Query         gi|254780406|ref|YP_003064819.1| putative ribosomal large subunit pseudouridine synthase B [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 354
No_of_seqs    197 out of 4149
Neff          8.4 
Searched_HMMs 39220
Date          Sun May 29 16:19:50 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780406.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK10700 23S rRNA pseudouridyl 100.0       0       0  520.4  25.5  240   12-252     1-248 (291)
  2 PRK10475 23S rRNA pseudouridin 100.0       0       0  514.1  25.6  234   10-250     3-238 (290)
  3 COG1187 RsuA 16S rRNA uridine- 100.0       0       0  492.4  24.0  237   12-248     1-245 (248)
  4 PRK10839 16S rRNA pseudouridyl 100.0       0       0  474.7  22.2  227   14-244     1-230 (231)
  5 PRK11394 23S rRNA pseudouridin 100.0       0       0  360.3  14.7  167   70-238    26-207 (207)
  6 cd02556 PseudoU_synth_RluB Pse 100.0       0       0  348.1  14.4  165   74-238     1-167 (167)
  7 TIGR00093 TIGR00093 conserved  100.0       0       0  343.0  12.1  160   79-238     1-185 (185)
  8 cd02553 PseudoU_synth_RsuA Pse 100.0       0       0  339.3  14.1  163   74-241     1-167 (167)
  9 cd02555 PSSA_1 PSSA_1: Pseudou 100.0       0       0  337.3  14.1  165   72-240     3-175 (177)
 10 cd02554 PseudoU_synth_RluF Pse 100.0       0       0  332.9  14.9  164   74-243     1-164 (164)
 11 cd02566 PseudoU_synth_RluE Pse 100.0       0       0  310.7  13.5  152   75-228     1-168 (168)
 12 cd02870 PseudoU_synth_RsuA_lik 100.0 8.7E-39 2.2E-43  264.1  11.2  146   75-220     1-146 (146)
 13 TIGR00005 rluA_subfam pseudour 100.0 8.3E-32 2.1E-36  220.2  10.6  212    9-222     1-262 (337)
 14 PRK11180 rluD 23S rRNA pseudou 100.0 3.8E-31 9.7E-36  216.0   9.7  215    6-222    10-255 (325)
 15 COG0564 RluA Pseudouridylate s 100.0 3.6E-30 9.2E-35  209.8  11.9  216    5-223     4-252 (289)
 16 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 8.1E-31 2.1E-35  213.9   8.5  146   75-220     1-154 (154)
 17 PRK11025 23S rRNA pseudouridyl 100.0   1E-29 2.6E-34  207.0   8.7  215    6-224    12-265 (317)
 18 cd02558 PSRA_1 PSRA_1: Pseudou  99.9 6.6E-24 1.7E-28  170.4   7.5  183   39-224     3-209 (246)
 19 pfam00849 PseudoU_synth_2 RNA   99.8 2.2E-20 5.7E-25  148.2   4.5  133   75-207     1-151 (151)
 20 cd02557 PseudoU_synth_ScRIB2 P  99.8 3.5E-19 8.9E-24  140.6   5.2  154   69-224    19-189 (213)
 21 PRK11112 tRNA pseudouridine sy  99.8 2.7E-19   7E-24  141.3   3.8  155   69-225     5-186 (257)
 22 PRK10158 23S rRNA/tRNA pseudou  99.8   1E-18 2.6E-23  137.8   5.7  152   69-222    17-183 (219)
 23 KOG1919 consensus               99.7 2.7E-17   7E-22  128.7  10.0  204   16-222    46-282 (371)
 24 cd02563 PseudoU_synth_TruC tRN  99.7 2.9E-18 7.4E-23  134.8   4.6  154   69-224     4-184 (223)
 25 cd02869 PseudoU_synth_RluCD_li  99.7 3.4E-17 8.7E-22  128.1   4.3  149   75-225     1-168 (185)
 26 TIGR01621 RluA-like pseudourid  99.4 2.1E-13 5.2E-18  104.3   2.8  140   70-214     6-161 (222)
 27 cd00165 S4 S4/Hsp/ tRNA synthe  99.1 2.8E-10 7.1E-15   84.6   6.2   66   14-79      1-70  (70)
 28 smart00363 S4 S4 RNA-binding d  99.0 6.5E-10 1.7E-14   82.3   6.0   55   14-68      1-56  (60)
 29 pfam01479 S4 S4 domain. The S4  98.9 2.9E-09 7.4E-14   78.2   4.5   47   14-60      1-48  (48)
 30 COG1188 Ribosome-associated he  98.5 2.3E-07   6E-12   66.2   5.3   51   11-62      6-57  (100)
 31 TIGR03069 PS_II_S4 photosystem  98.5 3.2E-07 8.1E-12   65.3   5.6   53   12-64    182-234 (257)
 32 COG1189 Predicted rRNA methyla  98.5 4.8E-07 1.2E-11   64.2   6.3   55   12-66      1-56  (245)
 33 TIGR01017 rpsD_bact ribosomal   98.4 3.3E-07 8.5E-12   65.2   3.6   53   14-66    100-153 (217)
 34 COG0522 RpsD Ribosomal protein  98.3 1.7E-06 4.4E-11   60.7   5.9   56   14-69     94-150 (205)
 35 COG2302 Uncharacterized conser  98.2 1.7E-06 4.2E-11   60.8   4.7   58    7-64    174-231 (257)
 36 PRK04270 H/ACA RNA-protein com  98.2 4.4E-06 1.1E-10   58.1   6.1  152   66-227    15-188 (300)
 37 PRK12565 30S ribosomal protein  98.2 4.4E-06 1.1E-10   58.1   5.8   53   14-66     88-141 (197)
 38 PRK10348 ribosome-associated h  98.1 3.7E-06 9.4E-11   58.6   5.0   56    8-64      3-59  (133)
 39 PRK04099 truB tRNA pseudouridi  98.1 1.5E-05 3.9E-10   54.7   8.1  144   74-227     3-202 (272)
 40 CHL00113 rps4 ribosomal protei  98.1 4.5E-06 1.2E-10   58.1   4.6   53   14-66     89-142 (201)
 41 cd02868 PseudoU_synth_hTruB2_l  98.1 1.5E-05 3.8E-10   54.8   7.0  156   75-233     2-217 (226)
 42 PRK00020 truB tRNA pseudouridi  98.1 8.3E-06 2.1E-10   56.4   5.6  156   73-245    10-224 (244)
 43 TIGR00478 tly hemolysin A; Int  98.0 6.4E-06 1.6E-10   57.1   4.4   53   15-67      1-54  (240)
 44 PRK00989 truB tRNA pseudouridi  98.0 3.4E-05 8.7E-10   52.5   7.9  146   73-227     9-209 (235)
 45 PRK05327 rpsD 30S ribosomal pr  98.0 8.9E-06 2.3E-10   56.2   4.7   53   14-66     92-145 (201)
 46 PRK02193 truB tRNA pseudouridi  98.0 3.4E-05 8.6E-10   52.6   7.3  155   75-243     2-215 (279)
 47 PRK01851 truB tRNA pseudouridi  98.0 4.3E-05 1.1E-09   51.9   7.7  151   73-233    17-224 (310)
 48 cd02572 PseudoU_synth_hDyskeri  97.9 6.3E-05 1.6E-09   50.9   8.3  144   74-227     3-170 (182)
 49 PRK05033 truB tRNA pseudouridi  97.9 4.5E-05 1.1E-09   51.8   7.3  145   73-227    12-212 (314)
 50 PRK00130 truB tRNA pseudouridi  97.9   5E-05 1.3E-09   51.5   7.4  143   74-227     3-202 (289)
 51 PRK04642 truB tRNA pseudouridi  97.9 6.4E-05 1.6E-09   50.8   7.4  146   72-227     9-211 (300)
 52 cd02573 PseudoU_synth_EcTruB P  97.9 5.3E-05 1.3E-09   51.3   6.5  143   75-227     2-203 (277)
 53 PRK11507 hypothetical protein;  97.8 4.2E-05 1.1E-09   51.9   5.5   62    8-69      6-68  (70)
 54 PRK01528 truB tRNA pseudouridi  97.8 7.9E-05   2E-09   50.2   6.7  145   73-227     3-205 (293)
 55 PRK03287 truB tRNA pseudouridi  97.8 0.00013 3.3E-09   48.8   7.7  149   71-227     7-214 (298)
 56 cd00506 PseudoU_synth_TruB_lik  97.8 9.6E-05 2.5E-09   49.7   6.9  143   75-227     2-203 (210)
 57 PRK05389 truB tRNA pseudouridi  97.6 0.00021 5.3E-09   47.6   6.9  151   73-233    13-221 (305)
 58 PRK02484 truB tRNA pseudouridi  97.6 0.00027 6.8E-09   46.9   6.7  144   74-227     4-210 (293)
 59 PRK01550 truB tRNA pseudouridi  97.6 0.00032 8.2E-09   46.4   6.9  145   74-227     3-210 (307)
 60 PRK02755 truB tRNA pseudouridi  97.6 0.00059 1.5E-08   44.7   8.2  144   75-227     4-205 (291)
 61 PRK13354 tyrosyl-tRNA syntheta  97.5 0.00047 1.2E-08   45.3   7.5   48   11-58    339-387 (405)
 62 COG2501 S4-like RNA binding pr  97.4 0.00049 1.3E-08   45.2   5.8   63    7-69      5-68  (73)
 63 PRK05912 tyrosyl-tRNA syntheta  97.4 0.00044 1.1E-08   45.5   5.5   39   16-54    337-376 (402)
 64 cd01291 PseudoU_synth PseudoU_  97.1 0.00036 9.2E-09   46.1   2.4   86   79-209     2-87  (87)
 65 PRK04051 rps4p 30S ribosomal p  97.0  0.0018 4.6E-08   41.7   5.9   55   14-68    103-161 (177)
 66 TIGR02988 YaaA_near_RecF S4 do  96.9  0.0017 4.5E-08   41.8   5.0   55   10-64      5-60  (60)
 67 COG0130 TruB Pseudouridine syn  96.9  0.0011 2.8E-08   43.0   3.8  144   74-227    16-184 (271)
 68 cd02867 PseudoU_synth_TruB_4 P  96.8  0.0045 1.2E-07   39.2   6.5  151   75-227     2-234 (312)
 69 PTZ00155 40S ribosomal protein  96.7  0.0027 6.8E-08   40.6   4.6   54   14-67    107-164 (188)
 70 TIGR00425 CBF5 rRNA pseudourid  96.2   0.036 9.1E-07   33.5   7.8  166   70-245    31-231 (326)
 71 PTZ00118 40S ribosomal protein  96.0   0.092 2.3E-06   30.9   9.0  124   12-150    40-165 (262)
 72 TIGR01018 rpsD_arch ribosomal   95.7  0.0069 1.8E-07   38.0   2.3   50   14-63    112-164 (170)
 73 PRK04313 30S ribosomal protein  94.9   0.062 1.6E-06   32.0   5.2   53   12-64     36-90  (237)
 74 PTZ00223 40S ribosomal protein  94.8   0.085 2.2E-06   31.1   5.7   74   12-90     37-112 (273)
 75 COG1471 RPS4A Ribosomal protei  93.9    0.24 6.1E-06   28.3   6.3   37   27-63     56-92  (241)
 76 KOG2559 consensus               86.8     1.5 3.9E-05   23.2   4.9   37  199-235   220-263 (318)
 77 KOG3301 consensus               84.6       1 2.7E-05   24.3   3.2   49   10-58     93-142 (183)
 78 KOG2623 consensus               83.6     2.9 7.4E-05   21.5   5.1   20  116-135   152-171 (467)
 79 pfam06353 DUF1062 Protein of u  81.7     2.1 5.3E-05   22.4   3.7   49   73-135     8-56  (142)
 80 COG4332 Uncharacterized protei  79.3     2.3 5.8E-05   22.1   3.3  120   56-214    31-155 (203)
 81 pfam01509 TruB_N TruB family p  77.6     1.6 4.1E-05   23.1   2.1   49  106-156     7-55  (149)
 82 TIGR00431 TruB tRNA pseudourid  77.5    0.49 1.2E-05   26.4  -0.6   70   75-151     4-73  (236)
 83 pfam05910 DUF868 Plant protein  74.8     3.2 8.2E-05   21.2   3.0   12  209-220   181-192 (272)
 84 TIGR02414 pepN_proteo aminopep  70.9       4  0.0001   20.6   2.8   62   39-101    55-128 (898)
 85 COG4043 Preprotein translocase  70.5     4.8 0.00012   20.1   3.1   43   26-68      6-48  (111)
 86 PRK10590 ATP-dependent RNA hel  67.7     9.4 0.00024   18.3   9.0   13  232-244   345-357 (457)
 87 KOG4655 consensus               66.3     3.8 9.8E-05   20.7   1.9   42   27-68    121-165 (181)
 88 pfam02824 TGS TGS domain. The   57.1      11 0.00029   17.8   3.0   22   40-62     37-58  (60)
 89 cd01668 TGS_RelA_SpoT TGS_RelA  57.0      11 0.00028   17.9   2.9   23   39-62     36-58  (60)
 90 PRK08857 para-aminobenzoate sy  55.8     6.6 0.00017   19.2   1.6   99  121-225     2-106 (192)
 91 pfam05949 DUF881 Bacterial pro  55.7      15 0.00039   16.9   4.0   31   39-69     61-91  (150)
 92 PRK08007 para-aminobenzoate sy  55.1     6.5 0.00017   19.3   1.5  100  121-225     2-106 (187)
 93 PRK02491 putative deoxyribonuc  53.7      15 0.00039   16.9   3.2   30  187-216   129-158 (328)
 94 pfam06668 ITI_HC_C Inter-alpha  49.0      20  0.0005   16.2   5.0   11   40-50      4-14  (188)
 95 cd01616 TGS The TGS domain, na  48.3      17 0.00044   16.6   2.7   22   40-62     37-58  (60)
 96 COG4909 PduC Propanediol dehyd  48.1      10 0.00027   18.0   1.6   57    1-68      1-57  (554)
 97 cd07973 Spt4 Transcription elo  47.5      21 0.00053   16.1   3.3   49  115-163    44-93  (98)
 98 PRK07649 para-aminobenzoate/an  43.4      11 0.00028   17.9   1.1   99  121-224     2-105 (195)
 99 PRK05670 anthranilate synthase  42.9      19 0.00047   16.4   2.2   98  121-223     2-104 (192)
100 PRK02967 nickel responsive reg  42.2      24  0.0006   15.7   2.7   34  188-225    95-128 (138)
101 KOG2529 consensus               39.6      19 0.00048   16.3   1.8  157   74-240    69-250 (395)
102 TIGR00601 rad23 UV excision re  39.0      10 0.00027   18.0   0.4   33  203-235    31-66  (453)
103 pfam02597 ThiS ThiS family. Th  38.3      29 0.00073   15.2   3.1   44   11-62     18-63  (70)
104 PRK06774 para-aminobenzoate sy  36.6      15 0.00038   17.0   0.9  100  121-225     2-106 (191)
105 COG2104 ThiS Sulfur transfer p  36.4      31 0.00079   15.0   2.9   42   13-62     17-61  (68)
106 PRK04460 nickel responsive reg  33.6      34 0.00087   14.7   2.6   20   14-33     17-36  (139)
107 PRK00630 nickel responsive reg  32.6      35  0.0009   14.6   2.6   24   14-37     20-44  (143)
108 PRK06065 acetyl-CoA acetyltran  30.7      31  0.0008   15.0   1.8   16   16-32     38-53  (393)
109 PRK11092 bifunctional (p)ppGpp  30.1      39   0.001   14.4   3.0   60  183-246   452-513 (702)
110 TIGR01687 moaD_arch MoaD famil  30.1      37 0.00095   14.5   2.1   26   37-62     57-86  (93)
111 TIGR01278 DPOR_BchB light-inde  29.9      38 0.00098   14.4   2.1   40  171-215   160-199 (562)
112 pfam05597 Phasin Poly(hydroxya  28.7      41  0.0011   14.2   3.2   24   13-36     93-116 (132)
113 cd00986 PDZ_LON_protease PDZ d  27.7      40   0.001   14.3   1.9   17   54-70     25-42  (79)
114 KOG3449 consensus               27.1      44  0.0011   14.0   2.1   17  197-213    19-35  (112)
115 PRK10872 relA GDP/GTP pyrophos  26.5      45  0.0012   14.0   3.3   20   70-89    305-324 (743)
116 pfam11685 DUF3281 Protein of u  26.0      46  0.0012   13.9   1.9   12  110-121   119-130 (269)
117 PRK06059 lipid-transfer protei  25.2      44  0.0011   14.1   1.7   18   16-34     31-48  (399)
118 PRK06488 sulfur carrier protei  25.2      48  0.0012   13.8   3.1   41   14-62     15-58  (65)
119 CHL00101 trpG anthranilate syn  25.2      36 0.00092   14.6   1.3   99  122-225     3-106 (190)
120 KOG2582 consensus               25.0      26 0.00067   15.4   0.6   20   75-94    182-201 (422)
121 PRK01002 nickel responsive reg  24.8      49  0.0012   13.8   2.6   20   14-33     17-36  (141)
122 PRK07855 lipid-transfer protei  24.4      48  0.0012   13.8   1.8   14  201-214   272-285 (386)
123 PRK08313 acetyl-CoA acetyltran  23.2      48  0.0012   13.8   1.6   17   17-34     34-50  (391)
124 PTZ00246 proteasome subunit al  22.6      53  0.0014   13.5   1.8   95  135-252   150-245 (253)
125 TIGR02542 B_forsyth_147 Bacter  22.5      37 0.00094   14.5   0.9  101  128-236    26-127 (154)
126 cd06555 ASCH_PF0470_like ASC-1  22.5      53  0.0014   13.5   1.7   34   31-64      9-42  (109)
127 TIGR01670 YrbI-phosphatas 3-de  21.2      44  0.0011   14.1   1.1   18  117-134    12-29  (154)
128 pfam10574 UPF0552 Uncharacteri  21.0      58  0.0015   13.3   5.2   95  148-245    19-120 (224)
129 KOG2553 consensus               21.0      58  0.0015   13.3   3.0   25  184-208   262-288 (416)
130 KOG0151 consensus               20.9      58  0.0015   13.3   2.9   24  221-244   719-745 (877)
131 pfam12471 GTP_CH_N GTP cyclohy  20.5      57  0.0015   13.3   1.5   15  156-170   137-151 (195)
132 PRK06365 acetyl-CoA acetyltran  20.4      59  0.0015   13.2   1.7   17   15-32     30-46  (415)

No 1  
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=100.00  E-value=0  Score=520.41  Aligned_cols=240  Identities=39%  Similarity=0.563  Sum_probs=222.1

Q ss_pred             CCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECC--CCEEEECCEECCCCCCE----EEEECCCCCEEE
Q ss_conf             734478899988687789999999869869999992406878079--99799999892255643----896027875156
Q gi|254780406|r   12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEVDGVPLRKAERT----RLWLYHKPIGLV   85 (354)
Q Consensus        12 ~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~--~d~v~vdg~~i~~~~~~----~~~~~~KP~g~~   85 (354)
                      ..||||||||++|+||||+||+||.+|+|+|||++++ ++.+|+.  +|.|+|||++|.+.+..    +||+||||.|++
T Consensus         1 m~eRL~K~LA~~G~~SRReae~lI~~GrV~VNG~v~~-lg~~v~~~~~~~V~vDG~~i~~~~~~~~~~~~l~l~KP~G~v   79 (291)
T PRK10700          1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAK-LGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGEL   79 (291)
T ss_pred             CHHHHHHHHHHCCCCHHHHHHHHHHCCEEEECCEECC-CCCEECCCCCCEEEECCEEEECCCCCCCCEEEEEEECCCEEE
T ss_conf             9179999999878943999999998694998999955-688265899988999999943245544301468998785775


Q ss_pred             ECCCCCCCCCCCCEEECCC-CCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             3144333364421011023-432002665543323202223676410001234457404775211245564678887400
Q gi|254780406|r   86 TTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG  164 (354)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~-~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g  164 (354)
                      ||..|+++++++|+.++.. ..+|++|||||+||||||||||||+|+|+|+||+++++|+|+|+|+++++++.++.|..|
T Consensus        80 ~T~~D~~~r~tV~dllp~~~~~rl~~VGRLD~dT~GLLLlTNDG~La~rL~hP~~~v~K~Y~V~v~g~i~~~~l~~l~~G  159 (291)
T PRK10700         80 CTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRG  159 (291)
T ss_pred             CCCCCCCCCCCHHHHCCCCCCCCEEEECCCCCCCCCCEEECCCHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHCC
T ss_conf             46677557983778463223664556305788887728983877999862488679877999998887999999999769


Q ss_pred             HHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEEC-CCCCCCCEEECCHHHHHH
Q ss_conf             0008767503430364026880799999951842899999998398686889758705451-875547488679999987
Q gi|254780406|r  165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE  243 (354)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l-~~L~~G~~r~l~~~e~~~  243 (354)
                      +.++|+.+.+..+.+....+.++|++|+|+|||||||||||+++|++|++|+||+||+|+| ++||+|+||+||.+||..
T Consensus       160 v~ledg~~~~~~i~~~~~~~~~~~~~i~L~EGrnrqIRRMf~~~G~~V~~LkRi~iG~i~L~~~Lp~G~wR~Lt~~Ev~~  239 (291)
T PRK10700        160 VQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNY  239 (291)
T ss_pred             CEECCCEEEEEEEEEECCCCCCEEEEEEEEECCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCCCEECCHHHHHH
T ss_conf             77678014679998844778857999999969688999999985997918899998776358999896771899999999


Q ss_pred             HHHHHHHHC
Q ss_conf             532100000
Q gi|254780406|r  244 QLGPHLLEE  252 (354)
Q Consensus       244 l~~~~~~~~  252 (354)
                      |..+.....
T Consensus       240 Lr~~v~l~~  248 (291)
T PRK10700        240 LRELVELPP  248 (291)
T ss_pred             HHHHCCCCC
T ss_conf             999819991


No 2  
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=100.00  E-value=0  Score=514.08  Aligned_cols=234  Identities=26%  Similarity=0.394  Sum_probs=216.9

Q ss_pred             CCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCC--CCEEEEECCCCCEEEEC
Q ss_conf             6773447889998868778999999986986999999240687807999799999892255--64389602787515631
Q gi|254780406|r   10 NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--ERTRLWLYHKPIGLVTT   87 (354)
Q Consensus        10 ~~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~--~~~~~~~~~KP~g~~~~   87 (354)
                      ..+++|||||||++|+||||+||+||.+|+|+|||++|+ ++++|+++|.|.|||+.|.+.  +...||+||||.|++||
T Consensus         3 ~~~~~RL~K~LA~~G~~SRReAe~lI~~GrV~VNGk~v~-~g~~V~~~D~V~vdg~~i~~~~~~~~~yi~lnKP~G~v~t   81 (290)
T PRK10475          3 PDSSTRLNKYISESGICSRREADRYIEQGNVFINGKRAT-IGDQVKPGDVVKVNGQLIEPREAEDLVLIALNKPVGIVST   81 (290)
T ss_pred             CCCCCHHHHHHHHCCCCHHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEECCEECCCCCCCCEEEEEEECCCCCCCC
T ss_conf             988614999998777835999999998597898999957-9888699998999998912336676399999589870677


Q ss_pred             CCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             44333364421011023432002665543323202223676410001234457404775211245564678887400000
Q gi|254780406|r   88 HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI  167 (354)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~  167 (354)
                      ..|. .+.+++++++. ..++++|||||+||+|||||||||+|+++|+||+++++|+|+|+|+++++++.++.|..|+.+
T Consensus        82 ~~d~-~r~ti~d~l~~-~~rl~pVGRLD~dSeGLLlLTNDG~l~~~l~hP~~~i~K~Y~V~v~g~i~~~~l~~l~~Gv~i  159 (290)
T PRK10475         82 TEDG-ERDNIVDFVNH-SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI  159 (290)
T ss_pred             CCCC-CCCCEEECCCC-CCCEEECCCCCCCCCCEEEECCCHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHCCCEE
T ss_conf             7667-89864641477-563505046687776759985987999987357678955999998985899999998589656


Q ss_pred             CCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHHHH
Q ss_conf             87675034303640268807999999518428999999983986868897587054518755474886799999875321
Q gi|254780406|r  168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP  247 (354)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~l~~~  247 (354)
                      +++.+.+|.+...    ..+|++|+|+||+||||||||+++|++|.+|+||+||+|.|++|++|+||+|+++||.+|++.
T Consensus       160 ~g~~~~~~~v~~~----~~~~~~i~L~EGknRqIRRm~~~~g~~V~~L~Ri~iG~i~L~~L~~G~wR~Lt~~Ei~~l~~~  235 (290)
T PRK10475        160 LGTVTKKCKVKKE----APFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL  235 (290)
T ss_pred             CCEECCEEEEEEC----CCCEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCCEECCHHHHHHHHHH
T ss_conf             8886011499964----897899999868049999999985997817899998887858989987158999999999976


Q ss_pred             HHH
Q ss_conf             000
Q gi|254780406|r  248 HLL  250 (354)
Q Consensus       248 ~~~  250 (354)
                      ...
T Consensus       236 ~~~  238 (290)
T PRK10475        236 IEN  238 (290)
T ss_pred             HHC
T ss_conf             534


No 3  
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=492.41  Aligned_cols=237  Identities=39%  Similarity=0.617  Sum_probs=220.6

Q ss_pred             CCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCC-CEEEECCEECCCCCCEEEEECCCCCEEEECCCC
Q ss_conf             7344788999886877899999998698699999924068780799-979999989225564389602787515631443
Q gi|254780406|r   12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSD   90 (354)
Q Consensus        12 ~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~-d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~   90 (354)
                      .++|||||||++|+||||+|++||++|+|+|||+++++++.+|+++ |.|.|||+++...+...|||||||.|++||..|
T Consensus         1 ~~~RL~K~La~~G~~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~llnKP~G~v~s~~D   80 (248)
T COG1187           1 DSMRLNKFLAEAGVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLLNKPRGYVSSTED   80 (248)
T ss_pred             CCCCHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEECCCCEEECCCCCEEEECCEEEECCCCCEEEEEECCCCEEECCCC
T ss_conf             95206899987477788999999973987889999224776727987689989988112666469999899876926668


Q ss_pred             CCCCCCCCEEECC---CCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             3336442101102---3432002665543323202223676410001234457404775211245564678887400000
Q gi|254780406|r   91 PDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI  167 (354)
Q Consensus        91 ~~~~~~~~~~~~~---~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~  167 (354)
                      +.+++|+++.++.   ...++++|||||+||||||||||||+|+|+|+||+++++|+|+|+|.++++++.++.|+.|+.+
T Consensus        81 ~~gr~tv~D~lp~~~~~~~~~~pvGRLD~dTeGLLLLTnDG~la~rL~~P~~~~~K~Y~v~v~g~~~~~~l~~l~~Gv~l  160 (248)
T COG1187          81 DEGRPTVFDLLPERLPRKKRLFPVGRLDKDTEGLLLLTNDGELAHRLMHPSSEVEKEYLVRVEGPVTEEDLEKLRKGVTL  160 (248)
T ss_pred             CCCCCEEEEECCCCCCCCCCEEECCCCCCCCEEEEEEECCHHHHHHHCCCCCCCCEEEEEEEECCCCHHHHHHHHCCCEE
T ss_conf             89981600025543466663334266577771279995787898875288889977999999258998999998578386


Q ss_pred             CCEEEECCC-EEEEECCC-CEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECCCC--CCCCEEECCHHHHHH
Q ss_conf             876750343-03640268-80799999951842899999998398686889758705451875--547488679999987
Q gi|254780406|r  168 QGICYGDMQ-VTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVSKKILRE  243 (354)
Q Consensus       168 ~~~~~~~~~-~~~~~~~~-~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~~L--~~G~~r~l~~~e~~~  243 (354)
                      +|+.+.|+. +.+..... .++|++|+|+|||||||||||+++|++|.+|+|++||+|.|++|  ++|+||+|+..|+..
T Consensus       161 ~d~~~~~~~~~~l~~~~~~~~s~~~itl~EGrnrQVRRm~~a~G~~V~~L~R~r~G~l~L~~L~l~~G~~R~L~~~E~~~  240 (248)
T COG1187         161 DDGETKPAKPASLEKEPGKNNSWLRITLTEGRNRQVRRMFEAVGLEVLRLKRIRIGPLSLGDLPLPPGEWRELTLEEIAQ  240 (248)
T ss_pred             CCCCCCCCEEEEEEECCCCCCEEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEEEEEECCCCCCCCCEEEECCHHHHHH
T ss_conf             67356601047898317887469999995784789999999849967489999870167289888882058998999999


Q ss_pred             HHHHH
Q ss_conf             53210
Q gi|254780406|r  244 QLGPH  248 (354)
Q Consensus       244 l~~~~  248 (354)
                      |....
T Consensus       241 l~~~~  245 (248)
T COG1187         241 LRKLV  245 (248)
T ss_pred             HHHHH
T ss_conf             99875


No 4  
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=100.00  E-value=0  Score=474.66  Aligned_cols=227  Identities=26%  Similarity=0.412  Sum_probs=208.2

Q ss_pred             HHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEECCCCCEEEECCCCCCC
Q ss_conf             44788999886877899999998698699999924068780799979999989225564389602787515631443333
Q gi|254780406|r   14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG   93 (354)
Q Consensus        14 ~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~~~~   93 (354)
                      ||||||||++|+||||+|++||.+|+|+|||++|++++++|+++|.|.|||+++.......||++|||+|++||..|+.+
T Consensus         1 mRL~K~La~~g~~SRR~ae~lI~~GrV~VNg~~v~~~~~~V~~~~~v~vdg~~i~~~~~~~y~~lnKP~G~v~s~~d~~~   80 (231)
T PRK10839          1 MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVKNAAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDH   80 (231)
T ss_pred             CCHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEECCCEECCCCCCEEEEEECCCCCCCCCCCCCC
T ss_conf             93789998878956999999998797999999914588084999869991958614668689999899875347889999


Q ss_pred             CCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEE--
Q ss_conf             644210110234320026655433232022236764100012344574047752112455646788874000008767--
Q gi|254780406|r   94 RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--  171 (354)
Q Consensus        94 ~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~--  171 (354)
                      +++++...+....++++|||||+||||||||||||+|+++|+||+++++|+|+|+|+++++++.+.+|..|+.+++..  
T Consensus        81 ~~~~~~l~~~~~~~l~~vGRLD~ds~GLlllTnDg~l~~~l~~P~~~i~k~Y~V~v~~~i~~~~l~~l~~Gv~i~~~~~~  160 (231)
T PRK10839         81 PTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDL  160 (231)
T ss_pred             CCEEEECCCCCCCCEEEEECCCCCCCCEEEECCCHHHHHHCCCCCCCCCEEEEEEECCCCCHHHHHHHHCCCEECCEECC
T ss_conf             72698637655563577004688987769976888999535187689978999998987999999999679698782311


Q ss_pred             EECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEEC-CCCCCCCEEECCHHHHHHH
Q ss_conf             503430364026880799999951842899999998398686889758705451-8755474886799999875
Q gi|254780406|r  172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ  244 (354)
Q Consensus       172 ~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l-~~L~~G~~r~l~~~e~~~l  244 (354)
                      ++|+.+...    ..+|++|+|+||+||||||||+++|++|.+|+||+||+|+| ++|++|+||+||++||..|
T Consensus       161 ~~~~~v~~~----~~~~~~i~l~eGk~rqIRrmf~~~g~~V~~L~Ri~iG~i~L~~dL~~G~~R~Lt~~Ei~~l  230 (231)
T PRK10839        161 TKPAVLEVI----TPTQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGGITLDADLAPGEYRPLTEEEIASV  230 (231)
T ss_pred             EEEEEEEEC----CCCEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEEECEECCCCCCCCCEEECCHHHHHHC
T ss_conf             603699984----8969999996687679999999859989899999990552389999975019999999742


No 5  
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=100.00  E-value=0  Score=360.31  Aligned_cols=167  Identities=31%  Similarity=0.529  Sum_probs=157.3

Q ss_pred             CCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEE
Q ss_conf             56438960278751563144333364421011023432002665543323202223676410001234457404775211
Q gi|254780406|r   70 AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF  149 (354)
Q Consensus        70 ~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v  149 (354)
                      ..+..||++|||+|++||..|+.+++||+++++.  .++++|||||+||+|||||||||+|+++|+||+++++|+|.|+|
T Consensus        26 ~~p~r~illnKP~G~i~T~~D~~gR~tV~dllp~--~~l~pVGRLD~dSeGLLLlTNDG~la~~L~hP~~~i~K~Y~V~v  103 (207)
T PRK11394         26 NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV--QGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQV  103 (207)
T ss_pred             CCCCEEEEEECCCCEEECCCCCCCCCCHHHHCCC--CCCEECCCCCCCCCCEEEECCCHHHHHHHHCCCCCCCEEEEEEE
T ss_conf             9998899998999858688899999767896885--67457777678987729980878999875256579778999999


