Query         gi|254780128|ref|YP_003064541.1| VRR-NUC domain-containing protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 103
No_of_seqs    109 out of 449
Neff          6.0 
Searched_HMMs 13730
Date          Sun May 22 11:09:01 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780128.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 d1ob8a_ c.52.1.18 (A:) Hollida  97.5 0.00067 4.9E-08   42.8  10.1   67   12-79      2-73  (124)
  2 d1hh1a_ c.52.1.18 (A:) Archaea  97.0  0.0017 1.2E-07   40.3   7.9   73   13-86      2-83  (132)
  3 d1gefa_ c.52.1.18 (A:) Archaea  96.1  0.0076 5.5E-07   36.4   6.2   74   10-87      4-81  (120)
  4 d1rzna_ c.52.1.28 (A:) Recombi  94.4    0.19 1.3E-05   28.0  11.2   74   11-85      3-104 (165)
  5 d1y1oa_ c.52.1.28 (A:) Recombi  94.0    0.23 1.6E-05   27.5  10.8   75   11-86      4-106 (168)
  6 d1vsra_ c.52.1.15 (A:) Very sh  88.8    0.87 6.3E-05   24.0   8.0   70   14-86      2-93  (134)
  7 d1kl7a_ c.79.1.1 (A:) Threonin  66.2     3.1 0.00023   20.6   3.7   41   60-100   184-225 (511)
  8 d1xmxa_ c.52.1.26 (A:) Hypothe  60.2     5.6 0.00041   19.0   4.2   22   41-63    294-315 (385)
  9 d1t0fa2 c.52.1.16 (A:7-168) Tn  49.5     8.1 0.00059   18.1   3.5   48   40-87    106-159 (162)
 10 d1t47a1 d.32.1.3 (A:16-178) 4-  46.8      10 0.00075   17.5   7.4   88   12-100    16-104 (163)
 11 d1zj8a2 d.58.36.1 (A:10-161) S  42.3     9.5 0.00069   17.7   3.0   51   51-101    83-144 (152)
 12 d1zj8a1 d.58.36.1 (A:327-406)   31.1      18  0.0013   15.9   6.8   54   47-101    11-75  (80)
 13 d2akja1 d.58.36.1 (A:346-430)   30.3      19  0.0014   15.9   3.2   29   49-77     16-44  (85)
 14 d1vb3a1 c.79.1.1 (A:1-428) Thr  28.3      16  0.0012   16.3   2.3   38   60-100   158-198 (428)
 15 d1dcea2 b.7.4.1 (A:242-350) Ra  24.4     9.9 0.00072   17.6   0.6   43   25-68     13-57  (109)
 16 d1y88a2 c.52.1.30 (A:3-127) Hy  22.3      27  0.0019   15.0   7.8   71   14-85      4-84  (125)
 17 d1loua_ d.58.14.1 (A:) Ribosom  22.0      26  0.0019   15.0   2.4   58    9-69     14-77  (97)
 18 d1aopa1 d.58.36.1 (A:81-145) S  21.9      13 0.00096   16.8   0.9   47   55-101     2-60  (65)
 19 d1p90a_ c.55.5.2 (A:) NafY cor  21.9      23  0.0017   15.3   2.1   66   37-102    23-111 (123)
 20 d2akja2 d.58.36.1 (A:22-174) F  20.2      22  0.0016   15.5   1.7   51   51-101    83-145 (153)
 21 d1b04a_ d.142.2.2 (A:) Adenyla  20.2      29  0.0021   14.7   5.3   48   53-100   218-269 (312)
 22 d1rkqa_ c.108.1.10 (A:) Hypoth  20.1      29  0.0021   14.7   5.0   22    7-30     20-41  (271)

No 1  
>d1ob8a_ c.52.1.18 (A:) Holliday-junction resolvase SSO1176 {Sulfolobus solfataricus [TaxId: 2287]}
Probab=97.49  E-value=0.00067  Score=42.77  Aligned_cols=67  Identities=16%  Similarity=0.125  Sum_probs=53.7

Q ss_pred             HHHHHHHHHHHHHCCCEEEEEECCC--CCCCCEEEEECCCCCEEEEEEECCCCC---CCHHHHHHHHHHHHCC
Q ss_conf             9999999999997898999981188--898743999906982999999768988---6889999999999789
Q gi|254780128|r   12 KDVEKRLVTGAKKLDCWVRKASFVG--RRGCPDRLIITPNGGLWWIEVKKPTGR---LSHQQMSEIEELRRRG   79 (103)
Q Consensus        12 ~~ie~~l~~~lk~~G~~~~K~~~~g--~~GvPDli~~~~~g~~~fIEvK~~~gk---ls~~Q~~~~~~l~~~G   79 (103)
                      +..|+.+++.+...|+.+.+..+.|  ..+.||++.. ++++++-||+|+.++.   ++..|...+..+.+..
T Consensus         2 ~~~ERelv~~l~~~gf~vvR~~gSGs~~~~~pDllA~-~~~~~~~IEvKst~~~kiyi~~eqie~L~~f~~~f   73 (124)
T d1ob8a_           2 KNAERELVSILRGEGFNAVRIPTSNSSPNPLPDIFAT-KGNTLLSIECKSTWENKVKVKEHQVRKLLDFLSMF   73 (124)
T ss_dssp             HHHHHHHHHHHHHTTCEEEECCC-----CCSCSEEEE-ETTEEEEEEEEEESSSEEEECHHHHHHHHHHHHTS
T ss_pred             CHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCEEEE-CCCEEEEEEEEECCCCEEEECHHHHHHHHHHHHHC
T ss_conf             5699999999986994399923578988889878985-79869999998535985998799999999999971


