Query         gi|255764506|ref|YP_003065297.2| GTP cyclohydrolase I [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 205
No_of_seqs    115 out of 1575
Neff          5.5 
Searched_HMMs 39220
Date          Tue May 31 14:43:59 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 255764506.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00063 folE GTP cyclohydrol 100.0       0       0  552.9  17.2  180   21-203     1-183 (183)
  2 PRK09347 folE GTP cyclohydrola 100.0       0       0  522.6  21.2  186   14-203     1-186 (186)
  3 COG0302 FolE GTP cyclohydrolas 100.0       0       0  522.9  19.6  187   14-204     8-195 (195)
  4 cd00642 GTP_cyclohydro1 GTP cy 100.0       0       0  518.2  21.5  184   17-203     2-185 (185)
  5 PRK12606 GTP cyclohydrolase I; 100.0       0       0  517.6  21.6  184   17-203     1-184 (185)
  6 KOG2698 consensus              100.0       0       0  468.6  12.6  185   16-204    62-247 (247)
  7 pfam01227 GTP_cyclohydroI GTP  100.0 5.1E-34 1.3E-38  231.7  11.7   86  100-185     1-86  (86)
  8 PRK13258 7-cyano-7-deazaguanin  98.0   9E-05 2.3E-09   50.7  10.0   99   61-160     9-107 (127)
  9 TIGR03139 QueF-II 7-cyano-7-de  97.9 0.00026 6.5E-09   47.9  10.0   93   67-160     5-97  (115)
 10 cd00651 TFold Tunnelling fold   97.4  0.0036 9.3E-08   40.7  10.7  105   81-185     2-122 (122)
 11 COG0780 Enzyme related to GTP   97.3  0.0031 7.9E-08   41.2   9.7   82   82-163    41-122 (149)
 12 TIGR02750 TraN_Ftype type-F co  54.9     5.9 0.00015   20.9   1.2   16  119-134   592-607 (683)
 13 PRK11245 folX D-erythro-7,8-di  52.0      21 0.00054   17.4   3.7   84   80-163     5-104 (120)
 14 PRK11792 queF 7-cyano-7-deazag  50.9      22 0.00057   17.3   7.4   69   90-160   177-245 (274)
 15 KOG3203 consensus               45.0      25 0.00063   17.0   3.1   46  122-167    20-73  (165)
 16 PTZ00126 tyrosyl-tRNA syntheta  44.9      16 0.00041   18.2   2.1   71   82-152   303-374 (399)
 17 PRK12355 conjugal transfer mat  44.0      12  0.0003   19.0   1.4   16  119-135   532-547 (612)
 18 TIGR00313 cobQ cobyric acid sy  42.0      16  0.0004   18.2   1.7   29  176-205   438-466 (502)
 19 PRK05337 beta-hexosaminidase;   41.8      31 0.00079   16.4   3.7  125   26-175   107-260 (336)
 20 PRK11593 folB bifunctional dih  40.6      32 0.00082   16.3   4.1   80   82-161     3-98  (119)
 21 pfam09710 Trep_dent_lipo Trepo  35.8      12  0.0003   19.0   0.3   75   10-84    160-235 (394)
 22 pfam05997 Nop52 Nucleolar prot  34.4      29 0.00074   16.6   2.1   16   15-30     14-29  (212)
 23 TIGR02393 RpoD_Cterm RNA polym  33.8      33 0.00084   16.2   2.3   38   16-53     84-125 (240)
 24 KOG3230 consensus               32.4      21 0.00055   17.4   1.2   31   15-46    153-183 (224)
 25 TIGR01754 flav_RNR ribonucleot  30.8      31  0.0008   16.3   1.8   59  139-200    14-78  (145)
 26 cd02691 PurM-like2 AIR synthas  30.6      47  0.0012   15.3   3.1   15  142-156   107-121 (346)
 27 COG0399 WecE Predicted pyridox  27.6      53  0.0013   15.0   2.8   87   79-170   190-292 (374)
 28 COG2345 Predicted transcriptio  27.1      38 0.00097   15.8   1.7   76   25-102    89-168 (218)
 29 cd00915 MD-1_MD-2 MD-1 and MD-  26.8      54  0.0014   14.9   2.4   13  102-114    36-48  (130)
 30 pfam09626 DHC Dihaem cytochrom  26.4      55  0.0014   14.8   2.6   46  103-153     6-58  (118)
 31 PRK10557 hypothetical protein;  25.8      57  0.0014   14.8   3.5   19  174-192   146-164 (178)
 32 PRK05568 flavodoxin; Provision  24.9      56  0.0014   14.8   2.2   29   17-45     14-42  (142)
 33 pfam06962 rRNA_methylase Putat  24.6      59  0.0015   14.6   3.2   42  104-160    51-92  (140)
 34 cd05087 PTKc_Aatyk1_Aatyk3 Cat  24.5      59  0.0015   14.7   2.3   47  107-154    74-120 (269)
 35 TIGR02026 BchE magnesium-proto  23.5      63  0.0016   14.5   2.3   47    7-56    346-393 (506)
 36 pfam08879 WRC WRC. The WRC dom  23.2      16 0.00041   18.2  -0.8   12   89-100    23-34  (46)
 37 TIGR00083 ribF riboflavin bios  22.5      66  0.0017   14.4   2.9   42   70-111   189-232 (296)
 38 pfam01340 MetJ Met Apo-repress  22.3      36 0.00092   16.0   0.8   16   21-36     84-99  (104)
 39 pfam08921 DUF1904 Domain of un  22.3      53  0.0013   15.0   1.7   37  125-161    59-95  (107)
 40 PRK09271 flavodoxin; Provision  22.3      61  0.0016   14.6   2.0   21   17-37     13-33  (160)
 41 TIGR00632 vsr DNA mismatch end  21.9      27 0.00068   16.8   0.1   33   20-52     42-81  (143)
 42 cd00490 Met_repressor_MetJ Met  21.5      39   0.001   15.7   0.9   16   21-36     84-99  (103)
 43 PHA00658 putative lysin         21.1      56  0.0014   14.8   1.6   82   20-102   595-676 (720)
 44 COG5441 Uncharacterized conser  20.9      50  0.0013   15.1   1.3   63   82-153   115-178 (401)
 45 cd01747 GATase1_Glutamyl_Hydro  20.9      71  0.0018   14.2   2.1   25   86-113   190-214 (273)
 46 PRK10416 cell division protein  20.7      46  0.0012   15.3   1.1   22   38-59    202-223 (499)
 47 COG1539 FolB Dihydroneopterin   20.5      72  0.0018   14.1   4.0   70   82-151     4-89  (121)
 48 pfam03652 UPF0081 Uncharacteri  20.1      52  0.0013   15.0   1.3   32  118-149    67-107 (134)
 49 TIGR00250 TIGR00250 conserved   20.1      37 0.00096   15.9   0.5   26  119-144    68-102 (133)
 50 pfam07893 DUF1668 Protein of u  20.0      31  0.0008   16.3   0.1   24   97-122   205-229 (330)

No 1  
>TIGR00063 folE GTP cyclohydrolase I; InterPro: IPR001474   GTP cyclohydrolase I (3.5.4.16 from EC) catalyzes the biosynthesis of formic acid and dihydroneopterin triphosphate from GTP. This reaction is the first step in the biosynthesis of tetrahydrofolate in prokaryotes, of tetrahydrobiopterin in vertebrates, and of pteridine-containing pigments in insects. The comparison of the sequence of the enzyme from bacterial and eukaryotic sources shows that the structure of this enzyme has been extremely well conserved throughout evolution .; GO: 0003934 GTP cyclohydrolase I activity, 0019438 aromatic compound biosynthetic process, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=552.92  Aligned_cols=180  Identities=49%  Similarity=0.823  Sum_probs=169.8

Q ss_pred             HHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHH-HHHHHCCCCCH-HHHHHHHCCCCCCCCCCEEEECCEEEEEECCCCE
Q ss_conf             999999999981478888100112678999999-99976086531-2344320256655667628961805877211002
Q gi|255764506|r   21 AKEAIRVILRWIGDDPDREGLKDTPDRVIKSYK-ELFAGYKQIPT-TQDTSRFHFGEASKYQDMVLIKDISFFSYCEHHI   98 (205)
Q Consensus        21 i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~-e~~~Gy~~~~~-~~~~~~~~~~~~~~~~~mVvv~~I~f~S~CEHHl   98 (205)
                      |+.+++++|++|||||+||||.+||+||||||. |+|+||+.++. ......   .+.+++||||+|+||.|||+|||||
T Consensus         1 i~~~~~~~l~~iGeD~~regL~~TP~RvAk~~~D~~f~G~~~~~~d~~~~~~---~f~~~~dEMV~V~DI~~~S~CEHHl   77 (183)
T TIGR00063         1 IEGAVRQILESIGEDLNREGLLETPKRVAKMYLDELFSGYDEANFDKKIKKA---IFQEKHDEMVLVRDIEFYSTCEHHL   77 (183)
T ss_pred             CHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHE---ECCCCCCEEEEEECCCEEECCHHHC
T ss_conf             9478899999808884667731124899999998864102556332144401---1058852688873241230333330


Q ss_pred             EEEEEEEEEEEECCC-CCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCCCCCE
Q ss_conf             346557899996388-5434677999999983154266899999999999732738479999948842522383559985
Q gi|255764506|r   99 LPIWGKIHLAYIPKK-HVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRDGLT  177 (205)
Q Consensus        99 lPf~G~~~IaYiP~~-~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~~~~s~  177 (205)
                      +||+|++||||||++ +|+|||||+|||++||||||+|||||.|||.|+++.|+|+||+|+++|+||||.||||++++|.
T Consensus        78 vpf~GK~~vaYIPk~GkViGLSKlaR~ve~farRlQvQERLT~QIa~a~~eiL~p~gVaVv~eA~H~Cm~~RGvrk~~s~  157 (183)
T TIGR00063        78 VPFDGKAHVAYIPKDGKVIGLSKLARIVEMFARRLQVQERLTKQIAEALQEILEPRGVAVVVEATHMCMKMRGVRKTGSI  157 (183)
T ss_pred             CCCCCCEEEEEECCCCEEEEHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEEEEECEECCCCC
T ss_conf             12458258998818964870668889999986265146889999999999873789828998656777653156529981


Q ss_pred             EEEEEEEEEECCCHHHHHHHHHHHCC
Q ss_conf             99967774430688999999998326
Q gi|255764506|r  178 TVTTAFTGEFSRDKGKTDFFLKMTHN  203 (205)
Q Consensus       178 ~~T~~~~G~F~~d~~~r~ef~~li~~  203 (205)
                      |+||+++|.|++|.++|+|||++|+.
T Consensus       158 tvTS~~~G~Fk~~~~TR~EFL~~~~~  183 (183)
T TIGR00063       158 TVTSALRGLFKKDQKTREEFLELIKR  183 (183)
T ss_pred             EEEEEEECCCHHHHHHHHHHHHHHCC
T ss_conf             68865422434246889999997159


