Query         gi|254780231|ref|YP_003064644.1| hypothetical protein CLIBASIA_00580 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 98
No_of_seqs    104 out of 559
Neff          5.4 
Searched_HMMs 13730
Date          Mon May 23 21:39:26 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780231.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 d1yh5a1 d.206.1.1 (A:1-100) Hy  99.9 1.8E-23 1.3E-27  158.3   7.5   74    2-82     15-88  (100)
  2 d1jrma_ d.206.1.1 (A:) Hypothe  99.9 1.8E-23 1.3E-27  158.2   6.2   86    2-95     14-100 (104)
  3 d1t6aa_ d.129.8.1 (A:) Rbstp22  69.2     1.5 0.00011   21.8   2.6   37   29-69     77-118 (124)
  4 d1uiza_ d.80.1.3 (A:) Micropha  64.7     3.8 0.00028   19.3   4.0   60    4-71     38-102 (115)
  5 d1jrob2 d.133.1.1 (B:124-777)   62.1     5.2 0.00038   18.5   5.0   46   29-74    353-398 (654)
  6 d1dpta_ d.80.1.3 (A:) D-dopach  61.4     4.7 0.00034   18.8   3.9   58    4-69     37-100 (117)
  7 d1b24a1 d.95.2.1 (A:7-99) DNA   59.4     4.7 0.00034   18.8   3.6   58   28-90     26-85  (93)
  8 d1v97a5 d.133.1.1 (A:695-1332)  48.9     8.6 0.00063   17.2   4.4   46   29-74    332-377 (638)
  9 d2gdga1 d.80.1.3 (A:1-114) Mic  48.2     8.9 0.00064   17.1   6.5   61    4-72     37-102 (114)
 10 d3dhxa1 d.58.18.13 (A:2-100) M  44.9     9.2 0.00067   17.0   3.2   52   41-95     28-86  (99)
 11 d2qswa1 d.58.18.13 (A:256-345)  42.6     9.8 0.00071   16.9   3.1   59   30-95     14-79  (90)
 12 d1szwa_ d.265.1.4 (A:) tRNA ps  42.0      11 0.00081   16.6   3.4   43   28-74     40-82  (341)
 13 d1rm6a2 d.133.1.1 (A:134-769)   39.8      12 0.00087   16.4   6.2   46   29-74    336-381 (636)
 14 d1hfoa_ d.80.1.3 (A:) Micropha  39.6      12 0.00088   16.3   6.5   61    4-72     37-102 (113)
 15 d1n62b2 d.133.1.1 (B:147-809)   34.2      15  0.0011   15.8   5.9   46   29-74    370-415 (663)
 16 d1ffvb2 d.133.1.1 (B:147-803)   27.6      19  0.0014   15.1   5.9   46   29-74    364-409 (657)
 17 d1mwwa_ d.80.1.4 (A:) Hypothet  25.1      21  0.0016   14.9   3.5   45   27-71     55-104 (120)
 18 d1y7ea1 b.49.3.1 (A:101-233) P  24.7      22  0.0016   14.8   2.7   33   32-64     90-126 (133)
 19 d1otfa_ d.80.1.1 (A:) 4-oxaloc  23.8      23  0.0016   14.7   3.1   23   46-68     20-42  (59)
 20 d1xdpa2 d.322.1.2 (A:107-314)   23.3      21  0.0016   14.9   2.2   30   41-70    158-187 (208)
 21 d2qrra1 d.58.18.13 (A:2-98) Me  22.8      24  0.0017   14.6   5.4   60   31-95     19-85  (97)

No 1  
>d1yh5a1 d.206.1.1 (A:1-100) Hypothetical protein YggU {Escherichia coli, o157 [TaxId: 562]}
Probab=99.88  E-value=1.8e-23  Score=158.26  Aligned_cols=74  Identities=24%  Similarity=0.341  Sum_probs=69.4

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCHHHEEEEECCCCCEEEEEECC
Q ss_conf             05999994186653023101456667776799999638767978899999999982998444799835577806999829
Q gi|254780231|r    2 CNVIVRLIPNAKKSGIASLEIPKDTSDTIHMKIKVTATPQKGKANKAMLAMLAKKLALSKSSLRMLSKQSSPLKIIYIDK   81 (98)
Q Consensus         2 ~~i~v~V~P~a~~~~I~g~~~~~d~~~~~~lkv~v~ApPv~GkAN~ali~~Lak~l~v~ks~I~I~~G~~sr~K~i~I~~   81 (98)
                      +.|.|+|+|||++++|.|+       ++++|+|+|+|||+||+||+||++|||++|++|||+|+|++|++||+|+++|.+
T Consensus        15 v~i~v~V~P~ak~~~i~~~-------~~~~l~v~v~app~~GkAN~ali~~Lak~l~v~ks~I~I~~G~tSr~K~i~I~~   87 (100)
T d1yh5a1          15 LVLRLYIQPKASRDSIVGL-------HGDEVKVAITAPPVDGQANSHLVKFLGKQFRVAKSQVVIEKGELGRHKQIKIIN   87 (100)
T ss_dssp             EEEEEECCBSCSSCCCCCC-------CSSCEECCBSSCSCTTTHHHHHHHHHHHHHTCCTTTEEEEECCSSSEEEEEEES
T ss_pred             EEEEEEEEECCCCCCCCCC-------CCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCEEEEEEC
T ss_conf             8999999759751432551-------199899999669977717899999999995997100899864777850899957


