Query         gi|254780124|ref|YP_003064537.1| hypothetical protein CLIBASIA_00015 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 388
No_of_seqs    219 out of 911
Neff          7.5 
Searched_HMMs 33803
Date          Sun May 22 08:23:30 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780124.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >3l0a_A Putative exonuclease;   99.9 3.6E-24 1.1E-28  177.9  16.3  225    5-247    17-263 (266)
  2 >3h4r_A Exodeoxyribonuclease 8  99.9 2.8E-23 8.4E-28  172.0  10.4  223    3-236     9-264 (265)
  3 >1w36_B RECB, exodeoxyribonucl  98.9 5.3E-10 1.6E-14   84.8   2.8  182    5-198    17-236 (246)
  4 >2vld_A NUCS, UPF0286 protein   84.8     2.6 7.5E-05   21.1  10.1   61   88-159    17-79  (130)
  5 >2p2w_A Citrate synthase; tran  50.0     8.7 0.00026   17.6   1.8   60  275-341    17-77  (101)
  6 >3h1t_A Type I site-specific r  41.1      21 0.00062   15.1   7.2   86  110-201    70-157 (178)
  7 >2elu_A Zinc finger protein 40  41.1      10 0.00031   17.1   1.0   13  224-236     8-20  (37)
  8 >1ckm_A MRNA capping enzyme; n  39.4      12 0.00035   16.8   1.1   28  115-142     3-31  (78)
  9 >3fov_A UPF0102 protein RPA032  37.4      24  0.0007   14.8   6.1   40  113-152    50-92  (134)
 10 >3kal_A Homoglutathione synthe  35.6      25 0.00075   14.6   3.0   34  267-300   134-167 (257)
 11 >2c6x_A Citrate synthase 1; tr  33.4      27 0.00081   14.4   2.7   37  275-318    18-54  (107)
 12 >1aj8_A Citrate synthase; hype  32.8      22 0.00065   15.0   1.6   37  276-319    59-95  (142)
 13 >1klr_A Zinc finger Y-chromoso  31.1      18 0.00052   15.6   0.9   11  227-237     4-14  (30)
 14 >1kea_A Possible G-T mismatche  30.1      23 0.00067   14.9   1.3   20  224-243    89-108 (110)
 15 >2ebb_A Pterin-4-alpha-carbino  27.3      28 0.00083   14.3   1.4   28  290-317    14-43  (101)
 16 >1csh_A Citrate synthase; lyas  26.7      35   0.001   13.6   4.5   39  273-318    24-62  (117)
 17 >1a6b_B Momulv, zinc finger pr  22.1      43  0.0013   13.1   1.9   21  222-242     7-31  (40)
 18 >3jst_A Putative pterin-4-alph  20.9      46  0.0014   12.9   4.8   28  290-317    17-47  (97)
 19 >1u6p_A GAG polyprotein; MLV,   20.6      46  0.0014   12.9   2.1   21  221-241    19-43  (56)
 20 >2hc4_A Vitamin D receptor; al  20.2      32 0.00095   13.9   0.5   10  226-235    27-36  (251)

No 1  
>>3l0a_A Putative exonuclease; RER070207002219, structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: PE4; 2.19A {Eubacterium rectale} (A:)
Probab=99.93  E-value=3.6e-24  Score=177.86  Aligned_cols=225  Identities=14%  Similarity=0.078  Sum_probs=146.2

Q ss_pred             CCCCCCCHHHHHC------CCHHHHHH--CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             5618423677871------83238862--138999898899989999999999724576534322010456453775788
Q gi|254780124|r    5 AFLSASSSHRWLK------CPIAPTLE--SKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTE   76 (388)
Q Consensus         5 A~LSpSs~~rwl~------CP~s~~Le--~~~pd~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e   76 (388)
                      ..||||++++|+.      ||.++.+.  .++|...+.++..||++|.++|...........   .......+.....+.
T Consensus        17 ~~~S~S~l~~~~~~~~~~~cp~~~~~~~~~~~~~~~~~a~~~Gt~iH~~le~~~~~~~~~~~---~~~~~~~~~~~~~~~   93 (266)
T 3l0a_A           17 EYXSVSGYKDFAGTYGKXPCEFYGXEKLNGRWEDEKSTALLVGSYVDSYFEGSLDQFKKDNP---EIFTQKGELKANFKQ   93 (266)
T ss_dssp             HCEEHHHHHHHHCBTTBCCCHHHHHHHHHTSCCCCCCHHHHHHHHHHHHHHTCHHHHHHHCG---GGBCTTSSBCHHHHH
T ss_pred             CCCCHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC---CCCCCCCHHHHHHHH
T ss_conf             65478689998449510007799999861767888987899978999998727676544173---100212056899999


Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCC--------------
Q ss_conf             999999999998503787368877553200044058999999998599799998113688767446--------------
Q gi|254780124|r   77 MASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAE--------------  142 (388)
Q Consensus        77 ~~~~v~~~~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~--------------  142 (388)
                      ....+..+..... .......+.|+.+....++..+.|++|+|+   +.+.|+|||||+.+.....              
T Consensus        94 ~~~~~~~~~~~~~-~~~~~~~~~E~~~~~~~~g~~l~GriD~id---~~~~IiDyKT~~~~~~~~~~~~~~~~~~~~~~~  169 (266)
T 3l0a_A           94 AEEIIARIERDEY-FXKYXSGQKQVIXTGELFGAKWKIKXDSYI---PGVAIVDLKVXASITDLKWVKDIGYLDFVRYWG  169 (266)
T ss_dssp             HHHHHHHHHTCHH-HHHHTTSEEEEEEEEEETTEEEEEEEEEEE---TTTEEEEEEEESCSSCCEEETTTEEECHHHHTT
T ss_pred             HHHHHHHHHHCCH-HHHHCCCCEEEEEEEEECCEEEEEEEEEEE---CCCEEEEEEECCCCCHHHCCCCHHHHHHHHHCC
T ss_conf             9999999995704-566435763789999876937651467993---687599954336565221244112355788608


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             68799999999998438356765138999998304887754302589889999999999999999857765304776678
Q gi|254780124|r  143 NNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYG  222 (388)
Q Consensus       143 ~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~  222 (388)
                      ...||.+|++++.+.++..      +.+.++..+......+.+.+++.+.+....+.+...+..+...     ..+.+++
T Consensus       170 y~~Ql~~Y~~~~~~~~~~~------~~~~~i~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~i~~~-----~~~~~~p  238 (266)
T 3l0a_A          170 YDIQGAVYQEIVRQNTGEK------LPFFIAGATKQTEPDIRIIHVTDNYLQEALHXVEXNXPRILRV-----KNGEVEP  238 (266)
T ss_dssp             HHHHHHHHHHHHHHHHSCC------CCEEEEEEECSSSCCEEEEEECHHHHHHHHHHHHHHHHHHHHH-----HTTSSCC
T ss_pred             HHHHHHHHHHHHHHHHCCC------CCEEEEEEECCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHH-----HCCCCCC
T ss_conf             3999999999999986898------7359999977898732388479899999999999999999999-----7598479


Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             8866667257644562013467876
Q gi|254780124|r  223 VNDDSCRFCRAKVRCPALSRHVLLE  247 (388)
Q Consensus       223 ~~g~~CrfC~~k~~Cra~a~~~l~~  247 (388)
                      .++++|+||+|+..|...-..+...
T Consensus       239 ~~~~~C~~C~~~~~c~~~~~~~~~~  263 (266)
T 3l0a_A          239 DRCELCDCCRHNRVLKKPISIXDLT  263 (266)
T ss_dssp             CCCSCSHHHHHHCCCCSCCCHHHHH
T ss_pred             CCCCCCCCCCCCCHHCCCCCHHHHH
T ss_conf             9999798861011011201199983


No 2  
>>3h4r_A Exodeoxyribonuclease 8; exonuclease, recombination, hydrolase; 2.80A {Escherichia coli k-12} (A:)
Probab=99.90  E-value=2.8e-23  Score=171.99  Aligned_cols=223  Identities=13%  Similarity=0.040  Sum_probs=140.4

Q ss_pred             CCCCCCCCCHHHHHCCCHHHHHHC--CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-------C-------
Q ss_conf             775618423677871832388621--389998988999899999999997245765343220104-------5-------
Q gi|254780124|r    3 HHAFLSASSSHRWLKCPIAPTLES--KIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLT-------F-------   66 (388)
Q Consensus         3 ~HA~LSpSs~~rwl~CP~s~~Le~--~~pd~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~-------~-------   66 (388)
                      .+..||+|++.+|+.||.+++|+.  +++.+.++++.+||++|.+++.+.+..............       .       
T Consensus         9 ~~~~~S~S~l~~~~~Cp~~~~~~~~~~~~~~~~~~~~~G~~~H~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (265)
T 3h4r_A            9 AGPGISKSQLDDIADTPALYLWRKNAPVDTTKTKTLDLGTAFHCRVLELEEFSNRFIVAPEFNRRTNAGKEEEKAFLMEC   88 (265)
T ss_dssp             --CCBCHHHHHHHHHCHHHHHHHTTSCCCCCCCSCCTHHHHHHHHHSSHHHHTCC-------------------------
T ss_pred             CCCCCCHHHHHHHHHCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             89983988999998599999999737899999779987299999874722321233246630234566667999998655


