Query         gi|254780245|ref|YP_003064658.1| 50S ribosomal protein L18 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 120
No_of_seqs    103 out of 1938
Neff          5.6 
Searched_HMMs 39220
Date          Tue May 24 05:18:53 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780245.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK05593 rplR 50S ribosomal pr 100.0       0       0  297.3  15.3  115    1-120     1-115 (115)
  2 TIGR00060 L18_bact ribosomal p 100.0       0       0  294.3  12.8  117    4-120     1-118 (118)
  3 CHL00139 rpl18 ribosomal prote 100.0 1.4E-45       0  291.9  12.4  109   11-120     1-109 (109)
  4 pfam00861 Ribosomal_L18p Ribos 100.0 5.2E-43       0  275.8  15.0  117    3-120     1-119 (119)
  5 COG0256 RplR Ribosomal protein 100.0   2E-40 5.6E-45  260.5  14.6  119    1-120     5-125 (125)
  6 cd00432 Ribosomal_L18_L5e Ribo 100.0 1.9E-34 4.8E-39  225.1  12.4   96   23-118     8-103 (103)
  7 PTZ00032 60S ribosomal protein 100.0 2.1E-32 5.3E-37  213.0  11.3   96   25-120   104-211 (211)
  8 PRK08569 rpl18p 50S ribosomal   99.6 8.5E-15 2.2E-19  108.6  10.1  102   16-119    24-129 (193)
  9 PTZ00069 60S ribosomal protein  99.2 4.4E-10 1.1E-14   80.7  11.2   95   25-119    47-173 (300)
 10 KOG3333 consensus               98.6 4.2E-07 1.1E-11   63.0   8.7   93   27-120    61-154 (188)
 11 PTZ00090 40S ribosomal protein  96.5   0.014 3.7E-07   36.1   7.2   91   24-119    97-188 (214)
 12 PRK05309 30S ribosomal protein  96.5   0.063 1.6E-06   32.3  10.3   87   27-119    17-104 (126)
 13 CHL00041 rps11 ribosomal prote  96.4   0.054 1.4E-06   32.7   9.9   87   27-119    14-101 (116)
 14 pfam00411 Ribosomal_S11 Riboso  96.4    0.06 1.5E-06   32.4   9.8   84   29-119     3-88  (109)
 15 TIGR03632 bact_S11 30S ribosom  96.2     0.1 2.6E-06   31.1  10.3   84   29-119     3-88  (108)
 16 KOG0875 consensus               95.6   0.026 6.6E-07   34.6   4.9   68   25-92     47-117 (264)
 17 PRK09607 rps11p 30S ribosomal   93.5    0.68 1.7E-05   26.2   9.3   89   28-119     8-103 (129)
 18 TIGR03628 arch_S11P archaeal r  91.6     1.2 3.1E-05   24.7  10.0   89   28-119     4-99  (114)
 19 COG0100 RpsK Ribosomal protein  87.5     2.5 6.5E-05   22.8   8.7   67   29-98     21-88  (129)
 20 PTZ00129 40S ribosomal protein  87.2     2.7 6.8E-05   22.7   7.2   89   28-119    29-124 (150)
 21 TIGR02360 pbenz_hydroxyl 4-hyd  81.9     2.3   6E-05   23.0   4.1   44   75-118    11-61  (393)
 22 pfam02065 Melibiase Melibiase.  81.0     3.5   9E-05   22.0   4.7   41   80-120    62-120 (395)
 23 COG3345 GalA Alpha-galactosida  76.6     5.2 0.00013   21.0   4.5   41   80-120   313-371 (687)
 24 PRK00072 hemC porphobilinogen   68.5      11 0.00027   19.1   5.0   41   37-89    258-298 (300)
 25 pfam03900 Porphobil_deamC Porp  68.1      11 0.00028   19.0   4.9   21   69-89     54-74  (74)
 26 pfam07355 GRDB Glycine/sarcosi  67.6      11 0.00028   19.0   4.5   36   61-96    312-347 (349)
 27 smart00812 Alpha_L_fucos Alpha  66.0      12 0.00031   18.8   4.9   42   79-120    84-144 (384)
 28 TIGR02298 HpaD_Fe 3,4-dihydrox  60.8     6.1 0.00015   20.5   2.1   26   71-96     88-114 (343)
 29 pfam01120 Alpha_L_fucos Alpha-  59.2      16 0.00041   18.0   5.0   45   76-120    92-155 (344)
 30 cd06290 PBP1_LacI_like_9 Ligan  56.4      18 0.00046   17.8   5.6   45   76-120   101-148 (265)
 31 pfam00875 DNA_photolyase DNA p  55.1      19 0.00048   17.6   4.7   44   77-120    76-120 (164)
 32 cd01574 PBP1_LacI Ligand-bindi  50.0      23 0.00058   17.1   5.5   43   77-119   103-148 (264)
 33 TIGR01035 hemA glutamyl-tRNA r  49.3      23 0.00059   17.1   3.6   46   71-120   190-237 (436)
 34 cd06294 PBP1_ycjW_transcriptio  47.1      25 0.00065   16.9   5.9   45   76-120   108-155 (270)
 35 cd01545 PBP1_SalR Ligand-bindi  47.0      25 0.00065   16.9   6.2   46   75-120   103-151 (270)
 36 cd06271 PBP1_AglR_RafR_like Li  46.8      26 0.00065   16.8   5.7   45   76-120   106-153 (268)
 37 KOG0104 consensus               46.6      26 0.00066   16.8   3.4   97   18-119    91-187 (902)
 38 PRK05477 gatB aspartyl/glutamy  45.7      21 0.00054   17.3   2.9   63   37-104    12-87  (479)
 39 cd06273 PBP1_GntR_like_1 This   43.4      29 0.00074   16.5   5.7   46   75-120   101-150 (268)
 40 cd06274 PBP1_FruR Ligand bindi  42.9      29 0.00075   16.5   6.1   45   76-120   102-149 (264)
 41 PRK07666 fabG 3-ketoacyl-(acyl  42.6      30 0.00076   16.4   3.9   43   73-119    14-56  (238)
 42 cd06277 PBP1_LacI_like_1 Ligan  41.0      31  0.0008   16.3   5.8   45   76-120   104-151 (268)
 43 cd06272 PBP1_hexuronate_repres  40.9      32 0.00081   16.3   5.8   46   75-120    96-144 (261)
 44 cd06270 PBP1_GalS_like Ligand   40.2      32 0.00083   16.2   5.9   45   76-120   102-149 (268)
 45 PRK05866 short chain dehydroge  39.3      33 0.00085   16.1   4.3   42   73-118    48-89  (290)
 46 cd06275 PBP1_PurR Ligand-bindi  38.6      34 0.00088   16.1   5.8   45   76-120   103-150 (269)
 47 TIGR03206 benzo_BadH 2-hydroxy  38.4      35 0.00088   16.1   3.9   43   73-119    11-53  (250)
 48 PRK13381 peptidase T; Provisio  38.2      35 0.00089   16.0   4.5   24   77-100    39-62  (413)
 49 PRK06181 short chain dehydroge  38.1      35 0.00089   16.0   4.5   40   74-117    10-49  (263)
 50 PRK10703 DNA-binding transcrip  38.0      35  0.0009   16.0   5.6   47   74-120   162-211 (335)
 51 pfam06370 DUF1069 Protein of u  36.4      19 0.00048   17.7   1.4   22   84-105   161-182 (206)
 52 TIGR00666 PBP4 D-alanyl-D-alan  34.6      28 0.00071   16.6   2.1   20  100-119    76-97  (427)
 53 cd00494 HMBS Hydroxymethylbila  32.9      43  0.0011   15.5   4.3   38   37-86    254-291 (292)
 54 PRK05650 short chain dehydroge  32.9      43  0.0011   15.5   4.2   21   77-97     12-32  (270)
 55 PRK10727 DNA-binding transcrip  32.8      43  0.0011   15.5   5.4   45   76-120   162-209 (342)
 56 PRK10014 DNA-binding transcrip  32.6      43  0.0011   15.5   6.1   47   74-120   166-215 (342)
 57 PRK08278 short chain dehydroge  32.4      43  0.0011   15.5   4.6   45   74-118    15-62  (273)
 58 KOG0408 consensus               31.1      46  0.0012   15.3   7.7   89   25-119    78-167 (190)
 59 PRK10423 transcriptional repre  30.2      47  0.0012   15.3   5.5   45   76-120   160-207 (327)
 60 PRK07454 short chain dehydroge  29.2      49  0.0013   15.2   3.9   42   73-118    14-55  (241)
 61 COG0299 PurN Folate-dependent   28.7      50  0.0013   15.1   4.2   37   81-119    42-81  (200)
 62 PRK08277 D-mannonate oxidoredu  28.7      50  0.0013   15.1   4.0   41   74-118    19-59  (278)
 63 cd06293 PBP1_LacI_like_11 Liga  28.5      51  0.0013   15.1   6.1   44   77-120   103-149 (269)
 64 cd06298 PBP1_CcpA_like Ligand-  28.5      51  0.0013   15.1   5.9   45   76-120   102-150 (268)
 65 PRK07775 short chain dehydroge  28.4      51  0.0013   15.1   4.4   41   73-117    18-58  (275)
 66 PRK08243 4-hydroxybenzoate 3-m  28.4      51  0.0013   15.1   4.1   12   94-105   260-271 (392)
 67 cd01543 PBP1_XylR Ligand-bindi  28.0      52  0.0013   15.0   6.0   46   75-120    94-141 (265)
 68 PRK11041 DNA-binding transcrip  27.8      52  0.0013   15.0   6.1   45   76-120   170-217 (341)
 69 PRK00819 RNA 2'-phosphotransfe  27.7      30 0.00078   16.4   1.3   22   98-119    93-114 (179)
 70 PRK08862 short chain dehydroge  27.5      53  0.0013   15.0   3.6   17   72-88    117-133 (227)
 71 pfam00289 CPSase_L_chain Carba  27.3      53  0.0014   15.0   3.2   49   69-120    53-101 (109)
 72 cd06291 PBP1_Qymf_like Ligand   27.3      53  0.0014   15.0   5.9   45   76-120    98-146 (265)
 73 cd06284 PBP1_LacI_like_6 Ligan  27.2      54  0.0014   14.9   5.9   45   76-120   101-148 (267)
 74 cd06280 PBP1_LacI_like_4 Ligan  26.8      54  0.0014   14.9   6.0   46   75-120   100-147 (263)
 75 PRK12857 putative aldolase; Re  26.7      55  0.0014   14.9   5.0   38   81-118    89-129 (284)
 76 cd06285 PBP1_LacI_like_7 Ligan  26.7      55  0.0014   14.9   5.9   44   77-120   101-147 (265)
 77 PRK07035 short chain dehydroge  26.6      55  0.0014   14.9   3.9   40   74-117    17-56  (252)
 78 PRK08185 hypothetical protein;  26.4      55  0.0014   14.9   5.1   39   80-118    82-123 (283)
 79 PRK12737 gatY tagatose-bisphos  26.4      55  0.0014   14.8   4.9   38   81-118    89-129 (284)
 80 PRK07832 short chain dehydroge  26.3      55  0.0014   14.8   4.6   38   75-116    10-47  (272)
 81 TIGR01830 3oxo_ACP_reduc 3-oxo  25.9      56  0.0014   14.8   4.9   44   73-119     6-49  (238)
 82 PRK12827 short chain dehydroge  25.9      57  0.0014   14.8   5.1   46   73-118    14-59  (251)
 83 PRK06457 pyruvate dehydrogenas  25.8      57  0.0015   14.8   4.9   16   97-114   424-439 (549)
 84 PRK06139 short chain dehydroge  25.7      57  0.0015   14.8   5.0   42   73-118    14-55  (324)
 85 PRK05653 fabG 3-ketoacyl-(acyl  25.0      59  0.0015   14.7   3.9   38   76-117    16-53  (246)
 86 COG3669 Alpha-L-fucosidase [Ca  24.9      45  0.0012   15.4   1.8   40   81-120    59-117 (430)
 87 pfam02776 TPP_enzyme_N Thiamin  24.8      59  0.0015   14.7   4.9   39   77-120     3-42  (172)
 88 COG1908 FrhD Coenzyme F420-red  24.5      60  0.0015   14.6   2.8   39   81-119    45-93  (132)
 89 PRK08945 short chain dehydroge  24.4      60  0.0015   14.6   4.2   27   69-95    124-150 (245)
 90 TIGR02867 spore_II_P stage II   24.2      61  0.0016   14.6   2.5   20   75-94     40-60  (221)
 91 COG4861 Uncharacterized protei  24.1      37 0.00095   15.9   1.2   48   69-118   144-192 (345)
 92 cd01575 PBP1_GntR Ligand-bindi  24.0      61  0.0016   14.6   6.0   46   75-120   101-149 (268)
 93 cd06267 PBP1_LacI_sugar_bindin  24.0      62  0.0016   14.6   5.6   45   76-120   102-149 (264)
 94 PRK10401 DNA-binding transcrip  23.6      63  0.0016   14.5   5.3   44   77-120   163-209 (346)
 95 PRK09526 lacI lac repressor; R  23.4      63  0.0016   14.5   5.4   44   76-119   167-213 (342)
 96 COG0064 GatB Asp-tRNAAsn/Glu-t  22.9      65  0.0016   14.5   3.6   63   37-104    13-89  (483)
 97 pfam02826 2-Hacid_dh_C D-isome  22.6      66  0.0017   14.4   3.1   24   76-99     46-69  (176)
 98 PRK07102 short chain dehydroge  22.6      66  0.0017   14.4   4.3   26   70-95    107-132 (243)
 99 KOG4691 consensus               22.5      48  0.0012   15.2   1.5   22   85-106   187-209 (227)
100 PRK06194 hypothetical protein;  22.2      67  0.0017   14.4   3.8   41   74-118    15-55  (301)
101 pfam12005 DUF3499 Protein of u  22.1      52  0.0013   15.0   1.6   46   73-118    40-89  (125)
102 TIGR01318 gltD_gamma_fam gluta  21.9      63  0.0016   14.5   2.0   23   76-98    153-175 (480)
103 COG0068 HypF Hydrogenase matur  21.7      68  0.0017   14.3   5.4   48   73-120   677-724 (750)
104 PRK07109 short chain dehydroge  21.6      69  0.0018   14.3   4.1   42   73-118    16-57  (338)
105 TIGR01235 pyruv_carbox pyruvat  21.5      69  0.0018   14.3   2.3   17   35-51    210-226 (1169)
106 COG1400 SEC65 Signal recogniti  21.3      61  0.0016   14.6   1.8   13   80-92     36-48  (93)
107 pfam01116 F_bP_aldolase Fructo  21.1      70  0.0018   14.2   5.0   38   81-118    87-127 (283)
108 PRK12738 kbaY tagatose-bisphos  21.1      71  0.0018   14.2   5.0   38   81-118    89-129 (286)
109 pfam03446 NAD_binding_2 NAD bi  21.0      71  0.0018   14.2   4.0   14   81-96    105-118 (163)
110 PRK06806 fructose-bisphosphate  21.0      71  0.0018   14.2   5.1   39   80-118    88-129 (281)
111 cd00947 TBP_aldolase_IIB Tagat  20.9      71  0.0018   14.2   5.0   38   81-118    84-124 (276)
112 cd07039 TPP_PYR_POX Pyrimidine  20.8      71  0.0018   14.2   4.9   39   77-120     2-41  (164)
113 cd06319 PBP1_ABC_sugar_binding  20.4      73  0.0019   14.1   6.3   52   68-119   101-157 (277)
114 KOG3396 consensus               20.4      73  0.0019   14.1   6.8   62   38-99     53-128 (150)
115 KOG1185 consensus               20.3      73  0.0019   14.1   4.3   38   78-120    17-54  (571)
116 pfam00532 Peripla_BP_1 family.  20.2      74  0.0019   14.1   5.4   45   76-120   106-154 (281)

No 1  
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=100.00  E-value=0  Score=297.25  Aligned_cols=115  Identities=49%  Similarity=0.736  Sum_probs=109.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHH
Q ss_conf             98879999989987768750578788249999638709999996279759999850210000013468667899999999
Q gi|254780245|r    1 MATKKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNL   80 (120)
Q Consensus         1 m~~k~~~~~kR~~R~R~k~k~~~~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~   80 (120)
                      ||+|++.+.||+.|+|+++.+++ ++|||+|||||+|||||||||.+++||||+||+|++++.    ++|+++|..||++
T Consensus         1 ~~~K~~~r~rR~~RiR~ki~~t~-~rpRL~VfrSnkhiyaQiIDD~~~~tl~saST~~k~~~~----~~n~~~A~~vG~~   75 (115)
T PRK05593          1 KMDKKEARLRRAKRVRKKISGTA-ERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDLKA----GGNKEAAKKVGKL   75 (115)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCC-CCCEEEEEECCCEEEEEEEECCCCCEEEEEECCCHHHHC----CCCHHHHHHHHHH
T ss_conf             98678999999999999972789-986799996088279999986999799997414244416----8849999999999


Q ss_pred             HHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             9999997799799983898631225999999999658789
Q gi|254780245|r   81 LVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        81 ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ||++++++||++|+||||||+|||||+||||++||+||+|
T Consensus        76 ia~~a~~~~I~~v~FDR~g~~YHGrvkalAd~aRe~Gl~F  115 (115)
T PRK05593         76 IAERAKAKGIKQVVFDRGGYKYHGRVKALADAAREAGLKF  115 (115)
T ss_pred             HHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHCCCCC
T ss_conf             9999998799889981899842239999999999848999


No 2  
>TIGR00060 L18_bact ribosomal protein L18; InterPro: IPR004389   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 is the ribosomal protein L18 family. The archaebacterial and eukaryotic type rpL18 is not included in this family.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=100.00  E-value=0  Score=294.25  Aligned_cols=117  Identities=48%  Similarity=0.705  Sum_probs=112.0

