Query         gi|254780753|ref|YP_003065166.1| peptide chain release factor 2 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 355
No_of_seqs    271 out of 3128
Neff          6.5 
Searched_HMMs 39220
Date          Sun May 29 23:36:38 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780753.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00020 prfB peptide chain r 100.0       0       0 1152.9  28.6  353    2-354    13-372 (373)
  2 TIGR00019 prfA peptide chain r 100.0       0       0 1025.1  24.2  336   15-354     9-362 (373)
  3 PRK00578 prfB peptide chain re 100.0       0       0  997.5  34.2  353    2-354    11-363 (367)
  4 PRK07245 consensus             100.0       0       0  989.8  32.2  335   19-355     1-335 (337)
  5 PRK00591 prfA peptide chain re 100.0       0       0  979.5  30.4  341   11-355     3-351 (360)
  6 PRK05589 peptide chain release 100.0       0       0  943.9  30.0  324   30-354     1-324 (325)
  7 PRK06746 peptide chain release 100.0       0       0  938.6  28.8  325   30-354     1-325 (326)
  8 PRK07342 peptide chain release 100.0       0       0  915.9  26.3  311   45-355     1-311 (322)
  9 COG0216 PrfA Protein chain rel 100.0       0       0  898.5  27.9  337   16-355     9-353 (363)
 10 PRK08787 peptide chain release 100.0       0       0  874.0  27.1  302   52-354     2-303 (313)
 11 KOG2726 consensus              100.0       0       0  709.4  24.9  321   24-355    51-377 (386)
 12 COG1186 PrfB Protein chain rel 100.0       0       0  636.2  18.0  238  117-354     1-238 (239)
 13 TIGR03072 release_prfH putativ 100.0       0       0  548.6  17.1  196  117-317     1-197 (200)
 14 PRK08179 prfH peptide chain re 100.0       0       0  533.5  18.4  199  117-320     2-201 (204)
 15 pfam00472 RF-1 RF-1 domain. Th 100.0 3.3E-36 8.5E-41  279.5   7.8  111  216-327     3-114 (114)
 16 pfam03462 PCRF PCRF domain. Th 100.0 4.2E-34 1.1E-38  264.5   8.4  110   75-184     2-115 (115)
 17 PRK09256 hypothetical protein;  99.6   1E-16 2.7E-21  140.2   3.6   68  219-286     6-97  (138)
 18 KOG3429 consensus               98.9 2.4E-09 6.2E-14   87.5   5.3   71  219-289    33-128 (172)
 19 PRK11147 ABC transporter ATPas  95.6    0.11 2.7E-06   32.9   8.2   21  218-239   337-357 (632)
 20 PRK10636 putative ABC transpor  94.8    0.33 8.5E-06   29.4   8.7   21  218-239   330-350 (638)
 21 TIGR00019 prfA peptide chain r  92.8    0.53 1.3E-05   27.9   6.7   88    4-102    14-104 (373)
 22 KOG0995 consensus               88.2     2.4 6.2E-05   23.2  10.3   69    2-72    221-291 (581)
 23 PRK05431 seryl-tRNA synthetase  80.3     5.2 0.00013   20.8  10.2   89   13-103     1-93  (422)
 24 TIGR03545 conserved hypothetic  77.8     6.2 0.00016   20.3   7.5   20  127-146   287-306 (554)
 25 COG0249 MutS Mismatch repair A  75.9     6.9 0.00018   20.0   9.9  153   12-180   308-473 (843)
 26 PRK11546 zraP zinc resistance   74.0     7.7  0.0002   19.6   6.0   37   18-56     65-101 (139)
 27 pfam07303 Occludin_ELL Occludi  72.1     8.5 0.00022   19.3   5.6   16   16-31     31-46  (101)
 28 KOG1086 consensus               69.3     9.6 0.00025   18.9   5.8   28   38-65    204-231 (594)
 29 TIGR01011 rpsB_bact ribosomal   68.7     9.2 0.00023   19.1   4.2   60   10-75     97-160 (227)
 30 PRK05729 valS valyl-tRNA synth  65.3      12 0.00029   18.4   5.3   10  306-315   406-415 (877)
 31 pfam08399 VWA_N VWA N-terminal  65.0     2.9 7.3E-05   22.7   1.0   19  239-260    55-73  (123)
 32 PRK05399 DNA mismatch repair p  64.7      12  0.0003   18.3  10.7  151   13-181   310-470 (848)
 33 pfam10458 Val_tRNA-synt_C Valy  63.7      12 0.00031   18.2   5.2   53   15-68     12-64  (66)
 34 KOG1697 consensus               57.4      10 0.00026   18.8   2.7  114   99-229    66-181 (275)
 35 KOG0994 consensus               55.1      17 0.00043   17.2   8.7   97   15-118  1202-1302(1758)
 36 TIGR02168 SMC_prok_B chromosom  54.8      17 0.00044   17.1  12.9   22  267-288   675-697 (1191)
 37 COG3378 Phage associated DNA p  54.7     9.9 0.00025   18.8   2.3   10  180-189   295-304 (517)
 38 COG4026 Uncharacterized protei  53.9      18 0.00045   17.0   6.3   12  153-164   221-232 (290)
 39 PRK07997 consensus              53.4      18 0.00046   17.0   4.5   86   22-109   175-289 (928)
 40 KOG3274 consensus               53.4      14 0.00035   17.8   2.9  105  138-255    76-185 (210)
 41 pfam00435 Spectrin Spectrin re  51.5      19 0.00049   16.8  10.3   85   15-103     9-93  (105)
 42 PRK08835 consensus              50.9      20  0.0005   16.7   5.5   88   22-109   175-289 (931)
 43 PRK09225 threonine synthase; V  49.5     5.6 0.00014   20.6   0.4   50  113-164    95-146 (465)
 44 PRK13520 L-tyrosine decarboxyl  49.2      16 0.00041   17.4   2.7   95   90-214    59-165 (375)
 45 PRK07456 consensus              45.9      23 0.00059   16.2   5.2   93   14-108   177-307 (975)
 46 pfam05192 MutS_III MutS domain  45.1      24 0.00061   16.1  11.7  130   13-154    53-192 (306)
 47 KOG4603 consensus               44.2      25 0.00063   16.0   7.7   12  135-146   155-166 (201)
 48 pfam05616 Neisseria_TspB Neiss  44.1      19  0.0005   16.7   2.5   93  110-216   197-318 (502)
 49 PRK00132 rpsI 30S ribosomal pr  43.4      14 0.00035   17.8   1.6   30  196-228     6-35  (130)
 50 pfam03962 Mnd1 Mnd1 family. Th  43.1      26 0.00065   15.9   8.1  119   34-156    55-177 (188)
 51 PRK00474 rps9p 30S ribosomal p  43.0      13 0.00034   17.9   1.5   32  197-233     5-36  (132)
 52 PRK06737 acetolactate synthase  42.7      14 0.00037   17.7   1.6   33  145-177    23-55  (76)
 53 pfam03357 Snf7 Snf7. This fami  42.1      26 0.00067   15.8  10.3   40   37-76     38-77  (169)
 54 PRK00294 hscB co-chaperone Hsc  41.1      27  0.0007   15.7   6.9   50   14-63     18-75  (173)
 55 PRK07898 consensus              40.6      28 0.00071   15.6   5.0   87   22-108   189-295 (902)
 56 pfam02815 MIR MIR domain. The   39.6      29 0.00073   15.5   4.4   36  230-265   120-155 (189)
 57 KOG0581 consensus               39.5      18 0.00045   17.0   1.7   55  200-262    54-108 (364)
 58 TIGR03627 arch_S9P archaeal ri  39.3      16 0.00042   17.3   1.5   32  197-233     3-34  (130)
 59 TIGR02194 GlrX_NrdH Glutaredox  39.0      14 0.00036   17.8   1.1   41  139-179    13-61  (72)
 60 PRK08928 consensus              38.6      30 0.00076   15.4   4.5   88   22-109   173-281 (861)
 61 COG1256 FlgK Flagellar hook-as  38.5      30 0.00076   15.4   7.5   19   16-34     87-105 (552)
 62 PRK01773 hscB co-chaperone Hsc  38.1      30 0.00077   15.4   6.8   49   14-62     16-72  (173)
 63 COG0172 SerS Seryl-tRNA synthe  38.1      30 0.00077   15.4   7.9   54   13-66      1-55  (429)
 64 pfam00380 Ribosomal_S9 Ribosom  37.4      20 0.00051   16.7   1.7   26  200-228     1-26  (121)
 65 COG0103 RpsI Ribosomal protein  36.9      21 0.00053   16.5   1.7   30  196-228     6-35  (130)
 66 pfam07050 consensus             36.8      32 0.00081   15.2   8.5   56    2-63      9-64  (145)
 67 CHL00079 rps9 ribosomal protei  36.6      18 0.00045   17.0   1.3   31  195-228     8-38  (134)
 68 pfam06160 EzrA Septation ring   36.4      32 0.00082   15.2   6.8   38   23-60     77-114 (559)
 69 KOG4519 consensus               36.2      32 0.00082   15.2   5.2   26  106-131   387-412 (459)
 70 cd01560 Thr-synth_2 Threonine   36.2     6.6 0.00017   20.1  -1.0   51  112-164    93-145 (460)
 71 cd02134 NusA_KH NusA_K homolog  35.2      13 0.00032   18.1   0.4   34  209-246    17-50  (61)
 72 PRK04778 septation ring format  34.5      34 0.00087   15.0   6.8   37   23-59     81-117 (569)
 73 PRK10329 glutaredoxin-like pro  34.2      18 0.00046   17.0   1.0   43  139-181    15-64  (81)
 74 pfam04983 RNA_pol_Rpb1_3 RNA p  33.9      30 0.00077   15.4   2.1   30  126-155   127-156 (158)
 75 pfam07962 Swi3 Replication For  33.3      36 0.00091   14.8   2.7   27  121-148    23-49  (84)
 76 cd04878 ACT_AHAS N-terminal AC  32.5      24 0.00062   16.0   1.5   40  136-176    13-52  (72)
 77 PRK08178 acetolactate synthase  32.3      31 0.00079   15.3   2.0   50  116-177    12-61  (96)
 78 PRK13182 racA polar chromosome  31.4      38 0.00098   14.6   6.6   21   86-106   131-151 (178)
 79 PTZ00086 40S ribosomal protein  31.1      28  0.0007   15.7   1.6   29  197-228    12-40  (147)
 80 PRK07556 consensus              31.1      39 0.00099   14.6   4.4   88   22-109   181-289 (977)
 81 PRK08385 nicotinate-nucleotide  31.1      36 0.00091   14.8   2.1   62  114-184    29-91  (279)
 82 TIGR02153 gatD_arch glutamyl-t  30.9      17 0.00044   17.1   0.5  113  125-255   149-292 (413)
 83 PRK08786 consensus              30.6      39   0.001   14.5   4.4   46   22-67    170-221 (927)
 84 PRK06887 consensus              30.3      40   0.001   14.5   5.2   88   22-109   175-289 (954)
 85 TIGR01219 Pmev_kin_ERG8 phosph  30.3      40   0.001   14.5   6.8   57  106-163   430-489 (499)
 86 COG0497 RecN ATPase involved i  30.2      40   0.001   14.5   9.8   10  247-256   485-494 (557)
 87 cd06891 PX_Vps17p The phosphoi  29.8      41   0.001   14.5   3.0   23  123-148    99-121 (140)
 88 KOG0081 consensus               29.7      41   0.001   14.4   2.4   30  199-240    31-60  (219)
 89 PHA00159 endonuclease I         29.5      23 0.00059   16.2   0.9   15  140-154   108-122 (149)
 90 CHL00100 ilvH acetohydroxyacid  29.5      30 0.00076   15.4   1.5   65  136-201    15-84  (172)
 91 cd01137 PsaA Metal binding pro  29.3      41  0.0011   14.4   7.0   20   31-50    115-134 (287)
 92 COG1196 Smc Chromosome segrega  29.0      42  0.0011   14.4   8.9   16  232-248   645-662 (1163)
 93 pfam05367 Phage_endo_I Phage e  28.9      24 0.00061   16.1   0.9   14  140-153   108-121 (149)
 94 COG5491 VPS24 Conserved protei  28.8      42  0.0011   14.3   9.2   65   14-78     52-120 (204)
 95 TIGR02090 LEU1_arch isopropylm  28.5      17 0.00042   17.2   0.0   15  172-189   276-290 (371)
 96 PRK11895 ilvH acetolactate syn  28.5      32 0.00082   15.2   1.5   62  136-198    15-81  (161)
 97 PRK08883 ribulose-phosphate 3-  28.3      43  0.0011   14.3   2.7   38  117-154   133-170 (220)
 98 pfam05055 DUF677 Protein of un  28.2      43  0.0011   14.3   8.8   98   33-146    56-157 (336)
 99 PRK05755 DNA polymerase I; Pro  28.1      43  0.0011   14.3   4.1   88   22-109   173-281 (889)
100 PRK08076 consensus              27.9      44  0.0011   14.2   3.5   96   14-109   160-283 (877)
101 pfam12112 DUF3579 Protein of u  27.9      29 0.00073   15.5   1.2   51  120-171    12-62  (93)
102 PRK05797 consensus              27.7      44  0.0011   14.2   4.0   88   22-109   175-284 (869)
103 TIGR02898 spore_YhcN_YlaJ spor  27.6      32 0.00081   15.2   1.4   20  160-179    81-101 (185)
104 pfam02403 Seryl_tRNA_N Seryl-t  27.5      44  0.0011   14.2  10.2   55   13-67      1-56  (108)
105 PRK08566 DNA-directed RNA poly  27.2      44  0.0011   14.2   2.0   31  175-211   298-329 (881)
106 PRK07737 fliD flagellar cappin  25.9      47  0.0012   14.0   6.3   58    5-73      3-60  (502)
107 TIGR00845 caca sodium/calcium   25.1      49  0.0012   13.9   3.1   35  205-241   573-617 (1067)
108 PRK11783 rlmL 23S rRNA m(2)G24  24.6      25 0.00064   15.9   0.4   38  117-159   309-354 (716)
109 pfam04800 ETC_C1_NDUFA4 ETC co  24.6      22 0.00056   16.4   0.1   17  142-158    62-78  (101)
110 COG1225 Bcp Peroxiredoxin [Pos  24.6      28 0.00072   15.6   0.7   86  116-216    32-146 (157)
111 pfam11926 DUF3444 Domain of un  24.0      28 0.00071   15.6   0.5   23  106-128   103-129 (216)
112 KOG3083 consensus               24.0      51  0.0013   13.7   2.9   18  236-256    81-98  (271)
113 PRK11020 hypothetical protein;  23.8      51  0.0013   13.7   5.7   61   15-75      6-68  (118)
114 KOG0544 consensus               23.8      35 0.00089   14.9   1.0   32  147-183    57-88  (108)
115 cd01989 STK_N The N-terminal d  23.3      46  0.0012   14.1   1.5   72  132-212    61-143 (146)
116 PRK05014 hscB co-chaperone Hsc  23.0      53  0.0014   13.6   7.0   60   14-75     15-74  (171)
117 KOG2148 consensus               22.9      53  0.0014   13.6  10.4   14  126-139   306-319 (867)
118 PRK07081 acyl carrier protein;  22.7     1.3 3.4E-05   25.1  -6.5   32  204-235    34-65  (83)
119 TIGR01169 rplA_bact ribosomal   22.0      19 0.00048   16.8  -0.7   48  214-274    35-88  (227)
120 PRK07417 arogenate dehydrogena  21.9      56  0.0014   13.5   4.3   13  116-131    85-97  (280)
121 KOG1760 consensus               21.9      56  0.0014   13.5   7.7   45   35-79     15-62  (131)
122 KOG4657 consensus               21.8      56  0.0014   13.5   6.6   75   40-119    48-123 (246)
123 pfam00834 Ribul_P_3_epim Ribul  21.7      56  0.0014   13.4   2.9   58  117-179   132-199 (201)
124 KOG1290 consensus               21.4      35 0.00089   14.9   0.6   42  109-150   134-181 (590)
125 pfam07851 TMPIT TMPIT-like pro  21.4      57  0.0015   13.4  10.1   43   79-126    64-106 (330)
126 cd04783 HTH_MerR1 Helix-Turn-H  21.3      57  0.0015   13.4   2.9   94    7-103     3-97  (126)
127 cd01145 TroA_c Periplasmic bin  21.0      58  0.0015   13.3   5.5   13   32-44    107-119 (203)
128 KOG4181 consensus               21.0      22 0.00056   16.4  -0.5   71  244-338   173-243 (491)
129 COG3978 Acetolactate synthase   20.2      60  0.0015   13.2   1.8   52  132-183    11-62  (86)
130 cd06145 REX1_like This subfami  20.1      44  0.0011   14.2   0.9   13  189-201    15-27  (150)

No 1  
>TIGR00020 prfB peptide chain release factor 2; InterPro: IPR004374 In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a superfamily IPR000352 from INTERPRO of RF-1, RF-2, mitochondrial, RF-H, etc proteins.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=1152.92  Aligned_cols=353  Identities=56%  Similarity=0.898  Sum_probs=350.4

Q ss_pred             CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             56899999886549899999999999987086600258999999999988999999999999998639999986310000
Q gi|254780753|r    2 KLSRQLNCLGGLFDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDD   81 (355)
Q Consensus         2 EL~~rl~~l~~~fDle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D   81 (355)
                      +|++|++.++++||++.++.||++|++++++|+||+||.+||.+.+|.+.|+..|+.|+++++.++|+.+|+||+.+++|
T Consensus        13 ~L~~rl~~~~~~Ld~e~~~~rle~le~e~~dP~fW~D~~rAq~v~~e~~~l~~~l~~~~~l~~~~~dl~~L~Ela~ee~d   92 (373)
T TIGR00020        13 ELASRLDDVRGILDPEKLKARLEELEKEMEDPNFWNDQERAQKVIKERSSLEEELDTLEELKNSLDDLSELLELAKEEDD   92 (373)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCH
T ss_conf             99989998775138668999999998775078666125899999999999998632799987553257889987437603


Q ss_pred             C------HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0------0234566765557740158998876303457662489982177870277899999998999987753113444
Q gi|254780753|r   82 C------SILQETSDNLQRIKLEVEYKQFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEAL  155 (355)
Q Consensus        82 ~------el~eE~~~el~~l~~~le~LE~~~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi  155 (355)
                      .      +.+.++..|++.|++.+.++|++.|||||+|.+||||+||||||||||||||+||+|||.||||+|||++|+|
T Consensus        93 ~aaasGm~~~~el~~El~~Le~~~~~lE~~~~LSgE~D~~nA~ltI~~GAGGTEa~DWa~ML~RMY~RWAE~rgykvE~l  172 (373)
T TIGR00020        93 EAAASGMETFAELEEELKALEKELEELELRTLLSGEYDANNAILTIQSGAGGTEAQDWASMLYRMYLRWAERRGYKVEIL  172 (373)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             57778999999999999999999999999997067577210633523877985166699999875357641057513563


Q ss_pred             HCCCCCCCCEEEEEEEEECCCCCHHHEEECCEEEEEEECCCCCCCEEEEEEEEEEECCCCCCC-CCCCCCCCEEEEEEEC
Q ss_conf             205454585013468850556100000101206898730466665035668878850344222-1112345503699853
Q gi|254780753|r  156 EIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDS-IEIEISESDCRIDTYR  234 (355)
Q Consensus       156 ~~~~~e~~GiK~~~~~I~G~~ayg~Lk~E~GvHRv~Ri~~~~s~gR~hTS~a~V~V~P~~~~~-~~i~i~~~dl~i~~~r  234 (355)
                      |+++||+||||||||.|+|+|||||||+|.||||||||||||+++|||||||+|.|+|++||. ++|+|+|.||||||||
T Consensus       173 D~~~geeAGIKSVT~~ikG~yAYG~Lk~E~GvHRLVRISPFDa~~rRHTSFasv~V~P~~Dd~tI~IeI~~~D~riD~YR  252 (373)
T TIGR00020       173 DYSEGEEAGIKSVTILIKGEYAYGYLKSEQGVHRLVRISPFDANARRHTSFASVEVMPEVDDDTIDIEIKPEDVRIDTYR  252 (373)
T ss_pred             ECCCCCCCCEEEEEEEEECCCCCCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEEEEE
T ss_conf             12678613401589998526533302268741787750666686953322688886240357445110688754686665


Q ss_pred             CCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEE
Q ss_conf             88865544273100358874697477665555522467999999999999999999999999998741332332221013
Q gi|254780753|r  235 ASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIGWGRQIRS  314 (355)
Q Consensus       235 ssg~ggq~vn~t~savri~H~ptgi~v~~q~~rsq~~Nk~~a~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~iRt  314 (355)
                      ||||||||||||||||||||+||||||+||++|||||||..||++||||||+++++|++++.+..++.|+.||||+||||
T Consensus       253 aSGAGGQhVNkTdSAVRITHiPTGiVv~CQ~eRSQ~kNK~~Amk~LKaKLYe~~~~k~~~~~~~~~~ek~eIgWG~QIRS  332 (373)
T TIGR00020       253 ASGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHKNKDSAMKVLKAKLYELEMEKEQAEKDAKEGEKSEIGWGNQIRS  332 (373)
T ss_pred             CCCCCCCCCCCCCCCEEEEEECCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE
T ss_conf             46898974214465326544358736851273046888999999999999998889998888763024677786451000


Q ss_pred             EECCCCCCCCCCCCCCEECCHHHHHCCCHHHHHHHHHHCC
Q ss_conf             0158568331111472507977871897799999997225
Q gi|254780753|r  315 YVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKATLAIK  354 (355)
Q Consensus       315 Y~~~p~~~v~DhR~~~~~~~~~~vl~G~ld~~i~a~l~~~  354 (355)
                      ||||||++|||||||++++|+.+||||+||.||+|||+|+
T Consensus       333 YVl~PY~~vKD~Rt~~E~gNv~AVlDGdID~FiE~~Lkwk  372 (373)
T TIGR00020       333 YVLHPYQLVKDLRTNYETGNVEAVLDGDIDEFIEAYLKWK  372 (373)
T ss_pred             EEECCHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHC
T ss_conf             0407613332201672357822575476547898887505


No 2  
>TIGR00019 prfA peptide chain release factor 1; InterPro: IPR004373 This family describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognise and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cut-off for this model. RF-1 does not have a translational frameshift.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=1025.15  Aligned_cols=336  Identities=38%  Similarity=0.575  Sum_probs=320.1

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHH
Q ss_conf             9899999999999987086600258999999999988999999999999998639999986310-000002345667655
Q gi|254780753|r   15 DWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALE-EDDCSILQETSDNLQ   93 (355)
Q Consensus        15 Dle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~e-e~D~el~eE~~~el~   93 (355)
                      .|+++..++.+|+..|+||++.+||+++++++||++.|++++..|.+|.+..++++++.+|++| .+|+||.++|..|+.
T Consensus         9 kL~~~~~~~~eL~~~L~dp~v~~d~~k~~~~~ke~~~l~~i~~~~~~~~~~~~~~~~A~~~l~E~~~D~El~elak~El~   88 (373)
T TIGR00019         9 KLESLEERYEELEELLSDPEVISDQDKLRKLSKEYSQLEEIVDKYEEYKKAQEDLKEAKELLEEKGDDKELRELAKEELE   88 (373)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             99999999999998506863113679999998862065689999999999999999999999742588658999999999


Q ss_pred             HHHHHHHHHH----HHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf             5774015899----887630345766248998217787027789999999899998775311344420545458501346
Q gi|254780753|r   94 RIKLEVEYKQ----FESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSAT  169 (355)
Q Consensus        94 ~l~~~le~LE----~~~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~  169 (355)
                      .++..+++||    +.|||+||+|.+||||||||||||+|||+||+||||||.||||.|||||+|++.+.++.||||+|+
T Consensus        89 ~l~~~~~~LE~~Lk~LLlPkDPND~kNv~lEiRaGtGGdEAalFagDLfrMY~rYAE~kgWkV~i~s~~~~~~GGyKE~I  168 (373)
T TIGR00019        89 ELEKEIEELEEQLKILLLPKDPNDEKNVILEIRAGTGGDEAALFAGDLFRMYSRYAESKGWKVEILSANETELGGYKEVI  168 (373)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCEEEE
T ss_conf             99988888999999726886976695348885079971479999987999988887437988999741157778703257


Q ss_pred             EEE--EC-------CCCCHHHEEECCEEEEEEECCCCCCCEEEEEEEEEEECCCCCCCCC-CCCCCCEEEEEEECCCCCC
Q ss_conf             885--05-------5610000010120689873046666503566887885034422211-1234550369985388865
Q gi|254780753|r  170 LLI--KG-------PNAYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDSIE-IEISESDCRIDTYRASGAG  239 (355)
Q Consensus       170 ~~I--~G-------~~ayg~Lk~E~GvHRv~Ri~~~~s~gR~hTS~a~V~V~P~~~~~~~-i~i~~~dl~i~~~rssg~g  239 (355)
                      |.|  +|       ++||+.||||||||||||||.|||+||+|||||||+|||++|| ++ |+|||+|||||||||||||
T Consensus       169 ~~ish~GasdGdav~gVys~LKFEsGvHRVQRVP~TES~GRiHTSaaTVAvlPE~eE-~E~v~InP~DLrIDtfRsSGaG  247 (373)
T TIGR00019       169 AEISHKGASDGDAVDGVYSRLKFESGVHRVQRVPVTESQGRIHTSAATVAVLPEVEE-VEEVKINPKDLRIDTFRSSGAG  247 (373)
T ss_pred             EEEECCCCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCCEEECHHHEEECCCCCC-CCCCCCCHHHCEEEEEECCCCC
T ss_conf             665305788863033156540010587303100231376925100111010577798-8975557605648476527898


Q ss_pred             CCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CCCCEEEEE
Q ss_conf             54427310035887469747766555552246799999999999999999999999999874133233---222101301
Q gi|254780753|r  240 GQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIG---WGRQIRSYV  316 (355)
Q Consensus       240 gq~vn~t~savri~H~ptgi~v~~q~~rsq~~Nk~~a~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~---~g~~iRtY~  316 (355)
                      |||||||||||||||+||||||+||+|||||+||++||++|+||||+.+.++++++....  ||.++|   |++||||||
T Consensus       248 GQ~VNtTdSAVRITHLPTGIVV~CQdErSQ~kNK~kAmk~L~ArL~~~~~~~~~~~~a~~--RksqVGSGDRSErIRTYN  325 (373)
T TIGR00019       248 GQHVNTTDSAVRITHLPTGIVVSCQDERSQHKNKDKAMKILRARLYEKEQEKQQAEQASD--RKSQVGSGDRSERIRTYN  325 (373)
T ss_pred             CCCCCCCCCCEEEEECCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHCCCCCHHCCCCCCC
T ss_conf             888665200002002688417885478520567999999999999999999999998750--466156654000355678


Q ss_pred             CCCCCCCCCCCCCCEECCHHHHHCCCHHHHHHHHHHCC
Q ss_conf             58568331111472507977871897799999997225
Q gi|254780753|r  317 LQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKATLAIK  354 (355)
Q Consensus       317 ~~p~~~v~DhR~~~~~~~~~~vl~G~ld~~i~a~l~~~  354 (355)
                      | ||+||||||+|+++++|+.||+|+||++|+|++...
T Consensus       326 f-PQNRvTDHRInlTly~L~~~l~G~LD~~i~aL~~~~  362 (373)
T TIGR00019       326 F-PQNRVTDHRINLTLYKLDEVLEGDLDEIIEALIAED  362 (373)
T ss_pred             C-CCCCCCHHHHCCHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             9-888530434401043045663067215778999999


No 3  
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=100.00  E-value=0  Score=997.50  Aligned_cols=353  Identities=58%  Similarity=0.896  Sum_probs=349.2

Q ss_pred             CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             56899999886549899999999999987086600258999999999988999999999999998639999986310000
Q gi|254780753|r    2 KLSRQLNCLGGLFDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDD   81 (355)
Q Consensus         2 EL~~rl~~l~~~fDle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D   81 (355)
                      +|.++++.++++||++.++.|+++|+.+|++|+||+||++|++++||++.|+++|+.|+.+.+.++|+.++.+|+.+++|
T Consensus        11 ~l~~rl~~l~~~ldle~l~~rl~ELe~~lsdP~~W~D~~~a~kl~kE~~~L~~~v~~~~~l~~~~~dl~~l~eL~~ee~D   90 (367)
T PRK00578         11 DLDERLENIRGVLDVDALKERLEELEAEAEDPDFWNDQERAQKVGKELSSLKAKLDTLENLRQRLDDLEELLELAEEEDD   90 (367)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999999987679999999999999986397054499999999999999999999999999999999999999864999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             00234566765557740158998876303457662489982177870277899999998999987753113444205454
Q gi|254780753|r   82 CSILQETSDNLQRIKLEVEYKQFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGE  161 (355)
Q Consensus        82 ~el~eE~~~el~~l~~~le~LE~~~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e  161 (355)
                      +++.+++..++..+...++++|+++||+||+|.+||||||||||||+||+|||+||||||+|||+++||++++++.++|+
T Consensus        91 ~el~eea~~el~~l~~~l~~lEl~~Llsd~~D~~naileI~aGaGG~EA~~~a~~L~rMY~r~ae~~g~k~~v~~~~~~~  170 (367)
T PRK00578         91 EETLAEAEAELKALEKKLAALELERLLSGEYDANNAILTIHAGAGGTEAQDWASMLLRMYLRWAERHGFKVEVLDYSEGE  170 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCC
T ss_conf             89999999999999999999999860489886788479998489960788999999999999998758863141037765