No 2  
>d1hh1a_ c.52.1.18 (A:) Archaeal Holliday junction resolvase Hjc {Archaeon Sulfolobus solfataricus [TaxId: 2287]}
Probab=97.01  E-value=0.0017  Score=40.33  Aligned_cols=73  Identities=26%  Similarity=0.358  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHHHCCCEEEEEECCC---CCCCCEEEEECCCCCEEEEEEECCCC-----CCCHHHHHHHHHH-HHCCCEEE
Q ss_conf             999999999997898999981188---89874399990698299999976898-----8688999999999-97898899
Q gi|254780128|r   13 DVEKRLVTGAKKLDCWVRKASFVG---RRGCPDRLIITPNGGLWWIEVKKPTG-----RLSHQQMSEIEEL-RRRGQRVK   83 (103)
Q Consensus        13 ~ie~~l~~~lk~~G~~~~K~~~~g---~~GvPDli~~~~~g~~~fIEvK~~~g-----kls~~Q~~~~~~l-~~~G~~~~   83 (103)
                      ..|+.++..+...|+.|.+..+.|   ..=.||++... ++.++-||||+..+     .++..|..-+..+ +..|....
T Consensus         2 ~~ERel~~~l~~~gFavvRapgSGs~~~~~~pDlvA~~-~~~~~~IEvKst~~~~~~iyi~~eqve~L~~f~~~fG~~p~   80 (132)
T d1hh1a_           2 AVERNIVSRLRDKGFAVVRAPASGSKRKDPIPDIIALK-NGVIILIEMKSRKDIEGKIYVRREQAEGIIEFARKSGGSLF   80 (132)
T ss_dssp             HHHHHHHHHHHHTTCEEEECCC-------CCCSEEEEE-TTEEEEEEECCEECTTSCEEECHHHHHHHHHHHHHHTCEEE
T ss_pred             HHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCEEECC-CCEEEEEEEEEECCCCCCEEECHHHHHHHHHHHHHCCCEEE
T ss_conf             78999999998589449994567888778998689526-98799999986157764389879999999999997599599


Q ss_pred             EEC
Q ss_conf             985
Q gi|254780128|r   84 VLV   86 (103)
Q Consensus        84 Vv~   86 (103)
                      ++.
T Consensus        81 iav   83 (132)
T d1hh1a_          81 LGV   83 (132)
T ss_dssp             EEE
T ss_pred             EEE
T ss_conf             999


No 3  
>d1gefa_ c.52.1.18 (A:) Archaeal Holliday junction resolvase Hjc {Archaeon Pyrococcus furiosus [TaxId: 2261]}
Probab=96.07  E-value=0.0076  Score=36.39  Aligned_cols=74  Identities=20%  Similarity=0.178  Sum_probs=51.1

Q ss_pred             CHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCC---CCHHHHHHHHHH-HHCCCEEEEE
Q ss_conf             999999999999997898999981188898743999906982999999768988---688999999999-9789889998
Q gi|254780128|r   10 TEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGR---LSHQQMSEIEEL-RRRGQRVKVL   85 (103)
Q Consensus        10 ~E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gk---ls~~Q~~~~~~l-~~~G~~~~Vv   85 (103)
                      +=+..|+.+++.+..+|+.+...-   .+|-||++... ++..+-||||+....   .+++|....-.. +..|....|+
T Consensus         4 KG~~~ERel~~~l~~~G~~~~R~~---~sg~~D~~a~~-~~~~~~IEvK~~~~~~~~~~~~~~eql~~~a~~~g~~P~la   79 (120)
T d1gefa_           4 KGAQAERELIKLLEKHGFAVVRSA---GSKKVDLVAGN-GKKYLCIEVKVTKKDHLYVGKRDMGRLIEFSRRFGGIPVLA   79 (120)
T ss_dssp             HHHHHHHHHHHHHHHTTCEEEEBG---GGSSCSEEEEC-SSCEEEEEEEEESSSCEEECHHHHHHHHHHHHHHTCEEEEE
T ss_pred             CHHHHHHHHHHHHHHCCCCEEECC---CCCCCCCCCCC-CCCEEEEECCCCCCCCEEECHHHHHHHHHHHHHCCCCEEEE
T ss_conf             343999999999986797699987---87788721378-88369998377104652429999999999998579936999


Q ss_pred             CC
Q ss_conf             59
Q gi|254780128|r   86 VS   87 (103)
Q Consensus        86 ~s   87 (103)
                      .-
T Consensus        80 ~K   81 (120)
T d1gefa_          80 VK   81 (120)
T ss_dssp             EE
T ss_pred             EE
T ss_conf             99


