Query         gi|254781061|ref|YP_003065474.1| putative iron-sulfur cluster assembly protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 428
No_of_seqs    179 out of 1810
Neff          8.4 
Searched_HMMs 33803
Date          Wed Jun  1 22:26:43 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781061.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1vh4_A SUFD protein; structur 100.0       0       0  649.9  36.1  415    4-422     2-424 (435)
  2 >1vh4_A SUFD protein; structur  98.4  0.0002 5.8E-09   51.2  19.3  172  143-319   174-353 (435)
  3 >3bul_A Methionine synthase; t  74.7     2.9 8.5E-05   20.8   3.1   31  360-390    20-51  (59)
  4 >1msk_A Cobalamin-dependent me  69.9     4.7 0.00014   19.3   3.3   31  360-390    23-54  (62)
  5 >3ihp_A Ubiquitin carboxyl-ter  67.2     4.1 0.00012   19.7   2.5   32  360-391     8-39  (70)
  6 >2o2k_A Methionine synthase; C  66.0     4.9 0.00015   19.1   2.7   37  361-402    23-60  (74)
  7 >3ip4_B Aspartyl/glutamyl-tRNA  61.9     9.3 0.00028   17.1   6.8   57  369-425     5-67  (119)
  8 >2au3_A DNA primase; zinc ribb  61.3       8 0.00024   17.6   3.1   10   34-43     30-39  (129)
  9 >3ic3_A Putative pyruvate dehy  51.5      14  0.0004   15.9   3.8   28  373-400    63-90  (101)
 10 >1dvp_A HRS, hepatocyte growth  51.0      14 0.00041   15.8   3.9   46    4-50     16-62  (73)
 11 >1whc_A RSGI RUH-027, UBA/UBX   50.5      11 0.00034   16.5   2.4   30  362-391     3-32  (64)
 12 >2crn_A Ubash3A protein; compa  49.3     8.9 0.00026   17.2   1.7   30  362-391     3-32  (64)
 13 >2if2_A Dephospho-COA kinase;   48.4      15 0.00045   15.6   3.3   73  345-418    39-121 (132)
 14 >2qsf_X RAD23, UV excision rep  48.1      15 0.00045   15.5   2.8   35  358-392    16-50  (67)
 15 >1vek_A UBP14, ubiquitin-speci  48.0      15 0.00045   15.5   3.6   32  360-391    21-52  (84)
 16 >1oqy_A HHR23A, UV excision re  45.9      14 0.00042   15.7   2.3   33  359-391     8-40  (60)
 17 >2dag_A Ubiquitin carboxyl-ter  43.6      18 0.00052   15.0   3.7   29  363-391     4-32  (74)
 18 >2dkj_A Serine hydroxymethyltr  42.9      18 0.00054   15.0   4.8   40  375-416   120-159 (163)
 19 >1yqf_A Hypothetical protein L  41.7      19 0.00056   14.8   3.6   39  360-398   147-189 (203)
 20 >2g3q_A Protein YBL047C; endoc  38.0      21 0.00063   14.5   2.9   29  365-393     1-29  (43)
 21 >2cpw_A CBL-interacting protei  36.1      22 0.00065   14.4   2.0   31  361-391    12-42  (64)
 22 >1wji_A Tudor domain containin  34.4      24 0.00071   14.1   3.9   32  362-393     3-34  (63)
 23 >1ify_A HHR23A, UV excision re  33.6      25 0.00073   14.0   2.3   31  363-393     3-33  (49)
 24 >2csb_A Topoisomerase V, TOP61  32.8      25 0.00075   13.9   3.1   15  377-391     2-16  (48)
 25 >1r5l_A Alpha-TTP, protein (al  32.2      26 0.00077   13.8   3.4   32  363-394    27-59  (74)
 26 >1dv0_A DNA repair protein HHR  32.1      18 0.00054   15.0   1.1   27  365-391     1-27  (47)
 27 >1aua_A Phosphatidylinositol t  32.0      26 0.00078   13.8   3.4   27  368-394    32-58  (73)
 28 >3eaf_A ABC transporter, subst  31.9      26 0.00078   13.8   3.2   50  375-424   136-190 (210)
 29 >1yqg_A Pyrroline-5-carboxylat  30.6      28 0.00082   13.6   3.9   36  375-410    16-55  (58)
 30 >2e1z_A Propionate kinase; TDC  30.4      28 0.00082   13.6   3.7   32  360-391    73-105 (220)
 31 >1wiv_A UBP14, ubiquitin-speci  30.3      28 0.00083   13.6   3.4   38  356-393    17-54  (73)
 32 >3ihp_A Ubiquitin carboxyl-ter  28.8      30 0.00087   13.4   3.9   33  361-393     7-39  (75)
 33 >1vg5_A RSGI RUH-014, rhomboid  28.0      30  0.0009   13.3   3.5   35  359-393    20-54  (73)
 34 >2v6z_M DNA polymerase epsilon  26.6      32 0.00095   13.2   2.8   33   21-55     20-52  (99)
 35 >2rcy_A Pyrroline carboxylate   25.7      33 0.00099   13.0   3.5   38  373-410    14-55  (58)
 36 >2izz_A Pyrroline-5-carboxylat  25.5      34 0.00099   13.0   3.3   38  373-410    15-56  (59)
 37 >2dak_A Ubiquitin carboxyl-ter  24.7      35   0.001   12.9   3.6   32  362-393     3-34  (63)
 38 >1wgn_A UBAP1, ubiquitin assoc  23.9      31 0.00093   13.2   1.1   31  362-392    13-43  (63)
 39 >3khy_A Propionate kinase; csg  23.5      36  0.0011   12.8   2.5   32  360-391    72-104 (212)
 40 >2ztd_A Holliday junction ATP-  23.0      37  0.0011   12.7   5.0   51  361-416     3-53  (58)
 41 >3c24_A Putative oxidoreductas  23.0      28 0.00082   13.6   0.7   28  363-390     6-34  (72)
 42 >2hoq_A Putative HAD-hydrolase  22.8      35   0.001   12.9   1.2   37   24-63      4-40  (83)
 43 >1ryp_D 20S proteasome; multic  22.8      38  0.0011   12.7   1.6   60  360-419   158-240 (241)
 44 >1bf6_A Phosphotriesterase hom  22.4      38  0.0011   12.6   2.3   27  365-391   113-139 (146)
 45 >1veg_A NEDD8 ultimate buster-  22.2      38  0.0011   12.6   3.4   38  355-392    16-53  (83)
 46 >3krn_A Protein C14A4.5, confi  21.1      40  0.0012   12.4   4.1   87  302-400     4-91  (102)
 47 >2ahr_A Putative pyrroline car  20.5      42  0.0012   12.3   3.3   37  374-410    15-55  (58)

No 1  
>>1vh4_A SUFD protein; structural genomics, protein binding protein; 1.75A {Escherichia coli} (A:)
Probab=100.00  E-value=0  Score=649.89  Aligned_cols=415  Identities=23%  Similarity=0.335  Sum_probs=371.7

Q ss_pred             CCHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCC-CCCCCHH
Q ss_conf             3279999999999998617-8877899999999999998283239972474258878977513576443211-1111000
Q gi|254781061|r    4 LTAVETMLLQSCDEACQKY-YRNQSVVAFRRRLLCDFRTQGLLPTRKIENWHYTDLKNILKVLPTNKNSIAT-LQKKYKP   81 (428)
Q Consensus         4 ~t~~~~~l~~~f~~~~~~~-~~~~~~~~~R~~a~~~F~~~G~lPtkK~E~WKyT~l~~l~~~~~~~~~~~~~-~~~~~~~   81 (428)
                      |++....+.+.+...++.. ..+.|+.++|++|++.|+++| ||++|+|.|||||++.+....+........ .......
T Consensus         2 m~~~~~~l~~~~~~~~s~~~~ep~wl~~~R~~a~~~~~~l~-~P~~~~e~wryt~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (435)
T 1vh4_A            2 LMAGLPNSSNALQQWHHLFEAEGTKRSPQAQQHLQQLLRTG-LPTRKHENWKYTPLEGLINSQFVSIAGEISPQQRDALA   80 (435)
T ss_dssp             ---------CHHHHHHHHHHC---CCCHHHHHHHHHHHHHC-CCCTTSTTCTTCCCHHHHTSCEECCCCCCCHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHC-CCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCHHHHHCC
T ss_conf             54558887699999999986227747599999999999829-78998708137987997454776557766800210001