Q ss_pred             CCCCCHHHHHHHHHHHHCCCEEEECCCEEEEE---------------CCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEE
Q ss_conf             24556467888740000087675034303640---------------268807999999518428999999983986868
Q gi|254780406|r  150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT---------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR  214 (354)
Q Consensus       150 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~---------------~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~  214 (354)
                      .+.++.+.+++|.+|+.++|+.+.|+.+.+..               ....++|++|+|+|||||||||||+++|++|.+
T Consensus       104 ~g~~~~~~l~~l~~Gv~i~dg~~~p~~~~~v~~~~~~~~~~~~~~~~~~~~~s~l~i~L~EGKnRqIRRmf~~~G~~V~~  183 (207)
T PRK11394        104 EGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLR  183 (207)
T ss_pred             CCCCCHHHHHHHHCCCEECCEEEEEEEEEEECCCCCCCCCCCCHHHCCCCCCCEEEEEEEECCCHHHHHHHHHCCCEEEE
T ss_conf             16899999999977978598476454899944742123457641110257865799999746359999999986997938


Q ss_pred             EEEEEECCEECCCCCCCCEEECCH
Q ss_conf             897587054518755474886799
Q gi|254780406|r  215 LIRISYGPFQLGTLLAGSTREVSK  238 (354)
Q Consensus       215 L~Rv~~G~~~l~~L~~G~~r~l~~  238 (354)
                      |+||+||+|.|++|++|+||+||.
T Consensus       184 L~Ri~iG~l~L~~L~~G~~ReLTe  207 (207)
T PRK11394        184 LIRYAMGDYSLDNLANGEWREATD  207 (207)
T ss_pred             EEEEEECCEECCCCCCCCCEECCC
T ss_conf             999998988739989988377969


No 6  
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. E.coli RluB makes psi2605 in 23S RNA.  psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.
Probab=100.00  E-value=0  Score=348.09  Aligned_cols=165  Identities=50%  Similarity=0.815  Sum_probs=159.5

Q ss_pred             EEEECCCCCEEEECCCCCCCCCCCCEEECC-CCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf             896027875156314433336442101102-3432002665543323202223676410001234457404775211245
Q gi|254780406|r   74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ  152 (354)
Q Consensus        74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~-~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~  152 (354)
                      +||++|||.|++||..|+.+++++++.++. ...++++|||||+||||||||||||+|+++|+||+++++|+|.|+++++
T Consensus         1 r~illnKP~G~v~s~~d~~~r~tv~dll~~~~~~rl~~vGRLD~ds~GLLLlTnDG~l~~~l~hP~~~i~k~Y~V~v~~~   80 (167)
T cd02556           1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ   80 (167)
T ss_pred             CEEEEECCCCEEECCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHCCCCCCCCEEEEEEECCC
T ss_conf             98999899998978629988975789655335557236413895767859992783675764098778857999997589


Q ss_pred             CCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEEC-CCCCCC
Q ss_conf             5646788874000008767503430364026880799999951842899999998398686889758705451-875547
Q gi|254780406|r  153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAG  231 (354)
Q Consensus       153 ~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l-~~L~~G  231 (354)
                      ++++.++++..|+.++++.++++.+.+......++|++|+|+||+||||||||+++|++|.+|+||+||+|+| ++|++|
T Consensus        81 ~~~~~l~~l~~Gv~i~~~~~~~~~v~~~~~~~~~~~~~i~l~eGk~rqIRrmf~~~g~~V~~L~Ri~iG~l~l~~dL~~G  160 (167)
T cd02556          81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG  160 (167)
T ss_pred             CCHHHHHHHHCCCEECCEEEEEEEEEEECCCCCCEEEEEEEECCCHHHHHHHHHHCCCEEEEEEEEEECCCCCCCCCCCC
T ss_conf             99999999877978799884006999962679967999999769468999999986998958999998885257898997


Q ss_pred             CEEECCH
Q ss_conf             4886799
Q gi|254780406|r  232 STREVSK  238 (354)
Q Consensus       232 ~~r~l~~  238 (354)
                      +||+|||
T Consensus       161 ~~R~LtP  167 (167)
T cd02556         161 QWEELPP  167 (167)
T ss_pred             CEEECCC
T ss_conf             4586989


No 7  
>TIGR00093 TIGR00093 conserved hypothetical protein; InterPro: IPR000748   Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. Several bacterial proteins from the Rsu family of pseudouridine synthases  have been shown to share regions of similarities, including Escherichia coli and Haemophilus influenzae 16S pseudouridylate 516 synthase (gene rsuA); E. coli hypothetical proteins yciL and ymfC and the corresponding H. influenzae proteins HI1199 and HI0694 respectively; Aquifex aeolicus hypothetical proteins AQ_554 and AQ_1464; Bacillus subtilis hypothetical proteins ypuL and ytzF; Borrelia burgdorferi hypothetical protein BB0129; Helicobacter pylori hypothetical protein HP1459; and Synechocystis sp. (strain PCC 6803) hypothetical proteins slr0361 and slr0612. These are proteins of from 25 to 40 kD which contain a number of conserved regions in their central section.; GO: 0003723 RNA binding, 0004730 pseudouridylate synthase activity, 0001522 pseudouridine synthesis.
Probab=100.00  E-value=0  Score=342.99  Aligned_cols=160  Identities=36%  Similarity=0.605  Sum_probs=153.2

Q ss_pred             CCCCEEEECCCCCCCCCCCCEEECCCC---CCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCH
Q ss_conf             787515631443333644210110234---32002665543323202223676410001234457404775211245564
Q gi|254780406|r   79 HKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ  155 (354)
Q Consensus        79 ~KP~g~~~~~~~~~~~~~~~~~~~~~~---~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~  155 (354)
                      |||.|++||..|+.++.++++.++...   .+|++|||||+||+|||||||||+|+++|+||.++++|+|.|+|++.+++
T Consensus         1 nKP~g~l~~~~Dp~~r~~~~~~l~~~~~~~~~~~a~GRLD~ds~GLlLLT~~G~L~~RL~~p~~~~eK~Y~V~v~g~v~~   80 (185)
T TIGR00093         1 NKPQGVLCTTDDPEGRKTVKDLLPKKLIRGKRLHAVGRLDRDSEGLLLLTNDGELQHRLTHPKFHHEKTYLVTVEGPVTD   80 (185)
T ss_pred             CCCCCEEECCCCCCCCCEEEECCCHHHHCCCCEEEEECCCCCCCCEEEECCCHHHHHHHHCCCCCCCCEEEEEECCCCCH
T ss_conf             99850443584988772350045202310574677402674562038990697999987176435896699995598588


Q ss_pred             HHHHHHHHHHHCCCEEEE--CCCEEEEECCC---------------CEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEE
Q ss_conf             678887400000876750--34303640268---------------8079999995184289999999839868688975
Q gi|254780406|r  156 DKLNLLKKGIVIQGICYG--DMQVTLDTQKG---------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI  218 (354)
Q Consensus       156 ~~~~~~~~g~~~~~~~~~--~~~~~~~~~~~---------------~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv  218 (354)
                      +.+..|++||.++|+.+.  ++.+.++.+..               ..|||.|||.||||||||||||++|++|.+|+|+
T Consensus        81 ~~~~~~~~Gv~L~~~~~~tk~a~~~~~~~~~~~~pr~ppir~r~~i~~S~l~~tl~EGRNRqvRRm~a~~G~~V~~L~R~  160 (185)
T TIGR00093        81 EDLEALRKGVQLEDGKTLTKPAKLKVISEPEDLWPRNPPIRERKSIPTSWLRVTLTEGRNRQVRRMFAAVGFPVLRLHRV  160 (185)
T ss_pred             HHHHHHHCCCEECCCCCCCCCEEEEEECCCCCCCCCCCCEEECCCCCCCEEEEEEEECCCHHHHHHHHHHCCEEEEEEEE
T ss_conf             89989871760058735644237787067131356787312003688225899996087068878889838903478988


Q ss_pred             EECCEEC-CC----CCCCCEEECCH
Q ss_conf             8705451-87----55474886799
Q gi|254780406|r  219 SYGPFQL-GT----LLAGSTREVSK  238 (354)
Q Consensus       219 ~~G~~~l-~~----L~~G~~r~l~~  238 (354)
                      +||++.| .+    |+.|+||+||+
T Consensus       161 ~iG~~~L~~~rGkvL~~G~wR~L~~  185 (185)
T TIGR00093       161 RIGDVSLDEGRGKVLPNGEWRELTD  185 (185)
T ss_pred             EECCEEECCCCCEECCCCCEEECCC
T ss_conf             6224342455743538983021889


No 8  
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
Probab=100.00  E-value=0  Score=339.32  Aligned_cols=163  Identities=32%  Similarity=0.497  Sum_probs=150.7

Q ss_pred             EEEECCCCCEEEECCCCCCCCCCCCEEECCCC--CCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC
Q ss_conf             89602787515631443333644210110234--3200266554332320222367641000123445740477521124
Q gi|254780406|r   74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG  151 (354)
Q Consensus        74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~--~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~  151 (354)
                      .|+++|||+|++||..|+.+ +++++.++...  .++++|||||+||||||||||||+|+++|+||+++++|+|+|+|++
T Consensus         1 VYillnKP~G~v~t~~d~~~-ktv~dll~~~~~~~~l~~vGRLD~~s~GLLLlTNDG~l~~~l~hP~~~i~K~Y~V~v~~   79 (167)
T cd02553           1 VYLMLNKPAGVVCATKDPHH-PTVIDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAG   79 (167)
T ss_pred             CEEEEECCCCEEECCCCCCC-CCHHHHCCCCCCCCCEEECCCCCCCCCCEEEECCCHHHHHHHHCCCCCCCEEEEEEECC
T ss_conf             99999889997969889999-97744335500367556744568997622999188889976414447888899998767


Q ss_pred             CCCHHHHHHHHHHHHCCCE-EEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECC-CCC
Q ss_conf             5564678887400000876-75034303640268807999999518428999999983986868897587054518-755
Q gi|254780406|r  152 QVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL  229 (354)
Q Consensus       152 ~~~~~~~~~~~~g~~~~~~-~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~-~L~  229 (354)
                      +++++++++|.+|+.++|+ .+.|+.+....    ++|++|+|+||+||||||||+++|++|.+|+||+||+|+|+ +|+
T Consensus        80 ~i~~~~l~~l~~Gv~i~dg~~~~~~~v~~~~----~~~~~i~l~eGknrqIRrm~~~~g~~V~~L~Rv~iG~l~L~~~L~  155 (167)
T cd02553          80 PLTEDDIEAFAEGVLLHDGYPTKPAKLEILS----PTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDDDLA  155 (167)
T ss_pred             CCCHHHHHHHHCCCEECCCCEEEEEEEEEEC----CCEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCC
T ss_conf             8999999999769896498597517999925----868999998884629999999869888589999981771599999


Q ss_pred             CCCEEECCHHHH
Q ss_conf             474886799999
Q gi|254780406|r  230 AGSTREVSKKIL  241 (354)
Q Consensus       230 ~G~~r~l~~~e~  241 (354)
                      +|+||+|+++||
T Consensus       156 ~G~~R~Lt~~Ei  167 (167)
T cd02553         156 PGEWRPLTEEEL  167 (167)
T ss_pred             CCCEEECCHHHC
T ss_conf             976138987879


No 9  
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.
Probab=100.00  E-value=0  Score=337.29  Aligned_cols=165  Identities=25%  Similarity=0.353  Sum_probs=150.8

Q ss_pred             CEEEEECCCCCEEEECCCCCCCCCC--------CCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEE
Q ss_conf             4389602787515631443333644--------21011023432002665543323202223676410001234457404
Q gi|254780406|r   72 RTRLWLYHKPIGLVTTHSDPDGRST--------VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR  143 (354)
Q Consensus        72 ~~~~~~~~KP~g~~~~~~~~~~~~~--------~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k  143 (354)
                      ++.|+++|||+|++||..|+...++        ....++.++.+++||||||+||||||||||||+|+++|+||+++++|
T Consensus         3 epvyllLnKP~G~v~t~~d~~~~~~~~~~~~~~~~~~l~~~~~rl~pVGRLD~~s~GLLllTNDG~l~~~l~~P~~~i~k   82 (177)
T cd02555           3 EPVTLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHFARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQ   82 (177)
T ss_pred             CCEEEEEECCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCEEEEEECCHHHHHHHCCCCCCCCE
T ss_conf             44999998998487077576678750133345410001022366216047899981189991888999875498668978


Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCE
Q ss_conf             77521124556467888740000087675034303640268807999999518428999999983986868897587054
Q gi|254780406|r  144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF  223 (354)
Q Consensus       144 ~Y~v~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~  223 (354)
                      +|+|+|+++++++.++.+..|+.+++..++|+.+....    ..+++|+|+||+||||||||+++|++|.+|+||+||+|
T Consensus        83 ~Y~V~v~~~~~~~~l~~l~~Gv~l~g~~~~~~~v~~~~----~~~~~i~l~eGknrqIRrm~~~~g~~V~~L~Ri~iG~l  158 (177)
T cd02555          83 EYLVEVRGELTAGGLERLNHGLTYDGRELPPAKVSWQN----EQRLRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRV  158 (177)
T ss_pred             EEEEEECCCCCHHHHHHHHCCEEECCEEECCEEEEEEC----CCEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEECCE
T ss_conf             99999898799999987528767899896786999957----99599999918416999999987997989999999888


Q ss_pred             ECCCCCCCCEEECCHHH
Q ss_conf             51875547488679999
Q gi|254780406|r  224 QLGTLLAGSTREVSKKI  240 (354)
Q Consensus       224 ~l~~L~~G~~r~l~~~e  240 (354)
                      +|++|++|+||+|+++|
T Consensus       159 ~L~~L~~G~wR~Lt~~E  175 (177)
T cd02555         159 SLGKLPLGQWRYLTTGE  175 (177)
T ss_pred             ECCCCCCCCCEECCCCC
T ss_conf             83889998831992426


No 10 
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Probab=100.00  E-value=0  Score=332.90  Aligned_cols=164  Identities=27%  Similarity=0.435  Sum_probs=152.1

Q ss_pred             EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCC
Q ss_conf             89602787515631443333644210110234320026655433232022236764100012344574047752112455
Q gi|254780406|r   74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV  153 (354)
Q Consensus        74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~  153 (354)
                      .|+++|||+|++||..+. +++++++.++.. .++++|||||.||||||||||||+|+++|+||+++++|+|.|++++++
T Consensus         1 vYillnKP~G~v~s~~~~-~~~~~~~~l~~~-~rl~~vGRLD~~s~GLLLlTNDg~l~~~L~hP~~~i~k~Y~V~~~~~i   78 (164)
T cd02554           1 VYIAYNKPVGIDCTLERA-DEDNIIDFVNPP-PRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPI   78 (164)
T ss_pred             CEEEEECCCCEEECCCCC-CCCCEEEECCCC-CCEEECCCCCCCCCCEEEEECCHHHHHHHCCCCCCCCCEEEEEECCCC
T ss_conf             999998999828387899-999669974886-777888678999856599957889997621998889629999995669


Q ss_pred             CHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCE
Q ss_conf             64678887400000876750343036402688079999995184289999999839868688975870545187554748
Q gi|254780406|r  154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST  233 (354)
Q Consensus       154 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~~L~~G~~  233 (354)
                      +++.++++.+|+.++++.+.|+.+....    +.|++|+|+||+||||||||+++|++|.+|+||+||+|+|++|++|+|
T Consensus        79 ~~~~l~~l~~Gi~i~~~~~~~~~v~~~~----~~~~~i~l~eGknrqIRrmf~~~g~~V~~L~Rv~~G~l~L~~L~~G~~  154 (164)
T cd02554          79 TDEFIEGMSNGVVILGTVTKPCKVERLA----KDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIELGDLAPGEW  154 (164)
T ss_pred             CHHHHHHHHCCEEECCEEEECEEEEEEC----CCEEEEEEEECCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCC
T ss_conf             9999998747859898898021999947----984999999267489999999869988489999988989399899782


Q ss_pred             EECCHHHHHH
Q ss_conf             8679999987
Q gi|254780406|r  234 REVSKKILRE  243 (354)
Q Consensus       234 r~l~~~e~~~  243 (354)
                      |+|+++||++
T Consensus       155 R~Lt~~Eike  164 (164)
T cd02554         155 RPLTDAELFE  164 (164)
T ss_pred             EECCHHHHCC
T ss_conf             6999899088


No 11 
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required.  Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.
Probab=100.00  E-value=0  Score=310.68  Aligned_cols=152  Identities=31%  Similarity=0.522  Sum_probs=141.0

Q ss_pred             EEECCCCCEEEECCCCC-CCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCC
Q ss_conf             96027875156314433-33644210110234320026655433232022236764100012344574047752112455
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV  153 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~-~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~  153 (354)
                      +|++|||+|++||..|+ .++++++++++.  +++++|||||+||||||||||||+|+++|+||+++++|+|+|+|++.+
T Consensus         1 ~i~lnKP~G~v~t~~d~~~~~~~v~d~~~~--~~l~~VGRLD~ds~GLLLlTnDG~l~~~L~hP~~~i~K~Y~v~v~g~~   78 (168)
T cd02566           1 LILFNKPYGVLSQFTDESEKHKTLKDYIDD--PGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVP   78 (168)
T ss_pred             CEEEECCCCEEECCCCCCCCCCEEHHHCCC--CCEEECCCCCCCCCCEEEEECCHHHHHHHHCCCCCCCEEEEEEECCCC
T ss_conf             989989999797966888999782440788--881784266789887599829699999873776799779999986679


Q ss_pred             CHHHHHHHHHHHHCCCEEEECCCEEEEE---------------CCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEE
Q ss_conf             6467888740000087675034303640---------------2688079999995184289999999839868688975
Q gi|254780406|r  154 DQDKLNLLKKGIVIQGICYGDMQVTLDT---------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI  218 (354)
Q Consensus       154 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~---------------~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv  218 (354)
                      +++.+..|.+|+.++++.+.|+.+....               ....++|++|+|+|||||||||||+++|++|.+|+||
T Consensus        79 ~~~~l~~l~~Gv~i~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~s~~~i~l~eGknrqIRrm~~~~g~~V~~L~Rv  158 (168)
T cd02566          79 TEDALEQLRNGVELGDGLTLPAKVEKVDEPPWLWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRV  158 (168)
T ss_pred             CHHHHHHHHCCCEECCEEEEEEEEEEECCCCCCCCCCCCCEEECCCCCEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEE
T ss_conf             99999998779697987864459999426544321256613201478348999996172199999999859969589999


Q ss_pred             EECCEECCCC
Q ss_conf             8705451875
Q gi|254780406|r  219 SYGPFQLGTL  228 (354)
Q Consensus       219 ~~G~~~l~~L  228 (354)
                      +||+|.|++|
T Consensus       159 ~~G~i~L~~L  168 (168)
T cd02566         159 SIGDIGLDNL  168 (168)
T ss_pred             EECCEECCCC
T ss_conf             9887884979


No 12 
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases  are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
Probab=100.00  E-value=8.7e-39  Score=264.11  Aligned_cols=146  Identities=38%  Similarity=0.583  Sum_probs=141.9

Q ss_pred             EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCC
Q ss_conf             96027875156314433336442101102343200266554332320222367641000123445740477521124556
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD  154 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~  154 (354)
                      |+++|||+|++|+..|+.++.++++.++....++++|||||++||||||||||++++++|++|+++++|+|++.|.|.++
T Consensus         1 yi~lnKP~G~~~~~~~~~~~~tv~~ll~~~~~~l~~V~RLD~~TsGLll~t~d~~~~~~l~~~~~~i~K~Y~a~v~g~~~   80 (146)
T cd02870           1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVPS   80 (146)
T ss_pred             CEEEECCCCCEECCCCCCCCCCHHHHHHHCCCCEEECCCCCCCCCCEEEEECCHHHHHHHHCCCCCCCEEEEEEEECCCC
T ss_conf             98999999828616699899857895430578672266689778765999579899998754035424699999902699


Q ss_pred             HHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEE
Q ss_conf             467888740000087675034303640268807999999518428999999983986868897587
Q gi|254780406|r  155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY  220 (354)
Q Consensus       155 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~  220 (354)
                      .+.+..+..|+.++++.+.++.+.+.......+|++|+|.|||+||||+||+++|++|.+|+||+|
T Consensus        81 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~s~l~v~l~tGR~hQIR~h~~~lg~pI~~L~Ri~i  146 (146)
T cd02870          81 EEELRRLRAGVELDDGKTAPAKVKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI  146 (146)
T ss_pred             HHHHHHHHCCEECCCCEEEEEEEEEECCCCCCEEEEEEECCCCHHHHHHHHHHCCCEEEEEEEEEC
T ss_conf             999999866645589887214899823789959999997899439999999984997967999979


No 13 
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family; InterPro: IPR006225    This is the RluD subfamily of pseudouridine synthases. In Escherichia coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917. RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homologue from E. coli outside this family, TruC (Q46918 from SWISSPROT), modifies uracil-65 in transfer RNAs to pseudouridine. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis.
Probab=99.97  E-value=8.3e-32  Score=220.15  Aligned_cols=212  Identities=24%  Similarity=0.317  Sum_probs=175.8

Q ss_pred             CCCCCHHHHHHHHHCCC-CCHHHHHHHHHCCCEEEC-CEECCCCCEEECCCCEEE-EC-------------CEE----CC
Q ss_conf             66773447889998868-778999999986986999-999240687807999799-99-------------989----22
Q gi|254780406|r    9 ENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIE-VD-------------GVP----LR   68 (354)
Q Consensus         9 ~~~~~~RL~K~la~~g~-~SRr~a~~lI~~G~V~Vn-g~~v~~~~~~v~~~d~v~-vd-------------g~~----i~   68 (354)
                      +...++||++||+...- .||..++++|++|.|.|| +.+..++.++|..+|.|. |+             .+|    ++
T Consensus         1 ~~~~g~Rld~~L~~~l~~~sr~~~~~~i~~G~V~vN~~~~~~~~~~~~~~g~~~~~v~~~~~~~~~~~~~~~~p~~l~l~   80 (337)
T TIGR00005         1 EEQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNKGKVTANPKLKIKDGDRITPVRVPEEQEELEVPVQDIPADLKLD   80 (337)
T ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCCEEECCCCCCCCCCEEECCCCEEECEECCCCCCCCCCCCCCCCCCCCCE
T ss_conf             97430269999999836788889999987496896376425674305238746601001464332357665673422113


Q ss_pred             -CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCC----------CEECCCCCCCCCCCEEEECCCCCCCCCCCC-
Q ss_conf             -55643896027875156314433336442101102343----------200266554332320222367641000123-
Q gi|254780406|r   69 -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVISVGRLDINTEGLLLLTNDGGLARVLEL-  136 (354)
Q Consensus        69 -~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~----------~~~~vgRLD~~t~GLlllTndg~l~~~l~~-  136 (354)
                       .+|+..+|++|||+|++|++.......||...|..+.+          ++++|+|||+||||||+++..-.-...|.. 
T Consensus        81 IlfEDe~i~vinKP~G~~vHP~~~~~~~Tv~~~L~~~~~~~~~gig~~~~~~~vHRLD~dTSGl~~vAK~~~A~~~L~~q  160 (337)
T TIGR00005        81 ILFEDEDILVINKPSGLVVHPGGGNSFGTVLNALLAHCPERLSGIGGVFRVGIVHRLDRDTSGLMVVAKTRLALRELQRQ  160 (337)
T ss_pred             EEEECCCEEEEECCCCEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECHHHHHHHHHH
T ss_conf             78750838999789875644888887354899999864766434576123613552477872589997086899999999


Q ss_pred             -CCCCCEEEEEEEECCCCC-HHHH-----------HHHHHHHHCCC---EEEECCCEEEEEC--CCCEEEEEEEEEECCH
Q ss_conf             -445740477521124556-4678-----------88740000087---6750343036402--6880799999951842
Q gi|254780406|r  137 -PSTQWLRVYRVRFHGQVD-QDKL-----------NLLKKGIVIQG---ICYGDMQVTLDTQ--KGSNAWVTVGLREGKN  198 (354)
Q Consensus       137 -p~~~~~k~Y~v~v~~~~~-~~~~-----------~~~~~g~~~~~---~~~~~~~~~~~~~--~~~~~~~~v~l~eGr~  198 (354)
                       ....+.|+|.+.|.|++. ....           ......|...+   +.-....+.+...  .+..+||++.|.+||+
T Consensus       161 l~~~~~~k~Y~A~V~G~~~~~~~~~~~~P~~r~~~~~~~~~v~~~~~~~GK~A~T~f~~~~~~A~~~~sl~~~~L~TGRT  240 (337)
T TIGR00005       161 LKERTVTKEYVALVHGEFDLSKKGTVDAPLGRVPNNRGKMAVAPSSEKEGKPAVTHFKVLERIADGNASLVECELETGRT  240 (337)
T ss_pred             HHHCCCEEEEEEEEECCCCCCCCEEEECCCCCCCCCCEEEEEEECCCCCCCEEEEEEEEEHHHCCCCCCEEEEEECCCCC
T ss_conf             98386117899998317688764478065323688602689976788889612342121001104452189998534897


Q ss_pred             HHHHHHHHHCCCEEEEEEEEEECC
Q ss_conf             899999998398686889758705
Q gi|254780406|r  199 REIKKVFEFFNWKVNRLIRISYGP  222 (354)
Q Consensus       199 ~qIrr~~~~~g~~V~~L~Rv~~G~  222 (354)
                      ||||.+|+++||++..-.  -||+
T Consensus       241 HQIRVHl~~~ghPl~gD~--~YG~  262 (337)
T TIGR00005       241 HQIRVHLQYLGHPLAGDP--LYGN  262 (337)
T ss_pred             HHHHHHHHHHCCCEECCC--CCCC
T ss_conf             389999997168531432--5688


No 14 
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=99.97  E-value=3.8e-31  Score=215.99  Aligned_cols=215  Identities=20%  Similarity=0.222  Sum_probs=165.6

Q ss_pred             CCCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCE----------EC---CCCC
Q ss_conf             4466677344788999886-87789999999869869999992406878079997999998----------92---2556
Q gi|254780406|r    6 IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----------PL---RKAE   71 (354)
Q Consensus         6 ~~~~~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~----------~i---~~~~   71 (354)
                      -++++..++|||+||+... ..||+.++++|++|.|+|||++++.+.++|..+|.|.++..          .+   ..+|
T Consensus        10 tV~~~~aG~RLD~fL~~~~~~~srs~i~k~ir~g~I~VNgk~v~k~~~~v~~GD~I~i~~~~~~~~~~~p~~~~l~IlyE   89 (325)
T PRK11180         10 TVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEAQDIPLDIVYE   89 (325)
T ss_pred             EECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCEEEE
T ss_conf             99910079739999997578889999999998698899999947821278899999981687763447722388518998


Q ss_pred             CEEEEECCCCCEEEECCCCCCCCCCCCEEECCCC------CCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEE
Q ss_conf             4389602787515631443333644210110234------3200266554332320222367641000123--4457404
Q gi|254780406|r   72 RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLR  143 (354)
Q Consensus        72 ~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~------~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k  143 (354)
                      +..++++|||.|++|+........++.+.+...+      .+...|+|||++|||||||+.+...+..|..  ....+.|
T Consensus        90 D~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~r~~iVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K  169 (325)
T PRK11180         90 DDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQKREITR  169 (325)
T ss_pred             CCCEEEEECCCCCEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCCCEEEEECCCHHHHHHHHHHHHHCCCCE
T ss_conf             38899998899944767989888779999987532104787676664279997414664175999999999997388965


Q ss_pred             EEEEEECCCCCHHHHHHH--HH-H-----H-HCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEE
Q ss_conf             775211245564678887--40-0-----0-0087675034303640268807999999518428999999983986868
Q gi|254780406|r  144 VYRVRFHGQVDQDKLNLL--KK-G-----I-VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR  214 (354)
Q Consensus       144 ~Y~v~v~~~~~~~~~~~~--~~-g-----~-~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~  214 (354)
                      +|++.|.|.++.......  .. .     + ....+......+.++......+++++.|.+||.||||.+|+++|++|..
T Consensus       170 ~Y~Alv~G~~~~~g~i~~pl~~~~~~~~~~~~~~~gk~A~T~~~vl~~~~~~slv~~~l~TGRtHQIRvHla~~G~PIvG  249 (325)
T PRK11180        170 EYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVG  249 (325)
T ss_pred             EEEEEEEEEECCCCEEECCCCCCCCCCEEEEECCCCEEECCHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHCCCCEEC
T ss_conf             99999810437996585420137766628997677702022101444358845799982758828999999987995637


Q ss_pred             EEEEEECC
Q ss_conf             89758705
Q gi|254780406|r  215 LIRISYGP  222 (354)
Q Consensus       215 L~Rv~~G~  222 (354)
                        -..||.
T Consensus       250 --D~~YG~  255 (325)
T PRK11180        250 --DQVYGG  255 (325)
T ss_pred             --CCCCCC
T ss_conf             --524688


No 15 
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=99.97  E-value=3.6e-30  Score=209.83  Aligned_cols=216  Identities=24%  Similarity=0.291  Sum_probs=163.6

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCE-------------EC-CCC
Q ss_conf             3446667734478899988687789999999869869999992406878079997999998-------------92-255
Q gi|254780406|r    5 NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-------------PL-RKA   70 (354)
Q Consensus         5 ~~~~~~~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~-------------~i-~~~   70 (354)
                      ..+.+...++||++||+....+||....++|++|.|.|||+++. ++++|..+|.|.+.-.             ++ ..+
T Consensus         4 ~~i~~~~~g~rld~~L~~l~~~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~Ily   82 (289)
T COG0564           4 FEVPEEEAGQRLDKFLAKLLPISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILY   82 (289)
T ss_pred             EEECCHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCEEECCEECC-CCEEECCCCEEEEECCCCCCCCCCCCCCCCCCEEE
T ss_conf             88361113547999998725747999999988898899999835-87160899999953565543334565477877799


Q ss_pred             CCEEEEECCCCCEEEECCCCCCCCCCCCEEECCC----CCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEEE
Q ss_conf             6438960278751563144333364421011023----43200266554332320222367641000123--44574047
Q gi|254780406|r   71 ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI----FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRV  144 (354)
Q Consensus        71 ~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~----~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k~  144 (354)
                      |+..++++|||+|++|+........++...+..+    ..++++|+|||++||||||++.+...+..|..  ....+.|+
T Consensus        83 ED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~  162 (289)
T COG0564          83 EDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKT  162 (289)
T ss_pred             ECCCEEEEECCCCCEECCCCCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHCCCCCEE
T ss_conf             76999999889997167798875267999998752334786435148899985699999599999999999851866179


Q ss_pred             EEEEECCCCCHHH--HHH---------HHHHHHCCC-EEEECCCEEEEECCCC-EEEEEEEEEECCHHHHHHHHHHCCCE
Q ss_conf             7521124556467--888---------740000087-6750343036402688-07999999518428999999983986
Q gi|254780406|r  145 YRVRFHGQVDQDK--LNL---------LKKGIVIQG-ICYGDMQVTLDTQKGS-NAWVTVGLREGKNREIKKVFEFFNWK  211 (354)
Q Consensus       145 Y~v~v~~~~~~~~--~~~---------~~~g~~~~~-~~~~~~~~~~~~~~~~-~~~~~v~l~eGr~~qIrr~~~~~g~~  211 (354)
                      |++.|.|.+..+.  ++.         ...-+...+ +...-..+.+....+. .+++++.+.+||+||||.+|+++|++
T Consensus       163 Y~Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~~~~~gk~A~T~~~~~~~~~~~~tlv~~~~~TGRTHQIRvHl~~lghP  242 (289)
T COG0564         163 YLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKEGSGKPAITHYEVLERFGDNYTLVELKPETGRTHQIRVHLAHLGHP  242 (289)
T ss_pred             EEEEEECCCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCEEEEEEEEEECCCCCEEEEEEECCCCHHHHHHHHHHCCCC
T ss_conf             99999685566687883541067677621699716889833799997206387628999996889851999999987997


Q ss_pred             EEEEEEEEECCE
Q ss_conf             868897587054
Q gi|254780406|r  212 VNRLIRISYGPF  223 (354)
Q Consensus       212 V~~L~Rv~~G~~  223 (354)
                      +..  ---||..
T Consensus       243 I~G--D~~Yg~~  252 (289)
T COG0564         243 IVG--DPLYGGK  252 (289)
T ss_pred             EEC--CCCCCCC
T ss_conf             438--7467874


No 16 
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors.  E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA.  Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved.  Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA.  psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=99.97  E-value=8.1e-31  Score=213.91  Aligned_cols=146  Identities=32%  Similarity=0.469  Sum_probs=128.4