Q ss_pred             -CCCCHHHHHHHHHHHHHHHHHHH-------CCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCC
Q ss_conf             -64537757889999999999985-------0378736887755320004405899999999859979999811368876
Q gi|254780124|r   67 -ENDTRIVDTEMASSVSMVLAYVR-------TFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVP  138 (388)
Q Consensus        67 -~~~~~~~~~e~~~~v~~~~~~~r-------~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~  138 (388)
                       ........+.+...+..++....       ..........|+.+.....+..+.|++|+|+  +|.+.|||||||+.+.
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~G~iD~i~--~~~~~IiDyKTg~~~~  166 (265)
T 3h4r_A           89 ASTGKTVITAEEGRKIELMYQSVMALPLGQWLVESAGHAESSIYWEDPETGILCRCRPDKII--PEFHWIMDVKTTADIQ  166 (265)
T ss_dssp             ---------CCCTTHHHHHHHHHTTSHHHHHHHSSSCBSSCCEEEECTTTCCEEEECCSEEE--GGGTEEEEEEEESCHH
T ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCEEEEEEEECCCCEEEEEEEEEEE--CCCCEEEEEEECCCHH
T ss_conf             53165421299999999999999829546766542023147899997676648888899997--7997488983026777


Q ss_pred             CC------CCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECC--CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             74------46687999999999984383567651389999983048--87754302589889999999999999999857
Q gi|254780124|r  139 VK------AENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVR--TGSPINEWVISADDLLEKAKEFKERGTLALSL  210 (388)
Q Consensus       139 v~------a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~--~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~  210 (388)
                      ..      ....+||.+|++++.+.++...     ....++.....  ....+.....+.+.+....+.+...+..+...
T Consensus       167 ~~~~~~~~~~~~~Ql~lY~~~l~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  241 (265)
T 3h4r_A          167 RFKTAYYDYRYHVQDAFYSDGYEAQFGVQP-----TFVFLVASTTIECGRYPVEIFMMGEEAKLAGQQEYHRNLRTLSDC  241 (265)
T ss_dssp             HHHHHHHHHTTTHHHHHHHHHHHHHHSSCC-----EEEEEEEESSCBTTBCCEEEEECCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHCCCCC-----CEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             653201233779999999999998429998-----639999983356776227999689999999999999999999999


Q ss_pred             HHHHHCCCCCC-CCCCCCCCCCCCCCC
Q ss_conf             76530477667-888666672576445
Q gi|254780124|r  211 KSKRAVSLEHY-GVNDDSCRFCRAKVR  236 (388)
Q Consensus       211 ~a~~~~~~~~~-~~~g~~CrfC~~k~~  236 (388)
                      ..    ++.++ ++++++|+||+||+.
T Consensus       242 ~~----~~~~~~~~~~~~C~~C~~k~~  264 (265)
T 3h4r_A          242 LN----TDEWPAIKTLSLPRWAKEYAN  264 (265)
T ss_dssp             HH----TCCCCCCCCCCCCTTCTTCC-
T ss_pred             HH----CCCCCCCCCCCCCCCCCCCCC
T ss_conf             96----697999864678845110005


No 3  
>>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} (B:886-964,B:1014-1180)
Probab=98.91  E-value=5.3e-10  Score=84.79  Aligned_cols=182  Identities=13%  Similarity=0.046  Sum_probs=91.4

Q ss_pred             CCCCCCCHHHHHCCCHHHHHHC---------CCCCCC-C-HH-----HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             5618423677871832388621---------389998-9-88-----999899999999997245765343220104564
Q gi|254780124|r    5 AFLSASSSHRWLKCPIAPTLES---------KIPQTT-S-IY-----ASEGTFAHNLLAHCLEQGVDAETVSHQKLTFEN   68 (388)
Q Consensus         5 A~LSpSs~~rwl~CP~s~~Le~---------~~pd~~-S-~a-----A~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~   68 (388)
                      +..|.|+..|-.+-+..-.+..         ..|+.+ | .+     |.-||+.|.++|..--   ..+...........
T Consensus        17 ~~~s~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~g~~~h~~~e~~~~---~~~~l~E~e~~~~l   93 (246)
T 1w36_B           17 RVTSYSGLQQRGHGIAQDLMPRLDVDAAGVASVVEEPTLTPHQFPRGASPGTFLHSLFEDLDF---ARNKQVEMEFYLPI   93 (246)
T ss_dssp             EEESSCSSSCSSCTTHHHHCTTSCTTCCCCCCSCCCSSCCGGGSCCSHHHHHHHHHHTTSCCS---GGGEEEEEEEEEEE
T ss_pred             CCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC---HHCCEECCCCCCCC
T ss_conf             013714543223555444455545554344321027767800057648669999999984889---20325412555234