Q ss_pred             HHHHHHHHHHHHHHHHCCCC-CCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             79999989987768750578-78824999963870999999627975999985021000001346866789999999999
Q gi|254780245|r    4 KKKVLARRISRIRRHLKSVS-RGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLV   82 (120)
Q Consensus         4 k~~~~~kR~~R~R~k~k~~~-~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia   82 (120)
                      ++..+.+|+.|++.||..+. ..+|||+|||||+|||||+|||.++.||+|+||+++++...+..++|.|+|+.||+++|
T Consensus         1 ~~~~r~rR~~Ri~~kl~~~~~~~rprl~VfrS~~hiYAQvIDd~~~~tlas~Stl~~~l~~~~~~~~n~~~a~~vG~~~A   80 (118)
T TIGR00060         1 KKSARLRRHKRIRKKLRGTGEANRPRLVVFRSNRHIYAQVIDDVKQVTLASASTLEKKLKEQLKSTGNKDAAKKVGKLVA   80 (118)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCEEEEEEECCCCEEEEEHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             91578899999999986214256836899861681789999858884787315566887765103789889999999999


Q ss_pred             HHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             99997799799983898631225999999999658789
Q gi|254780245|r   83 ERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        83 ~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ++++++||+.|+||||||+|||||+||||++||+||+|
T Consensus        81 ~rl~~kgi~~vvFDR~G~~YHGrv~ALAeaaRE~Gl~f  118 (118)
T TIGR00060        81 ERLIKKGINDVVFDRGGYKYHGRVAALAEAAREAGLNF  118 (118)
T ss_pred             HHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             99997277226852699622338999999999700359


No 3  
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=100.00  E-value=1.4e-45  Score=291.85  Aligned_cols=109  Identities=47%  Similarity=0.759  Sum_probs=105.7

Q ss_pred             HHHHHHHHHCCCCCCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99877687505787882499996387099999962797599998502100000134686678999999999999997799
Q gi|254780245|r   11 RISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGV   90 (120)
Q Consensus        11 R~~R~R~k~k~~~~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI   90 (120)
                      |++|+|+++++++ .+|||+|||||+|||||||||.+++||||+||++++++..++.++|+++|+.||++||++++++||
T Consensus         1 R~~RiR~ki~gt~-~rpRL~V~rSnkhiyaQiIDD~~g~tl~saST~~k~~~~~~~~~~n~e~A~~vG~~ia~~a~~~gI   79 (109)
T CHL00139          1 KHRRLRKKIQGTA-ERPRLSVFRSNKHIYAQIIDDTNGKTLVSCSTLDPDVKSNLSIGSTCDASKLVGQKLAKKSLKKGI   79 (109)
T ss_pred             CCHHHHHHCCCCC-CCCEEEEEECCCEEEEEEEECCCCCEEEEEECCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9466662604899-988899997088189999987999899996233677765514786699999999999999998799


Q ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             799983898631225999999999658789
Q gi|254780245|r   91 KSVYFDRGKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        91 ~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ++|+||||||+||||||||||++||+||+|
T Consensus        80 ~~VvFDRggy~YHGrVkalAd~aRe~GLkF  109 (109)
T CHL00139         80 TKVVFDRGGKLYHGRIKALAEAAREAGLQF  109 (109)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHCCCCC
T ss_conf             999985899842219999999999848989


No 4  
>pfam00861 Ribosomal_L18p Ribosomal L18p/L5e family. This family includes ribosomal proteins from the large subunit. This family includes L18 from bacteria and L5 from eukaryotes. It has been shown that the amino terminal 93 amino acids of the rat 60S ribosomal protein L5 are necessary and sufficient to bind 5S rRNA in vitro. Suggesting that the entire family has a function in rRNA binding.
Probab=100.00  E-value=5.2e-43  Score=275.78  Aligned_cols=117  Identities=49%  Similarity=0.682  Sum_probs=110.0

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCC--CCCCCCHHHHHHHHHH
Q ss_conf             87999998998776875057878824999963870999999627975999985021000001--3468667899999999
Q gi|254780245|r    3 TKKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSS--LKTGANIVAATAVGNL   80 (120)
Q Consensus         3 ~k~~~~~kR~~R~R~k~k~~~~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~--~~~~~ni~aA~~vG~~   80 (120)
                      .|+..+.+|+.|+|+++.+++ .+|||+||+||+|||||||||..+.||+++||++++++..  ....+|+++|++||++
T Consensus         1 ~k~~~r~~r~~rir~k~~~~~-~rpRL~V~rSNkhiyaQiIdd~~~~tl~saSt~~k~lkk~~~k~~~~n~~aA~~vG~~   79 (119)
T pfam00861         1 GKRRRRRRKRLRVRRKLKGTA-ERPRLVVRRSNKHIYAQIIDDTKGGTLVSASTLSKELKKYGLKGGGNNTAAAYLVGLL   79 (119)
T ss_pred             CCHHHHHHHHHHHHHHHCCCC-CCCEEEEEEECCEEEEEEEECCCCCEEEEEECCCHHHHHHCCCCCCCHHHHHHHHHHH
T ss_conf             927889999999997653899-9988999996894899999868998899997340567773444677649999999999


Q ss_pred             HHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             9999997799799983898631225999999999658789
Q gi|254780245|r   81 LVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        81 ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ||++++++||++|+||||||+|||||+||||++||+||+|
T Consensus        80 ia~ka~~~gi~~v~fDR~g~~yhGrvka~A~~aRe~Gl~F  119 (119)
T pfam00861        80 LAKRALKKGIAVVVFDRGGYTYHGRVFALAKGAREAGLNF  119 (119)
T ss_pred             HHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCC
T ss_conf             9999998799889983899844599999999999838889


No 5  
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=2e-40  Score=260.51  Aligned_cols=119  Identities=47%  Similarity=0.699  Sum_probs=110.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCC--CCCCCCCHHHHHHHH
Q ss_conf             988799999899877687505787882499996387099999962797599998502100000--134686678999999
Q gi|254780245|r    1 MATKKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRS--SLKTGANIVAATAVG   78 (120)
Q Consensus         1 m~~k~~~~~kR~~R~R~k~k~~~~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~--~~~~~~ni~aA~~vG   78 (120)
                      |+.++..+.||+.|+|.++.+. ..+|||+||+||+|||||||||..+.|++++||+++++..  +...++|+++|++||
T Consensus         5 ~~~rr~~~~kr~~r~R~kl~g~-~~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~~~N~~aA~~vG   83 (125)
T COG0256           5 VKFRRRRRGKRAYRIRKKLLGT-SGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGGNTEAAYLVG   83 (125)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCC-CCCCEEEEEEECCCEEEEEEECCCCCEEEEEECCHHHHHHHCCCCCCCCHHHHHHHH
T ss_conf             2557899876777777653068-999579999808938999997489966999871367776403257898789999999


Q ss_pred             HHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             999999997799799983898631225999999999658789
Q gi|254780245|r   79 NLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        79 ~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      +++|++++++||++|+|||+||+|||||+|+||++||+||+|
T Consensus        84 ~lia~ra~~kgi~~vVfdr~g~~yhgRV~Ala~~AreaGL~f  125 (125)
T COG0256          84 KLIAERALAKGIEEVVFDRGGYKYHGRVAALADGAREAGLEF  125 (125)
T ss_pred             HHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHCCCCC
T ss_conf             999999998599589983898865119999999999729679


No 6  
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e:  L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=100.00  E-value=1.9e-34  Score=225.05  Aligned_cols=96  Identities=51%  Similarity=0.744  Sum_probs=93.1

Q ss_pred             CCCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf             87882499996387099999962797599998502100000134686678999999999999997799799983898631
Q gi|254780245|r   23 SRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLY  102 (120)
Q Consensus        23 ~~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v~FDR~g~~y  102 (120)
                      ...+|||+||+||+|||||||||.+++||||+||+|+++++.+...+|+++|+.||++||++++++||++|+||||||+|
T Consensus         8 ~~~~pRl~V~~Snk~i~aqiid~~~~~tl~sasT~~~~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vvfDrg~~~y   87 (103)
T cd00432           8 TQERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFDRGGYRY   87 (103)
T ss_pred             CCCCCEEEEEEECCEEEEEEEECCCCCEEEEEECCHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCC
T ss_conf             89998899998189389999985999599999714065531236886299999999999999998799889986799976


Q ss_pred             HHHHHHHHHHHHHCCC
Q ss_conf             2259999999996587
Q gi|254780245|r  103 CGRIAALADAVRKGGV  118 (120)
Q Consensus       103 HGrvka~ad~~R~~Gl  118 (120)
                      ||||+||||++||+||
T Consensus        88 hgrv~a~a~~~re~Gl  103 (103)
T cd00432          88 HGRVKALAKGAREGGL  103 (103)
T ss_pred             CHHHHHHHHHHHHCCC
T ss_conf             3799999999998589


No 7  
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=99.98  E-value=2.1e-32  Score=212.96  Aligned_cols=96  Identities=30%  Similarity=0.482  Sum_probs=90.0

Q ss_pred             CCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCC------------CCCCCCHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             8824999963870999999627975999985021000001------------3468667899999999999999779979
Q gi|254780245|r   25 GRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSS------------LKTGANIVAATAVGNLLVERAVKVGVKS   92 (120)
Q Consensus        25 ~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~------------~~~~~ni~aA~~vG~~ia~r~~~~gI~~   92 (120)
                      .+|||.+.+||+||||.||||.+.++||..+|.++.+..-            .+.++|++||+.||++||++|+++||++
T Consensus       104 R~pRl~iK~Tnn~iyAtIvDDy~r~vlCf~cs~~~~lS~I~Gty~~k~tnr~~nnGg~i~aA~eVGk~IakkA~~kGI~~  183 (211)
T PTZ00032        104 RRPRLTLKNTNNQMYATIVDDYTRYVLCFTCTNFKYLSHIFGTYPTKATNRVRNNGGTIKAAYELGKLIGRKALSKGISK  183 (211)
T ss_pred             CCCCEEEECCCCEEEEEEECCCCCEEEEEECCCCCHHHHHHCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHCCCCE
T ss_conf             65306875267736787730200057999625882176663466666767375589765999999999999999879988


Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             9983898631225999999999658789
Q gi|254780245|r   93 VYFDRGKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        93 v~FDR~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      |+||||||+|||||+||||+|||+||+|
T Consensus       184 VvFDRggy~YHGRVkALAe~ARe~GL~F  211 (211)
T PTZ00032        184 VRFDRAHYKYAGKVEALAEGARAVGLQF  211 (211)
T ss_pred             EEECCCCCCCCHHHHHHHHHHHHHCCCC
T ss_conf             9987999732028999999999718899


No 8  
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=99.60  E-value=8.5e-15  Score=108.57  Aligned_cols=102  Identities=29%  Similarity=0.316  Sum_probs=90.4

Q ss_pred             HHHHCCCCCCCCEEEEEEECCCEEEEEEE--CCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             68750578788249999638709999996--2797599998502100000134686678999999999999997799799
Q gi|254780245|r   16 RRHLKSVSRGRLRLSVCRSSKHIYGQIID--DSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV   93 (120)
Q Consensus        16 R~k~k~~~~~~pRL~V~rSnkhiyAQiId--d~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v   93 (120)
                      |.++  ...++|||+|.+||++|.+||+.  ..++.|||||.|.|..-.++....+|++||++.|.++|.+++++|+++.
T Consensus        24 R~~L--l~s~k~R~VVR~TN~~ii~Qiv~~~~~GD~v~~sa~s~eL~kyG~k~~~~N~pAaYltGlL~gkral~~G~~ea  101 (193)
T PRK08569         24 RLKL--LLSGKPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSKELAKYGWKGDTGNTPAAYLTGLLAGKKALKAGVEEA  101 (193)
T ss_pred             HHHH--HHCCCCEEEEEECCCCEEEEEEEEECCCCEEEEEEEHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEE
T ss_conf             9999--85699759999738847999998607898999997652375568478877208999989999999997497637


Q ss_pred             EECCCCCCCH--HHHHHHHHHHHHCCCC
Q ss_conf             9838986312--2599999999965878
Q gi|254780245|r   94 YFDRGKHLYC--GRIAALADAVRKGGVS  119 (120)
Q Consensus        94 ~FDR~g~~yH--Grvka~ad~~R~~Gl~  119 (120)
                      ++|-|-.+..  +||.|...++-++||+
T Consensus       102 iLDiGL~~~t~G~rvfaalKGavDaGl~  129 (193)
T PRK08569        102 VLDIGLHRPTKGSRVFAALKGAVDAGLE  129 (193)
T ss_pred             EEECCCCCCCCCCCHHHHHHCCCCCCCC
T ss_conf             9840566465562068866323245611


No 9  
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=99.18  E-value=4.4e-10  Score=80.65  Aligned_cols=95  Identities=28%  Similarity=0.251  Sum_probs=78.9

Q ss_pred             CCCEEEEEEECCCEEEEEEE--CCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHC--------CCCE--
Q ss_conf             88249999638709999996--27975999985021000001346866789999999999999977--------9979--
Q gi|254780245|r   25 GRLRLSVCRSSKHIYGQIID--DSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKV--------GVKS--   92 (120)
Q Consensus        25 ~~pRL~V~rSnkhiyAQiId--d~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~--------gI~~--   92 (120)
                      -+|||+|.+||++|.+||+.  ..++.|+|+|.|.|..--+......|.+||+..|.++|.+++++        |+++  
T Consensus        47 pKyRlVVR~TN~~iicQiv~a~~~GD~v~~aA~s~EL~kyG~k~gltNyaAAY~TGlLlarR~L~kl~ld~~y~G~~e~~  126 (300)
T PTZ00069         47 PKYRLVVRITNKDIICQIVYAKIVGDKVVAAAYSHELPRFGIPVGLTNYAAAYATGLLLARRTLKKLKLADKFEGVKEAD  126 (300)
T ss_pred             CCCEEEEEEECCEEEEEEEEECCCCCEEEEEEECCHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCC
T ss_conf             87449999877828999998506898999985112042358878877408999989999999998606223315752145


Q ss_pred             ------------------EEECCCCCCC--HHHHHHHHHHHHHCCCC
Q ss_conf             ------------------9983898631--22599999999965878
Q gi|254780245|r   93 ------------------VYFDRGKHLY--CGRIAALADAVRKGGVS  119 (120)
Q Consensus        93 ------------------v~FDR~g~~y--HGrvka~ad~~R~~Gl~  119 (120)
                                        +++|-|-.+=  -.||.+...|+-++||.
T Consensus       127 g~~~~v~e~~~~~~rpFka~LDvGL~rtTtG~RVFaaLKGAvDgGl~  173 (300)
T PTZ00069        127 GSYYAVDEEDDEERRPFKAILDVGLARTTTGNRVFGALKGAVDGGLA  173 (300)
T ss_pred             CCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHCCCCCCCC
T ss_conf             75101222355787764799732544477653244532123357735


No 10 
>KOG3333 consensus
Probab=98.58  E-value=4.2e-07  Score=62.97  Aligned_cols=93  Identities=24%  Similarity=0.420  Sum_probs=78.0

Q ss_pred             CEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCC-CCHHH
Q ss_conf             24999963870999999627975999985021000001346866789999999999999977997999838986-31225
Q gi|254780245|r   27 LRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKH-LYCGR  105 (120)
Q Consensus        27 pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v~FDR~g~-~yHGr  105 (120)
                      +||-|-+|-.|..+-+.+-+ +.|++||||.|..++..+.++.|+.|+..||..||.||++.||+..++.-... .--..
T Consensus        61 h~lev~~~~~hveg~v~H~~-~gvvvSAST~EwaIk~qLYst~dtsA~~niGRVLAqRCLqsGI~fm~~~~t~ea~~~s~  139 (188)
T KOG3333          61 HRLEVIRTQHHVEGLVEHQN-GGVVVSASTREWAIKKQLYSTRDTSACENIGRVLAQRCLQSGINFMVYQPTPEAAASSS  139 (188)
T ss_pred             EEEEEEECCCCEEEEEEEEC-CCEEEEECCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCEECCCCCHHHCCCHH
T ss_conf             67887404641122356722-98899704551578987751463499887889999999982766332588834333158


Q ss_pred             HHHHHHHHHHCCCCC
Q ss_conf             999999999658789
Q gi|254780245|r  106 IAALADAVRKGGVSF  120 (120)
Q Consensus       106 vka~ad~~R~~Gl~F  120 (120)
                      .+-|-.++-|+|+-|
T Consensus       140 ~q~l~~a~~e~Gv~l  154 (188)
T KOG3333         140 MQRLQSAMTEGGVVL  154 (188)
T ss_pred             HHHHHHHHHHCCEEE
T ss_conf             999999987488653


No 11 
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=96.50  E-value=0.014  Score=36.12  Aligned_cols=91  Identities=18%  Similarity=0.258  Sum_probs=64.7

Q ss_pred             CCCCEEEEEEECCCEEEEEEECCCC-EEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf             7882499996387099999962797-599998502100000134686678999999999999997799799983898631
Q gi|254780245|r   24 RGRLRLSVCRSSKHIYGQIIDDSIG-HTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLY  102 (120)
Q Consensus        24 ~~~pRL~V~rSnkhiyAQiIdd~~~-~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v~FDR~g~~y  102 (120)
                      .++.++++.-|..+.+||+|+.... +|+...---.-.+...+-  ..-.-|+.+|+.||++|+-.||..|-.   .|+|
T Consensus        97 td~F~~V~ttsKNNvhaqvvNkS~nyrTvfgsfAGnVG~~K~~q--q~~kcAyRIGeniAkKcrRLGif~vdv---kFRr  171 (214)
T PTZ00090         97 TDRFMLVLTTSKNNVHAQLVNRSKNYKTVFGSFAGNVGFTKKLQ--QSERCAYRIGENIAKKCKRLGIFAVDV---KFRR  171 (214)
T ss_pred             CCEEEEEEECCCCCEEEEEEECCCCEEEEEEECCCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHCEEEEEH---HHHH
T ss_conf             76189999805774440110044440256531154210678876--300689999889999988728221104---6899