No 2  
>PRK09347 folE GTP cyclohydrolase I; Provisional
Probab=100.00  E-value=0  Score=522.58  Aligned_cols=186  Identities=51%  Similarity=0.878  Sum_probs=179.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEEECCEEEEEE
Q ss_conf             52248999999999999814788881001126789999999997608653123443202566556676289618058772
Q gi|255764506|r   14 KKPTVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHFGEASKYQDMVLIKDISFFSY   93 (205)
Q Consensus        14 ~~~~~~~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~e~~~Gy~~~~~~~~~~~~~~~~~~~~~~mVvv~~I~f~S~   93 (205)
                      .+|+.+++++||++||++||+||+|+||.+||+||||||.|+|+||+.+|+..+...|+    +.|++||+++||+|+|+
T Consensus         1 ~~~~~~~~e~av~~iL~~lGeD~~r~gL~~TP~Rvak~~~e~~~Gy~~~p~~~~~~~~~----~~~~~mViv~~I~f~S~   76 (186)
T PRK09347          1 NEPDKEKIEEAVREILEALGEDPDREGLLDTPKRVAKMYEELFSGYANDPKEVLNENFE----EVYDEMVLVKDIEFYST   76 (186)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCCC----CCCCCEEEEECCCEEEE
T ss_conf             96389999999999999967899941234579999999999855436896898741444----56884799927513786


Q ss_pred             CCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCC
Q ss_conf             11002346557899996388543467799999998315426689999999999973273847999994884252238355
Q gi|255764506|r   94 CEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKR  173 (205)
Q Consensus        94 CEHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~~  173 (205)
                      ||||||||+|++||||+|+++|+|||||+|||++||||||+|||||+|||++|++.|+|+||+|+++|+|+||.||||++
T Consensus        77 CEHHllPf~G~~~VaYiP~~~viGLSKl~Riv~~~arRlQvQErlT~qIa~~l~~~l~p~Gv~V~i~A~H~Cm~~RGv~~  156 (186)
T PRK09347         77 CEHHLLPFIGKAHVAYIPNGKVIGLSKIARIVDFFARRPQVQERLTAQIADALQEILGPRGVAVVIEAEHMCMTMRGVRK  156 (186)
T ss_pred             CCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCCCC
T ss_conf             42124534016999996488755655799999999738737889999999999983488968999988984152359889


Q ss_pred             CCCEEEEEEEEEEECCCHHHHHHHHHHHCC
Q ss_conf             998599967774430688999999998326
Q gi|255764506|r  174 DGLTTVTTAFTGEFSRDKGKTDFFLKMTHN  203 (205)
Q Consensus       174 ~~s~~~T~~~~G~F~~d~~~r~ef~~li~~  203 (205)
                      ++|.|+|++++|+|++|+++|+|||++|+.
T Consensus       157 ~~s~t~Ts~~~G~F~~d~~~R~Efl~~i~~  186 (186)
T PRK09347        157 PGSKTVTSALRGLFKTDPATRAEFLSLIRH  186 (186)
T ss_pred             CCCEEEEEEEEEEECCCHHHHHHHHHHHCC
T ss_conf             997499978788867898999999998429


No 3  
>COG0302 FolE GTP cyclohydrolase I [Coenzyme metabolism]
Probab=100.00  E-value=0  Score=522.86  Aligned_cols=187  Identities=49%  Similarity=0.884  Sum_probs=174.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHH-HHHHHCCCCCCCCCCEEEECCEEEEE
Q ss_conf             52248999999999999814788881001126789999999997608653123-44320256655667628961805877
Q gi|255764506|r   14 KKPTVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQ-DTSRFHFGEASKYQDMVLIKDISFFS   92 (205)
Q Consensus        14 ~~~~~~~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~e~~~Gy~~~~~~~-~~~~~~~~~~~~~~~mVvv~~I~f~S   92 (205)
                      +..+.+++++||++||+++||||+||||.+||+||||||.|+|+||+.+|... +...|    .+..++||+++||+|||
T Consensus         8 ~~~~~e~~e~avr~lL~~~Gedp~reGL~~TP~RVak~~~e~f~G~~~~~~~~~l~~~f----e~~~~emVlvkdI~f~S   83 (195)
T COG0302           8 RETDAERIEAAVRELLEALGEDPDREGLLETPKRVAKAYRELFSGYDEDPAEIVLEATF----EEDHDEMVLVKDIEFYS   83 (195)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCC----CCCCCCEEEEECCCEEE
T ss_conf             33348999999999999827997700334548999999999970007995786640421----23677589995441266


Q ss_pred             ECCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCC
Q ss_conf             21100234655789999638854346779999999831542668999999999997327384799999488425223835
Q gi|255764506|r   93 YCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIK  172 (205)
Q Consensus        93 ~CEHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~  172 (205)
                      +||||||||+|++||||||+|+|+|||||+|+|++||||||+|||||.|||++|++.|+|+||+|+|+|+||||.||||+
T Consensus        84 ~CEHHllPf~GkahVAYiP~gkV~GlSKiaRiV~~~arR~QvQErlT~qIA~al~~~L~p~GVaVvieA~HmCm~mRGv~  163 (195)
T COG0302          84 LCEHHLLPFFGKAHVAYIPDGKVIGLSKIARIVDIFARRLQVQERLTEQIADALQEILKPRGVAVVIEAEHMCMSMRGVR  163 (195)
T ss_pred             ECCCCCCCCCCEEEEEECCCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEHHCCCC
T ss_conf             23544243246589998269805207999999999961368999999999999998608685499997777120222746


Q ss_pred             CCCCEEEEEEEEEEECCCHHHHHHHHHHHCCC
Q ss_conf             59985999677744306889999999983268
Q gi|255764506|r  173 RDGLTTVTTAFTGEFSRDKGKTDFFLKMTHNQ  204 (205)
Q Consensus       173 ~~~s~~~T~~~~G~F~~d~~~r~ef~~li~~~  204 (205)
                      +++|.|+|++++|.|++|+++|.|||++|+.+
T Consensus       164 k~~s~t~Ts~~~G~F~~~~~~R~efl~li~~~  195 (195)
T COG0302         164 KPGSSTVTSALRGLFKEDAKTRAEFLRLIKGH  195 (195)
T ss_pred             CCCCEEEEEEEEEEECCCHHHHHHHHHHHHCC
T ss_conf             89965888765435536888899999987359


No 4  
>cd00642 GTP_cyclohydro1 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate.  The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria.  In vertebrates and insects it is the biosynthtic precursor of tetrahydrobiopterin (BH4) which is involved in the formation of catacholamines, nitric oxide, and the stimulation of T lymphocytes. The biosynthetic reaction of BH4 is controlled by a regulatory protein GFRP which mediates feedback inhibition of GTP-CH-I by BH4.  This inhibition is reversed by phenylalanine. The decameric GTP-CH-I forms a complex with two pentameric GFRP in the presence of phenylalanine or a combination of GTP and BH4, respectively.
Probab=100.00  E-value=0  Score=518.21  Aligned_cols=184  Identities=49%  Similarity=0.864  Sum_probs=174.3

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEEECCEEEEEECCC
Q ss_conf             48999999999999814788881001126789999999997608653123443202566556676289618058772110
Q gi|255764506|r   17 TVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHFGEASKYQDMVLIKDISFFSYCEH   96 (205)
Q Consensus        17 ~~~~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~e~~~Gy~~~~~~~~~~~~~~~~~~~~~~mVvv~~I~f~S~CEH   96 (205)
                      .++++++||++||++||+||+|+||.+||+||||||.|+|+||+.++.......++   +++|++||+++||+|+|+|||
T Consensus         2 ~i~~ie~av~~iL~~lGeD~~r~gL~~TP~Rvak~~~e~~~G~~~~~~~~~~~~~~---~~~~~~~V~~~~I~f~S~CEH   78 (185)
T cd00642           2 RLEKIAAAVREILELLGEDPNREGLLETPERVAKAYQEITSGYDQALNDPKNTAIF---DEDHDEMVIVKDITLFSMCEH   78 (185)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHHHCHHHHHHHHHHHHHCCCCCCHHHHCCCCC---CCCCCEEEEEECCCEEEECCC
T ss_conf             58999999999999967999950013579999999999973717892055316676---778871799918247884255


Q ss_pred             CEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCCCCC
Q ss_conf             02346557899996388543467799999998315426689999999999973273847999994884252238355998
Q gi|255764506|r   97 HILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRDGL  176 (205)
Q Consensus        97 HllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~~~~s  176 (205)
                      |||||+|++||||+|+++|+|||||+|||++||||||+|||||+|||++|++.|+|+||+|+++|+|+||.||||++++|
T Consensus        79 HllPf~G~~~VaYiP~~~viGLSKl~RiV~~~arRlQvQErlT~qIa~~l~~~l~~~gV~V~ieA~H~Cm~~RGv~~~~s  158 (185)
T cd00642          79 HLVPFYGKVHIAYIPKDKVIGLSKLARIVEFFSRRLQVQERLTKQIAVAIQEILGPQGVAVVIEATHMCMVMRGVRKPGS  158 (185)
T ss_pred             CCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCCCCCCC
T ss_conf             66616668999997688504389999999999648689989999999999984098978999998983176618889997


Q ss_pred             EEEEEEEEEEECCCHHHHHHHHHHHCC
Q ss_conf             599967774430688999999998326
Q gi|255764506|r  177 TTVTTAFTGEFSRDKGKTDFFLKMTHN  203 (205)
Q Consensus       177 ~~~T~~~~G~F~~d~~~r~ef~~li~~  203 (205)
                      .|+|++++|+|++|+++|+|||++|+.
T Consensus       159 ~t~T~~~~G~F~~d~~~R~Efl~~i~~  185 (185)
T cd00642         159 KTVTSAMLGVFKEDPKTREEFLRLIRK  185 (185)
T ss_pred             EEEEEEEEEEECCCHHHHHHHHHHHCC
T ss_conf             399988788947898999999997459


No 5  
>PRK12606 GTP cyclohydrolase I; Reviewed
Probab=100.00  E-value=0  Score=517.62  Aligned_cols=184  Identities=43%  Similarity=0.753  Sum_probs=174.9

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEEECCEEEEEECCC
Q ss_conf             48999999999999814788881001126789999999997608653123443202566556676289618058772110
Q gi|255764506|r   17 TVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHFGEASKYQDMVLIKDISFFSYCEH   96 (205)
Q Consensus        17 ~~~~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~e~~~Gy~~~~~~~~~~~~~~~~~~~~~~mVvv~~I~f~S~CEH   96 (205)
                      |.+++++||++||++||+||+|+||.+||+||||||.|+|+||..+|+..+...+   ..+++++||+++||+|+|+|||
T Consensus         1 D~~~ie~av~~lL~~lGeD~~regL~~TP~Rvak~~~e~~~G~~~~p~~~~~~~~---~~~~~~~mVvv~~I~f~S~CEH   77 (185)
T PRK12606          1 DPPALEAAYREILEALGEDPDREGLLDTPQRAAKAMQYLCDGYEQDPAEAVNGAL---FDSDNDEMVIVRDIELYSLCEH   77 (185)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCCCCHHHCHHHHHHHHHHHHCCCCCCHHHHCCCCC---CCCCCCCEEEEECCCEEEECCC
T ss_conf             9789999999999996799996310358999999999995686789578504667---7788884699818526785343


