PRK10476 multidrug resistance   33.1      29 0.00075   13.9   3.8   11  547-557   264-274 (348)
192 PRK10954 periplasmic protein d  32.5      11 0.00029   16.8  -0.2   13  346-358   144-156 (207)
193 TIGR02738 TrbB type-F conjugat  32.5      15 0.00037   16.0   0.3   34  366-400   133-168 (176)
194 PRK07726 DNA topoisomerase III  32.4      30 0.00076   13.9   1.9   27  233-260   306-332 (716)
195 LOAD_cold consensus             32.2      30 0.00077   13.8   4.6   33   43-75      2-35  (67)
196 TIGR02949 anti_SigH_actin anti  31.9      25 0.00065   14.4   1.5   51  312-362     7-60  (85)
197 PRK04323 hypothetical protein;  31.8      31 0.00079   13.8   3.2   16    5-20     42-57  (91)
198 cd01888 eIF2_gamma eIF2-gamma   31.5      31  0.0008   13.8   8.1   72  378-462   110-182 (203)
199 smart00778 Prim_Zn_Ribbon Zinc  31.3      19 0.00048   15.3   0.7   15  481-495     3-17  (37)
200 PRK02362 ski2-like helicase; P  31.0      32 0.00081   13.7   3.1   15  195-209   338-352 (736)
201 COG1097 RRP4 RNA-binding prote  30.4      32 0.00083   13.6   8.1   39   34-74     59-97  (239)
202 TIGR03655 anti_R_Lar restricti  30.4      19 0.00049   15.2   0.6   11  482-492     2-12  (53)
203 COG1411 Uncharacterized protei  30.3      33 0.00083   13.6   4.3   48  377-434   119-166 (229)
204 COG3634 AhpF Alkyl hydroperoxi  30.3      18 0.00047   15.4   0.5  125  299-449   140-278 (520)
205 PRK07399 DNA polymerase III su  30.2      33 0.00084   13.6   4.9   42  404-445   106-150 (314)
206 cd04171 SelB SelB subfamily.    30.0      33 0.00084   13.6   8.4   70  378-462    78-149 (164)
207 cd00105 KH-I K homology RNA-bi  29.9      33 0.00085   13.6   2.4   39  519-557     2-40  (64)
208 PRK05783 hypothetical protein;  29.8      33 0.00085   13.6   2.1   17  402-418    55-71  (84)
209 COG0557 VacB Exoribonuclease R  29.7      33 0.00085   13.6   5.2   91  313-415   366-464 (706)
210 KOG3013 consensus               29.4      34 0.00086   13.5   7.6  152   23-229    69-220 (301)
211 KOG0950 consensus               28.5      35 0.00089   13.4   2.2   44  418-461   340-385 (1008)
212 COG1352 CheR Methylase of chem  28.2      31  0.0008   13.7   1.4   32  349-380   215-246 (268)
213 KOG3558 consensus               28.2      35  0.0009   13.4   1.8   16  366-382   344-359 (768)
214 pfam08206 OB_RNB Ribonuclease   27.9      32 0.00083   13.7   1.5   15  176-190    34-48  (58)
215 PRK01033 imidazole glycerol ph  27.8      36 0.00092   13.3   3.3   19  408-426   155-173 (253)
216 PRK09098 type III secretion sy  27.8      36 0.00092   13.3   5.6   66  497-566   133-198 (229)
217 TIGR02499 HrpE_YscL_not type I  27.7      36 0.00092   13.3   3.9   65  496-566   105-174 (183)
218 pfam08273 Prim_Zn_Ribbon Zinc-  27.1      23 0.00058   14.7   0.6   14  481-494     3-16  (39)
219 TIGR01111 mtrA tetrahydrometha  26.8      31  0.0008   13.7   1.2   43  401-454   121-164 (246)
220 pfam08800 VirE_N VirE N-termin  26.8      37 0.00095   13.2   5.3   49  416-469    27-76  (136)
221 cd01887 IF2_eIF5B IF2/eIF5B (i  26.8      37 0.00095   13.2   7.0   69  378-462    77-149 (168)
222 PRK07085 diphosphate--fructose  26.5      38 0.00096   13.2   5.4   31  218-251   143-174 (557)
223 KOG0458 consensus               26.5      38 0.00097   13.2   6.4   83  377-468   281-374 (603)
224 PRK12564 carbamoyl phosphate s  26.4      38 0.00097   13.2   2.4   84  198-305    44-128 (355)
225 TIGR01523 ATPase-IID_K-Na pota  26.0      29 0.00073   14.0   0.9   56  474-529   517-580 (1001)
226 COG3585 MopI Molybdopterin-bin  25.9      39 0.00099   13.1   2.1   26   39-64      5-30  (69)
227 TIGR03598 GTPase_YsxC ribosome  25.6      39   0.001   13.1   6.1   55  408-462   119-173 (179)
228 smart00322 KH K homology RNA-b  25.6      31 0.00078   13.8   1.0   40  518-557     4-43  (69)
229 COG2260 Predicted Zn-ribbon RN  25.5      24 0.00062   14.5   0.5   19  479-497    15-33  (59)
230 TIGR01520 FruBisAldo_II_A fruc  25.4      17 0.00043   15.6  -0.4   79  285-369   267-345 (365)
231 COG1867 TRM1 N2,N2-dimethylgua  25.4      38 0.00098   13.1   1.5   58  441-498   193-274 (380)
232 PRK06921 hypothetical protein;  25.3      35 0.00089   13.4   1.2   22  493-514   193-214 (265)
233 PRK13586 1-(5-phosphoribosyl)-  25.1      40   0.001   13.0   4.7   19  408-426   148-166 (231)
234 pfam04208 MtrA Tetrahydrometha  25.1      40   0.001   13.0   2.6   56  387-453    99-154 (176)
235 pfam05772 NinB NinB protein. T  25.1      34 0.00087   13.5   1.1   35  225-259     4-38  (127)
236 PRK10611 chemotaxis methyltran  24.9      29 0.00074   14.0   0.8   21  363-383   250-270 (287)
237 COG0173 AspS Aspartyl-tRNA syn  24.8      39 0.00099   13.1   1.4   61  407-471   375-440 (585)
238 pfam03602 Cons_hypoth95 Conser  24.6      41   0.001   13.0   2.8   34  344-378   121-154 (181)
239 COG1329 Transcriptional regula  24.4      41  0.0011   12.9   1.9   35  293-327   104-139 (166)
240 COG5525 Bacteriophage tail ass  24.2      25 0.00065   14.4   0.4   33  349-387   420-452 (611)
241 pfam00313 CSD 'Cold-shock' DNA  23.6      43  0.0011   12.8   5.4   32   44-75      2-34  (66)
242 PRK02048 4-hydroxy-3-methylbut  23.6      12 0.00031   16.6  -1.4   27  460-490   501-527 (613)
243 pfam06075 DUF936 Plant protein  23.4      43  0.0011   12.8   4.3   44   44-90     27-72  (557)
244 COG5615 Predicted integral mem  23.1      43  0.0011   12.8   4.7   51  418-468    20-79  (161)
245 KOG0955 consensus               23.1      43  0.0011   12.8   1.5   38  348-389   598-635 (1051)
246 PRK06443 chorismate mutase; Va  22.8      44  0.0011   12.7   1.6   33  354-391   118-151 (177)
247 pfam11314 DUF3117 Protein of u  22.7      44  0.0011   12.7   1.4   13  362-374    22-34  (51)
248 KOG2268 consensus               22.7      15 0.00038   16.0  -1.1   65  352-450   205-279 (465)
249 TIGR01054 rgy reverse gyrase;   22.4      34 0.00088   13.5   0.7   86  379-470   321-410 (1843)
250 cd00453 FTBP_aldolase_II Fruct  22.3      39 0.00099   13.1   1.0   16  399-414   178-193 (340)
251 COG2804 PulE Type II secretory  22.3      23 0.00059   14.7  -0.2   66  192-262   208-275 (500)
252 PRK10767 chaperone protein Dna  22.2      16  0.0004   15.9  -1.1   43  479-527   178-220 (376)
253 COG4311 SoxD Sarcosine oxidase  21.9      32 0.00082   13.7   0.5   11  479-489     1-11  (97)
254 TIGR01275 ACC_deam_rel pyridox  21.7      46  0.0012   12.6   2.4   21  404-424   163-187 (339)
255 cd04617 CBS_pair_4 The CBS dom  21.6      46  0.0012   12.6   2.5   19  408-426    13-31  (118)
256 pfam01762 Galactosyl_T Galacto  21.3      47  0.0012   12.5   1.3   16  484-499   145-160 (196)
257 KOG3821 consensus               21.2      46  0.0012   12.6   1.2   26  481-506   253-278 (563)
258 PRK08084 DNA replication initi  21.1      48  0.0012   12.5   5.3  109  421-546    99-210 (235)
259 TIGR03572 WbuZ glycosyl amidat  21.0      48  0.0012   12.5   3.5   23  229-251    63-85  (232)
260 PRK01492 rnpA ribonuclease P;   21.0      48  0.0012   12.5   4.9   68  199-271    37-116 (118)
261 PRK06835 DNA replication prote  20.8      30 0.00077   13.9   0.2   20  259-278    68-87  (330)
262 cd01721 Sm_D3 The eukaryotic S  20.8      48  0.0012   12.4   2.3   24   38-61     18-41  (70)
263 pfam01440 Gemini_AL2 Geminivir  20.7      49  0.0012   12.4   1.4   14  360-373    30-43  (134)
264 TIGR02477 PFKA_PPi diphosphate  20.6      49  0.0012   12.4   5.8  193  343-558   318-549 (566)
265 TIGR01214 rmlD dTDP-4-dehydror  20.2      50  0.0013   12.4   2.6   13  241-253   153-165 (317)

No 1  
>PRK10811 rne ribonuclease E; Reviewed
Probab=100.00  E-value=0  Score=1291.31  Aligned_cols=498  Identities=44%  Similarity=0.690  Sum_probs=479.8

Q ss_pred             CCEEEEECCCCCEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCC
Q ss_conf             85268965289607999998998999996073346042878798997836388231353278977130222137121028
Q gi|254780751|r    2 ANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQI   81 (723)
Q Consensus         2 ~k~~lI~~~~~~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~i   81 (723)
                      .|+||||++|++|+||||++||+|.|||||+.++.+.+||||+|+|+||+|||||||||||.+|||||||+||+++||.-
T Consensus         1 mKrmLInat~~EE~RVAlvdg~~L~dldIE~~~~~q~kgNIYKGkV~rVePgLqAAFVDiG~eR~GFLp~kEI~~ey~~~   80 (1063)
T PRK10811          1 MKRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPA   80 (1063)
T ss_pred             CCEEEECCCCCCCEEEEEEECCEEEEEECCCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCCCCCCCHHHCCHHHCCC
T ss_conf             96267468884404799974999889862357765340542689997856886057772389755421688828654265


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             98899999998886311111000000011122334443344542222334455433222234321122111211000012
Q gi|254780751|r   82 PFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVP  161 (723)
Q Consensus        82 p~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (723)
                                                                                                     .
T Consensus        81 -------------------------------------------------------------------------------~   81 (1063)
T PRK10811         81 -------------------------------------------------------------------------------N   81 (1063)
T ss_pred             -------------------------------------------------------------------------------C
T ss_conf             -------------------------------------------------------------------------------5


Q ss_pred             CCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHC
Q ss_conf             23444421331068885799984033323456410123345765234422788751242046886899999999986300
Q gi|254780751|r  162 KKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEV  241 (723)
Q Consensus       162 ~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~  241 (723)
                      ....++++|+++|++||+|||||+|||+|+|||+|||+||||||||||||++++++||||||.+ ++|.+|+.++..+.+
T Consensus        82 ~~~~grp~I~dvLkeGQeILVQV~KEp~GtKGArLTT~ISLaGRYLVLMPn~~~~gGISRKIe~-eER~rLkeiL~~L~~  160 (1063)
T PRK10811         82 YSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEG-DDRTELKEALASLEL  160 (1063)
T ss_pred             CCCCCCCCHHHHCCCCCEEEEEEEECCCCCCCCCEEEEEEECCEEEEECCCCCCCCCEECCCCC-HHHHHHHHHHHHCCC
T ss_conf             3435687878836799989999966787897836642154342018982489877615147890-789999999971357


Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHH
Q ss_conf             25871699850455757999999999999999877642014322123456458888887523766311110353203667
Q gi|254780751|r  242 PAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREA  321 (723)
Q Consensus       242 ~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~~~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~  321 (723)
                      |+|||+||||+|.|++.++|.+|+.+|+++|+.|++.+....+|+|||++.+++.++||||++.++++|+||+.+.|+.+
T Consensus       161 Peg~GlIVRTAa~g~s~eeL~~Dl~~Ll~~W~~I~k~~~~~~AP~LIyqE~~li~R~iRD~l~~di~eIiVDd~e~ye~a  240 (1063)
T PRK10811        161 PEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELA  240 (1063)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHCCCCCCEEEEECHHHHHHH
T ss_conf             88826999757689999999999999999999999997358998687537548999999862177788999699999999


Q ss_pred             HHHHHHH-HHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHHH
Q ss_conf             8889876-310121122013442035677699999998422214367864998328806999823755444555114799
Q gi|254780751|r  322 KDFMKLL-MPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTAL  400 (723)
Q Consensus       322 ~~~~~~~-~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~l  400 (723)
                      ++|+..+ +|++..+|++|.+..|||++|+||.||+.+|+++||||||||||||+|||||+||||||+|++++|+|+|+|
T Consensus       241 k~~i~~l~~P~~~~kVklY~~~~PLF~~Y~IE~QIe~a~~rkV~LpSGGyIVID~TEALtaIDVNSGk~t~g~niEETal  320 (1063)
T PRK10811        241 RQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETAF  320 (1063)
T ss_pred             HHHHHHHCCCCCCCCEEEECCCCCHHHHHCHHHHHHHHHCCCEECCCCCEEEEECCCCEEEEEECCCCCCCCCCHHHHHH
T ss_conf             99999744733337458857998857770999999998459176798867998456040788616998888989999999


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHH
Q ss_conf             99999999999987310368638960334798888999999999973127872899860486148985156663011210
Q gi|254780751|r  401 QTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLEST  480 (723)
Q Consensus       401 ~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~  480 (723)
                      +||||||+||||||||||||||||||||||...+|++.|+++|+++|+.||+|+||+.||.||||||||||+|+||.+++
T Consensus       321 kTNLEAA~EIARQLRLRDLGGIIVIDFIDM~~~~nqr~Ve~~lr~alk~DRARiqig~IS~FGLlEMSRQRlrpSL~es~  400 (1063)
T PRK10811        321 NTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESS  400 (1063)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCEEEEHHHCCHHHHHHC
T ss_conf             99999999999999860268829997235896566999999999998637201033343676430323321014457542


Q ss_pred             CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHH-CCEEEEEECCCCC
Q ss_conf             023675465378606114689988788999730364310135769999987302379999999984-8879998478778
Q gi|254780751|r  481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARF-GVSINVVIGIELA  559 (723)
Q Consensus       481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~-~~~I~i~~d~~l~  559 (723)
                      ++.||+|+|+|.|++.+|+++.|||.|++++.+.++..+.+.+|++||.||||+||..|..||.++ ++.|.|+++++|.
T Consensus       401 ~~~CP~C~G~G~ir~~es~al~ilR~ieeea~k~~t~~v~~~vpv~va~yllNeKR~~i~~ie~r~~~v~~~~~pn~~~~  480 (1063)
T PRK10811        401 HHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQME  480 (1063)
T ss_pred             CCCCCCCCCCCEECCHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCC
T ss_conf             77488887700225728889999999999987557553999954999999876658999999975268339994898888


Q ss_pred             CCCEEEEECCCCCCCCCCCC
Q ss_conf             86338971554433333211
Q gi|254780751|r  560 DKLFYIEKGSPVQALVNTGH  579 (723)
Q Consensus       560 ~~~f~Ier~~~~~~~~~~~~  579 (723)
                      +|||.+.|.+.++.....+|
T Consensus       481 tp~~~~~r~r~~~~~~~~sy  500 (1063)
T PRK10811        481 TPHYSVLRVRKGEETPTLSY  500 (1063)
T ss_pred             CCCCEEEEECCCCCCCCCHH
T ss_conf             99826898307763441001


No 2  
>PRK11712 ribonuclease G; Provisional
Probab=100.00  E-value=0  Score=1157.64  Aligned_cols=487  Identities=32%  Similarity=0.521  Sum_probs=467.5

Q ss_pred             CCCEEEEECCCCCEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC
Q ss_conf             98526896528960799999899899999607334604287879899783638823135327897713022213712102
Q gi|254780751|r    1 MANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ   80 (723)
Q Consensus         1 M~k~~lI~~~~~~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~   80 (723)
                      |+++||||++ |+|||||+++||+|+||++|+..+.+++||||+|+|+||+|||||||||||.+|+||||++|++|.+..
T Consensus         1 M~~eilIn~~-~~E~RvAlle~g~L~el~iE~~~~~~~vGnIY~G~V~~V~pgl~AAFVdiG~~k~gFL~~~di~~~~~~   79 (489)
T PRK11712          1 MTAELLVNVT-PSETRVALIEGGILQEIHIEREAKRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTEC   79 (489)
T ss_pred             CCCEEEEECC-CCEEEEEEEECCEEEEEEEECCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCEEEEHHHCCCCHHC
T ss_conf             9856999789-983699999999999999855888776676699999430688776999847987428785543852111


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             89889999999888631111100000001112233444334454222233445543322223432112211121100001
Q gi|254780751|r   81 IPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDV  160 (723)
Q Consensus        81 ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (723)
                      ..                                                                            ..
T Consensus        80 ~~----------------------------------------------------------------------------~~   83 (489)
T PRK11712         80 VA----------------------------------------------------------------------------GE   83 (489)
T ss_pred             CC----------------------------------------------------------------------------CC
T ss_conf             33----------------------------------------------------------------------------32


Q ss_pred             CCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHH
Q ss_conf             22344442133106888579998403332345641012334576523442278875124204688689999999998630
Q gi|254780751|r  161 PKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLE  240 (723)
Q Consensus       161 ~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~  240 (723)
                      ........+|+++|++||.|||||+|||+|+|||+||++|||||||+||||+. .++||||||.++++|.+|+.++..+ 
T Consensus        84 ~~~~~~~~~I~~~l~~Gq~ilVQV~Ke~~~~KGa~lT~~isl~GRylVl~P~~-~~igiSrkI~~~~eR~rLk~i~~~~-  161 (489)
T PRK11712         84 EQKQFVVRDISELVRQGQDIMVQVVKDPLGTKGARLTTDITLPSRYLVFMPGA-SHVGVSQRIESEEERERLKKIVAPY-  161 (489)
T ss_pred             CCCCCCCCCHHHHCCCCCEEEEEEEECCCCCCCCCEEEEEEECCEEEEEECCC-CCCCCCCCCCCHHHHHHHHHHHHHC-
T ss_conf             23566646767746799989999962687898876751255453269995389-9876431679878999999988853-


Q ss_pred             CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHH
Q ss_conf             02587169985045575799999999999999987764201432212345645888888752376631111035320366
Q gi|254780751|r  241 VPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYRE  320 (723)
Q Consensus       241 ~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~~~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~  320 (723)
                      .|+++|+|+||+|++++.++|.+|+.+|.++|+.|.+++...++|+|||++++++.+++||+++.++++|+||+.+.|..
T Consensus       162 ~~~~~G~IiRT~a~~~~~e~l~~d~~~L~~~W~~I~~~~~~~~~p~ll~~e~~~~~r~lRD~~~~~~~~I~vD~~~~~~~  241 (489)
T PRK11712        162 CDEQGGFIIRTAAEGVGEEELAQDAAFLKRVWTKVMERKKRPQTRYQLYGELALAQRVLRDFVGAELDRIRVDSRLTYEE  241 (489)
T ss_pred             CCCCCCEEEECHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEECCCHHHHHHHHHHCCCCCCEEEECCHHHHHH
T ss_conf             88888669841320299999999999999999999999854999614642723899999984477652788578899999


Q ss_pred             HHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHHH
Q ss_conf             78889876310121122013442035677699999998422214367864998328806999823755444555114799
Q gi|254780751|r  321 AKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTAL  400 (723)
Q Consensus       321 ~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~l  400 (723)
                      +++|+..++|++..++++|.+..|||+.|+|+.||+++|+++||||||||||||+|||||+||||||+|+|++++|+|+|
T Consensus       242 ~~~~~~~~~p~~~~~v~~y~~~~plF~~y~ie~~I~~~l~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~g~~~~eet~~  321 (489)
T PRK11712        242 LKEFTSEYIPELTDKLEHYSGRQPIFDLYDVENEIQRALERKVELKSGGYLIIDQTEAMTTVDINTGAFVGHRNLEETIF  321 (489)
T ss_pred             HHHHHHHHCCCCCCEEEECCCCCHHHHHCCHHHHHHHHHCCEEECCCCCEEEEECCCCEEEEECCCCCCCCCCCHHHHHH
T ss_conf             99999875941001134326862177642899999997168077389878999426100798505765457777678899


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHH
Q ss_conf             99999999999987310368638960334798888999999999973127872899860486148985156663011210
Q gi|254780751|r  401 QTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLEST  480 (723)
Q Consensus       401 ~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~  480 (723)
                      +||||||+||||||||||||||||||||||++++|+++|+++|+++|++|+++++|++||+||||||||||+|+||.+++
T Consensus       322 ~tNlEAA~EIaRQLRLRnigGiIvIDFIDM~~~~~~~~V~~~l~~~l~~Dr~k~~v~~is~lGLvEmTRkR~r~sl~~~~  401 (489)
T PRK11712        322 NTNIEATQAIARQLRLRNLGGIIIIDFIDMNNEDHRRRVLHSLEQALSKDRVKTNINGFSQLGLVEMTRKRTRESLEHVL  401 (489)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCEEEEEEHHCCCCHHHHC
T ss_conf             98999999999998635578869998447998688999999999997468987078564777207996221033757770


Q ss_pred             CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCC
Q ss_conf             02367546537860611468998878899973036431013576999998730237999999998488799984787788
Q gi|254780751|r  481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELAD  560 (723)
Q Consensus       481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~  560 (723)
                      +++||+|+|+|+|+|.+|+|++|+|+|.+.+...+.+.+.+.+||+|+.||+|+++..|.+||.+++.+|.|.+||+++.
T Consensus       402 ~~~Cp~C~G~G~v~s~et~~~~i~R~i~~~~~~~~~~~i~v~~~~~v~~~l~~~~~~~l~~lE~~~~~~i~i~~d~~~~~  481 (489)
T PRK11712        402 CGECPTCHGRGTVKTVETVCYEIMREIVRVHHAYDSDRFLVYASPAVAEALKGEESHALAELEVFIGKQVKVQIEPLYNQ  481 (489)
T ss_pred             CCCCCCCCCEEEECCHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHCCCHHHHHHHHHHHCCCEEEEECCCCCC
T ss_conf             78699889872655899999999999999986578873999988999999871578999999998599389995899886


Q ss_pred             CCEEEE
Q ss_conf             633897
Q gi|254780751|r  561 KLFYIE  566 (723)
Q Consensus       561 ~~f~Ie  566 (723)
                      ++|.|-
T Consensus       482 e~~~iv  487 (489)
T PRK11712        482 EQFDVV  487 (489)
T ss_pred             CCEEEE
T ss_conf             763899


No 3  
>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=100.00  E-value=0  Score=1139.00  Aligned_cols=453  Identities=43%  Similarity=0.680  Sum_probs=412.3

Q ss_pred             EEEEEEEE-CCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf             07999998-99899999607334604287879899783638823135327897713022213712102898899999998
Q gi|254780751|r   14 ETRVVVLR-DNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKE   92 (723)
Q Consensus        14 e~Rvav~e-~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~   92 (723)
                      |+|||+|+ +|.|.||+||+....+.+||||||+|+||+|||||||||||..||||||++||+++|+..+.....     
T Consensus         1 e~r~Al~~~~~~l~el~ier~~~~~~~GnIY~G~V~~vlPsl~AAFvdiG~~~~GFLh~sdi~~~~~~~~~~~~~-----   75 (464)
T TIGR00757         1 ETRVALVELGGQLQELIIERPKSRQLVGNIYKGRVTRVLPSLQAAFVDIGLEKNGFLHASDIGENSEKLEQLVDT-----   75 (464)
T ss_pred             CEEEEEEEECCEEEEEEEECCHHHCCHHHHHHCEEEEECCCCCEEEEECCCCCCCCCCHHHCCCCHHHHHHHHHC-----
T ss_conf             958999961877999998431110110023202020220376447742068835563033203324568888620-----


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             88631111100000001112233444334454222233445543322223432112211121100001223444421331
Q gi|254780751|r   93 SNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQE  172 (723)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~  172 (723)
                      ...                       .+..+.....           .............-+.+...........++|++
T Consensus        76 d~~-----------------------NA~~~a~~~~-----------~~~~~~~~kp~~~~QS~~~~~~~~~~~~~~I~e  121 (464)
T TIGR00757        76 DDD-----------------------NAEAEAAPAE-----------AKREAGQEKPEEIIQSSGDELERRQSKTASISE  121 (464)
T ss_pred             CCC-----------------------CCCCCCCHHH-----------HHHHHHCCCCHHHHCCCHHHHHHHHCCCCCHHH
T ss_conf             212-----------------------5767788233-----------220100136213202530245543135435266


Q ss_pred             CCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC--CEEEEE
Q ss_conf             068885799984033323456410123345765234422788751242046886899999999986300258--716998
Q gi|254780751|r  173 VIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAG--MGVILR  250 (723)
Q Consensus       173 ~lk~gq~ilVQV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~--~G~IiR  250 (723)
                      +|++||.|||||+|||+|+|||+|||+||||||||||||++++.+||||||.+.++|.+||+++.+...|.+  ||+|||
T Consensus       122 ~L~~gq~vlVQV~Kep~G~KGArLTt~ISlpGrYlVlmP~~~~~~g~SRri~~~~eR~rLK~~~~~~~~p~~nt~G~IiR  201 (464)
T TIGR00757       122 LLRPGQSVLVQVVKEPRGNKGARLTTDISLPGRYLVLMPNTSHQVGVSRRIESEEERERLKKLLRSEVLPEGNTMGLIIR  201 (464)
T ss_pred             HHCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEEEEEE
T ss_conf             61288858999885267898873546622462107855788943203441288245899999999853888770468998


Q ss_pred             EECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCHHHHHHHHHCCCCCCEEECCC----CCHHHHHHHHH
Q ss_conf             5045575799999999999999987764201432212-345645888888752376631111035----32036678889
Q gi|254780751|r  251 TAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHL-VYEEGNLIKRAIRDLYCKDISEIIVSG----EKGYREAKDFM  325 (723)
Q Consensus       251 T~a~~~~~~~l~~d~~~L~~~w~~i~~~~~~~~~p~l-i~~~~~~~~~~ird~~~~~~~~i~vd~----~~~~~~~~~~~  325 (723)
                      |||+++++++|.+|+++|++.|+.|++++....+|++ ||+|++++.++|||+++.++.+|+||+    ..+|..+.+|+
T Consensus       202 Taa~g~~~~~l~~D~~~L~~~W~~i~~~~~~~~~p~l~l~~E~~~i~r~~rD~~~~~~~~i~id~PaG~~~~y~~~~~~~  281 (464)
T TIGR00757       202 TAAEGASEEELKKDLEELLRKWEKIKEKAQKRSAPILELYEEDDIIKRVLRDYLDTDVKEIVIDSPAGMKEIYEEIKEFI  281 (464)
T ss_pred             ECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHH
T ss_conf             40379998999999999999899999985047854101124504789999985101257789728610799999999985


Q ss_pred             H-HHHHCCCCHHHHCCCCCH-HHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCC-CHHHHHHH
Q ss_conf             8-763101211220134420-35677699999998422214367864998328806999823755444555-11479999
Q gi|254780751|r  326 K-LLMPSYARIVRQYEDPHP-IFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHC-IEDTALQT  402 (723)
Q Consensus       326 ~-~~~p~~~~~v~~~~~~~~-lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~-~e~t~l~t  402 (723)
                      . .++|+...++.+|.+..| ||+.|+||.+|++||+|+||||||||||||+|||||+||||||+||+.++ +|||+|+|
T Consensus       282 ~~~~~Pe~~~Kl~~y~~~~p~~F~~f~ie~~i~~a~~r~V~L~SGGyivId~TEAlt~IDVNSG~~t~~~~n~EET~~~t  361 (464)
T TIGR00757       282 QDLVAPELVSKLKLYEGSLPPLFEGFQIEKQIEKALSRKVWLPSGGYIVIDQTEALTVIDVNSGRFTGKRNNLEETALNT  361 (464)
T ss_pred             HCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCEEECCCCCEEEECCCCCEEEEEECCCHHHCCCCCCHHHHHHH
T ss_conf             00147314541443037788766533368999998388575588878876587403787604503112578723568888


Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCC
Q ss_conf             99999999998731036863896033479888899999999997312787289986048614898515666301121002
Q gi|254780751|r  403 NLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTK  482 (723)
Q Consensus       403 NleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~  482 (723)
                      |||||+||||||||||||||||||||||.+.+||+.|++.|+++|+.||+|++|.+||.||||||||||.|+||.|.+++
T Consensus       362 NLEAA~EiArQLrLRnlGGiiiiDFIDM~~~k~~~~vl~~l~~~l~~DraR~~i~~~s~lGLvEmTRkR~r~SL~e~~~~  441 (464)
T TIGR00757       362 NLEAAKEIARQLRLRNLGGIIIIDFIDMKSEKNRRRVLERLKEALSRDRARIQILGISELGLVEMTRKRLRESLMEVLGE  441 (464)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHCCCCHHHHHCC
T ss_conf             89999999877521015847999510698866689999999999861663100110130103333042326743655247


Q ss_pred             CCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             36754653786061146899887
Q gi|254780751|r  483 VCTYCKGAGYIRSQSSVALSILR  505 (723)
Q Consensus       483 ~c~~c~g~g~~~~~~~~~~~~~r  505 (723)
                      .||+|+|+|+|++.+++++.|+|
T Consensus       442 ~CP~C~G~G~v~~~e~~~~~i~R  464 (464)
T TIGR00757       442 TCPHCSGRGIVKTSETVLLEIER  464 (464)
T ss_pred             CCCCCCCEEEEECCCCHHHHCCC
T ss_conf             88874741278326500021029


No 4  
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=944.98  Aligned_cols=485  Identities=47%  Similarity=0.717  Sum_probs=471.1

Q ss_pred             CCEEEEECCCCCEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCC
Q ss_conf             85268965289607999998998999996073346042878798997836388231353278977130222137121028
Q gi|254780751|r    2 ANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQI   81 (723)
Q Consensus         2 ~k~~lI~~~~~~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~i   81 (723)
                      .|+||||+++ +|||||++++|.|.||+||+..+.+++||||+|+|+||+|||||||||||.+||||||++||++ ||+.
T Consensus         1 ~k~~~i~~~~-~e~rva~v~~~~l~el~ie~~~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~   78 (487)
T COG1530           1 MKKMLINATQ-EETRVAVVDGGALQELDIERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRA   78 (487)
T ss_pred             CCEEEEECCC-CEEEEEEEECCEEEEEEEECCCCEEEECCCEEEEECCCCCCCHHHEEECCCCCCCEEEECCCCH-HHHH
T ss_conf             9507985265-4169999968877999980477376306716888623176632220551687660688410553-4420


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             98899999998886311111000000011122334443344542222334455433222234321122111211000012
Q gi|254780751|r   82 PFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVP  161 (723)
Q Consensus        82 p~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (723)
                      +.++                                                                            
T Consensus        79 ~~~~----------------------------------------------------------------------------   82 (487)
T COG1530          79 VLEE----------------------------------------------------------------------------   82 (487)
T ss_pred             CCCC----------------------------------------------------------------------------
T ss_conf             0023----------------------------------------------------------------------------


Q ss_pred             CCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHC
Q ss_conf             23444421331068885799984033323456410123345765234422788751242046886899999999986300
Q gi|254780751|r  162 KKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEV  241 (723)
Q Consensus       162 ~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~  241 (723)
                             +|+++++.||.++|||+|+|+|+|||+||++||++|||+||||+.+..+++|++|.+..+|.+|+.++..+..
T Consensus        83 -------~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT~~Is~~grylVl~p~~~~~g~is~ri~~~~er~~Lk~~~~~l~~  155 (487)
T COG1530          83 -------KIKVRLRGGQATLVQVVKEPRGTKGARLTTDISLAGRYLVLMPNAPDVGGISRRIEGEIERERLKEIVRELVD  155 (487)
T ss_pred             -------CCEEEECCCCEEEEEEEEECCCCCCCCCEEEEEECEEEEEECCCCCCCCCEEEEECCHHHHHHHHHHHHHCCC
T ss_conf             -------5005541786289999862576603421247860315899758987636421282887887767999860327


Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHH
Q ss_conf             25871699850455757999999999999999877642014322123456458888887523766311110353203667
Q gi|254780751|r  242 PAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREA  321 (723)
Q Consensus       242 ~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~~~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~  321 (723)
                      |.+||+|+||++++++.++|.+|+++|...|+.|+..+....+|++||++.+++.+++||+++.++.+|+||+...|..+
T Consensus       156 ~~~~g~iiRTa~~g~~~eel~~d~~~l~~~w~~i~~~~~~~~ap~ll~~e~~~v~r~~rd~~~~~~~~I~Vd~~~~~~~~  235 (487)
T COG1530         156 PGGMGLIIRTAGEGASEEELRRDLDYLRRLWEAILERAKKRPAPGLLYEETSLVVRVIRDYVGKDITEIVVDGKEAYLEA  235 (487)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEEEECCCCCCCCEEEECCCHHHHHH
T ss_conf             67842899640368468999999999998888998876237998699744761478752014676665998370588999


Q ss_pred             HHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHHHH
Q ss_conf             88898763101211220134420356776999999984222143678649983288069998237554445551147999
Q gi|254780751|r  322 KDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQ  401 (723)
Q Consensus       322 ~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~l~  401 (723)
                      +.|+..++|+...++++|.+..|+|+.|+++.||..+++|+||||||||||||+|||||+||||||++++.+++++|+++
T Consensus       236 ~~~~~~~~~~~~~~l~~~~~~~~~f~~~~ie~~i~~al~r~V~L~sGG~~vId~tEAlt~IDVnsg~~~~~~~~eeta~~  315 (487)
T COG1530         236 KEFILEIMPELRSKLKLYRGTTPLFALFGIEEQIARALERKVQLPSGGYLVIDPTEALTVIDVNSGRFTGAGDLEETAVN  315 (487)
T ss_pred             HHHHHHCCHHHHHHEEECCCCCCCCCHHHHHHHHHHHHHHEEECCCCCCEEEECCCEEEEEECCCCCCCCCCCHHHHHHH
T ss_conf             99887537122110476468873012356999999765406736889824673130138997157642366746776666


Q ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHC
Q ss_conf             99999999999873103686389603347988889999999999731278728998604861489851566630112100
Q gi|254780751|r  402 TNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTT  481 (723)
Q Consensus       402 tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~  481 (723)
                      ||||||.|||||||||||||||+||||||...++++.|+.+|+++|+.|++++++++||+|||+||||||.++||.+.++
T Consensus       316 tNleAa~eiarqlrlR~lgGiIiIDfIdm~~~~~~~~v~~~l~~~l~~dr~r~~i~~~s~~Gl~emtR~R~~~sl~~~~~  395 (487)
T COG1530         316 TNLEAAEEIARQLRLRNLGGIIIIDFIDMTEESHQRLVLERLRRALKRDRARIQIGRISELGLLEMTRKRTRESLLEVLS  395 (487)
T ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEECCCCCCEEEE
T ss_conf             20788999998872325577599983304125555889999999861588621124542267438998814777744566


Q ss_pred             CCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHC-CEEEEEECCCCCC
Q ss_conf             236754653786061146899887889997303643101357699999873023799999999848-8799984787788
Q gi|254780751|r  482 KVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFG-VSINVVIGIELAD  560 (723)
Q Consensus       482 ~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~-~~I~i~~d~~l~~  560 (723)
                      ++||+|.|+|++++.+++++.++|.|+.++.......+.+.+++.++.|++|+++..+..+|...+ ..+.+..++.+++
T Consensus       396 ~~cp~c~G~g~v~~~~~~~~~i~R~i~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~e~~~~~~~i~~~~~~~~~~  475 (487)
T COG1530         396 ERCPGCKGTGHVRSTESELLHILRYIEEEADINKTPEVGVEVPPAVAKYLLNEERGAIAELELFKGYLRVRLRVDDRVEQ  475 (487)
T ss_pred             EECCCCEEEEEEECCCHHHHHHHCCCHHHHCCCCCCCCEEEECHHHHHHHCCCCCCHHHHHHHHCCCEEEEEEECHHHCC
T ss_conf             38898501589943814412332002454401467500489506665554156430256787630552489740212155


Q ss_pred             CCEEEEECCCC
Q ss_conf             63389715544
Q gi|254780751|r  561 KLFYIEKGSPV  571 (723)
Q Consensus       561 ~~f~Ier~~~~  571 (723)
                      ++|.+.+....
T Consensus       476 ~~~~~~~~~~~  486 (487)
T COG1530         476 EQYEVVRLREG  486 (487)
T ss_pred             CCEEEEEECCC
T ss_conf             55057642147


No 5  
>pfam10150 RNase_E_G Ribonuclease E/G family. Ribonuclease E and Ribonuclease G are related enzymes that cleave a wide variety of RNAs.
Probab=100.00  E-value=0  Score=652.56  Aligned_cols=271  Identities=51%  Similarity=0.800  Sum_probs=266.3

Q ss_pred             CCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             45765234422788751242046886899999999986300258716998504557579999999999999998776420
Q gi|254780751|r  201 SLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELAL  280 (723)
Q Consensus       201 sl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~~  280 (723)
                      ||||||+||||+. .++||||||.+.++|.+|+.++..+ .|+++|+|+||+|++++.++|.+|+.+|.++|+.|.+.+.
T Consensus         1 sL~GRylVl~P~~-~~igiSrKI~d~~eR~rLk~i~~~~-~~~~~GiIiRT~A~~~~~e~l~~e~~~L~~~w~~i~~~~~   78 (271)
T pfam10150         1 SLPGRYLVLMPNS-PGIGISRKIEDEEERKRLKEILESL-KPEGMGLIIRTAAEGASEEELAADLEYLLKLWEEILKKAK   78 (271)
T ss_pred             CCCCCEEEEECCC-CCEEECCCCCCHHHHHHHHHHHHHH-CCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9886049995599-9707607889869999999999973-8898229997765689999999999999999999999984


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf             14322123456458888887523766311110353203667888987631012112201344203567769999999842
Q gi|254780751|r  281 NSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQ  360 (723)
Q Consensus       281 ~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~  360 (723)
                      ..++|+|||++++++.+++||+++.++++|+||+.+.|+.+++|+..++|....++.+|.+..|||+.|+|+.||+.||+
T Consensus        79 ~~~~p~ll~~~~~~~~~~lrD~~~~~~~~IivDd~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lF~~~~ie~~i~~~~~  158 (271)
T pfam10150        79 SAKAPSLLYEELDLVLRALRDLLNPDVDEIIVDDREAYEKLKEFLKEFAPELAKKVELYEGERPLFDLYGIEEQIEKALS  158 (271)
T ss_pred             CCCCCEEEEECCCHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHCCHHHHHHHHHC
T ss_conf             59998598838858999999726533509995688999999999998681111121021478886764585999999844


Q ss_pred             CCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             22143678649983288069998237554445551147999999999999998731036863896033479888899999
Q gi|254780751|r  361 TEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVE  440 (723)
Q Consensus       361 ~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~  440 (723)
                      ++||||||||||||+||||||||||||+++++++.++|+|+||||||+||||||||||||||||||||||++.+++++|+
T Consensus       159 ~~V~L~sGG~lvIe~TEAlt~IDVNSG~~~~~~~~e~t~l~~NleAa~EIarQlrLRni~GiIvIDFIdm~~~~~~~~v~  238 (271)
T pfam10150       159 RKVWLKSGGYLVIEQTEALTAIDVNSGKFTGKRNLEETALKTNLEAAKEIARQLRLRNLGGIIVIDFIDMEDEEHRRQVL  238 (271)
T ss_pred             CCEEECCCCEEEEECCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHH
T ss_conf             85891899779994251478985046655566777888999999999999999985688883999778889878899999


Q ss_pred             HHHHHHHHHCCCCEEEEEECCCCEEEEECCCCC
Q ss_conf             999997312787289986048614898515666
Q gi|254780751|r  441 KKLKESLKKDRARVQVGAISNFGLLEMSRQRIR  473 (723)
Q Consensus       441 ~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r  473 (723)
                      +.|+++|++|+++++|++||+||||||||||+|
T Consensus       239 ~~l~~~~~~D~~~~~i~~~T~lGL~E~tRkR~r  271 (271)
T pfam10150       239 RALKEALKRDRAKTQILGITELGLVEMTRKRTR  271 (271)
T ss_pred             HHHHHHHHHCCCCCEEECCCCCEEEEEEECCCC
T ss_conf             999999850999867936788714899750469


No 6  
>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=99.95  E-value=3.4e-28  Score=215.02  Aligned_cols=87  Identities=46%  Similarity=0.785  Sum_probs=79.1

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             34604287879899783638823135327897713022213712102898899999998886311111000000011122
Q gi|254780751|r   34 HKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVT  113 (723)
Q Consensus        34 ~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~  113 (723)
                      ++.+++||||+|+|+||+|||||||||||.+++||||++|+.+.||.                                 
T Consensus         2 ~~~~~vGnIY~GkV~~v~p~i~AAFVdiG~~k~gfL~~~d~~~~~~~---------------------------------   48 (88)
T cd04453           2 NREPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFK---------------------------------   48 (88)
T ss_pred             CCCCCCCCEEEEEEEEECCCCCEEEEECCCCCCEEEECHHCCHHHHC---------------------------------
T ss_conf             87561124899999886668748999658986899990345723513---------------------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCC
Q ss_conf             33444334454222233445543322223432112211121100001223444421331068885799984033323456
Q gi|254780751|r  114 IPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKG  193 (723)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kg  193 (723)
                                                                          +..+|.+.|++||.|||||+|||+++||
T Consensus        49 ----------------------------------------------------~~~~~~~~l~~G~~ilVQV~Ke~~~~Kg   76 (88)
T cd04453          49 ----------------------------------------------------KHKKIAKLLKEGQEILVQVVKEPIGTKG   76 (88)
T ss_pred             ----------------------------------------------------CCCCHHHHCCCCCEEEEEEEECCCCCCC
T ss_conf             ----------------------------------------------------5788778377999999999766879978


Q ss_pred             CCCCCCCCCCCC
Q ss_conf             410123345765
Q gi|254780751|r  194 AAVTTYLSLAGR  205 (723)
Q Consensus       194 a~lT~~isl~Gr  205 (723)
                      |+||++|||+||
T Consensus        77 p~lT~~isl~Gr   88 (88)
T cd04453          77 PRLTTNISLPGR   88 (88)
T ss_pred             CEEEEEEECCCC
T ss_conf             608845872889


