Query         gi|254780136|ref|YP_003064549.1| ribonucleotide-diphosphate reductase subunit beta [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 125
No_of_seqs    106 out of 1338
Neff          7.1 
Searched_HMMs 39220
Date          Sun May 29 15:11:24 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780136.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK07209 ribonucleotide-diphos 100.0 1.4E-45       0  299.5  13.5  125    1-125   267-391 (391)
  2 PRK12759 bifunctional gluaredo 100.0 7.4E-42       0  275.3  13.1  125    1-125   279-405 (410)
  3 PRK09101 nrdB ribonucleotide-d 100.0 3.1E-35 7.8E-40  235.1  12.0  121    1-121   236-362 (376)
  4 PTZ00211 ribonucleotide reduct 100.0 1.2E-34   3E-39  231.5  12.9  115    1-124   204-318 (330)
  5 COG0208 NrdF Ribonucleotide re 100.0 4.8E-34 1.2E-38  227.8  12.6  121    1-122   218-338 (348)
  6 PRK09614 nrdF ribonucleotide-d 100.0 1.2E-32   3E-37  219.3  12.6  122    1-125   197-320 (325)
  7 PRK13966 nrdF2 ribonucleotide- 100.0 9.3E-31 2.4E-35  207.8  12.0  120    1-123   194-316 (324)
  8 PRK13965 ribonucleotide-diphos 100.0   7E-29 1.8E-33  196.4  11.8  122    1-125   207-332 (337)
  9 KOG1567 consensus              100.0   7E-29 1.8E-33  196.4   9.1  113    2-123   219-331 (344)
 10 PRK13967 nrdF1 ribonucleotide- 100.0 3.3E-28 8.5E-33  192.3  11.2  119    1-122   192-313 (322)
 11 cd01049 RNRR2 Ribonucleotide R  99.9 4.3E-26 1.1E-30  179.4  12.2  100    1-100   187-287 (288)
 12 pfam00268 Ribonuc_red_sm Ribon  99.9 3.4E-22 8.7E-27  155.8  10.2   88    1-94    191-278 (281)
 13 cd07911 RNRR2_Rv0233_like Ribo  99.5 1.4E-13 3.6E-18  103.4   9.0   84    1-86    187-270 (280)
 14 PRK08326 ribonucleotide-diphos  99.0 4.4E-09 1.1E-13   76.1   8.8   97    1-99    206-307 (318)
 15 cd07911 RNRR2_Rv0233_like Ribo  94.9   0.056 1.4E-06   32.9   4.9   57   30-86    211-267 (280)
 16 pfam11266 DUF3066 Protein of u  92.4    0.81 2.1E-05   25.8   7.2   76    1-84    131-207 (219)
 17 TIGR01647 ATPase-IIIA_H plasma  90.5    0.35   9E-06   28.0   3.7   27   73-99      7-44  (835)
 18 TIGR00289 TIGR00289 conserved   82.4     1.3 3.3E-05   24.6   2.9   74   31-116    72-146 (227)
 19 pfam10603 consensus             71.3     9.2 0.00023   19.4   5.0   40   35-75      2-41  (55)
 20 pfam02007 MtrH Tetrahydrometha  58.4      16 0.00041   17.9   3.9   44   31-75     46-89  (296)
 21 TIGR00956 3a01205 Pleiotropic   45.6      26 0.00067   16.6   3.7   55   56-118  1051-1111(1466)
 22 PRK00979 tetrahydromethanopter  44.8      27 0.00069   16.6   4.3   44   31-75     51-94  (310)
 23 pfam08671 SinI Anti-repressor   43.5      10 0.00025   19.2   0.9   27   45-71      2-28  (30)
 24 TIGR01125 TIGR01125 MiaB-like   41.8     8.1 0.00021   19.7   0.3   51   43-93    321-374 (475)
 25 KOG2067 consensus               36.0      28 0.00071   16.5   2.2   53   20-73    147-201 (472)
 26 cd01050 Acyl_ACP_Desat Acyl AC  35.6      38 0.00096   15.7   4.1   23    2-24    189-211 (297)
 27 TIGR02094 more_P_ylases alpha-  35.1      25 0.00064   16.8   1.9  110    5-120   280-418 (618)
 28 TIGR01502 B_methylAsp_ase meth  33.5      26 0.00066   16.7   1.7   59   32-101   179-248 (414)
 29 pfam11251 DUF3050 Protein of u  32.5      42  0.0011   15.4   4.0   71   11-83     31-122 (232)
 30 TIGR00988 hip integration host  29.9      47  0.0012   15.1   3.9   32   12-43      4-35  (94)
 31 pfam03405 FA_desaturase_2 Fatt  27.0      53  0.0013   14.8   3.4   23    2-24    195-217 (330)
 32 pfam07132 consensus             25.7      54  0.0014   14.8   2.3   62   12-76    271-333 (377)
 33 PRK10853 hypothetical protein;  25.6      46  0.0012   15.2   1.9   43   75-117    18-63  (118)
 34 TIGR00693 thiE thiamine-phosph  22.3      16  0.0004   18.0  -1.0   45   44-88     93-141 (210)
 35 pfam11583 AurF P-aminobenzoate  21.8      66  0.0017   14.2   4.8   21    1-21    115-135 (295)
 36 TIGR01114 mtrH N5-methyltetrah  21.1      51  0.0013   14.9   1.4   50   21-74     44-93  (323)
 37 PRK06267 hypothetical protein;  20.2      63  0.0016   14.3   1.7   53   32-89    153-208 (324)

No 1  
>PRK07209 ribonucleotide-diphosphate reductase subunit beta; Validated
Probab=100.00  E-value=1.4e-45  Score=299.52  Aligned_cols=125  Identities=68%  Similarity=1.164  Sum_probs=123.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      +|||++|+.|++.||++++.|+|++||++++++|++|+++||++|.+|+++++|.|++|||++++++||+|+|||||.+|
T Consensus       267 ~RDEslH~~f~~~li~~i~~EnP~l~t~e~~~~i~~~~~eAVelE~~f~~d~lp~gilGlna~~~~~YI~yiAdrRL~qL  346 (391)
T PRK07209        267 LRDESMHLNFGIDLINQIKLENPHLWTAEFQAEIRELILEAVELEYRYARDTMPRGVLGLNASMFKDYLRFIANRRLQQI  346 (391)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             20278899999999999874184227778999999999999999999999754688789899999999999998999987


Q ss_pred             CCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCCCC
Q ss_conf             978788987888689999834665732131003333430657789
Q gi|254780136|r   81 GLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELKWD  125 (125)
Q Consensus        81 Gl~~~f~~~~nPl~W~~~~~~~~~~~nFFE~r~t~Y~k~~~~~~D  125 (125)
                      |++|+|+.++||||||++.+++++++||||+|||+||+||+++||
T Consensus       347 Gl~~~y~~~~NPfpWm~e~idl~~~tNFFE~RVteYq~~g~l~wd  391 (391)
T PRK07209        347 GLDPLYPGTENPFPWMSEMIDLKKEKNFFETRVIEYQTGGALSWD  391 (391)
T ss_pred             CCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCHHHHHCCCCCCCC
T ss_conf             999878999998007998627332135133208776206657889


No 2  
>PRK12759 bifunctional gluaredoxin/ribonucleoside-diphosphate reductase subunit beta; Provisional
Probab=100.00  E-value=7.4e-42  Score=275.29  Aligned_cols=125  Identities=32%  Similarity=0.582  Sum_probs=120.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9403789999999999999677000311229999999999999999985763087601-889999999999999999998
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFV-GLNAPSCEQYMQFIANRRCHQ   79 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~-Gl~~~~~~~Yiky~an~rL~~   79 (125)
                      +|||++|++|+|.||+++++|+|++++++++++|++++++||++|.+|++.++|.+.+ |||+++|++||+|+|||||.+
T Consensus       279 ~RDEglH~eFa~~Lf~~~~~e~p~i~~~~~~~~I~~ii~eAVeiE~~Fi~~alp~~~I~Gmn~~~m~qYIeyVADRlL~q  358 (410)
T PRK12759        279 IRDESMHVEGNAALFRIYCQENPYIVDNEFKKEIYLMASKAVELEDRFIELAYELGTIEGLKADEVKQYIRHITDRRLNQ  358 (410)
T ss_pred             ECCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             12013368999999999976371207778999999999999999999999746667789989999999999999999998