Q ss_pred             HCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHCCCCHHHCCCCCCCCCCHHHHHHHHHCCCCEEEEEECCEEECCCEEEE
Q ss_conf             01581599983465420004457541005652124201000134555445667887521387487730544770230343
Q gi|254781061|r   82 LVADSIQLSISQQPSSSILKEKNIEVLPFSHIENTDENSYCLEPLSEHDTIGYINGILSNDGYKVVIPDECQLNVPLELQ  161 (428)
Q Consensus        82 ~~~d~~~i~~~~~~~~~~l~~~~i~~~~~~~~~~~~~~~~~~~~~~~~d~f~~LN~A~~~~g~~I~V~~~~~~~~PI~i~  161 (428)
                      ...+...+++.++.+.+.++..........   ...............++|.+||.|++++|++|+||+++++++||+++
T Consensus        81 ~~~~~~~~~~v~g~~~~~~~~l~~~~~~~~---~~~~~~~~~~~~~~~~~~~aln~a~~~~g~~i~v~~~~~~~~Pi~i~  157 (435)
T 1vh4_A           81 LTLDSVRLVFVDGRYVPALSDATEGSGYEV---SINDDRQGLPDAIQAEVFLHLTESLAQSVTHIAVKRGQRPAKPLLLM  157 (435)
T ss_dssp             CCCCSEEEEEETTEECGGGSCCCTTSSCEE---EEESCCTTCCCCSSCCHHHHHHHHHCSCEEEEEECTTCCCSSCEEEE
T ss_pred             CCCCCEEEEEECCEECCCCCCCCCCCCEEE---ECHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCEEECCCCEEE
T ss_conf             346760599778888120156755676076---23777753054442257899876230233201014524750453036


Q ss_pred             EECCC------CCCCEEEEEECCCCCCEEEEEECCCCCCCCEEECCCEEEEECCCCEEEEEECCCCCCCEEEEEECEEEE
Q ss_conf             20223------222101210017986135553035667552010031289964886376630024565301432000112
Q gi|254781061|r  162 AIQCG------GQMHLRYPISFGMNSRTTVVERYTTLTNDNSFVSSIADIKVGEGADITWVIVLDQGIEDTHLGQLRVIL  235 (428)
Q Consensus       162 ~~~~~------~~~~~r~~I~v~~ns~~~iiE~~~~~~~~~~~~n~~~ei~l~~~A~l~~~~iq~~~~~s~~~~~~~~~~  235 (428)
                      ++..+      ...++|++|++++||+++|+|.|.+.....+|++.++++++++||+|+|+.+|+++..++++...++.+
T Consensus       158 ~~~~~~~~~~~~~~~~~~~i~~~~~s~~~iie~~~~~~~~~~~~~~~~ei~~~~~A~l~~~~i~~~~~~~~~~~~~~~~~  237 (435)
T 1vh4_A          158 HITQGVAGEEVNTAHYRHHLDLAEGAEATVIEHFVSLNDARHFTGARFTINVAANAHLQHIKLAFENPLSHHFAHNDLLL  237 (435)
T ss_dssp             EEECCCSSSCEEEEEEEEEEEECTTCEEEEEEEEEESSSSCEEEEEEEEEEECTTCEEEEEEEECCCTTCEEEEEEEEEE
T ss_pred             EEECCCCCCCCCCEEEEEEEEECCCCHHHHHHHHCCCCCHHHHCCCEEEEEECCCCEEEEHHHHHCCCCCCCCCHHHHHH
T ss_conf             75036454444420157899742530345555421221001000421689841443343001343034432120222102


Q ss_pred             CCCCCEEEEEEECCCCCEEEEEEEEEECCCCEEEEEEEEECCCCCCHHHHHHHHHCCCCCEEEEEEEEEECCCCEEEEEC
Q ss_conf             03551467786425651244335665135412466334422744100111222212777526888730004885278741
Q gi|254781061|r  236 EKKSSLKVFVLNIGQGLSRRELSIDVKGEESQFMLRGINLLSGKAHSDLSMFLRHKVPNTCSTSVIRNIVLEKSTGVFQG  315 (428)
Q Consensus       236 ~~~S~~~~~~~~~Gg~~~R~~i~i~L~Ge~a~~~~~g~~l~~~~q~~D~~~~i~H~~~~t~S~~~~k~vl~d~s~~vf~G  315 (428)
                      +++|++++.++.+||+++|+++.+.|.|+||+++++|++++.++|+.|+++.|+|.+|+|+|+|++|||+.|+|+++|+|
T Consensus       238 ~~~a~~~~~~~~~g~~~~~~~~~~~l~g~~a~~~~~g~~~~~~~q~~d~~~~v~h~~~~t~s~~~~k~vl~d~s~~vf~G  317 (435)
T 1vh4_A          238 AEDATAFSHSFLLGGAVLRHNTSTQLNGENSTLRINSLAMPVKNEVCDTRTWLEHNKGFCNSRQLHKTIVSDKGRAVFNG  317 (435)
T ss_dssp             CTTCEEEEEEEECCCSEEEEEEEEEECSTTCEEEEEEEECCCTTCEEEEEEEEEECSSSCEEEEEEEEEECTTCEEEEEE
T ss_pred             CCCCCEEEEEECCCCCEEEEECCCCCCCCHHHEEEEECCCCCCCHHHHHHHHHHCCCCCCCCEEHHCCCCCCCCEEEEEE
T ss_conf             35652389864156511110011114400111001102456630364543222015553222002103333686269854


Q ss_pred             CCCCCCCCCCCCCCEEEEEEEECCCEEEEEEEEEEEECCCCEEEEEEEECCCCHHHHHHHHHCCCCHHHHHHHHHHHHHH
Q ss_conf             01013664100000000046612871798121247713873365542212389999999994688989999999999999
Q gi|254781061|r  316 AVHVSSEAQGSNARMTANTLLFSNEGSFYVKPELEIFADDVQCGHGATISDINPEHLYYLMARGISKNQACSMLSHAFMS  395 (428)
Q Consensus       316 ~i~V~~~a~~t~~~q~~~~llLs~~a~~~s~P~LeI~~ddV~~~Hgatvg~id~e~lfYl~sRGi~~~~A~~lli~gF~~  395 (428)
                      +|+|.++|+||+|+|.|++||||++|+++|+|.|||++|||+|+||||||+||+|||||||||||++++|++||+.||++
T Consensus       318 ~i~i~~~A~~s~a~q~~~~LlLs~~A~~~s~P~LeI~~dDV~~sHgAtvG~id~e~LFYL~SRGi~~~~A~~Llv~gF~~  397 (435)
T 1vh4_A          318 LINVAQHAIKTDGQMTNNNLLMGKLAEVDTKPQLEIYADDVKCSHGATVGRIDDEQIFYLRSRGINQQDAQQMIIYAFAA  397 (435)
T ss_dssp             EEEECTTCTTEEEEEEEEEEECSTTCEEEEEEEEEECCSSEEEEEEEEEECCCHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHHEEEECCCCEEEECCEEEEECCCEEEEEEEECCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             40336663166767655406505884166562389963972699402146789899999987699999999999999899


Q ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             998858978999999999999974138
Q gi|254781061|r  396 EIVEDLNDQVLQFSIEEILSSWLKNNS  422 (428)
Q Consensus       396 ~~i~~i~~~~~~~~~~~~i~~~l~~~~  422 (428)
                      |++++||++.+|+++.+.|++||....
T Consensus       398 ~vl~~i~~e~lr~~i~~~i~~~l~~~~  424 (435)
T 1vh4_A          398 ELTEALRDEGLKQQVLARIGQRLPGGA  424 (435)
T ss_dssp             HHHTTCCCHHHHHHHHHHHHTTSTTC-
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             999869859999999999998611422


No 2  
>>1vh4_A SUFD protein; structural genomics, protein binding protein; 1.75A {Escherichia coli} (A:)
Probab=98.42  E-value=0.0002  Score=51.20  Aligned_cols=172  Identities=9%  Similarity=-0.013  Sum_probs=120.4

Q ss_pred             CEEEEEECCEEECCCEEEEEECCCC---CCCEEEEEECCCCCCEEEEEECCCCCCCCEEECCCEEEEECCCCEEEEEECC
Q ss_conf             7487730544770230343202232---2210121001798613555303566755201003128996488637663002
Q gi|254781061|r  143 GYKVVIPDECQLNVPLELQAIQCGG---QMHLRYPISFGMNSRTTVVERYTTLTNDNSFVSSIADIKVGEGADITWVIVL  219 (428)
Q Consensus       143 g~~I~V~~~~~~~~PI~i~~~~~~~---~~~~r~~I~v~~ns~~~iiE~~~~~~~~~~~~n~~~ei~l~~~A~l~~~~iq  219 (428)
                      ...|.+.+|.++.  |...+...+.   ..+..+.|.+++||+++++.......  ..+....+.+.++++|.++++.+.
T Consensus       174 ~~~i~~~~~s~~~--iie~~~~~~~~~~~~~~~~ei~~~~~A~l~~~~i~~~~~--~~~~~~~~~~~~~~~a~~~~~~~~  249 (435)
T 1vh4_A          174 RHHLDLAEGAEAT--VIEHFVSLNDARHFTGARFTINVAANAHLQHIKLAFENP--LSHHFAHNDLLLAEDATAFSHSFL  249 (435)
T ss_dssp             EEEEEECTTCEEE--EEEEEEESSSSCEEEEEEEEEEECTTCEEEEEEEECCCT--TCEEEEEEEEEECTTCEEEEEEEE
T ss_pred             EEEEEECCCCHHH--HHHHHCCCCCHHHHCCCEEEEEECCCCEEEEHHHHHCCC--CCCCCCHHHHHHCCCCCEEEEEEC
T ss_conf             7899742530345--555421221001000421689841443343001343034--432120222102356523898641