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCC------
Q ss_conf             53775788999999999998503787368877553200044058999999998599799998113688767446------
Q gi|254780124|r   69 DTRIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAE------  142 (388)
Q Consensus        69 ~~~~~~~e~~~~v~~~~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~------  142 (388)
                      ......+.+...+..       ......  .+..+.+......+.|+||||...+|++.|||||||+-......      
T Consensus        94 ~~~~~~~~l~~~l~~-------e~~~~~--~e~~l~~~~~~~~i~G~IDlv~~~dd~~~IIDYKT~~~~~~~~~~~~~al  164 (246)
T 1w36_B           94 SEPLIASQLDTLIRQ-------FDPLSA--GCPPLEFMQVRGMLKGFIDLVFRHEGRYYLLDYKSNWLGEDSSAYTQQAM  164 (246)
T ss_dssp             CSCCCHHHHHHHHHH-------HCSSTT--SCCCCCSCCCEEEEEEEEEEEEBSSSCBCCEEEECCCCCSSGGGSBHHHH
T ss_pred             CCCCCHHHHHHHHHH-------CCCCCC--CCCCCCCCCCEEEEEEEEEEEEEECCEEEEEECCCCCCCCCCCCCCHHHH
T ss_conf             631008789999973-------262001--25432344540269999999999999999997178998998300289999


Q ss_pred             --------CCHHHHHHHHHHHHHCCCCCCC----CCEEEEEEEEEECCCC----CCCCCCCCCHHHHHHHHH
Q ss_conf             --------6879999999999843835676----5138999998304887----754302589889999999
Q gi|254780124|r  143 --------NNTQLMLYACGALHQYGDIFGR----PEALTLTIIQPRVRTG----SPINEWVISADDLLEKAK  198 (388)
Q Consensus       143 --------~n~QL~lYALgA~~~~~~~~~~----~~~v~~~I~qpr~~~~----~~vs~~~~s~eeL~~~~~  198 (388)
                              ..+||.+|++++.+.++.....    .....+.-+.+|..+.    ..+-.+..+.+.+..+.+
T Consensus       165 ~~~~~~~~Y~~QL~lYa~AL~~~~~~~V~~~ly~l~~G~vi~iflrg~~~~~~~~G~~~~~~~~e~i~~l~~  236 (246)
T 1w36_B          165 AAAMQAHRYDLQYQLYTLALHRYLRHRIADYDYEHHFGGVIYLFLRGVDKEHPQQGIYTTRPNAGLIALMDE  236 (246)
T ss_dssp             HHHHHHTTTHHHHHHHHHHHHHHHHHHSSSCCHHHHCCCCEEEESSSCCTTCTTBSCCBCCCCSSHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCEEEEEECCCCCCCCCCCEEECCCCHHHHHHHHH
T ss_conf             999987863999999999999997072679866650781799995798999999976841799999999999


No 4  
>>2vld_A NUCS, UPF0286 protein pyrab01260; endonuclease, hydrolase; 2.60A {Pyrococcus abyssi} (A:122-251)
Probab=84.81  E-value=2.6  Score=21.14  Aligned_cols=61  Identities=18%  Similarity=0.241  Sum_probs=40.6

Q ss_pred             HHCCC-CCCEEEEEEEEEEECCCEEEEEEEEEEEEE-CCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             85037-873688775532000440589999999985-9979999811368876744668799999999998438
Q gi|254780124|r   88 VRTFS-GPFLSETEVPLEPFTTEPGATGTADILIFN-STQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYG  159 (388)
Q Consensus        88 ~r~~~-~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~-dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~  159 (388)
                      ..... +..++..|.++.        -|+||.+.++ +|.++||.+|.|+...   +.--|+..|+-.......
T Consensus        17 ~~~l~~g~~~v~~E~~~~--------~g~IDll~~d~~~~~ViIElK~~~~~~---~~i~Ql~~Y~~~~~~~~~   79 (130)
T 2vld_A           17 PRVIEEGFKPIYREKPIR--------HGIVDVXGVDKDGNIVVLELKRRKADL---HAVSQXKRYVDSLKEEYG   79 (130)
T ss_dssp             GGGTCTTCEEEEEEEEET--------TEEEEEEEECTTSCEEEEEECSSCBCH---HHHHHHHHHHHHHHHHHC
T ss_pred             HHHHCCCCEEEEEEEECC--------CCCEEEEEEECCCCEEEEEEEECCCCH---HHHHHHHHHHHHHHHCCC
T ss_conf             998678968999999718--------886689999179999999997047987---489999999999861259


