Query         gi|254781056|ref|YP_003065469.1| phage-related lysozyme [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 171
No_of_seqs    116 out of 863
Neff          7.3 
Searched_HMMs 39220
Date          Mon May 30 03:36:20 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781056.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 cd00737 endolysin_autolysin En 100.0 1.3E-43       0  279.9  13.9  133   28-164     1-133 (133)
  2 COG3772 Phage-related lysozyme 100.0   1E-40 2.8E-45  262.8  13.4  141   27-170     6-149 (152)
  3 pfam00959 Phage_lysozyme Phage 100.0 7.8E-33   2E-37  215.8  11.3  107   54-162     1-107 (108)
  4 cd00735 bacteriophage_T4-like_  99.9 6.1E-26 1.6E-30  174.7  10.0  127   32-159     2-153 (164)
  5 cd00442 lysozyme_like lysozyme  95.9  0.0054 1.4E-07   38.0   2.4   90   31-135     1-102 (105)
  6 pfam05838 DUF847 Predicted lys  79.8     2.6 6.7E-05   22.0   3.8   75   32-118     2-87  (87)
  7 COG3926 zliS Lysozyme family p  78.9     5.4 0.00014   20.2   9.2  131   30-166     6-165 (252)
  8 TIGR01833 HMG-CoA-S_euk hydrox  55.6     9.5 0.00024   18.7   2.4   38   44-85     24-61  (461)
  9 KOG4404 consensus               48.4      22 0.00056   16.6   8.4   34   36-69     67-107 (350)
 10 TIGR00553 pabB para-aminobenzo  47.6      10 0.00026   18.5   1.5   23   31-59    284-306 (368)
 11 TIGR00538 hemN oxygen-independ  46.8      11 0.00028   18.3   1.6   74   35-121   307-386 (462)
 12 TIGR00080 pimt protein-L-isoas  46.2     8.8 0.00023   18.9   1.0   78   26-117    22-106 (228)
 13 TIGR00972 3a0107s01c2 phosphat  42.1      11 0.00029   18.2   1.0   12   70-81    176-187 (248)
 14 TIGR01341 aconitase_1 aconitat  34.5      18 0.00047   17.0   1.1   22   97-118   274-295 (896)
 15 TIGR03245 arg_AOST_alph argini  33.2      38 0.00097   15.1   2.7   27   30-57    232-258 (336)
 16 TIGR02291 rimK_rel_E_lig alpha  33.1      37 0.00095   15.2   2.5   56   30-86     66-124 (320)
 17 COG1650 Uncharacterized protei  32.2      34 0.00087   15.4   2.2   23   71-93    155-177 (266)
 18 KOG1661 consensus               31.5      31  0.0008   15.6   1.9   20   40-62     43-62  (237)
 19 TIGR03244 arg_catab_AstA argin  30.5      42  0.0011   14.8   2.7   23   30-53    231-253 (336)
 20 TIGR03243 arg_catab_AOST argin  29.1      45  0.0011   14.7   2.7   11   40-50    240-250 (335)
 21 PRK10456 arginine succinyltran  28.9      45  0.0012   14.7   2.7   28   29-57    232-259 (344)
 22 cd01021 GEWL Goose Egg White L  28.8      45  0.0012   14.7   7.2   93   27-124    43-139 (166)
 23 PRK09499 sifB secreted effecto  27.7      47  0.0012   14.6   3.1   17  106-122   225-241 (316)
 24 pfam11363 DUF3164 Protein of u  26.3      50  0.0013   14.4   4.3   67   81-147    94-165 (195)
 25 TIGR02795 tol_pal_ybgF tol-pal  22.5      60  0.0015   14.0   3.4   13  132-144    88-100 (119)
 26 pfam08267 Meth_synt_1 Cobalami  22.5      60  0.0015   14.0   6.2   15  132-146    97-111 (310)
 27 cd02064 Flavokinase_C Riboflav  22.2      42  0.0011   14.9   1.2   37  120-156   143-179 (179)
 28 TIGR01503 MthylAspMut_E methyl  21.3      63  0.0016   13.8   3.2   39   16-63    217-255 (481)
 29 TIGR00565 trpE_proteo anthrani  21.1      30 0.00076   15.7   0.2   26   31-62    423-452 (505)
 30 COG3941 Mu-like prophage prote  20.9      64  0.0016   13.8   6.2   72   70-147   176-247 (633)

No 1  
>cd00737 endolysin_autolysin Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell walls. Similarly, bacteria produce autolysins to facilitate the biosynthesis of its cell wall hetropolymer peptidoglycan and cell division.  Both endolysin and autolysin enzymes cleave the glycosidic beta 1,4-bonds between the N-acetylmuramic acid and the N-acetylglucosamine of the peptidoglycan.
Probab=100.00  E-value=1.3e-43  Score=279.88  Aligned_cols=133  Identities=46%  Similarity=0.840  Sum_probs=127.1

Q ss_pred             CCHHHHHHHHHHCCCCEEEECCCCCCCCEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH
Q ss_conf             89999999997538422000378888770234887773206886499999999999999999999971110135999999
Q gi|254781056|r   28 VPNALIKMLKEFEGLRLTAYRDIGGGAWTIGYGHTGSDVTEGMTITEKEAEDFLLKDASKSLNLLLESSPALKSTSENRL  107 (171)
Q Consensus        28 ~s~~~i~lik~~EG~~~~~Y~D~~~g~~TIGyG~t~~~v~~g~~iT~~~a~~ll~~di~~~~~~~~~~~~~~~~l~~~~~  107 (171)
                      +|+++|+|||.||||+++||+| ++|+||||||||++ ++.|+++|++||+++|..|+++++..+.+.++  .+|+|++|
T Consensus         1 is~~gi~~ik~~EG~~~~~Y~D-~~G~~TIGyGht~~-~~~g~~iT~~ea~~ll~~dl~~~~~~v~~~~~--~~l~~~~~   76 (133)
T cd00737           1 ISQAGLALIKRFEGCRLTPYKD-PAGVWTIGYGHTGG-VVPGMTITEEQADALLAKDLAKAERAVNRAVK--VPLTQNQF   76 (133)
T ss_pred             CCHHHHHHHHHHHCCCCEEEEC-CCCCEEEEECCCCC-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC--CCCCHHHH
T ss_conf             9989999999983882032778-99984781086248-88998409999999999999999999998668--99999999


Q ss_pred             HHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCEECCHHHHHHHHH
Q ss_conf             998766413682010271688999879989999999997408983361069999999
Q gi|254781056|r  108 VAVADFVFNLGIGNYNKSTFKQRVDAQDWEKAAEECKKWTKAGGKVLPGLVKRRDAE  164 (171)
Q Consensus       108 ~ALvs~ayN~G~~~~~~s~~~~~l~~gd~~~a~~e~~~w~~~ggk~~~GL~~RR~~E  164 (171)
                      |||+||+||+|+++++.|++++.+|+|||.+||++|++|+++||++++||++||++|
T Consensus        77 ~Alvs~ayN~G~g~~~~st~~~~ln~G~~~~a~~~~~~w~~~~g~~~~GL~~RR~~E  133 (133)
T cd00737          77 DALVSFAFNVGAGAFRTSTLLRKLNAGDWAGACAQLPRWVKAGGKVLPGLVRRREAE  133 (133)
T ss_pred             HHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCEECHHHHHHHHCC
T ss_conf             999998760686633252899999877999999999834324979858789888449