No 7  
>PRK07252 hypothetical protein; Provisional
Probab=98.34  E-value=8.1e-07  Score=66.46  Aligned_cols=40  Identities=23%  Similarity=0.419  Sum_probs=36.5

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf             428787989978363882313532789771302221371210
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY   79 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~   79 (723)
                      .+|.+|.|+|++|.|-  +|||+++.+..||+|.|||.+.|.
T Consensus         2 kvGdiv~G~V~~I~~f--GaFV~l~~gv~GLiHISEis~~~v   41 (120)
T PRK07252          2 KIGDKLKGTITGIKPY--GAFVALENGTTGLIHISEIKTGFI   41 (120)
T ss_pred             CCCCEEEEEEEEEECC--EEEEEECCCCEEEEEHHHHCCCCC
T ss_conf             8888999999999754--579995799578888666010200


No 8  
>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=98.19  E-value=3.2e-06  Score=62.28  Aligned_cols=38  Identities=32%  Similarity=0.549  Sum_probs=34.6

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf             8787989978363882313532789771302221371210
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY   79 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~   79 (723)
                      |.||.|+|++|.|  -.|||+++.+..||||.|||.++|.
T Consensus         1 G~vv~G~V~~I~~--fGaFV~l~~g~~GL~HiSeis~~~v   38 (69)
T cd05692           1 GSVVEGTVTRLKP--FGAFVELGGGISGLVHISQIAHKRV   38 (69)
T ss_pred             CCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHHCCCCC
T ss_conf             9999999999985--3899996899889999698345655


No 9  
>PRK08582 hypothetical protein; Provisional
Probab=98.19  E-value=2.7e-06  Score=62.85  Aligned_cols=40  Identities=25%  Similarity=0.385  Sum_probs=36.1

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf             428787989978363882313532789771302221371210
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY   79 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~   79 (723)
                      -+|+||.|+|++|.|-  .|||+|+.+..||+|.+||..+|-
T Consensus         4 evG~iv~G~V~~I~~f--GaFV~l~~g~~GLvHISeis~~~V   43 (139)
T PRK08582          4 EVGSKLQGKVTGITNF--GAFVELPEGKTGLVHISEVADNYV   43 (139)
T ss_pred             CCCCEEEEEEEEEECC--EEEEEECCCCEEEEEHHHHCCCCC
T ss_conf             4787999999899641--789995699667887366256656


No 10 
>PRK05807 hypothetical protein; Provisional
Probab=98.14  E-value=3.4e-06  Score=62.11  Aligned_cols=39  Identities=23%  Similarity=0.396  Sum_probs=34.7

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf             428787989978363882313532789771302221371210
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY   79 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~   79 (723)
                      .+|+||.|+|++|.|=  .|||+++ ++.||+|++||...|-
T Consensus         4 evG~iv~G~V~~I~~f--GaFV~l~-g~~GLvHISEis~~~V   42 (136)
T PRK05807          4 EAGSILEGTVVNITNF--GAFVEVE-GKTGLVHISEVADTYV   42 (136)
T ss_pred             CCCCEEEEEEEEEECC--EEEEEEC-CEEEEEEHHHHCCCCC
T ss_conf             5788999999999724--4799978-9276898567077643


No 11 
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.12  E-value=1.2e-05  Score=58.37  Aligned_cols=125  Identities=18%  Similarity=0.298  Sum_probs=82.8

Q ss_pred             CCCCCEEEEEEEEECCCCCEEEEEEC--CCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             04287879899783638823135327--8977130222137121028988999999988863111110000000111223
Q gi|254780751|r   37 QIKGNIYLAKVTRVEPSLQAAFVDYG--GNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTI  114 (723)
Q Consensus        37 ~~~GnIY~G~V~~V~p~lqAAFVdiG--~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  114 (723)
                      .-.|.|+.|+|++|.+  .+|||++.  .+..||+|+|||.+.+.                                   
T Consensus         6 Pe~g~~v~~~V~~i~~--~Ga~v~l~ey~~~eG~i~isEis~~~v-----------------------------------   48 (262)
T PRK03987          6 PEEGELVVGTVKEVKD--FGAFVTLDEYPGKEGFIHISEVASGWV-----------------------------------   48 (262)
T ss_pred             CCCCCEEEEEEEEEEC--CEEEEEECCCCCCCEEEEHHHCCHHHH-----------------------------------
T ss_conf             9999889999999956--679999356599316788798346775-----------------------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCC
Q ss_conf             34443344542222334455433222234321122111211000012234444213310688857999840333234564
Q gi|254780751|r  115 PNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGA  194 (723)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga  194 (723)
                                                                           .+|.+++++||.+.|+|.+=-      
T Consensus        49 -----------------------------------------------------~~i~d~~k~G~~v~~kVi~vd------   69 (262)
T PRK03987         49 -----------------------------------------------------KNIRDYVKEGQKVVCKVIRVD------   69 (262)
T ss_pred             -----------------------------------------------------HCHHHHCCCCCEEEEEEEEEC------
T ss_conf             -----------------------------------------------------199985158988999999883------


Q ss_pred             CCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCC--CCHHHHHHHHHH-HHHH
Q ss_conf             1012334576523442278875124204688689999999998630025871699850455--757999999999-9999
Q gi|254780751|r  195 AVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGAS--RTKIEIKRDFEY-LMRL  271 (723)
Q Consensus       195 ~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~--~~~~~l~~d~~~-L~~~  271 (723)
                                      |..+ .+.+|.|-.++++++...+......   -..-|+|.+|..  .+.+++...+.. |.+.
T Consensus        70 ----------------~~kg-~IdLS~k~Vs~~e~~~~~~~~k~~k---~a~~il~~va~~~~~~~ee~~~~i~~~l~~~  129 (262)
T PRK03987         70 ----------------PKKG-HIDLSLKRVNEHQRREKIQEWKNEQ---KAEKLLELAAEKLGKDLEEAWEEVGYKLEEE  129 (262)
T ss_pred             ----------------CCCC-EEEEECCCCCHHHHHHHHHHHHHHH---HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             ----------------8788-7871104499899999999999999---9999999999982989899999999999998


Q ss_pred             HHHHHH
Q ss_conf             998776
Q gi|254780751|r  272 WDNVRE  277 (723)
Q Consensus       272 w~~i~~  277 (723)
                      |.....
T Consensus       130 yg~~y~  135 (262)
T PRK03987        130 FGDLYD  135 (262)
T ss_pred             HCCHHH
T ss_conf             560989


No 12 
>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=98.10  E-value=5.8e-06  Score=60.55  Aligned_cols=39  Identities=21%  Similarity=0.361  Sum_probs=34.7

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEEC--CCCCCCCCHHHCCCCC
Q ss_conf             4287879899783638823135327--8977130222137121
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYG--GNRHGFLPFLEIHPDY   78 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG--~~k~gFL~~~ei~~~y   78 (723)
                      ..|+||.|+|++|.|  -+|||+++  .+..||+|.+||.+.+
T Consensus         2 e~G~iv~G~V~~i~~--~GafV~l~e~~g~eGlihiSEis~~~   42 (76)
T cd04452           2 EEGELVVVTVKSIAD--MGAYVSLLEYGNIEGMILLSELSRRR   42 (76)
T ss_pred             CCCCEEEEEEEEEEC--CEEEEEECCCCCCEEEEEHHHCCCCC
T ss_conf             889999999999973--46999973369919999979968451


No 13 
>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=98.04  E-value=7.9e-06  Score=59.59  Aligned_cols=38  Identities=21%  Similarity=0.290  Sum_probs=33.3

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEE-CCCCCCCCCHHHCCCC
Q ss_conf             428787989978363882313532-7897713022213712
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDY-GGNRHGFLPFLEIHPD   77 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdi-G~~k~gFL~~~ei~~~   77 (723)
                      .+|.||.|+|++|.|=  .|||+| |.++.|++|.|||.+.
T Consensus         2 evg~i~~G~V~~i~~f--GAFV~i~g~~~~GLvHiSeis~~   40 (73)
T cd05686           2 ALYQIFKGEVASVTEY--GAFVKIPGCRKQGLVHKSHMSSC   40 (73)
T ss_pred             CCCCEEEEEEEEEEEC--CEEEEECCCCCCEEEEEECCCCC
T ss_conf             7886999999899753--23999089884355995605412


No 14 
>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=97.99  E-value=1.1e-05  Score=58.54  Aligned_cols=39  Identities=13%  Similarity=0.140  Sum_probs=34.2

Q ss_pred             CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEEC
Q ss_conf             310135769999987302379999999984887999847
Q gi|254780751|r  517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIG  555 (723)
Q Consensus       517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d  555 (723)
                      .-.++.++|+-..-+.+..-..|..|.+++|++|.|..|
T Consensus       551 ~i~~~~i~~~ki~~vIG~gGk~Ik~i~~~tg~~I~i~dd  589 (684)
T TIGR03591       551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD  589 (684)
T ss_pred             EEEEEEECHHHHHHEECCCCHHHHHHHHHHCCEEEEECC
T ss_conf             579999787886650787528898999988988998589


No 15 
>PRK08059 general stress protein 13; Validated
Probab=97.98  E-value=1.1e-05  Score=58.54  Aligned_cols=41  Identities=24%  Similarity=0.370  Sum_probs=36.1

Q ss_pred             CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf             6042878798997836388231353278977130222137121
Q gi|254780751|r   36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY   78 (723)
Q Consensus        36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y   78 (723)
                      ..-+|.||.|+|++|.|  -+|||+++.+-.||||++||...+
T Consensus         3 k~kvGdiv~G~V~~I~~--fG~FV~l~~gv~GLihiSEls~~~   43 (119)
T PRK08059          3 QYEVGVVVTGKVTGIQD--YGAFVALDEETQGLVHISEITHGF   43 (119)
T ss_pred             CCCCCCEEEEEEEEEEC--EEEEEEEECCCEEEEEHHHHCCCC
T ss_conf             78999999999999974--048999943953788878824566


No 16 
>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=97.97  E-value=1.6e-05  Score=57.38  Aligned_cols=37  Identities=27%  Similarity=0.493  Sum_probs=33.6

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf             878798997836388231353278977130222137121
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY   78 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y   78 (723)
                      |.||.|+|++|.|  =.|||+++.+..||+|.|||.+++
T Consensus         1 G~iv~G~V~~i~~--fG~FV~l~~g~~GLiHiSeis~~~   37 (68)
T cd04472           1 GKIYEGKVVKIKD--FGAFVEILPGKDGLVHISELSDER   37 (68)
T ss_pred             CCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHHCCCC
T ss_conf             9999999999973--299999579962488868934565


No 17 
>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=97.95  E-value=1.8e-05  Score=57.06  Aligned_cols=40  Identities=40%  Similarity=0.635  Sum_probs=36.0

Q ss_pred             CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf             042878798997836388231353278977130222137121
Q gi|254780751|r   37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY   78 (723)
Q Consensus        37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y   78 (723)
                      ..+|.|+.|+|.+|.+  .+|||++|.+-.||+|.+++++++
T Consensus         2 ~~~G~iv~G~V~~i~~--~G~fV~l~~~~~g~v~~s~ls~~~   41 (74)
T pfam00575         2 PEEGDVVKGTVTRVTK--GGAFVDLGNGVEGFIPISEISDDR   41 (74)
T ss_pred             CCCCCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHCCCCC
T ss_conf             8899999999999987--759999789979999844613655


No 18 
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.91  E-value=1.8e-05  Score=57.09  Aligned_cols=39  Identities=15%  Similarity=0.154  Sum_probs=33.8

Q ss_pred             CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEEC
Q ss_conf             310135769999987302379999999984887999847
Q gi|254780751|r  517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIG  555 (723)
Q Consensus       517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d  555 (723)
                      +-..+.++|+-..-+.+..-..|..|.+.+|++|.|..|
T Consensus       554 ~i~~~~i~~~ki~~vIG~gGk~Ik~i~e~tg~~Idi~dd  592 (694)
T PRK11824        554 RIETIKIDPDKIRDVIGPGGKTIREITEETGAKIDIEDD  592 (694)
T ss_pred             EEEEEEECHHHHHHEECCCHHHHHHHHHHHCCEEEEECC
T ss_conf             799999787986650686338899999988988999689


No 19 
>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=97.87  E-value=3.2e-05  Score=55.39  Aligned_cols=40  Identities=23%  Similarity=0.345  Sum_probs=34.8

Q ss_pred             CCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCC
Q ss_conf             460428787989978363882313532789771302221371
Q gi|254780751|r   35 KKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHP   76 (723)
Q Consensus        35 ~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~   76 (723)
                      +.--+|.||.|+|++|.+  =.|||+++.+..|.+|.|++..
T Consensus        12 ~dlevG~~y~G~V~~v~~--fGaFV~l~~~~~GLiHiS~l~~   51 (77)
T cd04473          12 EDLEVGKLYKGKVNGVAK--YGVFVDLNDHVRGLIHRSNLLR   51 (77)
T ss_pred             CCCCCCCEEEEEEEEEEE--CCEEEECCCCCEEEEEEHHCCC
T ss_conf             035239999999988966--2889992699879689316668


No 20 
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=97.84  E-value=1.6e-05  Score=57.38  Aligned_cols=79  Identities=24%  Similarity=0.348  Sum_probs=63.4

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             42878798997836388231353278977130222137121028988999999988863111110000000111223344
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPND  117 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  117 (723)
                      -+|+++.|+|+.|-|=  .|||++-.+..|+.|+|||.-.|-.                                     
T Consensus         4 kvG~~l~GkItgI~~y--GAFV~l~~g~tGLVHISEIa~~fVk-------------------------------------   44 (129)
T COG1098           4 KVGSKLKGKITGITPY--GAFVELEGGKTGLVHISEIADGFVK-------------------------------------   44 (129)
T ss_pred             CCCCEEEEEEEEEEEC--CEEEEECCCCCCEEEEHHHHHHHHH-------------------------------------
T ss_conf             3464678889756743--3489823997314883575443677-------------------------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCC
Q ss_conf             43344542222334455433222234321122111211000012234444213310688857999840333234564101
Q gi|254780751|r  118 HSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVT  197 (723)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT  197 (723)
                                                                         .|.+.|++||+|.|||.-=..       .
T Consensus        45 ---------------------------------------------------dI~d~L~vG~eV~vKVl~ide-------~   66 (129)
T COG1098          45 ---------------------------------------------------DIHDHLKVGQEVKVKVLDIDE-------N   66 (129)
T ss_pred             ---------------------------------------------------HHHHHHCCCCEEEEEEEEECC-------C
T ss_conf             ---------------------------------------------------399884278879999972146-------8


Q ss_pred             CCCCCCCCCEEECCCC
Q ss_conf             2334576523442278
Q gi|254780751|r  198 TYLSLAGRYSVLMPNT  213 (723)
Q Consensus       198 ~~isl~Gry~Vl~P~~  213 (723)
                      ..|||.=|-+...|..
T Consensus        67 GKisLSIr~~~e~pe~   82 (129)
T COG1098          67 GKISLSIRKLEEEPEK   82 (129)
T ss_pred             CCCCEEHHHHHHCCCC
T ss_conf             9703356876647443


No 21 
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.84  E-value=2.9e-05  Score=55.70  Aligned_cols=38  Identities=18%  Similarity=0.281  Sum_probs=33.4

Q ss_pred             CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf             6042878798997836388231353278977130222137
Q gi|254780751|r   36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH   75 (723)
Q Consensus        36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~   75 (723)
                      .-..|.|..|+|..|..  ..+|||+|.--.||+|..|+.
T Consensus        30 ~i~~G~iV~G~Vv~I~~--d~v~VDiG~KsEG~Ip~~E~~   67 (489)
T PRK13806         30 NVRVGDRIKAAIVAIGE--DSVFVATGSKVDGVIDRRELE   67 (489)
T ss_pred             CCCCCCEEEEEEEEEEC--CEEEEEECCCEEEEEEHHHHC
T ss_conf             77799889999999979--989999689828995899925


No 22 
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.83  E-value=3.4e-05  Score=55.20  Aligned_cols=40  Identities=25%  Similarity=0.465  Sum_probs=31.5

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf             346042878798997836388231353278977130222137
Q gi|254780751|r   34 HKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH   75 (723)
Q Consensus        34 ~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~   75 (723)
                      ......|.|..|.|+.|.+..  ||||+|.--.||+|.+|+.
T Consensus        16 ~~~~~~G~vV~G~Vv~i~~~~--v~Vdig~Kseg~ip~~E~~   55 (541)
T COG0539          16 DEEFEPGDVVKGTVVSIEKDG--VLVDIGGKSEGVIPISEFS   55 (541)
T ss_pred             HHCCCCCCEEEEEEEEEECCE--EEEEECCCCCCEEEHHHCC
T ss_conf             311688878999999993884--9998367615576889805


No 23 
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=97.81  E-value=4.1e-05  Score=54.64  Aligned_cols=70  Identities=23%  Similarity=0.367  Sum_probs=58.8

Q ss_pred             CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             28787989978363882313532789771302221371210289889999999888631111100000001112233444
Q gi|254780751|r   39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDH  118 (723)
Q Consensus        39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  118 (723)
                      .|.||.|+|+++.+  ..+||++|.+-.||||++++.+.|.                                       
T Consensus         2 ~G~iv~g~V~~v~~--~g~~v~i~~~~~g~l~~~~l~~~~~---------------------------------------   40 (72)
T smart00316        2 VGDVVEGTVTEITP--FGAFVDLGNGVEGLIPISELSDKRV---------------------------------------   40 (72)
T ss_pred             CCCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHCCCCCC---------------------------------------
T ss_conf             99899999999978--7399997699899998075055554---------------------------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCCC
Q ss_conf             33445422223344554332222343211221112110000122344442133106888579998403332345641012
Q gi|254780751|r  119 SLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTT  198 (723)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~  198 (723)
                                                                       ..+.+.++.||.|-++|.+-...++...||.
T Consensus        41 -------------------------------------------------~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~   71 (72)
T smart00316       41 -------------------------------------------------KDPEEVLKVGDEVKVKVLSVDEEKGRIILSL   71 (72)
T ss_pred             -------------------------------------------------CCHHHEECCCCEEEEEEEEEECCCCEEEEEE
T ss_conf             -------------------------------------------------7846836389899999999999999999985


No 24 
>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=97.65  E-value=0.0001  Score=51.93  Aligned_cols=39  Identities=31%  Similarity=0.337  Sum_probs=34.1

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEE-CCCCCCCCCHHHCCCCC
Q ss_conf             428787989978363882313532-78977130222137121
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDY-GGNRHGFLPFLEIHPDY   78 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdi-G~~k~gFL~~~ei~~~y   78 (723)
                      .+|.+|.|+|++|.|  =+|||++ |.+-.||+|.+|+.+++
T Consensus         1 kVG~~v~G~V~~i~~--fG~FV~l~g~~i~GLvHiSels~~~   40 (77)
T cd05708           1 KVGQKIDGTVRRVED--YGVFIDIDGTNVSGLCHKSEISDNR   40 (77)
T ss_pred             CCCCEEEEEEEEEEC--EEEEEEECCCCEEEEEEHHHHCCCC
T ss_conf             998999999999964--1789996789807998878817565


No 25 
>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=97.63  E-value=1e-04  Score=51.95  Aligned_cols=36  Identities=28%  Similarity=0.530  Sum_probs=31.4

Q ss_pred             CCEEEEEEEEECCCCCEEEEEEC---CCCCCCCCHHHCCCC
Q ss_conf             87879899783638823135327---897713022213712
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYG---GNRHGFLPFLEIHPD   77 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG---~~k~gFL~~~ei~~~   77 (723)
                      |+||.|+|++|.|  -+|||++.   .+..|++|.|||.++
T Consensus         1 G~i~~G~V~~i~~--fGaFV~l~~~~~~~~GLvHiSeis~~   39 (79)
T cd05684           1 GKIYKGKVTSIMD--FGCFVQLEGLKGRKEGLVHISQLSFE   39 (79)
T ss_pred             CCEEEEEEEEEEE--EEEEEEEECCCCCCEEEEEHHHCCCC
T ss_conf             9999999989975--33999996788980678995681575


No 26 
>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=97.58  E-value=0.00015  Score=50.81  Aligned_cols=40  Identities=23%  Similarity=0.399  Sum_probs=35.5

Q ss_pred             CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf             042878798997836388231353278977130222137121
Q gi|254780751|r   37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY   78 (723)
Q Consensus        37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y   78 (723)
                      -.+|.|+.|+|++|.|  -++||+++.+-.||+|.+++...+
T Consensus        12 lk~G~iv~G~V~~i~~--~G~FV~l~~~v~Glv~~s~ls~~~   51 (83)
T cd04461          12 LKPGMVVHGYVRNITP--YGVFVEFLGGLTGLAPKSYISDEF   51 (83)
T ss_pred             CCCCCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHCCCCC
T ss_conf             7999999999999927--819999569948998999968642


No 27 
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.55  E-value=0.00015  Score=50.68  Aligned_cols=40  Identities=28%  Similarity=0.513  Sum_probs=34.8

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf             346042878798997836388231353278977130222137
Q gi|254780751|r   34 HKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH   75 (723)
Q Consensus        34 ~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~   75 (723)
                      ......|.|..|+|..|.+  ..+|||||....||||.+|+.
T Consensus        26 ~~~~k~GdiVeG~V~~I~~--~~v~VdiG~k~eG~i~~~E~s   65 (314)
T PRK07400         26 DYHFKPGDIVNGTVFSLEP--KGALIDIGAKTAAFMPLQEMS   65 (314)
T ss_pred             HCCCCCCCEEEEEEEEEEC--CEEEEEECCCEEEEEEHHHHC
T ss_conf             2369999989999999979--989999779807999999936


No 28 
>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=97.49  E-value=0.00022  Score=49.59  Aligned_cols=38  Identities=26%  Similarity=0.423  Sum_probs=34.0

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf             8787989978363882313532789771302221371210
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY   79 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~   79 (723)
                      |.||.|+|++|.|  -.|||++|.+-.||+|.+++...|.
T Consensus         1 G~iv~G~V~~i~~--fG~FV~l~~~~~GLvhisels~~~~   38 (68)
T cd05685           1 GMVLEGVVTNVTD--FGAFVDIGVKQDGLIHISKMADRFV   38 (68)
T ss_pred             CCEEEEEEEEEEC--EEEEEEECCCCEEEEECHHHCCCCC
T ss_conf             9999999999965--2899991499789998189767876


No 29 
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.48  E-value=0.00018  Score=50.15  Aligned_cols=10  Identities=30%  Similarity=0.614  Sum_probs=3.6

Q ss_pred             HHCCCCEEEE
Q ss_conf             1036863896
Q gi|254780751|r  416 LRDLAGLIVV  425 (723)
Q Consensus       416 LRnlgGiIvI  425 (723)
                      +.|=.|.|+.
T Consensus       362 ~ed~~G~i~L  371 (670)
T PRK00087        362 LENEDGYVVL  371 (670)
T ss_pred             EECCCCCEEE
T ss_conf             8689982998


No 30 
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.46  E-value=0.00021  Score=49.76  Aligned_cols=62  Identities=23%  Similarity=0.315  Sum_probs=48.7

Q ss_pred             CCEEEEEEEECCEEEEEE--ECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf             960799999899899999--6073346042878798997836388231353278977130222137
Q gi|254780751|r   12 VEETRVVVLRDNRVEELD--FESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH   75 (723)
Q Consensus        12 ~~e~Rvav~e~g~l~e~~--~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~   75 (723)
                      +.-.+||+-+-|--.||.  +|..-+.-..|.|..|+|..|.+.  .+|||||.--.||+|.+|+.
T Consensus         6 ~~~~~~~~~~~~S~edf~~~le~s~k~~~eGdIV~GtVv~I~~d--~VlVDIG~KsEGiIP~~E~s   69 (484)
T PRK07899          6 VTSPQVAVNDIGSAEDFLAAIDKTIKYFNDGDIVEGTVVKVDRD--EVLLDIGYKTEGVIPSRELS   69 (484)
T ss_pred             CCCCEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEEEEEEECC--EEEEEECCCEEEEEEHHHHC
T ss_conf             88760676589999999998887873588998899999999789--89998268704787999946


No 31 
>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=97.40  E-value=0.00026  Score=49.05  Aligned_cols=36  Identities=25%  Similarity=0.434  Sum_probs=32.1

Q ss_pred             CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC
Q ss_conf             287879899783638823135327897713022213712
Q gi|254780751|r   39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD   77 (723)
Q Consensus        39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~   77 (723)
                      .|.||.|+|++|.|  -+|||+++ +-.||+|.+|+++.
T Consensus         1 eG~iv~g~V~~i~~--fG~FV~l~-gi~Glihisels~~   36 (68)
T cd05688           1 EGDVVEGTVKSITD--FGAFVDLG-GVDGLLHISDMSWG   36 (68)
T ss_pred             CCCEEEEEEEEEEC--CEEEEEEC-CEEEEEECHHHCCC
T ss_conf             99999999999956--38899979-98999984364666


No 32 
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.38  E-value=0.00029  Score=48.76  Aligned_cols=38  Identities=24%  Similarity=0.392  Sum_probs=33.8

Q ss_pred             CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf             6042878798997836388231353278977130222137
Q gi|254780751|r   36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH   75 (723)
Q Consensus        36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~   75 (723)
                      ..-.|.|..|+|.+|.+  +.+|||+|.--.|++|..|+.
T Consensus        17 ~~~~G~iV~G~Vv~i~~--~~v~VdiG~K~eG~I~~~E~~   54 (556)
T PRK06299         17 ELREGSIVKGTVVAIDK--DYVLVDVGLKSEGRIPLEEFK   54 (556)
T ss_pred             CCCCCCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHHC
T ss_conf             78899989999999979--999999688835787999934


No 33 
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.37  E-value=0.00024  Score=49.24  Aligned_cols=37  Identities=27%  Similarity=0.405  Sum_probs=22.1

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC
Q ss_conf             4287879899783638823135327897713022213712
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD   77 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~   77 (723)
                      ..|.++.|+|++|.+  -+||||+| +-.||||.+||.+.
T Consensus       190 ~~G~vv~G~V~~i~~--~GaFVdlg-gvdGllhiseiSw~  226 (556)
T PRK06299        190 EEGQVVEGVVKNITD--YGAFVDLG-GVDGLLHITDISWK  226 (556)
T ss_pred             CCCCEEEEEEEEEEC--CCEEEEEC-CEEEEEEHHHCCCC
T ss_conf             479727899999705--75899958-95899985671556


No 34 
>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=97.36  E-value=0.00037  Score=47.99  Aligned_cols=37  Identities=27%  Similarity=0.517  Sum_probs=33.5

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf             878798997836388231353278977130222137121
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY   78 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y   78 (723)
                      |.|+.|.|++|.|.  .|||++..+-.||+|.+||..+|
T Consensus         1 G~vv~G~V~~i~~~--G~fV~~~~~i~Glvp~seis~~~   37 (70)
T cd05698           1 GLKTHGTIVKVKPN--GCIVSFYNNVKGFLPKSELSEAF   37 (70)
T ss_pred             CCEEEEEEEEEECC--CEEEEECCCCEEEEEHHHHCCCC
T ss_conf             99999999999817--18999489969998989928320


No 35 
>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=97.35  E-value=0.00043  Score=47.53  Aligned_cols=35  Identities=29%  Similarity=0.509  Sum_probs=31.8

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCC
Q ss_conf             8787989978363882313532789771302221371
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHP   76 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~   76 (723)
                      |.|..|+|..|.+  ..||||||..-.||||.+|+..
T Consensus         1 G~iV~G~V~~i~~--~gv~Vdig~k~eG~ip~~E~s~   35 (70)
T cd05687           1 GDIVKGTVVSVDD--DEVLVDIGYKSEGIIPISEFSD   35 (70)
T ss_pred             CCEEEEEEEEEEC--CEEEEEECCCCCEEEEHHHHCC
T ss_conf             9989999999978--8699996898502689999453


No 36 
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.35  E-value=0.0002  Score=49.87  Aligned_cols=62  Identities=10%  Similarity=0.012  Sum_probs=28.1

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHH-------HHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCE
Q ss_conf             9985045575799999999999999987-------7642014322123456458888887523766311
Q gi|254780751|r  248 ILRTAGASRTKIEIKRDFEYLMRLWDNV-------RELALNSVAPHLVYEEGNLIKRAIRDLYCKDISE  309 (723)
Q Consensus       248 IiRT~a~~~~~~~l~~d~~~L~~~w~~i-------~~~~~~~~~p~li~~~~~~~~~~ird~~~~~~~~  309 (723)
                      -|-..|...+++.+..-+.+-+...+.+       ........-+........-+...+++.+..++.+
T Consensus       187 MVE~~a~~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~~~~~~~~~~~l~~~i~~~~~~~l~~  255 (692)
T COG1185         187 MVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSLDEELEAKVRDLAEDELKE  255 (692)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             043466668889999999988898999999999999973765532335686489999999986788999


No 37 
>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=97.33  E-value=0.00048  Score=47.19  Aligned_cols=38  Identities=21%  Similarity=0.305  Sum_probs=34.4

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC
Q ss_conf             4287879899783638823135327897713022213712
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD   77 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~   77 (723)
                      -.|.+|.|+|++|.+  -+|||+|+.+-.|++|.||+.+.
T Consensus         2 ~~G~~v~G~V~~It~--fG~FV~i~~g~eGLvHiSelsw~   39 (72)
T cd05689           2 PEGTRLFGKVTNLTD--YGCFVELEEGVEGLVHVSEMDWT   39 (72)
T ss_pred             CCCCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHCCCC
T ss_conf             889999999989947--62399966993899997663165


No 38 
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.29  E-value=0.00049  Score=47.15  Aligned_cols=83  Identities=19%  Similarity=0.214  Sum_probs=67.0

Q ss_pred             CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             04287879899783638823135327897713022213712102898899999998886311111000000011122334
Q gi|254780751|r   37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPN  116 (723)
Q Consensus        37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (723)
                      -..|.+..|+|+++-|  ..||||||. =.|+||.+||.+.+-.                                    
T Consensus       190 l~~G~vV~G~V~~It~--~GafVdigG-vdGLlHiseiS~~rv~------------------------------------  230 (541)
T COG0539         190 LEVGEVVEGVVKNITD--YGAFVDIGG-VDGLLHISEISWKRVD------------------------------------  230 (541)
T ss_pred             CCCCCEEEEEEEEEEC--CCEEEEECC-EEEEEEHHHCCCCCCC------------------------------------
T ss_conf             7887669999998615--747999257-1668864760655558------------------------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCC
Q ss_conf             44334454222233445543322223432112211121100001223444421331068885799984033323456410
Q gi|254780751|r  117 DHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAV  196 (723)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~l  196 (723)
                                                                          .-.++++.||+|-|+|.+--..++--.|
T Consensus       231 ----------------------------------------------------~P~~vvkvGd~VkvkVi~~D~e~~RVsL  258 (541)
T COG0539         231 ----------------------------------------------------HPSEVVKVGDEVKVKVISLDEERGRVSL  258 (541)
T ss_pred             ----------------------------------------------------CHHHHCCCCCEEEEEEEEECCCCCEEEE
T ss_conf             ----------------------------------------------------9899535698899999997267886999


Q ss_pred             CCCCCCCCCCEEEC
Q ss_conf             12334576523442
Q gi|254780751|r  197 TTYLSLAGRYSVLM  210 (723)
Q Consensus       197 T~~isl~Gry~Vl~  210 (723)
                      |..-++++.|.-+-
T Consensus       259 SlK~l~~dPw~~i~  272 (541)
T COG0539         259 SLKQLEEDPWEGIE  272 (541)
T ss_pred             EEHHCCCCCHHHHH
T ss_conf             94650469477776


No 39 
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.28  E-value=0.00073  Score=45.93  Aligned_cols=39  Identities=26%  Similarity=0.463  Sum_probs=33.6

Q ss_pred             CCCCCCEEEEEEEEECCCCCEEEEEE-CCCCCCCCCHHHCCC
Q ss_conf             60428787989978363882313532-789771302221371
Q gi|254780751|r   36 KQIKGNIYLAKVTRVEPSLQAAFVDY-GGNRHGFLPFLEIHP   76 (723)
Q Consensus        36 ~~~~GnIY~G~V~~V~p~lqAAFVdi-G~~k~gFL~~~ei~~   76 (723)
                      .-.+|.|..|+|.+|.+  ..+|||+ |..-.||+|.+|+..
T Consensus        14 ~i~~G~iV~G~V~~I~~--~~v~Vdi~G~k~eG~I~~~E~s~   53 (390)
T PRK06676         14 EVEVGDVVTGEVLKVED--KQVFVNIEGYKVEGVIPISELSN   53 (390)
T ss_pred             CCCCCCEEEEEEEEEEC--CEEEEEECCCEEEEEEEHHHHCC
T ss_conf             68999989999999989--98999933863589999999456


No 40 
>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=97.25  E-value=0.00066  Score=46.26  Aligned_cols=37  Identities=38%  Similarity=0.515  Sum_probs=33.6

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf             878798997836388231353278977130222137121
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY   78 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y   78 (723)
                      |.|+.|+|++|.|.  .|||++|.+-.||+|.+|+.+++
T Consensus         1 G~iV~G~V~~i~~~--G~fV~l~~~v~G~ih~sels~~~   37 (73)
T cd05691           1 GSIVTGKVTEVDAK--GATVKLGDGVEGFLRAAELSRDR   37 (73)
T ss_pred             CCEEEEEEEEEECC--CEEEEECCCCEEEEEHHHCCCCH
T ss_conf             99999999999778--68999289969999989978211


No 41 
>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=97.21  E-value=0.00095  Score=45.16  Aligned_cols=40  Identities=25%  Similarity=0.319  Sum_probs=36.2

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf             428787989978363882313532789771302221371210
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY   79 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~   79 (723)
                      .+|.|+-|+|++|-|.  .|||++|.+-.|+.|.+|+..+|-
T Consensus         2 kvG~~l~G~Vt~V~~~--g~fV~L~~~~~Glvhisel~dd~~   41 (73)
T cd05706           2 KVGDILPGRVTKVNDR--YVLVQLGNKVTGPSFITDALDDYS   41 (73)
T ss_pred             CCCCEEEEEEEEECCC--EEEEEECCCCEEEEEHHHHCCCCC
T ss_conf             8898999999998888--799990899479999899304601


No 42 
>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=97.17  E-value=0.00097  Score=45.10  Aligned_cols=36  Identities=19%  Similarity=0.355  Sum_probs=32.9

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC
Q ss_conf             87879899783638823135327897713022213712
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD   77 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~   77 (723)
                      |.+|.|+|++|.+-  .|||++..+-.||+|.+|+.++
T Consensus         1 G~~v~G~V~~i~~f--G~FV~l~~gieGLvHiselsw~   36 (69)
T cd05690           1 GTVVSGKIKSITDF--GIFVGLDGGIDGLVHISDISWT   36 (69)
T ss_pred             CCEEEEEEEEECCC--EEEEEECCCCEEEEEHHHHCCC
T ss_conf             99999999999131--8999976996599994882456


No 43 
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.04  E-value=0.001  Score=44.85  Aligned_cols=37  Identities=27%  Similarity=0.372  Sum_probs=23.8

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC
Q ss_conf             4287879899783638823135327897713022213712
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD   77 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~   77 (723)
                      ..|.|+.|+|+++.+=  .||||+| +-.||||++||.+.
T Consensus       207 ~~G~vveG~Vk~It~f--GAFVDLG-GVDGLvHiSEiSW~  243 (484)
T PRK07899        207 QKGQVRKGVVSSIVNF--GAFVDLG-GVDGLVHVSELSWK  243 (484)
T ss_pred             CCCCEEEEEEEEECCC--EEEEEEC-CEEEEEEHHHCCCC
T ss_conf             7898799999982164--6899955-72378981340356


No 44 
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=96.94  E-value=0.0023  Score=42.51  Aligned_cols=35  Identities=20%  Similarity=0.235  Sum_probs=19.6

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf             42878798997836388231353278977130222137
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH   75 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~   75 (723)
                      ..|.+..|+|..+.+|  .+||+++ +-.||||+|++.
T Consensus       117 ~~~~~V~gkV~~~~kg--G~~V~i~-gl~gFiP~Sqls  151 (314)
T PRK07400        117 KEDATVRSEVFATNRG--GALVRIE-GLRGFIPGSHIS  151 (314)
T ss_pred             HCCCEEEEEEEEEECC--CEEEEEC-CEEEEEEHHHCC
T ss_conf             2598799999999638--4899976-865685524516


No 45 
>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=96.94  E-value=0.0016  Score=43.48  Aligned_cols=38  Identities=18%  Similarity=0.334  Sum_probs=34.0

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf             8787989978363882313532789771302221371210
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY   79 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~   79 (723)
                      |.|-.|.|++|.+  -+|||++|.+-.|+.|++++...|-
T Consensus         1 G~~v~G~V~~i~~--~G~FV~l~~~~~glVhiselsd~fV   38 (68)
T cd05707           1 GDVVRGFVKNIAN--NGVFVTLGRGVDARVRVSELSDSYL   38 (68)
T ss_pred             CCEEEEEEEEECC--CCEEEEECCCCEEEEEHHHHCHHHH
T ss_conf             9998999998036--4079991799679999599172356


No 46 
>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=96.90  E-value=0.0016  Score=43.54  Aligned_cols=34  Identities=18%  Similarity=0.346  Sum_probs=29.8

Q ss_pred             EEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf             798997836388231353278977130222137121
Q gi|254780751|r   43 YLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY   78 (723)
Q Consensus        43 Y~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y   78 (723)
                      +.|+|+++.+.  .|||+++.+..||+|.+++.+.+
T Consensus         1 v~G~V~~i~~~--G~fV~~~~~~~gli~~s~~s~~~   34 (65)
T cd00164           1 VTGKVVSITKF--GVFVELEDGVEGLVHISELSDKF   34 (65)
T ss_pred             CEEEEEEEECC--EEEEEECCCEEEEEEHHHHCCCC
T ss_conf             98999999784--59999898717889888916765


No 47 
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=96.79  E-value=0.0012  Score=44.39  Aligned_cols=39  Identities=26%  Similarity=0.402  Sum_probs=31.0

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf             42878798997836388231353278977130222137121
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY   78 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y   78 (723)
                      .+|.++.|+|+++.|  -.||||+|.+-.||||.+||.+..
T Consensus       200 ~~G~vv~G~V~~i~~--~GaFVdl~~GvdGllHiSeiSw~r  238 (489)
T PRK13806        200 KEGDVLEGTVTRLAP--FGAFVEIAPGVEGMVHISELSWSR  238 (489)
T ss_pred             CCCCEECEEEEEECC--CEEEEEECCCCEEEEEHHHCCCCC
T ss_conf             148800429999757--538999379807999835558656


No 48 
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=96.78  E-value=0.0017  Score=43.32  Aligned_cols=13  Identities=23%  Similarity=0.388  Sum_probs=6.6

Q ss_pred             ECCCCCEEEEEEC
Q ss_conf             3638823135327
Q gi|254780751|r   50 VEPSLQAAFVDYG   62 (723)
Q Consensus        50 V~p~lqAAFVdiG   62 (723)
                      |-..|+-.|+|=|
T Consensus        54 lA~~LG~~yLDTG   66 (863)
T PRK12269         54 LASRLGAQCLNTG   66 (863)
T ss_pred             HHHHHCCEEECCC
T ss_conf             9998299588748


No 49 
>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=96.71  E-value=0.0032  Score=41.48  Aligned_cols=40  Identities=20%  Similarity=0.371  Sum_probs=35.7

Q ss_pred             CCCEEEEEEEEECCCCCEEEEEEC-CCCCCCCCHHHCCCCCCC
Q ss_conf             287879899783638823135327-897713022213712102
Q gi|254780751|r   39 KGNIYLAKVTRVEPSLQAAFVDYG-GNRHGFLPFLEIHPDYYQ   80 (723)
Q Consensus        39 ~GnIY~G~V~~V~p~lqAAFVdiG-~~k~gFL~~~ei~~~y~~   80 (723)
                      +|++|.|+|+.|.|.  ++||++. ..-.||+|++++..|||.
T Consensus         1 IG~~f~g~I~~v~~~--GiFV~l~~~~ieGli~~~~l~~d~y~   41 (83)
T cd04471           1 VGEEFDGVISGVTSF--GLFVELDNLTVEGLVHVSTLGDDYYE   41 (83)
T ss_pred             CCCEEEEEEEEEEEE--EEEEEEECCCEEEEEECCCCCCCCEE
T ss_conf             999999999989830--69999828873999982214567224


No 50 
>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=96.71  E-value=0.0038  Score=40.96  Aligned_cols=34  Identities=21%  Similarity=0.543  Sum_probs=31.9

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf             878798997836388231353278977130222137
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH   75 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~   75 (723)
                      |.|..|+|++|.|-  +|||+++.+-.||.|.+++.
T Consensus         1 G~iv~G~V~~i~~f--G~fV~l~~~i~Glv~~s~ls   34 (69)
T cd05697           1 GQVVKGTIRKLRPS--GIFVKLSDHIKGLVPPMHLA   34 (69)
T ss_pred             CCEEEEEEEEECCC--EEEEEECCCEEEEEEHHHHC
T ss_conf             99999999997384--27999579906998789908


No 51 
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=96.60  E-value=0.004  Score=40.81  Aligned_cols=36  Identities=31%  Similarity=0.528  Sum_probs=17.7

Q ss_pred             CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf             04287879899783638823135327897713022213
Q gi|254780751|r   37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI   74 (723)
Q Consensus        37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei   74 (723)
                      -..|+|-.|+|..|...  .+|||||.--.||+|.+|+
T Consensus       302 ~~~G~iV~G~Vv~v~~~--~v~VDiG~KseG~Ip~~E~  337 (670)
T PRK00087        302 IRRGDIVKGTVVSVNEN--EVFVDVGYKSEGVIPLEEL  337 (670)
T ss_pred             CCCCCEEEEEEEEEECC--EEEEEECCCCCEEEEHHHH
T ss_conf             77898799999999389--8999836784368889993


No 52 
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=96.50  E-value=0.006  Score=39.59  Aligned_cols=14  Identities=29%  Similarity=0.477  Sum_probs=5.3

Q ss_pred             CCCCEEEEEECCCC
Q ss_conf             78728998604861
Q gi|254780751|r  450 DRARVQVGAISNFG  463 (723)
Q Consensus       450 D~~~~~v~~it~lG  463 (723)
                      |-..-.|-.||.||
T Consensus       495 ~vv~G~VKnitdyG  508 (863)
T PRK12269        495 DSVSGVVKSFTSFG  508 (863)
T ss_pred             CEEEEEEEECCCCE
T ss_conf             77889998315640


No 53 
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.24  E-value=0.011  Score=37.68  Aligned_cols=39  Identities=31%  Similarity=0.437  Sum_probs=33.5

Q ss_pred             CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf             042878798997836388231353278977130222137121
Q gi|254780751|r   37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY   78 (723)
Q Consensus        37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y   78 (723)
                      ...|.++.|+|+++.+|  ++||+++ +-.||||.+++...|
T Consensus       103 ~~~g~~v~g~V~~~~kg--G~~V~~~-gv~gFlP~S~ls~~~  141 (390)
T PRK06676        103 FEEGEVVEVKVTEVVKG--GLVVDVG-GVRGFIPASLISTRF  141 (390)
T ss_pred             HHCCCEEEEEEEEEECC--CEEEEEC-CCEEEEEHHHCCCCC
T ss_conf             53797799999999558--5999976-816877548725644


