Query         gi|254780187|ref|YP_003064600.1| 30S ribosomal protein S4 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 206
No_of_seqs    159 out of 1658
Neff          5.4 
Searched_HMMs 39220
Date          Mon May 23 13:10:36 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780187.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01017 rpsD_bact ribosomal  100.0       0       0  583.5  15.1  204    3-206     1-217 (217)
  2 PRK05327 rpsD 30S ribosomal pr 100.0       0       0  538.9  18.7  201    1-206     1-201 (201)
  3 PRK12565 30S ribosomal protein 100.0       0       0  531.5  19.2  196    1-206     1-197 (197)
  4 CHL00113 rps4 ribosomal protei 100.0       0       0  531.6  18.8  198    1-206     1-199 (201)
  5 COG0522 RpsD Ribosomal protein 100.0       0       0  427.3  14.5  202    1-206     1-205 (205)
  6 pfam00163 Ribosomal_S4 Ribosom  99.9 2.9E-28 7.3E-33  204.0   6.5   91    2-93      1-94  (94)
  7 KOG3301 consensus               99.8 3.9E-21 9.9E-26  157.8   3.9  130    1-136     1-139 (183)
  8 TIGR01018 rpsD_arch ribosomal   99.7 2.5E-18 6.4E-23  139.5   3.5   57   91-147   109-167 (170)
  9 PRK04051 rps4p 30S ribosomal p  99.7 1.8E-16 4.6E-21  127.5   7.5   60   90-149    99-160 (177)
 10 PTZ00155 40S ribosomal protein  99.6 1.6E-15   4E-20  121.5   5.8   59   90-148   103-163 (188)
 11 smart00363 S4 S4 RNA-binding d  99.2 1.2E-11 3.1E-16   96.2   4.9   54   94-147     1-54  (60)
 12 pfam01479 S4 S4 domain. The S4  99.2 8.7E-12 2.2E-16   97.1   3.6   48   94-141     1-48  (48)
 13 cd00165 S4 S4/Hsp/ tRNA synthe  99.1 6.1E-11 1.6E-15   91.6   4.8   56   94-149     1-56  (70)
 14 COG1189 Predicted rRNA methyla  98.5 2.4E-07   6E-12   68.4   5.4   52   94-145     3-54  (245)
 15 COG1188 Ribosome-associated he  98.4 3.3E-07 8.3E-12   67.5   4.1   58   91-149     6-63  (100)
 16 TIGR00478 tly hemolysin A; Int  98.3 5.3E-07 1.4E-11   66.1   4.2   54   95-148     1-54  (240)
 17 TIGR03069 PS_II_S4 photosystem  98.3 9.2E-07 2.3E-11   64.6   4.9   55   93-148   183-237 (257)
 18 PRK10348 ribosome-associated h  98.2 1.4E-06 3.7E-11   63.3   3.7   53   93-146     8-60  (133)
 19 PRK10839 16S rRNA pseudouridyl  98.2 3.3E-06 8.4E-11   61.0   5.3   53   94-147     1-53  (231)
 20 COG2302 Uncharacterized conser  98.1 4.4E-06 1.1E-10   60.1   4.9   54   94-148   181-234 (257)
 21 PRK11180 rluD 23S rRNA pseudou  97.8   5E-05 1.3E-09   53.3   5.2   53   94-146    18-70  (325)
 22 PRK11025 23S rRNA pseudouridyl  97.6 0.00012 3.2E-09   50.7   5.3   50   94-144    20-69  (317)
 23 KOG4655 consensus               97.6 1.9E-05 4.9E-10   56.0   0.6   71   88-158   101-173 (181)
 24 COG0564 RluA Pseudouridylate s  97.5 0.00042 1.1E-08   47.3   7.1   53   91-145    10-62  (289)
 25 PRK10475 23S rRNA pseudouridin  97.5  0.0002   5E-09   49.4   5.1   51   94-146     7-57  (290)
 26 COG1187 RsuA 16S rRNA uridine-  97.1  0.0013 3.4E-08   44.1   5.5   53   93-146     2-55  (248)
 27 PRK13354 tyrosyl-tRNA syntheta  96.7  0.0038 9.7E-08   41.1   5.3  100   49-148   291-396 (405)
 28 PRK10700 23S rRNA pseudouridyl  96.6   0.005 1.3E-07   40.4   5.6   53   93-146     2-55  (291)
 29 PRK11507 hypothetical protein;  96.5  0.0044 1.1E-07   40.7   4.7   52   95-146    13-64  (70)
 30 TIGR02988 YaaA_near_RecF S4 do  96.4  0.0057 1.4E-07   40.0   4.8   50   96-145    11-60  (60)
 31 PRK04313 30S ribosomal protein  96.4   0.004   1E-07   40.9   3.7   44  102-145    47-90  (237)
 32 PTZ00223 40S ribosomal protein  96.4  0.0039   1E-07   41.0   3.7   44  102-145    48-91  (273)
 33 PTZ00118 40S ribosomal protein  96.2  0.0056 1.4E-07   40.0   3.8   44  102-145    51-94  (262)
 34 COG2501 S4-like RNA binding pr  96.2   0.013 3.3E-07   37.7   5.4   51   96-146    14-64  (73)
 35 TIGR00005 rluA_subfam pseudour  95.8    0.02   5E-07   36.5   5.1   87   93-184     5-95  (337)
 36 PRK05912 tyrosyl-tRNA syntheta  95.7   0.013 3.4E-07   37.6   3.9   89   48-141   286-382 (402)
 37 COG1471 RPS4A Ribosomal protei  95.4   0.016 4.1E-07   37.0   3.4   44  102-145    50-93  (241)
 38 COG0162 TyrS Tyrosyl-tRNA synt  93.9    0.37 9.6E-06   28.2   7.4   86   49-135   288-377 (401)
 39 TIGR01687 moaD_arch MoaD famil  80.6       1 2.6E-05   25.3   1.9   60   81-145    24-88  (93)
 40 cd00754 MoaD MoaD family. Memb  79.0       4  0.0001   21.5   4.5   52   81-145    24-75  (80)
 41 KOG0378 consensus               67.3     3.3 8.3E-05   22.1   1.7   43  102-144    51-93  (263)
 42 TIGR01647 ATPase-IIIA_H plasma  67.0     3.9 9.8E-05   21.6   2.0   65  113-178    95-163 (835)
 43 pfam00498 FHA FHA domain. The   66.1     6.4 0.00016   20.2   3.0   26  118-143    41-66  (67)
 44 pfam02597 ThiS ThiS family. Th  64.6     5.8 0.00015   20.4   2.6   28  118-145    36-65  (70)
 45 KOG2623 consensus               63.8     7.6 0.00019   19.7   3.0   39   98-136   403-441 (467)
 46 pfam00122 E1-E2_ATPase E1-E2 A  61.6     4.7 0.00012   21.0   1.6   52  119-178    36-87  (222)
 47 cd01668 TGS_RelA_SpoT TGS_RelA  61.2       7 0.00018   19.9   2.5   23  121-144    37-59  (60)
 48 KOG1919 consensus               58.5      15 0.00039   17.7   4.9   46   96-143    47-92  (371)
 49 pfam02824 TGS TGS domain. The   55.9      10 0.00027   18.8   2.6   23  120-143    36-58  (60)
 50 TIGR01344 malate_syn_A malate   55.4     7.5 0.00019   19.7   1.8   35  107-141   441-476 (522)
 51 cd01616 TGS The TGS domain, na  53.6      11 0.00028   18.7   2.4   22  121-143    37-58  (60)
 52 TIGR00398 metG methionyl-tRNA   52.5     6.5 0.00017   20.1   1.1   33  109-141   327-361 (573)
 53 TIGR01832 kduD 2-deoxy-D-gluco  50.8     6.7 0.00017   20.1   1.0   69  101-173   113-192 (249)
 54 TIGR02375 pseudoazurin pseudoa  47.9      23 0.00058   16.6   4.2   25  126-150    12-37  (123)
 55 cd01089 PA2G4-like Related to   47.2      15 0.00037   17.9   2.2   25  120-144    62-92  (228)
 56 PRK06488 sulfur carrier protei  46.8      19 0.00048   17.2   2.7   41   95-144    16-59  (65)
 57 PRK05659 sulfur carrier protei  45.0      19 0.00047   17.2   2.5   23  121-143    34-59  (66)
 58 cd00060 FHA Forkhead associate  44.8      24 0.00062   16.4   3.0   16  166-181    56-71  (102)
 59 COG0474 MgtA Cation transport   44.0      14 0.00035   18.0   1.7   81   90-179   108-195 (917)
 60 pfam07828 PA-IL PA-IL-like pro  43.4      14 0.00034   18.1   1.6   28  119-146     4-31  (121)
 61 cd00430 PLPDE_III_AR Type III   42.5      22 0.00057   16.6   2.6   30   96-125   125-156 (367)
 62 PRK11930 putative bifunctional  42.0      21 0.00055   16.8   2.4   30   96-125   586-617 (824)
 63 COG2104 ThiS Sulfur transfer p  41.2      24 0.00062   16.4   2.6   23  121-143    36-61  (68)
 64 PRK09940 transcriptional regul  39.2      31 0.00079   15.7   3.0   28   58-86    219-246 (253)
 65 cd00565 ThiS ThiS (ThiaminS) i  39.0      26 0.00067   16.2   2.5   23  121-143    33-58  (65)
 66 cd03190 GST_C_ECM4_like GST_C   38.2      28  0.0007   16.1   2.5   26   86-111     9-34  (142)
 67 cd06826 PLPDE_III_AR2 Type III  37.5      30 0.00078   15.8   2.6   27  100-126   130-160 (365)
 68 PRK07440 hypothetical protein;  37.4      33 0.00084   15.6   2.9   23  121-143    38-63  (70)
 69 cd06827 PLPDE_III_AR_proteobac  37.2      30 0.00076   15.8   2.5   29   97-125   122-152 (354)
 70 TIGR01683 thiS thiamine biosyn  36.7      34 0.00086   15.5   2.9   23  121-143    33-58  (65)
 71 TIGR00691 spoT_relA RelA/SpoT   35.2      36 0.00091   15.3   3.0   24  104-127   573-596 (741)
 72 PRK08053 sulfur carrier protei  34.2      37 0.00094   15.2   2.7   24  121-144    34-60  (66)
 73 TIGR01266 fum_ac_acetase fumar  34.0      27 0.00069   16.1   1.9   36   97-141   330-365 (436)
 74 PRK11033 zntA zinc/cadmium/mer  32.1      40   0.001   15.0   4.7   64  108-179   227-294 (739)
 75 pfam02563 Poly_export Polysacc  31.3      29 0.00075   15.9   1.7   17  128-144     7-23  (83)
 76 smart00736 CADG Dystroglycan-t  29.3      40   0.001   15.0   2.1   23  161-185    41-63  (97)
 77 PRK13340 alanine racemase; Rev  29.1      45  0.0011   14.7   2.4   27   99-125   167-197 (404)
 78 TIGR01523 ATPase-IID_K-Na pota  29.1      37 0.00095   15.2   1.9   40  106-145   106-146 (1001)
 79 KOG0202 consensus               28.3      38 0.00097   15.2   1.9   67  107-180   104-171 (972)
 80 pfam02042 RWP-RK RWP-RK domain  28.0      10 0.00027   18.8  -1.1   13   10-22     34-46  (52)
 81 PRK06944 sulfur carrier protei  27.8      47  0.0012   14.5   2.4   23  121-143    33-58  (65)
 82 pfam00842 Ala_racemase_C Alani  27.1      48  0.0012   14.5   2.5   42  104-147    40-95  (125)
 83 COG4043 Preprotein translocase  26.9      38 0.00098   15.1   1.7   41  101-144     3-43  (111)
 84 PRK10517 magnesium-transportin  26.4      28 0.00072   16.0   0.9   48  124-178   170-217 (900)
 85 COG0787 Alr Alanine racemase [  26.1      50  0.0013   14.4   2.8   12   96-107   128-139 (360)
 86 PRK09393 ftrA transcriptional   26.1      51  0.0013   14.4   2.3   57   58-118   238-306 (320)
 87 KOG3312 consensus               25.5      38 0.00098   15.1   1.5   20   97-116   156-175 (186)
 88 cd01669 TGS_Ygr210_C TGS_Ygr21  25.4      35 0.00089   15.4   1.3   22  122-144    54-75  (76)
 89 PRK00053 alr alanine racemase;  25.4      52  0.0013   14.3   2.5   12   96-107   124-135 (360)
 90 PRK07696 sulfur carrier protei  24.9      53  0.0014   14.2   2.8   23  121-143    35-60  (67)
 91 PRK03646 dadX alanine racemase  24.5      54  0.0014   14.2   2.5   30   96-125   123-154 (355)
 92 PRK00133 metG methionyl-tRNA s  24.3      42  0.0011   14.9   1.5   18  113-130   313-330 (666)
 93 KOG4383 consensus               23.4      57  0.0014   14.0   2.3   29  122-150   161-189 (1354)
 94 TIGR02299 HpaE 5-carboxymethyl  23.3      32 0.00081   15.7   0.7   32   92-140   262-293 (494)
 95 PRK06083 sulfur carrier protei  22.3      59  0.0015   13.9   2.4   23  121-143    37-62  (69)
 96 TIGR02170 thyX thymidylate syn  21.4      52  0.0013   14.3   1.5   21  107-127    87-108 (259)
 97 TIGR01517 ATPase-IIB_Ca calciu  21.3      62  0.0016   13.8   2.9   26  120-145   160-185 (885)
 98 pfam07299 FBP Fibronectin-bind  21.2      61  0.0016   13.8   1.8   24   61-84     81-104 (208)
 99 pfam12331 DUF3636 Protein of u  21.1      63  0.0016   13.7   2.4   39   82-120    98-142 (155)
100 pfam10614 Tafi-CsgF Curli prod  20.9      64  0.0016   13.7   6.1   48   82-144    67-123 (142)
101 TIGR01940 nqrE NADH:ubiquinone  20.8      64  0.0016   13.7   2.1   20   87-112    94-113 (203)
102 TIGR01828 pyru_phos_dikin pyru  20.7      64  0.0016   13.7   2.2   23  123-145   501-525 (920)
103 pfam09285 Elong-fact-P_C Elong  20.7      64  0.0016   13.7   2.4   26  120-146    24-49  (56)
104 TIGR03164 UHCUDC OHCU decarbox  20.2      54  0.0014   14.2   1.4   21   79-99    114-134 (157)
105 TIGR01838 PHA_synth_I poly(R)-  20.2      66  0.0017   13.6   1.8   38  108-145   394-437 (541)

No 1  
>TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This family consists of organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00  E-value=0  Score=583.48  Aligned_cols=204  Identities=45%  Similarity=0.788  Sum_probs=192.4

Q ss_pred             CCCCCEEEEEEECCCCCCCC--CCCCHHC---CC--CCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             64487123520058888888--8770001---36--899877654-4334135899999988485551565479999999
Q gi|254780187|r    3 KRESSKHKIDRRIGENLWGR--PKSPVNT---RS--YGPGLHGQR-RKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIF   74 (206)
Q Consensus         3 r~~gpk~K~~RrlG~~l~~~--~k~~~~~---r~--~~pGqhg~~-r~~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~   74 (206)
                      ||+||++|+|||||++|||+  .+....+   |+  |||||||++ ++.|.||||+||+||||||++||.|+||||++||
T Consensus         1 Ry~Gp~~k~~RRlG~~l~g~~~~~~~~~K~k~r~~~~~PGQHG~~~r~~K~SdYg~QL~EKQKl~~~YG~i~EkQfr~~f   80 (217)
T TIGR01017         1 RYTGPKFKLSRRLGVSLFGKSGSRKLLLKGKIRPFLYPPGQHGQRFRRKKLSDYGLQLQEKQKLKFMYGMITEKQFRKYF   80 (217)
T ss_pred             CCCCCCCEEEHEECCEECCCCCCCCHHHHCCCCCCCCCCCCCCHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHH
T ss_conf             94255401100002101368776551120120114688887641104667764567789989998625974413778899


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHH--
Q ss_conf             875303344302689999988888998621212478878876249787888894135348338847886110022699--
Q gi|254780187|r   75 KEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLAS--  152 (206)
Q Consensus        75 ~~A~~~~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~--  152 (206)
                      ++|.+.+|+||++||.+||+||||||||||||+||++|||||+||||+|||++||||||+|+|||+|+|+||+++.+.  
T Consensus        81 ~~A~~~~GntGe~LL~~LE~RLDNvVYRlGfA~Tr~~ARQLVsHGhi~vNGk~VdIPSy~v~~Gd~i~ikEk~~~~~~sn  160 (217)
T TIGR01017        81 KEAKKLKGNTGENLLELLESRLDNVVYRLGFAPTRRAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLSN  160 (217)
T ss_pred             HHHHCCCCHHHHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHHCCEEEECCEEECCCEEEECCCCEEEEEECCCCCCHHH
T ss_conf             99843787278999998611001010212712007876356408807879818522406707998899810320353567


Q ss_pred             HHHHHHHC--CCCCCCEEEECCCCCEEEEEECCCCCC-CCCCCCCCCCCEEEEEECC
Q ss_conf             99877521--689996278812431899996788421-1246753466316775049
Q gi|254780187|r  153 VLEASQLA--ERDVPEYISVNHDNMVATFVRIPSSLK-DVPYPVIMQPNLVVEFYSR  206 (206)
Q Consensus       153 i~~~~~~~--~~~~P~wLevd~~~l~g~v~~~P~r~e-~i~~p~~ine~LVVEyYSR  206 (206)
                      |.++++..  .+.+|+|||||.++|.|+|++.|+.++ +.++|+.+||+||||||||
T Consensus       161 i~~~~E~~~~~~~~P~~Le~d~~~~~G~~~~~Pe~~qir~~l~~~ine~lvvE~YSk  217 (217)
T TIGR01017       161 IKENLELAGIQRNIPSWLEVDKDKLEGKVLRVPELDQIRSELPLPINEQLVVEYYSK  217 (217)
T ss_pred             HHHHHHHCCCCCCCCCEEEEECCCCEEEEEECCCCCCCCCCCCCCCEEEEEEEEECC
T ss_conf             888765200023678636776575079998778721112003536405788665059