Q ss_pred             C
Q ss_conf             9
Q gi|254780231|r   82 D   82 (98)
Q Consensus        82 ~   82 (98)
                      .
T Consensus        88 ~   88 (100)
T d1yh5a1          88 P   88 (100)
T ss_dssp             C
T ss_pred             C
T ss_conf             5


No 2  
>d1jrma_ d.206.1.1 (A:) Hypothetical protein MTH637 {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}
Probab=99.88  E-value=1.8e-23  Score=158.22  Aligned_cols=86  Identities=24%  Similarity=0.349  Sum_probs=77.6

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCHHHEEEEECCCCCEEEEEECC
Q ss_conf             05999994186653023101456667776799999638767978899999999982998444799835577806999829
Q gi|254780231|r    2 CNVIVRLIPNAKKSGIASLEIPKDTSDTIHMKIKVTATPQKGKANKAMLAMLAKKLALSKSSLRMLSKQSSPLKIIYIDK   81 (98)
Q Consensus         2 ~~i~v~V~P~a~~~~I~g~~~~~d~~~~~~lkv~v~ApPv~GkAN~ali~~Lak~l~v~ks~I~I~~G~~sr~K~i~I~~   81 (98)
                      +.|.|+|+|||++++|.|++     .|+++|+|+|+|||+||+||+||++|||++|+   |+|+|++|++||+|+++|.|
T Consensus        14 v~i~v~V~P~A~~~~i~g~~-----~~~~~l~V~v~app~dGkAN~ali~~Lak~lk---s~I~I~~G~tSR~K~i~I~g   85 (104)
T d1jrma_          14 LLVNIEVSPASGKFGIPSYN-----EWRKRIEVKIHSPPQKGKANREIIKEFSETFG---RDVEIVSGQKSRQKTIRIQG   85 (104)
T ss_dssp             EEEEEESCCCSSSCCCCCCC-----TTTTCCCCCCCTTCCCCCHHHHHHHHHHHHHS---SEEEECSCGGGSEEEEEEES
T ss_pred             EEEEEEEEECCCCCEEEEEC-----CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHC---CCEEEEECCCCCCEEEEEEC
T ss_conf             99999986099854464160-----77998999995699777689999999999868---98899846877850899908


Q ss_pred             -CHHHHHHHHHHHHH
Q ss_conf             -98999999975230
Q gi|254780231|r   82 -DCKEITELLQNNDS   95 (98)
Q Consensus        82 -~~~~i~~~L~~~~s   95 (98)
                       +.+++.++|+...-
T Consensus        86 ~~~~~~~~~L~~~lg  100 (104)
T d1jrma_          86 MGRDLFLKLVSEKFG  100 (104)
T ss_dssp             CCHHHHHHHHHHTSC
T ss_pred             CCHHHHHHHHHHHHC
T ss_conf             999999999999866


No 3  
>d1t6aa_ d.129.8.1 (A:) Rbstp2229 protein {Bacillus stearothermophilus [TaxId: 1422]}
Probab=69.19  E-value=1.5  Score=21.76  Aligned_cols=37  Identities=35%  Similarity=0.460  Sum_probs=24.7

Q ss_pred             CCEEEEEEECCC-----CCCHHHHHHHHHHHHHHCCCHHHEEEEEC
Q ss_conf             767999996387-----67978899999999982998444799835
Q gi|254780231|r   29 TIHMKIKVTATP-----QKGKANKAMLAMLAKKLALSKSSLRMLSK   69 (98)
Q Consensus        29 ~~~lkv~v~ApP-----v~GkAN~ali~~Lak~l~v~ks~I~I~~G   69 (98)
                      ++.--|.|.-||     .+|||| |.|+||||.|.   ....+-.|
T Consensus        77 ~e~sfIqi~LP~~AT~GDKgKAN-EfckfLAKkL~---geL~LFNG  118 (124)
T d1t6aa_          77 GEETFIDIALPPGATHGDKGKAN-EFSKWLAKTLG---GELHLFSG  118 (124)
T ss_dssp             TTEEEEEEECCTTCCHHHHHHHH-HHHHHHHHHHC---EEEECTTS
T ss_pred             CCEEEEEEECCCCCCCCCCHHHH-HHHHHHHHHHH---CEEEEECC
T ss_conf             86146999879998877622276-89999999741---01467546