Q ss_pred             CCCCCEEEEEECEEEECCCCCEEEEEEECCCCCEEE--EEEEEEECCCCEEEEEEEEECCCCCC--HHHHHHHHHCCCCC
Q ss_conf             456530143200011203551467786425651244--33566513541246633442274410--01112222127775
Q gi|254781061|r  220 DQGIEDTHLGQLRVILEKKSSLKVFVLNIGQGLSRR--ELSIDVKGEESQFMLRGINLLSGKAH--SDLSMFLRHKVPNT  295 (428)
Q Consensus       220 ~~~~~s~~~~~~~~~~~~~S~~~~~~~~~Gg~~~R~--~i~i~L~Ge~a~~~~~g~~l~~~~q~--~D~~~~i~H~~~~t  295 (428)
                      ..+..+. ........+++|.++...+.++.+-.+.  ...+...|+++.+++....++.++.+  +.=...|.+.+..|
T Consensus       250 ~g~~~~~-~~~~~~l~g~~a~~~~~g~~~~~~~q~~d~~~~v~h~~~~t~s~~~~k~vl~d~s~~vf~G~i~i~~~A~~s  328 (435)
T 1vh4_A          250 LGGAVLR-HNTSTQLNGENSTLRINSLAMPVKNEVCDTRTWLEHNKGFCNSRQLHKTIVSDKGRAVFNGLINVAQHAIKT  328 (435)
T ss_dssp             CCCSEEE-EEEEEEECSTTCEEEEEEEECCCTTCEEEEEEEEEECSSSCEEEEEEEEEECTTCEEEEEEEEEECTTCTTE
T ss_pred             CCCCEEE-EECCCCCCCCHHHEEEEECCCCCCCHHHHHHHHHHCCCCCCCCEEHHCCCCCCCCEEEEEEEECCCCCCHHH
T ss_conf             5651111-001111440011100110245663036454322201555322200210333368626985440336663166


Q ss_pred             EEEEEEEEEECC-CCEEEEECCCCC
Q ss_conf             268887300048-852787410101
Q gi|254781061|r  296 CSTSVIRNIVLE-KSTGVFQGAVHV  319 (428)
Q Consensus       296 ~S~~~~k~vl~d-~s~~vf~G~i~V  319 (428)
                      .+.|..++++-+ .|+..=.-.+.|
T Consensus       329 ~a~q~~~~LlLs~~A~~~s~P~LeI  353 (435)
T 1vh4_A          329 DGQMTNNNLLMGKLAEVDTKPQLEI  353 (435)
T ss_dssp             EEEEEEEEEECSTTCEEEEEEEEEE
T ss_pred             HHHHHHHEEEECCCCEEEECCEEEE
T ss_conf             7676554065058841665623899


No 3  
>>3bul_A Methionine synthase; transferase, reactivation conformation, cobalamin, intermodular interactions, amino-acid biosynthesis, cobalt; HET: B12; 2.30A {Escherichia coli} (A:252-273,A:543-579)
Probab=74.73  E-value=2.9  Score=20.80  Aligned_cols=31  Identities=16%  Similarity=0.343  Sum_probs=26.4

Q ss_pred             EEEEECCCCHHHHH-HHHHCCCCHHHHHHHHH
Q ss_conf             54221238999999-99946889899999999
Q gi|254781061|r  360 HGATISDINPEHLY-YLMARGISKNQACSMLS  390 (428)
Q Consensus       360 Hgatvg~id~e~lf-Yl~sRGi~~~~A~~lli  390 (428)
                      ..-+||+|+++|+- |-+-||++.+++++.|-
T Consensus        20 ~~~~VGKI~kDQVeDYA~RKg~~leeaERWLa   51 (59)
T 3bul_A           20 QAYAVAQIQRDQVEDYARRKGMSVTEVERWLA   51 (59)
T ss_dssp             GGCCCCCBCHHHHHHHHHHTTCCHHHHHHHTG
T ss_pred             CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             66737867688999999865999999998740


No 4  
>>1msk_A Cobalamin-dependent methionine synthase; methyltransferase, transferase, methionine biosynthesis, vitamin B12; HET: SAM; 1.80A {Escherichia coli K12} (A:1-25,A:295-331)
Probab=69.87  E-value=4.7  Score=19.27  Aligned_cols=31  Identities=16%  Similarity=0.343  Sum_probs=25.9

Q ss_pred             EEEEECCCCHHHHH-HHHHCCCCHHHHHHHHH
Q ss_conf             54221238999999-99946889899999999
Q gi|254781061|r  360 HGATISDINPEHLY-YLMARGISKNQACSMLS  390 (428)
Q Consensus       360 Hgatvg~id~e~lf-Yl~sRGi~~~~A~~lli  390 (428)
                      ..-+||+|++||+- |-.-||++.+++++.|-
T Consensus        23 ~~yaVGKI~kDQveDYA~RKg~~~~e~ERWLa   54 (62)
T 1msk_A           23 QAYAVAQIQRDQVEDYARRKGMSVTEVERWLA   54 (62)
T ss_dssp             TTCCCCCBCHHHHHHHHHHHTCCHHHHHHHHG
T ss_pred             CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             67826756688999999974999999998740


No 5  
>>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens} (A:637-706)
Probab=67.18  E-value=4.1  Score=19.68  Aligned_cols=32  Identities=6%  Similarity=0.081  Sum_probs=27.7

Q ss_pred             EEEEECCCCHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             54221238999999999468898999999999
Q gi|254781061|r  360 HGATISDINPEHLYYLMARGISKNQACSMLSH  391 (428)
Q Consensus       360 Hgatvg~id~e~lfYl~sRGi~~~~A~~lli~  391 (428)
                      .......+|++.|-.|++.|++++.|++-|..
T Consensus         8 ~~~~~~~~d~~~i~~L~~MGF~~~~a~kAL~~   39 (70)
T 3ihp_A            8 DEPKAPMLDESVIIQLVEMGFPMDACRKAVYY   39 (70)
T ss_dssp             ---------CHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             23345544415565676438887875666652


No 6  
>>2o2k_A Methionine synthase; C-shaped, twisted anti-parallel beta sheet, beta-meander region, transferase; 1.60A {Homo sapiens} (A:1-24,A:306-355)
Probab=66.00  E-value=4.9  Score=19.09  Aligned_cols=37  Identities=16%  Similarity=0.262  Sum_probs=28.5

Q ss_pred             EEEECCCCHHHHH-HHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             4221238999999-99946889899999999999999988589
Q gi|254781061|r  361 GATISDINPEHLY-YLMARGISKNQACSMLSHAFMSEIVEDLN  402 (428)
Q Consensus       361 gatvg~id~e~lf-Yl~sRGi~~~~A~~lli~gF~~~~i~~i~  402 (428)
                      +-+||+|++||+- |-.-||++.++|++.|     .+.+..-|
T Consensus        23 ~~aVGKI~kDQVeDYA~RKG~~leeaERWL-----APnL~Ydp   60 (74)
T 2o2k_A           23 SEAVGKISKDQVEDYALRKNISVAEVEKWL-----GPILGYDT   60 (74)
T ss_dssp             GCCCCCBCHHHHHHHHHHHTCCHHHHHHHT-----GGGBSCC-
T ss_pred             CCCCCCCCHHHHHHHHHHCCCCHHHHHHHH-----CCCCCCCC
T ss_conf             681575668999999987499999999985-----10117892


No 7  
>>3ip4_B Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; multi protein complex, ligase, ATP-binding, nucleotide- binding; 1.90A {Staphylococcus aureus subsp} PDB: 2df4_B 2dqn_B* 2g5h_B 2g5i_B* 2f2a_B (B:293-411)
Probab=61.87  E-value=9.3  Score=17.07  Aligned_cols=57  Identities=14%  Similarity=0.187  Sum_probs=44.2

Q ss_pred             HHHHHHHHHC-CCCHHHHHHHH----HHHHHHHHHHHCCCH-HHHHHHHHHHHHHHHHCCCCC
Q ss_conf             9999999946-88989999999----999999998858978-999999999999974138761
Q gi|254781061|r  369 PEHLYYLMAR-GISKNQACSML----SHAFMSEIVEDLNDQ-VLQFSIEEILSSWLKNNSANM  425 (428)
Q Consensus       369 ~e~lfYl~sR-Gi~~~~A~~ll----i~gF~~~~i~~i~~~-~~~~~~~~~i~~~l~~~~~~~  425 (428)
                      ++..=.|++. ||+..+|+.|+    +..|+.++++...+. .+.+|+...+-+.|++++..+
T Consensus         5 ~~~~~Rl~~~ygLs~~~A~~L~~~~~l~~yFe~~~~~~~~~k~~anwi~~el~~~ln~~~~~~   67 (119)
T 3ip4_B            5 DERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVEL   67 (119)
T ss_dssp             HHHHHHHHHTSCCCHHHHHHHTSSHHHHHHHHHHHTTTCCHHHHHHHHHTHHHHHHHHTTCCG
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999998709987875543100677888887764366348899999999988754025644


No 8  
>>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus} (A:96-224)
Probab=61.34  E-value=8  Score=17.55  Aligned_cols=10  Identities=10%  Similarity=0.125  Sum_probs=3.7