No 2  
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=100.00  E-value=0  Score=538.92  Aligned_cols=201  Identities=51%  Similarity=0.871  Sum_probs=193.8

Q ss_pred             CCCCCCCEEEEEEECCCCCCCCCCCCHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHC
Q ss_conf             97644871235200588888888770001368998776544334135899999988485551565479999999875303
Q gi|254780187|r    1 MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRS   80 (206)
Q Consensus         1 M~r~~gpk~K~~RrlG~~l~~~~k~~~~~r~~~pGqhg~~r~~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~~~A~~~   80 (206)
                      ||||+||++|+|||||++||+++++++++|++||||||++++ |.|+||+||+||||+||+|| ++||||++||++|.++
T Consensus         1 MsRy~GPk~Ki~RRlG~~l~g~~k~~~~rr~~~PGqhG~~r~-k~S~Yg~qL~eKQK~r~~Yg-~~EkQ~~~~~~~A~r~   78 (201)
T PRK05327          1 MARYTGPKCKLSRRLGTDLFGKSKDKLEKRPYPPGQHGQRRK-KLSDYGLQLREKQKLKRIYG-VLEKQFRNYFKEAARR   78 (201)
T ss_pred             CCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHC
T ss_conf             986447686730107999788887713368999998887877-65389999999999999829-7799999999998526


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHC
Q ss_conf             34430268999998888899862121247887887624978788889413534833884788611002269999877521
Q gi|254780187|r   81 RGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLA  160 (206)
Q Consensus        81 ~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~  160 (206)
                      +|+||++||++||+||||+|||+|||+|+++|||||+||||+|||++||||||+|+|||+|+++++++++..+.++.+..
T Consensus        79 ~G~Tg~~Ll~lLE~RLD~vv~r~g~a~t~~~ARQ~v~Hghi~vNg~~v~ips~~~k~gd~i~vkeks~~~~~v~~~~~~~  158 (201)
T PRK05327         79 KGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALELA  158 (201)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHEEEEEEEEECCEEECCCCEECCCCCEEEECCCCCCHHHHHHHHHHC
T ss_conf             99689999999999988999871410588886200644059989998357874738999999770002459999999705


Q ss_pred             CCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf             6899962788124318999967884211246753466316775049
Q gi|254780187|r  161 ERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR  206 (206)
Q Consensus       161 ~~~~P~wLevd~~~l~g~v~~~P~r~e~i~~p~~ine~LVVEyYSR  206 (206)
                      .+.+|+||++|.++++|++++.|++ +|  +|+.+||+||||||||
T Consensus       159 ~~~~P~wL~~d~~~l~g~v~~~P~r-~~--i~~~vne~LVVEyYSr  201 (201)
T PRK05327        159 ERGVPSWLEVDKDKLEGTFKRLPER-SE--IPAPINEQLIVELYSR  201 (201)
T ss_pred             CCCCCCEEEEECCCCEEEEEECCCH-HH--CCCCCCCCEEEEEECC
T ss_conf             8999985897566788999843687-88--8977772379986149


No 3  
>PRK12565 30S ribosomal protein S4; Provisional
Probab=100.00  E-value=0  Score=531.46  Aligned_cols=196  Identities=39%  Similarity=0.661  Sum_probs=186.1

Q ss_pred             CCCCCCCEEEEEEECCCCCCCCCCCCHHCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             97644871235200588888888770001368998776544-33413589999998848555156547999999987530
Q gi|254780187|r    1 MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRR-KSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADR   79 (206)
Q Consensus         1 M~r~~gpk~K~~RrlG~~l~~~~k~~~~~r~~~pGqhg~~r-~~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~~~A~~   79 (206)
                      ||||+||++|+|||+|++||++++      +++|||||+.+ ++|.|+||+||+||||+||+|| ++|+||++||++|.+
T Consensus         1 MaRy~GPk~K~~RRlG~~l~g~~k------~~~pGqhg~~r~r~K~S~Yg~qL~EKQKlr~~YG-v~EkQfr~y~~~A~r   73 (197)
T PRK12565          1 MARMRGPRFKLSRRLGVNIYGHPK------AMKRAQHGNSRERKKLSEYGIQLLEKQKLRAYYG-VLEKQFRRYVKKAMK   73 (197)
T ss_pred             CCCCCCCHHHHHHCCCCCCCCCCC------CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHH
T ss_conf             987458774531016897679998------8799877757788876779999999999999849-888999999999985


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHH
Q ss_conf             33443026899999888889986212124788788762497878888941353483388478861100226999987752
Q gi|254780187|r   80 SRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQL  159 (206)
Q Consensus        80 ~~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~  159 (206)
                      ++|+||++||++||+||||||||+|||+|+++|||||+||||+|||++||||||+|+|||+|+++++++++..+.++.+.
T Consensus        74 ~~G~Tg~~Ll~lLE~RLDnvv~R~gfa~t~~~ARQlV~Hghi~vng~kVdIPSy~vk~GDvI~vkeks~~~~~v~~~~~~  153 (197)
T PRK12565         74 SKEVTGEVLLQLLECRLDNVVYRIGFASSIRQARQMVNHGHILVNGKKVNIPSYEVKVGDEITLREKSRKNEEFAENFLD  153 (197)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCEEECCCCEEEECHHHCCHHHHHHHHHH
T ss_conf             48977999999999866677113441057999866740788897998955887670699999973322133899999972


Q ss_pred             CCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf             16899962788124318999967884211246753466316775049
Q gi|254780187|r  160 AERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR  206 (206)
Q Consensus       160 ~~~~~P~wLevd~~~l~g~v~~~P~r~e~i~~p~~ine~LVVEyYSR  206 (206)
                      .....|+||++|.++++|++++.|++ +|  +|+.+||+||||||||
T Consensus       154 ~~~~~p~wL~~d~~~~~g~v~~~P~r-~~--i~~~ine~lVVEyYSr  197 (197)
T PRK12565        154 LRLFSLPYIEKDEDKFSGRLIRLPER-EE--IPIEVNEQLVVELYSK  197 (197)
T ss_pred             CCCCCCCEEEEECCCCEEEEEECCCH-HH--CCCCCCCCEEEEECCC
T ss_conf             68899983887577788999934078-88--8998761479885479


No 4  
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=100.00  E-value=0  Score=531.60  Aligned_cols=198  Identities=35%  Similarity=0.524  Sum_probs=185.5

Q ss_pred             CCCCCCCEEEEEEECCCCCCCCCCCCHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHC
Q ss_conf             97644871235200588888888770001368998776544334135899999988485551565479999999875303
Q gi|254780187|r    1 MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRS   80 (206)
Q Consensus         1 M~r~~gpk~K~~RrlG~~l~~~~k~~~~~r~~~pGqhg~~r~~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~~~A~~~   80 (206)
                      ||||+||++|+|||||...+.+.|++  +|+++|||||++  +|.|+||+||+||||+||+|| |+||||++||++|.++
T Consensus         1 MaRy~GP~~K~~RRlG~l~g~~~k~~--kr~~~pGqhg~~--rK~S~Yg~qL~EKQKlr~~YG-v~EkQfr~y~~~A~r~   75 (201)
T CHL00113          1 MSRYRGPRLKKIRRLGALPGLTSKRP--KRGSDLGNQSRS--GKKSQYRIRLEEKQKLRFNYG-LTERQLLKYVRIARKA   75 (201)
T ss_pred             CCCCCCCHHHEECCCCCCCCCCCCCC--CCCCCCCCCCCC--CCCCHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHC
T ss_conf             98655767550215888856675443--689999878888--840689999999999999808-5499999999999865


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHC
Q ss_conf             34430268999998888899862121247887887624978788889413534833884788611002269999877521
Q gi|254780187|r   81 RGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLA  160 (206)
Q Consensus        81 ~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~  160 (206)
                      +|+||+|||++||+||||||||+|||+|+++|||||+||||+|||++||||||+|+|||+|++++++++...+.++++..
T Consensus        76 ~G~Tg~~Ll~lLE~RLDnvVyRlGfA~Tr~~ARQlV~HgHi~VNgkkVnIPSy~vk~GDvI~v~~ks~~~~~v~~~~~~~  155 (201)
T CHL00113         76 KGSTGQVLLQLLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPRDIITIKDKQKSRALIQNNLDSS  155 (201)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHEEECCEEEECCEEECCCCEEEECCCEEEECCCCCCHHHHHHHHHHC
T ss_conf             89689999999999999999870540588876105846629989989337875842799899753444458999999731


Q ss_pred             -CCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf             -6899962788124318999967884211246753466316775049
Q gi|254780187|r  161 -ERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR  206 (206)
Q Consensus       161 -~~~~P~wLevd~~~l~g~v~~~P~r~e~i~~p~~ine~LVVEyYSR  206 (206)
                       ...+|+||++|.++++|++++.|++ +|  +|+.+||+||||||||
T Consensus       156 ~~~~~p~wl~~d~~~~~g~v~~~P~r-~~--i~~~i~e~LIVE~YSr  199 (201)
T CHL00113        156 KLEELPNHLTFHKFQLKGLVNQIIDR-KW--VGLKINELLVVEYYSR  199 (201)
T ss_pred             CCCCCCCCEEEECCCCEEEEEECCCH-HH--CCCCCCCCEEEEEECC
T ss_conf             55799980186554588999606876-77--8977764579998067


No 5  
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=427.33  Aligned_cols=202  Identities=44%  Similarity=0.704  Sum_probs=188.7

Q ss_pred             CCCCCCCEEEEEEECCCCCCCCCCC-CHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             9764487123520058888888877-000136899877654433413589999998848555156547999999987530
Q gi|254780187|r    1 MSKRESSKHKIDRRIGENLWGRPKS-PVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADR   79 (206)
Q Consensus         1 M~r~~gpk~K~~RrlG~~l~~~~k~-~~~~r~~~pGqhg~~r~~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~~~A~~   79 (206)
                      |+||.||+.|++||+|.++|++... ...+++++|||||+.+.++.|+||.||+||||++++|| +.|+||+++|.+|..
T Consensus         1 M~r~~~~~~K~~rr~g~~~~~~~~~~~~~~~~~~pGqhk~~~~~k~s~yg~qL~ekqkl~~~yg-~~ekqf~~~l~~a~~   79 (205)
T COG0522           1 MARYPGPKKKLSRRLGFNPWLKERLCKERKLPYKPGQHGQERWKKLSDYGLQLREKQKLRAFYG-VLEKQFRRYLKEAGR   79 (205)
T ss_pred             CCCCCCCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHC
T ss_conf             9987673204210068776777778877612788564621677799999999999777652023-779999999999705


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHH
Q ss_conf             33443026899999888889986212124788788762497878888941353483388478861100226999987752
Q gi|254780187|r   80 SRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQL  159 (206)
Q Consensus        80 ~~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~  159 (206)
                      .+|+|+.+++.+||+||||+|||+|||+|+.+|||||+||||.|||++||||||+|++||+|+|++++++...+..+.+.
T Consensus        80 l~g~~~~~~~~~LErRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~~~~~~~~~~  159 (205)
T COG0522          80 LKGVTGLNLLALLERRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSPIKIKEALEL  159 (205)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCEEECCCCEEEEECCCCCHHHHHHHHHH
T ss_conf             57708889999999887899998404135999998840662899999952673796377788752034542555554653


Q ss_pred             C--CCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf             1--6899962788124318999967884211246753466316775049
Q gi|254780187|r  160 A--ERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR  206 (206)
Q Consensus       160 ~--~~~~P~wLevd~~~l~g~v~~~P~r~e~i~~p~~ine~LVVEyYSR  206 (206)
                      +  ...+|+|+++|.+++.|++.+.|++.+   +|..+||+||||||||
T Consensus       160 ~~~~~~~~~~~e~d~~~~~~~~~~~p~~~~---~~~~~~e~~ive~ys~  205 (205)
T COG0522         160 AAQRGIPPAWLEVDEEKLEGTFKRLPERSD---LPAPINEQLIVEFYSK  205 (205)
T ss_pred             HHHCCCCHHHHHCCHHHHCEEEEECCCCCC---CCCCCCHHEEEEEECC
T ss_conf             310147604542453330033100784001---6888781048851329


No 6  
>pfam00163 Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain. This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices.
Probab=99.95  E-value=2.9e-28  Score=204.04  Aligned_cols=91  Identities=32%  Similarity=0.448  Sum_probs=84.3

Q ss_pred             CCCCCCEEEEEEECCCCCCCCCCC-CHHCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             764487123520058888888877-00013689987765443--341358999999884855515654799999998753
Q gi|254780187|r    2 SKRESSKHKIDRRIGENLWGRPKS-PVNTRSYGPGLHGQRRK--SKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEAD   78 (206)
Q Consensus         2 ~r~~gpk~K~~RrlG~~l~~~~k~-~~~~r~~~pGqhg~~r~--~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~~~A~   78 (206)
                      |||+||++|+|||+|+++|++.+. ...+.+++|||||+.++  +|+|+||+||.||||+||+|| |+|+||++||++|.
T Consensus         1 aRy~GP~~K~~RR~g~~~~~~~~~~~~~~~~~~pg~hg~~~~~~rk~S~Yg~qL~EKQklr~~YG-l~ErQfr~y~~~A~   79 (94)
T pfam00163         1 SRYRGPTLKLPRRLGELPRLTAKTKLAGEYGLRPGQHGWRVKKGRRLSRYLLRLDEKQKLRFFYG-LLERQLRRYGVLAK   79 (94)
T ss_pred             CCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC-HHHHHHHHHHHHHH
T ss_conf             96657554431789998677677767676778999865344576526189887864307999805-30999999999997


Q ss_pred             HCCCCCCHHHHHHHH
Q ss_conf             033443026899999
Q gi|254780187|r   79 RSRGDTSHNLISFLE   93 (206)
Q Consensus        79 ~~~g~t~~~ll~~LE   93 (206)
                      +++|+||+||+++||
T Consensus        80 k~~G~TG~~Ll~lLE   94 (94)
T pfam00163        80 KLDGSLGLNLLDLLE   94 (94)
T ss_pred             CCCCCHHHHHHHHHC
T ss_conf             479877999999809


No 7  
>KOG3301 consensus
Probab=99.82  E-value=3.9e-21  Score=157.79  Aligned_cols=130  Identities=18%  Similarity=0.171  Sum_probs=104.3

Q ss_pred             CCCCCCCE--EEEEEECCCCCCCCCCCCHHCCCCCCCCCCCCCCCCHHHHHHH----HHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             97644871--2352005888888887700013689987765443341358999----99988485551565479999999
Q gi|254780187|r    1 MSKRESSK--HKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQ----LRAKQKMKKYYGDISEKKFRSIF   74 (206)
Q Consensus         1 M~r~~gpk--~K~~RrlG~~l~~~~k~~~~~r~~~pGqhg~~r~~k~S~yg~q----L~eKQKlr~~YG~~~ekq~~~~~   74 (206)
                      |.+|.+|+  |+..|..++.-.-...-..+++-..    ...+.-+-+.|+.+    +.++|++ |.|+ ..+.++.+|-
T Consensus         1 ~k~y~~PRrpfek~Rld~elkl~g~yglknk~elw----r~~~~l~K~r~aaR~ll~~k~p~rl-f~g~-allrrLvr~g   74 (183)
T KOG3301           1 SKTYKTPRRPFEKERLDAELKLVGEYGLKNKRELW----RVSRSLSKIRYAARELLDEKDPKRL-FEGN-ALLRRLVRYG   74 (183)
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHH----HHHHHHHHHHHHHHHHHCCCCHHHH-HCCH-HHHHHHHHHH
T ss_conf             98557898708888887660123212654305999----9999999999999986401267777-4000-8999999985


Q ss_pred             HHH---HHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEEC
Q ss_conf             875---30334430268999998888899862121247887887624978788889413534833
Q gi|254780187|r   75 KEA---DRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCK  136 (206)
Q Consensus        75 ~~A---~~~~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k  136 (206)
                      ..+   .+..++++..+..+||+|||++||++|+|.|+.+||++|.|+||.|++++||||||+|+
T Consensus        75 ~l~e~~~Kldyvl~l~ie~fLErRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vr  139 (183)
T KOG3301          75 VLDERKNKLDYVLALTVEDFLERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVR  139 (183)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCEEEECCCEEEE
T ss_conf             32012343137799899999999999999998665442788987427607615757624654566


No 8  
>TIGR01018 rpsD_arch ribosomal protein S4; InterPro: IPR005710   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This model finds eukaryotic ribosomal protein S9 as well as eukaryotic and archaeal ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=99.72  E-value=2.5e-18  Score=139.55  Aligned_cols=57  Identities=40%  Similarity=0.614  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCC--CEEEECCHH
Q ss_conf             999888889986212124788788762497878888941353483388--478861100
Q gi|254780187|r   91 FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEG--DVIEVKQKS  147 (206)
Q Consensus        91 ~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~g--d~I~~~~ks  147 (206)
                      .||+||+++||+.|+|.|+.||||||.||||-|||++||+|||+|+.+  |.|++...|
T Consensus       109 ~LERRLQT~Vyk~GLArTi~~ARqLi~hGHI~v~Gr~v~~Psy~V~~e~e~kI~fa~~S  167 (170)
T TIGR01018       109 VLERRLQTLVYKKGLARTIKQARQLIVHGHIAVDGRRVTSPSYIVRREEEDKIDFARSS  167 (170)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHCCEEEEECEEEECCEEEECCCEEEECCCCCCCCCCCCC
T ss_conf             55345678999863022632343023203388768477358616746554421205688


No 9  
>PRK04051 rps4p 30S ribosomal protein S4; Validated
Probab=99.67  E-value=1.8e-16  Score=127.52  Aligned_cols=60  Identities=40%  Similarity=0.520  Sum_probs=56.4