No 4  
>d1uiza_ d.80.1.3 (A:) Microphage migration inhibition factor (MIF) {African clawed frog (Xenopus laevis) [TaxId: 8355]}
Probab=64.70  E-value=3.8  Score=19.34  Aligned_cols=60  Identities=12%  Similarity=0.157  Sum_probs=38.3

Q ss_pred             EEEEEECCCCCCEEEEECCCCCCCCCCEEEEEEECCC-CC----CHHHHHHHHHHHHHHCCCHHHEEEEECCC
Q ss_conf             9999941866530231014566677767999996387-67----97889999999998299844479983557
Q gi|254780231|r    4 VIVRLIPNAKKSGIASLEIPKDTSDTIHMKIKVTATP-QK----GKANKAMLAMLAKKLALSKSSLRMLSKQS   71 (98)
Q Consensus         4 i~v~V~P~a~~~~I~g~~~~~d~~~~~~lkv~v~ApP-v~----GkAN~ali~~Lak~l~v~ks~I~I~~G~~   71 (98)
                      |.|.+.|+..-. ..|       .......+.|++-- .+    .+..+++++||.+.|+||+.+|-|..-..
T Consensus        38 vmv~v~~~~~m~-fgg-------s~~P~a~~~v~siG~l~~~~n~~~s~~i~~~l~~~LgI~~~Riyi~f~d~  102 (115)
T d1uiza_          38 IAIHIVPDQIMS-FGD-------STDPCAVCSLCSIGKIGGPQNKSYTKLLCDILTKQLNIPANRVYINYYDL  102 (115)
T ss_dssp             CEEEEECSCEEE-ETT-------BCSSCEEEEEEESSCCSHHHHHHHHHHHHHHHHHHHCCCGGGEEEEEEEC
T ss_pred             EEEEECCCCEEE-ECC-------CCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEC
T ss_conf             999983896079-679-------89968999999976888135599999999999987499956499999978


No 5  
>d1jrob2 d.133.1.1 (B:124-777) Xanthine dehydrogenase chain B, C-terminal domain {Rhodobacter capsulatus [TaxId: 1061]}
Probab=62.11  E-value=5.2  Score=18.52  Aligned_cols=46  Identities=13%  Similarity=0.163  Sum_probs=40.9

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCHHHEEEEECCCCCE
Q ss_conf             7679999963876797889999999998299844479983557780
Q gi|254780231|r   29 TIHMKIKVTATPQKGKANKAMLAMLAKKLALSKSSLRMLSKQSSPL   74 (98)
Q Consensus        29 ~~~lkv~v~ApPv~GkAN~ali~~Lak~l~v~ks~I~I~~G~~sr~   74 (98)
                      ++.+.|+..+.....=.+..+....|+.|++|..+|++..|-|+..
T Consensus       353 DG~v~v~~g~~d~GQG~~T~~aQiaAe~LGi~~e~V~v~~~DT~~~  398 (654)
T d1jrob2         353 DGSVALNHGGTEMGQGLHAKMVQVAAAVLGIDPVQVRITATDTSKV  398 (654)
T ss_dssp             TSCEEEEESCCCSSSCHHHHHHHHHHHHHTSCGGGEEECCEETTTS
T ss_pred             CCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEECCCCCC
T ss_conf             9988998387678986788899999998589620369994268888


No 6  
>d1dpta_ d.80.1.3 (A:) D-dopachrome tautomerase {Human (Homo sapiens) [TaxId: 9606]}
Probab=61.42  E-value=4.7  Score=18.79  Aligned_cols=58  Identities=16%  Similarity=0.255  Sum_probs=37.5

Q ss_pred             EEEEEECCCCCCEEEEECCCCCCCCCCEEEEEEECC-----CCCC-HHHHHHHHHHHHHHCCCHHHEEEEEC
Q ss_conf             999994186653023101456667776799999638-----7679-78899999999982998444799835
Q gi|254780231|r    4 VIVRLIPNAKKSGIASLEIPKDTSDTIHMKIKVTAT-----PQKG-KANKAMLAMLAKKLALSKSSLRMLSK   69 (98)
Q Consensus         4 i~v~V~P~a~~~~I~g~~~~~d~~~~~~lkv~v~Ap-----Pv~G-kAN~ali~~Lak~l~v~ks~I~I~~G   69 (98)
                      +.|.+.|+..-. ..|       ..+.+.-+.|++.     |++. +.-+++++||.+.||||+.+|-|..-
T Consensus        37 vmV~v~~~~~m~-fgG-------s~eP~a~~~l~sig~~~~~e~n~~~s~~i~~~l~~~LgI~~~RiyI~f~  100 (117)
T d1dpta_          37 VNVTVRPGLAMA-LSG-------STEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFF  100 (117)
T ss_dssp             CEEEEECSCCCC-BTT-------BCSSCEEEEEEEESSSCSHHHHHHHHHHHHHHHHHHHTCCGGGEEEEEE
T ss_pred             EEEEEECCCCEE-ECC-------CCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEE
T ss_conf             999997597569-779-------8996799999982587867788999999999999872979675999999