Q ss_pred             CEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCCCCC
Q ss_conf             02346557899996388543467799999998315426689999999999973273847999994884252238355998
Q gi|255764506|r   97 HILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRDGL  176 (205)
Q Consensus        97 HllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~~~~s  176 (205)
                      |||||+|++||||||+++|+|||||+|||++||||||+|||||+|||++|++.|+|+||+|+++|+|+||.||||++++|
T Consensus        78 HllPf~G~ahVaYiP~~~viGLSKl~Riv~~~arRlQ~QErlT~qIa~~l~~~l~~~gVaV~i~A~H~Cm~~RGv~~~~s  157 (185)
T PRK12606         78 HLLPFIGKAHVAYLPGGRVLGLSKIARIVDMFARRLQIQENLTRQIATAVVTVTQARGVAVVIEAEHMCMMMRGVEKQNS  157 (185)
T ss_pred             CCEEEEEEEEEEEECCCCEECHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCCCCCCC
T ss_conf             42047768999996898013568999999999728548989999999999984198978999998982074459889997


Q ss_pred             EEEEEEEEEEECCCHHHHHHHHHHHCC
Q ss_conf             599967774430688999999998326
Q gi|255764506|r  177 TTVTTAFTGEFSRDKGKTDFFLKMTHN  203 (205)
Q Consensus       177 ~~~T~~~~G~F~~d~~~r~ef~~li~~  203 (205)
                      .|+|++++|+|++|+++|+|||++|+.
T Consensus       158 ~t~T~~~~G~F~~d~~~R~Efl~~i~~  184 (185)
T PRK12606        158 RMITSVMLGAFRDSAQTRNEFLRLIGR  184 (185)
T ss_pred             EEEEEEEEEEECCCHHHHHHHHHHHCC
T ss_conf             499988788957898999999997566


No 6  
>KOG2698 consensus
Probab=100.00  E-value=0  Score=468.59  Aligned_cols=185  Identities=44%  Similarity=0.787  Sum_probs=172.7

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHH-HHHHHCCCCCCCCCCEEEECCEEEEEEC
Q ss_conf             248999999999999814788881001126789999999997608653123-4432025665566762896180587721
Q gi|255764506|r   16 PTVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQ-DTSRFHFGEASKYQDMVLIKDISFFSYC   94 (205)
Q Consensus        16 ~~~~~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~e~~~Gy~~~~~~~-~~~~~~~~~~~~~~~mVvv~~I~f~S~C   94 (205)
                      ....++..|+++||..|||||+|.||.+||.|+|||+..|+.||++.-... +...|    .++++|||+|+||+.||||
T Consensus        62 ~~lp~m~~a~~siL~~LGEdp~RqgLl~TP~R~aKaMl~Ftkgy~~~l~dvlN~Avf----dedhdEmvivkdiemfSmC  137 (247)
T KOG2698          62 EVLPEMANAYSSILKSLGEDPNRQGLLKTPERAAKAMLYFTKGYEQNLNDVLNEAVF----DEDHDEMVIVKDIEMFSMC  137 (247)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CCCCCEEEEEECCHHHHHH
T ss_conf             673999999999998736892220222187999999999986288789998521203----6666525888500687776


Q ss_pred             CCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCCC
Q ss_conf             10023465578999963885434677999999983154266899999999999732738479999948842522383559
Q gi|255764506|r   95 EHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRD  174 (205)
Q Consensus        95 EHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~~~  174 (205)
                      ||||+||+|++||||||+++|+||||++|||++|+||||+|||||+|||.+|.+.++|.||+|++||.||||.||||++.
T Consensus       138 EHHLvPF~GkVhIGY~pnkkvlGlSklarIve~ysrrLQVQERlTkQIA~a~s~~v~p~gVaVV~Ea~HmCMVmRGvqK~  217 (247)
T KOG2698         138 EHHLVPFYGKVHIGYIPNKKVLGLSKLARIVEMYSRRLQVQERLTKQIAVALSQAVQPAGVAVVVEATHMCMVMRGVQKI  217 (247)
T ss_pred             HHCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCEEEEEEECCCCC
T ss_conf             64356501257774226874104799999999998999999999999999999861866649998505454321033315


Q ss_pred             CCEEEEEEEEEEECCCHHHHHHHHHHHCCC
Q ss_conf             985999677744306889999999983268
Q gi|255764506|r  175 GLTTVTTAFTGEFSRDKGKTDFFLKMTHNQ  204 (205)
Q Consensus       175 ~s~~~T~~~~G~F~~d~~~r~ef~~li~~~  204 (205)
                      +|+|+|++++|+|.+|+.+|+|||++|+.+
T Consensus       218 ~SsTvTs~mlGvFr~d~ktReeFl~li~~~  247 (247)
T KOG2698         218 GSSTVTSTMLGVFRDDPKTREEFLNLINSR  247 (247)
T ss_pred             CCCHHHHHHHHHHCCCCHHHHHHHHHHCCC
T ss_conf             762222543210156833699999984269


No 7  
>pfam01227 GTP_cyclohydroI GTP cyclohydrolase I. This family includes GTP cyclohydrolase enzymes and a family of related bacterial proteins.
Probab=100.00  E-value=5.1e-34  Score=231.73  Aligned_cols=86  Identities=56%  Similarity=0.956  Sum_probs=85.2

Q ss_pred             EEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCCCCCEEE
Q ss_conf             46557899996388543467799999998315426689999999999973273847999994884252238355998599
Q gi|255764506|r  100 PIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRDGLTTV  179 (205)
Q Consensus       100 Pf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~~~~s~~~  179 (205)
                      ||+|++||||+|+++|+|||||+|+|++||+|||+|||||+|||++|++.|+|+||+|.++|+|+||.+||++++++.|+
T Consensus         1 P~~G~~~IaYiP~~~viGlskl~riv~~fa~R~q~QErlt~~Ia~~l~~~l~p~gv~V~~~a~H~C~~~RGv~~~~~~~~   80 (86)
T pfam01227         1 PFFGKAHIAYIPNGKVIGLSKLARYVDSFARRLQVQERLTNQIADALVEALKPKGVAVVIEAEHLCMTMRGVRKPGSKTV   80 (86)
T ss_pred             CEEEEEEEEEECCCEEEEHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCCCCCCCEEE
T ss_conf             94789999995599266078999999999747646899999999999984098979999999997676538889997699


Q ss_pred             EEEEEE
Q ss_conf             967774
Q gi|255764506|r  180 TTAFTG  185 (205)
Q Consensus       180 T~~~~G  185 (205)
                      |++++|
T Consensus        81 T~~~~G   86 (86)
T pfam01227        81 TSALRG   86 (86)
T ss_pred             EEEEEC
T ss_conf             966379


No 8  
>PRK13258 7-cyano-7-deazaguanine reductase; Provisional
Probab=98.01  E-value=9e-05  Score=50.68  Aligned_cols=99  Identities=19%  Similarity=0.177  Sum_probs=78.4

Q ss_pred             CCCHHHHHHHHCCCCCCCCCCEEEECCEEEEEECCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf             65312344320256655667628961805877211002346557899996388543467799999998315426689999
Q gi|255764506|r   61 QIPTTQDTSRFHFGEASKYQDMVLIKDISFFSYCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTM  140 (205)
Q Consensus        61 ~~~~~~~~~~~~~~~~~~~~~mVvv~~I~f~S~CEHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~  140 (205)
                      ..|...+..+|+++... .+-.|-..-=.|+|+|.=.=+|=+|++.|-|+|+++++-+-.|-...--|-..---.|..++
T Consensus         9 ~~p~~~~Le~f~n~~~~-~~y~i~~~~~EFtslCPvTgQPDfa~i~I~Y~p~~~~vE~KSLk~Yl~sfRn~~~FHE~~~~   87 (127)
T PRK13258          9 FSPEPEVLETFPNPHPG-RDYTIRFTCPEFTSLCPKTGQPDFATIVIDYIPDKKCVESKSLKLYLFSFRNHGIFHEDCTN   87 (127)
T ss_pred             CCCCHHHHCCCCCCCCC-CCEEEEEECCCEEECCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHCCHHHHHHHH
T ss_conf             99798991036899999-77899994575375277879995599999980798634789999999999861447999999


Q ss_pred             HHHHHHHHHCCCCCEEEEEE
Q ss_conf             99999997327384799999
Q gi|255764506|r  141 QIAHAIESSTDSKGVAVLIE  160 (205)
Q Consensus       141 qIa~~l~~~l~~~gv~V~i~  160 (205)
                      +|.+.|.+.++|+-..|...
T Consensus        88 ~I~~dl~~~~~P~~l~V~~~  107 (127)
T PRK13258         88 RILDDLVALLDPKWLRVGGD  107 (127)
T ss_pred             HHHHHHHHHCCCCEEEEEEE
T ss_conf             99999997559739999999


No 9  
>TIGR03139 QueF-II 7-cyano-7-deazaguanine reductase. The enzymatic step represents the first point at which the biosynthesis of queuosine in bacteria and eukaryotes is distinguished from the biosynthesis of archaeosine in archaea.
Probab=97.85  E-value=0.00026  Score=47.86  Aligned_cols=93  Identities=17%  Similarity=0.182  Sum_probs=76.1

Q ss_pred             HHHHHCCCCCCCCCCEEEECCEEEEEECCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             44320256655667628961805877211002346557899996388543467799999998315426689999999999
Q gi|255764506|r   67 DTSRFHFGEASKYQDMVLIKDISFFSYCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAI  146 (205)
Q Consensus        67 ~~~~~~~~~~~~~~~mVvv~~I~f~S~CEHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l  146 (205)
                      +..+|+++... .+-.|-..-=+|+|+|.=-=+|=+|++.|-|+|+++++-+..|-....-|-..---.|..+.+|.+.|
T Consensus         5 ~Le~f~N~~~~-~~y~i~~~~pEFtslCPvTgQPDfati~I~Y~p~~~~vE~kSLk~Yl~SfRn~~~FHE~~~~~I~~dl   83 (115)
T TIGR03139         5 LLEAFPNPYPD-RDYTIEFVCPEFTSLCPKTGQPDFATIVISYIPDQRCVELKSLKLYLFSFRNHGIFHENVTNTILDDL   83 (115)
T ss_pred             HCCCCCCCCCC-CCEEEEEECCCEEECCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             71004999999-87799994575377388889996389999984897733889999999997545750899999999999


Q ss_pred             HHHCCCCCEEEEEE
Q ss_conf             97327384799999
Q gi|255764506|r  147 ESSTDSKGVAVLIE  160 (205)
Q Consensus       147 ~~~l~~~gv~V~i~  160 (205)
                      .+.++|+-+.|...
T Consensus        84 ~~~~~P~~l~V~g~   97 (115)
T TIGR03139        84 VKLLQPRYLRVIGD   97 (115)
T ss_pred             HHHCCCCEEEEEEE
T ss_conf             97569629999999


No 10 
>cd00651 TFold Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1),  6-pyrovoyl tetrahydropterin synthetase (PTPS), and uricase (UO,uroate/urate oxidase). They bind to substrates belonging to the purine or pterin families, and share a fold-related binding site with a glutamate or glutamine residue anchoring the substrate and a lot of conserved interactions. They also share a similar oligomerization mode: several T-folds join together to form a beta(2n)alpha(n) barrel, then two barrels join together in a head-to-head fashion to made up the native enzymes. The functional enzyme is a tetramer for UO, a hexamer for PTPS, an octamer for DHNA/DHNTPE and a decamer for GTPCH-1. The substrate is located in a deep and narrow pocket at the interface between monomers. In PTPS, the active site is located at the interface of thr
Probab=97.41  E-value=0.0036  Score=40.72  Aligned_cols=105  Identities=19%  Similarity=0.124  Sum_probs=83.1