Q ss_pred             HHHHHHHHCC
Q ss_conf             9999999828
Q gi|254781061|r   34 RLLCDFRTQG   43 (428)
Q Consensus        34 ~a~~~F~~~G   43 (428)
                      +|++=+++.|
T Consensus        30 ~a~~YL~~Rg   39 (129)
T 2au3_A           30 EASEYVKSRG   39 (129)
T ss_dssp             HHHHHHHHTT
T ss_pred             HHHHHHHHCC
T ss_conf             7999988648


No 9  
>>3ic3_A Putative pyruvate dehydrogenase; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; HET: MSE BGC; 1.80A {Rhodopseudomonas palustris} (A:)
Probab=51.50  E-value=14  Score=15.89  Aligned_cols=28  Identities=14%  Similarity=0.248  Sum_probs=24.5

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999468898999999999999999885
Q gi|254781061|r  373 YYLMARGISKNQACSMLSHAFMSEIVED  400 (428)
Q Consensus       373 fYl~sRGi~~~~A~~lli~gF~~~~i~~  400 (428)
                      -|-++-|+++++|..+|+.+|-.|+.+.
T Consensus        63 aya~~~g~~~~eal~~I~~~F~~E~~~P   90 (101)
T 3ic3_A           63 SYARESEYTEDEALERIVEXFEAELSRP   90 (101)
T ss_dssp             HHHHTSSCCHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             9987128999999999999998875587


No 10 
>>1dvp_A HRS, hepatocyte growth factor-regulated tyrosine kinase substrate; VHS, FYVE, zinc finger, superhelix; HET: CIT; 2.00A {Drosophila melanogaster} (A:84-156)
Probab=51.01  E-value=14  Score=15.83  Aligned_cols=46  Identities=11%  Similarity=0.197  Sum_probs=26.1

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCC-CCCCCCC
Q ss_conf             3279999999999998617887789999999999999828-3239972
Q gi|254781061|r    4 LTAVETMLLQSCDEACQKYYRNQSVVAFRRRLLCDFRTQG-LLPTRKI   50 (428)
Q Consensus         4 ~t~~~~~l~~~f~~~~~~~~~~~~~~~~R~~a~~~F~~~G-~lPtkK~   50 (428)
                      .+.|+..+++....+....++...+.-++ +++..++..| .||..+.
T Consensus        16 ~~~Vk~kiL~li~~Wa~~f~~~~~l~~i~-~~Y~~Lk~~G~~FP~~~~   62 (73)
T 1dvp_A           16 HENVRQKMLELVQTWAYAFRSSDKYQAIK-DTMTILKAKGHTFPELRE   62 (73)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTTCSSCCHHH-HHHHHHHHTTCCCCCCCC
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCCCCHHHH-HHHHHHHHCCCCCCCCCC
T ss_conf             88999999999999999807884408999-999999977866665431


No 11 
>>1whc_A RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain, structural genomics, riken structural genomics/proteomics initiative, unknown function; NMR {Mus musculus} (A:)
Probab=50.49  E-value=11  Score=16.45  Aligned_cols=30  Identities=20%  Similarity=0.182  Sum_probs=25.7

Q ss_pred             EEECCCCHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             221238999999999468898999999999
Q gi|254781061|r  362 ATISDINPEHLYYLMARGISKNQACSMLSH  391 (428)
Q Consensus       362 atvg~id~e~lfYl~sRGi~~~~A~~lli~  391 (428)
                      +..-.+|++.|=.|+.-|+++..|++-|..
T Consensus         3 ~~~~~~d~~~l~~L~eMGF~~~~a~kAL~~   32 (64)
T 1whc_A            3 SGSSGAELTALESLIEMGFPRGRAEKALAL   32 (64)
T ss_dssp             CCCCCCCCCHHHHHHTTTCCHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             887756999999999959999999999999


No 12 
>>2crn_A Ubash3A protein; compact three-helix bundle, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:)
Probab=49.33  E-value=8.9  Score=17.22  Aligned_cols=30  Identities=27%  Similarity=0.261  Sum_probs=25.6

Q ss_pred             EEECCCCHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             221238999999999468898999999999
Q gi|254781061|r  362 ATISDINPEHLYYLMARGISKNQACSMLSH  391 (428)
Q Consensus       362 atvg~id~e~lfYl~sRGi~~~~A~~lli~  391 (428)
                      +..-.+|++.|=.|++-|++++.|++-|..
T Consensus         3 ~~~~~~d~~~l~~L~eMGF~~~~a~kAL~~   32 (64)
T 2crn_A            3 SGSSGSSPSLLEPLLAMGFPVHTALKALAA   32 (64)
T ss_dssp             CSSCCCSCSSHHHHHHTSCCHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             887898848888999836738999999998


No 13 
>>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 3.00A {Aquifex aeolicus VF5} (A:1-30,A:103-204)
Probab=48.36  E-value=15  Score=15.55  Aligned_cols=73  Identities=10%  Similarity=-0.041  Sum_probs=45.4

Q ss_pred             EEEEE-EEECCCCEEEEEEEECCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHH-HHHH----CCC----HHHHHHHHHHH
Q ss_conf             12124-77138733655422123899999999946889899999999999999-9885----897----89999999999
Q gi|254781061|r  345 VKPEL-EIFADDVQCGHGATISDINPEHLYYLMARGISKNQACSMLSHAFMSE-IVED----LND----QVLQFSIEEIL  414 (428)
Q Consensus       345 s~P~L-eI~~ddV~~~Hgatvg~id~e~lfYl~sRGi~~~~A~~lli~gF~~~-~i~~----i~~----~~~~~~~~~~i  414 (428)
                      -.|.| |.. -+-.|..=-+|.-=.+.++=-+|+||+++++|++.+-.=.-.+ -+..    |.+    +.+++.+...+
T Consensus        39 EiPLLfEsg-~~~~~D~Vi~V~a~~e~ri~Rl~~Rg~S~eea~~Ri~sQ~s~eeK~~~AD~VIdN~gsle~L~~qV~~ll  117 (132)
T 2if2_A           39 EASLLVEKG-TYKNYDKLIVVYAPYEVCKERAIKRGXSEEDFERRWKKQXPIEEKVKYADYVIDNSGSIEETYKQVKKVY  117 (132)
T ss_dssp             ECSCSTTTT-CGGGSSEEEEECCCHHHHHHHHHHTCCCHHHHHHHHTTSCCHHHHGGGCSEECCCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHCC-CCCCCCEEEEEECCHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHCCEEEECCCCHHHHHHHHHHHH
T ss_conf             344221024-4422667999852200178898702588999999999679989989859999989999999999999999


Q ss_pred             HHHH
Q ss_conf             9997
Q gi|254781061|r  415 SSWL  418 (428)
Q Consensus       415 ~~~l  418 (428)
                      ++.+
T Consensus       118 ~~L~  121 (132)
T 2if2_A          118 EELT  121 (132)
T ss_dssp             HTTC
T ss_pred             HHHH
T ss_conf             9982


No 14 
>>2qsf_X RAD23, UV excision repair protein RAD23; alpha-beta structure, beta hairpin, transglutaminase fold, DNA-damage recognition, DNA repair; HET: DNA; 2.35A {Saccharomyces cerevisiae} PDB: 2qsg_X* 2qsh_X* 1x3z_B* 1x3w_B* 3esw_B* (X:105-171)
Probab=48.11  E-value=15  Score=15.53  Aligned_cols=35  Identities=6%  Similarity=0.059  Sum_probs=30.5

Q ss_pred             EEEEEEECCCCHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             65542212389999999994688989999999999
Q gi|254781061|r  358 CGHGATISDINPEHLYYLMARGISKNQACSMLSHA  392 (428)
Q Consensus       358 ~~Hgatvg~id~e~lfYl~sRGi~~~~A~~lli~g  392 (428)
                      ..++.++...+++.|==|++=|+++..|++-|...
T Consensus        16 ~~~~~~~~~~~~~~i~~L~~MGF~~~~a~~AL~~~   50 (67)
T 2qsf_X           16 GSFQVDYTPEDDQAISRLCELGFERDLVIQVYFAC   50 (67)
T ss_dssp             -EECCCCCHHHHHHHHHHHTTTCCHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             87766788114999999998499999999999990


No 15 
>>1vek_A UBP14, ubiquitin-specific protease 14, putative; UBA domain, three helix bundle, ubiquitin associated domain, structural genomics; NMR {Arabidopsis thaliana} (A:)
Probab=47.98  E-value=15  Score=15.51  Aligned_cols=32  Identities=16%  Similarity=0.077  Sum_probs=26.6

Q ss_pred             EEEEECCCCHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             54221238999999999468898999999999
Q gi|254781061|r  360 HGATISDINPEHLYYLMARGISKNQACSMLSH  391 (428)
Q Consensus       360 Hgatvg~id~e~lfYl~sRGi~~~~A~~lli~  391 (428)
                      -+.....+|++.|=.|++-|+++..|++-|..
T Consensus        21 ~~~~~~~~d~~~l~~L~~MGF~~~~a~kAL~~   52 (84)
T 1vek_A           21 MESAQPVANEEIVAQLVSMGFSQLHCQKAAIN   52 (84)
T ss_dssp             CCSCCCCCCHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             67688989999999999959999999999999