No 7  
>d1b24a1 d.95.2.1 (A:7-99) DNA endonuclease I-dmoI {Archaeon Desulfurococcus mobilis [TaxId: 2274]}
Probab=59.43  E-value=4.7  Score=18.80  Aligned_cols=58  Identities=12%  Similarity=0.272  Sum_probs=36.5

Q ss_pred             CCCEEEEEEECCCCCC-HHHH-HHHHHHHHHHCCCHHHEEEEECCCCCEEEEEECCCHHHHHHHH
Q ss_conf             7767999996387679-7889-9999999982998444799835577806999829989999999
Q gi|254780231|r   28 DTIHMKIKVTATPQKG-KANK-AMLAMLAKKLALSKSSLRMLSKQSSPLKIIYIDKDCKEITELL   90 (98)
Q Consensus        28 ~~~~lkv~v~ApPv~G-kAN~-ali~~Lak~l~v~ks~I~I~~G~~sr~K~i~I~~~~~~i~~~L   90 (98)
                      .+..++|-++...+.- +-|. -+.++|-+.|++ +|.|.+++|.+--.  +++  ++..+-..+
T Consensus        26 ~RtEYRVViTQK~e~~i~~~~a~m~~~Ll~EL~l-kSkvQvi~G~tR~E--vRV--SSK~L~~~F   85 (93)
T d1b24a1          26 NRSEYRVVITQKSENLIKQHIAPLMQFLIDELNV-KSKIQIVKGDTRYE--LRV--SSKKLYYYF   85 (93)
T ss_dssp             TCEEEEEEEEESCHHHHHHTHHHHHHHHHHHTTC-CCCCEEEECSSCEE--EEE--ECHHHHHHH
T ss_pred             CCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCCC-CCEEEEEECCCEEE--EEE--EHHHHHHHH
T ss_conf             9748999998431879999899999999998097-75489971770699--996--078899999


No 8  
>d1v97a5 d.133.1.1 (A:695-1332) Xanthine oxidase, C-terminal domain {Cow (Bos taurus) [TaxId: 9913]}
Probab=48.93  E-value=8.6  Score=17.21  Aligned_cols=46  Identities=11%  Similarity=0.120  Sum_probs=39.4

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCHHHEEEEECCCCCE
Q ss_conf             7679999963876797889999999998299844479983557780
Q gi|254780231|r   29 TIHMKIKVTATPQKGKANKAMLAMLAKKLALSKSSLRMLSKQSSPL   74 (98)
Q Consensus        29 ~~~lkv~v~ApPv~GkAN~ali~~Lak~l~v~ks~I~I~~G~~sr~   74 (98)
                      ++.+.|+..+.....=.+..+....|+.|++|..+|+++.|-|+..
T Consensus       332 dG~v~v~~g~~d~GqG~~T~~aqi~Ae~LGi~~~~V~v~~~dT~~~  377 (638)
T d1v97a5         332 DGSVLVSHGGTEMGQGLHTKMVQVASKALKIPISKIYISETSTNTV  377 (638)
T ss_dssp             TSCEEEEESCCCSSSCHHHHHHHHHHHHHTSCGGGEECCCEETTTS
T ss_pred             CCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCHHEEEEEECCCCCC
T ss_conf             9974884476554630256798876765255401266420257778


No 9  
>d2gdga1 d.80.1.3 (A:1-114) Microphage migration inhibition factor (MIF) {Mouse (Mus musculus) [TaxId: 10090]}
Probab=48.17  E-value=8.9  Score=17.14  Aligned_cols=61  Identities=11%  Similarity=0.211  Sum_probs=38.8