Q ss_pred             CEEEECCEEEEEECC----CCEEEEEEEEEEEEECCCCC----------CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             628961805877211----00234655789999638854----------3467799999998315426689999999999
Q gi|255764506|r   81 DMVLIKDISFFSYCE----HHILPIWGKIHLAYIPKKHV----------IGLSKLVRILEVYSRRLQIQERLTMQIAHAI  146 (205)
Q Consensus        81 ~mVvv~~I~f~S~CE----HHllPf~G~~~IaYiP~~~v----------iGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l  146 (205)
                      +.+.++|+.+++.+.    .+.++-...++|..-.+...          +.-..+.+++..+..+.+++|+++.+||..|
T Consensus         2 d~i~l~~l~~~~~~G~~~~e~~~~q~~~vdV~~~~d~~~a~~~d~l~~t~~y~~v~~~v~~~~~~~~liE~lae~ia~~i   81 (122)
T cd00651           2 DGVRVKDLLKVTRLGFVTLERTVGQIFEVDVTLSWDGKKAAASDDVATDTVYNTIYRLAKEYVEGSQLIERLAEEIAYLI   81 (122)
T ss_pred             CEEEEECCEEEEEEECCHHHHHCCCEEEEEEEEEECCCCCCCCCCHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             88999587999997088899830987999999996373001558888738999999999999736326999999999999


Q ss_pred             HHHCC--CCCEEEEEEEEEEEEEECCCCCCCCEEEEEEEEE
Q ss_conf             97327--3847999994884252238355998599967774
Q gi|255764506|r  147 ESSTD--SKGVAVLIEGQHMCMSMRGIKRDGLTTVTTAFTG  185 (205)
Q Consensus       147 ~~~l~--~~gv~V~i~A~H~Cm~~RGv~~~~s~~~T~~~~G  185 (205)
                      .+...  ...|.|.+...|.|+..|+|..+......+..+|
T Consensus        82 ~~~f~~~~~~v~v~v~kp~a~~~~~~v~~~~~~~~~~i~r~  122 (122)
T cd00651          82 AEHFLSSVAEVKVEEKKPHAVIPDRGVFKPTDSPGVTIERG  122 (122)
T ss_pred             HHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEEEECC
T ss_conf             98513545389999969999987556533346427999629


No 11 
>COG0780 Enzyme related to GTP cyclohydrolase I [General function prediction only]
Probab=97.34  E-value=0.0031  Score=41.16  Aligned_cols=82  Identities=18%  Similarity=0.199  Sum_probs=74.1

Q ss_pred             EEEECCEEEEEECCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             28961805877211002346557899996388543467799999998315426689999999999973273847999994
Q gi|255764506|r   82 MVLIKDISFFSYCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEG  161 (205)
Q Consensus        82 mVvv~~I~f~S~CEHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A  161 (205)
                      .+.+--=.|.|.|.=-=+|=+|.+.|-|+|++.++-+-.|-+...-|-.+--.+|..+++|++.|.+.++|+-+.|...-
T Consensus        41 ~~~l~~~ef~S~CpiTgqPD~~ti~I~Y~p~~~~ve~ksLk~yl~SFR~h~~fHE~c~~~I~~dl~~~l~P~~l~V~~~~  120 (149)
T COG0780          41 LVKLVSPEFKSLCPITGQPDFATIYIEYIPDKACVESKSLKLYLFSFRNHGIFHEQCANRIFNDLKALLKPEYLEVYGKF  120 (149)
T ss_pred             EEEEECCCCEECCCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEE
T ss_conf             89994162012587769997379999982751434168899999987431148999999999999987398789999998


Q ss_pred             EE
Q ss_conf             88
Q gi|255764506|r  162 QH  163 (205)
Q Consensus       162 ~H  163 (205)
                      .+
T Consensus       121 ~p  122 (149)
T COG0780         121 TP  122 (149)
T ss_pred             EC
T ss_conf             53


No 12 
>TIGR02750 TraN_Ftype type-F conjugative transfer system mating-pair stabilization protein TraN; InterPro: IPR014121   TraN is a large cysteine-rich outer membrane protein involved in the mating-pair stabilisation (adhesin) component of the F-type conjugative plasmid transfer system. TraN is believed to interact with the core type IV secretion system apparatus through the TraV protein , , ..
Probab=54.91  E-value=5.9  Score=20.86  Aligned_cols=16  Identities=44%  Similarity=0.563  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHCCCCC
Q ss_conf             7799999998315426
Q gi|255764506|r  119 SKLVRILEVYSRRLQI  134 (205)
Q Consensus       119 SKl~Riv~~~a~RlQ~  134 (205)
                      |||||||..-+++.||
T Consensus       592 SKLArIVQ~QG~~gQL  607 (683)
T TIGR02750       592 SKLARIVQEQGRKGQL  607 (683)
T ss_pred             HHHHHHHHHHCCCCCC
T ss_conf             0554576741788717


No 13 
>PRK11245 folX D-erythro-7,8-dihydroneopterin triphosphate 2'-epimerase; Provisional
Probab=52.04  E-value=21  Score=17.43  Aligned_cols=84  Identities=13%  Similarity=0.223  Sum_probs=55.8

Q ss_pred             CCEEEECCEEEEEEC---CC---CEEEEEEEEEEEEECC--------CCCCCHHHHHHHHHHH--HCCCCCHHHHHHHHH
Q ss_conf             762896180587721---10---0234655789999638--------8543467799999998--315426689999999
Q gi|255764506|r   80 QDMVLIKDISFFSYC---EH---HILPIWGKIHLAYIPK--------KHVIGLSKLVRILEVY--SRRLQIQERLTMQIA  143 (205)
Q Consensus        80 ~~mVvv~~I~f~S~C---EH---HllPf~G~~~IaYiP~--------~~viGlSKl~Riv~~~--a~RlQ~QErlT~qIa  143 (205)
                      .+.|.++|+.++..=   +|   +-+|+.=.+.+.|=.+        ...+--+++...+.-+  +++.++.|+|+.+||
T Consensus         5 ~d~I~I~~L~v~~~IGV~~~Er~~~Q~v~idl~i~~d~~~a~~sDdi~dtvdY~~i~~~i~~~v~~~~f~LlE~LA~~ia   84 (120)
T PRK11245          5 AAIIRIKNLRLRTFIGIKEEEINNRQDVVINVTIHYPADKARTSDDIDDALNYRTITKNIIQHVENNRFSLLEKLTQDVL   84 (120)
T ss_pred             CCEEEECCCEEEEEECCCHHHHCCCCEEEEEEEEECCCHHHCCCCCHHHHEEHHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             55899938799999778989975698899999992374131035778880479999999999996497123999999999


Q ss_pred             HHHHHHCCCCCEEEEEEEEE
Q ss_conf             99997327384799999488
Q gi|255764506|r  144 HAIESSTDSKGVAVLIEGQH  163 (205)
Q Consensus       144 ~~l~~~l~~~gv~V~i~A~H  163 (205)
                      +.+.+.-....|-|.++=-|
T Consensus        85 ~~ll~~~~v~~v~v~v~KP~  104 (120)
T PRK11245         85 DIAREHPWVTYAEVEIDKPH  104 (120)
T ss_pred             HHHHCCCCCCEEEEEEECCH
T ss_conf             99964689868999998953


No 14 
>PRK11792 queF 7-cyano-7-deazaguanine reductase; Provisional
Probab=50.88  E-value=22  Score=17.27  Aligned_cols=69  Identities=23%  Similarity=0.338  Sum_probs=57.3

Q ss_pred             EEEECCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             87721100234655789999638854346779999999831542668999999999997327384799999
Q gi|255764506|r   90 FFSYCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIE  160 (205)
Q Consensus        90 f~S~CEHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~  160 (205)
                      |.|.|..-=+|=+|.+.|-|-..+  +--..|-+.+--|-.-----|.-..+|...|++.+.|.-..|...
T Consensus       177 lRSnCPVT~QPDWatI~I~y~G~~--Id~~~Ll~YliSfR~h~~FHE~CvE~If~dl~~~~~p~~L~V~~~  245 (274)
T PRK11792        177 LKSNCLVTGQPDWGSVQIRYRGKK--IDREGLLRYLISFRQHNEFHEQCVERIFTDIMRFCQPEKLTVYAR  245 (274)
T ss_pred             HHHCCCCCCCCCCEEEEEEEECCC--CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             530687779998189999996874--699999999998721464089999999999997569877999999


No 15 
>KOG3203 consensus
Probab=44.96  E-value=25  Score=16.99  Aligned_cols=46  Identities=24%  Similarity=0.327  Sum_probs=20.3

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHC--------CCCCEEEEEEEEEEEEE
Q ss_conf             99999983154266899999999999732--------73847999994884252
Q gi|255764506|r  122 VRILEVYSRRLQIQERLTMQIAHAIESST--------DSKGVAVLIEGQHMCMS  167 (205)
Q Consensus       122 ~Riv~~~a~RlQ~QErlT~qIa~~l~~~l--------~~~gv~V~i~A~H~Cm~  167 (205)
                      +|+=.++..+-|.-+||+.+||..|...-        +..+..|+++|++.-|+
T Consensus        20 aRvW~vvDa~~q~lGrLAs~ia~~L~GkhKPiYhP~~DcGD~VVV~N~~~Ia~s   73 (165)
T KOG3203          20 ARVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKIAFS   73 (165)
T ss_pred             HHHHEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCHHHEEC
T ss_conf             665125334567568999999999860467764876677887999545564412


No 16 
>PTZ00126 tyrosyl-tRNA synthetase; Provisional
Probab=44.86  E-value=16  Score=18.17  Aligned_cols=71  Identities=10%  Similarity=0.107  Sum_probs=55.2

Q ss_pred             EEEECCEEEEEECCCCEEEEEEEEEEEEECC-CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCC
Q ss_conf             2896180587721100234655789999638-8543467799999998315426689999999999973273
Q gi|255764506|r   82 MVLIKDISFFSYCEHHILPIWGKIHLAYIPK-KHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDS  152 (205)
Q Consensus        82 mVvv~~I~f~S~CEHHllPf~G~~~IaYiP~-~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~  152 (205)
                      +-.+.+-|+..+++|+++|.+|...|-=-++ |--+-.+.+..+..-|...---.-.|-.-+|++|.+.|+|
T Consensus       303 p~~ve~NPvLe~~kyvIfP~~~~f~V~R~ek~GG~~ty~s~eeLe~dy~~g~LHP~DLK~ava~~Ln~iL~P  374 (399)
T PTZ00126        303 PGVIEGNPIIAYFKSIVFPKFNSFTIERKEKNGGDVTYNTYEELEADYLSGALHPADLKPALAKYLNLMLQP  374 (399)
T ss_pred             CCCCCCCCHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             988687839999887320457835885675558877155899999999759989899999999999999999


