Query         gi|254780547|ref|YP_003064960.1| OmpA/MotB [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 160
No_of_seqs    126 out of 4755
Neff          8.2 
Searched_HMMs 13730
Date          Wed Jun  1 10:28:42 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780547.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 d2aizp1 d.79.7.1 (P:1-134) Pep 100.0 6.1E-31 4.5E-35  197.0  11.6  104   50-153    30-134 (134)
  2 d2hqsc1 d.79.7.1 (C:68-173) Pe 100.0 3.4E-30 2.5E-34  192.7   9.3  103   50-152     2-105 (106)
  3 d1r1ma_ d.79.7.1 (A:) Outer me 100.0 5.3E-30 3.9E-34  191.6   7.3  111   46-156     8-139 (140)
  4 d1gvha3 c.25.1.5 (A:254-396) F  62.6     3.3 0.00024   19.1   3.3   28  105-132   114-141 (143)
  5 d1cqxa3 c.25.1.5 (A:262-403) F  60.2     2.4 0.00017   19.9   2.2   29  104-132   111-139 (142)
  6 d1qy7a_ d.58.5.1 (A:) PII (pro  58.4     4.4 0.00032   18.4   3.3   54  103-156    10-68  (112)
  7 d2ns1b1 d.58.5.1 (B:1-112) PII  55.9       6 0.00044   17.6   3.7   54  103-156    10-68  (112)
  8 d1krha2 c.25.1.2 (A:206-338) B  51.5     7.3 0.00053   17.1   3.8   27  105-131   107-133 (133)
  9 d1tvca2 c.25.1.2 (A:111-251) M  48.0     5.7 0.00042   17.7   2.6   26  106-131   113-138 (141)
 10 d1z2la1 c.56.5.4 (A:4-212,A:33  41.5      10 0.00076   16.2   6.4   56   79-134    70-128 (293)
 11 d3tgla_ c.69.1.17 (A:) Triacyl  34.7      13 0.00098   15.6   6.3   54   72-138   122-178 (265)
 12 d2piia_ d.58.5.1 (A:) PII (pro  32.5      15  0.0011   15.3   4.6   54  103-156    10-68  (112)
 13 d2eyqa2 c.37.1.19 (A:349-465)   28.9     8.3  0.0006   16.8   0.9   48   63-123    17-64  (117)
 14 d2cz4a1 d.58.5.1 (A:1-100) Hyp  26.9      18  0.0013   14.8   4.2   48  104-155    16-64  (100)
 15 d1tiaa_ c.69.1.17 (A:) Triacyl  20.4      25  0.0018   14.0   6.1   55   69-138   124-179 (271)
 16 d1vfja_ d.58.5.1 (A:) PII (pro  20.3      25  0.0018   14.0   4.6   54  103-156    10-68  (116)

No 1  
>d2aizp1 d.79.7.1 (P:1-134) Peptidoglycan-associated lipoprotein, PAL, periplasmic domain {Haemophilus influenzae [TaxId: 727]}
Probab=99.97  E-value=6.1e-31  Score=197.02  Aligned_cols=104  Identities=40%  Similarity=0.714  Sum_probs=99.6

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHHHHHHCCC-EEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             100220475224324799999998430256-0589999722665333320011133799999999852898606999970
Q gi|254780547|r   50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus        50 ~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~-~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      ..|||++||+.|+++++..|+.++.+|+.+ +.+|.|.||||..|+.+||+.||++||++|++||+++||+++||.+.||
T Consensus        30 ~~I~F~~~s~~L~~~~~~~L~~la~~l~~~~~~~i~I~GhtD~~g~~~~N~~LS~~RA~~V~~~L~~~Gi~~~ri~~~g~  109 (134)
T d2aizp1          30 NTVYFGFDKYDITGEYVQILDAHAAYLNATPAAKVLVEGNTDERGTPEYNIALGQRRADAVKGYLAGKGVDAGKLGTVSY  109 (134)
T ss_dssp             CEEECCTTCCCCCHHHHHHHHHHHHHHHHSTTCCEEEEEECCSSSCHHHHHHHHHHHHHHHHHHHHHTTCCGGGEEEEEC
T ss_pred             CEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEC
T ss_conf             81883799812498899999999999986999689996043433221110137899999999899771875345513775