No 4  
>d1rzna_ c.52.1.28 (A:) Recombination protein U (RecU)/PBP related factor A (PrfA) {Bacillus subtilis [TaxId: 1423]}
Probab=94.44  E-value=0.19  Score=28.01  Aligned_cols=74  Identities=14%  Similarity=0.109  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEECC---------------------CCCCCCEEEEECCCCCEEEEEEECCCC-------
Q ss_conf             9999999999999789899998118---------------------889874399990698299999976898-------
Q gi|254780128|r   11 EKDVEKRLVTGAKKLDCWVRKASFV---------------------GRRGCPDRLIITPNGGLWWIEVKKPTG-------   62 (103)
Q Consensus        11 E~~ie~~l~~~lk~~G~~~~K~~~~---------------------g~~GvPDli~~~~~g~~~fIEvK~~~g-------   62 (103)
                      |..|......+..+.-+.+.|.-.|                     ..+.-||...++ .|+++..|.|...+       
T Consensus         3 E~~In~tn~~Y~~~~~A~I~K~PtPi~~vkv~~~~r~~~~I~~Ayf~~kSt~DY~Gvy-kG~~I~FEAKeT~nktsFpl~   81 (165)
T d1rzna_           3 EDDLNETNKYYLTNQIAVIHKKPTPVQIVNVHYPKRSAAVIKEAYFKQSSTTDYNGIY-KGRYIDFEAKETKNKTSFPLQ   81 (165)
T ss_dssp             HHHHHHHHHHHHHTTSCEEEECCCCEEC---------------CEECCCSSCSEEEEE-TTEEEEEEEEECCCSSEEEGG
T ss_pred             HHHHHHHHHHHHHCCEEEEEEECCCEEEEEECCCCCCCCEEEEEEECCCCCCCCEEEE-CCEEEEEECCCCCCCCCCCHH
T ss_conf             8999999999997798999970788389962577666534444796357888702477-789999983354676722334


Q ss_pred             CCCHHHHHHHHHHHHCCCEEEEE
Q ss_conf             86889999999999789889998
Q gi|254780128|r   63 RLSHQQMSEIEELRRRGQRVKVL   85 (103)
Q Consensus        63 kls~~Q~~~~~~l~~~G~~~~Vv   85 (103)
                      ...++|...++.+.++|+.++++
T Consensus        82 ni~~HQi~~L~~~~~~gGI~F~i  104 (165)
T d1rzna_          82 NFHDHQIEHMKQVKAQDGICFVI  104 (165)
T ss_dssp             GSCHHHHHHHHHHHHTTCEEEEE
T ss_pred             HCCHHHHHHHHHHHHCCCEEEEE
T ss_conf             37799999999999789989999


No 5  
>d1y1oa_ c.52.1.28 (A:) Recombination protein U (RecU)/PBP related factor A (PrfA) {Bacillus stearothermophilus [TaxId: 1422]}
Probab=94.03  E-value=0.23  Score=27.48  Aligned_cols=75  Identities=13%  Similarity=0.124  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHHHHHCCCEEEE---------EECCC------------CCCCCEEEEECCCCCEEEEEEECCC-C------
Q ss_conf             999999999999978989999---------81188------------8987439999069829999997689-8------
Q gi|254780128|r   11 EKDVEKRLVTGAKKLDCWVRK---------ASFVG------------RRGCPDRLIITPNGGLWWIEVKKPT-G------   62 (103)
Q Consensus        11 E~~ie~~l~~~lk~~G~~~~K---------~~~~g------------~~GvPDli~~~~~g~~~fIEvK~~~-g------   62 (103)
                      |..|......+..+.-+.+.|         +..+.            .+.-||.+.++ .|+++..|.|... .      
T Consensus         4 E~~In~tn~~Y~~~~~A~I~K~ptPi~~vkvd~~~r~~a~i~~ayf~~kSt~DY~Gvy-~G~~I~FEAKeT~~ktsFpl~   82 (168)
T d1y1oa_           4 EDDLNATNEYYRERGIAVIHKKPTPVQIVRVDYPKRSAAVITEAYFRQASTTDYNGVY-RGKYIDFEAKETKNKTAFPLK   82 (168)
T ss_dssp             HHHHHHHHHHHHHTTSCEEEECCCCEEEEEEECCSSSCCEEEEEEECCCSSCSEEEEE-TTEEEEEEEEEECCSSEEEGG
T ss_pred             HHHHHHHHHHHHHCCEEEEEEECCCEEEEEECCCCCCCCEEEEEEECCCCCCCEEEEE-CCEEEEEEEEECCCCCEECHH
T ss_conf             9999999999997797999970798389961577665644677796467988755675-565899996303688704533


Q ss_pred             CCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             868899999999997898899985
Q gi|254780128|r   63 RLSHQQMSEIEELRRRGQRVKVLV   86 (103)
Q Consensus        63 kls~~Q~~~~~~l~~~G~~~~Vv~   86 (103)
                      ..+++|...++.+.++|+.++++=
T Consensus        83 ni~~HQi~~L~~~~~~gGI~F~iI  106 (168)
T d1y1oa_          83 NFHAHQIRHMEQVVAHGGICFAIL  106 (168)
T ss_dssp             GSCHHHHHHHHHHHHTTCEEEEEE
T ss_pred             HCCHHHHHHHHHHHHCCCEEEEEE
T ss_conf             077999999999997899799999