Q ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCC--CEEEECCHHHH
Q ss_conf             9999888889986212124788788762497878888941353483388--47886110022
Q gi|254780187|r   90 SFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEG--DVIEVKQKSKQ  149 (206)
Q Consensus        90 ~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~g--d~I~~~~ksk~  149 (206)
                      .+||+|||++|||+|||+|+.+|||||.||||.|||++|++|||+|+..  |.|++.+.|+-
T Consensus        99 ~~l~RRL~~vv~r~~~a~si~~Ar~lI~hgHi~V~~~~v~~Ps~~V~r~~Ed~I~~~~~S~i  160 (177)
T PRK04051         99 DILERRLQTIVYRKGLARTPKQARQLIVHGHIAVNGRRVTSPGYLVSREEEDKIDYYPTSPL  160 (177)
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEECCCCEEEEECCCCCEEECCCCCC
T ss_conf             99996888999880566889999999747828999999536865886556685463179977


No 10 
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=99.59  E-value=1.6e-15  Score=121.46  Aligned_cols=59  Identities=27%  Similarity=0.428  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCC--CEEEECCHHH
Q ss_conf             9999888889986212124788788762497878888941353483388--4788611002
Q gi|254780187|r   90 SFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEG--DVIEVKQKSK  148 (206)
Q Consensus        90 ~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~g--d~I~~~~ksk  148 (206)
                      .+||+||+++||++|||.|+.+|||||.||||.|||++||+|||+|..+  |.|++.+.|-
T Consensus       103 ~~l~RRLqt~v~~~glA~si~~Ar~lI~hgHI~V~~~~V~~Ps~lV~r~~Ed~I~~~~~Sp  163 (188)
T PTZ00155        103 DILERRLQTKVFKLGLAKSVHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIAFALTSP  163 (188)
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHEECCEEEECCEEECCCCEEEEECCCCCEEEECCCC
T ss_conf             8998767689998601158898888834462889998953774588605446445436898


No 11 
>smart00363 S4 S4 RNA-binding domain.
Probab=99.22  E-value=1.2e-11  Score=96.21  Aligned_cols=54  Identities=39%  Similarity=0.576  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHH
Q ss_conf             888889986212124788788762497878888941353483388478861100
Q gi|254780187|r   94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKS  147 (206)
Q Consensus        94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ks  147 (206)
                      +|||.++.++||+.|+.+|+++|.||+|.|||++++.|||.|++||.|++..+.
T Consensus         1 ~RLD~~l~~~~~~~Sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I~~~~~~   54 (60)
T smart00363        1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKE   54 (60)
T ss_pred             CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECCCC
T ss_conf             978899998387047999999998491798999947898898999999998850


No 12 
>pfam01479 S4 S4 domain. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA.
Probab=99.21  E-value=8.7e-12  Score=97.13  Aligned_cols=48  Identities=46%  Similarity=0.652  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEE
Q ss_conf             888889986212124788788762497878888941353483388478
Q gi|254780187|r   94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVI  141 (206)
Q Consensus        94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I  141 (206)
                      +|||.+++++||++|+.+|+++|.||+|.|||++++.|||.|++||+|
T Consensus         1 ~RLd~~l~~~~~~~Sr~~a~~~I~~G~V~VNg~~v~~~~~~v~~gD~i   48 (48)
T pfam01479         1 MRLDKVLARLGLASSRSEARQLIRHGHVRVNGKVVKDPSYRVKPGDVI   48 (48)
T ss_pred             CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCCC
T ss_conf             966799998676148999999998897798999957898688992999


No 13 
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site;  Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=99.13  E-value=6.1e-11  Score=91.65  Aligned_cols=56  Identities=50%  Similarity=0.711  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHH
Q ss_conf             88888998621212478878876249787888894135348338847886110022
Q gi|254780187|r   94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQ  149 (206)
Q Consensus        94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~  149 (206)
                      +|||.++.++|++.|+.+|+++|.||+|.|||+.++.||+.|++||.|++.+....
T Consensus         1 ~RLd~~l~~~~~~~Sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~gd~i~i~~~~~~   56 (70)
T cd00165           1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIE   56 (70)
T ss_pred             CCHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEECCCCCC
T ss_conf             94889998748715899999999819389899995888889899999998787788


No 14 
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=98.49  E-value=2.4e-07  Score=68.40  Aligned_cols=52  Identities=31%  Similarity=0.345  Sum_probs=50.8

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC
Q ss_conf             8888899862121247887887624978788889413534833884788611
Q gi|254780187|r   94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ  145 (206)
Q Consensus        94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~  145 (206)
                      +|||..+++.|++.||..|+-+|..|.|.|||.+|+.||+.|+.++.|++.+
T Consensus         3 ~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~   54 (245)
T COG1189           3 MRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKG   54 (245)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEECC
T ss_conf             2389999973533209999999876857889999427652458986378756


No 15 
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=98.38  E-value=3.3e-07  Score=67.48  Aligned_cols=58  Identities=26%  Similarity=0.391  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHH
Q ss_conf             99988888998621212478878876249787888894135348338847886110022
Q gi|254780187|r   91 FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQ  149 (206)
Q Consensus        91 ~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~  149 (206)
                      -.++|||-.|.-++|..|+.-|.-+|.-|+|.|||..+ .||..|++||+|+|+-..+.
T Consensus         6 ~~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~~~   63 (100)
T COG1188           6 ADRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGNKE   63 (100)
T ss_pred             CCCEEHHHHHHHHHHHHHHHHHHHHHHCCEEEECCEEC-CCCCCCCCCCEEEEEECCCE
T ss_conf             65165678887887742289999998779698999675-65561477989999957818


No 16 
>TIGR00478 tly hemolysin A; InterPro: IPR004538 Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture. The mechanism of action is not well defined. Hemolysin A is induced by sodium ribonucleate, and is produced by pathogenic bacterial strains. Hemolysin A from Treponema hyodysenteriae causes swine dysentry.; GO: 0003723 RNA binding, 0019836 hemolysis by symbiont of host red blood cells.
Probab=98.34  E-value=5.3e-07  Score=66.11  Aligned_cols=54  Identities=26%  Similarity=0.316  Sum_probs=51.5

Q ss_pred             HHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHH
Q ss_conf             888899862121247887887624978788889413534833884788611002
Q gi|254780187|r   95 RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK  148 (206)
Q Consensus        95 RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk  148 (206)
                      |||++|++-||+.||..|..+|.-|.|.||+++|+.||..|+..+.|++.+...
T Consensus         1 RLD~lLv~rgl~~sR~~Ak~lI~kG~V~VN~~~v~KP~~~v~~~~~i~l~~~~~   54 (240)
T TIGR00478         1 RLDILLVKRGLVESREKAKRLILKGEVLVNKKKVDKPSALVDKDAKIELVQNPL   54 (240)
T ss_pred             CCHHHHHHHCHHHHHHHHHHHHHCCCEEECCEEECCCCCEECCCCCEEEECCCC
T ss_conf             903677650114578999999873945555765208860441676034414777


No 17 
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=98.31  E-value=9.2e-07  Score=64.57  Aligned_cols=55  Identities=22%  Similarity=0.244  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHH
Q ss_conf             98888899862121247887887624978788889413534833884788611002
Q gi|254780187|r   93 ESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK  148 (206)
Q Consensus        93 E~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk  148 (206)
                      -.|||+|+= ++|--||..|.++|..|.|.||++.++.|||.|++||+||++-.-+
T Consensus       183 SlRLDavvs-~~~~~SRska~~lI~~g~V~vN~~~v~~~s~~v~~gDiiSvRG~GR  237 (257)
T TIGR03069       183 SLRIDAIAS-AGFGLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGKGR  237 (257)
T ss_pred             CCCHHHHHH-HHHCCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEEECCCE
T ss_conf             213899999-8866579999999884968989999057875668999999906717


No 18 
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=98.19  E-value=1.4e-06  Score=63.30  Aligned_cols=53  Identities=26%  Similarity=0.338  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCH
Q ss_conf             988888998621212478878876249787888894135348338847886110
Q gi|254780187|r   93 ESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK  146 (206)
Q Consensus        93 E~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~k  146 (206)
                      .+|||--|+-+.|+.|+..|-+.|.-|||.|||.. ..||..|++||+|+|+..
T Consensus         8 k~RiDkwLW~aRffKTRslA~~a~~~G~V~vnG~~-~Kps~~V~~GD~l~i~~~   60 (133)
T PRK10348          8 EVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQG   60 (133)
T ss_pred             CEEEHHHHHHHEEHHHHHHHHHHHHCCCEEECCEE-CCCCCCCCCCCEEEEEEC
T ss_conf             05402003152010009999999987988989988-688887689999999869


No 19 
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=98.18  E-value=3.3e-06  Score=60.98  Aligned_cols=53  Identities=17%  Similarity=0.180  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHH
Q ss_conf             888889986212124788788762497878888941353483388478861100
Q gi|254780187|r   94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKS  147 (206)
Q Consensus        94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ks  147 (206)
                      +||+-++-.+|+| ||.+|..||..|.|.|||+.|+.|++.|.++|.|.+..+.
T Consensus         1 mRL~K~La~~g~~-SRR~ae~lI~~GrV~VNg~~v~~~~~~V~~~~~v~vdg~~   53 (231)
T PRK10839          1 MRLDKFIAQQLGV-SRAIAGREIRGNRVTVDGEIVKNAAFKLLPEHDVAYDGNP   53 (231)
T ss_pred             CCHHHHHHHCCCC-CHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEECCCE
T ss_conf             9378999887895-6999999998797999999914588084999869991958


No 20 
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=98.11  E-value=4.4e-06  Score=60.15  Aligned_cols=54  Identities=30%  Similarity=0.452  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHH
Q ss_conf             8888899862121247887887624978788889413534833884788611002
Q gi|254780187|r   94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK  148 (206)
Q Consensus        94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk  148 (206)
                      .|||.++=- +|--||..|.|+|..|.|.||.+.|+.+||.|..||.||++-.-+
T Consensus       181 lRLD~vis~-~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG~GR  234 (257)
T COG2302         181 LRLDVVISE-GFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRGFGR  234 (257)
T ss_pred             HHHHHHHHH-HHHHHHHHHHHHHHCCCEEEEEEEECCCCCEECCCCEEEEECCCC
T ss_conf             407999998-876559999998773732771299126663322498999840451


No 21 
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=97.76  E-value=5e-05  Score=53.32  Aligned_cols=53  Identities=19%  Similarity=0.271  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCH
Q ss_conf             88888998621212478878876249787888894135348338847886110
Q gi|254780187|r   94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK  146 (206)
Q Consensus        94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~k  146 (206)
                      .|||..+-+.-=..|+...+++|..|.|.|||++++.|++.|+.||+|++...
T Consensus        18 ~RLD~fL~~~~~~~srs~i~k~ir~g~I~VNgk~v~k~~~~v~~GD~I~i~~~   70 (325)
T PRK11180         18 QRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAE   70 (325)
T ss_pred             CHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCCCCCCCCEEEECCC
T ss_conf             73999999757888999999999869889999994782127889999998168


No 22 
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=97.60  E-value=0.00012  Score=50.73  Aligned_cols=50  Identities=16%  Similarity=0.232  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEEC
Q ss_conf             888889986212124788788762497878888941353483388478861
Q gi|254780187|r   94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVK  144 (206)
Q Consensus        94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~  144 (206)
                      +|||..+-..=-.-|+...+.+|..|.|.|||+++ .|||.|+.||+|++.
T Consensus        20 ~RLD~fL~~~l~~~srs~i~klir~g~V~VNg~~v-k~~~~l~~GD~I~i~   69 (317)
T PRK11025         20 QRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIP   69 (317)
T ss_pred             CHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEC-CCCCCCCCCCEEEEC
T ss_conf             75999999756626999999999869989999995-710465799999988


No 23 
>KOG4655 consensus
Probab=97.56  E-value=1.9e-05  Score=56.00  Aligned_cols=71  Identities=25%  Similarity=0.309  Sum_probs=62.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEEC--CCCEEEECCHHHHHHHHHHHHH
Q ss_conf             8999998888899862121247887887624978788889413534833--8847886110022699998775
Q gi|254780187|r   88 LISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCK--EGDVIEVKQKSKQLASVLEASQ  158 (206)
Q Consensus        88 ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k--~gd~I~~~~ksk~~~~i~~~~~  158 (206)
                      --+++++||-.|..++++|.|...|--+|.||||.|.-+.|+-|+|+|.  ..|.|+.-+.||....+.+-++
T Consensus       101 vssfCrRRLP~Vm~~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~mEDfvtWvd~SKIKr~v~~yn~  173 (181)
T KOG4655         101 VSSFCRRRLPVVMGRLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLVTRSMEDFVTWVDSSKIKRKVLEYND  173 (181)
T ss_pred             HHHHHHHCCCEEEEECHHHHHHHHHHHHHHCCCEEECCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             6777630465133402001669999999981853517800047257742226656424226889999998648


No 24 
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=97.52  E-value=0.00042  Score=47.30  Aligned_cols=53  Identities=26%  Similarity=0.368  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC
Q ss_conf             9998888899862121247887887624978788889413534833884788611
Q gi|254780187|r   91 FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ  145 (206)
Q Consensus        91 ~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~  145 (206)
                      .-.+|||..+-.+.- .|+.....++..|.|.|||++++ +++.+++||+|++..
T Consensus        10 ~~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~   62 (289)
T COG0564          10 EAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPL   62 (289)
T ss_pred             HCCCCHHHHHHHHCC-CCHHHHHHHHHCCCEEECCEECC-CCEEECCCCEEEEEC
T ss_conf             135479999987257-47999999988898899999835-871608999999535


No 25 
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=97.49  E-value=0.0002  Score=49.43  Aligned_cols=51  Identities=22%  Similarity=0.442  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCH
Q ss_conf             88888998621212478878876249787888894135348338847886110
Q gi|254780187|r   94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK  146 (206)
Q Consensus        94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~k  146 (206)
                      .||+-+|=++|+| |+.+|-+||..|.|.|||+.++ ++..|.++|.|.+..+
T Consensus         7 ~RL~K~LA~~G~~-SRReAe~lI~~GrV~VNGk~v~-~g~~V~~~D~V~vdg~   57 (290)
T PRK10475          7 TRLNKYISESGIC-SRREADRYIEQGNVFINGKRAT-IGDQVKPGDVVKVNGQ   57 (290)
T ss_pred             CHHHHHHHHCCCC-HHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEECCE
T ss_conf             1499999877783-5999999998597898999957-9888699998999998


No 26 
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=97.08  E-value=0.0013  Score=44.09  Aligned_cols=53  Identities=26%  Similarity=0.385  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCC-EEEECCH
Q ss_conf             98888899862121247887887624978788889413534833884-7886110
Q gi|254780187|r   93 ESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGD-VIEVKQK  146 (206)
Q Consensus        93 E~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd-~I~~~~k  146 (206)
                      .+|||-++-++|+| |+.+|.+||..|.|.|||+.++.+...+.+++ +|.+..+
T Consensus         2 ~~RL~K~La~~G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~   55 (248)
T COG1187           2 SMRLNKFLAEAGVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGK   55 (248)
T ss_pred             CCCHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEEECCCCEEECCCCCEEEECCE
T ss_conf             52068999874777-8899999997398788999922477672798768998998


No 27 
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=96.70  E-value=0.0038  Score=41.11  Aligned_cols=100  Identities=16%  Similarity=0.234  Sum_probs=61.9

Q ss_pred             HHHHHHHHHHHHHHCCCC----HHHHHHHHHHHHHCCCCCCHHHHHHH--HHHHHHHHHHHCCCCCHHHHHHHHHCCCEE
Q ss_conf             999999884855515654----79999999875303344302689999--988888998621212478878876249787
Q gi|254780187|r   49 GLQLRAKQKMKKYYGDIS----EKKFRSIFKEADRSRGDTSHNLISFL--ESRLDTIVYRAKFVPTIFAARQFVNHRHVL  122 (206)
Q Consensus        49 g~qL~eKQKlr~~YG~~~----ekq~~~~~~~A~~~~g~t~~~ll~~L--E~RLD~~v~r~g~a~t~~~Arq~v~hg~i~  122 (206)
                      +....+..-.+.+||.-.    ++.|..+|....-......-.+....  ..-|-.++..+|+++|..+||.+|..|-|.
T Consensus       291 aKk~LA~Eit~lvHG~e~a~~A~~~~~~lF~~~~l~e~ip~~~~~~~~~~~~~l~dlLv~~gl~~SksEARRlI~qGgV~  370 (405)
T PRK13354        291 AKMILAEEITRFYHGEEALLAAEEIFKALFQAGEIPQEIPEIPTIQSSKETKNIVDLLVDLGLAPSKREARRLINNGAVK  370 (405)
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEE
T ss_conf             99999999999836999999999999999678998000875410001257888999999839867889999999859989


Q ss_pred             ECCEEEECCCEEECCCCEEEECCHHH
Q ss_conf             88889413534833884788611002
Q gi|254780187|r  123 VNGRSVNIGSYRCKEGDVIEVKQKSK  148 (206)
Q Consensus       123 vng~~v~~ps~~~k~gd~I~~~~ksk  148 (206)
                      |||.+|+-|.+.+.++|.+-++-..|
T Consensus       371 INgekV~D~~~~l~~~~~llLr~GKK  396 (405)
T PRK13354        371 INGEKVTDVGTDVTVENSLIIQVGKK  396 (405)
T ss_pred             ECCEEECCCCCCCCCCCCEEEEECCC
T ss_conf             89999328876446899489982681