Q ss_pred             EEECCCCCEEEECCCCCCCCCCCCEEECCC-CCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCC
Q ss_conf             960278751563144333364421011023-4320026655433232022236764100012344574047752112455
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV  153 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~-~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~  153 (354)
                      ++++|||.|++|++.+.....++++.+... ..++++|||||++||||||||+|+++++.|+++...+.|+|++.|.|.+
T Consensus         1 iivvnKP~G~~~~~~~~~~~~~~~~~l~~~~~~~l~~vhRLDr~TSGlll~ak~~~~~~~l~~~~~~v~K~Y~a~v~g~~   80 (154)
T cd02550           1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL   80 (154)
T ss_pred             CEEEECCCCCEEECCCCCCCCCHHHHHHHHCCCCEEEECCCCCCCCCCEEECCCHHHHHHHHHHHCCCCEEEEEEEEEEC
T ss_conf             99999999971858999999709999875179861371268999978567737989999998500565057999998727


Q ss_pred             CHHHHHHHHHHH-------HCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEE
Q ss_conf             646788874000-------0087675034303640268807999999518428999999983986868897587
Q gi|254780406|r  154 DQDKLNLLKKGI-------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY  220 (354)
Q Consensus       154 ~~~~~~~~~~g~-------~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~  220 (354)
                      ..+.+..+..+.       ..+++......+.+.......+|+++.|.|||+||||+||+++|++|++|+||+|
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~slv~~~l~TGR~HQIR~hl~~~G~PIl~l~R~ri  154 (154)
T cd02550          81 DEEGIEDLATVRRGRLSGLVDEGVPLAVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI  154 (154)
T ss_pred             CHHHHEECCCCCCCCCEEEECCCCEECCCEEEEECCCCCCEEEEEEECCCCCHHHHHHHHHCCCEEEEEEEEEC
T ss_conf             85882444456424551266599620432889931479948999997988669999999986993956899879


No 17 
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=99.96  E-value=1e-29  Score=207.01  Aligned_cols=215  Identities=16%  Similarity=0.198  Sum_probs=158.9

Q ss_pred             CCCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC--------EEC---------
Q ss_conf             4466677344788999886-8778999999986986999999240687807999799999--------892---------
Q gi|254780406|r    6 IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--------VPL---------   67 (354)
Q Consensus         6 ~~~~~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg--------~~i---------   67 (354)
                      .+++++.++||++||+... ..||+.++++|++|.|+|||+.++ ++++|..+|.|++..        .++         
T Consensus        12 ~V~~~~~G~RLD~fL~~~l~~~srs~i~klir~g~V~VNg~~vk-~~~~l~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~   90 (317)
T PRK11025         12 AISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIK-PEYKLEAGDEVRIPPVRVAEREEEAVSPHLQKVAA   90 (317)
T ss_pred             EECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf             98930079759999997566269999999998699899999957-10465799999988866564445778855110024


Q ss_pred             ----CCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCC---CCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CC
Q ss_conf             ----25564389602787515631443333644210110234---3200266554332320222367641000123--44
Q gi|254780406|r   68 ----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PS  138 (354)
Q Consensus        68 ----~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~---~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~  138 (354)
                          ..+|+..++++|||+|++++........ +.+.+....   ..+..|+|||++||||||++.+...+..|..  ..
T Consensus        91 l~~~IlyED~~llvvnKPaGl~vhp~~~~~~~-~~~~l~~~~~~~~~~~iVHRLDr~TSGllv~AK~~~a~~~l~~~f~~  169 (317)
T PRK11025         91 LADVILYEDDHILVLNKPSGTAVHGGSGLSFG-VIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRE  169 (317)
T ss_pred             CCCEEEEECCCEEEEECCCCCEECCCCCCHHH-HHHHHHHHCCCCCCCCCEECCCCCCCEEEEEECCHHHHHHHHHHHHH
T ss_conf             55607994798899977435622688873168-99999975888876781312699874268871689999999999973


Q ss_pred             CCCEEEEEEEECCCCCHHHH--H------HHHHH---HH-CCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHH
Q ss_conf             57404775211245564678--8------87400---00-0876750343036402688079999995184289999999
Q gi|254780406|r  139 TQWLRVYRVRFHGQVDQDKL--N------LLKKG---IV-IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE  206 (354)
Q Consensus       139 ~~~~k~Y~v~v~~~~~~~~~--~------~~~~g---~~-~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~  206 (354)
                      ..|.|+|++.|.|.+....-  +      .+..+   +. ..++......+.+.......+++++.+.+||.||||.+|+
T Consensus       170 r~v~K~Y~Alv~G~~~~~~~~i~~pl~~~~~~~~~~~~~~~~~gk~a~T~~~v~~~~~~~sLv~~~~~TGRtHQIRvHla  249 (317)
T PRK11025        170 KGMQKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRASPVTGRTHQIRVHTQ  249 (317)
T ss_pred             CCCCCEEEEEEECCCCCCCCEEEEEECCCCCCCCCEEEECCCCCCCCHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHH
T ss_conf             72575599998276367788796100046676764566227777764101446765278640057558075899999998


Q ss_pred             HCCCEEEEEEEEEECCEE
Q ss_conf             839868688975870545
Q gi|254780406|r  207 FFNWKVNRLIRISYGPFQ  224 (354)
Q Consensus       207 ~~g~~V~~L~Rv~~G~~~  224 (354)
                      ++|++|..-  ..||.-.
T Consensus       250 ~~G~PI~GD--~~YG~~~  265 (317)
T PRK11025        250 YAGHPIAFD--DRYGDRE  265 (317)
T ss_pred             HCCCCEECC--CCCCCCC
T ss_conf             779968385--2028742


No 18 
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=99.90  E-value=6.6e-24  Score=170.39  Aligned_cols=183  Identities=15%  Similarity=0.120  Sum_probs=133.6

Q ss_pred             CEEECCEECCCCCEEECCCCEEEE-----CCEECC-----CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCC--C
Q ss_conf             869999992406878079997999-----998922-----5564389602787515631443333644210110234--3
Q gi|254780406|r   39 RVKVNGILLERAAVNVMSTDHIEV-----DGVPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--S  106 (354)
Q Consensus        39 ~V~Vng~~v~~~~~~v~~~d~v~v-----dg~~i~-----~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~--~  106 (354)
                      .|+|||+.|+ +.++|.++|.|.+     +..++.     .+|+..++++|||+|+++++.......++...+....  .
T Consensus         3 ~v~~~G~~v~-~~~~l~~Gd~v~~~~~~~~e~p~p~~l~IlyEDd~llVVnKPaGl~vhP~~~~~~~tl~~~l~~~~~~~   81 (246)
T cd02558           3 VVDADGEPLD-PDSPYRPGTFVWYYRELPDEPPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTGNP   81 (246)
T ss_pred             EECCCCEECC-CCCEECCCCEEEEEECCCCCCCCCCCCCEEEECCCEEEEECCCCCCEEECCCCCCCHHHHHHHHHCCCC
T ss_conf             8880997979-998727999999980589999999989989978999999999998576189972017999998840998


Q ss_pred             CEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEEEEEEEECCCCCHHHHHHHHH----H------HHCCCEEEEC
Q ss_conf             200266554332320222367641000123--445740477521124556467888740----0------0008767503
Q gi|254780406|r  107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKK----G------IVIQGICYGD  174 (354)
Q Consensus       107 ~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k~Y~v~v~~~~~~~~~~~~~~----g------~~~~~~~~~~  174 (354)
                      .+++|+|||++||||||++.+...+..|..  ....+.|+|++.+.+......-.....    +      ...++.....
T Consensus        82 ~~~~VHRLDr~TSGllv~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~A~  161 (246)
T cd02558          82 DLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAPYVPALTFPLTVRSRIVKGRGFFQAREVEGEPNAE  161 (246)
T ss_pred             CCCEECCCCCCCCEEEEEECCHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCEEECCCCCCCCCCEEEECCCCCCCEE
T ss_conf             65473467998746999988999999999986468452799999983377678636636557887644898058998769


Q ss_pred             CCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEE
Q ss_conf             43036402688079999995184289999999839868688975870545
Q gi|254780406|r  175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ  224 (354)
Q Consensus       175 ~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~  224 (354)
                      ..+.+.......+.+++.+.+||+||||.+|+++|++|..-.  .||+..
T Consensus       162 T~~~~l~~~~~~slv~~~~~TGRtHQIRvHla~iGhPIvGD~--~Yg~~~  209 (246)
T cd02558         162 TRIELLARRGGWGLYRLSPHTGKTHQLRVHMAALGVPILNDP--FYPVLL  209 (246)
T ss_pred             EEEEEEEECCCEEEEEEEECCCCHHHHHHHHHHCCCCCCCCC--CCCCCC
T ss_conf             999999983985899999687862999999998799350783--777644


No 19 
>pfam00849 PseudoU_synth_2 RNA pseudouridylate synthase. Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.
Probab=99.80  E-value=2.2e-20  Score=148.17  Aligned_cols=133  Identities=20%  Similarity=0.184  Sum_probs=97.1

Q ss_pred             EEECCCCCEEEECCCCCCCCCCCCEEEC---CCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEEEEEEEE
Q ss_conf             9602787515631443333644210110---2343200266554332320222367641000123--4457404775211
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRF  149 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~---~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k~Y~v~v  149 (354)
                      |+++|||+|+.|+..+.....++.....   ....++++|||||++|||||||++|.+.++.|..  +...+.|+|++.|
T Consensus         1 ~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~f~~~~v~K~Y~a~v   80 (151)
T pfam00849         1 YIVVNKPAGVPVHPTDLSDLLSLTELLLVAELGKFRLYPVHRLDRDTSGLLLLAKDGEAANKLNKLFPERKVEKEYLALV   80 (151)
T ss_pred             CEEEECCCCCEEECCCCCCCCCHHHHHHHHCCCCCCEEEECCCCCCCCCEEEECCCHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             99999999985821899878628886555515997355851778888544786232688888999866535542899999


Q ss_pred             CCCCCHHHHHHHHH----------HHHCCCEEEECCCEEEEEC---CCCEEEEEEEEEECCHHHHHHHHHH
Q ss_conf             24556467888740----------0000876750343036402---6880799999951842899999998
Q gi|254780406|r  150 HGQVDQDKLNLLKK----------GIVIQGICYGDMQVTLDTQ---KGSNAWVTVGLREGKNREIKKVFEF  207 (354)
Q Consensus       150 ~~~~~~~~~~~~~~----------g~~~~~~~~~~~~~~~~~~---~~~~~~~~v~l~eGr~~qIrr~~~~  207 (354)
                      .+++..+.......          .....++......+.++..   ....+++++.|.+||+||||.||++
T Consensus        81 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~~~slv~~~l~TGR~HQIRvhlas  151 (151)
T pfam00849        81 DGPEEEEGTIKAPIKKDKNKVPRRKKEELDGKKAVTHLRVLRSGSKIEDVSLVELELVTGRKHQIRAHLAA  151 (151)
T ss_pred             ECCCCCCCEEEEECCCCCCCCEEEEEECCCCCCCCEEEEEEEECCCCCCEEEEEEEECCCHHHHHHHHHCC
T ss_conf             67778770898101136777727987569984242599998872568996999999672837999998669


No 20 
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved.   The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Probab=99.77  E-value=3.5e-19  Score=140.63  Aligned_cols=154  Identities=19%  Similarity=0.198  Sum_probs=107.3

Q ss_pred             CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCC--CCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEEE
Q ss_conf             556438960278751563144333364421011023--43200266554332320222367641000123--44574047
Q gi|254780406|r   69 KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRV  144 (354)
Q Consensus        69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~--~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k~  144 (354)
                      .+|+..++++|||.|+.++........++...+...  ...+++|+|||++|||||||+.+.+.+..|..  ....+.|+
T Consensus        19 lyED~~iiVVnKP~Gl~~~p~~~~~~~~l~~~l~~~~~~~~~~~vHRLDr~TSGllv~Ak~~~a~~~l~~~f~~~~v~K~   98 (213)
T cd02557          19 VHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGLTELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKE   98 (213)
T ss_pred             EEECCCEEEEECCCCCCEECCCCCCCCHHHHHHHHHCCCCCCCEEECCCCCCCCEEEEECCHHHHHHHHHHHHCCCCCEE
T ss_conf             99689999999999986803899872479999997679987626405688876528997457899999999724756359


Q ss_pred             EEEEECCCCCHHHHH--------HHHHHH---HCCCEEEECCCEEEEE--CCCCEEEEEEEEEECCHHHHHHHHHHCCCE
Q ss_conf             752112455646788--------874000---0087675034303640--268807999999518428999999983986
Q gi|254780406|r  145 YRVRFHGQVDQDKLN--------LLKKGI---VIQGICYGDMQVTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWK  211 (354)
Q Consensus       145 Y~v~v~~~~~~~~~~--------~~~~g~---~~~~~~~~~~~~~~~~--~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~  211 (354)
                      |++.|.|.+......        ......   ...++......+.+..  .....+++++.+.+||+||||.+|+++|++
T Consensus        99 Y~Alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~sll~~~~~TGRtHQIRvhla~lG~P  178 (213)
T cd02557          99 YLARVKGEFPDGEVVVDQPIGLVSPKGGLRNDVDEKGKDARTIFKRLSYNGDLNTSVVLCKPITGRTHQIRVHLQYLGHP  178 (213)
T ss_pred             EEEEEEEECCCCEEEEECCCCEECCCCCEEEEECCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHCCCC
T ss_conf             99999726588838995321000776725885148886431699999983889989999995878889999999987995


Q ss_pred             EEEEEEEEECCEE
Q ss_conf             8688975870545
Q gi|254780406|r  212 VNRLIRISYGPFQ  224 (354)
Q Consensus       212 V~~L~Rv~~G~~~  224 (354)
                      ++.  -..||+..
T Consensus       179 IvG--D~~YG~~~  189 (213)
T cd02557         179 IVN--DPIYNNLG  189 (213)
T ss_pred             EEC--CCCCCCCC
T ss_conf             718--51329856


No 21 
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=99.76  E-value=2.7e-19  Score=141.31  Aligned_cols=155  Identities=16%  Similarity=0.183  Sum_probs=103.8

Q ss_pred             CCCCEEEEECCCCCEEEECCCCCCCCC--CCCEEECC-CCCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEE
Q ss_conf             556438960278751563144333364--42101102-343200266554332320222367641000123--4457404
Q gi|254780406|r   69 KAERTRLWLYHKPIGLVTTHSDPDGRS--TVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLR  143 (354)
Q Consensus        69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~--~~~~~~~~-~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k  143 (354)
                      .+|+.+++++|||+|++|+........  .++..+.. ....+++|+|||++||||||++.+...+..|..  ....+.|
T Consensus         5 lyED~~llVVnKPaGl~vh~~~~~~~~~~~~~~~l~~~~~~~~~~VHRLDr~TSGllv~AK~~~a~~~L~~~f~~~~v~K   84 (257)
T PRK11112          5 LYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIGQHVFTAHRLDRPTSGVLLMALSSEAARLLAQQFEQHQIQK   84 (257)
T ss_pred             EEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHHHCCCCE
T ss_conf             99669899999999986479988878519999999875277653205778987517999689999999999987576863


Q ss_pred             EEEEEECCCCCHHHHH---------HHHHHHHCCCEEEECC--CEEEEE-----------CCCCEEEEEEEEEECCHHHH
Q ss_conf             7752112455646788---------8740000087675034--303640-----------26880799999951842899
Q gi|254780406|r  144 VYRVRFHGQVDQDKLN---------LLKKGIVIQGICYGDM--QVTLDT-----------QKGSNAWVTVGLREGKNREI  201 (354)
Q Consensus       144 ~Y~v~v~~~~~~~~~~---------~~~~g~~~~~~~~~~~--~~~~~~-----------~~~~~~~~~v~l~eGr~~qI  201 (354)
                      +|++.|.|.+......         .+...+...+...+++  .+....           .....+++++.+.+||.|||
T Consensus        85 ~Y~Alv~G~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~~~~~~~sLv~~~p~TGRtHQI  164 (257)
T PRK11112         85 TYHAIVRGWLMEEAVLDYPLKEELDKIADKFAREDKEPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPKTGRKHQL  164 (257)
T ss_pred             EEEEEEEEECCCCCEEEEECCCCCCCCCCEEECCCCCCEEEEEEEEEEEEEEEECCCCCCCCCCEEEEEEECCCCCHHHH
T ss_conf             99999964538997685243446665563130228986363454111026875101232467857999996486852999


Q ss_pred             HHHHHHCCCEEEEEEEEEECCEEC
Q ss_conf             999998398686889758705451
Q gi|254780406|r  202 KKVFEFFNWKVNRLIRISYGPFQL  225 (354)
Q Consensus       202 rr~~~~~g~~V~~L~Rv~~G~~~l  225 (354)
                      |.+|+++|++|+.  -..||+...
T Consensus       165 RvHla~lGhPIvG--D~~YG~~~~  186 (257)
T PRK11112        165 RRHMAHLRHPIIG--DSKHGDLRQ  186 (257)
T ss_pred             HHHHHHCCCCEEC--CCCCCCCCC
T ss_conf             9999987996757--725587544


No 22 
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=99.75  E-value=1e-18  Score=137.76  Aligned_cols=152  Identities=14%  Similarity=0.178  Sum_probs=105.9

Q ss_pred             CCCCEEEEECCCCCEEEECCCCC-CCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEEEE
Q ss_conf             55643896027875156314433-336442101102343200266554332320222367641000123--445740477
Q gi|254780406|r   69 KAERTRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVY  145 (354)
Q Consensus        69 ~~~~~~~~~~~KP~g~~~~~~~~-~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k~Y  145 (354)
                      .+|+..++++|||.|++++...- ....++...+....+...+|+|||++|||||||+.+.+.+..|..  ....+.|+|
T Consensus        17 lyED~~llvvnKP~gl~~~pg~~~~~~~~~~~~~~~~~~~~~~vHRLDr~TSGlll~AK~~~a~~~l~~~f~~r~v~K~Y   96 (219)
T PRK10158         17 LYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQY   96 (219)
T ss_pred             EEECCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCEE
T ss_conf             99799999999999982079976456206999877407866634778999753699978999999998878737467379


Q ss_pred             EEEECCCCCHHHHH-H----------HHHHHHCCCEEEECCCEEEEE-CCCCEEEEEEEEEECCHHHHHHHHHHCCCEEE
Q ss_conf             52112455646788-8----------740000087675034303640-26880799999951842899999998398686
Q gi|254780406|r  146 RVRFHGQVDQDKLN-L----------LKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN  213 (354)
Q Consensus       146 ~v~v~~~~~~~~~~-~----------~~~g~~~~~~~~~~~~~~~~~-~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~  213 (354)
                      ++.|.|.+....-. .          ....+..+.+......+.+.. .....+++++.+.+||+||||.+|+++|+++.
T Consensus        97 lA~v~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~~~lv~l~p~TGRtHQIRvhla~lG~PIv  176 (219)
T PRK10158         97 VARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPIL  176 (219)
T ss_pred             EEEEECCCCCCCCCCCCCEEECCCCCCCEEEECCCCCCCCEEEEEEEECCCCEEEEEEEECCCCHHHHHHHHHHCCCCEE
T ss_conf             99983686643561124525047777616997246741215899999738985999998666851899999998799274


Q ss_pred             EEEEEEECC
Q ss_conf             889758705
Q gi|254780406|r  214 RLIRISYGP  222 (354)
Q Consensus       214 ~L~Rv~~G~  222 (354)
                      .-  .-||.
T Consensus       177 GD--~~Yg~  183 (219)
T PRK10158        177 GD--RFYAS  183 (219)
T ss_pred             CC--CCCCC
T ss_conf             78--77788


No 23 
>KOG1919 consensus
Probab=99.73  E-value=2.7e-17  Score=128.71  Aligned_cols=204  Identities=20%  Similarity=0.232  Sum_probs=142.1

Q ss_pred             HHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEE--C--C-----EECC-CCCCEEEEECCCCCEE
Q ss_conf             788999886-87789999999869869999992406878079997999--9--9-----8922-5564389602787515
Q gi|254780406|r   16 VSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--D--G-----VPLR-KAERTRLWLYHKPIGL   84 (354)
Q Consensus        16 L~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~v--d--g-----~~i~-~~~~~~~~~~~KP~g~   84 (354)
                      |..+++... .-.|-..+..|+.|.|+|||+.+. ..+.+..+|.|..  .  .     .++. ..++..|+++|||.|+
T Consensus        46 ~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~~-v~~i~k~~d~l~~~vhrh~p~~~~~~~~Iv~ed~~~vVvnKP~gi  124 (371)
T KOG1919          46 LVDVFVSEFRLRERAYYESAIKLGRVTVNGEQVR-VSLIVKNGDVLCHTVHRHEPPVAYLPIRIVFEDKDYVVVNKPHGI  124 (371)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHCCCEEECCEEEE-EEEEECCCCEEEEEECCCCCCCCCCCCCEEEECCCEEEEECCCCC
T ss_conf             7799989875371576665653686588858600-478712588887764047887544344158853998999589987


Q ss_pred             EECCCCCCCCCCCCEEECCC--CCCEECCCCCCCCCCCEEEECCCCCCCCCCCCC--CCCCEEEE-EEEECCCCCHHHHH
Q ss_conf             63144333364421011023--432002665543323202223676410001234--45740477-52112455646788
Q gi|254780406|r   85 VTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVY-RVRFHGQVDQDKLN  159 (354)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~--~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p--~~~~~k~Y-~v~v~~~~~~~~~~  159 (354)
                      .+++.......++...+...  ...+.+++|||+.|||||+|..+-+-+..+...  ...+.|+| .+.|.+.+......
T Consensus       125 pVhp~g~~~~n~i~~~l~~~~~~~~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~  204 (371)
T KOG1919         125 PVHPTGRYRENTITKILAALHKVEGLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLRKRTVKKEYVVARVEGPFPVVGEV  204 (371)
T ss_pred             CEECCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEECHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCEE
T ss_conf             54016854436536888874145566232246766564489985655768999997435410379999972457877627


Q ss_pred             HHHH-----------HHHCCC------EEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECC
Q ss_conf             8740-----------000087------67503430364026880799999951842899999998398686889758705
Q gi|254780406|r  160 LLKK-----------GIVIQG------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP  222 (354)
Q Consensus       160 ~~~~-----------g~~~~~------~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~  222 (354)
                      ....           ++.-.+      +......+......+..+|+++-+.+||.||||.+|+++|+++.  --.-|++
T Consensus       205 ~i~~~~~~~~~~~~~~l~~~~~~~~~~~k~a~T~~~~~~~~~~ss~V~~~PlTGRtHQIRvHlq~lG~PI~--gD~~Y~~  282 (371)
T KOG1919         205 EIKEPIGEEERPLRMGLNAVGVRDEVAAKDAKTLFKVLSYDGGSSLVECRPLTGRTHQIRVHLQYLGHPIA--GDPKYGN  282 (371)
T ss_pred             EECCCCCCCCCCCCEEEEECCCCCCCCCCCCEEEEEECCCCCCEEEEEEECCCCCHHHHHHHHHHHCCCCC--CCCCCCC
T ss_conf             71787553456651576401224444565644688872348966999963267967999999997199857--8855666


No 24 
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. TruC makes psi65 in tRNAs.  This psi residue is not universally conserved.
Probab=99.73  E-value=2.9e-18  Score=134.84  Aligned_cols=154  Identities=19%  Similarity=0.195  Sum_probs=100.3

Q ss_pred             CCCCEEEEECCCCCEEEECCCCCCCCCC--CCEEECCC-CCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEE
Q ss_conf             5564389602787515631443333644--21011023-43200266554332320222367641000123--4457404
Q gi|254780406|r   69 KAERTRLWLYHKPIGLVTTHSDPDGRST--VFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLR  143 (354)
Q Consensus        69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~~--~~~~~~~~-~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k  143 (354)
                      .+|+..++++|||.|+.|+........+  .+..+... ...+++|+|||++|||||||+.+.+.+..|..  ....+.|
T Consensus         4 vyED~~ilvvnKP~Gl~~hp~~~~~~~~~~~~~~~~~~~~~~~~~vHRLDr~TSGllv~Ak~~~a~~~l~~~f~~~~v~K   83 (223)
T cd02563           4 LYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLGQHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHK   83 (223)
T ss_pred             EEECCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEECCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCC
T ss_conf             99679999999999982658999988369999998875378753404778987635999845899999999987551122


Q ss_pred             EEEEEECCCCCHHHHHH--H-------HHHHHCCCEEEECC--CEEEE-----------ECCCCEEEEEEEEEECCHHHH
Q ss_conf             77521124556467888--7-------40000087675034--30364-----------026880799999951842899
Q gi|254780406|r  144 VYRVRFHGQVDQDKLNL--L-------KKGIVIQGICYGDM--QVTLD-----------TQKGSNAWVTVGLREGKNREI  201 (354)
Q Consensus       144 ~Y~v~v~~~~~~~~~~~--~-------~~g~~~~~~~~~~~--~~~~~-----------~~~~~~~~~~v~l~eGr~~qI  201 (354)
                      +|++.|.|.+.......  +       .......+....++  .....           ......+++++.+.+||+|||
T Consensus        84 ~Y~Alv~G~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGRtHQI  163 (223)
T cd02563          84 TYLAVVRGYVPESGTIDYPLSEELDKLADKFASDDKAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVELTPHTGRKHQL  163 (223)
T ss_pred             EEEEEEEEECCCCCEEEEECCCCCCCCCCEEEECCCCCCCEEEEEEEEEEEECCEEECCCCCCCEEEEEEEECCCCHHHH
T ss_conf             69999984079998798654546775563687427887634889887655320001011477747999999676870899


Q ss_pred             HHHHHHCCCEEEEEEEEEECCEE
Q ss_conf             99999839868688975870545
Q gi|254780406|r  202 KKVFEFFNWKVNRLIRISYGPFQ  224 (354)
Q Consensus       202 rr~~~~~g~~V~~L~Rv~~G~~~  224 (354)
                      |.+|+++|+++..-  .-||.-.
T Consensus       164 RvHla~lG~PIvGD--~~YG~~~  184 (223)
T cd02563         164 RRHLAHIRHPIIGD--TTHGDGR  184 (223)
T ss_pred             HHHHHHCCCCEECC--CCCCCCC
T ss_conf             99999879978277--2568754


No 25 
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA.  Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors.  E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA.  Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved.  Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA.  psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=99.67  E-value=3.4e-17  Score=128.10  Aligned_cols=149  Identities=20%  Similarity=0.191  Sum_probs=110.3

Q ss_pred             EEECCCCCEEEECCCCCCCCCCCCEE------ECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCC--CCCCEEEEE
Q ss_conf             96027875156314433336442101------1023432002665543323202223676410001234--457404775
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDPDGRSTVFDN------LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR  146 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~~~~~~~~~~------~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p--~~~~~k~Y~  146 (354)
                      ++++|||.|+.++........++...      .......+++|+|||++|+||||++.+...+..|...  ...+.|.|.
T Consensus         1 ~lvvnKP~gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl~l~Ak~~~~~~~l~~~~~~~~~~K~Y~   80 (185)
T cd02869           1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL   80 (185)
T ss_pred             CEEEECCCCCCEECCCCCCCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCEEEECHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             99999999983648989988589999999998648998653434789887561888660999999987446564403999


Q ss_pred             EEECCCCCHHHHHHHH-----------HHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEE
Q ss_conf             2112455646788874-----------00000876750343036402688079999995184289999999839868688
Q gi|254780406|r  147 VRFHGQVDQDKLNLLK-----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL  215 (354)
Q Consensus       147 v~v~~~~~~~~~~~~~-----------~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L  215 (354)
                      +.+.|.+.........           .-....++...-..+.+.......+++++.+.+||.||||.+|+++|+++  +
T Consensus        81 a~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~slv~~~~~TGR~HQIR~hla~lg~PI--v  158 (185)
T cd02869          81 ALVDGKPPEDEGTIDAPLGRKKRKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPI--V  158 (185)
T ss_pred             EEECCCCCCCCCEEECCEEECCCCCCEEEEECCCCCEEEEEHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHCCCCE--E
T ss_conf             99667656576568221441566671389856998476200134553798699998816587799999999879967--4


Q ss_pred             EEEEECCEEC
Q ss_conf             9758705451
Q gi|254780406|r  216 IRISYGPFQL  225 (354)
Q Consensus       216 ~Rv~~G~~~l  225 (354)
                      --..||...-
T Consensus       159 GD~~Yg~~~~  168 (185)
T cd02869         159 GDPKYGGKAS  168 (185)
T ss_pred             CCCCCCCCCC
T ss_conf             8635698533


No 26 
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621; InterPro: IPR006508   These sequences represent a clade within the pseudouridine synthase superfamily. The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences in this family are most closely related to RluA ; only Neisseria does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity..
Probab=99.37  E-value=2.1e-13  Score=104.30  Aligned_cols=140  Identities=15%  Similarity=0.176  Sum_probs=100.0

Q ss_pred             CCCEEEEECCCCCEEEECCCCCCCCCCCCEEECC--CCCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEEEE
Q ss_conf             5643896027875156314433336442101102--343200266554332320222367641000123--445740477
Q gi|254780406|r   70 AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVY  145 (354)
Q Consensus        70 ~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~--~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k~Y  145 (354)
                      +.-..++++|||.|+.+|.++.+  .-+...+..  ..++++.|+|||+.|||||||+-+-+-|..|..  ....|+|+|
T Consensus         6 f~H~DF~~INK~~giSVHkD~ge--tgL~~~vA~Qlgv~~vwLvHRLDK~TSGiLllAlNaesAselS~~Fa~~ki~KtY   83 (222)
T TIGR01621         6 FRHSDFVLINKSEGISVHKDDGE--TGLLREVAKQLGVEKVWLVHRLDKVTSGILLLALNAESASELSRLFAKKKIKKTY   83 (222)
T ss_pred             EECCCEEEEECCCCEEEEECCCC--HHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHCHHHHHHHHHHHHCCEEEEEE
T ss_conf             53686789867998327725711--1389999998189808998700034468999860478999998765217066677


Q ss_pred             EEEECCCCCHH------HHHHHHHHHHC-----C-CEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEE
Q ss_conf             52112455646------78887400000-----8-767503430364026880799999951842899999998398686
Q gi|254780406|r  146 RVRFHGQVDQD------KLNLLKKGIVI-----Q-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN  213 (354)
Q Consensus       146 ~v~v~~~~~~~------~~~~~~~g~~~-----~-~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~  213 (354)
                      ++--+..+...      .+++-+.|..=     | --.+++..+.+   ...--.|-+..++||+||||.-|.++|.+|+
T Consensus        84 LAls~~KPkKKQGlI~GdMeksR~g~WKL~~~~eNpAiTrF~S~s~---a~~lRLFilkPhTGKTHQlRVAmKSlGSpIl  160 (222)
T TIGR01621        84 LALSDKKPKKKQGLIIGDMEKSRRGAWKLVRSKENPAITRFESVSI---AEKLRLFILKPHTGKTHQLRVAMKSLGSPIL  160 (222)
T ss_pred             EECCCCCCCCCCCEEECCHHHHHCCCCHHCCCCCCCEECCEEEEEE---CCCCCEEEECCCCCCHHHHHHHHHHCCCCCC
T ss_conf             6313689874442025571242000100027898960111245652---3888637556899963788788877276300


Q ss_pred             E
Q ss_conf             8
Q gi|254780406|r  214 R  214 (354)
Q Consensus       214 ~  214 (354)
                      .
T Consensus       161 G  161 (222)
T TIGR01621       161 G  161 (222)
T ss_pred             C
T ss_conf             5


No 27 
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site;  Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=99.07  E-value=2.8e-10  Score=84.56  Aligned_cols=66  Identities=32%  Similarity=0.478  Sum_probs=55.6

Q ss_pred             HHHHHHHHHC-CCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCC---CCCEEEEECC
Q ss_conf             4478899988-6877899999998698699999924068780799979999989225---5643896027
Q gi|254780406|r   14 QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---AERTRLWLYH   79 (354)
Q Consensus        14 ~RL~K~la~~-g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~---~~~~~~~~~~   79 (354)
                      +||++||+.+ +.+||++|.++|.+|.|+|||+++++++++|.++|.|+++++....   +++..++++|
T Consensus         1 ~RLd~~l~~~~~~~Sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~gd~i~i~~~~~~~~i~~~~~~~~~i~   70 (70)
T cd00165           1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYEDKKLLVVN   70 (70)
T ss_pred             CCHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEECCCCCCCCEEEECCCEEEEC
T ss_conf             9488999874871589999999981938989999588888989999999878778867323269899969


No 28 
>smart00363 S4 S4 RNA-binding domain.
Probab=99.01  E-value=6.5e-10  Score=82.27  Aligned_cols=55  Identities=38%  Similarity=0.579  Sum_probs=50.2

Q ss_pred             HHHHHHHHHCCC-CCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC
Q ss_conf             447889998868-7789999999869869999992406878079997999998922
Q gi|254780406|r   14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR   68 (354)
Q Consensus        14 ~RL~K~la~~g~-~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~   68 (354)
                      .|||+||+..|+ +||++|+++|..|.|+|||++++++++.|.++|.|+++++...
T Consensus         1 ~RLD~~l~~~~~~~Sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I~~~~~~~~   56 (60)
T smart00363        1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK   56 (60)
T ss_pred             CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECCCCCC
T ss_conf             97889999838704799999999849179899994789889899999999885003