No 16 
>>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} (A:309-368)
Probab=45.94  E-value=14  Score=15.75  Aligned_cols=33  Identities=12%  Similarity=0.028  Sum_probs=27.6

Q ss_pred             EEEEEECCCCHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             554221238999999999468898999999999
Q gi|254781061|r  359 GHGATISDINPEHLYYLMARGISKNQACSMLSH  391 (428)
Q Consensus       359 ~Hgatvg~id~e~lfYl~sRGi~~~~A~~lli~  391 (428)
                      ...++..+.++++|=.|++=|++++.|++-|..
T Consensus         8 ~~~~~~~~~~e~~i~~L~~MGF~~~~a~~AL~~   40 (60)
T 1oqy_A            8 MNYIQVTPQEKEAIERLKALGFPESLVIQAYFA   40 (60)
T ss_dssp             CSSCCCCTTTHHHHHHHHHHTCCSHHHHHHTSS
T ss_pred             CCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             787889989999999999849998999999998


No 17 
>>2dag_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5 (USP 5), UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:)
Probab=43.58  E-value=18  Score=15.05  Aligned_cols=29  Identities=10%  Similarity=0.122  Sum_probs=25.3

Q ss_pred             EECCCCHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             21238999999999468898999999999
Q gi|254781061|r  363 TISDINPEHLYYLMARGISKNQACSMLSH  391 (428)
Q Consensus       363 tvg~id~e~lfYl~sRGi~~~~A~~lli~  391 (428)
                      +...+|++.|=-|+.-|+++..|++-|..
T Consensus         4 ~~~~~d~~~l~~L~eMGF~~~~a~kAL~~   32 (74)
T 2dag_A            4 GSSGLDESVIIQLVEMGFPMDACRKAVYY   32 (74)
T ss_dssp             CCCSSCHHHHHHHHHHSCCHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             88998999999999959999999999999


No 18 
>>2dkj_A Serine hydroxymethyltransferase; PLP dependent enzyme, structural genomics, NPPSFA; HET: PLP; 1.15A {Thermus thermophilus HB8} (A:1-32,A:277-407)
Probab=42.89  E-value=18  Score=14.97  Aligned_cols=40  Identities=8%  Similarity=0.173  Sum_probs=32.1

Q ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             994688989999999999999998858978999999999999
Q gi|254781061|r  375 LMARGISKNQACSMLSHAFMSEIVEDLNDQVLQFSIEEILSS  416 (428)
Q Consensus       375 l~sRGi~~~~A~~lli~gF~~~~i~~i~~~~~~~~~~~~i~~  416 (428)
                      +.+||+.+++-+.  +-.|+..++....++.+|..+.+...+
T Consensus       120 iTtRG~~e~d~~~--IA~lI~~vL~~~~~e~ik~~V~~L~~~  159 (163)
T 2dkj_A          120 ITTRGFTPEEMPL--VAELIDRALLEGPSEALREEVRRLALA  159 (163)
T ss_dssp             HHHTTCCGGGHHH--HHHHHHHHHHHCCCHHHHHHHHHHHHT
T ss_pred             HHHCCCCHHHHHH--HHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             9857998899999--999999999649869999999999982


No 19 
>>1yqf_A Hypothetical protein LMAJ011689; structural genomics, PSI, protein structure initiative, structural genomics of pathogenic protozoa consortium; 2.30A {Leishmania major} (A:)
Probab=41.70  E-value=19  Score=14.85  Aligned_cols=39  Identities=18%  Similarity=0.354  Sum_probs=27.8

Q ss_pred             EEEEECCCCHH----HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             54221238999----9999994688989999999999999998
Q gi|254781061|r  360 HGATISDINPE----HLYYLMARGISKNQACSMLSHAFMSEIV  398 (428)
Q Consensus       360 Hgatvg~id~e----~lfYl~sRGi~~~~A~~lli~gF~~~~i  398 (428)
                      -|.-...||++    -+=||..|||+.+-|..|.-.....|--
T Consensus       147 ~GP~f~~LD~~Lq~~~~~yL~erGI~~~la~fl~~~~~~kE~~  189 (203)
T 1yqf_A          147 TGPLVHELDYDLLNCVMTYLEKRGVDEKLGEFVVLYSFWAEQQ  189 (203)
T ss_dssp             CCCCGGGSBHHHHHHHHHHHHHTTCSHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             7988021389999999999999399999999999999999999


No 20 
>>2g3q_A Protein YBL047C; endocytosis, solution structure, UBA domain, endocytosis/signaling protein complex; NMR {Saccharomyces cerevisiae} (A:)
Probab=38.02  E-value=21  Score=14.46  Aligned_cols=29  Identities=14%  Similarity=0.125  Sum_probs=24.6

Q ss_pred             CCCCHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             23899999999946889899999999999
Q gi|254781061|r  365 SDINPEHLYYLMARGISKNQACSMLSHAF  393 (428)
Q Consensus       365 g~id~e~lfYl~sRGi~~~~A~~lli~gF  393 (428)
                      ++.|++.+=-|+.=|+++++|++-|....
T Consensus         1 s~~~~~~v~~L~~MGF~~~~a~~AL~~~~   29 (43)
T 2g3q_A            1 TTPKSLAVEELSGMGFTEEEAHNALEKCN   29 (43)
T ss_dssp             CCHHHHHHHHHHTTTSCHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf             98849999999976999999999999929


No 21 
>>2cpw_A CBL-interacting protein STS-1 variant; ubiquitin associated domain, UBA, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens} (A:)
Probab=36.12  E-value=22  Score=14.38  Aligned_cols=31  Identities=16%  Similarity=0.122  Sum_probs=26.7

Q ss_pred             EEEECCCCHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             4221238999999999468898999999999
Q gi|254781061|r  361 GATISDINPEHLYYLMARGISKNQACSMLSH  391 (428)
Q Consensus       361 gatvg~id~e~lfYl~sRGi~~~~A~~lli~  391 (428)
                      ....-.+|++.|=.|++=|+++..|++-|..
T Consensus        12 ~~~~~~~d~~~v~~L~~MGF~~~~a~kAL~~   42 (64)
T 2cpw_A           12 QRPGTIKHGSALDVLLSMGFPRARAQKALAS   42 (64)
T ss_dssp             CSSCSSSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             9998898999999999969989999999999


No 22 
>>1wji_A Tudor domain containing protein 3; UBA domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} (A:)
Probab=34.42  E-value=24  Score=14.06  Aligned_cols=32  Identities=19%  Similarity=0.163  Sum_probs=26.8

Q ss_pred             EEECCCCHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             22123899999999946889899999999999
Q gi|254781061|r  362 ATISDINPEHLYYLMARGISKNQACSMLSHAF  393 (428)
Q Consensus       362 atvg~id~e~lfYl~sRGi~~~~A~~lli~gF  393 (428)
                      ++.-.+|++.|=-|++=|+++..|++-|....
T Consensus         3 ~~~~~~~~~~i~~L~~MGF~~~~a~~AL~~~~   34 (63)
T 1wji_A            3 SGSSGVDEKALKHITEMGFSKEASRQALMDNG   34 (63)
T ss_dssp             SSCCSSCHHHHHHHHTTTCCHHHHHHHHHHTT
T ss_pred             CCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHC
T ss_conf             88775599999999996999999999999959


No 23 
>>1ify_A HHR23A, UV excision repair protein RAD23 homolog A; ubiquitin associated domain, UBA domain, ubiquitin proteosome pathway, DNA binding protein; NMR {Homo sapiens} (A:)
Probab=33.61  E-value=25  Score=13.97  Aligned_cols=31  Identities=13%  Similarity=0.229  Sum_probs=25.9

Q ss_pred             EECCCCHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             2123899999999946889899999999999
Q gi|254781061|r  363 TISDINPEHLYYLMARGISKNQACSMLSHAF  393 (428)
Q Consensus       363 tvg~id~e~lfYl~sRGi~~~~A~~lli~gF  393 (428)
                      ..++.|++.+=.|+.=|++++.|++-|....
T Consensus         3 ~~~~~~e~~v~~L~~MGF~~~~a~~AL~~~~   33 (49)
T 1ify_A            3 VTGSEYETMLTEIMSMGYERERVVAALRASY   33 (49)
T ss_dssp             CCSHHHHHHHHHHHHTTCCHHHHHHHHHTTT
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             2421699999999980027999999999871


No 24 
>>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix- hairpin-helix, HHH motif, three helix bundle; 2.30A {Methanopyrus kandleri} (A:472-519)
Probab=32.84  E-value=25  Score=13.89  Aligned_cols=15  Identities=33%  Similarity=0.596  Sum_probs=12.7

Q ss_pred             HCCCCHHHHHHHHHH
Q ss_conf             468898999999999
Q gi|254781061|r  377 ARGISKNQACSMLSH  391 (428)
Q Consensus       377 sRGi~~~~A~~lli~  391 (428)
                      -|||+++.|++++-.
T Consensus         2 irgidreraerllkk   16 (48)
T 2csb_A            2 IRGIDRERAERLLKK   16 (48)
T ss_dssp             STTCCHHHHHHHHHH
T ss_pred             ECCCCHHHHHHHHHH
T ss_conf             016568999999998