No 28 
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=96.64  E-value=0.005  Score=40.36  Aligned_cols=53  Identities=17%  Similarity=0.283  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCE-EECCCCEEEECCH
Q ss_conf             98888899862121247887887624978788889413534-8338847886110
Q gi|254780187|r   93 ESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY-RCKEGDVIEVKQK  146 (206)
Q Consensus        93 E~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~-~~k~gd~I~~~~k  146 (206)
                      +.|||-++-++|+| |+.+|.++|.-|.|.|||++++.... .+.++|.|.+..+
T Consensus         2 ~eRL~K~LA~~G~~-SRReae~lI~~GrV~VNG~v~~lg~~v~~~~~~~V~vDG~   55 (291)
T PRK10700          2 SEKLQKVLARAGHG-SRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGH   55 (291)
T ss_pred             HHHHHHHHHHCCCC-HHHHHHHHHHCCEEEECCEECCCCCEECCCCCCEEEECCE
T ss_conf             17999999987894-3999999998694998999955688265899988999999


No 29 
>PRK11507 hypothetical protein; Provisional
Probab=96.52  E-value=0.0044  Score=40.69  Aligned_cols=52  Identities=12%  Similarity=0.115  Sum_probs=48.1

Q ss_pred             HHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCH
Q ss_conf             8888998621212478878876249787888894135348338847886110
Q gi|254780187|r   95 RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK  146 (206)
Q Consensus        95 RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~k  146 (206)
                      .|+.++--.|++.|=-+|..+|.-|.|.|||..-+.-...+..||+|++...
T Consensus        13 eL~~lLK~~glv~sGg~AK~~Ia~G~V~VnGevEtRKr~Ki~~GdvV~f~g~   64 (70)
T PRK11507         13 ELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGH   64 (70)
T ss_pred             EHHHHHHHCCCCCCCHHHHHHEECCEEEECCEEEEEEEEEEECCCEEEECCE
T ss_conf             0888884717204658778654187689999996331025108999999999


No 30 
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014330   This small protein has a single S4 domain (IPR002942 from INTERPRO); it is also found in bacterial S4 ribosomal proteins, some pseudouridine synthases and tyrosyl-tRNA synthetases.   The S4 domain may bind RNA. Members of this protein are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members that are not near recF are found instead near dnaA and/or dnaN, the usual neighbours of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage..
Probab=96.44  E-value=0.0057  Score=39.98  Aligned_cols=50  Identities=28%  Similarity=0.357  Sum_probs=46.1

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC
Q ss_conf             88899862121247887887624978788889413534833884788611
Q gi|254780187|r   96 LDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ  145 (206)
Q Consensus        96 LD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~  145 (206)
                      ||-+|=-+|.+.|=-+|.+++.-+.|+|||+.-+.-+--|.+||+|+|.+
T Consensus        11 LgQlLK~~~~i~sGG~AK~fL~e~~V~vNGe~e~RRGkKL~~gD~i~i~~   60 (60)
T TIGR02988        11 LGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIPD   60 (60)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEECC
T ss_conf             76786688562282578898706955547844045887004896688269


No 31 
>PRK04313 30S ribosomal protein S4e; Validated
Probab=96.37  E-value=0.004  Score=40.93  Aligned_cols=44  Identities=25%  Similarity=0.305  Sum_probs=41.3

Q ss_pred             HHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC
Q ss_conf             62121247887887624978788889413534833884788611
Q gi|254780187|r  102 RAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ  145 (206)
Q Consensus       102 r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~  145 (206)
                      ++++|.|..+|+.++..|.|+|||+...-+.|.+-.-|+||+-+
T Consensus        47 ~L~~a~t~rEak~Il~~~~V~VDG~vr~d~~~pvGlmDVisi~~   90 (237)
T PRK04313         47 VLGYADTAREARKIISEGKVLVDGRVRKDYKFPVGLMDVISIPE   90 (237)
T ss_pred             HHHHHCCHHHHHHHHHCCEEEECCEEEECCCCCCCEEEEEEECC
T ss_conf             77250448899998648859989999603788754167998647


No 32 
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=96.37  E-value=0.0039  Score=41.00  Aligned_cols=44  Identities=25%  Similarity=0.357  Sum_probs=41.5

Q ss_pred             HHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC
Q ss_conf             62121247887887624978788889413534833884788611
Q gi|254780187|r  102 RAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ  145 (206)
Q Consensus       102 r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~  145 (206)
                      ++++|.|..+|+.++..|+|+|||++.+-+.|.+-.-||||+-.
T Consensus        48 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvG~MDVIsI~k   91 (273)
T PTZ00223         48 RLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPK   91 (273)
T ss_pred             HHCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCEEEEEEECC
T ss_conf             64521657999999877937977999655899885789999857


No 33 
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=96.21  E-value=0.0056  Score=40.03  Aligned_cols=44  Identities=23%  Similarity=0.259  Sum_probs=41.4

Q ss_pred             HHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC
Q ss_conf             62121247887887624978788889413534833884788611
Q gi|254780187|r  102 RAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ  145 (206)
Q Consensus       102 r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~  145 (206)
                      ++++|.|..+|+.++..|+|+|||+..+-+.|.+-.-|+||+-.
T Consensus        51 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvG~MDVIsI~k   94 (262)
T PTZ00118         51 RLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTK   94 (262)
T ss_pred             HHCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEECC
T ss_conf             64522658999999867908889999534899874678999856


No 34 
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=96.16  E-value=0.013  Score=37.68  Aligned_cols=51  Identities=24%  Similarity=0.363  Sum_probs=46.0

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCH
Q ss_conf             888998621212478878876249787888894135348338847886110
Q gi|254780187|r   96 LDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK  146 (206)
Q Consensus        96 LD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~k  146 (206)
                      |+-++--+|+..|=-+|.++++-|.|+|||..-|.-.-.+..||+|++.+.
T Consensus        14 L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~~   64 (73)
T COG2501          14 LGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPGQ   64 (73)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCEEEECCEEECCCCCEEECCCEEEECCE
T ss_conf             999998749505747888998779189888663016776016989998997


No 35 
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family; InterPro: IPR006225    This is the RluD subfamily of pseudouridine synthases. In Escherichia coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917. RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homologue from E. coli outside this family, TruC (Q46918 from SWISSPROT), modifies uracil-65 in transfer RNAs to pseudouridine. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis.
Probab=95.82  E-value=0.02  Score=36.46  Aligned_cols=87  Identities=20%  Similarity=0.275  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHCCCEEEC-CEEEECCCEEECCCCEEE-ECCHHHHHHHHHHHHHHCCCCCCC--EE
Q ss_conf             98888899862121247887887624978788-889413534833884788-611002269999877521689996--27
Q gi|254780187|r   93 ESRLDTIVYRAKFVPTIFAARQFVNHRHVLVN-GRSVNIGSYRCKEGDVIE-VKQKSKQLASVLEASQLAERDVPE--YI  168 (206)
Q Consensus        93 E~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vn-g~~v~~ps~~~k~gd~I~-~~~ksk~~~~i~~~~~~~~~~~P~--wL  168 (206)
                      -.|||.++-..=--.|+....++|.+|.|.|| ++....+++.++.||.|+ |.=.....     ..+......|.  -|
T Consensus         5 g~Rld~~L~~~l~~~sr~~~~~~i~~G~V~vN~~~~~~~~~~~~~~g~~~~~v~~~~~~~-----~~~~~~~~~p~~l~l   79 (337)
T TIGR00005         5 GQRLDDFLASLLPDLSRSRIQKLIENGQVKVNKGKVTANPKLKIKDGDRITPVRVPEEQE-----ELEVPVQDIPADLKL   79 (337)
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHHCCCEEECCCCCCCCCCEEECCCCEEECEECCCCCC-----CCCCCCCCCCCCCCC
T ss_conf             026999999983678888999998749689637642567430523874660100146433-----235766567342211


Q ss_pred             EECCCCCEEEEEECCC
Q ss_conf             8812431899996788
Q gi|254780187|r  169 SVNHDNMVATFVRIPS  184 (206)
Q Consensus       169 evd~~~l~g~v~~~P~  184 (206)
                      ++=++.=...++.-|.
T Consensus        80 ~IlfEDe~i~vinKP~   95 (337)
T TIGR00005        80 DILFEDEDILVINKPS   95 (337)
T ss_pred             EEEEECCCEEEEECCC
T ss_conf             3787508389997898


No 36 
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=95.73  E-value=0.013  Score=37.59  Aligned_cols=89  Identities=22%  Similarity=0.335  Sum_probs=56.5

Q ss_pred             HHHHHHHHHHHHHHHCCC----CHHHHHHHHHHHHHCCCCCCHHHH----HHHHHHHHHHHHHHCCCCCHHHHHHHHHCC
Q ss_conf             899999988485551565----479999999875303344302689----999988888998621212478878876249
Q gi|254780187|r   48 FGLQLRAKQKMKKYYGDI----SEKKFRSIFKEADRSRGDTSHNLI----SFLESRLDTIVYRAKFVPTIFAARQFVNHR  119 (206)
Q Consensus        48 yg~qL~eKQKlr~~YG~~----~ekq~~~~~~~A~~~~g~t~~~ll----~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg  119 (206)
                      .+....+..-.+.++|.=    .++.+..+|..     +...+.+-    .--+..+=.++..+|+++|..+||.+|..|
T Consensus       286 ~aqk~LA~Evt~lvHGe~~a~~A~~~~~~lF~~-----~~~~~dlp~~~~~~~~~~i~dlLv~~gl~~SksEARRlI~qG  360 (402)
T PRK05912        286 EAKKVLAEEITALFHGEEAAEAAEEAFEALFLK-----GLIPDDLPEVELDEAGIGLVDLLVEAGLVPSKSEARRLIQQG  360 (402)
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC-----CCCCCCCCEEEECCCCCCHHHHHHHCCCCCCHHHHHHHHHCC
T ss_conf             589999999999855999999999999999658-----998234885770689988999999868867889999999819


Q ss_pred             CEEECCEEEECCCEEECCCCEE
Q ss_conf             7878888941353483388478
Q gi|254780187|r  120 HVLVNGRSVNIGSYRCKEGDVI  141 (206)
Q Consensus       120 ~i~vng~~v~~ps~~~k~gd~I  141 (206)
                      -|.|||.+|+-|.+.+...|.+
T Consensus       361 gV~IN~~kI~D~~~~l~~~~l~  382 (402)
T PRK05912        361 AVKINGEKVSDPDYVFTEADLL  382 (402)
T ss_pred             CEEECCEEECCCCCCCCHHHCC
T ss_conf             9898999964955422787805


No 37 
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=95.42  E-value=0.016  Score=37.04  Aligned_cols=44  Identities=23%  Similarity=0.297  Sum_probs=40.4

Q ss_pred             HHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC
Q ss_conf             62121247887887624978788889413534833884788611
Q gi|254780187|r  102 RAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ  145 (206)
Q Consensus       102 r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~  145 (206)
                      .|++|.+..+||-+++.|+|+|||+...-.-|.|-.-|+|++-+
T Consensus        50 ~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~   93 (241)
T COG1471          50 YLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPK   93 (241)
T ss_pred             HHHHCCCHHHHHHHHHCCCEEECCEEECCCCCCCCEEEEEEECC
T ss_conf             87762234889998766957988898013557840689999768


No 38 
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=93.92  E-value=0.37  Score=28.17  Aligned_cols=86  Identities=26%  Similarity=0.341  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHHHHHCCC----CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEEC
Q ss_conf             99999988485551565----47999999987530334430268999998888899862121247887887624978788
Q gi|254780187|r   49 GLQLRAKQKMKKYYGDI----SEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVN  124 (206)
Q Consensus        49 g~qL~eKQKlr~~YG~~----~ekq~~~~~~~A~~~~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vn  124 (206)
                      ...+.++-..+..||.=    .+..+.+.|... ......-..|-..++..+=..+.-+|+++|+.+||.+|..|-+.+|
T Consensus       288 ~k~~LA~e~~~~~hG~~~a~~a~~~~~~~F~~g-~~~~l~~~dlk~~~~~~~~~~lv~~~L~psr~earr~i~~g~v~in  366 (401)
T COG0162         288 AKKLLAKEVTKLVHGEEAAEAAEEEFEKLFSEG-LPENLPPADLKQKLEDGLVDLLVDAGLAPSRSEARRLIQQGGVKIN  366 (401)
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCEEEC
T ss_conf             999887786675258899999999999998457-8354897998554167799999984461129999752315877888


Q ss_pred             CEEEECCCEEE
Q ss_conf             88941353483
Q gi|254780187|r  125 GRSVNIGSYRC  135 (206)
Q Consensus       125 g~~v~~ps~~~  135 (206)
                      |.+|.-..+.+
T Consensus       367 ~~~v~d~~~~~  377 (401)
T COG0162         367 GEKVEDENYVL  377 (401)
T ss_pred             CEECCCCCCCH
T ss_conf             87525634221


No 39 
>TIGR01687 moaD_arch MoaD family protein; InterPro: IPR010038   Members of this family appear to be archaeal and bacterial (proteobacteria and Thermus) versions of MoaD, subunit 1 of molybdopterin converting factor..
Probab=80.63  E-value=1  Score=25.33  Aligned_cols=60  Identities=30%  Similarity=0.374  Sum_probs=41.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH-HHHHHHCCCEEECCE-EEEC---CCEEECCCCEEEECC
Q ss_conf             3443026899999888889986212124788-788762497878888-9413---534833884788611
Q gi|254780187|r   81 RGDTSHNLISFLESRLDTIVYRAKFVPTIFA-ARQFVNHRHVLVNGR-SVNI---GSYRCKEGDVIEVKQ  145 (206)
Q Consensus        81 ~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~-Arq~v~hg~i~vng~-~v~~---ps~~~k~gd~I~~~~  145 (206)
                      .|.|...||+.|-+|--..     |..=+.. --..+..=.|+|||+ =|+.   -++.||-||+|+|=|
T Consensus        24 ~g~tv~dll~~l~~~Yp~~-----~~e~~~et~~~~~~~v~ilvNGran~~~l~GL~~~LkdGD~vai~P   88 (93)
T TIGR01687        24 DGKTVGDLLEELSSRYPKE-----FSELFKETGLGLVPNVIILVNGRANVDWLEGLETELKDGDVVAIFP   88 (93)
T ss_pred             CCCCHHHHHHHHHHHCCHH-----HHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCEEEEEC
T ss_conf             9980799899988615655-----6665147788764657898516414322036575232787567506


No 40 
>cd00754 MoaD MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit  is inserted into the lare subunit to form the active site.  The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=79.05  E-value=4  Score=21.47  Aligned_cols=52  Identities=25%  Similarity=0.383  Sum_probs=37.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC
Q ss_conf             34430268999998888899862121247887887624978788889413534833884788611
Q gi|254780187|r   81 RGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ  145 (206)
Q Consensus        81 ~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~  145 (206)
                      .+.|...|+..|..+-...            .-.+-.+-.+.||++.++ .+..++.||.|.+=|
T Consensus        24 ~~~Tv~~L~~~L~~~~~~~------------~~~~~~~~~iavN~~~~~-~~~~l~~gdEva~~P   75 (80)
T cd00754          24 EGATVGELLDALEARYPGL------------LEELLARVRIAVNGEYVR-LDTPLKDGDEVAIIP   75 (80)
T ss_pred             CCCCHHHHHHHHHHHCCHH------------HHHHHHCEEEEECCEECC-CCCCCCCCCEEEEEC
T ss_conf             9988999999999878176------------764310409988879836-771569999999979


No 41 
>KOG0378 consensus
Probab=67.25  E-value=3.3  Score=22.07  Aligned_cols=43  Identities=21%  Similarity=0.315  Sum_probs=38.3

Q ss_pred             HHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEEC
Q ss_conf             6212124788788762497878888941353483388478861
Q gi|254780187|r  102 RAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVK  144 (206)
Q Consensus       102 r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~  144 (206)
                      |+.+|.+-..+.|+....+|.|||+.-+-++|..---|+|++-
T Consensus        51 ~Lkya~~~~e~~~I~~qr~i~v~gkvrt~~~yp~g~mDvisie   93 (263)
T KOG0378          51 RLKYALNGKEVKKILMQREIKVDGKVRTDSTYPAGFMDVISIE   93 (263)
T ss_pred             HHHHHHCCHHHHHHHHHHHHHCCCEEECCCCCCCCEEEEEEEC
T ss_conf             5555304108889887766530545641666765203688720


No 42 
>TIGR01647 ATPase-IIIA_H plasma-membrane proton-efflux P-type ATPase; InterPro: IPR006534   These sequences represent the plasma membrane proton efflux P-type ATPase found in plants, fungi, protozoa, slime molds and archaea. The best studied representative is from yeast . ; GO: 0016887 ATPase activity, 0015992 proton transport, 0016021 integral to membrane.
Probab=66.98  E-value=3.9  Score=21.61  Aligned_cols=65  Identities=18%  Similarity=0.249  Sum_probs=43.3

Q ss_pred             HHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHH---HHHHHHHHHHHC-CCCCCCEEEECCCCCEEE
Q ss_conf             887624978788889413534833884788611002---269999877521-689996278812431899
Q gi|254780187|r  113 RQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK---QLASVLEASQLA-ERDVPEYISVNHDNMVAT  178 (206)
Q Consensus       113 rq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk---~~~~i~~~~~~~-~~~~P~wLevd~~~l~g~  178 (206)
                      .-|...-.|.=+|+=+++||-.|=|||+|.++-..=   +...+....+.. +. ---||+||...|+|.
T Consensus        95 ~~Lap~A~V~RDG~W~~~~A~~LVPGDvv~l~~GdivPAD~~l~~g~~qhPfdh-eevy~~vDqaALTGE  163 (835)
T TIGR01647        95 QSLAPKAKVLRDGKWQEIPAKELVPGDVVRLKLGDIVPADCRLFEGDPQHPFDH-EEVYIKVDQAALTGE  163 (835)
T ss_pred             HHCCCCEEEEECCEEEECCCCCCCCCCEEEEECCCEEECCCEEECCCCCCCCCC-CCCCEEEECHHHCCC
T ss_conf             627885099778867761502279763898720764012406725777888764-534337622110477