No 17 
>PRK12355 conjugal transfer mating pair stabilization protein TraN; Reviewed
Probab=43.99  E-value=12  Score=18.95  Aligned_cols=16  Identities=44%  Similarity=0.580  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHCCCCCH
Q ss_conf             77999999983154266
Q gi|255764506|r  119 SKLVRILEVYSRRLQIQ  135 (205)
Q Consensus       119 SKl~Riv~~~a~RlQ~Q  135 (205)
                      |||+|||+--+|. ||.
T Consensus       532 SkLArIiqeQgr~-QLg  547 (612)
T PRK12355        532 SKLARIIQEQGRP-QLG  547 (612)
T ss_pred             CHHHHHHHHHHHH-HHC
T ss_conf             6999999998599-748


No 18 
>TIGR00313 cobQ cobyric acid synthase CobQ; InterPro: IPR004459 Cobyric acid synthase (CobQ) catalyses amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide in the biosynthesis of cobalamin. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolysed for each amidation .; GO: 0003824 catalytic activity, 0009236 cobalamin biosynthetic process.
Probab=41.99  E-value=16  Score=18.23  Aligned_cols=29  Identities=17%  Similarity=0.290  Sum_probs=13.8

Q ss_pred             CEEEEEEEEEEECCCHHHHHHHHHHHCCCC
Q ss_conf             859996777443068899999999832688
Q gi|255764506|r  176 LTTVTTAFTGEFSRDKGKTDFFLKMTHNQR  205 (205)
Q Consensus       176 s~~~T~~~~G~F~~d~~~r~ef~~li~~~r  205 (205)
                      -...-+++.|.| +|-..|+.|.+++|+||
T Consensus       438 g~~~GtYlHGlF-~N~~fRry~~N~LR~Rk  466 (502)
T TIGR00313       438 GNVWGTYLHGLF-ENYEFRRYFLNLLRKRK  466 (502)
T ss_pred             CEEEECHHCCCH-HHHHHHHHHHHHHCCCC
T ss_conf             103121003300-11236667763100026


No 19 
>PRK05337 beta-hexosaminidase; Provisional
Probab=41.77  E-value=31  Score=16.40  Aligned_cols=125  Identities=17%  Similarity=0.167  Sum_probs=69.2

Q ss_pred             HHHHHHHCCCCC--------C-------HHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCC---CCCCCCCCEEEECC
Q ss_conf             999998147888--------8-------10011267899999999976086531234432025---66556676289618
Q gi|255764506|r   26 RVILRWIGDDPD--------R-------EGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHF---GEASKYQDMVLIKD   87 (205)
Q Consensus        26 ~~lL~~LGeDp~--------r-------egL~~TP~Rvak~~~e~~~Gy~~~~~~~~~~~~~~---~~~~~~~~mVvv~~   87 (205)
                      ..-|+++|.|.+        .       =...+.|+.|+++=..+.+|+...--....+-|+-   ...+.|-++.++ +
T Consensus       107 a~eL~a~Gin~nfAPVlDl~~~~~vIg~RsFg~dp~~V~~la~a~i~G~~~~Gv~~~~KHFPGHG~~~~DSH~~lp~~-~  185 (336)
T PRK05337        107 AAELRACGIDLSFAPVLDLDGISAVIGDRAFHRDPQVVAALASAFIDGMHAAGMAATGKHFPGHGAVEADSHVETPVD-E  185 (336)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEHHCCCCCCCCCCCCCCCCCCCC-C
T ss_conf             999998098844065504789986657888889999999999999998885693022121788888778887677777-7


Q ss_pred             EEEEEECCCCEEEE----------EEEEEEEEEC-CCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEE
Q ss_conf             05877211002346----------5578999963-885434677999999983154266899999999999732738479
Q gi|255764506|r   88 ISFFSYCEHHILPI----------WGKIHLAYIP-KKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVA  156 (205)
Q Consensus        88 I~f~S~CEHHllPf----------~G~~~IaYiP-~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~  156 (205)
                      -+.-.+.++.|+||          .-.+||.|-- +....++|+..                   |-+-|-+.++=+||.
T Consensus       186 ~s~~~l~~~Dl~PF~~li~~~~~~vM~aHv~yp~iD~~PAs~S~~~-------------------i~~iLR~~lgF~Gvi  246 (336)
T PRK05337        186 RPLEEIRAEDMAPFRALIDGGLDAVMPAHVIYPQVDPQPAGFSRYW-------------------LQDILRQELGFDGVI  246 (336)
T ss_pred             CCHHHHHHCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCHHH-------------------HHHHHHHHCCCCCEE
T ss_conf             7899998436478999986698616762433466689877379999-------------------999999755998489


Q ss_pred             EEEEEEEEEEEECCCCCCC
Q ss_conf             9999488425223835599
Q gi|255764506|r  157 VLIEGQHMCMSMRGIKRDG  175 (205)
Q Consensus       157 V~i~A~H~Cm~~RGv~~~~  175 (205)
                      +.     -|+.|.|+....
T Consensus       247 iS-----DDL~M~a~~~~~  260 (336)
T PRK05337        247 FS-----DDLSMEGAAVAG  260 (336)
T ss_pred             EC-----CCCCCCCHHHCC
T ss_conf             76-----275861113249


No 20 
>PRK11593 folB bifunctional dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase; Provisional
Probab=40.60  E-value=32  Score=16.28  Aligned_cols=80  Identities=14%  Similarity=0.203  Sum_probs=50.2

Q ss_pred             EEEECCEEEEEEC------CCCEEEEEEEEEEEEEC------C--CCCCCHHHHHHHHHHH--HCCCCCHHHHHHHHHHH
Q ss_conf             2896180587721------10023465578999963------8--8543467799999998--31542668999999999
Q gi|255764506|r   82 MVLIKDISFFSYC------EHHILPIWGKIHLAYIP------K--KHVIGLSKLVRILEVY--SRRLQIQERLTMQIAHA  145 (205)
Q Consensus        82 mVvv~~I~f~S~C------EHHllPf~G~~~IaYiP------~--~~viGlSKl~Riv~~~--a~RlQ~QErlT~qIa~~  145 (205)
                      .|.++|+.++...      -..-+||.=.+.+.+-.      +  ...+--+.+...+..+  +++..+.|.|+.+||+.
T Consensus         3 ~I~I~~L~v~~~iGv~~~Er~~~Q~~~idl~l~~d~~~a~~sDdl~~tvdY~~v~~~i~~~~~~~~~~LiEtLAe~ia~~   82 (119)
T PRK11593          3 IVFIEQLSVITTIGVYDWEQTIEQKLVFDIEMAWDNRKAAKSDDVADCLSYADIAETVISHVEGARFALVERVAEEVAEL   82 (119)
T ss_pred             EEEECCCEEEEEECCCHHHHCCCCEEEEEEEEEECCHHHCCCCCHHHCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             99997879999978898996799779999999417246256875443248999999999999679914199999999999


Q ss_pred             HHHHCCCCCEEEEEEE
Q ss_conf             9973273847999994
Q gi|255764506|r  146 IESSTDSKGVAVLIEG  161 (205)
Q Consensus       146 l~~~l~~~gv~V~i~A  161 (205)
                      |.+.-+...|-|.++-
T Consensus        83 ll~~f~v~~v~v~v~K   98 (119)
T PRK11593         83 LLARFNSPWVRIKLSK   98 (119)
T ss_pred             HHHHCCCCEEEEEEEC
T ss_conf             9965897679999989


No 21 
>pfam09710 Trep_dent_lipo Treponema clustered lipoprotein (Trep_dent_lipo). This entry represents a family of six predicted lipoproteins from a region of about 20 tandemly arranged genes in the Treponema denticola genome. Two other neighbouring genes share the lipoprotein signal peptide region but do not show more extensive homology. The function of this locus is unknown.
Probab=35.76  E-value=12  Score=19.00  Aligned_cols=75  Identities=13%  Similarity=0.104  Sum_probs=52.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHH-HHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEE
Q ss_conf             3666522489999999999998147888810011267899999-99997608653123443202566556676289
Q gi|255764506|r   10 NMKLKKPTVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSY-KELFAGYKQIPTTQDTSRFHFGEASKYQDMVL   84 (205)
Q Consensus        10 ~~~~~~~~~~~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~-~e~~~Gy~~~~~~~~~~~~~~~~~~~~~~mVv   84 (205)
                      +.++-....+.++.-|-..+...-.||+++.+..-=+|+..-| .+-+.+|.+.|...+.-..-++.+.|||+-+|
T Consensus       160 E~ni~~i~~~~i~~qvHG~i~e~e~d~~kd~~IklFE~Y~n~~Tk~~~~~~~~y~y~vlDYVkGNFTnSGyDEYiV  235 (394)
T pfam09710       160 ELNIGVINEELIENQVHGSVYEMENDPKKDEMIKLFEDYENTYTKVKTNKYKQYDYRVLDYVKGNFTNSGYDEYIV  235 (394)
T ss_pred             CCCEEEECHHHHHHHHCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCCCCCEEEE
T ss_conf             4870365035554320326765134857455568899875420231005656675587675324666788643899


No 22 
>pfam05997 Nop52 Nucleolar protein,Nop52. Nop52 believed to be involved in the generation of 28S rRNA.
Probab=34.39  E-value=29  Score=16.55  Aligned_cols=16  Identities=31%  Similarity=0.372  Sum_probs=6.0

Q ss_pred             CCCHHHHHHHHHHHHH
Q ss_conf             2248999999999999
Q gi|255764506|r   15 KPTVEEAKEAIRVILR   30 (205)
Q Consensus        15 ~~~~~~i~~av~~lL~   30 (205)
                      +..++++-+.++..|.
T Consensus        14 k~~Rd~al~~L~~~L~   29 (212)
T pfam05997        14 KETRDKALRSLRKYLS   29 (212)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             1079999999999998


No 23 
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD; InterPro: IPR012760   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.    With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .   This entry represents the C-terminal region of sigma 70 (RpoD) which contains the well-conserved regions 2, 3 and 4. Region 2 of sigma-70 is the most conserved region of the entire protein. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime , . The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation , . Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .Region 4 is involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=33.82  E-value=33  Score=16.23  Aligned_cols=38  Identities=26%  Similarity=0.398  Sum_probs=29.4

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCHHHCC----CHHHHHHHHH
Q ss_conf             2489999999999998147888810011----2678999999
Q gi|255764506|r   16 PTVEEAKEAIRVILRWIGDDPDREGLKD----TPDRVIKSYK   53 (205)
Q Consensus        16 ~~~~~i~~av~~lL~~LGeDp~regL~~----TP~Rvak~~~   53 (205)
                      .+++++...-+.|+..+|.||+.|.|.+    ++++|..-..
T Consensus        84 ETINk~~~~~R~l~Q~~Gr~Pt~EelAe~~g~~~~Kv~~i~~  125 (240)
T TIGR02393        84 ETINKLIKAERKLLQELGREPTDEELAERMGLPVEKVREIKK  125 (240)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             788899999899998728899877899870899899999998