No 54 
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=95.94  E-value=0.029  Score=34.80  Aligned_cols=38  Identities=24%  Similarity=0.472  Sum_probs=32.1

Q ss_pred             CCCCCEEEEEEEEECCCCCEEEEEEC--CCCCCCCCHHHCCC
Q ss_conf             04287879899783638823135327--89771302221371
Q gi|254780751|r   37 QIKGNIYLAKVTRVEPSLQAAFVDYG--GNRHGFLPFLEIHP   76 (723)
Q Consensus        37 ~~~GnIY~G~V~~V~p~lqAAFVdiG--~~k~gFL~~~ei~~   76 (723)
                      .-.|.|-.|+|++|..  -+|||.+-  .|+.||+|+||+..
T Consensus         9 PeeGEiVv~tV~~V~~--~GA~v~L~EY~g~Eg~ihiSEvas   48 (269)
T COG1093           9 PEEGEIVVGTVKQVAD--YGAYVELDEYPGKEGFIHISEVAS   48 (269)
T ss_pred             CCCCCEEEEEEEEEEC--CCCEEEEECCCCEEEEEEHHHHHH
T ss_conf             9888689999998604--642798420599622677899877


No 55 
>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=95.57  E-value=0.036  Score=34.14  Aligned_cols=41  Identities=22%  Similarity=0.391  Sum_probs=37.3

Q ss_pred             CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC
Q ss_conf             287879899783638823135327897713022213712102
Q gi|254780751|r   39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ   80 (723)
Q Consensus        39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~   80 (723)
                      .|.|-.|+|++|.|+. .+||.++.++.|..|+.|+.-+|-.
T Consensus         3 ~G~i~~G~V~kV~p~~-Gl~Vqlp~g~~G~V~itdl~D~y~~   43 (72)
T cd05704           3 EGAVTLGMVTKVIPHS-GLTVQLPFGKTGLVSIFHLSDSYTE   43 (72)
T ss_pred             CCCEEEEEEEEECCCC-CEEEECCCCCEEEEEEEEECCCCCC
T ss_conf             8747403999972898-5699848996668999971474544


No 56 
>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=95.49  E-value=0.051  Score=33.11  Aligned_cols=38  Identities=24%  Similarity=0.295  Sum_probs=33.7

Q ss_pred             CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCC
Q ss_conf             0428787989978363882313532789771302221371
Q gi|254780751|r   37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHP   76 (723)
Q Consensus        37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~   76 (723)
                      ..+|++..|+|+.|.+.  .-|||||..-+|+||++|++.
T Consensus         4 P~~GD~ViG~V~~i~~~--~w~vdi~s~~~a~L~ls~v~~   41 (86)
T cd05789           4 PEVGDVVIGRVTEVGFK--RWKVDINSPYDAVLPLSEVNL   41 (86)
T ss_pred             CCCCCEEEEEEEEEECC--CEEEECCCCEEEEEEHHHCCC
T ss_conf             98899999999998088--189974996077987454467


No 57 
>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=95.24  E-value=0.037  Score=34.10  Aligned_cols=38  Identities=29%  Similarity=0.393  Sum_probs=32.6

Q ss_pred             CEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCC
Q ss_conf             78798997836388231353278977130222137121028
Q gi|254780751|r   41 NIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQI   81 (723)
Q Consensus        41 nIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~i   81 (723)
                      .+|-|.|+.|..-  .|||++|. -.|++|++++..|||..
T Consensus         1 Ev~eG~Vs~Vt~f--G~FV~L~~-ieGLvHiS~l~dD~~~f   38 (99)
T cd04460           1 EVVEGEVVEVVDF--GAFVRIGP-VDGLLHISQIMDDYISY   38 (99)
T ss_pred             CEEEEEEEEEEEC--CEEEEECC-CEEEEEHHHCCCCEEEE
T ss_conf             9799999958825--66999328-10689936757843998


No 58 
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=95.18  E-value=0.044  Score=33.57  Aligned_cols=15  Identities=47%  Similarity=0.623  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999987
Q gi|254780751|r  400 LQTNLEAAEEIARQL  414 (723)
Q Consensus       400 l~tNleAA~EIaRQl  414 (723)
                      |.+-+.-|..|||-|
T Consensus       441 L~v~~r~aVSIaRrl  455 (780)
T COG2183         441 LDVSLRGAVSIARRL  455 (780)
T ss_pred             CCHHHHHHHHHHHHH
T ss_conf             966677687798862


No 59 
>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=94.98  E-value=0.086  Score=31.54  Aligned_cols=34  Identities=32%  Similarity=0.421  Sum_probs=29.7

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf             4287879899783638823135327897713022213
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI   74 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei   74 (723)
                      ..|.|.-|.|+++.+  ...|||+| .-.|+||-+|.
T Consensus         2 k~geiv~G~V~r~~~--~~v~vdlg-~~eailp~~eq   35 (67)
T cd04455           2 REGEIVTGIVKRVDR--GNVIVDLG-KVEAILPKKEQ   35 (67)
T ss_pred             CCCCEEEEEEEEEEC--CCEEEEEC-CCEEECCHHHC
T ss_conf             878889999999808--97999989-94897378995


No 60 
>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=94.76  E-value=0.066  Score=32.33  Aligned_cols=35  Identities=29%  Similarity=0.475  Sum_probs=15.7

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf             87879899783638823135327897713022213
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI   74 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei   74 (723)
                      |.|-.|+|..|-.+=.-+|||+|+=--|-+|.+|+
T Consensus        20 G~i~~G~VV~i~~ndd~v~VDvG~KsEg~ip~~Ef   54 (534)
T TIGR00717        20 GSIVKGTVVKINKNDDTVFVDVGLKSEGRIPVEEF   54 (534)
T ss_pred             CCEEEEEEEEEECCCCEEEEEEECCCCCCCCHHHC
T ss_conf             85553278998168889999831563123417682


No 61 
>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=94.57  E-value=0.095  Score=31.25  Aligned_cols=37  Identities=22%  Similarity=0.252  Sum_probs=18.9

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCC
Q ss_conf             428787989978363882313532789771302221371
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHP   76 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~   76 (723)
                      -.|.--.|||+++.|  =.|||||..|=-||+|.|||.|
T Consensus       286 ~~G~~~~G~Vt~~~d--yGvFvEi~eGiEGlvH~SE~sW  322 (534)
T TIGR00717       286 PVGDKIKGRVTNLTD--YGVFVEIEEGIEGLVHVSEISW  322 (534)
T ss_pred             CCCCEEEEEEEEECC--CEEEEEECCCCEEEECCEEEEC
T ss_conf             899788999998837--7079992389423423144405


No 62 
>PTZ00248 eukaryotic translation initiation factor 2 alpha subunit; Provisional
Probab=94.18  E-value=0.079  Score=31.82  Aligned_cols=89  Identities=17%  Similarity=0.269  Sum_probs=65.8

Q ss_pred             CCCCCCEEEEEEEEECCCCCEEEEEEC--CCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             604287879899783638823135327--897713022213712102898899999998886311111000000011122
Q gi|254780751|r   36 KQIKGNIYLAKVTRVEPSLQAAFVDYG--GNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVT  113 (723)
Q Consensus        36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG--~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~  113 (723)
                      -.-.|.|-.++|++|..  .+|||.+-  .+..||+|+|||.+-                                    
T Consensus        14 ~Pe~~e~V~~~V~~i~~--~gayV~LlEY~~~egmI~~sEls~r------------------------------------   55 (324)
T PTZ00248         14 YPEENDLVMVKVNRIEE--MGVYVSLLEYDDIEGMILLSELSKR------------------------------------   55 (324)
T ss_pred             CCCCCCEEEEEEEEEEC--CEEEEEEEEECCCCCEEEHHHHHHH------------------------------------
T ss_conf             99988889999999802--5689998400882221468886378------------------------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCC
Q ss_conf             33444334454222233445543322223432112211121100001223444421331068885799984033323456
Q gi|254780751|r  114 IPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKG  193 (723)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kg  193 (723)
                                                                          +-.+|+.+|+.|+.+.|+|.+=-     
T Consensus        56 ----------------------------------------------------rir~I~k~ikvG~~~v~~VlRVD-----   78 (324)
T PTZ00248         56 ----------------------------------------------------RIRSINKLVKVGRHEVVLVLRVD-----   78 (324)
T ss_pred             ----------------------------------------------------HHHHHHHHHCCCCEEEEEEEEEC-----
T ss_conf             ----------------------------------------------------88637887106877899999985-----


Q ss_pred             CCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf             41012334576523442278875124204688689999999998
Q gi|254780751|r  194 AAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIAR  237 (723)
Q Consensus       194 a~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~  237 (723)
                                       +..++ +-+|+|-...++...-.+-..
T Consensus        79 -----------------~~KGy-IDLS~rrVs~ed~~kCeery~  104 (324)
T PTZ00248         79 -----------------KDKGY-IDLSKRRVTPEDIIKCEEKFS  104 (324)
T ss_pred             -----------------CCCCC-EECHHHCCCHHHHHHHHHHHH
T ss_conf             -----------------87782-444150299889999999998


No 63 
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=93.94  E-value=0.18  Score=29.27  Aligned_cols=34  Identities=26%  Similarity=0.369  Sum_probs=28.8

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf             4287879899783638823135327897713022213
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI   74 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei   74 (723)
                      .+|.|..|.|.|+.++  ..|||+|. -.|+||.+|.
T Consensus       133 r~GeiV~G~V~r~~~~--~~~Vdlg~-~ea~LP~~eq  166 (353)
T PRK12327        133 REGDIVTGTVQRDDNR--FVYVNLGK-IEAVLPPAEQ  166 (353)
T ss_pred             HCCCEEEEEEEEECCC--CEEEEECC-EEEECCHHHC
T ss_conf             4396699999997588--58999788-2464687986


No 64 
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=93.78  E-value=0.54  Score=25.98  Aligned_cols=65  Identities=25%  Similarity=0.294  Sum_probs=50.4

Q ss_pred             CEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC
Q ss_conf             60799999899899999607334604287879899783638823135327897713022213712102
Q gi|254780751|r   13 EETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ   80 (723)
Q Consensus        13 ~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~   80 (723)
                      .|-+|.-=++....+.-+.---=+..+|-|..|+|+.+..  ..|||.+|. -.+|+|.+.+.+||+.
T Consensus        55 ~eG~I~~gdG~~~~~V~F~~ivfrPf~~EVv~g~V~~~~~--~G~fv~~Gp-~d~~vh~sqi~dd~~~  119 (182)
T PRK08563         55 GEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEVVEVVE--FGAFVRIGP-VDGLLHISQIMDDYIS  119 (182)
T ss_pred             CCCEEEECCCCEEEEEEEEEEEEECCCCCEEEEEEEEEEC--CEEEEEEEC-CCEEEEHHHCCCCCCE
T ss_conf             4998991999899999978999941368489999999966--769999846-6117609994777623


No 65 
>PRK11642 exoribonuclease R; Provisional
Probab=92.68  E-value=0.26  Score=28.27  Aligned_cols=90  Identities=16%  Similarity=0.172  Sum_probs=45.8

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCC---
Q ss_conf             35320366788898763101211220134-42035677699999998422214367864998328806999823755---
Q gi|254780751|r  313 SGEKGYREAKDFMKLLMPSYARIVRQYED-PHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGR---  388 (723)
Q Consensus       313 d~~~~~~~~~~~~~~~~p~~~~~v~~~~~-~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~---  388 (723)
                      ...-.|..+..++..- +...   ..|.. ...|...+.+-..+.....      .-|.|-+|..|+-...|-+..-   
T Consensus       378 ~arLTY~~v~~il~g~-~~~~---~~~~~~~~~L~~L~~l~~~L~~~R~------~rGai~fd~~E~~~~ld~~g~i~~i  447 (813)
T PRK11642        378 HARLTYTKVWHILQGD-QDLR---EQYAPLVKHLEELHNLYKVLDKARE------ERGGISFESEEAKFIFNAERRIERI  447 (813)
T ss_pred             CCEECHHHHHHHHHCC-HHHH---HHHHHHHHHHHHHHHHHHHHHHHHH------HCCCCCCCCCCCEEEECCCCCCCCE
T ss_conf             8362399999998188-5444---4556799999999999999999999------7789665677644897788873424


Q ss_pred             -----CCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             -----444555114799999999999999
Q gi|254780751|r  389 -----STREHCIEDTALQTNLEAAEEIAR  412 (723)
Q Consensus       389 -----~~~~~~~e~t~l~tNleAA~EIaR  412 (723)
                           .....=+|+..+.+|..||+-+..
T Consensus       448 ~~~~r~~ah~LIEE~Ml~AN~~vA~~l~~  476 (813)
T PRK11642        448 EQTQRNDAHKLIEECMILANISAARFVEK  476 (813)
T ss_pred             EECCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             76223505678999999999999999997


No 66 
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=92.37  E-value=0.46  Score=26.47  Aligned_cols=52  Identities=19%  Similarity=0.206  Sum_probs=34.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHH-HHHHHHCCCCHHHH
Q ss_conf             4322123456458888887523766311110353203667888-98763101211220
Q gi|254780751|r  282 SVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDF-MKLLMPSYARIVRQ  338 (723)
Q Consensus       282 ~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~-~~~~~p~~~~~v~~  338 (723)
                      -+..+|+..-..-+..+++.+-+..++-|..+++.     ..| ...+.|.....|..
T Consensus       246 DpVGAcVG~rGsRI~~I~~EL~gEkIDIi~~s~d~-----~~fi~nAlsPA~v~~V~i  298 (428)
T PRK09202        246 DPVGACVGMRGSRIQAISNELNGEKIDIILWSDDP-----AQFIINALSPAEVSSIVV  298 (428)
T ss_pred             CCCEEEECCCCCCHHHHHHHHCCCEEEEEECCCCH-----HHHHHHHCCCCCCEEEEE
T ss_conf             85137777886429999987467768999678888-----999998179421218997


No 67 
>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=92.24  E-value=0.4  Score=26.88  Aligned_cols=34  Identities=32%  Similarity=0.466  Sum_probs=31.6

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf             878798997836388231353278977130222137
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH   75 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~   75 (723)
                      |.+-.|+|+.|-|  -.+||.++.+-+|+.|++||.
T Consensus         1 G~vv~g~V~sik~--~~l~V~L~d~~~GrVhiSei~   34 (70)
T cd05702           1 GDLVKAKVKSVKP--TQLNVQLADNVHGRIHVSEVF   34 (70)
T ss_pred             CCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHCC
T ss_conf             9779999999946--708999689957789845521


No 68 
>PRK00499 rnpA ribonuclease P; Reviewed
Probab=91.88  E-value=0.73  Score=25.08  Aligned_cols=62  Identities=24%  Similarity=0.238  Sum_probs=45.0

Q ss_pred             CCEEEECCCCHHHHHHHHHHHHHHH--------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5124204688689999999998630--------0258716998504557579999999999999998776
Q gi|254780751|r  216 GETISRKITNPVDRKNLKEIARGLE--------VPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRE  277 (723)
Q Consensus       216 ~~~iSrki~~~~~r~~l~~~~~~~~--------~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~  277 (723)
                      |+.+|+|+.+.-.|.+++..+.++.        .+.++=+|.|..+.+++..+|..|+..|+..-.-+.+
T Consensus        42 G~~vsKKvg~AV~RNriKR~lRe~~R~~~~~l~~g~DiViiar~~~~~~~~~~l~~~l~~ll~Ka~ll~~  111 (116)
T PRK00499         42 GISVSKKIGNAVVRNRVKRLIRESFRELKDEIKKGYDFVVIARKPAEDLDYEEIKKSLIHVLKKAKLYNK  111 (116)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCC
T ss_conf             9998044675237889999999999974650588975999968654549999999999999998264000


No 69 
>KOG1070 consensus
Probab=91.84  E-value=0.53  Score=26.07  Aligned_cols=66  Identities=21%  Similarity=0.411  Sum_probs=52.6

Q ss_pred             CCEEEEEEEECCEEEEEEECCCC--CCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf             96079999989989999960733--460428787989978363882313532789771302221371210
Q gi|254780751|r   12 VEETRVVVLRDNRVEELDFESEH--KKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY   79 (723)
Q Consensus        12 ~~e~Rvav~e~g~l~e~~~e~~~--~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~   79 (723)
                      ..+-|||+.-.+.|++....-+.  ...+.|-||+|.|.++-+  +.|||.+=.+-.||+|.+++.-+|-
T Consensus       570 ~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~--~g~~V~F~g~lsGf~p~s~~sd~~v  637 (1710)
T KOG1070         570 RDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKE--NGAFVTFTGGLSGFAPVSEMSDDFV  637 (1710)
T ss_pred             CCCCEEEEEECHHHHCCCCCCCCCHHHCCCCCEEEEEEEEECC--CCEEEEECCCCCCCCCHHHHHHHHH
T ss_conf             3687258882233431468886425335878368987765426--8728995676565664454310121


No 70 
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=91.82  E-value=1  Score=24.16  Aligned_cols=54  Identities=20%  Similarity=0.247  Sum_probs=40.4

Q ss_pred             ECCEEEEEEECCCCCC----------CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf             8998999996073346----------042878798997836388231353278977130222137
Q gi|254780751|r   21 RDNRVEELDFESEHKK----------QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH   75 (723)
Q Consensus        21 e~g~l~e~~~e~~~~~----------~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~   75 (723)
                      +-|.-+++|+-.....          ..+|.-=.++|+.|-+.|. ||||.|..|.-|+|.+|..
T Consensus        45 evGdev~vFiY~D~~~rl~aTt~~p~~tvg~~g~~~Vv~v~~~lG-aFlD~Gl~KDl~vp~~elp  108 (287)
T COG2996          45 EVGDEVTVFIYVDSEDRLIATTREPKATVGEYGWLKVVEVNKDLG-AFLDWGLPKDLLVPLDELP  108 (287)
T ss_pred             CCCCEEEEEEEECCCCCEEHEEECCEEEECCEEEEEEEEECCCCC-EEEECCCCCCEEEEHHHCC
T ss_conf             137689999998887763010104137405323799998737751-5896598700361625364


No 71 
>PTZ00162 RNA polymerase II subunit 7; Provisional
Probab=90.75  E-value=1.3  Score=23.45  Aligned_cols=63  Identities=24%  Similarity=0.230  Sum_probs=49.2

Q ss_pred             CEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf             607999998998999996073346042878798997836388231353278977130222137121
Q gi|254780751|r   13 EETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY   78 (723)
Q Consensus        13 ~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y   78 (723)
                      .|-+|---++......-++-.-=+..+|-|.-|.|++|.+  .+|||++|.=. +|+|.+-|.+||
T Consensus        55 ~~G~I~~gdG~v~~~V~f~aivfkP~~~EVvdg~V~~v~~--~G~fv~~GPl~-~fv~~s~i~~d~  117 (170)
T PTZ00162         55 EPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNK--LGFFAQAGPLK-IFVSRTAIPPNF  117 (170)
T ss_pred             CCCEEEECCCCEEEEEEEEEEEEECCCCCEEEEEEEEEEC--CEEEEEECCEE-EEEEHHHCCCCC
T ss_conf             5797995898699999999999933679899999999964--07999912808-998989999864


No 72 
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=90.07  E-value=0.8  Score=24.84  Aligned_cols=58  Identities=19%  Similarity=0.247  Sum_probs=46.5

Q ss_pred             CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECC
Q ss_conf             0236754653786061146899887889997303643101357699999873023799999999848879998478
Q gi|254780751|r  481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGI  556 (723)
Q Consensus       481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~  556 (723)
                      .-.||.|+|.-.--|...+|..+-+.|++....+.+                  +.+-+..+.++||-.|...|.-
T Consensus        40 ~lRCpvCq~qsi~~S~a~~A~dmR~~I~~~i~~G~s------------------d~eI~~~l~~RYG~~Il~~Pp~   97 (126)
T TIGR03147        40 SLRCPQCQNQNLVESNSPIAYDLRHEVYSMVNEGKS------------------NQQIIDFMTARFGDFVLYNPPF   97 (126)
T ss_pred             HCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHCCCC------------------HHHHHHHHHHHCCCEEEECCCC
T ss_conf             168877799774007619999999999999985999------------------8999999999708828753999


No 73 
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=89.61  E-value=1.1  Score=23.91  Aligned_cols=52  Identities=21%  Similarity=0.181  Sum_probs=35.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHH-HHHHHCCCCHHHH
Q ss_conf             43221234564588888875237663111103532036678889-8763101211220
Q gi|254780751|r  282 SVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFM-KLLMPSYARIVRQ  338 (723)
Q Consensus       282 ~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~-~~~~p~~~~~v~~  338 (723)
                      -+..+|+..-..-+..+++.+-+..++-|..+++.     ..|+ ..+.|.....|..
T Consensus       251 DpVGAcVG~kG~RI~~I~~EL~gEkIDii~~s~d~-----~~fi~nALsPA~V~~V~i  303 (375)
T PRK12328        251 DPVGATVGVKGVRINAVSKELNGENIDCIEYSNIP-----EIFIARALAPAIILSVKI  303 (375)
T ss_pred             CCEEEEECCCCCCHHHHHHHHCCCEEEEEECCCCH-----HHHHHHCCCCCCCEEEEE
T ss_conf             74047888886309999998579627899778888-----999986378553018999


No 74 
>pfam03918 CcmH Cytochrome C biogenesis protein. Members of this family include NrfF, CcmH, CycL, Ccl2.
Probab=89.38  E-value=0.88  Score=24.54  Aligned_cols=58  Identities=19%  Similarity=0.238  Sum_probs=46.1

Q ss_pred             CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECC
Q ss_conf             0236754653786061146899887889997303643101357699999873023799999999848879998478
Q gi|254780751|r  481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGI  556 (723)
Q Consensus       481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~  556 (723)
                      .-.||.|+|.-.--|...+|..+-+.|++....+.+                  +.+-+..+-++||-.|...+--
T Consensus        37 ~lRCpvCq~qsi~dS~a~iA~dmR~~i~~~i~~G~s------------------d~eI~~~~~~rYG~~Vl~~Pp~   94 (145)
T pfam03918        37 ELRCPVCQNQSIADSNAPLARDLRLEVREMLVEGKS------------------DEEIIDYMVARYGDFVLYKPPL   94 (145)
T ss_pred             HCCCCCCCCCCHHCCCHHHHHHHHHHHHHHHHCCCC------------------HHHHHHHHHHHCCCCEEECCCC
T ss_conf             278888799765007779999999999999985999------------------9999999998638615555999


No 75 
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=89.24  E-value=1.1  Score=23.99  Aligned_cols=58  Identities=17%  Similarity=0.244  Sum_probs=45.9

Q ss_pred             CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECC
Q ss_conf             0236754653786061146899887889997303643101357699999873023799999999848879998478
Q gi|254780751|r  481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGI  556 (723)
Q Consensus       481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~  556 (723)
                      .-.||.|.|.-.--|...+|..+-..|++....+.+                  ..+-+..+.++||-.|...+.-
T Consensus        40 elRCpvCq~qsi~~S~s~iA~dmR~~Ir~~i~~G~s------------------d~eI~~~l~~rYG~~Il~~Pp~   97 (126)
T PRK10144         40 QLRCPQCQNQNLLESNAPVAVSMRHQVYSMVAEGKS------------------EVEIIGWMTERYGDFVRYNPPL   97 (126)
T ss_pred             HCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHCCCC------------------HHHHHHHHHHHCCCEEEEECCC
T ss_conf             278877899884115779999999999999986999------------------9999999998648849861899


No 76 
>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=88.94  E-value=1.5  Score=22.95  Aligned_cols=23  Identities=43%  Similarity=0.612  Sum_probs=19.9

Q ss_pred             CCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf             0428787989978363882313532
Q gi|254780751|r   37 QIKGNIYLAKVTRVEPSLQAAFVDY   61 (723)
Q Consensus        37 ~~~GnIY~G~V~~V~p~lqAAFVdi   61 (723)
                      ..+|+|-.|||++|-|  +.|+|+|
T Consensus         4 P~vGdiV~~rVtrv~~--~~a~v~I   26 (92)
T cd05791           4 PKVGSIVIARVTRINP--RFAKVDI   26 (92)
T ss_pred             CCCCCEEEEEEEEECC--CEEEEEE
T ss_conf             8899999999999711--3789999


No 77 
>PRK01732 rnpA ribonuclease P; Reviewed
Probab=87.75  E-value=2  Score=21.99  Aligned_cols=61  Identities=21%  Similarity=0.342  Sum_probs=45.8

Q ss_pred             CCEEEEC-CCCHHHHHHHHHHHHHHH-------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5124204-688689999999998630-------025871699850455757999999999999999877642
Q gi|254780751|r  216 GETISRK-ITNPVDRKNLKEIARGLE-------VPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELA  279 (723)
Q Consensus       216 ~~~iSrk-i~~~~~r~~l~~~~~~~~-------~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~  279 (723)
                      |+.||+| +...-.|.++|.++.+.-       .+.++=+|+|..+.+.+..+|..++..|   |..+...+
T Consensus        48 Gl~VsKK~v~~AV~RNRiKR~iRE~fR~~~~~l~~~DiVviar~~~~~~~~~~l~~~L~~l---~~kl~r~~  116 (119)
T PRK01732         48 GLTVAKKNVKRAHERNRIKRLTRESFRLRQHELPAMDFVVVAKKGVADLDNRALSEALEKL---WRRHCRLA  116 (119)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHH---HHHHHHHH
T ss_conf             9999765563267888999999999984802289860999956875538999999999999---99998750


No 78 
>PRK01313 rnpA ribonuclease P; Reviewed
Probab=87.68  E-value=1.8  Score=22.35  Aligned_cols=58  Identities=12%  Similarity=0.179  Sum_probs=43.5

Q ss_pred             CCCEEEECCCCHHHHHHHHHHHHHH---------HCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf             7512420468868999999999863---------002587169985045575799999999999999
Q gi|254780751|r  215 KGETISRKITNPVDRKNLKEIARGL---------EVPAGMGVILRTAGASRTKIEIKRDFEYLMRLW  272 (723)
Q Consensus       215 ~~~~iSrki~~~~~r~~l~~~~~~~---------~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w  272 (723)
                      -|..+|+|+-+.-.|.+.+..+.++         ..+.++-+|.|..+.+++.++|..|+...++..
T Consensus        53 vG~tvsKKvGnAV~RNRiKRrlRe~~r~~~~~~~~~g~D~ViiaR~~a~~~~f~~L~~dL~~alk~~  119 (133)
T PRK01313         53 VGFTVTKKNGNAVERNRIRRRLKEAVRVHAGRDMAPGTDYVIVARRDALNAPFSQLTEELSRRIEAK  119 (133)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCHHCCCCHHHHHHHHHHHHHHH
T ss_conf             8899841235167788999999999998605306899708999371110299999999999999983


No 79 
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=86.74  E-value=2.3  Score=21.61  Aligned_cols=38  Identities=32%  Similarity=0.328  Sum_probs=32.5

Q ss_pred             CCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf             4604287879899783638823135327897713022213
Q gi|254780751|r   35 KKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI   74 (723)
Q Consensus        35 ~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei   74 (723)
                      -...+|++-.|+|+.|-++  .=+||||.--+||||+++.
T Consensus        58 Y~P~~GD~VIG~V~~v~~~--~W~VDI~s~~~a~L~~s~~   95 (232)
T PRK04163         58 YIPKKGDLVIGKVTDVGFS--GWEVDINSPYKAILPVSEV   95 (232)
T ss_pred             CCCCCCCEEEEEEEEECCC--EEEEECCCCCEEEECHHHC
T ss_conf             0587699899999983187--1799869960558524445


No 80 
>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=86.66  E-value=2  Score=22.05  Aligned_cols=35  Identities=29%  Similarity=0.489  Sum_probs=28.5

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEEC-CCCCCCCCHHHC
Q ss_conf             4287879899783638823135327-897713022213
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYG-GNRHGFLPFLEI   74 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG-~~k~gFL~~~ei   74 (723)
                      ..|.+.-|-|+-|+-  ...-+|+| .+-.||||.+|+
T Consensus         3 ~~g~~l~a~V~SvED--HGyild~Gi~~~~gFl~~k~~   38 (74)
T cd05694           3 VEGMVLSGCVSSVED--HGYILDIGIPGTTGFLPKKDA   38 (74)
T ss_pred             CCCCEEEEEEEEEEC--CEEEEECCCCCCEEEEEHHHC
T ss_conf             678299999856714--418998477772667301334


No 81 
>PRK03031 rnpA ribonuclease P; Reviewed
Probab=86.14  E-value=1.3  Score=23.32  Aligned_cols=58  Identities=19%  Similarity=0.306  Sum_probs=37.9

Q ss_pred             CCEEEECCC-CHHHH----HHHHHHHHHH----HCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf             512420468-86899----9999999863----0025871699850455757999999999999999
Q gi|254780751|r  216 GETISRKIT-NPVDR----KNLKEIARGL----EVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWD  273 (723)
Q Consensus       216 ~~~iSrki~-~~~~r----~~l~~~~~~~----~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~  273 (723)
                      |+.+|+|+. +.-.|    +++++++...    ..+.++=+|.|..+.+.+.++|..|+..|+..-.
T Consensus        50 G~~VsKKvgk~AV~RNriKR~lRe~~r~~~~~l~~g~diViiar~~~~~~~~~~l~~el~~lL~kA~  116 (122)
T PRK03031         50 GISISQKVSKKAVVRNRLKRQIRAAIRQLLPRIAPGWDLVIIVKPGASECNYEQFLQELEQLLIQAE  116 (122)
T ss_pred             EEEEEEECCCCCEEECCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             9999620054402204122008999998676238896699997887565999999999999999847


No 82 
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase; InterPro: IPR014069    The of the characterization of two proteins from Streptomyces coelicolor ahs been presented . The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. It has also been shown that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase ..
Probab=85.27  E-value=0.3  Score=27.75  Aligned_cols=162  Identities=16%  Similarity=0.189  Sum_probs=77.9

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCC--CCHHHH---
Q ss_conf             999999998731036863896033479888899999999997312787289986048614898515666--301121---
Q gi|254780751|r  405 EAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIR--SSVLES---  479 (723)
Q Consensus       405 eAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r--~sl~e~---  479 (723)
                      .-.+.|.|+.-|.+---|=-=-.-|++.-...-.+.-+..-..--.|..|||.|+|-|.+|.|..+=-.  |....-   
T Consensus       326 ~~~~~~~r~~~~~~~~r~dGrG~~dir~l~~ev~~~Pr~hGsa~f~rGetq~lGv~tl~ml~m~q~~d~l~P~~~~ry~h  405 (725)
T TIGR02696       326 AVTKKLVRERVLKEGVRIDGRGLTDIRSLSAEVEVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPVTSKRYLH  405 (725)
T ss_pred             HHHHHHHHHHHHHCCCEECCCCHHHHHHHHCCEEEECCCCCHHHHHCCCEEEEHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             99999999888623620136764455521000024133101023205760354034778888876553116202300110


Q ss_pred             HCCCCCCCCC-EEEEECCH----------------------HHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCC-H
Q ss_conf             0023675465-37860611----------------------4689988788999730364310135769999987302-3
Q gi|254780751|r  480 TTKVCTYCKG-AGYIRSQS----------------------SVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQ-K  535 (723)
Q Consensus       480 ~~~~c~~c~g-~g~~~~~~----------------------~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~-k  535 (723)
                      .+.-.|+..| +|+|-|+.                      ..-+ ..|.+.+....+....+--.|...++.+-.+- .
T Consensus       406 ~yn~PPys~Ge~GrvG~PkrreiGhG~laeral~PvlP~~e~fPy-air~vseal~snGstsmGsvCastl~l~~aGvPl  484 (725)
T TIGR02696       406 HYNFPPYSTGETGRVGSPKRREIGHGALAERALVPVLPSREEFPY-AIRQVSEALGSNGSTSMGSVCASTLSLLNAGVPL  484 (725)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCH-HHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCC
T ss_conf             037887566764566887532025650221100034467665636-8999988741577630357899999998648862


Q ss_pred             HHHHH-----------HHHHHHCCEEEEE-ECCCCCCCCEEEEE
Q ss_conf             79999-----------9999848879998-47877886338971
Q gi|254780751|r  536 RATIV-----------EYEARFGVSINVV-IGIELADKLFYIEK  567 (723)
Q Consensus       536 r~~l~-----------~lE~~~~~~I~i~-~d~~l~~~~f~Ier  567 (723)
                      +..++           +-+.+|-.--.|. +++.+...+|++.-
T Consensus       485 ~~~vaGiamGl~~~~~~~~~~y~~ltdi~Gaeda~GdmdfkvaG  528 (725)
T TIGR02696       485 KAPVAGIAMGLISDEVDGETRYVALTDILGAEDALGDMDFKVAG  528 (725)
T ss_pred             CCCHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCEEECC
T ss_conf             00020122222222003542567642011320102553212214


No 83 
>PRK00396 rnpA ribonuclease P; Reviewed
Probab=84.39  E-value=3  Score=20.86  Aligned_cols=62  Identities=21%  Similarity=0.314  Sum_probs=45.3

Q ss_pred             CCEEEEC-CCCHHHHHHHHHHHHHHH-------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             5124204-688689999999998630-------0258716998504557579999999999999998776420
Q gi|254780751|r  216 GETISRK-ITNPVDRKNLKEIARGLE-------VPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELAL  280 (723)
Q Consensus       216 ~~~iSrk-i~~~~~r~~l~~~~~~~~-------~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~~  280 (723)
                      |+.|||| +...-.|.++|.++.+.-       .+.++=+|.|..+...+-.+|..++..   +|..+.....
T Consensus        49 Gl~VsKK~vk~AV~RNriKR~iRE~FR~~~~~L~~~DiVViar~~~~~l~n~el~~~L~~---lw~rL~r~~~  118 (134)
T PRK00396         49 GLVIGKKSVKLAVQRNRLKRLMRESFRLNQDSLAGWDIVIVARKGLGELENPELHQQFGK---LWKRLARSRP  118 (134)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCHHHCCHHHHHHHHHH---HHHHHHHCCC
T ss_conf             899866555057778889999999999573007998989993777002499999999999---9999985579


No 84 
>pfam01630 Glyco_hydro_56 Hyaluronidase.
Probab=84.26  E-value=1.6  Score=22.82  Aligned_cols=33  Identities=27%  Similarity=0.421  Sum_probs=16.3

Q ss_pred             HHHHHHHHHH-HHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             1479999999-99999998731036863896033
Q gi|254780751|r  396 EDTALQTNLE-AAEEIARQLRLRDLAGLIVVDFI  428 (723)
Q Consensus       396 e~t~l~tNle-AA~EIaRQlRLRnlgGiIvIDFI  428 (723)
                      ....|...|+ |.+.|...|.-+|-+||-||||=
T Consensus        79 Q~g~L~~HL~ka~~dI~~~ip~~~f~GLaVIDwE  112 (339)
T pfam01630        79 QLGSLTAHLAKAKKDIEHYIPDPDFNGLAVIDWE  112 (339)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEECC
T ss_conf             8577999999999989985789999841898754


No 85 
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=84.17  E-value=3  Score=20.80  Aligned_cols=65  Identities=25%  Similarity=0.335  Sum_probs=51.8

Q ss_pred             CCEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf             96079999989989999960733460428787989978363882313532789771302221371210
Q gi|254780751|r   12 VEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY   79 (723)
Q Consensus        12 ~~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~   79 (723)
                      -+|-+|..-+++.-.+.-++-.-=....|.|--|.|..+..  -.|||.+| --.||+|.+.|..||+
T Consensus        54 igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~~--~G~fV~ig-p~dglvh~sqi~dd~~  118 (183)
T COG1095          54 IGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVE--FGAFVRIG-PLDGLVHVSQIMDDYI  118 (183)
T ss_pred             EECCEEECCCCCEEEEEEEEEEEEEECCCCEEEEEEEEEEE--CCEEEEEC-CCCCCCCHHHCCCCCC
T ss_conf             20457862999679999999999970356389999999961--44699963-6222113866657532


No 86 
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=84.10  E-value=3.1  Score=20.78  Aligned_cols=32  Identities=19%  Similarity=0.174  Sum_probs=23.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCCCEEECCC
Q ss_conf             32212345645888888752376631111035
Q gi|254780751|r  283 VAPHLVYEEGNLIKRAIRDLYCKDISEIIVSG  314 (723)
Q Consensus       283 ~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~  314 (723)
                      ...+|+..-..-+..+++.+-+..++-|..+.
T Consensus       279 PVGaCVG~rG~RIq~I~~EL~gEkIDii~ws~  310 (457)
T PRK12329        279 PVGACIGARGSRIQQVVNELRGEKIDVIRWSP  310 (457)
T ss_pred             CEEEEECCCCCCHHHHHHHHCCCEEEEEECCC
T ss_conf             31478889974299999885796389997578


No 87 
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=83.66  E-value=3.2  Score=20.66  Aligned_cols=42  Identities=14%  Similarity=0.208  Sum_probs=28.3

Q ss_pred             CCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCC
Q ss_conf             645888888752376631111035320366788898763101
Q gi|254780751|r  291 EGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSY  332 (723)
Q Consensus       291 ~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~~~~~p~~  332 (723)
                      +..-+..+|+.+-+..-.-|+|+.+...-..-+|+-.+.|.-
T Consensus       526 D~~rLi~~L~~Lrd~GNTVlVVEHD~~~i~~AD~iIDlGPgA  567 (944)
T PRK00349        526 DNDRLIETLKRLRDLGNTLIVVEHDEDTIRAADYIVDIGPGA  567 (944)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHCCEEEEECCCC
T ss_conf             999999999999857985999835687775287789717877


No 88 
>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=83.29  E-value=3.3  Score=20.55  Aligned_cols=157  Identities=15%  Similarity=0.123  Sum_probs=70.7

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCH---HHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCC--
Q ss_conf             35320366788898763101211---2201344203567769999999842221436786499832880699982375--
Q gi|254780751|r  313 SGEKGYREAKDFMKLLMPSYARI---VRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSG--  387 (723)
Q Consensus       313 d~~~~~~~~~~~~~~~~p~~~~~---v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG--  387 (723)
                      ...-+|.++.+++..-.......   -.+...=.+++..|.|=..-.         ..=|+|=+|-.||=+.+|=|-=  
T Consensus       393 ~~R~TY~~Vn~~~~g~~~~~~~~~Gy~~~~~~l~~~~~L~~~L~~~R---------~~rG~IdFd~~E~k~ilDe~G~~~  463 (755)
T TIGR02063       393 KARLTYTQVNDILEGKDALEDKEYGYAPLKEMLKNLEELYKILRKKR---------KKRGAIDFDSKEAKIILDENGKPI  463 (755)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH---------HHCCCCCCCCCCCEEEECCCCEEE
T ss_conf             64457789999764985699963587115777998999999999877---------651881237764179987884289


Q ss_pred             ------CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCC-CCHHHHHHHHHHHHHHHHHCCC----CEEE
Q ss_conf             ------5444555114799999999999999873103686389603347-9888899999999997312787----2899
Q gi|254780751|r  388 ------RSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDM-EEKKNNRSVEKKLKESLKKDRA----RVQV  456 (723)
Q Consensus       388 ------~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM-~~~~~~~~v~~~l~~~l~~D~~----~~~v  456 (723)
                            +....+=+|+--+..|--||.-.-+.+..-+.+ +=.|==|.= .+.+.-..+.+.| ..|.-.-.    -.++
T Consensus       464 ~I~~~~R~~A~klIEefM~~ANe~vA~~~~~~~~~~~~~-~P~~YRvH~~P~~~kl~~l~~fl-~~lG~~~~~~G~~~~~  541 (755)
T TIGR02063       464 DIVPRERGDAHKLIEEFMIVANETVAEFLEKKLKKNKAK-LPFIYRVHEKPSEEKLQNLREFL-KELGLTLKGGGTSDKI  541 (755)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCEEEEECCCCCHHHHHHHHHHH-HHCCCEECCCCCCCCC
T ss_conf             989841333222368889999999999999888875489-95167647899889999999999-8718154488888875


Q ss_pred             EEECCCCEEEEECCCCCCCHHHHH
Q ss_conf             860486148985156663011210
Q gi|254780751|r  457 GAISNFGLLEMSRQRIRSSVLEST  480 (723)
Q Consensus       457 ~~it~lGLlEltRkR~r~sl~e~~  480 (723)
                      .+-+==-|||..+.|--..|.+++
T Consensus       542 ~P~~~~~~le~~~~~P~~~l~~~~  565 (755)
T TIGR02063       542 QPKDLQKLLEKVKGRPEEELINTV  565 (755)
T ss_pred             CHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf             869999999984088438999999


No 89 
>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=83.18  E-value=2.4  Score=21.48  Aligned_cols=36  Identities=22%  Similarity=0.047  Sum_probs=30.7

Q ss_pred             CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf             04287879899783638823135327897713022213
Q gi|254780751|r   37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI   74 (723)
Q Consensus        37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei   74 (723)
                      ..+|+|-.|+|+.|-+.  -++|||+.--.+.|+.+.+
T Consensus         4 P~vGDvVigrV~~v~~~--~w~vdI~~~~~a~l~~~~~   39 (82)
T cd04454           4 PDVGDIVIGIVTEVNSR--FWKVDILSRGTARLEDSSA   39 (82)
T ss_pred             CCCCCEEEEEEEEECCC--EEEEEECCCEEEEEEEHHC
T ss_conf             98999999999997078--1899968632889730216


No 90 
>TIGR02349 DnaJ_bact chaperone protein DnaJ; InterPro: IPR012724    Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle.   Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate.  DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately.    This entry mostly consists of bacterial forms of DnaJ. The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Most such proteins are not included in this family, though some chloroplast homologues are included; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding, 0009408 response to heat.
Probab=82.09  E-value=0.58  Score=25.78  Aligned_cols=25  Identities=20%  Similarity=0.611  Sum_probs=11.8

Q ss_pred             HHHHCCCCCCCCCEEEEECCHHHHH
Q ss_conf             1210023675465378606114689
Q gi|254780751|r  477 LESTTKVCTYCKGAGYIRSQSSVAL  501 (723)
Q Consensus       477 ~e~~~~~c~~c~g~g~~~~~~~~~~  501 (723)
                      -....++|+.|+|.|+++...++.+
T Consensus       224 G~ii~~~C~~C~G~G~~~~~~~~~v  248 (386)
T TIGR02349       224 GKIIKEPCSTCKGKGRVKERKTISV  248 (386)
T ss_pred             EEEEECCCCCCCCCEEEEEEEEEEE
T ss_conf             3896336899887406988889999


No 91 
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=81.32  E-value=3.9  Score=20.07  Aligned_cols=55  Identities=24%  Similarity=0.261  Sum_probs=33.1