Q ss_pred             CCCEEEEEEEEECCCCCHHHEEECCEEEEEEECCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCC
Q ss_conf             58501346885055610000010120689873046666503566887885034422211123455036998538886554
Q gi|254780753|r  162 EAGIKSATLLIKGPNAYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQ  241 (355)
Q Consensus       162 ~~GiK~~~~~I~G~~ayg~Lk~E~GvHRv~Ri~~~~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~rssg~ggq  241 (355)
                      .||||+|+|.|+|+||||+||+|+|||||||||||+++||||||||+|+|+|+++++++|+|+|+||+||||||||||||
T Consensus       171 ~~Gik~~~~~i~G~~ayg~Lk~E~GvHRv~Ri~~~es~gr~hTS~a~V~V~P~~~~~~~i~i~~~dl~id~~RssGaGGQ  250 (367)
T PRK00578        171 EAGIKSATLKIKGPYAYGYLKSEKGVHRLVRISPFDSAGRRHTSFASVEVYPEVDDDIEIEINPKDLRIDTYRSSGAGGQ  250 (367)
T ss_pred             CCCCCEEEEEEECCCHHHHHCCCCCCEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCC
T ss_conf             56600589998346534332225762135646985788865777569999626776435778821335898646899877


Q ss_pred             CCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCC
Q ss_conf             42731003588746974776655555224679999999999999999999999999987413323322210130158568
Q gi|254780753|r  242 HVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIGWGRQIRSYVLQPYQ  321 (355)
Q Consensus       242 ~vn~t~savri~H~ptgi~v~~q~~rsq~~Nk~~a~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~iRtY~~~p~~  321 (355)
                      |||||+|||||||+||||+|+||+|||||+||++||++|++|||+++++++.++....++.+..++||+||||||||||+
T Consensus       251 ~VNkt~sAVRitH~PTGivv~cq~eRSQ~~Nk~~A~~~L~akL~~~~~~~~~~~~~~~r~~~~~~~~g~~IRtY~f~p~~  330 (367)
T PRK00578        251 HVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASAMKMLKAKLYELELEKRAAEKDALRGEKKDIGWGSQIRSYVLHPYQ  330 (367)
T ss_pred             CCCCCCCEEEEEEECCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf             75752333799972586499955602189899999999999999999999999999976441357653656442478987


Q ss_pred             CCCCCCCCCEECCHHHHHCCCHHHHHHHHHHCC
Q ss_conf             331111472507977871897799999997225
Q gi|254780753|r  322 MVKDLRTNIEKTSPSDVLDGDLDDFMKATLAIK  354 (355)
Q Consensus       322 ~v~DhR~~~~~~~~~~vl~G~ld~~i~a~l~~~  354 (355)
                      ||||||||++++|++.||+|+||+||+|||+|+
T Consensus       331 rV~DhR~~~~~~~l~~vl~G~ld~~I~a~L~~~  363 (367)
T PRK00578        331 MVKDLRTGYETGNTQAVLDGDLDGFIEAYLRWR  363 (367)
T ss_pred             CCCCCCCCCEECCHHHHHCCCHHHHHHHHHHHH
T ss_conf             474005697357757874888599999999877


No 4  
>PRK07245 consensus
Probab=100.00  E-value=0  Score=989.76  Aligned_cols=335  Identities=45%  Similarity=0.748  Sum_probs=328.1

Q ss_pred             HHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf             99999999998708660025899999999998899999999999999863999998631000000234566765557740
Q gi|254780753|r   19 AVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSILQETSDNLQRIKLE   98 (355)
Q Consensus        19 ~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D~el~eE~~~el~~l~~~   98 (355)
                      +++++.+|+.+|++|+||+||++|++++||++.|+++++.|+.++..++|+..+.+|+.+  |+++.+|+..++..+.+.
T Consensus         1 l~~~l~eLe~~~s~Pd~w~D~~ka~kl~ke~~~L~~~v~~~~~l~~~~~d~e~l~el~~e--de~~~~El~~~~~~l~~~   78 (337)
T PRK07245          1 MEEEIALLENHMTEPDFWNDNIAAQKTSQELNELKGKYDTFHNMQELSDETELLLEMLDE--DDSLKEELEENLMQLDKI   78 (337)
T ss_pred             CHHHHHHHHHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHHHHH
T ss_conf             958999999986297033099999999999999999999999999999999999986607--998999999999999999


Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCCC
Q ss_conf             15899887630345766248998217787027789999999899998775311344420545458501346885055610
Q gi|254780753|r   99 VEYKQFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAY  178 (355)
Q Consensus        99 le~LE~~~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~ay  178 (355)
                      ++++++.+||+||+|.+||||||||||||+||||||+||||||+|||+++||++++++.++|++||||+|+|.|+|+|||
T Consensus        79 ~~~le~~lll~~~~D~~naileIrAGaGG~EA~dwA~mL~RMY~R~aE~~gwk~evl~~~~ge~~GiK~vt~~I~G~~aY  158 (337)
T PRK07245         79 MGAYEMTLLLSEPYDHNNAILEIHPGSGGTEAQDWGDLLLRMYTRFGNANGFKVEVLDYQAGDEAGIKSVTLSFEGPNAY  158 (337)
T ss_pred             HHHHHHHHCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCCCCEEEEEEECCCCC
T ss_conf             99999986669987678837999789896799999999999999999976994012106886545600579999647877


Q ss_pred             HHHEEECCEEEEEEECCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCH
Q ss_conf             00001012068987304666650356688788503442221112345503699853888655442731003588746974
Q gi|254780753|r  179 GWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTG  258 (355)
Q Consensus       179 g~Lk~E~GvHRv~Ri~~~~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~ptg  258 (355)
                      |+||+|+|||||||||||||+||||||||+|+|+|+++|+++|+|+|+||+|||||||||||||||||+|||||||+|||
T Consensus       159 g~Lk~EsGVHRv~Risp~es~gRrhTS~asV~VlP~~dd~i~i~i~~~Dlridt~RssGaGGQ~VNkt~SAVRitH~PTG  238 (337)
T PRK07245        159 GLLKSEMGVHRLVRISPFDSAKRRHTSFASVEVMPELDDTIEVEVRDDDIKMDTFRSGGAGGQNVNKVSTGVRLTHIPTG  238 (337)
T ss_pred             CCEEECCCCEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEEEEEECCC
T ss_conf             70331375202476799888886665678999953557654567887563899875799998886765226899972586


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCEECCHHHH
Q ss_conf             77665555522467999999999999999999999999998741332332221013015856833111147250797787
Q gi|254780753|r  259 VVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSDV  338 (355)
Q Consensus       259 i~v~~q~~rsq~~Nk~~a~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~iRtY~~~p~~~v~DhR~~~~~~~~~~v  338 (355)
                      |+|+||+|||||+||++||++|+||||+++.+++.++.+..++.+..++||+||||||||||+||||||||++++|+++|
T Consensus       239 i~v~cq~eRSQ~~Nk~~A~~~L~akL~~~~~~~~~~e~~~~~~~~~~~~~g~~IRtY~~~p~~~V~DhRt~~~~~~~~~v  318 (337)
T PRK07245        239 IVVSSTVDRTQYGNRDRAMKMLQAKLYQLEQEKKAQEVDALKGDKKEITWGSQIRSYVFTPYTMVKDHRTNFELAQVDKV  318 (337)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCEECCHHHH
T ss_conf             69996574368999999999999999999999999899986415212665576615167898837420669744784787


Q ss_pred             HCCCHHHHHHHHHHCCC
Q ss_conf             18977999999972259
Q gi|254780753|r  339 LDGDLDDFMKATLAIKK  355 (355)
Q Consensus       339 l~G~ld~~i~a~l~~~~  355 (355)
                      |+|+||+||+|||+||.
T Consensus       319 ldG~ld~fi~a~l~~~~  335 (337)
T PRK07245        319 MDGEINGFIDAYLKWRI  335 (337)
T ss_pred             HCCCHHHHHHHHHHHHH
T ss_conf             58775999999997540


No 5  
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=100.00  E-value=0  Score=979.48  Aligned_cols=341  Identities=38%  Similarity=0.574  Sum_probs=325.2

Q ss_pred             HHHCC-HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             86549-89999999999998708660025899999999998899999999999999863999998631000000234566
Q gi|254780753|r   11 GGLFD-WDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSILQETS   89 (355)
Q Consensus        11 ~~~fD-le~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D~el~eE~~   89 (355)
                      ..||+ ++.++.|+++|+.+|++|+||+||++|++++||++.|+++++.|+.+.+..+|+.++.+|+.+++|+++.+++.
T Consensus         3 ~~m~~kLe~l~~rl~eLe~~ls~p~fW~D~~~a~kl~kE~~~L~~~v~~~~~l~~~~~dl~el~eLl~ee~D~el~e~a~   82 (360)
T PRK00591          3 PSMLDKLEALEERYEELEALLSDPEVISDQKRFRKLSKEYAELEPIVEAYREYKQAEEDLEDAKELLKEESDPEMREMAK   82 (360)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             79999999999999999998729852129999999999999999999999999999998999999986279978999999


Q ss_pred             HHHHHHHHHHHHHH----HHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCE
Q ss_conf             76555774015899----88763034576624899821778702778999999989999877531134442054545850
Q gi|254780753|r   90 DNLQRIKLEVEYKQ----FESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGI  165 (355)
Q Consensus        90 ~el~~l~~~le~LE----~~~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~Gi  165 (355)
                      +++..+...++++|    ..+||+||+|.+||||||||||||+||||||+||||||+|||+++||+++++++++|++|||
T Consensus        83 ~El~~l~~~l~~lE~eL~~lLlp~d~~D~~nailEIrAGAGGtEA~dwA~mL~RMY~RwAE~~g~k~evid~s~ge~aGi  162 (360)
T PRK00591         83 EELKELEERLEELEEELKILLLPKDPNDDKNVILEIRAGTGGDEAALFAGDLFRMYSRYAERQGWKVEILSASEGELGGY  162 (360)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCH
T ss_conf             99999999999999999998379997756785899965888748999999999999999986799715602577655650


Q ss_pred             EEEEEEEECCCCCHHHEEECCEEEEEEECCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCC
Q ss_conf             13468850556100000101206898730466665035668878850344222111234550369985388865544273
Q gi|254780753|r  166 KSATLLIKGPNAYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNT  245 (355)
Q Consensus       166 K~~~~~I~G~~ayg~Lk~E~GvHRv~Ri~~~~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~  245 (355)
                      |+|||.|+|+|||||||+|+|||||||||||||+||||||||+|+|+|++++ ++|+|+|+||+||||||||||||||||
T Consensus       163 Ksat~~I~G~~AYg~Lk~EsGVHRvvRip~~es~gR~HTSfasV~V~P~~~~-~~i~i~~~dl~idt~RssGaGGQhVNk  241 (360)
T PRK00591        163 KEIIASISGDGVYSKLKFESGVHRVQRVPATESQGRIHTSAATVAVLPEAEE-VEVEINPKDLRIDTFRSSGAGGQHVNT  241 (360)
T ss_pred             HEEEEEEECHHHHHHHHHCCCCCCEECCCCCCCCCCEEEEEEEEEEECCCCC-CCCCCCCCCEEEEEEECCCCCCCCCCC
T ss_conf             2168887170688776323775412306985667856640047897067643-102568540258875357999887676


Q ss_pred             CCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---CCEEEEECCCCCC
Q ss_conf             1003588746974776655555224679999999999999999999999999987413323322---2101301585683
Q gi|254780753|r  246 TDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIGWG---RQIRSYVLQPYQM  322 (355)
Q Consensus       246 t~savri~H~ptgi~v~~q~~rsq~~Nk~~a~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~g---~~iRtY~~~p~~~  322 (355)
                      |+|||||||+||||+|.||++||||+||++||++|++|||+++.+++.++....  ++.++|||   +||||||| ||+|
T Consensus       242 t~saVritH~ptgi~v~cq~ersQ~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~--r~~~i~~g~rs~~iRtY~~-p~~~  318 (360)
T PRK00591        242 TDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEAAT--RKSQVGSGDRSERIRTYNF-PQGR  318 (360)
T ss_pred             CCCEEEEEECCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHCCCCCCCCCCCCCCC-CCCC
T ss_conf             343268986167559985460227889999999999999999999999999998--8865137770007507718-9886


Q ss_pred             CCCCCCCCEECCHHHHHCCCHHHHHHHHHHCCC
Q ss_conf             311114725079778718977999999972259
Q gi|254780753|r  323 VKDLRTNIEKTSPSDVLDGDLDDFMKATLAIKK  355 (355)
Q Consensus       323 v~DhR~~~~~~~~~~vl~G~ld~~i~a~l~~~~  355 (355)
                      |||||||++++|++.||||+||+||+|+|.+.+
T Consensus       319 v~DhR~~~~~~~~~~vldG~ld~~I~a~~~~~~  351 (360)
T PRK00591        319 VTDHRINLTLYKLDEVMEGDLDELIDALIAEDQ  351 (360)
T ss_pred             CCCCCCCCEECCHHHHHCCCHHHHHHHHHHHHH
T ss_conf             500135986468577748876999999999999


No 6  
>PRK05589 peptide chain release factor 2; Provisional
Probab=100.00  E-value=0  Score=943.89  Aligned_cols=324  Identities=48%  Similarity=0.814  Sum_probs=315.3

Q ss_pred             HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             70866002589999999999889999999999999986399999863100000023456676555774015899887630
Q gi|254780753|r   30 TEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSILQETSDNLQRIKLEVEYKQFESLLS  109 (355)
Q Consensus        30 lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D~el~eE~~~el~~l~~~le~LE~~~Lls  109 (355)
                      |++|+||+||++|++++||++.|+++|+.|+.+.+.++|+.++.+|+.+ +|.+++.++..++..+...++++++++||+
T Consensus         1 m~dPd~W~D~~~a~~l~kE~~~l~~~v~~~~~l~~~~~dl~~l~el~ee-ed~~~~~e~~~e~~~l~~~l~~le~~~Ll~   79 (325)
T PRK05589          1 MQEPNFWNDIKKAQEITSEEKYLKDKIDKYNSLRNRIEDIEVLKEMMEE-EDEESAKEIISEVKNIKEEIDNFKIETLLS   79 (325)
T ss_pred             CCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9893032099999999999999999999999999999999999998738-999999999999999999999999984579


Q ss_pred             CCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCCCHHHEEECCEEE
Q ss_conf             34576624899821778702778999999989999877531134442054545850134688505561000001012068
Q gi|254780753|r  110 GEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHR  189 (355)
Q Consensus       110 ~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~ayg~Lk~E~GvHR  189 (355)
                      +|+|.+||||||||||||+||||||+||||||+|||+++||++++++.++|+.||||+|++.|+|+||||+||+|+||||
T Consensus        80 ~~~D~~naileIrAGaGG~EA~dwA~~L~RMY~r~Ae~~gwk~evid~~~ge~gGiK~v~~~I~G~~ayg~Lk~E~GvHR  159 (325)
T PRK05589         80 GEYDRNNAILTLHSGVGGTDAQDWTEMLLRMYTRWAEKKGYKVEIIDLLEGDEAGIKSVTLKITGEFAYGYLKAEKGIHR  159 (325)
T ss_pred             CCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHCCCCCCCCCCCEEEEEECCHHHHHHHCCCCCCE
T ss_conf             98878985899965889779999999999999999987599501043176545781003899855125655421577511


Q ss_pred             EEEECCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHH
Q ss_conf             98730466665035668878850344222111234550369985388865544273100358874697477665555522
Q gi|254780753|r  190 LVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQ  269 (355)
Q Consensus       190 v~Ri~~~~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~ptgi~v~~q~~rsq  269 (355)
                      ||||||||++||||||||+|+|+|+++++++|+|+|+||+|||||||||||||||||+|||||||+||||+|+||+||||
T Consensus       160 vqRip~~es~gR~hTS~a~V~VlP~~~~~~~i~i~~~dl~id~~rssG~GGQ~VNkt~sAVRitH~PTGi~v~cq~eRSQ  239 (325)
T PRK05589        160 LVRISPFNANGKRQTSFASVEVLPELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQ  239 (325)
T ss_pred             EEECCCCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCEEEEEEEECCCEEEEECCCCCH
T ss_conf             46448877788548775788994576665447777356428988789998787776120489997058649996585648


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCEECCHHHHHCCCHHHHHHH
Q ss_conf             46799999999999999999999999999874133233222101301585683311114725079778718977999999
Q gi|254780753|r  270 HKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKA  349 (355)
Q Consensus       270 ~~Nk~~a~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~iRtY~~~p~~~v~DhR~~~~~~~~~~vl~G~ld~~i~a  349 (355)
                      |+||++||++|++|||+++.+++.+.....++++.+++||+||||||||||+||||||||++++|+++||+|+||+||+|
T Consensus       240 ~~Nk~~A~~~L~arL~~~~~~~~~~~~~~~~~~~~~~~~g~~iRtY~~~p~~~V~DhR~g~~~~~l~~vl~Gdld~fI~a  319 (325)
T PRK05589        240 HSNKDTAMKMLKSKLVELKERAHKEKIEDLTGELKDMGWGSQIRSYVFHPYNLVKDHRTGVETSNVDSVMDGDIDIFITQ  319 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCHHHHHCCCHHHHHHH
T ss_conf             99999999999999999999999999999860645677424631027789983741166970277477658773999999


Q ss_pred             HHHCC
Q ss_conf             97225
Q gi|254780753|r  350 TLAIK  354 (355)
Q Consensus       350 ~l~~~  354 (355)
                      ||+|-
T Consensus       320 ~l~~~  324 (325)
T PRK05589        320 YLKGN  324 (325)
T ss_pred             HHHHC
T ss_conf             99722


No 7  
>PRK06746 peptide chain release factor 2; Provisional
Probab=100.00  E-value=0  Score=938.55  Aligned_cols=325  Identities=51%  Similarity=0.793  Sum_probs=321.5

Q ss_pred             HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             70866002589999999999889999999999999986399999863100000023456676555774015899887630
Q gi|254780753|r   30 TEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSILQETSDNLQRIKLEVEYKQFESLLS  109 (355)
Q Consensus        30 lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D~el~eE~~~el~~l~~~le~LE~~~Lls  109 (355)
                      |++|+||+||++|++++||++.|+++|+.|+.+...++|++++.+|+.+++|+++.+++..++..+.+.++++|+++||+
T Consensus         1 M~~p~fWdD~~~A~~i~kE~s~l~~~v~~~~~l~~~~~dl~~l~eL~~ee~D~el~ee~~~el~~l~~~i~~lE~~~lls   80 (326)
T PRK06746          1 MMGAGFWDDQQGAQAVINEANALKDMVGKFRQLDETFENLEITHELLKEEYDEDLHEELESEVKGLIQEMNEYELQLLLS   80 (326)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             98977786999999999999999999999999999999799999998548998999999999999999999999985449


Q ss_pred             CCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCCCHHHEEECCEEE
Q ss_conf             34576624899821778702778999999989999877531134442054545850134688505561000001012068
Q gi|254780753|r  110 GEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHR  189 (355)
Q Consensus       110 ~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~ayg~Lk~E~GvHR  189 (355)
                      ||+|.+||||||||||||+||||||+||||||+|||+++||++++++.++|++||||+|+|.|+|+||||+||+|+||||
T Consensus        81 ~~~D~~naileI~aGaGG~EA~~~a~~L~rMY~r~ae~~g~~~~~~~~~~~~~~Gik~~~~~i~G~~ayg~Lk~E~GvHR  160 (326)
T PRK06746         81 DPYDKNNAILELHPGAGGTESQDWGSMLLRMYTRWAEKRGFKVETVDYLPGDEAGIKSVTLLIKGHNAYGYLKAEKGVHR  160 (326)
T ss_pred             CCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEE
T ss_conf             98767884899978989779999999999999999997598579972057777886246799960454201012576213


Q ss_pred             EEEECCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHH
Q ss_conf             98730466665035668878850344222111234550369985388865544273100358874697477665555522
Q gi|254780753|r  190 LVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQ  269 (355)
Q Consensus       190 v~Ri~~~~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~ptgi~v~~q~~rsq  269 (355)
                      |||||||+++||||||||+|+|+|+++++++++|+|+||+|||||||||||||||||+|||||||+||||+|+||+||||
T Consensus       161 v~Ris~~~s~gr~hTS~a~V~V~P~~~~~~~i~i~~~dl~id~~rssG~GGQ~VN~t~SAVRitH~PTGi~v~cq~eRSQ  240 (326)
T PRK06746        161 LVRISPFDSSGRRHTSFVSCEVVPEFNDEVEIEVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQ  240 (326)
T ss_pred             EEECCCCCCCCCEEEEEEEEEEECCCCCCCCCCCCHHHHCEEECCCCCCCCCCCCCCCCEEEEEEECCCEEEEECCCCCH
T ss_conf             46458878888668777899997266754335688677143201179998787665030499998157669995685577


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCEECCHHHHHCCCHHHHHHH
Q ss_conf             46799999999999999999999999999874133233222101301585683311114725079778718977999999
Q gi|254780753|r  270 HKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKA  349 (355)
Q Consensus       270 ~~Nk~~a~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~iRtY~~~p~~~v~DhR~~~~~~~~~~vl~G~ld~~i~a  349 (355)
                      |+||++||++|++|||+.++++++++....++.+..++||+||||||||||+||||||||++++|+++||+|+||+||+|
T Consensus       241 ~~Nk~~Al~~L~arL~~~~~e~~~~~~~~~r~~~~~~~~g~~IRtY~~~p~~~V~DhR~~~~~~~~~~vl~G~ld~fI~a  320 (326)
T PRK06746        241 IKNREHAMKMLKAKLYQKKLEEQQAELDEIRGEQKEIGWGSQIRSYVFHPYSLVKDHRTNTEVGNVQAVMDGEIDPFIDA  320 (326)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCHHHHHCCCHHHHHHH
T ss_conf             99999999999999999999999999999874535785525631526789883662055975678478658873999999


Q ss_pred             HHHCC
Q ss_conf             97225
Q gi|254780753|r  350 TLAIK  354 (355)
Q Consensus       350 ~l~~~  354 (355)
                      ||+||
T Consensus       321 ~l~~r  325 (326)
T PRK06746        321 YLRSR  325 (326)
T ss_pred             HHHCC
T ss_conf             99755


No 8  
>PRK07342 peptide chain release factor 2; Provisional
Probab=100.00  E-value=0  Score=915.88  Aligned_cols=311  Identities=70%  Similarity=1.133  Sum_probs=306.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECC
Q ss_conf             99999889999999999999986399999863100000023456676555774015899887630345766248998217
Q gi|254780753|r   45 LMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSILQETSDNLQRIKLEVEYKQFESLLSGEADSNDAYLEVHAG  124 (355)
Q Consensus        45 l~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D~el~eE~~~el~~l~~~le~LE~~~Lls~e~D~~nailEI~AG  124 (355)
                      |+||++.|+++|+.|+.+.+.++|+.+|.+|+.+++|+++.+++..++..+...++++++.+||++|+|.+|||||||||
T Consensus         1 l~kE~~~L~~~v~~~~~l~~~l~d~~el~el~~ee~D~e~~~e~~~~l~~l~~~l~~lel~~Ll~~~~D~~~aileIraG   80 (322)
T PRK07342          1 LMRERQQLEDSINGINHLEQTLNDNIELIAMGEEEGDKSIVEDAEKTIRDLKDEIDRRQIDALLSGEADANDTYLEVHAG   80 (322)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECC
T ss_conf             94318999999999999999987599999997569998999999999999999999999985469988888858999688


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCCCHHHEEECCEEEEEEECCCCCCCEEEE
Q ss_conf             78702778999999989999877531134442054545850134688505561000001012068987304666650356
Q gi|254780753|r  125 AGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHRLVRISPYDSNSRRHT  204 (355)
Q Consensus       125 aGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~ayg~Lk~E~GvHRv~Ri~~~~s~gR~hT  204 (355)
                      |||+||||||+||||||+|||+++||++++++.++|+.||||+|+|.|+|+||||+||+|+||||||||||||++|||||
T Consensus        81 aGG~EA~~fA~~L~rMY~r~ae~~g~k~evid~~~g~~~Gik~~~~~i~G~~ayg~Lk~E~GvHRv~Ri~~~es~gr~hT  160 (322)
T PRK07342         81 AGGTESQDWASMLLRMYTRWAERQGRKVEVLEVHDGEEAGIKSATILVKGHNAYGWLKTESGVHRLVRISPYDSNARRHT  160 (322)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCEEEEEEECCCHHHHHHHCCCCCEEEECCCCCCCCCEEE
T ss_conf             89579999999999999999987798789963167656771059999964767776420468530586598588886687


Q ss_pred             EEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             68878850344222111234550369985388865544273100358874697477665555522467999999999999
Q gi|254780753|r  205 SFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKL  284 (355)
Q Consensus       205 S~a~V~V~P~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~ptgi~v~~q~~rsq~~Nk~~a~~~l~~~l  284 (355)
                      |||+|+|+|+++|+++|+|+|+||+|||||||||||||||||+|||||||+||||+|+||+|||||+||++||++|++||
T Consensus       161 S~asV~VlP~~~d~~~i~i~~~Dlridt~RssGaGGQ~VNkt~SAVRitH~PTGivV~cq~eRSQ~~Nk~~Am~~LrarL  240 (322)
T PRK07342        161 SFASIWVYPVIDDNIEVDVNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSMLRARL  240 (322)
T ss_pred             EEEEEEEEECCCCCCCCCCCHHHCCEEEEECCCCCCCCCCCCCCEEEEEEECCCEEEEECCCCCHHHHHHHHHHHHHHHH
T ss_conf             66799998244664335698336127875679999877776242489997068669996685438999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCEECCHHHHHCCCHHHHHHHHHHCCC
Q ss_conf             99999999999999874133233222101301585683311114725079778718977999999972259
Q gi|254780753|r  285 YELELQKREEIANIGESSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKATLAIKK  355 (355)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~g~~iRtY~~~p~~~v~DhR~~~~~~~~~~vl~G~ld~~i~a~l~~~~  355 (355)
                      |++++++++++.+..++++.+++||+||||||||||+||||||||++++|+++||+|+||+||+|||+||.
T Consensus       241 ~~~e~~k~~~~~~~~~~~~~~~~~g~qIRtY~f~P~~~V~DhRt~~~~~~~~~vldG~ld~fI~a~L~~r~  311 (322)
T PRK07342        241 YEEELKKREEATNAAEASKTDIGWGHQIRSYVLQPYQLVKDLRTGVESTNPQDVLDGDLDEFMEAALAHRI  311 (322)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCHHHHHCCCHHHHHHHHHHHHH
T ss_conf             99999999999999874310365315522615479886760366978778478658873999999999886


No 9  
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=898.47  Aligned_cols=337  Identities=38%  Similarity=0.563  Sum_probs=320.1

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             89999999999998708660025899999999998899999999999999863999998631000000234566765557
Q gi|254780753|r   16 WDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSILQETSDNLQRI   95 (355)
Q Consensus        16 le~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D~el~eE~~~el~~l   95 (355)
                      ++.+..|+.+|+..|++|++.+|++++++++||++.|+++++.|.+|++..+++.++.+|+.++.|++|.+++.+++..+
T Consensus         9 l~~~~~r~~el~~~L~~p~v~~d~~~~~~lske~a~l~~iv~~~~~~~~~~~~l~~a~~~l~~~~D~em~ema~~Ei~~~   88 (363)
T COG0216           9 LESLLERYEELEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQEDLEDAKEMLAEEKDPEMREMAEEEIKEL   88 (363)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             99999999999998539633369999999999998888999999999999999999999983568878999999999999


Q ss_pred             HHHHHHH----HHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEE
Q ss_conf             7401589----988763034576624899821778702778999999989999877531134442054545850134688
Q gi|254780753|r   96 KLEVEYK----QFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLL  171 (355)
Q Consensus        96 ~~~le~L----E~~~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~  171 (355)
                      +..+..|    +..+||+||+|++||||||||||||+||++||++|||||.|||+.+||+++|++.++++.||||++++.
T Consensus        89 ~~~~~~le~~L~~lLlPkDpnd~knvilEIRagtGGdEAalFagDLfrMY~rYAe~kgWk~ei~s~se~~~GG~kEii~~  168 (363)
T COG0216          89 EAKIEELEEELKILLLPKDPNDDKNIILEIRAGTGGDEAALFAGDLFRMYSRYAESKGWKVEILSASESELGGYKEIIAS  168 (363)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEEE
T ss_conf             99899999999986289998877776899706888159999999999999999975798799941586667880489999