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHC-CCCCC
Q ss_conf             59787889878886899998346657321310033334306-57789
Q gi|254780136|r   80 IGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA-ELKWD  125 (125)
Q Consensus        80 lGl~~~f~~~~nPl~W~~~~~~~~~~~nFFE~r~t~Y~k~~-~~~~D  125 (125)
                      ||++|+|++++||+|||++.+++.++|||||+|||+||||| +++||
T Consensus       359 LG~~kiy~~~~NPf~wMe~il~~~~ktNFFE~RVtEYqkagv~g~wd  405 (410)
T PRK12759        359 LGLKEIYNIEKNPLTWLEWILNGADHTNFFENRVTEYEVAGLTGSWD  405 (410)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCHH
T ss_conf             69998789999982799998767555775677688776277576488


No 3  
>PRK09101 nrdB ribonucleotide-diphosphate reductase subunit beta; Reviewed
Probab=100.00  E-value=3.1e-35  Score=235.05  Aligned_cols=121  Identities=27%  Similarity=0.470  Sum_probs=112.7

Q ss_pred             CCHHHHHHHHHHHHHHHHH--HHCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCCCHHHHHHHHHHHHHH
Q ss_conf             9403789999999999999--6770003--112299999999999999999857630876-0188999999999999999
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIK--IENPHLW--TKEFQQKSRTMLHEATLLEIAYAHETMPKG-FVGLNAPSCEQYMQFIANR   75 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~--~e~pe~~--~~~~~~~i~~~~~eave~E~~~~~~~~~~~-~~Gl~~~~~~~Yiky~an~   75 (125)
                      .|||++|+.+++.+|+.++  +++|++.  ++++++++++|+++||++|++|++|+|++| ++|||++.|++||+|+||+
T Consensus       236 ~rDE~~Hl~~~~~ii~~l~~~~e~pe~~~~~~e~~~~v~~m~~~ave~E~~wa~ylf~~G~iiGLn~~~l~~Yi~ylan~  315 (376)
T PRK09101        236 ARDEALHLTGTQHMLNLMRSGKDDPEMAEIAEECKQECYDLFVQAAEQEKEWADYLFKDGSMIGLNKDILCQYVEYITNI  315 (376)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             97199899999999999985389827889999999999999999999999999996669971688999999999999999


Q ss_pred             HHHHCCCCCCCCCCCCCHHHHHHHHCCCC-CCCCCCCCHHHHHHHCC
Q ss_conf             99985978788987888689999834665-73213100333343065
Q gi|254780136|r   76 RCHQIGLEPLFKYTENPFPWMSEVIDLKK-EKNFFETRVTEYQQGAE  121 (125)
Q Consensus        76 rL~~lGl~~~f~~~~nPl~W~~~~~~~~~-~~nFFE~r~t~Y~k~~~  121 (125)
                      ||++||++|+|+..+||+|||+.|+++++ ++||||+++|+|.+|+.
T Consensus       316 Rl~~lGl~~~y~~~~NPlpWm~~~~~~~~~q~a~qE~evtsY~~g~~  362 (376)
T PRK09101        316 RMQAVGLDLPFQTRSNPIPWINTWLVSDNVQVAPQEVEVSSYLVGQI  362 (376)
T ss_pred             HHHHCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCEEEECC
T ss_conf             99976999999999998458999865576746731201300112142


No 4  
>PTZ00211 ribonucleotide reductase small subunit; Provisional
Probab=100.00  E-value=1.2e-34  Score=231.48  Aligned_cols=115  Identities=30%  Similarity=0.648  Sum_probs=106.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      .|||++|+.|++.|++.++.+.|       ++.+++|+++||++|.+|+.++++.+++|||++++++||+|+||+||++|
T Consensus       204 ~RDE~~H~~f~~~l~~~l~~e~~-------~e~v~~~~~eAvelE~~f~~~~~~~~~iGl~~e~l~~Yi~y~An~rL~~L  276 (330)
T PTZ00211        204 SRDEGLHTDFACLLYSHLKNKLP-------RERVQEIIKDAVEIEREFICDALPVDLIGMNSRLMAQYIEFVADRLLVSL  276 (330)
T ss_pred             HCCHHHHHHHHHHHHHHHHHCCC-------HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             82099999999999999756299-------99999999999999999999873678669999999999999999999987


Q ss_pred             CCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCCC
Q ss_conf             97878898788868999983466573213100333343065778
Q gi|254780136|r   81 GLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELKW  124 (125)
Q Consensus        81 Gl~~~f~~~~nPl~W~~~~~~~~~~~nFFE~r~t~Y~k~~~~~~  124 (125)
                      |++|+|++ +||+|||+ .+++.+++||||+|||+|+|||++.+
T Consensus       277 G~~~~f~~-~nP~~w~~-~~~~~~ktnFFE~r~t~Y~kag~~~~  318 (330)
T PTZ00211        277 GYEKIYNS-KNPFDWME-MISLQGKTNFFEKKVGEYQKAGVMSE  318 (330)
T ss_pred             CCCCCCCC-CCCCHHHH-HHCCCCCCCCCCCCHHHHHHCCCCCC
T ss_conf             99988899-99845899-85468888876677888877035645


No 5  
>COG0208 NrdF Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism]
Probab=100.00  E-value=4.8e-34  Score=227.80  Aligned_cols=121  Identities=40%  Similarity=0.742  Sum_probs=116.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      +|||++|+.+++.+|+.++.+.|+++++++++.+++++.+||++|++|+.++++ |++|||.+++++||+|+||+||++|
T Consensus       218 ~RDE~~H~~~~~~l~~~~~~e~~~~~t~e~~~~~~~l~~~ave~E~~y~~~~~~-~~~Glt~d~~~~Yi~y~ankrL~~l  296 (348)
T COG0208         218 IRDEALHLYFIGYLIQRLVAENPELWTAELKDEIYDLFKEAVELEKEYAEYLYP-GILGLTEDLVKQYIRYNANKRLQNL  296 (348)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             977999998999999999873838556888999999999999999999998735-6579988999999999987999975


Q ss_pred             CCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHCCC
Q ss_conf             978788987888689999834665732131003333430657
Q gi|254780136|r   81 GLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAEL  122 (125)
Q Consensus        81 Gl~~~f~~~~nPl~W~~~~~~~~~~~nFFE~r~t~Y~k~~~~  122 (125)
                      |++|+|+...||+||++.++++++++||||+|+++|+||+..
T Consensus       297 G~~~~y~~~~NP~~~~~~~~~~~~~~dFFe~~~ssY~~~~~~  338 (348)
T COG0208         297 GLEPLYPAEENPIPWIELSLSADEKTDFFEGRVSSYQKGSVA  338 (348)
T ss_pred             CCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCHHHHHHCC
T ss_conf             999889987896579986234333577500464167761045


No 6  
>PRK09614 nrdF ribonucleotide-diphosphate reductase subunit beta; Reviewed
Probab=100.00  E-value=1.2e-32  Score=219.33  Aligned_cols=122  Identities=28%  Similarity=0.425  Sum_probs=108.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      +|||++|+.+++.|++++++|+|++++++++++|++|+++||++|++|++++++  ++|+ +++|++||+|+||+||++|
T Consensus       197 ~RDE~lH~~~~~~l~~~l~~e~p~~~~~~~~~~i~~~~~eave~E~~~~~~~~~--~~Gl-~~~~~~Yi~y~an~~L~~l  273 (325)
T PRK09614        197 IRDESLHGYYIGYLFQAGLEELPELEQEELKDEIYDLLYELYENEEAYTELLYD--ILGL-TEDVKKYIRYNANKALMNL  273 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCC-HHHHHHHHHHHHHHHHHHC
T ss_conf             987888899999999999863988557999999999999999999999999855--4787-8999999999999999977