Q ss_pred             EEEEEECCCCCCEEEEECCCCCCCCCCEEEEEEECCC-CCCH----HHHHHHHHHHHHHCCCHHHEEEEECCCC
Q ss_conf             9999941866530231014566677767999996387-6797----8899999999982998444799835577
Q gi|254780231|r    4 VIVRLIPNAKKSGIASLEIPKDTSDTIHMKIKVTATP-QKGK----ANKAMLAMLAKKLALSKSSLRMLSKQSS   72 (98)
Q Consensus         4 i~v~V~P~a~~~~I~g~~~~~d~~~~~~lkv~v~ApP-v~Gk----AN~ali~~Lak~l~v~ks~I~I~~G~~s   72 (98)
                      +.|.+.|+..-. ..|       ..+.+.-+.|++-- .+..    -.+++++||++.||||..+|-|..-..+
T Consensus        37 vmV~v~~~~~m~-fgG-------s~~P~a~~~l~siG~~~~~~n~~~s~~i~~~l~~~LgI~~~RiyI~f~d~~  102 (114)
T d2gdga1          37 IAVHVVPDQLMT-FSG-------TNDPCALCSLHSIGKIGGAQNRNYSKLLCGLLSDRLHISPDRVYINYYDMN  102 (114)
T ss_dssp             CEEEEECSCEEE-ETT-------BCSSCEEEEEEESSCCSHHHHHHHHHHHHHHHHHHHCCCGGGEEEEEEECC
T ss_pred             EEEEEECCCCEE-ECC-------CCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECC
T ss_conf             899996798727-768-------899779999998068997888999999999999983979565999999788


No 10 
>d3dhxa1 d.58.18.13 (A:2-100) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}
Probab=44.92  E-value=9.2  Score=17.04  Aligned_cols=52  Identities=8%  Similarity=0.106  Sum_probs=39.7

Q ss_pred             CCCHHHHHHHHHHHHHHCCCHHHEEEEECCCCCEE-------EEEECCCHHHHHHHHHHHHH
Q ss_conf             67978899999999982998444799835577806-------99982998999999975230
Q gi|254780231|r   41 QKGKANKAMLAMLAKKLALSKSSLRMLSKQSSPLK-------IIYIDKDCKEITELLQNNDS   95 (98)
Q Consensus        41 v~GkAN~ali~~Lak~l~v~ks~I~I~~G~~sr~K-------~i~I~~~~~~i~~~L~~~~s   95 (98)
                      ....|++-++.-|++.|++   ++.|+.|.-.+..       ++.+.|+.+++.+.++...+
T Consensus        28 ~g~~a~~Piis~l~~~~~v---~vnIL~g~i~~i~~~~~G~Lil~l~g~~~~i~~al~~L~~   86 (99)
T d3dhxa1          28 TGQSVDAPLLSETARRFNV---NNNIISAQMDYAGGVKFGIMLTEMHGTQQDTQAAIAWLQE   86 (99)
T ss_dssp             EEECTTCCHHHHHHHHSCC---EEEEEEEEEEEETTEEEEEEEEEEESCHHHHHHHHHHHHH
T ss_pred             ECCCCCCCHHHHHHHHHCC---CEEEEEEEEEEECCEEEEEEEEEEECCHHHHHHHHHHHHH
T ss_conf             0897686199999998599---6699998627808842799999950898999999999998


No 11 
>d2qswa1 d.58.18.13 (A:256-345) Methionine import ATP-binding protein MetN2 {Enterococcus faecalis [TaxId: 1351]}
Probab=42.60  E-value=9.8  Score=16.88  Aligned_cols=59  Identities=5%  Similarity=0.120  Sum_probs=41.9

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHCCCHHHEEEEECCCCC-------EEEEEECCCHHHHHHHHHHHHH
Q ss_conf             67999996387679788999999999829984447998355778-------0699982998999999975230
Q gi|254780231|r   30 IHMKIKVTATPQKGKANKAMLAMLAKKLALSKSSLRMLSKQSSP-------LKIIYIDKDCKEITELLQNNDS   95 (98)
Q Consensus        30 ~~lkv~v~ApPv~GkAN~ali~~Lak~l~v~ks~I~I~~G~~sr-------~K~i~I~~~~~~i~~~L~~~~s   95 (98)
                      ..+++..    ....|++.++.-|++.|++   ++.|++|.-..       .=++++.|+++++.+.++...+
T Consensus        14 ~lvrl~f----~g~~a~~Pvis~l~r~~~i---~vnIL~g~i~~i~~~~~G~L~l~l~G~~~~i~~al~~L~~   79 (90)
T d2qswa1          14 KIVRLLF----HGEQAKLPIISHIVQEYQV---EVSIIQGNIQQTKQGAVGSLYIQLLGEEQNILAAIEGLRK   79 (90)
T ss_dssp             EEEEEEE----ESCSCSSCHHHHHHHHHTC---EEEEEEEEEEEETTEEEEEEEEEEESCHHHHHHHHHHHHH
T ss_pred             EEEEEEE----CCCCCCCCHHHHHHHHHCC---CEEEEEEEEEEECCCCEEEEEEEEECCHHHHHHHHHHHHH
T ss_conf             8999998----4986586499999998599---2899998708708963799999997899999999999998