No 6  
>d1vsra_ c.52.1.15 (A:) Very short patch repair (VSR) endonuclease {Escherichia coli [TaxId: 562]}
Probab=88.81  E-value=0.87  Score=23.95  Aligned_cols=70  Identities=17%  Similarity=0.151  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEE--------ECCCCCCCHHHH--------------HH
Q ss_conf             99999999997898999981188898743999906982999999--------768988688999--------------99
Q gi|254780128|r   14 VEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEV--------KKPTGRLSHQQM--------------SE   71 (103)
Q Consensus        14 ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEv--------K~~~gkls~~Q~--------------~~   71 (103)
                      ||..+.+.|.+.|.+ |+...+.-+|-|| |++.+-.-++||-=        +. ...|..+..              ..
T Consensus         2 ~E~~lr~~L~~~G~R-yR~~~k~lpG~PD-iv~~~~k~aIfvdGcFWH~h~c~~-~~~Pktn~efW~~Ki~~N~~RD~~~   78 (134)
T d1vsra_           2 IEKRLASLLTGQGLA-FRVQDASLPGRPD-FVVDEYRCVIFTHGCFWHHHHCYL-FKVPATRTEFWLEKIGKNVERDRRD   78 (134)
T ss_dssp             CCHHHHHHHHHTTCC-CEESCTTSTTCCS-EEEGGGTEEEEEECTTTTTCSSTT-CCCCSSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCE-EEECCCCCCCCCC-EEECCCCEEEEECCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             789999999978986-8864888999988-963376389997174036899655-6899855799999999888879999


Q ss_pred             HHHHHHCCCEEEEEC
Q ss_conf             999997898899985
Q gi|254780128|r   72 IEELRRRGQRVKVLV   86 (103)
Q Consensus        72 ~~~l~~~G~~~~Vv~   86 (103)
                      .+.|.++|+.|.+++
T Consensus        79 ~~~L~~~GW~vl~iW   93 (134)
T d1vsra_          79 ISRLQELGWRVLIVW   93 (134)
T ss_dssp             HHHHHHTTCEEEEEE
T ss_pred             HHHHHHCCCEEEEEE
T ss_conf             999998889899996


No 7  
>d1kl7a_ c.79.1.1 (A:) Threonine synthase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Probab=66.16  E-value=3.1  Score=20.61  Aligned_cols=41  Identities=15%  Similarity=0.306  Sum_probs=32.5

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCEEEEE-CCHHHHHHHHHHHHH
Q ss_conf             89886889999999999789889998-598999999999986
Q gi|254780128|r   60 PTGRLSHQQMSEIEELRRRGQRVKVL-VSMEEVDNFLEELAC  100 (103)
Q Consensus        60 ~~gkls~~Q~~~~~~l~~~G~~~~Vv-~s~edv~~~l~~l~~  100 (103)
                      |.|+.|+-|+..+.-..+.+..+.-| =++||++.++.++-.
T Consensus       184 P~~~vS~iQ~~Qmtt~~~~Nv~~i~v~G~fDDcq~~vk~~f~  225 (511)
T d1kl7a_         184 PTGRISPIQEEQMTTVPDENVQTLSVTGTFDNCQDIVKAIFG  225 (511)
T ss_dssp             ETTSSCHHHHHHHHHCCCTTEEEEEESSCHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHH
T ss_conf             688886678998740377659999843676778899999973


No 8  
>d1xmxa_ c.52.1.26 (A:) Hypothetical protein VC1899 {Vibrio cholerae [TaxId: 666]}
Probab=60.24  E-value=5.6  Score=19.03  Aligned_cols=22  Identities=32%  Similarity=0.226  Sum_probs=16.5

Q ss_pred             CEEEEECCCCCEEEEEEECCCCC
Q ss_conf             43999906982999999768988
Q gi|254780128|r   41 PDRLIITPNGGLWWIEVKKPTGR   63 (103)
Q Consensus        41 PDli~~~~~g~~~fIEvK~~~gk   63 (103)
                      =|++++ .+++.++||||+.+-+
T Consensus       294 lDv~~~-~~~~l~~IECKt~~~~  315 (385)
T d1xmxa_         294 LDVATV-VNNKLHIIECKTKGMR  315 (385)
T ss_dssp             EEEEEE-ETTEEEEEEEESSCCC
T ss_pred             EEEEEE-ECCEEEEEEECCCCCC
T ss_conf             689999-7999999995688877


No 9  
>d1t0fa2 c.52.1.16 (A:7-168) TnsA endonuclease, N-terminal domain {Escherichia coli [TaxId: 562]}
Probab=49.51  E-value=8.1  Score=18.10  Aligned_cols=48  Identities=15%  Similarity=0.132  Sum_probs=31.6

Q ss_pred             CCEEEEECCCCC--EEEEEEECCCCC--CCHHHHHHH--HHHHHCCCEEEEECC
Q ss_conf             743999906982--999999768988--688999999--999978988999859
Q gi|254780128|r   40 CPDRLIITPNGG--LWWIEVKKPTGR--LSHQQMSEI--EELRRRGQRVKVLVS   87 (103)
Q Consensus        40 vPDli~~~~~g~--~~fIEvK~~~gk--ls~~Q~~~~--~~l~~~G~~~~Vv~s   87 (103)
                      .||+++.+.||.  .+.+|||-...-  .+-.++..+  ...+..|....|+-.
T Consensus       106 TtDFLV~~~dG~~~~~a~eVKp~~~l~~~r~~eKleier~yw~~~Gi~~~ivTE  159 (162)
T d1t0fa2         106 STDFLVDCKDGPFEQFAIQVKPAAALQDERTLEKLELERRYWQQKQIPWFIFTD  159 (162)
T ss_dssp             EEEEEEEESSSSCSEEEEEECCGGGGGCHHHHHHHHHHHHHHHHHTCCEEEECG
T ss_pred             ECCEEEEEECCCEEEEEEEECCHHHHCCHHHHHHHHHHHHHHHHCCCCEEEECC
T ss_conf             225899981897889999965568842977999999999999984994899736