Q ss_pred             CEEEEEEECCC-CCCCCCCCEEEEEEEEECCCCCEEEEEE----C------CCCCCCCCHHHCCCCCC
Q ss_conf             98999996073-3460428787989978363882313532----7------89771302221371210
Q gi|254780751|r   23 NRVEELDFESE-HKKQIKGNIYLAKVTRVEPSLQAAFVDY----G------GNRHGFLPFLEIHPDYY   79 (723)
Q Consensus        23 g~l~e~~~e~~-~~~~~~GnIY~G~V~~V~p~lqAAFVdi----G------~~k~gFL~~~ei~~~y~   79 (723)
                      +++.-+.-... ......|.|-+|+|++|  ..|+|-|.|    |      ....|-+|++.+...|+
T Consensus        47 n~~~~V~p~~~~~~~~K~GdiV~grV~~v--~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~  112 (188)
T COG1096          47 NRVISVKPGKKTPPLPKGGDIVYGRVTDV--REQRALVRIVGVEGKERELATSGAADIHVSQVRDGYV  112 (188)
T ss_pred             CEEEEECCCCCCCCCCCCCCEEEEEEEEC--CCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCC
T ss_conf             44999524777777689887999999532--6608999999994333367887402589782023111


No 92 
>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=81.30  E-value=3.9  Score=20.06  Aligned_cols=23  Identities=43%  Similarity=0.712  Sum_probs=19.1

Q ss_pred             CCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf             0428787989978363882313532
Q gi|254780751|r   37 QIKGNIYLAKVTRVEPSLQAAFVDY   61 (723)
Q Consensus        37 ~~~GnIY~G~V~~V~p~lqAAFVdi   61 (723)
                      ..+|+|-++||+||-+  +-|+++|
T Consensus         2 P~vGdiV~arVtrv~~--~~a~~~I   24 (72)
T pfam10447         2 PKVGDIVLARVTRVTP--RQAYCEI   24 (72)
T ss_pred             CCCCCEEEEEEEEECH--HEEEEEE
T ss_conf             9899999999999750--1579999


No 93 
>TIGR02349 DnaJ_bact chaperone protein DnaJ; InterPro: IPR012724    Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle.   Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate.  DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately.    This entry mostly consists of bacterial forms of DnaJ. The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Most such proteins are not included in this family, though some chloroplast homologues are included; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding, 0009408 response to heat.
Probab=81.18  E-value=0.24  Score=28.45  Aligned_cols=44  Identities=18%  Similarity=0.227  Sum_probs=28.6

Q ss_pred             HCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf             00236754653786061146899887889997303643101357699999
Q gi|254780751|r  480 TTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVL  529 (723)
Q Consensus       480 ~~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~  529 (723)
                      +..+||.|+|+|.|-+..      +..=.=.......+.|.|.+|+-|.+
T Consensus       213 ~~~tC~~C~G~G~ii~~~------C~~C~G~G~~~~~~~~~v~IPaGV~~  256 (386)
T TIGR02349       213 QQQTCPTCGGEGKIIKEP------CSTCKGKGRVKERKTISVKIPAGVDT  256 (386)
T ss_pred             EEEECCCCCCEEEEEECC------CCCCCCCEEEEEEEEEEEECCCCCCC
T ss_conf             858778858423896336------89988740698888999961799888


No 94 
>pfam07092 DUF1356 Protein of unknown function (DUF1356). This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown.
Probab=79.34  E-value=0.62  Score=25.58  Aligned_cols=34  Identities=26%  Similarity=0.614  Sum_probs=26.1

Q ss_pred             EEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCCCCEEEEECC
Q ss_conf             8998604861489851566630112100236754653786061
Q gi|254780751|r  454 VQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQ  496 (723)
Q Consensus       454 ~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c~g~g~~~~~  496 (723)
                      -+-+.|+.|--+|.|-+         -+-.||.|+|+|+|...
T Consensus        13 ~~~~~~~~fpyveftg~---------~~vtCPTCqGtGrIp~e   46 (231)
T pfam07092        13 NREGDIAQFPYVEFTGR---------DSITCPTCQGTGRIPRE   46 (231)
T ss_pred             CCCCCHHHCCEEEECCC---------CCEECCCCCCCCCCCCC
T ss_conf             54676210856665178---------85046877677616823


No 95 
>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=76.01  E-value=2.5  Score=21.38  Aligned_cols=34  Identities=32%  Similarity=0.504  Sum_probs=28.3

Q ss_pred             CCEEE-EEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf             87879-899783638823135327897713022213
Q gi|254780751|r   40 GNIYL-AKVTRVEPSLQAAFVDYGGNRHGFLPFLEI   74 (723)
Q Consensus        40 GnIY~-G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei   74 (723)
                      |.|+. .+|++|.|++. +|+++|.+-.||.|++.+
T Consensus         1 G~i~~~~~V~~v~~~~G-~~~~l~~g~~gfvhiS~l   35 (71)
T cd05696           1 GAVVDSVKVTKVEPDLG-AVFELKDGLLGFVHISHL   35 (71)
T ss_pred             CCCCCEEEEEEECCCCC-EEEEECCCCEEEEEEHHC
T ss_conf             96233405999858853-799969996899996012


No 96 
>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=75.95  E-value=3.3  Score=20.56  Aligned_cols=33  Identities=30%  Similarity=0.401  Sum_probs=28.7

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf             878798997836388231353278977130222137
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH   75 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~   75 (723)
                      |.+-.|+|+....|  +.+|+++ +-.||||.|.+.
T Consensus         1 g~~v~g~I~~~~kG--G~~v~~~-gv~~FiP~Sq~~   33 (67)
T cd04465           1 GEIVEGKVTEKVKG--GLIVDIE-GVRAFLPASQVD   33 (67)
T ss_pred             CCEEEEEEEEEECC--CEEEEEC-CEEEEEECHHCC
T ss_conf             99999999999857--1999999-999998802525


No 97 
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=75.25  E-value=2.8  Score=21.09  Aligned_cols=49  Identities=24%  Similarity=0.333  Sum_probs=35.4

Q ss_pred             EEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf             999996073346042878798997836388231353278977130222137
Q gi|254780751|r   25 VEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH   75 (723)
Q Consensus        25 l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~   75 (723)
                      +.-|+.--.-...-.|-+|+|.|.+|+.  =.|||++...--|.+|-++..
T Consensus       108 vy~l~~~c~~~Dve~g~~Y~g~v~~v~~--~GvFv~Ln~~v~GL~~~~d~~  156 (715)
T COG1107         108 VYVLDNSCTMEDVEAGKYYKGIVSRVEK--YGVFVELNSHVRGLIHRRDLG  156 (715)
T ss_pred             EEEECCCCCHHHCCCCEEEECCCCCHHH--HCCEEECCHHHHCCCCCCCCC
T ss_conf             6996355662003464054031021434--065243373543344401247


No 98 
>PRK04820 rnpA ribonuclease P; Reviewed
Probab=75.14  E-value=5.8  Score=18.85  Aligned_cols=60  Identities=27%  Similarity=0.431  Sum_probs=42.4

Q ss_pred             CCEEEECCC-CHHHHHHHHHHHHHHH-------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             512420468-8689999999998630-------02587169985045575799999999999999987764
Q gi|254780751|r  216 GETISRKIT-NPVDRKNLKEIARGLE-------VPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVREL  278 (723)
Q Consensus       216 ~~~iSrki~-~~~~r~~l~~~~~~~~-------~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~  278 (723)
                      |..||||.. ..-.|.++|.++.+.-       .+.++=+|.|-.+...+-.+|..-   |.++|..+-..
T Consensus        51 GL~VsKK~~k~AV~RNRIKR~iREsFRl~Q~~Lp~~DiVVlaR~g~~~l~N~el~~~---l~kLw~r~~~~  118 (145)
T PRK04820         51 GMAVSRKVDTRAVGRNRIKRVLRDAMRHLLPELAGGDYVIVARSAAAKATNPQIRDA---FLRLLRRAGAL  118 (145)
T ss_pred             EEEEECHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCHHHCCHHHHHHH---HHHHHHHHCCC
T ss_conf             789751224566788889999999999731138888889993677344051999999---99999980468


No 99 
>TIGR02642 phage_xxxx uncharacterized phage protein; InterPro: IPR013464    This uncharacterised protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus (strain YJ016), Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to the phage lambda antitermination protein Q..
Probab=74.26  E-value=1.2  Score=23.70  Aligned_cols=48  Identities=13%  Similarity=0.203  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHC-CCCCCCCCEEEEECCHH
Q ss_conf             999999731278728998604861489851566630112100-23675465378606114
Q gi|254780751|r  440 EKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTT-KVCTYCKGAGYIRSQSS  498 (723)
Q Consensus       440 ~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~-~~c~~c~g~g~~~~~~~  498 (723)
                      ...|++.+...-+..+..|=           =.+.++..--. ..|++|+|+|.+....-
T Consensus       168 ~~~Lrd~a~~~a~~~~~CP~-----------C~Gtg~~~~~~P~~C~~C~G~G~~~~~~e  216 (270)
T TIGR02642       168 RRALRDYAVAKAAESRKCPR-----------CRGTGLRLRRQPEECDKCAGTGRLLPTVE  216 (270)
T ss_pred             HHHHHHHHHHHHHHCCCCCC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCHH
T ss_conf             88899999998741488798-----------65667888977887777786433030089


No 100
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=73.32  E-value=1.8  Score=22.32  Aligned_cols=19  Identities=32%  Similarity=0.555  Sum_probs=12.3

Q ss_pred             HHHHHCCCCCCCCCEEEEE
Q ss_conf             1121002367546537860
Q gi|254780751|r  476 VLESTTKVCTYCKGAGYIR  494 (723)
Q Consensus       476 l~e~~~~~c~~c~g~g~~~  494 (723)
                      ...++..+||.|+|+|.+.
T Consensus       178 g~~~~~~~C~~C~G~G~~i  196 (371)
T COG0484         178 GFFSFQQTCPTCNGTGKII  196 (371)
T ss_pred             EEEEEEEECCCCCCCEEEC
T ss_conf             5899999899976612389


No 101
>TIGR01213 TIGR01213 conserved hypothetical protein TIGR01213; InterPro: IPR005912    The members of this family of conserved hypothetical proteins show a low level of similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs.  .
Probab=72.42  E-value=1.1  Score=23.75  Aligned_cols=39  Identities=8%  Similarity=0.114  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEE-CCC
Q ss_conf             769999999842221436786499832880699982-375
Q gi|254780751|r  349 SGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDV-NSG  387 (723)
Q Consensus       349 y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDV-NSG  387 (723)
                      -.|..++.+=|.+.+--..|-..=.|.=++++.||+ -+.
T Consensus       149 EsiK~E~nRE~GK~~~~rtG~~~d~e~PD~v~~v~~r~~~  188 (450)
T TIGR01213       149 ESIKREFNRELGKLLAKRTGKEVDFERPDIVVMVEFREAE  188 (450)
T ss_pred             CCHHHHHCCCHHEEEEEECCCCCCCCCCCEEEEEECCCCC
T ss_conf             8624551610100231002724447888379998247776


No 102
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=72.07  E-value=3.1  Score=20.71  Aligned_cols=12  Identities=17%  Similarity=0.476  Sum_probs=5.1

Q ss_pred             HHHHHHHHHCCC
Q ss_conf             999987310368
Q gi|254780751|r  409 EIARQLRLRDLA  420 (723)
Q Consensus       409 EIaRQlRLRnlg  420 (723)
                      .+|-|+-+-|+-
T Consensus       193 k~aee~g~~~ie  204 (354)
T COG1568         193 KVAEELGYNNIE  204 (354)
T ss_pred             HHHHHHCCCCHH
T ss_conf             999984833155


No 103
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=70.97  E-value=7.2  Score=18.19  Aligned_cols=99  Identities=23%  Similarity=0.187  Sum_probs=64.5

Q ss_pred             CCCCCCCCEEEEECCCEEE----EEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEE-EECCCCCCHHHH
Q ss_conf             2143678649983288069----99823755444555114799999999999999873103686389-603347988889
Q gi|254780751|r  362 EVTLPSRGYVIINQTEALV----SIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIV-VDFIDMEEKKNN  436 (723)
Q Consensus       362 ~V~L~sGG~lvIe~TEALt----~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIv-IDFIdM~~~~~~  436 (723)
                      .|||-+-..+-++-++--+    .||.=|.-+-|+.|     +.+-+.+|-+.+.+-.+.+ +-||+ -||||+..    
T Consensus       312 ~~~lF~s~~~~~el~~k~~~~~e~i~fL~~~f~GGTD-----~~~~l~~al~~~k~~~~~~-adiv~ITDg~~~~~----  381 (437)
T COG2425         312 YVILFDSEVIEYELYEKKIDIEELIEFLSYVFGGGTD-----ITKALRSALEDLKSRELFK-ADIVVITDGEDERL----  381 (437)
T ss_pred             EEEEECCCCEEEEECCCCCCHHHHHHHHHHHCCCCCC-----HHHHHHHHHHHHHCCCCCC-CCEEEEECCHHHHH----
T ss_conf             8999525202555057745799999999650689888-----5899999999864366567-77899804376654----


Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEECCCC---EEEEECC
Q ss_conf             999999999731278728998604861---4898515
Q gi|254780751|r  437 RSVEKKLKESLKKDRARVQVGAISNFG---LLEMSRQ  470 (723)
Q Consensus       437 ~~v~~~l~~~l~~D~~~~~v~~it~lG---LlEltRk  470 (723)
                      ..++....+..+...++..-+=|+..|   |+.|+..
T Consensus       382 ~~~~~~v~e~~k~~~~rl~aV~I~~~~~~~l~~Isd~  418 (437)
T COG2425         382 DDFLRKVKELKKRRNARLHAVLIGGYGKPGLMRISDH  418 (437)
T ss_pred             HHHHHHHHHHHHHHHCEEEEEEECCCCCCCCCEECEE
T ss_conf             6789999999887543489999647898660001114


No 104
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=70.90  E-value=7.2  Score=18.18  Aligned_cols=13  Identities=38%  Similarity=0.856  Sum_probs=7.0

Q ss_pred             HCCCCCCCCCEEE
Q ss_conf             0023675465378
Q gi|254780751|r  480 TTKVCTYCKGAGY  492 (723)
Q Consensus       480 ~~~~c~~c~g~g~  492 (723)
                      +..+||.|+|+..
T Consensus       397 s~~~C~~C~G~RL  409 (935)
T COG0178         397 SEKPCPSCKGTRL  409 (935)
T ss_pred             CCCCCCCCCCCCC
T ss_conf             4274887888605


No 105
>pfam00825 Ribonuclease_P Ribonuclease P.
Probab=70.83  E-value=7.3  Score=18.17  Aligned_cols=57  Identities=23%  Similarity=0.358  Sum_probs=38.4

Q ss_pred             CCCEEEECCCC-HHHHHHHHHHHHHH----H--C--CCCCEEEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf             75124204688-68999999999863----0--0--258716998504557579999999999999
Q gi|254780751|r  215 KGETISRKITN-PVDRKNLKEIARGL----E--V--PAGMGVILRTAGASRTKIEIKRDFEYLMRL  271 (723)
Q Consensus       215 ~~~~iSrki~~-~~~r~~l~~~~~~~----~--~--~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~  271 (723)
                      -|+.+|+|+-+ .-.|.+++..+.+.    .  .  +.++=+|+|..+.+.+..+|..|+..|+..
T Consensus        40 ~G~~vsKK~g~~AV~RNriKR~lRe~~r~~~~~l~~~~d~Vvi~r~~~~~~~~~~l~~~l~~ll~k  105 (107)
T pfam00825        40 LGISVSKKVGKRAVVRNRIKRLLREAFRLNKDRLPPGLDIVVIARKGALEADFAELLKELEKLLKK  105 (107)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHH
T ss_conf             899995513636889889999999999973510588977999978754549999999999999997


No 106
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=70.66  E-value=7.3  Score=18.14  Aligned_cols=42  Identities=12%  Similarity=0.139  Sum_probs=28.7

Q ss_pred             CCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCC
Q ss_conf             645888888752376631111035320366788898763101
Q gi|254780751|r  291 EGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSY  332 (723)
Q Consensus       291 ~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~~~~~p~~  332 (723)
                      +..-+..+|+.+-+..-.-|+|+.++..-..-+|+-.+.|.-
T Consensus       513 D~~rLi~~L~~Lrd~GNTViVVEHD~~~i~~AD~iIDiGPgA  554 (1809)
T PRK00635        513 DTHKLIQVIKKLRDQGNTVLLVEHDEQMISLADRIIDIGPGA  554 (1809)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHCCEEEECCCCC
T ss_conf             899999999999856997999966899996277789617887


No 107
>pfam03589 Antiterm Antitermination protein.
Probab=69.28  E-value=2.8  Score=21.03  Aligned_cols=31  Identities=32%  Similarity=0.478  Sum_probs=24.9

Q ss_pred             HHHHCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             1210023675465378606114689988788
Q gi|254780751|r  477 LESTTKVCTYCKGAGYIRSQSSVALSILRSV  507 (723)
Q Consensus       477 ~e~~~~~c~~c~g~g~~~~~~~~~~~~~r~i  507 (723)
                      .-..+..|+.|+|.|+-+-+.+.|++.+..+
T Consensus        28 G~pvfk~c~rc~g~G~sr~~~~~a~~ai~~~   58 (95)
T pfam03589        28 GVPVFKTCERCGGRGYSRLDSTEAIEALCKY   58 (95)
T ss_pred             CCCEEEECCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             9751434777789785989709999999987


No 108
>PRK00588 rnpA ribonuclease P; Reviewed
Probab=69.04  E-value=7.9  Score=17.91  Aligned_cols=58  Identities=17%  Similarity=0.353  Sum_probs=39.9

Q ss_pred             CCCEEEECCCCHHHHHHH----HHHHHHH--HCCCCCEEEEE--EECCCCCHHHHHHHHHHHHHHH
Q ss_conf             751242046886899999----9999863--00258716998--5045575799999999999999
Q gi|254780751|r  215 KGETISRKITNPVDRKNL----KEIARGL--EVPAGMGVILR--TAGASRTKIEIKRDFEYLMRLW  272 (723)
Q Consensus       215 ~~~~iSrki~~~~~r~~l----~~~~~~~--~~~~~~G~IiR--T~a~~~~~~~l~~d~~~L~~~w  272 (723)
                      -|..+||++-+.-.|.+.    +.++...  ..|.|.-++||  ..|+.++..+|..|++..+..-
T Consensus        45 vG~vVSK~VGnAV~RnrVkRrLR~~~r~~l~~lp~g~~vVvrAlp~aa~as~~eL~~~l~~~l~ra  110 (116)
T PRK00588         45 VGLIIAKSVGSAVERHRVARRLRHVARPMLKELHPSDRVVIRALPSSRHVSSARLEQQLRCGLRRA  110 (116)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             899982310004678899999999999987407998879999588747489999999999999999


No 109
>PRK02083 imidazole glycerol phosphate synthase subunit HisF; Provisional
Probab=68.95  E-value=6.6  Score=18.43  Aligned_cols=16  Identities=6%  Similarity=0.196  Sum_probs=6.0

Q ss_pred             HHHHHHHHCCCCEEEE
Q ss_conf             9998731036863896
Q gi|254780751|r  410 IARQLRLRDLAGLIVV  425 (723)
Q Consensus       410 IaRQlRLRnlgGiIvI  425 (723)
                      .+.++.=.++|.|++.
T Consensus       158 ~i~~~~~~g~geil~t  173 (253)
T PRK02083        158 WAKEVQELGAGEILLT  173 (253)
T ss_pred             HHHHHHHCCCCEEEEE
T ss_conf             9999875698789999


No 110
>PRK05973 replicative DNA helicase; Provisional
Probab=68.83  E-value=7.2  Score=18.18  Aligned_cols=85  Identities=18%  Similarity=0.251  Sum_probs=52.2

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHH----HHHHHHHHHHHHCCCCEEEEEECCCC-EEEEECCCCCCCHHH-
Q ss_conf             999999998731036863896033479888899----99999999731278728998604861-489851566630112-
Q gi|254780751|r  405 EAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNR----SVEKKLKESLKKDRARVQVGAISNFG-LLEMSRQRIRSSVLE-  478 (723)
Q Consensus       405 eAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~----~v~~~l~~~l~~D~~~~~v~~it~lG-LlEltRkR~r~sl~e-  478 (723)
                      ..+.+|+|+|+=-.=+|+||||++-..+.+++.    .+.+.||...+.=  .+-|+-+|+|. =+| +|...||-+.+ 
T Consensus       133 i~~~~i~rrl~~~~~~~LIVIDYLQLM~~~r~~~eiseisRsLK~lAkEl--~vPVvaLSQLnRs~E-~R~dKrP~lSDL  209 (237)
T PRK05973        133 ICADYIIARLASAPRGTLVVIDYLQLLDQRREKPDLSVQVRALKSFARKR--GVILVFISQIDRSFD-PASKPLPDIRDV  209 (237)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEECHHHHCCCCCCCCHHHHHHHHHHHHHHH--CCCEEEEECCCCCCC-CCCCCCCCCCCC
T ss_conf             33999999985278996899976775266778866899999999999986--993999400364322-356789974013


Q ss_pred             ---------HHCCCCCCCCCEEE
Q ss_conf             ---------10023675465378
Q gi|254780751|r  479 ---------STTKVCTYCKGAGY  492 (723)
Q Consensus       479 ---------~~~~~c~~c~g~g~  492 (723)
                               .|...|-.-+|.-.
T Consensus       210 Rlpnp~dl~lf~k~~fl~~g~~~  232 (237)
T PRK05973        210 RLPNPLDLSLFDKACFLNNGEIR  232 (237)
T ss_pred             CCCCCCHHHHHCHHEEECCCEEE
T ss_conf             69982104230321031277378


No 111
>KOG1067 consensus
Probab=68.49  E-value=6.7  Score=18.41  Aligned_cols=34  Identities=6%  Similarity=0.159  Sum_probs=21.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCC
Q ss_conf             1432212345645888888752376631111035
Q gi|254780751|r  281 NSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSG  314 (723)
Q Consensus       281 ~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~  314 (723)
                      ..+.|.+++..++-+...++++....+..+..|.
T Consensus       270 ~Kr~~~~~~~p~pel~K~v~~la~erl~~vftd~  303 (760)
T KOG1067         270 QKREPQKLFLPDPELVKHVHKLAMERLYAVFTDY  303 (760)
T ss_pred             CCCCHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             6243244428987899999999999999985253


No 112
>PRK13597 imidazole glycerol phosphate synthase subunit HisF; Provisional
Probab=68.15  E-value=7.1  Score=18.23  Aligned_cols=16  Identities=19%  Similarity=0.293  Sum_probs=7.3

Q ss_pred             HHHHCCCCCCEEECCC
Q ss_conf             8752376631111035
Q gi|254780751|r  299 IRDLYCKDISEIIVSG  314 (723)
Q Consensus       299 ird~~~~~~~~i~vd~  314 (723)
                      +..++...++.|++..
T Consensus        90 ~~~ll~~GadkViigS  105 (252)
T PRK13597         90 ARKLLLSGADKVSVNS  105 (252)
T ss_pred             HHHHHHCCCCEEEECH
T ss_conf             9999856987798326


No 113
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=67.94  E-value=8.3  Score=17.76  Aligned_cols=57  Identities=19%  Similarity=0.220  Sum_probs=40.7

Q ss_pred             CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEEC
Q ss_conf             023675465378606114689988788999730364310135769999987302379999999984887999847
Q gi|254780751|r  481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIG  555 (723)
Q Consensus       481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d  555 (723)
                      .-.||.|.+.-..-|...+|..+-..+.+....+++                  +.+.+..+-.+||-.|...+-
T Consensus        44 ~LRCp~CQNqsIadSnA~IA~DlR~~V~e~l~eGkS------------------~~qIid~mVaRYG~FVly~Pp  100 (153)
T COG3088          44 ELRCPQCQNQSIADSNAPIARDLRHQVYELLQEGKS------------------DQQIIDYMVARYGEFVLYKPP  100 (153)
T ss_pred             HCCCCCCCCCCHHHHCCHHHHHHHHHHHHHHHCCCC------------------HHHHHHHHHHHHCCEEEECCC
T ss_conf             638875789773320667899999999999985786------------------899999999853463432699


No 114
>pfam00684 DnaJ_CXXCXGXG DnaJ central domain (4 repeats). The central cysteine-rich (CR) domain of DnaJ proteins contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DNAJ cysteine rich domain and various hydrophobic peptides has been found.
Probab=67.82  E-value=3.9  Score=20.07  Aligned_cols=21  Identities=24%  Similarity=0.442  Sum_probs=14.7

Q ss_pred             CHHHHHCCCCCCCCCEEEEEC
Q ss_conf             011210023675465378606
Q gi|254780751|r  475 SVLESTTKVCTYCKGAGYIRS  495 (723)
Q Consensus       475 sl~e~~~~~c~~c~g~g~~~~  495 (723)
                      .+.-.+..+|+.|+|+|++..
T Consensus        48 ~~~~~~~~~C~~C~G~G~~i~   68 (79)
T pfam00684        48 GGVFQFQQTCPACGGTGKIIE   68 (79)
T ss_pred             CEEEEEEEECCCCCCEEEEEC
T ss_conf             835886889966886461889


No 115
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=67.45  E-value=8.5  Score=17.70  Aligned_cols=24  Identities=29%  Similarity=0.339  Sum_probs=19.8

Q ss_pred             CCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf             60428787989978363882313532
Q gi|254780751|r   36 KQIKGNIYLAKVTRVEPSLQAAFVDY   61 (723)
Q Consensus        36 ~~~~GnIY~G~V~~V~p~lqAAFVdi   61 (723)
                      -..+|+|-.|+|++|-+.+  |+|+|
T Consensus        61 ~p~vGdiVig~V~~v~~~~--a~v~I   84 (187)
T PRK09521         61 LLKKGDIVYGRVVDVKEQR--ALVRI   84 (187)
T ss_pred             CCCCCCEEEEEEEEECCCE--EEEEE
T ss_conf             8898999999999954767--99999


No 116
>COG0594 RnpA RNase P protein component [Translation, ribosomal structure and biogenesis]
Probab=66.77  E-value=8.7  Score=17.61  Aligned_cols=57  Identities=23%  Similarity=0.307  Sum_probs=41.4

Q ss_pred             CCEEEE-CCCCHHHHHHHHHHHHHH-------HCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf             512420-468868999999999863-------002587169985045575799999999999999
Q gi|254780751|r  216 GETISR-KITNPVDRKNLKEIARGL-------EVPAGMGVILRTAGASRTKIEIKRDFEYLMRLW  272 (723)
Q Consensus       216 ~~~iSr-ki~~~~~r~~l~~~~~~~-------~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w  272 (723)
                      |+.||+ ++...-.|.+.+..+.+.       ..+.++=+|+|..+.+.+-.++.+++.+++..-
T Consensus        44 GlsVsKkk~~~AV~RNRiKR~iRe~~r~~~~~~~~~d~Viiar~~~~~~~~~~l~~~L~~~l~~~  108 (117)
T COG0594          44 GLTVSKKKVGNAVERNRIKRLIREAFRLLQHLLPGFDIVIIARKGFLELDFSELEKELSQLLKRA  108 (117)
T ss_pred             EEEEECHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             99998600241246789999999999962531898609999778867779899999999999861


No 117
>PRK03220 consensus
Probab=66.32  E-value=7.9  Score=17.91  Aligned_cols=19  Identities=11%  Similarity=0.011  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHCCCCEEEEE
Q ss_conf             9999987310368638960
Q gi|254780751|r  408 EEIARQLRLRDLAGLIVVD  426 (723)
Q Consensus       408 ~EIaRQlRLRnlgGiIvID  426 (723)
                      .+.+.++.=.++|.||+-|
T Consensus       162 ~~~i~~~~~~g~geil~td  180 (257)
T PRK03220        162 VEWAARGAELGVGEILLNS  180 (257)
T ss_pred             HHHHHHHHHCCCCEEEEEE
T ss_conf             9999998626988899998


No 118
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=65.43  E-value=5.6  Score=18.95  Aligned_cols=154  Identities=14%  Similarity=0.181  Sum_probs=82.7

Q ss_pred             HHHHHHCCCC---EEEEECCCCCCHHHH------HHHHHHHHHHHHHCCCCEEEEE---ECCCCEE--------------
Q ss_conf             9873103686---389603347988889------9999999997312787289986---0486148--------------
Q gi|254780751|r  412 RQLRLRDLAG---LIVVDFIDMEEKKNN------RSVEKKLKESLKKDRARVQVGA---ISNFGLL--------------  465 (723)
Q Consensus       412 RQlRLRnlgG---iIvIDFIdM~~~~~~------~~v~~~l~~~l~~D~~~~~v~~---it~lGLl--------------  465 (723)
                      +.++|-+=.|   +--|..|||+...-.      ..+++.+++.|.++..-.-+..   ++.+=+.              
T Consensus       373 ~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~  452 (730)
T COG1198         373 KLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDS  452 (730)
T ss_pred             EEEECCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCCCEEECCCCCCCCCCCCCCC
T ss_conf             89970354555678762587356665546775799999999999842986899971677654004256898024899995


Q ss_pred             EEECCCCCCCH-------HHHHCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCC------CCCHHHHHHHH
Q ss_conf             98515666301-------121002367546537860611468998878899973036431013------57699999873
Q gi|254780751|r  466 EMSRQRIRSSV-------LESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIV------HTHSDVVLYLL  532 (723)
Q Consensus       466 EltRkR~r~sl-------~e~~~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v------~~~~~va~~ll  532 (723)
                      =||=-+-+..|       .+.....||.|++. +++..-+=...+..++....-..+.-.+-.      ..+-....-+.
T Consensus       453 ~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~-~L~~~G~GterieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~  531 (730)
T COG1198         453 PLTLHKATGQLRCHYCGYQEPIPQSCPECGSE-HLRAVGPGTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFA  531 (730)
T ss_pred             CEEEECCCCEEEECCCCCCCCCCCCCCCCCCC-EEEEECCCHHHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             12786479806707799989988779899997-36996461999999999878999479984666664356899999975


Q ss_pred             CCHHHHHHHHH--------HHHCCEEEEEECCCCCCCCEEEE
Q ss_conf             02379999999--------98488799984787788633897
Q gi|254780751|r  533 NQKRATIVEYE--------ARFGVSINVVIGIELADKLFYIE  566 (723)
Q Consensus       533 n~kr~~l~~lE--------~~~~~~I~i~~d~~l~~~~f~Ie  566 (723)
                      +.+-+-|....        -.++.-..+.+|..|..|+|+-.
T Consensus       532 ~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRAs  573 (730)
T COG1198         532 NGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRAS  573 (730)
T ss_pred             CCCCCEEECCHHHHCCCCCCCCEEEEEEECHHHHCCCCCCHH
T ss_conf             799886634166642788666318999963143158884357


No 119
>KOG1015 consensus
Probab=65.10  E-value=7.1  Score=18.23  Aligned_cols=135  Identities=13%  Similarity=0.101  Sum_probs=65.6

Q ss_pred             CCCCEEECCCCCHHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEE
Q ss_conf             66311110353203667888987631012112201344203567769999999842221436786499832880699982
Q gi|254780751|r  305 KDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDV  384 (723)
Q Consensus       305 ~~~~~i~vd~~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDV  384 (723)
                      ..+..++|-.+  .+.+..++..+...+.. + ...+...+|..-.+-.-=++.+--.-|-.+||-.+|-.+=-  -|= 
T Consensus       726 lg~ktaLvV~P--lNt~~NW~~EFekWm~~-~-e~~~~leV~eL~~vkr~e~R~~~L~~W~~~ggVmIiGYdmy--RnL-  798 (1567)
T KOG1015         726 LGFKTALVVCP--LNTALNWMNEFEKWMEG-L-EDDEKLEVSELATVKRPEERSYMLQRWQEDGGVMIIGYDMY--RNL-  798 (1567)
T ss_pred             CCCCEEEEECC--HHHHHHHHHHHHHHCCC-C-CCCCCCEEEHHHHCCCHHHHHHHHHHHHHCCCEEEEEHHHH--HHH-
T ss_conf             47856899723--59988999999986124-2-22466212021202674889999999975297799736888--877-


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCC
Q ss_conf             375544455511479999999999999987310368638960334798888999999999973127872899860486
Q gi|254780751|r  385 NSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNF  462 (723)
Q Consensus       385 NSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~l  462 (723)
                      --|+..+..         |   ++|+.++--+++=--|+|.|=-..- +...-.|-++|....-+  .|+-+.| |+|
T Consensus       799 a~gr~vk~r---------k---~ke~f~k~lvdpGPD~vVCDE~HiL-KNeksa~Skam~~irtk--RRI~LTG-TPL  860 (1567)
T KOG1015         799 AQGRNVKSR---------K---LKEIFNKALVDPGPDFVVCDEGHIL-KNEKSAVSKAMNSIRTK--RRIILTG-TPL  860 (1567)
T ss_pred             HCCCCHHHH---------H---HHHHHHHHCCCCCCCEEEECCHHHH-CCCHHHHHHHHHHHHHH--EEEEEEC-CCH
T ss_conf             514560356---------7---9999998605789976872421221-35247899999987764--0477526-711


No 120
>PRK01659 consensus
Probab=64.74  E-value=9.5  Score=17.35  Aligned_cols=15  Identities=7%  Similarity=0.078  Sum_probs=5.3

Q ss_pred             HHHHHHHHCCCCEEE
Q ss_conf             999873103686389
Q gi|254780751|r  410 IARQLRLRDLAGLIV  424 (723)
Q Consensus       410 IaRQlRLRnlgGiIv  424 (723)
                      .+.++.-.+.|.||+
T Consensus       158 ~i~~~~~~g~geil~  172 (252)
T PRK01659        158 WAKEAVRLGAGEILL  172 (252)
T ss_pred             HHHHHHHCCCCEEEE
T ss_conf             999999769977999


No 121
>TIGR02034 CysN sulfate adenylyltransferase, large subunit; InterPro: IPR011779    Metabolic assimilation of sulphur from inorganic sulphate, requires sulphate activation by coupling to a nucleoside, for the production of high-energy nucleoside phosphosulphates. This pathway appears to be similar in all prokaryotic organisms. Activation is first achieved through sulphation of sulphate with ATP by sulphate adenylyltransferase (ATP sulphurylase) to produce 5'-phosphosulphate (APS), coupled by GTP hydrolysis. Subsequently, APS is phosphorylated by an APS kinase to produce 3'-phosphoadenosine-5'-phosphosulphate (PAPS) . In Escherichia coli, ATP sulphurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulphur-containing amino acids . Homologous to this E. coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulphurase and APS kinase activity, yet are involved in Nod factor sulphation, and sulphation of other macromolecules . With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulphurase) and cysC (APS kinase) , .; GO: 0016772 transferase activity transferring phosphorus-containing groups.
Probab=64.24  E-value=0.82  Score=24.76  Aligned_cols=69  Identities=20%  Similarity=0.142  Sum_probs=47.5

Q ss_pred             CCCCCCCCCCEEEEECCCEEE-EEEECCCCCCCCCCCH-H-HHHHHHHHHHHHHHH--HHHHHCCCCEEEEECC
Q ss_conf             222143678649983288069-9982375544455511-4-799999999999999--8731036863896033
Q gi|254780751|r  360 QTEVTLPSRGYVIINQTEALV-SIDVNSGRSTREHCIE-D-TALQTNLEAAEEIAR--QLRLRDLAGLIVVDFI  428 (723)
Q Consensus       360 ~~~V~L~sGG~lvIe~TEALt-~IDVNSG~~~~~~~~e-~-t~l~tNleAA~EIaR--QlRLRnlgGiIvIDFI  428 (723)
                      .+..||+.|+..|==.-.++. .+|||+.+....+.++ = .+=.+||.-+++|+=  ==.=|-+||+|+||=.
T Consensus       328 G~~Y~lk~g~~~v~a~v~~I~~~vdvn~~~~~~A~~L~GLN~iG~v~l~~~~~~~fd~Y~~nR~tG~FILIDr~  401 (411)
T TIGR02034       328 GRSYLLKLGTRKVRASVTAIKHKVDVNTLEKNAAKELEGLNEIGLVNLSLDEPIAFDAYAENRTTGAFILIDRL  401 (411)
T ss_pred             CCEEEEEECCEEEEEEEEEEEEEECCCCCCHHHHHHHHCCCCEEEEEEEECCCCCCCCHHHCCCCEEEEEEECC
T ss_conf             95378873242775899877799724643102212310687057999830661013542218841027999846


No 122
>PRK04281 consensus
Probab=62.86  E-value=10  Score=17.12  Aligned_cols=18  Identities=17%  Similarity=0.315  Sum_probs=7.9

Q ss_pred             HHHHHHHHHCCCCEEEEE
Q ss_conf             999987310368638960
Q gi|254780751|r  409 EIARQLRLRDLAGLIVVD  426 (723)
Q Consensus       409 EIaRQlRLRnlgGiIvID  426 (723)
                      |.+.++.=.++|.+|+-|
T Consensus       158 ~~~~~~~~~g~geil~td  175 (254)
T PRK04281        158 EWAVEMQKRGAGEILLTG  175 (254)
T ss_pred             HHHHHHHHCCCCEEEEEE
T ss_conf             999998752998999988


No 123
>PRK06937 type III secretion system protein; Reviewed
Probab=61.62  E-value=11  Score=16.97  Aligned_cols=50  Identities=14%  Similarity=0.149  Sum_probs=38.0

Q ss_pred             CCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEE
Q ss_conf             6431013576999998730237999999998488799984787788633897
Q gi|254780751|r  515 TAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIE  566 (723)
Q Consensus       515 ~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ie  566 (723)
                      ..+.++++|||+-...+.............  -..|.|.+|+.|.+..+.++
T Consensus       129 ~~~~v~I~V~P~d~~~v~~~~~~~~~~~~~--~~~l~I~~D~~L~~g~CvlE  178 (204)
T PRK06937        129 NQKQVVVRVAPDQAGAVREQIAKVLKDFPG--VGYLEVVADARLDQGGCILE  178 (204)
T ss_pred             CCCEEEEEECHHHHHHHHHHHHHHHHHCCC--CCEEEEEECCCCCCCCEEEE
T ss_conf             597399999946699999999999972888--85079852898899975995


No 124
>PRK04390 rnpA ribonuclease P; Reviewed
Probab=61.39  E-value=11  Score=16.94  Aligned_cols=56  Identities=18%  Similarity=0.210  Sum_probs=43.8

Q ss_pred             CCEEEECCCC-HHHHHHHHHHHHHHH-------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf             5124204688-689999999998630-------0258716998504557579999999999999
Q gi|254780751|r  216 GETISRKITN-PVDRKNLKEIARGLE-------VPAGMGVILRTAGASRTKIEIKRDFEYLMRL  271 (723)
Q Consensus       216 ~~~iSrki~~-~~~r~~l~~~~~~~~-------~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~  271 (723)
                      |+.||||... .-.|.++|.++.+.-       .+.++=+++|..+...+-.+|..+++.|.-.
T Consensus        48 GlvVsKK~~~~AV~RNriKR~iRE~FR~~q~~L~~~DiVV~ar~~~~~~dn~~l~~~L~~L~~~  111 (121)
T PRK04390         48 GLVVGKKTAKRANERNYMKRVIRDWFRLNKNRLPPQDFVVRVHRKFDRATAKQARAELAQLMFG  111 (121)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHH
T ss_conf             7998631213477777899999999986611189978999945444526999999999999843


No 125
>KOG3409 consensus
Probab=61.23  E-value=11  Score=16.92  Aligned_cols=57  Identities=26%  Similarity=0.243  Sum_probs=33.1

Q ss_pred             EEECCCCCEEEEEEEE--CCEEEEEEECCCCC---CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf             8965289607999998--99899999607334---604287879899783638823135327897713022213
Q gi|254780751|r    6 LIDASHVEETRVVVLR--DNRVEELDFESEHK---KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI   74 (723)
Q Consensus         6 lI~~~~~~e~Rvav~e--~g~l~e~~~e~~~~---~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei   74 (723)
                      .|.|+... ++  +.+  .+++.=..++...-   -..+|.|-++||.++  +++-|=|||       |++.|.
T Consensus        33 yI~aS~ag-~~--~~~~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~i--~~rfAkv~I-------~~V~d~   94 (193)
T KOG3409          33 YIFASVAG-VN--FRDNLVQKIEVVSVEKQLFNELLPFVGAIVTARVSRI--NLRFAKVDI-------LSVGDK   94 (193)
T ss_pred             EEEECCCC-CE--EECCCCCCEEEEEECCCCHHHCCCCCCCEEEEEEEEE--CCCEEEEEE-------EEECCE
T ss_conf             69851466-16--5437765224665226514330776576799998762--441356789-------998679


No 126
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=60.63  E-value=4.4  Score=19.64  Aligned_cols=22  Identities=9%  Similarity=0.303  Sum_probs=14.6

Q ss_pred             HHHHCCCCCCCCCCEEEEECCC
Q ss_conf             9984222143678649983288
Q gi|254780751|r  356 DSLHQTEVTLPSRGYVIINQTE  377 (723)
Q Consensus       356 ~~~~~~~V~L~sGG~lvIe~TE  377 (723)
                      -.=|.+.+|.+-|+|+++|+.|
T Consensus        30 P~KFRk~iWiKRG~fVlvd~~~   51 (78)
T cd05792          30 PTKFRKNIWIKRGDFVLVEPIE   51 (78)
T ss_pred             CHHHHCCEEEECCCEEEEEECC
T ss_conf             1334316899718999997604


No 127
>PRK02621 consensus
Probab=59.83  E-value=12  Score=16.76  Aligned_cols=16  Identities=13%  Similarity=0.295  Sum_probs=6.7

Q ss_pred             HHHHHHHCCCCEEEEE
Q ss_conf             9987310368638960
Q gi|254780751|r  411 ARQLRLRDLAGLIVVD  426 (723)
Q Consensus       411 aRQlRLRnlgGiIvID  426 (723)
                      +..+-=.++|.||+.|
T Consensus       160 ~~~~~~~g~geil~td  175 (254)
T PRK02621        160 AEEVAERGAGEILLTS  175 (254)
T ss_pred             HHHHHHHCCCEEEEEE
T ss_conf             9887762889699988


No 128
>PRK05054 exoribonuclease II; Provisional
Probab=59.53  E-value=12  Score=16.73  Aligned_cols=92  Identities=11%  Similarity=0.113  Sum_probs=46.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCC-
Q ss_conf             0353203667888987631012112201344203567769999999842221436786499832880699982375544-
Q gi|254780751|r  312 VSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRST-  390 (723)
Q Consensus       312 vd~~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~-  390 (723)
                      +...-.|.++.+++........       ....+-.....-.++..++  +-|=..+|.|.++..|+-...|-| |..+ 
T Consensus       308 S~~rLtY~~V~~~l~~~~~~~~-------~~~~l~~~l~~L~~la~~l--~~~R~~~g~~~~d~pe~~~~ld~~-g~~~~  377 (644)
T PRK05054        308 SKAKLAYDNVSDWLENGGNWQP-------ESEAIAQQIRLLHQFCLAR--SEWRKNHALVFKDRPDYRFELGEK-GEVLD  377 (644)
T ss_pred             ECCEECHHHHHHHHHCCCCCCC-------CCHHHHHHHHHHHHHHHHH--HHHHHHCCCCCCCCCCEEEEECCC-CCEEE
T ss_conf             4872539999999845876675-------4088999999999999999--976752876324686359998899-98735