Q ss_pred             HHHHHHHHHHHHHCCCC
Q ss_conf             22599999999965878
Q gi|254780245|r  103 CGRIAALADAVRKGGVS  119 (120)
Q Consensus       103 HGrvka~ad~~R~~Gl~  119 (120)
                      --||..+..+.-.+||+
T Consensus       172 imRve~vlqa~~a~~l~  188 (214)
T PTZ00090        172 IMRVETVLQAFYANGLQ  188 (214)
T ss_pred             HHHHHHHHHHHHHCCCC
T ss_conf             99999999999973762


No 12 
>PRK05309 30S ribosomal protein S11; Validated
Probab=96.46  E-value=0.063  Score=32.31  Aligned_cols=87  Identities=23%  Similarity=0.243  Sum_probs=65.6

Q ss_pred             CEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCCCCCCHHH
Q ss_conf             2499996387099999962797599998502100000134686678999999999999997799799-983898631225
Q gi|254780245|r   27 LRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRGKHLYCGR  105 (120)
Q Consensus        27 pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~g~~yHGr  105 (120)
                      =-+.|+-|..|....|. |.+|.+|+..|+-...|++..+  +.--||..+++.+++++++.||..| ++=+|- = -||
T Consensus        17 GivhI~ss~NNTiitlT-D~~Gn~l~~~S~G~~gfKg~rK--~T~~Aa~~aa~~~~~~~~~~Gi~~v~V~ikG~-G-~GR   91 (126)
T PRK05309         17 GVAHIHATFNNTIVTIT-DRQGNAISWASAGGSGFKGSRK--STPYAAQVAAEDAAKKAKEHGMKTVEVFVKGP-G-SGR   91 (126)
T ss_pred             EEEEEEECCCCEEEEEE-CCCCCEEEEEECCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHCCCEEEEEEEECC-C-CCH
T ss_conf             08999944798899998-3999999998077502588765--66669999999999999972971999999778-8-338


Q ss_pred             HHHHHHHHHHCCCC
Q ss_conf             99999999965878
Q gi|254780245|r  106 IAALADAVRKGGVS  119 (120)
Q Consensus       106 vka~ad~~R~~Gl~  119 (120)
                      -.+ .-++...||+
T Consensus        92 ~~a-ir~L~~~gik  104 (126)
T PRK05309         92 ESA-IRALQAAGLE  104 (126)
T ss_pred             HHH-HHHHHHCCCE
T ss_conf             999-9999878988


No 13 
>CHL00041 rps11 ribosomal protein S11
Probab=96.44  E-value=0.054  Score=32.69  Aligned_cols=87  Identities=18%  Similarity=0.199  Sum_probs=66.1

Q ss_pred             CEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCCCCCCHHH
Q ss_conf             2499996387099999962797599998502100000134686678999999999999997799799-983898631225
Q gi|254780245|r   27 LRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRGKHLYCGR  105 (120)
Q Consensus        27 pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~g~~yHGr  105 (120)
                      -.+.|+.|..|....+. |.+|.+++.+|+=...|++..+  ..--||..+++.+++++++.||+.| ++=+| .= .||
T Consensus        14 Gi~hI~~t~NNTiitlT-D~~Gn~l~~~S~G~~gfKg~rK--~T~~Aa~~aa~~~~~~a~~~Gi~~v~v~vkG-~G-~GR   88 (116)
T CHL00041         14 GVIHIQASFNNTIVTVT-DVRGRVISWSSAGACGFKGRRK--GTPFAAQTAAENAIRTVIDQGMKRAEVMIKG-PG-LGR   88 (116)
T ss_pred             EEEEEEECCCCEEEEEE-CCCCCEEEEECCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHCCCEEEEEEEEC-CC-CCH
T ss_conf             79999944798899998-4999999998077311588876--8988999999999999997398499999978-88-458


Q ss_pred             HHHHHHHHHHCCCC
Q ss_conf             99999999965878
Q gi|254780245|r  106 IAALADAVRKGGVS  119 (120)
Q Consensus       106 vka~ad~~R~~Gl~  119 (120)
                      -.+ .-++...||+
T Consensus        89 ~~a-ik~l~~~glk  101 (116)
T CHL00041         89 DTA-LRAIRRSGLK  101 (116)
T ss_pred             HHH-HHHHHHCCCE
T ss_conf             999-9999878988


No 14 
>pfam00411 Ribosomal_S11 Ribosomal protein S11.
Probab=96.39  E-value=0.06  Score=32.43  Aligned_cols=84  Identities=21%  Similarity=0.218  Sum_probs=61.9

Q ss_pred             EEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC-CCCCHHHH
Q ss_conf             99996387099999962797599998502100000134686678999999999999997799799-98389-86312259
Q gi|254780245|r   29 LSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRG-KHLYCGRI  106 (120)
Q Consensus        29 L~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~-g~~yHGrv  106 (120)
                      +-|+-|..|....+- |..|.+++..|+-..-|++..+  +.-.||..+++.+++++++.||..| ++=+| |.   ||-
T Consensus         3 vhi~~t~NNTiitlT-D~~G~~l~~~S~G~~gfKg~rK--~T~~Aa~~aa~~~~~~~~~~gi~~v~v~ikG~G~---Gr~   76 (109)
T pfam00411         3 AHIQASFNNTIVTVT-DVIGRVVSWSSAGGCGFKGSRK--STPYAAQTAAENAAKIAKEQGIKALEVKIKGPGP---GRE   76 (109)
T ss_pred             EEEEECCCCEEEEEE-CCCCCEEEEEECCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCC---CHH
T ss_conf             999925788899998-5998999999578765588876--8989999999999999998198599999988998---789


Q ss_pred             HHHHHHHHHCCCC
Q ss_conf             9999999965878
Q gi|254780245|r  107 AALADAVRKGGVS  119 (120)
Q Consensus       107 ka~ad~~R~~Gl~  119 (120)
                      .+ ..++...||+
T Consensus        77 ~a-ir~l~~~gl~   88 (109)
T pfam00411        77 SA-LRALARSGLR   88 (109)
T ss_pred             HH-HHHHHHCCCE
T ss_conf             99-9999877998


No 15 
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=96.23  E-value=0.1  Score=31.09  Aligned_cols=84  Identities=23%  Similarity=0.265  Sum_probs=63.0

Q ss_pred             EEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC-CCCCHHHH
Q ss_conf             99996387099999962797599998502100000134686678999999999999997799799-98389-86312259
Q gi|254780245|r   29 LSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRG-KHLYCGRI  106 (120)
Q Consensus        29 L~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~-g~~yHGrv  106 (120)
                      +-|+-|..|..+.|- |.+|.+++.+|+=...|++..+  +.--||..+++.+++++++.||+.| ++=+| |.   ||-
T Consensus         3 ~hI~~s~NNTiit~T-d~~Gn~~~~~S~G~~gfKg~rK--~T~~Aa~~aa~~~~~~~~~~gi~~v~V~ikG~G~---Gr~   76 (108)
T TIGR03632         3 AHIHATFNNTIVTIT-DPQGNVLSWASAGAVGFKGSKK--STPYAAQLAAEDAAKKAKEFGMKTVDVYVKGPGA---GRE   76 (108)
T ss_pred             EEEEECCCCEEEEEE-CCCCCEEEEEECCCEECCCCCC--CCHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCC---CHH
T ss_conf             999935787899998-7999999999477333277655--8889999999999999997096199999968997---479


Q ss_pred             HHHHHHHHHCCCC
Q ss_conf             9999999965878
Q gi|254780245|r  107 AALADAVRKGGVS  119 (120)
Q Consensus       107 ka~ad~~R~~Gl~  119 (120)
                      . +.-+++..||+
T Consensus        77 ~-air~l~~~glk   88 (108)
T TIGR03632        77 S-AIRALQAAGLE   88 (108)
T ss_pred             H-HHHHHHHCCCE
T ss_conf             9-99999988988


No 16 
>KOG0875 consensus
Probab=95.58  E-value=0.026  Score=34.59  Aligned_cols=68  Identities=25%  Similarity=0.148  Sum_probs=54.3

Q ss_pred             CCCEEEEEEECCCEEEEEEEC--CCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHC-CCCE
Q ss_conf             882499996387099999962--7975999985021000001346866789999999999999977-9979
Q gi|254780245|r   25 GRLRLSVCRSSKHIYGQIIDD--SIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKV-GVKS   92 (120)
Q Consensus        25 ~~pRL~V~rSnkhiyAQiIdd--~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~-gI~~   92 (120)
                      -++||.|..+|+.+.+||+..  +...+++++-+.|..-.+......|-.||...|-+||.++++. |..+
T Consensus        47 ~kyR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s~elpkyg~~~GLtNyaAay~TglLLarR~l~~~gmD~  117 (264)
T KOG0875          47 PKYRMIVRVINKDIICQIAYATIEGDVIVRAAYAHELPKYGVKVGLTNYAAAYCTGLLLACRLLKRFGMDK  117 (264)
T ss_pred             CCEEEEEEEECHHHHHHHHHHEECCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             73389999824046888776321323999720133466555554640168887667899999998708610


No 17 
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=93.50  E-value=0.68  Score=26.18  Aligned_cols=89  Identities=19%  Similarity=0.038  Sum_probs=57.3

Q ss_pred             EEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC-CC-CC--
Q ss_conf             499996387099999962797599998502100000134686678999999999999997799799-98389-86-31--
Q gi|254780245|r   28 RLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRG-KH-LY--  102 (120)
Q Consensus        28 RL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~-g~-~y--  102 (120)
                      -+.|+-|-.|..+.|-|-....+++..|.-.-.+.+..  .+.--||..+++.+++++++.||+.| ++=+| |+ +=  
T Consensus         8 ivhI~asfNNTivtvTD~~G~~~~~~ssgg~~~k~~~k--K~Tp~AAq~aae~~~~~a~~~Gi~~v~V~vkG~G~~~~k~   85 (129)
T PRK09607          8 IAHIYASFNNTIITITDLTGAETIAKVSGGMVVKADRD--EPSPYAAMQAAFRAAELAKDKGITGVHIKVRAPGGNGSKT   85 (129)
T ss_pred             EEEEEECCCCEEEEEECCCCCEEEEEECCCCEECCCCC--CCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCC
T ss_conf             99999368985999985999969999477630048887--6898999999999999999769858999998378777678


Q ss_pred             --HHHHHHHHHHHHHCCCC
Q ss_conf             --22599999999965878
Q gi|254780245|r  103 --CGRIAALADAVRKGGVS  119 (120)
Q Consensus       103 --HGrvka~ad~~R~~Gl~  119 (120)
                        -||-.|+ -++...||+
T Consensus        86 pGpGr~~ai-r~l~~~Gl~  103 (129)
T PRK09607         86 PGPGAQAAI-RALARAGLR  103 (129)
T ss_pred             CCCCHHHHH-HHHHHCCCE
T ss_conf             884289999-999868978


No 18 
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=91.60  E-value=1.2  Score=24.67  Aligned_cols=89  Identities=18%  Similarity=0.073  Sum_probs=56.6

Q ss_pred             EEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC-CC-----
Q ss_conf             499996387099999962797599998502100000134686678999999999999997799799-98389-86-----
Q gi|254780245|r   28 RLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRG-KH-----  100 (120)
Q Consensus        28 RL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~-g~-----  100 (120)
                      .+-|+-|-.|-...|-|.....+++..|.-.--+++..  .+.--||....+.+++++++.|+..| ++=|| |.     
T Consensus         4 i~hI~atfNNTiitvTD~~G~~~~~~ssgg~~~~~~~~--K~Tp~AAq~aae~~a~~~~~~Gi~~v~V~ikG~G~n~~~~   81 (114)
T TIGR03628         4 IAHIYSSFNNTIITITDITGAETIARSSGGMVVKADRD--ESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQKS   81 (114)
T ss_pred             EEEEECCCCCEEEEEECCCCCEEEEEECCCCEECCCCC--CCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCC
T ss_conf             99999168985999985999979999668746518887--7888999999999999999869849999999478787778


Q ss_pred             CCHHHHHHHHHHHHHCCCC
Q ss_conf             3122599999999965878
Q gi|254780245|r  101 LYCGRIAALADAVRKGGVS  119 (120)
Q Consensus       101 ~yHGrvka~ad~~R~~Gl~  119 (120)
                      .=-||-.|+ -++...||+
T Consensus        82 pGpGresAi-ral~~~Gl~   99 (114)
T TIGR03628        82 PGPGAQAAI-RALARAGLR   99 (114)
T ss_pred             CCCCHHHHH-HHHHHCCCE
T ss_conf             986289999-999868979


No 19 
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=87.54  E-value=2.5  Score=22.78  Aligned_cols=67  Identities=24%  Similarity=0.193  Sum_probs=50.8

Q ss_pred             EEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC
Q ss_conf             99996387099999962797599998502100000134686678999999999999997799799-98389
Q gi|254780245|r   29 LSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRG   98 (120)
Q Consensus        29 L~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~   98 (120)
                      .-|+.|-.|-...+ .|..|.+++.+|+=..-|++..  .+.--||...++..++.+++.||+.| ++=+|
T Consensus        21 ahI~asfNNTivti-tD~~Gn~i~wassG~~gfk~~r--k~tpyAA~~aa~~aa~~a~e~Gi~~v~v~vkg   88 (129)
T COG0100          21 AHIHASFNNTIVTI-TDLTGNVIIWASSGGMGFKGSR--KSTPYAAQLAAEDAAKKAKEHGIKSVEVKVKG   88 (129)
T ss_pred             EEEECCCCCCEEEE-CCCCCCEEEEEECCCCEECCCC--CCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEC
T ss_conf             89972678858974-0789988999704762474788--88868999999999999997085479999968


No 20 
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=87.24  E-value=2.7  Score=22.67  Aligned_cols=89  Identities=21%  Similarity=0.163  Sum_probs=54.5

Q ss_pred             EEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC--CCCCH-
Q ss_conf             499996387099999962797599998502100000134686678999999999999997799799-98389--86312-
Q gi|254780245|r   28 RLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRG--KHLYC-  103 (120)
Q Consensus        28 RL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~--g~~yH-  103 (120)
                      -.-|+=|-.|....|-|.....|+++ |+-...++.... .+.-=||....+..|+++++.||+.| +.=|+  |.+-+ 
T Consensus        29 vaHI~ASfNNTIVtvTD~~G~~t~~~-sSGg~~~k~~r~-ksTPyAAq~AAe~aa~~a~e~Gi~~v~V~vrg~Gg~~~k~  106 (150)
T PTZ00129         29 VAHVFASFNDTFIHITDLSGRETLVR-VTGGMKVKADRD-ESSPYAAMMAAQDAAARAKELGITAVHVKLRATGGTRSKT  106 (150)
T ss_pred             EEEEECCCCCEEEEEECCCCCEEEEE-ECCCCEEECCCC-CCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCC
T ss_conf             99998245871899873999989999-689726857877-7887999999999999999819818999998247876788


Q ss_pred             ---HHHHHHHHHHHHCCCC
Q ss_conf             ---2599999999965878
Q gi|254780245|r  104 ---GRIAALADAVRKGGVS  119 (120)
Q Consensus       104 ---Grvka~ad~~R~~Gl~  119 (120)
                         ||=.|+= ++...||+
T Consensus       107 PGpGresAIR-aL~~~Gl~  124 (150)
T PTZ00129        107 PGPGAQSALR-SLARSGLK  124 (150)
T ss_pred             CCCCHHHHHH-HHHHCCCE
T ss_conf             9864667789-98747988


No 21 
>TIGR02360 pbenz_hydroxyl 4-hydroxybenzoate 3-monooxygenase; InterPro: IPR012733   4-hydroxybenzoate 3-monooxygenase is a flavoprotein that converts its substrate to 3,4-dihydroxybenzoate, which subsequently enters the beta-ketioadipate pathway of aromatic degradation, using molecular oxygen and NADPH as shown below . 4-hydroxybenzoate + NADPH + O(2) = 3,4-dihydroxybenzoate + NADP(+) + H(2)O 4-hydroxybenzoate is an intermediate in the degradation of lignin and other aromatic plant compounds, and this enzyme is found extensively in soil bacteria.   This enzyme is a homodimer where each subunit is composed of three distinct domains: an N-terminal flavin-binding domain with a beta-alpha-beta fold, a small substrate-binding domain composed of a single alpha helix and beta-sheet, and a C-terminal helical domain . The active site is found at the interface of all three domains. Catalysis occurs by a two-step reaction. In the first step, flavin is reduced by NADPH. Subsequently, the reduced flavin is oxygenated to a hydroperoxide which transfers the hydroxyl group to the substrate, forming 3,4-dihydroxybenzoate.; GO: 0018659 4-hydroxybenzoate 3-monooxygenase activity, 0050660 FAD binding, 0043639 benzoate catabolic process.
Probab=81.90  E-value=2.3  Score=22.99  Aligned_cols=44  Identities=36%  Similarity=0.538  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCCCH-HHHHH------HHHHHHHCCC
Q ss_conf             99999999999977997999838986312-25999------9999996587
Q gi|254780245|r   75 TAVGNLLVERAVKVGVKSVYFDRGKHLYC-GRIAA------LADAVRKGGV  118 (120)
Q Consensus        75 ~~vG~~ia~r~~~~gI~~v~FDR~g~~yH-Grvka------~ad~~R~~Gl  118 (120)
                      -=-|-+|++.+.++||..|++.|-.-.|= |||.|      ++|=++++|+
T Consensus        11 GPsGLLLGQLLh~~GId~viLEr~~~dYVlgRIRAGvLE~g~v~LL~~agv   61 (393)
T TIGR02360        11 GPSGLLLGQLLHKAGIDTVILERKSRDYVLGRIRAGVLEQGTVDLLREAGV   61 (393)
T ss_pred             CHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             735789999998669858997235722343321012357899999987223