No 2  
>COG3772 Phage-related lysozyme (muraminidase) [General function prediction only]
Probab=100.00  E-value=1e-40  Score=262.76  Aligned_cols=141  Identities=42%  Similarity=0.763  Sum_probs=133.6

Q ss_pred             CCCHHHHHHHHHHCCCCEEEECCCCCCCCEECCCCCCCCCCCCCCCCHHHHHHH--HHHHHHHHHHHHHHHCCCCCCCCH
Q ss_conf             489999999997538422000378888770234887773206886499999999--999999999999971110135999
Q gi|254781056|r   27 PVPNALIKMLKEFEGLRLTAYRDIGGGAWTIGYGHTGSDVTEGMTITEKEAEDF--LLKDASKSLNLLLESSPALKSTSE  104 (171)
Q Consensus        27 ~~s~~~i~lik~~EG~~~~~Y~D~~~g~~TIGyG~t~~~v~~g~~iT~~~a~~l--l~~di~~~~~~~~~~~~~~~~l~~  104 (171)
                      .+|..+++|||.|||+++.||.| ++|+||||||||++++.+|+++|++||++.  |..|+..++..+++.+.  .+|+|
T Consensus         6 ~~s~~gi~lIk~~EG~~~~pY~d-~~GvwTIgyGhT~~~v~pg~t~t~~e~~~~~~l~~d~~~~~~~v~~~~~--~~l~~   82 (152)
T COG3772           6 SISEIGIALIKEFEGCRLDPYRD-PAGVWTIGYGHTGKPVGPGMTLTKEECDQANALERDLAEAERAVNRYIK--VPLTQ   82 (152)
T ss_pred             CCCHHHHHHHHHHHCCCCCCCCC-CCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCCCH
T ss_conf             14588899999975467764167-9987788628857888898422176899987788788887898887438--89875


Q ss_pred             HHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH-CCCCEECCHHHHHHHHHHHHHHH
Q ss_conf             9999987664136820102716889998799899999999974-08983361069999999999740
Q gi|254781056|r  105 NRLVAVADFVFNLGIGNYNKSTFKQRVDAQDWEKAAEECKKWT-KAGGKVLPGLVKRRDAEVKLLLE  170 (171)
Q Consensus       105 ~~~~ALvs~ayN~G~~~~~~s~~~~~l~~gd~~~a~~e~~~w~-~~ggk~~~GL~~RR~~E~~l~l~  170 (171)
                      +|||||+||+||+|++.+..||+++.+|+|||.++|.++.+|. ++|+++++||++||++|.+||+.
T Consensus        83 ~q~dalvsf~fN~G~~~~~~Stl~r~inaGd~~~a~~~~~rw~~~~g~~~l~gL~~RR~~E~aL~~~  149 (152)
T COG3772          83 PQFDALVSFAYNIGAGNFFSSTLLRRINAGDWSGACEQLRRWIKAGGGKVLPGLVRRREAERALFLW  149 (152)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHEECCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             5777888888742601232689999987688046788734622348963027899989999999862


No 3  
>pfam00959 Phage_lysozyme Phage lysozyme. This family includes lambda phage lysozyme and E. coli endolysin.
Probab=100.00  E-value=7.8e-33  Score=215.78  Aligned_cols=107  Identities=33%  Similarity=0.413  Sum_probs=104.1

Q ss_pred             CCEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHC
Q ss_conf             77023488777320688649999999999999999999997111013599999999876641368201027168899987
Q gi|254781056|r   54 AWTIGYGHTGSDVTEGMTITEKEAEDFLLKDASKSLNLLLESSPALKSTSENRLVAVADFVFNLGIGNYNKSTFKQRVDA  133 (171)
Q Consensus        54 ~~TIGyG~t~~~v~~g~~iT~~~a~~ll~~di~~~~~~~~~~~~~~~~l~~~~~~ALvs~ayN~G~~~~~~s~~~~~l~~  133 (171)
                      +||||||||+++|++|+++|++||+++|..|+.+++..+.+.++  .+|+|++||||+||+||+|+++++.||+++.+|+
T Consensus         1 ~wTIg~G~~~~~v~~g~~~T~~ea~~ll~~d~~~~~~~v~~~~~--~~l~q~~~dAlvs~ayN~G~g~~~~St~~r~ln~   78 (108)
T pfam00959         1 YWTIGIGHYGTDVSPHPRITKSTAAGRYQFDLDTAERGIKQYGK--VDFSPNRQDALVSLAFNVGCGARGFSTLLRAGNQ   78 (108)
T ss_pred             CEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC--CCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHC
T ss_conf             90488698999988899439999999999999999999998668--7999999999988631057775541469999978


Q ss_pred             CCHHHHHHHHHHHHCCCCEECCHHHHHHH
Q ss_conf             99899999999974089833610699999
Q gi|254781056|r  134 QDWEKAAEECKKWTKAGGKVLPGLVKRRD  162 (171)
Q Consensus       134 gd~~~a~~e~~~w~~~ggk~~~GL~~RR~  162 (171)
                      |||..+|++|.+|+++||++++||++||+
T Consensus        79 g~~~~a~~~~~~w~~~gGk~~~GL~~RR~  107 (108)
T pfam00959        79 GQWVLACSAIWKSLKAGGKEYNGLKRRRE  107 (108)
T ss_pred             CCHHHHHHHHHHHHHCCCEECHHHHHHCC
T ss_conf             89999999998774419998634675337


No 4  
>cd00735 bacteriophage_T4-like_lysozyme Bacteriophage T4-like lysozymes hydrolyse the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in peptidoglycan heteropolymers of prokaryotic cell walls.  Members include a variety of bacteriophages (T4, RB49, RB69, Aeh1) as well as Dictyostelium.
Probab=99.93  E-value=6.1e-26  Score=174.71  Aligned_cols=127  Identities=29%  Similarity=0.480  Sum_probs=106.8

Q ss_pred             HHHHHHHHCCCCEEEECCCCCCCCEECCCCCCCC-------------------CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999997538422000378888770234887773-------------------206886499999999999999999999
Q gi|254781056|r   32 LIKMLKEFEGLRLTAYRDIGGGAWTIGYGHTGSD-------------------VTEGMTITEKEAEDFLLKDASKSLNLL   92 (171)
Q Consensus        32 ~i~lik~~EG~~~~~Y~D~~~g~~TIGyG~t~~~-------------------v~~g~~iT~~~a~~ll~~di~~~~~~~   92 (171)
                      +++.||.+||+|+++|+|+ .|+|||||||++.+                   ...+.++|+++++.+|.+|++.+...+
T Consensus         2 L~e~ik~~EG~r~~~Y~Ds-~G~~TIGiGhlI~~~~~~~~~~~~~e~~~~~g~~~~~~~is~e~~~~lf~~Di~~a~~~~   80 (164)
T cd00735           2 IAEMLRQDEGLRLKVYWDT-EGYPTIGIGHLITRKKTKDLNAINSELSKQIGREVTNGVITSEEVEALFEKDLAKAQRDI   80 (164)
T ss_pred             HHHHHHHCCCEECCEEECC-CCCEEEEECEEECCCCCCCCCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             7899998078124025669-998147655250465420000000012254186267887389999999999999999999