Q ss_pred             EECCCCCHHHEEECCEEEEEEECCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEE
Q ss_conf             50556100000101206898730466665035668878850344222111234550369985388865544273100358
Q gi|254780753|r  172 IKGPNAYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVR  251 (355)
Q Consensus       172 I~G~~ayg~Lk~E~GvHRv~Ri~~~~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savr  251 (355)
                      |+|.+||+.||||+|||||||||.|+|+||+|||+|+|+|||++++..+++|+|+||||||||||||||||||||+||||
T Consensus       169 I~G~gvys~LKfEsGvHRVQRVP~TEsqGRIHTStaTVaVlPE~ee~~ei~I~~~DlrIDt~RsSGaGGQhVNtTdSAVR  248 (363)
T COG0216         169 ISGKGVYSRLKFESGVHRVQRVPATESQGRIHTSAATVAVLPEVEEVEEIEINPKDLRIDTFRSSGAGGQHVNTTDSAVR  248 (363)
T ss_pred             EECCCHHHHHHHCCCCCCEECCCCCCCCCCEEECCEEEEECCCCCCCCCCCCCHHHCEEEEEECCCCCCCCCCCCCHHHE
T ss_conf             84365455410315765221066655788314000168862787753346447788347655437898887665131101


Q ss_pred             EEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CCCCEEEEECCCCCCCCCCCC
Q ss_conf             87469747766555552246799999999999999999999999999874133233---222101301585683311114
Q gi|254780753|r  252 ITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIG---WGRQIRSYVLQPYQMVKDLRT  328 (355)
Q Consensus       252 i~H~ptgi~v~~q~~rsq~~Nk~~a~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~---~g~~iRtY~~~p~~~v~DhR~  328 (355)
                      |||+||||||+||+|||||+||++||++|+||||+.+.++++++....  ++.++|   |+++|||||| ||+||||||+
T Consensus       249 iTHlPTGIvV~cQderSQ~kNk~kAmkvL~ARl~~~~~~~~~~~~~~~--RksqVGSGDRSErIRTYNf-PQnRVTDHRI  325 (363)
T COG0216         249 ITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEASE--RKSQVGSGDRSERIRTYNF-PQNRVTDHRI  325 (363)
T ss_pred             EEECCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHCCCCCHHHHHHCCCC-CCCCCCCHHC
T ss_conf             431477369984462456651999999999999999999999999988--8873377742542103578-8776510103


Q ss_pred             CCEECCHHHHHCC-CHHHHHHHHHHCCC
Q ss_conf             7250797787189-77999999972259
Q gi|254780753|r  329 NIEKTSPSDVLDG-DLDDFMKATLAIKK  355 (355)
Q Consensus       329 ~~~~~~~~~vl~G-~ld~~i~a~l~~~~  355 (355)
                      |+++++|+.||+| +||++|+|++.+.|
T Consensus       326 ~lTl~kLd~vm~gG~LDeii~aLi~~~q  353 (363)
T COG0216         326 NLTLYKLDEVMEGGKLDEIIDALIAEDQ  353 (363)
T ss_pred             CCCCCCHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             6610458888646857899999999999


No 10 
>PRK08787 peptide chain release factor 2; Provisional
Probab=100.00  E-value=0  Score=874.00  Aligned_cols=302  Identities=54%  Similarity=0.874  Sum_probs=296.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHH
Q ss_conf             99999999999999863999998631000000234566765557740158998876303457662489982177870277
Q gi|254780753|r   52 LDNAISFIKEIQDRLCDNLILLELALEEDDCSILQETSDNLQRIKLEVEYKQFESLLSGEADSNDAYLEVHAGAGGTESQ  131 (355)
Q Consensus        52 L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D~el~eE~~~el~~l~~~le~LE~~~Lls~e~D~~nailEI~AGaGG~EA~  131 (355)
                      |++.|+.|+.+.+.++|+.+|++|+.+++|+++.+++..++..+...++++|+++||+||+|.+||||||||||||+|||
T Consensus         2 Lek~v~~~~~l~~~l~D~~el~ela~~E~d~~~~~e~~~~l~~l~~~~~~le~~~ll~~~~D~~~aileI~aGaGG~EA~   81 (313)
T PRK08787          2 LEKTVIGIADVLSGLADAGELLDLAESEQDEDTALAVIADLDKYQAHVEKLEFQRMFSGQMDGANAFVDIQAGAGGTEAQ   81 (313)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCHHHH
T ss_conf             58899999999976266999999988589989999999999999999999999863599775678489991689958999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCCCHHHEEECCEEEEEEECCCCCCCEEEEEEEEEEE
Q ss_conf             89999999899998775311344420545458501346885055610000010120689873046666503566887885
Q gi|254780753|r  132 DWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWV  211 (355)
Q Consensus       132 dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~ayg~Lk~E~GvHRv~Ri~~~~s~gR~hTS~a~V~V  211 (355)
                      |||+||||||+|||+++||++++++.++|++||||+|+++|+|+||||+||+|+|||||||||||+++||||||||+|+|
T Consensus        82 dwA~~L~rMY~r~ae~~g~k~ev~~~~~~~~~Giks~t~~i~G~~ayg~Lk~E~GvHRl~Ris~~~s~gr~hTS~asV~V  161 (313)
T PRK08787         82 DWAEILLRMYLRWAESRGWKTELMEVSGGEVAGIKSATVRIEGEYAYGWLKTEIGVHRLVRKSPFDSDNRRHTSFTSVFV  161 (313)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEEEEECCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEEEE
T ss_conf             99999999999999876983799844776657803568999447756632145873204846995778727864237999


Q ss_pred             CCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             03442221112345503699853888655442731003588746974776655555224679999999999999999999
Q gi|254780753|r  212 YPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQK  291 (355)
Q Consensus       212 ~P~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~ptgi~v~~q~~rsq~~Nk~~a~~~l~~~l~~~~~~~  291 (355)
                      +|+++++++++|+|+||+|||||||||||||||||+|||||||+||||+|+||+|||||+||++||++|++|||++++++
T Consensus       162 ~P~~~~~~~i~i~~~Dlrid~~RssGaGGQ~VNkt~SAVRitH~PTGivV~cq~eRSQ~~Nk~~A~~~LkarL~~~e~~k  241 (313)
T PRK08787        162 SPEVDDNIEIDINPADLRTDVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKMLAAKLYELEVQK  241 (313)
T ss_pred             ECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEEEEEECCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             56646544575775665899875799998987886005899984287799966855389999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCEECCHHHHHCCCHHHHHHHHHHCC
Q ss_conf             999999987413323322210130158568331111472507977871897799999997225
Q gi|254780753|r  292 REEIANIGESSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKATLAIK  354 (355)
Q Consensus       292 ~~~~~~~~~~~~~~~~~g~~iRtY~~~p~~~v~DhR~~~~~~~~~~vl~G~ld~~i~a~l~~~  354 (355)
                      ++++.+..++++.+++||+|||||||+ |+||||||||++++|+++||+|+||+||+|||+|.
T Consensus       242 ~~~e~~~~~~~~~~~~~g~qIRtY~~~-~~rVkDhRtg~~~~~~~~vldG~ld~fI~a~L~~~  303 (313)
T PRK08787        242 RNAEKDALEATKSDIGWGSQIRNYVLD-QSRIKDLRTGIERSDTQKVLDGDLDEFVEASLKAG  303 (313)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCC-CCCCCCCCCCCEECCHHHHHCCCHHHHHHHHHHHH
T ss_conf             999999987502247642673573179-98355206697767846764877399999999862


No 11 
>KOG2726 consensus
Probab=100.00  E-value=0  Score=709.37  Aligned_cols=321  Identities=38%  Similarity=0.602  Sum_probs=278.5

Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHH----HHHHHHHHHHH
Q ss_conf             99999870866002589999999999889999999999999986399999863100000023456----67655577401
Q gi|254780753|r   24 SFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSILQET----SDNLQRIKLEV   99 (355)
Q Consensus        24 ~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D~el~eE~----~~el~~l~~~l   99 (355)
                      ...+..+.+-++|+|+.+   +...++.|...-..+.++..    ++.|..+   .+|++|..++    .....++...+
T Consensus        51 ~~~~~~~~~~~~~~~~~~---l~~~~~~l~~~~~~~~~~~~----lk~l~~~---~e~e~~~~~a~~E~~~~~~~i~~~~  120 (386)
T KOG2726          51 KVQEAASNDSDLWDDPAE---LDEVLNALSDRMKLVRELKS----LKSLIKE---GEDEDMDELAEEEAEEISKEIERSL  120 (386)
T ss_pred             HHHHHHHCHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH----HHHHHHH---CCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             557876240245543488---99999999999999997650----9999862---0428899999999999999999999


Q ss_pred             HHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCCCH
Q ss_conf             58998876303457662489982177870277899999998999987753113444205454585013468850556100
Q gi|254780753|r  100 EYKQFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYG  179 (355)
Q Consensus       100 e~LE~~~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~ayg  179 (355)
                      .+|+..+||++|+|.++|+|||+|||||+||++||.||++||.+||+++||++++++..+++.+|||+|+++|+|++|||
T Consensus       121 ~~l~~~lLp~~~~D~~~~iiev~aGaGG~Ea~ift~el~~MY~~~a~~~~w~~~~l~~~~~~~~Gi~~At~~i~G~~ayg  200 (386)
T KOG2726         121 HELELSLLPSDPYDAEACIIEVRAGAGGQEAQIFTMELVDMYQKYAERLGWKARVLEKAPGESGGIKSATLEIEGESAYG  200 (386)
T ss_pred             HHHHHHHCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEHHCCCCCCCCCEEEEEEECCCCHHH
T ss_conf             99999726877465237589982788857999999999999999998606640451117753345001366763500122


Q ss_pred             HHEEECCEEEEEEECCCCCCCEEEEEEEEEEECCCCC-CCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCH
Q ss_conf             0001012068987304666650356688788503442-221112345503699853888655442731003588746974
Q gi|254780753|r  180 WLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVD-DSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTG  258 (355)
Q Consensus       180 ~Lk~E~GvHRv~Ri~~~~s~gR~hTS~a~V~V~P~~~-~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~ptg  258 (355)
                      +|+||+|||||||+|+|+++||+|||||+|+|+|.+. +++++.++++||+|++||||||||||||||+|||||+|+|||
T Consensus       201 ~l~~E~GvHRv~r~p~~e~~gr~htstasV~ViP~~~~~~~~~~~~~~dl~i~~~R~~G~GGQhvNktdsaVrl~HiPTG  280 (386)
T KOG2726         201 YLKFEAGVHRVQRVPSTETSGRRHTSTASVAVIPQPGRDEVDVEIDEKDLRIETFRASGPGGQHVNKTDSAVRLTHIPTG  280 (386)
T ss_pred             EEECCCCCCCEEECCCCCCCCCCCCCCCEEEEECCCCCCCCCEECCCHHEEEEECCCCCCCCCCCCCCCCCEEEEEECCC
T ss_conf             15415764444666876655651136543798546788765611472033677323678875655433440589860674


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCCCCEEEEECCCCCCCCCCCCCCEECCHHH
Q ss_conf             776655555224679999999999999999999999999987413-3233222101301585683311114725079778
Q gi|254780753|r  259 VVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGESSK-TEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSD  337 (355)
Q Consensus       259 i~v~~q~~rsq~~Nk~~a~~~l~~~l~~~~~~~~~~~~~~~~~~~-~~~~~g~~iRtY~~~p~~~v~DhR~~~~~~~~~~  337 (355)
                      |+|+||+|||||+||++||++|++||++++..+...+....+..+ +...|+++|||||| ||+||||||+|++++++.+
T Consensus       281 Ivv~cq~eRSq~~Nr~~A~~~L~akL~~~~~~~~~~~~~~~r~~qv~s~~rsekiRTy~~-~q~rv~D~r~~~~~~d~~~  359 (386)
T KOG2726         281 IVVECQEERSQHKNRALALKRLRAKLAVIYREEKSEEEKKKRKAQVGSLKRSEKIRTYNF-KQDRVTDHRIGLESHDLES  359 (386)
T ss_pred             EEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHCEEECCC-CCCCHHHHHHCCCCCCHHH
T ss_conf             699961377688659999999999999998741217765200876255470112100225-7650233310332025588


Q ss_pred             HHCCCHHHHHHHHHHCCC
Q ss_conf             718977999999972259
Q gi|254780753|r  338 VLDGDLDDFMKATLAIKK  355 (355)
Q Consensus       338 vl~G~ld~~i~a~l~~~~  355 (355)
                      ||+|+||+||.+++.|++
T Consensus       360 ~l~G~Ld~li~~~~~~~~  377 (386)
T KOG2726         360 FLDGNLDELIEALLSLRR  377 (386)
T ss_pred             HHHCCHHHHHHHHHHHHH
T ss_conf             874248999999998766


No 12 
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=636.24  Aligned_cols=238  Identities=68%  Similarity=1.044  Sum_probs=235.3

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCCCHHHEEECCEEEEEEECCC
Q ss_conf             48998217787027789999999899998775311344420545458501346885055610000010120689873046
Q gi|254780753|r  117 AYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHRLVRISPY  196 (355)
Q Consensus       117 ailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~ayg~Lk~E~GvHRv~Ri~~~  196 (355)
                      |||+|+||||||||||||.||||||+|||+++||++|++++++||++|+||++|.|+|+|||||||.|.||||+||+|||
T Consensus         1 ~~l~i~~g~gg~e~~dw~~~l~rmy~r~a~~~g~~~e~l~~~~g~~~g~ks~~~~~~g~~a~g~~~~e~g~hrlvr~Spf   80 (239)
T COG1186           1 AYLTIHAGAGGTEAQDWASMLLRMYTRWAERKGFKVEVLDTSDGEEAGIKSATLKIKGENAYGYLKTETGVHRLVRISPF   80 (239)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEEEEECHHHHHHHHHHCCEEEEEEECCC
T ss_conf             97997279885588999999999999999875985899860477304510379999646888888763254677850687


Q ss_pred             CCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             66650356688788503442221112345503699853888655442731003588746974776655555224679999
Q gi|254780753|r  197 DSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQA  276 (355)
Q Consensus       197 ~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~ptgi~v~~q~~rsq~~Nk~~a  276 (355)
                      ++++||||||++|.|+|+++++++++|+++||+|||||||||||||||||+|||||||+||||+|.||.+||||+|++.|
T Consensus        81 ~~~~~R~tsf~~v~v~p~~~~~i~i~I~~~dl~idt~RASGaGGQhVNKt~SAVrlth~ptgivv~cq~eRSq~~n~~~a  160 (239)
T COG1186          81 DSNGRRHTSFASVEVFPELDISIEIEIPDDDLRIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALA  160 (239)
T ss_pred             CCCCCCCCCEEEEEECCCCCCCCCEECCCCCEEEEEEECCCCCCCCCCCCCCCEEEEECCCCCEECCHHHHHHHHHHHHH
T ss_conf             75664155333310047777653100485216999887579998865552442899986777775188899999879999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCEECCHHHHHCCCHHHHHHHHHHCC
Q ss_conf             999999999999999999999987413323322210130158568331111472507977871897799999997225
Q gi|254780753|r  277 WNMLRAKLYELELQKREEIANIGESSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKATLAIK  354 (355)
Q Consensus       277 ~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~iRtY~~~p~~~v~DhR~~~~~~~~~~vl~G~ld~~i~a~l~~~  354 (355)
                      |.+|+++||..+.+++.++.+..++.+..++||+|||+|+|+|+..|+|||++++..|.+.||||++|.||+++|+|+
T Consensus       161 ~~~l~~kL~~~~~~~Rsqe~n~~~a~~k~i~wg~qirsyv~~p~~~vKd~Rt~~E~~~~~~v~dg~~~~~~~~~l~~~  238 (239)
T COG1186         161 RKMLKGKLYILAQEKRSQEKNRERALKKLIGWGNQIRSYVLDPYQPTKDLRTGVERRNKSKVLDGDKDGFIKAYLKWD  238 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHEECCHHHHHHHHHHHHHHHHHHCC
T ss_conf             998777999998898999998999876677887732126788643466532100123578764324778877554035


No 13 
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=100.00  E-value=0  Score=548.58  Aligned_cols=196  Identities=31%  Similarity=0.434  Sum_probs=187.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCEEEEEEEEECCCCCHHHEEECCEEEEEEECC
Q ss_conf             4899821778702778999999989999877531134442054545-850134688505561000001012068987304
Q gi|254780753|r  117 AYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEE-AGIKSATLLIKGPNAYGWLKGEQGVHRLVRISP  195 (355)
Q Consensus       117 ailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~-~GiK~~~~~I~G~~ayg~Lk~E~GvHRv~Ri~~  195 (355)
                      +||||+||+||+||++||+||||||+|||+++||++++++.++++. ||||+|++.|+|++||++|+.|.|+||+|+.||
T Consensus         1 vileIraG~GG~Ea~lfa~~L~rMY~r~a~~~gwk~evi~~~~~~~~Gg~ksv~~~i~G~~~~~~~~~~~G~~~~v~~sp   80 (200)
T TIGR03072         1 ILLQLSSAQGPAECCLAVAKALERLTREAAARGVRVEVLEQEPGEVPGTLRSALVSLDGEAAAALADRWEGTLLWICPSP   80 (200)
T ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEEEEEEEECCEEEEEEECCCEEEEEECC
T ss_conf             98999389986999999999999999999985998999857777779950899999995043078887756179996679


Q ss_pred             CCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHH
Q ss_conf             66665035668878850344222111234550369985388865544273100358874697477665555522467999
Q gi|254780753|r  196 YDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQ  275 (355)
Q Consensus       196 ~~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~ptgi~v~~q~~rsq~~Nk~~  275 (355)
                      |...++|||||++|.++|+..     +|+|+||+|||||||||||||||||+|||||||+||||+|.||+|||||+||++
T Consensus        81 ~~~~~~r~t~~v~v~~~~~~~-----ei~~~Dlridt~RssGaGGQhVNkT~SAVRitH~PTGi~V~~q~eRSQ~~Nk~~  155 (200)
T TIGR03072        81 YRPHHRRKNWFIGVQRFSASE-----EATEDEIRFETLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRL  155 (200)
T ss_pred             CCCCCCEEEEEEEEEECCCCC-----CCCCHHEEEEEEECCCCCCCCCCCCCCEEEEEECCCCEEEEECCCCCHHHHHHH
T ss_conf             767786799999977516557-----888123489998736899885077563499997488479997585547999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEC
Q ss_conf             999999999999999999999998741332332221013015
Q gi|254780753|r  276 AWNMLRAKLYELELQKREEIANIGESSKTEIGWGRQIRSYVL  317 (355)
Q Consensus       276 a~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~iRtY~~  317 (355)
                      ||++|++||++++.+++++.....+..+..++||++|||||-
T Consensus       156 Al~~L~arL~~~~~~~~~~~~~~r~~~~~~~~Rs~kIRTYng  197 (200)
T TIGR03072       156 ATLLLAVRLADLQQEQAAALRAERRTAHHQIERGNPVRVFKG  197 (200)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECC
T ss_conf             999999999999999999999999866798725687251279


No 14 
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=100.00  E-value=0  Score=533.50  Aligned_cols=199  Identities=29%  Similarity=0.402  Sum_probs=188.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-EEEEEEEEECCCCCHHHEEECCEEEEEEECC
Q ss_conf             489982177870277899999998999987753113444205454585-0134688505561000001012068987304
Q gi|254780753|r  117 AYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAG-IKSATLLIKGPNAYGWLKGEQGVHRLVRISP  195 (355)
Q Consensus       117 ailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~G-iK~~~~~I~G~~ayg~Lk~E~GvHRv~Ri~~  195 (355)
                      +||||+||+||+||++||+||||||+|||+++||++++++.++++.+| ||++++.|+|++||++|+.|.|+|+.|+.||
T Consensus         2 vileI~aG~GG~Ea~~fa~~L~rmy~r~a~~~g~~~eil~~~~~~~~g~~ks~~~~i~G~~a~~~l~~~~G~v~~V~~sp   81 (204)
T PRK08179          2 ILLQLSSAQGPAECCLAVAKALERLTKEAARQKVRVEVLETETGRYPDTLRSALVSLDGENAWALAESWCGTIQWICPSP   81 (204)
T ss_pred             EEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEEEEEEECCHHHHHEEECCEEEEEEECC
T ss_conf             89999089896999999999999999999885997999847887779835999999982465330000554379897679


Q ss_pred             CCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHH
Q ss_conf             66665035668878850344222111234550369985388865544273100358874697477665555522467999
Q gi|254780753|r  196 YDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQ  275 (355)
Q Consensus       196 ~~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~ptgi~v~~q~~rsq~~Nk~~  275 (355)
                      |...++|||||++|.++|.     +++++|+||+|||||||||||||||||+|||||||+||||+|.||+|||||+||++
T Consensus        82 ~~~~~~R~~~~v~v~~~~~-----~~~~~~~Dlridt~RssG~GGQhVNkT~SAVRitH~PTGi~V~~q~eRSQ~~Nk~~  156 (204)
T PRK08179         82 YRPHHGRKNWFVGIGRFSA-----DEQEQSDEIRYETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRL  156 (204)
T ss_pred             CCCCCCEEEEEEEEEEECC-----CCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEECCCCEEEEECCCCCHHHHHHH
T ss_conf             8887755999999876077-----66778633489999747998875046552499997588779997163358999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCC
Q ss_conf             999999999999999999999998741332332221013015856
Q gi|254780753|r  276 AWNMLRAKLYELELQKREEIANIGESSKTEIGWGRQIRSYVLQPY  320 (355)
Q Consensus       276 a~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~iRtY~~~p~  320 (355)
                      ||++|++||++.+.+++.+.....+..+..++||++||||.+.+.
T Consensus       157 A~~~L~arL~~~~~~~~~~~~~~r~~~~~~~~Rg~~IRtY~g~~f  201 (204)
T PRK08179        157 ARLLIAWKLEQQQQEQSAALKSQRRMFHHQIERGNPRRVFTGMAF  201 (204)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCCC
T ss_conf             999999999999999999999999866686215788067618988


No 15 
>pfam00472 RF-1 RF-1 domain. This domain is found in peptide chain release factors such as RF-1 and RF-2, and a number of smaller proteins of unknown function. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis.
Probab=100.00  E-value=3.3e-36  Score=279.47  Aligned_cols=111  Identities=55%  Similarity=0.825  Sum_probs=103.5

Q ss_pred             CCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             22211123455036998538886554427310035887469747766555552246799999999999999999999999
Q gi|254780753|r  216 DDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEI  295 (355)
Q Consensus       216 ~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~ptgi~v~~q~~rsq~~Nk~~a~~~l~~~l~~~~~~~~~~~  295 (355)
                      ++.++|+|+++||+|+|||||||||||||||+|||||+|+||||+|.||++|||++||+.||++|+++|++++.+++...
T Consensus         3 ~~~~~i~i~~~dl~~~~~RssGpGGQ~VNKt~saV~l~h~ptgi~v~~q~~RSq~~Nr~~A~~~L~~~l~~~~~~k~~~~   82 (114)
T pfam00472         3 DEEVEIEIPPSDLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNREKALERLKAKLYEAELQKKREE   82 (114)
T ss_pred             CCCCCEECCHHHEEEEEEECCCCCCCCCCHHHEEEEEEECCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88511141879948998887898656547204158999847648999707788899999999999999999988899999


Q ss_pred             HHHHHHHH-HHCCCCCCEEEEECCCCCCCCCCC
Q ss_conf             99987413-323322210130158568331111
Q gi|254780753|r  296 ANIGESSK-TEIGWGRQIRSYVLQPYQMVKDLR  327 (355)
Q Consensus       296 ~~~~~~~~-~~~~~g~~iRtY~~~p~~~v~DhR  327 (355)
                      .+..++.+ ..++||++|||||| ||++|||||
T Consensus        83 ~~~~r~~~~~~~~~~~kiRtY~~-~~~~Vkd~R  114 (114)
T pfam00472        83 TKPTRKSQVRRGDRKEKIRTYNF-PQGRVKDHR  114 (114)
T ss_pred             HHHHHHHHCCCCCCCCCCCCEEC-CCCCCCCCC
T ss_conf             87998600366855466001337-877767697


No 16 
>pfam03462 PCRF PCRF domain. This domain is found in peptide chain release factors.
Probab=100.00  E-value=4.2e-34  Score=264.46  Aligned_cols=110  Identities=46%  Similarity=0.660  Sum_probs=104.1

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH----HHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6310000002345667655577401589988----763034576624899821778702778999999989999877531
Q gi|254780753|r   75 LALEEDDCSILQETSDNLQRIKLEVEYKQFE----SLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKF  150 (355)
Q Consensus        75 La~ee~D~el~eE~~~el~~l~~~le~LE~~----~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gw  150 (355)
                      ++.+++|+++.+++..++..+...++.++.+    ++|++|+|.+||||||||||||+||||||+||||||+|||+++||
T Consensus         2 l~~~e~D~e~~~~a~~e~~~l~~~l~~le~~l~~~llp~~~~D~~~~ilEI~aGaGG~EA~~fa~~L~rMY~r~ae~~gw   81 (115)
T pfam03462         2 LLEEEDDPELRELAEEELEELEKELEELEKELLNLLLPLDPYDDKNAILEIRAGAGGTEAQLFAEDLLRMYQRYAERKGW   81 (115)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             02107998999999999999999999999999997079997766786899936889689999999999999999997799


Q ss_pred             HHHHHHCCCCCCCCEEEEEEEEECCCCCHHHEEE
Q ss_conf             1344420545458501346885055610000010
Q gi|254780753|r  151 KTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGE  184 (355)
Q Consensus       151 k~evi~~~~~e~~GiK~~~~~I~G~~ayg~Lk~E  184 (355)
                      +++|+++++++.||||+|+|.|+|++|||+||+|
T Consensus        82 ~~evl~~~~~e~gG~k~a~~~I~G~~aYg~Lk~E  115 (115)
T pfam03462        82 KVEVLDYSEGEEGGIKEATLEIEGEGAYGYLKFE  115 (115)
T ss_pred             EEEEEECCCCCCCCEEEEEEEEECCCHHHHCCCC
T ss_conf             8899755887777547999999863858753388


No 17 
>PRK09256 hypothetical protein; Provisional
Probab=99.64  E-value=1e-16  Score=140.16  Aligned_cols=68  Identities=34%  Similarity=0.484  Sum_probs=62.9

Q ss_pred             CCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEE------ECCCH------------------HHHHHHHHHHHHHHHH
Q ss_conf             11123455036998538886554427310035887------46974------------------7766555552246799
Q gi|254780753|r  219 IEIEISESDCRIDTYRASGAGGQHVNTTDSAVRIT------HIPTG------------------VVVQCQQERSQHKNKA  274 (355)
Q Consensus       219 ~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~------H~ptg------------------i~v~~q~~rsq~~Nk~  274 (355)
                      ..|.|+++||.+.+.|||||||||||||+|+|.|.      |+|++                  |+|.||+.|||++|++
T Consensus         6 ~~i~Ip~~el~~~f~RSsGPGGQnVNKv~Tkv~Lr~~~~~s~lp~~~k~rl~~~~~~ri~~~g~lvI~s~~~RsQ~~Nr~   85 (138)
T PRK09256          6 RRLVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQERNRE   85 (138)
T ss_pred             CCEEECHHHCEEEEEECCCCCCCCCCCEEEEEEEEECCCCCCCCHHHHHHHHHHHHCCCCCCCEEEEEECCCCCHHHHHH
T ss_conf             87378769907777775799876423000027889633014699999999999862651779739999745269999899


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780753|r  275 QAWNMLRAKLYE  286 (355)
Q Consensus       275 ~a~~~l~~~l~~  286 (355)
                      .|+..|...|..
T Consensus        86 ~a~~rL~~li~~   97 (138)
T PRK09256         86 DALERLAALIRA   97 (138)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999998


No 18 
>KOG3429 consensus
Probab=98.89  E-value=2.4e-09  Score=87.49  Aligned_cols=71  Identities=32%  Similarity=0.445  Sum_probs=59.4

Q ss_pred             CCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEEC-------C------------------CHHHHHHHHHHHHHHHH
Q ss_conf             1112345503699853888655442731003588746-------9------------------74776655555224679
Q gi|254780753|r  219 IEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHI-------P------------------TGVVVQCQQERSQHKNK  273 (355)
Q Consensus       219 ~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~-------p------------------tgi~v~~q~~rsq~~Nk  273 (355)
                      ..-.|+-+-+.|.+.||||||||||||..|-|-++-.       |                  .-|++.++..||||.|.
T Consensus        33 ~~g~ipld~~~i~y~RSSGPGGQNVNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~Ni  112 (172)
T KOG3429          33 FKGKIPLDQLEISYSRSSGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKNI  112 (172)
T ss_pred             CCCCCCHHHEEEEEEECCCCCCCCCCCCCCEEEEEEECCHHHHCCHHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHCCH
T ss_conf             58878631647887405799876520214438999750136561199999999998876425764899415047766259


Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999
Q gi|254780753|r  274 AQAWNMLRAKLYELEL  289 (355)
Q Consensus       274 ~~a~~~l~~~l~~~~~  289 (355)
                      +.|+..|++-+++.+.
T Consensus       113 aDcleKlr~~I~~~~~  128 (172)
T KOG3429         113 ADCLEKLRDIIRAAEQ  128 (172)
T ss_pred             HHHHHHHHHHHHHHHC
T ss_conf             9999999999999860