Q ss_pred             CCCCCCCCCCCCHHHHHHHH-CCCCCCCCCCCCHHHHHHHCCC-CCC
Q ss_conf             97878898788868999983-4665732131003333430657-789
Q gi|254780136|r   81 GLEPLFKYTENPFPWMSEVI-DLKKEKNFFETRVTEYQQGAEL-KWD  125 (125)
Q Consensus        81 Gl~~~f~~~~nPl~W~~~~~-~~~~~~nFFE~r~t~Y~k~~~~-~~D  125 (125)
                      |++|+|+...+|.+||+.+. ++.+++||||+|||+|+||+.. .||
T Consensus       274 G~~~~f~~~~~~p~w~~~~~~~~~~~tnFFE~r~t~Y~k~~~~~~~D  320 (325)
T PRK09614        274 GLEPLYPEEEVNPIWLNGLSNNADENHDFFEGKGTSYSKGSVEATFD  320 (325)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCC
T ss_conf             99988999889977999988577804589878711323156678843


No 7  
>PRK13966 nrdF2 ribonucleotide-diphosphate reductase subunit beta; Provisional
Probab=99.97  E-value=9.3e-31  Score=207.82  Aligned_cols=120  Identities=20%  Similarity=0.294  Sum_probs=110.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      +|||++|+.+...+++....+.|+.+++++++.+++++.++|++|++|++++++.  +||+. ++++||+|+||+||++|
T Consensus       194 ~RDEs~H~~~~~~l~~~~~~~~~~~~~~e~~~~i~~~~~~~v~~E~~~~~~l~~~--~GL~~-dv~~Yi~Y~ANrrL~~L  270 (324)
T PRK13966        194 IRDEAVHGYYIGYKFQRGLALVDDVTRAELKDYTYELLFELYDNEVEYTQDLYDE--VGLTE-DVKKFLRYNANKALMNL  270 (324)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCCHH-HHHHHHHHHHHHHHHHC
T ss_conf             9837888879999999988854877689999999999999999999999987523--79489-99999999999999978


Q ss_pred             CCCCCCCCC---CCCHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCC
Q ss_conf             978788987---8886899998346657321310033334306577
Q gi|254780136|r   81 GLEPLFKYT---ENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELK  123 (125)
Q Consensus        81 Gl~~~f~~~---~nPl~W~~~~~~~~~~~nFFE~r~t~Y~k~~~~~  123 (125)
                      |++|+|+..   .||++|+....++.+++||||+|||+|++|++..
T Consensus       271 Gl~~~fp~~~~~~nP~~~~~~~~~~~~~~nFFE~r~t~Y~~g~~~~  316 (324)
T PRK13966        271 GYEALFPRDETDVNPAILSALSPNADENHDFFSGSGSSYVIGKAVV  316 (324)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCC
T ss_conf             8998899745788946699862256753786788700214165667


No 8  
>PRK13965 ribonucleotide-diphosphate reductase subunit beta; Provisional
Probab=99.96  E-value=7e-29  Score=196.42  Aligned_cols=122  Identities=20%  Similarity=0.209  Sum_probs=100.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      +|||++|+.+++.+++...++.+...+++++++|++|+++||++|++|++++++.  +|++ +++++||+|+||+||.+|
T Consensus       207 ~RDEslH~~~~~~~~~~~~~~~~~e~~~e~~~~v~~~~~~aVelE~~~~~~~~~~--~gl~-~~l~~YI~YiANrrL~~L  283 (337)
T PRK13965        207 LRDKVIHNYYSGYKYQQKVARLSPEKQAEMKAFVFDLLYELIDLEKAYLRELYAG--FDLA-EDAIRFSLYNAGKFLQNL  283 (337)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCHH-HHHHHHHHHHHHHHHHHC
T ss_conf             8704888889999999998742987789999999999999999999999999836--7769-999999999999999977


Q ss_pred             CCCCCCCCCC-CCHHHHHHHHCCC--CCCCCCCCCHHHHHHHCCC-CCC
Q ss_conf             9787889878-8868999983466--5732131003333430657-789
Q gi|254780136|r   81 GLEPLFKYTE-NPFPWMSEVIDLK--KEKNFFETRVTEYQQGAEL-KWD  125 (125)
Q Consensus        81 Gl~~~f~~~~-nPl~W~~~~~~~~--~~~nFFE~r~t~Y~k~~~~-~~D  125 (125)
                      |++|+|++.+ +|.||+..+++..  +++||||+|||+|+||++- .||
T Consensus       284 Gl~~~y~~~~~~~~P~~~~~~~~~~~~~~dFFE~r~t~Y~~g~~~~~~d  332 (337)
T PRK13965        284 GYESPFTEEETRVSPEVFAQLSARADENHDFFSGNGSSYVMGITEETTD  332 (337)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCHHHHEECCCCCC
T ss_conf             9988899867888814589760478867785477721002100578823


No 9  
>KOG1567 consensus
Probab=99.96  E-value=7e-29  Score=196.40  Aligned_cols=113  Identities=34%  Similarity=0.625  Sum_probs=106.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             40378999999999999967700031122999999999999999998576308760188999999999999999999859
Q gi|254780136|r    2 RDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIG   81 (125)
Q Consensus         2 RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~lG   81 (125)
                      |||.+|+.|+|.++..+++       ++..+.|++++.+||++|.+|....+|..++|+|+..|++||+|+||+.|..||
T Consensus       219 rdeglh~dFacll~~~l~~-------kp~~~ri~eII~eAV~IEqef~~eaLPv~liGMN~~lM~qYIEFVADrLL~~lG  291 (344)
T KOG1567         219 RDEGLHCDFACLLFSHLKK-------KPNEERIEEIITEAVEIEQEFLTEALPVNLIGMNCDLMSQYIEFVADRLLVELG  291 (344)
T ss_pred             HCCCCCCCHHHHHHHHHHH-------CCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             0247761199999999860-------897899999999999999999871165455345788999999999999999848


Q ss_pred             CCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCC
Q ss_conf             787889878886899998346657321310033334306577
Q gi|254780136|r   82 LEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELK  123 (125)
Q Consensus        82 l~~~f~~~~nPl~W~~~~~~~~~~~nFFE~r~t~Y~k~~~~~  123 (125)
                      +++.|++ +||++||+ .+...++|||||+||++||++|+.+
T Consensus       292 ~~K~Yn~-~NPFdfME-nISl~GKTNFFEKrVseYQk~~vMs  331 (344)
T KOG1567         292 NEKYYNA-ENPFDFME-NISLAGKTNFFEKRVSEYQKAGVMS  331 (344)
T ss_pred             CCCEECC-CCCHHHHH-HHHHCCCCCHHHHHHHHHHHCHHCC
T ss_conf             5502057-88168888-7353254415776567765010024


No 10 
>PRK13967 nrdF1 ribonucleotide-diphosphate reductase subunit beta; Provisional
Probab=99.95  E-value=3.3e-28  Score=192.30  Aligned_cols=119  Identities=21%  Similarity=0.328  Sum_probs=101.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      +|||++|+.+...+++....+.|+..++++++.+.++++++|++|++|+.++++.  +|++. ++.+||+|+||+||.+|
T Consensus       192 ~RDEslH~~~~~~~~~~~~~~~~~~~~~e~~e~~~~~~~~~v~~Ei~~~~~l~~~--lGl~~-dv~~YI~YiANrrL~~L  268 (322)
T PRK13967        192 IRDEAVHGYYIGYKCQRGLADLTDAERADHREYTCELLHTLYANEIDYAHDLYDE--LGWTD-DVLPYMRYNANKALANL  268 (322)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCHH-HHHHHHHHHHHHHHHHC
T ss_conf             9828888999999999874523787789999999999999999999999998712--28689-99999989999999978


Q ss_pred             CCCCCCCCCC-CCHHHHHHHHC--CCCCCCCCCCCHHHHHHHCCC
Q ss_conf             9787889878-88689999834--665732131003333430657
Q gi|254780136|r   81 GLEPLFKYTE-NPFPWMSEVID--LKKEKNFFETRVTEYQQGAEL  122 (125)
Q Consensus        81 Gl~~~f~~~~-nPl~W~~~~~~--~~~~~nFFE~r~t~Y~k~~~~  122 (125)
                      |++|+|+... +|.||+...++  +.+++||||+|+|+|+||++-
T Consensus       269 Gl~p~y~~~~~~~nP~~~~~~~~~~~~~~dFFe~r~t~Y~k~~~~  313 (322)
T PRK13967        269 GYQPAFDRDTCQVNPAVRAALDPGAGENHDFFSGSGSSYVMGTHQ  313 (322)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCHHCCCC
T ss_conf             899999985577883668875768763268557886400432566