Q ss_pred             HHH---CCCCCCCCHHHHHHHHHHHHCCCCCCCCC-HHHHHHHHCCCHHHHHHHHH--HHHCCCCEECCHHHH
Q ss_conf             971---11013599999999876641368201027-16889998799899999999--974089833610699
Q gi|254781056|r   93 LES---SPALKSTSENRLVAVADFVFNLGIGNYNK-STFKQRVDAQDWEKAAEECK--KWTKAGGKVLPGLVK  159 (171)
Q Consensus        93 ~~~---~~~~~~l~~~~~~ALvs~ayN~G~~~~~~-s~~~~~l~~gd~~~a~~e~~--~w~~~ggk~~~GL~~  159 (171)
                      .+.   .+.|..++..++.+|++|+||+|.+++.+ .+++++|++|||..|+.||+  +|.++.+++..-|..
T Consensus        81 ~~~~~~~~~~~~l~~~~q~~li~M~FnLG~~~l~kFkkm~~ai~~~d~~~Aa~EmldS~WakQtp~Ra~rl~~  153 (164)
T cd00735          81 MSNPKLSPVYKKLNASRQMALENMVFQMGVGGVAKFKNSLRAMAAKDWKEAYKGLRDSLWANQTPGRASRVIS  153 (164)
T ss_pred             HHHHCCCCCCCCCCHHHHHHHHEEEECCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHCHHHHHHHHH
T ss_conf             9834227410129999998854135426764588899999999838999999999849553127499999999


No 5  
>cd00442 lysozyme_like lysozyme_like domain.  This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides.
Probab=95.89  E-value=0.0054  Score=38.04  Aligned_cols=90  Identities=20%  Similarity=0.247  Sum_probs=59.2

Q ss_pred             HHHHHHHHHCCCCEEEECCC-------CCCCCEECC-CCCCCC----CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99999997538422000378-------888770234-887773----206886499999999999999999999971110
Q gi|254781056|r   31 ALIKMLKEFEGLRLTAYRDI-------GGGAWTIGY-GHTGSD----VTEGMTITEKEAEDFLLKDASKSLNLLLESSPA   98 (171)
Q Consensus        31 ~~i~lik~~EG~~~~~Y~D~-------~~g~~TIGy-G~t~~~----v~~g~~iT~~~a~~ll~~di~~~~~~~~~~~~~   98 (171)
                      +.|++|+..||-++++|+|-       ..+.+|||. |||..-    ...|..+             +-.++...+.+. 
T Consensus         1 ai~~~l~~~Eg~~lk~~k~~g~~~~~~~~r~ygiG~~q~t~~~~~~~~~~g~~l-------------k~~~~~~~~~~~-   66 (105)
T cd00442           1 AIIDMLASSEGTDLKAYKDRGHGTLNPGERGYGIGLYQLTSRWSDAYRARGIGL-------------KLLAQLILKLFN-   66 (105)
T ss_pred             CHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHH-------------HHHHHHHHHHCC-
T ss_conf             955664322366566666788763485423431258899989899998604017-------------789998787639-


Q ss_pred             CCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCC
Q ss_conf             1359999999987664136820102716889998799
Q gi|254781056|r   99 LKSTSENRLVAVADFVFNLGIGNYNKSTFKQRVDAQD  135 (171)
Q Consensus        99 ~~~l~~~~~~ALvs~ayN~G~~~~~~s~~~~~l~~gd  135 (171)
                       ++..+.+...+++-+|+.+...+.+++..+.+.-.+
T Consensus        67 -~~~~~k~~~~~~~~~~~~~~~~~~~~~~vrq~~~i~  102 (105)
T cd00442          67 -PKVQDKQALQQIKNAGALIMSSFRSRGAVRQLILIN  102 (105)
T ss_pred             -CCHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHHH
T ss_conf             -312459999999866860243034411588988751


No 6  
>pfam05838 DUF847 Predicted lysozyme (DUF847). This family consists of several hypothetical bacterial sequences as well as one viral sequence, the function of this family is unknown. However, these proteins are predicted to be related to lysozyme enzymes.
Probab=79.81  E-value=2.6  Score=22.04  Aligned_cols=75  Identities=25%  Similarity=0.294  Sum_probs=40.9

Q ss_pred             HHHHHHHHCCC-CEEEECCCCCCCCEECCCCCCC--------CCCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             99999975384-2200037888877023488777--------32068--8649999999999999999999997111013
Q gi|254781056|r   32 LIKMLKEFEGL-RLTAYRDIGGGAWTIGYGHTGS--------DVTEG--MTITEKEAEDFLLKDASKSLNLLLESSPALK  100 (171)
Q Consensus        32 ~i~lik~~EG~-~~~~Y~D~~~g~~TIGyG~t~~--------~v~~g--~~iT~~~a~~ll~~di~~~~~~~~~~~~~~~  100 (171)
                      .++.|-+|||- +..|- | ++|. | -||.|..        ++..+  ..+|+++|.++..++.=..        ....
T Consensus         2 ~~~~il~~EGGy~ndP~-D-~GG~-T-~~GIt~~~~~~~~~~~~~~~dvr~Lt~~~a~~IY~~~YW~~--------~~~d   69 (87)
T pfam05838         2 IFDRILSHEGGYVNDPK-D-PGGA-T-NFGITAATARALGYGDVDAGDIKALTRDQAVAIYRADYWDR--------PRAD   69 (87)
T ss_pred             HHHHHHHHCCCCCCCCC-C-CCCC-C-CHHHHHHHHHHHCCCCCCHHHHHHCCHHHHHHHHHHHCCCC--------CCHH
T ss_conf             79999987178779999-9-9984-0-48871989998368999868898789999999999974180--------3542


Q ss_pred             CCCHHHHHHHHHHHHCCC
Q ss_conf             599999999876641368
Q gi|254781056|r  101 STSENRLVAVADFVFNLG  118 (171)
Q Consensus       101 ~l~~~~~~ALvs~ayN~G  118 (171)
                      .|++..-.++.|++.|.|
T Consensus        70 ~lp~~la~~~fD~aVN~G   87 (87)
T pfam05838        70 LLPPAVAYQLFDAAVNSG   87 (87)
T ss_pred             HCCHHHHHHHHCCCEECC
T ss_conf             189888088820012173


No 7  
>COG3926 zliS Lysozyme family protein [General function prediction only]
Probab=78.86  E-value=5.4  Score=20.20  Aligned_cols=131  Identities=20%  Similarity=0.160  Sum_probs=65.5

Q ss_pred             HHHHHHHHHHCCCCEEEECCCCCCCCEECCCCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
Q ss_conf             9999999975384220003788887702348877732-068864999999999999999999999711101359999999
Q gi|254781056|r   30 NALIKMLKEFEGLRLTAYRDIGGGAWTIGYGHTGSDV-TEGMTITEKEAEDFLLKDASKSLNLLLESSPALKSTSENRLV  108 (171)
Q Consensus        30 ~~~i~lik~~EG~~~~~Y~D~~~g~~TIGyG~t~~~v-~~g~~iT~~~a~~ll~~di~~~~~~~~~~~~~~~~l~~~~~~  108 (171)
                      +..|+.|-.+||=...-=+| ++|. | -+|.|..-. -.|...|+.+...|-.......+..--=.....+.|+...--
T Consensus         6 ~~~~~~V~s~EGGY~d~PkD-PGGa-T-n~GIT~~T~~A~G~~~S~~~vr~mT~aeA~~Iy~~~YW~k~~~D~lP~gVd~   82 (252)
T COG3926           6 NQAIPRVLSHEGGYADHPKD-PGGA-T-NWGITKRTLSAWGYNVSKADVRAMTRAEATAIYREEYWNKVGGDDLPAGVDY   82 (252)
T ss_pred             HHHHHHHHHCCCCCCCCCCC-CCCC-C-CHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHH
T ss_conf             77766786403676689999-8974-4-1438799999738778889999988999999999986400476768852004