No 22 
>pfam02065 Melibiase Melibiase.
Probab=81.03  E-value=3.5  Score=21.95  Aligned_cols=41  Identities=27%  Similarity=0.439  Sum_probs=35.3

Q ss_pred             HHHHHHHHCCCCEEEECCCC------------------CCCHHHHHHHHHHHHHCCCCC
Q ss_conf             99999997799799983898------------------631225999999999658789
Q gi|254780245|r   80 LLVERAVKVGVKSVYFDRGK------------------HLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        80 ~ia~r~~~~gI~~v~FDR~g------------------~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      .||+.|.+.||+-+|.|-|=                  .+|-+=++.|+|.+++.|++|
T Consensus        62 ~la~~Aa~lGvE~FVlDDGWFg~R~~D~~gLGDW~v~~~kfP~GL~~l~d~v~~~GM~F  120 (395)
T pfam02065        62 DLADEAADLGIELFVLDDGWFGGRNDDNSSLGDWFVNEQKFPNGLKPLADHVHSLGMEF  120 (395)
T ss_pred             HHHHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHHHHHCCCCE
T ss_conf             99999997398699981787789999887773816165005898799999999739843


No 23 
>COG3345 GalA Alpha-galactosidase [Carbohydrate transport and metabolism]
Probab=76.61  E-value=5.2  Score=20.95  Aligned_cols=41  Identities=29%  Similarity=0.408  Sum_probs=34.9

Q ss_pred             HHHHHHHHCCCCEEEECCCCC------------------CCHHHHHHHHHHHHHCCCCC
Q ss_conf             999999977997999838986------------------31225999999999658789
Q gi|254780245|r   80 LLVERAVKVGVKSVYFDRGKH------------------LYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        80 ~ia~r~~~~gI~~v~FDR~g~------------------~yHGrvka~ad~~R~~Gl~F  120 (120)
                      .+++.+++-|++-++.|-|-+                  +|-+-|..++++++|+|++|
T Consensus       313 e~vk~akk~gvE~FvlDDGwfg~rndd~~slGDWlv~seKfPsgiE~li~~I~e~Gl~f  371 (687)
T COG3345         313 ENVKEAKKFGVELFVLDDGWFGGRNDDLKSLGDWLVNSEKFPSGIEELIEAIAENGLIF  371 (687)
T ss_pred             HHHHHHHHCCEEEEEECCCCCCCCCCCHHHHHCEECCHHHCCCCHHHHHHHHHHCCCCC
T ss_conf             99998863682799973500156676312332114336435520899999999728764


No 24 
>PRK00072 hemC porphobilinogen deaminase; Reviewed
Probab=68.51  E-value=11  Score=19.09  Aligned_cols=41  Identities=22%  Similarity=0.194  Sum_probs=28.5

Q ss_pred             CEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             09999996279759999850210000013468667899999999999999779
Q gi|254780245|r   37 HIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVG   89 (120)
Q Consensus        37 hiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~g   89 (120)
                      ++.+.+.+..+...+. .+           ..++++.|..+|..+|+.+++.|
T Consensus       258 ~l~~~v~s~dG~~~i~-~~-----------~~g~~~~a~~lG~~la~~Ll~~G  298 (300)
T PRK00072        258 HLRGLVGSPDGSRIIR-EE-----------RIGNGADAEALGIELAEELLAQG  298 (300)
T ss_pred             EEEEEEECCCCCEEEE-EE-----------EEECHHHHHHHHHHHHHHHHHCC
T ss_conf             9999999899987999-99-----------98579999999999999999757


No 25 
>pfam03900 Porphobil_deamC Porphobilinogen deaminase, C-terminal domain.
Probab=68.12  E-value=11  Score=19.04  Aligned_cols=21  Identities=29%  Similarity=0.434  Sum_probs=18.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHCC
Q ss_conf             667899999999999999779
Q gi|254780245|r   69 ANIVAATAVGNLLVERAVKVG   89 (120)
Q Consensus        69 ~ni~aA~~vG~~ia~r~~~~g   89 (120)
                      ++++.|..+|..+|+.++++|
T Consensus        54 g~~~~a~~lG~~lA~~Ll~~G   74 (74)
T pfam03900        54 GDIEDAEELGKKLAEELLAQG   74 (74)
T ss_pred             ECHHHHHHHHHHHHHHHHHCC
T ss_conf             858999999999999999683


No 26 
>pfam07355 GRDB Glycine/sarcosine/betaine reductase selenoprotein B (GRDB). This family represents a conserved region approximately 350 residues long within the selenoprotein B component of the bacterial glycine, sarcosine and betaine reductase complexes.
Probab=67.59  E-value=11  Score=19.00  Aligned_cols=36  Identities=17%  Similarity=0.347  Sum_probs=29.1

Q ss_pred             HCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEC
Q ss_conf             000134686678999999999999997799799983
Q gi|254780245|r   61 LRSSLKTGANIVAATAVGNLLVERAVKVGVKSVYFD   96 (120)
Q Consensus        61 ~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v~FD   96 (120)
                      +......+..++.|+..|+.||+.+++.||..|.+-
T Consensus       312 fytT~G~gT~v~~ak~fg~eia~~L~~~gVdAvILT  347 (349)
T pfam07355       312 FYSTVGNGTSVANSKKFAKEIVKKLKEDGVDAVILT  347 (349)
T ss_pred             EEEECCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             689527981089999999999999998499989970


No 27 
>smart00812 Alpha_L_fucos Alpha-L-fucosidase. O-Glycosyl hydrolases (EC 3.2.1.-) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site PUBMED:. Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'. Family 29 encompasses alpha-L-fucosidases, which is a lysosomal enzyme responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Deficiency of alpha-L-fucosidase results in the lysosomal storage disease fucosidosis.
Probab=66.00  E-value=12  Score=18.78  Aligned_cols=42  Identities=31%  Similarity=0.384  Sum_probs=30.2

Q ss_pred             HHHHHHHHHCCCCEEEEC---CCCC--------CC-------H-HHHHHHHHHHHHCCCCC
Q ss_conf             999999997799799983---8986--------31-------2-25999999999658789
Q gi|254780245|r   79 NLLVERAVKVGVKSVYFD---RGKH--------LY-------C-GRIAALADAVRKGGVSF  120 (120)
Q Consensus        79 ~~ia~r~~~~gI~~v~FD---R~g~--------~y-------H-Grvka~ad~~R~~Gl~F  120 (120)
                      +..|+.++++|-+=|+|-   .-||        .|       + --|++|++++|+.||+|
T Consensus        84 ~~Wa~lak~AGaKY~V~TaKHHDGF~lwdS~~s~~n~~~~gpkrDiv~el~~A~rk~Glk~  144 (384)
T smart00812       84 EEWADLFKKAGAKYVVLTAKHHDGFCLWDSKYSNWNAVDTGPKRDLVGELADAVRKRGLKF  144 (384)
T ss_pred             HHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCEE
T ss_conf             9999999984995477521304774146788999866567887667999999998769769


No 28 
>TIGR02298 HpaD_Fe 3,4-dihydroxyphenylacetate 2,3-dioxygenase; InterPro: IPR011984    This enzyme catalyses the ring-opening step in the degradation of 4-hydroxyphenylacetate ..
Probab=60.80  E-value=6.1  Score=20.55  Aligned_cols=26  Identities=31%  Similarity=0.378  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEE-EEC
Q ss_conf             78999999999999997799799-983
Q gi|254780245|r   71 IVAATAVGNLLVERAVKVGVKSV-YFD   96 (120)
Q Consensus        71 i~aA~~vG~~ia~r~~~~gI~~v-~FD   96 (120)
                      -.+|---=+.|+++|+|.+|+.| |||
T Consensus        88 Rq~AidghkEi~~rakE~~VdTivVfD  114 (343)
T TIGR02298        88 RQAAIDGHKEISRRAKEMGVDTIVVFD  114 (343)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             289999988886431004686699963


No 29 
>pfam01120 Alpha_L_fucos Alpha-L-fucosidase.
Probab=59.24  E-value=16  Score=18.05  Aligned_cols=45  Identities=24%  Similarity=0.229  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHCCCCEEEEC---CCCC---------------CCH-HHHHHHHHHHHHCCCCC
Q ss_conf             999999999997799799983---8986---------------312-25999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFD---RGKH---------------LYC-GRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FD---R~g~---------------~yH-Grvka~ad~~R~~Gl~F  120 (120)
                      .-.+..++.++++|-+-++|-   .-||               .++ --|+.|++++|+.||+|
T Consensus        92 fd~~~Wa~~ak~AGakY~vlTaKHHDGF~lwdS~~t~~n~~~~~~krDiv~el~~A~rk~Glk~  155 (344)
T pfam01120        92 FDADEWAKLAKAAGAKYVVLTTKHHDGFTMWDSKYSDWNSVDTGPKRDIVGELAKACRKNGIKF  155 (344)
T ss_pred             CCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCEE
T ss_conf             7999999999985996588613415775257788999877678999776999999999859867


No 30 
>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=56.35  E-value=18  Score=17.75  Aligned_cols=45  Identities=18%  Similarity=0.275  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCC---CCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             99999999999779979998389---8631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRG---KHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~---g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ..|..+++.+.++|..++.|=.+   ..-.-.|...|-+++++.|+++
T Consensus       101 ~~~~~~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~g~~~  148 (265)
T cd06290         101 QGGYLATQHLIDLGHRRIAHITGPRGHIDARDRLAGYRKALEEAGLEV  148 (265)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999998299865560488787019999999999999869999


No 31 
>pfam00875 DNA_photolyase DNA photolyase. This domain binds a light harvesting cofactor.
Probab=55.07  E-value=19  Score=17.63  Aligned_cols=44  Identities=32%  Similarity=0.521  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHCCCCEEEECCCCCCCH-HHHHHHHHHHHHCCCCC
Q ss_conf             999999999977997999838986312-25999999999658789
Q gi|254780245|r   77 VGNLLVERAVKVGVKSVYFDRGKHLYC-GRIAALADAVRKGGVSF  120 (120)
Q Consensus        77 vG~~ia~r~~~~gI~~v~FDR~g~~yH-Grvka~ad~~R~~Gl~F  120 (120)
                      ..+.|.+.+.+-+|+.|+|++.--.|. -|-.++.+.+.+.|++|
T Consensus        76 ~~~~l~~l~~~~~i~~v~~n~~~~~~~~~rd~~v~~~l~~~~i~~  120 (164)
T pfam00875        76 PAEVLPELAKELGASAVYWNRDYEPYERRRDAAVKEALREAGIEV  120 (164)
T ss_pred             HHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCEE
T ss_conf             589999999967999999916789899999999999998547469


No 32 
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=49.98  E-value=23  Score=17.14  Aligned_cols=43  Identities=16%  Similarity=0.206  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             999999999977997999838---9863122599999999965878
Q gi|254780245|r   77 VGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVS  119 (120)
Q Consensus        77 vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~  119 (120)
                      .|..+++.+.++|.+++.|=-   +..-...|...|-+++++.|+.
T Consensus       103 ~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~G~~~al~~~~i~  148 (264)
T cd01574         103 GARLATEHLLELGHRTIAHVAGPEEWLSARARLAGWRAALEAAGIA  148 (264)
T ss_pred             HHHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             9999999999849982732589977757999999999999986989


No 33 
>TIGR01035 hemA glutamyl-tRNA reductase; InterPro: IPR000343   Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway . The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin .   The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA.   The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III.   Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) .   This entry represents glutamyl-tRNA reductase (1.2.1.70 from EC), which reduces glutamyl-tRNA to glutamate-1-semialdehyde during the first stage of tetrapyrrole biosynthesis by the C5 pathway , . This enzyme required NADPH as a coenzyme.; GO: 0008883 glutamyl-tRNA reductase activity, 0050661 NADP binding, 0033014 tetrapyrrole biosynthetic process.
Probab=49.33  E-value=23  Score=17.08  Aligned_cols=46  Identities=26%  Similarity=0.397  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEE-EECCCCCCCHHHHHHHHHHHHH-CCCCC
Q ss_conf             78999999999999997799799-9838986312259999999996-58789
Q gi|254780245|r   71 IVAATAVGNLLVERAVKVGVKSV-YFDRGKHLYCGRIAALADAVRK-GGVSF  120 (120)
Q Consensus        71 i~aA~~vG~~ia~r~~~~gI~~v-~FDR~g~~yHGrvka~ad~~R~-~Gl~F  120 (120)
                      +-.|-..|.|.|+-+..+||.+| +..|+-.    |=..||+-+.+ .++.|
T Consensus       190 liGAGeMg~Lva~~L~~~~v~~~~i~NRt~~----rA~~LA~e~~~P~~~~f  237 (436)
T TIGR01035       190 LIGAGEMGELVAKHLREKGVGKVLIANRTYE----RAEKLAKELGGPEAVKF  237 (436)
T ss_pred             EEECCHHHHHHHHHHHHCCCCEEEEECCCHH----HHHHHHHHCCCCCCCCC
T ss_conf             9827457999999996489528988556778----99999987078664544


No 34 
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=47.05  E-value=25  Score=16.87  Aligned_cols=45  Identities=22%  Similarity=0.321  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCCC---CCCHHHHHHHHHHHHHCCCCC
Q ss_conf             999999999997799799983898---631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRGK---HLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~g---~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      .-|..+++.+.+.|-.+|.|=.+.   ....-|...|.+++++.|+.+
T Consensus       108 ~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~  155 (270)
T cd06294         108 QAGYDATEYLIKLGHKKIAFVGGDLDLEVTQDRLQGYKQALEDHGIPD  155 (270)
T ss_pred             HHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999997699569998189986589999999999999869997


No 35 
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=47.01  E-value=25  Score=16.86  Aligned_cols=46  Identities=17%  Similarity=0.331  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCCC---HHHHHHHHHHHHHCCCCC
Q ss_conf             9999999999997799799983898631---225999999999658789
Q gi|254780245|r   75 TAVGNLLVERAVKVGVKSVYFDRGKHLY---CGRIAALADAVRKGGVSF  120 (120)
Q Consensus        75 ~~vG~~ia~r~~~~gI~~v~FDR~g~~y---HGrvka~ad~~R~~Gl~F  120 (120)
                      ...|..+++.+.++|-+++.|=.+.-.+   .-|.+.|-+++.+.|+.+
T Consensus       103 ~~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~R~~Gf~~a~~~~gi~~  151 (270)
T cd01545         103 RAAAREMTRHLIDLGHRRIAFIAGPPDHRASAERLEGYRDALAEAGLPL  151 (270)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             9999999999997499659993699777369999999999999839997


No 36 
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso
Probab=46.78  E-value=26  Score=16.84  Aligned_cols=45  Identities=18%  Similarity=0.219  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCC---CCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             99999999999779979998389---8631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRG---KHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~---g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      .-|..+++.+.++|-.+|.|=-+   ..-..-|...|.+++++.|+.+
T Consensus       106 ~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gl~~  153 (268)
T cd06271         106 AAAYQAVRRLIALGHRRIALLNPPEDLTFAQHRRAGYRRALAEAGLPL  153 (268)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999998598748754887546079999999999999839997


No 37 
>KOG0104 consensus
Probab=46.57  E-value=26  Score=16.83  Aligned_cols=97  Identities=16%  Similarity=0.084  Sum_probs=57.9

Q ss_pred             HHCCCCCCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECC
Q ss_conf             75057878824999963870999999627975999985021000001346866789999999999999977997999838
Q gi|254780245|r   18 HLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSVYFDR   97 (120)
Q Consensus        18 k~k~~~~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v~FDR   97 (120)
                      .+-+.+-.-| ++.+.+.+|-+-++++|+.-.||+.--+.+-++.-+---.-...-|..    +|+-..+.-|+.+++--
T Consensus        91 ~llgk~~~~~-~v~ly~~~~p~~e~v~d~~rstV~F~i~d~~~ysvEellAMil~~a~~----~ae~~a~~~Ikd~ViTV  165 (902)
T KOG0104          91 DLLGKSLDDP-TVDLYQKRFPFFELVEDPQRSTVVFKISDQEEYSVEELLAMILQYAKS----LAEEYAKQPIKDMVITV  165 (902)
T ss_pred             HHHCCCCCCC-HHHHHHHCCCCEEECCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH----HHHHHHHCCHHHEEEEC
T ss_conf             8747645770-888987118763421367664378981785416799999999999999----99998736143269967


Q ss_pred             CCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             9863122599999999965878
Q gi|254780245|r   98 GKHLYCGRIAALADAVRKGGVS  119 (120)
Q Consensus        98 ~g~~yHGrvka~ad~~R~~Gl~  119 (120)
                      .+|-=.--=.|+.++++=+||+
T Consensus       166 P~~F~qaeR~all~Aa~iagl~  187 (902)
T KOG0104         166 PPFFNQAERRALLQAAQIAGLN  187 (902)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCH
T ss_conf             8645889999999898862851


No 38 
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=45.73  E-value=21  Score=17.32  Aligned_cols=63  Identities=17%  Similarity=0.127  Sum_probs=30.9

Q ss_pred             CEEEEEEECCCCEEEEEEEECCC------------HHCCCCCCCCCHHHHHHHHHHHHHHHHHCCC-CEEEECCCCCCCH
Q ss_conf             09999996279759999850210------------0000134686678999999999999997799-7999838986312
Q gi|254780245|r   37 HIYGQIIDDSIGHTLVSASSLNE------------PLRSSLKTGANIVAATAVGNLLVERAVKVGV-KSVYFDRGKHLYC  103 (120)
Q Consensus        37 hiyAQiIdd~~~~tl~saST~~k------------~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI-~~v~FDR~g~~yH  103 (120)
                      -|++|+  +++.+-.|+++|...            .+-+.++. -| +.|-..+-.+|..+ .-.| ..+.|||-.|-|.
T Consensus        12 EiH~qL--~t~tKlF~~~~~~~~~~pNt~v~~v~~~~PG~lP~-lN-~~av~~ai~~a~al-~~~i~~~~~f~RK~YfYp   86 (479)
T PRK05477         12 EVHVQL--NTKSKIFSGCSTEFGAEPNTNVCPVCLGLPGALPV-LN-KEAVEKAIKAGLAL-NCEIAKRSVFDRKNYFYP   86 (479)
T ss_pred             EEEEEE--CCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCCCCC-CC-HHHHHHHHHHHHHC-CCCCCCCCEECCCCCCCC
T ss_conf             998770--79968578999878999766638420068988776-69-99999999999983-986463315502346689