Q ss_pred             --------CCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             --------45551147999999999999998
Q gi|254780751|r  391 --------REHCIEDTALQTNLEAAEEIARQ  413 (723)
Q Consensus       391 --------~~~~~e~t~l~tNleAA~EIaRQ  413 (723)
                              ...=+|+-.+.+|..+|+-+..+
T Consensus       378 i~~~~r~~ah~LIEE~MllAN~~vA~~l~~~  408 (644)
T PRK05054        378 IVAEPRRIANRIVEESMIAANICAARVLRDK  408 (644)
T ss_pred             EEEEECCHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             8985332788899999999999999999861


No 129
>cd01889 SelB_euk SelB subfamily.  SelB is an elongation factor needed for the co-translational incorporation of selenocysteine.  Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin.  In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu).  It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner.  This allows insertion of selenocysteine at in-frame UGA stop codons.  In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence).  The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation.  Archaeal and animal mechanisms of selenocysteine incorporation are more complex.  Although the SECIS elements have different secondary structures and conserved elements between archaea and euk
Probab=59.49  E-value=12  Score=16.72  Aligned_cols=70  Identities=19%  Similarity=0.182  Sum_probs=39.0

Q ss_pred             EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHH----HH-CCC
Q ss_conf             0699982375544455511479999999999999987310368638960334798888999999999973----12-787
Q gi|254780751|r  378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESL----KK-DRA  452 (723)
Q Consensus       378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l----~~-D~~  452 (723)
                      |+.+||.+.|-.      .+|         +|..+.+++.++-.||+|-=||+-+....+..++.+++.+    .. ...
T Consensus        95 ailvVda~~G~~------~QT---------~eh~~~~~~~~~~~iv~iNK~D~v~~~~~~~~~~~i~~~l~~~l~~~~~~  159 (192)
T cd01889          95 MLLVVDATKGIQ------TQT---------AECLVIGEILCKKLIVVLNKIDLIPEEERERKIEKMKKKLQKTLEKTRFK  159 (192)
T ss_pred             CEEEEECCCCCC------HHH---------HHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             279998788887------899---------99999999858997999974127881577999999999999998653899


Q ss_pred             CEEEEEECCC
Q ss_conf             2899860486
Q gi|254780751|r  453 RVQVGAISNF  462 (723)
Q Consensus       453 ~~~v~~it~l  462 (723)
                      ...+.++|.+
T Consensus       160 ~~~iipiSA~  169 (192)
T cd01889         160 NSPIIPVSAK  169 (192)
T ss_pred             CCEEEEEECC
T ss_conf             9849995789


No 130
>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=58.95  E-value=12  Score=16.66  Aligned_cols=41  Identities=17%  Similarity=0.385  Sum_probs=35.3

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC
Q ss_conf             4287879899783638823135327897713022213712102
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ   80 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~   80 (723)
                      ..|-+-+|.|+.|-+  ...+|-+..+-.||.++.+|...|-+
T Consensus         2 ~~G~lvLG~V~~I~~--~~l~isLP~~L~G~V~it~ISd~~t~   42 (100)
T cd05693           2 SEGMLVLGQVKEITK--LDLVISLPNGLTGYVPITNISDAYTE   42 (100)
T ss_pred             CCCCEEEEEEEEECC--CCEEEECCCCCEEEEEHHHHHHHHHH
T ss_conf             889899999989846--63899858985899887885299999


No 131
>KOG2228 consensus
Probab=58.95  E-value=12  Score=16.66  Aligned_cols=83  Identities=23%  Similarity=0.220  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCC-CEEEEECCCCCCCHHH
Q ss_conf             999999999999987310368638960334798888999999999973127872899860486-1489851566630112
Q gi|254780751|r  400 LQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNF-GLLEMSRQRIRSSVLE  478 (723)
Q Consensus       400 l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~l-GLlEltRkR~r~sl~e  478 (723)
                      +.|.--|.++|+|||-+++-.+  ++-|  |.-.++-.+++..|+..-..-..+ .|.=+-.| +.+.++||-+=-.|.+
T Consensus        89 ~~~dk~al~~I~rql~~e~~~~--~k~~--gsfte~l~~lL~~L~~~~~~t~~~-ViFIldEfDlf~~h~rQtllYnlfD  163 (408)
T KOG2228          89 LQTDKIALKGITRQLALELNRI--VKSF--GSFTENLSKLLEALKKGDETTSGK-VIFILDEFDLFAPHSRQTLLYNLFD  163 (408)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHH--HEEE--CCCCHHHHHHHHHHHCCCCCCCCE-EEEEEEHHHCCCCCHHHHHHHHHHH
T ss_conf             0155899999999999997532--1242--253346999999873378778851-9998310002464035678999988


Q ss_pred             HHC-CCCCCC
Q ss_conf             100-236754
Q gi|254780751|r  479 STT-KVCTYC  487 (723)
Q Consensus       479 ~~~-~~c~~c  487 (723)
                      ... -..|+|
T Consensus       164 isqs~r~Pic  173 (408)
T KOG2228         164 ISQSARAPIC  173 (408)
T ss_pred             HHHHCCCCEE
T ss_conf             8762479869


No 132
>pfam02108 FliH Flagellar assembly protein FliH.
Probab=58.17  E-value=12  Score=16.57  Aligned_cols=59  Identities=17%  Similarity=0.099  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHC--CCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEEE
Q ss_conf             88788999730--364310135769999987302379999999984887999847877886338971
Q gi|254780751|r  503 ILRSVEEYLLQ--YTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEK  567 (723)
Q Consensus       503 ~~r~i~~~~~~--~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ier  567 (723)
                      ++..+++....  .....+.+++||+-..++.....+.    ..  ...+.|.+|+++..-.+.|+-
T Consensus        52 i~~~v~~al~~l~~~~~~v~I~v~P~D~~~l~~~~~~~----~~--~~~~~l~~D~~l~~Ggc~iet  112 (128)
T pfam02108        52 ILALVREALAALPVLSGKVTLRLNPDDLALVEEHLGDE----LK--ARGWRLVADPSLSRGGCRIES  112 (128)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEECHHHHHHHHHHHHHH----HC--CCCEEEEECCCCCCCCEEEEE
T ss_conf             99999999997134478749998899999999988642----22--277489868987899889997


No 133
>COG1317 FliH Flagellar biosynthesis/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=57.40  E-value=13  Score=16.49  Aligned_cols=48  Identities=19%  Similarity=0.143  Sum_probs=38.8

Q ss_pred             CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEEE
Q ss_conf             4310135769999987302379999999984887999847877886338971
Q gi|254780751|r  516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEK  567 (723)
Q Consensus       516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ier  567 (723)
                      ...+.++|||+-..++...+-.++......    +.|.+|+++..-.+.|+-
T Consensus       157 ~~~i~l~VnP~d~e~i~~~~~~~~~~~~~~----l~l~~D~~l~~GgC~IeT  204 (234)
T COG1317         157 AAAITLRVNPDDLEIIRQQLDEELSLLGWR----LELVADPALSPGGCIIET  204 (234)
T ss_pred             CCCEEEEECHHHHHHHHHHHHHHHHHCCCE----EEECCCCCCCCCCEEEEE
T ss_conf             667389988888999999988887424520----243258887899649983


No 134
>cd00881 GTP_translation_factor GTP translation factor family.  This family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation.  In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function.
Probab=56.93  E-value=13  Score=16.44  Aligned_cols=59  Identities=24%  Similarity=0.275  Sum_probs=46.9

Q ss_pred             CEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             80699982375544455511479999999999999987310368638960334798888999999999973127
Q gi|254780751|r  377 EALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKD  450 (723)
Q Consensus       377 EALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D  450 (723)
                      =|+.+||.+.|-.               .-..|+.+.++..++.-+|+|-=||+..+++..++++.+++.|...
T Consensus        88 ~ailvVda~~G~~---------------~qt~~~~~~~~~~~~p~iv~iNKiD~~~~~~~~~~~~ei~~~l~~~  146 (189)
T cd00881          88 GAILVVDANEGVQ---------------PQTREHLRIAREGGLPIIVAINKIDRVGEEDLEEVLREIKELLGLI  146 (189)
T ss_pred             EEEEEEECCCCCC---------------HHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             5699998798998---------------7899999999976998799998971877562999999999998753


No 135
>PRK11032 hypothetical protein; Provisional
Probab=56.87  E-value=6.4  Score=18.55  Aligned_cols=53  Identities=13%  Similarity=0.275  Sum_probs=36.2

Q ss_pred             HHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHH-HCCCCCCCCCEEEEECC
Q ss_conf             9997312787289986048614898515666301121-00236754653786061
Q gi|254780751|r  443 LKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLES-TTKVCTYCKGAGYIRSQ  496 (723)
Q Consensus       443 l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~-~~~~c~~c~g~g~~~~~  496 (723)
                      |.+-|+.. ..-+.+.|+.+|-|-=..=--...+... ...+||.|+|+.+.|-+
T Consensus       104 l~~dl~h~-g~Y~sGEivg~G~LvC~~Cg~~~~~~~~~~ippCp~Cg~~~F~R~p  157 (160)
T PRK11032        104 VFQDLNHH-GVYHSGEVVGLGNLVCEKCHHHLAFYTPEVLPLCPKCGHDQFQRRP  157 (160)
T ss_pred             HHHHHCCC-CEEECCEEEECCEEEHHHCCCEEEEECCCCCCCCCCCCCCEEEECC
T ss_conf             99984357-7243560532556657428987787468779888779997674089


No 136
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU; InterPro: IPR014088   Members of this protein family include S-adenosylmethionine-dependent C-20 methyltransferase (BchU), part of the pathway of bacteriochlorophyll c production in photosynthetic green sulphur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produce bacteriochlorophyll d..
Probab=56.39  E-value=9.2  Score=17.46  Aligned_cols=33  Identities=24%  Similarity=0.277  Sum_probs=27.9

Q ss_pred             CCHHHHH--HHHHHHHHHHHCCCCC--CCCCCEEEEE
Q ss_conf             4203567--7699999998422214--3678649983
Q gi|254780751|r  342 PHPIFFR--SGIEVQLDSLHQTEVT--LPSRGYVIIN  374 (723)
Q Consensus       342 ~~~lf~~--y~ie~~i~~~~~~~V~--L~sGG~lvIe  374 (723)
                      +.-||.+  |..++|+..++-+|-+  |+|||-|.|=
T Consensus       217 DAVLF~RILY~~N~Ql~T~l~~KAyDAl~SGGR~LIL  253 (306)
T TIGR02716       217 DAVLFSRILYSANEQLSTILLKKAYDALRSGGRLLIL  253 (306)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEE
T ss_conf             1656778876446789999999887522578807865


No 137
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=55.99  E-value=11  Score=16.92  Aligned_cols=34  Identities=26%  Similarity=0.650  Sum_probs=24.3

Q ss_pred             CCCEEEEEEEEECCC--CCEEEEEECCCCCCCCCHHHC
Q ss_conf             287879899783638--823135327897713022213
Q gi|254780751|r   39 KGNIYLAKVTRVEPS--LQAAFVDYGGNRHGFLPFLEI   74 (723)
Q Consensus        39 ~GnIY~G~V~~V~p~--lqAAFVdiG~~k~gFL~~~ei   74 (723)
                      =|.-|.|+|+.+.+.  ..--|||||...  .++.++|
T Consensus        15 D~~wYRa~I~~~~~~~~~~V~fvDyGn~e--~V~~~~l   50 (57)
T smart00333       15 DGEWYRARIIKVDGEQLYEVFFIDYGNEE--VVPPSDL   50 (57)
T ss_pred             CCCEEEEEEEEECCCCEEEEEEECCCCEE--EECHHHH
T ss_conf             89899999999999997999997689849--9859990


No 138
>PRK08903 hypothetical protein; Validated
Probab=55.77  E-value=13  Score=16.31  Aligned_cols=109  Identities=12%  Similarity=0.039  Sum_probs=59.8

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCCCCEEEEECCHHH
Q ss_conf             86389603347988889999999999731278728998604861489851566630112100236754653786061146
Q gi|254780751|r  420 AGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSV  499 (723)
Q Consensus       420 gGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c~g~g~~~~~~~~  499 (723)
                      ..+|+||-|+--....+..+...+..+....+...-+..-..--.+.+. .+++.-|.-.+            +......
T Consensus        91 ~d~l~iDDi~~i~~~~q~~lF~l~N~~~~~~~~~ll~s~~~~p~~l~~~-~DL~SRl~~gl------------~~~i~~p  157 (227)
T PRK08903         91 AELYAVDDVERLDDAQQIALFNLFNRVRAHGKTALLVAGPAAPLALDVR-EDLRTRLGWGL------------VYEVKPL  157 (227)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHCCCC-HHHHHHHHCCC------------EEEEECC
T ss_conf             8989996411489569999999999999729948997189971201200-89999993897------------3899797


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             8998878899973036431013576999998730237999999998
Q gi|254780751|r  500 ALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEAR  545 (723)
Q Consensus       500 ~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~  545 (723)
                      -.+..+.|-......    -.+.++.+|+.||+..-...+..|+.-
T Consensus       158 dde~~~~iL~~~a~~----rgl~l~~~v~~yl~~r~~R~~~~L~~~  199 (227)
T PRK08903        158 SDEDKIAALKAAAAE----RGLQLADEVPDYLLTHFRRDMPSLMAL  199 (227)
T ss_pred             CHHHHHHHHHHHHHH----CCCCCCHHHHHHHHHHHCCCHHHHHHH
T ss_conf             999999999999996----299998899999999834789999999


No 139
>PRK02747 consensus
Probab=55.66  E-value=13  Score=16.30  Aligned_cols=19  Identities=11%  Similarity=0.179  Sum_probs=8.9

Q ss_pred             HHHHHHHHHHCCCCEEEEE
Q ss_conf             9999987310368638960
Q gi|254780751|r  408 EEIARQLRLRDLAGLIVVD  426 (723)
Q Consensus       408 ~EIaRQlRLRnlgGiIvID  426 (723)
                      .+.+.++-=.++|.|++-|
T Consensus       159 ~~~~~~~~~~G~geil~td  177 (257)
T PRK02747        159 VEFAQKVVSLGAGEILLTS  177 (257)
T ss_pred             HHHHHHHHHCCCCEEEEEE
T ss_conf             9999999970998899998


No 140
>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=55.31  E-value=13  Score=16.31  Aligned_cols=38  Identities=21%  Similarity=0.419  Sum_probs=33.2

Q ss_pred             CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf             28787989978363882313532789771302221371210
Q gi|254780751|r   39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY   79 (723)
Q Consensus        39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~   79 (723)
                      -|.|..|-|++|-|  +.+||.+|..-.|...++.+. +||
T Consensus         3 eGq~vRGyVk~v~~--~GvFv~Ls~~v~grv~~~nls-~~~   40 (74)
T cd05705           3 EGQLLRGYVSSVTK--QGVFFRLSSSIVGRVLFQNVT-KYF   40 (74)
T ss_pred             CCCEEEEEEEECCC--CCEEEEECCCEEEEEEEECCC-HHH
T ss_conf             88798999998268--739999568748999970036-212


No 141
>TIGR00393 kpsF sugar isomerase, KpsF/GutQ family; InterPro: IPR004800 This is a family of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. The group includes GutQ, a protein of the glucitol operon and KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of Escherichia coli.; GO: 0016853 isomerase activity, 0005975 carbohydrate metabolic process.
Probab=53.39  E-value=14  Score=16.12  Aligned_cols=41  Identities=34%  Similarity=0.507  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEECCC--CEEEEECCCCCCCHH
Q ss_conf             99999999973127872899860486--148985156663011
Q gi|254780751|r  437 RSVEKKLKESLKKDRARVQVGAISNF--GLLEMSRQRIRSSVL  477 (723)
Q Consensus       437 ~~v~~~l~~~l~~D~~~~~v~~it~l--GLlEltRkR~r~sl~  477 (723)
                      ++++-+.++.++.+..=.+|.+=|.|  -|+||||+|++-.+.
T Consensus       151 ~kLL~kV~dlm~t~d~lP~v~~tas~~DAL~e~~~~~LG~~~v  193 (272)
T TIGR00393       151 RKLLVKVKDLMQTDDELPLVAPTASFKDALLEMSRKRLGLAVV  193 (272)
T ss_pred             HHHHHHHHHHHCCCCCCCCEECCCCCEEEEEEEECCCCCEEEE
T ss_conf             7888876776406656782223677202102331378617999


No 142
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=53.35  E-value=13  Score=16.43  Aligned_cols=34  Identities=32%  Similarity=0.651  Sum_probs=24.7

Q ss_pred             CCCEEEEEEEEEC--CCCCEEEEEECCCCCCCCCHHHC
Q ss_conf             2878798997836--38823135327897713022213
Q gi|254780751|r   39 KGNIYLAKVTRVE--PSLQAAFVDYGGNRHGFLPFLEI   74 (723)
Q Consensus        39 ~GnIY~G~V~~V~--p~lqAAFVdiG~~k~gFL~~~ei   74 (723)
                      -|.-|.|+|..+.  ....--|||||....  +++++|
T Consensus        11 d~~wyRa~I~~i~~~~~~~V~f~DyG~~~~--v~~~~l   46 (48)
T cd04508          11 DGKWYRAKITSILSDGKVEVFFVDYGNTEV--VPLSDL   46 (48)
T ss_pred             CCCEEEEEEEEECCCCEEEEEEECCCCEEE--EEHHHC
T ss_conf             997999999998899969999988996699--889997


No 143
>PRK03459 rnpA ribonuclease P; Reviewed
Probab=52.66  E-value=15  Score=15.98  Aligned_cols=60  Identities=20%  Similarity=0.283  Sum_probs=40.7

Q ss_pred             CCCEEEECCCCHHHHHHH----HHHHHHH--HCCCCCEE--EEEEECCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             751242046886899999----9999863--00258716--998504557579999999999999998
Q gi|254780751|r  215 KGETISRKITNPVDRKNL----KEIARGL--EVPAGMGV--ILRTAGASRTKIEIKRDFEYLMRLWDN  274 (723)
Q Consensus       215 ~~~~iSrki~~~~~r~~l----~~~~~~~--~~~~~~G~--IiRT~a~~~~~~~l~~d~~~L~~~w~~  274 (723)
                      -|..+||++-+.-.|.+.    +.++...  ..|.|.-+  +.+..|+.++..+|..|++.++.....
T Consensus        57 vG~vVSK~VGnAVvRnrVkRrLR~~~~~~~~~lp~g~~vVVrA~p~aa~as~~eL~~~l~~~L~r~~~  124 (129)
T PRK03459         57 FGLVVSKAVGNAVVRHRVSRRLRHICASIVDKSPETHHVVIRALPGAATASSAELERDIRAGLGKLSR  124 (129)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             79997032211567889999999999987741899965999948870307999999999999999864


No 144
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'; InterPro: IPR012758   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.    This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0008270 zinc ion binding, 0006350 transcription.
Probab=51.68  E-value=16  Score=15.87  Aligned_cols=231  Identities=17%  Similarity=0.233  Sum_probs=116.3

Q ss_pred             CCCEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC-
Q ss_conf             4421331068885799984033323456410123345765234422788751242046886899999999986300258-
Q gi|254780751|r  166 RQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAG-  244 (723)
Q Consensus       166 ~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~-  244 (723)
                      --|-++..|..||.||-        |--|-| -.+|+.|.-+..||+...=.+.-                  ...|.+ 
T Consensus       425 pGw~VERHL~dGDiVLF--------NRQPSL-HRmSmMgH~VkVLPgkTFRLNLa------------------VCPPYNA  477 (901)
T TIGR02390       425 PGWVVERHLIDGDIVLF--------NRQPSL-HRMSMMGHKVKVLPGKTFRLNLA------------------VCPPYNA  477 (901)
T ss_pred             CCCEEEEEECCCCEEEE--------CCCCCH-HHHHHCCCEEEECCCCCCCCCCC------------------CCCCCCC
T ss_conf             99789987126888766--------588642-02101144546788885213667------------------7728887


Q ss_pred             ------CEE-EEEEECCCCCHHHHHHHHHHHHHHHHHHHHH-----------------HCCC-CCCCCCCCCCCHHHHHH
Q ss_conf             ------716-9985045575799999999999999987764-----------------2014-32212345645888888
Q gi|254780751|r  245 ------MGV-ILRTAGASRTKIEIKRDFEYLMRLWDNVREL-----------------ALNS-VAPHLVYEEGNLIKRAI  299 (723)
Q Consensus       245 ------~G~-IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~-----------------~~~~-~~p~li~~~~~~~~~~i  299 (723)
                            |-+ +++       .||=.+|...|+..-+.|..-                 +.-+ +...+-.++.-.++...
T Consensus       478 DFDGDEMNlHV~Q-------~EEarAEA~~lM~V~~hI~tPRyGGPIIGg~~D~IsGaYLLT~k~~~~t~~ev~~iL~~~  550 (901)
T TIGR02390       478 DFDGDEMNLHVPQ-------TEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTVKSTLFTKEEVVTILKKA  550 (901)
T ss_pred             CCCCCCCCCCCCC-------CHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHC
T ss_conf             8887603764025-------733589999985411101468876401102567888888865047776889999999860


Q ss_pred             HHHCCCCCCEE-ECCCCCH----HHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHH---HHCCCCCCCCCCEE
Q ss_conf             75237663111-1035320----3667888987631012112201344203567769999999---84222143678649
Q gi|254780751|r  300 RDLYCKDISEI-IVSGEKG----YREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDS---LHQTEVTLPSRGYV  371 (723)
Q Consensus       300 rd~~~~~~~~i-~vd~~~~----~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~---~~~~~V~L~sGG~l  371 (723)
                        -+..+..+- .|+...-    |-.=++.+..+.|+..+              +..-.++.+   .....-.=|+-.|+
T Consensus       551 --~~~~~~~~~~~ie~~~~eGrdywTGK~ifS~~LP~dLn--------------~~~~a~~~~G~c~~C~~e~Cp~D~Yv  614 (901)
T TIGR02390       551 --GLKGEPEEPKAIEKPKEEGRDYWTGKQIFSAFLPEDLN--------------FEFRAKVCSGKCEACKKEECPHDAYV  614 (901)
T ss_pred             --CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCC--------------EEEECCCCCCCCCCCCCCCCCCCCEE
T ss_conf             --76778766663317786675322103555420788777--------------21401367885001003679986578


Q ss_pred             EEECCCEEE-EEEECCCCCCCC-CCCHHHHHHHHHHHH--------HHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             983288069-998237554445-551147999999999--------9999987310368638960334798888999999
Q gi|254780751|r  372 IINQTEALV-SIDVNSGRSTRE-HCIEDTALQTNLEAA--------EEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEK  441 (723)
Q Consensus       372 vIe~TEALt-~IDVNSG~~~~~-~~~e~t~l~tNleAA--------~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~  441 (723)
                      ||.-=.=|- |||=++=..-.+ +=+..-+.+-=-|+|        +=-.|-|-||.++  +=||=||. .++..+++.+
T Consensus       615 VI~NG~Ll~GViDk~a~G~e~g~~il~~i~~~yG~e~ar~~lD~~trL~i~~i~~~GfT--~g~~D~dI-P~eA~~~I~~  691 (901)
T TIGR02390       615 VIKNGKLLKGVIDKKAIGAEKGDKILDRIVREYGPEAARRFLDSVTRLAIRFIELRGFT--TGIDDIDI-PKEAKEEIEE  691 (901)
T ss_pred             EEECCEEEEEECCHHHCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCC--CCCCCCCC-CHHHHHHHHH
T ss_conf             98668043203020112746637899999876074689999999999999987551660--13360104-6789999999


Q ss_pred             HHHHHHHH
Q ss_conf             99997312
Q gi|254780751|r  442 KLKESLKK  449 (723)
Q Consensus       442 ~l~~~l~~  449 (723)
                      .++.|.++
T Consensus       692 ~i~~A~~~  699 (901)
T TIGR02390       692 LIEKAEKR  699 (901)
T ss_pred             HHHHHHHH
T ss_conf             99999999


No 145
>KOG0546 consensus
Probab=51.26  E-value=7.9  Score=17.92  Aligned_cols=37  Identities=16%  Similarity=0.043  Sum_probs=21.1

Q ss_pred             HHHCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCC
Q ss_conf             2100236754653786061146899887889997303
Q gi|254780751|r  478 ESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQY  514 (723)
Q Consensus       478 e~~~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~  514 (723)
                      -+++.+||||+|.-.|...-.-...+.|.|+......
T Consensus       126 FITT~p~PHLdGkHVVFGqVI~G~~VVr~IEn~~~d~  162 (372)
T KOG0546         126 FITTVPTPHLDGKHVVFGQVIKGKEVVREIENLETDE  162 (372)
T ss_pred             EEECCCCCCCCCCEEEEEEEEECHHHHHHHHCCCCCC
T ss_conf             8967777776882468866764535899975455566


No 146
>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=50.29  E-value=16  Score=15.73  Aligned_cols=161  Identities=25%  Similarity=0.287  Sum_probs=92.9

Q ss_pred             CCCCCCEEEEEEEE--ECCCCC--EEEEEE-CCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             60428787989978--363882--313532-7897713022213712102898899999998886311111000000011
Q gi|254780751|r   36 KQIKGNIYLAKVTR--VEPSLQ--AAFVDY-GGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHG  110 (723)
Q Consensus        36 ~~~~GnIY~G~V~~--V~p~lq--AAFVdi-G~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~  110 (723)
                      +..+|.|--|+|.|  +..+=+  ..|||+ |.. .||||=+|.-|.                                 
T Consensus       142 ~~~~g~~i~g~V~r~d~~~~~~~~g~~v~l~g~~-e~~lp~~e~iP~---------------------------------  187 (366)
T TIGR01953       142 KSKVGEIISGTVKRVDVNKEGNETGLIVELAGKT-EAILPKKEQIPG---------------------------------  187 (366)
T ss_pred             HHHHCEEEEEEEEEEEECCCCCCCEEEEEECCCE-EEECCHHHCCCC---------------------------------
T ss_conf             3331808999999975257875210799985750-252135337888---------------------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCE---EEEEEECC
Q ss_conf             122334443344542222334455433222234321122111211000012234444213310688857---99984033
Q gi|254780751|r  111 DVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQI---LLVQIVKE  187 (723)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~---ilVQV~ke  187 (723)
                                                                                   +-++.|+.   ++..|.+.
T Consensus       188 -------------------------------------------------------------E~~~~Gd~i~~~~~eV~~~  206 (366)
T TIGR01953       188 -------------------------------------------------------------EKFRIGDRIKAYVYEVRKT  206 (366)
T ss_pred             -------------------------------------------------------------CCCCCCCEEEEEEEEEEEC
T ss_conf             -------------------------------------------------------------7523588899999999986


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCC--CC----EEEEEEECCCCCHHHH
Q ss_conf             32345641012334576523442278875124204688689999999998630025--87----1699850455757999
Q gi|254780751|r  188 ERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPA--GM----GVILRTAGASRTKIEI  261 (723)
Q Consensus       188 ~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~--~~----G~IiRT~a~~~~~~~l  261 (723)
                      +.|. -                    + -+-+||.  +.   ..++.++. +.+|+  +.    --|.|-+|.-+--..-
T Consensus       207 ~~g~-~--------------------~-~i~lSRt--~p---~fl~~Ll~-~EvPEI~dG~veIk~iAR~pG~R~KiAV~  258 (366)
T TIGR01953       207 AKGG-L--------------------P-QIILSRT--HP---EFLKELLK-LEVPEIADGIVEIKKIAREPGSRTKIAVE  258 (366)
T ss_pred             CCCC-E--------------------E-EEEEECC--CH---HHHHHHHH-CCCCEEECCEEEEEEEECCCCCCCEEEEE
T ss_conf             8896-6--------------------8-9999708--97---99999986-16965417819999998178876135788


Q ss_pred             H-HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHH-HHHHCCCCHHHH
Q ss_conf             9-9999999999987764201432212345645888888752376631111035320366788898-763101211220
Q gi|254780751|r  262 K-RDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMK-LLMPSYARIVRQ  338 (723)
Q Consensus       262 ~-~d~~~L~~~w~~i~~~~~~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~~-~~~p~~~~~v~~  338 (723)
                      . .|              ..--+-.+|+-.-..-+.-+++.|-+..++-|..+.+.     ..|+. .+.|.....|..
T Consensus       259 SH~d--------------~~iDPvGAcvG~~G~Ri~~i~~EL~gEkIDii~y~~d~-----~~Fi~nAL~PA~V~~v~i  318 (366)
T TIGR01953       259 SHND--------------ENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDP-----AEFIANALSPAEVISVEI  318 (366)
T ss_pred             EECC--------------CCCCEEEEEECCCCCCHHHHHHHHCCCEEEEEECCCCH-----HHHHHHHCCCCEECEEEE
T ss_conf             5078--------------99870465888988654333887478717898368887-----999997418631211489


No 147
>TIGR00137 gid gid protein; InterPro: IPR004417 The gid proteins are present in relatively few bacteria but very tightly conserved where they occur. The function of these proteins is unknown. They are closely related to gidA (glucose-inhibited division protein A), which appears to be present in all complete eubacterial genomes so far and in Saccharomyces cerevisiae..
Probab=49.92  E-value=11  Score=16.81  Aligned_cols=37  Identities=30%  Similarity=0.420  Sum_probs=29.7

Q ss_pred             EEEEEEECCCC-CEEEEEEC-CCCCCCCCHHHCCCCCCC
Q ss_conf             98997836388-23135327-897713022213712102
Q gi|254780751|r   44 LAKVTRVEPSL-QAAFVDYG-GNRHGFLPFLEIHPDYYQ   80 (723)
Q Consensus        44 ~G~V~~V~p~l-qAAFVdiG-~~k~gFL~~~ei~~~y~~   80 (723)
                      -++|-|..|+| ||-||=+| ..||-|..-..+--.||+
T Consensus       298 QkrVfrLIPgLeNaefVR~GvMHRNTFInSp~lL~~~l~  336 (444)
T TIGR00137       298 QKRVFRLIPGLENAEFVRLGVMHRNTFINSPKLLTASLQ  336 (444)
T ss_pred             CCEEEECCCCCCCEEEEEECCCCCCCCCCCHHHHHHHHC
T ss_conf             551444057843147885074311111276356557530


No 148
>PRK00694 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated
Probab=49.59  E-value=7.2  Score=18.20  Aligned_cols=61  Identities=20%  Similarity=0.351  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCC
Q ss_conf             99999999998731036863896033479888899999999997312787289986048614898515666301121002
Q gi|254780751|r  403 NLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTK  482 (723)
Q Consensus       403 NleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~  482 (723)
                      -+.||..+ =-|-+=+||-.|.|++-++.....+.                      +.||+||=+|-|+    ..+=+-
T Consensus       459 ~i~aa~d~-GsLL~DGlGDGI~i~~~~~~~~~~~~----------------------laF~ILQAaR~R~----sKTEYI  511 (606)
T PRK00694        459 AISIATEF-GALLLDGLGEAVLLDLPNIPLSDVRT----------------------IAFGTLQSAGVRL----VKTEYI  511 (606)
T ss_pred             HHHHHHHH-HHHHHCCCCCEEEEECCCCCHHHHHH----------------------HHHHHHHHHCCCC----CCCCEE
T ss_conf             99999874-05664577655898479886778888----------------------8888888757443----356166


Q ss_pred             CCCCCCCE
Q ss_conf             36754653
Q gi|254780751|r  483 VCTYCKGA  490 (723)
Q Consensus       483 ~c~~c~g~  490 (723)
                      +||-|+=|
T Consensus       512 SCPSCGRT  519 (606)
T PRK00694        512 SCPGCGRT  519 (606)
T ss_pred             ECCCCCCC
T ss_conf             58987752


No 149
>PRK06328 type III secretion system protein; Validated
Probab=48.67  E-value=17  Score=15.56  Aligned_cols=50  Identities=12%  Similarity=0.119  Sum_probs=37.5

Q ss_pred             CCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEE
Q ss_conf             6431013576999998730237999999998488799984787788633897
Q gi|254780751|r  515 TAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIE  566 (723)
Q Consensus       515 ~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ie  566 (723)
                      ..+.++++|||+-..++...+......+  .....+.|.+|+.+..-.+.|+
T Consensus       130 ~~~~V~IrV~P~d~~~V~~~~~~L~~~~--~~~~~L~i~~D~~l~~GgCiIE  179 (223)
T PRK06328        130 QNKHIIIHVNPKDLAIVEQNRPELKKIV--EYADSLILSPKADVTPGGCIIE  179 (223)
T ss_pred             HCCEEEEEECHHHHHHHHHHHHHHHHHC--CCCCCEEEEECCCCCCCCEEEE
T ss_conf             1881799988876999999899999746--7777626730898799986995


No 150
>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=46.46  E-value=17  Score=15.54  Aligned_cols=35  Identities=17%  Similarity=0.218  Sum_probs=31.0

Q ss_pred             CCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEE
Q ss_conf             01357699999873023799999999848879998
Q gi|254780751|r  519 IIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVV  553 (723)
Q Consensus       519 i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~  553 (723)
                      ..+.+|+....||.+.+-..|.+|++.+++.|.|-
T Consensus         2 ~~i~vp~~~h~~iIG~~G~~i~~i~~~~~~~I~~P   36 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFP   36 (62)
T ss_pred             CEEEECHHHCCCEECCCCCCHHHHHHHHCCEEEEC
T ss_conf             48998978819758899973999999859799958


No 151
>cd04731 HisF The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.
Probab=46.41  E-value=19  Score=15.33  Aligned_cols=22  Identities=18%  Similarity=0.342  Sum_probs=10.1

Q ss_pred             HHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             9999999863002587169985
Q gi|254780751|r  230 KNLKEIARGLEVPAGMGVILRT  251 (723)
Q Consensus       230 ~~l~~~~~~~~~~~~~G~IiRT  251 (723)
                      ..++++...+.+|-.+|==|||
T Consensus        61 ~~i~~i~~~~~~pi~vGGGIrs   82 (243)
T cd04731          61 DVVERVAEEVFIPLTVGGGIRS   82 (243)
T ss_pred             HHHHHHHHHCCCCEEEEEEEEE
T ss_conf             9999999867986899850664


No 152
>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=46.18  E-value=19  Score=15.30  Aligned_cols=35  Identities=20%  Similarity=0.338  Sum_probs=30.6

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCC
Q ss_conf             8787989978363882313532789771302221371
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHP   76 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~   76 (723)
                      |..+.|-|.++  +-...||.+..+-.|.+++.|+.-
T Consensus         1 G~~v~gfV~n~--~~~~~wv~iSp~V~gri~~l~lSd   35 (73)
T cd05703           1 GQEVTGFVNNV--SKEFVWLTISPDVKGRIPLLDLSD   35 (73)
T ss_pred             CCEEEEEEEEC--CCCEEEEEECCCEEEEEEHHHHCC
T ss_conf             98799999972--598499998888189997054268


No 153
>COG1278 CspC Cold shock proteins [Transcription]
Probab=46.14  E-value=19  Score=15.30  Aligned_cols=34  Identities=12%  Similarity=0.161  Sum_probs=27.2

Q ss_pred             EEEEEEECCCCCEEEEEECCC-CCCCCCHHHCCCC
Q ss_conf             989978363882313532789-7713022213712
Q gi|254780751|r   44 LAKVTRVEPSLQAAFVDYGGN-RHGFLPFLEIHPD   77 (723)
Q Consensus        44 ~G~V~~V~p~lqAAFVdiG~~-k~gFL~~~ei~~~   77 (723)
                      -|.|+-.-+.....||-=..+ +.-|.|++.|...
T Consensus         3 ~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~   37 (67)
T COG1278           3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRA   37 (67)
T ss_pred             CCEEEEEECCCCCEEECCCCCCCCEEEEEEEECCC
T ss_conf             61688850898633707899985779980125127


No 154
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=45.26  E-value=10  Score=17.05  Aligned_cols=49  Identities=16%  Similarity=0.152  Sum_probs=28.3

Q ss_pred             CCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf             2278875124204688689999999998630025871699850455757999999999999999
Q gi|254780751|r  210 MPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWD  273 (723)
Q Consensus       210 ~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~  273 (723)
                      +|+.+.+++-||+...-.+.+... +|         |     ...+|+.++|++-+..|...|.
T Consensus         7 ~~~~~~~~~~~~~~~~v~~t~yY~-iL---------G-----V~~~As~~EIKKAYRKLA~KyH   55 (422)
T PTZ00037          7 FPFDGMPGGHARRKREVDNEKLYE-VL---------N-----LSKDCTESEIKKAYRKLAIKHH   55 (422)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCHH-HH---------C-----CCCCCCHHHHHHHHHHHHHHHC
T ss_conf             887778776777888787676568-65---------9-----8999899999999999999849


No 155
>cd01890 LepA LepA subfamily.  LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome.  LepA is ubiquitous in bacteria and eukaryota (e.g. yeast GUF1p), but is missing from archaea.  This pattern of phyletic distribution suggests that LepA evolved through a duplication of the EF-G gene in bacteria, followed by early transfer into the eukaryotic lineage, most likely from the promitochondrial endosymbiont.  Yeast GUF1p is not essential and mutant cells did not reveal any marked phenotype.
Probab=45.17  E-value=19  Score=15.20  Aligned_cols=66  Identities=18%  Similarity=0.214  Sum_probs=44.7

Q ss_pred             EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             06999823755444555114799999999999999873103686389603347988889999999999731278728998
Q gi|254780751|r  378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVG  457 (723)
Q Consensus       378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~  457 (723)
                      |+.+||.++|=.      .+         .++..++.+.+++.-|++|-=||.. ..+..++.+.|++.+.-|...  +.
T Consensus        94 allVVda~~Gv~------~q---------T~~~~~~a~~~~~p~ivviNKiD~~-~ad~~~v~~~i~~~~g~~~~~--~v  155 (179)
T cd01890          94 ALLLVDATQGVE------AQ---------TLANFYLALENNLEIIPVINKIDLP-SADPERVKQQIEDVLGLDPSE--AI  155 (179)
T ss_pred             EEEEEECCCCCC------HH---------HHHHHHHHHHCCCCEEEEEECCCCC-CCCHHHHHHHHHHHHCCCCCC--EE
T ss_conf             789986477873------74---------8999999987699889998655567-789999999999986889767--48


Q ss_pred             EECC
Q ss_conf             6048
Q gi|254780751|r  458 AISN  461 (723)
Q Consensus       458 ~it~  461 (723)
                      ++|.
T Consensus       156 ~vSA  159 (179)
T cd01890         156 LVSA  159 (179)
T ss_pred             EEEC
T ss_conf             8437


No 156
>KOG2002 consensus
Probab=43.84  E-value=20  Score=15.06  Aligned_cols=15  Identities=27%  Similarity=0.426  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999873
Q gi|254780751|r  401 QTNLEAAEEIARQLR  415 (723)
Q Consensus       401 ~tNleAA~EIaRQlR  415 (723)
                      +-|+..|..|.+|+|
T Consensus       659 kg~~~~A~dIFsqVr  673 (1018)
T KOG2002         659 KGRFSEARDIFSQVR  673 (1018)
T ss_pred             CCCCHHHHHHHHHHH
T ss_conf             368138999999999


No 157
>PHA02114 hypothetical protein
Probab=43.70  E-value=20  Score=15.05  Aligned_cols=23  Identities=52%  Similarity=0.651  Sum_probs=19.9

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             71699850455757999999999
Q gi|254780751|r  245 MGVILRTAGASRTKIEIKRDFEY  267 (723)
Q Consensus       245 ~G~IiRT~a~~~~~~~l~~d~~~  267 (723)
                      |-+|+||+++|.+.+.|+..+..
T Consensus         1 mklilrta~~gkt~eaiksa~~a   23 (127)
T PHA02114          1 MKLILRTANAGKTQEAIKSAFEA   23 (127)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
T ss_conf             92576506786408999999987


No 158
>KOG0712 consensus
Probab=43.40  E-value=9.3  Score=17.43  Aligned_cols=33  Identities=21%  Similarity=0.483  Sum_probs=22.0

Q ss_pred             EEEECCCCCCCHHHHHCCCCCCCCCEEEEECCH
Q ss_conf             898515666301121002367546537860611
Q gi|254780751|r  465 LEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQS  497 (723)
Q Consensus       465 lEltRkR~r~sl~e~~~~~c~~c~g~g~~~~~~  497 (723)
                      +....+++.|.+.+++...|.-|+|+|...+..
T Consensus       154 v~~~~~~~gPg~~qs~q~~C~~C~G~G~~~~~k  186 (337)
T KOG0712         154 VQTRTRQMGPGMVQSPQLVCDSCNGSGETISLK  186 (337)
T ss_pred             CEEEEEECCCCCCCCCEEEECCCCCCCCCCCCC
T ss_conf             114776425653002245740678851031366


No 159
>TIGR01544 HAD-SF-IE HAD-superfamily (subfamily IE) hydrolase, TIGR01544; InterPro: IPR006434   This family is a small group of metazoan sequences with one sequence from Arabidopsis thaliana. The sequences from mouse are annotated as pyrimidine 5-nucleotidases, apparently in reference to HSPC233, the human homolog. However, no such annotation can currently be found for this gene. This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily (IPR005834 from INTERPRO). All of the conserved catalytic motifs  are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches of that subfamily (IA-ID) as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB..
Probab=42.91  E-value=20  Score=15.08  Aligned_cols=45  Identities=22%  Similarity=0.349  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCCCCE
Q ss_conf             999999999731278728998604861489851566630112100236754653
Q gi|254780751|r  437 RSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGA  490 (723)
Q Consensus       437 ~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c~g~  490 (723)
                      ..|++.+++....-.+|+||  ||.|- +-|||++...      .+.||.|+|-
T Consensus        12 t~Ve~ii~~~v~GGa~k~~i--isDFD-yTlsrf~~e~------G~r~pt~hgi   56 (287)
T TIGR01544        12 TEVEEIIRELVVGGAEKLQI--ISDFD-YTLSRFATED------GERVPTSHGI   56 (287)
T ss_pred             HHHHHHHHHHEECCCCCEEE--EEECC-CCHHHHHHHC------CCCCCCCCCC
T ss_conf             89999987431068765689--85236-4122323115------8605520010


No 160
>PRK06669 fliH flagellar assembly protein H; Validated
Probab=42.90  E-value=21  Score=14.97  Aligned_cols=49  Identities=16%  Similarity=0.206  Sum_probs=37.9

Q ss_pred             CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEE
Q ss_conf             431013576999998730237999999998488799984787788633897
Q gi|254780751|r  516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIE  566 (723)
Q Consensus       516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ie  566 (723)
                      ...|.++|||+=..|+..++......+..  ...|.|.+|+.+..-.+.|+
T Consensus       197 ~~~I~I~Vnp~Dye~v~e~k~el~~~l~~--~~~i~I~~D~~l~~GgciIe  245 (268)
T PRK06669        197 ATDITIRVNPEDYEYVKEQKDELISLLDS--EAHLKIYEDEAISKGGCIIE  245 (268)
T ss_pred             CCEEEEEECHHHHHHHHHHHHHHHHHHCC--CCCEEEEECCCCCCCCEEEE
T ss_conf             78189998888899999848999987457--77769976788899987996


No 161
>TIGR00459 aspS_bact aspartyl-tRNA synthetase; InterPro: IPR004524   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Aspartyl tRNA synthetase 6.1.1.12 from EC is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module .     This family represents aspartyl-tRNA synthetases from the bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). ; GO: 0000166 nucleotide binding, 0004815 aspartate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006422 aspartyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=42.42  E-value=6.7  Score=18.43  Aligned_cols=56  Identities=14%  Similarity=0.159  Sum_probs=24.6