No 19 
>PRK11147 ABC transporter ATPase component; Reviewed
Probab=95.63  E-value=0.11  Score=32.89  Aligned_cols=21  Identities=19%  Similarity=0.472  Sum_probs=12.2

Q ss_pred             CCCCCCCCCEEEEEEECCCCCC
Q ss_conf             2111234550369985388865
Q gi|254780753|r  218 SIEIEISESDCRIDTYRASGAG  239 (355)
Q Consensus       218 ~~~i~i~~~dl~i~~~rssg~g  239 (355)
                      ++++.|...| +|-..=.+|+|
T Consensus       337 ~vsl~i~~Ge-~ialvG~NGsG  357 (632)
T PRK11147        337 DFSAQVQRGD-KIALIGPNGCG  357 (632)
T ss_pred             EECCCCCCCC-EEEEECCCCCC
T ss_conf             5333357887-79998898842


No 20 
>PRK10636 putative ABC transporter ATP-binding protein; Provisional
Probab=94.82  E-value=0.33  Score=29.38  Aligned_cols=21  Identities=29%  Similarity=0.458  Sum_probs=12.2

Q ss_pred             CCCCCCCCCEEEEEEECCCCCC
Q ss_conf             2111234550369985388865
Q gi|254780753|r  218 SIEIEISESDCRIDTYRASGAG  239 (355)
Q Consensus       218 ~~~i~i~~~dl~i~~~rssg~g  239 (355)
                      ++++.|.+.|. |-..=.+|+|
T Consensus       330 ~vsl~i~~Ger-iaIvG~NGsG  350 (638)
T PRK10636        330 SIKLNLVPGSR-IGLLGRNGAG  350 (638)
T ss_pred             CCCCEECCCCE-EEEECCCCCC
T ss_conf             77505637847-9997478713


No 21 
>TIGR00019 prfA peptide chain release factor 1; InterPro: IPR004373 This family describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognise and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cut-off for this model. RF-1 does not have a translational frameshift.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=92.81  E-value=0.53  Score=27.94  Aligned_cols=88  Identities=19%  Similarity=0.185  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHCC---HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             899999886549---89999999999998708660025899999999998899999999999999863999998631000
Q gi|254780753|r    4 SRQLNCLGGLFD---WDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEED   80 (355)
Q Consensus         4 ~~rl~~l~~~fD---le~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~   80 (355)
                      ..+...|...|.   +-.=..|+.++.++.+++      .......++|..+.+-++.-+.+...-.+.++|.|||++| 
T Consensus        14 ~~~~~eL~~~L~dp~v~~d~~k~~~~~ke~~~l------~~i~~~~~~~~~~~~~~~~A~~~l~E~~~D~El~elak~E-   86 (373)
T TIGR00019        14 EERYEELEELLSDPEVISDQDKLRKLSKEYSQL------EEIVDKYEEYKKAQEDLKEAKELLEEKGDDKELRELAKEE-   86 (373)
T ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCH------HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH-
T ss_conf             999999998506863113679999998862065------6899999999999999999999997425886589999999-


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0002345667655577401589
Q gi|254780753|r   81 DCSILQETSDNLQRIKLEVEYK  102 (355)
Q Consensus        81 D~el~eE~~~el~~l~~~le~L  102 (355)
                          ++++.....+|+..|.-|
T Consensus        87 ----l~~l~~~~~~LE~~Lk~L  104 (373)
T TIGR00019        87 ----LEELEKEIEELEEQLKIL  104 (373)
T ss_pred             ----HHHHHHHHHHHHHHHHHH
T ss_conf             ----999998888899999972


No 22 
>KOG0995 consensus
Probab=88.22  E-value=2.4  Score=23.21  Aligned_cols=69  Identities=7%  Similarity=0.006  Sum_probs=53.5

Q ss_pred             CHHHHHHHHH--HHCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5689999988--6549899999999999987086600258999999999988999999999999998639999
Q gi|254780753|r    2 KLSRQLNCLG--GLFDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLIL   72 (355)
Q Consensus         2 EL~~rl~~l~--~~fDle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL   72 (355)
                      |++.+|..+-  -.++++.++....+|+.+++  ..-.+|.+-+.+-+.++.|+.-++.|..+.+...+-...
T Consensus       221 Elk~~l~~~~~~i~~~ie~l~~~n~~l~e~i~--e~ek~~~~~eslre~~~~L~~D~nK~~~y~~~~~~k~~~  291 (581)
T KOG0995         221 ELKHRLEKYFTSIANEIEDLKKTNRELEEMIN--EREKDPGKEESLREKKARLQDDVNKFQAYVSQMKSKKQH  291 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999998889999989988999999999--986375357789999999876899999999988764288


No 23 
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=80.27  E-value=5.2  Score=20.82  Aligned_cols=89  Identities=13%  Similarity=0.130  Sum_probs=49.8

Q ss_pred             HCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCHHH---HHH
Q ss_conf             5498999999999999870866002589999999999889999999999999986399999863100-000023---456
Q gi|254780753|r   13 LFDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEE-DDCSIL---QET   88 (355)
Q Consensus        13 ~fDle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee-~D~el~---eE~   88 (355)
                      |+|+.-++.-.+.+...+..-++-.|.++..++-.+...+...++.+..-++.+..  ++-.+.+.. +..++.   .++
T Consensus         1 MLDik~IReNpe~v~~~lkkR~~~~~id~il~lD~~rr~l~~e~e~Lr~erN~iSK--~Ig~~kk~g~~~~~l~~~~~~l   78 (422)
T PRK05431          1 MLDIKLIRENPDAVKEKLAKRGDPLDVDELLELDEERRELQTETEELQAERNALSK--EIGQAKAKGEDAEELIAEVKEL   78 (422)
T ss_pred             CCCHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHCCCCHHHHHHHHHHH
T ss_conf             98878987499999999986598451999999999999999999999999999999--9999874897799999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             676555774015899
Q gi|254780753|r   89 SDNLQRIKLEVEYKQ  103 (355)
Q Consensus        89 ~~el~~l~~~le~LE  103 (355)
                      .+++..++..+.+++
T Consensus        79 k~~i~~le~~~~~~~   93 (422)
T PRK05431         79 KEEIKALEAELKELE   93 (422)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999999999999999


No 24 
>TIGR03545 conserved hypothetical protein TIGR03545. This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair.
Probab=77.76  E-value=6.2  Score=20.30  Aligned_cols=20  Identities=15%  Similarity=0.268  Sum_probs=15.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q ss_conf             70277899999998999987
Q gi|254780753|r  127 GTESQDWANMLLRMYTRWAE  146 (355)
Q Consensus       127 G~EA~dwA~~L~rMY~r~ae  146 (355)
                      |++++.|++.++.-|.+..-
T Consensus       287 g~~i~~~~~~~~~~y~~~~p  306 (554)
T TIGR03545       287 GEEIRRYLQTAYDYYDQAEP  306 (554)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             69999999999999998766


No 25 
>COG0249 MutS Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=75.94  E-value=6.9  Score=19.96  Aligned_cols=153  Identities=18%  Similarity=0.212  Sum_probs=87.9

Q ss_pred             HHCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             65498999999999999870866002589999999999889999999----------99999998639999986310000
Q gi|254780753|r   12 GLFDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISF----------IKEIQDRLCDNLILLELALEEDD   81 (355)
Q Consensus        12 ~~fDle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~----------~~~l~~~l~Dl~eL~ELa~ee~D   81 (355)
                      -..|.+++..|++-++....++.+..   ..+..++....++.++..          +-.+...+.-+.++..+......
T Consensus       308 PL~~~~~I~~Rld~Ve~l~~~~~l~~---~L~~~L~~v~DleRl~~Rl~~~~~~~rDl~~l~~~l~~~~~i~~~l~~~~~  384 (843)
T COG0249         308 PLLDKEEIEERLDAVEELKDNPELRE---KLREMLKKVPDLERLLSRLSLGRASPRDLLRLRDSLEKIPEIFKLLSSLKS  384 (843)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             03589999999999999986568999---999998507679999999973799865699999999988999999852543


Q ss_pred             CHHHHHHHHHHHHHH---HHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             002345667655577---40158998876303457662489982177870277899999998999987753113444205
Q gi|254780753|r   82 CSILQETSDNLQRIK---LEVEYKQFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIH  158 (355)
Q Consensus        82 ~el~eE~~~el~~l~---~~le~LE~~~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~  158 (355)
                      ..........+..+.   +....++....+..|..-++  --|+.|        |-.+|..+=.-+-..+.|-.++... 
T Consensus       385 ~~~l~~~~~~i~~~~~~~e~~~ll~~~i~~~~~~~~~~--~ii~~g--------~~~eLd~lr~~~~~~~~~i~~le~~-  453 (843)
T COG0249         385 ESDLLLLLEDIESLDYLAELLELLETAINEDPPLAVRD--GIIKEG--------YNIELDELRDLLNNAKEWIAKLELE-  453 (843)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHCCH--HHHHCC--------HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_conf             02356776444313407999999998721166233015--577511--------0399999999998889999999998-


Q ss_pred             CCCCCCEEEEEEEEECCCCCHH
Q ss_conf             4545850134688505561000
Q gi|254780753|r  159 DGEEAGIKSATLLIKGPNAYGW  180 (355)
Q Consensus       159 ~~e~~GiK~~~~~I~G~~ayg~  180 (355)
                      +-+.-||++  ++|.-..+|||
T Consensus       454 ~r~~~gi~s--lki~~n~v~Gy  473 (843)
T COG0249         454 ERERTGIKS--LKIKYNKVYGY  473 (843)
T ss_pred             HHHHCCCCH--HHHHHHCCCEE
T ss_conf             888649721--21122034605


No 26 
>PRK11546 zraP zinc resistance protein; Provisional
Probab=73.97  E-value=7.7  Score=19.62  Aligned_cols=37  Identities=11%  Similarity=0.087  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999998708660025899999999998899999
Q gi|254780753|r   18 NAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAI   56 (355)
Q Consensus        18 ~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV   56 (355)
                      ++..+-.||++.++.++-  |.+++.+++||.+.|+..+
T Consensus        65 qL~aKr~ElNALL~at~P--D~~kI~avakEis~LR~kl  101 (139)
T PRK11546         65 QLVSKRYEYNALLTANPP--DSSKINAVAKEMETLRQSL  101 (139)
T ss_pred             HHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHHHHHH
T ss_conf             999989999999806997--7999999999999999999


No 27 
>pfam07303 Occludin_ELL Occludin homology domain. This domain represents a conserved region approximately 100 residues long within eukaryotic occludin proteins and the RNA polymerase II elongation factor ELL. Occludin is an integral membrane protein that localizes to tight junctions, while ELL is an elongation factor that can increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by polymerase at multiple sites along the DNA. This shared domain is thought to mediate protein interactions.
Probab=72.11  E-value=8.5  Score=19.32  Aligned_cols=16  Identities=25%  Similarity=0.335  Sum_probs=7.8

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             8999999999999870
Q gi|254780753|r   16 WDNAVQRLSFLNTKTE   31 (355)
Q Consensus        16 le~~~~rl~eLE~~ls   31 (355)
                      ++.+..+|.+|+.+|.
T Consensus        31 v~~v~~kf~~L~~~l~   46 (101)
T pfam07303        31 VDAINKRLQQLDAELD   46 (101)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999999999997


No 28 
>KOG1086 consensus
Probab=69.35  E-value=9.6  Score=18.91  Aligned_cols=28  Identities=7%  Similarity=0.139  Sum_probs=19.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5899999999998899999999999999
Q gi|254780753|r   38 NVIEAKMLMRERQHLDNAISFIKEIQDR   65 (355)
Q Consensus        38 D~~kAqkl~KE~s~L~~iV~~~~~l~~~   65 (355)
                      |..+.++++|+.+.|+.+.+..+.+...
T Consensus       204 ee~k~eKiskR~~aleev~n~vk~l~em  231 (594)
T KOG1086         204 EEHKLEKISKRVKALEEVNNNVKLLEEM  231 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999998999999899999999


No 29 
>TIGR01011 rpsB_bact ribosomal protein S2; InterPro: IPR005706   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    This family describes the bacterial, mitochondrial and chloroplast forms of ribosomal protein S2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=68.74  E-value=9.2  Score=19.08  Aligned_cols=60  Identities=20%  Similarity=0.212  Sum_probs=28.2

Q ss_pred             HHHHCC----HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             886549----899999999999987086600258999999999988999999999999998639999986
Q gi|254780753|r   10 LGGLFD----WDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLEL   75 (355)
Q Consensus        10 l~~~fD----le~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~EL   75 (355)
                      |||||=    +-+-.+||++||+...+..|=.=+    |  ||...|....+.++.+..-+.|++.|=.+
T Consensus        97 LGGMLTNf~TirkSi~kL~~lE~~~~~g~~~~Lt----K--KE~~~L~Re~~KL~k~LgGIk~M~~lPd~  160 (227)
T TIGR01011        97 LGGMLTNFKTIRKSIKKLKKLEKMEEDGTFDVLT----K--KEILMLSREKEKLEKNLGGIKDMKKLPDL  160 (227)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCC----C--CCHHHHHHHHHHHHHHHHHHHHHHCCCCE
T ss_conf             4640024799999999999999877613312477----0--00776789999986553002545316970


No 30 
>PRK05729 valS valyl-tRNA synthetase; Reviewed
Probab=65.26  E-value=12  Score=18.36  Aligned_cols=10  Identities=30%  Similarity=0.999  Sum_probs=5.6

Q ss_pred             CCCCCCEEEE
Q ss_conf             3322210130
Q gi|254780753|r  306 IGWGRQIRSY  315 (355)
Q Consensus       306 ~~~g~~iRtY  315 (355)
                      .-||.+|=-|
T Consensus       406 r~WG~piPvw  415 (877)
T PRK05729        406 LWWGHRIPAW  415 (877)
T ss_pred             CCCCCCEEEE
T ss_conf             4468842589


No 31 
>pfam08399 VWA_N VWA N-terminal. This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, pfam00092) and Cache (pfam02743) domains. It has been found in vertebrates, Drosophila and C. elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits.
Probab=65.02  E-value=2.9  Score=22.69  Aligned_cols=19  Identities=42%  Similarity=0.525  Sum_probs=16.1

Q ss_pred             CCCCCCCCCEEEEEEECCCHHH
Q ss_conf             5544273100358874697477
Q gi|254780753|r  239 GGQHVNTTDSAVRITHIPTGVV  260 (355)
Q Consensus       239 ggq~vn~t~savri~H~ptgi~  260 (355)
                      -+..||++-|||   |+||+|-
T Consensus        55 ~~~~Vn~~~S~V---hiPt~Vy   73 (123)
T pfam08399        55 NNLPVNTSVSSV---QLPTNVY   73 (123)
T ss_pred             CCCCCCCEEEEE---ECCCCCC
T ss_conf             786110634127---8576403


No 32 
>PRK05399 DNA mismatch repair protein; Provisional
Probab=64.73  E-value=12  Score=18.30  Aligned_cols=151  Identities=18%  Similarity=0.194  Sum_probs=73.1

Q ss_pred             HCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             54989999999999998708660025899999999998899999999----------99999986399999863100000
Q gi|254780753|r   13 LFDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFI----------KEIQDRLCDNLILLELALEEDDC   82 (355)
Q Consensus        13 ~fDle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~----------~~l~~~l~Dl~eL~ELa~ee~D~   82 (355)
                      ..|++.+..|++-++..+.++.+.+   ..+..++...+++.++..+          -.+...+.-+..+.++..   +.
T Consensus       310 L~d~~~I~~RldaVe~l~~~~~~~~---~lr~~Lk~i~DlERllsRi~~~~~~prDl~~L~~sL~~~~~i~~~l~---~~  383 (848)
T PRK05399        310 LRDREAINARLDAVEELLDNPLLRE---DLRELLKGVYDLERILSRVALGRANPRDLAALRDSLEALPELKELLE---ES  383 (848)
T ss_pred             CCCHHHHHHHHHHHHHHHHCHHHHH---HHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH---CC
T ss_conf             6277899999999999974979999---99999854898899999998089788999999999999999999984---67


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             02345667655577401589988763034576624899821778702778999999989999877531134442054545
Q gi|254780753|r   83 SILQETSDNLQRIKLEVEYKQFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEE  162 (355)
Q Consensus        83 el~eE~~~el~~l~~~le~LE~~~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~  162 (355)
                      .++..+...+..+....+.++.......|..-++-- -|++|.-        .+|-..=.-..+.+.|-.++. ..+-+.
T Consensus       384 ~~l~~l~~~l~~~~~l~~~i~~~i~~~~p~~~~dg~-~Ik~G~d--------~eLDelr~~~~~~~~~l~~le-~~er~~  453 (848)
T PRK05399        384 PLLAELLAQLDPLPELADLLERAIVEEPPLLIRDGG-VIADGYD--------AELDELRALSDNGKDWLAELE-ARERER  453 (848)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHCCCCC-EECCCCC--------HHHHHHHHHHHHHHHHHHHHH-HHHHHH
T ss_conf             789999885314899999999987105575543688-6358879--------889999999986899999999-999987


Q ss_pred             CCEEEEEEEEECCCCCHHH
Q ss_conf             8501346885055610000
Q gi|254780753|r  163 AGIKSATLLIKGPNAYGWL  181 (355)
Q Consensus       163 ~GiK~~~~~I~G~~ayg~L  181 (355)
                      -||++  ++|.-..++||+
T Consensus       454 tgI~s--LKi~yn~v~GY~  470 (848)
T PRK05399        454 TGISS--LKVGYNKVFGYY  470 (848)
T ss_pred             CCCCC--CCHHHCCCCEEE
T ss_conf             08651--101114752289


No 33 
>pfam10458 Val_tRNA-synt_C Valyl tRNA synthetase tRNA binding arm. This domain is found at the C-terminus of Valyl tRNA synthetases.
Probab=63.67  E-value=12  Score=18.16  Aligned_cols=53  Identities=13%  Similarity=0.273  Sum_probs=37.7

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             989999999999998708660025899999999998899999999999999863
Q gi|254780753|r   15 DWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCD   68 (355)
Q Consensus        15 Dle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~D   68 (355)
                      +++.+...+..++..|+.|+|.+.-.. .-+-++...+...-..+..+...+..
T Consensus        12 el~kl~~~i~~~~~kL~N~~Fv~kAP~-~VV~~er~kl~~~~~~~~~l~~~L~~   64 (66)
T pfam10458        12 ELAKLQKEIERLQKKLSNPGFVAKAPA-EVVEEEKAKLAEYEEQLEKLKERLSQ   64 (66)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999987787677770989-99999999999999999999999987


No 34 
>KOG1697 consensus
Probab=57.35  E-value=10  Score=18.76  Aligned_cols=114  Identities=14%  Similarity=0.037  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCC
Q ss_conf             15899887630345766248998217787027789--9999998999987753113444205454585013468850556
Q gi|254780753|r   99 VEYKQFESLLSGEADSNDAYLEVHAGAGGTESQDW--ANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPN  176 (355)
Q Consensus        99 le~LE~~~Lls~e~D~~nailEI~AGaGG~EA~dw--A~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~  176 (355)
                      +++...-+.|++-+|.+.-..-   ++++.|-.-|  ..|++-|-..-+....-..+-+-.++....       +..--.
T Consensus        66 id~ai~~l~psg~~d~~arp~m---~~~~~et~~~~ll~di~~~~~~~~~~~~~s~~~l~s~p~~~~-------e~~f~~  135 (275)
T KOG1697          66 IDRAISYLFPSGLFDPNARPVM---AFQFDETKYYQLLHDIGVLTNKLAKLYSISIEHLLSSPYSAI-------EEKFLK  135 (275)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCC---CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH-------HHHHHH
T ss_conf             6878887463123573346420---136785048999999876654566531067887761714577-------799999


Q ss_pred             CCHHHEEECCEEEEEEECCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEE
Q ss_conf             10000010120689873046666503566887885034422211123455036
Q gi|254780753|r  177 AYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCR  229 (355)
Q Consensus       177 ayg~Lk~E~GvHRv~Ri~~~~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~  229 (355)
                      .|-...-|.|---+.    ....|||.||.|.|.|.|--.   .|.||-.|+.
T Consensus       136 ~~~k~~~~~g~~~~~----~~~~g~rK~a~A~V~v~~GtG---k~~vNg~~~~  181 (275)
T KOG1697         136 RFRKPLDESGKPEVR----IIAVGRRKCARATVKVQPGTG---KFDVNGRDLD  181 (275)
T ss_pred             HHHHCCCCCCCCCEE----EEECCCEECCEEEEEEECCCE---EEEECCHHHH
T ss_conf             987302546887514----661254000113799956840---4876560277


No 35 
>KOG0994 consensus
Probab=55.11  E-value=17  Score=17.17  Aligned_cols=97  Identities=14%  Similarity=0.126  Sum_probs=50.4

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             98999999999999870866002589999999999889999999----99999998639999986310000002345667
Q gi|254780753|r   15 DWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISF----IKEIQDRLCDNLILLELALEEDDCSILQETSD   90 (355)
Q Consensus        15 Dle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~----~~~l~~~l~Dl~eL~ELa~ee~D~el~eE~~~   90 (355)
                      ++..+.+++.++...+++|++-.  ....++.+....|++.|..    +-+++..+.|+.....++..  |   ++-+..
T Consensus      1202 ~f~~me~kl~~ir~il~~~svs~--~~i~~l~~~~~~lr~~l~~~~e~L~~~E~~Lsdi~~~~~~a~~--~---LesLq~ 1274 (1758)
T KOG0994        1202 RFLDMEEKLEEIRAILSAPSVSA--EDIAQLASATESLRRQLQALTEDLPQEEETLSDITNSLPLAGK--D---LESLQR 1274 (1758)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH--H---HHHHHH
T ss_conf             79999999999999864898547--8899999999999999999875415666436665421650455--6---899998


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCEE
Q ss_conf             6555774015899887630345766248
Q gi|254780753|r   91 NLQRIKLEVEYKQFESLLSGEADSNDAY  118 (355)
Q Consensus        91 el~~l~~~le~LE~~~Lls~e~D~~nai  118 (355)
                      +...+.....+|+-.+-+-.+.|-..|+
T Consensus      1275 ~~~~l~~~~keL~e~~~~ik~sdi~GA~ 1302 (1758)
T KOG0994        1275 EFNGLLTTYKELREQLEKIKESDILGAF 1302 (1758)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf             9999999999999998876316703578


No 36 
>TIGR02168 SMC_prok_B chromosome segregation protein SMC; InterPro: IPR011890   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . The smc gene is often associated with scpB (IPR005234 from INTERPRO) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle , , .; GO: 0005515 protein binding, 0005524 ATP binding, 0005694 chromosome.
Probab=54.77  E-value=17  Score=17.13  Aligned_cols=22  Identities=23%  Similarity=0.258  Sum_probs=9.9

Q ss_pred             HHHHHHHHH-HHHHHHHHHHHHH
Q ss_conf             522467999-9999999999999
Q gi|254780753|r  267 RSQHKNKAQ-AWNMLRAKLYELE  288 (355)
Q Consensus       267 rsq~~Nk~~-a~~~l~~~l~~~~  288 (355)
                      .+...++.. .+.-|..++-.++
T Consensus       675 ~~~~l~r~~~ei~~l~~~~~~~~  697 (1191)
T TIGR02168       675 NSSILERRRIEIEELEEEIEELE  697 (1191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             12346888999999999999999


No 37 
>COG3378 Phage associated DNA primase [General function prediction only]
Probab=54.66  E-value=9.9  Score=18.83  Aligned_cols=10  Identities=20%  Similarity=0.212  Sum_probs=3.5

Q ss_pred             HHEEECCEEE
Q ss_conf             0001012068
Q gi|254780753|r  180 WLKGEQGVHR  189 (355)
Q Consensus       180 ~Lk~E~GvHR  189 (355)
                      +|.-|++|-.
T Consensus       295 ~l~~~~~lK~  304 (517)
T COG3378         295 RLDDEGKLKA  304 (517)
T ss_pred             CCCCCCCEEE
T ss_conf             0035566366


No 38 
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=53.89  E-value=18  Score=17.03  Aligned_cols=12  Identities=25%  Similarity=0.443  Sum_probs=5.6

Q ss_pred             HHHHCCCCCCCC
Q ss_conf             444205454585
Q gi|254780753|r  153 EALEIHDGEEAG  164 (355)
Q Consensus       153 evi~~~~~e~~G  164 (355)
                      +.++.+|-+.-|
T Consensus       221 et~~l~p~die~  232 (290)
T COG4026         221 ETLNLAPKDIEG  232 (290)
T ss_pred             HHHCCCCHHCCC
T ss_conf             884568232155


No 39 
>PRK07997 consensus
Probab=53.39  E-value=18  Score=16.98  Aligned_cols=86  Identities=14%  Similarity=0.116  Sum_probs=48.5

Q ss_pred             HHHHHHHHHHCC--------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHH----
Q ss_conf             999999987086--------6002589999999999889999999999999-----------98639999986310----
Q gi|254780753|r   22 RLSFLNTKTEDP--------HLWQNVIEAKMLMRERQHLDNAISFIKEIQD-----------RLCDNLILLELALE----   78 (355)
Q Consensus        22 rl~eLE~~lsdp--------~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~-----------~l~Dl~eL~ELa~e----   78 (355)
                      ++-.+-..+.|+        .+  -++-|.++.+++.+|+.+++..+++..           .+.+-++..-|.++    
T Consensus       175 qv~D~laL~GDsSDNIPGVpGI--G~KTA~kLL~eyGsLE~I~~n~d~i~g~~~r~~~kl~e~L~~~ke~A~LSkeLvTI  252 (928)
T PRK07997        175 LIIDFLALMGDSSDNIPGVPGV--GEKTAQALLQGLGGLDTLYAEPEKIAGLSFRGAKTMAAKLEQNKEVAYLSYQLATI  252 (928)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCC--CHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8899999728865688999975--48999999998277999998098604542211778999999729999999987465


Q ss_pred             CCCCHH------HHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             000002------3456676555774015899887630
Q gi|254780753|r   79 EDDCSI------LQETSDNLQRIKLEVEYKQFESLLS  109 (355)
Q Consensus        79 e~D~el------~eE~~~el~~l~~~le~LE~~~Lls  109 (355)
                      ..|..+      +.--......+...++++|+..|++
T Consensus       253 ~~Dvpl~~~l~~l~~~~~d~e~L~~lf~elEFksll~  289 (928)
T PRK07997        253 KTDVELELTCEQLEVQQPDAEELLGLFKKYEFKRWTA  289 (928)
T ss_pred             HCCCCCCCCHHHHCCCCCCHHHHHHHHHHCCCHHHHH
T ss_conf             1366778998994548999999999999808778999


No 40 
>KOG3274 consensus
Probab=53.38  E-value=14  Score=17.82  Aligned_cols=105  Identities=20%  Similarity=0.255  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCE-EEEEEEEECCCCCHHHEEECCEEEEEEECCCCCCCEEEEEEEEEEECCCCC
Q ss_conf             9989999877531134442054545850-134688505561000001012068987304666650356688788503442
Q gi|254780753|r  138 LRMYTRWAEKRKFKTEALEIHDGEEAGI-KSATLLIKGPNAYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVD  216 (355)
Q Consensus       138 ~rMY~r~ae~~gwk~evi~~~~~e~~Gi-K~~~~~I~G~~ayg~Lk~E~GvHRv~Ri~~~~s~gR~hTS~a~V~V~P~~~  216 (355)
                      +|=|..=+.-+.=.+..|+  ..|..-+ =+|.+.+.-+.++.+|-+|-|+|- +||-=++..|..-|+|---.|.|+- 
T Consensus        76 l~eYaltsAl~DsRF~PIs--r~ELp~L~CsvslL~nFE~i~d~lDWevG~HG-IrieF~~e~g~krsATyLPeVa~EQ-  151 (210)
T KOG3274          76 LREYALTSALKDSRFPPIS--REELPSLQCSVSLLTNFEDIFDYLDWEVGVHG-IRIEFTNETGTKRSATYLPEVAAEQ-  151 (210)
T ss_pred             HHHHHHHHHHHCCCCCCCC--HHHCCCEEEEEEEECCCHHCCCCCCEEECCCE-EEEEEECCCCCEEEEEECCCCHHHC-
T ss_conf             7888888876204689877--32417438777753364120353220100332-8999973789584212356321121-


Q ss_pred             CCCCCCCCCCEEEEEE----ECCCCCCCCCCCCCCEEEEEEEC
Q ss_conf             2211123455036998----53888655442731003588746
Q gi|254780753|r  217 DSIEIEISESDCRIDT----YRASGAGGQHVNTTDSAVRITHI  255 (355)
Q Consensus       217 ~~~~i~i~~~dl~i~~----~rssg~ggq~vn~t~savri~H~  255 (355)
                         .  .+.    |+|    -|-+|-+|-=-+-..+++++|--
T Consensus       152 ---g--Wd~----~eTidsLirKaGY~g~It~~~r~~I~ltRY  185 (210)
T KOG3274         152 ---G--WDQ----IETIDSLIRKAGYKGPITEELRKSIKLTRY  185 (210)
T ss_pred             ---C--CCH----HHHHHHHHHHCCCCCCCCHHHHHHEEEEEE
T ss_conf             ---8--748----888999998447777567898712035674