No 11 
>cd01049 RNRR2 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain. Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha-
Probab=99.94  E-value=4.3e-26  Score=179.45  Aligned_cols=100  Identities=41%  Similarity=0.762  Sum_probs=95.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      .|||++|+.|++.+++++++++|+++++++++.|++++++||++|.+|++++++.|++|++++++++||+|+||+||.+|
T Consensus       187 ~rDE~lH~~f~~~l~~~l~~e~~~~~~~~~~~~i~~~~~eav~~E~~~~~~~~~~~i~gl~~~~~~~yi~y~an~~l~~l  266 (288)
T cd01049         187 SRDESLHGDFACLLIRELLNENPELFTEEFKEEVYELIKEAVELEKEFARDLLPDGILGLNKEDMKQYIEYVANRRLENL  266 (288)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             99899999999999999886298856566799999999999999999999980688689899999999999999999977


Q ss_pred             CCCCCCCCC-CCCHHHHHHHH
Q ss_conf             978788987-88868999983
Q gi|254780136|r   81 GLEPLFKYT-ENPFPWMSEVI  100 (125)
Q Consensus        81 Gl~~~f~~~-~nPl~W~~~~~  100 (125)
                      |++|+|++. +||+|||+...
T Consensus       267 G~~~~f~~~~~nP~~~~~~~~  287 (288)
T cd01049         267 GLEKLFNVEDKNPFDWMELIS  287 (288)
T ss_pred             CCCCCCCCCCCCCHHHHHHHC
T ss_conf             999999999999777998751


No 12 
>pfam00268 Ribonuc_red_sm Ribonucleotide reductase, small chain.
Probab=99.88  E-value=3.4e-22  Score=155.77  Aligned_cols=88  Identities=31%  Similarity=0.460  Sum_probs=80.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      +|||++|+.|++.||+++++++     ++.++.|++++++||++|++|++++++.+++|||+++|++||+|+||+||++|
T Consensus       191 ~RDE~lH~~f~~~l~~~~~~~~-----~~~~~~v~~~~~eave~E~~~~~~~~~~~~~gl~~~~~~~Yi~y~an~~L~~L  265 (281)
T pfam00268       191 SRDEALHTDAACLLYNNYLGLE-----KPEPKRIYKLFREAVEIEIEFIEAAAPVDVHGMNVRAIKQYIEFSADRLLVAI  265 (281)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHC-----CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             9989999999999999998735-----85499999999999999999999867788389799999999999999999977


Q ss_pred             CCCCCCCCCCCCHH
Q ss_conf             97878898788868
Q gi|254780136|r   81 GLEPLFKYTENPFP   94 (125)
Q Consensus        81 Gl~~~f~~~~nPl~   94 (125)
                      |++|+|++ +||+.
T Consensus       266 G~~~~f~~-~NPf~  278 (281)
T pfam00268       266 GYKPLFNV-PNPFF  278 (281)
T ss_pred             CCCCCCCC-CCCCC
T ss_conf             99998999-89899


No 13 
>cd07911 RNRR2_Rv0233_like Ribonucleotide Reductase R2-like protein, ferritin-like diiron-binding domain. Rv0233 is a Mycobacterium tuberculosis ribonucleotide reductase R2 protein with a  heterodinuclear manganese/iron-carboxylate cofactor located in its metal center. The Rv0233-like family may represent a structural/functional counterpart of the evolutionary ancestor of the RNRR2's (Ribonucleotide Reductase, R2/beta subunit) and the bacterial multicomponent monooxygenases.  RNRR2s belong to a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in prokaryotes and archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites.
Probab=99.50  E-value=1.4e-13  Score=103.36  Aligned_cols=84  Identities=20%  Similarity=0.169  Sum_probs=75.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      .|||++|+.||+.+++.++.|+|++| +.+++.+.+++..|++++ +++..+++.+++|++++.+.+|+.++|++||..|
T Consensus       187 ~RDE~~H~~fg~~l~~~l~~e~p~~~-d~~~e~~~el~~~av~~~-~~~~~~~~~~~~g~~~~~f~~Y~~~~a~~rLg~i  264 (280)
T cd07911         187 GDDESRHIAWGTFTCRRLVAADDANW-DVFEERMNELVPHALGLI-DEIFELYDEMPFGLDPDELMQYAVDQFQRRLGYI  264 (280)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCHHHH-HHHHHHHHHHHHHHHHHH-HHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             98899999999999999998695678-999999999999999999-9998515655668899999999999999874488


Q ss_pred             CCCCCC
Q ss_conf             978788
Q gi|254780136|r   81 GLEPLF   86 (125)
Q Consensus        81 Gl~~~f   86 (125)
                      +-.+-.
T Consensus       265 ~~~~~~  270 (280)
T cd07911         265 ERARGQ  270 (280)
T ss_pred             HHHCCC
T ss_conf             785299


No 14 
>PRK08326 ribonucleotide-diphosphate reductase subunit beta; Validated
Probab=98.96  E-value=4.4e-09  Score=76.07  Aligned_cols=97  Identities=22%  Similarity=0.253  Sum_probs=80.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      .|||+.|+.||.++++.++.|+|++| +.+.+.+.+++..|+-+ .+|+..+++.-..||+.+.+.+|+++++++||..|
T Consensus       206 ~RDE~rHi~~g~~~~~rlv~e~~~~~-~~~~e~~~el~~~a~~~-~~~~~~~~~~~~~~l~~~~~~~ya~~~~~~Rl~~i  283 (318)
T PRK08326        206 GDDESRHIAFGTYTCRRLVAADDSNW-DVFEERMNELIPLALGL-IDEGFALYDVIPFGLSKDEFMQYAADKGQRRLGTI  283 (318)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCHHHH-HHHHHHHHHHHHHHHHH-HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             61599999999999999986088889-99999999999999877-52441036668889998999999999998889999


Q ss_pred             C---CCCCCCC--CCCCHHHHHHH
Q ss_conf             9---7878898--78886899998
Q gi|254780136|r   81 G---LEPLFKY--TENPFPWMSEV   99 (125)
Q Consensus        81 G---l~~~f~~--~~nPl~W~~~~   99 (125)
                      +   ..|+...  +..|..+-+..
T Consensus       284 ~~ar~~~~~~~~~~~~~~~~~~~~  307 (318)
T PRK08326        284 SRARGRPLAEIDLDYSPLQLEDTF  307 (318)
T ss_pred             HHHCCCCCHHCCCCCCHHHHHHHH
T ss_conf             974199700305778989999886


No 15 
>cd07911 RNRR2_Rv0233_like Ribonucleotide Reductase R2-like protein, ferritin-like diiron-binding domain. Rv0233 is a Mycobacterium tuberculosis ribonucleotide reductase R2 protein with a  heterodinuclear manganese/iron-carboxylate cofactor located in its metal center. The Rv0233-like family may represent a structural/functional counterpart of the evolutionary ancestor of the RNRR2's (Ribonucleotide Reductase, R2/beta subunit) and the bacterial multicomponent monooxygenases.  RNRR2s belong to a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in prokaryotes and archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites.
Probab=94.88  E-value=0.056  Score=32.89  Aligned_cols=57  Identities=9%  Similarity=-0.054  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             299999999999999999857630876018899999999999999999985978788
Q gi|254780136|r   30 FQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLF   86 (125)
Q Consensus        30 ~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~lGl~~~f   86 (125)
                      ..+.+.+.+.+.++.+.+++.++.+....|+-..+...|++|++|+.++.||+-.-.
T Consensus       211 ~~d~~~e~~~el~~~av~~~~~~~~~~~~~~~g~~~~~f~~Y~~~~a~~rLg~i~~~  267 (280)
T cd07911         211 NWDVFEERMNELVPHALGLIDEIFELYDEMPFGLDPDELMQYAVDQFQRRLGYIERA  267 (280)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             789999999999999999999998515655668899999999999999874488785