Q ss_pred             CCCCCCCCCCCHHHHHCCCEEEEEE
Q ss_conf             7448989987877984299189999
Q gi|254780547|r  129 GKEMPSVYGHDEDAYAKNRRAIVFL  153 (160)
Q Consensus       129 G~~~P~~~~~~~~~~~~NRRVei~i  153 (160)
                      |+++|+.++.++++|++||||||+.
T Consensus       110 G~~~P~~~~~~~~~~~~NRRVeiv~  134 (134)
T d2aizp1         110 GEEKPAVLGHDEAAYSKNRRAVLAY  134 (134)
T ss_dssp             TTTSCSSCSCSHHHHHHHSEEEEEC
T ss_pred             CCCCCCCCCCCHHHHHCCCCEEEEC
T ss_conf             4337578891977986239899959


No 2  
>d2hqsc1 d.79.7.1 (C:68-173) Peptidoglycan-associated lipoprotein, PAL, periplasmic domain {Escherichia coli [TaxId: 562]}
Probab=99.96  E-value=3.4e-30  Score=192.69  Aligned_cols=103  Identities=45%  Similarity=0.745  Sum_probs=99.2

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHHHHHHCCC-EEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             100220475224324799999998430256-0589999722665333320011133799999999852898606999970
Q gi|254780547|r   50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus        50 ~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~-~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      +.|||++||++|++++...|+.++.+|+.+ +.+|.|+||||..|+.+||+.||++||++|++||++.||++++|.+.||
T Consensus         2 ~~iyF~~~s~~l~~~~~~~L~~l~~~l~~~~~~~i~I~GhtD~~g~~~~N~~LS~~RA~~V~~~L~~~Gi~~~ri~~~g~   81 (106)
T d2hqsc1           2 NIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSY   81 (106)
T ss_dssp             CEEECCTTCCCCCGGGHHHHHHHHHHHHHCTTCCEEEEECCCSSSCHHHHHHHHHHHHHHHHHHHHHTTCCGGGEEEEEC
T ss_pred             CEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEE
T ss_conf             98994799773898899999999999986899579998433422104666558899876799999866986644899983


Q ss_pred             CCCCCCCCCCCHHHHHCCCEEEEE
Q ss_conf             744898998787798429918999
Q gi|254780547|r  129 GKEMPSVYGHDEDAYAKNRRAIVF  152 (160)
Q Consensus       129 G~~~P~~~~~~~~~~~~NRRVei~  152 (160)
                      |+++|++++.+++++++||||||+
T Consensus        82 G~~~p~~~~~~~~~~~~NRRVeii  105 (106)
T d2hqsc1          82 GKEKPAVLGHDEAAYSKNRRAVLV  105 (106)
T ss_dssp             TTSSCSSCSSSHHHHHHHSEEEEE
T ss_pred             CCCCCCCCCCCHHHHHHCCCEEEE
T ss_conf             564767899097799714949996


No 3  
>d1r1ma_ d.79.7.1 (A:) Outer membrane protein class 4, RmpM, C-terminal domain {Neisseria meningitidis [TaxId: 487]}
Probab=99.96  E-value=5.3e-30  Score=191.57  Aligned_cols=111  Identities=29%  Similarity=0.371  Sum_probs=101.7