No 5  
>>2p2w_A Citrate synthase; transferase, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: FLC; 1.90A {Thermotoga maritima} (A:213-313)
Probab=49.98  E-value=8.7  Score=17.63  Aligned_cols=60  Identities=25%  Similarity=0.315  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHCCC-CHHHHHHHHHH
Q ss_conf             99999999999789847852320588878611698999999986165100000138-98899997400
Q gi|254780124|r  275 KACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFKRILK-TPKELEQLYKE  341 (388)
Q Consensus       275 ~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~~~~~~~~~~~l~-~~~~~ek~~~~  341 (388)
                      .++++++...+.+|+.+|||       |.|.|++.|--...|.+...+.....+++ .-.++|+++.+
T Consensus        17 ~~~~~~i~~~l~~~~~i~Gf-------GH~vy~~~DPR~~~l~~~~~~~~~~~~~~~~a~~ie~~~~~   77 (101)
T 2p2w_A           17 DRVEEFVQKCLKEKRKIMGF-------GHRVYKTYDPRAVFLKRVLQEHFPDSKLFRIASKLEEYIVS   77 (101)
T ss_dssp             GGHHHHHHHHHHHTCCCTTB-------CCSSCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             12799999999638766676-------75321013420577887888751147899999999999985


No 6  
>>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus} (A:1-169,A:362-370)
Probab=41.12  E-value=21  Score=15.15  Aligned_cols=86  Identities=14%  Similarity=0.057  Sum_probs=49.9

Q ss_pred             EEEEEEEEEEEE-ECCE-EEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCC
Q ss_conf             058999999998-5997-99998113688767446687999999999984383567651389999983048877543025
Q gi|254780124|r  110 PGATGTADILIF-NSTQ-WIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWV  187 (388)
Q Consensus       110 ~~~~GtiD~I~~-~dg~-l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~  187 (388)
                      ....|++|.+.. .++. +.||.-|.-....  .+.-.|+.-||...-..|..+.++..   ..++.........++. -
T Consensus        70 ~~~~~r~Dy~l~~~~~~p~~viEaK~~~~~l--~~~~~Q~~~Ya~~~~~~~~ilTNG~~---~~~~~~~~~~~~~~~~-~  143 (178)
T 3h1t_A           70 RGEQKRADYLLKYTRDFPIAVVEAKPENSPV--GQGXQQAKDYAEILGLKFAYSTNGHE---ILEFDYTTGEEQLLSR-F  143 (178)
T ss_dssp             ECCCCEEEEEEEEETTEEEEEEEECCTTSCG--GGSHHHHHHHHHHHTCSEEEEECSSC---EEEEETTTCCEEEESS-C
T ss_pred             CCCCCCCCEEEECCCCCEEEEEECCCCCCCH--HHHHHHHHHHHHHCCCCEEEEECCCE---EEEEECCCCCCCCCCC-C
T ss_conf             6887875089987799089999637897799--99999999978866887799979964---8986469997313356-6


Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             89889999999999
Q gi|254780124|r  188 ISADDLLEKAKEFK  201 (388)
Q Consensus       188 ~s~eeL~~~~~~v~  201 (388)
                      .+.++|..+.....
T Consensus       144 ~~~~~l~~~~~~~k  157 (178)
T 3h1t_A          144 PTPDELFKRLCGDE  157 (178)
T ss_dssp             CCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             78368999997420


No 7  
>>2elu_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2elw_A (A:)
Probab=41.06  E-value=10  Score=17.15  Aligned_cols=13  Identities=38%  Similarity=0.956  Sum_probs=9.4

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             8666672576445
Q gi|254780124|r  224 NDDSCRFCRAKVR  236 (388)
Q Consensus       224 ~g~~CrfC~~k~~  236 (388)
                      -..|||||+-|-.
T Consensus         8 ikqhcrfckkkys   20 (37)
T 2elu_A            8 IKQHCRFCKKKYS   20 (37)
T ss_dssp             CCCEETTTTEECS
T ss_pred             HHHHHHHHHHHHH
T ss_conf             8999999998878


No 8  
>>1ckm_A MRNA capping enzyme; nucleotidyltransferase; HET: GTP; 2.50A {Paramecium bursaria chlorella virus 1} (A:240-317)
Probab=39.36  E-value=12  Score=16.80  Aligned_cols=28  Identities=29%  Similarity=0.296  Sum_probs=23.8