No 43 
>pfam00498 FHA FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
Probab=66.10  E-value=6.4  Score=20.18  Aligned_cols=26  Identities=35%  Similarity=0.562  Sum_probs=18.6

Q ss_pred             CCCEEECCEEEECCCEEECCCCEEEE
Q ss_conf             49787888894135348338847886
Q gi|254780187|r  118 HRHVLVNGRSVNIGSYRCKEGDVIEV  143 (206)
Q Consensus       118 hg~i~vng~~v~~ps~~~k~gd~I~~  143 (206)
                      -.-..|||+++..-.+.|++||+|.+
T Consensus        41 ~nGt~vNg~~i~~~~~~L~~GD~i~i   66 (67)
T pfam00498        41 TNGTFVNGQRLGPEPVRLKDGDVIRL   66 (67)
T ss_pred             CCCEEECCEECCCCCEECCCCCEEEE
T ss_conf             86859999996788769999999984


No 44 
>pfam02597 ThiS ThiS family. ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS. MoaD, a protein involved sulphur transfer in molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.
Probab=64.57  E-value=5.8  Score=20.44  Aligned_cols=28  Identities=29%  Similarity=0.338  Sum_probs=22.4

Q ss_pred             CCCEEECCEEEECC--CEEECCCCEEEECC
Q ss_conf             49787888894135--34833884788611
Q gi|254780187|r  118 HRHVLVNGRSVNIG--SYRCKEGDVIEVKQ  145 (206)
Q Consensus       118 hg~i~vng~~v~~p--s~~~k~gd~I~~~~  145 (206)
                      .=.|.|||..|...  ++.|+.||.|++-+
T Consensus        36 ~v~v~vN~~~v~~~~~~~~L~~gD~v~ivp   65 (70)
T pfam02597        36 RVAVAVNGEIVPRSQADTPLKDGDEVAIIP   65 (70)
T ss_pred             CEEEEECCEECCCCCCCCCCCCCCEEEEEC
T ss_conf             889999999867856776779999999978


No 45 
>KOG2623 consensus
Probab=63.80  E-value=7.6  Score=19.67  Aligned_cols=39  Identities=21%  Similarity=0.203  Sum_probs=33.2

Q ss_pred             HHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEEC
Q ss_conf             899862121247887887624978788889413534833
Q gi|254780187|r   98 TIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCK  136 (206)
Q Consensus        98 ~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k  136 (206)
                      -.+..++.++|...||.+|..|-|.||+++|..+|-.+-
T Consensus       403 ~l~~ka~~~~s~~~a~r~i~qG~vslnh~~v~~es~~~~  441 (467)
T KOG2623         403 DLLRKASRFPSGKEARRMIQQGGVSLNHEKVRDESVSIA  441 (467)
T ss_pred             HHHHHHHCCCCCHHHHHHHHCCCEEECCCCCCCCHHHCC
T ss_conf             999874037885889999871656666730367002014


No 46 
>pfam00122 E1-E2_ATPase E1-E2 ATPase.
Probab=61.58  E-value=4.7  Score=21.03  Aligned_cols=52  Identities=17%  Similarity=0.253  Sum_probs=34.8

Q ss_pred             CCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEE
Q ss_conf             978788889413534833884788611002269999877521689996278812431899
Q gi|254780187|r  119 RHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVAT  178 (206)
Q Consensus       119 g~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~~~~~P~wLevd~~~l~g~  178 (206)
                      -.|.-||+...+|+-.+.+||+|.+++..+--.-.        .-+-.-+++|...++|.
T Consensus        36 ~~V~rdG~~~~v~~~~l~~GDiv~v~~G~~IPaDg--------~vi~g~~~vdes~lTGE   87 (222)
T pfam00122        36 VTVIRDGKEEEIPADELVVGDIVLLKPGDRVPADG--------RIIEGSLEVDESALTGE   87 (222)
T ss_pred             EEEEECCEEEEEEHHHCCCCCEEEECCCCEEECCC--------EEECCCEEEEEHHHCCC
T ss_conf             89998999999888997889999989999962174--------57518389972220686


No 47 
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs.  The function of the TGS domain is unknown.
Probab=61.16  E-value=7  Score=19.92  Aligned_cols=23  Identities=39%  Similarity=0.512  Sum_probs=18.5

Q ss_pred             EEECCEEEECCCEEECCCCEEEEC
Q ss_conf             878888941353483388478861
Q gi|254780187|r  121 VLVNGRSVNIGSYRCKEGDVIEVK  144 (206)
Q Consensus       121 i~vng~~v~~ps~~~k~gd~I~~~  144 (206)
                      ..|||+.+. .++.++.||+|++-
T Consensus        37 a~vNg~~~~-l~~~L~~GD~VeIi   59 (60)
T cd01668          37 AKVNGKLVP-LSTVLKDGDIVEII   59 (60)
T ss_pred             EEECCEECC-CCCCCCCCCEEEEE
T ss_conf             999999989-87682899999987


No 48 
>KOG1919 consensus
Probab=58.54  E-value=15  Score=17.69  Aligned_cols=46  Identities=26%  Similarity=0.253  Sum_probs=34.6

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEE
Q ss_conf             888998621212478878876249787888894135348338847886
Q gi|254780187|r   96 LDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEV  143 (206)
Q Consensus        96 LD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~  143 (206)
                      +|.++.+.. +....-.+..|.+|-+.|||..+. .++.++.||+|..
T Consensus        47 ~~~~~~ef~-~~~~~~~~~~i~~g~v~~n~~~~~-v~~i~k~~d~l~~   92 (371)
T KOG1919          47 VDVFVSEFR-LRERAYYESAIKLGRVTVNGEQVR-VSLIVKNGDVLCH   92 (371)
T ss_pred             HHHHHHHHH-CCCHHHHHHHHHCCCEEECCEEEE-EEEEECCCCEEEE
T ss_conf             799989875-371576665653686588858600-4787125888877


No 49 
>pfam02824 TGS TGS domain. The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=55.88  E-value=10  Score=18.80  Aligned_cols=23  Identities=35%  Similarity=0.498  Sum_probs=17.6

Q ss_pred             CEEECCEEEECCCEEECCCCEEEE
Q ss_conf             787888894135348338847886
Q gi|254780187|r  120 HVLVNGRSVNIGSYRCKEGDVIEV  143 (206)
Q Consensus       120 ~i~vng~~v~~ps~~~k~gd~I~~  143 (206)
                      ...|||+.++ +++.++.||+|++
T Consensus        36 ~A~VnG~~v~-l~~~L~~gd~V~I   58 (60)
T pfam02824        36 GAKVNGQRVG-LDHVLEDGDVVEI   58 (60)
T ss_pred             EEEECCEECC-CCCCCCCCCEEEE
T ss_conf             7899988876-2112489999998


No 50 
>TIGR01344 malate_syn_A malate synthase A; InterPro: IPR006252   These sequences represent plant malate synthase and one of two bacterial forms, designated malate synthase A. This enzyme and isocitrate lyase are the two characteristic enzymes of the glyoxylate shunt. The shunt enables the cell to use acetyl-CoA to generate increased levels of TCA cycle intermediates for biosynthetic pathways such as gluconeogenesis.; GO: 0004474 malate synthase activity, 0006097 glyoxylate cycle.
Probab=55.37  E-value=7.5  Score=19.72  Aligned_cols=35  Identities=23%  Similarity=0.251  Sum_probs=26.3

Q ss_pred             CCHHHHHHHHHCCCEEEC-CEEEECCCEEECCCCEE
Q ss_conf             247887887624978788-88941353483388478
Q gi|254780187|r  107 PTIFAARQFVNHRHVLVN-GRSVNIGSYRCKEGDVI  141 (206)
Q Consensus       107 ~t~~~Arq~v~hg~i~vn-g~~v~~ps~~~k~gd~I  141 (206)
                      -||.|-=|+|.||-++=| |.+||--=+.=--++.+
T Consensus       441 ISR~Q~WQWi~~G~~L~dtG~~VT~eL~r~~l~~E~  476 (522)
T TIGR01344       441 ISRAQIWQWIKHGVVLEDTGRKVTPELFRDLLKEEM  476 (522)
T ss_pred             HHHHHHHHHHHCCCCEECCCCEECHHHHHHHHHHHH
T ss_conf             877579999980851114775006789999999889


No 51 
>cd01616 TGS The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=53.61  E-value=11  Score=18.70  Aligned_cols=22  Identities=41%  Similarity=0.738  Sum_probs=16.8

Q ss_pred             EEECCEEEECCCEEECCCCEEEE
Q ss_conf             87888894135348338847886
Q gi|254780187|r  121 VLVNGRSVNIGSYRCKEGDVIEV  143 (206)
Q Consensus       121 i~vng~~v~~ps~~~k~gd~I~~  143 (206)
                      ..|||+.++ .|+.|+.||+|+|
T Consensus        37 a~Vng~~~~-l~~~L~~gd~V~I   58 (60)
T cd01616          37 ALVNGQLVD-LSYTLQDGDTVSI   58 (60)
T ss_pred             EEECCEECC-CCCCCCCCCEEEE
T ss_conf             999999965-1669999999999


No 52 
>TIGR00398 metG methionyl-tRNA synthetase; InterPro: IPR002304   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .    Methionyl-tRNA synthetase (6.1.1.10 from EC) is an alpha 2 dimer that belongs to class Ia. In some species (archaea, eubacteria and eukaryota) a coding sequence, similar to the C-term end of MetRS, is present as an independent gene which is a tRNA binding domain as a dimer. In eubacteria, MetRS can also be splitted in two sub-classes corresponding to the presence of one or two CXXC domain specific to zinc binding. The crystal structures of a number of methionyl-tRNA synthases are known , , .; GO: 0000166 nucleotide binding, 0004825 methionine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006431 methionyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=52.53  E-value=6.5  Score=20.14  Aligned_cols=33  Identities=15%  Similarity=0.182  Sum_probs=22.9

Q ss_pred             HHHHHHHHHCCCEEECCEEEEC-CCEEECCCC-EE
Q ss_conf             7887887624978788889413-534833884-78
Q gi|254780187|r  109 IFAARQFVNHRHVLVNGRSVNI-GSYRCKEGD-VI  141 (206)
Q Consensus       109 ~~~Arq~v~hg~i~vng~~v~~-ps~~~k~gd-~I  141 (206)
                      ..--.|+++||++.++|.++.. -+.-|.|-| .|
T Consensus       327 ~~lP~q~~~hGyl~~eG~KMSKS~G~vv~~~~~~~  361 (573)
T TIGR00398       327 LPLPTQVFAHGYLTVEGQKMSKSLGNVVDPEDDLL  361 (573)
T ss_pred             HHHHHHHEEEEEEEECCEEECCCCCCEECHHHHHH
T ss_conf             02121324301688478443232475323217876


No 53 
>TIGR01832 kduD 2-deoxy-D-gluconate 3-dehydrogenase; InterPro: IPR011286   This entry describes 2-deoxy-D-gluconate 3-dehydrogenase (also called 2-keto-3-deoxygluconate oxidoreductase), a member of the family of short-chain-alcohol dehydrogenases (IPR002198 from INTERPRO). This protein has been characterised in Erwinia chrysanthemi as an enzyme of pectin degradation .; GO: 0008678 2-deoxy-D-gluconate 3-dehydrogenase activity, 0051287 NAD binding.
Probab=50.83  E-value=6.7  Score=20.06  Aligned_cols=69  Identities=28%  Similarity=0.413  Sum_probs=42.4

Q ss_pred             HHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEEC--CHHHHHHH-HH--HHHHHCCC------CCCCEEE
Q ss_conf             86212124788788762497878888941353483388478861--10022699-99--87752168------9996278
Q gi|254780187|r  101 YRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVK--QKSKQLAS-VL--EASQLAER------DVPEYIS  169 (206)
Q Consensus       101 ~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~--~ksk~~~~-i~--~~~~~~~~------~~P~wLe  169 (206)
                      ...=|.-|...|||++..|+   .||+|||.|.+==-|=+ .|-  .-||.-.. +.  -+.|-+..      -.|.|++
T Consensus       113 lk~vF~l~q~~a~~~l~~G~---~GkiiNIAS~LSFQGGi-rVPsYTASK~~v~GlTk~lAnEWa~~ginVNAIAPGY~~  188 (249)
T TIGR01832       113 LKSVFFLTQAAAKQFLKQGR---GGKIINIASLLSFQGGI-RVPSYTASKHGVAGLTKLLANEWAAKGINVNAIAPGYME  188 (249)
T ss_pred             HHHHHHHHHHHHHHHHHCCC---CCCEEEEHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCC
T ss_conf             89999999999999996489---95057514234422675-512466667777778999998998738815311588766


Q ss_pred             ECCC
Q ss_conf             8124
Q gi|254780187|r  170 VNHD  173 (206)
Q Consensus       170 vd~~  173 (206)
                      .|..
T Consensus       189 T~NT  192 (249)
T TIGR01832       189 TNNT  192 (249)
T ss_pred             CCCC
T ss_conf             4551


No 54 
>TIGR02375 pseudoazurin pseudoazurin; InterPro: IPR012745   Pseudoazurin, also called cupredoxin, is a small, blue periplasmic protein with a single bound copper atom. Pseudoazurin is related to plastocyanins. Several examples of pseudoazurin are encoded by a neighbouring gene for, or have been shown to transfer electrons to, copper-containing nitrite reductases (IPR012746 from INTERPRO) of the same species.; GO: 0005507 copper ion binding.
Probab=47.86  E-value=23  Score=16.60  Aligned_cols=25  Identities=20%  Similarity=0.250  Sum_probs=19.2

Q ss_pred             EEEECCCE-EECCCCEEEECCHHHHH
Q ss_conf             89413534-83388478861100226
Q gi|254780187|r  126 RSVNIGSY-RCKEGDVIEVKQKSKQL  150 (206)
Q Consensus       126 ~~v~~ps~-~~k~gd~I~~~~ksk~~  150 (206)
                      ..|.=|+| ++.|||.|++-+..|.+
T Consensus        12 ~MVFEPA~i~a~pGDtv~FvPtDKGH   37 (123)
T TIGR02375        12 AMVFEPAYIKAAPGDTVTFVPTDKGH   37 (123)
T ss_pred             EEEECCCEEEECCCCEEEEECCCCCC
T ss_conf             77617633665389768775288876


No 55 
>cd01089 PA2G4-like Related to aminopepdidase M, this family contains proliferation-associated protein 2G4. Family members have been implicated in cell cycle control.
Probab=47.16  E-value=15  Score=17.87  Aligned_cols=25  Identities=28%  Similarity=0.508  Sum_probs=19.6

Q ss_pred             CEEECCEEEE-CC-----CEEECCCCEEEEC
Q ss_conf             7878888941-35-----3483388478861
Q gi|254780187|r  120 HVLVNGRSVN-IG-----SYRCKEGDVIEVK  144 (206)
Q Consensus       120 ~i~vng~~v~-~p-----s~~~k~gd~I~~~  144 (206)
                      -+.||...+- ||     ++.++.||+|++.
T Consensus        62 CiSvNe~v~HGiP~~~~~~~~L~~GDiV~iD   92 (228)
T cd01089          62 CISVNNCVCHFSPLKSDATYTLKDGDVVKID   92 (228)
T ss_pred             EECCCCEEECCCCCCCCCCCCCCCCCEEEEE
T ss_conf             7502544456899988887354689989997


No 56 
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=46.78  E-value=19  Score=17.16  Aligned_cols=41  Identities=24%  Similarity=0.340  Sum_probs=27.7

Q ss_pred             HHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEE---CCCEEECCCCEEEEC
Q ss_conf             88889986212124788788762497878888941---353483388478861
Q gi|254780187|r   95 RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVN---IGSYRCKEGDVIEVK  144 (206)
Q Consensus        95 RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~---~ps~~~k~gd~I~~~  144 (206)
                      -|+.++-.+|+.....         -+-|||..|-   ..++.++.||.|++-
T Consensus        16 tl~~Ll~elg~~~~~v---------AvAvN~~~Vpr~~~~~~~L~eGDriEIv   59 (65)
T PRK06488         16 TLALLLAELGYEGNWL---------ATAVNGELVHSEARAQFVLHEGDRIEIL   59 (65)
T ss_pred             HHHHHHHHCCCCCCCE---------EEEECCEEECHHHHCCCCCCCCCEEEEE
T ss_conf             8999999729888808---------9998999874245054517999999996


No 57 
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=44.99  E-value=19  Score=17.17  Aligned_cols=23  Identities=48%  Similarity=0.618  Sum_probs=13.2

Q ss_pred             EEECCEEEEC---CCEEECCCCEEEE
Q ss_conf             8788889413---5348338847886
Q gi|254780187|r  121 VLVNGRSVNI---GSYRCKEGDVIEV  143 (206)
Q Consensus       121 i~vng~~v~~---ps~~~k~gd~I~~  143 (206)
                      |-||+.+|..   +++.|+.||.|++
T Consensus        34 VevN~~ivpr~~~~~~~L~egD~iEI   59 (66)
T PRK05659         34 VEVNGEIVPRSQHASTALREGDVVEI   59 (66)
T ss_pred             EEECCEECCHHHHCCCCCCCCCEEEE
T ss_conf             99899881778957265899999999


No 58 
>cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
Probab=44.84  E-value=24  Score=16.43  Aligned_cols=16  Identities=19%  Similarity=0.301  Sum_probs=9.7

Q ss_pred             CEEEECCCCCEEEEEE
Q ss_conf             6278812431899996
Q gi|254780187|r  166 EYISVNHDNMVATFVR  181 (206)
Q Consensus       166 ~wLevd~~~l~g~v~~  181 (206)
                      .|.-.|.....|+++.
T Consensus        56 ~~~~~d~~S~nGt~vn   71 (102)
T cd00060          56 GVVLIDLGSTNGTFVN   71 (102)
T ss_pred             EEEEEECCCCCCEEEC
T ss_conf             6999989987468999