No 25 
>>1r5l_A Alpha-TTP, protein (alpha-tocopherol transfer protein); ataxia with vitamin E deficiency, transport protein; HET: MSE VIV; 1.50A {Homo sapiens} (A:1-74)
Probab=32.23  E-value=26  Score=13.82  Aligned_cols=32  Identities=19%  Similarity=0.248  Sum_probs=24.0

Q ss_pred             EECCCCHH-HHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             21238999-999999468898999999999999
Q gi|254781061|r  363 TISDINPE-HLYYLMARGISKNQACSMLSHAFM  394 (428)
Q Consensus       363 tvg~id~e-~lfYl~sRGi~~~~A~~lli~gF~  394 (428)
                      .....|+. -|-||++|..+-+.|.+||..-+-
T Consensus        27 ~~~~~dD~~llrFLrarkf~ve~A~~~l~~~~~   59 (74)
T 1r5l_A           27 APLPLTDSFLLRFLRARDFDLDLAWRLLKNYYK   59 (74)
T ss_dssp             SSSCCCHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             999999899999985658999999999999999


No 26 
>>1dv0_A DNA repair protein HHR23A; helical bundle, DNA binding protein; HET: DNA; NMR {Homo sapiens} (A:)
Probab=32.10  E-value=18  Score=14.96  Aligned_cols=27  Identities=15%  Similarity=0.084  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             238999999999468898999999999
Q gi|254781061|r  365 SDINPEHLYYLMARGISKNQACSMLSH  391 (428)
Q Consensus       365 g~id~e~lfYl~sRGi~~~~A~~lli~  391 (428)
                      ++.|++.+=-|++=|+++..|++.|+.
T Consensus         1 t~~de~~i~~L~~MGF~~~~a~~AL~~   27 (47)
T 1dv0_A            1 GSQEKEAIERLKALGFPESLVIQAYFA   27 (47)
T ss_dssp             --CCHHHHTTTTTTTCCHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             916899999999839988899999998


No 27 
>>1aua_A Phosphatidylinositol transfer protein SEC14P; phospholipid-binding protein, peripheral golgi membrane protein, phospholipid exchange; HET: BOG; 2.50A {Saccharomyces cerevisiae} (A:21-93)
Probab=31.99  E-value=26  Score=13.79  Aligned_cols=27  Identities=22%  Similarity=0.222  Sum_probs=20.1

Q ss_pred             CHHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             999999999468898999999999999
Q gi|254781061|r  368 NPEHLYYLMARGISKNQACSMLSHAFM  394 (428)
Q Consensus       368 d~e~lfYl~sRGi~~~~A~~lli~gF~  394 (428)
                      |.--+=||++|+.+-++|.+||...+-
T Consensus        32 D~~LlRFLrAr~~~v~~A~~~l~~~l~   58 (73)
T 1aua_A           32 DSTLLRFLRARKFDVQLAKEMFENCEK   58 (73)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             999999998758999999999999999


No 28 
>>3eaf_A ABC transporter, substrate binding protein; PSI2, NYSGXRC, structural genomics, protein structure initiative; 2.00A {Aeropyrum pernix} (A:1-121,A:262-350)
Probab=31.86  E-value=26  Score=13.78  Aligned_cols=50  Identities=24%  Similarity=0.262  Sum_probs=39.6

Q ss_pred             HHHCCCCHHHHHHHHHHHHHHH-----HHHHCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9946889899999999999999-----9885897899999999999997413876
Q gi|254781061|r  375 LMARGISKNQACSMLSHAFMSE-----IVEDLNDQVLQFSIEEILSSWLKNNSAN  424 (428)
Q Consensus       375 l~sRGi~~~~A~~lli~gF~~~-----~i~~i~~~~~~~~~~~~i~~~l~~~~~~  424 (428)
                      -+..|.++++-.--.+.||.+-     .|+....+.++++--+.+.+.|+.+.-.
T Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  190 (210)
T 3eaf_A          136 ARXNGVSEDQINLRVVQGFVNVWLLIKAIESVTSQDLQERGGEALKEALEANTFD  190 (210)
T ss_dssp             HHHTTCCGGGCCHHHHHHHHHHHHHHHHHTTSCHHHHHHHTHHHHHHHHHHCCBC
T ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCC
T ss_conf             9985699998875999999999999999999747489988899999998518866


No 29 
>>1yqg_A Pyrroline-5-carboxylate reductase; structural genomics, PSI, protein structure initiative, midwest center for structural genomics; 1.90A {Neisseria meningitidis MC58} (A:167-224)
Probab=30.60  E-value=28  Score=13.63  Aligned_cols=36  Identities=17%  Similarity=0.255  Sum_probs=24.3

Q ss_pred             HHHCCCCHHHHHHHHHHHHHHHHH--HH--CCCHHHHHHH
Q ss_conf             994688989999999999999998--85--8978999999
Q gi|254781061|r  375 LMARGISKNQACSMLSHAFMSEIV--ED--LNDQVLQFSI  410 (428)
Q Consensus       375 l~sRGi~~~~A~~lli~gF~~~~i--~~--i~~~~~~~~~  410 (428)
                      -..-||++++|++|..+.|+.-.-  .+  ..-+.+++.+
T Consensus        16 gv~~Gl~~~~A~~lv~qt~~Gsa~ll~~~~~~p~~L~~~V   55 (58)
T 1yqg_A           16 AIRQGFDXAEARALSLATFKGAVALAEQTGEDFEKLQKNV   55 (58)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHT
T ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHC
T ss_conf             5513830767788999999999999986599999999876


No 30 
>>2e1z_A Propionate kinase; TDCD, native, acetate kinase, nucleotide, AP4A, ADP, ATP, AMPPNP, transferase; HET: B4P; 1.98A {Salmonella typhimurium} (A:174-393)
Probab=30.42  E-value=28  Score=13.61  Aligned_cols=32  Identities=9%  Similarity=0.226  Sum_probs=26.9

Q ss_pred             EEEEECCCCHHHHHHHHH-CCCCHHHHHHHHHH
Q ss_conf             542212389999999994-68898999999999
Q gi|254781061|r  360 HGATISDINPEHLYYLMA-RGISKNQACSMLSH  391 (428)
Q Consensus       360 Hgatvg~id~e~lfYl~s-RGi~~~~A~~lli~  391 (428)
                      -+.-.|.||+..++||+- -|++.++..++|..
T Consensus        73 m~tRsG~ldp~~l~~l~~~~~~s~~e~~~~Ln~  105 (220)
T 2e1z_A           73 MGTRSGDVDFGAMAWIAKETGQTLSDLERVVNK  105 (220)
T ss_dssp             CSSCCCSCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHC
T ss_conf             789899988189999998709999999998630


No 31 
>>1wiv_A UBP14, ubiquitin-specific protease 14; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Arabidopsis thaliana} (A:)
Probab=30.34  E-value=28  Score=13.60  Aligned_cols=38  Identities=18%  Similarity=0.211  Sum_probs=32.2

Q ss_pred             CEEEEEEEECCCCHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             33655422123899999999946889899999999999
Q gi|254781061|r  356 VQCGHGATISDINPEHLYYLMARGISKNQACSMLSHAF  393 (428)
Q Consensus       356 V~~~Hgatvg~id~e~lfYl~sRGi~~~~A~~lli~gF  393 (428)
                      ....+.......|++.|=-|++=|++++.|++-|....
T Consensus        17 ~~~~~~~~~~~~~~~~i~~L~~MGF~~~~a~~AL~~~~   54 (73)
T 1wiv_A           17 IDAPISHQTSDIDQSSVDTLLSFGFAEDVARKALKASG   54 (73)
T ss_dssp             SSCCSCCSSCSSCHHHHHHHHHHTCCHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf             67887778899899999999946999999999999919


No 32 
>>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens} (A:707-781)
Probab=28.81  E-value=30  Score=13.42  Aligned_cols=33  Identities=18%  Similarity=0.202  Sum_probs=27.9

Q ss_pred             EEEECCCCHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             422123899999999946889899999999999
Q gi|254781061|r  361 GATISDINPEHLYYLMARGISKNQACSMLSHAF  393 (428)
Q Consensus       361 gatvg~id~e~lfYl~sRGi~~~~A~~lli~gF  393 (428)
                      ..+....|++.|=.|+.=|++++.|++-|..-.
T Consensus         7 ~~~~~~~~~~~i~~L~~MGF~~~~a~~AL~~~~   39 (75)
T 3ihp_A            7 SAAADPPPEDCVTTIVSMGFSRDQALKALRATN   39 (75)
T ss_dssp             ------CCHHHHHHHHTTTCCHHHHHHHHHHTT
T ss_pred             CCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf             001355547765104541679999999998626


No 33 
>>1vg5_A RSGI RUH-014, rhomboid family protein; UBA domain, cDNA, structural genomics, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} (A:)
Probab=27.96  E-value=30  Score=13.32  Aligned_cols=35  Identities=20%  Similarity=0.157  Sum_probs=29.7