No 24 
>KOG3230 consensus
Probab=32.40  E-value=21  Score=17.38  Aligned_cols=31  Identities=26%  Similarity=0.378  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCHHHCCCHH
Q ss_conf             22489999999999998147888810011267
Q gi|255764506|r   15 KPTVEEAKEAIRVILRWIGDDPDREGLKDTPD   46 (205)
Q Consensus        15 ~~~~~~i~~av~~lL~~LGeDp~regL~~TP~   46 (205)
                      ..+.++.++-|...|..||.|.+.+ |..+|.
T Consensus       153 ~edEEEtd~lvnqVLDEiGvdl~~q-L~~~P~  183 (224)
T KOG3230         153 DEDEEETDDLVNQVLDEIGVDLASQ-LSSLPS  183 (224)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCHHHH-HCCCCC
T ss_conf             3206779999999999974118888-603763


No 25 
>TIGR01754 flav_RNR ribonucleotide reductase-associated flavodoxin, putative; InterPro: IPR010088   This entry represents a family of proteins found immediately downstream of ribonucleotide reductase genes in Xyella fastidiosa and some Gram-positive bacteria. It appears to be a highly divergent flavodoxin of the short chain type, more like the flavodoxins of the sulphate-reducing genus Desulfovibrio than like the NifF flavodoxins associated with nitrogen fixation..
Probab=30.76  E-value=31  Score=16.34  Aligned_cols=59  Identities=15%  Similarity=0.175  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHCCCCCEEEE-EEEEEEEEEECCCCCCCCEEEEEEEEEEECCC-----HHHHHHHHHH
Q ss_conf             99999999973273847999-99488425223835599859996777443068-----8999999998
Q gi|255764506|r  139 TMQIAHAIESSTDSKGVAVL-IEGQHMCMSMRGIKRDGLTTVTTAFTGEFSRD-----KGKTDFFLKM  200 (205)
Q Consensus       139 T~qIa~~l~~~l~~~gv~V~-i~A~H~Cm~~RGv~~~~s~~~T~~~~G~F~~d-----~~~r~ef~~l  200 (205)
                      |++||+.|.+.|..+|+-|= |+-.=.-..   -..-+-..-+-.++|.|-.|     ...+.+...|
T Consensus        14 T~eVA~~I~~~l~~~G~eVDW~~~r~~~La---~~pldPe~ydL~~LGtwT~~~GrTP~e~KdFiaEl   78 (145)
T TIGR01754        14 TKEVADIIRDILEKDGHEVDWVEFRISTLA---DAPLDPEDYDLYLLGTWTVERGRTPDEMKDFIAEL   78 (145)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEEECCHHHH---CCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHH
T ss_conf             789999999999847977676640004642---46789986315774312235789966689999999


No 26 
>cd02691 PurM-like2 AIR synthase (PurM) related protein, archaeal subgroup 2 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two conserved domains and seem to dimerize. The N-terminal domain forms the dimer interface and is a putative ATP binding domain.
Probab=30.61  E-value=47  Score=15.29  Aligned_cols=15  Identities=13%  Similarity=0.448  Sum_probs=5.2

Q ss_pred             HHHHHHHHCCCCCEE
Q ss_conf             999999732738479
Q gi|255764506|r  142 IAHAIESSTDSKGVA  156 (205)
Q Consensus       142 Ia~~l~~~l~~~gv~  156 (205)
                      |...+....+.-||.
T Consensus       107 i~~~m~~aa~~~gV~  121 (346)
T cd02691         107 FTAGVTAVSEATGVP  121 (346)
T ss_pred             HHHHHHHHHHHCCCC
T ss_conf             999999999985998


No 27 
>COG0399 WecE Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]
Probab=27.57  E-value=53  Score=14.96  Aligned_cols=87  Identities=21%  Similarity=0.277  Sum_probs=53.2

Q ss_pred             CCCEEEECCEEEEEECCCCEEEEEEEE----------EEEEECC----CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             676289618058772110023465578----------9999638----85434677999999983154266899999999
Q gi|255764506|r   79 YQDMVLIKDISFFSYCEHHILPIWGKI----------HLAYIPK----KHVIGLSKLVRILEVYSRRLQIQERLTMQIAH  144 (205)
Q Consensus        79 ~~~mVvv~~I~f~S~CEHHllPf~G~~----------~IaYiP~----~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~  144 (205)
                      .++||+-.|=.++.-|.  .+.++|..          .+||=-+    ---+|+.+|.|+-++..+|-.+-++..+..++
T Consensus       190 EGGav~tnd~ela~k~~--~lr~hG~~~~~~~~y~~~~~G~N~rm~~iqAAigl~QL~~l~~~~~~R~~~a~~Y~~~l~~  267 (374)
T COG0399         190 EGGAVVTNDEELAEKAR--SLRNHGLSRDAVFKYLHEELGYNYRLTEIQAAIGLAQLERLDEINERRREIAQIYAEALKG  267 (374)
T ss_pred             CCEEEEECCHHHHHHHH--HHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             75079838899999999--9998376778665643521330038779999999999988899999999999999998610


Q ss_pred             H--HHHHCCCCCEEEEEEEEEEEEEECC
Q ss_conf             9--9973273847999994884252238
Q gi|255764506|r  145 A--IESSTDSKGVAVLIEGQHMCMSMRG  170 (205)
Q Consensus       145 ~--l~~~l~~~gv~V~i~A~H~Cm~~RG  170 (205)
                      .  +.-...+.+.   ..+.|++....-
T Consensus       268 ~~~~~~p~~~~~~---~~~~~~~~i~~~  292 (374)
T COG0399         268 LPGITLPPEPDGA---VHAWHLYTILVD  292 (374)
T ss_pred             CCCCCCCCCCCCC---EEEEEEEEEEEC
T ss_conf             7874335789876---123036689826


No 28 
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=27.08  E-value=38  Score=15.84  Aligned_cols=76  Identities=14%  Similarity=0.119  Sum_probs=32.7

Q ss_pred             HHHHHHHHCCCCCCHHHCCC----HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEEECCEEEEEECCCCEEE
Q ss_conf             99999981478888100112----67899999999976086531234432025665566762896180587721100234
Q gi|255764506|r   25 IRVILRWIGDDPDREGLKDT----PDRVIKSYKELFAGYKQIPTTQDTSRFHFGEASKYQDMVLIKDISFFSYCEHHILP  100 (205)
Q Consensus        25 v~~lL~~LGeDp~regL~~T----P~Rvak~~~e~~~Gy~~~~~~~~~~~~~~~~~~~~~~mVvv~~I~f~S~CEHHllP  100 (205)
                      ...+|+.|.++..++.+..-    .+|....|.....| +.+....+....+.-+..+|-.-.-.-+..-+++|||| .|
T Consensus        89 ~~~~l~~l~~~~G~~~l~~~l~~r~~~~~~~~~~~~~~-~~~~ee~~e~Lv~l~~~~gy~~e~~~~~~~~~~l~e~n-CP  166 (218)
T COG2345          89 ALALLDALEETGGEEALNAFLEKRAQAIGAQYRPAMGG-DADLEEKVERLVELLSDLGYMPELRPVDNGRVQLIEHN-CP  166 (218)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECC-CC
T ss_conf             99999999985459999999999999999997624788-89999999999999985786654523589863887418-82


Q ss_pred             EE
Q ss_conf             65
Q gi|255764506|r  101 IW  102 (205)
Q Consensus       101 f~  102 (205)
                      |+
T Consensus       167 i~  168 (218)
T COG2345         167 IS  168 (218)
T ss_pred             HH
T ss_conf             38


No 29 
>cd00915 MD-1_MD-2 MD-1 and MD-2 are cofactors required for LPS signaling through cell surface receptors. MD-2 and its binding partner, Toll-like receptor 4 (TLR4), are essential for the innate immune responses of mammalian cells to bacterial lipopolysaccharide (LPS); MD-2 directly binds the lipid A moiety of LPS. The TLR4-like receptor, RP105, which mediates LPS-induced lymphocyte proliferation, interacts with MD-1; MD-1 enhances RP105-mediated LPS-induced growth of B cells. These proteins belong to the ML domain family.
Probab=26.79  E-value=54  Score=14.90  Aligned_cols=13  Identities=23%  Similarity=0.496  Sum_probs=9.3

Q ss_pred             EEEEEEEEECCCC
Q ss_conf             5578999963885
Q gi|255764506|r  102 WGKIHLAYIPKKH  114 (205)
Q Consensus       102 ~G~~~IaYiP~~~  114 (205)
                      .|.+|++|||..-
T Consensus        36 ~~~l~~~~I~R~d   48 (130)
T cd00915          36 NGFIRIKFILRRD   48 (130)
T ss_pred             CEEEEEEEEEHHH
T ss_conf             4699999988323


No 30 
>pfam09626 DHC Dihaem cytochrome c. Dihaem cytochrome c (DHC) is a soluble c-type cytochrome that folds into two distinct domains, each binding a single haem group and connected by a small linker region. Despite little sequence similarity, the N-terminal domain (residues 12-75) is a class I type cytochrome c, that binds one of the haems, but the domain surrounding the other haem is structurally unique. DHC binds electrostatically to an oxygen-binding protein, sphaeroides haem protein (SHP), as a component of a conserved electron transfer pathway. DHC acts as the physiological electron donor for SHP during phototrophic growth. In certain species DHC is found upstream of pfam01292.
Probab=26.43  E-value=55  Score=14.84  Aligned_cols=46  Identities=13%  Similarity=0.312  Sum_probs=27.7

Q ss_pred             EEEEEEEECC-------CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             5789999638-------85434677999999983154266899999999999732738
Q gi|255764506|r  103 GKIHLAYIPK-------KHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSK  153 (205)
Q Consensus       103 G~~~IaYiP~-------~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~  153 (205)
                      |.||+||=|+       .+|+     ..+-++|+....+-+.-..+|-+.|.....+.
T Consensus         6 gsCH~AyPP~lLP~~SW~~im-----~~l~~HFG~~asld~~~~~~I~~yL~~naa~~   58 (118)
T pfam09626         6 GSCHMAYPPELLPAASWRKIM-----ADLDDHFGTDASLDPPTRALIWAYLRANAADL   58 (118)
T ss_pred             CCCCCCCCCCCCCHHHHHHHH-----HHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             027740694528999999999-----73775258686878789999999999825334


No 31 
>PRK10557 hypothetical protein; Provisional
Probab=25.81  E-value=57  Score=14.77  Aligned_cols=19  Identities=5%  Similarity=-0.080  Sum_probs=9.3

Q ss_pred             CCCEEEEEEEEEEECCCHH
Q ss_conf             9985999677744306889
Q gi|255764506|r  174 DGLTTVTTAFTGEFSRDKG  192 (205)
Q Consensus       174 ~~s~~~T~~~~G~F~~d~~  192 (205)
                      ..+...|..+.|.-+.+|.
T Consensus       146 ~~~~~~~v~L~~~~~~~P~  164 (178)
T PRK10557        146 GFSPVLTLNLRAASKGEPQ  164 (178)
T ss_pred             CCCEEEEEEEEEECCCCCC
T ss_conf             8843799998552034998


No 32 
>PRK05568 flavodoxin; Provisional
Probab=24.90  E-value=56  Score=14.79  Aligned_cols=29  Identities=10%  Similarity=-0.008  Sum_probs=19.7