No 29 
>pfam01479 S4 S4 domain. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA.
Probab=98.85  E-value=2.9e-09  Score=78.16  Aligned_cols=47  Identities=38%  Similarity=0.591  Sum_probs=44.7

Q ss_pred             HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEE
Q ss_conf             4478899988687-7899999998698699999924068780799979
Q gi|254780406|r   14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI   60 (354)
Q Consensus        14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v   60 (354)
                      +||++||+..|+| ||++|.++|.+|.|+|||++++++++.|.++|.|
T Consensus         1 ~RLd~~l~~~~~~~Sr~~a~~~I~~G~V~VNg~~v~~~~~~v~~gD~i   48 (48)
T pfam01479         1 MRLDKVLARLGLASSRSEARQLIRHGHVRVNGKVVKDPSYRVKPGDVI   48 (48)
T ss_pred             CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCCC
T ss_conf             966799998676148999999998897798999957898688992999


No 30 
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=98.48  E-value=2.3e-07  Score=66.16  Aligned_cols=51  Identities=29%  Similarity=0.314  Sum_probs=47.0

Q ss_pred             CCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEE
Q ss_conf             77344788999886-87789999999869869999992406878079997999
Q gi|254780406|r   11 FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        11 ~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      ...+||||||.-+. +-+|.-|+.+|+.|+|.|||+.+ .++..|..+|.|+|
T Consensus         6 ~~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i   57 (100)
T COG1188           6 ADRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTI   57 (100)
T ss_pred             CCCEEHHHHHHHHHHHHHHHHHHHHHHCCEEEECCEEC-CCCCCCCCCCEEEE
T ss_conf             65165678887887742289999998779698999675-65561477989999


No 31 
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=98.46  E-value=3.2e-07  Score=65.31  Aligned_cols=53  Identities=15%  Similarity=0.234  Sum_probs=51.2

Q ss_pred             CCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC
Q ss_conf             73447889998868778999999986986999999240687807999799999
Q gi|254780406|r   12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG   64 (354)
Q Consensus        12 ~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg   64 (354)
                      .+.|||.++|....+||.+|..+|++|+|+||+++++++++.|.++|.|.|-|
T Consensus       182 sSlRLDavvs~~~~~SRska~~lI~~g~V~vN~~~v~~~s~~v~~gDiiSvRG  234 (257)
T TIGR03069       182 ASLRIDAIASAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRG  234 (257)
T ss_pred             CCCCHHHHHHHHHCCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEEEC
T ss_conf             12138999998866579999999884968989999057875668999999906


No 32 
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=98.45  E-value=4.8e-07  Score=64.21  Aligned_cols=55  Identities=27%  Similarity=0.383  Sum_probs=50.3

Q ss_pred             CCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE
Q ss_conf             734478899988687-7899999998698699999924068780799979999989
Q gi|254780406|r   12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP   66 (354)
Q Consensus        12 ~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~   66 (354)
                      ..+||+.+|.+.|++ ||..|..+|.+|.|.|||..|+.|++.|+.++.|+|.+..
T Consensus         1 ~k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~~~   56 (245)
T COG1189           1 NKMRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEE   56 (245)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEECCCC
T ss_conf             93238999997353320999999987685788999942765245898637875666


No 33 
>TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709   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 , .   The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This family consists of organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=98.36  E-value=3.3e-07  Score=65.18  Aligned_cols=53  Identities=25%  Similarity=0.438  Sum_probs=49.4

Q ss_pred             HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE
Q ss_conf             4478899988687-7899999998698699999924068780799979999989
Q gi|254780406|r   14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP   66 (354)
Q Consensus        14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~   66 (354)
                      .|||-++-++|+| ||+.|.+|+..|-|.|||++|+-|++.|.++|.|.|-.+.
T Consensus       100 ~RLDNvVYRlGfA~Tr~~ARQLVsHGhi~vNGk~VdIPSy~v~~Gd~i~ikEk~  153 (217)
T TIGR01017       100 SRLDNVVYRLGFAPTRRAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKS  153 (217)
T ss_pred             CCCCCEEECCCCHHHHHHHHHHHHCCEEEECCEEECCCEEEECCCCEEEEEECC
T ss_conf             100101021271200787635640880787981852240670799889981032


No 34 
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=98.29  E-value=1.7e-06  Score=60.71  Aligned_cols=56  Identities=25%  Similarity=0.396  Sum_probs=50.7

Q ss_pred             HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCC
Q ss_conf             4478899988687-7899999998698699999924068780799979999989225
Q gi|254780406|r   14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK   69 (354)
Q Consensus        14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~   69 (354)
                      -|||-++-.+|++ |+++|.+||..|.|.|||++|+.|++.|.++|.|.|+.+.-..
T Consensus        94 rRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~  150 (205)
T COG0522          94 RRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSP  150 (205)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCEEECCCCEEEEECCCCCH
T ss_conf             887899998404135999998840662899999952673796377788752034542


No 35 
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=98.22  E-value=1.7e-06  Score=60.79  Aligned_cols=58  Identities=26%  Similarity=0.370  Sum_probs=53.5

Q ss_pred             CCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC
Q ss_conf             4666773447889998868778999999986986999999240687807999799999
Q gi|254780406|r    7 VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG   64 (354)
Q Consensus         7 ~~~~~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg   64 (354)
                      ++-.-.+.|||.++|...-.||..|.+||+.|+|+||.++|+++.+.|..+|.|.+-|
T Consensus       174 ~~~~vsSlRLD~vis~~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG  231 (257)
T COG2302         174 LDVTVSSLRLDVVISEGFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRG  231 (257)
T ss_pred             EEEEEEHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCEECCCCEEEEEC
T ss_conf             7654212407999998876559999998773732771299126663322498999840


No 36 
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=98.18  E-value=4.4e-06  Score=58.12  Aligned_cols=152  Identities=19%  Similarity=0.201  Sum_probs=93.3

Q ss_pred             ECCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEE
Q ss_conf             92255643896027875156314433336442101102343200266554332320222367641000123445740477
Q gi|254780406|r   66 PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY  145 (354)
Q Consensus        66 ~i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y  145 (354)
                      +|.-.-..-++++|||.|+.++..=..-+..    +  ...+....|-||-..+|+|++.-..  +.++..--....|+|
T Consensus        15 ~~~~~~~~Gil~idKP~G~TS~~vv~~vrk~----l--~~kKvGH~GTLDP~AtGvL~i~~G~--aTK~~~~l~~~~K~Y   86 (300)
T PRK04270         15 PIEEYINYGVVNLDKPPGPTSHEVAAWVRDI----L--GVEKAGHGGTLDPKVTGVLPVALGK--ATKVVQALLESPKEY   86 (300)
T ss_pred             CHHHHHHCCEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEECH--HHHHHHHHCCCCCEE
T ss_conf             9999972999999689899989999999998----5--8884687867897462337888679--888869867589458


Q ss_pred             EEEE--CCCCCHHHHHHHHHHHHCCCEEEECCC--------------EEEEECCCCEEEEEEEEEECCHHHHHHHHHHCC
Q ss_conf             5211--245564678887400000876750343--------------036402688079999995184289999999839
Q gi|254780406|r  146 RVRF--HGQVDQDKLNLLKKGIVIQGICYGDMQ--------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN  209 (354)
Q Consensus       146 ~v~v--~~~~~~~~~~~~~~g~~~~~~~~~~~~--------------~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g  209 (354)
                      .+++  ..+++.+.+......+.-.-.+..|..              +.+..-+.....++|.-.-|-|  ||-++..+|
T Consensus        87 ~~~~~l~~~~~~~~i~~~l~~f~G~i~Q~PP~~SAvKr~~R~~~I~~~~ll~~~~~~~~~~v~cskGTY--IRsL~~DiG  164 (300)
T PRK04270         87 VCVMHLHGDVPEEKIREVFKEFTGEIYQKPPLKSAVKRRLRIRTIYELEILEIDGRDVLFRVGCESGTY--IRKLCHDIG  164 (300)
T ss_pred             EEEEECCCCCCHHHHHHHHHHCCCEEEECCCHHHHHCCCCCCCEEEEEEEEEEECCEEEEEEEECCCCC--HHHHHHHHH
T ss_conf             771013999999999999997785352069736640455567469999988860886999999789847--899999999


Q ss_pred             ------CEEEEEEEEEECCEECCC
Q ss_conf             ------868688975870545187
Q gi|254780406|r  210 ------WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       210 ------~~V~~L~Rv~~G~~~l~~  227 (354)
                            -.+..|.|+++|+|.+.+
T Consensus       165 ~~Lg~~a~m~~LrRt~~G~F~~~~  188 (300)
T PRK04270        165 EALGTGAHMRELRRTRTGPFTEDE  188 (300)
T ss_pred             HHHCCCEEEEEEEEEEECCCCHHH
T ss_conf             984986686353514783717898


No 37 
>PRK12565 30S ribosomal protein S4; Provisional
Probab=98.16  E-value=4.4e-06  Score=58.13  Aligned_cols=53  Identities=26%  Similarity=0.379  Sum_probs=49.2

Q ss_pred             HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE
Q ss_conf             4478899988687-7899999998698699999924068780799979999989
Q gi|254780406|r   14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP   66 (354)
Q Consensus        14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~   66 (354)
                      .|||-++-++|++ ||.+|.+||..|.|.|||+.|+-|++.|.++|.|+|..+.
T Consensus        88 ~RLDnvv~R~gfa~t~~~ARQlV~Hghi~vng~kVdIPSy~vk~GDvI~vkeks  141 (197)
T PRK12565         88 CRLDNVVYRIGFASSIRQARQMVNHGHILVNGKKVNIPSYEVKVGDEITLREKS  141 (197)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCEEECCCCEEEECHHH
T ss_conf             866677113441057999866740788897998955887670699999973322


No 38 
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=98.14  E-value=3.7e-06  Score=58.62  Aligned_cols=56  Identities=18%  Similarity=0.148  Sum_probs=49.0

Q ss_pred             CCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC
Q ss_conf             66677344788999886-8778999999986986999999240687807999799999
Q gi|254780406|r    8 QENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG   64 (354)
Q Consensus         8 ~~~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg   64 (354)
                      ++....+||||||..+= +-||.-|-.+|..|+|+|||+.++ |+..|.++|.|+|--
T Consensus         3 ~~p~~k~RiDkwLW~aRffKTRslA~~a~~~G~V~vnG~~~K-ps~~V~~GD~l~i~~   59 (133)
T PRK10348          3 EKPAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSK-PSKIVELNATLTLRQ   59 (133)
T ss_pred             CCCCCCEEEHHHHHHHEEHHHHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEEEE
T ss_conf             887550540200315201000999999998798898998868-888768999999986


No 39 
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=98.13  E-value=1.5e-05  Score=54.69  Aligned_cols=144  Identities=19%  Similarity=0.181  Sum_probs=88.0

Q ss_pred             EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC--
Q ss_conf             896027875156314433336442101102343200266554332320222367641000123445740477521124--
Q gi|254780406|r   74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG--  151 (354)
Q Consensus        74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~--  151 (354)
                      -++++|||.|+.++..=..-+.    .+  ...+....|-||-..+|||++.-.  -+.+|..--....|+|.+++.-  
T Consensus         3 gil~i~KP~G~TS~~vv~~vkk----~l--~~kKvGH~GTLDP~AtGvLiv~~G--~aTKl~~~l~~~~K~Y~a~i~lG~   74 (272)
T PRK04099          3 RLFVANKPPGLSSNAFLSRLKR----KY--GVKKAGFSGTLDPFAKGVLIVAFG--QYTKLFRFLDKTPKTYKATLWLGA   74 (272)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH----HH--CCCCCCCCCCCCCCCCCEEEEEEC--HHHHHHHHHCCCCCEEEEEEEECC
T ss_conf             3999618998998999999999----84--998446370569866045999988--776311766778827999999886


Q ss_pred             -----------------CCCHHHHHHHHHHHHCCCEE--------------------------EECCCE-----EEEECC
Q ss_conf             -----------------55646788874000008767--------------------------503430-----364026
Q gi|254780406|r  152 -----------------QVDQDKLNLLKKGIVIQGIC--------------------------YGDMQV-----TLDTQK  183 (354)
Q Consensus       152 -----------------~~~~~~~~~~~~g~~~~~~~--------------------------~~~~~~-----~~~~~~  183 (354)
                                       +++.+.++.....+.-.-..                          ..+..+     .+..-.
T Consensus        75 ~TdT~D~e~i~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySA~Kv~Gkr~YelAR~G~~ve~~~r~v~I~~i~ll~~~  154 (272)
T PRK04099         75 KSPSLDIENIESIEIIKPFDLADLEKIIKSLQGEISYTPPKFSAKKINGTRAYELARKGEEFELKPIQMEIFECKILSYN  154 (272)
T ss_pred             CCCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCHHHHHHHCCHHHHHHHHCCCCCCCCCEEEEEEEEEEEEEC
T ss_conf             14788745136744689999999999999777018983888996301454399998669730357579999999999612


Q ss_pred             CCEEEEEEEEEECCHHHHHHHHHHCCC------EEEEEEEEEECCEECCC
Q ss_conf             880799999951842899999998398------68688975870545187
Q gi|254780406|r  184 GSNAWVTVGLREGKNREIKKVFEFFNW------KVNRLIRISYGPFQLGT  227 (354)
Q Consensus       184 ~~~~~~~v~l~eGr~~qIrr~~~~~g~------~V~~L~Rv~~G~~~l~~  227 (354)
                      .....++|....|-|  ||-++.-+|.      .+..|.|+++|+|.|.+
T Consensus       155 ~p~~~f~v~cSkGTY--IRSLa~Dig~~Lg~~a~l~~L~Rt~~G~F~le~  202 (272)
T PRK04099        155 HPFLTFEITVSEGAY--IRSYAELFAKKLGVNGTLSSLERISEGKFVYEN  202 (272)
T ss_pred             CCEEEEEEEECCCCC--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH
T ss_conf             986999999869595--889999998985991898342821681717787


No 40 
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=98.09  E-value=4.5e-06  Score=58.06  Aligned_cols=53  Identities=17%  Similarity=0.359  Sum_probs=49.4

Q ss_pred             HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE
Q ss_conf             4478899988687-7899999998698699999924068780799979999989
Q gi|254780406|r   14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP   66 (354)
Q Consensus        14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~   66 (354)
                      .|||-++-++|++ ||.+|.+||..|.|.|||+.|+-|++.|.++|+|+|..+.
T Consensus        89 ~RLDnvVyRlGfA~Tr~~ARQlV~HgHi~VNgkkVnIPSy~vk~GDvI~v~~ks  142 (201)
T CHL00113         89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPRDIITIKDKQ  142 (201)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHEEECCEEEECCEEECCCCEEEECCCEEEECCCC
T ss_conf             999999987054058887610584662998998933787584279989975344


No 41 
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=98.07  E-value=1.5e-05  Score=54.81  Aligned_cols=156  Identities=22%  Similarity=0.236  Sum_probs=84.8

Q ss_pred             EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCC-C-CCCCCCCCCCCCCEEEEEEEECC-
Q ss_conf             96027875156314433336442101102343200266554332320222367-6-41000123445740477521124-
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND-G-GLARVLELPSTQWLRVYRVRFHG-  151 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTnd-g-~l~~~l~~p~~~~~k~Y~v~v~~-  151 (354)
                      ++++|||.|+.++..=..-...+...+.. .......|-||-.++|||++.-. + .+...|+  .....|+|.+++.- 
T Consensus         2 il~v~KP~G~TS~~vv~~v~~~l~k~~~~-~kk~g~~GTLDP~AtGvLvi~vG~aTKl~~~l~--~~~~~K~Y~~~~~lG   78 (226)
T cd02868           2 LFAVYKPPGVHWKHVRDTIESNLLKYFPE-DKVLVGVHRLDAFSSGVLVLGVNHGNKLLSHLY--SNHPTRVYTIRGLLG   78 (226)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHHCC-CEEEECCCCCCCCCCCCEEEEECHHHHHHHHHH--CCCCCEEEEEEEEEC
T ss_conf             89997599998999999999999766417-746960888897560338999887772569986--689976999999975


Q ss_pred             -------------------CCCHHHHHHHHHHHHCCCEEEE--------------------------CCC-----EEEEE
Q ss_conf             -------------------5564678887400000876750--------------------------343-----03640
Q gi|254780406|r  152 -------------------QVDQDKLNLLKKGIVIQGICYG--------------------------DMQ-----VTLDT  181 (354)
Q Consensus       152 -------------------~~~~~~~~~~~~g~~~~~~~~~--------------------------~~~-----~~~~~  181 (354)
                                         +++.+.++.....+.-.-....                          +-.     +.+..
T Consensus        79 ~~TdT~D~~G~v~~~~~~~~i~~~~i~~~l~~~~g~~~q~pP~~SA~k~~GkraYelAR~G~~~~~~~r~v~I~~i~l~~  158 (226)
T cd02868          79 KATENFFHTGRVIEKTTYDHITREKIERLLAVIQSGHQQKAFELCSVDDQSQQAAELAARGLIRPADKSPPIIYGIRLLE  158 (226)
T ss_pred             CCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHCCCEEEECCCHHEEEECCHHHHHHHHCCCCCCCCCCCEEEEEEEEEE
T ss_conf             65479899708797358987999999999997158705857622357708812899986899766788734999999985


Q ss_pred             CCCCEEEEEEEEEECCHHHHHHHHHHCCC------EEEEEEEEEECCEECCC-CCCCCE
Q ss_conf             26880799999951842899999998398------68688975870545187-554748
Q gi|254780406|r  182 QKGSNAWVTVGLREGKNREIKKVFEFFNW------KVNRLIRISYGPFQLGT-LLAGST  233 (354)
Q Consensus       182 ~~~~~~~~~v~l~eGr~~qIrr~~~~~g~------~V~~L~Rv~~G~~~l~~-L~~G~~  233 (354)
                      -+.....++|.-.-|.=-.||-+..-+|.      .+..|.|+++|+|.+++ |..=+|
T Consensus       159 ~~~p~~~~~v~cs~gtGtYIRsLa~DlG~~Lg~~a~l~~LrRt~~G~f~i~~al~~~~~  217 (226)
T cd02868         159 FRPPEFTLEVQCINETQEYLRKLIHEIGLELRSSAVCTQVRRTRDGPFTVDDALLRKQW  217 (226)
T ss_pred             ECCCEEEEEEEEECCCHHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHHCCCHHHC
T ss_conf             06998999999992867618999999998739927997789788967969995397778


No 42 
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=98.07  E-value=8.3e-06  Score=56.38  Aligned_cols=156  Identities=22%  Similarity=0.254  Sum_probs=92.0

Q ss_pred             EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf             38960278751563144333364421011023432002665543323202223676410001234457404775211245
Q gi|254780406|r   73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ  152 (354)
Q Consensus        73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~  152 (354)
                      .-++++|||.|+.++..=..-+..    +  ...++...|-||-..+|||++.-..  +.++..--.+..|+|.+++.--
T Consensus        10 ~G~l~idKP~G~TS~~vv~~vkk~----l--~~kKvGH~GTLDP~AtGvLiv~vG~--aTKl~~~~~~~~K~Y~a~i~lG   81 (244)
T PRK00020         10 DGVLLLDKPVGLSSNHALQRAKRT----V--DAAKAGHTGTLDPFATGLLVCCMGR--ATKISGRMLEADKTYQATLQFG   81 (244)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEECH--HHHHHHHHCCCCCEEEEEEEEC
T ss_conf             779997169989989999999998----2--9871577866797551418999673--7676597668992799999978


Q ss_pred             ----------------------CCHHHHHHHHHHHH--------------CCCE------------EEECCC-----EEE
Q ss_conf             ----------------------56467888740000--------------0876------------750343-----036
Q gi|254780406|r  153 ----------------------VDQDKLNLLKKGIV--------------IQGI------------CYGDMQ-----VTL  179 (354)
Q Consensus       153 ----------------------~~~~~~~~~~~g~~--------------~~~~------------~~~~~~-----~~~  179 (354)
                                            ++++.+......+.              +++.            ...+-.     +.+
T Consensus        82 ~~TdT~D~eG~v~~~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~GkrlY~lAR~G~~v~~~~R~v~I~~iel  161 (244)
T PRK00020         82 EETDSGDLTGHIVARAPDGFAGVEEAALRDVLSRFVGTIEQIPPMYSALKRDGKPLYEYARAGIELDRPPRQVTIRHIEL  161 (244)
T ss_pred             CCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCEECCCCEEEEEEEEEE
T ss_conf             76677676551564146767888999999999971686501498899756235428999977963214754899999999


Q ss_pred             EECCCCEEEEEEEEEECCHHHHHHHHHHCCC------EEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHH
Q ss_conf             4026880799999951842899999998398------68688975870545187554748867999998753
Q gi|254780406|r  180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNW------KVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL  245 (354)
Q Consensus       180 ~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~------~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~l~  245 (354)
                      ..-......++|.-..|-|  ||-++..+|.      .+..|.|+++|+|.+++-       ++-++|+.+.
T Consensus       162 l~~~~~~~~~~v~cSkGTY--IRSLa~Dig~~Lg~~a~l~~L~Rt~~G~f~l~~a-------i~ld~l~~~~  224 (244)
T PRK00020        162 LSFSGMQAQIDVACSKGTY--IRTLAQDIGRALGCHAHLAALRRTHVGPFSLDRA-------VTLEALQAMP  224 (244)
T ss_pred             EEECCCEEEEEEEECCCEE--EHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHHC-------CCHHHHHHCC
T ss_conf             8732886899999769668--1638999999859957986749526747087986-------7899998473


No 43 
>TIGR00478 tly hemolysin A; InterPro: IPR004538 Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture. The mechanism of action is not well defined. Hemolysin A is induced by sodium ribonucleate, and is produced by pathogenic bacterial strains. Hemolysin A from Treponema hyodysenteriae causes swine dysentry.; GO: 0003723 RNA binding, 0019836 hemolysis by symbiont of host red blood cells.
Probab=98.03  E-value=6.4e-06  Score=57.09  Aligned_cols=53  Identities=26%  Similarity=0.421  Sum_probs=48.9

Q ss_pred             HHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEEC
Q ss_conf             478899988687-78999999986986999999240687807999799999892
Q gi|254780406|r   15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL   67 (354)
Q Consensus        15 RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i   67 (354)
                      ||+-.|...|+| ||.+|.++|.+|.|.||++.|+.|+..|+.++.|+|-..+.
T Consensus         1 RLD~lLv~rgl~~sR~~Ak~lI~kG~V~VN~~~v~KP~~~v~~~~~i~l~~~~~   54 (240)
T TIGR00478         1 RLDILLVKRGLVESREKAKRLILKGEVLVNKKKVDKPSALVDKDAKIELVQNPL   54 (240)
T ss_pred             CCHHHHHHHCHHHHHHHHHHHHHCCCEEECCEEECCCCCEECCCCCEEEECCCC
T ss_conf             903677650114578999999873945555765208860441676034414777


No 44 
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=98.01  E-value=3.4e-05  Score=52.51  Aligned_cols=146  Identities=12%  Similarity=0.028  Sum_probs=80.6

Q ss_pred             EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf             38960278751563144333364421011023432002665543323202223676410001234457404775211245
Q gi|254780406|r   73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ  152 (354)
Q Consensus        73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~  152 (354)
                      .-++++|||+|+.++..=..-+..    +  ...++...|-||-..+|||++.-.. -+.+|..--....|+|.+++.--
T Consensus         9 ~GillidKP~G~TS~~vv~~vkk~----l--~~kKvGH~GTLDP~AtGvLiv~iG~-~~Tkl~~~~~~~~K~Y~a~i~lG   81 (235)
T PRK00989          9 EGILLVDKPQGRTSFSLIRALTKL----I--GVKKIGHAGTLDPFATGVMVMLIGR-KFTRLSDILLFEDKEYAAIAHLG   81 (235)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEECCC-CCCCHHHHHCCCCCEEEEEEEEC
T ss_conf             819999789999989999999998----5--8774687867797443528884074-51127898675784699999989


Q ss_pred             -------------------CCHHHHHHHHHHHHCCCEEEEC--------------------------C----CEEEEECC
Q ss_conf             -------------------5646788874000008767503--------------------------4----30364026
Q gi|254780406|r  153 -------------------VDQDKLNLLKKGIVIQGICYGD--------------------------M----QVTLDTQK  183 (354)
Q Consensus       153 -------------------~~~~~~~~~~~g~~~~~~~~~~--------------------------~----~~~~~~~~  183 (354)
                                         ++.+++......+.-.-.+..|                          .    .+.+..-+
T Consensus        82 ~~TdT~D~eG~i~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAiKv~Gkr~Y~lAR~g~~ve~~~r~v~I~~~l~~~~  161 (235)
T PRK00989         82 TTTDSYDCDGKVVGRSKKIPTLEEVLEAASYFQGEIQQVPPMFSAKKVQGKKLYEYARQGLSIERRHSTVQVHLQITKYE  161 (235)
T ss_pred             CCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHCCCEEECCCCCEEEEECCCCHHHHHHCCCEECCCCEEEEEEEEEEECC
T ss_conf             84777666785532148899999999999973387314188620588847068999867860115745899999997425


Q ss_pred             CCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC
Q ss_conf             88079999995184289999999839------868688975870545187
Q gi|254780406|r  184 GSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       184 ~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~  227 (354)
                      .....|+|.-..|-|  ||-++..+|      -.+..|.|+++|+|.+.+
T Consensus       162 ~~~~~~~v~cSkGTY--IRSLa~Dig~~Lg~~a~l~~L~Rt~~G~f~l~~  209 (235)
T PRK00989        162 YPLLHFVVQCSKGTY--IRSIAHELGTMLGCGAYLEELRRLRSGSFSIDQ  209 (235)
T ss_pred             CCEEEEEEEECCCCC--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH
T ss_conf             882899999899356--999999999986984898551864683838899


No 45 
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=98.00  E-value=8.9e-06  Score=56.20  Aligned_cols=53  Identities=26%  Similarity=0.433  Sum_probs=49.0

Q ss_pred             HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE
Q ss_conf             4478899988687-7899999998698699999924068780799979999989
Q gi|254780406|r   14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP   66 (354)
Q Consensus        14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~   66 (354)
                      .|||-++-++|++ |+.+|.+||..|.|.|||+.|+.|++.|.++|.|.|..+.
T Consensus        92 ~RLD~vv~r~g~a~t~~~ARQ~v~Hghi~vNg~~v~ips~~~k~gd~i~vkeks  145 (201)
T PRK05327         92 RRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVIEVREKS  145 (201)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHEEEEEEEEECCEEECCCCEECCCCCEEEECCCC
T ss_conf             998899987141058888620064405998999835787473899999977000


No 46 
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=97.97  E-value=3.4e-05  Score=52.56  Aligned_cols=155  Identities=16%  Similarity=0.135  Sum_probs=89.6

Q ss_pred             EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC---
Q ss_conf             96027875156314433336442101102343200266554332320222367641000123445740477521124---
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG---  151 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~---  151 (354)
                      ++++|||.|+.++..=..-+.    .  ....++...|-||-..+|||++.-..  +.++..--....|+|.+++.-   
T Consensus         2 illi~KP~G~TS~~vv~~vkk----~--~~~kKvGH~GTLDP~AtGvL~v~~G~--aTK~~~~~~~~~K~Y~~~~~lG~~   73 (279)
T PRK02193          2 ITLLYKPKKISSFKFIRQFSK----T--NLIKKIGHAGTLDPLATGLLLVATDE--DTKLLDYLDQKTKTYLAKIQLGFW   73 (279)
T ss_pred             EEEEECCCCCCHHHHHHHHHH----H--HCCCCCCCCCCCCCCCEEEEEEEECH--HHHHCHHHCCCCCEEEEEEEECCC
T ss_conf             899989998998999999999----8--39995361746798674479999786--651264554578269999996775


Q ss_pred             -----------------CCCHHHHHHHHHHHHCCCEEE--------------------------ECCCE-----EEEECC
Q ss_conf             -----------------556467888740000087675--------------------------03430-----364026
Q gi|254780406|r  152 -----------------QVDQDKLNLLKKGIVIQGICY--------------------------GDMQV-----TLDTQK  183 (354)
Q Consensus       152 -----------------~~~~~~~~~~~~g~~~~~~~~--------------------------~~~~~-----~~~~~~  183 (354)
                                       .++.+.+......+.-.-.+.                          .+..+     .+..-+
T Consensus        74 TdT~D~eG~v~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~GkrlY~lAR~g~~ve~~~r~v~I~~~~l~~~~  153 (279)
T PRK02193         74 STTYDSEGQIINVSSNIKVTKDNLEQALNRFSGSQKQVPPVFSAKKVNGKRAYHYARQGKQIELKPIEIKISKIILINFD  153 (279)
T ss_pred             CCCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCEEECCCEEEEEEEEEEEEEC
T ss_conf             77656777456304899999999999999667878982888996231563589898668543056478999999999841


Q ss_pred             --CCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCCCCCCCEEECCHHHHHH
Q ss_conf             --88079999995184289999999839------8686889758705451875547488679999987
Q gi|254780406|r  184 --GSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE  243 (354)
Q Consensus       184 --~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~  243 (354)
                        .....++|.-.-|-|  ||-++..+|      -.+..|.|+++|+|.++++..    -|.+.++-+
T Consensus       154 ~~~~~~~~~v~CSkGTY--IRsLa~Dig~~Lg~~a~~~~L~Rt~~G~f~~~~~~~----~l~~~~l~~  215 (279)
T PRK02193        154 EKLQNCVFMWQVSRGTY--IRSLIDDIGKMLKTRAYMDDLERTKIGNLDKNFLNQ----SLKPQDIID  215 (279)
T ss_pred             CCCCEEEEEEEECCCCC--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHHHHH----HCCHHHHCC
T ss_conf             78974999999899768--999999999986984798353977786859668761----089778568


No 47 
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=97.97  E-value=4.3e-05  Score=51.91  Aligned_cols=151  Identities=17%  Similarity=0.155  Sum_probs=90.2

Q ss_pred             EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC-
Q ss_conf             3896027875156314433336442101102343200266554332320222367641000123445740477521124-
Q gi|254780406|r   73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-  151 (354)
Q Consensus        73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~-  151 (354)
                      .-++++|||.|+.++..=..-+.    .+  ...+....|-||-..+|||++.-.  -+.++..--....|+|.+++.- 
T Consensus        17 ~G~l~idKP~G~TS~~vv~~vk~----~~--~~kKvGH~GTLDP~AtGvL~v~~G--~aTK~~~~~~~~~K~Y~~~~~lG   88 (310)
T PRK01851         17 DGVLLLDKPVGLSSNDALIRAKR----LL--LAKKAGHTGTLDPLASGLLPLCFG--EATKFSQDLLEADKTYEATMRLG   88 (310)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH----HH--CCCCCCCCCCCCCCCCCEEEEEEC--HHHHHHHHHCCCCCEEEEEEEEC
T ss_conf             78999705998998999999999----85--888457786779734040689978--87733177576980899999989


Q ss_pred             ------------------CCCHHHHHHHHHHHHC--------------CCE--------------EEECCC---EEEEEC
Q ss_conf             ------------------5564678887400000--------------876--------------750343---036402
Q gi|254780406|r  152 ------------------QVDQDKLNLLKKGIVI--------------QGI--------------CYGDMQ---VTLDTQ  182 (354)
Q Consensus       152 ------------------~~~~~~~~~~~~g~~~--------------~~~--------------~~~~~~---~~~~~~  182 (354)
                                        .++.+.++.....+.-              ++.              ..+.+.   +.+..-
T Consensus        89 ~~TdT~D~~G~v~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAiKv~GkrlY~lAR~G~~ve~~~R~v~I~~i~l~~~  168 (310)
T PRK01851         89 VRTTTGDAEGEVLDTRPVSCDRAAVEAALARFVGEIVQVPPMYSALKRDGKPLYEYARAGQTVEREGRRVTIRALDLLAC  168 (310)
T ss_pred             CCCCCCCCCCCEECCCCCCCCHHHHHHHHHHCCCCEEECCCHHHHEEECCHHHHHHHHCCCCEEEEEEEEEEEEEEEEEC
T ss_conf             86777787787720367999999999999967751676597068344458878999857886055028999999999723


Q ss_pred             CCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC-CCCCCE
Q ss_conf             688079999995184289999999839------868688975870545187-554748
Q gi|254780406|r  183 KGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT-LLAGST  233 (354)
Q Consensus       183 ~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~-L~~G~~  233 (354)
                      ......++|.-..|-|  ||-++.-+|      -.+..|.|+++|+|.+.+ +..-++
T Consensus       169 ~~~~~~~~v~CSkGTY--IRsLa~Dig~~Lg~~a~l~~LrRt~~G~f~~~~a~~Le~l  224 (310)
T PRK01851        169 ALPDVTFRVTCSKGTY--VRTLAEDIGEALGCGAHLTMLRRTGVGALTLEHAVTLDAL  224 (310)
T ss_pred             CCCCEEEEEEECCCEE--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHHCCCHHHH
T ss_conf             7982899999889616--6999999999869856982419667877266877089999