No 10 
>d1t47a1 d.32.1.3 (A:16-178) 4-hydroxyphenylpyruvate dioxygenase, HppD {Streptomyces avermitilis [TaxId: 33903]}
Probab=46.81  E-value=10  Score=17.46  Aligned_cols=88  Identities=6%  Similarity=-0.068  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCC-CEEEEECCHHH
Q ss_conf             99999999999978989999811888987439999069829999997689886889999999999789-88999859899
Q gi|254780128|r   12 KDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRG-QRVKVLVSMEE   90 (103)
Q Consensus        12 ~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G-~~~~Vv~s~ed   90 (103)
                      +++++.+..+.+.+|............+.-........|.. .+++-.+.+..++.-..+...+...| +...++-.++|
T Consensus        16 ~D~~~a~~fY~~~lGf~~v~~~~~~~~~~~~~~~~l~~~~~-~i~l~~~~~~~~~~~~~~~~~~~~~g~G~~hiaf~VdD   94 (163)
T d1t47a1          16 GNAKQAAHYYSTAFGMQLVAYSGPENGSRETASYVLTNGSA-RFVLTSVIKPATPWGHFLADHVAEHGDGVVDLAIEVPD   94 (163)
T ss_dssp             SCHHHHHHHHHHTSCCEEEEEESGGGTCCSEEEEEEEETTE-EEEEEEESSCCSHHHHHHHHHHHHHCSEEEEEEEECSC
T ss_pred             CCHHHHHHHHHHHHCCEEEEEECCCCCCEEEEEEEEECCCE-EEEEECCCCCCCCCCCCCCHHHHCCCCCEEEEEEEECC
T ss_conf             89999999999975995996641335652599999716988-89990367887743333220234079845999996087


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999986
Q gi|254780128|r   91 VDNFLEELAC  100 (103)
Q Consensus        91 v~~~l~~l~~  100 (103)
                      +++.++.+.+
T Consensus        95 id~a~~~l~~  104 (163)
T d1t47a1          95 ARAAHAYAIE  104 (163)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
T ss_conf             9999999998


No 11 
>d1zj8a2 d.58.36.1 (A:10-161) Sulfite reductase NirA {Mycobacterium tuberculosis [TaxId: 1773]}
Probab=42.26  E-value=9.5  Score=17.66  Aligned_cols=51  Identities=14%  Similarity=0.261  Sum_probs=36.9

Q ss_pred             CEEEEEEECCCCCCCHHHHHHHHHHHH-CC-CEEEEE---------CCHHHHHHHHHHHHHH
Q ss_conf             299999976898868899999999997-89-889998---------5989999999999863
Q gi|254780128|r   51 GLWWIEVKKPTGRLSHQQMSEIEELRR-RG-QRVKVL---------VSMEEVDNFLEELACT  101 (103)
Q Consensus        51 ~~~fIEvK~~~gkls~~Q~~~~~~l~~-~G-~~~~Vv---------~s~edv~~~l~~l~~t  101 (103)
                      .++++=++.|+|.++++|...+..+.+ .| ....+.         =..+++.+++++|.+.
T Consensus        83 ~~fmvRvr~p~G~lt~~Ql~~la~ia~~yg~g~i~iTtRQ~iql~gI~~~~l~~i~~~L~~~  144 (152)
T d1zj8a2          83 KYFMMRVRCDGGALSAAALRTLGQISTEFARDTADISDRQNVQYHWIEVENVPEIWRRLDDV  144 (152)
T ss_dssp             EEEEEEEBCGGGEECHHHHHHHHHHHHHHSTTEEEECTTSCEEEEEECGGGHHHHHHHHHTT
T ss_pred             CEEEEEEECCCCEECHHHHHHHHHHHHHHCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHC
T ss_conf             66999982589772699999999999984899701568732784698888999999999984


No 12 
>d1zj8a1 d.58.36.1 (A:327-406) Sulfite reductase NirA {Mycobacterium tuberculosis [TaxId: 1773]}
Probab=31.07  E-value=18  Score=15.94  Aligned_cols=54  Identities=20%  Similarity=0.349  Sum_probs=38.4

Q ss_pred             CCCCCEEEEEEECCCCCCCHHHHHHHHHHHH-CCC-EEEE-------E--CCHHHHHHHHHHHHHH
Q ss_conf             0698299999976898868899999999997-898-8999-------8--5989999999999863
Q gi|254780128|r   47 TPNGGLWWIEVKKPTGRLSHQQMSEIEELRR-RGQ-RVKV-------L--VSMEEVDNFLEELACT  101 (103)
Q Consensus        47 ~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~-~G~-~~~V-------v--~s~edv~~~l~~l~~t  101 (103)
                      -+||. ++|=++.|.|++++.|...+..+.+ .|. ...+       +  =..+++.+++++|.+.
T Consensus        11 q~dG~-~~vri~~p~G~it~~ql~~la~ia~~yg~g~i~lTtrq~l~l~~i~~~~~~~v~~~L~~~   75 (80)
T d1zj8a1          11 LKNGL-NAVGVAPIAGRVSGTILTAVADLMARAGSDRIRFTPYQKLVILDIPDALLDDLIAGLDAL   75 (80)
T ss_dssp             CTTSS-EEEEEBCBTTEEEHHHHHHHHHHHHHHTCCCEEECTTSCEEEEEECHHHHHHHHHHHHHT
T ss_pred             ECCCC-EEEEEECCCCEECHHHHHHHHHHHHHHCCCEEEECCCCCEEECCCCHHHHHHHHHHHHHC
T ss_conf             05970-999994668599999999999999973999498879875897589989999999999986