No 16 
>pfam11266 DUF3066 Protein of unknown function (DUF3066). This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=92.45  E-value=0.81  Score=25.81  Aligned_cols=76  Identities=16%  Similarity=0.219  Sum_probs=42.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9403789999999999999677000311229999999999999999985763087-601889999999999999999998
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPK-GFVGLNAPSCEQYMQFIANRRCHQ   79 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~-~~~Gl~~~~~~~Yiky~an~rL~~   79 (125)
                      |+||.+|+.||..-++.-.        +.+++++.+.-++..-+-..-.+.+-++ .++|+.++.+.+=.--.-...|..
T Consensus       131 VkDEy~HLN~Ge~WLk~~f--------~~~k~el~~AN~~nLPlv~~ML~qV~~Da~vL~Meke~lvedFmi~Y~eAL~~  202 (219)
T pfam11266       131 VKDEYTHLNFGEEWLKANF--------ETSKEELEEANRENLPLVWKMLNQVADDAAVLGMDKEALVEDFMIAYGEALTN  202 (219)
T ss_pred             HHHHHHHCCHHHHHHHHHH--------HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf             7447776026899999999--------99999999988861639999999998789997788999999999999999997


Q ss_pred             CCCCC
Q ss_conf             59787
Q gi|254780136|r   80 IGLEP   84 (125)
Q Consensus        80 lGl~~   84 (125)
                      ||+..
T Consensus       203 IGf~~  207 (219)
T pfam11266       203 IGFTT  207 (219)
T ss_pred             CCCCH
T ss_conf             59758


No 17 
>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=90.54  E-value=0.35  Score=28.03  Aligned_cols=27  Identities=30%  Similarity=0.534  Sum_probs=21.6

Q ss_pred             HHHHHHHCCCCCCCCCCC-----------CCHHHHHHH
Q ss_conf             999999859787889878-----------886899998
Q gi|254780136|r   73 ANRRCHQIGLEPLFKYTE-----------NPFPWMSEV   99 (125)
Q Consensus        73 an~rL~~lGl~~~f~~~~-----------nPl~W~~~~   99 (125)
                      |.+||..-|...+.+.+.           ||||||-|.
T Consensus         7 A~~RL~~yGpN~l~Ekk~~~ll~FL~f~WnPlsWvmE~   44 (835)
T TIGR01647         7 AKKRLAKYGPNELPEKKVSPLLKFLSFMWNPLSWVMEA   44 (835)
T ss_pred             HHHHHHHCCCCCCCCCCCCHHHHHHHHHHCHHHHHHHH
T ss_conf             99999742888785534225999977520724899999


No 18 
>TIGR00289 TIGR00289 conserved hypothetical protein TIGR00289; InterPro: IPR005237   This family of conserved hypothetical proteins has no known function. Homologous proteins related to MJ0570 of Methanococcus jannaschii include both the apparent orthologs in the family, the much longer protein YLR143W from Saccharomyces cerevisiae (Baker's yeast), and second homologous proteins from Archaeoglobus fulgidus and Pyrococcus horikoshii that appear to represent a second orthologous group..
Probab=82.37  E-value=1.3  Score=24.57  Aligned_cols=74  Identities=12%  Similarity=0.273  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC-CCCCHHHHHHHHCCCCCCCCC
Q ss_conf             9999999999999999985763087601889999999999999999998597878898-788868999983466573213
Q gi|254780136|r   31 QQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKY-TENPFPWMSEVIDLKKEKNFF  109 (125)
Q Consensus        31 ~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~lGl~~~f~~-~~nPl~W~~~~~~~~~~~nFF  109 (125)
                      +++|-++..+.-++...=++-+...       ..-=+|=|-|.|+.|+.+|++.+=|- .+||++||...++     --|
T Consensus        72 EkEVedLag~l~~lderGvea~~~G-------a~~S~YQK~Rid~vCrelGlks~APLW~~dPle~~~~~V~-----e~F  139 (227)
T TIGR00289        72 EKEVEDLAGQLEELDERGVEAVVIG-------AIESEYQKSRIDKVCRELGLKSIAPLWHKDPLEYLLEEVA-----EKF  139 (227)
T ss_pred             CCHHHHHHHHHHHHHHCCCCEEEEC-------CEECCHHHHHHHHHHHHHCCHHCCCCCCCCHHHHHHHHHH-----CCC
T ss_conf             2117666215544553054547885-------3410112335778877714100276013481799999862-----336


Q ss_pred             CCCHHHH
Q ss_conf             1003333
Q gi|254780136|r  110 ETRVTEY  116 (125)
Q Consensus       110 E~r~t~Y  116 (125)
                      +.++++=
T Consensus       140 ~v~iv~V  146 (227)
T TIGR00289       140 EVIIVSV  146 (227)
T ss_pred             EEEEEEE
T ss_conf             0899999


No 19 
>pfam10603 consensus
Probab=71.29  E-value=9.2  Score=19.40  Aligned_cols=40  Identities=10%  Similarity=0.029  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             99999999999998576308760188999999999999999
Q gi|254780136|r   35 RTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANR   75 (125)
Q Consensus        35 ~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~   75 (125)
                      ++++..|..+|.+|..|.- .=+.|-|.++++.-|+-+.+.
T Consensus         2 kk~yerA~KlEqef~e~Ft-aiVqGdt~e~i~~qvK~vI~~   41 (55)
T pfam10603         2 KKTYERALKLEQEFGEYFT-AIVQGDSLEEIYTQIKSVIEE   41 (55)
T ss_pred             CHHHHHHHHHHHHHHHHCE-EEEECCCHHHHHHHHHHHHHH
T ss_conf             0699999999999998712-545089899999999999998


No 20 
>pfam02007 MtrH Tetrahydromethanopterin S-methyltransferase MtrH subunit. The enzyme tetrahydromethanopterin S-methyltransferase EC:2.1.1.86 is composed of eight subunits. The enzyme is a membrane- associated enzyme complex which catalyses an energy-conserving, sodium-ion-translocating step in methanogenesis from hydrogen and carbon dioxide.
Probab=58.40  E-value=16  Score=17.93  Aligned_cols=44  Identities=11%  Similarity=0.262  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             999999999999999998576308760188999999999999999
Q gi|254780136|r   31 QQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANR   75 (125)
Q Consensus        31 ~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~   75 (125)
                      ++....++....++......-.+ .+++|-|.+.|..||+|+++.
T Consensus        46 k~~Ae~Lin~q~elsd~TGnp~~-~qI~g~t~EA~~kYidfv~~i   89 (296)
T pfam02007        46 REAAEALINTQEELSDETGNPYL-VQIFGETPEAIIRYIDFVADV   89 (296)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEE-EEEECCCHHHHHHHHHHHHCC
T ss_conf             89999999999988775589657-776448989999988876325


No 21 
>TIGR00956 3a01205 Pleiotropic Drug Resistance (PDR) Family protein; InterPro: IPR005285   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    This family includes transporters, whose physiological function is not yet established. These proteins are thought to confer resistance to the chemicals cycloheximide and sulphomethuron methyl, BFA, azole antifungal agents, other antifungal agents: amorolfine and terbinafine. Some of them could serve as an efflux pump of various antibiotics..
Probab=45.62  E-value=26  Score=16.65  Aligned_cols=55  Identities=31%  Similarity=0.486  Sum_probs=40.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCC----CCCCCCCCC--CHHHHHH
Q ss_conf             60188999999999999999999859787889878886899998346----657321310--0333343
Q gi|254780136|r   56 GFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDL----KKEKNFFET--RVTEYQQ  118 (125)
Q Consensus        56 ~~~Gl~~~~~~~Yiky~an~rL~~lGl~~~f~~~~nPl~W~~~~~~~----~~~~nFFE~--r~t~Y~k  118 (125)
                      |.+|=|...|.+|-+-       .-|-.|.= .+.||-.||-+.+.+    .-++||||.  .+++|+.
T Consensus      1051 GdlG~n~~T~inYFEa-------~hGA~kCp-~~~NPAEwmLeViGAApga~~~~Dy~E~W~nS~ey~~ 1111 (1466)
T TIGR00956      1051 GDLGENSKTLINYFEA-------KHGAPKCP-EDANPAEWMLEVIGAAPGAKANQDYHEVWRNSSEYQA 1111 (1466)
T ss_pred             CCCCHHHHHHHHHHHH-------HCCCCCCC-CCCCCHHHHHHHHCCCCCCCCCCHHHHHHCCCHHHHH
T ss_conf             7513135899988866-------53788985-8876345587774468777633006756258388999