Q ss_pred             H
Q ss_conf             2
Q gi|254780245|r  104 G  104 (120)
Q Consensus       104 G  104 (120)
                      -
T Consensus        87 D   87 (479)
T PRK05477         87 D   87 (479)
T ss_pred             C
T ss_conf             8


No 39 
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational
Probab=43.43  E-value=29  Score=16.53  Aligned_cols=46  Identities=17%  Similarity=0.283  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCC----CHHHHHHHHHHHHHCCCCC
Q ss_conf             999999999999779979998389863----1225999999999658789
Q gi|254780245|r   75 TAVGNLLVERAVKVGVKSVYFDRGKHL----YCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        75 ~~vG~~ia~r~~~~gI~~v~FDR~g~~----yHGrvka~ad~~R~~Gl~F  120 (120)
                      ..-|..+++.+.++|.+++.|=-+...    ..-|...|.+++++.|+..
T Consensus       101 ~~~~~~~~~~L~~~G~~~i~~i~~~~~~~~~~~~R~~gf~~al~~~~~~~  150 (268)
T cd06273         101 REAGRLAARHLIALGHRRIAMIFGPTQGNDRARARRAGVRAALAEAGLEL  150 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999999999872987479994687777789999999999999809998


No 40 
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=42.91  E-value=29  Score=16.48  Aligned_cols=45  Identities=16%  Similarity=0.137  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             9999999999977997999838---98631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      .-|..+++.+.++|-.+|.|=-   +.....-|.+.|.+++++.|+.+
T Consensus       102 ~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~  149 (264)
T cd06274         102 DGAAELTRELLAAPPEEVLFLGGLPELSPSRERLAGFRQALADAGLPV  149 (264)
T ss_pred             HHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999998599669997689877309999999999999779987


No 41 
>PRK07666 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=42.55  E-value=30  Score=16.45  Aligned_cols=43  Identities=26%  Similarity=0.375  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             99999999999999779979998389863122599999999965878
Q gi|254780245|r   73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVS  119 (120)
Q Consensus        73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~  119 (120)
                      ++.-+|+.+|+..-+.|.+-+..||...    ++..+++.+++.|.+
T Consensus        14 as~GIG~aiA~~la~~Ga~V~l~~r~~~----~l~~~~~~i~~~g~~   56 (238)
T PRK07666         14 AGRGIGRAVAIALAKEGVNVGLLARSEE----NLKAVAKEVEAEGVK   56 (238)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCCC
T ss_conf             3778999999999987998999989999----999999999955992


No 42 
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=41.05  E-value=31  Score=16.31  Aligned_cols=45  Identities=16%  Similarity=0.212  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCC---CCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             99999999999779979998389---8631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRG---KHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~---g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ..|..+++.+.++|-..|.|=-+   ..-..-|...|.+++++.|+++
T Consensus       104 ~a~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~R~~Gf~~al~~~gl~~  151 (268)
T cd06277         104 SGAYAATEYLIEKGHRKIGFVGDPLYSPSFEERYEGYKKALLDHGIPF  151 (268)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999997099836997278888129999999999999859999


No 43 
>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor 
Probab=40.90  E-value=32  Score=16.29  Aligned_cols=46  Identities=15%  Similarity=0.145  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             99999999999977997999838---98631225999999999658789
Q gi|254780245|r   75 TAVGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        75 ~~vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ...|..+++.+.++|-..|.|=-   ..+-..-|...|.++++++|+.+
T Consensus        96 ~~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~gf~~al~~~g~~~  144 (261)
T cd06272          96 EKAMELAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCDENGISI  144 (261)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             9999999999998699828996698887359999999999999859985


No 44 
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=40.19  E-value=32  Score=16.23  Aligned_cols=45  Identities=20%  Similarity=0.303  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCCC---CCCHHHHHHHHHHHHHCCCCC
Q ss_conf             999999999997799799983898---631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRGK---HLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~g---~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ..|..+++.+.++|-.++.|=-+.   .-..-|...|-+++.++|+.+
T Consensus       102 ~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~gl~~  149 (268)
T cd06270         102 QGGYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALAEAGIAL  149 (268)
T ss_pred             HHHHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999998399838984598888319999999999999859997


No 45 
>PRK05866 short chain dehydrogenase; Provisional
Probab=39.35  E-value=33  Score=16.15  Aligned_cols=42  Identities=26%  Similarity=0.398  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             9999999999999977997999838986312259999999996587
Q gi|254780245|r   73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV  118 (120)
Q Consensus        73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl  118 (120)
                      ++.=+|..+|+..-+.|-+-+..||+..    ++.++++.+.+.|-
T Consensus        48 assGIG~aiA~~la~~Ga~Vvl~~R~~~----~l~~~~~~i~~~g~   89 (290)
T PRK05866         48 ASSGIGEAAAEKFARRGATVVAVARRKD----LLDAVADRITAAGG   89 (290)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCC
T ss_conf             1309999999999986998999989999----99999999996499


No 46 
>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a 
Probab=38.56  E-value=34  Score=16.07  Aligned_cols=45  Identities=18%  Similarity=0.233  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             9999999999977997999838---98631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ..|.++++.+.++|-.+++|=-   +.+-..-|...|.+++.+.|++|
T Consensus       103 ~~~~~a~~~Li~~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~i~~  150 (269)
T cd06275         103 EGGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPV  150 (269)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999998299717755699777169999999999999859997


No 47 
>TIGR03206 benzo_BadH 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase. Members of this protein family are the enzyme 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase. The enzymatic properties were confirmed experimentally in Rhodopseudomonas palustris; the enzyme is homotetrameric, and not sensitive to oxygen. This enzyme is part of proposed pathway for degradation of benzoyl-CoA to 3-hydroxypimeloyl-CoA that differs from the analogous in Thauera aromatica. It also may occur in degradation of the non-aromatic compound cyclohexane-1-carboxylate.
Probab=38.44  E-value=35  Score=16.06  Aligned_cols=43  Identities=21%  Similarity=0.338  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             99999999999999779979998389863122599999999965878
Q gi|254780245|r   73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVS  119 (120)
Q Consensus        73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~  119 (120)
                      ++.-+|..++++..+.|-+-+.+||+..    .+..+++.+++.|-+
T Consensus        11 ~s~GIG~aia~~la~~Ga~V~i~~r~~~----~~~~~~~~l~~~g~~   53 (250)
T TIGR03206        11 GGGGIGGATCRRFAEEGAKVAVFDLNRE----AAEKVAADIRAKGGN   53 (250)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCCC
T ss_conf             5768999999999987999999979889----999999999953992


No 48 
>PRK13381 peptidase T; Provisional
Probab=38.23  E-value=35  Score=16.04  Aligned_cols=24  Identities=17%  Similarity=0.374  Sum_probs=8.3

Q ss_pred             HHHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             999999999977997999838986
Q gi|254780245|r   77 VGNLLVERAVKVGVKSVYFDRGKH  100 (120)
Q Consensus        77 vG~~ia~r~~~~gI~~v~FDR~g~  100 (120)
                      +++.|++.+++.|++.|..|-.||
T Consensus        39 la~~L~~eL~~lGl~~v~~d~~g~   62 (413)
T PRK13381         39 LAKLLAKELRELGLEDIVIDEHAI   62 (413)
T ss_pred             HHHHHHHHHHHCCCEEEEECCCEE
T ss_conf             999999999976993688669759


No 49 
>PRK06181 short chain dehydrogenase; Provisional
Probab=38.13  E-value=35  Score=16.03  Aligned_cols=40  Identities=28%  Similarity=0.473  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             99999999999997799799983898631225999999999658
Q gi|254780245|r   74 ATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGG  117 (120)
Q Consensus        74 A~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~G  117 (120)
                      +.-+|..+|+..-+.|-+-+..||+..    ++.++++.+++.|
T Consensus        10 ssGIG~a~A~~la~~Ga~vvl~~r~~~----~l~~~~~~l~~~g   49 (263)
T PRK06181         10 SEGIGRALAVRLARAGARLVLAARNEE----RLASLAQELANYG   49 (263)
T ss_pred             CCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCC
T ss_conf             019999999999987998999988999----9999999999549


No 50 
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=38.02  E-value=35  Score=16.02  Aligned_cols=47  Identities=19%  Similarity=0.270  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEECCC---CCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             9999999999999779979998389---8631225999999999658789
Q gi|254780245|r   74 ATAVGNLLVERAVKVGVKSVYFDRG---KHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        74 A~~vG~~ia~r~~~~gI~~v~FDR~---g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ...-|.+.++.+.+.|-.+|.|=-+   ......|...|.+++++.|+.+
T Consensus       162 ~~~~~~~a~~~L~~~Ghr~Ia~i~~~~~~~~~~~R~~gf~~al~~~gl~~  211 (335)
T PRK10703        162 AFEGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKV  211 (335)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             79999999999997599869999588765217899999999999859998


No 51 
>pfam06370 DUF1069 Protein of unknown function (DUF1069). This family consists of several Maize streak virus 21.7 kDa proteins. The function of this family is unknown.
Probab=36.45  E-value=19  Score=17.65  Aligned_cols=22  Identities=32%  Similarity=0.598  Sum_probs=18.0

Q ss_pred             HHHHCCCCEEEECCCCCCCHHH
Q ss_conf             9997799799983898631225
Q gi|254780245|r   84 RAVKVGVKSVYFDRGKHLYCGR  105 (120)
Q Consensus        84 r~~~~gI~~v~FDR~g~~yHGr  105 (120)
                      +....|+.+|.|.-||.+|||-
T Consensus       161 rssgigvdevtyasggdryhgg  182 (206)
T pfam06370       161 RSSGIGVDEVTYASGGDRYHGG  182 (206)
T ss_pred             ECCCCCCEEEEECCCCCCCCCC
T ss_conf             4067661057761578624589


No 52 
>TIGR00666 PBP4 D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase; InterPro: IPR000667   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This family of serine peptidases belong to MEROPS peptidase family S13 (D-Ala-D-Ala carboxypeptidase C, clan SE). The predicted active site residues for members of this family and family S12 occur in the motif SXXK.    D-Ala-D-Ala carboxypeptidase C is involved in the metabolism of cell components ; it is synthesised with a leader peptide to target it to the cell membrane . After cleavage of the leader peptide, the enzyme is retained in the membrane by a C-terminal anchor . There are three families of serine-type D-Ala-D-Ala peptidase (designated S11, S12 and S13), which are also known as low molecular weight penicillin-binding proteins . Family S13 comprises D-Ala-D-Ala peptidases that have sufficient sequence similarity around their active sites to assume a distant evolutionary relationship to other clan members; members of the S13 family also bind penicillin and have D-amino-peptidase activity. Proteases of family S11 have exclusive D-Ala-D-Ala peptidase activity, while some members of S12 are C beta-lactamases . ; GO: 0004185 serine carboxypeptidase activity, 0006508 proteolysis.
Probab=34.63  E-value=28  Score=16.61  Aligned_cols=20  Identities=35%  Similarity=0.732  Sum_probs=13.2

Q ss_pred             CCCHH--HHHHHHHHHHHCCCC
Q ss_conf             63122--599999999965878
Q gi|254780245|r  100 HLYCG--RIAALADAVRKGGVS  119 (120)
Q Consensus       100 ~~yHG--rvka~ad~~R~~Gl~  119 (120)
                      --|||  |+..+++.++..|++
T Consensus        76 tWyhGaar~~~l~~~LK~~GV~   97 (427)
T TIGR00666        76 TWYHGAARLDKLVEELKKSGVK   97 (427)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCC
T ss_conf             2012478999999999864880


No 53 
>cd00494 HMBS Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12.  HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB).  HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II.  HMBS is found in all organisms except viruses.
Probab=32.91  E-value=43  Score=15.53  Aligned_cols=38  Identities=18%  Similarity=0.210  Sum_probs=23.4

Q ss_pred             CEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             09999996279759999850210000013468667899999999999999
Q gi|254780245|r   37 HIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAV   86 (120)
Q Consensus        37 hiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~   86 (120)
                      ++.+.+.+..+...+. .+           -.++.+.|..+|..+|+.++
T Consensus       254 ~l~~~v~s~DG~~~~~-~~-----------~~g~~~~a~~lG~~lA~~Ll  291 (292)
T cd00494         254 KLKGLVGSPDGKRLIE-GE-----------VRGNIEDAEELGKKLAEELL  291 (292)
T ss_pred             EEEEEEECCCCCEEEE-EE-----------EEECHHHHHHHHHHHHHHHH
T ss_conf             9999999888987999-99-----------99778999999999999971


No 54 
>PRK05650 short chain dehydrogenase; Provisional
Probab=32.89  E-value=43  Score=15.53  Aligned_cols=21  Identities=19%  Similarity=0.235  Sum_probs=6.9

Q ss_pred             HHHHHHHHHHHCCCCEEEECC
Q ss_conf             999999999977997999838
Q gi|254780245|r   77 VGNLLVERAVKVGVKSVYFDR   97 (120)
Q Consensus        77 vG~~ia~r~~~~gI~~v~FDR   97 (120)
                      +|..+|+...+.|..-+..||
T Consensus        12 IG~alA~~la~~G~~V~l~~r   32 (270)
T PRK05650         12 LGRAIALRWAREGWRLALADV   32 (270)
T ss_pred             HHHHHHHHHHHCCCEEEEEEC
T ss_conf             999999999988998999979


No 55 
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=32.77  E-value=43  Score=15.51  Aligned_cols=45  Identities=13%  Similarity=0.112  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCCC---CCCHHHHHHHHHHHHHCCCCC
Q ss_conf             999999999997799799983898---631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRGK---HLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~g---~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      .-|.+.++.+.+.|-.+|.|=-+.   .-...|...|-+++++.||.+
T Consensus       162 ~~~~~a~~~L~~~Ghr~Ia~i~~~~~~~~~~~R~~g~~~al~~~gl~~  209 (342)
T PRK10727        162 YGAWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGYYDALAESGIPA  209 (342)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999997499759999689888359999999999999769999


No 56 
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=32.60  E-value=43  Score=15.50  Aligned_cols=47  Identities=21%  Similarity=0.347  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEECCC--CCCCH-HHHHHHHHHHHHCCCCC
Q ss_conf             9999999999999779979998389--86312-25999999999658789
Q gi|254780245|r   74 ATAVGNLLVERAVKVGVKSVYFDRG--KHLYC-GRIAALADAVRKGGVSF  120 (120)
Q Consensus        74 A~~vG~~ia~r~~~~gI~~v~FDR~--g~~yH-Grvka~ad~~R~~Gl~F  120 (120)
                      -...|..+++.+.+.|-..|.|=-+  ..... -|...|-+++++.|+.|
T Consensus       166 ~~~~~~~a~~~L~~~Ghr~Ia~i~~~~~~~~~~~R~~gf~~al~~~~l~~  215 (342)
T PRK10014        166 NMQAAQLLTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYCATLLKFGLPF  215 (342)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             69999999999987599869999578886339999999999999769998


No 57 
>PRK08278 short chain dehydrogenase; Provisional
Probab=32.41  E-value=43  Score=15.48  Aligned_cols=45  Identities=20%  Similarity=0.255  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEECCCCC---CCHHHHHHHHHHHHHCCC
Q ss_conf             999999999999977997999838986---312259999999996587
Q gi|254780245|r   74 ATAVGNLLVERAVKVGVKSVYFDRGKH---LYCGRIAALADAVRKGGV  118 (120)
Q Consensus        74 A~~vG~~ia~r~~~~gI~~v~FDR~g~---~yHGrvka~ad~~R~~Gl  118 (120)
                      +.-+|..+|+++.+.|-+-+..+|+..   +..|.+.+.++.+++.|-
T Consensus        15 s~GIG~aiA~~la~~Ga~Vvi~~r~~~~~~~l~~~~~~~a~e~~~~g~   62 (273)
T PRK08278         15 SRGIGLAIALRAARDGANIVIAAKTAEPHPKLPGTIHTAAAEIEAAGG   62 (273)
T ss_pred             CCHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             659999999999987998999967722213345489999999997499


No 58 
>KOG0408 consensus
Probab=31.11  E-value=46  Score=15.35  Aligned_cols=89  Identities=26%  Similarity=0.306  Sum_probs=63.1

Q ss_pred             CCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCCCCCCH
Q ss_conf             882499996387099999962797599998502100000134686678999999999999997799799-9838986312
Q gi|254780245|r   25 GRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRGKHLYC  103 (120)
Q Consensus        25 ~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~g~~yH  103 (120)
                      +-|=..|.-|-.|-.+||. |..+.++...|---.-|+...+.  .--||.-.|-..+.+++++|+..| +--+|  +=-
T Consensus        78 eiPi~hIraS~NNTivtVt-d~kg~vi~~~ScgteGFrntrkg--T~iAaQtaavaa~~r~v~~G~~~vrV~VkG--lGp  152 (190)
T KOG0408          78 EIPIIHIRASFNNTIVTVT-DVKGEVISWSSCGTEGFRNTRKG--TPIAAQTAAVAAIRRAVDQGMQTVRVRVKG--LGP  152 (190)
T ss_pred             CCCEEEEEECCCCEEEEEE-CCCCCEEEEEECCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHCCEEEEEEEEC--CCC
T ss_conf             0546899853787089998-06884898850242012356668--850677777899999997163699999845--886