Q ss_pred             HHHHHHHCCCCCCCCCHHHHH-HHH--------------------C----CCHHHHHHHHHHHHCCCCE---ECCHHHHH
Q ss_conf             987664136820102716889-998--------------------7----9989999999997408983---36106999
Q gi|254781056|r  109 AVADFVFNLGIGNYNKSTFKQ-RVD--------------------A----QDWEKAAEECKKWTKAGGK---VLPGLVKR  160 (171)
Q Consensus       109 ALvs~ayN~G~~~~~~s~~~~-~l~--------------------~----gd~~~a~~e~~~w~~~ggk---~~~GL~~R  160 (171)
                      ++.|++-|.|++.-  .++++ .++                    .    +-..++|++-..|.+..+.   +-+| ..|
T Consensus        83 avfD~AVNsGp~rA--a~~LQkal~~~~~v~~DGvIG~~TLaAl~~~~~~~~i~~~~d~r~a~l~~l~tf~tfg~G-w~~  159 (252)
T COG3926          83 AVFDAAVNSGPGRA--AKWLQKALGPAYTVRVDGVIGAQTLAALKKDPANDLIGRICDARLAFLKHLSTFGTFGKG-WTA  159 (252)
T ss_pred             HHHHHHHCCCCCHH--HHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCHHHHCCH-HHH
T ss_conf             56534541684169--999999856577666567624888998871653137888888999998555508665122-888


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254781056|r  161 RDAEVK  166 (171)
Q Consensus       161 R~~E~~  166 (171)
                      |.++..
T Consensus       160 rV~~vr  165 (252)
T COG3926         160 RVAEVR  165 (252)
T ss_pred             HHHHHH
T ss_conf             899999


No 8  
>TIGR01833 HMG-CoA-S_euk hydroxymethylglutaryl-CoA synthase; InterPro: IPR010122   Synonym(s): 3-hydroxy-3-methylglutaryl-coenzyme A synthase, HMG-CoA synthase.    Hydroxymethylglutaryl-CoA synthase (2.3.3.10 from EC) catalyses the condensation of acetyl-CoA with acetoacetyl-CoA to produce HMG-CoA and CoA, the second reaction in the mevalonate-dependent isoprenoid biosynthesis pathway. HMG-CoA synthase contains an important catalytic cysteine residue that acts as a nucleophile in the first step of the reaction: the acetylation of the enzyme by acetyl-CoA (its first substrate) to produce an acetyl-enzyme thioester, releasing the reduced coenzyme A. The subsequent nucleophilic attack on acetoacetyl-CoA (its second substrate) leads to the formation of HMG-CoA .   HMG-CoA synthase occurs in eukaryotes, archaea and certain bacteria . In vertebrates, there are two isozymes located in different subcellular compartments: a cytosolic form that is the starting point of the mevalonate pathway (leads to cholesterol and other sterolic and isoprenoid compounds), and a mitochondrial form responsible for ketone body biosynthesis. HMG-CoA is also found in other eukaryotes such as insects, plants and fungi . In bacteria, isoprenoid precursors are generally synthesised via an alternative, non-mevalonate pathway, however a number of Gram-positive pathogens utilise a mevalonate pathway involving HMG-CoA synthase that is parallel to that found in eukaryotes , .   This entry is specific for eukaryotic HMG-CoA synthase enzymes.; GO: 0004421 hydroxymethylglutaryl-CoA synthase activity, 0008299 isoprenoid biosynthetic process.
Probab=55.64  E-value=9.5  Score=18.72  Aligned_cols=38  Identities=26%  Similarity=0.533  Sum_probs=20.6

Q ss_pred             EEEECCCCCCCCEECCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             200037888877023488777320688649999999999999
Q gi|254781056|r   44 LTAYRDIGGGAWTIGYGHTGSDVTEGMTITEKEAEDFLLKDA   85 (171)
Q Consensus        44 ~~~Y~D~~~g~~TIGyG~t~~~v~~g~~iT~~~a~~ll~~di   85 (171)
                      ++.|...+.|.+|||-|-+    +.|..-.+|++..|-..-+
T Consensus        24 LE~yDgVs~GKYTiGLGq~----~mgFc~drEDI~Sl~LTvv   61 (461)
T TIGR01833        24 LEKYDGVSAGKYTIGLGQT----KMGFCTDREDINSLCLTVV   61 (461)
T ss_pred             HHHHCCCCCCCEEECCCCC----CCEEECCCCHHHHHHHHHH
T ss_conf             8632688889503423566----2000022101566658999


No 9  
>KOG4404 consensus
Probab=48.36  E-value=22  Score=16.55  Aligned_cols=34  Identities=26%  Similarity=0.413  Sum_probs=16.9

Q ss_pred             HHHHCCCCEEEECCCCCC-------CCEECCCCCCCCCCCC
Q ss_conf             997538422000378888-------7702348877732068
Q gi|254781056|r   36 LKEFEGLRLTAYRDIGGG-------AWTIGYGHTGSDVTEG   69 (171)
Q Consensus        36 ik~~EG~~~~~Y~D~~~g-------~~TIGyG~t~~~v~~g   69 (171)
                      |-+-|.-+.-+-+|.++-       +-||||||+.+.-..|
T Consensus        67 i~~s~ph~ag~qWkF~GaFYFa~TVItTIGyGhstP~T~~G  107 (350)
T KOG4404          67 ILKSEPHKAGPQWKFAGAFYFATTVITTIGYGHSTPSTDGG  107 (350)
T ss_pred             HHHCCCCCCCCCCCCCCCEEEEEEEEEEECCCCCCCCCCCC
T ss_conf             98237401366542475147888888642367788877676


No 10 
>TIGR00553 pabB para-aminobenzoate synthase, component I; InterPro: IPR005802   Para-aminobenzoate synthase component I (pabB) is closely related to anthranilate synthase component I (trpE). The apparent orthologs of pabB in Aquifex aeolicus and Helicobacter pylori score well below most TrpE proteins because of a different architecture, in which the less strongly conserved N-terminal domain is absent. The noise cut off is set to exclude most examples of TrpE.; GO: 0009396 folic acid and derivative biosynthetic process.
Probab=47.63  E-value=10  Score=18.49  Aligned_cols=23  Identities=35%  Similarity=0.654  Sum_probs=19.3

Q ss_pred             HHHHHHHHHCCCCEEEECCCCCCCCEECC
Q ss_conf             99999997538422000378888770234
Q gi|254781056|r   31 ALIKMLKEFEGLRLTAYRDIGGGAWTIGY   59 (171)
Q Consensus        31 ~~i~lik~~EG~~~~~Y~D~~~g~~TIGy   59 (171)
                      .++++|+.+|..+--+|  |+    ||||
T Consensus       284 RAMeII~elE~~~RG~Y--cG----aiG~  306 (368)
T TIGR00553       284 RAMEIIKELEKQPRGVY--CG----AIGY  306 (368)
T ss_pred             HHHHHHHHHCCCCCCCC--HH----HHHH
T ss_conf             99999998636888951--00----1330