Q ss_pred             HHHCCEEEEECCCCCCCHHHHHHHHHHHHHHCCC-EEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEE
Q ss_conf             5203100220475224324799999998430256-058999972266533332001113379999999985289860699
Q gi|254780547|r   46 SSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMK  124 (160)
Q Consensus        46 ~~~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~-~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~  124 (160)
                      ..++..+||++||+.|++++++.|+.++.+|+++ ..+|.|+||||.+|+.+||+.||++||++|++||++.|++++||.
T Consensus         8 i~l~~~~~F~~~s~~l~~~~~~~L~~l~~~l~~~~~~~i~I~GhtD~~G~~~~N~~LS~~RA~~V~~~L~~~Gi~~~ri~   87 (140)
T d1r1ma_           8 ISLSAKTLFGFDKDSLRAEAQDNLKVLAQRLSRTNIQSVRVEGHTDFMGSDKYNQALSERRAYVVANNLVSNGVPVSRIS   87 (140)
T ss_dssp             EEEEHHHHHTTSSSCCCHHHHHHHHHHHHHHTTSCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHHHHHHTTCCGGGEE
T ss_pred             EEECCCEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEE
T ss_conf             99777306628974279899999999999872199708999986065442121036788999999999997599937599


Q ss_pred             EEEECCCCCCCCCCCHHHHHC--------------------CCEEEEEEEEC
Q ss_conf             997074489899878779842--------------------99189999713
Q gi|254780547|r  125 VTSYGKEMPSVYGHDEDAYAK--------------------NRRAIVFLKGC  156 (160)
Q Consensus       125 ~~g~G~~~P~~~~~~~~~~~~--------------------NRRVei~i~~~  156 (160)
                      +.|||+++|+..+.++.+++.                    ||||||.|+..
T Consensus        88 ~~g~Ge~~P~~~n~~~~~~~~~~~~~~~~~nr~~~i~~~~~nRRVEi~v~~~  139 (140)
T d1r1ma_          88 AVGLGESQAQMTQVCEAEVAKLGAKVSKAKKREALIACIEPDRRVDVKIRSI  139 (140)
T ss_dssp             EEECTTTTCCCHHHHHHHHHTCCSSCCSSHHHHHHHHHTGGGSEEEEEEEEE
T ss_pred             EEEEECCCCCCCCCCHHHHHHCCCHHHHHHHHHHHHHCCCCCCCEEEEEEEC
T ss_conf             9997257877889698898530220123320255550468998589999825


No 4  
>d1gvha3 c.25.1.5 (A:254-396) Flavohemoglobin, C-terminal domain {Escherichia coli [TaxId: 562]}
Probab=62.57  E-value=3.3  Score=19.08  Aligned_cols=28  Identities=11%  Similarity=0.168  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHCCCCCEEEEEEEECCCC
Q ss_conf             7999999998528986069999707448
Q gi|254780547|r  105 RAYAVFNYFVARGISASRMKVTSYGKEM  132 (160)
Q Consensus       105 RA~aV~~~L~~~Gi~~~ri~~~g~G~~~  132 (160)
                      -.++|.++|.+.|++.++|....||.++
T Consensus       114 m~~~v~~~L~~~G~~~~~i~~E~F~~~~  141 (143)
T d1gvha3         114 FMQFTAKQLVDLGVKQENIHYECFGPHK  141 (143)
T ss_dssp             HHHHHHHHHHHTTCCGGGEEEECSSSCC
T ss_pred             HHHHHHHHHHHCCCCHHHEEEECCCCCC
T ss_conf             9999999999859999998986468975


No 5  
>d1cqxa3 c.25.1.5 (A:262-403) Flavohemoglobin, C-terminal domain {Alcaligenes eutrophus [TaxId: 106590]}
Probab=60.23  E-value=2.4  Score=19.93  Aligned_cols=29  Identities=14%  Similarity=0.261  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHCCCCCEEEEEEEECCCC
Q ss_conf             37999999998528986069999707448
Q gi|254780547|r  104 RRAYAVFNYFVARGISASRMKVTSYGKEM  132 (160)
Q Consensus       104 ~RA~aV~~~L~~~Gi~~~ri~~~g~G~~~  132 (160)
                      .-.++|++.|.+.|+++++|....||.+.
T Consensus       111 ~m~~~v~~~L~~~G~~~~~i~~E~Fg~~~  139 (142)
T d1cqxa3         111 PFMRMQHDALKNLGIHEARIHYEVFGPDL  139 (142)
T ss_dssp             HHHHHHHHHHHHTTCCGGGEEECCCSSCT
T ss_pred             HHHHHHHHHHHHCCCCHHHEEEEECCCCC
T ss_conf             68999999999859988879997158986