Q ss_pred             EEEEEECCCCHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             55422123899999999946889899999999999
Q gi|254781061|r  359 GHGATISDINPEHLYYLMARGISKNQACSMLSHAF  393 (428)
Q Consensus       359 ~Hgatvg~id~e~lfYl~sRGi~~~~A~~lli~gF  393 (428)
                      .+.......|+++|==|++=|+++++|++-|....
T Consensus        20 ~~~~~~~~~~e~~i~~L~~MGF~~~~a~~AL~~~~   54 (73)
T 1vg5_A           20 PQSQGRVAASEEQIQKLVAMGFDRTQVEVALAAAD   54 (73)
T ss_dssp             SSSCCCSCCCHHHHHHHHTTTCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHC
T ss_conf             88888878689999999993999999999999958


No 34 
>>2v6z_M DNA polymerase epsilon subunit 2; DNA replication, DPOE2, transferase, AAA protein family; HET: DNA; NMR {Homo sapiens} (M:)
Probab=26.62  E-value=32  Score=13.16  Aligned_cols=33  Identities=24%  Similarity=0.364  Sum_probs=15.5

Q ss_pred             HCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             17887789999999999999828323997247425
Q gi|254781061|r   21 KYYRNQSVVAFRRRLLCDFRTQGLLPTRKIENWHY   55 (428)
Q Consensus        21 ~~~~~~~~~~~R~~a~~~F~~~G~lPtkK~E~WKy   55 (428)
                      .++-+.....+|++....|+=.| | .-|.|.=+|
T Consensus        20 ~~~~~~~~~~LRk~IvsaFkL~G-l-~Lr~EAs~Y   52 (99)
T 2v6z_M           20 RLQVDMAPERLRSRALSAFKLRG-L-LLRGEAIKY   52 (99)
T ss_dssp             -----CCHHHHHHHHHHHHHHTT-C-EECHHHHHH
T ss_pred             HHHHHHCHHHHHHHHHHHHHHHC-E-EECHHHHHH
T ss_conf             77620088999999998861200-0-353889999


No 35 
>>2rcy_A Pyrroline carboxylate reductase; malaria, structural genomics, pyrroline reductase, oxidoreductase, structural genomics consortium; HET: NAP; 2.30A {Plasmodium falciparum 3D7} (A:169-226)
Probab=25.66  E-value=33  Score=13.04  Aligned_cols=38  Identities=13%  Similarity=0.125  Sum_probs=25.4

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHH--HH--CCCHHHHHHH
Q ss_conf             99994688989999999999999998--85--8978999999
Q gi|254781061|r  373 YYLMARGISKNQACSMLSHAFMSEIV--ED--LNDQVLQFSI  410 (428)
Q Consensus       373 fYl~sRGi~~~~A~~lli~gF~~~~i--~~--i~~~~~~~~~  410 (428)
                      -.-...||++++|++|..+.|..-.-  .+  .+-+.+++.+
T Consensus        14 ~a~v~~Gl~~~~A~~l~~qt~~Gsa~ll~~s~~~p~~l~~~V   55 (58)
T 2rcy_A           14 DAGVKNGLSRELSKNLVLQTIKGSVEXVKKSDQPVQQLKDNI   55 (58)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCSSCHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHC
T ss_conf             886507971567689999999999887504799999999847


No 36 
>>2izz_A Pyrroline-5-carboxylate reductase 1; amino-acid biosynthesis, NADP, oxidoreductase, proline biosynthesis; HET: NAD; 1.95A {Homo sapiens} PDB: 2ger_A 2gr9_A* 2gra_A* (A:198-256)
Probab=25.48  E-value=34  Score=13.01  Aligned_cols=38  Identities=11%  Similarity=0.090  Sum_probs=25.6

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHH--HHH--CCCHHHHHHH
Q ss_conf             9999468898999999999999999--885--8978999999
Q gi|254781061|r  373 YYLMARGISKNQACSMLSHAFMSEI--VED--LNDQVLQFSI  410 (428)
Q Consensus       373 fYl~sRGi~~~~A~~lli~gF~~~~--i~~--i~~~~~~~~~  410 (428)
                      -.-...||++++|++|..+.|..-+  +.+  ..-..+++.+
T Consensus        15 ~agv~~Gl~~~~A~~l~~~~~~Gta~ll~~s~~~p~~L~~~V   56 (59)
T 2izz_A           15 DGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNV   56 (59)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCSSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHC
T ss_conf             988764236888898999999999999987299999999807


No 37 
>>2dak_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5, USP 5, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:)
Probab=24.74  E-value=35  Score=12.92  Aligned_cols=32  Identities=19%  Similarity=0.188  Sum_probs=26.5

Q ss_pred             EEECCCCHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             22123899999999946889899999999999
Q gi|254781061|r  362 ATISDINPEHLYYLMARGISKNQACSMLSHAF  393 (428)
Q Consensus       362 atvg~id~e~lfYl~sRGi~~~~A~~lli~gF  393 (428)
                      +....+|++.|=-|++=|+++..|++-|....
T Consensus         3 ~~~~~~~~~~i~~L~~MGF~~~~a~~AL~~~~   34 (63)
T 2dak_A            3 SGSSGPPEDCVTTIVSMGFSRDQALKALRATN   34 (63)
T ss_dssp             CCSCCCCHHHHHHHHHHTCCHHHHHHHHHHTT
T ss_pred             CCCCCCCHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf             88899899999999996999999999999909


No 38 
>>1wgn_A UBAP1, ubiquitin associated protein; ubiquitin associated protein 1 (UBAP1), UBA domain, structural genomics; NMR {Homo sapiens} (A:)
Probab=23.94  E-value=31  Score=13.22  Aligned_cols=31  Identities=10%  Similarity=0.067  Sum_probs=25.5

Q ss_pred             EEECCCCHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             2212389999999994688989999999999
Q gi|254781061|r  362 ATISDINPEHLYYLMARGISKNQACSMLSHA  392 (428)
Q Consensus       362 atvg~id~e~lfYl~sRGi~~~~A~~lli~g  392 (428)
                      ......+++.|=-|++=|++++.|++-|...
T Consensus        13 ~~~~~~~~~~i~~L~~MGF~~~~a~~AL~~~   43 (63)
T 1wgn_A           13 QMLSPSERQCVETVVNMGYSYECVLRAMKKK   43 (63)
T ss_dssp             HTCCHHHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             3468057999999998699899999999992


No 39 
>>3khy_A Propionate kinase; csgid, IDP01739, ATP-binding, nucleotide-binding, transferase, structural genomics; 1.98A {Francisella tularensis subsp} (A:159-370)
Probab=23.50  E-value=36  Score=12.76  Aligned_cols=32  Identities=22%  Similarity=0.374  Sum_probs=27.9

Q ss_pred             EEEEECCCCHHHHHHHHHC-CCCHHHHHHHHHH
Q ss_conf             5422123899999999946-8898999999999
Q gi|254781061|r  360 HGATISDINPEHLYYLMAR-GISKNQACSMLSH  391 (428)
Q Consensus       360 Hgatvg~id~e~lfYl~sR-Gi~~~~A~~lli~  391 (428)
                      -|.-.|.||+..++||+-. |++.++.+++|-.
T Consensus        72 m~tRsG~idp~~l~~l~~~~~~s~~~l~~~Ln~  104 (212)
T 3khy_A           72 XGTRSGCIDPSIFAYISDNLGWSVTEITNXLNK  104 (212)
T ss_dssp             CSSCCCSCCTTHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             899888988499999999749999999999635


No 40 
>>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A (A:155-212)
Probab=22.99  E-value=37  Score=12.69  Aligned_cols=51  Identities=14%  Similarity=0.109  Sum_probs=35.4

Q ss_pred             EEEECCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             42212389999999994688989999999999999998858978999999999999
Q gi|254781061|r  361 GATISDINPEHLYYLMARGISKNQACSMLSHAFMSEIVEDLNDQVLQFSIEEILSS  416 (428)
Q Consensus       361 gatvg~id~e~lfYl~sRGi~~~~A~~lli~gF~~~~i~~i~~~~~~~~~~~~i~~  416 (428)
                      .++.+..-+|.+-=|.+-|+++.+|.+.+-.-     ...-|+..+.+.|...+..
T Consensus         3 ~~~~~~~~~da~~AL~aLGy~~~ea~~av~~v-----~~~~~~~~~~elIr~ALk~   53 (58)
T 2ztd_A            3 STNGHAVRSPVVEALVGLGFAAKQAEEATDTV-----LAANHDATTSSALRSALSL   53 (58)
T ss_dssp             -----CCHHHHHHHHHHTTCCHHHHHHHHHHH-----HHHCTTCCHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHH-----HHCCCCCCHHHHHHHHHHH
T ss_conf             35653216899999997599989999999999-----8408999999999999999


No 41 
>>3c24_A Putative oxidoreductase; YP_511008.1, structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: MSE; 1.62A {Jannaschia SP} (A:196-267)
Probab=22.97  E-value=28  Score=13.63  Aligned_cols=28  Identities=14%  Similarity=0.168  Sum_probs=17.3

Q ss_pred             EECCCCHHHHHHHHHC-CCCHHHHHHHHH
Q ss_conf             2123899999999946-889899999999
Q gi|254781061|r  363 TISDINPEHLYYLMAR-GISKNQACSMLS  390 (428)
Q Consensus       363 tvg~id~e~lfYl~sR-Gi~~~~A~~lli  390 (428)
                      |.+..=.|++-=--.| |++++.|+.+|.
T Consensus         6 ~ll~~mreA~dE~V~r~GVP~~aArdfLl   34 (72)
T 3c24_A            6 PFVETXVHAVDECADRYGIDRQAALDFXI   34 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             99999999999999984998999999986