Q ss_pred             EEEEEEEE-CCEEEEEEEECCCCCCCCCC
Q ss_conf             99999985-99799998113688767446
Q gi|254780124|r  115 TADILIFN-STQWIIVDFKYGAGVPVKAE  142 (388)
Q Consensus       115 tiD~I~~~-dg~l~IiDyKtGk~~~v~a~  142 (388)
                      |+|.|+.+ +|++-|.|=|-++.+++...
T Consensus         3 TvDFiim~~~GTiGi~DP~~rkNv~vgK~   31 (78)
T 1ckm_A            3 TIDFIIMSEDGTIGIFDPNLRKNVPVGKL   31 (78)
T ss_dssp             CEEEEECSTTCCEEEEETTTTEEEECCCC
T ss_pred             CEEEEEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf             17999993478644215543235754545


No 9  
>>3fov_A UPF0102 protein RPA0323; structural genomics, APC7380, PSI-2, protein structure initiative; 1.88A {Rhodopseudomonas palustris CGA009} (A:)
Probab=37.42  E-value=24  Score=14.78  Aligned_cols=40  Identities=18%  Similarity=0.122  Sum_probs=27.7

Q ss_pred             EEEEEEEEEECCEEEEEEEECCCC--CCCCCCCCH-HHHHHHH
Q ss_conf             999999998599799998113688--767446687-9999999
Q gi|254780124|r  113 TGTADILIFNSTQWIIVDFKYGAG--VPVKAENNT-QLMLYAC  152 (388)
Q Consensus       113 ~GtiD~I~~~dg~l~IiDyKtGk~--~~v~a~~n~-QL~lYAL  152 (388)
                      .|=||.|..++++|+.|.-||.++  .+.++-+.. |-.+...
T Consensus        50 ~GEIDlIa~~~~~LvFVEVK~R~~~~~~~eav~~~K~~ri~~a   92 (134)
T 3fov_A           50 CGEIDLVAQRDALVAFVEVKARGNVDDAAYAVTPRQQSRIVAA   92 (134)
T ss_dssp             TEEEEEEEEETTEEEEEEEEEC------CCCCCHHHHHHHHHH
T ss_pred             CCCCCEEEECCCEEEEEEEEEECCCCCHHHCCCHHHHHHHHHH
T ss_conf             9960679981999999998874488997673999999999999


No 10 
>>3kal_A Homoglutathione synthetase; dimer, ATP-grAsp domain; HET: ADP HGS; 1.90A {Glycine max} PDB: 3kak_A* 3kaj_A* (A:1-100,A:144-229,A:429-499)
Probab=35.58  E-value=25  Score=14.59  Aligned_cols=34  Identities=6%  Similarity=0.120  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCC
Q ss_conf             3899999999999999999789847852320588
Q gi|254780124|r  267 ISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGR  300 (388)
Q Consensus       267 ~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr  300 (388)
                      -..|-.++..+..|.+++.-....+..-.+.++.
T Consensus       134 FggLst~v~~lHkyll~~~g~~~~l~~k~iPeN~  167 (257)
T 3kal_A          134 FALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANN  167 (257)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHTCCGGGSCCCC
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             1026789999999999852433345545588871


No 11 
>>2c6x_A Citrate synthase 1; tricarboxylic acid cycle, transferase, allosteric enzyme, enzyme thermostability; HET: COZ CIT; 3.4A {Bacillus subtilis} (A:213-319)
Probab=33.41  E-value=27  Score=14.36  Aligned_cols=37  Identities=24%  Similarity=0.516  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             99999999999789847852320588878611698999999986
Q gi|254780124|r  275 KACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS  318 (388)
Q Consensus       275 ~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~  318 (388)
                      +++++|..+.+.+|+.+|||       |.|.|++.|-=...|+.
T Consensus        18 ~~~~~~i~~~l~~~~~i~Gf-------GHrvyk~~DPRa~~l~~   54 (107)
T 2c6x_A           18 EHAEAYLKEKLEKGERLMGF-------GHRVYKTKDPRAEALRQ   54 (107)
T ss_dssp             TTHHHHHHHHHHTTCCCTTB-------CCSSCSSCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHCCCCCCCC-------CCCCCCCCHHHHHHHHH
T ss_conf             01799999999669945145-------66425566067889999