No 6  
>d1qy7a_ d.58.5.1 (A:) PII (product of glnB) {Cyanobacteria (Synechococcus sp.) pcc 7942 [TaxId: 1131]}
Probab=58.40  E-value=4.4  Score=18.39  Aligned_cols=54  Identities=11%  Similarity=0.116  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHCCCCCE-EEEEEEECCCCCCCCCCCHH----HHHCCCEEEEEEEEC
Q ss_conf             3379999999985289860-69999707448989987877----984299189999713
Q gi|254780547|r  103 LRRAYAVFNYFVARGISAS-RMKVTSYGKEMPSVYGHDED----AYAKNRRAIVFLKGC  156 (160)
Q Consensus       103 ~~RA~aV~~~L~~~Gi~~~-ri~~~g~G~~~P~~~~~~~~----~~~~NRRVei~i~~~  156 (160)
                      ..|.+.|++.|.+.|++.= -.++.|+|............    ..-.-+++|++++.-
T Consensus        10 p~k~~~v~~AL~~~G~~g~Tv~~v~G~G~~~g~~~~~~~~~~~~~~~~k~~ieivv~d~   68 (112)
T d1qy7a_          10 PFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGAEYTVEFLQKLKLEIVVEDA   68 (112)
T ss_dssp             GGGHHHHHHHHHHTTCCCCEEEEEEEEEEEECCCSSCTTSSEEEEEEEEEEEEEEECGG
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCCEECCCEEEECCCCEEEEEEEECHH
T ss_conf             89999999999967997689964288757788542234613351205459999998789


No 7  
>d2ns1b1 d.58.5.1 (B:1-112) PII-homolog GlnK {Shigella flexneri [TaxId: 623]}
Probab=55.93  E-value=6  Score=17.59  Aligned_cols=54  Identities=11%  Similarity=0.047  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHHCCCCCE-EEEEEEECCCCCCCCCC---C-HHHHHCCCEEEEEEEEC
Q ss_conf             3379999999985289860-69999707448989987---8-77984299189999713
Q gi|254780547|r  103 LRRAYAVFNYFVARGISAS-RMKVTSYGKEMPSVYGH---D-EDAYAKNRRAIVFLKGC  156 (160)
Q Consensus       103 ~~RA~aV~~~L~~~Gi~~~-ri~~~g~G~~~P~~~~~---~-~~~~~~NRRVei~i~~~  156 (160)
                      -.|.+.|++.|.+.|++.= -..+.|+|...+.....   . ....-.-.++|++++.-
T Consensus        10 p~k~~~V~~AL~~~G~~g~Tv~~v~G~G~~~~~~~~~~g~~~~~~~~~k~~ieivv~d~   68 (112)
T d2ns1b1          10 PFKLEDVREALSSIGIQGLTVTEVKGFGRQKGHAELYRGAEFSVNFLPKVKIDVAIADD   68 (112)
T ss_dssp             GGGHHHHHHHHHHTTCCCCEEEEEEECSSSCCCCEEETTEEECCCCEEEEEEEEEEEGG
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCEECCCEEEEEEEEEEEEEEEECHH
T ss_conf             89999999999978997189997205315678641443630132111178999998549


No 8  
>d1krha2 c.25.1.2 (A:206-338) Benzoate dioxygenase reductase {Acinetobacter sp. [TaxId: 472]}
Probab=51.51  E-value=7.3  Score=17.11  Aligned_cols=27  Identities=15%  Similarity=0.281  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHCCCCCEEEEEEEECCC
Q ss_conf             799999999852898606999970744
Q gi|254780547|r  105 RAYAVFNYFVARGISASRMKVTSYGKE  131 (160)
Q Consensus       105 RA~aV~~~L~~~Gi~~~ri~~~g~G~~  131 (160)
                      -.++|++.|.+.|+++++|....||.+
T Consensus       107 m~~~v~~~L~~~Gv~~~~i~~E~F~~s  133 (133)
T d1krha2         107 MVEAVRSWLDTQGIQPANFLFEKFSAN  133 (133)
T ss_dssp             HHHHHHHHHHHHTCCCSEEEEEEECCC
T ss_pred             HHHHHHHHHHHCCCCHHHEEEEECCCC
T ss_conf             999999999985999899899834599