No 41 
>pfam00435 Spectrin Spectrin repeat. Spectrin repeats are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference. The spectrin repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.
Probab=51.50  E-value=19  Score=16.78  Aligned_cols=85  Identities=12%  Similarity=0.117  Sum_probs=55.8

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             98999999999999870866002589999999999889999999999999986399999863100000023456676555
Q gi|254780753|r   15 DWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSILQETSDNLQR   94 (355)
Q Consensus        15 Dle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D~el~eE~~~el~~   94 (355)
                      +.+.+..=+.+-+..++++++..|+..++.+.+++..++.-+.....-...+.+....+ +.....+   ...+...+..
T Consensus         9 ~~~el~~Wl~e~~~~l~~~~~~~d~~~~~~l~~~h~~l~~ei~~~~~~i~~l~~~g~~L-~~~~~~~---~~~i~~~~~~   84 (105)
T pfam00435         9 DADDLESWIEEKEALLSSEDYGKDLEEVEALLKKHKALEAELAAHQDRVEQLNELAEKL-IDEGHYA---SEEIQERLEE   84 (105)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCCC---HHHHHHHHHH
T ss_conf             99999999999998864987789999999999999999999998888999999999999-8739995---6889999999


Q ss_pred             HHHHHHHHH
Q ss_conf             774015899
Q gi|254780753|r   95 IKLEVEYKQ  103 (355)
Q Consensus        95 l~~~le~LE  103 (355)
                      +...-+.|.
T Consensus        85 l~~~W~~L~   93 (105)
T pfam00435        85 LNERWEQLL   93 (105)
T ss_pred             HHHHHHHHH
T ss_conf             999999999


No 42 
>PRK08835 consensus
Probab=50.91  E-value=20  Score=16.71  Aligned_cols=88  Identities=18%  Similarity=0.088  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHCCC-----CCC-CHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHH----CC
Q ss_conf             9999999870866-----002-58999999999988999999999999-----------998639999986310----00
Q gi|254780753|r   22 RLSFLNTKTEDPH-----LWQ-NVIEAKMLMRERQHLDNAISFIKEIQ-----------DRLCDNLILLELALE----ED   80 (355)
Q Consensus        22 rl~eLE~~lsdp~-----fW~-D~~kAqkl~KE~s~L~~iV~~~~~l~-----------~~l~Dl~eL~ELa~e----e~   80 (355)
                      ++-.+-..+.|+.     +=. -++-|.++.+++.+|+.+++..+++.           ..+.+-.+..-|.++    ..
T Consensus       175 qviD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~Iy~nld~Ik~~~~rg~kk~~ekL~e~~e~A~LSk~LaTI~~  254 (931)
T PRK08835        175 LIIDYLALMGDKVDNIPGVPGVGDKTATALLQGIGGLDALYDNLDDIAALGFRGSKTMAKKLVDNKDNAYLSYELATIKL  254 (931)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             98999997188646889999745888999999848699999769861444331056899999987999999898742033


Q ss_pred             CCHHH---HH---HHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             00023---45---6676555774015899887630
Q gi|254780753|r   81 DCSIL---QE---TSDNLQRIKLEVEYKQFESLLS  109 (355)
Q Consensus        81 D~el~---eE---~~~el~~l~~~le~LE~~~Lls  109 (355)
                      |-.+-   ++   -.-...++...++++|+..|++
T Consensus       255 Dvpl~~~le~l~~~~pd~~~L~~~f~eleFksll~  289 (931)
T PRK08835        255 DVELEETPESLLKQEPNKDELIKLYGQLTFKSWLN  289 (931)
T ss_pred             CCCCCCCHHHHHCCCCCHHHHHHHHHHHHCHHHHH
T ss_conf             55678898997307999999999999974789999


No 43 
>PRK09225 threonine synthase; Validated
Probab=49.50  E-value=5.6  Score=20.59  Aligned_cols=50  Identities=26%  Similarity=0.338  Sum_probs=35.6

Q ss_pred             CCCCEEEEEECCCCCHHHH-HH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             7662489982177870277-89-9999998999987753113444205454585
Q gi|254780753|r  113 DSNDAYLEVHAGAGGTESQ-DW-ANMLLRMYTRWAEKRKFKTEALEIHDGEEAG  164 (355)
Q Consensus       113 D~~nailEI~AGaGG~EA~-dw-A~~L~rMY~r~ae~~gwk~evi~~~~~e~~G  164 (355)
                      +++--+||+--|-  |=|- |+ ++.|.+|+..+..+++=++-|+-.+.||-|+
T Consensus        95 ~~~~~vlELfHGP--T~AFKD~alq~l~~l~~~~l~~~~~~~~Il~ATSGDTG~  146 (465)
T PRK09225         95 DENLYVLELFHGP--TLAFKDFALQFLAQLLEYFLKKRGEKITILGATSGDTGS  146 (465)
T ss_pred             CCCEEEEEECCCC--CCHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHH
T ss_conf             5982798841088--531122589999999999974067506999738885089


No 44 
>PRK13520 L-tyrosine decarboxylase; Provisional
Probab=49.25  E-value=16  Score=17.35  Aligned_cols=95  Identities=17%  Similarity=0.124  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEE--
Q ss_conf             765557740158998876303457662489982177870277899999998999987753113444205454585013--
Q gi|254780753|r   90 DNLQRIKLEVEYKQFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKS--  167 (355)
Q Consensus        90 ~el~~l~~~le~LE~~~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~--  167 (355)
                      ....+++.++-.. +..|+..| |....+     -+|||||.+.|--.+|   .+                  ++++.  
T Consensus        59 P~~~~mE~~vv~~-~a~l~g~p-~~~G~~-----tsGGTes~l~Al~aaR---~~------------------~~~~~p~  110 (375)
T PRK13520         59 PGTAKLEREVVRM-LGELLHLP-DAYGYI-----TSGGTEANIQAVRAAR---NL------------------ADAEKPN  110 (375)
T ss_pred             HHHHHHHHHHHHH-HHHHCCCC-CCEEEE-----ECHHHHHHHHHHHHHH---HH------------------CCCCCCE
T ss_conf             7799999999999-99980999-880899-----5618999999999997---62------------------6899987


Q ss_pred             EEEEEECCCCCHHHEEECCEEEEEEECCCCCCCEEE----------EEEEEEEECCC
Q ss_conf             468850556100000101206898730466665035----------66887885034
Q gi|254780753|r  168 ATLLIKGPNAYGWLKGEQGVHRLVRISPYDSNSRRH----------TSFSSIWVYPV  214 (355)
Q Consensus       168 ~~~~I~G~~ayg~Lk~E~GvHRv~Ri~~~~s~gR~h----------TS~a~V~V~P~  214 (355)
                      +++.....+++...-.--|+ ++++||..+ ++|..          ..++-|...|.
T Consensus       111 iv~~~~aH~s~~Kaa~~~gi-~~~~vp~d~-~~~~d~~~l~~~i~~~ti~vvatagt  165 (375)
T PRK13520        111 IVVPESAHFSFDKAADMLGL-ELRRAPLDE-DYRVDVKSVEDLIDDNTIGIVGIAGT  165 (375)
T ss_pred             EEEECCCHHHHHHHHHHCCC-EEEEEEECC-CCCCCHHHHHHHHHHCCEEEEEECCC
T ss_conf             99967316999999997495-569940388-88698999999886495799992588


No 45 
>PRK07456 consensus
Probab=45.90  E-value=23  Score=16.19  Aligned_cols=93  Identities=20%  Similarity=0.147  Sum_probs=51.1

Q ss_pred             CCHHHHHHH-------HHHHHHHHHCC--------CCCCCHHHHHHHHHHHHHHHHHHHHHHHH--------------HH
Q ss_conf             498999999-------99999987086--------60025899999999998899999999999--------------99
Q gi|254780753|r   14 FDWDNAVQR-------LSFLNTKTEDP--------HLWQNVIEAKMLMRERQHLDNAISFIKEI--------------QD   64 (355)
Q Consensus        14 fDle~~~~r-------l~eLE~~lsdp--------~fW~D~~kAqkl~KE~s~L~~iV~~~~~l--------------~~   64 (355)
                      +|.+...++       +-.+-..+.|+        .+  -++-|.++.+++.+|+.+++..+++              ..
T Consensus       177 ~d~~~V~ek~GV~P~qiiD~lAL~GDsSDNIPGVpGI--G~KTA~kLL~eyGsLE~Iyen~d~i~~~k~~~~~IKgkl~e  254 (975)
T PRK07456        177 INEAGVKEKLGVAPEQVVDLKALTGDSSDNIPGVKGV--GPKTAINLLKENGDLDGIYKALDEIEGEKAYRGAIKGALKK  254 (975)
T ss_pred             ECHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCC--CHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCHHHHH
T ss_conf             2699999986959899899999728865688999985--59999999998499999998287620011111234448899


Q ss_pred             HHHHHHHHH----HHHHHCCCCHHH-----HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             986399999----863100000023-----45667655577401589988763
Q gi|254780753|r   65 RLCDNLILL----ELALEEDDCSIL-----QETSDNLQRIKLEVEYKQFESLL  108 (355)
Q Consensus        65 ~l~Dl~eL~----ELa~ee~D~el~-----eE~~~el~~l~~~le~LE~~~Ll  108 (355)
                      .+.+-.+..    +|+.=..|..+-     .--.-....+...++++|+..|+
T Consensus       255 ~L~~~~d~A~LSkeLvTI~~Dvpl~~~~dl~~~~~d~~~L~~lf~elEF~sLl  307 (975)
T PRK07456        255 KLKNDKDNAYLSRFLAEILVDVPLPLDESLELTGFDQELLSPLLEKLELNSLL  307 (975)
T ss_pred             HHHHHHHHHHHHHHHHHEEECCCCCCCHHHCCCCCCHHHHHHHHHHHCCHHHH
T ss_conf             99997999998899765001798886555426899999999999995547899


No 46 
>pfam05192 MutS_III MutS domain III. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam01624 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterized in.
Probab=45.13  E-value=24  Score=16.11  Aligned_cols=130  Identities=18%  Similarity=0.179  Sum_probs=59.1

Q ss_pred             HCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             54989999999999998708660025899999999998899999999----------99999986399999863100000
Q gi|254780753|r   13 LFDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFI----------KEIQDRLCDNLILLELALEEDDC   82 (355)
Q Consensus        13 ~fDle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~----------~~l~~~l~Dl~eL~ELa~ee~D~   82 (355)
                      ..|++.+..|++-++..+..+++.+   ..+..+|....++.++..+          ..+.+.+.-+..+.++..+.+..
T Consensus        53 l~d~~~I~~R~d~Ve~l~~~~~~~~---~l~~~Lk~i~Dlerl~~ri~~~~~~~~~~~~l~~~l~~i~~i~~~l~~~~~~  129 (306)
T pfam05192        53 LRDREEINARLDAVEELLEDPELRQ---TLRELLKRVPDLERLLSRLALGRANPRDLLRLRDSLERLPTIKELLEELDSP  129 (306)
T ss_pred             CCCHHHHHHHHHHHHHHHHCHHHHH---HHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCH
T ss_conf             6699999999999999985989999---9999986489789999999828978899999999999999999999857884


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             023456676555774015899887630345766248998217787027789999999899998775311344
Q gi|254780753|r   83 SILQETSDNLQRIKLEVEYKQFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEA  154 (355)
Q Consensus        83 el~eE~~~el~~l~~~le~LE~~~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~ev  154 (355)
                      ............+....+.++-...+..+....+++ -|++|.-.        +|-.+...|.+-..+-.++
T Consensus       130 ~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~-~i~~g~~~--------~LD~~~~~~~~~~~~l~~~  192 (306)
T pfam05192       130 LLLKELRKSIDDLSELLDLLETAINEDPPLLIREGG-VIKSGYDA--------ELDELRDLRDEAKEWIAEL  192 (306)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHCCHHHHCCCCC-EECCCCCH--------HHHHHHHHHHHHHHHHHHH
T ss_conf             678888744234899999999998246176556788-54899887--------8999999999789999999


No 47 
>KOG4603 consensus
Probab=44.22  E-value=25  Score=16.01  Aligned_cols=12  Identities=17%  Similarity=0.576  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999998999987
Q gi|254780753|r  135 NMLLRMYTRWAE  146 (355)
Q Consensus       135 ~~L~rMY~r~ae  146 (355)
                      +-.+|||.+||.
T Consensus       155 ~~v~~~y~~~~~  166 (201)
T KOG4603         155 EQVYREYQKYCK  166 (201)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 48 
>pfam05616 Neisseria_TspB Neisseria meningitidis TspB protein. This family consists of several Neisseria meningitidis TspB virulence factor proteins.
Probab=44.06  E-value=19  Score=16.74  Aligned_cols=93  Identities=16%  Similarity=0.215  Sum_probs=45.0

Q ss_pred             CCCCCCCEEEEEECC----CCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHCCCC-----------CCCCEEEEEEEEE
Q ss_conf             345766248998217----7870277899999998999987753-11344420545-----------4585013468850
Q gi|254780753|r  110 GEADSNDAYLEVHAG----AGGTESQDWANMLLRMYTRWAEKRK-FKTEALEIHDG-----------EEAGIKSATLLIK  173 (355)
Q Consensus       110 ~e~D~~nailEI~AG----aGG~EA~dwA~~L~rMY~r~ae~~g-wk~evi~~~~~-----------e~~GiK~~~~~I~  173 (355)
                      ..+--..|+.-.+.|    .-|+++-.|+.--|.|-.||.|... =|++.|....-           ..-||++      
T Consensus       197 ~~y~~~~c~f~wNGg~C~V~~g~d~r~~isfsl~rn~kykEemdakK~eEIlslkvDaNPd~fI~aTGyPgY~E------  270 (502)
T pfam05616       197 RNYNFSRCYFNWNGGNCNVGKGDDARSFISFSLIRNPKYKEEMDAKKLEEILSLKVDANPDKYIQATGYPGYSE------  270 (502)
T ss_pred             HHCCCCCCEEECCCCCCEECCCCCCCCEEEEEEEECCCHHHHCCHHHHHHHHHHCCCCCCCCCEECCCCCCCCC------
T ss_conf             10144676575058754332587622147899870764054407577899875013689862111378876333------


Q ss_pred             CCCCCHHHEEECCEEEEEEE-CCCCCCCE-EE-----------EEEEEEEECCCCC
Q ss_conf             55610000010120689873-04666650-35-----------6688788503442
Q gi|254780753|r  174 GPNAYGWLKGEQGVHRLVRI-SPYDSNSR-RH-----------TSFSSIWVYPVVD  216 (355)
Q Consensus       174 G~~ayg~Lk~E~GvHRv~Ri-~~~~s~gR-~h-----------TS~a~V~V~P~~~  216 (355)
                            ..+-..|+  +|-+ |.|+-+|+ .|           .++|.|.|.|-++
T Consensus       271 ------~vkV~~GT--~V~mGPVt~~nG~pvqvv~tfg~dsqGNtta~Vq~i~rPd  318 (502)
T pfam05616       271 ------KVEVAPGT--KVNMGPVTDRNGNPVQVVATFGRDSQGNTTVDVQVIPRPD  318 (502)
T ss_pred             ------CCCCCCCC--EEEECCCCCCCCCEEEEEEEECCCCCCCEEEEEEECCCCC
T ss_conf             ------32138987--6752686588998678998755678996256557435898


No 49 
>PRK00132 rpsI 30S ribosomal protein S9; Reviewed
Probab=43.38  E-value=14  Score=17.82  Aligned_cols=30  Identities=20%  Similarity=0.348  Sum_probs=22.0

Q ss_pred             CCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEE
Q ss_conf             666650356688788503442221112345503
Q gi|254780753|r  196 YDSNSRRHTSFSSIWVYPVVDDSIEIEISESDC  228 (355)
Q Consensus       196 ~~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl  228 (355)
                      |-+.|||.||.|.|.+.|--   -.|.||..++
T Consensus         6 ~~~~GrRKtaiArv~l~~G~---G~i~INgk~~   35 (130)
T PRK00132          6 YYGTGRRKSAVARVRLKPGS---GKITVNGRDL   35 (130)
T ss_pred             EEEECCCCCEEEEEEEECCC---CEEEECCEEH
T ss_conf             99855760589999998688---5799958129


No 50 
>pfam03962 Mnd1 Mnd1 family. This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.
Probab=43.09  E-value=26  Score=15.89  Aligned_cols=119  Identities=13%  Similarity=0.222  Sum_probs=65.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             6002589999999999889999999999999986399999863100-000023456676555774015899887630345
Q gi|254780753|r   34 HLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEE-DDCSILQETSDNLQRIKLEVEYKQFESLLSGEA  112 (355)
Q Consensus        34 ~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee-~D~el~eE~~~el~~l~~~le~LE~~~Lls~e~  112 (355)
                      =||+=|..+..  +....+...-..+..+...+.++..-++-++.. ++.+-...+..++..+...++.|..++.--...
T Consensus        55 ~yWsFps~~~~--~~~~~~~~L~~~~~~~~~~i~~l~~~i~~~k~~r~~~~er~~ll~~l~~l~~~~~~L~~el~~~~~~  132 (188)
T pfam03962        55 YYWSFPSQAKN--KLKTRLEKLKKELEELKQRIAELQAQIEKLKVGREETEERTELLEELKQLEKELKKLKAELEKYEKN  132 (188)
T ss_pred             EEEECCHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             67658679999--9999999999999999999999999999998658551669999999999999999999999998836


Q ss_pred             CCCCEEEEEECCC--CCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Q ss_conf             7662489982177--8702778999999989999877-531134442
Q gi|254780753|r  113 DSNDAYLEVHAGA--GGTESQDWANMLLRMYTRWAEK-RKFKTEALE  156 (355)
Q Consensus       113 D~~nailEI~AGa--GG~EA~dwA~~L~rMY~r~ae~-~gwk~evi~  156 (355)
                      |+. .|=.++..+  -=..|.-|+..+|-+ .-|+.+ -|..-+.++
T Consensus       133 Dp~-~i~~~~~~~~~~~~aanrWTDNI~~l-~~~~~kk~g~~~~~l~  177 (188)
T pfam03962       133 DPE-RIEKLKEETKVAKEAANRWTDNIFSL-ESYLSKKFGLDEEQLR  177 (188)
T ss_pred             CHH-HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHCCCCHHHHH
T ss_conf             999-99999999999999999988319999-9999986299999999


No 51 
>PRK00474 rps9p 30S ribosomal protein S9P; Reviewed
Probab=42.96  E-value=13  Score=17.88  Aligned_cols=32  Identities=13%  Similarity=0.158  Sum_probs=23.5

Q ss_pred             CCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             6665035668878850344222111234550369985
Q gi|254780753|r  197 DSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTY  233 (355)
Q Consensus       197 ~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~  233 (355)
                      -+.|||.||.|.|.+.|-   +-.|.||..++  +.|
T Consensus         5 ~atGrRKtaiArv~l~~G---~G~i~INgk~~--~~y   36 (132)
T PRK00474          5 ITSGKRKTAIARATIKEG---KGRVRINGVPL--ELY   36 (132)
T ss_pred             EEECCCCCEEEEEEEECC---CCEEEECCEEH--HHH
T ss_conf             876787667999999828---73598898758--996


No 52 
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=42.70  E-value=14  Score=17.67  Aligned_cols=33  Identities=12%  Similarity=0.308  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCC
Q ss_conf             877531134442054545850134688505561
Q gi|254780753|r  145 AEKRKFKTEALEIHDGEEAGIKSATLLIKGPNA  177 (355)
Q Consensus       145 ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~a  177 (355)
                      +.++||+.+-+...+++..|+...|+-+.|+..
T Consensus        23 FsrRGyNI~SL~Vg~te~~~~SRmTivv~gd~~   55 (76)
T PRK06737         23 FARRGYYISSLNLNERDTSGVSEMKLTAVCTEN   55 (76)
T ss_pred             HHCCCCCEEEEEECCCCCCCCEEEEEEEECCCH
T ss_conf             621665711256746679982079999977813


No 53 
>pfam03357 Snf7 Snf7. This family of proteins are involved in protein sorting and transport from the endosome to the vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes play an important role in the degradation of both lipids and cellular proteins. In order to perform this degradative function, vacuoles/lysosomes contain numerous hydrolases which have been transported in the form of inactive precursors via the biosynthetic pathway and are proteolytically activated upon delivery to the vacuole/lysosome. The delivery of transmembrane proteins, such as activated cell surface receptors to the lumen of the vacuole/lysosome, either for degradation/downregulation, or in the case of hydrolases, for proper localisation, requires the formation of multivesicular bodies (MVBs). These late endosomal structures are formed by invaginating and budding of the limiting membrane into the lumen of the compartment. During this process, a subset of the endosomal membrane proteins is sorted into the form
Probab=42.15  E-value=26  Score=15.80  Aligned_cols=40  Identities=15%  Similarity=0.199  Sum_probs=28.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2589999999999889999999999999986399999863
Q gi|254780753|r   37 QNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELA   76 (355)
Q Consensus        37 ~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa   76 (355)
                      ++...|..+.|....+++.++.+......++.+..-++-+
T Consensus        38 g~k~~A~~~lk~kk~~ek~~~~~~~~~~~L~~~~~~ie~a   77 (169)
T pfam03357        38 GNKDAALILLKQKKRYEKQLDQLDGQLANLEQVRMAIENA   77 (169)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6399999999999999999999999999999999999999


No 54 
>PRK00294 hscB co-chaperone HscB; Provisional
Probab=41.14  E-value=27  Score=15.69  Aligned_cols=50  Identities=16%  Similarity=0.102  Sum_probs=28.0

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCHHHHHH--------HHHHHHHHHHHHHHHHHHH
Q ss_conf             4989999999999998708660025899999--------9999988999999999999
Q gi|254780753|r   14 FDWDNAVQRLSFLNTKTEDPHLWQNVIEAKM--------LMRERQHLDNAISFIKEIQ   63 (355)
Q Consensus        14 fDle~~~~rl~eLE~~lsdp~fW~D~~kAqk--------l~KE~s~L~~iV~~~~~l~   63 (355)
                      +|...+..++..|..++-=--|-+-+...+.        |++-|..|+.-+.....+.
T Consensus        18 iD~~~L~~~y~~LQ~~~HPDrf~~~s~~e~~~a~~~sa~iN~AY~tLk~pl~RA~yLL   75 (173)
T PRK00294         18 LDLDQLATRYRELAREVHPDRFADAPEREQRLALERSAALNEAYQTLKSAPRRARYLL   75 (173)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             7999999999999998695736798999999999999999999999759999999999


No 55 
>PRK07898 consensus
Probab=40.58  E-value=28  Score=15.63  Aligned_cols=87  Identities=16%  Similarity=0.144  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHCCC-----CCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH----CCCCHH---
Q ss_conf             9999999870866-----002-589999999999889999999999999986----39999986310----000002---
Q gi|254780753|r   22 RLSFLNTKTEDPH-----LWQ-NVIEAKMLMRERQHLDNAISFIKEIQDRLC----DNLILLELALE----EDDCSI---   84 (355)
Q Consensus        22 rl~eLE~~lsdp~-----fW~-D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~----Dl~eL~ELa~e----e~D~el---   84 (355)
                      ++-.+-..+.|+.     +=. -++-|.++..+|.+|+.+++..++++..+.    +-.+..-|.++    ..|-.+   
T Consensus       189 qviD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~I~~n~d~IkgK~~e~L~~~~d~a~LSk~LvTI~~Dvpl~~~  268 (902)
T PRK07898        189 QYPDFAALRGDPSDNLPGIPGVGEKTAAKWIAQYGSLDGLVDHADEIKGKVGDALRANLESVVRNRELTELVRDVPLPVT  268 (902)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             99999998188645799999844788999999767789999998752157788999659999998998688754888878


Q ss_pred             ---HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---345667655577401589988763
Q gi|254780753|r   85 ---LQETSDNLQRIKLEVEYKQFESLL  108 (355)
Q Consensus        85 ---~eE~~~el~~l~~~le~LE~~~Ll  108 (355)
                         +.-..-....+...+++||+..|+
T Consensus       269 le~l~~~~~d~~~L~~lf~eLEF~sL~  295 (902)
T PRK07898        269 PDDLRLQPWDRDAVHRLFDDLEFRVLR  295 (902)
T ss_pred             HHHHCCCCCCHHHHHHHHHHHCCHHHH
T ss_conf             887124899999999999984667899


No 56 
>pfam02815 MIR MIR domain. The MIR (protein mannosyltransferase, IP3R and RyR) domain is a domain that may have a ligand transferase function.
Probab=39.62  E-value=29  Score=15.53  Aligned_cols=36  Identities=25%  Similarity=0.419  Sum_probs=27.6

Q ss_pred             EEEECCCCCCCCCCCCCCEEEEEEECCCHHHHHHHH
Q ss_conf             998538886554427310035887469747766555
Q gi|254780753|r  230 IDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQ  265 (355)
Q Consensus       230 i~~~rssg~ggq~vn~t~savri~H~ptgi~v~~q~  265 (355)
                      ++.-...|.+...|-..+|-+||.|..||.-+...+
T Consensus       120 ~~~~~~~~~~~~~ik~~~s~frL~H~~tgc~L~s~~  155 (189)
T pfam02815       120 FELKSTTGMGQDRIKPGDSKVRLRHACTGCWLFSHN  155 (189)
T ss_pred             EEECCCCCCCCCEEEEEEEEEEEEECCCCEEEEECC
T ss_conf             763367777778389811599999999688998689


No 57 
>KOG0581 consensus
Probab=39.51  E-value=18  Score=17.04  Aligned_cols=55  Identities=29%  Similarity=0.318  Sum_probs=33.9

Q ss_pred             CEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCHHHHH
Q ss_conf             503566887885034422211123455036998538886554427310035887469747766
Q gi|254780753|r  200 SRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQ  262 (355)
Q Consensus       200 gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~ptgi~v~  262 (355)
                      ++.-+|........+++++ +..|...||..--.=.+|.|| .|      ....|+|||....
T Consensus        54 ~~~~~~~~~~~~~~~l~~~-~~~i~~~dle~~~~lG~G~gG-~V------~kv~Hk~t~~i~A  108 (364)
T KOG0581          54 PLSKISLSSSSANSELSED-DNGISLSDLERLGVLGSGNGG-TV------YKVRHKPTGKIYA  108 (364)
T ss_pred             CCCCCCCCCCCCCCCCCCC-CCCCCHHHHHHHHHCCCCCCC-EE------EEEEECCCCEEEE
T ss_conf             6433322454432234665-333377775423112467873-79------9999737885899


No 58 
>TIGR03627 arch_S9P archaeal ribosomal protein S9P. This model describes exclusively the archaeal ribosomal protein S9P. Homologous eukaryotic and bacterial ribosomal proteins are excluded from this model.
Probab=39.25  E-value=16  Score=17.29  Aligned_cols=32  Identities=13%  Similarity=0.158  Sum_probs=22.9

Q ss_pred             CCCCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             6665035668878850344222111234550369985
Q gi|254780753|r  197 DSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTY  233 (355)
Q Consensus       197 ~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~  233 (355)
                      -+.|||.||.|.|.+.|--   -.|.||..++  +.|
T Consensus         3 ~~tGrRKtaiA~v~l~~G~---G~i~VNg~~~--~~~   34 (130)
T TIGR03627         3 ITSGKRKTAIARATIREGK---GRVRINGVPV--ELY   34 (130)
T ss_pred             EEECCCCCEEEEEEEECCC---EEEEECCEEH--HHH
T ss_conf             5567680779999999171---7999999879--994


No 59 
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH; InterPro: IPR011909   Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system .    Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond.   Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed  that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro.    NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterised by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase .; GO: 0006118 electron transport, 0045454 cell redox homeostasis.
Probab=39.04  E-value=14  Score=17.75  Aligned_cols=41  Identities=20%  Similarity=0.449  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCC-------CEEEEEEEEE-CCCCCH
Q ss_conf             9899998775311344420545458-------5013468850-556100
Q gi|254780753|r  139 RMYTRWAEKRKFKTEALEIHDGEEA-------GIKSATLLIK-GPNAYG  179 (355)
Q Consensus       139 rMY~r~ae~~gwk~evi~~~~~e~~-------GiK~~~~~I~-G~~ayg  179 (355)
                      .|=-||-+.+|..+|.++++.-+++       ||+.|=+-+. |..++.
T Consensus        13 kmTKk~L~~~~i~Fe~inid~~pea~d~vk~lGF~~~PVi~~~g~~~~S   61 (72)
T TIGR02194        13 KMTKKALEEHGIAFEEINIDEQPEAVDYVKALGFRQVPVIVAEGDESWS   61 (72)
T ss_pred             CHHHHHHHHCCCCEEEEECCCCHHHHHHHHHCCCEECCEEEECCCEEEE
T ss_conf             1577667637996157635888437899987486307626767970021