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCHHHCCCH
Q ss_conf             48999999999999814788881001126
Q gi|255764506|r   17 TVEEAKEAIRVILRWIGDDPDREGLKDTP   45 (205)
Q Consensus        17 ~~~~i~~av~~lL~~LGeDp~regL~~TP   45 (205)
                      +.+++.+++.+=|+.-|.+..--.+.++.
T Consensus        14 nTe~mA~~Iaegl~~~Gv~V~~~~~~~~~   42 (142)
T PRK05568         14 NTEAMANLIAEGAKENGLEVKLLNVSEAS   42 (142)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEEEECCCC
T ss_conf             49999999999998669839999800499


No 33 
>pfam06962 rRNA_methylase Putative rRNA methylase. This family contains a number of putative rRNA methylases. Note that many family members are hypothetical proteins.
Probab=24.62  E-value=59  Score=14.63  Aligned_cols=42  Identities=14%  Similarity=0.338  Sum_probs=26.4

Q ss_pred             EEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             789999638854346779999999831542668999999999997327384799999
Q gi|255764506|r  104 KIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIE  160 (205)
Q Consensus       104 ~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~  160 (205)
                      .-+.||+|++-               +....+-.-|-.=-++..+.|.|.|+.+++-
T Consensus        51 ~FNLGYLPggD---------------k~i~T~~~tTi~Al~~al~lL~~gG~i~i~~   92 (140)
T pfam06962        51 IFNLGYLPGGD---------------KSITTKPDTTLEAIKKLLELLKPGGLIILVI   92 (140)
T ss_pred             EEECCCCCCCC---------------CCCEECCHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             99667688999---------------8758777209999999999636698999999


No 34 
>cd05087 PTKc_Aatyk1_Aatyk3 Catalytic Domain of the Protein Tyrosine Kinases, Apoptosis-associated tyrosine kinases 1 and 3. Protein Tyrosine Kinase (PTK) family; Apoptosis-associated tyrosine kinase 1 (Aatyk1) and Aatyk3; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Aatyk1 and Aatyk3 are members of the Aatyk subfamily of proteins. Aatyk3 is a receptor kinase containing a transmembrane segment and a long C-terminal cytoplasmic tail with a catalytic domain. Aatyk1 has a similar domain arrangement but without the transmembrane segment and is thus, a cytoplasmic (or nonreceptor) kinase. The expression of Aatyk1 (also referred simply as Aatyk) is upregulated during growth arrest and apoptosis in myeloid cells
Probab=24.46  E-value=59  Score=14.66  Aligned_cols=47  Identities=15%  Similarity=0.277  Sum_probs=23.2

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCC
Q ss_conf             999638854346779999999831542668999999999997327384
Q gi|255764506|r  107 LAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKG  154 (205)
Q Consensus       107 IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~g  154 (205)
                      .-|.|+|.+-.+=+-.|..+....-+....++..|||.++.- |+.++
T Consensus        74 ~Ey~~~GsL~~~l~~~~~~~~~~~~~~~~~~~~~qia~gl~y-LH~~~  120 (269)
T cd05087          74 MEFCPLGDLKGYLRSCRAAELMTPDPRTLQRMACEIASGLLH-LHKHN  120 (269)
T ss_pred             EECCCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHH-HHHCC
T ss_conf             981689869999874454455783899999999999999999-95299


No 35 
>TIGR02026 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase; InterPro: IPR011772    This entry respresents the cobalamin-dependent oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under anaerobic conditions . This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under anaerobic conditions (a separate enzyme, AcsF, acts under aerobic conditions). This entry identifies two clades of sequences, one from photosynthetic, non-cyanobacterial bacteria and another including Synechocystis and several non-photosynthetic bacteria. The function of the Synechocystis gene is supported by gene clustering with other photosynthetic genes, so the purpose of the gene in the non-photosynthetic bacteria is uncertain. Note that homologues of this gene are not found in plants which rely solely on the aerobic cyclase.; GO: 0016709 oxidoreductase activity acting on paired donors with incorporation or reduction of molecular oxygen NADH or NADPH as one donor and incorporation of one atom of oxygen, 0050661 NADP binding, 0015995 chlorophyll biosynthetic process.
Probab=23.46  E-value=63  Score=14.49  Aligned_cols=47  Identities=34%  Similarity=0.478  Sum_probs=38.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHH-HCCCHHHHHHHHHHHH
Q ss_conf             1013666522489999999999998147888810-0112678999999999
Q gi|255764506|r    7 GVFNMKLKKPTVEEAKEAIRVILRWIGDDPDREG-LKDTPDRVIKSYKELF   56 (205)
Q Consensus         7 ~~~~~~~~~~~~~~i~~av~~lL~~LGeDp~reg-L~~TP~Rvak~~~e~~   56 (205)
                      +-|=++++....+.++++.+.+|.+   |||--. +.=||-|.+..|.++-
T Consensus       346 A~fi~g~e~~~~~~~~etyr~~ldw---~PD~~~w~~yTPwpft~lf~~l~  393 (506)
T TIGR02026       346 AQFIVGLENETDETLEETYRQLLDW---DPDLANWLMYTPWPFTSLFEELS  393 (506)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCC---CCCHHHHCCCCCCCCHHHHHHHC
T ss_conf             0024254358756899999997337---83324214558987636788630


No 36 
>pfam08879 WRC WRC. The WRC domain, named after the conserved Trp-Arg-Cys motif, contains two distinctive features: a putative nuclear localisation signal and a zinc-finger motif (C3H). It is suggested that the WRC domain functions in DNA binding.
Probab=23.19  E-value=16  Score=18.17  Aligned_cols=12  Identities=25%  Similarity=0.382  Sum_probs=9.4

Q ss_pred             EEEEECCCCEEE
Q ss_conf             587721100234
Q gi|255764506|r   89 SFFSYCEHHILP  100 (205)
Q Consensus        89 ~f~S~CEHHllP  100 (205)
                      +-.++||+||.-
T Consensus        23 ~~~~~Ce~H~~~   34 (46)
T pfam08879        23 PGKKLCERHLHR   34 (46)
T ss_pred             CCCCHHHHHHHH
T ss_conf             870188998860


No 37 
>TIGR00083 ribF riboflavin biosynthesis protein RibF; InterPro: IPR002606   Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme , the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family . The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases .   This entry represents the bifunctional enzyme, FAD synthetase / riboflavin kinase.; GO: 0003919 FMN adenylyltransferase activity, 0008531 riboflavin kinase activity, 0009231 riboflavin biosynthetic process.
Probab=22.46  E-value=66  Score=14.37  Aligned_cols=42  Identities=12%  Similarity=0.033  Sum_probs=31.6

Q ss_pred             HHCCCCCCCCCCEEEECCEEEEEECCCCEE--EEEEEEEEEEEC
Q ss_conf             202566556676289618058772110023--465578999963
Q gi|255764506|r   70 RFHFGEASKYQDMVLIKDISFFSYCEHHIL--PIWGKIHLAYIP  111 (205)
Q Consensus        70 ~~~~~~~~~~~~mVvv~~I~f~S~CEHHll--Pf~G~~~IaYiP  111 (205)
                      .|+.-|-.=.+.++.++.-...-.-.-|=.  ||.|+++|||.|
T Consensus       189 GFPTANi~L~~~~~~~~~g~y~~~~~~~~~dv~~~GV~NiG~RP  232 (296)
T TIGR00083       189 GFPTANIKLKNQVLPLKGGYYVVVVLLNGEDVPYPGVGNIGKRP  232 (296)
T ss_pred             CCCCCCCCCCCCEEECCCEEEEEEEEECCCEEEEEEEEECCCCC
T ss_conf             47525645677543047158999985176000330134508876


No 38 
>pfam01340 MetJ Met Apo-repressor, MetJ.
Probab=22.34  E-value=36  Score=15.99  Aligned_cols=16  Identities=44%  Similarity=0.619  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHHHCCCC
Q ss_conf             9999999999814788
Q gi|255764506|r   21 AKEAIRVILRWIGDDP   36 (205)
Q Consensus        21 i~~av~~lL~~LGeDp   36 (205)
                      +-+.++.+++++|.||
T Consensus        84 iP~~ak~~m~~~Gi~~   99 (104)
T pfam01340        84 IPEAAKEIMRELGIDP   99 (104)
T ss_pred             CCHHHHHHHHHHCCCH
T ss_conf             6099999999919983


No 39 
>pfam08921 DUF1904 Domain of unknown function (DUF1904). This domain is found in a set of hypothetical bacterial proteins.
Probab=22.34  E-value=53  Score=14.95  Aligned_cols=37  Identities=19%  Similarity=0.299  Sum_probs=29.7

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             9998315426689999999999973273847999994
Q gi|255764506|r  125 LEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEG  161 (205)
Q Consensus       125 v~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A  161 (205)
                      |-||.|-.++|.++.+-|-+++.+..+-..|+|.-.+
T Consensus        59 VlWF~R~qe~~d~vA~~It~~v~~~~~~~~V~V~F~~   95 (107)
T pfam08921        59 VLWFPRDQETQDLVAQIITEAVRAVNGLQDVAVIFTA   95 (107)
T ss_pred             EEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEE
T ss_conf             9980389899999999999999843899739999996


No 40 
>PRK09271 flavodoxin; Provisional
Probab=22.32  E-value=61  Score=14.56  Aligned_cols=21  Identities=14%  Similarity=0.061  Sum_probs=15.7

Q ss_pred             CHHHHHHHHHHHHHHHCCCCC
Q ss_conf             489999999999998147888
Q gi|255764506|r   17 TVEEAKEAIRVILRWIGDDPD   37 (205)
Q Consensus        17 ~~~~i~~av~~lL~~LGeDp~   37 (205)
                      +.+++++.|.+-|+..|-+++
T Consensus        13 NTE~vA~~I~~~l~~~G~eV~   33 (160)
T PRK09271         13 NTREVARMIAARCEEAGHAVT   33 (160)
T ss_pred             CHHHHHHHHHHHHHHCCCEEE
T ss_conf             689999999999997698237


No 41 
>TIGR00632 vsr DNA mismatch endonuclease Vsr; InterPro: IPR004603   This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine . GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine . The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology . ; GO: 0004519 endonuclease activity, 0006298 mismatch repair.
Probab=21.88  E-value=27  Score=16.80  Aligned_cols=33  Identities=39%  Similarity=0.656  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHCC----C---CCCHHHCCCHHHHHHHH
Q ss_conf             999999999998147----8---88810011267899999
Q gi|255764506|r   20 EAKEAIRVILRWIGD----D---PDREGLKDTPDRVIKSY   52 (205)
Q Consensus        20 ~i~~av~~lL~~LGe----D---p~regL~~TP~Rvak~~   52 (205)
                      ++|.+++++|-+||.    |   -+++||.+||.=|.+.|
T Consensus        42 ~pE~~l~s~L~~lGlryRkdfl~~~~~G~~g~PD~vf~~~   81 (143)
T TIGR00632        42 KPEKALASLLFALGLRYRKDFLLRDKDGLPGTPDIVFKEY   81 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCC
T ss_conf             1789999999998899888987523689854675443473


No 42 
>cd00490 Met_repressor_MetJ Met Repressor, MetJ.  MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine.  MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence.  MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=21.45  E-value=39  Score=15.75  Aligned_cols=16  Identities=31%  Similarity=0.547  Sum_probs=5.4