No 11 
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase; InterPro: IPR004558   This family represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. HemN catalyses the anaerobic transformation of coproporhyrinogen-III into protoporphyrinogen-IX during porphyrin biosynthesis. Several species, including Escherichia coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity, IPR004559 from INTERPRO. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterised protein.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin biosynthetic process, 0005737 cytoplasm.
Probab=46.76  E-value=11  Score=18.30  Aligned_cols=74  Identities=19%  Similarity=0.285  Sum_probs=44.5

Q ss_pred             HHHHHCCCCEEEECCCCCCCCEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH-CCCCCC--CCHH---HHH
Q ss_conf             9997538422000378888770234887773206886499999999999999999999971-110135--9999---999
Q gi|254781056|r   35 MLKEFEGLRLTAYRDIGGGAWTIGYGHTGSDVTEGMTITEKEAEDFLLKDASKSLNLLLES-SPALKS--TSEN---RLV  108 (171)
Q Consensus        35 lik~~EG~~~~~Y~D~~~g~~TIGyG~t~~~v~~g~~iT~~~a~~ll~~di~~~~~~~~~~-~~~~~~--l~~~---~~~  108 (171)
                      |=.+|-||-.+.      +.-|+|+|.|.-. -.++.+++      -.++++.+++.+..- .|.|..  |++.   +++
T Consensus       307 L~RNFQGYTT~~------~~~lLG~GvtSIs-m~~D~Y~Q------N~K~L~~Y~~~lD~~~~pv~rG~~L~~dD~iRr~  373 (462)
T TIGR00538       307 LHRNFQGYTTKK------ETDLLGFGVTSIS-MLGDVYAQ------NYKTLKDYYKALDEGKLPVERGVALSQDDLIRRE  373 (462)
T ss_pred             CCCCCCCCCCCC------CCEEEEECHHHHH-HHCCCCCC------CCHHHHHHHHHHHCCCCCEEECEECCCCCCHHHH
T ss_conf             000576522489------7215630110211-20021225------5366888987520057845105100612220288


Q ss_pred             HHHHHHHCCCCCC
Q ss_conf             9876641368201
Q gi|254781056|r  109 AVADFVFNLGIGN  121 (171)
Q Consensus       109 ALvs~ayN~G~~~  121 (171)
                      ++.+|.=|++...
T Consensus       374 VI~~lmcnl~l~y  386 (462)
T TIGR00538       374 VIKELMCNLKLDY  386 (462)
T ss_pred             HHHHHHHHCCCCH
T ss_conf             9999986237666


No 12 
>TIGR00080 pimt protein-L-isoaspartate O-methyltransferase; InterPro: IPR000682 Protein-L-isoaspartate(D-aspartate) O-methyltransferase () (PCMT)  (which is also known as L-isoaspartyl protein carboxyl methyltransferase) is an enzyme that catalyzes the transfer of a methyl group from S- adenosylmethionine to the free carboxyl groups of D-aspartyl or L-isoaspartyl residues in a variety of peptides and proteins. The enzyme does not act on normal L-aspartyl residues L-isoaspartyl and D-aspartyl are the products of the spontaneous deamidation and/or isomerization of normal L-aspartyl and L- asparaginyl residues in proteins. PCMT plays a role in the repair and/or degradation of these damaged proteins; the enzymatic methyl esterification of the abnormal residues can lead to their conversion to normal L-aspartyl residues. The SAM domain is present in most of these proteins.; GO: 0004719 protein-L-isoaspartate (D-aspartate) O-methyltransferase activity, 0006464 protein modification process.
Probab=46.20  E-value=8.8  Score=18.90  Aligned_cols=78  Identities=22%  Similarity=0.271  Sum_probs=48.3

Q ss_pred             CCCCHHHHHHHHH--HCCC-----CEEEECCCCCCCCEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             7489999999997--5384-----22000378888770234887773206886499999999999999999999971110
Q gi|254781056|r   26 IPVPNALIKMLKE--FEGL-----RLTAYRDIGGGAWTIGYGHTGSDVTEGMTITEKEAEDFLLKDASKSLNLLLESSPA   98 (171)
Q Consensus        26 ~~~s~~~i~lik~--~EG~-----~~~~Y~D~~~g~~TIGyG~t~~~v~~g~~iT~~~a~~ll~~di~~~~~~~~~~~~~   98 (171)
                      ...|+..+|.++.  -|-|     ...||.|.+   ..||||-|.+.     +++-..+.++|+++|....+.+ ..-. 
T Consensus        22 ~~~~~~v~~Al~~v~Re~F~P~~fk~~AY~~~a---l~ig~~qtiS~-----p~mvA~m~~yL~nhL~~~~~vL-eiG~-   91 (228)
T TIGR00080        22 FIKSKRVLDALKSVPREEFVPEAFKEAAYEDAA---LEIGYGQTISA-----PHMVAKMTEYLENHLKPGAKVL-EIGT-   91 (228)
T ss_pred             CCCCHHHHHHHHCCCCCCCCCHHHHHCCCCCCC---CCCCCCCEECC-----HHHHHHHHHHHHHHCCCCCEEE-EECC-
T ss_conf             566878999974187623367166637852552---00256762440-----7899999998885214035566-5047-


Q ss_pred             CCCCCHHHHHHHHHHHHCC
Q ss_conf             1359999999987664136
Q gi|254781056|r   99 LKSTSENRLVAVADFVFNL  117 (171)
Q Consensus        99 ~~~l~~~~~~ALvs~ayN~  117 (171)
                          =..=+.|.++..+.-
T Consensus        92 ----GSGY~aavlA~~v~~  106 (228)
T TIGR00080        92 ----GSGYQAAVLAEIVGR  106 (228)
T ss_pred             ----CCHHHHHHHHHHHHC
T ss_conf             ----855899999998713


No 13 
>TIGR00972 3a0107s01c2 phosphate ABC transporter, ATP-binding protein; InterPro: IPR005670   This is a family of phosphate transport system permease proteins.; GO: 0005315 inorganic phosphate transmembrane transporter activity, 0015114 phosphate transmembrane transporter activity, 0006817 phosphate transport, 0016020 membrane.
Probab=42.06  E-value=11  Score=18.25  Aligned_cols=12  Identities=17%  Similarity=0.335  Sum_probs=4.7

Q ss_pred             CCCCHHHHHHHH
Q ss_conf             864999999999
Q gi|254781056|r   70 MTITEKEAEDFL   81 (171)
Q Consensus        70 ~~iT~~~a~~ll   81 (171)
                      |||+-.+.++|.
T Consensus       176 DPIaT~~IEeLi  187 (248)
T TIGR00972       176 DPIATGKIEELI  187 (248)
T ss_pred             CHHHHHHHHHHH
T ss_conf             877899999999