No 12 
>d1szwa_ d.265.1.4 (A:) tRNA pseudouridine synthase TruD {Escherichia coli [TaxId: 562]}
Probab=41.97  E-value=11  Score=16.56  Aligned_cols=43  Identities=16%  Similarity=0.259  Sum_probs=34.6

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCHHHEEEEECCCCCE
Q ss_conf             77679999963876797889999999998299844479983557780
Q gi|254780231|r   28 DTIHMKIKVTATPQKGKANKAMLAMLAKKLALSKSSLRMLSKQSSPL   74 (98)
Q Consensus        28 ~~~~lkv~v~ApPv~GkAN~ali~~Lak~l~v~ks~I~I~~G~~sr~   74 (98)
                      .|+++-+.|.-   .|.-+.+++..||+.|+++.++|.. .|.+.|.
T Consensus        40 ~G~~~~~~l~K---~~~dT~~ai~~Lar~l~v~~~~i~y-AG~KDk~   82 (341)
T d1szwa_          40 EGEHILVRILK---NGCNTRFVADALAKFLKIHAREVSF-AGQKDKH   82 (341)
T ss_dssp             CSSEEEEEEEE---SSSCHHHHHHHHHHHTTCCGGGEEE-SCCCCTT
T ss_pred             CCCEEEEEEEE---CCCCHHHHHHHHHHHHCCCHHHEEE-CCCCCCC
T ss_conf             76789999998---8899999999999983998444315-5356576


No 13 
>d1rm6a2 d.133.1.1 (A:134-769) 4-hydroxybenzoyl-CoA reductase alpha subunit HrcA, C-terminal domain {Thauera aromatica [TaxId: 59405]}
Probab=39.81  E-value=12  Score=16.36  Aligned_cols=46  Identities=17%  Similarity=0.128  Sum_probs=39.9

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCHHHEEEEECCCCCE
Q ss_conf             7679999963876797889999999998299844479983557780
Q gi|254780231|r   29 TIHMKIKVTATPQKGKANKAMLAMLAKKLALSKSSLRMLSKQSSPL   74 (98)
Q Consensus        29 ~~~lkv~v~ApPv~GkAN~ali~~Lak~l~v~ks~I~I~~G~~sr~   74 (98)
                      ++.+.|.........=.+..+....|+.|++|..+|++..|-|+..
T Consensus       336 dG~v~v~~g~~d~GqG~~T~~~QiaAe~LGi~~e~V~v~~~DT~~~  381 (636)
T d1rm6a2         336 DGGITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALT  381 (636)
T ss_dssp             TCCEEEEECCCCSSSCHHHHHHHHHHHHHTCCGGGEEEEESBTTTS
T ss_pred             CCCEEEECCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf             9976885154465444431055646777396643232102466645


No 14 
>d1hfoa_ d.80.1.3 (A:) Microphage migration inhibition factor (MIF) {Trichinella spiralis [TaxId: 6334]}
Probab=39.55  E-value=12  Score=16.33  Aligned_cols=61  Identities=13%  Similarity=0.098  Sum_probs=38.5

Q ss_pred             EEEEEECCCCCCEEEEECCCCCCCCCCEEEEEEECCC-CCC----HHHHHHHHHHHHHHCCCHHHEEEEECCCC
Q ss_conf             9999941866530231014566677767999996387-679----78899999999982998444799835577
Q gi|254780231|r    4 VIVRLIPNAKKSGIASLEIPKDTSDTIHMKIKVTATP-QKG----KANKAMLAMLAKKLALSKSSLRMLSKQSS   72 (98)
Q Consensus         4 i~v~V~P~a~~~~I~g~~~~~d~~~~~~lkv~v~ApP-v~G----kAN~ali~~Lak~l~v~ks~I~I~~G~~s   72 (98)
                      |.|.+.|+..-. ..       |....+.-+.|++-. .+.    +..+++++||.+.|+||+.+|-|..-..+
T Consensus        37 vmV~v~~~~~m~-fg-------Gs~eP~a~~~l~sig~l~~~~n~~~s~~i~~~l~~~LgI~~~RiyI~f~d~~  102 (113)
T d1hfoa_          37 VAVHINTDQQLS-FG-------GSTNPAAFGTLMSIGGIEPSRNRDHSAKLFDHLNTKLGIPKNRMYIHFVNLN  102 (113)
T ss_dssp             CEEEEECSCEEE-ET-------TBCSSCEEEEEEESSSCSHHHHHHHHHHHHHHHHHHHCCCGGGEEEEEEECC
T ss_pred             EEEEECCCCCEE-EC-------CCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECC
T ss_conf             899981897279-76-------9899679999999358996883899999999999971979364999999788