No 59 
>COG0474 MgtA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=44.03  E-value=14  Score=18.05  Aligned_cols=81  Identities=17%  Similarity=0.230  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHHHHCCCC------CHHHHHHHH-HCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf             999988888998621212------478878876-2497878888941353483388478861100226999987752168
Q gi|254780187|r   90 SFLESRLDTIVYRAKFVP------TIFAARQFV-NHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAER  162 (206)
Q Consensus        90 ~~LE~RLD~~v~r~g~a~------t~~~Arq~v-~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~~~  162 (206)
                      ..+=..+-|.++.  |..      +..+-+++. .+-+|.-||+.+.+|+-.|-|||+|.+.....- +.   -..+.+ 
T Consensus       108 ~I~~~i~~n~~~g--~~qe~~a~~~l~~lk~~~~~~~~V~R~g~~~~i~a~eLVpGDiV~l~~gd~v-PA---D~rLl~-  180 (917)
T COG0474         108 VILLVVVINALLG--FVQEYRAEKALEALKKMSSPKAKVLRDGKFVEIPASELVPGDIVLLEAGDVV-PA---DLRLLE-  180 (917)
T ss_pred             HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHCCCCCEEEEECCCEEEEEHHHCCCCCEEEECCCCCC-CC---CEEEEE-
T ss_conf             2688999998888--8776624899999984187855999779489974888666887998159971-58---777885-


Q ss_pred             CCCCEEEECCCCCEEEE
Q ss_conf             99962788124318999
Q gi|254780187|r  163 DVPEYISVNHDNMVATF  179 (206)
Q Consensus       163 ~~P~wLevd~~~l~g~v  179 (206)
                       . +-|.||.+.|+|.=
T Consensus       181 -~-~~l~VdEs~LTGES  195 (917)
T COG0474         181 -S-SDLEVDESALTGES  195 (917)
T ss_pred             -C-CCCEEECHHCCCCC
T ss_conf             -4-77678931136776


No 60 
>pfam07828 PA-IL PA-IL-like protein. The members of this family are similar to the galactophilic lectin-1 expressed by P. aeruginosa ((PA-IL). Lectins recognising specific carbohydrates found on the surface of host cells are known to be involved in the initiation of infections by this organism. The protein is thought to be organized into an extensive network of beta-sheets, as is the case with many other lectins.
Probab=43.45  E-value=14  Score=18.07  Aligned_cols=28  Identities=25%  Similarity=0.265  Sum_probs=21.4

Q ss_pred             CCEEECCEEEECCCEEECCCCEEEECCH
Q ss_conf             9787888894135348338847886110
Q gi|254780187|r  119 RHVLVNGRSVNIGSYRCKEGDVIEVKQK  146 (206)
Q Consensus       119 g~i~vng~~v~~ps~~~k~gd~I~~~~k  146 (206)
                      |-|..|..-=...+..+++||+||+-.+
T Consensus         4 G~VpAnae~gq~Tglilk~GD~IsivA~   31 (121)
T pfam07828         4 GEVLANAEAGKSTGIILKPGDTISIVAA   31 (121)
T ss_pred             CCCCCHHHCCCCCEEEECCCCEEEEEEE
T ss_conf             6455400059952068627989988561


No 61 
>cd00430 PLPDE_III_AR Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase. This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in peptidoglycan biosynthesis. AR catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. SerRac converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. murF catalyzes the addition of D-Ala-D-Ala to UDPMurNAc-tripeptide, the final step in the synthesis of the cytoplasmic precursor of bacterial cell wall peptidoglycan. Members of this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with activ
Probab=42.50  E-value=22  Score=16.64  Aligned_cols=30  Identities=20%  Similarity=0.150  Sum_probs=12.5

Q ss_pred             HHHHHHHHCCCCC--HHHHHHHHHCCCEEECC
Q ss_conf             8889986212124--78878876249787888
Q gi|254780187|r   96 LDTIVYRAKFVPT--IFAARQFVNHRHVLVNG  125 (206)
Q Consensus        96 LD~~v~r~g~a~t--~~~Arq~v~hg~i~vng  125 (206)
                      +|+=.-|+||.+.  ...++.+-.+.++.+-|
T Consensus       125 iDTGM~RlG~~~~e~~~~~~~l~~~~~l~~~g  156 (367)
T cd00430         125 IDTGMGRLGFRPEEAEELLEALKALPGLELEG  156 (367)
T ss_pred             EECCCCCCCCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             80688757889799999999998689961889


No 62 
>PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional
Probab=42.05  E-value=21  Score=16.77  Aligned_cols=30  Identities=23%  Similarity=0.278  Sum_probs=13.9

Q ss_pred             HHHHHHHHCCCCC--HHHHHHHHHCCCEEECC
Q ss_conf             8889986212124--78878876249787888
Q gi|254780187|r   96 LDTIVYRAKFVPT--IFAARQFVNHRHVLVNG  125 (206)
Q Consensus        96 LD~~v~r~g~a~t--~~~Arq~v~hg~i~vng  125 (206)
                      +|+=.-|+||.+.  ...++.+-...++.+-|
T Consensus       586 iDTGM~RlGf~~~e~~~l~~~l~~~~~l~~~g  617 (824)
T PRK11930        586 IDTGMHRLGFEPEDIPELIERLKKQSAVIVRS  617 (824)
T ss_pred             ECCCCCCCCCCHHHHHHHHHHHHHCCCCCEEE
T ss_conf             75999978599899999999998289985536


No 63 
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=41.16  E-value=24  Score=16.40  Aligned_cols=23  Identities=52%  Similarity=0.537  Sum_probs=9.6

Q ss_pred             EEECCEEEEC---CCEEECCCCEEEE
Q ss_conf             8788889413---5348338847886
Q gi|254780187|r  121 VLVNGRSVNI---GSYRCKEGDVIEV  143 (206)
Q Consensus       121 i~vng~~v~~---ps~~~k~gd~I~~  143 (206)
                      +.|||..|-.   ..+.|+.||.|++
T Consensus        36 v~vNg~iVpr~~~~~~~l~~gD~iev   61 (68)
T COG2104          36 VAVNGEIVPRSQWADTILKEGDRIEV   61 (68)
T ss_pred             EEECCEECCCHHHHHCCCCCCCEEEE
T ss_conf             99889982504632013158998999


No 64 
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=39.20  E-value=31  Score=15.74  Aligned_cols=28  Identities=18%  Similarity=0.326  Sum_probs=11.8

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHHCCCCCCH
Q ss_conf             85551565479999999875303344302
Q gi|254780187|r   58 MKKYYGDISEKKFRSIFKEADRSRGDTSH   86 (206)
Q Consensus        58 lr~~YG~~~ekq~~~~~~~A~~~~g~t~~   86 (206)
                      .|.+|| ++-+||...++.-.+..-+||.
T Consensus       219 FK~~fG-iTP~qy~~~~r~q~~~~~~~~~  246 (253)
T PRK09940        219 FRKHFG-NSPKRVSKEYRCQRHTGMNTGN  246 (253)
T ss_pred             HHHHHC-CCCHHHHHHHHHHHHCCCCCCC
T ss_conf             998819-7918999999999863766564


No 65 
>cd00565 ThiS ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria.  The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=39.00  E-value=26  Score=16.20  Aligned_cols=23  Identities=43%  Similarity=0.525  Sum_probs=8.9

Q ss_pred             EEECCEEEEC---CCEEECCCCEEEE
Q ss_conf             8788889413---5348338847886
Q gi|254780187|r  121 VLVNGRSVNI---GSYRCKEGDVIEV  143 (206)
Q Consensus       121 i~vng~~v~~---ps~~~k~gd~I~~  143 (206)
                      |.+||..|..   .++.++.||.|++
T Consensus        33 V~~N~~ivpk~~~~~~~l~~gD~iEi   58 (65)
T cd00565          33 VEVNGEIVPRSEWADTELQEGDRIEI   58 (65)
T ss_pred             EEECCEECCHHHCCCCCCCCCCEEEE
T ss_conf             99999980878928100899899999


No 66 
>cd03190 GST_C_ECM4_like GST_C family, ECM4-like subfamily; composed of predominantly uncharacterized and taxonomically diverse proteins with similarity to the translation product of the Saccharomyces cerevisiae gene ECM4.  ECM4, a gene of unknown function, is involved in cell surface biosynthesis and architecture. S. cerevisiae ECM4 mutants show increased amounts of the cell wall hexose, N-acetylglucosamine. More recently, global gene expression analysis shows that ECM4 is upregulated during genotoxic conditions and together with the expression profiles of 18 other genes could potentially differentiate between genotoxic and cytotoxic insults in yeast.
Probab=38.16  E-value=28  Score=16.06  Aligned_cols=26  Identities=27%  Similarity=0.382  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             26899999888889986212124788
Q gi|254780187|r   86 HNLISFLESRLDTIVYRAKFVPTIFA  111 (206)
Q Consensus        86 ~~ll~~LE~RLD~~v~r~g~a~t~~~  111 (206)
                      +.+-..+-.-+-|-|||+|||.|-.+
T Consensus         9 d~~n~~iy~~iNnGVYk~GFA~tQ~a   34 (142)
T cd03190           9 DELNEWIYDNINNGVYKAGFATTQEA   34 (142)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHH
T ss_conf             99999998866506525366799999


No 67 
>cd06826 PLPDE_III_AR2 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2. This subfamily is composed of bacterial alanine racemases (EC 5.1.1.1) with similarity to Yersinia pestis and Vibrio cholerae alanine racemase (AR) 2. ARs catalyze the interconversion between L- and D-alanine, an essential component of the peptidoglycan layer of bacterial cell walls. These proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=37.48  E-value=30  Score=15.79  Aligned_cols=27  Identities=11%  Similarity=0.015  Sum_probs=15.0

Q ss_pred             HHHHCCCCC----HHHHHHHHHCCCEEECCE
Q ss_conf             986212124----788788762497878888
Q gi|254780187|r  100 VYRAKFVPT----IFAARQFVNHRHVLVNGR  126 (206)
Q Consensus       100 v~r~g~a~t----~~~Arq~v~hg~i~vng~  126 (206)
                      .-|+||..+    ...+.++....++.+.|-
T Consensus       130 M~RlG~~~~~~~~~~~~~~~~~~~~l~i~Gi  160 (365)
T cd06826         130 MSRNGLELSTAQGKEDAVAIATLPNLKIVGI  160 (365)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             7757867340789999999973899857999


No 68 
>PRK07440 hypothetical protein; Provisional
Probab=37.40  E-value=33  Score=15.56  Aligned_cols=23  Identities=26%  Similarity=0.406  Sum_probs=8.8

Q ss_pred             EEECCEEEEC---CCEEECCCCEEEE
Q ss_conf             8788889413---5348338847886
Q gi|254780187|r  121 VLVNGRSVNI---GSYRCKEGDVIEV  143 (206)
Q Consensus       121 i~vng~~v~~---ps~~~k~gd~I~~  143 (206)
                      |-+|+.++..   ++..++.||.|++
T Consensus        38 VE~N~~Iv~r~~~~~~~l~~gD~iEI   63 (70)
T PRK07440         38 VEYNGEILHRQFWEQTQVQPGDRLEI   63 (70)
T ss_pred             EEECCEEECHHHCCCEECCCCCEEEE
T ss_conf             99688670867707106799999999


No 69 
>cd06827 PLPDE_III_AR_proteobact Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases. This subfamily is composed mainly of proteobacterial alanine racemases (EC 5.1.1.1), fold type III PLP-dependent enzymes that catalyze the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. hese proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=37.18  E-value=30  Score=15.85  Aligned_cols=29  Identities=21%  Similarity=0.122  Sum_probs=13.8

Q ss_pred             HHHHHHHCCCCCH--HHHHHHHHCCCEEECC
Q ss_conf             8899862121247--8878876249787888
Q gi|254780187|r   97 DTIVYRAKFVPTI--FAARQFVNHRHVLVNG  125 (206)
Q Consensus        97 D~~v~r~g~a~t~--~~Arq~v~hg~i~vng  125 (206)
                      |+=.-|+||.+.-  ..+.++-.+.++.+-|
T Consensus       122 DTGM~RlG~~~~e~~~~~~~l~~~~~l~~~g  152 (354)
T cd06827         122 DSGMHRLGFSPEEYAAAYQRLKASPNVASIV  152 (354)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCEEE
T ss_conf             5788857899899999999998589985689


No 70 
>TIGR01683 thiS thiamine biosynthesis protein ThiS; InterPro: IPR010035   This entry identifies the ThiS family, which are thiamine-biosynthesis proteins related to MoaD (IPR010034 from INTERPRO). MoaD is a molybdenum cofactor biosynthesis protein. Both ThiS and MoaD proteins are involved in sulphur transfer..
Probab=36.74  E-value=34  Score=15.50  Aligned_cols=23  Identities=48%  Similarity=0.499  Sum_probs=12.4

Q ss_pred             EEECCEEEE---CCCEEECCCCEEEE
Q ss_conf             878888941---35348338847886
Q gi|254780187|r  121 VLVNGRSVN---IGSYRCKEGDVIEV  143 (206)
Q Consensus       121 i~vng~~v~---~ps~~~k~gd~I~~  143 (206)
                      |-||+.+|.   -+++.|+.||.|+|
T Consensus        33 ve~N~~ivp~~~w~~~~l~~gD~iEi   58 (65)
T TIGR01683        33 VEVNGEIVPRSEWEDTILKEGDRIEI   58 (65)
T ss_pred             EEECCEEECCCCCCCEEECCCCEEEE
T ss_conf             98698340834567510158985889


No 71 
>TIGR00691 spoT_relA RelA/SpoT family protein; InterPro: IPR004811   The functions of Escherichia coli RelA and SpoT differ somewhat. RelA (2.7.6.5 from EC) produces pppGpp (or ppGpp) from ATP and GTP (or GDP). SpoT (3.1.7.2 from EC) degrades ppGpp, but may also act as a secondary ppGpp synthetase. The two proteins are strongly similar. In many species, a single homolog to SpoT and RelA appears responsible for both ppGpp synthesis and ppGpp degradation.     (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.  ; GO: 0015969 guanosine tetraphosphate metabolic process.
Probab=35.24  E-value=36  Score=15.35  Aligned_cols=24  Identities=13%  Similarity=-0.057  Sum_probs=12.7

Q ss_pred             CCCCCHHHHHHHHHCCCEEECCEE
Q ss_conf             121247887887624978788889
Q gi|254780187|r  104 KFVPTIFAARQFVNHRHVLVNGRS  127 (206)
Q Consensus       104 g~a~t~~~Arq~v~hg~i~vng~~  127 (206)
                      -.|+.+++-+.+=.++++.++|--
T Consensus       573 ~~a~~p~~~~~~~~~~~~~i~g~~  596 (741)
T TIGR00691       573 FPAVNPRRPKVTENSSFVSIEGIE  596 (741)
T ss_pred             CCCCCCCCCHHHCCCCEEECCCCC
T ss_conf             456788874000566412316755


No 72 
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=34.22  E-value=37  Score=15.24  Aligned_cols=24  Identities=21%  Similarity=0.234  Sum_probs=18.2

Q ss_pred             EEECCEEEE---CCCEEECCCCEEEEC
Q ss_conf             878888941---353483388478861
Q gi|254780187|r  121 VLVNGRSVN---IGSYRCKEGDVIEVK  144 (206)
Q Consensus       121 i~vng~~v~---~ps~~~k~gd~I~~~  144 (206)
                      |-||+.+|-   -+++.|+.||.|++-
T Consensus        34 vAiN~~vVPRs~W~~~~L~egD~I~i~   60 (66)
T PRK08053         34 LAINQQIVPREQWAQHIVQDGDQILLF   60 (66)
T ss_pred             EEECCEEECHHHCCCCCCCCCCEEEEE
T ss_conf             998897855788665316899999999


No 73 
>TIGR01266 fum_ac_acetase fumarylacetoacetase; InterPro: IPR005959   Fumarylacetoacetase (3.7.1.2 from EC; also known as fumarylacetoacetate hydrolase or FAH) catalyses the hydrolytic cleavage of a carbon-carbon bond in fumarylacetoacetate to yield fumarate and acetoacetate as the final step in phenylalanine and tyrosine degradation . This is an essential metabolic function in humans, the lack of FAH causing type I tyrosinaemia, which is associated with liver and kidney abnormalities and neurological disorders , . The enzyme mechanism involves a catalytic metal ion, a Glu/His catalytic dyad, and a charged oxyanion hole . FAH folds into two domains: an N-terminal domain SH3-like beta-barrel, and a C-terminal with an unusual fold consisting of three layers of beta-sheet structures .; GO: 0004334 fumarylacetoacetase activity, 0009072 aromatic amino acid family metabolic process.
Probab=34.05  E-value=27  Score=16.11  Aligned_cols=36  Identities=25%  Similarity=0.526  Sum_probs=31.8

Q ss_pred             HHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEE
Q ss_conf             889986212124788788762497878888941353483388478
Q gi|254780187|r   97 DTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVI  141 (206)
Q Consensus        97 D~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I  141 (206)
                      +.+|.|++|-.=.+.-.|++.|-  +|||       ..|++||..
T Consensus       330 ~~~~~~sN~k~lywt~~Q~laHH--~vnG-------CnL~~GDLl  365 (436)
T TIGR01266       330 PQVICRSNFKHLYWTLAQMLAHH--SVNG-------CNLRPGDLL  365 (436)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCC--EECC-------CCCCCCCEE
T ss_conf             11444543266787686452011--0016-------768767501


No 74 
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=32.10  E-value=40  Score=15.02  Aligned_cols=64  Identities=14%  Similarity=0.171  Sum_probs=40.2