No 9  
>d1tvca2 c.25.1.2 (A:111-251) Methane monooxygenase component C, MmoC {Methylococcus capsulatus [TaxId: 414]}
Probab=47.95  E-value=5.7  Score=17.70  Aligned_cols=26  Identities=15%  Similarity=0.192  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHCCCCCEEEEEEEECCC
Q ss_conf             99999999852898606999970744
Q gi|254780547|r  106 AYAVFNYFVARGISASRMKVTSYGKE  131 (160)
Q Consensus       106 A~aV~~~L~~~Gi~~~ri~~~g~G~~  131 (160)
                      .++|++.|.+.|+++++|....||.+
T Consensus       113 ~~~v~~~l~~~Gv~~~~i~~E~F~~~  138 (141)
T d1tvca2         113 IDAACELVRSRGIPGEQVFFEKFLPS  138 (141)
T ss_dssp             HHHHHHHHHHHCCCCSEEEECCCSSS
T ss_pred             HHHHHHHHHHCCCCHHHEEEEECCCC
T ss_conf             99999999983999899788746477


No 10 
>d1z2la1 c.56.5.4 (A:4-212,A:330-413) Allantoate amidohydrolase AllC catalytic domain {Escherichia coli [TaxId: 562]}
Probab=41.53  E-value=10  Score=16.19  Aligned_cols=56  Identities=14%  Similarity=0.192  Sum_probs=39.2

Q ss_pred             CEEEEEE-EEECCCC-CCCCCCCHHHHHHHHHHHHHHHHCCCCCE-EEEEEEECCCCCC
Q ss_conf             6058999-9722665-33332001113379999999985289860-6999970744898
Q gi|254780547|r   79 HDCDFLI-EGHADEL-GSRNSSIALGLRRAYAVFNYFVARGISAS-RMKVTSYGKEMPS  134 (160)
Q Consensus        79 ~~~~i~I-~GhtD~~-Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~-ri~~~g~G~~~P~  134 (160)
                      ++...++ -+|-|.. ..-.|.-.|+--=+..+...|.+.|+.+. .|.++.|..++..
T Consensus        70 ~~~~~v~iGSHlDtV~~gG~~Dg~~Gv~a~le~~~~l~~~~~~~~~~i~vv~f~~EEg~  128 (293)
T d1z2la1          70 YPQEVVLSGSHIDTVVNGGNLDGQFGALAAWLAIDWLKTQYGAPLRTVEVVAMAEEEGS  128 (293)
T ss_dssp             EEEEEEEEEEECCCCTTBCSSTTHHHHHHHHHHHHHHHHHHCSCSEEEEEEEESCSSCC
T ss_pred             CCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCC
T ss_conf             87762686220265898888787402799999987787608878999611221146456


No 11 
>d3tgla_ c.69.1.17 (A:) Triacylglycerol lipase {Rhizomucor miehei [TaxId: 4839]}
Probab=34.71  E-value=13  Score=15.56  Aligned_cols=54  Identities=20%  Similarity=0.278  Sum_probs=36.7