Q ss_pred             HHHHHHHHHHHHCCCC
Q ss_conf             2599999999965878
Q gi|254780245|r  104 GRIAALADAVRKGGVS  119 (120)
Q Consensus       104 Grvka~ad~~R~~Gl~  119 (120)
                      ||..|+ .+++-.||.
T Consensus       153 GRmsa~-kgl~m~Gl~  167 (190)
T KOG0408         153 GRMSAL-KGLRMGGLL  167 (190)
T ss_pred             CHHHHH-HHHHHCCEE
T ss_conf             478887-655215569


No 59 
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=30.22  E-value=47  Score=15.26  Aligned_cols=45  Identities=18%  Similarity=0.254  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCC---CCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             99999999999779979998389---8631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRG---KHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~---g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      .-|.+.++.+.++|-..|.|=-+   .....-|...|-+++++.||.+
T Consensus       160 ~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~R~~gf~~al~~~gl~~  207 (327)
T PRK10423        160 LGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNI  207 (327)
T ss_pred             HHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999997599749996688766179999999999999859998


No 60 
>PRK07454 short chain dehydrogenase; Provisional
Probab=29.25  E-value=49  Score=15.16  Aligned_cols=42  Identities=26%  Similarity=0.383  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             9999999999999977997999838986312259999999996587
Q gi|254780245|r   73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV  118 (120)
Q Consensus        73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl  118 (120)
                      ++.-+|..+|++.-+.|.+-+..||...    ++..+++.+++.|.
T Consensus        14 as~GIG~a~A~~la~~G~~V~l~~R~~~----~l~~~~~e~~~~g~   55 (241)
T PRK07454         14 ASRGIGKATALAFAKAGWDLALVARSQD----ALEALAEELRSTGV   55 (241)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCC
T ss_conf             5878999999999987998999989999----99999999996599


No 61 
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=28.66  E-value=50  Score=15.10  Aligned_cols=37  Identities=35%  Similarity=0.478  Sum_probs=27.1

Q ss_pred             HHHHHHHCCCCEEEECCCCCCCHHH---HHHHHHHHHHCCCC
Q ss_conf             9999997799799983898631225---99999999965878
Q gi|254780245|r   81 LVERAVKVGVKSVYFDRGKHLYCGR---IAALADAVRKGGVS  119 (120)
Q Consensus        81 ia~r~~~~gI~~v~FDR~g~~yHGr---vka~ad~~R~~Gl~  119 (120)
                      --++|.+.||..++||+..|.  +|   -.++++.+++.+..
T Consensus        42 ~lerA~~~gIpt~~~~~k~~~--~r~~~d~~l~~~l~~~~~d   81 (200)
T COG0299          42 ALERAAKAGIPTVVLDRKEFP--SREAFDRALVEALDEYGPD   81 (200)
T ss_pred             HHHHHHHCCCCEEEECCCCCC--CHHHHHHHHHHHHHHCCCC
T ss_conf             999999849988974445678--7789999999999852999


No 62 
>PRK08277 D-mannonate oxidoreductase; Provisional
Probab=28.65  E-value=50  Score=15.09  Aligned_cols=41  Identities=17%  Similarity=0.434  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             999999999999977997999838986312259999999996587
Q gi|254780245|r   74 ATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV  118 (120)
Q Consensus        74 A~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl  118 (120)
                      +.-+|.-+|+...+.|-+-+..||+..    .+.++++.+++.|-
T Consensus        19 s~GIG~aia~~la~~Ga~V~i~~~~~~----~~~~~~~~l~~~g~   59 (278)
T PRK08277         19 GGVLGGAMAKELARAGAKVAILDRNQE----KAEAVVEEIKANGG   59 (278)
T ss_pred             CCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCC
T ss_conf             748999999999987998999979889----99999999984599


No 63 
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=28.53  E-value=51  Score=15.08  Aligned_cols=44  Identities=18%  Similarity=0.243  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHCCCCEEEECCCCC---CCHHHHHHHHHHHHHCCCCC
Q ss_conf             999999999977997999838986---31225999999999658789
Q gi|254780245|r   77 VGNLLVERAVKVGVKSVYFDRGKH---LYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        77 vG~~ia~r~~~~gI~~v~FDR~g~---~yHGrvka~ad~~R~~Gl~F  120 (120)
                      -|+++++.+.+.|-.++.|=.+..   -..-|...|-+++++.|+.+
T Consensus       103 ~~~~~~~~L~~~G~~~I~~i~~~~~~~~~~~R~~G~~~a~~~~~~~~  149 (269)
T cd06293         103 GGRLATRHLARAGHRRIAFVGGPDALISARERYAGYREALAEAHIPE  149 (269)
T ss_pred             HHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             99999999998299838995488776339999999999999769999


No 64 
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=28.53  E-value=51  Score=15.08  Aligned_cols=45  Identities=22%  Similarity=0.245  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCCCCCC----HHHHHHHHHHHHHCCCCC
Q ss_conf             999999999997799799983898631----225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRGKHLY----CGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~g~~y----HGrvka~ad~~R~~Gl~F  120 (120)
                      .-|..+++.+.++|-.+|.|=-+....    .=|...|-+++.+.|+.+
T Consensus       102 ~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~~R~~gf~~a~~~~g~~~  150 (268)
T cd06298         102 KAAFEATELLIKNGHKKIAFISGPLEDSINGDERLAGYKEALSEANIEF  150 (268)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             9999999999972996699996787776259999999999999849997


No 65 
>PRK07775 short chain dehydrogenase; Provisional
Probab=28.37  E-value=51  Score=15.07  Aligned_cols=41  Identities=17%  Similarity=0.259  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             999999999999997799799983898631225999999999658
Q gi|254780245|r   73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGG  117 (120)
Q Consensus        73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~G  117 (120)
                      ++.-+|..+|+++-+.|.+-+..+|...    ++.++++.+++.|
T Consensus        18 AssGIG~aiA~~la~~G~~V~l~~R~~e----~l~~~~~~l~~~g   58 (275)
T PRK07775         18 ASSGIGAATAIELAAHGFPVALGARRVE----KCEEIVDKIRADG   58 (275)
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCC
T ss_conf             2359999999999987998999989899----9999999999649


No 66 
>PRK08243 4-hydroxybenzoate 3-monooxygenase; Validated
Probab=28.36  E-value=51  Score=15.06  Aligned_cols=12  Identities=0%  Similarity=-0.144  Sum_probs=5.5

Q ss_pred             EECCCCCCCHHH
Q ss_conf             983898631225
Q gi|254780245|r   94 YFDRGKHLYCGR  105 (120)
Q Consensus        94 ~FDR~g~~yHGr  105 (120)
                      .|+++-+.+|.+
T Consensus       260 ~~~~sv~~lrs~  271 (392)
T PRK08243        260 SIEKSIAPLRSF  271 (392)
T ss_pred             EEEEEEEEHHHH
T ss_conf             345666205655


No 67 
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=27.98  E-value=52  Score=15.02  Aligned_cols=46  Identities=22%  Similarity=0.313  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHCCCCEEEECC--CCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             99999999999977997999838--98631225999999999658789
Q gi|254780245|r   75 TAVGNLLVERAVKVGVKSVYFDR--GKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        75 ~~vG~~ia~r~~~~gI~~v~FDR--~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ...|.+.++.+.+.|-..|.|=-  ....-+-|...|.+++++.|+.+
T Consensus        94 ~~~~~~a~~~L~~~Ghr~I~~ig~~~~~~~~~R~~Gf~~al~~~g~~~  141 (265)
T cd01543          94 AAIGRMAAEHFLERGFRHFAFYGLPGARWSDEREEAFRQLVAEAGYEC  141 (265)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999999869974999899988069999999999999779997


No 68 
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=27.78  E-value=52  Score=15.00  Aligned_cols=45  Identities=20%  Similarity=0.243  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCC---CCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             99999999999779979998389---8631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRG---KHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~---g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      .-|...++.+.+.|-..|.|=-+   ....+-|...|.++++++|+.+
T Consensus       170 ~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~R~~G~~~al~~~gl~~  217 (341)
T PRK11041        170 TAAFEAVNYLYELGHKRIACIAGPEEMPLCHYRLQGYVQALRRCGITV  217 (341)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999997499769999689877689999999999999869999


No 69 
>PRK00819 RNA 2'-phosphotransferase-like protein; Reviewed
Probab=27.70  E-value=30  Score=16.39  Aligned_cols=22  Identities=23%  Similarity=0.489  Sum_probs=16.8

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             9863122599999999965878
Q gi|254780245|r   98 GKHLYCGRIAALADAVRKGGVS  119 (120)
Q Consensus        98 ~g~~yHGrvka~ad~~R~~Gl~  119 (120)
                      ..+.|||--..+.+.+++.||+
T Consensus        93 p~~lyHGT~~~~~~~I~~~GL~  114 (179)
T PRK00819         93 PQFLYHGTARRFLDSILEQGIK  114 (179)
T ss_pred             CCEEEECCCHHHHHHHHHHCCC
T ss_conf             8666734579999999996687


No 70 
>PRK08862 short chain dehydrogenase; Provisional
Probab=27.49  E-value=53  Score=14.97  Aligned_cols=17  Identities=24%  Similarity=0.208  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHHHHHHHC
Q ss_conf             89999999999999977
Q gi|254780245|r   72 VAATAVGNLLVERAVKV   88 (120)
Q Consensus        72 ~aA~~vG~~ia~r~~~~   88 (120)
                      .....+....+...++.
T Consensus       117 ~~~~~~~~~~~~~m~~~  133 (227)
T PRK08862        117 STLFTYGQVAAERMRKR  133 (227)
T ss_pred             HHHHHHHHHHHHHHHHC
T ss_conf             69999999999999966


No 71 
>pfam00289 CPSase_L_chain Carbamoyl-phosphate synthase L chain, N-terminal domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117.
Probab=27.34  E-value=53  Score=14.95  Aligned_cols=49  Identities=18%  Similarity=0.207  Sum_probs=39.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             6678999999999999997799799983898631225999999999658789
Q gi|254780245|r   69 ANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        69 ~ni~aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      +....+++-.+.|-+-+.+.|+..|.   +||-|----..||+.+.++|+.|
T Consensus        53 ~~~~~~Yl~~~~Ii~ia~~~~~~aih---pGyGflsEn~~fa~~~~~~Gi~f  101 (109)
T pfam00289        53 GPASESYLNIERILDIAEKEGADAIH---PGYGFLSENAEFAEACEKAGITF  101 (109)
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCCEEE---CCCCCCCCCHHHHHHHHHCCCEE
T ss_conf             98321113799999999981889687---79762335999999999888989


No 72 
>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription
Probab=27.32  E-value=53  Score=14.95  Aligned_cols=45  Identities=20%  Similarity=0.291  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCCCC---C-CHHHHHHHHHHHHHCCCCC
Q ss_conf             9999999999977997999838986---3-1225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRGKH---L-YCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~g~---~-yHGrvka~ad~~R~~Gl~F  120 (120)
                      ..|.++++.+.+.|-.+|.|=-+..   - -+-|...|-+++++.|+.+
T Consensus        98 ~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~  146 (265)
T cd06291          98 EGGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGLEV  146 (265)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             9999999999973996499996688887489999999999999769996


No 73 
>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=27.20  E-value=54  Score=14.94  Aligned_cols=45  Identities=18%  Similarity=0.314  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             9999999999977997999838---98631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ..|+.+++.+.++|-.++.|=-   +..-.-=|.+.|.+++++.|+.+
T Consensus       101 ~a~~~~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~  148 (267)
T cd06284         101 AAARLAVDHLISLGHRRIALITGPRDNPLARDRLEGYRQALAEAGLPA  148 (267)
T ss_pred             HHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999997099769996288887259999999999999839985


No 74 
>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=26.81  E-value=54  Score=14.90  Aligned_cols=46  Identities=26%  Similarity=0.235  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEC--CCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             9999999999997799799983--898631225999999999658789
Q gi|254780245|r   75 TAVGNLLVERAVKVGVKSVYFD--RGKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        75 ~~vG~~ia~r~~~~gI~~v~FD--R~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ..-|..+++.+.++|-.+|.|=  ...+...-|...|.+++.+.|+.+
T Consensus       100 ~~~~~~a~~~L~~~Ghr~I~~l~g~~~~~~~~R~~Gf~~al~~~gi~~  147 (263)
T cd06280         100 RAAARTLVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMRRHGLAP  147 (263)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999998608966999938998439999999999999769997


No 75 
>PRK12857 putative aldolase; Reviewed
Probab=26.70  E-value=55  Score=14.89  Aligned_cols=38  Identities=21%  Similarity=0.244  Sum_probs=30.0

Q ss_pred             HHHHHHHCCCCEEEECCCCCCCH---HHHHHHHHHHHHCCC
Q ss_conf             99999977997999838986312---259999999996587
Q gi|254780245|r   81 LVERAVKVGVKSVYFDRGKHLYC---GRIAALADAVRKGGV  118 (120)
Q Consensus        81 ia~r~~~~gI~~v~FDR~g~~yH---Grvka~ad~~R~~Gl  118 (120)
                      ..+++++.|.+.|.||-+.+.|.   -..+.+++-++..|+
T Consensus        89 ~i~~ai~~Gf~SVM~DgS~l~~eeNi~~Tk~vv~~ah~~gv  129 (284)
T PRK12857         89 QVMKCIRNGFTSVMIDGSKLPLEENIALTKKVVEIAHAVGV  129 (284)
T ss_pred             HHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999980998799728989999999999999999987089


No 76 
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=26.68  E-value=55  Score=14.88  Aligned_cols=44  Identities=18%  Similarity=0.315  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHCCCCEEEECCCCC---CCHHHHHHHHHHHHHCCCCC
Q ss_conf             999999999977997999838986---31225999999999658789
Q gi|254780245|r   77 VGNLLVERAVKVGVKSVYFDRGKH---LYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        77 vG~~ia~r~~~~gI~~v~FDR~g~---~yHGrvka~ad~~R~~Gl~F  120 (120)
                      -|.++++.+.++|-.++.|=.+..   .-..|...|-+++.++|+.+
T Consensus       101 ~~~~~~~~Li~~G~~~i~~l~~~~~~~~~~~R~~Gf~~a~~~~~~~~  147 (265)
T cd06285         101 GGRLATRHLLDLGHRRIAVLAGPDYASTARDRLAGFRAALAEAGIEV  147 (265)
T ss_pred             HHHHHHHHHHHHCCCCEEECCCCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             99999999998388658754788777059999999999999869998


No 77 
>PRK07035 short chain dehydrogenase; Provisional
Probab=26.62  E-value=55  Score=14.88  Aligned_cols=40  Identities=20%  Similarity=0.324  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             99999999999997799799983898631225999999999658
Q gi|254780245|r   74 ATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGG  117 (120)
Q Consensus        74 A~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~G  117 (120)
                      +.-+|..+|+.+.+.|-.-+..||...    .+.++++.+++.|
T Consensus        17 s~GIG~aia~~la~~Ga~V~i~~r~~~----~l~~~~~~i~~~g   56 (252)
T PRK07035         17 SRGIGEAIAKLLAQQGAHVIVSSRKLD----GCQAVADAIVAAG   56 (252)
T ss_pred             CCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCC
T ss_conf             749999999999987998999979889----9999999999649


No 78 
>PRK08185 hypothetical protein; Provisional
Probab=26.44  E-value=55  Score=14.86  Aligned_cols=39  Identities=28%  Similarity=0.286  Sum_probs=30.2

Q ss_pred             HHHHHHHHCCCCEEEECCCCCCCHH---HHHHHHHHHHHCCC
Q ss_conf             9999999779979998389863122---59999999996587
Q gi|254780245|r   80 LLVERAVKVGVKSVYFDRGKHLYCG---RIAALADAVRKGGV  118 (120)
Q Consensus        80 ~ia~r~~~~gI~~v~FDR~g~~yHG---rvka~ad~~R~~Gl  118 (120)
                      ...+++.+.|.+.|.||-+.+.|.-   +.+.+++-++..|+
T Consensus        82 e~~~~ai~~GFsSVM~DgS~lp~eeNi~~Tk~vv~~ah~~gv  123 (283)
T PRK08185         82 EDVMRAIRCGFTSVMIDGSLLPYEENVALTKEVVELAHKVGV  123 (283)
T ss_pred             HHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             999999982998798638989999999999999999986598


No 79 
>PRK12737 gatY tagatose-bisphosphate aldolase; Reviewed
Probab=26.37  E-value=55  Score=14.85  Aligned_cols=38  Identities=13%  Similarity=0.280  Sum_probs=29.2

Q ss_pred             HHHHHHHCCCCEEEECCCCCCCHH---HHHHHHHHHHHCCC
Q ss_conf             999999779979998389863122---59999999996587
Q gi|254780245|r   81 LVERAVKVGVKSVYFDRGKHLYCG---RIAALADAVRKGGV  118 (120)
Q Consensus        81 ia~r~~~~gI~~v~FDR~g~~yHG---rvka~ad~~R~~Gl  118 (120)
                      ..++|++.|.+.|.||-+.+.|.-   ..+.+++-++..|+
T Consensus        89 ~~~~ai~~GftSVM~DgS~lp~eeNi~~T~~vv~~Ah~~gv  129 (284)
T PRK12737         89 DIKKKVRAGIRSVMIDGSHLSFEENIAIVKEVVEFCHRYDA  129 (284)
T ss_pred             HHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999981998798709999999999999999998645288


No 80 
>PRK07832 short chain dehydrogenase; Provisional
Probab=26.35  E-value=55  Score=14.85  Aligned_cols=38  Identities=18%  Similarity=0.212  Sum_probs=15.7

Q ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHC
Q ss_conf             999999999999779979998389863122599999999965
Q gi|254780245|r   75 TAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKG  116 (120)
Q Consensus        75 ~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~  116 (120)
                      .=+|..+|....+.|..-+..||+.-    .+.++++.++..
T Consensus        10 sGIG~a~A~~la~~Ga~v~l~~r~~~----~l~~~~~~l~~~   47 (272)
T PRK07832         10 SGIGRATALRLAAQGAELFLTDRDAD----GLAQTVADARAL   47 (272)
T ss_pred             HHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHC
T ss_conf             19999999999988998999989889----999999999845