No 22 
>PRK00979 tetrahydromethanopterin S-methyltransferase subunit H; Provisional
Probab=44.80  E-value=27  Score=16.57  Aligned_cols=44  Identities=11%  Similarity=0.286  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             999999999999999998576308760188999999999999999
Q gi|254780136|r   31 QQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANR   75 (125)
Q Consensus        31 ~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~   75 (125)
                      ++....++....++......-.+ .+++|-|.+.+..||+|+++.
T Consensus        51 k~~Ae~Lin~q~elsd~tGnp~~-~qI~g~t~EA~~kYidfv~~~   94 (310)
T PRK00979         51 KEAAEALINRQAELSDITGNPYI-LQIFGETGEAIEKYIDFVSEI   94 (310)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEE-EEEECCCHHHHHHHHHHHHHC
T ss_conf             89999999999988774589657-776448989999998877404


No 23 
>pfam08671 SinI Anti-repressor SinI. SinR is a pleiotropic regulator of several late growth processes. It is a tetrameric DNA binding protein whose activity is down-regulated thorough the formation of a SinI:SinR protein complex. When complexed with SinI, the SinR tetramer is disrupted such that is no longer able to bind DNA.
Probab=43.54  E-value=10  Score=19.20  Aligned_cols=27  Identities=11%  Similarity=0.272  Sum_probs=20.7

Q ss_pred             HHHHHHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf             999857630876018899999999999
Q gi|254780136|r   45 EIAYAHETMPKGFVGLNAPSCEQYMQF   71 (125)
Q Consensus        45 E~~~~~~~~~~~~~Gl~~~~~~~Yiky   71 (125)
                      ..+|...+..--..|++++++.+|+.+
T Consensus         2 D~EW~~Li~EA~~~Gis~ee~r~fL~~   28 (30)
T pfam08671         2 DQEWVQLIKEAMEAGLSKEEFREFLEF   28 (30)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHHC
T ss_conf             579999999999814679999999850


No 24 
>TIGR01125 TIGR01125 MiaB-like tRNA modifying enzyme YliG, TIGR01125; InterPro: IPR005840   This is a family of mainly hypothetical proteins of unknown function. .
Probab=41.85  E-value=8.1  Score=19.73  Aligned_cols=51  Identities=16%  Similarity=0.259  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCC---CCCCCCCCCCH
Q ss_conf             9999985763087601889999999999999999998597---87889878886
Q gi|254780136|r   43 LLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGL---EPLFKYTENPF   93 (125)
Q Consensus        43 e~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~lGl---~~~f~~~~nPl   93 (125)
                      ..+...++-.|=.|.+|=|.|+...=.+|+-.-++..+|.   .|.-+...++|
T Consensus       321 ~~P~~vlRttfIVGFPGETEEdF~eL~~Fv~e~~~D~lG~F~YS~eEgt~A~~L  374 (475)
T TIGR01125       321 KVPDAVLRTTFIVGFPGETEEDFQELLDFVEEGQFDRLGVFTYSPEEGTDAFAL  374 (475)
T ss_pred             HCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCHHHCC
T ss_conf             556617722468868899878899999998520215000020783236603507


No 25 
>KOG2067 consensus
Probab=36.02  E-value=28  Score=16.47  Aligned_cols=53  Identities=17%  Similarity=0.316  Sum_probs=27.9

Q ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCHHHHHHHHHHHH
Q ss_conf             6770003112299999999999999999857630--87601889999999999999
Q gi|254780136|r   20 IENPHLWTKEFQQKSRTMLHEATLLEIAYAHETM--PKGFVGLNAPSCEQYMQFIA   73 (125)
Q Consensus        20 ~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~--~~~~~Gl~~~~~~~Yiky~a   73 (125)
                      -|..++|+++ +--..+|+.+|.=..-..+.-.+  ...+.+||.+.+.+|++|.-
T Consensus       147 ~E~~el~~~P-e~lL~e~iH~Aay~~ntlg~pl~cp~~~i~~I~~~~l~~yl~~~y  201 (472)
T KOG2067         147 YEIEELWMRP-EPLLTEMIHSAAYSGNTLGLPLLCPEENIDKINREVLEEYLKYFY  201 (472)
T ss_pred             HECCCCCCCC-HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             0112002482-366999999987356765555538745531303999999998617


No 26 
>cd01050 Acyl_ACP_Desat Acyl ACP desaturase, ferritin-like diiron-binding domain. Acyl-Acyl Carrier Protein Desaturase (Acyl_ACP_Desat) is a mu-oxo-bridged diiron-carboxylate enzyme, which belongs to a broad superfamily of ferritin-like proteins and catalyzes the NADPH and O2-dependent formation of a cis-double bond in acyl-ACPs.  Acyl-ACP desaturases are found in higher plants and a few bacterial species (Mycobacterium tuberculosis, M. leprae, M. avium and Streptomyces avermitilis, S. coelicolor). In plants, Acyl-ACP desaturase is a plastid-localized, covalently ACP linked, soluble desaturase that introduces the first double bound into saturated fatty acids, resulting in the corresponding monounsaturated fatty acid.  Members of this class of soluble desaturases are specific for a particular substrate chain length and introduce the double bond between specific carbon atoms. For example, delta 9 stearoyl-ACP is specific for stearic acid and introduces a double bond between carbon 9 and 1
Probab=35.58  E-value=38  Score=15.69  Aligned_cols=23  Identities=26%  Similarity=0.377  Sum_probs=19.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             40378999999999999967700
Q gi|254780136|r    2 RDESLHLNFGIDVINQIKIENPH   24 (125)
Q Consensus         2 RDE~lH~~~~~~l~~~l~~e~pe   24 (125)
                      .||++|..|..+++..+.+=.|.
T Consensus       189 ~DE~rH~~fYr~iv~~~le~dPd  211 (297)
T cd01050         189 ADEARHEAFYRDIVEALFELDPD  211 (297)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCH
T ss_conf             16889999999999999833936


No 27 
>TIGR02094 more_P_ylases alpha-glucan phosphorylases; InterPro: IPR011834    This family consists of known phosphorylases, and homologues believed to share the function of using inorganic phosphate to cleave an alpha 1,4 linkage between the terminal glucose residue and the rest of the polymer (maltodextrin, glycogen, etc.). The name of the glucose storage polymer substrate, and therefore the name of this enzyme, depends on the chain lengths and branching patterns. A number of the members of this family have been shown to operate on small maltodextrins, as may be obtained by utilization of exogenous sources. This family represents a distinct clade from the related families: Glycogen/starch/alpha-glucan phosphorylase and Glycosyl transferase, family 35.; GO: 0004645 phosphorylase activity, 0030170 pyridoxal phosphate binding, 0005975 carbohydrate metabolic process.
Probab=35.13  E-value=25  Score=16.76  Aligned_cols=110  Identities=11%  Similarity=0.101  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHHHHHHHHCCCC---------------CC-----HHHHHHHHHHHH-HHHHHHHHHH-HHHCCCCCC----
Q ss_conf             789999999999999677000---------------31-----122999999999-9999999985-763087601----
Q gi|254780136|r    5 SLHLNFGIDVINQIKIENPHL---------------WT-----KEFQQKSRTMLH-EATLLEIAYA-HETMPKGFV----   58 (125)
Q Consensus         5 ~lH~~~~~~l~~~l~~e~pe~---------------~~-----~~~~~~i~~~~~-eave~E~~~~-~~~~~~~~~----   58 (125)
                      -||...+++|+..|=...|+-               |.     +.++...-+.++ +-...+.-|. -+-+|+..+    
T Consensus       280 kLHg~VSr~Mw~~Lyp~~~p~EvPI~~vTNGVH~pTW~~~~~~~L~~~~~g~~w~W~~~~~~~~w~~~~~iPDeeLW~~h  359 (618)
T TIGR02094       280 KLHGEVSRKMWADLYPGVEPEEVPIGYVTNGVHLPTWVAPELAELYERYLGENWRWEDLASEEIWEAIDDIPDEELWEVH  359 (618)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCEEECCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             88899999986311688780204356311885675537878999998507864223047876799874118968999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHC---CCCCCCCCCCCHHHHHHHC
Q ss_conf             8899999999999999999985978788987888689999834---6657321310033334306
Q gi|254780136|r   59 GLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVID---LKKEKNFFETRVTEYQQGA  120 (125)
Q Consensus        59 Gl~~~~~~~Yiky~an~rL~~lGl~~~f~~~~nPl~W~~~~~~---~~~~~nFFE~r~t~Y~k~~  120 (125)
                      .-.+..|..|||..+..++..=|.      +..++.+....+|   .+..|==|..|.+.|..+.
T Consensus       360 ~~~K~~Li~~ir~~~~~~~~~~~~------~~~~~~~~~~~lD~~~p~~LtIGFARRfAtYKRa~  418 (618)
T TIGR02094       360 LKLKAELIDYIRRRLREQLLRRGA------DAAELKATDRLLDAKSPDVLTIGFARRFATYKRAT  418 (618)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCC------CHHHHHHHHHHCCCCCCCCCEECHHHCCCCCCCHH
T ss_conf             998999999999999998885036------86688888641464578852522122276002613