No 13 
>d2akja1 d.58.36.1 (A:346-430) Ferredoxin--nitrite reductase, NIR {Spinach (Spinacia oleracea) [TaxId: 3562]}
Probab=30.35  E-value=19  Score=15.87  Aligned_cols=29  Identities=28%  Similarity=0.590  Sum_probs=25.2

Q ss_pred             CCCEEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             98299999976898868899999999997
Q gi|254780128|r   49 NGGLWWIEVKKPTGRLSHQQMSEIEELRR   77 (103)
Q Consensus        49 ~g~~~fIEvK~~~gkls~~Q~~~~~~l~~   77 (103)
                      +...++|=++.|.|++++.|...+..+.+
T Consensus        16 ~~g~~~vri~~p~G~lt~~ql~~la~ia~   44 (85)
T d2akja1          16 QQGLSFVGLHIPVGRLQADEMEELARIAD   44 (85)
T ss_dssp             STTEEEEEECCGGGEECHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECCCCEECHHHHHHHHHHHH
T ss_conf             79869999976895929999999999999


No 14 
>d1vb3a1 c.79.1.1 (A:1-428) Threonine synthase {Escherichia coli [TaxId: 562]}
Probab=28.32  E-value=16  Score=16.28  Aligned_cols=38  Identities=13%  Similarity=0.186  Sum_probs=27.1

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCEEEE---ECCHHHHHHHHHHHHH
Q ss_conf             8988688999999999978988999---8598999999999986
Q gi|254780128|r   60 PTGRLSHQQMSEIEELRRRGQRVKV---LVSMEEVDNFLEELAC  100 (103)
Q Consensus        60 ~~gkls~~Q~~~~~~l~~~G~~~~V---v~s~edv~~~l~~l~~  100 (103)
                      |.|+.|+.|+..+..   .|..+.|   =-++||++.++.++-.
T Consensus       158 P~g~vS~~Q~~Qmtt---~g~nv~vi~V~G~fDDcq~lvk~~f~  198 (428)
T d1vb3a1         158 PRGKISPLQEKLFCT---LGGNIETVAIDGDFDACQALVKQAFD  198 (428)
T ss_dssp             ETTCSCHHHHHHHHS---CCTTEEEEEEESCHHHHHHHHHHGGG
T ss_pred             CCCCCCHHHHHHHHH---CCCCCEEEECCCCHHHHHHHHHHHHH
T ss_conf             688875899988764---46771378427875478999988764


No 15 
>d1dcea2 b.7.4.1 (A:242-350) Rab geranylgeranyltransferase alpha-subunit, insert domain {Rat (Rattus norvegicus) [TaxId: 10116]}
Probab=24.42  E-value=9.9  Score=17.55  Aligned_cols=43  Identities=16%  Similarity=0.105  Sum_probs=32.4

Q ss_pred             CCCEEEEEECCC--CCCCCEEEEECCCCCEEEEEEECCCCCCCHHH
Q ss_conf             898999981188--89874399990698299999976898868899
Q gi|254780128|r   25 LDCWVRKASFVG--RRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQ   68 (103)
Q Consensus        25 ~G~~~~K~~~~g--~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q   68 (103)
                      .++...-|..|-  .+|.-+|+++. ||...++|-.+|.|+.++.|
T Consensus        13 e~~l~v~FSrpv~v~~~~~~L~L~~-Dg~p~~veWRtp~gr~r~s~   57 (109)
T d1dcea2          13 EACLSVCFSRPLTVGSRMGTLLLMV-DEAPLSVEWRTPDGRNRPSH   57 (109)
T ss_dssp             TTEEEEEEEEEECTTBTTBCEEEEE-SSSEECCCCBCTTSSCCSEE
T ss_pred             CCEEEEEECCCEECCCCCCEEEEEE-CCCCEEEEEECCCCCCCCCC
T ss_conf             6748999625134066655179996-79827999768998667583


No 16 
>d1y88a2 c.52.1.30 (A:3-127) Hypothetical protein AF1548, N-terminal domain {Archaeoglobus fulgidus [TaxId: 2234]}
Probab=22.29  E-value=27  Score=14.96  Aligned_cols=71  Identities=10%  Similarity=-0.002  Sum_probs=40.6

Q ss_pred             HHHHHHHHH-HHCCCEEEE---EECCCCCCCCEEEEECCCCCEEEEEEECCCC--CCCHHHHHHHH----HHHHCCCEEE
Q ss_conf             999999999-978989999---8118889874399990698299999976898--86889999999----9997898899
Q gi|254780128|r   14 VEKRLVTGA-KKLDCWVRK---ASFVGRRGCPDRLIITPNGGLWWIEVKKPTG--RLSHQQMSEIE----ELRRRGQRVK   83 (103)
Q Consensus        14 ie~~l~~~l-k~~G~~~~K---~~~~g~~GvPDli~~~~~g~~~fIEvK~~~g--kls~~Q~~~~~----~l~~~G~~~~   83 (103)
                      .+.+++..+ ++.|+.+-.   +...+..+=-|+++. +++..+.||||.-..  .....|.....    .+...|+...
T Consensus         4 ~~~~lva~ll~~~Gy~v~~~v~v~g~~~d~gvDiia~-~~~~~~~VQcK~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~   82 (125)
T d1y88a2           4 FQGHMVARLLEEHGFETKTNVIVQGNCVEQEIDVVAE-RDGERYMIECKFHNIPVYTGLKEAMYTYARFLDVEKHGFTQP   82 (125)
T ss_dssp             HHHHHHHHHHHTTTCEEEEEEEEECSSSEEEEEEEEE-ETTEEEEEEECCCSSSCEECHHHHHHHHHHHHHHGGGTCSEE
T ss_pred             HHHHHHHHHHHHCCCCEECCEEEEECCCCCEEEEEEE-CCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCEE
T ss_conf             6999999999986996504679945145602899997-399089999998326778884568888876511332289869