No 12 
>>1aj8_A Citrate synthase; hyperthermostable, lyase; HET: COA CIT; 1.90A {Pyrococcus furiosus} (A:1-39,A:218-320)
Probab=32.80  E-value=22  Score=15.01  Aligned_cols=37  Identities=24%  Similarity=0.437  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             99999999997898478523205888786116989999999861
Q gi|254780124|r  276 ACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSV  319 (388)
Q Consensus       276 ~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~~  319 (388)
                      +++++....+.+|+.+|||       |.|.|++.|-=+..|.+.
T Consensus        59 ~~~~~i~~~l~~~~~ipGF-------GHrvyk~~DPRa~~L~~~   95 (142)
T 1aj8_A           59 KVEEWFFKALQQKRKIMGA-------GHRVYKTYDPRARIFKKY   95 (142)
T ss_dssp             GHHHHHHHHHHHTCCCTTB-------CCSSCSSCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCCCCCC-------CCCCCCCCCHHHHHHHHH
T ss_conf             0699999861257654334-------763356653068899998


No 13 
>>1klr_A Zinc finger Y-chromosomal protein; transcription; NMR {Synthetic} (A:)
Probab=31.06  E-value=18  Score=15.62  Aligned_cols=11  Identities=18%  Similarity=0.781  Sum_probs=8.6

Q ss_pred             CCCCCCCCCCC
Q ss_conf             66725764456
Q gi|254780124|r  227 SCRFCRAKVRC  237 (388)
Q Consensus       227 ~CrfC~~k~~C  237 (388)
                      .|++|.||..=
T Consensus         4 ~Cq~C~~r~ad   14 (30)
T 1klr_A            4 QCQYCEFRSAD   14 (30)
T ss_dssp             CCSSSSCCCSC
T ss_pred             CCCCCCCCCCC
T ss_conf             04413001366


No 14 
>>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} (A:1-28,A:140-221)
Probab=30.13  E-value=23  Score=14.89  Aligned_cols=20  Identities=15%  Similarity=0.436  Sum_probs=16.5

Q ss_pred             CCCCCCCCCCCCCCCHHHHH
Q ss_conf             86666725764456201346
Q gi|254780124|r  224 NDDSCRFCRAKVRCPALSRH  243 (388)
Q Consensus       224 ~g~~CrfC~~k~~Cra~a~~  243 (388)
                      ....|.-|+.+..|++..+.
T Consensus        89 k~P~C~~CPL~~~C~~~~~g  108 (110)
T 1kea_A           89 RKPKCEKCGMSKLCSYYEKC  108 (110)
T ss_dssp             SSCCGGGCTTTTTCHHHHTC
T ss_pred             CCCCCCCCCCCCCCCCCCCC
T ss_conf             89999889891019372776


No 15 
>>2ebb_A Pterin-4-alpha-carbinolamine dehydratase; coenzyme biosyntheses, GK1984, structural genomics, NPPSFA; 1.60A {Geobacillus kaustophilus} (A:)
Probab=27.28  E-value=28  Score=14.30  Aligned_cols=28  Identities=18%  Similarity=0.393  Sum_probs=17.3

Q ss_pred             CCCCCEECCCCCCCCCCC--CHHHHHHHHH
Q ss_conf             478523205888786116--9899999998
Q gi|254780124|r  290 EIQGYQLVEGRKGNRSFK--DINRAQELLT  317 (388)
Q Consensus       290 ~~~g~Klv~gr~~~r~~~--d~~~~~~~l~  317 (388)
                      ++|||+++.|+.=.|.|.  |-..+...+.
T Consensus        14 ~lpgW~~~d~~~l~r~f~f~~f~~a~~f~~   43 (101)
T 2ebb_A           14 KADGWKLADERWIVKKYRFQDYLQGIEFVR   43 (101)
T ss_dssp             TSTTCEEETTTEEEEEEECSSHHHHHHHHH
T ss_pred             CCCCCEECCCCCEEEEEEECCHHHHHHHHH
T ss_conf             498977628970999999799999999999


No 16 
>>1csh_A Citrate synthase; lyase(OXO-acid); HET: AMX; 1.65A {Gallus gallus} (A:272-388)
Probab=26.72  E-value=35  Score=13.63  Aligned_cols=39  Identities=18%  Similarity=0.350  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             9999999999999789847852320588878611698999999986
Q gi|254780124|r  273 YVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS  318 (388)
Q Consensus       273 w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~  318 (388)
                      ..++++++....+..|+.+|||       |.|.|++.|-=...|++
T Consensus        24 ~~~~a~~~v~~~l~~~~~i~Gf-------GH~vy~~~DPRa~~L~~   62 (117)
T 1csh_A           24 SDEKLRDYIWNTLNSGRVVPGY-------GHAVLRKTDPRYTCQRE   62 (117)
T ss_dssp             CHHHHHHHHHHHHHTTCCCTTB-------CCSSCCSCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCEEECC-------CCCCCCCCCCCHHHHHH
T ss_conf             8899999999744368776323-------76556788852389999