No 48 
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein).  Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene.  In addition dyskerin is likely to have a structural role in the telomerase complex.  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r
Probab=97.95  E-value=6.3e-05  Score=50.86  Aligned_cols=144  Identities=18%  Similarity=0.144  Sum_probs=87.5

Q ss_pred             EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC--
Q ss_conf             896027875156314433336442101102343200266554332320222367641000123445740477521124--
Q gi|254780406|r   74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG--  151 (354)
Q Consensus        74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~--  151 (354)
                      -++++|||.|+.++..=..-+..    +  ...++...|-||-..+|||++.-..  +.++..--....|+|.+++..  
T Consensus         3 Gil~idKP~G~TS~~vv~~ikk~----l--~~kKvGH~GTLDP~AtGvL~v~iG~--aTKl~~~~~~~~K~Y~~~~~f~~   74 (182)
T cd02572           3 GVINLDKPSGPSSHEVVAWIKRI----L--GVEKTGHSGTLDPKVTGCLPVCIDR--ATRLVKSQQEAGKEYVCVMRLHD   74 (182)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEECCH--HHHHHHHHCCCCEEEEEEEEECC
T ss_conf             89999579999989999999998----5--7664688977797554347763267--88999986779808998167078


Q ss_pred             CCCHHHHHHHHHHHHCCCEEEECC-----------CE---EEEECCC--CEEEEEEEEEECCHHHHHHHHHHCC------
Q ss_conf             556467888740000087675034-----------30---3640268--8079999995184289999999839------
Q gi|254780406|r  152 QVDQDKLNLLKKGIVIQGICYGDM-----------QV---TLDTQKG--SNAWVTVGLREGKNREIKKVFEFFN------  209 (354)
Q Consensus       152 ~~~~~~~~~~~~g~~~~~~~~~~~-----------~~---~~~~~~~--~~~~~~v~l~eGr~~qIrr~~~~~g------  209 (354)
                      .++.+.+......+.-.-....|.           .+   .+..-+.  ....++|+-..|-|  ||-+..-+|      
T Consensus        75 ~~~~~~i~~~l~~f~G~i~Q~PP~ySAvK~~~r~~~I~~~~~l~~~~~~~~~~f~v~cskGTY--IRSLa~Dig~~Lg~~  152 (182)
T cd02572          75 DVDEEKVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTY--IRTLCVHIGLLLGVG  152 (182)
T ss_pred             CCCHHHHHHHHHHCCEEEEECCCCHHHCCCCCCCCEEEEEEEEEECCCCCEEEEEEEECCCEE--HHHHHHHHHHHHCCC
T ss_conf             899999999999788037233785431214467627999999998188767999999679656--999999999986996


Q ss_pred             CEEEEEEEEEECCEECCC
Q ss_conf             868688975870545187
Q gi|254780406|r  210 WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       210 ~~V~~L~Rv~~G~~~l~~  227 (354)
                      -.+..|.|+++|+|.+.+
T Consensus       153 a~l~~L~Rt~~G~f~~ed  170 (182)
T cd02572         153 AHMQELRRTRSGPFSEED  170 (182)
T ss_pred             EEEEEEEEEEEECCCCHH
T ss_conf             799787957870887063


No 49 
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=97.93  E-value=4.5e-05  Score=51.77  Aligned_cols=145  Identities=14%  Similarity=0.133  Sum_probs=85.6

Q ss_pred             EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC-
Q ss_conf             3896027875156314433336442101102343200266554332320222367641000123445740477521124-
Q gi|254780406|r   73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-  151 (354)
Q Consensus        73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~-  151 (354)
                      .-++++|||.|+.++..=..-+..    +  ...++...|-||-..+|||++.-. + +.++..--....|+|.+++.- 
T Consensus        12 ~Gil~idKP~g~TS~~~v~~~kk~----~--~~kKvGH~GTLDP~AtGvL~i~~G-~-aTK~~~~~~~~~K~Y~~~~~lG   83 (314)
T PRK05033         12 NGVLLLDKPQGMSSNDALQKVKRI----Y--NANKAGHTGALDPLATGMLPICLG-E-ATKFSQFLLDSDKRYRVIAKLG   83 (314)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEEC-H-HHHHHHHHCCCCCEEEEEEEEC
T ss_conf             679998159999989999999998----5--888568785779756021899988-8-8704088668991799999978


Q ss_pred             ------------------CCCHHHHHHHHHHHHCCCEEE----------------------------ECC---CEEEEEC
Q ss_conf             ------------------556467888740000087675----------------------------034---3036402
Q gi|254780406|r  152 ------------------QVDQDKLNLLKKGIVIQGICY----------------------------GDM---QVTLDTQ  182 (354)
Q Consensus       152 ------------------~~~~~~~~~~~~g~~~~~~~~----------------------------~~~---~~~~~~~  182 (354)
                                        .++.+.+......+.-.-.+.                            +++   .+.+..-
T Consensus        84 ~~TdT~D~eG~i~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~Gkr~Y~lAR~G~~ve~~~R~v~I~~i~l~~~  163 (314)
T PRK05033         84 QRTDTSDADGQVVEERPVTFSAEQLAAALETFRGDIEQIPSMYSALKYQGKPLYEYARQGIEVPREARPITVYELLFIRH  163 (314)
T ss_pred             CCCCCCCCCCCEEECCCCCCCHHHHHHHHHHCCCCEEECCCHHHHEEECCHHHHHHHHCCCCEEECCEEEEEEEEEEEEE
T ss_conf             86566788887720368999999999999975584524588789542578609999877984142017989989999973


Q ss_pred             CCCEEEEEEEEEECCHHHHHHHHHHC------CCEEEEEEEEEECCEECCC
Q ss_conf             68807999999518428999999983------9868688975870545187
Q gi|254780406|r  183 KGSNAWVTVGLREGKNREIKKVFEFF------NWKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       183 ~~~~~~~~v~l~eGr~~qIrr~~~~~------g~~V~~L~Rv~~G~~~l~~  227 (354)
                      +.....++|.-.-|  ..||-++..+      +-.+..|.|+++|+|.+.+
T Consensus       164 ~~~~~~~~V~CSkG--TYIRSLa~Dig~~Lg~~a~l~~LrRt~vG~f~~~~  212 (314)
T PRK05033        164 EGNELELEVHCSKG--TYIRTIIDDLGEKLGCGAHVTYLRRLAVSKYPVER  212 (314)
T ss_pred             CCCEEEEEEEECCC--CCHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH
T ss_conf             28868999997897--23589999999875983797324853586818798


No 50 
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=97.92  E-value=5e-05  Score=51.49  Aligned_cols=143  Identities=17%  Similarity=0.167  Sum_probs=86.8

Q ss_pred             EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC-
Q ss_conf             8960278751563144333364421011023432002665543323202223676410001234457404775211245-
Q gi|254780406|r   74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-  152 (354)
Q Consensus        74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~-  152 (354)
                      -++++|||.|+.++..=..-+..      -...++...|-||-..+|||++.-..  +.++..--....|+|.+++.-- 
T Consensus         3 G~l~i~KP~g~TS~~vv~~vkk~------l~~kKvGH~GTLDP~AtGvL~v~~G~--aTK~~~~~~~~~K~Y~a~~~lG~   74 (289)
T PRK00130          3 GVINVYKPKGMTSFDVVRKIRKI------AKIKKVGHTGTLDPLASGVLPVCLGK--ATKIVDYIMEGKKVYRVELKLGT   74 (289)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH------HCCCCCCCCCCCCCCCCCEEEEEECH--HHHHHHHHCCCCEEEEEEEEECC
T ss_conf             79996089999989999999998------48885577846798560428999787--76143676799907999999787


Q ss_pred             ------------------CCHHHHHHHHHHH-----------------------------HCCCEEEECC---CEEEEEC
Q ss_conf             ------------------5646788874000-----------------------------0087675034---3036402
Q gi|254780406|r  153 ------------------VDQDKLNLLKKGI-----------------------------VIQGICYGDM---QVTLDTQ  182 (354)
Q Consensus       153 ------------------~~~~~~~~~~~g~-----------------------------~~~~~~~~~~---~~~~~~~  182 (354)
                                        ++.+.+......+                             .++- ..+++   .+.+..-
T Consensus        75 ~TdT~D~~G~i~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~~SA~Kv~GkrlY~lAR~G~~ve~-~~R~v~I~~i~l~~~  153 (289)
T PRK00130         75 TTDTYDREGEVLEEKEVSITEDEVEEAINSFIGEIDQVPPMYSALKINGVRLYELARKGIEVER-EARKITIYDICILSI  153 (289)
T ss_pred             CCCCCCCCCCEEEECCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCCCCC-CCEEEEEEEEEEECC
T ss_conf             5776546797876458998999999999975682625288789624159869999975875566-856999999998407


Q ss_pred             CCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC
Q ss_conf             688079999995184289999999839------868688975870545187
Q gi|254780406|r  183 KGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       183 ~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~  227 (354)
                      +.....++|.-..|-|  ||-++.-+|      -.+..|.|+++|+|.+.+
T Consensus       154 ~~~~~~~~v~CSkGTY--IRsLa~Dig~~Lg~~a~l~~L~Rt~vG~f~~~~  202 (289)
T PRK00130        154 DLPYVIFDVKCSKGTY--IRSLCYDIGEKLNVGATMWNLERLETGPFNIEE  202 (289)
T ss_pred             CCCEEEEEEEECCCEE--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH
T ss_conf             8996999999779557--799999999976984798664965786718899


No 51 
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=97.88  E-value=6.4e-05  Score=50.80  Aligned_cols=146  Identities=17%  Similarity=0.148  Sum_probs=86.2

Q ss_pred             CEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC
Q ss_conf             43896027875156314433336442101102343200266554332320222367641000123445740477521124
Q gi|254780406|r   72 RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG  151 (354)
Q Consensus        72 ~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~  151 (354)
                      -.-++++|||.|+.++..=..-+..    +  ...+....|-||-..+|||++.-.  -+.++..--....|+|.+++.-
T Consensus         9 m~Gil~idKP~g~TS~~vv~~vrr~----l--~~~KvGH~GTLDP~AtGvL~i~~g--~aTK~~~~~~~~~K~Y~~~~~l   80 (300)
T PRK04642          9 LHGILLLDKPAGLSSNNALQAARRL----L--RAEKGGHTGSLDPLATGLLPLCFG--EATKIAGLLLGSAKAYDAEIVL   80 (300)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEEC--HHHHHCHHHCCCCCEEEEEEEE
T ss_conf             6779997079989989999999998----6--898457685779856043789978--7651366656136643799998


Q ss_pred             --------------------CCCHHHHHHHHHHHH--------------CCCE--------------EEECCC---EEEE
Q ss_conf             --------------------556467888740000--------------0876--------------750343---0364
Q gi|254780406|r  152 --------------------QVDQDKLNLLKKGIV--------------IQGI--------------CYGDMQ---VTLD  180 (354)
Q Consensus       152 --------------------~~~~~~~~~~~~g~~--------------~~~~--------------~~~~~~---~~~~  180 (354)
                                          .++.+.+......+.              +++.              ..+.+.   +.+.
T Consensus        81 G~~TdT~D~~G~v~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~GkrlY~lAR~G~~ve~~~R~v~I~~l~ll  160 (300)
T PRK04642         81 GVTTDTDDADGQVLRERPVPDLSEAALQAALAPFIGRIQQQAPIYSALKQGGEPLYAKARRGEVIEAPVREVEVHAIEVL  160 (300)
T ss_pred             CCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHCCCHHHHHHHHCCCEEEECEEEEEEEEEEEE
T ss_conf             75136767778676405789889999999999777535652978897242882188887669703202089999999985


Q ss_pred             ECCCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC
Q ss_conf             02688079999995184289999999839------868688975870545187
Q gi|254780406|r  181 TQKGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       181 ~~~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~  227 (354)
                      .-......++|.-..|  -.||-++..+|      -.+..|.|+++|+|.+.+
T Consensus       161 ~~~~~~~~~~v~CskG--TYIRsLa~Dig~~Lg~~a~l~~LrRt~vG~f~~~~  211 (300)
T PRK04642        161 GYAAPRLRLRVTCGSG--TYIRSLARDLGEVLGCGAHIAALRRLWVEPFRAPQ  211 (300)
T ss_pred             ECCCCEEEEEEEECCC--CHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH
T ss_conf             0369859999998870--15999999999985985797021843786808798


No 52 
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  E. coli TruB and M.  tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved.  E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=97.85  E-value=5.3e-05  Score=51.34  Aligned_cols=143  Identities=21%  Similarity=0.222  Sum_probs=84.6

Q ss_pred             EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC---
Q ss_conf             96027875156314433336442101102343200266554332320222367641000123445740477521124---
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG---  151 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~---  151 (354)
                      ++++|||.|+.++..=..-+..    +  ...++...|-||-..+|||++.-.  -+.++..--.+..|+|.+++.-   
T Consensus         2 ~l~i~Kp~g~tS~~~v~~~k~~----~--~~kKvGH~GTLDP~AtGvL~i~~g--~aTKl~~~~~~~~K~Y~~~~~lG~~   73 (277)
T cd02573           2 ILLLDKPAGLTSHDVVQKVRRL----L--GTKKVGHTGTLDPLATGVLPIALG--EATKLSQYLLDADKTYRATVRLGEA   73 (277)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEEC--HHHHHHHHHCCCCCEEEEEEEECCC
T ss_conf             8999679999989999999998----5--888556375779766033789988--8870527867899179999998760


Q ss_pred             -----------------CCCHHHHHHHHHHHH--------------CCCE--------------EEECCC---EEEEECC
Q ss_conf             -----------------556467888740000--------------0876--------------750343---0364026
Q gi|254780406|r  152 -----------------QVDQDKLNLLKKGIV--------------IQGI--------------CYGDMQ---VTLDTQK  183 (354)
Q Consensus       152 -----------------~~~~~~~~~~~~g~~--------------~~~~--------------~~~~~~---~~~~~~~  183 (354)
                                       .++.+.+......+.              +++.              ..+.+.   +.+..-.
T Consensus        74 TdT~D~~G~i~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~GkrlY~lAR~G~~v~~~~r~v~I~~i~ll~~~  153 (277)
T cd02573          74 TDTDDAEGEIIETSPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKVNGKRLYELARAGEEVERPPRKVTIYSLELLSFD  153 (277)
T ss_pred             CCCCCCCCCEECCCCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCCCCCCCEEEEEEEEEEEEEC
T ss_conf             47655679871137899999999999999787707871988897464585199998779845568778999999998851


Q ss_pred             C--CEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC
Q ss_conf             8--8079999995184289999999839------868688975870545187
Q gi|254780406|r  184 G--SNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       184 ~--~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~  227 (354)
                      .  ....++|.-..|  -.||-++.-+|      -.+..|.|+++|+|.+.+
T Consensus       154 ~~~~~~~~~v~cSkG--TYIRsLa~Dig~~Lg~~a~l~~L~Rt~~G~f~~~~  203 (277)
T cd02573         154 PENPEADFEVECSKG--TYIRSLARDLGKALGCGAHLSALRRTRSGPFTLED  203 (277)
T ss_pred             CCCCEEEEEEEECCC--EEHHHHHHHHHHHHCCCEEEEEEECCEECCCCHHH
T ss_conf             789859999997786--33999999999985991898463820578869799


No 53 
>PRK11507 hypothetical protein; Provisional
Probab=97.81  E-value=4.2e-05  Score=51.94  Aligned_cols=62  Identities=16%  Similarity=0.281  Sum_probs=55.3

Q ss_pred             CCCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCC
Q ss_conf             6667734478899988687-7899999998698699999924068780799979999989225
Q gi|254780406|r    8 QENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK   69 (354)
Q Consensus         8 ~~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~   69 (354)
                      -+...-+.|.++|--+|+| |=-+|+.+|.+|.|+|||++-+.-..|+..+|.|+++|+.|..
T Consensus         6 L~~~~yIeL~~lLK~~glv~sGg~AK~~Ia~G~V~VnGevEtRKr~Ki~~GdvV~f~g~~i~V   68 (70)
T PRK11507          6 LGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQV   68 (70)
T ss_pred             CCCCCCEEHHHHHHHCCCCCCCHHHHHHEECCEEEECCEEEEEEEEEEECCCEEEECCEEEEE
T ss_conf             389871008888847172046587786541876899999963310251089999999999999


No 54 
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=97.80  E-value=7.9e-05  Score=50.24  Aligned_cols=145  Identities=18%  Similarity=0.108  Sum_probs=83.9

Q ss_pred             EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf             38960278751563144333364421011023432002665543323202223676410001234457404775211245
Q gi|254780406|r   73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ  152 (354)
Q Consensus        73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~  152 (354)
                      .-++++|||.|+.++..=..-+..    +  ...++...|-||-..+|||++.-..  +.++..--....|+|.+++.--
T Consensus         3 ng~l~i~KP~g~TS~~vv~~vkk~----~--~~~KvGH~GTLDP~AtGvL~i~~g~--aTK~~~~~~~~~K~Y~~~~~~G   74 (293)
T PRK01528          3 NYWLNIYKPRGISSAKLVSIVKKI----L--GKVKIGHAGTLDVEAEGILPLAVGE--ATKLIQLLIDAKKTYIFTVKFG   74 (293)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEECH--HHHHHHHHCCCCEEEEEEEEEC
T ss_conf             758998779999989999999998----4--8980576867887570158999786--6503378657980699999978


Q ss_pred             C-------------------CHHHHHHHHHHH--------------HCCCE------------EEECCCE-----EEEEC
Q ss_conf             5-------------------646788874000--------------00876------------7503430-----36402
Q gi|254780406|r  153 V-------------------DQDKLNLLKKGI--------------VIQGI------------CYGDMQV-----TLDTQ  182 (354)
Q Consensus       153 ~-------------------~~~~~~~~~~g~--------------~~~~~------------~~~~~~~-----~~~~~  182 (354)
                      .                   +.+.+......+              .+++.            ...+-.+     .+..-
T Consensus        75 ~~TdT~D~eG~ii~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkraY~lAR~G~~vel~~R~v~I~~l~ll~~  154 (293)
T PRK01528         75 KQTDSGDYAGKVIATKDYIPSQEEAYAVCSKFIGNVTQIPPAFSALKVNGVRAYKLAREGKEVELKPRNITIYDLKCLNF  154 (293)
T ss_pred             CCCCCCCCCCCEEECCCCCCCHHHHHHHHHHCCCCEEEECCHHHHHCCCCHHHHHHHHCCCEEECCCEEEEEEEEEEEEE
T ss_conf             84798886775874157899999999999857782799088899620067609999866972442767999999897640


Q ss_pred             CCCE--EEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC
Q ss_conf             6880--79999995184289999999839------868688975870545187
Q gi|254780406|r  183 KGSN--AWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       183 ~~~~--~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~  227 (354)
                      ...+  ..+.|.-.-|  -.||-++.-+|      -.+..|.|+++|+|.+.+
T Consensus       155 ~~~~~~~~f~v~CskG--TYIRSLa~Dlg~~Lg~~a~~~~LrRt~~G~F~~~~  205 (293)
T PRK01528        155 DEKNATATYYTECSKG--TYIRTLAEDLALSLQSLGFVIELRRTQVGIFKEEN  205 (293)
T ss_pred             CCCCCEEEEEEEECCC--EEHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH
T ss_conf             4778669999997897--05378999999985985687244876773878688


No 55 
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=97.79  E-value=0.00013  Score=48.84  Aligned_cols=149  Identities=15%  Similarity=0.158  Sum_probs=85.4

Q ss_pred             CCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEEC
Q ss_conf             64389602787515631443333644210110234320026655433232022236764100012344574047752112
Q gi|254780406|r   71 ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH  150 (354)
Q Consensus        71 ~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~  150 (354)
                      ...-++++|||.|+.++..=..-+..    +  ...++...|-||-..+|||++.-..  +.++..--.+..|+|.+++.
T Consensus         7 ~~sGil~idKP~G~TS~~vv~~vk~~----~--~~kKvGH~GTLDP~AtGvL~v~~G~--aTKl~~~~~~~~K~Y~a~~~   78 (298)
T PRK03287          7 TGSGLVVVDKPAGMTSHDVVARCRRI----F--GTRKVGHAGTLDPMATGVLVLGVER--ATKLLGHLVATDKSYTATIR   78 (298)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEECH--HHCCCHHHCCCCCEEEEEEE
T ss_conf             88789999479999989999999998----4--8983366857797460438999787--76218746557817999999


Q ss_pred             C--------------------CCCHHHHHHHHHHHHCCCEEEEC----------------------------CCE---EE
Q ss_conf             4--------------------55646788874000008767503----------------------------430---36
Q gi|254780406|r  151 G--------------------QVDQDKLNLLKKGIVIQGICYGD----------------------------MQV---TL  179 (354)
Q Consensus       151 ~--------------------~~~~~~~~~~~~g~~~~~~~~~~----------------------------~~~---~~  179 (354)
                      -                    .++.+.++.....+.-+-.+..|                            +.+   .+
T Consensus        79 lG~~TdT~D~eG~v~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~GkrlY~lAR~G~~ve~~~R~v~I~~~~l  158 (298)
T PRK03287         79 LGQTTSTDDAEGEVLSSAPASHLTEEAIAAAVAALTGEIMQVPSAVSAIKVDGKRAYARVRAGEEVELPARPVTISRFEV  158 (298)
T ss_pred             ECCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHCCCCEEEECCCHHEEEECCHHHHHHHHCCCCCCCCCEEEEEEEEEE
T ss_conf             89737776677877503679989999999999975762447077213233267989999975984205866899999999


Q ss_pred             EECCCCE--EEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC
Q ss_conf             4026880--79999995184289999999839------868688975870545187
Q gi|254780406|r  180 DTQKGSN--AWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       180 ~~~~~~~--~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~  227 (354)
                      ..-....  ..+.+.+.=++=-.||-++..+|      -.+..|.|+++|+|.+.+
T Consensus       159 ~~~~~~~~~~~~~~~V~CSkGTYIRSLa~Dlg~~Lg~~a~l~~LrRt~~G~f~~~~  214 (298)
T PRK03287        159 LAVRRDDAFIDLDVEVDCSSGTYIRALARDLGAALGVGGHLTALRRTRVGPFTLDQ  214 (298)
T ss_pred             EEECCCCCCCEEEEEEEECCCEEHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH
T ss_conf             85227777510799999679646799999999976985798554855685809799


No 56 
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M.  tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required.  E. coli TruB, M.  tuberculosis TruB and S. cerevisiae Pus4,  make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=97.78  E-value=9.6e-05  Score=49.69  Aligned_cols=143  Identities=17%  Similarity=0.112  Sum_probs=81.4

Q ss_pred             EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC--
Q ss_conf             960278751563144333364421011023432002665543323202223676410001234457404775211245--
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ--  152 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~--  152 (354)
                      ++++|||.|+.++..=..-+..    +  ...++...|.||-..+|||++--. + +.++..--....|+|.+++.--  
T Consensus         2 il~i~KP~G~TS~~vv~~vk~~----~--~~kKvGH~GTLDP~AtGvL~i~vG-~-aTK~~~~~~~~~K~Y~~~~~lG~~   73 (210)
T cd00506           2 LFAVDKPQGPSSHDVVDTIRRI----F--LAEKVGHGGTLDPFATGVLVVGIG-K-ATKLLKHLLAATKDYTAIGRLGQA   73 (210)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEEC-H-HHHHHHHHCCCCCEEEEEEEECCE
T ss_conf             8999679999989999999998----5--877357686669745242899977-8-887999875599778799998530


Q ss_pred             ------------------CCHHHHHHHHHHHHCCCEEEEC--------------------------CC-----EEEEECC
Q ss_conf             ------------------5646788874000008767503--------------------------43-----0364026
Q gi|254780406|r  153 ------------------VDQDKLNLLKKGIVIQGICYGD--------------------------MQ-----VTLDTQK  183 (354)
Q Consensus       153 ------------------~~~~~~~~~~~g~~~~~~~~~~--------------------------~~-----~~~~~~~  183 (354)
                                        ++.+.++.....+.-.-....|                          -.     +.+..-.
T Consensus        74 TdT~D~~G~i~~~~~~~~~~~~~i~~~l~~f~G~~~Q~PP~ySA~Kv~Gkr~Y~lAR~g~~v~~~~r~v~I~~~~ll~~~  153 (210)
T cd00506          74 TDTFDATGQVIEETPYDHITHEQLERALETLTGDIQQVPPLYSAVKRQGQRAYELARRGLLVPDEARPPTIYELLCIRFN  153 (210)
T ss_pred             ECCCCCCCCEECCCCCCCCCHHHHHHHHHHCCCCEEECCCHHHEEEECCCCHHHHHHCCCCCCCCCEEEEEEEEEEEEEC
T ss_conf             17999888621336899899999999998665776551855775631783489998668621346403489999999852


Q ss_pred             CCE--EEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC
Q ss_conf             880--79999995184289999999839------868688975870545187
Q gi|254780406|r  184 GSN--AWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       184 ~~~--~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~  227 (354)
                      ...  ..++|.-..|-|  ||.+..-+|      -.+..|.|+++|+|.+.+
T Consensus       154 ~~~~~~~~~v~cs~GTY--IRsLa~Dig~~Lg~~a~l~~LrRt~~G~f~~~~  203 (210)
T cd00506         154 PPHFLLEVEVVCETGTY--IRTLIHDLGLELGVGAHVTELRRTRVGPFKVEN  203 (210)
T ss_pred             CCCCEEEEEEEECCCCC--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH
T ss_conf             88878999999669727--999999999986998798378987786777898


No 57 
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=97.64  E-value=0.00021  Score=47.60  Aligned_cols=151  Identities=17%  Similarity=0.169  Sum_probs=86.7

Q ss_pred             EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf             38960278751563144333364421011023432002665543323202223676410001234457404775211245
Q gi|254780406|r   73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ  152 (354)
Q Consensus        73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~  152 (354)
                      .-++++|||.|+.++..=..-+..    +  ...++...|-||-..+|||++.-..  +.++..--....|+|.+++.--
T Consensus        13 ~G~l~idKP~G~TS~~vv~~vkk~----~--~~kKvGH~GTLDP~AtGvL~i~~G~--aTk~~~~~~~~~K~Y~~~~~lG   84 (305)
T PRK05389         13 SGWLILDKPAGMTSTEAVSKVKWL----F--DAQKAGHAGTLDPLASGVLPIALGE--ATKTVPYVMDGTKRYRFTVAWG   84 (305)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEECH--HHHHHHHHCCCCEEEEEEEEEC
T ss_conf             779998249999989999999998----5--8885677867798660238899887--7623367656880799999984


Q ss_pred             -------------------CCHHHHHHHHHHHH--------------CCCE--------------EEECCCE---EEEEC
Q ss_conf             -------------------56467888740000--------------0876--------------7503430---36402
Q gi|254780406|r  153 -------------------VDQDKLNLLKKGIV--------------IQGI--------------CYGDMQV---TLDTQ  182 (354)
Q Consensus       153 -------------------~~~~~~~~~~~g~~--------------~~~~--------------~~~~~~~---~~~~~  182 (354)
                                         ++.+.++.....+.              +++.              ..+.+.+   .+..-
T Consensus        85 ~~TdT~D~~G~v~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAiKv~Gkr~Y~lAR~G~~ve~~~R~v~I~~i~ll~~  164 (305)
T PRK05389         85 EERDTDDLEGEVTATSDKRPTDEEIRALLPAFTGVIMQVPPQFSAIKIDGERAYDLAREGETVELPPRPVEIDRLTLVDR  164 (305)
T ss_pred             CCCCCCCCCCCEEEECCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCCCCCCCEEEEEEEEEEEEC
T ss_conf             31335666885456258997599999999968761787288789644368019999877982135637999999899733


Q ss_pred             -CCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC-CCCCCE
Q ss_conf             -688079999995184289999999839------868688975870545187-554748
Q gi|254780406|r  183 -KGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT-LLAGST  233 (354)
Q Consensus       183 -~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~-L~~G~~  233 (354)
                       ......|+|.-.-|-  .||-++.-+|      -.+..|.|+++|+|.+.+ +..-++
T Consensus       165 ~~~~~~~f~v~CSkGT--YIRsLa~Dig~~Lg~~a~l~~LrRt~vG~f~~~~a~~le~l  221 (305)
T PRK05389        165 PDADHAVFEVECGKGT--YVRSLARDMGRALGCYGHIAALRRTWVGPFTEEDMITLDKL  221 (305)
T ss_pred             CCCCEEEEEEEECCCE--EHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHHCCCHHHH
T ss_conf             7899899999978963--76998999998759847984338446878287996689999


No 58 
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.58  E-value=0.00027  Score=46.90  Aligned_cols=144  Identities=13%  Similarity=0.083  Sum_probs=82.7

Q ss_pred             EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC--
Q ss_conf             896027875156314433336442101102343200266554332320222367641000123445740477521124--
Q gi|254780406|r   74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG--  151 (354)
Q Consensus        74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~--  151 (354)
                      -++++|||.|+.++..=..-+..+      ...++...|-||-..+|||++.-..  +.++..--....|+|.+++.-  
T Consensus         4 G~l~vdKP~G~TS~~vv~~ikk~~------~~kKvGH~GTLDP~AtGvL~v~~G~--aTkl~~~~~~~~K~Y~~~~~lG~   75 (293)
T PRK02484          4 GIINLKKEAGMTSHDAVFKLRKIL------QTKKIGHGGTLDPDVVGVLPIAVGK--ATRVIEYMTEAGKVYEGEVTLGY   75 (293)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH------CCCCCCCCCCCCCCCEEEEEEEECH--HHHHHHHHCCCCCEEEEEEEECC
T ss_conf             699972699999899999999984------8985565836798661268999788--77151876648938999999433


Q ss_pred             -------------------CCCHHHHHHHHHHH--------------HCCCE--------------EEECCCEEEE----
Q ss_conf             -------------------55646788874000--------------00876--------------7503430364----
Q gi|254780406|r  152 -------------------QVDQDKLNLLKKGI--------------VIQGI--------------CYGDMQVTLD----  180 (354)
Q Consensus       152 -------------------~~~~~~~~~~~~g~--------------~~~~~--------------~~~~~~~~~~----  180 (354)
                                         .++.+.++.....+              .+++.              ..+++.+.-.    
T Consensus        76 ~TdT~D~~G~ii~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAiKv~Gkr~Y~lAR~g~~ve~~~R~v~I~~~~l~~  155 (293)
T PRK02484         76 STTTEDASGEVVARTPVPAVLTEELVDQAMTSFTGKITQIPPMYSAVKVNGRKLYEYARAGEEVERPRRQVTISQFERTS  155 (293)
T ss_pred             CCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCCCCCCCEEEEEEEEEECC
T ss_conf             25666788866763477789999999999986874067659768962215567999987797034687789999988225


Q ss_pred             --ECCCC--EEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC
Q ss_conf             --02688--079999995184289999999839------868688975870545187
Q gi|254780406|r  181 --TQKGS--NAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       181 --~~~~~--~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~  227 (354)
                        .-+..  ...++|+-..|-|  ||-++.-+|      -.+..|.|+++|+|.+.+
T Consensus       156 ~~~~~~~~~~~~~~v~CSkGTY--IRsLa~Dlg~~Lg~~a~~~~LrRt~~G~F~~~~  210 (293)
T PRK02484        156 PLNFEDGLCRFSFKVACSKGTY--VRTLAVDLGRKLGYASHMSFLQRTASAGLTLED  210 (293)
T ss_pred             CCCCCCCCCEEEEEEEECCCEE--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH
T ss_conf             3335677506999999767447--389999999985993798563976785838798


No 59 
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=97.56  E-value=0.00032  Score=46.38  Aligned_cols=145  Identities=17%  Similarity=0.196  Sum_probs=82.5

Q ss_pred             EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC--
Q ss_conf             896027875156314433336442101102343200266554332320222367641000123445740477521124--
Q gi|254780406|r   74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG--  151 (354)
Q Consensus        74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~--  151 (354)
                      -++++|||.|+.++..=..-+...      ...++...|-||-..+|||++.-.-  +.++..--....|+|.+++.-  
T Consensus         3 Gil~idKP~G~TS~~vv~~vr~~l------~~kKvGH~GTLDP~AtGvL~i~iG~--aTKl~~~l~~~~K~Y~a~~~lG~   74 (307)
T PRK01550          3 GVVLLHKPKGMTSHDCVFKLRKIL------REKRIGHTGTLDPDVTGVLPICVGR--ATKIAQFLTSETKTYEGEVTLGF   74 (307)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHH------CCCCCCCCCCCCCCCEEEEEEEECC--CHHHCHHHCCCCCEEEEEEEEEE
T ss_conf             799970699899899999999984------8983464746798662169999780--00013444667834899999976