No 42 
>>2hoq_A Putative HAD-hydrolase PH1655; haloacid dehalogenase, structural genomics, NPPSFA; 1.70A {Pyrococcus horikoshii OT3} (A:13-95)
Probab=22.79  E-value=35  Score=12.86  Aligned_cols=37  Identities=16%  Similarity=0.304  Sum_probs=27.7

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             8778999999999999982832399724742588789775
Q gi|254781061|r   24 RNQSVVAFRRRLLCDFRTQGLLPTRKIENWHYTDLKNILK   63 (428)
Q Consensus        24 ~~~~~~~~R~~a~~~F~~~G~lPtkK~E~WKyT~l~~l~~   63 (428)
                      .+....--|+.|.+.-..-| ||...+|.++  -|..+.+
T Consensus         4 tS~~a~~ARk~Ai~~Mi~aG-L~~~~e~Ay~--~L~eiI~   40 (83)
T 2hoq_A            4 TSKLAEIARKNAIENMIRHG-LPVDFETAYS--ELIELIK   40 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT-CCSCHHHHHH--HHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHCC-CCCCHHHHHH--HHHHHHH
T ss_conf             87889999999999998737-9967999999--9999999


No 43 
>>1ryp_D 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} (D:)
Probab=22.78  E-value=38  Score=12.66  Aligned_cols=60  Identities=10%  Similarity=0.003  Sum_probs=42.4

Q ss_pred             EEEEECCCCHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHH--------------------HCCCHHHHHHHHHHHHH
Q ss_conf             5422123899999999946---889899999999999999988--------------------58978999999999999
Q gi|254781061|r  360 HGATISDINPEHLYYLMAR---GISKNQACSMLSHAFMSEIVE--------------------DLNDQVLQFSIEEILSS  416 (428)
Q Consensus       360 Hgatvg~id~e~lfYl~sR---Gi~~~~A~~lli~gF~~~~i~--------------------~i~~~~~~~~~~~~i~~  416 (428)
                      +.+++|.=.....-+|..+   .++.++|..++.+++..-.-.                    .++.+++.+++.+.-++
T Consensus       158 ~~~a~G~g~~~~~~~Le~~~~~~lt~~ea~~l~~~~l~~~~~~d~~s~~~iei~vi~kdg~~~~~~~~ei~~~l~~~~~~  237 (241)
T 1ryp_D          158 SAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQE  237 (241)
T ss_dssp             SEEEESTTHHHHHHHHHTTCCTTSCCCSHHHHHHHHHHHHHHHHCSCSTTEEEEEEETTTEEEECCHHHHHHHHHHHTHH
T ss_pred             EEEECCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCEEECCHHHHHHHHHHHHHH
T ss_conf             24504824899999999863105568999999999999999975589881699999889998997999999999999878


Q ss_pred             HHH
Q ss_conf             974
Q gi|254781061|r  417 WLK  419 (428)
Q Consensus       417 ~l~  419 (428)
                      +++
T Consensus       238 ~~~  240 (241)
T 1ryp_D          238 KQE  240 (241)
T ss_dssp             HHC
T ss_pred             HHC
T ss_conf             745


No 44 
>>1bf6_A Phosphotriesterase homology protein; hypothetical protein; 1.70A {Escherichia coli} (A:1-88,A:234-291)
Probab=22.45  E-value=38  Score=12.61  Aligned_cols=27  Identities=19%  Similarity=0.170  Sum_probs=18.1

Q ss_pred             CCCCHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             238999999999468898999999999
Q gi|254781061|r  365 SDINPEHLYYLMARGISKNQACSMLSH  391 (428)
Q Consensus       365 g~id~e~lfYl~sRGi~~~~A~~lli~  391 (428)
                      +-|-.+-+=+|+.||+++++-.+|++.
T Consensus       113 ~~i~~~~iP~L~~~Gv~~e~I~~ilv~  139 (146)
T 1bf6_A          113 DYLLTTFIPQLRQSGFSQADVDVMLRE  139 (146)
T ss_dssp             THHHHTHHHHHHHTTCCHHHHHHHHTH
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             069999999999759999999999999


No 45 
>>1veg_A NEDD8 ultimate buster-1; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Mus musculus} (A:)
Probab=22.23  E-value=38  Score=12.58  Aligned_cols=38  Identities=16%  Similarity=0.096  Sum_probs=31.5

Q ss_pred             CCEEEEEEEECCCCHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             73365542212389999999994688989999999999
Q gi|254781061|r  355 DVQCGHGATISDINPEHLYYLMARGISKNQACSMLSHA  392 (428)
Q Consensus       355 dV~~~Hgatvg~id~e~lfYl~sRGi~~~~A~~lli~g  392 (428)
                      +.........-.+|++.|=-|+.=|++++.|++-|...
T Consensus        16 ~~~~~~~~~~~~~~~~~i~~L~~MGF~~~~a~~AL~~~   53 (83)
T 1veg_A           16 DADPENNSRQASPSQESINQLVYMGFDTVVAEAALRVF   53 (83)
T ss_dssp             CSCSSCCSSSCCCCHHHHHHHHHHSCCHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             78876565547977888999998342388899999996


No 46 
>>3krn_A Protein C14A4.5, confirmed by transcript evidence; RNAse PH domain, homodimer, exosome, cell-death-related DNAse; 3.92A {Caenorhabditis elegans} (A:121-222)
Probab=21.12  E-value=40  Score=12.43  Aligned_cols=87  Identities=7%  Similarity=-0.044  Sum_probs=51.0

Q ss_pred             EEEECCCCEEEEECCCCCCCCCCCCCCCEEEEEE-EECCCEEEEEEEEEEEECCCCEEEEEEEECCCCHHHHHHHHHCCC
Q ss_conf             3000488527874101013664100000000046-612871798121247713873365542212389999999994688
Q gi|254781061|r  302 RNIVLEKSTGVFQGAVHVSSEAQGSNARMTANTL-LFSNEGSFYVKPELEIFADDVQCGHGATISDINPEHLYYLMARGI  380 (428)
Q Consensus       302 k~vl~d~s~~vf~G~i~V~~~a~~t~~~q~~~~l-lLs~~a~~~s~P~LeI~~ddV~~~Hgatvg~id~e~lfYl~sRGi  380 (428)
                      ++.+..-+-++.+|.+.|++...--......-.+ .++...+.            .+..--.+-|.+.+++++-.+.-|.
T Consensus         4 ~~~v~av~vg~i~g~~iiDPt~~E~~~s~~~l~va~~~~~~~~------------~~i~~~~~~g~~~~~~l~~al~~a~   71 (102)
T 3krn_A            4 ETVFCGVLIVRVKDELIIDPTAKQEAASTGRVLFSVCKGSDGH------------PEVCAMDAIGHWDFIQLEAAWSLAQ   71 (102)
T ss_dssp             TSCCCCCCCEECSSSEESSCCTTTTTSCC-CCCCEECCCSSSS------------CCEEEECCBSSCTTHHHHTHHHHTT
T ss_pred             CCCCCEEEEEEECCEEEECCCHHHHHCCCCEEEEEEECCCCCC------------EEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             4664237999985858878898999527854999997899983------------1999962468709999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q ss_conf             98999999999999999885
Q gi|254781061|r  381 SKNQACSMLSHAFMSEIVED  400 (428)
Q Consensus       381 ~~~~A~~lli~gF~~~~i~~  400 (428)
                      ..-....-+++.++.+...+
T Consensus        72 ~~~~~i~~~~~~~l~~~~~k   91 (102)
T 3krn_A           72 PSASAIFDFYKTVMKRKLSV   91 (102)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHCC
T ss_conf             99999999999999977461


No 47 
>>2ahr_A Putative pyrroline carboxylate reductase; pyrroline reductase, proline biosynthesis, NAD(P)binding protein, rossmann fold; HET: NAP; 2.15A {Streptococcus pyogenes m1 gas} (A:168-225)
Probab=20.50  E-value=42  Score=12.34  Aligned_cols=37  Identities=14%  Similarity=0.209  Sum_probs=24.5

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHH--HHH--CCCHHHHHHH
Q ss_conf             999468898999999999999999--885--8978999999
Q gi|254781061|r  374 YLMARGISKNQACSMLSHAFMSEI--VED--LNDQVLQFSI  410 (428)
Q Consensus       374 Yl~sRGi~~~~A~~lli~gF~~~~--i~~--i~~~~~~~~~  410 (428)
                      .-...||++++|++|..+-++.-.  +.+  ..-..+++.+
T Consensus        15 agv~~Gl~~~~A~~l~~qt~~Gsa~ll~~~~~~p~~L~~~V   55 (58)
T 2ahr_A           15 AGVKNGIPKAKALEIVTQTVLASASNLKTSSQSPHDFIDAI   55 (58)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHHHHHHHHHHSSSCHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHC
T ss_conf             55672266999999989999987888874799999999865


Done!