Q ss_pred             CHHHHHHHHH----CCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEEE
Q ss_conf             4788788762----49787888894135348338847886110022699998775216899962788124318999
Q gi|254780187|r  108 TIFAARQFVN----HRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATF  179 (206)
Q Consensus       108 t~~~Arq~v~----hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~~~~~P~wLevd~~~l~g~v  179 (206)
                      +..+.+.|..    .-.+.-||....+|.-.|++||+|.+++..+-=  +-..      -+-...++|...++|.-
T Consensus       227 a~~ai~~L~~l~P~~A~virdG~~~~Vp~~~l~~GDiV~V~~Ge~IP--aDG~------vv~G~s~vDES~LTGES  294 (739)
T PRK11033        227 ARQGVSALMALVPETATRLRDGEREEVAINSLRPGDVIEVAPGGRLP--ADGK------LLSPFASFDESALTGES  294 (739)
T ss_pred             HHHHHHHHHHCCCCEEEEEECCEEEEEEHHHCCCCCEEEECCCCEEE--CCEE------EECCEEEEECCCCCCCC
T ss_conf             99999998736999789998997999878997999999988999842--2279------97056888846869998


No 75 
>pfam02563 Poly_export Polysaccharide biosynthesis/export protein. This is a family of periplasmic proteins involved in polysaccharide biosynthesis and/or export.
Probab=31.31  E-value=29  Score=15.88  Aligned_cols=17  Identities=29%  Similarity=0.538  Sum_probs=13.9

Q ss_pred             EECCCEEECCCCEEEEC
Q ss_conf             41353483388478861
Q gi|254780187|r  128 VNIGSYRCKEGDVIEVK  144 (206)
Q Consensus       128 v~~ps~~~k~gd~I~~~  144 (206)
                      ..-+.|.+.|||+|++.
T Consensus         7 ~~~~~Y~lgpGD~l~i~   23 (83)
T pfam02563         7 AASPDYRLGPGDVLRIT   23 (83)
T ss_pred             CCCCCCEECCCCEEEEE
T ss_conf             79998888799999999


No 76 
>smart00736 CADG Dystroglycan-type cadherin-like domains. Cadherin-homologous domains present in metazoan dystroglycans and alpha/epsilon sarcoglycans, yeast Axl2p and in a very large protein from magnetotactic bacteria. Likely to bind calcium ions.
Probab=29.27  E-value=40  Score=14.99  Aligned_cols=23  Identities=22%  Similarity=0.538  Sum_probs=16.1

Q ss_pred             CCCCCCEEEECCCCCEEEEEECCCC
Q ss_conf             6899962788124318999967884
Q gi|254780187|r  161 ERDVPEYISVNHDNMVATFVRIPSS  185 (206)
Q Consensus       161 ~~~~P~wLevd~~~l~g~v~~~P~r  185 (206)
                      ...+|+||.+|...  +++...|..
T Consensus        41 ~~~LPsWl~fd~~t--~~l~G~P~~   63 (97)
T smart00736       41 GSALPSWLSFDSDT--GTLSGTPTN   63 (97)
T ss_pred             CCCCCCCEEEECCC--CEEEECCCC
T ss_conf             99899747990457--889964584


No 77 
>PRK13340 alanine racemase; Reviewed
Probab=29.15  E-value=45  Score=14.70  Aligned_cols=27  Identities=15%  Similarity=0.160  Sum_probs=15.8

Q ss_pred             HHHHHCCCCC----HHHHHHHHHCCCEEECC
Q ss_conf             9986212124----78878876249787888
Q gi|254780187|r   99 IVYRAKFVPT----IFAARQFVNHRHVLVNG  125 (206)
Q Consensus        99 ~v~r~g~a~t----~~~Arq~v~hg~i~vng  125 (206)
                      =.-|+||-++    ...+.++..+.++.+-|
T Consensus       167 GM~RlG~~~~~~~~~~~~~~i~~~~~l~v~G  197 (404)
T PRK13340        167 GMGRNGLDPSTFRGAWEAVRIATLPSLGIVG  197 (404)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCCCCCEEE
T ss_conf             8666798810289999999996089977789


No 78 
>TIGR01523 ATPase-IID_K-Na potassium/sodium efflux P-type ATPase, fungal-type; InterPro: IPR006414   Initially described as a calcium efflux ATPase , more recent work has shown that the Schizosaccharomyces pombe CTA3 gene is in fact a potassium ion efflux pump . These sequences form the clade which represents the fungal P-type ATPases which are responsible for potassium and sodium efflux. The degree to which these pumps show preference for sodium or potassium varies. This group of ATPases has been classified by phylogentic analysis as type IID . ; GO: 0015662 ATPase activity coupled to transmembrane movement of ions phosphorylative mechanism, 0006812 cation transport, 0016021 integral to membrane.
Probab=29.07  E-value=37  Score=15.21  Aligned_cols=40  Identities=25%  Similarity=0.287  Sum_probs=34.3

Q ss_pred             CCCHHHHHHHHH-CCCEEECCEEEECCCEEECCCCEEEECC
Q ss_conf             124788788762-4978788889413534833884788611
Q gi|254780187|r  106 VPTIFAARQFVN-HRHVLVNGRSVNIGSYRCKEGDVIEVKQ  145 (206)
Q Consensus       106 a~t~~~Arq~v~-hg~i~vng~~v~~ps~~~k~gd~I~~~~  145 (206)
                      .+|+..-|.|-+ .-||.-|||.-+|-|..|-|||++-++-
T Consensus       106 ~KTM~SL~~L~SP~AHV~R~~K~~~I~S~~~VPGD~~~~K~  146 (1001)
T TIGR01523       106 EKTMDSLKTLASPNAHVIRSSKSDAIDSKLLVPGDVVLLKV  146 (1001)
T ss_pred             HHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCEEEEEE
T ss_conf             45788865315886246517754432453227876799830


No 79 
>KOG0202 consensus
Probab=28.29  E-value=38  Score=15.16  Aligned_cols=67  Identities=22%  Similarity=0.306  Sum_probs=46.3

Q ss_pred             CCHHHHHHHHHC-CCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEEEE
Q ss_conf             247887887624-97878888941353483388478861100226999987752168999627881243189999
Q gi|254780187|r  107 PTIFAARQFVNH-RHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATFV  180 (206)
Q Consensus       107 ~t~~~Arq~v~h-g~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~~~~~P~wLevd~~~l~g~v~  180 (206)
                      +|+.+-+.++.+ +|++-+|+.-.+++..+-|||++.++-.-+-=+    -+.+.+  .-+ |++|...|+|.-.
T Consensus       104 kalEaLk~l~p~~~~V~R~gk~~~i~A~eLVPGDiV~l~vGDkVPA----DlRl~e--~~s-l~iDeS~LTGEs~  171 (972)
T KOG0202         104 KALEALKELVPPMAHVLRSGKLQHILARELVPGDIVELKVGDKIPA----DLRLIE--AKS-LRIDESSLTGESE  171 (972)
T ss_pred             HHHHHHHHCCCCCCEEEECCCCCCCCHHCCCCCCEEEEECCCCCCC----CEEEEE--EEE-EEEECCCCCCCCC
T ss_conf             8999998508964169844860340341068887899951880553----015876--430-0441121257764


No 80 
>pfam02042 RWP-RK RWP-RK domain. This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development.
Probab=27.97  E-value=10  Score=18.80  Aligned_cols=13  Identities=38%  Similarity=0.692  Sum_probs=6.3

Q ss_pred             EEEEECCCCCCCC
Q ss_conf             3520058888888
Q gi|254780187|r   10 KIDRRIGENLWGR   22 (206)
Q Consensus        10 K~~RrlG~~l~~~   22 (206)
                      |+||++|+.=|+.
T Consensus        34 k~CR~~gI~RWP~   46 (52)
T pfam02042        34 KICRQLGIPRWPH   46 (52)
T ss_pred             HHHHHCCCCCCCH
T ss_conf             9999879987857


No 81 
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=27.78  E-value=47  Score=14.55  Aligned_cols=23  Identities=30%  Similarity=0.408  Sum_probs=15.5

Q ss_pred             EEECCEEEEC---CCEEECCCCEEEE
Q ss_conf             8788889413---5348338847886
Q gi|254780187|r  121 VLVNGRSVNI---GSYRCKEGDVIEV  143 (206)
Q Consensus       121 i~vng~~v~~---ps~~~k~gd~I~~  143 (206)
                      +-||+..|-.   ..+.|+.||.|++
T Consensus        33 VavN~~~VPRs~~~~~~L~~GD~iei   58 (65)
T PRK06944         33 VAVNGNFVARTQHAARALAAGDRLDL   58 (65)
T ss_pred             EEECCEEECHHHHHHCCCCCCCEEEE
T ss_conf             99847980314533312789999999


No 82 
>pfam00842 Ala_racemase_C Alanine racemase, C-terminal domain.
Probab=27.14  E-value=48  Score=14.47  Aligned_cols=42  Identities=21%  Similarity=0.320  Sum_probs=25.4

Q ss_pred             CCCCCHHHHHHHHHCCCEEECCEEE-------------ECCC-EEECCCCEEEECCHH
Q ss_conf             1212478878876249787888894-------------1353-483388478861100
Q gi|254780187|r  104 KFVPTIFAARQFVNHRHVLVNGRSV-------------NIGS-YRCKEGDVIEVKQKS  147 (206)
Q Consensus       104 g~a~t~~~Arq~v~hg~i~vng~~v-------------~~ps-~~~k~gd~I~~~~ks  147 (206)
                      |+|--.+  |.+=+.+++++||++.             +++. -.+++||.+++=-..
T Consensus        40 GYaDG~~--r~~~~~~~v~i~g~~~pivGrIsMD~~~idv~~~~~~~~Gd~V~l~G~~   95 (125)
T pfam00842        40 GYADGYP--RALSNRGYVLINGKRAPIVGRVSMDQTMVDVTDIPDVKVGDEVTLFGPQ   95 (125)
T ss_pred             CCCCCCC--CCCCCCCEEEECCEEEEEECEECCCEEEEECCCCCCCCCCCEEEEECCC
T ss_conf             2335735--2067985899899993010726122589955688777789899998999


No 83 
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular    trafficking, secretion, and vesicular transport]
Probab=26.89  E-value=38  Score=15.14  Aligned_cols=41  Identities=15%  Similarity=0.110  Sum_probs=30.9

Q ss_pred             HHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEEC
Q ss_conf             86212124788788762497878888941353483388478861
Q gi|254780187|r  101 YRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVK  144 (206)
Q Consensus       101 ~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~  144 (206)
                      +++|+..   .-=.+|-.|.=.|-++.-+----.++|||.|.+.
T Consensus         3 ~~mgL~e---eylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~   43 (111)
T COG4043           3 HRMGLRE---EYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFN   43 (111)
T ss_pred             EEECHHH---HHHHHHHCCCCEEEEEECCHHHCCCCCCCEEEEC
T ss_conf             3300378---8999987044368999557766278989989983


No 84 
>PRK10517 magnesium-transporting ATPase MgtA; Provisional
Probab=26.35  E-value=28  Score=15.99  Aligned_cols=48  Identities=10%  Similarity=0.170  Sum_probs=29.8

Q ss_pred             CCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEE
Q ss_conf             8889413534833884788611002269999877521689996278812431899
Q gi|254780187|r  124 NGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVAT  178 (206)
Q Consensus       124 ng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~~~~~P~wLevd~~~l~g~  178 (206)
                      +|+.+.||+-.|-|||+|.+++..+-=+-.    ...+   -.-|.+|.+.|+|.
T Consensus       170 ~~~~~eIpa~eLVpGDIV~L~~Gd~VPAD~----rlie---~~~l~VDES~LTGE  217 (900)
T PRK10517        170 ENGWLELPIDQLVPGDIIKLAAGDMIPADL----RILQ---ARDLFVAQASLTGE  217 (900)
T ss_pred             CCEEEEEEHHHCCCCCEEEECCCCEEECCE----EEEE---ECCCEEEECCCCCC
T ss_conf             873789778988989789999999994128----9997---16877870123478


No 85 
>COG0787 Alr Alanine racemase [Cell envelope biogenesis, outer membrane]
Probab=26.13  E-value=50  Score=14.36  Aligned_cols=12  Identities=33%  Similarity=0.437  Sum_probs=6.6

Q ss_pred             HHHHHHHHCCCC
Q ss_conf             888998621212
Q gi|254780187|r   96 LDTIVYRAKFVP  107 (206)
Q Consensus        96 LD~~v~r~g~a~  107 (206)
                      +|+=.-|+||.+
T Consensus       128 iDTGM~RlG~~~  139 (360)
T COG0787         128 IDTGMNRLGLRP  139 (360)
T ss_pred             ECCCCCCCCCCH
T ss_conf             778987579884


No 86 
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=26.09  E-value=51  Score=14.35  Aligned_cols=57  Identities=19%  Similarity=0.211  Sum_probs=35.2

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHHCCCCCCHHHHH---------HH---HHHHHHHHHHHCCCCCHHHHHHHHHC
Q ss_conf             855515654799999998753033443026899---------99---98888899862121247887887624
Q gi|254780187|r   58 MKKYYGDISEKKFRSIFKEADRSRGDTSHNLIS---------FL---ESRLDTIVYRAKFVPTIFAARQFVNH  118 (206)
Q Consensus        58 lr~~YG~~~ekq~~~~~~~A~~~~g~t~~~ll~---------~L---E~RLD~~v~r~g~a~t~~~Arq~v~h  118 (206)
                      +--.-| ++++||.+.|+++..   .|-..++.         +|   +.-++.|-++.||...-...|.+-.+
T Consensus       238 lA~~~~-~S~R~l~R~Fk~~~G---~tp~~y~~~~Rl~~Ar~lL~~t~~si~~IA~~~Gf~~~s~F~r~Fk~~  306 (320)
T PRK09393        238 LAARAA-MSPRTFLRRFEAATG---MTPAEWLLRERLARARDLLESSALSIAQIAARAGFGSEESLRHHFRRR  306 (320)
T ss_pred             HHHHHC-CCHHHHHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             999978-798799989978869---699999999999999999876899999999995899999999999998


No 87 
>KOG3312 consensus
Probab=25.54  E-value=38  Score=15.13  Aligned_cols=20  Identities=25%  Similarity=0.154  Sum_probs=14.0

Q ss_pred             HHHHHHHCCCCCHHHHHHHH
Q ss_conf             88998621212478878876
Q gi|254780187|r   97 DTIVYRAKFVPTIFAARQFV  116 (206)
Q Consensus        97 D~~v~r~g~a~t~~~Arq~v  116 (206)
                      .|+---+|||||+.+|+|-.
T Consensus       156 qNlQK~LGfaPsRaaa~q~~  175 (186)
T KOG3312         156 QNLQKILGFAPSRAAAKQGG  175 (186)
T ss_pred             HHHHHHHCCCCCHHHHHCCC
T ss_conf             98999967698566761678


No 88 
>cd01669 TGS_Ygr210_C TGS_Ygr210_C: The C-terminal TGS domain of Ygr210 GTP-binding protein which is a member of Obg-like family of GTPases, and present in archaea. Several Obg-like family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=25.38  E-value=35  Score=15.39  Aligned_cols=22  Identities=36%  Similarity=0.545  Sum_probs=16.2

Q ss_pred             EECCEEEECCCEEECCCCEEEEC
Q ss_conf             78888941353483388478861
Q gi|254780187|r  122 LVNGRSVNIGSYRCKEGDVIEVK  144 (206)
Q Consensus       122 ~vng~~v~~ps~~~k~gd~I~~~  144 (206)
                      .+||++|- ..|.++-||+|+|-
T Consensus        54 a~~~r~v~-~d~~L~~gDvi~Iv   75 (76)
T cd01669          54 ARTGRRVG-EDYELKHRDVIKIV   75 (76)
T ss_pred             EECCCCCC-CCCCCCCCCEEEEE
T ss_conf             00587858-87284799999980


No 89 
>PRK00053 alr alanine racemase; Reviewed
Probab=25.36  E-value=52  Score=14.27  Aligned_cols=12  Identities=33%  Similarity=0.335  Sum_probs=5.8

Q ss_pred             HHHHHHHHCCCC
Q ss_conf             888998621212
Q gi|254780187|r   96 LDTIVYRAKFVP  107 (206)
Q Consensus        96 LD~~v~r~g~a~  107 (206)
                      +|+=.-|+||-+
T Consensus       124 iDTGM~RlG~~~  135 (360)
T PRK00053        124 VDTGMHRLGVRP  135 (360)
T ss_pred             ECCCCCCCCCCH
T ss_conf             858987478887


No 90 
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=24.89  E-value=53  Score=14.21  Aligned_cols=23  Identities=26%  Similarity=0.244  Sum_probs=10.2

Q ss_pred             EEECCEEEE---CCCEEECCCCEEEE
Q ss_conf             878888941---35348338847886
Q gi|254780187|r  121 VLVNGRSVN---IGSYRCKEGDVIEV  143 (206)
Q Consensus       121 i~vng~~v~---~ps~~~k~gd~I~~  143 (206)
                      |-+|+.+|.   .+++.++.||.|++
T Consensus        35 VE~N~eIvpr~~~~~~~L~~GD~iEI   60 (67)
T PRK07696         35 VERNKDILQKDDHTDTSVFDGDQIEI   60 (67)
T ss_pred             EEECCEECCHHHHCCEECCCCCEEEE
T ss_conf             99798575768809447799999999


No 91 
>PRK03646 dadX alanine racemase; Reviewed
Probab=24.54  E-value=54  Score=14.17  Aligned_cols=30  Identities=17%  Similarity=0.059  Sum_probs=18.6

Q ss_pred             HHHHHHHHCCCCCH--HHHHHHHHCCCEEECC
Q ss_conf             88899862121247--8878876249787888
Q gi|254780187|r   96 LDTIVYRAKFVPTI--FAARQFVNHRHVLVNG  125 (206)
Q Consensus        96 LD~~v~r~g~a~t~--~~Arq~v~hg~i~vng  125 (206)
                      +|+=.-|+||.+.-  ...+++...+++.+-|
T Consensus       123 iDTGM~RlG~~~~e~~~~~~~l~~~~~l~~~g  154 (355)
T PRK03646        123 VNSGMNRLGFQPERVQTVWQQLRAMGNVGEMT  154 (355)
T ss_pred             EECCCCCCCCCHHHHHHHHHHHHHCCCCCEEE
T ss_conf             90798778988578999999998489987589