No 28 
>TIGR01502 B_methylAsp_ase methylaspartate ammonia-lyase; InterPro: IPR006395   These sequences describe methylaspartate ammonia-lyase, also called beta-methylaspartase. It follows methylaspartate mutase (composed of S and E subunits) in one of several possible pathways of glutamate fermentation. .
Probab=33.47  E-value=26  Score=16.67  Aligned_cols=59  Identities=19%  Similarity=0.543  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCC-------CCCCHHHHHHHHHHHHHHHHHHCC----CCCCCCCCCCCHHHHHHHH
Q ss_conf             99999999999999998576308760-------188999999999999999999859----7878898788868999983
Q gi|254780136|r   32 QKSRTMLHEATLLEIAYAHETMPKGF-------VGLNAPSCEQYMQFIANRRCHQIG----LEPLFKYTENPFPWMSEVI  100 (125)
Q Consensus        32 ~~i~~~~~eave~E~~~~~~~~~~~~-------~Gl~~~~~~~Yiky~an~rL~~lG----l~~~f~~~~nPl~W~~~~~  100 (125)
                      ..+-+|+-..|        .+||-|+       +|+.-+.+-+||+|+.+|. .+||    |.|+|-+  .-+=|+=+.+
T Consensus       179 ~nvdkMilK~v--------dVLPHgLiNsve~k~G~dG~~l~EyvkWl~~R~-~~lgv~~gY~P~fH~--DVYG~iGe~f  247 (414)
T TIGR01502       179 RNVDKMILKEV--------DVLPHGLINSVEKKLGLDGEKLLEYVKWLSERI-AKLGVSEGYRPVFHV--DVYGTIGEEF  247 (414)
T ss_pred             HCHHHHHHHHC--------CCCCCCHHCCHHHHCCCCCHHHHHHHHHHHHHH-HHCCCCCCCCCEEEE--EECCHHHHHC
T ss_conf             13344223002--------557640120203222887115577888899988-750678898406887--5032334323


Q ss_pred             C
Q ss_conf             4
Q gi|254780136|r  101 D  101 (125)
Q Consensus       101 ~  101 (125)
                      +
T Consensus       248 g  248 (414)
T TIGR01502       248 G  248 (414)
T ss_pred             C
T ss_conf             8


No 29 
>pfam11251 DUF3050 Protein of unknown function (DUF3050). This bacterial family of proteins has no known function.
Probab=32.54  E-value=42  Score=15.39  Aligned_cols=71  Identities=15%  Similarity=0.282  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHH-----CCCCCCHHHHHHHHHHHHHHHHHHH-----------HHHHHHCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             99999999967-----7000311229999999999999999-----------9857630876018899999999999999
Q gi|254780136|r   11 GIDVINQIKIE-----NPHLWTKEFQQKSRTMLHEATLLEI-----------AYAHETMPKGFVGLNAPSCEQYMQFIAN   74 (125)
Q Consensus        11 ~~~l~~~l~~e-----~pe~~~~~~~~~i~~~~~eave~E~-----------~~~~~~~~~~~~Gl~~~~~~~Yiky~an   74 (125)
                      +..|++.++.+     -|  |.+.-...++..+.|.|--|.           -|--|+-...-+|-+...+..||+.+.+
T Consensus        31 FMSLlK~LQ~~ltc~~~P--W~P~~~~~~~RlINEIVl~EESD~~~~g~~~SHFElYl~AM~e~GA~t~~I~~fi~~l~~  108 (232)
T pfam11251        31 FMSLLKALQQQLTCTTVP--WVPPGNPELRRLINEIVLAEESDENLDGEHQSHFELYLDAMREVGADTSKIEAFLKLVQS  108 (232)
T ss_pred             HHHHHHHHHHHHCCCCCC--CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHC
T ss_conf             989999999853378888--789998159999999986530365779881149999999999938991789999999875


Q ss_pred             -----HHHHHCCCC
Q ss_conf             -----999985978
Q gi|254780136|r   75 -----RRCHQIGLE   83 (125)
Q Consensus        75 -----~rL~~lGl~   83 (125)
                           ..|...+++
T Consensus       109 g~~~~~al~~~~~p  122 (232)
T pfam11251       109 GTSVFEALAQADLP  122 (232)
T ss_pred             CCCHHHHHHHCCCC
T ss_conf             89999998764899


No 30 
>TIGR00988 hip integration host factor, beta subunit; InterPro: IPR005685   Integration host factor (IHF) is a heterodimeric protein consisting of alpha (IPR005684 from INTERPRO) and beta subunits. IHF binds the minor groove of DNA in a sequence-specific manner to induce a large bend. This bending stabilises distinct DNA conformations that are required during several bacterial processes, such as recombination, transposition, replication and transcription .; GO: 0003677 DNA binding, 0005694 chromosome.
Probab=29.87  E-value=47  Score=15.11  Aligned_cols=32  Identities=31%  Similarity=0.544  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             99999999677000311229999999999999
Q gi|254780136|r   12 IDVINQIKIENPHLWTKEFQQKSRTMLHEATL   43 (125)
Q Consensus        12 ~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave   43 (125)
                      ..||..+..++|++..+..+..|..|+.+..+
T Consensus         4 SELI~~i~~~~~~l~~k~VE~~v~~~lE~~~~   35 (94)
T TIGR00988         4 SELIERIATEQSHLFAKDVEKAVKTMLEEMIE   35 (94)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             78889987407875533389999999999999


No 31 
>pfam03405 FA_desaturase_2 Fatty acid desaturase.
Probab=26.98  E-value=53  Score=14.80  Aligned_cols=23  Identities=17%  Similarity=0.235  Sum_probs=19.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             40378999999999999967700
Q gi|254780136|r    2 RDESLHLNFGIDVINQIKIENPH   24 (125)
Q Consensus         2 RDE~lH~~~~~~l~~~l~~e~pe   24 (125)
                      -||++|-.|..+++..+.+-.|.
T Consensus       195 aDE~rH~~fYr~iv~~~~eldPd  217 (330)
T pfam03405       195 SDEKRHETAYTKIVEKLFELDPD  217 (330)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCH
T ss_conf             33778999999999999802932


No 32 
>pfam07132 consensus
Probab=25.75  E-value=54  Score=14.75  Aligned_cols=62  Identities=19%  Similarity=0.184  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCCCHHHHHHHHHHHHHHH
Q ss_conf             999999996770003112299999999999999999857630876-01889999999999999999
Q gi|254780136|r   12 IDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKG-FVGLNAPSCEQYMQFIANRR   76 (125)
Q Consensus        12 ~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~-~~Gl~~~~~~~Yiky~an~r   76 (125)
                      ++=|-.+..++||+|-|+-.++  .-..++-.-.+.|++ ++.+. -.|+|+..|.+|-|-..-..
T Consensus       271 AKEiGQFMDQYPEvFGKPqYQK--~~~s~~KtDdKSWAk-ALSkPDDDGMT~aSMdqF~kA~GMIK  333 (377)
T pfam07132       271 AKEIGQFMDQYPEIFGKPQYQK--DPWSSVKTDDKSWAK-ALSKPDDDGMTPASMEQFNKAKGMIK  333 (377)
T ss_pred             HHHHHHHHHHCHHHCCCCCCCC--CCCCCCCCCCHHHHH-HHCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             9999888764524308842236--887544545378999-72798767886340999999876788