No 14 
>TIGR01341 aconitase_1 aconitate hydratase 1; InterPro: IPR006249   Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop , . Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) . Below is a description of some of the multi-functional activities associated with different aconitases.   Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway . The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA.    Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) , . As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated .   IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis . Although IRP2 is homologous to IRP1, IPR2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes . In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system.   Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica , . In S.enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress.   This entry represents bacterial aconitase A (AcnA), eukaryotic cytosolic aconitase (cAcn/IRP1), iron regulatory protein 2 (IRP2), and a few mitochondrial aconitases (certain mAcn proteins, but not the majority of these enzymes).   More information about these proteins can be found at Protein of the Month: Aconitase .; GO: 0051539 4 iron 4 sulfur cluster binding, 0008152 metabolic process.
Probab=34.47  E-value=18  Score=17.01  Aligned_cols=22  Identities=27%  Similarity=0.374  Sum_probs=10.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCC
Q ss_conf             1013599999999876641368
Q gi|254781056|r   97 PALKSTSENRLVAVADFVFNLG  118 (171)
Q Consensus        97 ~~~~~l~~~~~~ALvs~ayN~G  118 (171)
                      +....|+-..++.+.+|+==.|
T Consensus       274 pg~~~LslaDRATIANM~PEYG  295 (896)
T TIGR01341       274 PGLKELSLADRATIANMAPEYG  295 (896)
T ss_pred             CCCCCCCCCCHHHHHCCCHHHH
T ss_conf             7620077633010322782045


No 15 
>TIGR03245 arg_AOST_alph arginine/ornithine succinyltransferase, alpha subunit. In some bacteria, including Pseudomonas aeruginosa, the astB gene (arginine N-succinyltransferase) is replaced by tandem paralogs that form a heterodimer. This heterodimer from P. aeruginosa is characterized as arginine and ornithine N-2 succinyltransferase (AOST). Members of this protein family represent the less widespread paralog, designated AruI, or arginine/ornithine succinyltransferase, alpha subunit.
Probab=33.17  E-value=38  Score=15.11  Aligned_cols=27  Identities=30%  Similarity=0.449  Sum_probs=12.1

Q ss_pred             HHHHHHHHHHCCCCEEEECCCCCCCCEE
Q ss_conf             9999999975384220003788887702
Q gi|254781056|r   30 NALIKMLKEFEGLRLTAYRDIGGGAWTI   57 (171)
Q Consensus        30 ~~~i~lik~~EG~~~~~Y~D~~~g~~TI   57 (171)
                      ..++.++++ |||+..-|.|.-.|=||+
T Consensus       232 ~pA~~lLe~-EGF~~~gyVDIFDgGP~l  258 (336)
T TIGR03245       232 RDNCQILNR-EGFEMDRYIDIFDGGPTL  258 (336)
T ss_pred             HHHHHHHHH-CCCCCCCCEECCCCCCEE
T ss_conf             899999997-389768964243688558


No 16 
>TIGR02291 rimK_rel_E_lig alpha-L-glutamate ligase homolog; InterPro: IPR011758   Members of this protein family contain a region of homology to the RimK family of alpha-L-glutamate ligases (IPR004666 from INTERPRO), various members of which modify the Glu-Glu C-terminus of ribosomal protein S6, or tetrahydromethanopterin, or a form of coenzyme F420 derivative. Members of this family are found so far in various Vibrio and Pseudomonas species and some other gamma and beta Proteobacteria. The function is unknown..
Probab=33.10  E-value=37  Score=15.19  Aligned_cols=56  Identities=16%  Similarity=0.242  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHCCCCEEEECCCCCCC-CEECCCCCCCC--CCCCCCCCHHHHHHHHHHHHH
Q ss_conf             9999999975384220003788887-70234887773--206886499999999999999
Q gi|254781056|r   30 NALIKMLKEFEGLRLTAYRDIGGGA-WTIGYGHTGSD--VTEGMTITEKEAEDFLLKDAS   86 (171)
Q Consensus        30 ~~~i~lik~~EG~~~~~Y~D~~~g~-~TIGyG~t~~~--v~~g~~iT~~~a~~ll~~di~   86 (171)
                      +..-++||.||+|+-+|=+- ++|. +-|=-+|...-  -..|..||++|.+.-..+-+.
T Consensus        66 ~~~~~ivkdh~dFVIKPAqG-sGG~GIlVit~r~~~ryr~~sG~~i~~eeiE~hvSniL~  124 (320)
T TIGR02291        66 KSLDDIVKDHEDFVIKPAQG-SGGDGILVITDRLDERYRKSSGALISKEEIERHVSNILA  124 (320)
T ss_pred             HHHHHHHCCCCCCEEECCCC-CCCCEEEEECCCCCCCEECCCCCCCCHHHHHHHHHHHHH
T ss_conf             43466627889836726606-798727997036688403541010154567788888887


No 17 
>COG1650 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.17  E-value=34  Score=15.40  Aligned_cols=23  Identities=22%  Similarity=0.273  Sum_probs=11.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             64999999999999999999999
Q gi|254781056|r   71 TITEKEAEDFLLKDASKSLNLLL   93 (171)
Q Consensus        71 ~iT~~~a~~ll~~di~~~~~~~~   93 (171)
                      .++.+++-+.+.+-+........
T Consensus       155 eW~d~~age~la~a~~eal~~~d  177 (266)
T COG1650         155 EWTDDEAGEILAEALEEALDNVD  177 (266)
T ss_pred             HHCCCCCHHHHHHHHHHHHCCCC
T ss_conf             50576311899999999853644


No 18 
>KOG1661 consensus
Probab=31.45  E-value=31  Score=15.64  Aligned_cols=20  Identities=35%  Similarity=0.509  Sum_probs=12.0

Q ss_pred             CCCCEEEECCCCCCCCEECCCCC
Q ss_conf             38422000378888770234887
Q gi|254781056|r   40 EGLRLTAYRDIGGGAWTIGYGHT   62 (171)
Q Consensus        40 EG~~~~~Y~D~~~g~~TIGyG~t   62 (171)
                      +++|..||.|   ..|-|||+.|
T Consensus        43 ~~~~~n~y~d---~pq~~G~n~~   62 (237)
T KOG1661          43 RSERTNPYMD---SPQKIGYNLT   62 (237)
T ss_pred             CCCCCCCCCC---CCCCCCCCEE
T ss_conf             1124687778---7655677548


No 19 
>TIGR03244 arg_catab_AstA arginine N-succinyltransferase. In many bacteria, the arginine succinyltransferase (ast) pathway operon consists of five genes, including this protein, arginine N-succinyltransferase (EC 2.3.1.109). In a few species, such as Pseudomonas aeruginosa, the member of this family is encoded adjacent to a paralog, and the two polypeptides form a heterodimeric enzyme, active on both arginine and ornithine. In such species, this polypeptide may be treated as the beta subunit of an enzyme that may be named either arginine N-succinyltransferase (AST) or arginine and orthithine N-succinyltransferase (AOST).
Probab=30.46  E-value=42  Score=14.84  Aligned_cols=23  Identities=35%  Similarity=0.563  Sum_probs=10.1

Q ss_pred             HHHHHHHHHHCCCCEEEECCCCCC
Q ss_conf             999999997538422000378888
Q gi|254781056|r   30 NALIKMLKEFEGLRLTAYRDIGGG   53 (171)
Q Consensus        30 ~~~i~lik~~EG~~~~~Y~D~~~g   53 (171)
                      ..+..++++ |||+..-|.|.-.|
T Consensus       231 ~pA~~lLe~-EGF~~~gyVDIFDg  253 (336)
T TIGR03244       231 RPALAMLES-EGFRYQGYVDIFDA  253 (336)
T ss_pred             HHHHHHHHH-CCCCCCCCEECCCC
T ss_conf             999999997-49975896534368


No 20 
>TIGR03243 arg_catab_AOST arginine and ornithine succinyltransferase subunits. In many bacteria, the sole member of this protein family is arginine N-succinyltransferase (EC 2.3.1.109), the AstA protein of the arginine succinyltransferase (ast) pathway. However, in Pseudomonas aeruginosa and several other species, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST).
Probab=29.12  E-value=45  Score=14.70  Aligned_cols=11  Identities=55%  Similarity=0.966  Sum_probs=4.4