Q ss_pred             -------------------CCCHHHHHHHHHHH-----------------------------HCCCEEEECCCEE---EE
Q ss_conf             -------------------55646788874000-----------------------------0087675034303---64
Q gi|254780406|r  152 -------------------QVDQDKLNLLKKGI-----------------------------VIQGICYGDMQVT---LD  180 (354)
Q Consensus       152 -------------------~~~~~~~~~~~~g~-----------------------------~~~~~~~~~~~~~---~~  180 (354)
                                         .++.+.++.....+                             .++- ..+++.+.   +.
T Consensus        75 ~TdT~D~~G~vi~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~GkrlY~lAR~G~~ve~-~~R~v~I~~~~ll  153 (307)
T PRK01550         75 STTTEDASGEVVETKHVDRVITRKEVEEVLAELTGTIEQMPPMFSAVKVNGKKLYEYARAGQEVER-PVRTITIHEFVLL  153 (307)
T ss_pred             ECCCCCCCCCEEEECCCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCCCCC-CCEEEEEEEEEEE
T ss_conf             468767787766404788899999999999967873635188899754334769999877882346-8668999999961


Q ss_pred             E----CCCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC
Q ss_conf             0----2688079999995184289999999839------868688975870545187
Q gi|254780406|r  181 T----QKGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       181 ~----~~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~  227 (354)
                      .    -++.+..+.+.+.=++=..||-+..-+|      -.+..|.|+++|+|.+.+
T Consensus       154 ~~~~~~~~~~~~~~~~v~CskGTYIRsLa~Dig~~Lg~~a~l~~L~Rt~~G~f~l~~  210 (307)
T PRK01550        154 DDREVFEGENISFRFRVTCSKGTYVRTLAVMIGEKLGFPSHMSHLVRTASGEFLLED  210 (307)
T ss_pred             CCCCCCCCCCCEEEEEEEECCCEEHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH
T ss_conf             452124555633899999889517699999999985983798353865786808798


No 60 
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=97.56  E-value=0.00059  Score=44.73  Aligned_cols=144  Identities=18%  Similarity=0.161  Sum_probs=78.3

Q ss_pred             EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC---
Q ss_conf             96027875156314433336442101102343200266554332320222367641000123445740477521124---
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG---  151 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~---  151 (354)
                      ++++|||.|+.++..=..-+.    .+  ...+....|-||-..+|||++.-.-  +.++..--.. .|+|.+++.-   
T Consensus         4 ~l~i~Kp~G~tS~~vv~~~k~----~~--~~kKvGH~GTLDP~AtGvL~i~~G~--aTk~~~~l~~-~K~Y~~~~~lG~~   74 (291)
T PRK02755          4 FLNLNKPAGWTSHDCVAKLRR----LL--RLKRVGHGGTLDPAATGVLPIAVGK--ATRLLPYLPS-GKAYKATVRFGLQ   74 (291)
T ss_pred             EEEEECCCCCCHHHHHHHHHH----HH--CCCCCCCCCCCCCCCCCEEEEEECH--HHEECCCCCC-CCEEEEEEEECCC
T ss_conf             999835998998999999999----85--8883677857797550528999765--7664300489-9589999998974


Q ss_pred             -----------------CCCHHHHHHHHHHH--------------HCCCEE------------EECCCEEE-----EE-C
Q ss_conf             -----------------55646788874000--------------008767------------50343036-----40-2
Q gi|254780406|r  152 -----------------QVDQDKLNLLKKGI--------------VIQGIC------------YGDMQVTL-----DT-Q  182 (354)
Q Consensus       152 -----------------~~~~~~~~~~~~g~--------------~~~~~~------------~~~~~~~~-----~~-~  182 (354)
                                       .++.+.++.....+              .+++..            ..+-.+.+     .. .
T Consensus        75 TdT~D~~G~i~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAiKv~GkrlY~lAR~G~~ve~~~R~v~I~~~~ll~~~  154 (291)
T PRK02755         75 TTTDDLTGEILASQPASHLSLAAVETALPQFLGKIEQIPPQYSAIQVEGKRLYDLARQGEAVEVPPRTVEVFSIDILDWR  154 (291)
T ss_pred             CCCCCCCCCCEEECCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHCCCHHHHHHHHCCCCCCCCCEEEEEEEEEEEECC
T ss_conf             66566678711336799899999999999736826254897895101572099998669803367789999999987104


Q ss_pred             CCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC
Q ss_conf             688079999995184289999999839------868688975870545187
Q gi|254780406|r  183 KGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       183 ~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~  227 (354)
                      ......+.+.+.=++=..||-+++-+|      -.+..|.|+++|+|.+.+
T Consensus       155 ~~~~~~~~~~v~CSkGTYIRsLa~Dig~~Lg~~a~l~~L~Rt~~G~f~~~~  205 (291)
T PRK02755        155 SGDFPELDVEIACGSGTYIRAIARDLGAVLGTGGTLAALIRTESSGFALED  205 (291)
T ss_pred             CCCCCEEEEEEEECCCHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH
T ss_conf             677846999999768611999999998976983898574964786708798


No 61 
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=97.53  E-value=0.00047  Score=45.33  Aligned_cols=48  Identities=25%  Similarity=0.442  Sum_probs=31.6

Q ss_pred             CCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCC
Q ss_conf             7734478899988687-78999999986986999999240687807999
Q gi|254780406|r   11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD   58 (354)
Q Consensus        11 ~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d   58 (354)
                      ....-|-.+|..+|+| |++||.++|++|-|+|||+.|+++.+.+..++
T Consensus       339 ~~~~~l~dlLv~~gl~~SksEARRlI~qGgV~INgekV~D~~~~l~~~~  387 (405)
T PRK13354        339 KETKNIVDLLVDLGLAPSKREARRLINNGAVKINGEKVTDVGTDVTVEN  387 (405)
T ss_pred             CCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCC
T ss_conf             5788899999983986788999999985998989999328876446899


No 62 
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=97.37  E-value=0.00049  Score=45.24  Aligned_cols=63  Identities=25%  Similarity=0.307  Sum_probs=56.1

Q ss_pred             CCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCC
Q ss_conf             466677344788999886-877899999998698699999924068780799979999989225
Q gi|254780406|r    7 VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK   69 (354)
Q Consensus         7 ~~~~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~   69 (354)
                      +..+.+-+-|++||--+| +-|=.+|+.+|.+|.|+|||++.+--+.|+..+|.|+++|..+..
T Consensus         5 ~~i~~e~I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~~~~~v   68 (73)
T COG2501           5 VLIKTEFITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPGQRYQV   68 (73)
T ss_pred             EEECCCEEEHHHHHHHHCCCCCCHHHHHHHHCCEEEECCEEECCCCCEEECCCEEEECCEEEEE
T ss_conf             8721351879999987495057478889987791898886630167760169899989978999


No 63 
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=97.36  E-value=0.00044  Score=45.54  Aligned_cols=39  Identities=28%  Similarity=0.457  Sum_probs=13.9

Q ss_pred             HHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEE
Q ss_conf             78899988687-7899999998698699999924068780
Q gi|254780406|r   16 VSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNV   54 (354)
Q Consensus        16 L~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v   54 (354)
                      |-.+|..+|+| |++||.++|++|-|+|||+.|.++.+.+
T Consensus       337 i~dlLv~~gl~~SksEARRlI~qGgV~IN~~kI~D~~~~l  376 (402)
T PRK05912        337 LVDLLVEAGLVPSKSEARRLIQQGAVKINGEKVSDPDYVF  376 (402)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCC
T ss_conf             9999998688678899999998199898999964955422


No 64 
>cd01291 PseudoU_synth PseudoU_synth:  Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
Probab=97.05  E-value=0.00036  Score=46.08  Aligned_cols=86  Identities=13%  Similarity=0.098  Sum_probs=55.6

Q ss_pred             CCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHH
Q ss_conf             78751563144333364421011023432002665543323202223676410001234457404775211245564678
Q gi|254780406|r   79 HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL  158 (354)
Q Consensus        79 ~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~  158 (354)
                      +||.+..+........     .+.....++..+|++|+.++|+.+++                 ++|.+++.        
T Consensus         2 ~K~~~~t~~~~~~~~~-----~~~~~~~~v~~aG~kDk~a~t~Q~~s-----------------n~f~i~lr--------   51 (87)
T cd01291           2 YKPGGDTMEAARQLAK-----LLGIPPKRVGYAGRKDKRAVTTQLVS-----------------NRFTITLR--------   51 (87)
T ss_pred             CCCCCCHHHHHHHHHH-----HHCCCHHHEEECCCCCCCEEEEEEEE-----------------EEEEEEEC--------
T ss_conf             6568789999999999-----82998777517446666554788764-----------------43589821--------


Q ss_pred             HHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCC
Q ss_conf             887400000876750343036402688079999995184289999999839
Q gi|254780406|r  159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN  209 (354)
Q Consensus       159 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g  209 (354)
                                   ..+..+..........++.++|  ++.+|++.|+..++
T Consensus        52 -------------~~~~~~~~~~~~~~~~~l~f~L--~~~~yat~~lrel~   87 (87)
T cd01291          52 -------------VKPLNLKWPEERKRALVLEFTL--PRGSYATMLLRELG   87 (87)
T ss_pred             -------------CCCCCCCCHHHHHHHEEEEEEC--CCCHHHHHHHHHCC
T ss_conf             -------------6466777678864115789852--67407899898619


No 65 
>PRK04051 rps4p 30S ribosomal protein S4; Validated
Probab=97.03  E-value=0.0018  Score=41.67  Aligned_cols=55  Identities=24%  Similarity=0.450  Sum_probs=46.7

Q ss_pred             HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECC--CCEEEE-CCEECC
Q ss_conf             4478899988687-789999999869869999992406878079--997999-998922
Q gi|254780406|r   14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEV-DGVPLR   68 (354)
Q Consensus        14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~--~d~v~v-dg~~i~   68 (354)
                      -||+-++...|++ |-.+|.+||..|-|.|||++|+.|++.|..  .|.|.+ ++-+|.
T Consensus       103 RRL~~vv~r~~~a~si~~Ar~lI~hgHi~V~~~~v~~Ps~~V~r~~Ed~I~~~~~S~i~  161 (177)
T PRK04051        103 RRLQTIVYRKGLARTPKQARQLIVHGHIAVNGRRVTSPGYLVSREEEDKIDYYPTSPLA  161 (177)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEECCCCEEEEECCCCCEEECCCCCCC
T ss_conf             68889998805668899999997478289999995368658865566854631799777


No 66 
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014330   This small protein has a single S4 domain (IPR002942 from INTERPRO); it is also found in bacterial S4 ribosomal proteins, some pseudouridine synthases and tyrosyl-tRNA synthetases.   The S4 domain may bind RNA. Members of this protein are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members that are not near recF are found instead near dnaA and/or dnaN, the usual neighbours of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage..
Probab=96.92  E-value=0.0017  Score=41.76  Aligned_cols=55  Identities=22%  Similarity=0.312  Sum_probs=49.7

Q ss_pred             CCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC
Q ss_conf             677344788999886-8778999999986986999999240687807999799999
Q gi|254780406|r   10 NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG   64 (354)
Q Consensus        10 ~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg   64 (354)
                      +.+-+-|++||=..+ +-|=.+|+.||.++.|.|||+..+-=|-|+.++|.|+|++
T Consensus         5 ~tEyITLgQlLK~~~~i~sGG~AK~fL~e~~V~vNGe~e~RRGkKL~~gD~i~i~~   60 (60)
T TIGR02988         5 KTEYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIPD   60 (60)
T ss_pred             CCCEECHHHHHHHHHHHCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEECC
T ss_conf             43416276786688562282578898706955547844045887004896688269


No 67 
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=96.90  E-value=0.0011  Score=43.04  Aligned_cols=144  Identities=13%  Similarity=0.036  Sum_probs=88.0

Q ss_pred             EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCC
Q ss_conf             89602787515631443333644210110234320026655433232022236764100012344574047752112455
Q gi|254780406|r   74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV  153 (354)
Q Consensus        74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~  153 (354)
                      -+++++||.|..++..-..-+..+      ...+....|-||-..+|+|.+.-+  -+.+|..--..-.|+|.+++.--.
T Consensus        16 Gil~ldKP~G~tS~~~v~~vkkil------~~~K~GH~GTLDP~atGvLpi~ig--~aTKl~~~l~~~~K~Y~a~~~lG~   87 (271)
T COG0130          16 GVINLDKPPGPTSHEVVAWVKRIL------GVEKAGHGGTLDPLATGVLPICLG--EATKLVQYLLDADKEYVATVRLGD   87 (271)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH------CCCCCCCCCCCCCCCCCEEEEEEC--HHHHHHHHHHHCCCEEEEEEEECC
T ss_conf             469840799997799999999985------864056463448743441888834--147489887208947999999677


Q ss_pred             C---HHHHHHHHHHHHCCCEEE-------------ECCCE---EEEECCCCEEEEEEEEEECCHHHHHHHHHHCC-----
Q ss_conf             6---467888740000087675-------------03430---36402688079999995184289999999839-----
Q gi|254780406|r  154 D---QDKLNLLKKGIVIQGICY-------------GDMQV---TLDTQKGSNAWVTVGLREGKNREIKKVFEFFN-----  209 (354)
Q Consensus       154 ~---~~~~~~~~~g~~~~~~~~-------------~~~~~---~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g-----  209 (354)
                      +   .+.+......+.-+=.+.             +.+.+   .+.........++|.-..|  ..||-+|.-+|     
T Consensus        88 ~t~~~e~i~~~l~~F~G~I~Q~PP~~SAvK~~v~~R~V~i~~l~~~~~~~~~~~~~v~CskG--TYIRtL~~DlG~~LG~  165 (271)
T COG0130          88 QTDSEEEVRAALEAFTGEIYQIPPMFSAVKREVERRKITIYDLLELDFDRNLVTLRVECSKG--TYIRTLARDLGEALGC  165 (271)
T ss_pred             CCCCHHHHHHHHHHCCEEEEECCCCHHHCCCEEEEEEEEEEEEEECCCCCCEEEEEEEEECC--CCHHHHHHHHHHHHCC
T ss_conf             57999999999986651058438703101346866799999866604777648999997068--5768889999998788


Q ss_pred             -CEEEEEEEEEECCEECCC
Q ss_conf             -868688975870545187
Q gi|254780406|r  210 -WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       210 -~~V~~L~Rv~~G~~~l~~  227 (354)
                       -++..|.|++.|+|.+.+
T Consensus       166 gahm~~LrRt~~g~f~~~~  184 (271)
T COG0130         166 GAHMSELRRTRVGPFSEED  184 (271)
T ss_pred             CCCHHHHCCCCCCCCCCCC
T ss_conf             5105552042246633023


No 68 
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved.  Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=96.83  E-value=0.0045  Score=39.17  Aligned_cols=151  Identities=13%  Similarity=0.101  Sum_probs=82.4

Q ss_pred             EEECCCCCEEEECCCCCCCCCC-----CCEEEC------------------CCCCCEECCCCCCCCCCCEEEECCCCCCC
Q ss_conf             9602787515631443333644-----210110------------------23432002665543323202223676410
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDPDGRST-----VFDNLP------------------SIFSRVISVGRLDINTEGLLLLTNDGGLA  131 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~~~~~~-----~~~~~~------------------~~~~~~~~vgRLD~~t~GLlllTndg~l~  131 (354)
                      ++++|||.|+.++..=..-+..     +|....                  ...-.+...|-||-..+|||++.-.-  +
T Consensus         2 i~~vdKP~GiTS~~vv~~lk~~f~~s~~f~~~~~~~~~~~~~~~~r~k~~~~~~~KvGH~GTLDP~AtGvL~i~~G~--a   79 (312)
T cd02867           2 VFAINKPSGITSAQVLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHGGTLDPLATGVLVVGVGA--G   79 (312)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCHHCCCCCCCCEEEECCCCCCCCCCEEEEEECH--H
T ss_conf             68874799999899999999983411102310222222101100000012457744402656787460338899875--4


Q ss_pred             CCCCCCCCCCEEEEEEEECC--------------------CCCHHHHHHHHHHHHC--------------CCEE------
Q ss_conf             00123445740477521124--------------------5564678887400000--------------8767------
Q gi|254780406|r  132 RVLELPSTQWLRVYRVRFHG--------------------QVDQDKLNLLKKGIVI--------------QGIC------  171 (354)
Q Consensus       132 ~~l~~p~~~~~k~Y~v~v~~--------------------~~~~~~~~~~~~g~~~--------------~~~~------  171 (354)
                      .++...-....|+|.+++.-                    .++.+.+......+.-              ++..      
T Consensus        80 TK~~~~~~~~~K~Y~a~~~lG~~TdT~D~eG~v~~~~~~~~~t~~~i~~~l~~F~G~i~Q~PP~ySA~Kv~GkrlYelAR  159 (312)
T cd02867          80 TKQLQDYLSCSKTYEATGLFGASTTTYDREGKILKKKPYSHITREDIEEVLAKFRGDIKQVPPLYSALKMDGKRLYEYAR  159 (312)
T ss_pred             HEECHHHCCCCCEEEEEEEECCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCCEEEECCHHHEEEECCEEHHHHHH
T ss_conf             40458666799179999998840578777787775057886889999999997788657648756834379988998986


Q ss_pred             ----------EECCCEE---EEECCCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC
Q ss_conf             ----------5034303---6402688079999995184289999999839------868688975870545187
Q gi|254780406|r  172 ----------YGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT  227 (354)
Q Consensus       172 ----------~~~~~~~---~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~  227 (354)
                                .+.+.+.   +.........+.+.+..++--.||.++.-+|      -++..|.|++.|++.-.+
T Consensus       160 ~G~~ver~i~~R~V~I~~l~l~~~~~~~~~~~~~v~cskGTYiRsla~dlg~~Lg~~ah~~~LrRt~~G~~~e~~  234 (312)
T cd02867         160 EGKPLPRPIERRQVVVSELLVKDWIEPGPLFTRTVEEEGKQYERSVVKMLGKELKTFAEVTELTATAEGDPVEEV  234 (312)
T ss_pred             CCCCCCCCCCCEEEEEEEEEEEECCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEEEHEEECCCCCCCCCCC
T ss_conf             897135777741699999998741588875999998179753889999986875886460104535458997222


No 69 
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=96.72  E-value=0.0027  Score=40.62  Aligned_cols=54  Identities=20%  Similarity=0.370  Sum_probs=45.8

Q ss_pred             HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECC--CCEEEEC-CEEC
Q ss_conf             4478899988687-789999999869869999992406878079--9979999-9892
Q gi|254780406|r   14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEVD-GVPL   67 (354)
Q Consensus        14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~--~d~v~vd-g~~i   67 (354)
                      -||+-++...|++ |-.+|-.||..|-|.|||++|+.|++.|..  .|.|.+. .-|+
T Consensus       107 RRLqt~v~~~glA~si~~Ar~lI~hgHI~V~~~~V~~Ps~lV~r~~Ed~I~~~~~Spl  164 (188)
T PTZ00155        107 RRLQTKVFKLGLAKSVHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIAFALTSPF  164 (188)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHEECCEEEECCEEECCCCEEEEECCCCCEEEECCCCC
T ss_conf             7676899986011588988888344628899989537745886054464454368988


No 70 
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative; InterPro: IPR004802   This family contains the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether the archaeal proteins in this family modify tRNA, rRNA, or both. .
Probab=96.20  E-value=0.036  Score=33.52  Aligned_cols=166  Identities=20%  Similarity=0.194  Sum_probs=107.2

Q ss_pred             CCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEE
Q ss_conf             56438960278751563144333364421011023432002665543323202223676410001234457404775211
Q gi|254780406|r   70 AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF  149 (354)
Q Consensus        70 ~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v  149 (354)
                      +-..=++.+.||.|-.+|.-.- +-.   .+|  +..+...-|-||---||.|++.=|-.----=+.....-|..+++++
T Consensus        31 yI~~Gvv~lDKP~gPsSHeV~~-Wvr---~iL--~veKtGH~GTLDPKVTGvLpv~ierATr~v~~~~~a~KEYVClmRL  104 (326)
T TIGR00425        31 YIRKGVVNLDKPSGPSSHEVVA-WVR---RIL--RVEKTGHGGTLDPKVTGVLPVCIERATRLVKSLQEAPKEYVCLMRL  104 (326)
T ss_pred             HHHCCEEEEECCCCCCCCEEHH-HHH---HHH--CCCCCCCCCCCCCCEEEEEEEEEHHHHHHHHHHHCCCCCEEEEEEE
T ss_conf             6206507876484188640102-212---101--0112465875788312462121000235644531699745997761


Q ss_pred             CCCCCHH-HHHHHHHHHHCCCEEEE--CCC--------------EEEEECCCCE--EEEEEEEEECCHHHHHHHHHHCCC
Q ss_conf             2455646-78887400000876750--343--------------0364026880--799999951842899999998398
Q gi|254780406|r  150 HGQVDQD-KLNLLKKGIVIQGICYG--DMQ--------------VTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNW  210 (354)
Q Consensus       150 ~~~~~~~-~~~~~~~g~~~~~~~~~--~~~--------------~~~~~~~~~~--~~~~v~l~eGr~~qIrr~~~~~g~  210 (354)
                      +.++..+ .+.+.-+-+  -|-.|+  |..              +.++.-++..  -.|+|.=.-|=|  ||.+|..+|.
T Consensus       105 H~~~~~e~~~~rvl~~f--~G~ifQrPPLksAVKr~LRvR~IYe~~llE~Dg~d~LvlFrv~CeaGTY--iRkLC~d~G~  180 (326)
T TIGR00425       105 HRDAKEEKDIERVLKEF--TGRIFQRPPLKSAVKRQLRVRTIYESELLEVDGKDRLVLFRVSCEAGTY--IRKLCVDIGE  180 (326)
T ss_pred             CHHHHHHHHHHHHHHHC--CCEEECCCCCHHHHCCCCCEEEEEEEEEEEECCCCCEEEEEEEECCCCC--HHHHHHHHHH
T ss_conf             20121257899998851--8303338862565223365016899887720799626899998757861--5687888867


Q ss_pred             ------EEEEEEEEEECCEE-------CCCCCCCCEEECCH---HHHHHHH
Q ss_conf             ------68688975870545-------18755474886799---9998753
Q gi|254780406|r  211 ------KVNRLIRISYGPFQ-------LGTLLAGSTREVSK---KILREQL  245 (354)
Q Consensus       211 ------~V~~L~Rv~~G~~~-------l~~L~~G~~r~l~~---~e~~~l~  245 (354)
                            +-.-|.|++-|.|.       |-||.=-+|-+-..   .+|+...
T Consensus       181 ~LG~GahMqELRRtrsG~f~E~d~~vtLhDllDAy~fw~e~gDE~yLR~~I  231 (326)
T TIGR00425       181 LLGTGAHMQELRRTRSGAFGERDDMVTLHDLLDAYVFWKEDGDESYLREVI  231 (326)
T ss_pred             HHCCCCCCCHHEEEEEECCCCCCCCEEHHHHHEEEEEEECCCCHHHHHHHH
T ss_conf             617672120010100102202467060420311102220378725656542


No 71 
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=95.95  E-value=0.092  Score=30.92  Aligned_cols=124  Identities=15%  Similarity=0.143  Sum_probs=68.7

Q ss_pred             CCHHHHHHHHHC-C-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEECCCCCEEEECCC
Q ss_conf             734478899988-6-87789999999869869999992406878079997999998922556438960278751563144
Q gi|254780406|r   12 TPQRVSKVIARA-G-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHS   89 (354)
Q Consensus        12 ~~~RL~K~la~~-g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~   89 (354)
                      +++=|.=||-+. + --+.|||...|.+|.|.|||++.++..+-|---|+|++..    ..+ .|-++|+.-.-+..+..
T Consensus        40 eslPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvG~MDVIsI~k----t~e-~yRvl~d~kGrf~l~~I  114 (262)
T PTZ00118         40 ECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTK----TNE-YFRLLYDTKGRFVPHKI  114 (262)
T ss_pred             CCCCCHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEECC----CCC-EEEEEECCCCEEEEEEC
T ss_conf             4554335643464522658999999867908889999534899874678999856----896-59999868970999988


Q ss_pred             CCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEEC
Q ss_conf             3333644210110234320026655433232022236764100012344574047752112
Q gi|254780406|r   90 DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH  150 (354)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~  150 (354)
                      +.+.-.  +.+.. .....+--|...      +++|.||.-. .+..|...+.-+..+.+.
T Consensus       115 ~~eEA~--~KLcK-V~K~~i~~g~iq------~~~thDGr~i-~~~d~~ik~~Dtv~i~l~  165 (262)
T PTZ00118        115 TNEEAK--YKLCR-VKKTFLGPKEVS------IAVTHDGRTI-RYVHPDVKVGDSLRLDLE  165 (262)
T ss_pred             CHHHHC--CEEEE-EEEEEECCCCEE------EEECCCCCEE-ECCCCCCCCCCEEEEECC
T ss_conf             967814--38999-999998689537------8872477668-326887666988999889


No 72 
>TIGR01018 rpsD_arch ribosomal protein S4; InterPro: IPR005710   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 , .   The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This model finds eukaryotic ribosomal protein S9 as well as eukaryotic and archaeal ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=95.66  E-value=0.0069  Score=37.99  Aligned_cols=50  Identities=18%  Similarity=0.406  Sum_probs=43.4

Q ss_pred             HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECC--CCEEEEC
Q ss_conf             4478899988687-789999999869869999992406878079--9979999
Q gi|254780406|r   14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEVD   63 (354)
Q Consensus        14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~--~d~v~vd   63 (354)
                      =|||=..-..|++ |=++|-+||-.|-|.|||++|+.|++-|.-  .|.|.+.
T Consensus       112 RRLQT~Vyk~GLArTi~~ARqLi~hGHI~v~Gr~v~~Psy~V~~e~e~kI~fa  164 (170)
T TIGR01018       112 RRLQTLVYKKGLARTIKQARQLIVHGHIAVDGRRVTSPSYIVRREEEDKIDFA  164 (170)
T ss_pred             HHHHHHHHHHHHCCCHHHCCEEEEECEEEECCEEEECCCEEEECCCCCCCCCC
T ss_conf             45678999863022632343023203388768477358616746554421205


No 73 
>PRK04313 30S ribosomal protein S4e; Validated
Probab=94.94  E-value=0.062  Score=31.99  Aligned_cols=53  Identities=21%  Similarity=0.286  Sum_probs=42.5

Q ss_pred             CCHHHHHHHHHC-C-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC
Q ss_conf             734478899988-6-8778999999986986999999240687807999799999
Q gi|254780406|r   12 TPQRVSKVIARA-G-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG   64 (354)
Q Consensus        12 ~~~RL~K~la~~-g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg   64 (354)
                      +++=|.=+|-+. + .-+.|||...|.+|.|.|||++.++..+-|---|+|++..
T Consensus        36 ~siPL~v~LRd~L~~a~t~rEak~Il~~~~V~VDG~vr~d~~~pvGlmDVisi~~   90 (237)
T PRK04313         36 SSLPLLIVLRDVLGYADTAREARKIISEGKVLVDGRVRKDYKFPVGLMDVISIPE   90 (237)
T ss_pred             CCCCCHHHHHHHHHHHCCHHHHHHHHHCCEEEECCEEEECCCCCCCEEEEEEECC
T ss_conf             5423389998777250448899998648859989999603788754167998647


No 74 
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=94.84  E-value=0.085  Score=31.12  Aligned_cols=74  Identities=15%  Similarity=0.065  Sum_probs=50.4

Q ss_pred             CCHHHHHHHHHC-C-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEECCCCCEEEECCC
Q ss_conf             734478899988-6-87789999999869869999992406878079997999998922556438960278751563144
Q gi|254780406|r   12 TPQRVSKVIARA-G-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHS   89 (354)
Q Consensus        12 ~~~RL~K~la~~-g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~   89 (354)
                      +++=|.=||-+. + .-+.|||...|.+|.|.|||++.++..+-|---|+|++..    . .+.|-++|+.-.-+..+..
T Consensus        37 eslPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvG~MDVIsI~k----t-~e~yRvl~D~kGr~~l~~I  111 (273)
T PTZ00223         37 ECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPK----T-GDRFRILYDVKGRFALVKV  111 (273)
T ss_pred             CCCCCHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCEEEEEEECC----C-CCEEEEEECCCCEEEEEEC
T ss_conf             4444257876564521657999999877937977999655899885789999857----8-8749999868962999984


Q ss_pred             C
Q ss_conf             3
Q gi|254780406|r   90 D   90 (354)
Q Consensus        90 ~   90 (354)
                      +
T Consensus       112 ~  112 (273)
T PTZ00223        112 S  112 (273)
T ss_pred             C
T ss_conf             9


No 75 
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=93.90  E-value=0.24  Score=28.31  Aligned_cols=37  Identities=22%  Similarity=0.331  Sum_probs=32.9

Q ss_pred             CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEEC
Q ss_conf             7899999998698699999924068780799979999
Q gi|254780406|r   27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD   63 (354)
Q Consensus        27 SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vd   63 (354)
                      .-|||...|.+|.|.|||++.++.-.-|---|+|++.
T Consensus        56 ~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip   92 (241)
T COG1471          56 NAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIP   92 (241)
T ss_pred             CHHHHHHHHHCCCEEECCEEECCCCCCCCEEEEEEEC
T ss_conf             3488999876695798889801355784068999976


No 76 
>KOG2559 consensus
Probab=86.80  E-value=1.5  Score=23.22  Aligned_cols=37  Identities=19%  Similarity=0.329  Sum_probs=29.8

Q ss_pred             HHHHHHHHHCCCE------EEEEEEEEECCEECC-CCCCCCEEE
Q ss_conf             8999999983986------868897587054518-755474886
Q gi|254780406|r  199 REIKKVFEFFNWK------VNRLIRISYGPFQLG-TLLAGSTRE  235 (354)
Q Consensus       199 ~qIrr~~~~~g~~------V~~L~Rv~~G~~~l~-~L~~G~~r~  235 (354)
                      -.+|.+...+|+.      .++|.|+++|+|.++ .|.+-+|-.
T Consensus       220 e~Lr~LVh~igl~L~T~a~c~qlrr~r~g~F~~d~aLLr~qw~L  263 (318)
T KOG2559         220 EMLRQLVHHIGLNLGTEATCIQLRRQRFGPFGSDNALLRKQWNL  263 (318)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCHHHHHHHHCC
T ss_conf             99999999974312541555242343257877518999986162


No 77 
>KOG3301 consensus
Probab=84.57  E-value=1  Score=24.29  Aligned_cols=49  Identities=18%  Similarity=0.357  Sum_probs=40.6

Q ss_pred             CCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCC
Q ss_conf             67734478899988687-78999999986986999999240687807999
Q gi|254780406|r   10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD   58 (354)
Q Consensus        10 ~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d   58 (354)
                      +.=..||+-.+...|++ |=-.|..||..+.|.|++++|.-|++.|....
T Consensus        93 ~fLErRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrlds  142 (183)
T KOG3301          93 DFLERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRLDS  142 (183)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCEEEECCCEEEEECH
T ss_conf             99999999999998665442788987427607615757624654566121


No 78 
>KOG2623 consensus
Probab=83.59  E-value=2.9  Score=21.47  Aligned_cols=20  Identities=10%  Similarity=0.287  Sum_probs=10.4

Q ss_pred             CCCCCEEEECCCCCCCCCCC
Q ss_conf             33232022236764100012
Q gi|254780406|r  116 INTEGLLLLTNDGGLARVLE  135 (354)
Q Consensus       116 ~~t~GLlllTndg~l~~~l~  135 (354)
                      --+.|=.+.-|+.+|-..+.
T Consensus       152 ~~s~g~~~ivnN~dW~~d~~  171 (467)
T KOG2623         152 GSSQGKYIIVNNSDWYKDIK  171 (467)
T ss_pred             CCCCCCEEEEECHHHHHHCH
T ss_conf             75668616750567762456


No 79 
>pfam06353 DUF1062 Protein of unknown function (DUF1062). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=81.65  E-value=2.1  Score=22.41  Aligned_cols=49  Identities=31%  Similarity=0.390  Sum_probs=25.4

Q ss_pred             EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCC
Q ss_conf             389602787515631443333644210110234320026655433232022236764100012
Q gi|254780406|r   73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE  135 (354)
Q Consensus        73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~  135 (354)
                      ..+|++     |-|+.++.-..-++|......   .+.-.-||.      |.+||-.+++.+.
T Consensus         8 LDvWLI-----YkC~~C~~TwN~ti~eR~~v~---~I~p~ll~~------f~~ND~~la~~~a   56 (142)
T pfam06353         8 LDVWLI-----YKCTKCDYTWNITIFERRNVR---SINPELLEA------LHSNDPGLARAYA   56 (142)
T ss_pred             EEEEEE-----EEECCCCCEECCCEEEECCCC---CCCHHHHHH------HHHCCHHHHHHHH
T ss_conf             348889-----871468684050114315812---079999998------9736999999994