Q ss_pred             CCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHH-HHHHHHHH
Q ss_conf             7887512420468868999999999863002587169985045575799999999999-99998776
Q gi|254780751|r  212 NTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLM-RLWDNVRE  277 (723)
Q Consensus       212 ~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~-~~w~~i~~  277 (723)
                      +..+..-|.|.--|++-|....=....+.  -.|.|        .+.+++..-++.|+ ..|..+..
T Consensus       222 G~drYyQIArCFRDEDLRADRQPEFTQiD--~E~SF--------~~~~~vm~l~E~l~~~vf~~v~~  278 (653)
T TIGR00459       222 GVDRYYQIARCFRDEDLRADRQPEFTQID--MEMSF--------MTQEDVMDLIEKLVSGVFKEVKG  278 (653)
T ss_pred             CCCCCEEEEEEECCCCCCCCCCCCCCHHH--HHHHC--------CCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             55531357889766256665778732442--63112--------89356899999999999999707


No 162
>pfam07013 DUF1314 Protein of unknown function (DUF1314). This family consists of several Alphaherpesvirus proteins of around 200 residues in length. The function of this family is unknown.
Probab=42.17  E-value=21  Score=14.96  Aligned_cols=37  Identities=27%  Similarity=0.296  Sum_probs=27.4

Q ss_pred             HHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCC
Q ss_conf             99998422214367864998328806999823755444555
Q gi|254780751|r  354 QLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHC  394 (723)
Q Consensus       354 ~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~  394 (723)
                      -++.+-.+.|.||.||++.|-.+-.-    +|+|+|+..+.
T Consensus         4 Ll~~L~GR~vDLPgG~el~I~~~~g~----~~~~~f~~~g~   40 (177)
T pfam07013         4 LLRSLRGRTVDLPGGGELFIFCNAGR----PVTGKFRRPGS   40 (177)
T ss_pred             HHHHHCCCEEECCCCCEEEEECCCCC----CEEEEECCCCC
T ss_conf             65344386164699986998558897----12788716986


No 163
>pfam02691 VacA Vacuolating cyotoxin. This family consists of Vacuolating cyotoxin proteins form Proteobacteria. These proteins are an important virulence determinate in H. pylori and induce cytoplasmic vacuolation in a variety of mammalian cell lines.
Probab=41.86  E-value=21  Score=14.90  Aligned_cols=32  Identities=16%  Similarity=0.133  Sum_probs=20.8

Q ss_pred             HHHHHHCCCCCCCCCCEEEEECC--------CEEEEEEEC
Q ss_conf             99998422214367864998328--------806999823
Q gi|254780751|r  354 QLDSLHQTEVTLPSRGYVIINQT--------EALVSIDVN  385 (723)
Q Consensus       354 ~i~~~~~~~V~L~sGG~lvIe~T--------EALt~IDVN  385 (723)
                      --..+|+--|..+||--|||+.-        .|.-+-||-
T Consensus       578 GtrsiysGGVkFK~GeKLVIde~Y~aPWNYFdarni~~VE  617 (1002)
T pfam02691       578 GTRPAFSGGVKFKGGEKLVIDEFYHAPWNYFDARNIKDVE  617 (1002)
T ss_pred             CCCCCCCCCEEECCCCEEEEEEHHCCCCHHCCCCCCCEEE
T ss_conf             7533301760653786577600111861010335652257


No 164
>cd00765 Pyrophosphate_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include pyrophosphate-dependent phosphofructokinases. These are found in bacteria as well as plants. These may be dimeric nonallosteric enzymes as in bacteria or allosteric heterotetramers as in plants.
Probab=40.90  E-value=22  Score=14.76  Aligned_cols=44  Identities=20%  Similarity=0.268  Sum_probs=23.5

Q ss_pred             EEEE-CCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHH
Q ss_conf             2420-4688689999999998630025871699850455757999999
Q gi|254780751|r  218 TISR-KITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRD  264 (723)
Q Consensus       218 ~iSr-ki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~~d  264 (723)
                      |.+| ||..++....-.+....+...   |++|=-....-+...+..+
T Consensus       143 ~sgr~ki~t~eq~~~~~~~~~~l~Ld---gLVIiGGddSnTnaa~LAE  187 (550)
T cd00765         143 CSGRTKIETEDQFKQAEETAKKLDLD---ALVVIGGDDSNTNAALLAE  187 (550)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCC---EEEEECCCCCHHHHHHHHH
T ss_conf             68856248999999999999985998---7999689873487999999


No 165
>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=40.87  E-value=22  Score=14.76  Aligned_cols=44  Identities=16%  Similarity=0.117  Sum_probs=36.7

Q ss_pred             CCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCC
Q ss_conf             01357699999873023799999999848879998478778863
Q gi|254780751|r  519 IIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKL  562 (723)
Q Consensus       519 i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~  562 (723)
                      +.+.+|...+..+.+..-..+.+|.+.+|.+|.|..++....++
T Consensus         2 ~rilvP~~~vG~vIGk~G~~I~~i~~~sga~I~i~~~~~~~~~e   45 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTE   45 (65)
T ss_pred             EEEEEEHHHEEEEECCCCHHHHHHHHHHCCEEEECCCCCCCCCC
T ss_conf             89998746722899799878999999849889999889999994


No 166
>PRK02145 consensus
Probab=40.76  E-value=23  Score=14.75  Aligned_cols=14  Identities=14%  Similarity=0.283  Sum_probs=5.1

Q ss_pred             HHHHHHHCCCCEEE
Q ss_conf             99873103686389
Q gi|254780751|r  411 ARQLRLRDLAGLIV  424 (723)
Q Consensus       411 aRQlRLRnlgGiIv  424 (723)
                      +.++-=.++|.|++
T Consensus       163 ~~~~~~~G~geil~  176 (257)
T PRK02145        163 ARKMAELGAGEILL  176 (257)
T ss_pred             HHHHHHCCCCEEEE
T ss_conf             56887618786899


No 167
>pfam06635 NolV Nodulation protein NolV. This family consists of several nodulation protein NolV sequences from different Rhizobium species. The function of this family is unclear.
Probab=40.73  E-value=23  Score=14.74  Aligned_cols=49  Identities=8%  Similarity=0.124  Sum_probs=33.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHCCHHHHHHHHHH-HHCCEEEEEECCCCCCCCEEEE
Q ss_conf             3643101357699999873023799999999-8488799984787788633897
Q gi|254780751|r  514 YTAHNIIVHTHSDVVLYLLNQKRATIVEYEA-RFGVSINVVIGIELADKLFYIE  566 (723)
Q Consensus       514 ~~~~~i~v~~~~~va~~lln~kr~~l~~lE~-~~~~~I~i~~d~~l~~~~f~Ie  566 (723)
                      .+.++++++|||.-+..|...    +.++.. .-.-+|.|.+||.|....+..+
T Consensus       128 ~~~keV~LhV~P~~ae~la~~----~ad~~~~~~~~~l~I~~Dp~L~~~~cvLe  177 (207)
T pfam06635       128 YKGAEVCLHVSPLKADLLARE----FADWDGLDGRPKLRIEADPALSADQCVLW  177 (207)
T ss_pred             HCCCEEEEEECHHHHHHHHHH----HHCCCCCCCCCEEEEEECCCCCCCCEEEE
T ss_conf             338728999888889999999----73310447886068721876687762664


No 168
>COG2895 CysN GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]
Probab=39.72  E-value=4.9  Score=19.36  Aligned_cols=31  Identities=16%  Similarity=0.164  Sum_probs=14.1

Q ss_pred             CCCCCCCCCCEEEEECCCEEE-EEEECCCCCC
Q ss_conf             222143678649983288069-9982375544
Q gi|254780751|r  360 QTEVTLPSRGYVIINQTEALV-SIDVNSGRST  390 (723)
Q Consensus       360 ~~~V~L~sGG~lvIe~TEALt-~IDVNSG~~~  390 (723)
                      .++.||+.|+--|--.-+++- .+|||+....
T Consensus       330 Gr~Y~lK~~t~~v~a~V~~i~~~ldvntl~~~  361 (431)
T COG2895         330 GRSYDLKIATRTVRARVEEIKHQLDVNTLEQE  361 (431)
T ss_pred             CCEEEEEECCEEEEEEEEEEEEEEECCCCCCC
T ss_conf             84688884124778986112789843500100


No 169
>pfam04025 DUF370 Domain of unknown function (DUF370). Bacterial domain of unknown function.
Probab=39.53  E-value=24  Score=14.62  Aligned_cols=27  Identities=30%  Similarity=0.316  Sum_probs=18.4

Q ss_pred             EEEEECCCCCEEEEEEE-ECCEEEEEEE
Q ss_conf             26896528960799999-8998999996
Q gi|254780751|r    4 KMLIDASHVEETRVVVL-RDNRVEELDF   30 (723)
Q Consensus         4 ~~lI~~~~~~e~Rvav~-e~g~l~e~~~   30 (723)
                      -.|||+|++..||.+++ +.|.++=.-+
T Consensus        37 g~lIDaT~GrkTRavii~DS~HviLSai   64 (73)
T pfam04025        37 GKLIDATYGRKTRAVIITDSGHVILSAL   64 (73)
T ss_pred             CCEEECCCCCEEEEEEEECCCCEEEEEC
T ss_conf             9089865696067999970893899705


No 170
>pfam04606 Ogr_Delta Ogr/Delta-like zinc finger. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F. This family also includes zinc fingers in recombinase proteins.
Probab=39.37  E-value=15  Score=15.89  Aligned_cols=19  Identities=21%  Similarity=0.497  Sum_probs=15.6

Q ss_pred             CCCCCCCEEEEECCHHHHH
Q ss_conf             3675465378606114689
Q gi|254780751|r  483 VCTYCKGAGYIRSQSSVAL  501 (723)
Q Consensus       483 ~c~~c~g~g~~~~~~~~~~  501 (723)
                      .||+|+..+++++...+..
T Consensus         1 ~CP~Cg~~a~irts~~~s~   19 (47)
T pfam04606         1 RCPHCGAKARIRTSRRLSA   19 (47)
T ss_pred             CCCCCCCCEEEEEHHHCCH
T ss_conf             9598898389968356297


No 171
>TIGR02836 spore_IV_A stage IV sporulation protein A; InterPro: IPR014201   This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. .
Probab=39.32  E-value=13  Score=16.40  Aligned_cols=37  Identities=24%  Similarity=0.571  Sum_probs=22.9

Q ss_pred             EEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCC-CHHHC
Q ss_conf             9996073346042878798997836388231353278977130-22213
Q gi|254780751|r   27 ELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFL-PFLEI   74 (723)
Q Consensus        27 e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL-~~~ei   74 (723)
                      .||+=+.=....-||||+|.|=-|-           .||.-|. -|-|+
T Consensus         3 ~~DiykDIAeRT~GdIYiGvVGpVR-----------TGKSTfIKkFMeL   40 (492)
T TIGR02836         3 KVDIYKDIAERTQGDIYIGVVGPVR-----------TGKSTFIKKFMEL   40 (492)
T ss_pred             CCCCEEEHHHCCCCCEEEEEECCCC-----------CCCCCHHHHEEHE
T ss_conf             8740210230168967898662742-----------7852111110010


No 172
>TIGR02533 type_II_gspE general secretory pathway protein E; InterPro: IPR013369    GspE, the E protein of the type II secretion system, is also referred to as the main terminal branch of the general secretion pathway. ; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=39.06  E-value=8  Score=17.86  Aligned_cols=80  Identities=26%  Similarity=0.419  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHH-----HHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCC
Q ss_conf             99999999999998731036863896033479888-----8999999999973127872899860486148985156663
Q gi|254780751|r  400 LQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKK-----NNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRS  474 (723)
Q Consensus       400 l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~-----~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~  474 (723)
                      |+||= ||--+.   ||+|+|   |=+|  |-...     .|+.| ++|...||.-...+.    ..+-++-++++-...
T Consensus       346 LHTND-AAgAvt---RL~DMG---vEPF--L~aSsl~GVLAQRLV-RrlCp~Cke~y~a~~----~~~~~~G~~~~~~~~  411 (495)
T TIGR02533       346 LHTND-AAGAVT---RLIDMG---VEPF--LLASSLLGVLAQRLV-RRLCPHCKEPYEATD----EELALLGISKKEPKK  411 (495)
T ss_pred             HHHHH-HHHHHH---HHHHCC---CCHH--HHHHHHHHHHHHHHH-HHCCCCCCCCCCCCH----HHHHHCCCCHHHHCC
T ss_conf             55401-544665---553258---6404--899999999986334-331514688899897----999854884021035


Q ss_pred             C---HHHHHCCCCCCCCCEEEE
Q ss_conf             0---112100236754653786
Q gi|254780751|r  475 S---VLESTTKVCTYCKGAGYI  493 (723)
Q Consensus       475 s---l~e~~~~~c~~c~g~g~~  493 (723)
                      .   ..=+=-.-||+|.++|+-
T Consensus       412 ~nGv~~lyr~~GC~~C~~~GY~  433 (495)
T TIGR02533       412 DNGVIILYRPVGCPACNHTGYR  433 (495)
T ss_pred             CCCEEEEECCCCCHHHCCCCCC
T ss_conf             7764899778764212788883


No 173
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).  During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=38.83  E-value=13  Score=16.41  Aligned_cols=78  Identities=14%  Similarity=0.204  Sum_probs=39.2

Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHHHHC----CCCEEEEEECCCCEEEEECCCCCCCHHHHH--CCCCCCCCCEEE
Q ss_conf             68638960334798888999999999973127----872899860486148985156663011210--023675465378
Q gi|254780751|r  419 LAGLIVVDFIDMEEKKNNRSVEKKLKESLKKD----RARVQVGAISNFGLLEMSRQRIRSSVLEST--TKVCTYCKGAGY  492 (723)
Q Consensus       419 lgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D----~~~~~v~~it~lGLlEltRkR~r~sl~e~~--~~~c~~c~g~g~  492 (723)
                      =.|.+.+-|-|-......++-  .+.|.+..+    ....-...-...-...+|=.-+-|-|....  +-.||.|.|.|.
T Consensus       229 ~~G~~~v~~~~~~~~~~~~~~--~~SE~~acp~~L~~~~~~f~~~~~c~~~~~s~~eLePRlFSFNSP~GaCp~C~GLG~  306 (956)
T TIGR00630       229 SEGLLEVEIEDDESPAEGKEE--LYSEKFACPARLEKSELLFSKNAACPECGFSLEELEPRLFSFNSPYGACPECSGLGI  306 (956)
T ss_pred             CCCEEEEEECCCCCCCCCHHH--HHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCE
T ss_conf             587489997367765410222--220210585122246666555337420462210036210332675777787455521


Q ss_pred             EECCHH
Q ss_conf             606114
Q gi|254780751|r  493 IRSQSS  498 (723)
Q Consensus       493 ~~~~~~  498 (723)
                      -.+.+.
T Consensus       307 ~~~~D~  312 (956)
T TIGR00630       307 KLEFDP  312 (956)
T ss_pred             EEEECH
T ss_conf             575061


No 174
>TIGR00340 zpr1_rel zinc finger protein ZPR1 homolog; InterPro: IPR004470   Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, however they are now recognised to bind DNA, RNA, protein and/or lipid substrates , , , , . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.    (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries).   This entry represents ZPR1-type zinc finger domains. ZPR1 was shown experimentally to bind approximately two moles of zinc, and has two copies of a domain homologous to this protein, each containing a putative zinc finger of the form CXXCX(25)CXXC. ZPR1 binds the tyrosine kinase domain of epidermal growth factor receptor but is displaced by receptor activation and autophosphorylation after which it redistributes in part to the nucleus. The proteins described by this family by analogy may be suggested to play a role in signal transduction as proven for other Z-finger binding proteins.   Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) . ZPR1 interacts with complexes formed by SMN , and may act as a modifier that effects the severity of SMA.   More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0008270 zinc ion binding.
Probab=38.34  E-value=11  Score=16.94  Aligned_cols=14  Identities=21%  Similarity=0.733  Sum_probs=6.3

Q ss_pred             CCCCCCEEEEECCH
Q ss_conf             67546537860611
Q gi|254780751|r  484 CTYCKGAGYIRSQS  497 (723)
Q Consensus       484 c~~c~g~g~~~~~~  497 (723)
                      ||.|+|.+..+.+.
T Consensus         1 CPVCGg~~~L~Av~   14 (168)
T TIGR00340         1 CPVCGGKRTLKAVT   14 (168)
T ss_pred             CCCCCCCCEEEEEE
T ss_conf             98638744157665


No 175
>PRK06032 fliH flagellar assembly protein H; Validated
Probab=38.03  E-value=25  Score=14.46  Aligned_cols=63  Identities=17%  Similarity=0.166  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHCC-CCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEEE
Q ss_conf             887889997303-64310135769999987302379999999984887999847877886338971
Q gi|254780751|r  503 ILRSVEEYLLQY-TAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEK  567 (723)
Q Consensus       503 ~~r~i~~~~~~~-~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ier  567 (723)
                      +...+++....- ....|.|.+++..+.-+...-..  ..-+.-|...|.|.+||.|..-+|+|+=
T Consensus       112 v~a~v~e~l~~l~~~P~LvIrV~~~l~e~l~~~le~--~a~~~Gf~Grl~i~~Dp~l~~GDcrieW  175 (208)
T PRK06032        112 ITALVRDCLRHLVATPHLVVRVNDALVEAARERLER--LARESGFEGRLVVLADPDIAPGDCRIEW  175 (208)
T ss_pred             HHHHHHHHHHHHHCCCEEEEEECHHHHHHHHHHHHH--HHHHCCCCCEEEEEECCCCCCCCEEEEE
T ss_conf             999999999987449728999787657999999999--9996698823898308998988658886


No 176
>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=37.95  E-value=16  Score=15.75  Aligned_cols=34  Identities=18%  Similarity=0.206  Sum_probs=31.2

Q ss_pred             CCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEE
Q ss_conf             0135769999987302379999999984887999
Q gi|254780751|r  519 IIVHTHSDVVLYLLNQKRATIVEYEARFGVSINV  552 (723)
Q Consensus       519 i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i  552 (723)
                      ..+.+|+....++.+.+-..+..|++.+++.|.|
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 177
>pfam07295 DUF1451 Protein of unknown function (DUF1451). This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=37.86  E-value=15  Score=16.05  Aligned_cols=44  Identities=18%  Similarity=0.268  Sum_probs=29.5

Q ss_pred             CEEEEEECCCCEEEEECCCCCCCHHHH-HCCCCCCCCCEEEEECC
Q ss_conf             289986048614898515666301121-00236754653786061
Q gi|254780751|r  453 RVQVGAISNFGLLEMSRQRIRSSVLES-TTKVCTYCKGAGYIRSQ  496 (723)
Q Consensus       453 ~~~v~~it~lGLlEltRkR~r~sl~e~-~~~~c~~c~g~g~~~~~  496 (723)
                      .-+.+.|..+|-|-=..=--...+... ...+||.|+|+.+.|-+
T Consensus       103 ~Y~sGEvvg~G~LvC~~Cg~~~~~~~p~~ip~Cp~Cg~~~F~R~~  147 (148)
T pfam07295       103 VYQSGEIVGLGTLVCENCGHMLTFYHPSVIPPCPKCGHTEFTRQP  147 (148)
T ss_pred             EEECCCEEECCEEEECCCCCEEEEECCCCCCCCCCCCCCEEECCC
T ss_conf             242460541645772368987887468768898779998253288


No 178
>PRK00964 tetrahydromethanopterin S-methyltransferase subunit A; Provisional
Probab=37.63  E-value=24  Score=14.54  Aligned_cols=56  Identities=25%  Similarity=0.336  Sum_probs=38.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             3755444555114799999999999999873103686389603347988889999999999731278
Q gi|254780751|r  385 NSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDR  451 (723)
Q Consensus       385 NSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~  451 (723)
                      +.|+-+|....--..-.++.+|.+..-+|+-        +||.||+   +|-..+..+.++|..+|+
T Consensus       101 ~~grIiGa~GaiPfieNi~~~av~rFq~qVe--------~vdlI~~---eD~~~I~a~I~ec~~kdP  156 (243)
T PRK00964        101 DGGRIIGAKGAIPFIENLPDEAVERFQQQVE--------IVDLIDT---EDPGAIAAAIKECIAKDP  156 (243)
T ss_pred             CCCCEECCCCCCCHHHHCCHHHHHHHHHHEE--------EEEEECC---CCHHHHHHHHHHHHCCCC
T ss_conf             8997825888863454099899999987457--------8863167---787999999999853899


No 179
>TIGR02405 trehalos_R_Ecol trehalose operon repressor; InterPro: IPR012771   Trehalose is a non-reducing disaccharide which can be used as both a carbon source and an osmoprotectant in bacteria. Trehalose uptake into the cytoplasm occurs via a trehalose-specific phosphotransferase system which phosphorylates trehalase to trehalose-6-phosphate (Tre6P) during transport into the cytoplasm, and a hydrolase which hydrolyses Tre6P to glucose and glucose-6-phophate.   This entry represents LacI-type TreR, a transcriptional repressor of trehalose uptake found mainly within the gamma-proteobacteria. It does not include the GntR-type TreR's such as those found in Bacillus species. It is capable of binding both the inducer Tre6P and trehalose. Binding of trehalose does not affect the repressor's affinity for its DNA binding site, while binding Tre6P substantially reduces its affinity. The repression activity of TreR is therefore regulated by the ratio of trehalose to Tre6P within the cell . The protein is composed of two domains, an N-terminal DNA-binding helix-turn-helix domain, and a C-terminal effector-binding domain which is homologous to that of LacI. The effector-binding domain is composed of two subdomains, both of which form an alpha-beta-alpha sandwhich, with the effector binding site located at the interface of these subdomains . Tre6P and trehalose bind competitively to this site, with the affinty for trehalose substantially lower than that for Tre6P.; GO: 0003677 DNA binding, 0016566 specific transcriptional repressor activity, 0005991 trehalose metabolic process, 0016481 negative regulation of transcription.
Probab=36.68  E-value=8.2  Score=17.81  Aligned_cols=90  Identities=16%  Similarity=0.290  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHH---HHHHCCCCEEEEEECCCCEEEEECCCC-CCCHHHHHCC
Q ss_conf             999999873103686389603347988889999999999---731278728998604861489851566-6301121002
Q gi|254780751|r  407 AEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKE---SLKKDRARVQVGAISNFGLLEMSRQRI-RSSVLESTTK  482 (723)
Q Consensus       407 A~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~---~l~~D~~~~~v~~it~lGLlEltRkR~-r~sl~e~~~~  482 (723)
                      ..|=-+||.+||+=|+|+-=|=-+..     +++..++.   .|.+|..+..=++.=..|.++|--+++ +++-.+.++-
T Consensus       104 ~~EHL~vL~~Rn~DGviLFGFtG~~e-----e~l~~w~~k~Vv~Ard~~gfsSVcYDd~Gai~llM~~ly~qG~r~ISfl  178 (311)
T TIGR02405       104 VNEHLSVLKKRNVDGVILFGFTGLDE-----EILESWRDKLVVLARDAKGFSSVCYDDIGAIKLLMAELYQQGHREISFL  178 (311)
T ss_pred             HHHHHHHHHHCCCCEEEECCCCCCCH-----HHHHHHCCCEEEEEEECCCEEEEEECHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             99999886550678479847657767-----8864420675899860675134521646799999999976277302251


Q ss_pred             CCCCCCC-EEEEECCHHHHH
Q ss_conf             3675465-378606114689
Q gi|254780751|r  483 VCTYCKG-AGYIRSQSSVAL  501 (723)
Q Consensus       483 ~c~~c~g-~g~~~~~~~~~~  501 (723)
                      -.|+|+- ||..|+.-.+++
T Consensus       179 GVd~sD~TTG~~Rh~aYla~  198 (311)
T TIGR02405       179 GVDDSDKTTGLLRHEAYLAY  198 (311)
T ss_pred             CCCCCCCCCCHHHHHHHHHH
T ss_conf             26988754241478999999


No 180
>pfam05262 Borrelia_P83 Borrelia P83/100 protein. This family consists of several Borrelia P83/P100 antigen proteins.
Probab=36.67  E-value=11  Score=16.84  Aligned_cols=11  Identities=36%  Similarity=0.860  Sum_probs=7.8

Q ss_pred             CCCEEEEEECC
Q ss_conf             88231353278
Q gi|254780751|r   53 SLQAAFVDYGG   63 (723)
Q Consensus        53 ~lqAAFVdiG~   63 (723)
                      +|.--||+|-+
T Consensus         8 N~~lEFvNy~G   18 (489)
T pfam05262         8 NMTLEFVNYKG   18 (489)
T ss_pred             CCCEEEEECCC
T ss_conf             38626874258


No 181
>PRK12366 replication factor A; Reviewed
Probab=35.79  E-value=12  Score=16.72  Aligned_cols=54  Identities=9%  Similarity=0.018  Sum_probs=42.9

Q ss_pred             HCCCCCCCCCCCCHHHHHHHHCCHHHHHHH------HHHHHCCEEEEEECCCCCCCCEEE
Q ss_conf             303643101357699999873023799999------999848879998478778863389
Q gi|254780751|r  512 LQYTAHNIIVHTHSDVVLYLLNQKRATIVE------YEARFGVSINVVIGIELADKLFYI  565 (723)
Q Consensus       512 ~~~~~~~i~v~~~~~va~~lln~kr~~l~~------lE~~~~~~I~i~~d~~l~~~~f~I  565 (723)
                      ....++.+.+.+--.-|.-|++-.++.|..      |+.-.|..+.|.+++++...++.+
T Consensus       570 LDDgTg~i~~~~y~~~vEeLl~m~~eElk~~~~~~~l~~~lG~e~~~~gn~~~~n~dl~~  629 (649)
T PRK12366        570 LDDGTGVINCRFYGNNVEKLTEMSKEELKNLNLDARLDDILGKEVVFYGNPSFRNDDLEF  629 (649)
T ss_pred             EECCCCEEEEEEECCCHHHHHCCCHHHHHHCCHHHHHHHHCCCEEEEEECCCCCCCCEEE
T ss_conf             977997599999336689885779899751212333566428559999524446751388


No 182
>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP).  It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
Probab=35.73  E-value=9.2  Score=17.46  Aligned_cols=62  Identities=19%  Similarity=0.178  Sum_probs=27.4

Q ss_pred             CCCCCCCCCCCCEEECCCCCC--CCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHH
Q ss_conf             101233457652344227887--5124204688689999999998630025871699850455757999
Q gi|254780751|r  195 AVTTYLSLAGRYSVLMPNTSK--GETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEI  261 (723)
Q Consensus       195 ~lT~~isl~Gry~Vl~P~~~~--~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l  261 (723)
                      ++++..+.-|.++|+-=-...  ...+..=--.++....++.++.     ...|+|+=|..-|..+...
T Consensus        33 Rvst~p~~~Ge~vvlRll~~~~~~~~L~~LG~~~~~~~~l~~~~~-----~~~GlilitGptGSGKtTt   96 (264)
T cd01129          33 RVSTLPTIYGESVVLRILDKKNQILDLEKLGLKPENLEIFRKLLE-----KPHGIILVTGPTGSGKTTT   96 (264)
T ss_pred             EEEECCCCCCCEEEEEEECCCCCCCCHHHHCCCHHHHHHHHHHHH-----CCCCEEEEECCCCCCHHHH
T ss_conf             999475799976999975776665798795799999999999970-----8998899978999977999


No 183
>TIGR01037 pyrD_sub1_fam dihydroorotate dehydrogenase family protein; InterPro: IPR005720   Dihydroorotate dehydrogenase (1.3.3.1 from EC) (DHOdehase) catalyzes the fourth step in the de novo biosynthesis of pyrimidine, the conversion of dihydroorotate into orotate. DHOdehase is a ubiquitous FAD flavoprotein. In bacteria (gene pyrD), DHOdease is located on the inner side of the cytosolic membrane. In some yeasts, such as in Saccharomyces cerevisiae (gene URA1, subfamily 2), it is a cytosolic protein while in other eukaryotes it is found in the mitochondria .    This describes dihydroorotate dehydrogenases subfamily 1 that includes a number of uncharacterised proteins and a domain of dihydropyrimidine dehydrogenase.; GO: 0004158 dihydroorotate oxidase activity, 0006207 'de novo' pyrimidine base biosynthetic process, 0005737 cytoplasm.
Probab=35.36  E-value=27  Score=14.18  Aligned_cols=46  Identities=15%  Similarity=0.240  Sum_probs=20.8

Q ss_pred             CCCCCCCC-EEEEECCHH-HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf             23675465-378606114-689988788999730364310135769999987
Q gi|254780751|r  482 KVCTYCKG-AGYIRSQSS-VALSILRSVEEYLLQYTAHNIIVHTHSDVVLYL  531 (723)
Q Consensus       482 ~~c~~c~g-~g~~~~~~~-~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~l  531 (723)
                      -+|||-.| .|.-.-.+. +++.+...+    ...-...+.+++.|.|.+++
T Consensus       129 ~SCPhvK~G~G~~iG~dP~l~~~vv~av----K~~~d~Pv~aKLsPNV~Di~  176 (308)
T TIGR01037       129 VSCPHVKGGGGIEIGQDPELSADVVKAV----KDKVDVPVFAKLSPNVTDIT  176 (308)
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHH----HCCCCCCEEEECCCCHHHHH
T ss_conf             7774434234655477877999999998----30007865786486566899


No 184
>cd04702 ASRGL1_like ASRGL1_like domains, a subfamily of the L-Asparaginase type 2-like enzymes. The wider family includes Glycosylasparaginase, Taspase 1 and  L-Asparaginase type 2 enzymes. The proenzymes undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue. ASRGL1, or asparaginase-like 1, has been cloned from mammalian testis cDNA libraries. It has been identified as a sperm antigen that may induce the production of autoantibodies following obstruction of the male reproductive tract, e.g. vasectomy.
Probab=35.28  E-value=27  Score=14.17  Aligned_cols=17  Identities=18%  Similarity=0.323  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             4799999999999999873
Q gi|254780751|r  397 DTALQTNLEAAEEIARQLR  415 (723)
Q Consensus       397 ~t~l~tNleAA~EIaRQlR  415 (723)
                      |.+++.++  |.+|+.+|+
T Consensus       186 E~iir~~~--A~~v~~~~~  202 (261)
T cd04702         186 ESIMKVVL--ARLILDHME  202 (261)
T ss_pred             HHHHHHHH--HHHHHHHHH
T ss_conf             99998869--999999998


No 185
>pfam00567 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. copies in the Drosophila Tudor protein.
Probab=34.76  E-value=28  Score=14.12  Aligned_cols=24  Identities=33%  Similarity=0.605  Sum_probs=9.2

Q ss_pred             CCEEEEEEEEECCC--CCEEEEEECC
Q ss_conf             87879899783638--8231353278
Q gi|254780751|r   40 GNIYLAKVTRVEPS--LQAAFVDYGG   63 (723)
Q Consensus        40 GnIY~G~V~~V~p~--lqAAFVdiG~   63 (723)
                      |.-|.|+|..+.++  ..--|||||.
T Consensus        63 ~~wyRa~I~~~~~~~~~~V~fvDyG~   88 (118)
T pfam00567        63 GKWYRAKILVSLDDGLVEVFFIDYGN   88 (118)
T ss_pred             CCEEEEEEEEECCCCEEEEEEEECCC
T ss_conf             94999999996699989999994697


No 186
>cd01883 EF1_alpha Eukaryotic elongation factor 1 (EF1) alpha subfamily.  EF1 is responsible for the GTP-dependent binding of aminoacyl-tRNAs to the ribosomes.  EF1 is composed of four subunits: the alpha chain which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains.  This subfamily is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF1-alpha) and eukaryotes (eEF1-alpha).  eEF1-alpha interacts with the actin of the eukaryotic cytoskeleton and may thereby play a role in cellular transformation and apoptosis.  EF-Tu can have no such role in bacteria.  In humans, the isoform eEF1A2 is overexpressed in 2/3 of breast cancers and has been identified as a putative oncogene.  This subfamily also includes Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation in
Probab=34.07  E-value=28  Score=14.04  Aligned_cols=94  Identities=23%  Similarity=0.244  Sum_probs=55.1

Q ss_pred             CEEEEEEECCCCCCCCCCC-HHHHHHHHHHHHHHHHHHHHHHCCCCEEE-EECCCCC----CHHHHHHHHHHHHHHHHHC
Q ss_conf             8069998237554445551-14799999999999999873103686389-6033479----8888999999999973127
Q gi|254780751|r  377 EALVSIDVNSGRSTREHCI-EDTALQTNLEAAEEIARQLRLRDLAGLIV-VDFIDME----EKKNNRSVEKKLKESLKKD  450 (723)
Q Consensus       377 EALt~IDVNSG~~~~~~~~-e~t~l~tNleAA~EIaRQlRLRnlgGiIv-IDFIdM~----~~~~~~~v~~~l~~~l~~D  450 (723)
                      =|+.+||.+.|-|..+-.. .+         .+|-++-+++-++.-||| |-=+|..    +++-...+.+.++..|++-
T Consensus       103 ~ailvvda~~g~~e~g~~~~~Q---------TreH~~l~~~lGik~iIVavNKMD~v~~~y~~~rf~~i~~~~~~~l~~~  173 (219)
T cd01883         103 VAVLVVDARKGEFEAGFEKGGQ---------TREHALLARTLGVKQLIVAVNKMDDVTVNWSEERYDEIKKELSPFLKKV  173 (219)
T ss_pred             EEEEEEECCCCCCCCCCCCCCH---------HHHHHHHHHHCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             6899998576751036677765---------9999999998499748999987536886525999999999999999982


Q ss_pred             ---CCCEEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCCCC
Q ss_conf             ---872899860486148985156663011210023675465
Q gi|254780751|r  451 ---RARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKG  489 (723)
Q Consensus       451 ---~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c~g  489 (723)
                         ...+.+.++|.|.=         .++.+ -++.||...|
T Consensus       174 g~~~~~~~~IPiSa~~G---------dNi~~-~s~~m~WY~G  205 (219)
T cd01883         174 GYNPKDVPFIPISGLTG---------DNLIE-KSENMPWYKG  205 (219)
T ss_pred             CCCCCCCEEEEEECCCC---------CCCCC-CCCCCCCCCC
T ss_conf             99956615999336766---------30466-7889989878


No 187
>COG2052 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.98  E-value=29  Score=14.03  Aligned_cols=19  Identities=47%  Similarity=0.635  Sum_probs=9.3

Q ss_pred             EEEEECCCCCEEEEEEEEC
Q ss_conf             2689652896079999989
Q gi|254780751|r    4 KMLIDASHVEETRVVVLRD   22 (723)
Q Consensus         4 ~~lI~~~~~~e~Rvav~e~   22 (723)
                      -||||||++.-||..++-|
T Consensus        41 ~~LIDATYGRrTRavii~D   59 (89)
T COG2052          41 GMLIDATYGRRTRAVIITD   59 (89)
T ss_pred             CCEEECCCCCEEEEEEEEC
T ss_conf             8277702485255799963


No 188
>PRK01172 ski2-like helicase; Provisional
Probab=33.78  E-value=29  Score=14.01  Aligned_cols=13  Identities=15%  Similarity=0.181  Sum_probs=5.3

Q ss_pred             CCCEEEECCCCHH
Q ss_conf             7512420468868
Q gi|254780751|r  215 KGETISRKITNPV  227 (723)
Q Consensus       215 ~~~~iSrki~~~~  227 (723)
                      +.+|.|--|.|.+
T Consensus       171 qiIgLSATi~N~~  183 (674)
T PRK01172        171 RILALSATVSNAN  183 (674)
T ss_pred             EEEEECCCCCCHH
T ss_conf             7997157868999


No 189
>pfam00009 GTP_EFTU Elongation factor Tu GTP binding domain. This domain contains a P-loop motif, also found in several other families such as pfam00071, pfam00025 and pfam00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.
Probab=33.35  E-value=29  Score=13.97  Aligned_cols=70  Identities=13%  Similarity=0.154  Sum_probs=44.5

Q ss_pred             EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHH----CCCC
Q ss_conf             069998237554445551147999999999999998731036863896033479888899999999997312----7872
Q gi|254780751|r  378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKK----DRAR  453 (723)
Q Consensus       378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~----D~~~  453 (723)
                      |+.+||.+.|-..      .         .+++.++++..++.-||+|-=||+-+.++..++.+.+.+.+-.    ....
T Consensus        94 ~vlVvda~~G~~~------q---------t~~~~~~~~~~~~p~iv~vNKiD~v~~~~~~~~~~e~~~~ll~~~~~~~~~  158 (185)
T pfam00009        94 AILVVDAVEGVMP------Q---------TREHLLLAKQLGVPIIVFINKMDRVDDAELDEVVEEISRELLEKYGFGGET  158 (185)
T ss_pred             CEEEEECCCCCCC------C---------CHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             4299986768532------3---------099999999828987999977327776769999999999988873248998


Q ss_pred             EEEEEECCC
Q ss_conf             899860486
Q gi|254780751|r  454 VQVGAISNF  462 (723)
Q Consensus       454 ~~v~~it~l  462 (723)
                      +.|+++|.+
T Consensus       159 ~pivpiSA~  167 (185)
T pfam00009       159 IPVIPGSAL  167 (185)
T ss_pred             CEEEEEECC
T ss_conf             869996789


No 190
>pfam01153 Glypican Glypican.
Probab=33.18  E-value=21  Score=14.94  Aligned_cols=26  Identities=19%  Similarity=0.524  Sum_probs=19.0

Q ss_pred             CCCCCCCCCEEEEECCHHHHHHHHHH
Q ss_conf             02367546537860611468998878
Q gi|254780751|r  481 TKVCTYCKGAGYIRSQSSVALSILRS  506 (723)
Q Consensus       481 ~~~c~~c~g~g~~~~~~~~~~~~~r~  506 (723)
                      ..-||||.|...++--..+++.++|-
T Consensus       247 M~YCp~C~G~~~~kPC~gyC~NVmrG  272 (559)
T pfam01153       247 MWYCPHCRGLSEVKPCRGYCLNVMRG  272 (559)
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             23585345878788836778998877


No 191
>PRK10476 multidrug resistance protein MdtN; Provisional
Probab=33.11  E-value=29  Score=13.94  Aligned_cols=11  Identities=27%  Similarity=0.220  Sum_probs=5.1

Q ss_pred             CCEEEEEECCC
Q ss_conf             88799984787
Q gi|254780751|r  547 GVSINVVIGIE  557 (723)
Q Consensus       547 ~~~I~i~~d~~  557 (723)
                      |-++.|..|..
T Consensus       264 Gq~v~I~~Da~  274 (348)
T PRK10476        264 GDCATVYSMID  274 (348)
T ss_pred             CCEEEEEEECC
T ss_conf             89899999768


No 192
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=32.53  E-value=11  Score=16.81  Aligned_cols=13  Identities=0%  Similarity=-0.100  Sum_probs=5.5

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             5677699999998
Q gi|254780751|r  346 FFRSGIEVQLDSL  358 (723)
Q Consensus       346 f~~y~ie~~i~~~  358 (723)
                      |..+.|...+.++
T Consensus       144 ~~Sf~V~~~v~~a  156 (207)
T PRK10954        144 WNSFVVKSLVAQQ  156 (207)
T ss_pred             HHCHHHHHHHHHH
T ss_conf             8588999999999


No 193
>TIGR02738 TrbB type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB; InterPro: IPR014109   This entry includes thiol-disulphide isomerase (TrbB), a protein that is involved in conjugative transfer of plasmid DNA, specifically in the F-type system. TrbB has been predicted to contain a thioredoxin fold, it also contains a conserved pair of cysteines and has been shown to function as a thiol disulphide isomerase by complementation of Escherichia coli DsbA mutants . TtbB is believed to be involved in pilin assembly . TrbB is closely related to TraF (IPR014110 from INTERPRO) though somewhat longer lacking the cysteine motif and is apparently not functional as a disulphide bond isomerase..
Probab=32.52  E-value=15  Score=16.04  Aligned_cols=34  Identities=24%  Similarity=0.430  Sum_probs=14.8

Q ss_pred             CCCCEEEEECCCEEEEEEECCCCCC--CCCCCHHHHH
Q ss_conf             6786499832880699982375544--4555114799
Q gi|254780751|r  366 PSRGYVIINQTEALVSIDVNSGRST--REHCIEDTAL  400 (723)
Q Consensus       366 ~sGG~lvIe~TEALt~IDVNSG~~~--~~~~~e~t~l  400 (723)
                      +||-|..|- |=||-.|=|||-++.  ..+..++.-|
T Consensus       133 ~~~ey~~~~-~PalFLvNvnt~~~~~v~~G~~~~~~L  168 (176)
T TIGR02738       133 PNGEYRPVV-TPALFLVNVNTRKAYPVLQGAVDEAEL  168 (176)
T ss_pred             CCCCCCEEC-CCEEEEECCCHHHHHHHHCCCCCHHHH
T ss_conf             889703010-232233315378887643387678999


No 194
>PRK07726 DNA topoisomerase III; Provisional
Probab=32.41  E-value=30  Score=13.90  Aligned_cols=27  Identities=22%  Similarity=0.150  Sum_probs=13.6

Q ss_pred             HHHHHHHHCCCCCEEEEEEECCCCCHHH
Q ss_conf             9999863002587169985045575799
Q gi|254780751|r  233 KEIARGLEVPAGMGVILRTAGASRTKIE  260 (723)
Q Consensus       233 ~~~~~~~~~~~~~G~IiRT~a~~~~~~~  260 (723)
                      ..+++.|.. .|+=---||.+.-.+.+.
T Consensus       306 l~iAQ~LYE-~glITYPRTDS~~ls~~~  332 (716)
T PRK07726        306 LDITQKLYQ-KGIVSYPRSDSNYVTQGE  332 (716)
T ss_pred             HHHHHHHHH-CCCEEECCCCCCCCCHHH
T ss_conf             999999985-696200687776479899


No 195
>LOAD_cold consensus
Probab=32.23  E-value=30  Score=13.84  Aligned_cols=33  Identities=12%  Similarity=0.064  Sum_probs=26.3

Q ss_pred             EEEEEEEECCCCCEEEEEECC-CCCCCCCHHHCC
Q ss_conf             798997836388231353278-977130222137
Q gi|254780751|r   43 YLAKVTRVEPSLQAAFVDYGG-NRHGFLPFLEIH   75 (723)
Q Consensus        43 Y~G~V~~V~p~lqAAFVdiG~-~k~gFL~~~ei~   75 (723)
                      +.|+|+.--+.=.=-||.--. ++.-|+|+++|.
T Consensus         2 ~~G~VK~f~~~kGfGFI~~~~g~~DvFvH~s~l~   35 (67)
T LOAD_cold         2 VKGTVKWFNVKKGFGFITPEDGGEDVFVHQSAIQ   35 (67)
T ss_pred             CCEEEEEEECCCCCEEEEECCCCCEEEEEHHHHC
T ss_conf             9869999989999478875799821899947814