No 92 
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=24.28  E-value=42  Score=14.89  Aligned_cols=18  Identities=17%  Similarity=0.309  Sum_probs=12.3

Q ss_pred             HHHHHCCCEEECCEEEEC
Q ss_conf             887624978788889413
Q gi|254780187|r  113 RQFVNHRHVLVNGRSVNI  130 (206)
Q Consensus       113 rq~v~hg~i~vng~~v~~  130 (206)
                      .++..||++.++|+++..
T Consensus       313 ~~v~~hg~l~~~G~KmSK  330 (666)
T PRK00133        313 TNVFAHGFLTVEGAKMSK  330 (666)
T ss_pred             CCCCCCCCEEECCEEEEC
T ss_conf             612114648778806001


No 93 
>KOG4383 consensus
Probab=23.37  E-value=57  Score=14.03  Aligned_cols=29  Identities=17%  Similarity=0.362  Sum_probs=24.0

Q ss_pred             EECCEEEECCCEEECCCCEEEECCHHHHH
Q ss_conf             78888941353483388478861100226
Q gi|254780187|r  122 LVNGRSVNIGSYRCKEGDVIEVKQKSKQL  150 (206)
Q Consensus       122 ~vng~~v~~ps~~~k~gd~I~~~~ksk~~  150 (206)
                      .-+|..++.|-..+-.||+|++++.....
T Consensus       161 fRDGhlm~lP~~LLVeGDiIa~RPGQeaf  189 (1354)
T KOG4383         161 FRDGHLMELPRILLVEGDIIAFRPGQEAF  189 (1354)
T ss_pred             HCCCEEEECCEEEEEECCEEEECCCCCCC
T ss_conf             51671440542688853478765886255


No 94 
>TIGR02299 HpaE 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase; InterPro: IPR011985    This entry represents the dehydrogenase responsible for the conversion of 5-carboxymethyl-2-hydroxymuconate semialdehyde to 5-carboxymethyl-2-hydroxymuconate (a tricarboxylic acid). This is the step in the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate following the oxidative opening of the aromatic ring ..
Probab=23.27  E-value=32  Score=15.66  Aligned_cols=32  Identities=25%  Similarity=0.336  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCE
Q ss_conf             9988888998621212478878876249787888894135348338847
Q gi|254780187|r   92 LESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDV  140 (206)
Q Consensus        92 LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~  140 (206)
                      |||=||.+||-                 -+..||+++|-.|-++=...+
T Consensus       262 LeRALDAvvF~-----------------IfS~NGeRCTasSRLL~~~sI  293 (494)
T TIGR02299       262 LERALDAVVFM-----------------IFSFNGERCTASSRLLVQESI  293 (494)
T ss_pred             HHHHHHHHHHH-----------------HHHCCCCCCCCCHHHHHHHCC
T ss_conf             44688899988-----------------760687501200134555042


No 95 
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=22.33  E-value=59  Score=13.89  Aligned_cols=23  Identities=30%  Similarity=0.345  Sum_probs=13.9

Q ss_pred             EEECCEEEEC---CCEEECCCCEEEE
Q ss_conf             8788889413---5348338847886
Q gi|254780187|r  121 VLVNGRSVNI---GSYRCKEGDVIEV  143 (206)
Q Consensus       121 i~vng~~v~~---ps~~~k~gd~I~~  143 (206)
                      |-||+.+|-.   +++.|+.||.|++
T Consensus        37 vaiN~~iVPRs~W~~~~l~~gD~Iei   62 (69)
T PRK06083         37 FAINNQVVPRSEWQSTVLSEGDAISL   62 (69)
T ss_pred             EEECCEEECHHHCCCCCCCCCCEEEE
T ss_conf             99778384356716045899999999


No 96 
>TIGR02170 thyX thymidylate synthase, flavin-dependent; InterPro: IPR003669   Thymidylate (dTMP) is an essential DNA precursor. There are two pathways for thymidylate synthesis, each utilising a different thymidylate synthase enzyme: ThyA (2.1.1.45 from EC) and ThyX (2.1.1.148 from EC) . Both enzymes convert dUMP to dTMP, but there is no sequence identity between the two enzymes, and their mechanisms of action differ . Only ThyX uses FAD as cofactor.   This entry represents the flavin-dependent enzyme ThyX, which is a homotetramer bound to four FAD molecules. Under oxygen-limiting conditions, thyX can complement a thyA mutation .; GO: 0050660 FAD binding, 0050797 thymidylate synthase (FAD) activity, 0006231 dTMP biosynthetic process.
Probab=21.43  E-value=52  Score=14.27  Aligned_cols=21  Identities=29%  Similarity=0.218  Sum_probs=18.3

Q ss_pred             CCHHHHHHHHHCCCE-EECCEE
Q ss_conf             247887887624978-788889
Q gi|254780187|r  107 PTIFAARQFVNHRHV-LVNGRS  127 (206)
Q Consensus       107 ~t~~~Arq~v~hg~i-~vng~~  127 (206)
                      -||..++|++.|.|. ..|-.-
T Consensus        87 ~sr~~~~Q~~RHR~~~S~~~~S  108 (259)
T TIGR02170        87 ASRSVAAQLVRHRIAFSYSVQS  108 (259)
T ss_pred             HHHHHHHHHHCCEEEEEEEECC
T ss_conf             3189999882063767773001


No 97 
>TIGR01517 ATPase-IIB_Ca calcium-translocating P-type ATPase, PMCA-type; InterPro: IPR006408   This family describes the P-type ATPase responsible for translocating calcium ions across the plasma membrane of eukaryotes , out of the cell. In some organisms, this type of pump may also be found in vacuolar membranes . In humans and mice, at least, there are multiple isoforms of the PMCA pump with overlapping but not redundant functions. Accordingly, there are no human diseases linked to PMCA defects, although alterations of PMCA function do elicit physiological effects . The calcium P-type ATPases have been characterised as Type IIB based on a phylogenetic analysis which distinguishes this group from the Type IIA SERCA calcium pump .; GO: 0005388 calcium-transporting ATPase activity, 0005509 calcium ion binding, 0005524 ATP binding, 0015085 calcium ion transmembrane transporter activity, 0006816 calcium ion transport, 0016020 membrane.
Probab=21.33  E-value=62  Score=13.76  Aligned_cols=26  Identities=19%  Similarity=0.429  Sum_probs=22.5

Q ss_pred             CEEECCEEEECCCEEECCCCEEEECC
Q ss_conf             78788889413534833884788611
Q gi|254780187|r  120 HVLVNGRSVNIGSYRCKEGDVIEVKQ  145 (206)
Q Consensus       120 ~i~vng~~v~~ps~~~k~gd~I~~~~  145 (206)
                      .+.=||+.+.|+=+.+.+||+|++.-
T Consensus       160 ~VIRgG~~~~Isi~d~~VGDi~sL~~  185 (885)
T TIGR01517       160 KVIRGGQEIQISIHDVVVGDIVSLST  185 (885)
T ss_pred             EEEECCEEEEEEEEEEEECCEEEEEE
T ss_conf             99787927898446888611899841


No 98 
>pfam07299 FBP Fibronectin-binding protein (FBP). This family consists of several bacterial fibronectin-binding proteins which are thought to be involved in virulence in Listeria species.
Probab=21.19  E-value=61  Score=13.82  Aligned_cols=24  Identities=4%  Similarity=0.285  Sum_probs=19.0

Q ss_pred             HHCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             515654799999998753033443
Q gi|254780187|r   61 YYGDISEKKFRSIFKEADRSRGDT   84 (206)
Q Consensus        61 ~YG~~~ekq~~~~~~~A~~~~g~t   84 (206)
                      -.-.++++|+.++|+++++.+-..
T Consensus        81 pF~~~s~~ql~KLF~K~KKLK~P~  104 (208)
T pfam07299        81 PFPSPTTQQLKKLFRKVKKLKIPN  104 (208)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCCCC
T ss_conf             889999899999825535027998


No 99 
>pfam12331 DUF3636 Protein of unknown function (DUF3636). This domain family is found in eukaryotes, and is approximately 160 amino acids in length.
Probab=21.08  E-value=63  Score=13.73  Aligned_cols=39  Identities=15%  Similarity=0.316  Sum_probs=32.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCHH------HHHHHHHCCC
Q ss_conf             44302689999988888998621212478------8788762497
Q gi|254780187|r   82 GDTSHNLISFLESRLDTIVYRAKFVPTIF------AARQFVNHRH  120 (206)
Q Consensus        82 g~t~~~ll~~LE~RLD~~v~r~g~a~t~~------~Arq~v~hg~  120 (206)
                      |...-.-.+.++.||..+-+=..||.+-+      ++.|+.+|--
T Consensus        98 g~~p~t~~~i~~lRleal~~Lt~~a~s~~~p~~~~g~~~lAshp~  142 (155)
T pfam12331        98 GEAPYTPDEICELRLEALSFLTSFAFSPYDPSQNHGGSALASHPT  142 (155)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCH
T ss_conf             889986899999999999999999617888320067889970813


No 100
>pfam10614 Tafi-CsgF Curli production assembly/transport component CsgF. Fimbriae are cell-surface protein polymers, of eg. E coli and Salmonella spp, that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), that differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae (Tafi) are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous m
Probab=20.90  E-value=64  Score=13.71  Aligned_cols=48  Identities=13%  Similarity=0.219  Sum_probs=33.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHC---------CCEEECCEEEECCCEEECCCCEEEEC
Q ss_conf             4430268999998888899862121247887887624---------97878888941353483388478861
Q gi|254780187|r   82 GDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNH---------RHVLVNGRSVNIGSYRCKEGDVIEVK  144 (206)
Q Consensus        82 g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~h---------g~i~vng~~v~~ps~~~k~gd~I~~~  144 (206)
                      ..+.+.|+..||+|+=+-+           +||++.-         |-+.+.|-.|.+    ++.+|-|.+.
T Consensus        67 nt~l~~F~~nLesriya~L-----------S~ql~d~~FGe~~~~sGt~~~~g~~I~~----~~~~~~i~lt  123 (142)
T pfam10614        67 NSQLDIFAQQLQSQLLSAL-----------ASQITTAIFGENPQESGTFSFGGTTISF----ARSDGQLQLT  123 (142)
T ss_pred             CCHHHHHHHHHHHHHHHHH-----------HHHHHHHHCCCCCCCCEEEEECCEEEEE----EECCCEEEEE
T ss_conf             5489999999999999999-----------9999875616888885079989989999----9889989999


No 101
>TIGR01940 nqrE NADH:ubiquinone oxidoreductase, Na(+)-translocating, E subunit; InterPro: IPR010967   NADH can be oxidized by the respiratory chain of bacteria via NADH:quinone oxidoreductases that belong to three distinct enzyme families: NDH-1, NDH-2, and NQR. The NQR-type enzymes are sodium-motive NADH:quinone oxidoreductases consisting of six subunits (NqrA-F) and several cofactors: FAD, 2 FMN, a 2Fe-2S cluster and riboflavin. The NADH:quinone oxidoreductase activity of these enzymes is stimulated by sodium ions and is coupled with pumping of Na+ but not H+. Subunits NqrA, NqrC and NqrF represent the three major subunits of the NQR complex, which are alpha, gamma and beta, respectively. Subunits NqrB, NqrD and NqrE are very hydrophobic polypeptides that were found to co-localise with the alpha subunit . This entry represents the NqrE subunit.; GO: 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0006118 electron transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=20.77  E-value=64  Score=13.69  Aligned_cols=20  Identities=35%  Similarity=0.778  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             68999998888899862121247887
Q gi|254780187|r   87 NLISFLESRLDTIVYRAKFVPTIFAA  112 (206)
Q Consensus        87 ~ll~~LE~RLD~~v~r~g~a~t~~~A  112 (206)
                      .|.|+||+=||      .|.|+.+.|
T Consensus        94 AlvQilEm~le------rF~p~LY~a  113 (203)
T TIGR01940        94 ALVQILEMVLE------RFSPSLYNA  113 (203)
T ss_pred             HHHHHHHHHHH------HCCHHHHHH
T ss_conf             99999999998------306778988


No 102
>TIGR01828 pyru_phos_dikin pyruvate, phosphate dikinase; InterPro: IPR010121   Pyruvate phosphate dikinase (PPDK, or pyruvate orthophosphate dikinase) is found in plants, bacteria and archaea. The amino acid sequence identity between bacterial and plant enzymes is high, and they are similar in sequence to other PEP-utilizing enzymes. PPDK catalyses the reversible conversion of ATP and pyruvate to AMP and PEP (phosphoenolpyruvate). In bacteria such as Clostridium symbiosum, PPDK uses Mg2+ and NH4+ ions as cofactors . The enzyme has three domains: the N- and C-terminal domains each have an active site centre that catalyses a different step in the reaction, and the middle domain has a carrier histidine residue that moves between the two active centres.   In plants, PPDK is localised predominantly in chloroplast stroma where it catalyses the rate-limiting step in the C4 photosynthetic pathway, namely the synthesis of PEP, which acts as the primary CO2 acceptor in C4 photosynthesis . PPDK activity in C4 plants is strictly regulated by light, its activity decreasing in darkness. This response is regulated by phosphorylation and dephosphorylation of the enzyme using ADP; such regulation is not seen in the bacterial form of the enzyme. PPDK is also found in C3 plants, but it is not known to have a photosynthetic role .; GO: 0050242 pyruvate phosphate dikinase activity.
Probab=20.70  E-value=64  Score=13.68  Aligned_cols=23  Identities=30%  Similarity=0.559  Sum_probs=18.1

Q ss_pred             ECCEEEECC--CEEECCCCEEEECC
Q ss_conf             888894135--34833884788611
Q gi|254780187|r  123 VNGRSVNIG--SYRCKEGDVIEVKQ  145 (206)
Q Consensus       123 vng~~v~~p--s~~~k~gd~I~~~~  145 (206)
                      ...|...++  +..++.||+|||.=
T Consensus       501 ~~~k~~~~g~Gg~~~~EGD~isiDG  525 (920)
T TIGR01828       501 EEKKTLTIGGGGRVIKEGDIISIDG  525 (920)
T ss_pred             CCCCEEEECCCCCEEECCEEEEEEC
T ss_conf             1048788888894774343799708


No 103
>pfam09285 Elong-fact-P_C Elongation factor P, C-terminal. Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology.
Probab=20.66  E-value=64  Score=13.68  Aligned_cols=26  Identities=27%  Similarity=0.510  Sum_probs=19.1

Q ss_pred             CEEECCEEEECCCEEECCCCEEEECCH
Q ss_conf             787888894135348338847886110
Q gi|254780187|r  120 HVLVNGRSVNIGSYRCKEGDVIEVKQK  146 (206)
Q Consensus       120 ~i~vng~~v~~ps~~~k~gd~I~~~~k  146 (206)
                      -++-||-.|..|.| ++.||.|.+...
T Consensus        24 A~letG~~i~VP~F-I~~Gd~I~VdT~   49 (56)
T pfam09285        24 ATLETGAEVQVPLF-IEEGEKIKVDTR   49 (56)
T ss_pred             EEECCCCEEECCCC-CCCCCEEEEECC
T ss_conf             89838989983874-048999999899


No 104
>TIGR03164 UHCUDC OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model.
Probab=20.17  E-value=54  Score=14.16  Aligned_cols=21  Identities=24%  Similarity=0.502  Sum_probs=16.9

Q ss_pred             HCCCCCCHHHHHHHHHHHHHH
Q ss_conf             033443026899999888889
Q gi|254780187|r   79 RSRGDTSHNLISFLESRLDTI   99 (206)
Q Consensus        79 ~~~g~t~~~ll~~LE~RLD~~   99 (206)
                      -.+|.+.+.+|..|++||+|-
T Consensus       114 ~v~g~~~~~IL~~l~~Rl~n~  134 (157)
T TIGR03164       114 AVKGKTKQSILAAFEARLNND  134 (157)
T ss_pred             EECCCCHHHHHHHHHHHHCCC
T ss_conf             538989999999999997699


No 105
>TIGR01838 PHA_synth_I poly(R)-hydroxyalkanoic acid synthase, class I; InterPro: IPR010963   This entry represents the class I subfamily of poly(R)-hydroxyalkanoate synthases, which polymerises hydroxyacyl-CoAs with three to five carbons in the hydroxyacyl backbone into aliphatic esters termed poly(R)-hydroxyalkanoic acids. These polymers accumulate as carbon and energy storage inclusions in many species and can amount to 90 percent of the dry weight of the cell.; GO: 0008415 acyltransferase activity, 0042619 poly-hydroxybutyrate biosynthetic process, 0005737 cytoplasm.
Probab=20.17  E-value=66  Score=13.61  Aligned_cols=38  Identities=21%  Similarity=0.316  Sum_probs=27.8

Q ss_pred             CHHHHHHHHHCCCEEECCEE-----EECCCEEEC-CCCEEEECC
Q ss_conf             47887887624978788889-----413534833-884788611
Q gi|254780187|r  108 TIFAARQFVNHRHVLVNGRS-----VNIGSYRCK-EGDVIEVKQ  145 (206)
Q Consensus       108 t~~~Arq~v~hg~i~vng~~-----v~~ps~~~k-~gd~I~~~~  145 (206)
                      ..+..-+|++.|.+.|+|.+     |++|+|.+. .-|-|..=.
T Consensus       394 ~lYl~N~L~~~g~l~~~G~~lDL~~vk~P~y~~at~eDHIApW~  437 (541)
T TIGR01838       394 NLYLQNELVSKGKLEVGGVRLDLSKVKVPVYIIATKEDHIAPWQ  437 (541)
T ss_pred             HHHHHCCCCCCCCEEECCEEEECCCCCCCEEEEECCCCCCCCCH
T ss_conf             53010111168854873246203424312457613444345827


Done!