Q ss_pred             HHHHHCC-CEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHC--CCCCEEEEEEEECCCCCCCCCC
Q ss_conf             9843025-60589999722665333320011133799999999852--8986069999707448989987
Q gi|254780547|r   72 LGSWLEK-HDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVAR--GISASRMKVTSYGKEMPSVYGH  138 (160)
Q Consensus        72 ia~~l~~-~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~--Gi~~~ri~~~g~G~~~P~~~~~  138 (160)
                      +...+++ ++.+|.|.||.           |+-.=|.-..-+|...  +++..++.+..||.  |..-+.
T Consensus       122 i~~~~~~~~~~~i~vtGHS-----------LGGAlA~L~a~~l~~~~~~~~~~~i~~~TFG~--PrvGn~  178 (265)
T d3tgla_         122 VLDQFKQYPSYKVAVTGHS-----------LGGATVLLCALDLYQREEGLSSSNLFLYTQGQ--PRVGDP  178 (265)
T ss_dssp             HHHHHHHCTTSEEEEEEET-----------HHHHHHHHHHHHHHHTCSSCCTTTEEEEEESC--CCCBCH
T ss_pred             HHHHHHHCCCCEEEEECCC-----------CHHHHHHHHHHHHHHHCCCCCCCCCCEEECCC--CCCCCH
T ss_conf             9999976899469984254-----------10789999999998733256754343453489--835888


No 12 
>d2piia_ d.58.5.1 (A:) PII (product of glnB) {Escherichia coli [TaxId: 562]}
Probab=32.49  E-value=15  Score=15.34  Aligned_cols=54  Identities=9%  Similarity=0.073  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHCCCCC-EEEEEEEECCCCCCCCCC---CH-HHHHCCCEEEEEEEEC
Q ss_conf             337999999998528986-069999707448989987---87-7984299189999713
Q gi|254780547|r  103 LRRAYAVFNYFVARGISA-SRMKVTSYGKEMPSVYGH---DE-DAYAKNRRAIVFLKGC  156 (160)
Q Consensus       103 ~~RA~aV~~~L~~~Gi~~-~ri~~~g~G~~~P~~~~~---~~-~~~~~NRRVei~i~~~  156 (160)
                      -.|.++|++.|.+.|++. .-..+.|+|...+.....   +. ...-.-+++|++++..
T Consensus        10 p~kl~~v~~aL~~~Gv~g~Tv~~v~G~G~~~~~~~~~~~~~~~~~~~~k~~ieivv~d~   68 (112)
T d2piia_          10 PFKLDDVREALAEVGITGMTVTEVKGFGRQKGHTELYRGAEYMVDFLPKVKIEIVVPDD   68 (112)
T ss_dssp             GGGHHHHHHHHHHHTCCCCEEEEEEECSCCTTCCCSCCCCSSCCCCEEEEEEEEEECGG
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCEEECCEEECCCCCEEEEEEEECHH
T ss_conf             89999999999968998599997427887555333340420030315357999998838


No 13 
>d2eyqa2 c.37.1.19 (A:349-465) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}
Probab=28.91  E-value=8.3  Score=16.79  Aligned_cols=48  Identities=19%  Similarity=0.185  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf             2479999999843025605899997226653333200111337999999998528986069
Q gi|254780547|r   63 PADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRM  123 (160)
Q Consensus        63 ~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri  123 (160)
                      ....+.++.+..|+++.+.+|+|.-+             |..|++...+.|.+.||++..+
T Consensus        17 ~~~~~p~~~L~~~i~~~~~~Vli~a~-------------s~g~~erl~e~L~~~~i~~~~~   64 (117)
T d2eyqa2          17 AQQKAPLDALRKFLETFDGPVVFSVE-------------SEGRREALGELLARIKIAPQRI   64 (117)
T ss_dssp             SSSSSTTHHHHHHHTTCCSCCCEEES-------------SHHHHHHHHHHHGGGTCCCEEC
T ss_pred             CCHHCHHHHHHHHHHHCCCEEEEEEC-------------CCCHHHHHHHHHHHCCCCCEEE
T ss_conf             02136999999999958983999979-------------9657999999999769982570