No 196
>TIGR02949 anti_SigH_actin anti-sigma factor, TIGR02949 family; InterPro: IPR014295   This is a group of anti-sigma factors that are associated in an apparent operon with sigma factors belonging to the sigma-70 family (IPR014293 from INTERPRO). They appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family, which is restricted to the Actinobacteria..
Probab=31.91  E-value=25  Score=14.38  Aligned_cols=51  Identities=14%  Similarity=0.107  Sum_probs=36.2

Q ss_pred             CCCCCH-HHHHHHHHHHHHH-CCCCHHHHCCCCCH-HHHHHHHHHHHHHHHCCC
Q ss_conf             035320-3667888987631-01211220134420-356776999999984222
Q gi|254780751|r  312 VSGEKG-YREAKDFMKLLMP-SYARIVRQYEDPHP-IFFRSGIEVQLDSLHQTE  362 (723)
Q Consensus       312 vd~~~~-~~~~~~~~~~~~p-~~~~~v~~~~~~~~-lf~~y~ie~~i~~~~~~~  362 (723)
                      +|..++ ...+.+|+-.-++ +...+++.|-+.-| -|..|++|.+|..++.+.
T Consensus         7 ~dC~evr~~~l~e~LDge~~~~~~~~l~~H~~~C~~Cl~~~dlE~~vr~~lk~~   60 (85)
T TIGR02949         7 TDCAEVRLDHLYEFLDGEMTEDDAERLRRHLEACPECLEEYDLEQAVRKLLKRC   60 (85)
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCHHHHHHHCHHHHHHHHHHHH
T ss_conf             784899999999985688988569999999863756688506889999999853


No 197
>PRK04323 hypothetical protein; Provisional
Probab=31.84  E-value=31  Score=13.80  Aligned_cols=16  Identities=44%  Similarity=0.582  Sum_probs=8.1

Q ss_pred             EEEECCCCCEEEEEEE
Q ss_conf             6896528960799999
Q gi|254780751|r    5 MLIDASHVEETRVVVL   20 (723)
Q Consensus         5 ~lI~~~~~~e~Rvav~   20 (723)
                      .|||+|++.-||.+++
T Consensus        42 ~lIDaT~GRkTRaVii   57 (91)
T PRK04323         42 KLIDATYGRKTRAVII   57 (91)
T ss_pred             CEEECCCCCEEEEEEE
T ss_conf             4787357960568999


No 198
>cd01888 eIF2_gamma eIF2-gamma (gamma subunit of initiation factor 2).  eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits.  The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit.  Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome.  The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B.  eIF2B is a heteropentamer, and the epsilon chain binds eIF2.  Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma.  It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role.  eIF2-gamma is found only in eukaryotes and archaea.  It is closely related to SelB, the sel
Probab=31.52  E-value=31  Score=13.76  Aligned_cols=72  Identities=21%  Similarity=0.234  Sum_probs=37.9

Q ss_pred             EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHH-CCCCEEE
Q ss_conf             069998237554445551147999999999999998731036863896033479888899999999997312-7872899
Q gi|254780751|r  378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKK-DRARVQV  456 (723)
Q Consensus       378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~-D~~~~~v  456 (723)
                      |+-+||.+-|-..     .+|  +-++    .+++.|-+.+|  ||+|-=||.-+.+...+.++.++..++. ....+.+
T Consensus       110 aiLvVdA~eG~~~-----~QT--~eH~----~l~~~lgv~~i--IV~vNKmDlv~~~~~~~~~~ei~~~l~~~~~~~~~i  176 (203)
T cd01888         110 ALLLIAANEPCPQ-----PQT--SEHL----AALEIMGLKHI--IIVQNKIDLVKEEQALENYEQIKKFVKGTIAENAPI  176 (203)
T ss_pred             EEEEEECCCCCCH-----HHH--HHHH----HHHHHCCCCCE--EEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf             6898643667750-----779--9999----99998499863--677507777886789999999999855216899859


Q ss_pred             EEECCC
Q ss_conf             860486
Q gi|254780751|r  457 GAISNF  462 (723)
Q Consensus       457 ~~it~l  462 (723)
                      .++|.+
T Consensus       177 IPiSA~  182 (203)
T cd01888         177 IPISAQ  182 (203)
T ss_pred             EEEECC
T ss_conf             991478


No 199
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=31.29  E-value=19  Score=15.26  Aligned_cols=15  Identities=27%  Similarity=0.585  Sum_probs=11.5

Q ss_pred             CCCCCCCCCEEEEEC
Q ss_conf             023675465378606
Q gi|254780751|r  481 TKVCTYCKGAGYIRS  495 (723)
Q Consensus       481 ~~~c~~c~g~g~~~~  495 (723)
                      ..+||.|+|+.+.+=
T Consensus         3 h~pCP~CGG~Drfrf   17 (37)
T smart00778        3 HGPCPNCGGSDRFRF   17 (37)
T ss_pred             CCCCCCCCCCCCEEE
T ss_conf             667886778655367


No 200
>PRK02362 ski2-like helicase; Provisional
Probab=31.05  E-value=32  Score=13.71  Aligned_cols=15  Identities=20%  Similarity=0.381  Sum_probs=6.2

Q ss_pred             CCCCCCCCCCCCEEE
Q ss_conf             101233457652344
Q gi|254780751|r  195 AVTTYLSLAGRYSVL  209 (723)
Q Consensus       195 ~lT~~isl~Gry~Vl  209 (723)
                      .|..-|.||-|-+|+
T Consensus       338 TLA~GVNLPAr~VIi  352 (736)
T PRK02362        338 TLAAGLNLPARRVII  352 (736)
T ss_pred             HHHCCCCCCEEEEEE
T ss_conf             665055785269998


No 201
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=30.45  E-value=32  Score=13.64  Aligned_cols=39  Identities=23%  Similarity=0.294  Sum_probs=34.0

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf             34604287879899783638823135327897713022213
Q gi|254780751|r   34 HKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI   74 (723)
Q Consensus        34 ~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei   74 (723)
                      .-..-+|++-.|+|.-|.+++  =+||||.--+|+||++++
T Consensus        59 ~YiP~~gD~VIG~I~~v~~~~--W~VDI~sp~~A~L~ls~~   97 (239)
T COG1097          59 RYIPEVGDVVIGKIIEVGPSG--WKVDIGSPYPALLSLSDF   97 (239)
T ss_pred             CCCCCCCCEEEEEEEEECCCC--EEEECCCCCCEEEEHHHH
T ss_conf             524888999999999971563--389728953237426662


No 202
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=30.36  E-value=19  Score=15.24  Aligned_cols=11  Identities=45%  Similarity=1.105  Sum_probs=6.5

Q ss_pred             CCCCCCCCEEE
Q ss_conf             23675465378
Q gi|254780751|r  482 KVCTYCKGAGY  492 (723)
Q Consensus       482 ~~c~~c~g~g~  492 (723)
                      .+||.|+|.-.
T Consensus         2 kpCPFCG~~~~   12 (53)
T TIGR03655         2 KPCPFCGGADV   12 (53)
T ss_pred             CCCCCCCCCHH
T ss_conf             88887897531


No 203
>COG1411 Uncharacterized protein related to proFAR isomerase (HisA) [General function prediction only]
Probab=30.33  E-value=33  Score=13.63  Aligned_cols=48  Identities=33%  Similarity=0.392  Sum_probs=36.5

Q ss_pred             CEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHH
Q ss_conf             8069998237554445551147999999999999998731036863896033479888
Q gi|254780751|r  377 EALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKK  434 (723)
Q Consensus       377 EALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~  434 (723)
                      .+-+++|||-|+--+.          ++|---|+.|-|--|..-|+||+|.=-.-..+
T Consensus       119 r~vvslD~k~~~Ll~~----------~~ed~le~Vk~l~~~~~~~lIvLDi~aVGt~~  166 (229)
T COG1411         119 RIVVSLDVKGGELLGP----------WLEDFLETVKDLNYRRDPGLIVLDIGAVGTKS  166 (229)
T ss_pred             CEEEEEECCCCEECCC----------CCHHHHHHHHHHHCCCCCCEEEEECCCCCCCC
T ss_conf             6699996478842377----------71048999998752578884999755433466


No 204
>COG3634 AhpF Alkyl hydroperoxide reductase, large subunit [Posttranslational modification, protein turnover, chaperones]
Probab=30.31  E-value=18  Score=15.37  Aligned_cols=125  Identities=18%  Similarity=0.196  Sum_probs=54.0

Q ss_pred             HHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEE----EEE
Q ss_conf             8752376631111035320366788898763101211220134420356776999999984222143678649----983
Q gi|254780751|r  299 IRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYV----IIN  374 (723)
Q Consensus       299 ird~~~~~~~~i~vd~~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~l----vIe  374 (723)
                      +....+..+.-.-+|+.--..++..---+..|.....-+.+.     --+..|++-+.++-       +|+--    -+.
T Consensus       140 ~msvlNp~I~H~~IdGa~Fq~Evear~IMaVPtvflnGe~fg-----~GRmtleeilaki~-------~gaa~~~ae~~~  207 (520)
T COG3634         140 LMSVLNPRIKHTAIDGALFQDEVEARNIMAVPTVFLNGEEFG-----QGRMTLEEILAKID-------TGAAKRDAEEFN  207 (520)
T ss_pred             HHHHCCCCCEEEEECCHHHHHHHHHCCCEECCEEEECCHHHC-----CCCEEHHHHHHHHC-------CCCCCCCHHHHH
T ss_conf             887608873367752166676787545100444888511214-----65105999999743-------776644667751


Q ss_pred             CCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHH-----HHHHCCCCEEE-----EECCCCCCHHHHHHHHHHHH
Q ss_conf             288069998237554445551147999999999999998-----73103686389-----60334798888999999999
Q gi|254780751|r  375 QTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQ-----LRLRDLAGLIV-----VDFIDMEEKKNNRSVEKKLK  444 (723)
Q Consensus       375 ~TEALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQ-----lRLRnlgGiIv-----IDFIdM~~~~~~~~v~~~l~  444 (723)
                      --+|.-+.=|-.|-.-.             .||.-.||-     |----.||.++     =.||....-+.. ++...|.
T Consensus       208 ~k~~yDVLvVGgGPAga-------------aAAIYaARKGiRTGl~aerfGGQvldT~~IENfIsv~~teGp-kl~~ale  273 (520)
T COG3634         208 AKDAYDVLVVGGGPAGA-------------AAAIYAARKGIRTGLVAERFGGQVLDTMGIENFISVPETEGP-KLAAALE  273 (520)
T ss_pred             CCCCCEEEEECCCCCHH-------------HHHHHHHHHCCHHHHHHHHHCCEECCCCCHHHEECCCCCCCH-HHHHHHH
T ss_conf             56883499986886316-------------789999861211100156518820000033330056545466-8999999


Q ss_pred             HHHHH
Q ss_conf             97312
Q gi|254780751|r  445 ESLKK  449 (723)
Q Consensus       445 ~~l~~  449 (723)
                      +.++.
T Consensus       274 ~Hv~~  278 (520)
T COG3634         274 AHVKQ  278 (520)
T ss_pred             HHHHH
T ss_conf             98764


No 205
>PRK07399 DNA polymerase III subunit delta'; Validated
Probab=30.19  E-value=33  Score=13.61  Aligned_cols=42  Identities=26%  Similarity=0.345  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHHHHCCCC---EEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             999999999873103686---389603347988889999999999
Q gi|254780751|r  404 LEAAEEIARQLRLRDLAG---LIVVDFIDMEEKKNNRSVEKKLKE  445 (723)
Q Consensus       404 leAA~EIaRQlRLRnlgG---iIvIDFIdM~~~~~~~~v~~~l~~  445 (723)
                      ++-.+++.+-+-++-..|   ++|||-+|+........+++.|.|
T Consensus       106 idqIR~l~~~l~~~p~~~~~kVvII~~ae~m~~~AaNaLLKtLEE  150 (314)
T PRK07399        106 LEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEE  150 (314)
T ss_pred             HHHHHHHHHHHCCCCCCCCCEEEEECCHHHCCHHHHHHHHHHHCC
T ss_conf             999999999973188568847999889787199999999986147


No 206
>cd04171 SelB SelB subfamily.  SelB is an elongation factor needed for the co-translational incorporation of selenocysteine.  Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin.  In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu).  It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons.  In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence).  The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation.  Archaeal and animal mechanisms of selenocysteine incorporation are more complex.  Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryo
Probab=30.04  E-value=33  Score=13.60  Aligned_cols=70  Identities=23%  Similarity=0.293  Sum_probs=43.0

Q ss_pred             EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC-CEEEEECCCCCCHHHHHHHHHHHHHHHHHCC-CCEE
Q ss_conf             0699982375544455511479999999999999987310368-6389603347988889999999999731278-7289
Q gi|254780751|r  378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLA-GLIVVDFIDMEEKKNNRSVEKKLKESLKKDR-ARVQ  455 (723)
Q Consensus       378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlg-GiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~-~~~~  455 (723)
                      ||.+||.+.|-.      ++|         .|+..-+++.++- .++|+-=+|+-+++....+.+.+++.++... ....
T Consensus        78 ~llVvda~~g~~------~q~---------~e~~~~~~~~~i~~~ivvlNK~D~v~~~~~~~~~~~i~~~l~~~~~~~~p  142 (164)
T cd04171          78 VLLVVAADEGIM------PQT---------REHLEILELLGIKRGLVVLTKADLVDEDWLELVEEEIRELLAGTFLADAP  142 (164)
T ss_pred             EEEEEECCCCCC------HHH---------HHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCE
T ss_conf             589986177888------889---------99999998738872787346342579789999999999999743999982


Q ss_pred             EEEECCC
Q ss_conf             9860486
Q gi|254780751|r  456 VGAISNF  462 (723)
Q Consensus       456 v~~it~l  462 (723)
                      +.++|.+
T Consensus       143 ii~iSA~  149 (164)
T cd04171         143 IFPVSAV  149 (164)
T ss_pred             EEEEECC
T ss_conf             9994698


No 207
>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=29.86  E-value=33  Score=13.58  Aligned_cols=39  Identities=21%  Similarity=0.130  Sum_probs=34.5

Q ss_pred             CCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC
Q ss_conf             013576999998730237999999998488799984787
Q gi|254780751|r  519 IIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE  557 (723)
Q Consensus       519 i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~  557 (723)
                      ..+.+|.....++.+.+-..|.+|++.+++.|.|.....
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 208
>PRK05783 hypothetical protein; Provisional
Probab=29.79  E-value=33  Score=13.57  Aligned_cols=17  Identities=29%  Similarity=0.462  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHHHC
Q ss_conf             99999999999873103
Q gi|254780751|r  402 TNLEAAEEIARQLRLRD  418 (723)
Q Consensus       402 tNleAA~EIaRQlRLRn  418 (723)
                      .-.+.+.+||.+|||=|
T Consensus        55 eA~~~v~~ic~~lrL~N   71 (84)
T PRK05783         55 EAQELALKLAKEMRLGN   71 (84)
T ss_pred             HHHHHHHHHHHHHHCCC
T ss_conf             99999999998620349


No 209
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=29.65  E-value=33  Score=13.55  Aligned_cols=91  Identities=19%  Similarity=0.156  Sum_probs=39.3

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEEC-------
Q ss_conf             3532036678889876310121122013442035677699999998422214367864998328806999823-------
Q gi|254780751|r  313 SGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVN-------  385 (723)
Q Consensus       313 d~~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVN-------  385 (723)
                      ...-.|.++...+....+...  -.+...-.+++..|.+-.+..         .+=|.|-|+-.|+-...|=+       
T Consensus       366 ~~rltY~~v~~~l~~~~~~~~--~~l~~~l~~~~~l~~~l~~~R---------~~rg~i~~~~~E~ki~~d~~~~~~~i~  434 (706)
T COG0557         366 AARLTYEEVQAILDGKEDDKY--APLLDSLLELLELAKILKKKR---------LSRGAIDFDTPEAKIVLDEEGRPVEIE  434 (706)
T ss_pred             HHHCCHHHHHHHHHCCCCCCC--CCCHHHHHHHHHHHHHHHHHH---------HHCCCCCCCCCCEEEEECCCCCCEEEE
T ss_conf             564479999998614553223--320588999999999999999---------868883557863158767888740688


Q ss_pred             CC-CCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             75-5444555114799999999999999873
Q gi|254780751|r  386 SG-RSTREHCIEDTALQTNLEAAEEIARQLR  415 (723)
Q Consensus       386 SG-~~~~~~~~e~t~l~tNleAA~EIaRQlR  415 (723)
                      -- +....+-+|+-.+..|..+|.- ..+..
T Consensus       435 ~~~r~~a~~lIee~Ml~AN~~vA~~-l~~~~  464 (706)
T COG0557         435 IRERLDAEKLIEEFMLLANETVAEH-LEKHK  464 (706)
T ss_pred             EECCCHHHHHHHHHHHHHHHHHHHH-HHHCC
T ss_conf             7305648989999999987999999-99708


No 210
>KOG3013 consensus
Probab=29.40  E-value=34  Score=13.53  Aligned_cols=152  Identities=14%  Similarity=0.165  Sum_probs=77.7

Q ss_pred             CEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98999996073346042878798997836388231353278977130222137121028988999999988863111110
Q gi|254780751|r   23 NRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEA  102 (723)
Q Consensus        23 g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~  102 (723)
                      ++|+-+.-=...-..-+|+|-.|||.-|-+-  -==||++...++.|.++-|+     +|+..--      +..+.+...
T Consensus        69 NkLi~V~plk~rY~pEvGDvVVgRV~eVq~K--RWkvd~nsk~d~vL~LsSvN-----LPGg~~R------Rk~~~DEl~  135 (301)
T KOG3013          69 NKLISVKPLKSRYAPEVGDVVVGRVIEVQQK--RWKVDLNSKQDAVLMLSSVN-----LPGGIQR------RKSEEDELQ  135 (301)
T ss_pred             CCEEEEEEHHHHCCCCCCCEEEEEEEEEECC--EEEEECCCCCCEEEEEECCC-----CCCHHHH------CCCHHHHHH
T ss_conf             4237886433203775577788876444023--35775166543378753024-----8861433------022356899


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEE
Q ss_conf             00000011122334443344542222334455433222234321122111211000012234444213310688857999
Q gi|254780751|r  103 VADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLV  182 (723)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilV  182 (723)
                      ..+-...||.....+-..-                     .++.-.              ...+.   ...=|-||-+||
T Consensus       136 MR~fl~egDLi~AEVQ~v~---------------------~dGs~s--------------LhTRS---~KYGKL~~G~lv  177 (301)
T KOG3013         136 MRSFLKEGDLIVAEVQNVF---------------------HDGSLS--------------LHTRS---LKYGKLGQGILV  177 (301)
T ss_pred             HHHHHHCCCEEHHHHHHHC---------------------CCCEEE--------------EEECC---HHCCCCCCCEEE
T ss_conf             9977550675317788761---------------------277378--------------77210---110651686599


Q ss_pred             EEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHH
Q ss_conf             84033323456410123345765234422788751242046886899
Q gi|254780751|r  183 QIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDR  229 (723)
Q Consensus       183 QV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r  229 (723)
                      ||----..   ..=|.+.+|||---|+.-.+++ +-+++.|++.++-
T Consensus       178 kVpp~Lvk---r~K~hfh~lp~g~~vIlG~NGy-IWv~~s~~~~~ee  220 (301)
T KOG3013         178 KVPPALVK---RSKTHFHNLPGGVDVILGCNGY-IWVGPSIKDQEEE  220 (301)
T ss_pred             EECHHHHH---HHHHHHCCCCCCEEEEEECCCE-EEECCCCCCCHHH
T ss_conf             71889962---5555530588870799824766-9950788860022


No 211
>KOG0950 consensus
Probab=28.54  E-value=35  Score=13.43  Aligned_cols=44  Identities=25%  Similarity=0.355  Sum_probs=30.5

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHH--HHCCCCEEEEEECC
Q ss_conf             368638960334798888999999999973--12787289986048
Q gi|254780751|r  418 DLAGLIVVDFIDMEEKKNNRSVEKKLKESL--KKDRARVQVGAISN  461 (723)
Q Consensus       418 nlgGiIvIDFIdM~~~~~~~~v~~~l~~~l--~~D~~~~~v~~it~  461 (723)
                      +.=|+||||=..|-.++++...++.|-..+  ..-.+-+|+.|||.
T Consensus       340 ~~~g~vvVdElhmi~d~~rg~~lE~~l~k~~y~~~~~~~~iIGMSA  385 (1008)
T KOG0950         340 DFLGMVVVDELHMIGDKGRGAILELLLAKILYENLETSVQIIGMSA  385 (1008)
T ss_pred             CCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHCCCCCEEEEEEEC
T ss_conf             3047289752246403563558999999999963256346765524


No 212
>COG1352 CheR Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]
Probab=28.24  E-value=31  Score=13.74  Aligned_cols=32  Identities=19%  Similarity=0.229  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCEEEEECCCEEE
Q ss_conf             76999999984222143678649983288069
Q gi|254780751|r  349 SGIEVQLDSLHQTEVTLPSRGYVIINQTEALV  380 (723)
Q Consensus       349 y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt  380 (723)
                      +.-+.|..-+-.=.=.|+.||+|+|-++|.+-
T Consensus       215 Fd~~~q~~il~~f~~~L~~gG~LflG~sE~~~  246 (268)
T COG1352         215 FDEETQERILRRFADSLKPGGLLFLGHSETIP  246 (268)
T ss_pred             ECHHHHHHHHHHHHHHHCCCCEEEECCCCCCC
T ss_conf             37899999999999974899789982676667


No 213
>KOG3558 consensus
Probab=28.16  E-value=35  Score=13.38  Aligned_cols=16  Identities=38%  Similarity=0.522  Sum_probs=11.9

Q ss_pred             CCCCEEEEECCCEEEEE
Q ss_conf             67864998328806999
Q gi|254780751|r  366 PSRGYVIINQTEALVSI  382 (723)
Q Consensus       366 ~sGG~lvIe~TEALt~I  382 (723)
                      ++|||+||+ |+|-|++
T Consensus       344 k~GGyvWlQ-TqATVi~  359 (768)
T KOG3558         344 KNGGYVWLQ-TQATVIY  359 (768)
T ss_pred             HCCCEEEEE-EEEEEEE
T ss_conf             449769998-6547985


No 214
>pfam08206 OB_RNB Ribonuclease B OB domain. This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.
Probab=27.94  E-value=32  Score=13.65  Aligned_cols=15  Identities=33%  Similarity=0.494  Sum_probs=10.8

Q ss_pred             CCCEEEEEEECCCCC
Q ss_conf             885799984033323
Q gi|254780751|r  176 NRQILLVQIVKEERG  190 (723)
Q Consensus       176 ~gq~ilVQV~ke~~~  190 (723)
                      -|+.|+|+|.+...+
T Consensus        34 ~GD~V~v~v~~~~~~   48 (58)
T pfam08206        34 HGDRVLVRITKGDRR   48 (58)
T ss_pred             CCCEEEEEEECCCCC
T ss_conf             999999999538889


No 215
>PRK01033 imidazole glycerol phosphate synthase subunit HisF; Provisional
Probab=27.78  E-value=36  Score=13.34  Aligned_cols=19  Identities=16%  Similarity=0.165  Sum_probs=9.4

Q ss_pred             HHHHHHHHHHCCCCEEEEE
Q ss_conf             9999987310368638960
Q gi|254780751|r  408 EEIARQLRLRDLAGLIVVD  426 (723)
Q Consensus       408 ~EIaRQlRLRnlgGiIvID  426 (723)
                      .+.++++.=.++|.||+-|
T Consensus       155 ~~~~~~~~~~g~geil~Td  173 (253)
T PRK01033        155 VEFAKQAEELGAGEIVLNS  173 (253)
T ss_pred             HHHHHHHHHCCCCEEEEEE
T ss_conf             9999998746977999987


No 216
>PRK09098 type III secretion system protein HrpB; Validated
Probab=27.77  E-value=36  Score=13.34  Aligned_cols=66  Identities=20%  Similarity=0.082  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEE
Q ss_conf             1468998878899973036431013576999998730237999999998488799984787788633897
Q gi|254780751|r  497 SSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIE  566 (723)
Q Consensus       497 ~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ie  566 (723)
                      ..+...+...++...  .....++|.|||+-.....+..-.....  ......|.|.+|+.|....+.++
T Consensus       133 ~aL~~ra~~~l~~~v--~~~~~l~VRVhPdD~d~ar~a~~~l~~~--~~~~~~i~Vv~D~~L~~G~CI~E  198 (229)
T PRK09098        133 AALFARAAQTLEGVL--DGASYLTVRVHPADLDAARRAFGALAAE--GGRNVPVEVVGDPRLAPGACVCE  198 (229)
T ss_pred             HHHHHHHHHHHHHHH--CCCCEEEEEECHHHHHHHHHHHHHHHHC--CCCCCCEEEECCCCCCCCCEEEE
T ss_conf             889999999999986--2466289998887799999989999864--69872137622787899986883


No 217
>TIGR02499 HrpE_YscL_not type III secretion apparatus protein, HrpE/YscL family; InterPro: IPR012842    This entry is related to IPR009335 from INTERPRO, but is broader. IPR009335 from INTERPRO describes HrpE-like proteins, components of bacterial type III secretion systems primarily in bacteria that infect plants. This entry also includes the homologous proteins of animal pathogens, such as YscL of Yersinia pestis. This entry excludes the related protein FliH of the bacterial flagellar apparatus (see IPR000563 from INTERPRO)..
Probab=27.75  E-value=36  Score=13.33  Aligned_cols=65  Identities=14%  Similarity=0.083  Sum_probs=44.0

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHH-----CCEEEEEECCCCCCCCEEEE
Q ss_conf             114689988788999730364310135769999987302379999999984-----88799984787788633897
Q gi|254780751|r  496 QSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARF-----GVSINVVIGIELADKLFYIE  566 (723)
Q Consensus       496 ~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~-----~~~I~i~~d~~l~~~~f~Ie  566 (723)
                      ...+...++|.+-.  .......++++|||+-..-+.    .+|.......     ...+.|.+|+.+.+..+.++
T Consensus       105 ~~~~~~~~lr~~~~--~~~~~~~~~l~vhP~~~~~~~----~~l~~~~~~~~~~~~~~~~~l~~D~~l~~g~~~l~  174 (183)
T TIGR02499       105 ESERLVRLLRQLLA--AVANQERLTLRVHPEQLDEVR----EALAELLALAPEFGLVGKWELEPDASLAPGACVLE  174 (183)
T ss_pred             HHHHHHHHHHHHHH--HHHCCCCCEEEECHHHHHHHH----HHHHHHHHHHCCCCCCCHHCCCCCHHHCCCCEEEE
T ss_conf             88999999999999--874457634676746799999----99998884202467421010276021078870675


No 218
>pfam08273 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase.
Probab=27.14  E-value=23  Score=14.72  Aligned_cols=14  Identities=29%  Similarity=0.693  Sum_probs=11.1

Q ss_pred             CCCCCCCCCEEEEE
Q ss_conf             02367546537860
Q gi|254780751|r  481 TKVCTYCKGAGYIR  494 (723)
Q Consensus       481 ~~~c~~c~g~g~~~  494 (723)
                      ..+||.|+|+.+.+
T Consensus         3 h~pCP~CGg~Drfr   16 (39)
T pfam08273         3 HGPCPNCGGSDRFR   16 (39)
T ss_pred             CCCCCCCCCCCCCE
T ss_conf             66777777857525


No 219
>TIGR01111 mtrA tetrahydromethanopterin S-methyltransferase, subunit A; InterPro: IPR005778    This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit A in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump.  5-methyl-5,6,7,8-tetrahydromethanopterin + 2-mercaptoethanesulphonate = 5,6,7,8-tetrahydromethanopterin + 2-(methylthio)ethanesulphonate.  Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0006814 sodium ion transport, 0005737 cytoplasm, 0012506 vesicle membrane.
Probab=26.84  E-value=31  Score=13.74  Aligned_cols=43  Identities=33%  Similarity=0.518  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHH-HHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             99999999999987-3103686389603347988889999999999731278728
Q gi|254780751|r  401 QTNLEAAEEIARQL-RLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARV  454 (723)
Q Consensus       401 ~tNleAA~EIaRQl-RLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~  454 (723)
                      .+|-||.+=-=+|| -        |||.||.   +|-.++.++.|+|+.||+-=.
T Consensus       121 N~n~eAveRF~~Q~Ve--------vV~LiD~---ED~g~I~~~vkEc~~KDPGAf  164 (246)
T TIGR01111       121 NINEEAVERFRKQIVE--------VVNLIDV---EDVGAITSKVKECVSKDPGAF  164 (246)
T ss_pred             CCCHHHHHHHHHHHHH--------HHCCCCC---CCHHHHHHHHHHHHCCCCCCC
T ss_conf             6876788998641310--------1111463---676789999885322786874


No 220
>pfam08800 VirE_N VirE N-terminal domain. This presumed domain is found at the N-terminus of VirE proteins.
Probab=26.78  E-value=37  Score=13.22  Aligned_cols=49  Identities=14%  Similarity=0.180  Sum_probs=29.3

Q ss_pred             HHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCC-CEEEEEECCCCEEEEEC
Q ss_conf             1036863896033479888899999999997312787-28998604861489851
Q gi|254780751|r  416 LRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRA-RVQVGAISNFGLLEMSR  469 (723)
Q Consensus       416 LRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~-~~~v~~it~lGLlEltR  469 (723)
                      |..-+|+|+|||=.+.. +   + +..++..+..|+. ...+...|.-||==+-|
T Consensus        27 l~~~sgli~lDiD~l~~-e---e-~~~~r~~l~~dp~t~~~FvSpSG~GvKi~V~   76 (136)
T pfam08800        27 MKAYNGLVCLDVDHLAK-E---E-LERVKQKAAALPYTVLAFISSSGRGVKIWVR   76 (136)
T ss_pred             HHHCCCEEEEEECCCCH-H---H-HHHHHHHHHCCCCEEEEEECCCCCEEEEEEE
T ss_conf             76368808998289998-9---9-9999999846994899998579987999999


No 221
>cd01887 IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily.  IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits.  As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states.  Eukaryotic IF2/eIF5Bs possess three characteristic segments, including a divergent N-terminal region followed by conserved central and C-terminal segments.  This core region is conserved among all known eukaryotic and archaeal IF2/eIF5Bs and eubacterial IF2s.
Probab=26.76  E-value=37  Score=13.22  Aligned_cols=69  Identities=17%  Similarity=0.197  Sum_probs=39.9

Q ss_pred             EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHH----HCCCC
Q ss_conf             06999823755444555114799999999999999873103686389603347988889999999999731----27872
Q gi|254780751|r  378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLK----KDRAR  453 (723)
Q Consensus       378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~----~D~~~  453 (723)
                      |+.+||...|-               .....|+..+++..++--++++--||..+ .+..++...+.+...    .....
T Consensus        77 ~ilvvda~~g~---------------~~~~~~~~~~l~~~~~p~ivviNKiD~~~-~~~~~v~~~l~~~~~~~~~~~~~~  140 (168)
T cd01887          77 AILVVAADDGV---------------MPQTIEAIKLAKAANVPFIVALNKIDKPN-ANPERVKNELSELGLQGEDEWGGD  140 (168)
T ss_pred             EEEEEECCCCC---------------CHHHHHHHHHHHHCCCCEEEEEECCCCCC-CCHHHHHHHHHHHHCCCHHHCCCC
T ss_conf             99998646675---------------45899999999876997899998930898-798999999999754524552898


Q ss_pred             EEEEEECCC
Q ss_conf             899860486
Q gi|254780751|r  454 VQVGAISNF  462 (723)
Q Consensus       454 ~~v~~it~l  462 (723)
                      ..+.++|.+
T Consensus       141 ~~iIpvSA~  149 (168)
T cd01887         141 VQIVPTSAK  149 (168)
T ss_pred             CEEEEEECC
T ss_conf             759999899


No 222
>PRK07085 diphosphate--fructose-6-phosphate 1-phosphotransferase; Provisional
Probab=26.55  E-value=38  Score=13.19  Aligned_cols=31  Identities=16%  Similarity=0.305  Sum_probs=16.8

Q ss_pred             EEEE-CCCCHHHHHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             2420-468868999999999863002587169985
Q gi|254780751|r  218 TISR-KITNPVDRKNLKEIARGLEVPAGMGVILRT  251 (723)
Q Consensus       218 ~iSr-ki~~~~~r~~l~~~~~~~~~~~~~G~IiRT  251 (723)
                      |.+| +|..++......+....+.+.   |++|=-
T Consensus       143 gs~r~ki~t~e~~~~~~~t~~~l~Ld---gLviiG  174 (557)
T PRK07085        143 GSGRTKIETEEQKEACLQTVKKLKLD---GLVIIG  174 (557)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCC---EEEEEC
T ss_conf             06865458999999999999985998---799979


No 223
>KOG0458 consensus
Probab=26.46  E-value=38  Score=13.18  Aligned_cols=83  Identities=22%  Similarity=0.251  Sum_probs=52.0

Q ss_pred             CEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE----ECCCCCCHHHHHHHHHHHHHHH----H
Q ss_conf             8069998237554445551147999999999999998731036863896----0334798888999999999973----1
Q gi|254780751|r  377 EALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVV----DFIDMEEKKNNRSVEKKLKESL----K  448 (723)
Q Consensus       377 EALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvI----DFIdM~~~~~~~~v~~~l~~~l----~  448 (723)
                      -|.-+||-|+|.|..+-.        +..-.+|+|+-||.-|+.-+||.    |-|+-.. .--.++-..|...|    .
T Consensus       281 ~avLvvd~s~~~FE~gfd--------~~gQtrEha~llr~Lgi~qlivaiNKmD~V~Wsq-~RF~eIk~~l~~fL~~~~g  351 (603)
T KOG0458         281 VAVLVVDASTGEFESGFD--------PGGQTREHALLLRSLGISQLIVAINKMDLVSWSQ-DRFEEIKNKLSSFLKESCG  351 (603)
T ss_pred             EEEEEEECCCCHHHHCCC--------CCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCH-HHHHHHHHHHHHHHHHHCC
T ss_conf             689999877543331348--------7986589999998749525888863010127538-8999999989999998528


Q ss_pred             HCCCCEEEEEECC---CCEEEEE
Q ss_conf             2787289986048---6148985
Q gi|254780751|r  449 KDRARVQVGAISN---FGLLEMS  468 (723)
Q Consensus       449 ~D~~~~~v~~it~---lGLlElt  468 (723)
                      ==..-+++.++|.   -+|....
T Consensus       352 f~es~v~FIPiSGl~GeNL~k~~  374 (603)
T KOG0458         352 FKESSVKFIPISGLSGENLIKIE  374 (603)
T ss_pred             CCCCCCCEEECCCCCCCCCCCCC
T ss_conf             50477656955465677621233


No 224
>PRK12564 carbamoyl phosphate synthase small subunit; Reviewed
Probab=26.37  E-value=38  Score=13.17  Aligned_cols=84  Identities=15%  Similarity=0.182  Sum_probs=52.5

Q ss_pred             CCCCCCCCCEEEC-CCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             2334576523442-278875124204688689999999998630025871699850455757999999999999999877
Q gi|254780751|r  198 TYLSLAGRYSVLM-PNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVR  276 (723)
Q Consensus       198 ~~isl~Gry~Vl~-P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~  276 (723)
                      |..|+.|.-+|++ |.-+. .|+..     ++       .. ...+.--|+|+|..+...+--.-...+...++      
T Consensus        44 TDPSY~gQIl~fTyP~IGN-yGv~~-----~d-------~E-S~~~~~~G~Iv~e~~~~~s~~~s~~sL~~~L~------  103 (355)
T PRK12564         44 TDPSYAGQIVTFTYPLIGN-YGVNR-----ED-------FE-SDRIHAKGLIVRELSRIPSNWRSEMSLDDYLK------  103 (355)
T ss_pred             CCCCCCCHHHEECCCCCCC-CCCCH-----HH-------HC-CCCCCEEEEEECCCCCCCCCCCCCCCHHHHHH------
T ss_conf             2877667300007767515-38894-----57-------15-56755106884146778884011069999999------


Q ss_pred             HHHCCCCCCCCCCCCCCHHHHHHHHHCCC
Q ss_conf             64201432212345645888888752376
Q gi|254780751|r  277 ELALNSVAPHLVYEEGNLIKRAIRDLYCK  305 (723)
Q Consensus       277 ~~~~~~~~p~li~~~~~~~~~~ird~~~~  305 (723)
                          ....|++-.-+--.+.+.||+.-.-
T Consensus       104 ----~~~IpgI~gVDTRaLtr~iR~~G~m  128 (355)
T PRK12564        104 ----EHGIPGISGIDTRALTRKLREKGAM  128 (355)
T ss_pred             ----HCCCCEEECCCHHHHHHHHHHCCCE
T ss_conf             ----7798428525389999999865980


No 225
>TIGR01523 ATPase-IID_K-Na potassium/sodium efflux P-type ATPase, fungal-type; InterPro: IPR006414   Initially described as a calcium efflux ATPase , more recent work has shown that the Schizosaccharomyces pombe CTA3 gene is in fact a potassium ion efflux pump . These sequences form the clade which represents the fungal P-type ATPases which are responsible for potassium and sodium efflux. The degree to which these pumps show preference for sodium or potassium varies. This group of ATPases has been classified by phylogentic analysis as type IID . ; GO: 0015662 ATPase activity coupled to transmembrane movement of ions phosphorylative mechanism, 0006812 cation transport, 0016021 integral to membrane.
Probab=26.03  E-value=29  Score=14.03  Aligned_cols=56  Identities=18%  Similarity=0.207  Sum_probs=32.4

Q ss_pred             CCHHHHHCCCCCCCCCEEE--------EECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf             3011210023675465378--------6061146899887889997303643101357699999
Q gi|254780751|r  474 SSVLESTTKVCTYCKGAGY--------IRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVL  529 (723)
Q Consensus       474 ~sl~e~~~~~c~~c~g~g~--------~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~  529 (723)
                      .+-.|...+.|....|+-.        ++..+|++.+-||-|--....-.........|-++|.
T Consensus       517 KGA~E~I~~~CS~~~G~~L~~~D~E~I~~~~~~L~~EGLRVL~lA~K~~~K~~~~~T~~R~~AE  580 (1001)
T TIGR01523       517 KGAVERILERCSSSYGSTLEDPDVELIIKNVESLAAEGLRVLALASKVIDKDDVNITLNRDVAE  580 (1001)
T ss_pred             CCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCHHH
T ss_conf             4057888865056788867654289999998886631255455664200021202356530100


No 226
>COG3585 MopI Molybdopterin-binding protein [Coenzyme metabolism]
Probab=25.91  E-value=39  Score=13.11  Aligned_cols=26  Identities=15%  Similarity=-0.022  Sum_probs=21.4

Q ss_pred             CCCEEEEEEEEECCCCCEEEEEECCC
Q ss_conf             28787989978363882313532789
Q gi|254780751|r   39 KGNIYLAKVTRVEPSLQAAFVDYGGN   64 (723)
Q Consensus        39 ~GnIY~G~V~~V~p~lqAAFVdiG~~   64 (723)
                      .-|+++|+|+.|++|+=-+-|++-.+
T Consensus         5 aRN~lKG~Vk~iv~G~Vnsev~iei~   30 (69)
T COG3585           5 ARNQLKGKVKEIVKGSVNSEVTIEIG   30 (69)
T ss_pred             HHHEECCEEEEEEECCCCEEEEEEEC
T ss_conf             24203518999998341018999808


No 227
>TIGR03598 GTPase_YsxC ribosome biogenesis GTP-binding protein YsxC/EngB. Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes.
Probab=25.58  E-value=39  Score=13.07  Aligned_cols=55  Identities=31%  Similarity=0.311  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCC
Q ss_conf             9999987310368638960334798888999999999973127872899860486
Q gi|254780751|r  408 EEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNF  462 (723)
Q Consensus       408 ~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~l  462 (723)
                      .+|+..|+-.+..=+||+-=+|.-+++.+.++++.+++.|..-.--..|..+|.+
T Consensus       119 ~~i~~~l~~~~kp~iivlNK~Dll~~~~~~~~~~~i~~~l~~~~~~~~v~~ISA~  173 (179)
T TIGR03598       119 LEMLEWLDERGIPVLIVLTKADKLKKSERNKQLKKIKKALKKDADDPSVQLFSSL  173 (179)
T ss_pred             HHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEECC
T ss_conf             9999999975998899997813069899999999999997336688948999799


No 228
>smart00322 KH K homology RNA-binding domain.
Probab=25.57  E-value=31  Score=13.82  Aligned_cols=40  Identities=25%  Similarity=0.243  Sum_probs=34.7

Q ss_pred             CCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC
Q ss_conf             1013576999998730237999999998488799984787
Q gi|254780751|r  518 NIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE  557 (723)
Q Consensus       518 ~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~  557 (723)
                      .+.+.+|.+...++.+.+-..+..|+..+++.|.+.....
T Consensus         4 ~~~i~vp~~~~g~iIG~~G~~i~~i~~~~~~~I~i~~~~~   43 (69)
T smart00322        4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS   43 (69)
T ss_pred             EEEEEECHHHCCEEECCCCCCHHHHHHHHCCEEEECCCCC
T ss_conf             9999989787685499998457999997288899779999


No 229
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=25.48  E-value=24  Score=14.51  Aligned_cols=19  Identities=16%  Similarity=0.457  Sum_probs=13.7

Q ss_pred             HHCCCCCCCCCEEEEECCH
Q ss_conf             1002367546537860611
Q gi|254780751|r  479 STTKVCTYCKGAGYIRSQS  497 (723)
Q Consensus       479 ~~~~~c~~c~g~g~~~~~~  497 (723)
                      ++.+.||.|+|.-.+-.+.
T Consensus        15 TLke~Cp~CG~~t~~~~Pp   33 (59)
T COG2260          15 TLKEKCPVCGGDTKVPHPP   33 (59)
T ss_pred             EECCCCCCCCCCCCCCCCC
T ss_conf             6113377888745467899


No 230
>TIGR01520 FruBisAldo_II_A fructose-bisphosphate aldolase, class II; InterPro: IPR006411   Members of this family are class II examples of the glycolytic enzyme fructose-bisphosphate aldolase (FBA). They represent one of two deeply split, architecturally distinct clades of the family that includes class II fructose-bisphosphate aldolases, tagatose-bisphosphate aldolases, and related uncharacterised proteins. This family is well-conserved and includes characterised FBA from Saccharomyces cerevisiae, Escherichia coli, and Corynebacterium glutamicum.; GO: 0004332 fructose-bisphosphate aldolase activity, 0006096 glycolysis.
Probab=25.44  E-value=17  Score=15.64  Aligned_cols=79  Identities=9%  Similarity=0.053  Sum_probs=53.8

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             21234564588888875237663111103532036678889876310121122013442035677699999998422214
Q gi|254780751|r  285 PHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVT  364 (723)
Q Consensus       285 p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~  364 (723)
                      -...|..++....-+++-....|.++-||.+--|..+.-.+..+ -.....|.--.+     .--+.|.=-.+.|+||||
T Consensus       267 ~fVFHGGSGSt~~Ei~ea~~yGVVKmN~DTDtQwA~~~Gi~~Y~-~~N~dyl~~~~G-----nP~g~~~PnKK~YDPRVW  340 (365)
T TIGR01520       267 FFVFHGGSGSTKQEIEEALSYGVVKMNVDTDTQWAYLEGILDYY-LNNEDYLQSQVG-----NPKGPEKPNKKFYDPRVW  340 (365)
T ss_pred             CEEEECCCCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHH-HHHHHHHCCCCC-----CCCCCCCCCCEEECCHHH
T ss_conf             41653775772899976533684788614311167764277665-310222026588-----888888898500376167