No 60 
>PRK08928 consensus
Probab=38.56  E-value=30  Score=15.42  Aligned_cols=88  Identities=15%  Similarity=0.151  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHCCC-----CCC-CHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHH----CCCCHHH-
Q ss_conf             9999999870866-----002-589999999999889999999999999-----98639999986310----0000023-
Q gi|254780753|r   22 RLSFLNTKTEDPH-----LWQ-NVIEAKMLMRERQHLDNAISFIKEIQD-----RLCDNLILLELALE----EDDCSIL-   85 (355)
Q Consensus        22 rl~eLE~~lsdp~-----fW~-D~~kAqkl~KE~s~L~~iV~~~~~l~~-----~l~Dl~eL~ELa~e----e~D~el~-   85 (355)
                      ++-++-..+.|+.     +=. -++-|.++..++.+|+.+++..+++..     .+.+-.+..-|.++    ..|-.+- 
T Consensus       173 qiiD~laL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~Iy~n~d~Ik~~K~re~L~e~ke~a~lSkeLvTI~~Dvpl~~  252 (861)
T PRK08928        173 KLLDVMALTGDRSDNIPGVPSIGPKTAAKLITQFGSLENILNSLDQISSNKQRETLQNSREQALISRQLIGLCSNVDLDF  252 (861)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             99999998087646889998856289999999679799999988611302467888855888999899864354788764


Q ss_pred             --HH---HHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             --45---6676555774015899887630
Q gi|254780753|r   86 --QE---TSDNLQRIKLEVEYKQFESLLS  109 (355)
Q Consensus        86 --eE---~~~el~~l~~~le~LE~~~Lls  109 (355)
                        +.   -......+...+++||+..|++
T Consensus       253 ~l~~l~~~~~d~~~L~~lf~elEF~sLlk  281 (861)
T PRK08928        253 DLNKLEWSPPNSEKLTGFLKKYEFKSLIK  281 (861)
T ss_pred             CHHHHCCCCCCHHHHHHHHHHHCCHHHHH
T ss_conf             67873448999999999999826789999


No 61 
>COG1256 FlgK Flagellar hook-associated protein [Cell motility and secretion]
Probab=38.46  E-value=30  Score=15.41  Aligned_cols=19  Identities=26%  Similarity=0.398  Sum_probs=10.7

Q ss_pred             HHHHHHHHHHHHHHHHCCC
Q ss_conf             8999999999999870866
Q gi|254780753|r   16 WDNAVQRLSFLNTKTEDPH   34 (355)
Q Consensus        16 le~~~~rl~eLE~~lsdp~   34 (355)
                      ++....-|.+|+..+++|+
T Consensus        87 ~~t~~~~L~~le~ll~~~~  105 (552)
T COG1256          87 LDTRASQLSQLESLLSEPS  105 (552)
T ss_pred             HHHHHHHHHHHHHHHCCCC
T ss_conf             9999999999999847976


No 62 
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=38.10  E-value=30  Score=15.37  Aligned_cols=49  Identities=16%  Similarity=0.097  Sum_probs=27.3

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH--------HHHHHHHHHHHHHHHHH
Q ss_conf             49899999999999987086600258999999--------99998899999999999
Q gi|254780753|r   14 FDWDNAVQRLSFLNTKTEDPHLWQNVIEAKML--------MRERQHLDNAISFIKEI   62 (355)
Q Consensus        14 fDle~~~~rl~eLE~~lsdp~fW~D~~kAqkl--------~KE~s~L~~iV~~~~~l   62 (355)
                      +|...+..++..|..++----|-+-+..-+.+        +.-|+.|+.-+....-+
T Consensus        16 ID~~~L~~~y~~LQ~~~HPDkf~~~s~~Ek~~s~~~Ss~iN~AY~tLkdpl~RA~YL   72 (173)
T PRK01773         16 LDQALLSERYLALQKSLHPDNFANSSAQEQRLAMQKSAEVNDALQILKDPILRAEAI   72 (173)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH
T ss_conf             799999999999999869685668999999999999999999999974888899999


No 63 
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=38.09  E-value=30  Score=15.37  Aligned_cols=54  Identities=15%  Similarity=0.089  Sum_probs=28.1

Q ss_pred             HCCHHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             549899999999999987086-600258999999999988999999999999998
Q gi|254780753|r   13 LFDWDNAVQRLSFLNTKTEDP-HLWQNVIEAKMLMRERQHLDNAISFIKEIQDRL   66 (355)
Q Consensus        13 ~fDle~~~~rl~eLE~~lsdp-~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l   66 (355)
                      |+|+.-++...+.+.+.+..- ..+.+-.+.-++-++...+...++.++...+.+
T Consensus         1 mld~k~ir~n~d~v~~~l~~r~~~~~~~~~~~~ld~~~r~~~~~~e~l~~~rn~~   55 (429)
T COG0172           1 MLDLKLIRENPDAVREKLKKRGGDALDVDKLLELDEERRKLLRELEELQAERNEL   55 (429)
T ss_pred             CCHHHHHHHCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9648776509999999876348837678999999999999999999999998899


No 64 
>pfam00380 Ribosomal_S9 Ribosomal protein S9/S16. This family includes small ribosomal subunit S9 from prokaryotes and S16 from eukaryotes.
Probab=37.44  E-value=20  Score=16.66  Aligned_cols=26  Identities=27%  Similarity=0.487  Sum_probs=19.1

Q ss_pred             CEEEEEEEEEEECCCCCCCCCCCCCCCEE
Q ss_conf             50356688788503442221112345503
Q gi|254780753|r  200 SRRHTSFSSIWVYPVVDDSIEIEISESDC  228 (355)
Q Consensus       200 gR~hTS~a~V~V~P~~~~~~~i~i~~~dl  228 (355)
                      |||.||.|.|.+.|--   -.|.||..++
T Consensus         1 GrRKtaiArv~l~~G~---G~i~INg~~~   26 (121)
T pfam00380         1 GRRKTAVARVWLKPGS---GKITINGKPL   26 (121)
T ss_pred             CCCCCEEEEEEEEECC---CEEEECCCCH
T ss_conf             9984589999998077---6799989328


No 65 
>COG0103 RpsI Ribosomal protein S9 [Translation, ribosomal structure and biogenesis]
Probab=36.93  E-value=21  Score=16.55  Aligned_cols=30  Identities=10%  Similarity=0.207  Sum_probs=20.6

Q ss_pred             CCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEE
Q ss_conf             666650356688788503442221112345503
Q gi|254780753|r  196 YDSNSRRHTSFSSIWVYPVVDDSIEIEISESDC  228 (355)
Q Consensus       196 ~~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl  228 (355)
                      +-+.|||.||.|.|.+.|. .  -.|.||..++
T Consensus         6 ~~~tGkRK~AvArv~l~~g-~--G~i~vNg~~~   35 (130)
T COG0103           6 VYTTGKRKSAVARVRLVPG-K--GKITVNGRPL   35 (130)
T ss_pred             EEEECCCCCEEEEEEEECC-C--CEEEECCCCH
T ss_conf             4640554326899999768-7--5899989189


No 66 
>pfam07050 consensus
Probab=36.75  E-value=32  Score=15.23  Aligned_cols=56  Identities=18%  Similarity=0.154  Sum_probs=27.1

Q ss_pred             CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             56899999886549899999999999987086600258999999999988999999999999
Q gi|254780753|r    2 KLSRQLNCLGGLFDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQ   63 (355)
Q Consensus         2 EL~~rl~~l~~~fDle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~   63 (355)
                      +|-...+.|..|+--......+..-++.+.      +..++|.+.+++..++...+.+..+-
T Consensus         9 ~Il~~a~eLa~mI~~se~~~~Y~~ak~~~~------~d~~~q~li~~f~~~ke~ye~~q~fg   64 (145)
T pfam07050         9 DILDQAEQLADMILQSEEVENYRKAKQALE------NDREAQQLIQEFLKLKEQYEEVQRFG   64 (145)
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHHHHH------CCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999981899999999999998------48999999999999999999999874


No 67 
>CHL00079 rps9 ribosomal protein S9
Probab=36.58  E-value=18  Score=17.03  Aligned_cols=31  Identities=23%  Similarity=0.313  Sum_probs=22.4

Q ss_pred             CCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCEE
Q ss_conf             4666650356688788503442221112345503
Q gi|254780753|r  195 PYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDC  228 (355)
Q Consensus       195 ~~~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl  228 (355)
                      -+-+.|||.||.|.|.+.|--.   .|.||..++
T Consensus         8 ~~y~tGkRKtsiArv~i~~GsG---~i~VN~k~l   38 (134)
T CHL00079          8 LYYGTGRRKCAVAQVRLVPGTG---EIIINGKPG   38 (134)
T ss_pred             EEEEECCCCCEEEEEEEECCCC---EEEEECCCH
T ss_conf             9998668705899999986983---699959709


No 68 
>pfam06160 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.
Probab=36.44  E-value=32  Score=15.19  Aligned_cols=38  Identities=5%  Similarity=0.037  Sum_probs=16.0

Q ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999987086600258999999999988999999999
Q gi|254780753|r   23 LSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIK   60 (355)
Q Consensus        23 l~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~   60 (355)
                      +.+++..+.+.+.++|.-++.+..+.++.+...++.++
T Consensus        77 l~~ie~~l~~ae~~~~~~rf~ka~~~i~~~~~~i~~~e  114 (559)
T pfam06160        77 LPDIEELLFEAEELNDKFRFLKAKKAIKEIEELLDTIE  114 (559)
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             25699999999999860628999999999999999999


No 69 
>KOG4519 consensus
Probab=36.22  E-value=32  Score=15.17  Aligned_cols=26  Identities=27%  Similarity=0.369  Sum_probs=15.1

Q ss_pred             HHHCCCCCCCCEEEEEECCCCCHHHH
Q ss_conf             76303457662489982177870277
Q gi|254780753|r  106 SLLSGEADSNDAYLEVHAGAGGTESQ  131 (355)
Q Consensus       106 ~Lls~e~D~~nailEI~AGaGG~EA~  131 (355)
                      .||.+-.--..+++---|||||-+|.
T Consensus       387 ~lLD~~~sl~GVl~~gvPGAGGfDAi  412 (459)
T KOG4519         387 QLLDSTMSLEGVLLAGVPGAGGFDAI  412 (459)
T ss_pred             HHHHHHHCCCCEEEECCCCCCCCCEE
T ss_conf             57666640566378446678874448


No 70 
>cd01560 Thr-synth_2 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria, archaebacteria and eubacterial groups. This CD, Thr-synth_2, includes enzymes from fungi and eubacterial groups, as well as, metazoan threonine synthase-like proteins.
Probab=36.16  E-value=6.6  Score=20.11  Aligned_cols=51  Identities=20%  Similarity=0.241  Sum_probs=35.8

Q ss_pred             CCCCCEEEEEECCCCCHHHH-HH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             57662489982177870277-89-9999998999987753113444205454585
Q gi|254780753|r  112 ADSNDAYLEVHAGAGGTESQ-DW-ANMLLRMYTRWAEKRKFKTEALEIHDGEEAG  164 (355)
Q Consensus       112 ~D~~nailEI~AGaGG~EA~-dw-A~~L~rMY~r~ae~~gwk~evi~~~~~e~~G  164 (355)
                      -+++.-+||.--|--  =|- |+ .+.|-+|+..+..+++=++.|+-.+.||-|+
T Consensus        93 l~~~~~vLELFHGPT--lAFKD~a~q~l~~l~~~~l~~~~~~~~Il~ATSGDTGs  145 (460)
T cd01560          93 LGDNLYVLELFHGPT--LAFKDMALQFLGRLLEYFLKRRNERITILVATSGDTGS  145 (460)
T ss_pred             ECCCCEEEEECCCCC--CHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHH
T ss_conf             149847887322884--14455689999999999974066347998578884189


No 71 
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2.   The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=35.21  E-value=13  Score=18.10  Aligned_cols=34  Identities=21%  Similarity=0.277  Sum_probs=19.3

Q ss_pred             EEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCC
Q ss_conf             88503442221112345503699853888655442731
Q gi|254780753|r  209 IWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTT  246 (355)
Q Consensus       209 V~V~P~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t  246 (355)
                      |.+.+..+....+.++++++    -.|=|.+||||+-.
T Consensus        17 V~i~~~~~~~~~V~V~~~~~----~~AIGk~G~Nvrla   50 (61)
T cd02134          17 VTVLDDEEKRARVVVPDDQL----GLAIGKGGQNVRLA   50 (61)
T ss_pred             EEECCCCCCEEEEEECHHHH----HHHHCCCCEEHHHH
T ss_conf             88447877379999885784----38766786709999


No 72 
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=34.53  E-value=34  Score=14.99  Aligned_cols=37  Identities=5%  Similarity=-0.021  Sum_probs=14.9

Q ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999998708660025899999999998899999999
Q gi|254780753|r   23 LSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFI   59 (355)
Q Consensus        23 l~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~   59 (355)
                      +.+++..+.+.+.++|.-++.+..+.++.+...++.+
T Consensus        81 l~~iee~l~~ae~~~~~~rf~kak~~l~~~~~~l~~~  117 (569)
T PRK04778         81 FPDIEELLFEAEDLNDKFRFFKAKHEINEIESLLDEI  117 (569)
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
T ss_conf             3569999999999987252899999999999999999


No 73 
>PRK10329 glutaredoxin-like protein; Provisional
Probab=34.22  E-value=18  Score=17.00  Aligned_cols=43  Identities=21%  Similarity=0.339  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCC-------CCEEEEEEEEECCCCCHHH
Q ss_conf             989999877531134442054545-------8501346885055610000
Q gi|254780753|r  139 RMYTRWAEKRKFKTEALEIHDGEE-------AGIKSATLLIKGPNAYGWL  181 (355)
Q Consensus       139 rMY~r~ae~~gwk~evi~~~~~e~-------~GiK~~~~~I~G~~ayg~L  181 (355)
                      .|=.||-+++|..|+++|++...+       .|++.+-+-+.|+..|.=+
T Consensus        15 ~aTKr~L~~~gI~y~~vdi~~dpea~~~vk~~G~~q~PVV~~~~~~wsGF   64 (81)
T PRK10329         15 HATKRAMESRGFDFEMINVDRVPEAADTLRAQGFRQLPVVIAGDLSWSGF   64 (81)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCHHHHHHHHHCCCCCCCEEEECCCEECCC
T ss_conf             98999999879942998589999999999976985599899699544360


No 74 
>pfam04983 RNA_pol_Rpb1_3 RNA polymerase Rpb1, domain 3. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Probab=33.91  E-value=30  Score=15.38  Aligned_cols=30  Identities=20%  Similarity=0.267  Sum_probs=20.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             870277899999998999987753113444
Q gi|254780753|r  126 GGTESQDWANMLLRMYTRWAEKRKFKTEAL  155 (355)
Q Consensus       126 GG~EA~dwA~~L~rMY~r~ae~~gwk~evi  155 (355)
                      |..+|..|...+.+|=.+|+...||.+-+-
T Consensus       127 G~~~~~~~ld~i~~l~~~~l~~~GfSvgi~  156 (158)
T pfam04983       127 GPEETVKFLDRLQKLGFRYLTKSGFSIGID  156 (158)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCEEEEEC
T ss_conf             989999999999999999999778679520


No 75 
>pfam07962 Swi3 Replication Fork Protection Component Swi3. Replication fork pausing is required to initiate a recombination events. More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1 Swi3, together with Swi1, define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilizes stalled replication forks. The Swi1-Swi3 complex is required for accurate replication, fork protection and replication checkpoint signalling
Probab=33.25  E-value=36  Score=14.85  Aligned_cols=27  Identities=33%  Similarity=0.514  Sum_probs=18.1

Q ss_pred             EECCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8217787027789999999899998775
Q gi|254780753|r  121 VHAGAGGTESQDWANMLLRMYTRWAEKR  148 (355)
Q Consensus       121 I~AGaGG~EA~dwA~~L~rMY~r~ae~~  148 (355)
                      ++...=|.|+.|.+ -|++||+.||..-
T Consensus        23 ~k~kgkghE~~DL~-~ll~~Yq~W~h~l   49 (84)
T pfam07962        23 FKFKGKGHEYSDLA-RLLQFYQLWAHDL   49 (84)
T ss_pred             CCCCCCCCHHHHHH-HHHHHHHHHHHHH
T ss_conf             78189998088999-9999999999800


No 76 
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=32.48  E-value=24  Score=16.02  Aligned_cols=40  Identities=28%  Similarity=0.502  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCC
Q ss_conf             99998999987753113444205454585013468850556
Q gi|254780753|r  136 MLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPN  176 (355)
Q Consensus       136 ~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~  176 (355)
                      .|.|+=.- ..++||+.+-+...+.+..|+...++-+.|+.
T Consensus        13 vL~Rit~l-F~rRg~NI~Sl~v~~te~~~~sR~tivv~~~~   52 (72)
T cd04878          13 VLNRISGL-FARRGFNIESLTVGPTEDPGISRITIVVEGDD   52 (72)
T ss_pred             HHHHHHHH-HHHCCCCEEEEEEEECCCCCEEEEEEEEECCH
T ss_conf             99999999-86078556789986137998489999997888


No 77 
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=32.33  E-value=31  Score=15.29  Aligned_cols=50  Identities=14%  Similarity=0.173  Sum_probs=37.7

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCC
Q ss_conf             24899821778702778999999989999877531134442054545850134688505561
Q gi|254780753|r  116 DAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNA  177 (355)
Q Consensus       116 nailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~a  177 (355)
                      +.+++=+||+-.-=|.+|            .++||+.+-+...+++..|+...|+.+.|+..
T Consensus        12 SvlV~N~pGVL~RV~gLF------------srRgyNIeSL~v~~te~~~~SRiTivv~~d~~   61 (96)
T PRK08178         12 ELTVRNHPGVMTHVCGLF------------ARRAFNVEGILCLPIQDSDKSRIWLLVNDDQR   61 (96)
T ss_pred             EEEEECCCCHHHHHHHHH------------HCCCCCCCEEEEEECCCCCCEEEEEEECCCCC
T ss_conf             999957787899998887------------50566812078851389981089999889844


No 78 
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=31.41  E-value=38  Score=14.64  Aligned_cols=21  Identities=10%  Similarity=0.147  Sum_probs=11.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             456676555774015899887
Q gi|254780753|r   86 QETSDNLQRIKLEVEYKQFES  106 (355)
Q Consensus        86 eE~~~el~~l~~~le~LE~~~  106 (355)
                      +|+...+..|+..+.++|-..
T Consensus       131 EEm~~~lq~Le~ri~klE~~~  151 (178)
T PRK13182        131 EEMLERIQKLEARLKKLEPIY  151 (178)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999861552


No 79 
>PTZ00086 40S ribosomal protein S16; Provisional
Probab=31.13  E-value=28  Score=15.66  Aligned_cols=29  Identities=10%  Similarity=-0.009  Sum_probs=20.9

Q ss_pred             CCCCEEEEEEEEEEECCCCCCCCCCCCCCCEE
Q ss_conf             66650356688788503442221112345503
Q gi|254780753|r  197 DSNSRRHTSFSSIWVYPVVDDSIEIEISESDC  228 (355)
Q Consensus       197 ~s~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl  228 (355)
                      .+.|||.||.|.|.+-|--   -.|.||..++
T Consensus        12 ~~~GrRKtAvArv~l~~G~---G~I~IN~k~~   40 (147)
T PTZ00086         12 QTFGKKKTAVAVATVTKGK---GLIKVNGVPL   40 (147)
T ss_pred             EEECCCCCEEEEEEEECCC---CEEEECCEEH
T ss_conf             9775474279999998897---5099989149


No 80 
>PRK07556 consensus
Probab=31.10  E-value=39  Score=14.60  Aligned_cols=88  Identities=16%  Similarity=0.224  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHCCC-----CCC-CHHHHHHHHHHHHHHHHHHHHHHHHH-HH----HHHHHHHHHHHHH----CCCCHH--
Q ss_conf             9999999870866-----002-58999999999988999999999999-99----8639999986310----000002--
Q gi|254780753|r   22 RLSFLNTKTEDPH-----LWQ-NVIEAKMLMRERQHLDNAISFIKEIQ-DR----LCDNLILLELALE----EDDCSI--   84 (355)
Q Consensus        22 rl~eLE~~lsdp~-----fW~-D~~kAqkl~KE~s~L~~iV~~~~~l~-~~----l~Dl~eL~ELa~e----e~D~el--   84 (355)
                      ++-++-..+.|+.     +=. -++-|.++..++..|+.+++..+++. ..    +.+-.+..-|.++    ..|-.+  
T Consensus       181 qv~D~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~Iy~n~deIk~~K~ke~L~~~~d~A~LSkeLaTI~~Dvpl~~  260 (977)
T PRK07556        181 KVVDVQALAGDSVDNVPGIPGIGIKTAAQLINEYGDLDTLLARAGEIKQPKRRETLIENAEQARISRQLVLLDTDVPLDV  260 (977)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             99999997187646789899854899999999757899999988650210277899857999999899867662798999


Q ss_pred             -HHHH---HHHHHHHHHHHHHHHHHHHHC
Q ss_conf             -3456---676555774015899887630
Q gi|254780753|r   85 -LQET---SDNLQRIKLEVEYKQFESLLS  109 (355)
Q Consensus        85 -~eE~---~~el~~l~~~le~LE~~~Lls  109 (355)
                       ++++   ......+..-+++||+..|++
T Consensus       261 ~le~l~~~~~d~~~L~~~f~eLEF~sLlk  289 (977)
T PRK07556        261 PLDDLAVREPDGPKLIAFLKAMEFTTLTR  289 (977)
T ss_pred             CHHHHCCCCCCHHHHHHHHHHHCCHHHHH
T ss_conf             98991458999999999999848277999


No 81 
>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=31.09  E-value=36  Score=14.85  Aligned_cols=62  Identities=24%  Similarity=0.178  Sum_probs=42.1

Q ss_pred             CCCEEEEEECCCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCCCHHHEEE
Q ss_conf             6624899821778702778-9999999899998775311344420545458501346885055610000010
Q gi|254780753|r  114 SNDAYLEVHAGAGGTESQD-WANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGE  184 (355)
Q Consensus       114 ~~nailEI~AGaGG~EA~d-wA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~ayg~Lk~E  184 (355)
                      +..+-..|.|...|.=|+. ||..+|+++       +.+++.. ...|+.-.-.++++.|+|+ +...|.+|
T Consensus        29 ~~~~~a~i~are~gV~~G~~~a~~i~~~~-------~~~~~~~-~~dG~~v~~g~~i~~i~G~-a~~il~~E   91 (279)
T PRK08385         29 DMNASAVIIAKQEGVIAGVEEARALFEHF-------GVAVEVK-KRDGETVKAGEVILELKGN-ARAILLVE   91 (279)
T ss_pred             CCEEEEEEEECCCEEEECHHHHHHHHHHC-------CCEEEEE-CCCCCEECCCCEEEEEEEC-HHHHHHHH
T ss_conf             96699999978998998699999999974-------9889999-2889890699899999987-89999999


No 82 
>TIGR02153 gatD_arch glutamyl-tRNA(Gln) amidotransferase, subunit D; InterPro: IPR011878    This peptide is found only in the Archaea. It is part of a heterodimer, with GatD (IPR004414 from INTERPRO), that acts as an amidotransferase on misacylated Glu-tRNA(Gln) to produce Gln-tRNA(Gln). The analogous amidotransferase found in bacteria is the GatABC system, although GatABC homologs in the Archaea appear to act instead on Asp-tRNA(Asn) .; GO: 0006450 regulation of translational fidelity.
Probab=30.86  E-value=17  Score=17.14  Aligned_cols=113  Identities=23%  Similarity=0.391  Sum_probs=61.2

Q ss_pred             CCCHHHHHH-HHHHHHHHHHHHHHHHHHHHHH---------------------HCCCCCCCCEEEEEEEEECCCCCHHHE
Q ss_conf             787027789-9999998999987753113444---------------------205454585013468850556100000
Q gi|254780753|r  125 AGGTESQDW-ANMLLRMYTRWAEKRKFKTEAL---------------------EIHDGEEAGIKSATLLIKGPNAYGWLK  182 (355)
Q Consensus       125 aGG~EA~dw-A~~L~rMY~r~ae~~gwk~evi---------------------~~~~~e~~GiK~~~~~I~G~~ayg~Lk  182 (355)
                      |=||+-+-| |+=|-     |+=+.|..+=|+                     .+..+..|-|.+|++--.|.--=.|.-
T Consensus       149 aHGTDTM~YTAaALS-----Fm~~~Gl~~PvVlVGAQRSSDRPSSDAa~NL~~A~~~A~~a~~aEV~VvMHG~tsD~yc~  223 (413)
T TIGR02153       149 AHGTDTMAYTAAALS-----FMFKTGLPVPVVLVGAQRSSDRPSSDAALNLIAAVRAATSAPIAEVVVVMHGETSDTYCL  223 (413)
T ss_pred             EECCCHHHHHHHHHH-----HHHHCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCEEE
T ss_conf             415874689999999-----999716999889985743588873137999999999833697100388840124886799


Q ss_pred             EECCEEEEEEECCCCCCCEEEEE----EEEEEECCCCCCCCCC-CCCCCE---EEEEEECCCCC-CCCCCCCCCEEEEEE
Q ss_conf             10120689873046666503566----8878850344222111-234550---36998538886-554427310035887
Q gi|254780753|r  183 GEQGVHRLVRISPYDSNSRRHTS----FSSIWVYPVVDDSIEI-EISESD---CRIDTYRASGA-GGQHVNTTDSAVRIT  253 (355)
Q Consensus       183 ~E~GvHRv~Ri~~~~s~gR~hTS----~a~V~V~P~~~~~~~i-~i~~~d---l~i~~~rssg~-ggq~vn~t~savri~  253 (355)
                          |||=+||      -|.|||    |=||.-+|...  ++. .+..+.   |+ +.||..|- +-.=-++-|..|=|.
T Consensus       224 ----~HRGVkV------RKMHTSRRDAF~SiN~~PiA~--~~~~~~~~~~~~~L~-~dYr~r~~~~le~~~~~EekVaLv  290 (413)
T TIGR02153       224 ----VHRGVKV------RKMHTSRRDAFQSINSIPIAK--VDPKSLKEKEIEKLR-EDYRRRGEKELELDDKFEEKVALV  290 (413)
T ss_pred             ----EECCCEE------ECCCCCCHHHHHCCCCCCCEE--ECCCCCCCCEEEEEE-EEEEECCCCCCCCCCCCCCEEEEE
T ss_conf             ----9658235------036588102553158865358--817778744077754-211313776532068877137999


Q ss_pred             EC
Q ss_conf             46
Q gi|254780753|r  254 HI  255 (355)
Q Consensus       254 H~  255 (355)
                      --
T Consensus       291 Kf  292 (413)
T TIGR02153       291 KF  292 (413)
T ss_pred             EE
T ss_conf             84


No 83 
>PRK08786 consensus
Probab=30.56  E-value=39  Score=14.54  Aligned_cols=46  Identities=17%  Similarity=0.154  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHCCC-----CCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999870866-----002-589999999999889999999999999986
Q gi|254780753|r   22 RLSFLNTKTEDPH-----LWQ-NVIEAKMLMRERQHLDNAISFIKEIQDRLC   67 (355)
Q Consensus        22 rl~eLE~~lsdp~-----fW~-D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~   67 (355)
                      ++-.+-..+.|+.     +=. -++-|.++..++.+|+.+++..++++..+.
T Consensus       170 qviD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~I~~n~d~IkgK~~  221 (927)
T PRK08786        170 QIVDLLALMGDTVDNVPGVEKCGPKTAAKWLAEYDSLDGVIANADKIKGKIG  221 (927)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             9999999808764678999985689999999975769999999875546678


No 84 
>PRK06887 consensus
Probab=30.28  E-value=40  Score=14.51  Aligned_cols=88  Identities=11%  Similarity=0.069  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHCCC-----CCC-CHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHH----CC
Q ss_conf             9999999870866-----002-58999999999988999999999999-----------998639999986310----00
Q gi|254780753|r   22 RLSFLNTKTEDPH-----LWQ-NVIEAKMLMRERQHLDNAISFIKEIQ-----------DRLCDNLILLELALE----ED   80 (355)
Q Consensus        22 rl~eLE~~lsdp~-----fW~-D~~kAqkl~KE~s~L~~iV~~~~~l~-----------~~l~Dl~eL~ELa~e----e~   80 (355)
                      ++-.+-..+.|+.     +=. -++-|.++.+++.+|+.+++..+++.           ..+.+-.+..-|.++    ..
T Consensus       175 qiiD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLe~Iy~nld~i~~~~~rg~~Kl~e~L~~~~e~a~LSk~LvtI~~  254 (954)
T PRK06887        175 LIIDYLALMGDSSDNIPGVAGVGEKTALGLLQGIGSMAEIYANLDKVAELPIRGAKKLGEKLLAEKANADLSYLLATIKT  254 (954)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCEEHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999997188524778878541699999999957799999869873255420057899999998998999998601455