No 14 
>d2cz4a1 d.58.5.1 (A:1-100) Hypothetical protein TTHA0516 {Thermus thermophilus [TaxId: 274]}
Probab=26.88  E-value=18  Score=14.77  Aligned_cols=48  Identities=8%  Similarity=-0.080  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHCCCCCEE-EEEEEECCCCCCCCCCCHHHHHCCCEEEEEEEE
Q ss_conf             3799999999852898606-999970744898998787798429918999971
Q gi|254780547|r  104 RRAYAVFNYFVARGISASR-MKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLKG  155 (160)
Q Consensus       104 ~RA~aV~~~L~~~Gi~~~r-i~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~~  155 (160)
                      .+++.|.+.|.+.|++.=- ..+.|+|........    .+..|=|+|+++..
T Consensus        16 ~~~~~v~~~L~~~Gv~G~Tv~~v~G~G~~~~~~~~----~~g~~v~Ieivv~~   64 (100)
T d2cz4a1          16 LLEKRLVEEVKRLGAKGYTITPARGEGSRGIRSVD----WEGQNIRLETIVSE   64 (100)
T ss_dssp             GGHHHHHHHHHHTTCCCCEEEEEBCTTCCCTTCSC----STTCEEEEEEEECH
T ss_pred             HHHHHHHHHHHHCCCCCEEEEECEEECCCCCCCCC----CCCCEEEEEEEECH
T ss_conf             88999999999789974699958898447877354----80422899999888


No 15 
>d1tiaa_ c.69.1.17 (A:) Triacylglycerol lipase {Penicillium camembertii [TaxId: 5075]}
Probab=20.42  E-value=25  Score=14.02  Aligned_cols=55  Identities=20%  Similarity=0.358  Sum_probs=34.6

Q ss_pred             HHHHHHHHCC-CEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCC
Q ss_conf             9999843025-605899997226653333200111337999999998528986069999707448989987
Q gi|254780547|r   69 LSNLGSWLEK-HDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGH  138 (160)
Q Consensus        69 L~~ia~~l~~-~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~G~~~P~~~~~  138 (160)
                      ++.+...+.+ ++.+|.|.||.           |+-.=|.-..-+|...+.+  .+.+..||.  |..-+.
T Consensus       124 ~~~i~~~~~~~~~~~i~iTGHS-----------LGGAlA~L~a~~l~~~~~~--~~~~~tfG~--PrvGn~  179 (271)
T d1tiaa_         124 IKELKEVVAQNPNYELVVVGHS-----------LGAAVATLAATDLRGKGYP--SAKLYAYAS--PRVGNA  179 (271)
T ss_pred             HHHHHHHHHHCCCCEEEEECCC-----------HHHHHHHHHHHHHHHCCCC--CCEEEEECC--CCCCCH
T ss_conf             9999999976899369985252-----------6899999999999872898--630798379--973789


No 16 
>d1vfja_ d.58.5.1 (A:) PII (product of glnB) {Thermus thermophilus [TaxId: 274]}
Probab=20.32  E-value=25  Score=14.01  Aligned_cols=54  Identities=13%  Similarity=0.086  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHHCCCCCE-EEEEEEECCCCCCCC---CCC-HHHHHCCCEEEEEEEEC
Q ss_conf             3379999999985289860-699997074489899---878-77984299189999713
Q gi|254780547|r  103 LRRAYAVFNYFVARGISAS-RMKVTSYGKEMPSVY---GHD-EDAYAKNRRAIVFLKGC  156 (160)
Q Consensus       103 ~~RA~aV~~~L~~~Gi~~~-ri~~~g~G~~~P~~~---~~~-~~~~~~NRRVei~i~~~  156 (160)
                      -.|...|++.|.+.|++.= -..+.|+|...+...   +.. ......-+++|++++.-
T Consensus        10 p~kl~~V~~aL~~~Gv~g~Tv~~v~G~G~~~~~~~~~~g~~~~~~~~~k~~ieivv~d~   68 (116)
T d1vfja_          10 PEKLNEVLKALFQAEVRGLTLSRVQGHGGETERVETYRGTTVKMELHEKVRLEIGVSEP   68 (116)
T ss_dssp             GGGHHHHHHHHHHTTCCCCEEEEEEEECTTCCCHHHHTTSCCSTTCEEEEEEEEEECGG
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEECCCCEEEEEEECHH
T ss_conf             89999999999868998589994070477654432022427772017745899998589


Done!