No 81 
>TIGR01830 3oxo_ACP_reduc 3-oxoacyl-(acyl-carrier-protein) reductase; InterPro: IPR011284   This entry represents 3-oxoacyl-[ACP] reductase, also called 3-ketoacyl-acyl carrier protein reductase, an enzyme of fatty acid biosynthesis found in many plant and bacterial species. This enzyme is involved in type II fatty acid biosynthesis, where the individual metabolic transformations are carried out by different enzymes rather than by a single enzyme as occurs in type I fatty acid biosynthesis .   Structural studies show that the enzyme is a tetramer which forms a typical Rossman fold , . Unlike other members of the short-chain dehydrogenase/reductase superfamily, the enzyme undergoes a marked conformational change upon binding of the NADP(H)cofactor. This conformational change aligns the side chains of the catalytic triad at the active site in an active conformation and increases the affinity of the enzyme for its substrate.; GO: 0004316 3-oxoacyl-[acyl-carrier-protein] reductase activity, 0051287 NAD binding, 0006633 fatty acid biosynthetic process.
Probab=25.94  E-value=56  Score=14.80  Aligned_cols=44  Identities=18%  Similarity=0.295  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             99999999999999779979998389863122599999999965878
Q gi|254780245|r   73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVS  119 (120)
Q Consensus        73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~  119 (120)
                      |+.=||.-||+++-+.|.+=++-||+...   .+.+++|.+++.|.+
T Consensus         6 asRGIG~AIA~~LA~~Ga~V~i~y~~~e~---~~~~~~~e~~~~G~~   49 (238)
T TIGR01830         6 ASRGIGRAIALKLAKEGAKVIITYRTSEE---GAEEVVEEIKELGVK   49 (238)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEECCCCHH---HHHHHHHHHHHCCCE
T ss_conf             78616799999998679959996598257---888999999856975


No 82 
>PRK12827 short chain dehydrogenase; Provisional
Probab=25.92  E-value=57  Score=14.80  Aligned_cols=46  Identities=15%  Similarity=0.166  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             9999999999999977997999838986312259999999996587
Q gi|254780245|r   73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV  118 (120)
Q Consensus        73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl  118 (120)
                      ++.-+|..+|++..+.|-+-++.|+....-.-...++++.+++.|-
T Consensus        14 as~GIG~aia~~la~~Ga~V~i~~~~~~~~~~~~~~~~~~~~~~g~   59 (251)
T PRK12827         14 GSGGLGRAIAVRLAADGADVIVLDIHPMRGRAEAEAVAALIEAAGG   59 (251)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHCCC
T ss_conf             2558999999999987998999848885328999999999996498


No 83 
>PRK06457 pyruvate dehydrogenase; Provisional
Probab=25.75  E-value=57  Score=14.78  Aligned_cols=16  Identities=19%  Similarity=0.243  Sum_probs=7.5

Q ss_pred             CCCCCCHHHHHHHHHHHH
Q ss_conf             898631225999999999
Q gi|254780245|r   97 RGKHLYCGRIAALADAVR  114 (120)
Q Consensus        97 R~g~~yHGrvka~ad~~R  114 (120)
                      =|++.|+  +.+|.-++|
T Consensus       424 DGsf~m~--~~EL~Ta~r  439 (549)
T PRK06457        424 DGGFAMT--MMELITAKK  439 (549)
T ss_pred             CCHHHCC--HHHHHHHHH
T ss_conf             6077514--899999999


No 84 
>PRK06139 short chain dehydrogenase; Provisional
Probab=25.66  E-value=57  Score=14.77  Aligned_cols=42  Identities=21%  Similarity=0.339  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             9999999999999977997999838986312259999999996587
Q gi|254780245|r   73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV  118 (120)
Q Consensus        73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl  118 (120)
                      ++.=||..+|+..-+.|-.-|..||+..    .+.++++.+++.|-
T Consensus        14 ASsGIG~aiA~~~A~~Ga~Vvl~~R~~~----~L~~~a~e~~~~G~   55 (324)
T PRK06139         14 ASSGIGRATAEAFARRGARLVLAARDEE----ALFEVAEECRALGA   55 (324)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCC
T ss_conf             2549999999999987998999989999----99999999995499


No 85 
>PRK05653 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Validated
Probab=24.99  E-value=59  Score=14.70  Aligned_cols=38  Identities=26%  Similarity=0.490  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             999999999997799799983898631225999999999658
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGG  117 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~G  117 (120)
                      -+|..+|+...+.|.+-+..||+..    ++..+.+.+.+.|
T Consensus        16 GIG~a~a~~la~~G~~V~~~~r~~~----~l~~~~~~~~~~~   53 (246)
T PRK05653         16 GIGRAIALRLAADGARVVIYDSNEE----AAEALAEELRAAG   53 (246)
T ss_pred             HHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCC
T ss_conf             8999999999987999999979999----9999999999659


No 86 
>COG3669 Alpha-L-fucosidase [Carbohydrate transport and metabolism]
Probab=24.90  E-value=45  Score=15.37  Aligned_cols=40  Identities=28%  Similarity=0.353  Sum_probs=22.4

Q ss_pred             HHHHHHHCCCCEEEEC---CCC-----CCCH-----------HHHHHHHHHHHHCCCCC
Q ss_conf             9999997799799983---898-----6312-----------25999999999658789
Q gi|254780245|r   81 LVERAVKVGVKSVYFD---RGK-----HLYC-----------GRIAALADAVRKGGVSF  120 (120)
Q Consensus        81 ia~r~~~~gI~~v~FD---R~g-----~~yH-----------Grvka~ad~~R~~Gl~F  120 (120)
                      .|...|++|-+.|+.-   .-|     -.||           --|..+|.++|+.||-|
T Consensus        59 War~fK~AGAKyvilvakHHDGFaLw~t~ys~wnsvk~GpKrDlVgela~Avr~qGL~F  117 (430)
T COG3669          59 WARLFKEAGAKYVILVAKHHDGFALWPTDYSVWNSVKRGPKRDLVGELAKAVREQGLRF  117 (430)
T ss_pred             HHHHHHHCCCCEEEEEEEECCCEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCEE
T ss_conf             99999971884799865403770423665300015540775118999999999728715


No 87 
>pfam02776 TPP_enzyme_N Thiamine pyrophosphate enzyme, N-terminal TPP binding domain.
Probab=24.83  E-value=59  Score=14.68  Aligned_cols=39  Identities=31%  Similarity=0.440  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHC-CCCC
Q ss_conf             9999999999779979998389863122599999999965-8789
Q gi|254780245|r   77 VGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKG-GVSF  120 (120)
Q Consensus        77 vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~-Gl~F  120 (120)
                      .++.|++.+++.||+.|.-==|+     .+-.|.|++.+. |++|
T Consensus         3 ~~~~i~~~L~~~Gv~~vFg~pG~-----~~~~l~~al~~~~~i~~   42 (172)
T pfam02776         3 GADALAEALKALGVDHVFGVPGG-----SILPLLDALAKSPGIRY   42 (172)
T ss_pred             HHHHHHHHHHHCCCCEEEEECCC-----CHHHHHHHHHHCCCCEE
T ss_conf             89999999998799999996897-----77999999986799769


No 88 
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=24.51  E-value=60  Score=14.64  Aligned_cols=39  Identities=18%  Similarity=0.311  Sum_probs=27.5

Q ss_pred             HHHHHHHCCCC----------EEEECCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             99999977997----------9998389863122599999999965878
Q gi|254780245|r   81 LVERAVKVGVK----------SVYFDRGKHLYCGRIAALADAVRKGGVS  119 (120)
Q Consensus        81 ia~r~~~~gI~----------~v~FDR~g~~yHGrvka~ad~~R~~Gl~  119 (120)
                      +.-+|..+|++          ++.|++|.|+-.-|+..+.+.+-|-||+
T Consensus        45 fvl~Al~~GaDGV~v~GC~~geCHy~~GN~ka~rR~~~lke~l~elgie   93 (132)
T COG1908          45 FVLKALRKGADGVLVAGCKIGECHYISGNYKAKRRMELLKELLKELGIE   93 (132)
T ss_pred             HHHHHHHCCCCEEEEECCCCCCEEEECCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999997389868993441561233016647999999999999994888


No 89 
>PRK08945 short chain dehydrogenase; Provisional
Probab=24.42  E-value=60  Score=14.63  Aligned_cols=27  Identities=22%  Similarity=0.236  Sum_probs=13.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             667899999999999999779979998
Q gi|254780245|r   69 ANIVAATAVGNLLVERAVKVGVKSVYF   95 (120)
Q Consensus        69 ~ni~aA~~vG~~ia~r~~~~gI~~v~F   95 (120)
                      .|..+...+-+.+....++.+--.|+|
T Consensus       124 vNl~g~~~l~~~~~p~m~~~~~G~Ii~  150 (245)
T PRK08945        124 VNVNATFMLTQALLPLLLKSPAASLVF  150 (245)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             675999999999999998779978999


No 90 
>TIGR02867 spore_II_P stage II sporulation protein P; InterPro: IPR010897   This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation .   SpoIIP is one of the three genes (spoIID, spoIIM and spoIIP, , , ), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers ..
Probab=24.23  E-value=61  Score=14.61  Aligned_cols=20  Identities=25%  Similarity=0.414  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHHHHC-CCCEEE
Q ss_conf             99999999999977-997999
Q gi|254780245|r   75 TAVGNLLVERAVKV-GVKSVY   94 (120)
Q Consensus        75 ~~vG~~ia~r~~~~-gI~~v~   94 (120)
                      ..||..|++.+-++ ||..++
T Consensus        40 ~~VG~~L~~~Le~~YGI~~~~   60 (221)
T TIGR02867        40 TKVGDRLAKELEEKYGIGAIH   60 (221)
T ss_pred             HHHHHHHHHHHHHHCCEEEEE
T ss_conf             067889999999828945786


No 91 
>COG4861 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.13  E-value=37  Score=15.87  Aligned_cols=48  Identities=19%  Similarity=0.188  Sum_probs=25.0

Q ss_pred             CCHHHHHHHHHHHHHHH-HHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             66789999999999999-977997999838986312259999999996587
Q gi|254780245|r   69 ANIVAATAVGNLLVERA-VKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV  118 (120)
Q Consensus        69 ~ni~aA~~vG~~ia~r~-~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl  118 (120)
                      -|-.+|..+|.+++.-. ...-+-+|.=--  ----|-++...|.+||.|+
T Consensus       144 ftp~raqv~~ALL~aP~lv~~P~REIAasA--gVsvGTa~~t~d~LrE~G~  192 (345)
T COG4861         144 FTPKRAQVVCALLDAPQLVDAPLREIAASA--GVSVGTAKETMDTLRETGF  192 (345)
T ss_pred             CCHHHHHHHHHHHCCHHHHCCHHHHHHHHC--CCEECHHHHHHHHHHHCCH
T ss_conf             886788899997558877544588887640--5101108888999886010


No 92 
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding, 
Probab=24.04  E-value=61  Score=14.59  Aligned_cols=46  Identities=15%  Similarity=0.243  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             99999999999977997999838---98631225999999999658789
Q gi|254780245|r   75 TAVGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        75 ~~vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ...|...++.+.++|-.+|.|=-   ......=|...|.+++.++|+..
T Consensus       101 ~~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~G~~~al~~~g~~~  149 (268)
T cd01575         101 AEAGRAMARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDP  149 (268)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             9999999999997499769998489887369999999999999769898


No 93 
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily.  In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=23.98  E-value=62  Score=14.58  Aligned_cols=45  Identities=20%  Similarity=0.324  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             9999999999977997999838---98631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      ..|..+++.+.+.|.++|.|=.   +..-..-|...|-+++.+.|+.+
T Consensus       102 ~a~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~  149 (264)
T cd06267         102 AGAYLAVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALEEAGIPL  149 (264)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999987188856896389877069999999999999869998


No 94 
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=23.55  E-value=63  Score=14.53  Aligned_cols=44  Identities=14%  Similarity=0.115  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHCCCCEEEECCCCC---CCHHHHHHHHHHHHHCCCCC
Q ss_conf             999999999977997999838986---31225999999999658789
Q gi|254780245|r   77 VGNLLVERAVKVGVKSVYFDRGKH---LYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        77 vG~~ia~r~~~~gI~~v~FDR~g~---~yHGrvka~ad~~R~~Gl~F  120 (120)
                      -|...++.+.+.|-..|.|=-+..   -..-|...|.+++++.||.+
T Consensus       163 g~~~a~~~L~~~GhrrI~~i~~~~~~~~~~~R~~G~~~al~~~gl~~  209 (346)
T PRK10401        163 GARMATRMLLNNGHQRIGYLSSSHGIEDDAMRKAGWLSALKEQGIIP  209 (346)
T ss_pred             HHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             99999999996299828999479887168999999999999849998


No 95 
>PRK09526 lacI lac repressor; Reviewed
Probab=23.44  E-value=63  Score=14.52  Aligned_cols=44  Identities=18%  Similarity=0.118  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHCCCCEEEEC---CCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             999999999997799799983---89863122599999999965878
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFD---RGKHLYCGRIAALADAVRKGGVS  119 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FD---R~g~~yHGrvka~ad~~R~~Gl~  119 (120)
                      .-|.++++.+.++|-..+.|=   ++..--+-|...|.+++++.|+.
T Consensus       167 ~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~R~~Gf~~~~~~~~l~  213 (342)
T PRK09526        167 DGTRLGVEHLVELGHQQIALLAGPLSSVSARLRLAGWLEYLTRNQLS  213 (342)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             99999999999759975999958976600999999999999977989


No 96 
>COG0064 GatB Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit (PET112 homolog) [Translation, ribosomal structure and biogenesis]
Probab=22.93  E-value=65  Score=14.46  Aligned_cols=63  Identities=17%  Similarity=0.133  Sum_probs=33.0

Q ss_pred             CEEEEEEECCCCEEEEEEEECCC-------------HHCCCCCCCCCHHHHHHHHHHHHHHHHHCCC-CEEEECCCCCCC
Q ss_conf             09999996279759999850210-------------0000134686678999999999999997799-799983898631
Q gi|254780245|r   37 HIYGQIIDDSIGHTLVSASSLNE-------------PLRSSLKTGANIVAATAVGNLLVERAVKVGV-KSVYFDRGKHLY  102 (120)
Q Consensus        37 hiyAQiIdd~~~~tl~saST~~k-------------~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI-~~v~FDR~g~~y  102 (120)
                      -|++|+  ....+..|+++|.--             .+-+.++. -|. .|-..+-.+| .++...| ...+|||..|-|
T Consensus        13 EvHvqL--~T~tKlFs~~~~~f~~a~PNtnv~pv~lglPGaLPv-lN~-~av~~ai~~~-lAL~~~i~~~~~FdRK~YFY   87 (483)
T COG0064          13 EVHVQL--NTKTKLFSGCSTDFGGAEPNTNVCPVCLGLPGALPV-LNK-EAVEKAIKAG-LALNCEINEKSVFDRKNYFY   87 (483)
T ss_pred             EEEEEE--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCH-HHHHHHHHHH-HHHCCEECCCEECCCCCCCC
T ss_conf             787786--157664678852126789977788500268987665-689-9999999964-53165625650316678899


Q ss_pred             HH
Q ss_conf             22
Q gi|254780245|r  103 CG  104 (120)
Q Consensus       103 HG  104 (120)
                      --
T Consensus        88 PD   89 (483)
T COG0064          88 PD   89 (483)
T ss_pred             CC
T ss_conf             98


No 97 
>pfam02826 2-Hacid_dh_C D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain. This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family pfam00389.
Probab=22.61  E-value=66  Score=14.42  Aligned_cols=24  Identities=25%  Similarity=0.462  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCCC
Q ss_conf             999999999997799799983898
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRGK   99 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~g   99 (120)
                      .+|+.+|++++..|.+-++|||..
T Consensus        46 ~IG~~va~~l~~fg~~V~~~d~~~   69 (176)
T pfam02826        46 RIGRAVARRLKAFGMKVIAYDRYP   69 (176)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCC
T ss_conf             999999999998398125437987


No 98 
>PRK07102 short chain dehydrogenase; Provisional
Probab=22.57  E-value=66  Score=14.41  Aligned_cols=26  Identities=23%  Similarity=0.172  Sum_probs=11.8

Q ss_pred             CHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             67899999999999999779979998
Q gi|254780245|r   70 NIVAATAVGNLLVERAVKVGVKSVYF   95 (120)
Q Consensus        70 ni~aA~~vG~~ia~r~~~~gI~~v~F   95 (120)
                      |.-+...+-..+.....+.+--.|++
T Consensus       107 N~~g~~~l~~~~~~~m~~~~~G~Iv~  132 (243)
T PRK07102        107 NFEGPIALLTLLANRFEARGSGTIVG  132 (243)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             98999999999999988723974999


No 99 
>KOG4691 consensus
Probab=22.52  E-value=48  Score=15.22  Aligned_cols=22  Identities=23%  Similarity=0.181  Sum_probs=17.1

Q ss_pred             HHH-CCCCEEEECCCCCCCHHHH
Q ss_conf             997-7997999838986312259
Q gi|254780245|r   85 AVK-VGVKSVYFDRGKHLYCGRI  106 (120)
Q Consensus        85 ~~~-~gI~~v~FDR~g~~yHGrv  106 (120)
                      +++ -.+..+..||.|.+||||-
T Consensus       187 AL~~p~~ynfAIdraGNky~vr~  209 (227)
T KOG4691         187 ALDSPKNYNFAIDRAGNKYVVRP  209 (227)
T ss_pred             HHCCCCCCCHHHCCCCCEEECCC
T ss_conf             97386433233112677333677