Q ss_pred             EE
Q ss_conf             98
Q gi|254780128|r   84 VL   85 (103)
Q Consensus        84 Vv   85 (103)
                      ++
T Consensus        83 ii   84 (125)
T d1y88a2          83 WI   84 (125)
T ss_dssp             EE
T ss_pred             EE
T ss_conf             99


No 17 
>d1loua_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus [TaxId: 274]}
Probab=21.98  E-value=26  Score=15.02  Aligned_cols=58  Identities=16%  Similarity=0.249  Sum_probs=36.5

Q ss_pred             CCHHHHH---HHHHHHHHHCCCEEEEEECCCCCCCCEEEEECC---CCCEEEEEEECCCCCCCHHHH
Q ss_conf             8999999---999999997898999981188898743999906---982999999768988688999
Q gi|254780128|r    9 QTEKDVE---KRLVTGAKKLDCWVRKASFVGRRGCPDRLIITP---NGGLWWIEVKKPTGRLSHQQM   69 (103)
Q Consensus         9 ~~E~~ie---~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~---~g~~~fIEvK~~~gkls~~Q~   69 (103)
                      .+|..++   .++.+.+++.||.+.+...-|.   =+|-....   .|.++++.+.+++..+....+
T Consensus        14 l~~~~~~~~~~~~~~~i~~~gg~i~~~e~~G~---r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~   77 (97)
T d1loua_          14 LDQSQLALEKEIIQRAAENYGARVEKVEELGL---RRLAYPIAKDPQGYFLWYQVEMPEDRVNDLAR   77 (97)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTCEEEEEEEEEE---EEEEEEETTEEEEEEEEEEEEECGGGHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCEEEEEEEEEE---EECCCCCCCCCEEEEEEEEEEECHHHHHHHHH
T ss_conf             99899999999999999868988999850077---82420246466369999999968999999999


No 18 
>d1aopa1 d.58.36.1 (A:81-145) Sulfite reductase, domains 1 and 3 {Escherichia coli [TaxId: 562]}
Probab=21.91  E-value=13  Score=16.81  Aligned_cols=47  Identities=13%  Similarity=0.301  Sum_probs=33.3

Q ss_pred             EEEECCCCCCCHHHHHHHHHHH-HCC--CEEEEE---------CCHHHHHHHHHHHHHH
Q ss_conf             9997689886889999999999-789--889998---------5989999999999863
Q gi|254780128|r   55 IEVKKPTGRLSHQQMSEIEELR-RRG--QRVKVL---------VSMEEVDNFLEELACT  101 (103)
Q Consensus        55 IEvK~~~gkls~~Q~~~~~~l~-~~G--~~~~Vv---------~s~edv~~~l~~l~~t  101 (103)
                      |=+|.|+|.++++|...+..+. +.|  ....+.         =..+++.+++++|.+.
T Consensus         2 iRiriPgG~it~~ql~~la~ia~kyg~~g~i~~TtRQ~iql~~v~~~~l~~v~~~L~~~   60 (65)
T d1aopa1           2 LRCRLPGGVITTKQWQAIDKFAGENTIYGSIRLTNRQTFQFHGILKKNVKPVHQMLHSV   60 (65)
T ss_dssp             EECCCGGGEEEHHHHHHHHHHHHHHBSSCCEEECTTSCEEECCBC-----CHHHHHHHT
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCCEEECCCCEEEECCCCHHHHHHHHHHHHHC
T ss_conf             78821897859999999999999966798365637315986798988999999999984


No 19 
>d1p90a_ c.55.5.2 (A:) NafY core domain {Azotobacter vinelandii [TaxId: 354]}
Probab=21.87  E-value=23  Score=15.31  Aligned_cols=66  Identities=9%  Similarity=0.024  Sum_probs=34.1