No 80 
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.35  E-value=2.3  Score=22.15  Aligned_cols=120  Identities=21%  Similarity=0.262  Sum_probs=60.1

Q ss_pred             CCCEEEECCEECCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCC--CCCEECCCCCCCCCCCEEEECCCCCCCCC
Q ss_conf             9997999998922556438960278751563144333364421011023--43200266554332320222367641000
Q gi|254780406|r   56 STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARV  133 (354)
Q Consensus        56 ~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~--~~~~~~vgRLD~~t~GLlllTndg~l~~~  133 (354)
                      .++.++|+-+-    +...+|+++     -|+.+|..+.-++|..++..  .+.++.           -|..||.+++++
T Consensus        31 cSg~fRvNAq~----K~LDvWlIY-----kC~~Cd~tWN~~IfeR~~~~~Iep~lle-----------al~~NDa~larr   90 (203)
T COG4332          31 CSGKFRVNAQG----KVLDVWLIY-----KCTHCDYTWNISIFERLNVSDIEPDLLE-----------ALMANDAALARR   90 (203)
T ss_pred             ECCCEEECCCC----CEEEEEEEE-----EEECCCCCCCHHHHHCCCCCCCCHHHHH-----------HHHCCCHHHHHH
T ss_conf             35727884788----378899999-----8504677256103101682008989999-----------998189999998


Q ss_pred             CCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHH---HHHHCCC
Q ss_conf             1234457404775211245564678887400000876750343036402688079999995184289999---9998398
Q gi|254780406|r  134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK---VFEFFNW  210 (354)
Q Consensus       134 l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr---~~~~~g~  210 (354)
                      .+... .+.+.-..++++..+                  -.++..+..+..+..-+++.|.--+.-|||-   +-+.+|+
T Consensus        91 ~afdl-a~lRr~~~r~~g~pd------------------~~i~krilge~~~~~~vel~l~~~~p~qlrl~~Ll~seL~L  151 (203)
T COG4332          91 FAFDL-AILRRNNARLSGFPD------------------FHIQKRILGEIASHAAVELSLRISRPFQLRLDRLLASELGL  151 (203)
T ss_pred             HHHHH-HHHHHCCCCCCCCCC------------------HHHHHHEECCCCCCEEEEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             87319-999720344457875------------------00311100574440027899745676065799999988583


Q ss_pred             EEEE
Q ss_conf             6868
Q gi|254780406|r  211 KVNR  214 (354)
Q Consensus       211 ~V~~  214 (354)
                      .-..
T Consensus       152 SrS~  155 (203)
T COG4332         152 SRSE  155 (203)
T ss_pred             CHHH
T ss_conf             7999


No 81 
>pfam01509 TruB_N TruB family pseudouridylate synthase (N terminal domain). Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA.
Probab=77.62  E-value=1.6  Score=23.11  Aligned_cols=49  Identities=24%  Similarity=0.164  Sum_probs=34.0

Q ss_pred             CCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHH
Q ss_conf             320026655433232022236764100012344574047752112455646
Q gi|254780406|r  106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD  156 (354)
Q Consensus       106 ~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~  156 (354)
                      .++...|.||-..+|||++.-+.  +.++..--....|+|.+++.--...+
T Consensus         7 kKvGH~GTLDP~AsGlL~i~ig~--~TK~~~~~~~~~K~Y~~~~~~G~~Td   55 (149)
T pfam01509         7 KKVGHTGTLDPLATGVLPVCVGK--ATKLLQYLLDADKEYRATIRLGVATD   55 (149)
T ss_pred             CCCCCCCCCCCCCEEEEEEEECH--HHHHHHHHCCCCCEEEEEEEECCCCC
T ss_conf             60242744698665689999987--87121887589817999998625668


No 82 
>TIGR00431 TruB tRNA pseudouridine synthase B; InterPro: IPR014780   TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific functions.; GO: 0003723 RNA binding, 0016439 tRNA-pseudouridine synthase activity, 0031119 tRNA pseudouridine synthesis.
Probab=77.47  E-value=0.49  Score=26.35  Aligned_cols=70  Identities=24%  Similarity=0.215  Sum_probs=48.3

Q ss_pred             EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC
Q ss_conf             96027875156314433336442101102343200266554332320222367641000123445740477521124
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG  151 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~  151 (354)
                      ++++|||.|..++..=..    |-.++  ..+++.+.|-||.-.+|+|++-= |.-+.+|..--..-+|+|.+...-
T Consensus         4 vLll~Kp~G~TSfd~~~~----v~rLl--~~kkvGHtGTLDp~A~G~L~~~v-Gr~aTkl~~yl~~~dK~Y~A~~~l   73 (236)
T TIGR00431         4 VLLLDKPQGMTSFDALAK----VRRLL--GVKKVGHTGTLDPFATGVLPILV-GRKATKLSPYLTDLDKEYEAEIRL   73 (236)
T ss_pred             CCCCCCCCCCCHHHHHHH----HHHHH--CCCCCCCCCCCCHHHHHHHHHHH-HHHHHHHHHHHCCCCCEEEEEEEC
T ss_conf             041557888788999999----99987--07852206665302410354223-001343433312647617999982


No 83 
>pfam05910 DUF868 Plant protein of unknown function (DUF868). This family consists of several hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Probab=74.78  E-value=3.2  Score=21.21  Aligned_cols=12  Identities=17%  Similarity=0.263  Sum_probs=6.2

Q ss_pred             CCEEEEEEEEEE
Q ss_conf             986868897587
Q gi|254780406|r  209 NWKVNRLIRISY  220 (354)
Q Consensus       209 g~~V~~L~Rv~~  220 (354)
                      |..|+..+|.++
T Consensus       181 gk~v~~VkrL~W  192 (272)
T pfam05910       181 GKVVVQVKRLQW  192 (272)
T ss_pred             CEEEEEEEEEEE
T ss_conf             999999987233


No 84 
>TIGR02414 pepN_proteo aminopeptidase N; InterPro: IPR012779   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.     The M1 family of zinc metallopeptidases contains a number of distinct, well-separated clades of proteins with aminopeptidase activity. Several are designated aminopeptidase N, 3.4.11.2 from EC, after the Escherichia coli enzyme, suggesting a similar activity profile (see P04825 from SWISSPROT for a description of catalytic activity).   This family of zinc metallopeptidases belong to MEROPS peptidase family M1 (aminopeptidase N, clan MA); the majority are identified as alanyl aminopeptidases (proteobacteria) that are closely related to Escherichia coli PepN and presumed to have a similar (not identical) function. Nearly all are found in proteobacteria, but members are found also in cyanobacteria, plants, and apicomplexan parasites , . This family differs greatly in sequence from the family of aminopeptidases typified by Streptomyces lividans PepN (IPR012778 from INTERPRO) and from the membrane bound aminopeptidase N family in animals.; GO: 0004179 membrane alanyl aminopeptidase activity, 0008270 zinc ion binding.
Probab=70.85  E-value=4  Score=20.59  Aligned_cols=62  Identities=19%  Similarity=0.222  Sum_probs=46.1

Q ss_pred             CEEECCEECCCCCEEECCCCEEEECCEEC------------CCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEE
Q ss_conf             86999999240687807999799999892------------2556438960278751563144333364421011
Q gi|254780406|r   39 RVKVNGILLERAAVNVMSTDHIEVDGVPL------------RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL  101 (354)
Q Consensus        39 ~V~Vng~~v~~~~~~v~~~d~v~vdg~~i------------~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~  101 (354)
                      .|+|||+....-+|.+++. ..+|.+.|-            .|.+.+-+.=++|=.|..||.|..+|-+-|.-++
T Consensus        55 si~idG~~L~~~~Y~~d~~-~LTI~~~P~~~~F~l~~~t~i~P~~Nt~L~GLY~SgG~fcTQCEAEGFRrITYf~  128 (898)
T TIGR02414        55 SIAIDGQPLAADDYQLDDE-SLTIASVPESKEFTLEIETEIKPEENTSLEGLYKSGGNFCTQCEAEGFRRITYFL  128 (898)
T ss_pred             EEEECCCEECCCCCEECCC-CCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCHHHCCCCEEEECCCCCCCCCCCC
T ss_conf             9986585205885367365-2325876898627999999986376772002020288407750577755002247


No 85 
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular    trafficking, secretion, and vesicular transport]
Probab=70.55  E-value=4.8  Score=20.13  Aligned_cols=43  Identities=21%  Similarity=0.260  Sum_probs=35.9

Q ss_pred             CCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC
Q ss_conf             7789999999869869999992406878079997999998922
Q gi|254780406|r   26 ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR   68 (354)
Q Consensus        26 ~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~   68 (354)
                      +-+-+--.+|++|+=+|.+.+...--.++.++|+|.++|..|.
T Consensus         6 gL~eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~~~l~   48 (111)
T COG4043           6 GLREEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNGDKLK   48 (111)
T ss_pred             CHHHHHHHHHHCCCCEEEEEECCHHHCCCCCCCEEEECCCEEE
T ss_conf             0378899998704436899955776627898998998388467


No 86 
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=67.73  E-value=9.4  Score=18.26  Aligned_cols=13  Identities=8%  Similarity=-0.181  Sum_probs=6.9

Q ss_pred             CEEECCHHHHHHH
Q ss_conf             4886799999875
Q gi|254780406|r  232 STREVSKKILREQ  244 (354)
Q Consensus       232 ~~r~l~~~e~~~l  244 (354)
                      .+-.++++|...+
T Consensus       345 ait~v~~~e~~~~  357 (457)
T PRK10590        345 ALSLVCVDEHKLL  357 (457)
T ss_pred             EEEEECHHHHHHH
T ss_conf             9998668999999


No 87 
>KOG4655 consensus
Probab=66.35  E-value=3.8  Score=20.72  Aligned_cols=42  Identities=26%  Similarity=0.396  Sum_probs=33.2

Q ss_pred             CHHHHHHHHHCCCEEECCEECCCCCEEECCC--CEEE-ECCEECC
Q ss_conf             7899999998698699999924068780799--9799-9998922
Q gi|254780406|r   27 SRREVERMIAQQRVKVNGILLERAAVNVMST--DHIE-VDGVPLR   68 (354)
Q Consensus        27 SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~--d~v~-vdg~~i~   68 (354)
                      |-.+|-++|++|-|.|--++|++|++.|..+  |-|+ ||...|+
T Consensus       121 ~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~mEDfvtWvd~SKIK  165 (181)
T KOG4655         121 SVKEAVRFVEQGHVRVGPKVVTDPAFLVTRSMEDFVTWVDSSKIK  165 (181)
T ss_pred             HHHHHHHHHHCCCEEECCEECCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             699999999818535178000472577422266564242268899


No 88 
>pfam02824 TGS TGS domain. The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=57.14  E-value=11  Score=17.77  Aligned_cols=22  Identities=27%  Similarity=0.302  Sum_probs=18.9

Q ss_pred             EEECCEECCCCCEEECCCCEEEE
Q ss_conf             69999992406878079997999
Q gi|254780406|r   40 VKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        40 V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      .+|||+.+ .+.+.+..+|+|++
T Consensus        37 A~VnG~~v-~l~~~L~~gd~V~I   58 (60)
T pfam02824        37 AKVNGQRV-GLDHVLEDGDVVEI   58 (60)
T ss_pred             EEECCEEC-CCCCCCCCCCEEEE
T ss_conf             89998887-62112489999998


No 89 
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs.  The function of the TGS domain is unknown.
Probab=57.03  E-value=11  Score=17.87  Aligned_cols=23  Identities=30%  Similarity=0.417  Sum_probs=18.9

Q ss_pred             CEEECCEECCCCCEEECCCCEEEE
Q ss_conf             869999992406878079997999
Q gi|254780406|r   39 RVKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        39 ~V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      -++|||+.+ .+.+.+..+|+|++
T Consensus        36 ~a~vNg~~~-~l~~~L~~GD~VeI   58 (60)
T cd01668          36 GAKVNGKLV-PLSTVLKDGDIVEI   58 (60)
T ss_pred             EEEECCEEC-CCCCCCCCCCEEEE
T ss_conf             999999998-98768289999998


No 90 
>PRK08857 para-aminobenzoate synthase component II; Provisional
Probab=55.82  E-value=6.6  Score=19.22  Aligned_cols=99  Identities=17%  Similarity=0.151  Sum_probs=60.0

Q ss_pred             EEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHH-HHHHCCCEEEECCCEEEEEC-----CCCEEEEEEEEE
Q ss_conf             022236764100012344574047752112455646788874-00000876750343036402-----688079999995
Q gi|254780406|r  121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQ-----KGSNAWVTVGLR  194 (354)
Q Consensus       121 LlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~~~-----~~~~~~~~v~l~  194 (354)
                      +||+-|-..+.+.|.+--.+..-...|.-...++.+.+..+. .++.+..|+-.|........     ...--  -+-|.
T Consensus         2 iLiiDn~DsfT~ni~~~l~~lg~~v~vv~~d~~~~~~i~~~~p~~IilS~GPg~p~~~~~~~~~~~~~~~~iP--ILGIC   79 (192)
T PRK08857          2 LLMIDNYDSFTYNLYQYFCELGAEVKVVRNDEIDIAGIEALNPSHLVISPGPCTPNEAGISLQAIEHFAGKLP--ILGVC   79 (192)
T ss_pred             EEEEECCCCHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHCCCCEEEECCCCCCHHHCCCCHHHHHHHCCCCC--EEEEC
T ss_conf             9999799977999999998779928999699899999984297959998999996782861466997357999--89987


Q ss_pred             ECCHHHHHHHHHHCCCEEEEEEEEEECCEEC
Q ss_conf             1842899999998398686889758705451
Q gi|254780406|r  195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL  225 (354)
Q Consensus       195 eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l  225 (354)
                      =|  ||+  |+.++|-+|.+++...+|....
T Consensus        80 lG--~Q~--ia~~~Gg~v~~~~~~~hG~~~~  106 (192)
T PRK08857         80 LG--HQA--IAQVFGGDVVRARQVMHGKTSP  106 (192)
T ss_pred             HH--HHH--HHHHHCCEEEECCCCEEEEEEE
T ss_conf             99--999--9998398299888432511579


No 91 
>pfam05949 DUF881 Bacterial protein of unknown function (DUF881). This family consists of a series of hypothetical bacterial proteins. One of the family members from Bacillus subtilis is thought to be involved in cell division and sporulation.
Probab=55.72  E-value=15  Score=16.91  Aligned_cols=31  Identities=23%  Similarity=0.335  Sum_probs=22.0

Q ss_pred             CEEECCEECCCCCEEECCCCEEEECCEECCC
Q ss_conf             8699999924068780799979999989225
Q gi|254780406|r   39 RVKVNGILLERAAVNVMSTDHIEVDGVPLRK   69 (354)
Q Consensus        39 ~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~   69 (354)
                      -|.|||+.+.....-...+..|.|||.++.+
T Consensus        61 AIsIng~Ri~~~s~Ir~~g~~i~Vng~~i~~   91 (150)
T pfam05949        61 AISINGQRITATTEIRCAGGTILVDGRPISP   91 (150)
T ss_pred             EEEECCEEECCEEEEEECCCEEEECCEEECC
T ss_conf             9999999972507999729989999999079


No 92 
>PRK08007 para-aminobenzoate synthase component II; Provisional
Probab=55.14  E-value=6.5  Score=19.28  Aligned_cols=100  Identities=17%  Similarity=0.126  Sum_probs=59.8

Q ss_pred             EEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHH-HHHHCCCEEEECCCEEEE----ECCCCEEEEEEEEEE
Q ss_conf             022236764100012344574047752112455646788874-000008767503430364----026880799999951
Q gi|254780406|r  121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLD----TQKGSNAWVTVGLRE  195 (354)
Q Consensus       121 LlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~----~~~~~~~~~~v~l~e  195 (354)
                      +||+-|-..+.+.|.+--.+..-+..|.-..+++.+.++.+. .++.+..|+-.|......    ...... .=-+-|.=
T Consensus         2 ILiIDn~DsFT~ni~~~l~~~g~~v~V~~~d~~~~~~i~~~~p~~IvlSpGPg~P~~~~~~~~~i~~~~~~-iPiLGICl   80 (187)
T PRK08007          2 ILLIDNYDSFTWNLYQYFCELGADVLVKRNDALTLADIDALKPQKIVISPGPCTPDEAGISLDVIRHYAGR-LPILGVCL   80 (187)
T ss_pred             EEEEECCCCHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHCCCCEEEECCCCCCHHHCCCCHHHHHHHCCC-CCEEEECH
T ss_conf             99996898189999999987799799993898999999842989799999999958908404689975389-98899879


Q ss_pred             CCHHHHHHHHHHCCCEEEEEEEEEECCEEC
Q ss_conf             842899999998398686889758705451
Q gi|254780406|r  196 GKNREIKKVFEFFNWKVNRLIRISYGPFQL  225 (354)
Q Consensus       196 Gr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l  225 (354)
                      |  ||+  |+.++|-+|.++....+|.-.+
T Consensus        81 G--~Q~--ia~~~Gg~v~~~~~~~hG~~~~  106 (187)
T PRK08007         81 G--HQA--MAQAFGGKVVRAAKVMHGKTSP  106 (187)
T ss_pred             H--HHH--HHHHCCCEEEECCCCCCCCCEE
T ss_conf             9--999--9998098073478320152069


No 93 
>PRK02491 putative deoxyribonucleotide triphosphate pyrophosphatase/unknown domain fusion protein; Reviewed
Probab=53.70  E-value=15  Score=16.92  Aligned_cols=30  Identities=30%  Similarity=0.494  Sum_probs=25.0

Q ss_pred             EEEEEEEEECCHHHHHHHHHHCCCEEEEEE
Q ss_conf             799999951842899999998398686889
Q gi|254780406|r  187 AWVTVGLREGKNREIKKVFEFFNWKVNRLI  216 (354)
Q Consensus       187 ~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~  216 (354)
                      +.+--|=.+||-+|.+.||+.+|++|..|.
T Consensus       129 tilIAT~N~GK~kEf~~l~~~~g~~V~sL~  158 (328)
T PRK02491        129 TILIATRNEGKTKEFRKLFGKLGYKVENLN  158 (328)
T ss_pred             EEEEEECCCCHHHHHHHHHHHCCCEEEEHH
T ss_conf             799983796569999998875495897887


No 94 
>pfam06668 ITI_HC_C Inter-alpha-trypsin inhibitor heavy chain C-terminus. This family represents the C-terminal region of inter-alpha-trypsin inhibitor heavy chains. Inter-alpha-trypsin inhibitors are glycoproteins with a high inhibitory activity against trypsin, built up from different combinations of four polypeptides: bikunin and the three heavy chains that belong to this family (HC1, HC2, HC3). The heavy chains do not have any protease inhibitory properties but have the capacity to interact in vitro and in vivo with hyaluronic acid, which promotes the stability of the extra-cellular matrix. All family members contain the pfam00092 domain.
Probab=48.97  E-value=20  Score=16.24  Aligned_cols=11  Identities=45%  Similarity=0.619  Sum_probs=7.7

Q ss_pred             EEECCEECCCC
Q ss_conf             69999992406
Q gi|254780406|r   40 VKVNGILLERA   50 (354)
Q Consensus        40 V~Vng~~v~~~   50 (354)
                      |.|||++|-.+
T Consensus         4 i~VNGqlIgak   14 (188)
T pfam06668         4 VTVNGQLIGAK   14 (188)
T ss_pred             EEEECEEECCC
T ss_conf             79806897388


No 95 
>cd01616 TGS The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=48.28  E-value=17  Score=16.61  Aligned_cols=22  Identities=23%  Similarity=0.391  Sum_probs=18.5

Q ss_pred             EEECCEECCCCCEEECCCCEEEE
Q ss_conf             69999992406878079997999
Q gi|254780406|r   40 VKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        40 V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      .+|||+.+ .+.+.+..+|+|++
T Consensus        37 a~Vng~~~-~l~~~L~~gd~V~I   58 (60)
T cd01616          37 ALVNGQLV-DLSYTLQDGDTVSI   58 (60)
T ss_pred             EEECCEEC-CCCCCCCCCCEEEE
T ss_conf             99999996-51669999999999


No 96 
>COG4909 PduC Propanediol dehydratase, large subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=48.07  E-value=10  Score=17.97  Aligned_cols=57  Identities=16%  Similarity=0.186  Sum_probs=37.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC
Q ss_conf             98653446667734478899988687789999999869869999992406878079997999998922
Q gi|254780406|r    1 MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR   68 (354)
Q Consensus         1 ~~~~~~~~~~~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~   68 (354)
                      |+.|.+-+-...|.++++|           +.++|++|.+-..-----.|+.++..+-+|++||++..
T Consensus         1 mrskrfe~lakrpvnqdgf-----------vkewieegfiamespndpkpsiki~ng~v~eldgk~~~   57 (554)
T COG4909           1 MRSKRFEDLAKRPVNQDGF-----------VKEWIEEGFIAMESPNDPKPSIKIKNGRVIELDGKLEH   57 (554)
T ss_pred             CCHHHHHHHHHCCCCCCCH-----------HHHHHHHCCEECCCCCCCCCCCEECCCEEEEECCCCCC
T ss_conf             9234678986287541212-----------66626521002238899999610115728863682312


No 97 
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles.   Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus.   Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=47.53  E-value=21  Score=16.10  Aligned_cols=49  Identities=16%  Similarity=0.241  Sum_probs=39.3

Q ss_pred             CCCCCCEEEECCC-CCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHH
Q ss_conf             4332320222367-641000123445740477521124556467888740
Q gi|254780406|r  115 DINTEGLLLLTND-GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK  163 (354)
Q Consensus       115 D~~t~GLlllTnd-g~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~  163 (354)
                      -.+.+|++-+.+- -.|+-+.+.-...+.-.|.+.|.|.+.++....|..
T Consensus        44 S~~F~G~Ial~~P~~SWvarw~ri~~~vpG~YAi~V~G~lp~~i~~~le~   93 (98)
T cd07973          44 SPNFEGIIALMDPEKSWVARWQRIDKFVPGIYAISVSGRLPEDIVEELES   93 (98)
T ss_pred             CCCCCEEEEEECCCCCHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHH
T ss_conf             67723278873685148999864467788758888458699899999998


No 98 
>PRK07649 para-aminobenzoate/anthranilate synthase glutamine amidotransferase component II; Validated
Probab=43.41  E-value=11  Score=17.88  Aligned_cols=99  Identities=14%  Similarity=0.109  Sum_probs=51.2

Q ss_pred             EEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHH-HHHHCCCEEEECCCEEEE----ECCCCEEEEEEEEEE
Q ss_conf             022236764100012344574047752112455646788874-000008767503430364----026880799999951
Q gi|254780406|r  121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLD----TQKGSNAWVTVGLRE  195 (354)
Q Consensus       121 LlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~----~~~~~~~~~~v~l~e  195 (354)
                      +||+-|-..+.+.|.+--.+.-.+..|.-...++.+.+..+. .++.+-.|+-.|......    .....+ .=-+-|.=
T Consensus         2 ILlIDn~DsFT~ni~~~l~~~g~~~~v~~~d~~~~~~i~~~~pd~IiLSpGPg~p~~~~~~~~~~~~~~~~-iPILGICl   80 (195)
T PRK07649          2 ILMIDNYDSFTYNLVQYLGELGQELVVKRNDEVTISDIENMKPDFLMISPGPCSPNEAGISMEVIRYFAGK-IPIFGVCL   80 (195)
T ss_pred             EEEEECCCCHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHCCCCEEEECCCCCCHHHCCCCHHHHHHHCCC-CCEEEECH
T ss_conf             99995898079999999997899799988996899999841989899889999957847614679975289-97843029


Q ss_pred             CCHHHHHHHHHHCCCEEEEEEEEEECCEE
Q ss_conf             84289999999839868688975870545
Q gi|254780406|r  196 GKNREIKKVFEFFNWKVNRLIRISYGPFQ  224 (354)
Q Consensus       196 Gr~~qIrr~~~~~g~~V~~L~Rv~~G~~~  224 (354)
                      |  ||+  |+.++|-+|.++....+|...
T Consensus        81 G--~Q~--ia~~~Gg~v~~~~~~~hG~~~  105 (195)
T PRK07649         81 G--HQS--IAQVFGGEVVRAERLMHGKTS  105 (195)
T ss_pred             H--HHH--HHHHCCCCEEECCCEEECEEE
T ss_conf             9--999--998739728337960764065


No 99 
>PRK05670 anthranilate synthase component II; Provisional
Probab=42.94  E-value=19  Score=16.41  Aligned_cols=98  Identities=17%  Similarity=0.099  Sum_probs=53.6

Q ss_pred             EEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHH-HHHHCCCEEEECCCEEE----EECCCCEEEEEEEEEE
Q ss_conf             022236764100012344574047752112455646788874-00000876750343036----4026880799999951
Q gi|254780406|r  121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTL----DTQKGSNAWVTVGLRE  195 (354)
Q Consensus       121 LlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~----~~~~~~~~~~~v~l~e  195 (354)
                      +||+.|-+.+.+.+.+.-.+.--...|.-...++.+.+..+. .|+.+-+|+-.|.....    ...-..+ .=-+-|.=
T Consensus         2 iLiiD~~dsfT~nI~~~lr~~g~~v~V~~~d~~~~~~i~~~~pdgiiLS~GPg~P~~~~~~~~~i~~~~~~-iPiLGICl   80 (192)
T PRK05670          2 ILLIDNYDSFTYNLVQYLGELGAEVVVYRNDEITLEEIEALAPDAIVLSPGPGTPAEAGISLELIREFAGK-VPILGVCL   80 (192)
T ss_pred             EEEEECCCCHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHCCCCEEEECCCCCCHHHCCCHHHHHHHHCCC-CCEEEEEH
T ss_conf             99996898689999999986899699998998999999850989899999999936605549999973469-97899847


Q ss_pred             CCHHHHHHHHHHCCCEEEEEEEEEECCE
Q ss_conf             8428999999983986868897587054
Q gi|254780406|r  196 GKNREIKKVFEFFNWKVNRLIRISYGPF  223 (354)
Q Consensus       196 Gr~~qIrr~~~~~g~~V~~L~Rv~~G~~  223 (354)
                      |  ||+  |+.++|-+|.++....+|..
T Consensus        81 G--~Ql--ia~~~Gg~v~~~~~~~hG~~  104 (192)
T PRK05670         81 G--HQA--IGEAFGGKVVRAKEIMHGKT  104 (192)
T ss_pred             H--HHH--HHHHCCCEEEECCCCCCCEE
T ss_conf             7--899--99871973888886363704


No 100
>PRK02967 nickel responsive regulator; Provisional
Probab=42.24  E-value=24  Score=15.74  Aligned_cols=34  Identities=12%  Similarity=0.130  Sum_probs=19.9

Q ss_pred             EEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEEC
Q ss_conf             99999951842899999998398686889758705451
Q gi|254780406|r  188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL  225 (354)
Q Consensus       188 ~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l  225 (354)
                      .+++.+..|...+|+.+...+.    .++=|++|.++|
T Consensus        95 CLEvivv~G~~~~i~~la~~l~----~~kGVk~gkL~~  128 (138)
T PRK02967         95 CLEVAVLKGDMGDVQHFADDVI----AERGVRHGHLQC  128 (138)
T ss_pred             CEEEEEEECCHHHHHHHHHHHH----CCCCEEEEEEEE
T ss_conf             2799999557899999999985----058978879999


No 101
>KOG2529 consensus
Probab=39.60  E-value=19  Score=16.35  Aligned_cols=157  Identities=15%  Similarity=0.020  Sum_probs=74.1

Q ss_pred             EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCC
Q ss_conf             89602787515631443333644210110234320026655433232022236764100012344574047752112455
Q gi|254780406|r   74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV  153 (354)
Q Consensus        74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~  153 (354)
                      -++.++||++-    +..+-..-+...+.  ....+..|-||-..+|-|+.++|-.  +++..-+....++|...+..-.
T Consensus        69 gv~~i~kpa~p----ss~e~~swvk~iL~--~ek~Gh~gTlDP~vtg~l~v~~~~~--tr~~~s~~s~gk~yvg~~~lt~  140 (395)
T KOG2529          69 GVINIDKPANP----SSHEVVSWVKNILR--VEKTGHSGTLDPEVTGCLIVCIDRA--TRLLKSQQSAGKEYVGIGKLTP  140 (395)
T ss_pred             CCEECCCCCCC----CHHHHHHHHHHHHH--HHHHCCCCCCCCCCCCEEEEEEECC--CCCCCCHHCCCCEEEEEEECCC
T ss_conf             74633689798----60788888888766--8870799888965232279996000--0242120105867999985475


Q ss_pred             CHH---HHHHHHHHHHCCCEEEECCCEE-----E---------EECCCCE--EEEEEEEEECCHHHHHHHHHHCC-----
Q ss_conf             646---7888740000087675034303-----6---------4026880--79999995184289999999839-----
Q gi|254780406|r  154 DQD---KLNLLKKGIVIQGICYGDMQVT-----L---------DTQKGSN--AWVTVGLREGKNREIKKVFEFFN-----  209 (354)
Q Consensus       154 ~~~---~~~~~~~g~~~~~~~~~~~~~~-----~---------~~~~~~~--~~~~v~l~eGr~~qIrr~~~~~g-----  209 (354)
                      ..+   .+.+...-.....+...|....     .         +......  -.+.+.+.+|-  -+|-||-++|     
T Consensus       141 ~v~~~~k~~~~~e~l~g~l~~~~pl~~~~kr~~~v~~~y~s~~ie~d~~~~l~~f~~~~~~~t--~~rt~~~~lg~ll~~  218 (395)
T KOG2529         141 EVEDALKLHQKLEHLYGALFQRPPLISAVKRVLRVRTLYESKIIEYDRDYPLLRFGVSCEAGT--YKRTMCVHLGLLLGF  218 (395)
T ss_pred             CHHHHHHHCCCHHHHHHHHCCCCCHHHHCCCEEEEECHHHHHCCCCCCCCHHCCCCCCCCCCC--HHHHHHHHHHHHHHH
T ss_conf             234566641213330043236782333114245740013331001130001003652334554--687777766157662


Q ss_pred             -CEEEEEEEEEECCEECCCCCCCCEEECCHHH
Q ss_conf             -8686889758705451875547488679999
Q gi|254780406|r  210 -WKVNRLIRISYGPFQLGTLLAGSTREVSKKI  240 (354)
Q Consensus       210 -~~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e  240 (354)
                       -+-.-++|++-|...=.++..-..-++..+.
T Consensus       219 g~k~~E~~r~r~~~~~E~~~~~t~~d~~~~q~  250 (395)
T KOG2529         219 GGKMQELRRVRSGICSEEDDMLTEHDEQDAQF  250 (395)
T ss_pred             CCHHHHHHHCCCCCCCCCCCCCCCCCCHHHHH
T ss_conf             30135332214555446666542000002566


No 102
>TIGR00601 rad23 UV excision repair protein Rad23; InterPro: IPR004806   All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. Rad23 contains a ubiquitin-like domain that interacts with catalytically active proteasomes and two ubiquitin (Ub)-associated (UBA) sequences that bind Ub. Rad23 interacts with ubiquitinated cellular proteins through the synergistic action of its UBA domains.    In humans, Rad23 complexes with the XPC protein.; GO: 0006289 nucleotide-excision repair, 0005634 nucleus.
Probab=38.98  E-value=10  Score=17.98  Aligned_cols=33  Identities=12%  Similarity=-0.006  Sum_probs=21.3

Q ss_pred             HHHHHCC---CEEEEEEEEEECCEECCCCCCCCEEE
Q ss_conf             9999839---86868897587054518755474886
Q gi|254780406|r  203 KVFEFFN---WKVNRLIRISYGPFQLGTLLAGSTRE  235 (354)
Q Consensus       203 r~~~~~g---~~V~~L~Rv~~G~~~l~~L~~G~~r~  235 (354)
                      ++=...|   |+|.+.|=|-=|.|--++-..++|.-
T Consensus        31 KI~~~~gkDa~pv~~qKLIY~GKiL~Dd~t~~Ey~I   66 (453)
T TIGR00601        31 KIEQEQGKDAYPVAQQKLIYSGKILSDDKTVSEYKI   66 (453)
T ss_pred             HHHHHCCCCCCCHHCCEEEECCCCCCCCCCHHHCCC
T ss_conf             999760873562002021004533167541544266


No 103
>pfam02597 ThiS ThiS family. ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS. MoaD, a protein involved sulphur transfer in molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.
Probab=38.28  E-value=29  Score=15.20  Aligned_cols=44  Identities=18%  Similarity=0.308  Sum_probs=30.2

Q ss_pred             CCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCC--CEEECCCCEEEE
Q ss_conf             7734478899988687789999999869869999992406--878079997999
Q gi|254780406|r   11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA--AVNVMSTDHIEV   62 (354)
Q Consensus        11 ~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~--~~~v~~~d~v~v   62 (354)
                      .++.-+..+|...++        ....=.|-|||++|...  .+.+.++|.|.+
T Consensus        18 ~~~~tv~~ll~~l~~--------~~~~v~v~vN~~~v~~~~~~~~L~~gD~v~i   63 (70)
T pfam02597        18 PEGATVAELLEALGL--------NPERVAVAVNGEIVPRSQADTPLKDGDEVAI   63 (70)
T ss_pred             CCCCCHHHHHHHHCC--------CCCCEEEEECCEECCCCCCCCCCCCCCEEEE
T ss_conf             999969999998388--------8888899999998678567767799999999