Q ss_pred             CCHH------HHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             0002------3456676555774015899887630
Q gi|254780753|r   81 DCSI------LQETSDNLQRIKLEVEYKQFESLLS  109 (355)
Q Consensus        81 D~el------~eE~~~el~~l~~~le~LE~~~Lls  109 (355)
                      |-.+      +..-......+...++++|+..+++
T Consensus       255 Dvpl~~~~~~l~~~~~d~~~L~~~f~elEFksll~  289 (954)
T PRK06887        255 DVELDVTPEQLLLGESNKDELIEYFARYEFKRWLN  289 (954)
T ss_pred             CCCCCCCHHHHCCCCCCHHHHHHHHHHHCCHHHHH
T ss_conf             78888998994448999999999999834858999


No 85 
>TIGR01219 Pmev_kin_ERG8 phosphomevalonate kinase; InterPro: IPR016005    Phosphomevalonate kinase (2.7.4.2 from EC) catalyzes the phosphorylation of 5-phosphomevalonate into 5-diphosphomevalonate, an essential step in isoprenoid biosynthesis via the mevalonate pathway. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the higher eukaryotic form and the ERG8 type . This model represents plant and fungal forms of the ERG8 type of phosphomevalonate kinase..
Probab=30.25  E-value=40  Score=14.51  Aligned_cols=57  Identities=21%  Similarity=0.285  Sum_probs=37.4

Q ss_pred             HHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHH--HHHHHHHHH-HHHHHHHHHCCCCCCC
Q ss_conf             763034576624899821778702778999999--989999877-5311344420545458
Q gi|254780753|r  106 SLLSGEADSNDAYLEVHAGAGGTESQDWANMLL--RMYTRWAEK-RKFKTEALEIHDGEEA  163 (355)
Q Consensus       106 ~Lls~e~D~~nailEI~AGaGG~EA~dwA~~L~--rMY~r~ae~-~gwk~evi~~~~~e~~  163 (355)
                      .||-+-.--..++.--=|||||-+|+ |+=-+-  ..-.+-+.. +.=+|-.+++++.+.|
T Consensus       430 ~lLD~~~~l~GVl~~gvPGAGGfDAi-f~it~~~~d~~~~~~~~w~~~~V~~ldV~~a~~G  489 (499)
T TIGR01219       430 SLLDDIESLEGVLLVGVPGAGGFDAI-FVITLNDVDLREKVIKAWKSDKVLALDVSEADDG  489 (499)
T ss_pred             HHHCCCCCCCCEEEEECCCCCHHHHH-HHHHHCCHHHHHHHHHHHHHCCCEEEEECCCCCC
T ss_conf             34302002586368852898547899-9887402126889987564268347760458774


No 86 
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=30.21  E-value=40  Score=14.50  Aligned_cols=10  Identities=30%  Similarity=0.743  Sum_probs=6.2

Q ss_pred             CEEEEEEECC
Q ss_conf             0035887469
Q gi|254780753|r  247 DSAVRITHIP  256 (355)
Q Consensus       247 ~savri~H~p  256 (355)
                      .--.+|||.|
T Consensus       485 ~QVl~VTHlP  494 (557)
T COG0497         485 HQVLCVTHLP  494 (557)
T ss_pred             CEEEEEECHH
T ss_conf             6499993578


No 87 
>cd06891 PX_Vps17p The phosphoinositide binding Phox Homology domain of yeast sorting nexin Vps17p. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Vsp17p forms a dimer with Vps5p, the yeast counterpart of human SNX1, and is part of the retromer complex that mediates the transport of the carboxypeptidase Y receptor Vps10p from endosomes to Golgi. Similar to Vps5p and SNX1, Vps17p harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvatur
Probab=29.85  E-value=41  Score=14.46  Aligned_cols=23  Identities=26%  Similarity=0.338  Sum_probs=17.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             17787027789999999899998775
Q gi|254780753|r  123 AGAGGTESQDWANMLLRMYTRWAEKR  148 (355)
Q Consensus       123 AGaGG~EA~dwA~~L~rMY~r~ae~~  148 (355)
                      +|+||+|   +..-+..|.++|..+-
T Consensus        99 ~g~~~~E---d~~~~~~~lQ~Wl~rV  121 (140)
T cd06891          99 YGSNNEE---DARKLKANLQRWFNRV  121 (140)
T ss_pred             CCCCCHH---HHHHHHHHHHHHHHHH
T ss_conf             8989778---9999999999999998


No 88 
>KOG0081 consensus
Probab=29.74  E-value=41  Score=14.45  Aligned_cols=30  Identities=33%  Similarity=0.630  Sum_probs=19.5

Q ss_pred             CCEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCC
Q ss_conf             650356688788503442221112345503699853888655
Q gi|254780753|r  199 NSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGG  240 (355)
Q Consensus       199 ~gR~hTS~a~V~V~P~~~~~~~i~i~~~dl~i~~~rssg~gg  240 (355)
                      .|+-||-|.+         ++-|+..++-   -+|+||||||
T Consensus        31 D~~F~~qFIs---------TVGIDFreKr---vvY~s~gp~g   60 (219)
T KOG0081          31 DGKFNTQFIS---------TVGIDFREKR---VVYNSSGPGG   60 (219)
T ss_pred             CCCCCCEEEE---------EEECCCCCCE---EEEECCCCCC
T ss_conf             7853343577---------7401344004---7883468998


No 89 
>PHA00159 endonuclease I
Probab=29.48  E-value=23  Score=16.20  Aligned_cols=15  Identities=27%  Similarity=0.552  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             899998775311344
Q gi|254780753|r  140 MYTRWAEKRKFKTEA  154 (355)
Q Consensus       140 MY~r~ae~~gwk~ev  154 (355)
                      -|-.||+++||++--
T Consensus       108 TYa~WCeKhgf~wa~  122 (149)
T PHA00159        108 SYAEWCEKHGILFAD  122 (149)
T ss_pred             CHHHHHHHCCCCCCC
T ss_conf             399999874997457


No 90 
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=29.47  E-value=30  Score=15.40  Aligned_cols=65  Identities=23%  Similarity=0.308  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECC-----CCCHHHEEECCEEEEEEECCCCCCCE
Q ss_conf             9999899998775311344420545458501346885055-----61000001012068987304666650
Q gi|254780753|r  136 MLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGP-----NAYGWLKGEQGVHRLVRISPYDSNSR  201 (355)
Q Consensus       136 ~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~-----~ayg~Lk~E~GvHRv~Ri~~~~s~gR  201 (355)
                      .|.|+=.- +.++||+.+-+...+++..|+...|+-+.|+     ..-..|.-=--||+|.-+++.++=.|
T Consensus        15 vL~RV~gl-FsrRgyNIeSL~V~~te~~~iSR~Tiv~~gd~~~ieQI~kQL~KLidVi~V~dlt~~~~v~R   84 (172)
T CHL00100         15 VLTRIAGL-FARRGFNIESLAVGPAEQIGISRITMVVPGDNRTIEQLTKQLYKLVNILKVQDITNIPSVER   84 (172)
T ss_pred             HHHHHHHH-HHCCCCCEEEEEEECCCCCCEEEEEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCCCHHHH
T ss_conf             99999999-85178672369972148998159999996899999999999955827026430678445643


No 91 
>cd01137 PsaA Metal binding protein PsaA.  These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species.  They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=29.31  E-value=41  Score=14.40  Aligned_cols=20  Identities=25%  Similarity=0.552  Sum_probs=15.1

Q ss_pred             HCCCCCCCHHHHHHHHHHHH
Q ss_conf             08660025899999999998
Q gi|254780753|r   31 EDPHLWQNVIEAKMLMRERQ   50 (355)
Q Consensus        31 sdp~fW~D~~kAqkl~KE~s   50 (355)
                      .||.+|-||..++.+.+.+.
T Consensus       115 ~DPHiWldp~~~~~~a~~I~  134 (287)
T cd01137         115 PDPHAWMSPKNAIIYVKNIA  134 (287)
T ss_pred             CCCCCCCCHHHHHHHHHHHH
T ss_conf             99863579999999999999


No 92 
>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]
Probab=28.97  E-value=42  Score=14.36  Aligned_cols=16  Identities=38%  Similarity=0.534  Sum_probs=7.5

Q ss_pred             EECCCCC--CCCCCCCCCE
Q ss_conf             8538886--5544273100
Q gi|254780753|r  232 TYRASGA--GGQHVNTTDS  248 (355)
Q Consensus       232 ~~rssg~--ggq~vn~t~s  248 (355)
                      .++.+|+  || ..++..+
T Consensus       645 ~~~~~G~~tGG-~~~~~~~  662 (1163)
T COG1196         645 LVEPSGSITGG-SRNKRSS  662 (1163)
T ss_pred             EEECCCCEECC-CCCCCCC
T ss_conf             88278421068-7455430


No 93 
>pfam05367 Phage_endo_I Phage endonuclease I. The bacteriophage endonuclease I is a nuclease that is selective for the structure of the four-way Holliday DNA junction.
Probab=28.93  E-value=24  Score=16.09  Aligned_cols=14  Identities=43%  Similarity=0.885  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             89999877531134
Q gi|254780753|r  140 MYTRWAEKRKFKTE  153 (355)
Q Consensus       140 MY~r~ae~~gwk~e  153 (355)
                      .|-.||+++||++-
T Consensus       108 TYa~WCeKhGf~wa  121 (149)
T pfam05367       108 TYAEWCEKHGFKFA  121 (149)
T ss_pred             CHHHHHHHCCCCCC
T ss_conf             39999987499745


No 94 
>COG5491 VPS24 Conserved protein implicated in secretion [Cell motility and secretion]
Probab=28.84  E-value=42  Score=14.34  Aligned_cols=65  Identities=22%  Similarity=0.169  Sum_probs=42.3

Q ss_pred             CCHHHHHHHHHHHHH----HHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             498999999999999----87086600258999999999988999999999999998639999986310
Q gi|254780753|r   14 FDWDNAVQRLSFLNT----KTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALE   78 (355)
Q Consensus        14 fDle~~~~rl~eLE~----~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~e   78 (355)
                      +-++....|+..+..    .++-..+-.|..++...+.|+..|..+...+....-.++-....++...+
T Consensus        52 srL~~~~sRLqs~~~~~~e~~~m~~v~~~~~~a~~~mnel~~i~ri~~~~et~~~~mE~~~~~le~m~e  120 (204)
T COG5491          52 SRLDASISRLQSLDTMLFEKVVMRQVSGDMAKAAMYMNELESIRRIMQLFETQFLALELVQLRLETMDE  120 (204)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999988999999999999874107899999887999999999999999999999999999999


No 95 
>TIGR02090 LEU1_arch isopropylmalate/citramalate/homocitrate synthases; InterPro: IPR011830   Methanogenic archaea contain three closely related homologs of the 2-isopropylmalate synthases (LeuA) represented by IPR005671 from INTERPRO. Two of these in Methanococcus janaschii (MJ1392 - CimA ; MJ0503 - AksA ) have been characterised as catalyzing alternative reactions leaving the third (MJ1195) as the presumptive LeuA enzyme. CimA is citramalate (2-methylmalate) synthase, which condenses acetyl-CoA with pyruvate. This enzyme is believed to be involved in the biosynthesis of isoleucine in methanogens and possibly other species lacking threonine dehydratase. AksA is a homocitrate synthase which also produces (homo)2-citrate and (homo)3-citrate in the biosynthesis of Coenzyme B which is restricted solely to methanogenic archaea. Methanogens, then should and apparently do contain all three of these enzymes. Unfortunately, phylogenetic trees do not resolve into three unambiguous clades, making assignment of function to particular genes problematic. Other archaea, which lack a threonine dehydratase (mainly Euryarchaeota), should contain both CimA and LeuA genes. This is true for archaeoglobus fulgidis, but not for the Pyrococci which have none in this clade, but one in IPR005671 from INTERPRO and one in IPR005675 from INTERPRO which may fulfil these roles. Proteins from other species, which have only one hit to this entry and lack threonine dehydratase, are very likely to be LeuA enzymes.; GO: 0046912 transferase activity transferring acyl groups acyl groups converted into alkyl on transfer, 0019752 carboxylic acid metabolic process.
Probab=28.49  E-value=17  Score=17.25  Aligned_cols=15  Identities=47%  Similarity=0.806  Sum_probs=9.9

Q ss_pred             EECCCCCHHHEEECCEEE
Q ss_conf             505561000001012068
Q gi|254780753|r  172 IKGPNAYGWLKGEQGVHR  189 (355)
Q Consensus       172 I~G~~ayg~Lk~E~GvHR  189 (355)
                      |-|++||+   +|||+|=
T Consensus       276 IVGeNAFa---HEsGIHv  290 (371)
T TIGR02090       276 IVGENAFA---HESGIHV  290 (371)
T ss_pred             CCCCCCCC---CCCHHHH
T ss_conf             32565000---1103558


No 96 
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=28.48  E-value=32  Score=15.17  Aligned_cols=62  Identities=19%  Similarity=0.298  Sum_probs=44.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCC-----CCHHHEEECCEEEEEEECCCCC
Q ss_conf             99998999987753113444205454585013468850556-----1000001012068987304666
Q gi|254780753|r  136 MLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPN-----AYGWLKGEQGVHRLVRISPYDS  198 (355)
Q Consensus       136 ~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~-----ayg~Lk~E~GvHRv~Ri~~~~s  198 (355)
                      -|.|+=. .+.++||+.+-+...+++..|+...|+.+.|+.     .-..|.-=--||.|.-..+.++
T Consensus        15 vL~Risg-lFsrRg~NI~SL~v~~te~~~iSR~Tiv~~g~~~~i~QI~kQL~KLidVi~V~dlt~~~~   81 (161)
T PRK11895         15 VLSRVAG-LFSRRGYNIESLTVAPTEDPGLSRITIVTSGDERVLEQITKQLNKLIDVLKVVDLTEEAH   81 (161)
T ss_pred             HHHHHHH-HHHCCCCCEEEEEEECCCCCCCEEEEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCCCE
T ss_conf             9999999-985068654666650247998159999996899999999999963214034664588540


No 97 
>PRK08883 ribulose-phosphate 3-epimerase; Provisional
Probab=28.31  E-value=43  Score=14.28  Aligned_cols=38  Identities=16%  Similarity=0.135  Sum_probs=27.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             48998217787027789999999899998775311344
Q gi|254780753|r  117 AYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEA  154 (355)
Q Consensus       117 ailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~ev  154 (355)
                      -+|.+.||-||..=..-+-+-.+...++...+|+++++
T Consensus       133 LvMtV~PGf~GQ~f~~~~l~Ki~~l~~~~~~~~~~~~I  170 (220)
T PRK08883        133 LLMSVNPGFGGQSFIPHTLDKLRAVRKMIDASGRDIRL  170 (220)
T ss_pred             EEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEE
T ss_conf             99874589887545577999999999988744998079


No 98 
>pfam05055 DUF677 Protein of unknown function (DUF677). This family consists of AT14A like proteins from Arabidopsis thaliana. At14a has a small domain that has sequence similarities to integrins from fungi, insects and humans. Transcripts of At14a are found in all Arabidopsis tissues and localizes partly to the plasma membrane.
Probab=28.22  E-value=43  Score=14.27  Aligned_cols=98  Identities=8%  Similarity=0.124  Sum_probs=51.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             66002589999999999889999999999999986399999863---100-00002345667655577401589988763
Q gi|254780753|r   33 PHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELA---LEE-DDCSILQETSDNLQRIKLEVEYKQFESLL  108 (355)
Q Consensus        33 p~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa---~ee-~D~el~eE~~~el~~l~~~le~LE~~~Ll  108 (355)
                      .++|+||+...=+..-...-.+..+.+..+.+-++.++.-.-+.   -.. +++....+.-.+-+...+-+++|.--.-.
T Consensus        56 edvw~n~eL~~LV~~YFesS~ktldfC~~Lekcv~rar~sql~I~~Al~qfe~e~~~~d~g~~~~ky~ktLeeL~~Fkaa  135 (336)
T pfam05055        56 EDVWENQDLFSLVNVYFESTKKTLDFCETLENCVERAERSQLLIREAVAQFEKESLDKDVGKKKKKYEKTLEELKKFKAM  135 (336)
T ss_pred             HHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             98860877999999999810999999999999999987321899999987654245555430235799999999988870


Q ss_pred             CCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             03457662489982177870277899999998999987
Q gi|254780753|r  109 SGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAE  146 (355)
Q Consensus       109 s~e~D~~nailEI~AGaGG~EA~dwA~~L~rMY~r~ae  146 (355)
                      .+|.|..+                |..+.-.||..+..
T Consensus       136 gnPF~~~~----------------f~~~Fq~vy~qq~~  157 (336)
T pfam05055       136 GDPFDGEE----------------FTTQFQSVYKQQVL  157 (336)
T ss_pred             CCCCCCHH----------------HHHHHHHHHHHHHH
T ss_conf             69998189----------------99999999999999


No 99 
>PRK05755 DNA polymerase I; Provisional
Probab=28.12  E-value=43  Score=14.26  Aligned_cols=88  Identities=17%  Similarity=0.164  Sum_probs=48.4

Q ss_pred             HHHHHHHHHHCCC-----CCC-CHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHH----CCCCHH--
Q ss_conf             9999999870866-----002-589999999999889999999999999-----98639999986310----000002--
Q gi|254780753|r   22 RLSFLNTKTEDPH-----LWQ-NVIEAKMLMRERQHLDNAISFIKEIQD-----RLCDNLILLELALE----EDDCSI--   84 (355)
Q Consensus        22 rl~eLE~~lsdp~-----fW~-D~~kAqkl~KE~s~L~~iV~~~~~l~~-----~l~Dl~eL~ELa~e----e~D~el--   84 (355)
                      ++-.+-..+.|+.     +=. -++.|.++.+++..|+.+++..+++..     .+.+-.+...+.++    ..|-.+  
T Consensus       173 q~~D~~aL~GD~sDNIPGVpGIG~KtA~kLl~~ygsle~i~~~~d~i~g~k~~~~l~~~~e~a~ls~~L~ti~~dvpl~~  252 (889)
T PRK05755        173 QIIDFLALMGDSSDNIPGVPGVGEKTAAKLLKEFGSLEGLYENLDEIKGKKLKEKLRENKEQAFLSRKLATIKTDVPLDV  252 (889)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             99999998088645789988626999999998678689999989852325678889846999999999856522898999


Q ss_pred             --HH--HHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             --34--56676555774015899887630
Q gi|254780753|r   85 --LQ--ETSDNLQRIKLEVEYKQFESLLS  109 (355)
Q Consensus        85 --~e--E~~~el~~l~~~le~LE~~~Lls  109 (355)
                        .+  --......+...++++|+..|++
T Consensus       253 ~le~l~~~~~d~~~l~~lf~elEFksLlk  281 (889)
T PRK05755        253 DLEDLELKPPDREKLIALLKKLEFKSLLR  281 (889)
T ss_pred             CHHHHCCCCCCHHHHHHHHHHHCCHHHHH
T ss_conf             99992258999999999999828599999


No 100
>PRK08076 consensus
Probab=27.92  E-value=44  Score=14.23  Aligned_cols=96  Identities=15%  Similarity=0.151  Sum_probs=52.9

Q ss_pred             CCHHHHHHH-------HHHHHHHHHCCC-----CCC-CHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHH
Q ss_conf             498999999-------999999870866-----002-589999999999889999999999999-----98639999986
Q gi|254780753|r   14 FDWDNAVQR-------LSFLNTKTEDPH-----LWQ-NVIEAKMLMRERQHLDNAISFIKEIQD-----RLCDNLILLEL   75 (355)
Q Consensus        14 fDle~~~~r-------l~eLE~~lsdp~-----fW~-D~~kAqkl~KE~s~L~~iV~~~~~l~~-----~l~Dl~eL~EL   75 (355)
                      +|.+...++       +-++-..+.|+.     +=. -++.|.++..++..|+.+++..+++..     .+.+-.+..-|
T Consensus       160 ~~~~~v~ek~Gv~P~q~~D~~aL~GDssDNIPGVpGiG~KtA~~ll~~~gsle~i~~~~~~ikg~k~re~L~e~~e~A~L  239 (877)
T PRK08076        160 YTPEALFEKYGLTPKQIIDMKGLMGDSSDNIPGVPGVGEKTAIKLLKQFGTVEEVLESIDEVSGKKLKEKLEENKEQALM  239 (877)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHCHHHHHH
T ss_conf             58999999979698999999997187646799999863799999999668668899877732644678898848999999


Q ss_pred             HHH----CCCCH----H--HHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             310----00000----2--3456676555774015899887630
Q gi|254780753|r   76 ALE----EDDCS----I--LQETSDNLQRIKLEVEYKQFESLLS  109 (355)
Q Consensus        76 a~e----e~D~e----l--~eE~~~el~~l~~~le~LE~~~Lls  109 (355)
                      .++    ..|..    +  +..-......+...++++|+..|++
T Consensus       240 SkeLaTI~~Dvpl~~~l~~l~~~~~d~~~L~~lf~eLEFksLl~  283 (877)
T PRK08076        240 SKELATIITDAPIEVTVDDLEYKGYEAEDVIPLFKELGFTSLLE  283 (877)
T ss_pred             HHHHHHHHCCCCCCCCHHHCCCCCCCHHHHHHHHHHCCHHHHHH
T ss_conf             99998853189899998881757999999999999806099999


No 101
>pfam12112 DUF3579 Protein of unknown function (DUF3579). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 98 to 126 amino acids in length. This protein has a conserved FRP sequence motif.
Probab=27.90  E-value=29  Score=15.55  Aligned_cols=51  Identities=16%  Similarity=0.290  Sum_probs=25.3

Q ss_pred             EEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEE
Q ss_conf             9821778702778999999989999877531134442054545850134688
Q gi|254780753|r  120 EVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLL  171 (355)
Q Consensus       120 EI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~  171 (355)
                      -|+.-------.|||+.|..+...|--.+...+... ..|.-.+|+|.+++.
T Consensus        12 GiT~~Gk~FRPSDWaERL~Gv~a~f~~~~r~~YSp~-~~P~~~~G~kcvvvd   62 (93)
T pfam12112        12 GVTRAGKTFRPSDWAERLCGVMSSFRPGGRLSYSPY-VRPGVIGGVKCVVVD   62 (93)
T ss_pred             EECCCCCCCCCCHHHHHHHHHHHHCCCCCCEEECCC-CCCEEECCEEEEEEC
T ss_conf             673899982885299997411540089994762675-454265885799986


No 102
>PRK05797 consensus
Probab=27.72  E-value=44  Score=14.21  Aligned_cols=88  Identities=18%  Similarity=0.218  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHCCC-----CCC-CHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHH----CCCCHH--
Q ss_conf             9999999870866-----002-589999999999889999999999999-----98639999986310----000002--
Q gi|254780753|r   22 RLSFLNTKTEDPH-----LWQ-NVIEAKMLMRERQHLDNAISFIKEIQD-----RLCDNLILLELALE----EDDCSI--   84 (355)
Q Consensus        22 rl~eLE~~lsdp~-----fW~-D~~kAqkl~KE~s~L~~iV~~~~~l~~-----~l~Dl~eL~ELa~e----e~D~el--   84 (355)
                      ++-.+-+.+.|+.     +=. -++.|.++..++.+|+.+++..+++..     .+.+-.+..-|.++    ..|-.+  
T Consensus       175 q~~D~~aL~GD~sDNIPGVpGIG~KTA~kLL~eyGsLE~I~~n~deIkgkk~~e~L~e~~d~a~LSkeLvTI~~Dvpl~~  254 (869)
T PRK05797        175 QFIDVKGLMGDKSDNIPGVPGIGEKTAFKLIKEYGSIENVLENIDNIKGKKLKENLEENREQAIFSKKLATIMRNVPIEI  254 (869)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             99999998088645789999878189999998678788999878850538899999954888899877774111798899


Q ss_pred             -HHHHH----HHHHHHHHHHHHHHHHHHHC
Q ss_conf             -34566----76555774015899887630
Q gi|254780753|r   85 -LQETS----DNLQRIKLEVEYKQFESLLS  109 (355)
Q Consensus        85 -~eE~~----~el~~l~~~le~LE~~~Lls  109 (355)
                       ++++.    -....+...++++|+..|++
T Consensus       255 ~le~l~~~~~~d~~~L~~~f~elEFksLl~  284 (869)
T PRK05797        255 DLEEIKSKEEYDIEKLRELFEKLEFKSLID  284 (869)
T ss_pred             CHHHHCCCCCCCHHHHHHHHHHHCCHHHHH
T ss_conf             989951478899999999999826599999


No 103
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein,  YhcN/YlaJ family; InterPro: IPR014247   This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain. .
Probab=27.62  E-value=32  Score=15.23  Aligned_cols=20  Identities=40%  Similarity=0.639  Sum_probs=15.5

Q ss_pred             CC-CCCEEEEEEEEECCCCCH
Q ss_conf             54-585013468850556100
Q gi|254780753|r  160 GE-EAGIKSATLLIKGPNAYG  179 (355)
Q Consensus       160 ~e-~~GiK~~~~~I~G~~ayg  179 (355)
                      .+ .-|||.|++-|.|.+||=
T Consensus        81 a~k~~gvk~A~vvi~g~~A~V  101 (185)
T TIGR02898        81 AKKVKGVKDATVVITGNRAYV  101 (185)
T ss_pred             HHHCCCCCEEEEEEECCEEEE
T ss_conf             862788621148874681589


No 104
>pfam02403 Seryl_tRNA_N Seryl-tRNA synthetase N-terminal domain. This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.
Probab=27.48  E-value=44  Score=14.18  Aligned_cols=55  Identities=16%  Similarity=0.147  Sum_probs=34.1

Q ss_pred             HCCHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             54989999999999998708660-02589999999999889999999999999986
Q gi|254780753|r   13 LFDWDNAVQRLSFLNTKTEDPHL-WQNVIEAKMLMRERQHLDNAISFIKEIQDRLC   67 (355)
Q Consensus        13 ~fDle~~~~rl~eLE~~lsdp~f-W~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~   67 (355)
                      |+|+.-++...+.+...+..-++ -.+.+....+-.+...+...++.+..-.+.+.
T Consensus         1 MlDik~ir~n~~~v~~~l~~R~~~~~~~~~i~~ld~~~r~~~~~~e~L~~~~N~~s   56 (108)
T pfam02403         1 MLDIKLIRENPEAVKEKLRKRGVDVLDVDELLELDEERRELQVELEELQAERNELS   56 (108)
T ss_pred             CCCHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98889988099999999988299887899999999999999999999999985989


No 105
>PRK08566 DNA-directed RNA polymerase subunit alpha; Validated
Probab=27.24  E-value=44  Score=14.21  Aligned_cols=31  Identities=19%  Similarity=0.195  Sum_probs=15.8

Q ss_pred             CCCCHHHEEECCEEEEEEECCCCCCCE-EEEEEEEEEE
Q ss_conf             561000001012068987304666650-3566887885
Q gi|254780753|r  175 PNAYGWLKGEQGVHRLVRISPYDSNSR-RHTSFSSIWV  211 (355)
Q Consensus       175 ~~ayg~Lk~E~GvHRv~Ri~~~~s~gR-~hTS~a~V~V  211 (355)
                      .+....|++-.|--|-      +=.|+ +-=|+-||..
T Consensus       298 k~i~q~L~gK~GrfR~------nlmGKRVd~saRSVIs  329 (881)
T PRK08566        298 KTLAQRLKGKEGRFRG------NLSGKRVNFSARTVIS  329 (881)
T ss_pred             CCHHHHHCCCCCEEEC------CCCCCCCCCCCEEEEC
T ss_conf             4188885466630100------2244533554303432


No 106
>PRK07737 fliD flagellar capping protein; Validated
Probab=25.89  E-value=47  Score=13.99  Aligned_cols=58  Identities=17%  Similarity=0.189  Sum_probs=45.8

Q ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999998865498999999999999870866002589999999999889999999999999986399999
Q gi|254780753|r    5 RQLNCLGGLFDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILL   73 (355)
Q Consensus         5 ~rl~~l~~~fDle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~   73 (355)
                      -|+.-+++-||++.+...|-+.|..         |  ..++.++...++..+..|..+++.+..+....
T Consensus         3 ~ri~GlgSGlD~~~iV~~Lv~aE~~---------p--~~~l~~~~~~~~~k~sa~~~l~s~l~~l~~~~   60 (502)
T PRK07737          3 TRITGLASGMDIDDIVSKLMKTERA---------P--LDKLTQKKQTLEWQRDSYREVNTKIKDLDDYI   60 (502)
T ss_pred             EECCEEECCCCHHHHHHHHHHHHHH---------H--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             3433034387899999999999998---------8--88999999999999999999999999999999