Q ss_pred             HHHHHHHHHHHHCCCC
Q ss_conf             9999999999814788
Q gi|255764506|r   21 AKEAIRVILRWIGDDP   36 (205)
Q Consensus        21 i~~av~~lL~~LGeDp   36 (205)
                      +-+.++.+++++|.||
T Consensus        84 iP~~ak~~m~~~Gi~~   99 (103)
T cd00490          84 IPEAAKELMREMGIEP   99 (103)
T ss_pred             CCHHHHHHHHHCCCCH
T ss_conf             6099999999909981


No 43 
>PHA00658 putative lysin
Probab=21.11  E-value=56  Score=14.77  Aligned_cols=82  Identities=21%  Similarity=0.371  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEEECCEEEEEECCCCEE
Q ss_conf             99999999999814788881001126789999999997608653123443202566556676289618058772110023
Q gi|255764506|r   20 EAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHFGEASKYQDMVLIKDISFFSYCEHHIL   99 (205)
Q Consensus        20 ~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~e~~~Gy~~~~~~~~~~~~~~~~~~~~~~mVvv~~I~f~S~CEHHll   99 (205)
                      .|...+..-|+-+|+||+-..-.-..+||-. +..|..||-........+.|+..+.+.+-+-...++-.+.......-+
T Consensus       595 aikagldtrlrmmgddptpkdgssdaervga-mrkfidgyfiaaqreagkkftdaeveqhldalfmknatvrgwfsnssv  673 (720)
T PHA00658        595 AIKAGLDTRLRMMGDDPTPKDGSSDAERVGA-MRKFIDGYFIAAQREAGKKFTDAEVEQHLDALFMKNATVRGWFSNSSV  673 (720)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHH-HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCC
T ss_conf             8861135667760799999888643888888-987621344466576444454588999999998515402221047876


Q ss_pred             EEE
Q ss_conf             465
Q gi|255764506|r  100 PIW  102 (205)
Q Consensus       100 Pf~  102 (205)
                      |+.
T Consensus       674 pil  676 (720)
T PHA00658        674 PIL  676 (720)
T ss_pred             CEE
T ss_conf             136


No 44 
>COG5441 Uncharacterized conserved protein [Function unknown]
Probab=20.92  E-value=50  Score=15.12  Aligned_cols=63  Identities=11%  Similarity=0.212  Sum_probs=48.3

Q ss_pred             EEEECCEEEEEECCCCEEEEEEEEEEEEECC-CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2896180587721100234655789999638-85434677999999983154266899999999999732738
Q gi|255764506|r   82 MVLIKDISFFSYCEHHILPIWGKIHLAYIPK-KHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSK  153 (205)
Q Consensus        82 mVvv~~I~f~S~CEHHllPf~G~~~IaYiP~-~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~  153 (205)
                      ++.+-.+-++.+-.-|++|..|...|.-+|. .-+-||-.+.|+|-.-|         ..+|+-+.....+|.
T Consensus       115 PlgvPK~mVST~Asgdv~pyv~~sDi~Mm~svtd~aGLNrisR~VLsnA---------a~aiag~a~~~~~~s  178 (401)
T COG5441         115 PLGVPKVMVSTLASGDVAPYVGVSDIIMMYSVTDMAGLNRISRVVLSNA---------AHAIAGMAKRPAEPS  178 (401)
T ss_pred             CCCCCCEEEEEEECCCCCCCCCHHHEEEEEECCCCCCCCHHHHHHHHHH---------HHHHHHHHHCCCCCC
T ss_conf             7677610256410267578777657253100143112348889999878---------899888873567898


No 45 
>cd01747 GATase1_Glutamyl_Hydrolase Type 1 glutamine amidotransferase (GATase1) domain found in gamma-Glutamyl Hydrolase. Type 1 glutamine amidotransferase (GATase1) domain found in gamma-Glutamyl Hydrolase. gamma-Glutamyl Hydrolase catalyzes the cleavage of the gamma-glutamyl chain of folylpoly-gamma-glutamyl substrates and is a central enzyme in folyl and antifolyl poly-gamma-glutamate metabolism. GATase activity involves the removal of the ammonia group from a glutamate molecule and its subsequent transfer to a specific substrate, thus creating a new carbon-nitrogen group on the substrate.  gamma-Glutamyl hydrolases belong to the triad family of amidotransferases having a conserved Cys-His-Glu catalytic triad in the glutaminase active site.
Probab=20.87  E-value=71  Score=14.17  Aligned_cols=25  Identities=32%  Similarity=0.517  Sum_probs=20.1

Q ss_pred             CCEEEEEECCCCEEEEEEEEEEEEECCC
Q ss_conf             1805877211002346557899996388
Q gi|255764506|r   86 KDISFFSYCEHHILPIWGKIHLAYIPKK  113 (205)
Q Consensus        86 ~~I~f~S~CEHHllPf~G~~~IaYiP~~  113 (205)
                      .+..|.|..||.--||+|+-+   -|-+
T Consensus       190 ~g~eFVStiE~k~YP~yg~Qf---HPEK  214 (273)
T cd01747         190 NGVEFISTVEAYKYPIYGVQW---HPEK  214 (273)
T ss_pred             CCCEEEEEEECCCCCEEEEEE---CCCC
T ss_conf             998898863032476466740---6875


No 46 
>PRK10416 cell division protein FtsY; Provisional
Probab=20.73  E-value=46  Score=15.32  Aligned_cols=22  Identities=23%  Similarity=0.406  Sum_probs=14.4

Q ss_pred             CHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             8100112678999999999760
Q gi|255764506|r   38 REGLKDTPDRVIKSYKELFAGY   59 (205)
Q Consensus        38 regL~~TP~Rvak~~~e~~~Gy   59 (205)
                      +.||.+|-..+...+..+|+|-
T Consensus       202 k~gL~kt~~~l~~~~~~lf~~k  223 (499)
T PRK10416        202 KRSLLKTKENLGSGFISLFRGK  223 (499)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9899999999999999986689


No 47 
>COG1539 FolB Dihydroneopterin aldolase [Coenzyme metabolism]
Probab=20.47  E-value=72  Score=14.11  Aligned_cols=70  Identities=21%  Similarity=0.363  Sum_probs=41.7

Q ss_pred             EEEECCEEEEEE-----CCCCE-EEEEEEEEEEEECC-----CC---CCCHHH-HHHHHHHH-HCCCCCHHHHHHHHHHH
Q ss_conf             289618058772-----11002-34655789999638-----85---434677-99999998-31542668999999999
Q gi|255764506|r   82 MVLIKDISFFSY-----CEHHI-LPIWGKIHLAYIPK-----KH---VIGLSK-LVRILEVY-SRRLQIQERLTMQIAHA  145 (205)
Q Consensus        82 mVvv~~I~f~S~-----CEHHl-lPf~G~~~IaYiP~-----~~---viGlSK-l~Riv~~~-a~RlQ~QErlT~qIa~~  145 (205)
                      -|.++++.|+..     .|+++ +||.=.+.++|=..     +.   -+--.- ..++.+++ .++..+.|+|+.+||+.
T Consensus         4 ~v~i~~l~~~~~iGv~~~E~~~~Q~~~Vdl~l~~d~~~A~~~Ddl~dtl~Y~~v~~~i~~~v~~~~~~LiE~lA~~ia~~   83 (121)
T COG1539           4 RVFIENLEFFAYIGVLDEERKLGQKFVVDLTLGYDLRKAAESDDLADTLNYAEVSELIKEIVEGKRFALIETLAEEIADL   83 (121)
T ss_pred             EEEECCEEEEEEECCCHHHHCCCCEEEEEEEEECCCHHHCCCCCHHHEECHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             89983469999973778996069719999999526045147663222536999999999998579534499999999999


Q ss_pred             HHHHCC
Q ss_conf             997327
Q gi|255764506|r  146 IESSTD  151 (205)
Q Consensus       146 l~~~l~  151 (205)
                      +...-.
T Consensus        84 l~~~~~   89 (121)
T COG1539          84 LLARFP   89 (121)
T ss_pred             HHHHCC
T ss_conf             986388


No 48 
>pfam03652 UPF0081 Uncharacterized protein family (UPF0081).
Probab=20.12  E-value=52  Score=14.97  Aligned_cols=32  Identities=28%  Similarity=0.327  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHHCCCCC---------HHHHHHHHHHHHHHH
Q ss_conf             67799999998315426---------689999999999973
Q gi|255764506|r  118 LSKLVRILEVYSRRLQI---------QERLTMQIAHAIESS  149 (205)
Q Consensus       118 lSKl~Riv~~~a~RlQ~---------QErlT~qIa~~l~~~  149 (205)
                      .|..++.+..|+++|+-         -||+|...|..+...
T Consensus        67 ~~~~~~~v~~f~~~L~~~~~i~v~~~DEr~TS~~A~~~l~~  107 (134)
T pfam03652        67 EGEQTKRVRKFARRLKKRFGLPVELVDERLTTVEAERILRE  107 (134)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHH
T ss_conf             08899999999999998619986886343279999999997


No 49 
>TIGR00250 TIGR00250 conserved hypothetical protein TIGR00250; InterPro: IPR005227   Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VIIcolicin E and RusA (IPR008822 from INTERPRO):  The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined.  The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex.   Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold.     Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes.   This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes.   The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma urealyticum (Q9PQY7 from SWISSPROT, ). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase . This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC . ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0004518 nuclease activity, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus.
Probab=20.10  E-value=37  Score=15.87  Aligned_cols=26  Identities=27%  Similarity=0.399  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHHCCCCCH---------HHHHHHHHH
Q ss_conf             77999999983154266---------899999999
Q gi|255764506|r  119 SKLVRILEVYSRRLQIQ---------ERLTMQIAH  144 (205)
Q Consensus       119 SKl~Riv~~~a~RlQ~Q---------ErlT~qIa~  144 (205)
                      +..+.=+..||+|++-|         ||||.-=|+
T Consensus        68 g~~~~~~~kFA~r~~~~~~v~v~l~DERL~t~~A~  102 (133)
T TIGR00250        68 GPLTKRAQKFAKRLEGRFGVPVELMDERLSTVEAE  102 (133)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHH
T ss_conf             50268889999886554066437861761378999


No 50 
>pfam07893 DUF1668 Protein of unknown function (DUF1668). The hypothetical proteins found in this family are expressed by Oryza sativa and are of unknown function.
Probab=20.02  E-value=31  Score=16.34  Aligned_cols=24  Identities=33%  Similarity=0.537  Sum_probs=18.4

Q ss_pred             CEEEEEEEEEEEEECC-CCCCCHHHHH
Q ss_conf             0234655789999638-8543467799
Q gi|255764506|r   97 HILPIWGKIHLAYIPK-KHVIGLSKLV  122 (205)
Q Consensus        97 HllPf~G~~~IaYiP~-~~viGlSKl~  122 (205)
                      -.|||.|+++  |.|. +--+|||.-.
T Consensus       205 w~LPF~G~a~--yv~el~lw~Gls~~~  229 (330)
T pfam07893       205 WTLPFDGQAE--YVPELDLWFGLSRGD  229 (330)
T ss_pred             CCCCCCCCEE--ECCCCCCEEEEECCC
T ss_conf             5067377278--741108079770379


Done!