No 104
>PRK06774 para-aminobenzoate synthase component II; Provisional
Probab=36.57  E-value=15  Score=17.00  Aligned_cols=100  Identities=15%  Similarity=0.106  Sum_probs=56.9

Q ss_pred             EEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHH-HHHHCCCEEEECCCEEEE----ECCCCEEEEEEEEEE
Q ss_conf             022236764100012344574047752112455646788874-000008767503430364----026880799999951
Q gi|254780406|r  121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLD----TQKGSNAWVTVGLRE  195 (354)
Q Consensus       121 LlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~----~~~~~~~~~~v~l~e  195 (354)
                      +||+-|-..+.+.|.|--.+..-+..|.-...++.+.+..+. .++.+..|+-.|......    ...... .=-+-|.=
T Consensus         2 ILiiDn~DsFT~nl~~~l~~~g~~v~V~~~d~~~~~~i~~~~p~~ivLSpGPG~P~~~~~~~~~i~~~~~~-iPILGICl   80 (191)
T PRK06774          2 LLLIDNYDSFTYNLYQYFCELGTEVMVKRNDELQLTDIEQLAPSHVVISPGPCTPNEAGISLAVIRHFADK-LPILGVCL   80 (191)
T ss_pred             EEEEECCCCHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHCCCCEEEECCCCCCHHHHCCHHHHHHHHCCC-CCEEEEHH
T ss_conf             99996999769999999987799599986998899999853999699999998967907306899974469-97886168


Q ss_pred             CCHHHHHHHHHHCCCEEEEEEEEEECCEEC
Q ss_conf             842899999998398686889758705451
Q gi|254780406|r  196 GKNREIKKVFEFFNWKVNRLIRISYGPFQL  225 (354)
Q Consensus       196 Gr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l  225 (354)
                      |  ||+  |+.++|-+|.++....+|....
T Consensus        81 G--~Q~--ia~~~Gg~v~~~~~~~hG~~~~  106 (191)
T PRK06774         81 G--HQA--LGQAFGARVVRARQVMHGKTSA  106 (191)
T ss_pred             H--HHH--HHHHCCCEEEECCCCEECEEEE
T ss_conf             7--999--8656098492899747570368


No 105
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=36.43  E-value=31  Score=15.02  Aligned_cols=42  Identities=31%  Similarity=0.437  Sum_probs=27.3

Q ss_pred             CHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCC---CCEEECCCCEEEE
Q ss_conf             3447889998868778999999986986999999240---6878079997999
Q gi|254780406|r   13 PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER---AAVNVMSTDHIEV   62 (354)
Q Consensus        13 ~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~---~~~~v~~~d~v~v   62 (354)
                      +..+.-+|++.|+-.+.-        -|.|||++|-.   ..+.++.+|.|+|
T Consensus        17 ~~tv~dLL~~l~~~~~~v--------av~vNg~iVpr~~~~~~~l~~gD~iev   61 (68)
T COG2104          17 GTTVADLLAQLGLNPEGV--------AVAVNGEIVPRSQWADTILKEGDRIEV   61 (68)
T ss_pred             CCCHHHHHHHHCCCCCEE--------EEEECCEECCCHHHHHCCCCCCCEEEE
T ss_conf             873999999729998559--------999889982504632013158998999


No 106
>PRK04460 nickel responsive regulator; Provisional
Probab=33.55  E-value=34  Score=14.73  Aligned_cols=20  Identities=25%  Similarity=0.506  Sum_probs=15.2

Q ss_pred             HHHHHHHHHCCCCCHHHHHH
Q ss_conf             44788999886877899999
Q gi|254780406|r   14 QRVSKVIARAGIASRREVER   33 (354)
Q Consensus        14 ~RL~K~la~~g~~SRr~a~~   33 (354)
                      .+|++++...|+-||++|-+
T Consensus        17 ~~lD~~i~~~Gy~nRSeaIR   36 (139)
T PRK04460         17 EKFDRLIEEKGYQNRSEAIR   36 (139)
T ss_pred             HHHHHHHHHCCCCCHHHHHH
T ss_conf             99999999809987889999


No 107
>PRK00630 nickel responsive regulator; Provisional
Probab=32.65  E-value=35  Score=14.64  Aligned_cols=24  Identities=29%  Similarity=0.526  Sum_probs=15.4

Q ss_pred             HHHHHHHHHCCCCCHHHHHH-HHHC
Q ss_conf             44788999886877899999-9986
Q gi|254780406|r   14 QRVSKVIARAGIASRREVER-MIAQ   37 (354)
Q Consensus        14 ~RL~K~la~~g~~SRr~a~~-lI~~   37 (354)
                      +.+++++...|+.||++|-+ +|+.
T Consensus        20 ~~~D~~i~~~Gy~nRSEaIRdliR~   44 (143)
T PRK00630         20 DELDNRIIKNGYSSRSELVRDLIRE   44 (143)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             9999999981999788999999999


No 108
>PRK06065 acetyl-CoA acetyltransferase; Provisional
Probab=30.71  E-value=31  Score=14.99  Aligned_cols=16  Identities=13%  Similarity=0.530  Sum_probs=7.5

Q ss_pred             HHHHHHHCCCCCHHHHH
Q ss_conf             78899988687789999
Q gi|254780406|r   16 VSKVIARAGIASRREVE   32 (354)
Q Consensus        16 L~K~la~~g~~SRr~a~   32 (354)
                      +.+-|.++|+ +.+++|
T Consensus        38 ~~~Al~DAGl-~~~dID   53 (393)
T PRK06065         38 ARQALDEAGL-ELKDID   53 (393)
T ss_pred             HHHHHHHCCC-CHHHCC
T ss_conf             9999998499-989989


No 109
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=30.06  E-value=39  Score=14.37  Aligned_cols=60  Identities=15%  Similarity=0.309  Sum_probs=30.3

Q ss_pred             CCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECC-CCC-CCCEEECCHHHHHHHHH
Q ss_conf             68807999999518428999999983986868897587054518-755-47488679999987532
Q gi|254780406|r  183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL-AGSTREVSKKILREQLG  246 (354)
Q Consensus       183 ~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~-~L~-~G~~r~l~~~e~~~l~~  246 (354)
                      ..+..|+.++.+.--...||++|......-.    +..|.--|. .|. .+....+..+.+..++.
T Consensus       452 ~Ps~~WL~fV~T~kARskIr~~lk~~~r~~~----i~~Gk~lL~~~l~~~~~l~~~~~~~l~~~~~  513 (702)
T PRK11092        452 RPNAAWLNFVVSSKARAKIRQLLKNLKRDDS----VSLGRRLLNHALGGSRKLDEIPQENIQRELD  513 (702)
T ss_pred             CCCHHHHHHHHCHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
T ss_conf             9897899763267889999999987558999----9999999999986256612289899999999


No 110
>TIGR01687 moaD_arch MoaD family protein; InterPro: IPR010038   Members of this family appear to be archaeal and bacterial (proteobacteria and Thermus) versions of MoaD, subunit 1 of molybdopterin converting factor..
Probab=30.05  E-value=37  Score=14.51  Aligned_cols=26  Identities=15%  Similarity=0.226  Sum_probs=20.1

Q ss_pred             CCCEEECCE-ECCC---CCEEECCCCEEEE
Q ss_conf             698699999-9240---6878079997999
Q gi|254780406|r   37 QQRVKVNGI-LLER---AAVNVMSTDHIEV   62 (354)
Q Consensus        37 ~G~V~Vng~-~v~~---~~~~v~~~d~v~v   62 (354)
                      .=.|.|||+ =|..   +.++++.+|.|.+
T Consensus        57 ~v~ilvNGran~~~l~GL~~~LkdGD~vai   86 (93)
T TIGR01687        57 NVIILVNGRANVDWLEGLETELKDGDVVAI   86 (93)
T ss_pred             EEEEEECCCCCCCCCCCCCCCCCCCCEEEE
T ss_conf             578985164143220365752327875675


No 111
>TIGR01278 DPOR_BchB light-independent protochlorophyllide reductase, B subunit; InterPro: IPR005969    Synonym: dark protochlorophyllide reductase    Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite .; GO: 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction.
Probab=29.85  E-value=38  Score=14.43  Aligned_cols=40  Identities=18%  Similarity=0.136  Sum_probs=23.4

Q ss_pred             EEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEE
Q ss_conf             750343036402688079999995184289999999839868688
Q gi|254780406|r  171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL  215 (354)
Q Consensus       171 ~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L  215 (354)
                      .+.+..|-+++-    +.|.+-.. --..+||||++.||.+|+-.
T Consensus       160 ~T~~psVNllGp----~~LGFH~r-~D~~elrrlL~~LG~evN~v  199 (562)
T TIGR01278       160 TTEKPSVNLLGP----ASLGFHHR-HDLIELRRLLKTLGIEVNVV  199 (562)
T ss_pred             CCCCCEEEECCC----CCCCCCCH-HHHHHHHHHHHHCCEEEEEE
T ss_conf             889623761141----13342321-03389999996589479897


No 112
>pfam05597 Phasin Poly(hydroxyalcanoate) granule associated protein (phasin). Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Probab=28.73  E-value=41  Score=14.22  Aligned_cols=24  Identities=46%  Similarity=0.729  Sum_probs=21.4

Q ss_pred             CHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             344788999886877899999998
Q gi|254780406|r   13 PQRVSKVIARAGIASRREVERMIA   36 (354)
Q Consensus        13 ~~RL~K~la~~g~~SRr~a~~lI~   36 (354)
                      .+|++++|...|+-|+++++.|.+
T Consensus        93 e~rV~~aL~rLGips~~di~~L~~  116 (132)
T pfam05597        93 DERVAKALNRLGVPSRKEVEALSA  116 (132)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             999999998569998999999999


No 113
>cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ domains a C-terminal beta-strand  is thought to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=27.72  E-value=40  Score=14.28  Aligned_cols=17  Identities=47%  Similarity=0.862  Sum_probs=9.5

Q ss_pred             ECCCCE-EEECCEECCCC
Q ss_conf             079997-99999892255
Q gi|254780406|r   54 VMSTDH-IEVDGVPLRKA   70 (354)
Q Consensus        54 v~~~d~-v~vdg~~i~~~   70 (354)
                      +..+|. +.|||+++.-.
T Consensus        25 Lk~GDvI~~vdGk~v~~~   42 (79)
T cd00986          25 LKAGDHIIAVDGKPFKEA   42 (79)
T ss_pred             CCCCCEEEEECCEECCCH
T ss_conf             778999999999895799


No 114
>KOG3449 consensus
Probab=27.15  E-value=44  Score=14.05  Aligned_cols=17  Identities=24%  Similarity=0.432  Sum_probs=11.9

Q ss_pred             CHHHHHHHHHHCCCEEE
Q ss_conf             42899999998398686
Q gi|254780406|r  197 KNREIKKVFEFFNWKVN  213 (354)
Q Consensus       197 r~~qIrr~~~~~g~~V~  213 (354)
                      .+.-|+.+|+++|.++-
T Consensus        19 sa~DikkIl~sVG~E~d   35 (112)
T KOG3449          19 SASDIKKILESVGAEID   35 (112)
T ss_pred             CHHHHHHHHHHHCCCCC
T ss_conf             78899999987173347


No 115
>PRK10872 relA GDP/GTP pyrophosphokinase; Provisional
Probab=26.51  E-value=45  Score=13.97  Aligned_cols=20  Identities=25%  Similarity=0.252  Sum_probs=14.5

Q ss_pred             CCCEEEEECCCCCEEEECCC
Q ss_conf             56438960278751563144
Q gi|254780406|r   70 AERTRLWLYHKPIGLVTTHS   89 (354)
Q Consensus        70 ~~~~~~~~~~KP~g~~~~~~   89 (354)
                      .....||...||.||-+=++
T Consensus       305 ~rfkDYIa~PK~NgYQSLHT  324 (743)
T PRK10872        305 DEFDDYVANPKPNGYQSIHT  324 (743)
T ss_pred             CHHHHHCCCCCCCCCEEEEE
T ss_conf             24665421789888306889


No 116
>pfam11685 DUF3281 Protein of unknown function (DUF3281). This family of bacterial proteins has no known function.
Probab=26.01  E-value=46  Score=13.93  Aligned_cols=12  Identities=33%  Similarity=0.490  Sum_probs=4.8

Q ss_pred             CCCCCCCCCCCE
Q ss_conf             266554332320
Q gi|254780406|r  110 SVGRLDINTEGL  121 (354)
Q Consensus       110 ~vgRLD~~t~GL  121 (354)
                      ++|.=-.-.+|.
T Consensus       119 ~~GsNtIsVSGt  130 (269)
T pfam11685       119 PVGSNTISVSGT  130 (269)
T ss_pred             CCCCCEEEEEEE
T ss_conf             567736887678


No 117
>PRK06059 lipid-transfer protein; Provisional
Probab=25.25  E-value=44  Score=14.06  Aligned_cols=18  Identities=28%  Similarity=0.484  Sum_probs=10.6

Q ss_pred             HHHHHHHCCCCCHHHHHHH
Q ss_conf             7889998868778999999
Q gi|254780406|r   16 VSKVIARAGIASRREVERM   34 (354)
Q Consensus        16 L~K~la~~g~~SRr~a~~l   34 (354)
                      +.+-|.++|+ ++.+++-+
T Consensus        31 ~~~AL~DAGl-~~~dVD~v   48 (399)
T PRK06059         31 ARAALADAGL-DWRQVQLV   48 (399)
T ss_pred             HHHHHHHCCC-CHHHCCEE
T ss_conf             9999985599-98994688


No 118
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=25.25  E-value=48  Score=13.83  Aligned_cols=41  Identities=24%  Similarity=0.339  Sum_probs=25.5

Q ss_pred             HHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCC---CCEEECCCCEEEE
Q ss_conf             447889998868778999999986986999999240---6878079997999
Q gi|254780406|r   14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLER---AAVNVMSTDHIEV   62 (354)
Q Consensus        14 ~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~---~~~~v~~~d~v~v   62 (354)
                      .-|+-.|+..|+..++-|        |-|||++|-.   ..+.+.++|.|+|
T Consensus        15 ~tl~~Ll~elg~~~~~vA--------vAvN~~~Vpr~~~~~~~L~eGDriEI   58 (65)
T PRK06488         15 TTLALLLAELGYEGNWLA--------TAVNGELVHSEARAQFVLHEGDRIEI   58 (65)
T ss_pred             HHHHHHHHHCCCCCCCEE--------EEECCEEECHHHHCCCCCCCCCEEEE
T ss_conf             689999997298888089--------99899987424505451799999999


No 119
>CHL00101 trpG anthranilate synthase component 2
Probab=25.20  E-value=36  Score=14.59  Aligned_cols=99  Identities=14%  Similarity=0.086  Sum_probs=51.4

Q ss_pred             EEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHH-HHHHCCCEEEECCCEEEEE----CCCCEEEEEEEEEEC
Q ss_conf             22236764100012344574047752112455646788874-0000087675034303640----268807999999518
Q gi|254780406|r  122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDT----QKGSNAWVTVGLREG  196 (354)
Q Consensus       122 lllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~~----~~~~~~~~~v~l~eG  196 (354)
                      ||+-|-..+.+.|.+.-.+..-...|.-...++.+.+..+. +|+.+-+|+-.|.......    .-... .=-+-|.=|
T Consensus         3 LiiD~~dsft~~i~r~lrelg~~~~v~~~d~~~~~~i~~~~p~gIILS~GPg~p~~~~~~~~~~~~~~~~-iPILGIClG   81 (190)
T CHL00101          3 LIIDNYDSFTYNLVQSLGELNSDLLVCRNDEIDLSKIKNLNPRHIIISPGPGHPRDSGISLDVISSYAPT-IPILGVCLG   81 (190)
T ss_pred             EEEECCCHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHCCCCEEEECCCCCCHHHCCCCHHHHHHHHCC-CCEEEECHH
T ss_conf             9997888089999999986899899986998999999707979899979999957857616899997149-987897398


Q ss_pred             CHHHHHHHHHHCCCEEEEEEEEEECCEEC
Q ss_conf             42899999998398686889758705451
Q gi|254780406|r  197 KNREIKKVFEFFNWKVNRLIRISYGPFQL  225 (354)
Q Consensus       197 r~~qIrr~~~~~g~~V~~L~Rv~~G~~~l  225 (354)
                        ||+  |..++|-+|.++....+|...+
T Consensus        82 --~Q~--ia~~~Gg~v~~~~~~~~G~~~~  106 (190)
T CHL00101         82 --HQS--IGYVYGGKIIKASKPMHGKTSL  106 (190)
T ss_pred             --HHH--HHHHCCCEEEECCCEEECCEEE
T ss_conf             --899--9887586499788204362479


No 120
>KOG2582 consensus
Probab=25.02  E-value=26  Score=15.44  Aligned_cols=20  Identities=20%  Similarity=0.142  Sum_probs=9.2

Q ss_pred             EEECCCCCEEEECCCCCCCC
Q ss_conf             96027875156314433336
Q gi|254780406|r   75 LWLYHKPIGLVTTHSDPDGR   94 (354)
Q Consensus        75 ~~~~~KP~g~~~~~~~~~~~   94 (354)
                      ++.|--=.|++|.......+
T Consensus       182 fL~Y~yYgg~iciglk~fe~  201 (422)
T KOG2582         182 FLLYLYYGGMICIGLKRFER  201 (422)
T ss_pred             HHHHHHHCCEEEECCCCHHH
T ss_conf             99999732144321263888


No 121
>PRK01002 nickel responsive regulator; Provisional
Probab=24.79  E-value=49  Score=13.78  Aligned_cols=20  Identities=35%  Similarity=0.494  Sum_probs=15.5

Q ss_pred             HHHHHHHHHCCCCCHHHHHH
Q ss_conf             44788999886877899999
Q gi|254780406|r   14 QRVSKVIARAGIASRREVER   33 (354)
Q Consensus        14 ~RL~K~la~~g~~SRr~a~~   33 (354)
                      ..|++++...|+-||++|-+
T Consensus        17 ~~lD~~i~~~Gy~nRSeaIR   36 (141)
T PRK01002         17 AEFDEIIEERGYASRSEAIR   36 (141)
T ss_pred             HHHHHHHHHCCCCCHHHHHH
T ss_conf             99999999809987889999


No 122
>PRK07855 lipid-transfer protein; Provisional
Probab=24.36  E-value=48  Score=13.79  Aligned_cols=14  Identities=0%  Similarity=0.003  Sum_probs=7.4

Q ss_pred             HHHHHHHCCCEEEE
Q ss_conf             99999983986868
Q gi|254780406|r  201 IKKVFEFFNWKVNR  214 (354)
Q Consensus       201 Irr~~~~~g~~V~~  214 (354)
                      .++.|+..|....+
T Consensus       272 a~~ay~~AGi~p~D  285 (386)
T PRK07855        272 ARQLWRQSGLGPAD  285 (386)
T ss_pred             HHHHHHHCCCCHHH
T ss_conf             99999984999788


No 123
>PRK08313 acetyl-CoA acetyltransferase; Provisional
Probab=23.18  E-value=48  Score=13.83  Aligned_cols=17  Identities=18%  Similarity=0.540  Sum_probs=7.1

Q ss_pred             HHHHHHCCCCCHHHHHHH
Q ss_conf             889998868778999999
Q gi|254780406|r   17 SKVIARAGIASRREVERM   34 (354)
Q Consensus        17 ~K~la~~g~~SRr~a~~l   34 (354)
                      ..=|+++|+ +.+++|.+
T Consensus        34 ~~Al~DAGl-~~~dID~~   50 (391)
T PRK08313         34 DRALADAGL-TFDDIDAV   50 (391)
T ss_pred             HHHHHHCCC-CHHHCCEE
T ss_conf             999997499-98998999


No 124
>PTZ00246 proteasome subunit alpha; Provisional
Probab=22.64  E-value=53  Score=13.51  Aligned_cols=95  Identities=17%  Similarity=0.126  Sum_probs=58.6

Q ss_pred             CCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEE
Q ss_conf             23445740477521124556467888740000087675034303640268807999999518428999999983986868
Q gi|254780406|r  135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR  214 (354)
Q Consensus       135 ~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~  214 (354)
                      +.| ......|....-|.=.......|.+...       .               .+++.|....-|+-+.+.+...+..
T Consensus       150 ~DP-sG~~~~~ka~AiG~gs~~a~~~LEk~y~-------~---------------~ms~eeai~lAi~aL~~~~~~~~~~  206 (253)
T PTZ00246        150 TDP-SGNYSGWKATAIGTNNQTAQSILKQEWK-------E---------------DMTLEQGLLLALKVLTKSMDSTTPK  206 (253)
T ss_pred             ECC-CCCEEEEEEEEECCCHHHHHHHHHHHCC-------C---------------CCCHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             879-8878545799989880899999987466-------9---------------9999999999999999998564798


Q ss_pred             EEEEEECCEECCC-CCCCCEEECCHHHHHHHHHHHHHHC
Q ss_conf             8975870545187-5547488679999987532100000
Q gi|254780406|r  215 LIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEE  252 (354)
Q Consensus       215 L~Rv~~G~~~l~~-L~~G~~r~l~~~e~~~l~~~~~~~~  252 (354)
                      -.-|.++=++..+ --...+|-|+++||++++.....+.
T Consensus       207 ~~~iEvavvt~~~~~~~~~~r~L~~~EI~~~l~~~~~~~  245 (253)
T PTZ00246        207 ADKIEVGYLSKGNGDGEPFQKMLSEKEIAELLKKYTQEY  245 (253)
T ss_pred             CCCEEEEEEECCCCCCCCCEEECCHHHHHHHHHHHHHHH
T ss_conf             883899999826888874158789999999999999887


No 125
>TIGR02542 B_forsyth_147 Bacteroides forsythus 147-residue repeat.
Probab=22.52  E-value=37  Score=14.53  Aligned_cols=101  Identities=18%  Similarity=0.130  Sum_probs=62.9

Q ss_pred             CCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEE-EECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHH
Q ss_conf             64100012344574047752112455646788874000008767-50343036402688079999995184289999999
Q gi|254780406|r  128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE  206 (354)
Q Consensus       128 g~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~  206 (354)
                      |+..+-++--.+-+...|+..+.|-+..-+    .+||.+..+. .....|.+.+.-+.+ -+.+.-.+=-+.+.|.||.
T Consensus        26 GKI~svI~~t~~p~~~~~l~~~~G~lE~~D----g~gi~IGs~~g~~~~sV~i~~TPsGN-~v~F~PYTlTy~~~r~~F~  100 (154)
T TIGR02542        26 GKIQSVITVTQYPMDNDALLRVRGTLEQVD----GNGIRIGSGQGITAASVRIKGTPSGN-NVIFPPYTLTYNELREIFR  100 (154)
T ss_pred             CCEEEEEEEECCCCCCCCEEEEEEEEEEEC----CCEEEECCCCCCCCCCEEEEECCCCC-CCCCCCCCCCHHHHHHHHC
T ss_conf             825789987315535541024542477025----87468717888512513770068988-5321883013567776631


Q ss_pred             HCCCEEEEEEEEEECCEECCCCCCCCEEEC
Q ss_conf             839868688975870545187554748867
Q gi|254780406|r  207 FFNWKVNRLIRISYGPFQLGTLLAGSTREV  236 (354)
Q Consensus       207 ~~g~~V~~L~Rv~~G~~~l~~L~~G~~r~l  236 (354)
                      .--+.-..+-|-.+   .-++||.|.||-=
T Consensus       101 E~~~~YQGITReQV---~rdGLP~G~YR~C  127 (154)
T TIGR02542       101 EPTMVYQGITREQV---LRDGLPEGSYRLC  127 (154)
T ss_pred             CCCEEECCCCHHHH---HHCCCCCCCEEEE
T ss_conf             67602237236887---5258999974576


No 126
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=22.47  E-value=53  Score=13.53  Aligned_cols=34  Identities=12%  Similarity=0.093  Sum_probs=28.0

Q ss_pred             HHHHHHCCCEEECCEECCCCCEEECCCCEEEECC
Q ss_conf             9999986986999999240687807999799999
Q gi|254780406|r   31 VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG   64 (354)
Q Consensus        31 a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg   64 (354)
                      --.+|++|.=+|-+.+...--.++.++|.|.+..
T Consensus         9 ~F~~Ik~G~KtIE~Rl~d~kr~~ik~GD~I~F~~   42 (109)
T cd06555           9 PFELIKSGKKTIEIRLNDEKRQQIKVGDKILFND   42 (109)
T ss_pred             HHHHHHCCCCEEEEECCCHHHHHCCCCCEEEEEE
T ss_conf             5899876997799982706787189999999998


No 127
>TIGR01670 YrbI-phosphatas 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family; InterPro: IPR010023    This entry is a part of the haloacid dehalogenase (HAD) superfamily of hydrolases from beta, gamma and epsilon proteobacteria, Aquifex, Fusobacterium, Porphyromonas and Methanosarcina. All characterised members of the HAD-superfamily hydrolase, subfamily IIIA and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs , all of which are found conserved in this family.    Lipopolysaccharides of Gram-negative bacteria consist of a heteropolysaccharide component (O-antigen) and a hydrophobic component (lipid A). Linking the two portions is 3-Deoxy-D-manno-octulosonate (KDO), an 8-carbon sugar. Biosynthesis of KDO linked to lipid A proceeds via five steps, one of which involves removal of a phosphate from KDO 8-P via the action of KDO 8-P phosphatase (3.1.3.45 from EC; IPR008230 from INTERPRO) . One member of this family, the YrbI protein from Haemophilus influenzae has been cloned, expressed, purified and found to be an active phosphatase. Furthermore, its crystal structure has been determined .   The sequence from Methanosarcina acetivorans, Q8TJL6 from SWISSPROT, is distinctive in that it is linked to an N-terminal cytidylyltransferase domain (IPR003329 from INTERPRO) and is annotated as acylneuraminate cytidylyltransferase. This may give some clue as the function of these phosphatases. Several eukaryotic sequences are also closely related to this family; one such sequence is the CMP-N-acetylneuraminic acid synthetase from mouse, but in this case as in the others the phosphatase domain is clearly inactive as many of the active site residues are not conserved.; GO: 0019143 3-deoxy-manno-octulosonate-8-phosphatase activity, 0009103 lipopolysaccharide biosynthetic process.
Probab=21.16  E-value=44  Score=14.07  Aligned_cols=18  Identities=22%  Similarity=0.410  Sum_probs=14.5

Q ss_pred             CCCCEEEECCCCCCCCCC
Q ss_conf             323202223676410001
Q gi|254780406|r  117 NTEGLLLLTNDGGLARVL  134 (354)
Q Consensus       117 ~t~GLlllTndg~l~~~l  134 (354)
                      -|.|++.+|++||....+
T Consensus        12 LtDGkiyyt~nGE~iK~F   29 (154)
T TIGR01670        12 LTDGKIYYTENGEEIKAF   29 (154)
T ss_pred             EECCEEEECCCCCEEEEE
T ss_conf             106706663888443120


No 128
>pfam10574 UPF0552 Uncharacterized protein family UPF0552. This family of proteins has no known function.
Probab=21.00  E-value=58  Score=13.30  Aligned_cols=95  Identities=16%  Similarity=0.283  Sum_probs=44.5

Q ss_pred             EECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCC-EEEEEEEEEECCHHHHHHHHHHCCCEE----EEEEEEEECC
Q ss_conf             11245564678887400000876750343036402688-079999995184289999999839868----6889758705
Q gi|254780406|r  148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVTVGLREGKNREIKKVFEFFNWKV----NRLIRISYGP  222 (354)
Q Consensus       148 ~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~-~~~~~v~l~eGr~~qIrr~~~~~g~~V----~~L~Rv~~G~  222 (354)
                      +..+..+++.. +-..|+.+++....+....+....+. .-++-+.|.  -.+-+||-|.+-|++|    ++-..|.-|-
T Consensus        19 ~~~g~w~P~~~-q~G~GvilEG~l~d~srH~itd~~~~k~Ry~vl~i~--~s~~hrR~Fd~~G~EiepnfS~t~kVntG~   95 (224)
T pfam10574        19 KFSGTWDPEVF-QSGDGVLLEGTLLDVSRHTITDQKNQKERYYVLYIR--PSRIHRRKFDSKGNEIEPNFSDTKKVNTGF   95 (224)
T ss_pred             CCCCCCCHHHH-CCCCEEEEEEEEEEEEEEEEECCCCCCEEEEEEEEE--CCHHHHHHCCCCCCCCCCCCCCCEEEEEEE
T ss_conf             05775074571-478648998798532467886278981579999982--145545322787768798755221542312


Q ss_pred             EECC-CC-CCCCEEECCHHHHHHHH
Q ss_conf             4518-75-54748867999998753
Q gi|254780406|r  223 FQLG-TL-LAGSTREVSKKILREQL  245 (354)
Q Consensus       223 ~~l~-~L-~~G~~r~l~~~e~~~l~  245 (354)
                      |.-. .. +.|+.-.|++.+|..|+
T Consensus        96 L~SsykVEAkG~tDrls~~~L~~lV  120 (224)
T pfam10574        96 LMSSYKVEAKGESDRLSEDQLSVLV  120 (224)
T ss_pred             EECEEEEEECCCCCCCCHHHHHHHH
T ss_conf             3000177742753434899999774


No 129
>KOG2553 consensus
Probab=20.98  E-value=58  Score=13.30  Aligned_cols=25  Identities=12%  Similarity=0.242  Sum_probs=18.3

Q ss_pred             CCEEEEEEEEEECC--HHHHHHHHHHC
Q ss_conf             88079999995184--28999999983
Q gi|254780406|r  184 GSNAWVTVGLREGK--NREIKKVFEFF  208 (354)
Q Consensus       184 ~~~~~~~v~l~eGr--~~qIrr~~~~~  208 (354)
                      ...-|+.|.|+.-.  .||||+|...+
T Consensus       262 ~~~e~V~i~i~GQSFMLHQIRKMVgla  288 (416)
T KOG2553         262 EGVEFVKIKIHGQSFMLHQIRKMVGLA  288 (416)
T ss_pred             CCCEEEEEEEECCHHHHHHHHHHHHHH
T ss_conf             782399999976105999999999999


No 130
>KOG0151 consensus
Probab=20.93  E-value=58  Score=13.30  Aligned_cols=24  Identities=17%  Similarity=0.158  Sum_probs=13.4

Q ss_pred             CCEECC--CCCCCCEEECCHH-HHHHH
Q ss_conf             054518--7554748867999-99875
Q gi|254780406|r  221 GPFQLG--TLLAGSTREVSKK-ILREQ  244 (354)
Q Consensus       221 G~~~l~--~L~~G~~r~l~~~-e~~~l  244 (354)
                      |-|.-+  +|.+|....+++. +.+.+
T Consensus       719 d~l~sg~~~lk~~~sv~~qpe~~~d~~  745 (877)
T KOG0151         719 DELESGERDLKPGSSVREQPENERDRL  745 (877)
T ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf             555778755788976014804677799


No 131
>pfam12471 GTP_CH_N GTP cyclohydrolase N terminal. This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. This family is the N terminal of GTP cyclohydrolase, the rate limiting enzyme in the synthesis of tetrahydrobiopterin.
Probab=20.54  E-value=57  Score=13.34  Aligned_cols=15  Identities=13%  Similarity=0.162  Sum_probs=5.5

Q ss_pred             HHHHHHHHHHHCCCE
Q ss_conf             678887400000876
Q gi|254780406|r  156 DKLNLLKKGIVIQGI  170 (354)
Q Consensus       156 ~~~~~~~~g~~~~~~  170 (354)
                      |..+.+..|-..-||
T Consensus       137 Ei~eAv~~GrL~~DG  151 (195)
T pfam12471       137 ELREAVAKGRLVPDG  151 (195)
T ss_pred             HHHHHHHCCCCCCCC
T ss_conf             799999849988887


No 132
>PRK06365 acetyl-CoA acetyltransferase; Provisional
Probab=20.41  E-value=59  Score=13.23  Aligned_cols=17  Identities=12%  Similarity=0.372  Sum_probs=8.9

Q ss_pred             HHHHHHHHCCCCCHHHHH
Q ss_conf             478899988687789999
Q gi|254780406|r   15 RVSKVIARAGIASRREVE   32 (354)
Q Consensus        15 RL~K~la~~g~~SRr~a~   32 (354)
                      =+.+=|.++|+ +.+++|
T Consensus        30 A~~~AL~DAGl-~~~dID   46 (415)
T PRK06365         30 AFDYAMNDAGL-TLADID   46 (415)
T ss_pred             HHHHHHHHCCC-CHHHCC
T ss_conf             99999997599-989969


Done!