No 15 
>d1n62b2 d.133.1.1 (B:147-809) Carbon monoxide (CO) dehydrogenase molybdoprotein {Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137]}
Probab=34.17  E-value=15  Score=15.82  Aligned_cols=46  Identities=9%  Similarity=0.135  Sum_probs=38.6

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCHHHEEEEECCCCCE
Q ss_conf             7679999963876797889999999998299844479983557780
Q gi|254780231|r   29 TIHMKIKVTATPQKGKANKAMLAMLAKKLALSKSSLRMLSKQSSPL   74 (98)
Q Consensus        29 ~~~lkv~v~ApPv~GkAN~ali~~Lak~l~v~ks~I~I~~G~~sr~   74 (98)
                      ++.+.|.+.+....-=.+..+....|+.||+|-.+|.+..|-|...
T Consensus       370 DG~v~v~~g~~d~GqG~~T~~~QiaAe~LGip~d~V~v~~~DT~~~  415 (663)
T d1n62b2         370 TGSVIARMGTKSQGQGHETTYAQIIATELGIPADDIMIEEGNTDTA  415 (663)
T ss_dssp             TSCEEEEESCCCSSSCHHHHHHHHHHHHHTCCGGGEEEECCBTTTS
T ss_pred             CCCEEEEECCCCCCCCCCHHHHHHHHHHHCCCHHHCCCCCCCCCCC
T ss_conf             9978775234456787413568999998399665433324778878


No 16 
>d1ffvb2 d.133.1.1 (B:147-803) Carbon monoxide (CO) dehydrogenase molybdoprotein {Hydrogenophaga pseudoflava [TaxId: 47421]}
Probab=27.57  E-value=19  Score=15.14  Aligned_cols=46  Identities=11%  Similarity=0.130  Sum_probs=39.0

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCHHHEEEEECCCCCE
Q ss_conf             7679999963876797889999999998299844479983557780
Q gi|254780231|r   29 TIHMKIKVTATPQKGKANKAMLAMLAKKLALSKSSLRMLSKQSSPL   74 (98)
Q Consensus        29 ~~~lkv~v~ApPv~GkAN~ali~~Lak~l~v~ks~I~I~~G~~sr~   74 (98)
                      ++.+.|+..+.....=.+..+....|+.|++|..+|.+..|-|+..
T Consensus       364 dG~v~v~~g~~e~GqG~~T~~aQiaAe~LGip~~~V~v~~~DT~~~  409 (657)
T d1ffvb2         364 TGSAIARMGTITQGQGHQTTYAQIIATELGIPSEVIQVEEGDTSTA  409 (657)
T ss_dssp             TSCEEEEESCCCSSSCHHHHHHHHHHHHHTCCGGGEEEECCBTTTS
T ss_pred             CCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCHHCCEECCCCCCCC
T ss_conf             3641022001234431135688777887188610031026887869


No 17 
>d1mwwa_ d.80.1.4 (A:) Hypothetical protein HI1388.1 {Haemophilus influenzae [TaxId: 727]}
Probab=25.07  E-value=21  Score=14.87  Aligned_cols=45  Identities=13%  Similarity=0.180  Sum_probs=29.8

Q ss_pred             CCCCEEEEEEECCC-CCCHHH----HHHHHHHHHHHCCCHHHEEEEECCC
Q ss_conf             77767999996387-679788----9999999998299844479983557
Q gi|254780231|r   27 SDTIHMKIKVTATP-QKGKAN----KAMLAMLAKKLALSKSSLRMLSKQS   71 (98)
Q Consensus        27 ~~~~~lkv~v~ApP-v~GkAN----~ali~~Lak~l~v~ks~I~I~~G~~   71 (98)
                      +....+.|.|..-+ ..-..+    +++.+.|++.+++|+.+|.|.--+.
T Consensus        55 rs~~~~~I~i~~~~grs~eqK~~l~~~lt~~l~~~lgi~~~~v~I~i~e~  104 (120)
T d1mwwa_          55 RSDDYTVIEINLMAGRMEGTKKRLIKMLFSELEYKLGIRAHDVEITIKEQ  104 (120)
T ss_dssp             SCTTCEEEEEEEETTCCHHHHHHHHHHHHHHHHHHHCCCGGGEEEEEEEE
T ss_pred             CCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC
T ss_conf             88987999999757999999999999999999998595907499999987


No 18 
>d1y7ea1 b.49.3.1 (A:101-233) Probable aminopeptidase ApeA {Borrelia burgdorferi [TaxId: 139]}
Probab=24.68  E-value=22  Score=14.82  Aligned_cols=33  Identities=24%  Similarity=0.469  Sum_probs=22.3