No 33 
>PRK10853 hypothetical protein; Provisional
Probab=25.62  E-value=46  Score=15.16  Aligned_cols=43  Identities=19%  Similarity=0.282  Sum_probs=16.8

Q ss_pred             HHHHHCCCCCCC-CCCCCCHH--HHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf             999985978788-98788868--99998346657321310033334
Q gi|254780136|r   75 RRCHQIGLEPLF-KYTENPFP--WMSEVIDLKKEKNFFETRVTEYQ  117 (125)
Q Consensus        75 ~rL~~lGl~~~f-~~~~nPl~--W~~~~~~~~~~~nFFE~r~t~Y~  117 (125)
                      +.|.+-|++-.| ++.++|++  -+..|+...+...+|-+|++.|-
T Consensus        18 kwL~~~~i~y~f~D~k~~~~~~~~l~~wl~~~G~~~liN~rgtt~R   63 (118)
T PRK10853         18 RWLEENGIDYRFHDYRVDGLDSELLNGFIAELGWEALLNTRGTTWR   63 (118)
T ss_pred             HHHHHCCCCCEEEECCCCCCCHHHHHHHHHHCCHHHHHCCCCCHHH
T ss_conf             9999879981896311469899999999996298987516663566


No 34 
>TIGR00693 thiE thiamine-phosphate pyrophosphorylase; InterPro: IPR003733   Thiamine monophosphate synthase (TMP) (2.5.1.3 from EC) catalyzes the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate in the thiamine biosynthesis pathway .   TENI, a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production belongs to this group .; GO: 0004789 thiamin-phosphate diphosphorylase activity, 0009228 thiamin biosynthetic process.
Probab=22.34  E-value=16  Score=17.98  Aligned_cols=45  Identities=20%  Similarity=0.389  Sum_probs=39.5

Q ss_pred             HHHHHHHHHCCCC-CCCCCHHHHHHHHHHHH---HHHHHHCCCCCCCCC
Q ss_conf             9999857630876-01889999999999999---999998597878898
Q gi|254780136|r   44 LEIAYAHETMPKG-FVGLNAPSCEQYMQFIA---NRRCHQIGLEPLFKY   88 (125)
Q Consensus        44 ~E~~~~~~~~~~~-~~Gl~~~~~~~Yiky~a---n~rL~~lGl~~~f~~   88 (125)
                      +..+.++.++|.. ++|+|...+.+-.+..+   +....=||+.|+|+-
T Consensus        93 ~p~~~aR~l~G~~~iiG~S~~~~~e~~~a~~C~~~~gaDY~G~Gp~fpT  141 (210)
T TIGR00693        93 LPVSEARKLLGPDKIIGVSTHNLEELAEAAACELKEGADYIGVGPIFPT  141 (210)
T ss_pred             CCHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHCCCCEEEECCCCCC
T ss_conf             9989999853899579853379899999998764078988886371158


No 35 
>pfam11583 AurF P-aminobenzoate N-oxygenase AurF. AurF is a metalloenzyme which is involved in the biosynthesis of antibiotic aureothin by catalysing the formation of p-nitrobenzoic acid from p-aminobenzoic acid. AurF is a non-heme di-iron monooxygenase which creates nitroarenes via the sequential oxidation of aminoarenes.
Probab=21.83  E-value=66  Score=14.20  Aligned_cols=21  Identities=29%  Similarity=0.226  Sum_probs=15.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHH
Q ss_conf             940378999999999999967
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIE   21 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e   21 (125)
                      +.||.-|+.+++.+++.+...
T Consensus       115 ~~DE~~H~~mf~~~~~~~g~~  135 (295)
T pfam11583       115 IVDECYHALMFQDAIERIGRL  135 (295)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             999998999999999998764


No 36 
>TIGR01114 mtrH N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit H; InterPro: IPR002856   This family of methyltransferases occurs in both archaea and bacteria. In archaea, members of this family (MtrH) are involved in the energy conservation step of methanogenesis, while in prokaryotes, members of this family whose function has been defined (CmuB) are involved in the metabolism of chloromethane.   In archaea the enzyme tetrahydromethanopterin S-methyltransferase is composed of eight subunits, MtrA-H. The enzyme is a membrane- associated enzyme complex which catalyzes an energy-conserving, sodium-ion-translocating step in methanogenesis from hydrogen and carbon dioxide . Subunit MtrH catalyzes the methylation reaction and was shown to exhibit methyltetrahydromethanopterin:cob(I)alamin methyltransferase activity . CH3-H4MPT + cob(I)alamin --> H4MPT + CH3-cob(III)alamin (H4MPT = tetrahydromethanopterin)   In bacteria, the pathway of chloromethane utilisation allows the microorganisms that possess it to grow with chloromethane as the sole carbon and energy source. It is initiated by a corrinoid-dependent methyltransferase system involving methyltransferase I (CmuA) and methyltransferase II (CmuB), which transfer the methyl group of chloromethane onto tetrahydrofolate . The methyl group of chloromethane is first transferred by the protein CmuA to its corrinoid moiety, from where it is transferred to tetrahydrofolate by CmuB, thereby yielding methyltetrahydrofolate , .   CmuB has methylcobalamin:tetrahydrofolate methyltransferase activity, and catalyzes the conversion of methylcobalamin and tetrahydrofolate to cob(I)alamin and methyltetrahydrofolate. CH3-cob(III)alamin + H4F --> CH3-H4F + cob(I)alamin (H4F = tetrahydromethanopterin); GO: 0008168 methyltransferase activity, 0006730 one-carbon compound metabolic process.
Probab=21.12  E-value=51  Score=14.88  Aligned_cols=50  Identities=12%  Similarity=0.280  Sum_probs=27.7

Q ss_pred             HCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             770003112299999999999999999857630876018899999999999999
Q gi|254780136|r   21 ENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIAN   74 (125)
Q Consensus        21 e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an   74 (125)
                      |..-+|+++   ...+++..-++++..=.+=.+ ..+.|=|.|.+..||+|+++
T Consensus        44 E~kGiFD~~---aAE~Li~~q~el~D~TGnP~~-~qi~G~tpEai~~Yldwv~~   93 (323)
T TIGR01114        44 EDKGIFDKA---AAEELIKTQEELSDVTGNPYV-VQIFGETPEAIVRYLDWVAD   93 (323)
T ss_pred             CCCCCCCHH---HHHHHHHHHHHHCCCCCCCEE-EEECCCCHHHHHHHHHHHEE
T ss_conf             667876478---999987421210356879604-53227887898877453031


No 37 
>PRK06267 hypothetical protein; Provisional
Probab=20.23  E-value=63  Score=14.35  Aligned_cols=53  Identities=19%  Similarity=0.206  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCC-CC--CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             9999999999999999857630876-01--8899999999999999999985978788987
Q gi|254780136|r   32 QKSRTMLHEATLLEIAYAHETMPKG-FV--GLNAPSCEQYMQFIANRRCHQIGLEPLFKYT   89 (125)
Q Consensus        32 ~~i~~~~~eave~E~~~~~~~~~~~-~~--Gl~~~~~~~Yiky~an~rL~~lGl~~~f~~~   89 (125)
                      +.-.++++.+-++-.+-+     -| |+  |=|.+++..-+.++-..-+.++|+.|.-++.
T Consensus       153 e~Ri~~l~~lk~~G~e~g-----sG~ivGlGET~ed~~~~~~~lkel~~d~I~I~~f~P~~  208 (324)
T PRK06267        153 DKIKEMLKKAKDLGLKTG-----ITIILGLGETEDDIELLLNLIEELNLDRITFYSLNPQK  208 (324)
T ss_pred             HHHHHHHHHHHHCCCCEE-----EEEEEECCCCHHHHHHHHHHHHHCCCCEEEECCCCCCC
T ss_conf             999999999998398320-----04687379889999999999997699976325845899


Done!