No 107
>TIGR00845 caca sodium/calcium exchanger 1; InterPro: IPR004836   Na^+/Ca^2+ exchange proteins are involved in maintaining Ca^2+ homeostasis in a wide variety of cell types. They are found in both the plasma membrane and intracellular organellar membranes, where they exchange Na^+ for Ca^2+ in an electrogenic manner. When located in the plasma membrane, they generally utilise the transmembrane (TM) Na^+ concentration gradient in order to extrude Ca^2+ from cells. Three mammalian isoforms have been cloned to date (NCX1-3), which consist of 920-970 amino acid residues that are predicted to possess 11 or 12 TM domains. Interestingly, they possess a short motif (~30 residues) that is similar to the Na^+/K^+-ATPase, although its function is unknown , .   NCX1 has been found to be predominantly expressed in the heart, where it plays an important role in excitation-contraction coupling, but it is also abundant in a variety of other tissues . NCX2 and NCX3 transcripts have been detected in the brain and skeletal muscle , . Homologous Na^+/Ca^2+ exchange proteins have also been found in Caenorhabditis elegans, Drosophila melanogaster and Loligo opalescens (California market squid). ; GO: 0005432 calcium:sodium antiporter activity, 0006816 calcium ion transport, 0016020 membrane.
Probab=25.12  E-value=49  Score=13.89  Aligned_cols=35  Identities=26%  Similarity=0.463  Sum_probs=22.4

Q ss_pred             EEEEEEECCCCCCC--------CCCCCCC--CEEEEEEECCCCCCCC
Q ss_conf             68878850344222--------1112345--5036998538886554
Q gi|254780753|r  205 SFSSIWVYPVVDDS--------IEIEISE--SDCRIDTYRASGAGGQ  241 (355)
Q Consensus       205 S~a~V~V~P~~~~~--------~~i~i~~--~dl~i~~~rssg~ggq  241 (355)
                      .+|||.||-  ||.        ..++|.+  -.+.+.++|.|||-|.
T Consensus       573 ~~ATv~ILD--DDHAGIF~f~~~~~~V~Es~G~~evkv~R~SGARG~  617 (1067)
T TIGR00845       573 LLATVMILD--DDHAGIFTFEEDVFHVSESIGELEVKVLRTSGARGT  617 (1067)
T ss_pred             CEEEEEEEE--CCCCCCCCEECCEEEEEEEEEEEEEEEEECCCCCCC
T ss_conf             546888874--588863213246589976665799999963688221


No 108
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=24.57  E-value=25  Score=15.95  Aligned_cols=38  Identities=13%  Similarity=0.259  Sum_probs=22.4

Q ss_pred             EEEEEECCCC---CHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHCCC
Q ss_conf             4899821778---70277899999998999987-----7531134442054
Q gi|254780753|r  117 AYLEVHAGAG---GTESQDWANMLLRMYTRWAE-----KRKFKTEALEIHD  159 (355)
Q Consensus       117 ailEI~AGaG---G~EA~dwA~~L~rMY~r~ae-----~~gwk~evi~~~~  159 (355)
                      .+|--+|==|   |++     ..|..+|..+.+     -.||++-|+.-.+
T Consensus       309 Gliv~NPPYGERLge~-----~~L~~LY~~lG~~lK~~f~GW~~~ilT~~~  354 (716)
T PRK11783        309 GLVISNPPYGERLGEE-----PALIALYSQLGRRLKKQFGGWNAALFSSSP  354 (716)
T ss_pred             CEEEECCCHHCCCCCC-----HHHHHHHHHHHHHHHHHCCCCEEEEEECCH
T ss_conf             2899678522013661-----468999999999999658998699997888


No 109
>pfam04800 ETC_C1_NDUFA4 ETC complex I subunit conserved region. Family of pankaryotic NADH-ubiquinone oxidoreductase subunits (EC:1.6.5.3) (EC:1.6.99.3) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein.
Probab=24.57  E-value=22  Score=16.35  Aligned_cols=17  Identities=18%  Similarity=0.327  Sum_probs=11.1

Q ss_pred             HHHHHHHHHHHHHHHCC
Q ss_conf             99987753113444205
Q gi|254780753|r  142 TRWAEKRKFKTEALEIH  158 (355)
Q Consensus       142 ~r~ae~~gwk~evi~~~  158 (355)
                      ..||+++||.++|++..
T Consensus        62 i~YA~k~gi~y~V~ep~   78 (101)
T pfam04800        62 IAFAERQGWEYDVEEPN   78 (101)
T ss_pred             HHHHHHCCCEEEEECCC
T ss_conf             99999849828995788


No 110
>COG1225 Bcp Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=24.55  E-value=28  Score=15.57  Aligned_cols=86  Identities=26%  Similarity=0.370  Sum_probs=48.2

Q ss_pred             CEEEEEECC--CCC--HHHHHHHHHHHHHH------------------HHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEE
Q ss_conf             248998217--787--02778999999989------------------99987753113444205454585013468850
Q gi|254780753|r  116 DAYLEVHAG--AGG--TESQDWANMLLRMY------------------TRWAEKRKFKTEALEIHDGEEAGIKSATLLIK  173 (355)
Q Consensus       116 nailEI~AG--aGG--~EA~dwA~~L~rMY------------------~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~  173 (355)
                      .++|-.-|.  +-|  +|||+|-..+ ..+                  .+|++++|.++.+++=..+..+          
T Consensus        32 ~VVLyFYPk~~TpgCT~Ea~~Frd~~-~ef~~~~a~V~GIS~Ds~~~~~~F~~k~~L~f~LLSD~~~~v~----------  100 (157)
T COG1225          32 PVVLYFYPKDFTPGCTTEACDFRDLL-EEFEKLGAVVLGISPDSPKSHKKFAEKHGLTFPLLSDEDGEVA----------  100 (157)
T ss_pred             CEEEEECCCCCCCCCHHHHHHHHHHH-HHHHHCCCEEEEEECCCHHHHHHHHHHHCCCCEEEECCCHHHH----------
T ss_conf             28999878899985169999999989-9998679789998089989999999982998556679737899----------


Q ss_pred             CCCCCHHHEEEC-------CEEEEEEECCCCCCCEEEEEEEEEEECCCCC
Q ss_conf             556100000101-------2068987304666650356688788503442
Q gi|254780753|r  174 GPNAYGWLKGEQ-------GVHRLVRISPYDSNSRRHTSFSSIWVYPVVD  216 (355)
Q Consensus       174 G~~ayg~Lk~E~-------GvHRv~Ri~~~~s~gR~hTS~a~V~V~P~~~  216 (355)
                        .+||-.+-..       |++|..-|  .|.+|++--.+--|-+-|.++
T Consensus       101 --~~ygv~~~k~~~gk~~~~~~R~Tfv--Id~dG~I~~~~~~v~~~~h~~  146 (157)
T COG1225         101 --EAYGVWGEKKMYGKEYMGIERSTFV--IDPDGKIRYVWRKVKVKGHAD  146 (157)
T ss_pred             --HHHCCCCCCCCCCCCCCCCCCEEEE--ECCCCEEEEEECCCCCCCCHH
T ss_conf             --9848663134576423322334899--899986999965899766199


No 111
>pfam11926 DUF3444 Domain of unknown function (DUF3444). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 210 amino acids in length. This domain is found associated with pfam00226. This domain has two conserved sequence motifs: FSH and FSH.
Probab=23.99  E-value=28  Score=15.65  Aligned_cols=23  Identities=13%  Similarity=0.190  Sum_probs=13.2

Q ss_pred             HHHCCC----CCCCCEEEEEECCCCCH
Q ss_conf             763034----57662489982177870
Q gi|254780753|r  106 SLLSGE----ADSNDAYLEVHAGAGGT  128 (355)
Q Consensus       106 ~Lls~e----~D~~nailEI~AGaGG~  128 (355)
                      .+||..    .....-..+|.|-.|-+
T Consensus       103 ~~FSH~v~~~~~~~r~~y~IyP~kGEV  129 (216)
T pfam11926       103 SMFSHQVVPEKKGRRNEYRIYPRKGEV  129 (216)
T ss_pred             CCEEEEEEEEECCCCCEEEEECCCCCE
T ss_conf             601578564665897679997998766


No 112
>KOG3083 consensus
Probab=23.97  E-value=51  Score=13.74  Aligned_cols=18  Identities=39%  Similarity=0.434  Sum_probs=14.5

Q ss_pred             CCCCCCCCCCCCEEEEEEECC
Q ss_conf             886554427310035887469
Q gi|254780753|r  236 SGAGGQHVNTTDSAVRITHIP  256 (355)
Q Consensus       236 sg~ggq~vn~t~savri~H~p  256 (355)
                      +-.--|+||.|   .||.|.|
T Consensus        81 GskdLQ~VniT---lril~rp   98 (271)
T KOG3083          81 GSKDLQNVNIT---LRILFRP   98 (271)
T ss_pred             CCHHHHCCCCE---EEEEECC
T ss_conf             73020105405---8999603


No 113
>PRK11020 hypothetical protein; Provisional
Probab=23.85  E-value=51  Score=13.73  Aligned_cols=61  Identities=20%  Similarity=0.285  Sum_probs=42.0

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHH
Q ss_conf             989999999999998708660025899999999998899999999999999--8639999986
Q gi|254780753|r   15 DWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDR--LCDNLILLEL   75 (355)
Q Consensus        15 Dle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~--l~Dl~eL~EL   75 (355)
                      ++..+..||+.+..++....--.|+.......+|+..|...|..++..++.  -.+...+..|
T Consensus         6 Elq~L~drLD~~r~Klaaa~~rgd~~~i~qf~~E~~~l~k~I~~lk~~q~~~lske~~~l~~l   68 (118)
T PRK11020          6 EIKRLSDRLDAIRHKLAAASLRGDADKIAQFEKEKATLEKEIARLKEVQSQKLSKEAQKLMKL   68 (118)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999998899999998899997478899999999999999999999889999988989998738


No 114
>KOG0544 consensus
Probab=23.75  E-value=35  Score=14.91  Aligned_cols=32  Identities=25%  Similarity=0.281  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEEEEEECCCCCHHHEE
Q ss_conf             7531134442054545850134688505561000001
Q gi|254780753|r  147 KRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKG  183 (355)
Q Consensus       147 ~~gwk~evi~~~~~e~~GiK~~~~~I~G~~ayg~Lk~  183 (355)
                      -+||.--+.-.|-|+.+     -+.|+.+||||--.+
T Consensus        57 IkGwdegv~qmsvGeka-----kLti~pd~aYG~~G~   88 (108)
T KOG0544          57 IKGWDEGVAQMSVGEKA-----KLTISPDYAYGPRGH   88 (108)
T ss_pred             EECHHHCCHHCCCCCCC-----EEEECCCCCCCCCCC
T ss_conf             60322321011536401-----016576312277888


No 115
>cd01989 STK_N The N-terminal domain of Eukaryotic Serine Threonine  kinases. The Serine Threonine  kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. The N-terminal domain is homologous to the USP family which has a ATP binding fold. The N-terminal domain  is predicted to be involved in ATP binding.
Probab=23.25  E-value=46  Score=14.07  Aligned_cols=72  Identities=19%  Similarity=0.318  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC----------CCEEEEEEEEECCCCCHHHEEECCEEEEEEECCCCCCCE
Q ss_conf             8999999989999877531134442054545----------850134688505561000001012068987304666650
Q gi|254780753|r  132 DWANMLLRMYTRWAEKRKFKTEALEIHDGEE----------AGIKSATLLIKGPNAYGWLKGEQGVHRLVRISPYDSNSR  201 (355)
Q Consensus       132 dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~----------~GiK~~~~~I~G~~ayg~Lk~E~GvHRv~Ri~~~~s~gR  201 (355)
                      .=+..|+.-|..+|..++-+++++-...++.          -|+.   .-|-|.-..|.++      |.-+-|..-+.--
T Consensus        61 ~~~~~ll~~~~~~C~~~~V~~e~~v~e~~d~~~~I~e~v~~~~i~---~LVmGs~~~~~~~------r~~~gs~vs~~v~  131 (146)
T cd01989          61 KEAKELLLPYRCFCSRKGVQCEDVVLEDDDVAKAIVEYVADHGIT---KLVMGASSDNHFS------MKFKKSDVASSVL  131 (146)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHCCCC---EEEECCCCCCCEE------EECCCCCHHHHHH
T ss_conf             999999999999998759728999983488889999999975998---9998627998514------5121786778998


Q ss_pred             EEE-EEEEEEEC
Q ss_conf             356-68878850
Q gi|254780753|r  202 RHT-SFSSIWVY  212 (355)
Q Consensus       202 ~hT-S~a~V~V~  212 (355)
                      +|. +|+.|.|.
T Consensus       132 ~~ap~~C~V~vV  143 (146)
T cd01989         132 KEAPDFCTVYVV  143 (146)
T ss_pred             HCCCCCCEEEEE
T ss_conf             379999859999


No 116
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=23.00  E-value=53  Score=13.61  Aligned_cols=60  Identities=10%  Similarity=0.055  Sum_probs=31.6

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             49899999999999987086600258999999999988999999999999998639999986
Q gi|254780753|r   14 FDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLEL   75 (355)
Q Consensus        14 fDle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~EL   75 (355)
                      +|...+..++..|..+.-=--|-+.+..-+.++-+.+.+  +=+.|..|++-+.-..=|+++
T Consensus        15 iD~~~L~~~y~~Lq~~~HPDkf~~~~~~e~~~a~~~ss~--iN~AY~tLk~pl~RA~yLL~L   74 (171)
T PRK05014         15 IDTQLLSLRYQELQRQVHPDKFANASEREQLAAVQQAAQ--INDAYQTLKHPLSRAEYMLSL   74 (171)
T ss_pred             CCHHHHHHHHHHHHHHHCHHHCCCCCHHHHHHHHHHHHH--HHHHHHHHCCHHHHHHHHHHH
T ss_conf             799999999999999869774058989999999999999--999999974889989999998


No 117
>KOG2148 consensus
Probab=22.90  E-value=53  Score=13.60  Aligned_cols=14  Identities=43%  Similarity=0.707  Sum_probs=11.1

Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             87027789999999
Q gi|254780753|r  126 GGTESQDWANMLLR  139 (355)
Q Consensus       126 GG~EA~dwA~~L~r  139 (355)
                      -|.|||.||+.-++
T Consensus       306 ~~ieact~aA~al~  319 (867)
T KOG2148         306 QGIEACTWAAKALR  319 (867)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             10799999999999


No 118
>PRK07081 acyl carrier protein; Provisional
Probab=22.71  E-value=1.3  Score=25.09  Aligned_cols=32  Identities=19%  Similarity=0.427  Sum_probs=14.6

Q ss_pred             EEEEEEEECCCCCCCCCCCCCCCEEEEEEECC
Q ss_conf             66887885034422211123455036998538
Q gi|254780753|r  204 TSFSSIWVYPVVDDSIEIEISESDCRIDTYRA  235 (355)
Q Consensus       204 TS~a~V~V~P~~~~~~~i~i~~~dl~i~~~rs  235 (355)
                      ||+++|.+|-.+++..+|+|++.-|.-.+|+|
T Consensus        34 sSl~tV~lMLaiEd~FdIeiPd~~L~r~~F~S   65 (83)
T PRK07081         34 SSLATVQLMLAIEDEFDIEIPDEMLNRKLFRS   65 (83)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCHHHHCHHHHHH
T ss_conf             27999999999999829808878838998865


No 119
>TIGR01169 rplA_bact ribosomal protein L1; InterPro: IPR005878   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    Ribosomal protein L1 is the largest protein from the large ribosomal subunit. In Escherichia coli, L1 is known to bind to the 23S rRNA. This model describe s bacterial and chloroplast ribosomal protein L1. Most mitochondrial L1 sequences are sufficiently divergent to be the contained in a different entry (IPR005879 from INTERPRO).; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=21.96  E-value=19  Score=16.84  Aligned_cols=48  Identities=31%  Similarity=0.513  Sum_probs=34.2

Q ss_pred             CCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCH------HHHHHHHHHHHHHHHH
Q ss_conf             442221112345503699853888655442731003588746974------7766555552246799
Q gi|254780753|r  214 VVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTG------VVVQCQQERSQHKNKA  274 (355)
Q Consensus       214 ~~~~~~~i~i~~~dl~i~~~rssg~ggq~vn~t~savri~H~ptg------i~v~~q~~rsq~~Nk~  274 (355)
                      ..|+++||.|+   |-||+-.|.    |+|+-|   |   -+|-|      +.|.|++++-.-+--+
T Consensus        35 KFDeTVeva~~---LG~DprKsD----Q~vRG~---v---vLP~GtGK~~RVaVfa~G~~~~eA~~A   88 (227)
T TIGR01169        35 KFDETVEVAIR---LGIDPRKSD----QQVRGT---V---VLPHGTGKTVRVAVFAKGEKAKEAKAA   88 (227)
T ss_pred             CCCCEEEEEEE---CCCCCCCCC----CEEEEE---E---ECCCCCCCCEEEEEECCCHHHHHHHHC
T ss_conf             43341788887---475885378----305113---8---657677862589997164348889870


No 120
>PRK07417 arogenate dehydrogenase; Reviewed
Probab=21.91  E-value=56  Score=13.47  Aligned_cols=13  Identities=15%  Similarity=0.373  Sum_probs=5.2

Q ss_pred             CEEEEEECCCCCHHHH
Q ss_conf             2489982177870277
Q gi|254780753|r  116 DAYLEVHAGAGGTESQ  131 (355)
Q Consensus       116 nailEI~AGaGG~EA~  131 (355)
                      +|+|.   -.|++-..
T Consensus        85 ~~iit---Dv~SvK~~   97 (280)
T PRK07417         85 EAIVT---DVGSVKEP   97 (280)
T ss_pred             CCEEE---ECHHHHHH
T ss_conf             84899---65223078


No 121
>KOG1760 consensus
Probab=21.85  E-value=56  Score=13.46  Aligned_cols=45  Identities=20%  Similarity=0.167  Sum_probs=25.4

Q ss_pred             CCCCHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             00258999999999---9889999999999999986399999863100
Q gi|254780753|r   35 LWQNVIEAKMLMRE---RQHLDNAISFIKEIQDRLCDNLILLELALEE   79 (355)
Q Consensus        35 fW~D~~kAqkl~KE---~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee   79 (355)
                      .|-|+.+..+.++-   ...++.-++..+.....++|...=++|+.++
T Consensus        15 t~EDQq~iN~Fsrl~~R~~~lk~dik~~k~~~enledA~~EieL~Ded   62 (131)
T KOG1760          15 TFEDQQNINEFSRLNSRKDDLKADIKEAKTEIENLEDASNEIELLDED   62 (131)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             488799899999987358899999999999998799877667322766


No 122
>KOG4657 consensus
Probab=21.84  E-value=56  Score=13.46  Aligned_cols=75  Identities=19%  Similarity=0.215  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCCCCCCEE
Q ss_conf             999999999988999999999999998639999986310000002345667655577401589988-7630345766248
Q gi|254780753|r   40 IEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSILQETSDNLQRIKLEVEYKQFE-SLLSGEADSNDAY  118 (355)
Q Consensus        40 ~kAqkl~KE~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D~el~eE~~~el~~l~~~le~LE~~-~Lls~e~D~~nai  118 (355)
                      ..|+.++.....++..+..+.+.++.+....+|+   .+.++..  .-++.++..+...++.++.. .+++.++|+.-+|
T Consensus        48 efar~lS~~~~e~e~l~~~l~etene~~~~neL~---~ek~~~q--~~ieqeik~~q~elEvl~~n~Q~lkeE~dd~kei  122 (246)
T KOG4657          48 EFARALSQSQVELENLKADLRETENELVKVNELK---TEKEARQ--MGIEQEIKATQSELEVLRRNLQLLKEEKDDSKEI  122 (246)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999988878999999999999999999999999---8888888--8789998888999999999888889875169999


Q ss_pred             E
Q ss_conf             9
Q gi|254780753|r  119 L  119 (355)
Q Consensus       119 l  119 (355)
                      |
T Consensus       123 I  123 (246)
T KOG4657         123 I  123 (246)
T ss_pred             H
T ss_conf             9


No 123
>pfam00834 Ribul_P_3_epim Ribulose-phosphate 3 epimerase family. This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.
Probab=21.71  E-value=56  Score=13.44  Aligned_cols=58  Identities=21%  Similarity=0.320  Sum_probs=36.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEE----------EEEEEECCCCCH
Q ss_conf             489982177870277899999998999987753113444205454585013----------468850556100
Q gi|254780753|r  117 AYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKS----------ATLLIKGPNAYG  179 (355)
Q Consensus       117 ailEI~AGaGG~EA~dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~----------~~~~I~G~~ayg  179 (355)
                      -+|.+.||-||..=..-+-.-.+-..++...+|+++++.  ..   ||++.          |-.-|.|.+.|+
T Consensus       132 LvMtV~PGf~GQ~f~~~~l~KI~~lr~~~~~~~~~~~I~--vD---GGIn~~ti~~l~~~Gad~~V~GSaiF~  199 (201)
T pfam00834       132 LLMSVNPGFGGQSFIPSVLPKIRKVRKMIDEGGLDTLIE--VD---GGVNLDNIPQIAEAGADVLVAGSAVFG  199 (201)
T ss_pred             EEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEE--EE---CCCCHHHHHHHHHCCCCEEEECCEECC
T ss_conf             998866898876456779999999999998269980799--98---988899999999879999997800245


No 124
>KOG1290 consensus
Probab=21.38  E-value=35  Score=14.93  Aligned_cols=42  Identities=12%  Similarity=0.202  Sum_probs=20.4

Q ss_pred             CCCCC-CCCEEEEE-----ECCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             03457-66248998-----21778702778999999989999877531
Q gi|254780753|r  109 SGEAD-SNDAYLEV-----HAGAGGTESQDWANMLLRMYTRWAEKRKF  150 (355)
Q Consensus       109 s~e~D-~~nailEI-----~AGaGG~EA~dwA~~L~rMY~r~ae~~gw  150 (355)
                      .||.| .+.|+|.+     ++|.-|.--|.--+-|=.=-++|..+-+|
T Consensus       134 ~Dp~~~~~~~VV~LlD~FkhsGpNG~HVCMVfEvLGdnLLklI~~s~Y  181 (590)
T KOG1290         134 GDPNDPGKKCVVQLLDHFKHSGPNGQHVCMVFEVLGDNLLKLIKYSNY  181 (590)
T ss_pred             CCCCCCCCCEEEEEECCCEECCCCCCEEEEEEHHHHHHHHHHHHHHCC
T ss_conf             598889973356630101313788747998816530679999998177


No 125
>pfam07851 TMPIT TMPIT-like protein. A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this.
Probab=21.37  E-value=57  Score=13.39  Aligned_cols=43  Identities=16%  Similarity=0.244  Sum_probs=29.2

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCC
Q ss_conf             000002345667655577401589988763034576624899821778
Q gi|254780753|r   79 EDDCSILQETSDNLQRIKLEVEYKQFESLLSGEADSNDAYLEVHAGAG  126 (355)
Q Consensus        79 e~D~el~eE~~~el~~l~~~le~LE~~~Lls~e~D~~nailEI~AGaG  126 (355)
                      +++.+.++++.+++.+-...+.+.| ..||+    .++.++.+--|.=
T Consensus        64 ~E~~~~~~~l~~~i~~r~~~l~dme-~~LP~----~nG~yL~l~LG~v  106 (330)
T pfam07851        64 PEDSELVEQLEEQIKERKNQFFDME-SFLPK----KNGLYLRLVLGNV  106 (330)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-HHCCC----CCCEEEEEECCCC
T ss_conf             7789999999999999999999998-64886----5886422111565


No 126
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.33  E-value=57  Score=13.39  Aligned_cols=94  Identities=15%  Similarity=-0.005  Sum_probs=50.5

Q ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHH
Q ss_conf             99988654989999999999998708660025899999999-99889999999999999986399999863100000023
Q gi|254780753|r    7 LNCLGGLFDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMR-ERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSIL   85 (355)
Q Consensus         7 l~~l~~~fDle~~~~rl~eLE~~lsdp~fW~D~~kAqkl~K-E~s~L~~iV~~~~~l~~~l~Dl~eL~ELa~ee~D~el~   85 (355)
                      +.++-..+.+....-|+-|=.-.+..|.--  ...++-... .+..| ..|..+..+--.++++.+++.+....+-.++.
T Consensus         3 IgevA~~~gvs~~TlRyYE~~GLl~~~~R~--~~gyR~Y~~~~l~rL-~~I~~~r~~G~sL~eI~~ll~~~~~~~~~~~~   79 (126)
T cd04783           3 IGELAKAAGVNVETIRYYQRRGLLPEPPRP--EGGYRRYPEETVTRL-RFIKRAQELGFTLDEIAELLELDDGTDCSEAR   79 (126)
T ss_pred             HHHHHHHHCCCHHHHHHHHHCCCCCCCCCC--CCCCCCCCHHHHHHH-HHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHH
T ss_conf             899999989398999999986998876318--999601779999999-99999998799899999997425699979999


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             456676555774015899
Q gi|254780753|r   86 QETSDNLQRIKLEVEYKQ  103 (355)
Q Consensus        86 eE~~~el~~l~~~le~LE  103 (355)
                      +.+...+..+...+.+|+
T Consensus        80 ~~l~~~~~~i~~~I~~L~   97 (126)
T cd04783          80 ELAEQKLAEVDEKIADLQ   97 (126)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999


No 127
>cd01145 TroA_c Periplasmic binding protein TroA_c.  These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=21.04  E-value=58  Score=13.35  Aligned_cols=13  Identities=31%  Similarity=0.764  Sum_probs=5.1

Q ss_pred             CCCCCCCHHHHHH
Q ss_conf             8660025899999
Q gi|254780753|r   32 DPHLWQNVIEAKM   44 (355)
Q Consensus        32 dp~fW~D~~kAqk   44 (355)
                      ||.+|-||..+..
T Consensus       107 dPH~Wldp~~~~~  119 (203)
T cd01145         107 NPHVWLDPNNAPA  119 (203)
T ss_pred             CCEECCCHHHHHH
T ss_conf             9801479999999


No 128
>KOG4181 consensus
Probab=21.00  E-value=22  Score=16.37  Aligned_cols=71  Identities=20%  Similarity=0.161  Sum_probs=34.5

Q ss_pred             CCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCC
Q ss_conf             73100358874697477665555522467999999999999999999999999998741332332221013015856833
Q gi|254780753|r  244 NTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIGWGRQIRSYVLQPYQMV  323 (355)
Q Consensus       244 n~t~savri~H~ptgi~v~~q~~rsq~~Nk~~a~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~iRtY~~~p~~~v  323 (355)
                      |-.++|.-+-|.-|...|-.- ---|..-|..-|.+|.+--.              +         .--|+|+|-|+.+-
T Consensus       173 ~~~d~a~~ll~~~tdf~VIgv-lG~QgsGKStllslLaans~--------------~---------~dyr~yvFRpvS~E  228 (491)
T KOG4181         173 IFNDNARKLLHKTTDFTVIGV-LGGQGSGKSTLLSLLAANSL--------------D---------YDYRQYVFRPVSPE  228 (491)
T ss_pred             CHHHHHHHHHHCCCCEEEEEE-ECCCCCCHHHHHHHHHCCCH--------------H---------HHHHHHHCCCCCHH
T ss_conf             123689999614898169974-04777548899999842684--------------7---------76677730357855


Q ss_pred             CCCCCCCEECCHHHH
Q ss_conf             111147250797787
Q gi|254780753|r  324 KDLRTNIEKTSPSDV  338 (355)
Q Consensus       324 ~DhR~~~~~~~~~~v  338 (355)
                      -|-+++.+++.++-+
T Consensus       229 a~E~~~~qt~~Id~~  243 (491)
T KOG4181         229 ADECIFAQTHKIDPN  243 (491)
T ss_pred             HHHHHCCCEECCCCC
T ss_conf             666530320033655


No 129
>COG3978 Acetolactate synthase (isozyme II), small (regulatory) subunit [Function unknown]
Probab=20.24  E-value=60  Score=13.23  Aligned_cols=52  Identities=17%  Similarity=0.248  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCCCHHHEE
Q ss_conf             8999999989999877531134442054545850134688505561000001
Q gi|254780753|r  132 DWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKG  183 (355)
Q Consensus       132 dwA~~L~rMY~r~ae~~gwk~evi~~~~~e~~GiK~~~~~I~G~~ayg~Lk~  183 (355)
                      .|+..++.=-+|--+.+||.+--++.++.-.||.-++-+.|.|+.++..|..
T Consensus        11 r~~pe~leRVLrvtrhRGF~vcamnmt~~~da~~~nie~tV~s~R~~~lL~~   62 (86)
T COG3978          11 RFNPETLERVLRVTRHRGFRVCAMNMTAAVDAGNANIELTVDSDRSVDLLTS   62 (86)
T ss_pred             CCCHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCEEEEEECCCCCHHHHHH
T ss_conf             6795899999988651575999852531123663059999858988689999


No 130
>cd06145 REX1_like This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of E.coli RNase T.
Probab=20.07  E-value=44  Score=14.18  Aligned_cols=13  Identities=31%  Similarity=0.580  Sum_probs=9.0

Q ss_pred             EEEEECCCCCCCE
Q ss_conf             8987304666650
Q gi|254780753|r  189 RLVRISPYDSNSR  201 (355)
Q Consensus       189 Rv~Ri~~~~s~gR  201 (355)
                      -|.|||..|..|.
T Consensus        15 ~LaRvsvVd~~g~   27 (150)
T cd06145          15 ELTRVTVVDENGK   27 (150)
T ss_pred             EEEEEEEECCCCC
T ss_conf             8999999938998


Done!