Q ss_pred             CCCCEEEECCC
Q ss_conf             38422000378
Q gi|254781056|r   40 EGLRLTAYRDI   50 (171)
Q Consensus        40 EG~~~~~Y~D~   50 (171)
                      |||+..-|.|.
T Consensus       240 EGF~~~gyVDI  250 (335)
T TIGR03243       240 EGFRYQGYVDI  250 (335)
T ss_pred             CCCCCCCCEEC
T ss_conf             39976896544


No 21 
>PRK10456 arginine succinyltransferase; Provisional
Probab=28.89  E-value=45  Score=14.68  Aligned_cols=28  Identities=32%  Similarity=0.440  Sum_probs=13.9

Q ss_pred             CHHHHHHHHHHCCCCEEEECCCCCCCCEE
Q ss_conf             99999999975384220003788887702
Q gi|254781056|r   29 PNALIKMLKEFEGLRLTAYRDIGGGAWTI   57 (171)
Q Consensus        29 s~~~i~lik~~EG~~~~~Y~D~~~g~~TI   57 (171)
                      +.-+..++.. |||+..-|.|.-.|-||+
T Consensus       232 t~pA~~lLe~-EGF~~~gyVDIFDaGP~l  259 (344)
T PRK10456        232 TAPARAVLEK-EGFRYRNYIDIFDGGPTL  259 (344)
T ss_pred             CHHHHHHHHH-CCCCCCCCEECCCCCCEE
T ss_conf             7999999997-489768955444788458


No 22 
>cd01021 GEWL Goose Egg White Lysozyme domain. Eukaryotic "goose-type" lysozymes (GEWL). These enzymes catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc).  Members include tunicate, Japanese flounder, ostrich, and mouse.
Probab=28.75  E-value=45  Score=14.66  Aligned_cols=93  Identities=15%  Similarity=0.158  Sum_probs=52.8

Q ss_pred             CCCHHHHHHHHHHCCCCEEEECCCCCCCCEECCCCC--CCC--CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             489999999997538422000378888770234887--773--2068864999999999999999999999711101359
Q gi|254781056|r   27 PVPNALIKMLKEFEGLRLTAYRDIGGGAWTIGYGHT--GSD--VTEGMTITEKEAEDFLLKDASKSLNLLLESSPALKST  102 (171)
Q Consensus        27 ~~s~~~i~lik~~EG~~~~~Y~D~~~g~~TIGyG~t--~~~--v~~g~~iT~~~a~~ll~~di~~~~~~~~~~~~~~~~l  102 (171)
                      -+-++.|.-|..-|.---.+-.| +.|.---|||-.  .+.  ...|...|++...+--. -+-...+.+.+.+|.|. .
T Consensus        43 ~idPAlIAaIiSRESraG~~L~~-Gwg~~g~g~GLMQvD~~~h~p~G~w~SeeHi~Q~t~-IL~~~I~~i~~kfP~Wt-~  119 (166)
T cd01021          43 CIDPAVIAAIISRESRAGKVLKN-GWGGAGNGFGLMQVDKRSHHPVGAWDSEEHLSQATE-ILIDRIKAIQRKFPTWT-K  119 (166)
T ss_pred             CCCHHHHHHHHHHHCCCCCHHHC-CCCCCCCEEEEEEECCCCCCCCCCCCHHHHHHHHHH-HHHHHHHHHHHHCCCCC-H
T ss_conf             99999999998743467732113-768888876677665876778877778999999999-99999999997089999-7


Q ss_pred             CHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             9999999876641368201027
Q gi|254781056|r  103 SENRLVAVADFVFNLGIGNYNK  124 (171)
Q Consensus       103 ~~~~~~ALvs~ayN~G~~~~~~  124 (171)
                      .|.-+.++.  +||.|++++..
T Consensus       120 eQ~LkGGia--AYn~G~~nV~s  139 (166)
T cd01021         120 EQQLKGGIS--AYNAGAGNVRS  139 (166)
T ss_pred             HHHHHHHHH--HHHCCCCCEEC
T ss_conf             888778899--98427664212


No 23 
>PRK09499 sifB secreted effector protein; Provisional
Probab=27.70  E-value=47  Score=14.55  Aligned_cols=17  Identities=18%  Similarity=0.114  Sum_probs=7.2

Q ss_pred             HHHHHHHHHHCCCCCCC
Q ss_conf             99998766413682010
Q gi|254781056|r  106 RLVAVADFVFNLGIGNY  122 (171)
Q Consensus       106 ~~~ALvs~ayN~G~~~~  122 (171)
                      |+.|+..-.-++|...+
T Consensus       225 qq~afletmsmcgLK~~  241 (316)
T PRK09499        225 KNKIAAKVIENTNLKNA  241 (316)
T ss_pred             HHHHHHHHHHHCCCCCC
T ss_conf             98999999986598667


No 24 
>pfam11363 DUF3164 Protein of unknown function (DUF3164). This family of proteins has no known function.
Probab=26.26  E-value=50  Score=14.39  Aligned_cols=67  Identities=15%  Similarity=0.240  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCC-CCCCCCHHHHHH----HHCCCHHHHHHHHHHHH
Q ss_conf             99999999999997111013599999999876641368-201027168899----98799899999999974
Q gi|254781056|r   81 LLKDASKSLNLLLESSPALKSTSENRLVAVADFVFNLG-IGNYNKSTFKQR----VDAQDWEKAAEECKKWT  147 (171)
Q Consensus        81 l~~di~~~~~~~~~~~~~~~~l~~~~~~ALvs~ayN~G-~~~~~~s~~~~~----l~~gd~~~a~~e~~~w~  147 (171)
                      |-..++.+...+..++..|..=.....-|||+-+|+.- .|.+..+.++..    ++.-+|..|-+++..-.
T Consensus        94 Fde~lqaAK~LIdeCi~~Ws~ga~~eiralV~~AF~~DK~G~i~~~~vL~Lrrl~I~D~rW~~AM~AI~dai  165 (195)
T pfam11363        94 FDERLQAAKALIDECLTEWSEGARAEIRALVTRAFQVDKEGNINTGRILSLRRLDIDDERWQRAMDAISDSI  165 (195)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf             586899999999999999754796889999999971387676559999878646779877999999999887


No 25 
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF; InterPro: IPR014162   Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, and a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction..
Probab=22.52  E-value=60  Score=13.96  Aligned_cols=13  Identities=31%  Similarity=0.269  Sum_probs=6.3

Q ss_pred             HCCCHHHHHHHHH
Q ss_conf             8799899999999
Q gi|254781056|r  132 DAQDWEKAAEECK  144 (171)
Q Consensus       132 ~~gd~~~a~~e~~  144 (171)
                      +.|+...||.-+.
T Consensus        88 ~~g~~~~A~~~l~  100 (119)
T TIGR02795        88 ELGDKEKAKATLQ  100 (119)
T ss_pred             HHCCHHHHHHHHH
T ss_conf             7289889999999