Q ss_pred             CCCCCEEEEECC--CCCEEEEEEEC-CC--CCC--CHHH----------------HHHHHHHHHCCCEEEEECCHHHHHH
Q ss_conf             898743999906--98299999976-89--886--8899----------------9999999978988999859899999
Q gi|254780128|r   37 RRGCPDRLIITP--NGGLWWIEVKK-PT--GRL--SHQQ----------------MSEIEELRRRGQRVKVLVSMEEVDN   93 (103)
Q Consensus        37 ~~GvPDli~~~~--~g~~~fIEvK~-~~--gkl--s~~Q----------------~~~~~~l~~~G~~~~Vv~s~edv~~   93 (103)
                      +-|-...+.++.  ++.+-++|.-. +.  +..  .+.|                ..-..+|++.|..++.+..-+.+++
T Consensus        23 HFG~A~~F~Iyev~~~~~~~ve~~~~~~~~~~~~~~~~~~~~~~~~~vvi~~~iG~~a~~~L~~~GI~vi~~~~~~~ie~  102 (123)
T d1p90a_          23 HFGSCLRFLVYQVSAKDASLVDIRSTLDVALAEDKNAWRVEQIQDCQVLYVVSIGGPAAAKVVRAGIHPLKKPKGCAAQE  102 (123)
T ss_dssp             BTTTCSEEEEEEEESSCEEEEEEEECGGGGGCSSHHHHHHHHTTTCSEEEESBCCHHHHHHHHHTTCEEEECTTCEEHHH
T ss_pred             CCCCCCEEEEEEECCCCEEEEEEECCCCCCCCCCCCHHHHHHHCCCCEEEECCCCHHHHHHHHHCCCEEEEECCCCCHHH
T ss_conf             57669889999962993799995414575656541067775307986999877786389999978958999189984999


Q ss_pred             HHHHHHHHC
Q ss_conf             999998630
Q gi|254780128|r   94 FLEELACTL  102 (103)
Q Consensus        94 ~l~~l~~t~  102 (103)
                      .|++++.+|
T Consensus       103 al~~l~~~l  111 (123)
T d1p90a_         103 AIAELQTVM  111 (123)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
T ss_conf             999999986


No 20 
>d2akja2 d.58.36.1 (A:22-174) Ferredoxin--nitrite reductase, NIR {Spinach (Spinacia oleracea) [TaxId: 3562]}
Probab=20.24  E-value=22  Score=15.51  Aligned_cols=51  Identities=20%  Similarity=0.391  Sum_probs=37.5

Q ss_pred             CEEEEEEECCCCCCCHHHHHHHHHHHHC-C--CEEEEE---------CCHHHHHHHHHHHHHH
Q ss_conf             2999999768988688999999999978-9--889998---------5989999999999863
Q gi|254780128|r   51 GLWWIEVKKPTGRLSHQQMSEIEELRRR-G--QRVKVL---------VSMEEVDNFLEELACT  101 (103)
Q Consensus        51 ~~~fIEvK~~~gkls~~Q~~~~~~l~~~-G--~~~~Vv---------~s~edv~~~l~~l~~t  101 (103)
                      ..+++=++.|+|.+++.|...+..+.+. |  +.+.+.         =..+++.+++++|.+.
T Consensus        83 g~FMvRlr~pgG~lt~~Ql~~ladiA~~yg~~G~l~lTtRQniql~gI~~~dl~~i~~~L~~~  145 (153)
T d2akja2          83 GRFMMRLKLPNGVTTSEQTRYLASVIKKYGKDGCADVTTRQNWQIRGVVLPDVPEIIKGLESV  145 (153)
T ss_dssp             TCEEEECCCGGGEEEHHHHHHHHHHHHTTGGGCCEEECTTSCEEEEEECGGGHHHHHHHHHTT
T ss_pred             CEEEEEEECCCEEECHHHHHHHHHHHHHHCCCCCEEECCCCEEEECCCCHHHHHHHHHHHHHC
T ss_conf             768999618981818999999999999978998675679863785688989999999999986


No 21 
>d1b04a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Bacillus stearothermophilus [TaxId: 1422]}
Probab=20.18  E-value=29  Score=14.70  Aligned_cols=48  Identities=15%  Similarity=0.175  Sum_probs=34.9

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHCCCEE----EEECCHHHHHHHHHHHHH
Q ss_conf             999997689886889999999999789889----998598999999999986
Q gi|254780128|r   53 WWIEVKKPTGRLSHQQMSEIEELRRRGQRV----KVLVSMEEVDNFLEELAC  100 (103)
Q Consensus        53 ~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~----~Vv~s~edv~~~l~~l~~  100 (103)
                      +..++=.+.......|...+..|+..|+.+    .++.+.+++.+++.++..
T Consensus       218 ~~y~~~~~~~~~~~~~~e~l~~L~~~gf~~~~~~~~~~~~~~v~~~~~~~~~  269 (312)
T d1b04a_         218 FVYGLADAEALGIASHSEALDYLQALGFKVNPERRRCANIDEVIAFVSEWHD  269 (312)
T ss_dssp             EEEEETTTTTTTCCBHHHHHHHHHHTTCCCCTTCEEESSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCHHHHHHHHHHHHH
T ss_conf             0011234545441219999999986376543423897999999999999996


No 22 
>d1rkqa_ c.108.1.10 (A:) Hypothetical protein YidA {Escherichia coli [TaxId: 562]}
Probab=20.13  E-value=29  Score=14.69  Aligned_cols=22  Identities=14%  Similarity=0.031  Sum_probs=11.4

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCEEE
Q ss_conf             488999999999999997898999
Q gi|254780128|r    7 HYQTEKDVEKRLVTGAKKLDCWVR   30 (103)
Q Consensus         7 h~~~E~~ie~~l~~~lk~~G~~~~   30 (103)
                      +-+++..+  ..++++...|..+.
T Consensus        20 ~~i~~~~~--~al~~L~~~gi~v~   41 (271)
T d1rkqa_          20 HTISPAVK--NAIAAARARGVNVV   41 (271)
T ss_dssp             SCCCHHHH--HHHHHHHHTTCEEE
T ss_pred             CCCCHHHH--HHHHHHHHCCCEEE
T ss_conf             95199999--99999997899999


Done!