No 100
>PRK06194 hypothetical protein; Provisional
Probab=22.24  E-value=67  Score=14.37  Aligned_cols=41  Identities=20%  Similarity=0.323  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             999999999999977997999838986312259999999996587
Q gi|254780245|r   74 ATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV  118 (120)
Q Consensus        74 A~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl  118 (120)
                      +.=+|..+|+++.+.|-+-|..||...    .+...++.+++.|.
T Consensus        15 ssGIG~a~A~~la~~Ga~Vvl~d~~~~----~l~~~~~~l~~~g~   55 (301)
T PRK06194         15 ASGFGREFARIGARLGMKLVLADVQQD----ALDRAVAELRAQGA   55 (301)
T ss_pred             CCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCC
T ss_conf             779999999999987998999979889----99999999984598


No 101
>pfam12005 DUF3499 Protein of unknown function (DUF3499). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 125 to 163 amino acids in length.
Probab=22.10  E-value=52  Score=15.02  Aligned_cols=46  Identities=24%  Similarity=0.178  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHHHH-CCCCEEEECCCC---CCCHHHHHHHHHHHHHCCC
Q ss_conf             999999999999997-799799983898---6312259999999996587
Q gi|254780245|r   73 AATAVGNLLVERAVK-VGVKSVYFDRGK---HLYCGRIAALADAVRKGGV  118 (120)
Q Consensus        73 aA~~vG~~ia~r~~~-~gI~~v~FDR~g---~~yHGrvka~ad~~R~~Gl  118 (120)
                      -++-+-..-|+++.. .|-+-|-.+-..   -.=.--+-||||++||+|-
T Consensus        40 h~yDLC~~Ha~rlTaP~GW~vvr~~~~~~~~~p~~dDL~ALAdAVREaar   89 (125)
T pfam12005        40 HSYDLCEEHAERLTAPLGWEVVRLAGEFAPAEPDEDDLVALADAVREAAR   89 (125)
T ss_pred             CHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             40465888986356888757786047777789777889999999987424


No 102
>TIGR01318 gltD_gamma_fam glutamate synthase, small subunit; InterPro: IPR006006    One pathway for the assimilation of ammonia and glutamate biosynthesis involves glutamate synthase (1.4.1.13 from EC) which transfers the amide group of glutamine to 2-oxoglutarate to yield two molecules of glutamate.  2 L-glutamate + NADP^+ = L-glutamine + 2-oxoglutarate + NADPH + H^+.    This model describes both glutatate synthase small subunit and closely related paralogs of unknown function from a number of gamma and alpha subdivision Proteobacteria, including Escherichia coli. ; GO: 0016639 oxidoreductase activity acting on the CH-NH2 group of donors NAD or NADP as acceptor, 0006537 glutamate biosynthetic process.
Probab=21.93  E-value=63  Score=14.50  Aligned_cols=23  Identities=30%  Similarity=0.453  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCC
Q ss_conf             99999999999779979998389
Q gi|254780245|r   76 AVGNLLVERAVKVGVKSVYFDRG   98 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~v~FDR~   98 (120)
                      =-|.-=|+.+.-.|++-+||||=
T Consensus       153 PAGLaCAD~L~RaGV~v~VfDRh  175 (480)
T TIGR01318       153 PAGLACADILARAGVQVVVFDRH  175 (480)
T ss_pred             CCHHHHHHHHHHCCCEEEEEECC
T ss_conf             60257999875178559997477


No 103
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=21.74  E-value=68  Score=14.31  Aligned_cols=48  Identities=29%  Similarity=0.336  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             999999999999997799799983898631225999999999658789
Q gi|254780245|r   73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      -|..+++++.+.++..||++|++-=|-+-=.=-++.+++.+-+.|++|
T Consensus       677 la~~~~e~~~~~a~~~gi~~V~lsGGVf~N~~l~~~~~~~lk~~~f~~  724 (750)
T COG0068         677 LAEGFAELAVELAKKYGINKVVLSGGVFQNRLLLERLAKYLKKEGFRF  724 (750)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEECCEEECHHHHHHHHHHHHHCCCEE
T ss_conf             999999999999986594279972776414999999999997539267


No 104
>PRK07109 short chain dehydrogenase; Provisional
Probab=21.63  E-value=69  Score=14.30  Aligned_cols=42  Identities=29%  Similarity=0.456  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             9999999999999977997999838986312259999999996587
Q gi|254780245|r   73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV  118 (120)
Q Consensus        73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl  118 (120)
                      ++.-||..+|+..-+.|..-+..+|+..    .+.++++.+++.|-
T Consensus        16 ASsGIGra~A~~fA~~Ga~Vvl~aR~~~----~L~~~a~e~~~~G~   57 (338)
T PRK07109         16 ASAGVGRATARAFARRGAKVVLLARGEE----GLEGLAAEIRAAGG   57 (338)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCC
T ss_conf             4349999999999987998999989999----99999999996398


No 105
>TIGR01235 pyruv_carbox pyruvate carboxylase; InterPro: IPR005930    In the postabsorptive state, blood glucose concentration is kept constant by a combination of glycogenolysis and gluconeogenesis. During prolonged fasting, when hepatic glycogen is exhausted, gluconeogenesis becomes the only source of plasma glucose. Gluconeogenesis (the production of new glucose molecules) occurs mainly in liver and, to a small extent, in kidneys.    Pyruvate carboxylase (6.4.1.1 from EC), a member of the biotin-dependent enzyme family, catalyses the ATP-dependent carboxylation of pyruvate to oxaloacetate, thus playing a crucial role in gluconeogenesis.  ATP + pyruvate + HCO3- = ADP + phosphate + oxaloacetate  Most well characterised forms of active enzyme consist of four identical subunits arranged in a tetrahedron-like structure. Each subunit contains three functional domains: the biotin carboxylation domain, the transcarboxylation domain and the biotin carboxyl carrier domain.; GO: 0004736 pyruvate carboxylase activity, 0006094 gluconeogenesis, 0005737 cytoplasm.
Probab=21.51  E-value=69  Score=14.28  Aligned_cols=17  Identities=35%  Similarity=0.554  Sum_probs=13.0

Q ss_pred             CCCEEEEEEECCCCEEE
Q ss_conf             87099999962797599
Q gi|254780245|r   35 SKHIYGQIIDDSIGHTL   51 (120)
Q Consensus        35 nkhiyAQiIdd~~~~tl   51 (120)
                      -|||-+||+-|..|.++
T Consensus       210 pkHiEvQ~LGD~~GNVV  226 (1169)
T TIGR01235       210 PKHIEVQLLGDKHGNVV  226 (1169)
T ss_pred             CCEEEEEEEECCCCCEE
T ss_conf             82078987634889878


No 106
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=21.31  E-value=61  Score=14.60  Aligned_cols=13  Identities=23%  Similarity=0.383  Sum_probs=6.4

Q ss_pred             HHHHHHHHCCCCE
Q ss_conf             9999999779979
Q gi|254780245|r   80 LLVERAVKVGVKS   92 (120)
Q Consensus        80 ~ia~r~~~~gI~~   92 (120)
                      .|++.+.+.|++-
T Consensus        36 ei~~a~~~LGl~~   48 (93)
T COG1400          36 EIAEALRELGLKP   48 (93)
T ss_pred             HHHHHHHHCCCCE
T ss_conf             9999999849974


No 107
>pfam01116 F_bP_aldolase Fructose-bisphosphate aldolase class-II.
Probab=21.09  E-value=70  Score=14.23  Aligned_cols=38  Identities=18%  Similarity=0.233  Sum_probs=26.4

Q ss_pred             HHHHHHHCCCCEEEECCCCCCCHH---HHHHHHHHHHHCCC
Q ss_conf             999999779979998389863122---59999999996587
Q gi|254780245|r   81 LVERAVKVGVKSVYFDRGKHLYCG---RIAALADAVRKGGV  118 (120)
Q Consensus        81 ia~r~~~~gI~~v~FDR~g~~yHG---rvka~ad~~R~~Gl  118 (120)
                      ..++|.+.|.+.|.||-+...|.-   ..+.+++-+...|+
T Consensus        87 ~~~~ai~~GftSVM~DgS~l~~eeNi~~T~~vv~~Ah~~gv  127 (283)
T pfam01116        87 GILEAIEAGFSSVMIDGSHLPFEENIAITKEVVEYAHARGV  127 (283)
T ss_pred             HHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999981998698638979999999999999999987398


No 108
>PRK12738 kbaY tagatose-bisphosphate aldolase; Reviewed
Probab=21.06  E-value=71  Score=14.23  Aligned_cols=38  Identities=18%  Similarity=0.319  Sum_probs=29.4

Q ss_pred             HHHHHHHCCCCEEEECCCCCCCH---HHHHHHHHHHHHCCC
Q ss_conf             99999977997999838986312---259999999996587
Q gi|254780245|r   81 LVERAVKVGVKSVYFDRGKHLYC---GRIAALADAVRKGGV  118 (120)
Q Consensus        81 ia~r~~~~gI~~v~FDR~g~~yH---Grvka~ad~~R~~Gl  118 (120)
                      ...+|.+.|.+.|.||-+.+.|.   -+.+.+++-++..|+
T Consensus        89 ~i~~ai~~GftSVM~DgS~lp~eeNi~~Tk~vv~~Ah~~gv  129 (286)
T PRK12738         89 DIRRKVHAGVRSAMIDGSHFPFAENVKLVKSVVDFCHSQDC  129 (286)
T ss_pred             HHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999977998798738999999999999999999847399


No 109
>pfam03446 NAD_binding_2 NAD binding domain of 6-phosphogluconate dehydrogenase. The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold.
Probab=21.01  E-value=71  Score=14.22  Aligned_cols=14  Identities=21%  Similarity=0.631  Sum_probs=6.9

Q ss_pred             HHHHHHHCCCCEEEEC
Q ss_conf             9999997799799983
Q gi|254780245|r   81 LVERAVKVGVKSVYFD   96 (120)
Q Consensus        81 ia~r~~~~gI~~v~FD   96 (120)
                      +++++.++|+.  ++|
T Consensus       105 ~~~~~~~~g~~--~lD  118 (163)
T pfam03446       105 LAKELKEKGIR--FLD  118 (163)
T ss_pred             HHHHHHHCCCC--CCC
T ss_conf             99987530344--347


No 110
>PRK06806 fructose-bisphosphate aldolase; Provisional
Probab=20.95  E-value=71  Score=14.21  Aligned_cols=39  Identities=18%  Similarity=0.316  Sum_probs=30.4

Q ss_pred             HHHHHHHHCCCCEEEECCCCCCCH---HHHHHHHHHHHHCCC
Q ss_conf             999999977997999838986312---259999999996587
Q gi|254780245|r   80 LLVERAVKVGVKSVYFDRGKHLYC---GRIAALADAVRKGGV  118 (120)
Q Consensus        80 ~ia~r~~~~gI~~v~FDR~g~~yH---Grvka~ad~~R~~Gl  118 (120)
                      ...++|.+.|.+.|.||-+...|.   -..+.++|-+...|+
T Consensus        88 e~i~~ai~~GfsSVM~DgS~l~~eeNi~~Tkevve~Ah~~gv  129 (281)
T PRK06806         88 EKIKEALEIGFTSVMFDGSHYPLEENIQKTKEIVELAKQYGA  129 (281)
T ss_pred             HHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             999999982998799609989999999999999999988598


No 111
>cd00947 TBP_aldolase_IIB Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as Na+. The type A and type B Class II FBPA's differ in the presence and absence of distinct indels in the sequence that result in differing loop lengths in the structures.
Probab=20.93  E-value=71  Score=14.21  Aligned_cols=38  Identities=24%  Similarity=0.420  Sum_probs=27.9

Q ss_pred             HHHHHHHCCCCEEEECCCCCCCHH---HHHHHHHHHHHCCC
Q ss_conf             999999779979998389863122---59999999996587
Q gi|254780245|r   81 LVERAVKVGVKSVYFDRGKHLYCG---RIAALADAVRKGGV  118 (120)
Q Consensus        81 ia~r~~~~gI~~v~FDR~g~~yHG---rvka~ad~~R~~Gl  118 (120)
                      ..+++.+.|.+.|.||-+.+.|.-   ..+.+++-+...|+
T Consensus        84 ~i~~ai~~Gf~SVM~DgS~lp~eeNi~~T~~vv~~ah~~gv  124 (276)
T cd00947          84 LIKRAIRAGFSSVMIDGSHLPFEENVAKTKEVVELAHAYGV  124 (276)
T ss_pred             HHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             99999983998798528989999999999999999998198


No 112
>cd07039 TPP_PYR_POX Pyrimidine (PYR) binding domain of POX. Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. Lactobacillus plantarum POX is a homotetramer (dimer-of-homodimers), having two active sites per homodimer lying between PYR and PP domains of differ
Probab=20.83  E-value=71  Score=14.20  Aligned_cols=39  Identities=41%  Similarity=0.630  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCC-CCC
Q ss_conf             99999999997799799983898631225999999999658-789
Q gi|254780245|r   77 VGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGG-VSF  120 (120)
Q Consensus        77 vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~G-l~F  120 (120)
                      |++.|++.+.+.||+.|.-=-|+     .+-.|.|++.+.+ ++|
T Consensus         2 va~~l~~~L~~~Gv~~vFg~pG~-----~~~~l~~al~~~~~i~~   41 (164)
T cd07039           2 VADVIVETLENWGVKRVYGIPGD-----SINGLMDALRREGKIEF   41 (164)
T ss_pred             HHHHHHHHHHHCCCCEEEEECCC-----CHHHHHHHHHHCCCCEE
T ss_conf             89999999998799999991783-----57999999986599739


No 113
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=20.43  E-value=73  Score=14.15  Aligned_cols=52  Identities=17%  Similarity=0.197  Sum_probs=36.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCC--CCEEEEC---CCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             8667899999999999999779--9799983---89863122599999999965878
Q gi|254780245|r   68 GANIVAATAVGNLLVERAVKVG--VKSVYFD---RGKHLYCGRIAALADAVRKGGVS  119 (120)
Q Consensus        68 ~~ni~aA~~vG~~ia~r~~~~g--I~~v~FD---R~g~~yHGrvka~ad~~R~~Gl~  119 (120)
                      ..|.+++..+|+.+++.+...+  -.+|.+-   .+..--.-|+..|-+++.+.|++
T Consensus       101 ~dn~~~g~~~g~~l~~~~~~~~~~~~~v~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~  157 (277)
T cd06319         101 SDNYEGAYDLGKFLAAAMKAQGWADGKVGMVAIPQKRKNGQKRTKGFKEAMKEAGCD  157 (277)
T ss_pred             EHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             235899999999999986764778866999965877623999999999999875997


No 114
>KOG3396 consensus
Probab=20.40  E-value=73  Score=14.14  Aligned_cols=62  Identities=19%  Similarity=0.341  Sum_probs=37.6

Q ss_pred             EEEEEEECCCCEEEEEEEEC--CCHHCCCCCCCCCHH--------HHHHHHHHHH----HHHHHCCCCEEEECCCC
Q ss_conf             99999962797599998502--100000134686678--------9999999999----99997799799983898
Q gi|254780245|r   38 IYGQIIDDSIGHTLVSASSL--NEPLRSSLKTGANIV--------AATAVGNLLV----ERAVKVGVKSVYFDRGK   99 (120)
Q Consensus        38 iyAQiIdd~~~~tl~saST~--~k~~~~~~~~~~ni~--------aA~~vG~~ia----~r~~~~gI~~v~FDR~g   99 (120)
                      .|.-+|.|.....++.+.|+  |+.|--.....+-+|        .-+.+|+++-    +.+++.|..++.+|+..
T Consensus        53 Y~i~Vied~~s~~vigtatL~IE~KfIh~~g~rGhiEDVVV~~~~rgk~LGkllv~~Lv~l~k~lgcYKi~LdC~~  128 (150)
T KOG3396          53 YYIVVIEDKESEKVIGTATLFIERKFIHGCGSRGHIEDVVVDSEYRGKQLGKLLVETLVDLAKSLGCYKIILDCDP  128 (150)
T ss_pred             EEEEEEEECCCCEEEEEEEEEEEHHHHHCCCCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCH
T ss_conf             7999999678672788877777666665044457514798675451567869999999999874282799996362


No 115
>KOG1185 consensus
Probab=20.25  E-value=73  Score=14.12  Aligned_cols=38  Identities=26%  Similarity=0.339  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             9999999997799799983898631225999999999658789
Q gi|254780245|r   78 GNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        78 G~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      |+++|+-++..||+.|.==-|+     -|-.+++++-..||+|
T Consensus        17 ~~~vA~~Lk~~gVe~iFgiVGi-----pV~el~~aaqalGIk~   54 (571)
T KOG1185          17 GELVAAVLKAQGVEYIFGIVGI-----PVIELAVAAQALGIKF   54 (571)
T ss_pred             HHHHHHHHHHCCCEEEEEEECC-----CHHHHHHHHHHCCCEE
T ss_conf             8999999997696299998162-----1079999999809868


No 116
>pfam00532 Peripla_BP_1 family. This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (pfam00356).
Probab=20.17  E-value=74  Score=14.11  Aligned_cols=45  Identities=13%  Similarity=0.106  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHCCCCE-EEEC---CCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             99999999999779979-9983---898631225999999999658789
Q gi|254780245|r   76 AVGNLLVERAVKVGVKS-VYFD---RGKHLYCGRIAALADAVRKGGVSF  120 (120)
Q Consensus        76 ~vG~~ia~r~~~~gI~~-v~FD---R~g~~yHGrvka~ad~~R~~Gl~F  120 (120)
                      .-|...++.+.+.|-.+ +.|-   .+..-..-|...|.+++++.|+.+
T Consensus       106 ~~~~~a~~~Li~~Ghrr~i~~~~~~~~~~~~~~R~~Gf~~al~~~g~~~  154 (281)
T pfam00532       106 QAGYESTQYLIAEGHKRPIAVMAGPASALTARERVQGFMAALAAAGREV  154 (281)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             9999999999983897704773078765078999999999999759999


Done!