Q ss_pred             CCCCC
Q ss_conf             36786
Q gi|254780751|r  365 LPSRG  369 (723)
Q Consensus       365 L~sGG  369 (723)
                      |+-|=
T Consensus       341 lR~gE  345 (365)
T TIGR01520       341 LREGE  345 (365)
T ss_pred             HHHHH
T ss_conf             67642


No 231
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=25.43  E-value=38  Score=13.13  Aligned_cols=58  Identities=14%  Similarity=0.157  Sum_probs=28.8

Q ss_pred             HHHHHHHHHCCCCEEEEEE-----------------------CCCCEEEEECCCC-CCCHHHHHCCCCCCCCCEEEEECC
Q ss_conf             9999973127872899860-----------------------4861489851566-630112100236754653786061
Q gi|254780751|r  441 KKLKESLKKDRARVQVGAI-----------------------SNFGLLEMSRQRI-RSSVLESTTKVCTYCKGAGYIRSQ  496 (723)
Q Consensus       441 ~~l~~~l~~D~~~~~v~~i-----------------------t~lGLlEltRkR~-r~sl~e~~~~~c~~c~g~g~~~~~  496 (723)
                      -..+.|.+-|++-.-+.-+                       .++|.+-.-++-. -.....-+.+.||+|+|.-++-.+
T Consensus       193 ~vaR~AAkyd~~i~Plls~~~dhY~Rvfv~v~rga~~ad~~~e~~g~~~~c~~cg~~~~~~~~~~~~c~~Cg~~~~~~GP  272 (380)
T COG1867         193 YVARTAAKYDKAIEPLLSLSIDHYVRVFVEVRRGARRADKLLENLGYIYHCSRCGEIVGSFREVDEKCPHCGGKVHLAGP  272 (380)
T ss_pred             HHHHHHHHHCCCCEEEEEEEECEEEEEEEEECCCCHHHHHHHHHCCCEEECCCCCCEECCCCCCCCCCCCCCCCCEECCC
T ss_conf             99999986356613677735331899999981473057789975470788266410003555444557766652002257


Q ss_pred             HH
Q ss_conf             14
Q gi|254780751|r  497 SS  498 (723)
Q Consensus       497 ~~  498 (723)
                      -+
T Consensus       273 lW  274 (380)
T COG1867         273 LW  274 (380)
T ss_pred             CC
T ss_conf             41


No 232
>PRK06921 hypothetical protein; Provisional
Probab=25.27  E-value=35  Score=13.44  Aligned_cols=22  Identities=14%  Similarity=-0.063  Sum_probs=9.1

Q ss_pred             EECCHHHHHHHHHHHHHHHHCC
Q ss_conf             6061146899887889997303
Q gi|254780751|r  493 IRSQSSVALSILRSVEEYLLQY  514 (723)
Q Consensus       493 ~~~~~~~~~~~~r~i~~~~~~~  514 (723)
                      -+..++..-+++.-|..-....
T Consensus       193 e~~te~~~~~lf~iIN~Ry~~~  214 (265)
T PRK06921        193 PRATEWQIEQTYSVVNYRYLNH  214 (265)
T ss_pred             CCCCHHHHHHHHHHHHHHHHCC
T ss_conf             7898899999999999999769


No 233
>PRK13586 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional
Probab=25.13  E-value=40  Score=13.02  Aligned_cols=19  Identities=16%  Similarity=0.223  Sum_probs=10.9

Q ss_pred             HHHHHHHHHHCCCCEEEEE
Q ss_conf             9999987310368638960
Q gi|254780751|r  408 EEIARQLRLRDLAGLIVVD  426 (723)
Q Consensus       408 ~EIaRQlRLRnlgGiIvID  426 (723)
                      .+.+.++.-.+++++|+-|
T Consensus       148 ~~~i~~~~~~g~~~ii~Td  166 (231)
T PRK13586        148 EDAISHVNSLESLGVIFTY  166 (231)
T ss_pred             HHHHHHHHHCCCCEEEEEE
T ss_conf             9999999975998899976


No 234
>pfam04208 MtrA Tetrahydromethanopterin S-methyltransferase, subunit A. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump.
Probab=25.07  E-value=40  Score=13.01  Aligned_cols=56  Identities=27%  Similarity=0.334  Sum_probs=34.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             5544455511479999999999999987310368638960334798888999999999973127872
Q gi|254780751|r  387 GRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRAR  453 (723)
Q Consensus       387 G~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~  453 (723)
                      |+-+|....--..-.++.+|.+.--+|+-        +||.|+   .+|-..+..+.++|..+|+.-
T Consensus        99 ~rIiGa~GaiPfieNi~~~aV~rFq~qVe--------~vd~i~---~eD~~~I~a~I~ec~~kdPGa  154 (176)
T pfam04208        99 GRIIGAEGAIPYIENIPEEAVERFQQQVE--------LVDLID---VEDLDEITKKVRECVSKDPGA  154 (176)
T ss_pred             CCEECCCCCCCHHHHCCHHHHHHHHHHEE--------EEEEEC---CCCHHHHHHHHHHHHHCCCCC
T ss_conf             97816888863555099999999986467--------876426---778899999999998449987


No 235
>pfam05772 NinB NinB protein. The ninR region of phage lambda contains two recombination genes, orf (ninB) and rap (ninG), that have roles when the RecF and RecBCD recombination pathways of E. coli, respectively, operate on phage lambda.
Probab=25.05  E-value=34  Score=13.49  Aligned_cols=35  Identities=14%  Similarity=0.127  Sum_probs=20.9

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHH
Q ss_conf             86899999999986300258716998504557579
Q gi|254780751|r  225 NPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKI  259 (723)
Q Consensus       225 ~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~  259 (723)
                      ++..|.+....+..+.+....+++|+---..++.+
T Consensus         4 ~~~~r~~ai~~I~~lP~d~~kp~vV~i~~~~Rtl~   38 (127)
T pfam05772         4 SPQIKQNAIQAILQLPVDPKKPLVVTIKERTRSLD   38 (127)
T ss_pred             CHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHH
T ss_conf             88999999999993899899974899518988877


No 236
>PRK10611 chemotaxis methyltransferase CheR; Provisional
Probab=24.87  E-value=29  Score=13.98  Aligned_cols=21  Identities=14%  Similarity=0.317  Sum_probs=14.4

Q ss_pred             CCCCCCCEEEEECCCEEEEEE
Q ss_conf             143678649983288069998
Q gi|254780751|r  363 VTLPSRGYVIINQTEALVSID  383 (723)
Q Consensus       363 V~L~sGG~lvIe~TEALt~ID  383 (723)
                      -.|.-||||++-++|.|.-++
T Consensus       250 ~~L~pgG~L~lG~sEsl~~~~  270 (287)
T PRK10611        250 PLLKPDGLLFAGHSENFSQLS  270 (287)
T ss_pred             HHHCCCCEEEEECCCCCCCCC
T ss_conf             986899289983887778877


No 237
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=24.77  E-value=39  Score=13.11  Aligned_cols=61  Identities=25%  Similarity=0.352  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHH-----CCCCEEEEEECCCCEEEEECCC
Q ss_conf             9999998731036863896033479888899999999997312-----7872899860486148985156
Q gi|254780751|r  407 AEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKK-----DRARVQVGAISNFGLLEMSRQR  471 (723)
Q Consensus       407 A~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~-----D~~~~~v~~it~lGLlEltRkR  471 (723)
                      ..+|..++-+-+ |++|.  |.-- +.+---..+-+|+-.+.+     |+-.-.++.++.|-|.|-.-.-
T Consensus       375 ~~~l~~~~~~~~-gD~if--f~A~-~~~~~~~~lGalR~~l~~~l~li~~~~~~f~WVvDFPlfE~~ee~  440 (585)
T COG0173         375 LEELIERLGAED-GDIIF--FVAD-KKKVVNKALGALRLKLGKELGLIDKDQFKFLWVVDFPLFEWDEEE  440 (585)
T ss_pred             HHHHHHHHCCCC-CCEEE--EECC-CHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCC
T ss_conf             999999828777-88899--9669-488999988999999888738778343248999706766775345


No 238
>pfam03602 Cons_hypoth95 Conserved hypothetical protein 95.
Probab=24.63  E-value=41  Score=12.95  Aligned_cols=34  Identities=18%  Similarity=0.280  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCE
Q ss_conf             03567769999999842221436786499832880
Q gi|254780751|r  344 PIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEA  378 (723)
Q Consensus       344 ~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEA  378 (723)
                      |.|....++.-++.+. ..=||..||.||||.--.
T Consensus       121 PPY~~~~~~~~l~~l~-~~~~l~~~~iiiiE~~~~  154 (181)
T pfam03602       121 PPYAKGLIEEALELLA-EKGWLNPNALIVVETESD  154 (181)
T ss_pred             CCCCCHHHHHHHHHHH-HCCCCCCCEEEEEEECCC
T ss_conf             9754206999999999-666657980999996687


No 239
>COG1329 Transcriptional regulators, similar to M. xanthus CarD [Transcription]
Probab=24.35  E-value=41  Score=12.92  Aligned_cols=35  Identities=23%  Similarity=0.260  Sum_probs=20.1

Q ss_pred             CHHHHHHHHHCCCCCCE-EECCCCCHHHHHHHHHHH
Q ss_conf             58888887523766311-110353203667888987
Q gi|254780751|r  293 NLIKRAIRDLYCKDISE-IIVSGEKGYREAKDFMKL  327 (723)
Q Consensus       293 ~~~~~~ird~~~~~~~~-i~vd~~~~~~~~~~~~~~  327 (723)
                      .-+-.++||++..+-.. .-......|+.+..++..
T Consensus       104 ~~~AevvrdL~r~~~qr~l~~~Er~ll~~A~~~l~~  139 (166)
T COG1329         104 IDIAEVVRDLYRRDKQRELSYSERRLLEKALQILAG  139 (166)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             789999999998640558996899999999999999


No 240
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=24.15  E-value=25  Score=14.38  Aligned_cols=33  Identities=15%  Similarity=0.191  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCC
Q ss_conf             769999999842221436786499832880699982375
Q gi|254780751|r  349 SGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSG  387 (723)
Q Consensus       349 y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG  387 (723)
                      -.....++.+|+++=.+-||.-+      -+-++=|+||
T Consensus       420 ed~~~~ld~~l~ktw~~asg~~M------~i~a~a~DtG  452 (611)
T COG5525         420 EDWLLRLDAYLNKTWPHASGIDM------PISAVAVDTG  452 (611)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCC------EEEEEEEECC
T ss_conf             57899999998520656788723------1578898348


No 241
>pfam00313 CSD 'Cold-shock' DNA-binding domain.
Probab=23.64  E-value=43  Score=12.83  Aligned_cols=32  Identities=19%  Similarity=0.317  Sum_probs=25.5

Q ss_pred             EEEEEEECCCCCEEEEEEC-CCCCCCCCHHHCC
Q ss_conf             9899783638823135327-8977130222137
Q gi|254780751|r   44 LAKVTRVEPSLQAAFVDYG-GNRHGFLPFLEIH   75 (723)
Q Consensus        44 ~G~V~~V~p~lqAAFVdiG-~~k~gFL~~~ei~   75 (723)
                      .|+|+-.-+.-.=-||.-. .+..-|+|.++|.
T Consensus         2 tG~VK~f~~~kGfGFI~~~~~~~DiFvH~s~l~   34 (66)
T pfam00313         2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQ   34 (66)
T ss_pred             CEEEEEEECCCCEEEEEECCCCCEEEEEHHHHC
T ss_conf             489999959999699997899846999926812


No 242
>PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional
Probab=23.58  E-value=12  Score=16.61  Aligned_cols=27  Identities=26%  Similarity=0.555  Sum_probs=19.4

Q ss_pred             CCCCEEEEECCCCCCCHHHHHCCCCCCCCCE
Q ss_conf             4861489851566630112100236754653
Q gi|254780751|r  460 SNFGLLEMSRQRIRSSVLESTTKVCTYCKGA  490 (723)
Q Consensus       460 t~lGLlEltRkR~r~sl~e~~~~~c~~c~g~  490 (723)
                      +.||+||=+|-|+.    .+=+-+||-|+-|
T Consensus       501 l~f~iLQa~r~R~~----kTeyIsCPsCGRT  527 (613)
T PRK02048        501 TAFGILQAGRIRTS----KTEYISCPGCGRT  527 (613)
T ss_pred             HHHHHHHHHCCCCC----CCCEEECCCCCCC
T ss_conf             88888887574433----5627758987652


No 243
>pfam06075 DUF936 Plant protein of unknown function (DUF936). This family consists of several hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Probab=23.41  E-value=43  Score=12.80  Aligned_cols=44  Identities=34%  Similarity=0.555  Sum_probs=25.2

Q ss_pred             EEEEEEECCCCCEEEEEECCCCCCC-CCHHHC-CCCCCCCCHHHHHHHH
Q ss_conf             9899783638823135327897713-022213-7121028988999999
Q gi|254780751|r   44 LAKVTRVEPSLQAAFVDYGGNRHGF-LPFLEI-HPDYYQIPFSDRQALL   90 (723)
Q Consensus        44 ~G~V~~V~p~lqAAFVdiG~~k~gF-L~~~ei-~~~y~~ip~~d~~~l~   90 (723)
                      |=.|+.|+|.|-+.  |+=.+ ||| |-++|- |.-|-.+|.+|-+-+|
T Consensus        27 LLQV~sIVPALag~--dLwpn-~GFylKVSDSsHStYVSLp~e~~DLIL   72 (557)
T pfam06075        27 LLQVTSIVPALAGS--DLWPN-HGFFLKVSDSSHSTYVSLSDEDDDLIL   72 (557)
T ss_pred             CEEEEEEEECCCCC--CCCCC-CCEEEEECCCCCCEEEECCHHHCHHHH
T ss_conf             23665442124568--86777-845898526665346756622110322


No 244
>COG5615 Predicted integral membrane protein [Function unknown]
Probab=23.15  E-value=43  Score=12.76  Aligned_cols=51  Identities=18%  Similarity=0.178  Sum_probs=36.9

Q ss_pred             CCCCEEEEECC-------CCCCHHHHHHHHHHHHHHHH-HCCCCEEEEEECCCCE-EEEE
Q ss_conf             36863896033-------47988889999999999731-2787289986048614-8985
Q gi|254780751|r  418 DLAGLIVVDFI-------DMEEKKNNRSVEKKLKESLK-KDRARVQVGAISNFGL-LEMS  468 (723)
Q Consensus       418 nlgGiIvIDFI-------dM~~~~~~~~v~~~l~~~l~-~D~~~~~v~~it~lGL-lElt  468 (723)
                      =+||.+++|||       -|.++..+.+.+...-..|. ---+-+-+..+|.-++ .||.
T Consensus        20 wIGGs~f~w~IlrPas~ka~~~~s~~~~~lg~I~rrF~~wvwatV~il~vsGv~~g~~~~   79 (161)
T COG5615          20 WIGGSFFIWFILRPASYKALEDESRRTKILGIIGRRFGWWVWATVAILPVSGVYLGYEYI   79 (161)
T ss_pred             HCCCEEEEEEEECHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCEEEEEEE
T ss_conf             706412576775576666440879888899999988676784631157702432556773


No 245
>KOG0955 consensus
Probab=23.13  E-value=43  Score=12.76  Aligned_cols=38  Identities=24%  Similarity=0.176  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCC
Q ss_conf             776999999984222143678649983288069998237554
Q gi|254780751|r  348 RSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRS  389 (723)
Q Consensus       348 ~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~  389 (723)
                      .+.|-..-..++.=+-.|.||+|-++|+-|+    |||...+
T Consensus       598 y~~iik~pm~~~tm~~k~~s~~y~tle~iee----d~~l~~~  635 (1051)
T KOG0955         598 YIDIIKKPMDFFTMRLKLESGAYSTLEPIEE----DVNLIVS  635 (1051)
T ss_pred             HHHHHCCCCCHHHHHHHHHCCHHHHHHHHHH----HHHHHHH
T ss_conf             8887257542455422100200222667777----6656666


No 246
>PRK06443 chorismate mutase; Validated
Probab=22.78  E-value=44  Score=12.72  Aligned_cols=33  Identities=21%  Similarity=0.322  Sum_probs=22.3

Q ss_pred             HHHHHHCCCCCCCCCCEEEEECCC-EEEEEEECCCCCCC
Q ss_conf             999984222143678649983288-06999823755444
Q gi|254780751|r  354 QLDSLHQTEVTLPSRGYVIINQTE-ALVSIDVNSGRSTR  391 (723)
Q Consensus       354 ~i~~~~~~~V~L~sGG~lvIe~TE-ALt~IDVNSG~~~~  391 (723)
                      -++..++     .+||.+||---- --++||+|||--++
T Consensus       118 s~e~gcs-----~~ggh~v~g~~~~~d~ivdi~sg~~~k  151 (177)
T PRK06443        118 SIEEGCS-----KAGGHVVIGLPDKDDHIVDINSGFPVK  151 (177)
T ss_pred             HHHHHHH-----HCCCEEECCCCCCCCEEEECCCCCEEE
T ss_conf             8997640-----348708427999887278638996344


No 247
>pfam11314 DUF3117 Protein of unknown function (DUF3117). This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=22.67  E-value=44  Score=12.70  Aligned_cols=13  Identities=23%  Similarity=0.526  Sum_probs=6.6

Q ss_pred             CCCCCCCCEEEEE
Q ss_conf             2143678649983
Q gi|254780751|r  362 EVTLPSRGYVIIN  374 (723)
Q Consensus       362 ~V~L~sGG~lvIe  374 (723)
                      +|+|..||.||+|
T Consensus        22 RvPleGGGRLVvE   34 (51)
T pfam11314        22 RVPLEGGGRLVVE   34 (51)
T ss_pred             EEECCCCCEEEEE
T ss_conf             9751788379999


No 248
>KOG2268 consensus
Probab=22.67  E-value=15  Score=15.99  Aligned_cols=65  Identities=17%  Similarity=0.256  Sum_probs=39.2

Q ss_pred             HHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             99999984222143678649983288069998237554445551147999999999999998731036863896033479
Q gi|254780751|r  352 EVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDME  431 (723)
Q Consensus       352 e~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~  431 (723)
                      ..-.+.+..-.|.|-.-|+|--|--|==.                                  -+++=++|+||||--|.
T Consensus       205 ~~ly~~lm~~Iv~la~~GlIHgDFNEFNi----------------------------------mv~dd~~i~vIDFPQmv  250 (465)
T KOG2268         205 PTLYDDLMGLIVRLANHGLIHGDFNEFNI----------------------------------MVKDDDKIVVIDFPQMV  250 (465)
T ss_pred             HHHHHHHHHHHHHHHHCCCEECCCCHHEE----------------------------------EEECCCCEEEEECHHHH
T ss_conf             89999999999999875933225305416----------------------------------87148977996345750


Q ss_pred             CHHHHH----------HHHHHHHHHHHHC
Q ss_conf             888899----------9999999973127
Q gi|254780751|r  432 EKKNNR----------SVEKKLKESLKKD  450 (723)
Q Consensus       432 ~~~~~~----------~v~~~l~~~l~~D  450 (723)
                      +-.|..          -|...|+.-+.-.
T Consensus       251 S~sh~nA~~YFdRDv~Ci~~fFrKkf~YE  279 (465)
T KOG2268         251 STSHPNAEYYFDRDVECIRAFFRKKFGYE  279 (465)
T ss_pred             CCCCCCCCEEECCCHHHHHHHHHHHCCCC
T ss_conf             46788631000144899999999961888


No 249
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.    Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=22.35  E-value=34  Score=13.46  Aligned_cols=86  Identities=20%  Similarity=0.205  Sum_probs=47.3

Q ss_pred             EEEEEECCCCCCCCCCCHHHHHH-HH--HHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             69998237554445551147999-99--9999999998731036863896033479888899999999997312787289
Q gi|254780751|r  379 LVSIDVNSGRSTREHCIEDTALQ-TN--LEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQ  455 (723)
Q Consensus       379 Lt~IDVNSG~~~~~~~~e~t~l~-tN--leAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~  455 (723)
                      |==-||-+|..+|=+|+.+++-. .+  -|+..|-+--++.=+=||||=+= +||-. +    .-+.+++.|+.-..+..
T Consensus       321 LL~FevG~~~~~GLRnvvD~y~~~~d~v~E~~~~sve~v~~LG~GGlVyvs-~~yG~-e----~a~ei~~~L~~~Gv~A~  394 (1843)
T TIGR01054       321 LLGFEVGKGSDTGLRNVVDVYEEDEDGVKEKLLESVELVKKLGKGGLVYVS-IDYGK-E----KAEEIKEFLREHGVKAV  394 (1843)
T ss_pred             HCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEE-CCCCH-H----HHHHHHHHHHHCCCEEE
T ss_conf             527100576422332138851148884468899999999984794399971-22255-8----99999999985794799


Q ss_pred             EEEE-CCCCEEEEECC
Q ss_conf             9860-48614898515
Q gi|254780751|r  456 VGAI-SNFGLLEMSRQ  470 (723)
Q Consensus       456 v~~i-t~lGLlEltRk  470 (723)
                      .+-- ++.++++.=++
T Consensus       395 ~~~~~k~~~~~~~F~~  410 (1843)
T TIGR01054       395 AYHAKKPKEDLEKFAE  410 (1843)
T ss_pred             EEEECCCCCCHHHHHC
T ss_conf             9840377320346634


No 250
>cd00453 FTBP_aldolase_II Fructose/tagarose-bisphosphate aldolase class II. This family includes fructose-1,6-bisphosphate (FBP) and tagarose 1,6-bisphosphate (TBP) aldolases. FBP-aldolase is homodimeric and used in gluconeogenesis and glycolysis; the enzyme controls the condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to yield fructose-1,6-bisphosphate. TBP-aldolase is tetrameric and produces tagarose-1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as Na+. Although structurally similar, the class I aldolases use a different mechanism and are believed to have an independent evolutionary origin.
Probab=22.34  E-value=39  Score=13.10  Aligned_cols=16  Identities=31%  Similarity=0.241  Sum_probs=7.2

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999999999987
Q gi|254780751|r  399 ALQTNLEAAEEIARQL  414 (723)
Q Consensus       399 ~l~tNleAA~EIaRQl  414 (723)
                      .+-|+-|-|.+.+.++
T Consensus       178 ~~yTdPeea~~fv~~t  193 (340)
T cd00453         178 ALYTQPEDVDYAYTEL  193 (340)
T ss_pred             CCCCCHHHHHHHHHHH
T ss_conf             4558989999999986


No 251
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=22.29  E-value=23  Score=14.69  Aligned_cols=66  Identities=20%  Similarity=0.170  Sum_probs=35.0

Q ss_pred             CCCCCCCCCCCCCCCEEEC--CCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHH
Q ss_conf             5641012334576523442--2788751242046886899999999986300258716998504557579999
Q gi|254780751|r  192 KGAAVTTYLSLAGRYSVLM--PNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIK  262 (723)
Q Consensus       192 Kga~lT~~isl~Gry~Vl~--P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~  262 (723)
                      -.-||+|-.++-|.-+|+-  +.......+.+-.........+..++   ..|  .|+|+-|-.-|..+....
T Consensus       208 vd~RvStlP~~~GEkvVlRil~~~~~~l~l~~Lg~~~~~~~~~~~~~---~~p--~GliLvTGPTGSGKTTTL  275 (500)
T COG2804         208 VDFRVSTLPTFYGEKVVLRILDKDQVILDLEKLGMSPFQLARLLRLL---NRP--QGLILVTGPTGSGKTTTL  275 (500)
T ss_pred             EEEEEECCCCCCCCEEEEEEECCCCCCCCHHHHCCCHHHHHHHHHHH---HCC--CEEEEEECCCCCCHHHHH
T ss_conf             88999557887785789998333124688878389988999999997---289--708999689999889999


No 252
>PRK10767 chaperone protein DnaJ; Provisional
Probab=22.21  E-value=16  Score=15.87  Aligned_cols=43  Identities=14%  Similarity=0.259  Sum_probs=20.2

Q ss_pred             HHCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHH
Q ss_conf             1002367546537860611468998878899973036431013576999
Q gi|254780751|r  479 STTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDV  527 (723)
Q Consensus       479 ~~~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~v  527 (723)
                      .+..+|+.|+|+|.+....      +..-.-.......+.|.|.+|+-+
T Consensus       178 ~~~~~C~~C~G~G~~i~~~------C~~C~G~g~v~~~k~l~V~Ip~G~  220 (376)
T PRK10767        178 AVQQTCPHCQGRGTLIKDP------CNKCHGHGRVEKSKTLSVKIPAGV  220 (376)
T ss_pred             EEEEECCCCCCCCEEECCC------CCCCCCCEEEEEEEEEEEEECCCC
T ss_conf             8887368766575693266------664478537865447998737987


No 253
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=21.86  E-value=32  Score=13.66  Aligned_cols=11  Identities=27%  Similarity=0.640  Sum_probs=7.4

Q ss_pred             HHCCCCCCCCC
Q ss_conf             10023675465
Q gi|254780751|r  479 STTKVCTYCKG  489 (723)
Q Consensus       479 ~~~~~c~~c~g  489 (723)
                      ++..+||+|+-
T Consensus         1 mlLI~CP~Cg~   11 (97)
T COG4311           1 MLLIPCPYCGE   11 (97)
T ss_pred             CCEECCCCCCC
T ss_conf             95001898887


No 254
>TIGR01275 ACC_deam_rel pyridoxal phosphate-dependent enzymes, D-cysteine desulfhydrase family; InterPro: IPR005966    Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy .   PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic .   This entry represents a family of pyridoxal phosphate-dependent enzymes closely related to (and often designated as) 1-aminocyclopropane-1-carboxylate deaminase. However, the members of this family are less well conserved.; GO: 0003824 catalytic activity, 0030170 pyridoxal phosphate binding.
Probab=21.70  E-value=46  Score=12.57  Aligned_cols=21  Identities=43%  Similarity=0.616  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHHHHHC----CCCEEE
Q ss_conf             999999999873103----686389
Q gi|254780751|r  404 LEAAEEIARQLRLRD----LAGLIV  424 (723)
Q Consensus       404 leAA~EIaRQlRLRn----lgGiIv  424 (723)
                      .+||.||+.||-++.    +.-|+|
T Consensus       163 v~A~~Ei~~QLN~~~d~vkfd~iVv  187 (339)
T TIGR01275       163 VEAVLEIAEQLNLESDEVKFDSIVV  187 (339)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCEEE
T ss_conf             9999999986078866420152689


No 255
>cd04617 CBS_pair_4 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=21.62  E-value=46  Score=12.56  Aligned_cols=19  Identities=37%  Similarity=0.448  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHCCCCEEEEE
Q ss_conf             9999987310368638960
Q gi|254780751|r  408 EEIARQLRLRDLAGLIVVD  426 (723)
Q Consensus       408 ~EIaRQlRLRnlgGiIvID  426 (723)
                      .|.++++.-+|+|++.|+|
T Consensus        13 ~eA~~~M~~~~ig~l~VVD   31 (118)
T cd04617          13 YDAIVTLFLEDVGSLFVVD   31 (118)
T ss_pred             HHHHHHHHHHCCCEEEEEC
T ss_conf             9999999983998799984


No 256
>pfam01762 Galactosyl_T Galactosyltransferase. This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2.
Probab=21.33  E-value=47  Score=12.52  Aligned_cols=16  Identities=25%  Similarity=0.436  Sum_probs=13.3

Q ss_pred             CCCCCCEEEEECCHHH
Q ss_conf             6754653786061146
Q gi|254780751|r  484 CTYCKGAGYIRSQSSV  499 (723)
Q Consensus       484 c~~c~g~g~~~~~~~~  499 (723)
                      =|+|.|.|+|.|.+.+
T Consensus       145 P~Y~~G~~YvlS~d~v  160 (196)
T pfam01762       145 PPYASGPFYLLSRDAA  160 (196)
T ss_pred             CCCCCCCEEEECHHHH
T ss_conf             8789888888669999


No 257
>KOG3821 consensus
Probab=21.23  E-value=46  Score=12.56  Aligned_cols=26  Identities=19%  Similarity=0.489  Sum_probs=20.1

Q ss_pred             CCCCCCCCCEEEEECCHHHHHHHHHH
Q ss_conf             02367546537860611468998878
Q gi|254780751|r  481 TKVCTYCKGAGYIRSQSSVALSILRS  506 (723)
Q Consensus       481 ~~~c~~c~g~g~~~~~~~~~~~~~r~  506 (723)
                      ..-||+|.|.-.++----.+..++|-
T Consensus       253 M~yCp~CqGl~~~kPC~gYC~NVmrG  278 (563)
T KOG3821         253 MIYCPHCQGLPSVKPCYGYCLNVMRG  278 (563)
T ss_pred             HHCCHHCCCCCCCCCCHHHHHHHHHH
T ss_conf             84363105877668707899999988


No 258
>PRK08084 DNA replication initiation factor; Provisional
Probab=21.12  E-value=48  Score=12.49  Aligned_cols=109  Identities=13%  Similarity=0.069  Sum_probs=58.3

Q ss_pred             CEEEEECCCCCC--HHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCCCCEEEEEC-CH
Q ss_conf             638960334798--888999999999973127872899860486148985156663011210023675465378606-11
Q gi|254780751|r  421 GLIVVDFIDMEE--KKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRS-QS  497 (723)
Q Consensus       421 GiIvIDFIdM~~--~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c~g~g~~~~-~~  497 (723)
                      .+|+||=||.-.  .+-+..+...+-.+....+.++-+..=..-.-+.+.-.+++.-|.-.+.         -.+.. .+
T Consensus        99 dll~iDDi~~i~g~~~~ee~lF~l~N~~~~~g~~~ll~ts~~~P~~l~~~l~DL~SRl~~g~~---------~~i~~~dd  169 (235)
T PRK08084         99 SLVCIDNIECIAGDELWEMAIFDLYNRILESGKTRLLITGDRPPRQLNLGLPDLASRLDWGQI---------YKLQPLSD  169 (235)
T ss_pred             CEEEEECHHHHCCCHHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHCCCCCHHHHHHHHCCCE---------EEECCCCH
T ss_conf             989982745546997899999999999998489669996798824302312889999956972---------78559998


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             4689988788999730364310135769999987302379999999984
Q gi|254780751|r  498 SVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARF  546 (723)
Q Consensus       498 ~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~  546 (723)
                      ..-..+++.   .     +..--+.++.+|+.||++.-...+..++.-.
T Consensus       170 e~~~~iL~~---~-----a~~rgl~l~~~V~~yl~~~~~R~~~~L~~~l  210 (235)
T PRK08084        170 EEKLQALQL---R-----ARLRGFELPEDVGRFLLKRLDREMRTLFMTL  210 (235)
T ss_pred             HHHHHHHHH---H-----HHHCCCCCCHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             999999999---9-----9973999998999999986158899999999


No 259
>TIGR03572 WbuZ glycosyl amidation-associated protein WbuZ. This clade of sequences is highly similar to the HisF protein, but generally represents the second HisF homolog in the genome where the other is an authentic HisF observed in the context of a complete histidine biosynthesis operon. The similarity between these WbuZ sequences and true HisFs is such that often the closest match by BLAST of a WbuZ is a HisF. Only by making a multiple sequence alignment is the homology relationship among the WbuZ sequences made apparent. WbuZ genes are invariably observed in the presence of a homolog of the HisH protein (designated WbuY) and a proposed N-acetyl sugar amidotransferase designated in WbuX in E. coli, IfnA in P. aeriginosa and PseA in C. jejuni. Similarly, this trio of genes is invariably found in the context of saccharide biosynthesis loci. It has been shown that the WbuYZ homologs are not essential components of the activity expressed by WbuX, leading to the proposal that these to pr
Probab=21.05  E-value=48  Score=12.48  Aligned_cols=23  Identities=17%  Similarity=0.212  Sum_probs=10.8

Q ss_pred             HHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             99999999863002587169985
Q gi|254780751|r  229 RKNLKEIARGLEVPAGMGVILRT  251 (723)
Q Consensus       229 r~~l~~~~~~~~~~~~~G~IiRT  251 (723)
                      ...++++...+.+|-.+|==|||
T Consensus        63 ~~~I~~i~~~~~ipi~vGGGIrs   85 (232)
T TIGR03572        63 FELISNLAEECFMPLTVGGGIRS   85 (232)
T ss_pred             HHHHHHHHHHCCCCEEEEECEEE
T ss_conf             99999999972985899713303


No 260
>PRK01492 rnpA ribonuclease P; Reviewed
Probab=20.99  E-value=48  Score=12.47  Aligned_cols=68  Identities=15%  Similarity=0.274  Sum_probs=41.7

Q ss_pred             CCCCCCCCEEECCCCCCCCEEEECCCCHHH-----HHHHHHHHHHHH-------CCCCCEEEEEEECCCCCHHHHHHHHH
Q ss_conf             334576523442278875124204688689-----999999998630-------02587169985045575799999999
Q gi|254780751|r  199 YLSLAGRYSVLMPNTSKGETISRKITNPVD-----RKNLKEIARGLE-------VPAGMGVILRTAGASRTKIEIKRDFE  266 (723)
Q Consensus       199 ~isl~Gry~Vl~P~~~~~~~iSrki~~~~~-----r~~l~~~~~~~~-------~~~~~G~IiRT~a~~~~~~~l~~d~~  266 (723)
                      .+-++++|-.++     |+.||||+....-     .++.+.++..+.       ....|=+|.|-.+....-+.+..|+.
T Consensus        37 ~i~~~Sk~~~fl-----GikvSkKvsKKAvvRNkIKRrIRhliR~il~~~~l~a~k~a~Iiiprkgf~e~~f~hl~~Elk  111 (118)
T PRK01492         37 KIFLESKYNTFL-----GIKVSRKLNKKAVVRNKIKRRIRHLIRIIVSDSSLKAIKFAMIIIPRKGFEEINFSHLNYELS  111 (118)
T ss_pred             CCCCCCCCCCEE-----EEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHHHHH
T ss_conf             666765577334-----467415433789999999999999999984553146664489999638832312999999999


Q ss_pred             HHHHH
Q ss_conf             99999
Q gi|254780751|r  267 YLMRL  271 (723)
Q Consensus       267 ~L~~~  271 (723)
                      .++..
T Consensus       112 ~~l~~  116 (118)
T PRK01492        112 KIILR  116 (118)
T ss_pred             HHHHH
T ss_conf             99864


No 261
>PRK06835 DNA replication protein DnaC; Validated
Probab=20.82  E-value=30  Score=13.87  Aligned_cols=20  Identities=10%  Similarity=-0.094  Sum_probs=8.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999987764
Q gi|254780751|r  259 IEIKRDFEYLMRLWDNVREL  278 (723)
Q Consensus       259 ~~l~~d~~~L~~~w~~i~~~  278 (723)
                      +.|..++..|...-..+...
T Consensus        68 ~~lk~~i~~L~~~k~~LL~~   87 (330)
T PRK06835         68 ESLKEKITDLRVKKSELLVS   87 (330)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999998


No 262
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation.  Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=20.77  E-value=48  Score=12.44  Aligned_cols=24  Identities=21%  Similarity=0.433  Sum_probs=20.2

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf             428787989978363882313532
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDY   61 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdi   61 (723)
                      .-|.+|.|++..+++.|+.-.-|.
T Consensus        18 KnG~~y~G~L~~~d~~MN~~L~~v   41 (70)
T cd01721          18 KTGEVYRGKLIEAEDNMNCQLKDV   41 (70)
T ss_pred             CCCEEEEEEEEEEECCCCCEEEEE
T ss_conf             899499999988702367499899


No 263
>pfam01440 Gemini_AL2 Geminivirus AL2 protein. Geminiviruses are small, ssDNA-containing plant viruses. Geminiviruses contain three ORFs (designated AL1, AL2, and AL3) that overlap and are specified by multiple polycistronic mRNAs. The AL2 gene product transactivates expression of TGMV coat protein gene, and BR1 movement protein.
Probab=20.69  E-value=49  Score=12.43  Aligned_cols=14  Identities=21%  Similarity=0.330  Sum_probs=5.8

Q ss_pred             CCCCCCCCCCEEEE
Q ss_conf             22214367864998
Q gi|254780751|r  360 QTEVTLPSRGYVII  373 (723)
Q Consensus       360 ~~~V~L~sGG~lvI  373 (723)
                      .|+|+|++|-++.|
T Consensus        30 RRRIDL~CGCS~yi   43 (134)
T pfam01440        30 RRRIDLPCGCSYYI   43 (134)
T ss_pred             CCCCCCCCCCEEEE
T ss_conf             54233057886987


No 264
>TIGR02477 PFKA_PPi diphosphate--fructose-6-phosphate 1-phosphotransferase; InterPro: IPR011183    Diphosphate--fructose-6-phosphate 1-phosphotransferase catalyses the addition of phosphate from diphosphate (PPi) to fructose 6-phosphate to give fructose 1,6-bisphosphate (2.7.1.90 from EC). The enzyme is also known as pyrophosphate-dependent phosphofructokinase. The usage of PPi-dependent enzymes in glycolysis presumably frees up ATP for other processes . IPR012828 from INTERPRO represents the ATP-dependent 6-phosphofructokinase enzyme contained within Phosphofructokinase. This entry contains primarily bacterial, plant alpha, and plant beta sequences. These may be dimeric nonallosteric enzymes (bacteria) or allosteric heterotetramers (plants) .   For additional information please see , , , .; GO: 0005524 ATP binding, 0047334 diphosphate-fructose-6-phosphate 1-phosphotransferase activity, 0006096 glycolysis, 0005945 6-phosphofructokinase complex.
Probab=20.64  E-value=49  Score=12.43  Aligned_cols=193  Identities=20%  Similarity=0.197  Sum_probs=108.9

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCC-CCCCCCCCHHHHHHHHHHHHHHHHHHHH--H-HC
Q ss_conf             203567769999999842221436786499832880699982375-5444555114799999999999999873--1-03
Q gi|254780751|r  343 HPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSG-RSTREHCIEDTALQTNLEAAEEIARQLR--L-RD  418 (723)
Q Consensus       343 ~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG-~~~~~~~~e~t~l~tNleAA~EIaRQlR--L-Rn  418 (723)
                      +-+++.+.+=.+|+.+|...+.==|             -|+ -.+ +..=...+...+.+|=.--=..|..||-  | ||
T Consensus       318 EFIPEv~~L~~ELn~~L~~~~~~F~-------------~i~-~~~~~~~~~~kLS~~~~~~f~~LP~~I~~QLLnil~RD  383 (566)
T TIGR02477       318 EFIPEVQALIKELNNLLAQNVEEFS-------------KIK-FEGRKDLVKSKLSPESKALFESLPETIRKQLLNILDRD  383 (566)
T ss_pred             ECCHHHHHHHHHHHHHHHCCCCHHC-------------CCC-HHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHCCC
T ss_conf             2026688999999865404762001-------------467-78899999862688899997407867999998752679


Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EEEECCC-CEEEEECCCCCCCHHHHHCCCCCCCCCEEE----
Q ss_conf             6863896033479888899999999997312787289-9860486-148985156663011210023675465378----
Q gi|254780751|r  419 LAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQ-VGAISNF-GLLEMSRQRIRSSVLESTTKVCTYCKGAGY----  492 (723)
Q Consensus       419 lgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~-v~~it~l-GLlEltRkR~r~sl~e~~~~~c~~c~g~g~----  492 (723)
                      =-|-|=|==|.-. +==-..|..+|.+..++-.-|.. +.++++| |= |     -|-++-.  .-.|.||.+.|+    
T Consensus       384 pHGNv~VS~IeTE-KLLi~lV~~~l~~~~~~g~yK~~~F~a~~HFFGY-E-----GRca~PS--nFDs~YcY~LGy~A~~  454 (566)
T TIGR02477       384 PHGNVQVSQIETE-KLLIELVQTELAKRKKEGEYKGKKFSAVSHFFGY-E-----GRCAFPS--NFDSDYCYALGYTAAI  454 (566)
T ss_pred             CCCCEEEEEECHH-HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC-C-----HHCCCCC--CCCHHHHHHHHHHHHH
T ss_conf             9885374211278-9999999999999986366467777754666553-0-----1126775--3210343578999999


Q ss_pred             ---------EECCHHHH----------------HHHHHHHHH----HHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHH
Q ss_conf             ---------60611468----------------998878899----9730364310135769999987302379999999
Q gi|254780751|r  493 ---------IRSQSSVA----------------LSILRSVEE----YLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYE  543 (723)
Q Consensus       493 ---------~~~~~~~~----------------~~~~r~i~~----~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE  543 (723)
                               +-++..+.                |.+.|+--.    ...+.-.++-.|.++...-.++.++.-.|..+=-
T Consensus       455 Ll~~g~TGYm~~i~NL~~p~~eW~~gg~PLt~mMn~E~R~G~PGass~~~PVIkKa~Vdl~G~pFk~f~~~R~~WA~~~~  534 (566)
T TIGR02477       455 LLANGLTGYMSTIKNLTNPAEEWIAGGVPLTMMMNMERRHGEPGASSIMKPVIKKALVDLEGKPFKKFASNRDKWALEDL  534 (566)
T ss_pred             HHHCCCCEEEEEECCCCCCHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             99716760455500115761240147622444412565457987521366655665547875457899999999988605


Q ss_pred             HHHCCEEEEEECCCC
Q ss_conf             984887999847877
Q gi|254780751|r  544 ARFGVSINVVIGIEL  558 (723)
Q Consensus       544 ~~~~~~I~i~~d~~l  558 (723)
                      -+|-..|++.....+
T Consensus       535 Y~fPGPiQy~Gp~~v  549 (566)
T TIGR02477       535 YVFPGPIQYFGPEEV  549 (566)
T ss_pred             CCCCCCEEECCCCCC
T ss_conf             779886663275322


No 265
>TIGR01214 rmlD dTDP-4-dehydrorhamnose reductase; InterPro: IPR005913    dTDP-4-dehydrorhamnose reductase (1.1.1.133 from EC) catalyzes the last of 4 steps in making dTDP-rhamnose, a precursor of LPS molecules such as core antigen and O-antigen.  dTDP-6-deoxy-L-mannose + NADP+ = dTDP-4-dehydro-6-deoxy-L-mannose + NADPH  ; GO: 0008831 dTDP-4-dehydrorhamnose reductase activity, 0045226 extracellular polysaccharide biosynthetic process.
Probab=20.24  E-value=50  Score=12.37  Aligned_cols=13  Identities=31%  Similarity=0.345  Sum_probs=8.3

Q ss_pred             CCCCCEEEEEEEC
Q ss_conf             0258716998504
Q gi|254780751|r  241 VPAGMGVILRTAG  253 (723)
Q Consensus       241 ~~~~~G~IiRT~a  253 (723)
                      .++.-.+||||+-
T Consensus       153 ~~~e~~lIvRTsW  165 (317)
T TIGR01214       153 GPDENALIVRTSW  165 (317)
T ss_pred             CCCCCEEEEEEEE
T ss_conf             7998578898521


Done!