Q ss_pred             EEEEEECCC----CCCHHHHHHHHHHHHHHCCCHHHE
Q ss_conf             999996387----679788999999999829984447
Q gi|254780231|r   32 MKIKVTATP----QKGKANKAMLAMLAKKLALSKSSL   64 (98)
Q Consensus        32 lkv~v~ApP----v~GkAN~ali~~Lak~l~v~ks~I   64 (98)
                      |..-+..-|    .+++....++++||+.++|...+|
T Consensus        90 L~pi~~~~p~~~~~~~~~k~~ll~lla~e~gi~~~Di  126 (133)
T d1y7ea1          90 LKILIGSLPIETKEKNKVKLATLQLIKEKYKIEEEDF  126 (133)
T ss_dssp             CCEEEECCCCSCSSSCHHHHHHHHHHHHHHCCCTTTT
T ss_pred             HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCHHHH
T ss_conf             3787655877665420579999999999969899994


No 19 
>d1otfa_ d.80.1.1 (A:) 4-oxalocrotonate tautomerase {Pseudomonas sp., DmpI [TaxId: 306]}
Probab=23.84  E-value=23  Score=14.73  Aligned_cols=23  Identities=17%  Similarity=0.229  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHHHCCCHHHEEEEE
Q ss_conf             89999999998299844479983
Q gi|254780231|r   46 NKAMLAMLAKKLALSKSSLRMLS   68 (98)
Q Consensus        46 N~ali~~Lak~l~v~ks~I~I~~   68 (98)
                      =+++.+.+++.+++|+.+|.++-
T Consensus        20 ~~~it~~~~~~~g~~~~~v~V~i   42 (59)
T d1otfa_          20 IRQVSEAMANSLDAPLERVRVLI   42 (59)
T ss_dssp             HHHHHHHHHHHHTCCGGGCEEEE
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEE
T ss_conf             99999999998495904299999


No 20 
>d1xdpa2 d.322.1.2 (A:107-314) Polyphosphate kinase, PPK {Escherichia coli [TaxId: 562]}
Probab=23.33  E-value=21  Score=14.86  Aligned_cols=30  Identities=17%  Similarity=0.239  Sum_probs=25.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCHHHEEEEECC
Q ss_conf             679788999999999829984447998355
Q gi|254780231|r   41 QKGKANKAMLAMLAKKLALSKSSLRMLSKQ   70 (98)
Q Consensus        41 v~GkAN~ali~~Lak~l~v~ks~I~I~~G~   70 (98)
                      +++..+.++.++|.+.|++.+.++-+.-|.
T Consensus       158 ~~~~mp~~~~~~L~~~l~l~~~d~~~~~G~  187 (208)
T d1xdpa2         158 YQRDMPNALVEVLREKLTISRYDSIVPGGR  187 (208)
T ss_dssp             ECTTCCHHHHHHHHHHTTCCSSSEEEECCS
T ss_pred             ECCCCCHHHHHHHHHHCCCCCCCEEEECCC
T ss_conf             347899999999999829694663741896


No 21 
>d2qrra1 d.58.18.13 (A:2-98) Methionine import ATP-binding protein MetN {Vibrio parahaemolyticus [TaxId: 670]}
Probab=22.77  E-value=24  Score=14.60  Aligned_cols=60  Identities=5%  Similarity=0.109  Sum_probs=42.9

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHCCCHHHEEEEECCCCCE-------EEEEECCCHHHHHHHHHHHHH
Q ss_conf             79999963876797889999999998299844479983557780-------699982998999999975230
Q gi|254780231|r   31 HMKIKVTATPQKGKANKAMLAMLAKKLALSKSSLRMLSKQSSPL-------KIIYIDKDCKEITELLQNNDS   95 (98)
Q Consensus        31 ~lkv~v~ApPv~GkAN~ali~~Lak~l~v~ks~I~I~~G~~sr~-------K~i~I~~~~~~i~~~L~~~~s   95 (98)
                      ..-++++=  ....|++.++.-|++.|++   ++.|+.|.-...       =.+.+.|+.+++.+.++...+
T Consensus        19 ~~llrl~f--~g~~a~~Pvis~l~~~~~i---~vnIL~g~i~~i~~~~~G~Lil~l~G~~~~~~~Al~~L~~   85 (97)
T d2qrra1          19 YPLVRMEF--TGATVDAPLMSQISRKYNI---DVSILSSDLDYAGGVKFGMMVAELFGNEQDDSAAIEYLRE   85 (97)
T ss_dssp             EEEEEEEE--CTTSCSSCHHHHHHHHSCC---EEEEEEEEEEEETTEEEEEEEEEEESCHHHHHHHHHHHHH
T ss_pred             CEEEEEEE--ECCCCCCHHHHHHHHHHCC---CEEEEEEEEEEECCEEEEEEEEEEECCHHHHHHHHHHHHH
T ss_conf             25999998--1887686399999998799---7299998528858854899999997899999999999998


Done!