No 17 
>>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus; HET: DNA; NMR {Synthetic} (B:)
Probab=22.09  E-value=43  Score=13.06  Aligned_cols=21  Identities=33%  Similarity=0.963  Sum_probs=14.8

Q ss_pred             CCCCCCCCCCCCC----CCCCHHHH
Q ss_conf             8886666725764----45620134
Q gi|254780124|r  222 GVNDDSCRFCRAK----VRCPALSR  242 (388)
Q Consensus       222 ~~~g~~CrfC~~k----~~Cra~a~  242 (388)
                      ....++|-||+-+    ..||.+-.
T Consensus         7 ~L~kDQCAyCke~GHW~~dCPk~~~   31 (40)
T 1a6b_B            7 QLDRDQCAYCKEKGHWAKDCPKKPR   31 (40)
T ss_dssp             SCCSSSCSSSCCTTCCTTSCSSSCC
T ss_pred             CCCCHHHHHHHHCCCHHHHCCCCCC
T ss_conf             6660163777534705430866778


No 18 
>>3jst_A Putative pterin-4-alpha-carbinolamine dehydratase; lyase, structural genomics, seattle structural genomics center for infectious disease; 2.10A {Brucella melitensis} (A:)
Probab=20.88  E-value=46  Score=12.90  Aligned_cols=28  Identities=39%  Similarity=0.744  Sum_probs=16.4

Q ss_pred             CCCCCEECCCCCC-CCCC--CCHHHHHHHHH
Q ss_conf             4785232058887-8611--69899999998
Q gi|254780124|r  290 EIQGYQLVEGRKG-NRSF--KDINRAQELLT  317 (388)
Q Consensus       290 ~~~g~Klv~gr~~-~r~~--~d~~~~~~~l~  317 (388)
                      ++|||++++|+.. .|.|  .|-..+...+.
T Consensus        17 ~l~~W~~~~d~~~l~r~f~f~~f~~a~~f~~   47 (97)
T 3jst_A           17 ALDGWQKVDGREAITRSFKFKDFSTAFGFMA   47 (97)
T ss_dssp             TSTTCEECTTSSCEEEEEECSSHHHHHHHHH
T ss_pred             CCCCCEEECCCCEEEEEEECCCHHHHHHHHH
T ss_conf             2999767479764999998598899999999


No 19 
>>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A mismatch, U-U mismatch, A-C mismatch, zinc finger, NC; HET: AP7; NMR {Moloney murine leukemia virus} (A:)
Probab=20.59  E-value=46  Score=12.86  Aligned_cols=21  Identities=29%  Similarity=0.858  Sum_probs=14.7

Q ss_pred             CCCCCCCCCCCCCC----CCCCHHH
Q ss_conf             78886666725764----4562013
Q gi|254780124|r  221 YGVNDDSCRFCRAK----VRCPALS  241 (388)
Q Consensus       221 ~~~~g~~CrfC~~k----~~Cra~a  241 (388)
                      ..-..++|-||+-+    .-||.+-
T Consensus        19 ppL~KDQCAyCKe~GHW~~dCPkk~   43 (56)
T 1u6p_A           19 SQLDRDQCAYCKEKGHWAKDCPKKP   43 (56)
T ss_dssp             TTCCTTBCSSSCCBSSCGGGCTTCC
T ss_pred             CCCCCCHHHHHHHCCCHHHHCCCCC
T ss_conf             9655116055511473020086667


No 20 
>>2hc4_A Vitamin D receptor; alpha helical sandwich, gene regulation; HET: VDX; 2.20A {Danio rerio} PDB: 2hbh_A* 2hcd_A* 3dr1_A* (A:1-150,A:202-302)
Probab=20.17  E-value=32  Score=13.90  Aligned_cols=10  Identities=20%  Similarity=0.291  Sum_probs=6.2

Q ss_pred             CCCCCCCCCC
Q ss_conf             6667257644
Q gi|254780124|r  226 DSCRFCRAKV  235 (388)
Q Consensus       226 ~~CrfC~~k~  235 (388)
                      ..|+||+|+-
T Consensus        27 n~Cq~CRlqK   36 (251)
T 2hc4_A           27 SYSDFVRFRP   36 (251)
T ss_dssp             TCGGGGGSCC
T ss_pred             CHHHHCCCCC
T ss_conf             5524304788


Done!