No 26 
>pfam08267 Meth_synt_1 Cobalamin-independent synthase, N-terminal domain. The N-terminal domain and C-terminal domains of cobalamin-independent synthases together define a catalytic cleft in the enzyme. The N-terminal domain is thought to bind the substrate, in particular, the negatively charged polyglutamate chain. The N-terminal domain is also thought to stabilize a loop from the C-terminal domain.
Probab=22.46  E-value=60  Score=13.96  Aligned_cols=15  Identities=27%  Similarity=0.399  Sum_probs=6.2

Q ss_pred             HCCCHHHHHHHHHHH
Q ss_conf             879989999999997
Q gi|254781056|r  132 DAQDWEKAAEECKKW  146 (171)
Q Consensus       132 ~~gd~~~a~~e~~~w  146 (171)
                      .+|+-+..+-+|.+|
T Consensus        97 ARG~~~~~a~eMtKW  111 (310)
T pfam08267        97 ARGNKDVPALEMTKW  111 (310)
T ss_pred             HHCCCCCCHHHHHHH
T ss_conf             708888861665512


No 27 
>cd02064 Flavokinase_C Riboflavin kinase (Flavokinase). This family represents the C-terminal region of the bifunctional riboflavin biosynthesis protein riboflavin kinase / FAD synthetase. These enzymes have both ATP:riboflavin. 5'-phospho transferase and ATP:FMN-adenylyltransferase activities . The C-terminal domain has FMN-adenylyltransferase activitie. They catalyse the 5'-phosphorylation of riboflavin to FMN and the adenylylation of FMN to FAD . A domain has been identified in the N-terminal region that is well conserved in all the bacterial FAD synthetases.This domain has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases .
Probab=22.22  E-value=42  Score=14.86  Aligned_cols=37  Identities=19%  Similarity=0.212  Sum_probs=24.4

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCEECCH
Q ss_conf             0102716889998799899999999974089833610
Q gi|254781056|r  120 GNYNKSTFKQRVDAQDWEKAAEECKKWTKAGGKVLPG  156 (171)
Q Consensus       120 ~~~~~s~~~~~l~~gd~~~a~~e~~~w~~~ggk~~~G  156 (171)
                      ..+.+|.+++.|..||.+.|.+-+-+...--|+|+.|
T Consensus       143 ~~ISSs~IR~~i~~G~i~~An~lLGr~y~i~G~Vi~G  179 (179)
T cd02064         143 EKVSSTRIREALAEGDVELANELLGRPYSISGTVVHG  179 (179)
T ss_pred             CEEEHHHHHHHHHCCCHHHHHHHCCCCCEEEEEEEEC
T ss_conf             1673899999998599999999819983788998059


No 28 
>TIGR01503 MthylAspMut_E methylaspartate mutase, E subunit; InterPro: IPR006396   Glutamate mutase (methylaspartate mutase) catalyses the reversible interconversion of L-glutamate and L-threo-3-methylaspartate, the first step in the pathway of glutamate fermentation . Catalysis is initiated using the cobalamin cofactor. The E subunit is the catalytic subunit (MutE) . ; GO: 0016866 intramolecular transferase activity, 0031419 cobalamin binding, 0019670 anaerobic glutamate catabolic process.
Probab=21.31  E-value=63  Score=13.82  Aligned_cols=39  Identities=28%  Similarity=0.440  Sum_probs=19.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEECCCCCCCCEECCCCCC
Q ss_conf             378754567774899999999975384220003788887702348877
Q gi|254781056|r   16 GMNGDDKHNKIPVPNALIKMLKEFEGLRLTAYRDIGGGAWTIGYGHTG   63 (171)
Q Consensus        16 ~~~~~~~~~~~~~s~~~i~lik~~EG~~~~~Y~D~~~g~~TIGyG~t~   63 (171)
                      +..||-.+|++..|=..++      |.-.-   .++....|||||..|
T Consensus       217 PLTgTLvPP~iS~si~i~E------~LLA~---eQGVk~itvGygq~G  255 (481)
T TIGR01503       217 PLTGTLVPPSISNSIQIIE------GLLAA---EQGVKNITVGYGQVG  255 (481)
T ss_pred             CCCCCCCCHHHHHHHHHHH------HHHHH---HCCCEEEEEEEECCC
T ss_conf             6642235067899999999------99887---649217885011004


No 29 
>TIGR00565 trpE_proteo anthranilate synthase component I; InterPro: IPR005257   This family represents anthranilate/para-aminobenzoate synthase component I from proteobacteria and actinobacteria.    This enzyme resembles some other chorismate-binding enzymes, including para-aminobenzoate synthase (pabB) and isochorismate synthase. There is a fairly deep split between two sets, seen in the pattern of gaps as well as in amino acid sequence differences. This group includes proteobacteria such as Escherichia coli and Helicobacter pylori but also the Gram-positive organism Corynebacterium glutamicum. The second group (IPR005256 from INTERPRO) includes eukaryotes, archaea, and most other bacterial lineages; sequences from the second group may resemble pabB more closely than other trpE from this group. ; GO: 0004049 anthranilate synthase activity, 0009058 biosynthetic process.
Probab=21.12  E-value=30  Score=15.75  Aligned_cols=26  Identities=27%  Similarity=0.663  Sum_probs=20.0

Q ss_pred             HHHHHHHHHCCCCEEEECCCCCCCCEECC----CCC
Q ss_conf             99999997538422000378888770234----887
Q gi|254781056|r   31 ALIKMLKEFEGLRLTAYRDIGGGAWTIGY----GHT   62 (171)
Q Consensus        31 ~~i~lik~~EG~~~~~Y~D~~~g~~TIGy----G~t   62 (171)
                      .||+||-+.|+-|.-.|=    |  .|||    ||.
T Consensus       423 ~A~qLIyq~E~qrRgSYG----G--aVGYlts~G~~  452 (505)
T TIGR00565       423 KAMQLIYQLENQRRGSYG----G--AVGYLTSEGDL  452 (505)
T ss_pred             HHHHHHHHHHCCCCCCCC----C--CCEEECCCCCC
T ss_conf             999999997168015667----6--42014158865


No 30 
>COG3941 Mu-like prophage protein [General function prediction only]
Probab=20.88  E-value=64  Score=13.76  Aligned_cols=72  Identities=15%  Similarity=0.177  Sum_probs=40.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             864999999999999999999999711101359999999987664136820102716889998799899999999974
Q gi|254781056|r   70 MTITEKEAEDFLLKDASKSLNLLLESSPALKSTSENRLVAVADFVFNLGIGNYNKSTFKQRVDAQDWEKAAEECKKWT  147 (171)
Q Consensus        70 ~~iT~~~a~~ll~~di~~~~~~~~~~~~~~~~l~~~~~~ALvs~ayN~G~~~~~~s~~~~~l~~gd~~~a~~e~~~w~  147 (171)
                      ..++.||+..+|.+-+.-+........   ...++.+...|.|=- -+|...+  +-+++.+....-..+.++|..|.
T Consensus       176 Gs~s~Eel~~lL~r~V~~~~~la~~a~---~g~t~~~l~kl~~~G-~lg~~aI--~aL~~~l~~qa~gAaKd~MktW~  247 (633)
T COG3941         176 GSLSMEELNQLLERGVPAKGRLADEAG---AGRTPAELSKLGSKG-KLGRDAI--RALFAGLGIQAKGAAKDQMKTWL  247 (633)
T ss_pred             CCCCHHHHHHHHHCCCHHHHHHHHHHH---CCCCHHHHHHHHHCC-CCCHHHH--HHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             767899999999735419999988761---577899999988534-5336679--99999987872223388999899


Done!